Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 123 of 131
Found at i:40498038 original size:18 final size:18
Alignment explanation
Indices: 40498015--40498060 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
40498005 TGAGTTTTCG
40498015 AATTTGAATAACTCGAAT
1 AATTTGAATAACTCGAAT
40498033 AATTTGAATAACTCGAAT
1 AATTTGAATAACTCGAAT
*
40498051 AATTCGAATA
1 AATTTGAATA
40498061 TCAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
AATTTGAATAACTCGAAT
Found at i:40498308 original size:30 final size:31
Alignment explanation
Indices: 40498274--40498333 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
40498264 AAACCTTTTA
*
40498274 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
40498304 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
40498334 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:40499220 original size:104 final size:104
Alignment explanation
Indices: 40499032--40499235 Score: 372
Period size: 104 Copynumber: 2.0 Consensus size: 104
40499022 TATTCCAACT
40499032 ATTCAAAAGAAATAAAATGCTCATTTTACAACCACAATTAAATCAAGAACACCATATCTATTCAA
1 ATTCAAAAGAAATAAAATGCTCATTTTACAACCACAATTAAATCAAGAACACCATATCTATTCAA
*
40499097 ACATATACCAATAATTTACTACTATTTTACACACAAACC
66 ACATATACCAATAAATTACTACTATTTTACACACAAACC
* *
40499136 ATTCAAAAGAAATAAAATGCTCATTTTACGACCATAATTAAATCAAGAACACCATATCTATTCAA
1 ATTCAAAAGAAATAAAATGCTCATTTTACAACCACAATTAAATCAAGAACACCATATCTATTCAA
*
40499201 ACATATACCGATAAATTACTACTATTTTACACACA
66 ACATATACCAATAAATTACTACTATTTTACACACA
40499236 TGTATGCATA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (104 bp):
ATTCAAAAGAAATAAAATGCTCATTTTACAACCACAATTAAATCAAGAACACCATATCTATTCAA
ACATATACCAATAAATTACTACTATTTTACACACAAACC
Found at i:40500910 original size:43 final size:43
Alignment explanation
Indices: 40500849--40500943 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 43
40500839 TTCTAGATAG
* *
40500849 GGTCTTACTTGAAAATACAAGTCGATGCCATCGTCCCAGACGT
1 GGTCTTACATGAAAATACAAGTCGATGCCATCGTCACAGACGT
* *
40500892 GGTCTTACATGAAAATACAAGTTGATGTCATCGTCACAGACGT
1 GGTCTTACATGAAAATACAAGTCGATGCCATCGTCACAGACGT
40500935 GGTCTTACA
1 GGTCTTACA
40500944 CAAAAACACT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (43 bp):
GGTCTTACATGAAAATACAAGTCGATGCCATCGTCACAGACGT
Found at i:40505061 original size:6 final size:6
Alignment explanation
Indices: 40505052--40505083 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
40505042 TTCTAGAAAA
*
40505052 CTCTCC CTCTCC CTCTCA CTCTCC CTCTCC CT
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CT
40505084 ATACCTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.62, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:40505775 original size:18 final size:19
Alignment explanation
Indices: 40505739--40505776 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
40505729 GAAAAAAAGG
*
40505739 AAAGAAAAGTAGAAGGAAA
1 AAAGAAAACTAGAAGGAAA
40505758 AAAGAAAACTAG-AGGAAA
1 AAAGAAAACTAGAAGGAAA
40505776 A
1 A
40505777 GGCTCCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.03, G:0.24, T:0.05
Consensus pattern (19 bp):
AAAGAAAACTAGAAGGAAA
Found at i:40508020 original size:18 final size:18
Alignment explanation
Indices: 40507993--40508035 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
40507983 CCCTCATCAT
* *
40507993 CTAAGCGGAAATAGAAAG
1 CTAAGGGGAAATAGAAAA
40508011 CTAAGGGGAAATAGAAAA
1 CTAAGGGGAAATAGAAAA
40508029 CTAAGGG
1 CTAAGGG
40508036 AAAGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.30, T:0.12
Consensus pattern (18 bp):
CTAAGGGGAAATAGAAAA
Found at i:40517066 original size:27 final size:26
Alignment explanation
Indices: 40517029--40517123 Score: 109
Period size: 27 Copynumber: 3.6 Consensus size: 26
40517019 ACTTACGACC
* *
40517029 GAAGGGCAAAATAACCGAAATACCCT
1 GAAGGGTAAAATGACCGAAATACCCT
*
40517055 CGAAGGGTAAAATGACCGATATACCCT
1 -GAAGGGTAAAATGACCGAAATACCCT
* * *
40517082 AAAGGATAAAATGATCGAAATACCCT
1 GAAGGGTAAAATGACCGAAATACCCT
*
40517108 TATAGGGTAAAATGAC
1 GA-AGGGTAAAATGAC
40517124 TGTTATACCC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 23 0.40
27 34 0.60
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (26 bp):
GAAGGGTAAAATGACCGAAATACCCT
Found at i:40517340 original size:26 final size:26
Alignment explanation
Indices: 40517311--40517365 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
40517301 TTTGCCACAT
*
40517311 ATACTGTTACTGGCACCTTCGCTGCG
1 ATACTGTTACTAGCACCTTCGCTGCG
* * * *
40517337 ATACTTTTACTAGCAGCTTTGCTGGG
1 ATACTGTTACTAGCACCTTCGCTGCG
40517363 ATA
1 ATA
40517366 TTGGTGTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (26 bp):
ATACTGTTACTAGCACCTTCGCTGCG
Found at i:40517502 original size:28 final size:28
Alignment explanation
Indices: 40517460--40517551 Score: 130
Period size: 28 Copynumber: 3.3 Consensus size: 28
40517450 GTTACATTAT
* *
40517460 CACACTGTTATTGTATCAGGCTAAGGTC
1 CACACTGTTACTGTATCGGGCTAAGGTC
* *
40517488 CACACTGTTACTGTATTGGGCTAAGGCC
1 CACACTGTTACTGTATCGGGCTAAGGTC
* *
40517516 CACACTATTACTATATCGGGCTAAGGTC
1 CACACTGTTACTGTATCGGGCTAAGGTC
40517544 CACACTGT
1 CACACTGT
40517552 ACTATTATTG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (28 bp):
CACACTGTTACTGTATCGGGCTAAGGTC
Found at i:40520781 original size:19 final size:20
Alignment explanation
Indices: 40520742--40520781 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
40520732 TAAATTGGGC
*
40520742 CCAAGAGCCCAAAACTGAGA
1 CCAAGAGCCCAAAAATGAGA
*
40520762 CCAAGA-CCCAAAAATTAGA
1 CCAAGAGCCCAAAAATGAGA
40520781 C
1 C
40520782 AAACCAAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.47, C:0.30, G:0.15, T:0.07
Consensus pattern (20 bp):
CCAAGAGCCCAAAAATGAGA
Found at i:40522333 original size:16 final size:16
Alignment explanation
Indices: 40522296--40522335 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
40522286 TTAATCAAAT
* *
40522296 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
40522312 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
40522328 TAAAATTA
1 TAAAATTA
40522336 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:40522363 original size:16 final size:16
Alignment explanation
Indices: 40522342--40522383 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
40522332 ATTATCAAAT
40522342 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
40522358 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
*
40522374 AATTAATTGT
1 TATTAATTGT
40522384 ATTAATTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (16 bp):
TATTAATTGTTAATTG
Found at i:40522365 original size:9 final size:9
Alignment explanation
Indices: 40522342--40522392 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
40522332 ATTATCAAAT
40522342 TATTAATTG
1 TATTAATTG
40522351 --TTAATTG
1 TATTAATTG
40522358 TATTAATTG
1 TATTAATTG
40522367 --TTAATTG
1 TATTAATTG
*
40522374 AATTAATTG
1 TATTAATTG
40522383 TATTAATTG
1 TATTAATTG
40522392 T
1 T
40522393 TGTAACAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
7 14 0.38
9 23 0.62
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (9 bp):
TATTAATTG
Found at i:40522385 original size:25 final size:25
Alignment explanation
Indices: 40522344--40522393 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
40522334 TATCAAATTA
40522344 TTAATTG-TTAATTGTATTAATTG-
1 TTAATTGATTAATTGTATTAATTGT
40522367 TTAATTGAATTAATTGTATTAATTGT
1 TTAATTG-ATTAATTGTATTAATTGT
40522393 T
1 T
40522394 GTAACAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.29
25 16 0.67
26 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (25 bp):
TTAATTGATTAATTGTATTAATTGT
Found at i:40522455 original size:68 final size:68
Alignment explanation
Indices: 40522380--40522515 Score: 247
Period size: 68 Copynumber: 2.0 Consensus size: 68
40522370 ATTGAATTAA
*
40522380 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAATAAAC-TTGATGTTTTATTAT
1 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTTGATGTTTT-TTAT
40522444 TATT
65 TATT
40522448 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTTGATGTTTTTTATT
1 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTTGATGTTTTTTATT
40522513 ATT
66 ATT
40522516 ATTTTATTTT
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 56 0.85
69 10 0.15
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (68 bp):
TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTTGATGTTTTTTATT
ATT
Found at i:40522794 original size:54 final size:54
Alignment explanation
Indices: 40522729--40522878 Score: 142
Period size: 65 Copynumber: 2.6 Consensus size: 54
40522719 CAAATAAAAA
*
40522729 AAACTTAAAATAAAAAACAATTATAATTTAAAAATAAGGAAATGAAAGTAAATG
1 AAACTTTAAATAAAAAACAATTATAATTTAAAAATAAGGAAATGAAAGTAAATG
***
40522783 AAACTTTAAATAAAAAACTATTAGTTGGATAAATTAGTTGGCCAATAAGGAAATGAAAGTAAATG
1 AAACTTTAAATAAAAAAC-A--A-TT--AT-AA-T--TT-AAAAATAAGGAAATGAAAGTAAATG
*
40522848 AAAC-TTAAATAAAAAACTATTAT-ATTTAAAA
1 AAACTTTAAATAAAAAACAATTATAATTTAAAA
40522879 TATATATATT
Statistics
Matches: 77, Mismatches: 8, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
52 1 0.01
53 2 0.03
54 17 0.22
55 2 0.03
56 1 0.01
57 1 0.01
58 4 0.05
60 4 0.05
61 3 0.04
62 1 0.01
64 15 0.19
65 26 0.34
ACGTcount: A:0.57, C:0.05, G:0.11, T:0.27
Consensus pattern (54 bp):
AAACTTTAAATAAAAAACAATTATAATTTAAAAATAAGGAAATGAAAGTAAATG
Found at i:40535804 original size:41 final size:41
Alignment explanation
Indices: 40535739--40535908 Score: 157
Period size: 41 Copynumber: 4.2 Consensus size: 41
40535729 CTAACTTTCA
* *
40535739 GGCTTTAGCGGCG-TTTTTAAAAAGCGTCGCTAATGCTCAG
1 GGCTTTAGCGACGCTTTTTAGAAAGCGTCGCTAATGCTCAG
* *
40535779 TGCTTTAGCGACGCTTTTTAGAAAGCGTCGCGAATGCTCAG
1 GGCTTTAGCGACGCTTTTTAGAAAGCGTCGCTAATGCTCAG
* * * *
40535820 GGTTTTATC-A-GCATTTTTGAGAAAGTGCCGCTAATGCTCAG
1 GGCTTTAGCGACGC-TTTTT-AGAAAGCGTCGCTAATGCTCAG
* ** * * * *
40535861 GGCTTTAGCGGCATTTTTTATAAAGCGCCTCGAATGCTCAG
1 GGCTTTAGCGACGCTTTTTAGAAAGCGTCGCTAATGCTCAG
*
40535902 GGATTTA
1 GGCTTTA
40535909 AAATAATTTA
Statistics
Matches: 105, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 17 0.16
41 81 0.77
42 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (41 bp):
GGCTTTAGCGACGCTTTTTAGAAAGCGTCGCTAATGCTCAG
Found at i:40535969 original size:7 final size:7
Alignment explanation
Indices: 40535957--40536140 Score: 52
Period size: 7 Copynumber: 25.7 Consensus size: 7
40535947 TATCACTATA
40535957 GTTTAGG
1 GTTTAGG
40535964 GTTTAGG
1 GTTTAGG
* *
40535971 GTATATG
1 GTTTAGG
*
40535978 GTTTAGA
1 GTTTAGG
40535985 GTTTAAGG
1 GTTT-AGG
40535993 G-TTA-G
1 GTTTAGG
**
40535998 GTGTTACCA
1 GT-TTA-GG
* *
40536007 TTTTAAG
1 GTTTAGG
*
40536014 GTTTATG
1 GTTTAGG
*
40536021 GATTATGG
1 GTTTA-GG
40536029 GTTTAGG
1 GTTTAGG
* *
40536036 GATTATG
1 GTTTAGG
*
40536043 GTTTATG
1 GTTTAGG
**
40536050 GTTTAAA
1 GTTTAGG
** *
40536057 GACTGGG
1 GTTTAGG
*
40536064 GTTTAAG
1 GTTTAGG
40536071 GTTTAGAG
1 GTTTAG-G
*
40536079 G-TTATGT
1 GTTTA-GG
*
40536086 GTTAAGG
1 GTTTAGG
40536093 GTTTATGG
1 GTTTA-GG
*
40536101 TTTTAGG
1 GTTTAGG
*
40536108 GTTTTAAG
1 G-TTTAGG
40536116 GTTTA-G
1 GTTTAGG
* *
40536122 ATTTATG
1 GTTTAGG
40536129 GTTTAGG
1 GTTTAGG
40536136 GTTTA
1 GTTTA
40536141 AATTAACTAG
Statistics
Matches: 125, Mismatches: 40, Indels: 24
0.66 0.21 0.13
Matches are distributed among these distances:
5 2 0.02
6 6 0.05
7 88 0.70
8 28 0.22
9 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.32, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:40536033 original size:15 final size:14
Alignment explanation
Indices: 40536013--40536050 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
40536003 ACCATTTTAA
40536013 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
40536027 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
40536042 GGTTTATGG
1 GGTTTATGG
40536051 TTTAAAGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:40536033 original size:22 final size:21
Alignment explanation
Indices: 40536008--40536055 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
40535998 GTGTTACCAT
*
40536008 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
* *
40536030 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
40536051 TTTAA
1 TTTAA
40536056 AGACTGGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:40536420 original size:21 final size:21
Alignment explanation
Indices: 40536391--40536542 Score: 127
Period size: 21 Copynumber: 7.3 Consensus size: 21
40536381 TTATGGTTAA
* *
40536391 TTTAAGGGTTAGGATTTAAGG
1 TTTAGGGGTTAGGAGTTAAGG
* *
40536412 TTTAGGGGTTAGTAGTTAGGG
1 TTTAGGGGTTAGGAGTTAAGG
* *
40536433 GTTAGGGGTTAAGAGTT-AGTG
1 TTTAGGGGTTAGGAGTTAAG-G
40536454 ATTTAGGGGTTAGGA--T--GG
1 -TTTAGGGGTTAGGAGTTAAGG
* *
40536472 TTTTA-GGGTTGGGATTTAAGG
1 -TTTAGGGGTTAGGAGTTAAGG
*
40536493 TTTAGGGGTTAGGAGTTAGGG
1 TTTAGGGGTTAGGAGTTAAGG
* *
40536514 GTTAGGGGTTAAGAGTTAAGG
1 TTTAGGGGTTAGGAGTTAAGG
40536535 ATTTAGGG
1 -TTTAGGG
40536543 ATTTAAGGGT
Statistics
Matches: 104, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
17 8 0.08
18 5 0.05
19 2 0.02
20 6 0.06
21 65 0.62
22 18 0.17
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (21 bp):
TTTAGGGGTTAGGAGTTAAGG
Found at i:40536423 original size:7 final size:7
Alignment explanation
Indices: 40536413--40536524 Score: 66
Period size: 7 Copynumber: 15.4 Consensus size: 7
40536403 GATTTAAGGT
40536413 TTAGGGG
1 TTAGGGG
**
40536420 TTAGTAG
1 TTAGGGG
40536427 TTAGGGG
1 TTAGGGG
40536434 TTAGGGG
1 TTAGGGG
* *
40536441 TTAAGAG
1 TTAGGGG
**
40536448 TTAGTGAT
1 TTAG-GGG
40536456 TTAGGGG
1 TTAGGGG
40536463 TTAGGATGG
1 TTAGG--GG
40536472 TTTTA-GGG
1 --TTAGGGG
*
40536480 TT-GGGAT
1 TTAGGG-G
* *
40536487 TTAAGGT
1 TTAGGGG
40536494 TTAGGGG
1 TTAGGGG
*
40536501 TTAGGAG
1 TTAGGGG
40536508 TTAGGGG
1 TTAGGGG
40536515 TTAGGGG
1 TTAGGGG
40536522 TTA
1 TTA
40536525 AGAGTTAAGG
Statistics
Matches: 81, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
6 4 0.05
7 61 0.75
8 10 0.12
9 2 0.02
10 1 0.01
11 3 0.04
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:40541125 original size:43 final size:43
Alignment explanation
Indices: 40541059--40541199 Score: 192
Period size: 43 Copynumber: 3.3 Consensus size: 43
40541049 TTTGCCAAAA
* * * *
40541059 TTAGTGGCGTTTGTTGGTAAAGCGCTGCTAAAGGTCATGTTTT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTTT
* ***
40541102 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGAACATGAGCT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTTT
**
40541145 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGTTTT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTTT
40541188 TTAGCGGCGTTT
1 TTAGCGGCGTTT
40541200 TTTCACATAA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTTT
Found at i:40546674 original size:35 final size:35
Alignment explanation
Indices: 40546628--40546698 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
40546618 TATTACATTA
* *
40546628 ATATATATTATTAGTACAATAGTATAGACGGATTG
1 ATATATATTATTAGTACAATAGTATAAACGAATTG
40546663 ATATATATTATTAGTACAATAGTATAAACGAATTG
1 ATATATATTATTAGTACAATAGTATAAACGAATTG
40546698 A
1 A
40546699 CAATTTGAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.37
Consensus pattern (35 bp):
ATATATATTATTAGTACAATAGTATAAACGAATTG
Found at i:40547943 original size:28 final size:28
Alignment explanation
Indices: 40547903--40547958 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
40547893 GTAATCATCT
40547903 CATCCAGAGTTACTAAATATATTTGAGA
1 CATCCAGAGTTACTAAATATATTTGAGA
40547931 CATCCAGAGTTACTAAATATATTTGAGA
1 CATCCAGAGTTACTAAATATATTTGAGA
40547959 TAGGGGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (28 bp):
CATCCAGAGTTACTAAATATATTTGAGA
Found at i:40550053 original size:29 final size:29
Alignment explanation
Indices: 40550021--40550088 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
40550011 ATTTAGTACA
*
40550021 TATACTTT-AATTTGATCAAATTTAATCTC
1 TATACTTTGAA-TTGATCAAATTTAATCCC
* *
40550050 TATACTCTTTGAATTGGTCAAGTTTAATCCC
1 TATA--CTTTGAATTGATCAAATTTAATCCC
40550081 TATACTTT
1 TATACTTT
40550089 TTAATTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 8 0.24
31 23 0.70
32 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.47
Consensus pattern (29 bp):
TATACTTTGAATTGATCAAATTTAATCCC
Found at i:40550077 original size:31 final size:30
Alignment explanation
Indices: 40550036--40550094 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
40550026 TTTAATTTGA
*
40550036 TCAAATTTAATCTCTATACTCTTTGAATTGG
1 TCAAATTTAATCCCTATACT-TTTGAATTGG
* *
40550067 TCAAGTTTAATCCCTATACTTTTTAATT
1 TCAAATTTAATCCCTATACTTTTGAATT
40550095 TTTAAAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (30 bp):
TCAAATTTAATCCCTATACTTTTGAATTGG
Found at i:40555742 original size:6 final size:6
Alignment explanation
Indices: 40555731--40555762 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
40555721 ATATAGACAA
40555731 GGGAGT GGGAGT GGGAGT GGGAGT GGGAGT GG
1 GGGAGT GGGAGT GGGAGT GGGAGT GGGAGT GG
40555763 AAAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.69, T:0.16
Consensus pattern (6 bp):
GGGAGT
Found at i:40572829 original size:20 final size:21
Alignment explanation
Indices: 40572804--40572846 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
40572794 CACATTAGTG
40572804 AACAAATATGAATAT-AAATA
1 AACAAATATGAATATGAAATA
**
40572824 AACAAATATTTATATGAAATA
1 AACAAATATGAATATGAAATA
40572845 AA
1 AA
40572847 ATAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (21 bp):
AACAAATATGAATATGAAATA
Found at i:40572855 original size:22 final size:20
Alignment explanation
Indices: 40572804--40572860 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
40572794 CACATTAGTG
**
40572804 AACAAATATGAATATAAATA
1 AACAAATATTTATATAAATA
40572824 AACAAATATTTATATGAAATAA
1 AACAAATATTTATAT-AAAT-A
*
40572846 AATAAATATTTATAT
1 AACAAATATTTATAT
40572861 TTAAAATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 13 0.41
21 4 0.12
22 15 0.47
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (20 bp):
AACAAATATTTATATAAATA
Found at i:40573308 original size:20 final size:20
Alignment explanation
Indices: 40573285--40573325 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40573275 TTAAATCAAT
*
40573285 TTGATTAAAATCAAATAAAA
1 TTGATTAAAATAAAATAAAA
**
40573305 TTGATTGGAATAAAATAAAA
1 TTGATTAAAATAAAATAAAA
40573325 T
1 T
40573326 CAAATAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
TTGATTAAAATAAAATAAAA
Found at i:40573326 original size:30 final size:30
Alignment explanation
Indices: 40573290--40573357 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
40573280 TCAATTTGAT
*
40573290 TAAAATCAAATAAAATTGATTGGAATAAAA
1 TAAAATCAAATAAAATAGATTGGAATAAAA
*
40573320 TAAAATCAAATAAAATAGATTGGAATCAAA
1 TAAAATCAAATAAAATAGATTGGAATAAAA
40573350 TAAAATCA
1 TAAAATCA
40573358 GGATATATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.25
Consensus pattern (30 bp):
TAAAATCAAATAAAATAGATTGGAATAAAA
Found at i:40573336 original size:20 final size:20
Alignment explanation
Indices: 40573313--40573355 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
40573303 AATTGATTGG
40573313 AATAAAATAAAATCAAATAA
1 AATAAAATAAAATCAAATAA
* * **
40573333 AATAGATTGGAATCAAATAA
1 AATAAAATAAAATCAAATAA
40573353 AAT
1 AAT
40573356 CAGGATATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (20 bp):
AATAAAATAAAATCAAATAA
Found at i:40580542 original size:92 final size:93
Alignment explanation
Indices: 40580397--40580582 Score: 340
Period size: 92 Copynumber: 2.0 Consensus size: 93
40580387 GTTGCAGGTA
40580397 CGTGCTTGAGGAGCGGTGTTTGCGGAGAAACGCCACGCGTGGAGGACGAAACTTGCGGCGACTGG
1 CGTGCTTGAGGAGCGGTGTTTGCGGAGAAACGCCACGCGTGGAGGACGAAACTTGCGGCGACTGG
40580462 AGACTGCGGTGGCCACTTG-TCGCTACCG
66 AGACTGCGGTGGCCACTTGCT-GCTACCG
40580490 CGTGCTTGA-GAGCGGTGTTTGCGGAGAAACGCCACGCGTGGAGGACGAAACTTGCGGCGACTGG
1 CGTGCTTGAGGAGCGGTGTTTGCGGAGAAACGCCACGCGTGGAGGACGAAACTTGCGGCGACTGG
*
40580554 AGACTGCGGTGGCTACTTGCTGCTACCG
66 AGACTGCGGTGGCCACTTGCTGCTACCG
40580582 C
1 C
40580583 CTAGGGTTTT
Statistics
Matches: 91, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
92 81 0.89
93 10 0.11
ACGTcount: A:0.18, C:0.25, G:0.38, T:0.19
Consensus pattern (93 bp):
CGTGCTTGAGGAGCGGTGTTTGCGGAGAAACGCCACGCGTGGAGGACGAAACTTGCGGCGACTGG
AGACTGCGGTGGCCACTTGCTGCTACCG
Found at i:40611911 original size:118 final size:118
Alignment explanation
Indices: 40611703--40611927 Score: 432
Period size: 118 Copynumber: 1.9 Consensus size: 118
40611693 ATTAGGCGCT
* *
40611703 GCATAGGTTTCCCGTCCCTGTTATACCCTTCCATCTGCTTCCCCTTTGTTTCTCTTCTGTTCCTT
1 GCATAGGTTTACCGTCCCTGTTATACCCTCCCATCTGCTTCCCCTTTGTTTCTCTTCTGTTCCTT
40611768 CTAGTCTCTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTGCCCTCTGTTC
66 CTAGTCTCTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTGCCCTCTGTTC
40611821 GCATAGGTTTACCGTCCCTGTTATACCCTCCCATCTGCTTCCCCTTTGTTTCTCTTCTGTTCCTT
1 GCATAGGTTTACCGTCCCTGTTATACCCTCCCATCTGCTTCCCCTTTGTTTCTCTTCTGTTCCTT
40611886 CTAGTCTCTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCT
66 CTAGTCTCTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCT
40611928 ACCGATTTGC
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.07, C:0.35, G:0.12, T:0.46
Consensus pattern (118 bp):
GCATAGGTTTACCGTCCCTGTTATACCCTCCCATCTGCTTCCCCTTTGTTTCTCTTCTGTTCCTT
CTAGTCTCTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTGCCCTCTGTTC
Found at i:40611950 original size:33 final size:34
Alignment explanation
Indices: 40611896--40611961 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
40611886 CTAGTCTCTG
* *
40611896 CCGATTTGCTCCCTCCGTTTCTTTTC-TTTTCTA
1 CCGATTTGCTCCCTCCATTTCTTCTCATTTTCTA
**
40611929 CCGATTTGCTCCCTTTATTTCTTCTCATTTTCT
1 CCGATTTGCTCCCTCCATTTCTTCTCATTTTCT
40611962 TTTCTGCCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 22 0.79
34 6 0.21
ACGTcount: A:0.08, C:0.32, G:0.08, T:0.53
Consensus pattern (34 bp):
CCGATTTGCTCCCTCCATTTCTTCTCATTTTCTA
Found at i:40613530 original size:23 final size:23
Alignment explanation
Indices: 40613504--40613548 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
40613494 TCGGTAGAAA
*
40613504 AGAAAAGAAAATAAACAGAGGGC
1 AGAAAAGAAAAGAAACAGAGGGC
*
40613527 AGAAAAGAAAAGAAACGGAGGG
1 AGAAAAGAAAAGAAACAGAGGG
40613549 AGCAAATCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.07, G:0.31, T:0.02
Consensus pattern (23 bp):
AGAAAAGAAAAGAAACAGAGGGC
Found at i:40615077 original size:13 final size:13
Alignment explanation
Indices: 40615059--40615083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40615049 ATTTCATGAG
40615059 GTGAAAAGAAAAC
1 GTGAAAAGAAAAC
40615072 GTGAAAAGAAAA
1 GTGAAAAGAAAA
40615084 AGGAGGCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.24, T:0.08
Consensus pattern (13 bp):
GTGAAAAGAAAAC
Found at i:40616644 original size:32 final size:32
Alignment explanation
Indices: 40616603--40616668 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
40616593 TTTTCTTTGC
40616603 ATTGCAAGTTGTCTCTGGATTATGTATTAATT
1 ATTGCAAGTTGTCTCTGGATTATGTATTAATT
40616635 ATTGCAAGTTGTCTCTGGATTATGTATTAATT
1 ATTGCAAGTTGTCTCTGGATTATGTATTAATT
40616667 AT
1 AT
40616669 CATGCTTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (32 bp):
ATTGCAAGTTGTCTCTGGATTATGTATTAATT
Found at i:40621933 original size:37 final size:37
Alignment explanation
Indices: 40621883--40621972 Score: 180
Period size: 37 Copynumber: 2.4 Consensus size: 37
40621873 TGGAAACAAC
40621883 AACGATTTACAGGCTTTTGTTTCAAAAAAAAAAAAAA
1 AACGATTTACAGGCTTTTGTTTCAAAAAAAAAAAAAA
40621920 AACGATTTACAGGCTTTTGTTTCAAAAAAAAAAAAAA
1 AACGATTTACAGGCTTTTGTTTCAAAAAAAAAAAAAA
40621957 AACGATTTACAGGCTT
1 AACGATTTACAGGCTT
40621973 GTCTGTAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (37 bp):
AACGATTTACAGGCTTTTGTTTCAAAAAAAAAAAAAA
Found at i:40622502 original size:25 final size:25
Alignment explanation
Indices: 40622464--40622514 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
40622454 GACAAGACAA
40622464 CATAGGATGCTTGTTTTAGTACGTT
1 CATAGGATGCTTGTTTTAGTACGTT
*
40622489 CATAGGATGTTTGTTTTAGTACGTT
1 CATAGGATGCTTGTTTTAGTACGTT
40622514 C
1 C
40622515 TTTCTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.45
Consensus pattern (25 bp):
CATAGGATGCTTGTTTTAGTACGTT
Found at i:40625011 original size:20 final size:21
Alignment explanation
Indices: 40624970--40625010 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40624960 TTTGCCCGGG
*
40624970 CCCAAAACTAAATAAATAAAA
1 CCCAAAACTAAAAAAATAAAA
40624991 CCCAAAA-TAAAAAAAATAAA
1 CCCAAAACT-AAAAAAATAAA
40625011 CATTCCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.71, C:0.17, G:0.00, T:0.12
Consensus pattern (21 bp):
CCCAAAACTAAAAAAATAAAA
Found at i:40626471 original size:21 final size:21
Alignment explanation
Indices: 40626441--40626503 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 21
40626431 TTTGAACCTT
40626441 TTTTTGTATTATTTATTTTAAA
1 TTTTT-TATTATTTATTTTAAA
*
40626463 TTTTTTATTATTTACTTTAAA
1 TTTTTTATTATTTATTTTAAA
40626484 TTTTTT-TGTATATTATTTTA
1 TTTTTTAT-TAT-TTATTTTA
40626504 TTTCATTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.03
21 24 0.65
22 12 0.32
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTTATTATTTATTTTAAA
Found at i:40626819 original size:18 final size:17
Alignment explanation
Indices: 40626789--40626822 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40626779 GCTATTATTC
40626789 AAAAAAGGAAATATTTT
1 AAAAAAGGAAATATTTT
*
40626806 AAAATAAGGCAATATTT
1 AAAA-AAGGAAATATTT
40626823 CGCGTTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (17 bp):
AAAAAAGGAAATATTTT
Found at i:40630337 original size:113 final size:110
Alignment explanation
Indices: 40630065--40630395 Score: 396
Period size: 113 Copynumber: 3.0 Consensus size: 110
40630055 AAAATAAGAA
* * * ** *
40630065 TTAGCGGCGCTTTTGCT-AAAGCGCCGC-AAAAAACTAAGCCCAACGATGCCGTTTTCTAAGCTT
1 TTAGCGGCGCTTTT-ATGAAAGCGCCGCAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTT
* * *
40630128 CTGGGGGGGTTTAGCGGCGTTTTTAATAATGCGCAGCTAATGCAGGGCT
65 -T-CGGGGGTTTAGCGGCGTTTTTAATAAAGCGC-GCTAATGCTGGGCT
* * * * *
40630177 TTAGCGGCGTTTTTATGGAAGCGACGCAAAAAAATTAAACCTAACGACACCGTTTTCTTTGCTTT
1 TTAGCGGCGCTTTTATGAAAGCGCCGCAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTTT
* * *
40630242 CGGGGGTTTAGCGGTGTTTTTAGTAAAGCGTCGCTAATGCTGGGTTT
66 CGGGGGTTTAGCGGCGTTTTTAATAAAGCG-CGCTAATGCTGGG-CT
*
40630289 TTAGTGGCGCTTTTATGAAAGCGCCGCAAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTT
1 TTAGCGGCGCTTTTATGAAAGCGCCGC-AAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTT
* *
40630354 TCAGGGTTTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCT
65 TCGGGGGTTTAGCGGCGTTTTTAATAAAGCG-CGCTAATGCT
40630396 CAGGGATTTA
Statistics
Matches: 186, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
111 38 0.20
112 47 0.25
113 101 0.54
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (110 bp):
TTAGCGGCGCTTTTATGAAAGCGCCGCAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTTT
CGGGGGTTTAGCGGCGTTTTTAATAAAGCGCGCTAATGCTGGGCT
Found at i:40630661 original size:31 final size:32
Alignment explanation
Indices: 40630626--40630688 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
40630616 GGTTTAAGGG
*
40630626 TTAGGTGTTATGATTT-AGGGGTTAGGGGGAT
1 TTAGGGGTTATGATTTAAGGGGTTAGGGGGAT
* *
40630657 TTAGGGGTTATGCTTTAAGGGGTTATGGGGAT
1 TTAGGGGTTATGATTTAAGGGGTTAGGGGGAT
40630689 ATATTTAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.19, C:0.02, G:0.41, T:0.38
Consensus pattern (32 bp):
TTAGGGGTTATGATTTAAGGGGTTAGGGGGAT
Found at i:40632717 original size:52 final size:52
Alignment explanation
Indices: 40632639--40633517 Score: 1704
Period size: 52 Copynumber: 16.9 Consensus size: 52
40632629 TGAAATAAGA
*
40632639 AAATTCAAACTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
*
40632691 AAATTCAAATTAGGTTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
*
40632743 AAATTCAAATTAGGTTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
*
40632795 AAATTCAAATTAGGTTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
*
40632847 AAATTCAAATTAGGTTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40632899 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40632951 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40633003 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40633055 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40633107 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40633159 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40633211 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40633263 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40633315 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40633367 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
40633419 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
*
40633471 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTAATAAT
1 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAAT
40633518 TTACATAACC
Statistics
Matches: 823, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 823 1.00
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.33
Consensus pattern (52 bp):
AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
Found at i:40641092 original size:19 final size:19
Alignment explanation
Indices: 40641068--40641110 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
40641058 TTATGTGCAT
*
40641068 ATATCACATCTAAGATTGC
1 ATATCACATCTAAGATTAC
**
40641087 ATATCATGTCTAAGATTAC
1 ATATCACATCTAAGATTAC
40641106 ATATC
1 ATATC
40641111 CTTGAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (19 bp):
ATATCACATCTAAGATTAC
Found at i:40642920 original size:2 final size:2
Alignment explanation
Indices: 40642913--40642938 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40642903 CCTTCATTGG
40642913 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
40642939 ATTTATTTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:40645352 original size:44 final size:45
Alignment explanation
Indices: 40645290--40645385 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 45
40645280 TCGTATATTC
* * *
40645290 TTTGA-TTCAGTATTTAAACATGTAATAACTGGTG-AAGCCAATG
1 TTTGAGTTCAGTATTTAAACAAGTAAGAACTGGTGAAAGCCAATA
* *
40645333 TTTGAGTTCTGTATTTAAACAAGTAAGAACTGGTGAAAGGCAATA
1 TTTGAGTTCAGTATTTAAACAAGTAAGAACTGGTGAAAGCCAATA
40645378 TTTGAGTT
1 TTTGAGTT
40645386 GAGAGAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 5 0.11
44 26 0.57
45 15 0.33
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.35
Consensus pattern (45 bp):
TTTGAGTTCAGTATTTAAACAAGTAAGAACTGGTGAAAGCCAATA
Found at i:40648554 original size:15 final size:15
Alignment explanation
Indices: 40648534--40648563 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40648524 ATAGCTTATA
40648534 GTACAAGTTAAATTT
1 GTACAAGTTAAATTT
*
40648549 GTACAATTTAAATTT
1 GTACAAGTTAAATTT
40648564 ATTTAATACT
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:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (15 bp):
GTACAAGTTAAATTT
Found at i:40648755 original size:31 final size:30
Alignment explanation
Indices: 40648696--40648761 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
40648686 TTTTTAATCA
* * *
40648696 CAAATGGTACTTAAATTATATTATGTTACT
1 CAAATGGTACCTAAATCATATTATGTTACC
40648726 CAAAGTGGTACCTAAATCATATT-TCGTTACC
1 CAAA-TGGTACCTAAATCATATTAT-GTTACC
40648757 CAAAT
1 CAAAT
40648762 TACCTCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (30 bp):
CAAATGGTACCTAAATCATATTATGTTACC
Found at i:40665533 original size:45 final size:45
Alignment explanation
Indices: 40665469--40665560 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
40665459 AAAGAAAAGA
40665469 ATGTGCATGAGATGCATTGTTGTTAATTCATTGACATGTATGTAT
1 ATGTGCATGAGATGCATTGTTGTTAATTCATTGACATGTATGTAT
40665514 ATGTGCATGAGATGCATTGTTGTTAATTCATTGACATGTATGTAT
1 ATGTGCATGAGATGCATTGTTGTTAATTCATTGACATGTATGTAT
40665559 AT
1 AT
40665561 ATGTATTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (45 bp):
ATGTGCATGAGATGCATTGTTGTTAATTCATTGACATGTATGTAT
Found at i:40675176 original size:17 final size:18
Alignment explanation
Indices: 40675151--40675185 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40675141 TTTAGTTTTC
*
40675151 AAATTAAAT-AAAGTAGA
1 AAATAAAATAAAAGTAGA
40675168 AAATAAAATAAAAGTAGA
1 AAATAAAATAAAAGTAGA
40675186 GGAAGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (18 bp):
AAATAAAATAAAAGTAGA
Found at i:40685520 original size:35 final size:35
Alignment explanation
Indices: 40685474--40685540 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
40685464 TAATTGACAG
40685474 ATTAACATAAAGACTGAAAGAAAGAAATAAAATCA
1 ATTAACATAAAGACTGAAAGAAAGAAATAAAATCA
40685509 ATTAACATAAAGACTGAAAGAAAGAAATAAAA
1 ATTAACATAAAGACTGAAAGAAAGAAATAAAA
40685541 GAATAAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.64, C:0.07, G:0.12, T:0.16
Consensus pattern (35 bp):
ATTAACATAAAGACTGAAAGAAAGAAATAAAATCA
Found at i:40691456 original size:25 final size:26
Alignment explanation
Indices: 40691423--40691471 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
40691413 AACTATTGCT
*
40691423 TTTTTACTATTTTGTTGCT-CTTTTC
1 TTTTAACTATTTTGTTGCTACTTTTC
40691448 TTTTAACTATTTTGTTGCTACTTT
1 TTTTAACTATTTTGTTGCTACTTT
40691472 CTTATTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.12, C:0.14, G:0.08, T:0.65
Consensus pattern (26 bp):
TTTTAACTATTTTGTTGCTACTTTTC
Found at i:40702176 original size:22 final size:22
Alignment explanation
Indices: 40702141--40702182 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40702131 TCCTTTTCAT
*
40702141 AATTTAAGCTTAATT-TTTATC
1 AATTTAAGCCTAATTCTTTATC
40702162 AATTTCAAGCCTAATTCTTTA
1 AATTT-AAGCCTAATTCTTTA
40702183 ATTTCTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (22 bp):
AATTTAAGCCTAATTCTTTATC
Found at i:40716682 original size:13 final size:13
Alignment explanation
Indices: 40716653--40716690 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
40716643 NNNNNNNNNN
40716653 TATTAAA-AATAT
1 TATTAAATAATAT
*
40716665 TATTAAATAATTT
1 TATTAAATAATAT
40716678 TATTAAAATAATA
1 TATT-AAATAATA
40716691 AATTATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 7 0.32
13 8 0.36
14 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATTAAATAATAT
Found at i:40718771 original size:18 final size:17
Alignment explanation
Indices: 40718732--40718784 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
40718722 ATTTAAAATA
*
40718732 ATTAATTTAACTATTAATT
1 ATTAATTTAA-T-TTTATT
40718751 ATTATATTTAATTTTATT
1 ATTA-ATTTAATTTTATT
*
40718769 ATTAATTTATTTTTAT
1 ATTAATTTAATTTTAT
40718785 AAATTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 11 0.35
18 9 0.29
19 5 0.16
20 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTAATTTAATTTTATT
Found at i:40718790 original size:21 final size:22
Alignment explanation
Indices: 40718766--40718816 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
40718756 ATTTAATTTT
40718766 ATTATTAATTT-ATTTTTATAA
1 ATTATTAATTTAATTTTTATAA
*
40718787 ATTATT-TTTTAATTTTTATAA
1 ATTATTAATTTAATTTTTATAA
40718808 ATTA-TAATT
1 ATTATTAATT
40718817 ACGGTTCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTATTAATTTAATTTTTATAA
Found at i:40727573 original size:22 final size:20
Alignment explanation
Indices: 40727536--40727581 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
40727526 CTCTTTCAAC
*
40727536 AAAAAAATTAAAAATTTCTA
1 AAAAAAATAAAAAATTTCTA
*
40727556 AAAAAAATCAAAATAATTTTTA
1 AAAAAAAT-AAAA-AATTTCTA
40727578 AAAA
1 AAAA
40727582 TCCAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 3 0.14
22 11 0.50
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAAATAAAAAATTTCTA
Found at i:40727592 original size:18 final size:19
Alignment explanation
Indices: 40727558--40727598 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40727548 AATTTCTAAA
*
40727558 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTAT
*
40727577 AAAAATCCAAAT-ATTTAT
1 AAAAATCAAAATAATTTAT
40727595 AAAA
1 AAAA
40727599 TTTCCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:40732671 original size:2 final size:2
Alignment explanation
Indices: 40732659--40732739 Score: 51
Period size: 2 Copynumber: 41.0 Consensus size: 2
40732649 ATAAGATAAA
* * * *
40732659 AT AT AT GT AT AT AT AT AT AT GT GT AT AT AT AT AT AG AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
40732700 AA AG AA ACT AT AT TT CA- AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
40732740 GAATACGTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
1 3 0.05
2 59 0.94
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:40732678 original size:14 final size:14
Alignment explanation
Indices: 40732659--40732692 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
40732649 ATAAGATAAA
40732659 ATATATGTATATAT
1 ATATATGTATATAT
*
40732673 ATATATGTGTATAT
1 ATATATGTATATAT
40732687 ATATAT
1 ATATAT
40732693 AGATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (14 bp):
ATATATGTATATAT
Found at i:40732678 original size:16 final size:16
Alignment explanation
Indices: 40732659--40732693 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
40732649 ATAAGATAAA
40732659 ATATATGTATATATAT
1 ATATATGTATATATAT
*
40732675 ATATGTGTATATATAT
1 ATATATGTATATATAT
40732691 ATA
1 ATA
40732694 GATATAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (16 bp):
ATATATGTATATATAT
Found at i:40733875 original size:27 final size:28
Alignment explanation
Indices: 40733827--40733881 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
40733817 GTTTTGGGCC
*
40733827 TGTTGGGTATTTGGGCTTGGTT-TAATT
1 TGTTGGGTACTTGGGCTTGGTTGTAATT
*
40733854 TGTTGGGT-CTTGGGTTTGGGTTGTAATT
1 TGTTGGGTACTTGGGCTT-GGTTGTAATT
40733882 GGGTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 12 0.50
28 5 0.21
ACGTcount: A:0.09, C:0.04, G:0.36, T:0.51
Consensus pattern (28 bp):
TGTTGGGTACTTGGGCTTGGTTGTAATT
Found at i:40734421 original size:132 final size:132
Alignment explanation
Indices: 40734197--40734465 Score: 432
Period size: 132 Copynumber: 2.0 Consensus size: 132
40734187 CATCATTGTT
40734197 GATCTGCTCCACTACTGCCTAGGGGGACAGAATCTACAATCTTCGACCTATTCCACTACTGCTTA
1 GATCTGCTCCACTACTGCCTAGGGGGACAGAATCTACAATCTTCGACCTATTCCACTACTGCTTA
* *
40734262 GGGTGATAGGGCTAACGGTTTAAATCTGCTTCTCCACTGTCTTGAGAAGATAAAATTCACCATCT
66 GGGTGATAGGACTAACGGATTAAATCTGCTTCTCCACTGTCTTGAGAAGATAAAATTCACCATCT
40734327 TC
131 TC
* * * *
40734329 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACCTATTCCACTATTGCTTA
1 GATCTGCTCCACTACTGCCTAGGGGGACAGAATCTACAATCTTCGACCTATTCCACTACTGCTTA
* * * *
40734394 GGAG-GATAGGACTAATGGATTAAATCTGCTTCTCCACTGTCTTGGGAAGGTAAGATTCACCATC
66 GG-GTGATAGGACTAACGGATTAAATCTGCTTCTCCACTGTCTTGAGAAGATAAAATTCACCATC
40734458 TTC
130 TTC
40734461 GATCT
1 GATCT
40734466 TCAATTTATT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
132 125 0.99
133 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
GATCTGCTCCACTACTGCCTAGGGGGACAGAATCTACAATCTTCGACCTATTCCACTACTGCTTA
GGGTGATAGGACTAACGGATTAAATCTGCTTCTCCACTGTCTTGAGAAGATAAAATTCACCATCT
TC
Found at i:40734540 original size:95 final size:95
Alignment explanation
Indices: 40734452--40734752 Score: 469
Period size: 95 Copynumber: 3.2 Consensus size: 95
40734442 GGTAAGATTC
* * *
40734452 ACCATCTTCGATCTTCAATTTATTCCACTGCCAACCAGAGAGATAGAATTATCGACTTCAATGTA
1 ACCATCTTTGATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTA
40734517 CTCCACTGTAGTCACAGAGAGGTAAAATCT
66 CTCCACTGTAGTCACAGAGAGGTAAAATCT
*
40734547 ACCATCTTTGATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTA
1 ACCATCTTTGATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTA
*
40734612 CTCCACTGTAATCACA-AGGAGGTAAAATCT
66 CTCCACTGTAGTCACAGA-GAGGTAAAATCT
* * * * *
40734642 GCCATCTTTGATCTTCAATCTATTCCACTGCTAACCAGAGAGATAGAATTATAGGTTTCAATATA
1 ACCATCTTTGATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTA
* *
40734707 CTCCACTGTAGTCACAGGGAGGTAGAATCT
66 CTCCACTGTAGTCACAGAGAGGTAAAATCT
*
40734737 GCCATCTTTGATCTTC
1 ACCATCTTTGATCTTC
40734753 TCCTTTTTGG
Statistics
Matches: 190, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
94 1 0.01
95 189 0.99
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (95 bp):
ACCATCTTTGATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTA
CTCCACTGTAGTCACAGAGAGGTAAAATCT
Found at i:40734874 original size:62 final size:62
Alignment explanation
Indices: 40734805--40734929 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 62
40734795 TTGCAAACTA
*
40734805 TGGTGTCTTCGATCTACTTCACTGTCAGTACAAGAAGGCAAGATCTGCTACCTTCAGTCTGC
1 TGGTGTCTTCGATCTACTTCACCGTCAGTACAAGAAGGCAAGATCTGCTACCTTCAGTCTGC
* * ** * * *
40734867 TGGTGTCTTTGATCTGCTTTGCCGTCAGTACAGGAAGGCAAGATCTGCTATCTTTAGTCTGC
1 TGGTGTCTTCGATCTACTTCACCGTCAGTACAAGAAGGCAAGATCTGCTACCTTCAGTCTGC
40734929 T
1 T
40734930 CCACTGTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (62 bp):
TGGTGTCTTCGATCTACTTCACCGTCAGTACAAGAAGGCAAGATCTGCTACCTTCAGTCTGC
Found at i:40735066 original size:45 final size:45
Alignment explanation
Indices: 40734938--40735326 Score: 200
Period size: 44 Copynumber: 8.8 Consensus size: 45
40734928 CTCCACTGTT
*
40734938 AATGCAGGAAGACAAGATCTGTTGTCTTCAACCAGC-TCTGCTA-C
1 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTC-GCTATC
* * * * * *
40734982 AACTG-A-GAGAGGCAAGGTTTG-TGTCTTCGACCTGATTCGCTATT
1 AA-TGCAGGA-AGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
*
40735026 AATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTTCGCTA-C
1 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
* * * * * * *
40735070 AA--CCGAGAGAGGCAAGGTTTG-TGTCTTCGATCTGCTTCGCTGTC
1 AATGCAG-GA-AGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
* *
40735114 AAGGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGC-TCTACTA-C
1 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTC-GCTATC
* * * * * * * * * *
40735158 AA-CCGAGAAAGGTAAGGTTTG-CGTCTTCGATCTGCTTCGCTGTC
1 AATGC-AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
* * * *
40735202 AAGGCAGGAAGGCAGGATCTGTTGTCTTCAACCAGCTCCACTA-C
1 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
* * * * * * *
40735246 AA--CCGAGAGAGGCAAGGTTTG-TGTCTTCGATCTGCTTCGCTGTC
1 AATGCAG-GA-AGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
* * * *
40735290 AAGGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCT
1 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCT
40735327 CCACTGCAAC
Statistics
Matches: 248, Mismatches: 72, Indels: 49
0.67 0.20 0.13
Matches are distributed among these distances:
42 4 0.02
43 67 0.27
44 110 0.44
45 63 0.25
46 4 0.02
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (45 bp):
AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
Found at i:40735403 original size:87 final size:87
Alignment explanation
Indices: 40734924--40736189 Score: 1569
Period size: 87 Copynumber: 14.5 Consensus size: 87
40734914 CTATCTTTAG
* * * * * ** * *
40734924 TCTGCTCCACTGTTAATGCAGGAAGACAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACTGA-
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
40734988 GAGAGGCAAGG-TTTGTGTCTTCGA
66 G-GAGGCAAGGCTTTGT-T-TTCGA
* * * * * * *
40735012 CCTGATTCGCTATTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTTCGCTACAACCGA-
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
40735076 GAGAGGCAAGG-TTTGTGTCTTCGA
66 G-GAGGCAAGGCTTTGT-T-TTCGA
* * * * * *
40735100 TCTGCTTCGCTGTCAAGGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTACTACAACCGA-
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
* * *
40735164 GAAAGGTAAGG-TTTGCGTCTTCGA
66 G-GAGGCAAGGCTTT--GTTTTCGA
* * * * * *
40735188 TCTGCTTCGCTGTCAAGGCAGGAAGGCAGGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
40735252 GAGAGGCAAGG-TTTGTGTCTTCGA
66 G-GAGGCAAGGCTTTGT-T-TTCGA
* * *
40735276 TCTGCTTCGCTGTCAAGGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
* *
40735341 GGAGGCAAGGTTTTGTGTTT-TA
66 GGAGGCAAGGCTTTGT-TTTCGA
* * * **
40735363 TCTGCTTCGCTGTTAATGTAGGAAGGTAAAATCTGCTATCTTCAACCAGCTCCACTATAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
* *
40735428 GGAGGCAGGGCTTTATTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
* *
40735450 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTACACTGCAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
**
40735515 GGAGGCAAGGCTTCATTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
* * * * * * *
40735537 TCTGCTTCGCTGTTAACGTAGAAAGACAAGATCTGCTATCTTTAACCAACTCCACTACAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
*
40735602 GGAGGCAAGGCTTTGTTTTTGA
66 GGAGGCAAGGCTTTGTTTTCGA
* * *
40735624 TCTACTTCGCTGTTAATGCAGGAAGGCAAAATCTGCTATCTTCAACCAGCTCCATTGCAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
40735689 GGAGGCAAGGCTTTGTTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
* *
40735711 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
*
40735776 GGAGGCAAGGCTTCGTTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
* * * *
40735798 TCTGCTTCGCTGTTAACGCGGGAAGGCAATATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
40735863 GGAGGCAAGGCTTTGTTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
* * *
40735885 TCTGCTTCGCTGTTAATGCAGGAAGACAAAATCTGTTATCTTCAACCAGCTCCACTGCAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
*
40735950 GGAGGCAAGGTTTTGTTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
* * * * *
40735972 TCTGCTTCGATGTTAATGTAGGAATGCAAGATCTACTATCTTTAACCAGCTCCACTGCAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
*
40736037 GGAGGCAAGGCTTCGTTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
* * * * * * * *
40736059 TCTACTTCGCTGTCAATGCAGGAAAGCAAGATCTGTTGTCTTCAACCAGCTCCATTGTAATCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
*
40736124 GGAGGCAAGGCTTTGCTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
* * *
40736146 TCTGCTTCACTGTTAACGCAGGAAAGCAAGATCTGCTATCTTCA
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCA
40736190 CTAATATGTT
Statistics
Matches: 1048, Mismatches: 123, Indels: 15
0.88 0.10 0.01
Matches are distributed among these distances:
86 5 0.00
87 734 0.70
88 299 0.29
89 8 0.01
90 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
GGAGGCAAGGCTTTGTTTTCGA
Found at i:40737890 original size:41 final size:41
Alignment explanation
Indices: 40737835--40737930 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
40737825 TCATTTCATA
* *
40737835 TTTTATTTTGACTTTGATTTTGATTTTAATTGATTTTCT-T-
1 TTTTCTTTTCACTTTGATTTTGATTTTAATT-ATTTTCTCTC
*
40737875 TTTTGCTTTTCACTTTGATTTTGATTTTAATTTTTTTCTCTC
1 TTTT-CTTTTCACTTTGATTTTGATTTTAATTATTTTCTCTC
40737917 TTTTCTTTTC-CTTT
1 TTTTCTTTTCACTTT
40737931 TTTTTTGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 14 0.28
41 32 0.64
42 4 0.08
ACGTcount: A:0.12, C:0.11, G:0.07, T:0.69
Consensus pattern (41 bp):
TTTTCTTTTCACTTTGATTTTGATTTTAATTATTTTCTCTC
Found at i:40742656 original size:12 final size:12
Alignment explanation
Indices: 40742639--40742704 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 12
40742629 GATAAGAAAC
40742639 AATAATATAAAT
1 AATAATATAAAT
*
40742651 AATAATATTAAT
1 AATAATATAAAT
40742663 AATAATA-ACAAT
1 AATAATATA-AAT
* *
40742675 AATGAAAAAAAAT
1 AAT-AATATAAAT
40742688 AAT-ATATTAAA-
1 AATAATA-TAAAT
40742699 AATAAT
1 AATAAT
40742705 GAGGAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 5 0.11
12 29 0.66
13 9 0.20
14 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (12 bp):
AATAATATAAAT
Found at i:40743340 original size:7 final size:6
Alignment explanation
Indices: 40743320--40743355 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
40743310 TATAGTTTTT
*
40743320 AAATAA AAAGAA AAATAA AAATAA AAATAA AGAATA
1 AAATAA AAATAA AAATAA AAATAA AAATAA A-AATA
40743356 CAAACAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:40743795 original size:27 final size:28
Alignment explanation
Indices: 40743747--40743801 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
40743737 GTTTTGGGCC
*
40743747 TGTTGGGTATTTGGGCTTGGTT-TAATT
1 TGTTGGGTACTTGGGCTTGGTTGTAATT
*
40743774 TGTTGGGT-CTTGGGTTTGGGTTGTAATT
1 TGTTGGGTACTTGGGCTT-GGTTGTAATT
40743802 GGGTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 12 0.50
28 5 0.21
ACGTcount: A:0.09, C:0.04, G:0.36, T:0.51
Consensus pattern (28 bp):
TGTTGGGTACTTGGGCTTGGTTGTAATT
Found at i:40745266 original size:10 final size:10
Alignment explanation
Indices: 40745251--40745412 Score: 94
Period size: 10 Copynumber: 16.2 Consensus size: 10
40745241 GAAGGAGAGG
40745251 GAAAGAAGAA
1 GAAAGAAGAA
40745261 GAAAGAAAGAAA
1 GAAAG-AAG-AA
40745273 GAAAGAA-AA
1 GAAAGAAGAA
40745282 GGAAAGAA-AA
1 -GAAAGAAGAA
* *
40745292 GGAAAGGAGAG
1 -GAAAGAAGAA
40745303 GAAAG-A-AA
1 GAAAGAAGAA
40745311 GAAA-AAGAA
1 GAAAGAAGAA
40745320 GGAAAGAA-AA
1 -GAAAGAAGAA
40745330 GGAAAGGAGAGAA
1 -GAAA-GA-AGAA
* *
40745343 GAAAAAAAAA
1 GAAAGAAGAA
40745353 GAAA-AAGAA
1 GAAAGAAGAA
40745362 GGAAAGAA-AA
1 -GAAAGAAGAA
*
40745372 GGAAAGGAGAA
1 -GAAAGAAGAA
40745383 GAGAAG-AGAA
1 GA-AAGAAGAA
*
40745393 -AAAAAAGAA
1 GAAAGAAGAA
40745402 G-AAGAAGAA
1 GAAAGAAGAA
40745411 GA
1 GA
40745413 GGGAAGGAAA
Statistics
Matches: 125, Mismatches: 9, Indels: 36
0.74 0.05 0.21
Matches are distributed among these distances:
8 8 0.06
9 22 0.18
10 63 0.50
11 18 0.14
12 12 0.10
13 2 0.02
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
GAAAGAAGAA
Found at i:40745287 original size:5 final size:5
Alignment explanation
Indices: 40745261--40745337 Score: 65
Period size: 5 Copynumber: 16.4 Consensus size: 5
40745251 GAAAGAAGAA
* * *
40745261 GAAA- GAAA- GAAA- GAAAG AAAAG GAAAG AAAAG GAAAG GAGAG GAAA-
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
* * *
40745307 GAAAG AAAAA G-AAG GAAAG AAAAG GAAAG GA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GA
40745338 GAGAAGAAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
4 19 0.33
5 39 0.67
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:40745297 original size:42 final size:42
Alignment explanation
Indices: 40745250--40745434 Score: 187
Period size: 42 Copynumber: 4.5 Consensus size: 42
40745240 AGAAGGAGAG
*
40745250 GGAAAGAAGAAGAAAGAAAGAAAGAAAGAA-AAGGAAAGAAAA
1 GGAAAGGAGAAGAAAGAAAGAAA-AAAGAAGAAGGAAAGAAAA
*
40745292 GGAAAGGAGAGGAAAGAAAG---AAA-AAGAAGGAAAGAAAA
1 GGAAAGGAGAAGAAAGAAAGAAAAAAGAAGAAGGAAAGAAAA
40745330 GGAAAGGAG-AG-AAGAAA-AAAAAAGAAAAAGAAGGAAAGAAAA
1 GGAAAGGAGAAGAAAGAAAGAAAAAAG---AAGAAGGAAAGAAAA
*
40745372 GGAAAGGAGAAGAGAAGAGAA-AAAAAAGAAGAA-G-AAGAAGA
1 GGAAAGGAGAAGA-AAGA-AAGAAAAAAGAAGAAGGAAAGAAAA
* *
40745413 GGGAAGGA-AAGAAAAAAAGAAA
1 GGAAAGGAGAAGAAAGAAAGAAA
40745435 TAAAAGGTAA
Statistics
Matches: 124, Mismatches: 6, Indels: 29
0.78 0.04 0.18
Matches are distributed among these distances:
36 6 0.05
37 3 0.02
38 29 0.23
39 6 0.05
40 4 0.03
41 13 0.10
42 43 0.35
43 7 0.06
45 4 0.03
46 9 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (42 bp):
GGAAAGGAGAAGAAAGAAAGAAAAAAGAAGAAGGAAAGAAAA
Found at i:40745307 original size:38 final size:37
Alignment explanation
Indices: 40745265--40745441 Score: 172
Period size: 38 Copynumber: 4.8 Consensus size: 37
40745255 GAAGAAGAAA
40745265 GAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGGAGAG
1 GAAAGAAAGAAA-AAAAGGAAAGAAAAGGAAAGGAGAG
40745303 GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAG
1 GAAAGAAAGAAAAA-AAGGAAAGAAAAGGAAAGGAGAG
*
40745341 AAGAAAAAAAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGA-
1 --G--AAAGAAAGAAAAA-AAGGAAAGAAAAGGAAAGGAGAG
* *
40745382 -AGAGAAGAGAAAAAAAAG-AAGAAGAA-G-AA-GAG-G
1 GAAAGAA-AGAAAAAAAGGAAAGAA-AAGGAAAGGAGAG
* *
40745415 GAAGGAAAGAAAAAAA-GAAATAAAAGG
1 GAAAGAAAGAAAAAAAGGAAAGAAAAGG
40745442 TAATTTTTAT
Statistics
Matches: 121, Mismatches: 7, Indels: 27
0.78 0.05 0.17
Matches are distributed among these distances:
32 3 0.02
33 17 0.14
34 6 0.05
35 6 0.05
36 9 0.07
37 9 0.07
38 35 0.29
40 1 0.01
42 35 0.29
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (37 bp):
GAAAGAAAGAAAAAAAGGAAAGAAAAGGAAAGGAGAG
Found at i:40745369 original size:80 final size:81
Alignment explanation
Indices: 40745250--40745430 Score: 232
Period size: 80 Copynumber: 2.2 Consensus size: 81
40745240 AGAAGGAGAG
40745250 GGAAA-GAAGAAGAAAGAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGGAG-AG-GAA-AGAAA
1 GGAAAGGAAGAAGAAA-AAA-AAAGAAA-AAAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAA
*
40745311 GAAAAAGAAGGA-AAGAAAA
63 -AAAAAGAAGAAGAAGAAAA
40745330 GGAAAGGAGAGAAGAAAAAAAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAA
1 GGAAAGGA-AGAAGAAAAAAAAAGAAAAA-AAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAA
*
40745395 AAAAGAAGAAGAAGAAGA
64 AAAAGAAGAAGAAGAAAA
*
40745413 GGGAAGG-A-AAGAAAAAAA
1 GGAAAGGAAGAAGAAAAAAA
40745431 GAAATAAAAG
Statistics
Matches: 91, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
79 2 0.02
80 43 0.47
81 8 0.09
82 21 0.23
83 17 0.19
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (81 bp):
GGAAAGGAAGAAGAAAAAAAAAGAAAAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAAAA
AAGAAGAAGAAGAAAA
Found at i:40746363 original size:319 final size:319
Alignment explanation
Indices: 40745768--40746862 Score: 1881
Period size: 319 Copynumber: 3.4 Consensus size: 319
40745758 AATTGTATAT
* * * * *
40745768 TTAATAAATTTTAAACATAATGCACTGAAATAATGTAAAATGATAAAATTAAAAATTACGGTATT
1 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATGATAAAATTAGAAATTAAGATATT
*
40745833 TTTTAAAGTAATATAATGCCGATAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTA
66 TTTTAAAGTAATATAATGCGGAT-AAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTA
* *
40745898 ACTTTTTTAAAAATTCAGAAATAATTAATGCAAATATTTCAAATAAAATACACTGAAATAATATA
130 ACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATACACTGAAATAATATA
* ***
40745963 AAATAATAAAATACGAAAATAAAATATTGGCATTGAAAGTAATAAAAATCGGG-AAATAATACGA
195 AAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACGA
* *
40746027 GCAAAGGGCATGGATAAGGGTTTTTTTCCTACACCAAATTAATTTAAAAAACACACTAAA
260 GCAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
*
40746087 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATGATAAAATTAGAAATTACGATATT
1 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATGATAAAATTAGAAATTAAGATATT
*
40746152 TTTTAAAATAATATAATGCGGATAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTAA
66 TTTTAAAGTAATATAATGCGGATAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTAA
40746217 CTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATACACTGAAATAATATAA
131 CTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATACACTGAAATAATATAA
40746282 AATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACGAG
196 AATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACGAG
* *
40746347 CAAAGGGCAGGGATAAGAGTTTTTTTCTTACACCAAATTAATTTAAAAAACAAACTAAA
261 CAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
40746406 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAA-GTATAAAATTAGAAATTAAGATAT
1 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATG-ATAAAATTAGAAATTAAGATAT
*
40746470 TTTTTAAAGTAATGA-AATGCGGAGAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACT
65 TTTTTAAAGTAAT-ATAATGCGGATAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACT
*
40746534 AACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATGCACTGAAATAATAT
129 AACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATACACTGAAATAATAT
40746599 AAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACG
194 AAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACG
*
40746664 AGCAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAACACACACTAAA
259 AGCAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
*
40746725 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTAAGATATT
1 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATGATAAAATTAGAAATTAAGATATT
* * * * * *
40746790 TTTTAAAGTAATAAAATACGGAGAAAAAAATAAGAACAAATGGCCGAAGTAAGAGTTTTTTACTA
66 TTTTAAAGTAATATAATGCGGA-TAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTA
40746855 ACTTTTTT
130 ACTTTTTT
40746863 TTCAACTTGC
Statistics
Matches: 741, Mismatches: 29, Indels: 11
0.95 0.04 0.01
Matches are distributed among these distances:
318 155 0.21
319 539 0.73
320 47 0.06
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (319 bp):
TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATGATAAAATTAGAAATTAAGATATT
TTTTAAAGTAATATAATGCGGATAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTAA
CTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATACACTGAAATAATATAA
AATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACGAG
CAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
Found at i:40748660 original size:18 final size:18
Alignment explanation
Indices: 40748637--40748673 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40748627 ATCCCAATGA
40748637 TTGCCACCACCTTCTTCT
1 TTGCCACCACCTTCTTCT
*
40748655 TTGCCACCAGCTTCTTCT
1 TTGCCACCACCTTCTTCT
40748673 T
1 T
40748674 CACCACCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.41, G:0.08, T:0.41
Consensus pattern (18 bp):
TTGCCACCACCTTCTTCT
Found at i:40748679 original size:18 final size:18
Alignment explanation
Indices: 40748640--40748681 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40748630 CCAATGATTG
**
40748640 CCACCACCTTCTTCTTTG
1 CCACCACCTTCTTCTTCA
*
40748658 CCACCAGCTTCTTCTTCA
1 CCACCACCTTCTTCTTCA
40748676 CCACCA
1 CCACCA
40748682 ATCATATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.48, G:0.05, T:0.31
Consensus pattern (18 bp):
CCACCACCTTCTTCTTCA
Found at i:40749386 original size:3 final size:3
Alignment explanation
Indices: 40749378--40749402 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40749368 NNNNNNNAAC
40749378 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
40749403 CTAACTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40749683 original size:27 final size:27
Alignment explanation
Indices: 40749645--40749735 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
40749635 ACGAGTAGTC
40749645 CCGCCAATCAGTATGGCACCATTGGTG
1 CCGCCAATCAGTATGGCACCATTGGTG
* *
40749672 CCGCCAACCAGTATGGCACCATCGGTG
1 CCGCCAATCAGTATGGCACCATTGGTG
*
40749699 CCGCCAATCAGT-TAGGCACCTTTGGTG
1 CCGCCAATCAGTAT-GGCACCATTGGTG
40749726 CCGCCAATCA
1 CCGCCAATCA
40749736 AAAACCCTCC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 1 0.02
27 57 0.98
ACGTcount: A:0.22, C:0.34, G:0.24, T:0.20
Consensus pattern (27 bp):
CCGCCAATCAGTATGGCACCATTGGTG
Found at i:40750007 original size:16 final size:17
Alignment explanation
Indices: 40749986--40750023 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 17
40749976 TTAAAAAATA
40749986 TTTTTTTCTT-TC-AAC
1 TTTTTTTCTTGTCAAAC
40750001 TTTTTTTCTTGTCAAAC
1 TTTTTTTCTTGTCAAAC
40750018 TTTTTT
1 TTTTTT
40750024 CTAAAGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
16 2 0.10
17 9 0.43
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTTTTCTTGTCAAAC
Found at i:40760156 original size:25 final size:28
Alignment explanation
Indices: 40760128--40760194 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 28
40760118 AAAAAAAAAA
40760128 CAAAATATTATAA-T-TTT-TTATTTAC
1 CAAAATATTATAATTATTTCTTATTTAC
40760153 CAAAATATTATAATTATTTCCATTATTTAC
1 CAAAATATTATAATTATTT-C-TTATTTAC
40760183 CAAAATA-TATAA
1 CAAAATATTATAA
40760195 AAAAAACCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 13 0.35
26 1 0.03
27 3 0.08
29 5 0.14
30 15 0.41
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (28 bp):
CAAAATATTATAATTATTTCTTATTTAC
Found at i:40760357 original size:4 final size:4
Alignment explanation
Indices: 40760348--40760473 Score: 57
Period size: 4 Copynumber: 31.0 Consensus size: 4
40760338 GAAGGAGAGG
* * *
40760348 GAAA GAAA GAAA GAAA GAAA GGAAG GAAG GAGAG GAAA GAAA G-AA -AAA
1 GAAA GAAA GAAA GAAA GAAA -GAAA GAAA GA-AA GAAA GAAA GAAA GAAA
* * * *
40760396 GAAG GAAA GAAAA GGAAA G-GA GAAA -AAA AAAA AAAA GGAAA GAATA
1 GAAA GAAA G-AAA -GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GAA-A
* *
40760442 AAAA G-AG GAAA GGAGAA GAAA -AAA GAAA GAAA
1 GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA
40760474 AGGAAAGGAG
Statistics
Matches: 97, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
3 14 0.14
4 57 0.59
5 23 0.24
6 3 0.03
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:40760434 original size:33 final size:34
Alignment explanation
Indices: 40760374--40760499 Score: 127
Period size: 33 Copynumber: 3.8 Consensus size: 34
40760364 GAAAGGAAGG
* * *
40760374 AAGGAGAGGA-AAGAAAGAAAAAGAAGGAAAGAA
1 AAGGAAAGGAGAAGAAAAAAAAAAAAGGAAAGAA
40760407 AAGGAAAGGAGAA-AAAAAAAAAAAAGGAAAGAA
1 AAGGAAAGGAGAAGAAAAAAAAAAAAGGAAAGAA
* * * *
40760440 TAA-AAAGAGGA-AAGGAGAAGAAAAAA-GAAAGAA
1 -AAGGAA-AGGAGAAGAAAAAAAAAAAAGGAAAGAA
*
40760473 AAGGAAAGGAGAAGAGAAAAAAAAAAG
1 AAGGAAAGGAGAAGAAAAAAAAAAAAG
40760500 ATGAAGAAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
32 6 0.08
33 51 0.69
34 17 0.23
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.01
Consensus pattern (34 bp):
AAGGAAAGGAGAAGAAAAAAAAAAAAGGAAAGAA
Found at i:40760500 original size:33 final size:32
Alignment explanation
Indices: 40760340--40760532 Score: 120
Period size: 33 Copynumber: 5.5 Consensus size: 32
40760330 GAGGGGGAGA
* *
40760340 AGGAGAGGGAAAGAAAGAAAGAAAGAAAGGAAGGAA
1 AGGAGAAGGAAA-AAAAAAAGAAAG-AA--AAGGAA
* *
40760376 GGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAA
1 AG-GA-GAAGGAAA-AAAAA-AA-GAAAGAAAAGGAA
** *
40760413 AGGAGAAAAAAAAAAAAAAGGAAAGAATAA-AAA
1 AGGAGAAGGAAAAAAAAAA-GAAAGAA-AAGGAA
*
40760446 GAGGA-AAGGAGAAGAAAAAAGAAAGAAAAGGAA
1 -AGGAGAAGGA-AAAAAAAAAGAAAGAAAAGGAA
* *
40760479 AGGAGAAGAGAAAAAAAAAAGATGAAGAAGAGGGA
1 AGGAGAAG-GAAAAAAAAAAGA--AAGAAAAGGAA
40760514 AGGAAGGAAGGAAAAAAAA
1 AGG-A-GAAGGAAAAAAAA
40760533 GAAAAAAAAG
Statistics
Matches: 129, Mismatches: 14, Indels: 28
0.75 0.08 0.16
Matches are distributed among these distances:
32 6 0.05
33 37 0.29
34 21 0.16
35 19 0.15
36 13 0.10
37 13 0.10
38 11 0.09
39 4 0.03
40 5 0.04
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (32 bp):
AGGAGAAGGAAAAAAAAAAGAAAGAAAAGGAA
Found at i:40760515 original size:29 final size:29
Alignment explanation
Indices: 40760447--40760500 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
40760437 GAATAAAAAG
*
40760447 AGGAAAGGAG-A-AGAAAAAAGAAAGAAA
1 AGGAAAGGAGAAGAGAAAAAAAAAAGAAA
40760474 AGGAAAGGAGAAGAGAAAAAAAAAAGA
1 AGGAAAGGAGAAGAGAAAAAAAAAAGA
40760501 TGAAGAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.42
28 1 0.04
29 13 0.54
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (29 bp):
AGGAAAGGAGAAGAGAAAAAAAAAAGAAA
Found at i:40760521 original size:66 final size:67
Alignment explanation
Indices: 40760378--40760543 Score: 173
Period size: 67 Copynumber: 2.5 Consensus size: 67
40760368 GGAAGGAAGG
* * *
40760378 AGAGGAAA-GAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAAAAAAAAAAAAAGGAAAGAATA
1 AGAGGAAAGGAAGGAAAAA-AAAGAAAGAAAAGGAAAGGAGAAAAAAAAAAAAAAGGAAAGAAGA
40760442 AAA
65 AAA
* *
40760445 AGAGGAAAGG-A-GAAGAAAAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAA-G-ATGAAG
1 AGAGGAAAGGAAGGAA-AAAAAAGAAAGAAAAGGAAAGGAGAA-AAAAAAAAAAAAGGAAAGAAG
*
40760506 AAGAG
64 AA-AA
* *
40760511 GGAAGG-AAGGAAGGAAAAAAAAGAAAAAAAAGG
1 AG-AGGAAAGGAAGGAAAAAAAAGAAAGAAAAGG
40760544 TAATTTTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
65 6 0.07
66 32 0.38
67 43 0.51
68 4 0.05
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (67 bp):
AGAGGAAAGGAAGGAAAAAAAAGAAAGAAAAGGAAAGGAGAAAAAAAAAAAAAAGGAAAGAAGAA
AA
Found at i:40760567 original size:18 final size:18
Alignment explanation
Indices: 40760544--40760580 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40760534 AAAAAAAAGG
40760544 TAATTTTTTT-TATAAATT
1 TAATTTTTTTGTA-AAATT
40760562 TAATTTTTTTGTAAAATT
1 TAATTTTTTTGTAAAATT
40760580 T
1 T
40760581 GGGTGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TAATTTTTTTGTAAAATT
Found at i:40765984 original size:18 final size:18
Alignment explanation
Indices: 40765958--40765992 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40765948 CCCAATGATC
40765958 GCCACCACCTGCTTCTTG
1 GCCACCACCTGCTTCTTG
* *
40765976 GCCAGCACCTTCTTCTT
1 GCCACCACCTGCTTCTT
40765993 CACCACCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.43, G:0.14, T:0.31
Consensus pattern (18 bp):
GCCACCACCTGCTTCTTG
Found at i:40766739 original size:11 final size:11
Alignment explanation
Indices: 40766719--40766758 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
40766709 TAAAAAATAC
40766719 CTTCTTTTTCT
1 CTTCTTTTTCT
*
40766730 CTTCTCTTTCT
1 CTTCTTTTTCT
40766741 C-TCTTTTTCT
1 CTTCTTTTTCT
40766751 CTTCTTTT
1 CTTCTTTT
40766759 CCATAGCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:40766746 original size:21 final size:20
Alignment explanation
Indices: 40766721--40766759 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
40766711 AAAAATACCT
40766721 TCTTTTTCTCTTCTCTTTCTC
1 TCTTTTTCTCTTCT-TTTCTC
40766742 TCTTTTTCTCTTCTTTTC
1 TCTTTTTCTCTTCTTTTC
40766760 CATAGCACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTTTCTCTTCTTTTCTC
Found at i:40766887 original size:27 final size:27
Alignment explanation
Indices: 40766843--40766916 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
40766833 AATACGAGTA
*
40766843 GTGCCGCCAGTGCCTTTGGCACCATTG
1 GTGCCGCCAATGCCTTTGGCACCATTG
** *
40766870 GTGCCGCCAATGGTTTTGGCACCTTTG
1 GTGCCGCCAATGCCTTTGGCACCATTG
* *
40766897 GTGCTGCCAATGCCATTGGC
1 GTGCCGCCAATGCCTTTGGC
40766917 CTGATTAGGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (27 bp):
GTGCCGCCAATGCCTTTGGCACCATTG
Found at i:40766993 original size:27 final size:29
Alignment explanation
Indices: 40766962--40767030 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 29
40766952 TTATTTTTTG
*
40766962 ATATATTTTGGTAAATAATAAAAATAATT
1 ATATATTTTGGTAAATAAAAAAAATAATT
*
40766991 ATAATATTTTGGTAAATAAAAAAAATTA-T
1 AT-ATATTTTGGTAAATAAAAAAAATAATT
40767020 A-ATATTTTGGT
1 ATATATTTTGGT
40767031 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 10 0.27
29 4 0.11
30 23 0.62
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAATAATT
Found at i:40766998 original size:30 final size:27
Alignment explanation
Indices: 40766964--40767030 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
40766954 ATTTTTTGAT
40766964 ATATTTTGGTAAATAATAAAAATAATTATA
1 ATATTTTGGTAAAT-A-AAAAA-AATTATA
40766994 ATATTTTGGTAAATAAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAAATTATA
40767021 ATATTTTGGT
1 ATATTTTGGT
40767031 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
27 17 0.46
28 5 0.14
29 1 0.03
30 14 0.38
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAATTATA
Found at i:40767715 original size:17 final size:18
Alignment explanation
Indices: 40767683--40767718 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40767673 ATATTATTTT
40767683 TTAATTATTTAAAATATA
1 TTAATTATTTAAAATATA
*
40767701 TTAATT-TTTATAATATA
1 TTAATTATTTAAAATATA
40767718 T
1 T
40767719 GACAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATTTAAAATATA
Found at i:40767988 original size:173 final size:174
Alignment explanation
Indices: 40767688--40768035 Score: 689
Period size: 173 Copynumber: 2.0 Consensus size: 174
40767678 ATTTTTTAAT
40767688 TATTTAAAATATATTAATTTTTATAATATATGACAAATATATTACCATATAAACCCAACCTAATA
1 TATTTAAAATATATTAATTTTTATAATATATGACAAATATATTACCATATAAACCCAACCTAATA
40767753 ACGCAATCACCTATGAACACAAAAATCTAATTAAACAACCCAATTAAAAAATAAAAAAATAAACA
66 ACGCAATCACCTATGAACACAAAAATCTAATTAAACAACCCAATTAAAAAATAAAAAAATAAACA
40767818 ACAAACTTTTAGAAAAACCCAAATAATCAATCTAGCTCATCCTA
131 ACAAACTTTTAGAAAAACCCAAATAATCAATCTAGCTCATCCTA
40767862 TATTTAAAAT-TATTAATTTTTATAATATATGACAAATATATTACCATATAAACCCAACCTAATA
1 TATTTAAAATATATTAATTTTTATAATATATGACAAATATATTACCATATAAACCCAACCTAATA
40767926 ACGCAATCACCTATGAACACAAAAATCTAATTAAACAACCCAATTAAAAAATAAAAAAATAAACA
66 ACGCAATCACCTATGAACACAAAAATCTAATTAAACAACCCAATTAAAAAATAAAAAAATAAACA
40767991 ACAAACTTTTAGAAAAACCCAAATAATCAATCTAGCTCATCCTA
131 ACAAACTTTTAGAAAAACCCAAATAATCAATCTAGCTCATCCTA
40768035 T
1 T
40768036 TTCCCCCAAA
Statistics
Matches: 174, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 164 0.94
174 10 0.06
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.27
Consensus pattern (174 bp):
TATTTAAAATATATTAATTTTTATAATATATGACAAATATATTACCATATAAACCCAACCTAATA
ACGCAATCACCTATGAACACAAAAATCTAATTAAACAACCCAATTAAAAAATAAAAAAATAAACA
ACAAACTTTTAGAAAAACCCAAATAATCAATCTAGCTCATCCTA
Found at i:40784673 original size:13 final size:13
Alignment explanation
Indices: 40784650--40784701 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
40784640 AGCACTCAAA
40784650 TTTTACAAAAGCAC
1 TTTT-CAAAAGCAC
* *
40784664 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
**
40784677 TTTTCAAAAATAC
1 TTTTCAAAAGCAC
40784690 TTTTCAAAAGCA
1 TTTTCAAAAGCA
40784702 ATAAAGAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 29 0.91
14 3 0.09
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:40786501 original size:2 final size:2
Alignment explanation
Indices: 40786494--40786519 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40786484 TCTTCCCTTC
40786494 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
40786520 GCTCAACACC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:40793925 original size:74 final size:75
Alignment explanation
Indices: 40793836--40793984 Score: 273
Period size: 74 Copynumber: 2.0 Consensus size: 75
40793826 ATTTTTTTAT
*
40793836 GAAATTATTTAATATATTTTATAATTATATTTTTTTAGAAAAACAATCTATTTGTATAAAAACTG
1 GAAATTATTTAATATATTTTATAATTATATTTTTTTAGAAAAACAATCTATTTGTAAAAAAACTG
*
40793901 ACTCATATCC
66 AATCATATCC
40793911 GAAATTATTT-ATATATTTTATAATTATATTTTTTTAGAAAAACAATCTATTTGTAAAAAAACTG
1 GAAATTATTTAATATATTTTATAATTATATTTTTTTAGAAAAACAATCTATTTGTAAAAAAACTG
40793975 AATCATATCC
66 AATCATATCC
40793985 AAGAATTTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 62 0.86
75 10 0.14
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (75 bp):
GAAATTATTTAATATATTTTATAATTATATTTTTTTAGAAAAACAATCTATTTGTAAAAAAACTG
AATCATATCC
Found at i:40794869 original size:18 final size:18
Alignment explanation
Indices: 40794846--40794888 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40794836 GTTCAATGTG
40794846 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
40794864 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
40794882 TAATTAA
1 TAATTAA
40794889 AAACCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:40796923 original size:8 final size:8
Alignment explanation
Indices: 40796910--40796974 Score: 76
Period size: 8 Copynumber: 7.9 Consensus size: 8
40796900 ATCACAATTT
40796910 AATAAACA
1 AATAAACA
40796918 AATAAACGA
1 AATAAAC-A
*
40796927 AATGAAATA
1 AAT-AAACA
* *
40796936 ATTGAACA
1 AATAAACA
40796944 AATAAACA
1 AATAAACA
*
40796952 AACAAACA
1 AATAAACA
40796960 AATAAACA
1 AATAAACA
40796968 AATAAAC
1 AATAAAC
40796975 CAACAACACC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
8 37 0.79
9 7 0.15
10 3 0.06
ACGTcount: A:0.69, C:0.12, G:0.05, T:0.14
Consensus pattern (8 bp):
AATAAACA
Found at i:40796955 original size:12 final size:12
Alignment explanation
Indices: 40796940--40796980 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
40796930 GAAATAATTG
40796940 AACAAATAAACA
1 AACAAATAAACA
* *
40796952 AACAAACAAATA
1 AACAAATAAACA
*
40796964 AACAAATAAACC
1 AACAAATAAACA
40796976 AACAA
1 AACAA
40796981 CACCACATGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.73, C:0.20, G:0.00, T:0.07
Consensus pattern (12 bp):
AACAAATAAACA
Found at i:40797184 original size:13 final size:13
Alignment explanation
Indices: 40797166--40797195 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40797156 TGACATAGTT
40797166 TAAAATAAATAAA
1 TAAAATAAATAAA
40797179 TAAAATAAATAAA
1 TAAAATAAATAAA
40797192 -AAAA
1 TAAAA
40797196 CACAGAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:40800168 original size:104 final size:104
Alignment explanation
Indices: 40800034--40800403 Score: 490
Period size: 104 Copynumber: 3.6 Consensus size: 104
40800024 AAAGAACTTA
* * *
40800034 GTTGCGAGCTTAACTCAGCTAACTTTTAATCATCAGCTGGGAATGTAGGTCCGCGAGCTGTTTCG
1 GTTGCGAGCTTAACTCAGCTAACATTTAATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
* *
40800099 GAGTTGCGAGCTTAACTCGACTAACCCAAATAACTGGAG
66 GAGTTGCGAGCTTAACTCGGCTAACTCAAATAACTGGAG
* * * * *
40800138 GTTGCGAGCTTAACTCAGCTAACCTTTAATCATTAGTTGGGAACGTAGGTCAGCAAGTTGTTTCG
1 GTTGCGAGCTTAACTCAGCTAACATTTAATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
* *
40800203 GAGTTACGAGCTTAACTCGGCTAACTCAAATAATTGGA-
66 GAGTTGCGAGCTTAACTCGGCTAACTCAAATAACTGGAG
* * * * * ** * **
40800241 GTTGTGAGCTTAACTCATCCAACATTTAATCATCAATTGGGAACATAGGTCCATGAGCTATTTTA
1 GTTGCGAGCTTAACTCAGCTAACATTTAATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
*
40800306 GAGTTGTGAGCTTAACTCGGCTAACTCAAATAACTGGAG
66 GAGTTGCGAGCTTAACTCGGCTAACTCAAATAACTGGAG
* * * *
40800345 GTTTCGAGCTTAACTCAGCTAACATTTAATCATTAGTTGGGAATGTAAGTCCGCGAGCT
1 GTTGCGAGCTTAACTCAGCTAACATTTAATCATCAGTTGGGAACGTAGGTCCGCGAGCT
40800404 ATTTTAAAGG
Statistics
Matches: 225, Mismatches: 40, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
103 85 0.38
104 140 0.62
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (104 bp):
GTTGCGAGCTTAACTCAGCTAACATTTAATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
GAGTTGCGAGCTTAACTCGGCTAACTCAAATAACTGGAG
Found at i:40800495 original size:69 final size:69
Alignment explanation
Indices: 40800382--40800580 Score: 204
Period size: 69 Copynumber: 2.9 Consensus size: 69
40800372 AATCATTAGT
* * **
40800382 TGGGAATGTAAGTCCGCGAGCTATTTTAAAGGCTACGATATTAAATCAGCGAGCCTTTATAATAT
1 TGGGAATGTAGGTCCGCGAGCTATTTGAAAGGCTACGATATTAAATCAAAGAGCCTTTATAATAT
*
40800447 CAGC
66 CAAC
* * ** * *
40800451 TGGGAATGTAGGTCCGTGAGCTGTTTGAGGGGCTGCGATCTTAAATCAAAGAGCCTTTATAATAT
1 TGGGAATGTAGGTCCGCGAGCTATTTGAAAGGCTACGATATTAAATCAAAGAGCCTTTATAATAT
40800516 CAAC
66 CAAC
* * * * * * *
40800520 TAGGAACGTAGGTCCGCAAGCTGCTTTTG--AGGTTACGATTTTAAATCAATGAGCCTTTATA
1 TGGGAATGTAGGTCCGCGAGCT--ATTTGAAAGGCTACGATATTAAATCAAAGAGCCTTTATA
40800581 TAGAAGGTCG
Statistics
Matches: 107, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
69 103 0.96
71 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (69 bp):
TGGGAATGTAGGTCCGCGAGCTATTTGAAAGGCTACGATATTAAATCAAAGAGCCTTTATAATAT
CAAC
Found at i:40800595 original size:16 final size:16
Alignment explanation
Indices: 40800576--40800607 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40800566 CAATGAGCCT
40800576 TTATATAGAAGGTCGC
1 TTATATAGAAGGTCGC
40800592 TTATATAGAAGGTCGC
1 TTATATAGAAGGTCGC
40800608 GGTATGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
TTATATAGAAGGTCGC
Found at i:40801465 original size:15 final size:15
Alignment explanation
Indices: 40801445--40801474 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40801435 CAAAATTTTG
40801445 ACAAGAACATAACAA
1 ACAAGAACATAACAA
40801460 ACAAGAACATAACAA
1 ACAAGAACATAACAA
40801475 TGTGATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (15 bp):
ACAAGAACATAACAA
Found at i:40802847 original size:86 final size:85
Alignment explanation
Indices: 40802692--40802859 Score: 284
Period size: 86 Copynumber: 2.0 Consensus size: 85
40802682 GGAATAAGAC
* *
40802692 ATTGTGCAAATCCAGTCCTTGAGAATTTGACCCTCTTCTCTTTTACTATTCTTTTTCATTATTTA
1 ATTGTGCAAATCCAGTCCCTGAGAATTTGACCCTCTTCCCTTTTACTATTCTTTTTCATTATTTA
40802757 TTAGGGAT-ATGATATTTGAT
66 TTAGGGATAAT-ATATTTGAT
*
40802777 ATTGTGCAAATCCAGTCCCTGAGAATTTGACCTTACTTCCCTTTTACTATTCTTTTTCATTATTT
1 ATTGTGCAAATCCAGTCCCTGAGAATTTGACCCT-CTTCCCTTTTACTATTCTTTTTCATTATTT
40802842 ATTAGGGATAATATATTT
65 ATTAGGGATAATATATTT
40802860 TTGCTGCTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
85 32 0.41
86 44 0.56
87 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.46
Consensus pattern (85 bp):
ATTGTGCAAATCCAGTCCCTGAGAATTTGACCCTCTTCCCTTTTACTATTCTTTTTCATTATTTA
TTAGGGATAATATATTTGAT
Found at i:40806340 original size:34 final size:35
Alignment explanation
Indices: 40806284--40806350 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
40806274 CAAACACCAA
* *
40806284 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
*
40806319 AAAACATTTTCCA-AAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAA
40806351 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
Found at i:40821242 original size:16 final size:16
Alignment explanation
Indices: 40821217--40821259 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
40821207 GATTGTAGCT
40821217 CTATTCAATTACAGCC
1 CTATTCAATTACAGCC
*
40821233 CTATTTAATTACAGCC
1 CTATTCAATTACAGCC
* *
40821249 TTATTCCATTA
1 CTATTCAATTA
40821260 GAGTGAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.40
Consensus pattern (16 bp):
CTATTCAATTACAGCC
Found at i:40822740 original size:21 final size:19
Alignment explanation
Indices: 40822714--40822753 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
40822704 TGCAATTTAA
40822714 TAATTTTCTTTTATGTTCTTT
1 TAATTTTCTTTT-T-TTCTTT
40822735 TAATTTTCTTTTTTTCTTT
1 TAATTTTCTTTTTTTCTTT
40822754 ATTTTCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (19 bp):
TAATTTTCTTTTTTTCTTT
Found at i:40822745 original size:11 final size:11
Alignment explanation
Indices: 40822714--40822746 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40822704 TGCAATTTAA
40822714 TAATTTTCTTT
1 TAATTTTCTTT
*
40822725 T-ATGTTCTTT
1 TAATTTTCTTT
40822735 TAATTTTCTTT
1 TAATTTTCTTT
40822746 T
1 T
40822747 TTTCTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.73
Consensus pattern (11 bp):
TAATTTTCTTT
Found at i:40822858 original size:32 final size:32
Alignment explanation
Indices: 40822797--40822861 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
40822787 TCCTCCCTTC
***
40822797 TCCATTTCTTTTAGTGTAATTTTTCTATGTTT
1 TCCATTTCTTTTAACATAATTTTTCTATGTTT
40822829 TCCATTTCTTTTAACATAACTTTTT-TATGTTT
1 TCCATTTCTTTTAACATAA-TTTTTCTATGTTT
40822861 T
1 T
40822862 TGAAACAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.18, C:0.14, G:0.06, T:0.62
Consensus pattern (32 bp):
TCCATTTCTTTTAACATAATTTTTCTATGTTT
Found at i:40827436 original size:16 final size:17
Alignment explanation
Indices: 40827405--40827438 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40827395 AATTTAACTT
40827405 TAATTAAATATTTAAAA
1 TAATTAAATATTTAAAA
*
40827422 TAATT-AATTTTTAAAA
1 TAATTAAATATTTAAAA
40827438 T
1 T
40827439 TATAAACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTAAATATTTAAAA
Done.