Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016160.1 Corchorus capsularis cultivar CVL-1 contig16181, 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: 45442
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:4685 original size:41 final size:41
Alignment explanation
Indices: 4564--4686 Score: 237
Period size: 41 Copynumber: 3.0 Consensus size: 41
4554 TACTAATGGG
*
4564 CCTAGGTCAATAGACTAATTTTATTGGTCTATGATGAGGAC
1 CCTAGGTCAATAGACTAATTTTATTGGTCTATGATGAGGGC
4605 CCTAGGTCAATAGACTAATTTTATTGGTCTATGATGAGGGC
1 CCTAGGTCAATAGACTAATTTTATTGGTCTATGATGAGGGC
4646 CCTAGGTCAATAGACTAATTTTATTGGTCTATGATGAGGGC
1 CCTAGGTCAATAGACTAATTTTATTGGTCTATGATGAGGGC
4687 ACTTGGGGCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 81 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.34
Consensus pattern (41 bp):
CCTAGGTCAATAGACTAATTTTATTGGTCTATGATGAGGGC
Found at i:5966 original size:20 final size:19
Alignment explanation
Indices: 5938--6000 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 19
5928 GACGTGACTT
*
5938 TTTTTTTTTTTTCATTTTCC
1 TTTTATTTTTTT-ATTTTCC
5958 TTTTATTTTCTTTATTTT-C
1 TTTTATTTT-TTTATTTTCC
5977 TTTTATTCTTTTTATTTTCC
1 TTTTATT-TTTTTATTTTCC
5997 TTTT
1 TTTT
6001 TTTCCTCTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 16 0.41
20 20 0.51
21 3 0.08
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTATTTTTTTATTTTCC
Found at i:6017 original size:40 final size:40
Alignment explanation
Indices: 5945--6020 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
5935 CTTTTTTTTT
*
5945 TTTTTCATTTTCCTTTTATTTTCTTTATTTTCTTTTATTC
1 TTTTTCATTTTCCTTTTATTTCCTTTATTTTCTTTTATTC
*
5985 TTTTT-ATTTTCCTTTT-TTTCCTCTTCTGTTTCTTTT
1 TTTTTCATTTTCCTTTTATTTCCT-TTAT-TTTCTTTT
6021 GCTTTCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 5 0.16
39 14 0.44
40 13 0.41
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (40 bp):
TTTTTCATTTTCCTTTTATTTCCTTTATTTTCTTTTATTC
Found at i:9779 original size:21 final size:21
Alignment explanation
Indices: 9736--9779 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
9726 AGATGCCATT
* **
9736 AAGATGCCATTTGATCCTTTG
1 AAGATGCCATTAGATCCGATG
*
9757 AAGATGCCATTAGGTCCGATG
1 AAGATGCCATTAGATCCGATG
9778 AA
1 AA
9780 AAGAGCAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (21 bp):
AAGATGCCATTAGATCCGATG
Found at i:11825 original size:28 final size:28
Alignment explanation
Indices: 11785--11841 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
11775 AAGCTGGTAG
*
11785 AATGCATTATACAGTTGTAAATGTAAGT
1 AATGCATTATACAATTGTAAATGTAAGT
*
11813 AATGCGTTATACAATTGTAAATGTAAGT
1 AATGCATTATACAATTGTAAATGTAAGT
11841 A
1 A
11842 CCTTAAACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (28 bp):
AATGCATTATACAATTGTAAATGTAAGT
Found at i:14313 original size:14 final size:14
Alignment explanation
Indices: 14274--14314 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
14264 TTATATACAT
14274 ATATATTAATAATAC
1 ATATATTAA-AATAC
14289 ATA-ATTAAAAT-C
1 ATATATTAAAATAC
14301 ATATATTATAAATA
1 ATATATTA-AAATA
14315 TGACCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 4 0.17
13 7 0.30
14 9 0.39
15 3 0.13
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATATTAAAATAC
Found at i:15115 original size:31 final size:31
Alignment explanation
Indices: 15080--15145 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
15070 AACTTTATGT
* *
15080 TTTCCGATTGTACCCTTATT-TTTAAAATATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
15111 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
15142 TTTC
1 TTTC
15146 TAAATTACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:15591 original size:24 final size:24
Alignment explanation
Indices: 15563--15611 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
15553 ATCGGGTCAA
*
15563 AGAGTTTGGGTCTTGATGGTCATG
1 AGAGTTTGGGTCCTGATGGTCATG
15587 AGAGTTTGGGTCCTGATGGTCATG
1 AGAGTTTGGGTCCTGATGGTCATG
15611 A
1 A
15612 TGTTCCACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.10, G:0.37, T:0.35
Consensus pattern (24 bp):
AGAGTTTGGGTCCTGATGGTCATG
Found at i:16956 original size:19 final size:20
Alignment explanation
Indices: 16929--16966 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
16919 TACTACTATT
16929 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
16949 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
16967 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:17160 original size:22 final size:22
Alignment explanation
Indices: 17132--17194 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
17122 TGTCTCTATG
17132 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
17154 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
17177 -GGTTATCAGAATTCCATA
1 TGGTTATCAAAATTTCATA
17195 GTGTGGTTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.03
22 30 0.88
23 3 0.09
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:17235 original size:22 final size:22
Alignment explanation
Indices: 17183--17239 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
17173 AGGAGGTTAT
* *
17183 CAGAATTCCATAGTGTGGTTAC
1 CAGAATTTCATAGTGTGATTAC
*
17205 TAGAATTTCATAGTGTGATTAC
1 CAGAATTTCATAGTGTGATTAC
* *
17227 CATATTTTCATAG
1 CAGAATTTCATAG
17240 GATCAGGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (22 bp):
CAGAATTTCATAGTGTGATTAC
Found at i:17340 original size:22 final size:22
Alignment explanation
Indices: 17312--17374 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
17302 TGTCTCTATG
17312 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
17334 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
17357 -GGTTATCAGAATTCCATA
1 TGGTTATCAAAATTTCATA
17375 GTGTGGTTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.03
22 30 0.88
23 3 0.09
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:17381 original size:180 final size:179
Alignment explanation
Indices: 17079--17446 Score: 718
Period size: 180 Copynumber: 2.1 Consensus size: 179
17069 AATTGGAAAG
17079 TATTGGGTTAGAAGAGTAGGTAATATTATGATTTTGATTTTCTTGTCTCTATGTGGTTATCAAAA
1 TATTGGGTTAGAAGAGTAGGTAATATTATGATTTTGATTTTCTTGTCTCTATGTGGTTATCAAAA
17144 TTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAGAATTCCATAGTGTGGTTACTAGA
66 TTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAGAATTCCATAGTGTGGTTACTAGA
17209 ATTTCATAGTGTGATTACCATATTTTCATAGGATCAGGTTATTAAAATC
131 ATTTCATAGTGTGATTACCATATTTTCATAGGATCAGGTTATTAAAATC
17258 TTATTGGGTTAGAAGAGTAGGTAATATTATGATTTTGATTTTCTTGTCTCTATGTGGTTATCAAA
1 -TATTGGGTTAGAAGAGTAGGTAATATTATGATTTTGATTTTCTTGTCTCTATGTGGTTATCAAA
17323 ATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAGAATTCCATAGTGTGGTTACTAG
65 ATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAGAATTCCATAGTGTGGTTACTAG
17388 AATTTCATAGTGTGATTACCATATTTTCATAGGATCAGGTTATTAAAATC
130 AATTTCATAGTGTGATTACCATATTTTCATAGGATCAGGTTATTAAAATC
*
17438 TCTTGGGTT
1 TATTGGGTT
17447 GGTTATTGAA
Statistics
Matches: 187, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
179 8 0.04
180 179 0.96
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (179 bp):
TATTGGGTTAGAAGAGTAGGTAATATTATGATTTTGATTTTCTTGTCTCTATGTGGTTATCAAAA
TTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAGAATTCCATAGTGTGGTTACTAGA
ATTTCATAGTGTGATTACCATATTTTCATAGGATCAGGTTATTAAAATC
Found at i:17415 original size:22 final size:22
Alignment explanation
Indices: 17363--17419 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
17353 AGGAGGTTAT
* *
17363 CAGAATTCCATAGTGTGGTTAC
1 CAGAATTTCATAGTGTGATTAC
*
17385 TAGAATTTCATAGTGTGATTAC
1 CAGAATTTCATAGTGTGATTAC
* *
17407 CATATTTTCATAG
1 CAGAATTTCATAG
17420 GATCAGGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (22 bp):
CAGAATTTCATAGTGTGATTAC
Found at i:17631 original size:22 final size:21
Alignment explanation
Indices: 17572--17868 Score: 138
Period size: 22 Copynumber: 13.3 Consensus size: 21
17562 TTCATTAAAT
*
17572 ATTTCATGAGGAGGTTATCAAA
1 ATTTCAT-AGAAGGTTATCAAA
* **
17594 ATTTTATAGTGTGGTTATCAAA
1 ATTTCATAG-AAGGTTATCAAA
17616 ATTTCATATGAAGGTTAT-AAA
1 ATTTCATA-GAAGGTTATCAAA
* * * *
17637 AGTCTCAATTTCATAAGGAGTACCAAA
1 A-TTTC-A--T-AGAAGG-TTATCAAA
*
17664 ATTTGATAGAAGGTTATC-AA
1 ATTTCATAGAAGGTTATCAAA
* *
17684 ATCTCATA-AAGTGATTATCGAA
1 ATTTCATAGAAG-G-TTATCAAA
*
17706 ATTTCATAGAGATCTGATTATCAAA
1 ATTTCATAGA-A---GGTTATCAAA
*
17731 ATTTCATAG-TGTTGTTATCAAA
1 ATTTCATAGAAG--GTTATCAAA
*
17753 ATTTCAAAGCAAGGTTATCAAA
1 ATTTCATAG-AAGGTTATCAAA
* *
17775 ATTACATA-ATGTGATTATCAAA
1 ATTTCATAGAAG-G-TTATCAAA
* * *
17797 ATTTCATAGAGGGGTCAACAAA
1 ATTTCATAGA-AGGTTATCAAA
*
17819 ATTTTATA-ACGAGGTTATCAAA
1 ATTTCATAGA--AGGTTATCAAA
*
17841 ATTTCATAAAGAGGTTATCAAA
1 ATTTCATAGA-AGGTTATCAAA
*
17863 TTTTCA
1 ATTTCA
17869 AAATGTGATT
Statistics
Matches: 212, Mismatches: 36, Indels: 54
0.70 0.12 0.18
Matches are distributed among these distances:
19 3 0.01
20 12 0.06
21 16 0.08
22 139 0.66
23 7 0.03
24 3 0.01
25 22 0.10
26 5 0.02
27 5 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
ATTTCATAGAAGGTTATCAAA
Found at i:17793 original size:44 final size:44
Alignment explanation
Indices: 17582--18176 Score: 198
Period size: 44 Copynumber: 13.4 Consensus size: 44
17572 ATTTCATGAG
* * * *
17582 GAGGTTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATATGA
1 GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCA-AAGA
* * * * *
17627 -AGGTTATAAAAGTCTCAATTTCATAA-G-GAGTACCAAAATTTGATAGA
1 GAGGTTAT-CAA-----AATTTCATAATGTGATTATCAAAATTTCAAAGA
* * * *
17674 -AGGTTATC-AAATCTCATAAAGTGATTATCGAAATTTCATAGA
1 GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGA
* *
17716 GATCTGATTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCAAAGCA
1 GA---GGTTATCAAAATTTCATAATG-TGATTATCAAAATTTCAAAG-A
* *
17764 -AGGTTATCAAAATTACATAATGTGATTATCAAAATTTCATAGA
1 GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGA
* * * * * * *
17807 GGGGTCAACAAAATTTTATAACGAGGTTATCAAAATTTCATAA-A
1 GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCA-AAGA
* *
17851 GAGGTTATCAAATTTTCAAAATGTGATTA-CAAGAATTTCATAGTGGTATTTCTGGA
1 GAGGTTATCAAAATTTCATAATGTGATTATCAA-AATTTCA-A-----A------GA
* * * * *
17907 GAGGTTATTAAAATTTCATAGTATGGTTA-CCAAA-TT--AAGA
1 GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGA
* * * * *
17947 -AGGTTATTAAACTTTTATTATG-GAGTAATCAAAATTTC-AAG-
1 GAGGTTATCAAAATTTCATAATGTGA-TTATCAAAATTTCAAAGA
* ** *
17988 GAGGATATCAAAA-TTCAGGGA-G-GA-TATCAAAATTTCATATGA
1 GAGGTTATCAAAATTTCA-TAATGTGATTATCAAAATTTCA-AAGA
* * * *
18030 -ATGTTATCAAAATTTCATAGT-TTAGTTTTCAAAATTTCACAAGA
1 GAGGTTATCAAAATTTCATAATGTGA-TTATCAAAATTTCA-AAGA
* * *
18074 G-GGTTATCAAAATTTCATAGTATGT-A-GATCAAAATTTCATAGG
1 GAGGTTATCAAAATTTCATA--ATGTGATTATCAAAATTTCAAAGA
** * * * ** * *
18117 GAGAATAACAAAATTTCATAATGAGGTTATCAAAAAATCATAGG
1 GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGA
*
18161 GAGGTAATCAAAATTT
1 GAGGTTATCAAAATTT
18177 GTAGTTATCA
Statistics
Matches: 405, Mismatches: 93, Indels: 105
0.67 0.15 0.17
Matches are distributed among these distances:
38 1 0.00
39 30 0.07
40 15 0.04
41 21 0.05
42 37 0.09
43 10 0.02
44 186 0.46
45 4 0.01
46 9 0.02
47 36 0.09
48 15 0.04
49 2 0.00
50 8 0.02
51 1 0.00
54 2 0.00
55 2 0.00
56 26 0.06
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGA
Found at i:17795 original size:66 final size:66
Alignment explanation
Indices: 17720--17868 Score: 174
Period size: 66 Copynumber: 2.3 Consensus size: 66
17710 CATAGAGATC
* ** * *
17720 TGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCAAGGTTATCAAAATTACATAA
1 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-CAAGGTTATCAAAATTACATAA
*
17784 TG
65 AG
* * *
17786 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAACGAGGTTATCAAAATTTCATAAA
1 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAACAAGGTTATCAAAATTACATAAA
17851 G
66 G
* * *
17852 AGGTTATCAAATTTTCA
1 TGATTATCAAAATTTCA
17869 AAATGTGATT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
66 68 0.97
67 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (66 bp):
TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAACAAGGTTATCAAAATTACATAAA
G
Found at i:17999 original size:20 final size:20
Alignment explanation
Indices: 17974--18024 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
17964 TTATGGAGTA
17974 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
17994 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
18013 ATCAAAATTTCA
1 ATCAAAATTTCA
18025 TATGAATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:18040 original size:22 final size:22
Alignment explanation
Indices: 17974--18571 Score: 224
Period size: 22 Copynumber: 27.6 Consensus size: 22
17964 TTATGGAGTA
*
17974 ATCAAAATTTCA-AGG-AGGAT
1 ATCAAAATTTCATAGGAAGGTT
* *
17994 ATCAAAA-TTC--AGGGAGGAT
1 ATCAAAATTTCATAGGAAGGTT
* *
18013 ATCAAAATTTCATATGAATGTT
1 ATCAAAATTTCATAGGAAGGTT
**
18035 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GAAGGTT
* * * *
18057 TTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATAGGAAGGTT
* * *
18079 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGAAGGT-T
* **
18101 ATCAAAATTTCATAGGGAGAAT
1 ATCAAAATTTCATAGGAAGGTT
* *
18123 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-AGGAAGGTT
** * *
18145 ATCAAAAAATCATAGGGAGGTA
1 ATCAAAATTTCATAGGAAGGTT
*
18167 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGAAGGTT
* * **
18183 ATCAAGATTTCATAAGAAAATT
1 ATCAAAATTTCATAGGAAGGTT
* *
18205 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGAAGG-TT
* *
18228 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGAAG-GTT
18251 ATCAAAATTTCATAGCG-AGGTT
1 ATCAAAATTTCATAG-GAAGGTT
* * *
18273 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATAG-GAAGGTT
* * *
18295 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATAG-GAAGGTT
18317 A-CTAACAA-TTCATATGG-AGGTT
1 ATC-AA-AATTTCATA-GGAAGGTT
* * * * *
18339 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-AGGAAGGTT
* *
18361 ATCAATATATCATATGG-AGGTT
1 ATCAAAATTTCATA-GGAAGGTT
* * **
18383 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GAAGGTT
*
18406 ATCAAAA-TTCATTGGGAA-GTT
1 ATCAAAATTTCA-TAGGAAGGTT
*
18427 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-GGAAGGT-T
* * * *
18450 -TCAAAATTCCTTAGGGAGATT
1 ATCAAAATTTCATAGGAAGGTT
* * *
18471 AACCAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
** * **
18493 AAAAAAAATT-ATAAAAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
* * * * **
18514 CTCGAAATTCCATAGTATCGTT
1 ATCAAAATTTCATAGGAAGGTT
*
18536 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
18558 ATCAAAATTTCATA
1 ATCAAAATTTCATA
18572 ATGGGATCAT
Statistics
Matches: 429, Mismatches: 113, Indels: 70
0.70 0.18 0.11
Matches are distributed among these distances:
16 8 0.02
17 4 0.01
18 3 0.01
19 17 0.04
20 10 0.02
21 40 0.09
22 286 0.67
23 60 0.14
24 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATAGGAAGGTT
Found at i:18232 original size:45 final size:44
Alignment explanation
Indices: 18180--18286 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 44
18170 AAAATTTGTA
* *
18180 GTTATCAAGATTTCATAAGAA-AATTATCAAAATTTTATAGGGAG
1 GTTATCAA-ATTTCATAAGAAGAATTATCAAAATTTCATAGCGAG
* * *
18224 GTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
1 G-TTATC-AAATTTCATAAGAAGAATTATCAAAATTTCATAGCGAG
18270 GTTATCACAATTTCATA
1 GTTATCA-AATTTCATA
18287 GTGTGATTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 2 0.04
45 28 0.53
46 23 0.43
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (44 bp):
GTTATCAAATTTCATAAGAAGAATTATCAAAATTTCATAGCGAG
Found at i:26088 original size:32 final size:32
Alignment explanation
Indices: 26042--26189 Score: 251
Period size: 32 Copynumber: 4.6 Consensus size: 32
26032 AAAAAGCCTT
*
26042 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
* *
26074 GCCGTCCTAGTGGGGAGGCTCGCCGTGGCAGA
1 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
26106 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
*
26138 GCCGTCCTAGTGGGGCGGCTAGCCGTTGCAGA
1 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
*
26170 GCCGTCCTAGTGGGGAGGCT
1 GCCGTCCTAGTGGGGCGGCT
26190 CCGCGTGGCT
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 109 1.00
ACGTcount: A:0.12, C:0.28, G:0.43, T:0.16
Consensus pattern (32 bp):
GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
Found at i:29610 original size:13 final size:13
Alignment explanation
Indices: 29592--29618 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29582 CTCTATTACC
29592 TCATAAATCATAT
1 TCATAAATCATAT
29605 TCATAAATCATAT
1 TCATAAATCATAT
29618 T
1 T
29619 TATTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:30794 original size:24 final size:25
Alignment explanation
Indices: 30762--30810 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
30752 TTGAATGATT
*
30762 GAGATTTG-AAAGTTTGAAGGTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
* *
30786 GAGAATTGAAAATTTTGAAGTTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
30811 AGGAAATGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.35
Consensus pattern (25 bp):
GAGAATTGAAAAGTTTGAAGGTTGA
Found at i:31140 original size:30 final size:31
Alignment explanation
Indices: 31104--31176 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
31094 GGTCAAAATG
* * *
31104 CAATTCAGGTTATAACGTTA-CCTCTTGTGT
1 CAATTCAGGATATAACGTTATCATCTTGTAT
* *
31134 CAATTCAGGATGTAACGTTATCATTTTGTAT
1 CAATTCAGGATATAACGTTATCATCTTGTAT
31165 CAATTCAGGATA
1 CAATTCAGGATA
31177 AAAATTGACA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (31 bp):
CAATTCAGGATATAACGTTATCATCTTGTAT
Found at i:32140 original size:21 final size:21
Alignment explanation
Indices: 32099--32141 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
32089 GAATAGTGTG
*
32099 GGTTATTCTTATTTTTAAGGT
1 GGTTATTCTTATTTTCAAGGT
* *
32120 GGTTGTTCTTATTTTCCAGGT
1 GGTTATTCTTATTTTCAAGGT
32141 G
1 G
32142 AAGTTCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.09, G:0.23, T:0.53
Consensus pattern (21 bp):
GGTTATTCTTATTTTCAAGGT
Found at i:33325 original size:18 final size:19
Alignment explanation
Indices: 33290--33328 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
33280 AACGTTCCGA
33290 AATCGCGTCAAATAGGGGC
1 AATCGCGTCAAATAGGGGC
* *
33309 AATC-CGTCTAATCGGGGC
1 AATCGCGTCAAATAGGGGC
33327 AA
1 AA
33329 AACCTTCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (19 bp):
AATCGCGTCAAATAGGGGC
Found at i:35519 original size:31 final size:31
Alignment explanation
Indices: 35495--35570 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
35485 TGGTCTGATG
* *
35495 TAGCCTTGCCATGTGGCA-TTTTGGTCCAAT
1 TAGCATTGCCACGTGGCATTTTTGGTCCAAT
* *
35525 TGGCATTGCCACGTGGCATTTTTGGTCCGAT
1 TAGCATTGCCACGTGGCATTTTTGGTCCAAT
*
35556 ATGGCATTGCCACGT
1 -TAGCATTGCCACGT
35571 CAGCAATACC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 15 0.38
31 11 0.28
32 14 0.35
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (31 bp):
TAGCATTGCCACGTGGCATTTTTGGTCCAAT
Found at i:35535 original size:30 final size:32
Alignment explanation
Indices: 35500--35570 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
35490 TGATGTAGCC
*
35500 TTGCCATGTGGCA-TTTTGGTCCAAT-TGGCA
1 TTGCCACGTGGCATTTTTGGTCCAATATGGCA
*
35530 TTGCCACGTGGCATTTTTGGTCCGATATGGCA
1 TTGCCACGTGGCATTTTTGGTCCAATATGGCA
35562 TTGCCACGT
1 TTGCCACGT
35571 CAGCAATACC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 12 0.32
31 11 0.30
32 14 0.38
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (32 bp):
TTGCCACGTGGCATTTTTGGTCCAATATGGCA
Found at i:37259 original size:73 final size:70
Alignment explanation
Indices: 37182--37335 Score: 168
Period size: 73 Copynumber: 2.1 Consensus size: 70
37172 TAATATATCA
* * * *
37182 AGTTTTTTAATTAAAATAGTAAAATGGTAAAATA-TAAGTAATAAGGATATTAAATTTAATTATA
1 AGTTTTTTAAGTAAAATAGTAAAA---TAAAATAGTAACT-ATAAAGATATTAAATTTAATTAAA
37246 TAAAAATAG
62 TAAAAATAG
* * *
37255 AGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTATATTTAATTAAAT
1 AG-TTTT--TTAAGTAAAATAGTAAAATAAAATAGTAACTATAAAGATATTAAATTTAATTAAAT
37320 AAAAATAG
63 AAAAATAG
37328 A-TTTTTTA
1 AGTTTTTTA
37336 GTTACATAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
69 2 0.03
71 4 0.06
73 40 0.58
74 7 0.10
76 16 0.23
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.39
Consensus pattern (70 bp):
AGTTTTTTAAGTAAAATAGTAAAATAAAATAGTAACTATAAAGATATTAAATTTAATTAAATAAA
AATAG
Found at i:37274 original size:68 final size:72
Alignment explanation
Indices: 37199--37338 Score: 189
Period size: 73 Copynumber: 2.0 Consensus size: 72
37189 TAATTAAAAT
* * * *
37199 AGTAAAATGGTAAAAT-ATA-AG-TA-ATAAGGATATTAAATTTAATTATATAAAAATAGAGTTT
1 AGTAAAATAGTAAAATAAAATAGTTACATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTT
37260 TTAGTTG
66 TTAGTTG
* *
37267 AGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTATATTTAATTAAATAAAAATAGATTT
1 AGTAAAATAGTAAAATAAAATAGTTAC-ATAAAGATATTAAATTTAATTAAATAAAAATAGAGTT
37332 TTTAGTT
65 TTTAGTT
37339 ACATAAAACT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
68 15 0.25
69 2 0.03
70 2 0.03
71 2 0.03
73 40 0.66
ACGTcount: A:0.50, C:0.01, G:0.11, T:0.38
Consensus pattern (72 bp):
AGTAAAATAGTAAAATAAAATAGTTACATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTT
TTAGTTG
Found at i:37385 original size:39 final size:39
Alignment explanation
Indices: 37318--37393 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
37308 ATTTAATTAA
*
37318 ATAAAAATAGATTTTTTAGTTACATAAAACTA-TAAAAAT
1 ATAAAAATAGAGTTTTTAGTTACATAAAA-TAGTAAAAAT
*
37357 ATAAAAATAGAGTTTTTAGTTGA-GTAAAATAGTAAAA
1 ATAAAAATAGAGTTTTTAGTT-ACATAAAATAGTAAAA
37394 TAAAATAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 2 0.06
39 30 0.91
40 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (39 bp):
ATAAAAATAGAGTTTTTAGTTACATAAAATAGTAAAAAT
Found at i:37455 original size:109 final size:111
Alignment explanation
Indices: 37243--37464 Score: 394
Period size: 109 Copynumber: 2.0 Consensus size: 111
37233 AAATTTAATT
37243 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTAT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTA-TATAAAGATATTAT
* *
37308 ATTTAATTAAATAAAAATAGATTTTTTAGTTACATAAAACTATAAAA
65 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
*
37355 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAG-T-TATAAATATATTATA
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATATAAAGATATTATA
37418 TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
66 TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
37464 A
1 A
37465 CTTAAACAAT
Statistics
Matches: 107, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
109 59 0.55
111 1 0.01
112 47 0.44
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (111 bp):
ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATATAAAGATATTATA
TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
Found at i:39203 original size:6 final size:6
Alignment explanation
Indices: 39192--39224 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
39182 CTGATCTGTA
39192 ATTGGG ATTGGG ATTGGG ATTGGG ATTGGG ATT
1 ATTGGG ATTGGG ATTGGG ATTGGG ATTGGG ATT
39225 ATATGACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.36
Consensus pattern (6 bp):
ATTGGG
Found at i:44770 original size:21 final size:18
Alignment explanation
Indices: 44729--44771 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 18
44719 CATATTACGT
*
44729 TTAATGAATTTATTTTGA
1 TTAATGAATTTATTTTAA
44747 TTAATAGAATTTGATTTTTAA
1 TTAAT-GAATTT-A-TTTTAA
44768 TTAA
1 TTAA
44772 CATGATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 1 0.05
21 9 0.43
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TTAATGAATTTATTTTAA
Done.