Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 77 of 189
Found at i:21566848 original size:43 final size:43
Alignment explanation
Indices: 21566785--21567052 Score: 351
Period size: 43 Copynumber: 6.3 Consensus size: 43
21566775 TTATAGAAAT
** *
21566785 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
* * *
21566828 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGTGCTTTT-CTAGA
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCA-C
* * * *
21566871 AAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTT-TCGC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
*
21566913 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
* * *
21566956 AAACACCGCTAAAGGCCATGTTCTTTAGCGGCACTTTTTCCAC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
** * *
21566999 AAACGCCATTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCAT
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
21567042 AAACGCCGCTA
1 AAACGCCGCTA
21567053 TTGTTTGGTG
Statistics
Matches: 192, Mismatches: 31, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
42 37 0.19
43 155 0.81
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
Found at i:21567013 original size:128 final size:128
Alignment explanation
Indices: 21566785--21567036 Score: 398
Period size: 128 Copynumber: 2.0 Consensus size: 128
21566775 TTATAGAAAT
* ** *
21566785 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTT
1 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCAAAAACACCGCTAAAGGCCATGTT
** *
21566850 CTTTAGCGGTGCTTTTCTAGAAAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCGC
66 CTTTAGCGGCACTTTTCCAGAAAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCGC
*
21566913 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAAAAACACCGCTAAAGGCCATGTT
1 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCAAAAACACCGCTAAAGGCCATGTT
* *
21566978 CTTTAGCGGCACTTTTTCCA-CAAACGCCATTAAAGGTCATGTTCTTTAGCGGCGCTTTT
66 CTTTAGCGGCAC-TTTTCCAGAAAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTT
21567037 CCCATAAACG
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
128 107 0.95
129 6 0.05
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (128 bp):
AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCAAAAACACCGCTAAAGGCCATGTT
CTTTAGCGGCACTTTTCCAGAAAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCGC
Found at i:21567038 original size:86 final size:86
Alignment explanation
Indices: 21566785--21567052 Score: 396
Period size: 86 Copynumber: 3.1 Consensus size: 86
21566775 TTATAGAAAT
* *
21566785 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTT
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCCGCAAACGCCGCTAAAGGCCATGTT
* *
21566850 CTTTAGCGGTGCTTTT-CTAGA
66 CTTTAGCGGCGCTTTTCCCA-A
*
21566871 AAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTTT-CGCAAACGCCGCTAAAGGCCATGTT
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCCGCAAACGCCGCTAAAGGCCATGTT
21566935 CTTTAGCGGCGCTTTTCCCAA
66 CTTTAGCGGCGCTTTTCCCAA
* * * * ** *
21566956 AAACACCGCTAAAGGCCATGTTCTTTAGCGGCACTTTTTCCACAAACGCCATTAAAGGTCATGTT
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCCGCAAACGCCGCTAAAGGCCATGTT
*
21567021 CTTTAGCGGCGCTTTTCCCAT
66 CTTTAGCGGCGCTTTTCCCAA
21567042 AAACGCCGCTA
1 AAACGCCGCTA
21567053 TTGTTTGGTG
Statistics
Matches: 165, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
85 76 0.46
86 89 0.54
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (86 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCCGCAAACGCCGCTAAAGGCCATGTT
CTTTAGCGGCGCTTTTCCCAA
Found at i:21567089 original size:86 final size:85
Alignment explanation
Indices: 21566807--21567096 Score: 294
Period size: 86 Copynumber: 3.4 Consensus size: 85
21566797 AGATCATGTT
* * * * *
21566807 CTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTTCTTTAGCGGTGCTTTT-CTAGA
1 CTTTAGCGGCGCTTTT-TCACAAACGCCACTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCA-A
* * * **
21566871 AAACGCCACTAAAGGTCATGTT
64 AAACACCGCTAAAGGCCATGGC
* *
21566893 CTTTAGCGGCGCTTTTTCGCAAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAAAA
1 CTTTAGCGGCGCTTTTTCACAAACGCCACTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAAAA
**
21566958 ACACCGCTAAAGGCCATGTT
66 ACACCGCTAAAGGCCATGGC
* * * *
21566978 CTTTAGCGGCACTTTTTCCACAAACGCCATTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCATA
1 CTTTAGCGGCGCTTTTT-CACAAACGCCACTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAAA
* ** ****
21567043 AACGCCGCTATTGTTTGGTGGC
65 AACACCGCTAAAG-GCCATGGC
* *
21567065 CTTTAGCGGCGCTTTTTTAAAAACGCCACTAA
1 CTTTAGCGGCGCTTTTTCACAAACGCCACTAA
21567097 TTTTGAGATT
Statistics
Matches: 176, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
85 76 0.43
86 82 0.47
87 18 0.10
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (85 bp):
CTTTAGCGGCGCTTTTTCACAAACGCCACTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAAAA
ACACCGCTAAAGGCCATGGC
Found at i:21567743 original size:17 final size:17
Alignment explanation
Indices: 21567721--21567780 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
21567711 ATATATTTTA
21567721 AAATTATTAAGTTATGT
1 AAATTATTAAGTTATGT
** *
21567738 AAATTATGCGAGTTGT-T
1 AAATTAT-TAAGTTATGT
*
21567755 AAGTTATTAAGTTATGT
1 AAATTATTAAGTTATGT
*
21567772 AAGTTATTA
1 AAATTATTA
21567781 TGTGAATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
16 5 0.15
17 24 0.71
18 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.45
Consensus pattern (17 bp):
AAATTATTAAGTTATGT
Found at i:21567766 original size:34 final size:36
Alignment explanation
Indices: 21567724--21567807 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 36
21567714 TATTTTAAAA
* *
21567724 TTATTAAGTTATGTAA-ATTATGCGAGTTGT-TAAG
1 TTATTAAGTTATGTAATATTATGCGAATTATATAAG
*
21567758 TTATTAAGTTATGTAAGTTATTATGTGAATTATATAAG
1 TTATTAAGTTATGTAA--TATTATGCGAATTATATAAG
21567796 TTATTAAGTTAT
1 TTATTAAGTTAT
21567808 ATGGTATGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 16 0.37
37 11 0.26
38 16 0.37
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.48
Consensus pattern (36 bp):
TTATTAAGTTATGTAATATTATGCGAATTATATAAG
Found at i:21567803 original size:46 final size:46
Alignment explanation
Indices: 21567748--21567908 Score: 133
Period size: 46 Copynumber: 3.3 Consensus size: 46
21567738 AAATTATGCG
*
21567748 AGTTGTTAAGTTATTAAGTTATGTAAGTTATTATGTGAATTATATA
1 AGTTATTAAGTTATTAAGTTATGTAAGTTATTATGTGAATTATATA
* * * * * *
21567794 AGTTATTAAGTTATATGGTATGACATATATATATATATGTATTATGTAAATTATGTG
1 AGTTATTAAG-T-TAT--TA--A-GT-TATGTA-A-GT-TATTATGTGAATTATATA
* * *
21567851 AGTTGTTAAGTTGTTCAGTTATGTAAGTTATTATGTGAATTATATA
1 AGTTATTAAGTTATTAAGTTATGTAAGTTATTATGTGAATTATATA
21567897 AGTTATTAAGTT
1 AGTTATTAAGTT
21567909 GGACATTTTT
Statistics
Matches: 87, Mismatches: 17, Indels: 22
0.69 0.13 0.17
Matches are distributed among these distances:
46 35 0.40
47 2 0.02
48 4 0.05
49 5 0.06
50 3 0.03
51 1 0.01
52 1 0.01
53 2 0.02
54 5 0.06
55 3 0.03
56 2 0.02
57 24 0.28
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.47
Consensus pattern (46 bp):
AGTTATTAAGTTATTAAGTTATGTAAGTTATTATGTGAATTATATA
Found at i:21567807 original size:8 final size:8
Alignment explanation
Indices: 21567724--21567780 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 8
21567714 TATTTTAAAA
21567724 TTATTAAG
1 TTATTAAG
*
21567732 TTATGTAAA
1 TTAT-TAAG
**
21567741 TTATGCGAG
1 TTAT-TAAG
*
21567750 TTGTTAAG
1 TTATTAAG
21567758 TTATTAAG
1 TTATTAAG
21567766 TTATGTAAG
1 TTAT-TAAG
21567775 TTATTA
1 TTATTA
21567781 TGTGAATTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
8 19 0.49
9 20 0.51
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (8 bp):
TTATTAAG
Found at i:21567809 original size:17 final size:17
Alignment explanation
Indices: 21567754--21567809 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
21567744 TGCGAGTTGT
*
21567754 TAAGTTATTAAGTTATG
1 TAAGTTATTAAGTTATA
*
21567771 TAAGTTATTATGTGAATTATA
1 TAAGTTATTA----AGTTATA
21567792 TAAGTTATTAAGTTATA
1 TAAGTTATTAAGTTATA
21567809 T
1 T
21567810 GGTATGACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 17 0.53
21 15 0.47
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (17 bp):
TAAGTTATTAAGTTATA
Found at i:21568545 original size:21 final size:21
Alignment explanation
Indices: 21568521--21568567 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
21568511 TTAACTATTT
* *
21568521 AAATTAGTTAATGATATTGTA
1 AAATTAGATAATGAAATTGTA
* *
21568542 AAATTAGATGATTAAATTGTA
1 AAATTAGATAATGAAATTGTA
21568563 AAATT
1 AAATT
21568568 TCAAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (21 bp):
AAATTAGATAATGAAATTGTA
Found at i:21570305 original size:31 final size:31
Alignment explanation
Indices: 21570262--21570321 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
21570252 ACAGCCGCCC
*
21570262 CAATTTATTGGCTAAGCCTAACAATGCCTAA
1 CAATGTATTGGCTAAGCCTAACAATGCCTAA
21570293 CAATGTATTGGCTAAGCCTAACAATGCCT
1 CAATGTATTGGCTAAGCCTAACAATGCCT
21570322 CCGCATCGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (31 bp):
CAATGTATTGGCTAAGCCTAACAATGCCTAA
Found at i:21572139 original size:100 final size:104
Alignment explanation
Indices: 21571956--21572164 Score: 291
Period size: 100 Copynumber: 2.0 Consensus size: 104
21571946 GCAAAATTTT
* * *
21571956 TTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAAAGTTTTTATTTTGTTTTTTTATAA
1 TTTCATTTTGAACAAAACGACACCGTTTTGCTATGCT--AAAG-TTTTATTTTGATTTTTTATAA
*
21572021 ATTGATTTATTTTTTGCGGCGTTTCTATAAAAAACGCTGCTA
63 ATTGATTTATTTTTTGCGGCGTTTCTATAAAAAACGCCGCTA
*
21572063 TTTCATTTTGAACAAAATGACACCGTTTTGCTATGCT-AA-TTTT-TTTT-ATTTTTTATAAATT
1 TTTCATTTTGAACAAAACGACACCGTTTTGCTATGCTAAAGTTTTATTTTGATTTTTTATAAATT
* * *
21572124 GATTTATTTTTTGCGGCGTTTTTATAGAAAATGCCGCTA
66 GATTTATTTTTTGCGGCGTTTCTATAAAAAACGCCGCTA
21572163 TT
1 TT
21572165 GCTTACAAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
100 50 0.53
101 4 0.04
102 4 0.04
104 2 0.02
107 34 0.36
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.48
Consensus pattern (104 bp):
TTTCATTTTGAACAAAACGACACCGTTTTGCTATGCTAAAGTTTTATTTTGATTTTTTATAAATT
GATTTATTTTTTGCGGCGTTTCTATAAAAAACGCCGCTA
Found at i:21572204 original size:115 final size:116
Alignment explanation
Indices: 21572063--21572287 Score: 398
Period size: 117 Copynumber: 1.9 Consensus size: 116
21572053 AACGCTGCTA
*
21572063 TTTCATTTTGAACAAAATGACACCGTTTTGCTATGCTAATTTTTTTTA-TTTTTTATAAATTGAT
1 TTTCATTTTGAACAAAACGACACCGTTTTGCTATGCTAATTTTTTTTATTTTTTTATAAATTGAT
*
21572127 TTATTTTTTGCGGCGTTTTTATAGAAAATGCCGCTATTGCTTACAAATTTT
66 TTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACAAATTTT
* *
21572178 TTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCTAATTTTTTTTATTTTTTTTATAAATTGA
1 TTTCATTTTGAACAAAACGACACCGTTTTGCTATGCTAATTTTTTTTA-TTTTTTTATAAATTGA
21572243 TTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTAC
65 TTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTAC
21572288 CTTTAGCGGC
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
115 45 0.43
117 59 0.57
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.49
Consensus pattern (116 bp):
TTTCATTTTGAACAAAACGACACCGTTTTGCTATGCTAATTTTTTTTATTTTTTTATAAATTGAT
TTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACAAATTTT
Found at i:21572513 original size:136 final size:136
Alignment explanation
Indices: 21572267--21572531 Score: 458
Period size: 136 Copynumber: 1.9 Consensus size: 136
21572257 CGTTTTTATA
21572267 GAAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATGT
1 GAAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATGT
* * **
21572332 TGAACAAAACGACGCCGTTTTGCTATTCTAATTTTTTTTATTTTTTTTATAAATTGATTTATTTT
66 TGAACAAAACAACGCCATTTTGCTATTCTAAAATTTTTTATTTTTTTTATAAATTGATTTATTTT
21572397 TTGCCT
131 TTGCCT
*
21572403 GAAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTT
1 GAAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATGT
* *
21572468 TGAACAAAATAACGCCATTTTGCTATTCTAAAAATTTTTTATTTTTTTTATAAGTTGATTTATT
66 TGAACAAAACAACGCCATTTTGCTATTCT-AAAATTTTTTATTTTTTTTATAAATTGATTTATT
21572532 ACCTTTAGCG
Statistics
Matches: 121, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
136 90 0.74
137 31 0.26
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (136 bp):
GAAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATGT
TGAACAAAACAACGCCATTTTGCTATTCTAAAATTTTTTATTTTTTTTATAAATTGATTTATTTT
TTGCCT
Found at i:21572687 original size:14 final size:14
Alignment explanation
Indices: 21572668--21572701 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
21572658 AACCTTAAAT
* *
21572668 CCCTAACTTTTAAC
1 CCCTAACATCTAAC
21572682 CCCTAACATCTAAC
1 CCCTAACATCTAAC
21572696 CCCTAA
1 CCCTAA
21572702 ACCCCTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.26
Consensus pattern (14 bp):
CCCTAACATCTAAC
Found at i:21572706 original size:8 final size:8
Alignment explanation
Indices: 21572693--21572727 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
21572683 CCTAACATCT
21572693 AACCCCTA
1 AACCCCTA
21572701 AACCCCTA
1 AACCCCTA
*
21572709 AACCACT-
1 AACCCCTA
21572716 AACCCCTA
1 AACCCCTA
21572724 AACC
1 AACC
21572728 TTAAATCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.40, C:0.49, G:0.00, T:0.11
Consensus pattern (8 bp):
AACCCCTA
Found at i:21572721 original size:23 final size:22
Alignment explanation
Indices: 21572679--21572727 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
21572669 CCTAACTTTT
21572679 AACCCCTAACATCTAACCCCTA
1 AACCCCTAACATCTAACCCCTA
21572701 AACCCCTAAACCA-CTAACCCCTA
1 AACCCCT-AA-CATCTAACCCCTA
21572724 AACC
1 AACC
21572728 TTAAATCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.28
23 16 0.64
24 2 0.08
ACGTcount: A:0.39, C:0.47, G:0.00, T:0.14
Consensus pattern (22 bp):
AACCCCTAACATCTAACCCCTA
Found at i:21572989 original size:22 final size:23
Alignment explanation
Indices: 21572964--21573007 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
21572954 CCCCTGAATC
*
21572964 CCTAA-CTTTTAATCCCTAAACA
1 CCTAACCTTTTAACCCCTAAACA
21572986 CCTAACCTTTTAACCCCTAAAC
1 CCTAACCTTTTAACCCCTAAAC
21573008 CTTAAATCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (23 bp):
CCTAACCTTTTAACCCCTAAACA
Found at i:21573492 original size:114 final size:114
Alignment explanation
Indices: 21573292--21573658 Score: 612
Period size: 114 Copynumber: 3.2 Consensus size: 114
21573282 TAAAATATTT
21573292 TTAGCGGCGCTTT-TCTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGC
1 TTAGCGGCGCTTTCT-TAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGC
21573356 TTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCA
65 TTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCA
*
21573406 TTAGCGGCGCTTTCTTCAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCT
1 TTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCT
*
21573471 TAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAATCCCTGAGCA
66 TAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCA
* * *
21573520 TTAGCGGTGCTTTCTTATAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCT
1 TTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCT
* * * * *
21573585 TAGGTTTTTTTGCAGTGCTTTACGAAAAATGCCGCTAAAG-CCTGAGCA
66 TAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCA
*
21573633 TTAGCGGCGCTTACTTAAAAACGCCG
1 TTAGCGGCGCTTTCTTAAAAACGCCG
21573659 TTAATGCTTA
Statistics
Matches: 236, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
113 30 0.13
114 205 0.87
115 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (114 bp):
TTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCT
TAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCA
Found at i:21573748 original size:12 final size:12
Alignment explanation
Indices: 21573731--21573756 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21573721 TTTTTTGTCC
21573731 AAATGCCGCTAA
1 AAATGCCGCTAA
21573743 AAATGCCGCTAA
1 AAATGCCGCTAA
21573755 AA
1 AA
21573757 GCCTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (12 bp):
AAATGCCGCTAA
Found at i:21574136 original size:6 final size:6
Alignment explanation
Indices: 21574101--21574125 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21574091 ATTATTTGTA
21574101 TGCTTT TGCTTT TGCTTT TGCTTT T
1 TGCTTT TGCTTT TGCTTT TGCTTT T
21574126 TTTTTGTTTT
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:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TGCTTT
Found at i:21579222 original size:159 final size:156
Alignment explanation
Indices: 21578976--21579284 Score: 356
Period size: 159 Copynumber: 2.0 Consensus size: 156
21578966 AGCAGTATCG
* * *
21578976 ACCTCACTAGTCTAGCCTTTTTTTTCTTCTTCATGACATATTTTAGGGTTGAATGGTCGTTGTAG
1 ACCTCACTAATCTAGCCTTTTTTTTCTTCTTCATGACATACTTTAGGGCTGAATGGTCGTTGTAG
* ** * *
21579041 ATATATGCTTGATTCACCATCAAAT-ATGGCCGA-AATTTTTCACATGTAGAAATAACTACTAAC
66 ATATATACTCAATTCACCATCAAATCAT-G-CGAGAATTTTTCACATGCAAAAATAACTACTAAC
*
21579104 ATCTCATTTTTAGTGGTAGTGTGCACCC
129 ATCTCATTTTCAGTGGTAGTGTGCACCC
*
21579132 ACCTCATTAATCTAGCCTTTGTTTATTTCTTCTTCATGACATACTTTAGGGCTGAATTGGTCAG-
1 ACCTCACTAATCTAGCC-TT-TTT-TTTCTTCTTCATGACATACTTTAGGGCTGAA-TGGTC-GT
*** * * * **
21579196 TGTAGATATATACTCAATT-TGTATCAAATCATGCTAGCATTTTTCACATGCAAAAATAATTGTT
61 TGTAGATATATACTCAATTCACCATCAAATCATGCGAGAATTTTTCACATGCAAAAATAACTACT
*
21579260 AACATCTCCTTTTCAGTGGTAGTGT
126 AACATCTCATTTTCAGTGGTAGTGT
21579285 AATTGCACTA
Statistics
Matches: 127, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
156 15 0.12
157 2 0.02
158 5 0.04
159 81 0.64
160 23 0.18
161 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (156 bp):
ACCTCACTAATCTAGCCTTTTTTTTCTTCTTCATGACATACTTTAGGGCTGAATGGTCGTTGTAG
ATATATACTCAATTCACCATCAAATCATGCGAGAATTTTTCACATGCAAAAATAACTACTAACAT
CTCATTTTCAGTGGTAGTGTGCACCC
Found at i:21582193 original size:27 final size:26
Alignment explanation
Indices: 21582156--21582235 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
21582146 TGTAATCATA
* *
21582156 TAGAGTACGCCACCAAGGCTATTCTT
1 TAGAGTTCGCCACCAAAGCTATTCTT
21582182 TCAGAGTTCGCCA-CAAAGCTTATTCATT
1 T-AGAGTTCGCCACCAAAGC-TATTC-TT
** *
21582210 TAGAGTTTTCCACAAAAGCTATTCTT
1 TAGAGTTCGCCACCAAAGCTATTCTT
21582236 AGCTTTTGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
26 8 0.18
27 29 0.64
28 8 0.18
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (26 bp):
TAGAGTTCGCCACCAAAGCTATTCTT
Found at i:21584583 original size:12 final size:12
Alignment explanation
Indices: 21584566--21584592 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21584556 AGAAAATAAT
21584566 AAAAAGATCATA
1 AAAAAGATCATA
21584578 AAAAAGATCATA
1 AAAAAGATCATA
21584590 AAA
1 AAA
21584593 TTGAACCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAAGATCATA
Found at i:21585931 original size:15 final size:15
Alignment explanation
Indices: 21585892--21585925 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
21585882 CATGAATTTG
* *
21585892 ACAGTACACCTTGTA
1 ACAGTACGCCCTGTA
21585907 ACAGTACGCCCTGTA
1 ACAGTACGCCCTGTA
21585922 ACAG
1 ACAG
21585926 CTCGCCTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (15 bp):
ACAGTACGCCCTGTA
Found at i:21590355 original size:23 final size:23
Alignment explanation
Indices: 21590328--21590376 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
21590318 TTGCAAAAAG
21590328 AAACTA-AAAATTAAACTTGAAT-T
1 AAACTAGAAAA-TAAA-TTGAATGT
21590351 AAACTAGAAAATAAATTGAATGT
1 AAACTAGAAAATAAATTGAATGT
21590374 AAA
1 AAA
21590377 AATCTCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.25
23 14 0.58
24 4 0.17
ACGTcount: A:0.59, C:0.06, G:0.08, T:0.27
Consensus pattern (23 bp):
AAACTAGAAAATAAATTGAATGT
Found at i:21598390 original size:16 final size:16
Alignment explanation
Indices: 21598366--21598396 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21598356 TGTTTCTGAG
*
21598366 CATGGCATACTGCATA
1 CATGACATACTGCATA
21598382 CATGACATACTGCAT
1 CATGACATACTGCAT
21598397 GGGGTTAGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (16 bp):
CATGACATACTGCATA
Found at i:21611464 original size:50 final size:49
Alignment explanation
Indices: 21611379--21611487 Score: 148
Period size: 50 Copynumber: 2.2 Consensus size: 49
21611369 GTACATGTAT
* *
21611379 GCTCATACGAGCTATGAATCAGTATGCTCTCACGAGCTGGAAATCAGTAA
1 GCTCATACGAGCTATGAATCAGTAAGCTCTAACGAGCTGG-AATCAGTAA
* * *
21611429 GCTCATACGAGCTGA-GAATTAGTAAGTTCTAACGAGCTGGAATCGGTAA
1 GCTCATACGAGCT-ATGAATCAGTAAGCTCTAACGAGCTGGAATCAGTAA
21611478 GCTCATACGA
1 GCTCATACGA
21611488 TCTGTGGTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
49 18 0.34
50 34 0.64
51 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (49 bp):
GCTCATACGAGCTATGAATCAGTAAGCTCTAACGAGCTGGAATCAGTAA
Found at i:21611477 original size:24 final size:24
Alignment explanation
Indices: 21611379--21611487 Score: 114
Period size: 25 Copynumber: 4.4 Consensus size: 24
21611369 GTACATGTAT
* *
21611379 GCTCATACGAGCTATGAATCAGTAT
1 GCTCATACGAGCT-GGAATCAGTAA
21611404 GCTC-TCACGAGCTGGAAATCAGTAA
1 GCTCAT-ACGAGCTGG-AATCAGTAA
*
21611429 GCTCATACGAGCTGAGAATTAGTAA
1 GCTCATACGAGCTG-GAATCAGTAA
* *
21611454 GTTC-TAACGAGCTGGAATCGGTAA
1 GCTCAT-ACGAGCTGGAATCAGTAA
21611478 GCTCATACGA
1 GCTCATACGA
21611488 TCTGTGGTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
24 18 0.25
25 51 0.72
26 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (24 bp):
GCTCATACGAGCTGGAATCAGTAA
Found at i:21614740 original size:20 final size:19
Alignment explanation
Indices: 21614715--21614752 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
21614705 TTATTGCTAA
21614715 ACCATTCCATTGCAATTTAC
1 ACCATTCCATTGC-ATTTAC
21614735 ACCATTCCATTGCATTTA
1 ACCATTCCATTGCATTTA
21614753 GGTTAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (19 bp):
ACCATTCCATTGCATTTAC
Found at i:21623591 original size:15 final size:15
Alignment explanation
Indices: 21623571--21623600 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21623561 AAAAATTGTA
21623571 AAACAATAATTAGGG
1 AAACAATAATTAGGG
21623586 AAACAATAATTAGGG
1 AAACAATAATTAGGG
21623601 GTTTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (15 bp):
AAACAATAATTAGGG
Found at i:21624672 original size:26 final size:26
Alignment explanation
Indices: 21624612--21624677 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
21624602 ACACCGCAGA
* *
21624612 TCTT-ATGAGCGTCCCGTTATATGGC
1 TCTTCATGAGCTTCCCGTTATAAGGC
21624637 TCTTCATGAGCTTCCCGGTTA-AAGGC
1 TCTTCATGAGCTTCCC-GTTATAAGGC
**
21624663 TCTTTGTGAGCTTCC
1 TCTTCATGAGCTTCC
21624678 TAATTAATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.11
26 27 0.77
27 4 0.11
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (26 bp):
TCTTCATGAGCTTCCCGTTATAAGGC
Found at i:21629502 original size:19 final size:18
Alignment explanation
Indices: 21629467--21629512 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
21629457 GATTGTTTAA
21629467 AATTTTAAAGCCTAAATTC
1 AATTTTAAAGCCTAAA-TC
21629486 AATTTTAAAGCAC-AAATC
1 AATTTTAAAGC-CTAAATC
*
21629504 ATTTTTAAA
1 AATTTTAAA
21629513 AAACATGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 10 0.40
19 14 0.56
20 1 0.04
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (18 bp):
AATTTTAAAGCCTAAATC
Found at i:21636690 original size:17 final size:17
Alignment explanation
Indices: 21636665--21636698 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21636655 AAGCAAACTC
*
21636665 AACAGAAACAAAATAAA
1 AACAAAAACAAAATAAA
*
21636682 AACAAAAACAAACTAAA
1 AACAAAAACAAAATAAA
21636699 TTGAAAATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.15, G:0.03, T:0.06
Consensus pattern (17 bp):
AACAAAAACAAAATAAA
Found at i:21639446 original size:49 final size:49
Alignment explanation
Indices: 21639388--21639485 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
21639378 TAATTGATCA
* *
21639388 AGAACATCTTTCCCTAATTAACATGTTATTAAAGACTAATTATAAGGGT
1 AGAACATCTTTCCATAATTAACATGTTATTAAAGAATAATTATAAGGGT
*
21639437 AGAACATCTTTCTATAATTAACATGTTATTAAAGAATAATTATAAGGGT
1 AGAACATCTTTCCATAATTAACATGTTATTAAAGAATAATTATAAGGGT
21639486 TCATTTACTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (49 bp):
AGAACATCTTTCCATAATTAACATGTTATTAAAGAATAATTATAAGGGT
Found at i:21658249 original size:20 final size:20
Alignment explanation
Indices: 21658211--21658249 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21658201 CTTAATCTAG
** *
21658211 GATAATTAGTTATTTAATTA
1 GATAATTAGGGATTCAATTA
21658231 GATAATTAGGGATTCAATT
1 GATAATTAGGGATTCAATT
21658250 GGTCATAGGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (20 bp):
GATAATTAGGGATTCAATTA
Found at i:21664227 original size:8 final size:8
Alignment explanation
Indices: 21664214--21664258 Score: 54
Period size: 8 Copynumber: 5.1 Consensus size: 8
21664204 TCATTTGAAC
21664214 ATAATTTT
1 ATAATTTT
21664222 ATAATTGTATAT
1 ATAA-T-T-T-T
21664234 ATAATTTT
1 ATAATTTT
21664242 ATAATTTT
1 ATAATTTT
21664250 ATAATTTT
1 ATAATTTT
21664258 A
1 A
21664259 GAAATTGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 22 0.67
9 2 0.06
10 2 0.06
11 2 0.06
12 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
ATAATTTT
Found at i:21664239 original size:20 final size:20
Alignment explanation
Indices: 21664214--21664252 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21664204 TCATTTGAAC
21664214 ATAATTTTATAATTGTATAT
1 ATAATTTTATAATTGTATAT
*
21664234 ATAATTTTATAATTTTATA
1 ATAATTTTATAATTGTATA
21664253 ATTTTAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
ATAATTTTATAATTGTATAT
Found at i:21668200 original size:18 final size:19
Alignment explanation
Indices: 21668169--21668204 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21668159 TTCCATTAGG
21668169 TTAATTTAGGTTAATTAAT
1 TTAATTTAGGTTAATTAAT
*
21668188 TTAA-TTAGTTTAATTAA
1 TTAATTTAGGTTAATTAA
21668205 AATATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TTAATTTAGGTTAATTAAT
Found at i:21672769 original size:27 final size:27
Alignment explanation
Indices: 21672739--21672796 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
21672729 TTGTCCTCCC
* *
21672739 CCTCATCATCA-TCTTCTTCTTCTTCAT
1 CCTCATCATCATTC-TCTTCCTCTTCAA
*
21672766 CCTCATCTTCATTCTCTTCCTCTTCAA
1 CCTCATCATCATTCTCTTCCTCTTCAA
21672793 CCTC
1 CCTC
21672797 TTTTTCCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (27 bp):
CCTCATCATCATTCTCTTCCTCTTCAA
Found at i:21672771 original size:21 final size:21
Alignment explanation
Indices: 21672741--21672784 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21672731 GTCCTCCCCC
21672741 TCATCATCATCTTC-TTCTTCT
1 TCATCATCATCTTCATTC-TCT
*
21672762 TCATCCTCATCTTCATTCTCT
1 TCATCATCATCTTCATTCTCT
21672783 TC
1 TC
21672785 CTCTTCAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.14, C:0.36, G:0.00, T:0.50
Consensus pattern (21 bp):
TCATCATCATCTTCATTCTCT
Found at i:21679355 original size:18 final size:18
Alignment explanation
Indices: 21679322--21679422 Score: 87
Period size: 18 Copynumber: 5.6 Consensus size: 18
21679312 GTGAACCTAT
*
21679322 TATGTTATTA-GCGAACC
1 TATGTTGTTAGGCGAACC
21679339 TATGTTGTTAGGCGAACC
1 TATGTTGTTAGGCGAACC
* * *
21679357 TATATTGCTATGCGAACC
1 TATGTTGTTAGGCGAACC
* * *
21679375 CATGTTATTATGCGAACC
1 TATGTTGTTAGGCGAACC
** *
21679393 TATAATGTTATGTGCAAACC
1 TATGTTGTTA-G-GCGAACC
21679413 TATGTTGTTA
1 TATGTTGTTA
21679423 TCCAAACCTT
Statistics
Matches: 65, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
17 9 0.14
18 42 0.65
20 14 0.22
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (18 bp):
TATGTTGTTAGGCGAACC
Found at i:21679359 original size:38 final size:37
Alignment explanation
Indices: 21679308--21679422 Score: 126
Period size: 38 Copynumber: 3.1 Consensus size: 37
21679298 ACTTATCCCC
*
21679308 TTAGGTGAACCTATTATGTTATTAGCGAACCTATGTTG
1 TTAGGCGAACCTATTATGTTATT-GCGAACCTATGTTG
* * *
21679346 TTAGGCGAACCTA-TATTGCTA-TGCGAACCCATGTTA
1 TTAGGCGAACCTATTA-TGTTATTGCGAACCTATGTTG
* * *
21679382 TTATGCGAACCTATAATGTTATGTGCAAACCTATGTTG
1 TTAGGCGAACCTATTATGTTAT-TGCGAACCTATGTTG
21679420 TTA
1 TTA
21679423 TCCAAACCTT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
36 28 0.44
37 4 0.06
38 31 0.49
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (37 bp):
TTAGGCGAACCTATTATGTTATTGCGAACCTATGTTG
Found at i:21679431 original size:38 final size:37
Alignment explanation
Indices: 21679314--21679423 Score: 132
Period size: 36 Copynumber: 2.9 Consensus size: 37
21679304 CCCCTTAGGT
* *
21679314 GAACCTATTATGTTATTAGCGAACCTATGTTGTTAGGC
1 GAACCTATAATGTTATT-GCGAACCTATGTTGTTATGC
* * * *
21679352 GAACCTATATTGCTA-TGCGAACCCATGTTATTATGC
1 GAACCTATAATGTTATTGCGAACCTATGTTGTTATGC
*
21679388 GAACCTATAATGTTATGTGCAAACCTATGTTGTTAT
1 GAACCTATAATGTTAT-TGCGAACCTATGTTGTTAT
21679424 CCAAACCTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
36 30 0.51
37 1 0.02
38 28 0.47
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (37 bp):
GAACCTATAATGTTATTGCGAACCTATGTTGTTATGC
Found at i:21680471 original size:6 final size:6
Alignment explanation
Indices: 21680429--21680476 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
21680419 GTATATGTAT
* * *
21680429 CATTTC TCATTTT CATTTT CATTTC CATTTC CATTTC CATTTC TATTT
1 CATTTC -CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
21680477 TGAGAAACCT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (6 bp):
CATTTC
Found at i:21685786 original size:22 final size:22
Alignment explanation
Indices: 21685761--21685830 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
21685751 TATTGTTTAG
21685761 TGTTGTTTTGCTGTCATTTTGA
1 TGTTGTTTTGCTGTCATTTTGA
* * *
21685783 TGTTATTTTGTTGTCATTTTGC
1 TGTTGTTTTGCTGTCATTTTGA
* * * * *
21685805 TATTGTATTGCTATTATTTTGT
1 TGTTGTTTTGCTGTCATTTTGA
21685827 TGTT
1 TGTT
21685831 ATTGTTTGGA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.11, C:0.07, G:0.19, T:0.63
Consensus pattern (22 bp):
TGTTGTTTTGCTGTCATTTTGA
Found at i:21685832 original size:11 final size:11
Alignment explanation
Indices: 21685761--21685833 Score: 56
Period size: 11 Copynumber: 6.6 Consensus size: 11
21685751 TATTGTTTAG
*
21685761 TGTTGTTTTGC
1 TGTTATTTTGC
* *
21685772 TGTCATTTTGA
1 TGTTATTTTGC
*
21685783 TGTTATTTTGT
1 TGTTATTTTGC
*
21685794 TGTCATTTTGC
1 TGTTATTTTGC
* * *
21685805 TATTGTATTGC
1 TGTTATTTTGC
* *
21685816 TATTATTTTGT
1 TGTTATTTTGC
21685827 TGTTATT
1 TGTTATT
21685834 GTTTGGATAT
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 47 1.00
ACGTcount: A:0.12, C:0.07, G:0.18, T:0.63
Consensus pattern (11 bp):
TGTTATTTTGC
Found at i:21685858 original size:36 final size:33
Alignment explanation
Indices: 21685785--21685860 Score: 80
Period size: 36 Copynumber: 2.2 Consensus size: 33
21685775 CATTTTGATG
* **
21685785 TTATTTTGTTGTCATTTTGCTATTGTATTGCTA
1 TTATTTTGTTGTCATTTTGATATTGTATAACTA
* *
21685818 TTATTTTGTTGTTATTGTTTGGATATTGTATAACTC
1 TTATTTTGTTGTCA-T-TTT-GATATTGTATAACTA
21685854 TTATTTT
1 TTATTTT
21685861 ATTATAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 13 0.37
34 1 0.03
35 3 0.09
36 18 0.51
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (33 bp):
TTATTTTGTTGTCATTTTGATATTGTATAACTA
Found at i:21695147 original size:17 final size:18
Alignment explanation
Indices: 21695110--21695144 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21695100 TCTCACTATG
21695110 TATATTAGAATTAAAAAA
1 TATATTAGAATTAAAAAA
21695128 TATATTA-AATGTAAAAA
1 TATATTAGAAT-TAAAAA
21695145 TATGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TATATTAGAATTAAAAAA
Found at i:21695843 original size:9 final size:9
Alignment explanation
Indices: 21695829--21695856 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
21695819 TATAGTTTGA
21695829 TATTCGAAT
1 TATTCGAAT
21695838 TATTCGAAT
1 TATTCGAAT
21695847 TATTCGAAT
1 TATTCGAAT
21695856 T
1 T
21695857 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:21695927 original size:9 final size:9
Alignment explanation
Indices: 21695910--21695940 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
21695900 TCGAGTTGAT
21695910 TCGAATAAC
1 TCGAATAAC
*
21695919 TCGATTAAC
1 TCGAATAAC
21695928 TCGAATAAC
1 TCGAATAAC
21695937 TCGA
1 TCGA
21695941 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:21703297 original size:30 final size:30
Alignment explanation
Indices: 21703263--21703320 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
21703253 TTATGGAATT
21703263 TAATATATACT-TCTTTTAATATTTTTATGA
1 TAATAT-TACTATCTTTTAATATTTTTATGA
** *
21703293 TAATATTTTTATCTTTTCATATTTTTAT
1 TAATATTACTATCTTTTAATATTTTTAT
21703321 AAAAGAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (30 bp):
TAATATTACTATCTTTTAATATTTTTATGA
Found at i:21704593 original size:16 final size:15
Alignment explanation
Indices: 21704560--21704589 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21704550 TTAAAATATT
*
21704560 TATTAAAATTAAAAA
1 TATTAAAATAAAAAA
21704575 TATTAAAATAAAAAA
1 TATTAAAATAAAAAA
21704590 ATATGTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TATTAAAATAAAAAA
Found at i:21704699 original size:14 final size:15
Alignment explanation
Indices: 21704672--21704705 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
21704662 CTTGACTTTG
21704672 TAAAAAGACATTTTC
1 TAAAAAGACATTTTC
*
21704687 TAAAAAG-CTTTTTC
1 TAAAAAGACATTTTC
21704701 TAAAA
1 TAAAA
21704706 TGTTGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (15 bp):
TAAAAAGACATTTTC
Found at i:21708771 original size:14 final size:14
Alignment explanation
Indices: 21708752--21708791 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
21708742 TTGATTGGCA
21708752 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
21708766 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
21708780 GGAAAATGTTTT
1 GTAAAATGTTTT
21708792 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:21708804 original size:34 final size:35
Alignment explanation
Indices: 21708760--21708826 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
21708750 CAGTAAAATG
* * *
21708760 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTAGAAAATATTTTAC
*
21708794 TTTTCTGTAAAATGACTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTAGAAAATATTTT
21708827 CTAGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTAGAAAATATTTTAC
Found at i:21708813 original size:20 final size:20
Alignment explanation
Indices: 21708775--21708814 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
21708765 CGTAAAATGA
**
21708775 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
21708795 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
21708815 AGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:21710202 original size:27 final size:27
Alignment explanation
Indices: 21710172--21710241 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
21710162 AATAATCAAT
*
21710172 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
21710199 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAAC-AATTCAAAACATATA
*
21710227 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
21710242 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:21711891 original size:40 final size:40
Alignment explanation
Indices: 21711847--21712215 Score: 152
Period size: 40 Copynumber: 9.1 Consensus size: 40
21711837 TTTATTATTT
21711847 AAGTTACCATGACTTAAAATATATTGATCATGTATTTATA
1 AAGTTACCATGACTTAAAATATATTGATCATGTATTTATA
21711887 AAGTTACCATGACTTAAAATATATTGATCATAGTTAATAATATGTTTCTATA
1 AAGTTACCATGACTTAAAATATATTGATCAT-G-------TA---TT-TATA
* *
21711939 AAGTTACCATGACGTAAAATATATTGATAATGTATTTATAA
1 AAGTTACCATGACTTAAAATATATTGATCATGTATTTAT-A
* * *
21711980 AGAGTTTTA-AATTA-TAATATAAAGT-TACCATGA-CATGTATTTATA
1 A-AG--TTACCATGACT--TA-AAA-TATA--TTGATCATGTATTTATA
* *
21712025 AAG--A-GATGTATTTAAAGATAAATATTGATCATGTA--T-TA
1 AAGTTACCATG-ACTTAAA-AT--ATATTGATCATGTATTTATA
* *
21712063 AAGTTACCATGACTTAAAATATCTT--TCATGTATTTGT-
1 AAGTTACCATGACTTAAAATATATTGATCATGTATTTATA
* * * * * * * *
21712100 TA-TATA--TTGA-TCATAGT-TAATAAT-ATGTTTTTATA
1 AAGT-TACCATGACTTAAAATATATTGATCATGTATTTATA
*
21712135 AAGTTACCATGACTTAAAAT-TATTCG-T-ACTGTTTTTATA
1 AAGTTACCATGACTTAAAATATATT-GATCA-TGTATTTATA
*
21712174 AAGTTACCATGACTTAAAATATATTGATCATGTTTTTATA
1 AAGTTACCATGACTTAAAATATATTGATCATGTATTTATA
21712214 AA
1 AA
21712216 TGTTGATGCT
Statistics
Matches: 252, Mismatches: 29, Indels: 96
0.67 0.08 0.25
Matches are distributed among these distances:
33 2 0.01
34 12 0.05
35 14 0.06
36 2 0.01
37 11 0.04
38 15 0.06
39 37 0.15
40 67 0.27
41 16 0.06
42 5 0.02
43 3 0.01
44 9 0.04
45 7 0.03
46 11 0.04
47 3 0.01
48 2 0.01
51 3 0.01
52 33 0.13
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (40 bp):
AAGTTACCATGACTTAAAATATATTGATCATGTATTTATA
Found at i:21712179 original size:39 final size:40
Alignment explanation
Indices: 21712124--21712215 Score: 145
Period size: 39 Copynumber: 2.3 Consensus size: 40
21712114 AGTTAATAAT
21712124 ATGTTTTTATAAAGTTACCATGACTTAAAAT-TATTCG-T-
1 ATGTTTTTATAAAGTTACCATGACTTAAAATATATT-GATC
21712162 ACTGTTTTTATAAAGTTACCATGACTTAAAATATATTGATC
1 A-TGTTTTTATAAAGTTACCATGACTTAAAATATATTGATC
21712203 ATGTTTTTATAAA
1 ATGTTTTTATAAA
21712216 TGTTGATGCT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
38 1 0.02
39 31 0.62
40 17 0.34
41 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (40 bp):
ATGTTTTTATAAAGTTACCATGACTTAAAATATATTGATC
Found at i:21719469 original size:49 final size:49
Alignment explanation
Indices: 21719246--21719469 Score: 272
Period size: 49 Copynumber: 4.6 Consensus size: 49
21719236 ATCACTAGGT
* * * *
21719246 TGGTTAACAACTAACATGCCCTACCAGAGACCCAGCACTTA--CACCAATC
1 TGGTTAGCAACTAACATGCCCTACCAGTGGCCCA-C-CTTATTCACCCATC
* * * ** * *
21719295 TGGTTAGCAATTAACATGTCCTACTAGTATCCCACCTTATTCGCACATC
1 TGGTTAGCAACTAACATGCCCTACCAGTGGCCCACCTTATTCACCCATC
* *
21719344 TGGTTAGCAACTAGCATGCCTTACCAGTGGCCCACCTTATTCACCCATC
1 TGGTTAGCAACTAACATGCCCTACCAGTGGCCCACCTTATTCACCCATC
* *
21719393 TGGTTAGCAACTAGCATGCCTTACCAGTGGCCCACCTTATTCACCCATC
1 TGGTTAGCAACTAACATGCCCTACCAGTGGCCCACCTTATTCACCCATC
*
21719442 TGGTTAGCAACTAACATGCCCTGCCAGT
1 TGGTTAGCAACTAACATGCCCTACCAGT
21719470 AATCTATCTT
Statistics
Matches: 151, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
47 4 0.03
48 1 0.01
49 146 0.97
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (49 bp):
TGGTTAGCAACTAACATGCCCTACCAGTGGCCCACCTTATTCACCCATC
Found at i:21723191 original size:76 final size:75
Alignment explanation
Indices: 21723065--21723288 Score: 288
Period size: 76 Copynumber: 2.9 Consensus size: 75
21723055 AAGGAGTGAT
* *
21723065 TGATATCGTCGGTTTATCCGACTAGCGCCG-AGCGCAAATCTTCGTTGGTATATCCAACTAATGC
1 TGATATCGTCGGTTTATCCGACTAGCG--GTAGCGCAAATCTTCGTTGGTATATCAAACTAGTGC
21723129 TGGGCACATATC
64 TGGGCACATATC
* * *
21723141 TGATATCGTCGGTTTATCCGACTAACGGTATGCACAAATCTTTGTTGGTATATCAAACTAGTGCT
1 TGATATCGTCGGTTTATCCGACTAGCGGTA-GCGCAAATCTTCGTTGGTATATCAAACTAGTGCT
* * *
21723206 GGACACATGTT
65 GGGCACATATC
* * * * *
21723217 TGATATCGTCAGTTTATCCGACTAGTGATGGGCGCAAATCTTCGTTGGTATATCTAACTAGTGCT
1 TGATATCGTCGGTTTATCCGACTAGCGGT-AGCGCAAATCTTCGTTGGTATATCAAACTAGTGCT
21723282 GGGCACA
65 GGGCACA
21723289 AATCATTGTC
Statistics
Matches: 128, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
74 1 0.01
75 1 0.01
76 126 0.98
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (75 bp):
TGATATCGTCGGTTTATCCGACTAGCGGTAGCGCAAATCTTCGTTGGTATATCAAACTAGTGCTG
GGCACATATC
Found at i:21723312 original size:36 final size:36
Alignment explanation
Indices: 21723222--21723324 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 36
21723212 ATGTTTGATA
* * * *
21723222 TCGTCAGTTTATCCGACTAGTGATGGGCGCAAATCT
1 TCGTCAGTTTATTCAACTAGTGCTGGGCACAAATCT
** *
21723258 TCGTTGGTATA-TCTAACTAGTGCTGGGCACAAATCAT
1 TCGTCAGTTTATTC-AACTAGTGCTGGGCACAAATC-T
21723295 T-GTCAGTTTATTCAACTAGTGCTGGGCACA
1 TCGTCAGTTTATTCAACTAGTGCTGGGCACA
21723325 CATTTGACAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
35 1 0.02
36 49 0.91
37 4 0.07
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (36 bp):
TCGTCAGTTTATTCAACTAGTGCTGGGCACAAATCT
Found at i:21726605 original size:13 final size:12
Alignment explanation
Indices: 21726584--21726616 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
21726574 ACCAAAATGA
21726584 AAAATAAAAGAT
1 AAAATAAAAGAT
21726596 AAAATGAAAAGAT
1 AAAAT-AAAAGAT
21726609 AAAATAAA
1 AAAATAAA
21726617 CACTTACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (12 bp):
AAAATAAAAGAT
Found at i:21729521 original size:26 final size:25
Alignment explanation
Indices: 21729482--21729637 Score: 136
Period size: 26 Copynumber: 6.0 Consensus size: 25
21729472 TTTAGTAGGT
*
21729482 TATGAGCCAGTGATTATTTAGCAAGC
1 TATGAG-CGGTGATTATTTAGCAAGC
* * *
21729508 TATCAGTCGTTGATTATTTAGCAGGC
1 TATGAG-CGGTGATTATTTAGCAAGC
*
21729534 TATGAGCTGGTGTTTATTTAGCAAGC
1 TATGAGC-GGTGATTATTTAGCAAGC
* *
21729560 TTTGAGCCGGTGATTATTTAGCAGGCC
1 TATGAG-CGGTGATTATTTAGCAAG-C
*
21729587 T-TGAGCTGGTAATTATTTCAGCAAGC
1 TATGAGC-GGTGATTATTT-AGCAAGC
*
21729613 TTTGAGCTGGTGAATTA-TTAGCAAG
1 TATGAGC-GGTG-ATTATTTAGCAAG
21729638 TATTGTGTAC
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
25 2 0.02
26 83 0.77
27 19 0.18
28 4 0.04
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (25 bp):
TATGAGCGGTGATTATTTAGCAAGC
Found at i:21729634 original size:53 final size:52
Alignment explanation
Indices: 21729456--21729635 Score: 184
Period size: 52 Copynumber: 3.4 Consensus size: 52
21729446 TTGTCAGGCC
* * * * ** *
21729456 TTGAGCCGATGATTTTTTTAGTAGGTTATGAGCCAGTGATTATTTAGCAAGCT
1 TTGAGCCGGTGA-TTATTTAGCAGGCTATGAGCTGGTAATTATTTAGCAAGCT
* * * * **
21729509 ATCAGTCGTTGATTATTTAGCAGGCTATGAGCTGGTGTTTATTTAGCAAGCT
1 TTGAGCCGGTGATTATTTAGCAGGCTATGAGCTGGTAATTATTTAGCAAGCT
21729561 TTGAGCCGGTGATTATTTAGCAGGCCT-TGAGCTGGTAATTATTTCAGCAAGCT
1 TTGAGCCGGTGATTATTTAGCAGG-CTATGAGCTGGTAATTATTT-AGCAAGCT
*
21729614 TTGAGCTGGTGAATTA-TTAGCA
1 TTGAGCCGGTG-ATTATTTAGCA
21729636 AGTATTGTGT
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
52 69 0.64
53 34 0.32
54 4 0.04
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (52 bp):
TTGAGCCGGTGATTATTTAGCAGGCTATGAGCTGGTAATTATTTAGCAAGCT
Found at i:21733820 original size:18 final size:18
Alignment explanation
Indices: 21733797--21733833 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21733787 GGAGTGCATT
21733797 ATATGAA-TGTGATAAGTG
1 ATATGAACT-TGATAAGTG
21733815 ATATGAACTTGATAAGTG
1 ATATGAACTTGATAAGTG
21733833 A
1 A
21733834 AAGTGTGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (18 bp):
ATATGAACTTGATAAGTG
Found at i:21740648 original size:25 final size:25
Alignment explanation
Indices: 21740611--21740661 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
21740601 TTGGGGGTAA
*
21740611 TAGGTCAATTGTTGGAAATCGCCAT
1 TAGGTCAACTGTTGGAAATCGCCAT
*
21740636 TAGGTCAACTGTTGGAAATCGTCAT
1 TAGGTCAACTGTTGGAAATCGCCAT
21740661 T
1 T
21740662 TTAGAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (25 bp):
TAGGTCAACTGTTGGAAATCGCCAT
Found at i:21745326 original size:10 final size:10
Alignment explanation
Indices: 21745311--21745337 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21745301 TATTATTTAT
21745311 TTAATTTAAA
1 TTAATTTAAA
21745321 TTAATTTAAA
1 TTAATTTAAA
21745331 TTAATTT
1 TTAATTT
21745338 TTCAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAATTTAAA
Found at i:21745351 original size:16 final size:17
Alignment explanation
Indices: 21745326--21745358 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
21745316 TTAAATTAAT
21745326 TTAAATTAATTTTTCAA
1 TTAAATTAATTTTTCAA
21745343 TTAAA-TAATTTTTCAA
1 TTAAATTAATTTTTCAA
21745359 CCTAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATTAATTTTTCAA
Found at i:21762960 original size:15 final size:16
Alignment explanation
Indices: 21762935--21762964 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21762925 ATGACATTTA
21762935 TTTATTAAATAAAACT
1 TTTATTAAATAAAACT
21762951 TTTA-TAAATAAAAC
1 TTTATTAAATAAAAC
21762965 AATTTAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTATTAAATAAAACT
Found at i:21763517 original size:20 final size:20
Alignment explanation
Indices: 21763492--21763529 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21763482 TAATTTTTCT
21763492 TTTTATACGAATTTTTATAA
1 TTTTATACGAATTTTTATAA
* *
21763512 TTTTATATGTATTTTTAT
1 TTTTATACGAATTTTTAT
21763530 TAAATCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTATACGAATTTTTATAA
Found at i:21764183 original size:20 final size:20
Alignment explanation
Indices: 21764160--21764197 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21764150 TTATAAAAAT
21764160 TAATTATATATATTAAATAA
1 TAATTATATATATTAAATAA
*
21764180 TAATTATTTATATTAAAT
1 TAATTATATATATTAAAT
21764198 TACTAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTATATATATTAAATAA
Found at i:21764375 original size:39 final size:40
Alignment explanation
Indices: 21764299--21764385 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 40
21764289 AAAATATATT
* * *
21764299 TAATACAATAAAATATTTATTATATTTATTTGTG-TTTTG
1 TAATATAATAAAACATTTATTATATTTATTGGTGTTTTTG
* *
21764338 TAATATAATAAAACATTTATTGTATTTA-TGGTAGTTTTTT
1 TAATATAATAAAACATTTATTATATTTATTGGT-GTTTTTG
21764378 TAATATAA
1 TAATATAA
21764386 ATATTTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 3 0.07
39 26 0.63
40 12 0.29
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (40 bp):
TAATATAATAAAACATTTATTATATTTATTGGTGTTTTTG
Found at i:21766154 original size:26 final size:26
Alignment explanation
Indices: 21766125--21766174 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
21766115 AATTAGAGTA
21766125 AGAGTTAGAGAATTCCTCGATTTTCT
1 AGAGTTAGAGAATTCCTCGATTTTCT
*
21766151 AGAGTTAGAGAATTTCTCGATTTT
1 AGAGTTAGAGAATTCCTCGATTTT
21766175 GCTAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (26 bp):
AGAGTTAGAGAATTCCTCGATTTTCT
Found at i:21767260 original size:3 final size:3
Alignment explanation
Indices: 21767248--21767306 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
21767238 TATTATATAT
*
21767248 TAA TATA TAA TAA -AA TAA -AG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21767292 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
21767307 AGAATTAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 3 0.06
3 45 0.88
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:21767337 original size:16 final size:16
Alignment explanation
Indices: 21767313--21767353 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
21767303 ATAAAGAATT
21767313 AAAAAGAAACA-AAGC
1 AAAAAGAAACAGAAGC
*
21767328 AAAAACGAAACAGAAGG
1 AAAAA-GAAACAGAAGC
21767345 AAAAAGAAA
1 AAAAAGAAA
21767354 GAAAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.73, C:0.10, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGAAACAGAAGC
Found at i:21768411 original size:24 final size:23
Alignment explanation
Indices: 21768371--21768466 Score: 113
Period size: 24 Copynumber: 4.0 Consensus size: 23
21768361 TCCTGAAATA
21768371 TGGCTCGTTGGAGCTTCCCGTTAT
1 TGGCTCGTT-GAGCTTCCCGTTAT
* *
21768395 TGGCTCGCTTGAACTTCCCGATAT
1 TGGCTCG-TTGAGCTTCCCGTTAT
*
21768419 TGGCTCGTATGAGCTTCCCGTTAA
1 TGGCTCGT-TGAGCTTCCCGTTAT
21768443 TGGCTC-TTCAGAGCTTCCCGTTAT
1 TGGCTCGTT--GAGCTTCCCGTTAT
21768467 ACAACTCACA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
22 1 0.02
23 2 0.03
24 57 0.92
25 2 0.03
ACGTcount: A:0.14, C:0.27, G:0.24, T:0.35
Consensus pattern (23 bp):
TGGCTCGTTGAGCTTCCCGTTAT
Found at i:21768460 original size:48 final size:49
Alignment explanation
Indices: 21768351--21768498 Score: 133
Period size: 48 Copynumber: 3.0 Consensus size: 49
21768341 GAAAAGCACT
* * *
21768351 TTCACGAGCTTCCTGAAATATGGCTCGT-TGGAGCTTCCCGTTATTGGCTCGC
1 TTCA-GAGCTTCCCGATATATGGCTCGTAT-GAGCTTCCCGTTAATGGCT--C
*
21768403 TT--GAACTTCCCGATAT-TGGCTCGTATGAGCTTCCCGTTAATGGCTC
1 TTCAGAGCTTCCCGATATATGGCTCGTATGAGCTTCCCGTTAATGGCTC
* *** **
21768449 TTCAGAGCTTCCCGTTATACAACTCACATGAGCTTCCCGTTATATGGCTC
1 TTCAGAGCTTCCCGATATATGGCTCGTATGAGCTTCCCGTTA-ATGGCTC
21768499 GAAAAAGCTT
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
46 3 0.04
48 38 0.47
49 30 0.38
50 7 0.09
52 2 0.03
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (49 bp):
TTCAGAGCTTCCCGATATATGGCTCGTATGAGCTTCCCGTTAATGGCTC
Found at i:21770009 original size:27 final size:27
Alignment explanation
Indices: 21769991--21770047 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
21769981 ACTAAAATGT
*
21769991 TATAACTTTTTTTATTTACCAAAAAATA
1 TATAA-TTTTTTTATTTACCAAAATATA
21770019 TATAATTTTTTTATTTACCAAAATATA
1 TATAATTTTTTTATTTACCAAAATATA
21770046 TA
1 TA
21770048 AAAAAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (27 bp):
TATAATTTTTTTATTTACCAAAATATA
Found at i:21770061 original size:11 final size:12
Alignment explanation
Indices: 21770047--21770077 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
21770037 CAAAATATAT
21770047 AAAAAAACA-AA
1 AAAAAAACAGAA
21770058 AAAAAAACAGAA
1 AAAAAAACAGAA
21770070 AAAAAAAC
1 AAAAAAAC
21770078 CTGAACTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAACAGAA
Found at i:21770145 original size:27 final size:27
Alignment explanation
Indices: 21770107--21770180 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
21770097 CCCTGGGTGG
21770107 AGGGAAGCAGGTTGGCGGCACCAAACA
1 AGGGAAGCAGGTTGGCGGCACCAAACA
****
21770134 AGGGAAGCAGGTTGGCGGCACCAGTGG
1 AGGGAAGCAGGTTGGCGGCACCAAACA
*
21770161 AGGGAACCAGGTTGGCGGCA
1 AGGGAAGCAGGTTGGCGGCA
21770181 ACACCCTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.27, C:0.20, G:0.43, T:0.09
Consensus pattern (27 bp):
AGGGAAGCAGGTTGGCGGCACCAAACA
Found at i:21770252 original size:18 final size:17
Alignment explanation
Indices: 21770229--21770306 Score: 72
Period size: 18 Copynumber: 4.5 Consensus size: 17
21770219 GAAGGAGAGG
21770229 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
21770247 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
21770264 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
21770280 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
21770298 GGAAAGAAA
1 GG-AAGAAA
21770307 AGGACAGGGG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
15 9 0.18
16 4 0.08
17 4 0.08
18 20 0.39
19 14 0.27
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:21770262 original size:10 final size:10
Alignment explanation
Indices: 21770231--21770302 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
21770221 AGGAGAGGGG
*
21770231 AAGAAGAAGA
1 AAGAAAAAGA
21770241 AAGAAAGGAAGA
1 AAGAAA--AAGA
21770253 AAGAAAAAGA
1 AAGAAAAAGA
* *
21770263 AGGAAAAGGA
1 AAGAAAAAGA
21770273 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
21770287 AAGAAAAAGA
1 AAGAAAAAGA
*
21770297 AGGAAA
1 AAGAAA
21770303 GAAAAGGACA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:21770262 original size:22 final size:23
Alignment explanation
Indices: 21770231--21770307 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 23
21770221 AGGAGAGGGG
*
21770231 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
21770253 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
21770275 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
21770301 AAGAAAA
1 AAGAAAA
21770308 GGACAGGGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 12 0.29
23 10 0.24
24 16 0.38
25 3 0.07
26 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:21770268 original size:14 final size:13
Alignment explanation
Indices: 21770234--21770307 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 13
21770224 AGAGGGGAAG
21770234 AAGAAGAAAG-AA
1 AAGAAGAAAGAAA
*
21770246 AGGAAGAAAGAAA
1 AAGAAGAAAGAAA
21770259 AAGAAGGAAAAGGAAA
1 AAGAA-G-AAA-GAAA
21770275 GGAGAGGAAAGAAAGAAA
1 --A-A-G-AAGAAAGAAA
21770293 AAGAAGGAAAGAAA
1 AAGAA-GAAAGAAA
21770307 A
1 A
21770308 GGACAGGGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
12 9 0.18
13 8 0.16
14 11 0.22
15 4 0.08
16 5 0.10
18 5 0.10
19 4 0.08
20 2 0.04
21 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAA
Found at i:21770307 original size:38 final size:35
Alignment explanation
Indices: 21770249--21770337 Score: 117
Period size: 38 Copynumber: 2.5 Consensus size: 35
21770239 GAAAGAAAGG
21770249 AAGAAAGAAAAAGAA-GGAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGGAAAAGGAAAGGAGAGGA
* *
21770283 AAGAAAGAAAAAGAAGGAAAGAAAAGGACAGGGGAGGA
1 AAGAAAGAAAAAGAAGG---GAAAAGGAAAGGAGAGGA
*
21770321 AAGAAAGAAAAATAAGG
1 AAGAAAGAAAAAGAAGG
21770338 CGTTTGAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
34 15 0.31
35 1 0.02
38 32 0.67
ACGTcount: A:0.64, C:0.01, G:0.34, T:0.01
Consensus pattern (35 bp):
AAGAAAGAAAAAGAAGGGAAAAGGAAAGGAGAGGA
Found at i:21770309 original size:10 final size:10
Alignment explanation
Indices: 21770251--21770310 Score: 54
Period size: 10 Copynumber: 6.2 Consensus size: 10
21770241 AAGAAAGGAA
*
21770251 GAAAGAAAAA
1 GAAAGAAAAG
*
21770261 GAAGGAAAAG
1 GAAAGAAAAG
* *
21770271 GAAAGGAGAG
1 GAAAGAAAAG
21770281 GAAAG-AAA-
1 GAAAGAAAAG
21770289 GAAA-AAGAAG
1 GAAAGAA-AAG
21770299 GAAAGAAAAG
1 GAAAGAAAAG
21770309 GA
1 GA
21770311 CAGGGGAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 5 0.12
9 4 0.10
10 29 0.73
11 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:21770310 original size:28 final size:28
Alignment explanation
Indices: 21770234--21770310 Score: 79
Period size: 34 Copynumber: 2.6 Consensus size: 28
21770224 AGAGGGGAAG
21770234 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
21770259 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
21770293 AAGAAGGAAAGAAAAGGA
1 AAGAAGGAAAGAAAAGGA
21770311 CAGGGGAGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
25 5 0.12
26 1 0.02
27 3 0.07
28 5 0.12
29 1 0.02
30 1 0.02
31 2 0.05
32 2 0.05
33 6 0.14
34 17 0.40
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:21771482 original size:17 final size:17
Alignment explanation
Indices: 21771460--21771496 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
21771450 AGTAAGATGT
21771460 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
21771477 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
21771494 CAT
1 CAT
21771497 CTTACCCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (17 bp):
CATGAATATTAGAATAG
Found at i:21772827 original size:17 final size:17
Alignment explanation
Indices: 21772807--21772839 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21772797 TTTTTTCCTC
*
21772807 TTTTTTATTTTTTTTGT
1 TTTTTTACTTTTTTTGT
21772824 TTTTTTACTTTTTTTG
1 TTTTTTACTTTTTTTG
21772840 ATATATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (17 bp):
TTTTTTACTTTTTTTGT
Found at i:21772871 original size:26 final size:28
Alignment explanation
Indices: 21772840--21772907 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
21772830 ACTTTTTTTG
21772840 ATATATTTTGGTAAAT-AAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAGTTAT
21772866 ATATATTTTGGTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAAT-AAAAAAAGTTAT
21772895 A-ATATTTTGGTAA
1 ATATATTTTGGTAA
21772908 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
26 16 0.41
28 18 0.46
29 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAGTTAT
Found at i:21772969 original size:19 final size:18
Alignment explanation
Indices: 21772945--21772984 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
21772935 TATAAAACCC
21772945 ATAATAAAACATTACAAAA
1 ATAATAAAACATTA-AAAA
*
21772964 ATAATAAAATATTAAAAA
1 ATAATAAAACATTAAAAA
21772982 ATA
1 ATA
21772985 CCAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAATAAAACATTAAAAA
Found at i:21772983 original size:18 final size:19
Alignment explanation
Indices: 21772945--21772995 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
21772935 TATAAAACCC
*
21772945 ATAATAAAACATTACAAAA
1 ATAATAAAATATTACAAAA
21772964 ATAATAAAATATTA-AAAA
1 ATAATAAAATATTACAAAA
**
21772982 ATACCAAAATATTA
1 ATAATAAAATATTA
21772996 TATATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (19 bp):
ATAATAAAATATTACAAAA
Found at i:21773728 original size:35 final size:36
Alignment explanation
Indices: 21773673--21773760 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 36
21773663 CCTTATTTTC
*
21773673 TTTTTTTTTC-CTTCCTTCCTTCCCTCTTCTTCTTCT
1 TTTTTTTTTCTCTTCCTTCCTTCCCTCTTCTT-TCCT
* *
21773709 TTTTTTTTTCTCTT-C-TCCTTTCCTTTTCTTTCCT
1 TTTTTTTTTCTCTTCCTTCCTTCCCTCTTCTTTCCT
21773743 TATTTTTCTTTCT-TTCCT
1 T-TTTTT-TTTCTCTTCCT
21773761 CCCCTTTCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
34 4 0.09
35 20 0.45
36 17 0.39
37 3 0.07
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (36 bp):
TTTTTTTTTCTCTTCCTTCCTTCCCTCTTCTTTCCT
Found at i:21773741 original size:10 final size:10
Alignment explanation
Indices: 21773726--21773788 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
21773716 TTCTCTTCTC
21773726 CTTTCCTTTT
1 CTTTCCTTTT
21773736 CTTTCCTTATT
1 CTTTCCTT-TT
21773747 -TTT-C-TTT
1 CTTTCCTTTT
***
21773754 CTTTCCTCCC
1 CTTTCCTTTT
21773764 CTTTCCTTTT
1 CTTTCCTTTT
* *
21773774 CCTTCTTTTT
1 CTTTCCTTTT
21773784 CTTTC
1 CTTTC
21773789 TTCCTTTCTT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
7 2 0.05
8 4 0.10
9 2 0.05
10 30 0.75
11 2 0.05
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:21773759 original size:28 final size:28
Alignment explanation
Indices: 21773726--21773800 Score: 73
Period size: 34 Copynumber: 2.5 Consensus size: 28
21773716 TTCTCTTCTC
21773726 CTTTCCTTTTCTTTCCTTATTTTTCTTT
1 CTTTCCTTTTCTTTCCTTATTTTTCTTT
*
21773754 CTTTCCTCCCCTTTCCTTTTCCTTCTTTTTCTTT
1 CTTTCCT----TTT-C-TTTCCTTATTTTTCTTT
21773788 C-TTCC-TTTCTTTC
1 CTTTCCTTTTCTTTC
21773801 TTCTTCTTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
26 4 0.10
27 1 0.03
28 10 0.25
32 3 0.08
33 5 0.12
34 17 0.43
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.65
Consensus pattern (28 bp):
CTTTCCTTTTCTTTCCTTATTTTTCTTT
Found at i:21773799 original size:18 final size:17
Alignment explanation
Indices: 21773670--21773810 Score: 67
Period size: 18 Copynumber: 8.0 Consensus size: 17
21773660 TTACCTTATT
*
21773670 TTCTTTTTTTTTCCTTCC
1 TTCTTTTTCTTT-CTTCC
* **
21773688 TTCCTTCCCTCTTCTT-C
1 TTCTTTTTCT-TTCTTCC
21773705 TTCTTTTT-TTT-TTCTC
1 TTCTTTTTCTTTCTTC-C
*
21773721 TTCTCCTTTCCTTTTCTTTCC
1 TTCT--TTTTC-TTTC-TTCC
*
21773742 TTATTTTTCTTTCTTTCC
1 TTCTTTTTCTTTC-TTCC
* ** *
21773760 TCCCCTTTCCTT-TTCC
1 TTCTTTTTCTTTCTTCC
21773776 TTCTTTTTCTTTCTTCC
1 TTCTTTTTCTTTCTTCC
21773793 TTTCTTTCTTC-TTCTTCC
1 -TTCTTT-TTCTTTCTTCC
21773811 CCTCTCCTTC
Statistics
Matches: 92, Mismatches: 19, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
14 2 0.02
15 2 0.02
16 18 0.20
17 10 0.11
18 41 0.45
19 9 0.10
20 3 0.03
21 4 0.04
22 3 0.03
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCTTTTTCTTTCTTCC
Found at i:21773801 original size:22 final size:23
Alignment explanation
Indices: 21773766--21773808 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
21773756 TTCCTCCCCT
*
21773766 TTCCTTTTCCTTCTTTTTCTTTC
1 TTCCTTTTCCTTCTTCTTCTTTC
*
21773789 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
21773809 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTTC
Found at i:21773961 original size:18 final size:17
Alignment explanation
Indices: 21773937--21773980 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
21773927 TCAGTTCAGG
21773937 TTTTTTTTTCTATTTTT
1 TTTTTTTTTCTATTTTT
* *
21773954 TATTTTTTTCTGTTTTT
1 TTTTTTTTTCTATTTTT
21773971 TTGTTTTTTT
1 TT-TTTTTTT
21773981 GGTAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTCTATTTTT
Found at i:21780465 original size:21 final size:21
Alignment explanation
Indices: 21780436--21780476 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
21780426 AGTCGTTGGT
*
21780436 AGGCTATGTCTCGAGACATGC
1 AGGCCATGTCTCGAGACATGC
21780457 AGGCCATGTCTCGAGACATG
1 AGGCCATGTCTCGAGACATG
21780477 TAGCCCCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (21 bp):
AGGCCATGTCTCGAGACATGC
Found at i:21782725 original size:13 final size:13
Alignment explanation
Indices: 21782709--21782750 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
21782699 AAATCTCAAA
21782709 ATTTACTTATAAT
1 ATTTACTTATAAT
* *
21782722 ATTTA-ATAT-GT
1 ATTTACTTATAAT
21782733 ATTTACTTATAAT
1 ATTTACTTATAAT
21782746 ATTTA
1 ATTTA
21782751 AAAAATTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 6 0.26
12 6 0.26
13 11 0.48
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (13 bp):
ATTTACTTATAAT
Found at i:21793730 original size:4 final size:4
Alignment explanation
Indices: 21793721--21793747 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21793711 CAAAACCAGC
21793721 AGTG AGTG AGTG AGTG AGTG AGTG AGT
1 AGTG AGTG AGTG AGTG AGTG AGTG AGT
21793748 CAGAGGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
AGTG
Found at i:21795283 original size:14 final size:14
Alignment explanation
Indices: 21795264--21795294 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21795254 AACATTTTAA
*
21795264 TGGAATGTAATTTT
1 TGGAATGTAATTGT
21795278 TGGAATGTAATTGT
1 TGGAATGTAATTGT
21795292 TGG
1 TGG
21795295 GGGAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (14 bp):
TGGAATGTAATTGT
Found at i:21804220 original size:27 final size:27
Alignment explanation
Indices: 21804187--21804273 Score: 131
Period size: 27 Copynumber: 3.2 Consensus size: 27
21804177 CTAAAATATA
* *
21804187 TAAAATGACCAAAATACCCTCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
21804214 TAAAATGACCGAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
*
21804241 TAAAATGATCGAAATACCCCCACT-GGG
1 TAAAATGACCGAAATACCCCCA-TAGGG
21804268 TAAAAT
1 TAAAAT
21804274 ACCTTATAGG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 55 0.98
28 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCCCATAGGG
Found at i:21804299 original size:71 final size:72
Alignment explanation
Indices: 21804197--21804344 Score: 201
Period size: 71 Copynumber: 2.1 Consensus size: 72
21804187 TAAAATGACC
* *
21804197 AAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCC
1 AAAATACCCTCATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCC
21804262 ACT-GGGT
66 A-TAGGGT
* ** * * *
21804269 AAAATA-CCTTATAGGGTAAAATAATTGAAATACCCTCGTAGGGTAAAATGACCGAAATACCCCT
1 AAAATACCCTCATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCC
21804333 ATAGGGT
66 ATAGGGT
21804340 AAAAT
1 AAAAT
21804345 GACTATTATA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 1 0.01
71 60 0.90
72 6 0.09
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (72 bp):
AAAATACCCTCATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCC
ATAGGGT
Found at i:21804345 original size:27 final size:26
Alignment explanation
Indices: 21804270--21804347 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 26
21804260 CCACTGGGTA
* * **
21804270 AAATACCTTATAGGGTAAAATAATTG
1 AAATACCCTATAGGGTAAAATGACCG
*
21804296 AAATACCCTCGTAGGGTAAAATGACCG
1 AAATACCCT-ATAGGGTAAAATGACCG
21804323 AAATACCCCTATAGGGTAAAATGAC
1 AAATA-CCCTATAGGGTAAAATGAC
21804348 TATTATACCC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.18
27 32 0.73
28 4 0.09
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (26 bp):
AAATACCCTATAGGGTAAAATGACCG
Found at i:21810444 original size:13 final size:12
Alignment explanation
Indices: 21810428--21810466 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
21810418 TTACAGTTAA
21810428 AGATAACAGAATC
1 AGATAACAGAA-C
21810441 AGATAAGCAGAAC
1 AGATAA-CAGAAC
21810454 AGATATACAGAAC
1 AGATA-ACAGAAC
21810467 CCTACCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (12 bp):
AGATAACAGAAC
Found at i:21812545 original size:37 final size:36
Alignment explanation
Indices: 21812477--21812594 Score: 144
Period size: 37 Copynumber: 3.5 Consensus size: 36
21812467 AACTATAAAG
*
21812477 GCCGAATGC--ACATAT-TCACTTATACCCACCTAT
1 GCCGAATGCATACATATATCACTTATATCCACCTAT
*
21812510 GCCGAATGCATACATATATACACTTATATCTACCTAT
1 GCCGAATGCATACATATAT-CACTTATATCCACCTAT
21812547 GCCGAATGCATACA-A-AT-A--TATATCCACCTAT
1 GCCGAATGCATACATATATCACTTATATCCACCTAT
*
21812578 GCCGAATGCCTACATAT
1 GCCGAATGCATACATAT
21812595 GCACACATAA
Statistics
Matches: 75, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
31 25 0.33
32 1 0.01
33 10 0.13
35 8 0.11
36 2 0.03
37 29 0.39
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (36 bp):
GCCGAATGCATACATATATCACTTATATCCACCTAT
Found at i:21812833 original size:41 final size:41
Alignment explanation
Indices: 21812783--21812992 Score: 339
Period size: 41 Copynumber: 5.1 Consensus size: 41
21812773 AATTCATCAT
*
21812783 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* *
21812824 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
21812865 ATTCAGATCACCGGCACTTAGCCTTCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
21812906 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * * *
21812947 ATTCATATCACCGACACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
21812988 ATTCA
1 ATTCA
21812993 ATTCACCAAT
Statistics
Matches: 158, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 158 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:21813254 original size:15 final size:17
Alignment explanation
Indices: 21813213--21813256 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
21813203 TTGTTCTATC
21813213 CACATATATATATTACA
1 CACATATATATATTACA
*
21813230 CACATATATATATT-CG
1 CACATATATATATTACA
21813246 CACAT-TATATA
1 CACATATATATA
21813257 AACACCACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 6 0.23
16 6 0.23
17 14 0.54
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.36
Consensus pattern (17 bp):
CACATATATATATTACA
Found at i:21822106 original size:43 final size:41
Alignment explanation
Indices: 21821957--21822113 Score: 111
Period size: 43 Copynumber: 3.7 Consensus size: 41
21821947 TGTGTTTTCG
* * * *
21821957 TGTAAGACCATGTCTGGGATATTGGCATCAGTTTGA-GATTTACA
1 TGTAAGACCACGTCTGGGACA-TGGCATC-GTAT-ATGA-TTGCA
* * * * *
21822001 TGTAAGACCATGTCTGGGACATCGACATTGTATATGATTTCG
1 TGTAAGACCACGTCTGGGACAT-GGCATCGTATATGATTGCA
* * *
21822043 TGTAAGACC-CTGTTTAGGACAGTGGCATCGATATTTGATTGCA
1 TGTAAGACCAC-GTCTGGGACA-TGGCATCG-TATATGATTGCA
21822086 TGTAAGACCACGTCTGGGACATTGGCAT
1 TGTAAGACCACGTCTGGGACA-TGGCAT
21822114 TGTACGATCT
Statistics
Matches: 90, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
42 26 0.29
43 39 0.43
44 25 0.28
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACATGGCATCGTATATGATTGCA
Found at i:21836118 original size:22 final size:21
Alignment explanation
Indices: 21836083--21836140 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
21836073 AAAAGGTATC
* * *
21836083 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
21836104 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
21836127 TGCATATCATATCT
1 TACAAATCATATCT
21836141 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:21836538 original size:18 final size:18
Alignment explanation
Indices: 21836507--21836556 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
21836497 TATATTATAA
21836507 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
21836525 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
21836543 TATTAA-TAATAAAA
1 TATTAATTAATAAAA
21836557 ACATCATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:21838491 original size:49 final size:47
Alignment explanation
Indices: 21838312--21838817 Score: 751
Period size: 47 Copynumber: 10.6 Consensus size: 47
21838302 CCCTTCGGGA
* * * * * *
21838312 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
21838359 CCTGTCACATATATACACTTTCACATTCGTCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
21838406 CTCATCACATATATACACTTTCACATTCATCTCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
21838453 CTTATCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
21838502 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
21838551 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
21838598 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
21838645 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
21838692 CTTATCACATATATATACACTTTCACATTCATCACATTGACCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
21838741 CTTATCTCATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTA--TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
21838790 CTTATCACATATATACACTTTCACATTC
1 CTTATCACATATATACACTTTCACATTC
21838818 CAATGAATAA
Statistics
Matches: 423, Mismatches: 30, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
47 247 0.58
49 173 0.41
51 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:21838738 original size:239 final size:239
Alignment explanation
Indices: 21838312--21838817 Score: 859
Period size: 239 Copynumber: 2.1 Consensus size: 239
21838302 CCCTTCGGGA
* * * * * *
21838312 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
* *
21838377 TTTCACATTCGTCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCTCATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
*
21838442 GGCCATTAGGCCTTATCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGCCTTAT
131 GGCCATTAGGCCTTATCACATATATATACACTTCCACATTCATCACATCGACCATTAGGCCTTAT
21838507 CACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
196 CACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
21838551 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
* *
21838616 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
* *
21838681 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGACCATTAGGCCTTAT
131 GGCCATTAGGCCTTATCACATATATATACACTTCCACATTCATCACATCGACCATTAGGCCTTAT
*
21838746 CTCATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
196 CACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
21838790 CTTATCACATATATACACTTTCACATTC
1 CTTATCACATATATACACTTTCACATTC
21838818 CAATGAATAA
Statistics
Matches: 250, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
239 250 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (239 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATATACACTTCCACATTCATCACATCGACCATTAGGCCTTAT
CACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:21840104 original size:8 final size:8
Alignment explanation
Indices: 21840091--21840118 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
21840081 TCGGTAATAC
21840091 GCATATAA
1 GCATATAA
21840099 GCATATAA
1 GCATATAA
21840107 GCATATAA
1 GCATATAA
21840115 GCAT
1 GCAT
21840119 GTCTCTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (8 bp):
GCATATAA
Found at i:21840454 original size:13 final size:13
Alignment explanation
Indices: 21840436--21840460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21840426 TACTAAATTT
21840436 TCATGGATTCAAA
1 TCATGGATTCAAA
21840449 TCATGGATTCAA
1 TCATGGATTCAA
21840461 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:21842493 original size:27 final size:27
Alignment explanation
Indices: 21842455--21842510 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
21842445 TGGTATATAA
21842455 TAAAGGAGAGTTCAGCCATAATACTTC
1 TAAAGGAGAGTTCAGCCATAATACTTC
* *
21842482 TAAAGGAGAGTTTAGTCATAATACTTC
1 TAAAGGAGAGTTCAGCCATAATACTTC
21842509 TA
1 TA
21842511 GTGGGGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (27 bp):
TAAAGGAGAGTTCAGCCATAATACTTC
Found at i:21842799 original size:21 final size:21
Alignment explanation
Indices: 21842760--21842799 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21842750 TTAAGAATTA
*
21842760 ATTTAATTTCATTGGATTATT
1 ATTTAATTTCATTGAATTATT
21842781 ATTTAATTT-ATTGTAATTA
1 ATTTAATTTCATTG-AATTA
21842800 AATAATTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (21 bp):
ATTTAATTTCATTGAATTATT
Done.