Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015401.1 Corchorus capsularis cultivar CVL-1 contig15422, 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: 96712
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:1379 original size:8 final size:8
Alignment explanation
Indices: 1366--1392 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1356 AAACATAGTT
1366 TTTTTTTC
1 TTTTTTTC
1374 TTTTTTTC
1 TTTTTTTC
1382 TTTTTTTC
1 TTTTTTTC
1390 TTT
1 TTT
1393 GATGTAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTC
Found at i:2714 original size:25 final size:25
Alignment explanation
Indices: 2663--2726 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
2653 GTCATCACAC
*
2663 AAAAATGGAAATC-TCCTTCAAATAA
1 AAAAATGGAAATCATACTTCAAA-AA
* *
2688 AAATATGGAAATCATACTTAAAAAA
1 AAAAATGGAAATCATACTTCAAAAA
*
2713 AAAAAAGGAAATCA
1 AAAAATGGAAATCA
2727 AGAGGTAGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 26 0.79
26 7 0.21
ACGTcount: A:0.59, C:0.11, G:0.09, T:0.20
Consensus pattern (25 bp):
AAAAATGGAAATCATACTTCAAAAA
Found at i:5509 original size:25 final size:25
Alignment explanation
Indices: 5475--5524 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5465 TCTACATACA
5475 GGTGACGAAAAGGTTACGTTTTTCT
1 GGTGACGAAAAGGTTACGTTTTTCT
5500 GGTGACGAAAAGGTTACGTTTTTCT
1 GGTGACGAAAAGGTTACGTTTTTCT
5525 TGGAATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (25 bp):
GGTGACGAAAAGGTTACGTTTTTCT
Found at i:12191 original size:20 final size:20
Alignment explanation
Indices: 12166--12207 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
12156 TTTAAATTAA
*
12166 TTAAATTCCACGTGGCTATT
1 TTAAATGCCACGTGGCTATT
12186 TTAAATGCCACGTGGCTATT
1 TTAAATGCCACGTGGCTATT
12206 TT
1 TT
12208 TGTTAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (20 bp):
TTAAATGCCACGTGGCTATT
Found at i:13286 original size:27 final size:28
Alignment explanation
Indices: 13230--13286 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
13220 TAACTATCCA
** *
13230 TTTTGGGACAAATTGGTCCCTTAACTTT
1 TTTTGGGACAAAAAGGCCCCTTAACTTT
13258 TTTTGGGACAAAAAGGCCCCTTAACTTT
1 TTTTGGGACAAAAAGGCCCCTTAACTTT
13286 T
1 T
13287 AAAAACGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (28 bp):
TTTTGGGACAAAAAGGCCCCTTAACTTT
Found at i:15793 original size:2 final size:2
Alignment explanation
Indices: 15786--15810 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15776 ATTAACCGTG
15786 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15811 TTAAATTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26095 original size:17 final size:18
Alignment explanation
Indices: 26073--26110 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
26063 GTTATCCAGC
*
26073 ACCTCATG-CTACCTTGT
1 ACCTCATGACTACCTGGT
26090 ACCTCATGACTACCTGGT
1 ACCTCATGACTACCTGGT
26108 ACC
1 ACC
26111 ATGAGAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.37, G:0.13, T:0.29
Consensus pattern (18 bp):
ACCTCATGACTACCTGGT
Found at i:29377 original size:14 final size:12
Alignment explanation
Indices: 29355--29389 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
29345 GAGTTCTTTT
29355 AAAAAAAAAAGAG
1 AAAAAAAAAAG-G
29368 AAAGAAAAAAAGG
1 AAA-AAAAAAAGG
29381 AAAAAAAAA
1 AAAAAAAAA
29390 GAAAGAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 7 0.33
14 8 0.38
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGG
Found at i:31264 original size:21 final size:21
Alignment explanation
Indices: 31236--31286 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
31226 TCTAGCTGGG
* *
31236 GACCCATGTGGTATGCTTGGC
1 GACCCATGTGGTATGCCTCGC
* *
31257 GCCCCATGTGGTTTGCCTCGC
1 GACCCATGTGGTATGCCTCGC
31278 GACCCATGT
1 GACCCATGT
31287 CCTCCAGTGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.12, C:0.31, G:0.29, T:0.27
Consensus pattern (21 bp):
GACCCATGTGGTATGCCTCGC
Found at i:31734 original size:26 final size:28
Alignment explanation
Indices: 31698--31763 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
31688 CAGCAACCCA
* *
31698 AAAATTGCAAAA-TTGCCGCAAGTA-CC
1 AAAATTCCAAAATTTGCCGCAACTAGCC
31724 AAAATTCCAAAATTTGCCGCAACTAGCC
1 AAAATTCCAAAATTTGCCGCAACTAGCC
*
31752 AAAATTCAAAAA
1 AAAATTCCAAAA
31764 CCCTGTAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 11 0.31
27 11 0.31
28 13 0.37
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.20
Consensus pattern (28 bp):
AAAATTCCAAAATTTGCCGCAACTAGCC
Found at i:47331 original size:10 final size:10
Alignment explanation
Indices: 47316--47381 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 10
47306 ATGTCACCAA
47316 GCCATGCCCG
1 GCCATGCCCG
47326 GCCATGTCCGCG
1 GCCATG-CC-CG
* *
47338 CACCATGCCCA
1 -GCCATGCCCG
47349 GCCATGTCCGCG
1 GCCATG-CC-CG
*
47361 CACCATGCCCG
1 -GCCATGCCCG
47372 GCCATGCCCG
1 GCCATGCCCG
47382 ACCAATGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
10 20 0.45
11 7 0.16
12 7 0.16
13 10 0.23
ACGTcount: A:0.14, C:0.48, G:0.26, T:0.12
Consensus pattern (10 bp):
GCCATGCCCG
Found at i:47343 original size:23 final size:23
Alignment explanation
Indices: 47317--47408 Score: 113
Period size: 23 Copynumber: 4.2 Consensus size: 23
47307 TGTCACCAAG
47317 CCATGCCCGGCCATGTCCGCGCA
1 CCATGCCCGGCCATGTCCGCGCA
*
47340 CCATGCCCAGCCATGTCCGCGCA
1 CCATGCCCGGCCATGTCCGCGCA
47363 CCATGCCCGGCCATG-CC-CG-A
1 CCATGCCCGGCCATGTCCGCGCA
**
47383 CCAATGCCATGCCA--TCCGCGCA
1 CC-ATGCCCGGCCATGTCCGCGCA
47405 CCAT
1 CCAT
47409 ACCGAGCCAC
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
20 5 0.08
21 15 0.25
22 5 0.08
23 36 0.59
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.13
Consensus pattern (23 bp):
CCATGCCCGGCCATGTCCGCGCA
Found at i:47696 original size:15 final size:14
Alignment explanation
Indices: 47676--47709 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
47666 TAACCCATAA
47676 TATTTTTCTTTGTTT
1 TATTTTTCTTT-TTT
47691 TATTTTTCTTTTTT
1 TATTTTTCTTTTTT
47705 T-TTTT
1 TATTTT
47710 AGGATTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 4 0.21
15 11 0.58
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.85
Consensus pattern (14 bp):
TATTTTTCTTTTTT
Found at i:49011 original size:12 final size:12
Alignment explanation
Indices: 48996--49035 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 12
48986 ATTATGCATG
48996 TTTTTATAGCTA
1 TTTTTATAGCTA
49008 TTTTTATA--TA
1 TTTTTATAGCTA
49018 TTTTT-T-GCTA
1 TTTTTATAGCTA
49028 TTTTTATA
1 TTTTTATA
49036 TGTGTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 1 0.04
10 14 0.58
11 1 0.04
12 8 0.33
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (12 bp):
TTTTTATAGCTA
Found at i:49043 original size:20 final size:20
Alignment explanation
Indices: 49004--49043 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48994 TGTTTTTATA
*
49004 GCTATTTTTATATATTTTTT
1 GCTATTTTTATATATGTTTT
*
49024 GCTATTTTTATATGTGTTTT
1 GCTATTTTTATATATGTTTT
49044 TACCCTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (20 bp):
GCTATTTTTATATATGTTTT
Found at i:56767 original size:7 final size:7
Alignment explanation
Indices: 56757--56843 Score: 50
Period size: 7 Copynumber: 11.9 Consensus size: 7
56747 TATATTTAAA
56757 ATATATT
1 ATATATT
56764 ATATA-T
1 ATATATT
56770 ATTATATT
1 A-TATATT
56778 ATATATT
1 ATATATT
* *
56785 TTTTATT
1 ATATATT
*
56792 ATATATAA
1 ATATAT-T
* **
56800 ATTTAAA
1 ATATATT
56807 ATATATT
1 ATATATT
56814 ATCTATATT
1 A--TATATT
56823 ATATATGT
1 ATATAT-T
* *
56831 TTTTATT
1 ATATATT
56838 ATATAT
1 ATATAT
56844 AAATAAATAA
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
6 2 0.03
7 40 0.67
8 11 0.18
9 7 0.12
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (7 bp):
ATATATT
Found at i:56789 original size:50 final size:50
Alignment explanation
Indices: 56732--56851 Score: 163
Period size: 50 Copynumber: 2.4 Consensus size: 50
56722 TCGAATAGAA
*
56732 ATTTTTTATAATATATATATTTAAAATATATTATATATATTATATTATAT
1 ATTTTTTATAATATATAAATTTAAAATATATTATATATATTATATTATAT
* * *
56782 ATTTTTTATTATATATAAATTTAAAATATATTATCTATATTATA-TATGT
1 ATTTTTTATAATATATAAATTTAAAATATATTATATATATTATATTATAT
*
56831 -TTTTATTATATATAAATAAAT
1 ATTTT-TTATA-ATATATAAAT
56852 AAAATTTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 4 0.06
49 8 0.13
50 50 0.81
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (50 bp):
ATTTTTTATAATATATAAATTTAAAATATATTATATATATTATATTATAT
Found at i:56842 original size:31 final size:28
Alignment explanation
Indices: 56758--56843 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 28
56748 ATATTTAAAA
*
56758 TATATTATATATATTATATTATATATTT
1 TATATTATATATATTTTATTATATATTT
* * **
56786 TTTATTATATATAAATTTAAAATATATTAT
1 TATATTATATAT-ATTTTATTATATATT-T
*
56816 CTATATTATATATGTTTTTATTATATAT
1 -TATATTATATAT-ATTTTATTATATAT
56844 AAATAAATAA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
28 11 0.25
29 11 0.25
30 1 0.02
31 21 0.48
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (28 bp):
TATATTATATATATTTTATTATATATTT
Found at i:56867 original size:46 final size:45
Alignment explanation
Indices: 56732--56868 Score: 91
Period size: 50 Copynumber: 2.9 Consensus size: 45
56722 TCGAATAGAA
* * * * *
56732 ATTTTTTATAATATATATATTTAAAATATATTATATATATTATATT
1 ATTTTTTATTATATATAAATATAAAATATATAAAATATATTATA-T
* * **
56778 ATATATTTT-TTATTATATATAAATTTAAAATATATTATCTATATTATAT
1 AT-T-TTTTATTA---TATATAAATATAAAATATATAAAATATATTATAT
56827 ATGTTTTTATTATATATAAATAAATAAAAT-T-TAAAATATATT
1 AT-TTTTTATTATATATAAAT--ATAAAATATATAAAATATATT
56869 TTAAATATAT
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
46 19 0.25
47 4 0.05
48 14 0.19
49 7 0.09
50 31 0.41
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (45 bp):
ATTTTTTATTATATATAAATATAAAATATATAAAATATATTATAT
Found at i:58158 original size:25 final size:25
Alignment explanation
Indices: 58110--58158 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
58100 GTAGTTCTTG
* *
58110 ATTGTTAGGATTTTGTTTAGGATTA
1 ATTGTTAGGATTTGGTTGAGGATTA
58135 ATTGTTA-GATTTGGTTGAGAGATT
1 ATTGTTAGGATTTGGTTGAG-GATT
58159 GAAAGAGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (25 bp):
ATTGTTAGGATTTGGTTGAGGATTA
Found at i:59037 original size:25 final size:25
Alignment explanation
Indices: 58989--59037 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
58979 TGTTAATTTG
*
58989 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAATGCTCAAA
* *
59014 TAGAGACCGAGTGAGAATGTTCAA
1 TAGAGACCGAGCGAGAATGCTCAA
59038 GATTGTTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.16, G:0.31, T:0.16
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAATGCTCAAA
Found at i:78597 original size:29 final size:31
Alignment explanation
Indices: 78538--78597 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
78528 AAAATGACTA
* *
78538 TATTTGATACATTTATAAAAGTTAAGTGACC
1 TATTTGAGACATATATAAAAGTTAAGTGACC
*
78569 TATTTGAGACATAT-TAAAA-TTCAGTGACC
1 TATTTGAGACATATATAAAAGTTAAGTGACC
78598 AAATTAGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 9 0.35
30 5 0.19
31 12 0.46
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (31 bp):
TATTTGAGACATATATAAAAGTTAAGTGACC
Found at i:81009 original size:41 final size:41
Alignment explanation
Indices: 80952--81029 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
80942 TCTCTGCTAG
*
80952 TTTTTCTTCTCTTTCAGCATCGTCTGAAGACGTTAAAACAA
1 TTTTTCTTCTCTTTCAGCATCGTCTCAAGACGTTAAAACAA
*
80993 TTTTTCTT-TACTTTCAGCATCGTCTCAGGACGTTAAA
1 TTTTTCTTCT-CTTTCAGCATCGTCTCAAGACGTTAAA
81030 CATTTGTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (41 bp):
TTTTTCTTCTCTTTCAGCATCGTCTCAAGACGTTAAAACAA
Found at i:81049 original size:41 final size:41
Alignment explanation
Indices: 80952--81049 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
80942 TCTCTGCTAG
*
80952 TTTTTC-TTCTCTTTCAGCATCGTCTGAAGACGTTAAAACAA
1 TTTTTCTTTCT-TTTCAGCATCGTCTCAAGACGTTAAAACAA
*
80993 TTTTTCTTTAC-TTTCAGCATCGTCTCAGGACGTT-AAAC-A
1 TTTTTCTTT-CTTTTCAGCATCGTCTCAAGACGTTAAAACAA
81032 TTTGTTACTTTCTTTTCA
1 TTT-TT-CTTTCTTTTCA
81050 TATGAATAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
39 4 0.08
40 7 0.14
41 36 0.72
42 2 0.04
43 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.45
Consensus pattern (41 bp):
TTTTTCTTTCTTTTCAGCATCGTCTCAAGACGTTAAAACAA
Found at i:88267 original size:2 final size:2
Alignment explanation
Indices: 88249--88293 Score: 65
Period size: 2 Copynumber: 22.0 Consensus size: 2
88239 AACTAGTTAA
88249 AT AT AT ACT AT AT -T AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
88292 AT
1 AT
88294 TATTTGAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 1 0.03
2 35 0.88
3 4 0.10
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:88626 original size:178 final size:176
Alignment explanation
Indices: 88315--88649 Score: 465
Period size: 178 Copynumber: 1.9 Consensus size: 176
88305 CCTCTGGAAA
* * * *
88315 TTACTAAAGGCTCCCATCAACTTTTAATATGGGAGAACCTTTTCACCCCCTTTTGGTCTTTTCTC
1 TTACTAAAGGCCCCCATCAACTTTTAATATGGGAGAACCTTATCACCCCCTTCTGGTCTTTTCCC
** * * *
88380 ATGTGGTTGATTACTAAAATATCCCCTAAGCCTAACATGTTTTCTTTAGATCCATTGCCTTTGTG
66 ACATGGTTGATTACTAAAATATCCCCTAAGCATAACATATTTTCTTCAGATCCATTGCCTTTGTG
88445 TGTAATTTGGCCATTGAGTTCTAATAAATGTTGTTCCCACAAAAAT
131 TGTAATTTGGCCATTGAGTTCTAATAAATGTTGTTCCCACAAAAAT
* * * *
88491 TTACTAAAGGATCCCCCATCAACTTTTAATGT-GGAGTGACCTTATCGCCCCGTTCTGGTCTTTT
1 TTACTAAAGG--CCCCCATCAACTTTTAATATGGGAG-AACCTTATCACCCCCTTCTGGTCTTTT
* * * *
88555 CCCACATTGTTGATTACTGAAATATCCCTTAAGCATAACATATTTTCTTCAGATCCATTGTCTTT
63 CCCACATGGTTGATTACTAAAATATCCCCTAAGCATAACATATTTTCTTCAGATCCATTGCCTTT
* *
88620 GTGTGTAATTTGGCCATTGGGTTCTGATAA
128 GTGTGTAATTTGGCCATTGAGTTCTAATAA
88650 GTTTACCACC
Statistics
Matches: 137, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
176 10 0.07
177 4 0.03
178 123 0.90
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (176 bp):
TTACTAAAGGCCCCCATCAACTTTTAATATGGGAGAACCTTATCACCCCCTTCTGGTCTTTTCCC
ACATGGTTGATTACTAAAATATCCCCTAAGCATAACATATTTTCTTCAGATCCATTGCCTTTGTG
TGTAATTTGGCCATTGAGTTCTAATAAATGTTGTTCCCACAAAAAT
Found at i:91977 original size:2 final size:2
Alignment explanation
Indices: 91970--91994 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91960 ACATACATAC
91970 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
91995 GCTAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:92665 original size:13 final size:13
Alignment explanation
Indices: 92647--92672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
92637 AGATTGAGAG
92647 GAAATAGAAAAAA
1 GAAATAGAAAAAA
92660 GAAATAGAAAAAA
1 GAAATAGAAAAAA
92673 ACTTAGGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (13 bp):
GAAATAGAAAAAA
Found at i:94223 original size:45 final size:46
Alignment explanation
Indices: 94158--94245 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
94148 AATAACATTT
* *
94158 AGTATATATATTAGCTTTATTTTGGTGAATTTCCTAGAGATGAAGG
1 AGTATATATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGG
* *
94204 AGTATA-ATATTAGTTTTATTTTGATGAATTACCTTGAGATGA
1 AGTATATATATTAGCTTTATTTTGATGAATTACCTAGAGATGA
94246 GGAAGTAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 32 0.84
46 6 0.16
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (46 bp):
AGTATATATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGG
Found at i:94673 original size:22 final size:23
Alignment explanation
Indices: 94634--94679 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
94624 AATTTACTAT
94634 TTTTATATTCATGATTAAGTGTG
1 TTTTATATTCATGATTAAGTGTG
*
94657 TTTTA-ATTACAT-ATTAATTGTG
1 TTTTATATT-CATGATTAAGTGTG
94679 T
1 T
94680 GTGGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.54
Consensus pattern (23 bp):
TTTTATATTCATGATTAAGTGTG
Found at i:95082 original size:15 final size:17
Alignment explanation
Indices: 95056--95087 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
95046 TCCTTATTCC
95056 TTTTTTATTTTA-CATT
1 TTTTTTATTTTATCATT
95072 TTTTTTA-TTTATCATT
1 TTTTTTATTTTATCATT
95088 CGACTTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTATTTTATCATT
Done.