Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009688.1 Corchorus olitorius cultivar O-4 contig09720, 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: 4963
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:2380 original size:655 final size:651
Alignment explanation
Indices: 1--2827 Score: 4748
Period size: 655 Copynumber: 4.3 Consensus size: 651
1 CAAGTTCAGTTTTTAGCCGAAATCGTGTACTAACTATCACGA-TTTTGGGCTAAAAACGCGTTTT
1 CAAG-TCAGTTTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGGCTAAAAACGCGTTTT
*
65 GGGGCCCCGGCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTACATATATCT
65 GGGGCCCCGGCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATATATCT
*
130 AGCCAAATCTGAGCCACAGTGGATTTAAGGATTTGTTTTTATGAGCATCTTAATCTTGTTTCGAT
130 AGCCAAATCTGAGCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGAT
195 TTAAATAAATAAATTCGAAAAAGAAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAATT
195 TTAAATAAATAAATTCG--AAA-AAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAA-T
260 TTTTTTGGCGTTGAAATATATA-TTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTT
256 TTTTTTGGCGTTGAAATATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTT
324 CGGGTCATTTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAA
321 CGGGTCATTTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAA
* *
389 CGCGTTCCGGAGCCCGACTCAATTTTGCATGATTTTTGGCACAAAGAGACCCTGAAATATCTATA
386 CGCGTTCCAGAGCCCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATA
454 TTCATCGAACTAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTTT
451 TTCATCGAACTAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTTT
*
519 TTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTTAAAAGCC
516 TTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTGAAAAGCC
584 CGTCAATCTTTTTGGCGTTGAAA-TATATATTTTTTCTGAGTATTTTGGCAAAAAAATTCAGGAA
581 CGTCAATCTTTTTGGCGTT-AAATTATATATTTTTTCTGAGTATTTTGGC-AAAAAATTCAGGAA
648 AAACTTCT
644 AAACTTCT
*
656 CAAGTCAGTTTTTAGACGAAATCGTGTACTAACTATCACGATTTTTGGGCTAAAAACGCGTTTT-
1 CAAGTCAGTTTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGGCTAAAAACGCGTTTTG
* *
720 GGGCCCCGGCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAAGATCTACATATATCTA
66 GGGCCCCGGCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATATATCTA
* *
785 GCCAAATCTGAGTCACAGTGGATTTAAGGATTTGTTTTTATGAGCATCTTAATCTTGTTTCGATT
131 GCCAAATCTGAGCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATT
850 TAAATAAATAAATTCGAAAAAGAAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAATTT
196 TAAATAAATAAATTCG--AAA-AAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAATTT
915 TTTTGGCGTTGAAATATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTTCG
258 TTTTGGCGTTGAAATATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTTCG
*
980 GGTCATTTTTTGGAAAATTTTAGCCGAAATCGTGTACGT-----T-ACTGTTTTTGGCTAAAAAT
323 GGTCATTTTTTGGAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACTGTTTTTGGCTAAAAAC
* *
1039 GCATTCCAGAGCCCGAGTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATAT
387 GCGTTCCAGAGCCCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATAT
* *
1104 TCATCGAACTAAATCTCAACCACATTGGATATAAGGATTTGGTTTTGCAAGCATCTAAATCTTTT
452 TCATCGAACTAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTTTT
*
1169 TTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTTAAAAGCCC
517 TTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTGAAAAGCCC
*
1234 GTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTTTGGTCAAAAAATTCAGGAAAA
582 GTCAATCTTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTTTGG-CAAAAAATTCAGGAAAA
1299 ACTTCT
646 ACTTCT
1305 CAAGTCAGTTTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGGCTAAAAACGCGTTTTG
1 CAAGTCAGTTTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGGCTAAAAACGCGTTTTG
*
1370 GGGCCCCGAGCTCAGTTATACATGATTTTAGGTAGAAAGACTTCTTGAAATATCTATATATATCT
66 GGGCCCCG-GCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATATATCT
*
1435 AGCCAAATCTGAGTCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGAT
130 AGCCAAATCTGAGCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGAT
1500 TTAAATAAATAAATTCGAAAAAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAA-TTTT
195 TTAAATAAATAAATTCGAAAAAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAATTTTT
* * *
1564 TTGGCGTTGAATTATATATTTTTTCCGAGTATTGAGGTAAAAAAATTGAGGAAAAACTTTTCGGG
260 TTGGCGTTGAAATATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTTCGGG
1629 TCATTTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCG
325 TCATTTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCG
*
1694 TTCCGGAGCCCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATATTCA
390 TTCCAGAGCCCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATATTCA
* * * * * * *
1759 TCCAACTAAATATCAACCACTTTGGATTTAAGGATTT-TCTTTACAAGCATCCAAATCTTTTTCC
455 TCGAACTAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTTTTTTC
* * * *
1823 G-TATTAATAAGAAATTAATTCGGAAAAAAAATTGAAAAACGATATTAAAATAGTGAAAAGCCCA
520 GAT-TTAATTAGAAATTAATTCGG-AAAAAAATTGAAAAACGATAGTAGAATAGTGAAAAGCCCG
* *
1887 TCAATCTTTTTGGCGTTAAATTATATTTTTTTTCTGAATATTTTGGCAAAAAATTCAGGAAAAAC
583 TCAATCTTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAAC
1952 TTCT
648 TTCT
* * * * *
1956 CAGGTCAATTTTTAGCCGAAATCGTGTACTAACTAACCATCACGATTTTT-AGTTAAAAACGTGT
1 CAAGTCAGTTTTTAGCCGAAATCGTGTACTAACT----ATCACGATTTTTGGGCTAAAAACGCGT
*
2020 TTTGGGGCCTCGGCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATAT-TC
62 TTTGGGGCCCCGGCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATAT-
** *
2084 ATCTAGCTGAATTTGAGCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTT
126 ATCTAGCCAAATCTGAGCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTT
*
2149 CGATTTAAATAAATAAATTCGAAAAAAATGGAAAATCGGTTTTAGAATCGTGAATAACCCTTAAT
191 CGATTTAAATAAATAAATTCGAAAAAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAAT
* * *
2214 TTTTATTGGCGTTGAATTATATATTTTCTCCGAGTATTGTGGTAAAAAAATTGAGGAAAAACTTT
256 TTTT-TTGGCGTTGAAATATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTT
2279 TCGGGTCATTTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAA
320 TCGGGTCATTTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAA
*
2344 ACGCGTTCCAGAGCCCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCATGAAATATCTAT
385 ACGCGTTCCAGAGCCCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTAT
*
2409 ATTCATCGAACTAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACAATCATCTAAATCTT
450 ATTCATCGAACTAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTT
* * *
2474 TTTTCTATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAAAGATATTAGAATAGTGAAAAGC
515 TTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTGAAAAGC
* * * * *
2539 CCGTCAATCTTTTTTGCATTGAATTATTTATTTTTTCAGAGTATTTTGGCAAAAAATTCAGGAAA
580 CCGTCAATCTTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAA
*
2604 AACTTTT
645 AACTTCT
* * * *
2611 CAGGTCAGTTTTTAGCCAAAATCGTATACTAACTATCACTATTTTTGGGCTAAAAACGCGTTTTG
1 CAAGTCAGTTTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGGCTAAAAACGCGTTTTG
2676 GGGCCCCGGCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATATATCTA
66 GGGCCCCGGCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATATATCTA
* * * *
2741 GCGAAATCTGAGCCACAATGAATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCAATT
131 GCCAAATCTGAGCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATT
2806 TAAATAAATAAATTCGAAAAAA
196 TAAATAAATAAATTCGAAAAAA
2828 GAGTCCCTGA
Statistics
Matches: 2055, Mismatches: 91, Indels: 55
0.93 0.04 0.02
Matches are distributed among these distances:
646 1 0.00
647 101 0.05
648 42 0.02
649 338 0.16
650 11 0.01
651 243 0.12
652 354 0.17
653 197 0.10
654 333 0.16
655 392 0.19
656 42 0.02
657 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (651 bp):
CAAGTCAGTTTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGGCTAAAAACGCGTTTTG
GGGCCCCGGCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATATATCTA
GCCAAATCTGAGCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATT
TAAATAAATAAATTCGAAAAAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAATTTTTT
TGGCGTTGAAATATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGT
CATTTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCGT
TCCAGAGCCCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATATTCAT
CGAACTAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTTTTTTCG
ATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTGAAAAGCCCGTCA
ATCTTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTC
T
Found at i:4116 original size:763 final size:767
Alignment explanation
Indices: 3215--4758 Score: 2512
Period size: 765 Copynumber: 2.0 Consensus size: 767
3205 TAAGGATTTG
* *
3215 TTTTTACGAGCATCTTAATCTTGTTTCGATTTAAATAAATAAATTCGACAAAAAAATGGAAAATC
1 TTTTTACGAGCATCTTAATCTTGTTTCGATTTAAATAAATAAATTCGAAAAAAAAAAGGAAAATC
* *
3280 GGTTTTAGAAGCGTGAATAACCCTTAATTTTTTTTGGCGTTGAAATATATATTTTTTCCAAGTAT
66 GGTATTAGAAGCGTGAATAACCCTTAATATTTTTTGGCGTTGAAATATATATTTTTTCCAAGTAT
* **
3345 TGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGTCATTTTTTGGAAAATTTTAGCCGAAATCGTG
131 TGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTCCAAAATTTTAGCCGAAATCGTG
* * * * *
3410 T-GTTA-CATCATTGTTTTTGGCTAAAAACGCGTTCCGGAGCCCGGCTCAATTTTGCATGATTTT
196 TACTAACCATCAATGTTTTTGGCTAAAAACGCGTTCCAGAGCCCGACTCAATTTTGCATGATTTT
*
3473 TGGCACAAAGAGTCCCTGAAATATCTATATTCATCGAACTAAATCTCAACCACATTGGATATAAG
261 TGGCACAAAGAGTCCATGAAATATCTATATTCATCGAACTAAATCTCAACCACATTGGATATAAG
3538 GATTTGTTTTTACAAGCATCTAAATCTTTTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATT
326 GATTTGTTTTTACAAGCATCTAAATCTTTTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATT
* *
3603 GAAAAACGATAGTAGAATAGTTAAAAGCCCGTCAATCTTTTTGACGTTGAAATATATATTTTTTC
391 GAAAAACGATAGTAGAATAGTGAAAAGCCCGTCAATCTTTTTGACATTGAAATATATATTTTTTC
* *
3668 TGAGTATTTTGGCT-AAAAATTTAGGAAAAACTTCTCAAGTCAGTTTTTAGCCGAAATCGTG-T-
456 TGAGTATTTTGG-TAAAAAATTCAGGAAAAACTTCTCAAGTCAGTTTTTAGCCAAAATCGTGATA
3730 ACTATCACGATTTTTGGGCTAAAAACGCGTTTTGGGGCCCCAACTCAGTTATACATGATTTTAGG
520 ACTATCACGATTTTTGGGCTAAAAACGCGTTTTGGGGCCCCAACTCAGTTATACATGATTTTAGG
* *
3795 TAGAAAGACTTCTTGAAATATCTATATAT-ATCTAGCCAAATCTGAGTCACAGTGGATTTAAGGA
585 CAGAAAGACTTCTTGAAATATCTATAT-TCATCTAGCCAAATCTGAGGCACAGTGGATTTAAGGA
*
3859 TTTGTTTTTACAAGCATCTTAATCTTCTTTCGATTTAAATAAATAAATT-TGAAAAAAAATGGAA
649 TTTGTTTTTACAAGCATCTTAATCTTCTTTCGATTTAAATAAATAAATTAAGAAAAAAAATGG-A
* * *
3923 AATCGGTTTTAGAAGCGTGAATAACCCTT-ATTTTTTTTGGCGTTGAATTATTTAC
713 AATCGGTATTAGAAGCGTGAAAAACCCTTCA-TTTTTTTGGCGTTGAATTATATAC
* * *
3978 TTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAAATGAATTCGAAAAAAAAAAGGAAAATT
1 TTTTTACGAGCATCTTAATCTTGTTTCGATTTAAATAAATAAATTCGAAAAAAAAAAGGAAAATC
* * *
4043 GGTATTAGAAGCGTTGAA-AACCCTTCATATTTTTTGGCGTTGAATTATATATTTTTTCCGAGTA
66 GGTATTAGAAGCG-TGAATAACCCTTAATATTTTTTGGCGTTGAAATATATATTTTTTCCAAGTA
*
4107 TTGTGGTAAAGAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTCCAAAATTTTAGCCGAAATCGT
130 TTGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTCCAAAATTTTAGCCGAAATCGT
4172 GTACTAACCATCAATGTTTTTGGCTAAAAACGCGTTCCAGAGCCCGACTCAATTTTGCATGATTT
195 GTACTAACCATCAATGTTTTTGGCTAAAAACGCGTTCCAGAGCCCGACTCAATTTTGCATGATTT
*
4237 TTGGCAGAAAGAGTCCATGAAATATCTATATTCATCGAACTAAATCTCAACCACATTGGATATAA
260 TTGGCACAAAGAGTCCATGAAATATCTATATTCATCGAACTAAATCTCAACCACATTGGATATAA
* *
4302 GGATTTGTTTTTACAATCATCTAAATCTTTTTTCTATTTAATTAGAAATTAATTCGGAAAAAAAT
325 GGATTTGTTTTTACAAGCATCTAAATCTTTTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAT
* ** *
4367 TGAAAAACGATATTAGAATAGTGAAAAGCCCGTCAATCTTTTTTTCATTGAATTATATATTTTTT
390 TGAAAAACGATAGTAGAATAGTGAAAAGCCCGTCAATCTTTTTGACATTGAAATATATATTTTTT
* *
4432 CTGAGTATTTTGGTAAAAAATTCAGGAAAAACTTTTCAGGTCAGTTTTTAGCCAAAATCGTGTAC
455 CTGAGTATTTTGGTAAAAAATTCAGGAAAAACTTCTCAAGTCAGTTTTTAGCCAAAATCGTG-A-
* **
4497 TAACTATCACGATTTTTGGTCTAAAAACGCGTTTTGGGGCCCCGGCTCAGTTATACATGATTTTA
518 TAACTATCACGATTTTTGGGCTAAAAACGCGTTTTGGGGCCCCAACTCAGTTATACATGATTTTA
4562 GGCAGAAAGACTTCTTGAAATATCTATATTCATCTAGCCAAATCTGAGGCACAGTGGATTTAAGG
583 GGCAGAAAGACTTCTTGAAATATCTATATTCATCTAGCCAAATCTGAGGCACAGTGGATTTAAGG
* * * *
4627 ATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAAATGAATTCGAAGAAAAAAAATG
648 ATTTGTTTTTACAAGCATCTTAATCTTCTTTCGATTTAAATAAATAAATT--AAGAAAAAAAATG
*
4692 GAAATCGGTATTAGAAGCGTGAAAAACCCTTCATTTTTTTGGCGTTGAATTATATAT
711 GAAATCGGTATTAGAAGCGTGAAAAACCCTTCATTTTTTTGGCGTTGAATTATATAC
*
4749 TTTTTCCGAG
1 TTTTTACGAG
4759 TATTGTGGTA
Statistics
Matches: 720, Mismatches: 48, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
763 177 0.25
764 7 0.01
765 295 0.41
768 2 0.00
769 167 0.23
771 59 0.08
772 13 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (767 bp):
TTTTTACGAGCATCTTAATCTTGTTTCGATTTAAATAAATAAATTCGAAAAAAAAAAGGAAAATC
GGTATTAGAAGCGTGAATAACCCTTAATATTTTTTGGCGTTGAAATATATATTTTTTCCAAGTAT
TGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTCCAAAATTTTAGCCGAAATCGTG
TACTAACCATCAATGTTTTTGGCTAAAAACGCGTTCCAGAGCCCGACTCAATTTTGCATGATTTT
TGGCACAAAGAGTCCATGAAATATCTATATTCATCGAACTAAATCTCAACCACATTGGATATAAG
GATTTGTTTTTACAAGCATCTAAATCTTTTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATT
GAAAAACGATAGTAGAATAGTGAAAAGCCCGTCAATCTTTTTGACATTGAAATATATATTTTTTC
TGAGTATTTTGGTAAAAAATTCAGGAAAAACTTCTCAAGTCAGTTTTTAGCCAAAATCGTGATAA
CTATCACGATTTTTGGGCTAAAAACGCGTTTTGGGGCCCCAACTCAGTTATACATGATTTTAGGC
AGAAAGACTTCTTGAAATATCTATATTCATCTAGCCAAATCTGAGGCACAGTGGATTTAAGGATT
TGTTTTTACAAGCATCTTAATCTTCTTTCGATTTAAATAAATAAATTAAGAAAAAAAATGGAAAT
CGGTATTAGAAGCGTGAAAAACCCTTCATTTTTTTGGCGTTGAATTATATAC
Found at i:4631 original size:323 final size:319
Alignment explanation
Indices: 3978--4963 Score: 1052
Period size: 323 Copynumber: 3.0 Consensus size: 319
3968 AATTATTTAC
* * * * **
3978 TTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAAATGAATTCGAAAAAAAAAAGGAAAATT
1 TTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTAAATGAATTCGAGAAAAAAAATGAAAAAC
* * * *
4043 GGTATTAGAAGCGTTG-AAAACCCTTCATATTTTTTGGCGTTGAATTATATATTTTTTCCGAGTA
66 GATATTAGAAGAG-TGAAAAACCCGTCAT-TTTTTTGGCATTGAATTATATATTTTTTCCGAGTA
*
4107 TTGTGGTAAAGAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTCCAAAATTTTAGCCGAAATCGT
129 TTGTGGTAAA-AAATTGAGGAAAAACTTTTCGGGTCAG----T------TTTTAGCCAAAATCGT
* * *
4172 GTACTAACCATCAATGTTTTTGGCTAAAAACGCGTTCCAGAGCCCGACTCAATTTTGCATGATTT
183 GTACTAACCATCAACGTTTTTGGCTAAAAACGCGTTCCAGAGCCCGACTCAATTATACATGATTT
* * * *
4237 TTGGCAGAAAGAGTCCATGAAATATCTATATTCATCGAACTAAATCTCAACCACATTGGATATAA
248 TAGGCAGAAAGACTCCATGAAATATCTATATTCATCGAACCAAATCTCAACCACAGTGGATATAA
4302 GGATTTG
313 GGATTTG
* * * * *
4309 TTTTTACAATCATCTAAATCTTTTTTCTATTTAATTAGAAATTAATTCG-GAAAAAAATTGAAAA
1 TTTTTACAAGCATCTAAATCTTGTTTCGATTTAATT--AAATGAATTCGAGAAAAAAAATGAAAA
* * * *
4373 ACGATATTAGAATAGTGAAAAGCCCGTCAATCTTTTTT-TCATTGAATTATATATTTTTTCTGAG
64 ACGATATTAGAAGAGTGAAAAACCCGTC-AT-TTTTTTGGCATTGAATTATATATTTTTTCCGAG
* * * *
4437 TATTTTGGTAAAAAATTCAGGAAAAACTTTTCAGGTCAGTTTTTAGCCAAAATCGTGTACTAACT
127 TATTGTGGTAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTAGCCAAAATCGTGTACTAACC
*** * * *
4502 ATC-ACGATTTTTGGTCTAAAAACGCGTTTTGGGGCCCCGGCTCAGTTATACATGATTTTAGGCA
192 ATCAACG-TTTTTGG-CTAAAAACGCGTTCCAGAG-CCCGACTCAATTATACATGATTTTAGGCA
* * * * * ** *
4566 GAAAGACTTCTTGAAATATCTATATTCATCTAGCCAAATCTGAGGCACAGTGGATTTAAGGATTT
254 GAAAGACTCCATGAAATATCTATATTCATCGAACCAAATCTCAACCACAGTGGATATAAGGATTT
4631 G
319 G
* * * *
4632 TTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAAATGAATTCGAAGAAAAAAAATGGAAAT
1 TTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTAAATGAATTCG-AGAAAAAAAATGAAAAA
* * * *
4697 CGGTATTAGAAGCGTGAAAAACCCTTCATTTTTTTGGCGTTGAATTATATATTTTTTCCGAGTAT
65 CGATATTAGAAGAGTGAAAAACCCGTCATTTTTTTGGCATTGAATTATATATTTTTTCCGAGTAT
* *
4762 TGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTT--CCAAAATTTTAGCTGAAATCG
130 TGTGGT-AAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTAGCCAAAA---TCG-TG-TA-C-
* * * *
4825 TGTACTATC-ACTGTTTTTGGCTAAAAACGCGTTCCAGAGCCCGACTCAATTTTGCATGATTTT-
187 T-AACCATCAAC-GTTTTTGGCTAAAAACGCGTTCCAGAGCCCGACTCAATTATACATGATTTTA
* * * * * *
4888 GGCACAAAGAGTCCCTGAAATATCTACATTCATCGAACTAAATCTCAACCACATTGGATATAAGG
250 GGCAGAAAGACTCCATGAAATATCTATATTCATCGAACCAAATCTCAACCACAGTGGATATAAGG
4953 ATTTG
315 ATTTG
4958 TTTTTA
1 TTTTTA
Statistics
Matches: 545, Mismatches: 90, Indels: 45
0.80 0.13 0.07
Matches are distributed among these distances:
320 2 0.00
321 55 0.10
322 48 0.09
323 178 0.33
324 2 0.00
325 2 0.00
326 64 0.12
327 22 0.04
328 16 0.03
329 15 0.03
330 1 0.00
331 58 0.11
332 64 0.12
333 18 0.03
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (319 bp):
TTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTAAATGAATTCGAGAAAAAAAATGAAAAAC
GATATTAGAAGAGTGAAAAACCCGTCATTTTTTTGGCATTGAATTATATATTTTTTCCGAGTATT
GTGGTAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTAGCCAAAATCGTGTACTAACCATCA
ACGTTTTTGGCTAAAAACGCGTTCCAGAGCCCGACTCAATTATACATGATTTTAGGCAGAAAGAC
TCCATGAAATATCTATATTCATCGAACCAAATCTCAACCACAGTGGATATAAGGATTTG
Done.