Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008668.1 Hibiscus syriacus cultivar Beakdansim tig00111671_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: 2122653
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1631363 original size:2 final size:2
Alignment explanation
Indices: 1631358--1631432 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
1631348 TCTCGTTGTC
1631358 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
1631400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1631433 ATACAATGTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1634134 original size:19 final size:16
Alignment explanation
Indices: 1634100--1634130 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1634090 TACAAAAATT
1634100 AATAATCCATAATATA
1 AATAATCCATAATATA
*
1634116 AATAATCCATTATAT
1 AATAATCCATAATAT
1634131 TATATATATA
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:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATCCATAATATA
Found at i:1635466 original size:60 final size:60
Alignment explanation
Indices: 1635366--1635502 Score: 220
Period size: 60 Copynumber: 2.3 Consensus size: 60
1635356 GACGCAGCAG
* *
1635366 CCGGTGACGAATCCGGTAACGACGTATCCCGCACCAACTGGAGGAGTCCCGGTGAGCACA
1 CCGGTGACGAATCCTGTAACGACGTATCCCGCACCAACTGGAGGAGTCCCAGTGAGCACA
* * *
1635426 CCGGTGACGAATCCTGTCACGACGTATCCCGCCCCGACTGGAGGAGTCCCAGTGAGCACA
1 CCGGTGACGAATCCTGTAACGACGTATCCCGCACCAACTGGAGGAGTCCCAGTGAGCACA
*
1635486 CCAGTGACGAATCCTGT
1 CCGGTGACGAATCCTGT
1635503 GCCTAATCCT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.23, C:0.33, G:0.28, T:0.15
Consensus pattern (60 bp):
CCGGTGACGAATCCTGTAACGACGTATCCCGCACCAACTGGAGGAGTCCCAGTGAGCACA
Found at i:1636608 original size:26 final size:26
Alignment explanation
Indices: 1636572--1636633 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
1636562 GAGTTGGGTG
1636572 ATTTCGAGTTTTAAAATTCTTTTGTC
1 ATTTCGAGTTTTAAAATTCTTTTGTC
1636598 ATTTCGAGTTTTAAAATTCTTTTGTC
1 ATTTCGAGTTTTAAAATTCTTTTGTC
1636624 ATTTCGAGTT
1 ATTTCGAGTT
1636634 CAGGGTCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53
Consensus pattern (26 bp):
ATTTCGAGTTTTAAAATTCTTTTGTC
Found at i:1638885 original size:32 final size:32
Alignment explanation
Indices: 1638844--1638912 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
1638834 AAACCTAAAC
* *
1638844 AATCTCCCTATGATTATACAGCAACAGAATTT
1 AATCTCCCTATGATTATACAGAAACAAAATTT
1638876 AATCTCCCTATGATTATACAGAAACAAAATTT
1 AATCTCCCTATGATTATACAGAAACAAAATTT
1638908 AATCT
1 AATCT
1638913 AAGTCGATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (32 bp):
AATCTCCCTATGATTATACAGAAACAAAATTT
Found at i:1643327 original size:55 final size:55
Alignment explanation
Indices: 1643253--1643363 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
1643243 ACGAGGAAAG
*
1643253 ACCACTACTTCAGCTGCACACAAGTAGAGCAAGAGCAGTAGTCCTTAAACAACTA
1 ACCACTACTTCAGCTGCACACAAGTAGAGCAACAGCAGTAGTCCTTAAACAACTA
1643308 ACCACTACTTCAGCTGCACACAAGTAGAGCAACAGCAGTAGTCCTTAAACAACTA
1 ACCACTACTTCAGCTGCACACAAGTAGAGCAACAGCAGTAGTCCTTAAACAACTA
1643363 A
1 A
1643364 AATGCAAATT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.18
Consensus pattern (55 bp):
ACCACTACTTCAGCTGCACACAAGTAGAGCAACAGCAGTAGTCCTTAAACAACTA
Found at i:1650027 original size:20 final size:20
Alignment explanation
Indices: 1649933--1650301 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1649923 GATTTTCCAT
* ** *
1649933 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1649953 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1649973 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1649993 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1650013 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1650033 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1650053 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1650073 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1650093 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1650113 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1650133 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1650153 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1650173 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1650193 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1650213 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1650233 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1650253 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1650273 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1650293 AATCACAAC
1 AATCGCAAC
1650302 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1651021 original size:24 final size:24
Alignment explanation
Indices: 1650982--1651028 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1650972 AAATTTGGTC
1650982 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1651006 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1651029 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1652344 original size:19 final size:19
Alignment explanation
Indices: 1652322--1652642 Score: 369
Period size: 19 Copynumber: 18.4 Consensus size: 19
1652312 CGGAAAATAC
*
1652322 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1652341 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1652355 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1652375 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1652389 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1652408 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1652427 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1652441 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1652460 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1652479 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1652498 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1652512 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1652531 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1652550 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1652564 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1652583 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1652597 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1652616 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1652635 AATCGCAA
1 AATCGCAA
1652643 CGAGATAATC
Statistics
Matches: 261, Mismatches: 10, Indels: 62
0.78 0.03 0.19
Matches are distributed among these distances:
14 56 0.21
15 2 0.01
16 22 0.08
17 20 0.08
18 3 0.01
19 145 0.56
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1652409 original size:33 final size:33
Alignment explanation
Indices: 1652322--1652623 Score: 243
Period size: 33 Copynumber: 8.8 Consensus size: 33
1652312 CGGAAAATAC
* *
1652322 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
1652355 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
1652389 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
1652427 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
1652460 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
1652498 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
1652531 AATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
1652563 GAATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 -AATCGCAATGCGAAATGAAAATCGCAACGAGAA
1652596 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
1652624 TGCGAAATGA
Statistics
Matches: 242, Mismatches: 9, Indels: 36
0.84 0.03 0.13
Matches are distributed among these distances:
32 2 0.01
33 141 0.58
34 31 0.13
35 10 0.04
36 9 0.04
37 2 0.01
38 47 0.19
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:1652569 original size:14 final size:14
Alignment explanation
Indices: 1652550--1652604 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
1652540 GCGAAATGAA
1652550 AATCGCAACGAAAG
1 AATCGCAACGAAAG
1652564 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1652581 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1652597 AATCGCAA
1 AATCGCAA
1652605 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.44
16 6 0.17
17 6 0.17
19 8 0.22
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1652680 original size:52 final size:52
Alignment explanation
Indices: 1652350--1652664 Score: 412
Period size: 52 Copynumber: 6.0 Consensus size: 52
1652340 AAATCCCAAC
1652350 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1652403 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
1652455 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* * *
1652505 ACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
1652562 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1652611 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1652663 AT
1 AT
1652665 TATAAACGCA
Statistics
Matches: 232, Mismatches: 15, Indels: 31
0.83 0.05 0.11
Matches are distributed among these distances:
47 9 0.04
48 1 0.00
49 5 0.02
50 10 0.04
51 7 0.03
52 170 0.73
53 16 0.07
54 1 0.00
56 1 0.00
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1652779 original size:19 final size:19
Alignment explanation
Indices: 1652671--1652771 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
1652661 AAATTATAAA
1652671 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1652690 CCGCATTGCGA-TTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1652709 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1652725 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1652742 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1652761 CGCATTGCGAT
1 CGCATTGCGAT
1652772 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
18 10 0.14
19 34 0.46
20 10 0.14
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1652779 original size:38 final size:37
Alignment explanation
Indices: 1652671--1652771 Score: 140
Period size: 33 Copynumber: 2.8 Consensus size: 37
1652661 AAATTATAAA
1652671 CGCATTGCGATTTTCATTTCCGCATTGCGATTTCATTT
1 CGCATTGCGATTTTCATTT-CGCATTGCGATTTCATTT
*
1652709 CGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTT
1652742 CGCATTGCGATTTTCATTTCGCATTGCGAT
1 CGCATTGCGATTTTCATTTCGCATTGCGAT
1652772 AGTCATTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
32 6 0.11
33 18 0.33
34 2 0.04
35 5 0.09
36 7 0.13
37 1 0.02
38 16 0.29
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (37 bp):
CGCATTGCGATTTTCATTTCGCATTGCGATTTCATTT
Found at i:1652897 original size:14 final size:14
Alignment explanation
Indices: 1652878--1652914 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1652868 CATCAATTAC
1652878 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1652892 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1652906 ACAAATCAA
1 ACAAATCAA
1652915 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1654914 original size:14 final size:14
Alignment explanation
Indices: 1654895--1654951 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1654885 GCGAAATGAA
*
1654895 AATCGCAACGACAG
1 AATCGCAACGAAAG
1654909 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1654926 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1654942 AATCGCAACG
1 AATCGCAACG
1654952 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1654922 original size:33 final size:33
Alignment explanation
Indices: 1654876--1654968 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1654866 GCGAAACCAA
*
1654876 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1654909 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1654942 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1654969 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1654933 original size:19 final size:19
Alignment explanation
Indices: 1654839--1654973 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1654829 TAGTTTACTT
* *
1654839 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1654859 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1654878 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1654897 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1654911 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1654930 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1654944 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1654963 TCGCAATGCGA
1 TCGCAACGCGA
1654974 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1654991 original size:19 final size:19
Alignment explanation
Indices: 1654969--1655097 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1654959 AAAATCGCAA
1654969 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1654988 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1655002 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1655021 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1655035 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1655054 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1655073 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1655093 TGCGA
1 TGCGA
1655098 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1655011 original size:33 final size:33
Alignment explanation
Indices: 1654969--1655060 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1654959 AAAATCGCAA
1654969 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1655002 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1655035 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1655061 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1655288 original size:93 final size:93
Alignment explanation
Indices: 1655129--1655595 Score: 918
Period size: 93 Copynumber: 5.0 Consensus size: 93
1655119 GCAAATTGAA
1655129 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1655194 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1655222 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1655287 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1655315 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1655380 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1655408 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1655472 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1655500 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
1655565 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1655593 ACT
1 ACT
1655596 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.25
93 280 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:1655566 original size:185 final size:186
Alignment explanation
Indices: 1655129--1655595 Score: 918
Period size: 185 Copynumber: 2.5 Consensus size: 186
1655119 GCAAATTGAA
1655129 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1655194 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
1655259 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
1655315 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1655380 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
1655444 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
1655500 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
1655565 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
1655596 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
185 154 0.55
186 126 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:1657303 original size:14 final size:14
Alignment explanation
Indices: 1657284--1657373 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1657274 TTGAAATGAA
1657284 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1657298 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1657315 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1657331 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1657350 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1657364 AATCGCAACG
1 AATCGCAACG
1657374 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1657321 original size:33 final size:33
Alignment explanation
Indices: 1657276--1657390 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1657266 TCTTTTGGTT
1657276 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1657309 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1657342 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1657375 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1657391 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1657322 original size:19 final size:18
Alignment explanation
Indices: 1657283--1657395 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1657273 GTTGAAATGA
1657283 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1657298 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1657315 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1657331 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1657348 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1657364 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1657381 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1657396 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1657426 original size:14 final size:14
Alignment explanation
Indices: 1657407--1657461 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1657397 TTTGGTTTCG
1657407 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1657421 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1657440 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1657454 CGTTGCGA
1 CGTTGCGA
1657462 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1657439 original size:33 final size:33
Alignment explanation
Indices: 1657391--1657461 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1657381 AAAATCGCAA
**
1657391 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1657424 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1657457 TGCGA
1 TGCGA
1657462 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1657469 original size:33 final size:33
Alignment explanation
Indices: 1657402--1657483 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1657392 GCGATTTTGG
***
1657402 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1657435 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1657468 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1657484 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1657488 original size:20 final size:20
Alignment explanation
Indices: 1657414--1657502 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1657404 TCGCGTTGCG
1657414 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1657434 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1657447 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1657467 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1657487 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1657503 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1657623 original size:33 final size:33
Alignment explanation
Indices: 1657581--1657651 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1657571 AATACTAACT
*
1657581 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1657614 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1657647 TGAAA
1 TGAAA
1657652 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1657885 original size:22 final size:22
Alignment explanation
Indices: 1657833--1657887 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1657823 TGGTTGTGAG
**
1657833 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1657855 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1657877 GGATTTCTTCG
1 GGATTTCTTCG
1657888 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1658058 original size:20 final size:20
Alignment explanation
Indices: 1658033--1658225 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
1658023 CTTTAAATAT
1658033 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1658053 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1658075 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1658094 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1658114 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1658134 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1658154 CACGTTGCAATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1658174 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1658194 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1658214 CGCGTTGCGATT
1 CGCGTTGCGATT
1658226 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1658220 original size:60 final size:60
Alignment explanation
Indices: 1658033--1658225 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
1658023 CTTTAAATAT
**
1658033 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1658094 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * * ** *
1658154 CACGTTGCAATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1658214 CGCGTTGCGATT
1 CGCGTTGCGATT
1658226 ATGGAAAATC
Statistics
Matches: 109, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 81 0.74
61 28 0.26
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1667268 original size:29 final size:29
Alignment explanation
Indices: 1667230--1667298 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
1667220 TAGATACAAC
1667230 GAAACAAACAAACCCTAAATATAGTACGA
1 GAAACAAACAAACCCTAAATATAGTACGA
1667259 GAAACAAACAAACCCTAAATATAGTACGA
1 GAAACAAACAAACCCTAAATATAGTACGA
1667288 GAAAC-AACAAA
1 GAAACAAACAAA
1667299 TTAAAAAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.58, C:0.20, G:0.10, T:0.12
Consensus pattern (29 bp):
GAAACAAACAAACCCTAAATATAGTACGA
Found at i:1671832 original size:2 final size:2
Alignment explanation
Indices: 1671825--1671855 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1671815 CAAATTTATC
1671825 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1671856 TTATTAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1676471 original size:10 final size:10
Alignment explanation
Indices: 1676456--1676480 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1676446 GCCTACAAAT
1676456 TATAAATAAA
1 TATAAATAAA
1676466 TATAAATAAA
1 TATAAATAAA
1676476 TATAA
1 TATAA
1676481 TTTTCAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATAAATAAA
Found at i:1682169 original size:162 final size:163
Alignment explanation
Indices: 1681902--1682230 Score: 624
Period size: 162 Copynumber: 2.0 Consensus size: 163
1681892 GGCAAATTCT
1681902 CCAGCAGGGATCGTTTTTCACGAGGTGGTTCTAAGGAACGGAGAGGTTTGAGGACCTCCAGGGGT
1 CCAGCAGGGATCGTTTTTCACGAGGTGGTTCTAAGGAACGGAGAGGTTTGAGGACCTCCAGGGGT
1681967 TGGGGTAATGGCCGAGATTCTGACAATGGGTTCCAAGGCGGAAGAAGCAGCTGGTCA-CTTCGAA
66 TGGGGTAATGGCCGAGATTCTGACAATGGGTTCCAAGGCGGAAGAAGCAGCTGGTCAGCTTCGAA
1682031 AAACAGTAGGGATGACTGGCTAATTGGTAGTAG
131 AAACAGTAGGGATGACTGGCTAATTGGTAGTAG
1682064 CCAGCAGGGATCGTTTTTCACGAGGTGGTTCTAAGGAACGGAGAGGTTTGAGGACCTCCAGGGGT
1 CCAGCAGGGATCGTTTTTCACGAGGTGGTTCTAAGGAACGGAGAGGTTTGAGGACCTCCAGGGGT
1682129 TGGGGTAATGGCCGAGATTCTGACAATGGGTTCCAAGGCGGAAGAAGCAGCTGGTCACGGGCTTC
66 TGGGGTAATGGCCGAGATTCTGACAATGGGTTCCAAGGCGGAAGAAGCAGCTGGTCA---GCTTC
1682194 GAAAAACAGTAGGGATGACTGGCTAATTGGTAGTAG
128 GAAAAACAGTAGGGATGACTGGCTAATTGGTAGTAG
1682230 C
1 C
1682231 AGATCAAAGA
Statistics
Matches: 163, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
162 122 0.75
166 41 0.25
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.22
Consensus pattern (163 bp):
CCAGCAGGGATCGTTTTTCACGAGGTGGTTCTAAGGAACGGAGAGGTTTGAGGACCTCCAGGGGT
TGGGGTAATGGCCGAGATTCTGACAATGGGTTCCAAGGCGGAAGAAGCAGCTGGTCAGCTTCGAA
AAACAGTAGGGATGACTGGCTAATTGGTAGTAG
Found at i:1684394 original size:75 final size:75
Alignment explanation
Indices: 1684301--1684455 Score: 265
Period size: 75 Copynumber: 2.1 Consensus size: 75
1684291 AAAATCGTGA
*
1684301 TGAAGCTCATGAAAGTGAAGACCAGATCAATGAGGAAGTACAAACTGCTCATATGAAAGAAAATT
1 TGAAGCTCATGAAAGTGAAGACCAGATCAATGAGGAAGTACAAACTGCTCATAGGAAAGAAAATT
1684366 CAGGTGAAAT
66 CAGGTGAAAT
* * * *
1684376 TGAAGCTCATGTAGGTGAAGGCCGGATCAATGAGGAAGTACAAACTGCTCATAGGAAAGAAAATT
1 TGAAGCTCATGAAAGTGAAGACCAGATCAATGAGGAAGTACAAACTGCTCATAGGAAAGAAAATT
1684441 CAGGTGAAAT
66 CAGGTGAAAT
1684451 TGAAG
1 TGAAG
1684456 AACTTTCACT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (75 bp):
TGAAGCTCATGAAAGTGAAGACCAGATCAATGAGGAAGTACAAACTGCTCATAGGAAAGAAAATT
CAGGTGAAAT
Found at i:1692721 original size:16 final size:16
Alignment explanation
Indices: 1692695--1692739 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1692685 TAATATTGAA
1692695 ACTCG-ACTCGAAAAG
1 ACTCGAACTCGAAAAG
1692710 ACTCGAACTCGAAAAG
1 ACTCGAACTCGAAAAG
*
1692726 ACTCAAACTC-AAAA
1 ACTCGAACTCGAAAA
1692740 AAAAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.47, C:0.27, G:0.13, T:0.13
Consensus pattern (16 bp):
ACTCGAACTCGAAAAG
Found at i:1702304 original size:33 final size:33
Alignment explanation
Indices: 1702262--1702374 Score: 131
Period size: 33 Copynumber: 3.4 Consensus size: 33
1702252 CGCAAAATGT
1702262 TATAATTTCAGTTAATAAGGATTTGAATAAGTA
1 TATAATTTCAGTTAATAAGGATTTGAATAAGTA
* *** *
1702295 TATAATTTCAGTAAATCACTCTCATTGGAA-AATGT-
1 TATAATTTCAGTTAAT-A--AGGATTTGAATAA-GTA
1702330 TATAATTTCAGTTAATAAGGATTTGAATAAGTA
1 TATAATTTCAGTTAATAAGGATTTGAATAAGTA
1702363 TATAATTTCAGT
1 TATAATTTCAGT
1702375 AAATCACTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
32 8 0.12
33 29 0.45
34 2 0.03
35 17 0.27
36 8 0.12
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (33 bp):
TATAATTTCAGTTAATAAGGATTTGAATAAGTA
Found at i:1702341 original size:35 final size:35
Alignment explanation
Indices: 1702295--1702405 Score: 131
Period size: 35 Copynumber: 3.2 Consensus size: 35
1702285 TGAATAAGTA
1702295 TATAATTTCAGTAAATCACTCTCATTGGAAAATGT
1 TATAATTTCAGTAAATCACTCTCATTGGAAAATGT
* *** *
1702330 TATAATTTCAGTTAAT-A--AGGATTTGAATAA-GT
1 TATAATTTCAGTAAATCACTCTCATTGGAA-AATGT
1702362 ATATAATTTCAGTAAATCACTCTCATTGGAAAATGT
1 -TATAATTTCAGTAAATCACTCTCATTGGAAAATGT
1702398 TATAATTT
1 TATAATTT
1702406 GTTTAAAGTG
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
32 8 0.13
33 17 0.28
34 2 0.03
35 25 0.42
36 8 0.13
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.40
Consensus pattern (35 bp):
TATAATTTCAGTAAATCACTCTCATTGGAAAATGT
Found at i:1702364 original size:68 final size:68
Alignment explanation
Indices: 1702255--1702405 Score: 302
Period size: 68 Copynumber: 2.2 Consensus size: 68
1702245 CTTCCTACGC
1702255 AAAATGTTATAATTTCAGTTAATAAGGATTTGAATAAGTATATAATTTCAGTAAATCACTCTCAT
1 AAAATGTTATAATTTCAGTTAATAAGGATTTGAATAAGTATATAATTTCAGTAAATCACTCTCAT
1702320 TGG
66 TGG
1702323 AAAATGTTATAATTTCAGTTAATAAGGATTTGAATAAGTATATAATTTCAGTAAATCACTCTCAT
1 AAAATGTTATAATTTCAGTTAATAAGGATTTGAATAAGTATATAATTTCAGTAAATCACTCTCAT
1702388 TGG
66 TGG
1702391 AAAATGTTATAATTT
1 AAAATGTTATAATTT
1702406 GTTTAAAGTG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 83 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (68 bp):
AAAATGTTATAATTTCAGTTAATAAGGATTTGAATAAGTATATAATTTCAGTAAATCACTCTCAT
TGG
Found at i:1712897 original size:8 final size:8
Alignment explanation
Indices: 1712824--1712922 Score: 75
Period size: 8 Copynumber: 12.9 Consensus size: 8
1712814 TTTATAACTG
1712824 TAAAA-AA
1 TAAAATAA
1712831 TAAAATAA
1 TAAAATAA
*
1712839 TTAAATAA
1 TAAAATAA
*
1712847 -AAAA-AT
1 TAAAATAA
1712853 TAAAA-AA
1 TAAAATAA
1712860 T-AAATAA
1 TAAAATAA
*
1712867 TACAATAA
1 TAAAATAA
*
1712875 TTAAATAA
1 TAAAATAA
*
1712883 TTAAATAA
1 TAAAATAA
1712891 -AATAATAA
1 TAA-AATAA
* *
1712899 CAAAATAT
1 TAAAATAA
1712907 TAAATATAA
1 TAAA-ATAA
1712916 TAAAATA
1 TAAAATA
1712923 TAACTTATAA
Statistics
Matches: 74, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
6 4 0.05
7 18 0.24
8 43 0.58
9 9 0.12
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (8 bp):
TAAAATAA
Found at i:1712898 original size:36 final size:36
Alignment explanation
Indices: 1712824--1712905 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 36
1712814 TTTATAACTG
1712824 TAAAAAATAAAATAATTAAATAAAAAAATTAAAAAA
1 TAAAAAATAAAATAATTAAATAAAAAAATTAAAAAA
* * **
1712860 TAAATAATACAATAATTAAATAATTAAA-TAAAATAA
1 TAAAAAATAAAATAATTAAATAAAAAAATTAAAA-AA
1712896 TAACAAAATA
1 TAA-AAAATA
1712906 TTAAATATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.13
36 29 0.74
37 5 0.13
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (36 bp):
TAAAAAATAAAATAATTAAATAAAAAAATTAAAAAA
Found at i:1712905 original size:16 final size:14
Alignment explanation
Indices: 1712826--1712898 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 14
1712816 TATAACTGTA
1712826 AAAAATAAAATAAT
1 AAAAATAAAATAAT
* *
1712840 -TAAATAAAAAAATT
1 AAAAATAAAATAA-T
1712854 AAAAA-ATAAATAAT
1 AAAAATA-AAATAAT
*
1712868 ACAATAATTAAATAAT
1 A-AA-AATAAAATAAT
*
1712884 -TAAATAAAATAAT
1 AAAAATAAAATAAT
1712897 AA
1 AA
1712899 CAAAATATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
13 20 0.45
14 5 0.11
15 10 0.23
16 9 0.20
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATAAAATAAT
Found at i:1712920 original size:17 final size:18
Alignment explanation
Indices: 1712890--1712923 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1712880 TAATTAAATA
1712890 AAATAATAACAAAATATT
1 AAATAATAACAAAATATT
*
1712908 AAAT-ATAATAAAATAT
1 AAATAATAACAAAATAT
1712924 AACTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAATAACAAAATATT
Found at i:1718724 original size:21 final size:21
Alignment explanation
Indices: 1718678--1718716 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1718668 TCCTAATTTA
*
1718678 AAACCCTAAATTGATAATCAC
1 AAACCCTAAATTCATAATCAC
1718699 AAACCCTAAA-TCATAATC
1 AAACCCTAAATTCATAATC
1718717 TCATAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.26, G:0.03, T:0.23
Consensus pattern (21 bp):
AAACCCTAAATTCATAATCAC
Found at i:1719678 original size:23 final size:23
Alignment explanation
Indices: 1719622--1719678 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
1719612 TCACCGAGGA
* *
1719622 CGGTGGCTCACCGACGACATCAT
1 CGGTGGCTCATCGACGACATCAC
* *
1719645 CGGTGGCTCATCGATGACCTCAC
1 CGGTGGCTCATCGACGACATCAC
1719668 CGGTGGCTCAT
1 CGGTGGCTCAT
1719679 TAACGGTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (23 bp):
CGGTGGCTCATCGACGACATCAC
Found at i:1720254 original size:21 final size:21
Alignment explanation
Indices: 1720230--1720288 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
1720220 ATTATCCAAT
* *
1720230 AAACTTGACATGCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
1720251 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
1720272 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
1720289 TAATAAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:1721874 original size:17 final size:17
Alignment explanation
Indices: 1721852--1721888 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1721842 CAAAACGTGT
*
1721852 GAATCAGCAGATTCGGC
1 GAATCAGCAGATTCAGC
1721869 GAATCAGCAGATTCAGC
1 GAATCAGCAGATTCAGC
1721886 GAA
1 GAA
1721889 GAGAAAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.16
Consensus pattern (17 bp):
GAATCAGCAGATTCAGC
Found at i:1721909 original size:20 final size:20
Alignment explanation
Indices: 1721885--1721969 Score: 93
Period size: 20 Copynumber: 4.2 Consensus size: 20
1721875 GCAGATTCAG
*
1721885 CGAAGAGAAAGTGAGATCGG
1 CGAAGAGAAAGTGAGATCGA
* *
1721905 CGAAGAGAAAGTGAAATCAA
1 CGAAGAGAAAGTGAGATCGA
*
1721925 CGAAGA-AACAG-CAGATTCGA
1 CGAAGAGAA-AGTGAGA-TCGA
*
1721945 CGAAGAGAAAGTAAGATCGA
1 CGAAGAGAAAGTGAGATCGA
1721965 CGAAG
1 CGAAG
1721970 CAGCAGCAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 4 0.07
20 45 0.83
21 5 0.09
ACGTcount: A:0.47, C:0.13, G:0.31, T:0.09
Consensus pattern (20 bp):
CGAAGAGAAAGTGAGATCGA
Found at i:1721949 original size:40 final size:40
Alignment explanation
Indices: 1721905--1721980 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
1721895 GTGAGATCGG
1721905 CGAAGAGAAAGTGAA-ATCAACGAAGAAACAGCAGATTCGA
1 CGAAGAGAAAGT-AAGATCAACGAAGAAACAGCAGATTCGA
* * *
1721945 CGAAGAGAAAGTAAGATCGACGAAGCAGCAGCAGAT
1 CGAAGAGAAAGTAAGATCAACGAAGAAACAGCAGAT
1721981 GGGTTTAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.47, C:0.16, G:0.28, T:0.09
Consensus pattern (40 bp):
CGAAGAGAAAGTAAGATCAACGAAGAAACAGCAGATTCGA
Found at i:1725296 original size:58 final size:56
Alignment explanation
Indices: 1725191--1725337 Score: 206
Period size: 58 Copynumber: 2.6 Consensus size: 56
1725181 TTTAAATTAA
* *
1725191 TTATTTAATTAATCATGTTCAATAAATAAATTATTTTCACTATTAATGATTATAAT
1 TTATTTAATTAATCATATTCAATAAATAAATTATTTTCAATATTAATGATTATAAT
* *
1725247 TTATTTAATTATTCATATTCAATACCAATAAATTATTTT-AATTTGTAATGATTATAAT
1 TTATTTAATTAATCATATTCAATA--AATAAATTATTTTCAATAT-TAATGATTATAAT
* *
1725305 TAATTTAATTAATCACATTCAATAAATAAATTA
1 TTATTTAATTAATCATATTCAATAAATAAATTA
1725338 CTTAACAAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
56 31 0.38
57 3 0.04
58 47 0.58
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (56 bp):
TTATTTAATTAATCATATTCAATAAATAAATTATTTTCAATATTAATGATTATAAT
Found at i:1726569 original size:6 final size:6
Alignment explanation
Indices: 1726558--1726584 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1726548 TGATGTCATC
1726558 GAGGGT GAGGGT GAGGGT GAGGGT GAG
1 GAGGGT GAGGGT GAGGGT GAGGGT GAG
1726585 AATTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.67, T:0.15
Consensus pattern (6 bp):
GAGGGT
Found at i:1738971 original size:2 final size:2
Alignment explanation
Indices: 1738964--1739049 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
1738954 ATTACCACTC
1738964 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
1739006 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
1739048 AT
1 AT
1739050 CCACTTAACC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1740214 original size:16 final size:16
Alignment explanation
Indices: 1740193--1740226 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1740183 AGCAATTTAC
1740193 TTAGCTTTTTCAAAAT
1 TTAGCTTTTTCAAAAT
1740209 TTAGCTTTTTCAAAAT
1 TTAGCTTTTTCAAAAT
1740225 TT
1 TT
1740227 CGCATTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAGCTTTTTCAAAAT
Found at i:1748595 original size:14 final size:14
Alignment explanation
Indices: 1748562--1748629 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
1748552 TTTTTTAAAT
1748562 TACATTATTAAAAA
1 TACATTATTAAAAA
1748576 T--A-TATTAAAAA
1 TACATTATTAAAAA
1748587 TACATTATTAATAATTA
1 TACATTATTAA-AA--A
* *
1748604 TAAATTTTTAAAAA
1 TACATTATTAAAAA
*
1748618 TACATTTTTAAA
1 TACATTATTAAA
1748630 TGTATTATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 10 0.22
12 1 0.02
13 1 0.02
14 19 0.42
15 2 0.04
16 2 0.04
17 10 0.22
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (14 bp):
TACATTATTAAAAA
Found at i:1748615 original size:31 final size:34
Alignment explanation
Indices: 1748580--1748646 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 34
1748570 TAAAAATATA
1748580 TTAAAAATACATTATT-AAT-AATTATAA-ATTT
1 TTAAAAATACATTATTAAATGAATTATAAGATTT
* *
1748611 TTAAAAATACATTTTTAAATGTATTATAAGATTT
1 TTAAAAATACATTATTAAATGAATTATAAGATTT
1748645 TT
1 TT
1748647 GTAGGTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 15 0.48
32 3 0.10
33 7 0.23
34 6 0.19
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (34 bp):
TTAAAAATACATTATTAAATGAATTATAAGATTT
Found at i:1748692 original size:17 final size:17
Alignment explanation
Indices: 1748670--1748703 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1748660 CGAGTTTGAC
1748670 TTCGAGCTTGAATCGAG
1 TTCGAGCTTGAATCGAG
1748687 TTCGAGCTTGAATCGAG
1 TTCGAGCTTGAATCGAG
1748704 CTCAAAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (17 bp):
TTCGAGCTTGAATCGAG
Found at i:1751413 original size:66 final size:66
Alignment explanation
Indices: 1751302--1751439 Score: 267
Period size: 66 Copynumber: 2.1 Consensus size: 66
1751292 TGTCGGGTGT
*
1751302 ACACAGTTTGGTTGTTTGCTTTTTGAAGAGGCTGCGAGGAAAAGATGATGGTATGCCTTGTGAAA
1 ACACCGTTTGGTTGTTTGCTTTTTGAAGAGGCTGCGAGGAAAAGATGATGGTATGCCTTGTGAAA
1751367 A
66 A
1751368 ACACCGTTTGGTTGTTTGCTTTTTGAAGAGGCTGCGAGGAAAAGATGATGGTATGCCTTGTGAAA
1 ACACCGTTTGGTTGTTTGCTTTTTGAAGAGGCTGCGAGGAAAAGATGATGGTATGCCTTGTGAAA
1751433 A
66 A
1751434 ACACCG
1 ACACCG
1751440 GAACAGCGTC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (66 bp):
ACACCGTTTGGTTGTTTGCTTTTTGAAGAGGCTGCGAGGAAAAGATGATGGTATGCCTTGTGAAA
A
Found at i:1752378 original size:31 final size:30
Alignment explanation
Indices: 1752305--1752379 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 30
1752295 ATATCATGTA
*
1752305 TCGAAAATGAGGATGTGAGTATATCACATG
1 TCGAAAATGATGATGTGAGTATATCACATG
1752335 TCGAAAACTGATGATGT-AGCATATATC-CAATG
1 TCGAAAA-TGATGATGTGAG--TATATCAC-ATG
1752367 TCGAAAATGATGA
1 TCGAAAATGATGA
1752380 CATTGCACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 9 0.22
31 15 0.38
32 16 0.40
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.27
Consensus pattern (30 bp):
TCGAAAATGATGATGTGAGTATATCACATG
Found at i:1752449 original size:26 final size:26
Alignment explanation
Indices: 1752392--1752443 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1752382 TTGCACATAC
1752392 CGCTCATTGAAAGTGGTGACATGAAT
1 CGCTCATTGAAAGTGGTGACATGAAT
1752418 CGCTCATTGAAAGTGGTGACATGAAT
1 CGCTCATTGAAAGTGGTGACATGAAT
1752444 GTCTCAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (26 bp):
CGCTCATTGAAAGTGGTGACATGAAT
Found at i:1760006 original size:17 final size:17
Alignment explanation
Indices: 1759985--1760017 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1759975 GTTTTAAAGT
1759985 TTTTTTAAAATA-TATA
1 TTTTTTAAAATACTATA
1760001 TTTTTTAAAATACTATA
1 TTTTTTAAAATACTATA
1760018 AAATCGACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTTAAAATACTATA
Found at i:1760427 original size:31 final size:29
Alignment explanation
Indices: 1760392--1760459 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1760382 AACAACACCC
1760392 TATAACCGTACTCAATCCAACATTTTATTAG
1 TATAACCG-ACTC-ATCCAACATTTTATTAG
* **
1760423 TATAACCGAGTCATCTTACATTTTATTAG
1 TATAACCGACTCATCCAACATTTTATTAG
1760452 TATAACCG
1 TATAACCG
1760460 GGATCATGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 23 0.68
30 3 0.09
31 8 0.24
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.37
Consensus pattern (29 bp):
TATAACCGACTCATCCAACATTTTATTAG
Found at i:1761483 original size:17 final size:17
Alignment explanation
Indices: 1761458--1761502 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1761448 GTATGTTGTT
*
1761458 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
1761475 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
*
1761492 CATTTATGCAT
1 CATTTAAGCAT
1761503 CTAGTTGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:1761562 original size:18 final size:18
Alignment explanation
Indices: 1761539--1761581 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1761529 CATGCATTTT
1761539 GTTCATTGAATAAAGTTA
1 GTTCATTGAATAAAGTTA
*
1761557 GTTCATTGAATAATGTTA
1 GTTCATTGAATAAAGTTA
*
1761575 TTTCATT
1 GTTCATT
1761582 AATCAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (18 bp):
GTTCATTGAATAAAGTTA
Found at i:1763522 original size:24 final size:24
Alignment explanation
Indices: 1763495--1763573 Score: 158
Period size: 24 Copynumber: 3.3 Consensus size: 24
1763485 AAGACTCCAC
1763495 TGTTGAGGGACATAGAGACAGACA
1 TGTTGAGGGACATAGAGACAGACA
1763519 TGTTGAGGGACATAGAGACAGACA
1 TGTTGAGGGACATAGAGACAGACA
1763543 TGTTGAGGGACATAGAGACAGACA
1 TGTTGAGGGACATAGAGACAGACA
1763567 TGTTGAG
1 TGTTGAG
1763574 AACCATTAGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.35, C:0.11, G:0.34, T:0.19
Consensus pattern (24 bp):
TGTTGAGGGACATAGAGACAGACA
Found at i:1765339 original size:14 final size:14
Alignment explanation
Indices: 1765322--1765351 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1765312 AAGTTTTTTT
1765322 AAATAATTTTTTAA
1 AAATAATTTTTTAA
*
1765336 AAATATTTTTTTAA
1 AAATAATTTTTTAA
1765350 AA
1 AA
1765352 TGCTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATAATTTTTTAA
Found at i:1765352 original size:13 final size:14
Alignment explanation
Indices: 1765315--1765352 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1765305 AGGAAAAAAG
1765315 TTTTTTT-AAATAA
1 TTTTTTTAAAATAA
*
1765328 TTTTTTAAAAAT-A
1 TTTTTTTAAAATAA
1765341 TTTTTTTAAAAT
1 TTTTTTTAAAAT
1765353 GCTATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTTTTAAAATAA
Found at i:1773792 original size:19 final size:19
Alignment explanation
Indices: 1773756--1773795 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1773746 AACACATTTG
* **
1773756 AATATCATCAAATTTTTTA
1 AATATCATAAAAAATTTTA
1773775 AATATCATAAAAAATTTTA
1 AATATCATAAAAAATTTTA
1773794 AA
1 AA
1773796 ATAATATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATCATAAAAAATTTTA
Found at i:1773797 original size:20 final size:19
Alignment explanation
Indices: 1773756--1773798 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1773746 AACACATTTG
* * *
1773756 AATATCATCAAATTTTTTA
1 AATATCATAAAAATTTTAA
1773775 AATATCATAAAAAATTTTAA
1 AATATCAT-AAAAATTTTAA
1773795 AATA
1 AATA
1773799 ATATTTAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATCATAAAAATTTTAA
Found at i:1774556 original size:35 final size:35
Alignment explanation
Indices: 1774508--1774617 Score: 125
Period size: 35 Copynumber: 3.1 Consensus size: 35
1774498 TCTAAACCTT
* *
1774508 AAATTGAAGTATTTTAGAATTTGAGGTTTAAAATTG
1 AAATTGAATTATTTTGGAATTTGAGGTTTAAAA-TG
*
1774544 -AATTGAATTATTTTGGAATTT-AGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGA-GGTTTAAAATG
* * * *
1774578 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGAGGTTTAAAATG
1774613 AAATT
1 AAATT
1774618 AAGGACTGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
34 3 0.05
35 62 0.95
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGAGGTTTAAAATG
Found at i:1774792 original size:29 final size:29
Alignment explanation
Indices: 1774759--1774822 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
1774749 ATAAATATTG
1774759 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1774788 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1774817 GGGGAC
1 GGGGAC
1774823 CTAAATGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.30, C:0.08, G:0.31, T:0.31
Consensus pattern (29 bp):
GGGGACTGTATTGCAAGTTTTAAAAGTTA
Found at i:1774831 original size:29 final size:29
Alignment explanation
Indices: 1774759--1774833 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
1774749 ATAAATATTG
* *
1774759 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1 GGGGACTGAAATGCAAGTTTTAAAAGTTA
* *
1774788 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1 GGGGACTGAAATGCAAGTTTTAAAAGTTA
1774817 GGGGACCT-AAATGCAAG
1 GGGGA-CTGAAATGCAAG
1774834 ATTCAGAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 41 0.95
30 2 0.05
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (29 bp):
GGGGACTGAAATGCAAGTTTTAAAAGTTA
Found at i:1775402 original size:38 final size:38
Alignment explanation
Indices: 1775351--1775434 Score: 168
Period size: 38 Copynumber: 2.2 Consensus size: 38
1775341 GACACCCTTT
1775351 TCTTCCTCCTATTATTCGTCATGTTGTCGTTGCCTTCG
1 TCTTCCTCCTATTATTCGTCATGTTGTCGTTGCCTTCG
1775389 TCTTCCTCCTATTATTCGTCATGTTGTCGTTGCCTTCG
1 TCTTCCTCCTATTATTCGTCATGTTGTCGTTGCCTTCG
1775427 TCTTCCTC
1 TCTTCCTC
1775435 GTCTATTTCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.07, C:0.31, G:0.14, T:0.48
Consensus pattern (38 bp):
TCTTCCTCCTATTATTCGTCATGTTGTCGTTGCCTTCG
Found at i:1780543 original size:12 final size:11
Alignment explanation
Indices: 1780506--1780542 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
1780496 ATACCTCAAT
1780506 AAAGAAGAGGAA
1 AAAGAA-AGGAA
1780518 AAAGAAAGGAA
1 AAAGAAAGGAA
1780529 AAAGAAAGGAA
1 AAAGAAAGGAA
1780540 AAA
1 AAA
1780543 AAAAACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (11 bp):
AAAGAAAGGAA
Found at i:1780934 original size:28 final size:28
Alignment explanation
Indices: 1780885--1780939 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1780875 GTGAAAATGA
*
1780885 ATTTAAAATTTTTATATTTTTAAAATAT
1 ATTTAAAATTTTTATATCTTTAAAATAT
* *
1780913 ATTTAATATTTTCTATA-CTTTATAATA
1 ATTTAAAATTTT-TATATCTTTAAAATA
1780940 ATAAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTAAAATTTTTATATCTTTAAAATAT
Found at i:1783269 original size:2 final size:2
Alignment explanation
Indices: 1783262--1783297 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1783252 GTTTGAGGCC
1783262 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
1783298 TGATTTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1787388 original size:12 final size:12
Alignment explanation
Indices: 1787371--1787395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1787361 AATGCGATGA
1787371 ACTTGAATTGTC
1 ACTTGAATTGTC
1787383 ACTTGAATTGTC
1 ACTTGAATTGTC
1787395 A
1 A
1787396 TTCAAATATG
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
ACTTGAATTGTC
Found at i:1788407 original size:17 final size:17
Alignment explanation
Indices: 1788385--1788419 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1788375 TGTTCCTTTC
1788385 ATTGTACTATATCATTT
1 ATTGTACTATATCATTT
* *
1788402 ATTGTATTATATCTTTT
1 ATTGTACTATATCATTT
1788419 A
1 A
1788420 CAATATTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.57
Consensus pattern (17 bp):
ATTGTACTATATCATTT
Found at i:1788575 original size:40 final size:40
Alignment explanation
Indices: 1788531--1788645 Score: 158
Period size: 40 Copynumber: 2.9 Consensus size: 40
1788521 AACTCCCAGT
1788531 ATCAATAATCAGTGAATAATAATGCACATAAAGTGTCAGC
1 ATCAATAATCAGTGAATAATAATGCACATAAAGTGTCAGC
* * * *
1788571 ATCAATAATCAATGAACATTAATGCACATAAAGTGTCAGT
1 ATCAATAATCAGTGAATAATAATGCACATAAAGTGTCAGC
* ** *
1788611 ATTAGGATTCAGTGAATAATAATGCACATAAAGTG
1 ATCAATAATCAGTGAATAATAATGCACATAAAGTG
1788646 AATGACAGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (40 bp):
ATCAATAATCAGTGAATAATAATGCACATAAAGTGTCAGC
Found at i:1791661 original size:13 final size:13
Alignment explanation
Indices: 1791657--1791690 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
1791647 CGTTCACCCG
1791657 ACCCGACCCGTTC
1 ACCCGACCCGTTC
1791670 ACCCGA-CCGTTC
1 ACCCGACCCGTTC
1791682 ACCCGACCC
1 ACCCGACCC
1791691 TACCCGTTGA
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:0.18, C:0.56, G:0.15, T:0.12
Consensus pattern (13 bp):
ACCCGACCCGTTC
Found at i:1791666 original size:18 final size:18
Alignment explanation
Indices: 1791643--1791708 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 18
1791633 GAAATGTTTT
1791643 GACCCGTTCACCCGACCC
1 GACCCGTTCACCCGACCC
1791661 GACCCGTT----C-ACCC
1 GACCCGTTCACCCGACCC
1791674 GA-CCGTTCACCCGACCC
1 GACCCGTTCACCCGACCC
* *
1791691 TACCCGTTGACCCGACCC
1 GACCCGTTCACCCGACCC
1791709 ATTGAACCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
12 5 0.12
13 6 0.15
14 1 0.03
16 1 0.03
17 5 0.12
18 22 0.55
ACGTcount: A:0.17, C:0.53, G:0.17, T:0.14
Consensus pattern (18 bp):
GACCCGTTCACCCGACCC
Found at i:1791682 original size:30 final size:30
Alignment explanation
Indices: 1791646--1791707 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1791636 ATGTTTTGAC
1791646 CCGTTCACCCGACCCGACCCGTTCACCCGA
1 CCGTTCACCCGACCCGACCCGTTCACCCGA
* *
1791676 CCGTTCACCCGACCCTACCCGTTGACCCGA
1 CCGTTCACCCGACCCGACCCGTTCACCCGA
1791706 CC
1 CC
1791708 CATTGAACCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.16, C:0.53, G:0.16, T:0.15
Consensus pattern (30 bp):
CCGTTCACCCGACCCGACCCGTTCACCCGA
Found at i:1791708 original size:13 final size:13
Alignment explanation
Indices: 1791686--1791724 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1791676 CCGTTCACCC
*
1791686 GACCCTACCCGTT
1 GACCCGACCCGTT
*
1791699 GACCCGACCCATT
1 GACCCGACCCGTT
*
1791712 GAACCGACCCGTT
1 GACCCGACCCGTT
1791725 AACCGTTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.21, C:0.44, G:0.18, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1794240 original size:47 final size:47
Alignment explanation
Indices: 1794182--1794274 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
1794172 CGATTGAATT
* *
1794182 TGATCTGATACTTGGCATGGATTCTGATCTGATATCTGACATGGATTC
1 TGATCTGATACTTGACATGGATTCTGATATGATA-CTGACATGGATTC
* * *
1794230 TGAT-TGATACTTGACTTGGATTCTTATATGATACTGACCTGGATT
1 TGATCTGATACTTGACATGGATTCTGATATGATACTGACATGGATT
1794275 TTTGTCTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 11 0.28
47 25 0.62
48 4 0.10
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (47 bp):
TGATCTGATACTTGACATGGATTCTGATATGATACTGACATGGATTC
Found at i:1794244 original size:23 final size:24
Alignment explanation
Indices: 1794182--1794274 Score: 111
Period size: 24 Copynumber: 4.0 Consensus size: 24
1794172 CGATTGAATT
*
1794182 TGATCTGATACTTGGCATGGATTC
1 TGATCTGATACTTGACATGGATTC
1794206 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
1794230 TGAT-TGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
1794253 TTATATGATAC-TGACCTGGATT
1 TGATCTGATACTTGACATGGATT
1794275 TTTGTCTGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
23 30 0.48
24 32 0.52
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:1794531 original size:24 final size:24
Alignment explanation
Indices: 1794504--1794622 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
1794494 TTCGATTTGA
* *
1794504 ATTCTGATCTGATACTTGGCATGG
1 ATTCTGATATGATACTTGACATGG
*
1794528 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* *
1794552 ATTCTGATTTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* *
1794576 ATTCTTATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
* *
1794600 ATTTTGATATGATACTTAACATG
1 ATTCTGATATGATACTTGACATG
1794623 AATTATGTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1794839 original size:2 final size:2
Alignment explanation
Indices: 1794832--1794858 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1794822 TGGATGAGGG
1794832 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 T
1794859 GTTTAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1799291 original size:24 final size:24
Alignment explanation
Indices: 1799264--1799382 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
1799254 TTCGATTTGA
1799264 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
1799288 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
1799312 ATTCTGATCTGATTCTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
1799336 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
1799360 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
1799383 AATTATGTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 82 0.98
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1799317 original size:12 final size:12
Alignment explanation
Indices: 1799280--1799342 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
1799270 ATCTGATACT
1799280 TGACATGGATTC
1 TGACATGGATTC
*
1799292 TGATAT-GATATC
1 TGACATGGAT-TC
1799304 TGACATGGATTC
1 TGACATGGATTC
1799316 TGATC-T-GATTC
1 TGA-CATGGATTC
*
1799327 TTGACTTGGATTC
1 -TGACATGGATTC
1799340 TGA
1 TGA
1799343 TCTGATACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
11 9 0.21
12 25 0.58
13 9 0.21
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:1799341 original size:72 final size:72
Alignment explanation
Indices: 1799246--1799382 Score: 206
Period size: 72 Copynumber: 1.9 Consensus size: 72
1799236 TGAAAATTTT
*
1799246 ATCTGATTTTCGATTTGAATTCTGATCTGATACTTGACATGGATTCTGATATGATA-TCTGACAT
1 ATCTGATTTTCGACTTGAATTCTGATCTGATACTTGACATGGATTCTGATATGATACT-TGACAT
1799310 GGATTCTG
65 GGATTCTG
* * *
1799318 ATCTGATTCTT-GACTTGGATTCTGATCTGATACTTGACCTGGATTTTGATATGATACTTGACAT
1 ATCTGATT-TTCGACTTGAATTCTGATCTGATACTTGACATGGATTCTGATATGATACTTGACAT
1799382 G
65 G
1799383 AATTATGTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
72 56 0.95
73 3 0.05
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (72 bp):
ATCTGATTTTCGACTTGAATTCTGATCTGATACTTGACATGGATTCTGATATGATACTTGACATG
GATTCTG
Found at i:1802197 original size:2 final size:2
Alignment explanation
Indices: 1802192--1802218 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1802182 ATTGTGTGTG
1802192 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 T
1802219 TAGCTCTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1804698 original size:14 final size:14
Alignment explanation
Indices: 1804681--1804730 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
1804671 TAAAAATATA
1804681 TTAAAAATACATTT
1 TTAAAAATACATTT
*
1804695 TTAATAATTATAAATTT
1 TTAA-AA--ATACATTT
1804712 TTAAAAATACATTT
1 TTAAAAATACATTT
1804726 TTAAA
1 TTAAA
1804731 TGTATTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 16 0.52
15 2 0.06
16 2 0.06
17 11 0.35
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAAAATACATTT
Found at i:1804716 original size:31 final size:34
Alignment explanation
Indices: 1804681--1804747 Score: 104
Period size: 31 Copynumber: 2.1 Consensus size: 34
1804671 TAAAAATATA
1804681 TTAAAAATACATTTTT-AAT-AATTATAA-ATTT
1 TTAAAAATACATTTTTAAATGAATTATAAGATTT
*
1804712 TTAAAAATACATTTTTAAATGTATTATAAGATTT
1 TTAAAAATACATTTTTAAATGAATTATAAGATTT
1804746 TT
1 TT
1804748 GTAGGTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 16 0.50
32 3 0.09
33 7 0.22
34 6 0.19
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (34 bp):
TTAAAAATACATTTTTAAATGAATTATAAGATTT
Found at i:1804793 original size:17 final size:17
Alignment explanation
Indices: 1804771--1804804 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1804761 CGAGTTTGAC
1804771 TTCGAGCTTGAATCGAG
1 TTCGAGCTTGAATCGAG
1804788 TTCGAGCTTGAATCGAG
1 TTCGAGCTTGAATCGAG
1804805 CTCAAAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (17 bp):
TTCGAGCTTGAATCGAG
Found at i:1808254 original size:31 final size:31
Alignment explanation
Indices: 1808182--1808262 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
1808172 AGATTTTCAT
* *
1808182 GTGTTGAAAATGATGATATGTCACATGTTAA
1 GTGTTGAAAGTGATGATATGTCACATGTCAA
*
1808213 GTGTCT-AAAGTGATGATATGTCACATGTCAC
1 GTGT-TGAAAGTGATGATATGTCACATGTCAA
1808244 GCT-TTGAAAGTGATGATAT
1 G-TGTTGAAAGTGATGATAT
1808263 TACATATGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 1 0.02
31 41 0.93
32 2 0.05
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (31 bp):
GTGTTGAAAGTGATGATATGTCACATGTCAA
Found at i:1808382 original size:31 final size:30
Alignment explanation
Indices: 1808309--1808383 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 30
1808299 ATATCATGTA
*
1808309 TCGAAAATGAGGATGTGAGTATATCACATG
1 TCGAAAATGATGATGTGAGTATATCACATG
1808339 TCGAAAACTGATGATGT-AGCATATATC-CAATG
1 TCGAAAA-TGATGATGTGAG--TATATCAC-ATG
1808371 TCGAAAATGATGA
1 TCGAAAATGATGA
1808384 CATTGCACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 9 0.22
31 15 0.38
32 16 0.40
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.27
Consensus pattern (30 bp):
TCGAAAATGATGATGTGAGTATATCACATG
Found at i:1808453 original size:26 final size:26
Alignment explanation
Indices: 1808396--1808447 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1808386 TTGCACATAC
1808396 CGCTCATTGAAAGTGGTGACATGAAT
1 CGCTCATTGAAAGTGGTGACATGAAT
1808422 CGCTCATTGAAAGTGGTGACATGAAT
1 CGCTCATTGAAAGTGGTGACATGAAT
1808448 GTCTCAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (26 bp):
CGCTCATTGAAAGTGGTGACATGAAT
Found at i:1816007 original size:17 final size:17
Alignment explanation
Indices: 1815986--1816018 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1815976 GTTTTAAAGT
1815986 TTTTTTAAAATA-TATA
1 TTTTTTAAAATACTATA
1816002 TTTTTTAAAATACTATA
1 TTTTTTAAAATACTATA
1816019 AAATCGACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTTAAAATACTATA
Found at i:1816428 original size:31 final size:29
Alignment explanation
Indices: 1816393--1816460 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1816383 AACAACACCC
1816393 TATAACCGTACTCAATCCAACATTTTATTAG
1 TATAACCG-ACTC-ATCCAACATTTTATTAG
* **
1816424 TATAACCGAGTCATCTTACATTTTATTAG
1 TATAACCGACTCATCCAACATTTTATTAG
1816453 TATAACCG
1 TATAACCG
1816461 GGATCATGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 23 0.68
30 3 0.09
31 8 0.24
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.37
Consensus pattern (29 bp):
TATAACCGACTCATCCAACATTTTATTAG
Found at i:1817483 original size:17 final size:17
Alignment explanation
Indices: 1817458--1817502 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1817448 GTATGTTGTT
*
1817458 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
1817475 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
*
1817492 CATTTATGCAT
1 CATTTAAGCAT
1817503 CTAGTTGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:1817559 original size:17 final size:18
Alignment explanation
Indices: 1817539--1817580 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1817529 CATGCATTTT
1817539 GTTCATTGAATAA-GTTA
1 GTTCATTGAATAATGTTA
1817556 GTTCATTGAATAATGTTA
1 GTTCATTGAATAATGTTA
*
1817574 TTTCATT
1 GTTCATT
1817581 AATCAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (18 bp):
GTTCATTGAATAATGTTA
Found at i:1819523 original size:24 final size:24
Alignment explanation
Indices: 1819496--1819550 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
1819486 AAGACTCCAC
1819496 TGTTGAGGGACATAGAGACAGACA
1 TGTTGAGGGACATAGAGACAGACA
1819520 TGTTGAGGGACATAGAGACAGACA
1 TGTTGAGGGACATAGAGACAGACA
1819544 TGTTGAG
1 TGTTGAG
1819551 AACCATTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.35, T:0.20
Consensus pattern (24 bp):
TGTTGAGGGACATAGAGACAGACA
Found at i:1821314 original size:14 final size:14
Alignment explanation
Indices: 1821297--1821326 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1821287 AAGTTTTTTT
1821297 AAATAATTTTTTAA
1 AAATAATTTTTTAA
*
1821311 AAATATTTTTTTAA
1 AAATAATTTTTTAA
1821325 AA
1 AA
1821327 TGCTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATAATTTTTTAA
Found at i:1821327 original size:13 final size:14
Alignment explanation
Indices: 1821290--1821327 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1821280 AGGAAAAAAG
1821290 TTTTTTT-AAATAA
1 TTTTTTTAAAATAA
*
1821303 TTTTTTAAAAAT-A
1 TTTTTTTAAAATAA
1821316 TTTTTTTAAAAT
1 TTTTTTTAAAAT
1821328 GCTATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTTTTAAAATAA
Found at i:1827864 original size:13 final size:13
Alignment explanation
Indices: 1827846--1827873 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1827836 CCACCGTACT
1827846 CCGCCGCCGACCA
1 CCGCCGCCGACCA
1827859 CCGCCGCCGACCA
1 CCGCCGCCGACCA
1827872 CC
1 CC
1827874 ATAACGGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.64, G:0.21, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGACCA
Found at i:1828691 original size:3 final size:3
Alignment explanation
Indices: 1828678--1828749 Score: 101
Period size: 3 Copynumber: 24.0 Consensus size: 3
1828668 GTAATATTTA
* * *
1828678 AAT AAT AAAT AAT ATT ACT ATT AAT AAT AAT AAT -AT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1828723 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1828750 TTAAAATGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.92
4 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1829028 original size:76 final size:76
Alignment explanation
Indices: 1828902--1829883 Score: 1743
Period size: 76 Copynumber: 13.0 Consensus size: 76
1828892 GGTCTTATGA
* *
1828902 ATGACCCTG-AGGGTTTGAAAGCATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* *
1828966 TAGGGCTTACAG
65 AAGGACTTACAG
* *
1828978 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAAGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
1829043 AGGGCTTACAG
66 AGGACTTACAG
1829054 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1829119 AGGACTTACAG
66 AGGACTTACAG
*
1829130 ATGACCCGAAGG-TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCCTGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1829193 AGGACTTACAG
66 AGGACTTACAG
1829204 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1829269 AGGACTTACAG
66 AGGACTTACAG
1829280 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1829345 AGGACTTACAG
66 AGGACTTACAG
1829356 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
1829421 AGGACTTACTG
66 AGGACTTACAG
*
1829432 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1829497 AGGACTTACAG
66 AGGACTTACAG
1829508 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1829573 AGGACTTACAG
66 AGGACTTACAG
1829584 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1829649 AGGACTTACAG
66 AGGACTTACAG
*
1829660 ATGA-CCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1829724 AGGACTTACAG
66 AGGACTTACAG
*
1829735 ATGACCCGAA-G----GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGG
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1829795 AGGACTTACAG
66 AGGACTTACAG
* *
1829806 ATGAACCG-AGGCTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCCGAAGGTTTTG-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1829870 AA-GACTTACAG
65 AAGGACTTACAG
1829881 ATG
1 ATG
1829884 TGGGAAATAG
Statistics
Matches: 879, Mismatches: 17, Indels: 21
0.96 0.02 0.02
Matches are distributed among these distances:
70 1 0.00
71 67 0.08
74 44 0.05
75 147 0.17
76 620 0.71
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:1830577 original size:21 final size:22
Alignment explanation
Indices: 1830553--1830602 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1830543 CATAAAGTTT
* *
1830553 TCATCTTGAAAGAGA-AATCTG
1 TCATCTTGAAAAAGAGAATCTA
*
1830574 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTGAAAAAGAGAATCTA
1830596 TCATCTT
1 TCATCTT
1830603 TGAAGAGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTGAAAAAGAGAATCTA
Found at i:1830599 original size:22 final size:23
Alignment explanation
Indices: 1830561--1830603 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1830551 TTTCATCTTG
*
1830561 AAAGAGAAATCTGTCATCTTTAA
1 AAAGAGAAATCTATCATCTTTAA
1830584 AAAGAG-AATCTATCATCTTT
1 AAAGAGAAATCTATCATCTTT
1830604 GAAGAGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (23 bp):
AAAGAGAAATCTATCATCTTTAA
Found at i:1831054 original size:54 final size:54
Alignment explanation
Indices: 1830972--1831133 Score: 243
Period size: 54 Copynumber: 3.0 Consensus size: 54
1830962 AGAATAGCAG
* *** *
1830972 GTTCGTAAAACATTTGATAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTAAGAT
* *
1831026 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTAAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTAAGAT
* *
1831080 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTGCCAAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTAAGAT
1831134 TTCTCAATCA
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 97 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTAAGAT
Found at i:1833520 original size:114 final size:114
Alignment explanation
Indices: 1833320--1833659 Score: 574
Period size: 114 Copynumber: 3.0 Consensus size: 114
1833310 GATCATGCAG
* * ** * *
1833320 TTCATCTTTCAATTCCAATGATCAGTTTTGGGGTTTC-TACCGAATCAGATCAGATAACTCAAAG
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGG-TTCATACCAAACCAGATCAGATAACTCAAAG
* * *
1833384 AACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
1833434 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1833499 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
1833548 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1833613 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTATTATGAGCA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
1833660 CATGGCACTT
Statistics
Matches: 215, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
113 3 0.01
114 212 0.99
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:1835499 original size:11 final size:11
Alignment explanation
Indices: 1835483--1835512 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1835473 TCAATTTTCC
1835483 TTTTTCTTTTT
1 TTTTTCTTTTT
1835494 TTTTTC-TTTT
1 TTTTTCTTTTT
1835504 TTTTTCTTT
1 TTTTTCTTT
1835513 CTTTGCTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1841669 original size:13 final size:13
Alignment explanation
Indices: 1841651--1841678 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1841641 CCACCGTACT
1841651 CCGCCGCCGACCA
1 CCGCCGCCGACCA
1841664 CCGCCGCCGACCA
1 CCGCCGCCGACCA
1841677 CC
1 CC
1841679 ATAACGGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.64, G:0.21, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGACCA
Found at i:1842496 original size:3 final size:3
Alignment explanation
Indices: 1842483--1842549 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
1842473 GTAATATTTA
* * *
1842483 AAT AAT AAAT AAT ATT ACT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
1842529 AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
1842550 TTAAAATGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:1842497 original size:18 final size:17
Alignment explanation
Indices: 1842474--1842549 Score: 66
Period size: 18 Copynumber: 4.2 Consensus size: 17
1842464 TTGGGCTTTG
1842474 TAATATTTAAATAATAAA
1 TAATATTTAAATAAT-AA
1842492 TAATATTACTATTAATAATAA
1 TAATATT--TA--AATAATAA
*
1842513 TAATA-AT-AATAATAA
1 TAATATTTAAATAATAA
*
1842528 TAATAATTTTAATAATAA
1 TAAT-ATTTAAATAATAA
1842546 TAAT
1 TAAT
1842550 TTAAAATGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
15 12 0.24
16 1 0.02
17 1 0.02
18 20 0.41
20 2 0.04
21 7 0.14
22 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATATTTAAATAATAA
Found at i:1846919 original size:18 final size:18
Alignment explanation
Indices: 1846893--1846927 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1846883 TCGAAAGGAC
*
1846893 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1846911 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1846928 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1850398 original size:19 final size:19
Alignment explanation
Indices: 1850374--1850413 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1850364 AACACATTTG
* *
1850374 AATATCATCAAATTTTTTA
1 AATATCATAAAATATTTTA
1850393 AATATCATAAAATATTTTA
1 AATATCATAAAATATTTTA
1850412 AA
1 AA
1850414 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATCATAAAATATTTTA
Found at i:1851174 original size:35 final size:35
Alignment explanation
Indices: 1851126--1851235 Score: 125
Period size: 35 Copynumber: 3.1 Consensus size: 35
1851116 TCTAAACCTT
* *
1851126 AAATTGAAGTATTTTAGAATTTGAGGTTTAAAATTG
1 AAATTGAATTATTTTGGAATTTGAGGTTTAAAA-TG
*
1851162 -AATTGAATTATTTTGGAATTT-AGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGA-GGTTTAAAATG
* * * *
1851196 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGAGGTTTAAAATG
1851231 AAATT
1 AAATT
1851236 AAGGAATGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
34 3 0.05
35 62 0.95
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGAGGTTTAAAATG
Done.