######################################### # # # BoBro version 1.20 output # # # ######################################### **************************************** INPUT DATA SUMMARY **************************************** Datafile: /home/www/html/bobro2/data/annotation/20161228201738g/ortholog_promoter/3112 Alphabet: A G C T Nucleotides composition: A: 0.29 G: 0.21 C: 0.21 T: 0.29 Sequences number: 43 Nucleotides number: 8965 Sequence name Length NC_000913_opr_3112_gi_16128515_16128516_145698227_16128518_+ 219 NC_013941_opr_674468_gi_291281941_291281942_291281943_291281944_+_0.697553743513714 299 NC_013941_opr_674368_gi_291281442_291281443_291281444_291281445_+_0.697553743513714 219 NC_013941_opr_674269_gi_291280959_291280960_291280961_291280962_291280963_291280964_291280965_-_0.697553743513714 270 NC_015761_opr_901534_gi_339998059_339998060_339998061_339998062_339998063_339998064_+_0.626192893401015 100 NC_015761_opr_901562_gi_339998198_339998199_339998200_339998201_339998202_339998203_-_0.626192893401015 79 NC_010658_opr_431474_gi_187732072_187731046_-_0.605817068503636 175 NC_010658_opr_431740_gi_187730523_187734022_187731105_187731051_-_0.605817068503636 299 NC_010658_opr_2309924_gi_187733887_-_0.605817068503636 299 NC_014562_opr_754086_gi_308186849_308186850_+_0.54286843145002 299 NC_014562_opr_2956850_gi_308189038_-_0.54286843145002 51 NC_013850_opr_662986_gi_288936738_288936739_288936740_288936741_-_0.530771789753826 299 NC_013850_opr_662418_gi_288933654_288933655_288933656_288933657_288933658_288933659_288933660_288933661_-_0.530771789753826 299 NC_013850_opr_662420_gi_288933674_288933675_288933676_288933677_+_0.530771789753826 95 NC_015224_opr_822737_gi_332159786_332159787_-_0.510371893104093 135 NC_015224_opr_3081924_gi_332159788_-_0.510371893104093 299 NC_013421_opr_628749_gi_261820376_261820377_-_0.452284263959391 299 NC_013421_opr_628816_gi_261820745_261820746_261820747_261820748_-_0.452284263959391 176 NC_010554_opr_417996_gi_197285323_197285324_197285325_197285326_197285327_-_0.435474912053323 61 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 299 NC_010554_opr_2276368_gi_197284164_+_0.435474912053323 239 NC_012962_opr_589185_gi_253989887_253989888_253989889_+_0.347544607610927 94 NC_012962_opr_2627875_gi_253987688_+_0.347544607610927 116 NC_014228_opr_2877151_gi_300722691_-_0.334597755650387 299 NC_014228_opr_715150_gi_300722689_300722690_-_0.334597755650387 100 NC_015460_opr_845286_gi_332288374_332288375_332288376_-_0.320342016305429 75 NC_015460_opr_3122764_gi_332288377_-_0.320342016305429 299 NC_015460_opr_3122885_gi_332288826_+_0.320342016305429 299 NC_012559_opr_2544128_gi_226941440_+_0.288132635253054 120 NC_008781_opr_261216_gi_121603060_121603061_-_0.280535241948032 251 NC_014924_opr_3030286_gi_319787622_+_0.278979085430698 299 NC_014924_opr_793544_gi_319787623_319787624_+_0.278979085430698 98 NC_009524_opr_2064415_gi_148653616_-_0.275396359365825 299 NC_009524_opr_317936_gi_148653613_148653614_148653615_-_0.275396359365825 107 NC_016010_opr_923186_gi_346724326_346724327_346724328_346724329_-_0.269746874046966 299 NC_015677_opr_3191825_gi_337279318_-_0.259375490349914 299 NC_014931_opr_795804_gi_319796189_319796190_319796191_-_0.247436689314392 218 NC_014931_opr_795211_gi_319793444_319793445_319793446_319793447_-_0.247436689314392 299 NC_008358_opr_220263_gi_114798718_114799312_114800318_114797879_+_0.237425198123888 299 NC_008343_opr_217622_gi_114327992_114327993_+_0.237119217751034 87 NC_011420_opr_479896_gi_209963504_209963505_+_0.233762301286904 139 NC_010577_opr_421368_gi_182680623_182680624_182680625_-_0.219922630560928 299 NC_015717_opr_892034_gi_338739850_338739851_338739852_338739853_-_0.216390795316916 60 **************************************** COMMAND LINE SUMMARY **************************************** Parameters: -k 3; -c 1.00; -o 5; -n 10; -L 12; -U 20; -R 2; -u 0.70; -e 3; -w 2.00; -b 0.95; -N 6; -F Seed size lower limit (-k) 3 Seed conservation level (-c) 1.00 Output motif number (-o) 5 Output motif number in each length (-n) 10 Motif length lower limit (-L) 12 Motif length upper limit (-U) 20 Motif length step (-R) 2 Motif similarity lower limit (-u) 0.70 Motif refine times (-e) 3 Two ends weight (-w) 2.00 Motif conservation level in background (-b) 0.95 Lower limit of motif conservation level (-N) 6 Fasta version (-F) On ********************************************************* Candidate Motif 1 ********************************************************* Motif length: 12 Motif number: 26 Seed number: 4 Motif Pvalue: 9.5E-28 (2702) ------------------- Motif Seed------------------ TTAAATATATTT TCAATTGTATTT TTATGTTTATTT TCAGGTTTATTT ------------------- Position weight matrix------------------ 1 2 3 4 5 6 7 8 9 10 11 12 A 0 0 4 2 1 0 1 0 4 0 0 0 G 0 0 0 1 2 0 1 0 0 0 0 0 C 0 2 0 0 0 0 0 0 0 0 0 0 T 4 2 0 1 1 4 2 4 0 4 4 4 IC 1.57 0.86 1.55 0.34 0.46 1.57 0.34 1.57 1.55 1.57 1.57 1.57 ------------------- Consensus sequences------------------ TCAAGTTTATTT ************ ************ ************ * * * ***** ------------------- Aligned Motif ------------------ #Motif Seq start end Motif Score Info >Motif-1 23 96 107 TTAAATATATTT 12.99 NC_012962_opr_2627875_gi_253987688_+_0.347544607610927 >Motif-1 5 8 19 TCAGGTTTATTT 12.96 NC_015761_opr_901534_gi_339998059_339998060_339998061_339998062_339998063_339998064_+_0.626192893401015 >Motif-1 33 231 242 TTATGTTTATTT 12.79 NC_009524_opr_2064415_gi_148653616_-_0.275396359365825 >Motif-1 39 117 128 TCAATTGTATTT 12.52 NC_008358_opr_220263_gi_114798718_114799312_114800318_114797879_+_0.237425198123888 >Motif-1 20 209 220 TTATATATATTT 12.10 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 >Motif-1 42 62 73 TCAATTAAATTT 11.73 NC_010577_opr_421368_gi_182680623_182680624_182680625_-_0.219922630560928 >Motif-1 21 228 239 TTAGGTTTACTT 11.09 NC_010554_opr_2276368_gi_197284164_+_0.435474912053323 >Motif-1 12 68 79 TTTATTTTATTT 10.97 NC_013850_opr_662986_gi_288936738_288936739_288936740_288936741_-_0.530771789753826 >Motif-1 4 50 61 TTAAATATACTT 10.85 NC_013941_opr_674269_gi_291280959_291280960_291280961_291280962_291280963_291280964_291280965_-_0.697553743513714 >Motif-1 24 208 219 TTTATTGAATTT 9.04 NC_014228_opr_2877151_gi_300722691_-_0.334597755650387 >Motif-1 27 216 227 TTATTAAAATTT 8.69 NC_015460_opr_3122764_gi_332288377_-_0.320342016305429 >Motif-1 20 227 238 TCAATAATACTT 8.43 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 >Motif-1 27 73 84 TTTTCTTTATTT 8.33 NC_015460_opr_3122764_gi_332288377_-_0.320342016305429 >Motif-1 28 57 68 TTAAAAACATTT 8.24 NC_015460_opr_3122885_gi_332288826_+_0.320342016305429 >Motif-1 24 199 210 TTATTAGAATTT 8.22 NC_014228_opr_2877151_gi_300722691_-_0.334597755650387 >Motif-1 1 94 105 TCATGTTCACTT 8.06 NC_000913_opr_3112_gi_16128515_16128516_145698227_16128518_+ >Motif-1 3 94 105 TCATGTTCACTT 8.06 NC_013941_opr_674368_gi_291281442_291281443_291281444_291281445_+_0.697553743513714 >Motif-1 40 6 17 TTATTTTTAGTT 7.91 NC_008343_opr_217622_gi_114327992_114327993_+_0.237119217751034 >Motif-1 28 202 213 TTTTGATTATTT 7.89 NC_015460_opr_3122885_gi_332288826_+_0.320342016305429 >Motif-1 3 169 180 TTCTTTATATTT 7.73 NC_013941_opr_674368_gi_291281442_291281443_291281444_291281445_+_0.697553743513714 >Motif-1 20 109 120 TTATTTTTATAT 7.73 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 >Motif-1 24 236 247 GTATTTTTATTT 7.73 NC_014228_opr_2877151_gi_300722691_-_0.334597755650387 >Motif-1 16 25 36 TTAGTAGGATTT 7.58 NC_015224_opr_3081924_gi_332159788_-_0.510371893104093 >Motif-1 20 105 116 TTATTTATTTTT 7.54 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 >Motif-1 27 79 90 TTATTTATATTG 7.53 NC_015460_opr_3122764_gi_332288377_-_0.320342016305429 >Motif-1 20 150 161 TCTTTATTATTT 7.40 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 ---------------------------------------------------- ********************************************************* Candidate Motif 2 ********************************************************* Motif length: 12 Motif number: 16 Seed number: 5 Motif Pvalue: 1.9E-14 (1372) ------------------- Motif Seed------------------ AATTTGAATAAT AATAACAATAAT AATATGGTTAAT AATATAGGTAAT AATAGGAATCAT ------------------- Position weight matrix------------------ 1 2 3 4 5 6 7 8 9 10 11 12 A 5 5 0 4 1 1 3 3 0 4 5 0 G 0 0 0 0 1 3 2 1 0 0 0 0 C 0 0 0 0 0 1 0 0 0 1 0 0 T 0 0 5 1 3 0 0 1 5 0 0 5 IC 1.59 1.59 1.61 0.94 0.46 0.72 0.88 0.45 1.61 1.02 1.59 1.61 ------------------- Consensus sequences------------------ AATATGAATAAT ************ ************ ************ **** **** ------------------- Aligned Motif ------------------ #Motif Seq start end Motif Score Info >Motif-2 23 17 28 AATATGGTTAAT 14.70 NC_012962_opr_2627875_gi_253987688_+_0.347544607610927 >Motif-2 23 33 44 AATATGGTTAAT 14.70 NC_012962_opr_2627875_gi_253987688_+_0.347544607610927 >Motif-2 24 273 284 AATATAGGTAAT 13.19 NC_014228_opr_2877151_gi_300722691_-_0.334597755650387 >Motif-2 4 53 64 AATATACTTAAT 13.14 NC_013941_opr_674269_gi_291280959_291280960_291280961_291280962_291280963_291280964_291280965_-_0.697553743513714 >Motif-2 12 137 148 AATTTGAATAAT 13.02 NC_013850_opr_662986_gi_288936738_288936739_288936740_288936741_-_0.530771789753826 >Motif-2 19 4 15 AATTGGATTAAT 12.83 NC_010554_opr_417996_gi_197285323_197285324_197285325_197285326_197285327_-_0.435474912053323 >Motif-2 14 40 51 AATAACAATAAT 12.37 NC_013850_opr_662420_gi_288933674_288933675_288933676_288933677_+_0.530771789753826 >Motif-2 20 282 293 AATAGGAATCAT 11.96 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 >Motif-2 27 268 279 AATTAACTTAAT 10.68 NC_015460_opr_3122764_gi_332288377_-_0.320342016305429 >Motif-2 10 79 90 AATATTCCTAAT 9.71 NC_014562_opr_754086_gi_308186849_308186850_+_0.54286843145002 >Motif-2 16 137 148 AATTACTTTAAT 9.19 NC_015224_opr_3081924_gi_332159788_-_0.510371893104093 >Motif-2 24 264 275 GATATGCGTAAT 8.49 NC_014228_opr_2877151_gi_300722691_-_0.334597755650387 >Motif-2 23 49 60 AATGTGGCTAAT 8.33 NC_012962_opr_2627875_gi_253987688_+_0.347544607610927 >Motif-2 23 58 69 AATAGCAATATT 8.18 NC_012962_opr_2627875_gi_253987688_+_0.347544607610927 >Motif-2 4 146 157 AATAGCAACAAT 8.16 NC_013941_opr_674269_gi_291280959_291280960_291280961_291280962_291280963_291280964_291280965_-_0.697553743513714 >Motif-2 12 21 32 AATAAAAATTAT 7.95 NC_013850_opr_662986_gi_288936738_288936739_288936740_288936741_-_0.530771789753826 ---------------------------------------------------- ********************************************************* Candidate Motif 3 ********************************************************* Motif length: 12 Motif number: 14 Seed number: 8 Motif Pvalue: 4.5E-12 (1134) ------------------- Motif Seed------------------ ATATTCCTTATT ATATTTCTTATT ATATCCCTTATT ATATGACTGATT ATATTTTAAATT CTATTTCTAATT ATATTCCTAATG ATATTACTAAAT ------------------- Position weight matrix------------------ 1 2 3 4 5 6 7 8 9 10 11 12 A 7 0 8 0 0 2 0 1 4 8 1 0 G 0 0 0 0 1 0 0 0 1 0 0 1 C 1 0 0 0 1 3 7 0 0 0 0 0 T 0 8 0 8 6 3 1 7 3 0 7 7 IC 1.20 1.67 1.65 1.67 0.80 0.36 1.56 1.17 0.40 1.65 1.17 1.22 ------------------- Consensus sequences------------------ ATATTCCTAATT ************ ************ ***** ****** ***** ** *** ------------------- Aligned Motif ------------------ #Motif Seq start end Motif Score Info >Motif-3 1 175 186 ATATTCCTTATT 14.15 NC_000913_opr_3112_gi_16128515_16128516_145698227_16128518_+ >Motif-3 3 175 186 ATATTTCTTATT 13.94 NC_013941_opr_674368_gi_291281442_291281443_291281444_291281445_+_0.697553743513714 >Motif-3 25 65 76 ATATCCCTTATT 13.18 NC_014228_opr_715150_gi_300722689_300722690_-_0.334597755650387 >Motif-3 10 80 91 ATATTCCTAATG 12.40 NC_014562_opr_754086_gi_308186849_308186850_+_0.54286843145002 >Motif-3 16 270 281 CTATTTCTAATT 12.18 NC_015224_opr_3081924_gi_332159788_-_0.510371893104093 >Motif-3 33 147 158 ATATGACTGATT 11.76 NC_009524_opr_2064415_gi_148653616_-_0.275396359365825 >Motif-3 34 77 88 ATATTTTAAATT 11.58 NC_009524_opr_317936_gi_148653613_148653614_148653615_-_0.275396359365825 >Motif-3 21 209 220 ATATTACTAAAT 11.52 NC_010554_opr_2276368_gi_197284164_+_0.435474912053323 >Motif-3 4 54 65 ATATACTTAATT 10.82 NC_013941_opr_674269_gi_291280959_291280960_291280961_291280962_291280963_291280964_291280965_-_0.697553743513714 >Motif-3 28 17 28 CTATCACTTATT 10.59 NC_015460_opr_3122885_gi_332288826_+_0.320342016305429 >Motif-3 20 213 224 ATATATTTTATT 10.25 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 >Motif-3 23 100 111 ATATATTTAAAT 8.10 NC_012962_opr_2627875_gi_253987688_+_0.347544607610927 >Motif-3 24 274 285 ATATAGGTAATT 7.78 NC_014228_opr_2877151_gi_300722691_-_0.334597755650387 >Motif-3 12 29 40 TTATTATTTATT 7.56 NC_013850_opr_662986_gi_288936738_288936739_288936740_288936741_-_0.530771789753826 ---------------------------------------------------- ********************************************************* Candidate Motif 4 ********************************************************* Motif length: 12 Motif number: 14 Seed number: 6 Motif Pvalue: 4.5E-12 (1134) ------------------- Motif Seed------------------ AAATATAAATTT AAATTGAAATTT AAATACCAATTT AAATAGACATTC AAATTTACATTT AAATTATTATTT ------------------- Position weight matrix------------------ 1 2 3 4 5 6 7 8 9 10 11 12 A 6 6 6 0 3 1 4 3 6 0 0 0 G 0 0 0 0 0 2 0 0 0 0 0 0 C 0 0 0 0 0 1 1 2 0 0 0 1 T 0 0 0 6 3 2 1 1 0 6 6 5 IC 1.62 1.62 1.62 1.64 0.69 0.10 0.55 0.43 1.62 1.64 1.64 1.11 ------------------- Consensus sequences------------------ AAATAGAAATTT ************ ************ ***** ****** **** **** ------------------- Aligned Motif ------------------ #Motif Seq start end Motif Score Info >Motif-4 9 28 39 AAATATAAATTT 14.45 NC_010658_opr_2309924_gi_187733887_-_0.605817068503636 >Motif-4 42 277 288 AAATTGAAATTT 14.42 NC_010577_opr_421368_gi_182680623_182680624_182680625_-_0.219922630560928 >Motif-4 27 202 213 AAATTTACATTT 14.07 NC_015460_opr_3122764_gi_332288377_-_0.320342016305429 >Motif-4 20 90 101 AAATAATAATTT 13.59 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 >Motif-4 8 171 182 AAATACCAATTT 13.13 NC_010658_opr_431740_gi_187730523_187734022_187731105_187731051_-_0.605817068503636 >Motif-4 12 37 26 AAATAATAATTT 12.59 NC_013850_opr_662986_gi_288936738_288936739_288936740_288936741_-_0.530771789753826 >Motif-4 42 113 102 AAATTTAAATTA 11.98 NC_010577_opr_421368_gi_182680623_182680624_182680625_-_0.219922630560928 >Motif-4 11 30 41 AAATAGACATTC 11.88 NC_014562_opr_2956850_gi_308189038_-_0.54286843145002 >Motif-4 4 61 72 TAATTTACATTT 11.59 NC_013941_opr_674269_gi_291280959_291280960_291280961_291280962_291280963_291280964_291280965_-_0.697553743513714 >Motif-4 12 20 31 AAATAAAAATTA 9.53 NC_013850_opr_662986_gi_288936738_288936739_288936740_288936741_-_0.530771789753826 >Motif-4 4 252 241 AAATTAATATTG 9.22 NC_013941_opr_674269_gi_291280959_291280960_291280961_291280962_291280963_291280964_291280965_-_0.697553743513714 >Motif-4 40 1 12 AAATATTATTTT 9.03 NC_008343_opr_217622_gi_114327992_114327993_+_0.237119217751034 >Motif-4 42 96 107 ACATACTAATTT 8.54 NC_010577_opr_421368_gi_182680623_182680624_182680625_-_0.219922630560928 >Motif-4 20 114 103 AAATAAATAATT 8.03 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 ---------------------------------------------------- ********************************************************* Candidate Motif 5 ********************************************************* Motif length: 20 Motif number: 13 Seed number: 5 Motif Pvalue: 6.4E-11 (1019) ------------------- Motif Seed------------------ TTTCTTTATATTCCTTATTT TTTCTTTATATTTCTTATTT ATTTATTCCACATTTTAATT TTTATATATCACGCATATTT TTATTTTATTTTCTTATCTT ------------------- Position weight matrix------------------ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 A 1 0 1 1 1 1 0 4 0 3 1 1 0 0 1 1 4 1 0 0 G 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 C 0 0 0 2 0 0 0 1 1 1 1 1 2 3 0 0 0 1 0 0 T 4 5 4 2 4 4 5 0 4 1 3 3 2 2 4 4 1 3 5 5 IC 0.96 1.61 0.96 0.39 0.96 0.96 1.61 1.02 1.03 0.44 0.45 0.45 0.47 0.97 0.96 0.96 0.94 0.45 1.61 1.61 ------------------- Consensus sequences------------------ TTTCTTTATATTCCTTATTT ******************** ******************** *** ******** ******* *** ***** *** ** ------------------- Aligned Motif ------------------ #Motif Seq start end Motif Score Info >Motif-5 1 168 187 TTTCTTTATATTCCTTATTT 20.90 NC_000913_opr_3112_gi_16128515_16128516_145698227_16128518_+ >Motif-5 3 168 187 TTTCTTTATATTTCTTATTT 20.69 NC_013941_opr_674368_gi_291281442_291281443_291281444_291281445_+_0.697553743513714 >Motif-5 9 77 96 TTTATATATCACGCATATTT 14.07 NC_010658_opr_2309924_gi_187733887_-_0.605817068503636 >Motif-5 4 6 25 TTATTTTATTTTCTTATCTT 12.68 NC_013941_opr_674269_gi_291280959_291280960_291280961_291280962_291280963_291280964_291280965_-_0.697553743513714 >Motif-5 17 214 233 ATTTATTCCACATTTTAATT 11.94 NC_013421_opr_628749_gi_261820376_261820377_-_0.452284263959391 >Motif-5 27 74 93 TTTCTTTATTTATATTGTTT 11.54 NC_015460_opr_3122764_gi_332288377_-_0.320342016305429 >Motif-5 20 95 114 ATAATTTCAATTATTTATTT 10.89 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 >Motif-5 33 42 61 TTTCTTTGAATACCTTTTGT 10.42 NC_009524_opr_2064415_gi_148653616_-_0.275396359365825 >Motif-5 4 10 29 TTTATTTTCTTATCTTACTC 10.29 NC_013941_opr_674269_gi_291280959_291280960_291280961_291280962_291280963_291280964_291280965_-_0.697553743513714 >Motif-5 20 208 227 ATTATATATATTTTATTATT 10.17 NC_010554_opr_417841_gi_197284431_197284432_197284433_197284434_-_0.435474912053323 >Motif-5 34 63 82 TTACCTTAGCTTTTATATTT 9.93 NC_009524_opr_317936_gi_148653613_148653614_148653615_-_0.275396359365825 >Motif-5 26 42 61 TTTTTATCATCTTTGTATTT 9.93 NC_015460_opr_845286_gi_332288374_332288375_332288376_-_0.320342016305429 >Motif-5 27 201 220 TAAATTTACATTTCTTTATT 9.74 NC_015460_opr_3122764_gi_332288377_-_0.320342016305429 ----------------------------------------------------