Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 23
Found at i:4410111 original size:22 final size:22
Alignment explanation
Indices: 4410083--4410147 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
4410073 AACAGTCAAC
*
4410083 GGTCAACAGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
4410105 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
4410127 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
4410148 TGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:4410171 original size:19 final size:19
Alignment explanation
Indices: 4410149--4410243 Score: 95
Period size: 19 Copynumber: 4.9 Consensus size: 19
4410139 GGTCGGGTCT
4410149 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
4410168 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
*
4410186 GAACCGGTTGAAACCGG-TCA
1 G-ACCGG-TCAAACCGGTTCA
* *
4410206 AACCGGTCAGAACCGGTTGAA
1 GACCGGTCA-AACCGGTT-CA
* *
4410227 AACCGGTTAAACCGGTT
1 GACCGGTCAAACCGGTT
4410244 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.05
19 36 0.55
20 17 0.26
21 9 0.14
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.17
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:4410174 original size:10 final size:9
Alignment explanation
Indices: 4410150--4410242 Score: 87
Period size: 9 Copynumber: 9.7 Consensus size: 9
4410140 GTCGGGTCTG
4410150 ACCGGTCAA
1 ACCGGTCAA
*
4410159 ACCGGTTCAG
1 ACCGG-TCAA
4410169 ACCGGTCAA
1 ACCGGTCAA
*
4410178 ACCGGTTCGA
1 ACCGG-TCAA
*
4410188 ACCGGTTGAA
1 ACCGG-TCAA
4410198 ACCGGTCAA
1 ACCGGTCAA
4410207 ACCGGTCAGA
1 ACCGGTCA-A
*
4410217 ACCGGTTGAAA
1 ACCGG-T-CAA
*
4410228 ACCGGTTAA
1 ACCGGTCAA
4410237 ACCGGT
1 ACCGGT
4410243 TTCCAGCAGC
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 32 0.45
10 31 0.44
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:4410201 original size:29 final size:28
Alignment explanation
Indices: 4410157--4410243 Score: 61
Period size: 29 Copynumber: 3.0 Consensus size: 28
4410147 CTGACCGGTC
*
4410157 AAACCGGTTCAGACCGGTCAAACCGGTTCG
1 AAACCGG-TCAAACCGGTCAAACCGGTT-G
* *
4410187 -AACCGGTTGAAACCGGTCAAACCGG-TC
1 AAACCGG-TCAAACCGGTCAAACCGGTTG
* *
4410214 AGAACCGGTTGAAAACCGGTTAAACCGGTT
1 A-AACCGG-T-CAAACCGGTCAAACCGGTT
4410244 TCCAGCAGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 31 0.65
30 15 0.31
31 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (28 bp):
AAACCGGTCAAACCGGTCAAACCGGTTG
Found at i:4417407 original size:7 final size:7
Alignment explanation
Indices: 4417395--4417421 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4417385 GTCAAAGAAA
4417395 GTCAACG
1 GTCAACG
4417402 GTCAACG
1 GTCAACG
4417409 GTCAACG
1 GTCAACG
4417416 GTCAAC
1 GTCAAC
4417422 AGTCGGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:4417433 original size:5 final size:5
Alignment explanation
Indices: 4417423--4417496 Score: 67
Period size: 5 Copynumber: 13.6 Consensus size: 5
4417413 ACGGTCAACA
* *
4417423 GTCGG GTCGG GTCGG GTCAACG GTCGG GTCGG GTCAACG GTCGG GTCGG
1 GTCGG GTCGG GTCGG GTC--GG GTCGG GTCGG GTC--GG GTCGG GTCGG
*
4417472 GTCGG GTCAATG GTCGG GTCGG GTC
1 GTCGG GTC--GG GTCGG GTCGG GTC
4417497 TGACCGGTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
5 45 0.79
7 12 0.21
ACGTcount: A:0.08, C:0.22, G:0.50, T:0.20
Consensus pattern (5 bp):
GTCGG
Found at i:4417442 original size:22 final size:22
Alignment explanation
Indices: 4417415--4417496 Score: 102
Period size: 22 Copynumber: 4.0 Consensus size: 22
4417405 AACGGTCAAC
4417415 GGTCAACAGTCGGGTCGGGTCG
1 GGTCAACAGTCGGGTCGGGTCG
4417437 GGTC-A-A--C-GGTCGGGTCG
1 GGTCAACAGTCGGGTCGGGTCG
*
4417454 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACAGTCGGGTCGGGTCG
**
4417476 GGTCAATGGTCGGGTCGGGTC
1 GGTCAACAGTCGGGTCGGGTC
4417497 TGACCGGTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
17 14 0.26
18 2 0.04
20 1 0.02
21 2 0.04
22 34 0.64
ACGTcount: A:0.11, C:0.22, G:0.48, T:0.20
Consensus pattern (22 bp):
GGTCAACAGTCGGGTCGGGTCG
Found at i:4417447 original size:17 final size:17
Alignment explanation
Indices: 4417427--4417474 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
4417417 TCAACAGTCG
4417427 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
4417444 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
4417461 GGTCGGGTCGGGTC
1 GGTCGGGTCGGGTC
4417475 GGGTCAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:4417466 original size:39 final size:39
Alignment explanation
Indices: 4417415--4417496 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
4417405 AACGGTCAAC
4417415 GGTCAACAGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
* *
4417454 GGTCAACGGTCGGGTCGGGTCGGGTCAATGGTCGGGTCG
1 GGTCAACAGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
4417493 GGTC
1 GGTC
4417497 TGACCGGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.11, C:0.22, G:0.48, T:0.20
Consensus pattern (39 bp):
GGTCAACAGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
Found at i:4417486 original size:17 final size:17
Alignment explanation
Indices: 4417427--4417496 Score: 86
Period size: 17 Copynumber: 3.8 Consensus size: 17
4417417 TCAACAGTCG
*
4417427 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAT
4417444 GGTCGGGTCGGGTCAACGGT
1 GGTCGGGTCGGGTCAA---T
4417464 CGGGTCGGGTCGGGTCAAT
1 --GGTCGGGTCGGGTCAAT
4417483 GGTCGGGTCGGGTC
1 GGTCGGGTCGGGTC
4417497 TGACCGGTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
17 30 0.64
19 1 0.02
22 16 0.34
ACGTcount: A:0.09, C:0.21, G:0.50, T:0.20
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAT
Found at i:4417520 original size:19 final size:19
Alignment explanation
Indices: 4417498--4417592 Score: 86
Period size: 19 Copynumber: 4.9 Consensus size: 19
4417488 GGTCGGGTCT
4417498 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
4417517 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
* *
4417535 GAACCGATTGAAACCGG-TCA
1 G-ACCG-GTCAAACCGGTTCA
* *
4417555 AACCGGTCAGAACCGGTTGAA
1 GACCGGTCA-AACCGGTT-CA
* *
4417576 AACCGGTTAAACCGGTT
1 GACCGGTCAAACCGGTT
4417593 TCCAGCAGCC
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
18 3 0.05
19 34 0.54
20 17 0.27
21 9 0.14
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.17
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:4417523 original size:10 final size:9
Alignment explanation
Indices: 4417499--4417591 Score: 78
Period size: 9 Copynumber: 9.7 Consensus size: 9
4417489 GTCGGGTCTG
4417499 ACCGGTCAA
1 ACCGGTCAA
*
4417508 ACCGGTTCAG
1 ACCGG-TCAA
4417518 ACCGGTCAA
1 ACCGGTCAA
*
4417527 ACCGGTTCGA
1 ACCGG-TCAA
* *
4417537 ACCGATTGAA
1 ACCG-GTCAA
4417547 ACCGGTCAA
1 ACCGGTCAA
4417556 ACCGGTCAGA
1 ACCGGTCA-A
*
4417566 ACCGGTTGAAA
1 ACCGG-T-CAA
*
4417577 ACCGGTTAA
1 ACCGGTCAA
4417586 ACCGGT
1 ACCGGT
4417592 TTCCAGCAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
9 32 0.47
10 28 0.41
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:4417550 original size:29 final size:31
Alignment explanation
Indices: 4417518--4417592 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
4417508 ACCGGTTCAG
4417518 ACCGGTCAAACCGGTTC-GAACCGATTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGATTGAAA
*
4417547 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGATTGAAA
*
4417577 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
4417593 TCCAGCAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.56
30 15 0.37
31 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGATTGAAA
Found at i:4417581 original size:30 final size:29
Alignment explanation
Indices: 4417535--4417591 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
4417525 AAACCGGTTC
4417535 GAACCGATTGAAACCGGTCAAACCGGTCA
1 GAACCGATTGAAACCGGTCAAACCGGTCA
* *
4417564 GAACCGGTTGAAAACCGGTTAAACCGGT
1 GAACCGATTG-AAACCGGTCAAACCGGT
4417592 TTCCAGCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.16
Consensus pattern (29 bp):
GAACCGATTGAAACCGGTCAAACCGGTCA
Found at i:4419517 original size:20 final size:20
Alignment explanation
Indices: 4419456--4419517 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
4419446 TGCGAAATAA
4419456 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
* * *
4419476 ACGTAGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATC
4419496 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
4419516 GC
1 GC
4419518 AACGCTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:4419646 original size:25 final size:25
Alignment explanation
Indices: 4419608--4419656 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
4419598 AAATCAATTA
*
4419608 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
4419633 AACATTGTTATGGGTACATTATTT
1 AACATTGTTATGGGTACATTATTT
4419657 AGAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:4420065 original size:18 final size:18
Alignment explanation
Indices: 4420044--4420080 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4420034 GTAATTGGAG
4420044 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
4420062 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
4420080 T
1 T
4420081 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:4420087 original size:24 final size:24
Alignment explanation
Indices: 4420036--4420088 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4420026 TTTCATATGT
* * *
4420036 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
4420060 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
4420084 AATTT
1 AATTT
4420089 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:4420434 original size:39 final size:39
Alignment explanation
Indices: 4420391--4420477 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
4420381 TCCGATGCTC
4420391 ATCAAAATCCAAAGCTCATATGGTACCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTACCAAGCAAAAGGAA
* *
4420430 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTACCAAGCAAAAGGAA
4420469 ATCAAAATC
1 ATCAAAATC
4420478 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTACCAAGCAAAAGGAA
Found at i:4421531 original size:22 final size:22
Alignment explanation
Indices: 4421481--4421531 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
4421471 GATGGAGATA
*
4421481 GACGGATTTCGTCAGAAATGTG
1 GACGGATTTCGTCAGAAATGGG
* * *
4421503 GATGGATTTTGTCAGAGATGGG
1 GACGGATTTCGTCAGAAATGGG
4421525 GACGGAT
1 GACGGAT
4421532 GTCGCCGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.37, T:0.27
Consensus pattern (22 bp):
GACGGATTTCGTCAGAAATGGG
Found at i:4421684 original size:20 final size:20
Alignment explanation
Indices: 4421659--4421739 Score: 87
Period size: 20 Copynumber: 4.0 Consensus size: 20
4421649 GCGTAAAAAC
4421659 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
4421679 ATTTGACTATCGCGTTGTGA
1 ATTTGACTTTCGCGTTGCGA
*
4421699 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
4421718 ATTT-ACATATTCGCGTTGCGA
1 ATTTGAC-T-TTCGCGTTGCGA
4421739 A
1 A
4421740 ATTGGAAACT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.04
19 6 0.12
20 38 0.76
21 4 0.08
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:4421716 original size:40 final size:40
Alignment explanation
Indices: 4421659--4421735 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
4421649 GCGTAAAAAC
4421659 ATTTGACTTTCGCGTTGCGAATTTGAC-TA-TCGCGTTGTGA
1 ATTTGACTTTCGCGTTGCG-ATTT-ACATATTCGCGTTGTGA
*
4421699 ATTTGAC-TTCTGTGTTGCGATTTACATATTCGCGTTG
1 ATTTGACTTTC-GCGTTGCGATTTACATATTCGCGTTG
4421736 CGAAATTGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
38 2 0.06
39 9 0.27
40 22 0.67
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (40 bp):
ATTTGACTTTCGCGTTGCGATTTACATATTCGCGTTGTGA
Found at i:4422909 original size:16 final size:16
Alignment explanation
Indices: 4422885--4422915 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4422875 TTTGACTAAC
*
4422885 TGTTGACTTTGACCAG
1 TGTTAACTTTGACCAG
4422901 TGTTAACTTTGACCA
1 TGTTAACTTTGACCA
4422916 AAAAGTCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (16 bp):
TGTTAACTTTGACCAG
Found at i:4423822 original size:26 final size:28
Alignment explanation
Indices: 4423771--4423832 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
4423761 GAAAAGATTG
*
4423771 AAATACCCTTCAACTGTAAAATAACC-A
1 AAATACCCATCAACTGTAAAATAACCTA
* *
4423798 AAATACCCAT-AAGTGTGAAATAACCTA
1 AAATACCCATCAACTGTAAAATAACCTA
4423825 AAATACCC
1 AAATACCC
4423833 CCAAGCCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 13 0.42
27 18 0.58
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.21
Consensus pattern (28 bp):
AAATACCCATCAACTGTAAAATAACCTA
Found at i:4428879 original size:105 final size:105
Alignment explanation
Indices: 4428707--4429645 Score: 1545
Period size: 105 Copynumber: 8.9 Consensus size: 105
4428697 TTGAACAAGT
* * *
4428707 TCTTCTCATTATGAACTTCTTCTTCTTTTATCGGATGAGTTCTTCTCATTATGAACTCTTCTGGA
1 TCTTCTCATTACGAAC--CTTC-TCCTTTA--GGACGAGTTCTTCTCATTATGAACTCTTCTGGA
* * * * *
4428772 AATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAAGGAACAAGC
61 AATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
*
4428817 TCTTCTCATTACGAACCTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
**
4428882 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATAC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
* *
4428922 TCTTCTCATTACGAACCTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATAT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
4428987 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
*
4429027 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTATTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
*
4429092 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAAGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
* * *
4429132 TCTTCTCATTATGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATAAACTCTTTTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* *
4429197 TGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGAACAGGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
4429237 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* * *
4429302 TGGTTCACCTCCTTCTGCAGTGTATTTGAAAGGAACTGGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
*
4429342 TCTTCTCATTATGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* *
4429407 TGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGAACAGGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
*
4429447 TCTTCTCATTACGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
*
4429512 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
* *
4429552 TCTTTTCATTACGAACCTTCTTCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* *
4429617 TGGGTCACCTCCTTCTGTGGTGGATTTGA
66 TGGTTCACCTCCTTCTGCGGTGGATTTGA
4429646 TTGTTGTTGA
Statistics
Matches: 781, Mismatches: 48, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
105 756 0.97
107 6 0.01
108 4 0.01
110 15 0.02
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (105 bp):
TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
Found at i:4430580 original size:8 final size:8
Alignment explanation
Indices: 4430567--4430684 Score: 102
Period size: 8 Copynumber: 15.0 Consensus size: 8
4430557 TTTCTTTTTC
4430567 TTTTCATT
1 TTTTCATT
4430575 TTTTCATT
1 TTTTCATT
* *
4430583 TTTTTAAT
1 TTTTCATT
*
4430591 TTTTCAAT
1 TTTTCATT
*
4430599 TTTTCAAT
1 TTTTCATT
*
4430607 TTTTCAAT
1 TTTTCATT
*
4430615 TTTTCAAT
1 TTTTCATT
4430623 TTTTCAATTT
1 TTTTC-A-TT
*
4430633 TTTTCTTTT
1 TTTTC-ATT
4430642 TTTTCATT
1 TTTTCATT
4430650 TTTT-A--
1 TTTTCATT
4430655 TTTTC--T
1 TTTTCATT
*
4430661 TTTTCACT
1 TTTTCATT
4430669 TTTTCATT
1 TTTTCATT
4430677 TTTTCATT
1 TTTTCATT
4430685 CATTCTTTTT
Statistics
Matches: 96, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
5 4 0.04
6 5 0.05
7 1 0.01
8 72 0.75
9 8 0.08
10 6 0.06
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTCATT
Found at i:4430658 original size:24 final size:24
Alignment explanation
Indices: 4430555--4430697 Score: 76
Period size: 24 Copynumber: 5.6 Consensus size: 24
4430545 CGAACCCTCC
4430555 TTTTTCTTTTTCTTTTCATTTTTTCAT
1 TTTTTC-TTTT-TTTTCATTTTTT-AT
** * *
4430582 TTTTT-TAATTTTTCAATTTTTCAA
1 TTTTTCTTTTTTTTC-ATTTTTTAT
** *
4430606 TTTTTC-AATTTTTCAATTTTTCAATT
1 TTTTTCTTTTTTTTC-ATTTTT-TA-T
4430632 TTTTTCTTTTTTTTCATTTTTTAT
1 TTTTTCTTTTTTTTCATTTTTTAT
4430656 TTTCTT-TTTCACTTTTTCATTTTTTCAT
1 TTT-TTCTTT---TTTTTCATTTTTT-AT
**
4430684 TCATTCTTTTTTTT
1 TTTTTCTTTTTTTT
4430698 TCAAGCATAG
Statistics
Matches: 94, Mismatches: 11, Indels: 24
0.73 0.09 0.19
Matches are distributed among these distances:
24 33 0.35
25 17 0.18
26 12 0.13
27 26 0.28
28 6 0.06
ACGTcount: A:0.14, C:0.13, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTCTTTTTTTTCATTTTTTAT
Found at i:4430663 original size:27 final size:26
Alignment explanation
Indices: 4430614--4430698 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 26
4430604 AATTTTTCAA
* *
4430614 TTTTTCAATTTTTCAATTTT-TTTCTTT
1 TTTTTC-ATTTTT-TATTTTCTTTTTTT
**
4430641 TTTTTCATTTTTTATTTTCTTTTTCAC
1 TTTTTCATTTTTTATTTTCTTTTT-TT
4430668 TTTTTCATTTTTTCATTCATTCTTTTTTT
1 TTTTTCATTTTTT-ATT--TTCTTTTTTT
4430697 TT
1 TT
4430699 CAAGCATAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 5 0.11
26 10 0.21
27 19 0.40
28 3 0.06
29 2 0.04
30 8 0.17
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTTCATTTTTTATTTTCTTTTTTT
Found at i:4434243 original size:14 final size:14
Alignment explanation
Indices: 4434224--4434250 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4434214 AAATGAATGT
4434224 AAAGAATGAAGAAC
1 AAAGAATGAAGAAC
4434238 AAAGAATGAAGAA
1 AAAGAATGAAGAA
4434251 TGAAAATGTA
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:0.67, C:0.04, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAGAATGAAGAAC
Found at i:4439719 original size:25 final size:25
Alignment explanation
Indices: 4439691--4439741 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4439681 AAGCAGCATC
4439691 ACCTAATTGTAGTCACCACATTTAT
1 ACCTAATTGTAGTCACCACATTTAT
4439716 ACCTAATTGTAGTCACCACATTTAT
1 ACCTAATTGTAGTCACCACATTTAT
4439741 A
1 A
4439742 GAGGAGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (25 bp):
ACCTAATTGTAGTCACCACATTTAT
Found at i:4444594 original size:21 final size:21
Alignment explanation
Indices: 4444568--4444616 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4444558 ATCATTTTTT
* *
4444568 ATTTTTAAAAATTTTGAAAATA
1 ATTTTCAAAAA-TTTGAAAACA
*
4444590 ATTTTCTAAAATTTGAAAACA
1 ATTTTCAAAAATTTGAAAACA
4444611 ATTTTC
1 ATTTTC
4444617 TAGGAGACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (21 bp):
ATTTTCAAAAATTTGAAAACA
Found at i:4444617 original size:21 final size:22
Alignment explanation
Indices: 4444575--4444618 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
4444565 TTTATTTTTA
*
4444575 AAAATTTTGAAAATAATTTTCT
1 AAAATTTTGAAAACAATTTTCT
4444597 AAAA-TTTGAAAACAATTTTCT
1 AAAATTTTGAAAACAATTTTCT
4444618 A
1 A
4444619 GGAGACATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (22 bp):
AAAATTTTGAAAACAATTTTCT
Found at i:4448400 original size:9 final size:9
Alignment explanation
Indices: 4448370--4448421 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 9
4448360 ATCTGCAAAA
4448370 AAATTAAAT
1 AAATTAAAT
*
4448379 -AAGTAAA-
1 AAATTAAAT
*
4448386 ATATTAAAT
1 AAATTAAAT
4448395 AAATTAAAT
1 AAATTAAAT
*
4448404 -ACTTAAAT
1 AAATTAAAT
4448412 AAATTAAAT
1 AAATTAAAT
4448421 A
1 A
4448422 CAAAAAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 18 0.53
9 16 0.47
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:4448402 original size:17 final size:17
Alignment explanation
Indices: 4448367--4448419 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
4448357 TATATCTGCA
* *
4448367 AAAAAATTAAAT-AAGT
1 AAAATATTAAATAAATT
4448383 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
4448400 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
4448417 AAA
1 AAA
4448420 TACAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 16 0.50
17 14 0.44
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:4448420 original size:17 final size:17
Alignment explanation
Indices: 4448373--4448433 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
4448363 TGCAAAAAAA
* *
4448373 TTAAATAAGTAAAATA-
1 TTAAATAAATTAAATAC
4448389 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
4448406 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
4448423 --AAA-AAATTAAA
1 TTAAATAAATTAAA
4448434 AATATAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.19
15 3 0.07
16 14 0.33
17 17 0.40
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:4448421 original size:33 final size:31
Alignment explanation
Indices: 4448373--4448433 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
4448363 TGCAAAAAAA
* *
4448373 TTAAATAAGTAAAATATTAAATAAATTAAATAC
1 TTAAATAAATAAAATA-CAAA-AAATTAAATAC
*
4448406 TTAAATAAATTAAATACAAAAAATTAAA
1 TTAAATAAATAAAATACAAAAAATTAAA
4448434 AATATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 8 0.32
32 3 0.12
33 14 0.56
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (31 bp):
TTAAATAAATAAAATACAAAAAATTAAATAC
Found at i:4449046 original size:18 final size:19
Alignment explanation
Indices: 4449011--4449047 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4449001 CACGGAATGT
4449011 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
4449031 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
4449048 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:4449973 original size:13 final size:14
Alignment explanation
Indices: 4449951--4449980 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4449941 TTATTAGTAT
4449951 TTTTTAAAATAATA
1 TTTTTAAAATAATA
4449965 TTTTT-AAATAATA
1 TTTTTAAAATAATA
4449978 TTT
1 TTT
4449981 AATAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTAAAATAATA
Found at i:4453878 original size:2 final size:2
Alignment explanation
Indices: 4453871--4453920 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
4453861 TGATATCCAA
4453871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4453911 GT AT AT AT AT
1 AT AT AT AT AT
4453921 TTTTATTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4453927 original size:22 final size:22
Alignment explanation
Indices: 4453890--4453946 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
4453880 TATATATATA
* *
4453890 TATATATATATATATTATATTG
1 TATATATATTTTTATTATATTG
*
4453912 TATATATATTTTTATTATTTTG
1 TATATATATTTTTATTATATTG
*
4453934 -ATATTATAATTTT
1 TATA-TATATTTTT
4453947 CAAACATTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TATATATATTTTTATTATATTG
Found at i:4461955 original size:27 final size:27
Alignment explanation
Indices: 4461925--4461978 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
4461915 GGAATTGCTG
4461925 TTGGCCTCTCTGTGGAAGGTCTTTTGA
1 TTGGCCTCTCTGTGGAAGGTCTTTTGA
4461952 TTGGCCTCTCTGTGGAAGGTCTTTTGA
1 TTGGCCTCTCTGTGGAAGGTCTTTTGA
4461979 ATTTAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.11, C:0.19, G:0.30, T:0.41
Consensus pattern (27 bp):
TTGGCCTCTCTGTGGAAGGTCTTTTGA
Found at i:4462948 original size:2 final size:2
Alignment explanation
Indices: 4462936--4462967 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4462926 ATCGTACAAC
4462936 AT AT AT A- 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 A
4462968 GAAATAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4463961 original size:2 final size:2
Alignment explanation
Indices: 4463956--4463980 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4463946 CATTTACCTT
4463956 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4463981 CTTATGGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4467899 original size:30 final size:29
Alignment explanation
Indices: 4467859--4467916 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
4467849 TAGATAATCT
4467859 TAATTAATTTTAT-GACTAAGTTTGAGGACA
1 TAATTAATTTTATAGA--AAGTTTGAGGACA
* *
4467889 TAATTGATTTTTTAGAAAGTTTGAGGAC
1 TAATTAATTTTATAGAAAGTTTGAGGAC
4467917 TTATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 11 0.44
31 2 0.08
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.41
Consensus pattern (29 bp):
TAATTAATTTTATAGAAAGTTTGAGGACA
Found at i:4468008 original size:32 final size:33
Alignment explanation
Indices: 4467946--4468008 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
4467936 ATTAAGATAT
*
4467946 TTATTTAAATATAAAATATAAATAATTATTAAG
1 TTATTCAAATATAAAATATAAATAATTATTAAG
*
4467979 TTATTCAATATATTAAATATAAA-AA-TATTA
1 TTATTCAA-ATATAAAATATAAATAATTATTA
4468009 CAAAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 5 0.19
33 9 0.33
34 13 0.48
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (33 bp):
TTATTCAAATATAAAATATAAATAATTATTAAG
Found at i:4475468 original size:27 final size:29
Alignment explanation
Indices: 4475438--4475495 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
4475428 ATCAATTATA
4475438 TATT-AAAA-TTATATC-AGAATACAACTT
1 TATTAAAAATTTA-ATCAAGAATACAACTT
4475465 TATTAAAAATTTGAATCAAGAATACAACTT
1 TATTAAAAATTT-AATCAAGAATACAACTT
4475495 T
1 T
4475496 GATAAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 4 0.15
28 4 0.15
29 5 0.19
30 14 0.52
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.36
Consensus pattern (29 bp):
TATTAAAAATTTAATCAAGAATACAACTT
Found at i:4476713 original size:38 final size:38
Alignment explanation
Indices: 4476647--4476813 Score: 261
Period size: 38 Copynumber: 4.4 Consensus size: 38
4476637 TTTATTTTGT
* *
4476647 TCGGTTCGGGTCGGG-TTTTTTAAGTGTGATATTTGGG
1 TCGGATCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
4476684 TC-GAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
1 TCGGA-TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
*
4476722 TCGGATCGGGTCGGG-TTTTTTAAGTGTGATATTTGGG
1 TCGGATCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
4476759 TC-GAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
1 TCGGA-TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
4476797 TCGGATCGGGTCGGGTT
1 TCGGATCGGGTCGGGTT
4476814 CAGGGTGAAA
Statistics
Matches: 120, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
36 3 0.03
37 45 0.38
38 68 0.57
39 4 0.03
ACGTcount: A:0.12, C:0.10, G:0.38, T:0.40
Consensus pattern (38 bp):
TCGGATCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
Found at i:4476737 original size:75 final size:75
Alignment explanation
Indices: 4476647--4476813 Score: 325
Period size: 75 Copynumber: 2.2 Consensus size: 75
4476637 TTTATTTTGT
*
4476647 TCGGTTCGGGTCGGGTTTTTTAAGTGTGATATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGT
1 TCGGATCGGGTCGGGTTTTTTAAGTGTGATATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGT
4476712 GATATTCGGG
66 GATATTCGGG
4476722 TCGGATCGGGTCGGGTTTTTTAAGTGTGATATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGT
1 TCGGATCGGGTCGGGTTTTTTAAGTGTGATATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGT
4476787 GATATTCGGG
66 GATATTCGGG
4476797 TCGGATCGGGTCGGGTT
1 TCGGATCGGGTCGGGTT
4476814 CAGGGTGAAA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 91 1.00
ACGTcount: A:0.12, C:0.10, G:0.38, T:0.40
Consensus pattern (75 bp):
TCGGATCGGGTCGGGTTTTTTAAGTGTGATATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGT
GATATTCGGG
Found at i:4477631 original size:16 final size:18
Alignment explanation
Indices: 4477610--4477655 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
4477600 TATGGAATTG
4477610 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
4477626 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
4477644 GATTCCAATTCC
1 GATTCCAATTCC
4477656 CTCATAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 12 0.43
17 1 0.04
18 15 0.54
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:4477936 original size:16 final size:17
Alignment explanation
Indices: 4477910--4477941 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4477900 GGTCACACAT
4477910 TAAATTTATTAATTTAA
1 TAAATTTATTAATTTAA
4477927 TAAA-TTATTAATTTA
1 TAAATTTATTAATTTA
4477942 TTATATTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATTTATTAATTTAA
Found at i:4481203 original size:17 final size:17
Alignment explanation
Indices: 4481181--4481217 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4481171 TAAATCAAGT
*
4481181 ATACAAAATTAAGTTTC
1 ATACAAAACTAAGTTTC
*
4481198 ATACAAAACTCAGTTTC
1 ATACAAAACTAAGTTTC
4481215 ATA
1 ATA
4481218 TACTGAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (17 bp):
ATACAAAACTAAGTTTC
Found at i:4483710 original size:16 final size:16
Alignment explanation
Indices: 4483689--4483727 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
4483679 TTACCTTATG
4483689 CCCATTCTGACTTGCC
1 CCCATTCTGACTTGCC
4483705 CCCATTCTGACTTGCC
1 CCCATTCTGACTTGCC
4483721 CCCATTC
1 CCCATTC
4483728 CACGAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.13, C:0.46, G:0.10, T:0.31
Consensus pattern (16 bp):
CCCATTCTGACTTGCC
Found at i:4486816 original size:23 final size:24
Alignment explanation
Indices: 4486766--4486816 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4486756 ATTGTCAATT
* *
4486766 TTTTTTTCATTTTTTATATATTAT
1 TTTTTTTCATTTCTTATATATTAG
4486790 TTTTTTTCATTTGCTT-TAT-TTAG
1 TTTTTTTCATTT-CTTATATATTAG
4486813 TTTT
1 TTTT
4486817 CAATAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 15 0.62
25 2 0.08
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTTTTCATTTCTTATATATTAG
Found at i:4487760 original size:16 final size:16
Alignment explanation
Indices: 4487739--4487781 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
4487729 GAGAGGCAAC
4487739 AAGAACAAAGAGAATA
1 AAGAACAAAGAGAATA
4487755 AAGAACAAAGAGAATA
1 AAGAACAAAGAGAATA
4487771 AAGAACAAAGA
1 AAGAACAAAGA
4487782 ACACAAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.70, C:0.07, G:0.19, T:0.05
Consensus pattern (16 bp):
AAGAACAAAGAGAATA
Found at i:4488286 original size:15 final size:15
Alignment explanation
Indices: 4488249--4488286 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4488239 CTTAGCAAGC
*
4488249 ACCACTCTGCATAGA
1 ACCACTTTGCATAGA
4488264 ACCACTTTGCATAGA
1 ACCACTTTGCATAGA
*
4488279 ACCTCTTT
1 ACCACTTT
4488287 AACAGACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.29
Consensus pattern (15 bp):
ACCACTTTGCATAGA
Found at i:4515403 original size:16 final size:16
Alignment explanation
Indices: 4515382--4515413 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4515372 CCTTTCCTAC
4515382 TCCTACTAATTAAAAA
1 TCCTACTAATTAAAAA
4515398 TCCTACTAATTAAAAA
1 TCCTACTAATTAAAAA
4515414 CGCTTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (16 bp):
TCCTACTAATTAAAAA
Found at i:4516556 original size:15 final size:15
Alignment explanation
Indices: 4516536--4516564 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4516526 TAAATTAAAG
4516536 TTAACAAATAATTTC
1 TTAACAAATAATTTC
4516551 TTAACAAATAATTT
1 TTAACAAATAATTT
4516565 GATAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAACAAATAATTTC
Found at i:4518101 original size:13 final size:13
Alignment explanation
Indices: 4518085--4518114 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4518075 TTTAATTACA
4518085 AAAATTAAAAATT
1 AAAATTAAAAATT
*
4518098 AAAATTAAAATTT
1 AAAATTAAAAATT
4518111 AAAA
1 AAAA
4518115 CATTCGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:4518273 original size:14 final size:14
Alignment explanation
Indices: 4518256--4518315 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 14
4518246 AATCAAAGGG
4518256 AAAAAATAAAAATA
1 AAAAAATAAAAATA
*
4518270 AAAAATAAAAAAATA
1 AAAAA-ATAAAAATA
* *
4518285 AAAGTAATAAAAGTA
1 AAA-AAATAAAAATA
*
4518300 ATAAAAT-AAAATA
1 AAAAAATAAAAATA
4518313 AAA
1 AAA
4518316 TCCATAATGG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
13 7 0.19
14 8 0.22
15 20 0.56
16 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:4518293 original size:9 final size:9
Alignment explanation
Indices: 4518281--4518305 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4518271 AAAATAAAAA
4518281 AATAAAAGT
1 AATAAAAGT
4518290 AATAAAAGT
1 AATAAAAGT
4518299 AATAAAA
1 AATAAAA
4518306 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (9 bp):
AATAAAAGT
Found at i:4520241 original size:124 final size:124
Alignment explanation
Indices: 4519963--4520636 Score: 870
Period size: 124 Copynumber: 5.5 Consensus size: 124
4519953 GGAAAGCTCA
* * * * *
4519963 TTCGCTGTGAAGTTGGGCTTTGAATTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTAAAGA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
* *
4520028 T-AGATGTTGTTGGTGGGCACGATAT-CTTCATCGTGAAGTTGAAATCGTGGATGGCC-C
66 TGA-ATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCAC
* *
4520085 ATTCGTTGTGAAGTTGAGCCTTAAATTGGATATCCTTCGTTGTGAAGTTGAAA-CTCAATCTAAA
1 -TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC-CAATCTAAA
4520149 GATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCAC
64 GATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCAC
* * *
4520210 TTCGTTGTGAAGTTGAGCCTTAAATTGGATATCCTTCGTCGTGAAGTTGAGATCCAACCTAAAGA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
* *
4520275 TGAATGTTGCTGGTGGCCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
66 TGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCAC
* *
4520334 TTCGTTGTGAAGTTGTGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATC-AACAG
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAA-AG
*
4520398 ATGAATGTTGCTGAT--GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCA-
65 ATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGC-CAC
* * * * * * *
4520456 TTCGTTGTGAAATTAAG--TT-AATTGGATATCATTTGTCATGAAGTTGAAATCCAATCTAGAGT
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
* * * * ** **
4520518 TGTATGCTGCTTGG-GTGAACGATATCCTTCGTCGTGAAGTTGAAATATTAAATGGCTCA-
66 TGAATGTTGC-TGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGC-CAC
* * * *
4520577 TTCGTTGTAAAGTTGAGCTTTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCT
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
4520637 TGTGTTGTTT
Statistics
Matches: 496, Mismatches: 41, Indels: 27
0.88 0.07 0.05
Matches are distributed among these distances:
119 45 0.09
120 5 0.01
121 52 0.10
122 54 0.11
123 85 0.17
124 253 0.51
125 2 0.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (124 bp):
TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
TGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCAC
Found at i:4520602 original size:243 final size:245
Alignment explanation
Indices: 4519985--4520636 Score: 874
Period size: 243 Copynumber: 2.7 Consensus size: 245
4519975 TTGGGCTTTG
* * *
4519985 AATTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTAAAGATAGATGTTG-TTGGTGGGCACG
1 AATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAG-TTGATGTTGCTTGG-GTGCACG
* *
4520049 ATAT-CTTCATCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAAATTG
64 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTG
*
4520113 GATATCCTTCGTTGTGAAGTTGAAA-CTCAATCTAAAGATGAATGTTGCTGGTGGGCACGATATC
129 GATATCCTTCGTTGTGAAGTTGAAATC-CAATCTAAAGATGAATGTTGCTGAT-GGCACGATATC
* *
4520177 CTTCGTCGTGAAGTTGAAATCGTGGATGGCCACTTCGTTGTGAAGTTGAGCCTTA
192 CTTCGTCGTGAAGTTGAAATCGTGGATGGCCACTTCGTTGTGAAATTAAG-CTTA
* * * *
4520232 AATTGGATATCCTTCGTCGTGAAGTTGAGATCCAACCTAAAGATGAATGTTGC-T-GGTGGCCAC
1 AATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAGTTG-ATGTTGCTTGGGT-G-CAC
* *
4520295 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGTGCCTTGAATT
63 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATT
**
4520360 GGATATCCTTCGTCATGAAGTTGAAATCCAATC-AACAGATGAATGTTGCTGAT-GCACGATATC
128 GGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAA-AGATGAATGTTGCTGATGGCACGATATC
4520423 CTTCGTCGTGAAGTTGAAATCGTGGATGGCTCA-TTCGTTGTGAAATTAAG-TT-
192 CTTCGTCGTGAAGTTGAAATCGTGGATGGC-CACTTCGTTGTGAAATTAAGCTTA
* * * * *
4520475 AATTGGATATCATTTGTCATGAAGTTGAAATCCAATCTAGAGTTGTATGCTGCTTGGGTGAACGA
1 AATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAGTTG-ATGTTGCTTGGGTGCACGA
** ** * * *
4520540 TATCCTTCGTCGTGAAGTTGAAATATTAAATGGCTCATTCGTTGTAAAGTTGAGCTTTGAATTGG
65 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGG
*
4520605 ATATCCTTTGTTGTGAAGTTGAAATCCAATCT
130 ATATCCTTCGTTGTGAAGTTGAAATCCAATCT
4520637 TGTGTTGTTT
Statistics
Matches: 356, Mismatches: 38, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
243 132 0.37
244 4 0.01
245 4 0.01
246 58 0.16
247 57 0.16
248 100 0.28
249 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (245 bp):
AATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAGTTGATGTTGCTTGGGTGCACGAT
ATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGA
TATCCTTCGTTGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGATGGCACGATATCCTTC
GTCGTGAAGTTGAAATCGTGGATGGCCACTTCGTTGTGAAATTAAGCTTA
Found at i:4525581 original size:5 final size:5
Alignment explanation
Indices: 4525546--4525626 Score: 53
Period size: 5 Copynumber: 15.8 Consensus size: 5
4525536 TCAAAGAGAA
* * *
4525546 AAAAT AAAAA ATAAAT AACAT AACAT AAAAAT AAAA- AAAAT AAAAAAT
1 AAAAT AAAAT A-AAAT AAAAT AAAAT -AAAAT AAAAT AAAAT --AAAAT
4525594 AAAA- AACAAT AAAAGT --AAT AAAAT AAAAT AAAA
1 AAAAT AA-AAT AAAA-T AAAAT AAAAT AAAAT AAAA
4525627 CCCATAATGG
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
3 1 0.02
4 8 0.13
5 37 0.60
6 11 0.18
7 5 0.08
ACGTcount: A:0.79, C:0.04, G:0.01, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:4525584 original size:36 final size:35
Alignment explanation
Indices: 4525544--4525626 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 35
4525534 AATCAAAGAG
*
4525544 AAAAAATAAAAAATAAATAAC-ATAACATAAAAATAA
1 AAAAAATAAAAAATAAAAAACAATAA-A-AAAAATAA
**
4525580 AAAAAATAAAAAATAAAAAACAATAAAAGTAATAA
1 AAAAAATAAAAAATAAAAAACAATAAAAAAAATAA
4525615 AATAAAATAAAA
1 AA-AAAATAAAA
4525627 CCCATAATGG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 8 0.19
36 30 0.71
37 4 0.10
ACGTcount: A:0.80, C:0.04, G:0.01, T:0.16
Consensus pattern (35 bp):
AAAAAATAAAAAATAAAAAACAATAAAAAAAATAA
Found at i:4526829 original size:3 final size:3
Alignment explanation
Indices: 4526823--4526862 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
4526813 AAATATATAT
*
4526823 TAA TAA TAA TAA TAA TAA TAT TAA TAAA TCAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TA
4526863 TTTTTTAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4528236 original size:20 final size:20
Alignment explanation
Indices: 4528192--4528236 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
4528182 CCCTTGATTG
*
4528192 CAACCTTCCCCATAAAACAA
1 CAACCTTCCCCATAAAAAAA
4528212 C-ACCTCTCCCC-TAAAAAAA
1 CAACCT-TCCCCATAAAAAAA
4528231 CAACCT
1 CAACCT
4528237 ATACATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (20 bp):
CAACCTTCCCCATAAAAAAA
Found at i:4533676 original size:19 final size:21
Alignment explanation
Indices: 4533652--4533695 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
4533642 TCTCTTTCAT
4533652 ATATCTCATG-TCACGT-ATC
1 ATATCTCATGATCACGTAATC
* *
4533671 ATATCTTATGATCATGTAATC
1 ATATCTCATGATCACGTAATC
4533692 ATAT
1 ATAT
4533696 TACTCATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 5 0.24
21 7 0.33
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (21 bp):
ATATCTCATGATCACGTAATC
Found at i:4534895 original size:61 final size:61
Alignment explanation
Indices: 4534776--4534889 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 61
4534766 ATCCCTTGAC
*
4534776 GGGTGCATCGATGCACTATCTGTGCATCGGTACATAAATCATTCGATGTTGTATTTTAAGG
1 GGGTGCATCGATGCACTATCTGTGCATCGATACATAAATCATTCGATGTTGTATTTTAAGG
***
4534837 GGGTGCATCGATGCA-TA-CTTGTGCATCGATACATGTGTCATTCGATGTT-TATT
1 GGGTGCATCGATGCACTATC-TGTGCATCGATACATAAATCATTCGATGTTGTATT
4534890 CTTTAAAGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 5 0.10
60 28 0.58
61 15 0.31
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (61 bp):
GGGTGCATCGATGCACTATCTGTGCATCGATACATAAATCATTCGATGTTGTATTTTAAGG
Found at i:4534903 original size:60 final size:61
Alignment explanation
Indices: 4534778--4534906 Score: 149
Period size: 60 Copynumber: 2.1 Consensus size: 61
4534768 CCCTTGACGG
* * *
4534778 GTGCATCGATGCACTATCTGTGCATCGGTACATAAATCATTCGATGTTGTATTTTAAGGGG
1 GTGCATCGATGCACTATCTGTGCATCGATACATAAATCATTCGATGTTGTATTTTAAGAGA
***
4534839 GTGCATCGATGCA-TA-CTTGTGCATCGATACATGTGTCATTCGATGTT-TATTCTTTAA-AGA
1 GTGCATCGATGCACTATC-TGTGCATCGATACATAAATCATTCGATGTTGTA-T-TTTAAGAGA
4534899 GTGCATCG
1 GTGCATCG
4534907 GTACACATTG
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
59 3 0.05
60 38 0.64
61 18 0.31
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (61 bp):
GTGCATCGATGCACTATCTGTGCATCGATACATAAATCATTCGATGTTGTATTTTAAGAGA
Found at i:4542970 original size:2 final size:2
Alignment explanation
Indices: 4542963--4542995 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4542953 ATTTTAAAAT
4542963 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4542996 TTTGATGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4543752 original size:124 final size:124
Alignment explanation
Indices: 4543532--4543779 Score: 487
Period size: 124 Copynumber: 2.0 Consensus size: 124
4543522 CACATCCTCA
4543532 CCAAATCCCAATCCGATCCTTTCGTCGTTCTCTCTCAGTATCTTTCGTCCCTCTCCCCAACCCTT
1 CCAAATCCCAATCCGATCCTTTCGTCGTTCTCTCTCAGTATCTTTCGTCCCTCTCCCCAACCCTT
4543597 ACCACTAATGAAGCCTCTCTCATTTTATCCCACGCCTTGAAATTCTTCCACTTTTGCAG
66 ACCACTAATGAAGCCTCTCTCATTTTATCCCACGCCTTGAAATTCTTCCACTTTTGCAG
*
4543656 CCAAATCCGAATCCGATCCTTTCGTCGTTCTCTCTCAGTATCTTTCGTCCCTCTCCCCAACCCTT
1 CCAAATCCCAATCCGATCCTTTCGTCGTTCTCTCTCAGTATCTTTCGTCCCTCTCCCCAACCCTT
4543721 ACCACTAATGAAGCCTCTCTCATTTTATCCCACGCCTTGAAATTCTTCCACTTTTGCAG
66 ACCACTAATGAAGCCTCTCTCATTTTATCCCACGCCTTGAAATTCTTCCACTTTTGCAG
4543780 AAAAGGCCAC
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.19, C:0.38, G:0.09, T:0.34
Consensus pattern (124 bp):
CCAAATCCCAATCCGATCCTTTCGTCGTTCTCTCTCAGTATCTTTCGTCCCTCTCCCCAACCCTT
ACCACTAATGAAGCCTCTCTCATTTTATCCCACGCCTTGAAATTCTTCCACTTTTGCAG
Found at i:4544628 original size:2 final size:2
Alignment explanation
Indices: 4544621--4544646 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4544611 ATATTTGTGA
4544621 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
4544647 CCTATTATCA
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:4546418 original size:103 final size:102
Alignment explanation
Indices: 4546237--4546431 Score: 318
Period size: 103 Copynumber: 1.9 Consensus size: 102
4546227 GTCACATGAT
* * *
4546237 AACTCTACCTGACTAGCTCGGGGTGGAAGGTATGCTCCTTTTTACTTAGAGTGTGGGATGGTTGT
1 AACTCTACCTGACTAGCTCGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGT
* * *
4546302 GTGATTAGCTGACTCTCCTTAAAGTATGCTTAAAAAA
66 GTGATAAGATGACTCCCCTTAAAGTATGCTTAAAAAA
4546339 AACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAG
1 AACTCTACCTGACTAGCTC-GGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAG
*
4546404 TGTGATAAGATGACTCCCCTTGAAGTAT
65 TGTGATAAGATGACTCCCCTTAAAGTAT
4546432 AAAACAAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 19 0.22
103 66 0.78
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (102 bp):
AACTCTACCTGACTAGCTCGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGT
GTGATAAGATGACTCCCCTTAAAGTATGCTTAAAAAA
Found at i:4548755 original size:20 final size:21
Alignment explanation
Indices: 4548726--4548785 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
4548716 GATTTCTGGA
4548726 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
4548747 CAA-GGGAATCAGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
4548767 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
4548786 CTCAAGCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.56
21 3 0.09
22 12 0.35
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:4548863 original size:23 final size:22
Alignment explanation
Indices: 4548819--4548863 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4548809 AATCTCATAG
*
4548819 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
4548841 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
4548864 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:4549810 original size:31 final size:31
Alignment explanation
Indices: 4549768--4549891 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
4549758 AGGGTCGAGG
4549768 GTTT-CCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4549798 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4549829 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
4549860 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
4549891 G
1 G
4549892 GTCTTTCGGG
Statistics
Matches: 89, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.04
31 84 0.94
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4552669 original size:16 final size:16
Alignment explanation
Indices: 4552648--4552690 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
4552638 GGTAATTAAA
4552648 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
4552664 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
4552681 GAGTGATAAG
1 GATTGATAAG
4552691 AACTGATGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:4553625 original size:22 final size:21
Alignment explanation
Indices: 4553575--4553632 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
4553565 TTTCTGGGAC
4553575 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCATTCA
*
4553596 A-GGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCATTCA
4553616 ATGGGGAATCGATACCC
1 A-GGGGAATCGATACCC
4553633 CTCAAGCGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 19 0.58
21 1 0.03
22 13 0.39
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCATTCA
Found at i:4553710 original size:23 final size:22
Alignment explanation
Indices: 4553666--4553710 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4553656 AATCTCATAG
*
4553666 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
4553688 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
4553711 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:4554657 original size:31 final size:31
Alignment explanation
Indices: 4554619--4554774 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
4554609 AGGGTCGAGG
4554619 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4554650 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4554681 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4554712 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
4554743 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
4554774 G
1 G
4554775 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4555262 original size:21 final size:21
Alignment explanation
Indices: 4555237--4555279 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4555227 AAAGAATATA
4555237 TTGTATAA-GCTTTGAATAATT
1 TTGTA-AATGCTTTGAATAATT
*
4555258 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTTTGAATAATT
4555279 T
1 T
4555280 AAATGTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (21 bp):
TTGTAAATGCTTTGAATAATT
Found at i:4560631 original size:23 final size:24
Alignment explanation
Indices: 4560600--4560666 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 24
4560590 ACTCACATAA
* *
4560600 TTGCACCGAAGTG-CCACATAGTT
1 TTGCCCCGAAGTGACCACATAGGT
4560623 TTGCCCCGAA-TGACCACATAGGT
1 TTGCCCCGAAGTGACCACATAGGT
*
4560646 TTGTCCCGAAG-GACCACATAG
1 TTGCCCCGAAGTGACCACATAG
4560667 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
22 2 0.05
23 37 0.95
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.22
Consensus pattern (24 bp):
TTGCCCCGAAGTGACCACATAGGT
Found at i:4561266 original size:18 final size:17
Alignment explanation
Indices: 4561243--4561280 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
4561233 TTCCTTTTTA
4561243 TGGTATCGATATCCACTT
1 TGGTATCGATA-CCACTT
*
4561261 TGGTATCGATACCATTT
1 TGGTATCGATACCACTT
4561278 TGG
1 TGG
4561281 CATTTTGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (17 bp):
TGGTATCGATACCACTT
Found at i:4570423 original size:2 final size:2
Alignment explanation
Indices: 4570416--4570440 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4570406 CAAAAGGCAA
4570416 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 A
4570441 GAACCATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4573277 original size:22 final size:22
Alignment explanation
Indices: 4573252--4573302 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
4573242 ATGATGTGTG
4573252 TGTGCAAGATGCGAGTCAGATA
1 TGTGCAAGATGCGAGTCAGATA
4573274 TGTGCAAGATGCGAGTCAGATA
1 TGTGCAAGATGCGAGTCAGATA
4573296 TGTGCAA
1 TGTGCAA
4573303 AATTAATCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (22 bp):
TGTGCAAGATGCGAGTCAGATA
Found at i:4574722 original size:11 final size:11
Alignment explanation
Indices: 4574706--4574730 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4574696 ATCTAAGGAA
4574706 ATACGATTAAT
1 ATACGATTAAT
4574717 ATACGATTAAT
1 ATACGATTAAT
4574728 ATA
1 ATA
4574731 TAGCATTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (11 bp):
ATACGATTAAT
Found at i:4575473 original size:103 final size:106
Alignment explanation
Indices: 4575222--4575584 Score: 371
Period size: 110 Copynumber: 3.3 Consensus size: 106
4575212 TAACTTTCAA
* * * * * * *
4575222 AAAAGTATCGATCATTTTTATAAAAAGTATCTATACTTTCAACATATTAAATAAATTTTATCAGT
1 AAAA-TATCTATCA-TTTTAT-AAAAGGATCGATACTTTCAACATA-TCAGTAAATTTTACCATT
* * *
4575287 TTTGTCATAATGAAACTGATTTGGTCATATTTATACTTGTTATATTGT
62 TTTGTCATAATGAAACTG-TTT-TTCATATTTTTAC-TATTATATTGT
* * *
4575335 AAAATATCGATAT-TTTTTATAAAATGATCGATACTTTCAACATATCAGTAAATTTTACCCTTTT
1 AAAATATC--TATCATTTTATAAAAGGATCGATACTTTCAACATATCAGTAAATTTTA-CCATTT
4575399 TTGT-ATAATGAAACTGTTTTTCATATTTTTAC-ATT-TA-TGT
63 TTGTCATAATGAAACTGTTTTTCATATTTTTACTATTATATTGT
4575439 AAAATATCTATCATTTTATAAAAGGATCGATACTTTCAACATATCAGATAAATTTTACCATTTTT
1 AAAATATCTATCATTTTATAAAAGGATCGATACTTTCAACATATCAG-TAAATTTTACCATTTTT
* *
4575504 GTCATAACGAAACTGGTTTTGTCATA-TTTTACTTGTTATATTGT
65 GTCATAATGAAACT-GTTTT-TCATATTTTTAC-TATTATATTGT
* * *
4575548 AAAATATCGATACATTTT-TGTAAAGTATCGATACTTT
1 AAAATATCTAT-CATTTTAT-AAAAGGATCGATACTTT
4575585 ATAGGCGCTA
Statistics
Matches: 215, Mismatches: 21, Indels: 31
0.81 0.08 0.12
Matches are distributed among these distances:
102 3 0.01
103 42 0.20
104 30 0.14
105 13 0.06
106 7 0.03
107 2 0.01
108 13 0.06
109 17 0.08
110 44 0.20
111 28 0.13
112 10 0.05
113 4 0.02
114 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (106 bp):
AAAATATCTATCATTTTATAAAAGGATCGATACTTTCAACATATCAGTAAATTTTACCATTTTTG
TCATAATGAAACTGTTTTTCATATTTTTACTATTATATTGT
Found at i:4576226 original size:111 final size:111
Alignment explanation
Indices: 4576015--4576490 Score: 608
Period size: 111 Copynumber: 4.3 Consensus size: 111
4576005 CAAAAAAAAA
* * * ** *
4576015 TATCAATCCTTTTTATAAAAAGTATTTATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGT
1 TATCTATCATTTTTAT-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGT
4576080 CATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAG
65 CATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAG
* * *
4576127 TATCTATCATTTTTATAAAAGGATCGATACTTTCAACTTATTAGGTAAGTTTTACCGTTTTTGTC
1 TATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTC
*
4576192 ATAATGAAACTGATTTTGTCATATTTTTACCTG-T-TATTGTAAAG
66 ATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAG
* *
4576236 TATCTATTATTTTTATAAAAGGA-CGATGCTTTCAACATATCAGGTAAATTTTAACCG-TTTT-T
1 TATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTT-ACCGTTTTTGT
** * *
4576298 CATAATGAAACTGGTTTTACCGTATTTTTACATGTTATATTGTAAAG
65 CATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAG
* * *
4576345 TAT-TGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTATCGGTTTTT
1 TATCT-ATCATTTTTAT-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTA-CCG-TTTT
* * * *
4576409 TCTCAT-ATGAAATTGGTTTTGTCATATTTTTACTTGTTATATTGTAAAA
62 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAG
* *
4576458 TATCGATACATTTTTAT-AAAGTATCGATACTTT
1 TATCTAT-CATTTTTATAAAAGGATCGATACTTT
4576491 ATAGGCGCTA
Statistics
Matches: 318, Mismatches: 34, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
107 30 0.09
108 31 0.10
109 58 0.18
110 9 0.03
111 103 0.32
112 29 0.09
113 46 0.14
114 12 0.04
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (111 bp):
TATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTC
ATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAG
Found at i:4577991 original size:19 final size:19
Alignment explanation
Indices: 4577955--4577992 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4577945 GCCCATAAAT
*
4577955 TATTATTTAGATTTTAATA
1 TATTATTTAGATTATAATA
4577974 TATTATTTCA-ATTATAATA
1 TATTATTT-AGATTATAATA
4577993 AGTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
TATTATTTAGATTATAATA
Found at i:4583404 original size:18 final size:18
Alignment explanation
Indices: 4583377--4583428 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
4583367 GTAGAATTTA
*
4583377 TCCCGTAGGACCACTGTG
1 TCCCGAAGGACCACTGTG
*
4583395 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTGTG
*
4583413 TCTCGAAGGACCACTG
1 TCCCGAAGGACCACTG
4583429 ATAATCCCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.19
Consensus pattern (18 bp):
TCCCGAAGGACCACTGTG
Found at i:4585277 original size:19 final size:21
Alignment explanation
Indices: 4585230--4585278 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
4585220 GGATATTACA
4585230 CTTCTTGTTTGGTTTCTTGGTG
1 CTTCTTGTTTGGTTTC-TGGTG
4585252 C-TC--GTTTGG-TTC-GGTG
1 CTTCTTGTTTGGTTTCTGGTG
4585268 CTTCTTGTTTG
1 CTTCTTGTTTG
4585279 TGCTGGCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
16 5 0.21
17 2 0.08
18 3 0.12
19 11 0.46
21 2 0.08
22 1 0.04
ACGTcount: A:0.00, C:0.16, G:0.29, T:0.55
Consensus pattern (21 bp):
CTTCTTGTTTGGTTTCTGGTG
Found at i:4586622 original size:2 final size:2
Alignment explanation
Indices: 4586609--4586646 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4586599 CGTCTGTCCT
*
4586609 TA TA TT 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
4586647 AATTATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4587105 original size:5 final size:5
Alignment explanation
Indices: 4587095--4587159 Score: 64
Period size: 5 Copynumber: 13.4 Consensus size: 5
4587085 TAGATATAAA
* * **
4587095 AAAAT AAAAT AAAAT -AAAT -AAAT AAATT CAACC AAAAT AAAA- AGAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT
4587143 AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AA
4587160 TAAATAAAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
4 9 0.18
5 40 0.80
6 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:4587902 original size:37 final size:35
Alignment explanation
Indices: 4587852--4587987 Score: 157
Period size: 37 Copynumber: 3.8 Consensus size: 35
4587842 GTGCTTGTGG
* * * * *
4587852 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-A-AAATCT
*
4587889 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT-CT
*
4587926 ATCCTATTTTTAGGAGTTTGAATCCTA-AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAATCT
*
4587960 ATCCTATTTTTAGGTGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
4587988 TAGGACGAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 27 0.31
35 4 0.05
36 3 0.03
37 53 0.61
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.43
Consensus pattern (35 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGAAAATCT
Found at i:4587963 original size:34 final size:35
Alignment explanation
Indices: 4587886--4587986 Score: 152
Period size: 34 Copynumber: 2.9 Consensus size: 35
4587876 TTAGTAGAAC
4587886 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
4587924 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
*
4587957 TCTATCCTATTTTTAGGTGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
4587987 GTAGGACGAA
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.45
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:4588737 original size:105 final size:106
Alignment explanation
Indices: 4588529--4588985 Score: 634
Period size: 105 Copynumber: 4.3 Consensus size: 106
4588519 GCATTGTTCC
* * * * * ** *
4588529 AAGTCCAATATCCTCCGTCGTGAAGTTTAAATTGGCTATGGAACAGGGAAATTGTTTGTTGACAA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
4588594 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
*
4588636 -AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
4588699 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4588740 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
4588804 GCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4588845 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
4588910 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
* *
4588952 -AGTGCCACGATATCCTCCGTTGTGGAGTTGAAAT
1 AAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
4588986 CGCGGATGGC
Statistics
Matches: 318, Mismatches: 26, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
104 1 0.00
105 198 0.62
106 92 0.29
107 4 0.01
109 23 0.07
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:4588882 original size:210 final size:213
Alignment explanation
Indices: 4588519--4588985 Score: 649
Period size: 211 Copynumber: 2.2 Consensus size: 213
4588509 CAAGTAAGTA
* * * *
4588519 GCATTGT-TCCAAGTCCAATATCCTCCGTCGTGAAGTTTAAATTGGCTATGGAACAGGGAAATTG
1 GCATTGTCTCGAAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTATGAAACAGGGAAATTG
** *
4588583 TTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCC
66 TTTGTTGACAACCAACCGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCC
* * * *
4588648 TTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAGCAGCGGTCCCTT
131 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTT
4588712 CGTCGTGAAGTTGAACTT
196 CGTCGTGAAGTTGAACTT
* * ** *
4588730 GCATTGTCT-GAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG
1 GCATTGTCTCGAAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTATGAAACAGGGAAATTG
* * *
4588794 -TTGTTGACAAGCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCT-GAAGTCCAATATC
66 TTTGTTGACAACCAACCGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTCG-AGTCCAATATC
4588857 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCT
130 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCT
*
4588922 TCGTTGTGAAGTTGAACTT
195 TCGTCGTGAAGTTGAACTT
** *
4588941 GTGTTGTCTCG-AGTGCCACGATATCCTCCGTTGTGGAGTTGAAAT
1 GCATTGTCTCGAAGT-CCA--ATATCCTCCGTTGTGAAGTTGAAAT
4588986 CGCGGATGGC
Statistics
Matches: 225, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
209 1 0.00
210 95 0.42
211 101 0.45
212 5 0.02
214 23 0.10
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (213 bp):
GCATTGTCTCGAAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTATGAAACAGGGAAATTG
TTTGTTGACAACCAACCGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCC
TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTT
CGTCGTGAAGTTGAACTT
Found at i:4589761 original size:65 final size:65
Alignment explanation
Indices: 4589589--4590042 Score: 313
Period size: 65 Copynumber: 6.7 Consensus size: 65
4589579 AAGATATCTG
* * * **
4589589 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
4589654 TT
64 TT
* *
4589656 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
4589721 T
65 T
* ** * *
4589722 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTTAAGAGAAACT--ATCTCAAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-
*
4589785 AGACAAAACT
61 AG-----ATT
* * * * * * * * * * *
4589795 TAGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * *
4589860 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
*
4589925 ACAAA-ATT
57 TCAAAGATT
* * * * * * *** *
4589933 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
4589997 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
4590043 AAAAGCAATC
Statistics
Matches: 306, Mismatches: 57, Indels: 50
0.74 0.14 0.12
Matches are distributed among these distances:
64 8 0.03
65 126 0.41
66 5 0.02
67 25 0.08
68 35 0.11
70 1 0.00
71 1 0.00
72 2 0.01
73 96 0.31
74 7 0.02
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:4589773 original size:36 final size:36
Alignment explanation
Indices: 4589721--4589983 Score: 254
Period size: 36 Copynumber: 7.4 Consensus size: 36
4589711 ATTCAAAGAT
* *
4589721 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
4589757 TTTGTTTTAAGAGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * *
4589793 CTTAGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * *
4589830 TTTGTTTCAAAGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
4589859 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
4589895 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
4589931 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
4589968 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
4589984 TGTTTTCAAT
Statistics
Matches: 184, Mismatches: 32, Indels: 22
0.77 0.13 0.09
Matches are distributed among these distances:
28 2 0.01
29 18 0.10
30 1 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 97 0.53
37 63 0.34
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:4589834 original size:138 final size:138
Alignment explanation
Indices: 4589670--4590042 Score: 478
Period size: 138 Copynumber: 2.7 Consensus size: 138
4589660 TTTCAAGAGT
* * * *
4589670 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
* *
4589735 AACTGTCTCAAGATAGACGAAATTTGTTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTT
66 AACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTT
*
4589800 CCAAAAGC
131 CCAAAAGA
* * * *
4589808 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
* * * * * *
4589873 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTT
66 AACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTT
* **
4589938 TCAAGGGA
131 CCAAAAGA
* * * * * * *
4589946 AACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAG
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTT-TGTTTCAAGGG
*
4590010 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
65 AAACTGTCTCAAGAGAGACAAAATTTGTTTTAA
4590043 AAAAGCAATC
Statistics
Matches: 200, Mismatches: 34, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
137 3 0.01
138 197 0.99
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (138 bp):
AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTT
CCAAAAGA
Found at i:4589890 original size:102 final size:102
Alignment explanation
Indices: 4589757--4589941 Score: 264
Period size: 102 Copynumber: 1.8 Consensus size: 102
4589747 ATAGACGAAA
* * *
4589757 TTTGTTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGCAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAG
*
4589822 AGACGAAA-TTTGTTTCAAAGAAAACATATTCAAATAT
65 AGACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
* * * * **
4589859 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
4589924 GACAAAATTTTGTTTCAA
66 GACAAAATTTTGTTTCAA
4589942 GGGAAACTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 26 0.36
102 46 0.64
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
Found at i:4590440 original size:18 final size:18
Alignment explanation
Indices: 4590405--4590440 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4590395 TGTTGAATCC
*
4590405 CCAAAAATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
*
4590423 CCAAAAATGCCCCCATAT
1 CCAAAAATGCCCCAATAT
4590441 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.33, G:0.06, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:4590832 original size:22 final size:22
Alignment explanation
Indices: 4590806--4590860 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4590796 TTGTGTTTGG
4590806 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
4590828 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
4590850 TCAAATGTTTG
1 TCAAAGGTTTG
4590861 ATGGGATATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:4591579 original size:7 final size:7
Alignment explanation
Indices: 4591511--4591582 Score: 54
Period size: 7 Copynumber: 9.3 Consensus size: 7
4591501 TTGATTCTTG
4591511 TTTTTTCC
1 TTTTTT-C
*
4591519 TTTTGCTC
1 TTTT-TTC
4591527 TTGTTTCTC
1 TT-TTT-TC
4591536 TTTTTTC
1 TTTTTTC
*
4591543 TTTGTTTT
1 TTT-TTTC
*
4591551 TTTTTTA
1 TTTTTTC
4591558 TTTTTTGC
1 TTTTTT-C
4591566 TTCTTTTC
1 TT-TTTTC
4591574 TTTTTTC
1 TTTTTTC
4591581 TT
1 TT
4591583 CTTGATTGGA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
7 21 0.40
8 21 0.40
9 11 0.21
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:4591583 original size:15 final size:15
Alignment explanation
Indices: 4591534--4591585 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
4591524 CTCTTGTTTC
4591534 TCTT-TTTTCTTTGTT
1 TCTTCTTTTCTTT-TT
* *
4591549 T-TTTTTTTATTTTT
1 TCTTCTTTTCTTTTT
4591563 TGCTTCTTTTCTTTTT
1 T-CTTCTTTTCTTTTT
4591579 TCTTCTT
1 TCTTCTT
4591586 GATTGGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 5 0.16
15 14 0.45
16 12 0.39
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (15 bp):
TCTTCTTTTCTTTTT
Found at i:4592745 original size:8 final size:8
Alignment explanation
Indices: 4592729--4592767 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
4592719 AATGTAGATG
4592729 AAAATGCA
1 AAAATGCA
*
4592737 AAAAGGCA
1 AAAATGCA
4592745 AAAATGC-
1 AAAATGCA
4592752 AAAATGCA
1 AAAATGCA
*
4592760 AGAATGCA
1 AAAATGCA
4592768 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:4592755 original size:15 final size:15
Alignment explanation
Indices: 4592729--4592767 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4592719 AATGTAGATG
4592729 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
4592745 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
4592760 AGAATGCA
1 AAAATGCA
4592768 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:4595269 original size:5 final size:5
Alignment explanation
Indices: 4595259--4595318 Score: 54
Period size: 5 Copynumber: 12.4 Consensus size: 5
4595249 TAGATATAAA
* * **
4595259 AAAAT AAAAT AAAAT -AAAT -AAAT AAATT CAACC AAAAT AAAA- AGAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT
4595307 AAAAT AAAAT AA
1 AAAAT AAAAT AA
4595319 TAAATAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 9 0.20
5 35 0.78
6 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:4596096 original size:37 final size:36
Alignment explanation
Indices: 4596014--4596149 Score: 161
Period size: 37 Copynumber: 3.8 Consensus size: 36
4596004 GTGCTTGTGG
* * * * * *
4596014 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-AAAATTCT
*
4596051 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATGT-T
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT-TCT
4596088 ATCCTATTTTTAGGAGTTTGAATCCT--AAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAATTCT
4596122 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
4596150 TAGGACGAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.01
34 32 0.37
37 52 0.60
38 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGAAAATTCT
Found at i:4596125 original size:34 final size:35
Alignment explanation
Indices: 4596048--4596148 Score: 152
Period size: 34 Copynumber: 2.9 Consensus size: 35
4596038 TTAGTAGAAC
*
4596048 TCTATCATATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
4596086 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
4596119 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
4596149 GTAGGACGAA
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.54
37 26 0.43
38 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:4598064 original size:58 final size:61
Alignment explanation
Indices: 4598000--4598140 Score: 159
Period size: 58 Copynumber: 2.4 Consensus size: 61
4597990 TTTTTATATA
*
4598000 TTTTAATTTCATC-CATAAACTATGA-CTATCATTCTAA-AT-ATCCTTAAAC-TTTTGAACG
1 TTTTAATTTCATCTC-CAAACTATGACCT-TCATTCTAATATGATCCTTAAACTTTTTGAACG
* * *
4598058 TTTTAATTTCATCTCCAAACTATGACCTTCATTCTAATTTGGTCCTTAAACTTTTTGAACA
1 TTTTAATTTCATCTCCAAACTATGACCTTCATTCTAATATGATCCTTAAACTTTTTGAACG
** *
4598119 TTCAAATTACATCT-CAAACTAT
1 TTTTAATTTCATCTCCAAACTAT
4598141 ACATATATAC
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
58 31 0.44
59 4 0.06
60 17 0.24
61 19 0.27
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.42
Consensus pattern (61 bp):
TTTTAATTTCATCTCCAAACTATGACCTTCATTCTAATATGATCCTTAAACTTTTTGAACG
Found at i:4598138 original size:60 final size:58
Alignment explanation
Indices: 4598016--4598140 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 58
4598006 TTTCATCCAT
* ** *
4598016 AAACTATGACTATCATTCTAAATATCCTTAAACTTTTGAACGTTTTAATTTCATCTCC
1 AAACTATGACTATCATTCTAAATATCCTTAAACTTTTGAACATTCAAATTACATCTCC
* *
4598074 AAACTATGACCT-TCATTCTAATTTGGTCCTTAAACTTTTTGAACATTCAAATTACATCT-C
1 AAACTATGA-CTATCATTCTAA-AT-ATCCTTAAAC-TTTTGAACATTCAAATTACATCTCC
4598134 AAACTAT
1 AAACTAT
4598141 ACATATATAC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
58 18 0.32
59 3 0.05
60 17 0.30
61 19 0.33
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.40
Consensus pattern (58 bp):
AAACTATGACTATCATTCTAAATATCCTTAAACTTTTGAACATTCAAATTACATCTCC
Found at i:4598332 original size:60 final size:60
Alignment explanation
Indices: 4598262--4598434 Score: 215
Period size: 60 Copynumber: 2.9 Consensus size: 60
4598252 TATTTGAATG
* * ** * *
4598262 AATTTGGGGATAAAATTAGAATATTCAAAAGTTTGGGGACTAATTTAGAAA-GAGGGTCAC
1 AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA-AAATAAGAGTCAC
*
4598322 AATTTAGGGATGAAATTAGAATGA-TCAAAAGTTTAAGGACTAATTTAAAATAAGAGTCAT
1 AATTTAGGGATGAAATTAGAAT-ATTCAAAAGTTTAAGGACTAATTTAAAATAAGAGTCAC
* * * *
4598382 AGTTTAAGGATGAAATTTGAATATTCAAAAGTTTAAGGACCAATTTAAAATAA
1 AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATAA
4598435 CTGTTATAAT
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
59 4 0.04
60 94 0.95
61 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.30
Consensus pattern (60 bp):
AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATAAGAGTCAC
Found at i:4598433 original size:29 final size:29
Alignment explanation
Indices: 4598346--4598433 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
4598336 ATTAGAATGA
*
4598346 TCAAAAGTTTAAGGACTAATTTAAAATAAGAG
1 TCAAAAGTTTAAGGACAAATTTAAAAT---AG
* * * *
4598378 TC-ATAGTTTAAGGATGAAATTT-GAATAT
1 TCAAAAGTTTAAGGA-CAAATTTAAAATAG
*
4598406 TCAAAAGTTTAAGGACCAATTTAAAATA
1 TCAAAAGTTTAAGGACAAATTTAAAATA
4598434 ACTGTTATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
28 8 0.18
29 15 0.34
31 14 0.32
32 7 0.16
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.32
Consensus pattern (29 bp):
TCAAAAGTTTAAGGACAAATTTAAAATAG
Found at i:4602154 original size:2 final size:2
Alignment explanation
Indices: 4602147--4602171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4602137 GTTTAAGGTG
4602147 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4602172 TGATATGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4602695 original size:22 final size:21
Alignment explanation
Indices: 4602661--4602701 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
4602651 ATAATTATTT
4602661 AAAAAATTAAATAAAAATATC
1 AAAAAATTAAATAAAAATATC
*
4602682 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
4602702 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATC
Found at i:4603813 original size:2 final size:2
Alignment explanation
Indices: 4603806--4603851 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4603796 ATTATAAATA
4603806 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
4603848 AT AT
1 AT AT
4603852 TAAAAAGGGT
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):
AT
Found at i:4604754 original size:15 final size:15
Alignment explanation
Indices: 4604736--4604791 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
4604726 TAACCGGTTT
4604736 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
* *
4604751 CGGTTTTTTTAAAAATC
1 CGG--TTTTAAAAAAAC
*
4604768 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
4604783 CGATTTTAA
1 CGGTTTTAA
4604792 TATTATTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 19 0.59
17 13 0.41
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:4604764 original size:17 final size:17
Alignment explanation
Indices: 4604739--4604789 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
4604729 CCGGTTTCGG
4604739 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
* *
4604756 TTTTTAAAAATCCGG--
1 TTTTAAAAAAACCGGTT
* *
4604771 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
4604788 TT
1 TT
4604790 AATATTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 11 0.42
17 15 0.58
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:4604869 original size:32 final size:33
Alignment explanation
Indices: 4604833--4604941 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 33
4604823 ACAAAGTTTA
*
4604833 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
4604865 CGATAAATTAAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
4604898 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
4604930 CGAT-AATTGAAA
1 CGATAAATTGAAA
4604942 CAAAGTTTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 7 0.10
32 14 0.19
33 51 0.71
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTGAAATACTTAAAAACTTCCAAGTT
Done.