Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012026.1 Corchorus capsularis cultivar CVL-1 contig12047, 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: 57879
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1764 original size:9 final size:10
Alignment explanation
Indices: 1741--1805 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
1731 CTATATGGCT
1741 TTTTTTAATA
1 TTTTTTAATA
*
1751 TTTTTTATTA
1 TTTTTTAATA
* *
1761 TTTTTCAAAA
1 TTTTTTAATA
**
1771 TTTTAAATATA
1 TTTTTTA-ATA
1782 TTTTTTAA-A
1 TTTTTTAATA
*
1791 ATTTTTAATA
1 TTTTTTAATA
1801 TTTTT
1 TTTTT
1806 AAAGTGGGTC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
9 8 0.19
10 27 0.64
11 7 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTTTAATA
Found at i:1783 original size:21 final size:21
Alignment explanation
Indices: 1759--1805 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1749 TATTTTTTAT
1759 TATTTTTCAAAATTTTAAATA
1 TATTTTTCAAAATTTTAAATA
* *
1780 TATTTTTTAAAATTTTTAATA
1 TATTTTTCAAAATTTTAAATA
1801 T-TTTT
1 TATTTT
1806 AAAGTGGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTCAAAATTTTAAATA
Found at i:1806 original size:9 final size:9
Alignment explanation
Indices: 1742--1807 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
1732 TATATGGCTT
1742 TTTTTAATA
1 TTTTTAATA
*
1751 TTTTTTATTA
1 -TTTTTAATA
*
1761 TTTTTCAAAA
1 TTTTT-AATA
*
1771 TTTTAAATATA
1 TTTT-TA-ATA
*
1782 TTTTTTAAAA
1 -TTTTTAATA
1792 TTTTTAATA
1 TTTTTAATA
1801 TTTTTAA
1 TTTTTAA
1808 AGTGGGTCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
9 20 0.45
10 17 0.39
11 3 0.07
12 4 0.09
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTTAATA
Found at i:1867 original size:31 final size:30
Alignment explanation
Indices: 1801--1869 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
1791 ATTTTTAATA
* * *
1801 TTTTTAAAGTGGGTCAAATAGGTACTGAAC
1 TTTTCAAAGTGGCTCAAATAGGTACTAAAC
*
1831 ATTTCAAAGTTGGCTCAAATAGGTACTAAAC
1 TTTTCAAAG-TGGCTCAAATAGGTACTAAAC
1862 TTTTCAAA
1 TTTTCAAA
1870 ATTGAATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33
Consensus pattern (30 bp):
TTTTCAAAGTGGCTCAAATAGGTACTAAAC
Found at i:3290 original size:31 final size:31
Alignment explanation
Indices: 3254--3317 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3244 ATAAATCCCA
3254 AATTTCCAATGCTTTTTGTTTGAATCAAATT
1 AATTTCCAATGCTTTTTGTTTGAATCAAATT
3285 AATTTCCAATGCTTTTTGTTTGAATCAAATT
1 AATTTCCAATGCTTTTTGTTTGAATCAAATT
3316 AA
1 AA
3318 AAGGAAGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (31 bp):
AATTTCCAATGCTTTTTGTTTGAATCAAATT
Found at i:4412 original size:25 final size:26
Alignment explanation
Indices: 4348--4413 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 26
4338 GCGGTAGAGA
*
4348 AAAAGAAGAAGAAAAGGGAGAAGAAAG
1 AAAAGAA-AACAAAAGGGAGAAGAAAG
* * *
4375 AGAA-AAGACAAAAGGGAGAA-AAAT
1 AAAAGAAAACAAAAGGGAGAAGAAAG
*
4399 AAAAGAAAATAAAAG
1 AAAAGAAAACAAAAG
4414 AAGAAGATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
24 6 0.19
25 20 0.65
26 2 0.06
27 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.03
Consensus pattern (26 bp):
AAAAGAAAACAAAAGGGAGAAGAAAG
Found at i:4583 original size:18 final size:18
Alignment explanation
Indices: 4560--4596 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4550 TTACACTCGT
4560 TGACGGATAACGAAAAAG
1 TGACGGATAACGAAAAAG
4578 TGACGGATAACGAAAAAG
1 TGACGGATAACGAAAAAG
4596 T
1 T
4597 AGCTAATTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.27, T:0.14
Consensus pattern (18 bp):
TGACGGATAACGAAAAAG
Found at i:7144 original size:27 final size:28
Alignment explanation
Indices: 7100--7159 Score: 95
Period size: 27 Copynumber: 2.1 Consensus size: 28
7090 TTTTCTTCCC
*
7100 ATTATATTAGTATTTTCTATTCTATTAGT
1 ATTACATTAGTA-TTTCTATTCTATTAGT
7129 ATTACATTAGTA-TTCTATTCTATTAGT
1 ATTACATTAGTATTTCTATTCTATTAGT
7156 ATTA
1 ATTA
7160 GAATAGGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 19 0.63
29 11 0.37
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.55
Consensus pattern (28 bp):
ATTACATTAGTATTTCTATTCTATTAGT
Found at i:7720 original size:4 final size:4
Alignment explanation
Indices: 7711--7741 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
7701 CAAAAAAAGA
*
7711 GAGT GAGT GAGT GAGT GAGT GAGT GGGT GAG
1 GAGT GAGT GAGT GAGT GAGT GAGT GAGT GAG
7742 AGAGGGAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.55, T:0.23
Consensus pattern (4 bp):
GAGT
Found at i:8333 original size:100 final size:101
Alignment explanation
Indices: 8147--8345 Score: 233
Period size: 100 Copynumber: 2.0 Consensus size: 101
8137 GAATGAGCCT
** *
8147 AAAAATGTTCAAAATGAAAATTTCTAGCAGGTTAATGTTTTTTTACACTTCATTATGCGAAAATA
1 AAAAATGTTCAAAATGAAAATTTCTAGCAGGTTAATG-TTTTTTACACTTCACAATGCAAAAATA
* * *
8212 AGAATTCCAGCACGTTAACATGTTCTCAGAAGTCCTA
65 AGAATTCCAGCACATCAACATGTTATCAGAAGTCCTA
* * *
8249 AAAAATGTTTCAGAAT-AAAATTT-TCAGCATGTTAATG-TTTTTATACTTCACAATGCAAAAAT
1 AAAAATG-TTCAAAATGAAAATTTCT-AGCAGGTTAATGTTTTTTACACTTCACAATGCAAAAAT
* * * *
8311 AAGCATTCCAGCATATCGACATGTTATTAGAAGTC
64 AAGAATTCCAGCACATCAACATGTTATCAGAAGTC
8346 ATATGAAATT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
100 49 0.60
101 1 0.01
102 25 0.30
103 7 0.09
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (101 bp):
AAAAATGTTCAAAATGAAAATTTCTAGCAGGTTAATGTTTTTTACACTTCACAATGCAAAAATAA
GAATTCCAGCACATCAACATGTTATCAGAAGTCCTA
Found at i:19426 original size:157 final size:156
Alignment explanation
Indices: 19218--19941 Score: 730
Period size: 156 Copynumber: 4.6 Consensus size: 156
19208 CTTGGCTAAG
* * * *
19218 TTTCATCCCAAACGGACTTA-AGATGAAAAACTTATGCACGTTTTTCAGTTAAGGACAGTTTGGG
1 TTTCATCTCAATCGGACTTAGA-ATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTGGG
** *
19282 GTGAGAAACC-AGTTCACCATGAAGGAGAGCTCTTTTTTACTTAGAATTTTTTCCATAATTTTAT
65 GTGAGAAACCAAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTTTTAT
19346 GGAGATAATCTAAGTCTCTTGGGCAAA
130 GGAGATAATCTAAGTCTCTTGGGCAAA
* ** * ***
19373 TTTCATCTCAATCAGACTTAAGATAAAAAAAAATTATGCATGTTTTTTGGTTAAGGACAGTTTGG
1 TTTCATCTCAATCGGACTT-AGA-ATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTGG
* * * * * * ** *
19438 GGTGAGAAAACTAGTTCACTATCATGGAGAGTTCGGTTTTACTTAGAATCCTTTCCATAGTTTTG
64 GGTGAGAAACCAAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTTTTA
*
19503 TGGAGATAATCTAAGTCTACTTATGG-AAA
129 TGGAGATAATCTAAGTCT-CTT-GGGCAAA
* * *
19532 -TTCAGTCT-TATTGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAAGACAGTTTGGG
1 TTTCA-TCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTGGG
* * * * * * **
19595 GTGTGTAACCAACTTCACTATGCTAGG-GAGTTCATTTTTACTTAGAATTTTTTCCATAGTTTTA
65 GTGAGAAACCAAGTTCACCATG-AAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTTTTA
* * * *
19659 TGG-GAATAACCTAAGCCTTTTGGTGGAAA
129 TGGAG-ATAATCTAAGTCTCTTGG-GCAAA
* * * * *
19688 -ATCAGCTTC-ATTGGACTTAGAATGAAAAACTTATGCACGTTTTTCATTTAAGGACAGTTTAGG
1 TTTCATC-TCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTGGG
* ** * ** * *
19751 GAGAGAAACCAAGTTCACCACAAAGGAGAGCTCGGTTTTACTTGGAATTTTTTTAATAGTCTTGT
65 GTGAGAAACCAAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTTTTAT
*
19816 GGAGATAATCTAAGTCCCTT-GGCAAA
130 GGAGATAATCTAAGTCTCTTGGGCAAA
** * *
19842 GTTTCATCTCAATATGACTTAGAATGAAAAACTTATGCTTCTTTTTCATTTAAGGACAGTTTGGG
1 -TTTCATCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTT-GG
* * *
19907 GGTGTGAAACCTAGTTCACCATGAAGGAGGGCTCG
64 GGTGAGAAACCAAGTTCACCATGAAGGAGAGCTCG
19942 AACCAAGCCA
Statistics
Matches: 462, Mismatches: 89, Indels: 34
0.79 0.15 0.06
Matches are distributed among these distances:
154 5 0.01
155 27 0.06
156 265 0.57
157 82 0.18
158 72 0.16
159 9 0.02
160 2 0.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (156 bp):
TTTCATCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTGGGG
TGAGAAACCAAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTTTTATG
GAGATAATCTAAGTCTCTTGGGCAAA
Found at i:20454 original size:31 final size:32
Alignment explanation
Indices: 20395--20469 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 32
20385 ATTTTTGGGT
** *
20395 ACCCGAACCCGAAATGACCTGAATCC-AAACG
1 ACCCGAACCCGAAATGACCCAAACCCAAAACG
* *
20426 ACCCGAACCCGAAATGTCCCAAACCCAAAATG
1 ACCCGAACCCGAAATGACCCAAACCCAAAACG
*
20458 ACTCGAACCCGA
1 ACCCGAACCCGA
20470 TTAACCCGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 22 0.59
32 15 0.41
ACGTcount: A:0.39, C:0.37, G:0.15, T:0.09
Consensus pattern (32 bp):
ACCCGAACCCGAAATGACCCAAACCCAAAACG
Found at i:20466 original size:16 final size:16
Alignment explanation
Indices: 20395--20469 Score: 80
Period size: 16 Copynumber: 4.8 Consensus size: 16
20385 ATTTTTGGGT
20395 ACCCGAACCCGAAATG
1 ACCCGAACCCGAAATG
* * *
20411 ACCTGAATCC-AAACG
1 ACCCGAACCCGAAATG
20426 ACCCGAACCCGAAATG
1 ACCCGAACCCGAAATG
* * *
20442 TCCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
*
20458 ACTCGAACCCGA
1 ACCCGAACCCGA
20470 TTAACCCGAT
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
15 12 0.27
16 33 0.73
ACGTcount: A:0.39, C:0.37, G:0.15, T:0.09
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:21773 original size:16 final size:16
Alignment explanation
Indices: 21748--21779 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21738 GAATTGTTAC
*
21748 GACCCGAACCCGAAAA
1 GACCCAAACCCGAAAA
21764 GACCCAAACCCGAAAA
1 GACCCAAACCCGAAAA
21780 CCCGAGGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.38, G:0.16, T:0.00
Consensus pattern (16 bp):
GACCCAAACCCGAAAA
Found at i:21867 original size:15 final size:17
Alignment explanation
Indices: 21832--21869 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
21822 AATCGAAAAC
21832 GACCC-AACCCAGAATT
1 GACCCGAACCCAGAATT
21848 GACCCGAACCCA-AA-T
1 GACCCGAACCCAGAATT
21863 GACCCGA
1 GACCCGA
21870 CATTTGAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.08
Consensus pattern (17 bp):
GACCCGAACCCAGAATT
Found at i:22053 original size:28 final size:28
Alignment explanation
Indices: 22021--22092 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
22011 ACTTGCTGTG
22021 TGATACATCAGAGGGAAGAATTTTCGCA
1 TGATACATCAGAGGGAAGAATTTTCGCA
* *
22049 TGATA-ATTCAAAGGGAAGAATTTTCGCC
1 TGATACA-TCAGAGGGAAGAATTTTCGCA
* *
22077 TGACACACCAGAGGGA
1 TGATACATCAGAGGGA
22093 GACGTCATAG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 35 0.95
29 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (28 bp):
TGATACATCAGAGGGAAGAATTTTCGCA
Found at i:26194 original size:21 final size:21
Alignment explanation
Indices: 26147--26199 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
26137 ACAGCAGCTG
*
26147 ATGGAGTCAACTGCTCGAATA
1 ATGGAGTCAAATGCTCGAATA
26168 ATGGAGTCAAATGCTC-AACTTA
1 ATGGAGTCAAATGCTCGAA--TA
26190 A-GGAGTCAAA
1 ATGGAGTCAAA
26200 CGACTTACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.83
22 3 0.10
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (21 bp):
ATGGAGTCAAATGCTCGAATA
Found at i:30615 original size:178 final size:177
Alignment explanation
Indices: 30308--30816 Score: 689
Period size: 178 Copynumber: 2.9 Consensus size: 177
30298 TAAACACAAA
* * * * * *
30308 TTATGTAATATTAAGTAGACC-ATCTATTTCCGTTAACCGAAACAACTAATTCTTTTGGAAGCAT
1 TTATATAATATTAAGTGGACCGA-CTATTACCGTTAATCGAAACAAC-AAAT-TTTTCGAAGCAT
*
30372 TTTTTATACCTTG-AACGTTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
63 TTTTTATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
* * *
30436 AACCTTTCAAGAGACACTTAAATCATCTCAATCATACATTTGGAGCAAAAG
127 AACCTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTAGAGCAAAAG
* *
30487 TTATATTATATTAAGTGGACCGACTATTACTGTTAATCGAAACAACAAATTTTTCAGAAGCATTT
1 TTATATAATATTAAGTGGACCGACTATTACCGTTAATCGAAACAACAAATTTTTC-GAAGCATTT
* * * *
30552 TTGATACTTGAAACATTAAATTTAGTTTTCAAGTCCTGCATGAAAGTTATAGATCATGGAACAAC
65 TTTATACTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
* *
30617 CTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTAGAGTAAAAG
130 CTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTAGAGCAAAAG
* * * *
30665 TTATATAATATTAAGTGGACCGTCTATTCCCGTTAATCGAAACAAGAAATTTTTCGAAAGCTTTT
1 TTATATAATATTAAGTGGACCGACTATTACCGTTAATCGAAACAACAAATTTTTCG-AAGCATTT
* * *
30730 TTTATACTTAAAACATTAAATTTAGTTTTCGAGACCTTCATGAAAGTTGTAGATCATGGAACAAT
65 TTTATACTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
* * * *
30795 TTTTTAATAGACATTTAAATCA
130 CTTTCAAGAGACACTTAAATCA
30817 CCTTAATCGG
Statistics
Matches: 290, Mismatches: 36, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
177 9 0.03
178 242 0.83
179 38 0.13
180 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (177 bp):
TTATATAATATTAAGTGGACCGACTATTACCGTTAATCGAAACAACAAATTTTTCGAAGCATTTT
TTATACTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAACC
TTTCAAGAGACACTTAAATCATCTCAATCAGACATCTAGAGCAAAAG
Found at i:32001 original size:2 final size:2
Alignment explanation
Indices: 31994--32026 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31984 TTTGGGTTGG
31994 AT 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 AT A
32027 AACCACAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32489 original size:2 final size:2
Alignment explanation
Indices: 32484--32508 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32474 CTAACACACT
32484 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 T
32509 TAATTTCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34702 original size:2 final size:2
Alignment explanation
Indices: 34682--34726 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
34672 TCTTTCTTCC
*
34682 TA TA TA GTA TC TA TA -A 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 TA TA TA TA TA TA TA
34724 TA T
1 TA T
34727 GATCTAGTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:43446 original size:22 final size:23
Alignment explanation
Indices: 43411--43457 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
43401 GTAGTTAATC
*
43411 ATAAATTAACTAATTAAA-ACTA
1 ATAAACTAACTAATTAAATACTA
*
43433 ATAAACTAAGTAATTAAATACTA
1 ATAAACTAACTAATTAAATACTA
43456 AT
1 AT
43458 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAACTAACTAATTAAATACTA
Found at i:43469 original size:22 final size:22
Alignment explanation
Indices: 43422--43471 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
43412 TAAATTAACT
*
43422 AATTAAAACTAATAAACTAAGT
1 AATTAAAACTAATAAACTAAGA
* *
43444 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAACTAAGA
43466 AATTAA
1 AATTAA
43472 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (22 bp):
AATTAAAACTAATAAACTAAGA
Found at i:43472 original size:15 final size:15
Alignment explanation
Indices: 43435--43473 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
43425 TAAAACTAAT
*
43435 AAACTAAGTAATTAA
1 AAACTAATTAATTAA
*
43450 ATACTAATTAATTAA
1 AAACTAATTAATTAA
*
43465 AAATTAATT
1 AAACTAATT
43474 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (15 bp):
AAACTAATTAATTAA
Found at i:43741 original size:21 final size:21
Alignment explanation
Indices: 43711--43754 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
43701 AAAAGTGTAA
*
43711 AAAAGGGGGGCGGTATTTAGC
1 AAAAGAGGGGCGGTATTTAGC
*
43732 AAAAGAGGGGCGGTGTTTAGC
1 AAAAGAGGGGCGGTATTTAGC
43753 AA
1 AA
43755 TCCAATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.41, T:0.18
Consensus pattern (21 bp):
AAAAGAGGGGCGGTATTTAGC
Found at i:44919 original size:38 final size:39
Alignment explanation
Indices: 44845--44919 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 39
44835 TTTTTTTTAA
*
44845 TTTAATTTTTCCTTCATATGTATGCTAATAAGTTTTTCC
1 TTTAAATTTTCCTTCATATGTATGCTAATAAGTTTTTCC
* *
44884 TTTAAATTTT-CTTGATTTGTATGCTAATCAA-TTTTT
1 TTTAAATTTTCCTTCATATGTATGCTAAT-AAGTTTTT
44920 ACTTGAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 21 0.66
39 11 0.34
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (39 bp):
TTTAAATTTTCCTTCATATGTATGCTAATAAGTTTTTCC
Found at i:49609 original size:16 final size:16
Alignment explanation
Indices: 49588--49627 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
49578 ATCTTGACAG
49588 AAACCAAAAGAAAAAA
1 AAACCAAAAGAAAAAA
49604 AAACC-AAAGAAAAAA
1 AAACCAAAAGAAAAAA
49619 AAACCAAAA
1 AAACCAAAA
49628 TCCGCGCGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.80, C:0.15, G:0.05, T:0.00
Consensus pattern (16 bp):
AAACCAAAAGAAAAAA
Found at i:57388 original size:37 final size:37
Alignment explanation
Indices: 57317--57390 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
57307 GGCTTTTGGC
* *
57317 CCATTTTGTGAGAGAAAGACGGCCCACGTGTTTGGGA
1 CCATTTTGTGAGAGAAAGACGACCCACGTATTTGGGA
* * * *
57354 CCATTTTGTGTGAGAGAGATGACCCATGTATTTGGGA
1 CCATTTTGTGAGAGAAAGACGACCCACGTATTTGGGA
57391 TTTTTGTGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.28
Consensus pattern (37 bp):
CCATTTTGTGAGAGAAAGACGACCCACGTATTTGGGA
Found at i:57733 original size:20 final size:19
Alignment explanation
Indices: 57707--57761 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
57697 GCCACGTCAT
*
57707 ATTTTTTGATTAAAAAATA
1 ATTTTTTTATTAAAAAATA
*
57726 ATTTTTTTA-AAAAATATATA
1 ATTTTTTTATTAAAA-A-ATA
57746 ATTTTTTT-TTAAAAAA
1 ATTTTTTTATTAAAAAA
57762 AATGGTGAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 15 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTTTTTATTAAAAAATA
Done.