Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010865.1 Corchorus capsularis cultivar CVL-1 contig10886, 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: 106981
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:347 original size:2 final size:2
Alignment explanation
Indices: 340--365 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
330 ATTTGGTTCA
340 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
366 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:1453 original size:322 final size:323
Alignment explanation
Indices: 369--1624 Score: 1686
Period size: 323 Copynumber: 3.9 Consensus size: 323
359 TGTGTGTATA
* * * * * * ***
369 TATATATATATTTCAGGGAGTTTTTGTGACAAAAATCATGCAAAATTGAATCAGTTTTCCGGAAC
1 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCAGGGCTCCGGAAC
** * * *
434 GTATTTTTAGCTAAAAACTGTAATGGTAACGTACACGATTTCGGCTAAAAACTG-CTCCGAAAA-
66 GCGTTTTTAGCTAAAAACCGTGATGGTTA-GTACACGATTTCGGCTAAAAACTGACT-CGAAAAT
** *
497 CATTTTTCTCAATTTTTTGCCACAATACTCA-AAAAAATATATT-ATTCAACGCCAAAAAGATTG
129 TTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATAT-TTAATTCAACACCAAAAAGATTG
* * **
560 AAGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCTGAATTAATTTATAATTAAATCG
193 ACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTGGTAATTAAATCG
* * **
625 AAATATGATTTAGATACTCGTAAAAACAAATCATTATATCCAATGTTGCTGACATTTGTTTCAAT
258 AAATATGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGCAGCTGACATTTGTTTCAAT
690 G
323 G
* * * *
691 TATATATATATTTCAGGGAGTCTTTGCGCCAAAAGTCATGCAAAATTGAGTTAGGGCTCCGGAAC
1 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCAGGGCTCCGGAAC
* ** * *
756 GCGTTTTTAGCCAAAAGTCGTGATTGTTAGTACACGATTTCGGCTAAAAACTGAC-CCAAAATTT
66 GCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACTCGAAAA--T
* * * *
820 TTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCGACGCTAAATAGATTGA
129 TTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAGATTGA
* * *
885 CAGGCATTTCACGCTTCTAATATCATTTTTTCATTTTTTTCCGAATTAATTGGTAATTAAATCGA
194 CGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTGGTAATTAAATCGA
* * * *
950 AATATGATTTAGATGCTCGTAAAAACAAATCCTAATAGCCAATGCAGCTGACATTTGGTTCATTG
259 AATATGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGCAGCTGACATTTGTTTCAATG
* * * * * *
1015 TATATAGATATTTCAAGGAGTTTTTGCGTCAGAAATCATGCAAAATTTAGTCGGGGCTCTGGAAC
1 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCAGGGCTCCGGAAC
* * *
1080 GTGTTTTTAG-TAAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTAACTCGAAAA-T
66 GCGTTTTTAGCT-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACTCGAAAATT
1143 TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAGATTGAC
130 TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAGATTGAC
* * * *
1208 GGGCTTTTCACTCTTGTAGTATCATTTTTTTCATTTTTTTCCGAATTAATTGGTAATTAAATCGA
195 GGGCTTTTCACGCTTCTAATATCA-TTTTTCCATTTTTTTCCGAATTAATTGGTAATTAAATCGA
*
1273 AATATGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGCGGCTGACATTTGTTTCAATG
259 AATATGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGCAGCTGACATTTGTTTCAATG
* * **
1338 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTTAGTCGGGGCTCTAGAAC
1 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCAGGGCTCCGGAAC
*
1403 GCGTTTTTAG-TAAAAACCGTGATGGTTAGTGCACGATTTCGGCTAAAAACTGACAT-GAAAATT
66 GCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGAC-TCGAAAATT
*
1466 TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAAATTTGA
130 TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAGA-TTGA
* * * * *
1531 CGGACTTTTCACGCTTCTATTATCGTTTTTCCA-TTTTTCCCGAATTAATTTGTAATTAAATCGA
194 CGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTGGTAATTAAATCGA
* * ** *
1595 AACAAGATCCAGATGCTCGTAAAGACAAAT
259 AATATGATTTAGATGCTCGTAAAAACAAAT
1625 AGTTAAATTG
Statistics
Matches: 829, Mismatches: 93, Indels: 24
0.88 0.10 0.03
Matches are distributed among these distances:
320 5 0.01
321 24 0.03
322 257 0.31
323 270 0.33
324 268 0.32
325 5 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (323 bp):
TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCAGGGCTCCGGAAC
GCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACTCGAAAATTT
TTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAGATTGACG
GGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTGGTAATTAAATCGAAA
TATGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGCAGCTGACATTTGTTTCAATG
Found at i:1692 original size:322 final size:322
Alignment explanation
Indices: 369--1704 Score: 1600
Period size: 322 Copynumber: 4.1 Consensus size: 322
359 TGTGTGTATA
* * * * * * * * *** *
369 TATATATATATTTCAGGGAGTTTTTGTGACAAAAATCATGCAAAATTGAATCAGTTTTCCGGAAC
1 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTTAGTCGGGGCTCTGGAAC
** * * * *
434 GTATTTTTAGCTAAAAACTGTAATGGTAACGTACACGATTTCGGCTAAAAACTG-CTCCGAAAAC
66 GCGTTTTTAGCTAAAAACCGTGATGGTTA-GTACACGATTTCGGCTAAAAACTGACT-CGAAAAT
* *
498 ATTTTTCTCAATTTTTTGCCACAATACTCA-AAAAAATATATT-ATTCAACGCCAAAAAGATTGA
129 TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATAT-TTAATTCAACACCAAAAAGATTGA
* * **
561 AGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCTGAATTAATTTATAATTAAATCGA
193 CGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTGGTAATTAAATCGA
* * ** *
626 AATATGATTTAGATACTCGTAAAAACAAAT-CATTATATCCAATGTTGCTGACATTTGTTTCAAT
258 AATATGATTTAGATGCTCGTAAAAACAAATAC-TTAAATCCAACATGGCTGACATTTGTTTCAAT
690 G
322 G
* * * * ** *
691 TATATATATATTTCAGGGAGTCTTTGCGCCAAAAGTCATGCAAAATTGAGTTAGGGCTCCGGAAC
1 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTTAGTCGGGGCTCTGGAAC
* ** * *
756 GCGTTTTTAGCCAAAAGTCGTGATTGTTAGTACACGATTTCGGCTAAAAACTGAC-CCAAAATTT
66 GCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACTCGAAAA---
* * * *
820 TTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCGACGCTAAATAGATTGA
128 TTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAGATTGA
* * *
885 CAGGCATTTCACGCTTCTAATATCATTTTTTCATTTTTTTCCGAATTAATTGGTAATTAAATCGA
193 CGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTGGTAATTAAATCGA
* * *
950 AATATGATTTAGATGCTCGTAAAAACAAAT-CCTAATAGCC-A-ATGCAGCTGACATTTGGTTCA
258 AATATGATTTAGATGCTCGTAAAAACAAATACTTAA-ATCCAACATG--GCTGACATTTGTTTCA
*
1012 TTG
320 ATG
* * *
1015 TATATAGATATTTCAAGGAGTTTTTGCGTCAGAAATCATGCAAAATTTAGTCGGGGCTCTGGAAC
1 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTTAGTCGGGGCTCTGGAAC
* * *
1080 GTGTTTTTAG-TAAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTAACTCGAAAATT
66 GCGTTTTTAGCT-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACTCGAAAATT
1144 TTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAGATTGACG
130 TTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAGATTGACG
* * * *
1209 GGCTTTTCACTCTTGTAGTATCATTTTTTTCATTTTTTTCCGAATTAATTGGTAATTAAATCGAA
195 GGCTTTTCACGCTTCTAATATCA-TTTTTCCATTTTTTTCCGAATTAATTGGTAATTAAATCGAA
* * ***
1274 ATATGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGCGGCTGACATTTGTTTCAATG
259 ATATGATTTAGATGCTCGTAAAAACAAATACTTAAATCCAACATGGCTGACATTTGTTTCAATG
*
1338 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTTAGTCGGGGCTCTAGAAC
1 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTTAGTCGGGGCTCTGGAAC
*
1403 GCGTTTTTAG-TAAAAACCGTGATGGTTAGTGCACGATTTCGGCTAAAAACTGACAT-GAAAATT
66 GCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGAC-TCGAAAA-T
*
1466 TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAAATTTGA
129 TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAGA-TTGA
* * * * *
1531 CGGACTTTTCACGCTTCTATTATCGTTTTTCCA-TTTTTCCCGAATTAATTTGTAATTAAATCGA
193 CGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTGGTAATTAAATCGA
* * ** * * ** * ** **
1595 AACAAGATCCAGATGCTCGTAAAGACAAATAGTTAAATTGAACATGGTTGGGATTCTG-TTCGTT
258 AATATGATTTAGATGCTCGTAAAAACAAATACTTAAATCCAACATGGCTGACATT-TGTTTCAAT
1659 G
322 G
* * * * *
1660 AATATAGATATTTGAATGAGTATTTTCGCCAAAAATCATGCAAAA
1 TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAA
1705 CTGAACCGGT
Statistics
Matches: 882, Mismatches: 113, Indels: 38
0.85 0.11 0.04
Matches are distributed among these distances:
320 5 0.01
321 24 0.03
322 317 0.36
323 265 0.30
324 265 0.30
325 6 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (322 bp):
TATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTTAGTCGGGGCTCTGGAAC
GCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACTCGAAAATTT
TTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACACCAAAAAGATTGACGG
GCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTGGTAATTAAATCGAAAT
ATGATTTAGATGCTCGTAAAAACAAATACTTAAATCCAACATGGCTGACATTTGTTTCAATG
Found at i:1995 original size:15 final size:15
Alignment explanation
Indices: 1968--2011 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
1958 AAGTTTCATG
1968 ATTATAA-ATTATAA
1 ATTATAATATTATAA
1982 ATTATAATATTAT-A
1 ATTATAATATTATAA
*
1996 ATTAAATATATTATAA
1 ATTATA-ATATTATAA
2012 TCGAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 13 0.50
15 12 0.46
16 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATAATATTATAA
Found at i:2157 original size:26 final size:27
Alignment explanation
Indices: 2123--2174 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
2113 TTTCCATAAT
*
2123 TAATAAAAAAATTGAATT-CTAAAAAA
1 TAATAAAAAAATTAAATTACTAAAAAA
*
2149 TAATAAAAAAGTTAAATTACTAAAAA
1 TAATAAAAAAATTAAATTACTAAAAA
2175 GAATATTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (27 bp):
TAATAAAAAAATTAAATTACTAAAAAA
Found at i:8637 original size:22 final size:24
Alignment explanation
Indices: 8591--8637 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
8581 ATTATTATTA
* *
8591 ATTAATATATATTATTAGTATAAT
1 ATTAATATATATTATTACTAAAAT
8615 ATTAATATAT-TTA-TACTAAAAT
1 ATTAATATATATTATTACTAAAAT
8637 A
1 A
8638 AGATTAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 10 0.48
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTAATATATATTATTACTAAAAT
Found at i:22796 original size:7 final size:7
Alignment explanation
Indices: 22784--22810 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
22774 GAATGGATAC
22784 TTCAAAG
1 TTCAAAG
22791 TTCAAAG
1 TTCAAAG
22798 TTCAAAG
1 TTCAAAG
22805 TTCAAA
1 TTCAAA
22811 CCTCAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (7 bp):
TTCAAAG
Found at i:28747 original size:6 final size:6
Alignment explanation
Indices: 28703--28743 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
28693 AGAAACCATC
* *
28703 CCAAAT CCAAAT CCAAAT CCAAAT CCAAAA CCAAAA CCAAA
1 CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAA
28744 ACCACTCTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.56, C:0.34, G:0.00, T:0.10
Consensus pattern (6 bp):
CCAAAT
Found at i:32685 original size:7 final size:7
Alignment explanation
Indices: 32673--32697 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32663 TTATGTACTA
32673 ATTTATT
1 ATTTATT
32680 ATTTATT
1 ATTTATT
32687 ATTTATT
1 ATTTATT
32694 ATTT
1 ATTT
32698 TCCTCATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTATT
Found at i:32977 original size:64 final size:64
Alignment explanation
Indices: 32877--33033 Score: 192
Period size: 64 Copynumber: 2.5 Consensus size: 64
32867 ACACCTCCAC
* * *
32877 GAATT-AAAATATTTTAAAATATTATCAATTTAGTATTATC-CCATGATATTACATTAGGCGAGT
1 GAATTAAAAATATTTTAAAATATTATTAATTCAGTATTATCTCAAT-ATATTACATTAGGCGAGT
* * ** *
32940 GAATTAAAAAAATTTTAAAATATTTTTAATTCAGTATTATCTCAATATATTAGTTTAGGTGAGT
1 GAATTAAAAATATTTTAAAATATTATTAATTCAGTATTATCTCAATATATTACATTAGGCGAGT
* * *
33004 GAACTACAAATATTTTTAAATATTATTAAT
1 GAATTAAAAATATTTTAAAATATTATTAAT
33034 AGCTTAATGG
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
63 5 0.06
64 71 0.90
65 3 0.04
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (64 bp):
GAATTAAAAATATTTTAAAATATTATTAATTCAGTATTATCTCAATATATTACATTAGGCGAGT
Found at i:36185 original size:89 final size:89
Alignment explanation
Indices: 36059--36228 Score: 295
Period size: 89 Copynumber: 1.9 Consensus size: 89
36049 CTTCCCTTCA
* * * *
36059 TCTCAATTTCTTTCATCCTTTCTCCCAAAGCATAACAACAATAAGCGTGAAAGCATCCACCGAAG
1 TCTCAATTGCTTCCATCCTTTCTCCCAAAGCATAACAACAATAAGCATAAAAGCATCCACCGAAG
36124 ATGTTTGTCTTAAACAAGTTATCC
66 ATGTTTGTCTTAAACAAGTTATCC
*
36148 TCTCAATTGCTTCCATCTTTTCTCCCAAAGCATAACAACAATAAGCATAAAAGCATCCACCGAAG
1 TCTCAATTGCTTCCATCCTTTCTCCCAAAGCATAACAACAATAAGCATAAAAGCATCCACCGAAG
36213 ATGTTTGTCTTAAACA
66 ATGTTTGTCTTAAACA
36229 TATAAATGAA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 76 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (89 bp):
TCTCAATTGCTTCCATCCTTTCTCCCAAAGCATAACAACAATAAGCATAAAAGCATCCACCGAAG
ATGTTTGTCTTAAACAAGTTATCC
Found at i:38570 original size:59 final size:60
Alignment explanation
Indices: 38501--38631 Score: 169
Period size: 61 Copynumber: 2.2 Consensus size: 60
38491 AAATTAGATA
* * * *
38501 AACATAAACAT-AAAAAA-ATAGAAACTA-TATGCTATACTATAAAGCATTAGATTTAGAAC
1 AACATAAACATAAAAAAATATAAAAAC-ACCAT-CTATACTAGAAAACATTAGATTTAGAAC
38560 AACATAAACATGAAAAAAATATAAAAACACCATCTATACTAGAAAACATTAGATTTAGAAC
1 AACATAAACAT-AAAAAAATATAAAAACACCATCTATACTAGAAAACATTAGATTTAGAAC
*
38621 AACAGAAACAT
1 AACATAAACAT
38632 GATCCGCATC
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
59 11 0.17
61 43 0.68
62 9 0.14
ACGTcount: A:0.56, C:0.14, G:0.08, T:0.22
Consensus pattern (60 bp):
AACATAAACATAAAAAAATATAAAAACACCATCTATACTAGAAAACATTAGATTTAGAAC
Found at i:40788 original size:28 final size:29
Alignment explanation
Indices: 40733--40788 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
40723 ACTATCTATT
* *
40733 TTGGGACAAATTGGCCCCTTAACTTTTTC
1 TTGGAACAAATTGACCCCTTAACTTTTTC
*
40762 TTGGAACAAATTGACCCTTTAACTTTT
1 TTGGAACAAATTGACCCCTTAACTTTT
40789 AAAAATGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (29 bp):
TTGGAACAAATTGACCCCTTAACTTTTTC
Found at i:41515 original size:28 final size:28
Alignment explanation
Indices: 41480--41559 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
41470 TCTCGTTTTT
41480 AAAAGTTAAGGGACCAATTTGTCCCAAA
1 AAAAGTTAAGGGACCAATTTGTCCCAAA
* *
41508 AAAAGTTAAGGGGCCAATTTATCCCAAA
1 AAAAGTTAAGGGACCAATTTGTCCCAAA
* *
41536 ATGGATAGTTAAGGGACTAATTTG
1 A---AAAGTTAAGGGACCAATTTG
41560 GGTATTAAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
28 27 0.63
31 16 0.37
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (28 bp):
AAAAGTTAAGGGACCAATTTGTCCCAAA
Found at i:42411 original size:72 final size:72
Alignment explanation
Indices: 42330--42466 Score: 256
Period size: 72 Copynumber: 1.9 Consensus size: 72
42320 TATTTTTGTA
* *
42330 TATCTATACTATATTAAAAAGTACGTTCAGCTGTAAAATTTTTGAATCGCCTATTATACCCTTAT
1 TATCTATACTATATTAAAAAGTACGTTCAGCTGTAAAACTTCTGAATCGCCTATTATACCCTTAT
42395 CTATATC
66 CTATATC
42402 TATCTATACTATATTAAAAAGTACGTTCAGCTGTAAAACTTCTGAATCGCCTATTATACCCTTAT
1 TATCTATACTATATTAAAAAGTACGTTCAGCTGTAAAACTTCTGAATCGCCTATTATACCCTTAT
42467 TTGTTAAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.39
Consensus pattern (72 bp):
TATCTATACTATATTAAAAAGTACGTTCAGCTGTAAAACTTCTGAATCGCCTATTATACCCTTAT
CTATATC
Found at i:42585 original size:70 final size:71
Alignment explanation
Indices: 42503--42722 Score: 291
Period size: 70 Copynumber: 3.1 Consensus size: 71
42493 CTGTTTAGGT
* * * *
42503 TTTTA-TAGTTTTATTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTAGTTTTATTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
42567 ATTTTA
66 ATTATA
*
42573 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
1 TTTTACTAGTTTTATTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
42637 ATTATA
66 ATTATA
* * ** * *
42643 TTTTACCATTTTACTATTTTATTCAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATA
1 TTTTACTAGTTT--TATTCAACT-AAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATA
42708 ACTATTATA
63 ACTATTATA
42717 TTTTAC
1 TTTTAC
42723 AATTTTACTA
Statistics
Matches: 133, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
70 68 0.51
71 5 0.04
73 5 0.04
74 55 0.41
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.50
Consensus pattern (71 bp):
TTTTACTAGTTTTATTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
ATTATA
Found at i:42696 original size:74 final size:73
Alignment explanation
Indices: 42522--42745 Score: 312
Period size: 74 Copynumber: 3.1 Consensus size: 73
42512 TTTATTCAAC
* * * * * *
42522 TAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTAC
1 TAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAATTTTAC
*
42587 TCA----AC
66 T-ATTTTAT
*
42592 TAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACCATTTTAC
1 TAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAATTTTAC
42657 TATTTTAT
66 TATTTTAT
*
42665 TCAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAATTTTA
1 T-AAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAATTTTA
42730 CTATTTTAGT
65 CTATTTTA-T
42740 TAAAAA
1 TAAAAA
42746 AAACTTGATA
Statistics
Matches: 139, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
69 1 0.01
70 60 0.43
73 2 0.01
74 74 0.53
75 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (73 bp):
TAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAATTTTAC
TATTTTAT
Found at i:43522 original size:78 final size:76
Alignment explanation
Indices: 43440--43670 Score: 314
Period size: 78 Copynumber: 3.1 Consensus size: 76
43430 TTATTTAGGT
* * *
43440 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATATAATAT-CTT-T-A-TA
1 TTTTATA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
43501 AT-TATTTT--A
65 TTATATTTTACA
*
43510 TTTTACTATTTTACTCAACTAAAAATTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTA-TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
43575 TTATATTTTACCA
65 TTATATTTTA-CA
*
43588 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTA-TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
43653 TTATATTTTACTA
65 TTATATTTTAC-A
43666 TTTTA
1 TTTTA
43671 ATTAAAAAAC
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
70 47 0.33
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 80 0.56
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (76 bp):
TTTTATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTAT
TATATTTTACA
Found at i:43526 original size:70 final size:70
Alignment explanation
Indices: 43440--43670 Score: 293
Period size: 70 Copynumber: 3.2 Consensus size: 70
43430 TTATTTAGGT
* * *
43440 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
43504 ATTTTA
65 ATTTTA
*
43510 TTTTACTATTTTACTCAACTAAAAATTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-T-A-TA
*
43575 TTATATTTTACCA
62 AT-TATTTT---A
* * *
43588 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
43653 TTATA
66 TTTTA
43658 TTTTACTATTTTA
1 TTTTACTATTTTA
43671 ATTAAAAAAC
Statistics
Matches: 141, Mismatches: 11, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
70 61 0.43
71 5 0.04
72 1 0.01
73 6 0.04
74 5 0.04
75 7 0.05
76 1 0.01
77 2 0.01
78 53 0.38
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:44215 original size:924 final size:930
Alignment explanation
Indices: 42408--44254 Score: 3225
Period size: 924 Copynumber: 2.0 Consensus size: 930
42398 TATCTATCTA
* * * *
42408 TACTATATTAAAAAGTACGTTCAGCTGTAAAACTTCTGAATCGCCTATTATACCCTTATTTGTTA
1 TACTATATTAAAAAGTACGTTAAGCTGTAAAACTTCTGAATCACCTATTATACCCTTAGTTGTCA
* * * *
42473 AATATATTTCTAAATTGCCACTGTTTAGGTTTTTATAGTTTTATTCAACTAAAAACTCTATTTTT
66 AATATATTTCTAAATTACCACTATTTAGGTTTTTATAGTTTTACTCAACTAAAAACTCTATTTTC
42538 ATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTACTCAACTAAAAACTCTA
131 ATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTACTCAACTAAAAACTCTA
*
42603 TTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACCATTTTACTATTTTATTCA
196 TTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACCATTTTACTATTTTATACA
42668 AAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAATTTTACTA
261 AAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATA--TT--AATTTTACTA
* *
42733 TTTTAGTTAAAAAAAACTTGATATATTAGTTTTATTAAATATATTTCTTGAATGACATTGTTTAA
322 TTTTAATT-AAAAAAACTTGATATATTAGTTTTATTAAATATATTTATTGAATGACATTGTTTAA
42798 ACTTTTACAATTTTTTTTAAAAATAAACTTTTGCAACTGAAAACACTATTTTTATTTAATTGAAT
386 ACTTTTACAATTTTTTTTAAAAATAAACTTTTGCAACTGAAAACACTATTTTTATTTAATTGAAT
42863 TCAATATTTTTATAATTATTTTACTTTTACCATTTTAATTTTAAAATTTTCAATTAAAATATAAA
451 TCAATATTTTTATAATTATTTTACTTTTACCATTTTAATTTTAAAATTTTCAATTAAAATATAAA
*
42928 CTAACAAAAGTATTATTATCAAGTTTAAAAATTAAAATAAATTGTCTAATCAATAATTATTCATA
516 CTAACAAAAGTATTACTATCAAGTTTAAAAATTAAAATAAATTGTCTAATCAATAATTATTCATA
42993 TTTTTTAAAACTAATTAAGTTAAAAATTTATTTAAATTATATAGTGATTGGTCTGTTTCTATTTT
581 TTTTTTAAAACTAATTAAGTTAAAAA--TATTTAAATTATATAGTGATTGGTCTGTTTCTATTTT
43058 TGGAGCATGTTGGTATAACAAGAATTTAAAGTTTTAAAAATGAGAAGAAGAGTAACATACAATTA
644 TGGAGCATGTTGGTATAACAAGAATTTAAAGTTTTAAAAATGAGAAGAAGAGTAACATACAATTA
* * *
43123 TTTCCTTTGACTTATAAATTTAGAGATGTCAATCGGGCAGGTTGGGTGGGTTTCGGGTTATCGTC
709 TTTCCTTTGACTTATAAAGTTAGAGATGTCAATCGGGCAGGTTGGGTGGATTTCGGATTATCGTC
43188 ACTTGGGTCCAGGTTTAATGAGTTAGGTAATTTTCTCGGATCATTCGGGTAATCGTTTATTTTTC
774 ACTTGGGTCCAGGTTTAATGAGTTAGGTAATTTTCTCGGATCATTCGGGTAATCGTTTATTTTTC
* *
43253 TGGTCAAATCGGGATCGATCGGATTGGACAAGTTATTGGGTTCATGTCATGTTTTGACAGCTTTA
839 TGGTCAAATCGGGATCGACCGGATTGGACAAGTTATTGGGTTCATGTCAAGTTTTGACAGCTTTA
43318 CTTATAATTAATGTGAGTGAAGACTAG
904 CTTATAATTAATGTGAGTGAAGACTAG
*
43345 TACTATATTAAAAAGTACGTTAAGCTGTAAAACTTTTGAATCACCTATTATACCCTTAGTTGTCA
1 TACTATATTAAAAAGTACGTTAAGCTGTAAAACTTCTGAATCACCTATTATACCCTTAGTTGTCA
*
43410 AATATATTTCTAAATTACCATTATTTAGGTTTTTATAGTTTTACTCAACTAAAAACTCTATTTTC
66 AATATATTTCTAAATTACCACTATTTAGGTTTTTATAGTTTTACTCAACTAAAAACTCTATTTTC
*
43475 ATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTACTCAACTAAAAATTCTA
131 ATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTACTCAACTAAAAACTCTA
43540 TTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACCATTTTACTATTTTACTCA
196 TTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACCATTTTACTATTTTA-T--
43605 ACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA-T-TA-T-ATTTTACTA
258 AC-AAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTAATTTTACTA
43666 TTTTAATT-AAAAAACTTGATATATTAGTTTT-TTAAAATATATTTATTGAATGACATTGTTTAA
322 TTTTAATTAAAAAAACTTGATATATTAGTTTTATT-AAATATATTTATTGAATGACATTGTTTAA
*
43729 ACTTTTACAAATTTTTTTTAAAAATAAACTTTTGCAACTGAAAATACTATTTTTATTTAATTGAA
386 ACTTTTAC-AATTTTTTTTAAAAATAAACTTTTGCAACTGAAAACACTATTTTTATTTAATTGAA
*
43794 TTCAATATTTTTATAATTATTTTATTTTTACCATTTTAATTTTAAAATTTTCAATTAAAATATAA
450 TTCAATATTTTTATAATTATTTTACTTTTACCATTTTAATTTTAAAATTTTCAATTAAAATATAA
* * *
43859 ACTAACAAAAGTATTACTATCAAGTTTAAAAGTTAAAATAAGTTGTCTAATCATTAATTATTCAT
515 ACTAACAAAAGTATTACTATCAAGTTTAAAAATTAAAATAAATTGTCTAATCAATAATTATTCAT
43924 A-TTTTTAAAACTAATTAAGTT-AAAA-ATTT-AA-T-TATAGTGATTGGTCTGTTTCTATTTTT
580 ATTTTTTAAAACTAATTAAGTTAAAAATATTTAAATTATATAGTGATTGGTCTGTTTCTATTTTT
43983 GGAGCATGTTGGTATAACAAGAATTTAAAGTTTTAAAAATGAGAAGAAGAGTAACATACAATTAT
645 GGAGCATGTTGGTATAACAAGAATTTAAAGTTTTAAAAATGAGAAGAAGAGTAACATACAATTAT
44048 TTCCTTTGACTTATAAAGTTAGAGATGTCAATCGGGCAGGTTGGGTGGATTTCGGATTATCGTCA
710 TTCCTTTGACTTATAAAGTTAGAGATGTCAATCGGGCAGGTTGGGTGGATTTCGGATTATCGTCA
* * *
44113 CTTGGGTCCAGGTTTACTGAGTTAGGTAATTTTCTCGGGTCATTCGGGTTATCGTTTATTTTTCT
775 CTTGGGTCCAGGTTTAATGAGTTAGGTAATTTTCTCGGATCATTCGGGTAATCGTTTATTTTTCT
44178 GGTCAAATCGGGATCGACCGGATTGGAC-AGCTTATTGGGTTCATGTCAAGTTTTGACAGCTTTA
840 GGTCAAATCGGGATCGACCGGATTGGACAAG-TTATTGGGTTCATGTCAAGTTTTGACAGCTTTA
44242 CTTATAATTAATG
904 CTTATAATTAATG
44255 GGTCACGTGC
Statistics
Matches: 875, Mismatches: 28, Indels: 27
0.94 0.03 0.03
Matches are distributed among these distances:
923 2 0.00
924 288 0.33
925 1 0.00
926 2 0.00
927 4 0.00
930 6 0.01
931 79 0.09
932 181 0.21
933 16 0.02
936 1 0.00
937 245 0.28
938 1 0.00
939 2 0.00
940 2 0.00
941 45 0.05
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (930 bp):
TACTATATTAAAAAGTACGTTAAGCTGTAAAACTTCTGAATCACCTATTATACCCTTAGTTGTCA
AATATATTTCTAAATTACCACTATTTAGGTTTTTATAGTTTTACTCAACTAAAAACTCTATTTTC
ATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTACTCAACTAAAAACTCTA
TTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACCATTTTACTATTTTATACA
AAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTAATTTTACTATTTT
AATTAAAAAAACTTGATATATTAGTTTTATTAAATATATTTATTGAATGACATTGTTTAAACTTT
TACAATTTTTTTTAAAAATAAACTTTTGCAACTGAAAACACTATTTTTATTTAATTGAATTCAAT
ATTTTTATAATTATTTTACTTTTACCATTTTAATTTTAAAATTTTCAATTAAAATATAAACTAAC
AAAAGTATTACTATCAAGTTTAAAAATTAAAATAAATTGTCTAATCAATAATTATTCATATTTTT
TAAAACTAATTAAGTTAAAAATATTTAAATTATATAGTGATTGGTCTGTTTCTATTTTTGGAGCA
TGTTGGTATAACAAGAATTTAAAGTTTTAAAAATGAGAAGAAGAGTAACATACAATTATTTCCTT
TGACTTATAAAGTTAGAGATGTCAATCGGGCAGGTTGGGTGGATTTCGGATTATCGTCACTTGGG
TCCAGGTTTAATGAGTTAGGTAATTTTCTCGGATCATTCGGGTAATCGTTTATTTTTCTGGTCAA
ATCGGGATCGACCGGATTGGACAAGTTATTGGGTTCATGTCAAGTTTTGACAGCTTTACTTATAA
TTAATGTGAGTGAAGACTAG
Found at i:48968 original size:30 final size:30
Alignment explanation
Indices: 48913--48980 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 30
48903 GTATATCTTT
48913 TCTTTTCTTTTTTCGCATCAAATATTATATA
1 TCTTTTCTTTTTTCGCATC-AATATTATATA
* *
48944 TCTTTTCTTTTTTTGACATC-ATATTGTATA
1 TCTTTTCTTTTTTCG-CATCAATATTATATA
48974 TCTTTTC
1 TCTTTTC
48981 ATGTTGTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 16 0.47
31 14 0.41
32 4 0.12
ACGTcount: A:0.21, C:0.16, G:0.04, T:0.59
Consensus pattern (30 bp):
TCTTTTCTTTTTTCGCATCAATATTATATA
Found at i:57567 original size:6 final size:6
Alignment explanation
Indices: 57534--57565 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
57524 TTGTGGGGTC
*
57534 TCTGGT TCTGGT TCTGGT TCTGGT TCAGGT TC
1 TCTGGT TCTGGT TCTGGT TCTGGT TCTGGT TC
57566 AGACATAGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.19, G:0.31, T:0.47
Consensus pattern (6 bp):
TCTGGT
Found at i:61151 original size:51 final size:51
Alignment explanation
Indices: 61091--61191 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
61081 AACCCTTAAG
* * *
61091 CAAGTTTTAACTTAGTTCAATCCTAAATTAATCGGGATCCAATGTAATTGT
1 CAAGTTTTAACATAGTTCAATCCCAAATTAATCGAGATCCAATGTAATTGT
** *
61142 CAAGTTTTAACATAGTTTGATCCCAAATTAATCGAGATCCAATGTGATTG
1 CAAGTTTTAACATAGTTCAATCCCAAATTAATCGAGATCCAATGTAATTG
61192 CAGGATACGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (51 bp):
CAAGTTTTAACATAGTTCAATCCCAAATTAATCGAGATCCAATGTAATTGT
Found at i:62067 original size:31 final size:31
Alignment explanation
Indices: 62018--62078 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
62008 ATGACAACTA
62018 TCTCTTAAATTTTCAAATTCAAGACATTTTG
1 TCTCTTAAATTTTCAAATTCAAGACATTTTG
* *
62049 TCTC-TAAACTTTTTAAATTCATGACATTTT
1 TCTCTTAAA-TTTTCAAATTCAAGACATTTT
62079 ATCCACTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.48
Consensus pattern (31 bp):
TCTCTTAAATTTTCAAATTCAAGACATTTTG
Found at i:68535 original size:32 final size:32
Alignment explanation
Indices: 68494--68558 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
68484 TTGTGAACGA
68494 GTAAAACCCAATTTCGTTCTTCAAGAGAAAGG
1 GTAAAACCCAATTTCGTTCTTCAAGAGAAAGG
68526 GTAAAACCCAATTTCGTTCTTCAAGAGAAAGG
1 GTAAAACCCAATTTCGTTCTTCAAGAGAAAGG
68558 G
1 G
68559 ACCAAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (32 bp):
GTAAAACCCAATTTCGTTCTTCAAGAGAAAGG
Found at i:69426 original size:6 final size:6
Alignment explanation
Indices: 69415--69441 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
69405 ATCTGCATAA
69415 GGGAGT GGGAGT GGGAGT GGGAGT GGG
1 GGGAGT GGGAGT GGGAGT GGGAGT GGG
69442 GGAGGAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.70, T:0.15
Consensus pattern (6 bp):
GGGAGT
Found at i:78495 original size:2 final size:2
Alignment explanation
Indices: 78488--78523 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
78478 TACATAAGAA
78488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78524 TCAATTAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81885 original size:30 final size:28
Alignment explanation
Indices: 81849--81926 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
81839 CATCAGAAAA
81849 GGGCTTATTTGGCCTTTTTAAAGAGTTCAG
1 GGGCTTATTTGGCCTTTTT-AA-AGTTCAG
**
81879 GGGCTTATTTGG-CTGCAATTAAAGTTCAG
1 GGGCTTATTTGGCCT--TTTTAAAGTTCAG
*
81908 GGGCTTATTTGGCCGTTTT
1 GGGCTTATTTGGCCTTTTT
81927 GTGTAAGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
28 2 0.05
29 21 0.52
30 15 0.38
31 2 0.05
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.40
Consensus pattern (28 bp):
GGGCTTATTTGGCCTTTTTAAAGTTCAG
Found at i:104023 original size:109 final size:109
Alignment explanation
Indices: 103827--104101 Score: 428
Period size: 109 Copynumber: 2.5 Consensus size: 109
103817 ACTATTATAG
* *
103827 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
103892 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
*
103941 TTTTATTCTATTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* **
104006 TTACCAAAAAATTTGGATATATTAATTTTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
104050 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
104102 TAAATTTTTT
Statistics
Matches: 153, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
108 7 0.05
109 121 0.79
110 3 0.02
111 2 0.01
114 20 0.13
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:106958 original size:2 final size:2
Alignment explanation
Indices: 106951--106981 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
106941 CAATAAATAA
106951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.