Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006154.1 Corchorus capsularis cultivar CVL-1 contig06172, 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: 18697
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:3564 original size:31 final size:30
Alignment explanation
Indices: 3523--3944 Score: 234
Period size: 35 Copynumber: 13.2 Consensus size: 30
3513 AATGTGAATC
*
3523 AGTAATAAGTAATTTAATTCAGGGTAATTA
1 AGTAATAAGTAACTTAATTCAGGGTAATTA
*
3553 AGTCAATAAGTAGCTTAATTCAGGGTAATTA
1 AGT-AATAAGTAACTTAATTCAGGGTAATTA
*
3584 AGTAAGTCAGTAATCAACTTAATTCAGGGTAATTA
1 AGTAA-T-A--AGT-AACTTAATTCAGGGTAATTA
*
3619 AGTAAGTCAGTAATCAACTTAATTCAGGGTAATTA
1 AGTAA-T-A--AGT-AACTTAATTCAGGGTAATTA
* * *
3654 AGTGAGTCATTAACTTAATTCAGGGTAATTA
1 AGT-AATAAGTAACTTAATTCAGGGTAATTA
* *
3685 AGTAATTCAATAATCAACTTAATTCAGGGTAGTTA
1 AGTAA-T--A-AGT-AACTTAATTCAGGGTAATTA
**
3720 AGTAAGCCAGTAA-TCAACTTAATTCAGACTAATTA
1 AGT-A---A-TAAGT-AACTTAATTCAGGGTAATTA
3755 AGTCAGTCAGTAA-TCAACTTAATTCAGGGTAATTA
1 AGT-A---A-TAAGT-AACTTAATTCAGGGTAATTA
*** * * *
3790 AGTAAT---TCAGGGTAATT-A-AGTAAGTC
1 AGTAATAAGT-AACTTAATTCAGGGTAATTA
** *
3816 AG--CGAA-TAACTTAATTCAGGGTAATAA
1 AGTAATAAGTAACTTAATTCAGGGTAATTA
* *
3843 AGTCAATAAGTAGCTTAATTCAGGGAAATTA
1 AGT-AATAAGTAACTTAATTCAGGGTAATTA
*
3874 AGTCAATAAGTAGCTTAATTCAGGGTAATTAAGTA
1 AGT-AATAAGTAACTTAATTCAGGGTAA-T---TA
3909 AGTCAATAAGTAACTTAATTCAGGGTAATTA
1 AGT-AATAAGTAACTTAATTCAGGGTAATTA
3940 AGTAA
1 AGTAA
3945 GGGTAATTAA
Statistics
Matches: 323, Mismatches: 41, Indels: 56
0.77 0.10 0.13
Matches are distributed among these distances:
25 6 0.02
26 9 0.03
27 7 0.02
28 8 0.02
30 11 0.03
31 104 0.32
32 4 0.01
34 6 0.02
35 162 0.50
36 3 0.01
37 1 0.00
39 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.32
Consensus pattern (30 bp):
AGTAATAAGTAACTTAATTCAGGGTAATTA
Found at i:3605 original size:35 final size:35
Alignment explanation
Indices: 3566--3799 Score: 359
Period size: 35 Copynumber: 6.8 Consensus size: 35
3556 CAATAAGTAG
3566 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
3601 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
*
3636 CTTAATTCAGGGTAATTAAGTGAGTCA-T--T-AA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
* *
3667 CTTAATTCAGGGTAATTAAGTAATTCAATAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
* *
3702 CTTAATTCAGGGTAGTTAAGTAAGCCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
** *
3737 CTTAATTCAGACTAATTAAGTCAGTCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
*
3772 CTTAATTCAGGGTAATTAAGTAATTCAG
1 CTTAATTCAGGGTAATTAAGTAAGTCAG
3800 GGTAATTAAG
Statistics
Matches: 179, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
31 27 0.15
32 2 0.01
34 2 0.01
35 148 0.83
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (35 bp):
CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
Found at i:3810 original size:53 final size:53
Alignment explanation
Indices: 3739--3845 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 53
3729 GTAATCAACT
* * *
3739 TAATTCAGACTAATTAAGTCAGTCAG-TAATCAACTTAATTCAGGGTAATTAAG
1 TAATTCAGACTAATTAAGTAAGTCAGCGAAT-AACTTAATTCAGGGTAATAAAG
**
3792 TAATTCAGGGTAATTAAGTAAGTCAGCGAATAACTTAATTCAGGGTAATAAAG
1 TAATTCAGACTAATTAAGTAAGTCAGCGAATAACTTAATTCAGGGTAATAAAG
3845 T
1 T
3846 CAATAAGTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 45 0.94
54 3 0.06
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (53 bp):
TAATTCAGACTAATTAAGTAAGTCAGCGAATAACTTAATTCAGGGTAATAAAG
Found at i:3831 original size:35 final size:31
Alignment explanation
Indices: 3792--3945 Score: 150
Period size: 31 Copynumber: 4.7 Consensus size: 31
3782 GGTAATTAAG
3792 TAATTCAGGGTAATTAAGTAAGTCAGCGAATAACT
1 TAATTCAGGGTAATTAAGTAAGT-A---AATAACT
* * *
3827 TAATTCAGGGTAATAAAGTCAA-TAAGTAGCT
1 TAATTCAGGGTAATTAAGT-AAGTAAATAACT
* * *
3858 TAATTCAGGGAAATTAAGTCAA-TAAGTAGCT
1 TAATTCAGGGTAATTAAGT-AAGTAAATAACT
3889 TAATTCAGGGTAATTAAGTAAGTCAATAAGTAACT
1 TAATTCAGGGTAATTAAGTAAGT--A-AA-TAACT
3924 TAATTCAGGGTAATTAAGTAAG
1 TAATTCAGGGTAATTAAGTAAG
3946 GGTAATTAAG
Statistics
Matches: 105, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.02
31 53 0.50
33 1 0.01
34 2 0.02
35 45 0.43
36 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (31 bp):
TAATTCAGGGTAATTAAGTAAGTAAATAACT
Found at i:3947 original size:14 final size:14
Alignment explanation
Indices: 3930--3956 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3920 AACTTAATTC
3930 AGGGTAATTAAGTA
1 AGGGTAATTAAGTA
3944 AGGGTAATTAAGT
1 AGGGTAATTAAGT
3957 TTAGTAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGTAATTAAGTA
Found at i:6961 original size:17 final size:16
Alignment explanation
Indices: 6927--6991 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 16
6917 TTCCCTCCTG
6927 AAAAGGAAAAAGAAGA
1 AAAAGGAAAAAGAAGA
* *
6943 AAAAGTGAAAAGGATGA
1 AAAAG-GAAAAAGAAGA
*
6960 AAAA--AAAATGAAGA
1 AAAAGGAAAAAGAAGA
*
6974 AAAAAGAGAAAAG-AGA
1 AAAAGGA-AAAAGAAGA
6990 AA
1 AA
6992 GAAGTTAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
14 12 0.30
16 11 0.28
17 17 0.43
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (16 bp):
AAAAGGAAAAAGAAGA
Found at i:7084 original size:12 final size:12
Alignment explanation
Indices: 7067--7108 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
7057 TCAAAAAATT
*
7067 ATTTTCGAAAAG
1 ATTTTCAAAAAG
7079 ATTTTCAAAAATG
1 ATTTTCAAAAA-G
7092 AGTTTTCAAAAAG
1 A-TTTTCAAAAAG
7105 -TTTT
1 ATTTT
7109 TAAAGTCGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.15
12 10 0.37
13 3 0.11
14 10 0.37
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (12 bp):
ATTTTCAAAAAG
Found at i:7097 original size:26 final size:26
Alignment explanation
Indices: 7054--7109 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
7044 CGAGAAGTAT
* *
7054 TTTTCAAAAAATTATTTTCGAAAAGA
1 TTTTCAAAAAATGATTTTCAAAAAGA
*
7080 TTTTC-AAAAATGAGTTTTCAAAAAGT
1 TTTTCAAAAAATGA-TTTTCAAAAAGA
7106 TTTT
1 TTTT
7110 AAAGTCGCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (26 bp):
TTTTCAAAAAATGATTTTCAAAAAGA
Found at i:7099 original size:14 final size:13
Alignment explanation
Indices: 7054--7103 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
7044 CGAGAAGTAT
*
7054 TTTTCAAAAAATTA
1 TTTTC-AAAAATGA
*
7068 TTTTCGAAAA-GA
1 TTTTCAAAAATGA
7080 TTTTCAAAAATGA
1 TTTTCAAAAATGA
7093 GTTTTCAAAAA
1 -TTTTCAAAAA
7104 GTTTTTAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 10 0.32
13 6 0.19
14 15 0.48
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:7771 original size:7 final size:7
Alignment explanation
Indices: 7759--7822 Score: 53
Period size: 7 Copynumber: 9.1 Consensus size: 7
7749 AGCGAACAAA
7759 AAAAAAG
1 AAAAAAG
7766 AAAAAAG
1 AAAAAAG
7773 AAGAAAA-
1 AA-AAAAG
*
7780 AAGAAA-
1 AAAAAAG
7786 AAAAAAG
1 AAAAAAG
7793 AGAAAAA-
1 A-AAAAAG
*
7800 AAGAAAG
1 AAAAAAG
*
7807 AGCAAAAG
1 A-AAAAAG
7815 AAAAAAG
1 AAAAAAG
7822 A
1 A
7823 GATGAAGCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
6 12 0.26
7 20 0.43
8 14 0.30
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:7771 original size:10 final size:10
Alignment explanation
Indices: 7756--7820 Score: 69
Period size: 10 Copynumber: 6.4 Consensus size: 10
7746 TGAAGCGAAC
7756 AAAAAAA-AA
1 AAAAAAAGAA
*
7765 GAAAAAAGAA
1 AAAAAAAGAA
*
7775 GAAAAAAGAA
1 AAAAAAAGAA
*
7785 AAAAAAAGAG
1 AAAAAAAGAA
7795 AAAAAAAGAA
1 AAAAAAAGAA
*
7805 AGAGCAAAAGAA
1 A-A-AAAAAGAA
7817 AAAA
1 AAAA
7821 GAGATGAAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
9 6 0.13
10 31 0.66
11 2 0.04
12 8 0.17
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:7813 original size:15 final size:13
Alignment explanation
Indices: 7756--7824 Score: 68
Period size: 15 Copynumber: 5.0 Consensus size: 13
7746 TGAAGCGAAC
*
7756 AAAAAAAAAGAAA
1 AAAAAAAAAGAGA
*
7769 AAAGAAGAAAAAAG-
1 AAA-AA-AAAAGAGA
7783 AAAAAAAAAGAGA
1 AAAAAAAAAGAGA
7796 AAAAAAGAAAGAGCA
1 AAAAAA-AAAGAG-A
7811 AAAGAAAAAAGAGA
1 AAA-AAAAAAGAGA
7825 TGAAGCTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
12 6 0.13
13 11 0.23
14 12 0.26
15 15 0.32
16 3 0.06
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAGA
Found at i:7813 original size:27 final size:29
Alignment explanation
Indices: 7755--7824 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 29
7745 GTGAAGCGAA
7755 CAAAAAAAAAGA-AAAAAGAAGAAAAAAG
1 CAAAAAAAAAGAGAAAAAGAAGAAAAAAG
*
7783 -AAAAAAAAAGAGAAAAA-AAG-AAAGAG
1 CAAAAAAAAAGAGAAAAAGAAGAAAAAAG
7809 CAAAAGAAAAAAGAGA
1 C-AAA-AAAAAAGAGA
7825 TGAAGCTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 5 0.14
27 14 0.38
28 8 0.22
29 10 0.27
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (29 bp):
CAAAAAAAAAGAGAAAAAGAAGAAAAAAG
Found at i:9386 original size:36 final size:35
Alignment explanation
Indices: 9339--9450 Score: 109
Period size: 36 Copynumber: 3.1 Consensus size: 35
9329 TCATTCAGTA
*
9339 CTTCAATTTATTTCAAAATGATCGAGGGTGGTCGTT
1 CTTCAATTTATTTCAAGATGATCGAGGGTGGTC-TT
* * * * * *
9375 CTTCAGTTTATTTC-AGTTGACCCAAGTTGGTCTT
1 CTTCAATTTATTTCAAGATGATCGAGGGTGGTCTT
* *
9409 CCATCAATTTATTTCAGGATGATCGAGGGTGGTCATT
1 -CTTCAATTTATTTCAAGATGATCGAGGGTGGTC-TT
9446 CTTCA
1 CTTCA
9451 GTATATTCCA
Statistics
Matches: 57, Mismatches: 16, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
34 2 0.04
35 24 0.42
36 29 0.51
37 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (35 bp):
CTTCAATTTATTTCAAGATGATCGAGGGTGGTCTT
Found at i:9473 original size:35 final size:34
Alignment explanation
Indices: 9363--9489 Score: 119
Period size: 35 Copynumber: 3.6 Consensus size: 34
9353 AAAATGATCG
*
9363 AGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACCC
1 AGGGTGGTC-TTCATCAGTTTATTTCAGTTGACCC
* * * * * *
9398 AAGTTGGTCTTCCATCAATTTATTTCAGGATGATCG
1 AGGGTGGTCTT-CATCAGTTTATTTCA-GTTGACCC
* * *
9434 AGGGTGGTCATTCTTCAGTATATTCCAGTTGACCC
1 AGGGTGGTC-TTCATCAGTTTATTTCAGTTGACCC
9469 AGGGTGGTCTTTCATCAGTTT
1 AGGGTGGTC-TTCATCAGTTT
9490 GTGTCGGAAT
Statistics
Matches: 70, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
34 2 0.03
35 43 0.61
36 23 0.33
37 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (34 bp):
AGGGTGGTCTTCATCAGTTTATTTCAGTTGACCC
Found at i:9502 original size:71 final size:71
Alignment explanation
Indices: 9341--9821 Score: 293
Period size: 71 Copynumber: 6.6 Consensus size: 71
9331 ATTCAGTACT
* * * * * *
9341 TCAATTTATTTCAAAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACCCAAGTTGGT
1 TCAATTTGTGTCAGAATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGACCCAGGGTGGT
*
9406 CTTCCA
66 CTTTCA
* * * * *
9412 TCAATTTATTTCAGGATGATCGAGGGTGGTCATTCTTCAGTATATTCCAGTTGACCCAGGGTGGT
1 TCAATTTGTGTCAGAATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGACCCAGGGTGGT
9477 CTTTCA
66 CTTTCA
* * * *
9483 TCAGTTTGTGTCGGAATGATCCAGGGT-G--A-TCTTC-CTTTA----A-TTGACCCAGGGTGGT
1 TCAATTTGTGTCAGAATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGACCCAGGGTGGT
*
9538 CTTTCT
66 CTTTCA
* ** * ** * * *
9544 TTAGGTTGAGTCAGAATGATCGAGGGTGGTTGTTCTTCAGTTTATTTCAGCTGACCCTGGGCGGT
1 TCAATTTGTGTCAGAATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGACCCAGGGTGGT
*
9609 CTTTCT
66 CTTTCA
* * *
9615 TGAATTTGTGTCAGAATGATCGAGGATGG-CTGTTCTTCAGGGTGGTTGTTCTTCAGTTTATTTC
1 TCAATTTGTGTCAGAATGATCGAGGGTGGTC-ATTCTTCA--------G-T-TT-A-----TTTC
*
9679 AGTTGACCCAGGGTGGTCTTTCTT
49 AGTTGACCCAGGGTGGTCTTTC-A
* * * *
9703 TCCAAAGTTTGCGTCGGAATGATCGAGGGTGGTCGTTCTTCAAGTTTATGTT-AGTTAACCCAGG
1 T-C-AA-TTTGTGTCAGAATGATCGAGGGTGGTCATTCTTC-AGTTTAT-TTCAGTTGACCCAGG
*
9767 GTGGTCTTTCT
61 GTGGTCTTTCA
* ** * * *
9778 TCGATTTGCATCAGAGTGATCGAGGGTGGTCGTTCTTCTGTTTA
1 TCAATTTGTGTCAGAATGATCGAGGGTGGTCATTCTTCAGTTTA
9822 GTTCGAAATA
Statistics
Matches: 330, Mismatches: 46, Indels: 68
0.74 0.10 0.15
Matches are distributed among these distances:
61 42 0.13
62 2 0.01
65 5 0.02
66 7 0.02
67 5 0.02
68 1 0.00
70 2 0.01
71 139 0.42
72 31 0.09
73 1 0.00
74 1 0.00
75 2 0.01
76 22 0.07
77 2 0.01
79 1 0.00
80 1 0.00
81 3 0.01
82 3 0.01
83 1 0.00
84 1 0.00
87 23 0.07
88 2 0.01
90 2 0.01
91 29 0.09
92 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.38
Consensus pattern (71 bp):
TCAATTTGTGTCAGAATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGACCCAGGGTGGT
CTTTCA
Found at i:9808 original size:72 final size:75
Alignment explanation
Indices: 9653--9821 Score: 222
Period size: 72 Copynumber: 2.3 Consensus size: 75
9643 GCTGTTCTTC
* * *
9653 AGGGTGGTTGTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTTCCAAAGTTTGCGTC
1 AGGGTGGTCGTTCTTCAGTTTATTTCAGTTAACCCAGGGTGGTCTTTCTTTCCAAAGTTTGCATC
*
9718 GGAATGATCG
66 AGAATGATCG
*
9728 AGGGTGGTCGTTCTTCAAGTTTATGTT-AGTTAACCCAGGGTGGTCTTTC-TT-C-GA-TTTGCA
1 AGGGTGGTCGTTCTTC-AGTTTAT-TTCAGTTAACCCAGGGTGGTCTTTCTTTCCAAAGTTTGCA
*
9788 TCAGAGTGATCG
64 TCAGAATGATCG
*
9800 AGGGTGGTCGTTCTTCTGTTTA
1 AGGGTGGTCGTTCTTCAGTTTA
9822 GTTCGAAATA
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
71 5 0.06
72 31 0.36
73 1 0.01
74 1 0.01
75 17 0.20
76 28 0.33
77 2 0.02
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.39
Consensus pattern (75 bp):
AGGGTGGTCGTTCTTCAGTTTATTTCAGTTAACCCAGGGTGGTCTTTCTTTCCAAAGTTTGCATC
AGAATGATCG
Found at i:13425 original size:35 final size:35
Alignment explanation
Indices: 13386--13852 Score: 660
Period size: 35 Copynumber: 13.7 Consensus size: 35
13376 TCAATAAGTG
13386 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
13421 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
13456 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
13491 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
* *
13526 CTTAATTCAAGGTAATTAAGTGAGTCA-T--T-AA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
* *
13557 CTTAATTCAGGGTAATTAAGTAATTCAATAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
* *
13592 CTTAATTCAAGGTAGTTAAGTAAGTCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
*
13627 CTTAATTCAGGGTAATTAAGTCAGTCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
*
13662 CTTAATTCAGGGTAATTAAGTAATTCAGTAATCAA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
*
13697 CTTAATTCAGGGTAATTAAGTAAGTCAGCGAAT-AA
1 CTTAATTCAGGGTAATTAAGTAAGTCAG-TAATCAA
* *
13732 CTTAATTCAGGGTAATTAAGTCAA-T-A--AGT-AG
1 CTTAATTCAGGGTAATTAAGT-AAGTCAGTAATCAA
* *
13763 CTTAATTCAGGGTAATTAAGTCAA-T-A--AGT-AG
1 CTTAATTCAGGGTAATTAAGT-AAGTCAGTAATCAA
*
13794 CTTAATTCAGGGTAATTAAGTAAGTCAATAAGT-AA
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAA-TCAA
13829 CTTAATTCAGGGTAATTAAGTAAG
1 CTTAATTCAGGGTAATTAAGTAAG
13853 GGCAATTAAG
Statistics
Matches: 401, Mismatches: 20, Indels: 22
0.91 0.05 0.05
Matches are distributed among these distances:
30 2 0.00
31 82 0.20
32 3 0.01
34 4 0.01
35 305 0.76
36 5 0.01
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (35 bp):
CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA
Found at i:13575 original size:171 final size:171
Alignment explanation
Indices: 13386--13852 Score: 668
Period size: 171 Copynumber: 2.7 Consensus size: 171
13376 TCAATAAGTG
13386 CTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTA
1 CTTAATTCAGGGTAATTAAGTAA-TCA-TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTA
13451 ATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGT
64 ATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGT
* *
13516 CAGTAATCAACTTAATTCAAGGTAATTAAGTGAGT-C-ATTAA
129 CAGTAATCAACTTAATTCAAGGTAATTAAGTAAGTACGAATAA
* *
13557 CTTAATTCAGGGTAATTAAGTAATTCAATAATCAACTTAATTCAAGGTAGTTAAGTAAGTCAGTA
1 CTTAATTCAGGGTAATTAAGTAA-TC-ATAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTA
* *
13622 ATCAACTTAATTCAGGGTAATTAAGTCAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAATT
64 ATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGT
*
13687 CAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGCGAATAA
129 CAGTAATCAACTTAATTCAAGGTAATTAAGTAAGT-A-CGAATAA
* *
13732 CTTAATTCAGGGTAATTAAGTCAAT-A-AGT-AGCTTAATTCAGGGTAATTAAGTCAA-T-A--A
1 CTTAATTCAGGGTAATTAAGT-AATCATAATCAACTTAATTCAGGGTAATTAAGT-AAGTCAGTA
* * *
13790 GT-AGCTTAATTCAGGGTAATTAAGTAAGTCAATAAGT-AACTTAATTCAGGGTAATTAAGTAAG
64 ATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-TCAACTTAATTCAGGGTAATTAAGTAAG
13853 GGCAATTAAG
Statistics
Matches: 271, Mismatches: 17, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
167 55 0.20
168 3 0.01
170 1 0.00
171 177 0.65
172 5 0.02
173 1 0.00
174 1 0.00
175 26 0.10
176 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (171 bp):
CTTAATTCAGGGTAATTAAGTAATCATAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCA
GTAATCAACTTAATTCAAGGTAATTAAGTAAGTACGAATAA
Found at i:15745 original size:18 final size:17
Alignment explanation
Indices: 15715--15748 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
15705 AAAATTAATA
15715 TTTTTAATGGTTTGATG
1 TTTTTAATGGTTTGATG
*
15732 TTTTTCATGTGTTTGAT
1 TTTTTAATG-GTTTGAT
15749 AATCCATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.03, G:0.21, T:0.62
Consensus pattern (17 bp):
TTTTTAATGGTTTGATG
Done.