Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005529.1 Corchorus capsularis cultivar CVL-1 contig05547, 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: 3329
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:894 original size:324 final size:325
Alignment explanation
Indices: 8--1466 Score: 2129
Period size: 324 Copynumber: 4.5 Consensus size: 325
1 AAAATCA
* * **
8 TTTCAGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTTTTGGCTAAAAACGTAT
1 TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACG--GTTTTTGGCTAAAAACGCGT
** * *
73 TCCGGAGACATGACTCAATTTTGCATGATTTTTTCGCAGAAAGACTCCTTGAAATATTTATATTC
64 TCCGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATCTATATTC
* * * * * *
138 ATCTAATCAAATCTCATCCATAATGGATTTAAGGATTTCTATTTACGAGCATCTGAATGTTTTTT
129 ATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTT
* * *
203 CGATTTATTTTGAAATAAAAGTTCGGAAAAAAAA-AGAAAAACGATATTAGAAGCGTGAAAAATC
194 CGATTTAATTTGAAATAAAAGTTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACC
* * * *
267 AAT--TTTTTTTGGCATTGATTTATATATTTTTTCTTAGTATTGTTGCAAAAAATTGAGGAAAAA
259 CATCATTTTTTGGGCGTTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGAAAAA
330 -T
324 CT
*
331 TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCCATCACGGTTTTTGGCT-CAAACGCGTT
1 TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA-CCATCACGGTTTTTGGCTAAAAACGCGTT
* * * *
395 TCGGAGACCCGACTCAATTTTGCATGATTTTTTTTGAAGAAAGACTCCTTGTAATATCTATATGC
65 CCGGAGACCCGACTCAATTTTGCATGA-TTTTTTTGCAGAAAGACTCCTTGAAATATCTATATTC
*
460 ATCTAACCAAATCTCAGCCACAATGGATTAAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTT
129 ATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTT
* *
525 CGATTTAATTTGAAATAAAAGTTCAG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAATC
194 CGATTTAATTTGAAATAAAAGTTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACC
589 CATCATTTTTTGGGCGTTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGAAAAA
259 CATCATTTTTTGGGCGTTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGAAAAA
654 CT
324 CT
*
656 TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACC-TCACGGTTTTTGTCTAAAAACGCGTTC
1 TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTC
*
720 CGGTGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCAT
66 CGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCAT
*
785 CTAACCAAATCTCAGCCACAATGGATTAAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCG
131 CTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCG
*
850 ATTTAATTTGAAATAAAAGTTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCA
196 ATTTAATTTGAAATAAAAGTTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCA
*
915 TCATTTTTTGGGCGTTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTAAGGAAAAACT
261 TCATTTTTTGGGCGTTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGAAAAACT
* *
980 TTTCGGGTCAATTTTTAGCCGAAATC--G---T---CA-C-C-GTTTTTGGCTAAAAATGCGTTT
1 TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTC
*
1034 CGGAGACCCGACTC-ATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATTTATATTCAT
66 CGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCAT
* * * *
1098 CCAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCTTTTGAATTTTGTTTCG
131 CTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCG
** * * *
1163 ATTTAATTAAAAAT-AAA-TTCGGGAGAAAAAATAGG-AAAACGATATTAGAAGGGTGAAGAACC
196 ATTTAATTTGAAATAAAAGTTC-GGAAAAAAAAT-GGAAAAACGATATTAGAAGCGTGAAAAACC
* * * * * * * *
1225 CTTAATTTTTTTGGCGTTGATTTCTATATTTTTTCTGAATGTTGTGGCAAAAAATTGAGGAAAAT
259 CATCATTTTTTGGGCGTTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGAAAAA
*
1290 CA
324 CT
* *
1292 TTTCGGGTCAATTATTAGCCGAAATCGTGTACTAACCATCACGTTTTTTTGGCTAAAAACGCGTT
1 TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACG-GTTTTTGGCTAAAAACGCGTT
* *
1357 CTGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCC-T-AAATATCCATATTCA
65 CCGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCA
* * *
1420 TCTAACCAAATTTCAGTCACAATTGATTTAAGGATTTCTTTTTACGA
130 TCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGA
1467 TCTGAATATT
Statistics
Matches: 1037, Mismatches: 75, Indels: 48
0.89 0.06 0.04
Matches are distributed among these distances:
311 3 0.00
312 119 0.11
313 123 0.12
314 33 0.03
315 1 0.00
316 2 0.00
317 1 0.00
319 1 0.00
320 2 0.00
321 39 0.04
322 156 0.15
323 228 0.22
324 262 0.25
325 67 0.06
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (325 bp):
TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTC
CGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCAT
CTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCG
ATTTAATTTGAAATAAAAGTTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCA
TCATTTTTTGGGCGTTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGGAAAAACT
Found at i:1272 original size:636 final size:641
Alignment explanation
Indices: 1--1466 Score: 2161
Period size: 636 Copynumber: 2.3 Consensus size: 641
* *
1 AAAATCATTTCAGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTTTTGGCTAAA
1 AAAAACATTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACG-TTTTTTTGGCTAAA
** ** * *
66 AACGTATTCCGGAGACATGACTCAATTTTGCATGATTTTTTCGCAGAAAGACTCCTTGAAATATT
65 AACGCGTTCCGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATC
* * * *
131 TATATTCATCTAATCAAATCTCATCCATAATGGATTTAAGGATTTCTATTTACGAGCATCTGAAT
130 TATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATCTGAAT
* * *
196 GTTTTTTCGATTTATTTTGAAATAAAAGTTCGGAAAAAAAAAGAAAAACGATATTAGAAGCGTGA
195 CTTGTTTCGATTTAATTTGAAATAAAAGTTCGGAAAAAAAAAGAAAAACGATATTAGAAGCGTGA
* * * *
261 AAAATCAATTTTTTTTGGCATTGATTTATATATTTTTTCTTAGTATTGTTGCAAAAAATTGAGGA
260 AAAACCAATTTTTTTGGGCATTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTAAGGA
*
326 AAAATTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCCATCACGGTTTTTGGCTCAAACG
325 AAAATTTTCGGGTCAATTTTTAGCCGAAATCG-G-A-T-A--CATCACGGTTTTTGGCTAAAACG
*
391 CGTTTCGGAGACCCGACTCAATTTTGCATGATTTTTTTTGAAGAAAGACTCCTTGTAATATCTAT
384 CGTTTCGGAGACCCGACTCAATTTTGCATGATTTTTTTTGAAGAAAGACTCCTTGAAATATCTAT
*
456 ATGCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATTTCTTTTTACGAGCATCTGAATCTT
449 ATGCATCCAACCAAATCTCAGCCACAATGGATTAAAGGATTTCTTTTTACGAGCATCTGAATCTT
**
521 GTTTCGATTTAATTTGAAATAAAAGTTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
514 GTTTCGATTTAATTAAAAATAAAAGTTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * *
586 ATCCATCATTTTTTGGGCGTTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGG
579 ACCCATAATTTTTTGGGCGTTGATTTATATATTTTTTCTGAATATTGTGGCAAAAAATTGAGG
* * *
649 AAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACC-TCACG-GTTTTTGTCTAAAA
1 AAAAACATTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTTTGGCTAAAA
*
712 ACGCGTTCCGGTGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATCT
66 ACGCGTTCCGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATCT
*
777 ATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATTTCTTTTTACGAGCATCTGAATC
131 ATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATCTGAATC
*
842 TTGTTTCGATTTAATTTGAAATAAAAGTTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGA
196 TTGTTTCGATTTAATTTGAAATAAAAGTTCGGAAAAAAAA-AGAAAAACGATATTAGAAGCGTGA
* * *
907 AAAGCCCATCATTTTTTGGGCGTTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTAAG
260 AAAACCAAT--TTTTTTGGGCATTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTAAG
*
972 GAAAAACTTTTCGGGTCAATTTTTAGCCGAAATC-G-T-CA-C-C-GTTTTTGGCTAAAAATGCG
323 GAAAAA-TTTTCGGGTCAATTTTTAGCCGAAATCGGATACATCACGGTTTTTGGCT-AAAACGCG
* *
1031 TTTCGGAGACCCGACTC-ATTTTGCATGA-TTTTTTTGCAGAAAGACTCCTTGAAATATTTATAT
386 TTTCGGAGACCCGACTCAATTTTGCATGATTTTTTTTGAAGAAAGACTCCTTGAAATATCTATAT
* * * * *
1094 TCATCCAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCTTTTGAATTTTGT
451 GCATCCAACCAAATCTCAGCCACAATGGATTAAAGGATTTCTTTTTACGAGCATCTGAATCTTGT
* * *
1159 TTCGATTTAATTAAAAAT-AAA-TTCGGGAGAAAAAATAGG-AAAACGATATTAGAAGGGTGAAG
516 TTCGATTTAATTAAAAATAAAAGTTC-AGA-AAAAAAT-GGAAAAACGATATTAGAAGCGTGAAA
* * * *
1221 AACCCTTAATTTTTTTGGCGTTGATTTCTATATTTTTTCTGAATGTTGTGGCAAAAAATTGAGG
578 AACCCATAATTTTTTGGGCGTTGATTTATATATTTTTTCTGAATATTGTGGCAAAAAATTGAGG
* *
1285 AAAATCATTTCGGGTCAATTATTAGCCGAAATCGTGTACTAACCATCACGTTTTTTTGGCTAAAA
1 AAAAACATTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTTTGGCTAAAA
* *
1350 ACGCGTTCTGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCC-T-AAATATCC
66 ACGCGTTCCGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATCT
* * *
1413 ATATTCATCTAACCAAATTTCAGTCACAATTGATTTAAGGATTTCTTTTTACGA
131 ATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGA
1467 TCTGAATATT
Statistics
Matches: 744, Mismatches: 64, Indels: 32
0.89 0.08 0.04
Matches are distributed among these distances:
634 3 0.00
635 5 0.01
636 289 0.39
637 29 0.04
638 88 0.12
639 1 0.00
640 2 0.00
644 1 0.00
645 167 0.22
646 29 0.04
647 6 0.01
648 97 0.13
649 27 0.04
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (641 bp):
AAAAACATTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTTTGGCTAAAA
ACGCGTTCCGGAGACCCGACTCAATTTTGCATGATTTTTTTGCAGAAAGACTCCTTGAAATATCT
ATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATCTGAATC
TTGTTTCGATTTAATTTGAAATAAAAGTTCGGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAA
AAACCAATTTTTTTGGGCATTGATTTATATATTTTTTCTTAGTATTGTGGCAAAAAATTAAGGAA
AAATTTTCGGGTCAATTTTTAGCCGAAATCGGATACATCACGGTTTTTGGCTAAAACGCGTTTCG
GAGACCCGACTCAATTTTGCATGATTTTTTTTGAAGAAAGACTCCTTGAAATATCTATATGCATC
CAACCAAATCTCAGCCACAATGGATTAAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCGA
TTTAATTAAAAATAAAAGTTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCATA
ATTTTTTGGGCGTTGATTTATATATTTTTTCTGAATATTGTGGCAAAAAATTGAGG
Found at i:1620 original size:209 final size:209
Alignment explanation
Indices: 1258--1675 Score: 626
Period size: 209 Copynumber: 2.0 Consensus size: 209
1248 CTATATTTTT
* * * * *
1258 TCTGAATGTTGTGGCAAAAAATTGAGGAAAATCATTTCGGGTCAATTATTAGCCGAAATCGTGTA
1 TCTGAATATTGTGGCAAAAAATTAAGGAAAAACATTTCCGGTCAATTATTAGCCCAAATCGTGTA
* * *
1323 CTAACCATCACGTTTTTTTGGCTAAAAACGCGTTCTGGAGACCCGACTCAATTTTGCATGATTTT
66 CTAACAATCACGGTTTTTTGGCTAAAAACGCGTTCCGGAGACCCGACTCAATTTTGCATGATTTT
* * *
1388 TTTGCAGAAAGACTCCTAAATATCCATATTCATCTAACCAAATTTCAG-TCACAATTGATTTAAG
131 TTTGCAGAAAGACTCCTAAATATCCATATTCATCTAACCAAATCTCAGCT-ACAATGGATATAAG
1452 GATTTCTTTTTACGA
195 GATTTCTTTTTACGA
* * *
1467 TCTGAATATTGTTGCAAAAAATTAAGGAAAAACTTTTCCGGTCAATTTTTAGCCCAAATCGTGTA
1 TCTGAATATTGTGGCAAAAAATTAAGGAAAAACATTTCCGGTCAATTATTAGCCCAAATCGTGTA
* *
1532 CTAACAATCACGGTTTTTT-GCTAAAAACGTGTTCCGGAGACCCGGCTCAATTTTGCATGA-TTT
66 CTAACAATCACGGTTTTTTGGCTAAAAACGCGTTCCGGAGACCCGACTCAATTTTGCATGATTTT
* *
1595 TTTGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCTACAATGGATATAA
131 TTTGCAGAAAGACTCC-T-AAATATCCATATTCATCTAACCAAATCTCAGCTACAATGGATATAA
1660 GGATTTCTTTTTACGA
194 GGATTTCTTTTTACGA
1676 GCATCTGAAT
Statistics
Matches: 188, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
207 19 0.10
208 39 0.21
209 129 0.69
210 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (209 bp):
TCTGAATATTGTGGCAAAAAATTAAGGAAAAACATTTCCGGTCAATTATTAGCCCAAATCGTGTA
CTAACAATCACGGTTTTTTGGCTAAAAACGCGTTCCGGAGACCCGACTCAATTTTGCATGATTTT
TTTGCAGAAAGACTCCTAAATATCCATATTCATCTAACCAAATCTCAGCTACAATGGATATAAGG
ATTTCTTTTTACGA
Found at i:2823 original size:972 final size:969
Alignment explanation
Indices: 1475--3329 Score: 3033
Period size: 972 Copynumber: 1.9 Consensus size: 969
1465 GATCTGAATA
*
1475 TTGTTGCAAAAAATTAAGGAAAAACTTTTCCGGTCAATTTTTAGCCCAAATCGTGTACTAACAAT
1 TTGTGGCAAAAAATTAAGGAAAAACTTTTCCGGTCAATTTTTAGCCCAAATCGTGTACTAACAAT
* * *
1540 CACGGTTTTTTGCTAAAAACGTGTTCCGGAGACCCGGCTCAATTTTGCATGATTTTTTGCAGAAA
66 CACGGTTTTTTGCTAAAAACATATTCCGGAGACCCGGCTAAATTTTGCATGATTTTTTGCAGAAA
* * *
1605 GACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCTACAATGGATATAAGGATTTCTTT
131 GACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACAATGGATATAAGGATTTCTTT
*
1670 TTACGAGCATCTGAATCTTGTTTCGATTTAATTTAAAATAAATTCGAAAAAAAATGGAAAAACGA
196 CTACGAGCATCTGAATCTTGTTTCGATTTAATTTAAAATAAATTCGAAAAAAAATGGAAAAACGA
* *
1735 TTTTAGAAGCATGAAAAACCCATCATTTTTTGGGTGTTGAATTATATATTTTTTATGAGTATTGT
261 TATTAGAAGCATGAAAAACCCATCATTTTTTGGGCGTTGAATTATATATTTTTTATGAGTATTGT
*
1800 CGCAAAAAATTGAGGAAAAACTTTTCTGGTTAGTTTTTAGCCGAAATCGTGTACTAACAATCACA
326 CGCAAAAAATTGAGGAAAAACTTTTCTGGTTAATTTTTAGCCGAAATCGTGTACTAACAATCACA
1865 GTTTTTTGCTAAAAACGCGTTCCAGAGACCCGGCTCAATTTTGCATGATTTTTTTGCA-AAAAGA
391 GTTTTTTGCTAAAAACGCGTTCCAGAGACCCGGCTCAATTTTGCATGATTTTTTTGCAGAAAAGA
* *
1929 CTTCTTGAAATATCTATATTCATCTAACTAAATCTCAGCCACCATGGATTTAAGGATTTCTTTTT
456 CTTCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACCATGGATTTAAGGATTTCTTTTT
*
1994 ACGAGCACCTGAATTTTGTTTCGATTTAATTAGAAAT-AAA-TTCGGAAAAAAAAACAACTGGAA
521 ACGAGCACCTGAATCTTGTTTCGATTTAATTAGAAATAAAAGTTCGG--AAAAAAA-AA-TGGAA
* *
2057 AAACGATA-TAAGATGCATGAAAAACCCTTCATTTTTTTGGTGTTGATTTATATACTTTTTCTGA
582 AAACGATATTAAGA-GCATGAAAAACCCATCATTTTTTTGGCGTTGATTTATATACTTTTTCTGA
* *
2121 GTATTGTCGCAATAAATTGAGGAAAAACTTTTCGGCTCAATTTTTAGCCCAAATCGTGTACTAAC
646 GTATTGTCGCAAAAAATTGAGGAAAAACTTTTCGGCTCAACTTTTAGCCCAAATCGTGTACTAAC
* * * *
2186 CATCGCA-G-TTTTTGGCTAAAAACGCGTTCCGGAG-CCCGGCTCAATTTTGCATGATTTTTTTG
711 C-GC-CACGTTTTTTGGCTAAAAACACATTCCGGAGACCCGGCTCAATTTGGCATGA-TTTTTTG
* * *
2248 CAGAAAGTCTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGAT
773 CACAAAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACAATGGATTTAAGGAT
* *
2313 TTCTTTTTACGAGCTTCTGAATTTTGTTTCGATTTAATTAAAAATAAATTCGGGAAAAAATAGGA
838 TTCTTTCTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATAAATTCGGGAAAAAATAGGA
2378 AAACGATATTAGAAGCGTGAAGAACCCTTAATTTTTTTTGGCGTTGATTTATATATTTTTCTGAG
903 AAACGATATTAGAAGCGTGAAGAACCCTTAATTTTTTTTGGCGTTGATTTATATATTTTTCTGAG
2443 TG
968 TG
* * * *
2445 TTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCAT
1 TTGTGGCAAAAAATTAAGGAAAAACTTTTCCGGTCAATTTTTAGCCCAAATCGTGTACTAACAAT
* *
2510 CACGTTTTTTTGGCTAAAAACATATTCCGGAGACCCGGCTAAATTTTGCATGATTTTTTGCCGAA
66 CACGGTTTTTT-GCTAAAAACATATTCCGGAGACCCGGCTAAATTTTGCATGATTTTTTGCAGAA
* * * *
2575 ATATTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACACTGGATTTAAGGATTTCTT
130 AGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACAATGGATATAAGGATTTCTT
*
2640 TCTACGAGCATCTGAATTTTGTTTCGATTTAA-TTAGAAATAAATTCGGAAAAAAAATGGAAAAA
195 TCTACGAGCATCTGAATCTTGTTTCGATTTAATTTA-AAATAAATTC-GAAAAAAAATGGAAAAA
*
2704 CGATATTAGAAGCGTGAAAAACCCATCATTTTTTGGGCGTTGAATTATATATTTTTTATGAGTAT
258 CGATATTAGAAGCATGAAAAACCCATCATTTTTTGGGCGTTGAATTATATATTTTTTATGAGTAT
2769 TGTCGCAAAAAATTGAGGAAAAACTTTTCTGGTTAATTTTTAGCCGAAATCGTGTACTAACAATC
323 TGTCGCAAAAAATTGAGGAAAAACTTTTCTGGTTAATTTTTAGCCGAAATCGTGTACTAACAATC
* * *
2834 ACAGTTTTTTGCTAAAAACGCGTTCCGGAGACCCGGCTCAATTTTGCATGATTTTTTTGTAGAAG
388 ACAGTTTTTTGCTAAAAACGCGTTCCAGAGACCCGGCTCAATTTTGCATGATTTTTTTGCAGAAA
*
2899 AGACTTCTTGAAATATCTATATTCATCTAACCAAATGTCAACCACCATGGATTTAAGGATTTCTT
453 AGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACCATGGATTTAAGGATTTCTT
* *
2964 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAAAGTTCGGAAAAAAAAATGGAAA
518 TTTACGAGCACCTGAATCTTGTTTCGATTTAATTAGAAATAAAAGTTCGGAAAAAAAAATGGAAA
* *
3029 AACGATATTAAGAGCGTGAAAAACCCATCATTTTTTTGGCGTTGATTTATATATTTTTTCTGAGT
583 AACGATATTAAGAGCATGAAAAACCCATCATTTTTTTGGCGTTGATTTATATACTTTTTCTGAGT
* * * * *
3094 GTTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAACTTTTAGCCGAAGTCGTGTACTAACCG
648 ATTGTCGCAAAAAATTGAGGAAAAACTTTTCGGCTCAACTTTTAGCCCAAATCGTGTACTAACCG
* * *
3159 CCACGTTTTTTTGGCTGAAAACATATTCCGGAGACCCGGCTCAATTTGGCATGATTTTTTGCTCA
713 CCACG-TTTTTTGGCTAAAAACACATTCCGGAGACCCGGCTCAATTTGGCATGATTTTTTGCACA
*
3224 AAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACACTGGATTTAAGGATTTCT
777 AAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCT
*
3289 TTCTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAAT
842 TTCTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAAT
Statistics
Matches: 817, Mismatches: 57, Indels: 20
0.91 0.06 0.02
Matches are distributed among these distances:
969 2 0.00
970 75 0.09
971 265 0.32
972 340 0.42
973 127 0.16
974 3 0.00
975 5 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (969 bp):
TTGTGGCAAAAAATTAAGGAAAAACTTTTCCGGTCAATTTTTAGCCCAAATCGTGTACTAACAAT
CACGGTTTTTTGCTAAAAACATATTCCGGAGACCCGGCTAAATTTTGCATGATTTTTTGCAGAAA
GACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACAATGGATATAAGGATTTCTTT
CTACGAGCATCTGAATCTTGTTTCGATTTAATTTAAAATAAATTCGAAAAAAAATGGAAAAACGA
TATTAGAAGCATGAAAAACCCATCATTTTTTGGGCGTTGAATTATATATTTTTTATGAGTATTGT
CGCAAAAAATTGAGGAAAAACTTTTCTGGTTAATTTTTAGCCGAAATCGTGTACTAACAATCACA
GTTTTTTGCTAAAAACGCGTTCCAGAGACCCGGCTCAATTTTGCATGATTTTTTTGCAGAAAAGA
CTTCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACCATGGATTTAAGGATTTCTTTTT
ACGAGCACCTGAATCTTGTTTCGATTTAATTAGAAATAAAAGTTCGGAAAAAAAAATGGAAAAAC
GATATTAAGAGCATGAAAAACCCATCATTTTTTTGGCGTTGATTTATATACTTTTTCTGAGTATT
GTCGCAAAAAATTGAGGAAAAACTTTTCGGCTCAACTTTTAGCCCAAATCGTGTACTAACCGCCA
CGTTTTTTGGCTAAAAACACATTCCGGAGACCCGGCTCAATTTGGCATGATTTTTTGCACAAAGA
CTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTCT
ACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATAAATTCGGGAAAAAATAGGAAAACGATA
TTAGAAGCGTGAAGAACCCTTAATTTTTTTTGGCGTTGATTTATATATTTTTCTGAGTG
Found at i:3156 original size:650 final size:647
Alignment explanation
Indices: 1473--3329 Score: 2851
Period size: 649 Copynumber: 2.9 Consensus size: 647
1463 ACGATCTGAA
* *
1473 TATTGTTGCAAAAAATTAAGGAAAAACTTTTCCGGTCAATTTTTAGCCCAAATCGTGTACTAACA
1 TATTGTCGCAAAAAATTGAGGAAAAACTTTT-CGGTCAATTTTTAGCCCAAATCGTGTACTAACA
* *
1538 ATCACGGTTTTTTGCTAAAAACGTGTTCCGGAGACCCGGCTCAATTTTGCATGA-TTTTTTGCAG
65 ATCACAGTTTTTTGCTAAAAACGCGTTCCGGAGACCCGGCTCAATTTTGCATGATTTTTTTGCAG
* * *
1602 AAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCTACAATGGATATAAGGATTTC
130 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTC
1667 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTAAAATAAATTC-GAAAAAAAATGGAAAA
195 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTAAAATAAATTCGGAAAAAAAATGGAAAA
* * * * * * *
1731 ACGATTTTAGAAGCATGAAAAACCCATCATTTTTTGGGTGTTGAATTATATATTTTTTATGAGTA
260 ACGATATTAGAAGCGTGAAAAACCCATCATTTTTTTGGCGTTGATTTATATATTTTTTCTGAGTG
* * * * *
1796 TTGTCGCAAAAAATTGAGGAAAAACTTTTCTGGTTAGTTTTTAGCCGAAATCGTGTACTAACAAT
325 TTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCAT
*** * *
1861 CACAG-TTTTTT-GCTAAAAACGCGTTCCAGAGACCCGGCTCAATTTTGCATGATTTTTTTGCAA
390 CAC-GTTTTTTTGGCTAAAAACATATTCCGGAGACCCGGCTCAATTTTGCATGA-TTTTTTGC-C
* *
1924 AAAGACTT-CTTGAAATATCTATATTCATCTAACTAAATCTCAGCCAC-CATGGATTTAAGGATT
452 AAAGA-TTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACAC-TGGATTTAAGGATT
* *
1987 TCTTTTTACGAGCACCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAACAAC
515 TCTTTCTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGG--AAAAAAACAAC
* * * * *
2052 TGGAAAAACGATATAAGATGCATGAAAAACCCTTCATTTTTTTGGTGTTGATTTATATACTTTTT
578 TGGAAAAACGATATAAGAAGCATGAAAAACCCATCATTTTTTGGGCGTTGAATTATATACTTTTT
*
2117 CTGAG
643 ATGAG
* *
2122 TATTGTCGCAATAAATTGAGGAAAAACTTTTCGGCTCAATTTTTAGCCCAAATCGTGTACTAACC
1 TATTGTCGCAAAAAATTGAGGAAAAACTTTTCGG-TCAATTTTTAGCCCAAATCGTGTACTAACA
* *
2187 ATCGCAGTTTTTGGCTAAAAACGCGTTCCGGAG-CCCGGCTCAATTTTGCATGATTTTTTTGCAG
65 ATCACAGTTTTTTGCTAAAAACGCGTTCCGGAGACCCGGCTCAATTTTGCATGATTTTTTTGCAG
*
2251 AAAGTCTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTC
130 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTC
* * * *
2316 TTTTTACGAGCTTCTGAATTTTGTTTCGATTTAATTAAAAATAAATTCGG-GAAAAAATAGG-AA
195 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTAAAATAAATTCGGAAAAAAAAT-GGAAA
* * *
2379 AACGATATTAGAAGCGTGAAGAACCCTTAATTTTTTTTGGCGTTGATTTATATA-TTTTTCTGAG
259 AACGATATTAGAAGCGTGAAAAACCCATCA-TTTTTTTGGCGTTGATTTATATATTTTTTCTGAG
2443 TGTTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACC
323 TGTTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACC
*
2508 ATCACGTTTTTTTGGCTAAAAACATATTCCGGAGACCCGGCTAAATTTTGCATGATTTTTTGCCG
388 ATCACGTTTTTTTGGCTAAAAACATATTCCGGAGACCCGGCTCAATTTTGCATGATTTTTTGCC-
*
2573 AAATATTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACACTGGATTTAAGGATTTC
452 AAAGATTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACACTGGATTTAAGGATTTC
2638 TTTCTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGG-AAAAAA-AA-TGGA
517 TTTCTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAACAACTGGA
* * *
2700 AAAACGATATTAGAAGCGTGAAAAACCCATCATTTTTTGGGCGTTGAATTATATATTTTTTATGA
582 AAAACGATATAAGAAGCATGAAAAACCCATCATTTTTTGGGCGTTGAATTATATACTTTTTATGA
2765 G
647 G
* *
2766 TATTGTCGCAAAAAATTGAGGAAAAACTTTTCTGGTTAATTTTTAGCCGAAATCGTGTACTAACA
1 TATTGTCGCAAAAAATTGAGGAAAAACTTTTC-GGTCAATTTTTAGCCCAAATCGTGTACTAACA
*
2831 ATCACAGTTTTTTGCTAAAAACGCGTTCCGGAGACCCGGCTCAATTTTGCATGATTTTTTTGTAG
65 ATCACAGTTTTTTGCTAAAAACGCGTTCCGGAGACCCGGCTCAATTTTGCATGATTTTTTTGCAG
* * * *
2896 AAGAGACTTCTTGAAATATCTATATTCATCTAACCAAATGTCAACCACCATGGATTTAAGGATTT
130 AA-AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTT
*
2961 CTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAAAGTTCGGAAAAAAAAATGG
194 CTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTAAAAT-AAA-TTCGG-AAAAAAAATGG
3026 AAAAACGATATTA-AGAGCGTGAAAAACCCATCATTTTTTTGGCGTTGATTTATATATTTTTTCT
256 AAAAACGATATTAGA-AGCGTGAAAAACCCATCATTTTTTTGGCGTTGATTTATATATTTTTTCT
* *
3090 GAGTGTTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAACTTTTAGCCGAAGTCGTGTACTA
320 GAGTGTTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTA
** * *
3155 ACCGCCACGTTTTTTTGGCTGAAAACATATTCCGGAGACCCGGCTCAATTTGGCATGATTTTTTG
385 ACCATCACGTTTTTTTGGCTAAAAACATATTCCGGAGACCCGGCTCAATTTTGCATGATTTTTTG
*
3220 CTCAAAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACACTGGATTTAAGGAT
450 C-CAAAGATTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACACTGGATTTAAGGAT
3285 TTCTTTCTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAAT
514 TTCTTTCTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAAT
Statistics
Matches: 1107, Mismatches: 80, Indels: 41
0.90 0.07 0.03
Matches are distributed among these distances:
644 150 0.14
645 36 0.03
646 102 0.09
647 3 0.00
648 31 0.03
649 454 0.41
650 330 0.30
651 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (647 bp):
TATTGTCGCAAAAAATTGAGGAAAAACTTTTCGGTCAATTTTTAGCCCAAATCGTGTACTAACAA
TCACAGTTTTTTGCTAAAAACGCGTTCCGGAGACCCGGCTCAATTTTGCATGATTTTTTTGCAGA
AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCT
TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTAAAATAAATTCGGAAAAAAAATGGAAAAA
CGATATTAGAAGCGTGAAAAACCCATCATTTTTTTGGCGTTGATTTATATATTTTTTCTGAGTGT
TGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATC
ACGTTTTTTTGGCTAAAAACATATTCCGGAGACCCGGCTCAATTTTGCATGATTTTTTGCCAAAG
ATTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACACTGGATTTAAGGATTTCTTTC
TACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAACAACTGGAAAAA
CGATATAAGAAGCATGAAAAACCCATCATTTTTTGGGCGTTGAATTATATACTTTTTATGAG
Done.