Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024838.1 Corchorus olitorius cultivar O-4 contig24871, 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: 27188
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:56 original size:40 final size:40
Alignment explanation
Indices: 1--201 Score: 186
Period size: 47 Copynumber: 4.7 Consensus size: 40
*
1 TTCCGGCGGGGAAGGGCAAACTGGGAACTTAAACAACACC
1 TTCCGGTGGGGAAGGGCAAACTGGGAACTTAAACAACACC
*
41 TTCCGGTGGGGAAGGGCAAATTGGGTAAAACAGACTTAAACAACACC
1 TTCCGGTGGGGAAGGGCAAACTGGG------A-ACTTAAACAACACC
* * *
88 TTCCGATGAGGAAGGGCAAACTGGGAAATTAAACAACACC
1 TTCCGGTGGGGAAGGGCAAACTGGGAACTTAAACAACACC
* * * *
128 TTCCGGTTGGGAAGGGCAAATTGGGTAAAGTAGACTTAAAAAAAACC
1 TTCCGGTGGGGAAGGGCAAACT-GG----G-A-ACTTAAACAACACC
*
175 TTCCGGTGAGGAAGGGCAAACTGGGAA
1 TTCCGGTGGGGAAGGGCAAACTGGGAA
202 AAGTAGACAA
Statistics
Matches: 131, Mismatches: 16, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
40 55 0.42
41 4 0.03
42 1 0.01
45 1 0.01
46 4 0.03
47 66 0.50
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.16
Consensus pattern (40 bp):
TTCCGGTGGGGAAGGGCAAACTGGGAACTTAAACAACACC
Found at i:101 original size:47 final size:45
Alignment explanation
Indices: 27--203 Score: 204
Period size: 47 Copynumber: 4.0 Consensus size: 45
17 CAAACTGGGA
* *
27 ACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAACAG
1 ACTTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGG-AAAA-AG
*
74 ACTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGG---AA-
1 ACTTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAAAG
* *
115 A-TTAAACAACACCTTCCGGTTG-GGAAGGGCAAATTGGGTAAAGTAG
1 ACTTAAACAACACCTTCCGG-TGAGGAAGGGCAAACTGGG-AAA-AAG
* *
161 ACTTAAAAAAAACCTTCCGGTGAGGAAGGGCAAACTGGGAAAA
1 ACTTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAA
204 GTAGACAACT
Statistics
Matches: 111, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
40 32 0.29
41 3 0.03
42 1 0.01
43 1 0.01
45 1 0.01
46 6 0.05
47 67 0.60
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (45 bp):
ACTTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAAAG
Found at i:147 original size:87 final size:87
Alignment explanation
Indices: 10--202 Score: 323
Period size: 87 Copynumber: 2.2 Consensus size: 87
1 TTCCGGCGG
*
10 GGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAACAGA
1 GGAAGGGCAAACTGGGAAATTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAACAGA
* *
75 CTTAAACAACACCTTCCGATGA
66 CTTAAAAAAAACCTTCCGATGA
* **
97 GGAAGGGCAAACTGGGAAATTAAACAACACCTTCCGGTTGGGAAGGGCAAATTGGGTAAAGTAGA
1 GGAAGGGCAAACTGGGAAATTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAACAGA
*
162 CTTAAAAAAAACCTTCCGGTGA
66 CTTAAAAAAAACCTTCCGATGA
184 GGAAGGGCAAACTGGGAAA
1 GGAAGGGCAAACTGGGAAA
203 AGTAGACAAC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 99 1.00
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.16
Consensus pattern (87 bp):
GGAAGGGCAAACTGGGAAATTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAACAGA
CTTAAAAAAAACCTTCCGATGA
Found at i:4754 original size:20 final size:20
Alignment explanation
Indices: 4729--4797 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
4719 GCAACTTAGA
4729 TATGCAAAATGCCATACAAC
1 TATGCAAAATGCCATACAAC
* *
4749 TATGCAAAAAAG-TA-ACTTAGA-
1 TATGC-AAAATGCCATAC--A-AC
4770 TATGCAAAATGCCATACAAC
1 TATGCAAAATGCCATACAAC
4790 TATGCAAA
1 TATGCAAA
4798 GAACCCCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 3 0.08
20 20 0.53
21 12 0.32
22 3 0.08
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (20 bp):
TATGCAAAATGCCATACAAC
Found at i:4768 original size:41 final size:41
Alignment explanation
Indices: 4707--4797 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
4697 CCGAATCATG
4707 AACTATGC--AAAAGCAACTTAGATATGCAAAATGCCATAC
1 AACTATGCAAAAAAGCAACTTAGATATGCAAAATGCCATAC
*
4746 AACTATGCAAAAAAGTAACTTAGATATGCAAAATGCCATAC
1 AACTATGCAAAAAAGCAACTTAGATATGCAAAATGCCATAC
4787 AACTATGCAAA
1 AACTATGCAAA
4798 GAACCCCTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 8 0.16
41 41 0.84
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (41 bp):
AACTATGCAAAAAAGCAACTTAGATATGCAAAATGCCATAC
Found at i:4968 original size:108 final size:107
Alignment explanation
Indices: 4756--4970 Score: 403
Period size: 108 Copynumber: 2.0 Consensus size: 107
4746 AACTATGCAA
*
4756 AAAAGTAACTTAGATATGCAAAATGCCATACAACTATGCAAAGAACCCCTTTGGCCTTTTCTTGA
1 AAAAGCAACTTAGATATGCAAAATGCCATACAACTATGCAAAGAACCCCTTTGGCCTTTTCTTGA
4821 GCTTTGAGCTAAATGTTAGGAAAAGCTAATCTATCAAGATGC
66 GCTTTGAGCTAAATGTTAGGAAAAGCTAATCTATCAAGATGC
4863 AAAAGCAACTTAGATATGCAAAATGCCATACAACTATGCAAAGAACCCCTTTTGGCCTTTTCTTG
1 AAAAGCAACTTAGATATGCAAAATGCCATACAACTATGCAAAGAACCCC-TTTGGCCTTTTCTTG
*
4928 AGCTTTGAGCTAAATGTTAGGAAAAGCTAATCTATTAAGATGC
65 AGCTTTGAGCTAAATGTTAGGAAAAGCTAATCTATCAAGATGC
4971 CATGCTCAAT
Statistics
Matches: 105, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
107 48 0.46
108 57 0.54
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (107 bp):
AAAAGCAACTTAGATATGCAAAATGCCATACAACTATGCAAAGAACCCCTTTGGCCTTTTCTTGA
GCTTTGAGCTAAATGTTAGGAAAAGCTAATCTATCAAGATGC
Found at i:5133 original size:27 final size:27
Alignment explanation
Indices: 5101--5172 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
5091 TCAATTAAGA
** *
5101 AAATGACCAAAATACCCTTAAATGTAC
1 AAATGACCAAAATACCCCCAAATATAC
* * *
5128 AAATGACCAAAATGCCCCCGAATATGC
1 AAATGACCAAAATACCCCCAAATATAC
*
5155 AAATGACCAAAATGCCCC
1 AAATGACCAAAATACCCC
5173 TAGGTGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCAAATATAC
Found at i:5659 original size:7 final size:8
Alignment explanation
Indices: 5639--5668 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
5629 TCTTCTTCTT
5639 TTTTCTTCA
1 TTTT-TTCA
5648 TTTTTTCA
1 TTTTTTCA
5656 TTTTTTCA
1 TTTTTTCA
5664 TTTTT
1 TTTTT
5669 ATGGGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:9811 original size:54 final size:54
Alignment explanation
Indices: 9672--10105 Score: 459
Period size: 54 Copynumber: 8.0 Consensus size: 54
9662 TTCTTAATCA
* ** *
9672 ACCGCACTGGATCAT-TTAAGATTCAAC-CTTGATCACGAAAACCTCTCTTGGAATG
1 ACCGCACTGGATCATCTGAAGA-TCAACTC-TGATCATTAAAAACT-TCTTGGAATG
* * * *
9727 ATCGCACTGGATCCAAT-TGAAAATCAACTCTGATCATCAAAAACGTCTTGGAATG
1 ACCGCACTGGAT-C-ATCTGAAGATCAACTCTGATCATTAAAAACTTCTTGGAATG
* * * * * *
9782 ACTGCACTGTATCAAT-TGAAGATCAACTCTGATCATTGAAAATTTTTTGGAAAG
1 ACCGCACTGGATC-ATCTGAAGATCAACTCTGATCATTAAAAACTTCTTGGAATG
* *
9836 ACCGCACTAGATCATCT-AGGATCAACTCTGATC-TCTAAAAACTTCTTGGAATG
1 ACCGCACTGGATCATCTGAAGATCAACTCTGATCAT-TAAAAACTTCTTGGAATG
* * *
9889 ACCGCACAGGATCATCTG-AGAATCAACTCTGATCATTAAAAACTTCTTGTAAGG
1 ACCGCACTGGATCATCTGAAG-ATCAACTCTGATCATTAAAAACTTCTTGGAATG
* * * * *
9943 ACCGCACTGGATCATATGGAGATCAACTCTGATCATCAAAAACGTCTTCGAATG
1 ACCGCACTGGATCATCTGAAGATCAACTCTGATCATTAAAAACTTCTTGGAATG
** * *
9997 ACCGCACTGGATCATCTGTGGATCAACTCTGATCATTGAAAACTTCATGGAATG
1 ACCGCACTGGATCATCTGAAGATCAACTCTGATCATTAAAAACTTCTTGGAATG
* * * *
10051 ACCGCACTGGATCATCTTAGGATCAACTCTGACCATTGAAAACTTCTTGGAATG
1 ACCGCACTGGATCATCTGAAGATCAACTCTGATCATTAAAAACTTCTTGGAATG
10105 A
1 A
10106 GATCAACTCT
Statistics
Matches: 321, Mismatches: 49, Indels: 19
0.83 0.13 0.05
Matches are distributed among these distances:
52 1 0.00
53 47 0.15
54 216 0.67
55 33 0.10
56 17 0.05
57 7 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (54 bp):
ACCGCACTGGATCATCTGAAGATCAACTCTGATCATTAAAAACTTCTTGGAATG
Found at i:10110 original size:35 final size:35
Alignment explanation
Indices: 10071--10659 Score: 714
Period size: 35 Copynumber: 16.8 Consensus size: 35
10061 ATCATCTTAG
* ** * *
10071 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
*
10106 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* * *
10141 GATCAACTTTGATCATCGAAAACTTCTTTAAA-GAA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACG-A
* * *
10176 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* * * *
10211 AATAAACTCTGATTAT-AAAAATTTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAA-CTTCTTGAAACGA
* * *
10246 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* * * *
10281 GATAAACTCTGATCATAAAAAACTACTTGAAGCGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* **
10316 GATCAACTCTGATAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* **
10351 GATCAACTCTGATAAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGAT-CATCAAAAACTTCTTGAAACGA
* *
10387 GATCAACTCTGATCATCGAAAACTTACTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTT-CTTGAAACGA
*
10423 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* *
10458 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* *
10493 GATCAATTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* *
10528 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
*
10563 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* * * *
10598 GATCACCTCTGATCATCGAAAATTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
** *
10633 GATCAACAATGATCATAAAAAACTTCT
1 GATCAACTCTGATCATCAAAAACTTCT
10660 CTGATCATAA
Statistics
Matches: 481, Mismatches: 67, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
34 5 0.01
35 403 0.84
36 73 0.15
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
Found at i:10199 original size:105 final size:104
Alignment explanation
Indices: 10071--10947 Score: 1007
Period size: 105 Copynumber: 8.5 Consensus size: 104
10061 ATCATCTTAG
* * * *
10071 GATCAACTCTGACCATTGAAAACTTCTTGGAATGAGATCAACTCTGATCATAAAAAACTTCTTGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
* *
10136 AACGAGATCAACTTTGATCATCGAAAACTTCTTTAAAGAA
66 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAG-A
* * * * **
10176 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGAAATAAACTCTGATTATAAAAATTTTCTTGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
*
10241 AACGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
66 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
* ** * * *
10281 GATAAACTCTGATCATAAAAAACTACTTG-AAGCGAGATCAACTCTGATAAAAAAAAACTTCTTG
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAG-GAGATCAACTCTGATCATAAAAAACTTCTTG
* ***
10345 AAACGAGATCAACTCTGATAAAAAAAAAACTTCTTGAAACGA
65 AAACGAGATCAACTCTGAT-CATCGAAAACTTCTTGAAA-GA
*
10387 GATCAACTCTGATCATCGAAAACTTACTTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTG
1 GATCAACTCTGATCATCGAAAACTT-CTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
*
10452 AAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
65 AAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
* * * **
10493 GATCAATTCTGATCATCAAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTTCTTGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
* **
10558 AAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGA
66 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
* * **
10598 GATCACCTCTGATCATCGAAAATTTCTTGAAAGGAGATCAACAATGATCATAAAAAACTTCTCTG
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCT-TG
*
10663 -ATC---AT-AA-----A--A---AAAACTTCTTGAAATGA
65 AAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
* * *
10689 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTGACCATAAAAAACTTTTTGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
* * * *
10754 AAGGAGATCAACTTTGATCATCGCAAACTTCTTAAAATGA
66 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
** * **
10794 GATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTTCTTGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
* * *
10859 AAGGAGATCAACTCTGATCAT--AGAACTTCTTGAAACGG
66 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
* * * *
10897 GATCAACTCTGATCATAGAAAGCTTCTTGAAATGAGATCAACTATGATCAT
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCAT
10948 CGAAAACCTC
Statistics
Matches: 662, Mismatches: 89, Indels: 44
0.83 0.11 0.06
Matches are distributed among these distances:
90 2 0.00
91 72 0.11
94 3 0.00
95 2 0.00
96 1 0.00
100 1 0.00
101 2 0.00
102 3 0.00
103 60 0.09
104 3 0.00
105 378 0.57
106 82 0.12
107 50 0.08
108 3 0.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (104 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGA
Found at i:10685 original size:91 final size:89
Alignment explanation
Indices: 10569--10748 Score: 279
Period size: 91 Copynumber: 2.0 Consensus size: 89
10559 AGGAGATCAA
* * *
10569 CTCTGATCATAAAAAACTTCTTGAAACGAGATCACCTCTGATCATCGAAAATTTCTTGAAAGGAG
1 CTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAG
*
10634 ATCAACAATGATCATAAAAAACTT
66 ATCAACAATGACCATAAAAAACTT
*
10658 CTCTGATCATAAAAAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGG
1 CTCTGATCAT--AAAAAACTTCTTGAAACGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGG
**
10723 AGATCAACTCTGACCATAAAAAACTT
64 AGATCAACAATGACCATAAAAAACTT
10749 TTTGAAAGGA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
89 10 0.12
91 72 0.88
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.26
Consensus pattern (89 bp):
CTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAG
ATCAACAATGACCATAAAAAACTT
Found at i:10715 original size:35 final size:35
Alignment explanation
Indices: 10658--10959 Score: 385
Period size: 35 Copynumber: 8.6 Consensus size: 35
10648 TAAAAAACTT
*
10658 CTCTGATCATAAAAAAAACTTCTTGAAATGAGATCAA
1 CTCTGATCAT--AGAAAACTTCTTGAAATGAGATCAA
*
10695 CTCTGATCA-ACGAAAACTTCTTGAAAGGAGATCAA
1 CTCTGATCATA-GAAAACTTCTTGAAATGAGATCAA
* * * *
10730 CTCTGACCATAAAAAACTTTTTGAAAGGAGATCAA
1 CTCTGATCATAGAAAACTTCTTGAAATGAGATCAA
* * * *
10765 CTTTGATCATCGCAAACTTCTTAAAATGAGATCAA
1 CTCTGATCATAGAAAACTTCTTGAAATGAGATCAA
*
10800 CTCTGATCATAAAAAACTTCTTGAAATGAGATCAA
1 CTCTGATCATAGAAAACTTCTTGAAATGAGATCAA
* *
10835 CTCTGATCATCGAAAACTTCTTGAAAGGAGATCAA
1 CTCTGATCATAGAAAACTTCTTGAAATGAGATCAA
* *
10870 CTCTGATCATAG--AACTTCTTGAAACGGGATCAA
1 CTCTGATCATAGAAAACTTCTTGAAATGAGATCAA
*
10903 CTCTGATCATAGAAAGCTTCTTGAAATGAGATCAA
1 CTCTGATCATAGAAAACTTCTTGAAATGAGATCAA
* * *
10938 CTATGATCATCGAAAACCTCTT
1 CTCTGATCATAGAAAACTTCTT
10960 ATGAAAGACC
Statistics
Matches: 230, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
33 31 0.13
34 1 0.00
35 188 0.82
36 1 0.00
37 9 0.04
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.27
Consensus pattern (35 bp):
CTCTGATCATAGAAAACTTCTTGAAATGAGATCAA
Found at i:10775 original size:161 final size:165
Alignment explanation
Indices: 10509--10960 Score: 553
Period size: 161 Copynumber: 2.7 Consensus size: 165
10499 TTCTGATCAT
*
10509 CAAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTG
1 CAAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTG
* * * *
10574 ATCATAAAAAACTTCTTGAAACGAGATCACCTCTGATCATCGAAAATTTCTTGAAAGGAGATCAA
66 ATCATAAAAAACTTCTTGAAACGAGATCAACTATGATCATCGAAAACTTCTTAAAAGGAGATCAA
10639 CAATGATCATAAAAAACTTCTCTG-AT-CAT-AA-A
131 CAATGATCATAAAAAACTTCT-TGAATACATCAACA
10671 -AAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTG
1 CAAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTG
* * * * * *
10735 ACCATAAAAAACTTTTTGAAAGGAGATCAACTTTGATCATCGCAAACTTCTTAAAATGAGATCAA
66 ATCATAAAAAACTTCTTGAAACGAGATCAACTATGATCATCGAAAACTTCTTAAAAGGAGATCAA
** *
10800 CTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGA
131 CAATGATCATAAAAAACTTCTTG-AAT-ACATCAA--C--A
*
10841 TCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATA-G--AACTTCTTGAAACGG-GATCA
1 -CA---AAAACTTCTTGAAATGAGATCAACTCTGATCA-ACGAAAACTTCTTGAAA-GGAGATCA
* * * *
10902 ACTCTGATCATAGAAAGCTTCTTGAAATGAGATCAACTATGATCATCGAAAACCTCTTA
60 ACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTATGATCATCGAAAACTTCTTA
10961 TGAAAGACCG
Statistics
Matches: 251, Mismatches: 22, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
160 2 0.01
161 138 0.55
162 2 0.01
164 2 0.01
165 2 0.01
170 1 0.00
172 1 0.00
173 68 0.27
174 2 0.01
175 32 0.13
176 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (165 bp):
CAAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTG
ATCATAAAAAACTTCTTGAAACGAGATCAACTATGATCATCGAAAACTTCTTAAAAGGAGATCAA
CAATGATCATAAAAAACTTCTTGAATACATCAACA
Found at i:10823 original size:196 final size:196
Alignment explanation
Indices: 10476--10855 Score: 544
Period size: 196 Copynumber: 1.9 Consensus size: 196
10466 CTGATCATCG
* * * *
10476 AAAACTTCTTGAAAGGAGATCAATTCTGATCATCAAAAACTTCTTGAAATGAGATCAACTCTGAT
1 AAAACTTCTTGAAAGGAGATCAACTCTGATCAACAAAAACTTCTTGAAAGGAGATCAACTCTGAC
** * *
10541 CATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCACCT
66 CATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTAAAACGAGATCAACT
** *
10606 CTGATCATCGAAAATTTCTTGAAAGGAGATCAACAATGATCATAAAAAACTTCTCTGATCATAAA
131 CTGATCATAAAAAACTTCTTGAAAGGAGATCAACAATGATCATAAAAAACTTCTCTGATCATAAA
10671 A
196 A
* *
10672 AAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTGAC
1 AAAACTTCTTGAAAGGAGATCAACTCTGATCAACAAAAACTTCTTGAAAGGAGATCAACTCTGAC
* * *** *
10737 CATAAAAAACTTTTTGAAAGGAGATCAACTTTGATCATCGCAAACTTCTTAAAATGAGATCAACT
66 CATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTAAAACGAGATCAACT
* ** **
10802 CTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTTCT
131 CTGATCATAAAAAACTTCTTGAAAGGAGATCAACAATGATCATAAAAAACTTCT
10856 TGAAAGGAGA
Statistics
Matches: 160, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
196 160 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (196 bp):
AAAACTTCTTGAAAGGAGATCAACTCTGATCAACAAAAACTTCTTGAAAGGAGATCAACTCTGAC
CATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTAAAACGAGATCAACT
CTGATCATAAAAAACTTCTTGAAAGGAGATCAACAATGATCATAAAAAACTTCTCTGATCATAAA
A
Found at i:10843 original size:231 final size:231
Alignment explanation
Indices: 10440--10880 Score: 747
Period size: 231 Copynumber: 1.9 Consensus size: 231
10430 TCTGATCATC
* *
10440 AAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAATTCTGA
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTGA
* * * *
10505 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAAC
66 CCATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCAAC
* *
10570 TCTGATCATAAAAAACTTCTTGAAACGAGATCACCTCTGATCATCGAAAATTTCTTGAAAGGAGA
131 TCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGA
10635 TCAACAATGATCATAAAAAACTTCTCTGATCATAAA
196 TCAACAATGATCATAAAAAACTTCTCTGATCATAAA
10671 AAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTGA
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTGA
* * * *
10736 CCATAAAAAACTTTTTGAAAGGAGATCAACTTTGATCATCGCAAACTTCTTAAAATGAGATCAAC
66 CCATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCAAC
*
10801 TCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGA
131 TCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGA
**
10866 TCAACTCTGATCATA
196 TCAACAATGATCATA
10881 GAACTTCTTG
Statistics
Matches: 195, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
231 195 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (231 bp):
AAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTGA
CCATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCAAC
TCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGA
TCAACAATGATCATAAAAAACTTCTCTGATCATAAA
Found at i:11034 original size:54 final size:54
Alignment explanation
Indices: 10949--11148 Score: 269
Period size: 54 Copynumber: 3.7 Consensus size: 54
10939 TATGATCATC
* * ** * *
10949 GAAAACCTCTTATGAAAGACCGCACAAGGTCATCTGAAGATCAACTTAGATTTCT
1 GAAAACTTC-TATGAAAGACCACACTGGGTCATCTTAAGATCAATTTAGATTTCT
* *
11004 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGAT-ATGTTTAGATCTCT
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCA-ATTTAGATTTCT
11058 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAATTTAGATCTT-T
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAATTTAGAT-TTCT
* *
11112 GAAAACTTCTATGAAAGACCATACTGGGTCATTTTAA
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
11149 ACACATGTAC
Statistics
Matches: 130, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
53 1 0.01
54 119 0.92
55 10 0.08
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (54 bp):
GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAATTTAGATTTCT
Found at i:11089 original size:108 final size:109
Alignment explanation
Indices: 10949--11148 Score: 305
Period size: 108 Copynumber: 1.8 Consensus size: 109
10939 TATGATCATC
*
10949 GAAAACCTCTTATGAAAGACCGCACAAGGTCATCTGAAGATCAACTTAGAT-TTCTGAAAACTTC
1 GAAAACCTCTTATGAAAGACCACACAAGGTCATCTGAAGATCAACTTAGATCTT-TGAAAACTTC
11013 TATGAAAGACCACACTGGGTCATCTTAAGATATGTTTAGATCTCT
65 TATGAAAGACCACACTGGGTCATCTTAAGATATGTTTAGATCTCT
* ** * *
11058 GAAAACTTC-TATGAAAGACCACACTGGGTCATCTTAAGATCAATTTAGATCTTTGAAAACTTCT
1 GAAAACCTCTTATGAAAGACCACACAAGGTCATCTGAAGATCAACTTAGATCTTTGAAAACTTCT
* *
11122 ATGAAAGACCATACTGGGTCATTTTAA
66 ATGAAAGACCACACTGGGTCATCTTAA
11149 ACACATGTAC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 72 0.88
109 10 0.12
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (109 bp):
GAAAACCTCTTATGAAAGACCACACAAGGTCATCTGAAGATCAACTTAGATCTTTGAAAACTTCT
ATGAAAGACCACACTGGGTCATCTTAAGATATGTTTAGATCTCT
Found at i:16348 original size:34 final size:34
Alignment explanation
Indices: 16303--16369 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
16293 GTTTTCTTAA
16303 ATGAAAATTCTAAACAGAGAACTAAGCAGGTTTG
1 ATGAAAATTCTAAACAGAGAACTAAGCAGGTTTG
* * *
16337 ATGAAACTTCTAAATAGAGACCTAAGCAGGTTT
1 ATGAAAATTCTAAACAGAGAACTAAGCAGGTTT
16370 ACTTGAACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.25
Consensus pattern (34 bp):
ATGAAAATTCTAAACAGAGAACTAAGCAGGTTTG
Found at i:16390 original size:31 final size:31
Alignment explanation
Indices: 16352--16410 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
16342 ACTTCTAAAT
*
16352 AGAGACCTAAGCAGGTTTACTTGAACGGGAC
1 AGAGACCTAAGCAGGTTTACTTAAACGGGAC
*
16383 AGAGACCTAAGCAGGTTTGCTTAAACGG
1 AGAGACCTAAGCAGGTTTACTTAAACGG
16411 AAATTCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (31 bp):
AGAGACCTAAGCAGGTTTACTTAAACGGGAC
Found at i:16496 original size:39 final size:38
Alignment explanation
Indices: 16381--16497 Score: 153
Period size: 39 Copynumber: 3.0 Consensus size: 38
16371 CTTGAACGGG
* * *
16381 ACAGAGACCTAAGCAGGTTTGCTTAAACGGAAATTCTAA
1 ACAGGGACCTAAGCAGGTTTTCTTAAAC-GAAATTCTGA
*
16420 ACAGGGACCTAAGCAGGTTTTACTTATACGAAATTCTGA
1 ACAGGGACCTAAGCAGGTTTT-CTTAAACGAAATTCTGA
* *
16459 ACGGGGACCTAAGCAGGTTTTCTTAAACATAAATTCTGA
1 ACAGGGACCTAAGCAGGTTTTCTTAAAC-GAAATTCTGA
16498 TGAGATTCTA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
38 6 0.09
39 57 0.83
40 6 0.09
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (38 bp):
ACAGGGACCTAAGCAGGTTTTCTTAAACGAAATTCTGA
Done.