Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014254.1 Corchorus capsularis cultivar CVL-1 contig14275, 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: 89492
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:585 original size:15 final size:15
Alignment explanation
Indices: 565--594 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
555 TTTATTAGAT
565 ATATATATATATATA
1 ATATATATATATATA
*
580 ATATATTTATATATA
1 ATATATATATATATA
595 GAGTCTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:2090 original size:108 final size:109
Alignment explanation
Indices: 1975--2232 Score: 437
Period size: 109 Copynumber: 2.3 Consensus size: 109
1965 AATATTGAAC
*
1975 TTAATTAAATGAAAATAGAGTTTTTAGTAAAATAAAATTGTATATTAG-AAAAATTTTAATATAT
1 TTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAATATAT
2039 CCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGAT
66 CCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGAT
*
2083 TTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTATAT
1 TTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAATATAT
2148 CCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGAT
66 CCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGAT
* *
2192 TTAATTTAATTGAATAAAATAGAGTTTCTAGTAGAATAAAA
1 TTAA-TTAAATG---AAAATAGAGTTTTTAGTAGAATAAAA
2233 CTATAATAGT
Statistics
Matches: 141, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
108 47 0.33
109 63 0.45
110 6 0.04
113 25 0.18
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAATATAT
CCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGAT
Found at i:2528 original size:34 final size:35
Alignment explanation
Indices: 2470--2553 Score: 120
Period size: 34 Copynumber: 2.4 Consensus size: 35
2460 TTTATGGTTT
*
2470 CGAATAAGTGGAGGGTTTTTTTTTTTTTGAG-CA-AA
1 CGAATAAGTGGA-GTTTTTTTTTTTTTTG-GCCACAA
2505 CGAATAAGTGGAGTTTTTTTTTTTTTTGGCCACAA
1 CGAATAAGTGGAGTTTTTTTTTTTTTTGGCCACAA
2540 CGAATAA-TGGAGTT
1 CGAATAAGTGGAGTT
2554 GATATGCATA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
33 1 0.02
34 24 0.52
35 21 0.46
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (35 bp):
CGAATAAGTGGAGTTTTTTTTTTTTTTGGCCACAA
Found at i:3372 original size:13 final size:13
Alignment explanation
Indices: 3354--3378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3344 CCTTCCCATC
3354 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
3367 TTTTCTTTTTTT
1 TTTTCTTTTTTT
3379 CCCTTTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:3884 original size:7 final size:7
Alignment explanation
Indices: 3872--3897 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3862 TATATAGCTG
3872 CTGAAAT
1 CTGAAAT
3879 CTGAAAT
1 CTGAAAT
3886 CTGAAAT
1 CTGAAAT
3893 CTGAA
1 CTGAA
3898 TCAAGTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (7 bp):
CTGAAAT
Found at i:5727 original size:16 final size:16
Alignment explanation
Indices: 5708--5871 Score: 195
Period size: 16 Copynumber: 10.3 Consensus size: 16
5698 CAGTTTTCTT
* *
5708 GGGTCATTCGGCTTTT
1 GGGTCATTCGGGTTTC
*
5724 GGGTCATTTGGG-TTC
1 GGGTCATTCGGGTTTC
*
5739 GGGTTATTCGGGTTTC
1 GGGTCATTCGGGTTTC
*
5755 GGGTCATTCGGGTCTC
1 GGGTCATTCGGGTTTC
* *
5771 GAGTCATACGGGTTTC
1 GGGTCATTCGGGTTTC
* *
5787 GGGTCATTCGAGTCTC
1 GGGTCATTCGGGTTTC
*
5803 GGGTCATACGGGTTTC
1 GGGTCATTCGGGTTTC
*
5819 GGGTCATTCGGGTCTC
1 GGGTCATTCGGGTTTC
* *
5835 GGGTCATACGGGTTCC
1 GGGTCATTCGGGTTTC
*
5851 GGGTCATTCGGGTCTC
1 GGGTCATTCGGGTTTC
5867 GGGTC
1 GGGTC
5872 TACCAGGTCT
Statistics
Matches: 122, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
15 12 0.10
16 110 0.90
ACGTcount: A:0.09, C:0.21, G:0.37, T:0.34
Consensus pattern (16 bp):
GGGTCATTCGGGTTTC
Found at i:5886 original size:32 final size:32
Alignment explanation
Indices: 5708--5871 Score: 240
Period size: 32 Copynumber: 5.2 Consensus size: 32
5698 CAGTTTTCTT
* * * *
5708 GGGTCATTCGGCTTTTGGGTCATTTGGGT-TC
1 GGGTCATACGGGTTTCGGGTCATTCGGGTCTC
* *
5739 GGGTTATTCGGGTTTCGGGTCATTCGGGTCTC
1 GGGTCATACGGGTTTCGGGTCATTCGGGTCTC
* *
5771 GAGTCATACGGGTTTCGGGTCATTCGAGTCTC
1 GGGTCATACGGGTTTCGGGTCATTCGGGTCTC
5803 GGGTCATACGGGTTTCGGGTCATTCGGGTCTC
1 GGGTCATACGGGTTTCGGGTCATTCGGGTCTC
*
5835 GGGTCATACGGGTTCCGGGTCATTCGGGTCTC
1 GGGTCATACGGGTTTCGGGTCATTCGGGTCTC
5867 GGGTC
1 GGGTC
5872 TACCAGGTCT
Statistics
Matches: 121, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
31 25 0.21
32 96 0.79
ACGTcount: A:0.09, C:0.21, G:0.37, T:0.34
Consensus pattern (32 bp):
GGGTCATACGGGTTTCGGGTCATTCGGGTCTC
Found at i:6743 original size:16 final size:16
Alignment explanation
Indices: 6722--6856 Score: 159
Period size: 16 Copynumber: 8.4 Consensus size: 16
6712 GGTTAACTTC
*
6722 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
6738 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
*
6754 TCGGGTCACTCGGGTT
1 TCGGGTCATTCGGGTT
*
6770 ACGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
6786 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
6802 AT-GGGTCATTCGGGTT
1 -TCGGGTCATTCGGGTT
6818 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
6834 GCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
6850 TCGGGTC
1 TCGGGTC
6857 GGATGGGTTC
Statistics
Matches: 101, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
15 5 0.05
16 91 0.90
17 5 0.05
ACGTcount: A:0.08, C:0.20, G:0.39, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:7249 original size:25 final size:24
Alignment explanation
Indices: 7215--7273 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
7205 TTCAAACCCT
*
7215 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAA-ATCTTC
*
7240 AAACTTCATTTTTAACAAATCTTC
1 AAACTTCATTTCTAACAAATCTTC
7264 AAA-TTCATTT
1 AAACTTCATTT
7274 TTCTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 8 0.25
25 17 0.53
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:7312 original size:26 final size:26
Alignment explanation
Indices: 7283--7350 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
7273 TTTCTTCATT
7283 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
7309 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
7335 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
7351 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:7351 original size:37 final size:36
Alignment explanation
Indices: 7292--7400 Score: 87
Period size: 37 Copynumber: 3.0 Consensus size: 36
7282 TTTAATCATA
* *
7292 AACTAATTAAATACT-AATTAATAATAAACTAATTAG
1 AACTAATTAAACA-TAAACTAATAATAAACTAATTAG
* **
7328 ATACTAATTAAACATAAACTAATAA-ACTAAGTAATTTT
1 A-ACTAATTAAACATAAACTAATAATA--AACTAATTAG
* * * *
7366 AATTAACTAATCATAAACTAATCATAAACTAATTA
1 AACTAATTAAACATAAACTAATAATAAACTAATTA
7401 ATATTAAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
36 10 0.18
37 38 0.67
38 9 0.16
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (36 bp):
AACTAATTAAACATAAACTAATAATAAACTAATTAG
Found at i:7386 original size:11 final size:11
Alignment explanation
Indices: 7370--7398 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
7360 AATTTTAATT
7370 AACTAATCATA
1 AACTAATCATA
7381 AACTAATCATA
1 AACTAATCATA
7392 AACTAAT
1 AACTAAT
7399 TAATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (11 bp):
AACTAATCATA
Found at i:7403 original size:52 final size:49
Alignment explanation
Indices: 7284--7403 Score: 111
Period size: 52 Copynumber: 2.4 Consensus size: 49
7274 TTCTTCATTT
* * * *
7284 TAATCATAAACTAATTAA-ATACTAATTAATAATAAACTAATTAGATAC
1 TAATCATAAACTAATTAATAAACTAAGTAATAATAAACTAATCAGAAAC
* * *
7332 TAAT--TAAACATAAACTAATAAACTAAGTAATTTTAATTAACTAATCATAAAC
1 TAATCATAAAC-T-AATTAATAAACTAAGTAA---TAATAAACTAATCAGAAAC
7384 TAATCATAAACTAATTAATA
1 TAATCATAAACTAATTAATA
7404 TTAAAAAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
46 5 0.09
47 1 0.02
48 9 0.16
49 9 0.16
52 26 0.46
53 1 0.02
54 5 0.09
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (49 bp):
TAATCATAAACTAATTAATAAACTAAGTAATAATAAACTAATCAGAAAC
Found at i:16818 original size:5 final size:5
Alignment explanation
Indices: 16810--16838 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
16800 TTTTCTTTTG
16810 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
16839 TTTTTATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:18662 original size:30 final size:30
Alignment explanation
Indices: 18622--18680 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
18612 TGTCTTCAAG
18622 TCCATAATAAGTCCTT-GGCGCATAATTCCT
1 TCCATAATAAG-CCTTGGGCGCATAATTCCT
* *
18652 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATAATTCC
18681 CTCCCCTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATAATTCCT
Found at i:19059 original size:30 final size:29
Alignment explanation
Indices: 19023--19129 Score: 88
Period size: 34 Copynumber: 3.3 Consensus size: 29
19013 TTCTCGTCAC
19023 CCAAAACAGATTTATTTTCAATGCTATCAA
1 CCAAAACAGA-TTATTTTCAATGCTATCAA
*
19053 CCAAAACAGGATTATTTGCAATGCTATGATCAAA
1 CCAAAACA-GATTATTTTCAATGC--T-ATC-AA
* * *
19087 CCAAAATAAAATTATTTTTAATGCTATGTTCAA
1 CCAAAA-CAGATTATTTTCAATGCTA---TCAA
19120 CCAAAACAGA
1 CCAAAACAGA
19130 ATTGTTTTAC
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
30 20 0.33
31 3 0.05
32 4 0.07
33 11 0.18
34 22 0.36
35 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (29 bp):
CCAAAACAGATTATTTTCAATGCTATCAA
Found at i:19194 original size:33 final size:32
Alignment explanation
Indices: 19157--19261 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 32
19147 ATTAGCATCC
* *
19157 AAAACAGATTTAGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTATCATCGCAAACAACA-CT
* *
19190 AAAACAGATTTAGTGTCATTGCAAACAACACT
1 AAAACAGATTTAGTATCATCGCAAACAACACT
** *
19222 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCGCAAACAACA-CT
19256 AAAACA
1 AAAACA
19262 CTCTTTTCAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 2 0.03
33 56 0.93
34 2 0.03
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.25
Consensus pattern (32 bp):
AAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:22115 original size:20 final size:20
Alignment explanation
Indices: 22090--22130 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
22080 TTCTAAAACC
22090 TATCCTAATAAAATCTTAAT
1 TATCCTAATAAAATCTTAAT
22110 TATCCTAATAAAATCTTAAT
1 TATCCTAATAAAATCTTAAT
22130 T
1 T
22131 TTGGGGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (20 bp):
TATCCTAATAAAATCTTAAT
Found at i:24631 original size:156 final size:157
Alignment explanation
Indices: 24445--24860 Score: 499
Period size: 156 Copynumber: 2.6 Consensus size: 157
24435 TTGGTTGGGT
* * * * *
24445 TCGAGCCCTCCTTCATGGTGAACTAGGTTTCACACCTCAAACTGTCCTTAAATGAAAAACATGCA
1 TCGAGCTCTCCTTGATGGTGAACTAGGTTTCACACCCCAGACTGTCCTTAAATGAAAAACAAGCA
*
24510 TAAGTTTTTCAT-TCTAAGTCTGATTGAGATGAAACTTTTCTA-AG-GGACTTAGATGATCTCCA
66 TAAGTTTTTCATCT-TAAGTCTGATTGAGATGAAACTTTTC-ACAGAGG-CTTAGATGATATCCA
**
24572 TAAGGCTATGG-AAAAAATTCTAAGTAAAA
128 TAAAACTATGGAAAAAAATTCTAAGTAAAA
* *
24601 TCGAGCTCTCCTTGGTGGTGAACTATGTTTCACACCCCAGACTGTCCTTAAATGAAAAACAAGCA
1 TCGAGCTCTCCTTGATGGTGAACTAGGTTTCACACCCCAGACTGTCCTTAAATGAAAAACAAGCA
* * * * *
24666 TAAGTTTTTCATCTTAAGTC-CAATAAGGCTG-AA-TTTTCACCAGTAGGCTTAGATTATATCCA
66 TAAGTTTTTCATCTTAAGTCTGATTGA-GATGAAACTTTTCA-CAG-AGGCTTAGATGATATCCA
*
24728 TAAAACTATGGAAAAAAAATTCTAAGTAAGA
128 TAAAACTATGG-AAAAAAATTCTAAGTAAAA
* **
24759 CCGAGCTCTCCTTGATGGTGAACT-GGTTTTCTTACCCCAGACTGTCCTTAAATGAAAAACAAGC
1 TCGAGCTCTCCTTGATGGTGAACTAGG-TTTCACACCCCAGACTGTCCTTAAATGAAAAACAAGC
* *
24823 ATAAGTTTTCCATCTTAAG-CATGTTTGAGATGAAACTT
65 ATAAGTTTTTCATCTTAAGTC-TGATTGAGATGAAACTT
24861 AGCCAAAATG
Statistics
Matches: 220, Mismatches: 27, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
153 1 0.00
154 5 0.02
155 7 0.03
156 101 0.46
157 5 0.02
158 95 0.43
159 4 0.02
160 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (157 bp):
TCGAGCTCTCCTTGATGGTGAACTAGGTTTCACACCCCAGACTGTCCTTAAATGAAAAACAAGCA
TAAGTTTTTCATCTTAAGTCTGATTGAGATGAAACTTTTCACAGAGGCTTAGATGATATCCATAA
AACTATGGAAAAAAATTCTAAGTAAAA
Found at i:34045 original size:87 final size:86
Alignment explanation
Indices: 33940--34124 Score: 266
Period size: 87 Copynumber: 2.1 Consensus size: 86
33930 TAAAAACTCT
*
33940 ATTTTTATTAATAAAATCTAATCTCTTTATAACTATTTTATCTCTAACA-TTTTACTATTTTAAT
1 ATTTTT-TTAATTAAATCTAATCTCTTTATAACTATTTTATCTCTAACATTTTTACTATTTTAA-
34004 TTTAAAAAACTTAGATATATTAAA
64 -TTAAAAAACTTAGATATATTAAA
* * * *
34028 ATTTTTTTAATTAAATCTAATCTCTTTATAATTATTTTATTTTTACCATTTTTACTATTTTAATT
1 ATTTTTTTAATTAAATCTAATCTCTTTATAACTATTTTATCTCTAACATTTTTACTATTTTAATT
* *
34093 ACAAAACTTAGATATATTAGA
66 AAAAAACTTAGATATATTAAA
34114 A-TTTTTTAATT
1 ATTTTTTTAATT
34125 TATTTCTTAA
Statistics
Matches: 89, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
85 10 0.11
86 22 0.25
87 37 0.42
88 20 0.22
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (86 bp):
ATTTTTTTAATTAAATCTAATCTCTTTATAACTATTTTATCTCTAACATTTTTACTATTTTAATT
AAAAAACTTAGATATATTAAA
Found at i:43498 original size:2 final size:2
Alignment explanation
Indices: 43491--43519 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43481 TATTATTATA
43491 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
43520 ATACAATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:43956 original size:101 final size:92
Alignment explanation
Indices: 43874--44040 Score: 280
Period size: 92 Copynumber: 1.8 Consensus size: 92
43864 ATGAGTTTGC
* *
43874 CTTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTTCATAATTGGGATAACTTTG
1 CTTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTCCATAATAGGGATAACTTTG
43939 CAGACCATTTGCTTTATCTTCATCCAA
66 CAGACCATTTGCTTTATCTTCATCCAA
* *
43966 CTTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTCCATGATAGGGATATCTTTT
1 CTTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTCCATAATAGGGATAAC-TTT
*
44031 GTAGACCATT
65 GCAGACCATT
44041 ATTTCATCCA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
92 57 0.83
93 12 0.17
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (92 bp):
CTTGCATTATTGACATAATTGGAGACAATTTTTGCAGAGATTCCTCCATAATAGGGATAACTTTG
CAGACCATTTGCTTTATCTTCATCCAA
Found at i:49231 original size:18 final size:18
Alignment explanation
Indices: 49208--49243 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
49198 AAAAATGTTT
*
49208 TTTTGAAGATTTTTTGGA
1 TTTTGAAAATTTTTTGGA
49226 TTTTGAAAATTTTTTGGA
1 TTTTGAAAATTTTTTGGA
49244 ATTTCATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (18 bp):
TTTTGAAAATTTTTTGGA
Found at i:50520 original size:2 final size:2
Alignment explanation
Indices: 50513--50539 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50503 CATTTTGTTT
50513 TA 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 TA T
50540 TTTACAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53160 original size:23 final size:23
Alignment explanation
Indices: 53128--53187 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 23
53118 AGGTGAATCA
53128 GTAA-TAAGTAACTTAATTCAGG
1 GTAATTAAGTAACTTAATTCAGG
53150 GTAATTAAGTAATTAACTTAATTCAGG
1 GTAATTAAG----TAACTTAATTCAGG
53177 GTAATTAAGTA
1 GTAATTAAGTA
53188 GTTCAATGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
22 4 0.12
23 6 0.18
27 23 0.70
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (23 bp):
GTAATTAAGTAACTTAATTCAGG
Found at i:53168 original size:27 final size:27
Alignment explanation
Indices: 53136--53187 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
53126 CAGTAATAAG
53136 TAACTTAATTCAGGGTAATTAAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTAAT
53163 TAACTTAATTCAGGGTAATTAAGTA
1 TAACTTAATTCAGGGTAATTAAGTA
53188 GTTCAATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (27 bp):
TAACTTAATTCAGGGTAATTAAGTAAT
Found at i:53362 original size:35 final size:35
Alignment explanation
Indices: 53150--53728 Score: 582
Period size: 35 Copynumber: 16.1 Consensus size: 35
53140 TTAATTCAGG
* *
53150 GTAATTAAGTAATTAACTTAATTCAGGGTAATTAA
1 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAA
*
53185 GTAGTTCAATGAGTAATCAACTTAATTCAGGGTAATTAA
1 GTAATTC----AGTAATCAACTTAATTCAGGGTAATTAA
* *
53224 GTAAATCGGTAAGAAGT-AACTTAATTCAGGGTAATTAA
1 GTAATTCAGT---AA-TCAACTTAATTCAGGGTAATTAA
*
53262 GTGAGTT-AGTAATAAGCAACTTAATTCAGGGTAATTAA
1 GT-AATTCAGTAAT---CAACTTAATTCAGGGTAATTAA
*
53300 GTGAGTT-AGTAATAAGCAACTTAATTCAGGGTAATTAA
1 GT-AATTCAGTAAT---CAACTTAATTCAGGGTAATTAA
53338 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAA
1 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAA
** * * *
53373 GCGAGTCAGCAGT-AACTTAATTCAGGGTAATTAA
1 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAA
53407 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAA
1 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAA
* * *
53442 GTGAGTCAGTGATAAGCAACTTAATTCAGGGTAATTAA
1 GTAATTCA--G-TAATCAACTTAATTCAGGGTAATTAA
* *
53480 GTGAGTCAGTAATCAACTTAATTCAGGGTAATTAA
1 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAA
* * *
53515 GTGAGTCAGTAATAAGCAACTTAATTAAGGG-AATTAA
1 GTAATTCAGTAAT---CAACTTAATTCAGGGTAATTAA
* * *
53552 GTAATTCGGTAATTAACTTAATTCAGGGTAATTAG
1 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAA
* *
53587 GTGAGTCAGTAATCAACTTAATTCAGGGTAATTAA
1 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAA
53622 GTAATTCAGTAAGT-AACTTAATTCAGGGTAATTAA
1 GTAATTCAGTAA-TCAACTTAATTCAGGGTAATTAA
* * *
53657 GTGAGTT-AATAATCAACTTAATTTAGGG-AAGTTAA
1 GT-AATTCAGTAATCAACTTAATTCAGGGTAA-TTAA
* * *
53692 GTAGTTCAATAAGT-AACTTAATTCAGGGAAATTAA
1 GTAATTCAGTAA-TCAACTTAATTCAGGGTAATTAA
53727 GT
1 GT
53729 TTAGTAAGAA
Statistics
Matches: 473, Mismatches: 42, Indels: 58
0.83 0.07 0.10
Matches are distributed among these distances:
34 50 0.11
35 219 0.46
36 8 0.02
37 20 0.04
38 141 0.30
39 35 0.07
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.32
Consensus pattern (35 bp):
GTAATTCAGTAATCAACTTAATTCAGGGTAATTAA
Found at i:53428 original size:142 final size:141
Alignment explanation
Indices: 53164--53728 Score: 669
Period size: 142 Copynumber: 3.9 Consensus size: 141
53154 TTAAGTAATT
*
53164 AACTTAATTCAGGGTAATTAAGTAGTTCAATGAGTAATCAACTTAATTCAGGGTAATTAAGTAAA
1 AACTTAATTCAGGGTAATTAAGTAATTC----AGTAATCAACTTAATTCAGGGTAATTAAG----
* *
53229 TCG-GTAAGAAGTAACTTAATTCAGGGTAATTAAGTGAGTT-AGTAATAAGCAACTTAATTCAGG
58 -CGAGTCAGAAGTAACTTAATTCAGGG-AATTAAGT-AATTCAGTAAT---CAACTTAATTCAGG
*
53292 GTAATTAAGTGAGTTAGTAATAAGC
117 GTAATTAAGTGAGTCAGTAATAAGC
53317 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGCGAGTCAG
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGCGAGTCAG
*
53382 CAGTAACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGTGAG
66 AAGTAACTTAATTCAGGG-AATTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGTGAG
*
53447 TCAGTGATAAGC
130 TCAGTAATAAGC
* * *
53459 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTGAGTCAG
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGCGAGTCAG
* * * * *
53524 TAATAAGCAACTTAATTAAGGGAATTAAGTAATTCGGTAATTAACTTAATTCAGGGTAATTAGGT
66 ----AAGTAACTTAATTCAGGGAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGT
53589 GAGTCAGTAAT---C
127 GAGTCAGTAATAAGC
* *
53601 AACTTAATTCAGGGTAATTAAGTAATTCAGTAAGT-AACTTAATTCAGGGTAATTAAGTGAGTTA
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAA-TCAACTTAATTCAGGGTAATTAAGCGAGTCA
* * * * *
53665 -ATAATCAACTTAATTTAGGGAAGTTAAGTAGTTCAATAAGT-AACTTAATTCAGGGAAATTAAG
65 GA-AGT-AACTTAATTCAGGGAA-TTAAGTAATTCAGTAA-TCAACTTAATTCAGGGTAATTAAG
53728 T
126 T
53729 TTAGTAAGAA
Statistics
Matches: 374, Mismatches: 27, Indels: 35
0.86 0.06 0.08
Matches are distributed among these distances:
137 1 0.00
138 1 0.00
139 15 0.04
140 34 0.09
141 1 0.00
142 159 0.43
143 1 0.00
144 5 0.01
145 86 0.23
146 15 0.04
149 29 0.08
153 27 0.07
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (141 bp):
AACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGCGAGTCAG
AAGTAACTTAATTCAGGGAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGTGAGT
CAGTAATAAGC
Found at i:53429 original size:180 final size:176
Alignment explanation
Indices: 53150--53727 Score: 638
Period size: 180 Copynumber: 3.2 Consensus size: 176
53140 TTAATTCAGG
* * *
53150 GTAATTAAGTAATTAACTTAATTCAGGGTAATTAAGTAGTTCAATGAGTAATCAACTTAATTCAG
1 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGAAG-TC-A-GAG---T-AACTTAATTCAG
*
53215 GGTAATTAAGTAAATCGGTAAGAAGT-AACTTAATTCAGGGTAATTAAGTGAGTTAGTAATAAGC
59 GGTAATTAAGTAAATCAGT---AA-TCAACTTAATTCAGGGTAATTAAGTGAGTTAGT-ATAAGC
53279 AACTTAATTCAGGGTAATTAAGTGAGTTAGTAATAAGCAACTTAATTCAGGGTAATTAA
119 AACTTAATTCAGGGTAATTAAGTGAGTTAGTAATAA-CAACTTAATTCAGGGTAATTAA
*
53338 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGCGAGTCAGCAGTAACTTAATTCAGGGTAA
1 GTAATTCAGTAATCAACTTAATTCAGGGTAATTAAG-AAGTCAG-AGTAACTTAATTCAGGGTAA
* *
53403 TTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGTGAGTCAGTGATAAGCAACTTAATT
64 TTAAGTAAATCAGTAATCAACTTAATTCAGGGTAATTAAGTGAGTTAGT-ATAAGCAACTTAATT
*
53468 CAGGGTAATTAAGTGAGTCAGTAAT--CAACTTAATTCAGGGTAATTAA
128 CAGGGTAATTAAGTGAGTTAGTAATAACAACTTAATTCAGGGTAATTAA
* * * * * *
53515 GTGAGTCAGTAATAAGCAACTTAATTAAGGG-AATTAAGTAATTCGGTAATTAACTTAATTCAGG
1 GTAATTCAGTAAT---CAACTTAATTCAGGGTAATTAAG-AAGTCAG--AGTAACTTAATTCAGG
* * * * *
53579 GTAATTAGGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGT-AATTCAG--TAAGTAACTT
60 GTAATTAAGTAAATCAGTAATCAACTTAATTCAGGGTAATTAAGTGAGTT-AGTATAAGCAACTT
* *
53641 AATTCAGGGTAATTAAGTGAGTTAATAAT--CAACTTAATTTAGGG-AAGTTAA
124 AATTCAGGGTAATTAAGTGAGTTAGTAATAACAACTTAATTCAGGGTAA-TTAA
* * *
53692 GTAGTTCAATAAGT-AACTTAATTCAGGGAAATTAAG
1 GTAATTCAGTAA-TCAACTTAATTCAGGGTAATTAAG
53728 TTTAGTAAGA
Statistics
Matches: 348, Mismatches: 31, Indels: 35
0.84 0.07 0.08
Matches are distributed among these distances:
174 13 0.04
175 7 0.02
176 2 0.01
177 95 0.27
178 1 0.00
179 14 0.04
180 144 0.41
183 29 0.08
184 1 0.00
186 1 0.00
187 3 0.01
188 36 0.10
189 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.32
Consensus pattern (176 bp):
GTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGAAGTCAGAGTAACTTAATTCAGGGTAATT
AAGTAAATCAGTAATCAACTTAATTCAGGGTAATTAAGTGAGTTAGTATAAGCAACTTAATTCAG
GGTAATTAAGTGAGTTAGTAATAACAACTTAATTCAGGGTAATTAA
Found at i:56871 original size:21 final size:22
Alignment explanation
Indices: 56847--56888 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
56837 ATGCTGTTGC
56847 TGCAG-TGGTAGAATGTGCTGT
1 TGCAGTTGGTAGAATGTGCTGT
* *
56868 TGCAGTTTGTAGAGTGTGCTG
1 TGCAGTTGGTAGAATGTGCTG
56889 CAGTAGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.17, C:0.10, G:0.38, T:0.36
Consensus pattern (22 bp):
TGCAGTTGGTAGAATGTGCTGT
Found at i:57030 original size:1 final size:1
Alignment explanation
Indices: 57024--57055 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
57014 AGCGTGCAGG
57024 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
57056 GGTAAGAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:57761 original size:29 final size:29
Alignment explanation
Indices: 57728--57789 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
57718 AACGGAGTTT
* *
57728 CAAAATAAAAGTTCAAGTGG-CAAAATGTC
1 CAAAAAAAAAATTCAA-TGGACAAAATGTC
**
57757 CAAAAAAAAAATTGGATGGACAAAATGTC
1 CAAAAAAAAAATTCAATGGACAAAATGTC
57786 CAAA
1 CAAA
57790 TATTACAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (29 bp):
CAAAAAAAAAATTCAATGGACAAAATGTC
Found at i:60017 original size:7 final size:7
Alignment explanation
Indices: 60007--60035 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
59997 AGACCTTGGT
60007 ACTCTCA
1 ACTCTCA
60014 ACTCTCA
1 ACTCTCA
60021 ACTCTCA
1 ACTCTCA
60028 ACTCTCA
1 ACTCTCA
60035 A
1 A
60036 ACTTTCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.41, G:0.00, T:0.28
Consensus pattern (7 bp):
ACTCTCA
Found at i:62349 original size:22 final size:23
Alignment explanation
Indices: 62306--62350 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
62296 TAGCCTTATG
62306 AAAATGCTTGTAATATTGATAAAAA
1 AAAATGCTTGTAATA-T-ATAAAAA
62331 AAAATGCTTGTAATA-ATAAA
1 AAAATGCTTGTAATATATAAA
62351 GGTTTTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
25 15 0.75
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31
Consensus pattern (23 bp):
AAAATGCTTGTAATATATAAAAA
Found at i:67425 original size:3 final size:3
Alignment explanation
Indices: 67419--67450 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
67409 AAAATAGTTA
67419 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
67451 ATATATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:69027 original size:2 final size:2
Alignment explanation
Indices: 69020--69050 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
69010 TATGTTAGTA
69020 AT AT AT 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 AT AT AT A
69051 CTAGTTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69138 original size:22 final size:21
Alignment explanation
Indices: 69105--69148 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
69095 AAATAAAATA
69105 TTCTTATGAAATAATGATAAT
1 TTCTTATGAAATAATGATAAT
* *
69126 TTCTCTATTAAATTATGATAAT
1 TTCT-TATGAAATAATGATAAT
69148 T
1 T
69149 ACACTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (21 bp):
TTCTTATGAAATAATGATAAT
Found at i:69155 original size:22 final size:22
Alignment explanation
Indices: 69113--69156 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
69103 TATTCTTATG
* *
69113 AAATAATGATAATTTCTCTATT
1 AAATAATGATAATTACACTATT
*
69135 AAATTATGATAATTACACTATT
1 AAATAATGATAATTACACTATT
69157 TTTTATGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATAATGATAATTACACTATT
Found at i:69509 original size:23 final size:23
Alignment explanation
Indices: 69439--69560 Score: 99
Period size: 23 Copynumber: 5.4 Consensus size: 23
69429 TCACACTCTG
* *
69439 AAATTTTGAT-AAT-TACACTATG
1 AAATTTTGATAAATCT-CCCTATA
* * * *
69461 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTCCCTATA
*
69483 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTCCCTATA
*
69506 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTCCCTATA
* * *
69529 AAATTTTAATAAAT-TCCTTATG
1 AAATTTTGATAAATCTCCCTATA
*
69551 AAATCTTGAT
1 AAATTTTGAT
69561 GGGTACAAAT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
22 40 0.49
23 42 0.51
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAATCTCCCTATA
Found at i:69541 original size:46 final size:45
Alignment explanation
Indices: 69456--69542 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
69446 GATAATTACA
* * * *
69456 CTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAATCTTC
1 CTATAAAATTGTGATAACCTCCCTATAAAATTTTAATAAATCTTC
*
69501 CTATAAAATTTTGATAAACCTCCCTATAAAATTTTAATAAAT
1 CTATAAAATTGTGAT-AACCTCCCTATAAAATTTTAATAAAT
69543 TCCTTATGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 13 0.36
46 23 0.64
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (45 bp):
CTATAAAATTGTGATAACCTCCCTATAAAATTTTAATAAATCTTC
Found at i:69617 original size:22 final size:22
Alignment explanation
Indices: 69258--69769 Score: 228
Period size: 22 Copynumber: 23.6 Consensus size: 22
69248 TTAATCTTCT
* *
69258 TATGAAATTTAGTTAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
69279 TTAAGAAAATTTTGA-AGACCTCAA
1 -TATG-AAATTTTGATA-ACCTCAC
* *
69303 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCTCAC
* *
69325 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
69348 TATGAGATGTTGAT-ACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * **
69368 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCAC
* * *
69391 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
69412 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* *
69435 TCTGAAATTTTGATAA-TTACAC
1 TATGAAATTTTGATAACCT-CAC
* *
69457 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
*
69479 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCTCAC
* *
69502 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
* * **
69525 TATAAAATTTTAATAAATTC-C
1 TATGAAATTTTGATAACCTCAC
* ***
69546 TTATGAAATCTTGAT-GGGT-AC
1 -TATGAAATTTTGATAACCTCAC
*
69567 ----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** *
69585 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * *
69607 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
69629 TAAGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
*
69651 TATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* * *
69673 TGTGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
69695 TATGAAATTTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
*
69717 TATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
69738 -CTG-AATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
69757 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
69770 TACTCCATAA
Statistics
Matches: 368, Mismatches: 85, Indels: 76
0.70 0.16 0.14
Matches are distributed among these distances:
16 9 0.02
17 1 0.00
18 1 0.00
19 18 0.05
20 14 0.04
21 25 0.07
22 221 0.60
23 75 0.20
24 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:69775 original size:19 final size:20
Alignment explanation
Indices: 69719--69769 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
69709 AACCTTCATA
69719 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
69739 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
69758 TGAAATTTTGAT
1 TGAAATTTTGAT
69770 TACTCCATAA
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:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:69908 original size:22 final size:22
Alignment explanation
Indices: 69875--70191 Score: 191
Period size: 22 Copynumber: 14.3 Consensus size: 22
69865 AATCACATTT
*
69875 TGAAA-TTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
69896 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
69918 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
69940 TGAAATTCTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
69962 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
** *
69984 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
70006 TGAAATTTTGATAATCTTTCTA
1 TGAAATTTTGATAACCTCTCTA
70028 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * * *
70052 TAAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
70074 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* * **
70094 TCAAATTTTGGTATTC-CT-TA
1 TGAAATTTTGATAACCTCTCTA
*
70114 TGAAATTGAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* *
70142 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* * *
70164 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTCTA
70186 TGAAAT
1 TGAAAT
70192 ATTTAATGAA
Statistics
Matches: 222, Mismatches: 55, Indels: 37
0.71 0.18 0.12
Matches are distributed among these distances:
20 13 0.06
21 34 0.15
22 140 0.63
23 2 0.01
24 7 0.03
25 11 0.05
26 7 0.03
27 1 0.00
28 7 0.03
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:69969 original size:44 final size:43
Alignment explanation
Indices: 69850--70019 Score: 137
Period size: 44 Copynumber: 3.9 Consensus size: 43
69840 AGAAATACCA
* * * *
69850 CTATGGAATTTTTG-TAATCACATTTTGAAA-TTTGATAACCTCT
1 CTAT-GAAATTTTGATAA-CACATTATGAAATTTTGATAACCCCG
* * * * * * *
69893 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAA-CACATTATGAAATTTTGATAACCCCG
* * *
69937 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAA-CACATTATGAAATTTTGATAACCCCG
* *
69981 CTTTGAAATTTTGATAACAACACTATGAAATTTTGATAA
1 CTATGAAATTTTGATAAC-ACATTATGAAATTTTGATAA
70020 TCTTTCTATA
Statistics
Matches: 99, Mismatches: 25, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
42 8 0.08
43 15 0.15
44 76 0.77
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (43 bp):
CTATGAAATTTTGATAACACATTATGAAATTTTGATAACCCCG
Found at i:70398 original size:22 final size:22
Alignment explanation
Indices: 70373--70430 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
70363 TACACTTTGG
*
70373 AATTTTGATAACC-TCCTCATGA
1 AATTTTGATAACCAT-CTCATAA
* * *
70395 AATTGTAATAACCATCTTATAA
1 AATTTTGATAACCATCTCATAA
*
70417 AATTTAGATAACCA
1 AATTTTGATAACCA
70431 CATAGAGACA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (22 bp):
AATTTTGATAACCATCTCATAA
Found at i:70628 original size:19 final size:20
Alignment explanation
Indices: 70597--70634 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
70587 TATTGACATT
70597 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
70616 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
70635 AATAATAGTA
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:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:71988 original size:36 final size:36
Alignment explanation
Indices: 71941--72044 Score: 172
Period size: 36 Copynumber: 2.9 Consensus size: 36
71931 GTACTTTTAG
**
71941 ACAATTTAACCTAAATTGCATGAATTTCAATCTGAT
1 ACAATTTAACCTAAATTGCATGAATTTCAATCAAAT
*
71977 ACAATTTAACCTAAATTGCATTAATTTCAATCAAAT
1 ACAATTTAACCTAAATTGCATGAATTTCAATCAAAT
*
72013 ACAATTTAACCTAAATTACATGAATTTCAATC
1 ACAATTTAACCTAAATTGCATGAATTTCAATC
72045 GCGTGGTGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (36 bp):
ACAATTTAACCTAAATTGCATGAATTTCAATCAAAT
Found at i:75850 original size:15 final size:15
Alignment explanation
Indices: 75830--75860 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
75820 TAATTGTGTC
75830 TAATGTGTAAAAGTA
1 TAATGTGTAAAAGTA
*
75845 TAATGTGTGAAAGTA
1 TAATGTGTAAAAGTA
75860 T
1 T
75861 GTGATTTGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (15 bp):
TAATGTGTAAAAGTA
Done.