Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold720
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: 4268
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1202 original size:476 final size:476
Alignment explanation
Indices: 1--2588 Score: 4840
Period size: 475 Copynumber: 5.5 Consensus size: 476
1 CCTAATAAGGATAAC-TG-TTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATCACTAGATTC
1 CCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAAT-ACTAGATTC
64 CTTGTTT-GCACATTTTAAGGCACAGACATAGACTTTATAATAATAGGTCG-AAGAAAACCTTTC
65 CTTGTTTGGCACATTTT-AGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTC
127 TTGAGAAACCAAAGC-TCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCC
129 TTGAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCC
191 TGAAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCT
194 TGAAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCT
256 ATC-AAAATGGCGGAATGAAAAGCTTTTTCTTGTGACACCAAAGCATCAATGTCCGTCTATCCTA
259 ATCAAAAATGGCGGAATGAAAAGC-TTTTCTTGTGACACCAAAGCATCAATGT-CGTCTATCCTA
320 ATGAAGGGAATGTGTTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATG
322 ATGAAGGGAATGTG-TTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATG
385 CTTGTCTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATG
386 CTTGTCTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATG
450 AGAAGAAAATCATCAATATCATTTAT
451 AGAAGAAAATCATCAATATCATTTAT
* *
476 CCTAATAAGGATAACATGTTTATAAGCCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
1 CCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
541 TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCG-AAGAAAACCTTTCTT
66 TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
605 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
131 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
670 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
196 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
735 CAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
261 CAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
800 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
326 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
865 CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAG
391 CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAG
930 AAAATCATCAATATCATTTAT
456 AAAATCATCAATATCATTTAT
*
951 CCTAATGAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
1 CCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
1016 TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
66 TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
1081 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
131 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
1146 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
196 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
* * * *
1211 CTAAAATGGCGGAATGAAAAGTTTTTCTTGTAACACCAAAGCATCAATGTCGTGTATCCTAATGA
261 CAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
*
1276 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTACGAGAATTGATGCTTGT
326 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
* * *
1341 CTTATTTAAAGGTTGAGCTTTGATTTTAAGGAAAATAAGGGCAAAGAAAAGATTTCCATGAAAAG
391 CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAG
1406 AAAATCATCAATATCATTTAT
456 AAAATCATCAATATCATTTAT
1427 CCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
1 CCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
1492 TTG-TTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
66 TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
1556 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
131 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
1621 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
196 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
1686 CAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
261 CAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
1751 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
326 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
*
1816 CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGGAAAGATTTCCATGAGAAG
391 CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAG
1881 AAAATCATCAATATCATTTAT
456 AAAATCATCAATATCATTTAT
* *
1902 CCTAATAAGGATAACATGTTTATAAGCCCCATTCAC-AGGTGTGTGAAGATCAATACTAGA-TCC
1 CCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
1965 TTGTTTGGCACA-TTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
66 TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
2029 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
131 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
2094 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
196 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
2159 CAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
261 CAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
2224 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
326 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
2289 CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAG
391 CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAG
2354 AAAATCATCAATATCATTTAT
456 AAAATCATCAATATCATTTAT
* *
2375 CCTAATGAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGAGTGAAGATCAATACTAGATTCC
1 CCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
*
2440 TTGTTTGGCACATTTTAGGCACAGACATAGACTATATAATAATAGGTCGAAAGAAAACCTTTCTT
66 TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
* * * ** *
2505 GAGAAGCTAAAGCTTCATTATCATGTATACTTATGAGAAGACTATATTTATGGTGCCTAAT-CTA
131 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
2569 AAAAGAATGGGGATTAGTAT
196 AAAAGAATGGGGATTAGTAT
2589 TGTAGACACT
Statistics
Matches: 2067, Mismatches: 36, Indels: 20
0.97 0.02 0.01
Matches are distributed among these distances:
473 436 0.21
474 55 0.03
475 736 0.36
476 631 0.31
477 189 0.09
478 20 0.01
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (476 bp):
CCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
CAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAG
AAAATCATCAATATCATTTAT
Found at i:1894 original size:951 final size:950
Alignment explanation
Indices: 1--2588 Score: 4836
Period size: 951 Copynumber: 2.7 Consensus size: 950
1 CCTAATAAGGATAACTG-TTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATCACTAGATTCC
1 CCTAATAAGGATAACTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAAT-ACTAGATTCC
65 TTGTTT-GCACATTTTAAGGCACAGACATAGACTTTATAATAATAGGTCG-AAGAAAACCTTTCT
65 TTGTTTGGCACATTTT-AGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCT
128 TGAGAAACCAAAGC-TCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCT
129 TGAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCT
192 GAAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTA
194 GAAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTA
257 TCAAAATGGCGGAATGAAAAGCTTTTTCTTGTGACACCAAAGCATCAATGTCCGTCTATCCTAAT
259 TCAAAATGGCGGAATGAAAAG-TTTTTCTTGTGACACCAAAGCATCAATGT-CGTCTATCCTAAT
322 GAAGGGAATGTGTTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCT
322 GAAGGGAATGTG-TTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCT
387 TGTCTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAG
386 TGTCTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAG
* *
452 AAGAAAATCATCAATATCATTTATCCTAATAAGGATAACATGTTTATAAGCCCCATTCACAAGGT
451 AAGAAAATCATCAATATCATTTATCCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGT
517 GTGTGAAGATCAATACTAGATTCCTTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATA
516 GTGTGAAGATCAATACTAGATTCCTTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATA
582 ATAGGTCG-AAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGA
581 ATAGGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGA
646 CTACGTTTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTAT
646 CTACGTTTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTAT
711 TTAAGAGGCAAACTTTCATTCTATCAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAG
711 TTAAGAGGCAAACTTTCATTCTATCAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAG
776 CATCAATGTCGTCTATCCTAATGAAGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAG
776 CATCAATGTCGTCTATCCTAATGAAGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAG
841 ATTGTTATGAGAATTGATGCTTGTCTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGG
841 ATTGTTATGAGAATTGATGCTTGTCTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGG
906 CAAAGAAAAGATTTCCATGAGAAGAAAATCATCAATATCATTTAT
906 CAAAGAAAAGATTTCCATGAGAAGAAAATCATCAATATCATTTAT
*
951 CCTAATGAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
1 CCTAATAAGGATAAC-TGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
1016 TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
65 TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
1081 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
130 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
1146 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
195 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
* *
1211 CTAAAATGGCGGAATGAAAAGTTTTTCTTGTAACACCAAAGCATCAATGTCGTGTATCCTAATGA
260 C-AAAATGGCGGAATGAAAAGTTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
*
1276 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTACGAGAATTGATGCTTGT
324 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
* * *
1341 CTTATTTAAAGGTTGAGCTTTGATTTTAAGGAAAATAAGGGCAAAGAAAAGATTTCCATGAAAAG
389 CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAG
1406 AAAATCATCAATATCATTTATCCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTG
454 AAAATCATCAATATCATTTATCCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTG
1471 TGAAGATCAATACTAGATTCCTTG-TTGGCACATTTTAGGCACAGACATAGACTTTATAATAATA
519 TGAAGATCAATACTAGATTCCTTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATA
1535 GGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTA
584 GGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTA
1600 CGTTTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTA
649 CGTTTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTA
1665 AGAGGCAAACTTTCATTCTATCAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCAT
714 AGAGGCAAACTTTCATTCTATCAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCAT
1730 CAATGTCGTCTATCCTAATGAAGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATT
779 CAATGTCGTCTATCCTAATGAAGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATT
1795 GTTATGAGAATTGATGCTTGTCTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAA
844 GTTATGAGAATTGATGCTTGTCTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAA
*
1860 AGGAAAGATTTCCATGAGAAGAAAATCATCAATATCATTTAT
909 AGAAAAGATTTCCATGAGAAGAAAATCATCAATATCATTTAT
*
1902 CCTAATAAGGATAACATGTTTATAAGCCCCATTCAC-AGGTGTGTGAAGATCAATACTAGA-TCC
1 CCTAATAAGGATAAC-TGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCC
1965 TTGTTTGGCACA-TTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
65 TTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTT
2029 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
130 GAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTG
2094 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
195 AAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTAT
*
2159 CAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
260 C-AAAATGGCGGAATGAAAAGTTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGA
2224 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
324 AGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGT
2289 CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAG
389 CTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAG
* *
2354 AAAATCATCAATATCATTTATCCTAATGAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGAG
454 AAAATCATCAATATCATTTATCCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTG
*
2419 TGAAGATCAATACTAGATTCCTTGTTTGGCACATTTTAGGCACAGACATAGACTATATAATAATA
519 TGAAGATCAATACTAGATTCCTTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATA
* * *
2484 GGTCGAAAGAAAACCTTTCTTGAGAAGCTAAAGCTTCATTATCATGTATACTTATGAGAAGACTA
584 GGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTA
** *
2549 TATTTATGGTGCCTAAT-CTAAAAAGAATGGGGATTAGTAT
649 CGTTTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTAT
2589 TGTAGACACT
Statistics
Matches: 1600, Mismatches: 30, Indels: 18
0.97 0.02 0.01
Matches are distributed among these distances:
948 478 0.30
949 131 0.08
950 83 0.05
951 647 0.40
952 97 0.06
953 145 0.09
954 19 0.01
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (950 bp):
CCTAATAAGGATAACTGTTTATAAGGCCCATTCACAAGGTGTGTGAAGATCAATACTAGATTCCT
TGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGGTCGAAAGAAAACCTTTCTTG
AGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACGTTTATGGTGCCTAATCCTGA
AAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAGAGGCAAACTTTCATTCTATC
AAAATGGCGGAATGAAAAGTTTTTCTTGTGACACCAAAGCATCAATGTCGTCTATCCTAATGAAG
GGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGTTATGAGAATTGATGCTTGTCT
TATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAGAAAAGATTTCCATGAGAAGAA
AATCATCAATATCATTTATCCTAATAAGGATAACGTGTTTATAAGGCCCATTCACAAGGTGTGTG
AAGATCAATACTAGATTCCTTGTTTGGCACATTTTAGGCACAGACATAGACTTTATAATAATAGG
TCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATACTTATGAGAAGACTACG
TTTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTATGACCATTCTTGTTTGTCTTATTTAAG
AGGCAAACTTTCATTCTATCAAAAATGGCGGAATGAAAAGCTTTTCTTGTGACACCAAAGCATCA
ATGTCGTCTATCCTAATGAAGGGAATGTGTTTTTGGGTGCAAATCTTGAAAAGAATGGAGATTGT
TATGAGAATTGATGCTTGTCTTATTTAATGGTTGAGCTTTGATTTTAAGGAGAATAAGGGCAAAG
AAAAGATTTCCATGAGAAGAAAATCATCAATATCATTTAT
Found at i:2935 original size:33 final size:33
Alignment explanation
Indices: 2898--2964 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2888 TTCAACGATT
2898 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2931 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2964 T
1 T
2965 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2936 original size:13 final size:13
Alignment explanation
Indices: 2918--2942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2908 CATAAAATGT
2918 TGTATCGATACAA
1 TGTATCGATACAA
2931 TGTATCGATACA
1 TGTATCGATACA
2943 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3020 original size:12 final size:12
Alignment explanation
Indices: 3003--3029 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2993 TACATTACTC
3003 ACATGTATCGAT
1 ACATGTATCGAT
3015 ACATGTATCGAT
1 ACATGTATCGAT
3027 ACA
1 ACA
3030 CTGATCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (12 bp):
ACATGTATCGAT
Found at i:3100 original size:51 final size:50
Alignment explanation
Indices: 3037--3154 Score: 177
Period size: 51 Copynumber: 2.3 Consensus size: 50
3027 ACACTGATCT
*
3037 TGTATCGATACATGCAGGCAAA-TTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGA-A-ACTATAAAA
*
3088 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGAAACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGAAACTATAAAA
3138 TGTATCG-TAACATGCAG
1 TGTATCGAT-ACATGCAG
3155 ATAATTTTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
49 1 0.02
50 22 0.35
51 23 0.37
52 17 0.27
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (50 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGAAACTATAAAA
Found at i:3811 original size:20 final size:20
Alignment explanation
Indices: 3786--3825 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3776 TGTTGGTATA
3786 TTTTCTGACTT-TGATTTTAT
1 TTTTCTG-CTTATGATTTTAT
*
3806 TTTTCTGCTTATGGTTTTAT
1 TTTTCTGCTTATGATTTTAT
3826 CATCATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (20 bp):
TTTTCTGCTTATGATTTTAT
Done.