Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012290.1 Corchorus olitorius cultivar O-4 contig12323, 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: 62038
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:7068 original size:15 final size:15
Alignment explanation
Indices: 7038--7079 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
7028 TTACTCTGCT
7038 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
7054 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
7069 TTGCTTTCTGT
1 TTGTTTTCTGT
7080 CAATCTCTGT
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:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:10709 original size:33 final size:32
Alignment explanation
Indices: 10659--10727 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
10649 CTGGATAGGA
10659 CCGGCCATACCCGAGCCACGCCGAGACACATGC
1 CCGGCCATACCCGAGCCA-GCCGAGACACATGC
* * * *
10692 CCGGCCATGGCCC-AGCCATCCGAGCCACCTGC
1 CCGGCCAT-ACCCGAGCCAGCCGAGACACATGC
10724 CCGG
1 CCGG
10728 TCTATCCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 15 0.48
33 13 0.42
34 3 0.10
ACGTcount: A:0.19, C:0.48, G:0.26, T:0.07
Consensus pattern (32 bp):
CCGGCCATACCCGAGCCAGCCGAGACACATGC
Found at i:11448 original size:15 final size:15
Alignment explanation
Indices: 11428--11461 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11418 TATTCTTTCA
*
11428 TGTGAATTAATTGTT
1 TGTGAATTAATTATT
*
11443 TGTGAATTAGTTATT
1 TGTGAATTAATTATT
11458 TGTG
1 TGTG
11462 TTTTCTGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (15 bp):
TGTGAATTAATTATT
Found at i:14791 original size:24 final size:22
Alignment explanation
Indices: 14737--14904 Score: 77
Period size: 22 Copynumber: 7.8 Consensus size: 22
14727 GATAAGCACA
*
14737 CTATGAAATTTCAATAACCTTC
1 CTATGAAATTTTAATAACCTTC
** *
14759 CTAAAAAATTTTAATAACTTGATC
1 CTATGAAATTTTAATAACCT--TC
*
14783 CTATGAAATTTTGATAACCTTC
1 CTATGAAATTTTAATAACCTTC
* *
14805 C----CAA--TTGATAA-CTTC
1 CTATGAAATTTTAATAACCTTC
** *
14820 CATATGAAATTTTGGTAACC-AC
1 C-TATGAAATTTTAATAACCTTC
* *
14842 ACTATGGAATTTTGATAACC-TC
1 -CTATGAAATTTTAATAACCTTC
*
14864 CTCATGAAATTATAATAACCATT-
1 CT-ATGAAATTTTAATAACC-TTC
* *
14887 TTATGAAATTTTGATAAC
1 CTATGAAATTTTAATAAC
14905 TACACAGAGA
Statistics
Matches: 111, Mismatches: 21, Indels: 28
0.69 0.13 0.17
Matches are distributed among these distances:
15 5 0.05
16 7 0.06
18 2 0.02
20 2 0.02
21 2 0.02
22 71 0.64
23 3 0.03
24 19 0.17
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTAATAACCTTC
Found at i:14883 original size:44 final size:44
Alignment explanation
Indices: 14809--14904 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 44
14799 ACCTTCCCAA
* * ** *
14809 TTGATAACTTCCATATGAAATTTTGGTAACCACACTATGGAATT
1 TTGATAACCTCCATATGAAATTATAATAACCACACTATGAAATT
***
14853 TTGATAACCTCC-TCATGAAATTATAATAACCATTTTATGAAATT
1 TTGATAACCTCCAT-ATGAAATTATAATAACCACACTATGAAATT
14897 TTGATAAC
1 TTGATAAC
14905 TACACAGAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.02
44 42 0.98
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TTGATAACCTCCATATGAAATTATAATAACCACACTATGAAATT
Found at i:15186 original size:22 final size:22
Alignment explanation
Indices: 15161--15315 Score: 105
Period size: 22 Copynumber: 7.0 Consensus size: 22
15151 TAAAATTGTG
*
15161 ATAACCATACTATGAAATTTCA
1 ATAACCATACTATGAAATTTTA
* * **
15183 ATAACCTTCCTAAAAAATTTTA
1 ATAACCATACTATGAAATTTTA
* * *
15205 ATAACTTGATCCTATGAAATTTTG
1 ATAAC--CATACTATGAAATTTTA
* *
15229 GTAACCATACTATGAAATTTTG
1 ATAACCATACTATGAAATTTTA
* * * *
15251 ATAACCTTCCCATGAAATTTTG
1 ATAACCATACTATGAAATTTTA
* * *
15273 ATAA-CTTCCATATGAAATTTTG
1 ATAACCATAC-TATGAAATTTTA
* *
15295 GTAACCACACTATGAAATTTT
1 ATAACCATACTATGAAATTTT
15316 GATATTAATG
Statistics
Matches: 107, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
21 5 0.05
22 84 0.79
23 2 0.02
24 16 0.15
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (22 bp):
ATAACCATACTATGAAATTTTA
Found at i:15269 original size:68 final size:66
Alignment explanation
Indices: 15153--15319 Score: 219
Period size: 68 Copynumber: 2.5 Consensus size: 66
15143 AAAACCAATA
* * ** *
15153 AAATTGTGATAACCATACTATGAAATTTCAATAACCTTCCTAAAAAATTTTAATAACTTGATCC-
1 AAATTTTGGTAACCATACTATGAAATTTTGATAACCTTCCCAAAAAATTTTAATAAC-T--TCCA
15217 TATG
63 TATG
** *
15221 AAATTTTGGTAACCATACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTCCATAT
1 AAATTTTGGTAACCATACTATGAAATTTTGATAACCTTCCCAAAAAATTTTAATAACTTCCATAT
15286 G
66 G
*
15287 AAATTTTGGTAACCACACTATGAAATTTTGATA
1 AAATTTTGGTAACCATACTATGAAATTTTGATA
15320 TTAATGAATT
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 3 0.03
66 36 0.40
67 1 0.01
68 49 0.55
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (66 bp):
AAATTTTGGTAACCATACTATGAAATTTTGATAACCTTCCCAAAAAATTTTAATAACTTCCATAT
G
Found at i:15316 original size:22 final size:22
Alignment explanation
Indices: 15216--15319 Score: 115
Period size: 22 Copynumber: 4.7 Consensus size: 22
15206 TAACTTGATC
* *
15216 CTATGAAATTTTGGTAACCATA
1 CTATGAAATTTTGATAACCACA
*
15238 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
15260 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
15283 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
15304 CTATGAAATTTTGATA
1 CTATGAAATTTTGATA
15320 TTAATGAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.01
21 2 0.03
22 65 0.94
24 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:18923 original size:150 final size:150
Alignment explanation
Indices: 18652--18953 Score: 586
Period size: 150 Copynumber: 2.0 Consensus size: 150
18642 ATTTTGAAAT
18652 TTTATATTCAAAAATCATTTTTAAACGAAAATTTTGTCAAAAATTGGGGAAAATAAAATCAAGTT
1 TTTATATTCAAAAATCATTTTTAAACGAAAATTTTGTCAAAAATTGGGGAAAATAAAATCAAGTT
18717 AAAAACAACAAGTTCTATCCTAGGTTCTCATGCAAACAAGGACTATCATATGACTCAATTATTCA
66 AAAAACAACAAGTTCTATCCTAGGTTCTCATGCAAACAAGGACTATCATATGACTCAATTATTCA
18782 AGCAATAAACCTATCTAGCA
131 AGCAATAAACCTATCTAGCA
18802 TTTATATTCAAAAATCATTTTTAAACGAAAATTTTGTCAAAAATTGGGGAAAATAAAATCAAGTT
1 TTTATATTCAAAAATCATTTTTAAACGAAAATTTTGTCAAAAATTGGGGAAAATAAAATCAAGTT
* *
18867 AAAAACAACAAGTTCTATCCTAGGTTTTCATGCAAACAAGGACTATCATATGACTCATTTATTCA
66 AAAAACAACAAGTTCTATCCTAGGTTCTCATGCAAACAAGGACTATCATATGACTCAATTATTCA
18932 AGCAATAAACCTATCTAGCA
131 AGCAATAAACCTATCTAGCA
18952 TT
1 TT
18954 CACTCCCCCC
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.31
Consensus pattern (150 bp):
TTTATATTCAAAAATCATTTTTAAACGAAAATTTTGTCAAAAATTGGGGAAAATAAAATCAAGTT
AAAAACAACAAGTTCTATCCTAGGTTCTCATGCAAACAAGGACTATCATATGACTCAATTATTCA
AGCAATAAACCTATCTAGCA
Found at i:29917 original size:22 final size:21
Alignment explanation
Indices: 29892--29947 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
29882 AATCCGTTCT
29892 CGGCCCGAAAGGGATTAGTCTC
1 CGGCCCGAAAGGGATTAGTC-C
* *
29914 CGGCGCGAAAAGGATTAGTCC
1 CGGCCCGAAAGGGATTAGTCC
*
29935 CAGGCCCAAAAGG
1 C-GGCCCGAAAGG
29948 CTCGGGGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.29, C:0.27, G:0.32, T:0.12
Consensus pattern (21 bp):
CGGCCCGAAAGGGATTAGTCC
Found at i:30881 original size:439 final size:441
Alignment explanation
Indices: 30061--30892 Score: 1133
Period size: 439 Copynumber: 1.9 Consensus size: 441
30051 AAACTCGTAG
* * *
30061 ATCAAATTTACCTTTCGGACACTTCATGAAAGTCGTAGATCATGCAGTAACCTTTTAAACGACAC
1 ATCAAATTTACCTTTCGGACACTTAACGAAAGTCGTAGATCATACAGTAACCTTTTAAACGACAC
* * * ** ***
30126 TTAAATAACATCAATCGGACATGTGGACCGAAAATTATACAATATATTGGATAGACCGGTGATCG
66 TTAAACAACATCAATCGGACAAGTGGACCGAAAATTATAC-AGATATTAAATAGACCGACAATCG
* *
30191 AAACCATAAAAATTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTCTGAGTTCTTCA
130 AAACCACAAAAATTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTCTGAGTTCTTCA
* * * *
30256 TGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACTTTAATCGGAAAAATAG
195 TGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATCGGAAAAACAA
* * * * * *
30321 AACAAAAAATACAAGAATAAAAGTCAAAGCGTTAAATCATCCAACCCATAATTGTTAAGGATTAA
260 AACAAAAAATAAAAGAATAAAAGCCAAAGCGTTAAATCATACAACCCAAAATTGTGAAGGACTAA
*
30386 ATAGCATAAAGCATAAAACTATGAGGATCATTTGATAAATAATCCAGCAAAAAAAAT-ATTGGTT
325 ATAGCATAAAGCATAAAACTATGAGGATCATTTGATAAATAATCCAACAAAAAAAATGATTGGTT
30450 TATGCAAACCAAACATAAAAATTCCCTCTTGAACCCTCCACAAAACTCATTA
390 TATGCAAACCAAACATAAAAATTCCCTCTTGAACCCTCCACAAAACTCATTA
* * *
30502 ATCAAATTTAGCTTTCAGG-CCCTTAACGAAAGTCGTAGATCATACAGTAACCTTTTAACCGACA
1 ATCAAATTTACCTTTC-GGACACTTAACGAAAGTCGTAGATCATACAGTAACCTTTTAAACGACA
*
30566 CTTGAACAATC-TCAATCGGACAAGTGGACCGAAAATTATAC-GATATTAAATAGACCGACAATC
65 CTTAAACAA-CATCAATCGGACAAGTGGACCGAAAATTATACAGATATTAAATAGACCGACAATC
* * *
30629 GAGACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTTTGAG-TCTTT
129 GAAACCACAAAAATTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTCTGAGTTC-TT
* * * * * *
30693 CATGAAAATTGTAGATCATGAAATTACGTTTTTATAGACATTTGAATCACCTTGATCGGACAAGC
193 CATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATCGGAAAAAC
* * * * *
30758 AAAACAAAAAATAAAAGAATTAAAGCCGAAA-CGTTCAGTCGTACAACCCAGAAATTGTGAGGGA
258 AAAACAAAAAATAAAAGAATAAAAGCC-AAAGCGTTAAATCATACAACCCA-AAATTGTGAAGGA
*
30822 CTAAATAGCATAAAGCATAAAAGTAT-AGAGATCATTTGATAAATGAA-CCAAC-AAAAAAATGA
321 CTAAATAGCATAAAGCATAAAACTATGAG-GATCATTTGATAAAT-AATCCAACAAAAAAAATGA
*
30884 TTTGTTTAT
384 TTGGTTTAT
30893 TGAGAGCGGG
Statistics
Matches: 339, Mismatches: 44, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
438 2 0.01
439 176 0.52
440 65 0.19
441 93 0.27
442 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (441 bp):
ATCAAATTTACCTTTCGGACACTTAACGAAAGTCGTAGATCATACAGTAACCTTTTAAACGACAC
TTAAACAACATCAATCGGACAAGTGGACCGAAAATTATACAGATATTAAATAGACCGACAATCGA
AACCACAAAAATTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTCTGAGTTCTTCAT
GAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATCGGAAAAACAAA
ACAAAAAATAAAAGAATAAAAGCCAAAGCGTTAAATCATACAACCCAAAATTGTGAAGGACTAAA
TAGCATAAAGCATAAAACTATGAGGATCATTTGATAAATAATCCAACAAAAAAAATGATTGGTTT
ATGCAAACCAAACATAAAAATTCCCTCTTGAACCCTCCACAAAACTCATTA
Found at i:31084 original size:2 final size:2
Alignment explanation
Indices: 31079--31111 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31069 TATATATTGT
31079 TA TA 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 T
31112 TATTTCTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33238 original size:14 final size:14
Alignment explanation
Indices: 33221--33254 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
33211 TGTGTGTGTG
33221 TGTGAGTGTGAGAT
1 TGTGAGTGTGAGAT
33235 TGTGAGTGTGAGAT
1 TGTGAGTGTGAGAT
33249 TGTGAG
1 TGTGAG
33255 AGAGAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (14 bp):
TGTGAGTGTGAGAT
Found at i:34616 original size:23 final size:23
Alignment explanation
Indices: 34590--34633 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
34580 TTAATACTAA
*
34590 TAAATACTAATAACA-AATTAATT
1 TAAA-ACTAATAAAACAATTAATT
*
34613 TAAAAGTAATAAAACAATTAA
1 TAAAACTAATAAAACAATTAA
34634 AACCTTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAAACTAATAAAACAATTAATT
Found at i:36839 original size:62 final size:61
Alignment explanation
Indices: 36721--36845 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 61
36711 ATACTCATTT
36721 TAGGCAAACAATTGGAGACATGAAGCATATTGCATTTATTAATTAGGTTTTCTGATATACA
1 TAGGCAAACAATTGGAGACATGAAGCATATTGCATTTATTAATTAGGTTTTCTGATATACA
**
36782 TAGGCAAACAATTGGAGACATGAAGCATTATTGCATTTATTAATTCTGTTTTCTGATATACA
1 TAGGCAAACAATTGGAGACATGAAGCA-TATTGCATTTATTAATTAGGTTTTCTGATATACA
36844 TA
1 TA
36846 CATTCCCTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 27 0.44
62 34 0.56
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (61 bp):
TAGGCAAACAATTGGAGACATGAAGCATATTGCATTTATTAATTAGGTTTTCTGATATACA
Found at i:37984 original size:73 final size:73
Alignment explanation
Indices: 37865--38012 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 73
37855 GATTCCCCTG
*
37865 ATTGTGTCTTATGCGGTTTATGCCCTGAAACCCGAGATTATTTATTCTTTTCATATGACTACTCG
1 ATTGTGTCTTATGCGGTTTATGCCCTGAAACCCGAGATCATTTATTCTTTTCATATGACTACTCG
37930 AGGAAGTT
66 AGGAAGTT
*
37938 ATTGTGTCTTATGCGGTTTATGCCCTGAAACCCGAGATCATTTATTCTTTTCATGTGACTACTCG
1 ATTGTGTCTTATGCGGTTTATGCCCTGAAACCCGAGATCATTTATTCTTTTCATATGACTACTCG
38003 AGGAAGTT
66 AGGAAGTT
38011 AT
1 AT
38013 GGGAACGTAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (73 bp):
ATTGTGTCTTATGCGGTTTATGCCCTGAAACCCGAGATCATTTATTCTTTTCATATGACTACTCG
AGGAAGTT
Found at i:38058 original size:62 final size:62
Alignment explanation
Indices: 37982--38106 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
37972 AGATCATTTA
37982 TTCTTTTCATGTGACTACTCGAGGAAGTTATGGGAACGTATTTTGCGTGCTTGTAACCTGAC
1 TTCTTTTCATGTGACTACTCGAGGAAGTTATGGGAACGTATTTTGCGTGCTTGTAACCTGAC
38044 TTCTTTTCATGTGACTACTCGAGGAAGTTATGGGAACGTATTTTGCGTGCTTGTAACCTGAC
1 TTCTTTTCATGTGACTACTCGAGGAAGTTATGGGAACGTATTTTGCGTGCTTGTAACCTGAC
38106 T
1 T
38107 AGACCTGCTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (62 bp):
TTCTTTTCATGTGACTACTCGAGGAAGTTATGGGAACGTATTTTGCGTGCTTGTAACCTGAC
Found at i:38215 original size:57 final size:58
Alignment explanation
Indices: 38127--38242 Score: 225
Period size: 57 Copynumber: 2.0 Consensus size: 58
38117 GCAATTGGCA
38127 TGGAGAGCTACAGTGGGCTACCACCAAGATTAAAGCAAAGTCTTTTCTTACTTT-GTC
1 TGGAGAGCTACAGTGGGCTACCACCAAGATTAAAGCAAAGTCTTTTCTTACTTTAGTC
38184 TGGAGAGCTACAGTGGGCTACCACCAAGATTAAAGCAAAGTCTTTTCTTACTTTAGTC
1 TGGAGAGCTACAGTGGGCTACCACCAAGATTAAAGCAAAGTCTTTTCTTACTTTAGTC
38242 T
1 T
38243 TGAAGCTTGC
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 54 0.93
58 4 0.07
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (58 bp):
TGGAGAGCTACAGTGGGCTACCACCAAGATTAAAGCAAAGTCTTTTCTTACTTTAGTC
Found at i:38298 original size:23 final size:23
Alignment explanation
Indices: 38272--38315 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
38262 TTAACGTAAA
38272 GCAAGGACCTTCAAAAGGAAAGT
1 GCAAGGACCTTCAAAAGGAAAGT
*
38295 GCAAGGACCTTCTAAAGGAAA
1 GCAAGGACCTTCAAAAGGAAA
38316 ATGCTCACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (23 bp):
GCAAGGACCTTCAAAAGGAAAGT
Found at i:41267 original size:17 final size:17
Alignment explanation
Indices: 41231--41268 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
41221 CTACTTTACT
*
41231 ATATATATATATATAGA
1 ATATATATATATACAGA
41248 ATATATAGTATATACA-A
1 ATATATA-TATATACAGA
41265 ATAT
1 ATAT
41269 TAAATATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (17 bp):
ATATATATATATACAGA
Found at i:44218 original size:22 final size:22
Alignment explanation
Indices: 44189--44335 Score: 124
Period size: 22 Copynumber: 6.8 Consensus size: 22
44179 TGAATATTTT
44189 TATGAAATTTTGATAACTACCA
1 TATGAAATTTTGATAACTACCA
* *
44211 TATTAAATTTTAATAACTACCA
1 TATGAAATTTTGATAACTACCA
*
44233 TATGAAATTTTGATAATTACC-
1 TATGAAATTTTGATAACTACCA
* * *
44254 TAT-ACAATTGTGATAAATTCCA
1 TATGA-AATTTTGATAACTACCA
* * *
44276 TAAGAAACTTTGATAACCTAACA
1 TATGAAATTTTGATAA-CTACCA
* * *
44299 -ATGAAATTTTAATAAACTTCCC
1 TATGAAATTTTGAT-AACTACCA
44321 TATG-AATTTTG-TAAC
1 TATGAAATTTTGATAAC
44336 ATTCCTATGA
Statistics
Matches: 98, Mismatches: 21, Indels: 14
0.74 0.16 0.11
Matches are distributed among these distances:
20 4 0.04
21 17 0.17
22 68 0.69
23 9 0.09
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCA
Found at i:44238 original size:44 final size:44
Alignment explanation
Indices: 44189--44335 Score: 142
Period size: 44 Copynumber: 3.4 Consensus size: 44
44179 TGAATATTTT
*
44189 TATGAAATTTTGATAACTACCATATTAAATTTTAATAACTACCA
1 TATGAAATTTTGATAACTACCATATTAAATTTTAATAACTTCCA
* * * *
44233 TATGAAATTTTGATAATTACC-TA-TACAATTGTGATAAATTCCA
1 TATGAAATTTTGATAACTACCATATTA-AATTTTAATAACTTCCA
* * * * *
44276 TAAGAAACTTTGATAACCTAACA-ATGAAATTTTAATAAACTTCCC
1 TATGAAATTTTGATAA-CTACCATATTAAATTTTAAT-AACTTCCA
44321 TATG-AATTTTG-TAAC
1 TATGAAATTTTGATAAC
44336 ATTCCTATGA
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
42 3 0.04
43 32 0.39
44 37 0.45
45 10 0.12
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACCATATTAAATTTTAATAACTTCCA
Found at i:49360 original size:22 final size:22
Alignment explanation
Indices: 49311--49361 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
49301 AAATATTACC
**
49311 ATAATTATTTTTGACAGCCATA
1 ATAATTATTTTTGACAGAAATA
*
49333 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGAC-AGAAATA
49356 A-AATTA
1 ATAATTA
49362 GGGAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGACAGAAATA
Found at i:57408 original size:16 final size:15
Alignment explanation
Indices: 57370--57411 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
57360 ACAGAGATTG
*
57370 ATAGAAAGCAATTAA
1 ATAGAAAACAATTAA
*
57385 AAAGAAAACAATTAA
1 ATAGAAAACAATTAA
57400 ACTAGAAAACAA
1 A-TAGAAAACAA
57412 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.14
Consensus pattern (15 bp):
ATAGAAAACAATTAA
Found at i:58180 original size:11 final size:11
Alignment explanation
Indices: 58164--58189 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
58154 CCTTTGCCTA
58164 AAAACTAGAAG
1 AAAACTAGAAG
58175 AAAACTAGAAG
1 AAAACTAGAAG
58186 AAAA
1 AAAA
58190 GAAATTATCT
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:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:61044 original size:20 final size:21
Alignment explanation
Indices: 61006--61044 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60996 GGGTGGCGCT
*
61006 GGTGGCCGGGCAGATGGCTCG
1 GGTGGCCGGGCACATGGCTCG
61027 GGTGGCCGGGC-CATGGCT
1 GGTGGCCGGGCACATGGCT
61045 TGGCATGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.08, C:0.26, G:0.51, T:0.15
Consensus pattern (21 bp):
GGTGGCCGGGCACATGGCTCG
Done.