Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008235.1 Hibiscus syriacus cultivar Beakdansim tig00110879_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: 820011
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:1426 original size:20 final size:20
Alignment explanation
Indices: 1398--1436 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1388 CAAGAAATTA
1398 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
1418 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1437 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:7003 original size:62 final size:63
Alignment explanation
Indices: 6906--7037 Score: 239
Period size: 62 Copynumber: 2.1 Consensus size: 63
6896 ATCATTAATG
6906 GATTTAAAAGAAATTCGCTTTTGTTTTCCTTTAGCACAAGCATCACAGATTTTACCATTA-CA
1 GATTTAAAAGAAATTCGCTTTTGTTTTCCTTTAGCACAAGCATCACAGATTTTACCATTATCA
*
6968 GATTTAAAAGAAATTCGCTTTTGTTTTCCTTTAGCACAAGCATCACAGATTTTATCATTATCA
1 GATTTAAAAGAAATTCGCTTTTGTTTTCCTTTAGCACAAGCATCACAGATTTTACCATTATCA
*
7031 AATTTAA
1 GATTTAA
7038 GCTTAGGCAA
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 59 0.88
63 8 0.12
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (63 bp):
GATTTAAAAGAAATTCGCTTTTGTTTTCCTTTAGCACAAGCATCACAGATTTTACCATTATCA
Found at i:10077 original size:64 final size:63
Alignment explanation
Indices: 9963--10087 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 63
9953 TGGACCCTTA
** *
9963 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTAAGAAAAA-CCTGAGTGCATCGATACATGGTAT
*
10027 GTGCATCGATGCATAAAATGCATTCGATGTTCAAGAAATTAA-TTGA-TGCATCGATACATGG
1 GTGCATCGATGCATAAAATGCATTCGATGTT-AAGAAA--AACCTGAGTGCATCGATACATGG
10088 ATTGGTGCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
64 45 0.83
65 7 0.13
67 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTAAGAAAAACCTGAGTGCATCGATACATGGTAT
Found at i:11007 original size:33 final size:33
Alignment explanation
Indices: 10958--11054 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
10948 TTTATTTTGT
*
10958 TCGGGTC-GGGTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGGTTTTTTAAGTGTGGTATTCGGG
10990 TCGGGTCGGGGTTTTTTAAGTGTGGTATTCGGG
1 TCGGGTCGGGGTTTTTTAAGTGTGGTATTCGGG
*
11023 TCGGGTCGGGATTTTTTAAGTGTGGTATTCGG
1 TCGGGTCGGGGTTTTTTAAGTGTGGTATTCGG
11055 ACCGACCCAA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 7 0.11
33 55 0.89
ACGTcount: A:0.11, C:0.09, G:0.39, T:0.40
Consensus pattern (33 bp):
TCGGGTCGGGGTTTTTTAAGTGTGGTATTCGGG
Found at i:27609 original size:3 final size:3
Alignment explanation
Indices: 27601--27642 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
27591 TATTTTTATT
*
27601 TAA TAA TAA TATA TAA TAA TAA TAA T-T TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27643 ATATGATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 31 0.89
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:39582 original size:21 final size:20
Alignment explanation
Indices: 39496--39653 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
39486 AAATGACCAA
**
39496 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
39515 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
39535 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
39555 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
39576 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
39597 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
39617 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
39638 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
39654 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:39669 original size:40 final size:40
Alignment explanation
Indices: 39620--39774 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
39610 CGATTTTCCA
* ** *
39620 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
39660 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
39700 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
39740 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
39775 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:39682 original size:20 final size:20
Alignment explanation
Indices: 39620--39773 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
39610 CGATTTTCCA
* ** *
39620 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
39640 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
39660 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
39680 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
39700 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
39720 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
39740 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
39761 AAATCGCAACGCG
1 AAATCGCAACGCG
39774 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:40195 original size:33 final size:33
Alignment explanation
Indices: 40156--40226 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
40146 TTCACTTAGA
*
40156 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
40189 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
40222 TTTCA
1 TTTCA
40227 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:40350 original size:20 final size:20
Alignment explanation
Indices: 40306--40415 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
40296 TGCAGAAGAG
*
40306 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
40327 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
40347 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
40368 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
40382 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
40401 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
40416 CGCAATGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:40363 original size:41 final size:38
Alignment explanation
Indices: 40299--40415 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
40289 TTCAATTTGC
* *
40299 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
40337 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
40378 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
40411 AGAAT
1 AGAAT
40416 CGCAATGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:40385 original size:14 final size:14
Alignment explanation
Indices: 40366--40420 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
40356 GAGAAATGAA
40366 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
40380 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
40399 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40413 AATCGCAA
1 AATCGCAA
40421 TGCGAAACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40398 original size:33 final size:33
Alignment explanation
Indices: 40358--40438 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
40348 CGCAACGAGA
40358 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
40391 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
40424 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
40439 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:40456 original size:19 final size:19
Alignment explanation
Indices: 40434--40527 Score: 82
Period size: 19 Copynumber: 5.5 Consensus size: 19
40424 GAAACCAAAA
*
40434 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40453 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
40467 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40486 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
40500 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40519 TCGCGTTGC
1 TCGCGTTGC
40528 CATTCTCTCG
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 19 0.33
16 6 0.10
17 6 0.10
19 27 0.47
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:40475 original size:14 final size:14
Alignment explanation
Indices: 40456--40545 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
40446 TTTCATTTCG
40456 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
40470 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
40489 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
40503 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
40522 CGTTGCCATTCTCT
1 CGTTGCGATTCTCT
40536 CGTTGCGATT
1 CGTTGCGATT
40546 TCATTTCAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
14 28 0.48
16 6 0.10
17 6 0.10
19 18 0.31
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:40481 original size:33 final size:33
Alignment explanation
Indices: 40439--40552 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
40429 CAAAATCGCA
40439 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
40472 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
40505 TTGCGATTTTCATTTCGCGTTGCCATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
40538 TTGCGA-TTTCATTTC
1 TTGCGATTTTCATTTC
40553 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 9 0.12
33 69 0.88
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:42403 original size:93 final size:93
Alignment explanation
Indices: 42244--42802 Score: 1072
Period size: 93 Copynumber: 6.1 Consensus size: 93
42234 TAGATTGCTT
*
42244 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
42309 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
42337 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
42402 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
42430 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
42494 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
42522 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
42586 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
42613 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
42678 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
42706 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
42771 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
42798 AGTAA
1 AGTAA
42803 TGCAATCCAT
Statistics
Matches: 460, Mismatches: 3, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
91 77 0.17
92 124 0.27
93 259 0.56
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:42659 original size:276 final size:278
Alignment explanation
Indices: 42244--42802 Score: 1070
Period size: 276 Copynumber: 2.0 Consensus size: 278
42234 TAGATTGCTT
42244 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
42309 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
42374 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
131 GTATATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
42439 GTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
196 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
42503 GTTTTGTCTTTTGGTTGAA
261 GTTTTGTCTTTTGGTTG-A
*
42522 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
42586 TTTGTC-TTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
42650 GTATATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
131 GTATATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
42715 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
196 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
42780 GTTTTGTCTTTTGGTTGA
261 GTTTTGTCTTTTGGTTGA
42798 AGTAA
1 AGTAA
42803 TGCAATCCAT
Statistics
Matches: 278, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
276 151 0.54
277 71 0.26
278 56 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (278 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
GTTTTGTCTTTTGGTTGA
Found at i:42890 original size:19 final size:19
Alignment explanation
Indices: 42850--42977 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
42840 TAGTTTACTT
* *
42850 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
42870 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
42889 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACCAAAA
*
42907 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
42921 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
42940 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
42954 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
42973 TCGCA
1 TCGCA
42978 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 36 0.41
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:42946 original size:33 final size:32
Alignment explanation
Indices: 42886--42977 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
42876 CGCGAAACCA
**
42886 AAATCGCAACGCGAAA-TGAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
42917 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
42950 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
42978 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.02
32 16 0.29
33 39 0.70
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:43000 original size:19 final size:19
Alignment explanation
Indices: 42973--43107 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
42963 GAAACCAAAA
*
42973 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
42992 TTGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
43008 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
43025 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
43041 T--CGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
**
43058 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
43077 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
43097 TCGTGTTGCGA
1 TCGCGTTGCGA
43108 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 11 0.12
19 45 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:43012 original size:14 final size:14
Alignment explanation
Indices: 42995--43051 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
42985 TTTCATTTTG
42995 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
43009 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
43026 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
43042 CGTTGCGATT
1 CGTTGCGATT
43052 TTTATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:43020 original size:33 final size:33
Alignment explanation
Indices: 42978--43070 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
42968 CAAAATCGCA
* *
42978 TTGCGATTTTCATTTTGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
43011 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
43044 TTGCGATTTTTATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
43071 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:45047 original size:14 final size:14
Alignment explanation
Indices: 45028--45066 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
45018 ATTGTTTAAT
45028 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
45042 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
45056 TGATTGTGTAA
1 TGATT-TGTAA
45067 TTGATGCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:45193 original size:19 final size:19
Alignment explanation
Indices: 45169--45285 Score: 181
Period size: 19 Copynumber: 6.4 Consensus size: 19
45159 AAAATTGACT
45169 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
45188 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
45207 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
45226 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
45240 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
45259 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
45279 ATCGCAA
1 ATCGCAA
45286 CGGGAGAATC
Statistics
Matches: 90, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 58 0.64
20 16 0.18
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:45248 original size:33 final size:36
Alignment explanation
Indices: 45169--45285 Score: 159
Period size: 33 Copynumber: 3.2 Consensus size: 36
45159 AAAATTGACT
45169 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
*
45207 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
45240 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GC-G-AATGAAA
45279 ATCGCAA
1 ATCGCAA
45286 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
33 29 0.41
34 1 0.01
35 1 0.01
36 3 0.04
38 27 0.38
39 10 0.14
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:45317 original size:53 final size:53
Alignment explanation
Indices: 45187--45304 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
45177 GCGAAATGAA
45187 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
*
45239 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
45292 AATCGCAATGCGA
1 AATCGCAATGCGA
45305 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:45322 original size:19 final size:19
Alignment explanation
Indices: 45294--45461 Score: 163
Period size: 19 Copynumber: 9.7 Consensus size: 19
45284 AACGGGAGAA
* *
45294 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
45313 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
45329 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
45346 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
45365 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
45381 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
45398 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
45416 TCCGCATTGCGA-TTTCA--
1 T-CGCATTGCGATTTTCATT
*
45433 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
45449 TCGCATTGCGATT
1 TCGCATTGCGATT
45462 CTCTCGTTGC
Statistics
Matches: 124, Mismatches: 8, Indels: 34
0.75 0.05 0.20
Matches are distributed among these distances:
13 5 0.04
14 17 0.14
15 1 0.01
16 15 0.12
17 15 0.12
18 8 0.06
19 63 0.51
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:45337 original size:33 final size:33
Alignment explanation
Indices: 45300--45475 Score: 148
Period size: 33 Copynumber: 5.2 Consensus size: 33
45290 AGAATCGCAA
*
45300 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
45333 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
45371 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
45404 TGCGA-TTTCATTTCCGCATTGCGATT-TCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
45436 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
45469 TGCGATT
1 TGCGATT
45476 GTAATTTCCG
Statistics
Matches: 113, Mismatches: 15, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
30 4 0.04
31 6 0.05
32 25 0.22
33 47 0.42
35 5 0.04
36 4 0.04
37 2 0.02
38 8 0.07
39 3 0.03
40 9 0.08
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:45357 original size:52 final size:52
Alignment explanation
Indices: 45294--45461 Score: 270
Period size: 52 Copynumber: 3.2 Consensus size: 52
45284 AACGGGAGAA
* *
45294 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
45346 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
45398 TCGCATTGCGA-TTTCATTTCCGCATTGCGATT-TCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATT
45449 TCGCATTGCGATT
1 TCGCATTGCGATT
45462 CTCTCGTTGC
Statistics
Matches: 110, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
51 35 0.32
52 75 0.68
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:47931 original size:24 final size:24
Alignment explanation
Indices: 47897--47943 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47887 CTGAAACATC
47897 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
47921 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
47944 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:48651 original size:20 final size:20
Alignment explanation
Indices: 48623--48932 Score: 352
Period size: 20 Copynumber: 15.5 Consensus size: 20
48613 AAATTTCAGT
* *
48623 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
48643 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
48663 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
48683 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
48703 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
48723 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
48743 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
48763 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
48783 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
48803 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
48823 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
48843 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
48863 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
48883 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
48903 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
48923 GTTGCGATTT
1 GTTGCGATTT
48933 TGGAAAATCG
Statistics
Matches: 256, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
20 255 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:48949 original size:21 final size:21
Alignment explanation
Indices: 48919--49001 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
48909 ATTTTCATAT
*
48919 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
48940 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
48961 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
48982 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
49002 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:48992 original size:42 final size:43
Alignment explanation
Indices: 48899--48997 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
48889 ATTTATGTGT
* *
48899 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
48940 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
48982 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
48998 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:49362 original size:36 final size:36
Alignment explanation
Indices: 49315--49387 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
49305 GGAAACTCGT
49315 AATAATGTTTCAATGTCTGCATCATTGCTGATTCCC
1 AATAATGTTTCAATGTCTGCATCATTGCTGATTCCC
49351 AATAATGTTTCAATGTCTGCATCATTGCTGATTCCC
1 AATAATGTTTCAATGTCTGCATCATTGCTGATTCCC
49387 A
1 A
49388 CATCAGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (36 bp):
AATAATGTTTCAATGTCTGCATCATTGCTGATTCCC
Found at i:54185 original size:3 final size:3
Alignment explanation
Indices: 54177--54203 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54167 AGAGAAAATC
54177 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
54204 AATATAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:55085 original size:12 final size:12
Alignment explanation
Indices: 55052--55090 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
55042 ATAGTTTTTG
*
55052 AATATAAATAAT
1 AATATAAATTAT
*
55064 AA-AAAAATTAT
1 AATATAAATTAT
55075 AATATAAATTAT
1 AATATAAATTAT
55087 AATA
1 AATA
55091 ATTCTAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATATAAATTAT
Found at i:57026 original size:64 final size:65
Alignment explanation
Indices: 56953--57108 Score: 235
Period size: 65 Copynumber: 2.4 Consensus size: 65
56943 ACACCCTATT
*
56953 TCGAATGCATTTTGTGTACCGATGCACA-ACCATGCATCGATGCACTCTTGAAT-TTATTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATCTT-TTGAAAC
57016 A
65 A
**
57017 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATCTTTTGAAACA
* * *
57082 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
57109 CCCAAGTGTA
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
64 28 0.33
65 54 0.64
66 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATCTTTTGAAACA
Found at i:57382 original size:19 final size:20
Alignment explanation
Indices: 57338--57382 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
57328 AAGAATTAAG
*
57338 AAGAAAAGCTAGAGAATCGA
1 AAGAGAAGCTAGAGAATCGA
57358 AA-AGAAGCTAGAGAATC-A
1 AAGAGAAGCTAGAGAATCGA
57376 AAGAGAA
1 AAGAGAA
57383 AGTATCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 18 0.78
20 2 0.09
ACGTcount: A:0.58, C:0.09, G:0.24, T:0.09
Consensus pattern (20 bp):
AAGAGAAGCTAGAGAATCGA
Found at i:59850 original size:21 final size:21
Alignment explanation
Indices: 59825--59876 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
59815 TTTACACTTG
59825 ATGCATCGATACAGCTTGACT
1 ATGCATCGATACAGCTTGACT
59846 ATGCATCGATACAGCTTGACT
1 ATGCATCGATACAGCTTGACT
59867 ATGCATCGAT
1 ATGCATCGAT
59877 GCACACACGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (21 bp):
ATGCATCGATACAGCTTGACT
Found at i:65574 original size:45 final size:44
Alignment explanation
Indices: 65510--65605 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 44
65500 TTTTGCATAA
*
65510 TGCATCGATACACTATGAAGCTGCA-TCGATGCA-TCCCTTTGAATG
1 TGCATCGATACACTATGAAGATGCACT-GATGCACT-CC-TTGAATG
*
65555 TGCATCGATACA-TCATGAAGATGCACTGATGTACTCCTTGAATG
1 TGCATCGATACACT-ATGAAGATGCACTGATGCACTCCTTGAATG
65599 TGCATCG
1 TGCATCG
65606 CTGCACACTG
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
44 15 0.33
45 29 0.63
46 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
TGCATCGATACACTATGAAGATGCACTGATGCACTCCTTGAATG
Found at i:65579 original size:21 final size:22
Alignment explanation
Indices: 65509--65579 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
65499 TTTTTGCATA
65509 ATGCATCGATACA-CTATGAAG
1 ATGCATCGATACATCTATGAAG
* * *
65530 CTGCATCGATGCATCCCTTTGAATG
1 ATGCATCGATACAT--CTATGAA-G
65555 -TGCATCGATACATC-ATGAAG
1 ATGCATCGATACATCTATGAAG
65575 ATGCA
1 ATGCA
65580 CTGATGTACT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.03
21 19 0.47
22 1 0.03
24 18 0.45
25 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (22 bp):
ATGCATCGATACATCTATGAAG
Found at i:68249 original size:19 final size:19
Alignment explanation
Indices: 68225--68270 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
68215 TTTTATGTAC
68225 CGATGCACATACCATGCAT
1 CGATGCACATACCATGCAT
68244 CGATGCACATACCATGCAT
1 CGATGCACATACCATGCAT
68263 CGATGCAC
1 CGATGCAC
68271 TCCATGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (19 bp):
CGATGCACATACCATGCAT
Found at i:72746 original size:44 final size:43
Alignment explanation
Indices: 72654--72773 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 43
72644 TTTATGTGCA
* * *
72654 ATGCATCGATACATTA-GAAAGTGTACCAATACATCCCTTGAAT
1 ATGCATCGATACACTATG-AAGTGCACCGATACATCCCTTGAAT
* *
72697 ATGCATCGATACACTATGAATGTGCACCGATGCATTCCTTGAAT
1 ATGCATCGATACACTATGAA-GTGCACCGATACATCCCTTGAAT
* *
72741 GTGCATCGATACACTATGAAGTGCATCGATACA
1 ATGCATCGATACACTATGAAGTGCACCGATACA
72774 CTCGTCGGGT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 28 0.42
44 39 0.58
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (43 bp):
ATGCATCGATACACTATGAAGTGCACCGATACATCCCTTGAAT
Found at i:72766 original size:20 final size:21
Alignment explanation
Indices: 72692--72775 Score: 100
Period size: 21 Copynumber: 4.0 Consensus size: 21
72682 ATACATCCCT
*
72692 TGAATATGCATCGATACACTA
1 TGAATGTGCATCGATACACTA
* *
72713 TGAATGTGCACCGATGCATTCCT-
1 TGAATGTGCATCGATACA---CTA
72736 TGAATGTGCATCGATACACTA
1 TGAATGTGCATCGATACACTA
72757 TGAA-GTGCATCGATACACT
1 TGAATGTGCATCGATACACT
72776 CGTCGGGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
20 17 0.31
21 19 0.35
23 16 0.30
24 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (21 bp):
TGAATGTGCATCGATACACTA
Found at i:73204 original size:21 final size:21
Alignment explanation
Indices: 73173--73218 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
73163 ATTTTTTTTG
73173 TTTTGATTTTAAAAATTGTTGT
1 TTTTGATTTTAAAAA-TGTTGT
**
73195 TTTTGA-TTTAATTATGTTGT
1 TTTTGATTTTAAAAATGTTGT
73215 TTTT
1 TTTT
73219 AAAACTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 6 0.27
22 6 0.27
ACGTcount: A:0.22, C:0.00, G:0.13, T:0.65
Consensus pattern (21 bp):
TTTTGATTTTAAAAATGTTGT
Found at i:73255 original size:13 final size:13
Alignment explanation
Indices: 73234--73267 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
73224 TTCATATTGA
*
73234 TTTTCAAACATCG
1 TTTTCAAACATAG
*
73247 TTTTTAAACATAG
1 TTTTCAAACATAG
73260 TTTTCAAA
1 TTTTCAAA
73268 ATTGCCTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:78442 original size:22 final size:22
Alignment explanation
Indices: 78429--78472 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
78419 TATATTTTAG
*
78429 TATGTATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
78451 TATGAATTGATTTATTTAAAAA
1 TATGAATTGATTTATTTTAAAA
78473 AATTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:78529 original size:31 final size:31
Alignment explanation
Indices: 78494--78552 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
78484 TAGTTTATGG
*
78494 ATTATTTAAATGTCAGTATTGTAAAACTAAA
1 ATTATTTAAATGTCAGTATTGCAAAACTAAA
*
78525 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATGTCAGTATTGCAAAACT
78553 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATGTCAGTATTGCAAAACTAAA
Found at i:82488 original size:32 final size:32
Alignment explanation
Indices: 82452--82528 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 32
82442 ACAAAGTTTA
* * *
82452 CGATAATTGAAATATTTAAATACTTTCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
82484 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
82517 CGATAATTGAAA
1 CGATAATTGAAA
82529 CAAAGTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 11 0.28
33 28 0.72
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:86173 original size:29 final size:29
Alignment explanation
Indices: 86140--86195 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
86130 TCCCAACACA
*
86140 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
86169 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
86196 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:86242 original size:23 final size:23
Alignment explanation
Indices: 86213--86288 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
86203 CTCGGTTGCC
86213 CTCGGATTCCCTCGCATAGCTCG
1 CTCGGATTCCCTCGCATAGCTCG
86236 CTCGGATTCCCTCGCATAGCTCG
1 CTCGGATTCCCTCGCATAGCTCG
*
86259 TTCGG-TTGCCCTCGCATAGCTCG
1 CTCGGATT-CCCTCGCATAGCTCG
*
86282 GTCGGAT
1 CTCGGAT
86289 GGCCTCGGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
22 2 0.04
23 46 0.94
24 1 0.02
ACGTcount: A:0.12, C:0.36, G:0.25, T:0.28
Consensus pattern (23 bp):
CTCGGATTCCCTCGCATAGCTCG
Found at i:86376 original size:29 final size:29
Alignment explanation
Indices: 86339--86396 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
86329 GCAATCTCTT
*
86339 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
86368 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
86397 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:97240 original size:6 final size:6
Alignment explanation
Indices: 97220--97265 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
97210 TATTATATCA
97220 TTTA-T TTTA-T TTTATT TTTATT TTTATT TTTATT TTTA-T TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
97265 T
1 T
97266 ATTTCTGTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 14 0.36
6 25 0.64
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:98561 original size:23 final size:23
Alignment explanation
Indices: 98535--98579 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
98525 CTGGACCTCC
98535 CATTCTAATTTATTTCATTTTAT
1 CATTCTAATTTATTTCATTTTAT
* *
98558 CATTCTGATTTATTTTATTTTA
1 CATTCTAATTTATTTCATTTTA
98580 ATTTAGTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.62
Consensus pattern (23 bp):
CATTCTAATTTATTTCATTTTAT
Found at i:100232 original size:150 final size:151
Alignment explanation
Indices: 100039--100339 Score: 579
Period size: 150 Copynumber: 2.0 Consensus size: 151
100029 AATATTGGTG
100039 ACGACTCCTCAAACCACGTTTTATTATTAAAAGATCACCAAATTATTCGAGACGAAATCTTTT-A
1 ACGACTCCTCAAACCACGTTTTATTATTAAAAGATCACCAAATTATTCGAGACGAAATCTTTTAA
100103 AAATTAGATTTTAAAAATTAAATTTTGTTTTTAAGAACAACCG-TTCGACACTGTACATACAATG
66 AAATTAGATTTT-AAAATTAAATTTTGTTTTTAAGAACAACCGTTTCGACACTGTACATACAATG
100167 TTGGCTTTCCTTATGTGAGTTT
130 TTGGCTTTCCTTATGTGAGTTT
100189 ACGACTCCTCAAACCACGTTTTATTATTAAAAGATCACCAAATTATTCGAGACGAAATCTTTTAA
1 ACGACTCCTCAAACCACGTTTTATTATTAAAAGATCACCAAATTATTCGAGACGAAATCTTTTAA
100254 AAATTAGATTTTAAAATTAAATTTTGTTTTTAAGAACAACCGTTTCGACACTGTACATACAATGT
66 AAATTAGATTTTAAAATTAAATTTTGTTTTTAAGAACAACCGTTTCGACACTGTACATACAATGT
100319 TGGCTTTCCTTATGTGAGTTT
131 TGGCTTTCCTTATGTGAGTTT
100340 TATAAGGTAC
Statistics
Matches: 149, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
150 93 0.62
151 56 0.38
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (151 bp):
ACGACTCCTCAAACCACGTTTTATTATTAAAAGATCACCAAATTATTCGAGACGAAATCTTTTAA
AAATTAGATTTTAAAATTAAATTTTGTTTTTAAGAACAACCGTTTCGACACTGTACATACAATGT
TGGCTTTCCTTATGTGAGTTT
Found at i:100704 original size:21 final size:21
Alignment explanation
Indices: 100680--100741 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
100670 GGTAGAGCGA
* *
100680 TACTTAAAATGTTATTTTTTC
1 TACTTAAAATATTATTTTTGC
** * *
100701 TACTGGAAATATTAATTTCGC
1 TACTTAAAATATTATTTTTGC
*
100722 TACTTAAAATAATATTTTTG
1 TACTTAAAATATTATTTTTG
100742 ATATTAACAT
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (21 bp):
TACTTAAAATATTATTTTTGC
Found at i:100792 original size:45 final size:42
Alignment explanation
Indices: 100741--100823 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 42
100731 TAATATTTTT
*
100741 GATATTAACATTTTTGGTAAAAAAATATTATTTTAAATAACGTCC
1 GATATTAACA-TTTT-G-AAAAAAATAATATTTTAAATAACGTCC
* *
100786 GATATTAATATTTTGATAAAAATAATATTTTAAATAAC
1 GATATTAACATTTTGAAAAAAATAATATTTTAAATAAC
100824 CTCTACTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 21 0.60
43 1 0.03
44 4 0.11
45 9 0.26
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (42 bp):
GATATTAACATTTTGAAAAAAATAATATTTTAAATAACGTCC
Found at i:101469 original size:2 final size:2
Alignment explanation
Indices: 101464--101528 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
101454 ATATATAAGA
101464 AT AT AT AT AT AT AT AT AT AT A- 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 AT AT
101505 AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
101529 ATTAGATTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 59 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:101743 original size:2 final size:2
Alignment explanation
Indices: 101736--101817 Score: 104
Period size: 2 Copynumber: 44.0 Consensus size: 2
101726 AATTCGTTAA
* *
101736 AT AT AT AT AT -T AT A- AT TT AT TT AT AT AT AT AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
101774 AT A- AT -T 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 AT AT
101814 AT AT
1 AT AT
101818 GATTAATCAA
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
1 6 0.09
2 64 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:108596 original size:14 final size:14
Alignment explanation
Indices: 108577--108603 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
108567 GATATAGTGA
108577 TTACTGATTATTGT
1 TTACTGATTATTGT
108591 TTACTGATTATTG
1 TTACTGATTATTG
108604 ATACTGGCAT
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:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (14 bp):
TTACTGATTATTGT
Found at i:109853 original size:16 final size:16
Alignment explanation
Indices: 109832--109872 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
109822 GATGTTTAAT
109832 TTAAATAAATTTAAAC
1 TTAAATAAATTTAAAC
* *
109848 TTAAATTAATTTTAAC
1 TTAAATAAATTTAAAC
109864 -TAAA-AAATT
1 TTAAATAAATT
109873 AAATCTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 4 0.18
15 4 0.18
16 14 0.64
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAATAAATTTAAAC
Found at i:112492 original size:23 final size:23
Alignment explanation
Indices: 112466--112525 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
112456 GCTCGTATAA
112466 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
112489 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
112512 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
112526 ATATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:113234 original size:64 final size:65
Alignment explanation
Indices: 113125--113270 Score: 215
Period size: 64 Copynumber: 2.2 Consensus size: 65
113115 TTTTTTTCAT
* * * *
113125 GGGGAATCGGTTCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATA-TCGTTGA
1 GGGGTATCGGTT-CCCCATGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTTGA
113189 -
65 G
*
113189 GGGGTATCGGTTCCCCATGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTTGA
1 GGGGTATCGGTTCCCCAT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTTGA
113254 G
65 G
113255 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
113271 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
63 5 0.07
64 46 0.62
65 7 0.09
66 16 0.22
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.32
Consensus pattern (65 bp):
GGGGTATCGGTTCCCCATGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTTGAG
Found at i:114843 original size:19 final size:19
Alignment explanation
Indices: 114821--114857 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
114811 CAAATTTCAT
114821 TTTGATTTTCAAAATCAAC
1 TTTGATTTTCAAAATCAAC
*
114840 TTTGTTTTTCAAAATCAA
1 TTTGATTTTCAAAATCAA
114858 ATCATTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (19 bp):
TTTGATTTTCAAAATCAAC
Found at i:116758 original size:40 final size:40
Alignment explanation
Indices: 116708--116817 Score: 157
Period size: 40 Copynumber: 2.8 Consensus size: 40
116698 CCTTACCTTT
* *
116708 GGTATCGATACCATATGAACAATATCGGTATTGTTCATGA
1 GGTATCGATACTATAAGAACAATATCGGTATTGTTCATGA
* * * * *
116748 GGTATCGATACTGTAAGAACAGTATTGATGTTGTTCATGA
1 GGTATCGATACTATAAGAACAATATCGGTATTGTTCATGA
116788 GGTATCGATACTATAAGAACAATATCGGTA
1 GGTATCGATACTATAAGAACAATATCGGTA
116818 CTTTTTGTCC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.32
Consensus pattern (40 bp):
GGTATCGATACTATAAGAACAATATCGGTATTGTTCATGA
Found at i:117848 original size:15 final size:14
Alignment explanation
Indices: 117803--117844 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
117793 ACTCCGATTC
117803 AACCTGTTGACTTT
1 AACCTGTTGACTTT
* **
117817 GACCCATTGACTTT
1 AACCTGTTGACTTT
117831 AACCTGTTGACTTT
1 AACCTGTTGACTTT
117845 TAACGTTCAC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.40
Consensus pattern (14 bp):
AACCTGTTGACTTT
Found at i:118866 original size:19 final size:20
Alignment explanation
Indices: 118842--118887 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
118832 GTAATAAAGG
118842 GTAAAATGGTCAATTGAT-A
1 GTAAAATGGTCAATTGATAA
118861 GTAAAATGGTCAATTGATAA
1 GTAAAATGGTCAATTGATAA
118881 GTAAAAT
1 GTAAAAT
118888 TTGTATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (20 bp):
GTAAAATGGTCAATTGATAA
Found at i:122037 original size:106 final size:109
Alignment explanation
Indices: 121851--122077 Score: 399
Period size: 106 Copynumber: 2.1 Consensus size: 109
121841 CACTCCCTTG
121851 GGTT-AATCATGGGACTATATATAGTGTACGGGTTGAGGATAATTATATGGTTTATTTTATTGTC
1 GGTTAAAT-ATGGGACTATATATAGTGTACGGGTTGAGGATAATTATATGGTTTATTTTATTGTC
121915 ACACTTATGAGATTTTACTGGATCAC-ATCC-ATATTACTATTAT
65 ACACTTATGAGATTTTACTGGATCACAATCCAATATTACTATTAT
*
121958 GGTTAAATATGGGACTATATATAGTGTACGGGTTGAGGA-CATTATATGGTTTATTTTATTGTCA
1 GGTTAAATATGGGACTATATATAGTGTACGGGTTGAGGATAATTATATGGTTTATTTTATTGTCA
122022 CACTTATGAGATTTTACTGGATCACAATCCATATATTACTATTAT
66 CACTTATGAGATTTTACTGGATCACAATCCA-ATATTACTATTAT
122067 GGTTAAATATG
1 GGTTAAATATG
122078 ATTTCTACTG
Statistics
Matches: 115, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
106 49 0.43
107 39 0.34
108 3 0.03
109 24 0.21
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (109 bp):
GGTTAAATATGGGACTATATATAGTGTACGGGTTGAGGATAATTATATGGTTTATTTTATTGTCA
CACTTATGAGATTTTACTGGATCACAATCCAATATTACTATTAT
Found at i:123301 original size:17 final size:17
Alignment explanation
Indices: 123279--123313 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
123269 GAGTATTTTT
123279 TTATTTGGGTTTTAAAA
1 TTATTTGGGTTTTAAAA
123296 TTATTTGGGTTTTAAAA
1 TTATTTGGGTTTTAAAA
123313 T
1 T
123314 ATTATTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (17 bp):
TTATTTGGGTTTTAAAA
Found at i:123399 original size:14 final size:14
Alignment explanation
Indices: 123377--123414 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
123367 GAGATTGGGC
123377 TGAATATAAATGAA
1 TGAATATAAATGAA
*
123391 TGAACATAAATGAA
1 TGAATATAAATGAA
*
123405 CGAATATAAA
1 TGAATATAAA
123415 CAAATGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (14 bp):
TGAATATAAATGAA
Found at i:123883 original size:32 final size:31
Alignment explanation
Indices: 123846--123923 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
123836 TCATATTATC
*
123846 TAAAATGATGATGTGATATATGTCACATCAT
1 TAAAATGATGATGTGATATATGTCACACCAT
* * * *
123877 TCAAAATAATGATGTGGTATGTGTCACGCCAT
1 T-AAAATGATGATGTGATATATGTCACACCAT
*
123909 TAAAATGATAATGTG
1 TAAAATGATGATGTG
123924 TGTCATGTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 13 0.33
32 26 0.67
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (31 bp):
TAAAATGATGATGTGATATATGTCACACCAT
Found at i:127084 original size:17 final size:19
Alignment explanation
Indices: 127058--127097 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
127048 GGGTAATTAA
127058 TGTATAGTAC-ATTAG-TT
1 TGTATAGTACTATTAGATT
*
127075 TGTATTGTACTATTAGATT
1 TGTATAGTACTATTAGATT
127094 TGTA
1 TGTA
127098 CTACAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 5 0.25
19 6 0.30
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.50
Consensus pattern (19 bp):
TGTATAGTACTATTAGATT
Found at i:127287 original size:2 final size:2
Alignment explanation
Indices: 127282--127311 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
127272 TAAAAAAACA
127282 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
127312 GTACACACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128334 original size:2 final size:2
Alignment explanation
Indices: 128327--128378 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
128317 GTTTTTAAGT
128327 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
128369 TA TA TA TA TA
1 TA TA TA TA TA
128379 ATTAATTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:132272 original size:15 final size:16
Alignment explanation
Indices: 132241--132284 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
132231 TAAAACGAAG
132241 ATAAAGAACATAAAAA
1 ATAAAGAACATAAAAA
132257 ATAAA-AACA-AATAAA
1 ATAAAGAACATAA-AAA
*
132272 ATAAAGAAAATAA
1 ATAAAGAACATAA
132285 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 12 0.50
16 8 0.33
17 2 0.08
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (16 bp):
ATAAAGAACATAAAAA
Found at i:132309 original size:55 final size:50
Alignment explanation
Indices: 132241--132391 Score: 139
Period size: 55 Copynumber: 2.9 Consensus size: 50
132231 TAAAACGAAG
* *
132241 ATAAA-GAACATAAAAAATAAAAACAAATAAAATAAAGAAAATAATATATAT
1 ATAAAGGAA-ATAAAAAATAAAAA-AAATAAAATAAAGAAAATAAAATAAAT
* *
132292 ATATA-TACAATAAATAAATAAAAACAAGAATAAAAAATAAAG-AAATAAAATAAAT
1 ATAAAGGA-AATAAA-AAAT-AAAA-AA-AAT--AAAATAAAGAAAATAAAATAAAT
*
132347 ATAAAGGAAATAAAAAATAAAAAAAATAATA-AAAGATAAATAAAA
1 ATAAAGGAAATAAAAAATAAAAAAAATAAAATAAAGA-AAATAAAA
132392 AGAAAGAGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
48 4 0.05
49 3 0.04
50 8 0.10
51 13 0.16
52 7 0.08
53 9 0.11
54 8 0.10
55 21 0.25
56 10 0.12
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.19
Consensus pattern (50 bp):
ATAAAGGAAATAAAAAATAAAAAAAATAAAATAAAGAAAATAAAATAAAT
Found at i:132332 original size:27 final size:25
Alignment explanation
Indices: 132300--132390 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 25
132290 ATATATATAC
132300 AATAAATAAATAAAAACAAGAATAAAA
1 AATAAATAAATAAAAA-AA-AATAAAA
* *
132327 AATAAAGAAATAAAATAAATATAAAGGA
1 AATAAATAAATAAAA-AAAAATAAA--A
132355 AATAAA-AAATAAAAAAAATAATAAAA
1 AATAAATAAAT-AAAAAAA-AATAAAA
*
132381 GATAAATAAA
1 AATAAATAAA
132391 AAGAAAGAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
26 11 0.20
27 26 0.48
28 17 0.31
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.16
Consensus pattern (25 bp):
AATAAATAAATAAAAAAAAATAAAA
Found at i:132341 original size:13 final size:13
Alignment explanation
Indices: 132265--132345 Score: 56
Period size: 13 Copynumber: 5.9 Consensus size: 13
132255 AAATAAAAAC
132265 AAATAAAATAAAG
1 AAATAAAATAAAG
* *
132278 AAAATAATATATATAT
1 -AAATAA-A-ATAAAG
* * *
132294 ATATACAATAAAT
1 AAATAAAATAAAG
132307 AAATAAAA-ACAAG
1 AAATAAAATA-AAG
*
132320 AATAAAAAATAAAG
1 AA-ATAAAATAAAG
132334 AAATAAAATAAA
1 AAATAAAATAAA
132346 TATAAAGGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
12 1 0.02
13 24 0.46
14 17 0.33
15 6 0.12
16 4 0.08
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (13 bp):
AAATAAAATAAAG
Found at i:132343 original size:20 final size:20
Alignment explanation
Indices: 132324--132361 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
132314 AACAAGAATA
132324 AAAAATAAA-GAAATAAAAT
1 AAAAATAAAGGAAATAAAAT
*
132343 AAATATAAAGGAAATAAAA
1 AAAAATAAAGGAAATAAAA
132362 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAAATAAAGGAAATAAAAT
Found at i:132379 original size:12 final size:11
Alignment explanation
Indices: 132323--132392 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
132313 AAACAAGAAT
132323 AAAAAATAAAGA
1 AAAAAATAAA-A
*
132335 AATAAAATAAAT
1 AA-AAAATAAAA
* ** *
132347 ATAAAGGAAAT
1 AAAAAATAAAA
132358 AAAAAATAAAA
1 AAAAAATAAAA
132369 AAAATAATAAAA
1 AAAA-AATAAAA
* *
132381 GATAAATAAAA
1 AAAAAATAAAA
132392 A
1 A
132393 GAAAGAGAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
11 25 0.56
12 12 0.27
13 8 0.18
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.16
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:132386 original size:35 final size:35
Alignment explanation
Indices: 132320--132386 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
132310 TAAAAACAAG
*
132320 AATAAAAAATAAAGAAATAAAATAAATATAAAGGA
1 AATAAAAAATAAAGAAATAAAATAAAGATAAAGGA
132355 AATAAAAAATAAA-AAA-AATAATAAAAGATAAA
1 AATAAAAAATAAAGAAATAA-AAT-AAAGATAAA
132387 TAAAAAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 2 0.07
34 6 0.21
35 21 0.72
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (35 bp):
AATAAAAAATAAAGAAATAAAATAAAGATAAAGGA
Found at i:132391 original size:19 final size:19
Alignment explanation
Indices: 132300--132392 Score: 75
Period size: 18 Copynumber: 4.9 Consensus size: 19
132290 ATATATATAC
* *
132300 AATAAATAAATAAAAACAAG
1 AATAAA-AAATAAAAAAAAT
*
132320 AATAAAAAAT-AAAGAAAT
1 AATAAAAAATAAAAAAAAT
* * **
132338 AA-AATAAATATAAAGGA-
1 AATAAAAAATAAAAAAAAT
132355 AATAAAAAATAAAAAAAAT
1 AATAAAAAATAAAAAAAAT
*
132374 AATAAAAGATAAATAAAAA
1 AATAAAAAATAAA-AAAAA
132393 GAAAGAGAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
17 8 0.14
18 21 0.38
19 16 0.29
20 11 0.20
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.16
Consensus pattern (19 bp):
AATAAAAAATAAAAAAAAT
Found at i:133519 original size:18 final size:16
Alignment explanation
Indices: 133496--133535 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
133486 AAAAATGTAA
133496 ATAATATATACATATTAT
1 ATAATATATAC--ATTAT
*
133514 ATAATATATGCATTAT
1 ATAATATATACATTAT
133530 ATAATA
1 ATAATA
133536 AGGGCGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
ATAATATATACATTAT
Found at i:135935 original size:23 final size:22
Alignment explanation
Indices: 135907--135955 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
135897 ACGAAGGATG
*
135907 AATTAAAATAATAAAGAAATTA
1 AATTAAAATAATAAAAAAATTA
*
135929 ATATT-AAATTATAAAAAAATTA
1 A-ATTAAAATAATAAAAAAATTA
135951 AATTA
1 AATTA
135956 TTTAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.13
22 17 0.74
23 3 0.13
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AATTAAAATAATAAAAAAATTA
Found at i:135997 original size:15 final size:16
Alignment explanation
Indices: 135977--136009 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
135967 GACACTAATA
135977 TTTTAAT-TTAAAATT
1 TTTTAATATTAAAATT
*
135992 TTTTAATATTTAAATT
1 TTTTAATATTAAAATT
136008 TT
1 TT
136010 ATAAATCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTAATATTAAAATT
Found at i:144665 original size:124 final size:124
Alignment explanation
Indices: 144528--144775 Score: 478
Period size: 124 Copynumber: 2.0 Consensus size: 124
144518 GTTTGTTAAA
144528 CGAGCCAAGCGAACTCGAGTATTACTGATCTCAACTCGAACTTGAAAACTTTAAAAGTAAGCTCA
1 CGAGCCAAGCGAACTCGAGTATTACTGATCTCAACTCGAACTTGAAAACTTTAAAAGTAAGCTCA
*
144593 ACTCGACTCAAACTTACGAGCTAAAAATTATCAAGTTCAACTCGAACTCGAAATATAAT
66 ACTCGACTCAAACTCACGAGCTAAAAATTATCAAGTTCAACTCGAACTCGAAATATAAT
*
144652 CGAGCCAAGCGAACTCGAGTATTACTGATCTCGACTCGAACTTGAAAACTTTAAAAGTAAGCTCA
1 CGAGCCAAGCGAACTCGAGTATTACTGATCTCAACTCGAACTTGAAAACTTTAAAAGTAAGCTCA
144717 ACTCGACTCAAACTCACGAGCTAAAAATTATCAAGTTCAACTCGAACTCGAAATATAAT
66 ACTCGACTCAAACTCACGAGCTAAAAATTATCAAGTTCAACTCGAACTCGAAATATAAT
144776 GTTGAAACTT
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 122 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (124 bp):
CGAGCCAAGCGAACTCGAGTATTACTGATCTCAACTCGAACTTGAAAACTTTAAAAGTAAGCTCA
ACTCGACTCAAACTCACGAGCTAAAAATTATCAAGTTCAACTCGAACTCGAAATATAAT
Found at i:146262 original size:3 final size:3
Alignment explanation
Indices: 146254--146308 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
146244 TCTTCAGTTT
* * * *
146254 AGC AGC AGC AGC AGC AGT AGC AGC AGC CGC AGC AGC CGC AGC AGC CGC
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC
146302 AGC AGC A
1 AGC AGC A
146309 TTTGTATTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.29, C:0.36, G:0.33, T:0.02
Consensus pattern (3 bp):
AGC
Found at i:146307 original size:18 final size:18
Alignment explanation
Indices: 146254--146308 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
146244 TCTTCAGTTT
* *
146254 AGCAGCAGCAGCAGCAGT
1 AGCAGCAGCCGCAGCAGC
146272 AGCAGCAGCCGCAGCAGC
1 AGCAGCAGCCGCAGCAGC
*
146290 CGCAGCAGCCGCAGCAGC
1 AGCAGCAGCCGCAGCAGC
146308 A
1 A
146309 TTTGTATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.29, C:0.36, G:0.33, T:0.02
Consensus pattern (18 bp):
AGCAGCAGCCGCAGCAGC
Found at i:146858 original size:3 final size:3
Alignment explanation
Indices: 146850--146948 Score: 148
Period size: 3 Copynumber: 33.0 Consensus size: 3
146840 TTCATTTAAA
* *
146850 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT AGT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
146898 ATT ATT ATT ATT ATT ATTT ATT A-T ATT ATT A-T ATT ATAT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
146943 ATT ATT
1 ATT ATT
146949 TAATAAATAA
Statistics
Matches: 88, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.05
3 78 0.89
4 6 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:147439 original size:10 final size:10
Alignment explanation
Indices: 147403--147447 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
147393 AACCAGAAGG
147403 ACAGAGAGCA
1 ACAGAGAGCA
* *
147413 ACAGACAGCC
1 ACAGAGAGCA
147423 ACAGAGAGCA
1 ACAGAGAGCA
* *
147433 ACGGAGAACA
1 ACAGAGAGCA
147443 ACAGA
1 ACAGA
147448 AAAACAGACG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.49, C:0.24, G:0.27, T:0.00
Consensus pattern (10 bp):
ACAGAGAGCA
Found at i:149324 original size:13 final size:15
Alignment explanation
Indices: 149293--149329 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
149283 TTATATGTTT
149293 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
149308 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
149321 TA-TTTATTT
1 TATTTTATTT
149330 TTCTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:156484 original size:114 final size:113
Alignment explanation
Indices: 156229--156536 Score: 443
Period size: 114 Copynumber: 2.8 Consensus size: 113
156219 ATGTAATTTG
*
156229 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TT-G--G-A---CAGAATCT
1 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCCCA-AAACT
*
156286 AATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGAC
65 AATCATTGGATTTGAAAAATGAATTTGCTCATAGTAGAAATAAGAAGAC
156335 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACT
1 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GAACCCCAAAACT
*
156400 AATCATTGGATTTGAAAAATGAATTTGCTCATAGTAGAAATAAGGAGAC
65 AATCATTGGATTTGAAAAATGAATTTGCTCATAGTAGAAATAAGAAGAC
* * * * *
156449 CCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAGAACC
1 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GAACCCCAAAACT
* *
156514 GATCATTGGAATTGAAAAATGAA
65 AATCATTGGATTTGAAAAATGAA
156537 CTGCATGATC
Statistics
Matches: 182, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
106 44 0.24
107 2 0.01
108 1 0.01
111 1 0.01
112 1 0.01
114 131 0.72
115 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (113 bp):
CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCCCAAAACTA
ATCATTGGATTTGAAAAATGAATTTGCTCATAGTAGAAATAAGAAGAC
Found at i:159027 original size:22 final size:22
Alignment explanation
Indices: 158959--159038 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
158949 TACATCTGCA
* *
158959 CTTTTTAAAGATAATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
** * * * *
158981 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGATAGATTCT
*
159003 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
159025 CTTTTCAAAAATGA
1 CTTTTCAAAGATGA
159039 AAGCTTTATG
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:159830 original size:76 final size:76
Alignment explanation
Indices: 159704--161485 Score: 3255
Period size: 76 Copynumber: 23.5 Consensus size: 76
159694 CTATTTCTTA
159704 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
159769 AACCTTCGGGT
66 AGCCTTCGGGT
* * *
159780 CATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
159845 AACCTTC-GGT
66 AGCCTTCGGGT
* *
159855 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
159920 AGCCTTCGGGT
66 AGCCTTCGGGT
159931 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
159995 AGCCTTCGGGT
66 AGCCTTCGGGT
*
160006 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
160071 AGCCTTCGGGT
66 AGCCTTCGGGT
*
160082 CATCTGTAGGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
160147 AGCCTTCGGGT
66 AGCCTTCGGGT
*
160158 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
160223 AGCCTTCGGGT
66 AGCCTTCGGGT
160234 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
160299 AGCCTTCGGGT
66 AGCCTTCGGGT
160310 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
160375 AACCTTCGGGT
66 AGCCTTCGGGT
* *
160386 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
160451 AGCCTTCGGGT
66 AGCCTTCGGGT
*
160462 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
160527 AAGCCTTCGGGT
65 AAGCCTTCGGGT
*
160539 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
160603 AGCCTTCGGGT
66 AGCCTTCGGGT
160614 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
160679 AGCCTTCGGGT
66 AGCCTTCGGGT
160690 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
160755 AGCCTTCGGGT
66 AGCCTTCGGGT
160766 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
160831 AACCTTCGGGT
66 AGCCTTCGGGT
* * *
160842 CATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
160907 AACCTTCGGGT
66 AGCCTTCGGGT
* *
160918 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
160983 AACCTTCGGGT
66 AGCCTTCGGGT
* *
160994 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
161059 AGCCTTCGGGT
66 AGCCTTCGGGT
161070 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
161135 AGCCTTCGGGT
66 AGCCTTCGGGT
*
161146 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
161211 AGCCTTCGGGT
66 AGCCTTCGGGT
161222 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
161287 AGCCTTCGGGT
66 AGCCTTCGGGT
161298 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
161363 AGCCTTCGGGT
66 AGCCTTCGGGT
*
161374 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
161439 AAACCTTCGGGT
65 AAGCCTTCGGGT
* *
161451 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
161486 CATTTCCATC
Statistics
Matches: 1667, Mismatches: 34, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
75 221 0.13
76 1326 0.80
77 120 0.07
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:161618 original size:3 final size:3
Alignment explanation
Indices: 161610--161725 Score: 178
Period size: 3 Copynumber: 38.0 Consensus size: 3
161600 TTCATTTAAA
* *
161610 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT AGT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
161658 ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
*
161704 AAT ATT ATAT ATT ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT
161726 TAATAAATAA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
3 98 0.95
4 5 0.05
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:162216 original size:10 final size:10
Alignment explanation
Indices: 162180--162224 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
162170 AACCAGAAGG
162180 ACAGAGAGCA
1 ACAGAGAGCA
* *
162190 ACAGACAGCC
1 ACAGAGAGCA
162200 ACAGAGAGCA
1 ACAGAGAGCA
* *
162210 ACGGAGAACA
1 ACAGAGAGCA
162220 ACAGA
1 ACAGA
162225 AAAACAGACG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.49, C:0.24, G:0.27, T:0.00
Consensus pattern (10 bp):
ACAGAGAGCA
Found at i:164540 original size:23 final size:23
Alignment explanation
Indices: 164510--164559 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
164500 TGACCAGGAA
164510 TATAAAATCTACATATCTTCTGG
1 TATAAAATCTACATATCTTCTGG
*
164533 TATAAAATCTACATATCTTTTGG
1 TATAAAATCTACATATCTTCTGG
164556 TATA
1 TATA
164560 TAGAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (23 bp):
TATAAAATCTACATATCTTCTGG
Found at i:169664 original size:21 final size:20
Alignment explanation
Indices: 169640--169684 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
169630 CAAAAAAATT
*
169640 AATATTATCTTT-TAAATAACA
1 AATATTAACTTTGTAAA-AA-A
169661 AATATTAACTTTGTAAAAAA
1 AATATTAACTTTGTAAAAAA
169681 AATA
1 AATA
169685 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (20 bp):
AATATTAACTTTGTAAAAAA
Found at i:188239 original size:3 final size:3
Alignment explanation
Indices: 188224--188285 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
188214 TTTTTCTTTT
* * * * * * *
188224 TTA TTA TTT TTA TTA TTA TAA TAA TTA TTA TAA TAA TAA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
188272 TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
188286 ATAATAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:188271 original size:30 final size:30
Alignment explanation
Indices: 188235--188296 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
188225 TATTATTTTT
188235 ATTATTATAATAATTATTA-TAATAATAATA
1 ATTATTAT-ATAATTATTATTAATAATAATA
* *
188265 ATTATTATTTTATTATTATTAATAATAATA
1 ATTATTATATAATTATTATTAATAATAATA
188295 AT
1 AT
188297 AAATAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTATTATATAATTATTATTAATAATAATA
Found at i:188290 original size:33 final size:32
Alignment explanation
Indices: 188233--188314 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 32
188223 TTTATTATTT
* *
188233 TTATTATTATAATAATTATTATAATAATAATAA
1 TTATTATT-TTATTATTATTATAATAATAATAA
188266 TTATTATTTTATTATTATTAATAATAATAATAA
1 TTATTATTTTATTATTATT-ATAATAATAATAA
*
188299 --ATAATTTTATTTATTA
1 TTATTATTTTA-TTATTA
188315 CAGGCCCAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
31 8 0.18
32 15 0.34
33 21 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TTATTATTTTATTATTATTATAATAATAATAA
Found at i:188995 original size:22 final size:22
Alignment explanation
Indices: 188944--188997 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
188934 GAATAGTGAT
188944 TGGTGGAC-GGAATAGTGACCGG
1 TGGTGG-CTGGAATAGTGACCGG
* * * *
188966 AGGCGGCTGGAATAGTGGCTGG
1 TGGTGGCTGGAATAGTGACCGG
188988 TGGTGGCTGG
1 TGGTGGCTGG
188998 CCGGTTCTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.17, C:0.13, G:0.50, T:0.20
Consensus pattern (22 bp):
TGGTGGCTGGAATAGTGACCGG
Found at i:190422 original size:25 final size:25
Alignment explanation
Indices: 190388--190437 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
190378 GATCAGGGGT
190388 ACTGAAGCATAAACATATAGTGATA
1 ACTGAAGCATAAACATATAGTGATA
*
190413 ACTGAAGCATAAACATGTAGTGATA
1 ACTGAAGCATAAACATATAGTGATA
190438 TGGTGTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (25 bp):
ACTGAAGCATAAACATATAGTGATA
Found at i:190524 original size:4 final size:4
Alignment explanation
Indices: 190515--190541 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
190505 ACCTATGTAA
190515 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
190542 ACAATAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:195112 original size:41 final size:42
Alignment explanation
Indices: 195046--195128 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
195036 AGAGATGATT
* * * *
195046 GATCAAGTAAAAAAGTTCTAGGATGATTCAAATGAACAAATG
1 GATCAAGCAAAAAAGATCCAGGATGATTCAAAGGAACAAATG
*
195088 GATCAAGCAAAAAA-ATCCAGGATGATTCAAAGGAGCAAATG
1 GATCAAGCAAAAAAGATCCAGGATGATTCAAAGGAACAAATG
195129 ACAAAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.64
42 13 0.36
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.19
Consensus pattern (42 bp):
GATCAAGCAAAAAAGATCCAGGATGATTCAAAGGAACAAATG
Found at i:199595 original size:18 final size:18
Alignment explanation
Indices: 199572--199644 Score: 110
Period size: 18 Copynumber: 3.9 Consensus size: 18
199562 AATGAATATT
199572 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
199590 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
199609 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
199628 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
199645 GATAATCCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 32 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:199627 original size:38 final size:38
Alignment explanation
Indices: 199571--199647 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
199561 CAATGAATAT
*
199571 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
*
199609 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
199647 T
1 T
199648 AATCCCTCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
Found at i:207883 original size:54 final size:54
Alignment explanation
Indices: 207818--207925 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
207808 TTATCGAGAA
* *
207818 ATCTGAGCAGAAGCTACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* *
207872 ATCTGTGCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
207926 CAGTGATTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (54 bp):
ATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:208318 original size:22 final size:22
Alignment explanation
Indices: 208290--208358 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
208280 CTACATCTAC
*
208290 ATTCTTCAAAGATGATAGATTT
1 ATTCTTCAAAGATGAAAGATTT
*
208312 ATTCTTCAAAGATGACAGATTCT
1 ATTCTTCAAAGATGAAAGATT-T
* *
208335 CTT-TTCAAAGATGAAAGCTTT
1 ATTCTTCAAAGATGAAAGATTT
208356 ATT
1 ATT
208359 GGATTTCTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 3 0.07
22 35 0.85
23 3 0.07
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (22 bp):
ATTCTTCAAAGATGAAAGATTT
Found at i:209264 original size:177 final size:177
Alignment explanation
Indices: 208968--209368 Score: 585
Period size: 177 Copynumber: 2.3 Consensus size: 177
208958 CCCAGAATTG
* * * *
208968 TAAGTCCTACGGGACATCCATAAGACCTTCAGTGCATGATGTTTTCAAATAAGATTTTAGAAACT
1 TAAGTCCTACGGGCCATCTATAAGACCTTCAGTGCAGGATGTTTTCAAATAAGATTCTAGAAACT
* *
209033 AAGCCTTCGGTGGCTTCCTAATTATCTCAAAAAAGTTGTTAAAGGAAGCTAAGCCTAATAAAGGG
66 AAGCCTTCGGTGGCTTCCTAATTATCTCAAAAAAGTTGTTAAAGGAAACTAAGCCTAACAAAGGG
*
209098 GTTCCTTGACAACTAAGAAACCAAGCCTTCGGGGGTTTCTTGATTTA
131 GTTCATTGACAACTAAGAAACCAAGCCTTCGGGGGTTTCTTGATTTA
209145 TAAGTCCTACGGGCCATCTATAAGACCTTCAGTGCAGGATGTTTTCAAATGAA-ATTCTAGAAAC
1 TAAGTCCTACGGGCCATCTATAAGACCTTCAGTGCAGGATGTTTTCAAAT-AAGATTCTAGAAAC
* *
209209 TAAGCCTTCAGG-GGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAACTAAGCCTAACAAAG
65 TAAGCCTTC-GGTGGCTTCCTAATTATCTCAAAAAAGTTGTTAAAGGAAACTAAGCCTAACAAAG
* * *
209273 GGGTTCATTGACAATTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTG
129 GGGTTCATTGACAACTAAGAAACCAAGCCTTCGGGGGTTTCTTGATTTA
* * * * * *
209322 TAAGTCTTTCAGGCCAT-TCATAAGACCTTC-GGGCAGAATATTTTCAA
1 TAAGTCCTACGGGCCATCT-ATAAGACCTTCAGTGCAGGATGTTTTCAA
209369 CATTTCCGTT
Statistics
Matches: 203, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
176 15 0.07
177 184 0.91
178 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (177 bp):
TAAGTCCTACGGGCCATCTATAAGACCTTCAGTGCAGGATGTTTTCAAATAAGATTCTAGAAACT
AAGCCTTCGGTGGCTTCCTAATTATCTCAAAAAAGTTGTTAAAGGAAACTAAGCCTAACAAAGGG
GTTCATTGACAACTAAGAAACCAAGCCTTCGGGGGTTTCTTGATTTA
Found at i:209718 original size:3 final size:3
Alignment explanation
Indices: 209703--209779 Score: 84
Period size: 3 Copynumber: 26.0 Consensus size: 3
209693 TTTTTCTTTT
* * * * * * *
209703 TTA TTA TTT TTA TTA TTA TAA TTA TAA TTA TAA TTA TAA TAA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
209751 TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
209780 AATAATTTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:216472 original size:70 final size:71
Alignment explanation
Indices: 216359--216497 Score: 178
Period size: 70 Copynumber: 2.0 Consensus size: 71
216349 TTACTGGTTC
* * *
216359 ACCTTTAATACATCTACATACAAATAATGACTTCTAAAGTGAGGATAAATATCAACCTTG-AAAG
1 ACCTTTAATACATCTACATACAAATAATAACTTCTAAAGTGAGGATAAATACCAAACTTGAAAAG
216423 AGCTGA
66 AGCTGA
**
216429 ACCTTTAATACATCTACA-AGCAAATTGTAACCATTC-AAA-TGAGGATAAATACCAAACTTGAA
1 ACCTTTAATACATCTACATA-CAAATAATAA-C-TTCTAAAGTGAGGATAAATACCAAACTTGAA
216491 AAGAGCT
63 AAGAGCT
216498 ATACACACAG
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
69 1 0.02
70 44 0.73
71 12 0.20
72 3 0.05
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (71 bp):
ACCTTTAATACATCTACATACAAATAATAACTTCTAAAGTGAGGATAAATACCAAACTTGAAAAG
AGCTGA
Found at i:223402 original size:21 final size:22
Alignment explanation
Indices: 223369--223411 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
223359 CTTTAAATGG
223369 TTTTTAATTAAGTCCCCATTAAT
1 TTTTTAA-TAAGTCCCCATTAAT
* *
223392 TTTTTAA-AAGTTCTCATTAA
1 TTTTTAATAAGTCCCCATTAA
223412 GGCTTAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTTTAATAAGTCCCCATTAAT
Found at i:233145 original size:22 final size:21
Alignment explanation
Indices: 233120--233168 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
233110 TTTTTATAAA
*
233120 ATTAATCAAATAATATATTAAT
1 ATTAATAAAATAATA-ATTAAT
* *
233142 ATTATTAAAATAATAATTATT
1 ATTAATAAAATAATAATTAAT
233163 ATTAAT
1 ATTAAT
233169 TTAAATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTAATAAAATAATAATTAAT
Found at i:233174 original size:22 final size:21
Alignment explanation
Indices: 233127--233180 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
233117 AAAATTAATC
233127 AAATAATATATTAATATTATTA
1 AAATAATA-ATTAATATTATTA
* *
233149 AAATAATAATTATTATTAATTT
1 AAATAATAATTAATATT-ATTA
233171 AAATATATAA
1 AAATA-ATAA
233181 CAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 8 0.29
22 16 0.57
23 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATAATAATTAATATTATTA
Found at i:234301 original size:3 final size:3
Alignment explanation
Indices: 234284--234354 Score: 78
Period size: 3 Copynumber: 24.3 Consensus size: 3
234274 TGGACCGTTG
234284 TAA TAA T-A TATA TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* *
234327 TAA TAT TTA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
234355 TTTAGTAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 44 0.76
4 6 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:234311 original size:20 final size:21
Alignment explanation
Indices: 234284--234352 Score: 115
Period size: 20 Copynumber: 3.4 Consensus size: 21
234274 TGGACCGTTG
234284 TAATAATATATATAATAATAA
1 TAATAATATATATAATAATAA
234305 T-ATAATATATATAAT-ATAA
1 TAATAATATATATAATAATAA
*
234324 TAATAATATTTATAATAATAA
1 TAATAATATATATAATAATAA
234345 TAATAATA
1 TAATAATA
234353 ATTTTAGTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
19 5 0.11
20 27 0.60
21 13 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATAATATATATAATAATAA
Found at i:234353 original size:15 final size:14
Alignment explanation
Indices: 234284--234354 Score: 90
Period size: 15 Copynumber: 4.9 Consensus size: 14
234274 TGGACCGTTG
234284 TAATAATATATATAA
1 TAATAATATA-ATAA
234299 TAATAATATAAT-A
1 TAATAATATAATAA
234312 TATATAATATAATAA
1 TA-ATAATATAATAA
*
234327 TAATATTTATAATAA
1 TAATA-ATATAATAA
234342 TAATAATAATAAT
1 TAATAAT-ATAAT
234355 TTTAGTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
13 3 0.06
14 16 0.32
15 31 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:235780 original size:76 final size:76
Alignment explanation
Indices: 234508--235753 Score: 2321
Period size: 76 Copynumber: 16.4 Consensus size: 76
234498 GAGGTCTTAA
* *
234508 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
234573 AGGCTTTTTGG
66 AGGCTTTTTGG
234584 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
234649 AGGCTTTTTGG
66 AGGCTTTTTGG
234660 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
234725 AGGCTTTTTGG
66 AGGCTTTTTGG
*
234736 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
234801 AGGCTTTTTGG
66 AGGCTTTTTGG
234812 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
234877 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
234888 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
234953 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
234964 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAAGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235029 AGGCTTTTTGG
66 AGGCTTTTTGG
235040 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235105 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
235116 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235181 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
235192 AAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235257 AGGCTTTTTGG
66 AGGCTTTTTGG
235268 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235333 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
235344 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235409 AGGCTTTTTGG
66 AGGCTTTTTGG
*
235420 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235485 AGGCTTTTTGG
66 AGGCTTTTTGG
*
235496 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235561 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
235572 AAACATCATGCATTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235637 AGGCTTTTTGG
66 AGGCTTTTTGG
*
235648 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235713 AGGCTTTTTGG
66 AGGCTTTTTGG
235724 AAACATCATGCACTGAAGGGCTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
235754 TGGGAAATAG
Statistics
Matches: 1137, Mismatches: 33, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 1137 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Done.