Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014911.1 Corchorus capsularis cultivar CVL-1 contig14932, 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: 76083
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:1617 original size:16 final size:16
Alignment explanation
Indices: 1578--1699 Score: 169
Period size: 16 Copynumber: 7.8 Consensus size: 16
1568 ATTGGGCGGG
*
1578 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGGGTATT
1593 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
1609 TTCGAGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
1625 TTCGGGTTCGAG-ATTT
1 TTCGGGTTCGGGTA-TT
*
1641 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTATT
1657 TTCGGGTTCGGGTA-T
1 TTCGGGTTCGGGTATT
*
1672 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTATT
1688 TTCGGGTTCGGG
1 TTCGGGTTCGGG
1700 CTAGGATCGG
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
15 29 0.31
16 66 0.69
ACGTcount: A:0.06, C:0.14, G:0.38, T:0.43
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:1618 original size:31 final size:32
Alignment explanation
Indices: 1578--1718 Score: 155
Period size: 31 Copynumber: 4.4 Consensus size: 32
1568 ATTGGGCGGG
*
1578 TTCGGGTTCGGG-TACTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTTATTTCGGGTTCGGGTATT
* *
1609 TTCGAGTTCGGG-TATTTTCGGGTTCGAG-ATTT
1 TTCGGGTTCGGGTTA-TTTCGGGTTCGGGTA-TT
*
1641 TTCGGGTTCGGGTTTTTTCGGGTTCGGGTA-T
1 TTCGGGTTCGGGTTATTTCGGGTTCGGGTATT
* **
1672 TTCGGGTTCGGGTTTTTTCGGGTTCGGGCTAGG
1 TTCGGGTTCGGGTTATTTCGGGTTCGGG-TATT
*
1705 ATCGGGTTCGGGTT
1 TTCGGGTTCGGGTT
1719 CGGGTTCACT
Statistics
Matches: 96, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
31 43 0.45
32 38 0.40
33 15 0.16
ACGTcount: A:0.06, C:0.14, G:0.38, T:0.41
Consensus pattern (32 bp):
TTCGGGTTCGGGTTATTTCGGGTTCGGGTATT
Found at i:1710 original size:48 final size:47
Alignment explanation
Indices: 1578--1717 Score: 174
Period size: 48 Copynumber: 2.9 Consensus size: 47
1568 ATTGGGCGGG
** *
1578 TTCGGGTTCGGGTACTTCGGGTTCGGGTATTTTCGAGTTCGGGTATT
1 TTCGGGTTCGGGTTTTTCGGGTTCGGGTATTTTCGGGTTCGGGTATT
* *
1625 TTCGGGTTCGAGATTTTTCGGGTTCGGGTTTTTTCGGGTTCGGGTA-T
1 TTCGGGTTCG-GGTTTTTCGGGTTCGGGTATTTTCGGGTTCGGGTATT
***
1672 TTCGGGTTCGGGTTTTTTCGGGTTCGGGCTAGGATCGGGTTCGGGT
1 TTCGGGTTCGGG-TTTTTCGGGTTCGGG-TATTTTCGGGTTCGGGT
1718 TCGGGTTCAC
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
46 1 0.01
47 36 0.45
48 43 0.54
ACGTcount: A:0.06, C:0.14, G:0.39, T:0.41
Consensus pattern (47 bp):
TTCGGGTTCGGGTTTTTCGGGTTCGGGTATTTTCGGGTTCGGGTATT
Found at i:2506 original size:16 final size:17
Alignment explanation
Indices: 2470--2524 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
2460 TATTTTGATC
* *
2470 TCGGGCTCGGGTCGTGT
1 TCGGGTTCGGGTCGGGT
2487 TCGGGTTCGGG-CGGGT
1 TCGGGTTCGGGTCGGGT
**
2503 TCGGGTT-GTCTCGGGT
1 TCGGGTTCGGGTCGGGT
2519 TCGGGT
1 TCGGGT
2525 ATTTTCGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 1 0.03
16 22 0.67
17 10 0.30
ACGTcount: A:0.00, C:0.20, G:0.49, T:0.31
Consensus pattern (17 bp):
TCGGGTTCGGGTCGGGT
Found at i:2532 original size:16 final size:16
Alignment explanation
Indices: 2498--2539 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
2488 CGGGTTCGGG
2498 CGGGTTCGGGTTGTCT
1 CGGGTTCGGGTTGTCT
*
2514 CGGGTTCGGGTAT-TTT
1 CGGGTTCGGGT-TGTCT
2530 CGGGTTCGGG
1 CGGGTTCGGG
2540 CGGGTTCGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.02, C:0.17, G:0.45, T:0.36
Consensus pattern (16 bp):
CGGGTTCGGGTTGTCT
Found at i:3279 original size:113 final size:114
Alignment explanation
Indices: 3147--3412 Score: 322
Period size: 114 Copynumber: 2.3 Consensus size: 114
3137 TTGGCCAAAG
* * *
3147 ACGCCGTTAAATGGTGGCGTCTGAAGTACGAGACGCCGCCATATTTAATCTTTTCGGAGAAATGT
1 ACGCCGCTAAATGGTGGCGTATGAAGTACGAGACGCCGCCATATTTAATCTTTTCGGAGAAATGC
*** * * * *
3212 AATTTGA-GTAAAAATGAAGCCTA-AAACATAGCGGCGTCTTGACCCTGA
66 AATGAAATCTAAAAATGAAGCCTAGAAA-ATAGCGGCCTCTTAACCCTAA
* * *
3260 ACGCCGCTAAATGGCGGCGTATGATA-TTCGAAACGCCGCCATATTTAATCTTTTCGGAGAAATG
1 ACGCCGCTAAATGGTGGCGTATGA-AGTACGAGACGCCGCCATATTTAATCTTTTCGGAGAAATG
3324 CAATGAAATCTAAAAATGAAGCCTAGAAAATAGCGGCCTCTTAACCCTAA
65 CAATGAAATCTAAAAATGAAGCCTAGAAAATAGCGGCCTCTTAACCCTAA
* * * * * *
3374 ACCCCGCTAAATAGTGGCGTTTGAGGTCCAAGACGCCGC
1 ACGCCGCTAAATGGTGGCGTATGAAGTACGAGACGCCGC
3413 TAAAAGGTGG
Statistics
Matches: 128, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
113 61 0.48
114 64 0.50
115 3 0.02
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (114 bp):
ACGCCGCTAAATGGTGGCGTATGAAGTACGAGACGCCGCCATATTTAATCTTTTCGGAGAAATGC
AATGAAATCTAAAAATGAAGCCTAGAAAATAGCGGCCTCTTAACCCTAA
Found at i:3414 original size:32 final size:31
Alignment explanation
Indices: 3372--3443 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
3362 TCTTAACCCT
* *
3372 AAACCCCGCTAAATA-GTGGCGTTTGAGGTCC
1 AAACGCCGCTAAA-AGGTGGCGTCTGAGGTCC
* *
3403 AAGACGCCGCTAAAAGGTGGCGTCTGATGTTC
1 AA-ACGCCGCTAAAAGGTGGCGTCTGAGGTCC
3435 AAACGCCGC
1 AAACGCCGC
3444 CATATTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
31 10 0.29
32 25 0.71
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (31 bp):
AAACGCCGCTAAAAGGTGGCGTCTGAGGTCC
Found at i:3526 original size:145 final size:145
Alignment explanation
Indices: 3260--3530 Score: 341
Period size: 145 Copynumber: 1.9 Consensus size: 145
3250 TTGACCCTGA
*
3260 ACGCCGCTAAATGGCGGCGTATGATATTCGAAACGCCGCCATATTTAATCTTTTCGGAGAAATGC
1 ACGCCGCTAAAAGGCGGCGTATGATATTCGAAACGCCGCCATATTTAATCTTTTCGGAGAAATGC
* * * *
3325 AATGAAATCTAAAAATGAAGCCTAGAAAATAGCGGCCTCTTAACCCTAAACCCCGCTAAATAGTG
66 AATG-AATCTAAAAATGAAGACTAAAAAATAACGGCCTCTTAACCCAAAACCCCGCTAAATAGTG
3390 GCGTTTGAGGTCCAAG
130 GCGTTTGAGGTCCAAG
* * * *
3406 ACGCCGCTAAAAGGTGGCGTCTGATGTTC-AAACGCCGCCATATTTAATTTTTTCGGAGAAATTG
1 ACGCCGCTAAAAGGCGGCGTATGATATTCGAAACGCCGCCATATTTAATCTTTTCGGAGAAA-T-
** * * * * *
3470 GCTTTTG-A-GTAAACATGAAGACTAAAAAATAACGGCGTCTTGACCCAAAACGCCGCTAAAT
64 GC-AATGAATCTAAAAATGAAGACTAAAAAATAACGGCCTCTTAACCCAAAACCCCGCTAAAT
3531 TAGAAAAATG
Statistics
Matches: 106, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
145 75 0.71
146 27 0.25
147 2 0.02
148 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (145 bp):
ACGCCGCTAAAAGGCGGCGTATGATATTCGAAACGCCGCCATATTTAATCTTTTCGGAGAAATGC
AATGAATCTAAAAATGAAGACTAAAAAATAACGGCCTCTTAACCCAAAACCCCGCTAAATAGTGG
CGTTTGAGGTCCAAG
Found at i:6245 original size:14 final size:14
Alignment explanation
Indices: 6226--6257 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
6216 TCTCACTTAG
6226 TTAATTAGTCATGT
1 TTAATTAGTCATGT
6240 TTAATTAGTCATGT
1 TTAATTAGTCATGT
6254 TTAA
1 TTAA
6258 AACCCTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (14 bp):
TTAATTAGTCATGT
Found at i:6738 original size:14 final size:15
Alignment explanation
Indices: 6696--6738 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
6686 TCTTTTTTTA
6696 CTGAAATTTTATAGTT
1 CTGAAATTTTATAG-T
6712 CTG-AATTTCTATA-T
1 CTGAAATTT-TATAGT
6726 CTGAAATTTTATA
1 CTGAAATTTTATA
6739 CTTGTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.32
15 10 0.40
16 7 0.28
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (15 bp):
CTGAAATTTTATAGT
Found at i:7239 original size:59 final size:60
Alignment explanation
Indices: 7147--7283 Score: 222
Period size: 59 Copynumber: 2.3 Consensus size: 60
7137 CGCCACTATA
* *
7147 TTTAAAAAAACCCTTACATATAGCGGCGTCTAAACGCCGCTACATTTAATTTGAGA-TTT
1 TTTAAAAAATCCCTTAAATATAGCGGCGTCTAAACGCCGCTACATTTAATTTGAGATTTT
* *
7206 TTTAAAAAATCCCTTAAATATAGCGGCGTCTAAACGCTGCTATATTTAATTTGAGATTTT
1 TTTAAAAAATCCCTTAAATATAGCGGCGTCTAAACGCCGCTACATTTAATTTGAGATTTT
7266 TTTAAGAAAATCCCTTAA
1 TTTAA-AAAATCCCTTAA
7284 TTGAGGTTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 52 0.72
60 8 0.11
61 12 0.17
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (60 bp):
TTTAAAAAATCCCTTAAATATAGCGGCGTCTAAACGCCGCTACATTTAATTTGAGATTTT
Found at i:7351 original size:56 final size:56
Alignment explanation
Indices: 7280--7396 Score: 209
Period size: 56 Copynumber: 2.1 Consensus size: 56
7270 AGAAAATCCC
7280 TTAA-TTGAGGTTTTTTTTAAACACTCTAAATAGCGGCGTCTAGACGCCGCTATAT
1 TTAATTTGAGGTTTTTTTTAAACACTCTAAATAGCGGCGTCTAGACGCCGCTATAT
*
7335 TTAATTTGAGGTTTTTTTTAAACACTCTAAATAGCGGCGTCTAGACGTCGCTATAT
1 TTAATTTGAGGTTTTTTTTAAACACTCTAAATAGCGGCGTCTAGACGCCGCTATAT
*
7391 ATAATT
1 TTAATT
7397 AAAAAAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 4 0.07
56 55 0.93
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (56 bp):
TTAATTTGAGGTTTTTTTTAAACACTCTAAATAGCGGCGTCTAGACGCCGCTATAT
Found at i:10325 original size:31 final size:32
Alignment explanation
Indices: 10287--10349 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
10277 GTCAGGTCGA
10287 GTTGAATTTGAGTCAGGTTAATTC-GGTTTGG
1 GTTGAATTTGAGTCAGGTTAATTCGGGTTTGG
*
10318 GTTGAATTTGGGTCAGGTTAATTCGGGTTTGG
1 GTTGAATTTGAGTCAGGTTAATTCGGGTTTGG
10350 TTTCAGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 23 0.77
32 7 0.23
ACGTcount: A:0.17, C:0.06, G:0.35, T:0.41
Consensus pattern (32 bp):
GTTGAATTTGAGTCAGGTTAATTCGGGTTTGG
Found at i:10336 original size:16 final size:15
Alignment explanation
Indices: 10298--10345 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
10288 TTGAATTTGA
10298 GTCAGGTTAATTCGG
1 GTCAGGTTAATTCGG
* ** *
10313 TTTGGGTTGAATTTGG
1 GTCAGGTT-AATTCGG
10329 GTCAGGTTAATTCGG
1 GTCAGGTTAATTCGG
10344 GT
1 GT
10346 TTGGTTTCAG
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.17, C:0.08, G:0.35, T:0.40
Consensus pattern (15 bp):
GTCAGGTTAATTCGG
Found at i:14507 original size:26 final size:26
Alignment explanation
Indices: 14458--14630 Score: 164
Period size: 26 Copynumber: 6.6 Consensus size: 26
14448 TAGTCAGTAA
*
14458 AAAAGAGTAAG-AAACAGT-ATTCAGT
1 AAAAGAGTAAGAAAAGAGTCA-TCAGT
*
14483 AAAAGAATAAGAAAAGAGTCATCAGT
1 AAAAGAGTAAGAAAAGAGTCATCAGT
*
14509 AAAAAGAGTAAGAAAAGAGCCATCAGT
1 -AAAAGAGTAAGAAAAGAGTCATCAGT
*
14536 AAAAAGAGTAAG-AAACAGT-ATTCAGT
1 -AAAAGAGTAAGAAAAGAGTCA-TCAGT
14562 AAGAAGAGT-AGAAAAGAGTCATCAGT
1 AA-AAGAGTAAGAAAAGAGTCATCAGT
*
14588 AAAAAGAGTAGGAAACA-A-T-ATTCAGT
1 -AAAAGAGTAAGAAA-AGAGTCA-TCAGT
14614 AAGAAGAGTAAGAAAAG
1 AA-AAGAGTAAGAAAAG
14631 CGCAATAGTA
Statistics
Matches: 126, Mismatches: 9, Indels: 25
0.79 0.06 0.16
Matches are distributed among these distances:
25 19 0.15
26 61 0.48
27 45 0.36
28 1 0.01
ACGTcount: A:0.55, C:0.08, G:0.22, T:0.16
Consensus pattern (26 bp):
AAAAGAGTAAGAAAAGAGTCATCAGT
Found at i:14515 original size:16 final size:16
Alignment explanation
Indices: 14494--14544 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
14484 AAAGAATAAG
14494 AAAAGAGTCATCAGTA
1 AAAAGAGTCATCAGTA
14510 AAAAGAGT-A--AG--
1 AAAAGAGTCATCAGTA
*
14521 AAAAGAGCCATCAGTA
1 AAAAGAGTCATCAGTA
14537 AAAAGAGT
1 AAAAGAGT
14545 AAGAAACAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
11 7 0.25
12 1 0.04
13 2 0.07
14 2 0.07
15 1 0.04
16 15 0.54
ACGTcount: A:0.55, C:0.10, G:0.22, T:0.14
Consensus pattern (16 bp):
AAAAGAGTCATCAGTA
Found at i:14555 original size:79 final size:80
Alignment explanation
Indices: 14451--14602 Score: 263
Period size: 79 Copynumber: 1.9 Consensus size: 80
14441 AAATTAGTAG
14451 TCAGTAAAAAAGAGTAAGAAACAGTATTCAGTAA-AAGAATAAGAAAAGAGTCATCAGTAAAAAG
1 TCAGTAAAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAAT-AGAAAAGAGTCATCAGTAAAAAG
14515 AGTAAGAAAAGAGCCA
65 AGTAAGAAAAGAGCCA
*
14531 TCAGT-AAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAGTAGAAAAGAGTCATCAGTAAAAAGA
1 TCAGTAAAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAATAGAAAAGAGTCATCAGTAAAAAGA
*
14595 GTAGGAAA
66 GTAAGAAA
14603 CAATATTCAG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
79 59 0.86
80 10 0.14
ACGTcount: A:0.55, C:0.08, G:0.22, T:0.16
Consensus pattern (80 bp):
TCAGTAAAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAATAGAAAAGAGTCATCAGTAAAAAGA
GTAAGAAAAGAGCCA
Found at i:14592 original size:52 final size:53
Alignment explanation
Indices: 14478--14630 Score: 213
Period size: 52 Copynumber: 2.9 Consensus size: 53
14468 GAAACAGTAT
* * *
14478 TCAGT-AAAAGAATAAGAAAAGAGTCA-TCAGTAAAAAGAGTAAGAAAAGAGCCA
1 TCAGTAAAAAGAGTAAG-AAACAGT-ATTCAGTAAGAAGAGTAAGAAAAGAGCCA
*
14531 TCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAGT-AGAAAAGAGTCA
1 TCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAGTAAGAAAAGAGCCA
* *
14583 TCAGTAAAAAGAGTAGGAAACAATATTCAGTAAGAAGAGTAAGAAAAG
1 TCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAGTAAGAAAAG
14631 CGCAATAGTA
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
52 50 0.55
53 31 0.34
54 10 0.11
ACGTcount: A:0.54, C:0.08, G:0.22, T:0.16
Consensus pattern (53 bp):
TCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAGTAAGAAAAGAGCCA
Found at i:14761 original size:14 final size:14
Alignment explanation
Indices: 14744--14812 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 14
14734 AATGGTAATT
14744 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAG
**
14758 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAG
**
14772 AAAAAAATAGTAAAG
1 AGTAAAA-AGTAAAG
**
14787 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAG
14801 AGTAAAAAGTAA
1 AGTAAAAAGTAA
14813 TCAGTAAAGA
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
14 32 0.76
15 10 0.24
ACGTcount: A:0.61, C:0.03, G:0.19, T:0.17
Consensus pattern (14 bp):
AGTAAAAAGTAAAG
Found at i:14779 original size:43 final size:43
Alignment explanation
Indices: 14708--14805 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
14698 AAAGGCAATC
* * **
14708 AGTAAAGAG-AGATCAGTAAAAAGTAAAATGGTAATTAGTAAAA
1 AGTAAAGAGTA-ATCAGTAAAAAGAAAAATAGTAAAGAGTAAAA
**
14751 AGTAAAGAGTAATCAGTAAAGAA-AAAAATAGTAAAGAGTAATC
1 AGTAAAGAGTAATCAGTAAA-AAGAAAAATAGTAAAGAGTAAAA
14794 AGTAAAGAGTAA
1 AGTAAAGAGTAA
14806 AAAGTAATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 44 0.94
44 3 0.06
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.19
Consensus pattern (43 bp):
AGTAAAGAGTAATCAGTAAAAAGAAAAATAGTAAAGAGTAAAA
Found at i:14783 original size:29 final size:28
Alignment explanation
Indices: 14747--14812 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 28
14737 GGTAATTAGT
14747 AAAAAGTAAAGAGTAATCAGTAAAGAAA
1 AAAAAGTAAAGAGTAATCAGTAAAGAAA
**
14775 AAAATAGTAAAGAGTAATCAGTAAAGAGT
1 AAAA-AGTAAAGAGTAATCAGTAAAGAAA
14804 AAAAAGTAA
1 AAAAAGTAA
14813 TCAGTAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 9 0.26
29 26 0.74
ACGTcount: A:0.62, C:0.03, G:0.18, T:0.17
Consensus pattern (28 bp):
AAAAAGTAAAGAGTAATCAGTAAAGAAA
Found at i:14806 original size:21 final size:21
Alignment explanation
Indices: 14780--14822 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
14770 AGAAAAAAAT
*
14780 AGTAAAGAGTAATCAGTAAAG
1 AGTAAAAAGTAATCAGTAAAG
14801 AGTAAAAAGTAATCAGTAAAG
1 AGTAAAAAGTAATCAGTAAAG
14822 A
1 A
14823 AAAAATAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.19
Consensus pattern (21 bp):
AGTAAAAAGTAATCAGTAAAG
Found at i:14832 original size:21 final size:21
Alignment explanation
Indices: 14787--14906 Score: 84
Period size: 21 Copynumber: 5.6 Consensus size: 21
14777 AATAGTAAAG
*
14787 AGTAATCAGTAAAGAGTAAAA-
1 AGTAATCAGTAAAGA-AAAAAT
14808 AGTAATCAGTAAAGAAAAAAT
1 AGTAATCAGTAAAGAAAAAAT
** * *
14829 AGTAAGGAGT-GAGAAGAAAT
1 AGTAATCAGTAAAGAAAAAAT
* * *
14849 CAGTAAAAT-GGTAAAGGAAAAAG
1 -AGT--AATCAGTAAAGAAAAAAT
* *
14872 AGTAATCAGTAAAGAGTAAGAT
1 AGTAATCAGTAAAGA-AAAAAT
14894 AGTAATCAGTAAA
1 AGTAATCAGTAAA
14907 TCAGTAATTA
Statistics
Matches: 76, Mismatches: 16, Indels: 13
0.72 0.15 0.12
Matches are distributed among these distances:
20 15 0.20
21 32 0.42
22 21 0.28
23 8 0.11
ACGTcount: A:0.55, C:0.04, G:0.23, T:0.18
Consensus pattern (21 bp):
AGTAATCAGTAAAGAAAAAAT
Found at i:14961 original size:55 final size:55
Alignment explanation
Indices: 14892--15140 Score: 332
Period size: 47 Copynumber: 4.8 Consensus size: 55
14882 AAAGAGTAAG
*
14892 ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCAAGGTA
1 ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTA
14947 ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA-G--
1 ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTA
14999 ---GTAAT-AGT-AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTA
1 ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTA
*
15049 AT-G------GT-AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGAA
1 ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTA
* * * *
15096 ATAGTAATCAGTAAATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAG
15141 TAAATTGATA
Statistics
Matches: 175, Mismatches: 6, Indels: 26
0.85 0.03 0.13
Matches are distributed among these distances:
47 83 0.47
48 5 0.03
49 5 0.03
52 1 0.01
54 3 0.02
55 78 0.45
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.25
Consensus pattern (55 bp):
ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTA
Found at i:15113 original size:102 final size:102
Alignment explanation
Indices: 14884--15140 Score: 334
Period size: 102 Copynumber: 2.5 Consensus size: 102
14874 TAATCAGTAA
14884 AGAGT-AAGATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCAAGGTAA
1 AGAGTCAAGATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCAAGGTAA
14948 TAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
66 TAG-----AGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
*
14990 AGAGTCAAG---GTAAT-AGT-AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAA
1 AGAGTCAAGATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCAAGGTAA
15050 T-G-GT-AATCAGTAATTAAGTAAAAAGAGATTAATC
66 TAGAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
* * * *
15084 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 AGAGTCAA-G--ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAG
15141 TAAATTGATA
Statistics
Matches: 137, Mismatches: 5, Indels: 22
0.84 0.03 0.13
Matches are distributed among these distances:
94 38 0.28
95 3 0.02
100 5 0.04
101 4 0.03
102 71 0.52
103 3 0.02
104 5 0.04
106 5 0.04
107 3 0.02
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (102 bp):
AGAGTCAAGATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCAAGGTAA
TAGAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
Found at i:15118 original size:15 final size:15
Alignment explanation
Indices: 15094--15126 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
15084 AGAGTCAAGG
15094 AAATAGTAATCA-GT
1 AAATAGTAATCAGGT
15108 AAATCAGTAATCAGGT
1 AAAT-AGTAATCAGGT
15124 AAA
1 AAA
15127 AAGATAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 8 0.47
16 5 0.29
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (15 bp):
AAATAGTAATCAGGT
Found at i:15171 original size:71 final size:71
Alignment explanation
Indices: 15095--15228 Score: 225
Period size: 71 Copynumber: 1.9 Consensus size: 71
15085 GAGTCAAGGA
* *
15095 AATAGTAATCAGTAAA-TCAGTAATCAGGTAAAAAGATAGTAATCAGTAAATTGATAATTAAGAG
1 AATAGTAATCAGTAAACT-AGTAATCAAGTAAAAAGATAGTAATCAGTAAATTGATAATAAAGAG
15159 TCCAGAT
65 TCCAGAT
*
15166 AATAGTAATCAGTAAACTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGATAATAAAGA
1 AATAGTAATCAGTAAACTAGTAATCAAGTAAAAAGATAGTAATCAGTAAATTGATAATAAAGA
15229 ATTAAAGTGA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 58 0.98
72 1 0.02
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.27
Consensus pattern (71 bp):
AATAGTAATCAGTAAACTAGTAATCAAGTAAAAAGATAGTAATCAGTAAATTGATAATAAAGAGT
CCAGAT
Found at i:15179 original size:37 final size:36
Alignment explanation
Indices: 15096--15228 Score: 127
Period size: 34 Copynumber: 3.8 Consensus size: 36
15086 AGTCAAGGAA
* *
15096 ATAGTAATCAGTAAA-TCAGTAA-TCAG-GTAAAAAG
1 ATAGTAATCAGTAAATTGA-TAATTAAGAGTAAAAAG
* *
15130 ATAGTAATCAGTAAATTGATAATTAAGAGTCCAGATA-
1 ATAGTAATCAGTAAATTGATAATTAAGAGT--AAAAAG
*
15167 ATAGTAATCAGTAAACT-AGTAATT-A-AGTAAAAAG
1 ATAGTAATCAGTAAATTGA-TAATTAAGAGTAAAAAG
*
15201 ATAGTAATCAGTAAATTGATAATAAAGA
1 ATAGTAATCAGTAAATTGATAATTAAGA
15229 ATTAAAGTGA
Statistics
Matches: 80, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
33 3 0.04
34 38 0.47
35 10 0.12
36 5 0.06
37 21 0.26
38 3 0.04
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (36 bp):
ATAGTAATCAGTAAATTGATAATTAAGAGTAAAAAG
Found at i:15616 original size:27 final size:25
Alignment explanation
Indices: 15542--15792 Score: 85
Period size: 27 Copynumber: 9.6 Consensus size: 25
15532 GCAAGTAAGA
* *
15542 TAAAAAAGAGTAAAAGAGAGTAATTAG
1 TAAAAAAGAGTAAAAGTG-GT-ATCAG
* *
15569 TAATAAAGAGTAAGAAATGGTGATCAG
1 TAAAAAAGAGTAA-AAGTGGT-ATCAG
15596 TAAAAAAGAGTGAAAAGTGGTATTCAG
1 TAAAAAAGAGT-AAAAGTGGTA-TCAG
* *
15623 T-AAAAAGGGATAAAA-----AT-GG
1 TAAAAAAGAG-TAAAAGTGGTATCAG
* * *
15642 TAAAAAAGTGTAAAAATGGTATTAAG
1 TAAAAAAGAGTAAAAGTGGTA-TCAG
* *
15668 TAAAAAGGGAGAGTAAAAAATGGTAATTAAG
1 TAAAAA---AGAGT-AAAAGTGGT-A-TCAG
15699 T-AAAAAGAGTAAAAAGTGGTATTCAG
1 TAAAAAAGAGT-AAAAGTGGTA-TCAG
*
15725 TAGAAGCAGAA-AG-AAAAGAGGTAATCAG
1 TA-AA--A-AAGAGTAAAAGTGGT-ATCAG
*
15753 TAAAAAAG-GTAAAATATGGTAATCAG
1 TAAAAAAGAGTAAAA-GTGGT-ATCAG
*
15779 T-ACAAAGAGTAAAA
1 TAAAAAAGAGTAAAA
15793 AATGGTAATT
Statistics
Matches: 179, Mismatches: 18, Indels: 55
0.71 0.07 0.22
Matches are distributed among these distances:
19 7 0.04
20 8 0.04
21 1 0.01
24 4 0.02
25 11 0.06
26 41 0.23
27 56 0.31
28 21 0.12
29 5 0.03
30 16 0.09
31 9 0.05
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.20
Consensus pattern (25 bp):
TAAAAAAGAGTAAAAGTGGTATCAG
Found at i:15646 original size:19 final size:18
Alignment explanation
Indices: 15622--15662 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
15612 GTGGTATTCA
15622 GTAAAAAGGGATAAAAATG
1 GTAAAAAGGG-TAAAAATG
*
15641 GTAAAAAAGTGTAAAAATG
1 GT-AAAAAGGGTAAAAATG
15660 GTA
1 GTA
15663 TTAAGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 12 0.60
20 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (18 bp):
GTAAAAAGGGTAAAAATG
Found at i:15672 original size:16 final size:16
Alignment explanation
Indices: 15651--15704 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
15641 GTAAAAAAGT
15651 GTAAAAATGGTATTAA
1 GTAAAAATGGTATTAA
* *
15667 GTAAAAA-GGGA--GA
1 GTAAAAATGGTATTAA
15680 GTAAAAAATGGTAATTAA
1 GT-AAAAATGGT-ATTAA
15698 GTAAAAA
1 GTAAAAA
15705 GAGTAAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 5 0.17
16 8 0.28
17 5 0.17
18 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (16 bp):
GTAAAAATGGTATTAA
Found at i:15775 original size:26 final size:26
Alignment explanation
Indices: 15641--15807 Score: 112
Period size: 26 Copynumber: 6.2 Consensus size: 26
15631 GATAAAAATG
* * *
15641 GTAAAAAAGTGTAAAAATGGTATTAA
1 GTAAAAAAGAGTAAAAATGGTAATCA
*
15667 GTAAAAAGGGAGAGTAAAAAATGGTAATTAA
1 GTAAAAA---AGAGT-AAAAATGGTAA-TCA
*
15698 GT-AAAAAGAGTAAAAAGTGGTATTCA
1 GTAAAAAAGAGTAAAAA-TGGTAATCA
15724 GTAGAAGCAGAA-AG-AAAAGA-GGTAATCA
1 GTA-AA--A-AAGAGTAAAA-ATGGTAATCA
15752 GTAAAAAAG-GTAAAATATGGTAATCA
1 GTAAAAAAGAGTAAAA-ATGGTAATCA
* *
15778 GT-ACAAAGAGTAAAAAATGGTAATTA
1 GTAAAAAAGAGT-AAAAATGGTAATCA
15804 GTAA
1 GTAA
15808 TCAAGAAATA
Statistics
Matches: 115, Mismatches: 8, Indels: 35
0.73 0.05 0.22
Matches are distributed among these distances:
24 3 0.03
25 11 0.10
26 39 0.34
27 17 0.15
28 12 0.10
29 8 0.07
30 18 0.16
31 7 0.06
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.21
Consensus pattern (26 bp):
GTAAAAAAGAGTAAAAATGGTAATCA
Found at i:29605 original size:167 final size:165
Alignment explanation
Indices: 29206--29648 Score: 611
Period size: 167 Copynumber: 2.7 Consensus size: 165
29196 TGAGTCATTT
*
29206 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAAT-CCCTCAAGAATCAAAAGTTAGGATAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * ** * *
29270 TTAAGTAATTTGCCAAGTAGGTAAAGACGAAAAATATTAGTTCTCTAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTG
* * *
29335 ATGGGGATCTTTTATTAATTCCATCACTCTATTCAA
130 ATAGGGATCTTTTAGTAATTCCATCACTCTATTAAA
* * * *
29371 GTCCATTGAGAAATGACAAAAAAGATTATTTATTTAATCCCCTCAAGAATCAAAAGTTAGAACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
*
29436 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCTT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACT-CAAAAGCAAGCCTT
* *
29501 GGTAGGGATCTTTTAGTATTTCCA-CTACTCTATTAAA
129 GATAGGGATCTTTTAGTAATTCCATC-ACTCTATTAAA
* * * *
29538 GTCAATCGAGAAATTACCAAAAAGTCTAGTTATTTAATCCCCTCAAAAATCAAAAGTTGGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
*
29603 TTAAGTAATCTGCCAAGTGGGAAAAGACGAAAAAAATTAGTTCTCT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT
29649 CGCTCCTCAT
Statistics
Matches: 244, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
165 34 0.14
166 71 0.29
167 139 0.57
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTGA
TAGGGATCTTTTAGTAATTCCATCACTCTATTAAA
Found at i:30213 original size:45 final size:45
Alignment explanation
Indices: 30164--30253 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
30154 GATTACTTCT
30164 CCAGCTCATCATTAATCCGAGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGAGGTAGGGATCTTTTAGTAATTCCAC
* *
30209 CCAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGAGGTAGGGATCTTTTAGTAATTCCAC
30254 TACTCTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGAGGTAGGGATCTTTTAGTAATTCCAC
Found at i:31819 original size:20 final size:20
Alignment explanation
Indices: 31794--31835 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31784 GATTTGGGTG
31794 ATCAACTTATCTTGATAAGT
1 ATCAACTTATCTTGATAAGT
31814 ATCAACTTATCTTGATAAGT
1 ATCAACTTATCTTGATAAGT
31834 AT
1 AT
31836 GAATGCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCAACTTATCTTGATAAGT
Found at i:33256 original size:55 final size:56
Alignment explanation
Indices: 33194--33298 Score: 176
Period size: 56 Copynumber: 1.9 Consensus size: 56
33184 TTTCTATCAA
* * *
33194 AAAAGTCCTCGAACACATGGGC-ATTCATAAGTCCCTAAACAGAGAGGCATCTCTC
1 AAAAGTCCTCAAACACAAGGGCAATTCATAAGTCCCTAAACACAGAGGCATCTCTC
33249 AAAAGTCCTCAAACACAAGGGCAATTCATAAGTCCCTAAACACAGAGGCA
1 AAAAGTCCTCAAACACAAGGGCAATTCATAAGTCCCTAAACACAGAGGCA
33299 ATTTTTCTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 20 0.43
56 26 0.57
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (56 bp):
AAAAGTCCTCAAACACAAGGGCAATTCATAAGTCCCTAAACACAGAGGCATCTCTC
Found at i:33271 original size:29 final size:26
Alignment explanation
Indices: 33194--33292 Score: 69
Period size: 29 Copynumber: 3.7 Consensus size: 26
33184 TTTCTATCAA
* *
33194 AAAAGTCCTCGAACACATGGGCATTC
1 AAAAGTCCTCAAACACAAGGGCATTC
* *
33220 ATAAGTCC-CTAAACA-GAGAGGCATCTCTC
1 AAAAGTCCTC-AAACACAAG-GGCA--T-TC
33249 AAAAGTCCTCAAACACAAGGGCAATTC
1 AAAAGTCCTCAAACACAAGGGC-ATTC
*
33276 ATAAGTCC-CTAAACACA
1 AAAAGTCCTC-AAACACA
33293 GAGGCAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
25 2 0.04
26 16 0.28
27 16 0.28
28 2 0.04
29 17 0.30
30 4 0.07
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.18
Consensus pattern (26 bp):
AAAAGTCCTCAAACACAAGGGCATTC
Found at i:33289 original size:27 final size:28
Alignment explanation
Indices: 33216--33301 Score: 90
Period size: 27 Copynumber: 3.1 Consensus size: 28
33206 ACACATGGGC
*
33216 ATTCATAAGTCCCTAAACA-GAGAGGCA
1 ATTCATAAGTCCCTAAACACAAGAGGCA
* *
33243 TCTCTCAAAAGT-CCTCAAACACAAG-GGCA
1 -AT-TCATAAGTCCCT-AAACACAAGAGGCA
33272 ATTCATAAGTCCCTAAACAC-AGAGGCA
1 ATTCATAAGTCCCTAAACACAAGAGGCA
33299 ATT
1 ATT
33302 TTTCTTCTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
26 2 0.04
27 20 0.42
28 8 0.17
29 16 0.33
30 2 0.04
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.20
Consensus pattern (28 bp):
ATTCATAAGTCCCTAAACACAAGAGGCA
Found at i:35786 original size:40 final size:40
Alignment explanation
Indices: 35742--35821 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
35732 CCACTCCAAC
*
35742 TTCCTACTGTAAAAGTCGACGCTCTTTTCAAGCAATGGGT
1 TTCCTACTGTAAAAGTCGACGCTCTTCTCAAGCAATGGGT
* * *
35782 TTCCTACTGTAGAAGTTGACGCTCTTCTCAATCAATGGGT
1 TTCCTACTGTAAAAGTCGACGCTCTTCTCAAGCAATGGGT
35822 GGCAGAGAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (40 bp):
TTCCTACTGTAAAAGTCGACGCTCTTCTCAAGCAATGGGT
Found at i:36712 original size:58 final size:58
Alignment explanation
Indices: 36642--36985 Score: 593
Period size: 58 Copynumber: 5.9 Consensus size: 58
36632 TATTCTCTTC
*
36642 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCTCTAAACACAAGAGGCATCTATACT-
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACAC-AGAGGCATCTATACTA
36700 AAAAGTCCTCAAACACAA-GGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
* *
36757 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCACTAAACACAAAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
* * *
36815 AAAAGTCCTCAAACAAAAGGGCATTCATAAGTCCCTGAACACAGAGGCATCTATACTG
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
*
36873 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGTGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
*
36931 AAAAGTCCTCAAACACAAGGGCATTCATAAGTTCCTAAACACAGAGGCATCTATA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA
36986 TCAAAGTCCC
Statistics
Matches: 270, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
56 15 0.06
57 40 0.15
58 215 0.80
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.20
Consensus pattern (58 bp):
AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
Found at i:36714 original size:32 final size:27
Alignment explanation
Indices: 36639--36973 Score: 171
Period size: 26 Copynumber: 11.7 Consensus size: 27
36629 TAATATTCTC
36639 TTCAAAAGTCCTCAAACACAAGGGCA-
1 TTCAAAAGTCCTCAAACACAAGGGCAT
*
36665 TTCATAAGT-CTCTAAACACAAGAGGCAT
1 TTCAAAAGTCCTC-AAACACAAG-GGCAT
36693 CTATACTAAAAGTCCTCAAACACAA-GGCA-
1 -T-T-C-AAAAGTCCTCAAACACAAGGGCAT
*
36722 TTCATAAGTCC-CTAAACAC-AGAGGCAT
1 TTCAAAAGTCCTC-AAACACAAG-GGCAT
36749 CTATACTAAAAAGTCCTCAAACACAAGGGCA-
1 -T-T-C--AAAAGTCCTCAAACACAAGGGCAT
* *
36780 TTCATAAGTCACT-AAACACAAAGGCAT
1 TTCAAAAGTC-CTCAAACACAAGGGCAT
*
36807 CTATACTAAAAAGTCCTCAAACAAAAGGGCA-
1 -T-T-C--AAAAGTCCTCAAACACAAGGGCAT
* *
36838 TTCATAAGTCC-CTGAACAC-AGAGGCAT
1 TTCAAAAGTCCTC-AAACACAAG-GGCAT
36865 CTATACTGAAAAGTCCTCAAACACAAGGGCA-
1 -T-T-C--AAAAGTCCTCAAACACAAGGGCAT
*
36896 TTCATAAGTCC-CTAAACAC-AGTGGCAT
1 TTCAAAAGTCCTC-AAACACAAG-GGCAT
36923 CTATACTAAAAAGTCCTCAAACACAAGGGCA-
1 -T-T-C--AAAAGTCCTCAAACACAAGGGCAT
*
36954 TTCATAAGTTCCT-AAACACA
1 TTCAAAAG-TCCTCAAACACA
36974 GAGGCATCTA
Statistics
Matches: 244, Mismatches: 17, Indels: 96
0.68 0.05 0.27
Matches are distributed among these distances:
24 2 0.01
25 22 0.09
26 83 0.34
27 11 0.05
28 9 0.04
29 9 0.04
30 13 0.05
31 3 0.01
32 80 0.33
33 12 0.05
ACGTcount: A:0.41, C:0.25, G:0.13, T:0.20
Consensus pattern (27 bp):
TTCAAAAGTCCTCAAACACAAGGGCAT
Found at i:41643 original size:35 final size:35
Alignment explanation
Indices: 41595--41679 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 35
41585 ATTTCATCAG
* * * *
41595 ATTCAGCACTTGGGGGCTGCAGAAACCCCTTCATC
1 ATTCAACACTTGGGGACTCCAGAAACCCATTCATC
* * * *
41630 ATTCAACAGTTGGGTACTCCAGAAACTCATTCTTC
1 ATTCAACACTTGGGGACTCCAGAAACCCATTCATC
* *
41665 ATTCAATATTTGGGG
1 ATTCAACACTTGGGG
41680 TCTTCAACAA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (35 bp):
ATTCAACACTTGGGGACTCCAGAAACCCATTCATC
Found at i:42131 original size:72 final size:73
Alignment explanation
Indices: 42046--42320 Score: 396
Period size: 72 Copynumber: 3.8 Consensus size: 73
42036 GTCTTCTTCT
* *
42046 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
1 TCATTGTGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATT
*
42111 ATCTTCCA
66 ATATTCCA
* * ***
42119 T-ATTGTGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTATGCGATT
1 TCATTGTGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATT
42183 ATATT-CA
66 ATATTCCA
* * **
42190 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAATCCTTCGCACAATCCTTATGTGATT
1 TCATTGTGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATT
*
42255 ATTTTCC-
66 ATATTCCA
*
42262 TCATTGTGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCCTACA
1 TCATTGTGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
42321 ACTACATTCT
Statistics
Matches: 181, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
71 26 0.14
72 153 0.85
73 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (73 bp):
TCATTGTGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATT
ATATTCCA
Found at i:42226 original size:144 final size:144
Alignment explanation
Indices: 42046--42317 Score: 458
Period size: 144 Copynumber: 1.9 Consensus size: 144
42036 GTCTTCTTCT
*
42046 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAATCCTTCGCACAATCCTTACATGATA
*
42111 ATCTTCCAT-ATTGTGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA-CCCT
66 ATCTTCC-TCATTGTGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCCT
42174 TATGCGATTATATTCA
129 TATGCGATTATATTCA
** *
42190 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAATCCTTCGCACAATCCTTATGTGATT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAATCCTTCGCACAATCCTTACATGATA
*
42255 ATTTTCCTCATTGTGATTGTAGCCGAGGCAGTTCCCACATTGGCAGTCCTTCGCACAATCCCT
66 ATCTTCCTCATTGTGATTGTAGCCGAGGCAGTTCCCACATTGGCAGTCCTTCGCACAATCCCT
42318 ACAACTACAT
Statistics
Matches: 120, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
143 20 0.17
144 100 0.83
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (144 bp):
TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAATCCTTCGCACAATCCTTACATGATA
ATCTTCCTCATTGTGATTGTAGCCGAGGCAGTTCCCACATTGGCAGTCCTTCGCACAATCCCTTA
TGCGATTATATTCA
Found at i:42997 original size:16 final size:16
Alignment explanation
Indices: 42976--43006 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42966 AACGGAAGGT
*
42976 TACCGCAGTAGAATGG
1 TACCGCAGCAGAATGG
42992 TACCGCAGCAGAATG
1 TACCGCAGCAGAATG
43007 TCGCCGCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (16 bp):
TACCGCAGCAGAATGG
Found at i:47138 original size:21 final size:21
Alignment explanation
Indices: 47099--47147 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
47089 TCAATGCTTT
**
47099 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
47121 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
47142 A-GAAGC
1 AGGAAGC
47148 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:54067 original size:20 final size:20
Alignment explanation
Indices: 54038--54086 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
54028 CAAAGCTACT
54038 ACCCAAAAGCCCAAGTTTAA
1 ACCCAAAAGCCCAAGTTTAA
*
54058 ACCCAGAAGCCCAAGTTTAGA
1 ACCCAAAAGCCCAAGTTTA-A
*
54079 GCCCAAAA
1 ACCCAAAA
54087 TGATAGCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.43, C:0.31, G:0.14, T:0.12
Consensus pattern (20 bp):
ACCCAAAAGCCCAAGTTTAA
Found at i:54717 original size:29 final size:29
Alignment explanation
Indices: 54685--54780 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
54675 GAAGAAGACC
54685 AGACCATGGTCGACCTTGAAAATTTAGAA
1 AGACCATGGTCGACCTTGAAAATTTAGAA
** * **
54714 AGACC-T-GTCTGAGGTCTGAAACTGAAGAAGA
1 AGACCATGGTC-GACCT-TGAAAATTTAG-A-A
*
54745 CCAGACCATGGTCGACCTTGAGAATTTAGAA
1 --AGACCATGGTCGACCTTGAAAATTTAGAA
54776 AGACC
1 AGACC
54781 TGTCCGAGGT
Statistics
Matches: 48, Mismatches: 11, Indels: 16
0.64 0.15 0.21
Matches are distributed among these distances:
27 3 0.06
28 4 0.08
29 18 0.38
30 1 0.02
31 2 0.04
32 1 0.02
33 12 0.25
34 4 0.08
35 3 0.06
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (29 bp):
AGACCATGGTCGACCTTGAAAATTTAGAA
Found at i:54717 original size:34 final size:34
Alignment explanation
Indices: 54679--54780 Score: 83
Period size: 34 Copynumber: 3.2 Consensus size: 34
54669 GAAACTGAAG
54679 AAGACCAGACCATGGTCGACCTTGAAAATTTAGA
1 AAGACCAGACCATGGTCGACCTTGAAAATTTAGA
* * * * **
54713 AAGACCTG-TC-TGAG--G-TC-TGAAACTGAAG-
1 AAGACCAGACCATG-GTCGACCTTGAAAATTTAGA
*
54741 AAGACCAGACCATGGTCGACCTTGAGAATTTAGA
1 AAGACCAGACCATGGTCGACCTTGAAAATTTAGA
54775 AAGACC
1 AAGACC
54781 TGTCCGAGGT
Statistics
Matches: 47, Mismatches: 13, Indels: 16
0.62 0.17 0.21
Matches are distributed among these distances:
28 7 0.15
29 10 0.21
30 3 0.06
31 2 0.04
32 3 0.06
33 9 0.19
34 13 0.28
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (34 bp):
AAGACCAGACCATGGTCGACCTTGAAAATTTAGA
Found at i:54730 original size:62 final size:62
Alignment explanation
Indices: 54653--54809 Score: 262
Period size: 62 Copynumber: 2.5 Consensus size: 62
54643 AAAAATTAAG
54653 GACCTGTCT-ACGGTCTGAAACTGAAGAAGACCAGACCATGGTCGACCTTGAAAATTTAGAAA
1 GACCTGTCTGA-GGTCTGAAACTGAAGAAGACCAGACCATGGTCGACCTTGAAAATTTAGAAA
*
54715 GACCTGTCTGAGGTCTGAAACTGAAGAAGACCAGACCATGGTCGACCTTGAGAATTTAGAAA
1 GACCTGTCTGAGGTCTGAAACTGAAGAAGACCAGACCATGGTCGACCTTGAAAATTTAGAAA
* **
54777 GACCTGTCCGAGGTCTGAAGTTGAAGAAGACCA
1 GACCTGTCTGAGGTCTGAAACTGAAGAAGACCA
54810 ATCCGTGGTC
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
62 89 0.99
63 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.20
Consensus pattern (62 bp):
GACCTGTCTGAGGTCTGAAACTGAAGAAGACCAGACCATGGTCGACCTTGAAAATTTAGAAA
Found at i:54757 original size:28 final size:28
Alignment explanation
Indices: 54664--54757 Score: 64
Period size: 28 Copynumber: 3.1 Consensus size: 28
54654 ACCTGTCTAC
54664 GGTCTGAAACTGAAGAAGACCAGACCAT
1 GGTCTGAAACTGAAGAAGACCAGACCAT
* ** * * *
54692 GGTCGACCTTGAAAATTTAGAAAGACCTGTCTGA-
1 GGT----C-TGAAACTGAAG-AAGACCAGAC-CAT
54726 GGTCTGAAACTGAAGAAGACCAGACCAT
1 GGTCTGAAACTGAAGAAGACCAGACCAT
54754 GGTC
1 GGTC
54758 GACCTTGAGA
Statistics
Matches: 46, Mismatches: 12, Indels: 16
0.62 0.16 0.22
Matches are distributed among these distances:
27 1 0.02
28 15 0.33
29 8 0.17
30 1 0.02
32 1 0.02
33 8 0.17
34 11 0.24
35 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (28 bp):
GGTCTGAAACTGAAGAAGACCAGACCAT
Found at i:63856 original size:29 final size:29
Alignment explanation
Indices: 63814--63878 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
63804 AGTGATCACC
*
63814 AAATACATGAACAAAGGGTACTGTAGGAA
1 AAATCCATGAACAAAGGGTACTGTAGGAA
*
63843 AAATCCATGAACAATGGGTACTGTAGGAA
1 AAATCCATGAACAAAGGGTACTGTAGGAA
63872 AAATCCA
1 AAATCCA
63879 AAAAGTCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (29 bp):
AAATCCATGAACAAAGGGTACTGTAGGAA
Found at i:66226 original size:24 final size:25
Alignment explanation
Indices: 66169--66227 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
66159 TTTCCAAGAT
66169 AAAAATTAAAAAAAATGAGTCTTTC
1 AAAAATTAAAAAAAATGAGTCTTTC
66194 -AAAATTAAATAAAAA-G-GT-TTTC
1 AAAAATTAAA-AAAAATGAGTCTTTC
66216 AAAAATATAAAA
1 AAAAAT-TAAAA
66228 TAATCAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
22 4 0.13
23 8 0.26
24 14 0.45
25 5 0.16
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (25 bp):
AAAAATTAAAAAAAATGAGTCTTTC
Found at i:71677 original size:49 final size:49
Alignment explanation
Indices: 71547--71862 Score: 429
Period size: 49 Copynumber: 6.4 Consensus size: 49
71537 CTTTGTCCGA
* * * * * *
71547 AAGGGCATTTTGGTAAATTGCAAGTGAAATATAAGTGCCTTCCGTCTGGG
1 AAGGGCATTTTGGGAAATAGCAGGT-AAAAATAAATGCCTTCCGTCCGGG
*
71597 AAGGGCATTTTGGGGAATAGCAGGTAAAAATAAATGCCTT-CGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
* * * *
71645 AAGGGCATTTTGGTAAATAGCAAGTGAAAAATAAGTGCCTTCCGTCTGGG
1 AAGGGCATTTTGGGAAATAGCAGGT-AAAAATAAATGCCTTCCGTCCGGG
* * *
71695 AAGGGCATTTTGGGGAGTAGCAGGTAAAAATAAATGACTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
* * * *
71744 AATGGCATTTTGGGAAATAGTAGGTAAAAA-AAATCCCTTCCGACCGGG
1 AAGGGCATTTTGGGAAATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
71792 AAGGGCATTTTGGGAAATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
*
71841 AAGGGCATTTTGAGAAATAGCA
1 AAGGGCATTTTGGGAAATAGCA
71863 AGTGAAAACT
Statistics
Matches: 232, Mismatches: 31, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
48 72 0.31
49 111 0.48
50 49 0.21
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (49 bp):
AAGGGCATTTTGGGAAATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
Found at i:71716 original size:98 final size:99
Alignment explanation
Indices: 71547--71870 Score: 494
Period size: 98 Copynumber: 3.3 Consensus size: 99
71537 CTTTGTCCGA
* *
71547 AAGGGCATTTTGGTAAATTGCAAGTGAAATATAAGTGCCTTCCGTCTGGGAAGGGCATTTTGGGG
1 AAGGGCATTTTGGTAAATAGCAAGTGAAAAATAAGTGCCTTCCGTCTGGGAAGGGCATTTTGGGG
71612 AATAGCAGGTAAAAATAAATGCCTT-CGTCCGGG
66 AATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
71645 AAGGGCATTTTGGTAAATAGCAAGTGAAAAATAAGTGCCTTCCGTCTGGGAAGGGCATTTTGGGG
1 AAGGGCATTTTGGTAAATAGCAAGTGAAAAATAAGTGCCTTCCGTCTGGGAAGGGCATTTTGGGG
* *
71710 AGTAGCAGGTAAAAATAAATGACTTCCGTCCGGG
66 AATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
* * * * * * * * *
71744 AATGGCATTTTGGGAAATAGTAGGT-AAAAA-AAATCCCTTCCGACCGGGAAGGGCATTTTGGGA
1 AAGGGCATTTTGGTAAATAGCAAGTGAAAAATAAGTGCCTTCCGTCTGGGAAGGGCATTTTGGGG
71807 AATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
66 AATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
71841 AAGGGCATTTTGAG-AAATAGCAAGTGAAAA
1 AAGGGCATTTTG-GTAAATAGCAAGTGAAAA
71871 CTGAAAAAAT
Statistics
Matches: 205, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
97 80 0.39
98 96 0.47
99 29 0.14
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (99 bp):
AAGGGCATTTTGGTAAATAGCAAGTGAAAAATAAGTGCCTTCCGTCTGGGAAGGGCATTTTGGGG
AATAGCAGGTAAAAATAAATGCCTTCCGTCCGGG
Done.