Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023278.1 Corchorus olitorius cultivar O-4 contig23311, 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: 87422
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:359 original size:15 final size:15
Alignment explanation
Indices: 333--370 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
323 TTTGCTTTGT
333 TTTCTAGTTTAATTGC
1 TTTCT-GTTTAATTGC
349 TTTCTGTTTAATTGC
1 TTTCTGTTTAATTGC
364 TTTCTGT
1 TTTCTGT
371 CAATCTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTGTTTAATTGC
Found at i:810 original size:24 final size:24
Alignment explanation
Indices: 768--834 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
758 TTGTTTTGTA
*
768 TTTTGCGTC-GAAAAAAAAAATAT
1 TTTTGCGTCATAAAAAAAAAATAT
* *
791 TTTTGCGTCATAAAAAAAAATTGT
1 TTTTGCGTCATAAAAAAAAAATAT
*
815 TTCTGCGTCATAAAAAAAAA
1 TTTTGCGTCATAAAAAAAAA
835 TTTCTTGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 9 0.23
24 30 0.77
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.31
Consensus pattern (24 bp):
TTTTGCGTCATAAAAAAAAAATAT
Found at i:835 original size:24 final size:22
Alignment explanation
Indices: 768--837 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 22
758 TTGTTTTGTA
768 TTTTGCGTCGA-AAAAAAAAATAT
1 TTTTGCGTC-ATAAAAAAAAAT-T
791 TTTTGCGTCATAAAAAAAAATT
1 TTTTGCGTCATAAAAAAAAATT
813 GTTTCTGCGTCATAAAAAAAAATT
1 -TTT-TGCGTCATAAAAAAAAATT
837 T
1 T
838 CTTGTTCCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.05
23 23 0.52
24 19 0.43
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (22 bp):
TTTTGCGTCATAAAAAAAAATT
Found at i:4003 original size:24 final size:21
Alignment explanation
Indices: 3948--4002 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
3938 CGGCCATTCA
* *
3948 CCGTGACACCACCGGTTAAGC
1 CCGTGCCACCACCGGCTAAGC
*
3969 CCGTGCCACCACCGGCTATGC
1 CCGTGCCACCACCGGCTAAGC
*
3990 CCGTGCCATCACC
1 CCGTGCCACCACC
4003 ATTCAGTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.45, G:0.22, T:0.15
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTAAGC
Found at i:7278 original size:15 final size:15
Alignment explanation
Indices: 7252--7289 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
7242 TTTGCTTTGT
7252 TTTCTAGTTTAATTGC
1 TTTCT-GTTTAATTGC
*
7268 TTTCTGTTTAATTGT
1 TTTCTGTTTAATTGC
7283 TTTCTGT
1 TTTCTGT
7290 CAATCTCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.63
Consensus pattern (15 bp):
TTTCTGTTTAATTGC
Found at i:19264 original size:254 final size:255
Alignment explanation
Indices: 18812--19321 Score: 986
Period size: 254 Copynumber: 2.0 Consensus size: 255
18802 GACATTCAAA
18812 CACACTTTTTGTGTTTTTCCCTTGTTTCAATCTTGTCTCCGGACACAAAAACACTGTACACGTGT
1 CACACTTTTTGTGTTTTTCCCTTGTTTCAATCTTGTCTCCGGACACAAAAACACTGTACACGTGT
18877 TTCTCTCCTATAAATAACAAATCAAATTGTTATTTTTCTTTTCAAATTCAATTGCAATCAAAGCA
66 TTCTCTCCTATAAATAACAAATCAAATTGTTATTTTTCTTTTCAAATTCAATTGCAATCAAAGCA
*
18942 GATCTCCCAGATCTGATCCAGATAGAGGAATACCCATAGAAGGAAATTAGTTTGTACGAATCCAA
131 GATCTCCCAGATCTGATCCAGATAGAGGAAGACCCATAGAAGGAAATTAGTTTGTACGAATCCAA
19007 TGATTTAAATGCTCCGGTGTGACTTTGATACAGTCCCCACAATCGCTCTGATCTTTTAAT
196 TGATTTAAATGCTCCGGTGTGACTTTGATACAGTCCCCACAATCGCTCTGATCTTTTAAT
*
19067 CACACTTTTTGTGTTTTTCCCTTGTTTCAATCTTGTCTCCGGAGACAAAAACACTGTACACGTGT
1 CACACTTTTTGTGTTTTTCCCTTGTTTCAATCTTGTCTCCGGACACAAAAACACTGTACACGTGT
19132 TTCTCTCCTATAAATAACAAATCAAATTGTTA-TTTTCTTTTCAAATTCAATTGCAATCAAAGCA
66 TTCTCTCCTATAAATAACAAATCAAATTGTTATTTTTCTTTTCAAATTCAATTGCAATCAAAGCA
19196 GATCTCCCAGATCTGATCCAGATAGAGGAAGACCCATAGAAGGAAATTAGTTTGTACGAATCCAA
131 GATCTCCCAGATCTGATCCAGATAGAGGAAGACCCATAGAAGGAAATTAGTTTGTACGAATCCAA
*
19261 TGATTTAAATGCTCCGGTGTGACTTTGATCCAGTCCCCACAATCGCTCTGATCTTTTAAT
196 TGATTTAAATGCTCCGGTGTGACTTTGATACAGTCCCCACAATCGCTCTGATCTTTTAAT
19321 C
1 C
19322 TGCTGCTCCA
Statistics
Matches: 252, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
254 156 0.62
255 96 0.38
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (255 bp):
CACACTTTTTGTGTTTTTCCCTTGTTTCAATCTTGTCTCCGGACACAAAAACACTGTACACGTGT
TTCTCTCCTATAAATAACAAATCAAATTGTTATTTTTCTTTTCAAATTCAATTGCAATCAAAGCA
GATCTCCCAGATCTGATCCAGATAGAGGAAGACCCATAGAAGGAAATTAGTTTGTACGAATCCAA
TGATTTAAATGCTCCGGTGTGACTTTGATACAGTCCCCACAATCGCTCTGATCTTTTAAT
Found at i:22994 original size:32 final size:32
Alignment explanation
Indices: 22957--23035 Score: 131
Period size: 32 Copynumber: 2.5 Consensus size: 32
22947 TTTTTTTACG
*
22957 GAAACGCCACTATTTAATGGCGTTTCCATACA
1 GAAACGCCGCTATTTAATGGCGTTTCCATACA
* *
22989 GAAACGCCGCTATTTAGTGGCGTTTCCATATA
1 GAAACGCCGCTATTTAATGGCGTTTCCATACA
23021 GAAACGCCGCTATTT
1 GAAACGCCGCTATTT
23036 TGGCTTCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (32 bp):
GAAACGCCGCTATTTAATGGCGTTTCCATACA
Found at i:23352 original size:45 final size:45
Alignment explanation
Indices: 23288--23376 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
23278 TCAGGGTAGA
23288 CAACTTATTGCCAATGGCTCGACCGAAGCCACAAGGAACTGCTGC
1 CAACTTATTGCCAATGGCTCGACCGAAGCCACAAGGAACTGCTGC
23333 CAACTTATTGCCAATGGCTCGACCGAAGCCACAAGGAACTGCTG
1 CAACTTATTGCCAATGGCTCGACCGAAGCCACAAGGAACTGCTG
23377 TCGCATCAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.18
Consensus pattern (45 bp):
CAACTTATTGCCAATGGCTCGACCGAAGCCACAAGGAACTGCTGC
Found at i:23590 original size:14 final size:14
Alignment explanation
Indices: 23571--23598 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23561 ACCGAATTCC
23571 ACCCAATAAAATAA
1 ACCCAATAAAATAA
23585 ACCCAATAAAATAA
1 ACCCAATAAAATAA
23599 GTCTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (14 bp):
ACCCAATAAAATAA
Found at i:27052 original size:133 final size:134
Alignment explanation
Indices: 26889--27185 Score: 449
Period size: 134 Copynumber: 2.2 Consensus size: 134
26879 AAACGCCACT
* * * *
26889 TAGTGGCGTTTCTAACA-AAAAACGCCGCTAAAT-GTCTTACTTTAT-TTCTAACTTTTCCTTTA
1 TAGTGGCGTTTCAAATACCAAAACGCCGCTAAATGGT-TTAATTTATCTTCTAACTTTTCCTTTA
*
26951 ATTATTTTTGGGGGAATTTTTCTCAACAATTTTTCTAAATAGCGGCGA-CTTTATATGAAACGCC
65 ATTATTTTTGGGGGAATTTTTCCCAACAATTTTTCTAAATAGCGGC-ATCTTTATATGAAACGCC
27015 ACTAAA
129 ACTAAA
* *
27021 TTGTGGCGTTTCAAATACCAAAACGCCGCTAAATGGTTTAATTTATCTTTTAACTTTTCCTTTAA
1 TAGTGGCGTTTCAAATACCAAAACGCCGCTAAATGGTTTAATTTATCTTCTAACTTTTCCTTTAA
* *
27086 TTATTTTTGGGGGAATTTTTCCCGACAATTTTTCTAAATAGCGGCATGTTTATATGAAACGCCAC
66 TTATTTTTGGGGGAATTTTTCCCAACAATTTTTCTAAATAGCGGCATCTTTATATGAAACGCCAC
27151 TAAA
131 TAAA
* *
27155 TAGTGGCGTTTCAGATACCAAGACGCCGCTA
1 TAGTGGCGTTTCAAATACCAAAACGCCGCTA
27186 TTTAGAACAA
Statistics
Matches: 149, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
132 14 0.09
133 24 0.16
134 111 0.74
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (134 bp):
TAGTGGCGTTTCAAATACCAAAACGCCGCTAAATGGTTTAATTTATCTTCTAACTTTTCCTTTAA
TTATTTTTGGGGGAATTTTTCCCAACAATTTTTCTAAATAGCGGCATCTTTATATGAAACGCCAC
TAAA
Found at i:36707 original size:30 final size:31
Alignment explanation
Indices: 36667--36725 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
36657 AACTCTTCTC
*
36667 TTATAAATGTTCTTGT-AAATGTGAAATCGA
1 TTATAAATGTTCTAGTAAAATGTGAAATCGA
*
36697 TTATACATGTTCTAGTAAAATGTGAAATC
1 TTATAAATGTTCTAGTAAAATGTGAAATC
36726 TATATATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (31 bp):
TTATAAATGTTCTAGTAAAATGTGAAATCGA
Found at i:44242 original size:21 final size:20
Alignment explanation
Indices: 44218--44262 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
44208 ATAGTTTAGA
* *
44218 TTTACTTTACTTTGCTTTGTT
1 TTTACTTTA-ATTGCTTTCTT
*
44239 TTTAGTTTAATTGCTTTCTT
1 TTTACTTTAATTGCTTTCTT
44259 TTTA
1 TTTA
44263 GTTAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTACTTTAATTGCTTTCTT
Found at i:53933 original size:15 final size:14
Alignment explanation
Indices: 53913--53948 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
53903 AATTCCCATC
53913 GAAAAAGAGAAAAA
1 GAAAAAGAGAAAAA
*
53927 TGAAAAAGAGAAGAA
1 -GAAAAAGAGAAAAA
53942 GAAAAAG
1 GAAAAAG
53949 GCACTTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (14 bp):
GAAAAAGAGAAAAA
Found at i:54425 original size:6 final size:7
Alignment explanation
Indices: 54395--54445 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
54385 AAAACAAAAC
*
54395 AAAAGTG
1 AAAATTG
54402 AAAATTG
1 AAAATTG
54409 AAAATTG
1 AAAATTG
54416 AAAA-TG
1 AAAATTG
54422 AAAA-TG
1 AAAATTG
54428 AAAATTG
1 AAAATTG
*
54435 AAAACTG
1 AAAATTG
54442 AAAA
1 AAAA
54446 AAGCATAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 12 0.29
7 29 0.71
ACGTcount: A:0.63, C:0.02, G:0.16, T:0.20
Consensus pattern (7 bp):
AAAATTG
Found at i:54752 original size:9 final size:9
Alignment explanation
Indices: 54738--54767 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
54728 TCTCAAGTGC
54738 AAACAAAAA
1 AAACAAAAA
54747 AAACAAAAA
1 AAACAAAAA
*
54756 AACCAAAAA
1 AAACAAAAA
54765 AAA
1 AAA
54768 AGAGGAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (9 bp):
AAACAAAAA
Found at i:55946 original size:123 final size:123
Alignment explanation
Indices: 55727--55981 Score: 474
Period size: 123 Copynumber: 2.1 Consensus size: 123
55717 AATTTCAGAA
*
55727 ACCTCCGGGTATTAATTTTGATAAATCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAA
1 ACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAA
55792 AGCTGCATTTAAGTTTCAAAATAAAAACCTTGCTCAAGGTCAAGTTTGCATTTGTAAG
66 AGCTGCATTTAAGTTTCAAAATAAAAACCTTGCTCAAGGTCAAGTTTGCATTTGTAAG
55850 ACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAA
1 ACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAA
* * *
55915 AGCTGGATTTAAGTTTCAAAATCAAAACCTTGCTCAAGTTCAAGTTTGCATTTGTAAG
66 AGCTGCATTTAAGTTTCAAAATAAAAACCTTGCTCAAGGTCAAGTTTGCATTTGTAAG
55973 ACCTCCGGG
1 ACCTCCGGG
55982 CACGATTCCA
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 128 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (123 bp):
ACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAA
AGCTGCATTTAAGTTTCAAAATAAAAACCTTGCTCAAGGTCAAGTTTGCATTTGTAAG
Found at i:55999 original size:145 final size:146
Alignment explanation
Indices: 55850--56174 Score: 571
Period size: 145 Copynumber: 2.2 Consensus size: 146
55840 CATTTGTAAG
55850 ACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAA
1 ACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAA
* *
55915 AGCTGGATTTAAGTTTCAAAATCAAAACCTTGCTCAAGTTCAAG-TTTGCATTTGTAAGACCTCC
66 AGCTGCATTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCAAGTTTTGCATTTGTAAGACCTCC
*
55979 GGGCACGATTCCAGAA
131 GGGCACAATTCCAGAA
55995 ACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAA
1 ACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAA
*
56060 AGCTGCATTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCC
66 AGCTGCATTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCAAGTTTTGCATTTGTAAGACCTCC
*
56125 GGGCACAATTTCAGAA
131 GGGCACAATTCCAGAA
* * *
56141 ACGTCCGGGTATTAATTCTGACAAGTCCTCCGGG
1 ACCTCCGGGTATTAATTCTGATAAATCCTCCGGG
56175 CATTCTATAT
Statistics
Matches: 171, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
145 106 0.62
146 65 0.38
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (146 bp):
ACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAA
AGCTGCATTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCAAGTTTTGCATTTGTAAGACCTCC
GGGCACAATTCCAGAA
Found at i:56308 original size:40 final size:40
Alignment explanation
Indices: 56224--57327 Score: 1396
Period size: 40 Copynumber: 27.7 Consensus size: 40
56214 TATGGGTTTT
* * * * *
56224 AATCCTGCTCAAGATCATTTCTTTA-CCAGTTAA--TCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
56261 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
56301 AATCCTGCTCAGGATCATTGCTGTATCAAATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
56341 AATCCTGCTCAGGATCATCT-TTTTATCAAATCAATTTCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
56381 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
56421 AATCCTGCTCAAGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
56461 AATCCTGCTCAAGATCATTGCTTTATCAAATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * *
56501 AATCCTGCTGAGGATCGTTGCTGTATCAAATTAATTT-AA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
56540 GAATCCTGCTCAGGATCATCT-TTTTATCAAATTAATTTCAA
1 -AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
* * *
56581 AATCCTACTCAGGATCATTGCTTTATCAAATTGATTTCCA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * **
56621 AATCCTGCTCAGGACCATCT-CTATATCAAATTAATTT-TG
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
* *
56660 AACCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * *
56700 AATCCTACTCAGGATCATCT-TTTTATCAAATTAATTGCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
* *
56740 AATCCTGCTAAGGATCATTGCTTTATCAAATTGATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
56780 AATCCTGCTCAGGATCATCT-CTATATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
*
56820 AATCCTTCTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
56860 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * *
56900 AATCCTGCTGAGGATCATTGCTGTATCAAATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
56940 AATCCTGCTCAGGATCATCT-TTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
* * *
56980 AATCCTGCTTAAGATCATTGCTTTATCAAATTGATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * *
57020 AATCCTGCTCATGATCATCT-CTATATCAAATTAATTTC-G
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
* *
57059 AACCCTGCTCAGGATCATTACTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
57099 AATCCTGCTCAGGATCATAT-TTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
* * * * *
57139 AACCCTGGTCAAGATCATTGCTTTATCAAACTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
57179 AATCCTGCTCAGGATCATTGCTTTATCAAATTAA--TCAC
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
57217 AATCCTGTTCAGGATCATTGCTTTATCAATTTAATTAATTTCCA
1 AATCCTGCTCAGGATCATTGCTTTATC-A---AATTAATTTCAA
** * * * *
57261 AATCCTATTCAGGATCATTGCCTCATCAAGTCAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
** *
57301 AATCCTATTCAGGATCATGGC-TTATCA
1 AATCCTGCTCAGGATCATTGCTTTATCA
57328 GTTGATTTCA
Statistics
Matches: 942, Mismatches: 96, Indels: 56
0.86 0.09 0.05
Matches are distributed among these distances:
37 23 0.02
38 37 0.04
39 77 0.08
40 762 0.81
41 10 0.01
42 6 0.01
43 1 0.00
44 26 0.03
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (40 bp):
AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
Found at i:57006 original size:399 final size:398
Alignment explanation
Indices: 56268--57306 Score: 1595
Period size: 399 Copynumber: 2.6 Consensus size: 398
56258 CAGAATCCTG
* * *
56268 CTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTGTATCAAATT
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTGCTCAGGATCATT-TTTTATCAAATT
* * * *
56333 AATTTCAGAATCCTGCTCAGGATCATCT-TTTTATCAAATCAATTTCAAAATCCTGCTCAGGATC
65 AATTTCAAAATCCTGCTAAGGATCAT-TGCTTTATCAAATTAATTTCAAAATCCTGCTCAGGATC
* *
56397 ATTGCTTTATCAAATTAATTTCAAAATCCTGCTCAAGATCATTGCTTTATCAAATTAATTTCAAA
129 ATTGCTTTATCAAATTAATTTCAAAATCCTTCTCAGGATCATTGCTTTATCAAATTAATTTCAAA
* *
56462 ATCCTGCTCAAGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTGAGGATCGTTGCTGTAT
194 ATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTGAGGATCATTGCTGTAT
56527 CAAATTAATTTAAGAATCCTGCTCAGGATCATCTTTTTATCAAATTAATTTCAAAATCCTACTCA
259 CAAATTAATTTAAGAATCCTGCTCAGGATCATCTTTTTATCAAATTAATTTCAAAATCCTACTCA
* *
56592 GGATCATTGCTTTATCAAATTGATTTCCAAATCCTGCTCAGGACCATCTCTATATCAAATTAATT
324 AGATCATTGCTTTATCAAATTGATTTCAAAATCCTGCTCAGGACCATCTCTATATCAAATTAATT
*
56657 TTGAACCCTA
389 TCGAACCCTA
*
56667 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTACTCAGGATCATCTTTTTATCAAATT
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTGCTCAGGATCAT-TTTTTATCAAATT
* *
56732 AATTGCAAAATCCTGCTAAGGATCATTGCTTTATCAAATTGATTTCAAAATCCTGCTCAGGATCA
65 AATTTCAAAATCCTGCTAAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTGCTCAGGATCA
*
56797 TCT-CTATATCAAATTAATTTCAAAATCCTTCTCAGGATCATTGCTTTATCAAATTAATTTCAAA
130 T-TGCTTTATCAAATTAATTTCAAAATCCTTCTCAGGATCATTGCTTTATCAAATTAATTTCAAA
56861 ATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTGAGGATCATTGCTGTAT
194 ATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTGAGGATCATTGCTGTAT
* * *
56926 CAAATTAATTTCAGAATCCTGCTCAGGATCATCTTTTTATCAAATTAATTTCAAAATCCTGCTTA
259 CAAATTAATTTAAGAATCCTGCTCAGGATCATCTTTTTATCAAATTAATTTCAAAATCCTACTCA
* *
56991 AGATCATTGCTTTATCAAATTGATTTCAAAATCCTGCTCATGATCATCTCTATATCAAATTAATT
324 AGATCATTGCTTTATCAAATTGATTTCAAAATCCTGCTCAGGACCATCTCTATATCAAATTAATT
*
57056 TCGAACCCTG
389 TCGAACCCTA
*
57066 CTCAGGATCATTACTTTATCAAATTAATTTCAAAATCCTGCTCAGGATCATATTTTTATCAAATT
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTGCTCAGGATCAT-TTTTTATCAAATT
* * * *
57131 AATTTCAAAACCCTGGTCAA-GATCATTGCTTTATCAAACTAATTTCAGAATCCTGCTCAGGATC
65 AATTTCAAAATCCTGCT-AAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTGCTCAGGATC
*
57195 ATTGCTTTATCAAATTAA--TCACAATCCTGT-TCAGGATCATTGCTTTATCAATTTAATTAATT
129 ATTGCTTTATCAAATTAATTTCAAAATCCT-TCTCAGGATCATTGCTTTATC-A---AATTAATT
* ** * * * * *
57257 TCCAAATCCTATTCAGGATCATTGCCTCATCAAGTCAATTTCAAAATCCT
189 TCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCT
57307 ATTCAGGATC
Statistics
Matches: 587, Mismatches: 43, Indels: 18
0.91 0.07 0.03
Matches are distributed among these distances:
397 28 0.05
398 4 0.01
399 501 0.85
400 4 0.01
401 50 0.09
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (398 bp):
CTCAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTGCTCAGGATCATTTTTTATCAAATTA
ATTTCAAAATCCTGCTAAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTGCTCAGGATCAT
TGCTTTATCAAATTAATTTCAAAATCCTTCTCAGGATCATTGCTTTATCAAATTAATTTCAAAAT
CCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTGAGGATCATTGCTGTATCA
AATTAATTTAAGAATCCTGCTCAGGATCATCTTTTTATCAAATTAATTTCAAAATCCTACTCAAG
ATCATTGCTTTATCAAATTGATTTCAAAATCCTGCTCAGGACCATCTCTATATCAAATTAATTTC
GAACCCTA
Found at i:57762 original size:13 final size:13
Alignment explanation
Indices: 57740--57801 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
57730 TTTTGCATTG
*
57740 CATTAACATATCA
1 CATTAGCATATCA
*
57753 TATTAGCATATCA
1 CATTAGCATATCA
* **
57766 CGTTAAAATATCA
1 CATTAGCATATCA
*
57779 GATTAGCATATCA
1 CATTAGCATATCA
*
57792 CATTTGCATA
1 CATTAGCATA
57802 GTATGTTTGC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (13 bp):
CATTAGCATATCA
Found at i:57771 original size:26 final size:26
Alignment explanation
Indices: 57742--57792 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
57732 TTGCATTGCA
* *
57742 TTAACATATCATATTAGCATATCACG
1 TTAAAATATCAGATTAGCATATCACG
57768 TTAAAATATCAGATTAGCATATCAC
1 TTAAAATATCAGATTAGCATATCAC
57793 ATTTGCATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (26 bp):
TTAAAATATCAGATTAGCATATCACG
Found at i:62226 original size:59 final size:60
Alignment explanation
Indices: 62149--62275 Score: 168
Period size: 59 Copynumber: 2.1 Consensus size: 60
62139 GTCAATTGGA
*
62149 AATTTATTATAACAACTTCTAGTGTAAATTGAAAAA-TAAAATTATGAAC-TTCAAGTGTC
1 AATTGATTATAACAACTTCTAGTGTAAATTGAAAAAGTAAAATTAT-AACATTCAAGTGTC
* * * *
62208 AATTGATTATGACAACTTCTGGTGTCAATTGAAAAAGTAAAATTATAACAGTTTCAGGTGTC
1 AATTGATTATAACAACTTCTAGTGTAAATTGAAAAAGTAAAATTATAACA--TTCAAGTGTC
62270 AATTGA
1 AATTGA
62276 AAATTAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
59 35 0.59
60 9 0.15
62 15 0.25
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (60 bp):
AATTGATTATAACAACTTCTAGTGTAAATTGAAAAAGTAAAATTATAACATTCAAGTGTC
Found at i:62295 original size:69 final size:68
Alignment explanation
Indices: 62208--62367 Score: 212
Period size: 68 Copynumber: 2.3 Consensus size: 68
62198 TTCAAGTGTC
* ** *
62208 AATTGATTATGACAACTTCTGGTGTCAATTGAAAAAGTAAAATTATAACAGTTTCAGGTGTCAAT
1 AATTAATTATGACAACTTCTGGTGTCAATTG-AAAAGTAAAATTATAACAACTTCAGGCGTCAAT
62273 TGAA
65 TGAA
* ** *
62277 AATTAATTATGACAACTTCTAGTGTCTGTTGAAAAGTAAAATTATGACAACTTCAGGCGTCAATT
1 AATTAATTATGACAACTTCTGGTGTCAATTGAAAAGTAAAATTATAACAACTTCAGGCGTCAATT
*
62342 GGA
66 GAA
* *
62345 AATTAATTACGACAGCTTCTGGT
1 AATTAATTATGACAACTTCTGGT
62368 AAAAGTAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
68 52 0.66
69 27 0.34
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (68 bp):
AATTAATTATGACAACTTCTGGTGTCAATTGAAAAGTAAAATTATAACAACTTCAGGCGTCAATT
GAA
Found at i:62302 original size:33 final size:34
Alignment explanation
Indices: 62208--62364 Score: 133
Period size: 33 Copynumber: 4.6 Consensus size: 34
62198 TTCAAGTGTC
*
62208 AATTGATTATGACAACTTCT-GGTGTCAATTGAAA
1 AATTAATTATGACAACTTCTAGGTGTCAATTG-AA
* * **
62242 AAGTAAAATTATAACAGTTTC-AGGTGTCAATTGAA
1 AA-T-TAATTATGACAACTTCTAGGTGTCAATTGAA
**
62277 AATTAATTATGACAACTTCTA-GTGTCTGTTGAA
1 AATTAATTATGACAACTTCTAGGTGTCAATTGAA
* * *
62310 AAGTAAAATTATGACAACTTC-AGGCGTCAATTGGA
1 AA-T-TAATTATGACAACTTCTAGGTGTCAATTGAA
* *
62345 AATTAATTACGACAGCTTCT
1 AATTAATTATGACAACTTCT
62365 GGTAAAAGTA
Statistics
Matches: 96, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
33 37 0.39
34 7 0.07
35 30 0.31
36 22 0.23
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (34 bp):
AATTAATTATGACAACTTCTAGGTGTCAATTGAA
Found at i:62727 original size:33 final size:33
Alignment explanation
Indices: 62690--62908 Score: 136
Period size: 33 Copynumber: 6.4 Consensus size: 33
62680 ACAGCTACAT
62690 GTGTCAATTAGAAAT-TAATTATGACAACTTCTG
1 GTGTCAATT-GAAATATAATTATGACAACTTCTG
* * ** **
62723 GTGTCAGTTGAAAATGTAAAATTACAACAACTTCAA
1 GTGTCAATTG-AAA--TATAATTATGACAACTTCTG
* * *
62759 ATGTCAATTAGAAAT-TAATAATGACAGCTTCTG
1 GTGTCAATT-GAAATATAATTATGACAACTTCTG
* * * ** * *
62792 ATATCAATTGAAAAGTAAAAAGAAGACAACTTCAG
1 GTGTCAATTG-AAA-TATAATTATGACAACTTCTG
* *
62827 GTGTCAATTGAAAAAATAAAATTACGACAACTTCTG
1 GTGTCAATTG---AAATATAATTATGACAACTTCTG
* * * *
62863 GTGTCAGTTGAAATTTAATTATGACAACGTATG
1 GTGTCAATTGAAATATAATTATGACAACTTCTG
62896 GTGTCAATTGAAA
1 GTGTCAATTGAAA
62909 AAAAAAATTA
Statistics
Matches: 141, Mismatches: 35, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
32 2 0.01
33 63 0.45
34 2 0.01
35 21 0.15
36 48 0.34
37 5 0.04
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (33 bp):
GTGTCAATTGAAATATAATTATGACAACTTCTG
Found at i:62753 original size:36 final size:35
Alignment explanation
Indices: 62713--62909 Score: 113
Period size: 36 Copynumber: 5.7 Consensus size: 35
62703 ATTAATTATG
*
62713 ACAACTTCTGGTGTCAGTTGAAAATGTAAAATTACA
1 ACAACTTCTGGTGTCAATTGAAAATGTAAAATTA-A
*** *
62749 ACAACTTCAAATGTCAATT-AGAAAT-TAATAA-T-G
1 ACAACTTCTGGTGTCAATTGA-AAATGTAA-AATTAA
* * * **
62782 ACAGCTTCTGATATCAATTGAAAA-GTAAAAAGAA
1 ACAACTTCTGGTGTCAATTGAAAATGTAAAATTAA
* ** *
62816 GACAACTTCAGGTGTCAATTGAAAAAATAAAATTACG
1 -ACAACTTCTGGTGTCAATTGAAAATGTAAAATTA-A
* * *
62853 ACAACTTCTGGTGTCAGTTG-AAAT-T-TAATTATG
1 ACAACTTCTGGTGTCAATTGAAAATGTAAAATTA-A
* *
62886 ACAACGTATGGTGTCAATTGAAAA
1 ACAACTTCTGGTGTCAATTGAAAA
62910 AAAAAATTAT
Statistics
Matches: 124, Mismatches: 27, Indels: 22
0.72 0.16 0.13
Matches are distributed among these distances:
32 2 0.02
33 44 0.35
34 5 0.04
35 28 0.23
36 45 0.36
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (35 bp):
ACAACTTCTGGTGTCAATTGAAAATGTAAAATTAA
Found at i:62930 original size:104 final size:105
Alignment explanation
Indices: 62706--62939 Score: 258
Period size: 104 Copynumber: 2.2 Consensus size: 105
62696 ATTAGAAATT
* * **
62706 AATTATGACAACTTCTGGTGTCAGTTGAAAATGTAAAATTACAACAACTTCAAATGTCAATTAGA
1 AATTATGACAACTTCAGGTGTCAATTGAAAAAATAAAATTACAACAACTTCAAATGTCAATTAGA
* * * *
62771 AATTAATAATGACAGCTTCTGATATCAATTGAAAAGTAAA
66 AATTAATAATGACAACGTATGATATCAATTGAAAAGAAAA
* * * *** *
62811 AA-GAAGACAACTTCAGGTGTCAATTGAAAAAATAAAATTACGACAACTTCTGGTGTCAGTT-GA
1 AATTATGACAACTTCAGGTGTCAATTGAAAAAATAAAATTACAACAACTTCAAATGTCAATTAGA
* * *
62874 AATTTAATTATGACAACGTATGGTGTCAATTGAAAA-AAAA
66 AA-TTAATAATGACAACGTATGATATCAATTGAAAAGAAAA
**
62914 AATTATGACATTTTCAGGTGTCAATT
1 AATTATGACAACTTCAGGTGTCAATT
62940 ATATATATAA
Statistics
Matches: 105, Mismatches: 22, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
103 9 0.09
104 94 0.90
105 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (105 bp):
AATTATGACAACTTCAGGTGTCAATTGAAAAAATAAAATTACAACAACTTCAAATGTCAATTAGA
AATTAATAATGACAACGTATGATATCAATTGAAAAGAAAA
Found at i:62934 original size:35 final size:35
Alignment explanation
Indices: 62706--62939 Score: 138
Period size: 35 Copynumber: 6.7 Consensus size: 35
62696 ATTAGAAATT
* * **
62706 AATTATGACAACTTCTGGTGTCAGTTGAAAATGTAA
1 AATTATGACAACTTCAGGTGTCAATTGAAAA-AAAA
** ** * **
62742 AATTACAACAACTTCAAATGTCAATT--AGAAATT
1 AATTATGACAACTTCAGGTGTCAATTGAAAAAAAA
* * * * * *
62775 AATAATGACAGCTTCTGATATCAATTGAAAAGTAAA
1 AATTATGACAACTTCAGGTGTCAATTGAAAA-AAAA
* *
62811 AA-GAAGACAACTTCAGGTGTCAATTGAAAAAATAA
1 AATTATGACAACTTCAGGTGTCAATTGAAAAAA-AA
* * * ***
62846 AATTACGACAACTTCTGGTGTCAGTTG--AAATTT
1 AATTATGACAACTTCAGGTGTCAATTGAAAAAAAA
*
62879 AATTATGACAACGT-ATGGTGTCAATTGAAAAAAAA
1 AATTATGACAACTTCA-GGTGTCAATTGAAAAAAAA
**
62914 AATTATGACATTTTCAGGTGTCAATT
1 AATTATGACAACTTCAGGTGTCAATT
62940 ATATATATAA
Statistics
Matches: 143, Mismatches: 46, Indels: 19
0.69 0.22 0.09
Matches are distributed among these distances:
33 41 0.29
34 6 0.04
35 52 0.36
36 44 0.31
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (35 bp):
AATTATGACAACTTCAGGTGTCAATTGAAAAAAAA
Found at i:65244 original size:29 final size:29
Alignment explanation
Indices: 65189--65245 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
65179 ATTGAAGATT
*
65189 CATTGAAGATAATTTCAAGATATGAAGAC
1 CATTGAAGATAATTTCAAGATAGGAAGAC
*
65218 CATTGAAGAATTATTTCAAGA-AGGAAGA
1 CATTGAAG-ATAATTTCAAGATAGGAAGA
65246 ATTGAGGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (29 bp):
CATTGAAGATAATTTCAAGATAGGAAGAC
Found at i:69303 original size:21 final size:21
Alignment explanation
Indices: 69260--69303 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
69250 TTACTTTTTC
*
69260 TTGCATTGCTTTGATTGATTA
1 TTGCATTGCTTTGATTGACTA
* *
69281 TTGCTTTGCTTTGATTGCCTA
1 TTGCATTGCTTTGATTGACTA
69302 TT
1 TT
69304 CCTTGATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (21 bp):
TTGCATTGCTTTGATTGACTA
Found at i:76263 original size:9 final size:9
Alignment explanation
Indices: 76245--76278 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
76235 CCTAGCGTTG
76245 TTCT-CTTC
1 TTCTACTTC
76253 TTCTACTTC
1 TTCTACTTC
76262 TTCTACTTC
1 TTCTACTTC
76271 TTCTACTT
1 TTCTACTT
76279 TCTACAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.09, C:0.32, G:0.00, T:0.59
Consensus pattern (9 bp):
TTCTACTTC
Found at i:76486 original size:20 final size:20
Alignment explanation
Indices: 76461--76499 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
76451 TTTACCTTTC
76461 ATTTGCTTTGGG-TTGTTGTT
1 ATTTGC-TTGGGATTGTTGTT
76481 ATTTGCTTGGGATTGTTGT
1 ATTTGCTTGGGATTGTTGT
76500 GAAATTCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.08, C:0.05, G:0.31, T:0.56
Consensus pattern (20 bp):
ATTTGCTTGGGATTGTTGTT
Found at i:76907 original size:33 final size:29
Alignment explanation
Indices: 76847--76904 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
76837 TTTTATAAGA
*
76847 AATATTTATTAATATGTAGTAAATATTAG
1 AATATTTATTAATATATAGTAAATATTAG
76876 AATATTTATTTAATATATAGTAAATATTA
1 AATATTTA-TTAATATATAGTAAATATTA
76905 TTAAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (29 bp):
AATATTTATTAATATATAGTAAATATTAG
Found at i:78500 original size:65 final size:65
Alignment explanation
Indices: 78375--78500 Score: 173
Period size: 65 Copynumber: 1.9 Consensus size: 65
78365 GCCTAATCGA
**
78375 GCTACTCGAATAAGCTCGACAGGCTACCACTCCCAAGAACTGAAAACACCAAATTTAAAAAATTT
1 GCTACTCGAATAAGCTCGACAGGCTACCACTCCCAAGAACTGAAAACACCAAATCCAAAAAATTT
* * * * *
78440 GCTACTCGGATAAGCTTGGCAGGCTACCACTCCCACA-AACTGGAAACACTAAATCCAAAAA
1 GCTACTCGAATAAGCTCGACAGGCTACCACTCCCA-AGAACTGAAAACACCAAATCCAAAAA
78501 TTTTACAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
65 52 0.98
66 1 0.02
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18
Consensus pattern (65 bp):
GCTACTCGAATAAGCTCGACAGGCTACCACTCCCAAGAACTGAAAACACCAAATCCAAAAAATTT
Found at i:79753 original size:25 final size:24
Alignment explanation
Indices: 79719--79767 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
79709 CGAGCATCAA
*
79719 ACTTTTTTATGCT-TTTATTAGTATT
1 ACTTATTTAT-CTATTT-TTAGTATT
79744 ACTTATTTATCTATTTTTAGTATT
1 ACTTATTTATCTATTTTTAGTATT
79768 TGATAATTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.63
Consensus pattern (24 bp):
ACTTATTTATCTATTTTTAGTATT
Found at i:84201 original size:16 final size:15
Alignment explanation
Indices: 84163--84202 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
84153 AGAGGTTGAA
*
84163 AGAAAGCAATTAAAC
1 AGAAAACAATTAAAC
*
84178 AAAAAACAATTAAAC
1 AGAAAACAATTAAAC
84193 TAGAAAACAA
1 -AGAAAACAA
84203 AACAAAGCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.68, C:0.12, G:0.07, T:0.12
Consensus pattern (15 bp):
AGAAAACAATTAAAC
Found at i:86694 original size:117 final size:117
Alignment explanation
Indices: 86567--86799 Score: 315
Period size: 117 Copynumber: 2.0 Consensus size: 117
86557 AAAATAGTGA
* * * * *
86567 AAATAAAATATTTGTAAGGATTTAGATTTAGTTA-AAAAAAAAATATTTTTTAGTAGACTAAAAC
1 AAATAAAATATTTATAAAGATTTAGATATA-TTATAAAAAAAAAGAGTTTTTAGTAGACTAAAAC
*
86631 TATAACAGTTTAAACGATGGCAGTTTAGAAATATATTAGAAAAATAAGGGTAC
65 TATAACAGTTTAAACAATGGCAGTTTAGAAATATATTAGAAAAATAAGGGTAC
** * *
86684 AAATAAAATATTTATAAAGATTTAGATATATTATTTAAAAATAGAGTTTTTAGTAGAGTAAAACT
1 AAATAAAATATTTATAAAGATTTAGATATATTATAAAAAAAAAGAGTTTTTAGTAGACTAAAACT
* ** * *
86749 ATAATAGTTTAAACAATGTTAGTTTAGAGATATGTTAGAAAAATAAGGGTA
66 ATAACAGTTTAAACAATGGCAGTTTAGAAATATATTAGAAAAATAAGGGTA
86800 TAGTGGTCGA
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
116 3 0.03
117 97 0.97
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.34
Consensus pattern (117 bp):
AAATAAAATATTTATAAAGATTTAGATATATTATAAAAAAAAAGAGTTTTTAGTAGACTAAAACT
ATAACAGTTTAAACAATGGCAGTTTAGAAATATATTAGAAAAATAAGGGTAC
Done.