Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 19 of 150
Found at i:5107445 original size:2 final size:2
Alignment explanation
Indices: 5107438--5107468 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5107428 TCAATTATCA
5107438 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 A
5107469 CATTTATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5110698 original size:22 final size:22
Alignment explanation
Indices: 5110671--5110713 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5110661 TACTTTTTAA
5110671 TTTAATTT-TTAATAGAATAATT
1 TTTAATTTATT-ATAGAATAATT
*
5110693 TTTAATTTATTATATAATAAT
1 TTTAATTTATTATAGAATAAT
5110714 ATTATTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAATTTATTATAGAATAATT
Found at i:5111213 original size:12 final size:13
Alignment explanation
Indices: 5111196--5111225 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5111186 GACTAAAAAA
5111196 TTCTTCTT-CTTT
1 TTCTTCTTCCTTT
5111208 TTCTTCTTCCTTT
1 TTCTTCTTCCTTT
5111221 TTCTT
1 TTCTT
5111226 TTTATGGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTCTTCTTCCTTT
Found at i:5114097 original size:22 final size:21
Alignment explanation
Indices: 5114063--5114103 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5114053 CATTTAATTA
*
5114063 ATTTTTTTAAATTTAAAAAAT
1 ATTTTTTAAAATTTAAAAAAT
*
5114084 ATTTTTTAATAATTTTAAAA
1 ATTTTTTAA-AATTTAAAAA
5114104 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTTAAAATTTAAAAAAT
Found at i:5114138 original size:33 final size:31
Alignment explanation
Indices: 5114066--5114179 Score: 149
Period size: 33 Copynumber: 3.6 Consensus size: 31
5114056 TTAATTAATT
* **
5114066 TTTTTAAATTTAAAAAATA-TTTTTTAATAA
1 TTTTTAAATTTTAAAAATAGTTTTTTTTTAA
*
5114096 TTTTAAAATTTTAAAAATAGTTTTCTTTTTAAA
1 TTTTTAAATTTTAAAAATAGTTTT-TTTTT-AA
5114129 TTTTTAAATTTTAAAAATAGTTTTTTTTCTGAA
1 TTTTTAAATTTTAAAAATAGTTTTTTTT-T-AA
5114162 TTTTTAAATTTTAAAAAT
1 TTTTTAAATTTTAAAAAT
5114180 TAATTAAATG
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
30 17 0.23
31 4 0.05
32 7 0.09
33 46 0.62
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (31 bp):
TTTTTAAATTTTAAAAATAGTTTTTTTTTAA
Found at i:5116250 original size:22 final size:22
Alignment explanation
Indices: 5116220--5116262 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5116210 ACAGCAGAAC
* *
5116220 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
5116242 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
5116263 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:5116484 original size:43 final size:43
Alignment explanation
Indices: 5116334--5116482 Score: 239
Period size: 43 Copynumber: 3.5 Consensus size: 43
5116324 ACGTCACTAA
* *
5116334 CTTTTGCGGCGCTTACGTAAAA-AAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-G-AAAACAAACGCCGCTAAAGATCATGCT
5116378 CTTTAGCGGCGCTTAGAAAACAAACGCCGCTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAACAAACGCCGCTAAAGATCATGCT
*
5116421 CTTTAGCGGCGCTTAGAAAACAAACGCC-CTAAAGATCACGCT
1 CTTTAGCGGCGCTTAGAAAACAAACGCCGCTAAAGATCATGCT
5116463 CTTTAGCGGCGCTTAGAAAA
1 CTTTAGCGGCGCTTAGAAAA
5116483 ACGCCACTAA
Statistics
Matches: 101, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
42 37 0.37
43 50 0.50
44 14 0.14
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (43 bp):
CTTTAGCGGCGCTTAGAAAACAAACGCCGCTAAAGATCATGCT
Found at i:5116964 original size:22 final size:21
Alignment explanation
Indices: 5116921--5116964 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
5116911 CCTTCTGTAA
* *
5116921 TGGAAAAAAAAAAGGTTGAGT
1 TGGAAAAAAAAAAGATTAAGT
*
5116942 TGGAAAAAGAAAAATATTAAGT
1 TGGAAAAA-AAAAAGATTAAGT
5116964 T
1 T
5116965 ATCATTAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (21 bp):
TGGAAAAAAAAAAGATTAAGT
Found at i:5117127 original size:22 final size:22
Alignment explanation
Indices: 5117097--5117139 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5117087 ACAGCAGAAC
* *
5117097 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
5117119 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
5117140 AACACCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:5117287 original size:43 final size:42
Alignment explanation
Indices: 5117213--5117522 Score: 358
Period size: 43 Copynumber: 7.3 Consensus size: 42
5117203 GTCACTAACT
5117213 TTTA-CGGCGCTTATGTAAAAAAACGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGCTTA-G-AAAAAAACGCCGCTAAAGATCATGTTC
* *
5117256 TTTAGCGGCGCTTAGAAAACAAACGCTGCTAAAGATCATGCTC
1 TTTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGTTC
* * *
5117299 TTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTC
1 TTTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGTTC
* *
5117342 TTTAGCGGCGCTTAG--AAAAACGCCCCTAAAGATCATGCTC
1 TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTC
* * * * *
5117382 TTTAGTGACGCTTATAAAAAAATGCCTCTAAAGATCATGTTC
1 TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTC
*
5117424 TTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTC
* * ** * *
5117466 TTTAGCGGTGCTTTGGAAGGAAACGCCTCTAAA-AGTAATGTTC
1 TTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTTC
*
5117509 TATAGCGGCGCTTA
1 TTTAGCGGCGCTTA
5117523 TTTCACAAAC
Statistics
Matches: 233, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
40 34 0.15
41 2 0.01
42 75 0.32
43 113 0.48
44 9 0.04
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTC
Found at i:5117974 original size:12 final size:12
Alignment explanation
Indices: 5117942--5117981 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5117932 TTTTGAACCT
* *
5117942 CTGCTTCTATTG
1 CTGCTTCTCTCG
5117954 CTGCTTCTCTCG
1 CTGCTTCTCTCG
*
5117966 CTGCTTCTCTCA
1 CTGCTTCTCTCG
5117978 CTGC
1 CTGC
5117982 GGCCTCTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.05, C:0.38, G:0.15, T:0.42
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:5117996 original size:21 final size:21
Alignment explanation
Indices: 5117966--5118034 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
5117956 GCTTCTCTCG
*
5117966 CTGCTTCTCTCACTGCGGCCT
1 CTGCTTCTCTCACTGCAGCCT
* * *
5117987 CTGTTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCACTGCAGCCT
* *
5118008 CTGCTTCCCTCACTGCCGCCT
1 CTGCTTCTCTCACTGCAGCCT
5118029 CTGCTT
1 CTGCTT
5118035 TAAGTTGCTG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.04, C:0.42, G:0.17, T:0.36
Consensus pattern (21 bp):
CTGCTTCTCTCACTGCAGCCT
Found at i:5123506 original size:16 final size:17
Alignment explanation
Indices: 5123485--5123583 Score: 73
Period size: 16 Copynumber: 5.9 Consensus size: 17
5123475 GATTTAGGAA
5123485 TAAGTTATGTA-TTATG
1 TAAGTTATGTAGTTATG
*
5123501 TAAGTTATGTAAGTTGTG
1 TAAGTTATGT-AGTTATG
* *
5123519 TAAGTTGTGTAAGTTGTG
1 TAAGTTATGT-AGTTATG
* *
5123537 T-A-TTATGAAACTTATG
1 TAAGTTATG-TAGTTATG
* *
5123553 TACGTTATGT-CTTATG
1 TAAGTTATGTAGTTATG
5123569 TAAGTTATGTA-TTAT
1 TAAGTTATGTAGTTAT
5123584 TATGTAAGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
16 39 0.57
17 2 0.03
18 27 0.40
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.47
Consensus pattern (17 bp):
TAAGTTATGTAGTTATG
Found at i:5123510 original size:9 final size:9
Alignment explanation
Indices: 5123485--5123592 Score: 86
Period size: 9 Copynumber: 12.6 Consensus size: 9
5123475 GATTTAGGAA
5123485 TAAGTTATG
1 TAAGTTATG
5123494 T-A-TTATG
1 TAAGTTATG
5123501 TAAGTTATG
1 TAAGTTATG
*
5123510 TAAGTTGTG
1 TAAGTTATG
*
5123519 TAAGTTGTG
1 TAAGTTATG
*
5123528 TAAGTTGTG
1 TAAGTTATG
5123537 T-A-TTATG
1 TAAGTTATG
* *
5123544 AAACTTATG
1 TAAGTTATG
*
5123553 TACGTTATG
1 TAAGTTATG
*
5123562 T--CTTATG
1 TAAGTTATG
5123569 TAAGTTATG
1 TAAGTTATG
5123578 TATTA-TTATG
1 TA--AGTTATG
5123588 TAAGT
1 TAAGT
5123593 AGGGATGTAG
Statistics
Matches: 82, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
7 16 0.20
8 5 0.06
9 53 0.65
10 7 0.09
11 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:5123674 original size:10 final size:11
Alignment explanation
Indices: 5123659--5123720 Score: 74
Period size: 12 Copynumber: 5.5 Consensus size: 11
5123649 TTTATGGATG
5123659 TTATGTA-TTA
1 TTATGTAGTTA
5123669 TTATGTA-TTA
1 TTATGTAGTTA
5123679 TTATGTAAGTTA
1 TTATGT-AGTTA
5123691 TTATGTAGGTTA
1 TTATGTA-GTTA
*
5123703 TTATGTAAGTCA
1 TTATGT-AGTTA
5123715 TTATGT
1 TTATGT
5123721 TGGTTATGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
10 16 0.34
11 2 0.04
12 28 0.60
13 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (11 bp):
TTATGTAGTTA
Found at i:5123693 original size:12 final size:12
Alignment explanation
Indices: 5123666--5123720 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
5123656 ATGTTATGTA
5123666 TTATTATGT-A-
1 TTATTATGTAAG
5123676 TTATTATGTAAG
1 TTATTATGTAAG
*
5123688 TTATTATGTAGG
1 TTATTATGTAAG
5123700 TTATTATGTAAG
1 TTATTATGTAAG
*
5123712 TCATTATGT
1 TTATTATGT
5123721 TGGTTATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
10 9 0.22
11 1 0.03
12 30 0.75
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:5123708 original size:24 final size:24
Alignment explanation
Indices: 5123659--5123727 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
5123649 TTTATGGATG
5123659 TTATGT-A-TTATTATGTA--TTA
1 TTATGTAAGTTATTATGTAGGTTA
5123679 TTATGTAAGTTATTATGTAGGTTA
1 TTATGTAAGTTATTATGTAGGTTA
* *
5123703 TTATGTAAGTCATTATGTTGGTTA
1 TTATGTAAGTTATTATGTAGGTTA
5123727 T
1 T
5123728 GTAAGTTGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.14
21 1 0.02
22 10 0.23
24 26 0.60
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.54
Consensus pattern (24 bp):
TTATGTAAGTTATTATGTAGGTTA
Found at i:5123729 original size:21 final size:22
Alignment explanation
Indices: 5123679--5123733 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
5123669 TTATGTATTA
*
5123679 TTATGTAAGTTATTATGTAGGTT
1 TTATGTAAGTCATTATGTAGG-T
*
5123702 ATTATGTAAGTCATTATGTTGG-
1 -TTATGTAAGTCATTATGTAGGT
5123724 TTATGTAAGT
1 TTATGTAAGT
5123734 TGTGATATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
24 19 0.66
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (22 bp):
TTATGTAAGTCATTATGTAGGT
Found at i:5123882 original size:19 final size:19
Alignment explanation
Indices: 5123858--5123920 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
5123848 ATGTATCAAT
5123858 TTTTAAAAATATATATAAA
1 TTTTAAAAATATATATAAA
* *
5123877 TTTTAAATATATATATATA
1 TTTTAAAAATATATATAAA
* *
5123896 -TATATAAACTATATATAAA
1 TTTTA-AAAATATATATAAA
*
5123915 TATTAA
1 TTTTAA
5123921 TAAGTTATGT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
18 3 0.09
19 29 0.85
20 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTTAAAAATATATATAAA
Found at i:5123886 original size:17 final size:17
Alignment explanation
Indices: 5123864--5123920 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
5123854 CAATTTTTAA
5123864 AAATATATATAAATTTT
1 AAATATATATAAATTTT
*
5123881 AAATATATATATATATATAT
1 AAATATATATA-A-AT-TTT
*
5123901 AAACTATATATAAATATT
1 AAA-TATATATAAATTTT
5123919 AA
1 AA
5123921 TAAGTTATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 11 0.33
18 4 0.12
19 4 0.12
20 6 0.18
21 8 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATATATAAATTTT
Found at i:5123923 original size:21 final size:20
Alignment explanation
Indices: 5123860--5123923 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
5123850 GTATCAATTT
5123860 TTAA-AAATATATATAAAT-
1 TTAATAAATATATATAAATA
*
5123878 TT--TAAATATATATATATA
1 TTAATAAATATATATAAATA
5123896 -TATATAAACTATATATAAATA
1 TTA-ATAAA-TATATATAAATA
5123917 TTAATAA
1 TTAATAA
5123924 GTTATGTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
17 14 0.38
18 2 0.05
20 4 0.11
21 15 0.41
22 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATAAATATATATAAATA
Found at i:5123935 original size:9 final size:9
Alignment explanation
Indices: 5123921--5124001 Score: 51
Period size: 9 Copynumber: 9.0 Consensus size: 9
5123911 TAAATATTAA
5123921 TAAGTTATG
1 TAAGTTATG
5123930 TAAGTTATG
1 TAAGTTATG
* *
5123939 TATTA-TAAATT
1 TA--AGT-TATG
*
5123950 TAAGTTGTG
1 TAAGTTATG
5123959 TAAGTTATG
1 TAAGTTATG
5123968 -AA-TTATG
1 TAAGTTATG
*
5123975 TAAGATATG
1 TAAGTTATG
* *
5123984 TAAATTACG
1 TAAGTTATG
*
5123993 TAAGATATG
1 TAAGTTATG
5124002 AAATTTGAAC
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
7 5 0.09
8 4 0.08
9 37 0.70
10 2 0.04
11 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (9 bp):
TAAGTTATG
Found at i:5123995 original size:18 final size:17
Alignment explanation
Indices: 5123958--5124006 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
5123948 TTTAAGTTGT
* *
5123958 GTAAGTTATG-AATTAT
1 GTAAGATATGAAATTAC
5123974 GTAAGATATGTAAATTAC
1 GTAAGATATG-AAATTAC
5123992 GTAAGATATGAAATT
1 GTAAGATATGAAATT
5124007 TGAACTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 9 0.31
17 5 0.17
18 15 0.52
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (17 bp):
GTAAGATATGAAATTAC
Found at i:5125765 original size:45 final size:45
Alignment explanation
Indices: 5125701--5125791 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
5125691 TGGAAGGAGG
* *
5125701 AAGGAGGCGATTTAGGGATTTCGGATTTCAAGAAATTAGGCAAGA
1 AAGGAGGCGATTTACGGATTTCGGAATTCAAGAAATTAGGCAAGA
* * *
5125746 AAGGAGGCGATTTTCGGATTTGGGAATTCAAGAAATTGGGCAAGA
1 AAGGAGGCGATTTACGGATTTCGGAATTCAAGAAATTAGGCAAGA
5125791 A
1 A
5125792 GGACGCAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (45 bp):
AAGGAGGCGATTTACGGATTTCGGAATTCAAGAAATTAGGCAAGA
Found at i:5127045 original size:7 final size:7
Alignment explanation
Indices: 5127033--5127079 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
5127023 TAAATTAAGC
5127033 ACCCTAA
1 ACCCTAA
5127040 ACCCTAA
1 ACCCTAA
*
5127047 ACCTTAA
1 ACCCTAA
*
5127054 ACCCCAA
1 ACCCTAA
*
5127061 ACTTCTAA
1 AC-CCTAA
5127069 ACCCTAA
1 ACCCTAA
5127076 ACCC
1 ACCC
5127080 ATAACACCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 28 0.85
8 5 0.15
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (7 bp):
ACCCTAA
Found at i:5127645 original size:114 final size:114
Alignment explanation
Indices: 5127495--5127904 Score: 470
Period size: 114 Copynumber: 3.6 Consensus size: 114
5127485 TTCTCGTGAA
* *
5127495 CGCCACTAATTCCAGTATACATCAAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGC
1 CGCCACTAATTCAAGTATACATCAAGATCTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGC
* * *
5127560 TTATAAGAAAGCGCCACTAATAGTATACTTTTGCGGCGTTTACGGAAAG
66 TTATAAGAAAGCGCCGCTAATAGTATACTTTTGCGGCGTTTCCAGAAAG
* * *
5127609 CGCCACTAATTCAAGTATACGTCAAGATCTAAACGCAGCGTTTAGGTTAATATATCTTGCGGCGC
1 CGCCACTAATTCAAGTATACATCAAGATCTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGC
* * * * * *
5127674 TTCTAATAAAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTG-AA-
66 TTATAAGAAAGCGCCGCTAATAGTATACTTTTGCGGCG--TT-TCCAGAAAG
* * * * * *
5127724 CGCCACTAACTCCAGTATACATCAAGATTTAAACGCAGCATTTCCGTTAATATATCTTGCGGCGC
1 CGCCACTAATTCAAGTATACATCAAGATCTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGC
* * *
5127789 TTCTAAGAAAGCGACGCTAATAGTATACTTTTGCGGCGTTTCCATAAAG
66 TTATAAGAAAGCGCCGCTAATAGTATACTTTTGCGGCGTTTCCAGAAAG
* * * * * * *
5127838 CGCCACTAATTCTAA-TATACCTCAATA-CCAAACTCTGCGTTTTGGTCT-GTATATATTGCGGC
1 CGCCACTAATTC-AAGTATACATCAAGATCTAAACGCAGCGTTTCGGT-TAATATATATTGCGGC
5127900 GCTTA
64 GCTTA
5127905 ACCAAAAGCA
Statistics
Matches: 248, Mismatches: 41, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
112 3 0.01
113 32 0.13
114 114 0.46
115 92 0.37
116 4 0.02
117 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (114 bp):
CGCCACTAATTCAAGTATACATCAAGATCTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGC
TTATAAGAAAGCGCCGCTAATAGTATACTTTTGCGGCGTTTCCAGAAAG
Found at i:5127777 original size:115 final size:114
Alignment explanation
Indices: 5127453--5127849 Score: 503
Period size: 115 Copynumber: 3.5 Consensus size: 114
5127443 GCTAACAAAT
* * *
5127453 AAGCGCTGCTAATAATATGATTTAGCGGCGATTTCTCGTGAACGCCACTAATTCCAGTATACATC
1 AAGCGCCGCTAATAATATAATTTAGCGGCG-TTTCTCCTGAACGCCACTAATTCCAGTATACATC
* *
5127518 AAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGCTTATAAGA
65 AAGATTTAAACGCAGCGTTTCGGTTAATATATCTTGCGGCGCTTCTAAGA
* * * * * * * *
5127568 AAGCGCCACTAATAGTATACTTTTGCGGCG-TT-TACGGAAAGCGCCACTAATTCAAGTATACGT
1 AAGCGCCGCTAATAATATAATTTAGCGGCGTTTCTCCTG-AA-CGCCACTAATTCCAGTATACAT
* * *
5127631 CAAGATCTAAACGCAGCGTTTAGGTTAATATATCTTGCGGCGCTTCTAATA
64 CAAGATTTAAACGCAGCGTTTCGGTTAATATATCTTGCGGCGCTTCTAAGA
*
5127682 AAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAACGCCACTAACTCCAGTATACATC
1 AAGCGCCGCTAATAATATAATTTAGCGGCG-TTTCTCCTGAACGCCACTAATTCCAGTATACATC
* *
5127747 AAGATTTAAACGCAGCATTTCCGTTAATATATCTTGCGGCGCTTCTAAGA
65 AAGATTTAAACGCAGCGTTTCGGTTAATATATCTTGCGGCGCTTCTAAGA
* * * * * *
5127797 AAGCGACGCTAATAGTATACTTTTGCGGCGTTTC-CATAAAGCGCCACTAATTC
1 AAGCGCCGCTAATAATATAATTTAGCGGCGTTTCTCCTGAA-CGCCACTAATTC
5127850 TAATATACCT
Statistics
Matches: 239, Mismatches: 37, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
112 2 0.01
113 8 0.03
114 107 0.45
115 115 0.48
116 4 0.02
117 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (114 bp):
AAGCGCCGCTAATAATATAATTTAGCGGCGTTTCTCCTGAACGCCACTAATTCCAGTATACATCA
AGATTTAAACGCAGCGTTTCGGTTAATATATCTTGCGGCGCTTCTAAGA
Found at i:5127840 original size:229 final size:229
Alignment explanation
Indices: 5127436--5127862 Score: 678
Period size: 229 Copynumber: 1.9 Consensus size: 229
5127426 TGAAGATCTT
* * *
5127436 TTGCGGCGCTAACAAATAAGCGCTGCTAATAATATGATTTAGCGGCGATTTCTCGTGAACGCCAC
1 TTGCGGCGCTAACAAATAAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAACGCCAC
* * *
5127501 TAATTCCAGTATACATCAAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGCTTATAA
66 TAACTCCAGTATACATCAAGATTTAAACGCAGCATTTCCGTTAATATATATTGCGGCGCTTATAA
* * *
5127566 GAAAGCGCCACTAATAGTATACTTTTGCGGCGTTTACGGAAAGCGCCACTAATTC-AAGTATACG
131 GAAAGCGACACTAATAGTATACTTTTGCGGCGTTTACAGAAAGCGCCACTAATTCTAA-TATACC
5127630 TCAAGATCTAAACGCAGCGTTTAGGTTAATATATC
195 TCAAGATCTAAACGCAGCGTTTAGGTTAATATATC
* *
5127665 TTGCGGCGCT-TCTAATAAAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAACGCCA
1 TTGCGGCGCTAACAAAT-AAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAACGCCA
* *
5127729 CTAACTCCAGTATACATCAAGATTTAAACGCAGCATTTCCGTTAATATATCTTGCGGCGCTTCTA
65 CTAACTCCAGTATACATCAAGATTTAAACGCAGCATTTCCGTTAATATATATTGCGGCGCTTATA
* * *
5127794 AGAAAGCGACGCTAATAGTATACTTTTGCGGCGTTTCCATAAAGCGCCACTAATTCTAATATACC
130 AGAAAGCGACACTAATAGTATACTTTTGCGGCGTTTACAGAAAGCGCCACTAATTCTAATATACC
5127859 TCAA
195 TCAA
5127863 TACCAAACTC
Statistics
Matches: 180, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
228 4 0.02
229 174 0.97
230 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (229 bp):
TTGCGGCGCTAACAAATAAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAACGCCAC
TAACTCCAGTATACATCAAGATTTAAACGCAGCATTTCCGTTAATATATATTGCGGCGCTTATAA
GAAAGCGACACTAATAGTATACTTTTGCGGCGTTTACAGAAAGCGCCACTAATTCTAATATACCT
CAAGATCTAAACGCAGCGTTTAGGTTAATATATC
Found at i:5130173 original size:13 final size:12
Alignment explanation
Indices: 5130134--5130186 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 12
5130124 AGTTCTTCAT
5130134 TGCTTTTAAAAAG
1 TGCTTTT-AAAAG
**
5130147 TGCTGTGGAAAAG
1 TGCT-TTTAAAAG
5130160 TGCTTTTAAGAAG
1 TGCTTTTAA-AAG
5130173 TGCTTTTGAAAAG
1 TGCTTTT-AAAAG
5130186 T
1 T
5130187 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 3 0.09
13 27 0.82
14 3 0.09
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
TGCTTTTAAAAG
Found at i:5130173 original size:26 final size:26
Alignment explanation
Indices: 5130134--5130186 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
5130124 AGTTCTTCAT
5130134 TGCTTTTAAAAAGTGCTGTGGAAAAG
1 TGCTTTTAAAAAGTGCTGTGGAAAAG
* * *
5130160 TGCTTTTAAGAAGTGCTTTTGAAAAG
1 TGCTTTTAAAAAGTGCTGTGGAAAAG
5130186 T
1 T
5130187 TTGGTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (26 bp):
TGCTTTTAAAAAGTGCTGTGGAAAAG
Found at i:5139238 original size:50 final size:50
Alignment explanation
Indices: 5139133--5139311 Score: 160
Period size: 50 Copynumber: 3.5 Consensus size: 50
5139123 GAGATGAGAC
* ***
5139133 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTAAGGTTATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGC---ACCGA-G--ATGAGAGGT
* * **
5139189 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGTGCCGAGATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGT
** * * **
5139239 CCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGT
* *
5139289 CTCATGTAAGACCATATCTGGGA
1 CCCATGTAAGACCATGTCTGGGA
5139312 TATGACATTT
Statistics
Matches: 102, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
50 67 0.66
52 1 0.01
53 1 0.01
56 33 0.32
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.24
Consensus pattern (50 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGT
Found at i:5139592 original size:12 final size:12
Alignment explanation
Indices: 5139575--5139613 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5139565 ATGAGTTATT
5139575 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
5139587 TAAGTAAACAAG
1 TAAGTAAGCAAG
5139599 TAAG-AGAGCAAG
1 TAAGTA-AGCAAG
5139611 TAA
1 TAA
5139614 AGAAGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 1 0.04
12 23 0.96
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:5142051 original size:64 final size:64
Alignment explanation
Indices: 5141967--5142125 Score: 219
Period size: 64 Copynumber: 2.5 Consensus size: 64
5141957 CACACTGCTC
* * * * *
5141967 GACACACGCCCGTGTCTCTTGCCCGTGTGACTCCAAAACTTAACTCAGTGAGTTACATGGCCTA
1 GACACACGCCAGTGTGTCTTGCCCGTGTGACTCCAAAACTTAACTCAGGGAGTTACACGACCTA
* * **
5142031 GACACACGCCAGTGTGTCTTGCCCATGTAACTCCAAGTCTTAACTCAGGGAGTTACACGACCTA
1 GACACACGCCAGTGTGTCTTGCCCGTGTGACTCCAAAACTTAACTCAGGGAGTTACACGACCTA
* *
5142095 GACAAACGCCTGTGTGTCTTGCCCGTGTGAC
1 GACACACGCCAGTGTGTCTTGCCCGTGTGAC
5142126 CCCTACACCT
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 82 1.00
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (64 bp):
GACACACGCCAGTGTGTCTTGCCCGTGTGACTCCAAAACTTAACTCAGGGAGTTACACGACCTA
Found at i:5151887 original size:11 final size:11
Alignment explanation
Indices: 5151871--5151895 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5151861 AATCACTTGG
5151871 TTCTATCGCAT
1 TTCTATCGCAT
5151882 TTCTATCGCAT
1 TTCTATCGCAT
5151893 TTC
1 TTC
5151896 ACTTTGACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (11 bp):
TTCTATCGCAT
Found at i:5160282 original size:20 final size:20
Alignment explanation
Indices: 5160257--5160294 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5160247 GTATGTAACA
5160257 TATATATA-TCATGACATACT
1 TATATATAGTCAT-ACATACT
5160277 TATATATAGTCATACATA
1 TATATATAGTCATACATA
5160295 ACATAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (20 bp):
TATATATAGTCATACATACT
Found at i:5163878 original size:24 final size:24
Alignment explanation
Indices: 5163850--5163902 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
5163840 ATTCGCAAGT
* *
5163850 TAAATAAATTATGCTAATAAATGC
1 TAAATAAATTATACTAATAAATAC
*
5163874 TAAATATATTATACTAATAAATAC
1 TAAATAAATTATACTAATAAATAC
5163898 TAAAT
1 TAAAT
5163903 TTTTTAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.36
Consensus pattern (24 bp):
TAAATAAATTATACTAATAAATAC
Found at i:5165884 original size:11 final size:11
Alignment explanation
Indices: 5165868--5165907 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5165858 GTTGCTGCGG
*
5165868 AAAAGAAGAAA
1 AAAAGAAGAGA
5165879 AAAAG-AGAGA
1 AAAAGAAGAGA
*
5165889 AAAAGAGGAGA
1 AAAAGAAGAGA
5165900 AAAAGAAG
1 AAAAGAAG
5165908 GTATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:5165971 original size:19 final size:21
Alignment explanation
Indices: 5165933--5165971 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5165923 AATAATTTAT
*
5165933 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
5165954 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
5165972 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:5166047 original size:3 final size:3
Alignment explanation
Indices: 5166041--5166090 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
5166031 ATTATTATTA
5166041 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
5166089 TT
1 TT
5166091 AGTATTAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:5169884 original size:160 final size:156
Alignment explanation
Indices: 5169450--5169894 Score: 458
Period size: 160 Copynumber: 2.8 Consensus size: 156
5169440 GCAAGTTGAA
*
5169450 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGACATTTTATT
**
5169515 ACTTT-AAAAAATCATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGTATTATGTTAT
66 ACTTTAAAAAAAT-ATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTAT
** **
5169579 TTCTTTATTAATTTAGTGTGTTTTTTT
130 TTCTTTATTAATTTAGTCCGAATTTTT
** * * * * *
5169606 AAATTAATTTAGTGTAAAAAAAACAACCCTTATTCTTAC--CC-TTTGCTCGTATTATTTTCCCG
1 AAA--AA---AGT-T-AGTAAAAC-ACTCTT-TACTT-CGGCCATTTGTTCGTATTTTTTTCTCG
* * * * *
5169668 A-ATTTTATTACTTCCAAAAAAA-AT-ATTATTTTCGT-ATTTTATTATTTTATATTATTTCATT
56 ACATTTTATTACTT-TAAAAAAATATCA-TAATTTC-TAATTTTATAATTTTACATTATTTCAGT
* **
5169729 ACATTTTGTTTAAAATTT-TTGTATTAATTTTTTCCGAATTTTT
118 ACATTATG-TT---ATTTCTT-TATTAATTTAGTCCGAATTTTT
5169772 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGACATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGACATTTTATT
5169837 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTA
66 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTA
5169895 CTTCGGCCTT
Statistics
Matches: 228, Mismatches: 35, Indels: 48
0.73 0.11 0.15
Matches are distributed among these distances:
156 4 0.02
157 4 0.02
158 9 0.04
159 33 0.14
160 49 0.21
161 8 0.04
162 49 0.21
163 27 0.12
164 15 0.07
165 6 0.03
166 24 0.11
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (156 bp):
AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGACATTTTATT
ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTATT
TCTTTATTAATTTAGTCCGAATTTTT
Found at i:5169920 original size:97 final size:99
Alignment explanation
Indices: 5169794--5169991 Score: 271
Period size: 98 Copynumber: 2.0 Consensus size: 99
5169784 AAAACACTCT
* * * *
5169794 TTACTTCGGCCATTTGTTCGTATTTTTTTCTCGACATTTTATTACTTT-AA-AAAAATATCA-TA
1 TTACTTCGGCCATTTGCTCGTATTATTTTC-CCAAATTTTATTACTTTCAATAAAAATAT-ATTA
5169856 ATTTC-TAATTTTATAATTTTACATTATTTCAGTACA
64 ATTTCGT-ATTTTATAATTTTACATTATTTCAGTACA
*
5169892 TTACTTCGGCC-TTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTATT
1 TTACTTCGGCCATTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTAAT
* *
5169956 TTCGTATTTTATTATTTTATATTATTTCAGTACA
66 TTCGTATTTTATAATTTTACATTATTTCAGTACA
5169990 TT
1 TT
5169992 TTGTGAGAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
96 15 0.17
97 19 0.21
98 54 0.61
99 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (99 bp):
TTACTTCGGCCATTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTAAT
TTCGTATTTTATAATTTTACATTATTTCAGTACA
Found at i:5171190 original size:3 final size:3
Alignment explanation
Indices: 5171156--5171237 Score: 78
Period size: 3 Copynumber: 27.0 Consensus size: 3
5171146 CCCTTTGTAG
* * *
5171156 TAT TTT TAT TAT T-T TGT TCAT TAT T-C TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
* *
5171200 TAT TAT TAT TATT TAT TATT TAA TAT TAT TTT TAT TAT
1 TAT TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT
5171238 CATCGTATTT
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
2 3 0.05
3 54 0.83
4 8 0.12
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5171211 original size:32 final size:33
Alignment explanation
Indices: 5171156--5171237 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 33
5171146 CCCTTTGTAG
* *
5171156 TATTTTTATTATT-TTGTTCATTATTCTATTA-T
1 TATTATTATTATTATTATTCATTATT-TATTATT
5171188 TATTATTATTATTATTATT-ATTATTTATTATT
1 TATTATTATTATTATTATTCATTATTTATTATT
* *
5171220 TAATATTATTTTTATTAT
1 TATTATTATTATTATTAT
5171238 CATCGTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
31 5 0.11
32 35 0.80
33 4 0.09
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.68
Consensus pattern (33 bp):
TATTATTATTATTATTATTCATTATTTATTATT
Found at i:5171618 original size:23 final size:22
Alignment explanation
Indices: 5171565--5171618 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
5171555 TATATATACC
* *
5171565 TATATATATACTTTTTATATTA
1 TATACATATACTTTTTATATGA
*
5171587 TATATATATACTTTTT-TATGA
1 TATACATATACTTTTTATATGA
5171608 TAGTTACATAT
1 TA--TACATAT
5171619 GTATAGATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 16 0.57
23 6 0.21
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (22 bp):
TATACATATACTTTTTATATGA
Found at i:5173287 original size:14 final size:14
Alignment explanation
Indices: 5173268--5173311 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
5173258 CCTTTCCTTG
5173268 TCTTTCCTTCTTTT
1 TCTTTCCTTCTTTT
5173282 TCTTT-C--C-TTT
1 TCTTTCCTTCTTTT
5173292 TCTTTCCTTCTTTT
1 TCTTTCCTTCTTTT
5173306 TCTTTC
1 TCTTTC
5173312 TTTCCTCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
13 2 0.08
14 14 0.54
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TCTTTCCTTCTTTT
Found at i:5173297 original size:4 final size:4
Alignment explanation
Indices: 5173268--5173372 Score: 55
Period size: 4 Copynumber: 26.5 Consensus size: 4
5173258 CCTTTCCTTG
* *
5173268 TCTT TCCT TC-T T-TT TCTT TCCTTT TCTT TCCT TC-T T-TT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT T-C-TT TCTT TCTT TCTT TCTT TCTT TCTT
* *
5173314 TCCTC TCATCT CCTT TCCTTT TCTT TC-T T-TT TCTT TCTT TCTT TCTT
1 T-CTT TC-T-T TCTT T-C-TT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
5173361 TC-T TC-T TCTT TC
1 TCTT TCTT TCTT TC
5173373 CATCTCCTTC
Statistics
Matches: 81, Mismatches: 6, Indels: 28
0.70 0.05 0.24
Matches are distributed among these distances:
3 18 0.22
4 47 0.58
5 9 0.11
6 7 0.09
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (4 bp):
TCTT
Found at i:5173330 original size:57 final size:58
Alignment explanation
Indices: 5173269--5173378 Score: 147
Period size: 57 Copynumber: 1.9 Consensus size: 58
5173259 CTTTCCTTGT
5173269 CTTTCCTTCTT-TTTCTTTC-CTTTTCTTTCCTTCTTT-TTCTTTCTTTCC-TCTCATCTC
1 CTTTCCTT-TTCTTTCTTTCTC-TTTCTTTCCTTCTTTCTTC-TTCTTTCCATCTCATCTC
* *
5173326 CTTTCCTTTTCTTTCTTTTTCTTTCTTTCTTTCTTTCTTCTTCTTTCCATCTC
1 CTTTCCTTTTCTTTCTTTCTCTTTCTTTCCTTCTTTCTTCTTCTTTCCATCTC
5173379 CTTCTCTTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
56 2 0.04
57 37 0.79
58 8 0.17
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (58 bp):
CTTTCCTTTTCTTTCTTTCTCTTTCTTTCCTTCTTTCTTCTTCTTTCCATCTCATCTC
Found at i:5173334 original size:24 final size:24
Alignment explanation
Indices: 5173252--5173373 Score: 97
Period size: 24 Copynumber: 5.5 Consensus size: 24
5173242 TTTTTTGTTC
*
5173252 TCTTCTCCTTTCCTTGTCTTTCCT
1 TCTTCTCCTTTCCTTTTCTTTCCT
* *
5173276 TCTTTTTCTTTCCTTTTCTTTCCT
1 TCTTCTCCTTTCCTTTTCTTTCCT
5173300 TC-T-T--TTT-C-TTTCTTTCCT
1 TCTTCTCCTTTCCTTTTCTTTCCT
*
5173318 CTCATCTCCTTTCCTTTTCTTT-CT
1 -TCTTCTCCTTTCCTTTTCTTTCCT
*
5173342 T-TT-T-CTTT-C-TTTCTTTCTT
1 TCTTCTCCTTTCCTTTTCTTTCCT
*
5173361 TCTTCTTCTTTCC
1 TCTTCTCCTTTCC
5173374 ATCTCCTTCT
Statistics
Matches: 81, Mismatches: 5, Indels: 25
0.73 0.05 0.23
Matches are distributed among these distances:
18 17 0.21
19 6 0.07
20 10 0.12
21 3 0.04
22 6 0.07
23 6 0.07
24 26 0.32
25 7 0.09
ACGTcount: A:0.01, C:0.32, G:0.01, T:0.66
Consensus pattern (24 bp):
TCTTCTCCTTTCCTTTTCTTTCCT
Found at i:5173339 original size:10 final size:10
Alignment explanation
Indices: 5173279--5173373 Score: 63
Period size: 10 Copynumber: 9.0 Consensus size: 10
5173269 CTTTCCTTCT
5173279 TTTTCTTTCC
1 TTTTCTTTCC
5173289 TTTTCTTTCC
1 TTTTCTTTCC
5173299 TTCTT-TTT-C
1 TT-TTCTTTCC
5173308 -TTTCTTTCC
1 TTTTCTTTCC
5173317 TCTCATCTCCTTTCC
1 T-T--T-T-CTTTCC
*
5173332 TTTTCTTTCT
1 TTTTCTTTCC
*
5173342 TTTTCTTTCTT
1 TTTTCTTTC-C
5173353 TCTTTCTTT-C
1 T-TTTCTTTCC
5173363 TTCTTCTTTCC
1 TT-TTCTTTCC
5173374 ATCTCCTTCT
Statistics
Matches: 70, Mismatches: 2, Indels: 25
0.72 0.02 0.26
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 3 0.04
10 36 0.51
11 7 0.10
12 8 0.11
13 1 0.01
14 2 0.03
15 7 0.10
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTCTTTCC
Found at i:5173350 original size:14 final size:14
Alignment explanation
Indices: 5173326--5173372 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5173316 CTCTCATCTC
*
5173326 CTTTCCTTTTCTTT
1 CTTTCTTTTTCTTT
5173340 CTTT-TTCTTTCTTT
1 CTTTCTT-TTTCTTT
5173354 CTTTCTTTCTTC-TT
1 CTTTCTTT-TTCTTT
5173368 CTTTC
1 CTTTC
5173373 CATCTCCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 1 0.03
14 23 0.79
15 5 0.17
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
CTTTCTTTTTCTTT
Found at i:5180337 original size:29 final size:29
Alignment explanation
Indices: 5180304--5180360 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
5180294 GGGCATCGAC
5180304 AAAGTCCTGTAGATCTCCTAAACACATGA
1 AAAGTCCTGTAGATCTCCTAAACACATGA
5180333 AAAGTCCTGTAGATCTCCTAAACACATG
1 AAAGTCCTGTAGATCTCCTAAACACATG
5180361 TCAAACTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (29 bp):
AAAGTCCTGTAGATCTCCTAAACACATGA
Found at i:5180630 original size:22 final size:22
Alignment explanation
Indices: 5180597--5180657 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
5180587 GCCCGGCCCG
* *
5180597 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
5180620 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
5180642 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
5180658 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:5180670 original size:16 final size:16
Alignment explanation
Indices: 5180633--5180672 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5180623 TTAATAAAAT
* *
5180633 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
5180649 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
5180665 TAAAATTA
1 TAAAATTA
5180673 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:5180943 original size:31 final size:33
Alignment explanation
Indices: 5180907--5180977 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 33
5180897 ATTTTTTAAA
*
5180907 CGGGCCTAAAATTTTGCCC-AAG-CCCATATTT
1 CGGGCCTAAAATTTTACCCAAAGCCCCATATTT
* *
5180938 CGGGCCTATATTTTTACCCAAAGCCTCCCATATTT
1 CGGGCCTAAAATTTTACCCAAAG-C-CCCATATTT
5180973 CGGGC
1 CGGGC
5180978 GGGCCGTCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 16 0.48
32 3 0.09
35 14 0.42
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.30
Consensus pattern (33 bp):
CGGGCCTAAAATTTTACCCAAAGCCCCATATTT
Found at i:5182122 original size:44 final size:44
Alignment explanation
Indices: 5181986--5182124 Score: 106
Period size: 44 Copynumber: 3.2 Consensus size: 44
5181976 AGTTGCAGAT
* *
5181986 CTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAGAC-TCAAAC
1 CTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGACAT-AAAC
* * * * * * * * * *
5182030 CTTGCC-TCTCT-CGGTTG-TGGTGGAGCTGGTTGAAGACAGCATAT
1 CTTGCCTTC-CTGC-ATTGACGGCGAAGCAGATCGAAGACA-TAAAC
5182074 CTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGACATAAAC
1 CTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGACATAAAC
5182118 CTTGCCT
1 CTTGCCT
5182125 CTCTCGGTTG
Statistics
Matches: 66, Mismatches: 22, Indels: 14
0.65 0.22 0.14
Matches are distributed among these distances:
43 15 0.23
44 33 0.50
45 18 0.27
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGACATAAAC
Found at i:5182584 original size:263 final size:260
Alignment explanation
Indices: 5181982--5182695 Score: 1088
Period size: 263 Copynumber: 2.7 Consensus size: 260
5181972 ATGAAGTTGC
* * *
5181982 AGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAGACTCAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* * **
5182047 TGGTGGAGCTGGTTGAAGACAGCATATCTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGAC
66 T-GTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAGAC
* *
5182112 ATAAACCTTGCCTCTCTCGGTTGTGATAGAGCCGGTTGAAGACAAAAGATCTTGCCTTCCTGCAT
130 ACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTT-CTGCAT
* *
5182177 TGACAGCGAAGCAGGTCGAAGACAAACCTTCCCTCTCTCTGTTGTGATGGAGCTGGTTGAAGACA
194 TGACAGCGAAGCAGGTCGAAGACAAACCTTCCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACA
5182242 AA
259 AA
*
5182244 AGATCTTGCCTTCCTGCATTGTCAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* * * ** *
5182309 TGATGGAGCTGGTTGAAGATAAAAGATCTTGCTTTCCTGCATTGACAACGAAAAAGGTCGAAGAC
66 TG-TGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAGAC
*
5182374 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCTGCATT
130 ACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCTGCATT
* *
5182439 GACAGCGAAGCAGGTTGAAGACACAAACCTTGCCTCTCTCGGTTATGATGGAGCTGGTTGAAGAC
195 GACAGCGAAGCAGGTCGAAG--ACAAACCTTCCCTCTCTCGGTTATGATGGAGCTGGTTGAAGAC
5182504 AAA
258 AAA
* *
5182507 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTA
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* *
5182572 TAGTGCAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAACGAAGCAGATCAAAGAC
66 T-GTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAGAC
* * * * *
5182637 ACAAACCTTGCCTCTCTCGATTG-CAGTAGAGCTGGTTAAAGATAACAGATCTTGCCTTC
130 ACAAACCTTGCCTCTCTCGGTTGTGA-TAGAGCTGGTTGAAGACAAAAGATCTTGCCTTC
5182696 CTGCGTTAAC
Statistics
Matches: 409, Mismatches: 38, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
261 27 0.07
262 170 0.42
263 211 0.52
264 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (260 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
TGTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAGACA
CAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCTGCATTG
ACAGCGAAGCAGGTCGAAGACAAACCTTCCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACAAA
Found at i:5182721 original size:88 final size:88
Alignment explanation
Indices: 5181982--5182699 Score: 1068
Period size: 88 Copynumber: 8.2 Consensus size: 88
5181972 ATGAAGTTGC
* * *
5181982 AGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAGACTCAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* **
5182047 TGGTGGAGCTGGTTGAAGACAGC
66 TGATGGAGCTGGTTGAAGACAAA
* * * *
5182070 ATATCTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGACATAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* *
5182135 TGATAGAGCCGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
5182158 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAG--ACAAACCTTCCCTCTCTCTGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
5182221 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
5182244 AGATCTTGCCTTCCTGCATTGTCAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
5182309 TGATGGAGCTGGTTGAAGATAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * **
5182332 AGATCTTGCTTTCCTGCATTGACAACGAAAAAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
5182397 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
5182420 AGATCTTGCCTT-CTGCATTGACAGCGAAGCAGGTTGAAGACACAAACCTTGCCTCTCTCGGTTA
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
5182484 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
5182507 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTA
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* *
5182572 T-AGTGCAGCTGGTTGAAGACAAC
66 TGA-TGGAGCTGGTTGAAGACAAA
* * * *
5182595 AGATCTTGCCTTCCTGCATTGACAACGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGATTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* * * * *
5182660 -CAGTAGAGCTGGTTAAAGATAAC
66 TGA-TGGAGCTGGTTGAAGACAAA
5182683 AGATCTTGCCTTCCTGC
1 AGATCTTGCCTTCCTGC
5182700 GTTAACAACG
Statistics
Matches: 577, Mismatches: 48, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
86 80 0.14
87 83 0.14
88 414 0.72
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:5183231 original size:20 final size:21
Alignment explanation
Indices: 5183208--5183246 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5183198 TGCCCAATAC
5183208 ACCT-AAACAAACCCAAATTG
1 ACCTAAAACAAACCCAAATTG
*
5183228 ACCTAAAACTAACCCAAAT
1 ACCTAAAACAAACCCAAAT
5183247 GCAGCCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.51, C:0.31, G:0.03, T:0.15
Consensus pattern (21 bp):
ACCTAAAACAAACCCAAATTG
Found at i:5184283 original size:3 final size:3
Alignment explanation
Indices: 5184254--5184320 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
5184244 TGTAGCATTT
* *
5184254 TTA TTA TT- TTG TTCA TTA TT- CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5184298 TTA TTTA ATA TTA TTT TTA TTA T
1 TTA -TTA TTA TTA TTA TTA TTA T
5184321 CATCGTATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
2 3 0.06
3 45 0.85
4 5 0.09
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5184655 original size:34 final size:30
Alignment explanation
Indices: 5184613--5184687 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 30
5184603 ATATGTTCTT
5184613 TATATTTTTATGATTCATATATATACCTATATA
1 TATATTTTTATGATT-ATATATATA--TATATA
5184646 TATACTTTTTAT-ATTATATATATATATATA
1 TATA-TTTTTATGATTATATATATATATATA
5184676 -AT-TTTTTATGAT
1 TATATTTTTATGAT
5184688 AGTTACATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
27 7 0.17
28 2 0.05
29 2 0.05
30 6 0.15
32 9 0.22
33 7 0.17
34 7 0.17
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (30 bp):
TATATTTTTATGATTATATATATATATATA
Found at i:5184671 original size:28 final size:28
Alignment explanation
Indices: 5184630--5184684 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 28
5184620 TTATGATTCA
5184630 TATATATACCTATATATATACTTTTTATAT
1 TATATATA-CTATATATA-ACTTTTTATAT
*
5184660 TATATATA-TATATATAATTTTTTAT
1 TATATATACTATATATAACTTTTTAT
5184685 GATAGTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 8 0.33
30 8 0.33
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TATATATACTATATATAACTTTTTATAT
Found at i:5184697 original size:27 final size:26
Alignment explanation
Indices: 5184641--5184702 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
5184631 ATATATACCT
* * *
5184641 ATATATATACTTTTTATATTATATAT
1 ATATATATAATTTTTATATGATATAC
5184667 ATATATATAATTTTT-TATGATAGTTAC
1 ATATATATAATTTTTATATGATA--TAC
*
5184694 ATATGTATA
1 ATATATATA
5184703 GATGTACATG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 6 0.20
26 14 0.47
27 10 0.33
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (26 bp):
ATATATATAATTTTTATATGATATAC
Found at i:5185331 original size:112 final size:112
Alignment explanation
Indices: 5185197--5185402 Score: 367
Period size: 112 Copynumber: 1.8 Consensus size: 112
5185187 TCAAAAAAGG
* * *
5185197 AAAATATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAACATGCCCTAAGGTGCT
*
5185262 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAA
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTTTAA
5185309 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAACATGCCCTAAGGTGCT
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAACATGCCCTAAGGTGCT
*
5185374 GGGTGTCGATTTTTCTCATTTAACCAAAT
66 GGGTGTCGATTTTTCTCATTCAACCAAAT
5185403 TGCTAAAACA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 89 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (112 bp):
AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAACATGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTTTAA
Found at i:5186208 original size:21 final size:21
Alignment explanation
Indices: 5186182--5186269 Score: 74
Period size: 21 Copynumber: 4.1 Consensus size: 21
5186172 AAATATATTT
*
5186182 TTTCTTTCCCTGTTCTCCTTC
1 TTTCTTTCCTTGTTCTCCTTC
**
5186203 TTTCTTTTTTTGTTCT-CTTC
1 TTTCTTTCCTTGTTCTCCTTC
* *
5186223 -TCCTTTCCTTGTCTTTCCTTC
1 TTTCTTTCCTTGT-TCTCCTTC
5186244 TTTTCTTTCCTT-TTCTTTCCTTC
1 -TTTCTTTCCTTGTTC--TCCTTC
5186267 TTT
1 TTT
5186270 TTCTTTCTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
19 9 0.17
20 6 0.12
21 18 0.35
22 4 0.08
23 15 0.29
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTCTTTCCTTGTTCTCCTTC
Found at i:5186240 original size:10 final size:10
Alignment explanation
Indices: 5186225--5186282 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
5186215 TTCTCTTCTC
*
5186225 CTTTCCTTGT
1 CTTTCCTTTT
5186235 CTTTCCTTCTTTT
1 CTTTCC---TTTT
5186248 CTTTCCTTTT
1 CTTTCCTTTT
5186258 CTTTCCTTCTT
1 CTTTCCTT-TT
5186269 -TTT-C-TTT
1 CTTTCCTTTT
5186276 CTTTCCT
1 CTTTCCT
5186283 CTCATCTCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
7 2 0.05
8 4 0.10
9 2 0.05
10 21 0.52
11 2 0.05
13 9 0.22
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:5186251 original size:23 final size:24
Alignment explanation
Indices: 5186225--5186276 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
5186215 TTCTCTTCTC
5186225 CTTTCCTTGTCTTTCCTTC-TTTT
1 CTTTCCTTGTCTTTCCTTCTTTTT
*
5186248 CTTTCCTTTTCTTTCCTTCTTTTT
1 CTTTCCTTGTCTTTCCTTCTTTTT
5186272 CTTTC
1 CTTTC
5186277 TTTCCTCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (24 bp):
CTTTCCTTGTCTTTCCTTCTTTTT
Found at i:5187441 original size:40 final size:36
Alignment explanation
Indices: 5187381--5187466 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
5187371 AAATTAGTAT
* * *
5187381 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATTGTTAGTTATTATTTTGAGTATAAA-AC
5187417 TAATTATTATTGTTAGTTACTATTATTTTGAGTATAAAAC
1 T-ATTATTATTGTTAG-T--TATTATTTTGAGTATAAAAC
5187457 TATTATTATT
1 TATTATTATT
5187467 TTTATTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.31
38 1 0.02
39 9 0.21
40 15 0.36
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTATTATTGTTAGTTATTATTTTGAGTATAAAAC
Found at i:5190953 original size:16 final size:15
Alignment explanation
Indices: 5190932--5190961 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5190922 CAAAAAAATA
5190932 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
5190948 TATTATTTTATATT
1 TATTATTTTATATT
5190962 ATTTCATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:5191012 original size:23 final size:25
Alignment explanation
Indices: 5190967--5191012 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
5190957 ATATTATTTC
*
5190967 ATTACATTTTGTTTGAAATTTTTGT
1 ATTACATTTTGTTTCAAATTTTTGT
5190992 ATTA-ATTTT-TTTCAAATTTTT
1 ATTACATTTTGTTTCAAATTTTT
5191013 AAAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 5 0.25
25 4 0.20
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (25 bp):
ATTACATTTTGTTTCAAATTTTTGT
Found at i:5191125 original size:160 final size:157
Alignment explanation
Indices: 5190887--5191763 Score: 648
Period size: 160 Copynumber: 5.6 Consensus size: 157
5190877 ATTCTTGCCC
*
5190887 TTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTT-TCATATTTTAT
1 TTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATAATTTCT-A-ATTTTAT
* *
5190951 TATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTTCAAATTTTTAAA
64 AATTTTACATTATTTCATTACATTTTGTTT-AAATTTTTGTATTAATTTTTTTCAAATTTTTAAA
5191016 AAATTTAGTAAAACACTTTTTACTTCGGCCA
128 AAA-TTAGTAAAACACTTTTTACTTCGGCCA
* * * * * *
5191047 TTTGTTCGTATTTTTTTCTCGGCATTTTATTACTT-TAAAAAAATATCATAATTTCTAATTTTGT
1 TTTGCTCGTATTATTTTC-CCGAATTTTATTACTTCCAAAAAAATAT-ATAATTTCTAATTTTAT
* * * * * *
5191111 AATTTTACATTATTTCAGTGCATTATG-TT-ATTTCTTTATTAATTTAGTATGTTTTTTAAAATT
64 AATTTTACATTATTTCATTACATTTTGTTTAAATT-TTT-GT-A-TTA--AT-TTTTTTCAAATT
* * * * * *
5191174 AATTTAGTGTAAAAA-AAATACAACCCTTATT-CTT--GCCC
122 --TTTA----AAAAATTAGTAAAACACTTTTTACTTCGGCCA
*
5191212 TTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGT-ATTTTAT
1 TTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATA-TAATTTC-TAATTTTAT
* * * * *
5191276 TATTTTATATTATTTCATTACATTTTTTTTAAAATTTTTGTATTAATTTTTTCCGAATTTTTAAA
64 AATTTTACATTATTTCATTACATTTTGTTT-AAATTTTTGTATTAATTTTTTTCAAATTTTTAAA
* *
5191341 AGAGTTAGTAAAACACTCTTTACTTCGGCCA
128 A-AATTAGTAAAACACTTTTTACTTCGGCCA
* * * * *
5191372 TTTGTTCGTATTTTTTTCTCGGTATTTTATTACTT--TAAAAAATATCATAATTTCTAATTTTAT
1 TTTGCTCGTATTATTTTC-CCGAATTTTATTACTTCCAAAAAAATAT-ATAATTTCTAATTTTAT
* * * * * **
5191435 AATTTTACATTATTTCAGTGCATTATG-TT--ATTTCTT-TATTAATTTAGTGT--GTTTTTTAA
64 AATTTTACATTATTTCATTACATTTTGTTTAAATTT-TTGTATTAATTT-TTTTCAAATTTTTAA
* **
5191494 ATTAATTTAGTGTAAAA-A------A-AAC--CCA
127 A--AAATTA--GTAAAACACTTTTTACTTCGGCCA
*** ** *
5191519 -ACCCTTATATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGT-ATTTTAT
1 TTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATA-TAATTTC-TAATTTTAT
* * * * * *
5191582 TATTTTAAATTATTTCAGTACATTATT-TTGAAATTTTTGTATTAATTTTTTCCAAATTTCTAAA
64 AATTTTACATTATTTCATTACATT-TTGTTTAAATTTTTGTATTAATTTTTTTCAAATTTTTAAA
5191646 AAAGTTAGTAAAACACTTTTTACTTCGGCCA
128 AAA-TTAGTAAAACACTTTTTACTTCGGCCA
* * * *
5191677 TTTGTTCATATTATTTTCTCGACATTTTATTACTT--TAAAAAATATCATAATTTCTAATTTTAT
1 TTTGCTCGTATTATTTTCCCGA-ATTTTATTACTTCCAAAAAAATAT-ATAATTTCTAATTTTAT
*
5191740 AATTTTACATTATTTCAGTACATT
64 AATTTTACATTATTTCATTACATT
5191764 ACTTCGGTCT
Statistics
Matches: 553, Mismatches: 102, Indels: 126
0.71 0.13 0.16
Matches are distributed among these distances:
145 14 0.03
146 11 0.02
147 46 0.08
148 9 0.02
149 7 0.01
150 17 0.03
151 7 0.01
154 8 0.01
155 21 0.04
156 7 0.01
157 20 0.04
158 56 0.10
159 66 0.12
160 87 0.16
161 47 0.08
162 3 0.01
163 2 0.00
164 29 0.05
165 63 0.11
166 8 0.01
167 6 0.01
168 14 0.03
170 5 0.01
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (157 bp):
TTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATAATTTCTAATTTTATAA
TTTTACATTATTTCATTACATTTTGTTTAAATTTTTGTATTAATTTTTTTCAAATTTTTAAAAAA
TTAGTAAAACACTTTTTACTTCGGCCA
Found at i:5191340 original size:325 final size:323
Alignment explanation
Indices: 5190750--5191764 Score: 1652
Period size: 325 Copynumber: 3.2 Consensus size: 323
5190740 TACTTCGGCC
5190750 ATTACTTTAAAAAATTATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTT
1 ATTACTTTAAAAAA-TATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTT
* * *
5190815 ATTTCTTTATTAATTTAGTGTGTTTTTTAAGTTAATTTAGTGTAAAAAAAATTTCAACCTTTATT
65 ATTTCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAA-TACAACCCTTATT
*
5190880 CTTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCATA
129 CTTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTA
* *
5190945 TTTTATTATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTTCAAATT
194 TTTTATTATTTTATATTATTTCATTACATTTTTTTTGAAATTTTTGTATTAATTTTTTCCAAATT
*
5191010 TTTAAAAAATTTAGTAAAACACTTTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTT
259 TTTAAAAAAGTTAGTAAAACACTTTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTT
*
5191075 ATTACTTTAAAAAAATATCATAATTTCTAATTTTGTAATTTTACATTATTTCAGTGCATTATGTT
1 ATTACTTT-AAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTT
*
5191140 ATTTCTTTATTAATTTAGTATGTTTTTTAAAATTAATTTAGTGTAAAAAAAATACAACCCTTATT
65 ATTTCTTTATTAATTTAGTGTGTTTTTT-AAATTAATTTAGTGTAAAAAAAATACAACCCTTATT
5191205 CTTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTA
129 CTTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTA
* *
5191270 TTTTATTATTTTATATTATTTCATTACATTTTTTTTAAAATTTTTGTATTAATTTTTTCCGAATT
194 TTTTATTATTTTATATTATTTCATTACATTTTTTTTGAAATTTTTGTATTAATTTTTTCCAAATT
* * *
5191335 TTTAAAAGAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGTATTTT
259 TTTAAAAAAGTTAGTAAAACACTTTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTT
5191400 ATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTA
1 ATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTA
5191465 TTTCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGT---AAAAA-A-AACCC--A----
66 TTTCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAATACAACCCTTATTCT
* *
5191519 -ACCC--T--T-ATATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATT
131 TGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATT
* * * *
5191578 TTATTATTTTAAATTATTTCAGTACA-TTATTTTGAAATTTTTGTATTAATTTTTTCCAAATTTC
196 TTATTATTTTATATTATTTCATTACATTTTTTTTGAAATTTTTGTATTAATTTTTTCCAAATTTT
* * *
5191642 TAAAAAAGTTAGTAAAACACTTTTTACTTCGGCCATTTGTTCATATTATTTTCTCGACATTTT
261 TAAAAAAGTTAGTAAAACACTTTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTT
*
5191705 ATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTA
1 ATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTA
5191765 CTTCGGTCTT
Statistics
Matches: 657, Mismatches: 31, Indels: 24
0.92 0.04 0.03
Matches are distributed among these distances:
305 150 0.23
306 76 0.12
307 1 0.00
309 1 0.00
311 3 0.00
316 1 0.00
318 5 0.01
319 1 0.00
320 5 0.01
323 15 0.02
324 82 0.12
325 289 0.44
326 28 0.04
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (323 bp):
ATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTA
TTTCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAATACAACCCTTATTCT
TGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATT
TTATTATTTTATATTATTTCATTACATTTTTTTTGAAATTTTTGTATTAATTTTTTCCAAATTTT
TAAAAAAGTTAGTAAAACACTTTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTT
Found at i:5191835 original size:98 final size:97
Alignment explanation
Indices: 5191665--5191861 Score: 249
Period size: 98 Copynumber: 2.0 Consensus size: 97
5191655 AAAACACTTT
* * *
5191665 TTACTTCGGCCATTTGTTCATATTATTTTCTCGACATTTTATTACTTTAAAAAATATCATAATTT
1 TTACTTCGGCCATTTGCTCATATTATTTTCTCCAAATTTTATTACTTTAAAAAATATCATAATTT
5191730 CTAATTTTATAATTTTACATTATTTCAGTACA
66 CTAATTTTATAATTTTACATTATTTCAGTACA
* *
5191762 TTACTTCGGTC-TTTGCTCGTATTATTTTC-CCAAATTTTATTACTTTCAATAAAAATAT-ATTA
1 TTACTTCGGCCATTTGCTCATATTATTTTCTCCAAATTTTATTACTTT--A-AAAAATATCA-TA
* * *
5191824 TTTTCGT-ATTTTATTATTTTATATTATTTCAGTACA
62 ATTTC-TAATTTTATAATTTTACATTATTTCAGTACA
5191860 TT
1 TT
5191862 TTGTGAGAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
95 15 0.17
96 16 0.18
97 12 0.14
98 43 0.49
99 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.52
Consensus pattern (97 bp):
TTACTTCGGCCATTTGCTCATATTATTTTCTCCAAATTTTATTACTTTAAAAAATATCATAATTT
CTAATTTTATAATTTTACATTATTTCAGTACA
Found at i:5192011 original size:256 final size:255
Alignment explanation
Indices: 5191526--5192020 Score: 789
Period size: 256 Copynumber: 1.9 Consensus size: 255
5191516 CCAACCCTTA
*
5191526 TATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTTTATTATTTTAAA
1 TATTATTTTCCCAAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTTTATTATTTTAAA
* * *
5191591 TTATTTCAGTACATTATTTTGAAATTTTTGTATTAATTTTTTCCAAATTTCTAAAAAAGTTAGTA
66 TTATTTCAGTACATTATTTAGAAATATTTGTATTAATTATTTCCAAATTTCTAAAAAAGTTAGTA
*
5191656 AAACACTTTTTACTTCGGCCATTTGTTCATATTATTTTCTCGACATTTTATTACTTTAAAAAATA
131 AAACACTTCTTACTTCGGCCATTTGTTCATATTATTTTCTCGACATTTTATTACTTTAAAAAATA
*
5191721 TCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTACTTCGGTCTTTGCTCG
196 TCATAAATTCTAATTTTATAATTTTACATTATTTCAGTACATTACTTCGGTCTTTGCTCG
* *
5191781 TATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTAT
1 TATTATTTTCCCAAATTTTATTACTTCCAA-AAAAATATATTATTTTCGTATTTTATTATTTTAA
** *
5191846 ATTATTTCAGTACATT-TTGTGAGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAAGTTA
65 ATTATTTCAGTACATTATT-T-AGAAATATTTGTATTAATTATTTCCAAATTTCTAAAAAAGTTA
* * *
5191910 GTAAAACAC-TCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCG-TATTTTATTACTTTAAAA
128 GTAAAACACTTCTTACTTCGGCCATTTGTTCATATTATTTTCT-CGACATTTTATTACTTTAAAA
* *
5191973 AATATCATAAATTCTAATTTTATAATTTTACGTTATTTCAGTGCATTA
192 AATATCATAAATTCTAATTTTATAATTTTACATTATTTCAGTACATTA
5192021 TGTTTGAAAT
Statistics
Matches: 220, Mismatches: 16, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
255 30 0.14
256 142 0.65
257 48 0.22
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (255 bp):
TATTATTTTCCCAAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTTTATTATTTTAAA
TTATTTCAGTACATTATTTAGAAATATTTGTATTAATTATTTCCAAATTTCTAAAAAAGTTAGTA
AAACACTTCTTACTTCGGCCATTTGTTCATATTATTTTCTCGACATTTTATTACTTTAAAAAATA
TCATAAATTCTAATTTTATAATTTTACATTATTTCAGTACATTACTTCGGTCTTTGCTCG
Found at i:5193838 original size:16 final size:15
Alignment explanation
Indices: 5193795--5193851 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
5193785 TTTACATACG
* *
5193795 TTTTATATTTTTTTA
1 TTTTATATATTTTAA
* *
5193810 TTTTATCTCTTTTAA
1 TTTTATATATTTTAA
5193825 CTTTTATATATTTTATA
1 -TTTTATATATTTTA-A
*
5193842 TTATATATAT
1 TTTTATATAT
5193852 ATATATACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.35
16 21 0.62
17 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTATATATTTTAA
Found at i:5196066 original size:19 final size:19
Alignment explanation
Indices: 5196026--5196067 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5196016 GTCTCTTTTC
* *
5196026 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
5196045 GCATTACATTACAT-CATAT
1 GCATT-CATTACATGCATAT
5196064 GCAT
1 GCAT
5196068 CAAACACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:5197980 original size:20 final size:20
Alignment explanation
Indices: 5197955--5197995 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
5197945 GCAAATGTTC
5197955 TTTCATTCTTT-ACGATTTTT
1 TTTCATTCTTTCA-GATTTTT
5197975 TTTCATTCTTTCAGATTTTT
1 TTTCATTCTTTCAGATTTTT
5197995 T
1 T
5197996 CTGCCAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTCATTCTTTCAGATTTTT
Found at i:5198939 original size:7 final size:7
Alignment explanation
Indices: 5198915--5198956 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
5198905 AGTGATGTGA
5198915 AAAAATG
1 AAAAATG
5198922 AAAAGAT-
1 AAAA-ATG
5198929 AAAAATG
1 AAAAATG
5198936 AAAAATG
1 AAAAATG
5198943 AAAAA-G
1 AAAAATG
5198949 TAAAAATG
1 -AAAAATG
5198957 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.10
7 25 0.81
8 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:5198941 original size:21 final size:21
Alignment explanation
Indices: 5198915--5198956 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5198905 AGTGATGTGA
5198915 AAAAATG-AAAAGATAAAAATG
1 AAAAATGAAAAAG-TAAAAATG
5198936 AAAAATGAAAAAGTAAAAATG
1 AAAAATGAAAAAGTAAAAATG
5198957 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAAGTAAAAATG
Found at i:5200306 original size:44 final size:44
Alignment explanation
Indices: 5200256--5200967 Score: 676
Period size: 44 Copynumber: 16.1 Consensus size: 44
5200246 GCAGATTTTA
* *
5200256 TCTTCATGTATTGACATGAAGTAGATCGAAAATAATGGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
* * *
5200300 TCTTCATGTATTGACATGAAGTAGATC-AGAGATAGTAAATCTTA
1 TCTTCATGTATTGACATGAAGTAGATCGA-AGATAATAGATCTTG
* *
5200344 TCTTCATGTATTGACATTAAGTAGATCGAAGATAATGGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
* * **
5200388 TCTTCATGTATTGACATGAAATAGATC-AGGGATAGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGA-AGATAATAGATCTTG
*** * *** *
5200432 TCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTG
1 TCTTCATGTA-TTGACATGAAGTAGATCGAAGATAATAGATCTTG
* * **
5200477 TCTTCATGTATTGACATGAAATAGATC-AGGGATAGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGA-AGATAATAGATCTTG
*** * ***
5200521 TCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATAGATCTTG
1 TCTTCATGTA-TTGACATGAAGTAGATCGAAGATAATAGATCTTG
***
5200566 TCTTCATGTATTGACATGAAGTAGATC-AGAGATGGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGA-AGATAATAGATCTTG
** * * *
5200610 TCTTCCCATAGTGGTG--GTGAAGTAGATCGAAGATAATGGATCTTA
1 TCTT--CAT-GTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
** *
5200655 TCTTCATGTATTGACATGAAGTAGATC-AGAGATAGCAGATCTTA
1 TCTTCATGTATTGACATGAAGTAGATCGA-AGATAATAGATCTTG
* *
5200699 TCTTCATGTATTGACATGAAGTTGATCGAAGATAATGGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
*
5200743 TCTTCATGTATTGACATGAAGTAGATC-AGAGA-AAGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGA-AGATAA-TAGATCTTG
* *
5200787 TCTTCATGTATT-AGCGTGAAGTAGATCGAAGA-AAGCAGATCTTG
1 TCTTCATGTATTGA-CATGAAGTAGATCGAAGATAA-TAGATCTTG
* * *
5200831 TCTTCATGTATTGGCGTGAAGTAGATCGAAGA-AAGTAGATCCTG
1 TCTTCATGTATTGACATGAAGTAGATCGAAGATAA-TAGATCTTG
* * *
5200875 TCTTCATGTATTGGCGTGAAGTAGATCGAAGA-AAGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGAAGATAA-TAGATCTTG
* * * **
5200919 TCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
5200963 TCTTC
1 TCTTC
5200968 CCATACTGGT
Statistics
Matches: 554, Mismatches: 91, Indels: 46
0.80 0.13 0.07
Matches are distributed among these distances:
42 4 0.01
43 12 0.02
44 438 0.79
45 90 0.16
46 6 0.01
47 4 0.01
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (44 bp):
TCTTCATGTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
Found at i:5200402 original size:88 final size:88
Alignment explanation
Indices: 5200245--5200967 Score: 904
Period size: 88 Copynumber: 8.2 Consensus size: 88
5200235 GTTGAAAAGC
* * * *
5200245 AGCAGATTTTATCTTCATGTATTGACATGAAGTAGATCGAAAATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
5200310 TTGACATGAAGTAGATCAGAGAT
66 TTGACATGAAGTAGATCAGAGAT
* * * * *
5200333 AGTAAATCTTATCTTCATGTATTGACATTAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
* *
5200398 TTGACATGAAATAGATCAGGGAT
66 TTGACATGAAGTAGATCAGAGAT
*** * **
5200421 AGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTA-TTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
* *
5200486 ATTGACATGAAATAGATCAGGGAT
65 ATTGACATGAAGTAGATCAGAGAT
*** * ** *
5200510 AGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATAGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTA-TTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
5200575 ATTGACATGAAGTAGATCAGAGAT
65 ATTGACATGAAGTAGATCAGAGAT
* ** *
5200599 GGCAGATCTTGTCTTCCCATAGTGGTG--GTGAAGTAGATCGAAGATAATGGATCTTATCTTCAT
1 AGCAGATCTTGTCTT--CAT-GTATTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCAT
5200662 GTATTGACATGAAGTAGATCAGAGAT
63 GTATTGACATGAAGTAGATCAGAGAT
* * *
5200688 AGCAGATCTTATCTTCATGTATTGACATGAAGTTGATCGAAGATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
*
5200753 TTGACATGAAGTAGATCAGAGAA
66 TTGACATGAAGTAGATCAGAGAT
5200776 AGCAGATCTTGTCTTCATGTATT-AGCGTGAAGTAGATCGAAGA-AA-GCAGATCTTGTCTTCAT
1 AGCAGATCTTGTCTTCATGTATTGA-CGTGAAGTAGATCGAAGATAATG--GATCTTGTCTTCAT
* * *
5200838 GTATTGGCGTGAAGTAGATC-GAAGAA
63 GTATTGACATGAAGTAGATCAG-AGAT
* * *
5200864 AGTAGATCCTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA-AA-GCAGATCTTGTCTTCATG
1 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATG
* * *
5200927 TATTGGCGTGAAGTAGATCAAAGAT
64 TATTGACATGAAGTAGATCAGAGAT
5200952 AGCAGATCTTGTCTTC
1 AGCAGATCTTGTCTTC
5200968 CCATACTGGT
Statistics
Matches: 573, Mismatches: 50, Indels: 24
0.89 0.08 0.04
Matches are distributed among these distances:
86 5 0.01
87 7 0.01
88 323 0.56
89 235 0.41
91 2 0.00
92 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (88 bp):
AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
TTGACATGAAGTAGATCAGAGAT
Found at i:5201041 original size:45 final size:45
Alignment explanation
Indices: 5200986--5201113 Score: 122
Period size: 45 Copynumber: 2.9 Consensus size: 45
5200976 GTGGCGAAGT
* *
5200986 AGATCGAAGATAACAAGTCTTATCCCCCTGAAGTTGCAGTGGGGC
1 AGATTGAAGATAACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGC
** *
5201031 AGATTGAAGATAGTGAA-TCTTATCTCCCTGAAGTTGCAGTGGAGC
1 AGATTGAAGATA-ACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGC
* *
5201076 -GAATT-AA-A-ACCACAGATCTTATCCCTCTGAAGTTGCAG
1 AG-ATTGAAGATAACA-AG-TCTTATCCCCCTGAAGTTGCAG
5201114 GAGAAAGCAG
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 2 0.03
43 1 0.01
44 23 0.33
45 40 0.58
46 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (45 bp):
AGATTGAAGATAACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGC
Found at i:5201110 original size:44 final size:45
Alignment explanation
Indices: 5201047--5201202 Score: 132
Period size: 44 Copynumber: 3.6 Consensus size: 45
5201037 AAGATAGTGA
5201047 ATCTTATCTCC-CTGAAGTTGCAGTGGAGCGAATTAAAACCACAG
1 ATCTTATCTCCTCTGAAGTTGCAGTGGAGCGAATTAAAACCACAG
* * *
5201091 ATCTTATC-CCTCTGAAGTTGCAG-GAGAAAGC-AGA-TCATATC-CAG
1 ATCTTATCTCCTCTGAAGTTGCAGTG-G--AGCGA-ATTAAAACCACAG
* * *
5201135 -TCTTATCTTCCT-TGAAGTTGCAATGGAGTGGATTAAAACCACAG
1 ATCTTATC-TCCTCTGAAGTTGCAGTGGAGCGAATTAAAACCACAG
* *
5201179 ATCTCATCT-ATCTGAAGTTGCAGT
1 ATCTTATCTCCTCTGAAGTTGCAGT
5201203 AGAGTAGATC
Statistics
Matches: 87, Mismatches: 12, Indels: 26
0.70 0.10 0.21
Matches are distributed among these distances:
42 3 0.03
43 15 0.17
44 50 0.57
45 15 0.17
46 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (45 bp):
ATCTTATCTCCTCTGAAGTTGCAGTGGAGCGAATTAAAACCACAG
Found at i:5202911 original size:2 final size:2
Alignment explanation
Indices: 5202904--5202930 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5202894 ATGCATAATT
5202904 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
5202931 TCCTTTTTTT
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:5203329 original size:20 final size:20
Alignment explanation
Indices: 5203291--5203336 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5203281 TTAACCATAC
5203291 ATCAAA-GTTATTTTCTTGA
1 ATCAAAGGTTATTTTCTTGA
* *
5203310 ATCAAAGGTTTTTTTTTTGA
1 ATCAAAGGTTATTTTCTTGA
*
5203330 ATAAAAG
1 ATCAAAG
5203337 CAATATTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (20 bp):
ATCAAAGGTTATTTTCTTGA
Found at i:5205146 original size:9 final size:8
Alignment explanation
Indices: 5205125--5205294 Score: 57
Period size: 8 Copynumber: 22.0 Consensus size: 8
5205115 ATACTTTTTT
5205125 TTCTTTCC
1 TTCTTTCC
*
5205133 CTCTTCTCC
1 TTCTT-TCC
5205142 TTCTTT-C
1 TTCTTTCC
*
5205149 TT-TTT-T
1 TTCTTTCC
5205155 TTCTCTT-C
1 TTCT-TTCC
*
5205163 TCCTTTCC
1 TTCTTTCC
5205171 TTTTCTTTCC
1 --TTCTTTCC
*
5205181 TTATTT--
1 TTCTTTCC
5205187 TTCTTT-C
1 TTCTTTCC
**
5205194 TT-TTTTT
1 TTCTTTCC
5205201 TTC-TT-C
1 TTCTTTCC
5205207 TTCTTTCC
1 TTCTTTCC
5205215 TTTTCTTTCC
1 --TTCTTTCC
5205225 TTCTTT--
1 TTCTTTCC
*
5205231 TTCTTTCT
1 TTCTTTCC
5205239 TTCTTTCC
1 TTCTTTCC
5205247 TCTCCTTTCC
1 T-T-CTTTCC
*
5205257 -T-TTTCT
1 TTCTTTCC
5205263 TTCTTT--
1 TTCTTTCC
*
5205269 TTCTTTCT
1 TTCTTTCC
5205277 TTCTTTCTTC
1 TTCTTTC--C
5205287 TTCTTTCC
1 TTCTTTCC
5205295 CTCTCCTTCT
Statistics
Matches: 126, Mismatches: 13, Indels: 46
0.68 0.07 0.25
Matches are distributed among these distances:
6 32 0.25
7 15 0.12
8 43 0.34
9 8 0.06
10 28 0.22
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (8 bp):
TTCTTTCC
Found at i:5205149 original size:4 final size:4
Alignment explanation
Indices: 5205142--5205293 Score: 76
Period size: 4 Copynumber: 37.8 Consensus size: 4
5205132 CCTCTTCTCC
*
5205142 TTCT TTCT TT-T TT-T TCTCT TCTCCT TTCCTT TTCT TTCCT TATTT TTCT
1 TTCT TTCT TTCT TTCT T-TCT T-T-CT TT-C-T TTCT TT-CT T-TCT TTCT
*
5205191 TTCT TT-T TT-T TTC- TTC- TTCT TTCCTT TTCT TTCC TTC- TT-T TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT-C-T TTCT TTCT TTCT TTCT TTCT
*
5205235 TTCT TTCT TTCCT CTCCT TTCCTT TTCT TTC- TT-T TTCT TTCT TTCT
1 TTCT TTCT TT-CT -TTCT TT-C-T TTCT TTCT TTCT TTCT TTCT TTCT
5205281 TTC- TTC- TTCT TTC
1 TTCT TTCT TTCT TTC
5205294 CCTCTCCTTC
Statistics
Matches: 124, Mismatches: 5, Indels: 38
0.74 0.03 0.23
Matches are distributed among these distances:
3 31 0.25
4 58 0.47
5 21 0.17
6 14 0.11
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:5205180 original size:10 final size:10
Alignment explanation
Indices: 5205142--5205294 Score: 93
Period size: 10 Copynumber: 14.8 Consensus size: 10
5205132 CCTCTTCTCC
5205142 TTCTTT-CTT
1 TTCTTTCCTT
*
5205151 TTTTTTCTCTT
1 TTCTTTC-CTT
*
5205162 CTCCTTTCCTT
1 -TTCTTTCCTT
5205173 TTCTTTCCTT
1 TTCTTTCCTT
5205183 ATT-TTTCTTTCTT
1 -TTCTTTC---CTT
* *
5205196 TTTTTTTCTT
1 TTCTTTCCTT
5205206 CTTCTTTCCTT
1 -TTCTTTCCTT
5205217 TTCTTTCCTT
1 TTCTTTCCTT
*
5205227 CTT-TTTCTTTCT
1 -TTCTTTC-CT-T
*
5205239 TTCTTTCCTC
1 TTCTTTCCTT
*
5205249 TCCTTTCCTT
1 TTCTTTCCTT
*
5205259 TTCTTTCTTT
1 TTCTTTCCTT
5205269 TTCTTT-C-T
1 TTCTTTCCTT
5205277 TTCTTT-CTT
1 TTCTTTCCTT
5205286 CTTCTTTCC
1 -TTCTTTCC
5205295 CTCTCCTTCT
Statistics
Matches: 113, Mismatches: 15, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
8 8 0.07
9 6 0.05
10 58 0.51
11 23 0.20
12 12 0.11
13 6 0.05
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (10 bp):
TTCTTTCCTT
Found at i:5205190 original size:14 final size:13
Alignment explanation
Indices: 5205151--5205294 Score: 85
Period size: 14 Copynumber: 10.0 Consensus size: 13
5205141 CTTCTTTCTT
5205151 TTTTTTCTCTTCTCC
1 TTTTTT-TCTT-TCC
5205166 TTTCCTTTTCTTTCC
1 TTT--TTTTCTTTCC
*
5205181 TTATTTTTCTTTCTT
1 TT-TTTTTCTTTC-C
*
5205196 TTTTTTTCTTCTTC
1 TTTTTTTCTT-TCC
5205210 TTTCCTTTTCTTTCC
1 TTT--TTTTCTTTCC
5205225 TTCTTTTTCTTT-C
1 TT-TTTTTCTTTCC
* *
5205238 TTTCTTTCCTCTCC
1 TTT-TTTTCTTTCC
*
5205252 TTTCCTTTTCTTTCT
1 TTT--TTTTCTTTCC
5205267 TTTTCTTTCTTT-C
1 TTTT-TTTCTTTCC
5205280 TTTCTTCTTCTTTCC
1 TTT-TT-TTCTTTCC
5205295 CTCTCCTTCT
Statistics
Matches: 104, Mismatches: 10, Indels: 30
0.72 0.07 0.21
Matches are distributed among these distances:
12 1 0.01
13 14 0.13
14 46 0.44
15 27 0.26
16 13 0.12
17 3 0.03
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTCTTTCC
Found at i:5205211 original size:34 final size:34
Alignment explanation
Indices: 5205142--5205285 Score: 134
Period size: 34 Copynumber: 4.1 Consensus size: 34
5205132 CCTCTTCTCC
* * * *
5205142 TTCTTT-CTTTTTTT-TCTCTTCTCCTTTCCT-T
1 TTCTTTCCTTTTTTTCTTTCTTTTTCTTTCTTCT
*
5205173 TTCTTTCCTTATTTTTCTTTCTTTTTTTTTCTTC-
1 TTCTTTCCTT-TTTTTCTTTCTTTTTCTTTCTTCT
*
5205207 TTCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCT
1 TTCTTTCCTTTT-TTTCTTTCTTTTTCTTTC-TTCT
*
5205243 TTCCTCTCCTTTCCTTTTCTTTCTTTTTCTTTCTTTCT
1 TT-CTTTCCTTT--TTTTCTTTCTTTTTCTTTC-TTCT
5205281 TTCTT
1 TTCTT
5205286 CTTCTTTCCC
Statistics
Matches: 93, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
31 6 0.06
32 3 0.03
33 7 0.08
34 37 0.40
35 3 0.03
36 2 0.02
37 10 0.11
38 24 0.26
39 1 0.01
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (34 bp):
TTCTTTCCTTTTTTTCTTTCTTTTTCTTTCTTCT
Found at i:5205242 original size:38 final size:38
Alignment explanation
Indices: 5205146--5205294 Score: 144
Period size: 44 Copynumber: 3.7 Consensus size: 38
5205136 TTCTCCTTCT
*
5205146 TTCTTTTT-TTTC--TCTTCTCCTTTCCTTTTCTTTCC
1 TTCTTTTTCTTTCTTTCTTCTTCTTTCCTTTTCTTTCC
*
5205181 TTATTTTTCTTTCTTTTTTTTTCTTCTTCTTTCCTTTTCTTTCC
1 TTCTTTTTCTTTC------TTTCTTCTTCTTTCCTTTTCTTTCC
5205225 TTCTTTTTCTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTT-C
1 TTCTTTTTCTTTCTTTC-TT-CT-T-CTTTCCTTTTCTTTCC
*
5205266 TTTTTCTTTCTTTCTTTCTTCTTCTTTCC
1 TTCTT-TTTCTTTCTTTCTTCTTCTTTCC
5205295 CTCTCCTTCT
Statistics
Matches: 96, Mismatches: 4, Indels: 25
0.77 0.03 0.20
Matches are distributed among these distances:
35 7 0.07
36 4 0.04
38 10 0.10
39 3 0.03
40 4 0.04
41 8 0.08
42 26 0.27
44 34 0.35
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (38 bp):
TTCTTTTTCTTTCTTTCTTCTTCTTTCCTTTTCTTTCC
Found at i:5210013 original size:19 final size:19
Alignment explanation
Indices: 5209972--5210013 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5209962 CGTCTCTTTT
* *
5209972 TGCATTCATTTCATGCATT
1 TGCATTCATTGCATGCATA
5209991 TGCATTTCATTGCAT-CATA
1 TGCA-TTCATTGCATGCATA
5210010 TGCA
1 TGCA
5210014 CTAAACACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (19 bp):
TGCATTCATTGCATGCATA
Found at i:5212732 original size:46 final size:47
Alignment explanation
Indices: 5212627--5212766 Score: 210
Period size: 47 Copynumber: 3.0 Consensus size: 47
5212617 CTAAAAGGTG
5212627 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
* *
5212674 GGGCCAAGGTGAAAGCCTACAAAGGGCTCTTTGAGTCAAAAAAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
* * * * *
5212721 -GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
5212767 AAGGAGAGGC
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
46 39 0.46
47 45 0.54
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (47 bp):
GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
Found at i:5212767 original size:47 final size:46
Alignment explanation
Indices: 5212628--5212766 Score: 197
Period size: 46 Copynumber: 3.0 Consensus size: 46
5212618 TAAAAGGTGG
*
5212628 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAAG
1 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGT-AAAAAAAAAAA
* * *
5212675 GGCCAAGGTGAAAGCCTACAAAGGGCTCTTTGAGTCAAAAAAAAAA
1 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTAAAAAAAAAAA
* * * *
5212721 GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAAA
1 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTAAAAAAAAAAA
5212767 AAGGAGAGGC
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 48 0.59
47 33 0.41
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.13
Consensus pattern (46 bp):
GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTAAAAAAAAAAA
Found at i:5214330 original size:133 final size:133
Alignment explanation
Indices: 5214034--5214532 Score: 561
Period size: 133 Copynumber: 3.8 Consensus size: 133
5214024 TGAATACAAA
* * *
5214034 AGATCTTGTCTTCCCATACTGATGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATT
* * *** * * *
5214099 GGCGTGAAGCAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGGAGTAGATCGAAGA
66 GGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCGAAGA
* *
5214164 AAGT
130 TAGC
*** * * * * * * * *
5214168 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGCAGATCCTGTCTTCCTATATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATT
* * * *
5214232 GGTAGTGAAGTGGATCGAAGAT-GCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGA
66 GG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGA
5214296 TAGC
130 TAGC
** *
5214300 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGTGAGCAAATCTTATCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATT
* * ** * *
5214365 GGCGTGAAGTAGATTGAAGAAAATAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGAT
66 GGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAT
*
5214430 AAC
131 AGC
* * * *
5214433 AGATCTTCTCTTCCCATACTGGTGGCGAAGTAAATCGAAGAAAGCAGGTCTTGTCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATT
* * *
5214498 GGCGTGAAGTAGATCGAATATCGCAGATCTGGTCT
66 GGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCT
5214533 CTCTGAAGTT
Statistics
Matches: 297, Mismatches: 65, Indels: 7
0.80 0.18 0.02
Matches are distributed among these distances:
132 51 0.17
133 213 0.72
134 33 0.11
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (133 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATT
GGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAT
AGC
Found at i:5214401 original size:177 final size:177
Alignment explanation
Indices: 5214034--5214445 Score: 511
Period size: 177 Copynumber: 2.3 Consensus size: 177
5214024 TGAATACAAA
* * * * * *
5214034 AGATCTTGTCTTCCCATACTGATGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACT
1 AGATCTTGTCTTCCTATACTGGTAGTGAAGTAGATCAAAG-ATGCAGATCTTATCTTCATGTACT
* *
5214099 GGCGTGAAGCAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGGAGTAGATCGAAGA
65 AGCGTGAAGCAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
* * * * *
5214164 AAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGC
130 AAGCAAATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAAC
* * * * * *
5214212 AGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCATGTATTA
1 AGATCTTGTCTTCCTATACTGGTAGTGAAGTAGATCAAAGATGCAGATCTTATCTTCATGTACTA
* * **
5214277 GCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGTG
66 GCGTGAAGCAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
* ** *
5214342 AGCAAATCTTATCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAAT
131 AGCAAATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAAC
* * * * *
5214389 AGATCTTGTCTTCATGTACTGGCA-TGAAGTAGATCAAAGATAACAGATCTTCTCTTC
1 AGATCTTGTCTTCCTATACTGGTAGTGAAGTAGATCAAAGAT-GCAGATCTTATCTTC
5214446 CCATACTGGT
Statistics
Matches: 198, Mismatches: 35, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
176 15 0.08
177 151 0.76
178 32 0.16
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (177 bp):
AGATCTTGTCTTCCTATACTGGTAGTGAAGTAGATCAAAGATGCAGATCTTATCTTCATGTACTA
GCGTGAAGCAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
AGCAAATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAAC
Found at i:5214410 original size:89 final size:89
Alignment explanation
Indices: 5214034--5214401 Score: 495
Period size: 89 Copynumber: 4.1 Consensus size: 89
5214024 TGAATACAAA
* *
5214034 AGATCTTGTCTTCCCATACTGATGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTACT
*
5214099 GGCGTGAAGCAGATCAAAGATAGC
66 GGCGTGAAGTAGATCAAAGATAGC
* * *
5214123 AGATCTTGTCTTCCCATACTGGTGGCGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTACT
5214188 GGCGTGAAGTAGATCAAAGATAGC
66 GGCGTGAAGTAGATCAAAGATAGC
* * * * * * * * *
5214212 AGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAG-ATGCAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTACT
* *
5214276 AGCGTGAAGTAGATCGAAGATAGC
66 GGCGTGAAGTAGATCAAAGATAGC
** * *
5214300 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGTGAGCAAATCTTATCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTACT
** * **
5214365 GGCGTGAAGTAGATTGAAGAAAAT
66 GGCGTGAAGTAGATCAAAGATAGC
5214389 AGATCTTGTCTTC
1 AGATCTTGTCTTC
5214402 ATGTACTGGC
Statistics
Matches: 245, Mismatches: 33, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
88 77 0.31
89 168 0.69
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (89 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTACT
GGCGTGAAGTAGATCAAAGATAGC
Found at i:5219540 original size:12 final size:12
Alignment explanation
Indices: 5219523--5219550 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5219513 CGTTACATTC
5219523 GATCACCGAAGT
1 GATCACCGAAGT
5219535 GATCACCGAAGT
1 GATCACCGAAGT
5219547 GATC
1 GATC
5219551 TTGTAAAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (12 bp):
GATCACCGAAGT
Found at i:5220724 original size:60 final size:59
Alignment explanation
Indices: 5220649--5220833 Score: 254
Period size: 60 Copynumber: 3.2 Consensus size: 59
5220639 AGTGGTTTCG
* *
5220649 CATGTAATAATGTGACTCGCATGTAATAACATATTATTGACTCGCATAAGCAATGATTCA
1 CATGTAATAATGTGACTCGCATGTAATAACATATCATTGACTCGCATAA-CAATGGTTCA
* *
5220709 CATGTAATAATGTGACTTGCATGTAATAACATATCATTGACTCGCATAAACAGTGGTTCA
1 CATGTAATAATGTGACTCGCATGTAATAACATATCATTGACTCGCAT-AACAATGGTTCA
* *
5220769 CATGTAATAATGTGACTCACATG---T--CATATCATTGACTTGCATGAACAATGGTTCA
1 CATGTAATAATGTGACTCGCATGTAATAACATATCATTGACTCGCAT-AACAATGGTTCA
5220824 CATGTAATAA
1 CATGTAATAA
5220834 CATATACTTG
Statistics
Matches: 115, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
55 38 0.33
57 1 0.01
60 74 0.64
61 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (59 bp):
CATGTAATAATGTGACTCGCATGTAATAACATATCATTGACTCGCATAACAATGGTTCA
Found at i:5223312 original size:114 final size:113
Alignment explanation
Indices: 5223111--5223459 Score: 501
Period size: 114 Copynumber: 3.1 Consensus size: 113
5223101 CCTTTTTGAA
* * *
5223111 TTTTTTTTAAACTTTTTTCGTATACTAGTGCCGACCATTGACATGAAAAAAGTAAAAAAAAAATT
1 TTTTTTTT-AACTTTTTTCGTATACTGGTGCTG-CCATTGACACGAAAAAAGT-AAAAAAAAATT
*
5223176 CCAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAC
63 CCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAC
5223227 TTTTTTTTAACTTTTTTCGTATACTGGTGCTTGCCATTGACACGAAAAAAGT-AAAAAAAATTCT
1 TTTTTTTTAACTTTTTTCGTATACTGGTGC-TGCCATTGACACGAAAAAAGTAAAAAAAAATTC-
*
5223291 CATAAAGGTGGTGCCGACCATTGGCAGGCCACCACCAAATTTTTTTTT--
64 CATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAC
*
5223339 TTACTTTTTTAACTTTTTTCGTATAATGGTGCCTGCCATTGACAC-AAAAAAGTAAAAAAAAAAT
1 TT--TTTTTTAACTTTTTTCGTATACTGGTG-CTGCCATTGACACGAAAAAAGT-AAAAAAAAAT
* **
5223403 CCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCA-CAAATTTTTTTAAAC
62 TCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAC
5223454 TTTTTT
1 TTTTTT
5223460 CGTATATTGG
Statistics
Matches: 214, Mismatches: 10, Indels: 21
0.87 0.04 0.09
Matches are distributed among these distances:
112 2 0.01
113 34 0.16
114 117 0.55
115 52 0.24
116 9 0.04
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (113 bp):
TTTTTTTTAACTTTTTTCGTATACTGGTGCTGCCATTGACACGAAAAAAGTAAAAAAAAATTCCA
TAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAC
Found at i:5223336 original size:102 final size:101
Alignment explanation
Indices: 5223227--5223502 Score: 320
Period size: 114 Copynumber: 2.6 Consensus size: 101
5223217 TTTTTTTTAC
* * *
5223227 TTTTTTTTAACTTTTTTCGTATACTGGTGCTTGCCATTGACACGAAAAAAGTAAAAAAAATTCTC
1 TTTTTTTTAACTTTTTTCGTATAATGGTGC-TGCCATTGACACGAAAAAAGTAAAAAAAAATCCC
5223292 ATAAAGGTGGTGCCGACCATTGGCAGGCCACCACCAAA
65 ATAAAGGTGGTGCCGACCATTGGCAGGCCACCA-CAAA
5223330 TTTTTTTTTTTACTTTTTTAACTTTTTTCGTATAATGGTGCCTGCCATTGACAC-AAAAAAGTAA
1 ---------TT--TTTTTTAACTTTTTTCGTATAATGGTG-CTGCCATTGACACGAAAAAAGT-A
*
5223394 AAAAAAAATCCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAA
53 AAAAAAAATCCCATAAAGGTGGTGCCGACCATTGGCAGGCCACCACAAA
* * * *
5223443 TTTTTTTAAACTTTTTTCGTATATTGGTGCCGACCATTGACAAGAAAAAAAGTAAAAAAA
1 TTTTTTTTAACTTTTTTCGTATAATGGTGCTG-CCATTGACACG-AAAAAAGTAAAAAAA
5223503 CAAGTTTTCT
Statistics
Matches: 149, Mismatches: 8, Indels: 23
0.83 0.04 0.13
Matches are distributed among these distances:
101 2 0.01
102 34 0.23
103 7 0.05
104 10 0.07
112 2 0.01
113 12 0.08
114 81 0.54
115 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (101 bp):
TTTTTTTTAACTTTTTTCGTATAATGGTGCTGCCATTGACACGAAAAAAGTAAAAAAAAATCCCA
TAAAGGTGGTGCCGACCATTGGCAGGCCACCACAAA
Found at i:5227921 original size:35 final size:35
Alignment explanation
Indices: 5227872--5227938 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
5227862 GAGAAATCCA
*
5227872 ACGGTAAACGTTGTGGATTATGTAGGTTAAGTCCG
1 ACGGTAAACATTGTGGATTATGTAGGTTAAGTCCG
*
5227907 ACGGTAAGCATTGTGGATTATGTAGGTTAAGT
1 ACGGTAAACATTGTGGATTATGTAGGTTAAGT
5227939 GGTCATAGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.31, T:0.33
Consensus pattern (35 bp):
ACGGTAAACATTGTGGATTATGTAGGTTAAGTCCG
Found at i:5231500 original size:51 final size:48
Alignment explanation
Indices: 5231422--5231520 Score: 171
Period size: 51 Copynumber: 2.0 Consensus size: 48
5231412 TAGTCTCCGG
5231422 GTGAATTTAATTTTTTTAGGGGTTAAAATTAAATTGTAATTTTTACGA
1 GTGAATTTAATTTTTTTAGGGGTTAAAATTAAATTGTAATTTTTACGA
5231470 GTGAATTTAAATTTTTTTTAGGGGGTTAAAATTAAATTGTAATTTTTACGA
1 GTGAATTT-AA-TTTTTTTA-GGGGTTAAAATTAAATTGTAATTTTTACGA
5231521 TAGTAAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
48 8 0.17
49 2 0.04
50 8 0.17
51 30 0.62
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.47
Consensus pattern (48 bp):
GTGAATTTAATTTTTTTAGGGGTTAAAATTAAATTGTAATTTTTACGA
Found at i:5235337 original size:38 final size:40
Alignment explanation
Indices: 5235269--5235363 Score: 94
Period size: 38 Copynumber: 2.5 Consensus size: 40
5235259 ATATATATAC
5235269 TAAA-TAAATTAATAATA-AAATAATAAAATA-TCATTTAA
1 TAAATTAAATTAA-AATATAAATAATAAAATATTCATTTAA
* *
5235307 -AAATTAAATTAAAATATAAATAA-ACTAATATTTATTTAA
1 TAAATTAAATTAAAATATAAATAATA-AAATATTCATTTAA
*
5235346 TTAATT-AATATAAAATAT
1 TAAATTAAAT-TAAAATAT
5235364 CACCAACATC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
37 8 0.17
38 18 0.38
39 10 0.21
40 12 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (40 bp):
TAAATTAAATTAAAATATAAATAATAAAATATTCATTTAA
Found at i:5237462 original size:2 final size:2
Alignment explanation
Indices: 5237457--5237482 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5237447 GCATTTTTCT
5237457 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5237483 CACGTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5244971 original size:25 final size:26
Alignment explanation
Indices: 5244915--5244978 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
5244905 TTGAGCCAGT
*
5244915 ATTCTTTTATTCTTTTTTTCGAGTAATT
1 ATTCTTTTATTCTTTTTTTC--GTAATC
5244943 ATTCTTTTATTC-TTTTTTC-TACATC
1 ATTCTTTTATTCTTTTTTTCGTA-ATC
5244968 ATTC-TTTATTC
1 ATTCTTTTATTC
5244979 ATTTCATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 9 0.26
25 6 0.18
27 7 0.21
28 12 0.35
ACGTcount: A:0.17, C:0.16, G:0.03, T:0.64
Consensus pattern (26 bp):
ATTCTTTTATTCTTTTTTTCGTAATC
Found at i:5248506 original size:1 final size:1
Alignment explanation
Indices: 5248500--5248609 Score: 58
Period size: 1 Copynumber: 110.0 Consensus size: 1
5248490 TACTTTTCTT
* * * * * * * * * * *
5248500 AAAAAAAAGAAAAGAAAAGAAAAAAAGAAAAAATAAAAATAAAATAAAATAAAAAAGAAAGAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
5248565 AAAAGAAAAAGAAAAAAAAGAAAGAAAGAAAAGAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5248610 GGAAAAGGAG
Statistics
Matches: 73, Mismatches: 36, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.04
Consensus pattern (1 bp):
A
Found at i:5248514 original size:5 final size:5
Alignment explanation
Indices: 5248500--5248616 Score: 92
Period size: 5 Copynumber: 25.0 Consensus size: 5
5248490 TACTTTTCTT
* * *
5248500 AAAA- AAAAG AAAAG AAAAG -AAA- AAAAG AAAA- AATA- AAAAT AAAAT
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
* *
5248545 AAAAT AAAAA AGAAAG -AAAG AAAAG AAAAAG AAAA- AAAAG -AAAG -AAAG
1 AAAAG AAAAG A-AAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG
*
5248593 AAAAG AAAAG AAAA- AAAGG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
5248617 GAGAGGCCAA
Statistics
Matches: 97, Mismatches: 6, Indels: 19
0.80 0.05 0.16
Matches are distributed among these distances:
4 35 0.36
5 54 0.56
6 8 0.08
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:5248525 original size:13 final size:13
Alignment explanation
Indices: 5248509--5248615 Score: 94
Period size: 13 Copynumber: 8.1 Consensus size: 13
5248499 TAAAAAAAAG
5248509 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
5248522 AAAAGAAAA-AATA
1 AAAAGAAAAGAA-A
* *
5248535 AAAATAAAATAAA
1 AAAAGAAAAGAAA
*
5248548 ATAA-AAAAGAAA
1 AAAAGAAAAGAAA
*
5248560 GAAAGAAAAGAAAA
1 AAAAGAAAAG-AAA
*
5248574 AGAAAAAAAAGAAA
1 A-AAAGAAAAGAAA
*
5248588 GAAAGAAAAGAAA
1 AAAAGAAAAGAAA
5248601 AGAAA-AAAAGGAAA
1 A-AAAGAAAA-GAAA
5248615 A
1 A
5248616 GGAGAGGCCA
Statistics
Matches: 77, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
12 11 0.14
13 42 0.55
14 16 0.21
15 8 0.10
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (13 bp):
AAAAGAAAAGAAA
Found at i:5248616 original size:28 final size:28
Alignment explanation
Indices: 5248500--5248616 Score: 125
Period size: 28 Copynumber: 4.2 Consensus size: 28
5248490 TACTTTTCTT
*
5248500 AAAAAAAAGAAAAGAAAAGAAAA-AAAG
1 AAAAGAAAGAAAAGAAAAGAAAAAAAAG
* * *
5248527 AAAA-AATA-AAAATAAAATAAAATAAAAA
1 AAAAGAA-AGAAAAGAAAAGAAAA-AAAAG
5248555 AGAAAGAAAGAAAAGAAAAAGAAAAAAAAG
1 A-AAAGAAAGAAAAG-AAAAGAAAAAAAAG
*
5248585 -AAAGAAAGAAAAGAAAAGAAAAAAAGG
1 AAAAGAAAGAAAAGAAAAGAAAAAAAAG
5248612 AAAAG
1 AAAAG
5248617 GAGAGGCCAA
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
26 14 0.19
27 18 0.24
28 21 0.28
29 4 0.05
30 10 0.13
31 8 0.11
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (28 bp):
AAAAGAAAGAAAAGAAAAGAAAAAAAAG
Found at i:5249920 original size:87 final size:87
Alignment explanation
Indices: 5249774--5250318 Score: 582
Period size: 87 Copynumber: 6.4 Consensus size: 87
5249764 GGTGAAACAG
5249774 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
5249839 GTGGAGAGGATTAACATTCAGA
66 GTGGAGAGGATTAACATTCAGA
5249861 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
*
5249926 GTGGAGCGGATTAACATTCAGA
66 GTGGAGAGGATTAACATTCAGA
* * * *
5249948 TCTTATCTCCCTGAAGTTGTAGTGGAACAGACAGAAGAAATCAATCCTATTTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
* *
5250013 GTGGAGCGGATTAACATCCAGA
66 GTGGAGAGGATTAACATTCAGA
** * * * * *
5250035 TCTTATCTTTCTGAGGTTGCA---GAG-AG-CAGATCG-CATCCAGTCTTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAT-CAATCCTATCTCCCTGAAGTTG
* * ** * *
5250094 CAGGGGAGTAGACAGAAAAAATCA-A
64 CAGTGGAG-AG-GATTAACATTCAGA
* ** * ** *
5250119 TCCTATCTCCCTGAAGTTGCAGTGGAGC-G---GATTAACATCCAGATCTTATCTTTCTGAGGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA-AT-CA-ATCCTATCTCCCTGAAGTT
* *
5250180 GCAG-AGAGCA-GA-TCACATTCAG-
63 GCAGTGGAG-AGGATTAACATTCAGA
*
5250202 TCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
* *
5250267 GTGGAGCGGATTAACATCCAGA
66 GTGGAGAGGATTAACATTCAGA
** * *
5250289 TCTTATCTTTCTGAGGTTGCAG-AGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
5250319 TCACATCCAG
Statistics
Matches: 379, Mismatches: 59, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
82 6 0.02
83 59 0.16
84 42 0.11
85 15 0.04
86 26 0.07
87 231 0.61
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
GTGGAGAGGATTAACATTCAGA
Found at i:5250094 original size:40 final size:40
Alignment explanation
Indices: 5249771--5250359 Score: 271
Period size: 44 Copynumber: 13.8 Consensus size: 40
5249761 ACCGGTGAAA
*
5249771 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAT-
1 CAGTCTTATCTCCCTGAAGTTGCA---GAG-AG-CAGATA-ACATC
* * * *
5249815 CAATCCTATCTCCCTGAAGTTGCAGTGGAG-AGGATTAACATT
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCA-GA-TAACATC
*
5249857 CAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAT-
1 CAG-TCTTATCTCCCTGAAGTTGCA---GAG-AG-CAGATA-ACATC
* * * * *
5249902 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATT
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-TAACATC
* * *
5249944 CAGATCTTATCTCCCTGAAGTTGTAGTGGAACAGACAGA-AGAAAT-
1 CAG-TCTTATCTCCCTGAAGTTGCA---G-AGAG-CAGATA-ACATC
* * * * * *
5249989 CAATCCTATTTCCCTGAAGTTGTAGTGGAGCGGATTAACATC
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-TAACATC
** * **
5250031 CAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
1 CAG-TCTTATCTCCCTGAAGTTGCAGAGAGCAGATAACATC
* *
5250072 CAGTCTTATCTCCCTGAAGTTGCAGGGGAGTAGACAGAAAAAAT-
1 CAGTCTTATCTCCCTGAAGTTGCA---GAG-AG-CAGATAACATC
* * * *
5250116 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATC
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-TAACATC
** * * *
5250158 CAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCACATT
1 CAG-TCTTATCTCCCTGAAGTTGCAGAGAGCAGATAACATC
*
5250199 CAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGA-AGAAAT-
1 CAGTCTTATCTCCCTGAAGTTGCA---GAG-AG-CAGATA-ACATC
* * * *
5250243 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATC
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-TAACATC
** * *
5250285 CAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCACATC
1 CAG-TCTTATCTCCCTGAAGTTGCAGAGAGCAGATAACATC
* *
5250326 CAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCAGA
5250360 CAGAAGAAAT
Statistics
Matches: 412, Mismatches: 85, Indels: 99
0.69 0.14 0.17
Matches are distributed among these distances:
39 1 0.00
40 68 0.17
41 63 0.15
42 36 0.09
43 97 0.24
44 109 0.26
45 20 0.05
46 12 0.03
47 5 0.01
48 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (40 bp):
CAGTCTTATCTCCCTGAAGTTGCAGAGAGCAGATAACATC
Found at i:5250107 original size:127 final size:127
Alignment explanation
Indices: 5249939--5250421 Score: 840
Period size: 127 Copynumber: 3.8 Consensus size: 127
5249929 GAGCGGATTA
* * * * *
5249939 ACATTCAGATCTTATCTCCCTGAAGTTGTAGTGGAACAGACAGAAGAAATCAATCCTATTTCCCT
1 ACATCCAG-TCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCT
*
5250004 GAAGTTGTAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
65 GAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
* * *
5250067 GCATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGTAGACAGAAAAAATCAATCCTATCTCCCTG
1 ACATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
5250132 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
66 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
*
5250194 ACATTCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
1 ACATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
5250259 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
66 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
* *
5250321 ACATCCAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
1 ACATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
*
5250386 AAGTTGCAGTGGAGCGGATTAACATCTAGATCTTAT
66 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTAT
5250422 GAGAGCAGAT
Statistics
Matches: 338, Mismatches: 17, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
127 332 0.98
128 6 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (127 bp):
ACATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
Found at i:5250295 original size:214 final size:216
Alignment explanation
Indices: 5249767--5250318 Score: 669
Period size: 214 Copynumber: 2.6 Consensus size: 216
5249757 ACAAACCGGT
5249767 GAAA-CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
1 GAAATCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
* * *
5249831 AAGTTGCAGTGGAGAGGATTAACATTCAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA
66 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGA
* *
5249896 AGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATTCAGATCTTATCTCCCTG
131 AAAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTG
* *
5249961 AAGTTGTAGTGGAACAGACAGAA
196 AAGTTGCAGTAGAACAGAC--AA
* * * * ** * **
5249984 GAAATCAATCCTATTTCCCTGAAGTTGTAGTGGAGC-G---GATTAACATCCAGATCTTATCTTT
1 GAAATCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA-AT-CA-ATCCTATCTCC
* * * ** *
5250045 CTGAGGTTGCAG-AGAGCAGA-TCGCATCCAG-TCTTATCTCCCTGAAGTTGCAGGGGAGTAGAC
63 CTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTGAAGTTGCAGGGGAGCAGAC
**
5250107 AGAAAAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTT
128 AGAAAAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCC
* *
5250172 CTGAGGTTGCAG-AGAGCAGATC-A
193 CTGAAGTTGCAGTAGAACAGA-CAA
* * *
5250195 -CATTCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
1 GAAATCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
** * *
5250259 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCA-GAGAGCAGA
66 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTGAAGTTGCAGGGGAGCAGA
5250319 TCACATCCAG
Statistics
Matches: 275, Mismatches: 48, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
210 28 0.10
211 21 0.08
212 8 0.03
213 23 0.08
214 128 0.47
215 9 0.03
216 7 0.03
217 24 0.09
218 27 0.10
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (216 bp):
GAAATCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGA
AAAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTG
AAGTTGCAGTAGAACAGACAA
Found at i:5251455 original size:21 final size:21
Alignment explanation
Indices: 5251430--5251469 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5251420 GGTCCCCTTG
5251430 TTTTTACATTT-TTTTAAATCA
1 TTTTT-CATTTCTTTTAAATCA
*
5251451 TTTTTTATTTCTTTTAAAT
1 TTTTTCATTTCTTTTAAAT
5251470 TTCGTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTCATTTCTTTTAAATCA
Found at i:5259333 original size:42 final size:43
Alignment explanation
Indices: 5259230--5259494 Score: 211
Period size: 43 Copynumber: 6.3 Consensus size: 43
5259220 TTATGTGGAA
* * * *
5259230 AAACGCCGCTATAGAACATGACCTTTTGCTGCG-TTTT--TA-
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
** * * * *
5259269 TGACGCCGCTATAGGACATGACCTTTAGCGGTGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
5259312 AAACGCCACTAAAGAA-ATGACCTTTAACGGCACTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
5259354 AAACGGCGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
5259397 AAACGCCGCTATAA-AACATGATC-TTAGCGGTGCTTTCCCCAC
1 AAACGCCGCTA-AAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * ** * * *
5259439 AAATGCTGCTAAAGAACAGGACTTTTAGTTGCGCTTTTACTAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
*
5259482 AAACGCCACTAAA
1 AAACGCCGCTAAA
5259495 TGTCATGTTC
Statistics
Matches: 175, Mismatches: 43, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
39 27 0.15
40 4 0.02
41 2 0.01
42 67 0.38
43 74 0.42
44 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:5259391 original size:43 final size:43
Alignment explanation
Indices: 5259230--5259476 Score: 227
Period size: 42 Copynumber: 5.9 Consensus size: 43
5259220 TTATGTGGAA
* * *
5259230 AAACGCCGCTATAGAACATGACCTTTTGCTGCG-TTTT--TA-
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
** * * *
5259269 TGACGCCGCTATAGGACATGACCTTTAGCGGTGCTTTTTCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
5259312 AAACGCCACTAAAGAA-ATGACCTTTAACGGCACTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
5259354 AAACGGCGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
5259397 AAACGCCGCTATAAAACATGATC-TTAGCGGTGCTTTCCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * * **
5259439 AAATGCTGCTAAAGAACAGGACTTTTAGTTGCGCTTTT
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTT
5259477 ACTAAAAACG
Statistics
Matches: 163, Mismatches: 39, Indels: 8
0.78 0.19 0.04
Matches are distributed among these distances:
39 27 0.17
40 4 0.02
42 68 0.42
43 64 0.39
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:5259438 original size:85 final size:84
Alignment explanation
Indices: 5259275--5259494 Score: 228
Period size: 85 Copynumber: 2.6 Consensus size: 84
5259265 TTTATGACGC
* * * *
5259275 CGCTATAGGACATGACCTTTAGCGGTGCTTTTTCCACAAACGCCACTAAAGAAATGACCTTTAAC
1 CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTAAAGAAATGACCTTTAAC
*
5259340 GGCACTTTTCCCACAAACGG
66 GGCACTTTCCCCACAAA-GG
* *
5259360 CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCGCTATAA-AACATGATC-TTA
1 CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTA-AAGAA-ATGACCTTTA
* ** *
5259423 GCGGTGCTTTCCCCACAAATG
64 ACGGCACTTTCCCCACAAAGG
* * * * * * *
5259444 CTGCTAAAGAACAGGACTTTTAGTTGCGCTTTTACTAAAAACGCCACTAAA
1 C-GCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTAAA
5259495 TGTCATGTTC
Statistics
Matches: 113, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
84 4 0.04
85 102 0.90
86 7 0.06
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (84 bp):
CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTAAAGAAATGACCTTTAAC
GGCACTTTCCCCACAAAGG
Found at i:5264584 original size:40 final size:40
Alignment explanation
Indices: 5264529--5264608 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5264519 ATATATTCTG
5264529 TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
1 TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
5264569 TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
1 TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
5264609 AGGCTGTTGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (40 bp):
TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
Found at i:5264820 original size:15 final size:15
Alignment explanation
Indices: 5264796--5264825 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5264786 TCCGATCCAC
*
5264796 CCTCCTAAACATTTT
1 CCTCCCAAACATTTT
5264811 CCTCCCAAACATTTT
1 CCTCCCAAACATTTT
5264826 AAGTGAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (15 bp):
CCTCCCAAACATTTT
Found at i:5265351 original size:20 final size:20
Alignment explanation
Indices: 5265326--5265366 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5265316 GAAAAATTTG
5265326 TACTCCATTTCGATAGTCAT
1 TACTCCATTTCGATAGTCAT
5265346 TACTCCATTTCGATAGTCAT
1 TACTCCATTTCGATAGTCAT
5265366 T
1 T
5265367 GCTTACCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (20 bp):
TACTCCATTTCGATAGTCAT
Done.