Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 18 of 207
Found at i:5348795 original size:119 final size:120
Alignment explanation
Indices: 5348478--5348822 Score: 613
Period size: 120 Copynumber: 2.9 Consensus size: 120
5348468 TTTATAAAGT
*
5348478 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCA
1 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
*
5348543 TATATTTTAATTAAAATATATTCAATAATAATTAT-TTCAAATTATATTTTATAGC
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGC
5348598 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
* *
5348663 TATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTCTAGT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGC
* *
5348718 TTCATATATTATGA-TTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
5348782 TATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
5348823 ATATGATTAA
Statistics
Matches: 218, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
119 90 0.41
120 126 0.58
121 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
TATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGC
Found at i:5348796 original size:18 final size:17
Alignment explanation
Indices: 5348768--5348802 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5348758 ATTATTAAGA
*
5348768 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5348785 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5348803 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5349016 original size:44 final size:44
Alignment explanation
Indices: 5348958--5349055 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 44
5348948 GCTATTACAC
*
5348958 ATTCATTCCATTCAACCAAACACA-AGAA-TACTATTACGCCTCT
1 ATTCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCT
* * *
5349001 ATTCTATTACATTCAACCAAATAATTGAATTGCTATTACGCCTCT
1 ATTC-ATTACATTCAACCAAACAATAGAATTACTATTACGCCTCT
5349046 ATTCCATTAC
1 ATT-CATTAC
5349056 CCCTCTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
43 5 0.11
44 19 0.40
45 22 0.47
46 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.34
Consensus pattern (44 bp):
ATTCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCT
Found at i:5349060 original size:16 final size:16
Alignment explanation
Indices: 5349035--5349067 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5349025 TTGAATTGCT
*
5349035 ATTACGCCTCTATTCC
1 ATTACCCCTCTATTCC
5349051 ATTACCCCTCTATTCC
1 ATTACCCCTCTATTCC
5349067 A
1 A
5349068 ATAGAACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.39, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACCCCTCTATTCC
Found at i:5349518 original size:4 final size:4
Alignment explanation
Indices: 5349509--5349541 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
5349499 TGATAAGAAC
5349509 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
5349542 TAAAATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:5361587 original size:6 final size:6
Alignment explanation
Indices: 5361576--5361604 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5361566 GGAAGAGAGC
5361576 GAAATA GAAATA GAAATA GAAATA GAAAT
1 GAAATA GAAATA GAAATA GAAATA GAAAT
5361605 GGGAAGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
GAAATA
Found at i:5367037 original size:25 final size:25
Alignment explanation
Indices: 5367009--5367149 Score: 92
Period size: 25 Copynumber: 5.6 Consensus size: 25
5366999 AATAACGGGT
* *
5367009 AGCTCTAAAGAGCTATTAATCAGGA
1 AGCTCCAAAGAGCCATTAATCAGGA
* * **
5367034 AGCTCCAAATAACCA-TATATTGGGA
1 AGCTCCAAAGAGCCATTA-ATCAGGA
* * *
5367059 AG-TTCAAGCGAGCCA-T-ATCGGGA
1 AGCTCCAA-AGAGCCATTAATCAGGA
* *
5367082 AGCTCCATAGAGCAATTAATCAGGA
1 AGCTCCAAAGAGCCATTAATCAGGA
* *
5367107 AGCTCATAAAGAGCCTTTAATCAGGA
1 AGCTC-CAAAGAGCCATTAATCAGGA
*
5367133 AGCTCACGAAGAGCCAT
1 AGCTC-CAAAGAGCCAT
5367150 ATATCAGAAC
Statistics
Matches: 87, Mismatches: 23, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
23 13 0.15
24 10 0.11
25 34 0.39
26 30 0.34
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (25 bp):
AGCTCCAAAGAGCCATTAATCAGGA
Found at i:5367126 original size:26 final size:26
Alignment explanation
Indices: 5367079--5367147 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
5367069 AGCCATATCG
* **
5367079 GGAAGCTC-CATAGAGCAATTAATCA
1 GGAAGCTCACAAAGAGCCTTTAATCA
*
5367104 GGAAGCTCATAAAGAGCCTTTAATCA
1 GGAAGCTCACAAAGAGCCTTTAATCA
*
5367130 GGAAGCTCACGAAGAGCC
1 GGAAGCTCACAAAGAGCC
5367148 ATATATCAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 8 0.22
26 29 0.78
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCTTTAATCA
Found at i:5367155 original size:26 final size:26
Alignment explanation
Indices: 5367098--5367164 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
5367088 ATAGAGCAAT
* *
5367098 TAATCAGGAAGCTCATAAAGAGCCTT
1 TAATCAGGAAGCTCACAAAGAGCCTA
*
5367124 TAATCAGGAAGCTCACGAAGAGCC-A
1 TAATCAGGAAGCTCACAAAGAGCCTA
5367149 TATATCA-GAACGCTCA
1 TA-ATCAGGAA-GCTCA
5367165 TAAGAGTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 5 0.14
26 31 0.86
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAGCCTA
Found at i:5369469 original size:14 final size:14
Alignment explanation
Indices: 5369450--5369482 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5369440 CAAATTACAT
5369450 GTTAGAATAGTATC
1 GTTAGAATAGTATC
5369464 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
5369478 ATTAG
1 GTTAG
5369483 CAAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:5373254 original size:51 final size:51
Alignment explanation
Indices: 5373193--5373307 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
5373183 TCCTCTCTAA
*
5373193 TCCTTTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
* *
5373244 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCTATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
5373295 TCC-CATCAATTTC
1 TCCTC-TCAATTTC
5373308 ATTTTTTAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 1 0.02
51 59 0.98
ACGTcount: A:0.29, C:0.28, G:0.00, T:0.43
Consensus pattern (51 bp):
TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
Found at i:5373350 original size:21 final size:21
Alignment explanation
Indices: 5373326--5373365 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5373316 AAATAATTTT
*
5373326 AAATAATTTTATATTTTTTAA
1 AAATAATTTTAAATTTTTTAA
5373347 AAATAATTTTAAATTTTTT
1 AAATAATTTTAAATTTTTT
5373366 TATATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATAATTTTAAATTTTTTAA
Found at i:5373350 original size:31 final size:30
Alignment explanation
Indices: 5373308--5373373 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
5373298 CATCAATTTC
5373308 ATTTTTTAAAATAATTTTAAATAATTTTAT
1 ATTTTTTAAAATAATTTTAAATAATTTTAT
**
5373338 ATTTTTTAAAAATAATTTTAAATTTTTTTAT
1 ATTTTTT-AAAATAATTTTAAATAATTTTAT
5373369 ATTTT
1 ATTTT
5373374 CATCAATGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTTTTTAAAATAATTTTAAATAATTTTAT
Found at i:5374466 original size:7 final size:7
Alignment explanation
Indices: 5374454--5374478 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5374444 AGTCGATTGA
5374454 TATTTAG
1 TATTTAG
5374461 TATTTAG
1 TATTTAG
5374468 TATTTAG
1 TATTTAG
5374475 TATT
1 TATT
5374479 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:5375684 original size:71 final size:71
Alignment explanation
Indices: 5375566--5375750 Score: 325
Period size: 71 Copynumber: 2.6 Consensus size: 71
5375556 TATTTAAATT
*
5375566 TATTATTTGATATAATAAATTAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATATAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
5375631 TTTTGA
66 TTTTGA
* * *
5375637 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATATAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
5375702 TTTTGA
66 TTTTGA
5375708 TATTATTTGATATAATAAAATAGAAGTTCTATTTGATGTAATA
1 TATTATTTGATATAATAAAATAGAAGTT-TATTTGATGTAATA
5375751 AAAACCCTAA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 94 0.88
72 13 0.12
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.45
Consensus pattern (71 bp):
TATTATTTGATATAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
TTTTGA
Found at i:5375772 original size:18 final size:18
Alignment explanation
Indices: 5375749--5375802 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 18
5375739 TTTGATGTAA
5375749 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAATTTAAT
5375767 TAAAAACCCTAACATAATTTAAT
1 TAAAAA-CC---C-TAATTTAAT
5375790 TAAAAACCCTAAT
1 TAAAAACCCTAAT
5375803 CCTAACCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
18 10 0.32
19 3 0.10
22 3 0.10
23 15 0.48
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAACCCTAATTTAAT
Found at i:5375784 original size:23 final size:23
Alignment explanation
Indices: 5375758--5375801 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
5375748 ATAAAAACCC
5375758 TAATTTAATTAAAAACCCTAACA
1 TAATTTAATTAAAAACCCTAACA
5375781 TAATTTAATTAAAAACCCTAA
1 TAATTTAATTAAAAACCCTAA
5375802 TCCTAACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (23 bp):
TAATTTAATTAAAAACCCTAACA
Found at i:5375807 original size:29 final size:29
Alignment explanation
Indices: 5375771--5376019 Score: 392
Period size: 29 Copynumber: 8.6 Consensus size: 29
5375761 TTTAATTAAA
*
5375771 AACCCTAACATAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
5375800 AATCCTAACCTAATTTAATTAGAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
5375829 AACACTAACCTAATTTAATTAAAAAGCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
5375858 AACCCTAACCTAATTTAATTAAAAACCTT
1 AACCCTAACCTAATTTAATTAAAAACCCT
5375887 AACCCTAACCTAATTTAATTAAAAATCCACT
1 AACCCTAACCTAATTTAATTAAAAA-CC-CT
* *
5375918 -GCCATAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
5375946 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
5375975 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
5376004 AGCCCTAACCTAATTT
1 AACCCTAACCTAATTT
5376020 TACTAATCAT
Statistics
Matches: 201, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
28 2 0.01
29 174 0.87
30 24 0.12
31 1 0.00
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.29
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:5375955 original size:117 final size:116
Alignment explanation
Indices: 5375771--5376019 Score: 401
Period size: 117 Copynumber: 2.1 Consensus size: 116
5375761 TTTAATTAAA
* *
5375771 AACCCTAACATAATTTAATTAAAAACCCTAATCCTAACCTAATTTAATTAGAAACCCTAACACTA
1 AACCCTAACCTAATTTAATTAAAAACCCTAATCCTAACCTAATTTAATTAAAAACCCTAACACTA
* *
5375836 ACCTAATTTAATTAAAAAGCCTAACCCTAACCTAATTTAATTAAAAACCTT
66 ACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
* * *
5375887 AACCCTAACCTAATTTAATTAAAAATCC-ACTGCCATAACCTAATTTAATTAAAAACCCTAACCC
1 AACCCTAACCTAATTTAATTAAAAACCCTAAT-CC-TAACCTAATTTAATTAAAAACCCTAACAC
5375951 TAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
64 TAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
*
5376004 AGCCCTAACCTAATTT
1 AACCCTAACCTAATTT
5376020 TACTAATCAT
Statistics
Matches: 123, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
115 2 0.02
116 28 0.23
117 93 0.76
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.29
Consensus pattern (116 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAATCCTAACCTAATTTAATTAAAAACCCTAACACTA
ACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
Found at i:5376080 original size:55 final size:55
Alignment explanation
Indices: 5376014--5376121 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
5376004 AGCCCTAACC
*
5376014 TAATTTTACTAATCATTAACACAATTTTTAGACTTAATAATTTTACATAATTTGA
1 TAATTTTACTAACCATTAACACAATTTTTAGACTTAATAATTTTACATAATTTGA
*
5376069 TAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTT
1 TAATTTTACTAACCATTAACACAATTTTTAGACTTAATAATTTTACATAATTT
5376122 TACATAATGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (55 bp):
TAATTTTACTAACCATTAACACAATTTTTAGACTTAATAATTTTACATAATTTGA
Found at i:5376120 original size:10 final size:10
Alignment explanation
Indices: 5376105--5376129 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5376095 TTTGGACTTA
5376105 ATAATTTTAC
1 ATAATTTTAC
5376115 ATAATTTTAC
1 ATAATTTTAC
5376125 ATAAT
1 ATAAT
5376130 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:5379526 original size:124 final size:125
Alignment explanation
Indices: 5379218--5379565 Score: 601
Period size: 124 Copynumber: 2.8 Consensus size: 125
5379208 CCCAAACTTG
*
5379218 CTACTGTAGCAAAATCGCGTCCACGAA-GGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAATCGCGTCCAC-AAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTG
5379282 GTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
65 GTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* * **
5379343 CAACTGTAGCAAAATCGCGTCCACGAGAACACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACAAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
5379408 TAGAAGCAATTTTATACTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
*
5379467 CTACTGTAGCAAAATCGCGTCCACAAGGGCCCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACAAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
5379532 TAGAAGCGATTTTATACTATTTGTTCAGAAACGT
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGT
5379566 TAACTCGAAA
Statistics
Matches: 209, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
124 117 0.56
125 92 0.44
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAATCGCGTCCACAAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:5380107 original size:35 final size:35
Alignment explanation
Indices: 5380061--5380133 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
5380051 ATTTTCCAAT
*
5380061 AACTAAAAATAAAATCAAT-CAAA-TATAAAGAAAAA
1 AACTAAAAATAAAAT-AATCCAAACTA-AAAAAAAAA
5380096 AACTAAAAATAAAATAATCCAAACTAAAAAAAAAA
1 AACTAAAAATAAAATAATCCAAACTAAAAAAAAAA
5380131 AAC
1 AAC
5380134 AGTAAAACTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
34 3 0.09
35 30 0.86
36 2 0.06
ACGTcount: A:0.73, C:0.11, G:0.01, T:0.15
Consensus pattern (35 bp):
AACTAAAAATAAAATAATCCAAACTAAAAAAAAAA
Found at i:5380644 original size:14 final size:15
Alignment explanation
Indices: 5380625--5380653 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5380615 CTTTCAATTA
5380625 GTTGATTTT-TTTTT
1 GTTGATTTTCTTTTT
5380639 GTTGATTTTCTTTTT
1 GTTGATTTTCTTTTT
5380654 CTGATCGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.14, T:0.76
Consensus pattern (15 bp):
GTTGATTTTCTTTTT
Found at i:5385263 original size:6 final size:6
Alignment explanation
Indices: 5385252--5385305 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
5385242 TTTTTTAAAA
* * *
5385252 ATATTT ATATTT ATATTA AT-TTT A-ATTT AATATTT TTATAT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT -ATATTT ATATTT ATATTT
5385299 -TATTT AT
1 ATATTT AT
5385306 TAAATTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
5 11 0.29
6 23 0.61
7 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATATTT
Found at i:5385291 original size:25 final size:26
Alignment explanation
Indices: 5385261--5385318 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
5385251 AATATTTATA
*
5385261 TTTATATTA-ATTTTAATTTA-ATATT
1 TTTATATTATATTTT-ATTTATAAATT
5385286 TTTATA-TATATTTTATTTATTAAATT
1 TTTATATTATATTTTATTTA-TAAATT
5385312 TTTATAT
1 TTTATAT
5385319 ATACAGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 7 0.25
25 11 0.39
26 10 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTATATTATATTTTATTTATAAATT
Found at i:5386046 original size:31 final size:31
Alignment explanation
Indices: 5386008--5386067 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5385998 AAAACTATAA
5386008 AAAAAAAAGATAAAATTTCAAAAAAAAATAC
1 AAAAAAAAGATAAAATTTCAAAAAAAAATAC
** *
5386039 AAAAAAAATTTAAAATTTCATAAAAAAAT
1 AAAAAAAAGATAAAATTTCAAAAAAAAAT
5386068 TATAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.22
Consensus pattern (31 bp):
AAAAAAAAGATAAAATTTCAAAAAAAAATAC
Found at i:5386082 original size:20 final size:20
Alignment explanation
Indices: 5386032--5386083 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
5386022 ATTTCAAAAA
5386032 AAAATA-CA-AAAAAAATTT
1 AAAATATCATAAAAAAATTT
*
5386050 AAAATTTCATAAAAAAATTAT
1 AAAATATCATAAAAAAATT-T
5386071 AAAATATC-TAAAA
1 AAAATATCATAAAA
5386084 CACATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 5 0.17
19 2 0.07
20 14 0.48
21 8 0.28
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATATCATAAAAAAATTT
Found at i:5386090 original size:21 final size:22
Alignment explanation
Indices: 5386032--5386096 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 22
5386022 ATTTCAAAAA
5386032 AAAATA-CA-AAAAAAATT--T
1 AAAATATCATAAAAAAATTAAT
*
5386050 AAAATTTCATAAAAAAATT-AT
1 AAAATATCATAAAAAAATTAAT
*
5386071 AAAATATC-TAAAACACATTAAT
1 AAAATATCATAAAA-AAATTAAT
5386093 AAAA
1 AAAA
5386097 AATGTATCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 14 0.36
21 12 0.31
22 6 0.15
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAATATCATAAAAAAATTAAT
Found at i:5389829 original size:90 final size:90
Alignment explanation
Indices: 5389671--5389851 Score: 292
Period size: 90 Copynumber: 2.0 Consensus size: 90
5389661 ATCCATATAC
* * *
5389671 ATTCTGTGACAAAAAGCATATAAATATAATGTTCATCGTCACATTATCTTTAATTCTTGGAGGTT
1 ATTCTGTGACAAAAAGCATATAAATATAACGTTCATCGTCACATTATATTTAATTCTTAGAGGTT
*
5389736 TTTTTTTACATTTGTTGGAACATTT
66 TTTTTTTACATTTATTGGAACATTT
*
5389761 ATTCTGTGACAAAAAGCATATAAATGTAACGTTCATCGTCACATTATATATTAAATTCTTAGA-G
1 ATTCTGTGACAAAAAGCATATAAATATAACGTTCATCGTCACATTATAT-TT-AATTCTTAGAGG
5389825 TTTTTTTTTACATTTATTGGAACATTT
64 TTTTTTTTTACATTTATTGGAACATTT
5389852 GATTGCTCCA
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
90 46 0.55
91 29 0.35
92 9 0.11
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (90 bp):
ATTCTGTGACAAAAAGCATATAAATATAACGTTCATCGTCACATTATATTTAATTCTTAGAGGTT
TTTTTTTACATTTATTGGAACATTT
Found at i:5398259 original size:28 final size:28
Alignment explanation
Indices: 5398223--5398277 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
5398213 ATGCCTACAA
*
5398223 GTAGTCATTCATCTTGAACCTAAATCTT
1 GTAGGCATTCATCTTGAACCTAAATCTT
*
5398251 GTAGGCATTCATCTTGAACCTGAATCT
1 GTAGGCATTCATCTTGAACCTAAATCT
5398278 GATCATTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (28 bp):
GTAGGCATTCATCTTGAACCTAAATCTT
Found at i:5406608 original size:15 final size:16
Alignment explanation
Indices: 5406588--5406624 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5406578 ACAAAATCAA
5406588 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
5406603 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
5406619 ATAAAA
1 ATAAAA
5406625 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:5406803 original size:60 final size:60
Alignment explanation
Indices: 5406739--5406860 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
5406729 ATACTAAACT
* * * * *
5406739 AAACACAACAATTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
5406799 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
5406859 AA
1 AA
5406861 TATTCATACA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.07
60 52 0.93
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:5406965 original size:19 final size:19
Alignment explanation
Indices: 5406938--5406974 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5406928 TTATAAAATA
5406938 ATTACAATATTCATACAAC
1 ATTACAATATTCATACAAC
*
5406957 ATTATAATATTCATACAA
1 ATTACAATATTCATACAA
5406975 AATACTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTACAATATTCATACAAC
Found at i:5406983 original size:19 final size:19
Alignment explanation
Indices: 5406943--5406983 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5406933 AAATAATTAC
*
5406943 AATATTCATACAACATTAT
1 AATATTCATACAACAATAT
5406962 AATATTCATACAA-AATACT
1 AATATTCATACAACAATA-T
5406981 AAT
1 AAT
5406984 CAAAAACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (19 bp):
AATATTCATACAACAATAT
Found at i:5406991 original size:80 final size:80
Alignment explanation
Indices: 5406837--5407234 Score: 383
Period size: 80 Copynumber: 4.7 Consensus size: 80
5406827 AATTACTAAC
* *
5406837 AAATTAATTATAAAATAATTACAATATTCATACAAACAATATTACAATATTCATACAAAATACAA
1 AAATTAATTATAAAATAATTACAATATTCATAC-AAC---ATTATAATATTCATACAAAATACTA
*
5406902 ATCCAAAACTATAAATACA
62 ATCAAAAACTATAAATACA
5406921 AAATTAATTATAAAATAATTACAATATTCATACAACATTATAATATTCATACAAAATACTAATCA
1 AAATTAATTATAAAATAATTACAATATTCATACAACATTATAATATTCATACAAAATACTAATCA
5406986 AAAACTATAAATACA
66 AAAACTATAAATACA
* * *
5407001 AAATTAATTATAAAATAATTACAA-AAT--TACAACATTCATACAAAAT--TACAAAATTACAAT
1 AAATTAATTATAAAATAATTACAATATTCATACAACATT-ATA-ATATTCATACAAAA-TAC--T
* *
5407061 ATTTATACAAAATATTAATCAAAAACTATA
61 A---AT-CAAAA-ACT-AT---AAA-TACA
* *
5407091 AATATAAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTATACTATTCATACAAAAT
1 AA-AT-----TAATTATAAAATAATTACAATATTCATAC--AACATTATAATATTCATACAAAAT
* *
5407156 ACTAATCCAAAACAATAAATACA
58 ACTAATCAAAAACTATAAATACA
* * *
5407179 AAATTAATTATAAAATAATTATAATATTCATACAAAATTATAATATTTATACAAAA
1 AAATTAATTATAAAATAATTACAATATTCATACAACATTATAATATTCATACAAAA
5407235 AATTACAATA
Statistics
Matches: 266, Mismatches: 20, Indels: 60
0.77 0.06 0.17
Matches are distributed among these distances:
77 16 0.06
78 6 0.02
79 5 0.02
80 88 0.33
82 28 0.11
83 5 0.02
84 38 0.14
85 2 0.01
86 2 0.01
87 2 0.01
88 5 0.02
89 6 0.02
90 5 0.02
91 2 0.01
92 2 0.01
93 1 0.00
94 4 0.02
95 2 0.01
96 20 0.08
97 2 0.01
98 2 0.01
99 5 0.02
100 6 0.02
101 12 0.05
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (80 bp):
AAATTAATTATAAAATAATTACAATATTCATACAACATTATAATATTCATACAAAATACTAATCA
AAAACTATAAATACA
Found at i:5407030 original size:8 final size:8
Alignment explanation
Indices: 5407017--5407059 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
5407007 ATTATAAAAT
5407017 AATTACAA
1 AATTACAA
5407025 AATTACAA
1 AATTACAA
*
5407033 CATTCATACAA
1 -AAT--TACAA
5407044 AATTACAA
1 AATTACAA
5407052 AATTACAA
1 AATTACAA
5407060 TATTTATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 21 0.70
9 2 0.07
10 2 0.07
11 5 0.17
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (8 bp):
AATTACAA
Found at i:5407053 original size:27 final size:27
Alignment explanation
Indices: 5407017--5407073 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
5407007 ATTATAAAAT
5407017 AATTACAAAATTACAACATTCATACAA
1 AATTACAAAATTACAACATTCATACAA
* *
5407044 AATTACAAAATTACAATATTTATACAA
1 AATTACAAAATTACAACATTCATACAA
5407071 AAT
1 AAT
5407074 ATTAATCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (27 bp):
AATTACAAAATTACAACATTCATACAA
Found at i:5407138 original size:21 final size:21
Alignment explanation
Indices: 5407108--5407255 Score: 94
Period size: 21 Copynumber: 7.2 Consensus size: 21
5407098 AATTAATTAT
5407108 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
* *
5407130 AAAAAATTATACTATTCATAC
1 AAAAAATTACAATATTCATAC
* * *
5407151 --AAAA-TACTA-ATCCAAAAC
1 AAAAAATTACAATATTC-ATAC
* * * *
5407169 AATAAA-TACAAAATTAATTAT
1 AAAAAATTACAATATTCA-TAC
*
5407190 AAAATAATTATAATATTCATAC
1 AAAA-AATTACAATATTCATAC
* *
5407212 --AAAATTATAATATTTATAC
1 AAAAAATTACAATATTCATAC
*
5407231 AAAAAATTACAATATACATAC
1 AAAAAATTACAATATTCATAC
5407252 AAAA
1 AAAA
5407256 TTACTCATTG
Statistics
Matches: 95, Mismatches: 22, Indels: 19
0.70 0.16 0.14
Matches are distributed among these distances:
17 3 0.03
18 5 0.05
19 20 0.21
20 10 0.11
21 41 0.43
22 8 0.08
23 8 0.08
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:5407219 original size:19 final size:19
Alignment explanation
Indices: 5407195--5407258 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
5407185 ATTATAAAAT
5407195 AATTATAATATTCATACAA
1 AATTATAATATTCATACAA
*
5407214 AATTATAATATTTATACAAAA
1 AATTATAATATTCATAC--AA
* *
5407235 AATTACAATATACATACAA
1 AATTATAATATTCATACAA
5407254 AATTA
1 AATTA
5407259 CTCATTGGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 23 0.59
21 16 0.41
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (19 bp):
AATTATAATATTCATACAA
Found at i:5407237 original size:82 final size:80
Alignment explanation
Indices: 5407047--5407234 Score: 286
Period size: 82 Copynumber: 2.3 Consensus size: 80
5407037 CATACAAAAT
* * * *
5407047 TACAAAATTACAATATTTATACAAAATATTAATCAAAAACTATAAATATAAAATTAATTATAAAA
1 TACAAAATTATAATATTTATACAAAATACTAATCAAAAACAATAAATACAAAATTAATTATAAAA
5407112 TAATTACAATATTCA
66 TAATTACAATATTCA
* * *
5407127 TACAAAAAATTATACTATTCATACAAAATACTAATCCAAAACAATAAATACAAAATTAATTATAA
1 TAC--AAAATTATAATATTTATACAAAATACTAATCAAAAACAATAAATACAAAATTAATTATAA
*
5407192 AATAATTATAATATTCA
64 AATAATTACAATATTCA
5407209 TACAAAATTATAATATTTATACAAAA
1 TACAAAATTATAATATTTATACAAAA
5407235 AATTACAATA
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
80 24 0.25
82 72 0.75
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.32
Consensus pattern (80 bp):
TACAAAATTATAATATTTATACAAAATACTAATCAAAAACAATAAATACAAAATTAATTATAAAA
TAATTACAATATTCA
Found at i:5407305 original size:27 final size:27
Alignment explanation
Indices: 5407264--5407336 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
5407254 AATTACTCAT
*
5407264 TGGCGCCTCCCTATGAGTCACTTTTAA
1 TGGCGCCTCCCTATGAGGCACTTTTAA
*
5407291 TGGCGCCTCCTTATGAGGCACTTTTAA
1 TGGCGCCTCCCTATGAGGCACTTTTAA
*
5407318 TGGTGCCTCCCTATGAGGC
1 TGGCGCCTCCCTATGAGGC
5407337 GCCACCCGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.16, C:0.29, G:0.23, T:0.32
Consensus pattern (27 bp):
TGGCGCCTCCCTATGAGGCACTTTTAA
Found at i:5408649 original size:15 final size:14
Alignment explanation
Indices: 5408601--5408646 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
5408591 TTATTGTAGA
5408601 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
5408615 TTTAATTTAATTA-GT
1 TTTAATTT--TTATAT
5408630 TTTAATTTTTATAT
1 TTTAATTTTTATAT
5408644 TTT
1 TTT
5408647 TAAAATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 12 0.44
15 9 0.33
16 3 0.11
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:5417308 original size:24 final size:24
Alignment explanation
Indices: 5417276--5417324 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5417266 GGATAATTCA
* *
5417276 ACTTACTTAGGGTTGAGGTAAGTT
1 ACTTACTTAAGATTGAGGTAAGTT
5417300 ACTTACTTAAGATTGAGGTAAGTT
1 ACTTACTTAAGATTGAGGTAAGTT
5417324 A
1 A
5417325 TACTATGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (24 bp):
ACTTACTTAAGATTGAGGTAAGTT
Found at i:5423606 original size:43 final size:43
Alignment explanation
Indices: 5423558--5423645 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
5423548 TCAACCACAT
* * *
5423558 ATCAAATTTAAAGATCAACAAAAGATTGATGCACAAGTAAAGC
1 ATCAAATGTAAACATCAACAAAAGATGGATGCACAAGTAAAGC
5423601 ATCAAATGTAAACATCAACAAAAGATGGATGCACAAGTAAAGC
1 ATCAAATGTAAACATCAACAAAAGATGGATGCACAAGTAAAGC
5423644 AT
1 AT
5423646 GAAGTTACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (43 bp):
ATCAAATGTAAACATCAACAAAAGATGGATGCACAAGTAAAGC
Found at i:5425425 original size:15 final size:15
Alignment explanation
Indices: 5425405--5425435 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5425395 TGAGATTGTG
5425405 AATGAGGAAAATATT
1 AATGAGGAAAATATT
5425420 AATGAGGAAAATATT
1 AATGAGGAAAATATT
5425435 A
1 A
5425436 TATTCCACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (15 bp):
AATGAGGAAAATATT
Found at i:5425776 original size:30 final size:30
Alignment explanation
Indices: 5425742--5425804 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
5425732 ACTTATTTTA
5425742 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* * *
5425772 TTGTTGATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
5425802 TTG
1 TTG
5425805 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:5427396 original size:17 final size:17
Alignment explanation
Indices: 5427349--5427388 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5427339 GAATTTAGAA
* *
5427349 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTATT
5427365 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTATT
5427382 GAATTTT
1 GAATTTT
5427389 TTGGTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (17 bp):
GAATTTTGTGATTTATT
Found at i:5428683 original size:46 final size:46
Alignment explanation
Indices: 5428613--5428751 Score: 233
Period size: 46 Copynumber: 3.0 Consensus size: 46
5428603 CATGGCAAAG
*
5428613 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
5428659 TGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
5428705 TGTGAAAAGTAGGTATGGTATTCCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
5428751 T
1 T
5428752 ATAGCCTTGT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:5440420 original size:13 final size:13
Alignment explanation
Indices: 5440402--5440442 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
5440392 TATCATATTT
5440402 TATATTTCAAAAA
1 TATATTTCAAAAA
5440415 TATATTT-ATAAAA
1 TATATTTCA-AAAA
5440428 -ATATTTCAAAAA
1 TATATTTCAAAAA
5440440 TAT
1 TAT
5440443 TTTATTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATTTCAAAAA
Found at i:5451974 original size:23 final size:24
Alignment explanation
Indices: 5451948--5452001 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
5451938 GACGGCTGGT
5451948 GAGAGGAAGACAAGT-G-GAGAAAG
1 GAGAGGAA-ACAAGTGGAGAGAAAG
* *
5451971 GAGATTGAAACACGTGGAGAGAAAG
1 GAGA-GGAAACAAGTGGAGAGAAAG
5451996 GAGAGG
1 GAGAGG
5452002 TGGGGAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 9 0.36
24 5 0.20
25 11 0.44
ACGTcount: A:0.44, C:0.06, G:0.43, T:0.07
Consensus pattern (24 bp):
GAGAGGAAACAAGTGGAGAGAAAG
Found at i:5453519 original size:3 final size:3
Alignment explanation
Indices: 5453511--5453536 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5453501 GTCCACAGTT
5453511 AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AG
5453537 GCATTGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:5456316 original size:520 final size:519
Alignment explanation
Indices: 5455335--5456377 Score: 2041
Period size: 520 Copynumber: 2.0 Consensus size: 519
5455325 ACAATATAAG
5455335 AGGAGTTCGACTACATCTATTTAAGGGTTAAACAACCTTGCTATAGTCAATGTATAATAGAATAA
1 AGGAGTTCGACTACATCTATTTAAGGGTTAAACAACCTTGCTATAGTCAATGTATAATAGAATAA
*
5455400 GCATAGTCCTATACAAGAGGAGTTCGGCCCTCGGTCCTTCGCCCTATAGATCCTCCTATTTTGCC
66 GCATAGTCCTATACAAGAGGAGTTCGGCCCTCGGTCCTTCGCCCCATAGATCCTCCTATTTTGCC
5455465 TTTCTATTTTATTTCTTTAACACGTAACGAGATTCGGGTCACACAACTCTAACATTGAAAGAAAA
131 TTTCTATTTTATTTCTTTAACACGTAACGAGATTCGGGTCACACAACTCTAACATTGAAAGAAAA
5455530 ACCTAAAGCCCACAAGGACAAAATGAAGATTAAGTAATAATCACATCGTCCAACACCATTCAGGT
196 ACCTAAAGCCCACAAGGACAAAATGAAGATTAAGTAATAATCACATCGTCCAACACCATTCAGGT
*
5455595 AGCCCAAACCAAAATCAAAAGAGCAATAATTACCTATGGACCGATGGATGAGACTGTGAGTAACC
261 AGCCCAAACCAAAATCAAAAGAGCAATAATTACCTATGGACCGATGGATGAGACTGTAAGTAACC
5455660 TCATTGGTAAATCAAGGAACAAAACGAAAAGTGATAAGATCAAAATTAATACAAAGTCTGCGAGC
326 TCATTGGTAAATCAAGGAACAAAACGAAAAGTGATAAGATCAAAATTAATACAAAGTCTGCGAGC
*
5455725 CTCTACAAGCTCCTTCCCTGTCAATTGATCTCCAATGAATTAAAAAGACACTTAATGCTTTAAAC
391 CTCTACAAGCTCCTTCCCTGTCAATTGATCTCCAATGAATTAAAAAAACACTTAATGCTTTAAAC
5455790 ATTTTTTTTTTGCCATAAAAAGGAACTTCATTACCATAAGGGAAAAAAGATACAAACAAAACAAA
456 A-TTTTTTTTTGCCATAAAAAGGAACTTCATTACCATAAGGGAAAAAAGATACAAACAAAACAAA
5455855 AGGAGTTCGACTACATCTATTTAAGGGTTAAACAACCTTGCTATAGTCAATGTATAATAGAATAA
1 AGGAGTTCGACTACATCTATTTAAGGGTTAAACAACCTTGCTATAGTCAATGTATAATAGAATAA
5455920 GCATAGTCCTATACAAGAGGAGTTCGGCCCTCGGTCCTTCGCCCCATAGATCCTCCTATTTTGCC
66 GCATAGTCCTATACAAGAGGAGTTCGGCCCTCGGTCCTTCGCCCCATAGATCCTCCTATTTTGCC
5455985 TTTCTATTTTATTTCTTTAACACGTAACGAGATTCGGGTCACACAACTCTAACATTGAAAGAAAA
131 TTTCTATTTTATTTCTTTAACACGTAACGAGATTCGGGTCACACAACTCTAACATTGAAAGAAAA
*
5456050 ACCTAAAGCCCACAAGGACAAAATGAAGATTAAGTAATAATCATATCGTCCAACACCATTCAGGT
196 ACCTAAAGCCCACAAGGACAAAATGAAGATTAAGTAATAATCACATCGTCCAACACCATTCAGGT
5456115 AGCCCAAACCAAAATCAAAAGAGCAATAATTACCTATGGACCGATGGATGAGACTGTAAGTAACC
261 AGCCCAAACCAAAATCAAAAGAGCAATAATTACCTATGGACCGATGGATGAGACTGTAAGTAACC
5456180 TCATTGGTAAATCAAGGAACAAAACGAAAAGTGATAAGATCAAAATTAATACAAAGTCTGCGAGC
326 TCATTGGTAAATCAAGGAACAAAACGAAAAGTGATAAGATCAAAATTAATACAAAGTCTGCGAGC
5456245 CTCTACAAGCTCCTTCCCTGTCAATTGATCTCCAATGAATTAAAAAAACACTTAATGCTTTAAAC
391 CTCTACAAGCTCCTTCCCTGTCAATTGATCTCCAATGAATTAAAAAAACACTTAATGCTTTAAAC
5456310 ATTTTTTTTTGCCATAAAAAGGAACTTCATTACCATAAGGGAAAAAAGATACAAACAAAACAAA
456 ATTTTTTTTTGCCATAAAAAGGAACTTCATTACCATAAGGGAAAAAAGATACAAACAAAACAAA
5456374 AGGA
1 AGGA
5456378 AACATGCTGA
Statistics
Matches: 519, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
519 67 0.13
520 452 0.87
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.26
Consensus pattern (519 bp):
AGGAGTTCGACTACATCTATTTAAGGGTTAAACAACCTTGCTATAGTCAATGTATAATAGAATAA
GCATAGTCCTATACAAGAGGAGTTCGGCCCTCGGTCCTTCGCCCCATAGATCCTCCTATTTTGCC
TTTCTATTTTATTTCTTTAACACGTAACGAGATTCGGGTCACACAACTCTAACATTGAAAGAAAA
ACCTAAAGCCCACAAGGACAAAATGAAGATTAAGTAATAATCACATCGTCCAACACCATTCAGGT
AGCCCAAACCAAAATCAAAAGAGCAATAATTACCTATGGACCGATGGATGAGACTGTAAGTAACC
TCATTGGTAAATCAAGGAACAAAACGAAAAGTGATAAGATCAAAATTAATACAAAGTCTGCGAGC
CTCTACAAGCTCCTTCCCTGTCAATTGATCTCCAATGAATTAAAAAAACACTTAATGCTTTAAAC
ATTTTTTTTTGCCATAAAAAGGAACTTCATTACCATAAGGGAAAAAAGATACAAACAAAACAAA
Found at i:5457823 original size:27 final size:28
Alignment explanation
Indices: 5457793--5457926 Score: 107
Period size: 27 Copynumber: 5.0 Consensus size: 28
5457783 GCTCTAAAGT
* *
5457793 AATCTAAT-TAGAGTACCCCACAAAGGC
1 AATCTAATACAGAGTACGCCACAAAGGC
* **
5457820 AATC-CATACAGAGTATACCACAAAGGC
1 AATCTAATACAGAGTACGCCACAAAGGC
* *
5457847 AACCT-ATACAGAGTACGCCACAAAGGT
1 AATCTAATACAGAGTACGCCACAAAGGC
* * *
5457874 GAT-TCATTCAGAGTACGCCACAAAGGC
1 AATCTAATACAGAGTACGCCACAAAGGC
* * * *
5457901 TATCT-ATACAAAGTATGCCCCAAAGG
1 AATCTAATACAGAGTACGCCACAAAGG
5457927 TGATTCATTC
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
26 3 0.03
27 82 0.95
28 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (28 bp):
AATCTAATACAGAGTACGCCACAAAGGC
Found at i:5457861 original size:54 final size:54
Alignment explanation
Indices: 5457802--5457953 Score: 144
Period size: 54 Copynumber: 2.8 Consensus size: 54
5457792 TAATCTAATT
*
5457802 AGAGTACCCCACAAAGGCAATCCATACAGAGTATACCACAAAGGCAACCTATAC
1 AGAGTACCCCACAAAGGCAATCCATACAGAGTACACCACAAAGGCAACCTATAC
* ** * * * * *
5457856 AGAGTACGCCACAAAGGTGATTCATTCAGAGTACGCCACAAAGGCTATCTATAC
1 AGAGTACCCCACAAAGGCAATCCATACAGAGTACACCACAAAGGCAACCTATAC
* * ** * * *
5457910 AAAGTATGCCC-CAAAGGTGATTCATTCAGAGTACACTACAAAGG
1 AGAGTA-CCCCACAAAGGCAATCCATACAGAGTACACCACAAAGG
5457954 TTGACAGAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 81 0.98
55 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (54 bp):
AGAGTACCCCACAAAGGCAATCCATACAGAGTACACCACAAAGGCAACCTATAC
Found at i:5457942 original size:27 final size:27
Alignment explanation
Indices: 5457855--5457954 Score: 114
Period size: 27 Copynumber: 3.7 Consensus size: 27
5457845 GCAACCTATA
5457855 CAGAGTACGCCACAAAGGTGATTCATT
1 CAGAGTACGCCACAAAGGTGATTCATT
*
5457882 CAGAGTACGCCACAAAGGCT-A-TCTATA
1 CAGAGTACGCCACAAAGG-TGATTC-ATT
* * *
5457909 CAAAGTATGCCCCAAAGGTGATTCATT
1 CAGAGTACGCCACAAAGGTGATTCATT
* *
5457936 CAGAGTACACTACAAAGGT
1 CAGAGTACGCCACAAAGGT
5457955 TGACAGAATG
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
26 3 0.05
27 53 0.90
28 3 0.05
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (27 bp):
CAGAGTACGCCACAAAGGTGATTCATT
Found at i:5458342 original size:20 final size:22
Alignment explanation
Indices: 5458303--5458342 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
5458293 TCAAGCAGAC
*
5458303 TAACTTATATCTTCTTTAATCA
1 TAACTTATATCTTCTATAATCA
5458325 TAACTT-TAT-TTCTATAAT
1 TAACTTATATCTTCTATAAT
5458343 TGTATAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (22 bp):
TAACTTATATCTTCTATAATCA
Found at i:5463573 original size:20 final size:20
Alignment explanation
Indices: 5463541--5463594 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
5463531 TATATAAATA
*
5463541 ATTTTAAAAAATAAAAACAC
1 ATTTTATAAAATAAAAACAC
* *
5463561 A-TTTATAATAAT-ATAACTC
1 ATTTTATAA-AATAAAAACAC
5463580 ATTTTATAAAATAAA
1 ATTTTATAAAATAAA
5463595 TAGTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTTTATAAAATAAAAACAC
Found at i:5471185 original size:29 final size:29
Alignment explanation
Indices: 5471152--5471209 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
5471142 ATTTTATTGT
5471152 TAATTTTGTTATTATTTTAAAGGCATTTG
1 TAATTTTGTTATTATTTTAAAGGCATTTG
*
5471181 TAATTTTGTTATTATTTTATAGGCATTTG
1 TAATTTTGTTATTATTTTAAAGGCATTTG
5471210 CTTGTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (29 bp):
TAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:5476470 original size:23 final size:23
Alignment explanation
Indices: 5476443--5476487 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5476433 AGTCATGGTT
*
5476443 TTTGATTACTTTCATTAGTCACG
1 TTTGATTACTTTCACTAGTCACG
*
5476466 TTTGATTACTTTCGCTAGTCAC
1 TTTGATTACTTTCACTAGTCAC
5476488 ATCAATATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (23 bp):
TTTGATTACTTTCACTAGTCACG
Found at i:5489194 original size:6 final size:6
Alignment explanation
Indices: 5489183--5489207 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5489173 AACAAGAAGA
5489183 GATGTG GATGTG GATGTG GATGTG G
1 GATGTG GATGTG GATGTG GATGTG G
5489208 GGCGAGGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GATGTG
Found at i:5489781 original size:20 final size:19
Alignment explanation
Indices: 5489738--5489789 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
5489728 AATAACATCA
5489738 AAACAACAACAAACAGTAG
1 AAACAACAACAAACAGTAG
* * *
5489757 AAACAACAGCAAAGTAGTGG
1 AAACAACAACAAA-CAGTAG
*
5489777 AAACAATAACAAA
1 AAACAACAACAAA
5489790 ACACAATAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.62, C:0.17, G:0.13, T:0.08
Consensus pattern (19 bp):
AAACAACAACAAACAGTAG
Found at i:5490469 original size:20 final size:20
Alignment explanation
Indices: 5490444--5490483 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5490434 AATATTTTCC
*
5490444 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
5490464 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
5490484 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:5490489 original size:34 final size:35
Alignment explanation
Indices: 5490432--5490498 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
5490422 CAAACACTAG
*
5490432 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
5490467 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
5490499 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5497306 original size:21 final size:22
Alignment explanation
Indices: 5497251--5497312 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
5497241 TATAAAAAAT
*
5497251 AATTTATTACAAAAAAATTAGA
1 AATTAATTACAAAAAAATTAGA
* *
5497273 AA--AATTTATAAAAATATTAGA
1 AATTAA-TTACAAAAAAATTAGA
*
5497294 AATTAATTAAAAACAAAAT
1 AATTAATTACAAA-AAAAT
5497313 ATATAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
20 1 0.03
21 16 0.52
22 8 0.26
23 6 0.19
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (22 bp):
AATTAATTACAAAAAAATTAGA
Found at i:5497328 original size:27 final size:26
Alignment explanation
Indices: 5497283--5497334 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
5497273 AAAATTTATA
*
5497283 AAAATATTAGAAATTAATTA-AAAAC
1 AAAATATTAAAAATTAATTATAAAAC
5497308 AAAATATATAAAAATTAAATTATAAAA
1 AAAATAT-TAAAAATT-AATTATAAAA
5497335 TTTTATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 7 0.30
27 5 0.22
28 4 0.17
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
AAAATATTAAAAATTAATTATAAAAC
Found at i:5498680 original size:2 final size:2
Alignment explanation
Indices: 5498673--5498710 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
5498663 ATATTTATAC
* *
5498673 AG AG AG AG AG AG AG GG AG AG AG AG AG AA AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5498711 TTAATTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5499082 original size:6 final size:6
Alignment explanation
Indices: 5499075--5499135 Score: 83
Period size: 6 Copynumber: 10.7 Consensus size: 6
5499065 CAAACCACAA
* *
5499075 CAACAA CAACAG CATCAG C-A-A- CAACAG CAACAG CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
5499120 CAACAG CAACAG CAAC
1 CAACAG CAACAG CAAC
5499136 GGGAACATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 1 0.02
6 45 0.92
ACGTcount: A:0.51, C:0.34, G:0.13, T:0.02
Consensus pattern (6 bp):
CAACAG
Found at i:5499098 original size:15 final size:15
Alignment explanation
Indices: 5499072--5499130 Score: 73
Period size: 15 Copynumber: 3.7 Consensus size: 15
5499062 CGGCAAACCA
*
5499072 CAACAACAACAACAG
1 CAACAGCAACAACAG
*
5499087 CATCAGCAACAACAG
1 CAACAGCAACAACAG
5499102 CAACAGCAACAGCAACAG
1 CAACAGC-A-A-CAACAG
5499120 CAACAGCAACA
1 CAACAGCAACA
5499131 GCAACGGGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
15 21 0.55
16 2 0.05
17 2 0.05
18 13 0.34
ACGTcount: A:0.53, C:0.34, G:0.12, T:0.02
Consensus pattern (15 bp):
CAACAGCAACAACAG
Found at i:5499098 original size:21 final size:21
Alignment explanation
Indices: 5499072--5499135 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
5499062 CGGCAAACCA
*
5499072 CAACAACAACAACAGCATCAG
1 CAACAACAACAACAGCAACAG
*
5499093 CAACAACAGCAACAGCAACAG
1 CAACAACAACAACAGCAACAG
*
5499114 ---CAACAGCAACAGCAACAG
1 CAACAACAACAACAGCAACAG
5499132 CAAC
1 CAAC
5499136 GGGAACATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 18 0.47
21 20 0.53
ACGTcount: A:0.52, C:0.34, G:0.12, T:0.02
Consensus pattern (21 bp):
CAACAACAACAACAGCAACAG
Found at i:5505370 original size:39 final size:41
Alignment explanation
Indices: 5505292--5505378 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 41
5505282 TAAAAAGTAT
* * * *
5505292 TTATATTAACAAATACTACCATAAATATAATAGATATTTT-C
1 TTATATTAAAAAACACTA-CATAAATATAATAAACATTTTAC
5505333 TTATATTAAAAAACACTA-ATAAATATAATAAACATTTTAC
1 TTATATTAAAAAACACTACATAAATATAATAAACATTTTAC
5505373 -TATATT
1 TTATATT
5505379 TAATATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 24 0.59
40 1 0.02
41 16 0.39
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.39
Consensus pattern (41 bp):
TTATATTAAAAAACACTACATAAATATAATAAACATTTTAC
Found at i:5510908 original size:19 final size:19
Alignment explanation
Indices: 5510884--5510923 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5510874 ATTTTTAAAA
5510884 AATTATATCTT-TATTTTTT
1 AATTAT-TCTTATATTTTTT
*
5510903 AATTATTTTTATATTTTTT
1 AATTATTCTTATATTTTTT
5510922 AA
1 AA
5510924 ATTTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
AATTATTCTTATATTTTTT
Found at i:5511144 original size:20 final size:20
Alignment explanation
Indices: 5511098--5511145 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5511088 CTGTTTTTTA
*
5511098 TTTTATATATTATAATATAAT
1 TTTTA-ATATTATAACATAAT
*
5511119 TATTAATATTATGAACAT-AT
1 TTTTAATATTAT-AACATAAT
5511139 TTTTAAT
1 TTTTAAT
5511146 GGTTTGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTAATATTATAACATAAT
Found at i:5515865 original size:19 final size:20
Alignment explanation
Indices: 5515838--5515880 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
5515828 GTCCACGTGT
*
5515838 AATTCATAAAAAT-TTAAAA
1 AATTAATAAAAATATTAAAA
*
5515857 AATTAATAAAAATATTTAAA
1 AATTAATAAAAATATTAAAA
5515877 AATT
1 AATT
5515881 CAACAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTAATAAAAATATTAAAA
Found at i:5516904 original size:7 final size:7
Alignment explanation
Indices: 5516894--5516923 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5516884 AAATTTTACG
5516894 TTTTTAT
1 TTTTTAT
5516901 TTTTTAT
1 TTTTTAT
5516908 TTTTTAT
1 TTTTTAT
5516915 TTTTTAT
1 TTTTTAT
5516922 TT
1 TT
5516924 CAGTCGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:5533888 original size:33 final size:32
Alignment explanation
Indices: 5533803--5533992 Score: 100
Period size: 33 Copynumber: 5.7 Consensus size: 32
5533793 GTTTTCTTTG
** * *
5533803 TGCCATAGTCCAACTATGATCTTACA-CATGCAT
1 TGCCATAACCCAACTATGGTCTTACATCA-G-AA
* * * *
5533836 TACCATGACCCAACCATGGTCTTACATTC-GTAG
1 TGCCATAACCCAACTATGGTCTTACA-TCAG-AA
* * *
5533869 TGTCATAACTCAATTATGGTCTTATCATCAGAA
1 TGCCATAACCCAACTATGGTCTTA-CATCAGAA
*
5533902 TGCCATAACCCAACTATGGTCTTACTTAT-AAATA
1 TGCCATAACCCAACTATGGTCTTAC--ATCAGA-A
** *
5533936 CTGCCATAGTCCAACCATGGTCTTACATTCA-AA
1 -TGCCATAACCCAACTATGGTCTTACA-TCAGAA
**
5533969 TAGCCATAACCCAGTTATGGTCTT
1 T-GCCATAACCCAACTATGGTCTT
5533993 TTCATTAAAA
Statistics
Matches: 119, Mismatches: 27, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
32 2 0.02
33 85 0.71
34 8 0.07
35 24 0.20
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (32 bp):
TGCCATAACCCAACTATGGTCTTACATCAGAA
Found at i:5533950 original size:35 final size:34
Alignment explanation
Indices: 5533901--5534061 Score: 109
Period size: 35 Copynumber: 4.7 Consensus size: 34
5533891 TATCATCAGA
*
5533901 ATGCCATAACCCAACTATGGTCTTACTTATAAAT
1 ATGCCATAATCCAACTATGGTCTTACTTATAAAT
* * *
5533935 ACTGCCATAGTCCAACCATGGTCTTACATT-CAAAT
1 A-TGCCATAATCCAACTATGGTCTTAC-TTATAAAT
* **
5533970 A-GCCATAACCCAGTTATGGTCTT--TTCATTAAA-
1 ATGCCATAATCCAACTATGGTCTTACTT-A-TAAAT
* *
5534002 ATGCCAT-ATCTCAGCTATAGTCTTACTTATAAAT
1 ATGCCATAATC-CAACTATGGTCTTACTTATAAAT
* ** *
5534036 ACTACCATGGTCCAACCATGGTCTTA
1 A-TGCCATAATCCAACTATGGTCTTA
5534062 TCCGTCAATT
Statistics
Matches: 97, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
30 2 0.02
32 3 0.03
33 40 0.41
34 3 0.03
35 45 0.46
36 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (34 bp):
ATGCCATAATCCAACTATGGTCTTACTTATAAAT
Found at i:5533977 original size:101 final size:101
Alignment explanation
Indices: 5533845--5534061 Score: 292
Period size: 101 Copynumber: 2.1 Consensus size: 101
5533835 TTACCATGAC
* * * * *
5533845 CCAACCATGGTCTTACATTCGTAGTGTCATAACTCAATTATGGTCTTATCATCAGAATGCCATAA
1 CCAACCATGGTCTTACATTCGAAATGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAA
* *
5533910 CCCAACTATGGTCTTACTTATAAATACTGCCATAGT
66 CCCAACTATAGTCTTACTTATAAATACTACCATAGT
* * *
5533946 CCAACCATGGTCTTACATTC-AAATAGCCATAACCCAGTTATGGTCTTTTCATTAAAATGCCATA
1 CCAACCATGGTCTTACATTCGAAAT-GCCATAACCCAATTATGGTCTTATCATCAAAATGCCATA
* * * *
5534010 TCTCAGCTATAGTCTTACTTATAAATACTACCATGGT
65 ACCCAACTATAGTCTTACTTATAAATACTACCATAGT
5534047 CCAACCATGGTCTTA
1 CCAACCATGGTCTTA
5534062 TCCGTCAATT
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
100 2 0.02
101 99 0.98
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (101 bp):
CCAACCATGGTCTTACATTCGAAATGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAA
CCCAACTATAGTCTTACTTATAAATACTACCATAGT
Found at i:5534008 original size:33 final size:33
Alignment explanation
Indices: 5533872--5534009 Score: 102
Period size: 33 Copynumber: 4.1 Consensus size: 33
5533862 TTCGTAGTGT
* * * * *
5533872 CATAACTCAATTATGGTCTTATCATCAGAATGC
1 CATAACCCAACTATGGTCTTTTCATTAAAATGC
5533905 CATAACCCAACTATGGTCTTACTT-A-TAAATACTGC
1 CATAACCCAACTATGGTCTT--TTCATTAAA-A-TGC
** * * *
5533940 CATAGTCCAACCATGGTC-TTACATTCAAATAGC
1 CATAACCCAACTATGGTCTTTTCATTAAAAT-GC
**
5533973 CATAACCCAGTTATGGTCTTTTCATTAAAATGC
1 CATAACCCAACTATGGTCTTTTCATTAAAATGC
5534006 CATA
1 CATA
5534010 TCTCAGCTAT
Statistics
Matches: 80, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
32 2 0.03
33 43 0.54
34 16 0.20
35 19 0.24
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (33 bp):
CATAACCCAACTATGGTCTTTTCATTAAAATGC
Found at i:5534025 original size:33 final size:34
Alignment explanation
Indices: 5533961--5534025 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 34
5533951 CATGGTCTTA
* * *
5533961 CATTCAAATAGCCATAACCCAGTTATGGTCTTTT
1 CATTAAAATAGCCATAACCCAGCTATAGTCTTTT
* *
5533995 CATTAAAAT-GCCATATCTCAGCTATAGTCTT
1 CATTAAAATAGCCATAACCCAGCTATAGTCTT
5534026 ACTTATAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
33 18 0.69
34 8 0.31
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (34 bp):
CATTAAAATAGCCATAACCCAGCTATAGTCTTTT
Found at i:5536778 original size:25 final size:23
Alignment explanation
Indices: 5536734--5536794 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
5536724 TGGTATTTAA
*
5536734 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
5536758 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
5536783 ATATTATTAAAT
1 ATATAATTAAAT
5536795 GAATTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:5537091 original size:3 final size:3
Alignment explanation
Indices: 5537083--5537114 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5537073 AAATGATTAA
5537083 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5537115 ATTGTGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5538621 original size:51 final size:45
Alignment explanation
Indices: 5538511--5538615 Score: 165
Period size: 45 Copynumber: 2.3 Consensus size: 45
5538501 ATGTGCCGAC
*
5538511 TACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGT
* * *
5538556 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATAATGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGT
*
5538601 CACTGTTACTGTTAC
1 TACTGTTACTGTTAC
5538616 TGTTACCATT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGT
Found at i:5541152 original size:17 final size:17
Alignment explanation
Indices: 5541130--5541238 Score: 87
Period size: 17 Copynumber: 6.5 Consensus size: 17
5541120 ACGACTATAC
5541130 TTTATATGCAAGTTGTG
1 TTTATATGCAAGTTGTG
** *
5541147 TTTATATGTGAGTTGTC
1 TTTATATGCAAGTTGTG
* *
5541164 TTTATATGTAAGCTG-G
1 TTTATATGCAAGTTGTG
* * *
5541180 GTTATATGCGAGTTGTA
1 TTTATATGCAAGTTGTG
* * * *
5541197 TGTATATGCGAGCTATG
1 TTTATATGCAAGTTGTG
*
5541214 TTTATACGCAAGTTGTG
1 TTTATATGCAAGTTGTG
5541231 -TTATATGC
1 TTTATATGC
5541239 GAACTGCGTT
Statistics
Matches: 69, Mismatches: 22, Indels: 3
0.73 0.23 0.03
Matches are distributed among these distances:
16 18 0.26
17 51 0.74
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (17 bp):
TTTATATGCAAGTTGTG
Found at i:5541193 original size:33 final size:34
Alignment explanation
Indices: 5541129--5541270 Score: 110
Period size: 33 Copynumber: 4.2 Consensus size: 34
5541119 AACGACTATA
* * *
5541129 CTTTATATGCAAGTTGTGTTTATATGTGAGTTGT
1 CTTTATATGCAAGCTGTGGTTATATGCGAGTTGT
*
5541163 CTTTATATGTAAGCTG-GGTTATATGCGAGTTGT
1 CTTTATATGCAAGCTGTGGTTATATGCGAGTTGT
* * * * * * *
5541196 ATGTATATGCGAGCTATGTTTATACGCAAGTTGT
1 CTTTATATGCAAGCTGTGGTTATATGCGAGTTGT
* * * * *
5541230 -GTTATATGCGAA-CTGCGTTTATATGTGTGTTGT
1 CTTTATATGC-AAGCTGTGGTTATATGCGAGTTGT
5541263 CTTTATAT
1 CTTTATAT
5541271 TCGAGCTATG
Statistics
Matches: 83, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
33 48 0.58
34 35 0.42
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (34 bp):
CTTTATATGCAAGCTGTGGTTATATGCGAGTTGT
Found at i:5541194 original size:50 final size:50
Alignment explanation
Indices: 5541131--5541270 Score: 145
Period size: 50 Copynumber: 2.8 Consensus size: 50
5541121 CGACTATACT
* *
5541131 TTATATGCAAGTTGTGTTTATATGTGAGTTGTCTTTATATGTAAGCTGGG
1 TTATATGCGAGTTGTGTTTATATGTGAGTTGTCTTTATATGCAAGCTGGG
* * * * * * * * *
5541181 TTATATGCGAGTTGTATGTATATGCGAGCTATGTTTATACGCAAGTTGTG
1 TTATATGCGAGTTGTGTTTATATGTGAGTTGTCTTTATATGCAAGCTGGG
** * *
5541231 TTATATGCGAACTGCGTTTATATGTGTGTTGTCTTTATAT
1 TTATATGCGAGTTGTGTTTATATGTGAGTTGTCTTTATAT
5541271 TCGAGCTATG
Statistics
Matches: 68, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (50 bp):
TTATATGCGAGTTGTGTTTATATGTGAGTTGTCTTTATATGCAAGCTGGG
Found at i:5545639 original size:5 final size:5
Alignment explanation
Indices: 5545629--5545654 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5545619 TGAGCATTCG
5545629 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
5545655 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:5548853 original size:50 final size:50
Alignment explanation
Indices: 5548778--5548876 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
5548768 TTCAGAATTC
*
5548778 TGACTTCTGATATATAAAACATAAGGAAGAATACGTTTTGTTGGTAAAAT
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTTGGTAAAAT
* *
5548828 TGACTTCTGGTATATAAAACATAAGGAAGGATACATTTTGTTGGTAAAA
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTTGGTAAAA
5548877 AACTGACTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.33
Consensus pattern (50 bp):
TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTTGGTAAAAT
Found at i:5557482 original size:24 final size:24
Alignment explanation
Indices: 5557455--5557506 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
5557445 TGAGGGGGAG
5557455 TATTGAGAATCTTTGATTATTTGA
1 TATTGAGAATCTTTGATTATTTGA
5557479 TATTGAGAATCTTTGATTATTTGA
1 TATTGAGAATCTTTGATTATTTGA
5557503 TATT
1 TATT
5557507 ATTAAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.15, T:0.52
Consensus pattern (24 bp):
TATTGAGAATCTTTGATTATTTGA
Found at i:5566982 original size:15 final size:14
Alignment explanation
Indices: 5566951--5566980 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5566941 TCATATAAAA
5566951 TTATTAAAGATGAT
1 TTATTAAAGATGAT
*
5566965 TTATTTAAGATGAT
1 TTATTAAAGATGAT
5566979 TT
1 TT
5566981 TAAATTGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TTATTAAAGATGAT
Found at i:5575671 original size:23 final size:24
Alignment explanation
Indices: 5575627--5575673 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5575617 TTTTTTTTAA
* * *
5575627 TTTCGAATTTAAATCGAGTTAAAT
1 TTTCGAATTCAAATCAACTTAAAT
5575651 TTTCGAATTCAAAT-AACTTAAAT
1 TTTCGAATTCAAATCAACTTAAAT
5575674 AAATCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (24 bp):
TTTCGAATTCAAATCAACTTAAAT
Found at i:5589536 original size:19 final size:19
Alignment explanation
Indices: 5589487--5589538 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
5589477 TTCTCATAAA
5589487 AAATATTAAAAA-ATTATG
1 AAATATTAAAAATATTATG
* * * *
5589505 AAAAATCATAAATATTATT
1 AAATATTAAAAATATTATG
5589524 AAATATTAAAAATAT
1 AAATATTAAAAATAT
5589539 ACAATCACAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATATTAAAAATATTATG
Found at i:5596641 original size:24 final size:24
Alignment explanation
Indices: 5596589--5596641 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
5596579 CTAATTTTTT
* *
5596589 AGAA-TAATATATTTAAATTTTAA
1 AGAATTAATATATTTAAAGTGTAA
*
5596612 AAAATTAATATTATTTAAAGTGT-A
1 AGAATTAATA-TATTTAAAGTGTAA
5596636 AGAATT
1 AGAATT
5596642 GCATTATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.12
24 11 0.46
25 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (24 bp):
AGAATTAATATATTTAAAGTGTAA
Found at i:5600126 original size:27 final size:27
Alignment explanation
Indices: 5599999--5600130 Score: 174
Period size: 27 Copynumber: 4.9 Consensus size: 27
5599989 TTTCATCTCC
*
5599999 TAGGGGTATTTCGATCATTTTACCCTA
1 TAGGGGTATTTCGGTCATTTTACCCTA
* *
5600026 TGGGGGTATTTCGGCCATTTTACCCTA
1 TAGGGGTATTTCGGTCATTTTACCCTA
* * *
5600053 TAGGGGTATTTCAGTCATTTAACCTTA
1 TAGGGGTATTTCGGTCATTTTACCCTA
**
5600080 TAATGGTATTTCGGTCATTTTACCCTA
1 TAGGGGTATTTCGGTCATTTTACCCTA
* *
5600107 TAGGGGTATTTTGGTTATTTTACC
1 TAGGGGTATTTCGGTCATTTTACC
5600131 TATTTTTGGG
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (27 bp):
TAGGGGTATTTCGGTCATTTTACCCTA
Found at i:5600756 original size:73 final size:73
Alignment explanation
Indices: 5600637--5600779 Score: 225
Period size: 73 Copynumber: 2.0 Consensus size: 73
5600627 GAAAATCAAT
* *
5600637 TGTCGAAACCATCTTTTCCAAAATTTGAAAAAATAGGGATCGACTTTTAAAATGAAAGCTGGAGT
1 TGTCGAAACCATCTTTTACAAAATTTGAAAAAATAGGGATCGACTTTTAAAATGAAAACTGGAGT
5600702 CGCCAAGC
66 CGCCAAGC
* *
5600710 TGTCGAAACCATCTTTTACGAAATTTGAAAAACA-GGGGATCGACTTTTAAAATGAAAACTGGAG
1 TGTCGAAACCATCTTTTACAAAATTTGAAAAA-ATAGGGATCGACTTTTAAAATGAAAACTGGAG
*
5600774 TTGCCA
65 TCGCCA
5600780 CCGATCTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 63 0.98
74 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (73 bp):
TGTCGAAACCATCTTTTACAAAATTTGAAAAAATAGGGATCGACTTTTAAAATGAAAACTGGAGT
CGCCAAGC
Found at i:5601662 original size:27 final size:26
Alignment explanation
Indices: 5601606--5601663 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
5601596 GTTAACACTT
* *
5601606 AAAAACTAAAGAATTTAAAGTTCATC
1 AAAAACTAAAGAAATTAAAGTGCATC
* * *
5601632 AAAACACTAAATAAATTAATGTGCATG
1 AAAA-ACTAAAGAAATTAAAGTGCATC
5601659 AAAAA
1 AAAAA
5601664 TGTATGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.57, C:0.10, G:0.09, T:0.24
Consensus pattern (26 bp):
AAAAACTAAAGAAATTAAAGTGCATC
Found at i:5603857 original size:43 final size:44
Alignment explanation
Indices: 5603808--5604128 Score: 145
Period size: 43 Copynumber: 7.5 Consensus size: 44
5603798 ATACGATCTA
*
5603808 CTCCACTACTGCTT-AGGGAGATAAGATCTATTATTTTAATCCG
1 CTCCACTACTGCTTCAGGGAGATAAGATCTATTATTTCAATCCG
* ** * * * *
5603851 CTCCACTGCAACTTCAGGGAGATAGGAT-TGATT-TCTCAGTCTG
1 CTCCACTACTGCTTCAGGGAGATAAGATCT-ATTATTTCAATCCG
* * ** * *
5603894 CCCCACT-GTGACTTCAAGGG-GATAAGA-CT-CGA-TGCAATCTG
1 CTCCACTACTG-CTTC-AGGGAGATAAGATCTATTATTTCAATCCG
* *
5603935 CTCCACTACTGCTT-AGGGAGATAAGATCTATTGTTTTAATCCG
1 CTCCACTACTGCTTCAGGGAGATAAGATCTATTATTTCAATCCG
* ** * * *
5603978 CTCCACTGCAACTTCAGGGAGATAGGAT-TGATT-TTTCAGTCTG
1 CTCCACTACTGCTTCAGGGAGATAAGATCT-ATTATTTCAATCCG
* * ** * * *
5604021 CCCCACT-GTGACTTCAAGGG-GATAAGA-CT-CGA-TGCGATCTG
1 CTCCACTACTG-CTTC-AGGGAGATAAGATCTATTATTTCAATCCG
* * * *
5604062 CTCCACTACTGCTT-AAGGAGATAAGATCTATTGTTTTAATCCA
1 CTCCACTACTGCTTCAGGGAGATAAGATCTATTATTTCAATCCG
* **
5604105 CTCCACTGCAACTTCAGGGAGATA
1 CTCCACTACTGCTTCAGGGAGATA
5604129 GGATTGATTT
Statistics
Matches: 197, Mismatches: 58, Indels: 45
0.66 0.19 0.15
Matches are distributed among these distances:
39 7 0.04
40 14 0.07
41 34 0.17
42 4 0.02
43 92 0.47
44 46 0.23
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTCAGGGAGATAAGATCTATTATTTCAATCCG
Found at i:5603950 original size:127 final size:127
Alignment explanation
Indices: 5603763--5604155 Score: 687
Period size: 127 Copynumber: 3.1 Consensus size: 127
5603753 TCGACTTCAA
* * *
5603763 TCTGCTCCACTGTGACTTCAAGGGGATAAGACTCGATACGATCTACTCCACTACTGCTTAGGGAG
1 TCTGCCCCACTGTGACTTCAAGGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAGGGAG
*
5603828 ATAAGATCTATTATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTCAG
66 ATAAGATCTATTGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTCAG
*
5603890 TCTGCCCCACTGTGACTTCAAGGGGATAAGACTCGATGCAATCTGCTCCACTACTGCTTAGGGAG
1 TCTGCCCCACTGTGACTTCAAGGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAGGGAG
*
5603955 ATAAGATCTATTGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTTTCAG
66 ATAAGATCTATTGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTCAG
*
5604017 TCTGCCCCACTGTGACTTCAAGGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAAGGAG
1 TCTGCCCCACTGTGACTTCAAGGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAGGGAG
* *
5604082 ATAAGATCTATTGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTCCTG
66 ATAAGATCTATTGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCT-CAG
*
5604145 TCTGCTCCACT
1 TCTGCCCCACT
5604156 ATTGCTTAGG
Statistics
Matches: 253, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
127 241 0.95
128 12 0.05
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (127 bp):
TCTGCCCCACTGTGACTTCAAGGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAGGGAG
ATAAGATCTATTGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTCAG
Found at i:5604285 original size:87 final size:87
Alignment explanation
Indices: 5604194--5604438 Score: 235
Period size: 87 Copynumber: 2.8 Consensus size: 87
5604184 TCCAACCTAT
* * *
5604194 TCCACTACTGGTCAGGGACATAGGACTT-GTGGCTTAAATCTGTTTCCCTACTCATGGGAAAGAT
1 TCCACTACTGCTCAGGGACATAAGA-TTAATGGCTTAAATCTGTTTCCCTACTCATGGGAAAGAT
* *
5604258 AAGATTCGCCGTTTTGGATCTGC
65 AAGATTCGCCGTCTTCGATCTGC
* * * * * *
5604281 TCCACTATTGCTTAGGGAGATAAGATTAATGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATG
1 TCCACTACTGCTCAGGGACATAAGATTAATGGCTTAAATCTGTTTCCCTACTCATGGGAAAGATA
*
5604346 AGATTCGCCGTCTTCGATCTGTT
66 AGATTCGCCGTCTTCGATCTG-C
** * ** * *** * *
5604369 TCC-CTACT-CTTGGGGAAGATAAGATTCGTAGCTCGGATCTGTTTCCCTACTCCTGGGGAAGAT
1 TCCACTACTGCTCAGGG-ACATAAGATTAATGGCTTAAATCTGTTTCCCTACTCATGGGAAAGAT
5604432 AAGATTC
65 AAGATTC
5604439 ATAGCTTGGA
Statistics
Matches: 134, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
86 8 0.06
87 123 0.92
88 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (87 bp):
TCCACTACTGCTCAGGGACATAAGATTAATGGCTTAAATCTGTTTCCCTACTCATGGGAAAGATA
AGATTCGCCGTCTTCGATCTGC
Found at i:5604350 original size:43 final size:43
Alignment explanation
Indices: 5604231--5604570 Score: 369
Period size: 43 Copynumber: 7.9 Consensus size: 43
5604221 TGTGGCTTAA
* * ** *
5604231 ATCTGTTTCCCTACTCATGGGAAAGATAAGATTCGCCGTTTTGG
1 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTAG-CTTGG
* * * * ** * **
5604275 ATCTG-CTCCACTATTGCTTAGGG-AGATAAGATTAATGGCTTAA
1 ATCTGTTTCC-CTACT-CCTGGGGAAGATAAGATTCGTAGCTTGG
* ** *
5604318 ATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCG
1 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTAG-CTTGG
* *
5604362 ATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGTAGCTCGG
1 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTAGCTTGG
*
5604405 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCATAGCTTGG
1 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTAGCTTGG
** *
5604448 ATCTCATTCCCTACTCCTGGGGAAGATAAGATTCGCAGCTTGG
1 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTAGCTTGG
* **
5604491 ATCTCTTTCCCTACTCCCAGGGAAGATAAGATTCGTAGCTTGG
1 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTAGCTTGG
* *
5604534 ATCTGTTTCCTTACTCCTGGGGAAGATAAGATCCGTA
1 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTA
5604571 ATATTCACTG
Statistics
Matches: 246, Mismatches: 45, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
42 5 0.02
43 177 0.72
44 60 0.24
45 4 0.02
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (43 bp):
ATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTAGCTTGG
Found at i:5605803 original size:14 final size:13
Alignment explanation
Indices: 5605780--5605837 Score: 64
Period size: 15 Copynumber: 4.2 Consensus size: 13
5605770 AGCCTCTCCA
5605780 TTTTACTTTTCATT
1 TTTTA-TTTTCATT
5605794 TTTTCATTTTCATTT
1 TTTT-ATTTTCA-TT
5605809 TTTTATTTTTCATCT
1 TTTTA-TTTTCAT-T
5605824 TTTTATTTT-ATT
1 TTTTATTTTCATT
5605836 TT
1 TT
5605838 ATTGTCTCGT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 2 0.05
14 16 0.40
15 19 0.47
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTTCATT
Found at i:5605812 original size:15 final size:14
Alignment explanation
Indices: 5605780--5605837 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
5605770 AGCCTCTCCA
5605780 TTTTACTTTTCATTT
1 TTTTA-TTTTCATTT
*
5605795 TTTCATTTTCATTT
1 TTTTATTTTCATTT
*
5605809 TTTTATTTTTCATCT
1 TTTTA-TTTTCATTT
5605824 TTTTATTTT-ATTT
1 TTTTATTTTCATTT
5605837 T
1 T
5605838 ATTGTCTCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 4 0.11
14 17 0.45
15 17 0.45
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTTCATTT
Found at i:5605818 original size:29 final size:28
Alignment explanation
Indices: 5605780--5605837 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
5605770 AGCCTCTCCA
5605780 TTTTACTTTTCAT-TTTTTCATTTTCATTT
1 TTTTACTTTTCATCTTTTT-ATTTT-ATTT
*
5605809 TTTTATTTTTCATCTTTTTATTTTATTT
1 TTTTACTTTTCATCTTTTTATTTTATTT
5605837 T
1 T
5605838 ATTGTCTCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 17 0.63
30 5 0.19
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTACTTTTCATCTTTTTATTTTATTT
Found at i:5606912 original size:12 final size:12
Alignment explanation
Indices: 5606895--5606919 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5606885 ATGAGTACCG
5606895 AAGAATGTATAA
1 AAGAATGTATAA
5606907 AAGAATGTATAA
1 AAGAATGTATAA
5606919 A
1 A
5606920 TTCATTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
AAGAATGTATAA
Found at i:5610070 original size:73 final size:73
Alignment explanation
Indices: 5609951--5610107 Score: 262
Period size: 73 Copynumber: 2.2 Consensus size: 73
5609941 GCATCCCCAG
**
5609951 TGGAGTCGCCAAGCTGTCGAAACCATCTTTTCTAAAATTTGAAAAAATGGGGATCGACTTTTAAA
1 TGGAGTCGCCAAGCTGTCGAAACCATCTTTTCTAAAATTTGAAAAAACAGGGATCGACTTTTAAA
5610016 ATGAAAAC
66 ATGAAAAC
*
5610024 TGGAGTCGCCAAGCTGTCGAAACCATCTTTTCTGAAA-TTGAAAAAAACAGGGATCGACTTTTAA
1 TGGAGTCGCCAAGCTGTCGAAACCATCTTTTCTAAAATTTG-AAAAAACAGGGATCGACTTTTAA
*
5610088 AATTAAAAC
65 AATGAAAAC
5610097 TGGAGTCGCCA
1 TGGAGTCGCCA
5610108 CCGAGCTTTT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
72 3 0.04
73 76 0.96
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (73 bp):
TGGAGTCGCCAAGCTGTCGAAACCATCTTTTCTAAAATTTGAAAAAACAGGGATCGACTTTTAAA
ATGAAAAC
Found at i:5610989 original size:27 final size:26
Alignment explanation
Indices: 5610933--5610990 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
5610923 GTTAACACTT
* *
5610933 AAAAACTAAAGAATTTAAAGTTCATC
1 AAAAACTAAAGAAATTAAAGTGCATC
* * *
5610959 AAAACACTAAATAAATTAATGTGCATG
1 AAAA-ACTAAAGAAATTAAAGTGCATC
5610986 AAAAA
1 AAAAA
5610991 TGTATGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.57, C:0.10, G:0.09, T:0.24
Consensus pattern (26 bp):
AAAAACTAAAGAAATTAAAGTGCATC
Found at i:5624077 original size:4 final size:4
Alignment explanation
Indices: 5624068--5624134 Score: 55
Period size: 4 Copynumber: 16.2 Consensus size: 4
5624058 CTAACTTTTC
* * *
5624068 TCTT TCTT TCTT TCTCT T-TT TCTT TCCTT TCTT TCCT TCTC TGTT TCGTT
1 TCTT TCTT TCTT TCT-T TCTT TCTT T-CTT TCTT TCTT TCTT TCTT TC-TT
* *
5624118 TCTT TCTC TCAT TCTT T
1 TCTT TCTT TCTT TCTT T
5624135 ATCTATTTCT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
3 2 0.04
4 37 0.76
5 10 0.20
ACGTcount: A:0.01, C:0.28, G:0.03, T:0.67
Consensus pattern (4 bp):
TCTT
Found at i:5624086 original size:21 final size:21
Alignment explanation
Indices: 5624062--5624126 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
5624052 GAAACCCTAA
5624062 CTTTTCTCTTTCTTTCTTTCT
1 CTTTTCTCTTTCTTTCTTTCT
5624083 CTTTT-TCTTTCCTTTCTTTC-
1 CTTTTCTCTTT-CTTTCTTTCT
* *
5624103 CTTCTCTGTTTCGTTTCTTTCT
1 CTTTTCTCTTTC-TTTCTTTCT
5624125 CT
1 CT
5624127 CATTCTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 10 0.26
21 26 0.68
22 2 0.05
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (21 bp):
CTTTTCTCTTTCTTTCTTTCT
Found at i:5624099 original size:25 final size:26
Alignment explanation
Indices: 5624064--5624124 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
5624054 AACCCTAACT
* *
5624064 TTTCTCTTTCTTTCTTTCTCTTTTTC-
1 TTTC-CTTTCTTTCCTTCTCTGTTTCG
5624090 TTTCCTTTCTTTCCTTCTCTGTTTCG
1 TTTCCTTTCTTTCCTTCTCTGTTTCG
5624116 TTT-CTTTCT
1 TTTCCTTTCT
5624125 CTCATTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (26 bp):
TTTCCTTTCTTTCCTTCTCTGTTTCG
Found at i:5624132 original size:25 final size:25
Alignment explanation
Indices: 5624068--5624132 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
5624058 CTAACTTTTC
* *
5624068 TCTTTCTTTCTTTCTCTTTTTC-TT
1 TCTTTCTTTCATTCTCTGTTTCGTT
*
5624092 TCCTTTCTTTCCTTCTCTGTTTCGTT
1 T-CTTTCTTTCATTCTCTGTTTCGTT
*
5624118 TCTTTCTCTCATTCT
1 TCTTTCTTTCATTCT
5624133 TTATCTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.03
25 31 0.89
26 3 0.09
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (25 bp):
TCTTTCTTTCATTCTCTGTTTCGTT
Found at i:5624167 original size:5 final size:5
Alignment explanation
Indices: 5624157--5624228 Score: 144
Period size: 5 Copynumber: 14.4 Consensus size: 5
5624147 TTCTTTTACT
5624157 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
5624207 TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TA
5624229 CTTAACTTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 67 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:5625442 original size:21 final size:22
Alignment explanation
Indices: 5625400--5625449 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
5625390 CTTTTATTCG
* *
5625400 AAACATGTGATTTAATGGCTAA
1 AAACATGTGATTTAAAGACTAA
*
5625422 AAACATG-GCTTTAAAGACTAA
1 AAACATGTGATTTAAAGACTAA
5625443 ATAACAT
1 A-AACAT
5625450 TTAAAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (22 bp):
AAACATGTGATTTAAAGACTAA
Found at i:5627813 original size:15 final size:16
Alignment explanation
Indices: 5627785--5627815 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5627775 TTAATAAAAG
5627785 TATTTTTAATTAATAT
1 TATTTTTAATTAATAT
5627801 TATTTTT-ATTAATAT
1 TATTTTTAATTAATAT
5627816 ACTAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAATTAATAT
Found at i:5629039 original size:22 final size:22
Alignment explanation
Indices: 5629013--5629060 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
5629003 TATTTTTCAC
*
5629013 TATTGTTTTGCTGCCATTTTGA
1 TATTGTTTTGCTACCATTTTGA
*
5629035 TATTGTTTTGCTACCATTTTGC
1 TATTGTTTTGCTACCATTTTGA
5629057 TATT
1 TATT
5629061 ATTGTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (22 bp):
TATTGTTTTGCTACCATTTTGA
Found at i:5631400 original size:31 final size:31
Alignment explanation
Indices: 5631365--5631432 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
5631355 TTTTGGGTTC
* *
5631365 AATTTGATACCTAAGCTTCACACTTTTTAC-T
1 AATTTGACACCTAAACTTCACACTTTTT-CTT
* *
5631396 AATTTCACACCTAAACTTGACACTTTTTCTT
1 AATTTGACACCTAAACTTCACACTTTTTCTT
5631427 AATTTG
1 AATTTG
5631433 GTACTTAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (31 bp):
AATTTGACACCTAAACTTCACACTTTTTCTT
Found at i:5631498 original size:90 final size:90
Alignment explanation
Indices: 5631307--5631499 Score: 212
Period size: 90 Copynumber: 2.1 Consensus size: 90
5631297 TAATATAAAC
* * * * *
5631307 ATTTGATATCTGAATTTGACACTTTTTCTTAATTTGGTATCTAAGAGTTTTTGGGTTCAATTTGA
1 ATTTGATACCTAAACTTGACACTTTTTCTTAATTTGGTATCTAAGACTTTTTGGGGTCAATTTGA
5631372 TACCTAAGCTTCACACTTTTTACTA
66 TACCTAAGCTTCACACTTTTTACTA
* * *
5631397 ATTTCACACCTAAACTTGACACTTTTTCTTAATTTGGTA-CTTAA-TCTTTTTGGGGTCAAATTT
1 ATTTGATACCTAAACTTGACACTTTTTCTTAATTTGGTATC-TAAGACTTTTTGGGGTC-AATTT
* * * ** *
5631460 GGTATCTGAA-CTTGATTCTTTTTCCTA
64 GATACCT-AAGCTTCACACTTTTTACTA
5631487 ATTTGATACCTAA
1 ATTTGATACCTAA
5631500 TCTTTTTTTT
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
89 11 0.13
90 71 0.85
91 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.46
Consensus pattern (90 bp):
ATTTGATACCTAAACTTGACACTTTTTCTTAATTTGGTATCTAAGACTTTTTGGGGTCAATTTGA
TACCTAAGCTTCACACTTTTTACTA
Found at i:5631969 original size:32 final size:32
Alignment explanation
Indices: 5631932--5632001 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
5631922 AGCTTAGGTG
5631932 CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
1 CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
* *** * *
5631964 CCAAATTGGGCCTAAAATATTAAGTTTAAGTA
1 CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
5631996 CCAAAT
1 CCAAAT
5632002 ATTATATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (32 bp):
CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
Found at i:5633597 original size:13 final size:13
Alignment explanation
Indices: 5633563--5633598 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
5633553 TTATATACAC
5633563 TTAAAAATT-ATA
1 TTAAAAATTAATA
5633575 -TAAAAA-TAATA
1 TTAAAAATTAATA
5633586 TTAAAAATTAATA
1 TTAAAAATTAATA
5633599 CGTGTAGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.05
11 9 0.43
12 6 0.29
13 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAATTAATA
Found at i:5634909 original size:30 final size:29
Alignment explanation
Indices: 5634873--5634934 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
5634863 ACTTAACAAG
5634873 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAA-AAAATTAA
* *
5634903 CAAATGTCTTTAAAATAATAATAAATTAA
1 CAAATGTCTCTAAAATAATAAAAAATTAA
5634932 CAA
1 CAA
5634935 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.29
Consensus pattern (29 bp):
CAAATGTCTCTAAAATAATAAAAAATTAA
Found at i:5644313 original size:73 final size:73
Alignment explanation
Indices: 5644194--5644337 Score: 225
Period size: 73 Copynumber: 2.0 Consensus size: 73
5644184 ATTGTCTCAG
* * * *
5644194 GGTAGGTCACTTTATAACCTTACCCTCAATTGGGAGCATGCAATTGTTATCAATACCTTGTCATA
1 GGTAGGTCACTTTATAACCTTACCCTCAATTGGGAGCAAGAAATTGTTATCAATACATTGCCATA
5644259 ACACACAT
66 ACACACAT
** *
5644267 GGTAGGTCACTTTATAACCTTACCCTTGATTGGGGGCAAGAAATTGTTATCAATACATTGCCATA
1 GGTAGGTCACTTTATAACCTTACCCTCAATTGGGAGCAAGAAATTGTTATCAATACATTGCCATA
5644332 ACACAC
66 ACACAC
5644338 CTTGCCACCC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (73 bp):
GGTAGGTCACTTTATAACCTTACCCTCAATTGGGAGCAAGAAATTGTTATCAATACATTGCCATA
ACACACAT
Done.