Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016650.1 Corchorus olitorius cultivar O-4 contig16683, 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: 146578
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7687 original size:18 final size:18
Alignment explanation
Indices: 7664--7710 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
7654 AGCTGCTGAT
7664 GAAGATGATATAAATC-AC
1 GAAGATGATA-AAATCAAC
* *
7682 GAAGATGAGAAAATCAAT
1 GAAGATGATAAAATCAAC
7700 GAAGATGATAA
1 GAAGATGATAA
7711 TAGAGGAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.19
Consensus pattern (18 bp):
GAAGATGATAAAATCAAC
Found at i:12156 original size:23 final size:19
Alignment explanation
Indices: 12114--12152 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12104 TAGAAATATA
12114 CCATAAATAAACTACATAC
1 CCATAAATAAACTACATAC
12133 CCATAAATAAACTACATAC
1 CCATAAATAAACTACATAC
12152 C
1 C
12153 TACCAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (19 bp):
CCATAAATAAACTACATAC
Found at i:12238 original size:49 final size:49
Alignment explanation
Indices: 12181--12278 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
12171 ATTACAAACA
12181 AACTCACATTCCGTGAGAGTTGAACCTAAGACCTCTTGGTCTAGGTAGG
1 AACTCACATTCCGTGAGAGTTGAACCTAAGACCTCTTGGTCTAGGTAGG
*
12230 AACTCACATTCCGTGAGAGTTGAACCTAAGACCTCTTGGTTTAGGTAGG
1 AACTCACATTCCGTGAGAGTTGAACCTAAGACCTCTTGGTCTAGGTAGG
12279 CTGGAACTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (49 bp):
AACTCACATTCCGTGAGAGTTGAACCTAAGACCTCTTGGTCTAGGTAGG
Found at i:13121 original size:80 final size:80
Alignment explanation
Indices: 13008--13164 Score: 287
Period size: 80 Copynumber: 2.0 Consensus size: 80
12998 GCATTCGTTC
*
13008 TGCAACTCCCCCTCATTTTCATTTCCCTTCCCAAAATAGGTTTTTCAGCCAACCCATCTTCAAAA
1 TGCAACTCCCCCTCATTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
13073 GTCGTCTAAGATCCA
66 GTCGTCTAAGATCCA
* *
13088 TGCAACTCCCCCTCGTTTTTATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
1 TGCAACTCCCCCTCATTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
13153 GTCGTCTAAGAT
66 GTCGTCTAAGAT
13165 TCGAAACCTC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.25, C:0.33, G:0.10, T:0.32
Consensus pattern (80 bp):
TGCAACTCCCCCTCATTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
GTCGTCTAAGATCCA
Found at i:14758 original size:21 final size:22
Alignment explanation
Indices: 14718--14758 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
14708 GACAAACTCG
*
14718 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
14740 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
14759 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:16220 original size:22 final size:23
Alignment explanation
Indices: 16171--16221 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
16161 TTTTGCCTGA
16171 ACATATCTAATCTAATCTAACTAC
1 ACATATCTAATCT-ATCTAACTAC
16195 ACATATCTAA-CT-TCTAACTTAC
1 ACATATCTAATCTATCTAAC-TAC
16217 ACATA
1 ACATA
16222 AAGAGTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.23
22 8 0.31
23 2 0.08
24 10 0.38
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.33
Consensus pattern (23 bp):
ACATATCTAATCTATCTAACTAC
Found at i:16315 original size:13 final size:13
Alignment explanation
Indices: 16297--16321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16287 CTCCTCAACT
16297 TCCAATTTGAAAA
1 TCCAATTTGAAAA
16310 TCCAATTTGAAA
1 TCCAATTTGAAA
16322 CACGCAGGTC
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TCCAATTTGAAAA
Found at i:21344 original size:18 final size:18
Alignment explanation
Indices: 21321--21363 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
21311 TAAAAGGGTG
21321 GGAAAGTTCACTTTCCCA
1 GGAAAGTTCACTTTCCCA
21339 GGAAAGTTCACTTTCCCA
1 GGAAAGTTCACTTTCCCA
21357 GGAAAGT
1 GGAAAGT
21364 GTTACTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (18 bp):
GGAAAGTTCACTTTCCCA
Found at i:24836 original size:3 final size:3
Alignment explanation
Indices: 24823--24857 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
24813 GGTGAAGAGA
*
24823 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
24858 ACAGTGAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:27487 original size:21 final size:21
Alignment explanation
Indices: 27463--27507 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27453 TTGATATTAT
*
27463 TTAGCAATTGTACAGATTAGA
1 TTAGCAATTGTACAGATGAGA
** *
27484 TTAGTTATTGTACATATGAGA
1 TTAGCAATTGTACAGATGAGA
27505 TTA
1 TTA
27508 TTAGAGCAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.40
Consensus pattern (21 bp):
TTAGCAATTGTACAGATGAGA
Found at i:33816 original size:135 final size:136
Alignment explanation
Indices: 33569--33819 Score: 434
Period size: 135 Copynumber: 1.9 Consensus size: 136
33559 AAAAAAAAAA
* * *
33569 AATTCACCTTTACCTCAATTTTTCTCATCACCACATTCATTTGGTCTACTATTTGTATGGTTTTT
1 AATTCACCTTTACCTCAATTTTTCTCATCACCACATTCATTTGGGCTACTATTTGCATGATTTTT
*
33634 GTGTCTTTTCACCTTGGTTATTTTGTTATTTCATGTGATTGCAAGGCTAAAACTATAAAAGCTGA
66 GTGTCTTTTCACCTTGATTATTTTGTTATTTCATGTGATTGCAAGGCTAAAACTATAAAAGCTGA
33699 ACCTAG
131 ACCTAG
33705 AATT-ACCTTTAGCC-CAATTTTTCTCATCACCACATTCATTTGGGCTACTATTTGCATGATTTT
1 AATTCACCTTTA-CCTCAATTTTTCTCATCACCACATTCATTTGGGCTACTATTTGCATGATTTT
*
33768 TGTGTCTTTTCACCTTGATTTTTTTGTTATTTCATGTGATTGCAAGGCTAAA
65 TGTGTCTTTTCACCTTGATTATTTTGTTATTTCATGTGATTGCAAGGCTAAA
33820 TATGTCATTC
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
135 103 0.94
136 6 0.06
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (136 bp):
AATTCACCTTTACCTCAATTTTTCTCATCACCACATTCATTTGGGCTACTATTTGCATGATTTTT
GTGTCTTTTCACCTTGATTATTTTGTTATTTCATGTGATTGCAAGGCTAAAACTATAAAAGCTGA
ACCTAG
Found at i:34139 original size:19 final size:19
Alignment explanation
Indices: 34115--34162 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
34105 ATAACCAGGT
34115 CAGGTGTTGGCTCATAGGC
1 CAGGTGTTGGCTCATAGGC
34134 CAGGTGTTGGCTCATAGGC
1 CAGGTGTTGGCTCATAGGC
*
34153 TAGGTGTTGG
1 CAGGTGTTGG
34163 TTTGGGCCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.15, C:0.17, G:0.40, T:0.29
Consensus pattern (19 bp):
CAGGTGTTGGCTCATAGGC
Found at i:37458 original size:12 final size:12
Alignment explanation
Indices: 37441--37465 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37431 CGACACCCTT
37441 AGGAAAAACTAG
1 AGGAAAAACTAG
37453 AGGAAAAACTAG
1 AGGAAAAACTAG
37465 A
1 A
37466 AAAATAGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.24, T:0.08
Consensus pattern (12 bp):
AGGAAAAACTAG
Found at i:40081 original size:21 final size:21
Alignment explanation
Indices: 40052--40103 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
40042 ATCTCGAAAT
**
40052 GGTGATGGCACGGGCTTGGCC
1 GGTGATGGCACGGGCTTAACC
*
40073 GGTGGTGGCACGGGCTTAACC
1 GGTGATGGCACGGGCTTAACC
40094 GGTGATGGCA
1 GGTGATGGCA
40104 AGGTGTTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.13, C:0.21, G:0.46, T:0.19
Consensus pattern (21 bp):
GGTGATGGCACGGGCTTAACC
Found at i:44298 original size:20 final size:22
Alignment explanation
Indices: 44260--44299 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
44250 TCGACACCCT
*
44260 TAGGAAAAACTAGAGGAAAAAC
1 TAGGAAAAACTAGAAGAAAAAC
44282 TAGG-AAAA-TAGAAGAAAA
1 TAGGAAAAACTAGAAGAAAA
44300 GAAATTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.62, C:0.05, G:0.23, T:0.10
Consensus pattern (22 bp):
TAGGAAAAACTAGAAGAAAAAC
Found at i:47996 original size:18 final size:18
Alignment explanation
Indices: 47973--48052 Score: 160
Period size: 18 Copynumber: 4.4 Consensus size: 18
47963 GGCGTTTGTC
47973 GCTTCCTCTCGGCGCCGT
1 GCTTCCTCTCGGCGCCGT
47991 GCTTCCTCTCGGCGCCGT
1 GCTTCCTCTCGGCGCCGT
48009 GCTTCCTCTCGGCGCCGT
1 GCTTCCTCTCGGCGCCGT
48027 GCTTCCTCTCGGCGCCGT
1 GCTTCCTCTCGGCGCCGT
48045 GCTTCCTC
1 GCTTCCTC
48053 ATCTCTGGGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.00, C:0.45, G:0.26, T:0.29
Consensus pattern (18 bp):
GCTTCCTCTCGGCGCCGT
Found at i:49821 original size:28 final size:29
Alignment explanation
Indices: 49785--49862 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 29
49775 TTCAAAGTAC
* * *
49785 AAGGTTAAAACTGTAAATTTA-ACCTTCT
1 AAGGGTAAAACGGTAAATTTATACATTCT
*
49813 AAGGGTAAAACGGT-AATTTATTCATTCT
1 AAGGGTAAAACGGTAAATTTATACATTCT
* *
49841 TAGGGTAAAACGGTAATTTTAT
1 AAGGGTAAAACGGTAAATTTAT
49863 GCCCATACAG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.14
28 30 0.71
29 6 0.14
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (29 bp):
AAGGGTAAAACGGTAAATTTATACATTCT
Found at i:50957 original size:30 final size:30
Alignment explanation
Indices: 50923--50993 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 30
50913 CCAACCTGCT
50923 CAGGCCCGCGCTAGCTGGCCCAGCACGCAC
1 CAGGCCCGCGCTAGCTGGCCCAGCACGCAC
* *
50953 CAGGCCTGCGCGCTAGCTGGCCCAGCGCGCGC
1 CAGGCC--CGCGCTAGCTGGCCCAGCACGCAC
50985 CAGGCCCGC
1 CAGGCCCGC
50994 TAGGCTGGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 9 0.24
32 28 0.76
ACGTcount: A:0.13, C:0.46, G:0.34, T:0.07
Consensus pattern (30 bp):
CAGGCCCGCGCTAGCTGGCCCAGCACGCAC
Found at i:50982 original size:17 final size:17
Alignment explanation
Indices: 50929--50982 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
50919 TGCTCAGGCC
50929 CGCGCTAGCTGGCCCAG
1 CGCGCTAGCTGGCCCAG
* * * *
50946 CACGC-ACCAGG-CCTG
1 CGCGCTAGCTGGCCCAG
50961 CGCGCTAGCTGGCCCAG
1 CGCGCTAGCTGGCCCAG
50978 CGCGC
1 CGCGC
50983 GCCAGGCCCG
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 7 0.26
16 8 0.30
17 12 0.44
ACGTcount: A:0.13, C:0.44, G:0.33, T:0.09
Consensus pattern (17 bp):
CGCGCTAGCTGGCCCAG
Found at i:57377 original size:62 final size:62
Alignment explanation
Indices: 57252--57378 Score: 175
Period size: 62 Copynumber: 2.0 Consensus size: 62
57242 GGTTTTGGTT
* * * * *
57252 TATGGCAAGTAGATTTTCATGGTGTAAATATAATCACTACATTGGTGGAGGGGATCTTCATG
1 TATGGCAAGTAGATTTTCATAGAGAAAAAATAATCACTACATTGGTGGAGGGGACCTTCATG
* *
57314 TATGGCAAGTAGATTTTCGTAGAGAAAAAATAGTCACTACATTGGTGGAGGGGACCCTT-ATG
1 TATGGCAAGTAGATTTTCATAGAGAAAAAATAATCACTACATTGGTGGAGGGGA-CCTTCATG
57376 TAT
1 TAT
57379 AAAGAAGAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 54 0.95
63 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (62 bp):
TATGGCAAGTAGATTTTCATAGAGAAAAAATAATCACTACATTGGTGGAGGGGACCTTCATG
Found at i:57501 original size:17 final size:17
Alignment explanation
Indices: 57474--57508 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
57464 TGTGTTTGCG
57474 TGTCTTCAATTTATCTAT
1 TGTCTTCAATTTAT-TAT
57492 TGTC-TCAATTTATTAT
1 TGTCTTCAATTTATTAT
57508 T
1 T
57509 TCAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 9 0.53
18 4 0.24
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.57
Consensus pattern (17 bp):
TGTCTTCAATTTATTAT
Found at i:59905 original size:17 final size:17
Alignment explanation
Indices: 59854--59905 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
59844 TGTAGGTAAG
* *
59854 TTGTTATTTTGTTAATT
1 TTGTTATATTGTTAACT
*
59871 TTTTTATATTCGTT-ACT
1 TTGTTATATT-GTTAACT
*
59888 TTGTTATCTTGTTAACT
1 TTGTTATATTGTTAACT
59905 T
1 T
59906 ATCTGATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 3 0.11
17 22 0.79
18 3 0.11
ACGTcount: A:0.17, C:0.08, G:0.10, T:0.65
Consensus pattern (17 bp):
TTGTTATATTGTTAACT
Found at i:60557 original size:2 final size:2
Alignment explanation
Indices: 60544--60578 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
60534 ATAAAACATG
*
60544 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60579 TCGTGGAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64811 original size:3 final size:3
Alignment explanation
Indices: 64803--64842 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
64793 ATAGTGATTT
* *
64803 TTA TTA TTA TTA TAA TT- CTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
64843 GTGTTGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:67818 original size:42 final size:42
Alignment explanation
Indices: 67759--67841 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
67749 AACAATAATT
67759 AATATTAGCTTTATTTTGATGAATTATCTAAAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTATCTAAAGATGGAGTAG
* *
67801 AATATTAGCTTTATTTTGATGAATTTTCTAGAGATGGAGTA
1 AATATTAGCTTTATTTTGATGAATTATCTAAAGATGGAGTA
67842 AAATTTACGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTATCTAAAGATGGAGTAG
Found at i:69740 original size:22 final size:22
Alignment explanation
Indices: 69714--69766 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
69704 CGTGTTGTGC
*
69714 CAAAATTTAATAAGGAGCTTAT
1 CAAAATTTAATAAGGAACTTAT
* *
69736 CAAAATTTCATAATGAACTTAT
1 CAAAATTTAATAAGGAACTTAT
69758 CAAGAATTT
1 CAA-AATTT
69767 TCATAAGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (22 bp):
CAAAATTTAATAAGGAACTTAT
Found at i:72061 original size:17 final size:17
Alignment explanation
Indices: 72041--72097 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
72031 AGATCACTAA
72041 TGATCTTGCAACACCAG
1 TGATCTTGCAACACCAG
*
72058 TGATCTTGCAACACCGG
1 TGATCTTGCAACACCAG
*
72075 TGATCTTAG-ATCACCAG
1 TGATCTT-GCAACACCAG
72092 TGATCT
1 TGATCT
72098 GGAGGTAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 35 0.97
18 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (17 bp):
TGATCTTGCAACACCAG
Found at i:80487 original size:16 final size:18
Alignment explanation
Indices: 80466--80510 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
80456 CCTCCATTTC
80466 TCTTTTT-TT-TTTTTTG
1 TCTTTTTCTTATTTTTTG
*
80482 TCTTTTTCTTATTTTTTTT
1 TCTTTTTCTTA-TTTTTTG
80501 TCTTTTTCTT
1 TCTTTTTCTT
80511 GTCTCTTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 7 0.28
17 2 0.08
19 16 0.64
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.84
Consensus pattern (18 bp):
TCTTTTTCTTATTTTTTG
Found at i:80489 original size:24 final size:24
Alignment explanation
Indices: 80462--80518 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
80452 CTTTCCTCCA
80462 TTTCTCTTTTTTTTTT-TTTGTCT
1 TTTCTCTTTTTTTTTTCTTTGTCT
*
80485 TTT-TCTTATTTTTTTTTCTTTTTCT
1 TTTCTC-T-TTTTTTTTTCTTTGTCT
*
80510 TGTCTCTTT
1 TTTCTCTTT
80519 GCTTGCTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 2 0.07
23 4 0.14
24 11 0.39
25 9 0.32
26 2 0.07
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.81
Consensus pattern (24 bp):
TTTCTCTTTTTTTTTTCTTTGTCT
Found at i:80498 original size:19 final size:19
Alignment explanation
Indices: 80474--80510 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
80464 TCTCTTTTTT
80474 TTTTTTTGTCTTTTTCTTA
1 TTTTTTTGTCTTTTTCTTA
*
80493 TTTTTTTTTCTTTTTCTT
1 TTTTTTTGTCTTTTTCTT
80511 GTCTCTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (19 bp):
TTTTTTTGTCTTTTTCTTA
Found at i:80517 original size:26 final size:25
Alignment explanation
Indices: 80468--80517 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
80458 TCCATTTCTC
*
80468 TTTTTTTTTTTTTGTCTTTTTCTTA
1 TTTTTTTTTTTTTGTCTTTCTCTTA
80493 TTTTTTTTTCTTTT-TCTTGTCTCTT
1 TTTTTTTTT-TTTTGTCTT-TCTCTT
80518 TGCTTGCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (25 bp):
TTTTTTTTTTTTTGTCTTTCTCTTA
Found at i:83092 original size:65 final size:64
Alignment explanation
Indices: 82987--83111 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 64
82977 TGCTTGCTAT
* * ** *
82987 TGATTCCAATTTTCTGCACTAGCCCTTGCATGGGTAGGCCAAGGATACCTCATGCATGGGTTGGA
1 TGATTCAAACTTTCTGCACTAGCCCAGGCATGGGTAGGCC-AGGATACCCCATGCATGGGTTGGA
* *
83052 TGATTCAAACTTTCTGCACTAGCCCAGGCGTGGGGT-GGCCAGGGTACCCCATGCATGGGT
1 TGATTCAAACTTTCTGCACTAGCCCAGGCAT-GGGTAGGCCAGGATACCCCATGCATGGGT
83112 AGGACCAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 18 0.35
65 30 0.58
66 4 0.08
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.26
Consensus pattern (64 bp):
TGATTCAAACTTTCTGCACTAGCCCAGGCATGGGTAGGCCAGGATACCCCATGCATGGGTTGGA
Found at i:84309 original size:21 final size:21
Alignment explanation
Indices: 84283--84323 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
84273 TTTAAACCCT
84283 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
84304 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
84324 GGGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:84775 original size:21 final size:22
Alignment explanation
Indices: 84733--84775 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
84723 ACAAGCACTT
**
84733 ATGCAAAGAATGGATGCCATGG
1 ATGCAAAGAATGGAAACCATGG
*
84755 ATGC-AAGAATGGAAACTATGG
1 ATGCAAAGAATGGAAACCATGG
84776 CTAAAGCTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.19
Consensus pattern (22 bp):
ATGCAAAGAATGGAAACCATGG
Found at i:93486 original size:57 final size:57
Alignment explanation
Indices: 93399--93510 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 57
93389 AAAGATTGAT
* *
93399 TTTAAGGGTATGCACTAAACGTAAATTATTTATTTC-TAGGGTTTTAGGAAAAAAAAC
1 TTTAAGGGTATGCACTAAACGTAAAATATTTATTACTTAGGGTTTTA-GAAAAAAAAC
* * *
93456 TTTAAGGGTATGCCCTAAACTTAAAATATTTGTTACTTAGGGTTTTAGAAAAAAA
1 TTTAAGGGTATGCACTAAACGTAAAATATTTATTACTTAGGGTTTTAGAAAAAAA
93511 TATTAAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
57 39 0.80
58 10 0.20
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (57 bp):
TTTAAGGGTATGCACTAAACGTAAAATATTTATTACTTAGGGTTTTAGAAAAAAAAC
Found at i:96859 original size:12 final size:12
Alignment explanation
Indices: 96842--96871 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
96832 AGACCCTACA
96842 ATGAAAAGGCAC
1 ATGAAAAGGCAC
*
96854 ATGAAAATGCAC
1 ATGAAAAGGCAC
96866 ATGAAA
1 ATGAAA
96872 CCCACGCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (12 bp):
ATGAAAAGGCAC
Found at i:102193 original size:23 final size:23
Alignment explanation
Indices: 102163--102335 Score: 201
Period size: 23 Copynumber: 7.7 Consensus size: 23
102153 AAATAATTAA
* *
102163 AACAACATTTTGAACAGCAAAAT
1 AACAACATTTTCAACAGCAAAAC
*
102186 AACAACATTTTCAACAGAAAAAC
1 AACAACATTTTCAACAGCAAAAC
* * * *
102209 AACAGCAATTTCAACACCAAAAT
1 AACAACATTTTCAACAGCAAAAC
* * *
102232 AGCAGCATTTTCAATAGCAAAAC
1 AACAACATTTTCAACAGCAAAAC
* *
102255 AGCAGCATTTTCAACA-CAAAAC
1 AACAACATTTTCAACAGCAAAAC
*
102277 AACAACATTTTCAACA--ATAA-
1 AACAACATTTTCAACAGCAAAAC
102297 AACAACATTTTCAACAGCAAAAC
1 AACAACATTTTCAACAGCAAAAC
102320 AACAACATTTTCAACA
1 AACAACATTTTCAACA
102336 AAAAAGAAAC
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.12
21 3 0.02
22 23 0.18
23 87 0.67
ACGTcount: A:0.51, C:0.23, G:0.06, T:0.20
Consensus pattern (23 bp):
AACAACATTTTCAACAGCAAAAC
Found at i:106598 original size:20 final size:20
Alignment explanation
Indices: 106573--106611 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
106563 CTTCCAATCA
106573 TCAATCAAATTGTAAACCTC
1 TCAATCAAATTGTAAACCTC
106593 TCAATCAAATTGTAAACCT
1 TCAATCAAATTGTAAACCT
106612 TTTCACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (20 bp):
TCAATCAAATTGTAAACCTC
Found at i:107519 original size:22 final size:22
Alignment explanation
Indices: 107493--107554 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
107483 TATTCATTTA
* *
107493 TGAAATAGTGTTGTATCAATTC
1 TGAAATACTGTTCTATCAATTC
107515 TGAAATACTGTTCTATCAATTC
1 TGAAATACTGTTCTATCAATTC
107537 TGAAATACTGTTCTATCA
1 TGAAATACTGTTCTATCA
107555 TCTTAATAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (22 bp):
TGAAATACTGTTCTATCAATTC
Found at i:110064 original size:20 final size:20
Alignment explanation
Indices: 110020--110057 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
110010 AGTTCAATTT
*
110020 CTGAGATAGAGAAAGAGAAA
1 CTGAGAAAGAGAAAGAGAAA
*
110040 CTGAGAAAGAGAGAGAGA
1 CTGAGAAAGAGAAAGAGA
110058 GAGTGAGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.05, G:0.34, T:0.08
Consensus pattern (20 bp):
CTGAGAAAGAGAAAGAGAAA
Found at i:113456 original size:2 final size:2
Alignment explanation
Indices: 113449--113476 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
113439 TACTAGTATG
113449 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
113477 CATTATACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:121744 original size:38 final size:38
Alignment explanation
Indices: 121687--121797 Score: 156
Period size: 38 Copynumber: 2.9 Consensus size: 38
121677 GAATTTCCTT
*
121687 CAAGT-TTTTCAAAGCTTTCAAATTCGGAAAGTTCCCAC
1 CAAGTCTTTTC-AAGTTTTCAAATTCGGAAAGTTCCCAC
121725 CAAGTCTTTTCAAGTTTTCAAATTCGGAAAGTTCCCAC
1 CAAGTCTTTTCAAGTTTTCAAATTCGGAAAGTTCCCAC
* *
121763 CAAGTCTTTT--AGTTTTCAATTTAGGAAAAGTTCCC
1 CAAGTCTTTTCAAGTTTTCAAATTCGG-AAAGTTCCC
121798 GTCATTTTCG
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
36 13 0.19
37 9 0.13
38 41 0.60
39 5 0.07
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.35
Consensus pattern (38 bp):
CAAGTCTTTTCAAGTTTTCAAATTCGGAAAGTTCCCAC
Found at i:123998 original size:11 final size:11
Alignment explanation
Indices: 123982--124007 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
123972 AGATAATTTC
123982 TTTTCTTCTAG
1 TTTTCTTCTAG
123993 TTTTCTTCTAG
1 TTTTCTTCTAG
124004 TTTT
1 TTTT
124008 TTAGGGCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:125121 original size:32 final size:33
Alignment explanation
Indices: 125085--125149 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
125075 TGCGTTTTTC
*
125085 TTTTTCTTTGCGT-TTT-ATTCTGAAAAAAAATA
1 TTTTTCTTTGCGTCTTTAATT-TAAAAAAAAATA
125117 TTTTTCTTTGCGTCTTTAATTTAAAAAAAAATA
1 TTTTTCTTTGCGTCTTTAATTTAAAAAAAAATA
125150 ATAATTTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.43
33 14 0.47
34 3 0.10
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (33 bp):
TTTTTCTTTGCGTCTTTAATTTAAAAAAAAATA
Found at i:129167 original size:11 final size:11
Alignment explanation
Indices: 129151--129176 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
129141 AGATAATTTC
129151 TTTTCTTCTAG
1 TTTTCTTCTAG
129162 TTTTCTTCTAG
1 TTTTCTTCTAG
129173 TTTT
1 TTTT
129177 TTAGGGCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:133252 original size:69 final size:69
Alignment explanation
Indices: 133190--133330 Score: 228
Period size: 69 Copynumber: 2.0 Consensus size: 69
133180 TTCCATTTGT
* *** *
133190 CAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCAAGCGGTAAGGGCTTTTCCAC
1 CAAACTCGTTTCCATACGAGTCAATTCAAGCATTGGTTCCATCCAAGCAACAAGGGCTTTTCCAT
133255 AAGC
66 AAGC
*
133259 CAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCAACAAGGGCTTTTCCAT
1 CAAACTCGTTTCCATACGAGTCAATTCAAGCATTGGTTCCATCCAAGCAACAAGGGCTTTTCCAT
133324 AAGC
66 AAGC
133328 CAA
1 CAA
133331 CCTCAATGAG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (69 bp):
CAAACTCGTTTCCATACGAGTCAATTCAAGCATTGGTTCCATCCAAGCAACAAGGGCTTTTCCAT
AAGC
Found at i:133510 original size:47 final size:47
Alignment explanation
Indices: 133441--133768 Score: 453
Period size: 47 Copynumber: 7.0 Consensus size: 47
133431 ATACAGGTAA
* * *
133441 TCTTTTCTCGCTTCCATGCGAGTTTGCAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCATGCGAGTCTACGATTTAGTGACCAAAGTTGG
* *
133488 TCTTTTCTTGCTTCCATGCGAGTCTACTATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCATGCGAGTCTACGATTTAGTGACCAAAGTTGG
* * *
133535 TCTTTTCTCGCTTCCACGTGAGTCTACGATTTAGTGACAAAAGTTGG
1 TCTTTTCTCGCTTCCATGCGAGTCTACGATTTAGTGACCAAAGTTGG
*
133582 T-TATTTTTCGCTTCCATGCGAGTCTACGATTTAGTGACCAAAGTTGG
1 TCT-TTTCTCGCTTCCATGCGAGTCTACGATTTAGTGACCAAAGTTGG
* * * * *
133629 GCTTCTCTCGCTTCCATGTGAGTCCACGATTTGGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCATGCGAGTCTACGATTTAGTGACCAAAGTTGG
* *
133676 TCTTTTCTCGCTTCCATGCGA-ACTTACAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCATGCGAGTC-TACGATTTAGTGACCAAAGTTGG
* * *
133723 TCTTTTCTCGCTTCCATGCGAGTCTACTATTTGGTGACCACAGTTG
1 TCTTTTCTCGCTTCCATGCGAGTCTACGATTTAGTGACCAAAGTTG
133769 ACAGTTGTTT
Statistics
Matches: 247, Mismatches: 30, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
46 2 0.01
47 243 0.98
48 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCATGCGAGTCTACGATTTAGTGACCAAAGTTGG
Found at i:133807 original size:22 final size:22
Alignment explanation
Indices: 133782--133988 Score: 104
Period size: 22 Copynumber: 9.2 Consensus size: 22
133772 GTTGTTTAAT
133782 TTCAATTCTTCAAATTCAATTC
1 TTCAATTCTTCAAATTCAATTC
* *
133804 TTCAATGCTTCAATTTCAATT-
1 TTCAATTCTTCAAATTCAATTC
* ** *
133825 TCTCAATGCTTCGTATTCAATAC
1 T-TCAATTCTTCAAATTCAATTC
* *
133848 TTCAATGCTTCAATTTCAATTC
1 TTCAATTCTTCAAATTCAATTC
***
133870 TTCAAATTCAATCCTTCTGCTTCAA-T-
1 TTC-AA-T---T-CTTCAAATTCAATTC
*
133896 TTCAATTCTTCAAATTCAATCC
1 TTCAATTCTTCAAATTCAATTC
**
133918 TTCAATGT-TTTGAATTCAATTC
1 TTCAAT-TCTTCAAATTCAATTC
133940 TTCAATGT-TTC-AATTCCAATGT-
1 TTCAAT-TCTTCAAATT-CAAT-TC
*** *
133962 TTCAACGGTTCAATTTCAATTC
1 TTCAATTCTTCAAATTCAATTC
133984 TTCAA
1 TTCAA
133989 ATTCAATCCT
Statistics
Matches: 144, Mismatches: 25, Indels: 32
0.72 0.12 0.16
Matches are distributed among these distances:
20 9 0.06
21 7 0.05
22 103 0.72
23 8 0.06
24 2 0.01
25 2 0.01
26 3 0.02
27 1 0.01
28 9 0.06
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (22 bp):
TTCAATTCTTCAAATTCAATTC
Found at i:133943 original size:36 final size:36
Alignment explanation
Indices: 133804--134024 Score: 209
Period size: 36 Copynumber: 6.0 Consensus size: 36
133794 AATTCAATTC
* * **
133804 TTCAATGCTTCAAT--TTCAATTTCTCAATGCTTCGTA
1 TTCAATCCTTCAATGCTTCAA-TT-TCAATTCTTCAAA
*
133840 TTCAATACTTCAATGCTTCAATTTCAATTCTTCAAA
1 TTCAATCCTTCAATGCTTCAATTTCAATTCTTCAAA
133876 TTCAATCCTTC--TGCTTCAATTTCAATTCTTCAAA
1 TTCAATCCTTCAATGCTTCAATTTCAATTCTTCAAA
* * *
133910 TTCAATCCTTCAATGTTTTGAA-TTCAATTCTTCAATGT
1 TTCAATCCTTCAATG-CTTCAATTTCAATTCTTCAA--A
* *
133948 TTCAATTCCAATGTTTCAACGGTTCAATTTCAATTCTTCAAA
1 TTCAA-TCC-----TTCAATGCTTCAATTTCAATTCTTCAAA
*
133990 TTCAATCCTTCAATGTTTCAATTTCAATTCTTCAA
1 TTCAATCCTTCAATGCTTCAATTTCAATTCTTCAA
134025 TGCATCAATT
Statistics
Matches: 157, Mismatches: 14, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
34 34 0.22
36 73 0.46
37 6 0.04
38 10 0.06
39 3 0.02
41 3 0.02
42 5 0.03
43 4 0.03
44 19 0.12
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (36 bp):
TTCAATCCTTCAATGCTTCAATTTCAATTCTTCAAA
Found at i:134025 original size:14 final size:14
Alignment explanation
Indices: 133779--134003 Score: 74
Period size: 14 Copynumber: 15.2 Consensus size: 14
133769 ACAGTTGTTT
133779 AATTTCAATTCTTC
1 AATTTCAATTCTTC
*
133793 AAATTCAATTCTTC
1 AATTTCAATTCTTC
133807 AATGCTTCAA-T-TTC
1 AAT--TTCAATTCTTC
133821 AATTTCTCAATGCTTCGTATTC
1 AA-TT-TCAA---TTC---TTC
*
133843 AATACTTCAATGCTTC
1 AAT--TTCAATTCTTC
133859 AATTTCAATTCTTC
1 AATTTCAATTCTTC
*
133873 AAATTCAATCCTTCTGCTTC
1 AATTTCAA----T-T-CTTC
133893 AATTTCAATTCTTC
1 AATTTCAATTCTTC
* *
133907 AAATTCAATCCTTC
1 AATTTCAATTCTTC
* *
133921 AA--T--GTT-TTG
1 AATTTCAATTCTTC
133930 AA-TTCAATTCTTC
1 AATTTCAATTCTTC
133943 AATGTTTCAATTC--C
1 AA--TTTCAATTCTTC
***
133957 AATGTTTCAACGGTTC
1 AA--TTTCAATTCTTC
133973 AATTTCAATTCTTC
1 AATTTCAATTCTTC
* *
133987 AAATTCAATCCTTC
1 AATTTCAATTCTTC
134001 AAT
1 AAT
134004 GTTTCAATTT
Statistics
Matches: 160, Mismatches: 22, Indels: 58
0.67 0.09 0.24
Matches are distributed among these distances:
9 4 0.03
10 2 0.01
12 3 0.02
13 5 0.03
14 93 0.58
15 3 0.02
16 23 0.14
18 2 0.01
19 3 0.02
20 11 0.07
21 1 0.01
22 9 0.06
23 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (14 bp):
AATTTCAATTCTTC
Found at i:134032 original size:22 final size:22
Alignment explanation
Indices: 133976--134035 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
133966 ACGGTTCAAT
* *
133976 TTCAATTCTTCAAATTCAATCC
1 TTCAATGCTTCAATTTCAATCC
* *
133998 TTCAATGTTTCAATTTCAATTC
1 TTCAATGCTTCAATTTCAATCC
*
134020 TTCAATGCATCAATTT
1 TTCAATGCTTCAATTT
134036 ACTTCAACGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.45
Consensus pattern (22 bp):
TTCAATGCTTCAATTTCAATCC
Found at i:134073 original size:56 final size:56
Alignment explanation
Indices: 134006--134350 Score: 582
Period size: 56 Copynumber: 6.1 Consensus size: 56
133996 CCTTCAATGT
* *
134006 TTCAATTTCAATTCTTCAATGCATCAATTTACTTCAACGATCCAGAGTGGTCTTTC
1 TTCAATTTCAATTATTCAATGCATCAATTTACTTCAACGATCCAGGGTGGTCTTTC
* *
134062 TTCAATTTCAATTCTTCAATGCATCAATTTACCTCAACGATCCAGGGTGGTCTTTC
1 TTCAATTTCAATTATTCAATGCATCAATTTACTTCAACGATCCAGGGTGGTCTTTC
*
134118 TTCAATTTCAATTATCCAATGCATCAATTTACTTCAACGATCCAGGGTGGTCTTTC
1 TTCAATTTCAATTATTCAATGCATCAATTTACTTCAACGATCCAGGGTGGTCTTTC
*
134174 TTCAATTTCAATTATTCAATGCATAAATTTACTTCAACGATCCAGGGTGGTCTTTC
1 TTCAATTTCAATTATTCAATGCATCAATTTACTTCAACGATCCAGGGTGGTCTTTC
134230 TTCAATTTCAATTATTCAATGCATCAATTTACTTCAACGATCCAGGGTGGTCTTTC
1 TTCAATTTCAATTATTCAATGCATCAATTTACTTCAACGATCCAGGGTGGTCTTTC
* * * *
134286 TTCAATTTCAATTATTCAATGCTTCAATTTATTTCAGAAAGATCGAGGGTGGTCTTTC
1 TTCAATTTCAATTATTCAATGCATCAATTTACTTC--AACGATCCAGGGTGGTCTTTC
134344 TTCAATT
1 TTCAATT
134351 CTTTAGTTCT
Statistics
Matches: 275, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
56 249 0.91
58 26 0.09
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (56 bp):
TTCAATTTCAATTATTCAATGCATCAATTTACTTCAACGATCCAGGGTGGTCTTTC
Found at i:134458 original size:36 final size:36
Alignment explanation
Indices: 134357--134444 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
134347 AATTCTTTAG
** * * *
134357 TTCTTCAATTTATTCCAAAATGATCGAGGGTAGTCT
1 TTCTTCAATTTATTTTAGAAGGATCCAGGGTAGTCT
* *
134393 TTCTTCAGTTTATTTTAGAAGGATCCAGGGTGGTCT
1 TTCTTCAATTTATTTTAGAAGGATCCAGGGTAGTCT
134429 TTCTTCAATTTATTTT
1 TTCTTCAATTTATTTT
134445 CGATTGATGC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (36 bp):
TTCTTCAATTTATTTTAGAAGGATCCAGGGTAGTCT
Found at i:138286 original size:16 final size:15
Alignment explanation
Indices: 138248--138276 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
138238 GCAGAGGTTG
138248 AAAGAAAACAATTAA
1 AAAGAAAACAATTAA
138263 AAAGAAAACAATTA
1 AAAGAAAACAATTA
138277 TACTAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAGAAAACAATTAA
Found at i:142141 original size:16 final size:15
Alignment explanation
Indices: 142103--142144 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
142093 ACAGAGATTG
*
142103 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
142118 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
142133 ACTAGAAAACAA
1 AC-AGAAAACAA
142145 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:143703 original size:14 final size:15
Alignment explanation
Indices: 143684--143713 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
143674 CAATCAAAGC
143684 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
143698 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
143713 A
1 A
143714 TTAAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:144096 original size:21 final size:20
Alignment explanation
Indices: 144070--144117 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
144060 GGAATGGCGA
**
144070 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGG-ATAACCGGTGG
*
144091 TGGCACGGGTTAACCGGTGG
1 TGGCACGGGATAACCGGTGG
144111 TGGCACG
1 TGGCACG
144118 ATGAATGGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.12, C:0.23, G:0.48, T:0.17
Consensus pattern (20 bp):
TGGCACGGGATAACCGGTGG
Found at i:144395 original size:21 final size:21
Alignment explanation
Indices: 144358--144397 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
144348 TCGGGCATGA
*
144358 GGCGCGGAGGGTAGCACGGAT
1 GGCGCGGAGGGAAGCACGGAT
144379 GGCGCGGA-GGAAGGCACGG
1 GGCGCGGAGGGAA-GCACGG
144398 CTAGCCGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.20, C:0.20, G:0.55, T:0.05
Consensus pattern (21 bp):
GGCGCGGAGGGAAGCACGGAT
Done.