Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014898.1 Corchorus capsularis cultivar CVL-1 contig14919, 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: 56760
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1313 original size:18 final size:18
Alignment explanation
Indices: 1292--1347 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
1282 TGCAAAACCC
1292 GTGGCAAATTGAAAAGTT
1 GTGGCAAATTGAAAAGTT
*
1310 GTGGCAAA--G----GTC
1 GTGGCAAATTGAAAAGTT
1322 GTGGCAAATTGAAAAGTT
1 GTGGCAAATTGAAAAGTT
1340 GTGGCAAA
1 GTGGCAAA
1348 GGCCGTGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 10 0.33
14 1 0.03
16 1 0.03
18 18 0.60
ACGTcount: A:0.36, C:0.09, G:0.32, T:0.23
Consensus pattern (18 bp):
GTGGCAAATTGAAAAGTT
Found at i:1325 original size:30 final size:30
Alignment explanation
Indices: 1290--1360 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
1280 GCTGCAAAAC
1290 CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
1 CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
*
1320 TCGTGGCAAATTGAAAAGTTGTGGCAAAGG
1 CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
*
1350 CCGTGCCAAAT
1 CCGTGGCAAAT
1361 AGCCACGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.21
Consensus pattern (30 bp):
CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
Found at i:2386 original size:18 final size:18
Alignment explanation
Indices: 2365--2420 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
2355 TGCAAAACCC
2365 GTGGCAAATTGAAAAGTT
1 GTGGCAAATTGAAAAGTT
*
2383 GTGGCAAA--G----GTC
1 GTGGCAAATTGAAAAGTT
2395 GTGGCAAATTGAAAAGTT
1 GTGGCAAATTGAAAAGTT
2413 GTGGCAAA
1 GTGGCAAA
2421 GGCCGTGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 10 0.33
14 1 0.03
16 1 0.03
18 18 0.60
ACGTcount: A:0.36, C:0.09, G:0.32, T:0.23
Consensus pattern (18 bp):
GTGGCAAATTGAAAAGTT
Found at i:2398 original size:30 final size:30
Alignment explanation
Indices: 2363--2433 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
2353 GCTGCAAAAC
2363 CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
1 CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
*
2393 TCGTGGCAAATTGAAAAGTTGTGGCAAAGG
1 CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
*
2423 CCGTGCCAAAT
1 CCGTGGCAAAT
2434 AGCCACGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.21
Consensus pattern (30 bp):
CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
Found at i:2401 original size:529 final size:536
Alignment explanation
Indices: 955--2618 Score: 2336
Period size: 529 Copynumber: 3.1 Consensus size: 536
945 TCATTGGTTG
* ** * * * *
955 GATGTATAATTTCGTGTAAAATAGTTTTGGTATTGGAAAAGAAATCAAAATTGTGTAC-ATG-GT
1 GATGTAGAATTTAATGTAAAATAG-TTTGGGAGTGGAAAA-AAATCAAAATTGT-AACTA-GACT
* * *
1018 ATAATTAGCAAAATGTATAT-GTAATACTT-TCTATGAATATACACTACTAACACATTTGTATAT
62 -TAATTAGCTAAATGTAT-TCGTAGTA-TTATCTATG-AT-CACACTACTAACACATTTGTATAT
** ** *
1081 TATGACAATGTACAAAGATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTGGGGG
122 TATGACTTTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGG
*
1146 ACAATATAGAATTTTGAGATGATATAAAAGCAATTATGTGATCATTAGCCAATTACTAACTCATA
187 ACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCATTAGCCAATTACTAACTCATA
* *
1211 TAAGTATAGGGTTTGACGTCAATCATCTCTCAATTTGCCACGGCCTTTGCCACGGGTAGCTGTAA
252 TAAGTATAGGGTTTGAGGTCAATCATCTCTCAATTCGCCACGGCCTTTG-C-C--G-A----TAA
1276 ACCCGCTGCAAAACCCGTGGCAAATTGAAAAGTTGTGGCAAAGGTCGTGGCAAATTGAAAAGTTG
308 ACCCGCTGCAAAACCCGTGGCAAATTGAAAAGTTGTGGCAAAGG-CGT-GC---------A---G
1341 TGGCAAAGGCCGTGCCAAATAGCCACGACTTTTCCCACGG---TTAAGAAACCCGTTTCAAAAAC
359 TGGCAAAGGCCGTGCCAAATAGCCACGACTTTTCCCACGGTTTTTAAGAAACCCGTTTCAAAAAC
1403 CGTGGCAAATGTAGAATTCATGTCTAAGAATTTTACCCTAAACAAAGATAATTTGATGTTCCCAT
424 CGTGGCAAATGTAGAATTCATGTCTAAGAATTTTACCCTAAACAAAGATAATTTGATGTTCCCAT
*
1468 AAAATTAAAGCTTTTTACGGTACCATATTGTGTTTAGCTCGAGTATTT
489 AAAATTAAAGCTTTTTATGGTACCATATTGTGTTTAGCTCGAGTATTT
1516 GATGTAGAATTTAATGTAAAATAGTTTGGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAAT
1 GATGTAGAATTTAATGTAAAATAGTTTGGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAAT
* * *
1581 TAGCTAAATGTATTCGTAGTATTATCTATGATCACACTACTAACGCAGTTGTATATTATGAGTTT
66 TAGCTAAATGTATTCGTAGTATTATCTATGATCACACTACTAACACATTTGTATATTATGACTTT
** *
1646 GTGTAAAGATTCAACGAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGGATAATATAG
131 GTGTAAAGATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGGACAATATAG
* *
1711 AATTTTGAGATGATATAAATGCAATTATGTGATCATTAGCCAATTACCAACTCATATATGTATAG
196 AATTTTGAGATGATATAAATGCAATTATGTGATCATTAGCCAATTACTAACTCATATAAGTATAG
1776 GGTTTGAGGTCAATCATCTCTCAATTCGCCACGGCCTTTGCCACGGGAATCTGTAAACCCGCTGC
261 GGTTTGAGGTCAATCATCTCTCAATTCGCCACGGCCTTTG-C-C--G-A----TAAACCCGCTGC
1841 AAAACCCGTGGCAAATTGAAAA---GT----------T---GTGGCAAAGGCCGTGCCAAATAGC
317 AAAACCCGTGGCAAATTGAAAAGTTGTGGCAAAGGCGTGCAGTGGCAAAGGCCGTGCCAAATAGC
1890 CACGACTTTTCCCACGGTTTTTAAGAAACCCGTTTCAAAAACCGTGGCAAATGTAGAATTCATGT
382 CACGACTTTTCCCACGGTTTTTAAGAAACCCGTTTCAAAAACCGTGGCAAATGTAGAATTCATGT
*
1955 CTAAGAATTTTACCCTAAACAAAGATAATTTGATGTTCCCATAAAATTAAAGGTTTTTATGGTAC
447 CTAAGAATTTTACCCTAAACAAAGATAATTTGATGTTCCCATAAAATTAAAGCTTTTTATGGTAC
*
2020 CATTTTGTGTTTAGCTCGAGTATTT
512 CATATTGTGTTTAGCTCGAGTATTT
2045 GATGTAGAATTTAATGTAAAATAGTTTGGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAAT
1 GATGTAGAATTTAATGTAAAATAGTTTGGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAAT
* *
2110 TGGCTAAATGTATTCGTAGTATTATCTATGATCACACTAGTAACACATTTGTATATTATGACTTT
66 TAGCTAAATGTATTCGTAGTATTATCTATGATCACACTACTAACACATTTGTATATTATGACTTT
2175 GTGTAAAGATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGGACAATATAG
131 GTGTAAAGATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGGACAATATAG
*
2240 AATTTTGAGATGATATAAATGCAATTATGTGATCATTAGTCAATTACTAACTCATATAAGTATAG
196 AATTTTGAGATGATATAAATGCAATTATGTGATCATTAGCCAATTACTAACTCATATAAGTATAG
2305 GGTTTGAGGTCAATCATCTCTCAATTCGCCACGGCCTTTG-C-A-AAACCCGCTGCAAAACCCGT
261 GGTTTGAGGTCAATCATCTCTCAATTCGCCACGGCCTTTGCCGATAAACCCGCTGCAAAACCCGT
2367 GGCAAATTGAAAAGTTGTGGCAAAGGTCGTGGCAAATTGAAAAGTTGTGGCAAAGGCCGTGCCAA
326 GGCAAATTGAAAAGTTGTGGCAAAGG-CGT-GC---------A---GTGGCAAAGGCCGTGCCAA
*
2432 ATAGCCACGACTTTTCCCACGGTTTTTAAGAAACCCGTTTCAAAAACTGTGGCAAATGTAGAATT
377 ATAGCCACGACTTTTCCCACGGTTTTTAAGAAACCCGTTTCAAAAACCGTGGCAAATGTAGAATT
*
2497 CATGTCTAAGAATTTTACCCTAAACAAAGATAATTTGATGTTCCCATAAAATTAAAACTTTTTAT
442 CATGTCTAAGAATTTTACCCTAAACAAAGATAATTTGATGTTCCCATAAAATTAAAGCTTTTTAT
*
2562 GGTACCATATTGTGTTTAACTCGAGTATTT
507 GGTACCATATTGTGTTTAGCTCGAGTATTT
2592 GATGTAGAATTTAATGTAAAATAGTTT
1 GATGTAGAATTTAATGTAAAATAGTTT
2619 AGACTTAATT
Statistics
Matches: 1019, Mismatches: 47, Indels: 88
0.88 0.04 0.08
Matches are distributed among these distances:
517 33 0.03
520 2 0.00
522 1 0.00
526 42 0.04
529 421 0.41
531 1 0.00
542 1 0.00
547 201 0.20
553 2 0.00
556 231 0.23
557 5 0.00
558 30 0.03
559 15 0.01
560 13 0.01
561 21 0.02
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (536 bp):
GATGTAGAATTTAATGTAAAATAGTTTGGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAAT
TAGCTAAATGTATTCGTAGTATTATCTATGATCACACTACTAACACATTTGTATATTATGACTTT
GTGTAAAGATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGGACAATATAG
AATTTTGAGATGATATAAATGCAATTATGTGATCATTAGCCAATTACTAACTCATATAAGTATAG
GGTTTGAGGTCAATCATCTCTCAATTCGCCACGGCCTTTGCCGATAAACCCGCTGCAAAACCCGT
GGCAAATTGAAAAGTTGTGGCAAAGGCGTGCAGTGGCAAAGGCCGTGCCAAATAGCCACGACTTT
TCCCACGGTTTTTAAGAAACCCGTTTCAAAAACCGTGGCAAATGTAGAATTCATGTCTAAGAATT
TTACCCTAAACAAAGATAATTTGATGTTCCCATAAAATTAAAGCTTTTTATGGTACCATATTGTG
TTTAGCTCGAGTATTT
Found at i:4074 original size:26 final size:25
Alignment explanation
Indices: 4037--4087 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
4027 TTTTGCAACA
4037 ACATGATCCTCTCTCCTTAGTGATT
1 ACATGATCCTCTCTCCTTAGTGATT
*
4062 ACATGATATCTCTCTCCTTAGTGATT
1 ACATGAT-CCTCTCTCCTTAGTGATT
4088 CAGAGTAGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (25 bp):
ACATGATCCTCTCTCCTTAGTGATT
Found at i:8102 original size:23 final size:23
Alignment explanation
Indices: 8073--8147 Score: 98
Period size: 23 Copynumber: 3.2 Consensus size: 23
8063 TTTCTTTGTT
8073 TTTTTGGAACTCCTTAGTGAGAG
1 TTTTTGGAACTCCTTAGTGAGAG
* *
8096 TTTTTGGTACTCCTTTA-TGAGAA
1 TTTTTGGAACTCC-TTAGTGAGAG
*
8119 TTTTTGGAACTCCTTTGTGAGAG
1 TTTTTGGAACTCCTTAGTGAGAG
8142 CTTTTT
1 -TTTTT
8148 TTATTGTCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
22 2 0.05
23 34 0.77
24 8 0.18
ACGTcount: A:0.19, C:0.13, G:0.21, T:0.47
Consensus pattern (23 bp):
TTTTTGGAACTCCTTAGTGAGAG
Found at i:9180 original size:53 final size:53
Alignment explanation
Indices: 9111--9213 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
9101 GACGTGGCAC
* **
9111 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* * * *
9164 GCCACATGTATCAAAAAGTTACACATGTCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
9214 GACACGTGAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:9230 original size:31 final size:31
Alignment explanation
Indices: 9163--9261 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 31
9153 CAAAAAGTCG
* * *
9163 TGCCACATGTATCAAAAAGTTACACATGTCA
1 TGCCACATGTATCAAAAAGTGACACGTGACA
* * *
9194 CGCCACGTGTACCAAAAAGTGACACGTGACA
1 TGCCACATGTATCAAAAAGTGACACGTGACA
* * * *
9225 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTATCAAAAAGTGACACGTGACA
9256 TGCCAC
1 TGCCAC
9262 GTGCACAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (31 bp):
TGCCACATGTATCAAAAAGTGACACGTGACA
Found at i:11446 original size:23 final size:23
Alignment explanation
Indices: 11420--11467 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
11410 TCATTAGATG
11420 CGAGTGTGGTAGTTAATTTCGGA
1 CGAGTGTGGTAGTTAATTTCGGA
11443 CGAGTGTGGTAGTTAATTTCGGA
1 CGAGTGTGGTAGTTAATTTCGGA
11466 CG
1 CG
11468 GAGCTAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.10, G:0.35, T:0.33
Consensus pattern (23 bp):
CGAGTGTGGTAGTTAATTTCGGA
Found at i:12010 original size:49 final size:49
Alignment explanation
Indices: 11935--12030 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
11925 GTTTCAAACC
11935 CGGAACCTCCCACAAGAAGCCCCAAACTCTTAACCACTGGGTGTCCCCT
1 CGGAACCTCCCACAAGAAGCCCCAAACTCTTAACCACTGGGTGTCCCCT
* *
11984 CGGAACCTCCCACAAGAAGTCTCAAACTCTTAACCACTGGGTGTCCC
1 CGGAACCTCCCACAAGAAGCCCCAAACTCTTAACCACTGGGTGTCCC
12031 TTGGGACTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.27, C:0.39, G:0.17, T:0.18
Consensus pattern (49 bp):
CGGAACCTCCCACAAGAAGCCCCAAACTCTTAACCACTGGGTGTCCCCT
Found at i:12400 original size:57 final size:58
Alignment explanation
Indices: 12311--12425 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 58
12301 ATTGACCCGA
**
12311 GTTTTGTCCCCATGACGTGTCATGGTTAGTCATCTCATATTATATAGCAAAACTCCAC
1 GTTTTGTCCCCATGACGTGTCATGACTAGTCATCTCATATTATATAGCAAAACTCCAC
12369 GTTTTG-CCCCATGACGTGTCATGACTAGTCATCTCATATTATATAGCAAAACTCCAC
1 GTTTTGTCCCCATGACGTGTCATGACTAGTCATCTCATATTATATAGCAAAACTCCAC
12426 TTAGATGACC
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 49 0.89
58 6 0.11
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (58 bp):
GTTTTGTCCCCATGACGTGTCATGACTAGTCATCTCATATTATATAGCAAAACTCCAC
Found at i:14300 original size:34 final size:34
Alignment explanation
Indices: 14262--14331 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
14252 ATAAATATGC
14262 AACGCCCATGGCATGATGAAGAGTGATAGCTAAA
1 AACGCCCATGGCATGATGAAGAGTGATAGCTAAA
14296 AACGCCCATGGCATGATGAAGAGTGATAGCTAAA
1 AACGCCCATGGCATGATGAAGAGTGATAGCTAAA
14330 AA
1 AA
14332 GTCTATTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (34 bp):
AACGCCCATGGCATGATGAAGAGTGATAGCTAAA
Found at i:22296 original size:17 final size:17
Alignment explanation
Indices: 22274--22310 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
22264 ATATAATAAA
22274 TAAAACATTTAGAAAAT
1 TAAAACATTTAGAAAAT
22291 TAAAACATTTAGAAAAT
1 TAAAACATTTAGAAAAT
22308 TAA
1 TAA
22311 CTATTGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (17 bp):
TAAAACATTTAGAAAAT
Found at i:22368 original size:15 final size:15
Alignment explanation
Indices: 22348--22377 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
22338 TGTCAAGTGT
22348 CACTTAATGAGAGTC
1 CACTTAATGAGAGTC
22363 CACTTAATGAGAGTC
1 CACTTAATGAGAGTC
22378 TTGTACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
CACTTAATGAGAGTC
Found at i:23250 original size:12 final size:12
Alignment explanation
Indices: 23229--23261 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
23219 GCATGGAAAG
*
23229 AATAATTGTTCA
1 AATAAATGTTCA
23241 AATAAATGTTCA
1 AATAAATGTTCA
23253 AATAAATGT
1 AATAAATGT
23262 CCAACCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (12 bp):
AATAAATGTTCA
Found at i:25037 original size:14 final size:15
Alignment explanation
Indices: 25008--25042 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
24998 TATATTTTTA
25008 ATTTATAATATTTCT
1 ATTTATAATATTTCT
*
25023 ATTTGTAAT-TTTCT
1 ATTTATAATATTTCT
25037 ATTTAT
1 ATTTAT
25043 TTTTTATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (15 bp):
ATTTATAATATTTCT
Found at i:32298 original size:15 final size:15
Alignment explanation
Indices: 32267--32358 Score: 69
Period size: 16 Copynumber: 5.8 Consensus size: 15
32257 GTTTTCTCTT
*
32267 GTCATTCGGGTTTCGG
1 GTCATT-GGGTCTCGG
32283 GTCATCTGGGT-TCGG
1 GTCAT-TGGGTCTCGG
* *
32298 GTTATTCCGGTCTCGG
1 GTCATT-GGGTCTCGG
32314 GTCAGTTGGGTCTCGG
1 GTCA-TTGGGTCTCGG
* *
32330 GTCATACGGGTTTCGG
1 GTCAT-TGGGTCTCGG
*
32346 GACATTCGGGTCT
1 GTCATT-GGGTCT
32359 TGGTTTCGGG
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
14 1 0.02
15 12 0.20
16 45 0.74
17 3 0.05
ACGTcount: A:0.09, C:0.21, G:0.37, T:0.34
Consensus pattern (15 bp):
GTCATTGGGTCTCGG
Found at i:32613 original size:42 final size:42
Alignment explanation
Indices: 32550--32631 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
32540 TTGATATTAA
*
32550 TTTTGAATATTAAATATATAATTAATTATCAGGTGGGGTAAG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTAAG
32592 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
32632 TGTGTCAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTAAG
Found at i:33226 original size:33 final size:32
Alignment explanation
Indices: 33180--33259 Score: 106
Period size: 33 Copynumber: 2.5 Consensus size: 32
33170 ATATGGGTCT
* * *
33180 CAGGTCATTCGGGTTTCGGGTTATCTGGGTTA
1 CAGGTCATTCGGGTCTCGGGTAATCTAGGTTA
* *
33212 CGGGTTCATTCGGGTCTCGGGTAATCTAGGTTG
1 CAGG-TCATTCGGGTCTCGGGTAATCTAGGTTA
33245 CAGGTCATTCGGGTC
1 CAGGTCATTCGGGTC
33260 ACAGGTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 14 0.34
33 27 0.66
ACGTcount: A:0.12, C:0.19, G:0.35, T:0.34
Consensus pattern (32 bp):
CAGGTCATTCGGGTCTCGGGTAATCTAGGTTA
Found at i:35239 original size:90 final size:90
Alignment explanation
Indices: 35085--35264 Score: 299
Period size: 90 Copynumber: 2.0 Consensus size: 90
35075 CTTCCAATCC
35085 CCATTTTGCTTCTTTTTGCCTCCTTGGCTCTGATATCCTCTTATTCTTTCTGTTTCATCAACTCC
1 CCATTTTGCTTCTTTTTGCCTCCTTGGCTCTGATATCCTCTTATTCTTTCTGTTTCATCAACTCC
*
35150 GCAAGATCAATATTTGGATTTAGAG
66 GCAAGATCAAAATTTGGATTTAGAG
* *
35175 CCATTTTGCTTCTTTTTGCCTCCTTGGCTCTGATATCCTCTTTTTCTTTTTGTTTCAT-ATACTC
1 CCATTTTGCTTCTTTTTGCCTCCTTGGCTCTGATATCCTCTTATTCTTTCTGTTTCATCA-ACTC
**
35239 CTTAAGATCAAAATTTGGATTTAGAG
65 CGCAAGATCAAAATTTGGATTTAGAG
35265 TAAGTGATAA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
89 1 0.01
90 83 0.99
ACGTcount: A:0.18, C:0.23, G:0.13, T:0.47
Consensus pattern (90 bp):
CCATTTTGCTTCTTTTTGCCTCCTTGGCTCTGATATCCTCTTATTCTTTCTGTTTCATCAACTCC
GCAAGATCAAAATTTGGATTTAGAG
Found at i:40341 original size:32 final size:32
Alignment explanation
Indices: 40289--40371 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
40279 ATCTTCTTTG
* * *
40289 TTGAGAACCAAACATTAAATTCCAAAGCATAAA
1 TTGA-AACCAAACCTGAAATTCCAAAGAATAAA
40322 TTGAAACCAAACCTGAAATTCCAAAGAATAAA
1 TTGAAACCAAACCTGAAATTCCAAAGAATAAA
*
40354 TTGAAACCAAAGCTGAAA
1 TTGAAACCAAACCTGAAA
40372 AGCAGCGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 42 0.91
33 4 0.09
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.19
Consensus pattern (32 bp):
TTGAAACCAAACCTGAAATTCCAAAGAATAAA
Found at i:40656 original size:11 final size:10
Alignment explanation
Indices: 40638--40671 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
40628 GAAATTCGTG
40638 TTTTGAAGAT
1 TTTTGAAGAT
40648 TTCTTGAAGAT
1 TT-TTGAAGAT
40659 ATTTTGAAGAT
1 -TTTTGAAGAT
40670 TT
1 TT
40672 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:47728 original size:15 final size:16
Alignment explanation
Indices: 47701--47730 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47691 CTTCTCAGCC
47701 ACAAAACAAGAAAAGA
1 ACAAAACAAGAAAAGA
47717 ACAAAA-AAGAAAAG
1 ACAAAACAAGAAAAG
47731 GGGTTGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (16 bp):
ACAAAACAAGAAAAGA
Found at i:48857 original size:18 final size:18
Alignment explanation
Indices: 48834--48870 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
48824 GCCAAAGTGA
48834 TAAAGGCTTAACTTTTGG
1 TAAAGGCTTAACTTTTGG
48852 TAAAGGCTTAACTTTTGG
1 TAAAGGCTTAACTTTTGG
48870 T
1 T
48871 GGGAGGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (18 bp):
TAAAGGCTTAACTTTTGG
Found at i:52197 original size:26 final size:26
Alignment explanation
Indices: 52157--52207 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
52147 TCAAACTTTG
* *
52157 GGATTTTGAGTAAGAGATAAAAATTT
1 GGATTTAGAGGAAGAGATAAAAATTT
52183 GGATTTAGAGGAAGAGATAAAAATT
1 GGATTTAGAGGAAGAGATAAAAATT
52208 CATCCATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.29
Consensus pattern (26 bp):
GGATTTAGAGGAAGAGATAAAAATTT
Found at i:55618 original size:20 final size:21
Alignment explanation
Indices: 55582--55627 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
55572 ATAGTTTAGA
*
55582 TTTAATTTACTTTGCTTTATT
1 TTTAATTTACATTGCTTTATT
*
55603 TTTAATTTA-ATTGCTTTCTT
1 TTTAATTTACATTGCTTTATT
55623 TTTAA
1 TTTAA
55628 GTAATCTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTAATTTACATTGCTTTATT
Found at i:55919 original size:17 final size:18
Alignment explanation
Indices: 55889--55922 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55879 TCTAAAAAAA
55889 AAAAAATTGCGTCGAAAG
1 AAAAAATTGCGTCGAAAG
*
55907 AAAAAA-TGTGTCGAAA
1 AAAAAATTGCGTCGAAA
55923 ATAAATTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.18
Consensus pattern (18 bp):
AAAAAATTGCGTCGAAAG
Done.