Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006421.1 Hibiscus syriacus cultivar Beakdansim tig00015494_pilon, 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: 177031
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4358 original size:19 final size:19
Alignment explanation
Indices: 4334--4370 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4324 AATGACCAAC
* *
4334 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
4353 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
4371 CAGTATCACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:4421 original size:20 final size:20
Alignment explanation
Indices: 4396--4524 Score: 136
Period size: 20 Copynumber: 6.3 Consensus size: 20
4386 GTTTCCAGAT
4396 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
4416 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* * **
4436 TTGCAACGCTATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
4457 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
**
4477 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
*
4498 TCGCAACGCTATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
4518 TTGCAAC
1 TCGCAAC
4525 ACTAAATTTC
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
19 4 0.04
20 54 0.61
21 27 0.30
22 4 0.04
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:4464 original size:21 final size:21
Alignment explanation
Indices: 4438--4506 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
4428 TCTGACTATT
*
4438 GCAACGCTATAATACATAATC
1 GCAACGCGATAATACATAATC
**
4459 GCAACGCGATTCTGAC-T-ATC
1 GCAACGCGATAAT-ACATAATC
4479 GCAACGCGATAATACATAATC
1 GCAACGCGATAATACATAATC
4500 GCAACGC
1 GCAACGC
4507 TATTCTGACT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.05
20 15 0.38
21 21 0.52
22 2 0.05
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (21 bp):
GCAACGCGATAATACATAATC
Found at i:4545 original size:41 final size:41
Alignment explanation
Indices: 4415--4524 Score: 193
Period size: 41 Copynumber: 2.7 Consensus size: 41
4405 GATTCTGACT
4415 ATCGCAACGCGATTCTGACTATTGCAACGCTATAATACATA
1 ATCGCAACGCGATTCTGACTATTGCAACGCTATAATACATA
* *
4456 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
1 ATCGCAACGCGATTCTGACTATTGCAACGCTATAATACATA
*
4497 ATCGCAACGCTATTCTGACTATTGCAAC
1 ATCGCAACGCGATTCTGACTATTGCAAC
4525 ACTAAATTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (41 bp):
ATCGCAACGCGATTCTGACTATTGCAACGCTATAATACATA
Found at i:5336 original size:24 final size:24
Alignment explanation
Indices: 5302--5355 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5292 GTATTCGAAA
5302 TTTGATATTGGTCAATACCCAGAC
1 TTTGATATTGGTCAATACCCAGAC
* * *
5326 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
5350 TTTGAT
1 TTTGAT
5356 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:7837 original size:140 final size:136
Alignment explanation
Indices: 7664--7938 Score: 469
Period size: 140 Copynumber: 2.0 Consensus size: 136
7654 GCAAACGTTG
7664 TATTATGTATATTTATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTG
1 TATTATGTATATTTATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTG
* *
7729 AACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAATGTGA
66 AACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATT-ATTTGAATATCGCAACGCGA
7794 ATTTGAT
130 ATTTGAT
*
7801 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTATA-TTTA--TGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
7866 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTTTTTGAATATTGCAACGC
63 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTATTTGAATATCGCAACGC
7931 GAATTTGA
128 GAATTTGA
7939 CTATCGCAAC
Statistics
Matches: 130, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
137 10 0.08
138 4 0.03
139 22 0.17
140 94 0.72
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (136 bp):
TATTATGTATATTTATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTG
AACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTATTTGAATATCGCAACGCGAA
TTTGAT
Found at i:7947 original size:20 final size:20
Alignment explanation
Indices: 7914--8124 Score: 104
Period size: 20 Copynumber: 11.6 Consensus size: 20
7904 TTACACATTT
* *
7914 TTTGAATATTGCAACGCGAA
1 TTTGACTATCGCAACGCGAA
*
7934 TTTGACTATCGCAACGCAAA
1 TTTGACTATCGCAACGCGAA
* *
7954 TTTGATTATCGCAACTC-AA
1 TTTGACTATCGCAACGCGAA
* *
7973 ----A-AACCGCAACGCGAA
1 TTTGACTATCGCAACGCGAA
*
7988 TTTGACTATCGCAACTC-AA
1 TTTGACTATCGCAACGCGAA
*
8007 ----A-AATCGCAA--CGAA
1 TTTGACTATCGCAACGCGAA
* *
8020 TTTAACTATCGCAACGTGAA
1 TTTGACTATCGCAACGCGAA
* * *
8040 TTTGATTATCGCAACGGGTA
1 TTTGACTATCGCAACGCGAA
*
8060 TTTGACTATCGCAACGAGAA
1 TTTGACTATCGCAACGCGAA
* *
8080 ----A--ATCGCAAAGCGTA
1 TTTGACTATCGCAACGCGAA
*
8094 TTAGACTATCGCAACGCGAA
1 TTTGACTATCGCAACGCGAA
*
8114 -TTGACTTTCGC
1 TTTGACTATCGC
8125 GTTGCGATTT
Statistics
Matches: 143, Mismatches: 28, Indels: 41
0.67 0.13 0.19
Matches are distributed among these distances:
12 1 0.01
13 2 0.01
14 25 0.17
15 4 0.03
16 1 0.01
17 1 0.01
18 8 0.06
19 14 0.10
20 87 0.61
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (20 bp):
TTTGACTATCGCAACGCGAA
Found at i:7990 original size:34 final size:34
Alignment explanation
Indices: 7943--8034 Score: 134
Period size: 34 Copynumber: 2.8 Consensus size: 34
7933 ATTTGACTAT
* *
7943 CGCAACGCAAATTTGATTATCGCAACTCAAAAAC
1 CGCAACGCGAATTTGACTATCGCAACTCAAAAAC
*
7977 CGCAACGCGAATTTGACTATCGCAACTCAAAAAT
1 CGCAACGCGAATTTGACTATCGCAACTCAAAAAC
*
8011 CGCAA--CGAATTTAACTATCGCAAC
1 CGCAACGCGAATTTGACTATCGCAAC
8035 GTGAATTTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 18 0.33
34 36 0.67
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (34 bp):
CGCAACGCGAATTTGACTATCGCAACTCAAAAAC
Found at i:8065 original size:72 final size:74
Alignment explanation
Indices: 7977--8115 Score: 187
Period size: 72 Copynumber: 1.9 Consensus size: 74
7967 ACTCAAAAAC
*
7977 CGCAACGCGAATTTGACTATCGCAACTCA-AAAATCGC-AA-CGAATTTA-ACTATCGCAACGTG
1 CGCAACGCGAATTTGACTATCGCAAC-CAGAAAATCGCAAAGCGAA-TTAGACTATCGCAACGCG
8038 AATTTGATTAT
64 AATTTGATTAT
* * * *
8049 CGCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAACGCGAA
1 CGCAACGCGAATTTGACTATCGCAACCAGAAAATCGCAAAGCGAATTAGACTATCGCAACGCGAA
8114 TT
66 TT
8116 GACTTTCGCG
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
71 1 0.02
72 32 0.55
73 5 0.09
74 20 0.34
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (74 bp):
CGCAACGCGAATTTGACTATCGCAACCAGAAAATCGCAAAGCGAATTAGACTATCGCAACGCGAA
TTTGATTAT
Found at i:8143 original size:20 final size:21
Alignment explanation
Indices: 8114--8171 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
8104 GCAACGCGAA
8114 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
8134 TTG-GCTTTCGCATTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
8154 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
8172 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.43
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:8309 original size:29 final size:28
Alignment explanation
Indices: 8275--8329 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
8265 ATAAGAATTA
*
8275 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAA-ATTAAACAAATCAACT
**
8304 TTTACAAATCAAATTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
8330 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:8312 original size:14 final size:14
Alignment explanation
Indices: 8293--8329 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
8283 TCAATATTAA
*
8293 ACAAATCAACTTTT
1 ACAAATCAAATTTT
8307 ACAAATCAAATTTT
1 ACAAATCAAATTTT
8321 ACAAATCAA
1 ACAAATCAA
8330 TTAAACAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAAATTTT
Found at i:10321 original size:19 final size:20
Alignment explanation
Indices: 10290--10331 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
10280 ATAGTTTCTA
10290 AAACTTAAAATCGCAACACG
1 AAACTTAAAATCGCAACACG
10310 AAACTT-AAATCGCAACACG
1 AAACTTAAAATCGCAACACG
10329 AAA
1 AAA
10332 ATGACTATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.52, C:0.24, G:0.10, T:0.14
Consensus pattern (20 bp):
AAACTTAAAATCGCAACACG
Found at i:10343 original size:20 final size:20
Alignment explanation
Indices: 10299--10365 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
10289 AAAACTTAAA
* * *
10299 ATCGCAACACGAAACTTA-A
1 ATCGCAACACGAAAATGACT
10318 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
10338 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
10358 ATCGCAAC
1 ATCGCAAC
10366 GGGATAATCG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 16 0.39
20 25 0.61
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:10411 original size:33 final size:33
Alignment explanation
Indices: 10358--10437 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
10348 GAATTTGACT
* * * * *
10358 ATCGCAACGGGATAATCGCAATGCGAAATAAAA
1 ATCGCAACGAGAAAAACGCAACGCGAAACAAAA
*
10391 ATCGCAACGAGAAAAACGCAACGCGAAACCAAA
1 ATCGCAACGAGAAAAACGCAACGCGAAACAAAA
* *
10424 TTCGCAACGTGAAA
1 ATCGCAACGAGAAA
10438 CTAAATTCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAAAAACGCAACGCGAAACAAAA
Found at i:10431 original size:19 final size:19
Alignment explanation
Indices: 10407--10447 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
10397 ACGAGAAAAA
10407 CGCAACGCGAAACCAAATT
1 CGCAACGCGAAACCAAATT
* *
10426 CGCAACGTGAAACTAAATT
1 CGCAACGCGAAACCAAATT
10445 CGC
1 CGC
10448 GTTGCGATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.15
Consensus pattern (19 bp):
CGCAACGCGAAACCAAATT
Found at i:10479 original size:14 final size:14
Alignment explanation
Indices: 10460--10492 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
10450 TGCGATAGTC
*
10460 ATTTTCGCATTGCG
1 ATTTTCACATTGCG
10474 ATTTTCACATTGCG
1 ATTTTCACATTGCG
10488 ATTTT
1 ATTTT
10493 TATTTCGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (14 bp):
ATTTTCACATTGCG
Found at i:10539 original size:20 final size:20
Alignment explanation
Indices: 10514--10562 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
10504 GCGATTATCC
10514 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
10534 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
10554 CGTTGCGAT
1 CGTTGCGAT
10563 TTAAGTTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:12579 original size:20 final size:19
Alignment explanation
Indices: 12458--12594 Score: 106
Period size: 20 Copynumber: 7.2 Consensus size: 19
12448 GAAACTTAAA
* *
12458 ATCGCAACACGAAAATGACT
1 ATCGCAACGC-AAATTGACT
*
12478 ATCGCAACGCGAATTTGACT
1 ATCGCAACGC-AAATTGACT
*
12498 ATCGCAACG-AGA-T-A--
1 ATCGCAACGCAAATTGACT
**
12512 ATCGCAACGCAGAA-TGAAA
1 ATCGCAACGCA-AATTGACT
* *
12531 ATCGCAACACGAAAATGACT
1 ATCGCAACGC-AAATTGACT
12551 ATCGCAACGCAAATTTGACT
1 ATCGCAACGCAAA-TTGACT
12571 ATCGCAACGCAAATTTGACT
1 ATCGCAACGCAAA-TTGACT
12591 ATCG
1 ATCG
12595 TTGCGATTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 3 0.03
17 2 0.02
18 1 0.01
19 14 0.14
20 68 0.69
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (19 bp):
ATCGCAACGCAAATTGACT
Found at i:13187 original size:20 final size:20
Alignment explanation
Indices: 13162--13253 Score: 73
Period size: 20 Copynumber: 4.6 Consensus size: 20
13152 ATTTTATATT
13162 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* *
13182 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAGA
* *
13202 TTCGCATTGCGATA-T-ACGTA
1 ATCGCGTTGCGATAGTCA-G-A
* * *
13222 TTCGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAGA
13242 ATCGCGTTGCGA
1 ATCGCGTTGCGA
13254 ATCTGGAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 54 0.93
21 1 0.02
22 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:13647 original size:2 final size:2
Alignment explanation
Indices: 13640--13680 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
13630 TAATACAAAA
13640 AT AT AT AT AT 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 AT AT AT AT AT A
13681 AACTAACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18507 original size:17 final size:17
Alignment explanation
Indices: 18485--18525 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
18475 ATGGTTTTCA
18485 GAACCGGACCGGTTAGC
1 GAACCGGACCGGTTAGC
18502 GAACCGGACCGGTTAGC
1 GAACCGGACCGGTTAGC
18519 GAACCGG
1 GAACCGG
18526 TCATGCTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.37, T:0.10
Consensus pattern (17 bp):
GAACCGGACCGGTTAGC
Found at i:25335 original size:14 final size:14
Alignment explanation
Indices: 25318--25344 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25308 AATATTTGAA
25318 AATGAAATCAGGAT
1 AATGAAATCAGGAT
25332 AATGAAATCAGGA
1 AATGAAATCAGGA
25345 GAATTATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.22, T:0.19
Consensus pattern (14 bp):
AATGAAATCAGGAT
Found at i:26017 original size:17 final size:18
Alignment explanation
Indices: 25981--26021 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
25971 ATATTATGTA
*
25981 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
25999 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
26016 TTTACT
1 TTTACT
26022 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:29498 original size:4 final size:4
Alignment explanation
Indices: 29489--29640 Score: 288
Period size: 4 Copynumber: 38.2 Consensus size: 4
29479 AAATGATGAC
*
29489 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
29537 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
29585 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -TGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
29632 ATGT ATGT A
1 ATGT ATGT A
29641 AAGGGTTATA
Statistics
Matches: 145, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
3 3 0.02
4 142 0.98
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:29927 original size:30 final size:30
Alignment explanation
Indices: 29882--29984 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
29872 TAGTTCTTCG
* *
29882 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
29912 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
29942 GACCTCTGGATAGTTACCGAAGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
29972 GACCTCTGGATAG
1 GACCTCTGGATAG
29985 GTCCTTCGGA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:31621 original size:16 final size:16
Alignment explanation
Indices: 31600--31630 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31590 TATTTTTTCA
31600 AATAATCATAATAAAC
1 AATAATCATAATAAAC
*
31616 AATAATTATAATAAA
1 AATAATCATAATAAA
31631 AAATTATAAC
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:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATCATAATAAAC
Found at i:36038 original size:2 final size:2
Alignment explanation
Indices: 36031--36075 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
36021 AATTAAAATT
36031 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36073 TA T
1 TA T
36076 GTATTTTATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36774 original size:25 final size:25
Alignment explanation
Indices: 36740--36791 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
36730 AAAGAAAAGG
36740 AACATTAGGGTTTTAATTCTTATCT
1 AACATTAGGGTTTTAATTCTTATCT
*
36765 AACATTAGGGTTTTATTTCTTATCT
1 AACATTAGGGTTTTAATTCTTATCT
36790 AA
1 AA
36792 TTTTCTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (25 bp):
AACATTAGGGTTTTAATTCTTATCT
Found at i:37229 original size:23 final size:23
Alignment explanation
Indices: 37180--37230 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
37170 GTGTTATATT
**
37180 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
37203 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
37226 ATATT
1 ATATT
37231 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:37286 original size:19 final size:19
Alignment explanation
Indices: 37218--37298 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
37208 TTAAATATCT
37218 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
37237 TTATTAGATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
37256 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
37276 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
37294 -TATTA
1 TTATTA
37299 TTTTTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:37319 original size:27 final size:25
Alignment explanation
Indices: 37252--37339 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 25
37242 AGATTAATAT
*
37252 TAAATATATAAATAATATTATTCATTA
1 TAAATA-ATAAATAATATTATT-TTTA
* *
37279 TTAATAATTTAATAATATTATTTTTA
1 TAAATAA-TAAATAATATTATTTTTA
* *
37305 TGAAATTAATAAATAATATAAATTTTA
1 T-AAA-TAATAAATAATATTATTTTTA
*
37332 TTAATAAT
1 TAAATAAT
37340 TTATTATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
25 4 0.08
26 7 0.14
27 36 0.72
28 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
TAAATAATAAATAATATTATTTTTA
Found at i:37453 original size:32 final size:32
Alignment explanation
Indices: 37386--37455 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
37376 ATATTATTAT
* * *
37386 AATATAATTGATTATTTTATTATAATATTAAA
1 AATATAATTGATTATATTATTAAAACATTAAA
37418 AATATAA-T-ATTATATTATTAGAAACATTAATA
1 AATATAATTGATTATATTATTA-AAACATTAA-A
37450 AATATA
1 AATATA
37456 TTTTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 11 0.33
31 8 0.24
32 14 0.42
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (32 bp):
AATATAATTGATTATATTATTAAAACATTAAA
Found at i:37514 original size:24 final size:25
Alignment explanation
Indices: 37467--37515 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
37457 TTTAATAATT
*
37467 AATATTTTGATTAAAATGATATTAA
1 AATATTTTGATTAAAATGAAATTAA
* *
37492 AATATTTT-ATTAATATTAAATTAA
1 AATATTTTGATTAAAATGAAATTAA
37516 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
AATATTTTGATTAAAATGAAATTAA
Found at i:43286 original size:16 final size:17
Alignment explanation
Indices: 43265--43296 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43255 TGGTCAATTT
43265 TTTAAAATTT-TTATTA
1 TTTAAAATTTATTATTA
43281 TTTAAAATTTATTATT
1 TTTAAAATTTATTATT
43297 GATAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAAATTTATTATTA
Found at i:43293 original size:14 final size:15
Alignment explanation
Indices: 43274--43306 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
43264 TTTTAAAATT
43274 TTTATTATT-TAAAA
1 TTTATTATTATAAAA
43288 TTTATTATTGATAAAA
1 TTTATTATT-ATAAAA
43304 TTT
1 TTT
43307 GAAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTATTATTATAAAA
Found at i:43356 original size:2 final size:2
Alignment explanation
Indices: 43351--43386 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
43341 AGAAGTAATT
43351 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43387 ATTATTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46200 original size:17 final size:17
Alignment explanation
Indices: 46178--46216 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
46168 TGAATCAAAT
46178 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
46195 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
46212 -AATTA
1 TAATTA
46217 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:49710 original size:25 final size:25
Alignment explanation
Indices: 49688--49736 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
49678 GAGGCTTCTG
49688 CTTCTAGCAAAGTCTCTCCCTTCAA
1 CTTCTAGCAAAGTCTCTCCCTTCAA
49713 CTTCTAGCAAAGTCTCTCCCTTCA
1 CTTCTAGCAAAGTCTCTCCCTTCA
49737 GCATGTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.37, G:0.08, T:0.33
Consensus pattern (25 bp):
CTTCTAGCAAAGTCTCTCCCTTCAA
Found at i:59523 original size:30 final size:30
Alignment explanation
Indices: 59489--59546 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
59479 AGTGCTCCAT
* * *
59489 AGGTCGTCGTGTGTTCCTGGACACCTATAG
1 AGGTCGTCATGTGCTCCTAGACACCTATAG
*
59519 AGGTCGTCATGTGCTCCTAGAGACCTAT
1 AGGTCGTCATGTGCTCCTAGACACCTAT
59547 GGTGGTCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (30 bp):
AGGTCGTCATGTGCTCCTAGACACCTATAG
Found at i:60311 original size:6 final size:7
Alignment explanation
Indices: 60295--60325 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
60285 AATTGCAAAA
60295 AAAATTT
1 AAAATTT
60302 AAAA-TT
1 AAAATTT
60308 AAAATTT
1 AAAATTT
60315 AAAATTT
1 AAAATTT
60322 AAAA
1 AAAA
60326 AACTGATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
AAAATTT
Found at i:60313 original size:13 final size:14
Alignment explanation
Indices: 60295--60325 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
60285 AATTGCAAAA
60295 AAAATTTAAAA-TT
1 AAAATTTAAAATTT
60308 AAAATTTAAAATTT
1 AAAATTTAAAATTT
60322 AAAA
1 AAAA
60326 AACTGATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATTTAAAATTT
Found at i:60782 original size:16 final size:16
Alignment explanation
Indices: 60759--60803 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
60749 TCGTTGTGAA
60759 AAAAAGAAAAATAAAG
1 AAAAAGAAAAATAAAG
* *
60775 ATAAAGAAAACTAAAG
1 AAAAAGAAAAATAAAG
*
60791 AAAAATAAAAATA
1 AAAAAGAAAAATA
60804 TATAAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (16 bp):
AAAAAGAAAAATAAAG
Found at i:60862 original size:4 final size:4
Alignment explanation
Indices: 60849--60882 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
60839 AAAGAAATAG
60849 AAAT -AAT AAAT AAAT AAAT AAAT AAAT ATAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AA
60883 GATATAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
4 21 0.75
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:60911 original size:9 final size:8
Alignment explanation
Indices: 60844--60946 Score: 52
Period size: 9 Copynumber: 12.1 Consensus size: 8
60834 CAAAAAAAGA
60844 AATAGAAAT
1 AATA-AAAT
60853 AAT-AAAT
1 AATAAAAT
60860 AA-ATAAAT
1 AATA-AAAT
60868 AAATAAATAT
1 -AATAAA-AT
60878 AATAAGATAT
1 AATAA-A-AT
**
60888 AAT-ATTT
1 AATAAAAT
60895 AATAAAAT
1 AATAAAAT
60903 AAGTAAAAT
1 AA-TAAAAT
*
60912 AAAAAAAAT
1 -AATAAAAT
60921 AATAAACAT
1 AATAAA-AT
60930 ATATAAAA-
1 A-ATAAAAT
*
60938 ATTAAAAT
1 AATAAAAT
60946 A
1 A
60947 TTAGGAAAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
7 15 0.20
8 15 0.20
9 28 0.37
10 17 0.23
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (8 bp):
AATAAAAT
Found at i:60937 original size:18 final size:18
Alignment explanation
Indices: 60853--60937 Score: 59
Period size: 18 Copynumber: 4.6 Consensus size: 18
60843 AAATAGAAAT
*
60853 AATAAAT-AAATAAAT-A
1 AATAAATAAAATAAGTAA
*
60869 AATAAATATAATAAGATATA
1 AATAAATAAAATAAG-TA-A
*
60889 ATATTTAATAAAATAAGTAA
1 A-A-TAAATAAAATAAGTAA
*
60909 AATAAAAAAAATAA-TAA
1 AATAAATAAAATAAGTAA
*
60926 ACATATATAAAA
1 A-ATAAATAAAA
60938 ATTAAAATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.13
17 9 0.17
18 19 0.35
19 1 0.02
20 4 0.07
21 3 0.06
22 11 0.20
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.27
Consensus pattern (18 bp):
AATAAATAAAATAAGTAA
Found at i:64707 original size:14 final size:14
Alignment explanation
Indices: 64688--64716 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
64678 TTAATCCGAT
64688 ATATTACTGATTAA
1 ATATTACTGATTAA
64702 ATATTACTGATTAA
1 ATATTACTGATTAA
64716 A
1 A
64717 ATCAAAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATTACTGATTAA
Found at i:68588 original size:14 final size:14
Alignment explanation
Indices: 68553--68592 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
68543 TTTTTTTTGT
68553 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
* *
68566 ATTTATGTTCGTTC
1 GTTTGTGTTCGTTC
68580 GTTTGTGTTCGTT
1 GTTTGTGTTCGTT
68593 TATATTCGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.05, C:0.10, G:0.25, T:0.60
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:72647 original size:3 final size:3
Alignment explanation
Indices: 72639--72685 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
72629 CTGCAAGATG
* *
72639 TAA TAA TAA TAA TAA TAA AAA TAA AAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
72686 TTTTTAACCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:72760 original size:24 final size:24
Alignment explanation
Indices: 72732--72781 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
72722 ATTATCATAT
*
72732 TAGATTATTTATCATAAATTATTA
1 TAGATTATTTACCATAAATTATTA
72756 TAGATTATTTACCATAAATTATTA
1 TAGATTATTTACCATAAATTATTA
72780 TA
1 TA
72782 TTGGGTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (24 bp):
TAGATTATTTACCATAAATTATTA
Found at i:80294 original size:18 final size:18
Alignment explanation
Indices: 80271--80306 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
80261 TTAGCTTGCC
80271 CTGTTTTATTTAGTTTCA
1 CTGTTTTATTTAGTTTCA
80289 CTGTTTTATTTAGTTTCA
1 CTGTTTTATTTAGTTTCA
80307 TTTTTCTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (18 bp):
CTGTTTTATTTAGTTTCA
Found at i:83820 original size:24 final size:24
Alignment explanation
Indices: 83775--83820 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
83765 GATCATTAGG
* *
83775 TGTACAAAGGGCACCAGGTATTCT
1 TGTACAAAGAGCACCAGATATTCT
83799 TGTACAAAAGAGCA-CAGATATT
1 TGTAC-AAAGAGCACCAGATATT
83821 TGCTGCTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (24 bp):
TGTACAAAGAGCACCAGATATTCT
Found at i:88184 original size:2 final size:2
Alignment explanation
Indices: 88177--88214 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
88167 TGGTTAAATA
88177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88215 CACTTTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93042 original size:28 final size:28
Alignment explanation
Indices: 92998--93051 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
92988 AAGTCAACGG
92998 GTTGACTCGGACAAGTTAACTCAGACAA
1 GTTGACTCGGACAAGTTAACTCAGACAA
* * *
93026 GTTGACTCGGACGAGTTGACTGAGAC
1 GTTGACTCGGACAAGTTAACTCAGAC
93052 GAGTCAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (28 bp):
GTTGACTCGGACAAGTTAACTCAGACAA
Found at i:93055 original size:14 final size:14
Alignment explanation
Indices: 92998--93046 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
92988 AAGTCAACGG
92998 GTTGACTCGGACAA
1 GTTGACTCGGACAA
* *
93012 GTTAACTCAGACAA
1 GTTGACTCGGACAA
*
93026 GTTGACTCGGACGA
1 GTTGACTCGGACAA
93040 GTTGACT
1 GTTGACT
93047 GAGACGAGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (14 bp):
GTTGACTCGGACAA
Found at i:94731 original size:21 final size:21
Alignment explanation
Indices: 94705--94758 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
94695 GTTTCCAGAT
*
94705 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
94726 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
94747 TCGCAATGCGAA
1 TCGCAATGCGAA
94759 TATGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:94797 original size:21 final size:21
Alignment explanation
Indices: 94773--94832 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
94763 TAAATCGCAA
*
94773 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAATTCGCGT
*
94794 TGCGATAGTCGAAATTCGCGT
1 TGCGATAGTCCAAATTCGCGT
**
94815 TGCGATTTTCCAAATTCG
1 TGCGATAGTCCAAATTCG
94833 ACTATTGCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (21 bp):
TGCGATAGTCCAAATTCGCGT
Found at i:94924 original size:23 final size:21
Alignment explanation
Indices: 94858--94945 Score: 74
Period size: 21 Copynumber: 4.2 Consensus size: 21
94848 ACTTTGACTA
* * *
94858 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCAAAT
*
94878 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAAT
* *
94899 TCGCATTTCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAAT
*
94922 TCG--TTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAT
94941 TCGCA
1 TCGCA
94946 ACGACTGGTG
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
19 11 0.21
20 12 0.23
21 19 0.36
23 11 0.21
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:94927 original size:111 final size:110
Alignment explanation
Indices: 94718--94931 Score: 258
Period size: 111 Copynumber: 1.9 Consensus size: 110
94708 CAACGCGAAC
94718 TTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 TTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
* *
94783 CAAGTTCGCGTTGCGATAGTCGAAATTCGCGTTGCGATTTTCCAAA
66 CAAGTTCGCATTGCGATAGTCCAAATTC-CGTTGCGATTTTCCAAA
* * * *
94829 TTCGACTATTGCAACT-CGAACTTTGACTATCGCATTGCG-AT-T-TACATATTCGCATTGCGAT
1 TTCGACTATCGCAA-TGCGAACTTGGACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGAT
* *
94890 AGTCCAAGTTCGCATTTCGATTTATTCCAAATT-CGTTGCGAT
62 AGTCCAAGTTCGCATTGCGA--TAGTCCAAATTCCGTTGCGAT
94932 AGTCCAAAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
108 2 0.02
109 2 0.02
110 3 0.03
111 72 0.81
112 1 0.01
113 9 0.10
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (110 bp):
TTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
CAAGTTCGCATTGCGATAGTCCAAATTCCGTTGCGATTTTCCAAA
Found at i:95781 original size:90 final size:90
Alignment explanation
Indices: 95674--95847 Score: 255
Period size: 90 Copynumber: 1.9 Consensus size: 90
95664 AATTTAGAAT
* *
95674 AAATCGCATCGCGAACTTCGACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCGA
1 AAATCGCAACGCGAACTTCGACTATCGCAATGCG-AT-T-TACATATTCGCAATGCGATAGTCCA
*
95736 AGTTCGCGTTGCGATAGTCGAATTTGGA
63 AGTTCGCATTGCGATAGTCGAATTTGGA
* *
95764 AAATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 AAATCGCAACGCGAACTTCGACTATCGCAATGCGATTTACATATTCGCAATGCGATAGTCCAAGT
95829 TCGCATTGCGATAGTCGAA
66 TCGCATTGCGATAGTCGAA
95848 GTTCGTGTTG
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
87 2 0.03
88 2 0.03
89 3 0.04
90 69 0.91
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (90 bp):
AAATCGCAACGCGAACTTCGACTATCGCAATGCGATTTACATATTCGCAATGCGATAGTCCAAGT
TCGCATTGCGATAGTCGAATTTGGA
Found at i:95860 original size:21 final size:21
Alignment explanation
Indices: 95807--95852 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
95797 GATTTACATA
95807 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
95828 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
95849 TTCG
1 TTCG
95853 TGTTGCGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:100228 original size:13 final size:13
Alignment explanation
Indices: 100210--100234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100200 AGTGCATGTG
100210 TCCAACACTTGAA
1 TCCAACACTTGAA
100223 TCCAACACTTGA
1 TCCAACACTTGA
100235 TTTTCAAGGA
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:0.36, C:0.32, G:0.08, T:0.24
Consensus pattern (13 bp):
TCCAACACTTGAA
Found at i:105033 original size:2 final size:2
Alignment explanation
Indices: 105026--105051 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
105016 AAGTTGTAGC
105026 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
105052 AAGCAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:123441 original size:14 final size:15
Alignment explanation
Indices: 123394--123443 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 15
123384 TTGTTTCAAC
* *
123394 ATTTTGAATTGTTTG
1 ATTTTGGATTGTTGG
123409 ATTTTGTGGATTGTTGG
1 A-TTT-TGGATTGTTGG
123426 ATTTTGGATT-TTGG
1 ATTTTGGATTGTTGG
123440 ATTT
1 ATTT
123444 AAAATGGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 8 0.26
15 7 0.23
16 6 0.19
17 10 0.32
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:123721 original size:14 final size:13
Alignment explanation
Indices: 123687--123718 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
123677 GGGAGAAGTG
123687 TGTTTTAAGTGTA
1 TGTTTTAAGTGTA
123700 TGTTTTAAGTGTA
1 TGTTTTAAGTGTA
123713 TGTTTT
1 TGTTTT
123719 TAAAATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (13 bp):
TGTTTTAAGTGTA
Found at i:124728 original size:17 final size:19
Alignment explanation
Indices: 124696--124731 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
124686 CATATATCTC
124696 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
124715 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
124732 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:129504 original size:64 final size:65
Alignment explanation
Indices: 129393--129543 Score: 182
Period size: 64 Copynumber: 2.3 Consensus size: 65
129383 TCTTTCAATG
* * * * * *
129393 AAGGTATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTT-
129457 A
65 A
* * *
129458 AAGG-ATGCATCGATGCATTATC-TATGCATCGATGTATCAAAGGCATTCGATGTTCTTCTTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTA
129521 AAGGAATGCATCGATGCACTTAT
1 AAGGAATGCATCGATGCA-TTAT
129544 GAATGTGCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 5 0.07
64 61 0.81
65 9 0.12
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (65 bp):
AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTA
Found at i:130996 original size:17 final size:17
Alignment explanation
Indices: 130970--131008 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
130960 AGTTTGTGCA
130970 ATTC-AAGCCAATTTTC
1 ATTCAAAGCCAATTTTC
130986 ATTCAAAGCCAATTTTC
1 ATTCAAAGCCAATTTTC
131003 ATTCAA
1 ATTCAA
131009 TATTCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (17 bp):
ATTCAAAGCCAATTTTC
Found at i:133607 original size:55 final size:54
Alignment explanation
Indices: 133522--133653 Score: 219
Period size: 55 Copynumber: 2.4 Consensus size: 54
133512 GTGTTTCTCC
* **
133522 TTCTTTCATACAACCTTTCCTTTTACAAAATGTAAAACCATTGCATTAATATTG
1 TTCTTTCATACAACTTTTCCTTTTACAAAATGTAAAACCATTGCAAGAATATTG
133576 TCTCTTTCATACAACTTTTCCTTTTACAAAATGTAAAACCATTGCAAGAATATTG
1 T-TCTTTCATACAACTTTTCCTTTTACAAAATGTAAAACCATTGCAAGAATATTG
*
133631 TGCTTTCATACAACTTTTCCTTT
1 TTCTTTCATACAACTTTTCCTTT
133654 GCAATCCACT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 22 0.30
55 51 0.70
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (54 bp):
TTCTTTCATACAACTTTTCCTTTTACAAAATGTAAAACCATTGCAAGAATATTG
Found at i:135177 original size:64 final size:63
Alignment explanation
Indices: 135108--135264 Score: 176
Period size: 64 Copynumber: 2.4 Consensus size: 63
135098 TTGAAGGTGT
** *
135108 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCA-ATTAGT
1 ATCGATGCACAGGTA-TGCATCGATGCATC-CCATTAATAAT-AAAACAGCGAATGCATATTA-T
135170 GC
62 GC
* * *
135172 ATCGATGCATAAGGCATGCATCGATGCATCCCATTAATAATAAAACAGCGAATGCATTTTATGC
1 ATCGATGCA-CAGGTATGCATCGATGCATCCCATTAATAATAAAACAGCGAATGCATATTATGC
*
135236 ATCGATGCACAAGTATTGCATCGATGCAT
1 ATCGATGCACAGGTA-TGCATCGATGCAT
135265 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 65 0.82
65 11 0.14
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (63 bp):
ATCGATGCACAGGTATGCATCGATGCATCCCATTAATAATAAAACAGCGAATGCATATTATGC
Found at i:135679 original size:29 final size:29
Alignment explanation
Indices: 135641--135743 Score: 170
Period size: 29 Copynumber: 3.5 Consensus size: 29
135631 TATGTGATAT
* *
135641 GAGAACATGACATGAGCTATATAATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
135671 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
135700 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
135729 GAGAAATGACATGAG
1 GAGAAATGACATGAG
135744 TATATGAACA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
29 64 0.93
30 5 0.07
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:135853 original size:15 final size:15
Alignment explanation
Indices: 135835--135868 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
135825 GAGGGTATAA
135835 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
135850 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
135865 TAGT
1 TAGT
135869 GGTTCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:142141 original size:64 final size:64
Alignment explanation
Indices: 142070--142226 Score: 187
Period size: 64 Copynumber: 2.5 Consensus size: 64
142060 TTGAAGGTGT
**
142070 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCA-ATTAGT
1 ATCGATGCACAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
142132 GC
63 GC
* * *
142134 ATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
* *
142198 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAGGTAGTGCATCGATGCAT
142227 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 65 0.82
65 11 0.14
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:142642 original size:29 final size:29
Alignment explanation
Indices: 142603--142712 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
142593 TATGTGATAT
*
142603 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAACTACATGATCACAA
142633 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAACTACATGATCACAA
142662 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAACTACATGATCACAA
*
142691 GAGAAATGACATG-AGTACATGA
1 GAGAAATGACATGAACTACATGA
142713 ACATATAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 8 0.10
29 65 0.83
30 5 0.06
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAACTACATGATCACAA
Found at i:142815 original size:15 final size:15
Alignment explanation
Indices: 142797--142830 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
142787 GAGGGTATAA
142797 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
142812 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
142827 TAGT
1 TAGT
142831 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:143830 original size:30 final size:31
Alignment explanation
Indices: 143788--143864 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
143778 ATAATGGTGG
*
143788 AATGATCATTTTGTTACAAATCGATCACGTT
1 AATGACCATTTTGTTACAAATCGATCACGTT
* *
143819 AGTGA-CATTTTGTTACAAATCGATCATGTT
1 AATGACCATTTTGTTACAAATCGATCACGTT
*
143849 AATGACCAATTTGTTA
1 AATGACCATTTTGTTA
143865 ATTTTAACAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 28 0.68
31 13 0.32
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (31 bp):
AATGACCATTTTGTTACAAATCGATCACGTT
Found at i:162584 original size:19 final size:19
Alignment explanation
Indices: 162560--162611 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
162550 AATGCAATTC
162560 GTGCATCGATGCATAAGTA
1 GTGCATCGATGCATAAGTA
*
162579 GTGCATTGATGCATAAGTA
1 GTGCATCGATGCATAAGTA
162598 GTGCATCGATGCAT
1 GTGCATCGATGCAT
162612 CACATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (19 bp):
GTGCATCGATGCATAAGTA
Found at i:162590 original size:83 final size:83
Alignment explanation
Indices: 162496--162675 Score: 229
Period size: 83 Copynumber: 2.2 Consensus size: 83
162486 TTGTTTGAAT
* ** **
162496 GTGCACCGATGCATTGGTAGTGCATCGATGCACTC-TTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCA-TCACATTAATAATAAA-ACATCGAATGCAATT
*
162559 CGTGCATCGATGCATAAGTA
64 CGTGCATCGATGCATAAGGA
* * * * *
162579 GTGCATTGATGCATAAGTAGTGCATCGATGCATCACATTAATAGTGAAACATCGAATGTAATTGG
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCACATTAATAATAAAACATCGAATGCAATTCG
162644 TGCATCGATGCATAAGGA
66 TGCATCGATGCATAAGGA
162662 GTGCATCGATGCAT
1 GTGCATCGATGCAT
162676 CCCAACAATA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
82 2 0.02
83 77 0.93
84 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (83 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCACATTAATAATAAAACATCGAATGCAATTCG
TGCATCGATGCATAAGGA
Found at i:163006 original size:26 final size:26
Alignment explanation
Indices: 162977--163031 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
162967 TGTTGATTTT
162977 TATA-ATACAGTAGTTGTGA-ACATGCA
1 TATAGATA-AGTA-TTGTGATACATGCA
*
163003 TATATGATAATTATTGTGATACATGCA
1 TATA-GATAAGTATTGTGATACATGCA
163030 TA
1 TA
163032 AGACATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 10 0.40
27 12 0.48
28 3 0.12
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (26 bp):
TATAGATAAGTATTGTGATACATGCA
Found at i:163065 original size:12 final size:12
Alignment explanation
Indices: 163048--163082 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
163038 ATATATGTTC
163048 ATGTGATATGAT
1 ATGTGATATGAT
163060 ATGTGATATGAT
1 ATGTGATATGAT
163072 ATGTGATATGA
1 ATGTGATATGA
163083 GAACATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:163140 original size:29 final size:29
Alignment explanation
Indices: 163098--163171 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
163088 TGATATGAAG
163098 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
163127 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
163156 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
163172 ACATATGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:163274 original size:15 final size:15
Alignment explanation
Indices: 163256--163288 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
163246 GAGGATATAA
163256 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
163271 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
163286 TAG
1 TAG
163289 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:169558 original size:64 final size:61
Alignment explanation
Indices: 169421--169643 Score: 194
Period size: 64 Copynumber: 3.5 Consensus size: 61
169411 TTGTTTGAAT
* ** ** *
169421 GTGCATTGATGCATTGGTAGTGCATCGATGCACTCTTTTAAAATAAACATCGAATGTAATTC
1 GTGCATCGATGCATAAGTAGTGCATCGATGCA-TCCATTAAAATAAACATCGAATGCAATTC
* * * *
169483 ATGCATCGATGCATAAGTAGTGCATCGATGCATCACATTAATAGTGAAATATCGAATGCAATTG
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATC-CATTAA-AAT-AAACATCGAATGCAATTC
* ** * * ** *
169547 GTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATACTACATCGAATACCTTTT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCAT-CCATTAA-AATA-AACATCGAATGCAATTC
* * *
169611 ATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCAT
169644 ACCTTCATTA
Statistics
Matches: 131, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
61 2 0.02
62 32 0.24
63 3 0.02
64 93 0.71
65 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (61 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCATTAAAATAAACATCGAATGCAATTC
Found at i:170031 original size:28 final size:28
Alignment explanation
Indices: 169987--170059 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
169977 TGATATGAAG
*
169987 TGACATGAGCTACATGATCACCAGAGAAA
1 TGACATGA-CTACATGATCACAAGAGAAA
170016 TGACATGACTACATGATCACAAGAGAAA
1 TGACATGACTACATGATCACAAGAGAAA
*
170044 TGACATGAGTACATGA
1 TGACATGACTACATGA
170060 ACAAATGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 34 0.81
29 8 0.19
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (28 bp):
TGACATGACTACATGATCACAAGAGAAA
Found at i:170158 original size:15 final size:15
Alignment explanation
Indices: 170140--170172 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
170130 GAGGGTATAA
170140 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
170155 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
170170 TAG
1 TAG
170173 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:173691 original size:124 final size:120
Alignment explanation
Indices: 173503--173746 Score: 418
Period size: 124 Copynumber: 2.0 Consensus size: 120
173493 TTTTTGTTGG
173503 TAATTAATAATTATATGTTAATATGAAAAGTATAGCCAATTTTGTAGCTGCTAGCTGTAGTTTTA
1 TAATTAATAATTATATGTTAATATGAAAAGTATAGCCAATTTTGTAGCTGCTAGCTGTAGTTTTA
173568 GATAAATAATAGACCATCATTGTGCTGTTTATACTTTATCCAAGGGTAAAGTATTGTAGA
66 GATAAATAATAGACCATCATTGTG-TGTTT-TAC-TTATCCAAGGGTAAA--ATTGTAGA
*
173628 TAATTAATAATTATATGTTAATATG-AAAGTATAGCCAATTTTGTAGTTGCTAGCTGTAGTTTTA
1 TAATTAATAATTATATGTTAATATGAAAAGTATAGCCAATTTTGTAGCTGCTAGCTGTAGTTTTA
*
173692 GATAAATAATAGACCATCATTGTGTGTTTTACTTATCTAAGGGTAAAATTGTAGA
66 GATAAATAATAGACCATCATTGTGTGTTTTACTTATCCAAGGGTAAAATTGTAGA
173747 ATTGTATGTA
Statistics
Matches: 117, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
119 8 0.07
121 14 0.12
122 3 0.03
123 5 0.04
124 62 0.53
125 25 0.21
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (120 bp):
TAATTAATAATTATATGTTAATATGAAAAGTATAGCCAATTTTGTAGCTGCTAGCTGTAGTTTTA
GATAAATAATAGACCATCATTGTGTGTTTTACTTATCCAAGGGTAAAATTGTAGA
Found at i:175959 original size:15 final size:15
Alignment explanation
Indices: 175936--175968 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
175926 TTCTTAGTTT
175936 TTTAATTTTTTAGTA
1 TTTAATTTTTTAGTA
*
175951 TTTATTTTTTTAGTA
1 TTTAATTTTTTAGTA
175966 TTT
1 TTT
175969 GTATATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (15 bp):
TTTAATTTTTTAGTA
Found at i:175959 original size:23 final size:23
Alignment explanation
Indices: 175933--175997 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
175923 GTGTTCTTAG
175933 TTTTTTAAT-TTTTTAGTATTTAT
1 TTTTTTAATATTTTTA-TATTTAT
* *
175956 TTTTTTAGTATTTGTATATTTAT
1 TTTTTTAATATTTTTATATTTAT
*
175979 TTTTTAAATATTTTTATAT
1 TTTTTTAATATTTTTATAT
175998 CGATATTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 31 0.86
24 5 0.14
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.71
Consensus pattern (23 bp):
TTTTTTAATATTTTTATATTTAT
Done.