Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024016.1 Corchorus olitorius cultivar O-4 contig24049, 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: 78380
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:7552 original size:9 final size:9
Alignment explanation
Indices: 7538--7562 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
7528 GTCGGTTTCA
7538 GGTCTGTCG
1 GGTCTGTCG
7547 GGTCTGTCG
1 GGTCTGTCG
7556 GGTCTGT
1 GGTCTGT
7563 TTCTATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.44, T:0.36
Consensus pattern (9 bp):
GGTCTGTCG
Found at i:8440 original size:13 final size:13
Alignment explanation
Indices: 8417--8523 Score: 75
Period size: 13 Copynumber: 8.5 Consensus size: 13
8407 TAATGGAAAT
8417 AGAAA-TGATTTC
1 AGAAACTGATTTC
*
8429 AAAAACTGATTTC
1 AGAAACTGATTTC
*
8442 AGAAACTGATTTT
1 AGAAACTGATTTC
**
8455 AGAAACTGAAATC
1 AGAAACTGATTTC
8468 AG--ACTGA-TTC
1 AGAAACTGATTTC
* *
8478 AGAATCTGAAATT-
1 AGAAACTG-ATTTC
8491 AG--ACTGATTTC
1 AGAAACTGATTTC
*
8502 AGAATCATTGATTTC
1 AGAA--ACTGATTTC
8517 AGAAACT
1 AGAAACT
8524 ACAAACAACA
Statistics
Matches: 73, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
10 7 0.10
11 10 0.14
12 7 0.10
13 35 0.48
14 2 0.03
15 12 0.16
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (13 bp):
AGAAACTGATTTC
Found at i:8507 original size:24 final size:24
Alignment explanation
Indices: 8446--8507 Score: 90
Period size: 23 Copynumber: 2.6 Consensus size: 24
8436 GATTTCAGAA
* *
8446 ACTGATTTTAGAAACTGAAATCAG
1 ACTGATTTCAGAATCTGAAATCAG
*
8470 ACTGA-TTCAGAATCTGAAATTAG
1 ACTGATTTCAGAATCTGAAATCAG
8493 ACTGATTTCAGAATC
1 ACTGATTTCAGAATC
8508 ATTGATTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (24 bp):
ACTGATTTCAGAATCTGAAATCAG
Found at i:9170 original size:29 final size:30
Alignment explanation
Indices: 9118--9177 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
9108 GAAGTTCGTG
* * *
9118 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTCAAGAATTATTTCAAGA
9149 TTTGAAGA-CATTCAAGAATTATTTCAAGA
1 TTTGAAGACCATTCAAGAATTATTTCAAGA
9178 GGAAAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 18 0.69
31 8 0.31
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTCAAGAATTATTTCAAGA
Found at i:10840 original size:19 final size:18
Alignment explanation
Indices: 10816--10851 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10806 TGAAGACTTA
*
10816 TTGAAGACTATTTGAAGAT
1 TTGAAGACCA-TTGAAGAT
10835 TTGAAGACCATTGAAGA
1 TTGAAGACCATTGAAGA
10852 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGACCATTGAAGAT
Found at i:12691 original size:36 final size:36
Alignment explanation
Indices: 12623--12692 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
12613 AGTCTCTGCG
* *
12623 TTTCTGCGTTTTTAACCTAAAAAAAATCGTTTTTCT
1 TTTCTGCGTTTTTAACATAAAAAAAAACGTTTTTCT
* *
12659 TTTCTGCGTTTTT-TCTATAAAAAAAAAGGTTTTT
1 TTTCTGCGTTTTTAAC-ATAAAAAAAAACGTTTTT
12693 TTGCGTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.03
36 28 0.97
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.49
Consensus pattern (36 bp):
TTTCTGCGTTTTTAACATAAAAAAAAACGTTTTTCT
Found at i:12781 original size:24 final size:25
Alignment explanation
Indices: 12727--12830 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
12717 TGCGTTTTTG
* * *
12727 AAAAAAAAAGTTGTGTTTTGCGTCAAG
1 AAAAAAAAAATTGT-TTTTGAGTC-AT
*
12754 AAAAAAAAAATTG-TTTTGATTCAT
1 AAAAAAAAAATTGTTTTTGAGTCAT
* *
12778 -AAAAAAAAGTTGTTTTTGCGTCAT
1 AAAAAAAAAATTGTTTTTGAGTCAT
** *
12802 AAAAAAAAAAGAGTTTTTGCGTCAT
1 AAAAAAAAAATTGTTTTTGAGTCAT
12827 AAAA
1 AAAA
12831 TTTTTTTTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
23 11 0.17
24 10 0.15
25 32 0.49
27 12 0.18
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (25 bp):
AAAAAAAAAATTGTTTTTGAGTCAT
Found at i:12820 original size:49 final size:50
Alignment explanation
Indices: 12728--12830 Score: 140
Period size: 49 Copynumber: 2.1 Consensus size: 50
12718 GCGTTTTTGA
* *
12728 AAAAAAAAGTTGTGTTTTGCGTCAAGAAAAAAAAAATTGTTTTGATTCAT
1 AAAAAAAAGTTGTGTTTTGCGTCAAGAAAAAAAAAAGTGTTTTGAGTCAT
*
12778 AAAAAAAAGTTGT-TTTTGCGTCATA-AAAAAAAAAGAGT-TTTTGCGTCAT
1 AAAAAAAAGTTGTGTTTTGCGTCA-AGAAAAAAAAA-AGTGTTTTGAGTCAT
12827 AAAA
1 AAAA
12831 TTTTTTTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
49 32 0.67
50 16 0.33
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.32
Consensus pattern (50 bp):
AAAAAAAAGTTGTGTTTTGCGTCAAGAAAAAAAAAAGTGTTTTGAGTCAT
Found at i:17984 original size:29 final size:30
Alignment explanation
Indices: 17930--17989 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
17920 GAAGTTCGTG
* * *
17930 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
17961 TTTGAAGA-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACCATTGAAGAATAATTTCAAGA
17990 GGAAAGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 18 0.69
31 8 0.31
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATAATTTCAAGA
Found at i:19387 original size:15 final size:15
Alignment explanation
Indices: 19367--19395 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19357 TTGTTTCCTA
19367 GTTTAATTGTTTTCG
1 GTTTAATTGTTTTCG
19382 GTTTAATTGTTTTC
1 GTTTAATTGTTTTC
19396 TTTCAACCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.17, T:0.62
Consensus pattern (15 bp):
GTTTAATTGTTTTCG
Found at i:23816 original size:29 final size:29
Alignment explanation
Indices: 23784--23848 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
23774 TTTTTCTGAT
* *
23784 TTTGTTTAAGTGCGGGTTGTGCACTTGTG
1 TTTGTTTAAGTGCGGGTTGGGCACTTGGG
* *
23813 TTTGTTCAAGTGTGGGTTGGGCACTTGGG
1 TTTGTTTAAGTGCGGGTTGGGCACTTGGG
*
23842 ATTGTTT
1 TTTGTTT
23849 TGAGTGTGGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.11, C:0.09, G:0.35, T:0.45
Consensus pattern (29 bp):
TTTGTTTAAGTGCGGGTTGGGCACTTGGG
Found at i:30733 original size:18 final size:19
Alignment explanation
Indices: 30701--30737 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
30691 CTGTTCTTCT
30701 TTTTCTCTTCAAGTTTTAG
1 TTTTCTCTTCAAGTTTTAG
*
30720 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCAAGTTTTAG
30738 GGTTAGGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.62
Consensus pattern (19 bp):
TTTTCTCTTCAAGTTTTAG
Found at i:33212 original size:153 final size:158
Alignment explanation
Indices: 32915--33226 Score: 472
Period size: 153 Copynumber: 2.0 Consensus size: 158
32905 GATAACCAGG
* *
32915 TTTAATTAGCAATGTAAATCTTATTTTCGCCATAGTTGACGGCTGGAGTGTCTTTTATTTCTCTC
1 TTTAATTAGCAATGTAAATCTTATTTTCACCATAGTTGACGGCTGGAGTGTCTTTTATGTCTCTC
* *
32980 TCTTTTTTTTCCCTACAAGTTTGATTTTTATTTCAAGGTACTGAATAATACAATTGACTAATATG
66 TCTTCTTTTTCCCTACAAGTTTGATTTTTACTTCAAGGTACTGAATAATACAATTGACTAATATG
* *
33045 TTTGACAGCTTGAAGATGGACCTCATCA
131 TTCGACAGCTTGAAGATAGACCTCATCA
* *
33073 TTTAATTAGCAATGTAAATCTTATTTTTACCATAGTTGACGGCTTGAGTGT-TTTT-TGT-T-TC
1 TTTAATTAGCAATGTAAATCTTATTTTCACCATAGTTGACGGCTGGAGTGTCTTTTATGTCTCTC
* * *
33134 TCTTCTTTTT-CCTGCACGTTTGATTTTTACTTCAAGGTTCTGAATAATACAATTGACTAATATG
66 TCTTCTTTTTCCCTACAAGTTTGATTTTTACTTCAAGGTACTGAATAATACAATTGACTAATATG
* *
33198 TTCGACTGCTTGAAGATAGACGTCATCA
131 TTCGACAGCTTGAAGATAGACCTCATCA
33226 T
1 T
33227 CACGGTTATG
Statistics
Matches: 141, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
153 75 0.53
154 11 0.08
155 1 0.01
156 2 0.01
157 4 0.03
158 48 0.34
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.43
Consensus pattern (158 bp):
TTTAATTAGCAATGTAAATCTTATTTTCACCATAGTTGACGGCTGGAGTGTCTTTTATGTCTCTC
TCTTCTTTTTCCCTACAAGTTTGATTTTTACTTCAAGGTACTGAATAATACAATTGACTAATATG
TTCGACAGCTTGAAGATAGACCTCATCA
Found at i:36681 original size:35 final size:35
Alignment explanation
Indices: 36641--36715 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
36631 AGTTCGTTTA
*
36641 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
36676 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
36711 TGTTC
1 TGTTC
36716 GTTTATATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (35 bp):
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
Found at i:36778 original size:16 final size:16
Alignment explanation
Indices: 36757--36788 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36747 TATAATTATT
36757 TATATATTAATAATAA
1 TATATATTAATAATAA
*
36773 TATATATTATTAATAA
1 TATATATTAATAATAA
36789 AAATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:36783 original size:19 final size:19
Alignment explanation
Indices: 36741--36793 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
36731 GAACGTTCGT
* *
36741 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
36761 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
*
36779 TTATTAATAAAAATA
1 TTATTAATAATAATA
36794 ATAATATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:36795 original size:25 final size:27
Alignment explanation
Indices: 36765--36814 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
36755 TTTATATATT
36765 AATAATAATA-TATATTAT-TAATAAA
1 AATAATAATATTATATTATCTAATAAA
*
36790 AATAATAATATTCTATTATCTAATA
1 AATAATAATATTATATTATCTAATA
36815 TATTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
AATAATAATATTATATTATCTAATAAA
Found at i:36936 original size:18 final size:18
Alignment explanation
Indices: 36909--36943 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36899 AATTATTATA
36909 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
36927 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
36944 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:54952 original size:22 final size:21
Alignment explanation
Indices: 54918--54979 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
54908 CTTACCTTTA
*
54918 TCTTTTTCATTTTCGTTATTT-T
1 TCTTTTT-ATTTTTGTT-TTTGT
54940 TCTTTTTATTTTTGTTTTTGT
1 TCTTTTTATTTTTGTTTTTGT
* *
54961 TTTTGTTTATTTTTATTTT
1 TCTT-TTTATTTTTGTTTT
54980 CTTTGTTACT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.09
21 12 0.34
22 20 0.57
ACGTcount: A:0.08, C:0.06, G:0.06, T:0.79
Consensus pattern (21 bp):
TCTTTTTATTTTTGTTTTTGT
Found at i:54965 original size:12 final size:12
Alignment explanation
Indices: 54933--54968 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
54923 TTCATTTTCG
*
54933 TTATTTTTCTTT
1 TTATTTTTGTTT
54945 TTATTTTTGTTT
1 TTATTTTTGTTT
*
54957 TTGTTTTTGTTT
1 TTATTTTTGTTT
54969 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.03, G:0.08, T:0.83
Consensus pattern (12 bp):
TTATTTTTGTTT
Found at i:62365 original size:18 final size:18
Alignment explanation
Indices: 62342--62377 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
62332 TATATGTTAC
62342 TAATGGACAAATGAAGAT
1 TAATGGACAAATGAAGAT
62360 TAATGGACAAATGAAGAT
1 TAATGGACAAATGAAGAT
62378 AAATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (18 bp):
TAATGGACAAATGAAGAT
Found at i:62648 original size:18 final size:18
Alignment explanation
Indices: 62625--62660 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
62615 TATATGTTAC
62625 TAATGGACAAATGAAGAT
1 TAATGGACAAATGAAGAT
62643 TAATGGACAAATGAAGAT
1 TAATGGACAAATGAAGAT
62661 AAATATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (18 bp):
TAATGGACAAATGAAGAT
Found at i:63082 original size:27 final size:28
Alignment explanation
Indices: 63043--63117 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
63033 AGGTGATCCT
63043 AGAATGACCAAAATGCCCCT-GAATGT-
1 AGAATGACCAAAATGCCCCTGGAATGTG
* *
63069 ACGAATGACCAAAATGCCCCTGGATTTTG
1 A-GAATGACCAAAATGCCCCTGGAATGTG
*
63098 AAAATGACCAAAATGCCCCT
1 AGAATGACCAAAATGCCCCT
63118 AGATGACCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 1 0.02
27 19 0.44
28 22 0.51
29 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (28 bp):
AGAATGACCAAAATGCCCCTGGAATGTG
Found at i:63714 original size:50 final size:50
Alignment explanation
Indices: 63585--64077 Score: 779
Period size: 50 Copynumber: 9.8 Consensus size: 50
63575 ATGTTTGAAC
* * **
63585 TGACTCGTGTGGAAACGAGTTCGGCTTGTGGAAAAGCCTACGTGGCTTGGATGGT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA--T-G-TT-GATAAT
63640 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
63690 TGACTCGTATGGAAACGAGTTTGGCTTGTGAAAAAGCCTATGTTAATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
63740 TGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
63790 TGACTCGTATGAAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
63840 TGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * *
63890 TGATTCGTATGGAAACGAGTTTGGCTTATGGAAAAGTCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
63940 TGACTCGTATGGAAACGAGTTTGGCCTATGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
63990 TGACTCGTATGGAAACGAGTTTGGCCTATGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
64040 TGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
64078 AAAGCATTCG
Statistics
Matches: 416, Mismatches: 22, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
50 374 0.90
51 2 0.00
52 1 0.00
53 1 0.00
55 38 0.09
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:65935 original size:76 final size:76
Alignment explanation
Indices: 65785--65936 Score: 166
Period size: 76 Copynumber: 2.0 Consensus size: 76
65775 ACAATGACCC
* *
65785 CGACTCCACCTGGGCGCACACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCACACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
*
65850 GGGCAGTGTCA
66 GGACAGTGTCA
* * * * **
65861 CGACTCCAGCTGGGTGCCCACATGGTCTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCACACATGGT-TGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
65923 GATGGACTGTGTCA
63 GATGGACAGTGTCA
65937 TAGCTCATCA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.86
77 5 0.08
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCACACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGACAGTGTCA
Found at i:66976 original size:50 final size:50
Alignment explanation
Indices: 66830--66979 Score: 246
Period size: 50 Copynumber: 3.0 Consensus size: 50
66820 CGTCAAGGTC
* * *
66830 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* *
66880 CTTTGAAAAGCAAATTTTGATCTTCAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
*
66930 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
66980 TTGTAAAACT
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 92 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
Found at i:67635 original size:19 final size:18
Alignment explanation
Indices: 67597--67636 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
67587 ATTTGATTTG
*
67597 ATTTTTTTGTTTTTTGTT
1 ATTTTTTTATTTTTTGTT
*
67615 ATTTTTTTATTGTTTTTTT
1 ATTTTTTTATT-TTTTGTT
67634 ATT
1 ATT
67637 GATTGATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.82
Consensus pattern (18 bp):
ATTTTTTTATTTTTTGTT
Found at i:68601 original size:76 final size:74
Alignment explanation
Indices: 68475--68618 Score: 184
Period size: 76 Copynumber: 1.9 Consensus size: 74
68465 ATTCAATCAC
* *
68475 CTCGAAATCATTGTTTTGACCAAAACTGATTTTGAAACATCTTTTGATTAAAACACTGTCATTCC
1 CTCGAAATCATAGTTTTGACCAAAACTGATTTTGAAACA-CTTTTGATTAAAACAC-ATCATTCC
68540 TTTGTTCACAA
64 TTTGTTCACAA
** *
68551 CTCGAAATCATAGTTTTGATTAAAACTGATTTTTTTGAAA-A-TTTTGATTAAAACTCATCATTC
1 CTCGAAATCATAGTTTTGACCAAAACTGA---TTTTGAAACACTTTTGATTAAAACACATCATTC
68614 CTTTG
63 CTTTG
68619 CTCATAGTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
75 11 0.18
76 40 0.67
78 1 0.02
79 8 0.13
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (74 bp):
CTCGAAATCATAGTTTTGACCAAAACTGATTTTGAAACACTTTTGATTAAAACACATCATTCCTT
TGTTCACAA
Found at i:73198 original size:16 final size:16
Alignment explanation
Indices: 73173--73205 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
73163 GAGGACATGA
*
73173 TTTGAGAAAAACCTTT
1 TTTGAAAAAAACCTTT
73189 TTTGAAAAAAACCTTT
1 TTTGAAAAAAACCTTT
73205 T
1 T
73206 ATTACCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTTGAAAAAAACCTTT
Found at i:74593 original size:30 final size:30
Alignment explanation
Indices: 74548--74685 Score: 208
Period size: 29 Copynumber: 4.6 Consensus size: 30
74538 AGCAATTGAC
*
74548 AGAAAAAATGGCGAAATTGCAGTAATTAAA
1 AGAAAAAAAGGCGAAATTGCAGTAATTAAA
* * *
74578 AGAATAAAGGGCGAAATTGAAGTAATTAAA
1 AGAAAAAAAGGCGAAATTGCAGTAATTAAA
74608 AGAAAAAAAGG-GAAATTGCAGTAATTAAA
1 AGAAAAAAAGGCGAAATTGCAGTAATTAAA
74637 AGAAAAAAAGG-GAAATTGCAGTAATTAAA
1 AGAAAAAAAGGCGAAATTGCAGTAATTAAA
*
74666 AGCAAAAAAGGGCGAAATTG
1 AG-AAAAAAAGGCGAAATTG
74686 AAAAAAAAAT
Statistics
Matches: 99, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
29 48 0.48
30 44 0.44
31 7 0.07
ACGTcount: A:0.55, C:0.05, G:0.22, T:0.17
Consensus pattern (30 bp):
AGAAAAAAAGGCGAAATTGCAGTAATTAAA
Found at i:75361 original size:14 final size:15
Alignment explanation
Indices: 75324--75361 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
75314 AGAGAGCCTC
75324 ATGTTGTTGTGTGTG
1 ATGTTGTTGTGTGTG
75339 A-GTTGTTGTGTGTG
1 ATGTTGTTGTGTGTG
75353 ATGTT-TTGT
1 ATGTTGTTGT
75362 TTTTTCTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.08, C:0.00, G:0.37, T:0.55
Consensus pattern (15 bp):
ATGTTGTTGTGTGTG
Found at i:76403 original size:18 final size:18
Alignment explanation
Indices: 76380--76415 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
76370 TATATGTTAC
76380 TAATGGACAAATGAAGAT
1 TAATGGACAAATGAAGAT
76398 TAATGGACAAATGAAGAT
1 TAATGGACAAATGAAGAT
76416 AAATATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (18 bp):
TAATGGACAAATGAAGAT
Found at i:77360 original size:42 final size:42
Alignment explanation
Indices: 77299--77385 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
77289 GGAATAAATG
* *
77299 TTACCCATTTTACTTATATTGGCATTATCTTACTTTGTCTCA
1 TTACCCATTTTACTCATATTGGCATTATCTTACCTTGTCTCA
* *
77341 TTACCCATTTTAGTCATATTGGCATTGTCTTACCTTGTCTCA
1 TTACCCATTTTACTCATATTGGCATTATCTTACCTTGTCTCA
77383 TTA
1 TTA
77386 GATTGCATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.48
Consensus pattern (42 bp):
TTACCCATTTTACTCATATTGGCATTATCTTACCTTGTCTCA
Done.