Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020389.1 Corchorus olitorius cultivar O-4 contig20422, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 67186
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:745 original size:21 final size:21
Alignment explanation
Indices: 719--758 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
709 CTACAATACT
* *
719 AAAAATCGTGATGATTATTAC
1 AAAAATCCTGATGAATATTAC
740 AAAAATCCTGATGAATATT
1 AAAAATCCTGATGAATATT
759 TTTCCTCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (21 bp):
AAAAATCCTGATGAATATTAC
Found at i:1252 original size:21 final size:21
Alignment explanation
Indices: 1226--1265 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1216 CTACAATACT
*
1226 AAAAATCATGATGATTATTAC
1 AAAAATCATGATGAATATTAC
*
1247 AAAAATCGTGATGAATATT
1 AAAAATCATGATGAATATT
1266 TTTCCTCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (21 bp):
AAAAATCATGATGAATATTAC
Found at i:1273 original size:507 final size:505
Alignment explanation
Indices: 285--1726 Score: 2471
Period size: 507 Copynumber: 2.8 Consensus size: 505
275 CCTTGGAACG
*
285 CATTTTTAGCCAAAAATCGTGATGATTATTACACG-TTTCGGCTAAAATTTTGTAAAAATTGA-C
1 CATTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
* *
348 GTGAAAGATATTTCCTTC-ATTTTTTGGCTAAAATACTCATAAAAATGTATAAAATTTGAGACCA
66 G-GAAAGATATTTCC-TCAATTTTTT-GCTAAAATACTCATAAAAATGTATAAAATTTAACACCA
* *
412 AAAATATTGAAGGGTTTTTTACTCTTCTACTATCGTTTTTCCTACTTTTTCCGAATGAATTTCTA
128 AAAATATTGAAGGGTTTTTTACGCTTCTATTATCGTTTTTCCTACTTTTTCCGAATGAATTTCTA
477 GTTAAGTCAAAACAAGATTTAGATGCTCTTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
193 GTTAAGTCAAAACAAGATTTAGATGCTCTTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* * *
542 TGACTAGATGAATATAGATATTTCAAGGACTCTTGGCGCCAAAAATCATACACAACTGACCCAGA
258 TGATTAGATGAATATAGATATTTCAAGGACTCTTGGCGCCAAAAATCATACACAACTGACCCGGG
* *
607 CCCCGGAACGCATTTTTAGCAATAAAGAAAAACCGTGATGTTACATGATTTCGGCTAATATTTTG
323 GCCCGGAACGCGTTTTTAGCAATAAAGAAAAACCGTGATGTTACATGATTTCGGCTAATATTTTG
*
672 CAAAAATTGACCCGAAATATTTTTCCTCAATTTTTAGCTACAATACTAAAAATCGTGATGATTAT
388 C-AAAATTGACCCGAAATATTTTTCCTCAATTTTTAGCTACAATACTAAAAATCATGATGATTAT
*
737 TACAAAAATCCTGATGAATATTTTTCCTCAATTTTTAGCTACAATACTAAAAAT
452 TACAAAAATCCTGATGAATATTTTTCCTCAATTTGTAGCTACAATACTAAAAAT
*
791 CGTTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
1 CATTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
856 GGAAAGATATTTCCTCAATTTTTTGCTAAAATACTCATAAAAATGTATAAAATTTAACACCAAAA
66 GGAAAGATATTTCCTCAATTTTTTGCTAAAATACTCATAAAAATGTATAAAATTTAACACCAAAA
*
921 ATGTTGAAGGGTTTTTTACGCTTCTATTATCGTTTTTCCTACTTTTTCCGAATGAATTTCTAGTT
131 ATATTGAAGGGTTTTTTACGCTTCTATTATCGTTTTTCCTACTTTTTCCGAATGAATTTCTAGTT
986 AAGTCAAAACAAGATTTAGATGCTCTTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA
196 AAGTCAAAACAAGATTTAGATGCTCTTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA
1051 TTAGATGAATATAGATATTTCAAGGACTCTTGGCGCCAAAAATCATACACAACTGACCCGGGGCC
261 TTAGATGAATATAGATATTTCAAGGACTCTTGGCGCCAAAAATCATACACAACTGACCCGGGGCC
1116 CTGGAACGCGTTTTTAGCAATAAAGAAAAACCGTGATGTTACATGATTTCGGCTAATATTTTGCA
326 C-GGAACGCGTTTTTAGCAATAAAGAAAAACCGTGATGTTACATGATTTCGGCTAATATTTTGCA
*
1181 ATAATTGAACCGAAATATTTTTCCTCAATTTTTAGCTACAATACTAAAAATCATGATGATTATTA
390 A-AATTGACCCGAAATATTTTTCCTCAATTTTTAGCTACAATACTAAAAATCATGATGATTATTA
* *
1246 CAAAAATCGTGATGAATATTTTTCCTCAATTTGTAGCTACGATACTAAAAAT
454 CAAAAATCCTGATGAATATTTTTCCTCAATTTGTAGCTACAATACTAAAAAT
* * * *
1298 CATTTTTAGCCAATAATCGTGATGATTATTACACGATTTCAGCTAAAATTTTACAAAAATTGACA
1 CATTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
* *
1363 GGAAAGATATTTCCTCAATTGTTTGCTGAAATACTCATAAAAAATGTAT-AAATTTCAACACCAA
66 GGAAAGATATTTCCTCAATTTTTTGCTAAAATACTCAT-AAAAATGTATAAAATTT-AACACCAA
1427 AAATATTGAA-GGTTTTTTACGCTTCTATTATCGTTTTTCCTACTTTTTCCGAATGAATTTCTAG
129 AAATATTGAAGGGTTTTTTACGCTTCTATTATCGTTTTTCCTACTTTTTCCGAATGAATTTCTAG
* **
1491 TTAAGTCAAAACAAGATTTAGATGCTCTTAAAAACTAATCCTTAAATCCAATGTCACTGAGATTT
194 TTAAGTCAAAACAAGATTTAGATGCTCTTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
*
1556 GATTAGATGAATATAGATATTTCAAGGACTCTTGGCGCCAAAAAATCAAACACAACTGACCCGGG
259 GATTAGATGAATATAGATATTTCAAGGACTCTTGGCGCC-AAAAATCATACACAACTGACCCGGG
* *
1621 GTCCCGGAGCGCGTTTTTAGCAATAAAGAAAAACCGTGATGTTACACGATTTCGGCTAATATTTT
323 G-CCCGGAACGCGTTTTTAGCAATAAAGAAAAACCGTGATGTTACATGATTTCGGCTAATATTTT
* *
1686 GCAAAAGTTGACCCAAAATATTTTTTCTCAATTTTTAGCTA
387 GCAAAA-TTGACCCGAAATATTTTTCCTCAATTTTTAGCTA
1727 AAAAACTCAT
Statistics
Matches: 892, Mismatches: 34, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
506 266 0.30
507 476 0.53
508 147 0.16
509 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (505 bp):
CATTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
GGAAAGATATTTCCTCAATTTTTTGCTAAAATACTCATAAAAATGTATAAAATTTAACACCAAAA
ATATTGAAGGGTTTTTTACGCTTCTATTATCGTTTTTCCTACTTTTTCCGAATGAATTTCTAGTT
AAGTCAAAACAAGATTTAGATGCTCTTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA
TTAGATGAATATAGATATTTCAAGGACTCTTGGCGCCAAAAATCATACACAACTGACCCGGGGCC
CGGAACGCGTTTTTAGCAATAAAGAAAAACCGTGATGTTACATGATTTCGGCTAATATTTTGCAA
AATTGACCCGAAATATTTTTCCTCAATTTTTAGCTACAATACTAAAAATCATGATGATTATTACA
AAAATCCTGATGAATATTTTTCCTCAATTTGTAGCTACAATACTAAAAAT
Found at i:3968 original size:331 final size:329
Alignment explanation
Indices: 3452--4795 Score: 1197
Period size: 331 Copynumber: 4.0 Consensus size: 329
3442 GATTCAGTTT
* * *
3452 GATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAA-AATCATTTAAAACTGA-ACGGGGCC
1 GATGAATATAAATATTTCAAGGAGTCTCGGCGCCAAAAATAATGA---AAAACTGAGTCGGGGCC
* * * * *
3515 TC-AGAACGCATTTTTAGCCAAACACCATGATGAT-TATTAGGCAATTTCAGCTAAAATTTTGCA
63 CCGA-AACGCGTTTTTAGCCAAAAACCATGATG-TGTA-CACG-AATTTCAGCTAAAATTTTGCA
* * * * * *
3578 AAAATTGACCCG-AAAGATATTTTCTCAATTTTTAG-TCATAATACTGATAAAAAATATATATAA
124 AAAAATGAACCGAAAAGAT-TTTCCTCAATTTTTGGCT-AAAATACTCAT--AAAATATATATAA
* *
3641 TTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTTTAATATCGTTTTTCATATTTTATTTAAG
185 TTCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTT-TCT-A-
* * * *
3706 AATTAATTTCTAATTAAATCGGAACAAAATTCAGATGCTTGTAAAAACAAATTTTTACATACAAT
247 AATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATTCTTAAATACAAT
* *
3771 GTGGCTAAGATTTTATTA
312 GTGGCTGAGATTTGATTA
* * *
3789 GATGAATATAAATATTTCAAGGAGTGTCGGCGACAAAAATAATGAAAAACTGAGTCGCGGCCCCG
1 GATGAATATAAATATTTCAAGGAGTCTCGGCGCCAAAAATAATGAAAAACTGAGTCGGGGCCCCG
*
3854 AAACGCGTTTTTAGCCAAAAACCATGATG-GT-CACGATTTTC-GCTAAAATTTTGCAAAAAATG
66 AAACGCGTTTTTAGCCAAAAACCATGATGTGTACACGAATTTCAGCTAAAATTTTGCAAAAAATG
** * *
3916 GTCCGAAAA-ATTTATCCTCAATTTTTGGATAAAATACTCATAAAATATATATAA-TCTAACTCC
131 AACCGAAAAGATTT-TCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTC-AACGCC
* * * * * * * *
3979 AAAAAGATTGGAGGACTTTTCGCGCTTTTAATTTTGTTTTTGATATTTTTCTGAATTAATTTCTA
194 AAAAAAATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATTAATTTCTA
* * * * *
4044 ATTAAATCGAAACAAGATTTTCATATGCTTGTAAAAACAAATTCTTAAATACGATGTGGCTGATA
259 ATTAAATCGAAACAA-A-ATTCAGATGCTCGTAAAAACAAATTCTTAAATACAATGTGGCTGAGA
4109 TTTGATTA
322 TTTGATTA
* ** * * * * * * * *
4117 AATGAATATGGATATTTTAAGGAGTTTTGACGCCAAAAATATTGCAAAACTGAGTCGGGGCTCAG
1 GATGAATATAAATATTTCAAGGAGTCTCGGCGCCAAAAATAATGAAAAACTGAGTCGGGGCCCCG
* * ** * * * *
4182 -AACACTTTTTTAGCCAAAAACTGTGATAATTATTACAC-AATTTCGGCTAAAATTTTGTAAAAA
66 AAACGCGTTTTTAGCCAAAAACCATGAT--GT-GTACACGAATTTCAGCTAAAATTTTGCAAAAA
* * * * * *
4245 TTG-ACCCAAAAGATATTTCCTCAATTTTTGGCTAAAATGCGCATATAA-ATATATAATTTAACG
128 ATGAACCGAAAAGAT-TTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACG
* * * * * *
4308 CCAAAAAGATTGAAGGGCTTTTGACG-TTTCTAATATCGTTTTTCCTTTTTTTTCCACATTAATT
192 CCAAAAAAATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTT-CATATTTTTCTAAATTAATT
* * * * *
4372 TGTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTCGCTGA
255 TCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATTCTTAAATACAATGTGGCTGA
4437 GATTTGATTA
320 GATTTGATTA
* * * * * * ** *
4447 GATGAATATAAATATTTCAAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGAGCCAAGTCCCCG
1 GATGAATATAAATATTTCAAGGAGTCTCGGCGCCAAAAATAATGAAAAACTGAGTCGGGGCCCCG
* * *
4512 GAATGCGTTTTTAGCCAAAAACCGTGATGGTTTGTTAGTACAC-AATTT-AGGCTAAAATTTTGC
66 AAACGCGTTTTTAGCCAAAAACC---AT-G-ATG-T-GTACACGAATTTCA-GCTAAAATTTTGC
*
4575 -AAAAATTAACACG-AAAGATTTCTCCTCAATTTTTGGCTAAAATACTCATAAAA-ATATATAAT
123 AAAAAATGAAC-CGAAAAGATTT-TCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAAT
* * * * ** * * * *
4637 TTAACACC-AAAAAATTGGAGGGCTTTTTATACTTTTGATATCATATTTCTTATTTTTCTAAATT
186 TCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATT
* * * * * * *
4701 AATATCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATTTTTAAATCCAATATTG
251 AATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATTCTTAAATACAATGTGG
*
4766 TTGAGATTT-AGTTA
316 CTGAGATTTGA-TTA
*
4780 GAT-AATGTAAAGTATT
1 GATGAATATAAA-TATT
4796 AAACCAATTT
Statistics
Matches: 826, Mismatches: 146, Indels: 74
0.79 0.14 0.07
Matches are distributed among these distances:
326 26 0.03
327 24 0.03
328 103 0.12
329 59 0.07
330 99 0.12
331 120 0.15
332 101 0.12
333 93 0.11
334 36 0.04
335 89 0.11
336 35 0.04
337 37 0.04
338 4 0.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (329 bp):
GATGAATATAAATATTTCAAGGAGTCTCGGCGCCAAAAATAATGAAAAACTGAGTCGGGGCCCCG
AAACGCGTTTTTAGCCAAAAACCATGATGTGTACACGAATTTCAGCTAAAATTTTGCAAAAAATG
AACCGAAAAGATTTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACGCCAA
AAAAATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATTAATTTCTAAT
TAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATTCTTAAATACAATGTGGCTGAGATTTG
ATTA
Found at i:5164 original size:15 final size:16
Alignment explanation
Indices: 5146--5175 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5136 ATAAATGATA
5146 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
5161 ATATTATAATCTAAA
1 ATATTATAATCTAAA
5176 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:5239 original size:20 final size:20
Alignment explanation
Indices: 5214--5252 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5204 TATAGTGGAT
5214 TATTGTAATTAAAAATAATA
1 TATTGTAATTAAAAATAATA
5234 TATTGTAATTAAAAATAAT
1 TATTGTAATTAAAAATAAT
5253 TAATTACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TATTGTAATTAAAAATAATA
Found at i:5263 original size:20 final size:20
Alignment explanation
Indices: 5220--5264 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5210 GGATTATTGT
**
5220 AATTAAAAATAATATATTGT
1 AATTAAAAATAATATATTAC
5240 AATTAAAAATAAT-TAATTAC
1 AATTAAAAATAATAT-ATTAC
5260 AATTA
1 AATTA
5265 TAGTGGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTAAAAATAATATATTAC
Found at i:8109 original size:28 final size:28
Alignment explanation
Indices: 8042--8124 Score: 125
Period size: 28 Copynumber: 3.0 Consensus size: 28
8032 ACAAATCCAA
*
8042 TGTAAACTCAATTGGCAAATTGGGTCA--
1 TGTAAACTTAATT-GCAAATTGGGTCATC
8069 TGTAAACTTAATTGCAAATTGGGTCATC
1 TGTAAACTTAATTGCAAATTGGGTCATC
*
8097 TGTAACCTTAATTGCAAATTGGGTCATC
1 TGTAAACTTAATTGCAAATTGGGTCATC
8125 GTAGTTCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
26 13 0.25
27 12 0.23
28 27 0.52
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (28 bp):
TGTAAACTTAATTGCAAATTGGGTCATC
Found at i:11352 original size:33 final size:33
Alignment explanation
Indices: 11305--11369 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
11295 AGTTAAGTTT
*
11305 ATGCAATTTGAAAAGATGGGAACACCATTAATC
1 ATGCAATTTAAAAAGATGGGAACACCATTAATC
*
11338 ATGCAATTTAAAAAGATGGGAACACTATTAAT
1 ATGCAATTTAAAAAGATGGGAACACCATTAAT
11370 AGAAGTCAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (33 bp):
ATGCAATTTAAAAAGATGGGAACACCATTAATC
Found at i:28011 original size:96 final size:94
Alignment explanation
Indices: 27847--28037 Score: 301
Period size: 96 Copynumber: 2.0 Consensus size: 94
27837 TATGAAGTTA
* *
27847 CATTGCGACAGTTGCAATCTGCATCAAAAGTAGAGGAAAACTCCCACAACGGAAAACTTGAAGAT
1 CATTGCAACAGTTGCAATCTGCATCAAAAGTAGAGGAAAACTACCACAACGGAAAACTTGAAGAT
*
27912 AAGGCAGCGACAATCAGGCACTAAAAAAGT
66 AAGGCAGCGAC-ATCAGACACTAAAAAAGT
* * *
27942 CATTGCAACAGTTGCAGGTCTGCATCAAAAGTAGAGGAAAACTACCACGACGGAAAACTTGAAGT
1 CATTGCAACAGTTGCA-ATCTGCATCAAAAGTAGAGGAAAACTACCACAACGGAAAACTTGAAGA
*
28007 TAAGGCAGCGACATCAGACACTAAAATAGT
65 TAAGGCAGCGACATCAGACACTAAAAAAGT
28037 C
1 C
28038 GTCTAATGAA
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 32 0.36
96 56 0.64
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (94 bp):
CATTGCAACAGTTGCAATCTGCATCAAAAGTAGAGGAAAACTACCACAACGGAAAACTTGAAGAT
AAGGCAGCGACATCAGACACTAAAAAAGT
Found at i:37345 original size:2 final size:2
Alignment explanation
Indices: 37338--37368 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
37328 AACTAGCTCC
37338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37369 ACTTCTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37565 original size:3 final size:3
Alignment explanation
Indices: 37557--37593 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
37547 TCCATCCTAA
37557 TAT TAT TAT TAT TAT TA- TAT TA- TAT ATAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TA
37594 ACTTAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:37578 original size:17 final size:17
Alignment explanation
Indices: 37556--37591 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
37546 GTCCATCCTA
37556 ATATTAT-TATTATTATT
1 ATATTATATA-TATTATT
37573 ATATTATATATATTATT
1 ATATTATATATATTATT
37590 AT
1 AT
37592 TAACTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTATATATATTATT
Found at i:40668 original size:20 final size:21
Alignment explanation
Indices: 40640--40682 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
40630 GACAACCAAA
*
40640 TTGGTTAAAAACAATGCA-TT
1 TTGGCTAAAAACAATGCACTT
40660 TTGGCTAAAAACAATGCACTT
1 TTGGCTAAAAACAATGCACTT
40681 TT
1 TT
40683 TGTGTTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (21 bp):
TTGGCTAAAAACAATGCACTT
Found at i:47170 original size:16 final size:16
Alignment explanation
Indices: 47149--47183 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
47139 AAGACTCTAG
47149 TTATAATAACTTATTA
1 TTATAATAACTTATTA
47165 TTATAATAACTTATTA
1 TTATAATAACTTATTA
47181 TTA
1 TTA
47184 GTTCTTAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATAATAACTTATTA
Found at i:52057 original size:12 final size:12
Alignment explanation
Indices: 52040--52087 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
52030 TTATGTTCGT
52040 TTATATTATATA
1 TTATATTATATA
52052 TTATATTATATA
1 TTATATTATATA
*
52064 TAATAATTATAT-
1 TTAT-ATTATATA
*
52076 TTTTATT-TATA
1 TTATATTATATA
52087 T
1 T
52088 AAATATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 3 0.10
11 4 0.13
12 17 0.55
13 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATATTATATA
Found at i:52073 original size:25 final size:23
Alignment explanation
Indices: 52044--52089 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
52034 GTTCGTTTAT
52044 ATTATATATTATATTATATATAATA
1 ATTATAT-TTATATT-TATATAATA
*
52069 ATTATATTTTTATTTATATAA
1 ATTATATTTATATTTATATAA
52090 ATATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTATATTTATATTTATATAATA
Found at i:52095 original size:23 final size:24
Alignment explanation
Indices: 52042--52095 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
52032 ATGTTCGTTT
52042 ATATTATATATTATATTATATATA
1 ATATTATATATTATATTATATATA
*
52066 ATAATTATAT-TTTTATT-TATATAA
1 AT-ATTATATATTATATTATATAT-A
52090 ATATTA
1 ATATTA
52096 AAAATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 9 0.33
24 11 0.41
25 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATATTATATATTATATTATATATA
Found at i:52134 original size:42 final size:39
Alignment explanation
Indices: 52059--52156 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 39
52049 ATATTATATT
* *
52059 ATATATAATAATTATATTTTTATTTATATAAATATTAAAA
1 ATATAT-ATAATTATATTTTAATTTATATAAATAATAAAA
* * *
52099 ATATATATACTTATATTTTAATTTTTATTCCAAATAATATAA
1 ATATATATAATTATATTTTAATTTATA-T--AAATAATAAAA
*
52141 ATATTTATAAATTATA
1 ATATATAT-AATTATA
52157 ATAGTATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 18 0.38
40 7 0.15
42 16 0.34
43 6 0.13
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (39 bp):
ATATATATAATTATATTTTAATTTATATAAATAATAAAA
Found at i:53058 original size:12 final size:13
Alignment explanation
Indices: 53035--53066 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
53025 AAATATAGAC
53035 ATATATATTTTTA
1 ATATATATTTTTA
53048 ATATATA-TTTTA
1 ATATATATTTTTA
53060 ATATATA
1 ATATATA
53067 CATAGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATATATTTTTA
Found at i:54101 original size:24 final size:21
Alignment explanation
Indices: 54052--54095 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
54042 CAAAATTTTC
54052 ATTTAATAAGATAAAAAATAT
1 ATTTAATAAGATAAAAAATAT
* *
54073 ATTTAATAATAT-AATAATAT
1 ATTTAATAAGATAAAAAATAT
54093 ATT
1 ATT
54096 ATTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTAATAAGATAAAAAATAT
Found at i:57999 original size:15 final size:14
Alignment explanation
Indices: 57980--58006 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57970 ACTTGGTAAA
57980 AAAAAAGAAAATCT
1 AAAAAAGAAAATCT
57994 AAAAAAGAAAATC
1 AAAAAAGAAAATC
58007 AAGTTGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.11
Consensus pattern (14 bp):
AAAAAAGAAAATCT
Found at i:58137 original size:2 final size:2
Alignment explanation
Indices: 58132--58160 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
58122 CTCCCCCCAT
58132 TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
58161 ATTGTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:58245 original size:2 final size:2
Alignment explanation
Indices: 58238--58270 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
58228 CTTCCACCCA
58238 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
58271 CACAGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:60487 original size:43 final size:43
Alignment explanation
Indices: 60439--60522 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
60429 AGGGTTCTAA
* * *
60439 TATGATTTTATTACAAATTA-CCTGACTCTCTTGATTTCAGTAG
1 TATGATTTGATCACAAATTATCC-GACTCTCTTAATTTCAGTAG
* *
60482 TATGATTTGATCACAGATTATCCGGCTCTCTTAATTTCAGT
1 TATGATTTGATCACAAATTATCCGACTCTCTTAATTTCAGT
60523 GATCAGAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 33 0.94
44 2 0.06
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (43 bp):
TATGATTTGATCACAAATTATCCGACTCTCTTAATTTCAGTAG
Found at i:67144 original size:2 final size:2
Alignment explanation
Indices: 67137--67183 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
67127 CACAGACTGC
67137 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
67179 AG AG A
1 AG AG A
67184 TGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.