Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012484.1 Corchorus capsularis cultivar CVL-1 contig12505, 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: 67468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8499 original size:32 final size:34
Alignment explanation
Indices: 8456--8523 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
8446 TTCCTAAACC
8456 AATTTAGGTTTTC-A-AATTAGAATTTTAATTTT
1 AATTTAGGTTTTCTAGAATTAGAATTTTAATTTT
* * * *
8488 AATTTATGTTTTCTAGATTTAGGATTTTATTTTT
1 AATTTAGGTTTTCTAGAATTAGAATTTTAATTTT
8522 AA
1 AA
8524 GCATCTTAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 12 0.40
33 1 0.03
34 17 0.57
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (34 bp):
AATTTAGGTTTTCTAGAATTAGAATTTTAATTTT
Found at i:11449 original size:15 final size:16
Alignment explanation
Indices: 11429--11462 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11419 GATTGCTTTC
*
11429 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
11444 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
11460 TTA
1 TTA
11463 ATTCTTCTTT
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:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:13707 original size:2 final size:2
Alignment explanation
Indices: 13700--13727 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13690 CTAAAATTTC
13700 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
13728 ATAAAAGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15469 original size:12 final size:12
Alignment explanation
Indices: 15452--15476 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15442 CTTTTTTTGA
15452 TCTAATTAATGT
1 TCTAATTAATGT
15464 TCTAATTAATGT
1 TCTAATTAATGT
15476 T
1 T
15477 TGAAACATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TCTAATTAATGT
Found at i:15582 original size:12 final size:12
Alignment explanation
Indices: 15565--15598 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15555 GAGGGAGGTA
*
15565 TATAATTATAAT
1 TATAATAATAAT
15577 TATAATAATAAT
1 TATAATAATAAT
*
15589 AATAATAATA
1 TATAATAATA
15599 TAATGATTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TATAATAATAAT
Found at i:17717 original size:6 final size:6
Alignment explanation
Indices: 17706--17730 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17696 GGCCTAGCCA
17706 TTTTGG TTTTGG TTTTGG TTTTGG T
1 TTTTGG TTTTGG TTTTGG TTTTGG T
17731 GCTGGGCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (6 bp):
TTTTGG
Found at i:18004 original size:15 final size:16
Alignment explanation
Indices: 17984--18089 Score: 106
Period size: 16 Copynumber: 6.7 Consensus size: 16
17974 CTTGAACCTG
*
17984 AACCCG-AAAAGCTTA
1 AACCCGAAAAAGCTCA
* * *
17999 AACCCGAAAAAACCCG
1 AACCCGAAAAAGCTCA
18015 AACCCGAAAAAGCTCA
1 AACCCGAAAAAGCTCA
* * *
18031 AACCCGAAAAAACACG
1 AACCCGAAAAAGCTCA
* * *
18047 AACCCGAAAAAACCCG
1 AACCCGAAAAAGCTCA
*
18063 AATCCGAAAAAGCTCA
1 AACCCGAAAAAGCTCA
18079 AACCCGAAAAA
1 AACCCGAAAAA
18090 ACCCGAATCC
Statistics
Matches: 74, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
15 6 0.08
16 68 0.92
ACGTcount: A:0.52, C:0.31, G:0.12, T:0.05
Consensus pattern (16 bp):
AACCCGAAAAAGCTCA
Found at i:18018 original size:16 final size:16
Alignment explanation
Indices: 17999--18104 Score: 131
Period size: 16 Copynumber: 6.6 Consensus size: 16
17989 GAAAAGCTTA
17999 AACCCGAAAAAACCCG
1 AACCCGAAAAAACCCG
* * *
18015 AACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCG
*
18031 AACCCGAAAAAACACG
1 AACCCGAAAAAACCCG
18047 AACCCGAAAAAACCCG
1 AACCCGAAAAAACCCG
* * * *
18063 AATCCGAAAAAGCTCA
1 AACCCGAAAAAACCCG
18079 AACCCGAAAAAACCCG
1 AACCCGAAAAAACCCG
*
18095 AATCCGAAAA
1 AACCCGAAAA
18105 TTTATGAAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 74 1.00
ACGTcount: A:0.52, C:0.32, G:0.12, T:0.04
Consensus pattern (16 bp):
AACCCGAAAAAACCCG
Found at i:18034 original size:32 final size:32
Alignment explanation
Indices: 17978--18089 Score: 127
Period size: 32 Copynumber: 3.5 Consensus size: 32
17968 AACCCGCTTG
* *
17978 AACCTGAACCCG-AAAAGCTTAAACCCGAAAA
1 AACCCGAACCCGAAAAAGCTCAAACCCGAAAA
18009 AACCCGAACCCGAAAAAGCTCAAACCCGAAAA
1 AACCCGAACCCGAAAAAGCTCAAACCCGAAAA
* * * * *
18041 AACACGAACCCGAAAAAACCCGAATCCGAAAA
1 AACCCGAACCCGAAAAAGCTCAAACCCGAAAA
* * *
18073 AGCTCAAACCCGAAAAA
1 AACCCGAACCCGAAAAA
18090 ACCCGAATCC
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
31 11 0.16
32 59 0.84
ACGTcount: A:0.51, C:0.31, G:0.12, T:0.05
Consensus pattern (32 bp):
AACCCGAACCCGAAAAAGCTCAAACCCGAAAA
Found at i:18070 original size:48 final size:48
Alignment explanation
Indices: 17999--18104 Score: 185
Period size: 48 Copynumber: 2.2 Consensus size: 48
17989 GAAAAGCTTA
17999 AACCCGAAAAAACCCGAACCCGAAAAAGCTCAAACCCGAAAAAACACG
1 AACCCGAAAAAACCCGAACCCGAAAAAGCTCAAACCCGAAAAAACACG
* *
18047 AACCCGAAAAAACCCGAATCCGAAAAAGCTCAAACCCGAAAAAACCCG
1 AACCCGAAAAAACCCGAACCCGAAAAAGCTCAAACCCGAAAAAACACG
*
18095 AATCCGAAAA
1 AACCCGAAAA
18105 TTTATGAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.52, C:0.32, G:0.12, T:0.04
Consensus pattern (48 bp):
AACCCGAAAAAACCCGAACCCGAAAAAGCTCAAACCCGAAAAAACACG
Found at i:18280 original size:15 final size:15
Alignment explanation
Indices: 18257--18316 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
18247 CAGAACCCGA
* *
18257 ACCCGAATTAACATG
1 ACCCAAATTAACCTG
*
18272 ACCCAAATTAACCCG
1 ACCCAAATTAACCTG
*
18287 AACCCGAATTAACCTG
1 -ACCCAAATTAACCTG
18303 ACCCAAATTCAACC
1 ACCCAAATT-AACC
18317 CGAACCCGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 20 0.54
16 17 0.46
ACGTcount: A:0.40, C:0.35, G:0.08, T:0.17
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:18287 original size:31 final size:32
Alignment explanation
Indices: 18250--18325 Score: 136
Period size: 31 Copynumber: 2.4 Consensus size: 32
18240 ACCCAAACAG
18250 AACCCGAACCCGAATTAACATGACCCAAATT-
1 AACCCGAACCCGAATTAACATGACCCAAATTC
*
18281 AACCCGAACCCGAATTAACCTGACCCAAATTC
1 AACCCGAACCCGAATTAACATGACCCAAATTC
18313 AACCCGAACCCGA
1 AACCCGAACCCGA
18326 CTCAAGCCCG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 30 0.70
32 13 0.30
ACGTcount: A:0.39, C:0.37, G:0.11, T:0.13
Consensus pattern (32 bp):
AACCCGAACCCGAATTAACATGACCCAAATTC
Found at i:23665 original size:72 final size:73
Alignment explanation
Indices: 23515--23666 Score: 211
Period size: 72 Copynumber: 2.1 Consensus size: 73
23505 TTGAAGATCT
* * * * *
23515 TGGTTCGTGGGATTCTAGTTTTGATGCAAAGTTTTCTGTTGAAGTCTTGAGATTGTCAAAAATTG
1 TGGTTTGTGGGATTCTAGTTTGGATGCAAAATTTTCTGCTGAAATCTTGAGATTGTCAAAAATTG
23580 ACTTTGAA
66 ACTTTGAA
* *
23588 T-GTTTGTGGGATTCTAGTTTGGATGCAAAATTTTCTGCTGAAATTTTTAGATTGTCAAAAATTG
1 TGGTTTGTGGGATTCTAGTTTGGATGCAAAATTTTCTGCTGAAATCTTGAGATTGTCAAAAATTG
23652 A-TCTTG-A
66 ACT-TTGAA
23659 TGGTTTGT
1 TGGTTTGT
23667 TTGAAAAAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
71 3 0.04
72 66 0.94
73 1 0.01
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (73 bp):
TGGTTTGTGGGATTCTAGTTTGGATGCAAAATTTTCTGCTGAAATCTTGAGATTGTCAAAAATTG
ACTTTGAA
Found at i:26354 original size:3 final size:3
Alignment explanation
Indices: 26348--26386 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
26338 AACAACTATA
26348 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26387 ATACTATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:26557 original size:13 final size:13
Alignment explanation
Indices: 26539--26565 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26529 CTCTATAACC
26539 TCATAAATCATAT
1 TCATAAATCATAT
26552 TCATAAATCATAT
1 TCATAAATCATAT
26565 T
1 T
26566 TATTATATTT
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:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:26728 original size:19 final size:19
Alignment explanation
Indices: 26688--26724 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
26678 AGTTTTTGAG
*
26688 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
26707 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
26725 ATAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:30543 original size:33 final size:33
Alignment explanation
Indices: 30447--30614 Score: 249
Period size: 33 Copynumber: 5.3 Consensus size: 33
30437 TCTTTTCACG
* *
30447 CAAAACAGAATTATTTTCAATGC---CATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
* *
30477 CAAAACAGAATTATTTTCAATGC---CATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
30507 CAAAACAGAATTATTTGCAATGCTATGATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
30540 CAAAACAGAATTATTTGCAATGCTATGATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
*
30573 CAAAACAGAATTATTTGCAATGCTATGATCGAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
30606 CAAAACAGA
1 CAAAACAGA
30615 TTTGTTTTCA
Statistics
Matches: 132, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
30 52 0.39
33 80 0.61
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (33 bp):
CAAAACAGAATTATTTGCAATGCTATGATCAAC
Found at i:30642 original size:66 final size:66
Alignment explanation
Indices: 30447--30647 Score: 218
Period size: 66 Copynumber: 3.1 Consensus size: 66
30437 TCTTTTCACG
* * * * *
30447 CAAAACAGAATTATTTTCAATGC---CATCAACCAAAACAGAATTATTTTCAATGCCAT---CAA
1 CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCAA
30506 C
66 C
* * *
30507 CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCAA
30572 C
66 C
* * * * *
30573 CAAAACAGAATTATTTGCAATGCTATGATCGACCAAAACAGATTTGTTTTC-ATCACAATTAGCA
1 CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAAT-ACAATGAGCA
*
30637 TC
65 AC
30639 CAAAACAGA
1 CAAAACAGA
30648 TTTAGTATCA
Statistics
Matches: 121, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
60 22 0.18
63 30 0.25
65 2 0.02
66 67 0.55
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.27
Consensus pattern (66 bp):
CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCAA
C
Found at i:30677 original size:33 final size:33
Alignment explanation
Indices: 30639--30741 Score: 136
Period size: 33 Copynumber: 3.2 Consensus size: 33
30629 AATTAGCATC
*
30639 CAAAACAGATTTAGTATCATCACAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
* * *
30672 TAAAACAGATTTAGTGTCATTGCAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
** *
30705 CAAATTAGGTTTAGTATCATCGCAAACAACA-T
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
30737 CAAAA
1 CAAAA
30742 AGACTCTTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
32 5 0.08
33 54 0.92
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:32227 original size:8 final size:8
Alignment explanation
Indices: 32214--32244 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
32204 CTGGTCGAAT
32214 TTTTTTTA
1 TTTTTTTA
32222 TTTTTTTA
1 TTTTTTTA
32230 TTTTTTTA
1 TTTTTTTA
*
32238 TATTTTT
1 TTTTTTT
32245 CGATATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:33921 original size:30 final size:30
Alignment explanation
Indices: 33880--33954 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
33870 CGGGTTGTGC
*** *
33880 CCGGTCTTGTGCGATTGGACCATGCCATGG
1 CCGGTCTTGTGCGATCCCACCATGCAATGG
* *
33910 CCGGTCATGTGCGATCCCTCCATGCAATGG
1 CCGGTCTTGTGCGATCCCACCATGCAATGG
33940 CCGGTCTTGTGCGAT
1 CCGGTCTTGTGCGAT
33955 GGCATCCTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.13, C:0.29, G:0.31, T:0.27
Consensus pattern (30 bp):
CCGGTCTTGTGCGATCCCACCATGCAATGG
Found at i:35571 original size:19 final size:18
Alignment explanation
Indices: 35538--35573 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
35528 TTGAAATAAT
35538 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
35556 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
35574 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:35774 original size:20 final size:21
Alignment explanation
Indices: 35736--35774 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
35726 TAGAAAATAA
*
35736 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
35757 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
35775 ACAGCCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:41592 original size:33 final size:33
Alignment explanation
Indices: 41551--41662 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 33
41541 GCCGCGCAAC
** *
41551 ACCGGCCACATGACTTAGAGATGCCCGGCCACC
1 ACCGGCCACATGACTTAGCCATGCCCGGCCACA
*
41584 ACCGGCCACATGACTCAGCCATGCCCGGCCACA
1 ACCGGCCACATGACTTAGCCATGCCCGGCCACA
*
41617 ACCGGCCACATGACTTGGCCATGCCCGGCCACA
1 ACCGGCCACATGACTTAGCCATGCCCGGCCACA
*
41650 ACCAGCCACATGA
1 ACCGGCCACATGA
41663 TCCTTTAACT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.25, C:0.42, G:0.22, T:0.11
Consensus pattern (33 bp):
ACCGGCCACATGACTTAGCCATGCCCGGCCACA
Found at i:42690 original size:12 final size:12
Alignment explanation
Indices: 42675--42700 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42665 GAAAAATATC
42675 AAAAAAATAAAA
1 AAAAAAATAAAA
42687 AAAAAAATAAAA
1 AAAAAAATAAAA
42699 AA
1 AA
42701 CTTTTCGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:44184 original size:21 final size:21
Alignment explanation
Indices: 44158--44199 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
44148 GCACTTGTGA
*
44158 CCGGCCACACGATTTGGAGAT
1 CCGGCCACACGACTTGGAGAT
*
44179 CCGGCCACGCGACTTGGAGAT
1 CCGGCCACACGACTTGGAGAT
44200 GCCCGACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17
Consensus pattern (21 bp):
CCGGCCACACGACTTGGAGAT
Found at i:44221 original size:33 final size:33
Alignment explanation
Indices: 44179--44318 Score: 149
Period size: 33 Copynumber: 4.2 Consensus size: 33
44169 ATTTGGAGAT
*
44179 CCGGCCACGCGACTTGGAGATGCCCGACCATCA
1 CCGGCCACGCGACTTGGAGATGCCCGGCCATCA
*
44212 CCGGCCACGCGACTCGGAGATGCCCGGCCATCA
1 CCGGCCACGCGACTTGGAGATGCCCGGCCATCA
* * * *
44245 CCGGCCAGGCGACATGGACATGCTCGGCCA-CAA
1 CCGGCCACGCGACTTGGAGATGCCCGGCCATC-A
*** **
44278 CCGGCCAAATGACTTGGCCATGCCCGGCCA-CAA
1 CCGGCCACGCGACTTGGAGATGCCCGGCCATC-A
44311 CCGGCCAC
1 CCGGCCAC
44319 ATGATCCTTT
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
32 1 0.01
33 91 0.99
ACGTcount: A:0.21, C:0.41, G:0.28, T:0.10
Consensus pattern (33 bp):
CCGGCCACGCGACTTGGAGATGCCCGGCCATCA
Found at i:46904 original size:33 final size:33
Alignment explanation
Indices: 46819--46911 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
46809 TTTTAGATGT
* * * *
46819 TGTTTGCGATGATACTAAACCTAATTTGAGTGT
1 TGTTTGCGATGATACTAAATCTATTTTAAGTGA
* *
46852 TGTTTGCAATGACACTAAATCTATTTTAAGTGA
1 TGTTTGCGATGATACTAAATCTATTTTAAGTGA
* *
46885 TGTTTGTGATGATACTAAATCTGTTTT
1 TGTTTGCGATGATACTAAATCTATTTT
46912 GGATGCTAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (33 bp):
TGTTTGCGATGATACTAAATCTATTTTAAGTGA
Found at i:48782 original size:21 final size:21
Alignment explanation
Indices: 48757--48796 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
48747 ACTTGTGACC
48757 GGCCACGCGACTTGGAGATCT
1 GGCCACGCGACTTGGAGATCT
48778 GGCCACGCGACTTGGAGAT
1 GGCCACGCGACTTGGAGAT
48797 GCCCGACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.17
Consensus pattern (21 bp):
GGCCACGCGACTTGGAGATCT
Found at i:48820 original size:33 final size:33
Alignment explanation
Indices: 48778--48915 Score: 163
Period size: 33 Copynumber: 4.2 Consensus size: 33
48768 TTGGAGATCT
*
48778 GGCCACGCGACTTGGAGATGCCCGACCATCACC
1 GGCCACGCGACTTGGAGATGCCCGGCCATCACC
*
48811 GGCCACGCGACTCGGAGATGCCCGGCCATCACC
1 GGCCACGCGACTTGGAGATGCCCGGCCATCACC
* *
48844 GGCCACGCGACATGGACATGCCCGGCCA-CAACC
1 GGCCACGCGACTTGGAGATGCCCGGCCATC-ACC
*** **
48877 GGCCAAATGACTTGGCCATGCCCGGCCA-CAACC
1 GGCCACGCGACTTGGAGATGCCCGGCCATC-ACC
48910 GGCCAC
1 GGCCAC
48916 ATGATCCTTT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 1 0.01
33 92 0.99
ACGTcount: A:0.22, C:0.41, G:0.28, T:0.09
Consensus pattern (33 bp):
GGCCACGCGACTTGGAGATGCCCGGCCATCACC
Found at i:51717 original size:11 final size:11
Alignment explanation
Indices: 51700--51731 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
51690 ATTGTCTTCA
51700 AATCTTCAAAT
1 AATCTTCAAAT
*
51711 TATCTTCAAAT
1 AATCTTCAAAT
51722 AATCTTCAAA
1 AATCTTCAAA
51732 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:56817 original size:13 final size:14
Alignment explanation
Indices: 56793--56822 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
56783 AAATTAAAAT
56793 TAAATCTAACTAAG
1 TAAATCTAACTAAG
56807 TAAAT-TAACTAAG
1 TAAATCTAACTAAG
56820 TAA
1 TAA
56823 GCAATCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (14 bp):
TAAATCTAACTAAG
Found at i:58323 original size:20 final size:21
Alignment explanation
Indices: 58285--58323 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
58275 TAGAAAATAA
*
58285 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
58306 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
58324 AAAGCCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:60555 original size:11 final size:12
Alignment explanation
Indices: 60526--60559 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
60516 AAATTATGCA
60526 TATTTTTATAGC
1 TATTTTTATAGC
60538 TATTTTTATAGC
1 TATTTTTATAGC
60550 TATTTTTATA
1 TATTTTTATA
60560 TAAAAGCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (12 bp):
TATTTTTATAGC
Found at i:60641 original size:109 final size:109
Alignment explanation
Indices: 60450--60656 Score: 414
Period size: 109 Copynumber: 1.9 Consensus size: 109
60440 AAACTTGCCA
60450 ATAAAAGCTCTTAAAACATGATTCATTAATCGCATGAATGTACTAGGTGCATTAGTGATCGGGCC
1 ATAAAAGCTCTTAAAACATGATTCATTAATCGCATGAATGTACTAGGTGCATTAGTGATCGGGCC
60515 AAAATTATGCATATTTTTATAGCTATTTTTATAGCTATTTTTAT
66 AAAATTATGCATATTTTTATAGCTATTTTTATAGCTATTTTTAT
60559 ATAAAAGCTCTTAAAACATGATTCATTAATCGCATGAATGTACTAGGTGCATTAGTGATCGGGCC
1 ATAAAAGCTCTTAAAACATGATTCATTAATCGCATGAATGTACTAGGTGCATTAGTGATCGGGCC
60624 AAAATTATGCATATTTTTATAGCTATTTTTATA
66 AAAATTATGCATATTTTTATAGCTATTTTTATA
60657 TACTTTTTTG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 98 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (109 bp):
ATAAAAGCTCTTAAAACATGATTCATTAATCGCATGAATGTACTAGGTGCATTAGTGATCGGGCC
AAAATTATGCATATTTTTATAGCTATTTTTATAGCTATTTTTAT
Found at i:60839 original size:11 final size:10
Alignment explanation
Indices: 60821--60854 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
60811 GAAGTTCGTG
60821 TTTTGAAGAT
1 TTTTGAAGAT
60831 TTCTTGAAGAT
1 TT-TTGAAGAT
60842 ATTTTGAAGAT
1 -TTTTGAAGAT
60853 TT
1 TT
60855 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:61780 original size:21 final size:21
Alignment explanation
Indices: 61754--61795 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
61744 TCCCTGTCTT
61754 TACCACTACAATTTGCCTAAC
1 TACCACTACAATTTGCCTAAC
61775 TACCACTACAATTTGCCTAAC
1 TACCACTACAATTTGCCTAAC
61796 AAAGTGGCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCACTACAATTTGCCTAAC
Found at i:62787 original size:20 final size:20
Alignment explanation
Indices: 62762--62802 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
62752 TTGTAATCCC
62762 AATCTCTTCAAGAAATGAAA
1 AATCTCTTCAAGAAATGAAA
*
62782 AATCTCTTCGAGAAATGAAA
1 AATCTCTTCAAGAAATGAAA
62802 A
1 A
62803 TGATTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (20 bp):
AATCTCTTCAAGAAATGAAA
Found at i:62822 original size:2 final size:2
Alignment explanation
Indices: 62817--62852 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
62807 TCTTCTCTCA
62817 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62853 AAATTAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.