Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007352.1 Corchorus capsularis cultivar CVL-1 contig07373, 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: 33556
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:3556 original size:22 final size:22
Alignment explanation
Indices: 3528--3573 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3518 CAATTCAAGC
* * *
3528 ATCATGTCAGGCTGATGATCAT
1 ATCATGTCAAGCTCATAATCAT
3550 ATCATGTCAAGCTCATAATCAT
1 ATCATGTCAAGCTCATAATCAT
3572 AT
1 AT
3574 GATATATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (22 bp):
ATCATGTCAAGCTCATAATCAT
Found at i:6798 original size:49 final size:50
Alignment explanation
Indices: 6722--6836 Score: 144
Period size: 49 Copynumber: 2.3 Consensus size: 50
6712 AAATGTGAAG
* * ** *
6722 AGAAAACT-GGACCATCCGACCGGGAAGGGGCATTTTGGG-AATAAAGAA
1 AGAAAACTGGGACCTTCCAACCAAGAAGGGGCATTTTGGGAAACAAAGAA
*
6770 AGAAAACTGGGACCTTCCAACCAAGAAGGGGCATTTTGGGAAACAAATAA
1 AGAAAACTGGGACCTTCCAACCAAGAAGGGGCATTTTGGGAAACAAAGAA
* *
6820 AGAGAACAGGGACCTTC
1 AGAAAACTGGGACCTTC
6837 TGACCTGGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 8 0.14
49 27 0.47
50 22 0.39
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.15
Consensus pattern (50 bp):
AGAAAACTGGGACCTTCCAACCAAGAAGGGGCATTTTGGGAAACAAAGAA
Found at i:7290 original size:32 final size:32
Alignment explanation
Indices: 7244--7307 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
7234 ATTTCATCAT
* *
7244 TTACTTAAAGGTTCAAT-TTTTATTTACAAAAA
1 TTACTTAAAAGTTCAATGTTTTAATTA-AAAAA
7276 TTACTTAAAAGTTCAATGTTTTAATTAAAAAA
1 TTACTTAAAAGTTCAATGTTTTAATTAAAAAA
7308 CTCAATCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (32 bp):
TTACTTAAAAGTTCAATGTTTTAATTAAAAAA
Found at i:7545 original size:51 final size:51
Alignment explanation
Indices: 7456--7631 Score: 246
Period size: 51 Copynumber: 3.5 Consensus size: 51
7446 ACCACACTTC
* ** * *
7456 TATTTACAAATTAATCATCAA-TTCCATCATTTGGTTCAAAGATATCATTTT
1 TATTTACAAATTAATCA-CAAGTTCAATCATTTAATTCAAAGCTCTCATTTT
*
7507 TATTTACAAATTAATCACAAGTTCAATCACTTAATTCAAAGCTCTCATTTT
1 TATTTACAAATTAATCACAAGTTCAATCATTTAATTCAAAGCTCTCATTTT
* *
7558 TATTTACAAATTACTTACAAGTTCAATCATTTAATTCAAAGCTCTCATTTT
1 TATTTACAAATTAATCACAAGTTCAATCATTTAATTCAAAGCTCTCATTTT
* *
7609 TATTTACAAATTACTCAAAAGTT
1 TATTTACAAATTAATCACAAGTT
7632 TAATTATTAG
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
50 3 0.03
51 110 0.97
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (51 bp):
TATTTACAAATTAATCACAAGTTCAATCATTTAATTCAAAGCTCTCATTTT
Found at i:9773 original size:20 final size:20
Alignment explanation
Indices: 9748--9786 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9738 AAAAAGAGCA
9748 CCAATTTGCAAATCAAATGT
1 CCAATTTGCAAATCAAATGT
*
9768 CCAATTTGTAAATCAAATG
1 CCAATTTGCAAATCAAATG
9787 CCTTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
CCAATTTGCAAATCAAATGT
Found at i:9952 original size:14 final size:14
Alignment explanation
Indices: 9933--9960 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9923 TGATATTAAT
9933 CTAAATGGACTAAA
1 CTAAATGGACTAAA
9947 CTAAATGGACTAAA
1 CTAAATGGACTAAA
9961 GTTAATATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
CTAAATGGACTAAA
Found at i:10331 original size:27 final size:28
Alignment explanation
Indices: 10284--10360 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 28
10274 AAGTGAACTT
10284 AAAATGACCAAAATACCCCCTAAATGCA
1 AAAATGACCAAAATACCCCCTAAATGCA
* * **
10312 AAAATGACCAAAATA-TCCCTGAATGTG
1 AAAATGACCAAAATACCCCCTAAATGCA
* *
10339 AAAACGACCAAAATGCCCCCTA
1 AAAATGACCAAAATACCCCCTA
10361 GGTGACGATA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.47, C:0.27, G:0.10, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATACCCCCTAAATGCA
Found at i:11732 original size:8 final size:7
Alignment explanation
Indices: 11706--11752 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
11696 ACCCTAGAGC
*
11706 TTTCTTC
1 TTTCTTT
*
11713 TTTATTT
1 TTTCTTT
11720 TTTCTTGT
1 TTTCTT-T
11728 TTTC-TT
1 TTTCTTT
11734 TTTCTTT
1 TTTCTTT
11741 CTTTCTTT
1 -TTTCTTT
11749 TTTC
1 TTTC
11753 ATTGCACTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
6 5 0.15
7 17 0.50
8 12 0.35
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTCTTT
Found at i:12503 original size:33 final size:33
Alignment explanation
Indices: 12428--12514 Score: 149
Period size: 32 Copynumber: 2.7 Consensus size: 33
12418 TTGTAACATT
*
12428 TTTTTGGAAACCATGACTCTCTTTTGAAAAACA
1 TTTTTGAAAACCATGACTCTCTTTTGAAAAACA
*
12461 -TTTTGAAAACCTTGACTCTCTTTTGAAAAACA
1 TTTTTGAAAACCATGACTCTCTTTTGAAAAACA
12493 TTTTTGAAAACCATGACTCTCT
1 TTTTTGAAAACCATGACTCTCT
12515 ACCATTCCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 30 0.60
33 20 0.40
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (33 bp):
TTTTTGAAAACCATGACTCTCTTTTGAAAAACA
Found at i:17308 original size:49 final size:49
Alignment explanation
Indices: 17233--17566 Score: 283
Period size: 49 Copynumber: 6.9 Consensus size: 49
17223 AAATGTGAAG
* * * *
17233 AGAAAACT-GGACCATCTGACCGGGAAGGGGCATTTTGGGAATAAAGAA
1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAAATAA
* ** * * *
17281 AGAAAACTGGGACCTTCCAACCAGGAA-GAGCA----GGAAACAAATAA
1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAAATAA
* * * * ** *
17325 AGAGAACAGGGACCTTTCGACTGGGAAAGGGCATTTTAGAAAATGAATAA
1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTT-GGGAATAAATAA
* ** * *
17375 AGAAAACAGGGACCTTTTGACTGGGAAGGGGCATTTTGGAAACAAATAA
1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAAATAA
* * *
17424 AGAAAACAGTGACCTTCCGACTGGGAAGGGGCTTTTTGGGAA-ACAGATAA
1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATA-A-ATAA
* * *
17474 AGGAAA-TAGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGA-AA
1 AGAAAACT-GGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAA-ATAA
* *
17523 AGAAAACTGTGACCTTCCGACTGGGAAGGGGC-TTTTTGGAATAA
1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAA
17567 GAAAAGCAGA
Statistics
Matches: 236, Mismatches: 38, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
44 30 0.13
45 4 0.02
48 25 0.11
49 90 0.38
50 86 0.36
51 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.29, T:0.19
Consensus pattern (49 bp):
AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAAATAA
Found at i:17397 original size:50 final size:50
Alignment explanation
Indices: 17254--17563 Score: 295
Period size: 50 Copynumber: 6.4 Consensus size: 50
17244 CCATCTGACC
* * * * * *
17254 GGGAAGGGGCATTTTGGGAATA-AAGAAAGAAAACTGGGACCTTCCAACC
1 GGGAAGGGGCATTTTGGAAACAGAATAAAGAAAACAGGGACCTTCCGACT
* * * *
17303 AGGAA-GAGCA----GGAAACA-AATAAAGAGAACAGGGACCTTTCGACT
1 GGGAAGGGGCATTTTGGAAACAGAATAAAGAAAACAGGGACCTTCCGACT
* * **
17347 GGGAAAGGGCATTTTAGAAA-ATGAATAAAGAAAACAGGGACCTTTTGACT
1 GGGAAGGGGCATTTTGGAAACA-GAATAAAGAAAACAGGGACCTTCCGACT
*
17397 GGGAAGGGGCATTTTGGAAACA-AATAAAGAAAACAGTGACCTTCCGACT
1 GGGAAGGGGCATTTTGGAAACAGAATAAAGAAAACAGGGACCTTCCGACT
* * * *
17446 GGGAAGGGGCTTTTTGGGAAACAG-ATAAAGGAAATAGGGACCTTCCGACC
1 GGGAAGGGGCATTTT-GGAAACAGAATAAAGAAAACAGGGACCTTCCGACT
* *
17496 GGGAAGGGGCATTTTTGGAATA-AG-A-AAAGAAAACTGTGACCTTCCGACT
1 GGGAAGGGGCA-TTTTGGAA-ACAGAATAAAGAAAACAGGGACCTTCCGACT
*
17545 GGGAAGGGGCTTTTTGGAA
1 GGGAAGGGGCATTTTGGAA
17564 TAAGAAAAGC
Statistics
Matches: 217, Mismatches: 32, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
44 30 0.14
45 4 0.02
48 13 0.06
49 75 0.35
50 89 0.41
51 6 0.03
ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19
Consensus pattern (50 bp):
GGGAAGGGGCATTTTGGAAACAGAATAAAGAAAACAGGGACCTTCCGACT
Found at i:17561 original size:99 final size:100
Alignment explanation
Indices: 17254--17561 Score: 325
Period size: 99 Copynumber: 3.2 Consensus size: 100
17244 CCATCTGACC
* * * * * * *
17254 GGGAAGGGGCATTTTGGG--AATAAAGAAAGAAAACTGGGACCTTCCAACCAGGAA-GAGCA---
1 GGGAAGGGGCTTTTTGGGAAAATGAATAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTT
* * *
17313 -GGAAACAAATAAAGAGAACAGGGACCTTTCGACT
66 TGGAAACAAATAAAGAAAACAGTGACCTTCCGACT
* * * ** *
17347 GGGAAAGGGCATTTT-AGAAAATGAATAAAGAAAACAGGGACCTTTTGACTGGGAAGGGGCATTT
1 GGGAAGGGGCTTTTTGGGAAAATGAATAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTT
17411 TGGAAACAAATAAAGAAAACAGTGACCTTCCGACT
66 TGGAAACAAATAAAGAAAACAGTGACCTTCCGACT
* *
17446 GGGAAGGGGCTTTTTGGGAAACA-G-ATAAAGGAAATAGGGACCTTCCGACCGGGAAGGGGCATT
1 GGGAAGGGGCTTTTTGGGAAA-ATGAATAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCA-T
* *
17509 TTTGGAATA-AGA-AAAGAAAACTGTGACCTTCCGACT
64 TTTGGAA-ACAAATAAAGAAAACAGTGACCTTCCGACT
17545 GGGAAGGGGCTTTTTGG
1 GGGAAGGGGCTTTTTGG
17562 AATAAGAAAA
Statistics
Matches: 180, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
92 1 0.01
93 14 0.08
94 28 0.16
95 4 0.02
99 116 0.64
100 15 0.08
101 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19
Consensus pattern (100 bp):
GGGAAGGGGCTTTTTGGGAAAATGAATAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTT
TGGAAACAAATAAAGAAAACAGTGACCTTCCGACT
Found at i:17669 original size:40 final size:40
Alignment explanation
Indices: 17576--17910 Score: 331
Period size: 40 Copynumber: 8.1 Consensus size: 40
17566 AGAAAAGCAG
* *
17576 ACAACACCTTCC-AGTGAGGAAGGGCACGA-TAGGAAATCTAA
1 ACAACACCTTCCGA-TGAGGAAGGGCA-AACTGGGAAA-CTAA
* *
17617 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAACTTA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACTAA
* *
17657 ACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAGACTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACTAA
* * *
17697 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATTCGGCAACTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACT-G------GGAAACTAA
*
17744 ACAACACC-TCTCGACTG-GGAAGGGC-AAGTCGGGAAAACTAA
1 ACAACACCTTC-CGA-TGAGGAAGGGCAAACT-GGG-AAACTAA
**
17785 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACTAA
*
17825 ACAACACCTTCCGATGGGGAAGGGCAAAACT-GGAAACTAA
1 ACAACACCTTCCGATGAGGAAGGGC-AAACTGGGAAACTAA
* * * *
17865 ACAACACCTTTCGGTGAGGAAGGGCAAACTGAGAATAATAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-ACTAA
17906 ACAAC
1 ACAAC
17911 TAAACAACAT
Statistics
Matches: 250, Mismatches: 26, Indels: 36
0.80 0.08 0.12
Matches are distributed among these distances:
39 5 0.02
40 134 0.54
41 72 0.29
42 6 0.02
46 6 0.02
47 25 0.10
48 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (40 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACTAA
Found at i:17793 original size:128 final size:128
Alignment explanation
Indices: 17613--17857 Score: 365
Period size: 128 Copynumber: 1.9 Consensus size: 128
17603 GATAGGAAAT
* *
17613 CTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAACTTAACAACACCTTCCGGTGAGGAA
1 CTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGATGAGGAA
*
17678 GGGCAAACTGGGAGA-CTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGTAATTCGGCAA
66 GGGCAAACTGGGA-ATCTAAACAACACCTTCCGATGGGGAAGGGCAAAACTGGTAATTCGGCAA
*
17740 CTAAACAACACC-TCTCGACT-GGGAAGGGC-AAGTCGGGAAAACTAAACAACACCTTCCGATGA
1 CTAAACAACACCTTC-CGA-TGGGGAAGGGCAAACT-GGG-AAACTAAACAACACCTTCCGATGA
*
17802 GGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGATGGGGAAGGGCAAAACTGG
62 GGAAGGGCAAACTGGGAATCTAAACAACACCTTCCGATGGGGAAGGGCAAAACTGG
17858 AAACTAAACA
Statistics
Matches: 107, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
126 5 0.05
127 28 0.26
128 67 0.63
129 7 0.07
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.15
Consensus pattern (128 bp):
CTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGATGAGGAA
GGGCAAACTGGGAATCTAAACAACACCTTCCGATGGGGAAGGGCAAAACTGGTAATTCGGCAA
Found at i:17967 original size:49 final size:48
Alignment explanation
Indices: 17860--17989 Score: 140
Period size: 49 Copynumber: 2.7 Consensus size: 48
17850 AAAACTGGAA
* * *
17860 ACTAAACAACACCTTTCGGTGAGGAAGGGCAAACTGAGAATAATAAAC
1 ACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATAACAAAC
* * *
17908 AACTAAACAACATCTTCCGATGAGGAAGGGCAGACTGGGAATCAGACAAAC
1 -ACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAAT-A-ACAAAC
*
17959 -CTAGACAACACCTTCC-AGTG-GGAAGGGCAAA
1 ACTAAACAACACCTTCCGA-TGAGGAAGGGCAAA
17990 TTAGGAATTT
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
48 11 0.16
49 52 0.75
50 1 0.01
51 5 0.07
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.15
Consensus pattern (48 bp):
ACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATAACAAAC
Found at i:17997 original size:48 final size:45
Alignment explanation
Indices: 17692--18082 Score: 169
Period size: 47 Copynumber: 8.7 Consensus size: 45
17682 AAACTGGGAG
* * * *
17692 ACTAAACAACACCTTCCGGTGGGGAAGGGCAAACT-GGTAATTCGGCA
1 ACTAGACAACACCTTCCGAT-GGGAAGGGCAAAATAGG-AATT-GACA
* * * *
17739 ACTAAACAACACC-TCTCGACTGGGAAGGGC-AAGTCGG----GAAA
1 ACTAGACAACACCTTC-CGA-TGGGAAGGGCAAAATAGGAATTGACA
* * *
17780 ACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATT----
1 ACTAGACAACACCTTCCGATG-GGAAGGGCAAAATAGGAATTGACA
*
17822 --TAAACAACACCTTCCGATGGGGAAGGGCAAAACT--G----GA-A
1 ACTAGACAACACCTTCCGAT-GGGAAGGGCAAAA-TAGGAATTGACA
* * * * *
17860 ACTAAACAACACCTTTCGGTGAGGAAGGGCAAACT-GAGAATAATAAACA
1 ACTAGACAACACCTTCCGATG-GGAAGGGCAAAATAG-GAAT--T-GACA
* * * * * *
17909 ACTAAACAACATCTTCCGATGAGGAAGGGCAGACTGGGAATCAGACAA
1 ACTAGACAACACCTTCCGATG-GGAAGGGCAAAATAGGAAT-TGAC-A
*
17957 ACCTAGACAACACCTTCC-AGTGGGAAGGGCAAATTAGGAATTTGACA
1 A-CTAGACAACACCTTCCGA-TGGGAAGGGCAAAATAGGAA-TTGACA
* * *
18004 ACTAAACAACACCTTCCAACTGGGAATGGCAAAATAGGAAATTGACA
1 ACTAGACAACACCTTCCGA-TGGGAAGGGCAAAATAGG-AATTGACA
* *
18051 ACTAGACAACACCTTTCGTCTGGGAAGGGCAA
1 ACTAGACAACACCTTCCG-ATGGGAAGGGCAA
18083 TACCGGAAAT
Statistics
Matches: 275, Mismatches: 33, Indels: 72
0.72 0.09 0.19
Matches are distributed among these distances:
39 3 0.01
40 58 0.21
41 29 0.11
42 7 0.03
46 20 0.07
47 79 0.29
48 25 0.09
49 53 0.19
50 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (45 bp):
ACTAGACAACACCTTCCGATGGGAAGGGCAAAATAGGAATTGACA
Found at i:18776 original size:32 final size:32
Alignment explanation
Indices: 18730--18793 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
18720 ATTTCATCAT
* *
18730 TTACTTAAAGGTTCAAT-TTTTATTTACAAAAA
1 TTACTTAAAAGTTCAATGTTTTAATTA-AAAAA
18762 TTACTTAAAAGTTCAATGTTTTAATTAAAAAA
1 TTACTTAAAAGTTCAATGTTTTAATTAAAAAA
18794 CTCAATCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (32 bp):
TTACTTAAAAGTTCAATGTTTTAATTAAAAAA
Found at i:18994 original size:51 final size:51
Alignment explanation
Indices: 18929--19102 Score: 180
Period size: 51 Copynumber: 3.5 Consensus size: 51
18919 AAGACCACAC
* * **
18929 TTTTATTTACAAATTAATCATCAA-TTCCATCATTTGGTTCAAAGATATCAT
1 TTTTATTTACAAATTAATCA-CAAGTTCAATCACTTAATTCAAAGATATCAT
* *
18980 TTTTATTTACAAATTAATCACAAGTTCAATCACTTAATTCAAAGCTCTCAT
1 TTTTATTTACAAATTAATCACAAGTTCAATCACTTAATTCAAAGATATCAT
* * * * *
19031 TTTTATTTGCAAATTACTTACAAGTTCAATCATTTAATTC-----TCTCAT
1 TTTTATTTACAAATTAATCACAAGTTCAATCACTTAATTCAAAGATATCAT
* *
19077 TTTTATTTACAAATTACTCAAAAGTT
1 TTTTATTTACAAATTAATCACAAGTT
19103 TAATTATTAG
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
46 29 0.27
50 3 0.03
51 77 0.71
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.44
Consensus pattern (51 bp):
TTTTATTTACAAATTAATCACAAGTTCAATCACTTAATTCAAAGATATCAT
Found at i:19498 original size:13 final size:14
Alignment explanation
Indices: 19477--19508 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
19467 TCTTTTCCTC
19477 CTTTGTTTTTTTCT
1 CTTTGTTTTTTTCT
19491 CTTT-TTTTTTTCT
1 CTTTGTTTTTTTCT
19504 CTTTG
1 CTTTG
19509 CTGACTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (14 bp):
CTTTGTTTTTTTCT
Found at i:23830 original size:28 final size:28
Alignment explanation
Indices: 23777--23832 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
23767 GGGGGCATGG
*
23777 TTCTTCTTTAACTTTCCTTTATTTACTA
1 TTCTTCTTTAACTTTCCTTTAGTTACTA
* *
23805 TTCTTGTTTAA-TTTCCTTGTGGTTACTA
1 TTCTTCTTTAACTTTCCTT-TAGTTACTA
23833 ACTTCTCTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.16, C:0.18, G:0.07, T:0.59
Consensus pattern (28 bp):
TTCTTCTTTAACTTTCCTTTAGTTACTA
Found at i:27480 original size:16 final size:16
Alignment explanation
Indices: 27456--27486 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27446 GGAATGATAG
*
27456 GTTTTAATCAAAGCAT
1 GTTTCAATCAAAGCAT
27472 GTTTCAATCAAAGCA
1 GTTTCAATCAAAGCA
27487 ATAGTTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (16 bp):
GTTTCAATCAAAGCAT
Found at i:28069 original size:44 final size:44
Alignment explanation
Indices: 28019--28158 Score: 226
Period size: 44 Copynumber: 3.1 Consensus size: 44
28009 AGCAACGATT
* *
28019 GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGGTTTGACAAAATG
1 GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATG
* *
28063 GTTTTCAAAAAGAGTCATTGTTTTCAAAAGGTTTTGATAAAACG
1 GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATG
28107 GTTTTTCAAAAAGGAGTCATGGTTTTCAAAAGGTTTTGATAAAATG
1 G-TTTTCAAAAA-GAGTCATGGTTTTCAAAAGGTTTTGATAAAATG
28153 GTTTTC
1 GTTTTC
28159 CAAAGTTGTG
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
44 41 0.47
45 15 0.17
46 32 0.36
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (44 bp):
GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATG
Found at i:28541 original size:32 final size:32
Alignment explanation
Indices: 28504--28574 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
28494 AAAGAAATTA
* *
28504 AAAAAAAAAGAAGAGAAAATTGAAAGTGAAAGT
1 AAAAAAAAA-AAGAGAAAATTGAAAGTAAAAGG
*
28537 AAAAAAAAAAAGTGAAAATTGAAAGTAAAAGG
1 AAAAAAAAAAAGAGAAAATTGAAAGTAAAAGG
28569 AAAAAA
1 AAAAAA
28575 TTGAAAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 26 0.74
33 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.11
Consensus pattern (32 bp):
AAAAAAAAAAAGAGAAAATTGAAAGTAAAAGG
Found at i:28564 original size:26 final size:27
Alignment explanation
Indices: 28530--28581 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
28520 AAATTGAAAG
28530 TGAAAGTAAAA-AAAAAAAGTGAAAAT
1 TGAAAGTAAAAGAAAAAAAGTGAAAAT
* *
28556 TGAAAGTAAAAGGAAAAAATTGAAAA
1 TGAAAGTAAAAGAAAAAAAGTGAAAA
28582 GAAAGTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (27 bp):
TGAAAGTAAAAGAAAAAAAGTGAAAAT
Found at i:28566 original size:19 final size:19
Alignment explanation
Indices: 28518--28572 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 19
28508 AAAAAGAAGA
*
28518 GAAAATTGAAAGTGAAAGT
1 GAAAATTGAAAGTAAAAGT
28537 -AAAA---AAA--AAAAGT
1 GAAAATTGAAAGTAAAAGT
28550 GAAAATTGAAAGTAAAAG-
1 GAAAATTGAAAGTAAAAGT
28568 GAAAA
1 GAAAA
28573 AATTGAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 13
0.67 0.02 0.30
Matches are distributed among these distances:
13 5 0.17
14 4 0.14
15 3 0.10
17 3 0.10
18 9 0.31
19 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (19 bp):
GAAAATTGAAAGTAAAAGT
Found at i:28585 original size:25 final size:25
Alignment explanation
Indices: 28519--28595 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
28509 AAAAGAAGAG
* *
28519 AAAATTGAAAGTGAAAGTAAAA-AAA
1 AAAATTGAAA-AGAAAGTAAAAGGAA
*
28544 AAAAGTGAAAATTGAAAGTAAAAGGAA
1 AAAATTGAAAA--GAAAGTAAAAGGAA
*
28571 AAAATTGAAAAGAAAGTGAAAGGAA
1 AAAATTGAAAAGAAAGTAAAAGGAA
28596 GGGTGAGGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 22 0.50
26 10 0.23
27 12 0.27
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.14
Consensus pattern (25 bp):
AAAATTGAAAAGAAAGTAAAAGGAA
Found at i:28935 original size:13 final size:13
Alignment explanation
Indices: 28901--28943 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
28891 GTAAAAAATG
28901 AAAGAAAAA-AAA
1 AAAGAAAAAGAAA
28913 AGAAG-AAAAGAAA
1 A-AAGAAAAAGAAA
*
28926 AAAGAAAAAGGAA
1 AAAGAAAAAGAAA
28939 AAAGA
1 AAAGA
28944 GGATGAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 8 0.30
13 19 0.70
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:28942 original size:7 final size:7
Alignment explanation
Indices: 28893--28941 Score: 55
Period size: 7 Copynumber: 6.7 Consensus size: 7
28883 AAGTGCATGT
28893 AAAAAATG
1 AAAAAA-G
28901 AAAGAAA-
1 AAA-AAAG
28908 AAAAAAG
1 AAAAAAG
28915 AAGAAAAG
1 AA-AAAAG
28923 AAAAAAG
1 AAAAAAG
*
28930 AAAAAGG
1 AAAAAAG
28937 AAAAA
1 AAAAA
28942 GAGGATGAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
6 3 0.08
7 21 0.57
8 10 0.27
9 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:29290 original size:50 final size:50
Alignment explanation
Indices: 29231--29331 Score: 148
Period size: 50 Copynumber: 2.0 Consensus size: 50
29221 GAAGTTTTAT
* * * *
29231 AATAAGATTGCATTTCATTTGTGAGTCCAATATCAAGATTCGATTTTCAA
1 AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGATTTTCAA
* *
29281 AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTTGCTTTTCAA
1 AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGATTTTCAA
29331 A
1 A
29332 GGGCATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (50 bp):
AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGATTTTCAA
Found at i:30009 original size:68 final size:68
Alignment explanation
Indices: 29853--30097 Score: 296
Period size: 68 Copynumber: 3.6 Consensus size: 68
29843 AATGCTTCGA
* * * * *
29853 CTTTTCCATAAGTCAAACTCGTTTCCACACGAGTCAATTGAAGCTTTGGTTCCATCCAAGCATTC
1 CTTTTCCACAAGTCAAACTCGTTTCCACACGAGCCAATT-TAGCATTGGTTCCATCCAAGCA-AC
*
29918 AGGGG
64 AGAGG
* * *
29923 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGCCACTTTAGCCTTGGTTCCATCCAAGCAACAG
1 CTTTTCCACAAGTCAAACTCGTTTCCACACGAGCCAATTTAGCATTGGTTCCATCCAAGCAACAG
29988 AGG
66 AGG
* ** *
29991 CTTTTCCACAAG-CTAAACTCGTTTCCATACGAGATAGTTTAAGCATTGGTTCCATCCAAGCAAC
1 CTTTTCCACAAGTC-AAACTCGTTTCCACACGAGCCAATTT-AGCATTGGTTCCATCCAAGCAAC
*
30055 A-TGG
64 AGAGG
* *
30059 CTTTTCCACAAGTCAAACTCGTTTCCATAAGAGCCAATT
1 CTTTTCCACAAGTCAAACTCGTTTCCACACGAGCCAATT
30098 CAAGTAGCAT
Statistics
Matches: 154, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
67 1 0.01
68 74 0.48
69 44 0.29
70 35 0.23
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (68 bp):
CTTTTCCACAAGTCAAACTCGTTTCCACACGAGCCAATTTAGCATTGGTTCCATCCAAGCAACAG
AGG
Found at i:30321 original size:47 final size:47
Alignment explanation
Indices: 30236--30725 Score: 560
Period size: 47 Copynumber: 10.4 Consensus size: 47
30226 ATTCAAGCAA
* *
30236 TCTTCTCTCGCTTCCACGCGAGTTTGCAACTCAGTGACCAAAGTTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
** * * *
30283 TCTTCTCTCGCTTCCATACGAATTTTCAATTTAATGACCAAAGTTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* * *
30330 TATTCTCTCGCTTCCACGCGAGTTTGCAACTCAGTGACCAAAGTTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* *
30377 TCTTCTCTCGCTTCCACGCGAGCTTGCAATTTATTGACCAAAGTTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
*
30424 TCTTCTCTCGCTTCCACGC-AGGTTCT-CAATTTAGTGGCCAAAGTTGG
1 TCTTCTCTCGCTTCCACGCGA-GTT-TGCAATTTAGTGACCAAAGTTGG
* *
30471 -CTTTCTCTCGCTTCCACGCGAATTCT-CAATTCAGTGACCAAAGTTGG
1 TC-TTCTCTCGCTTCCACGCGAGTT-TGCAATTTAGTGACCAAAGTTGG
* *
30518 TCTTCTCTCGCTTCCATGCGAGTTTGCAATTTAGTGGCCAAAGTTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* * * * *
30565 -CATTTTCTCG-TTTCACGCGAGTTTACAGTTTGGTGACCAAAGTTGG
1 TC-TTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* * * * * * *
30611 TCTTTTCGCGCTTCCATGCGAGTCTACAATCTAATGACCAAAGTTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* * * * * *
30658 TCTTTTCTCGCTTCCAGGCGAGTCTACAATTTAGTGACAAAAATTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* *
30705 TCTTTTATCGCTTCCACGCGA
1 TCTTCTCTCGCTTCCACGCGA
30726 ATCTGCAAGG
Statistics
Matches: 381, Mismatches: 53, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
46 41 0.11
47 337 0.88
48 3 0.01
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.34
Consensus pattern (47 bp):
TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
Found at i:31631 original size:6 final size:6
Alignment explanation
Indices: 31620--31646 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31610 AAAGCAAAGC
31620 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
31647 GCAGAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:32450 original size:6 final size:6
Alignment explanation
Indices: 32439--32472 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
32429 GAGATTAATT
32439 GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA GTGT
1 GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA GTGT
32473 GTGATTTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (6 bp):
GTGTAA
Found at i:32618 original size:10 final size:10
Alignment explanation
Indices: 32603--32628 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
32593 GAGGACTCTA
32603 GAATTTTCTG
1 GAATTTTCTG
32613 GAATTTTCTG
1 GAATTTTCTG
32623 GAATTT
1 GAATTT
32629 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Done.