Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014508.1 Corchorus capsularis cultivar CVL-1 contig14529, 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: 2944
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:768 original size:322 final size:320
Alignment explanation
Indices: 1--1889 Score: 1953
Period size: 322 Copynumber: 5.8 Consensus size: 320
* * * *
1 GTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGA
1 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
** * * * * * *
66 AGTCTTTACGCCAGAAA-TCATGCAAAATTGAGCCAGGGCTCC-GGAACTCCT-TTTTTAG-CAA
66 AGTCTTTTTGCCA-AAAGTTATGCAAAACTGAGTC-GGGGTCCTGAAACT--TGTTTTTAGCCCA
** ** * * *
127 AAAAGCTATGATAATTAGTGCATGATTTCAGCTAAAATTTTTGCAAAAACTGGCCCGAAAAGTTT
127 AAAA-CCGTGATGGTTAGTACACGATTTCAGC---------T--AAAAACTGACCCGAAAA-TTT
* * * * * ** * * ** * *
192 ATCCTTAGTTTTTTGCCCCTTTACTCTGAAAAAATATATAATTCAAGGCCAAAATGATTGA-ATA
179 TTTCTCAATTTTTTGCCACAATACTCAGAAAAGATATATAATTCAACACCAAAAAGATTGACA-G
** ** * * *
256 TTTTTTCACCCTTCTAATATCGTTTTTTCATTTTTTTTCTCGAATTTATTTTTAATTAAATCGAA
243 GCTTTTCACGGTTCTAATATCG-TTTTCCA-ATTTTTT-TCGAA-TTAATTTTAATTAAATCGAA
*
321 ACAAGATTCAGAAGCCC
304 ACAAGATTCAGAAGCTC
*
338 GTAAAAACAAATCCTTAAAACCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATCTT-AAG
1 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATAT-TTCAAG
*** * * * *
402 GAAAAATTCTT-CCAAAAGTTATACAAAACTGAGCCGGAGTCCTGAAACTTGTTTTTAGCCCAAA
65 G-AGTCTTTTTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACTTGTTTTTAGCCCAAA
*
466 AACCGTGATGGTTAGTACACGACTTCAGCTAAAAACTGACCCGAAAATTTTCTTCTCAATTTTTT
129 AACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAAATTTT-TTCTCAATTTTTT
* *
531 GCCACAATACTCAGAAAAGATATATAGTTCAACACCAAAAAGATTGATAGGCTTTTCACGGTTCT
193 GCCACAATACTCAGAAAAGATATATAATTCAACACCAAAAAGATTGACAGGCTTTTCACGGTTCT
*
596 AATATCGTTTTCCAATTTGTTTTCGAATTAATTTTAATTAAATCGAAATAAGATTCAGAAGCTC
258 AATATCGTTTTCCAATTT-TTTTCGAATTAATTTTAATTAAATCGAAACAAGATTCAGAAGCTC
* *
660 GTAAAAACAAATCCTTAAAACCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGG
1 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
* * *
725 AGTCTTTTTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACGTGTTTTTAACCGAAAAA
66 AGTCTTTTTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACTTGTTTTTAGCCCAAAAA
** *
790 CTATGATGGTTAGTACACGATTTCAGTTAAAAACTGACCCGAAAATATTTTTCTCAATTTTTTGC
131 CCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAAAT-TTTTTCTCAATTTTTTGC
* * *
855 CACAATACTCAGAAAACATATATAATTCAACGA-CTAAAAGATTGACGGGCTTTTCACGGTTCTA
195 CACAATACTCAGAAAAGATATATAATTCAAC-ACCAAAAAGATTGACAGGCTTTTCACGGTTCTA
* * * *
919 AT-TGGTTTTCCAATATTTTTTCGAATTAATTTTAATTAAATCAAAACAAGATTAAGATGCTC
259 ATATCGTTTTCCAAT-TTTTTTCGAATTAATTTTAATTAAATCGAAACAAGATTCAGAAGCTC
* * * * *
981 GTAAAAATAAATCCTTATATCCAATGTGGCTGAAATTTGGTTCGATGAATATAGATATTTGAAGG
1 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
* ** * * * * * * *
1046 ATTCTTTACGCCAAAAATCATGCAAAATTGA-TCCGGGGCTCC-GGAACTCGTTTGTAG-CAAAA
66 AGTCTTTTTGCCAAAAGTTATGCAAAACTGAGT-CGGGG-TCCTGAAACTTGTTTTTAGCCCAAA
* * *
1108 AACTGTGAT-GTTAGTACACGATATTTGCTAAAATTTTTGC-AAAAAATGGCCCGAAAAGTTTTT
129 AACCGTGATGGTTAGTACACG--ATTT-C----A-----GCTAAAAACTGACCCGAAAA-TTTTT
* * ** * * * * **
1171 CCTCAAATTTTTTG-CTCAATACTCTTAAAAAATATATAATACAACGCCAAAAAAATTGA-ATAT
181 TCTC-AATTTTTTGCCACAATACTCAGAAAAGATATATAATTCAACACCAAAAAGATTGACA-GG
* * * * *
1234 TTTTTCACGCTTCAAATATCGTTTTTTC-ATTTTTTCTCGAATTTATTTCTAATTAAATCGAAAC
244 CTTTTCACGGTTCTAATATCG-TTTTCCAATTTTTT-TCGAATTAATTT-TAATTAAATCGAAAC
*
1298 AAAATTCAGAAGCTC
306 AAGATTCAGAAGCTC
*
1313 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAAG
1 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
*
1378 AG-CTTTTCTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACGTGTTTTTAGCCCAAAA
66 AGTCTTTT-TGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACTTGTTTTTAGCCCAAAA
* * * * *
1442 ACCGTGATGGTTAATACACGATTTCAACTAAAAACTAACCCGAAAATATTATTCTCAATTTTTTA
130 ACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAAAT-TTTTTCTCAATTTTTTG
* * ** * *
1507 CCACAATACTAAAAAAAGATATATAATTCAACGGCTAAAAGATTGACAGACTTTTCACGGTTCTA
194 CCACAATACTCAGAAAAGATATATAATTCAACACCAAAAAGATTGACAGGCTTTTCACGGTTCTA
*
1572 ATATCGTTTTCCAATTTTTTTTCTGAATTAATTTTAATTAAATCGAAACAAGATTTA-AATGCTC
259 ATATCGTTTTCCAA-TTTTTTTC-GAATTAATTTTAATTAAATCGAAACAAGATTCAGAA-GCTC
* * *
1636 GTAAAAACAAATCCTTACATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATATCAAGG
1 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
* * * * *
1701 AGTCTTTCTGCCAAAAGTTATGCATAACTGAGCCGGAGTCCTGAAACTTTTTTTTAGCCCAAAAA
66 AGTCTTTTTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACTTGTTTTTAGCCCAAAAA
* * * * *
1766 TCATGATGGTTAGTACACAATTTCAGCTAAAAGCTGACCTGAAAATATTTTTTCTCAATTTTTTT
131 CCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCG-AAA-ATTTTTTCTCAA-TTTTTT
* *
1831 GCCACAATACTCAGAAAAGATATATAATTCAACACCAAAAAAATTTGACGGGCTTTTCA
193 GCCACAATACTCAGAAAAGATATATAATTCAACACCAAAAAGA-TTGACAGGCTTTTCA
1890 ATTTTAATTA
Statistics
Matches: 1307, Mismatches: 191, Indels: 119
0.81 0.12 0.07
Matches are distributed among these distances:
319 11 0.01
320 13 0.01
321 161 0.12
322 283 0.22
323 262 0.20
324 44 0.03
325 126 0.10
326 15 0.01
327 2 0.00
330 77 0.06
331 34 0.03
332 130 0.10
333 13 0.01
334 10 0.01
335 1 0.00
336 35 0.03
337 85 0.07
338 5 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (320 bp):
GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
AGTCTTTTTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACTTGTTTTTAGCCCAAAAA
CCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAAATTTTTTCTCAATTTTTTGCC
ACAATACTCAGAAAAGATATATAATTCAACACCAAAAAGATTGACAGGCTTTTCACGGTTCTAAT
ATCGTTTTCCAATTTTTTTCGAATTAATTTTAATTAAATCGAAACAAGATTCAGAAGCTC
Found at i:1354 original size:653 final size:654
Alignment explanation
Indices: 220--1716 Score: 1889
Period size: 653 Copynumber: 2.3 Consensus size: 654
210 CTTTACTCTG
* * * * **
220 AAAAA-ATATATAATTCAA-GGCCAAAATGATTGA-ATATTTTTTCACCCTTCTAATATCGTTTT
1 AAAAACATATATAATTCAACGACTAAAA-GATTGACAGA-CTTTTCACGGTTCTAATATCG-TTT
* * * * * *
282 TTC-ATTTTTTTTCTCGAATTTATTTTTAATTAAATCGAAACAAGATTCAGAA-GCCCGTAAAAA
63 TCCAATATTTTTTCT-GAA-TTAATTTTAATTAAATCAAAACAAGATTTA-AATGCTCGTAAAAA
* * * * * * ****
345 CAAATCCTTAAAACCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATCTTAAGGAAAAATT
125 CAAATCCTTACATCCAATGTGGCTGAAATTTGGTTCGATGAATATAGATATATCAAGGAGTCTTT
* * * * * * * * * * * *
410 CTTCCAAAAGTTATACAAAACTGAGCCGGAG-TCCTGAAACTTGTTTTTAGCCCAAAAACCGTGA
190 CTGCCAAAAATCATGCAAAATTGATCCGGGGCTCC-GGAACTCGTTTGTAG-CAAAAAACTGTGA
* * *
474 TGGTTAGTACACG--ACTT-C----A-----GCTAAAAACTGACCCGAAAATTTTCTTCTCAATT
253 T-GTTAGTACACGATATTTGCTAAAATTTTTGC-AAAAAATGACCCGAAAATTTTCTCCTCAATT
* * * * *
527 TTTTGCCACAATACTCAGAAAAGATATATAGTTCAACACCAAAAAGATTGATAGGCTTTTCACGG
316 TTTTGCCACAATACTCAGAAAAAATATATAATACAACACCAAAAAAATTGATAGGCTTTTCACGC
* * *
592 TTCTAATATCGTTTTCCAATTTGTTTTCGAATTAATTTTAATTAAATCGAAATAAGATTCAGAAG
381 TTCAAATATCGTTTTCCAATTTGTTTTCGAATTAATTTTAATTAAATCGAAACAAAATTCAGAAG
657 CTCGTAAAAACAAATCCTTAAAACCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCA
446 CTCGTAAAAACAAATCCTTAAAACCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCA
* *
722 AGGAGTCTTTT-TGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACGTGTTTTTAACCGA
511 AAGAG-CTTTTCTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACGTGTTTTTAACCCA
* * ** * *
786 AAAACTATGATGGTTAGTACACGATTTCAGTTAAAAACTGACCCGAAAATATTTTTCTCAATTTT
575 AAAACCATGATGGTTAATACACGATTTCAACTAAAAACTAACCCGAAAATATTATTCTCAATTTT
* *
851 TTGCCACAATACTCA
640 TTACCACAATACTAA
* * * *
866 GAAAACATATATAATTCAACGACTAAAAGATTGACGGGCTTTTCACGGTTCTAAT-TGGTTTTCC
1 AAAAACATATATAATTCAACGACTAAAAGATTGACAGACTTTTCACGGTTCTAATATCGTTTTCC
*
930 AATATTTTTTC-GAATTAATTTTAATTAAATCAAAACAAGA-TTAAGATGCTCGTAAAAATAAAT
66 AATATTTTTTCTGAATTAATTTTAATTAAATCAAAACAAGATTTAA-ATGCTCGTAAAAACAAAT
* * * *
993 CCTTATATCCAATGTGGCTGAAATTTGGTTCGATGAATATAGATATTTGAAGGATTCTTTAC-GC
130 CCTTACATCCAATGTGGCTGAAATTTGGTTCGATGAATATAGATATATCAAGGAGTCTTT-CTGC
1057 CAAAAATCATGCAAAATTGATCCGGGGCTCCGGAACTCGTTTGTAGCAAAAAACTGTGATGTTAG
194 CAAAAATCATGCAAAATTGATCCGGGGCTCCGGAACTCGTTTGTAGCAAAAAACTGTGATGTTAG
*
1122 TACACGATATTTGCTAAAATTTTTGCAAAAAATGGCCCGAAAAGTTTT-TCCTCAAATTTTTTG-
259 TACACGATATTTGCTAAAATTTTTGCAAAAAATGACCCGAAAA-TTTTCTCCTC-AATTTTTTGC
* ** * **
1185 CTCAATACTCTTAAAAAATATATAATACAACGCCAAAAAAATTGAATA-TTTTTTCACGCTTCAA
322 CACAATACTCAGAAAAAATATATAATACAACACCAAAAAAATTG-ATAGGCTTTTCACGCTTCAA
* *
1249 ATATCGTTTTTTC-ATTT-TTTCTCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGAAGCT
386 ATATCG-TTTTCCAATTTGTTT-TCGAATTAATTT-TAATTAAATCGAAACAAAATTCAGAAGCT
* *
1312 CGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAA
448 CGTAAAAACAAATCCTTAAAACCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAA
*
1377 GAGCTTTTCTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACGTGTTTTTAGCCCAAAA
513 GAGCTTTTCTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACGTGTTTTTAACCCAAAA
*
1442 ACCGTGATGGTTAATACACGATTTCAACTAAAAACTAACCCGAAAATATTATTCTCAATTTTTTA
578 ACCATGATGGTTAATACACGATTTCAACTAAAAACTAACCCGAAAATATTATTCTCAATTTTTTA
1507 CCACAATACTAA
643 CCACAATACTAA
* *
1519 AAAAAGATATATAATTCAACGGCTAAAAGATTGACAGACTTTTCACGGTTCTAATATCGTTTTCC
1 AAAAACATATATAATTCAACGACTAAAAGATTGACAGACTTTTCACGGTTCTAATATCGTTTTCC
* *
1584 AATTTTTTTTCTGAATTAATTTTAATTAAATCGAAACAAGATTTAAATGCTCGTAAAAACAAATC
66 AATATTTTTTCTGAATTAATTTTAATTAAATCAAAACAAGATTTAAATGCTCGTAAAAACAAATC
*
1649 CTTACATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATATCAAGGAGTCTTTCTGCCA
131 CTTACATCCAATGTGGCTGAAATTTGGTTCGATGAATATAGATATATCAAGGAGTCTTTCTGCCA
1714 AAA
196 AAA
1717 GTTATGCATA
Statistics
Matches: 733, Mismatches: 87, Indels: 53
0.84 0.10 0.06
Matches are distributed among these distances:
641 12 0.02
642 15 0.02
643 125 0.17
644 8 0.01
645 5 0.01
646 15 0.02
647 33 0.05
648 7 0.01
651 3 0.00
652 93 0.13
653 287 0.39
654 19 0.03
655 107 0.15
656 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (654 bp):
AAAAACATATATAATTCAACGACTAAAAGATTGACAGACTTTTCACGGTTCTAATATCGTTTTCC
AATATTTTTTCTGAATTAATTTTAATTAAATCAAAACAAGATTTAAATGCTCGTAAAAACAAATC
CTTACATCCAATGTGGCTGAAATTTGGTTCGATGAATATAGATATATCAAGGAGTCTTTCTGCCA
AAAATCATGCAAAATTGATCCGGGGCTCCGGAACTCGTTTGTAGCAAAAAACTGTGATGTTAGTA
CACGATATTTGCTAAAATTTTTGCAAAAAATGACCCGAAAATTTTCTCCTCAATTTTTTGCCACA
ATACTCAGAAAAAATATATAATACAACACCAAAAAAATTGATAGGCTTTTCACGCTTCAAATATC
GTTTTCCAATTTGTTTTCGAATTAATTTTAATTAAATCGAAACAAAATTCAGAAGCTCGTAAAAA
CAAATCCTTAAAACCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAAGAGCTTTT
CTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACGTGTTTTTAACCCAAAAACCATGAT
GGTTAATACACGATTTCAACTAAAAACTAACCCGAAAATATTATTCTCAATTTTTTACCACAATA
CTAA
Found at i:2086 original size:975 final size:950
Alignment explanation
Indices: 2--2014 Score: 2622
Period size: 975 Copynumber: 2.1 Consensus size: 950
1 G
* * ** *
2 TAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGAA
1 TAAAAACAAATCCTTATATCCAATGTGGCTGAAATTTGGTAAGATGAATATAGATATTTCAAGGA
* * * * * * * **
67 GTCTTTACGCCAGAAATCATGCAAAATTGAGCCAGGGCTCCGGAACTCCTTTTTTAGCAAAAAAG
66 GTCTTTACACCAAAAATCATGCAAAATTGATCCGGGGCACCGGAAC-ACATTTGCAGCAAAAAA-
* * * * * *
132 CTATGATAATTAGTGCATGAT-TTCAGCTAAAATTTTTGCAAAAACTGGCCCGAAAAGTTTATCC
129 CTGTGAT-GTTAGTACACGATATT-TGCTAAAATTTTTGCAAAAAATGGCCCGAAAAGTTTATCC
* * ** * * **
196 TTAGTTTTTTGCCCCTTTACTCTGAAAAAATATATAATTCAAGGCCAAAATGATTGAATATTTTT
192 TAAATTTTTTGCCCCAATACTCTGAAAAAATATATAATACAACGCCAAAAAAATTGAATATTTTT
* * *
261 TCACCCTTCTAATATCGTTTTTTCATTTTTTTTCTCGAATTTATTTTTAATTAAATCGAAACAAG
257 TCACCCTTCAAATATCGTTTTTTCA-TTTTTTTCTCGAATTTATTTCTAATTAAATCGAAACAAA
326 ATTCAGAAGCCCGTAAAAACAAATCCTTAAAACCAATGTGGCTGAGATTTGGTTAGATGAATATA
321 ATTCAGAAGCCCGTAAAAACAAATCCTTAAAACCAATGTGGCTGAGATTTGGTTAGATGAATATA
* * *
391 GATATCTTAAGGAAAAATTCTTCCAAAAGTTATACAAAACTGAGCCGGAGTCCTGAAACTTGTTT
386 GATATCTTAAAGAAAAATTCTGCCAAAAGTTATACAAAACTGAGCCGGAGTCCTGAAACGTGTTT
* * * * *
456 TTAGCCCAAAAACCGTGATGGTTAGTACACGACTTCAGCTAAAAACTGACCCGAAAATTTTCTTC
451 TTAGCCCAAAAACCGTGATGGTTAATACACGACTTCAACTAAAAACTAACCCGAAAATATTATTC
* * * * * *
521 TCAATTTTTTGCCACAATACTCAGAAAAGATATATAGTTCAACACCAAAAAGATTGATAGGCTTT
516 TCAATTTTTTACCACAATACTAAAAAAAGATATATAATTCAACACCAAAAAGATTGACAGACTTT
*
586 TCACGGTTCTAATATCGTTTTCCAATTTGTTTTCGAATTAATTTTAATTAAATCGAAATAAGATT
581 TCACGGTTCTAATATCGTTTTCCAATTTGTTTTCGAATTAATTTTAATTAAATCGAAACAAGATT
651 CAGAAGCTCGTAAAAACAAATCCTTAAAACCAATGTGGCTAAGATTTGGTTAGATGAATATAGAT
646 CAGAAGCTCGTAAAAACAAATCCTTAAAACCAATGTGGCTAAGATTTGGTTAGATGAATATAGAT
* * * *
716 ATTTCAAGGAGTCTTTTTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACGTGTTTTTA
711 ATATCAAGGAGTCTTTCTGCCAAAAGTTATGCAAAACTGAGCCGGAGTCCTGAAACGTGTTTTTA
* * *
781 ACCGAAAAACTATGATGGTTAGTACACGATTTCAGTTAAAAACTGACCCGAAAATATTTTTCTCA
776 ACCCAAAAACTATGATGGTTAGTACACAATTTCAGCTAAAAACTGACCCGAAAATATTTTTCTCA
* *
846 ATTTTTTGCCACAATACTCAGAAAACATATATAATTCAACGACTAAAAGATTGACGGGCTTTTCA
841 ATTTTTTGCCACAATACTCAGAAAACATATATAATTCAACGACCAAAAGA-T-A---G-ATTTCA
911 CGGTTCTAATTGGTTTTCCAATATTTTTTCGAATTAATTTTAATTAAATCAAAACAAGATTAAGA
900 CGG-------TGG---T-C---A--TTTTC--A--AATTTTAATTAAATCAAAACAAGATTAAGA
*
976 TGCTCG
945 TGCTCA
* ** *
982 TAAAAATAAATCCTTATATCCAATGTGGCTGAAATTTGGTTCGATGAATATAGATATTTGAAGGA
1 TAAAAACAAATCCTTATATCCAATGTGGCTGAAATTTGGTAAGATGAATATAGATATTTCAAGGA
* * * * * *
1047 TTCTTTACGCCAAAAATCATGCAAAATTGATCCGGGGCTCCGGAACTCGTTTGTAGCAAAAAACT
66 GTCTTTACACCAAAAATCATGCAAAATTGATCCGGGGCACCGGAACACATTTGCAGCAAAAAACT
*
1112 GTGATGTTAGTACACGATATTTGCTAAAATTTTTGCAAAAAATGGCCCGAAAAGTTTTTCCTCAA
131 GTGATGTTAGTACACGATATTTGCTAAAATTTTTGCAAAAAATGGCCCGAAAAGTTTATCCT-AA
* *
1177 ATTTTTTG-CTCAATACTCTTAAAAAATATATAATACAACGCCAAAAAAATTGAATATTTTTTCA
195 ATTTTTTGCCCCAATACTCTGAAAAAATATATAATACAACGCCAAAAAAATTGAATATTTTTTCA
*
1241 CGCTTCAAATATCGTTTTTTCA-TTTTTTCTCGAATTTATTTCTAATTAAATCGAAACAAAATTC
260 CCCTTCAAATATCGTTTTTTCATTTTTTTCTCGAATTTATTTCTAATTAAATCGAAACAAAATTC
* *
1305 AGAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
325 AGAAGCCCGTAAAAACAAATCCTTAAAACCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
**** * * *
1370 T-TTCAAAGAGCTTTTCTGCCAAAAGTTATGCAAAACTGAGTCGGGGTCCTGAAACGTGTTTTTA
390 TCTT-AAAGAAAAATTCTGCCAAAAGTTATACAAAACTGAGCCGGAGTCCTGAAACGTGTTTTTA
*
1434 GCCCAAAAACCGTGATGGTTAATACACGATTTCAACTAAAAACTAACCCGAAAATATTATTCTCA
454 GCCCAAAAACCGTGATGGTTAATACACGACTTCAACTAAAAACTAACCCGAAAATATTATTCTCA
** *
1499 ATTTTTTACCACAATACTAAAAAAAGATATATAATTCAACGGCTAAAAGATTGACAGACTTTTCA
519 ATTTTTTACCACAATACTAAAAAAAGATATATAATTCAACACCAAAAAGATTGACAGACTTTTCA
* *
1564 CGGTTCTAATATCGTTTTCCAATTTTTTTTCTGAATTAATTTTAATTAAATCGAAACAAGATTTA
584 CGGTTCTAATATCGTTTTCCAATTTGTTTTC-GAATTAATTTTAATTAAATCGAAACAAGATTCA
* * * *
1629 -AATGCTCGTAAAAACAAATCCTTACATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATA
648 GAA-GCTCGTAAAAACAAATCCTTAAAACCAATGTGGCTAAGATTTGGTTAGATGAATATAGATA
* * * *
1693 TATCAAGGAGTCTTTCTGCCAAAAGTTATGCATAACTGAGCCGGAGTCCTGAAACTTTTTTTTAG
712 TATCAAGGAGTCTTTCTGCCAAAAGTTATGCAAAACTGAGCCGGAGTCCTGAAACGTGTTTTTAA
* *
1758 CCCAAAAA-TCATGATGGTTAGTACACAATTTCAGCTAAAAGCTGACCTGAAAATATTTTTTCTC
777 CCCAAAAACT-ATGATGGTTAGTACACAATTTCAGCTAAAAACTGACCCGAAAATA-TTTTTCTC
* *
1822 AATTTTTTTGCCACAATACTCAGAAAAGATATATAATTCAAC-ACCAAAA-A-A-ATTTGAC-G-
840 AA-TTTTTTGCCACAATACTCAGAAAACATATATAATTCAACGACCAAAAGATAGATTTCACGGT
* *
1881 GG-C-TTTTC-AATTTTAATTAAATCGAAACAAGATTCAGATGCTCA
904 GGTCATTTTCAAATTTTAATTAAATCAAAACAAGATTAAGATGCTCA
*
1925 TAAAAACAAATCCTTATATCC-ATGTGGCT-AAGGTTTGGTAAGATGAATATAGATATTTCAAGG
1 TAAAAACAAATCCTTATATCCAATGTGGCTGAA-ATTTGGTAAGATGAATATAGATATTTCAAGG
* *
1988 AGTCTTT-CTACCAAAAGTTATGCAAAA
65 AGTCTTTAC-ACCAAAAATCATGCAAAA
2015 CTTAGCGGGG
Statistics
Matches: 927, Mismatches: 96, Indels: 58
0.86 0.09 0.05
Matches are distributed among these distances:
941 3 0.00
942 56 0.06
943 53 0.06
948 5 0.01
954 1 0.00
959 2 0.00
967 1 0.00
968 5 0.01
973 1 0.00
974 2 0.00
975 302 0.33
976 194 0.21
977 132 0.14
978 54 0.06
979 14 0.02
980 102 0.11
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (950 bp):
TAAAAACAAATCCTTATATCCAATGTGGCTGAAATTTGGTAAGATGAATATAGATATTTCAAGGA
GTCTTTACACCAAAAATCATGCAAAATTGATCCGGGGCACCGGAACACATTTGCAGCAAAAAACT
GTGATGTTAGTACACGATATTTGCTAAAATTTTTGCAAAAAATGGCCCGAAAAGTTTATCCTAAA
TTTTTTGCCCCAATACTCTGAAAAAATATATAATACAACGCCAAAAAAATTGAATATTTTTTCAC
CCTTCAAATATCGTTTTTTCATTTTTTTCTCGAATTTATTTCTAATTAAATCGAAACAAAATTCA
GAAGCCCGTAAAAACAAATCCTTAAAACCAATGTGGCTGAGATTTGGTTAGATGAATATAGATAT
CTTAAAGAAAAATTCTGCCAAAAGTTATACAAAACTGAGCCGGAGTCCTGAAACGTGTTTTTAGC
CCAAAAACCGTGATGGTTAATACACGACTTCAACTAAAAACTAACCCGAAAATATTATTCTCAAT
TTTTTACCACAATACTAAAAAAAGATATATAATTCAACACCAAAAAGATTGACAGACTTTTCACG
GTTCTAATATCGTTTTCCAATTTGTTTTCGAATTAATTTTAATTAAATCGAAACAAGATTCAGAA
GCTCGTAAAAACAAATCCTTAAAACCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATATC
AAGGAGTCTTTCTGCCAAAAGTTATGCAAAACTGAGCCGGAGTCCTGAAACGTGTTTTTAACCCA
AAAACTATGATGGTTAGTACACAATTTCAGCTAAAAACTGACCCGAAAATATTTTTCTCAATTTT
TTGCCACAATACTCAGAAAACATATATAATTCAACGACCAAAAGATAGATTTCACGGTGGTCATT
TTCAAATTTTAATTAAATCAAAACAAGATTAAGATGCTCA
Found at i:2855 original size:24 final size:21
Alignment explanation
Indices: 2815--2862 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 21
2805 GTGATTTTAT
2815 ATAGTAGTAAAATAAGATAAG
1 ATAGTAGTAAAATAAGATAAG
2836 ATAGTAAGATAAATATAAGATAAG
1 ATAGT-AG-TAAA-ATAAGATAAG
2860 ATA
1 ATA
2863 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 5 0.21
22 2 0.08
23 4 0.17
24 13 0.54
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (21 bp):
ATAGTAGTAAAATAAGATAAG
Found at i:2879 original size:2 final size:2
Alignment explanation
Indices: 2874--2941 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
2864 ATATATATAT
2874 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2916 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
2942 TAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.