Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 191 of 210
Found at i:56261911 original size:21 final size:22
Alignment explanation
Indices: 56261872--56261924 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
56261862 TTCTCTTAAA
56261872 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
56261894 CTCTCAATTTCCTTCAAAAAAT-
1 CTCTCAAATTCCTTC-CAAAATC
56261916 CTCTCAAAT
1 CTCTCAAAT
56261925 CCATATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:56261983 original size:29 final size:29
Alignment explanation
Indices: 56261952--56262013 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
56261942 GTCCATTCAA
56261952 TTTCATTTTTTTAAAGAAAATTTTAAAAAT
1 TTTCATTTTTTTAAA-AAAATTTTAAAAAT
* * *
56261982 TTTTATTTTTTTAAAATAATTTTAAAATT
1 TTTCATTTTTTTAAAAAAATTTTAAAAAT
56262011 TTT
1 TTT
56262014 AATATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTCATTTTTTTAAAAAAATTTTAAAAAT
Found at i:56261992 original size:30 final size:28
Alignment explanation
Indices: 56261956--56262014 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 28
56261946 ATTCAATTTC
56261956 ATTTTTTTAAAGAAAATTTTAAAAATTTTT
1 ATTTTTTTAAA-AAAATTTT-AAAATTTTT
*
56261986 ATTTTTTTAAAATAATTTTAAAATTTTT
1 ATTTTTTTAAAAAAATTTTAAAATTTTT
56262014 A
1 A
56262015 ATATTTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 10 0.36
29 7 0.25
30 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
ATTTTTTTAAAAAAATTTTAAAATTTTT
Found at i:56262021 original size:28 final size:30
Alignment explanation
Indices: 56261960--56262021 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
56261950 AATTTCATTT
* *
56261960 TTTTAAAGAAAATTTTAAAAATTTTTATTT
1 TTTTAAAGAAAATTTTAAAAATTTTTAATA
*
56261990 TTTTAAA-ATAATTTT-AAAATTTTTAATA
1 TTTTAAAGAAAATTTTAAAAATTTTTAATA
56262018 TTTT
1 TTTT
56262022 CAACAATGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 15 0.52
29 7 0.24
30 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTAAAGAAAATTTTAAAAATTTTTAATA
Found at i:56262021 original size:29 final size:30
Alignment explanation
Indices: 56261959--56262021 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
56261949 CAATTTCATT
*
56261959 TTTTTAAAGAAAATTTTAAAAATTTTTATT
1 TTTTTAAAGAAAATTTTAAAAATTTTTATA
*
56261989 TTTTTAAA-ATAATTTT-AAAATTTTTAATA
1 TTTTTAAAGAAAATTTTAAAAATTTTT-ATA
56262018 TTTT
1 TTTT
56262022 CAACAATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 9 0.30
29 13 0.43
30 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTTAAAGAAAATTTTAAAAATTTTTATA
Found at i:56264006 original size:24 final size:24
Alignment explanation
Indices: 56263987--56264034 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
56263977 TTCAAACTCT
**
56263987 GTCACCGTTCATGATGCAAACACC
1 GTCACCGTTCACAATGCAAACACC
*
56264011 GTCGCCGTTCACAATGCAAACACC
1 GTCACCGTTCACAATGCAAACACC
56264035 TCCACATACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.19
Consensus pattern (24 bp):
GTCACCGTTCACAATGCAAACACC
Found at i:56264402 original size:29 final size:29
Alignment explanation
Indices: 56264320--56264649 Score: 341
Period size: 29 Copynumber: 11.5 Consensus size: 29
56264310 TATAATTTGT
*
56264320 TTAAAAACCC-AACCCTAACCTAATTTAA
1 TTAAAAACCCTAACCCTAATCTAATTTAA
* * * *
56264348 TTAAAAACCCTAAACTCAAACCTAATTAAA
1 TTAAAAACCCT-AACCCTAATCTAATTTAA
*
56264378 TTAAAAACCCTAACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAATCTAATTTAA
* * *
56264407 TTAAAAACCTTAAACCCAAATCTAATTAAA
1 TTAAAAACCCT-AACCCTAATCTAATTTAA
* *
56264437 TTAAAAACCCTGACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAATCTAATTTAA
* * * * *
56264466 TTAAAAATCCTAAACCTTGACCTAATTAAA
1 TTAAAAACCCT-AACCCTAATCTAATTTAA
* *
56264496 TTAAAAACCCTAACCCCAATTTAATTTAA
1 TTAAAAACCCTAACCCTAATCTAATTTAA
* * *
56264525 TTAAAAACCCTAACCCTAACCCATTTTAA
1 TTAAAAACCCTAACCCTAATCTAATTTAA
* *
56264554 TTAAAAATCCTAACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAATCTAATTTAA
* * * *
56264583 TTAAAATCCCTAACCCTAACCCATTTTAA
1 TTAAAAACCCTAACCCTAATCTAATTTAA
56264612 TTAAAAACCCTAACCC--A--T--TTTAA
1 TTAAAAACCCTAACCCTAATCTAATTTAA
56264635 TTAAAAACCCTAACC
1 TTAAAAACCCTAACC
56264650 ATTAACAAAA
Statistics
Matches: 249, Mismatches: 49, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
23 20 0.08
27 1 0.00
28 10 0.04
29 145 0.58
30 73 0.29
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.30
Consensus pattern (29 bp):
TTAAAAACCCTAACCCTAATCTAATTTAA
Found at i:56264565 original size:23 final size:23
Alignment explanation
Indices: 56264536--56264649 Score: 102
Period size: 23 Copynumber: 4.4 Consensus size: 23
56264526 TAAAAACCCT
56264536 AACCCTAACCCATTTTAATTAAA
1 AACCCTAACCCATTTTAATTAAA
*
56264559 AATCCTAACCCTAATTTAATTTAATTAAA
1 AACCCTAACCC--A--T--TTTAATTAAA
*
56264588 ATCCCTAACCCTAACCCATTTTAATTAAA
1 AACCCT------AACCCATTTTAATTAAA
56264617 AACCCTAACCCATTTTAATTAAA
1 AACCCTAACCCATTTTAATTAAA
56264640 AACCCTAACC
1 AACCCTAACC
56264650 ATTAACAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 24
0.73 0.04 0.23
Matches are distributed among these distances:
23 37 0.49
25 1 0.01
27 1 0.01
29 29 0.39
31 1 0.01
33 1 0.01
35 5 0.07
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (23 bp):
AACCCTAACCCATTTTAATTAAA
Found at i:56264577 original size:58 final size:59
Alignment explanation
Indices: 56264320--56264636 Score: 417
Period size: 59 Copynumber: 5.4 Consensus size: 59
56264310 TATAATTTGT
** * *
56264320 TTAAAAACCC-AACCCTAACCTAATTTAATTAAAAACCCTAAACTCAAACCTAATTAAA
1 TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAA
* * *
56264378 TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCTTAAACCCAAATCTAATTAAA
1 TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAA
* * * *
56264437 TTAAAAACCCTGACCCTAATTTAATTTAATTAAAAATCCTAAACCTTGACCTAATTAAA
1 TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAA
* * * *
56264496 TTAAAAACCCTAACCCCAATTTAATTTAATTAAAAACCCT-AACCCTAACCCATTTTAA
1 TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAA
* * * * *
56264554 TTAAAAATCCTAACCCTAATTTAATTTAATTAAAATCCCT-AACCCTAACCCATTTTAA
1 TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAA
*
56264612 TTAAAAACCCTAACCC-ATTTTAATT
1 TTAAAAACCCTAACCCTAATTTAATT
56264637 AAAAACCCTA
Statistics
Matches: 233, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
57 8 0.03
58 93 0.40
59 132 0.57
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.31
Consensus pattern (59 bp):
TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAA
Found at i:56264652 original size:22 final size:23
Alignment explanation
Indices: 56264594--56264649 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
56264584 TAAAATCCCT
56264594 AACCCTAACCCATTTTAATTAAA
1 AACCCTAACCCATTTTAATTAAA
56264617 AACCCTAACCCATTTTAATTAAA
1 AACCCTAACCCATTTTAATTAAA
56264640 AACCCTAACC
1 AACCCTAACC
56264650 ATTAACAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (23 bp):
AACCCTAACCCATTTTAATTAAA
Found at i:56267995 original size:124 final size:124
Alignment explanation
Indices: 56267774--56268054 Score: 424
Period size: 124 Copynumber: 2.3 Consensus size: 124
56267764 CCACGAGGGC
* * *
56267774 GCGATTTGACACTATTTGCTCAGAAACATCAAAAAATAATTATTTCCTACATGACCAACTGTAGC
1 GCGATTTTATACTATTTGCTCAGAAACGTC-AAAAATAATTATTTCCTACATGACCAACTGTAGC
* **
56267839 GAAATCGAGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCA
65 GAAATCGAGTCCACGAGGGCACGATTTCACAATTTCTTCTC-TGATAGCATCCTGGTAGAA
*
56267899 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAA-AATTATTTCTTACATGACCAACTGTAGC
1 GCGATTTTATACTATTTGCTCAG-AAACGTCAAAAATAATTATTTCCTACATGACCAACTGTAGC
*
56267963 GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAA
65 GAAATCGAGTCCACGAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAA
*
56268023 GCAATTTTATACTATTTGAC-CAGAAACGTCAA
1 GCGATTTTATACTATTTG-CTCAGAAACGTCAA
56268055 CTCGAAATAA
Statistics
Matches: 144, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
123 10 0.07
124 101 0.70
125 27 0.19
126 6 0.04
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (124 bp):
GCGATTTTATACTATTTGCTCAGAAACGTCAAAAATAATTATTTCCTACATGACCAACTGTAGCG
AAATCGAGTCCACGAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAA
Found at i:56270834 original size:30 final size:30
Alignment explanation
Indices: 56270794--56270852 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
56270784 TAGTGAAAAG
* * *
56270794 GTAATAAAATAATGAAAAAACAAGAAAATA
1 GTAACAAAATAATAAAAAAACAACAAAATA
* *
56270824 GTAACAAAATATTAAAAAAATAACAAAAT
1 GTAACAAAATAATAAAAAAACAACAAAAT
56270853 TTTTTGCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (30 bp):
GTAACAAAATAATAAAAAAACAACAAAATA
Found at i:56272005 original size:20 final size:20
Alignment explanation
Indices: 56271977--56272015 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56271967 AATGATTTGA
*
56271977 TTAAATAAATTATTAAAAAT
1 TTAAATAAAATATTAAAAAT
*
56271997 TTAATTAAAATATTAAAAA
1 TTAAATAAAATATTAAAAA
56272016 AAATTGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAATAAAATATTAAAAAT
Found at i:56273555 original size:43 final size:42
Alignment explanation
Indices: 56273489--56273714 Score: 186
Period size: 43 Copynumber: 5.3 Consensus size: 42
56273479 CTAATGGCAG
* * *
56273489 TTTAT-TTGCAAAAATGTTATGCATCCACAACATAATGGAAGTT
1 TTTATCTT-CAAATATGTTGTGCATCCACAAC-TAGTGGAAGTT
* * * * *
56273532 TTTATCTTCAAATATGTTGTGCATCCATAGCCCAGTAGTAGTT
1 TTTATCTTCAAATATGTTGTGCATCCACA-ACTAGTGGAAGTT
* * * * *
56273575 TTTATCTACAAGTATGTTGTGCATCTACAACCTAGTGGCAGCT
1 TTTATCTTCAAATATGTTGTGCATCCACAA-CTAGTGGAAGTT
* * * * *
56273618 TTTAT-ATCAAATATGTTGTGCAACAACAACCAGTGAAAGTT
1 TTTATCTTCAAATATGTTGTGCATCCACAACTAGTGGAAGTT
* * * *
56273659 TTTATCTGCAAATATGTTGTGCATCTACAACTCAATGGTAGTT
1 TTTATCTTCAAATATGTTGTGCATCCACAACT-AGTGGAAGTT
*
56273702 TTTATCTGCAAAT
1 TTTATCTTCAAAT
56273715 CAGTGGTAGT
Statistics
Matches: 144, Mismatches: 34, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
41 13 0.09
42 40 0.28
43 88 0.61
44 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (42 bp):
TTTATCTTCAAATATGTTGTGCATCCACAACTAGTGGAAGTT
Found at i:56273647 original size:42 final size:42
Alignment explanation
Indices: 56273587--56273681 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
56273577 TATCTACAAG
* * **
56273587 TATGTTGTGCATCTACAACCTAGTGGCAGCTTTTATAT-CAAA
1 TATGTTGTGCAACAACAACC-AGTGAAAGCTTTTATATGCAAA
* *
56273629 TATGTTGTGCAACAACAACCAGTGAAAGTTTTTATCTGCAAA
1 TATGTTGTGCAACAACAACCAGTGAAAGCTTTTATATGCAAA
56273671 TATGTTGTGCA
1 TATGTTGTGCA
56273682 TCTACAACTC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 13 0.28
42 33 0.72
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (42 bp):
TATGTTGTGCAACAACAACCAGTGAAAGCTTTTATATGCAAA
Found at i:56273676 original size:84 final size:86
Alignment explanation
Indices: 56273489--56273707 Score: 230
Period size: 84 Copynumber: 2.6 Consensus size: 86
56273479 CTAATGGCAG
* * * * * *
56273489 TTTATTTGCAAAAATGTTATGCATCCACAACATAATGGAAGTTTTTATCTTCAAATATGTTGTGC
1 TTTATCTGCAAATATGTTGTGCATCTACAACATAATGGAAGCTTTTATCATCAAATATGTTGTGC
* * * * *
56273554 ATCCATAGCCCAGTAGTAGTT
66 AACAACAGACCAGTAGAAGTT
* * * * *
56273575 TTTATCTACAAGTATGTTGTGCATCTACAACCTAGTGGCAGCTTTTAT-ATCAAATATGTTGTGC
1 TTTATCTGCAAATATGTTGTGCATCTACAACATAATGGAAGCTTTTATCATCAAATATGTTGTGC
56273639 AACAACA-ACCAGT-GAAAGTT
66 AACAACAGACCAGTAG-AAGTT
* *
56273659 TTTATCTGCAAATATGTTGTGCATCTACAAC-TCAATGGTAGTTTTTATC
1 TTTATCTGCAAATATGTTGTGCATCTACAACAT-AATGGAAGCTTTTATC
56273708 TGCAAATCAG
Statistics
Matches: 109, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
83 2 0.02
84 50 0.46
85 19 0.17
86 38 0.35
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (86 bp):
TTTATCTGCAAATATGTTGTGCATCTACAACATAATGGAAGCTTTTATCATCAAATATGTTGTGC
AACAACAGACCAGTAGAAGTT
Found at i:56289051 original size:23 final size:23
Alignment explanation
Indices: 56289025--56289146 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
56289015 ATAAGTGCAA
*
56289025 CACTGATATGTAGCCGAAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
*
56289048 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
56289071 CACTGAAATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
56289094 CACT-ATTATGTAGCCGAAGCTAC
1 CACTGA-TATGTAGCCGAAGCTAC
* *
56289117 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
56289140 CACTGAT
1 CACTGAT
56289147 CAATAACACT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
22 1 0.01
23 85 0.98
24 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:56289095 original size:46 final size:46
Alignment explanation
Indices: 56289025--56289144 Score: 195
Period size: 46 Copynumber: 2.6 Consensus size: 46
56289015 ATAAGTGCAA
* *
56289025 CACTGATATGTAGCCGAAGTTACCACTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
* *
56289071 CACTGAAATGTAACCGAAGCTACCACTATTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
*
56289117 CACTGAAACGTAGCCGAAGCTACCACTG
1 CACTGAAATGTAGCCGAAGCTACCACTG
56289145 ATCAATAACA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
Found at i:56290580 original size:41 final size:40
Alignment explanation
Indices: 56290489--56290599 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 40
56290479 CGACTTCAAG
* * *
56290489 TCGATGAGGCACTGGGTGCCAA-TT-C-ACTTCGGTTTAA
1 TCGATGAGACACTGGGTGTCAATTTACTACTTCGATTTAA
*
56290526 TCGATGAGACACTGGGTGTCAATTTACTACTTCGAATTTAT
1 TCGATGAGACACTGGGTGTCAATTTACTACTTCG-ATTTAA
56290567 TCGATGAGACACTGGGTGTCAATTTACTACTTC
1 TCGATGAGACACTGGGTGTCAATTTACTACTTC
56290600 AAAATATCCG
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
37 20 0.30
38 2 0.03
39 1 0.02
40 6 0.09
41 37 0.56
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAATTTACTACTTCGATTTAA
Found at i:56290623 original size:40 final size:41
Alignment explanation
Indices: 56290527--56290624 Score: 144
Period size: 41 Copynumber: 2.4 Consensus size: 41
56290517 TCGGTTTAAT
** *
56290527 CGATGAGACACTGGGTGTCAATTTACTACTTCGAATTTATT
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGAAAATATC
56290568 CGATGAGACACTGGGTGTCAATTTACTACTTC-AAAATATC
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGAAAATATC
* *
56290608 CGATGAGGCATTGGGTG
1 CGATGAGACACTGGGTG
56290625 CCAAACTGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
40 20 0.38
41 32 0.62
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (41 bp):
CGATGAGACACTGGGTGTCAATTTACTACTTCGAAAATATC
Found at i:56292227 original size:23 final size:23
Alignment explanation
Indices: 56292201--56292248 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
56292191 GTATTACAAC
* *
56292201 GCAATTCATTCTGGCACTACGAT
1 GCAACTCATTCTAGCACTACGAT
*
56292224 GCAACTCATTCTAGCACTTCGAT
1 GCAACTCATTCTAGCACTACGAT
56292247 GC
1 GC
56292249 GTTACAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (23 bp):
GCAACTCATTCTAGCACTACGAT
Found at i:56295014 original size:45 final size:45
Alignment explanation
Indices: 56294963--56295078 Score: 126
Period size: 45 Copynumber: 2.6 Consensus size: 45
56294953 CGTTGGTTGA
*
56294963 AAACGAGTAAGACTATAGCTGAAAGACGCTATAACATCACGAATC
1 AAACGAGTAAGACTATAGTTGAAAGACGCTATAACATCACGAATC
* * * ** * *
56295008 AAACGAGTAA-AATCATAGTTGAAAAATGCTATGGCATCATGATTC
1 AAACGAGTAAGACT-ATAGTTGAAAGACGCTATAACATCACGAATC
* *
56295053 AAACGTGTAAGACCATAGTTGAAAGA
1 AAACGAGTAAGACTATAGTTGAAAGA
56295079 TACAATGACA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
44 2 0.04
45 54 0.95
46 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.22
Consensus pattern (45 bp):
AAACGAGTAAGACTATAGTTGAAAGACGCTATAACATCACGAATC
Found at i:56295206 original size:47 final size:45
Alignment explanation
Indices: 56295060--56295221 Score: 191
Period size: 45 Copynumber: 3.6 Consensus size: 45
56295050 TTCAAACGTG
* * **
56295060 TAAGACCATAGTTGAAAGATACAATGAC-ACTATATAAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAAC-ATATCGAAAATGAA
* *
56295105 TAAGACCATAGTTGAAAGACATTATGACAATATATCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATATCGAAAATGAA
* * * *
56295150 TAAGGCCATAATTGAAAGACACTATGGCAACATGATGGAGAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAACAT-ATCGA-AAATGAA
*
56295197 TAAGACCATAGTTGAAAGGCACTAT
1 TAAGACCATAGTTGAAAGACACTAT
56295222 AACATCAGGT
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 65 0.66
46 5 0.05
47 29 0.29
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGACAACATATCGAAAATGAA
Found at i:56295244 original size:92 final size:92
Alignment explanation
Indices: 56295098--56295270 Score: 204
Period size: 92 Copynumber: 1.9 Consensus size: 92
56295088 ACTATATAAA
* * * * * *
56295098 AAATGAATAAGACCATAGTTGAAAGACATTATGACAATATATCGAAAATGAATAAGGCCATAATT
1 AAATGAATAAGACCATAGTTGAAAGACACTATAACAATAGATCGAAAATAAATAAGACCATAACT
*
56295163 GAAAGACACTATGGCAACATGATGGAG
66 GAAAGACACCATGGCAACATGATGGAG
* * * ** **
56295190 AAATGAATAAGACCATAGTTGAAAGGCACTATAAC-ATCAGGTTGGGAATAAATAAGACCATGGC
1 AAATGAATAAGACCATAGTTGAAAGACACTATAACAAT-AGATCGAAAATAAATAAGACCATAAC
56295254 TGAAAGACACCATGGCA
65 TGAAAGACACCATGGCA
56295271 TCCTTCAACC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
91 2 0.03
92 64 0.97
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (92 bp):
AAATGAATAAGACCATAGTTGAAAGACACTATAACAATAGATCGAAAATAAATAAGACCATAACT
GAAAGACACCATGGCAACATGATGGAG
Found at i:56299899 original size:14 final size:15
Alignment explanation
Indices: 56299868--56299900 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
56299858 ATTAGTTGTA
*
56299868 ATGTTTTACTATGTC
1 ATGTTTTACTATGGC
56299883 ATGTTTTA-TATGGC
1 ATGTTTTACTATGGC
56299897 ATGT
1 ATGT
56299901 ACCTAAGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.52
Consensus pattern (15 bp):
ATGTTTTACTATGGC
Found at i:56300982 original size:40 final size:40
Alignment explanation
Indices: 56300927--56301052 Score: 252
Period size: 40 Copynumber: 3.1 Consensus size: 40
56300917 CTTACTAAGC
56300927 ATTGTTGTTGCTTACCTTAGTTGTTTTCTTTCCCTCGTAG
1 ATTGTTGTTGCTTACCTTAGTTGTTTTCTTTCCCTCGTAG
56300967 ATTGTTGTTGCTTACCTTAGTTGTTTTCTTTCCCTCGTAG
1 ATTGTTGTTGCTTACCTTAGTTGTTTTCTTTCCCTCGTAG
56301007 ATTGTTGTTGCTTACCTTAGTTGTTTTCTTTCCCTCGTAG
1 ATTGTTGTTGCTTACCTTAGTTGTTTTCTTTCCCTCGTAG
56301047 ATTGTT
1 ATTGTT
56301053 ACCTTGCAGA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 86 1.00
ACGTcount: A:0.10, C:0.19, G:0.17, T:0.53
Consensus pattern (40 bp):
ATTGTTGTTGCTTACCTTAGTTGTTTTCTTTCCCTCGTAG
Found at i:56303301 original size:2 final size:2
Alignment explanation
Indices: 56303294--56303325 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56303284 GTCATTTAAA
56303294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56303326 TACATTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56305948 original size:2 final size:2
Alignment explanation
Indices: 56305941--56305967 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56305931 GAGACAAAAG
56305941 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 A
56305968 CATGTCACAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56307202 original size:19 final size:17
Alignment explanation
Indices: 56307174--56307213 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
56307164 TTATAAATTT
*
56307174 TTAAACAAATTAATATAAA
1 TTAAA-AAAATAA-ATAAA
56307193 TTAAAAAAATAAATAAA
1 TTAAAAAAATAAATAAA
56307210 TTAA
1 TTAA
56307214 CCATGGTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 6 0.30
19 5 0.25
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TTAAAAAAATAAATAAA
Found at i:56309392 original size:53 final size:53
Alignment explanation
Indices: 56309331--56309433 Score: 206
Period size: 53 Copynumber: 1.9 Consensus size: 53
56309321 ATCCGTTGGC
56309331 CTAATTCTCCATGGCGACTACTGCAGGTATTTTAGTTTTACATTATCAATTGT
1 CTAATTCTCCATGGCGACTACTGCAGGTATTTTAGTTTTACATTATCAATTGT
56309384 CTAATTCTCCATGGCGACTACTGCAGGTATTTTAGTTTTACATTATCAAT
1 CTAATTCTCCATGGCGACTACTGCAGGTATTTTAGTTTTACATTATCAAT
56309434 CGTCATTGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (53 bp):
CTAATTCTCCATGGCGACTACTGCAGGTATTTTAGTTTTACATTATCAATTGT
Found at i:56326747 original size:119 final size:119
Alignment explanation
Indices: 56326536--56326772 Score: 465
Period size: 119 Copynumber: 2.0 Consensus size: 119
56326526 GTTCCTGCTT
56326536 CCGATTTGCTTAATAGTTAAATAAGTTCAATAGTGATGGCTGGTTTGCGATTCTTGCTTTTGCCT
1 CCGATTTGCTTAATAGTTAAATAAGTTCAATAGTGATGGCTGGTTTGCGATTCTTGCTTTTGCCT
56326601 AAGTTCCTGTTTTTTTATACTTGCTTAGAGGCCGCCACATTTCATCTTCTTGTC
66 AAGTTCCTGTTTTTTTATACTTGCTTAGAGGCCGCCACATTTCATCTTCTTGTC
56326655 CCGATTTGCTTAATAGTTAAATAAGTTCAATAGTGATGGCTGGTTTGCGATTCTTGCTTTTGCCT
1 CCGATTTGCTTAATAGTTAAATAAGTTCAATAGTGATGGCTGGTTTGCGATTCTTGCTTTTGCCT
*
56326720 AAGTTCCTGTTTTTTTATACTTGCTTAGAGGCCGCCACATTTCTTCTTCTTGT
66 AAGTTCCTGTTTTTTTATACTTGCTTAGAGGCCGCCACATTTCATCTTCTTGT
56326773 TTTTTTTTTC
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 117 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (119 bp):
CCGATTTGCTTAATAGTTAAATAAGTTCAATAGTGATGGCTGGTTTGCGATTCTTGCTTTTGCCT
AAGTTCCTGTTTTTTTATACTTGCTTAGAGGCCGCCACATTTCATCTTCTTGTC
Found at i:56326847 original size:16 final size:16
Alignment explanation
Indices: 56326826--56326859 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56326816 AACTTTTAAG
56326826 TGAATAAAAAAAACAA
1 TGAATAAAAAAAACAA
* *
56326842 TGAATAGAAAAAAGAA
1 TGAATAAAAAAAACAA
56326858 TG
1 TG
56326860 GATACACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.15, T:0.15
Consensus pattern (16 bp):
TGAATAAAAAAAACAA
Found at i:56329220 original size:25 final size:25
Alignment explanation
Indices: 56329184--56329243 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
56329174 TGCAAGCAGT
* *
56329184 TTTATAG-ATTGATGTAGTTTGTCG
1 TTTATAGTTTTGATGTAGTTTGTAG
56329208 TTTATAGTTTTGATGTAGTTTGTAG
1 TTTATAGTTTTGATGTAGTTTGTAG
*
56329233 TTTATGGTTTT
1 TTTATAGTTTT
56329244 TCTGTTAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 7 0.22
25 25 0.78
ACGTcount: A:0.18, C:0.02, G:0.23, T:0.57
Consensus pattern (25 bp):
TTTATAGTTTTGATGTAGTTTGTAG
Found at i:56331084 original size:63 final size:63
Alignment explanation
Indices: 56331006--56331195 Score: 330
Period size: 63 Copynumber: 3.0 Consensus size: 63
56330996 TTTTCAATAT
*
56331006 TTATATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAAGAAC
1 TTATATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAAC
*
56331069 TTATATCAGTTATAGTTCTGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAAC
1 TTATATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAAC
* *
56331132 -T-TATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGCGGATGGGATATCAACAAC
1 TTATATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAAC
56331193 TTA
1 TTA
56331196 GCATGAATCA
Statistics
Matches: 120, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
61 57 0.47
62 2 0.02
63 61 0.51
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31
Consensus pattern (63 bp):
TTATATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAAC
Found at i:56331167 original size:61 final size:61
Alignment explanation
Indices: 56331009--56331195 Score: 320
Period size: 61 Copynumber: 3.0 Consensus size: 61
56330999 TCAATATTTA
*
56331009 TATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAAGAACTT
1 TATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAAC-T
*
56331071 ATATCAGTTATAGTTCTGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAACT
1 -TATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAACT
* *
56331133 TATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGCGGATGGGATATCAACAACT
1 TATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAACT
56331194 TA
1 TA
56331196 GCATGAATCA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
61 60 0.50
62 1 0.01
63 58 0.49
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (61 bp):
TATCAGTTATAGTTCCGCTGGTAGAGTGCTATCGAAATAAGTGAATGGGATATCAACAACT
Found at i:56338590 original size:2 final size:2
Alignment explanation
Indices: 56338583--56338612 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
56338573 GTCTGAAGAG
*
56338583 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56338613 CCAATCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56345537 original size:17 final size:19
Alignment explanation
Indices: 56345502--56345544 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
56345492 AAAAATTAAA
56345502 AAAT-ATTTTATACTTTTT
1 AAATAATTTTATACTTTTT
56345520 AAATAATTTT-TA-TTTTT
1 AAATAATTTTATACTTTTT
*
56345537 AAAAAATT
1 AAATAATT
56345545 AATTAATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 6 0.26
19 5 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATAATTTTATACTTTTT
Found at i:56347726 original size:2 final size:2
Alignment explanation
Indices: 56347719--56347763 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
56347709 AAAAGCAATA
*
56347719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56347761 AT A
1 AT A
56347764 AAAGAGAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:56348392 original size:60 final size:60
Alignment explanation
Indices: 56348320--56348432 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
56348310 AATTTGACAC
* *
56348320 TTTTTTCCTAATTTGATACTTAAAATTTTTTTGGGTCCAATTTGGTACCTAAACTTCATA
1 TTTTTTCCTAATTTGATACTTAAAATTTTTTTAGGTCCAATTTGATACCTAAACTTCATA
* * ** *
56348380 TTTTTTCTTAATTTGGTACTTAATCTTTTTTTAGGTTCAATTTGATACCTAAA
1 TTTTTTCCTAATTTGATACTTAAAATTTTTTTAGGTCCAATTTGATACCTAAA
56348433 TTTGTTAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (60 bp):
TTTTTTCCTAATTTGATACTTAAAATTTTTTTAGGTCCAATTTGATACCTAAACTTCATA
Found at i:56348645 original size:4 final size:4
Alignment explanation
Indices: 56348636--56348667 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
56348626 TCAATTAATA
56348636 AAAT AAAT AAAT AAAT AAAT AAAT AAACT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAA
56348668 AGTAATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:56348902 original size:32 final size:32
Alignment explanation
Indices: 56348840--56348978 Score: 141
Period size: 31 Copynumber: 4.5 Consensus size: 32
56348830 ACCTCCCAAA
* * *
56348840 AAGTTTAAGTACCAACTTAAG-AAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGGAAAAAAGTGTC
*
56348871 AAGTTTAGGTATCAAATTAGGAAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGGAAAAAAGTGTC
*
56348903 AAGTTTGGGTACCAAATT-GGACCAAAAA-----
1 AAGTTTAGGTACCAAATTAGGA--AAAAAGTGTC
* *
56348931 AAGATTAGGTACCAAATTA-GAAAAAAGTGCC
1 AAGTTTAGGTACCAAATTAGGAAAAAAGTGTC
56348962 AAGTTTAGGTACCAAAT
1 AAGTTTAGGTACCAAAT
56348979 ATTATATTAA
Statistics
Matches: 90, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
26 5 0.06
28 18 0.20
31 36 0.40
32 26 0.29
33 5 0.06
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (32 bp):
AAGTTTAGGTACCAAATTAGGAAAAAAGTGTC
Found at i:56348970 original size:91 final size:92
Alignment explanation
Indices: 56348785--56348978 Score: 268
Period size: 91 Copynumber: 2.1 Consensus size: 92
56348775 AACAAAAAAA
** *
56348785 AGGTACCAAATTAGGAAAAAGAGTCAAGTTCGGGTACCAAATTGGACCTCCCAAAAAGTTTAAGT
1 AGGTACCAAATTAGGAAAAAGAGTCAAGTTCGGGTACCAAATTGGACCTCAAAAAAAGATTAAGT
* *
56348850 ACCAACTTAAGAAAAAGTGTCAAGTTT
66 ACCAAATTAAGAAAAAGTGCCAAGTTT
* * * *
56348877 AGGTATCAAATTAGGAAAAAAGTGTCAAGTTTGGGTACCAAATTGGA-C-CAAAAAAAGATTAGG
1 AGGTACCAAATTAGG-AAAAAGAGTCAAGTTCGGGTACCAAATTGGACCTCAAAAAAAGATTAAG
56348940 TACCAAATT-AGAAAAAAGTGCCAAGTTT
65 TACCAAATTAAG-AAAAAGTGCCAAGTTT
56348968 AGGTACCAAAT
1 AGGTACCAAAT
56348979 ATTATATTAA
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
90 2 0.02
91 44 0.49
92 15 0.17
93 29 0.32
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (92 bp):
AGGTACCAAATTAGGAAAAAGAGTCAAGTTCGGGTACCAAATTGGACCTCAAAAAAAGATTAAGT
ACCAAATTAAGAAAAAGTGCCAAGTTT
Found at i:56356099 original size:12 final size:12
Alignment explanation
Indices: 56356084--56356108 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56356074 TACAATAAGC
56356084 AAAAAAATATTT
1 AAAAAAATATTT
56356096 AAAAAAATATTT
1 AAAAAAATATTT
56356108 A
1 A
56356109 TTCTGAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAAAATATTT
Found at i:56356819 original size:29 final size:31
Alignment explanation
Indices: 56356748--56356824 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
56356738 TTAACGGCTC
* *
56356748 AGTGACTAAAATGTTACAATACGATAACGTA
1 AGTGACTAAAATGTAACAATACGATAACATA
* *
56356779 AGTGACTAAAATGTAACATTTC-A-AACATA
1 AGTGACTAAAATGTAACAATACGATAACATA
56356808 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
56356825 TTGAGGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 22 0.52
30 1 0.02
31 19 0.45
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (31 bp):
AGTGACTAAAATGTAACAATACGATAACATA
Found at i:56357254 original size:27 final size:27
Alignment explanation
Indices: 56357203--56357279 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 27
56357193 GGGTATGGTG
* * *
56357203 CCTATCTGATAGGCGACACCAGTGATC
1 CCTATCTGATAGGCGGCACTAGTGACC
* *
56357230 CCTATTTGATAGGCGGCACTGGTGACC
1 CCTATCTGATAGGCGGCACTAGTGACC
* *
56357257 CCTATCTCATAGGTGGCACTAGT
1 CCTATCTGATAGGCGGCACTAGT
56357280 ACCATTTCCC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (27 bp):
CCTATCTGATAGGCGGCACTAGTGACC
Found at i:56357395 original size:18 final size:18
Alignment explanation
Indices: 56357363--56357413 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
56357353 AGAGAGGTAG
*
56357363 AAGAGAAGAATGAAAGAA
1 AAGAGAAGAAAGAAAGAA
* *
56357381 AATAGGAGAAAGAAAGAA
1 AAGAGAAGAAAGAAAGAA
56357399 AAGAGAAGAAAGAAA
1 AAGAGAAGAAAGAAA
56357414 ATGTATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (18 bp):
AAGAGAAGAAAGAAAGAA
Found at i:56361556 original size:3 final size:3
Alignment explanation
Indices: 56361487--56361541 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
56361477 TGCTCTCTCA
56361487 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
56361535 -TC TTC TT
1 TTC TTC TT
56361542 TAAAGATTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:56361734 original size:31 final size:31
Alignment explanation
Indices: 56361693--56361751 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
56361683 GACCAGGGGT
*
56361693 GTGCTGCCTCTCCAGTAGGCACGACCAGCTA
1 GTGCCGCCTCTCCAGTAGGCACGACCAGCTA
*
56361724 GTGCCGCCTCTCCAGTAGGCATGACCAG
1 GTGCCGCCTCTCCAGTAGGCACGACCAG
56361752 TGCTGCTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.19, C:0.36, G:0.27, T:0.19
Consensus pattern (31 bp):
GTGCCGCCTCTCCAGTAGGCACGACCAGCTA
Found at i:56368373 original size:23 final size:23
Alignment explanation
Indices: 56368316--56368377 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
56368306 AGCAAGCAAA
* *
56368316 AAGATAAAAAA-AATATAAGAAG
1 AAGAAAAAAAAGAAAATAAGAAG
*
56368338 AAGAAAAACAAAGAAAATAGGAA-
1 AAGAAAAA-AAAGAAAATAAGAAG
56368361 AAGAAACAAAAAGAAAA
1 AAGAAA-AAAAAGAAAA
56368378 GAACGATAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 7 0.21
23 17 0.50
24 10 0.29
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (23 bp):
AAGAAAAAAAAGAAAATAAGAAG
Found at i:56373384 original size:9 final size:9
Alignment explanation
Indices: 56373365--56373393 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
56373355 GACTGAATTT
56373365 TAAAT-ATA
1 TAAATAATA
56373373 TAAATAATA
1 TAAATAATA
56373382 TAAATAATA
1 TAAATAATA
56373391 TAA
1 TAA
56373394 CATCACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAATAATA
Found at i:56377356 original size:11 final size:11
Alignment explanation
Indices: 56377342--56377390 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
56377332 AAATAGTGAA
*
56377342 AAAATAATAAG
1 AAAATAACAAG
*
56377353 AAAATAACAAC
1 AAAATAACAAG
*
56377364 AAAATAATAA-
1 AAAATAACAAG
*
56377374 AAAATAGCAAG
1 AAAATAACAAG
56377385 AAAATA
1 AAAATA
56377391 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 8 0.25
11 24 0.75
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.14
Consensus pattern (11 bp):
AAAATAACAAG
Found at i:56377379 original size:21 final size:22
Alignment explanation
Indices: 56377342--56377390 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
56377332 AAATAGTGAA
56377342 AAAATAATAAGAAAATAACAAC
1 AAAATAATAAGAAAATAACAAC
* *
56377364 AAAATAATAA-AAAATAGCAAG
1 AAAATAATAAGAAAATAACAAC
56377385 AAAATA
1 AAAATA
56377391 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.14
Consensus pattern (22 bp):
AAAATAATAAGAAAATAACAAC
Found at i:56377990 original size:91 final size:92
Alignment explanation
Indices: 56377850--56378022 Score: 235
Period size: 91 Copynumber: 1.9 Consensus size: 92
56377840 GATATTTATC
* * * *
56377850 TTTTATAAAAAAGTTTAATGTGGTACTTATATTTTGAAAATGTCAAATGTGGTA-TATGAGCTAT
1 TTTTATAAAAAAGTTCAATGTGATACTTACATTTTGAAAATGTCAAATGTGGTACT-TGAACTAT
**
56377914 CAATTTGTGTATTATTTAGTACATGTAT
65 CAACCTGTGTATTATTTAGTACATGTAT
* *
56377942 TTTTATAAAATA-TTCAATGTGATACTTACCTTTTGAAAATGTTC-AATGTGGTACTTGAACTAT
1 TTTTATAAAAAAGTTCAATGTGATACTTACATTTTGAAAATG-TCAAATGTGGTACTTGAACTAT
56378005 CAACCTGTGTATTATTTA
65 CAACCTGTGTATTATTTA
56378023 TGGTATCTGG
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
91 57 0.80
92 14 0.20
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (92 bp):
TTTTATAAAAAAGTTCAATGTGATACTTACATTTTGAAAATGTCAAATGTGGTACTTGAACTATC
AACCTGTGTATTATTTAGTACATGTAT
Found at i:56379464 original size:192 final size:192
Alignment explanation
Indices: 56379225--56379570 Score: 548
Period size: 192 Copynumber: 1.8 Consensus size: 192
56379215 GGAAAAAATG
*
56379225 ATGATTTTAAGTTGAAAGTGTGGTGTGAGTTTACAAAAATTACACAAAAGCATGATTATAATCAT
1 ATGATTTTAAGTTGAAAGTATGGTGTGAGTTTACAAAAATTACACAAAAGCATGATTATAATCAT
* * * * *
56379290 GCTAATGGAAAATCTTGTAGATGAAATGAACTAACCATATGTTTTGAAGAAGAAAAGTGATGTTT
66 GCTAATAGAAAATCTTGTAGATGAAATGAACCAACCATATGTTTTGAAAAAGAAAAATGATCTTT
* *
56379355 GGCAAGAGAGAAAATGAGAAAAAAAAATGACAACCGACAGTGGTGGGGGGGGGGGGAGGACA
131 GGCAAGAAAAAAAATGAGAAAAAAAAATGACAACCGACAGTGGTGGGGGGGGGGGGAGGACA
*
56379417 ATGATTTTAAGTTGAAAGTATGGTGTGGGTTTACAAAAATTACACAAAAGCATGATTATAATCAT
1 ATGATTTTAAGTTGAAAGTATGGTGTGAGTTTACAAAAATTACACAAAAGCATGATTATAATCAT
* * * * * *
56379482 GGTAATAGAAAATCTTGTAGGTGAAATGAGCCAACTATGTGTTTTGAAAAAGAAAAATGGTCTTT
66 GCTAATAGAAAATCTTGTAGATGAAATGAACCAACCATATGTTTTGAAAAAGAAAAATGATCTTT
*
56379547 GGCAAGAAAAAAAATGAGAGAAAA
131 GGCAAGAAAAAAAATGAGAAAAAA
56379571 TTTTTTGTTA
Statistics
Matches: 138, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
192 138 1.00
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.26
Consensus pattern (192 bp):
ATGATTTTAAGTTGAAAGTATGGTGTGAGTTTACAAAAATTACACAAAAGCATGATTATAATCAT
GCTAATAGAAAATCTTGTAGATGAAATGAACCAACCATATGTTTTGAAAAAGAAAAATGATCTTT
GGCAAGAAAAAAAATGAGAAAAAAAAATGACAACCGACAGTGGTGGGGGGGGGGGGAGGACA
Found at i:56391101 original size:99 final size:99
Alignment explanation
Indices: 56390965--56392037 Score: 1975
Period size: 99 Copynumber: 10.8 Consensus size: 99
56390955 TCGGGGAAGC
* * * * * *
56390965 AAGATTTGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTTGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
56391030 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
66 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
56391064 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
*
56391129 AGCTTCAATATGTTCCGTTGCATCGCCTGAAGGT
66 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
*
56391163 AAGATTCGCTGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
* *
56391228 AGCTTCAATCTGTTTCGTTGCATCGCCTAAAGGT
66 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
56391262 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
*
56391327 AGCTTCAATCTGTTCCGTTGCATCGCCTGAATGT
66 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
* *
56391361 AAGATTCGACGTTGTGGCTTCGATATTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
56391426 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
66 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
*
56391460 AAGATTCGCCGTTGTGGCTTCGATATTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
56391525 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
66 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
56391559 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
*
56391624 AGCTTCAATCTGTTCCGTTGCATCGCCTGAATGT
66 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
* *
56391658 AAGATTCGACGTTGTGGCTTCGATATTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
56391723 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
66 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
*
56391757 AAGATTCGCCGTTGTGGCTTCGATATTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
56391822 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
66 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
56391856 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
56391921 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
66 AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
*
56391955 AAGATTCGCCGTTGTGGCTTCGATATTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
56392020 AGCTTCAATCTGTTCCGT
66 AGCTTCAATCTGTTCCGT
56392038 NNNNNNNNNN
Statistics
Matches: 947, Mismatches: 27, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 947 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (99 bp):
AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGT
AGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
Found at i:56404309 original size:11 final size:12
Alignment explanation
Indices: 56404286--56404314 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
56404276 TATTTGATTG
56404286 TAATATCAATAA
1 TAATATCAATAA
56404298 TAATAT-AATAA
1 TAATATCAATAA
56404309 TAATAT
1 TAATAT
56404315 TATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATATCAATAA
Found at i:56404321 original size:23 final size:23
Alignment explanation
Indices: 56404286--56404334 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
56404276 TATTTGATTG
*
56404286 TAATATCAATAA-TAATATAATAA
1 TAATATCAATAATTAAT-TAAAAA
* *
56404309 TAATATTATTAATTAATTAAAAA
1 TAATATCAATAATTAATTAAAAA
56404332 TAA
1 TAA
56404335 AATAGCAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATATCAATAATTAATTAAAAA
Found at i:56405903 original size:29 final size:31
Alignment explanation
Indices: 56405871--56405935 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
56405861 GCCCAATGTA
*
56405871 CAATTATATACA-TAAACTTTAATTTT-ATT
1 CAATTATATACACAAAACTTTAATTTTAATT
56405900 CAATTATATACACAAAACTTTAATTTTAATT
1 CAATTATATACACAAAACTTTAATTTTAATT
56405931 CAATT
1 CAATT
56405936 TTCCCTTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 12 0.36
30 13 0.39
31 8 0.24
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (31 bp):
CAATTATATACACAAAACTTTAATTTTAATT
Found at i:56406307 original size:35 final size:36
Alignment explanation
Indices: 56406227--56406310 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 36
56406217 TAAGCCGAAG
* * * *
56406227 ACCCTAAACCATG-GACCTTGAACCCTAGACTTTGG
1 ACCCTAAACCCTGAGACCCTGAACCCTAAACTTTGA
*
56406262 ACCCTAAACCCTGAG-CCCTGAACCTTAAACTTTGA
1 ACCCTAAACCCTGAGACCCTGAACCCTAAACTTTGA
56406297 ACCCTAAACCCTGA
1 ACCCTAAACCCTGA
56406311 AACACTGGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 42 0.98
36 1 0.02
ACGTcount: A:0.31, C:0.35, G:0.13, T:0.21
Consensus pattern (36 bp):
ACCCTAAACCCTGAGACCCTGAACCCTAAACTTTGA
Found at i:56406425 original size:28 final size:28
Alignment explanation
Indices: 56406377--56406452 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
56406367 GTCTAGGTTC
*
56406377 CAAGGTTT-AGGATTCAAGGTCC-GAGATA
1 CAAGGTTTAAGG-TCCAAGGTCCAGAG-TA
* * *
56406405 CAAGGTTTAAGGTCCATGGTCCATAGTC
1 CAAGGTTTAAGGTCCAAGGTCCAGAGTA
56406433 CAAGGTTTAAGGTCCAAGGT
1 CAAGGTTTAAGGTCCAAGGT
56406453 TCATGTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 36 0.88
29 5 0.12
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (28 bp):
CAAGGTTTAAGGTCCAAGGTCCAGAGTA
Found at i:56406447 original size:14 final size:14
Alignment explanation
Indices: 56406405--56406453 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
56406395 GTCCGAGATA
56406405 CAAGGTTTAAGGTC
1 CAAGGTTTAAGGTC
* **
56406419 CATGGTCCATA-GTC
1 CAAGGTTTA-AGGTC
56406433 CAAGGTTTAAGGTC
1 CAAGGTTTAAGGTC
56406447 CAAGGTT
1 CAAGGTT
56406454 CATGTTAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (14 bp):
CAAGGTTTAAGGTC
Found at i:56409474 original size:3 final size:3
Alignment explanation
Indices: 56409448--56409714 Score: 100
Period size: 3 Copynumber: 87.7 Consensus size: 3
56409438 AAAAAAAGGA
* * * * *
56409448 AAT AGT AAT AGT AAT AAT ACT AAT AAT AAT AAAT AAT GAT TAT AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA-T
* *
56409495 AGAT GAGA- AAT AAG GA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 A-AT -A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
56409541 AA- AA- AAT AAT GAT TAT AAGT AGAT GAGA- AAT -AT GGA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T A-AT -A-AT AAT AAT -AAT AAT AAT
* * * *
56409583 AAT AAT AAT AAT CAT AAT AAT AAAT AAT AGT AAT AAT ATT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
* ** ** * * *
56409629 AATT CAT AAT AAT GTT AAT AGG AAC AA- AAT AAC AAT AAT ACT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** ** * * * *
56409674 AAT GCT GGT AAT AAT AAG GAT AAT AAT AGT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
56409715 AAAGGTCAAT
Statistics
Matches: 196, Mismatches: 51, Indels: 34
0.70 0.18 0.12
Matches are distributed among these distances:
2 12 0.06
3 161 0.82
4 15 0.08
5 8 0.04
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:56409556 original size:66 final size:66
Alignment explanation
Indices: 56409448--56409605 Score: 262
Period size: 66 Copynumber: 2.4 Consensus size: 66
56409438 AAAAAAAGGA
* * * *
56409448 AATAGTAATAGTAATAATACTAATAATAATAAATAATGATTATAAGTAGATGAGAAATAAGGAAA
1 AATAATAATAATAATAATAATAATAATAAAAAATAATGATTATAAGTAGATGAGAAATAAGGAAA
56409513 T
66 T
*
56409514 AATAATAATAATAATAATAATAATAATAAAAAATAATGATTATAAGTAGATGAGAAATATGGAAA
1 AATAATAATAATAATAATAATAATAATAAAAAATAATGATTATAAGTAGATGAGAAATAAGGAAA
56409579 T
66 T
*
56409580 AATAATAATAATAATCATAATAATAA
1 AATAATAATAATAATAATAATAATAA
56409606 ATAATAGTAA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 86 1.00
ACGTcount: A:0.59, C:0.01, G:0.10, T:0.29
Consensus pattern (66 bp):
AATAATAATAATAATAATAATAATAATAAAAAATAATGATTATAAGTAGATGAGAAATAAGGAAA
T
Found at i:56409609 original size:25 final size:25
Alignment explanation
Indices: 56409580--56409641 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
56409570 ATATGGAAAT
*
56409580 AATAATAATAATAATCA-TAATAATA
1 AATAATAATAATAAT-ATTAACAATA
*
56409605 AATAATAGTAATAATATTAACAATA
1 AATAATAATAATAATATTAACAATA
* *
56409630 ATTCATAATAAT
1 AATAATAATAAT
56409642 GTTAATAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 1 0.03
25 30 0.97
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (25 bp):
AATAATAATAATAATATTAACAATA
Found at i:56409637 original size:28 final size:28
Alignment explanation
Indices: 56409511--56409676 Score: 99
Period size: 28 Copynumber: 5.9 Consensus size: 28
56409501 GAAATAAGGA
*
56409511 AATAAT-AATAATAATAATAATAATAAT
1 AATAATAAATAATAATAATAATAATAAC
* * *
56409538 AATAAAAAATAATGATTATAAGTAGATGAGA-
1 AATAATAAATAATAATAATAA-TA-AT-A-AC
* *
56409569 AAT-ATGGAAATAATAATAATAATAATCAT
1 AATAAT--AAATAATAATAATAATAATAAC
* *
56409598 AATAATAAATAATAGTAATAATATTAAC
1 AATAATAAATAATAATAATAATAATAAC
** ** **
56409626 AATAATTCATAATAATGTTAATAGGAAC
1 AATAATAAATAATAATAATAATAATAAC
* *
56409654 AA-AAT-AACAATAATACTAATAAT
1 AATAATAAATAATAATAATAATAAT
56409677 GCTGGTAATA
Statistics
Matches: 106, Mismatches: 24, Indels: 19
0.71 0.16 0.13
Matches are distributed among these distances:
26 12 0.11
27 8 0.08
28 54 0.51
29 5 0.05
30 7 0.07
31 6 0.06
32 14 0.13
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.30
Consensus pattern (28 bp):
AATAATAAATAATAATAATAATAATAAC
Found at i:56409811 original size:15 final size:13
Alignment explanation
Indices: 56409778--56409816 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
56409768 TAAATACAAT
*
56409778 AAAAAGTAAAAGA
1 AAAAAATAAAAGA
56409791 AAAAAATAAAATGA
1 AAAAAATAAAA-GA
56409805 AATAAAATAAAA
1 AA-AAAATAAAA
56409817 AGAATGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 4 0.17
15 9 0.39
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (13 bp):
AAAAAATAAAAGA
Found at i:56410281 original size:24 final size:24
Alignment explanation
Indices: 56410249--56410296 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
56410239 TTACCAGAGT
56410249 TCATCGGGGAAAGGCCATTTTGGC
1 TCATCGGGGAAAGGCCATTTTGGC
56410273 TCATCGGGGAAAGGCCATTTTGGC
1 TCATCGGGGAAAGGCCATTTTGGC
56410297 CGTTTCTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (24 bp):
TCATCGGGGAAAGGCCATTTTGGC
Found at i:56411239 original size:44 final size:44
Alignment explanation
Indices: 56411171--56411413 Score: 188
Period size: 44 Copynumber: 5.6 Consensus size: 44
56411161 GATGCGATCT
* *
56411171 GCTCTACTGCAACTTCAGAGAGATAAGATCCGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGAGAGATAAGATCAGTGGTTTTAATCC
* * * * * * *
56411215 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCT
1 GCTCCACTGCAACTTCAGAGAGATAAGATCAGTGGTTTTAATCC
* * ** *
56411259 GCTCCGCTGCAACTTCAGGGAGATAAGATTGGT-ATCTTTAA-CC
1 GCTCCACTGCAACTTCAGAGAGATAAGATCAGTGGT-TTTAATCC
* * * * * *** *
56411302 TGCTCCACTACAACTTCAGGGAGATAAGGT--TTGGATGCGATCT
1 -GCTCCACTGCAACTTCAGAGAGATAAGATCAGTGGTTTTAATCC
* * * *
56411345 GCTCTACTGTAACTTTAGAGAGATAAGATCAGTGGTTTTAATTC
1 GCTCCACTGCAACTTCAGAGAGATAAGATCAGTGGTTTTAATCC
*
56411389 GCCCCACTGCAACTTCAGAGAGATA
1 GCTCCACTGCAACTTCAGAGAGATA
56411414 GGATTGACTT
Statistics
Matches: 150, Mismatches: 43, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
42 26 0.17
43 2 0.01
44 122 0.81
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATCAGTGGTTTTAATCC
Found at i:56411275 original size:88 final size:86
Alignment explanation
Indices: 56411161--56411418 Score: 288
Period size: 88 Copynumber: 3.0 Consensus size: 86
56411151 AATAAAGTCT
* *
56411161 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCGTGGTTTTAATCCGCTCCACTGCA
1 GATGCAATCTGCTCTACTGCAACTTCAGAGAGATAAGATCAGTGGTTTTAATCCGCTCCACTGCA
56411226 ACTTCAGGGAGATAGGATTAGTA
66 ACTTCAGGGAGATAGGATT--TA
* * ** * ** * *
56411249 GCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGT-ATCTTTAA-CCTGCTCCACTA
1 GATGCAATCTGCTCTACTGCAACTTCAGAGAGATAAGATCAGTGGT-TTTAATCC-GCTCCACTG
*
56411312 CAACTTCAGGGAGATAAGG-TTTG
64 CAACTTCAGGGAGAT-AGGATTTA
* * * * *
56411335 GATGCGATCTGCTCTACTGTAACTTTAGAGAGATAAGATCAGTGGTTTTAATTCGCCCCACTGCA
1 GATGCAATCTGCTCTACTGCAACTTCAGAGAGATAAGATCAGTGGTTTTAATCCGCTCCACTGCA
*
56411400 ACTTCAGAGAGATAGGATT
66 ACTTCAGGGAGATAGGATT
56411419 GACTTCTTTG
Statistics
Matches: 138, Mismatches: 26, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
85 3 0.02
86 62 0.45
87 5 0.04
88 65 0.47
89 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (86 bp):
GATGCAATCTGCTCTACTGCAACTTCAGAGAGATAAGATCAGTGGTTTTAATCCGCTCCACTGCA
ACTTCAGGGAGATAGGATTTA
Found at i:56411481 original size:45 final size:46
Alignment explanation
Indices: 56411430--56411784 Score: 427
Period size: 45 Copynumber: 8.0 Consensus size: 46
56411420 ACTTCTTTGA
56411430 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATGC-GCTATCTTCAG
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATGCTGCTATCTTCAG
* *
56411475 TCTGCTTCGCTGTCAGTACAGGAAGGCAAG--GCTGGTGTCTTC-G
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATGCTGCTATCTTCAG
56411518 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAT-CTGCTATCTTCAG
1 -TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATGCTGCTATCTTCAG
* * *
56411564 TCTGC-TCACTGTCAGTACAGGAAGGCAAG--GCTGGTGTCTTC-G
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATGCTGCTATCTTCAG
* *
56411606 ATCTGCTTCACTGTCAGTACAAGG-AGGTAAGAT-CTGCTATCTTCAG
1 -TCTGCTTCGCTGTCAGTAC-AGGAAGGCAAGATGCTGCTATCTTCAG
* *
56411652 TCTACTCCGCTGTCAGTACAGGAAGGCAAGAT-CTGCTATCTTCAG
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATGCTGCTATCTTCAG
* * *
56411697 TCTGCTCCGCTGTCAGTACAGGAAGG-AA-AGGCTGGTATCTTC-G
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATGCTGCTATCTTCAG
* * *
56411740 ATCTACTTCGTTGTCAGTACAGGAAGGCAAGAT-CTGCTATTTTCA
1 -TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATGCTGCTATCTTCA
56411785 ATAATCTGTT
Statistics
Matches: 269, Mismatches: 23, Indels: 35
0.82 0.07 0.11
Matches are distributed among these distances:
42 1 0.00
43 19 0.07
44 117 0.43
45 129 0.48
46 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (46 bp):
TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATGCTGCTATCTTCAG
Found at i:56411736 original size:89 final size:89
Alignment explanation
Indices: 56411423--56411779 Score: 438
Period size: 89 Copynumber: 4.0 Consensus size: 89
56411413 AGGATTGACT
* * *
56411423 TCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATGC-GCTATCTTCAGTCTGCTTCGCTG
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGAAAGA-GCTGCTATCTTCAGTCTACTTCGCTG
* *
56411487 TCAGTACAGGAAGGCAAGGCTGGTG
65 TCAGTACAGGAAGGCAAGGCTGCTA
* * * *
56411512 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGC-TCACTGT
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGAAAGAGCTGCTATCTTCAGTCTACTTCGCTGT
* *
56411576 CAGTACAGGAAGGCAAGGCTGGTG
66 CAGTACAGGAAGGCAAGGCTGCTA
* * * *
56411600 TCTTCGATCTGCTTCACTGTCAGTACAAGG-AGGTAAGATCTGCTATCTTCAGTCTACTCCGCTG
1 TCTTCGATCTGCTTCGCTGTCAGTAC-AGGAAGGAAAGAGCTGCTATCTTCAGTCTACTTCGCTG
*
56411664 TCAGTACAGGAAGGCAAGATCTGCTA
65 TCAGTACAGGAAGGCAAG-GCTGCTA
* * *
56411690 TCTTC-AGTCTGCTCCGCTGTCAGTACAGGAAGGAAAG-GCTGGTATCTTC-GATCTACTTCGTT
1 TCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGAAAGAGCTGCTATCTTCAG-TCTACTTCGCT
*
56411752 GTCAGTACAGGAAGGCAAGATCTGCTA
64 GTCAGTACAGGAAGGCAAG-GCTGCTA
56411779 T
1 T
56411780 TTTCAATAAT
Statistics
Matches: 243, Mismatches: 18, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
88 82 0.34
89 129 0.53
90 32 0.13
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.28
Consensus pattern (89 bp):
TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGAAAGAGCTGCTATCTTCAGTCTACTTCGCTGT
CAGTACAGGAAGGCAAGGCTGCTA
Found at i:56414110 original size:66 final size:64
Alignment explanation
Indices: 56414025--56414158 Score: 153
Period size: 66 Copynumber: 2.0 Consensus size: 64
56414015 ATTTTGAAGC
* *
56414025 TGTAGCTAGAGTGCATCATACTTTCTGCTCTG-CTCTGCTTCCCTCGCTACTGCCTCCGCTTTAA
1 TGTAGCTAGAGTGCATCATA-TTT-T-CTCTGACTCAGCTTCCCTCGATACTGCCTCCGCTTTAA
56414089 GT
63 GT
* * * * *
56414091 TGTAGCTAGAGTTCTTCATATTTTCTTTGAACCTCAGCTTCTCTCGATGCTGCCTCCGCTTTAAG
1 TGTAGCTAGAGTGCATCATATTTTCTCTG-A-CTCAGCTTCCCTCGATACTGCCTCCGCTTTAAG
56414156 T
64 T
56414157 TG
1 TG
56414159 AGCAATTTGC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
63 4 0.07
64 1 0.02
65 3 0.05
66 50 0.86
ACGTcount: A:0.15, C:0.28, G:0.18, T:0.39
Consensus pattern (64 bp):
TGTAGCTAGAGTGCATCATATTTTCTCTGACTCAGCTTCCCTCGATACTGCCTCCGCTTTAAGT
Found at i:56416388 original size:10 final size:10
Alignment explanation
Indices: 56416368--56416424 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
56416358 ACCAGCAATA
56416368 ATGTAATATAT
1 ATGT-ATATAT
56416379 ATGTATATAT
1 ATGTATATAT
56416389 ATGTATATAT
1 ATGTATATAT
* *
56416399 ATGTGTATGT
1 ATGTATATAT
* *
56416409 GTGCATATAT
1 ATGTATATAT
56416419 ATGTAT
1 ATGTAT
56416425 GCGCCCTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
10 34 0.89
11 4 0.11
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (10 bp):
ATGTATATAT
Found at i:56423114 original size:21 final size:21
Alignment explanation
Indices: 56423072--56423114 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
56423062 TTTTTTCTGA
* *
56423072 AATAAAATTGTGTCTTGTATC
1 AATAAAATTGTGTCATGCATC
56423093 AATAAAATTGTGTCATGCATC
1 AATAAAATTGTGTCATGCATC
56423114 A
1 A
56423115 TCCAATCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (21 bp):
AATAAAATTGTGTCATGCATC
Found at i:56423959 original size:107 final size:107
Alignment explanation
Indices: 56423773--56424061 Score: 479
Period size: 107 Copynumber: 2.7 Consensus size: 107
56423763 TTTTGTTGGT
* * *
56423773 TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTGATTTGTTAGTGAGTAGAAGAT
1 TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAAGAT
*
56423838 GAAATTGGAAATTGTTGCATTTGTTTTGATTTTGTTCTTGAA
66 GAAATTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGAA
* *
56423880 TTGTTCTGGCAGTTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAAGAT
1 TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAAGAT
* *
56423945 GAAATTGGAAATTGTTGCATTTGTTTTGATATTGTTTTTGAT
66 GAAATTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGAA
* *
56423987 TTGTTTTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAATAT
1 TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAAGAT
*
56424052 GAAACTGGAA
66 GAAATTGGAA
56424062 CTTGATTTGT
Statistics
Matches: 169, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 169 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (107 bp):
TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAAGAT
GAAATTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGAA
Found at i:56423981 original size:11 final size:11
Alignment explanation
Indices: 56423965--56424009 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
56423955 ATTGTTGCAT
56423965 TTGTTTTGATA
1 TTGTTTTGATA
56423976 TTGTTTTTGAT-
1 TTG-TTTTGATA
*
56423987 TTGTTTTGGAAA
1 TTGTTTT-GATA
56423999 TTGTTTTGATA
1 TTGTTTTGATA
56424010 GTCTGCTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 4 0.14
11 11 0.38
12 14 0.48
ACGTcount: A:0.18, C:0.00, G:0.20, T:0.62
Consensus pattern (11 bp):
TTGTTTTGATA
Found at i:56423985 original size:12 final size:12
Alignment explanation
Indices: 56423968--56424009 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
56423958 GTTGCATTTG
56423968 TTTTGATATTGT
1 TTTTGATATTGT
56423980 TTTTGAT-TTGT
1 TTTTGATATTGT
* *
56423991 TTTGGAAATTG-
1 TTTTGATATTGT
56424002 TTTTGATA
1 TTTTGATA
56424010 GTCTGCTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (12 bp):
TTTTGATATTGT
Found at i:56424005 original size:23 final size:23
Alignment explanation
Indices: 56423963--56424037 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
56423953 AAATTGTTGC
*
56423963 ATTTGTTTT-GATATTGTTTTTG
1 ATTTGTTTTGGAAATTGTTTTTG
56423985 ATTTGTTTTGGAAATTG-TTTTG
1 ATTTGTTTTGGAAATTGTTTTTG
* * *
56424007 A-TAGTCTGCTGGAAATTGTTCTTG
1 ATTTGT-T-TTGGAAATTGTTTTTG
56424031 ATTTGTT
1 ATTTGTT
56424038 AGTCAGTAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.07
22 16 0.37
23 15 0.35
24 6 0.14
25 3 0.07
ACGTcount: A:0.17, C:0.04, G:0.21, T:0.57
Consensus pattern (23 bp):
ATTTGTTTTGGAAATTGTTTTTG
Found at i:56429539 original size:11 final size:11
Alignment explanation
Indices: 56429523--56429549 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
56429513 TAGAAATTAG
56429523 TTTGTGAAACT
1 TTTGTGAAACT
56429534 TTTGTGAAACT
1 TTTGTGAAACT
56429545 TTTGT
1 TTTGT
56429550 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:56431024 original size:62 final size:64
Alignment explanation
Indices: 56430958--56431085 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 64
56430948 TTGATTTTAG
* * **
56430958 TAAATTAATATAAGAACATTTTATTATTA-AATTTTATTTAA-TAT-TAATTATT-TTAAATTAT
1 TAAATTAATATAAGAA-AATTTATTATCACAATTTTATGAAATTATAT-ATTATTATTAAATTAT
56431019 A
64 A
*
56431020 TAAATTCATATAAGAAAATTTATTATCACGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTAATATAAGAAAATTTATTATCAC-AATTTTATGAAATTATATATTATTATTAAATTATA
56431085 T
1 T
56431086 TTAATAATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
61 10 0.18
62 15 0.27
63 10 0.18
64 9 0.16
65 12 0.21
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (64 bp):
TAAATTAATATAAGAAAATTTATTATCACAATTTTATGAAATTATATATTATTATTAAATTATA
Found at i:56431056 original size:44 final size:43
Alignment explanation
Indices: 56431007--56431135 Score: 102
Period size: 47 Copynumber: 2.9 Consensus size: 43
56430997 AATATTAATT
*
56431007 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCACGA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTAT-AAGA
* * * **
56431051 ATTTTATGAAATTATATATTATT-AT-TAA-ATTATATTTAATAATAATT
1 A-TTT-T-AAATTATATA-AATTCATATAAGA--AAATTT-ATTATAAGA
*
56431098 ATTTTAAATTATACAAATTCATATAAGAAAATTTATTA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTA
56431136 GTTATAATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
43 6 0.09
44 17 0.26
45 8 0.12
46 8 0.12
47 19 0.29
48 7 0.11
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (43 bp):
ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATAAGA
Found at i:56431272 original size:16 final size:15
Alignment explanation
Indices: 56431251--56431280 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
56431241 TAAATTCATA
56431251 TAAGAATTTTGATTAT
1 TAAGAATTTT-ATTAT
56431267 TAAGAATTTTATTA
1 TAAGAATTTTATTA
56431281 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (15 bp):
TAAGAATTTTATTAT
Found at i:56431281 original size:120 final size:120
Alignment explanation
Indices: 56431151--56431688 Score: 927
Period size: 120 Copynumber: 4.5 Consensus size: 120
56431141 AATTATTTTA
* *
56431151 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
* *
56431215 TATAGTGTCATATATTATGATTTGAGTAAATTCATATAAGAATTTTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
56431271 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
* *
56431335 TATAGTGTCATATATTATGATTTGAGTAAATTCATATAAGAATTTTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
56431391 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
56431456 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
56431511 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
56431576 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTAGTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
56431631 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
56431689 ATGATTAAAT
Statistics
Matches: 406, Mismatches: 10, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
120 398 0.98
121 8 0.02
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:56431300 original size:18 final size:17
Alignment explanation
Indices: 56431272--56431306 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56431262 ATTATTAAGA
*
56431272 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
56431289 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
56431307 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:56431392 original size:16 final size:15
Alignment explanation
Indices: 56431371--56431400 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
56431361 TAAATTCATA
56431371 TAAGAATTTTGATTAT
1 TAAGAATTTT-ATTAT
56431387 TAAGAATTTTATTA
1 TAAGAATTTTATTA
56431401 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (15 bp):
TAAGAATTTTATTAT
Found at i:56431420 original size:18 final size:17
Alignment explanation
Indices: 56431392--56431426 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56431382 ATTATTAAGA
*
56431392 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
56431409 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
56431427 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:56431506 original size:66 final size:65
Alignment explanation
Indices: 56431429--56431618 Score: 197
Period size: 66 Copynumber: 3.1 Consensus size: 65
56431419 AAATATATTT
56431429 AATAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATAATAATTATGTTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
56431494 G
65 G
* * * * * * *
56431495 AATATTAATTAT-TAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-T
1 AATAATAATTATGTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
*
56431548 T
65 G
56431549 AATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATAATAATTATGTTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
56431614 G
65 G
56431615 AATA
1 AATA
56431619 TTGATTAGTA
Statistics
Matches: 94, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
54 15 0.16
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.11
60 8 0.09
61 10 0.11
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 19 0.20
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (65 bp):
AATAATAATTATGTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:56431546 original size:16 final size:16
Alignment explanation
Indices: 56431525--56431571 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
56431515 TTATTAAATT
56431525 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
56431541 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
56431556 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
56431572 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:56431666 original size:16 final size:16
Alignment explanation
Indices: 56431645--56431686 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
56431635 TTATTAAATT
*
56431645 ATATATTTTAATTATA
1 ATATATTTTAATAATA
56431661 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
56431676 AT-TATGTTTAA
1 ATATAT-TTTAA
56431687 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:56431671 original size:15 final size:15
Alignment explanation
Indices: 56431636--56431677 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
56431626 GTAAGAATTT
*
56431636 TATTAAATTAT-ATA
1 TATTTAATTATAATA
56431650 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
56431664 TATTTAATAATAAT
1 TATTTAATTATAAT
56431678 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:56434351 original size:38 final size:38
Alignment explanation
Indices: 56434309--56434386 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
56434299 CCAATTATGG
56434309 TTTGCATGTAAGAACTCATCATCGTACCATTATTTCTA
1 TTTGCATGTAAGAACTCATCATCGTACCATTATTTCTA
56434347 TTTGCATGTAAGAACTCATCATCGTACCATTATTTCTA
1 TTTGCATGTAAGAACTCATCATCGTACCATTATTTCTA
56434385 TT
1 TT
56434387 AAATGTGGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (38 bp):
TTTGCATGTAAGAACTCATCATCGTACCATTATTTCTA
Found at i:56435643 original size:87 final size:87
Alignment explanation
Indices: 56435497--56435670 Score: 339
Period size: 87 Copynumber: 2.0 Consensus size: 87
56435487 TCATTCTTCC
56435497 ATTTTCAATATGCAAAATGAAAATTCAGCTGCTATAACTCTGGCTTCAATGTGTAAGCTGTGACA
1 ATTTTCAATATGCAAAATGAAAATTCAGCTGCTATAACTCTGGCTTCAATGTGTAAGCTGTGACA
*
56435562 TGTATTACGGCCAAATCGCTTT
66 TGTATCACGGCCAAATCGCTTT
56435584 ATTTTCAATATGCAAAATGAAAATTCAGCTGCTATAACTCTGGCTTCAATGTGTAAGCTGTGACA
1 ATTTTCAATATGCAAAATGAAAATTCAGCTGCTATAACTCTGGCTTCAATGTGTAAGCTGTGACA
56435649 TGTATCACGGCCAAATCGCTTT
66 TGTATCACGGCCAAATCGCTTT
56435671 GGATTTAGGT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (87 bp):
ATTTTCAATATGCAAAATGAAAATTCAGCTGCTATAACTCTGGCTTCAATGTGTAAGCTGTGACA
TGTATCACGGCCAAATCGCTTT
Found at i:56436090 original size:42 final size:43
Alignment explanation
Indices: 56435955--56436134 Score: 170
Period size: 43 Copynumber: 4.2 Consensus size: 43
56435945 TGAAAAAAAT
* * * *
56435955 GCCGCTATAGAACATGA-CATGTT-GCGGTGCTTTTATTAAAAAC
1 GCCGCTAAAGAACATGATC-T-TTAGCGGCGCTTTTATCACAAAC
* * * *
56435998 ACCGCTAAAGAACATGACCTTTAGCGGCACCTTTATCACAAAC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAAC
*** ** *
56436041 ATTGCTAAAGAGA-ATGAT-TTTAGCGGCTTTTTTTTCACAAAC
1 GCCGCTAAAGA-ACATGATCTTTAGCGGCGCTTTTATCACAAAC
*
56436083 GCCGCTAAAGAACATGATCTTTAGTGGCGCTTTTATCACAAAC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAAC
56436126 GCCGCTAAA
1 GCCGCTAAA
56436135 AGTACCGTTC
Statistics
Matches: 111, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.01
42 35 0.32
43 73 0.66
44 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (43 bp):
GCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAAC
Found at i:56436147 original size:43 final size:43
Alignment explanation
Indices: 56435978--56436154 Score: 144
Period size: 43 Copynumber: 4.1 Consensus size: 43
56435968 ATGACATGTT
* * * * * *
56435978 GCGGTGCTTTTATTAAAAACACCGCTAAAGAACATGACCTTTA
1 GCGGCGCTTTTATCACAAACGCCGCTAAAGAACACGATCTTTA
* * *** *
56436021 GCGGCACCTTTATCACAAACATTGCTAAAGAGA-ATGAT-TTTA
1 GCGGCGCTTTTATCACAAACGCCGCTAAAGA-ACACGATCTTTA
** * *
56436063 GCGGCTTTTTTTTCACAAACGCCGCTAAAGAACATGATCTTTA
1 GCGGCGCTTTTATCACAAACGCCGCTAAAGAACACGATCTTTA
* * *
56436106 GTGGCGCTTTTATCACAAACGCCGCTAAAAGTAC-CGTTCTTTA
1 GCGGCGCTTTTATCACAAACGCCGCT-AAAGAACACGATCTTTA
56436149 GCGGCG
1 GCGGCG
56436155 TTTATGAAAA
Statistics
Matches: 107, Mismatches: 23, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
41 1 0.01
42 33 0.31
43 66 0.62
44 7 0.07
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (43 bp):
GCGGCGCTTTTATCACAAACGCCGCTAAAGAACACGATCTTTA
Found at i:56436360 original size:28 final size:29
Alignment explanation
Indices: 56436320--56436381 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
56436310 CTATAAAATA
56436320 ATAAATCCTAAAC-CACAAACTCTAA-CCC
1 ATAAATCCTAAACTCA-AAACTCTAATCCC
56436348 ATAAACTCC-AAACTCAAAACTCTAATCCC
1 ATAAA-TCCTAAACTCAAAACTCTAATCCC
56436377 A-AAAT
1 ATAAAT
56436382 AATAAACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
27 1 0.03
28 21 0.68
29 9 0.29
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.19
Consensus pattern (29 bp):
ATAAATCCTAAACTCAAAACTCTAATCCC
Found at i:56436639 original size:40 final size:41
Alignment explanation
Indices: 56436562--56436659 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 41
56436552 GCTTTTTGCG
*
56436562 AAAAGCGCCGCTAATGCTCGATCTATAGTGG--TGTTTTTCA
1 AAAAGCGCCGCTAATGCTCGATCTATAGTGGCAT-TTTTTAA
* *
56436602 ACAAGCGCCGCTAATTCTCGATCTATTA-TGGCATTTTTTAA
1 AAAAGCGCCGCTAATGCTCGATCTA-TAGTGGCATTTTTTAA
*
56436643 AAAAGCGCCACTAATGC
1 AAAAGCGCCGCTAATGC
56436660 CACTAAAGCT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
40 26 0.53
41 22 0.45
42 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (41 bp):
AAAAGCGCCGCTAATGCTCGATCTATAGTGGCATTTTTTAA
Found at i:56436745 original size:40 final size:41
Alignment explanation
Indices: 56436701--56436810 Score: 134
Period size: 40 Copynumber: 2.7 Consensus size: 41
56436691 CAACTTTTTT
* *
56436701 GCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGATCTA-TA
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATTA
* * *
56436741 GCGGCATTTTTCAAATATCGCCACTAATGCTCGATCTATTA
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATTA
* * *
56436782 -CGGCATTTTTTAAAAAGTGCTGCTAATGC
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGC
56436811 CACTAAAGCT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 56 0.97
41 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (41 bp):
GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATTA
Found at i:56436768 original size:152 final size:150
Alignment explanation
Indices: 56436498--56436933 Score: 545
Period size: 152 Copynumber: 2.8 Consensus size: 150
56436488 AAAAATGCCG
* * * * *
56436498 CTAATGCCACTAAAGCTCAACAACAAACAACTCTGTTTT-CTCAACTTTTTTGAGGCTTTTTGCG
1 CTAATGCCACTAAAGCTCAACAAC-AAC--GT-TGTTTTGCTCAACTTTTTTGCGGCGTTTTCCA
* ** *
56436562 AAAAGCGCCGCTAATGCTCGATCTATAGTGGTGTTTTTCAACAAGCGCCGCTAATTCTCGATCTA
62 AAAAGCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAA-AAGCGCCGCTAATGCTCGATCTA
*
56436627 TTATGGCATTTTTTAAAAAAGCGCCA
126 TTACGGCATTTTTT-AAAAAGCGCCA
56436653 CTAATGCCACTAAAGCTCAACAACAACGTTGTTTTGCTCAACTTTTTTGCGGCGTTTTCCAAAAA
1 CTAATGCCACTAAAGCTCAACAACAACGTTGTTTTGCTCAACTTTTTTGCGGCGTTTTCCAAAAA
* *
56436718 GCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAATATCGCCACTAATGCTCGATCTATTAC
66 GCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAA-AGCGCCGCTAATGCTCGATCTATTAC
* **
56436783 GGCATTTTTTAAAAAGTGCTG
130 GGCATTTTTTAAAAAGCGCCA
* * *
56436804 CTAATGCCACTAAAGCTCAACAACAAACAACG-TGTTTTGCTCAACTTTTTTACGGTGTTTTCTG
1 CTAATGCCACTAAAGCT---CAAC-AACAACGTTGTTTTGCTCAACTTTTTTGCGGCGTTTTC-C
** *
56436868 AAAAA-TACCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCT
61 AAAAAGCGCCGCTAATGCTCGATCTATAGCGGCATTTTTC-AAAAGCGCCGCTAATGCTCGATCT
56436932 AT
125 AT
56436934 AGCGACGTTT
Statistics
Matches: 250, Mismatches: 23, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
151 32 0.13
152 92 0.37
154 87 0.35
155 39 0.16
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (150 bp):
CTAATGCCACTAAAGCTCAACAACAACGTTGTTTTGCTCAACTTTTTTGCGGCGTTTTCCAAAAA
GCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAGCGCCGCTAATGCTCGATCTATTACG
GCATTTTTTAAAAAGCGCCA
Found at i:56436893 original size:154 final size:153
Alignment explanation
Indices: 56436488--56436933 Score: 577
Period size: 154 Copynumber: 2.9 Consensus size: 153
56436478 CGTTTTTATC
*
56436488 AAAAA-TGCCGCTAATGCCACTAAAGCTCAACAACAAACAACTCTGTTTT-CTCAACTTTTTTGA
1 AAAAAGTGCCGCTAATGCCACTAAAGCTCAACAACAAACAAC-GTGTTTTGCTCAACTTTTTT-A
* * **
56436551 -GGCT-TTTTGCGAAAAGCGCCGCTAATGCTCGATCTATAGTGGTGTTTTTCAACAAGCGCCGCT
64 CGG-TGTTTT-CGAAAAACGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAA-AAGCGCCGCT
* *
56436614 AATTCTCGATCTATTATGGCATTTTTTA
126 AATGCTCGATCTATTACGGCATTTTTTA
* * *
56436642 AAAAAGCGCCACTAATGCCACTAAAGCT---CAAC-AACAACGTTGTTTTGCTCAACTTTTTTGC
1 AAAAAGTGCCGCTAATGCCACTAAAGCTCAACAACAAACAACG-TGTTTTGCTCAACTTTTTTAC
* * * *
56436703 GGCGTTTTCCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAATATCGCCACTAA
65 GGTGTTTTCGAAAAA-CGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAA-AGCGCCGCTAA
56436768 TGCTCGATCTATTACGGCATTTTTT-
128 TGCTCGATCTATTACGGCATTTTTTA
*
56436793 AAAAAGTGCTGCTAATGCCACTAAAGCTCAACAACAAACAACGTGTTTTGCTCAACTTTTTTACG
1 AAAAAGTGCCGCTAATGCCACTAAAGCTCAACAACAAACAACGTGTTTTGCTCAACTTTTTTACG
**
56436858 GTGTTTTCTGAAAAATACCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAAGCGCCGCTAAT
66 GTGTTTTC-GAAAAACGCCGCTAATGCTCGATCTATAGCGGCATTTTTC-AAAAGCGCCGCTAAT
*
56436923 GCTCGACCTAT
129 GCTCGATCTAT
56436934 AGCGACGTTT
Statistics
Matches: 254, Mismatches: 25, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
151 43 0.17
152 87 0.34
154 89 0.35
155 35 0.14
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (153 bp):
AAAAAGTGCCGCTAATGCCACTAAAGCTCAACAACAAACAACGTGTTTTGCTCAACTTTTTTACG
GTGTTTTCGAAAAACGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAGCGCCGCTAATGC
TCGATCTATTACGGCATTTTTTA
Found at i:56436924 original size:40 final size:41
Alignment explanation
Indices: 56436875--56436972 Score: 128
Period size: 40 Copynumber: 2.4 Consensus size: 41
56436865 CTGAAAAATA
* *
56436875 CCGCTAATGCTCGATCTATAGCGGC-ATT-TTTCAAAAAGCG
1 CCGCTAATGCTCGACCTATAGCGACGATTGTTTCAAAAA-CG
* *
56436915 CCGCTAATGCTCGACCTATAGCGACGTTTGTTTCAGAAACG
1 CCGCTAATGCTCGACCTATAGCGACGATTGTTTCAAAAACG
*
56436956 CCGCTAATGCTTGACCT
1 CCGCTAATGCTCGACCT
56436973 CTTGCGGCGT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
40 23 0.45
41 20 0.39
42 8 0.16
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
CCGCTAATGCTCGACCTATAGCGACGATTGTTTCAAAAACG
Found at i:56436972 original size:41 final size:40
Alignment explanation
Indices: 56436875--56437002 Score: 150
Period size: 41 Copynumber: 3.1 Consensus size: 40
56436865 CTGAAAAATA
* *
56436875 CCGCTAATGCTCGATCTATAGCGGC-ATTTTTCAAAAAGCG
1 CCGCTAATGCTCGACCTATAGCGGCGTTTTTTCAAAAA-CG
* *
56436915 CCGCTAATGCTCGACCTATAGCGACGTTTGTTTCAGAAACG
1 CCGCTAATGCTCGACCTATAGCGGCGTTT-TTTCAAAAACG
* * * *
56436956 CCGCTAATGCTTGACCTCTTGCGGCGTTTTTGTCATAAACG
1 CCGCTAATGCTCGACCTATAGCGGCGTTTTT-TCAAAAACG
56436997 CCGCTA
1 CCGCTA
56437003 TAACTCTAAC
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
40 25 0.33
41 43 0.57
42 8 0.11
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (40 bp):
CCGCTAATGCTCGACCTATAGCGGCGTTTTTTCAAAAACG
Found at i:56444317 original size:24 final size:25
Alignment explanation
Indices: 56444261--56444310 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
56444251 TTCATTTCTT
*
56444261 ATATATATACTAATTAATAATAATA
1 ATATATATACTAATTAATAAAAATA
*
56444286 ATAAATAT-CTAATTAATAACAAATA
1 ATATATATACTAATTAATAA-AAATA
56444311 TTTATATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATATATACTAATTAATAAAAATA
Found at i:56445109 original size:87 final size:87
Alignment explanation
Indices: 56444998--56445176 Score: 227
Period size: 87 Copynumber: 2.1 Consensus size: 87
56444988 CAAGTTGCCA
* **
56444998 ATAATGCGGACGAGCCACCAGAAATACAGATAAACTGCCAATACAATTGA-GGTAAACCGCCAAT
1 ATAATGCGGACGAGCCACCAGAAATACAGATAAACTGCCAATACAATT-ACAGTAAACAACCAAT
* *
56445062 AATAGATTGCAGACAAGCTGTTG
65 AAGAGATTGCAGACAAGCTGTCG
* * * *
56445085 ATAATGTGGACGAGGCC-CTAGAAATACAGATAAACTGTCAATATAATTACAGTAAACAACCAAT
1 ATAATGCGGACGA-GCCACCAGAAATACAGATAAACTGCCAATACAATTACAGTAAACAACCAAT
* *
56445149 AAGATATTGCAGACGAGCTGTCG
65 AAGAGATTGCAGACAAGCTGTCG
56445172 ATAAT
1 ATAAT
56445177 TTTGTGGGCA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
86 1 0.01
87 75 0.95
88 3 0.04
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (87 bp):
ATAATGCGGACGAGCCACCAGAAATACAGATAAACTGCCAATACAATTACAGTAAACAACCAATA
AGAGATTGCAGACAAGCTGTCG
Found at i:56450695 original size:19 final size:19
Alignment explanation
Indices: 56450650--56450696 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
56450640 TATGTATATC
* * * *
56450650 TATATATGTATATTAAAAT
1 TATATAAGTACATAAAAAA
56450669 TATA-AAGTACATAAAAAA
1 TATATAAGTACATAAAAAA
56450687 TATATAAGTA
1 TATATAAGTA
56450697 ATTATACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (19 bp):
TATATAAGTACATAAAAAA
Found at i:56450822 original size:3 final size:3
Alignment explanation
Indices: 56450816--56450844 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
56450806 CTACTACTAC
56450816 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
56450845 GTAACCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:56453164 original size:20 final size:20
Alignment explanation
Indices: 56453128--56453168 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
56453118 TTAACTTTCT
56453128 TTATATATTCTTTAAAAATA
1 TTATATATTCTTTAAAAATA
*
56453148 TTATA-ATTTTTTGAAAAATA
1 TTATATATTCTTT-AAAAATA
56453168 T
1 T
56453169 AAAATTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTATATATTCTTTAAAAATA
Found at i:56453203 original size:20 final size:19
Alignment explanation
Indices: 56453167--56453202 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56453157 TTTGAAAAAT
*
56453167 ATAAA-ATTTGGAATTTTC
1 ATAAATATTTTGAATTTTC
56453185 ATAAATATTTTGAATTTT
1 ATAAATATTTTGAATTTT
56453203 TGAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (19 bp):
ATAAATATTTTGAATTTTC
Found at i:56453386 original size:16 final size:16
Alignment explanation
Indices: 56453349--56453388 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
56453339 TTGACTCAAA
56453349 AAATTCGAATAACTTG
1 AAATTCGAATAACTTG
*
56453365 --ATTCGATTAACTTG
1 AAATTCGAATAACTTG
56453379 AAATTCGAAT
1 AAATTCGAAT
56453389 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
14 13 0.65
16 7 0.35
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (16 bp):
AAATTCGAATAACTTG
Found at i:56456998 original size:16 final size:14
Alignment explanation
Indices: 56456969--56457002 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
56456959 GAATCAGATT
56456969 TTTTTATTTTAATAA
1 TTTTTATTTTAAT-A
56456984 TTTTTATTTTAAATA
1 TTTTTATTTT-AATA
56456999 TTTT
1 TTTT
56457003 AATGATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTATTTTAATA
Found at i:56458456 original size:31 final size:31
Alignment explanation
Indices: 56458368--56458456 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 31
56458358 ATAAAATCTC
* * * * *
56458368 TAAACATTTTAATTATACTTACCAAAATTTT
1 TAAAAATTTTAATTAAACCTCCCAAAACTTT
* * * *
56458399 TAGAAATTCTTACTAAAACC-CTCAAAACTTT
1 TAAAAATT-TTAATTAAACCTCCCAAAACTTT
56458430 TAAAAATTTTAATTAAACCTCCCAAAA
1 TAAAAATTTTAATTAAACCTCCCAAAA
56458457 ATTAATGCTA
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
30 9 0.21
31 27 0.63
32 7 0.16
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.36
Consensus pattern (31 bp):
TAAAAATTTTAATTAAACCTCCCAAAACTTT
Found at i:56460981 original size:29 final size:29
Alignment explanation
Indices: 56460948--56461003 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
56460938 TTTGATCTTT
**
56460948 ATATTCTTATAATGTTTTTAATTAGTTTA
1 ATATTCTTATAATGTAATTAATTAGTTTA
*
56460977 ATATTTTTATAATGTAATTAATTAGTT
1 ATATTCTTATAATGTAATTAATTAGTT
56461004 CATATAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (29 bp):
ATATTCTTATAATGTAATTAATTAGTTTA
Found at i:56462956 original size:12 final size:12
Alignment explanation
Indices: 56462930--56462963 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
56462920 TAATGATACA
56462930 AATAGTAAC-AT
1 AATAGTAACAAT
56462941 AATAGTAACAAT
1 AATAGTAACAAT
*
56462953 AATAATAACAA
1 AATAGTAACAA
56462964 CAAAAGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (12 bp):
AATAGTAACAAT
Found at i:56465853 original size:27 final size:27
Alignment explanation
Indices: 56465815--56465868 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
56465805 GTTACTTGAG
*
56465815 TTACTAAATTACTTCAAGTTTAAAACT
1 TTACTAAATTACTTCAAATTTAAAACT
56465842 TTACTAAATTACTTCAAATTTAAAACT
1 TTACTAAATTACTTCAAATTTAAAACT
56465869 AACTTAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.41
Consensus pattern (27 bp):
TTACTAAATTACTTCAAATTTAAAACT
Found at i:56466188 original size:12 final size:12
Alignment explanation
Indices: 56466171--56466195 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56466161 TAACATCAAT
56466171 GGGGTGATAGAC
1 GGGGTGATAGAC
56466183 GGGGTGATAGAC
1 GGGGTGATAGAC
56466195 G
1 G
56466196 CAGGGGCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.52, T:0.16
Consensus pattern (12 bp):
GGGGTGATAGAC
Found at i:56467847 original size:60 final size:58
Alignment explanation
Indices: 56467686--56467878 Score: 156
Period size: 60 Copynumber: 3.2 Consensus size: 58
56467676 TAATAAATTT
* * * *
56467686 AGGTACCAAATTGAACCTAAAAAAAAGCTTAGGTACCAAATTAAGAAGACAAAAAGCCAAGTTC
1 AGGTACTAAATTG-AGC-AAAAAAAAGCTTAGGTACCAAATT-AG--GA-AAAATGACAAGTTC
* ** * *
56467750 A-GTACCAAATTGAGCCCAAAAAAGTTTAAGTACCAAATTAGGAAAAAGTGACAAGTTC
1 AGGTACTAAATTGAGCAAAAAAAAGCTTAGGTACCAAATTAGGAAAAA-TGACAAGTTC
* * * * *
56467808 AGGTACTAAATTGGGCAAAAAAAAAGGTTAGGTACCAAATTAGAAAAAAAT-ATAAAGTTT
1 AGGTACTAAATTGAGC-AAAAAAAAGCTTAGGTACCAAATTAG-GAAAAATGA-CAAGTTC
56467868 AGGTACTAAAT
1 AGGTACTAAAT
56467879 GTTATATTAA
Statistics
Matches: 108, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
57 4 0.04
58 11 0.10
59 13 0.12
60 41 0.38
61 25 0.23
62 2 0.02
63 11 0.10
64 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (58 bp):
AGGTACTAAATTGAGCAAAAAAAAGCTTAGGTACCAAATTAGGAAAAATGACAAGTTC
Found at i:56467873 original size:31 final size:30
Alignment explanation
Indices: 56467769--56467878 Score: 105
Period size: 31 Copynumber: 3.6 Consensus size: 30
56467759 TTGAGCCCAA
* *
56467769 AAAAGTTTAAGTACCAAATTAGGAAAAAGT
1 AAAAGTTTAGGTACCAAATTAGGAAAAAAT
* * * * *
56467799 GACAAGTTCAGGTACTAAATTGGGCAAAAA-
1 -AAAAGTTTAGGTACCAAATTAGGAAAAAAT
* *
56467829 AAAAGGTTAGGTACCAAATTAGAAAAAAAT
1 AAAAGTTTAGGTACCAAATTAGGAAAAAAT
*
56467859 ATAAAGTTTAGGTACTAAAT
1 A-AAAGTTTAGGTACCAAAT
56467879 GTTATATTAA
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
29 22 0.36
30 1 0.02
31 38 0.62
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.24
Consensus pattern (30 bp):
AAAAGTTTAGGTACCAAATTAGGAAAAAAT
Found at i:56473789 original size:7 final size:7
Alignment explanation
Indices: 56473777--56473801 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56473767 AAATTAATCC
56473777 TAAATTT
1 TAAATTT
56473784 TAAATTT
1 TAAATTT
56473791 TAAATTT
1 TAAATTT
56473798 TAAA
1 TAAA
56473802 ATGTAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:56478734 original size:21 final size:23
Alignment explanation
Indices: 56478709--56478750 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56478699 CAAACTTATA
56478709 CTAGGAG-G-GCACGTGTTAATC
1 CTAGGAGAGAGCACGTGTTAATC
*
56478730 CTAGGAGAGAGTACGTGTTAA
1 CTAGGAGAGAGCACGTGTTAA
56478751 CATGCATGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (23 bp):
CTAGGAGAGAGCACGTGTTAATC
Found at i:56479536 original size:19 final size:19
Alignment explanation
Indices: 56479512--56479549 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
56479502 ATTTTCCGGA
56479512 AAATGATTTACTTTTCTAG
1 AAATGATTTACTTTTCTAG
56479531 AAATGATTTACTTTTCTAG
1 AAATGATTTACTTTTCTAG
56479550 TGTTTGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
AAATGATTTACTTTTCTAG
Found at i:56489183 original size:34 final size:33
Alignment explanation
Indices: 56489120--56489184 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
56489110 AGGTTAATTT
* **
56489120 TTTTTTATTTTGATTTTTTATTATAAATAAACC
1 TTTTTTATTTTCATTTTTTAACATAAATAAACC
56489153 TTTTTTATTTTCACTTTTATTAACAT-AATAAA
1 TTTTTTATTTTCA-TTTT-TTAACATAAATAAA
56489185 ATAAAGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 12 0.44
34 10 0.37
35 5 0.19
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (33 bp):
TTTTTTATTTTCATTTTTTAACATAAATAAACC
Done.