Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006681.1 Corchorus capsularis cultivar CVL-1 contig06702, 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: 15378
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7639 original size:15 final size:15
Alignment explanation
Indices: 7621--7651 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7611 TTACTTTTAC
*
7621 TACTTTTATCATTTT
1 TACTTTTACCATTTT
7636 TACTTTTACCATTTT
1 TACTTTTACCATTTT
7651 T
1 T
7652 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:7651 original size:24 final size:24
Alignment explanation
Indices: 7606--7679 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
7596 TATTGATTAC
* *
7606 CATTTTTACTTTTACTACTTTTAT
1 CATTTTTACTTTTACCATTTTTAT
*
7630 CATTTTTACTTTTACCATTTTTCT
1 CATTTTTACTTTTACCATTTTTAT
* *
7654 TACTCTTTTACTTAATACCATTTTTA
1 CA-T-TTTTACTT-TTACCATTTTTA
7680 ATTAATACCA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 22 0.54
25 1 0.02
26 8 0.20
27 10 0.24
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (24 bp):
CATTTTTACTTTTACCATTTTTAT
Found at i:7693 original size:15 final size:16
Alignment explanation
Indices: 7659--7694 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
7649 TTTCTTACTC
*
7659 TTTTACTTAATACCAT
1 TTTTAATTAATACCAT
7675 TTTTAATTAATACCAT
1 TTTTAATTAATACCAT
7691 TTTT
1 TTTT
7695 TTGACCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAATTAATACCAT
Found at i:7725 original size:17 final size:17
Alignment explanation
Indices: 7703--7751 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
7693 TTTTGACCTT
*
7703 CTTACTTAATACCATAC
1 CTTACTTGATACCATAC
7720 CTTACTTGATACCATAC
1 CTTACTTGATACCATAC
7737 CTTACTTGATACCAT
1 CTTACTTGATACCAT
7752 TGTTGACCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.37
Consensus pattern (17 bp):
CTTACTTGATACCATAC
Found at i:7725 original size:60 final size:60
Alignment explanation
Indices: 7661--7777 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
7651 TCTTACTCTT
** *
7661 TTACTTAATACCAT-TTTTAATTAATACCATTTTTTTGACC-TTCTTACTTAATACCATACC
1 TTACTTAATACCATACCTTAATTAATACCA--TTGTTGACCTTTCTTACTTAATACCATACC
* * * *
7721 TTACTTGATACCATACCTTACTTGATACCATTGTTGACCTTTTTTACTTAATACCAT
1 TTACTTAATACCATACCTTAATTAATACCATTGTTGACCTTTCTTACTTAATACCAT
7778 TTTTGATCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 8 0.17
60 29 0.60
61 11 0.23
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.45
Consensus pattern (60 bp):
TTACTTAATACCATACCTTAATTAATACCATTGTTGACCTTTCTTACTTAATACCATACC
Found at i:7774 original size:26 final size:26
Alignment explanation
Indices: 7738--7798 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
7728 ATACCATACC
*
7738 TTACTTGATACCATTGTTGACCTTTT
1 TTACTTAATACCATTGTTGACCTTTT
* *
7764 TTACTTAATACCATTTTTGATCTTTT
1 TTACTTAATACCATTGTTGACCTTTT
7790 TTACTTAAT
1 TTACTTAAT
7799 TCCACTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.54
Consensus pattern (26 bp):
TTACTTAATACCATTGTTGACCTTTT
Found at i:7807 original size:26 final size:26
Alignment explanation
Indices: 7738--7807 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
7728 ATACCATACC
*
7738 TTACTTGATACCA-TTGTTGACCTTTT
1 TTACTTAATACCACTT-TTGACCTTTT
* *
7764 TTACTTAATACCATTTTTGATCTTTT
1 TTACTTAATACCACTTTTGACCTTTT
*
7790 TTACTTAATTCCACTTTT
1 TTACTTAATACCACTTTT
7808 ACTTAATACC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 37 0.95
27 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (26 bp):
TTACTTAATACCACTTTTGACCTTTT
Found at i:7809 original size:16 final size:16
Alignment explanation
Indices: 7788--7826 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
7778 TTTTGATCTT
*
7788 TTTTACTTAATTCCAC
1 TTTTACTTAATACCAC
*
7804 TTTTACTTAATACCAT
1 TTTTACTTAATACCAC
7820 TTTTACT
1 TTTTACT
7827 CTTTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTACTTAATACCAC
Found at i:7856 original size:25 final size:24
Alignment explanation
Indices: 7803--7912 Score: 103
Period size: 24 Copynumber: 4.9 Consensus size: 24
7793 CTTAATTCCA
7803 CTTTTACTTAATACCATTTTTACT
1 CTTTTACTTAATACCATTTTTACT
*
7827 CTTTTATTTAATACCATTTTTGAC-
1 CTTTTACTTAATACCATTTTT-ACT
7851 CTTTTTACTTAATACC------A-T
1 C-TTTTACTTAATACCATTTTTACT
*
7869 C-TTTACTTAATACAATTTTTACT
1 CTTTTACTTAATACCATTTTTACT
**
7892 CTTTTGTTTAATACCATTTTT
1 CTTTTACTTAATACCATTTTT
7913 TACCTTAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
16 12 0.17
18 2 0.03
22 1 0.01
23 2 0.03
24 37 0.54
25 15 0.22
ACGTcount: A:0.25, C:0.18, G:0.02, T:0.55
Consensus pattern (24 bp):
CTTTTACTTAATACCATTTTTACT
Found at i:7875 original size:16 final size:16
Alignment explanation
Indices: 7854--7891 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
7844 TTTTGACCTT
*
7854 TTTACTTAATACCATC
1 TTTACTTAATACAATC
*
7870 TTTACTTAATACAATT
1 TTTACTTAATACAATC
7886 TTTACT
1 TTTACT
7892 CTTTTGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTACTTAATACAATC
Found at i:7887 original size:41 final size:41
Alignment explanation
Indices: 7829--7923 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
7819 TTTTTACTCT
* *
7829 TTTATTTAATACCATTTTTGAC-CTTTT-TACTTAATACCA-TC
1 TTTACTTAATACAATTTTT-ACTCTTTTGT--TTAATACCATTC
*
7870 TTTACTTAATACAATTTTTACTCTTTTGTTTAATACCATTT
1 TTTACTTAATACAATTTTTACTCTTTTGTTTAATACCATTC
7911 TTTACCTTAATAC
1 TTTA-CTTAATAC
7924 CATCTTTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
40 11 0.23
41 27 0.57
42 9 0.19
ACGTcount: A:0.27, C:0.18, G:0.02, T:0.53
Consensus pattern (41 bp):
TTTACTTAATACAATTTTTACTCTTTTGTTTAATACCATTC
Found at i:7887 original size:65 final size:65
Alignment explanation
Indices: 7721--7968 Score: 253
Period size: 65 Copynumber: 3.9 Consensus size: 65
7711 ATACCATACC
* * * * * *
7721 TTACTTGATACCATACCTTACTTGATACCATTGTTGACCTTTTTTACTTAATACCATTTTTGATC
1 TTACTTAATACCAT-CTTTACTTAATACCATT-TTTA-CTCTTTTATTTAATACCATTTTTGA-C
*
7786 TTTT
62 CTTT
*
7790 TTACTTAATTCCA-CTTTTACTTAATACCATTTTTACTCTTTTATTTAATACCATTTTTGACCTT
1 TTACTTAATACCATC-TTTACTTAATACCATTTTTACTCTTTTATTTAATACCATTTTTGACCTT
7854 T
65 T
* * *
7855 TTACTTAATACCATCTTTACTTAATACAATTTTTACTCTTTTGTTTAATACCATTTTTTA-C---
1 TTACTTAATACCATCTTTACTTAATACCATTTTTACTCTTTTATTTAATACCATTTTTGACCTTT
* * *
7916 ---CTTAATACCATCTTT-CTTTGATACCATTTTTACTCTCTTGTTTAATACCATTT
1 TTACTTAATACCATCTTTAC-TTAATACCATTTTTACTCTTTTATTTAATACCATTT
7969 ATTTACTCTT
Statistics
Matches: 161, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
57 1 0.01
58 48 0.30
64 1 0.01
65 58 0.36
66 24 0.15
67 4 0.02
68 14 0.09
69 11 0.07
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.52
Consensus pattern (65 bp):
TTACTTAATACCATCTTTACTTAATACCATTTTTACTCTTTTATTTAATACCATTTTTGACCTTT
Found at i:7927 original size:58 final size:58
Alignment explanation
Indices: 7852--7979 Score: 188
Period size: 58 Copynumber: 2.2 Consensus size: 58
7842 ATTTTTGACC
*
7852 TTTTTA-CTTAATACCATCTTTAC-TTAATACAATTTTTACTCTTTTGTTTAATACCAT
1 TTTTTACCTTAATACCATCTTT-CTTTAATACAATTTTTACTCTCTTGTTTAATACCAT
* *
7909 TTTTTACCTTAATACCATCTTTCTTTGATACCATTTTTACTCTCTTGTTTAATACCAT
1 TTTTTACCTTAATACCATCTTTCTTTAATACAATTTTTACTCTCTTGTTTAATACCAT
7967 TTATTTACTCTTA
1 TT-TTTAC-CTTA
7980 GTATCATTTA
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
57 7 0.11
58 48 0.75
59 5 0.08
60 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.02, T:0.53
Consensus pattern (58 bp):
TTTTTACCTTAATACCATCTTTCTTTAATACAATTTTTACTCTCTTGTTTAATACCAT
Found at i:8580 original size:149 final size:140
Alignment explanation
Indices: 8422--8732 Score: 367
Period size: 149 Copynumber: 2.2 Consensus size: 140
8412 TCACTCAACT
* * * *
8422 CTTAATTACTGATTTACTGATTATCATCACTTTGACTCTTCATTATCGATTTACTGATT-A-C-C
1 CTTAATTACTGATTTACTGATTACCATCACCTTGACTCTTAATTATCAATTTACTGATTGATCTC
8484 ATTTTAACCTTGACTCTTGATTACTGACTTTACTGATCACTATTACCTTGACTCTTAATTATCAA
66 -TTTTAA-C-TGA--CTT-A-T--TGA-TTTACTGATCACTATTACCTTGACTCTTAATTATC-A
*
8549 TTTACTGATTAATCTCTTTTTA
120 CTTACTGATTAATCTC-TTTTA
* * * *
8571 CTTAATTACTGACTTGCTGATTACCATTACCTTGACTCTTAATTATCAATTTGCTGATTGATCTC
1 CTTAATTACTGATTTACTGATTACCATCACCTTGACTCTTAATTATCAATTTACTGATTGATCTC
* * * * *
8636 TTTTTACTGACTTATTGATTTACTGATTACTATTGCCTTGATTCTTGATTATCACTTACTGATTA
66 TTTTAACTGACTTATTGATTTACTGATCACTATTACCTTGACTCTTAATTATCACTTACTGATTA
8701 ATCTCTTTTA
131 ATCTCTTTTA
8711 CTTAATTACTGATTTACTGATT
1 CTTAATTACTGATTTACTGATT
8733 TCTACTTTTT
Statistics
Matches: 143, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
140 25 0.17
141 16 0.11
142 31 0.22
143 3 0.02
145 1 0.01
146 1 0.01
147 3 0.02
149 54 0.38
150 2 0.01
151 6 0.04
152 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (140 bp):
CTTAATTACTGATTTACTGATTACCATCACCTTGACTCTTAATTATCAATTTACTGATTGATCTC
TTTTAACTGACTTATTGATTTACTGATCACTATTACCTTGACTCTTAATTATCACTTACTGATTA
ATCTCTTTTA
Found at i:8607 original size:71 final size:71
Alignment explanation
Indices: 8503--8732 Score: 311
Period size: 71 Copynumber: 3.3 Consensus size: 71
8493 TTGACTCTTG
*
8503 ATTACTGACTTTACTGATCACTATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTT
1 ATTACTGAC-TTACTGATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTT
8568 TTACTTA
65 TTACTTA
* * * *
8575 ATTACTGACTTGCTGATTACCATTACCTTGACTCTTAATTATCAATTTGCTGATTGATCTCTTTT
1 ATTACTGACTTACTGATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTTT
*
8640 TACTGA
66 TACTTA
* * * * * * *
8646 CTTATTGATTTACTGATTACTATTGCCTTGATTCTTGATTATC-ACTTACTGATTAATCTC-TTT
1 ATTACTGACTTACTGATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTTT
8709 TACTTA
66 TACTTA
*
8715 ATTACTGATTTACTGATT
1 ATTACTGACTTACTGATT
8733 TCTACTTTTT
Statistics
Matches: 138, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
69 24 0.17
70 14 0.10
71 91 0.66
72 9 0.07
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (71 bp):
ATTACTGACTTACTGATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTTT
TACTTA
Found at i:8625 original size:37 final size:37
Alignment explanation
Indices: 8419--8629 Score: 148
Period size: 37 Copynumber: 5.7 Consensus size: 37
8409 TAATCACTCA
* * * *
8419 ACTCTTAATTA-CTGATTTACTGATTATCATCACTTTG
1 ACTCTTAATTATC-AATTTACTGATTACCATTACCTTG
* *
8456 ACTCTTCATTATCGATTTACTGATTACCATTTTAACCTTG
1 ACTCTTAATTATCAATTTACTGATTACCA--TT-ACCTTG
* * * * *
8496 ACTCTTGATTACTGACTTTACTGATCACTATTACCTTG
1 ACTCTTAATTA-TCAATTTACTGATTACCATTACCTTG
8534 ACTCTTAATTATCAATTTACTGATTA--A-T-CTCTT-
1 ACTCTTAATTATCAATTTACTGATTACCATTAC-CTTG
** * * *
8567 TTTACTTAATTA-CTGACTTGCTGATTACCATTACCTTG
1 ACT-CTTAATTATC-AATTTACTGATTACCATTACCTTG
*
8605 ACTCTTAATTATCAATTTGCTGATT
1 ACTCTTAATTATCAATTTACTGATT
8630 GATCTCTTTT
Statistics
Matches: 137, Mismatches: 23, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
33 3 0.02
34 22 0.16
35 1 0.01
36 1 0.01
37 59 0.43
38 20 0.15
39 3 0.02
40 15 0.11
41 13 0.09
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.45
Consensus pattern (37 bp):
ACTCTTAATTATCAATTTACTGATTACCATTACCTTG
Found at i:12369 original size:71 final size:71
Alignment explanation
Indices: 12237--12619 Score: 466
Period size: 71 Copynumber: 5.3 Consensus size: 71
12227 AAAAAGTAGA
* * * *
12237 AATCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATCAGTAAAGTGATAATCAAGAATCAAGGC
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGT
12301 AATAGT
66 AATAGT
* * * * *
12307 AATCAGTAAATCAGTAAGTCAGTAAAAAGAGATCAATCAGCAAATTGATATTTAAGAGTCAAGGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGT
*
12372 AATGGT
66 AATAGT
* *
12378 AATCAGCAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGT
*
12443 AATGGT
66 AATAGT
* *
12449 AATCAGCAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGT
12514 AATAGT
66 AATAGT
* * * *
12520 GATCAGTAAAGTCAGTAATCAAGAGTCAATGTAAA-A-ATGGTAATCAGTAAATCGATAATAAAG
1 AATCAGTAAA-TCAGTAAT-TA-AGT-AA---AAAGAGAT--TAATCAGTAAATTGATAATTAAG
* * *
12583 AGTCAAAGTGATGGT
57 AGTCAAGGTAATAGT
12598 AATCAGTAAATCAGTAATTAAG
1 AATCAGTAAATCAGTAATTAAG
12620 AGTTGAGTGA
Statistics
Matches: 274, Mismatches: 29, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
70 21 0.08
71 180 0.66
72 8 0.03
73 1 0.00
74 3 0.01
75 4 0.01
76 3 0.01
77 9 0.03
78 45 0.16
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (71 bp):
AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGT
AATAGT
Found at i:12382 original size:37 final size:37
Alignment explanation
Indices: 12341--12622 Score: 149
Period size: 37 Copynumber: 7.7 Consensus size: 37
12331 AAAAGAGATC
*
12341 AATCAGCAAATTGATATTTAAGAGTCAAGGTAATGGT
1 AATCAGCAAATTGATAATTAAGAGTCAAGGTAATGGT
* * * *
12378 AATCAGC-AAGTCAGTAATT-A-AGTAAAAAG-AGAT--T
1 AATCAGCAAATTGA-TAATTAAGAGT-CAAGGTA-ATGGT
*
12412 AATCAGTAAATTGATAATTAAGAGTCAAGGTAATGGT
1 AATCAGCAAATTGATAATTAAGAGTCAAGGTAATGGT
* * * *
12449 AATCAGC-AAGTCAGTAATT-A-AGTAAAAAG-AGAT--T
1 AATCAGCAAATTGA-TAATTAAGAGT-CAAGGTA-ATGGT
* *
12483 AATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGT
1 AATCAGCAAATTGATAATTAAGAGTCAAGGTAATGGT
* * * * * *
12520 GATCAGTAAAGTCAGTAATCAAGAGTCAATGTAAAAATGGT
1 AATCAGCAAATTGA-TAATTAAGAGTCAAGGT---AATGGT
* * * * *
12561 AATCAGTAAATCGATAATAAAGAGTCAAAGTGATGGT
1 AATCAGCAAATTGATAATTAAGAGTCAAGGTAATGGT
* *
12598 AATCAGTAAA-TCAGTAATTAAGAGT
1 AATCAGCAAATTGA-TAATTAAGAGT
12623 TGAGTGATTA
Statistics
Matches: 186, Mismatches: 36, Indels: 46
0.69 0.13 0.17
Matches are distributed among these distances:
34 24 0.13
35 28 0.15
36 29 0.16
37 60 0.32
38 15 0.08
40 15 0.08
41 15 0.08
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.27
Consensus pattern (37 bp):
AATCAGCAAATTGATAATTAAGAGTCAAGGTAATGGT
Found at i:13143 original size:18 final size:16
Alignment explanation
Indices: 13097--13147 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
13087 TAAACAAGAG
*
13097 AGTAAAAATGGTATCA
1 AGTAAAAATGGTATTA
*
13113 AGTAAAGATGGTATTA
1 AGTAAAAATGGTATTA
13129 AGGTCAAAAATGGTATTA
1 A-GT-AAAAATGGTATTA
13147 A
1 A
13148 ACAAAAGCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 15 0.50
17 2 0.07
18 13 0.43
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (16 bp):
AGTAAAAATGGTATTA
Found at i:13178 original size:25 final size:23
Alignment explanation
Indices: 13128--13220 Score: 125
Period size: 24 Copynumber: 3.8 Consensus size: 23
13118 AGATGGTATT
13128 AAGGTCAAAAATGGTATTAAACAA
1 AAGGT-AAAAATGGTATTAAACAA
13152 AAGCGTAAAAATGGTATTAAGTA-AA
1 AAG-GTAAAAATGGTATTAA--ACAA
13177 AAGGTCAAAAATGGTATTAAACAA
1 AAGGT-AAAAATGGTATTAAACAA
13201 AAGAGTAAAAATGGTATTAA
1 AAG-GTAAAAATGGTATTAA
13221 GTAAAAGTGG
Statistics
Matches: 63, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.02
24 38 0.60
25 23 0.37
26 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.18, T:0.23
Consensus pattern (23 bp):
AAGGTAAAAATGGTATTAAACAA
Found at i:13200 original size:49 final size:48
Alignment explanation
Indices: 13128--13331 Score: 195
Period size: 49 Copynumber: 4.4 Consensus size: 48
13118 AGATGGTATT
13128 AAGGTCAAAAATGGTATTAAACAAAAGCGTAAAAATGGTATTAAGTAAA
1 AAGGTCAAAAATGGTATTAAACAAAAG-GTAAAAATGGTATTAAGTAAA
13177 AAGGTCAAAAATGGTATTAAACAAAAGAGTAAAAATGGTATTAAGT-AA
1 AAGGTCAAAAATGGTATTAAACAAAAG-GTAAAAATGGTATTAAGTAAA
*
13225 AA-G-------TGGTATTAAGTAAAAAAGGTCAAAAATGGTATTAAGTAAA
1 AAGGTCAAAAATGGTATTAA--ACAAAAGGT-AAAAATGGTATTAAGTAAA
* ** *
13268 AAGGGTCAAAAATGGTA-TCAA-GTAAGGT----ATGGTATTAAGTAAG
1 AA-GGTCAAAAATGGTATTAAACAAAAGGTAAAAATGGTATTAAGTAAA
13311 AAGGTCAAAAAATGGTATTAA
1 AAGGTC-AAAAATGGTATTAA
13332 GTAAAAGAGT
Statistics
Matches: 133, Mismatches: 7, Indels: 35
0.76 0.04 0.20
Matches are distributed among these distances:
40 9 0.07
41 2 0.02
42 26 0.20
43 30 0.23
44 2 0.02
45 1 0.01
47 1 0.01
48 9 0.07
49 46 0.35
51 2 0.02
52 5 0.04
ACGTcount: A:0.50, C:0.04, G:0.21, T:0.24
Consensus pattern (48 bp):
AAGGTCAAAAATGGTATTAAACAAAAGGTAAAAATGGTATTAAGTAAA
Found at i:13225 original size:16 final size:16
Alignment explanation
Indices: 13204--13243 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
13194 TAAACAAAAG
13204 AGTAAAAATGGTATTA
1 AGTAAAAATGGTATTA
*
13220 AGTAAAAGTGGTATTA
1 AGTAAAAATGGTATTA
13236 AGTAAAAA
1 AGTAAAAA
13244 AGGTCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.28
Consensus pattern (16 bp):
AGTAAAAATGGTATTA
Found at i:13226 original size:24 final size:24
Alignment explanation
Indices: 13134--13343 Score: 148
Period size: 26 Copynumber: 9.1 Consensus size: 24
13124 TATTAAGGTC
** *
13134 AAAAATGGTATTAAACAAAAGCGT
1 AAAAATGGTATTAAGTAAAAGAGT
13158 AAAAATGGTATTAAGTAAAA-AGGT
1 AAAAATGGTATTAAGTAAAAGA-GT
**
13182 CAAAAATGGTATTAAACAAAAGAGT
1 -AAAAATGGTATTAAGTAAAAGAGT
13207 AAAAATGGTATTAAGT-AAA-AG-
1 AAAAATGGTATTAAGTAAAAGAGT
*
13228 -----TGGTATTAAGTAAAAAAGGT
1 AAAAATGGTATTAAGTAAAAGA-GT
*
13248 CAAAAATGGTATTAAGTAAAAAGGGT
1 -AAAAATGGTATTAAGT-AAAAGAGT
*
13274 CAAAAATGGTATCAAGT--AAG-GT
1 -AAAAATGGTATTAAGTAAAAGAGT
13296 ----ATGGTATTAAGTAAGAAG-GT
1 AAAAATGGTATTAAGTAA-AAGAGT
13316 CAAAAAATGGTATTAAGTAAAAGAGT
1 --AAAAATGGTATTAAGTAAAAGAGT
13342 AA
1 AA
13344 GAAAAATGGT
Statistics
Matches: 151, Mismatches: 11, Indels: 48
0.72 0.05 0.23
Matches are distributed among these distances:
16 11 0.07
17 14 0.09
18 1 0.01
19 1 0.01
20 5 0.03
22 4 0.03
23 6 0.04
24 36 0.24
25 23 0.15
26 46 0.30
27 4 0.03
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.24
Consensus pattern (24 bp):
AAAAATGGTATTAAGTAAAAGAGT
Found at i:13264 original size:42 final size:40
Alignment explanation
Indices: 13183--13269 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 40
13173 TAAAAAGGTC
*
13183 AAAAATGGTATTAAACAAAAGAGTAAAAATGGTATTAAGT
1 AAAAATGGTATTAAAAAAAAGAGTAAAAATGGTATTAAGT
*
13223 AAAAGTGGTATTAAGTAAAAAAG-GTCAAAAATGGTATTAAGT
1 AAAAATGGTATTAA--AAAAAAGAGT-AAAAATGGTATTAAGT
13265 AAAAA
1 AAAAA
13270 GGGTCAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 13 0.32
41 2 0.05
42 26 0.63
ACGTcount: A:0.55, C:0.02, G:0.18, T:0.24
Consensus pattern (40 bp):
AAAAATGGTATTAAAAAAAAGAGTAAAAATGGTATTAAGT
Found at i:13268 original size:91 final size:92
Alignment explanation
Indices: 13113--13285 Score: 264
Period size: 91 Copynumber: 1.9 Consensus size: 92
13103 AATGGTATCA
* *
13113 AGTAAAGATGGTATTAAGGTCAAAAATGGTATTAAACAAAAGCGTAAAAATGGTATTAAGTAAAA
1 AGTAAAAATGGTATTAAGGTCAAAAATGGTATTAAAAAAAAGCGTAAAAATGGTATTAAGTAAAA
13178 A-GGTCAAAAATGGTATTAAACAAAAG
66 AGGGTCAAAAATGGTATTAAACAAAAG
*
13204 AGTAAAAATGGTATTAA-GT-AAAAGTGGTATTAAGTAAAAAAG-GTCAAAAATGGTATTAAGTA
1 AGTAAAAATGGTATTAAGGTCAAAAATGGTATTAA--AAAAAAGCGT-AAAAATGGTATTAAGTA
13266 AAAAGGGTCAAAAATGGTAT
63 AAAAGGGTCAAAAATGGTAT
13286 CAAGTAAGGT
Statistics
Matches: 75, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
89 13 0.17
90 4 0.05
91 43 0.57
92 15 0.20
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.24
Consensus pattern (92 bp):
AGTAAAAATGGTATTAAGGTCAAAAATGGTATTAAAAAAAAGCGTAAAAATGGTATTAAGTAAAA
AGGGTCAAAAATGGTATTAAACAAAAG
Found at i:13301 original size:43 final size:43
Alignment explanation
Indices: 13253--13335 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
13243 AAGGTCAAAA
13253 ATGGTATTAAGTAAAAAGGGTC-AAAAATGGTATCAAGTAAGGT
1 ATGGTATTAAGTAAAAA-GGTCAAAAAATGGTATCAAGTAAGGT
* *
13296 ATGGTATTAAGTAAGAAGGTCAAAAAATGGTATTAAGTAA
1 ATGGTATTAAGTAAAAAGGTCAAAAAATGGTATCAAGTAA
13336 AAGAGTAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 4 0.11
43 33 0.89
ACGTcount: A:0.46, C:0.04, G:0.24, T:0.27
Consensus pattern (43 bp):
ATGGTATTAAGTAAAAAGGTCAAAAAATGGTATCAAGTAAGGT
Found at i:13332 original size:26 final size:27
Alignment explanation
Indices: 13296--13363 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
13286 CAAGTAAGGT
*
13296 ATGGTATTAAGTAAGAAG-GTCA-AAAA
1 ATGGTATTAAGTAA-AAGAGTAAGAAAA
13322 ATGGTATTAAGTAAAAGAGTAAGAAAA
1 ATGGTATTAAGTAAAAGAGTAAGAAAA
*
13349 ATGGTA-AAAGTAAAA
1 ATGGTATTAAGTAAAA
13364 ATGATAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 3 0.08
26 25 0.66
27 10 0.26
ACGTcount: A:0.54, C:0.01, G:0.22, T:0.22
Consensus pattern (27 bp):
ATGGTATTAAGTAAAAGAGTAAGAAAA
Found at i:13332 original size:69 final size:65
Alignment explanation
Indices: 13159--13343 Score: 250
Period size: 68 Copynumber: 2.8 Consensus size: 65
13149 CAAAAGCGTA
*
13159 AAAATGGTATTAAGTAAAAAGGTCAAAAATGGTATTAA--ACAAAAGAGTAAAAATGGTATTAAG
1 AAAATGGTATTAAGTAAAAAGGTCAAAAATGGTATTAAGTA-AAAAGAGTAAAAATGGTATCAAG
13222 T
65 T
*
13223 AAAAGTGGTATTAAGTAAAAAAGGTCAAAAATGGTATTAAGTAAAAAGGGTCAAAAATGGTATCA
1 AAAA-TGGTATTAAGT-AAAAAGGTCAAAAATGGTATTAAGTAAAAAGAGT-AAAAATGGTATCA
13288 AGT
63 AGT
* *
13291 AAGGTATGGTATTAAGTAAGAAGGTCAAAAAATGGTATTAAGT-AAAAGAGTAA
1 AA--AATGGTATTAAGTAAAAAGGTC-AAAAATGGTATTAAGTAAAAAGAGTAA
13344 GAAAAATGGT
Statistics
Matches: 108, Mismatches: 5, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
64 4 0.04
65 11 0.10
66 23 0.21
67 9 0.08
68 33 0.31
69 27 0.25
70 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.22, T:0.24
Consensus pattern (65 bp):
AAAATGGTATTAAGTAAAAAGGTCAAAAATGGTATTAAGTAAAAAGAGTAAAAATGGTATCAAGT
Found at i:13360 original size:69 final size:64
Alignment explanation
Indices: 13159--13363 Score: 250
Period size: 69 Copynumber: 3.1 Consensus size: 64
13149 CAAAAGCGTA
** *
13159 AAAATGGTATTAAGTAAAAAGGTCAAAAATGGTATTAAACAAAAGAGTAAAAATGGTATTAAGT
1 AAAATGGTATTAAGTAAAAAGGTCAAAAATGGTATTAAGTAAAAGAGTAAAAATGGTATAAAGT
* *
13223 AAAAGTGGTATTAAGTAAAAAAGGTCAAAAATGGTATTAAGTAAAAAGGGTCAAAAATGGTATCA
1 AAAA-TGGTATTAAGT-AAAAAGGTCAAAAATGGTATTAAGT-AAAAGAGT-AAAAATGGTATAA
13288 AGT
62 AGT
* *
13291 AAGGTATGGTATTAAGTAAGAAGGTCAAAAAATGGTATTAAGTAAAAGAGTAAGAAAAATGGTA-
1 AA--AATGGTATTAAGTAAAAAGGTC-AAAAATGGTATTAAGTAAAAGAGT---AAAAATGGTAT
13355 AAAGT
60 AAAGT
13360 AAAA
1 AAAA
13364 ATGATAAAAG
Statistics
Matches: 122, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
64 4 0.03
65 11 0.09
66 23 0.19
67 8 0.07
68 32 0.26
69 33 0.27
70 11 0.09
ACGTcount: A:0.52, C:0.03, G:0.21, T:0.23
Consensus pattern (64 bp):
AAAATGGTATTAAGTAAAAAGGTCAAAAATGGTATTAAGTAAAAGAGTAAAAATGGTATAAAGT
Found at i:13394 original size:15 final size:15
Alignment explanation
Indices: 13345--13375 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13335 AAAGAGTAAG
*
13345 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
13360 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
13375 A
1 A
13376 GTAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Found at i:14432 original size:15 final size:16
Alignment explanation
Indices: 14397--14432 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
14387 TAGGCACACA
*
14397 AAAAATGGTATTAATT
1 AAAAATGGTATTAAGT
14413 AAAAATGGTATTAAGT
1 AAAAATGGTATTAAGT
14429 AAAA
1 AAAA
14433 GAGTAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (16 bp):
AAAAATGGTATTAAGT
Found at i:14489 original size:15 final size:15
Alignment explanation
Indices: 14440--14470 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14430 AAAGAGTAAG
*
14440 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
14455 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
14470 A
1 A
14471 GTAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Done.