Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012402.1 Corchorus olitorius cultivar O-4 contig12435, 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: 25125
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:894 original size:103 final size:102
Alignment explanation
Indices: 590--896 Score: 445
Period size: 103 Copynumber: 3.0 Consensus size: 102
580 CGGATTTTTC
* * *
590 TGTAGTAATTTCCGTTGGAACAATTTATTTTGGCGCAAAATATTTGAACTAGCGGGAATTCAAAT
1 TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTTGAA-GAGCGGGAATTCAAAT
*
655 TTTAATTTGACACGAAAATTAAATTCGTTGCAAAAATT
65 TTTAATTTGACACGAAAATTAAATTCGTTGCAAAATTT
693 TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTT-AATCGAGCGGGAATTCAAA
1 TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTTGAA--GAGCGGGAATTCAAA
* ** *
757 TTTTGATTTGTTACGAAAACTAAATTCGTTGCAAAATTT
64 TTTTAATTTGACACGAAAATTAAATTCGTTGCAAAATTT
* *
796 TGTAATAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATTTTTGAGAGAGCGGGAATTCAAAT
1 TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTTGA-AGAGCGGGAATTCAAAT
* * * *
861 TTTAATTTGCCACGAAAATTAATTTTGTGGCAAAAT
65 TTTAATTTGACACGAAAATTAAATTCGTTGCAAAAT
897 CTGTAGCAAA
Statistics
Matches: 184, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
102 2 0.01
103 180 0.98
104 1 0.01
105 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (102 bp):
TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTTGAAGAGCGGGAATTCAAATT
TTAATTTGACACGAAAATTAAATTCGTTGCAAAATTT
Found at i:5962 original size:54 final size:53
Alignment explanation
Indices: 5904--6060 Score: 170
Period size: 54 Copynumber: 2.8 Consensus size: 53
5894 AATTAAAGAG
* *
5904 TAAAATGAAATTTGATAGTCAAAGAGTAAAAGGAAATTGGTAAATTTGGTTAAT
1 TAAAAGGAAATTTGATAATCAAAGAGTAAAAGGAAATTGGTAAATTTGG-TAAT
* * *
5958 TAAAAGGAAATTTGGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAAT
1 TAAAAGGAAATTTGATAATCAAAGAGTAAAAGGAAATTGGTAAATTTGGTAAT
* * *
6011 TAAAGAGTAAAATGAATTGGGTAATTAAAGAGTAAAAGGAAATTTGGTAA
1 TAAA-AG-GAAAT---TT-GATAATCAAAGAGTAAAAGGAAA-TTGGTAA
6061 TTAAAGAGTA
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
53 8 0.09
54 46 0.52
55 4 0.04
58 2 0.02
59 23 0.26
60 6 0.07
ACGTcount: A:0.47, C:0.01, G:0.22, T:0.30
Consensus pattern (53 bp):
TAAAAGGAAATTTGATAATCAAAGAGTAAAAGGAAATTGGTAAATTTGGTAAT
Found at i:5994 original size:26 final size:26
Alignment explanation
Indices: 5958--6075 Score: 139
Period size: 26 Copynumber: 4.3 Consensus size: 26
5948 TTTGGTTAAT
5958 TAAAAGGAAATTTGGTAATTAAAGAG
1 TAAAAGGAAATTTGGTAATTAAAGAG
5984 TAAAAGGAAATTGGTTAATTTGGTAATTAAAGAG
1 TAAAAGG--A------AATTTGGTAATTAAAGAG
* *
6018 TAAAATG-AATTGGGTAATTAAAGAG
1 TAAAAGGAAATTTGGTAATTAAAGAG
6043 TAAAAGGAAATTTGGTAATTAAAGAG
1 TAAAAGGAAATTTGGTAATTAAAGAG
6069 TAAAAGG
1 TAAAAGG
6076 CATTGTTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
25 23 0.29
26 31 0.39
28 1 0.01
34 24 0.30
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (26 bp):
TAAAAGGAAATTTGGTAATTAAAGAG
Found at i:6009 original size:34 final size:33
Alignment explanation
Indices: 5966--6036 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 33
5956 ATTAAAAGGA
*
5966 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
1 AATTTGGTAATTAAAGAGTAAAAGG-AATTGGGT
*
6000 AATTTGGTAATTAAAGAGTAAAATGAATTGGGT
1 AATTTGGTAATTAAAGAGTAAAAGGAATTGGGT
6033 AATT
1 AATT
6037 AAAGAGTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 11 0.31
34 24 0.69
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.34
Consensus pattern (33 bp):
AATTTGGTAATTAAAGAGTAAAAGGAATTGGGT
Found at i:6551 original size:25 final size:26
Alignment explanation
Indices: 6521--6569 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
6511 GAAATTGGTT
6521 AATTT-GGTAATTAAAGAGTAAAATG
1 AATTTGGGTAATTAAAGAGTAAAATG
6546 AATTTGGGTAATTAAAGAGTAAAA
1 AATTTGGGTAATTAAAGAGTAAAA
6570 GGAAAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (26 bp):
AATTTGGGTAATTAAAGAGTAAAATG
Found at i:6586 original size:36 final size:36
Alignment explanation
Indices: 6546--6650 Score: 176
Period size: 35 Copynumber: 2.9 Consensus size: 36
6536 GAGTAAAATG
6546 AATTTGGGTAATTAAAGAGTAAAAGGAAAATTGGGA
1 AATTTGGGTAATTAAAGAGTAAAAGGAAAATTGGGA
*
6582 AATTT-GGTAATTAAAGAGTAAAATGAAAATTGGGA
1 AATTTGGGTAATTAAAGAGTAAAAGGAAAATTGGGA
* *
6617 AATTTGGTTAATTAAAGAGTAAAAGGAAAGTTGG
1 AATTTGGGTAATTAAAGAGTAAAAGGAAAATTGG
6651 TTAATTAAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
35 34 0.53
36 30 0.47
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.28
Consensus pattern (36 bp):
AATTTGGGTAATTAAAGAGTAAAAGGAAAATTGGGA
Found at i:6597 original size:27 final size:27
Alignment explanation
Indices: 6579--6920 Score: 271
Period size: 26 Copynumber: 13.0 Consensus size: 27
6569 AGGAAAATTG
6579 GGAAATTTGGTAATTAAAGAGTAAAATGAAAATT
1 GGAAATTTGGTAATTAAAGAG-----T-AAAA-T
6613 GGGAAATTTGGTTAATTAAAGAGTAAAA-
1 GG-AAATTTGG-TAATTAAAGAGTAAAAT
* *
6641 GGAAAGTTGGTTAATTAAAGGGTAAAA-
1 GGAAATTTGG-TAATTAAAGAGTAAAAT
6668 GGAAATTTGGTAATTAAAGAGTAAAAT
1 GGAAATTTGGTAATTAAAGAGTAAAAT
*
6695 GG-AATTGGGTAATTAAAGAGTAAAAT
1 GGAAATTTGGTAATTAAAGAGTAAAAT
6721 -GAAA-TTGGTTAATTAAAGAGTAAAA-
1 GGAAATTTGG-TAATTAAAGAGTAAAAT
*
6746 AGAAATTT-G---TT----AGTAAAA-
1 GGAAATTTGGTAATTAAAGAGTAAAAT
*
6764 GGAAATTTAGTAATTAAAGAGTAAAAT
1 GGAAATTTGGTAATTAAAGAGTAAAAT
* * *
6791 -GAAATTAGGTAATTGAACAGTAAAA-
1 GGAAATTTGGTAATTAAAGAGTAAAAT
6816 GG-AATGTT-GTAAATTAAAGAGTAAAA-
1 GGAAAT-TTGGT-AATTAAAGAGTAAAAT
* * *
6842 GGGAATTCGGTAATTAAAGAATAAAAT
1 GGAAATTTGGTAATTAAAGAGTAAAAT
* *
6869 -GAAA-TTGGACAATTAAAGAGTAAGA-
1 GGAAATTTGG-TAATTAAAGAGTAAAAT
*
6894 GAAAATTTGGTAATTAAAGAGTAAAAT
1 GGAAATTTGGTAATTAAAGAGTAAAAT
6921 TTAGTAATTT
Statistics
Matches: 258, Mismatches: 24, Indels: 59
0.76 0.07 0.17
Matches are distributed among these distances:
18 14 0.05
19 1 0.00
22 4 0.02
25 12 0.05
26 154 0.60
27 45 0.17
28 2 0.01
30 4 0.02
31 1 0.00
34 2 0.01
35 8 0.03
36 11 0.04
ACGTcount: A:0.49, C:0.01, G:0.22, T:0.27
Consensus pattern (27 bp):
GGAAATTTGGTAATTAAAGAGTAAAAT
Found at i:6691 original size:26 final size:26
Alignment explanation
Indices: 6614--6919 Score: 305
Period size: 26 Copynumber: 12.0 Consensus size: 26
6604 ATGAAAATTG
6614 GGAAATTTGGTTAATTAAAGAGTAAAA
1 GGAAATTTGG-TAATTAAAGAGTAAAA
* *
6641 GGAAAGTTGGTTAATTAAAGGGTAAAA
1 GGAAATTTGG-TAATTAAAGAGTAAAA
6668 GGAAATTTGGTAATTAAAGAGTAAAA
1 GGAAATTTGGTAATTAAAGAGTAAAA
*
6694 TGG-AATTGGGTAATTAAAGAGTAAAA
1 -GGAAATTTGGTAATTAAAGAGTAAAA
*
6720 TGAAA-TTGGTTAATTAAAGAGTAAAA
1 GGAAATTTGG-TAATTAAAGAGTAAAA
*
6746 AGAAATTT-G---TT----AGTAAAA
1 GGAAATTTGGTAATTAAAGAGTAAAA
*
6764 GGAAATTTAGTAATTAAAGAGTAAAA
1 GGAAATTTGGTAATTAAAGAGTAAAA
* * * *
6790 TGAAATTAGGTAATTGAACAGTAAAA
1 GGAAATTTGGTAATTAAAGAGTAAAA
6816 GG-AATGTT-GTAAATTAAAGAGTAAAA
1 GGAAAT-TTGGT-AATTAAAGAGTAAAA
* * *
6842 GGGAATTCGGTAATTAAAGAATAAAA
1 GGAAATTTGGTAATTAAAGAGTAAAA
* * *
6868 TGAAA-TTGGACAATTAAAGAGTAAGA
1 GGAAATTTGG-TAATTAAAGAGTAAAA
*
6894 GAAAATTTGGTAATTAAAGAGTAAAA
1 GGAAATTTGGTAATTAAAGAGTAAAA
6920 TTTAGTAATT
Statistics
Matches: 231, Mismatches: 30, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
18 14 0.06
19 1 0.00
22 4 0.02
25 12 0.05
26 153 0.66
27 47 0.20
ACGTcount: A:0.50, C:0.01, G:0.22, T:0.27
Consensus pattern (26 bp):
GGAAATTTGGTAATTAAAGAGTAAAA
Found at i:6778 original size:44 final size:44
Alignment explanation
Indices: 6713--6796 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
6703 GTAATTAAAG
* *
6713 AGTAAAATGAAATTGGTTAATTAAAGAGTAAAAAGAAATTTGTT
1 AGTAAAAGGAAATTAGTTAATTAAAGAGTAAAAAGAAATTTGTT
*
6757 AGTAAAAGGAAATTTAG-TAATTAAAGAGTAAAATGAAATT
1 AGTAAAAGGAAA-TTAGTTAATTAAAGAGTAAAAAGAAATT
6797 AGGTAATTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 33 0.92
45 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (44 bp):
AGTAAAAGGAAATTAGTTAATTAAAGAGTAAAAAGAAATTTGTT
Found at i:6831 original size:96 final size:96
Alignment explanation
Indices: 6662--6841 Score: 272
Period size: 96 Copynumber: 1.9 Consensus size: 96
6652 TAATTAAAGG
* * * *
6662 GTAAAAGGAAATTTGGTAATTAAAGAGTAAAATGGAATTGGGTAATTAAAGAGTAAAATGAAATT
1 GTAAAAGGAAATTTAGTAATTAAAGAGTAAAATGAAATTAGGTAATTAAACAGTAAAATGAAATT
*
6727 GGTTAATTAAAGAGTAAAAAGAAATTTGTTA
66 GGTAAATTAAAGAGTAAAAAGAAATTTGTTA
* *
6758 GTAAAAGGAAATTTAGTAATTAAAGAGTAAAATGAAATTAGGTAATTGAACAGTAAAA-GGAATG
1 GTAAAAGGAAATTTAGTAATTAAAGAGTAAAATGAAATTAGGTAATTAAACAGTAAAATGAAAT-
*
6822 TTGTAAATTAAAGAGTAAAA
65 TGGTAAATTAAAGAGTAAAA
6842 GGGAATTCGG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
95 4 0.05
96 71 0.95
ACGTcount: A:0.51, C:0.01, G:0.21, T:0.28
Consensus pattern (96 bp):
GTAAAAGGAAATTTAGTAATTAAAGAGTAAAATGAAATTAGGTAATTAAACAGTAAAATGAAATT
GGTAAATTAAAGAGTAAAAAGAAATTTGTTA
Found at i:6920 original size:21 final size:20
Alignment explanation
Indices: 6890--6929 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
6880 ATTAAAGAGT
*
6890 AAGAGAAAATTTGGTAATTA
1 AAGAGAAAATTTAGTAATTA
6910 AAGAGTAAAATTTAGTAATT
1 AAGAG-AAAATTTAGTAATT
6930 TGGTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (20 bp):
AAGAGAAAATTTAGTAATTA
Found at i:7124 original size:20 final size:20
Alignment explanation
Indices: 7091--7134 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
7081 AAAAAGAGGT
7091 AAAATGAAATTTTGGTAATTA
1 AAAATGAAATTTTGGTAA-TA
7112 AAAATGAAA-TTTGGTAATA
1 AAAATGAAATTTTGGTAATA
7131 AAAA
1 AAAA
7135 AAAAGGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 8 0.35
21 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.32
Consensus pattern (20 bp):
AAAATGAAATTTTGGTAATA
Found at i:7136 original size:21 final size:21
Alignment explanation
Indices: 7091--7135 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
7081 AAAAAGAGGT
*
7091 AAAATGAAATTTTGGTAATTA
1 AAAATGAAATTTTGGTAATAA
7112 AAAATGAAA-TTTGGTAATAA
1 AAAATGAAATTTTGGTAATAA
7132 AAAA
1 AAAA
7136 AAAGGAGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (21 bp):
AAAATGAAATTTTGGTAATAA
Found at i:9405 original size:22 final size:21
Alignment explanation
Indices: 9362--9405 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
9352 ATTGAGCCGG
*
9362 TTTATATCAAAGGTTGATTAT
1 TTTATATCAAAGGTTGAGTAT
* *
9383 TTTATATCTAAGTTTTGAGTAT
1 TTTATATCAAAG-GTTGAGTAT
9405 T
1 T
9406 AAGTATTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.52
Consensus pattern (21 bp):
TTTATATCAAAGGTTGAGTAT
Found at i:10079 original size:26 final size:24
Alignment explanation
Indices: 10050--10144 Score: 95
Period size: 25 Copynumber: 3.8 Consensus size: 24
10040 ATCTTACACT
*
10050 TGATTACTCTTTTACTTCTTGATTAC
1 TGATTACTCTTTTAC-TCTT-TTTAC
*
10076 TGATTACCATTTTTTACTCTTTTTAC
1 TGATTA-C-TCTTTTACTCTTTTTAC
10102 TGATTAC-CGTTTTTACTCTTTTTAC
1 TGATTACTC--TTTTACTCTTTTTAC
*
10127 TGATTACT-TTTTTCTCTT
1 TGATTACTCTTTTACTCTT
10145 GCTGACTACT
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
23 9 0.15
25 23 0.38
26 16 0.27
27 5 0.08
28 7 0.12
ACGTcount: A:0.17, C:0.19, G:0.06, T:0.58
Consensus pattern (24 bp):
TGATTACTCTTTTACTCTTTTTAC
Found at i:10120 original size:25 final size:26
Alignment explanation
Indices: 10072--10133 Score: 108
Period size: 25 Copynumber: 2.4 Consensus size: 26
10062 TACTTCTTGA
*
10072 TTACTGATTACCATTTTTTACTCTTT
1 TTACTGATTACCAGTTTTTACTCTTT
10098 TTACTGATTACC-GTTTTTACTCTTT
1 TTACTGATTACCAGTTTTTACTCTTT
10123 TTACTGATTAC
1 TTACTGATTAC
10134 TTTTTTCTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 23 0.66
26 12 0.34
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (26 bp):
TTACTGATTACCAGTTTTTACTCTTT
Found at i:10191 original size:36 final size:37
Alignment explanation
Indices: 10163--10390 Score: 256
Period size: 36 Copynumber: 6.3 Consensus size: 37
10153 CTCTTACTAG
10163 TTTGCTGATTACTATTACCATTTTTACTCTTTACT-T
1 TTTGCTGATTACTATTACCATTTTTACTCTTTACTCT
* *
10199 TTTGCTGATTGCTATTACCA-TTTTACTGTTTACTCT
1 TTTGCTGATTACTATTACCATTTTTACTCTTTACTCT
* * *
10235 TTTACTGATTACTATTATTC-TTTTTACTCTTTACT-A
1 TTTGCTGATTACTATTA-CCATTTTTACTCTTTACTCT
* * *
10271 TTTGCTCATTACTATTACTA-TTTTACTGTTTACTCT
1 TTTGCTGATTACTATTACCATTTTTACTCTTTACTCT
* *
10307 TTTACTGATTACTATTACTC-TTTTTACTCTTTAC-CC
1 TTTGCTGATTACTATTAC-CATTTTTACTCTTTACTCT
* * *
10343 TTTGCTCATTACTATTACCA-TTTTATTGTTTACTCT
1 TTTGCTGATTACTATTACCATTTTTACTCTTTACTCT
*
10379 TTTACTGATTAC
1 TTTGCTGATTAC
10391 ACTTTACTCT
Statistics
Matches: 158, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
35 38 0.24
36 94 0.59
37 26 0.16
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.55
Consensus pattern (37 bp):
TTTGCTGATTACTATTACCATTTTTACTCTTTACTCT
Found at i:10232 original size:72 final size:71
Alignment explanation
Indices: 10167--10390 Score: 349
Period size: 72 Copynumber: 3.1 Consensus size: 71
10157 TACTAGTTTG
* * *
10167 CTGATTACTATTACCATTTTTACTCTTTACTTTTTGCTGATTGCTATTACCATTTTACTGTTTAC
1 CTGATTACTATTACC-TTTTTACTCTTTACTATTTGCTCATTACTATTACCATTTTACTGTTTAC
10232 TCTTTTA
65 TCTTTTA
* *
10239 CTGATTACTATTATTCTTTTTACTCTTTACTATTTGCTCATTACTATTACTATTTTACTGTTTAC
1 CTGATTACTATTA-CCTTTTTACTCTTTACTATTTGCTCATTACTATTACCATTTTACTGTTTAC
10304 TCTTTTA
65 TCTTTTA
** *
10311 CTGATTACTATTACTCTTTTTACTCTTTACCCTTTGCTCATTACTATTACCATTTTATTGTTTAC
1 CTGATTACTATTAC-CTTTTTACTCTTTACTATTTGCTCATTACTATTACCATTTTACTGTTTAC
10376 TCTTTTA
65 TCTTTTA
10383 CTGATTAC
1 CTGATTAC
10391 ACTTTACTCT
Statistics
Matches: 140, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
72 139 0.99
73 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.54
Consensus pattern (71 bp):
CTGATTACTATTACCTTTTTACTCTTTACTATTTGCTCATTACTATTACCATTTTACTGTTTACT
CTTTTA
Found at i:10275 original size:108 final size:114
Alignment explanation
Indices: 10113--10359 Score: 296
Period size: 108 Copynumber: 2.2 Consensus size: 114
10103 GATTACCGTT
* *
10113 TTTACTCTTTTTACTGATTACT-TTTTTCTCTTGCTGACTACTCTTACTAGTTTGCTGATTACTA
1 TTTACTC-TTTTACTGATTACTATTATTCTCTT-CTGACTACTCTTACTAGTTTGCTCATTACTA
* * *
10177 TTACCATTTTTACTCTTTACT-TTTTGCTGATTGCTATTAC-CATTTTACTG
64 TTACCA-TTTTACTCTTTACTCTTTTACTGATTACTATTACTCATTTTACTC
*
10227 TTTACTCTTTTACTGATTACTATTATTCT-TT-TTACT-CT-TTACTA-TTTGCTCATTACTATT
1 TTTACTCTTTTACTGATTACTATTATTCTCTTCTGACTACTCTTACTAGTTTGCTCATTACTATT
* * *
10287 ACTATTTTACTGTTTACTCTTTTACTGATTACTATTACTCTTTTTACTC
66 ACCATTTTACTCTTTACTCTTTTACTGATTACTATTACTCATTTTACTC
* * *
10336 TTTAC-CCTTTGCTCATTACTATTA
1 TTTACTCTTTTACTGATTACTATTA
10360 CCATTTTATT
Statistics
Matches: 118, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
107 13 0.11
108 51 0.43
109 19 0.16
110 2 0.02
111 4 0.03
113 16 0.14
114 13 0.11
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (114 bp):
TTTACTCTTTTACTGATTACTATTATTCTCTTCTGACTACTCTTACTAGTTTGCTCATTACTATT
ACCATTTTACTCTTTACTCTTTTACTGATTACTATTACTCATTTTACTC
Found at i:10331 original size:22 final size:21
Alignment explanation
Indices: 10300--10340 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
10290 ATTTTACTGT
*
10300 TTACTCTTTTACTGATTACTA
1 TTACTCTTTTACTCATTACTA
*
10321 TTACTCTTTTTACTCTTTAC
1 TTACTC-TTTTACTCATTAC
10341 CCTTTGCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.56
Consensus pattern (21 bp):
TTACTCTTTTACTCATTACTA
Found at i:10435 original size:35 final size:35
Alignment explanation
Indices: 10396--10474 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
10386 ATTACACTTT
*
10396 ACTCTTTACTGACTATTATTACTCATTTACTGATG
1 ACTCTTTACTGACTACTATTACTCATTTACTGATG
* * * *
10431 ACTCTTTATTGATTACTATTACTCCTTTACTGATT
1 ACTCTTTACTGACTACTATTACTCATTTACTGATG
10466 ACTCTTTAC
1 ACTCTTTAC
10475 CATTTCTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (35 bp):
ACTCTTTACTGACTACTATTACTCATTTACTGATG
Found at i:10446 original size:21 final size:21
Alignment explanation
Indices: 10422--10468 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
10412 TATTACTCAT
*
10422 TTACTGATGACT-CTTTATTGA
1 TTACT-ATGACTCCTTTACTGA
*
10443 TTACTATTACTCCTTTACTGA
1 TTACTATGACTCCTTTACTGA
10464 TTACT
1 TTACT
10469 CTTTACCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (21 bp):
TTACTATGACTCCTTTACTGA
Found at i:10461 original size:14 final size:14
Alignment explanation
Indices: 10220--10447 Score: 63
Period size: 15 Copynumber: 15.9 Consensus size: 14
10210 CTATTACCAT
*
10220 TTTACTGTTTACTC
1 TTTACTGATTACTC
*
10234 TTTTACTGATTACTA
1 -TTTACTGATTACTC
* **
10249 TTATTCTTTTTACTC
1 TT-TACTGATTACTC
*
10264 TTTACT-ATTTGCTC
1 TTTACTGA-TTACTC
* *
10278 ATTACT-ATTACTAT
1 TTTACTGATTACT-C
*
10292 TTTACTGTTTACTC
1 TTTACTGATTACTC
10306 TTTTACTGATTACT-
1 -TTTACTGATTACTC
* **
10320 ATTACTCTTTTTACTC
1 TTTA--CTGATTACTC
*** *
10336 TTTACCCTTTGCTC
1 TTTACTGATTACTC
*
10350 ATTACT-ATTAC-C
1 TTTACTGATTACTC
* *
10362 ATTTTATTGTTTACTC
1 --TTTACTGATTACTC
*
10378 TTTTACTGATTACAC
1 -TTTACTGATTACTC
** *
10393 TTTACTCTTTACTG
1 TTTACTGATTACTC
** *
10407 ACTA-TTATTACTC
1 TTTACTGATTACTC
*
10420 ATTTACTGATGACTC
1 -TTTACTGATTACTC
*
10435 TTTATTGATTACT
1 TTTACTGATTACT
10448 ATTACTCCTT
Statistics
Matches: 151, Mismatches: 48, Indels: 29
0.66 0.21 0.13
Matches are distributed among these distances:
12 1 0.01
13 16 0.11
14 61 0.40
15 69 0.46
16 4 0.03
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (14 bp):
TTTACTGATTACTC
Found at i:10734 original size:31 final size:32
Alignment explanation
Indices: 10635--10754 Score: 161
Period size: 32 Copynumber: 3.8 Consensus size: 32
10625 TTACTCTTTA
* *
10635 AATTAGATTACTAATTACTATTTTACCTTTTG
1 AATTTGATTACTAATTACCATTTTACCTTTTG
** *
10667 AATTTGATTGTTAATTACTATTTTACCCTTTTG
1 AATTTGATTACTAATTACCATTTTA-CCTTTTG
*
10700 AATTTGATTACTAATTACCA-TTTACCATTTG
1 AATTTGATTACTAATTACCATTTTACCTTTTG
*
10731 AATTTGATTACTAGTTACCATTTT
1 AATTTGATTACTAATTACCATTTT
10755 GCTCTTTACT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 25 0.32
32 29 0.37
33 24 0.31
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.50
Consensus pattern (32 bp):
AATTTGATTACTAATTACCATTTTACCTTTTG
Found at i:17262 original size:23 final size:22
Alignment explanation
Indices: 17233--17275 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
17223 AAAAAAGATT
17233 TTTTTTTGTTTTTGCGTTTTTAA
1 TTTTTTTG-TTTTGCGTTTTTAA
*
17256 TTTTTTTGTTTTGTGTTTTT
1 TTTTTTTGTTTTGCGTTTTT
17276 GGAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.05, C:0.02, G:0.14, T:0.79
Consensus pattern (22 bp):
TTTTTTTGTTTTGCGTTTTTAA
Found at i:17323 original size:28 final size:29
Alignment explanation
Indices: 17292--17346 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
17282 AAAAAAGAGA
* *
17292 GTTTTTACATTTTCTGAAA-AAAAAAATT
1 GTTTCTACATTTTCAGAAAGAAAAAAATT
* *
17320 GTTTCTGCGTTTTCAGAAAGAAAAAAA
1 GTTTCTACATTTTCAGAAAGAAAAAAA
17347 AATATATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (29 bp):
GTTTCTACATTTTCAGAAAGAAAAAAATT
Found at i:24635 original size:25 final size:25
Alignment explanation
Indices: 24582--24641 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
24572 GTTAAAAATA
**
24582 AAAAAT-ATAAATTATATATAATATT
1 AAAAATAAT-AATTATATATAATAAC
24607 AAAAATAATAATTATATAT-ATAAAC
1 AAAAATAATAATTATATATAAT-AAC
24632 AAAAA-AATAA
1 AAAAATAATAA
24642 AATAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 7 0.23
25 22 0.71
26 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
AAAAATAATAATTATATATAATAAC
Found at i:24941 original size:116 final size:118
Alignment explanation
Indices: 24788--25001 Score: 342
Period size: 117 Copynumber: 1.8 Consensus size: 118
24778 GTTTAAAAAT
24788 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATACCCTTATAAC-T
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATACCCTTATAACTT
*
24852 ATTTTATTTTTACCATTTTAATATTTTAATTAAAAAAATTAAATATATTATAC
66 ATTTTATTTTTACCATTTTAATAATTTAATTAAAAAAATTAAATATATTATAC
** * * *
24905 TTTTATAGTTTTGCTCAA-TAAAAATTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTT
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATACCCTTATAACTT
* *
24969 TTTTTATTTTTACCATTTTACTAATTTAATTAA
66 ATTTTATTTTTACCATTTTAATAATTTAATTAA
25002 TTAAAAAAAC
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
116 41 0.47
117 47 0.53
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.51
Consensus pattern (118 bp):
TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATACCCTTATAACTT
ATTTTATTTTTACCATTTTAATAATTTAATTAAAAAAATTAAATATATTATAC
Done.