Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013088.1 Corchorus capsularis cultivar CVL-1 contig13109, 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: 64536
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:3788 original size:30 final size:29
Alignment explanation
Indices: 3752--3853 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 29
3742 CTGTGTTATA
*
3752 TGTGTTTGGGGACTTTATTATAGATGCCTC
1 TGTGTTTAGGGACTTTA-TATAGATGCCTC
*
3782 TGTGTTTAGGGACTTTAATATGGATGCC-C
1 TGTGTTTAGGGACTTT-ATATAGATGCCTC
* *
3811 TTGTGCTT-GAGGACTTTGATGTAGATGCCTC
1 -TGTGTTTAG-GGACTTT-ATATAGATGCCTC
3842 TGTGTTTAGGGA
1 TGTGTTTAGGGA
3854 TGAATACCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
29 2 0.03
30 55 0.92
31 3 0.05
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.40
Consensus pattern (29 bp):
TGTGTTTAGGGACTTTATATAGATGCCTC
Found at i:3877 original size:52 final size:53
Alignment explanation
Indices: 3808--3990 Score: 237
Period size: 53 Copynumber: 3.4 Consensus size: 53
3798 AATATGGATG
*
3808 CCCTTGTGCTTGAGGACTTTGATGTAGA-TGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGTTTGAGGACTTTGATGTAGAGTGCCTCTGTGTTTAGGGATGAATA
3860 CCCTTGTGTTTGAGGACTTTTGA-G-AGAGGTGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGTTTGAGGAC-TTTGATGTAGA-GTGCCTCTGTGTTTAGGGATGAATA
* * * *
3913 CCCTTGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGACTTATAAATG
1 CCCTTGTGTTTGAGGACTTTGATGTAG-AGTGCCTCTGTGTTTAGGG----ATGAATA
3971 CCCTTGTGTTTGAGGACTTT
1 CCCTTGTGTTTGAGGACTTT
3991 AGTTATTGGG
Statistics
Matches: 116, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
51 3 0.03
52 22 0.19
53 46 0.40
54 19 0.16
55 1 0.01
58 25 0.22
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (53 bp):
CCCTTGTGTTTGAGGACTTTGATGTAGAGTGCCTCTGTGTTTAGGGATGAATA
Found at i:6176 original size:21 final size:22
Alignment explanation
Indices: 6150--6198 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
6140 ATCTTGGAAA
* *
6150 ACTCAAATCTGATTTCTT-TAG
1 ACTCAAATCGGATGTCTTATAG
*
6171 ACTCAACTCGGATGTCTTATAG
1 ACTCAAATCGGATGTCTTATAG
6193 -CTCAAA
1 ACTCAAA
6199 GAGGAAGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (22 bp):
ACTCAAATCGGATGTCTTATAG
Found at i:11975 original size:30 final size:30
Alignment explanation
Indices: 11935--11993 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
11925 TGTCTTCAAG
11935 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCGCATCATTCCT
*
11965 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATCATTCC
11994 CTCCCCCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCT
Found at i:12414 original size:33 final size:33
Alignment explanation
Indices: 12372--12513 Score: 248
Period size: 33 Copynumber: 4.3 Consensus size: 33
12362 TTCTTTTCAC
* **
12372 CCAAAACAGAATTATTTTCAATATTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
12405 CCAAAACAGAAATATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
12438 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
12471 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
12504 CCAAAACAGA
1 CCAAAACAGA
12514 TTTGTTTTCA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 104 1.00
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:12541 original size:66 final size:66
Alignment explanation
Indices: 12372--12546 Score: 217
Period size: 66 Copynumber: 2.7 Consensus size: 66
12362 TTCTTTTCAC
* ** *
12372 CCAAAACAGAATTATTTTCAATATTATGATCAACCAAAACAGAAATATTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAGAAATATTTGCAATGCTATGATCA
12437 A
66 A
* * * *
12438 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAGAAATATTTGCAATGCTATGATCA
12503 A
66 A
* * * * *
12504 CCAAAACAGATTTGTTTTC-ATCACAATTAGCATCCAAAACAGA
1 CCAAAACAGAATTATTTGCAAT-ACAATGAGCAACCAAAACAGA
12547 TTTAGTATCA
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 2 0.02
66 94 0.98
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.27
Consensus pattern (66 bp):
CCAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAGAAATATTTGCAATGCTATGATCA
A
Found at i:12576 original size:33 final size:33
Alignment explanation
Indices: 12539--12643 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 33
12529 ATTAGCATCC
*
12539 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
12572 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
12605 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
12638 AAAACA
1 AAAACA
12644 CTCTCTTCAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 1 0.02
33 58 0.98
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:14040 original size:10 final size:9
Alignment explanation
Indices: 14021--14055 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
14011 TCTGGTCGAA
14021 ATTTTTTTT
1 ATTTTTTTT
14030 ATTTATTTTT
1 ATTT-TTTTT
14040 ATTTTTTTAT
1 ATTTTTTT-T
14050 ATTTTT
1 ATTTTT
14056 CGATATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:14156 original size:8 final size:8
Alignment explanation
Indices: 14128--14161 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
14118 GAATTGGCTA
14128 TGAATTTT
1 TGAATTTT
*
14136 TGAAGTTTC
1 TGAA-TTTT
14145 TGAATTTT
1 TGAATTTT
14153 TGAATTTT
1 TGAATTTT
14161 T
1 T
14162 CAAGAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:23142 original size:48 final size:48
Alignment explanation
Indices: 23086--23366 Score: 228
Period size: 48 Copynumber: 5.7 Consensus size: 48
23076 TAAGAGAATG
* * * *
23086 GTGCCTTCCGTCCGGGAATGGCGTTTTAGGAAAAACAGGTAAAAATTA
1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAACAGGTAAAAATAA
* * *
23134 GTGCCTTCCATCCGGGAAGGGCATTTTGGGACAAAGCAGG-AAAAACAA
1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGA-AAAACAGGTAAAAATAA
* ** * * *
23182 GTGCCTTCCATCTAGGAAGGGCATTTTTGGAAAATAGCAAGT-TAAATAA
1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAA-A-CAGGTAAAAATAA
*
23231 GTGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAAA-ACGAGTAAAAATTAAATA
1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAACA-G-GTAAAAA-T--A-A
* ** ** **
23284 GCGCCTTCCGTCCGGGAAGGGTGTTTTGGG-AAAAGTGTGCGAAAATAA
1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAACAG-GTAAAAATAA
* * *
23332 GCGCCTTCTGTCCGGGAAGGGCATTTTTGGAAAAA
1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAA
23367 GTAAGCAAAA
Statistics
Matches: 189, Mismatches: 31, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
46 1 0.01
47 3 0.02
48 91 0.48
49 54 0.29
50 1 0.01
51 1 0.01
52 11 0.06
53 27 0.14
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (48 bp):
GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAACAGGTAAAAATAA
Found at i:23236 original size:49 final size:48
Alignment explanation
Indices: 23086--23400 Score: 226
Period size: 48 Copynumber: 6.4 Consensus size: 48
23076 TAAGAGAATG
* * * * * *
23086 GTGCCTTCCGTCCGGGAATGGCGTTTTAGGAAAAA-CAGGTAAAAATTA
1 GTGCCTTCCATCCGGGAAGGGCATTTTTGGAAAAAGCAAG-AAAAATAA
* * * *
23134 GTGCCTTCCATCCGGGAAGGGCATTTTGGGACAAAGCAGGAAAAACAA
1 GTGCCTTCCATCCGGGAAGGGCATTTTTGGAAAAAGCAAGAAAAATAA
** **
23182 GTGCCTTCCATCTAGGAAGGGCATTTTTGGAAAATAGCAAGTTAAATAA
1 GTGCCTTCCATCCGGGAAGGGCATTTTTGGAAAA-AGCAAGAAAAATAA
* * *
23231 GTGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAAAACGAGTAAAAATTAAATA
1 GTGCCTTCCATCCGGGAAGGGCATTTTTGGAAAAAGCAAG-AAAAA-T--A-A
* * * *** *
23284 GCGCCTTCCGTCCGGGAAGGG--TGTTTTGGGAAAAGTGTGCGAAAATAA
1 GTGCCTTCCATCCGGGAAGGGCAT-TTTTGGAAAAAGCAAG-AAAAATAA
* ** *
23332 GCGCCTTCTGTCCGGGAAGGGCATTTTTGGAAAAAGTAAGCAAAAACTAA
1 GTGCCTTCCATCCGGGAAGGGCATTTTTGGAAAAAGCAAG-AAAAA-TAA
*
23382 CGT--CTTCCATCTGGGAAGG
1 -GTGCCTTCCATCCGGGAAGG
23401 ACCTTCTGGG
Statistics
Matches: 217, Mismatches: 38, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
48 91 0.42
49 80 0.37
50 5 0.02
51 3 0.01
52 17 0.08
53 21 0.10
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.23
Consensus pattern (48 bp):
GTGCCTTCCATCCGGGAAGGGCATTTTTGGAAAAAGCAAGAAAAATAA
Found at i:23316 original size:53 final size:53
Alignment explanation
Indices: 23136--23466 Score: 205
Period size: 49 Copynumber: 6.6 Consensus size: 53
23126 AAAAATTAGT
* * * * *
23136 GCCTTCCATCCGGGAAGGGCATTTTGGGACAAAGC-AG-GAAAA--ACA-AGT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCGAGCAAAAATTAAATAGC
* ** * * * *
23184 GCCTTCCATCTAGGAAGGGCATTTTTGG-AAAA--TAGC--AAGTTAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCGAGCAAAAATTAAAT-AGC
* * *
23233 GCCTTCCGTCCGGGAAGGGCATTTTTGGAAAAAACGAGTAAAAATTAAATAGC
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCGAGCAAAAATTAAATAGC
** * * *
23286 GCCTTCCGTCCGGGAAGGGTGTTTTGGG-AAAAGTGTGCGAAAA-T--A-AGC
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCGAGCAAAAATTAAATAGC
* * ** *
23334 GCCTTCTGTCCGGGAAGGGCATTTTTGGAAAAAGTAAGCAAAAACT--A-A-C
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCGAGCAAAAATTAAATAGC
* * * * * * * *
23383 GTCTTCCATCTGGGAAGGACCTTCTGGGAAAAAGCGAGTAATAATTAAATAGC
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCGAGCAAAAATTAAATAGC
**
23436 GCCTTCCGTCCGGGAAGGGTGTTTTGGGAAA
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAA
23467 TAGCAAGTAA
Statistics
Matches: 218, Mismatches: 48, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
45 2 0.01
46 2 0.01
47 5 0.02
48 52 0.24
49 75 0.34
50 7 0.03
51 2 0.01
52 13 0.06
53 52 0.24
54 8 0.04
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (53 bp):
GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCGAGCAAAAATTAAATAGC
Found at i:23339 original size:150 final size:151
Alignment explanation
Indices: 23086--23480 Score: 400
Period size: 150 Copynumber: 2.6 Consensus size: 151
23076 TAAGAGAATG
* * * *
23086 GTGCCTTCCGTCCGGGAATGGCGTTTTAGG-AAAAAC-AGGTAAAAA-T---TAGTGCCTTCCAT
1 GTGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAAACGA-GTAAAAATTAAATAGCGCCTTCCGT
** * *
23145 CCGGGAAGGGCATTTTGGGACAAAGCAGGAAAAACAAGTGCCTTCCATCTAGGAAGGGCATTTTT
65 CCGGGAAGGGTGTTTTGGGA-AAAGCAGGAAAAACAAGCGCCTTCCATCCAGGAAGGGCATTTTT
**
23210 GGAAAATAGCAAG-TTAAA-TAA-
129 GGAAAA-AGCAAGCAAAAACTAAC
*
23231 GTGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAAAACGAGTAAAAATTAAATAGCGCCTTCCGTC
1 GTGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAAACGAGTAAAAATTAAATAGCGCCTTCCGTC
* * * ** *
23296 CGGGAAGGGTGTTTTGGGAAAAG-TGTGCGAAAATAAGCGCCTTCTGTCCGGGAAGGGCATTTTT
66 CGGGAAGGGTGTTTTGGGAAAAGCAG-G-AAAAACAAGCGCCTTCCATCCAGGAAGGGCATTTTT
*
23360 GGAAAAAGTAAGCAAAAACTAAC
129 GGAAAAAGCAAGCAAAAACTAAC
* * * * * * * *
23383 GT--CTTCCATCTGGGAAGGACCTTCTGGGAAAAAGCGAGTAATAATTAAATAGCGCCTTCCGTC
1 GTGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAAACGAGTAAAAATTAAATAGCGCCTTCCGTC
*
23446 CGGGAAGGGTGTTTTGGGAAATAGCAAGTAAAAAC
66 CGGGAAGGGTGTTTTGGGAAA-AGC-AGGAAAAAC
23481 TGAAAGTTAA
Statistics
Matches: 206, Mismatches: 30, Indels: 22
0.80 0.12 0.09
Matches are distributed among these distances:
145 27 0.13
146 13 0.06
147 2 0.01
148 1 0.00
149 10 0.05
150 141 0.68
151 9 0.04
152 2 0.01
153 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.23
Consensus pattern (151 bp):
GTGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAAACGAGTAAAAATTAAATAGCGCCTTCCGTC
CGGGAAGGGTGTTTTGGGAAAAGCAGGAAAAACAAGCGCCTTCCATCCAGGAAGGGCATTTTTGG
AAAAAGCAAGCAAAAACTAAC
Found at i:23476 original size:53 final size:52
Alignment explanation
Indices: 23326--23478 Score: 123
Period size: 53 Copynumber: 3.0 Consensus size: 52
23316 AAGTGTGCGA
* * * *
23326 AAATAAGCGCCTTCTGTCCGGGAAGGGCATTTTTGGAAAAAGTAAG-CAAA--
1 AAAT-AGCGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAATT
* * * * * * * * *
23376 AACTAACGTCTTCCATCTGGGAAGGACCTTCTGGGAAAAAGCGAGTAATAATT
1 AAATAGCGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAA-AATT
** *
23429 AAATAGCGCCTTCCGTCCGGGAAGGGTGTTTTGGGAAATAGCAAGTAAAA
1 AAATAGCGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAA
23479 ACTGAAAGTT
Statistics
Matches: 75, Mismatches: 24, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
49 30 0.40
50 4 0.05
51 2 0.03
52 2 0.03
53 37 0.49
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (52 bp):
AAATAGCGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAATT
Found at i:24845 original size:18 final size:18
Alignment explanation
Indices: 24804--24838 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24794 TAATCTAAAG
*
24804 CTTTTTCTTTTTTGTTTC
1 CTTTTTCTGTTTTGTTTC
*
24822 CGTTTTCTGTTTTGTTT
1 CTTTTTCTGTTTTGTTT
24839 TTTTTTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.74
Consensus pattern (18 bp):
CTTTTTCTGTTTTGTTTC
Found at i:30817 original size:7 final size:7
Alignment explanation
Indices: 30807--30834 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
30797 CAGAGGGGAG
30807 AGAAGAA
1 AGAAGAA
30814 AGAAGAA
1 AGAAGAA
30821 AGAAGAA
1 AGAAGAA
30828 AGAAGAA
1 AGAAGAA
30835 GCGACATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:31002 original size:24 final size:25
Alignment explanation
Indices: 30975--31029 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
30965 AAAATGTTGT
*
30975 AGCCAAGCAATTAAGAA-ATGCCGC
1 AGCCAAGCAATGAAGAATATGCCGC
* * **
30999 AGCCCAGTAATGAAGAATATGTGGC
1 AGCCAAGCAATGAAGAATATGCCGC
31024 AGCCAA
1 AGCCAA
31030 ATATCTATGC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.15
Consensus pattern (25 bp):
AGCCAAGCAATGAAGAATATGCCGC
Found at i:31162 original size:27 final size:27
Alignment explanation
Indices: 31124--31254 Score: 127
Period size: 27 Copynumber: 5.1 Consensus size: 27
31114 CCGAGTAAGA
31124 TGCCGCATCAACCCAAAATTGCAAAGT
1 TGCCGCATCAACCCAAAATTGCAAAGT
*
31151 TGCCGCAGCAACCCAAAATTGCCATAA-T
1 TGCCGCATCAACCCAAAATTG-CA-AAGT
* * * * *
31179 TG-C-CA-C-A-GC--TAGT-CGAAGA
1 TGCCGCATCAACCCAAAATTGCAAAGT
31198 TGCCGCATCAACCCAAAATTGCAAAGT
1 TGCCGCATCAACCCAAAATTGCAAAGT
31225 TGCCGCATCAACCCAAAATTGCAAAGT
1 TGCCGCATCAACCCAAAATTGCAAAGT
31252 TGC
1 TGC
31255 TACAACTAGC
Statistics
Matches: 82, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
18 2 0.02
19 3 0.04
20 1 0.01
21 4 0.05
22 1 0.01
23 2 0.02
24 2 0.02
25 1 0.01
26 4 0.05
27 55 0.67
28 5 0.06
29 2 0.02
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (27 bp):
TGCCGCATCAACCCAAAATTGCAAAGT
Found at i:31267 original size:27 final size:27
Alignment explanation
Indices: 31206--31276 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
31196 GATGCCGCAT
* *
31206 CAACCCAAAATTGCAAAGTTGCCGCAT
1 CAACCCAAAATTGCAAAGTTGCCACAA
*
31233 CAACCCAAAATTGCAAAGTTGCTACAA
1 CAACCCAAAATTGCAAAGTTGCCACAA
* * *
31260 CTAGCCAAAATTACAAA
1 CAACCCAAAATTGCAAA
31277 AATCCCGCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.44, C:0.27, G:0.11, T:0.18
Consensus pattern (27 bp):
CAACCCAAAATTGCAAAGTTGCCACAA
Found at i:31287 original size:27 final size:27
Alignment explanation
Indices: 31257--31324 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
31247 AAAGTTGCTA
*
31257 CAACTAGCCAAAATTACAAAAATCCC-G
1 CAACAAGCCAAAATTACAAAAA-CCCTG
* * *
31284 CAACCAGCCAAAATTGCAAGAACCCTG
1 CAACAAGCCAAAATTACAAAAACCCTG
*
31311 CAACAAGACAAAAT
1 CAACAAGCCAAAAT
31325 CGCCAAGGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.49, C:0.29, G:0.10, T:0.12
Consensus pattern (27 bp):
CAACAAGCCAAAATTACAAAAACCCTG
Found at i:38809 original size:33 final size:33
Alignment explanation
Indices: 38769--38850 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
38759 GGCATGGGTG
* *
38769 GCACGGCAGTGGCCTGCAATGGCCGGGTAGGTA
1 GCACGGCAGAGGCCTGCAATGGCCGGGCAGGTA
* * * * *
38802 GCGCGGCAGAGGACTGGAATGGCTGGGCAGGTG
1 GCACGGCAGAGGCCTGCAATGGCCGGGCAGGTA
38835 GCACGGCAGAGGCCTG
1 GCACGGCAGAGGCCTG
38851 GCTCGGTGCA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.18, C:0.23, G:0.46, T:0.12
Consensus pattern (33 bp):
GCACGGCAGAGGCCTGCAATGGCCGGGCAGGTA
Found at i:48256 original size:6 final size:6
Alignment explanation
Indices: 48245--48283 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
48235 ATTAATCTGC
48245 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
48284 GCTTTGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (6 bp):
TTTAGA
Found at i:59062 original size:21 final size:21
Alignment explanation
Indices: 59038--59086 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
59028 CAGCTGGGGG
* * *
59038 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
59059 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
59080 CCCATGT
1 CCCATGT
59087 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:61679 original size:33 final size:34
Alignment explanation
Indices: 61618--61695 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
61608 ATGCTGGATT
* * *
61618 TTGAGTTTTGAACATGAGATGCAGATTTTGAACA
1 TTGAATTTTGAACATGAAATGCAAATTTTGAACA
**
61652 TTGAATTTTGAA-ATGAAATGCAAATTTTGAATT
1 TTGAATTTTGAACATGAAATGCAAATTTTGAACA
61685 TTGAATTTTGA
1 TTGAATTTTGA
61696 TTTTCGAAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 28 0.72
34 11 0.28
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (34 bp):
TTGAATTTTGAACATGAAATGCAAATTTTGAACA
Found at i:61938 original size:28 final size:29
Alignment explanation
Indices: 61896--61953 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
61886 TTTTGAAGAA
*
61896 TGAACCATGTAATGCAGGTTTTG-AATTT
1 TGAACCATGTAATGCAGATTTTGAAATTT
*
61924 TGAACCATG-AGATGCTGATTTTGAAATTT
1 TGAACCATGTA-ATGCAGATTTTGAAATTT
61953 T
1 T
61954 ATTTTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 1 0.04
28 19 0.73
29 6 0.23
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (29 bp):
TGAACCATGTAATGCAGATTTTGAAATTT
Found at i:61990 original size:28 final size:28
Alignment explanation
Indices: 61947--62017 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
61937 GCTGATTTTG
*
61947 AAATTTT-ATTTTTGAATAATGAAATGC
1 AAATTTTGAATTTTGAATAATGAAATGC
61974 AAATTTTGAATTTTGAATAATGAAATGC
1 AAATTTTGAATTTTGAATAATGAAATGC
* *
62002 AAACTTTGAACTTTGA
1 AAATTTTGAATTTTGA
62018 TTTTCGAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.41
Consensus pattern (28 bp):
AAATTTTGAATTTTGAATAATGAAATGC
Found at i:62105 original size:28 final size:28
Alignment explanation
Indices: 62074--62132 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
62064 TTTTGAAGAA
* *
62074 TGAACCATGAAATGCAGGTTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAACTT
* *
62102 TGAACCATGAGATGCTGATTTTGAACTT
1 TGAACCATGAAATGCAGATTTTGAACTT
62130 TGA
1 TGA
62133 TTTTTGAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (28 bp):
TGAACCATGAAATGCAGATTTTGAACTT
Found at i:62132 original size:35 final size:35
Alignment explanation
Indices: 62093--62171 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
62083 AAATGCAGGT
* *
62093 TTTGAATTTTGAACCATGAGATGCTG-ATTTTGAAC
1 TTTGAATTTTGAACAATGAAATGC-GAATTTTGAAC
* *
62128 TTTGATTTTTGAATAATGAAATGCGAATTTTGAAC
1 TTTGAATTTTGAACAATGAAATGCGAATTTTGAAC
62163 TTT-AATTTT
1 TTTGAATTTT
62172 CAAAGAATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
34 6 0.16
35 32 0.84
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (35 bp):
TTTGAATTTTGAACAATGAAATGCGAATTTTGAAC
Found at i:62185 original size:150 final size:149
Alignment explanation
Indices: 61978--62254 Score: 405
Period size: 150 Copynumber: 1.8 Consensus size: 149
61968 AAATGCAAAT
* * * * *
61978 TTTGAATTTTGAATAATGAAATGCAAACTTTGAACTTTGATTTTCGAAGGATAGAATGTTGATAT
1 TTTGAATTTTGAATAATGAAATGCAAACTTTGAACTTTAATTTTCAAAGAATAGAATGCTGAAAT
* *
62043 GCAAGTTTTGAATTTTGATTTTTTTGAAGAAT-GAA-CCATGAAATGCAGGTTTTGAATTTTGAA
66 GCAAGTTTTGAATTTTGA--CTTTTGAAGAATAGAATCC-TGAAATGCAAGTTTTGAATTTTGAA
62106 CCATGAGATGCTGATTTTGAAC
128 CCATGAGATGCTGATTTTGAAC
* * *
62128 TTTGATTTTTGAATAATGAAATGCGAATTTTGAACTTTAATTTTCAAAGAATAGAATGCTGAAAT
1 TTTGAATTTTGAATAATGAAATGCAAACTTTGAACTTTAATTTTCAAAGAATAGAATGCTGAAAT
*
62193 GCAAGTTTTGAATTTTGACTTTTGAAGAATGAGAATGCTGAAATGCAAGTTTTGAATTTTGA
66 GCAAGTTTTGAATTTTGACTTTTGAAGAAT-AGAATCCTGAAATGCAAGTTTTGAATTTTGA
62255 CTTTTGAAGA
Statistics
Matches: 113, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
148 11 0.10
150 101 0.89
151 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.39
Consensus pattern (149 bp):
TTTGAATTTTGAATAATGAAATGCAAACTTTGAACTTTAATTTTCAAAGAATAGAATGCTGAAAT
GCAAGTTTTGAATTTTGACTTTTGAAGAATAGAATCCTGAAATGCAAGTTTTGAATTTTGAACCA
TGAGATGCTGATTTTGAAC
Found at i:62237 original size:44 final size:44
Alignment explanation
Indices: 62144--62296 Score: 192
Period size: 44 Copynumber: 3.5 Consensus size: 44
62134 TTTTGAATAA
* * *
62144 TGAAATGCGAA-TTTTGAACTTT-AATTTTCAAAGAAT-AGAATGC
1 TGAAATGC-AAGTTTTGAATTTTGACTTTT-GAAGAATGAGAATGC
62187 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAGAATGC
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAGAATGC
*
62231 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATG-G-A-CC
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAGAATGC
*
62272 ATGAAATGCAGGTTTTGAATTTTGA
1 -TGAAATGCAAGTTTTGAATTTTGA
62297 ACCATGAGAT
Statistics
Matches: 101, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
41 1 0.01
42 26 0.26
43 25 0.25
44 49 0.49
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (44 bp):
TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAGAATGC
Found at i:62275 original size:192 final size:192
Alignment explanation
Indices: 61994--62444 Score: 703
Period size: 192 Copynumber: 2.3 Consensus size: 192
61984 TTTTGAATAA
** * * *
61994 TGAAATGCAAACTTTGAACTTTGA-TTTTCGAAGGAT-AGAATGTTGATATGCAAGTTTTGAATT
1 TGAAATGCAAGTTTTGAATTTTGACTTTT-GAAGAATGAGAATG-TGAAATGCAAGTTTTGAATT
*
62057 TTGATTTTTTTGAAGAATGAACCATGAAATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATT
64 TTGA-TCTTTTGAAGAATGAACCATGAAATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATT
*
62122 TTGAACTTTGATTTTTGAATAATGAAATGCGAATTTTGAACTTTAATTTTCAAAGAATAGAATGC
128 TTGAACTTTGATTTTTGAATAATGAAATGCAAATTTTGAACTTTAATTTTCAAAGAATAGAATGC
62187 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAGAATGCTGAAATGCAAGTTTTGAATTT
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAGAATG-TGAAATGCAAGTTTTGAATTT
*
62252 TGA-CTTTTGAAGAATGGACCATGAAATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATTTT
65 TGATCTTTTGAAGAATGAACCATGAAATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATTTT
* * * *
62316 GAAGTTTGATTTTTGAATAATGAAATGCAAATTTTGAACTTTGATTTTCGAAGGATAGAATGC
130 GAACTTTGATTTTTGAATAATGAAATGCAAATTTTGAACTTTAATTTTCAAAGAATAGAATGC
** *
62379 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGA-ACCGTGAAATGCAGGTTTTGAATTTT
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAGAATGTGAAATGCAAGTTTTGAATTTT
62443 GA
66 GA
62445 ACCATGAGAT
Statistics
Matches: 240, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
190 23 0.10
191 2 0.01
192 155 0.65
193 27 0.11
194 33 0.14
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (192 bp):
TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAGAATGTGAAATGCAAGTTTTGAATTTT
GATCTTTTGAAGAATGAACCATGAAATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATTTTG
AACTTTGATTTTTGAATAATGAAATGCAAATTTTGAACTTTAATTTTCAAAGAATAGAATGC
Found at i:62288 original size:150 final size:146
Alignment explanation
Indices: 61984--62439 Score: 400
Period size: 150 Copynumber: 3.1 Consensus size: 146
61974 AAATTTTGAA
* * * *
61984 TTTTGAATAATGAAATGCAAACTTTGAACTTTGATTTTCGAAGGATAGAATGTTGATATGCAAGT
1 TTTTGAATAATGAAATGCGAATTTTGAACTTTGATTTTC-AAGAATAGAATG-TGAAATGCAAGT
* * **
62049 TTTGAATTTTGATTTTTTTGAAGAAT-GAA-CCATGAAATGCAGGTTTTGAATTTTGAAC-CATG
64 TTTGAATTTTGA---TTTTGAAGAATAGAATGC-TGAAATGCAAGTTTTGAATTTTG-ACTTTTG
*** * *
62111 -AG-ATGCTGATTTTGAACTTTG-A-T
124 AAGAATG--GACCATGAA--ATGCAGG
*
62134 TTTTGAATAATGAAATGCGAATTTTGAACTTTAATTTTCAAAGAATAGAATGCTGAAATGCAAGT
1 TTTTGAATAATGAAATGCGAATTTTGAACTTTGATTTTC-AAGAATAGAATG-TGAAATGCAAGT
62199 TTTGAATTTTGACTTTTGAAGAATGAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAG
64 TTTGAATTTTGA-TTTTGAAGAAT-AGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAG
62264 AATGGACCATGAAATGCAGG
127 AATGGACCATGAAATGCAGG
* * *
62284 TTTTGAATTTTGAACCATGAGATGCTG-ATTTTGAAGTTTGATTTT--TGAAT--AA--TGAAAT
1 TTTTGAA---T--A--ATGAAATGC-GAATTTTGAACTTTGATTTTCAAGAATAGAATGTGAAAT
* * *
62342 GCAAATTTTGAACTTTGATTTTCGAAGGATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTT
58 GCAAGTTTTGAATTTTGATTTT-GAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTT
* *
62407 TGAAGAATGAACCGTGAAATGCAGG
122 TGAAGAATGGACCATGAAATGCAGG
62432 TTTTGAAT
1 TTTTGAAT
62440 TTTGAACCAT
Statistics
Matches: 263, Mismatches: 26, Indels: 39
0.80 0.08 0.12
Matches are distributed among these distances:
145 1 0.00
148 82 0.31
149 31 0.12
150 110 0.42
151 3 0.01
152 5 0.02
153 1 0.00
154 4 0.02
155 1 0.00
157 24 0.09
158 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (146 bp):
TTTTGAATAATGAAATGCGAATTTTGAACTTTGATTTTCAAGAATAGAATGTGAAATGCAAGTTT
TGAATTTTGATTTTGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATG
GACCATGAAATGCAGG
Found at i:62300 original size:28 final size:28
Alignment explanation
Indices: 62269--62324 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
62259 TGAAGAATGG
* *
62269 ACCATGAAATGCAGGTTTTGAATTTTGA
1 ACCATGAAATGCAGATTTTGAAGTTTGA
* *
62297 ACCATGAGATGCTGATTTTGAAGTTTGA
1 ACCATGAAATGCAGATTTTGAAGTTTGA
62325 TTTTTGAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (28 bp):
ACCATGAAATGCAGATTTTGAAGTTTGA
Found at i:62324 original size:35 final size:35
Alignment explanation
Indices: 62285--62363 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 35
62275 AAATGCAGGT
* * ** *
62285 TTTGAATTTTGAACCATGAGATGCTGATTTTGAAG
1 TTTGAATTTTGAACAATGAAATGCAAATTTTGAAC
* *
62320 TTTGATTTTTGAATAATGAAATGCAAATTTTGAAC
1 TTTGAATTTTGAACAATGAAATGCAAATTTTGAAC
62355 TTTG-ATTTT
1 TTTGAATTTT
62364 CGAAGGATAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 4 0.11
35 32 0.89
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.46
Consensus pattern (35 bp):
TTTGAATTTTGAACAATGAAATGCAAATTTTGAAC
Found at i:62435 original size:42 final size:43
Alignment explanation
Indices: 62336--62444 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
62326 TTTTGAATAA
* * * *
62336 TGAAATGCAAATTTTGAACTTTGATTTTCGAAGGATAGAATGC
1 TGAAATGCAAGTTTTGAATTTTGATTTTCGAAGAATAGAACGC
62379 TGAAATGCAAGTTTTGAATTTTGACTTTT-GAAGAAT-GAAC-C
1 TGAAATGCAAGTTTTGAATTTTGA-TTTTCGAAGAATAGAACGC
*
62420 GTGAAATGCAGGTTTTGAATTTTGA
1 -TGAAATGCAAGTTTTGAATTTTGA
62445 ACCATGAGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.02
42 26 0.44
43 28 0.47
44 4 0.07
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (43 bp):
TGAAATGCAAGTTTTGAATTTTGATTTTCGAAGAATAGAACGC
Found at i:62445 original size:28 final size:28
Alignment explanation
Indices: 62414--62473 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
62404 TTTTGAAGAA
* *
62414 TGAACCGTGAAATGCAGGTTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAATTT
* *
62442 TGAACCATGAGATGCTGATTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAATTT
62470 TGAA
1 TGAA
62474 TTTTGAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (28 bp):
TGAACCATGAAATGCAGATTTTGAATTT
Found at i:62471 original size:7 final size:7
Alignment explanation
Indices: 62459--62522 Score: 128
Period size: 7 Copynumber: 9.1 Consensus size: 7
62449 TGAGATGCTG
62459 ATTTTGA
1 ATTTTGA
62466 ATTTTGA
1 ATTTTGA
62473 ATTTTGA
1 ATTTTGA
62480 ATTTTGA
1 ATTTTGA
62487 ATTTTGA
1 ATTTTGA
62494 ATTTTGA
1 ATTTTGA
62501 ATTTTGA
1 ATTTTGA
62508 ATTTTGA
1 ATTTTGA
62515 ATTTTGA
1 ATTTTGA
62522 A
1 A
62523 GACTTTTGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 57 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (7 bp):
ATTTTGA
Found at i:62507 original size:148 final size:148
Alignment explanation
Indices: 62187--62515 Score: 507
Period size: 148 Copynumber: 2.2 Consensus size: 148
62177 AATAGAATGC
*
62187 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAGAATGCTGAAATGCAAGTTTTGAATTT
1 TGAAATGCAAATTTTGAATTTTGA-TTTTGAAGAATGAGAATGCTGAAATGCAAGTTTTGAATTT
*
62252 TGACTTTTGAAGAATGGACCATGAAATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATTTTG
65 TGACTTTTGAAGAATGAACCATGAAATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATTTTG
*
62317 AAGTTTGATTTTTGAATAA
130 AAGTTTGAATTTTGAATAA
* *
62336 TGAAATGCAAATTTTGAACTTTGATTTTCGAAGGAT-AGAATGCTGAAATGCAAGTTTTGAATTT
1 TGAAATGCAAATTTTGAATTTTGATTTT-GAAGAATGAGAATGCTGAAATGCAAGTTTTGAATTT
*
62400 TGACTTTTGAAGAATGAACCGTGAAATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATTTTG
65 TGACTTTTGAAGAATGAACCATGAAATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATTTTG
* **
62465 AATTTTGAATTTTGAATTT
130 AAGTTTGAATTTTGAATAA
* ***
62484 TGAATTTTGAATTTTGAATTTTGAATTTTGAA
1 TGAAATGCAAATTTTGAATTTTG-ATTTTGAA
62516 TTTTGAAGAC
Statistics
Matches: 164, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
148 131 0.80
149 33 0.20
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (148 bp):
TGAAATGCAAATTTTGAATTTTGATTTTGAAGAATGAGAATGCTGAAATGCAAGTTTTGAATTTT
GACTTTTGAAGAATGAACCATGAAATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATTTTGA
AGTTTGAATTTTGAATAA
Found at i:62690 original size:37 final size:38
Alignment explanation
Indices: 62648--63123 Score: 392
Period size: 37 Copynumber: 12.8 Consensus size: 38
62638 TGGTTTTTGA
*
62648 ACACCTAAACAGGGAACATAAACAA-GATTTTGATGAG
1 ACACCTAAACAGGGAACTTAAACAAGGATTTTGATGAG
* *
62685 ACACCTAAACAGGG-ACTTTAAATAAGGA-TTTGATAAG
1 ACACCTAAACAGGGAAC-TTAAACAAGGATTTTGATGAG
* ** * * *
62722 AAACCTAAACAGACATCTTGAACAAGG--TTTGATGAC
1 ACACCTAAACAGGGAACTTAAACAAGGATTTTGATGAG
* * *
62758 ACACCTAAACAGGTACCTTAAACAAGGATTTTGATAAG
1 ACACCTAAACAGGGAACTTAAACAAGGATTTTGATGAG
* *
62796 AAACCTCAACA-GGAATCTTAAACAA-GATTTTGATGAG
1 ACACCTAAACAGGGAA-CTTAAACAAGGATTTTGATGAG
* * * *
62833 ACACATAAACAGGGACCTTAAACAAGGA-TTTCATAAG
1 ACACCTAAACAGGGAACTTAAACAAGGATTTTGATGAG
*
62870 AAACCTAAACA-GGAATCTTAAACAA-GATTTTGATGAG
1 ACACCTAAACAGGGAA-CTTAAACAAGGATTTTGATGAG
* * *
62907 ACACCTAAACAGGGACCTTAAACAAGGA-TTTAATAAG
1 ACACCTAAACAGGGAACTTAAACAAGGATTTTGATGAG
* * *
62944 AAACCTTAACA-TGAATCTTAAACAA-GATTTTGATGAG
1 ACACCTAAACAGGGAA-CTTAAACAAGGATTTTGATGAG
* * * *
62981 ACACCTAAACAGGGACCTTAAACAAGGA-TTTAATAAT
1 ACACCTAAACAGGGAACTTAAACAAGGATTTTGATGAG
* * * **
63018 AAACCTAAACA-GGAATTATAAACAGGGA-TTTGACAAG
1 ACACCTAAACAGGGAACT-TAAACAAGGATTTTGATGAG
* * * * * * *
63055 AAACCCAAACAGGGATCTTGAACAATGATTTTTATGAA
1 ACACCTAAACAGGGAACTTAAACAAGGATTTTGATGAG
* *
63093 ACACCTAAATA-GGAACCTTAAATAAGGATTT
1 ACACCTAAACAGGGAA-CTTAAACAAGGATTT
63124 GATAAGAGAC
Statistics
Matches: 344, Mismatches: 75, Indels: 39
0.75 0.16 0.09
Matches are distributed among these distances:
36 44 0.13
37 229 0.67
38 71 0.21
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (38 bp):
ACACCTAAACAGGGAACTTAAACAAGGATTTTGATGAG
Found at i:62728 original size:74 final size:74
Alignment explanation
Indices: 62650--63085 Score: 585
Period size: 74 Copynumber: 5.9 Consensus size: 74
62640 GTTTTTGAAC
* * *
62650 ACCTAAACAGGGAA-CATAAACAAGATTTTGATGAGACACCTAAACAGGGACTTTAAATAAGGAT
1 ACCTAAACA-GGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGAT
*
62714 TTGATAAGAA
65 TTAATAAGAA
* * * *
62724 ACCTAAACA-GACATCTTGAACAAG-GTTTGATGACACACCTAAACAGGTACCTTAAACAAGGAT
1 ACCTAAACAGGA-ATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGA-
*
62787 TTTGATAAGAA
64 TTTAATAAGAA
* *
62798 ACCTCAACAGGAATCTTAAACAAGATTTTGATGAGACACATAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
*
62863 TCATAAGAA
66 TAATAAGAA
62872 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
62937 TAATAAGAA
66 TAATAAGAA
* *
62946 ACCTTAACATGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
*
63011 TAATAATAA
66 TAATAAGAA
* ** * * * * *
63020 ACCTAAACAGGAAT-TATAAACAGGGA-TTTGACAAGAAACCCAAACAGGGATCTTGAACAATGA
1 ACCTAAACAGGAATCT-TAAACA-AGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGA
63083 TTT
64 TTT
63086 TTATGAAACA
Statistics
Matches: 325, Mismatches: 30, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
72 2 0.01
73 35 0.11
74 250 0.77
75 38 0.12
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (74 bp):
ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
TAATAAGAA
Found at i:64057 original size:87 final size:87
Alignment explanation
Indices: 63911--64078 Score: 264
Period size: 87 Copynumber: 1.9 Consensus size: 87
63901 TAATTGATGC
* * * *
63911 CCCAAACCTTCTTCCAATTTGGTCATGTATTGATATTCCCAACTCAATTGATGTTTCTGGATCAG
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
63976 CTTCTCACCTCAAGAATTATTT
66 CTTCTCACCTCAAGAATTATTT
*
63998 CCCAAATCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
* * *
64063 TTTCTCATCTTAAGAA
66 CTTCTCACCTCAAGAA
64079 ACTTTCAAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (87 bp):
CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
CTTCTCACCTCAAGAATTATTT
Found at i:64225 original size:23 final size:23
Alignment explanation
Indices: 64199--64244 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
64189 CAATTTGAAC
*
64199 CTTTTGATTTTTCTTTCTTTTTT
1 CTTTTGACTTTTCTTTCTTTTTT
** *
64222 CTTTTTCCTTTTCTTTTTTTTTT
1 CTTTTGACTTTTCTTTCTTTTTT
64245 TGAAATTGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (23 bp):
CTTTTGACTTTTCTTTCTTTTTT
Done.