Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008475.1 Hibiscus syriacus cultivar Beakdansim tig00111303_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: 982705
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 4
Found at i:298778 original size:32 final size:32
Alignment explanation
Indices: 298733--298822 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
298723 CACTCTTTTC
*
298733 GCCCTTCCACTATCGGTAGCTTATTACCGTAA
1 GCCCTTCCACTATCGGTAGCTTATTAACGTAA
* * *
298765 GCCCTTCCGCTATCGGTAGCTTACTAATGTAA
1 GCCCTTCCACTATCGGTAGCTTATTAACGTAA
* *
298797 GCCCTTCCACCATGGGTAGCTTATTA
1 GCCCTTCCACTATCGGTAGCTTATTA
298823 TTGTAGGCTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (32 bp):
GCCCTTCCACTATCGGTAGCTTATTAACGTAA
Found at i:304005 original size:18 final size:18
Alignment explanation
Indices: 303982--304028 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
303972 GACCGGTCAC
303982 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
304000 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
*
304018 GACCCGACCCG
1 AACCCGACCCG
304029 TTGACCGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.51, G:0.19, T:0.09
Consensus pattern (18 bp):
AACCCGACCCGACCCGTT
Found at i:304021 original size:8 final size:8
Alignment explanation
Indices: 304010--304056 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
304000 AACCCGACCC
304010 GACCCGTT
1 GACCCGTT
304018 GACCC---
1 GACCCGTT
304023 GACCCGTT
1 GACCCGTT
304031 GA-CCGTT
1 GACCCGTT
304038 GACCCGTT
1 GACCCGTT
304046 GA-CCGTT
1 GACCCGTT
304053 GACC
1 GACC
304057 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:304021 original size:13 final size:13
Alignment explanation
Indices: 304005--304049 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
303995 CCGTTAACCC
304005 GACCCGACCCGTT
1 GACCCGACCCGTT
304018 GACCCGACCCGTT
1 GACCCGACCCGTT
*
304031 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
304046 GACC
1 GACC
304050 GTTGACCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.16, C:0.42, G:0.24, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:304038 original size:7 final size:7
Alignment explanation
Indices: 304026--304057 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
304016 TTGACCCGAC
304026 CCGTTGA
1 CCGTTGA
304033 CCGTTGA
1 CCGTTGA
304040 CCCGTTGA
1 -CCGTTGA
304048 CCGTTGA
1 CCGTTGA
304055 CCG
1 CCG
304058 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:304043 original size:15 final size:15
Alignment explanation
Indices: 304010--304056 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
304000 AACCCGACCC
*
304010 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
304023 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
304038 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
304053 GACC
1 GACC
304057 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:305510 original size:25 final size:26
Alignment explanation
Indices: 305478--305526 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
305468 AATGACCCAA
305478 GAATATCC-CAAGCTCAGAAATGATT
1 GAATATCCTCAAGCTCAGAAATGATT
* *
305503 GAATATCCTCGAGCTCTGAAATGA
1 GAATATCCTCAAGCTCAGAAATGA
305527 ATGGAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (26 bp):
GAATATCCTCAAGCTCAGAAATGATT
Found at i:306538 original size:48 final size:48
Alignment explanation
Indices: 306486--306617 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
306476 AATATTTTAC
*
306486 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
306534 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
306582 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
306618 CTGATTTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:306624 original size:24 final size:24
Alignment explanation
Indices: 306503--306617 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
306493 TCGATTTGAT
306503 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
306527 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
306551 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
306575 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
306598 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
306618 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:306640 original size:24 final size:24
Alignment explanation
Indices: 306554--306627 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
306544 ACATGGATTC
* * *
306554 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
306578 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
306602 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
306626 TG
1 TG
306628 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:308815 original size:18 final size:18
Alignment explanation
Indices: 308792--308838 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
308782 GACCGGTCAC
308792 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
308810 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
*
308828 GACCCGACCCG
1 AACCCGACCCG
308839 TTGACCGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.51, G:0.19, T:0.09
Consensus pattern (18 bp):
AACCCGACCCGACCCGTT
Found at i:308831 original size:8 final size:8
Alignment explanation
Indices: 308820--308866 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
308810 AACCCGACCC
308820 GACCCGTT
1 GACCCGTT
308828 GACCC---
1 GACCCGTT
308833 GACCCGTT
1 GACCCGTT
308841 GA-CCGTT
1 GACCCGTT
308848 GACCCGTT
1 GACCCGTT
308856 GA-CCGTT
1 GACCCGTT
308863 GACC
1 GACC
308867 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:308831 original size:13 final size:13
Alignment explanation
Indices: 308815--308859 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
308805 CCGTTAACCC
308815 GACCCGACCCGTT
1 GACCCGACCCGTT
308828 GACCCGACCCGTT
1 GACCCGACCCGTT
*
308841 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
308856 GACC
1 GACC
308860 GTTGACCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.16, C:0.42, G:0.24, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:308848 original size:7 final size:7
Alignment explanation
Indices: 308836--308867 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
308826 TTGACCCGAC
308836 CCGTTGA
1 CCGTTGA
308843 CCGTTGA
1 CCGTTGA
308850 CCCGTTGA
1 -CCGTTGA
308858 CCGTTGA
1 CCGTTGA
308865 CCG
1 CCG
308868 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:308853 original size:15 final size:15
Alignment explanation
Indices: 308820--308866 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
308810 AACCCGACCC
*
308820 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
308833 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
308848 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
308863 GACC
1 GACC
308867 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:310330 original size:26 final size:26
Alignment explanation
Indices: 310290--310339 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
310280 AATGACCCAA
310290 GAATATCCCCAAGCTCAGAAATGATT
1 GAATATCCCCAAGCTCAGAAATGATT
* * *
310316 GAATATCCTCGAGCTCTGAAATGA
1 GAATATCCCCAAGCTCAGAAATGA
310340 ATGGAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (26 bp):
GAATATCCCCAAGCTCAGAAATGATT
Found at i:311349 original size:48 final size:48
Alignment explanation
Indices: 311297--311428 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
311287 AATATTTTAC
*
311297 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
311345 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
311393 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
311429 CTGATTTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:311435 original size:24 final size:24
Alignment explanation
Indices: 311314--311428 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
311304 TCGATTTGAT
311314 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
311338 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
311362 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
311386 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
311409 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
311429 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:311451 original size:24 final size:24
Alignment explanation
Indices: 311365--311438 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
311355 ACATGGATTC
* * *
311365 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
311389 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
311413 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
311437 TG
1 TG
311439 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:313626 original size:18 final size:18
Alignment explanation
Indices: 313603--313649 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
313593 GACCGGTCAC
313603 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
313621 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
*
313639 GACCCGACCCG
1 AACCCGACCCG
313650 TTGACCGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.51, G:0.19, T:0.09
Consensus pattern (18 bp):
AACCCGACCCGACCCGTT
Found at i:313642 original size:8 final size:8
Alignment explanation
Indices: 313631--313677 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
313621 AACCCGACCC
313631 GACCCGTT
1 GACCCGTT
313639 GACCC---
1 GACCCGTT
313644 GACCCGTT
1 GACCCGTT
313652 GA-CCGTT
1 GACCCGTT
313659 GACCCGTT
1 GACCCGTT
313667 GA-CCGTT
1 GACCCGTT
313674 GACC
1 GACC
313678 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:313642 original size:13 final size:13
Alignment explanation
Indices: 313626--313670 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
313616 CCGTTAACCC
313626 GACCCGACCCGTT
1 GACCCGACCCGTT
313639 GACCCGACCCGTT
1 GACCCGACCCGTT
*
313652 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
313667 GACC
1 GACC
313671 GTTGACCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.16, C:0.42, G:0.24, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:313659 original size:7 final size:7
Alignment explanation
Indices: 313647--313678 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
313637 TTGACCCGAC
313647 CCGTTGA
1 CCGTTGA
313654 CCGTTGA
1 CCGTTGA
313661 CCCGTTGA
1 -CCGTTGA
313669 CCGTTGA
1 CCGTTGA
313676 CCG
1 CCG
313679 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:313664 original size:15 final size:15
Alignment explanation
Indices: 313631--313677 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
313621 AACCCGACCC
*
313631 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
313644 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
313659 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
313674 GACC
1 GACC
313678 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:315139 original size:26 final size:26
Alignment explanation
Indices: 315099--315148 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
315089 AATGACCCAA
315099 GAATATCCCCAAGCTCAGAAATGATT
1 GAATATCCCCAAGCTCAGAAATGATT
* * *
315125 GAATATCCTCGAGCTCTGAAATGA
1 GAATATCCCCAAGCTCAGAAATGA
315149 ATGGAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (26 bp):
GAATATCCCCAAGCTCAGAAATGATT
Found at i:316160 original size:48 final size:48
Alignment explanation
Indices: 316108--316239 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
316098 AATATTTTAC
*
316108 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
316156 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
316204 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
316240 CTGATTTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:316246 original size:24 final size:24
Alignment explanation
Indices: 316125--316239 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
316115 TCGATTTGAT
316125 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
316149 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
316173 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
316197 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
316220 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
316240 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:316262 original size:24 final size:24
Alignment explanation
Indices: 316176--316249 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
316166 ACATGGATTC
* * *
316176 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
316200 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
316224 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
316248 TG
1 TG
316250 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:320239 original size:31 final size:31
Alignment explanation
Indices: 320201--320271 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
320191 CGAAGTACAT
*
320201 GACGTCTTCCCATAAGACGATCGAAACACCC
1 GACGTCTTCCCAGAAGACGATCGAAACACCC
320232 GACGTCTTCCCAGAAGACGATCGAAACACCC
1 GACGTCTTCCCAGAAGACGATCGAAACACCC
*
320263 GATGTCTTC
1 GACGTCTTC
320272 AAGGTTTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18
Consensus pattern (31 bp):
GACGTCTTCCCAGAAGACGATCGAAACACCC
Found at i:339228 original size:20 final size:21
Alignment explanation
Indices: 339205--339285 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 21
339195 TTAGTGCAGA
339205 GGGAATCGATACCCCCATGA-
1 GGGAATCGATACCCCCATGAG
* *
339225 GGGAA-CTGATTCCCCCTTTGAAG
1 GGGAATC-GATACCCCC-ATG-AG
* *
339248 GGGAACCGATTCCCCC-T-AG
1 GGGAATCGATACCCCCATGAG
339267 GGGAATCGATACCCCCATG
1 GGGAATCGATACCCCCATG
339286 GGGTTCTGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
19 17 0.34
20 14 0.28
21 3 0.06
22 1 0.02
23 14 0.28
24 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.19
Consensus pattern (21 bp):
GGGAATCGATACCCCCATGAG
Found at i:342273 original size:51 final size:51
Alignment explanation
Indices: 342212--342335 Score: 151
Period size: 51 Copynumber: 2.4 Consensus size: 51
342202 GTAAAGCGCA
* * * *
342212 CCCCCTGAACCGCGCTATATGCTGATTTGG-CACCACGTGGAGTATAGCACG
1 CCCCCTGAACCGCGCTATACGCTGACTGGGTCA-CACGTGGAGTATAACACG
** * * *
342263 TGCCCTGAACCGCGCTATACGCTGACTGGGTTACACGTGGGGTATAACGCG
1 CCCCCTGAACCGCGCTATACGCTGACTGGGTCACACGTGGAGTATAACACG
342314 CCCCCTGAACCGCGCTATACGC
1 CCCCCTGAACCGCGCTATACGC
342336 CACGTAGGGG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 60 0.98
52 1 0.02
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (51 bp):
CCCCCTGAACCGCGCTATACGCTGACTGGGTCACACGTGGAGTATAACACG
Found at i:346011 original size:35 final size:34
Alignment explanation
Indices: 345926--346012 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
345916 ATTTGATATT
*
345926 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
345960 TAAATGATAACCAAATTACAATAACTGATATTAAAT-G
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
*
345997 TTAATA-AACAAAATTA
1 TAAATACAACAAAATTA
346013 ACTAAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 7 0.16
38 7 0.16
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:348285 original size:111 final size:110
Alignment explanation
Indices: 348148--348360 Score: 399
Period size: 111 Copynumber: 1.9 Consensus size: 110
348138 ATTACAAAAA
*
348148 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
348213 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTCGAGATAT
66 AATT-AAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
348259 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
348324 AATTAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
66 AATTAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
348361 AGATATATGA
Statistics
Matches: 100, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
110 32 0.32
111 68 0.68
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (110 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:348694 original size:50 final size:50
Alignment explanation
Indices: 348640--348765 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
348630 GGATACCCAG
* * *
348640 GTATAGCGCGGATCAGGGAGCGCGCTATACCCATGTGGCGTCAGATCACC
1 GTATAGCGCGGATCAGGGAGCGCGCTATACCCACGTGGCGCCAAATCACC
* ** * * * *
348690 GTATATCGCGGGGCAGGGGGCGCGCTATGCCCACGTGGTGCCAAATCAGC
1 GTATAGCGCGGATCAGGGAGCGCGCTATACCCACGTGGCGCCAAATCACC
*
348740 GTATAGCGC-GATTCAGGGAGTGCGCT
1 GTATAGCGCGGA-TCAGGGAGCGCGCT
348766 TTACTGCTAC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
49 1 0.02
50 59 0.98
ACGTcount: A:0.20, C:0.26, G:0.36, T:0.18
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGAGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:348834 original size:16 final size:16
Alignment explanation
Indices: 348813--348848 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
348803 ACCAGTATTA
*
348813 GATCGATAAATATACT
1 GATCGATAAATATACC
348829 GATCGATAAATATACC
1 GATCGATAAATATACC
348845 GATC
1 GATC
348849 ACCGATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (16 bp):
GATCGATAAATATACC
Found at i:348911 original size:20 final size:20
Alignment explanation
Indices: 348883--348928 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
348873 CCTTTTATCT
*
348883 CCATCATCCTTCAATCCATC
1 CCATTATCCTTCAATCCATC
348903 CCATTATCCTTCAATCCATC
1 CCATTATCCTTCAATCCATC
348923 CC-TTAT
1 CCATTAT
348929 ATATATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (20 bp):
CCATTATCCTTCAATCCATC
Found at i:354734 original size:95 final size:95
Alignment explanation
Indices: 354571--354742 Score: 344
Period size: 95 Copynumber: 1.8 Consensus size: 95
354561 TAATTGACAT
354571 GCACTGGTGTTGTCACACCATATGACTGGCTCTTCTTTATGACAGACACCAAGTTCTGTAAGCAA
1 GCACTGGTGTTGTCACACCATATGACTGGCTCTTCTTTATGACAGACACCAAGTTCTGTAAGCAA
354636 GGCTCTAACCCATTCGCGCTCATAGCCACA
66 GGCTCTAACCCATTCGCGCTCATAGCCACA
354666 GCACTGGTGTTGTCACACCATATGACTGGCTCTTCTTTATGACAGACACCAAGTTCTGTAAGCAA
1 GCACTGGTGTTGTCACACCATATGACTGGCTCTTCTTTATGACAGACACCAAGTTCTGTAAGCAA
354731 GGCTCTAACCCA
66 GGCTCTAACCCA
354743 GACTGCATCT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 77 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (95 bp):
GCACTGGTGTTGTCACACCATATGACTGGCTCTTCTTTATGACAGACACCAAGTTCTGTAAGCAA
GGCTCTAACCCATTCGCGCTCATAGCCACA
Found at i:357247 original size:18 final size:18
Alignment explanation
Indices: 357224--357276 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
357214 GTTCTTAAGG
357224 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
357242 AGTGGTCCTTCTGGACAT
1 AGTGGTCCTTCGGGACAT
*
357260 AGTGGTTCTTCGGGACA
1 AGTGGTCCTTCGGGACA
357277 AATATACAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:360227 original size:22 final size:22
Alignment explanation
Indices: 360196--360238 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
360186 CATAGCATAA
*
360196 TATCGGTACCATAGTA-GGGTAG
1 TATCGATACCAT-GTATGGGTAG
360218 TATCGATACCATGTATGGGTA
1 TATCGATACCATGTATGGGTA
360239 TCAATACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (22 bp):
TATCGATACCATGTATGGGTAG
Found at i:360637 original size:54 final size:54
Alignment explanation
Indices: 360572--360692 Score: 197
Period size: 54 Copynumber: 2.2 Consensus size: 54
360562 ACCAGATAGG
* *
360572 CACTAATTGTGCATTTCACGGAATTCATCCTATGTGGATAAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATAAATAACCGTTTCGA
* *
360626 CACTAAGTGTGCATTTCACTAAATTCATCCTATGTGGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATAAATAACCGTTTCGA
*
360680 CACTATGTGTGCA
1 CACTAAGTGTGCA
360693 AAACCACAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATAAATAACCGTTTCGA
Found at i:361064 original size:68 final size:68
Alignment explanation
Indices: 360952--361206 Score: 359
Period size: 68 Copynumber: 3.8 Consensus size: 68
360942 AAAGATTAAT
* *
360952 GGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCGGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATTCCGGTTAGATGAAAGGCTAAGTGCCTT
*
361017 TAA
66 TGA
* * * *
361020 GGTCTAACTGTGCATTTGACAGAAATGTGTCAATTATTCTGGTTAGATGAAAGGCCAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATTCCGGTTAGATGAAAGGCTAAGTGCCTT
361085 TGA
66 TGA
*
361088 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGT-CGGTTAGATGAAAGGCTAAGTGTCT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTAT-TCCGGTTAGATGAAAGGCTAAGTGCCT
361152 TTGA
65 TTGA
* * ** * * *
361156 GGCCTAGCTTTGCATTTGGTAGAAAGATGTCAATTATACCAGTTAGATGAA
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATTCCGGTTAGATGAA
361207 CGGTTAAATA
Statistics
Matches: 166, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
68 165 0.99
69 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATTCCGGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:361295 original size:81 final size:81
Alignment explanation
Indices: 361156--361474 Score: 381
Period size: 81 Copynumber: 3.9 Consensus size: 81
361146 GTGTCTTTGA
* * * *
361156 GGCCTAGCTT-TGCATTTGGTAGAAAGATGTCAATTATACCAGTTAGATGAACGGTTAAATACCA
1 GGCCTAG-TTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCG
361220 TTGAGTAAAAGATTAAT
65 TTGAGTAAAAGATTAAT
* * * * *
361237 GGCCTAGTTGTGCACTTGGCAGAAAGGTGTTAATTATGTCAGTTAGATGAACGATTAAATATCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
361302 TGAGTAAAAGATTAAT
66 TGAGTAAAAGATTAAT
* **
361318 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATTGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
* *
361383 TAAGTAAAAGAATAAT
66 TGAGTAAAAGATTAAT
* * * * * * * * * *
361399 AGACTAGATGTGCATTTGACAGAAAAGTGTCAAATATG-CAATTAAGATGAAAGGCTAAATACCT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTT-AGATGAACGGTTAAATACCG
*
361463 TTGGGTAAAAGA
65 TTGAGTAAAAGA
361475 ATAAAGGAAT
Statistics
Matches: 205, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
80 6 0.03
81 199 0.97
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.29
Consensus pattern (81 bp):
GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
TGAGTAAAAGATTAAT
Found at i:361660 original size:46 final size:46
Alignment explanation
Indices: 361543--361660 Score: 173
Period size: 46 Copynumber: 2.6 Consensus size: 46
361533 GTAAACAATA
* * *
361543 CATGAAAGGATACCATAAATGAAATATATAATATCGTAAATAAGGG
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGCGTAAATAAGGG
* *
361589 CATGAAATGATGCCATAAATGAAATGTATAATAGCGTATATAAGGG
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGCGTAAATAAGGG
* *
361635 CATGAAAGGATGTCATAATTGAAATG
1 CATGAAAGGATGCCATAAATGAAATG
361661 CATATGGGTG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.25
Consensus pattern (46 bp):
CATGAAAGGATGCCATAAATGAAATGTATAATAGCGTAAATAAGGG
Found at i:364919 original size:17 final size:16
Alignment explanation
Indices: 364895--364937 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
364885 GTTACAAGAT
364895 TGCTAACAACTCTAAC
1 TGCTAACAACTCTAAC
*
364911 TGACTAACAA-ACTAAC
1 TG-CTAACAACTCTAAC
364927 TGC-AACAACTC
1 TGCTAACAACTC
364938 CAAGAGCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 9 0.39
17 7 0.30
ACGTcount: A:0.42, C:0.30, G:0.07, T:0.21
Consensus pattern (16 bp):
TGCTAACAACTCTAAC
Found at i:369728 original size:17 final size:15
Alignment explanation
Indices: 369704--369736 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
369694 CTTACACATT
369704 TGAAAAAAATTCTATA
1 TGAAAAAAA-TCTATA
369720 TGAAAAAAATCTATA
1 TGAAAAAAATCTATA
369735 TG
1 TG
369737 TATATCGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (15 bp):
TGAAAAAAATCTATA
Found at i:373929 original size:22 final size:22
Alignment explanation
Indices: 373890--373944 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
373880 AATAAGATCG
*
373890 AAAACGTGTCA-AAAGATAAAA
1 AAAATGTGTCATAAAGATAAAA
373911 AAAATGTGTCATAAAGATAAAA
1 AAAATGTGTCATAAAGATAAAA
*
373933 AAATTGTGTCAT
1 AAAATGTGTCAT
373945 GAACTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.24
Consensus pattern (22 bp):
AAAATGTGTCATAAAGATAAAA
Found at i:373953 original size:22 final size:22
Alignment explanation
Indices: 373890--373954 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
373880 AATAAGATCG
* *
373890 AAAACGTGTCA-AAAGATAAAA
1 AAAATGTGTCATAAACATAAAA
*
373911 AAAATGTGTCATAAAGATAAAA
1 AAAATGTGTCATAAACATAAAA
* * *
373933 AAATTGTGTCATGAACTTAAAA
1 AAAATGTGTCATAAACATAAAA
373955 TGATTAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
21 10 0.26
22 28 0.74
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.23
Consensus pattern (22 bp):
AAAATGTGTCATAAACATAAAA
Found at i:377474 original size:22 final size:23
Alignment explanation
Indices: 377449--377499 Score: 95
Period size: 22 Copynumber: 2.3 Consensus size: 23
377439 GTAGTGAGTC
377449 AAGCATCAATAACTCAG-TGGAA
1 AAGCATCAATAACTCAGTTGGAA
377471 AAGCATCAATAACTCAGTTGGAA
1 AAGCATCAATAACTCAGTTGGAA
377494 AAGCAT
1 AAGCAT
377500 TCTATTTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.20
Consensus pattern (23 bp):
AAGCATCAATAACTCAGTTGGAA
Found at i:379392 original size:16 final size:17
Alignment explanation
Indices: 379359--379395 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
379349 ATGGGATGAA
379359 AAAAATAGTATTATTCT
1 AAAAATAGTATTATTCT
379376 AAAAAT-GTAATTA-TCT
1 AAAAATAGT-ATTATTCT
379392 AAAA
1 AAAA
379396 TAATACACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (17 bp):
AAAAATAGTATTATTCT
Found at i:382755 original size:15 final size:15
Alignment explanation
Indices: 382735--382765 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
382725 GATTAAAAGC
382735 TTTGTAATGGAAGTT
1 TTTGTAATGGAAGTT
382750 TTTGTAATGGAAGTT
1 TTTGTAATGGAAGTT
382765 T
1 T
382766 GTATGTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (15 bp):
TTTGTAATGGAAGTT
Found at i:382877 original size:22 final size:21
Alignment explanation
Indices: 382844--382884 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
382834 ATAAACTTTG
382844 ATTTTTTGCATTGTGCATTTA
1 ATTTTTTGCATTGTGCATTTA
* *
382865 ATTTTTCTTCATTTTGCATT
1 ATTTTT-TGCATTGTGCATT
382885 GAACTGCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.61
Consensus pattern (21 bp):
ATTTTTTGCATTGTGCATTTA
Found at i:385973 original size:15 final size:15
Alignment explanation
Indices: 385955--385995 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
385945 TCATTGTCCC
385955 TTTCAACATTACTCA
1 TTTCAACATTACTCA
385970 TTTCAACATTACTCA
1 TTTCAACATTACTCA
385985 TTTCAACATTA
1 TTTCAACATTA
385996 TCCATTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTCAACATTACTCA
Found at i:386018 original size:60 final size:60
Alignment explanation
Indices: 385954--386319 Score: 310
Period size: 60 Copynumber: 6.1 Consensus size: 60
385944 CTCATTGTCC
* * * *
385954 CTTTCAACATT-ACTCATTTCAACATTACTCATTTCAACATTATCCATTTCTACACCAACA
1 CTTTCAACATTGTC-CATTTCTACACTACCCATTTCAACATTATCCATTTCTACACCAACA
* * * * * *
386014 CTTTCAACATTGTCCCTTTCAACACTACCCATTTCAACATTGTCCCTTTCTACA-CTACC
1 CTTTCAACATTGTCCATTTCTACACTACCCATTTCAACATTATCCATTTCTACACCAACA
* * * **
386073 CATTTCAACATTGTCCCTTTCTACACTACCCATTTTAGCATTATCCATTTCTACACCAGTA
1 C-TTTCAACATTGTCCATTTCTACACTACCCATTTCAACATTATCCATTTCTACACCAACA
* * * * * ** * * * *
386134 CTTTCAGCACTATCCATTTCTACACCA-CCACTTTCAGCATTGCCCCTTTCAACA-CTACC
1 CTTTCAACATTGTCCATTTCTACACTACCCA-TTTCAACATTATCCATTTCTACACCAACA
* * * * * *
386193 CATTTCAGCATTGTCCCTTTCTACACTACCCATTTCAACAGTATCTATTTCTGCACCACCA
1 C-TTTCAACATTGTCCATTTCTACACTACCCATTTCAACATTATCCATTTCTACACCAACA
* * * * * *
386254 CTTTCAGCATTATCCATTTCTACACCA-CCACTTTCAGCATTATCCACTTCTACACCACCA
1 CTTTCAACATTGTCCATTTCTACACTACCCA-TTTCAACATTATCCATTTCTACACCAACA
386314 CTTTCA
1 CTTTCA
386320 TAACAACCAC
Statistics
Matches: 244, Mismatches: 54, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
59 12 0.05
60 223 0.91
61 9 0.04
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (60 bp):
CTTTCAACATTGTCCATTTCTACACTACCCATTTCAACATTATCCATTTCTACACCAACA
Found at i:386019 original size:30 final size:30
Alignment explanation
Indices: 385985--386319 Score: 230
Period size: 30 Copynumber: 11.2 Consensus size: 30
385975 ACATTACTCA
*
385985 TTTCAACATTATCCATTTCTACACCAACAC
1 TTTCAGCATTATCCATTTCTACACCAACAC
* * * * * *
386015 TTTCAACATTGTCCCTTTCAACA-CTACCC
1 TTTCAGCATTATCCATTTCTACACCAACAC
* * * * *
386044 ATTTCAACATTGTCCCTTTCTACA-CTACCC
1 -TTTCAGCATTATCCATTTCTACACCAACAC
* * * * *
386074 ATTTCAACATTGTCCCTTTCTACA-CTACCC
1 -TTTCAGCATTATCCATTTCTACACCAACAC
* **
386104 ATTTTAGCATTATCCATTTCTACACCAGTAC
1 -TTTCAGCATTATCCATTTCTACACCAACAC
* *
386135 TTTCAGCACTATCCATTTCTACACCACCAC
1 TTTCAGCATTATCCATTTCTACACCAACAC
** * * * *
386165 TTTCAGCATTGCCCCTTTCAACA-CTACCC
1 TTTCAGCATTATCCATTTCTACACCAACAC
* * * *
386194 ATTTCAGCATTGTCCCTTTCTACA-CTACCC
1 -TTTCAGCATTATCCATTTCTACACCAACAC
* * * * *
386224 ATTTCAACAGTATCTATTTCTGCACCACCAC
1 -TTTCAGCATTATCCATTTCTACACCAACAC
*
386255 TTTCAGCATTATCCATTTCTACACCACCAC
1 TTTCAGCATTATCCATTTCTACACCAACAC
* *
386285 TTTCAGCATTATCCACTTCTACACCACCAC
1 TTTCAGCATTATCCATTTCTACACCAACAC
386315 TTTCA
1 TTTCA
386320 TAACAACCAC
Statistics
Matches: 259, Mismatches: 42, Indels: 8
0.84 0.14 0.03
Matches are distributed among these distances:
29 7 0.03
30 247 0.95
31 5 0.02
ACGTcount: A:0.26, C:0.36, G:0.04, T:0.34
Consensus pattern (30 bp):
TTTCAGCATTATCCATTTCTACACCAACAC
Found at i:386084 original size:120 final size:120
Alignment explanation
Indices: 385983--386308 Score: 449
Period size: 120 Copynumber: 2.7 Consensus size: 120
385973 CAACATTACT
* * * * *
385983 CATTTCAACATTATCCATTTCTACACCAACACTTTCAACATTGTCCCTTTCAACACTACC-CATT
1 CATTTCAACATTATCCATTTCTACACCAACACTTTCAGCATTATCCATTTCTACACCACCAC-TT
*
386047 TCAACATTGTCCCTTTCTACACTACCCATTTCAACATTGTCCCTTTCTACACTACC
65 TCAGCATTGTCCCTTTCTACACTACCCATTTCAACATTGTCCCTTTCTACACTACC
* * ** *
386103 CATTTTAGCATTATCCATTTCTACACCAGTACTTTCAGCACTATCCATTTCTACACCACCACTTT
1 CATTTCAACATTATCCATTTCTACACCAACACTTTCAGCATTATCCATTTCTACACCACCACTTT
* * *
386168 CAGCATTGCCCCTTTCAACACTACCCATTTCAGCATTGTCCCTTTCTACACTACC
66 CAGCATTGTCCCTTTCTACACTACCCATTTCAACATTGTCCCTTTCTACACTACC
* * * *
386223 CATTTCAACAGTATCTATTTCTGCACCACCACTTTCAGCATTATCCATTTCTACACCACCACTTT
1 CATTTCAACATTATCCATTTCTACACCAACACTTTCAGCATTATCCATTTCTACACCACCACTTT
*
386288 CAGCATTATCCAC-TTCTACAC
66 CAGCATTGTCC-CTTTCTACAC
386309 CACCACTTTC
Statistics
Matches: 179, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
120 177 0.99
121 2 0.01
ACGTcount: A:0.26, C:0.36, G:0.04, T:0.34
Consensus pattern (120 bp):
CATTTCAACATTATCCATTTCTACACCAACACTTTCAGCATTATCCATTTCTACACCACCACTTT
CAGCATTGTCCCTTTCTACACTACCCATTTCAACATTGTCCCTTTCTACACTACC
Found at i:386302 original size:16 final size:16
Alignment explanation
Indices: 386251--386302 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
386241 TTCTGCACCA
386251 CCACTTTCAGCATTAT
1 CCACTTTCAGCATTAT
**
386267 CCA-TTTCTA-CACCA-
1 CCACTTTC-AGCATTAT
386281 CCACTTTCAGCATTAT
1 CCACTTTCAGCATTAT
386297 CCACTT
1 CCACTT
386303 CTACACCACC
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 10 0.36
ACGTcount: A:0.25, C:0.37, G:0.04, T:0.35
Consensus pattern (16 bp):
CCACTTTCAGCATTAT
Found at i:386991 original size:14 final size:16
Alignment explanation
Indices: 386972--387004 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
386962 TGGTCTACAA
386972 CAATATA-AAACAT-T
1 CAATATACAAACATGT
386986 CAATATACAAACATGT
1 CAATATACAAACATGT
387002 CAA
1 CAA
387005 AACCACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.24
Consensus pattern (16 bp):
CAATATACAAACATGT
Found at i:390895 original size:2 final size:2
Alignment explanation
Indices: 390888--390931 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
390878 AAGGTAATCC
390888 AT AT 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 AT AT
390930 AT
1 AT
390932 TAAATTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:391991 original size:17 final size:17
Alignment explanation
Indices: 391969--392006 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
391959 CTTCTTTTTG
391969 CTTTCTGTTATGATTTC
1 CTTTCTGTTATGATTTC
391986 CTTTCTGTTATGATTTC
1 CTTTCTGTTATGATTTC
392003 CTTT
1 CTTT
392007 GTAGGCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.61
Consensus pattern (17 bp):
CTTTCTGTTATGATTTC
Found at i:397652 original size:110 final size:110
Alignment explanation
Indices: 397538--397942 Score: 331
Period size: 110 Copynumber: 3.6 Consensus size: 110
397528 TTTAAAAAAT
** *
397538 AATTATTAGACTATTTATTTTGATTTTACCTATTAAGTTGTATTTGAGTAGTTTGGTAAGTTTAG
1 AATTATTAGACTATTTATTTTGATTTTACAGATTAAATTGTATTTGAGTAGTTTGGTAAGTTTAG
* * *
397603 TT-TAGTTTAGTTCAATTTAAATTTTATTTTTTATTGAGT-AATATA
66 TTATAATTTAGTT-AATTTAAGTTTAATTTTTTATT-AGTAAATATA
* * * * * * *
397648 AATTATGATATTGA-TTATTTTTATTTTAGAGATTAAATCGTATTTGAGTAGTTTTGTAAGTTTA
1 AATTATTAGACT-ATTTATTTTGATTTTACAGATTAAATTGTATTTGAGTAGTTTGGTAAGTTTA
* * * * *
397712 GTGTAAAATATA-TT-GTTTAGGGTTTAGAGTTTTTATT-GTAAATATA
65 GT-TATAATTTAGTTAATTTA-AGTTTA-ATTTTTTATTAGTAAATATA
* * *
397758 AAGTAATTAGACTATTTATTTTGATTTTACAGATTAAATTGTATTCGAGTGGTTTGGTAAGTTTA
1 AA-TTATTAGACTATTTATTTTGATTTTACAGATTAAATTGTATTTGAGTAGTTTGGTAAGTTT-
* * * * * *
397823 ATTTATATTTTTTGTGTATTTTTAGTATAATTTTGGGTT-TTAGTTTAAATTATA
64 AGTTATA-ATTTAGT-TAATTTAAGTTTAATTTT---TTATTAG--TAAA-TATA
* * * *
397877 AA-TATTAGACTATTTATTTTGATTTTATATATTAAGTTGTATTTGAGTGGTTTGGTAAGTTTAG
1 AATTATTAGACTATTTATTTTGATTTTACAGATTAAATTGTATTTGAGTAGTTTGGTAAGTTTAG
397941 TT
66 TT
397943 TAAATTATAA
Statistics
Matches: 231, Mismatches: 44, Indels: 34
0.75 0.14 0.11
Matches are distributed among these distances:
109 6 0.03
110 66 0.29
111 65 0.28
112 8 0.03
113 5 0.02
114 5 0.02
115 5 0.02
116 6 0.03
117 55 0.24
118 4 0.02
119 6 0.03
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.52
Consensus pattern (110 bp):
AATTATTAGACTATTTATTTTGATTTTACAGATTAAATTGTATTTGAGTAGTTTGGTAAGTTTAG
TTATAATTTAGTTAATTTAAGTTTAATTTTTTATTAGTAAATATA
Found at i:406747 original size:61 final size:61
Alignment explanation
Indices: 406682--406809 Score: 247
Period size: 61 Copynumber: 2.1 Consensus size: 61
406672 AAGGGTATCA
*
406682 ATACTGAAGTATAGTATTGATACCACAGTAAGGAAGTATCGATATTGTACCTTGGGTACCG
1 ATACTAAAGTATAGTATTGATACCACAGTAAGGAAGTATCGATATTGTACCTTGGGTACCG
406743 ATACTAAAGTATAGTATTGATACCACAGTAAGGAAGTATCGATATTGTACCTTGGGTACCG
1 ATACTAAAGTATAGTATTGATACCACAGTAAGGAAGTATCGATATTGTACCTTGGGTACCG
406804 ATACTA
1 ATACTA
406810 CTCATATGGA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (61 bp):
ATACTAAAGTATAGTATTGATACCACAGTAAGGAAGTATCGATATTGTACCTTGGGTACCG
Found at i:407244 original size:44 final size:44
Alignment explanation
Indices: 407151--407263 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
407141 TATTCATGCT
* * * * * *
407151 ATGTGATATTGATTTCCGTGATTACATGAATATGTTATACAAGCT
1 ATGTGATA-TGATCTACGTGATTACACGAACATGTGATACAAGCC
*
407196 ATGTGATATGATCTACGTGATTACACGAACATGTGATATAAGCC
1 ATGTGATATGATCTACGTGATTACACGAACATGTGATACAAGCC
* * *
407240 ATGTGACATGACCTGCGTGATTAC
1 ATGTGATATGATCTACGTGATTAC
407264 TTGTCTATGT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
44 50 0.86
45 8 0.14
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (44 bp):
ATGTGATATGATCTACGTGATTACACGAACATGTGATACAAGCC
Found at i:407443 original size:23 final size:23
Alignment explanation
Indices: 407374--407432 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
407364 GTTCTACGCA
* * * *
407374 GTCATTTGGGATAATTCTACGTG
1 GTCATTCGGGACAATACTATGTG
*
407397 GTCTTTCGGGACAATACTATGTG
1 GTCATTCGGGACAATACTATGTG
407420 GTCATTCGGGACA
1 GTCATTCGGGACA
407433 TTTTTATGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (23 bp):
GTCATTCGGGACAATACTATGTG
Found at i:417026 original size:21 final size:21
Alignment explanation
Indices: 417001--417050 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
416991 AATTCGCTTT
417001 TGCCTTAGCATCAGAATCTGG
1 TGCCTTAGCATCAGAATCTGG
*
417022 TGCCTTGGCATCAGAATCTGG
1 TGCCTTAGCATCAGAATCTGG
417043 TGCCTTAG
1 TGCCTTAG
417051 TAGAATCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (21 bp):
TGCCTTAGCATCAGAATCTGG
Found at i:417389 original size:21 final size:21
Alignment explanation
Indices: 417338--417382 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
417328 AGACCAGCTA
*
417338 TGACT-TTGAAGTAAGGCGCCT
1 TGACTATT-AAGTAAAGCGCCT
*
417359 TGACTATTAAGTAAAGCTCCT
1 TGACTATTAAGTAAAGCGCCT
417380 TGA
1 TGA
417383 TTTTTAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (21 bp):
TGACTATTAAGTAAAGCGCCT
Found at i:425147 original size:19 final size:20
Alignment explanation
Indices: 425116--425153 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
425106 ATGTGTTAAA
425116 GTGATATATGTTGA-TTTTT
1 GTGATATATGTTGAGTTTTT
425135 GTGAGTATA-GTTGAGTTTT
1 GTGA-TATATGTTGAGTTTT
425154 AAGTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (20 bp):
GTGATATATGTTGAGTTTTT
Found at i:425387 original size:20 final size:20
Alignment explanation
Indices: 425362--425424 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
425352 TTCATAGAGA
425362 ATCGATACTGAAGTAGTAGT
1 ATCGATACTGAAGTAGTAGT
* *
425382 ATCGATAC--CA-T-G-GGT
1 ATCGATACTGAAGTAGTAGT
*
425397 ATCGATATTGAAGTAGTAGT
1 ATCGATACTGAAGTAGTAGT
425417 ATCGATAC
1 ATCGATAC
425425 CATGGGTATC
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
15 9 0.28
16 1 0.03
17 2 0.06
18 2 0.06
19 1 0.03
20 17 0.53
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (20 bp):
ATCGATACTGAAGTAGTAGT
Found at i:425409 original size:35 final size:35
Alignment explanation
Indices: 425362--425439 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
425352 TTCATAGAGA
425362 ATCGATACTGAAGTAGTAGTATCGATACCATGGGT
1 ATCGATACTGAAGTAGTAGTATCGATACCATGGGT
*
425397 ATCGATATTGAAGTAGTAGTATCGATACCATGGGT
1 ATCGATACTGAAGTAGTAGTATCGATACCATGGGT
*
425432 ATCAATAC
1 ATCGATAC
425440 CGTTGTCTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (35 bp):
ATCGATACTGAAGTAGTAGTATCGATACCATGGGT
Found at i:426173 original size:23 final size:24
Alignment explanation
Indices: 426120--426173 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
426110 AGAGTCAAGG
*
426120 TTTCTACGTTGTCCTTCGGGATAA
1 TTTCTACGTAGTCCTTCGGGATAA
*
426144 TTT-TACGTAGTCCTTCGGGA-CA
1 TTTCTACGTAGTCCTTCGGGATAA
426166 TTTCTACG
1 TTTCTACG
426174 CGGTGCTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 4 0.15
23 20 0.74
24 3 0.11
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTCTACGTAGTCCTTCGGGATAA
Found at i:427988 original size:12 final size:12
Alignment explanation
Indices: 427971--427995 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
427961 AGTATCTCAG
427971 AGAGGTAGAGGA
1 AGAGGTAGAGGA
427983 AGAGGTAGAGGA
1 AGAGGTAGAGGA
427995 A
1 A
427996 TAAGTCAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.48, T:0.08
Consensus pattern (12 bp):
AGAGGTAGAGGA
Found at i:430178 original size:38 final size:38
Alignment explanation
Indices: 430108--430183 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
430098 TTTCCCGTTC
* *
430108 AACCACCAACCTACTAGGGTTATTAAGGGATAATTAAT
1 AACCACCAACCTACCAGGGTTATTAAGAGATAATTAAT
**
430146 AACCACCAACCTACCCA-GGTTATTATTAGATAATTAAT
1 AACCACCAACCTA-CCAGGGTTATTAAGAGATAATTAAT
430184 GTTGCCATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 31 0.94
39 2 0.06
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (38 bp):
AACCACCAACCTACCAGGGTTATTAAGAGATAATTAAT
Found at i:430218 original size:25 final size:25
Alignment explanation
Indices: 430190--430247 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
430180 TAATGTTGCC
* *
430190 ATTATTTTTTATCATTATAATGAAT
1 ATTATTTTTCATCATTATAATAAAT
*
430215 ATTATTTTTCGTCATTATAATAAAT
1 ATTATTTTTCATCATTATAATAAAT
430240 ATTATTTT
1 ATTATTTT
430248 CCTATTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (25 bp):
ATTATTTTTCATCATTATAATAAAT
Found at i:432297 original size:29 final size:30
Alignment explanation
Indices: 432245--432312 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
432235 AAAAACTTTC
*
432245 AATTAAATCCTCAAATTTCACC-AATTTTT
1 AATTAAATCCTCAAATTTCACCAAATATTT
**
432274 AATTAAATCCTCAAATTTTGCCAAAATATTT
1 AATTAAATCCTCAAATTTCACC-AAATATTT
432305 AATTAAAT
1 AATTAAAT
432313 ATTTTTTCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 20 0.59
31 14 0.41
ACGTcount: A:0.43, C:0.16, G:0.01, T:0.40
Consensus pattern (30 bp):
AATTAAATCCTCAAATTTCACCAAATATTT
Found at i:439321 original size:29 final size:29
Alignment explanation
Indices: 439279--439335 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
439269 TTTTAAAAAC
*
439279 TTTCAATTAAATCCTTAAATTTCACCAAT
1 TTTCAATTAAATCCTCAAATTTCACCAAT
*
439308 TTTCAATTAAATCCTCAAATTTCGCCAA
1 TTTCAATTAAATCCTCAAATTTCACCAA
439336 AATATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.39
Consensus pattern (29 bp):
TTTCAATTAAATCCTCAAATTTCACCAAT
Found at i:441602 original size:64 final size:65
Alignment explanation
Indices: 441451--441604 Score: 215
Period size: 65 Copynumber: 2.4 Consensus size: 65
441441 ATTGAAAATT
* * * *
441451 GAATGCGTTTTATGCATTGATGCACATACCATGCATCGATGCACTCAGGTTTTTATGAAAACATC
1 GAATGCATTTTATGCATAGATGCACATAACATGCATCGATGCACTCAGGTATTTATGAAAACATC
* *
441516 GAATGCATTTGATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-T-AAAACA
1 GAATGCATTTTATGCATAGATGCACATA-ACATGCATCGATGCACTCAGG-TATTTATGAAAACA
441578 TC
64 TC
441580 GAATGCATTTTATGCATAGATGCAC
1 GAATGCATTTTATGCATAGATGCAC
441605 CCTTAGTGCA
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 32 0.40
65 44 0.55
66 4 0.05
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (65 bp):
GAATGCATTTTATGCATAGATGCACATAACATGCATCGATGCACTCAGGTATTTATGAAAACATC
Found at i:449565 original size:65 final size:64
Alignment explanation
Indices: 449496--449619 Score: 171
Period size: 64 Copynumber: 1.9 Consensus size: 64
449486 AATGCATTTT
*
449496 ATGCATCGATGCACTCAGGA-T-TTTATGAAAACATCGAATGCATTTGGTGCATCGATGCACAAG
1 ATGCATCGATGCACTCA-GACTATTT-T-AAAACATCGAATGCATTTGATGCATCGATGCACAAG
449559 AC
63 AC
** *
449561 ATGCATCGATGTTCTCAGACTATTTTAAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACTCAGACTATTTTAAAACATCGAATGCATTTGATGCATCGATGCAC
449620 CCTTAGTGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
64 33 0.62
65 17 0.32
66 3 0.06
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACTCAGACTATTTTAAAACATCGAATGCATTTGATGCATCGATGCACAAGAC
Found at i:453064 original size:24 final size:24
Alignment explanation
Indices: 453027--453075 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
453017 GACGCATTAT
* *
453027 TGGTCTCAACGCATGCAAAACGAA
1 TGGTCCCAAAGCATGCAAAACGAA
*
453051 TGGTCCCAAAGCATGCAGAACGAA
1 TGGTCCCAAAGCATGCAAAACGAA
453075 T
1 T
453076 CTACGCGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (24 bp):
TGGTCCCAAAGCATGCAAAACGAA
Found at i:484516 original size:21 final size:21
Alignment explanation
Indices: 484490--484540 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
484480 TAGATTTATT
484490 GAAAATGAAAAAT-TAATATAA
1 GAAAAT-AAAAATGTAATATAA
*
484511 GAAAATAAAGATGTAATATAA
1 GAAAATAAAAATGTAATATAA
484532 -AAAATAAAA
1 GAAAATAAAA
484541 GGAAATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (21 bp):
GAAAATAAAAATGTAATATAA
Found at i:484547 original size:19 final size:21
Alignment explanation
Indices: 484504--484552 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
484494 ATGAAAAATT
* *
484504 AATATAAGAAAATAAAGATGT
1 AATATAAGAAAATAAAGAGGA
484525 AATATAA-AAAATAAA-AGGA
1 AATATAAGAAAATAAAGAGGA
484544 AATA-AAGAA
1 AATATAAGAA
484553 GATTGAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 2 0.08
19 8 0.32
20 8 0.32
21 7 0.28
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.18
Consensus pattern (21 bp):
AATATAAGAAAATAAAGAGGA
Found at i:485004 original size:17 final size:18
Alignment explanation
Indices: 484982--485019 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
484972 TATTAATAAT
*
484982 TTTATAA-TCTTTTAAAA
1 TTTATAAGTATTTTAAAA
*
484999 TTTATAAGTATTTTATAA
1 TTTATAAGTATTTTAAAA
485017 TTT
1 TTT
485020 TTTAAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTATAAGTATTTTAAAA
Found at i:488559 original size:12 final size:13
Alignment explanation
Indices: 488526--488563 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
488516 AAATACATAA
488526 ATATATTTAATAT
1 ATATATTTAATAT
*
488539 ATTTATTTAATAT
1 ATATATTTAATAT
488552 A-ATATTTAATAT
1 ATATATTTAATAT
488564 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:488615 original size:23 final size:22
Alignment explanation
Indices: 488577--488631 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 22
488567 TAGTTATAAT
488577 TTTTACAT-TATAATCGAAACA
1 TTTTACATATATAATCGAAACA
488598 TTTTACATAATATAATCGAAACA
1 TTTTACAT-ATATAATCGAAACA
488621 -TTTACATATAT
1 TTTTACATATAT
488632 TATTAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 12 0.38
22 7 0.22
23 13 0.41
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.40
Consensus pattern (22 bp):
TTTTACATATATAATCGAAACA
Found at i:489944 original size:28 final size:28
Alignment explanation
Indices: 489874--490028 Score: 166
Period size: 28 Copynumber: 5.4 Consensus size: 28
489864 CCGTTGACCA
* *
489874 GGTGCTATTTTGAGAATTAATTCGAAAT
1 GGTGCTATTTTGGGAATTAATTTGAAAT
489902 GGGGTGCTATTTTGGGAATTAATTTGAAAT
1 --GGTGCTATTTTGGGAATTAATTTGAAAT
*
489932 GGTGCTATTTTGGGAATTAATTTAAAAT
1 GGTGCTATTTTGGGAATTAATTTGAAAT
* * *
489960 GGTGCTACTTTGGGAATTAATTCGAAAAA
1 GGTGCTATTTTGGGAATTAATTTG-AAAT
* * * * * *
489989 GATACTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTT-GAAAT
490018 GGTGCTATTTT
1 GGTGCTATTTT
490029 TATAAAATGG
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
28 48 0.45
29 32 0.30
30 26 0.25
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.41
Consensus pattern (28 bp):
GGTGCTATTTTGGGAATTAATTTGAAAT
Found at i:491148 original size:117 final size:116
Alignment explanation
Indices: 490937--491227 Score: 408
Period size: 117 Copynumber: 2.5 Consensus size: 116
490927 GGAAGTATTT
* * * *
490937 CAGGCTCCTTTTCTATGTGCTCA-GTTAAAGTCCTTACTGGTGTGCAGGTGGGTGCATGGTTCTG
1 CAGGCTCCTTTGCT-TGTGCTCAGGAT-AAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATG
*
491001 GGGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACTG
64 GGGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGAGAAGTTATTACTG
491054 CAGGCTCCTTTGCTGTGTGCTCAGGATAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGG
1 CAGGCTCCTTTGCT-TGTGCTCAGGATAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGG
* *
491119 GGAACCTACACATTGTAGTGA-TGGAAGTGACTGGATGGAGACGTTATTATTG
65 GGAACCTACACATTGTAGTGATTGG-AGTGACTGGATGGAGAAGTTATTACTG
** * * *
491171 CAGGCTCCTCGGCTTCGTGCTTAGGGTAAGTCC-TATTGGTGTGCAGGTGGGTGTATG
1 CAGGCTCCTTTGCTT-GTGCTCAGGATAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
491228 TTTTGGGAAA
Statistics
Matches: 158, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
116 27 0.17
117 129 0.82
118 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (116 bp):
CAGGCTCCTTTGCTTGTGCTCAGGATAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGGG
GAACCTACACATTGTAGTGATTGGAGTGACTGGATGGAGAAGTTATTACTG
Found at i:491265 original size:117 final size:116
Alignment explanation
Indices: 490964--491265 Score: 268
Period size: 117 Copynumber: 2.6 Consensus size: 116
490954 TGCTCAGTTA
* * * * * ** * **
490964 AAGTCCTTACTGGTGTGCAGGTGGGTGCATGGTTCTGGGGAACCTACACATTGTAGTGATTGGAG
1 AAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGGGAAACATACAAAAAGTAG-AAACGGAG
* **
491029 TGACTGGATGGGGAAGTTATTACTGCAGGCTCCTTTGCTGTGTGCTCAGGAT
65 TGACTGGATGGAGAAGTTATTACTGCAGGCTCCTCGGCTGTGTGCTCAGGAT
* * * ** ** *
491081 AAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGGGGAACCTACACATTGTAGTGATGGAAG
1 AAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGGGAAACATACAAAAAGTAGAAACGG-AG
* * * *
491146 TGACTGGATGGAGACGTTATTATTGCAGGCTCCTCGGCT-TCGTGCTTAGGGT
65 TGACTGGATGGAGAAGTTATTACTGCAGGCTCCTCGGCTGT-GTGCTCAGGAT
* * * *
491198 AAGTCC-TATTGGTGTGCAGGTGGGTGTAT-GTTTTGGGAAAATATATAAAAAGATAGAAACCGG
1 AAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGGG-AAACATACAAAAAG-TAGAAA-CGG
491261 AGTGA
63 AGTGA
491266 TTGAATGAAA
Statistics
Matches: 156, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
115 7 0.04
116 33 0.21
117 114 0.73
118 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.33, T:0.30
Consensus pattern (116 bp):
AAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGGGAAACATACAAAAAGTAGAAACGGAGT
GACTGGATGGAGAAGTTATTACTGCAGGCTCCTCGGCTGTGTGCTCAGGAT
Found at i:491557 original size:18 final size:17
Alignment explanation
Indices: 491522--491560 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
491512 TTCGTTTTGA
491522 ATATATTTGTATTATTT
1 ATATATTTGTATTATTT
491539 ATAT-TTTGTTATGTATTT
1 ATATATTTG-TAT-TATTT
491557 ATAT
1 ATAT
491561 CTAATGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (17 bp):
ATATATTTGTATTATTT
Found at i:496582 original size:2 final size:2
Alignment explanation
Indices: 496577--496612 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
496567 AAAAAAAAAA
496577 AT AT AT -T 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 A
496613 ATTGTAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:497482 original size:29 final size:29
Alignment explanation
Indices: 497397--497494 Score: 124
Period size: 29 Copynumber: 3.3 Consensus size: 29
497387 ACTGTAAATG
* **
497397 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTTGAAAAA
**
497426 GGTATTATTTTGGGAATTAATTTGAAAAA
1 GGTGCTATTTTGGGAATTAATTTGAAAAA
* *
497455 GGTGCTATTTTGGGAATTATTTTAAAAACA
1 GGTGCTATTTTGGGAATTAATTTGAAAA-A
497485 GGTGCTATTT
1 GGTGCTATTT
497495 CTGTAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
29 48 0.81
30 11 0.19
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTTGAAAAA
Found at i:498999 original size:117 final size:116
Alignment explanation
Indices: 498788--499079 Score: 440
Period size: 117 Copynumber: 2.5 Consensus size: 116
498778 GGAAGTATTT
*
498788 CAGGCTCCTTTGCTATGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGCATGGTTCTGC
1 CAGGCTCCTTTGCT-TGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGC
* * * *
498853 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACTG
65 GGAACCTACACATTGTAGTGATAGAAGTGACTGGATAGAGAAGTTATTACTG
* *
498905 CAGGCTCCTTTGCTGTGTGCTCAGGATAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCT-TGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGC
* *
498970 GGAACCTACACATTGTAGTGATAGAAGTGACTGGATAGAGATGTTATTATTG
65 GGAACCTACACATTGTAGTGATAGAAGTGACTGGATAGAGAAGTTATTACTG
* * * *
499022 CAGGCTCCTTGGCTTCGTGCTTAGGGTAAGTCCGTACTGGTGTGCATGTGGGTGTATG
1 CAGGCTCCTTTGCTT-GTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
499080 TTTTGTGAAA
Statistics
Matches: 159, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
116 1 0.01
117 158 0.99
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.32
Consensus pattern (116 bp):
CAGGCTCCTTTGCTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGCG
GAACCTACACATTGTAGTGATAGAAGTGACTGGATAGAGAAGTTATTACTG
Found at i:502552 original size:105 final size:105
Alignment explanation
Indices: 502406--502675 Score: 423
Period size: 105 Copynumber: 2.6 Consensus size: 105
502396 TTTGTTGGAT
* *
502406 GAGTTCTTCTTATTATGAACTCTTCTGGAAATGTTGATTCACCTCATTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAA
* * *
502471 GGAACATGTTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GAAACAGGATCTTCTCATTACGAACCTTCTCCTTTAAGAC
* * ** *
502511 GAGTTCTTCTCATTATGAACTCTTTTGGAAATGTTGGTTCACCTCCTTCTACGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAA
* * *
502576 GAAATAGGATCTTCTCATTACGAACCTTCTCTTTTAGGAC
66 GAAACAGGATCTTCTCATTACGAACCTTCTCCTTTAAGAC
502616 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATT
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATT
502676 ATAGTTGTTG
Statistics
Matches: 147, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 147 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAA
GAAACAGGATCTTCTCATTACGAACCTTCTCCTTTAAGAC
Found at i:503602 original size:8 final size:8
Alignment explanation
Indices: 503589--503657 Score: 56
Period size: 8 Copynumber: 8.9 Consensus size: 8
503579 GAAACCTCCT
503589 TTTTTTTC
1 TTTTTTTC
503597 -TTTTTT-
1 TTTTTTTC
*
503603 TTTTCTTC
1 TTTTTTTC
*
503611 ATTTTTTC
1 TTTTTTTC
*
503619 ATTTTTTC
1 TTTTTTTC
*
503627 ATTTTTTC
1 TTTTTTTC
503635 --TTTTTC
1 TTTTTTTC
503641 ATTTTTTCTC
1 -TTTTTT-TC
503651 TTTTTTT
1 TTTTTTT
503658 TATTTTTCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
6 6 0.12
7 11 0.21
8 23 0.44
9 10 0.19
10 2 0.04
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:508674 original size:2 final size:2
Alignment explanation
Indices: 508667--508712 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
508657 ATTATATCAT
508667 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
508709 TA TA
1 TA TA
508713 ATGATTAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:521475 original size:16 final size:17
Alignment explanation
Indices: 521454--521487 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
521444 TTTTTTTATT
*
521454 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
521470 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
521487 A
1 A
521488 AAAATATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:522071 original size:3 final size:3
Alignment explanation
Indices: 522063--522095 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
522053 CACGTCATAG
522063 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
522096 TTGTAGTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:525969 original size:14 final size:14
Alignment explanation
Indices: 525950--525990 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
525940 ATAACTTTAA
525950 ATAAAATTTGAATT
1 ATAAAATTTGAATT
* *
525964 ATAAAATATGATTT
1 ATAAAATTTGAATT
525978 AT-AAATTT-AATT
1 ATAAAATTTGAATT
525990 A
1 A
525991 ATTTATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 4 0.17
13 5 0.22
14 14 0.61
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (14 bp):
ATAAAATTTGAATT
Found at i:530182 original size:2 final size:2
Alignment explanation
Indices: 530175--530200 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
530165 TAAATCTTTA
530175 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
530201 TAAAAACTTA
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):
AT
Found at i:537948 original size:20 final size:20
Alignment explanation
Indices: 537923--537962 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
537913 CCATGTTAAA
537923 AAGGTTTTTGCAGTGAAAAT
1 AAGGTTTTTGCAGTGAAAAT
537943 AAGGTTTTTGCAGTGAAAAT
1 AAGGTTTTTGCAGTGAAAAT
537963 GGCCCCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (20 bp):
AAGGTTTTTGCAGTGAAAAT
Found at i:543722 original size:16 final size:16
Alignment explanation
Indices: 543701--543733 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
543691 TGGTGATGTA
543701 TGTATTC-ATTCACTCT
1 TGTATTCTATTCA-TCT
543717 TGTATTCTATTCATCT
1 TGTATTCTATTCATCT
543733 T
1 T
543734 TAGAGATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.55
Consensus pattern (16 bp):
TGTATTCTATTCATCT
Found at i:549423 original size:31 final size:31
Alignment explanation
Indices: 549268--549409 Score: 257
Period size: 31 Copynumber: 4.6 Consensus size: 31
549258 AGGGTCGAAG
549268 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
549299 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
549330 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
549361 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
549392 GTTTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
549410 AAATCTATGG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:550148 original size:21 final size:21
Alignment explanation
Indices: 550122--550163 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
550112 TCGAAGTTTC
* *
550122 ATGCATTGGTGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
550143 ATGCATCGATGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
550164 GGTTAATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
ATGCATCGATGCACTGTAGCA
Found at i:550573 original size:13 final size:13
Alignment explanation
Indices: 550555--550581 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
550545 ATAAATAGCA
550555 TGTCTCCATTCGG
1 TGTCTCCATTCGG
550568 TGTCTCCATTCGG
1 TGTCTCCATTCGG
550581 T
1 T
550582 TGATTCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.30, G:0.22, T:0.41
Consensus pattern (13 bp):
TGTCTCCATTCGG
Found at i:553952 original size:22 final size:22
Alignment explanation
Indices: 553924--553977 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
553914 TAAAATATGG
*
553924 AATGAACAGTACTGTGAACAAT
1 AATGAACAGTACCGTGAACAAT
*
553946 AATGAACAGTGCCGTGAACAAT
1 AATGAACAGTACCGTGAACAAT
553968 ACCATGAACA
1 A--ATGAACA
553978 ATGAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 21 0.75
24 7 0.25
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (22 bp):
AATGAACAGTACCGTGAACAAT
Found at i:554839 original size:32 final size:31
Alignment explanation
Indices: 554723--554844 Score: 106
Period size: 31 Copynumber: 3.9 Consensus size: 31
554713 CCTCGGAAAC
* * * *
554723 TGTCCATA-GGTCCGAAGAACCTAGGTAAAT
1 TGTCCATATGTTCCGTAGAACATAGGTAATT
* *
554753 TATCCATATGTTCCTTAGAACATAGGT-ATAT
1 TGTCCATATGTTCCGTAGAACATAGGTAAT-T
* * * *
554784 TGTTCATATATACCG-AAAGACATAGGTAATT
1 TGTCCATATGTTCCGTAGA-ACATAGGTAATT
554815 CTGTCCATATGTTCCGTAGAACATAGGTAA
1 -TGTCCATATGTTCCGTAGAACATAGGTAA
554845 ACCCTCGACT
Statistics
Matches: 70, Mismatches: 16, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
30 10 0.14
31 34 0.49
32 24 0.34
33 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (31 bp):
TGTCCATATGTTCCGTAGAACATAGGTAATT
Found at i:558068 original size:27 final size:27
Alignment explanation
Indices: 558027--558119 Score: 168
Period size: 27 Copynumber: 3.4 Consensus size: 27
558017 GATAATAGCT
*
558027 CTGAATCATTCAGAATGTACTTCTGTA
1 CTGAATCATTCAGAATGTACTTCTGTG
*
558054 CTAAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
558081 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
558108 CTGAATCATTCA
1 CTGAATCATTCA
558120 ACACTGTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTG
Found at i:560240 original size:3 final size:3
Alignment explanation
Indices: 560222--560302 Score: 99
Period size: 3 Copynumber: 26.7 Consensus size: 3
560212 TGTAATATTA
* * * *
560222 AAT AAT ATAT ATT AAT AAT AAT AAT AAT AAT AAT AAT TAT TAT TAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
560268 AAT TAT AAT AAT AAT TAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
560303 ATAACATTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 66 0.96
4 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:560795 original size:113 final size:113
Alignment explanation
Indices: 560528--561311 Score: 1251
Period size: 113 Copynumber: 7.0 Consensus size: 113
560518 TAGAGTCATT
* ** * *
560528 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC-T--T-CTTCTCCTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*** ** * *
560589 TTATGAACT-TTTCTGGAAAAATTGACCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
*
560636 CAAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
560700 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
*
560748 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
**
560813 TTATGAACTCGATTTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
*
560861 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTATTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
560926 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
560974 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTC-AG--ATGAGTTCTTC
* *** **
561039 TCATTATGAACTC-TACTTGGAAATTTTAATCCATCAAGTGATAAATTTGAG
63 TCATTATGAACTCGAAC-TGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
561090 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* *
561155 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
561203 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGA-TTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
561267 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTT
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTT
561312 AAATCTTTGC
Statistics
Matches: 631, Mismatches: 34, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
107 27 0.04
108 6 0.01
110 1 0.00
111 30 0.05
112 88 0.14
113 370 0.59
114 4 0.01
115 4 0.01
116 101 0.16
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
Found at i:561077 original size:342 final size:338
Alignment explanation
Indices: 560528--561311 Score: 1249
Period size: 342 Copynumber: 2.3 Consensus size: 338
560518 TAGAGTCATT
* ** * *
560528 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC-T--T-CTTCTCCTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*** ** * *
560589 TTATGAACT-TTTCTGGAAAAATTGACCCATCAAGTGATGGATTTGAGCAAAAGTTGAACAAATT
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGTTGAACAAATT
*
560653 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
131 CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
**
560718 AAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
196 AAAGCTAATCCATCAAGTGATAAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
** *
560783 CTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGATTTGGAAAAGCTAATCCATCAAG
261 CTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAG
*
560848 TGATGGATTTGAG
326 TGATAGATTTGAG
*
560861 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTATTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
560926 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAA-GTTGAACAAAT
*
560991 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAAGTAATGAGTTCTTCTCATTATGAACTC-TAC
130 TCTTCTCATTATGAACTTCTTCATCCTTCTTC-AG--ATGAGTTCTTCTCATTATGAACTCGAAC
***
561055 TTGGAAATTTTAATCCATCAAGTGATAAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATG
192 -TGGAAAAGCTAATCCATCAAGTGATAAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATG
*
561120 AACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCA
256 AACTTCTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCA
561185 TCAAGTGATAGATTTGAG
321 TCAAGTGATAGATTTGAG
561203 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGA-TTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
561267 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTT
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTT
561312 AAATCTTTGC
Statistics
Matches: 415, Mismatches: 26, Indels: 12
0.92 0.06 0.03
Matches are distributed among these distances:
333 33 0.08
334 1 0.00
336 1 0.00
337 29 0.07
338 36 0.09
339 42 0.10
340 2 0.00
341 55 0.13
342 216 0.52
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (338 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGTTGAACAAATT
CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
AAAGCTAATCCATCAAGTGATAAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
CTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAG
TGATAGATTTGAG
Found at i:561144 original size:229 final size:225
Alignment explanation
Indices: 560528--561311 Score: 1256
Period size: 229 Copynumber: 3.5 Consensus size: 225
560518 TAGAGTCATT
* ** * *
560528 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC-T--T-CTTCTCCTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * ** * *
560589 TTATGAACTTTTCTGGAAAAATTGACCCATCAAGTGATGGATTTGAGCAAAA-GTTGAACAAATT
66 TTATGAACTCTACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
*
560653 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
131 CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
560718 AAAGCTAATCCATCAAGTGATGGATTTGAG
196 AAAGCTAATCCATCAAGTGATGGATTTGAG
*
560748 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* *
560813 TTATGAACTCGATTTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTCTA-CTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
*
560878 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTATTCTCATTATGAACTCGAACTGG
130 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
560943 AAAAGCTAATCCATCAAGTGATGGATTTGAG
195 AAAAGCTAATCCATCAAGTGATGGATTTGAG
560974 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTC-AG--ATGAGTTCTTC
*** **
561039 TCATTATGAACTCTACTTGGAAATTTTAATCCATCAAGTGATAAATTTGAGCAAAAGGTTGAACA
63 TCATTATGAACTCTAC-TGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACA
561104 AATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAAC
127 AATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAAC
* *
561169 TGGAAAAGATAATCCATCAAGTGATAGATTTGAG
192 TGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
561203 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGA-TTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*
561267 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTT
66 TTATGAACTC-TACTGGAAAAGCTAATCCATCAAGTGATGGATTT
561312 AAATCTTTGC
Statistics
Matches: 520, Mismatches: 33, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
220 33 0.06
221 1 0.00
223 1 0.00
224 29 0.06
225 80 0.15
226 159 0.31
227 2 0.00
228 2 0.00
229 213 0.41
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (225 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
AAAGCTAATCCATCAAGTGATGGATTTGAG
Found at i:562207 original size:83 final size:83
Alignment explanation
Indices: 562027--562406 Score: 681
Period size: 83 Copynumber: 4.6 Consensus size: 83
562017 GGTTCCTACT
* * *
562027 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATAC-TCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
562091 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
562109 AAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCTAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
562174 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
562192 AAACCAGATCAGATAACTCAAAGAACACTTACAGAAGATACTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
562257 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
*
562275 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
562340 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
562358 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA
562407 CATTGCATTT
Statistics
Matches: 288, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
82 52 0.18
83 236 0.82
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
TCAATGATTGGTTCTGCC
Found at i:563217 original size:16 final size:18
Alignment explanation
Indices: 563181--563223 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
563171 AATAAAAGAG
*
563181 TAAATTGAATTTTCGAAA
1 TAAATTGAATTCTCGAAA
563199 TAAATTGAA-TCTC-AAA
1 TAAATTGAATTCTCGAAA
563215 TAAATTGAA
1 TAAATTGAA
563224 CTTGAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 12 0.50
17 3 0.12
18 9 0.38
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (18 bp):
TAAATTGAATTCTCGAAA
Found at i:563231 original size:16 final size:15
Alignment explanation
Indices: 563181--563242 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 15
563171 AATAAAAGAG
563181 TAAATTGAATTTTCGAAA
1 TAAATTGAA--TT-GAAA
*
563199 TAAATTGAATCTCAAA
1 TAAATTGAAT-TGAAA
563215 TAAATTGAACTTGAAA
1 TAAATTGAA-TTGAAA
* *
563231 TAGATAGAATTG
1 TAAATTGAATTG
563243 TATTCAAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.08
16 24 0.63
17 2 0.05
18 9 0.24
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (15 bp):
TAAATTGAATTGAAA
Found at i:570886 original size:15 final size:15
Alignment explanation
Indices: 570863--570894 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
570853 TGAAATGAAT
570863 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
570878 AATGCATGTATGCAA
1 AATGAATGTATGCAA
570893 AA
1 AA
570895 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:574914 original size:13 final size:13
Alignment explanation
Indices: 574890--574922 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
574880 TCGATATTGA
574890 AAAATAAA-TATT
1 AAAATAAATTATT
574902 AAAATAAATTATT
1 AAAATAAATTATT
574915 AAAA-AAAT
1 AAAATAAAT
574923 AAATTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATAAATTATT
Found at i:576332 original size:11 final size:12
Alignment explanation
Indices: 576316--576377 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
576306 TTTGGGCTTG
576316 TAATATTAA-AA
1 TAATATTAATAA
576327 TAATATATTAATAA
1 T-A-ATATTAATAA
*
576341 TAATATT-ATTA
1 TAATATTAATAA
* *
576352 TATTATTAATTA
1 TAATATTAATAA
*
576364 TAATAATAATAA
1 TAATATTAATAA
576376 TA
1 TA
576378 TAAATAACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
11 10 0.24
12 21 0.50
13 8 0.19
14 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:578332 original size:26 final size:26
Alignment explanation
Indices: 578285--578335 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
578275 ATGAAAGTAT
*
578285 GAATTAAAAGAAAAATTGAAAAAAAG
1 GAATTAAAAGAAAAAATGAAAAAAAG
*
578311 GAATTAAAAATAAAAAAT-AAAAAAA
1 GAATT-AAAAGAAAAAATGAAAAAAA
578336 TAATTGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.16
Consensus pattern (26 bp):
GAATTAAAAGAAAAAATGAAAAAAAG
Found at i:579707 original size:13 final size:13
Alignment explanation
Indices: 579681--579715 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
579671 CAATCCAGGC
579681 GACATACG-GGGT
1 GACATACGAGGGT
579693 GACATACGAGGGT
1 GACATACGAGGGT
579706 GACATACGAG
1 GACATACGAG
579716 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:579804 original size:28 final size:32
Alignment explanation
Indices: 579731--579923 Score: 201
Period size: 32 Copynumber: 6.2 Consensus size: 32
579721 TACGAGTCAT
* *
579731 ACGAGCCAATGGGGAGGATGCAACGAGCCAT--
1 ACGAGCCAATGGGGAGCATGC-ACGAGCAATAG
579762 ACGAGCCAATGGGGAGCATGCA-G-G-AATAG
1 ACGAGCCAATGGGGAGCATGCACGAGCAATAG
* *
579791 A-GAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAATGGGGAGCATGC-ACGAGCAATAG
* *
579823 ACGAGCC-ATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAATGGGGAGCATGC-ACGAGCAATAG
579855 ACGAGCCAATGGGGAGCATGCA-G-G-AATAG
1 ACGAGCCAATGGGGAGCATGCACGAGCAATAG
* *
579884 A-GAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAATGGGGAGCATGC-ACGAGCAATAG
579916 ACGAGCCA
1 ACGAGCCA
579924 TACGAGCCAA
Statistics
Matches: 141, Mismatches: 8, Indels: 24
0.82 0.05 0.14
Matches are distributed among these distances:
27 2 0.01
28 39 0.28
29 8 0.06
30 4 0.03
31 23 0.16
32 41 0.29
33 24 0.17
ACGTcount: A:0.34, C:0.22, G:0.34, T:0.11
Consensus pattern (32 bp):
ACGAGCCAATGGGGAGCATGCACGAGCAATAG
Found at i:579896 original size:93 final size:91
Alignment explanation
Indices: 579729--579924 Score: 356
Period size: 93 Copynumber: 2.1 Consensus size: 91
579719 TATACGAGTC
*
579729 ATACGAGCCAATGGGGAGGATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGA
1 ATACGAGCC-ATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGA
579794 GCCAATGGGGAGCATGCAACGAGCCAT
65 GCCAATGGGGAGCATGCAACGAGCCAT
579821 ATACGAGCCATGGGGAGCATGCAACGAGCCATATACGAGCCAATGGGGAGCATGCAGGAATAGAG
1 ATACGAGCCATGGGGAGCATGCAACGAGCC--ATACGAGCCAATGGGGAGCATGCAGGAATAGAG
579886 AGCCAATGGGGAGCATGCAACGAGCCAT
64 AGCCAATGGGGAGCATGCAACGAGCCAT
579914 ATACGAGCCAT
1 ATACGAGCCAT
579925 ACGAGCCAAT
Statistics
Matches: 101, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
91 20 0.20
92 9 0.09
93 72 0.71
ACGTcount: A:0.34, C:0.21, G:0.33, T:0.12
Consensus pattern (91 bp):
ATACGAGCCATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGAG
CCAATGGGGAGCATGCAACGAGCCAT
Found at i:579910 original size:61 final size:64
Alignment explanation
Indices: 579729--579923 Score: 248
Period size: 61 Copynumber: 3.2 Consensus size: 64
579719 TATACGAGTC
* * *
579729 ATACGAGCCAATGGGGAGGATGCAACGAGCCATACGAGCCAATGGGGAGCATGC-A-G-G-AAT
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATAAGAGCCAATGGGGAGCATGCAACGAGCCAT
*
579789 AGA-GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCC-ATGGGGAGCATGCAACGAGCCA
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATA-A-GAGCCAATGGGGAGCATGCAACGAGCCA
579852 T
64 T
*
579853 ATACGAGCCAATGGGGAGCATGC-A-G-G-AATAGAGAGCCAATGGGGAGCATGCAACGAGCCAT
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATA-AGAGCCAATGGGGAGCATGCAACGAGCCAT
579914 ATACGAGCCA
1 ATACGAGCCA
579924 TACGAGCCAA
Statistics
Matches: 120, Mismatches: 7, Indels: 15
0.85 0.05 0.11
Matches are distributed among these distances:
59 29 0.24
60 20 0.17
61 43 0.36
62 2 0.02
63 2 0.02
64 5 0.04
65 19 0.16
ACGTcount: A:0.34, C:0.22, G:0.33, T:0.11
Consensus pattern (64 bp):
ATACGAGCCAATGGGGAGCATGCAACGAGCCATAAGAGCCAATGGGGAGCATGCAACGAGCCAT
Found at i:580005 original size:29 final size:29
Alignment explanation
Indices: 579973--580034 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
579963 ATGCAGCCTA
579973 GGCGACCTTGTAGGTCGCCATGTAGTCCC
1 GGCGACCTTGTAGGTCGCCATGTAGTCCC
580002 GGCGACCTTGTAGGTCGCCATGTAGTCCC
1 GGCGACCTTGTAGGTCGCCATGTAGTCCC
580031 GGCG
1 GGCG
580035 CCATTCCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.13, C:0.31, G:0.34, T:0.23
Consensus pattern (29 bp):
GGCGACCTTGTAGGTCGCCATGTAGTCCC
Done.