Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012056.1 Corchorus capsularis cultivar CVL-1 contig12077, 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: 31450
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:186 original size:2 final size:2
Alignment explanation
Indices: 179--204 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
169 GCTAAACTAC
179 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
205 ACTTAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:803 original size:24 final size:24
Alignment explanation
Indices: 757--809 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
747 TTTAATCTTT
**
757 ATATATATTGATAATAATGTTATA
1 ATATATATTGATAATAAACTTATA
*
781 TTATATATT-ATCAATAAACTTATA
1 ATATATATTGAT-AATAAACTTATA
805 ATATA
1 ATATA
810 AAAGATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (24 bp):
ATATATATTGATAATAAACTTATA
Found at i:953 original size:22 final size:22
Alignment explanation
Indices: 928--987 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
918 ACCCAAGCCT
928 GAACCCAACCCGAGCCAAACCC
1 GAACCCAACCCGAGCCAAACCC
* *
950 GAACCCTACCCGAGACCGAACCC
1 GAACCCAACCCGAG-CCAAACCC
**
973 G-ACATAACCCGAGCC
1 GAACCCAACCCGAGCC
988 CGAAAAAGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.06
22 22 0.69
23 8 0.25
ACGTcount: A:0.33, C:0.47, G:0.17, T:0.03
Consensus pattern (22 bp):
GAACCCAACCCGAGCCAAACCC
Found at i:1584 original size:17 final size:15
Alignment explanation
Indices: 1546--1579 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1536 AATTATCTGT
* *
1546 AAATAAATTATTAAA
1 AAATTAATTACTAAA
1561 AAATTAATTACTAAA
1 AAATTAATTACTAAA
1576 AAAT
1 AAAT
1580 GTTAAAATTC
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:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTAATTACTAAA
Found at i:1706 original size:18 final size:18
Alignment explanation
Indices: 1669--1706 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1659 AAACTTGGAA
1669 TATAAAAATGAACATCAT
1 TATAAAAATGAACATCAT
1687 TATAACAAATGAACAT-AT
1 TATAA-AAATGAACATCAT
1705 TA
1 TA
1707 ATGAGTGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (18 bp):
TATAAAAATGAACATCAT
Found at i:2339 original size:178 final size:180
Alignment explanation
Indices: 2034--2362 Score: 488
Period size: 178 Copynumber: 1.8 Consensus size: 180
2024 GTTTAAGCGA
* * * *
2034 ATTAAGGGTTAAGTAATTAAAATATTCAATTTTATAAATTTAAGTAACCAAATTGCCCAAGCCCG
1 ATTAAGGGTTAAGTAATTAAAATATTCAATTTTACAAATTTAAATAAACAAATTGCCCAAACCCG
* *
2099 CCCCGTCCCGTGAGCACCTCGAGTGCCACATAAGTGAATTAAAGGTTAAGTGATTAAAATA-T-T
66 CCCCGGCCCCTGAGCACCTCGAGTGCCACATAAGTGAATTAAAGGTTAAGTGATTAAAATATTAT
2162 CAATTTTACAAATTTAAGTGTCTAAATCGTTGCGCATGCCACTTAAGTAG
131 CAATTTTACAAATTTAAGTGTCTAAATCGTTGCGCATGCCACTTAAGTAG
* *
2212 ATTAATGGTTAAGTGATTAAAATATTCAATTTTACAAATTTAAATAAACAAATTGCCCAAACCCG
1 ATTAAGGGTTAAGTAATTAAAATATTCAATTTTACAAATTTAAATAAACAAATTGCCCAAACCCG
* * *
2277 GCTCGGCCCACTGA-CACCTCTAGTGCCACGA-AAGCT-AATTAAAGGTTAAGTGATTAAAATAT
66 CCCCGGCCC-CTGAGCACCTCGAGTGCCAC-ATAAG-TGAATTAAAGGTTAAGTGATTAAAATAT
2339 TGATCAATTTTACAAATTTAAGTG
128 T-ATCAATTTTACAAATTTAAGTG
2363 AAAAAAACAA
Statistics
Matches: 134, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
178 107 0.80
179 6 0.04
181 21 0.16
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (180 bp):
ATTAAGGGTTAAGTAATTAAAATATTCAATTTTACAAATTTAAATAAACAAATTGCCCAAACCCG
CCCCGGCCCCTGAGCACCTCGAGTGCCACATAAGTGAATTAAAGGTTAAGTGATTAAAATATTAT
CAATTTTACAAATTTAAGTGTCTAAATCGTTGCGCATGCCACTTAAGTAG
Found at i:7154 original size:19 final size:19
Alignment explanation
Indices: 7112--7154 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
7102 AATTTAAATT
*
7112 TTTTTAAATCTGTTTTTCA
1 TTTTCAAATCTGTTTTTCA
*
7131 CTTTCAAATCT-TTTTATCA
1 TTTTCAAATCTGTTTT-TCA
7150 TTTTC
1 TTTTC
7155 TTTTTTAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.21, C:0.16, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTCAAATCTGTTTTTCA
Found at i:12189 original size:42 final size:42
Alignment explanation
Indices: 12130--12211 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
12120 AAGCGAGCTT
12130 ATTGCAGAATCATGTGCAGGCCACCCGGTGATTTGTAGACTA
1 ATTGCAGAATCATGTGCAGGCCACCCGGTGATTTGTAGACTA
12172 ATTGCAGAATCATGTGCAGGCCACCCGGTGATTTGTAGAC
1 ATTGCAGAATCATGTGCAGGCCACCCGGTGATTTGTAGAC
12212 CAGCAGACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (42 bp):
ATTGCAGAATCATGTGCAGGCCACCCGGTGATTTGTAGACTA
Found at i:14739 original size:32 final size:32
Alignment explanation
Indices: 14688--14757 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
14678 TTATATATAG
* *
14688 CGGCATTTGGGACCGTAGACGCCACCATTTAA
1 CGGCGTTTAGGACCGTAGACGCCACCATTTAA
* * *
14720 CGGCGTTTAGGACCTTAGACGCCACTATTTAG
1 CGGCGTTTAGGACCGTAGACGCCACCATTTAA
14752 CGGCGT
1 CGGCGT
14758 CTGGGTTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (32 bp):
CGGCGTTTAGGACCGTAGACGCCACCATTTAA
Found at i:17629 original size:16 final size:16
Alignment explanation
Indices: 17608--17639 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17598 AATCCTACAT
*
17608 GAACAAGCAGACAAAA
1 GAACAAGCAAACAAAA
17624 GAACAAGCAAACAAAA
1 GAACAAGCAAACAAAA
17640 AGAGAAAATA
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:0.66, C:0.19, G:0.16, T:0.00
Consensus pattern (16 bp):
GAACAAGCAAACAAAA
Found at i:18746 original size:51 final size:50
Alignment explanation
Indices: 18656--18994 Score: 374
Period size: 51 Copynumber: 6.7 Consensus size: 50
18646 TTTTAATAAC
* * * * * * *
18656 TTAAGTAATTGGTAATTAAAAATGTCATCTTTGAGTAAAAGATTGAATTT
1 TTAAGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTT
*
18706 TTAGAGTAATTAGTAAATAAGGATTTAACCTTTGAATAAAAGATTGAATTT
1 TTA-AGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTT
* * * * * ** *
18757 TTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATCT
1 TTAAGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTT
18807 TTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTTGAATTT
1 TTA-AGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGA-TTGAATTT
* * * *** ** *
18859 TTAAGTAATTGGTAAATAAAAATGTCGTCTTTGGGTAAAAGATTGAATCT
1 TTAAGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTT
* *
18909 TTAGAGTGATTAGTAAATAAAGATTTAACCTTTGAATAGAAGATTGAATTT
1 TTA-AGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTT
* *
18960 TTAAGTAATTAGTAAATAAA-ATGTCACCTTTGAAT
1 TTAAGTAATTAGTAAATAAAGATTTAACCTTTGAAT
18995 TAGAAGTTTA
Statistics
Matches: 237, Mismatches: 48, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
49 13 0.05
50 70 0.30
51 144 0.61
52 10 0.04
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.37
Consensus pattern (50 bp):
TTAAGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTT
Found at i:19024 original size:203 final size:203
Alignment explanation
Indices: 18656--19030 Score: 565
Period size: 203 Copynumber: 1.8 Consensus size: 203
18646 TTTTAATAAC
* *
18656 TTAAGTAATTGGTAATTAAAAATGTCATCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTA
1 TTAAGTAATTGGTAAATAAAAATGTCATCTTTGAGTAAAAGATTGAATCTTTAGAGTAATTAGTA
* * *
18721 AATAAGGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATC
66 AATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCACC
* * *
18786 TTTGGGTAAAAGATTGAATCTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGAT
131 TTTGAGTAAAAGATTAAATCTTTAGAGCAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGAT
18851 TTGAATTT
196 TTGAATTT
* * *
18859 TTAAGTAATTGGTAAATAAAAATGTCGTCTTTGGGTAAAAGATTGAATCTTTAGAGTGATTAGTA
1 TTAAGTAATTGGTAAATAAAAATGTCATCTTTGAGTAAAAGATTGAATCTTTAGAGTAATTAGTA
*
18924 AATAAAGATTTAACCTTTGAATAGAAGATTGAATTTTTAAGTAATTAGTAAAT-AAAATGTCACC
66 AATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCACC
* * * * *
18988 TTTGAATTAGAAGTTTAAACTTTTTAGA-CCATTAGTAAATAAA
131 TTTG-AGTAAAAGATTAAA-TCTTTAGAGCAATTAGTAAATAAA
19031 TTGATTAGTT
Statistics
Matches: 153, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
202 14 0.09
203 132 0.86
204 7 0.05
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (203 bp):
TTAAGTAATTGGTAAATAAAAATGTCATCTTTGAGTAAAAGATTGAATCTTTAGAGTAATTAGTA
AATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCACC
TTTGAGTAAAAGATTAAATCTTTAGAGCAATTAGTAAATAAAGATTTAACCTTTGAATAAAAGAT
TTGAATTT
Found at i:19046 original size:102 final size:101
Alignment explanation
Indices: 18656--18991 Score: 575
Period size: 101 Copynumber: 3.3 Consensus size: 101
18646 TTTTAATAAC
* * *
18656 TTAAGTAATTGGTAATTAAAAATGTCATCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTA
1 TTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATCTTTAGAGTAATTAGTA
*
18721 AATAAGGATTTAACCTTTGAATAAAAGATTGAATTT
66 AATAAAGATTTAACCTTTGAATAAAAGATTGAATTT
18757 TTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATCTTTAGAGTAATTAGTA
1 TTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATCTTTAGAGTAATTAGTA
18822 AATAAAGATTTAACCTTTGAATAAAAGATTTGAATTT
66 AATAAAGATTTAACCTTTGAATAAAAGA-TTGAATTT
* *
18859 TTAAGTAATTGGTAAATAAAAATGTCGTCTTTGGGTAAAAGATTGAATCTTTAGAGTGATTAGTA
1 TTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATCTTTAGAGTAATTAGTA
*
18924 AATAAAGATTTAACCTTTGAATAGAAGATTGAATTT
66 AATAAAGATTTAACCTTTGAATAAAAGATTGAATTT
* *
18960 TTAAGTAATTAGTAAAT-AAAATGTCACCTTTG
1 TTAAGTAATTGGTAAATAAAAATGTCATCTTTG
18992 AATTAGAAGT
Statistics
Matches: 224, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
100 13 0.06
101 113 0.50
102 98 0.44
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (101 bp):
TTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATCTTTAGAGTAATTAGTA
AATAAAGATTTAACCTTTGAATAAAAGATTGAATTT
Found at i:19733 original size:29 final size:29
Alignment explanation
Indices: 19700--19788 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
19690 AAAAGAGATT
19700 AATCAGAGTCAAAGTAACAGTAATCAGTA
1 AATCAGAGTCAAAGTAACAGTAATCAGTA
* * *
19729 AATCAGTAAT-TAAGTAA-A--AA-GAGGT-
1 AATCAG-AGTCAAAGTAACAGTAATCA-GTA
* *
19754 AATCAAAGTCAAAGTAGCAGTAATCAGTA
1 AATCAGAGTCAAAGTAACAGTAATCAGTA
19783 AATCAG
1 AATCAG
19789 TAATTAAGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 16
0.63 0.13 0.24
Matches are distributed among these distances:
24 2 0.05
25 11 0.26
26 5 0.12
28 5 0.12
29 18 0.42
30 2 0.05
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.21
Consensus pattern (29 bp):
AATCAGAGTCAAAGTAACAGTAATCAGTA
Found at i:19842 original size:55 final size:55
Alignment explanation
Indices: 19689--19961 Score: 406
Period size: 55 Copynumber: 5.0 Consensus size: 55
19679 ATAAAGAAAA
*
19689 AAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTAAATCAGTAATTAAGT
1 AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGT
* * **
19744 AAAAAGAG-GTAATCAAAGTCAAAGTAGCAGTAATCAGTAAATCAGTAATTAAGT
1 AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGT
* * **
19798 AAAAAGAGATTAATCAGAGTTAAGGTAATAGTGGTCAGTAAATCAGTAATTAAGT
1 AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGT
*
19853 AAAAAGAGATTAATCAGAGTCAAAGTAATAGAAATCAGTAAATCAGTAATTAAGT
1 AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGT
* * *
19908 GAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATTAGTAAATC-GATAATTAAG
1 AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAG-TAATTAAG
19962 AGCTAAAATG
Statistics
Matches: 196, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
54 52 0.27
55 144 0.73
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (55 bp):
AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGT
Found at i:20251 original size:43 final size:42
Alignment explanation
Indices: 20198--20536 Score: 263
Period size: 43 Copynumber: 7.7 Consensus size: 42
20188 TAAATTAGTA
*
20198 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAGC
* * * * *
20241 AAGAATAAAATAGTAGTCAGTAAAGAGTAAATA-GTAATTAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAGC
* * * *
20283 AAGAGTAATAA-AGTAATAAGTAAGAAGTAAAAGGAAATCAGT
1 AAGAGTAA-AATAGTAATCAGTAAAAAGTAAAAGGTAATCAGC
* * *
20325 AAGAGTAAAA-AGGTGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGT-AAAAGGTAATCAGC
* * *
20368 AAGAAGTAAAA-AGGTAATCAGTAAAAAGCAAAAGGCAATCAGTA
1 AAG-AGTAAAATA-GTAATCAGTAAAAAGTAAAAGGTAATCAG-C
* * * * *
20412 AAAAGTAAAAGAGTAATCAGTAAAAAAGGAACAGGAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT-AAAAA-G--TA--AAA-GGTAATCAG--C
* * *
20463 AAGAGTAAAATGGCAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAGC
*
20506 AAGAGTAAAATAGTAATCAGTACAAAGTAAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA
20537 GAATAATCAG
Statistics
Matches: 238, Mismatches: 41, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
41 4 0.02
42 58 0.24
43 98 0.41
44 30 0.13
45 9 0.04
46 2 0.01
47 3 0.01
49 4 0.02
50 12 0.05
51 18 0.08
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAGC
Found at i:20274 original size:21 final size:21
Alignment explanation
Indices: 20194--20550 Score: 164
Period size: 21 Copynumber: 16.3 Consensus size: 21
20184 ATGGTAAATT
20194 AGTAAAGAGTAAAATAGTAATC
1 AGTAAAGAGT-AAATAGTAATC
*
20216 AGTAAAAAGTAAGA-AGGTAATC
1 AGTAAAGAGTAA-ATA-GTAATC
* *
20238 A--ACAAGAATAAAATAGTAGTC
1 AGTA-AAGAGT-AAATAGTAATC
*
20259 AGTAAAGAGTAAATAGTAATT
1 AGTAAAGAGTAAATAGTAATC
* *
20280 AGT-AAGAGTAATAAAGTAATA
1 AGTAAAGAGTAA-ATAGTAATC
*
20301 AGT-AAGAAGTAAA-AGGAAATC
1 AGTAAAG-AGTAAATA-GTAATC
* *
20322 AGT-AAGAGTAAAAAGGTGATC
1 AGTAAAGAGTAAATA-GTAATC
*
20343 AGTAAAGAGTAAAAAGCTAATC
1 AGTAAAGAGTAAATAG-TAATC
* *
20365 AG-CAAGAAGTAAAAAGGTAATC
1 AGTAAAG-AGTAAATA-GTAATC
* * *
20387 AGTAAAAAGCAAA-AGGCAATC
1 AGTAAAGAGTAAATA-GTAATC
* *
20408 AGTAAAAAGTAAAAGAGTAATC
1 AGTAAAGAGT-AAATAGTAATC
*
20430 AGTAAAAAAGGAACAGGAAATAGTAATC
1 AGT---AAA-G---AGTAAATAGTAATC
* *
20458 AGTAAAAGAGTAAAATGGCAATC
1 AGT-AAAGAGT-AAATAGTAATC
*
20481 AGTAAAAAGTAAGA-AGGTAATC
1 AGTAAAGAGTAA-ATA-GTAATC
20503 A--ACAAGAGTAAAATAGTAATC
1 AGTA-AAGAGT-AAATAGTAATC
* *
20524 AGTACAA-AGTAAAGAATAATC
1 AGTA-AAGAGTAAATAGTAATC
20545 AGTAAA
1 AGTAAA
20551 ATAGTGATGG
Statistics
Matches: 269, Mismatches: 33, Indels: 68
0.73 0.09 0.18
Matches are distributed among these distances:
20 19 0.07
21 107 0.40
22 99 0.37
23 21 0.08
25 4 0.01
26 4 0.01
28 13 0.05
29 2 0.01
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.18
Consensus pattern (21 bp):
AGTAAAGAGTAAATAGTAATC
Found at i:20433 original size:15 final size:15
Alignment explanation
Indices: 20415--20470 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
20405 ATCAGTAAAA
20415 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* *
20430 AGTAAAAAAGGAA-C
1 AGTAAAAGAGTAATC
* *
20444 AG-GAAATAGTAATC
1 AGTAAAAGAGTAATC
20458 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
20471 AATGGCAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 7 0.22
14 6 0.19
15 19 0.59
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:22835 original size:21 final size:22
Alignment explanation
Indices: 22806--22849 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
22796 TTTTTCTGTC
22806 ATCTGTATAATATATG-ATATTA
1 ATCTGTATAATAT-TGCATATTA
*
22828 ATCT-TATATTATTGCATATTA
1 ATCTGTATAATATTGCATATTA
22849 A
1 A
22850 CGTACAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 14 0.70
22 4 0.20
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (22 bp):
ATCTGTATAATATTGCATATTA
Found at i:25607 original size:42 final size:43
Alignment explanation
Indices: 25535--25625 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 43
25525 AGTGCATTAC
* *
25535 CTAA-ATTCTACTTCATCTCTAGGTAATTCATCAAAATAAA-T
1 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAGT
* *
25576 CTAATATTTTACTCCATCTTTAGATAATTCATCAAAATAAAGT
1 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAGT
25619 -TAATATT
1 CTAATATT
25626 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 4 0.09
42 39 0.89
43 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (43 bp):
CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAGT
Found at i:26785 original size:30 final size:30
Alignment explanation
Indices: 26735--26805 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
26725 TTGTCACGTA
* * *
26735 AACT-TCAATTTTTGACATTTTACCCCCTT
1 AACTCTCAATTTTAGACATTTTACCCACTG
* * *
26764 AACTCTTAATTTTAGATATTTTGCCCACTG
1 AACTCTCAATTTTAGACATTTTACCCACTG
26794 AACTCTCAATTT
1 AACTCTCAATTT
26806 GAGTCTCTGT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
AACTCTCAATTTTAGACATTTTACCCACTG
Found at i:26927 original size:31 final size:31
Alignment explanation
Indices: 26886--26997 Score: 138
Period size: 31 Copynumber: 3.7 Consensus size: 31
26876 GTCGGACAGA
* *
26886 GTTTTTGACGTTTTGTCCCCTGAACTTGTAT
1 GTTTTGGACGTTTTGCCCCCTGAACTTGTAT
* *
26917 GTTTTGGACGTTTTACCCCTTGAACTTGTAT
1 GTTTTGGACGTTTTGCCCCCTGAACTTGTAT
* * *
26948 GTTTTAGACGTTTTGCCCCCGGGACTT-TA-
1 GTTTTGGACGTTTTGCCCCCTGAACTTGTAT
*
26977 ATTTTGGACGTTTTGCCCCCT
1 GTTTTGGACGTTTTGCCCCCT
26998 AAGCAATAAG
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
29 18 0.26
30 2 0.03
31 49 0.71
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (31 bp):
GTTTTGGACGTTTTGCCCCCTGAACTTGTAT
Found at i:28242 original size:15 final size:15
Alignment explanation
Indices: 28206--28247 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
28196 GTACGAAAAT
28206 ATCTAAAATAATCCTA
1 ATCTAAAATAAT-CTA
28222 AT-TAAAATAAT-TA
1 ATCTAAAATAATCTA
28235 AGTCTAAAATAAT
1 A-TCTAAAATAAT
28248 AATTAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 1 0.04
15 18 0.75
16 2 0.08
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (15 bp):
ATCTAAAATAATCTA
Done.