Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018331.1 Corchorus olitorius cultivar O-4 contig18364, 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: 37255
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:10895 original size:30 final size:30
Alignment explanation
Indices: 10861--10917 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
10851 TAGTCCTCAA
* * *
10861 TGTATTTGAATTATATCCAAACTCATATAT
1 TGTATTTCAATCATACCCAAACTCATATAT
*
10891 TGTATTTCACTCATACCCAAACTCATA
1 TGTATTTCAATCATACCCAAACTCATA
10918 AATACTCTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (30 bp):
TGTATTTCAATCATACCCAAACTCATATAT
Found at i:11949 original size:19 final size:17
Alignment explanation
Indices: 11927--11961 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
11917 TACTACTAAT
11927 AGAAAAACAAAAGTAAAAA
1 AGAAAAA-AAAA-TAAAAA
11946 AGAAAAAAAAATAAAA
1 AGAAAAAAAAATAAAA
11962 TAAAATTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.83, C:0.03, G:0.09, T:0.06
Consensus pattern (17 bp):
AGAAAAAAAAATAAAAA
Found at i:13171 original size:125 final size:125
Alignment explanation
Indices: 13002--13685 Score: 743
Period size: 125 Copynumber: 5.5 Consensus size: 125
12992 CAAACGTTTG
* * * * *
13002 TAAATATCGGAACAAG--TTTCACATCAATTGATCTCGACGTATTCCGACATTTGTAAGTGTTGG
1 TAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGACATCTGTAAGCGTTGG
* * * * * *
13065 TTTAGATATTATATAGGGACATTTATTAAACGTCGCTACAAAATACTATACCGACCCTTG
66 TATAGATATTATATCGTGACATTTATTAAACGTCGCTATAAAATACTATACCGACCATTA
* * *
13125 TAAATGTCGGAATAAGTTTTTCACATCATTTGATTTTGACGTATTCCGACATTTGTAAGCGTTGG
1 TAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGACATCTGTAAGCGTTGG
* * * * * *
13190 TATAGATATTATATCGTGACAATTATTACACGTCGCAACAAAATACTATACCGACCCTTG
66 TATAGATATTATATCGTGACATTTATTAAACGTCGCTATAAAATACTATACCGACCATTA
* ** * * * *
13250 TAAATGCCGGAACAAGTTGTTT-AGGTCATTTGATTTCGATGTATTCCGACTTTTGTAAGTGTTG
1 TAAATGTCGGAACAAGTT-TTTCACATCATTTGATTTCGACGTATTCCGACATCTGTAAGCGTTG
* * * * *
13314 GTATAGATATTATATCGTGACATTTATTAAACGTTGCAATAGAACACTATACCGACAATTA
65 GTATAGATATTATATCGTGACATTTATTAAACGTCGCTATAAAATACTATACCGACCATTA
* * * * * * * *
13375 CAAACGTCGGAACAAGTTCTTCACATTATTTAATTTTGACATATTCCGACATCTATAAGCGTTGG
1 TAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGACATCTGTAAGCGTTGG
* * * * *
13440 TATAAATATTATATCGTGACATTTATTAGACGTCACTTTAAGAA-A-TATACCGACGATTA
66 TATAGATATTATATCGTGACATTTATTAAACGTCGCTATAA-AATACTATACCGACCATTA
* * * * * *
13499 CAAATGTCGGAACAAGTTCTTCACATCATTTCAGTTCGAC-AATTCCGACATCTGTAAACGTTGG
1 TAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGACATCTGTAAGCGTTGG
* * * * *
13563 TATAGATATTATATCGTCACATTGATTAAACGTCACTATAAAAAAC-ATACCGACGATTA
66 TATAGATATTATATCGTGACATTTATTAAACGTCGCTATAAAATACTATACCGACCATTA
* * * * * *
13622 TAAATGTCGGAACAAGTTGTACAAATTATTTGAGTTCGACATATTCCGACATCTGTAAGCGTTG
1 TAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGACATCTGTAAGCGTTG
13686 AATCGTGACA
Statistics
Matches: 480, Mismatches: 73, Indels: 15
0.85 0.13 0.03
Matches are distributed among these distances:
122 2 0.00
123 119 0.25
124 71 0.15
125 283 0.59
126 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (125 bp):
TAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGACATCTGTAAGCGTTGG
TATAGATATTATATCGTGACATTTATTAAACGTCGCTATAAAATACTATACCGACCATTA
Found at i:15992 original size:73 final size:73
Alignment explanation
Indices: 15873--16021 Score: 289
Period size: 73 Copynumber: 2.0 Consensus size: 73
15863 GGTAAAGGGG
15873 TGAAAAGGGATCAATTTGGATTCACACTTGTGAACTTATCAAAATTAGTTCACACTAGGGTGAAG
1 TGAAAAGGGATCAATTTGGATTCACACTTGTGAACTTATCAAAATTAGTTCACACTAGGGTGAAG
15938 GCAGCTGA
66 GCAGCTGA
*
15946 TGAAAAGGGATCAATTTGGATTCACACTTGTGAACTTATCAAAATTAGTTCACACTGGGGTGAAG
1 TGAAAAGGGATCAATTTGGATTCACACTTGTGAACTTATCAAAATTAGTTCACACTAGGGTGAAG
16011 GCAGCTGA
66 GCAGCTGA
16019 TGA
1 TGA
16022 GCCATTTGTC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (73 bp):
TGAAAAGGGATCAATTTGGATTCACACTTGTGAACTTATCAAAATTAGTTCACACTAGGGTGAAG
GCAGCTGA
Found at i:16766 original size:215 final size:213
Alignment explanation
Indices: 16350--17414 Score: 1140
Period size: 215 Copynumber: 5.0 Consensus size: 213
16340 CAAAAAACGT
* * * * * * *
16350 TAAA-AAGAGCAACGTTATTAGAAAACGTTATTAAAATTT-ATAAAGAGTCGCAAGGTACTGCGA
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACT-CAATTTAAAAAAGAGTCGCAAGGTATTGCGA
* * * * * *
16413 CGTTTATTAAAAAAGACACGTA-TTT-AAGCGACGTTTACCCT-A-AACGTTGTCATAAATGTCG
65 CATTTATT-AAAATGTCA--TATTTTAAAACGACGTTT--CATAACAACGTTGTTATAAATGTCG
* * * * * *
16474 GAGAAGTCTATTTTAAAGAGAC-GTTGTTAAAAATGTCGCATGATTGAACAACATTTGAGATAAA
125 GAAAAGTCTATCTTAAAGCGACATTTGTTAAAAATGTCGCATTATTGAACGACATTTGAGA-AAA
* * *
16538 CGTCTCAACAAACGTCGCAAAAGTA
189 CGTCGCTACAAACGTCGCAAAAGCA
* * * * * * *
16563 TAACCAAGAGCGACTTTATTAAAAAACGTCACTCAGTTTAAAAAAGAGTCACAATGTACTGTGAC
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGGTATTGCGAC
* * *
16628 ATTTATTAAAATGTCATATTTTAAAACGACGTTTTATAACAACGTTTTTATAAATGTTGGAAAAG
66 ATTTATTAAAATGTCATATTTTAAAACGACGTTTCATAACAACGTTGTTATAAATGTCGGAAAAG
*
16693 TCTATCTTAAAGCGACATTTCTTAATAAATGTCGCATTATTGAACGACATTTGAGAAACACGTCG
131 TCTATCTTAAAGCGACATTTGTTAA-AAATGTCGCATTATTGAACGACATTTGAGAAA-ACGTCG
16758 CTACAAACGTCGCAAAAGCA
194 CTACAAACGTCGCAAAAGCA
* * *
16778 TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAGTTTAAAAAAGAGTCGTAATGTATTGCGAC
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGGTATTGCGAC
* * *
16843 ATTTATTAAAATGTCATATTTTAAAACGACGGTTT-ATAACAACATTCTTATAAATGTTGGAAAA
66 ATTTATTAAAATGTCATATTTTAAAACGAC-GTTTCATAACAACGTTGTTATAAATGTCGGAAAA
* ** * *
16907 GTCTATCTTAAAGCGACGTTTGTTGATTAATGTCAC-TTGATTGAATGACATTTGAGAAACACGT
130 GTCTATCTTAAAGCGACATTTGTT-AAAAATGTCGCATT-ATTGAACGACATTTGAGAAA-ACGT
* *
16971 TGCTACAAACGTTGCAAAAGCA
192 CGCTACAAACGTCGCAAAAGCA
* * *
16993 TAAACTAGAGCGACGTTATTAAAAAACGTCACTCAAATTAAAAAAGAGTCGCAAGGTATTGTGAC
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGGTATTGCGAC
* * *
17058 ATTTATCAAAATGTCATATTTTAAAACGACGTTTCCCT-A-AACGTTGTTATAAATGTCGGAGAA
66 ATTTATTAAAATGTCATATTTTAAAACGACGTTT-CATAACAACGTTGTTATAAATGTCGGAAAA
* * * * * * * *
17121 GTATGTCCTAAAGCGACATTTGTTAAAAACGTCG--TTA-AGAA--ACGTTGTTAAGAAAAATGT
130 GTCTATCTTAAAGCGACATTTGTTAAAAATGTCGCATTATTGAACGAC-AT-TTGAG-AAAACGT
* *
17181 CGTTACAAACGTCACACAAA-CA
192 CGCTACAAACGTCGCA-AAAGCA
* * *
17203 TAAACTAGAGCGACATTATTAAAAAACGTCACTCAATTTAAAAAAGTGTCGCAAGGTGA-TGCGA
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGGT-ATTGCGA
* * ** * *
17267 CATTTATTAAAATGTTATATATTAAAACGACGTTTCGGAAAAACGTTGCTATAAATGTCGGAAAA
65 CATTTATTAAAATGTCATATTTTAAAACGACGTTTCATAACAACGTTGTTATAAATGTCGGAAAA
* * * *
17332 GTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATGATTGAACGACGTTTGAGAAAACGTCT
130 GTCTATCTTAAAGCGACATTTGTT-AAAAATGTCGCATTATTGAACGACATTTGAGAAAACGTCG
*
17397 CTACAAACATCGCAAAAG
194 CTACAAACGTCGCAAAAG
17415 AAATAATTAA
Statistics
Matches: 724, Mismatches: 100, Indels: 55
0.82 0.11 0.06
Matches are distributed among these distances:
208 2 0.00
209 2 0.00
210 115 0.16
211 53 0.07
212 15 0.02
213 68 0.09
214 124 0.17
215 336 0.46
216 7 0.01
217 2 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (213 bp):
TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGGTATTGCGAC
ATTTATTAAAATGTCATATTTTAAAACGACGTTTCATAACAACGTTGTTATAAATGTCGGAAAAG
TCTATCTTAAAGCGACATTTGTTAAAAATGTCGCATTATTGAACGACATTTGAGAAAACGTCGCT
ACAAACGTCGCAAAAGCA
Found at i:17165 original size:13 final size:13
Alignment explanation
Indices: 17142--17175 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
17132 AGCGACATTT
17142 GTTAA-AAACGTC
1 GTTAAGAAACGTC
*
17154 GTTAAGAAACGTT
1 GTTAAGAAACGTC
17167 GTTAAGAAA
1 GTTAAGAAA
17176 AATGTCGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (13 bp):
GTTAAGAAACGTC
Found at i:17343 original size:425 final size:427
Alignment explanation
Indices: 16391--17414 Score: 1232
Period size: 425 Copynumber: 2.4 Consensus size: 427
16381 TAAAATTTAT
* * * * ** * * ***
16391 AAAGAGTCGCAAGGTACTGCGACGTTTATTAAAAAAGACACGTATTTAAGCGAC-GTTTACCCTA
1 AAAGAGTCGCAAGGTATTGCGACATTTATT-AAAATGTCATATATTAAAACGACGGTTTA-GAAA
* * *
16455 AACGTTG-TCATAAATGTCGGAGAAGTCTATTTTAAAGAGACG-TTGTT-AAAAATGTCGCATGA
64 AACGTTGCT-ATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATGA
* * * * *
16517 TTGAACAACATTTGAGATAAACGTCTCAACAAACGTCGCAAAAGTATAACCAAGAGCGACTTTAT
128 TTGAACGACATTTGAGA-AAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTAT
** * *
16582 TAAAAAACGTCACTCAGTTTAAAAAAGAGTCACAATGTACTGTGACATTTATTAAAATGTCATAT
192 TAAAAAACGTCACTCAAATTAAAAAAGAGTCACAAGGTACTGTGACATTTATCAAAATGTCATAT
* * * * *
16647 TTTAAAACGACGTTTTATAACAACGTTTTTATAAATGTTGGAAAAGTCTATCTTAAAGCGACATT
257 TTTAAAACGACGTTTCATAACAACGTTGTTATAAATGTCGGAAAAGTATATCCTAAAGCGACATT
* * * * *
16712 TCTTAATAAATGTCGCATTATTGAACGACATTTGAGAAACACGTCGCTACAAACGTCGCAAAAGC
322 TCTTAATAAACGTCG-ATTATAGAACGA-ATTTAAGAAAAACGTCGCTACAAACGTCACAAAAGC
* *
16777 ATAAACAAGAGCGACGTTATTAAAAAACGTCACTCAGTTTAAA
385 ATAAACAAGAGCGACATTATTAAAAAACGTCACTCAATTTAAA
* * * * *
16820 AAAGAGTCGTAATGTATTGCGACATTTATTAAAATGTCATATTTTAAAACGACGGTTTATAACAA
1 AAAGAGTCGCAAGGTATTGCGACATTTATTAAAATGTCATATATTAAAACGACGGTTTAGAAAAA
* * ** * *
16885 CATT-CTTATAAATGTTGGAAAAGTCTATCTTAAAGCGACGTTTGTTGATTAATGTCACTTGATT
66 CGTTGC-TATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATGATT
* * *
16949 GAATGACATTTGAGAAACACGT-TGCTACAAACGTTGCAAAAGCATAAACTAGAGCGACGTTATT
130 GAACGACATTTGAGAAA-ACGTCT-CTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTATT
* *
17013 AAAAAACGTCACTCAAATTAAAAAAGAGTCGCAAGGTATTGTGACATTTATCAAAATGTCATATT
193 AAAAAACGTCACTCAAATTAAAAAAGAGTCACAAGGTACTGTGACATTTATCAAAATGTCATATT
* * *
17078 TTAAAACGACGTTTCCCT-A-AACGTTGTTATAAATGTCGGAGAAGTATGTCCTAAAGCGACATT
258 TTAAAACGACGTTT-CATAACAACGTTGTTATAAATGTCGGAAAAGTATATCCTAAAGCGACATT
* * * *
17141 TGTTAA-AAACGTCG-TTA-AGAAACG-TTGTTAAGAAAAATGTCGTTACAAACGTCACACAAA-
322 TCTTAATAAACGTCGATTATAG-AACGAAT-TTAAGAAAAACGTCGCTACAAACGTCACA-AAAG
*
17201 CATAAACTAGAGCGACATTATTAAAAAACGTCACTCAATTTAAA
384 CATAAACAAGAGCGACATTATTAAAAAACGTCACTCAATTTAAA
* * *
17245 AAAGTGTCGCAAGGTGA-TGCGACATTTATTAAAATGTTATATATTAAAACGAC-GTTTCGGAAA
1 AAAGAGTCGCAAGGT-ATTGCGACATTTATTAAAATGTCATATATTAAAACGACGGTTT-AGAAA
17308 AACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATGAT
64 AACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATGAT
* *
17373 TGAACGACGTTTGAGAAAACGTCTCTACAAACATCGCAAAAG
129 TGAACGACATTTGAGAAAACGTCTCTACAAACGTCGCAAAAG
17415 AAATAATTAA
Statistics
Matches: 504, Mismatches: 76, Indels: 35
0.82 0.12 0.06
Matches are distributed among these distances:
424 25 0.05
425 188 0.37
426 12 0.02
428 57 0.11
429 83 0.16
430 138 0.27
431 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (427 bp):
AAAGAGTCGCAAGGTATTGCGACATTTATTAAAATGTCATATATTAAAACGACGGTTTAGAAAAA
CGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATGATTG
AACGACATTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTATTAAA
AAACGTCACTCAAATTAAAAAAGAGTCACAAGGTACTGTGACATTTATCAAAATGTCATATTTTA
AAACGACGTTTCATAACAACGTTGTTATAAATGTCGGAAAAGTATATCCTAAAGCGACATTTCTT
AATAAACGTCGATTATAGAACGAATTTAAGAAAAACGTCGCTACAAACGTCACAAAAGCATAAAC
AAGAGCGACATTATTAAAAAACGTCACTCAATTTAAA
Found at i:18449 original size:104 final size:104
Alignment explanation
Indices: 18268--18476 Score: 364
Period size: 104 Copynumber: 2.0 Consensus size: 104
18258 TAATAGTTGT
* *
18268 AACACAAGTTAGAATGTAGTTAATCCACTTAAATGGGAACCCATGTCTTGCCAAAAGTTATTCTA
1 AACACAAGTTAGAATGTAGTTAATCCACTTAAATGGGAACCCATGTCTTGCCAAAACTTATGCTA
*
18333 GGAAAGTTCAACTGATTAGGTTAGTAGTTAATCAACACA
66 GGAAAGTCCAACTGATTAGGTTAGTAGTTAATCAACACA
* *
18372 AACACAAGTTAGAATGTAGTTAATCCACTTATATGGGAACCCATGTCTTGCCAAAACTTGTGCTA
1 AACACAAGTTAGAATGTAGTTAATCCACTTAAATGGGAACCCATGTCTTGCCAAAACTTATGCTA
*
18437 GGAAAGTCCAACTGATTAGGTTAGTAGTTAATCCACACA
66 GGAAAGTCCAACTGATTAGGTTAGTAGTTAATCAACACA
18476 A
1 A
18477 TTTCTATCAA
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (104 bp):
AACACAAGTTAGAATGTAGTTAATCCACTTAAATGGGAACCCATGTCTTGCCAAAACTTATGCTA
GGAAAGTCCAACTGATTAGGTTAGTAGTTAATCAACACA
Found at i:24675 original size:123 final size:122
Alignment explanation
Indices: 24441--24764 Score: 326
Period size: 123 Copynumber: 2.6 Consensus size: 122
24431 TTAACCGAAC
24441 GAACCAAAAACTATTTTTGTAAAACATTAACCGAACCGAAGTATCCTATTCCGAACATTAACCGA
1 GAACCAAAAACTATTTTTGTAAAACATTAACCGAACCGAAGTATCCTATTCCGAACATTAACCGA
* *
24506 ACCGAAATATTTCGATTAACCGACCAAATGATATTTTAACATAAATTTAAAATTTAT
66 ACCGAAATATATCGATCAACCGACCAAATGATATTTTAACATAAATTTAAAATTTAT
* * *** *
24563 GAACCAAATACTATTTTTTGTAAAACATTAATCGAGTTGAAGTATCTTATTCCGAACATTAACCG
1 GAACCAAAAACTA-TTTTTGTAAAACATTAACCGAACCGAAGTATCCTATTCCGAACATTAACCG
* * * * * **
24628 AACTGAAATATATCGGTCAACCGATC-GATTATATTTTAATTTAAAATTTATTAACCGAATTAGT
65 AACCGAAATATATCGATCAACCGACCAAATGATATTTTAACAT-AAA--T-TTAA---AATT--T
24692 AT
121 AT
* * * ** * * * * *
24694 TAACCGAATACTACATATGTAAAACATTTACCGAACCGAAGTTTCCTATTCCGAGCATTAATCGA
1 GAACCAAAAACTATTTTTGTAAAACATTAACCGAACCGAAGTATCCTATTCCGAACATTAACCGA
24759 ACCGAA
66 ACCGAA
24765 GTATTTCAGT
Statistics
Matches: 162, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
122 24 0.15
123 70 0.43
125 1 0.01
126 4 0.02
129 4 0.02
130 45 0.28
131 14 0.09
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (122 bp):
GAACCAAAAACTATTTTTGTAAAACATTAACCGAACCGAAGTATCCTATTCCGAACATTAACCGA
ACCGAAATATATCGATCAACCGACCAAATGATATTTTAACATAAATTTAAAATTTAT
Found at i:30364 original size:2 final size:2
Alignment explanation
Indices: 30357--30394 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
30347 GTATAGTTAG
30357 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30395 GTGTATATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32045 original size:12 final size:14
Alignment explanation
Indices: 32005--32047 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
31995 TTGTAATGTA
32005 ATAT-TGTATAGAT
1 ATATATGTATAGAT
*
32018 GTATATGTATAGAT
1 ATATATGTATAGAT
32032 ATATAT-TATA-AT
1 ATATATGTATAGAT
32044 ATAT
1 ATAT
32048 GTTTCTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 6 0.22
13 7 0.26
14 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (14 bp):
ATATATGTATAGAT
Found at i:36307 original size:16 final size:16
Alignment explanation
Indices: 36261--36313 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
36251 TGAGAGGAAA
* *
36261 GAAATAGGATGGAAAG
1 GAAATAGGAGGGAAGG
*
36277 GAAATAGAAAGGGAAGG
1 GAAATAG-GAGGGAAGG
36294 GAAATAGTGA-GGAAGG
1 GAAATAG-GAGGGAAGG
36310 GAAA
1 GAAA
36314 GGAAGTCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.51, C:0.00, G:0.40, T:0.09
Consensus pattern (16 bp):
GAAATAGGAGGGAAGG
Found at i:36374 original size:17 final size:16
Alignment explanation
Indices: 36349--36391 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
36339 TTGGTAGGAT
*
36349 GGAAAGGAAATAGAAA
1 GGAAGGGAAATAGAAA
**
36365 GGGAAGGGAAATAGTGA
1 -GGAAGGGAAATAGAAA
36382 GGAAGGGAAA
1 GGAAGGGAAA
36392 GGAAGTCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.42, T:0.07
Consensus pattern (16 bp):
GGAAGGGAAATAGAAA
Found at i:36394 original size:78 final size:78
Alignment explanation
Indices: 36265--36425 Score: 313
Period size: 78 Copynumber: 2.1 Consensus size: 78
36255 AGGAAAGAAA
36265 TAGGATGGAAAGGAAATAGAAAGGGAAGGGAAATAGTGAGGAAGGGAAAGGAAGTCATATTTCCT
1 TAGGATGGAAAGGAAATAGAAAGGGAAGGGAAATAGTGAGGAAGGGAAAGGAAGTCATATTTCCT
*
36330 CCATCATGTTTGG
66 CCATCATGTCTGG
36343 TAGGATGGAAAGGAAATAGAAAGGGAAGGGAAATAGTGAGGAAGGGAAAGGAAGTCATATTTCCT
1 TAGGATGGAAAGGAAATAGAAAGGGAAGGGAAATAGTGAGGAAGGGAAAGGAAGTCATATTTCCT
36408 CCATCATGTCTGG
66 CCATCATGTCTGG
36421 TAGGA
1 TAGGA
36426 AGTAAAGAGA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.39, C:0.08, G:0.34, T:0.20
Consensus pattern (78 bp):
TAGGATGGAAAGGAAATAGAAAGGGAAGGGAAATAGTGAGGAAGGGAAAGGAAGTCATATTTCCT
CCATCATGTCTGG
Done.