Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 19 of 163
Found at i:6487050 original size:22 final size:22
Alignment explanation
Indices: 6487001--6487044 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6486991 TTTTTTCAAG
*
6487001 AATATTTATATTATTTTAATTT
1 AATATTTATAATATTTTAATTT
*
6487023 AATATTTTTAATATTTT-ATTT
1 AATATTTATAATATTTTAATTT
6487044 A
1 A
6487045 TTTATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATATTTATAATATTTTAATTT
Found at i:6487799 original size:16 final size:17
Alignment explanation
Indices: 6487772--6487805 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6487762 CGACCCACCC
*
6487772 ATATTAATTTTTTTATA
1 ATATTAATTTTTATATA
6487789 ATATT-ATTTTTATATA
1 ATATTAATTTTTATATA
6487805 A
1 A
6487806 AAATAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTAATTTTTATATA
Found at i:6488523 original size:25 final size:24
Alignment explanation
Indices: 6488472--6488534 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
6488462 TTTTGAGCAA
* *
6488472 TTTAATTTTTTTCTTTTATGTTTT
1 TTTAATTTCTTTCTTTTATCTTTT
6488496 TTTAACTTTCTTTCTTTT-TCTTTAT
1 TTTAA-TTTCTTTCTTTTATCTTT-T
6488521 TTTCAATTCTCTTT
1 TTT-AATT-TCTTT
6488535 TGCTTCTCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 9 0.27
25 17 0.52
26 7 0.21
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTAATTTCTTTCTTTTATCTTTT
Found at i:6489742 original size:23 final size:23
Alignment explanation
Indices: 6489716--6489764 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
6489706 ACGAGATTTC
6489716 TTAAAAA-TATATAAATA-ATTACA
1 TTAAAAATTA-ATAAA-ACATTACA
*
6489739 TTAATAATTAATAAAACATTACA
1 TTAAAAATTAATAAAACATTACA
6489762 TTA
1 TTA
6489765 CCATTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 1 0.04
23 20 0.87
24 2 0.09
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAAAATTAATAAAACATTACA
Found at i:6492932 original size:22 final size:24
Alignment explanation
Indices: 6492907--6492951 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
6492897 CGTGACAATT
6492907 AATTAGTTTTTA-A-AATTTTTAA
1 AATTAGTTTTTATATAATTTTTAA
*
6492929 AATTATTTTTTATATAATTTTTA
1 AATTAGTTTTTATATAATTTTTA
6492952 TACTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 1 0.05
24 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
AATTAGTTTTTATATAATTTTTAA
Found at i:6492959 original size:33 final size:32
Alignment explanation
Indices: 6492913--6492974 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
6492903 AATTAATTAG
*
6492913 TTTTTAAAATTTTTAAAATTATTTTTTATATAA
1 TTTTTAAAATTTTTAAAA-TACTTTTTATATAA
* *
6492946 TTTTTATACTTTTTAAAATACTTTTTATA
1 TTTTTAAAATTTTTAAAATACTTTTTATA
6492975 ATTGATGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 10 0.38
33 16 0.62
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTTAAAATTTTTAAAATACTTTTTATATAA
Found at i:6499888 original size:17 final size:16
Alignment explanation
Indices: 6499866--6499913 Score: 66
Period size: 13 Copynumber: 3.1 Consensus size: 16
6499856 ATAATTTTAA
6499866 AATATAATTTAAAATTG
1 AATATAATTT-AAATTG
6499883 AATATAATTT-AA-T-
1 AATATAATTTAAATTG
6499896 AATATAATTTAAATTG
1 AATATAATTTAAATTG
6499912 AA
1 AA
6499914 CGATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 10 0.36
14 3 0.11
15 3 0.11
16 2 0.07
17 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
AATATAATTTAAATTG
Found at i:6499920 original size:30 final size:29
Alignment explanation
Indices: 6499854--6499920 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 29
6499844 ATGAACCGAT
6499854 AGATAATTTTAAAATATAATTTAAAATTGA
1 AGATAA-TTTAAAATATAATTTAAAATTGA
*
6499884 ATATAATTTAATAATATAATTT-AAATTGA
1 AGATAATTTAA-AATATAATTTAAAATTGA
6499913 ACGATAAT
1 A-GATAAT
6499921 AATTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (29 bp):
AGATAATTTAAAATATAATTTAAAATTGA
Found at i:6503311 original size:15 final size:16
Alignment explanation
Indices: 6503291--6503321 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6503281 ACATGTTTAA
6503291 TATTTTT-ATATAATT
1 TATTTTTAATATAATT
6503306 TATTTTTAATATAATT
1 TATTTTTAATATAATT
6503322 ATTATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAATATAATT
Found at i:6525528 original size:14 final size:13
Alignment explanation
Indices: 6525494--6525541 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
6525484 ATCAATAAAA
6525494 TTTATTGAAAATT
1 TTTATTGAAAATT
*
6525507 TTTGTTGAAAATT
1 TTTATTGAAAATT
6525520 TTTATTTG-AAA--
1 TTTA-TTGAAAATT
6525531 TTTATTGAAAA
1 TTTATTGAAAA
6525542 AAATAACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 18 0.58
14 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (13 bp):
TTTATTGAAAATT
Found at i:6526473 original size:23 final size:23
Alignment explanation
Indices: 6526447--6526502 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
6526437 CTTGTATCAG
6526447 TTTAGTTTAAATTCATTTTATCT
1 TTTAGTTTAAATTCATTTTATCT
*
6526470 TTTAGTTTAAATTTATTTTATCT
1 TTTAGTTTAAATTCATTTTATCT
6526493 TTATA-TTTAA
1 TT-TAGTTTAA
6526503 TTTTTTGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 29 0.94
24 2 0.06
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTAGTTTAAATTCATTTTATCT
Found at i:6542010 original size:5 final size:5
Alignment explanation
Indices: 6541997--6542029 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
6541987 AACATTAACC
*
6541997 TATAC TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT
6542030 GCTTCCTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:6543050 original size:27 final size:23
Alignment explanation
Indices: 6542998--6543043 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6542988 AACTTTAACA
6542998 TTACCTTGTTTAGAAGGACTGAT
1 TTACCTTGTTTAGAAGGACTGAT
6543021 TTACCTTGTTTAGAAGGACTGAT
1 TTACCTTGTTTAGAAGGACTGAT
6543044 GGTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (23 bp):
TTACCTTGTTTAGAAGGACTGAT
Found at i:6546222 original size:10 final size:10
Alignment explanation
Indices: 6546208--6546241 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
6546198 AGGTATGGTT
*
6546208 TGTATTGTAT
1 TGTATTGTAG
6546218 TGTATTGTAG
1 TGTATTGTAG
*
6546228 TCTATTGTAG
1 TGTATTGTAG
6546238 TGTA
1 TGTA
6546242 ATCTATACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.03, G:0.24, T:0.53
Consensus pattern (10 bp):
TGTATTGTAG
Found at i:6553323 original size:3 final size:3
Alignment explanation
Indices: 6553315--6553345 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6553305 ACAATTAGAG
*
6553315 AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
6553346 AATGAATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6559932 original size:5 final size:5
Alignment explanation
Indices: 6559924--6559951 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
6559914 GAATGCGAAT
6559924 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
6559952 AATTGAAGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:6562805 original size:15 final size:16
Alignment explanation
Indices: 6562787--6562821 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
6562777 TGGGTTCCAA
6562787 AATTTGGTTTT-AAAG
1 AATTTGGTTTTCAAAG
6562802 AA-TTGGTTTTCAAAG
1 AATTTGGTTTTCAAAG
6562817 AATTT
1 AATTT
6562822 TAAACATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.44
15 8 0.44
16 2 0.11
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (16 bp):
AATTTGGTTTTCAAAG
Found at i:6563069 original size:16 final size:17
Alignment explanation
Indices: 6563050--6563087 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
6563040 AATATTAAAA
6563050 CTAATG-CATAAAACTT
1 CTAATGACATAAAACTT
*
6563066 CTAATGTAGATAAAACTT
1 CTAATG-ACATAAAACTT
6563084 CTAA
1 CTAA
6563088 GTCACAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (17 bp):
CTAATGACATAAAACTT
Found at i:6563741 original size:21 final size:21
Alignment explanation
Indices: 6563710--6563764 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
6563700 GGTGGTGTCG
* * *
6563710 AAGTATAAGAGATATGTATCG
1 AAGTATGAGAGATATATATCA
* *
6563731 GAGTATGAGAGATGTATATCA
1 AAGTATGAGAGATATATATCA
6563752 AAGTATGAGAGAT
1 AAGTATGAGAGAT
6563765 GTGTTAGGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.27, T:0.27
Consensus pattern (21 bp):
AAGTATGAGAGATATATATCA
Found at i:6569510 original size:26 final size:26
Alignment explanation
Indices: 6569480--6569533 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
6569470 TCACTTTCAT
*
6569480 GTGACATCGTCAAATAGGACCATAAA
1 GTGACATCGTCAAATACGACCATAAA
6569506 GTGACATCGTCAAATACGACCATAAA
1 GTGACATCGTCAAATACGACCATAAA
6569532 GT
1 GT
6569534 CTAGGCCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (26 bp):
GTGACATCGTCAAATACGACCATAAA
Found at i:6574563 original size:5 final size:5
Alignment explanation
Indices: 6574553--6574580 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
6574543 GAAAGCGAAT
6574553 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
6574581 AATTCAAGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:6575134 original size:24 final size:23
Alignment explanation
Indices: 6575089--6575135 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
6575079 AAGCAATACT
*
6575089 ACATGCATAAGTAAGACTAAAAA
1 ACATGCATAAGAAAGACTAAAAA
6575112 ACATGCCATAAGAAGAGAC-AAAAA
1 ACATG-CATAAGAA-AGACTAAAAA
6575136 CATCTAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13
Consensus pattern (23 bp):
ACATGCATAAGAAAGACTAAAAA
Found at i:6575547 original size:21 final size:21
Alignment explanation
Indices: 6575487--6575549 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
6575477 TTCTTCTCTG
* *
6575487 CTCTGCTTCCCTCACTGCAGC
1 CTCTGCTTCCCTCGCTGCTGC
* * *
6575508 CTCTGCTGCTCTCGTTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
6575529 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
6575550 ATCAACTTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.03, C:0.44, G:0.19, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCTGC
Found at i:6575623 original size:86 final size:87
Alignment explanation
Indices: 6575507--6575709 Score: 300
Period size: 86 Copynumber: 2.3 Consensus size: 87
6575497 CTCACTGCAG
* * * * * *
6575507 CCTCTGCTGCTCTCGTTGCTGCCTCTGCTTCCCTCGCTGCTGCATCAACTTTAAGTTGTAGCTGG
1 CCTCAGCTTCTCTCGATGCTGCCTCTGCTTCCCTCACCGCTGCATCAACTCTAAGTTGTAGCTGG
*
6575572 AGTTCTTTATATTTTCTTTGAA
66 AGTTCTTCATATTTTCTTTGAA
***
6575594 CCTCAGCTTCTCTC-ATGCTGCCTCTGCTTCCCTCACCGCTGCATTTGCTCTAAGTTGTAGCTGG
1 CCTCAGCTTCTCTCGATGCTGCCTCTGCTTCCCTCACCGCTGCATCAACTCTAAGTTGTAGCTGG
6575658 AGTTCTTCATATTTTCTTTGAA
66 AGTTCTTCATATTTTCTTTGAA
*
6575680 CCTTAGCTTCTCTCGATGCTGCCTCTGCTT
1 CCTCAGCTTCTCTCGATGCTGCCTCTGCTT
6575710 TAAGTTGAGT
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 77 0.74
87 27 0.26
ACGTcount: A:0.12, C:0.30, G:0.17, T:0.40
Consensus pattern (87 bp):
CCTCAGCTTCTCTCGATGCTGCCTCTGCTTCCCTCACCGCTGCATCAACTCTAAGTTGTAGCTGG
AGTTCTTCATATTTTCTTTGAA
Found at i:6577468 original size:41 final size:40
Alignment explanation
Indices: 6577423--6577550 Score: 123
Period size: 41 Copynumber: 3.1 Consensus size: 40
6577413 ATGTTTTTTT
*
6577423 GCGGCACTTTCACAAAAACGCAGCTAAAACCCTGAGCTTTA
1 GCGGCACTTTCA-AAAAACGCAGCTAAAACCCTGAGCATTA
* * * * * *
6577464 GCGGCGCCTTTCTAAAAATGCCGCTAAAACCCCGAACATTA
1 GCGGC-ACTTTCAAAAAACGCAGCTAAAACCCTGAGCATTA
* * *
6577505 GCGGCGCTTAAT-AAAAAACGCTGCTAAAACCCTGAGCATTG
1 GCGGCACTT--TCAAAAAACGCAGCTAAAACCCTGAGCATTA
6577546 GCGGC
1 GCGGC
6577551 GCTATTTTAA
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
40 3 0.04
41 61 0.87
42 6 0.09
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (40 bp):
GCGGCACTTTCAAAAAACGCAGCTAAAACCCTGAGCATTA
Found at i:6577562 original size:82 final size:82
Alignment explanation
Indices: 6577436--6577594 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 82
6577426 GCACTTTCAC
*
6577436 AAAAACGCAGCTAAAACCCTGAGCTTTAGCGGCGCCTTTCTAAAAATGCCGCTAAAACCC-CGAA
1 AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCCTTTCTAAAAATGCCGCTAAAACCCAC-AA
6577500 CATTAGCGGCGCTTAATA
65 CATTAGCGGCGCTTAATA
* * * **
6577518 AAAAACGCTGCTAAAACCCTGAGCATTGGCGGCG-CTATTTTAAAAATGCCTTTAAAACCCACAA
1 AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCCT-TTCTAAAAATGCCGCTAAAACCCACAA
6577582 CATTAGCGGCGCT
65 CATTAGCGGCGCT
6577595 ACTCCAGAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 2 0.03
82 66 0.96
83 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (82 bp):
AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCCTTTCTAAAAATGCCGCTAAAACCCACAAC
ATTAGCGGCGCTTAATA
Found at i:6577563 original size:41 final size:40
Alignment explanation
Indices: 6577436--6577563 Score: 139
Period size: 41 Copynumber: 3.1 Consensus size: 40
6577426 GCACTTTCAC
* *
6577436 AAAAACGCAGCTAAAACCCTGAGCTTTAGCGGCGCCTTTCT
1 AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCG-CTTTTT
* * * * * *
6577477 AAAAATGCCGCTAAAACCCCGAACATTAGCGGCGCTTAATA
1 AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCTT-TTT
* *
6577518 AAAAACGCTGCTAAAACCCTGAGCATTGGCGGCGCTATTTT
1 AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCT-TTTT
6577559 AAAAA
1 AAAAA
6577564 TGCCTTTAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
40 3 0.04
41 66 0.94
42 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (40 bp):
AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCTTTTT
Found at i:6577574 original size:41 final size:40
Alignment explanation
Indices: 6577446--6577594 Score: 138
Period size: 41 Copynumber: 3.6 Consensus size: 40
6577436 AAAAACGCAG
* * * *
6577446 CTAAAACCCTGAGCTTTAGCGGCGCCTTTCTAAAAATGCCG
1 CTAAAACCCTGAACATTAGCGGCG-CTTTATAAAAATGCCT
* * *
6577487 CTAAAACCCCGAACATTAGCGGCGCTTAATAAAAA-ACGCT
1 CTAAAACCCTGAACATTAGCGGCGCTTTATAAAAATGC-CT
* * *
6577527 GCTAAAACCCTGAGCATTGGCGGCGCTATTTTAAAAATGCCT
1 -CTAAAACCCTGAACATTAGCGGCGCT-TTATAAAAATGCCT
* **
6577569 TTAAAACCCACAACATTAGCGGCGCT
1 CTAAAACCCTGAACATTAGCGGCGCT
6577595 ACTCCAGAAA
Statistics
Matches: 86, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
39 1 0.01
40 10 0.12
41 65 0.76
42 9 0.10
43 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (40 bp):
CTAAAACCCTGAACATTAGCGGCGCTTTATAAAAATGCCT
Found at i:6577894 original size:37 final size:37
Alignment explanation
Indices: 6577850--6577924 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
6577840 AGTTAGGGGG
6577850 TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
1 TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
*
6577887 TTTAGAAGATGATGAACAGGATGCAAAAAGTGGGGTT
1 TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
6577924 T
1 T
6577925 CTTATTATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.04, G:0.32, T:0.25
Consensus pattern (37 bp):
TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
Found at i:6583272 original size:21 final size:21
Alignment explanation
Indices: 6583242--6583281 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6583232 CCTCAATGCA
* *
6583242 ATTGGGTCATTGCGAGATGAC
1 ATTGGCTCATTACGAGATGAC
6583263 ATTGGCTCATTACGAGATG
1 ATTGGCTCATTACGAGATG
6583282 TAGTTAGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (21 bp):
ATTGGCTCATTACGAGATGAC
Found at i:6587669 original size:26 final size:26
Alignment explanation
Indices: 6587527--6587678 Score: 62
Period size: 26 Copynumber: 5.9 Consensus size: 26
6587517 AAACAATTTT
* * *
6587527 AAACAATTTAAAATAAACATTACATG
1 AAACAATTTAAAATAAATAATATATG
* * * * * **
6587553 AAATAGTTTAAAAGAAATGACACGT-
1 AAACAATTTAAAATAAATAATATATG
* * *
6587578 AAA-AATCTAAAATAAAGAATATACATA
1 AAACAATTTAAAATAAATAATAT--ATG
* *
6587605 AAACAGTTTAAGAT-AA-AATA-ATAG
1 AAACAATTTAAAATAAATAATATAT-G
**
6587629 AAAGCAATTCGAAATAAATAATATATG
1 AAA-CAATTTAAAATAAATAATATATG
**
6587656 AAACAATTTAAAATTGATAATAT
1 AAACAATTTAAAATAAATAATAT
6587679 CAAACAGTTT
Statistics
Matches: 89, Mismatches: 28, Indels: 18
0.66 0.21 0.13
Matches are distributed among these distances:
23 2 0.02
24 15 0.17
25 10 0.11
26 40 0.45
27 13 0.15
28 9 0.10
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (26 bp):
AAACAATTTAAAATAAATAATATATG
Found at i:6587720 original size:14 final size:14
Alignment explanation
Indices: 6587701--6587731 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6587691 TATGAACAAT
6587701 ATAAATAAAATGAA
1 ATAAATAAAATGAA
*
6587715 ATAAATAAAATGTA
1 ATAAATAAAATGAA
6587729 ATA
1 ATA
6587732 TGTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (14 bp):
ATAAATAAAATGAA
Found at i:6587776 original size:26 final size:26
Alignment explanation
Indices: 6587741--6587790 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
6587731 ATGTTTAAAA
6587741 AATAATAATAATGAATATAA-AAATTCG
1 AATAATAATAAT-AA-ATAACAAATTCG
6587768 AATAA-AATAATAAATAACAAATT
1 AATAATAATAATAAATAACAAATT
6587791 AAAGGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.18
25 7 0.32
26 6 0.27
27 5 0.23
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (26 bp):
AATAATAATAATAAATAACAAATTCG
Found at i:6588535 original size:15 final size:16
Alignment explanation
Indices: 6588515--6588545 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6588505 ATTATTTAGT
6588515 ATAAAAG-GAAAAAAA
1 ATAAAAGAGAAAAAAA
6588530 ATAAAAGAGAAAAAAA
1 ATAAAAGAGAAAAAAA
6588546 TCGAACAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (16 bp):
ATAAAAGAGAAAAAAA
Found at i:6612001 original size:69 final size:69
Alignment explanation
Indices: 6611886--6612209 Score: 323
Period size: 69 Copynumber: 4.9 Consensus size: 69
6611876 AAGCTTACAA
*
6611886 CTTCAAAATAGCTCGCGGACCTACGCT-CCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCG
1 CTTCAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCG
6611950 CAGC
66 CAGC
* * ** * * *
6611954 CTTCAAAACAGCTCGTGAACCTACATTCCCAACTGATATTATAAAGGCTCACCAGTTTAAGATCA
1 CTTCAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCG
6612019 CAGC
66 CAGC
* * * * * * *
6612023 CTCCAAAACAGTTCACGGACCTATGCTCCCAGCTAATATTATAAAGGCTCGCTGGTTTAAGATCG
1 CTTCAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCG
*
6612088 CAAC
66 CAGC
* ** * *
6612092 CTCCAAAACA--------A-C-A--CTCCCAGTTGATATTATAAAGACTCGCCGGTCTAAGATCG
1 CTTCAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCG
6612145 CAGC
66 CAGC
* * * * *
6612149 CTCCAAAATAGCTCGCGGACCTACGTTCCCAATTGATATTATAAAGGCTCGCTGGTTTAAG
1 CTTCAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAG
6612210 CCTCAAAAAC
Statistics
Matches: 208, Mismatches: 35, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
57 47 0.23
59 1 0.00
60 1 0.00
61 1 0.00
65 1 0.00
66 1 0.00
67 1 0.00
68 22 0.11
69 133 0.64
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (69 bp):
CTTCAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCG
CAGC
Found at i:6612141 original size:57 final size:57
Alignment explanation
Indices: 6612048--6612156 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
6612038 CGGACCTATG
* * *
6612048 CTCCCAGCTAATATTATAAAGGCTCGCTGGTTTAAGATCGCAACCTCCAAAACAACA
1 CTCCCAGCTAATATTATAAAGACTCGCCGGTCTAAGATCGCAACCTCCAAAACAACA
* * *
6612105 CTCCCAGTTGATATTATAAAGACTCGCCGGTCTAAGATCGCAGCCTCCAAAA
1 CTCCCAGCTAATATTATAAAGACTCGCCGGTCTAAGATCGCAACCTCCAAAA
6612157 TAGCTCGCGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (57 bp):
CTCCCAGCTAATATTATAAAGACTCGCCGGTCTAAGATCGCAACCTCCAAAACAACA
Found at i:6612268 original size:62 final size:62
Alignment explanation
Indices: 6612146--6612271 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 62
6612136 CTAAGATCGC
* * * * * * ** *
6612146 AGCCTCCAAAATAGCTCGCGGACCTACGTTCCCAATTGATATTATAAAGGCTCGCTGGTTTA
1 AGCCTCAAAAACAGCTCACGGACCTAAGTTCCCAACTAATATTATAAAGGCTAACCGGTTTA
* *
6612208 AGCCTCAAAAACAGCTCACGGACCTAAGTTCCTAGCTAATATTATAAAGGCTAACCGGTTTA
1 AGCCTCAAAAACAGCTCACGGACCTAAGTTCCCAACTAATATTATAAAGGCTAACCGGTTTA
6612270 AG
1 AG
6612272 ATCGTAACCT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (62 bp):
AGCCTCAAAAACAGCTCACGGACCTAAGTTCCCAACTAATATTATAAAGGCTAACCGGTTTA
Found at i:6614625 original size:22 final size:22
Alignment explanation
Indices: 6614583--6614627 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6614573 TATAATAAGA
**
6614583 TTTTAATTTAACATGCTTAATT
1 TTTTAATTTAACATGAATAATT
*
6614605 TTTTAATTTAACTTGAATAATT
1 TTTTAATTTAACATGAATAATT
6614627 T
1 T
6614628 CACTCGATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAATTTAACATGAATAATT
Found at i:6615960 original size:23 final size:20
Alignment explanation
Indices: 6615913--6615949 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
6615903 CAGTTAGTTT
*
6615913 TATGAGGTGGAATTAATTAA
1 TATGACGTGGAATTAATTAA
6615933 -ATGACGTGGAATTAATT
1 TATGACGTGGAATTAATT
6615950 TAAGATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (20 bp):
TATGACGTGGAATTAATTAA
Found at i:6617211 original size:521 final size:521
Alignment explanation
Indices: 6616230--6617260 Score: 2035
Period size: 521 Copynumber: 2.0 Consensus size: 521
6616220 TAAAAAATGG
6616230 GTCAGGCTGGGCCAGGCTCGGGCTTAGGAATTTTTTCTTGAGCCGGGCTTGGACAAAATTTCAGG
1 GTCAGGCTGGGCCAGGCTCGGGCTTAGGAATTTTTTCTTGAGCCGGGCTTGGACAAAATTTCAGG
6616295 CTCATTTTCAGGCCGGGCCAGGGCCTAGGACGTGGGCCAAAATTTTTTCTGGGCTCAGCCCGACC
66 CTCATTTTCAGGCCGGGCCAGGGCCTAGGACGTGGGCCAAAATTTTTTCTGGGCTCAGCCCGACC
6616360 CAGCCCATGAACACCTCTAAATTTATCCTGTCCTTTTTCTTTTTATTTTGAATGTAATAAACTCA
131 CAGCCCATGAACACCTCTAAATTTATCCTGTCCTTTTTCTTTTTATTTTGAATGTAATAAACTCA
6616425 AAGTGCTTACTTCAAACTATTAAAAGTAAAAGAAGCCATTTGCTTTATCTAAACCCAAGTATTGT
196 AAGTGCTTACTTCAAACTATTAAAAGTAAAAGAAGCCATTTGCTTTATCTAAACCCAAGTATTGT
6616490 AAAATCTCCTAAAAAAAAGGACACCTTCCTTATTATCATAAATCAATTTGGCGATTCCATCGGCA
261 AAAATCTCCTAAAAAAAAGGACACCTTCCTTATTATCATAAATCAATTTGGCGATTCCATCGGCA
6616555 ACTTGATTATTCTTCTTGGGAGCATACCTGAAAAACCACAATCTTCCATATTTTAATATATGTTT
326 ACTTGATTATTCTTCTTGGGAGCATACCTGAAAAACCACAATCTTCCATATTTTAATATATGTTT
6616620 GGTTCTTCTAACCAAGGTTGAATTTGCATCCGTTGATTGTCTATCTTCAATGACTTTAATCATTT
391 GGTTCTTCTAACCAAGGTTGAATTTGCATCCGTTGATTGTCTATCTTCAATGACTTTAATCATTT
* *
6616685 CCATGCTATCCGTATGAATCAACACTCTCTCATATCTTCGTTTGTTTAAAATAGTTTTATTAAAA
456 CCATGCTATCCGTATGAATCAACACACTCTCATATCTTCGTTTATTTAAAATAGTTTTATTAAAA
6616750 A
521 A
6616751 GTCAGGCTGGGCCAGGCTCGGGCTTAGGAATTTTTTCTTGAGCCGGGCTTGGACAAAATTTCAGG
1 GTCAGGCTGGGCCAGGCTCGGGCTTAGGAATTTTTTCTTGAGCCGGGCTTGGACAAAATTTCAGG
6616816 CTCATTTTCAGGCCGGGCCAGGGCCTAGGACGTGGGCCAAAATTTTTTCTGGGCTCAGCCCGACC
66 CTCATTTTCAGGCCGGGCCAGGGCCTAGGACGTGGGCCAAAATTTTTTCTGGGCTCAGCCCGACC
6616881 CAGCCCATGAACACCTCTAAATTTATCCTGTCCTTTTTCTTTTTATTTTGAATGTAATAAACTCA
131 CAGCCCATGAACACCTCTAAATTTATCCTGTCCTTTTTCTTTTTATTTTGAATGTAATAAACTCA
6616946 AAGTGCTTACTTCAAACTATTAAAAGTAAAAGAAGCCATTTGCTTTATCTAAACCCAAGTATTGT
196 AAGTGCTTACTTCAAACTATTAAAAGTAAAAGAAGCCATTTGCTTTATCTAAACCCAAGTATTGT
6617011 AAAATCTCCTAAAAAAAAGGACACCTTCCTTATTATCATAAATCAATTTGGCGATTCCATCGGCA
261 AAAATCTCCTAAAAAAAAGGACACCTTCCTTATTATCATAAATCAATTTGGCGATTCCATCGGCA
6617076 ACTTGATTATTCTTCTTGGGAGCATACCTGAAAAACCACAATCTTCCATATTTTAATATATGTTT
326 ACTTGATTATTCTTCTTGGGAGCATACCTGAAAAACCACAATCTTCCATATTTTAATATATGTTT
6617141 GGTTCTTCTAACCAAGGTTGAATTTGCATCCGTTGATTGTCTATCTTCAATGACTTTAATCATTT
391 GGTTCTTCTAACCAAGGTTGAATTTGCATCCGTTGATTGTCTATCTTCAATGACTTTAATCATTT
*
6617206 CCATGCTATCCGTATGAATCAACACACTCTCCTATCTTCGTTTATTTAAAATAGT
456 CCATGCTATCCGTATGAATCAACACACTCTCATATCTTCGTTTATTTAAAATAGT
6617261 CAGCCCATCC
Statistics
Matches: 507, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
521 507 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (521 bp):
GTCAGGCTGGGCCAGGCTCGGGCTTAGGAATTTTTTCTTGAGCCGGGCTTGGACAAAATTTCAGG
CTCATTTTCAGGCCGGGCCAGGGCCTAGGACGTGGGCCAAAATTTTTTCTGGGCTCAGCCCGACC
CAGCCCATGAACACCTCTAAATTTATCCTGTCCTTTTTCTTTTTATTTTGAATGTAATAAACTCA
AAGTGCTTACTTCAAACTATTAAAAGTAAAAGAAGCCATTTGCTTTATCTAAACCCAAGTATTGT
AAAATCTCCTAAAAAAAAGGACACCTTCCTTATTATCATAAATCAATTTGGCGATTCCATCGGCA
ACTTGATTATTCTTCTTGGGAGCATACCTGAAAAACCACAATCTTCCATATTTTAATATATGTTT
GGTTCTTCTAACCAAGGTTGAATTTGCATCCGTTGATTGTCTATCTTCAATGACTTTAATCATTT
CCATGCTATCCGTATGAATCAACACACTCTCATATCTTCGTTTATTTAAAATAGTTTTATTAAAA
A
Found at i:6619257 original size:14 final size:13
Alignment explanation
Indices: 6619224--6619254 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6619214 TAAATTAATT
6619224 TTTTAA-TAAAAA
1 TTTTAATTAAAAA
6619236 TTTTAATTAAAAA
1 TTTTAATTAAAAA
6619249 TTTTAA
1 TTTTAA
6619255 ATTTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAATTAAAAA
Found at i:6625850 original size:13 final size:14
Alignment explanation
Indices: 6625827--6625870 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
6625817 TTTTAGATTA
6625827 AAATATTATTTTTT
1 AAATATTATTTTTT
6625841 AAAT-TTATTTTTATT
1 AAATATTA-TTTT-TT
6625856 GAAATATTATTTTTT
1 -AAATATTATTTTTT
6625871 TTATAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 4 0.15
16 8 0.31
17 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
AAATATTATTTTTT
Found at i:6632391 original size:18 final size:19
Alignment explanation
Indices: 6632368--6632408 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
6632358 AGCACCACCT
*
6632368 ATAAAAAATAAA-AATTTA
1 ATAAAAAATAAATAAATTA
6632386 AT-AAAAATAAATAAATTA
1 ATAAAAAATAAATAAATTA
6632404 ATAAA
1 ATAAA
6632409 TTAAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 9 0.45
18 9 0.45
19 2 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAAAAATAAATAAATTA
Found at i:6632393 original size:17 final size:18
Alignment explanation
Indices: 6632371--6632408 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
6632361 ACCACCTATA
*
6632371 AAAAATAAA-AATTTAAT
1 AAAAATAAATAAATTAAT
6632388 AAAAATAAATAAATTAAT
1 AAAAATAAATAAATTAAT
6632406 AAA
1 AAA
6632409 TTAAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATAAATAAATTAAT
Found at i:6636460 original size:69 final size:68
Alignment explanation
Indices: 6636375--6636851 Score: 452
Period size: 69 Copynumber: 7.2 Consensus size: 68
6636365 CTTGCAACTT
* *
6636375 CAAAATAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCAGTTTAAGATCCCAG
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCC-GTTTAAGATCGCAG
*
6636440 CCTT
65 CCTC
* *
6636444 CAAGACAGCTCTCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCGATTTAAGATCGCAG
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCG-TTTAAGATCGCAG
*
6636509 CCTT
65 CCTC
* ** * *
6636513 CAAAACAGCTCGCGAACCTACATTCCCAACTGATATTATAAAGGCTCACCAGTTTAAGATCGTAG
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCC-GTTTAAGATCGCAG
6636578 CCTC
65 CCTC
* * * * * *
6636582 CAAAACAACTCACGGACCTACGCTCCCAGCTAATATTATAAAGGCTCGCTGGTTTAAGATCGCAA
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGC-CGTTTAAGATCGCAG
6636647 CCTC
65 CCTC
** * *
6636651 CAAAACA--------A-C-A--CTCCCAGTTGATATTATAAAGACTCGCCGATCTAAGATCGCAG
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCG-TTTAAGATCGCAG
6636704 CCTC
65 CCTC
* * **
6636708 CAAAACAGCTCGCGGACCTACGTTCCCAATTGATATTATAAAGGCTCGTTGGTTT-A-A--G--G
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCG-CCGTTTAAGATCGCAG
6636767 -CTC
65 CCTC
* * * * ** * *
6636770 CAAAACAGCTCACGGACCTACGTTCCCAGCTAATATTATAAAGGCTAACCGGTTTAAGATCGTAA
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCC-GTTTAAGATCGCAG
6636835 CCTC
65 CCTC
*
6636839 CAAAGCAGCTCGC
1 CAAAACAGCTCGC
6636852 AAACCTGCGT
Statistics
Matches: 337, Mismatches: 46, Indels: 50
0.78 0.11 0.12
Matches are distributed among these distances:
56 1 0.00
57 46 0.14
59 1 0.00
60 1 0.00
61 1 0.00
62 49 0.15
63 2 0.01
64 1 0.00
65 2 0.01
66 2 0.01
67 2 0.01
68 2 0.01
69 225 0.67
70 2 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (68 bp):
CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCGTTTAAGATCGCAGC
CTC
Found at i:6636697 original size:57 final size:57
Alignment explanation
Indices: 6636604--6636714 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
6636594 CGGACCTACG
* * * *
6636604 CTCCCAGCTAATATTATAAAGGCTCGCTGGTTTAAGATCGCAACCTCCAAAACAACA
1 CTCCCAGCTAATATTATAAAGACTCGCCGATCTAAGATCGCAACCTCCAAAACAACA
* * *
6636661 CTCCCAGTTGATATTATAAAGACTCGCCGATCTAAGATCGCAGCCTCCAAAACA
1 CTCCCAGCTAATATTATAAAGACTCGCCGATCTAAGATCGCAACCTCCAAAACA
6636715 GCTCGCGGAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (57 bp):
CTCCCAGCTAATATTATAAAGACTCGCCGATCTAAGATCGCAACCTCCAAAACAACA
Found at i:6636824 original size:62 final size:62
Alignment explanation
Indices: 6636705--6636827 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 62
6636695 AGATCGCAGC
* * * ****
6636705 CTCCAAAACAGCTCGCGGACCTACGTTCCCAATTGATATTATAAAGGCTCGTTGGTTTAAGG
1 CTCCAAAACAGCTCACGGACCTACGTTCCCAACTAATATTATAAAGGCTAACCGGTTTAAGG
*
6636767 CTCCAAAACAGCTCACGGACCTACGTTCCCAGCTAATATTATAAAGGCTAACCGGTTTAAG
1 CTCCAAAACAGCTCACGGACCTACGTTCCCAACTAATATTATAAAGGCTAACCGGTTTAAG
6636828 ATCGTAACCT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (62 bp):
CTCCAAAACAGCTCACGGACCTACGTTCCCAACTAATATTATAAAGGCTAACCGGTTTAAGG
Found at i:6636902 original size:257 final size:262
Alignment explanation
Indices: 6636405--6636908 Score: 615
Period size: 257 Copynumber: 1.9 Consensus size: 262
6636395 CGCTCCCAAC
* * * * *
6636405 TGATATTATAAAGGCTCGCCAGTTTAAGATCCCAGCCTTCAAGACAGCTCTCGGACCTACGCTCC
1 TGATATTATAAAGACTCGCCAGTCTAAGATCCCAGCCTCCAAAACAGCTCGCGGACCTACGCTCC
* *
6636470 CAACTGATATTATAAAGGCTCGCCGATTTAAGATCGCAGCCTTCAAAACAGCTCGCGAACCTACA
66 CAACTGATATTATAAAGGCTCGCCGATTTAAGA-CG-AGCCTCCAAAACAGCTCACGAACCTACA
* * * **
6636535 TTCCCAACTGATATTATAAAGGCTCACCAGTTTAAGATCGTAGCCTCCAAAACAACTCACGGACC
129 TTCCCAACTAATATTATAAAGGCTAACCAGTTTAAGATCGTAACCTCCAAAACAACTCACAAACC
* *
6636600 TACGCTCCCAGCTAATATTATAAAGGCTCGCTGGTTTAAGATCGCAACCTCCAAAACAACACTCC
194 TACGCTCCCAGCTAATATTATAAAGGCTAGCTGATTTAAGATCGCAACCTCCAAAACAACACTCC
6636665 CAGT
259 CAGT
* *
6636669 TGATATTATAAAGACTCGCC-GATCTAAGATCGCAGCCTCCAAAACAGCTCGCGGACCTACGTTC
1 TGATATTATAAAGACTCGCCAG-TCTAAGATCCCAGCCTCCAAAACAGCTCGCGGACCTACGCTC
* ** * * *
6636733 CCAATTGATATTATAAAGGCTCGTTGGTTT-A-A-G-G-CTCCAAAACAGCTCACGGACCTACGT
65 CCAACTGATATTATAAAGGCTCGCCGATTTAAGACGAGCCTCCAAAACAGCTCACGAACCTACAT
* * * * *
6636793 TCCCAGCTAATATTATAAAGGCTAACCGGTTTAAGATCGTAACCTCCAAAGCAGCTCGCAAACCT
130 TCCCAACTAATATTATAAAGGCTAACCAGTTTAAGATCGTAACCTCCAAAACAACTCACAAACCT
* * ** * * * * *
6636858 GCGTTCTTAGCTGATATTATAAAGGTTAGTTGATTTAGGATCGCAGCCTCC
195 ACGCTCCCAGCTAATATTATAAAGGCTAGCTGATTTAAGATCGCAACCTCC
6636909 GAACAGTTCG
Statistics
Matches: 203, Mismatches: 36, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
257 117 0.58
258 1 0.00
260 1 0.00
262 1 0.00
263 2 0.01
264 81 0.40
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (262 bp):
TGATATTATAAAGACTCGCCAGTCTAAGATCCCAGCCTCCAAAACAGCTCGCGGACCTACGCTCC
CAACTGATATTATAAAGGCTCGCCGATTTAAGACGAGCCTCCAAAACAGCTCACGAACCTACATT
CCCAACTAATATTATAAAGGCTAACCAGTTTAAGATCGTAACCTCCAAAACAACTCACAAACCTA
CGCTCCCAGCTAATATTATAAAGGCTAGCTGATTTAAGATCGCAACCTCCAAAACAACACTCCCA
GT
Found at i:6637917 original size:36 final size:37
Alignment explanation
Indices: 6637876--6637948 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 37
6637866 TAATAAATAT
6637876 ATATTTTTTATTTTTTATTTTTAAAA-ATATTTAAAA
1 ATATTTTTTATTTTTTATTTTTAAAATATATTTAAAA
*
6637912 ATATTTTTTATTTTTTATTTTTAAAATATTTTTAAAA
1 ATATTTTTTATTTTTTATTTTTAAAATATATTTAAAA
6637949 TAAGTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (37 bp):
ATATTTTTTATTTTTTATTTTTAAAATATATTTAAAA
Found at i:6637957 original size:37 final size:36
Alignment explanation
Indices: 6637880--6637957 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 36
6637870 AAATATATAT
*
6637880 TTTTTATTTTTTATTTTTAAAAATATTTAAAAATAT
1 TTTTTATTTTTTATTTTTAAAAATATTTAAAAATAG
*
6637916 TTTTTATTTTTTATTTTT-AAAATATTTTTAAAATAAG
1 TTTTTATTTTTTATTTTTAAAAATA-TTTAAAAAT-AG
6637953 TTTTT
1 TTTTT
6637958 TAATTTTCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 6 0.16
36 26 0.68
37 6 0.16
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (36 bp):
TTTTTATTTTTTATTTTTAAAAATATTTAAAAATAG
Found at i:6640175 original size:4 final size:4
Alignment explanation
Indices: 6640166--6640237 Score: 68
Period size: 4 Copynumber: 19.5 Consensus size: 4
6640156 ATCGGGGAGG
* *
6640166 AAGA AAGA AAGG AAGA AAGA AA-A AAAA AAGA AA-A AGAGA AAGA AAG-
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA
6640212 AAGA AAG- AAG- AAG- AAG- AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
6640238 AAGAAGAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
3 20 0.33
4 38 0.63
5 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:6640199 original size:6 final size:6
Alignment explanation
Indices: 6640181--6640268 Score: 74
Period size: 6 Copynumber: 14.5 Consensus size: 6
6640171 AGAAAGGAAG
* *
6640181 AAAGAA AAA-AA AAAGAA AAAGAG AAAGAA AGAAGAA AGAAGAA GAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA A-AAGAA AAAGAA
* * *
6640230 GAAAGAA AAAGAA GAA-AA AAATAA AATA-AA AAATAA AAA
1 -AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAA
6640269 ATTTTCAACA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
5 10 0.14
6 42 0.60
7 18 0.26
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:6640205 original size:23 final size:23
Alignment explanation
Indices: 6640179--6640248 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
6640169 AAAGAAAGGA
6640179 AGAAAGAAAAAAAAAAGAAAAAG
1 AGAAAGAAAAAAAAAAGAAAAAG
* * *
6640202 AGAAAGAAAGAAGAAAGAAGAAG
1 AGAAAGAAAAAAAAAAGAAAAAG
6640225 A-AGAAGAAAGAAAAAGAAGAAAAA
1 AGA-AAGAAA-AAAAA-AAGAAAAA
6640249 AATAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 27 0.71
24 3 0.08
25 7 0.18
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (23 bp):
AGAAAGAAAAAAAAAAGAAAAAG
Found at i:6640241 original size:16 final size:16
Alignment explanation
Indices: 6640165--6640245 Score: 89
Period size: 16 Copynumber: 5.2 Consensus size: 16
6640155 GATCGGGGAG
*
6640165 GAAGAAAG-AAAGGAA
1 GAAGAAAGAAAAAGAA
6640180 GAAAGAAA-AAAAA-AA
1 G-AAGAAAGAAAAAGAA
*
6640195 GAA-AAAGAGAAAGAAA
1 GAAGAAAGAAAAAG-AA
*
6640211 GAAGAAAGAAGAAGAA
1 GAAGAAAGAAAAAGAA
6640227 GAAGAAAGAAAAAGAA
1 GAAGAAAGAAAAAGAA
6640243 GAA
1 GAA
6640246 AAAAATAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
13 3 0.05
14 6 0.11
15 4 0.07
16 34 0.62
17 8 0.15
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
GAAGAAAGAAAAAGAA
Found at i:6640255 original size:16 final size:16
Alignment explanation
Indices: 6640177--6640255 Score: 65
Period size: 16 Copynumber: 4.8 Consensus size: 16
6640167 AGAAAGAAAG
6640177 GAAGAAAGAAAAAA-AA
1 GAAGAAA-AAAAAAGAA
6640193 -AAGAAAAAGAGAAAGAAA
1 GAAGAAAAA-A-AAAG-AA
* *
6640211 GAAGAAAGAAGAAGAA
1 GAAGAAAAAAAAAGAA
*
6640227 GAAGAAAGAAAAAGAA
1 GAAGAAAAAAAAAGAA
6640243 GAA-AAAAATAAAA
1 GAAGAAAAA-AAAA
6640256 TAAAAAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.04
15 11 0.21
16 27 0.51
17 3 0.06
18 3 0.06
19 7 0.13
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (16 bp):
GAAGAAAAAAAAAGAA
Found at i:6640426 original size:25 final size:24
Alignment explanation
Indices: 6640398--6640448 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
6640388 CAAAATAGAA
6640398 AAAGAAGCAGCAGAAAAA-AAGAAAG
1 AAAGAAGCAG-A-AAAAAGAAGAAAG
6640423 AAAGAAGCAGAAAAAAGAAGAAAG
1 AAAGAAGCAGAAAAAAGAAGAAAG
6640447 AA
1 AA
6640449 GCAGGCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.20
24 10 0.40
25 10 0.40
ACGTcount: A:0.71, C:0.06, G:0.24, T:0.00
Consensus pattern (24 bp):
AAAGAAGCAGAAAAAAGAAGAAAG
Found at i:6640443 original size:20 final size:22
Alignment explanation
Indices: 6640398--6640452 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
6640388 CAAAATAGAA
*
6640398 AAAG-AAGCAGCAGAAAAAAAG
1 AAAGAAAGAAGCAGAAAAAAAG
6640419 AAAGAAAGAAGCAG-AAAAAAG
1 AAAGAAAGAAGCAGAAAAAAAG
6640440 -AAGAAAGAAGCAG
1 AAAGAAAGAAGCAG
6640453 GCCATTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 13 0.41
21 11 0.34
22 8 0.25
ACGTcount: A:0.67, C:0.07, G:0.25, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAGCAGAAAAAAAG
Found at i:6640596 original size:13 final size:13
Alignment explanation
Indices: 6640578--6640621 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
6640568 GCAGGGCAAA
6640578 AAAAAAAGAGAAG
1 AAAAAAAGAGAAG
*
6640591 AAAAAAAGGGAAG
1 AAAAAAAGAGAAG
6640604 -AAAAAAGA-AA-
1 AAAAAAAGAGAAG
6640614 AAAAAAAG
1 AAAAAAAG
6640622 TTCAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 9 0.32
12 7 0.25
13 12 0.43
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAAG
Found at i:6640790 original size:8 final size:7
Alignment explanation
Indices: 6640760--6640796 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
6640750 TATTTTTGTA
*
6640760 TTTATAT
1 TTTAAAT
6640767 TTTAAAT
1 TTTAAAT
6640774 TTTAAAT
1 TTTAAAT
*
6640781 TTTAAAA
1 TTTAAAT
6640788 TTTAAAT
1 TTTAAAT
6640795 TT
1 TT
6640797 AATTCAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAAAT
Found at i:6640820 original size:23 final size:24
Alignment explanation
Indices: 6640778--6640823 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
6640768 TTAAATTTTA
6640778 AATTTTAAAATTTAAATTTAATTC
1 AATTTTAAAATTTAAATTTAATTC
* *
6640802 AATTTT-AATTTTAATTTTAATT
1 AATTTTAAAATTTAAATTTAATT
6640824 TATTTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTTTAAAATTTAAATTTAATTC
Found at i:6640825 original size:11 final size:11
Alignment explanation
Indices: 6640786--6640829 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
6640776 TAAATTTTAA
*
6640786 AATTTAAATTT
1 AATTTAATTTT
*
6640797 AATTCAATTTT
1 AATTTAATTTT
6640808 AATTTTAATTTT
1 AA-TTTAATTTT
6640820 AATTT-ATTTT
1 AATTTAATTTT
6640830 GAATACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 10 0.34
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
AATTTAATTTT
Found at i:6640995 original size:18 final size:19
Alignment explanation
Indices: 6640974--6641022 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
6640964 AATCTCATGG
6640974 TTTCAAAAAATTTC-TATC
1 TTTCAAAAAATTTCGTATC
** *
6640992 TTTCAAAATTTTTCGTGTC
1 TTTCAAAAAATTTCGTATC
6641011 -TTCAAAAAATTT
1 TTTCAAAAAATTT
6641023 TTCTCGTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (19 bp):
TTTCAAAAAATTTCGTATC
Found at i:6641021 original size:20 final size:21
Alignment explanation
Indices: 6640996--6641040 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
6640986 TCTATCTTTC
6640996 AAAA-TTTT-TCGTGTCTTCAA
1 AAAATTTTTCTCGTGT-TTCAA
6641016 AAAATTTTTCTCGTGTTTCAA
1 AAAATTTTTCTCGTGTTTCAA
6641037 AAAA
1 AAAA
6641041 AAATATTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.17
21 13 0.57
22 6 0.26
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (21 bp):
AAAATTTTTCTCGTGTTTCAA
Found at i:6641200 original size:18 final size:18
Alignment explanation
Indices: 6641179--6641241 Score: 74
Period size: 17 Copynumber: 3.5 Consensus size: 18
6641169 TTTGTGTAAA
*
6641179 AAAAATTTCCCGTGTTTC
1 AAAAATTTCTCGTGTTTC
* *
6641197 AAAAATTT-TCTTGTTTT
1 AAAAATTTCTCGTGTTTC
*
6641214 AAAAAATTCTCGTGTTTTC
1 AAAAATTTCTCGTG-TTTC
6641233 AAAAATTTC
1 AAAAATTTC
6641242 AGTGTTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 13 0.36
18 12 0.33
19 11 0.31
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.44
Consensus pattern (18 bp):
AAAAATTTCTCGTGTTTC
Found at i:6641211 original size:17 final size:18
Alignment explanation
Indices: 6641179--6641240 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
6641169 TTTGTGTAAA
*
6641179 AAAAATTTCCCGTG-TTTC
1 AAAAATTT-TCGTGTTTTC
* *
6641197 AAAAATTTTCTTGTTTTA
1 AAAAATTTTCGTGTTTTC
*
6641215 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
6641233 AAAAATTT
1 AAAAATTT
6641241 CAGTGTTTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 3 0.08
18 33 0.92
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:6641246 original size:18 final size:17
Alignment explanation
Indices: 6641179--6641248 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
6641169 TTTGTGTAAA
6641179 AAAAATTTCCCGTG-TTTC
1 AAAAATTT--CGTGTTTTC
* *
6641197 AAAAATTTTCTTGTTTTA
1 AAAAA-TTTCGTGTTTTC
6641215 AAAAATTCTCGTGTTTTC
1 AAAAATT-TCGTGTTTTC
6641233 AAAAATTTCAGTGTTT
1 AAAAATTTC-GTGTTT
6641249 ATTTCGATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.16
18 34 0.77
19 3 0.07
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:6641248 original size:36 final size:36
Alignment explanation
Indices: 6641178--6641248 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
6641168 GTTTGTGTAA
*
6641178 AAAAAATTTCCCGTGTTTCAAAAATTTTCTTGTTTT
1 AAAAAATTTCCCGTGTTTCAAAAATTTTCGTGTTTT
*
6641214 AAAAAA-TTCTCGTGTTTTCAAAAA-TTTCAGTGTTT
1 AAAAAATTTCCCGTG-TTTCAAAAATTTTC-GTGTTT
6641249 ATTTCGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 11 0.35
36 20 0.65
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (36 bp):
AAAAAATTTCCCGTGTTTCAAAAATTTTCGTGTTTT
Found at i:6641354 original size:17 final size:17
Alignment explanation
Indices: 6641319--6641408 Score: 85
Period size: 17 Copynumber: 5.3 Consensus size: 17
6641309 TTTTTTTTTT
* *
6641319 AATTTGCGT-TTTGAAA
1 AATTTTCGTGTTTCAAA
*
6641335 AATTCTCGTGTTTCAAA
1 AATTTTCGTGTTTCAAA
* *
6641352 AATTGTCGTGTTTTAAAAA
1 AATTTTCGTG-TTT-CAAA
*
6641371 AATTTTCGTGTTTCTAA
1 AATTTTCGTGTTTCAAA
*
6641388 AATTTTCATG-TTCAAA
1 AATTTTCGTGTTTCAAA
6641404 AATTT
1 AATTT
6641409 CGTTTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
16 17 0.28
17 26 0.43
18 6 0.10
19 12 0.20
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (17 bp):
AATTTTCGTGTTTCAAA
Found at i:6641373 original size:19 final size:19
Alignment explanation
Indices: 6641332--6641389 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
6641322 TTGCGTTTTG
*
6641332 AAAAATTCTCGTG-TTT-C
1 AAAAATTCTCGTGTTTTAA
*
6641349 AAAAATTGTCGTGTTTTAA
1 AAAAATTCTCGTGTTTTAA
*
6641368 AAAAATTTTCGTGTTTCTAA
1 AAAAATTCTCGTGTTT-TAA
6641388 AA
1 AA
6641390 TTTTCATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.34
18 3 0.09
19 15 0.43
20 5 0.14
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (19 bp):
AAAAATTCTCGTGTTTTAA
Found at i:6647310 original size:114 final size:115
Alignment explanation
Indices: 6647171--6647406 Score: 447
Period size: 114 Copynumber: 2.1 Consensus size: 115
6647161 GAAAATGAGC
*
6647171 AAATTGATCTCTCTCAACAAAAATTACAAAAAAAATCAAAATAATTTTCAAAATTTTTAACTATT
1 AAATTAATCTCTCTCAACAAAAATTACAAAAAAAATCAAAATAATTTTCAAAATTTTTAACTATT
6647236 TATAAAAATTTCAAAAAATATATATGTAAAAAATATATAAAGAAATTTAA
66 TATAAAAATTTCAAAAAATATATATGTAAAAAATATATAAAGAAATTTAA
6647286 AAATTAATCTCTCTC-ACAAAAATTACAAAAAAAATCAAAATAATTTTCAAAATTTTTAACTATT
1 AAATTAATCTCTCTCAACAAAAATTACAAAAAAAATCAAAATAATTTTCAAAATTTTTAACTATT
*
6647350 TATAAAAATTTCAAAAAATATATATGTAAAAAATTTATAAAGAAATTTAA
66 TATAAAAATTTCAAAAAATATATATGTAAAAAATATATAAAGAAATTTAA
6647400 AAATTAA
1 AAATTAA
6647407 AAATTTTCTA
Statistics
Matches: 119, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
114 105 0.88
115 14 0.12
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.33
Consensus pattern (115 bp):
AAATTAATCTCTCTCAACAAAAATTACAAAAAAAATCAAAATAATTTTCAAAATTTTTAACTATT
TATAAAAATTTCAAAAAATATATATGTAAAAAATATATAAAGAAATTTAA
Found at i:6648097 original size:4 final size:4
Alignment explanation
Indices: 6648088--6648159 Score: 68
Period size: 4 Copynumber: 19.5 Consensus size: 4
6648078 ATCGGGGAGG
* *
6648088 AAGA AAGA AAGG AAGA AAGA AA-A AAAA AAGA AA-A AGAGA AAGA AAG-
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA
6648134 AAGA AAG- AAG- AAG- AAG- AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
6648160 AAGAAGAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
3 20 0.33
4 38 0.63
5 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:6648121 original size:6 final size:6
Alignment explanation
Indices: 6648103--6648190 Score: 74
Period size: 6 Copynumber: 14.5 Consensus size: 6
6648093 AGAAAGGAAG
* *
6648103 AAAGAA AAA-AA AAAGAA AAAGAG AAAGAA AGAAGAA AGAAGAA GAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA A-AAGAA AAAGAA
* * *
6648152 GAAAGAA AAAGAA GAA-AA AAATAA AATA-AA AAATAA AAA
1 -AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAA
6648191 ATTTTCAACA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
5 10 0.14
6 42 0.60
7 18 0.26
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:6648127 original size:23 final size:23
Alignment explanation
Indices: 6648101--6648170 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
6648091 AAAGAAAGGA
6648101 AGAAAGAAAAAAAAAAGAAAAAG
1 AGAAAGAAAAAAAAAAGAAAAAG
* * *
6648124 AGAAAGAAAGAAGAAAGAAGAAG
1 AGAAAGAAAAAAAAAAGAAAAAG
6648147 A-AGAAGAAAGAAAAAGAAGAAAAA
1 AGA-AAGAAA-AAAAA-AAGAAAAA
6648171 AATAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 27 0.71
24 3 0.08
25 7 0.18
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (23 bp):
AGAAAGAAAAAAAAAAGAAAAAG
Found at i:6648163 original size:16 final size:16
Alignment explanation
Indices: 6648087--6648167 Score: 89
Period size: 16 Copynumber: 5.2 Consensus size: 16
6648077 GATCGGGGAG
*
6648087 GAAGAAAG-AAAGGAA
1 GAAGAAAGAAAAAGAA
6648102 GAAAGAAA-AAAAA-AA
1 G-AAGAAAGAAAAAGAA
*
6648117 GAA-AAAGAGAAAGAAA
1 GAAGAAAGAAAAAG-AA
*
6648133 GAAGAAAGAAGAAGAA
1 GAAGAAAGAAAAAGAA
6648149 GAAGAAAGAAAAAGAA
1 GAAGAAAGAAAAAGAA
6648165 GAA
1 GAA
6648168 AAAAATAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
13 3 0.05
14 6 0.11
15 4 0.07
16 34 0.62
17 8 0.15
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
GAAGAAAGAAAAAGAA
Found at i:6648177 original size:16 final size:16
Alignment explanation
Indices: 6648099--6648177 Score: 65
Period size: 16 Copynumber: 4.8 Consensus size: 16
6648089 AGAAAGAAAG
6648099 GAAGAAAGAAAAAA-AA
1 GAAGAAA-AAAAAAGAA
6648115 -AAGAAAAAGAGAAAGAAA
1 GAAGAAAAA-A-AAAG-AA
* *
6648133 GAAGAAAGAAGAAGAA
1 GAAGAAAAAAAAAGAA
*
6648149 GAAGAAAGAAAAAGAA
1 GAAGAAAAAAAAAGAA
6648165 GAA-AAAAATAAAA
1 GAAGAAAAA-AAAA
6648178 TAAAAAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.04
15 11 0.21
16 27 0.51
17 3 0.06
18 3 0.06
19 7 0.13
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (16 bp):
GAAGAAAAAAAAAGAA
Found at i:6648348 original size:25 final size:24
Alignment explanation
Indices: 6648320--6648370 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
6648310 CAAAATAGAA
6648320 AAAGAAGCAGCAGAAAAA-AAGAAAG
1 AAAGAAGCAG-A-AAAAAGAAGAAAG
6648345 AAAGAAGCAGAAAAAAGAAGAAAG
1 AAAGAAGCAGAAAAAAGAAGAAAG
6648369 AA
1 AA
6648371 GCAGGCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.20
24 10 0.40
25 10 0.40
ACGTcount: A:0.71, C:0.06, G:0.24, T:0.00
Consensus pattern (24 bp):
AAAGAAGCAGAAAAAAGAAGAAAG
Found at i:6648365 original size:20 final size:22
Alignment explanation
Indices: 6648320--6648374 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
6648310 CAAAATAGAA
*
6648320 AAAG-AAGCAGCAGAAAAAAAG
1 AAAGAAAGAAGCAGAAAAAAAG
6648341 AAAGAAAGAAGCAG-AAAAAAG
1 AAAGAAAGAAGCAGAAAAAAAG
6648362 -AAGAAAGAAGCAG
1 AAAGAAAGAAGCAG
6648375 GCCATTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 13 0.41
21 11 0.34
22 8 0.25
ACGTcount: A:0.67, C:0.07, G:0.25, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAGCAGAAAAAAAG
Found at i:6648518 original size:13 final size:13
Alignment explanation
Indices: 6648500--6648543 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
6648490 GCAGGGCAAA
6648500 AAAAAAAGAGAAG
1 AAAAAAAGAGAAG
*
6648513 AAAAAAAGGGAAG
1 AAAAAAAGAGAAG
6648526 -AAAAAAGA-AA-
1 AAAAAAAGAGAAG
6648536 AAAAAAAG
1 AAAAAAAG
6648544 TTCAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 9 0.32
12 7 0.25
13 12 0.43
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAAG
Found at i:6648712 original size:8 final size:7
Alignment explanation
Indices: 6648682--6648718 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
6648672 TATTTTTGTA
*
6648682 TTTATAT
1 TTTAAAT
6648689 TTTAAAT
1 TTTAAAT
6648696 TTTAAAT
1 TTTAAAT
*
6648703 TTTAAAA
1 TTTAAAT
6648710 TTTAAAT
1 TTTAAAT
6648717 TT
1 TT
6648719 AATTCAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAAAT
Found at i:6648742 original size:23 final size:24
Alignment explanation
Indices: 6648700--6648745 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
6648690 TTAAATTTTA
6648700 AATTTTAAAATTTAAATTTAATTC
1 AATTTTAAAATTTAAATTTAATTC
* *
6648724 AATTTT-AATTTTAATTTTAATT
1 AATTTTAAAATTTAAATTTAATT
6648746 TATTTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTTTAAAATTTAAATTTAATTC
Found at i:6648747 original size:11 final size:11
Alignment explanation
Indices: 6648708--6648751 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
6648698 TAAATTTTAA
*
6648708 AATTTAAATTT
1 AATTTAATTTT
*
6648719 AATTCAATTTT
1 AATTTAATTTT
6648730 AATTTTAATTTT
1 AA-TTTAATTTT
6648742 AATTT-ATTTT
1 AATTTAATTTT
6648752 GAATACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 10 0.34
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
AATTTAATTTT
Found at i:6648941 original size:27 final size:27
Alignment explanation
Indices: 6648911--6648966 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
6648901 CAAAATAATT
*
6648911 TTCAAAA-ATTCAAAATAAATTTTAAAA
1 TTCAAAATATTCAAAA-AAATTCTAAAA
* *
6648938 TTCAAAATATTTATAAAAATTCTAAAA
1 TTCAAAATATTCAAAAAAATTCTAAAA
6648965 TT
1 TT
6648967 TATAGTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (27 bp):
TTCAAAATATTCAAAAAAATTCTAAAA
Found at i:6648958 original size:19 final size:19
Alignment explanation
Indices: 6648894--6648965 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
6648884 AAATTACAAA
*
6648894 AAAAAATCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
6648913 CAAAAATTCAAAATAAATTTT
1 -AAAAATTCAAAAT-AATTTT
6648934 -AAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
6648952 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
6648966 TTATAGTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 19 0.40
20 17 0.36
21 6 0.13
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:6652414 original size:14 final size:13
Alignment explanation
Indices: 6652381--6652411 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6652371 TAAATTAATT
6652381 TTTTAA-TAAAAA
1 TTTTAATTAAAAA
6652393 TTTTAATTAAAAA
1 TTTTAATTAAAAA
6652406 TTTTAA
1 TTTTAA
6652412 ATTTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAATTAAAAA
Found at i:6653434 original size:29 final size:29
Alignment explanation
Indices: 6653389--6653451 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
6653379 ATTAGATTTG
* *
6653389 AAATTTTAAAATTTAAAAATA-AAGTGATT
1 AAATTTTAAAATATAAAAATATAA-AGATT
6653418 AAATTTCTAAAA-ATAAAAATATAAAGATT
1 AAATTT-TAAAATATAAAAATATAAAGATT
6653447 AAATT
1 AAATT
6653452 ACAAATATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (29 bp):
AAATTTTAAAATATAAAAATATAAAGATT
Found at i:6664139 original size:17 final size:17
Alignment explanation
Indices: 6664100--6664133 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6664090 CTCTTCCTCC
6664100 GATTTCTTCTCATCTAG
1 GATTTCTTCTCATCTAG
6664117 GATTTCTTCTCATCTAG
1 GATTTCTTCTCATCTAG
6664134 CGTTTCAGTG
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:0.18, C:0.24, G:0.12, T:0.47
Consensus pattern (17 bp):
GATTTCTTCTCATCTAG
Found at i:6664659 original size:40 final size:39
Alignment explanation
Indices: 6664572--6664659 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
6664562 NNNNNNNNCC
** *
6664572 CAACCCAATAAAACTAAAACTAAAGTTTACCCAATTACT
1 CAACCCAATAAAACTAAAACTAAAGACTACCCAATTACA
* * **
6664611 CAATCCAATAAAATTAAAACTAAAAGACTACCCAATTTGA
1 CAACCCAATAAAACTAAAACT-AAAGACTACCCAATTACA
6664651 CAACCCAAT
1 CAACCCAAT
6664660 TTACTAAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 19 0.47
40 21 0.52
ACGTcount: A:0.50, C:0.25, G:0.03, T:0.22
Consensus pattern (39 bp):
CAACCCAATAAAACTAAAACTAAAGACTACCCAATTACA
Found at i:6664746 original size:9 final size:9
Alignment explanation
Indices: 6664734--6664828 Score: 129
Period size: 9 Copynumber: 10.4 Consensus size: 9
6664724 AAATAAAAAA
6664734 AATTCGGGT
1 AATTCGGGT
6664743 AATTCGGGT
1 AATTCGGGT
*
6664752 ATTTTTC-GGT
1 A--ATTCGGGT
*
6664762 AATTCGGTT
1 AATTCGGGT
*
6664771 AATTCGGTT
1 AATTCGGGT
6664780 AATTCGGGT
1 AATTCGGGT
*
6664789 AATTCGGTT
1 AATTCGGGT
6664798 AATTCGGGT
1 AATTCGGGT
6664807 AATTCGGGT
1 AATTCGGGT
6664816 AATTCGGGT
1 AATTCGGGT
6664825 AATT
1 AATT
6664829 TTTAACCAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
8 3 0.04
9 67 0.87
10 4 0.05
11 3 0.04
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:6665876 original size:36 final size:36
Alignment explanation
Indices: 6665819--6665888 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
6665809 ACTAACTAAT
* *
6665819 GTAAACCATAAACCCCTAACCCCTATCCCCTAAATC
1 GTAAAACATAAACCCCTAACCCCTAACCCCTAAATC
* *
6665855 GTAAAACATAAA-CCGTAAACCCCTAACCCTTAAA
1 GTAAAACATAAACCCCT-AACCCCTAACCCCTAAA
6665889 CCCCAACCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 3 0.10
36 26 0.90
ACGTcount: A:0.41, C:0.36, G:0.04, T:0.19
Consensus pattern (36 bp):
GTAAAACATAAACCCCTAACCCCTAACCCCTAAATC
Found at i:6665897 original size:14 final size:15
Alignment explanation
Indices: 6665870--6665900 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
6665860 ACATAAACCG
6665870 TAAACCCCTAACCCT
1 TAAACCCCTAACCCT
6665885 TAAACCCC-AACCCT
1 TAAACCCCTAACCCT
6665899 TA
1 TA
6665901 TAACTGTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAACCCCTAACCCT
Found at i:6667131 original size:41 final size:41
Alignment explanation
Indices: 6667023--6667227 Score: 245
Period size: 41 Copynumber: 5.0 Consensus size: 41
6667013 TATGATAAAT
* *
6667023 CTGAGCATTAGCGGCGCTTCTTCATAAACGCCGCTAAA--A
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
* *
6667062 ATAGAGTATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
1 CT-GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
* * *
6667104 CTGAGCACTAGTGGCGCTTCTTTAAAAACGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
*
6667145 CTAAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAG-C
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
* * * * * *
6667185 CTCGAGCATTAGAGGCACTTTTTAAAAAAAGCCGCTAATGCC
1 CT-GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
6667227 C
1 C
6667228 CCAAAAACTC
Statistics
Matches: 141, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 37 0.26
41 100 0.71
42 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
Found at i:6667314 original size:39 final size:38
Alignment explanation
Indices: 6667278--6667410 Score: 122
Period size: 40 Copynumber: 3.3 Consensus size: 38
6667268 CGCTTTTTGG
6667278 AAAACGCCGCTAATGCTCATTTTTAGTGGCGTTTTTTA
1 AAAACGCCGCTAATGCTCATTTTTAGTGGCGTTTTTTA
* * * * * *
6667316 AAAAGTGCAGCTAATACTCGATCTTTAGTGACGTTTTTTTT
1 AAAA-CGCCGCTAATGCTC-ATTTTTAGTGGCG-TTTTTTA
* * *
6667357 AAAGCGCCACTAATGCTTGATTTTTAGTGGCGTTTTTTA
1 AAAACGCCGCTAATGC-TCATTTTTAGTGGCGTTTTTTA
*
6667396 TCCAAACGCCGCTAA
1 --AAAACGCCGCTAA
6667411 AAGCCTGTTT
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
38 4 0.06
39 17 0.24
40 30 0.42
41 20 0.28
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (38 bp):
AAAACGCCGCTAATGCTCATTTTTAGTGGCGTTTTTTA
Found at i:6667351 original size:40 final size:41
Alignment explanation
Indices: 6667278--6667395 Score: 138
Period size: 40 Copynumber: 3.0 Consensus size: 41
6667268 CGCTTTTTGG
6667278 AAAA-CGCC-GCTAATGCTC-ATTTTTAGTGGCGTTTTTTA
1 AAAAGCGCCAGCTAATGCTCGATTTTTAGTGGCGTTTTTTA
* * * * *
6667316 AAAAGTG-CAGCTAATACTCGATCTTTAGTGACGTTTTTTT
1 AAAAGCGCCAGCTAATGCTCGATTTTTAGTGGCGTTTTTTA
* *
6667356 TAAAGCGCCA-CTAATGCTTGATTTTTAGTGGCGTTTTTTA
1 AAAAGCGCCAGCTAATGCTCGATTTTTAGTGGCGTTTTTTA
6667396 TCCAAACGCC
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
38 5 0.08
39 10 0.16
40 47 0.73
41 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (41 bp):
AAAAGCGCCAGCTAATGCTCGATTTTTAGTGGCGTTTTTTA
Found at i:6672520 original size:35 final size:36
Alignment explanation
Indices: 6672480--6672548 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 36
6672470 TAAAATTATG
* *
6672480 AAAA-TGTAAAAAGATATATATATATATATAAAAAT
1 AAAAGTGTAAAAAGATATAGATACATATATAAAAAT
* *
6672515 AAAATGTGTAAACAGATGTAGATACATATATAAA
1 AAAA-GTGTAAAAAGATATAGATACATATATAAA
6672549 TTATACAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 4 0.14
37 24 0.86
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.29
Consensus pattern (36 bp):
AAAAGTGTAAAAAGATATAGATACATATATAAAAAT
Found at i:6672963 original size:3 final size:3
Alignment explanation
Indices: 6672955--6673005 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
6672945 AAGATGAAAC
*
6672955 TAA TAA TAA TTAA TAG TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6673000 TAA TAA
1 TAA TAA
6673006 CACTAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6672997 original size:20 final size:20
Alignment explanation
Indices: 6672955--6673017 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
6672945 AAGATGAAAC
*
6672955 TAATAATAATTAATAGTAATAA
1 TAATAATAA-TAATA-AAATAA
6672977 TAATAATAATAATAAAATAA
1 TAATAATAATAATAAAATAA
* *
6672997 TAATAATAACACTAAAATAA
1 TAATAATAATAATAAAATAA
6673017 T
1 T
6673018 TAGTTAAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 24 0.63
21 5 0.13
22 9 0.24
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (20 bp):
TAATAATAATAATAAAATAA
Found at i:6673017 original size:14 final size:14
Alignment explanation
Indices: 6672955--6673005 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
6672945 AAGATGAAAC
*
6672955 TAATAAT-AATTAA
1 TAATAATAAAATAA
*
6672968 TAGTAATAATAATAA
1 TAATAATAA-AATAA
6672983 TAATAATAAAATAA
1 TAATAATAAAATAA
6672997 TAATAATAA
1 TAATAATAA
6673006 CACTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.18
14 15 0.45
15 12 0.36
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
TAATAATAAAATAA
Found at i:6674941 original size:2 final size:2
Alignment explanation
Indices: 6674934--6674960 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6674924 TTTCTGCTAA
6674934 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
6674961 TTTTTTTACA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:6679271 original size:31 final size:32
Alignment explanation
Indices: 6679236--6679305 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
6679226 AATTTTTTAA
* *
6679236 TTAAATTTAGCTCTTAA-TCTTTTAAAAAGAG
1 TTAAATTTAACTATTAATTCTTTTAAAAAGAG
* *
6679267 TTAAATTTAATTATTAATTTTTTTAAAAAGAG
1 TTAAATTTAACTATTAATTCTTTTAAAAAGAG
6679299 TTAAATT
1 TTAAATT
6679306 AAATTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.41
32 20 0.59
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (32 bp):
TTAAATTTAACTATTAATTCTTTTAAAAAGAG
Found at i:6680277 original size:28 final size:28
Alignment explanation
Indices: 6680237--6680292 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
6680227 AGGTCCTTTG
6680237 GATTTTCCTTGGTTCACACGTGAATTAA
1 GATTTTCCTTGGTTCACACGTGAATTAA
6680265 GATTTTCCTTGGTTCACACGTGAATTAA
1 GATTTTCCTTGGTTCACACGTGAATTAA
6680293 CTTCCTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (28 bp):
GATTTTCCTTGGTTCACACGTGAATTAA
Found at i:6691860 original size:20 final size:21
Alignment explanation
Indices: 6691820--6691872 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
6691810 AAATACAAAT
*
6691820 ATAATCATAATATATATTCAA
1 ATAATCATAATATATAATCAA
*
6691841 ATAATTATAA-ATATAATCAA
1 ATAATCATAATATATAATCAA
6691861 ATCAAT-ATAATA
1 AT-AATCATAATA
6691873 CACAATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAATCATAATATATAATCAA
Found at i:6692304 original size:59 final size:59
Alignment explanation
Indices: 6692175--6692317 Score: 146
Period size: 59 Copynumber: 2.4 Consensus size: 59
6692165 AAGAAATATC
* * * *
6692175 AAGGATTAACTTGGATAAAAAAAAGTTCAGGCATCAAAGTGGATACAATTGTCAAGCTT
1 AAGGACTAACTTGGACAAAAAAAAGTTCAGGCATCAAAGTGAAAACAATTGTCAAGCTT
* * * * *
6692234 AAGGACCAACTTGGACAAATAAAAGTTCAGGC-CCTAATGTGAAAACAATTGTTAAG-TT
1 AAGGACTAACTTGGACAAAAAAAAGTTCAGGCATC-AAAGTGAAAACAATTGTCAAGCTT
* *
6692292 CAGAGACTAACTTGAAACAAAAAAAA
1 AAG-GACTAACTTG-GACAAAAAAAA
6692318 AATTTTAAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
58 5 0.07
59 54 0.79
60 9 0.13
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.22
Consensus pattern (59 bp):
AAGGACTAACTTGGACAAAAAAAAGTTCAGGCATCAAAGTGAAAACAATTGTCAAGCTT
Found at i:6692658 original size:1 final size:1
Alignment explanation
Indices: 6692652--6692688 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
6692642 TCCCTTCTTC
* *
6692652 TTTTTTTTTTTTTTTTTTTTTTTTCTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6692689 GCTTAAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:6715481 original size:21 final size:21
Alignment explanation
Indices: 6715453--6715514 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
6715443 ACTTCTATTT
*
6715453 AACCCTTATGGGTTTTTGTTC
1 AACCCTTATGGGTTTCTGTTC
* * * * *
6715474 AACTCTTACGAGCTTCCGTTC
1 AACCCTTATGGGTTTCTGTTC
6715495 AACCCTTATGGGTTTCTGTT
1 AACCCTTATGGGTTTCTGTT
6715515 TAGCTCTCAT
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
AACCCTTATGGGTTTCTGTTC
Found at i:6715529 original size:42 final size:42
Alignment explanation
Indices: 6715382--6715537 Score: 111
Period size: 42 Copynumber: 3.7 Consensus size: 42
6715372 CGTGTTTACT
* * * * * *
6715382 TTTC-GTTTAGCTCTCACGAGCTTCTGTTTAACTCATATGAG
1 TTTCTGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGG
* * * * ** *
6715423 TTTCCGTTCAGCT-TTATTGAACTTCTATTTAACCCTTATGGG
1 TTTCTGTTCAGCTCTCA-CGAGCTTCCGTTCAACCCTTATGGG
* * *
6715465 TTTTTGTTCAACTCTTACGAGCTTCCGTTCAACCCTTATGGG
1 TTTCTGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGG
* *
6715507 TTTCTGTTTAGCTCTCATGAGC-TCCTGTTCA
1 TTTCTGTTCAGCTCTCACGAGCTTCC-GTTCA
6715538 GCCTTCGGGC
Statistics
Matches: 90, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
41 9 0.10
42 78 0.87
43 3 0.03
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGG
Found at i:6721021 original size:3 final size:3
Alignment explanation
Indices: 6721013--6721038 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6721003 TGGTCAGTGT
6721013 CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CT
6721039 TTTAGATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:6727824 original size:14 final size:14
Alignment explanation
Indices: 6727805--6727833 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6727795 ATCATTTCAC
6727805 TATTATGTTGTTAT
1 TATTATGTTGTTAT
6727819 TATTATGTTGTTAT
1 TATTATGTTGTTAT
6727833 T
1 T
6727834 GTATAACTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (14 bp):
TATTATGTTGTTAT
Found at i:6728988 original size:27 final size:28
Alignment explanation
Indices: 6728951--6729007 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
6728941 TTGACTGGAT
* *
6728951 TTTAATAATTTTTATTTTTAATATTTCA
1 TTTAATAATTTTTAGTATTAATATTTCA
*
6728979 TTTAAT-ATTTTTGGTATTAATATTTCA
1 TTTAATAATTTTTAGTATTAATATTTCA
6729006 TT
1 TT
6729008 AAAGTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTAATAATTTTTAGTATTAATATTTCA
Found at i:6729315 original size:11 final size:11
Alignment explanation
Indices: 6729299--6729332 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
6729289 TTTTCCCAAT
6729299 TTTTACTATTA
1 TTTTACTATTA
*
6729310 TTTTACTACTA
1 TTTTACTATTA
*
6729321 TTTTACCATTA
1 TTTTACTATTA
6729332 T
1 T
6729333 GCTGTTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTACTATTA
Found at i:6729961 original size:29 final size:28
Alignment explanation
Indices: 6729886--6729957 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 28
6729876 AGATAAATCT
*
6729886 TAAAATTATACATGAATTTTAATTTAATG
1 TAAAATTATACATGAATTTTAATTT-AGG
*
6729915 TATAATTATATACATGAATTTTAATTT-GG
1 TA-AAAT-TATACATGAATTTTAATTTAGG
6729944 TAAAATTATACATG
1 TAAAATTATACATG
6729958 TGAAACTCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 8 0.21
28 3 0.08
29 5 0.13
30 3 0.08
31 19 0.50
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (28 bp):
TAAAATTATACATGAATTTTAATTTAGG
Found at i:6731026 original size:123 final size:124
Alignment explanation
Indices: 6730832--6731358 Score: 734
Period size: 123 Copynumber: 4.2 Consensus size: 124
6730822 TTTGCAGTCA
* * * * * *
6730832 CGCCCACGTGTACGCGCTTTTGCTACAGTCGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTG
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCAAGTTGACGTTTATG
*
6730897 AGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCG
66 AGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCG
* * *
6730956 CGCCCTCCTAGACGCGCTTTTGCTACAGTAGGT-CTGAAAAAATTATTTCAAGTTGACGTTTATG
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCAAGTTGACGTTTATG
* * * * *
6731020 AGCAAATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAGAAGAATTTGTGAAATCG
66 AGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCG
6731079 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGT-CTGAAAAAATTATTTCAAGTTGACGTTTATG
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCAAGTTGACGTTTATG
* * * *
6731143 AGCAAATAGTATAAAAAACGCTTCAAGTAGGATGTTATTTGAGAAGAATTTCTGAAATCG
66 AGCAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCG
* * * ** * * *
6731203 CGCCCTCGTGGACGCACTTTTGCTACAGTTGGTCCTGGTAGAATTAATTTCGAGTTGACGTTTCT
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATT-ATTTCAAGTTGACGTTTAT
* * * *
6731268 GAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTTTATGAGAAGAATTTATGAAATCG
65 GAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCG
*
6731328 CGCCCACGTGGACGCGCTTTTGCTATAGTAG
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAG
6731359 CATGTATGGG
Statistics
Matches: 354, Mismatches: 46, Indels: 5
0.87 0.11 0.01
Matches are distributed among these distances:
123 153 0.43
124 96 0.27
125 75 0.21
126 30 0.08
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (124 bp):
CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCAAGTTGACGTTTATG
AGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCG
Found at i:6731335 original size:249 final size:247
Alignment explanation
Indices: 6730832--6731358 Score: 804
Period size: 249 Copynumber: 2.1 Consensus size: 247
6730822 TTTGCAGTCA
* * * * *
6730832 CGCCCACGTGTACGCGCTTTTGCTACAGTCGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTG
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAAGTTGACGTTTATG
* *
6730897 AGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGCGCCCT
66 AGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCGCCCT
*
6730962 CCTAGACGCGCTTTTGCTACAGTAGGTCTGAAAAAATTATTTCAAGTTGACGTTTATGAGCAAAT
131 CCTAGACGCACTTTTGCTACAGTAGGTCTGAAAAAATTATTTCAAGTTGACGTTTATGAGCAAAT
*
6731027 AGTATAAAATCGCTTCTACCAAGATGCTTTATGAGAAGAATTTGTGAAATCG
196 AGTATAAAATCGCTTCTACCAAGATGCTTTATGAGAAGAATTTATGAAATCG
*
6731079 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGT-CTGAAAAAATTATTTCAAGTTGACGTTTATG
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAAGTTGACGTTTATG
* * *
6731143 AGCAAATAGTATAAAAAACGCTTCAAGTAGGATGTTATTTGAGAAGAATTTCTGAAATCGCGCCC
66 AGCAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCGCCC
* * * ** * * *
6731208 TCGTGGACGCACTTTTGCTACAGTTGGTCCTGGTAGAATTAATTTCGAGTTGACGTTTCTGAGCA
130 TCCTAGACGCACTTTTGCTACAGTAGGT-CTGAAAAAATT-ATTTCAAGTTGACGTTTATGAGCA
* *
6731273 AATAGTATAAAATCGCTTCTAGCAGGATGCTTTATGAGAAGAATTTATGAAATCG
193 AATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAGAAGAATTTATGAAATCG
*
6731328 CGCCCACGTGGACGCGCTTTTGCTATAGTAG
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAG
6731359 CATGTATGGG
Statistics
Matches: 253, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
246 39 0.15
247 102 0.40
248 8 0.03
249 104 0.41
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (247 bp):
CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAAGTTGACGTTTATG
AGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCGCCCT
CCTAGACGCACTTTTGCTACAGTAGGTCTGAAAAAATTATTTCAAGTTGACGTTTATGAGCAAAT
AGTATAAAATCGCTTCTACCAAGATGCTTTATGAGAAGAATTTATGAAATCG
Found at i:6733561 original size:29 final size:29
Alignment explanation
Indices: 6733512--6733567 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
6733502 TAATGGTTAA
* *
6733512 TTTAGGTTTTACGATTTAGGGTTTAGGTT
1 TTTAGGTTTTAAGATTAAGGGTTTAGGTT
6733541 TTTAGGTTTTAA-AGTTAAGGGTTTAGG
1 TTTAGGTTTTAAGA-TTAAGGGTTTAGG
6733568 ATATAGGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.21, C:0.02, G:0.29, T:0.48
Consensus pattern (29 bp):
TTTAGGTTTTAAGATTAAGGGTTTAGGTT
Found at i:6733575 original size:43 final size:42
Alignment explanation
Indices: 6733512--6733678 Score: 144
Period size: 43 Copynumber: 3.9 Consensus size: 42
6733502 TAATGGTTAA
* * *
6733512 TTTAGGTTTTACGATTTAGGGTTTAGGTTTTTAGGTTTTAAAG
1 TTTAGGGTTTAAGATATAGGGTTTAGGTTTTTAGG-TTTAAAG
* * * *
6733555 TTAAGGGTTTAGGATATAGGG-TTAGAGGTTTTAGGTTAAAAG
1 TTTAGGGTTTAAGATATAGGGTTTAG-GTTTTTAGGTTTAAAG
* * *
6733597 TTTAGGGTTTTAAG-TAAAAGGTTTAAGGTTTTTAGGTTTAGAG
1 TTTAGGG-TTTAAGATATAGGGTTT-AGGTTTTTAGGTTTAAAG
* *
6733640 TTTAGGGTTTTAAGTTA-AAGGTTATA-GTTTTTAGGTTTA
1 TTTAGGG-TTTAAGATATAGGGTT-TAGGTTTTTAGGTTTA
6733679 GGGTTAATGG
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
42 34 0.32
43 66 0.63
44 5 0.05
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.46
Consensus pattern (42 bp):
TTTAGGGTTTAAGATATAGGGTTTAGGTTTTTAGGTTTAAAG
Found at i:6733605 original size:21 final size:21
Alignment explanation
Indices: 6733532--6733676 Score: 98
Period size: 21 Copynumber: 6.8 Consensus size: 21
6733522 ACGATTTAGG
* *
6733532 GTTTAGGTTTTTAGGTTTTAAA
1 GTTTAGGGTTTTAGG-TTAAAA
* * * *
6733554 GTTAAGGG-TTTAGGATATAG
1 GTTTAGGGTTTTAGGTTAAAA
*
6733574 GGTTAGAGGTTTTAGGTTAAAA
1 GTTTAG-GGTTTTAGGTTAAAA
*
6733596 GTTTAGGGTTTTAAG-TAAAA
1 GTTTAGGGTTTTAGGTTAAAA
* * *
6733616 GGTTTAAGGTTTTTAGGTTTAGA
1 -GTTT-AGGGTTTTAGGTTAAAA
* *
6733639 GTTTAGGGTTTTAAGTTAAAG
1 GTTTAGGGTTTTAGGTTAAAA
*
6733660 GTTATA-GTTTTTAGGTT
1 GTT-TAGGGTTTTAGGTT
6733677 TAGGGTTAAT
Statistics
Matches: 93, Mismatches: 24, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
20 11 0.12
21 44 0.47
22 35 0.38
23 3 0.03
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.45
Consensus pattern (21 bp):
GTTTAGGGTTTTAGGTTAAAA
Found at i:6733624 original size:7 final size:7
Alignment explanation
Indices: 6733614--6733914 Score: 91
Period size: 7 Copynumber: 42.0 Consensus size: 7
6733604 TTTTAAGTAA
6733614 AAGGTTT
1 AAGGTTT
6733621 AAGGTTTT
1 AAGG-TTT
*
6733629 TAGGTTT
1 AAGGTTT
6733636 -AGAGTTT
1 AAG-GTTT
*
6733643 AGGGTTTT
1 AAGG-TTT
*
6733651 AA-GTTA
1 AAGGTTT
6733657 AAGG-TT
1 AAGGTTT
*
6733663 ATAGTTTT
1 A-AGGTTT
*
6733671 TAGGTTT
1 AAGGTTT
*
6733678 -AGGGTT
1 AAGGTTT
6733684 AATGGTTTTT
1 AA-GG--TTT
*
6733694 AA-TTTT
1 AAGGTTT
*
6733700 AAAGTTT
1 AAGGTTT
6733707 AAGGTTTT
1 AAGG-TTT
6733715 AAGGTTTT
1 AAGG-TTT
*
6733723 AAAGTTTT
1 -AAGGTTT
*
6733731 TAGGTTT
1 AAGGTTT
6733738 -AGAGTTT
1 AAG-GTTT
6733745 -AGTGTTT
1 AAG-GTTT
6733752 -AGAGTTT
1 AAG-GTTT
6733759 -AGAGTTT
1 AAG-GTTT
6733766 AAGGTTTTT
1 AAGG--TTT
6733775 AA-G-TT
1 AAGGTTT
*
6733780 AATAG-TT
1 AA-GGTTT
*
6733787 ATGGTTT
1 AAGGTTT
6733794 -AGAGTTT
1 AAG-GTTT
6733801 AGAGGTTTT
1 A-AGG-TTT
6733810 AA-G-TT
1 AAGGTTT
6733815 AAGGTTT
1 AAGGTTT
*
6733822 AGGGTTT
1 AAGGTTT
6733829 -AGTGTTT
1 AAG-GTTT
6733836 AAGGTTT
1 AAGGTTT
*
6733843 AGGGTTT
1 AAGGTTT
6733850 AAGGTTTTT
1 AAGG--TTT
6733859 AA-GTTT
1 AAGGTTT
6733865 AAAGGTTT
1 -AAGGTTT
*
6733873 -AGAATTT
1 AAG-GTTT
*
6733880 AGGGTTT
1 AAGGTTT
6733887 AAGGTTT
1 AAGGTTT
6733894 -AGAGTTT
1 AAG-GTTT
6733901 AAGGTTT
1 AAGGTTT
6733908 AAGGTTT
1 AAGGTTT
6733915 TTAAGTTAAG
Statistics
Matches: 228, Mismatches: 29, Indels: 74
0.69 0.09 0.22
Matches are distributed among these distances:
5 8 0.04
6 31 0.14
7 122 0.54
8 44 0.19
9 19 0.08
10 4 0.02
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (7 bp):
AAGGTTT
Found at i:6733672 original size:64 final size:64
Alignment explanation
Indices: 6733576--6733717 Score: 144
Period size: 64 Copynumber: 2.2 Consensus size: 64
6733566 GGATATAGGG
* * * *
6733576 TTAGAGGTTTTAGGTTAAAAGTTTAGGGTTTTAAGTAAAAGGTTTAA-GGTTTTTAGGTTTAGAG
1 TTAG-GGTTTTAAGTTAAAAGTTTAGGGTTTTAAGT-AAAGGGTTAATGGTTTTTAAGTTTAAAG
6733640 T
64 T
* * * ** *
6733641 TTAGGGTTTTAAGTTAAAGGTTATA-GTTTTTAGGTTTAGGGTTAATGGTTTTTAATTTTAAAGT
1 TTAGGGTTTTAAGTTAAAAGTT-TAGGGTTTTAAGTAAAGGGTTAATGGTTTTTAAGTTTAAAGT
*
6733705 TTAAGGTTTTAAG
1 TTAGGGTTTTAAG
6733718 GTTTTAAAGT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
63 7 0.11
64 51 0.80
65 6 0.09
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.46
Consensus pattern (64 bp):
TTAGGGTTTTAAGTTAAAAGTTTAGGGTTTTAAGTAAAGGGTTAATGGTTTTTAAGTTTAAAGT
Found at i:6733691 original size:42 final size:43
Alignment explanation
Indices: 6733531--6733721 Score: 153
Period size: 43 Copynumber: 4.5 Consensus size: 43
6733521 TACGATTTAG
* * *
6733531 GGTTT-AGGTTTTTAGGTTTTAAAGTTAAGGG-TTT-AGGATATA
1 GGTTTAAGGTTTTTAGG-TTTAGAGTTAAGGGTTTTAAGTA-AAA
* * * *
6733573 GGGTTAGAGG-TTTTAGGTTAAAAGTTTAGGGTTTTAAGTAAAA
1 GGTTTA-AGGTTTTTAGGTTTAGAGTTAAGGGTTTTAAGTAAAA
* *
6733616 GGTTTAAGGTTTTTAGGTTTAGAGTTTAGGGTTTTAAGTTAAA
1 GGTTTAAGGTTTTTAGGTTTAGAGTTAAGGGTTTTAAGTAAAA
* * * *
6733659 GG-TTATA-GTTTTTAGGTTTAGGGTTAATGGTTTTTAATTTTAAA
1 GGTTTA-AGGTTTTTAGGTTTAGAGTTAA-GGGTTTTAA-GTAAAA
*
6733703 -GTTTAAGGTTTTAAGGTTT
1 GGTTTAAGGTTTTTAGGTTT
6733722 TAAAGTTTTT
Statistics
Matches: 125, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
42 40 0.32
43 60 0.48
44 25 0.20
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (43 bp):
GGTTTAAGGTTTTTAGGTTTAGAGTTAAGGGTTTTAAGTAAAA
Found at i:6733708 original size:23 final size:22
Alignment explanation
Indices: 6733580--6733729 Score: 82
Period size: 21 Copynumber: 7.0 Consensus size: 22
6733570 ATAGGGTTAG
* *
6733580 AGGTTTT-AGGTTAAAAGTTTA
1 AGGTTTTAAGTTTTAAAGTTTA
* *
6733601 GGGTTTTAAG--TAAAAGGTTTA
1 AGGTTTTAAGTTTTAAA-GTTTA
* * *
6733622 AGGTTTTTAGGTTTAGAGTTTA
1 AGGTTTTAAGTTTTAAAGTTTA
* *
6733644 GGGTTTTAAG--TTAAAGGTTA
1 AGGTTTTAAGTTTTAAAGTTTA
* * * *
6733664 TA-GTTTTTAGGTTT-AGGGTTA
1 -AGGTTTTAAGTTTTAAAGTTTA
6733685 ATGGTTTTTAA-TTTTAAAGTTTA
1 A-GG-TTTTAAGTTTTAAAGTTTA
6733708 AGGTTTTAAGGTTTTAAAGTTT
1 AGGTTTTAA-GTTTTAAAGTTT
6733730 TTAGGTTTAG
Statistics
Matches: 100, Mismatches: 16, Indels: 24
0.71 0.11 0.17
Matches are distributed among these distances:
20 21 0.21
21 31 0.31
22 23 0.23
23 25 0.25
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (22 bp):
AGGTTTTAAGTTTTAAAGTTTA
Found at i:6733717 original size:8 final size:8
Alignment explanation
Indices: 6733704--6733737 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
6733694 AATTTTAAAG
6733704 TTTAAGGT
1 TTTAAGGT
6733712 TTTAAGGT
1 TTTAAGGT
*
6733720 TTTAAAGT
1 TTTAAGGT
*
6733728 TTTTAGGT
1 TTTAAGGT
6733736 TT
1 TT
6733738 AGAGTTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.56
Consensus pattern (8 bp):
TTTAAGGT
Done.