Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023681.1 Corchorus olitorius cultivar O-4 contig23714, 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: 92994
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:6527 original size:5 final size:5
Alignment explanation
Indices: 6519--6548 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
6509 ACTTCCCTCC
*
6519 CCTTT CCTTT CCTTT CCTTC CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
6549 AATTACTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (5 bp):
CCTTT
Found at i:6738 original size:16 final size:15
Alignment explanation
Indices: 6696--6744 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
6686 CTGGGCGGTT
6696 TTCGGGTC-ATCTGGG
1 TTCGGGTCAATC-GGG
* *
6711 TTCGGATTAATCGGG
1 TTCGGGTCAATCGGG
6726 TCTCGGGTCAATCGGG
1 T-TCGGGTCAATCGGG
6742 TTC
1 TTC
6745 AGTTGAGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.12, C:0.20, G:0.35, T:0.33
Consensus pattern (15 bp):
TTCGGGTCAATCGGG
Found at i:11617 original size:16 final size:17
Alignment explanation
Indices: 11596--11627 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11586 TAAATTGCGT
11596 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
11612 TTTATTTTTCTATTTT
1 TTTATTTTTCTATTTT
11628 AATTTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Found at i:22057 original size:16 final size:16
Alignment explanation
Indices: 22034--22075 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
22024 ACTTATAAAT
* *
22034 TCTCGGGTTATTCGGG
1 TCTCGGGTCATTCAGG
*
22050 TTTCGGGTCATTCAGG
1 TCTCGGGTCATTCAGG
22066 TCTCGGGTCA
1 TCTCGGGTCA
22076 GCCGGGTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.10, C:0.21, G:0.33, T:0.36
Consensus pattern (16 bp):
TCTCGGGTCATTCAGG
Found at i:23861 original size:14 final size:15
Alignment explanation
Indices: 23822--23865 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
23812 TTCCCCCGAC
23822 CCTCTCTCTCTTC-T
1 CCTCTCTCTCTTCTT
23836 CCAT-TCTCTCTTCTT
1 CC-TCTCTCTCTTCTT
23851 CCTCTCT-TCTTCTT
1 CCTCTCTCTCTTCTT
23865 C
1 C
23866 ACCGTCACCG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.52
Consensus pattern (15 bp):
CCTCTCTCTCTTCTT
Found at i:24526 original size:21 final size:21
Alignment explanation
Indices: 24501--24545 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
24491 TGTGTTTGCT
*
24501 GTTTTGCTATATAATGATTTA
1 GTTTTGCTATATAAAGATTTA
24522 GTTTTGCTATATAAAGATTTA
1 GTTTTGCTATATAAAGATTTA
24543 GTT
1 GTT
24546 GAATGATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (21 bp):
GTTTTGCTATATAAAGATTTA
Found at i:25470 original size:21 final size:23
Alignment explanation
Indices: 25446--25502 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 23
25436 AAATCCAAGC
25446 TTTAACCATAAAAAC-CAT-TTT
1 TTTAACCATAAAAACACATGTTT
* *
25467 TTTAA-AAGAAAAAACACATGTTT
1 TTTAACCA-TAAAAACACATGTTT
*
25490 ATTAACCATAAAA
1 TTTAACCATAAAA
25503 GACTAACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
20 1 0.04
21 11 0.41
22 3 0.11
23 11 0.41
24 1 0.04
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.32
Consensus pattern (23 bp):
TTTAACCATAAAAACACATGTTT
Found at i:26112 original size:16 final size:16
Alignment explanation
Indices: 26088--26130 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
26078 GTTATTTACC
26088 TTAATTAAATTTTACA-A
1 TTAA-TAAATTTTA-ATA
26105 TTAATAAATTTTAATA
1 TTAATAAATTTTAATA
*
26121 ATAATAAATT
1 TTAATAAATT
26131 ACACAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 19 0.79
17 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAATAAATTTTAATA
Found at i:28216 original size:31 final size:31
Alignment explanation
Indices: 28149--28230 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
28139 ATTTCATTAA
* *
28149 TTTCCAAAATCTTCTTTTGG-GTTTCTTTAT
1 TTTCCAAAATCTTCTTTTGGAATTACTTTAT
*
28179 TCTCCAAAATCTTCTTTTGGAATTAAC-TTAT
1 TTTCCAAAATCTTCTTTTGGAATT-ACTTTAT
28210 TTTCCAAAATCTTCTTTTGGA
1 TTTCCAAAATCTTCTTTTGGA
28231 TTTGCTTAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
30 19 0.41
31 26 0.57
32 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (31 bp):
TTTCCAAAATCTTCTTTTGGAATTACTTTAT
Found at i:32137 original size:13 final size:13
Alignment explanation
Indices: 32119--32143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32109 TAATCAAAAG
32119 CAAAATGGTTTCC
1 CAAAATGGTTTCC
32132 CAAAATGGTTTC
1 CAAAATGGTTTC
32144 TTATTAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
CAAAATGGTTTCC
Found at i:32919 original size:50 final size:50
Alignment explanation
Indices: 32844--33299 Score: 587
Period size: 50 Copynumber: 9.3 Consensus size: 50
32834 TGATCAACTT
*
32844 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACTGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * * *
32894 CTTTGAACTGTCTTCAAATTCAATCTTAAAAGGATCGTCTCCCGCATATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
32944 CTTTGAATTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
32994 CTTTGAACTGTCTTCCAATTCAATCTTAAATGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
33044 CTTTGAACTATCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTCATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
33094 CTTTGAACTGTCTTCCAATTCAATCTTAAAACGG-CCGTCTTCCGTTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAA-GGACCGTCTTCCGCTTATC
* ** * * * *
33144 CTTTGAACTG---T-C----C--TC-T-AATGGATTGTCTCCCGATCAACTT
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCT-TA-TC
* *
33184 CTTTGAACTGACTTCGAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * * *
33234 CTTTGAACTGTCTTCCAATTCAATATTAAAAGGATCGTCTCCCGCTTAAC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
33284 CTTTGAACTGTCTTCC
1 CTTTGAACTGTCTTCC
33300 GCTTATCCTT
Statistics
Matches: 351, Mismatches: 39, Indels: 32
0.83 0.09 0.08
Matches are distributed among these distances:
37 2 0.01
38 10 0.03
39 2 0.01
40 13 0.04
42 1 0.00
43 1 0.00
46 1 0.00
47 1 0.00
48 1 0.00
50 302 0.86
51 4 0.01
52 13 0.04
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.36
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:33006 original size:23 final size:23
Alignment explanation
Indices: 32980--33059 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
32970 TAAAAGGACC
32980 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
** * *
33003 GTCTTCCAATTCAAT-CTTAAATGGACC
1 GTCTTCCGCTT--ATCCTT---TGAACT
33030 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
*
33053 ATCTTCC
1 GTCTTCC
33060 AATTCAATCT
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
23 19 0.45
24 3 0.07
25 4 0.10
26 3 0.07
27 13 0.31
ACGTcount: A:0.19, C:0.30, G:0.11, T:0.40
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTTGAACT
Found at i:33307 original size:73 final size:73
Alignment explanation
Indices: 33220--33372 Score: 270
Period size: 73 Copynumber: 2.1 Consensus size: 73
33210 TAAAAGGACC
*
33220 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATATTAAAAGGATCGTCTCCCGCTTAACC
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATATTAAAAGGACCGTCTCCCGCTTAACC
33285 TTTGAACT
66 TTTGAACT
* * *
33293 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCC
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATATTAAAAGGACCGTCTCCCGCTTAACC
33358 TTTGAACT
66 TTTGAACT
33366 GTCTTCC
1 GTCTTCC
33373 AATTCAATCT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (73 bp):
GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATATTAAAAGGACCGTCTCCCGCTTAACC
TTTGAACT
Found at i:33320 original size:23 final size:23
Alignment explanation
Indices: 33270--33422 Score: 96
Period size: 23 Copynumber: 6.3 Consensus size: 23
33260 TAAAAGGATC
* *
33270 GTCTCCCGCTTAACCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
33293 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
** * * *
33316 GTCTTCCAATTCAAT-CTTAAAAGGACC
1 GTCTTCCGCTT--ATCCTT---TGAACT
33343 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
** *
33366 GTCTTCCAATTCAAT-CTTAAATGGA-T
1 GTCTTCCGCTT--ATCCTT---TGAACT
33392 CGTCTTCCGCTTATCCTTTGAACT
1 -GTCTTCCGCTTATCCTTTGAACT
33416 GTCTTCC
1 GTCTTCC
33423 AATTCAATCT
Statistics
Matches: 98, Mismatches: 18, Indels: 28
0.68 0.12 0.19
Matches are distributed among these distances:
23 52 0.53
24 7 0.07
25 8 0.08
26 7 0.07
27 24 0.24
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTTGAACT
Found at i:33347 original size:50 final size:50
Alignment explanation
Indices: 33293--33564 Score: 436
Period size: 50 Copynumber: 5.4 Consensus size: 50
33283 CCTTTGAACT
33293 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
* *
33343 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAATGGATC
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
33393 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
* * *
33443 ATCTTCCGTTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGGCC
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
* * * * * *
33493 GTCTTCCGTTTATCCTTTGAACTGTCCTCTAATTCAAGCTTAAAAAGATC
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
*
33543 GTCTTCTGCTTATCCTTTGAAC
1 GTCTTCCGCTTATCCTTTGAAC
33565 ATTACTTTCC
Statistics
Matches: 206, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 206 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.38
Consensus pattern (50 bp):
GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
Found at i:33403 original size:123 final size:123
Alignment explanation
Indices: 33184--33422 Score: 424
Period size: 123 Copynumber: 1.9 Consensus size: 123
33174 CGATCAACTT
*
33184 CTTTGAACTGACTTCGAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
1 CTTTGAACTGACTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
33249 CAATTCAATATTAAAAGGATCGTCTCCCGCTTAACCTTTGAACTGTCTTCCGCTTATC
66 CAATTCAATATTAAAAGGATCGTCTCCCGCTTAACCTTTGAACTGTCTTCCGCTTATC
*
33307 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
1 CTTTGAACTGACTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
* * * *
33372 CAATTCAATCTTAAATGGATCGTCTTCCGCTTATCCTTTGAACTGTCTTCC
66 CAATTCAATATTAAAAGGATCGTCTCCCGCTTAACCTTTGAACTGTCTTCC
33423 AATTCAATCT
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 110 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (123 bp):
CTTTGAACTGACTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
CAATTCAATATTAAAAGGATCGTCTCCCGCTTAACCTTTGAACTGTCTTCCGCTTATC
Found at i:43535 original size:31 final size:29
Alignment explanation
Indices: 43494--43573 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
43484 GCTAAATATC
*
43494 CAAAAAAATCCCTTACGTTTTCCCTTTGGGA
1 CAAAATAATCCCTTACGTTTT-CCTTT-GGA
* ** *
43525 CAAAATAATCCCTTATGTTTTTGTTTTGA
1 CAAAATAATCCCTTACGTTTTCCTTTGGA
*
43554 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTACGTTT
43574 CAAAAATGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 20 0.48
30 3 0.07
31 19 0.45
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (29 bp):
CAAAATAATCCCTTACGTTTTCCTTTGGA
Found at i:53586 original size:54 final size:51
Alignment explanation
Indices: 53476--53586 Score: 127
Period size: 51 Copynumber: 2.1 Consensus size: 51
53466 GTCTCTGCAT
* *
53476 TTTTTATCT-AAAAAAAAAGATTTTGTTTTTCTTTTATTTTTCTTCTTTGCG
1 TTTTT-TCTAAAAAAAAAAGATTTCGTTTTGCTTTTATTTTTCTTCTTTGCG
*
53527 TTTTTTCTAAAAAAAAAAGATTTCGATTTTGCGTTTTTAATTTTTGTGT-TTTGCG
1 TTTTTTCTAAAAAAAAAAGATTTCG-TTTTGC--TTTT-ATTTTTCT-TCTTTGCG
53582 TTTTT
1 TTTTT
53587 GAAAAGAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
50 3 0.06
51 20 0.39
52 5 0.10
54 4 0.08
55 18 0.35
56 1 0.02
ACGTcount: A:0.23, C:0.08, G:0.11, T:0.58
Consensus pattern (51 bp):
TTTTTTCTAAAAAAAAAAGATTTCGTTTTGCTTTTATTTTTCTTCTTTGCG
Found at i:53604 original size:26 final size:26
Alignment explanation
Indices: 53575--53650 Score: 102
Period size: 25 Copynumber: 2.9 Consensus size: 26
53565 AATTTTTGTG
*
53575 TTTTGCGTTTT-TGAAAAGAAAAAAAAT
1 TTTTACGTTTTCT-AAAA-AAAAAAAAT
53602 TTTTACGTTTTCT-AAAAAAAAAAAT
1 TTTTACGTTTTCTAAAAAAAAAAAAT
*
53627 TTTTACGTTTTCTTAAAAAAAAAA
1 TTTTACGTTTTCTAAAAAAAAAAA
53651 TTGTTTCTGC
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 22 0.48
26 13 0.28
27 10 0.22
28 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (26 bp):
TTTTACGTTTTCTAAAAAAAAAAAAT
Found at i:53627 original size:25 final size:25
Alignment explanation
Indices: 53593--53652 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
53583 TTTTGAAAAG
53593 AAAAAAAATTTTTACGTTTTCTAAA
1 AAAAAAAATTTTTACGTTTTCTAAA
*
53618 AAAAAAAATTTTTACGTTTTCTTAA
1 AAAAAAAATTTTTACGTTTTCTAAA
53643 AAAAAAAATT
1 AAAAAAAATT
53653 GTTTCTGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (25 bp):
AAAAAAAATTTTTACGTTTTCTAAA
Found at i:56550 original size:21 final size:21
Alignment explanation
Indices: 56526--56569 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
56516 GCCATGGCCC
56526 GGCCACCCGAGCCACCTGCCT
1 GGCCACCCGAGCCACCTGCCT
* * * *
56547 GGCCATCCGTGCTACTTGCCT
1 GGCCACCCGAGCCACCTGCCT
56568 GG
1 GG
56570 TTAAGCTTGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.11, C:0.43, G:0.27, T:0.18
Consensus pattern (21 bp):
GGCCACCCGAGCCACCTGCCT
Found at i:62406 original size:4 final size:4
Alignment explanation
Indices: 62395--62570 Score: 91
Period size: 4 Copynumber: 44.5 Consensus size: 4
62385 AAGATTTTTT
* *
62395 TTTA -TTA TTTA TTTCTA TTTA TCTA TTTA TTTA TTT- TTAA CTATTA
1 TTTA TTTA TTTA -TT-TA TTTA TTTA TTTA TTTA TTTA TTTA -T-TTA
* * ** *
62441 TCTA TTTA TTTA -CTA TTTA TCTT- TTTA TTTA TTTTA ACTA -TTA TCTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA -TTTA TTTA TTTA TTTA
* * * *
62488 TTTA TTTA TTAA TTTA ATTA -TTA TCTA TTTA TTTA -CTA TTTA TCTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
* ** *
62534 TTTA TTTA TTAA TTTA GCTA -TTA TCTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
62571 ATTATTATCC
Statistics
Matches: 129, Mismatches: 27, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
3 20 0.16
4 91 0.71
5 14 0.11
6 4 0.03
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:62421 original size:8 final size:8
Alignment explanation
Indices: 62395--62642 Score: 93
Period size: 8 Copynumber: 31.9 Consensus size: 8
62385 AAGATTTTTT
62395 TTTAT-TA
1 TTTATCTA
62402 TTTATTTCTA
1 TTTA--TCTA
62412 TTTATCTA
1 TTTATCTA
*
62420 TTTATTTA
1 TTTATCTA
*
62428 TTTTTAACTA
1 --TTTATCTA
62438 -TTATCTA
1 TTTATCTA
62445 TTTATTTACTA
1 TTTA--T-CTA
*
62456 TTTATCTT
1 TTTATCTA
*
62464 TTTATTTA
1 TTTATCTA
*
62472 TTTTAACTA
1 -TTTATCTA
62481 -TTATCTA
1 TTTATCTA
*
62488 TTTATTTA
1 TTTATCTA
* *
62496 TTAATTTA
1 TTTATCTA
*
62504 ATTAT-TA
1 TTTATCTA
* *
62511 TCTATTTA
1 TTTATCTA
62519 TTTA-CTA
1 TTTATCTA
62526 TTTATC--
1 TTTATCTA
62532 TTT-T-TA
1 TTTATCTA
62538 TTTAT-TAA
1 TTTATCT-A
*
62546 TTTAGCTA
1 TTTATCTA
62554 -TTATCTA
1 TTTATCTA
*
62561 TTTATTTA
1 TTTATCTA
62569 -TTAT-TA
1 TTTATCTA
62575 -TTATCCT-
1 TTTAT-CTA
62582 TTT-T-TA
1 TTTATCTA
** *
62588 GCTACCTA
1 TTTATCTA
62596 TTTATCTA
1 TTTATCTA
62604 -TTATTCTA
1 TTTA-TCTA
*
62612 TGTATCTA
1 TTTATCTA
62620 TTTATCT-
1 TTTATCTA
*
62627 TTATACCTA
1 TT-TATCTA
62636 TTTATCT
1 TTTATCT
62643 TTTTTTATTA
Statistics
Matches: 181, Mismatches: 31, Indels: 57
0.67 0.12 0.21
Matches are distributed among these distances:
5 2 0.01
6 13 0.07
7 45 0.25
8 88 0.49
9 13 0.07
10 13 0.07
11 7 0.04
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.63
Consensus pattern (8 bp):
TTTATCTA
Found at i:62476 original size:43 final size:44
Alignment explanation
Indices: 62396--62563 Score: 177
Period size: 43 Copynumber: 3.8 Consensus size: 44
62386 AGATTTTTTT
62396 TTAT-TATTTATTT-CTATTTATCTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
*
62438 TTATCTATTTATTTACTATTTATCTTTTTATTTA-TTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
* * *
62481 TTATCTATTTATTTATTAATTTAAT-TA-TTATCTATTTATTTACTA
1 TTATCTATTTATTTACT-ATTT-ATCTATTTATTTATTT-TTAACTA
* * * *
62526 TTTATCTTTTTATTTATTAATTTAGCTA-TTATCTATTT
1 -TTATCTATTTATTTACT-ATTTATCTATTTATTTATTT
62564 ATTTATTATT
Statistics
Matches: 111, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
42 4 0.04
43 40 0.36
44 25 0.23
45 9 0.08
46 33 0.30
ACGTcount: A:0.27, C:0.08, G:0.01, T:0.65
Consensus pattern (44 bp):
TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
Found at i:62510 original size:70 final size:71
Alignment explanation
Indices: 62389--62573 Score: 268
Period size: 70 Copynumber: 2.6 Consensus size: 71
62379 ACCAAAAAGA
* *
62389 TTTTTTTTTATTATTTATTTCTATTTATCTATTTATTTATT-TTTAACTATTATCTATTTATTTA
1 TTTTTATTTATTATTTA--ACTA-TTATCTATTTATTTATTATTTAACTATTATCTATTTATTTA
62453 CTATTTATC
63 CTATTTATC
*
62462 TTTTTATTTA-T-TTTAACTATTATCTATTTATTTATTAATTTAATTATTATCTATTTATTTACT
1 TTTTTATTTATTATTTAACTATTATCTATTTATTTATT-ATTTAACTATTATCTATTTATTTACT
62525 ATTTATC
65 ATTTATC
*
62532 TTTTTATTTATTAATTTAGCTATTATCTATTTATTTATTATT
1 TTTTTATTTATT-ATTTAACTATTATCTATTTATTTATTATT
62574 ATTATCCTTT
Statistics
Matches: 103, Mismatches: 4, Indels: 11
0.87 0.03 0.09
Matches are distributed among these distances:
68 17 0.17
69 3 0.03
70 41 0.40
71 5 0.05
72 4 0.04
73 33 0.32
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (71 bp):
TTTTTATTTATTATTTAACTATTATCTATTTATTTATTATTTAACTATTATCTATTTATTTACTA
TTTATC
Found at i:62511 original size:27 final size:25
Alignment explanation
Indices: 62403--62578 Score: 129
Period size: 25 Copynumber: 7.2 Consensus size: 25
62393 TTTTTATTAT
*
62403 TTATT-TCTATTTATCTATTTATTTA
1 TTATTATCTATTTATTTA-TTATTTA
* * *
62428 TTTTTAACTA-TTATCTATTTATTTA
1 TTATTATCTATTTATTTA-TTATTTA
* * *
62453 CTATTTATCTTTTTATTTATT-TTAA
1 TTA-TTATCTATTTATTTATTATTTA
*
62478 CTATTATCTATTTATTTATTAATTTAA
1 TTATTATCTATTTATTTATT-ATTT-A
*
62505 TTATTATCTATTTATTTACTATTTA
1 TTATTATCTATTTATTTATTATTTA
62530 TCT-TT-T-TATTTA-TTA--ATTTA
1 T-TATTATCTATTTATTTATTATTTA
*
62550 GCTATTATCTATTTATTTATTA-TTA
1 -TTATTATCTATTTATTTATTATTTA
62575 TTAT
1 TTAT
62579 CCTTTTTTAG
Statistics
Matches: 123, Mismatches: 14, Indels: 29
0.74 0.08 0.17
Matches are distributed among these distances:
20 6 0.05
21 2 0.02
22 4 0.03
23 12 0.10
24 23 0.19
25 33 0.27
26 18 0.15
27 25 0.20
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (25 bp):
TTATTATCTATTTATTTATTATTTA
Found at i:62544 original size:46 final size:46
Alignment explanation
Indices: 62395--62573 Score: 171
Period size: 46 Copynumber: 4.0 Consensus size: 46
62385 AAGATTTTTT
* * * *
62395 TTTAT-TATTTATTT-CT-ATTTATCTATTTATTTATTT-TTAACTA
1 TTTATCTATTTATTTATTAATTTAACTA-TTATCTATTTATTTACTA
* *
62438 -TTATCTATTTATTTACT-ATTTATCT-TT-T-TATTTATTTTAACTA
1 TTTATCTATTTATTTATTAATTTAACTATTATCTATTTA-TTT-ACTA
*
62481 -TTATCTATTTATTTATTAATTTAATTATTATCTATTTATTTACTA
1 TTTATCTATTTATTTATTAATTTAACTATTATCTATTTATTTACTA
* * *
62526 TTTATCTTTTTATTTATTAATTTAGCTATTATCTATTTATTTATTA
1 TTTATCTATTTATTTATTAATTTAACTATTATCTATTTATTTACTA
62572 TT
1 TT
62574 ATTATCCTTT
Statistics
Matches: 118, Mismatches: 8, Indels: 17
0.83 0.06 0.12
Matches are distributed among these distances:
40 5 0.04
41 1 0.01
42 8 0.07
43 29 0.25
44 16 0.14
45 6 0.05
46 47 0.40
47 6 0.05
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (46 bp):
TTTATCTATTTATTTATTAATTTAACTATTATCTATTTATTTACTA
Found at i:67392 original size:24 final size:26
Alignment explanation
Indices: 67361--67418 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
67351 ATAGGTTTAG
*
67361 AGATAAATAGATA-C-AAAGAATAAT
1 AGATAAATAGATAGCTAAAAAATAAT
*
67385 AGATAAATAGGTAGCTAAAAAATAAT
1 AGATAAATAGATAGCTAAAAAATAAT
67411 A-ATAAATA
1 AGATAAATA
67419 AATAAATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 12 0.40
25 8 0.27
26 10 0.33
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.22
Consensus pattern (26 bp):
AGATAAATAGATAGCTAAAAAATAAT
Found at i:67433 original size:19 final size:19
Alignment explanation
Indices: 67400--67653 Score: 133
Period size: 19 Copynumber: 13.4 Consensus size: 19
67390 AATAGGTAGC
67400 TAAA-AAATA-ATAATAAA
1 TAAATAAATAGATAATAAA
*
67417 TAAATAAATAGATAATAAC
1 TAAATAAATAGATAATAAA
* *
67436 TAAATTAATAAATAA-AAA
1 TAAATAAATAGATAATAAA
67454 T--ATAAATAG-TAAATAAA
1 TAAATAAATAGAT-AATAAA
*
67471 TAGAT-AATA-ATTAA-AAA
1 TAAATAAATAGA-TAATAAA
* *
67488 TAAATAAAAAAGATAA-ATAG
1 TAAAT-AAATAGATAATA-AA
67508 TAAATAAATAGATAATAGTTAA
1 TAAATAAATAGATAATA---AA
* * * *
67530 -AAATGTAACAAATAGTAAA
1 TAAAT-AAATAGATAATAAA
*
67549 TAAATAGATAATAGTTAA-AAA
1 TAAAT--A-AATAGATAATAAA
*
67570 TAAATAAATAGATAAATGAA
1 TAAATAAATAGAT-AATAAA
67590 -AAATAAATAGATAATAAAA
1 TAAATAAATAGATAAT-AAA
*
67609 AAAATAAATAG-TAAATAAA
1 TAAATAAATAGAT-AATAAA
*
67628 TAGATAAATAG-TGAATAAA
1 TAAATAAATAGAT-AATAAA
*
67647 TAGATAA
1 TAAATAA
67654 TAGTTAAAAA
Statistics
Matches: 187, Mismatches: 26, Indels: 46
0.72 0.10 0.18
Matches are distributed among these distances:
15 1 0.01
16 8 0.04
17 15 0.08
18 23 0.12
19 85 0.45
20 27 0.14
21 13 0.07
22 15 0.08
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (19 bp):
TAAATAAATAGATAATAAA
Found at i:67548 original size:37 final size:37
Alignment explanation
Indices: 67463--67657 Score: 176
Period size: 37 Copynumber: 5.3 Consensus size: 37
67453 ATATAAATAG
* **
67463 TAAATAAATAG-ATAATAATTA-A-AAATAAATAAAAA
1 TAAATAAATAGTA-AATAAATAGATAAATAGTTAAAAA
*
67498 -AGATAAATAGTAAATAAATAGAT-AATAGTTAAAAA
1 TAAATAAATAGTAAATAAATAGATAAATAGTTAAAAA
* *
67533 TGTAACAAATAGTAAATAAATAGAT-AATAGTTAAAAA
1 T-AAATAAATAGTAAATAAATAGATAAATAGTTAAAAA
67570 TAAATAAATAGATAAATGAAA-A-ATAAATAGATAATAAAAA
1 TAAATAAATAG-TAAAT-AAATAGATAAATAG-T--TAAAAA
*
67610 -AAATAAATAGTAAATAAATAGATAAATAGTGAATAAA
1 TAAATAAATAGTAAATAAATAGATAAATAGTTAA-AAA
*
67647 TAGAT-AATAGT
1 TAAATAAATAGT
67658 TAAAAATGTA
Statistics
Matches: 134, Mismatches: 11, Indels: 28
0.77 0.06 0.16
Matches are distributed among these distances:
34 16 0.12
35 12 0.09
36 12 0.09
37 56 0.42
38 14 0.10
39 18 0.13
40 6 0.04
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.26
Consensus pattern (37 bp):
TAAATAAATAGTAAATAAATAGATAAATAGTTAAAAA
Found at i:67552 original size:82 final size:75
Alignment explanation
Indices: 67457--67634 Score: 241
Period size: 82 Copynumber: 2.3 Consensus size: 75
67447 ATAAAAATAT
*
67457 AAATAGTAAATAAATAGATAATAATTAAAAATAAATAAAAAAGATAAAT-AGTAAATAAATAGAT
1 AAATAGTAAATAAATAGATAATAATTAAAAATAAAT-AAAAAGATAAATGA-AAAATAAATAGAT
67521 AATAGTTAAAAATGTAAC
64 AATA---AAAAA---AAC
* *
67539 AAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATGAAAAATAAATAGATAA
1 AAATAGTAAATAAATAGATAATAATTAAAAATAAATAAAAAGATAAATGAAAAATAAATAGATAA
*
67604 TAAAAAAAAT
66 TAAAAAAAAC
67614 AAATAGTAAATAAATAGATAA
1 AAATAGTAAATAAATAGATAA
67635 ATAGTGAATA
Statistics
Matches: 91, Mismatches: 4, Indels: 9
0.88 0.04 0.09
Matches are distributed among these distances:
75 23 0.25
78 5 0.05
81 27 0.30
82 36 0.40
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.25
Consensus pattern (75 bp):
AAATAGTAAATAAATAGATAATAATTAAAAATAAATAAAAAGATAAATGAAAAATAAATAGATAA
TAAAAAAAAC
Found at i:67648 original size:4 final size:4
Alignment explanation
Indices: 67400--67637 Score: 103
Period size: 4 Copynumber: 61.5 Consensus size: 4
67390 AATAGGTAGC
* * *
67400 TAAA -AAA T-AA T-AA TAAA TAAA TAAA TAGA T-AA TAAC TAAA TTAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
67444 TAAA TAAA -AATA TAAA T-AG TAAA TAAA TAGA T-AA T-AA TTAA -AAA
1 TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * *
67488 TAAA TAAA AAAGA TAAA T-AG TAAA TAAA TAGA TAATA GTTAA -AAA TGTAA
1 TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA T-AAA
* * * * *
67538 CAAA T-AG TAAA TAAA TAGA TAATA GTTAA -AAA TAAA TAAA TAGA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA TAAA TAAA
* * * * *
67586 TGAA -AAA TAAA TAGA T-AA TAAAA AAAA TAAA T-AG TAAA TAAA TAGA
1 TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA
67632 TAAA TA
1 TAAA TA
67638 GTGAATAAAT
Statistics
Matches: 171, Mismatches: 41, Indels: 44
0.67 0.16 0.17
Matches are distributed among these distances:
3 36 0.21
4 118 0.69
5 13 0.08
6 4 0.02
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.26
Consensus pattern (4 bp):
TAAA
Done.