Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009570.1 Corchorus capsularis cultivar CVL-1 contig09591, 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: 22113
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:843 original size:12 final size:12
Alignment explanation
Indices: 826--851 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
816 AATTTAATTA
826 GTGCAAGATTTT
1 GTGCAAGATTTT
838 GTGCAAGATTTT
1 GTGCAAGATTTT
850 GT
1 GT
852 AGTAATGACA
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:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (12 bp):
GTGCAAGATTTT
Found at i:1614 original size:26 final size:25
Alignment explanation
Indices: 1581--1629 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
1571 TATAGTTAAG
1581 TAATAGATAACTATAAAAA-ATAAAAA
1 TAATAGATAA--ATAAAAAGATAAAAA
1607 TAATAGATAAATAAAAAGATAAA
1 TAATAGATAAATAAAAAGATAAA
1630 TAGATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 5 0.23
26 10 0.45
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.22
Consensus pattern (25 bp):
TAATAGATAAATAAAAAGATAAAAA
Found at i:1670 original size:24 final size:24
Alignment explanation
Indices: 1582--1693 Score: 85
Period size: 24 Copynumber: 4.8 Consensus size: 24
1572 ATAGTTAAGT
1582 AATAGATAACTATAAA-AAATA-A-A
1 AATAGAT-A-TATAAACAAATAGATA
* * *
1605 AATA-ATAGATAAATAAAAAGATA
1 AATAGATATATAAACAAATAGATA
1628 AATAGATATATAAACAAATAGATA
1 AATAGATATATAAACAAATAGATA
*
1652 AATA-AGTATGTAAACAAAT--ATA
1 AATAGA-TATATAAACAAATAGATA
* * *
1674 TATATATATATAAATAAATA
1 AATAGATATATAAACAAATA
1694 ATAGCTTAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
20 5 0.07
21 5 0.07
22 20 0.27
23 11 0.15
24 32 0.44
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (24 bp):
AATAGATATATAAACAAATAGATA
Found at i:1756 original size:17 final size:16
Alignment explanation
Indices: 1735--1849 Score: 86
Period size: 14 Copynumber: 7.7 Consensus size: 16
1725 AAAATAAAAG
*
1735 ATAAATAAATAATAGTA
1 ATAAATAGATAATAG-A
*
1752 TTAAATAGATAATAGA
1 ATAAATAGATAATAGA
1768 ATAAATAGATAAT--A
1 ATAAATAGATAATAGA
*
1782 ATAAATA-ATAAT--T
1 ATAAATAGATAATAGA
* * *
1795 ACAAATAGATAAGAAA
1 ATAAATAGATAATAGA
*
1811 ATAAATAG-TGATAG-
1 ATAAATAGATAATAGA
*
1825 ATAGATAGATAAT--A
1 ATAAATAGATAATAGA
1839 ATAAATAGATA
1 ATAAATAGATA
1850 GATAAAGAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
13 11 0.14
14 29 0.37
15 6 0.08
16 20 0.25
17 13 0.16
ACGTcount: A:0.61, C:0.01, G:0.10, T:0.28
Consensus pattern (16 bp):
ATAAATAGATAATAGA
Found at i:1791 original size:43 final size:41
Alignment explanation
Indices: 1725--1849 Score: 114
Period size: 43 Copynumber: 3.0 Consensus size: 41
1715 AGGATATACT
*
1725 AAAATAAA-AGATA-AATAAATAATAGTATTAAATAGATAAT
1 AAAATAAATAGATATAATAAATAATA-TATTAAATAGATAAG
*
1765 AGAATAAATAGATAATAATAAATAATA-ATTACAAATAGATAAG
1 AAAATAAATAGAT-ATAATAAATAATATATT--AAATAGATAAG
* *
1808 AAAATAAATAG-TGATAGATAGATAGATAATAATAAATAGATA
1 AAAATAAATAGAT-ATA-ATAAATA-AT-ATATTAAATAGATA
1850 GATAAAGAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
40 7 0.10
41 7 0.10
42 5 0.07
43 37 0.53
44 11 0.16
45 1 0.01
46 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.26
Consensus pattern (41 bp):
AAAATAAATAGATATAATAAATAATATATTAAATAGATAAG
Found at i:3268 original size:35 final size:35
Alignment explanation
Indices: 3185--3723 Score: 613
Period size: 35 Copynumber: 15.5 Consensus size: 35
3175 TAATCGTTGG
* *
3185 AAACTTCATGGAATGAAATCAACTCTGACCTCT-A
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
**
3219 AAACTTCTTAAAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
*
3254 AAACTTCTTGAAATGAGATCAACTCTGACCTCTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGA-C-CTCTGA
*
3291 AAACTTCTTGGAATGAGATCAATTCTGACCTCTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGA-C-CTCTGA
3328 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
3363 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
*
3398 AAACTTCTTGAAATGAGATCAACTCTGACCTCTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGA-C-CTCTGA
3435 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
* *
3470 AAACTTCTTGGAATGAGATCAACTCTGATCATC-GG
1 AAACTTCTTGGAATGAGATCAACTCTGA-CCTCTGA
* *
3505 AAACTTCTTGGAAT--GATCAACTCTGATCGT-TGG
1 AAACTTCTTGGAATGAGATCAACTCTGA-CCTCTGA
* * *
3538 AAACTT-TTTGAATGAGATCAACTCTGATCTTTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
* * *
3572 AAACCTT-TT-GAATGAGATGAACTCTGATCATC-GG
1 AAA-CTTCTTGGAATGAGATCAACTCTGA-CCTCTGA
* * *
3606 AAACTTCTTAGAAT--GATCAACTCTGATCGT-TGG
1 AAACTTCTTGGAATGAGATCAACTCTGA-CCTCTGA
* * *
3639 AAACTT-TTTGAATGAGATCAACTCTGATCTTTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
** * *
3673 AAACTT-TTTTAATGAGATCAACTATGATCT-TCGAA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCT-G-A
3708 AAACTTCTTGGAATGA
1 AAACTTCTTGGAATGA
3724 CCGCACTGGG
Statistics
Matches: 452, Mismatches: 32, Indels: 40
0.86 0.06 0.08
Matches are distributed among these distances:
32 12 0.03
33 51 0.11
34 112 0.25
35 162 0.36
36 14 0.03
37 101 0.22
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (35 bp):
AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
Found at i:3320 original size:72 final size:71
Alignment explanation
Indices: 3185--3723 Score: 609
Period size: 72 Copynumber: 7.7 Consensus size: 71
3175 TAATCGTTGG
* * * **
3185 AAACTTCATGGAATGAAATCAACTCTGAC-CTCT-AAAACTTCTTAAAATGAGATCAACTCTGAC
1 AAACTTCTTGAAATGAGATCAACTCTGACTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGAC
3248 CTCTGA
66 CTCTGA
*
3254 AAACTTCTTGAAATGAGATCAACTCTGACCTCTCTGAAAACTTCTTGGAATGAGATCAATTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGA-CTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA
3319 CCTCTCTGA
65 -C-CTCTGA
*
3328 AAACTTCTTGGAATGAGATCAACTCTGAC-CTCTGAAAACTTCTTGGAATGAGATCAACTCTGAC
1 AAACTTCTTGAAATGAGATCAACTCTGACTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGAC
3392 CTCTGA
66 CTCTGA
3398 AAACTTCTTGAAATGAGATCAACTCTGACCTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGA-CTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA
3463 CCTCTGA
65 CCTCTGA
* *
3470 AAACTTCTTGGAATGAGATCAACTCTGA-TCATC-GGAAACTTCTTGGAAT--GATCAACTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACTC-TCTGAAAACTTCTTGGAATGAGATCAACTCTGA
* *
3531 TCGT-TGG
65 -CCTCTGA
* * *
3538 AAACTTTTTG-AATGAGATCAACTCTGA-TCTTTGAAAACCTT-TT-GAATGAGATGAACTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACTCTCTGAAAA-CTTCTTGGAATGAGATCAACTCTGA
* *
3599 TCATC-GG
65 -CCTCTGA
* *
3606 AAACTTCTT-AGAAT--GATCAACTCTGA-TCGT-TGGAAACTT-TTTGAATGAGATCAACTCTG
1 AAACTTCTTGA-AATGAGATCAACTCTGACTC-TCTGAAAACTTCTTGGAATGAGATCAACTCTG
* *
3665 ATCTTTGA
64 ACCTCTGA
** *
3673 AAACTT-TTTTAATGAGATCAACTATGA-TCT-TCGAAAAACTTCTTGGAATGA
1 AAACTTCTTGAAATGAGATCAACTCTGACTCTCT-G-AAAACTTCTTGGAATGA
3724 CCGCACTGGG
Statistics
Matches: 416, Mismatches: 29, Indels: 49
0.84 0.06 0.10
Matches are distributed among these distances:
66 16 0.04
67 70 0.17
68 65 0.16
69 36 0.09
70 59 0.14
71 8 0.02
72 127 0.31
73 2 0.00
74 33 0.08
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (71 bp):
AAACTTCTTGAAATGAGATCAACTCTGACTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGAC
CTCTGA
Found at i:3449 original size:107 final size:107
Alignment explanation
Indices: 3185--3723 Score: 648
Period size: 107 Copynumber: 5.1 Consensus size: 107
3175 TAATCGTTGG
* * **
3185 AAACTTCATGGAATGAAATCAACTCTGAC-CTCT-AAAACTTCTTAAAATGAGATCAACTCTGAC
1 AAACTTCTTGGAATGAGATCAACTCTGACTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGAC
* *
3248 CTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTCTGA
66 CTCTGAAAACTTCTTGGAATGAGATCAACTCTGATC-CTCTGA
*
3291 AAACTTCTTGGAATGAGATCAATTCTGACCTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGA-CTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA
3356 CCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA-CCTCTGA
65 CCTCTGAAAACTTCTTGGAATGAGATCAACTCTGATCCTCTGA
*
3398 AAACTTCTTGAAATGAGATCAACTCTGACCTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGA-CTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA
* *
3463 CCTCTGAAAACTTCTTGGAATGAGATCAACTCTGATCATC-GG
65 CCTCTGAAAACTTCTTGGAATGAGATCAACTCTGATCCTCTGA
* *
3505 AAACTTCTTGGAAT--GATCAACTCTGA-TCGT-TGGAAACTT-TTTGAATGAGATCAACTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACTC-TCTGAAAACTTCTTGGAATGAGATCAACTCTGA
* * * * *
3565 TCTTTGAAAACCTT-TT-GAATGAGATGAACTCTGATCATC-GG
65 CCTCTGAAAA-CTTCTTGGAATGAGATCAACTCTGATCCTCTGA
* * *
3606 AAACTTCTTAGAAT--GATCAACTCTGA-TCGT-TGGAAACTT-TTTGAATGAGATCAACTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACTC-TCTGAAAACTTCTTGGAATGAGATCAACTCTGA
* * ** * *
3666 TCTTTGAAAACTT-TTTTAATGAGATCAACTATGATCTTC-GAA
65 CCTCTGAAAACTTCTTGGAATGAGATCAACTCTGATCCTCTG-A
3708 AAACTTCTTGGAATGA
1 AAACTTCTTGGAATGA
3724 CCGCACTGGG
Statistics
Matches: 400, Mismatches: 23, Indels: 22
0.90 0.05 0.05
Matches are distributed among these distances:
100 5 0.01
101 113 0.28
102 43 0.11
103 13 0.03
104 1 0.00
105 12 0.03
106 25 0.06
107 119 0.30
108 8 0.02
109 61 0.15
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (107 bp):
AAACTTCTTGGAATGAGATCAACTCTGACTCTCTGAAAACTTCTTGGAATGAGATCAACTCTGAC
CTCTGAAAACTTCTTGGAATGAGATCAACTCTGATCCTCTGA
Found at i:3840 original size:109 final size:108
Alignment explanation
Indices: 3707--3910 Score: 320
Period size: 109 Copynumber: 1.9 Consensus size: 108
3697 TGATCTTCGA
* * *
3707 AAAACTTCTTGGAATGACCGCACTGGGTCGTCT-GACAATCAACTCTGATATTTGAAAACTTTTT
1 AAAACTTCTTGAAATGACCGCACTGGGTCGTCTGGA-AATCAACTCTGATATCTGAAAAC-TTCT
3771 TGAAATGACCGCACTAGGTCGCCTAGAAATCAACTCTAATATTTG
64 TGAAATGACCGCACTAGGTCGCCTAGAAATCAACTCTAATATTTG
*
3816 AAAACTTTTTGAAATGACCGCACTGGGTCGTCTGGAAATCAACTCTGATATCTGAAAACTTCTTG
1 AAAACTTCTTGAAATGACCGCACTGGGTCGTCTGGAAATCAACTCTGATATCTGAAAACTTCTTG
* * *
3881 AAATGACCGCACTGGGTCGTCTGGAAATCA
66 AAATGACCGCACTAGGTCGCCTAGAAATCA
3911 CTGAATAAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 32 0.37
109 53 0.61
110 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (108 bp):
AAAACTTCTTGAAATGACCGCACTGGGTCGTCTGGAAATCAACTCTGATATCTGAAAACTTCTTG
AAATGACCGCACTAGGTCGCCTAGAAATCAACTCTAATATTTG
Found at i:3854 original size:54 final size:54
Alignment explanation
Indices: 3689--3910 Score: 311
Period size: 54 Copynumber: 4.1 Consensus size: 54
3679 TTTTAATGAG
* * * *
3689 ATCAACTATGATCTTCGAAAAACTTCTTGGAATGACCGCACTGGGTCGTCT-GACA
1 ATCAACTCTGATATTTG-AAAACTTCTTGAAATGACCGCACTGGGTCGTCTGGA-A
* * * *
3744 ATCAACTCTGATATTTGAAAACTTTTTTGAAATGACCGCACTAGGTCGCCTAGAA
1 ATCAACTCTGATATTTGAAAAC-TTCTTGAAATGACCGCACTGGGTCGTCTGGAA
* *
3799 ATCAACTCTAATATTTGAAAACTTTTTGAAATGACCGCACTGGGTCGTCTGGAA
1 ATCAACTCTGATATTTGAAAACTTCTTGAAATGACCGCACTGGGTCGTCTGGAA
*
3853 ATCAACTCTGATATCTGAAAACTTCTTGAAATGACCGCACTGGGTCGTCTGGAA
1 ATCAACTCTGATATTTGAAAACTTCTTGAAATGACCGCACTGGGTCGTCTGGAA
3907 ATCA
1 ATCA
3911 CTGAATAAAA
Statistics
Matches: 151, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
54 89 0.59
55 60 0.40
56 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
ATCAACTCTGATATTTGAAAACTTCTTGAAATGACCGCACTGGGTCGTCTGGAA
Found at i:3959 original size:34 final size:34
Alignment explanation
Indices: 3910--4141 Score: 351
Period size: 34 Copynumber: 6.9 Consensus size: 34
3900 TCTGGAAATC
* * *
3910 ACTGAATAAAAACCGCCCTGGGTCAACTGAATAC
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATAA
*
3944 ACTGAAGAAAGACCGCCCTGGG--AACTGAATAC
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATAA
*
3976 ACTGAAGAAAGACCGCCTTGGGTCAACTGAATAA
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATAA
* *
4010 ACTGAAGAAAGATCGTCCTGGGTCAACTGAATAA
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATAA
4044 ACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAA
1 ACTGAAGAAAGACCGCCCTGGGTCAACTG-AATAA
*
4079 ACTTAAGAAAGACCGCCCTGGGTCAACTGAATAA
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATAA
* *
4113 ACTGAATAAAGACCGCCATGGGTCAACTG
1 ACTGAAGAAAGACCGCCCTGGGTCAACTG
4142 TACTTGACTC
Statistics
Matches: 182, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
32 31 0.17
34 118 0.65
35 33 0.18
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (34 bp):
ACTGAAGAAAGACCGCCCTGGGTCAACTGAATAA
Found at i:4110 original size:69 final size:68
Alignment explanation
Indices: 3910--4141 Score: 351
Period size: 69 Copynumber: 3.4 Consensus size: 68
3900 TCTGGAAATC
* * *
3910 ACTGAATAAAAACCGCCCTGGGTCAACTGAATACACTGAAGAAAGACCGCCCTGGG--AACTGAA
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAA
*
3973 TAC
66 TAA
* * *
3976 ACTGAAGAAAGACCGCCTTGGGTCAACTGAATAAACTGAAGAAAGATCGTCCTGGGTCAACTGAA
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAA
4041 TAA
66 TAA
*
4044 ACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTTAAGAAAGACCGCCCTGGGTCAACTGA
1 ACTGAAGAAAGACCGCCCTGGGTCAACTG-AATAAACTGAAGAAAGACCGCCCTGGGTCAACTGA
4109 ATAA
65 ATAA
* *
4113 ACTGAATAAAGACCGCCATGGGTCAACTG
1 ACTGAAGAAAGACCGCCCTGGGTCAACTG
4142 TACTTGACTC
Statistics
Matches: 150, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
66 50 0.33
68 37 0.25
69 63 0.42
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (68 bp):
ACTGAAGAAAGACCGCCCTGGGTCAACTGAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAA
TAA
Found at i:4124 original size:103 final size:99
Alignment explanation
Indices: 3910--4141 Score: 347
Period size: 103 Copynumber: 2.3 Consensus size: 99
3900 TCTGGAAATC
* *
3910 ACTGAATAAAAACCGCCCTGGGTCAACTGAATACACTGAAGAAAGACCGCCCTGGGAACTGAATA
1 ACTGAATAAAGACCG-CCTGGGTCAACTGAATAAACTGAAGAAAGACCGCCCTGGGAACTGAATA
* *
3975 CACTGAAGAAAGACCGCCTTGGGTCAACTGAATAA
65 AACTGAAGAAAGACCGCCCTGGGTCAACTGAATAA
* *
4010 ACTGAAGAAAGATCGTCCTGGGTCAACTGAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAA
1 ACTGAATAAAGACCG-CCTGGGTCAACTGAATAAACTGAAGAAAGACCGCCCTGGG--AACTG-A
*
4075 ATAAACTTAAGAAAGACCGCCCTGGGTCAACTGAATAA
62 ATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAATAA
4113 ACTGAATAAAGACCGCCATGGGTCAACTG
1 ACTGAATAAAGACCGCC-TGGGTCAACTG
4142 TACTTGACTC
Statistics
Matches: 118, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
100 51 0.43
102 7 0.06
103 60 0.51
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (99 bp):
ACTGAATAAAGACCGCCTGGGTCAACTGAATAAACTGAAGAAAGACCGCCCTGGGAACTGAATAA
ACTGAAGAAAGACCGCCCTGGGTCAACTGAATAA
Found at i:10374 original size:7 final size:7
Alignment explanation
Indices: 10360--10411 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
10350 TTCAAAAATT
10360 AAAA-AA
1 AAAACAA
10366 AAAACAA
1 AAAACAA
10373 AAAAC-A
1 AAAACAA
10379 AAAACAAA
1 AAAAC-AA
*
10387 AACAAAAA
1 AA-AACAA
10395 AAAACAA
1 AAAACAA
*
10402 AATACAA
1 AAAACAA
10409 AAA
1 AAA
10412 TCAGGAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 10 0.26
7 19 0.50
8 7 0.18
9 2 0.05
ACGTcount: A:0.87, C:0.12, G:0.00, T:0.02
Consensus pattern (7 bp):
AAAACAA
Found at i:10375 original size:19 final size:19
Alignment explanation
Indices: 10360--10411 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 19
10350 TTCAAAAATT
10360 AAAAA-AAAAACAAAAAAC
1 AAAAACAAAAACAAAAAAC
10378 AAAAACAAAAAC--AAAA-
1 AAAAACAAAAACAAAAAAC
10394 AAAAACAAAATACAAAAA
1 AAAAACAAAA-ACAAAAA
10412 TCAGGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.33
17 6 0.20
18 5 0.17
19 9 0.30
ACGTcount: A:0.87, C:0.12, G:0.00, T:0.02
Consensus pattern (19 bp):
AAAAACAAAAACAAAAAAC
Found at i:10376 original size:13 final size:13
Alignment explanation
Indices: 10360--10396 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
10350 TTCAAAAATT
10360 AAAAAAAAAACAA
1 AAAAAAAAAACAA
*
10373 AAAACAAAAACAA
1 AAAAAAAAAACAA
10386 AAACAAAAAAA
1 AAA-AAAAAAA
10397 AACAAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:10421 original size:23 final size:22
Alignment explanation
Indices: 10361--10411 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 22
10351 TCAAAAATTA
*
10361 AAAAAAAAACAAAAAACAAAAAC
1 AAAAACAAA-AAAAAACAAAAAC
10384 AAAAACAAAAAAAAACAAAATAC
1 AAAAACAAAAAAAAACAAAA-AC
10407 AAAAA
1 AAAAA
10412 TCAGGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (22 bp):
AAAAACAAAAAAAAACAAAAAC
Found at i:10906 original size:25 final size:26
Alignment explanation
Indices: 10858--10907 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
10848 TATAGTTAAG
10858 TAATAGATAACTATAAAAAAATAAAAA
1 TAATAGATAAC-ATAAAAAAATAAAAA
*
10885 TAATAGATAA-ATAAAAAGATAAA
1 TAATAGATAACATAAAAAAATAAA
10908 TAGATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.55
27 10 0.45
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (26 bp):
TAATAGATAACATAAAAAAATAAAAA
Found at i:10912 original size:8 final size:8
Alignment explanation
Indices: 10882--11152 Score: 71
Period size: 8 Copynumber: 35.1 Consensus size: 8
10872 AAAAAAATAA
10882 AAATA-AT
1 AAATAGAT
* *
10889 AGATAAAT
1 AAATAGAT
*
10897 AAAAAGAT
1 AAATAGAT
10905 AAATAGAT
1 AAATAGAT
* * *
10913 ATATAAAC
1 AAATAGAT
10921 AAATAGAT
1 AAATAGAT
10929 AAATA-AGT
1 AAATAGA-T
** *
10937 ATGTAAAT
1 AAATAGAT
*
10945 AAATATAT
1 AAATAGAT
*
10953 ATATATATAT
1 A-A-ATAGAT
*
10963 AAATAAAT
1 AAATAGAT
*
10971 -AATAGCT
1 AAATAGAT
*
10978 TAATAGAT
1 AAATAGAT
*
10986 AATTAGA-
1 AAATAGAT
* *
10993 AGGATATACT
1 A-AATAGA-T
11003 -AA-A-AT
1 AAATAGAT
11008 AAA-AGAT
1 AAATAGAT
*
11015 AAATAAAT
1 AAATAGAT
11023 -AATAGTATT
1 AAATAG-A-T
11032 AAATAGAT
1 AAATAGAT
11040 -AATAGAAT
1 AAATAG-AT
11048 AAATAGAT
1 AAATAGAT
11056 -AATA-AT
1 AAATAGAT
11062 AAATA-AT
1 AAATAGAT
* *
11069 -AAT-TAC
1 AAATAGAT
11075 AAATAGAT
1 AAATAGAT
*
11083 AAGA-AAAT
1 AA-ATAGAT
11091 AAATAG-T
1 AAATAGAT
11098 AAATAGAT
1 AAATAGAT
* *
11106 AAA-ACAA
1 AAATAGAT
11113 AAACTA-AGT
1 AAA-TAGA-T
*
11122 AGATAGAT
1 AAATAGAT
*
11130 AGATAGAT
1 AAATAGAT
11138 -AATA-AT
1 AAATAGAT
11144 AAATAGAT
1 AAATAGAT
11152 A
1 A
11153 GATAAAGAAA
Statistics
Matches: 196, Mismatches: 38, Indels: 59
0.67 0.13 0.20
Matches are distributed among these distances:
5 1 0.01
6 12 0.06
7 59 0.30
8 97 0.49
9 15 0.08
10 12 0.06
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (8 bp):
AAATAGAT
Found at i:10947 original size:4 final size:4
Alignment explanation
Indices: 10870--10972 Score: 55
Period size: 4 Copynumber: 25.0 Consensus size: 4
10860 ATAGATAACT
* * * * *
10870 ATAA AAAA ATAA AAATA ATAG ATAA ATAA A-AA GATAA ATAG ATAT ATAA
1 ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA
* * * * * * *
10919 ACAA ATAG ATAA ATAA GTAT GTAA ATAA ATATA TATAT ATAT ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A -ATAA ATAA ATAA ATAA
10969 ATAA
1 ATAA
10973 TAGCTTAATA
Statistics
Matches: 75, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
3 2 0.03
4 64 0.85
5 6 0.08
6 3 0.04
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:11069 original size:43 final size:40
Alignment explanation
Indices: 11003--11107 Score: 117
Period size: 43 Copynumber: 2.6 Consensus size: 40
10993 AGGATATACT
*
11003 AAAATAAA-AGATAAATAAATAATAGTATT-AAATAGATAAT
1 AAAATAAATAGATAAATAAATAATA--ATTAAAATAGATAAG
*
11043 AGAATAAATAGATAATAATAAATAATAATTACAAATAGATAAG
1 AAAATAAATAGAT-A-AATAAATAATAATTA-AAATAGATAAG
*
11086 AAAATAAATAG-TAAATAGATAA
1 AAAATAAATAGATAAATAAATAA
11108 AACAAAAACT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
40 15 0.27
41 8 0.14
42 2 0.04
43 31 0.55
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.26
Consensus pattern (40 bp):
AAAATAAATAGATAAATAAATAATAATTAAAATAGATAAG
Found at i:11102 original size:23 final size:22
Alignment explanation
Indices: 11007--11152 Score: 79
Period size: 22 Copynumber: 6.5 Consensus size: 22
10997 TATACTAAAA
*
11007 TAAA-AGATAAATAAATAATAGTAT
1 TAAATAGATAAA-AAATAA-A-TAG
*
11031 TAAATAGATAATAGAATAAATAG
1 TAAATAGATAA-AAAATAAATAG
* *
11054 -ATAATA-ATAAATAATAATTA-
1 TA-AATAGATAAAAAATAAATAG
*
11074 CAAATAGATAAGAAAATAAATAG
1 TAAATAGATAA-AAAATAAATAG
11097 TAAATAGATAAAACAA-AAACTAAG
1 TAAATAGATAAAA-AATAAA-T-AG
* * * *
11121 TAGATAGATAGATAGAT-AATAA
1 TAAATAGATA-AAAAATAAATAG
11143 TAAATAGATA
1 TAAATAGATA
11153 GATAAAGAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
20 4 0.04
21 13 0.13
22 28 0.29
23 20 0.20
24 19 0.19
25 13 0.13
26 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.25
Consensus pattern (22 bp):
TAAATAGATAAAAAATAAATAG
Found at i:16172 original size:20 final size:21
Alignment explanation
Indices: 16147--16189 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
16137 TAATCATGTC
*
16147 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
16167 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
16188 AA
1 AA
16190 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:16319 original size:2 final size:2
Alignment explanation
Indices: 16312--16343 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
16302 TATCTTTAAT
16312 TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16344 GAGTTTAGTT
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):
TA
Found at i:18313 original size:34 final size:31
Alignment explanation
Indices: 18233--18323 Score: 114
Period size: 31 Copynumber: 2.8 Consensus size: 31
18223 AGCACAAATG
*
18233 AATTTGATTAGTGCAA-GATTTTGTAGTATCT
1 AATTTAATTAGTG-AAGGATTTTGTAGTATCT
18264 AATTTAATTAGTGAAGGATTTTGTAGTAAT-T
1 AATTTAATTAGTGAAGGATTTTGTAGT-ATCT
18295 AATTTAATTATTAGTGAAGGATTTTGTAG
1 AATTT-A--ATTAGTGAAGGATTTTGTAG
18324 CAGCACAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
30 2 0.04
31 29 0.54
32 3 0.06
34 20 0.37
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (31 bp):
AATTTAATTAGTGAAGGATTTTGTAGTATCT
Found at i:22066 original size:28 final size:31
Alignment explanation
Indices: 22009--22073 Score: 100
Period size: 28 Copynumber: 2.2 Consensus size: 31
21999 TATCTAAAAA
*
22009 AATCCCTTATATTTTTCTTTTGGGACAAA-T
1 AATCCCTTATATTTTTCTTTTGGAACAAATT
22039 AATCCCTTATA-TTTT-TTTTGGAACAAATT
1 AATCCCTTATATTTTTCTTTTGGAACAAATT
22068 AATCCC
1 AATCCC
22074 CTACGTTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 11 0.33
29 11 0.33
30 11 0.33
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (31 bp):
AATCCCTTATATTTTTCTTTTGGAACAAATT
Done.