Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014278.1 Corchorus olitorius cultivar O-4 contig14311, 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: 148894
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:43 original size:33 final size:33
Alignment explanation
Indices: 1--75 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
* *
1 AGGGCGGCATGCCCATGGTCGTGTCGTCCTCAC
1 AGGGCGGCATGCCCATGGTCGTGCCGTACTCAC
34 AGGGCGGCATGCCCATGGTCGTGCCGTACTCAC
1 AGGGCGGCATGCCCATGGTCGTGCCGTACTCAC
67 AGGGCGGCA
1 AGGGCGGCA
76 CCGCGTCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.15, C:0.32, G:0.36, T:0.17
Consensus pattern (33 bp):
AGGGCGGCATGCCCATGGTCGTGCCGTACTCAC
Found at i:239 original size:33 final size:33
Alignment explanation
Indices: 202--282 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
192 CCTCTGGGGA
* **
202 CGGCACGACCATGGGCATGCCGTCCTCCTAGGG
1 CGGCATGACCATGGGCATGCCACCCTCCTAGGG
235 CGGCATGACCATGGGCATGCCACCCTCCTAGGG
1 CGGCATGACCATGGGCATGCCACCCTCCTAGGG
268 CGGCATGACCATGGG
1 CGGCATGACCATGGG
283 AGTGCCGCCC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.17, C:0.35, G:0.33, T:0.15
Consensus pattern (33 bp):
CGGCATGACCATGGGCATGCCACCCTCCTAGGG
Found at i:305 original size:33 final size:33
Alignment explanation
Indices: 199--293 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 33
189 CATCCTCTGG
* *
199 GGACGGCACGACCATGGGCATGCCGTCCTCCTA
1 GGACGGCATGACCATGGGCATGCCGCCCTCCTA
* *
232 GGGCGGCATGACCATGGGCATGCCACCCTCCTA
1 GGACGGCATGACCATGGGCATGCCGCCCTCCTA
*
265 GGGCGGCATGACCATGGG-AGTGCCGCCCT
1 GGACGGCATGACCATGGGCA-TGCCGCCCT
294 TGGAGGACGG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 1 0.02
33 55 0.98
ACGTcount: A:0.17, C:0.35, G:0.34, T:0.15
Consensus pattern (33 bp):
GGACGGCATGACCATGGGCATGCCGCCCTCCTA
Found at i:3585 original size:21 final size:21
Alignment explanation
Indices: 3559--3602 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3549 GTAATATATA
*
3559 ATTTCATCCCATCTTTGTTTG
1 ATTTCATCCCATCGTTGTTTG
3580 ATTTCATCCCATCGTTGTTTG
1 ATTTCATCCCATCGTTGTTTG
3601 AT
1 AT
3603 AAAACATACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.23, G:0.11, T:0.50
Consensus pattern (21 bp):
ATTTCATCCCATCGTTGTTTG
Found at i:3663 original size:12 final size:12
Alignment explanation
Indices: 3633--3663 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3623 CTTGGCAATC
*
3633 CGTGTTCCGTGT
1 CGTGTTTCGTGT
3645 CGTGTTTCGTGT
1 CGTGTTTCGTGT
3657 CGTGTTT
1 CGTGTTT
3664 ACATAGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.19, G:0.32, T:0.48
Consensus pattern (12 bp):
CGTGTTTCGTGT
Found at i:3782 original size:5 final size:5
Alignment explanation
Indices: 3772--3798 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3762 GTATACACGG
3772 GACAC GACAC GACAC GACAC GACAC GA
1 GACAC GACAC GACAC GACAC GACAC GA
3799 TTAAGCCGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.37, G:0.22, T:0.00
Consensus pattern (5 bp):
GACAC
Found at i:3885 original size:2 final size:2
Alignment explanation
Indices: 3878--3907 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3868 TTAACTAAAC
3878 TA 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 TA
3908 ATTAGAGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4249 original size:42 final size:43
Alignment explanation
Indices: 4178--4260 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
4168 CTTAAACGTG
* *
4178 TTAATCGTGTCTTGACACGATTAGGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTAGAACACGAAACACGATAATC
*
4221 TTAATCGTGTC-CGACACGATTCA-AACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATT-AGAACACGAAACACGATAA
4261 GTCAAACACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 24 0.67
43 12 0.33
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTAGAACACGAAACACGATAATC
Found at i:4256 original size:18 final size:19
Alignment explanation
Indices: 4233--4277 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
4223 AATCGTGTCC
4233 GACACGAT-TCAAACACGA
1 GACACGATATCAAACACGA
4251 GACACGATAAGTCAAACACGA
1 GACACGAT-A-TCAAACACGA
4272 -ACACGA
1 GACACGA
4278 CTAAACGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
20 6 0.25
21 10 0.42
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
GACACGATATCAAACACGA
Found at i:12521 original size:39 final size:37
Alignment explanation
Indices: 12463--12547 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 37
12453 GGCTGTGCAT
** *
12463 AGTGGACCCGTACCTCAGGGGGTTAAACAGATGGTAAAG
1 AGTGGACCCACACCACA-GGGGTTAAACAGATGGT-AAG
* *
12502 AGTGGACCCACACCACAGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCACACCACAGGGGTTAAACAGATGGTAAG
12539 AGTGGACCC
1 AGTGGACCC
12548 GTGCCTCAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
37 12 0.29
38 15 0.37
39 14 0.34
ACGTcount: A:0.29, C:0.21, G:0.32, T:0.18
Consensus pattern (37 bp):
AGTGGACCCACACCACAGGGGTTAAACAGATGGTAAG
Found at i:12558 original size:37 final size:38
Alignment explanation
Indices: 12463--12570 Score: 139
Period size: 37 Copynumber: 2.9 Consensus size: 38
12453 GGCTGTGCAT
* *
12463 AGTGGACCCGTACCTCAGGGGGTTAAACAGATGGTAAAG
1 AGTGGACCCGTACCTCA-GGGGTTAAACTGTTGGTAAAG
** *
12502 AGTGGACCCACACCACAGGGGTTAAACTGTTGGT-AAG
1 AGTGGACCCGTACCTCAGGGGTTAAACTGTTGGTAAAG
*
12539 AGTGGACCCGTGCCTCAGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGTTAAACTGTTGG
12571 CTAGACTCGA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
36 9 0.15
37 22 0.37
38 15 0.25
39 14 0.23
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.20
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGTTAAACTGTTGGTAAAG
Found at i:29792 original size:46 final size:46
Alignment explanation
Indices: 29725--29816 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
29715 TTTCTAAACA
29725 ATAGAAATTCAAAATACTCTAGATGGTATTAACCATGACAGGAAAT
1 ATAGAAATTCAAAATACTCTAGATGGTATTAACCATGACAGGAAAT
29771 ATAGAAATTCAAAATACTCTAGATGGTATTAACCATGACAGGAAAT
1 ATAGAAATTCAAAATACTCTAGATGGTATTAACCATGACAGGAAAT
29817 TGGAGACCTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (46 bp):
ATAGAAATTCAAAATACTCTAGATGGTATTAACCATGACAGGAAAT
Found at i:33548 original size:8 final size:8
Alignment explanation
Indices: 33535--33585 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 8
33525 TCCATTCTTT
33535 TTTTTTTC
1 TTTTTTTC
33543 TTTTTTTTC
1 -TTTTTTTC
33552 TTTTTTTTC
1 -TTTTTTTC
33561 TTTTTTT-
1 TTTTTTTC
33568 TTTACTTTTC
1 TTT--TTTTC
*
33578 TATTTTTC
1 TTTTTTTC
33586 ACTATAAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
7 3 0.08
8 12 0.32
9 21 0.55
10 2 0.05
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTC
Found at i:33552 original size:20 final size:20
Alignment explanation
Indices: 33529--33576 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
33519 CTTCATTCCA
33529 TTCTTTTTTTT-TTCTTTTTT
1 TTCTTTTTTTTCTT-TTTTTT
33549 TTCTTTTTTTTCTTTTTTTT
1 TTCTTTTTTTTCTTTTTTTT
33569 TTACTTTT
1 TT-CTTTT
33577 CTATTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (20 bp):
TTCTTTTTTTTCTTTTTTTT
Found at i:33576 original size:9 final size:9
Alignment explanation
Indices: 33534--33568 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
33524 TTCCATTCTT
33534 TTTTTTTTC
1 TTTTTTTTC
33543 TTTTTTTTC
1 TTTTTTTTC
33552 TTTTTTTTC
1 TTTTTTTTC
33561 TTTTTTTT
1 TTTTTTTT
33569 TTACTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:33583 original size:18 final size:18
Alignment explanation
Indices: 33538--33584 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
33528 ATTCTTTTTT
**
33538 TTTTCTTTTTTTTCTTTT
1 TTTTCTTTTTTTTCTTAC
33556 TTTTCTTTTTTTT-TTAC
1 TTTTCTTTTTTTTCTTAC
33573 TTTTCTATTTTT
1 TTTTCT-TTTTT
33585 CACTATAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTCTTTTTTTTCTTAC
Found at i:33584 original size:1 final size:1
Alignment explanation
Indices: 33532--33570 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
33522 CATTCCATTC
* * *
33532 TTTTTTTTTTCTTTTTTTTCTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33571 ACTTTTCTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:33584 original size:29 final size:29
Alignment explanation
Indices: 33529--33584 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
33519 CTTCATTCCA
* *
33529 TTCTTTTTTTTTTCTTTTTTTTCTTTTTT
1 TTCTTTTTTTTTTCTTTTCTATCTTTTTT
33558 TTCTTTTTTTTTTACTTTTCTAT-TTTT
1 TTCTTTTTTTTTT-CTTTTCTATCTTTT
33585 CACTATAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.86
Consensus pattern (29 bp):
TTCTTTTTTTTTTCTTTTCTATCTTTTTT
Found at i:42470 original size:16 final size:16
Alignment explanation
Indices: 42446--42480 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42436 TGACAGCATC
*
42446 AAATGAAAAATCAAGA
1 AAATAAAAAATCAAGA
*
42462 AAATAAAAAATTAAGA
1 AAATAAAAAATCAAGA
42478 AAA
1 AAA
42481 GAATGCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (16 bp):
AAATAAAAAATCAAGA
Found at i:48839 original size:20 final size:20
Alignment explanation
Indices: 48814--48853 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
48804 AATTACAAAC
48814 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
48834 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
48854 TTGAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:57868 original size:18 final size:20
Alignment explanation
Indices: 57823--57868 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
57813 TCTGATATAC
57823 TGAAAAT-ATATAAATGCTA
1 TGAAAATAATATAAATGCTA
57842 T-AAATATAATA-AAAT-CTA
1 TGAAA-ATAATATAAATGCTA
57860 TGAAAATAA
1 TGAAAATAA
57869 AAACATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 11 0.46
19 10 0.42
20 3 0.12
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (20 bp):
TGAAAATAATATAAATGCTA
Found at i:58065 original size:49 final size:47
Alignment explanation
Indices: 57971--58111 Score: 178
Period size: 49 Copynumber: 3.0 Consensus size: 47
57961 GAGCGTGCTT
* * *
57971 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG
58018 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG
* * *
58067 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGTAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAA
58112 GGATTGCTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
47 23 0.27
48 18 0.21
49 42 0.50
50 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Found at i:60721 original size:3 final size:3
Alignment explanation
Indices: 60715--60741 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
60705 GGAGGAGGAG
60715 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
60742 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:60967 original size:10 final size:10
Alignment explanation
Indices: 60950--60994 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
60940 AAAAGAAAGG
60950 AAAA-AAATA
1 AAAATAAATA
60959 AAAATAAATA
1 AAAATAAATA
*
60969 ATAATAAAT-
1 AAAATAAATA
60978 -AAATAAATA
1 AAAATAAATA
60987 AAAATAAA
1 AAAATAAA
60995 AGGAAAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 7 0.23
9 4 0.13
10 20 0.65
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAATAAATA
Found at i:60983 original size:18 final size:18
Alignment explanation
Indices: 60952--60994 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
60942 AAGAAAGGAA
60952 AAAAAT-AA-AAATAAAT
1 AAAAATAAATAAATAAAT
*
60968 AATAATAAATAAATAAAT
1 AAAAATAAATAAATAAAT
60986 AAAAATAAA
1 AAAAATAAA
60995 AGGAAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 5 0.22
17 2 0.09
18 16 0.70
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAATAAATAAATAAAT
Found at i:63824 original size:8 final size:8
Alignment explanation
Indices: 63813--63838 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
63803 CCAATCATCC
63813 ATTGTTGA
1 ATTGTTGA
63821 ATTGTTGA
1 ATTGTTGA
63829 ATTGTTGA
1 ATTGTTGA
63837 AT
1 AT
63839 CTGATTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (8 bp):
ATTGTTGA
Found at i:65197 original size:38 final size:38
Alignment explanation
Indices: 65146--65235 Score: 144
Period size: 38 Copynumber: 2.4 Consensus size: 38
65136 AATTATTAGT
*
65146 ATCTCTTAAATTTAATTGGCAGATTTTGTGACTAATAA
1 ATCTCTTAAATTTAATTGGCAGATTTTATGACTAATAA
* * *
65184 ATCTCTTAAATTTAATTTGCAGATTTTATGGCTAGTAA
1 ATCTCTTAAATTTAATTGGCAGATTTTATGACTAATAA
65222 ATCTCTTAAATTTA
1 ATCTCTTAAATTTA
65236 GTTAGTCTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (38 bp):
ATCTCTTAAATTTAATTGGCAGATTTTATGACTAATAA
Found at i:65906 original size:37 final size:37
Alignment explanation
Indices: 65865--65936 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
65855 GGGCTTGGAA
65865 CGGTTTTCAGTTTTGGGTTTTCTCTCCTTTTCAGTAT
1 CGGTTTTCAGTTTTGGGTTTTCTCTCCTTTTCAGTAT
65902 CGGTTTTCAGTTTTGGGTTTTCTCTCCTTTTCAGT
1 CGGTTTTCAGTTTTGGGTTTTCTCTCCTTTTCAGT
65937 GTCAGCTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.07, C:0.19, G:0.19, T:0.54
Consensus pattern (37 bp):
CGGTTTTCAGTTTTGGGTTTTCTCTCCTTTTCAGTAT
Found at i:66012 original size:30 final size:31
Alignment explanation
Indices: 65976--66036 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
65966 AATATTTGAT
*
65976 ACATTGTCAGTGCATCAA-TTCTAATTATTA
1 ACATTGTCAATGCATCAATTTCTAATTATTA
66006 ACATTGTCAATGCATCAATTTTCTAATTATT
1 ACATTGTCAATGCATCAA-TTTCTAATTATT
66037 TTAATTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 17 0.61
32 11 0.39
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (31 bp):
ACATTGTCAATGCATCAATTTCTAATTATTA
Found at i:66307 original size:47 final size:47
Alignment explanation
Indices: 66238--66331 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
66228 TGAAAGAGTG
*
66238 GATCATGTTCTTGCACAATGCCTAAAACTTTATTCATTGCTAGTAAA
1 GATCATGTGCTTGCACAATGCCTAAAACTTTATTCATTGCTAGTAAA
66285 GATCATGTGCTTGCACAATGCCTAAAACTTTATTCATTGCTAGTAAA
1 GATCATGTGCTTGCACAATGCCTAAAACTTTATTCATTGCTAGTAAA
66332 TAATCTGATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (47 bp):
GATCATGTGCTTGCACAATGCCTAAAACTTTATTCATTGCTAGTAAA
Found at i:80294 original size:17 final size:18
Alignment explanation
Indices: 80262--80300 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
80252 AACAGAAAAT
80262 ACACAATATAATTGAAGA
1 ACACAATATAATTGAAGA
*
80280 ACACATTAT-ATTGAAGA
1 ACACAATATAATTGAAGA
80297 ACAC
1 ACAC
80301 TTCTTCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.23
Consensus pattern (18 bp):
ACACAATATAATTGAAGA
Found at i:80364 original size:21 final size:22
Alignment explanation
Indices: 80325--80372 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
80315 TGAAGAACAT
80325 AGAACACACTCAATTATAATCGA
1 AGAACACACTCAA-TATAATCGA
*
80348 AGAACACACTCAA-ATAATTGA
1 AGAACACACTCAATATAATCGA
80369 AGAA
1 AGAA
80373 AAAAAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.46
23 13 0.54
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (22 bp):
AGAACACACTCAATATAATCGA
Found at i:80645 original size:39 final size:39
Alignment explanation
Indices: 80591--80672 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
80581 CTTCGGTATC
*
80591 TAAAATTTGATTTAAAACTCTTCTAAGTTAAAGATTAAA
1 TAAAACTTGATTTAAAACTCTTCTAAGTTAAAGATTAAA
* *
80630 TAAAACTTGATTTAAAACTCTTCTAGGTTGAAGATTAAA
1 TAAAACTTGATTTAAAACTCTTCTAAGTTAAAGATTAAA
80669 -AAAA
1 TAAAA
80673 GCCTAATTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 4 0.10
39 36 0.90
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (39 bp):
TAAAACTTGATTTAAAACTCTTCTAAGTTAAAGATTAAA
Found at i:80760 original size:13 final size:13
Alignment explanation
Indices: 80742--80768 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
80732 TGAACTCAAC
80742 TTTGTTAGAGCAA
1 TTTGTTAGAGCAA
80755 TTTGTTAGAGCAA
1 TTTGTTAGAGCAA
80768 T
1 T
80769 ATAAGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (13 bp):
TTTGTTAGAGCAA
Found at i:85962 original size:2 final size:2
Alignment explanation
Indices: 85950--85992 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
85940 AATATTTTAT
85950 TA TA TA T- TA TA TA 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 TA TA TA TA TA TA TA
85991 TA
1 TA
85993 GTAGTAAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:86378 original size:19 final size:19
Alignment explanation
Indices: 86338--86374 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
86328 AATTTTTAAG
86338 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
86357 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
86375 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:89858 original size:5 final size:5
Alignment explanation
Indices: 89848--89880 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
89838 TAATAATAGG
*
89848 TATAA TATAA TATAA TATAA TATAA TATTA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TAT
89881 GGATCAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TATAA
Found at i:90423 original size:4 final size:4
Alignment explanation
Indices: 90416--90444 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
90406 TAATTAGTGC
90416 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
90445 GACAAAGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:98479 original size:6 final size:6
Alignment explanation
Indices: 98454--98501 Score: 71
Period size: 6 Copynumber: 7.8 Consensus size: 6
98444 AACATCAGAC
98454 TAAAAA TATTAAAA -AAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TA--AAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
98502 CCCTCTCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 4 0.10
6 30 0.77
7 1 0.03
8 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:102327 original size:15 final size:17
Alignment explanation
Indices: 102307--102360 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 17
102297 TAAAACCAGA
*
102307 CATGCT-TTTGTAT-TT
1 CATGCTATTTATATCTT
102322 CATGCTATTTATATCTT
1 CATGCTATTTATATCTT
102339 CATATGCTATTTATATCTT
1 C--ATGCTATTTATATCTT
102358 CAT
1 CAT
102361 CCAACTATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 6 0.18
16 6 0.18
17 5 0.15
19 17 0.50
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (17 bp):
CATGCTATTTATATCTT
Found at i:102347 original size:19 final size:19
Alignment explanation
Indices: 102323--102360 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
102313 TTTGTATTTC
102323 ATGCTATTTATATCTTCAT
1 ATGCTATTTATATCTTCAT
102342 ATGCTATTTATATCTTCAT
1 ATGCTATTTATATCTTCAT
102361 CCAACTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (19 bp):
ATGCTATTTATATCTTCAT
Found at i:102936 original size:36 final size:36
Alignment explanation
Indices: 102895--103000 Score: 203
Period size: 36 Copynumber: 2.9 Consensus size: 36
102885 CAGCCAGAGT
*
102895 CTTGGCTACCCCAACCTCCACCGGAGCTCTGTCCGC
1 CTTGGCTACCCCAACCTCCACCAGAGCTCTGTCCGC
102931 CTTGGCTACCCCAACCTCCACCAGAGCTCTGTCCGC
1 CTTGGCTACCCCAACCTCCACCAGAGCTCTGTCCGC
102967 CTTGGCTACCCCAACCTCCACCAGAGCTCTGTCC
1 CTTGGCTACCCCAACCTCCACCAGAGCTCTGTCC
103001 TTGGTCCTTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.16, C:0.47, G:0.17, T:0.20
Consensus pattern (36 bp):
CTTGGCTACCCCAACCTCCACCAGAGCTCTGTCCGC
Found at i:103285 original size:30 final size:30
Alignment explanation
Indices: 103155--103284 Score: 242
Period size: 30 Copynumber: 4.3 Consensus size: 30
103145 CCTTCCACGT
103155 CCTCTACCTCCAAATCCTCCCCTGTCACCA
1 CCTCTACCTCCAAATCCTCCCCTGTCACCA
*
103185 CCTCTACCTCCAAATCCTCCCCTATCACCA
1 CCTCTACCTCCAAATCCTCCCCTGTCACCA
103215 CCTCTACCTCCAAATCCTCCCCTGTCACCA
1 CCTCTACCTCCAAATCCTCCCCTGTCACCA
*
103245 CCTCTACCTCTAAATCCTCCCCTGTCACCA
1 CCTCTACCTCCAAATCCTCCCCTGTCACCA
103275 CCTCTACCTC
1 CCTCTACCTC
103285 TGTGGCCACC
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 97 1.00
ACGTcount: A:0.20, C:0.53, G:0.02, T:0.25
Consensus pattern (30 bp):
CCTCTACCTCCAAATCCTCCCCTGTCACCA
Found at i:103329 original size:30 final size:30
Alignment explanation
Indices: 103289--103360 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
103279 TACCTCTGTG
103289 GCCACCTCTACCTCCATAGCTTTCTCCATC
1 GCCACCTCTACCTCCATAGCTTTCTCCATC
*
103319 GCCCCCTCTACCTCCATAGCTTTCTCCATC
1 GCCACCTCTACCTCCATAGCTTTCTCCATC
103349 GCCACCTCTACC
1 GCCACCTCTACC
103361 GCCAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.15, C:0.50, G:0.07, T:0.28
Consensus pattern (30 bp):
GCCACCTCTACCTCCATAGCTTTCTCCATC
Found at i:103581 original size:57 final size:57
Alignment explanation
Indices: 103514--103642 Score: 168
Period size: 57 Copynumber: 2.3 Consensus size: 57
103504 CATTTCCACT
* * * *
103514 TCCCGAGTTCCAATTGCTTTTCTGGCCCCAACCTGAACCCTGGCTTGCATCTCCAGG
1 TCCCGAGTTCCAATTGCTTTTCTGGCCCCAACCTGAACCCTGGCCTGCACCACCAGA
* * * *
103571 TCCCGAGTTCCAGTCGCTTTTCTTGCCCCAACCTGAATCCTGGCCTGCACCACCAGA
1 TCCCGAGTTCCAATTGCTTTTCTGGCCCCAACCTGAACCCTGGCCTGCACCACCAGA
* *
103628 ACCAGAGTTCCAATT
1 TCCCGAGTTCCAATT
103643 CCCCTTTTTA
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.19, C:0.37, G:0.18, T:0.26
Consensus pattern (57 bp):
TCCCGAGTTCCAATTGCTTTTCTGGCCCCAACCTGAACCCTGGCCTGCACCACCAGA
Found at i:104184 original size:288 final size:288
Alignment explanation
Indices: 103668--104205 Score: 864
Period size: 288 Copynumber: 1.9 Consensus size: 288
103658 AGAGTCTTGG
* *
103668 CCAGAATCACTGGTTCCAGCACCCCAGCTACTTTTTGTGCCCCAGTTTGAATTCTGATTTGCATC
1 CCAGAATCACTGGTTCCAGCACCCCAACTACTTTTTGTACCCCAGTTTGAATTCTGATTTGCATC
* * * **
103733 TGCAGTTCCTGAATCAGAGTCATTTTTCTTTCCCCAACTAGAACCTTTTGTTGCATCATCAGATC
66 TGCAGATCCTGAATCACAGTCATTTTTCCTTCCCCAACTAGAACCTTCGGTTGCATCATCAGATC
* ** *
103798 CAAAGTCTGAATTATTTTTCTTGGCCCAACCTTGATCCTGGTTTGCACTTCCTGAGTTCCAATTG
131 CAAAGTCTGAATCATTTTTCTTACCCCAACCTGGATCCTGGTTTGCACTTCCTGAGTTCCAATTG
* *
103863 CTTTTCTTACCCCAATCTGAACCCTGGCTTGCATCTCCAGCTCCTGATTTCCAATCGCTTTTCTT
196 CTTTTCTTACCCCAACCTGAACCCTGGCTTGCATCTCCAGCTCCTGAGTTCCAATCGCTTTTCTT
103928 GCCACACCCTGAATCATGGCCTGCACCA
261 GCCACACCCTGAATCATGGCCTGCACCA
103956 CCAGAATCACTGGTTCCAGCACCCCAACTACTTTTCT-TACCCCAGTTTGAATTCTGATTTGCAT
1 CCAGAATCACTGGTTCCAGCACCCCAACTACTTTT-TGTACCCCAGTTTGAATTCTGATTTGCAT
* * *
104020 CTGCAGATCCTGATTTC-CAGTCATTTTTCCTTCCCCAACTAGAATCTTCGGTTGCATTATCAGA
65 CTGCAGATCCTGA-ATCACAGTCATTTTTCCTTCCCCAACTAGAACCTTCGGTTGCATCATCAGA
*
104084 TCCAAAGTTTGAATCATTTTTCTTACCCCAACCTGGATCCTGGTTTGCACTTCCTGAGTTCCAAT
129 TCCAAAGTCTGAATCATTTTTCTTACCCCAACCTGGATCCTGGTTTGCACTTCCTGAGTTCCAAT
* * *
104149 TGCTTTTCTTGCCCCAACCTGAATCCTGGCTTGCATCTCCAGGTCCTGAGTTCCAAT
194 TGCTTTTCTTACCCCAACCTGAACCCTGGCTTGCATCTCCAGCTCCTGAGTTCCAAT
104206 TAGAATCCTT
Statistics
Matches: 228, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
288 225 0.99
289 3 0.01
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (288 bp):
CCAGAATCACTGGTTCCAGCACCCCAACTACTTTTTGTACCCCAGTTTGAATTCTGATTTGCATC
TGCAGATCCTGAATCACAGTCATTTTTCCTTCCCCAACTAGAACCTTCGGTTGCATCATCAGATC
CAAAGTCTGAATCATTTTTCTTACCCCAACCTGGATCCTGGTTTGCACTTCCTGAGTTCCAATTG
CTTTTCTTACCCCAACCTGAACCCTGGCTTGCATCTCCAGCTCCTGAGTTCCAATCGCTTTTCTT
GCCACACCCTGAATCATGGCCTGCACCA
Found at i:108163 original size:15 final size:15
Alignment explanation
Indices: 108143--108172 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
108133 TGAGCCCTCG
*
108143 CCTTTTTCACCTCCT
1 CCTTTTCCACCTCCT
108158 CCTTTTCCACCTCCT
1 CCTTTTCCACCTCCT
108173 TTATCAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.50, G:0.00, T:0.43
Consensus pattern (15 bp):
CCTTTTCCACCTCCT
Found at i:138273 original size:22 final size:22
Alignment explanation
Indices: 138245--138290 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
138235 AAAATCTCCT
138245 AATTCAACC-TCTGGAGAGGTCG
1 AATTCAACCTTC-GGAGAGGTCG
*
138267 AATTCAACCTTCGTAGAGGTCG
1 AATTCAACCTTCGGAGAGGTCG
138289 AA
1 AA
138291 ACAACAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (22 bp):
AATTCAACCTTCGGAGAGGTCG
Found at i:144065 original size:2 final size:2
Alignment explanation
Indices: 144054--144085 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
144044 ATTTTTAAAA
144054 AT AT -T AT AT AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
144086 TAAAATTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.