Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011441.1 Corchorus capsularis cultivar CVL-1 contig11462, 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: 44940
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1331 original size:33 final size:32
Alignment explanation
Indices: 1293--1354 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
1283 TTTGCTTCCA
* *
1293 AAAGTCGACTTGTGTAGTCGATTTGCTCCTTGT
1 AAAGTCGACTTGTATAGTCGACTT-CTCCTTGT
1326 AAAGTCGACTTGTATAGTCGACTTCTCCT
1 AAAGTCGACTTGTATAGTCGACTTCTCCT
1355 CCCAATAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (32 bp):
AAAGTCGACTTGTATAGTCGACTTCTCCTTGT
Found at i:1365 original size:33 final size:33
Alignment explanation
Indices: 1293--1369 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
1283 TTTGCTTCCA
* * ***
1293 AAAGTCGACTTGTGTAGTCGATTTGCTCCTTGT
1 AAAGTCGACTTGTATAGTCGACTTGCTCCTCCC
1326 AAAGTCGACTTGTATAGTCGACTT-CTCCTCCC
1 AAAGTCGACTTGTATAGTCGACTTGCTCCTCCC
1358 AATAGTCGACTT
1 AA-AGTCGACTT
1370 CTCCTCTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 7 0.18
33 31 0.82
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (33 bp):
AAAGTCGACTTGTATAGTCGACTTGCTCCTCCC
Found at i:1668 original size:22 final size:22
Alignment explanation
Indices: 1640--1683 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1630 CCTAATCTTC
*
1640 CTTGCATGTAGATGGCGCGGCA
1 CTTGCATGGAGATGGCGCGGCA
**
1662 CTTGCATGGATTTGGCGCGGCA
1 CTTGCATGGAGATGGCGCGGCA
1684 TTCCCCTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.23, G:0.36, T:0.25
Consensus pattern (22 bp):
CTTGCATGGAGATGGCGCGGCA
Found at i:2490 original size:15 final size:16
Alignment explanation
Indices: 2458--2491 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2448 AAAGAAGATT
*
2458 TAAAATTAAATCTAAC
1 TAAAAATAAATCTAAC
2474 TAAAAATAAAT-TAAC
1 TAAAAATAAATCTAAC
2489 TAA
1 TAA
2492 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAATAAATCTAAC
Found at i:3750 original size:19 final size:18
Alignment explanation
Indices: 3717--3752 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3707 TTGAAATAAT
3717 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
3735 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
3753 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:7715 original size:21 final size:21
Alignment explanation
Indices: 7685--7724 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
7675 CCTATGATTG
7685 GAGGTCTCTTATTTATATTTA
1 GAGGTCTCTTATTTATATTTA
*
7706 GAGGTTTCTTATTTATATT
1 GAGGTCTCTTATTTATATT
7725 AGAAAGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.15, T:0.55
Consensus pattern (21 bp):
GAGGTCTCTTATTTATATTTA
Found at i:7733 original size:21 final size:21
Alignment explanation
Indices: 7691--7736 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
7681 ATTGGAGGTC
*
7691 TCTTATTTATATTTAGAGGTT
1 TCTTATTTATATTTAGAAGTT
7712 TCTTATTTATA-TTAGAAAGTT
1 TCTTATTTATATTTAG-AAGTT
7733 TCTT
1 TCTT
7737 TCATATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.57
Consensus pattern (21 bp):
TCTTATTTATATTTAGAAGTT
Found at i:14136 original size:27 final size:26
Alignment explanation
Indices: 14104--14174 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
14094 GGTCGTCCAA
*
14104 GGGTATTTTGGTCATTTTCGCGCCCAG
1 GGGTATTTTGGTCATTTTCGC-ACCAG
14131 GGGTATTTTGGTCATTTTCGCACCAG
1 GGGTATTTTGGTCATTTTCGCACCAG
*
14157 GGGCATTTTGGTCATTTT
1 GGGTATTTTGGTCATTTT
14175 TACACTCGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
26 21 0.50
27 21 0.50
ACGTcount: A:0.13, C:0.18, G:0.28, T:0.41
Consensus pattern (26 bp):
GGGTATTTTGGTCATTTTCGCACCAG
Found at i:14187 original size:27 final size:26
Alignment explanation
Indices: 14108--14204 Score: 88
Period size: 27 Copynumber: 3.6 Consensus size: 26
14098 GTCCAAGGGT
** * *
14108 ATTTTGGTCATTTTCGCGCCCAGGGGT
1 ATTTTGGTCATTTTTAC-ACCAGGGGC
**
14135 ATTTTGGTCATTTTCGCACCAGGGGC
1 ATTTTGGTCATTTTTACACCAGGGGC
14161 ATTTTGGTCATTTTTACACTC-GAGGGC
1 ATTTTGGTCATTTTTACAC-CAG-GGGC
*
14188 ATTTTAGTCATTCTTTA
1 ATTTTGGTCATT-TTTA
14205 AGTTCACCTT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
26 25 0.40
27 33 0.53
28 4 0.06
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (26 bp):
ATTTTGGTCATTTTTACACCAGGGGC
Found at i:14767 original size:23 final size:22
Alignment explanation
Indices: 14724--14772 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
14714 CAAAAATAAG
14724 AATACAAAAAATATAATAATAGT
1 AATACAAAAAATATAATAATA-T
* *
14747 AATACAAGAATTA-AATAAATAT
1 AATACAAAAAATATAAT-AATAT
14769 AATA
1 AATA
14773 ATGCAGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (22 bp):
AATACAAAAAATATAATAATAT
Found at i:20906 original size:16 final size:17
Alignment explanation
Indices: 20869--20905 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
20859 AAGAGGTCGC
20869 AAAAAGAAAGAAAAAGA
1 AAAAAGAAAGAAAAAGA
20886 AAAAAG-AAG-AAAAGA
1 AAAAAGAAAGAAAAAGA
20901 AAAAA
1 AAAAA
20906 ACTAGGCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 3 0.15
17 6 0.30
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAGA
Found at i:20906 original size:17 final size:17
Alignment explanation
Indices: 20869--20906 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
20859 AAGAGGTCGC
*
20869 AAAAAGAAAGAAAAAGA
1 AAAAAGAAAGAAAAAAA
*
20886 AAAAAG-AAGAAAAGAA
1 AAAAAGAAAGAAAAAAA
20902 AAAAA
1 AAAAA
20907 CTAGGCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAA
Found at i:21053 original size:26 final size:26
Alignment explanation
Indices: 21024--21108 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
21014 TTGAAAACCT
21024 GAAAAAGGCGGCTCAAGTGAAGGATG
1 GAAAAAGGCGGCTCAAGTGAAGGATG
* ** * **
21050 G-AAAAGGAGGAACTTGAGTTGAA-AACCC
1 GAAAAAGGCGG--CTCAAG-TGAAGGA-TG
21078 GAAAAAGGCGGCTCAAGTGAAGGATG
1 GAAAAAGGCGGCTCAAGTGAAGGATG
21104 GAAAA
1 GAAAA
21109 GGAGGAACTT
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
25 8 0.20
26 10 0.24
27 10 0.24
28 5 0.12
29 8 0.20
ACGTcount: A:0.42, C:0.12, G:0.34, T:0.12
Consensus pattern (26 bp):
GAAAAAGGCGGCTCAAGTGAAGGATG
Found at i:21089 original size:54 final size:54
Alignment explanation
Indices: 21007--21160 Score: 238
Period size: 54 Copynumber: 2.9 Consensus size: 54
20997 ATCGGGGGTC
*
21007 ACTTGAGTTGAAAACCTGAAAAAGGCGGCTCAAGTGAAGGATGGAAAAGGAGGA
1 ACTTGAGTTGAAAACCCGAAAAAGGCGGCTCAAGTGAAGGATGGAAAAGGAGGA
21061 ACTTGAGTTGAAAACCCGAAAAAGGCGGCTCAAGTGAAGGATGGAAAAGGAGGA
1 ACTTGAGTTGAAAACCCGAAAAAGGCGGCTCAAGTGAAGGATGGAAAAGGAGGA
** * * *
21115 ACTTGAACTGAAAACCCGAAAAGGGCGACTCAGGTGGAA-GATGGAA
1 ACTTGAGTTGAAAACCCGAAAAAGGCGGCTCAAGT-GAAGGATGGAA
21161 GGACATAGTT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 90 0.97
55 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.32, T:0.14
Consensus pattern (54 bp):
ACTTGAGTTGAAAACCCGAAAAAGGCGGCTCAAGTGAAGGATGGAAAAGGAGGA
Found at i:24791 original size:19 final size:19
Alignment explanation
Indices: 24769--24811 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
24759 AATCCTTATT
*
24769 TAATATTTCTTTGAATAGA
1 TAATATTTCTTTGAATAAA
* *
24788 TAATTTTTTTTTGAATAAA
1 TAATATTTCTTTGAATAAA
24807 TAATA
1 TAATA
24812 ATCTTTTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (19 bp):
TAATATTTCTTTGAATAAA
Found at i:26106 original size:38 final size:38
Alignment explanation
Indices: 26046--26250 Score: 207
Period size: 38 Copynumber: 5.3 Consensus size: 38
26036 ACCCCAATAA
*
26046 AATTAAGAGTCAAAGTAATAGTAATCAGT-GAATTAAGT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAA-T
* * * * *
26084 AATTGAGAATCAAAGTAATAGTAATAATTAAAATTGAT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAAT
* *
26122 AATTAAGAGTCAAAGTAGTAGTAATCAGTAAAATTGAT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAAT
* * * * *
26160 AATTAAGAGTCAAAGCAAGAATGATCAGTAAAATTTAT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAAT
* * * *
26198 AATCAAGAGTCAAGGTAAAAATAGTAATCAGT-AAATCAGT
1 AATTAAGAGTCAAAGT---AATAGTAATCAGTAAAATTAAT
26238 AATTAAGAGTCAA
1 AATTAAGAGTCAA
26251 GGGATTAATC
Statistics
Matches: 136, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
38 104 0.76
39 5 0.04
40 17 0.12
41 10 0.07
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (38 bp):
AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAAT
Found at i:26515 original size:25 final size:26
Alignment explanation
Indices: 26465--26517 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
26455 AGTAAAAAGG
26465 ATATTAAGAGTAAAAAAAATGATATTAA
1 ATATTAAGAGT--AAAAAATGATATTAA
*
26493 ATATTAAGAGT-AAAAATGGTATTAA
1 ATATTAAGAGTAAAAAATGATATTAA
26518 GAAAAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 13 0.54
28 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (26 bp):
ATATTAAGAGTAAAAAATGATATTAA
Found at i:26517 original size:18 final size:18
Alignment explanation
Indices: 26494--26586 Score: 56
Period size: 16 Copynumber: 5.4 Consensus size: 18
26484 TGATATTAAA
26494 TATTAAGAGTAAAAATGG
1 TATTAAGAGTAAAAATGG
*
26512 TATTAAGA--AAAAATAG
1 TATTAAGAGTAAAAATGG
** **
26528 -AAAAATG-GT-ATCATGG
1 TATTAA-GAGTAAAAATGG
*
26544 T-TAAAGAGTAAAAA-GG
1 TATTAAGAGTAAAAATGG
26560 ATATTAAGAGTAAAAAATGG
1 -TATTAAGAGT-AAAAATGG
26580 TATTAAG
1 TATTAAG
26587 CAAAAAAGAG
Statistics
Matches: 55, Mismatches: 10, Indels: 19
0.65 0.12 0.23
Matches are distributed among these distances:
15 4 0.07
16 19 0.35
17 3 0.05
18 15 0.27
19 12 0.22
20 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.20, T:0.26
Consensus pattern (18 bp):
TATTAAGAGTAAAAATGG
Found at i:26575 original size:19 final size:18
Alignment explanation
Indices: 26547--26586 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
26537 ATCATGGTTA
26547 AAGAGTAAAAA-GGATATT
1 AAGAGTAAAAATGG-TATT
26565 AAGAGTAAAAAATGGTATT
1 AAGAGT-AAAAATGGTATT
26584 AAG
1 AAG
26587 CAAAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 12 0.60
20 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (18 bp):
AAGAGTAAAAATGGTATT
Found at i:26608 original size:96 final size:95
Alignment explanation
Indices: 26417--26802 Score: 510
Period size: 95 Copynumber: 4.0 Consensus size: 95
26407 AGGAGTAAAA
26417 AAGAAGAAGAAGAGAAAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAGTAAAAAA
1 AAGAA-AA-AAGAG-AAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAGT-AAAAA
*
26482 AATGATATTAAATATTAAGAGTAAAAATGGTATT
62 AATGGTATTAAATATTAAGAGTAAAAATGGTATT
* *
26516 AAGAAAAAATAGAAAAATGGTATCATGGT-TAAAGAGTAAAAAGGATATTAAGAGT-AAAAAATG
1 AAGAAAAAAGAGAAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAGTAAAAAAATG
**
26579 GTATTAAGCA-AAAAAGAGTAAAAAAATGGTATT
66 GTATTAA--ATATTAAGAGT--AAAAATGGTATT
* * *
26612 AAGTAAAAAGAGAAAAAAATGGTATCATGGTAAAGAGAGTAAAAAGGATATTAAGAAT-AAAAAA
1 AAG-AAAAA-AGAGAAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAGTAAAAAAA
*
26676 TGGTATTAAATATTATGAGTAAAAATGGTATT
64 TGGTATTAAATATTAAGAGTAAAAATGGTATT
* * *
26708 AAGTAAAAAGAGAAAAAATGGTATCATGGTAAAAAGGGTAAAAAGGGTATTAAAGAGTAAAAAAA
1 AAGAAAAAAGAG-AAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATT-AAGAGTAAAAAAA
*
26773 TGGTATTAAGTATTAAGAGTAAAAAATGGT
64 TGGTATTAAATATTAAGAGT-AAAAATGGT
26803 GGAAAATGTT
Statistics
Matches: 254, Mismatches: 21, Indels: 25
0.85 0.07 0.08
Matches are distributed among these distances:
93 14 0.06
94 10 0.04
95 65 0.26
96 52 0.20
97 34 0.13
98 36 0.14
99 43 0.17
ACGTcount: A:0.55, C:0.01, G:0.21, T:0.23
Consensus pattern (95 bp):
AAGAAAAAAGAGAAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAGTAAAAAAATG
GTATTAAATATTAAGAGTAAAAATGGTATT
Found at i:26610 original size:28 final size:27
Alignment explanation
Indices: 26565--26636 Score: 112
Period size: 28 Copynumber: 2.7 Consensus size: 27
26555 AAAGGATATT
26565 AAGAGT-AAAAAATGGTATTAAGCAAAA
1 AAGAGTAAAAAAATGGTATTAAG-AAAA
*
26592 AAGAGTAAAAAAATGGTATTAAGTAAA
1 AAGAGTAAAAAAATGGTATTAAGAAAA
26619 AAGAG-AAAAAAATGGTAT
1 AAGAGTAAAAAAATGGTAT
26637 CATGGTAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
26 13 0.30
27 14 0.33
28 16 0.37
ACGTcount: A:0.60, C:0.01, G:0.19, T:0.19
Consensus pattern (27 bp):
AAGAGTAAAAAAATGGTATTAAGAAAA
Found at i:26619 original size:26 final size:25
Alignment explanation
Indices: 26565--26802 Score: 139
Period size: 26 Copynumber: 9.6 Consensus size: 25
26555 AAAGGATATT
*
26565 AAGAGTAAAAAATGGTATTAAGCAAAA
1 AAGAGTAAAAAATGGTATTAAG--TAA
26592 AAGAGTAAAAAAATGGTATTAAGTAAA
1 AAGAGT-AAAAAATGGTATTAAGT-AA
* * *
26619 AAGAGAAAAAAATGGTATCATGGTAA
1 AAGAGTAAAAAATGGTATTA-AGTAA
26645 AGAGAGT-AAAAA-GGATATTAAG---
1 A-AGAGTAAAAAATGG-TATTAAGTAA
* *
26667 -A-A-TAAAAAATGGTATTAAATATT
1 AAGAGTAAAAAATGGTATTAAGTA-A
*
26690 ATGAGT-AAAAATGGTATTAAGTAAA
1 AAGAGTAAAAAATGGTATTAAGT-AA
* *
26715 AAGAG-AAAAAATGGTATCATGGTAAA
1 AAGAGTAAAAAATGGTATTA-AGT-AA
* *
26741 AAGGGT-AAAAAGGGTA-T---T-A
1 AAGAGTAAAAAATGGTATTAAGTAA
*
26760 AAGAGTAAAAAAATGGTATTAAGTATT
1 AAGAGT-AAAAAATGGTATTAAGTA-A
26787 AAGAGTAAAAAATGGT
1 AAGAGTAAAAAATGGT
26803 GGAAAATGTT
Statistics
Matches: 165, Mismatches: 20, Indels: 53
0.69 0.08 0.22
Matches are distributed among these distances:
18 1 0.01
19 18 0.11
20 3 0.02
21 10 0.06
22 1 0.01
25 36 0.22
26 55 0.33
27 25 0.15
28 16 0.10
ACGTcount: A:0.55, C:0.01, G:0.21, T:0.23
Consensus pattern (25 bp):
AAGAGTAAAAAATGGTATTAAGTAA
Found at i:26655 original size:28 final size:27
Alignment explanation
Indices: 26565--26656 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
26555 AAAGGATATT
**
26565 AAGAGT-AAAAAATGGTATTAAGCAAAA
1 AAGAGTAAAAAAATGGTATT-AGGTAAA
*
26592 AAGAGTAAAAAAATGGTATTAAGTAAA
1 AAGAGTAAAAAAATGGTATTAGGTAAA
*
26619 AAGAG-AAAAAAATGGTATCATGGTAAA
1 AAGAGTAAAAAAATGGTATTA-GGTAAA
*
26646 GAGAGTAAAAA
1 AAGAGTAAAAA
26657 GGATATTAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
26 14 0.25
27 24 0.43
28 18 0.32
ACGTcount: A:0.59, C:0.02, G:0.21, T:0.18
Consensus pattern (27 bp):
AAGAGTAAAAAAATGGTATTAGGTAAA
Found at i:26751 original size:194 final size:194
Alignment explanation
Indices: 26426--26782 Score: 576
Period size: 194 Copynumber: 1.8 Consensus size: 194
26416 AAAGAAGAAG
26426 AAGAGAAAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAGTAAAAAAAATGATATT
1 AAGAGAAAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAG-AAAAAAAATGATATT
* *
26491 AAATATTAAGAGTAAAAATGGTATTAAGAAAAAATAGAAAAATGGTATCATGGTTAAAGAGTAAA
65 AAATATTAAGAGTAAAAATGGTATTAAGAAAAAAGAGAAAAATGGTATCATGGTAAAAGAGTAAA
26556 AAGGATATT-AAGAGT-AAAAAATGGTATTAAGCAAAAAAGAGTAAAAAAATGGTATTAAGTAAA
130 AAGGATATTAAAGAGTAAAAAAATGGTATTAAGCAAAAAAGAGTAAAAAAATGGTATTAAGTAAA
* * *
26619 AAGAGAAAAAAATGGTATCATGGTAAAGAGAGTAAAAAGGATATTAAGA-ATAAAAAATGGTATT
1 AAGAG-AAAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAGAAAAAAAATGATATT
* * *
26683 AAATATTATGAGTAAAAATGGTATTAAGTAAAAAGAGAAAAAATGGTATCATGGTAAAAAGGGTA
65 AAATATTAAGAGTAAAAATGGTATTAAGAAAAAAGAG-AAAAATGGTATCATGGT-AAAAGAGTA
*
26748 AAAAGGGTATTAAAGAGTAAAAAAATGGTATTAAG
128 AAAAGGATATTAAAGAGTAAAAAAATGGTATTAAG
26783 TATTAAGAGT
Statistics
Matches: 150, Mismatches: 9, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
192 47 0.31
193 22 0.15
194 59 0.39
195 6 0.04
196 16 0.11
ACGTcount: A:0.55, C:0.01, G:0.20, T:0.23
Consensus pattern (194 bp):
AAGAGAAAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAGAAAAAAAATGATATTA
AATATTAAGAGTAAAAATGGTATTAAGAAAAAAGAGAAAAATGGTATCATGGTAAAAGAGTAAAA
AGGATATTAAAGAGTAAAAAAATGGTATTAAGCAAAAAAGAGTAAAAAAATGGTATTAAGTAAA
Found at i:34354 original size:13 final size:14
Alignment explanation
Indices: 34336--34366 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
34326 TTTCTTGCTT
34336 TTAAAAAAAA-TAA
1 TTAAAAAAAATTAA
34349 TTAAAAAAAATTAA
1 TTAAAAAAAATTAA
34363 TTAA
1 TTAA
34367 TCCATTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TTAAAAAAAATTAA
Found at i:35452 original size:21 final size:21
Alignment explanation
Indices: 35426--35474 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
35416 GCACTGGAGG
* * *
35426 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
35447 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
35468 ACATGGG
1 ACATGGG
35475 CCCCCAGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:40049 original size:21 final size:22
Alignment explanation
Indices: 40025--40384 Score: 115
Period size: 21 Copynumber: 16.5 Consensus size: 22
40015 ATCACTATTT
40025 TACTGATTA-TTCTTTACTTTG
1 TACTGATTACTTCTTTACTTTG
40046 TACTGATTACTAT-TTTACTCTTG
1 TACTGATTACT-TCTTTACT-TTG
*
40069 T--TGATTACCTTC-TTACTTTT
1 TACTGATTA-CTTCTTTACTTTG
* *
40089 TACTGATTACCAT-TTTACTCTTT
1 TACTGATTA-CTTCTTTACT-TTG
* * *
40112 TACTGATTACTATTTTCTGCTCCTTTTT
1 TACTGATTAC----TTCT-TTAC-TTTG
*
40140 TACTGATTAC-TCTTTTACTTTT
1 TACTGATTACTTC-TTTACTTTG
* * *
40162 TACTGATTGGC-T-TTTGCTTTT
1 TACTGATT-ACTTCTTTACTTTG
*
40183 TACTGATTACCT-TTTACTTCT-
1 TACTGATTACTTCTTTACTT-TG
*
40204 TACTAATTAGCTT-TTTACTCTT-
1 TACTGATTA-CTTCTTTACT-TTG
* *
40226 TACTGATCACCTT-TTTACTCT-
1 TACTGATTA-CTTCTTTACTTTG
* *
40247 TACTGATTTCCT-TTTACTTCT-
1 TACTGATTACTTCTTTACTT-TG
*
40268 TACTGATTACTAT-TTTACTCT-
1 TACTGATTACT-TCTTTACTTTG
* * *
40289 TATTGATTAC-TATTTACTTTT
1 TACTGATTACTTCTTTACTTTG
*
40310 TACTGACTACTAT-TTTACTCTTG
1 TACTGATTACT-TCTTTACT-TTG
*
40333 T--TGATTACCTTC-TTACTTTT
1 TACTGATTA-CTTCTTTACTTTG
40353 TACTGATTACTAT-TTTACTCTT-
1 TACTGATTACT-TCTTTACT-TTG
*
40375 TACTAATTAC
1 TACTGATTAC
40385 CATTTTACCC
Statistics
Matches: 271, Mismatches: 32, Indels: 71
0.72 0.09 0.19
Matches are distributed among these distances:
19 1 0.00
20 22 0.08
21 101 0.37
22 98 0.36
23 30 0.11
24 1 0.00
26 1 0.00
27 1 0.00
28 15 0.06
29 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (22 bp):
TACTGATTACTTCTTTACTTTG
Found at i:40095 original size:43 final size:42
Alignment explanation
Indices: 40037--40392 Score: 304
Period size: 43 Copynumber: 8.1 Consensus size: 42
40027 CTGATTATTC
* *
40037 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCT
* * *
40079 TCTTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTACTATTT
1 T-TTACTTTTTACTGATTACTATTTTACTC--TTATTGATTAC---CT
* * * * **
40127 TCTGCTCCTTTTTTACTGATTACTCTTTTACTTTTTACTGATTGGCT
1 T-T--TAC-TTTTTACTGATTACTATTTTAC-TCTTATTGATTACCT
* * * * *
40174 TTTGCTTTTTACTGATTAC-CTTTTACTTCTTACTAATTAGCTT
1 TTTACTTTTTACTGATTACTATTTTAC-TCTTATTGATTA-CCT
* * * *
40217 TTTACTCTTTACTGATCACCT-TTTTACTCTTACTGATTTCCT
1 TTTACTTTTTACTGATTA-CTATTTTACTCTTATTGATTACCT
*
40259 TTTACTTCTTACTGATTACTATTTTACTCTTATTGATTA-CT
1 TTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCT
* *
40300 ATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCT
* *
40343 TCTTACTTTTTACTGATTACTATTTTACTCTTTACTAATTACCAT
1 T-TTACTTTTTACTGATTACTATTTTACTC-TTATTGATTACC-T
40388 TTTAC
1 TTTAC
40393 CCTTTCAAAT
Statistics
Matches: 259, Mismatches: 36, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
41 4 0.02
42 88 0.34
43 95 0.37
44 22 0.08
45 11 0.04
46 1 0.00
47 2 0.01
48 4 0.02
50 11 0.04
51 20 0.08
52 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCT
Found at i:40095 original size:64 final size:64
Alignment explanation
Indices: 40022--40424 Score: 252
Period size: 64 Copynumber: 6.2 Consensus size: 64
40012 ACCATCACTA
* * *
40022 TTTTACTGATTATTCTTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCTTCTTACT
1 TTTTACTGATTATTCTTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCTTTTTACT
* * *
40086 TTTTACTGATTA-CCATTTTACTCTTTTACTGATTACTATTTTCTGCTCCTTTTTTACTGATTA-
1 TTTTACTGATTATTC--TTTACT-TTTTACTGATTACTA-TTT-TACT-C----TTATTGATTAC
40149 CTCTTTTACT
56 CT-TTTTACT
** * * * * *
40159 TTTTACTGATT-GGCTTTTGCTTTTTACTGATTAC-CTTTTACTTCTTACTAATTAGCTTTTTAC
1 TTTTACTGATTATTC-TTTACTTTTTACTGATTACTATTTTAC-TCTTATTGATTACCTTTTTAC
40222 T
64 T
* * * * * *
40223 CTTTACTGATCACCTT-TTTAC-TCTTACTGATTTC-CTTTTACTTCTTACTGATTA-CTATTTT
1 TTTTACTGATTA--TTCTTTACTTTTTACTGATTACTATTTTAC-TCTTATTGATTACCT-TTTT
40284 AC-
62 ACT
* * * * * * *
40286 TCTTATTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTCTTACT
1 TTTTACTGATTATTCTTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCTTTTTACT
* * * * ** * *
40350 TTTTACTGATTACTAT-TTTACTCTTTACTAATTACCATTTTACCCTT-TCAAATATCTTTTTAC
1 TTTTACTGATTA-T-TCTTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCTTTTTAC
40413 T
64 T
40414 TTTTACTGATT
1 TTTTACTGATT
40425 GCATGCTATT
Statistics
Matches: 270, Mismatches: 44, Indels: 50
0.74 0.12 0.14
Matches are distributed among these distances:
61 1 0.00
62 5 0.02
63 36 0.13
64 114 0.42
65 38 0.14
66 15 0.06
67 3 0.01
68 6 0.02
69 5 0.02
71 13 0.05
72 8 0.03
73 26 0.10
ACGTcount: A:0.20, C:0.19, G:0.06, T:0.55
Consensus pattern (64 bp):
TTTTACTGATTATTCTTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCTTTTTACT
Found at i:40121 original size:15 final size:15
Alignment explanation
Indices: 40103--40158 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
40093 GATTACCATT
40103 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
40118 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
40131 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
40146 TTACTCTTTTACT
1 TTACTCTTTTACT
40159 TTTTACTGAT
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:0.16, C:0.21, G:0.05, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:40217 original size:42 final size:42
Alignment explanation
Indices: 40136--40392 Score: 268
Period size: 42 Copynumber: 6.0 Consensus size: 42
40126 TTCTGCTCCT
* * ** *
40136 TTTTTACTGATTACTCTTTTACTTTTTACTGATTGGCTTTTGC
1 TTTTTACTGATTACTATTTTAC-TCTTACTGATTACCTTTTAC
* * *
40179 TTTTTACTGATTAC-CTTTTACTTCTTACTAATTAGCTTTTTAC
1 TTTTTACTGATTACTATTTTAC-TCTTACTGATTA-CCTTTTAC
* * *
40222 TCTTTACTGATCACCT-TTTTACTCTTACTGATTTCCTTTTAC
1 TTTTTACTGATTA-CTATTTTACTCTTACTGATTACCTTTTAC
* *
40264 TTCTTACTGATTACTATTTTACTCTTATTGATTA-CTATTTAC
1 TTTTTACTGATTACTATTTTACTCTTACTGATTACCT-TTTAC
* **
40306 TTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTCTTAC
1 TTTTTACTGATTACTATTTTACTCTTACTGATTACCTT-TTAC
*
40349 TTTTTACTGATTACTATTTTACTCTTTACTAATTACCATTTTAC
1 TTTTTACTGATTACTATTTTACTC-TTACTGATTACC-TTTTAC
40393 CCTTTCAAAT
Statistics
Matches: 182, Mismatches: 23, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.02
42 87 0.48
43 69 0.38
44 20 0.11
45 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.06, T:0.55
Consensus pattern (42 bp):
TTTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTAC
Found at i:41734 original size:49 final size:49
Alignment explanation
Indices: 41526--41781 Score: 307
Period size: 50 Copynumber: 5.1 Consensus size: 49
41516 AACTTTAATT
* * * **
41526 CAAAGATGACA-TTTTATTTACAAATTACTTTTAAAAAATCAATCTTTTATT
1 CAAAGATGACATTTTTACTTACTAATTAC---TAAAAATTCAATCTTTTACC
* * * **
41577 CAAAGGTGACATTTTTACTTATTAATTACTAGATAATTCAATCTTTTATT
1 CAAAGATGACATTTTTACTTACTAATTACTA-AAAATTCAATCTTTTACC
* * * * *
41627 CAAAGGTGGCACTTTTACTTATTAATTACTAAATAATTTAATCTTTTACC
1 CAAAGATGACATTTTTACTTACTAATTACTAAA-AATTCAATCTTTTACC
41677 CAAAGATGACATTTTTACTTACTAATTACTAAAAATTCAATCTTTTACC
1 CAAAGATGACATTTTTACTTACTAATTACTAAAAATTCAATCTTTTACC
41726 CAAAGATGACATTTTTACTTACTAATTACTAAAAATTCAATCTTGTTACAC
1 CAAAGATGACATTTTTACTTACTAATTACTAAAAATTCAATCTT-TTAC-C
41777 CAAAG
1 CAAAG
41782 GTCGGATCTT
Statistics
Matches: 183, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
49 62 0.34
50 91 0.50
51 16 0.09
52 14 0.08
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (49 bp):
CAAAGATGACATTTTTACTTACTAATTACTAAAAATTCAATCTTTTACC
Found at i:41757 original size:99 final size:98
Alignment explanation
Indices: 41526--41781 Score: 307
Period size: 99 Copynumber: 2.5 Consensus size: 98
41516 AACTTTAATT
* * * ** *
41526 CAAAGATGACATTTTATTTACAAATTACTTTTAAAAAATCAATCTTTTATTCAAAGGTGACATTT
1 CAAAGATGACATTTTACTTACTAATTAC---TAAAAATTCAATCTTTTACCCAAAGATGACATTT
* * **
41591 TTACTTATTAATTACTAGATAATTCAATCTTTTATT
63 TTACTTACTAATTACTAGAAAATTCAATCTTTTACC
* * * *
41627 CAAAGGTGGCACTTTTACTTATTAATTACTAAATAATTTAATCTTTTACCCAAAGATGACATTTT
1 CAAAGATGACA-TTTTACTTACTAATTACTAAA-AATTCAATCTTTTACCCAAAGATGACATTTT
41692 TACTTACTAATTACTA-AAAATTCAATCTTTTACC
64 TACTTACTAATTACTAGAAAATTCAATCTTTTACC
41726 CAAAGATGACATTTTTACTTACTAATTACTAAAAATTCAATCTTGTTACACCAAAG
1 CAAAGATGACA-TTTTACTTACTAATTACTAAAAATTCAATCTT-TTAC-CCAAAG
41782 GTCGGATCTT
Statistics
Matches: 132, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
98 10 0.08
99 52 0.39
100 47 0.36
101 9 0.07
102 14 0.11
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (98 bp):
CAAAGATGACATTTTACTTACTAATTACTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTA
CTTACTAATTACTAGAAAATTCAATCTTTTACC
Found at i:44078 original size:50 final size:50
Alignment explanation
Indices: 44002--44109 Score: 209
Period size: 50 Copynumber: 2.2 Consensus size: 50
43992 TGATTCCAAT
44002 GAGA-AATACCCTTTATGTTGTAGCCTAAAAGACCTGTAAACAAAAACTA
1 GAGAGAATACCCTTTATGTTGTAGCCTAAAAGACCTGTAAACAAAAACTA
44051 GAGAGAATACCCTTTATGTTGTAGCCTAAAAGACCTGTAAACAAAAACTA
1 GAGAGAATACCCTTTATGTTGTAGCCTAAAAGACCTGTAAACAAAAACTA
44101 GAGAGAATA
1 GAGAGAATA
44110 GTGAATATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 4 0.07
50 54 0.93
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (50 bp):
GAGAGAATACCCTTTATGTTGTAGCCTAAAAGACCTGTAAACAAAAACTA
Found at i:44557 original size:27 final size:27
Alignment explanation
Indices: 44499--44571 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
44489 AAGTGAACTT
* *
44499 AAAATGACCCAAGATACCCCTAAATGCC
1 AAAATGA-CCAAAATACCCCTAAATGCA
* * **
44527 AAAATGACCTAAATGCCCCTAGGTGCA
1 AAAATGACCAAAATACCCCTAAATGCA
44554 AAAATGACCAAAATACCC
1 AAAATGACCAAAATACCC
44572 TTGGACGACC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
27 30 0.81
28 7 0.19
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (27 bp):
AAAATGACCAAAATACCCCTAAATGCA
Done.