Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 176 of 222
Found at i:56553159 original size:24 final size:24
Alignment explanation
Indices: 56553094--56553147 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
56553084 TATTTCTAGA
* * *
56553094 ATATTTAGTATTTATGAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
56553118 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
56553142 ATATTT
1 ATATTT
56553148 GACTTTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:56555012 original size:20 final size:20
Alignment explanation
Indices: 56554987--56555024 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56554977 TTATAATTAA
56554987 AAGTTAAAACC-CTAAAATGT
1 AAGTT-AAACCTCTAAAATGT
56555007 AAGTTAAACCTCTAAAAT
1 AAGTTAAACCTCTAAAAT
56555025 ATAAAACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (20 bp):
AAGTTAAACCTCTAAAATGT
Found at i:56555060 original size:14 final size:13
Alignment explanation
Indices: 56555010--56555092 Score: 53
Period size: 14 Copynumber: 5.9 Consensus size: 13
56555000 AAAATGTAAG
*
56555010 TTAAACCTCTAAAA
1 TTAAACC-CTAAAC
*
56555024 TATAAAACCTAAAC
1 T-TAAACCCTAAAC
56555038 -TAGAGACCCTAAATC
1 TTA-A-ACCCTAAA-C
56555053 TTAAACCC-AAGAC
1 TTAAACCCTAA-AC
56555066 TCTAAACCCTTAAAC
1 T-TAAACCC-TAAAC
*
56555081 TCAAACCCTAAA
1 TTAAACCCTAAA
56555093 TATGATAGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
12 2 0.04
13 9 0.16
14 31 0.55
15 10 0.18
16 4 0.07
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.22
Consensus pattern (13 bp):
TTAAACCCTAAAC
Found at i:56555065 original size:21 final size:21
Alignment explanation
Indices: 56555041--56555093 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
56555031 CCTAAACTAG
56555041 AGACCCTAAATCTTAAACCCA
1 AGACCCTAAATCTTAAACCCA
* * *
56555062 AGACTCTAAACCCTTAAACTCA
1 AGACCCTAAA-TCTTAAACCCA
56555084 A-ACCCTAAAT
1 AGACCCTAAAT
56555094 ATGATAGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.43, C:0.32, G:0.04, T:0.21
Consensus pattern (21 bp):
AGACCCTAAATCTTAAACCCA
Found at i:56557381 original size:21 final size:20
Alignment explanation
Indices: 56557355--56557396 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
56557345 GCTGCAATTG
56557355 ATTTATTATATAAATTTTTTT
1 ATTTATTAT-TAAATTTTTTT
* *
56557376 ATTTATTGTTACATTTTTTT
1 ATTTATTATTAAATTTTTTT
56557396 A
1 A
56557397 ACTTTTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTATTATTAAATTTTTTT
Found at i:56558148 original size:26 final size:27
Alignment explanation
Indices: 56558100--56558152 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
56558090 ATTTAATATT
*
56558100 TTAATTTAATACTTAAAAAATAATAAA
1 TTAATATAATACTTAAAAAATAATAAA
*
56558127 TTAATATAATA-TTAAATAATAATAAA
1 TTAATATAATACTTAAAAAATAATAAA
56558153 AGCAAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
TTAATATAATACTTAAAAAATAATAAA
Found at i:56569403 original size:25 final size:25
Alignment explanation
Indices: 56569375--56569568 Score: 124
Period size: 25 Copynumber: 7.8 Consensus size: 25
56569365 TAGCTCGCAA
* * *
56569375 GAGCGTCCCGTTATTTAGCTCTTAT
1 GAGCTTCCCGTTATTTGGCTCTCAT
* * *
56569400 GAGCATCCCATTATATGGCTCTCAT
1 GAGCTTCCCGTTATTTGGCTCTCAT
* *
56569425 GAGCTTCTCGATATTTGGCTCTCAT
1 GAGCTTCCCGTTATTTGGCTCTCAT
* **
56569450 GAGCTTCCCGATTA-ATGGCTCTTTT
1 GAGCTTCCCG-TTATTTGGCTCTCAT
* * *
56569475 AAGCTTCCTGTT-TATGGCTCGT-AT
1 GAGCTTCCCGTTATTTGGCTC-TCAT
* * * *
56569499 GAGCTTTCCGATATTTGGCTCGCAA
1 GAGCTTCCCGTTATTTGGCTCTCAT
* *** *
56569524 GAACTTCCCGTTATACAGCTCACAT
1 GAGCTTCCCGTTATTTGGCTCTCAT
* *
56569549 GAGCTTCCCTTTATATGGCT
1 GAGCTTCCCGTTATTTGGCT
56569569 TGGAAGAGCT
Statistics
Matches: 127, Mismatches: 37, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
24 18 0.14
25 107 0.84
26 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (25 bp):
GAGCTTCCCGTTATTTGGCTCTCAT
Found at i:56571002 original size:17 final size:18
Alignment explanation
Indices: 56570876--56571032 Score: 85
Period size: 18 Copynumber: 8.8 Consensus size: 18
56570866 AACGCGAGAA
*
56570876 TTTTGAAACAC-AATAATT
1 TTTTAAAACACGAA-AATT
* *
56570894 TTTTGAGAACACGGAAA-T
1 TTTT-AAAACACGAAAATT
* * *
56570912 TTTTGAAATACGAGAA--
1 TTTTAAAACACGAAAATT
*
56570928 TTTTAGAAACAC-AAAAAT
1 TTTTA-AAACACGAAAATT
*
56570946 TTCTAAAACACGAAAATT
1 TTTTAAAACACGAAAATT
* * *
56570964 TTTGAAAACACGAGATTT
1 TTTTAAAACACGAAAATT
*
56570982 TTTTTAAACAC-AAAATTT
1 TTTTAAAACACGAAAA-TT
*
56571000 TTTTAAAAAACACGGAAA-T
1 TTTT--AAAACACGAAAATT
*
56571019 TTTTGAAACACGAA
1 TTTTAAAACACGAA
56571033 GTTTTTAAAA
Statistics
Matches: 104, Mismatches: 25, Indels: 21
0.69 0.17 0.14
Matches are distributed among these distances:
16 7 0.07
17 28 0.27
18 47 0.45
19 12 0.12
20 7 0.07
21 3 0.03
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (18 bp):
TTTTAAAACACGAAAATT
Found at i:56571038 original size:17 final size:17
Alignment explanation
Indices: 56570876--56571032 Score: 111
Period size: 17 Copynumber: 8.8 Consensus size: 17
56570866 AACGCGAGAA
56570876 TTTTGAAACAC-AATAATT
1 TTTTGAAACACGAA-AA-T
*
56570894 TTTTGAGAACACGGAAAT
1 TTTTGA-AACACGAAAAT
* *
56570912 TTTTGAAATACGAGAAT
1 TTTTGAAACACGAAAAT
* *
56570929 TTTAGAAACACAAAAAT
1 TTTTGAAACACGAAAAT
* *
56570946 TTCTAAAACACGAAAAT
1 TTTTGAAACACGAAAAT
**
56570963 TTTTGAAAACACGAGATTT
1 TTTTG-AAACACGA-AAAT
*
56570982 TTTTTAAACAC-AAAATTT
1 TTTTGAAACACGAAAA--T
* *
56571000 TTTTAAAAAACACGGAAAT
1 TTTT--GAAACACGAAAAT
56571019 TTTTGAAACACGAA
1 TTTTGAAACACGAA
56571033 GTTTTTAAAA
Statistics
Matches: 107, Mismatches: 23, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
16 1 0.01
17 46 0.43
18 32 0.30
19 18 0.17
20 7 0.07
21 3 0.03
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (17 bp):
TTTTGAAACACGAAAAT
Found at i:56571848 original size:6 final size:6
Alignment explanation
Indices: 56571839--56571889 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
56571829 TTTTTCTCTC
* ** *
56571839 CTTTTT CTTTTT CCTTTTT CTTCTT C-TTTT CTTTAA CTTTCT CTTTTT
1 CTTTTT CTTTTT -CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
56571887 CTT
1 CTT
56571890 CCTTTCAAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
5 4 0.11
6 26 0.72
7 6 0.17
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:56571849 original size:24 final size:24
Alignment explanation
Indices: 56571822--56571872 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
56571812 TATTTTTTAT
*
56571822 TTTTTTATTTTTCTCTCCT-TTTTC
1 TTTTTCATTTTTCT-TCCTCTTTTC
* *
56571846 TTTTTCCTTTTTCTTCTTCTTTTC
1 TTTTTCATTTTTCTTCCTCTTTTC
56571870 TTT
1 TTT
56571873 AACTTTCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTCATTTTTCTTCCTCTTTTC
Found at i:56572019 original size:19 final size:18
Alignment explanation
Indices: 56571993--56572039 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
56571983 CTTCCTTCCT
56571993 CCTTT-TCTTC-TTTTT-
1 CCTTTCTCTTCTTTTTTC
*
56572008 CTTTTCTCTTCTTTTTTC
1 CCTTTCTCTTCTTTTTTC
*
56572026 CCTTTCTCTCCTTT
1 CCTTTCTCTTCTTT
56572040 CCTTTCCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 5 0.19
18 12 0.46
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
CCTTTCTCTTCTTTTTTC
Found at i:56572031 original size:18 final size:17
Alignment explanation
Indices: 56571992--56572065 Score: 65
Period size: 15 Copynumber: 4.8 Consensus size: 17
56571982 TCTTCCTTCC
56571992 TCCTTT-TCTTC-TTTT
1 TCCTTTCTCTTCTTTTT
*
56572007 TCTTTTCTCTTCTTTTT
1 TCCTTTCTCTTCTTTTT
*
56572024 TCCCTTTCTC-TC--CTT
1 T-CCTTTCTCTTCTTTTT
56572039 TCCTTTC-C-TCTTTTT
1 TCCTTTCTCTTCTTTTT
56572054 T-CTTTCTCTTCT
1 TCCTTTCTCTTCT
56572066 ATTTCGGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
13 3 0.06
14 11 0.23
15 12 0.25
16 8 0.17
17 7 0.15
18 7 0.15
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TCCTTTCTCTTCTTTTT
Found at i:56572640 original size:30 final size:30
Alignment explanation
Indices: 56572577--56572738 Score: 96
Period size: 30 Copynumber: 5.4 Consensus size: 30
56572567 TTCTGGGGAA
* *** * *
56572577 AAAATGTAATTTTAAGAAAAACATGGGGCC
1 AAAATGTAATTTTGAGAAAGTTAAGGGGTC
*
56572607 AAAATGTAATTTCT-AGAAATTTAAGGGGTC
1 AAAATGTAATTT-TGAGAAAGTTAAGGGGTC
* *
56572637 AAAATGAAATTTTGAGAAAGTTAAAGGGTC
1 AAAATGTAATTTTGAGAAAGTTAAGGGGTC
* * * *
56572667 AAAGTGTAAATAT-AGGAAAGTTTA-GGGTCC
1 AAAATGTAATTTTGA-GAAAGTTAAGGGGT-C
* ** * *
56572697 AAAATGCAATTTAAAGAAAATTTAGGGGTC
1 AAAATGTAATTTTGAGAAAGTTAAGGGGTC
* *
56572727 TAAATGTGATTT
1 AAAATGTAATTT
56572739 ATATTTTTTT
Statistics
Matches: 104, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
29 6 0.06
30 92 0.88
31 6 0.06
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGTAATTTTGAGAAAGTTAAGGGGTC
Found at i:56572952 original size:5 final size:5
Alignment explanation
Indices: 56572942--56572967 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56572932 AAATATATAT
56572942 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
56572968 ACACGAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:56579476 original size:29 final size:29
Alignment explanation
Indices: 56579444--56579510 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
56579434 AACCAAAAAA
56579444 GGCCGTTTTTTTCAA-AATTTACCGAAATG
1 GGCCGTTTTTTT-AATAATTTACCGAAATG
* * *
56579473 GGCCGGTTTTTTAATTATTTACCGGAATG
1 GGCCGTTTTTTTAATAATTTACCGAAATG
*
56579502 GGCCATTTT
1 GGCCGTTTT
56579511 CCGCGAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.06
29 30 0.94
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (29 bp):
GGCCGTTTTTTTAATAATTTACCGAAATG
Found at i:56581785 original size:24 final size:24
Alignment explanation
Indices: 56581747--56581795 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
56581737 TGCCTTTGTA
**
56581747 AGTAGTTGTAGATATGGGAATTCT
1 AGTAGTTGTAGATATGAAAATTCT
56581771 AGTAGTTGT-GTATATGAAAATTCT
1 AGTAGTTGTAG-ATATGAAAATTCT
56581795 A
1 A
56581796 CTGTTCAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (24 bp):
AGTAGTTGTAGATATGAAAATTCT
Found at i:56585112 original size:58 final size:58
Alignment explanation
Indices: 56585022--56585138 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
56585012 TATAAAACAC
*
56585022 TGTTATGAAGTTTATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
1 TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
56585080 TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
1 TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
56585138 T
1 T
56585139 TAATGAATGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (58 bp):
TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
Found at i:56595000 original size:85 final size:79
Alignment explanation
Indices: 56594911--56595149 Score: 297
Period size: 85 Copynumber: 3.0 Consensus size: 79
56594901 GCGCTTACAG
* * *
56594911 AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTAGAAAAAAACGCCGCTAAATATCATG
1 AAAAAAC-CCGCTAAAGATCATGTTCTTTAGCGGCGTTAAGAAAAAAACGCCGCTAAAGATCATG
56594976 TTCTTTAGCGGCGCTTGT
65 TTCTTTAGCGGCGC---T
* *
56594994 GCAAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACACCGCTAAAGATCA
1 --AAAAAAC-CCGCTAAAGATCATGTTCTTTAGCGGCGTTAAGAAAAAAACGCCGCTAAAGATCA
56595059 TGTTCTTTAGCGGCGCT
63 TGTTCTTTAGCGGCGCT
* **
56595076 AAGAAAA----CTAAAGATCGTGTTCTTTAGCGGCGCTTGGGAAAAAAACGCCGCTAAAGATCAT
1 AA-AAAACCCGCTAAAGATCATGTTCTTTAGCGGCG-TTAAGAAAAAAACGCCGCTAAAGATCAT
56595137 GTTCTTTAGCGGC
64 GTTCTTTAGCGGC
56595150 ACTTTATTTA
Statistics
Matches: 141, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
76 24 0.17
77 37 0.26
80 2 0.01
81 4 0.03
82 1 0.01
85 73 0.52
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (79 bp):
AAAAAACCCGCTAAAGATCATGTTCTTTAGCGGCGTTAAGAAAAAAACGCCGCTAAAGATCATGT
TCTTTAGCGGCGCT
Found at i:56595017 original size:43 final size:42
Alignment explanation
Indices: 56594911--56595154 Score: 290
Period size: 42 Copynumber: 6.0 Consensus size: 42
56594901 GCGCTTACAG
* *
56594911 AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCG-TTTAGA
1 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTT-GA
* * *
56594953 AAAAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTGTGC
1 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTT-TGA
**
56594996 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGA
1 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGA
56595038 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGC--T--
1 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGA
* * *
56595076 AAGAAA-A---CTAAAGATCGTGTTCTTTAGCGGCGCTTGGGA
1 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTT-TGA
* *
56595115 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTT
1 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTT
56595155 ATTTACAAAC
Statistics
Matches: 174, Mismatches: 17, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
34 25 0.14
37 1 0.01
38 5 0.03
39 5 0.03
42 72 0.41
43 65 0.37
44 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (42 bp):
AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGA
Found at i:56595100 original size:76 final size:77
Alignment explanation
Indices: 56595007--56595149 Score: 243
Period size: 77 Copynumber: 1.9 Consensus size: 77
56594997 AAAAACACCG
56595007 CTAAAGATCATGTTCTTTAGCGGCGC-TAAGAAAAAAACACCGCTAAAGATCATGTTCTTTAGCG
1 CTAAAGATCATGTTCTTTAGCGGCGCTTAAGAAAAAAACACCGCTAAAGATCATGTTCTTTAGCG
56595071 GCGCTAAGAAAA
66 GCGCTAAGAAAA
* ** *
56595083 CTAAAGATCGTGTTCTTTAGCGGCGCTTGGGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCG
1 CTAAAGATCATGTTCTTTAGCGGCGCTTAAGAAAAAAACACCGCTAAAGATCATGTTCTTTAGCG
56595148 GC
66 GC
56595150 ACTTTATTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
76 25 0.40
77 37 0.60
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (77 bp):
CTAAAGATCATGTTCTTTAGCGGCGCTTAAGAAAAAAACACCGCTAAAGATCATGTTCTTTAGCG
GCGCTAAGAAAA
Found at i:56595187 original size:43 final size:42
Alignment explanation
Indices: 56595118--56595200 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
56595108 CTTGGGAAAA
*
56595118 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTTATTTAC
1 AAACGCCGCTAAAGATCATGTGCTTTAGCGGCAC-TTATTTAC
*
56595161 AAACGCCGCTAAA-AGT-AGTGTGCTTTAGCGGCGCTTATTT
1 AAACGCCGCTAAAGA-TCA-TGTGCTTTAGCGGCACTTATTT
56595201 CAGAAACACC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
42 8 0.22
43 28 0.78
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGTGCTTTAGCGGCACTTATTTAC
Found at i:56595730 original size:21 final size:21
Alignment explanation
Indices: 56595644--56595722 Score: 104
Period size: 21 Copynumber: 3.8 Consensus size: 21
56595634 GCTTCTCTCA
56595644 CTGCTTCTCTCGCTGCGGCAT
1 CTGCTTCTCTCGCTGCGGCAT
*
56595665 CTGCTTCTCTCACTGCGGCAT
1 CTGCTTCTCTCGCTGCGGCAT
* ** *
56595686 CTGCTTCTCTTGCTGTAGCCT
1 CTGCTTCTCTCGCTGCGGCAT
*
56595707 CTGCTTCCCTCGCTGC
1 CTGCTTCTCTCGCTGC
56595723 CGCCTCTGTT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.05, C:0.39, G:0.20, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCGGCAT
Found at i:56601254 original size:9 final size:9
Alignment explanation
Indices: 56601240--56601574 Score: 111
Period size: 9 Copynumber: 37.8 Consensus size: 9
56601230 TTTTTATGTA
56601240 TTATGTAAG
1 TTATGTAAG
*
56601249 TTATGTAAC
1 TTATGTAAG
*
56601258 TTACGTAAG
1 TTATGTAAG
** *
56601267 TTA-CCAAA
1 TTATGTAAG
*
56601275 TTAATGTATG
1 TT-ATGTAAG
56601285 TTATGTAAG
1 TTATGTAAG
56601294 -T-TGTAAG
1 TTATGTAAG
*
56601301 TTAT-TATG
1 TTATGTAAG
56601309 TATTATGTAAG
1 --TTATGTAAG
56601320 TTATGT-A-
1 TTATGTAAG
*
56601327 TTATGTAGG
1 TTATGTAAG
56601336 TTATGTAAG
1 TTATGTAAG
*
56601345 TTGTGTAAG
1 TTATGTAAG
* *
56601354 ATATTTAAG
1 TTATGTAAG
56601363 TTATGTAAG
1 TTATGTAAG
* *
56601372 TTTTG-CA-
1 TTATGTAAG
56601379 TTATGTAAG
1 TTATGTAAG
*
56601388 TTATGTATG
1 TTATGTAAG
*
56601397 CTATGT-A-
1 TTATGTAAG
*
56601404 TAATGTAAG
1 TTATGTAAG
* *
56601413 TTGT-TATG
1 TTATGTAAG
56601421 TATAATGTAAG
1 T-T-ATGTAAG
56601432 TTAATATGTAAG
1 -T--TATGTAAG
*
56601444 TAATGT-A-
1 TTATGTAAG
56601451 TTATGTAAG
1 TTATGTAAG
* *
56601460 TTTATATAAAAATT
1 -TTATGT---AA-G
*
56601474 TTATATAAG
1 TTATGTAAG
56601483 TTATGT-A-
1 TTATGTAAG
56601490 TTATGTAAGG
1 TTATGTAA-G
* *
56601500 TAACATATAAG
1 T--TATGTAAG
56601511 TTTATGTAAG
1 -TTATGTAAG
56601521 TTATG--A-
1 TTATGTAAG
56601527 --ATGTAAG
1 TTATGTAAG
56601534 TTATGT-A-
1 TTATGTAAG
56601541 TTATGTAAG
1 TTATGTAAG
* *
56601550 TTATTTAAA
1 TTATGTAAG
*
56601559 TTATTTAAG
1 TTATGTAAG
*
56601568 TTGTGTA
1 TTATGTA
56601575 TTATATAACT
Statistics
Matches: 238, Mismatches: 50, Indels: 76
0.65 0.14 0.21
Matches are distributed among these distances:
4 3 0.01
6 1 0.00
7 38 0.16
8 23 0.10
9 119 0.50
10 22 0.09
11 8 0.03
12 14 0.06
13 10 0.04
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:56601254 original size:16 final size:16
Alignment explanation
Indices: 56601233--56601578 Score: 128
Period size: 16 Copynumber: 20.7 Consensus size: 16
56601223 TGATATATTT
56601233 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
*
56601249 TTATGTAACTTACGTAAG
1 TTATGT-A-TTATGTAAG
*** *
56601267 TTACCAAATTAATGTATG
1 TTA-TGTATT-ATGTAAG
*
56601285 TTATGTAAGT-TGTAAG
1 TTATGT-ATTATGTAAG
56601301 TTATTATGTATTATGTAAG
1 ---TTATGTATTATGTAAG
*
56601320 TTATGTATTATGTAGG
1 TTATGTATTATGTAAG
*
56601336 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
* *
56601354 ATATTTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
* *
56601372 TTTTGCATTATGTAAG
1 TTATGTATTATGTAAG
56601388 TTATGTATGCTATGT-A-
1 TTATGTAT--TATGTAAG
* *
56601404 TAATGTA--A-GT-TG
1 TTATGTATTATGTAAG
*
56601416 TTATGTATAATGTAAG
1 TTATGTATTATGTAAG
56601432 TTA---A-TATGTAAG
1 TTATGTATTATGTAAG
*
56601444 TAATGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
56601460 TTTATATAAAAATTTTATATAAG
1 -TTATGT----A--TTATGTAAG
56601483 TTATGTATTATGTAAGG
1 TTATGTATTATGTAA-G
56601500 TAACATATAAGT-TTATGTAAG
1 T----TAT--GTATTATGTAAG
56601521 TTATG-A--ATGTAAG
1 TTATGTATTATGTAAG
56601534 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
56601550 TTATTTAAATTATTTAAG
1 TTATGT--ATTATGTAAG
*
56601568 TTGTGTATTAT
1 TTATGTATTAT
56601579 ATAACTCATG
Statistics
Matches: 249, Mismatches: 39, Indels: 84
0.67 0.10 0.23
Matches are distributed among these distances:
11 2 0.01
12 16 0.06
13 13 0.05
14 2 0.01
15 4 0.02
16 89 0.36
17 15 0.06
18 67 0.27
19 12 0.05
21 6 0.02
22 13 0.05
23 10 0.04
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:56601309 original size:19 final size:19
Alignment explanation
Indices: 56601285--56601323 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
56601275 TTAATGTATG
56601285 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
56601304 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
56601323 T
1 T
56601324 GTATTATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:56601345 original size:25 final size:24
Alignment explanation
Indices: 56601305--56601410 Score: 88
Period size: 25 Copynumber: 4.2 Consensus size: 24
56601295 TGTAAGTTAT
56601305 TATGTA-TTATGTAAGTTATGTAT
1 TATGTAGTTATGTAAGTTATGTAT
* *
56601328 TATGTAGGTTATGTAAGTTGTGTAAGA
1 TATGTA-GTTATGTAAGTTATGT-A-T
* * *
56601355 TATTTAAGTTATGTAAGTTTTGCAT
1 TATGT-AGTTATGTAAGTTATGTAT
* *
56601380 TATGTAAGTTATGTATGCTATGTAT
1 TATGT-AGTTATGTAAGTTATGTAT
*
56601405 AATGTA
1 TATGTA
56601411 AGTTGTTATG
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
23 6 0.09
24 1 0.02
25 38 0.58
26 2 0.03
27 18 0.27
28 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (24 bp):
TATGTAGTTATGTAAGTTATGTAT
Found at i:56601384 original size:52 final size:50
Alignment explanation
Indices: 56601278--56601394 Score: 137
Period size: 52 Copynumber: 2.3 Consensus size: 50
56601268 TACCAAATTA
* * * *
56601278 ATGTATGTTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTATGTATT
1 ATGTAAGTTATGTAAGTTGTAAGATATTAAG-ATTATGTAAGTTATGCATT
* *
56601329 ATGTAGGTTATGTAAGTTGTGTAAGATATTTAAG-TTATGTAAGTTTTGCATT
1 ATGTAAGTTATGTAAG-T-TGTAAGATA-TTAAGATTATGTAAGTTATGCATT
56601381 ATGTAAGTTATGTA
1 ATGTAAGTTATGTA
56601395 TGCTATGTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 15 0.26
52 30 0.53
53 8 0.14
54 4 0.07
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.48
Consensus pattern (50 bp):
ATGTAAGTTATGTAAGTTGTAAGATATTAAGATTATGTAAGTTATGCATT
Found at i:56601439 original size:19 final size:19
Alignment explanation
Indices: 56601398--56601441 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
56601388 TTATGTATGC
**
56601398 TATGTATAATGTAAGTTGT
1 TATGTATAATGTAAGTTAA
56601417 TATGTATAATGTAAGTTAA
1 TATGTATAATGTAAGTTAA
56601436 TATGTA
1 TATGTA
56601442 AGTAATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (19 bp):
TATGTATAATGTAAGTTAA
Found at i:56601532 original size:13 final size:15
Alignment explanation
Indices: 56601513--56601553 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
56601503 CATATAAGTT
56601513 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
56601527 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
56601541 TTATGTAAGTTAT
1 -TATGTAAGTTAT
56601554 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:56604923 original size:7 final size:7
Alignment explanation
Indices: 56604911--56605034 Score: 58
Period size: 7 Copynumber: 17.0 Consensus size: 7
56604901 CTTAATTGAC
56604911 ACCCTAA
1 ACCCTAA
56604918 ACCCTAA
1 ACCCTAA
56604925 ATCCCTAA
1 A-CCCTAA
*
56604933 CCCCTAA
1 ACCCTAA
*
56604940 CCCCTAA
1 ACCCTAA
*
56604947 ATCTCCTAG
1 A-C-CCTAA
*
56604956 TCCCTAA
1 ACCCTAA
*
56604963 ATTCCT-A
1 A-CCCTAA
*
56604970 ACCCTTA
1 ACCCTAA
56604977 ACTCCTAA
1 AC-CCTAA
*
56604985 CCCCTAA
1 ACCCTAA
56604992 ATCCCT-A
1 A-CCCTAA
56604999 ACCC-ATA
1 ACCCTA-A
56605006 ACCCTTAA
1 ACCC-TAA
*
56605014 ACCTTATA
1 ACCCTA-A
*
56605022 TCCC-AA
1 ACCCTAA
56605028 ACCCTAA
1 ACCCTAA
56605035 TAATCATATA
Statistics
Matches: 89, Mismatches: 15, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
6 10 0.11
7 47 0.53
8 27 0.30
9 5 0.06
ACGTcount: A:0.34, C:0.42, G:0.01, T:0.23
Consensus pattern (7 bp):
ACCCTAA
Found at i:56604932 original size:15 final size:15
Alignment explanation
Indices: 56604911--56605034 Score: 66
Period size: 15 Copynumber: 8.5 Consensus size: 15
56604901 CTTAATTGAC
56604911 ACCCTAAA-CCCTAA
1 ACCCTAAATCCCTAA
*
56604925 ATCCCT-AACCCCTAA
1 A-CCCTAAATCCCTAA
* *
56604940 CCCCTAAATCTCCTAG
1 ACCCTAAATC-CCTAA
* *
56604956 TCCCTAAATTCCT-A
1 ACCCTAAATCCCTAA
*
56604970 ACCCTTAA-CTCCTAA
1 ACCCTAAATC-CCTAA
*
56604985 CCCCTAAATCCCT-A
1 ACCCTAAATCCCTAA
56604999 ACCC-ATAA-CCCTTAA
1 ACCCTA-AATCCC-TAA
* *
56605014 ACCTTATATCCC-AA
1 ACCCTAAATCCCTAA
56605028 ACCCTAA
1 ACCCTAA
56605035 TAATCATATA
Statistics
Matches: 82, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
13 4 0.05
14 30 0.37
15 31 0.38
16 17 0.21
ACGTcount: A:0.34, C:0.42, G:0.01, T:0.23
Consensus pattern (15 bp):
ACCCTAAATCCCTAA
Found at i:56604961 original size:45 final size:44
Alignment explanation
Indices: 56604912--56604998 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 44
56604902 TTAATTGACA
56604912 CCCTAAA-CCCTAAATCCC-TAACCCCTAACCCCTAAATCTCCTAGT
1 CCCTAAATCCCT-AA-CCCTTAACCCCTAACCCCTAAATC-CCTAGT
* *
56604957 CCCTAAATTCCTAACCCTTAACTCCTAACCCCTAAATCCCTA
1 CCCTAAATCCCTAACCCTTAACCCCTAACCCCTAAATCCCTA
56604999 ACCCATAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
44 7 0.18
45 28 0.74
46 3 0.08
ACGTcount: A:0.31, C:0.44, G:0.01, T:0.24
Consensus pattern (44 bp):
CCCTAAATCCCTAACCCTTAACCCCTAACCCCTAAATCCCTAGT
Found at i:56605024 original size:29 final size:29
Alignment explanation
Indices: 56604920--56605031 Score: 84
Period size: 29 Copynumber: 3.8 Consensus size: 29
56604910 CACCCTAAAC
* *
56604920 CCTAAATCCCT-AACCCCTAACCCCTAAATCT
1 CCTAAA-CCCTAAATCCCTAACCCAT-AA-CT
** * *
56604951 CCTAGTCCCTAAATTCCTAACCCTTAACT
1 CCTAAACCCTAAATCCCTAACCCATAACT
*
56604980 CCTAACCCCTAAATCCCTAACCCATAAC-
1 CCTAAACCCTAAATCCCTAACCCATAACT
* * *
56605008 CCTTAAACCTTATATCCCAAACCC
1 CC-TAAACCCTAAATCCCTAACCC
56605032 TAATAATCAT
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
28 2 0.03
29 43 0.65
30 6 0.09
31 15 0.23
ACGTcount: A:0.32, C:0.43, G:0.01, T:0.24
Consensus pattern (29 bp):
CCTAAACCCTAAATCCCTAACCCATAACT
Found at i:56605831 original size:40 final size:41
Alignment explanation
Indices: 56605787--56605979 Score: 123
Period size: 40 Copynumber: 4.8 Consensus size: 41
56605777 TGTTTTTTTT
* *
56605787 GCGGCGCTTCA-ACAAAAATGCCGCTAAAACCTTAACATTA
1 GCGGCGCTTCACATAAAAACGCCGCTAAAACCTTAACATTA
* * * *
56605827 GCGGCG-TTTATCATAAAAACACCGCTAAAAATCTTAACTTTA
1 GCGGCGCTTCA-CATAAAAACGCCGCT-AAAACCTTAACATTA
* * * * *
56605869 GCGTCGCTT-ACATAAAAACGCCGGCTAAGACC-AAATATTT
1 GCGGCGCTTCACATAAAAACGCC-GCTAAAACCTTAACATTA
* * *
56605909 GCGGCGCTTCA-A-AGAAATCGCCACTAAATACCTTAACTTTA
1 GCGGCGCTTCACATA-AAAACGCCGCTAAA-ACCTTAACATTA
* * * *
56605950 GCGG-GGTTGA-TTAAAAACGCCACTAAAACC
1 GCGGCGCTTCACATAAAAACGCCGCTAAAACC
56605980 CCCGACCATT
Statistics
Matches: 117, Mismatches: 26, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
39 11 0.09
40 46 0.39
41 36 0.31
42 22 0.19
43 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (41 bp):
GCGGCGCTTCACATAAAAACGCCGCTAAAACCTTAACATTA
Found at i:56605852 original size:41 final size:40
Alignment explanation
Indices: 56605807--56605953 Score: 111
Period size: 41 Copynumber: 3.6 Consensus size: 40
56605797 AACAAAAATG
*
56605807 CCGCTAAAACCTTAACATTAGCGGCGTTTATCATAAAAACA
1 CCGCTAAAACCTTAACATTAGCGGCGCTTA-CATAAAAACA
* * * *
56605848 CCGCTAAAAATCTTAACTTTAGCGTCGCTTACATAAAAACG
1 CCGCT-AAAACCTTAACATTAGCGGCGCTTACATAAAAACA
* * * * *
56605889 CCGGCTAAGACC-AAATATTTGCGGCGCTT-CA-AAGAAATCG
1 CC-GCTAAAACCTTAACATTAGCGGCGCTTACATAA-AAA-CA
* *
56605929 CCACTAAATACCTTAACTTTAGCGG
1 CCGCTAAA-ACCTTAACATTAGCGG
56605954 GGTTGATTAA
Statistics
Matches: 82, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
38 2 0.02
39 9 0.11
40 19 0.23
41 28 0.34
42 24 0.29
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (40 bp):
CCGCTAAAACCTTAACATTAGCGGCGCTTACATAAAAACA
Found at i:56605896 original size:42 final size:42
Alignment explanation
Indices: 56605800--56605896 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
56605790 GCGCTTCAAC
* *
56605800 AAAAATGCCGCT-AAAACCTTAACATTAGCGGCGTTTATCAT
1 AAAAACGCCGCTAAAAACCTTAACATTAGCGGCGCTTATCAT
* * * *
56605841 AAAAACACCGCTAAAAATCTTAACTTTAGCGTCGCTTA-CAT
1 AAAAACGCCGCTAAAAACCTTAACATTAGCGGCGCTTATCAT
56605882 AAAAACGCCGGCTAA
1 AAAAACGCC-GCTAA
56605897 GACCAAATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 21 0.45
42 26 0.55
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAAACCTTAACATTAGCGGCGCTTATCAT
Found at i:56609572 original size:18 final size:18
Alignment explanation
Indices: 56609515--56609573 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
56609505 AAGGTAAAGG
*
56609515 TTTCTAACTCTCTTTTGC
1 TTTCTAACTCTCTTTTTC
* * * *
56609533 TCTCAAACTC-CTTTAATG
1 TTTCTAACTCTCTTT-TTC
56609551 TTTCTAACTCTCTTTTTC
1 TTTCTAACTCTCTTTTTC
56609569 TTTCT
1 TTTCT
56609574 GTAATGAGTT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
17 4 0.13
18 22 0.73
19 4 0.13
ACGTcount: A:0.15, C:0.27, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTCTAACTCTCTTTTTC
Found at i:56610174 original size:117 final size:119
Alignment explanation
Indices: 56609957--56610180 Score: 280
Period size: 118 Copynumber: 1.9 Consensus size: 119
56609947 GAAACAATTT
*
56609957 TTGGATTAGGCTTAAGAATTGATAACTGTTGTTTGTTGATAAGGTGCCTTGGCTTATATAGATGG
1 TTGGATTAGGCTTAAGAAATGATAACTGTTGTTTGTTGATAAGGTGCCTTGGCTTATATAGATGG
** * *
56610022 ATTTATATATCCAGTTGTAGTGTAATTAAGTGG-AAATTATGTGTTTTGTGTTG
66 ATGGAGATATCCAATTGTAGTGTAATTAAGTGGAAAATTATGTGTTTTGTGTTG
*
56610075 TTGG-TTAGGCTTAAGAAATGATAACTGTTGTTTGTTGAT-AGTGTTG-CTT-GCTTTAATATGG
1 TTGGATTAGGCTTAAGAAATGATAACTGTTGTTTGTTGATAAG-G-TGCCTTGGC-TT-ATATAG
* * **
56610136 ATGGATGGGGCTATTGAATTGTAGTGTAATTAAG-GGAAAATTATG
62 ATGGATGGAGATATCCAATTGTAGTGTAATTAAGTGGAAAATTATG
56610181 CATGTATGTC
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
116 4 0.04
117 42 0.46
118 45 0.49
ACGTcount: A:0.26, C:0.05, G:0.27, T:0.42
Consensus pattern (119 bp):
TTGGATTAGGCTTAAGAAATGATAACTGTTGTTTGTTGATAAGGTGCCTTGGCTTATATAGATGG
ATGGAGATATCCAATTGTAGTGTAATTAAGTGGAAAATTATGTGTTTTGTGTTG
Found at i:56611379 original size:37 final size:37
Alignment explanation
Indices: 56611336--56611424 Score: 160
Period size: 37 Copynumber: 2.4 Consensus size: 37
56611326 ATCATAAATA
*
56611336 AATAAACTAATCAATGTTCAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
56611373 AGTAAACTAATCAATGTTAAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
56611410 AATAAACTAATCAAT
1 AATAAACTAATCAAT
56611425 ATATTTATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (37 bp):
AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
Found at i:56614787 original size:91 final size:91
Alignment explanation
Indices: 56614640--56614847 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
56614630 TTGATTTTAG
* *
56614640 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
56614705 ATTTAACATTAATTATTTTAAATTGTA
65 ATGTAACAATAATTATTTTAAATTATA
*
56614732 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
56614797 TGTAATAATAATTATTTTAAATTATA
66 TGTAACAATAATTATTTTAAATTATA
*
56614823 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
56614848 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAACAATAATTATTTTAAATTATA
Found at i:56614816 original size:26 final size:28
Alignment explanation
Indices: 56614762--56614822 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
56614752 TATTATCAAG
* *
56614762 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
56614790 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
56614816 AATTATA
1 AATTATA
56614823 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:56614822 original size:44 final size:43
Alignment explanation
Indices: 56614680--56614822 Score: 112
Period size: 44 Copynumber: 3.2 Consensus size: 43
56614670 GAATTTTATG
* * *
56614680 AAATTATATATCATTATTAAATTATATTTAACATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
56614724 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
56614771 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
56614815 AAATTATA
1 AAATTATA
56614823 CAAATTCATA
Statistics
Matches: 75, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 10 0.13
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:56614991 original size:120 final size:120
Alignment explanation
Indices: 56614863--56615281 Score: 723
Period size: 120 Copynumber: 3.5 Consensus size: 120
56614853 AATTATTTTA
* *
56614863 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
*
56614927 TATAGTATCTTATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
56614983 AATTTTATTAAATTATATATTTTAATTAAAATATATTTGATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
56615048 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
56615103 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
*
56615168 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
56615223 AATTTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AA-TTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
56615282 ATGATTAAAC
Statistics
Matches: 286, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
120 230 0.80
121 51 0.18
122 5 0.02
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:56615012 original size:18 final size:17
Alignment explanation
Indices: 56614984--56615018 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56614974 ATTATTAAGA
*
56614984 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
56615001 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
56615019 TTGATAATAA
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:56615143 original size:15 final size:15
Alignment explanation
Indices: 56615108--56615159 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
56615098 TTAAGAATTT
*
56615108 TATTAAATTAT-ATA
1 TATTTAATTATAATA
56615122 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
56615136 TATTTAATAATAAT-
1 TATTTAATTATAATA
56615150 TATGTTAATT
1 TAT-TTAATT
56615160 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:56615259 original size:16 final size:16
Alignment explanation
Indices: 56615238--56615279 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
56615228 TTATTAAATT
*
56615238 ATATATTTTAATTATA
1 ATATATTTTAATAATA
56615254 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
56615269 AT-TATGTTTAA
1 ATATAT-TTTAA
56615280 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:56615264 original size:15 final size:15
Alignment explanation
Indices: 56615229--56615270 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
56615219 TAAGAATTTT
*
56615229 TATTAAATTAT-ATA
1 TATTTAATTATAATA
56615243 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
56615257 TATTTAATAATAAT
1 TATTTAATTATAAT
56615271 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:56615462 original size:5 final size:5
Alignment explanation
Indices: 56615452--56615477 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56615442 TGAGCATTCG
56615452 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
56615478 AATTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:56616458 original size:9 final size:9
Alignment explanation
Indices: 56616444--56616480 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
56616434 TATAGTTTGA
56616444 TATTCGAAT
1 TATTCGAAT
56616453 TATTCGAAT
1 TATTCGAAT
*
56616462 TATTCGAGT
1 TATTCGAAT
56616471 TATTCGAAT
1 TATTCGAAT
56616480 T
1 T
56616481 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:56616551 original size:9 final size:9
Alignment explanation
Indices: 56616534--56616564 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
56616524 TCGAGTTTAT
56616534 TCGAATAAC
1 TCGAATAAC
*
56616543 TCGATTAAC
1 TCGAATAAC
56616552 TCGAATAAC
1 TCGAATAAC
56616561 TCGA
1 TCGA
56616565 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:56617866 original size:13 final size:14
Alignment explanation
Indices: 56617836--56617871 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
56617826 AATCTCAAAC
56617836 CCTAAAC-TG-ATA
1 CCTAAACTTGAATA
56617848 CCTAAACTTGAAT-
1 CCTAAACTTGAATA
56617861 CCTAAACTTGA
1 CCTAAACTTGA
56617872 GATTTGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 13 0.59
14 2 0.09
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.28
Consensus pattern (14 bp):
CCTAAACTTGAATA
Found at i:56619914 original size:24 final size:23
Alignment explanation
Indices: 56619886--56619932 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
56619876 CTCTTCTGGG
56619886 TTTGCTTTTGTCTTCTATCTTGTT
1 TTTGCTTTTGTCTTCT-TCTTGTT
*
56619910 TTTGCTTTTTTCTTCTTCTTGTT
1 TTTGCTTTTGTCTTCTTCTTGTT
56619933 ATGTTATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.02, C:0.17, G:0.11, T:0.70
Consensus pattern (23 bp):
TTTGCTTTTGTCTTCTTCTTGTT
Found at i:56629002 original size:4 final size:4
Alignment explanation
Indices: 56628993--56629054 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
56628983 CCTGTCTAGG
* *
56628993 TTAT TTA- TT-T TTAT GTAT TAAT TT-- TTAT TTCATT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-A-T TTAT TTAT TTAT
56629039 TTAT TTATT TTAT TTA
1 TTAT TTA-T TTAT TTA
56629055 CTCATTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
2 2 0.04
3 4 0.09
4 32 0.68
5 6 0.13
6 3 0.06
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:56629062 original size:24 final size:22
Alignment explanation
Indices: 56628993--56629064 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 22
56628983 CCTGTCTAGG
*
56628993 TTATTTATTTTTATGTATTAATT-T
1 TTATTTA-TTTTATTTA-T-ATTAT
56629017 TTATTTCATTTTATTTAT-TTAT
1 TTATTT-ATTTTATTTATATTAT
56629039 TTATTTATTTTATTTACTCATTAT
1 TTATTTATTTTATTTA-T-ATTAT
56629063 TT
1 TT
56629065 CCTTTTTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
21 12 0.29
22 8 0.19
23 1 0.02
24 20 0.48
25 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (22 bp):
TTATTTATTTTATTTATATTAT
Found at i:56629070 original size:21 final size:22
Alignment explanation
Indices: 56629016--56629076 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
56629006 TGTATTAATT
* *
56629016 TTTATTTCATTTTATTTATTTA
1 TTTATTTCATTTTATTTACTCA
56629038 TTTATTT-ATTTTATTTACTCA
1 TTTATTTCATTTTATTTACTCA
*
56629059 -TTATTTCCTTTTTATTTA
1 TTTATTT-CATTTTATTTA
56629077 AAATTGGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.18
21 12 0.35
22 16 0.47
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTATTTCATTTTATTTACTCA
Found at i:56629136 original size:16 final size:18
Alignment explanation
Indices: 56629105--56629143 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
56629095 ATTTATTGTG
*
56629105 CATTTTTATTTATTATTT
1 CATTTTTATCTATTATTT
56629123 -ATTTTTATCT-TTATTT
1 CATTTTTATCTATTATTT
56629139 CATTT
1 CATTT
56629144 ACATTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
CATTTTTATCTATTATTT
Found at i:56629183 original size:20 final size:20
Alignment explanation
Indices: 56629114--56629174 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 20
56629104 GCATTTTTAT
*
56629114 TTATTATTTATTT-TTATCT
1 TTATTATTTATTTATTATCG
56629133 TTATTTCATTTACATTTATTATCG
1 TTA-TT-ATTT--ATTTATTATCG
56629157 TTATTATTTATTTATTAT
1 TTATTATTTATTTATTAT
56629175 TTTTCTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 3 0.08
20 11 0.31
21 4 0.11
22 4 0.11
23 6 0.17
24 8 0.22
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATTATTTATTTATTATCG
Found at i:56631865 original size:28 final size:28
Alignment explanation
Indices: 56631833--56631888 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
56631823 CAGTATGAGT
56631833 TTGTATACAAGGGAGATAATTACAAAAA
1 TTGTATACAAGGGAGATAATTACAAAAA
56631861 TTGTATACAAGGGAGATAATTACAAAAA
1 TTGTATACAAGGGAGATAATTACAAAAA
56631889 GAAAGTTTGT
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:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (28 bp):
TTGTATACAAGGGAGATAATTACAAAAA
Found at i:56643157 original size:30 final size:30
Alignment explanation
Indices: 56643123--56643183 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
56643113 GACGATATGA
*
56643123 TTGCCAAATCCTGAATAGAAAAGGAGCATG
1 TTGCCAAATCCCGAATAGAAAAGGAGCATG
56643153 TTGCCAAATCCCGAATAGAAAAGGAGCATG
1 TTGCCAAATCCCGAATAGAAAAGGAGCATG
56643183 T
1 T
56643184 ACAAGTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (30 bp):
TTGCCAAATCCCGAATAGAAAAGGAGCATG
Found at i:56646834 original size:89 final size:88
Alignment explanation
Indices: 56646691--56647402 Score: 430
Period size: 89 Copynumber: 7.8 Consensus size: 88
56646681 GTAACAATTT
** * * * * * *
56646691 ACAAATCTTATCTTTCTGAAGTTGTAATGGGGTAGATTGAAA-TTATAGATCTTATCTCCCTGAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTATAAATCTTATCTCCCTGAA
* * **
56646755 GTTACAGTGGATTAGATCAGAGATA
65 GTTGCAGTGAAGCAGAT-AGAGATA
* * * * *
56646780 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCTTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAG
* * * * *
56646845 TTGTAGTGAAGTAGGTTAAAAATAA
66 TTGCAGTGAAGCA-GATAGAGAT-A
* * * * **
56646870 ACAAATCTTATCTCCCTGAAATTGTAGTGGAGTAGATTGAAGACAAGCTACAAATCTTATCTCTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT----A-AAGCTATAAATCTTATCTCCC
* * **
56646935 TGAAGTTGCAGTGAAGCATATTAAAG-CC
61 TGAAGTTGCAGTGAAGCAGA-TAGAGATA
* * *
56646963 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAATTTTATCTCCTTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAG
* *
56647028 TTGCAGTGGAGCAGATTGA-ATA
66 TTGCAGTGAAGCAGATAGAGATA
** * * * * * * *
56647050 TAGTGAATCTTATCTCTCTGAAATTGTAGTAGAGTAGATTGAAGCTATAAATTTTATCTCCCTGA
1 -A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGA
* *
56647115 AGTTGCAGTGAAGCATATTGAAGATA
64 AGTTGCAGTGAAGCAGATAG-AGATA
** * * ** * *
56647141 ATGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAATCTTATTTCTCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAG
* * *
56647206 TTGCAGTGGAA-CATATTAAAGCTACAAGTT
66 TTGCAGT-GAAGCAGA-T--AG--A-GA-TA
* * *
56647236 ACAAA-CATTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAA--TATACGAATTTTATTTCCCTG
1 ACAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATA--AATCTTATCTCCCTG
* * * *
56647298 AAGTTGTAGTGAAACAGATTAAGGTACAAGTT
63 AAGTTGCAGTGAAGCAGA-T-A-G-A-GA-TA
* * * * * *** *
56647330 ACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAG
56647395 TTGCAGTG
66 TTGCAGTG
56647403 GAACGGATCT
Statistics
Matches: 500, Mismatches: 94, Indels: 53
0.77 0.15 0.08
Matches are distributed among these distances:
87 2 0.00
88 39 0.08
89 198 0.40
90 41 0.08
91 3 0.01
92 1 0.00
93 38 0.08
94 74 0.15
95 103 0.21
96 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (88 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAG
TTGCAGTGAAGCAGATAGAGATA
Found at i:56646998 original size:183 final size:177
Alignment explanation
Indices: 56646599--56647367 Score: 526
Period size: 184 Copynumber: 4.2 Consensus size: 177
56646589 CATTATGGCG
* * * * ** * ** * *
56646599 AATCTTATCTTCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAACCTTATCTCCTTGAAGTTG
* ** * * * *
56646664 CAGTGGAA-CAGATTAAAGTAACAATTTACAAATCTTATCTTTCTGAAGTTGTAATGGGGTAGAT
66 CAGT-GAAGCAGATT--A--AA-AA-TAACAAATCTTATCTCCCTGAAATTGTAGTAGAGTAGAT
** * * * * ** * * * *
56646728 TGAAATTATAGATCTTATCTCCCTGAAGTTACAGTGGATTAGATCAGAGATAGCA
124 TGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGAAGCATATTAAAGACA-CA
* * *
56646783 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAACCTTATCTCCTTGAAGTTG
* * * *
56646848 TAGTGAAGTAGGTTAAAAATAAACAAATCTTATCTCCCTGAAATTGTAGTGGAGTAGATTGAAGA
66 CAGTGAAGCAGATTAAAAAT-AACAAATCTTATCTCCCTGAAATTGTAGTAGAGTAGATT---G-
** *
56646913 CAAGCTACAAATCTTATCTCTTTGAAGTTGCAGTGAAGCATATTAAAGCCACA
126 -AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGAAGCATATTAAAGACACA
**
56646966 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAATTTTATCTCCTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAACCTTATCTCCTTGAAGTTG
* * * *** *
56647031 CAGTGGAGCAGATTGAATATAGTGAATCTTATCTCTCTGAAATTGTAGTAGAGTAGATTGAAGCT
66 CAGTGAAGCAGATTAAAAATAACAAATCTTATCTCCCTGAAATTGTAGTAGAGTAGATTGAAGCT
* * * *
56647096 ATAAATTTTATCTCCCTGAAGTTGCAGTGAAGCATATTGAAGATA-A
131 ACAAATCTTATCTCCCTGAAGTTGCAGTGAAGCATATTAAAGACACA
* * *
56647142 TGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--ATACCAATCTTAT-TTCTCTGA
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATA--AACCTTATCTCCT-TGA
* * * * *
56647204 AGTTGCAGTGGAA-CATATTAAAGCTACAAGTTACAAA-CATTATCTCCCTGAAGTTGCAGTGGA
61 AGTTGCAGT-GAAGCAGATT-AA---A-AA-TAACAAATC-TTATCTCCCTGAAATTGTAGTAGA
* ** * * * * * * *
56647267 GTAGATTAAATATACGAATTTTATTTCCCTGAAGTTGTAGTGAAACAGATTAAGGTACAAGTTAC
118 GTAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGAAGCATATTAAAG-AC-----AC
56647332 A
177 A
* * *
56647333 AATCTTATCTCCCTAAAGTTACAATGGAGCAGATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
56647368 GAAGATGCGA
Statistics
Matches: 471, Mismatches: 87, Indels: 49
0.78 0.14 0.08
Matches are distributed among these distances:
176 4 0.01
177 46 0.10
178 63 0.13
179 39 0.08
180 2 0.00
182 37 0.08
183 81 0.17
184 164 0.35
185 1 0.00
189 32 0.07
190 1 0.00
191 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (177 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAACCTTATCTCCTTGAAGTTG
CAGTGAAGCAGATTAAAAATAACAAATCTTATCTCCCTGAAATTGTAGTAGAGTAGATTGAAGCT
ACAAATCTTATCTCCCTGAAGTTGCAGTGAAGCATATTAAAGACACA
Found at i:56647089 original size:45 final size:44
Alignment explanation
Indices: 56646694--56647404 Score: 395
Period size: 44 Copynumber: 15.6 Consensus size: 44
56646684 ACAATTTACA
** * * * *
56646694 AATCTTATCTTTCTGAAGTTGTAATGGGGTAGATTGAA-ATTAT-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TATG
* ** *
56646737 AGATCTTATCTCCCTGAAGTTACAGTGGATTAGA-TCAGAGATA-G
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGATATG
* * * * *
56646781 CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATA
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATATG
* * * * * * * * **
56646827 AACCTTATCTCCTTGAAGTTGTAGTGAAGTAGGTTAAAAATAAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT--ATG
* * * **
56646873 AATCTTATCTCCCTGAAATTGTAGTGGAGTAGATTGAAGACAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG---A--TATG
** * * * ** **
56646922 AATCTTATCTCTTTGAAGTTGCAGTGAAGCATATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATATG
* ** *
56646966 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATATG
* * *
56647010 AATTTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAATATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-TG
* * * * * * *
56647055 AATCTTATCTCTCTGAAATTGTAGTAGAGTAGATTGAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATATG
* * *
56647099 AATTTTATCTCCCTGAAGTTGCAGTGAAGCATATTGAAGATAATG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ATG
**
56647144 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATATG
* * * * * * *
56647188 AATCTTATTTCTCTGAAGTTGCAGTGGAACATATTAAAGCTACAAGTTAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--A-TA--T-G
* * * * *
56647238 AAACATTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAATATACG
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATATG
* * * * * * **
56647283 AATTTTATTTCCCTGAAGTTGTAGTGAAACAGATTAAGGTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G---AAGATATG
* * * **
56647333 AATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGATGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATATG
*
56647377 AATCTTATTTCCCTGAAGTTGCAGTGGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGA
56647405 ACGGATCTTA
Statistics
Matches: 514, Mismatches: 124, Indels: 59
0.74 0.18 0.08
Matches are distributed among these distances:
43 3 0.01
44 260 0.51
45 108 0.21
46 38 0.07
47 2 0.00
48 1 0.00
49 36 0.07
50 36 0.07
51 30 0.06
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATATG
Found at i:56647113 original size:133 final size:133
Alignment explanation
Indices: 56646599--56647402 Score: 522
Period size: 139 Copynumber: 5.9 Consensus size: 133
56646589 CATTATGGCG
* * * * * * * *
56646599 AATCTTATCTTCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTA-CAAGTCTTATCTCCCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * * ** * * ** *
56646663 GCAGTGGAACAGATTAAAGTAACAATTTACAAATCTTATCTTTCTGAAGTTGTAATGGGGTAGAT
66 GCAGTAGAGCAGATTAAAG---C----TATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGAT
**
56646728 TGAAA-TTATA
124 T-AAAGAAATA
* * ** * *
56646738 GATCTTATCTCCCTGAAGTTACAGTGGATTAGA-TCAGAGATAGCAAATCTTATCTCTCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGATAGTAAATCTTATCTCTCTGAAGT
* * * * *
56646802 TGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCTTGAAGTTGTAGTGAAGTAGGTTAAAAA
65 TGCAGTAGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATT--AAA
* *
56646867 TAAACA
128 GAAATA
* * * * *
56646873 AATCTTATCTCCCTGAAATTGTAGTGGAGTAGATTGAAGACAAGCTACAAATCTTATCTCTTTGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TAG-T--AAATCTTATCTCTCTGA
* * * *
56646938 AGTTGCAGT-GAAGCATATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
62 AGTTGCAGTAG-AGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTA
**
56647002 AAGCCATA
126 AAGAAATA
* * * * *
56647010 AATTTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAATATAGTGAATCTTATCTCTCTGAAATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * * * * *
56647075 GTAGTAGAGTAGATTGAAGCTATAAATTTTATCTCCCTGAAGTTGCAGTGAAGCATATTGAAGAT
66 GCAGTAGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGA-
*
56647140 AATG
130 AATA
** *
56647144 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CCAATCTTATTTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * * * * *
56647208 GCAGTGGAACATATTAAAGCTACAAGTTACAAACATTATCTCCCTGAAGTTGCAGTGGAGTAGAT
66 GCAGTAGAGCAGATTAAAGCT---A--TA-AATC-TTATCTCCCTGAAGTTGCAGTGAAGCAGAT
* * **
56647273 TAAATATACG
124 TAAAGAAATA
* * * * * * *
56647283 AATTTTATTTCCCTGAAGTTGTAGTGAAACAGATT-AAGGTACAAGTTACAAATCTTATCTCCCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-G-A-TAG-T--AAATCTTATCTCTCT
* * * * * * *** *
56647347 AAAGTTACAATGGAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAGTTGCAGTG
60 GAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTGCAGTG
56647403 GAACGGATCT
Statistics
Matches: 523, Mismatches: 116, Indels: 53
0.76 0.17 0.08
Matches are distributed among these distances:
133 132 0.25
134 45 0.09
135 34 0.07
136 7 0.01
137 40 0.08
138 28 0.05
139 136 0.26
140 68 0.13
141 1 0.00
145 32 0.06
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (133 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
GCAGTAGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGAA
ATA
Found at i:56647367 original size:94 final size:95
Alignment explanation
Indices: 56647144--56647402 Score: 369
Period size: 94 Copynumber: 2.7 Consensus size: 95
56647134 GAAGATAATG
* *
56647144 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAATCTTATTTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTGAAGTTG
* *
56647209 CAGTGGAACATATTAAAGCTACAAGTTACA
66 CAGTGAAACAGATTAAAGCTACAAGTTACA
* * * *
56647239 AA-CATTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAATATACGAATTTTATTTCCCTGAAGTT
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTGAAGTT
* *
56647303 GTAGTGAAACAGATT-AAGGTACAAGTTACA
65 GCAGTGAAACAGATTAAAGCTACAAGTTACA
* * * *
56647333 AATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTGAAGTTG
56647398 CAGTG
66 CAGTG
56647403 GAACGGATCT
Statistics
Matches: 143, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
94 74 0.52
95 69 0.48
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (95 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTGAAGTTG
CAGTGAAACAGATTAAAGCTACAAGTTACA
Found at i:56647487 original size:44 final size:44
Alignment explanation
Indices: 56647421--56647522 Score: 150
Period size: 44 Copynumber: 2.3 Consensus size: 44
56647411 CTTATCTCCT
*
56647421 TAAAGTTGTAGTGGAGCAGATTGAAGCAACAAACCCTATACCTC
1 TAAAGTTGCAGTGGAGCAGATTGAAGCAACAAACCCTATACCTC
** * *
56647465 TAAAGTTGCAGTGGAGTGGATTGAAGCAACAAATCTTATACCTC
1 TAAAGTTGCAGTGGAGCAGATTGAAGCAACAAACCCTATACCTC
*
56647509 AAAAGTTGCAGTGG
1 TAAAGTTGCAGTGG
56647523 GTTAGAATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.25
Consensus pattern (44 bp):
TAAAGTTGCAGTGGAGCAGATTGAAGCAACAAACCCTATACCTC
Found at i:56648965 original size:9 final size:9
Alignment explanation
Indices: 56648942--56648977 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
56648932 ATGTATTACT
56648942 TTTTATTTCA
1 TTTTATTT-A
56648952 TTTTATTTA
1 TTTTATTTA
56648961 TTTTATTTA
1 TTTTATTTA
56648970 -TTTATTTA
1 TTTTATTTA
56648978 CTAATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 10 0.38
10 8 0.31
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:56648979 original size:38 final size:39
Alignment explanation
Indices: 56648920--56648999 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 39
56648910 CCTGTCTAGG
* **
56648920 TTATTTATTTTTATGTATTACTTTTTATTT-CATTTTAT
1 TTATTTATATTTATGTATTACTAATTATTTCCATTTTAT
* *
56648958 TTATTT-TATTTATTTATTTACTAATTATTTCCTTTTTAT
1 TTATTTATATTTATGTA-TTACTAATTATTTCCATTTTAT
56648997 TTA
1 TTA
56649000 AAAATGGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 8 0.23
38 17 0.49
39 10 0.29
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (39 bp):
TTATTTATATTTATGTATTACTAATTATTTCCATTTTAT
Found at i:56653744 original size:23 final size:23
Alignment explanation
Indices: 56653701--56653754 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
56653691 TATAATTTTT
* * *
56653701 TTTTAAATATCTTCATCTCTATA
1 TTTTATATATCTTCAACTCTACA
56653724 TTTTATATAT-TTCAACTTCTACA
1 TTTTATATATCTTCAAC-TCTACA
*
56653747 TATTATAT
1 TTTTATAT
56653755 TACTTGTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTATATATCTTCAACTCTACA
Found at i:56656780 original size:17 final size:17
Alignment explanation
Indices: 56656758--56656793 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
56656748 GGAATCTTAA
56656758 ATGGCTTAGGCATTGTG
1 ATGGCTTAGGCATTGTG
56656775 ATGGCTTAGGCATTGTG
1 ATGGCTTAGGCATTGTG
56656792 AT
1 AT
56656794 TGATCGAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.11, G:0.33, T:0.36
Consensus pattern (17 bp):
ATGGCTTAGGCATTGTG
Found at i:56662607 original size:36 final size:36
Alignment explanation
Indices: 56662533--56662607 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
56662523 TTTAATCATT
*
56662533 TTAATATTAAATTAATAAAATACTATTAATTAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAATAAGTA
*
56662569 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAA-TA
1 TTAATATTAAA-TTAATA-AAATACTATT-AAATAAGTA
56662605 TTA
1 TTA
56662608 TTTTTATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
35 6 0.18
36 21 0.62
37 7 0.21
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAATAAGTA
Found at i:56669551 original size:21 final size:20
Alignment explanation
Indices: 56669527--56669565 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
56669517 CAGAAACAAT
*
56669527 TATACAAATTAAATGCTAACA
1 TATAAAAATTAAAT-CTAACA
*
56669548 TATAAAAATTGAATCTAA
1 TATAAAAATTAAATCTAA
56669566 TCATGGCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (20 bp):
TATAAAAATTAAATCTAACA
Found at i:56672233 original size:15 final size:15
Alignment explanation
Indices: 56672186--56672235 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
56672176 CAATTCAAAT
*
56672186 AATCAATATATATTC
1 AATCAATATAAATTC
56672201 AAT-ATATATACCAATTC
1 AATCA-ATATA--AATTC
56672218 AATCAATATAAATTC
1 AATCAATATAAATTC
56672233 AAT
1 AAT
56672236 AAATTTATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
17 12 0.40
18 1 0.03
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCAATATAAATTC
Found at i:56672932 original size:14 final size:14
Alignment explanation
Indices: 56672913--56672940 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56672903 AACCCTTAAC
56672913 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
56672927 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
56672941 CCCTTCTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTCTTTTT
Found at i:56673031 original size:5 final size:5
Alignment explanation
Indices: 56673026--56673078 Score: 90
Period size: 5 Copynumber: 10.8 Consensus size: 5
56673016 TTTGTTTTAT
*
56673026 TATAT TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
56673075 TATA
1 TATA
56673079 CTTAATACTT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
4 4 0.09
5 42 0.91
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:56673091 original size:22 final size:24
Alignment explanation
Indices: 56673066--56673109 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
56673056 TATAATATAA
56673066 TATAATATATA-T-ACTTAATACT
1 TATAATATATATTAACTTAATACT
56673088 TATAATATATATTAACTTAATA
1 TATAATATATATTAACTTAATA
56673110 TAGTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
23 1 0.05
24 8 0.40
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (24 bp):
TATAATATATATTAACTTAATACT
Found at i:56673111 original size:20 final size:20
Alignment explanation
Indices: 56673043--56673127 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 20
56673033 TAATATAATA
56673043 TAATATAATATA-ATATAA-T
1 TAATATAATATATAT-TAACT
56673062 ATAATATAATATATA-T-ACT
1 -TAATATAATATATATTAACT
56673081 TAATACTTATAATATATATTAACT
1 T-A-A--TATAATATATATTAACT
* *
56673105 TAATATAGTTTATATTAACT
1 TAATATAATATATATTAACT
56673125 TAA
1 TAA
56673128 AGTTTTATGA
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.04
19 3 0.05
20 31 0.56
21 1 0.02
22 12 0.22
23 2 0.04
24 4 0.07
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (20 bp):
TAATATAATATATATTAACT
Found at i:56679387 original size:25 final size:25
Alignment explanation
Indices: 56679359--56679408 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
56679349 ACCAAGCATG
56679359 CTATAATACCCTCTAATTTGTTATT
1 CTATAATACCCTCTAATTTGTTATT
*
56679384 CTATAATGCCCTCTAATTTGTTATT
1 CTATAATACCCTCTAATTTGTTATT
56679409 GAATACTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (25 bp):
CTATAATACCCTCTAATTTGTTATT
Found at i:56683653 original size:11 final size:11
Alignment explanation
Indices: 56683637--56683688 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
56683627 TTATATCTTT
56683637 AATAATAATAC
1 AATAATAATAC
56683648 AATAATAATAC
1 AATAATAATAC
* **
56683659 TTATAAT-ATTT
1 -AATAATAATAC
56683670 AATAATAATAC
1 AATAATAATAC
56683681 AATAATAA
1 AATAATAA
56683689 AAAATGTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 5 0.15
11 23 0.70
12 5 0.15
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAATAATAC
Found at i:56683676 original size:33 final size:32
Alignment explanation
Indices: 56683616--56683688 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 32
56683606 TATGTTGAAT
*
56683616 AATAATAATACTTATATCTTTAATAATAATAC
1 AATAATAATACTTATATATTTAATAATAATAC
56683648 AATAATAATACTTATAATATTTAATAATAATAC
1 AATAATAATACTTAT-ATATTTAATAATAATAC
56683681 AATAATAA
1 AATAATAA
56683689 AAAATGTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 15 0.38
33 24 0.62
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (32 bp):
AATAATAATACTTATATATTTAATAATAATAC
Found at i:56686797 original size:14 final size:14
Alignment explanation
Indices: 56686778--56686816 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
56686768 TATATATGTA
56686778 AATATAATAATAAT
1 AATATAATAATAAT
56686792 AATATAATAATAAT
1 AATATAATAATAAT
*
56686806 AACA-AATAATA
1 AATATAATAATA
56686817 CAATAACAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (14 bp):
AATATAATAATAAT
Found at i:56689815 original size:55 final size:57
Alignment explanation
Indices: 56689711--56689817 Score: 130
Period size: 55 Copynumber: 1.9 Consensus size: 57
56689701 AATCTATTAT
* * * * * *
56689711 TATTTTTATTATTTATTTTTAACATAAATATGATTTTATTTATTATTTAATATTCAA
1 TATTTTTAATATATATTATTAACATAAATATGAATATATTAATTATTTAATATTCAA
56689768 TATTTTTAATATATATTATT-A-ATAAATATGAATATATATAATT-TTTAATA
1 TATTTTTAATATATATTATTAACATAAATATGAATATAT-TAATTATTTAATA
56689818 ATTTATTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
55 21 0.49
56 5 0.12
57 17 0.40
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (57 bp):
TATTTTTAATATATATTATTAACATAAATATGAATATATTAATTATTTAATATTCAA
Found at i:56690343 original size:11 final size:12
Alignment explanation
Indices: 56690280--56690344 Score: 77
Period size: 11 Copynumber: 5.8 Consensus size: 12
56690270 AACTAATCCT
56690280 CTCTCAAATTTC
1 CTCTCAAATTTC
56690292 CTCTC-AATTTC
1 CTCTCAAATTTC
*
56690303 CTCTC-AATTTG
1 CTCTCAAATTTC
56690314 CTCTCAAA-TTC
1 CTCTCAAATTTC
56690325 CT-TCCAAATTT-
1 CTCT-CAAATTTC
56690336 CTCTCAAAT
1 CTCTCAAAT
56690345 CCATATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
10 1 0.02
11 36 0.77
12 10 0.21
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.42
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:56690414 original size:51 final size:50
Alignment explanation
Indices: 56690308--56690403 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 50
56690298 ATTTCCTCTC
*
56690308 AATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAATCTT
1 AATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA-CAT
* * * *
56690359 AATTTGCTCTCAAGTTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 AATTTGCTCTCAAATTCCTTC-CAAATTTCTCTCAAATCCATATTT
56690404 TTAAATAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 2 0.05
51 38 0.95
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (50 bp):
AATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAACAT
Found at i:56692743 original size:21 final size:21
Alignment explanation
Indices: 56692739--56692994 Score: 275
Period size: 21 Copynumber: 12.0 Consensus size: 21
56692729 CTAAAAACCC
*
56692739 AAACCCTAACCCTTAACTTTA
1 AAACCCTAACCCTTAACTTAA
* *
56692760 AAATCCTAACCCTTAAATTAA
1 AAACCCTAACCCTTAACTTAA
* *
56692781 AACCCCTAAACCTTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
*
56692803 AAACCCTAAACCCTAAACATT--
1 AAACCCT-AACCCTTAAC-TTAA
*
56692824 AAACCCTAAACCCTTAACCTAA
1 AAACCCT-AACCCTTAACTTAA
*
56692846 AAACCCTAAACCCTTAACCTAA
1 AAACCCT-AACCCTTAACTTAA
*
56692868 AAACCTTAACCCTTAACTT-A
1 AAACCCTAACCCTTAACTTAA
* *
56692888 AAACCCTAACCTTTAAATTAA
1 AAACCCTAACCCTTAACTTAA
* *
56692909 AAACCCTAAACCTTTAACTTTA
1 AAACCCT-AACCCTTAACTTAA
* * * *
56692931 AAATCGTAACCCTTAAATAAA
1 AAACCCTAACCCTTAACTTAA
*
56692952 AAACCCTAACACTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
56692973 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
56692994 A
1 A
56692995 TATAATTTGA
Statistics
Matches: 198, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
20 18 0.09
21 106 0.54
22 72 0.36
23 2 0.01
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTAA
Found at i:56692811 original size:43 final size:42
Alignment explanation
Indices: 56692739--56692994 Score: 277
Period size: 43 Copynumber: 6.0 Consensus size: 42
56692729 CTAAAAACCC
* *
56692739 AAACCCT-AACCCTTAACTTTAAAATCCTAACCCTTAAATTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAAATTA
* *
56692780 AAACCCCTAAACCTTTAACTTAAAAACCCTAAACCCTAAACATT-
1 AAA-CCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAA-ATTA
* **
56692824 AAACCCTAAACCCTTAACCTAAAAACCCTAAACCCTTAACCTA
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAAATTA
* * *
56692867 AAAACCTTAACCCTTAACTT-AAAACCCTAACCTTTAAATTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAAATT-A
* * * * *
56692909 AAACCCTAAACCTTTAACTTTAAAATCGTAACCCTTAAATAAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAAAT-TA
* *
56692952 AAACCCT-AACACTTAACTTAAAAACCCTAACCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAAATTA
56692993 AA
1 AA
56692995 TATAATTTGA
Statistics
Matches: 178, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
41 15 0.08
42 57 0.32
43 92 0.52
44 11 0.06
45 3 0.02
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (42 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAAATTA
Found at i:56692842 original size:14 final size:14
Alignment explanation
Indices: 56692803--56692880 Score: 55
Period size: 14 Copynumber: 6.0 Consensus size: 14
56692793 TTTAACTTAA
*
56692803 AAACCCTAAACCCT
1 AAACCCTTAACCCT
*
56692817 AAA-CATTAAACCCT
1 AAACCCTT-AACCCT
56692831 AAACCCTTAA-CCT
1 AAACCCTTAACCCT
56692844 AAA-----AACCCT
1 AAACCCTTAACCCT
56692853 AAACCCTTAA-CCT
1 AAACCCTTAACCCT
*
56692866 AAAAACCTTAACCCT
1 -AAACCCTTAACCCT
56692881 TAACTTAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 19
0.68 0.05 0.26
Matches are distributed among these distances:
8 2 0.04
9 6 0.12
13 11 0.22
14 25 0.50
15 6 0.12
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACCCTTAACCCT
Found at i:56692884 original size:7 final size:7
Alignment explanation
Indices: 56692803--56692868 Score: 64
Period size: 7 Copynumber: 9.4 Consensus size: 7
56692793 TTTAACTTAA
56692803 AAACCCT
1 AAACCCT
56692810 AAACCCT
1 AAACCCT
**
56692817 AAACATT
1 AAACCCT
56692824 AAACCCT
1 AAACCCT
56692831 AAACCCT
1 AAACCCT
*
56692838 TAA-CCT
1 AAACCCT
56692844 AAAAACCCT
1 --AAACCCT
56692853 AAACCCT
1 AAACCCT
*
56692860 TAA-CCT
1 AAACCCT
56692866 AAA
1 AAA
56692869 AACCTTAACC
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
6 8 0.17
7 35 0.73
8 2 0.04
9 3 0.06
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:56696429 original size:125 final size:125
Alignment explanation
Indices: 56696167--56696733 Score: 832
Period size: 125 Copynumber: 4.5 Consensus size: 125
56696157 CCCAAACATG
*
56696167 CTACTGTAGCAAAAGTGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * *
56696232 TAGAAGCG-ATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGTAC
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* *
56696291 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * * *
56696355 CTTGCAGCGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTTCAGGAC
65 CTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
*
56696416 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
56696481 TTGAAGCGTTTTTTAAACTATTTACTCAGAAACGTCAACTCCAAATTATTTCTTCCAGGAC
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
* * * *
56696542 CAACTGTGGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
56696607 TTGAAGCGTTGTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGTAC
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * * * * * * *
56696667 CTACTGTAGCAAAAACGCGTACACGTGGACGCGACTTCAAAAATCCTTCTGATAAATCATACTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
56696732 TT
66 TT
56696734 TGATTTTATC
Statistics
Matches: 400, Mismatches: 39, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
123 2 0.00
124 65 0.16
125 215 0.54
126 118 0.29
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:56696647 original size:251 final size:249
Alignment explanation
Indices: 56696167--56696736 Score: 845
Period size: 251 Copynumber: 2.3 Consensus size: 249
56696157 CCCAAACATG
* *
56696167 CTACTGTAGCAAAAGTGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
* * * * * * *
56696232 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGTACCTACTG
66 TTGAAGCGATTTTAAACTATTTACTCAGAAACGTCAACTCCAAATTATTTTTCCAGGACCAACTG
* * *
56696297 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTTCTTGCAG
131 TAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGAAG
* * *
56696362 CGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTTCAGGAC
196 CGTTGTTTAAACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTCCAGGAC
56696416 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
*
56696481 TTGAAGCGTTTTTTAAACTATTTACTCAGAAACGTCAACTCCAAATTATTTCTTCCAGGACCAAC
66 TTGAAGCG-ATTTTAAACTATTTACTCAGAAACGTCAACTCCAAATTATTT-TTCCAGGACCAAC
*
56696546 TGTGGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTTG
129 TGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTG
* *
56696610 AAGCGTTGTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGTAC
193 AAGCGTTGTTTAAACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTCCAGGAC
* * * * * * * * *
56696667 CTACTGTAGCAAAAACGCGTACACGTGGACGCGACTTCAAAAATCCTTCTGATAAATCATACTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG-
56696732 TTTGA
65 TTTGA
56696737 TTTTATCTTA
Statistics
Matches: 289, Mismatches: 28, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
249 70 0.24
250 37 0.13
251 175 0.61
252 7 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (249 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
TTGAAGCGATTTTAAACTATTTACTCAGAAACGTCAACTCCAAATTATTTTTCCAGGACCAACTG
TAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGAAG
CGTTGTTTAAACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTCCAGGAC
Found at i:56696869 original size:8 final size:9
Alignment explanation
Indices: 56696849--56696885 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
56696839 TTTTTTCTCC
*
56696849 AAAACCCTA
1 AAAATCCTA
56696858 AAAATCCTA
1 AAAATCCTA
*
56696867 AAAACCCTA
1 AAAATCCTA
56696876 AAAATCCTA
1 AAAATCCTA
56696885 A
1 A
56696886 CGTGCGAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAATCCTA
Found at i:56696872 original size:18 final size:18
Alignment explanation
Indices: 56696849--56696885 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
56696839 TTTTTTCTCC
56696849 AAAACCCTAAAAATCCTA
1 AAAACCCTAAAAATCCTA
56696867 AAAACCCTAAAAATCCTA
1 AAAACCCTAAAAATCCTA
56696885 A
1 A
56696886 CGTGCGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAACCCTAAAAATCCTA
Found at i:56700212 original size:22 final size:24
Alignment explanation
Indices: 56700164--56700214 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
56700154 AATTCCCCCA
* *
56700164 AAAAGTAAAAATTTAAGTAATTCT
1 AAAAGTAAAAATTAAAGTAAATCT
*
56700188 AAAA-TAAAAATTAAAG-AAATGT
1 AAAAGTAAAAATTAAAGTAAATCT
56700210 AAAAG
1 AAAAG
56700215 GAGTAGGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 8 0.35
23 11 0.48
24 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (24 bp):
AAAAGTAAAAATTAAAGTAAATCT
Found at i:56706111 original size:24 final size:25
Alignment explanation
Indices: 56706084--56706138 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 25
56706074 GAAAAGGGAA
56706084 AAAAATCATTTT-TTCTTTACTAAT
1 AAAAATCATTTTGTTCTTTACTAAT
* * *
56706108 AAAAGTTATTTTGGATTGTTTACTAAT
1 AAAAATCATTTT-G-TTCTTTACTAAT
56706135 AAAA
1 AAAA
56706139 TTTAAATCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 10 0.40
27 15 0.60
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (25 bp):
AAAAATCATTTTGTTCTTTACTAAT
Found at i:56708893 original size:7 final size:7
Alignment explanation
Indices: 56708881--56708916 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
56708871 AAGTTTCTAA
56708881 CAAGCTT
1 CAAGCTT
56708888 CAAGCTT
1 CAAGCTT
56708895 CAAGCTT
1 CAAGCTT
56708902 CAAGCTT
1 CAAGCTT
56708909 CAAGCTT
1 CAAGCTT
56708916 C
1 C
56708917 TTCTTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.28
Consensus pattern (7 bp):
CAAGCTT
Found at i:56717836 original size:22 final size:20
Alignment explanation
Indices: 56717781--56717837 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
56717771 TAAATATATA
*
56717781 TTGAATAGTTATGTTTATTG
1 TTGAATAGTTATGTCTATTG
* * *
56717801 TT-AAAAGATGTGTCTATTCG
1 TTGAATAGTTATGTCTATT-G
56717821 TTTGAATAGTTATGTCT
1 -TTGAATAGTTATGTCT
56717838 TAATGAAGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
19 12 0.44
20 3 0.11
21 2 0.07
22 10 0.37
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.49
Consensus pattern (20 bp):
TTGAATAGTTATGTCTATTG
Found at i:56733814 original size:16 final size:18
Alignment explanation
Indices: 56733782--56733814 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56733772 ATTTCAAAAA
56733782 TTTTAATACATTACTATT
1 TTTTAATACATTACTATT
56733800 TTTTAA-ACATT-CTAT
1 TTTTAATACATTACTAT
56733815 GATATGACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAATACATTACTATT
Found at i:56736108 original size:20 final size:20
Alignment explanation
Indices: 56736083--56736121 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
56736073 TTCTCAATGT
56736083 CTCTTTTACACCGAAATTTC
1 CTCTTTTACACCGAAATTTC
56736103 CTCTTTTACACCGAAATTT
1 CTCTTTTACACCGAAATTT
56736122 AACGACCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.05, T:0.41
Consensus pattern (20 bp):
CTCTTTTACACCGAAATTTC
Found at i:56736982 original size:44 final size:44
Alignment explanation
Indices: 56736931--56737235 Score: 470
Period size: 44 Copynumber: 6.9 Consensus size: 44
56736921 CAAGATTTGT
*
56736931 TATCTTCGATCTACTTCATGTCAATACATGGAGATAAGATCCAA
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
* * *
56736975 TATCTTCGATCTACTTCATGTCAACACATGAAGATAAGATCTAC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
* * *
56737019 TATCTTTGATCTACTTCATGTCAATACATGAAGACAAGATCCAT
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
56737063 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
*
56737107 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTA
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATC--CAA
* *
56737153 TATC-T-GATCTACTTCATGTCAATACATGAAGACAAGATCCAT
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
* *
56737195 TATCTTCGATCCACTTCACGTCAATACATGAAGATAAGATC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATC
56737236 TGCTATATTT
Statistics
Matches: 238, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
42 5 0.02
43 1 0.00
44 225 0.95
45 1 0.00
46 6 0.03
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (44 bp):
TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
Found at i:56737250 original size:132 final size:132
Alignment explanation
Indices: 56736930--56737235 Score: 549
Period size: 132 Copynumber: 2.3 Consensus size: 132
56736920 ACAAGATTTG
*
56736930 TTATCTTCGATCTACTTCATGTCAATACATGGAGATAAGATCCAATATCTTCGATCTACTTCATG
1 TTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAATATCTTCGATCTACTTCATG
* *
56736995 TCAACACATGAAGATAAGATCTACTATCTTTGATCTACTTCATGTCAATACATGAAGACAAGATC
66 TCAACACATGAAGATAAGATCTACTATATCTGATCTACTTCATGTCAATACATGAAGACAAGATC
56737060 CA
131 CA
56737062 TTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAATATCTTCGATCTACTTCATG
1 TTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAATATCTTCGATCTACTTCATG
* *
56737127 TCAATACATGAAGATAAGATCTGCTATATCTGATCTACTTCATGTCAATACATGAAGACAAGATC
66 TCAACACATGAAGATAAGATCTACTATATCTGATCTACTTCATGTCAATACATGAAGACAAGATC
56737192 CA
131 CA
* *
56737194 TTATCTTCGATCCACTTCACGTCAATACATGAAGATAAGATC
1 TTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATC
56737236 TGCTATATTT
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 167 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (132 bp):
TTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAATATCTTCGATCTACTTCATG
TCAACACATGAAGATAAGATCTACTATATCTGATCTACTTCATGTCAATACATGAAGACAAGATC
CA
Found at i:56741298 original size:19 final size:20
Alignment explanation
Indices: 56741274--56741320 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
56741264 TAGTGGTGTT
* *
56741274 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
56741293 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
56741313 -AATGCAAA
1 TAATGCAAA
56741321 AAGAGACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:56743506 original size:3 final size:3
Alignment explanation
Indices: 56743493--56743545 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
56743483 TTGTATGTAC
* * * *
56743493 ATA AAA ATA ATA ATT A-A ATA ATA GTT A-A ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56743539 ATA ATA A
1 ATA ATA A
56743546 GGAGAAAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:56743513 original size:11 final size:11
Alignment explanation
Indices: 56743497--56743540 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
56743487 ATGTACATAA
56743497 AAATAATAATT
1 AAATAATAATT
*
56743508 AAATAATAGTT
1 AAATAATAATT
*
56743519 AAATAATAATA
1 AAATAATAATT
56743530 ATAATAATAAT
1 A-AATAATAAT
56743541 AATAAGGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AAATAATAATT
Found at i:56743584 original size:20 final size:19
Alignment explanation
Indices: 56743561--56743603 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
56743551 AAATAAATTT
*
56743561 AAAAGAGAACAAATTGCAAA
1 AAAAG-GAACAAATAGCAAA
* *
56743581 AAAAGGATCAAATAGTAAA
1 AAAAGGAACAAATAGCAAA
56743600 AAAA
1 AAAA
56743604 CTAAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.67, C:0.07, G:0.14, T:0.12
Consensus pattern (19 bp):
AAAAGGAACAAATAGCAAA
Found at i:56746659 original size:23 final size:24
Alignment explanation
Indices: 56746625--56746669 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
56746615 TACTTGATGA
56746625 AGAACTGATGGAAATA-CTGAAGC
1 AGAACTGATGGAAATATCTGAAGC
*
56746648 AGAA-TGATTGGACATATCTGAA
1 AGAACTGA-TGGAAATATCTGAA
56746670 AGAATTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 11 0.58
24 5 0.26
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.22
Consensus pattern (24 bp):
AGAACTGATGGAAATATCTGAAGC
Found at i:56753342 original size:21 final size:19
Alignment explanation
Indices: 56753309--56753350 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 19
56753299 TTTTGTGTTT
56753309 AATATTTTAATAAATTTGATA
1 AATATTTTAAT-AA-TTGATA
56753330 AATA-TTTATATAATTGATA
1 AATATTTTA-ATAATTGATA
56753349 AA
1 AA
56753351 AATATAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
AATATTTTAATAATTGATA
Found at i:56754135 original size:14 final size:14
Alignment explanation
Indices: 56754102--56754147 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
56754092 AGGAATAGGA
*
56754102 AATTTCATTAGATT
1 AATTTAATTAGATT
*
56754116 ATTTTAAGTTA-ATT
1 AATTTAA-TTAGATT
56754130 AATTTAATTAGATT
1 AATTTAATTAGATT
56754144 AATT
1 AATT
56754148 AATATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (14 bp):
AATTTAATTAGATT
Found at i:56757875 original size:24 final size:26
Alignment explanation
Indices: 56757833--56757883 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
56757823 TTATTCTATT
56757833 ATATTTGTATTATAATTTAAGT-TAA
1 ATATTTGTATTATAATTTAAGTGTAA
*
56757858 ATATTT-TATTATATTTTAAGTGTAA
1 ATATTTGTATTATAATTTAAGTGTAA
56757883 A
1 A
56757884 ACTAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (26 bp):
ATATTTGTATTATAATTTAAGTGTAA
Found at i:56759192 original size:28 final size:30
Alignment explanation
Indices: 56759129--56759192 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
56759119 AAAAAAAGCC
*
56759129 ATTTTTTAATAAAATTATGGAAATAAGTTA
1 ATTTTTTAATAAAATTATGGAAATAAGCTA
*
56759159 ATTTTTTAA-AAATTTATGGAAAT-AGACTA
1 ATTTTTTAATAAAATTATGGAAATAAG-CTA
56759188 ATTTT
1 ATTTT
56759193 GGTGTCCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 2 0.06
29 20 0.65
30 9 0.29
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (30 bp):
ATTTTTTAATAAAATTATGGAAATAAGCTA
Found at i:56760836 original size:28 final size:28
Alignment explanation
Indices: 56760787--56760844 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
56760777 TGTAACAGTT
* *
56760787 CAGATGTAGATGCAAAACAAATTAGATA
1 CAGATGTAGATACAAAACAAATCAGATA
*
56760815 CAGATGTAGA-ACAAATCAAAATCAGATA
1 CAGATGTAGATACAAAAC-AAATCAGATA
56760843 CA
1 CA
56760845 ATTTCCTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.19
Consensus pattern (28 bp):
CAGATGTAGATACAAAACAAATCAGATA
Found at i:56762238 original size:6 final size:6
Alignment explanation
Indices: 56762220--56762269 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
56762210 AATCAAAAGT
* * *
56762220 AAAGAA AATGAA AAAGAA ATAAGAA ATAAGAA AAATAA AAATAA AAAGAA
1 AAAGAA AAAGAA AAAGAA A-AAGAA A-AAGAA AAAGAA AAAGAA AAAGAA
56762270 GAAGGAACGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 26 0.67
7 13 0.33
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (6 bp):
AAAGAA
Found at i:56766992 original size:33 final size:32
Alignment explanation
Indices: 56766955--56767136 Score: 132
Period size: 35 Copynumber: 5.4 Consensus size: 32
56766945 ATAACCCAAT
*
56766955 TATGGTCTTATCATCAGAATGCCATAGTCCAGC
1 TATGGTCTTA-CATCAAAATGCCATAGTCCAGC
* *
56766988 TATGGTCTTACATATAAACACTGCCATAGCCCAGC
1 TATGGTCTTACAT-CAAA-A-TGCCATAGTCCAGC
* * * **
56767023 TATGGTCTTACATATAAACACTGCCCTGGTCCAAT
1 TATGGTCTTACAT-CAAA-A-TGCCATAGTCCAGC
* * * * *
56767058 TATGGTCTTACGTTCATAGTGCCAT-GACCTAGT
1 TATGGTCTTAC-ATCAAAATGCCATAGTCC-AGC
* *
56767091 TATGGTCTTATCATCAGAATGCTATAGTCCAGC
1 TATGGTCTTA-CATCAAAATGCCATAGTCCAGC
56767124 TATGGTCTTACAT
1 TATGGTCTTACAT
56767137 ATAAATACTG
Statistics
Matches: 121, Mismatches: 21, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
32 9 0.07
33 50 0.41
34 5 0.04
35 56 0.46
36 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (32 bp):
TATGGTCTTACATCAAAATGCCATAGTCCAGC
Found at i:56767022 original size:35 final size:35
Alignment explanation
Indices: 56766974--56767047 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
56766964 ATCATCAGAA
*
56766974 TGCCATAGTCCAGCTATGGTCTTACATATAAACAC
1 TGCCATAGCCCAGCTATGGTCTTACATATAAACAC
56767009 TGCCATAGCCCAGCTATGGTCTTACATATAAACAC
1 TGCCATAGCCCAGCTATGGTCTTACATATAAACAC
56767044 TGCC
1 TGCC
56767048 CTGGTCCAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (35 bp):
TGCCATAGCCCAGCTATGGTCTTACATATAAACAC
Found at i:56767062 original size:35 final size:35
Alignment explanation
Indices: 56766941--56767068 Score: 127
Period size: 35 Copynumber: 3.7 Consensus size: 35
56766931 ACATTCGTAG
* * * *
56766941 TGCCATAACCCAATTATGGTCTTATCAT-CAGA-A-
1 TGCCATAGCCCAACTATGGTCTTA-CATATAAACAC
* *
56766974 TGCCATAGTCCAGCTATGGTCTTACATATAAACAC
1 TGCCATAGCCCAACTATGGTCTTACATATAAACAC
*
56767009 TGCCATAGCCCAGCTATGGTCTTACATATAAACAC
1 TGCCATAGCCCAACTATGGTCTTACATATAAACAC
* * * *
56767044 TGCCCTGGTCCAATTATGGTCTTAC
1 TGCCATAGCCCAACTATGGTCTTAC
56767069 GTTCATAGTG
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 3 0.04
33 22 0.28
34 1 0.01
35 54 0.68
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (35 bp):
TGCCATAGCCCAACTATGGTCTTACATATAAACAC
Found at i:56767164 original size:101 final size:101
Alignment explanation
Indices: 56767013--56767203 Score: 292
Period size: 101 Copynumber: 1.9 Consensus size: 101
56767003 AAACACTGCC
* **
56767013 ATAGCCCAGCTATGGTCTTACATATAAACACTGCCCTGGTCCAATTATGGTCTTACGTTCATAGT
1 ATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTTCATAGT
* *
56767078 GCCATGACCTAGTTATGGTCTTATCATCAGAATGCT
66 GCCATAACCCAGTTATGGTCTTATCATCAGAATGCT
* * * * *
56767114 ATAGTCCAGCTATGGTCTTACATATAAATACTGTCATGGTCTAACCATGGTCTTATGTTCATAGT
1 ATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTTCATAGT
56767179 GCCATAACCCAGTTATGGTCTTATC
66 GCCATAACCCAGTTATGGTCTTATC
56767204 CGTTAATTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 80 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (101 bp):
ATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTTCATAGT
GCCATAACCCAGTTATGGTCTTATCATCAGAATGCT
Found at i:56781508 original size:29 final size:29
Alignment explanation
Indices: 56781458--56781516 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
56781448 TCCACTTTGA
* * * * *
56781458 CACGAATTCTCAACGAATAAGTTCTTCAC
1 CACGAACTCTAAACAAACAAGTTCTCCAC
56781487 CACGAACTCTAAACAAACAAGTTCTCCAC
1 CACGAACTCTAAACAAACAAGTTCTCCAC
56781516 C
1 C
56781517 TCTTCCACGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.37, C:0.32, G:0.08, T:0.22
Consensus pattern (29 bp):
CACGAACTCTAAACAAACAAGTTCTCCAC
Found at i:56788994 original size:67 final size:67
Alignment explanation
Indices: 56788911--56789046 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
56788901 ATGCCTCGAG
*
56788911 ACATGGCTTCATTATCTCAAGACATAAACTTGCATTTTGCTTGTTTGATCCCAAGATTGGTAACC
1 ACATGGCTTCATTATCTCAAGACATAAACTTGCATTTTGCTTGTTTGATCCCAAGATTCGTAACC
56788976 CA
66 CA
56788978 ACATGGCTTCATTATCTCAAGACATAAACTTGCATTTTGCTTGTTTGATCCCAAGATTCGTAACC
1 ACATGGCTTCATTATCTCAAGACATAAACTTGCATTTTGCTTGTTTGATCCCAAGATTCGTAACC
56789043 CA
66 CA
56789045 AC
1 AC
56789047 TTTGTATTTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (67 bp):
ACATGGCTTCATTATCTCAAGACATAAACTTGCATTTTGCTTGTTTGATCCCAAGATTCGTAACC
CA
Found at i:56789583 original size:34 final size:34
Alignment explanation
Indices: 56789540--56789608 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
56789530 TGTTTTCGAC
56789540 AATGGCTATTAGGAAATTAAGTCAATTTTTGAAA
1 AATGGCTATTAGGAAATTAAGTCAATTTTTGAAA
56789574 AATGGCTATTAGGAAATTAAGTCAATTTTTGAAA
1 AATGGCTATTAGGAAATTAAGTCAATTTTTGAAA
56789608 A
1 A
56789609 TGAGTTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (34 bp):
AATGGCTATTAGGAAATTAAGTCAATTTTTGAAA
Found at i:56802264 original size:138 final size:138
Alignment explanation
Indices: 56802007--56802546 Score: 647
Period size: 138 Copynumber: 3.9 Consensus size: 138
56801997 CTTGGTATTA
* * ** * **
56802007 TATAAAGGTTTGTCGGTTTGTGATCGCAACCTCCAAAAATAGCTAGTGGACCTACGCTTCCATAT
1 TATAAAGGTTTGTCGATTTATGATTACAACCTCCAAAAATAGCTAGTGGACCTACGCTCCCAGCT
* * * *
56802072 GATATTCCAAGAGCTCGTAGAGTTAAGCTTGCAACTCCAATATAGCTAAG-GGACCTACGCTCCC
66 GATATTCCAAGAGCTCGTAGAGTTAAGCTCGCAGCTCCAACACAGCT-AGCGGACCTACGCTCCC
56802136 AGTTGATGT
130 AGTTGATGT
* * *
56802145 TATAAAGGTTTG-CTGATTTATGATTGCAACCTCCAAAAATAACTAATGGACCTACGCTCCCAGC
1 TATAAAGGTTTGTC-GATTTATGATTACAACCTCCAAAAATAGCTAGTGGACCTACGCTCCCAGC
** * * *
56802209 TGATATTCTGAGAGCTCGCAAAGTTAAGCTCGCAGCTCCAACACAACTAGCGGACCTACGCTCCC
65 TGATATTCCAAGAGCTCGTAGAGTTAAGCTCGCAGCTCCAACACAGCTAGCGGACCTACGCTCCC
*
56802274 AGCTGATGT
130 AGTTGATGT
* * ** *
56802283 TATAAAGGTTTGTC-ATTTTATGATTACAACCTCCAAAAATAGCTAGCGAACCTATACTCCTAGC
1 TATAAAGGTTTGTCGA-TTTATGATTACAACCTCCAAAAATAGCTAGTGGACCTACGCTCCCAGC
* * * * * * *
56802347 T-AGTATTCCAAGAGCTCATAGATTTAAGGTCACAGCTCCAACACAGCTAGCGAACCTATGCTCT
65 TGA-TATTCCAAGAGCTCGTAGAGTTAAGCTCGCAGCTCCAACACAGCTAGCGGACCTACGCTCC
*
56802411 CAATTGATGT
129 CAGTTGATGT
* **
56802421 TATAAGGGTTTGTCGATTTATGATTACAACCTTTAAAAATAGCTAGTGGACCTACGCTCCCAGCT
1 TATAAAGGTTTGTCGATTTATGATTACAACCTCCAAAAATAGCTAGTGGACCTACGCTCCCAGCT
** * * *
56802486 GATATTCTGAGAGCTCGTAGAGTTAAGCTCGTAGCTCCAACACAGGTGGCGGACCTACGCT
66 GATATTCCAAGAGCTCGTAGAGTTAAGCTCGCAGCTCCAACACAGCTAGCGGACCTACGCT
56802547 ACCAACTTAC
Statistics
Matches: 336, Mismatches: 59, Indels: 14
0.82 0.14 0.03
Matches are distributed among these distances:
137 5 0.01
138 328 0.98
139 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (138 bp):
TATAAAGGTTTGTCGATTTATGATTACAACCTCCAAAAATAGCTAGTGGACCTACGCTCCCAGCT
GATATTCCAAGAGCTCGTAGAGTTAAGCTCGCAGCTCCAACACAGCTAGCGGACCTACGCTCCCA
GTTGATGT
Found at i:56802682 original size:17 final size:17
Alignment explanation
Indices: 56802662--56802768 Score: 124
Period size: 17 Copynumber: 6.3 Consensus size: 17
56802652 AAGTCTATTC
*
56802662 AAGTTCAGAATTTGCTT
1 AAGTTCAAAATTTGCTT
*
56802679 AAGTTCAAAAATTGCTT
1 AAGTTCAAAATTTGCTT
** *
56802696 AAGCCCAAAATTTGTTT
1 AAGTTCAAAATTTGCTT
*
56802713 AAGTTCAAAATGTGCTT
1 AAGTTCAAAATTTGCTT
* *
56802730 AAGTTCAAGATTTGATT
1 AAGTTCAAAATTTGCTT
*
56802747 AAATTCAAAATTTGCTT
1 AAGTTCAAAATTTGCTT
*
56802764 GAGTT
1 AAGTT
56802769 TACAAAAAGA
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 72 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (17 bp):
AAGTTCAAAATTTGCTT
Done.