Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 189 of 279
Found at i:61979184 original size:16 final size:15
Alignment explanation
Indices: 61979163--61979192 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
61979153 TTCAATTTTT
61979163 TGTATTGATCTTTCTG
1 TGTATTGAT-TTTCTG
61979179 TGTATTGATTTTCT
1 TGTATTGATTTTCT
61979193 CTTGATACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (15 bp):
TGTATTGATTTTCTG
Found at i:61988009 original size:8 final size:8
Alignment explanation
Indices: 61987996--61988021 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
61987986 TTTATGGTAA
61987996 AAATTGTG
1 AAATTGTG
61988004 AAATTGTG
1 AAATTGTG
61988012 AAATTGTG
1 AAATTGTG
61988020 AA
1 AA
61988022 TTATGTGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (8 bp):
AAATTGTG
Found at i:62011627 original size:24 final size:24
Alignment explanation
Indices: 62011600--62011650 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
62011590 GGTGAACTAA
62011600 TCATGTGACTTAATGATGAGCAAG
1 TCATGTGACTTAATGATGAGCAAG
62011624 TCATGTGACTTAATGATGAGCAAG
1 TCATGTGACTTAATGATGAGCAAG
62011648 TCA
1 TCA
62011651 CCTTCAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (24 bp):
TCATGTGACTTAATGATGAGCAAG
Found at i:62016594 original size:21 final size:21
Alignment explanation
Indices: 62016570--62016612 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
62016560 ATTGTTGATA
62016570 AGGAAGTTGCTACTACAGAAG
1 AGGAAGTTGCTACTACAGAAG
* *
62016591 AGGAAGTTGTTGCTACAGAAG
1 AGGAAGTTGCTACTACAGAAG
62016612 A
1 A
62016613 AGTTACTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (21 bp):
AGGAAGTTGCTACTACAGAAG
Found at i:62021980 original size:11 final size:11
Alignment explanation
Indices: 62021964--62021997 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
62021954 CCATATTAAT
62021964 TTTTTATATTA
1 TTTTTATATTA
*
62021975 TTTTTATATAA
1 TTTTTATATTA
*
62021986 TTTTTAAATTA
1 TTTTTATATTA
62021997 T
1 T
62021998 ATAATACATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:62022897 original size:18 final size:17
Alignment explanation
Indices: 62022873--62022921 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
62022863 CTAAAATATT
62022873 TTTTTTAAAATTTTATA
1 TTTTTTAAAATTTTATA
* *
62022890 TATTTTTAATATTTTTTA
1 T-TTTTTAAAATTTTATA
*
62022908 TTTTTTATAATTTT
1 TTTTTTAAAATTTT
62022922 TAAATAAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAAAATTTTATA
Found at i:62022922 original size:18 final size:18
Alignment explanation
Indices: 62022873--62022923 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
62022863 CTAAAATATT
*
62022873 TTTTTTAAAATTTTATATA
1 TTTTTTATAATTTT-TATA
*
62022892 TTTTTAAT-ATTTTT-TA
1 TTTTTTATAATTTTTATA
62022908 TTTTTTATAATTTTTA
1 TTTTTTATAATTTTTA
62022924 AATAAAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 9 0.33
17 7 0.26
18 5 0.19
19 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTATAATTTTTATA
Found at i:62024847 original size:32 final size:32
Alignment explanation
Indices: 62024806--62024870 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
62024796 CCCCTCAACA
62024806 TCCTATGATAAAGACCCATTGTCAGCATTGTT
1 TCCTATGATAAAGACCCATTGTCAGCATTGTT
62024838 TCCTATGATAAAGACCCATTGTCAGCATTGTT
1 TCCTATGATAAAGACCCATTGTCAGCATTGTT
62024870 T
1 T
62024871 GATAAATCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (32 bp):
TCCTATGATAAAGACCCATTGTCAGCATTGTT
Found at i:62028402 original size:39 final size:39
Alignment explanation
Indices: 62028352--62028432 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
62028342 ATGATAAATT
62028352 TTTATTTGGGTTAATATAATATTTGATATTTAAACTTTA
1 TTTATTTGGGTTAATATAATATTTGATATTTAAACTTTA
*
62028391 TTTATTTGGGTTAATATAATATTTGATATTTAAATTTTA
1 TTTATTTGGGTTAATATAATATTTGATATTTAAACTTTA
62028430 TTT
1 TTT
62028433 TTTTTGTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.57
Consensus pattern (39 bp):
TTTATTTGGGTTAATATAATATTTGATATTTAAACTTTA
Found at i:62028462 original size:20 final size:21
Alignment explanation
Indices: 62028424--62028462 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
62028414 TGATATTTAA
* *
62028424 ATTTTATTTTTTTTGTAATTT
1 ATTTTATTTTTGTTCTAATTT
62028445 ATTTT-TTTTTGTTCTAAT
1 ATTTTATTTTTGTTCTAAT
62028463 ATGATACCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (21 bp):
ATTTTATTTTTGTTCTAATTT
Found at i:62030559 original size:18 final size:18
Alignment explanation
Indices: 62030536--62030587 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
62030526 TAGCTTTTAT
62030536 CTTTTATCTTTATAATAG
1 CTTTTATCTTTATAATAG
*
62030554 CTTTTATAATTT-TAATAG
1 CTTTTAT-CTTTATAATAG
62030572 CTTTTATCTTTATAAT
1 CTTTTATCTTTATAAT
62030588 TTTTAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.58
Consensus pattern (18 bp):
CTTTTATCTTTATAATAG
Found at i:62039732 original size:31 final size:31
Alignment explanation
Indices: 62039697--62039759 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
62039687 CTTTATCTTT
62039697 TAGTGGCTTTTGTTTCATACAAGTTCTCATA
1 TAGTGGCTTTTGTTTCATACAAGTTCTCATA
*
62039728 TAGTGGCTTTTGTTTCATACTAGTTCTCATA
1 TAGTGGCTTTTGTTTCATACAAGTTCTCATA
62039759 T
1 T
62039760 TGCAATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.48
Consensus pattern (31 bp):
TAGTGGCTTTTGTTTCATACAAGTTCTCATA
Found at i:62047624 original size:25 final size:26
Alignment explanation
Indices: 62047588--62047642 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
62047578 AAGAGAGTAA
*
62047588 AGAATAAGAAAATATA-AGAGTAAAAG
1 AGAATAAGAAAATA-AGAGAGCAAAAG
62047614 AGAATAA-AAAATAAGAGAGCAAAAG
1 AGAATAAGAAAATAAGAGAGCAAAAG
62047639 AGAA
1 AGAA
62047643 CGGATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 1 0.04
25 19 0.70
26 7 0.26
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.11
Consensus pattern (26 bp):
AGAATAAGAAAATAAGAGAGCAAAAG
Found at i:62051449 original size:25 final size:25
Alignment explanation
Indices: 62051405--62051452 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
62051395 TACAGCCCCG
* *
62051405 ATAAGCTTCCTGTTGCATGGCTCAT
1 ATAAGCTTCCCGTTACATGGCTCAT
*
62051430 ATAAGCTTCCCGTTATATGGCTC
1 ATAAGCTTCCCGTTACATGGCTC
62051453 GAGAGAGGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (25 bp):
ATAAGCTTCCCGTTACATGGCTCAT
Found at i:62052921 original size:34 final size:34
Alignment explanation
Indices: 62052883--62052949 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
62052873 CCATTTATAT
62052883 ATTTGCACGAATTTAGTGAATAATAAAAATTTAC
1 ATTTGCACGAATTTAGTGAATAATAAAAATTTAC
62052917 ATTTGCACGAATTTAGTGAATAATAAAAATTTA
1 ATTTGCACGAATTTAGTGAATAATAAAAATTTA
62052950 TCTATTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (34 bp):
ATTTGCACGAATTTAGTGAATAATAAAAATTTAC
Found at i:62057761 original size:24 final size:24
Alignment explanation
Indices: 62057734--62057825 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
62057724 TGGCTCTTCG
*
62057734 GAGCTACCCG-TTATTGGCTCGCAT
1 GAGCTACCCGAATA-TGGCTCGCAT
* *
62057758 GAGCTTCCTGAATATGGCTCGCAT
1 GAGCTACCCGAATATGGCTCGCAT
* * *
62057782 GAGCTTCCTGAATATCGCTCGCAT
1 GAGCTACCCGAATATGGCTCGCAT
* *
62057806 GAGCTTCCTGAATATGGCTC
1 GAGCTACCCGAATATGGCTC
62057826 TTATGAGTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 60 0.97
25 2 0.03
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (24 bp):
GAGCTACCCGAATATGGCTCGCAT
Found at i:62057837 original size:24 final size:24
Alignment explanation
Indices: 62057748--62057825 Score: 147
Period size: 24 Copynumber: 3.2 Consensus size: 24
62057738 TACCCGTTAT
62057748 TGGCTCGCATGAGCTTCCTGAATA
1 TGGCTCGCATGAGCTTCCTGAATA
62057772 TGGCTCGCATGAGCTTCCTGAATA
1 TGGCTCGCATGAGCTTCCTGAATA
*
62057796 TCGCTCGCATGAGCTTCCTGAATA
1 TGGCTCGCATGAGCTTCCTGAATA
62057820 TGGCTC
1 TGGCTC
62057826 TTATGAGTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.29
Consensus pattern (24 bp):
TGGCTCGCATGAGCTTCCTGAATA
Found at i:62063875 original size:2 final size:2
Alignment explanation
Indices: 62063868--62063893 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62063858 AGCTTGCTTT
62063868 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
62063894 GGATTTCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:62064187 original size:24 final size:23
Alignment explanation
Indices: 62064160--62064211 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
62064150 GTTTTTGGTA
62064160 TTGTTCATCAATTCCTTTTTTGC
1 TTGTTCATCAATTCCTTTTTTGC
* *
62064183 GTTGTTCGTCACTTCCTTTTTTGC
1 -TTGTTCATCAATTCCTTTTTTGC
62064207 TTGTT
1 TTGTT
62064212 TTTTCAGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.08, C:0.21, G:0.13, T:0.58
Consensus pattern (23 bp):
TTGTTCATCAATTCCTTTTTTGC
Found at i:62065745 original size:6 final size:6
Alignment explanation
Indices: 62065737--62065770 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
62065727 TGGCCATGGC
* *
62065737 CTGCAC CTGCAA CTGCAA CTGCAA CTGCAG CTGC
1 CTGCAA CTGCAA CTGCAA CTGCAA CTGCAA CTGC
62065771 TTACATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.24, C:0.38, G:0.21, T:0.18
Consensus pattern (6 bp):
CTGCAA
Found at i:62070850 original size:29 final size:29
Alignment explanation
Indices: 62070794--62070850 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
62070784 ATAAAATGTT
* *
62070794 TAATGTAGTAATTGTACTATGAAAATATC
1 TAATGTAGTAATTGAACTATCAAAATATC
* * *
62070823 TAATGTGGTATTTGAACTATCAATATAT
1 TAATGTAGTAATTGAACTATCAAAATAT
62070851 GTTTTATTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (29 bp):
TAATGTAGTAATTGAACTATCAAAATATC
Found at i:62071480 original size:29 final size:28
Alignment explanation
Indices: 62071430--62071484 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
62071420 TTGACACTTC
* *
62071430 AAGTAAAGTATTACATTGGACATTTTCA
1 AAGTAAAGGATTACATTAGACATTTTCA
*
62071458 AAGTACAAGGATTATATTAGACATTTT
1 AAGTA-AAGGATTACATTAGACATTTT
62071485 ATGCAAGTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (28 bp):
AAGTAAAGGATTACATTAGACATTTTCA
Found at i:62072257 original size:6 final size:6
Alignment explanation
Indices: 62072248--62072296 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
62072238 CTTCCTACAC
62072248 TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA
1 TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA
62072296 T
1 T
62072297 ACGAGTGATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (6 bp):
TCTATA
Found at i:62075058 original size:12 final size:12
Alignment explanation
Indices: 62075043--62075068 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
62075033 TTTTATTATT
62075043 TAATTTATGCAA
1 TAATTTATGCAA
62075055 TAATTTATGCAA
1 TAATTTATGCAA
62075067 TA
1 TA
62075069 TTTTTTTGCT
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:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
TAATTTATGCAA
Found at i:62077174 original size:137 final size:137
Alignment explanation
Indices: 62076928--62077205 Score: 520
Period size: 137 Copynumber: 2.0 Consensus size: 137
62076918 CTGGTTCCTA
62076928 GATGATATATGATGTGTATATTGGGAAGAACCATTTCTTCTCTTCTTTATTTATTTAAAAAAAGA
1 GATGATATATGATGTGTATATTGGGAAGAACCATTTCTTCTCTTCTTTATTTATTTAAAAAAAGA
* * *
62076993 AAAGCATAAGAAATTTGTGGTGAAAATGGTATCTTATGTAAGATCTTTCCAAATGAGAATTTACA
66 AAAGAACAAGAAATTTGTGGTGAAAATGGTATCTTATGTAAGATCTTTCCAAATAAGAATTTACA
62077058 TGGCCCT
131 TGGCCCT
*
62077065 GATGATATATGATGTGTATATTGGGAAGAACCATTTCTTCTCTTCTTTATTTATTTTAAAAAAGA
1 GATGATATATGATGTGTATATTGGGAAGAACCATTTCTTCTCTTCTTTATTTATTTAAAAAAAGA
62077130 AAAGAACAAGAAATTTGTGGTGAAAATGGTATCTTATGTAAGATCTTTCCAAATAAGAATTTACA
66 AAAGAACAAGAAATTTGTGGTGAAAATGGTATCTTATGTAAGATCTTTCCAAATAAGAATTTACA
62077195 TGGCCCT
131 TGGCCCT
62077202 GATG
1 GATG
62077206 GTTGCATTTC
Statistics
Matches: 137, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (137 bp):
GATGATATATGATGTGTATATTGGGAAGAACCATTTCTTCTCTTCTTTATTTATTTAAAAAAAGA
AAAGAACAAGAAATTTGTGGTGAAAATGGTATCTTATGTAAGATCTTTCCAAATAAGAATTTACA
TGGCCCT
Found at i:62080786 original size:15 final size:15
Alignment explanation
Indices: 62080751--62080802 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
62080741 TTAAGAATTT
*
62080751 TATTAAATTAT-ATA
1 TATTTAATTATAATA
62080765 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
62080779 TATTTAATAATAAT-
1 TATTTAATTATAATA
62080793 TATGTTAATT
1 TAT-TTAATT
62080803 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:62080836 original size:120 final size:120
Alignment explanation
Indices: 62080689--62080918 Score: 460
Period size: 120 Copynumber: 1.9 Consensus size: 120
62080679 TTTGAGTAAA
62080689 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
62080754 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
62080809 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
62080874 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
62080919 TAAATATGAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 110 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (120 bp):
TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
Found at i:62080884 original size:61 final size:61
Alignment explanation
Indices: 62080699--62080886 Score: 208
Period size: 61 Copynumber: 3.1 Consensus size: 61
62080689 TTATAGTATC
62080699 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * * * *
62080760 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTA-AATT
62080819 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
62080880 ATATATT
1 ATATATT
62080887 TTAATTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 29 0.30
60 26 0.27
61 36 0.37
62 3 0.03
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:62080901 original size:16 final size:16
Alignment explanation
Indices: 62080880--62080921 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
62080870 TTATTAAATT
*
62080880 ATATATTTTAATTATA
1 ATATATTTTAATAATA
62080896 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
62080911 AT-TATGTTTAA
1 ATATAT-TTTAA
62080922 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:62080906 original size:15 final size:15
Alignment explanation
Indices: 62080871--62080912 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
62080861 TTAAGAATTT
*
62080871 TATTAAATTAT-ATA
1 TATTTAATTATAATA
62080885 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
62080899 TATTTAATAATAAT
1 TATTTAATTATAAT
62080913 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:62081147 original size:45 final size:43
Alignment explanation
Indices: 62081047--62081156 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
62081037 TTTTCCATTA
62081047 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
62081086 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
62081131 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
62081157 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:62081158 original size:16 final size:16
Alignment explanation
Indices: 62081137--62081204 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
62081127 GATTTGCTAT
*
62081137 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
62081153 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
62081169 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
62081185 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
62081201 TACA
1 TACA
62081205 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:62081269 original size:26 final size:25
Alignment explanation
Indices: 62081229--62081282 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 25
62081219 CCCTGATTAT
*
62081229 TTTACTTAGATATCAAAGTTTTCGA
1 TTTACTTAGAAATCAAAGTTTTCGA
62081254 TTTACTTACGAAATCAAAGTTTTCGA
1 TTTACTTA-GAAATCAAAGTTTTCGA
62081280 TTT
1 TTT
62081283 CAAGCAAGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (25 bp):
TTTACTTAGAAATCAAAGTTTTCGA
Found at i:62092067 original size:28 final size:28
Alignment explanation
Indices: 62092034--62092097 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
62092024 GGGCAAAGTA
62092034 TAATTTTACCTTTACTAATTTAAAATTT
1 TAATTTTACCTTTACTAATTTAAAATTT
62092062 TAATTTTACCTTTACTAATTTAAAATTT
1 TAATTTTACCTTTACTAATTTAAAATTT
*
62092090 TCATTTTA
1 TAATTTTA
62092098 GGGGGTCGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (28 bp):
TAATTTTACCTTTACTAATTTAAAATTT
Found at i:62092582 original size:21 final size:20
Alignment explanation
Indices: 62092535--62092583 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
62092525 GATCTTAATT
62092535 AAACTATT-A-TTTCAATAA
1 AAACTATTAATTTTCAATAA
**
62092553 AATGT-TTAATTTTCACATAA
1 AAACTATTAATTTTCA-ATAA
62092573 AAACTATTAAT
1 AAACTATTAAT
62092584 CATGTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
17 2 0.09
18 4 0.17
19 5 0.22
20 7 0.30
21 5 0.22
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (20 bp):
AAACTATTAATTTTCAATAA
Found at i:62092734 original size:32 final size:32
Alignment explanation
Indices: 62092698--62092760 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
62092688 TCATAAACTT
62092698 ATAAATTGA-TTATTTGAATTTAATAACTCATG
1 ATAAATTGATTTATTT-AATTTAATAACTCATG
* *
62092730 ATAAATTGATTTATTTATTTTGATAACTCAT
1 ATAAATTGATTTATTTAATTTAATAACTCAT
62092761 AAAAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (32 bp):
ATAAATTGATTTATTTAATTTAATAACTCATG
Found at i:62092763 original size:29 final size:29
Alignment explanation
Indices: 62092693--62092763 Score: 72
Period size: 32 Copynumber: 2.3 Consensus size: 29
62092683 AAGCATCATA
*
62092693 AACTTATAAATTGATTATTTGAATTTAAT
1 AACTCATAAATTGATTATTTGAATTTAAT
* *
62092722 AACTCATGATAAATTGATTTATTT-ATTTTGAT
1 AACTC---ATAAATTGA-TTATTTGAATTTAAT
62092754 AACTCATAAA
1 AACTCATAAA
62092764 AATTAATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
29 9 0.26
32 20 0.57
33 6 0.17
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (29 bp):
AACTCATAAATTGATTATTTGAATTTAAT
Found at i:62092849 original size:145 final size:144
Alignment explanation
Indices: 62092664--62092929 Score: 354
Period size: 145 Copynumber: 1.8 Consensus size: 144
62092654 TTCTACTTAA
* *
62092664 ATATTCTACTATGAATTTCAAGCATCATAAACTTATAAATTGATTATTTGAATTTAATAACTCAT
1 ATATTCTACTATGAATTTCAAGCATCATAAACTTATAAATTGATTACTTGAATTTAATAACACAT
* * * * *
62092729 GATAAATTGATTTATTTATTTTGATAACTCATAAAAATTAATTGAGCTTGTTAGATTTATGATCA
66 GATAAATT-AATTAATTAATTTGATAACTCATAAAAATTAATTAAACTTGTTAGATTTATGATCA
62092794 ATCACGTGTAAGAAT
130 ATCACGTGTAAGAAT
* * ** *
62092809 ATATTTTACTATGAATTTGGAA-CATCATATGCTTATAAATTGATTACTTGAGTTTAATAACACA
1 ATATTCTACTATGAATTT-CAAGCATCATAAACTTATAAATTGATTACTTGAATTTAATAACACA
* * ***
62092873 TTATTAATTAATTAATTAATTTGATAACTCATATTGATTAATTAAACTTGTTAGATT
65 TGATAAATTAATTAATTAATTTGATAACTCATAAAAATTAATTAAACTTGTTAGATT
62092930 AATAATCCTC
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
144 40 0.39
145 61 0.59
146 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (144 bp):
ATATTCTACTATGAATTTCAAGCATCATAAACTTATAAATTGATTACTTGAATTTAATAACACAT
GATAAATTAATTAATTAATTTGATAACTCATAAAAATTAATTAAACTTGTTAGATTTATGATCAA
TCACGTGTAAGAAT
Found at i:62094933 original size:113 final size:113
Alignment explanation
Indices: 62094793--62095215 Score: 389
Period size: 113 Copynumber: 3.7 Consensus size: 113
62094783 GTTTACCTTC
* * * *
62094793 AAGCGCCGCAAAAT-CCCTAAACCAAAACGCAGTGTTTTAGTGTTGATGTATACTAGAATTAGTG
1 AAGCGCCGCAAAATATCTTAAA--AAAACGCAGTGTTTTGGTCTTGATGTATACTAGAATTAGTG
* * * * *
62094857 GCGATTATGGGAAAACTCCGTTAAAGCAAGTATTAG-AGCGATCCGTGAA
64 GCGATTATGGAAAAACGCCGCTAAAGCAAGTATTAGCGGCGATTCGTGAA
* * *
62094906 AAGCGCTGCAAAAAATCTTAAAGAAAACGCA-TCGTTTTGGTCTTGATGTATATTAGAATTAGTG
1 AAGCGCCGCAAAATATCTTAAA-AAAACGCAGT-GTTTTGGTCTTGATGTATACTAGAATTAGTG
* * * *
62094970 GCGCTTA-AGAAAACACGCCGCTAAAG-AATGTATTAGCGGCGCTTCTTGAA
64 GCGATTATGGAAAA-ACGCCGCTAAAGCAA-GTATTAGCGGCGATTCGTGAA
* * * * *
62095020 AAGCGCCGCAAAATATCTT-AAAAAATGCAGAG-TTTGGTTTTGA-GTTATATTATAATTAGTGG
1 AAGCGCCGCAAAATATCTTAAAAAAACGCAGTGTTTTGGTCTTGATG-TATACTAGAATTAGTGG
* * * * **
62095082 CGATTATGGAAAAACGCTGCCAAAGCAAAGTATTAGCGGCGTTTTGTGGC
65 CGATTATGGAAAAACGCCGCTAAAGC-AAGTATTAGCGGCGATTCGTGAA
* * *
62095132 AAGTGCCGCAAAATATCTTAAAACAAAACGTAGCT-TTTTGGTCTTAATGTATACTAGAATTAGT
1 AAGCGCCGCAAAATATCTT-AAA-AAAACGCAG-TGTTTTGGTCTTGATGTATACTAGAATTAGT
* *
62095196 GACGCTTATGG-AAAACGCCG
63 GGCGATTATGGAAAAACGCCG
62095216 TCATGGTTTG
Statistics
Matches: 251, Mismatches: 43, Indels: 30
0.77 0.13 0.09
Matches are distributed among these distances:
110 1 0.00
111 41 0.16
112 54 0.22
113 75 0.30
114 33 0.13
115 15 0.06
116 31 0.12
117 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (113 bp):
AAGCGCCGCAAAATATCTTAAAAAAACGCAGTGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
GATTATGGAAAAACGCCGCTAAAGCAAGTATTAGCGGCGATTCGTGAA
Found at i:62095140 original size:112 final size:111
Alignment explanation
Indices: 62094835--62095154 Score: 290
Period size: 112 Copynumber: 2.9 Consensus size: 111
62094825 TGTTTTAGTG
* * * * ** * * *
62094835 TTGATGTATACTAGAATTAGTGGCGATTATGGGAAA-ACTCCGTTAAAGCAAGTATTAG-AGCGA
1 TTGATGTATATTAGAATTAGTGGCGATTA-AGAAAACACGCCGCCAAAGAAAGTATTAGCGGCGC
* * * * * **
62094898 TCCGTGAAAAGCGCTGCAAAAAATCTTAAAGAAAACGCATCGTTTTGGTC
65 TTCTTGAAAAGCGCCGCAAAATATCTT-AA-AAAATGCAGAG-TTTGGTC
* * *
62094948 TTGATGTATATTAGAATTAGTGGCGCTTAAGAAAACACGCCGCTAAAGAATGTATTAGCGGCGCT
1 TTGATGTATATTAGAATTAGTGGCGATTAAGAAAACACGCCGCCAAAGAAAGTATTAGCGGCGCT
*
62095013 TCTTGAAAAGCGCCGCAAAATATCTTAAAAAATGCAGAGTTTGGTT
66 TCTTGAAAAGCGCCGCAAAATATCTTAAAAAATGCAGAGTTTGGTC
* * *
62095059 TTGA-GTTATATTATAATTAGTGGCGATTATGGAAAA-ACGCTGCCAAAGCAAAGTATTAGCGGC
1 TTGATG-TATATTAGAATTAGTGGCGATTA-AGAAAACACGCCGCCAAAG-AAAGTATTAGCGGC
* ** *
62095122 G-TTTTGTGGCAAGTGCCGCAAAATATCTTAAAA
63 GCTTCT-TGAAAAGCGCCGCAAAATATCTTAAAA
62095155 CAAAACGTAG
Statistics
Matches: 173, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
110 1 0.01
111 44 0.25
112 55 0.32
113 47 0.27
114 26 0.15
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (111 bp):
TTGATGTATATTAGAATTAGTGGCGATTAAGAAAACACGCCGCCAAAGAAAGTATTAGCGGCGCT
TCTTGAAAAGCGCCGCAAAATATCTTAAAAAATGCAGAGTTTGGTC
Found at i:62095507 original size:75 final size:76
Alignment explanation
Indices: 62095400--62095589 Score: 249
Period size: 76 Copynumber: 2.5 Consensus size: 76
62095390 GAGACAAGCG
* * *
62095400 CCGCAAAATATCTTAACCAAAACGTAGAGTTTT-GTTTTGAGGTATATTAGAATTAGTGGCGCTT
1 CCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCTT
62095464 AAAGAAAAACA
66 AAAGAAAAACA
* *
62095475 CCGCAAAATATCTTAACCAAAACGCA-ATGTTTTGGTCTTGATGTATACTAGAGTTAGTGGCGCT
1 CCGCAAAATATCTTAACCAAAACGCAGA-GTTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCT
*** * * *
62095539 TGCGGGAAAGCG
65 TAAAGAAAAACA
*
62095551 CCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTT
1 CCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
62095590 AACCATGCAT
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
74 1 0.01
75 30 0.30
76 69 0.69
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (76 bp):
CCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCTT
AAAGAAAAACA
Found at i:62095716 original size:21 final size:21
Alignment explanation
Indices: 62095692--62095756 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 21
62095682 TGTTTTTGGA
62095692 TTACAGTTTAGGGTTTAGAGT
1 TTACAGTTTAGGGTTTAGAGT
* * *
62095713 TTACAATATA-GGTTTAGTGT
1 TTACAGTTTAGGGTTTAGAGT
*
62095733 TTTC-GATTTAGGGTTTGAGAGT
1 TTACAG-TTTAGGGTTT-AGAGT
62095755 TT
1 TT
62095757 GGTGATTAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 15 0.44
21 13 0.38
22 6 0.18
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (21 bp):
TTACAGTTTAGGGTTTAGAGT
Found at i:62098517 original size:27 final size:27
Alignment explanation
Indices: 62098482--62098549 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
62098472 AATAATAAAA
62098482 ATTTACCAAAATATTACAACTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTT
62098509 ATTTACCAAAATATTACAACTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTT
62098536 ATTTACCAAAATAT
1 ATTTACCAAAATAT
62098550 ATCAAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTTACCAAAATATTACAACTTTTTTT
Found at i:62098763 original size:41 final size:39
Alignment explanation
Indices: 62098718--62098840 Score: 130
Period size: 41 Copynumber: 3.1 Consensus size: 39
62098708 AAGGAGAGGA
62098718 AAGAAAGACAAGGAAAGGAGAAGAGAAAAAAGGAAAGAAAG
1 AAGAAAGA-AAGGAAAGGAGAAGAGAAAAAA-GAAAGAAAG
*
62098759 AAG-AAGAAAAGGAGAA-GAG-A-AGAAAAAAGAAGGAAAG
1 AAGAAAG-AAAGGA-AAGGAGAAGAGAAAAAAGAAAGAAAG
*
62098796 AAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAAGAAG-AAG
1 AA-GAAAGAAA-GGAAAGGAGAAGAGAAAAAAGA-AAGAAAG
62098837 AAGA
1 AAGA
62098841 GGGAAGAAAG
Statistics
Matches: 70, Mismatches: 3, Indels: 19
0.76 0.03 0.21
Matches are distributed among these distances:
37 10 0.14
38 14 0.20
39 10 0.14
40 14 0.20
41 20 0.29
42 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.33, T:0.00
Consensus pattern (39 bp):
AAGAAAGAAAGGAAAGGAGAAGAGAAAAAAGAAAGAAAG
Found at i:62098788 original size:23 final size:23
Alignment explanation
Indices: 62098745--62098849 Score: 75
Period size: 23 Copynumber: 4.8 Consensus size: 23
62098735 GAGAAGAGAA
*
62098745 AAAAGGA-AAGA-AAG-AAGAAG
1 AAAAGGAGAAGAGAAGAAAAAAG
62098765 AAAAGGAGAAGAGAAGAAAAAAG
1 AAAAGGAGAAGAGAAGAAAAAAG
*
62098788 --AAGGA-AAGA-AGGAAAGAAAGG
1 AAAAGGAGAAGAGAAGAAA-AAA-G
*
62098809 GAAAGGAGAAGAGAA-AAAAAAG
1 AAAAGGAGAAGAGAAGAAAAAAG
* *
62098831 AAGAAGAAG-AGGGAAGAAA
1 AA-AAGGAGAAGAGAAGAAA
62098850 GGGAAAAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
19 5 0.07
20 14 0.21
21 10 0.15
22 10 0.15
23 21 0.31
24 7 0.10
25 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAAAGGAGAAGAGAAGAAAAAAG
Found at i:62098805 original size:26 final size:26
Alignment explanation
Indices: 62098752--62098805 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
62098742 GAAAAAAGGA
* * *
62098752 AAGAAAGAAGAAGAAAAGGAGAAGAG
1 AAGAAAAAAGAAGAAAAGAAGAAAAG
* *
62098778 AAGAAAAAAGAAGGAAAGAAGGAAAG
1 AAGAAAAAAGAAGAAAAGAAGAAAAG
62098804 AA
1 AA
62098806 AGGGAAAGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (26 bp):
AAGAAAAAAGAAGAAAAGAAGAAAAG
Found at i:62098829 original size:44 final size:42
Alignment explanation
Indices: 62098729--62098855 Score: 142
Period size: 43 Copynumber: 3.1 Consensus size: 42
62098719 AGAAAGACAA
*
62098729 GGAAAGGAGAAGAG----AAAA-AAGGAAAGAAAGAAG-AA-
1 GGAAAGGAGAAGAGAAAAAAAAGAAGGAAAGAAGGAAGAAAG
*
62098764 GAAAAGGAGAAGAGAAGAAAAAAGAAGGAAAGAAGGAAAGAAAG
1 GGAAAGGAGAAGAGAA-AAAAAAGAAGGAAAGAAGG-AAGAAAG
* *
62098808 GGAAAGGAGAAGAGAAAAAAAAGAAGAAGAAGAGGGAAGAAAG
1 GGAAAGGAGAAGAGAAAAAAAAGAAGGA-AAGAAGGAAGAAAG
62098851 GGAAA
1 GGAAA
62098856 AAAAGGTAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
35 13 0.17
40 4 0.05
41 11 0.14
42 3 0.04
43 25 0.32
44 21 0.27
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (42 bp):
GGAAAGGAGAAGAGAAAAAAAAGAAGGAAAGAAGGAAGAAAG
Found at i:62098887 original size:19 final size:20
Alignment explanation
Indices: 62098863--62098901 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
62098853 AAAAAAAGGT
62098863 AATTTTATTTATAA-ATTTG
1 AATTTTATTTATAATATTTG
* *
62098882 AATTTTTTTTGTAATATTTG
1 AATTTTATTTATAATATTTG
62098902 TGTGTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
AATTTTATTTATAATATTTG
Found at i:62104903 original size:15 final size:12
Alignment explanation
Indices: 62104866--62104896 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
62104856 AAAAAAATTT
*
62104866 ATACTCAAAATA
1 ATACACAAAATA
62104878 ATACACAAAATA
1 ATACACAAAATA
62104890 ATACACA
1 ATACACA
62104897 CTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
ATACACAAAATA
Found at i:62104951 original size:26 final size:26
Alignment explanation
Indices: 62104902--62104954 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
62104892 ACACACTAAA
* *
62104902 ATTATTAATTTTATACTACGAATAAT
1 ATTAATAATTTTATACTACAAATAAT
62104928 ATTAATAATTTTATACT-CAAAATAAT
1 ATTAATAATTTTATACTAC-AAATAAT
62104954 A
1 A
62104955 CACACTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAATAATTTTATACTACAAATAAT
Found at i:62104996 original size:62 final size:61
Alignment explanation
Indices: 62104878--62104998 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 61
62104868 ACTCAAAATA
**
62104878 ATACACAAAATAATACACACTAAAATTATTAATTTTATACTACGAATAATATTAATAATTTT
1 ATACACAAAATAATACACACTAAAATTATTAATTTTATAC-AAAAATAATATTAATAATTTT
*
62104940 ATACTCAAAATAATACACACTAAAATTATTAATTTTACTA-AAAAACTAACTA-TAATAAT
1 ATACACAAAATAATACACACTAAAATTATTAATTTTA-TACAAAAA-TAA-TATTAATAAT
62104999 ACTAATTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 3 0.06
62 46 0.87
63 4 0.08
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (61 bp):
ATACACAAAATAATACACACTAAAATTATTAATTTTATACAAAAATAATATTAATAATTTT
Found at i:62105136 original size:3 final size:3
Alignment explanation
Indices: 62105128--62105159 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
62105118 TCTTAATACT
62105128 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
62105160 TAATAATAAT
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:62105246 original size:19 final size:21
Alignment explanation
Indices: 62105222--62105260 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
62105212 ACTACAACAA
*
62105222 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAATAATATAC
62105241 AAAATAATAACAATAATATA
1 AAAATAATAACAATAATATA
62105261 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATAATAACAATAATATAC
Found at i:62105557 original size:28 final size:28
Alignment explanation
Indices: 62105499--62105594 Score: 153
Period size: 27 Copynumber: 3.5 Consensus size: 28
62105489 TTTTTTTTAT
62105499 ATATTTTGGTAAAT-AAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
62105525 TATATTTTGGTAAATAAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAGTTGTA
62105554 ATATTTTGGTAAATAAAAAAAA-TTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
*
62105581 ATATTTTAGTAAAT
1 ATATTTTGGTAAAT
62105595 TTTTATTATT
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
27 32 0.48
28 32 0.48
29 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:62106097 original size:31 final size:31
Alignment explanation
Indices: 62106040--62106098 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
62106030 ATCTTTATAA
*
62106040 TTTTTAAAGAATTAAATTAAATTTTTATTAT
1 TTTTTAAAGAATTAAATTAAAATTTTATTAT
* *
62106071 TTTTTGAAGAGTT-AATATAAAATTTTAT
1 TTTTTAAAGAATTAAAT-TAAAATTTTAT
62106099 CATTACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.53
Consensus pattern (31 bp):
TTTTTAAAGAATTAAATTAAAATTTTATTAT
Found at i:62111798 original size:31 final size:31
Alignment explanation
Indices: 62111760--62111825 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
62111750 TACAATTTAG
*
62111760 TCACCAAACTATTCAAAA-GTTTTCATTTAAA
1 TCACCAAACTATTCAAAATGCTTT-ATTTAAA
*
62111791 TCACCAAACTATTCAAAATGCTTTATTTAAG
1 TCACCAAACTATTCAAAATGCTTTATTTAAA
62111822 TCAC
1 TCAC
62111826 TAAGCTGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (31 bp):
TCACCAAACTATTCAAAATGCTTTATTTAAA
Found at i:62113049 original size:13 final size:13
Alignment explanation
Indices: 62113031--62113065 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
62113021 TATCTCAGAG
* *
62113031 AATTTTCTGAAAC
1 AATTTTCTCAAAA
62113044 AATTTTCTCAAAA
1 AATTTTCTCAAAA
62113057 AATTTTCTC
1 AATTTTCTC
62113066 TCTACAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (13 bp):
AATTTTCTCAAAA
Found at i:62113264 original size:20 final size:21
Alignment explanation
Indices: 62113168--62113284 Score: 85
Period size: 21 Copynumber: 5.2 Consensus size: 21
62113158 ACTTAATCAT
62113168 TTTAATATTAAATTAATATAATA
1 TTTAATATTAAATTAAT-TAA-A
* *
62113191 CTTATCAAGATAAATATTAGATTAAA
1 -TT-T-AATATTAA-ATTA-ATTAAA
62113217 TTTAATATTAAATTAATTAAA
1 TTTAATATTAAATTAATTAAA
* *
62113238 TTCAATATTAAGA-TAA-TCAA
1 TTTAATATTAA-ATTAATTAAA
* *
62113258 TTTAATATTAAATGAATTTAA
1 TTTAATATTAAATTAATTAAA
62113279 TATTAA
1 T-TTAA
62113285 ATCTATTAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.01
20 15 0.20
21 23 0.30
22 9 0.12
23 6 0.08
24 3 0.04
25 3 0.04
26 7 0.09
27 7 0.09
28 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (21 bp):
TTTAATATTAAATTAATTAAA
Found at i:62113277 original size:16 final size:16
Alignment explanation
Indices: 62113256--62113286 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
62113246 TAAGATAATC
62113256 AATTTAATATTAAATG
1 AATTTAATATTAAATG
62113272 AATTTAATATTAAAT
1 AATTTAATATTAAAT
62113287 CTATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AATTTAATATTAAATG
Found at i:62115922 original size:104 final size:104
Alignment explanation
Indices: 62115787--62116052 Score: 462
Period size: 104 Copynumber: 2.6 Consensus size: 104
62115777 TTGTACATAA
** *
62115787 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
62115852 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
62115891 AGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
62115955 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * *
62115995 AGGGGTTGCTAAGTGATGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
62116053 AATAACGGTT
Statistics
Matches: 154, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
103 1 0.01
104 152 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:62126070 original size:21 final size:21
Alignment explanation
Indices: 62126046--62126087 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
62126036 TATGAGCAAC
62126046 AAAAGAAAAATGG-AAGTGAAG
1 AAAA-AAAAATGGAAAGTGAAG
* *
62126067 AAAAATAGATGGAAAGTGAAG
1 AAAAAAAAATGGAAAGTGAAG
62126088 GGTAGTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.12
Consensus pattern (21 bp):
AAAAAAAAATGGAAAGTGAAG
Found at i:62129232 original size:60 final size:60
Alignment explanation
Indices: 62129159--62129340 Score: 364
Period size: 60 Copynumber: 3.0 Consensus size: 60
62129149 ACAAGCCCTC
62129159 ACGCGTTTGAAAAGAAACGTGTTAAGCTCATGAAAGTTTAGTAAGCATATCAAGAATTTA
1 ACGCGTTTGAAAAGAAACGTGTTAAGCTCATGAAAGTTTAGTAAGCATATCAAGAATTTA
62129219 ACGCGTTTGAAAAGAAACGTGTTAAGCTCATGAAAGTTTAGTAAGCATATCAAGAATTTA
1 ACGCGTTTGAAAAGAAACGTGTTAAGCTCATGAAAGTTTAGTAAGCATATCAAGAATTTA
62129279 ACGCGTTTGAAAAGAAACGTGTTAAGCTCATGAAAGTTTAGTAAGCATATCAAGAATTTA
1 ACGCGTTTGAAAAGAAACGTGTTAAGCTCATGAAAGTTTAGTAAGCATATCAAGAATTTA
62129339 AC
1 AC
62129341 TTTGCATTTG
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 122 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (60 bp):
ACGCGTTTGAAAAGAAACGTGTTAAGCTCATGAAAGTTTAGTAAGCATATCAAGAATTTA
Found at i:62129693 original size:23 final size:23
Alignment explanation
Indices: 62129647--62129693 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
62129637 CACTAGCACC
* *
62129647 TGCACCGTAGTGCCATTTTTACT
1 TGCACCGTAGTGCCATTATCACT
62129670 TGCACCGTAGTGCCATTATCACT
1 TGCACCGTAGTGCCATTATCACT
62129693 T
1 T
62129694 TCGCGAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (23 bp):
TGCACCGTAGTGCCATTATCACT
Found at i:62132495 original size:41 final size:38
Alignment explanation
Indices: 62132450--62132542 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 38
62132440 AGCGGTATTT
62132450 TTAGCGGCGTTTGGACAAAAAACGCCGCTAAAAATCGAGCA
1 TTAGCGGCGTTTGG---AAAAACGCCGCTAAAAATCGAGCA
* *
62132491 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAAATTGAGCA
1 TTAGCGGCG--TTTGGAAAAACGCCGCTAAAAATCGAGCA
62132531 TTAGCGGCGTTT
1 TTAGCGGCGTTT
62132543 ATAAGGAAGC
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
38 3 0.06
40 32 0.67
41 9 0.19
43 4 0.08
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (38 bp):
TTAGCGGCGTTTGGAAAAACGCCGCTAAAAATCGAGCA
Found at i:62132737 original size:82 final size:83
Alignment explanation
Indices: 62132619--62132836 Score: 207
Period size: 83 Copynumber: 2.7 Consensus size: 83
62132609 GTTTTTGAAG
* * *
62132619 AAGCGTCGCTAATGTTGGGGGATTTAGCGGCGTTTTTGAAG-AAGCGTCGCTAATACTGAGGGAT
1 AAGCGCCGCTAATGTTGGGGCATTTAGCGGCGTTTTTGAAGAAAGCGCCGCTAATACTGAGGGAT
*
62132683 TTAGCGGCG-TTTTCTAGA
66 TTAGC-ACGTTTTTCTAGA
* * * * * ** *
62132701 AAGCGCCGCTAATGTTCTGGGCA-TTAGCGTCGTTTTTGAAGAAAGTGCCGCTATTGCTTTGGGT
1 AAGCGCCGCTAATGTT-GGGGCATTTAGCGGCGTTTTTGAAGAAAGCGCCGCTAATACTGAGGGA
*
62132765 TTTAGCACGTTTTTTTAGA
65 TTTAGCACGTTTTTCTAGA
** *
62132784 AAGCGCCGCTAAT-TCTCTAGGC-TTTAGCGGTGTTTTT--AGAAAGCGCCGCTAAT
1 AAGCGCCGCTAATGT-T-GGGGCATTTAGCGGCGTTTTTGAAGAAAGCGCCGCTAAT
62132837 GCTCGGAGGC
Statistics
Matches: 113, Mismatches: 18, Indels: 11
0.80 0.13 0.08
Matches are distributed among these distances:
81 14 0.12
82 35 0.31
83 64 0.57
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.33
Consensus pattern (83 bp):
AAGCGCCGCTAATGTTGGGGCATTTAGCGGCGTTTTTGAAGAAAGCGCCGCTAATACTGAGGGAT
TTAGCACGTTTTTCTAGA
Found at i:62132770 original size:42 final size:42
Alignment explanation
Indices: 62132589--62132839 Score: 207
Period size: 41 Copynumber: 6.1 Consensus size: 42
62132579 ATTTACTGAG
* *
62132589 GCTTTGGGGACTTTAGCTGCGTTTTTGAAG-AAGCGTCGCTAAT
1 GCTTT-GGGA-TTTAGCGGCGTTTTTGAAGAAAGCGCCGCTAAT
* *
62132632 G-TTGGGGGATTTAGCGGCGTTTTTGAAG-AAGCGTCGCTAAT
1 GCTT-TGGGATTTAGCGGCGTTTTTGAAGAAAGCGCCGCTAAT
* **
62132673 ACTGAGGGATTTAGCGGCGTTTTCT--AGAAAGCGCCGCTAAT
1 GCTTTGGGATTTAGCGGCGTTTT-TGAAGAAAGCGCCGCTAAT
* * *
62132714 G-TTCTGGGCA-TTAGCGTCGTTTTTGAAGAAAGTGCCGCTATT
1 GCTT-TGGG-ATTTAGCGGCGTTTTTGAAGAAAGCGCCGCTAAT
* * **
62132756 GCTTTGGGTTTTAGC-ACGTTTTTTTAGAAAGCGCCGCTAAT
1 GCTTTGGGATTTAGCGGCGTTTTTGAAGAAAGCGCCGCTAAT
* * * * *
62132797 TCTCTAGGCTTTAGCGGTGTTTTT--AGAAAGCGCCGCTAAT
1 GCTTTGGGATTTAGCGGCGTTTTTGAAGAAAGCGCCGCTAAT
62132837 GCT
1 GCT
62132840 CGGAGGCTTT
Statistics
Matches: 172, Mismatches: 25, Indels: 25
0.77 0.11 0.11
Matches are distributed among these distances:
40 22 0.13
41 108 0.63
42 39 0.23
43 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (42 bp):
GCTTTGGGATTTAGCGGCGTTTTTGAAGAAAGCGCCGCTAAT
Found at i:62132994 original size:21 final size:21
Alignment explanation
Indices: 62132968--62133008 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62132958 TTTATAGTGT
* *
62132968 AGGTTTAGGGTTTGGGGTTTG
1 AGGTTTAAGGTTTAGGGTTTG
62132989 AGGTTTAAGGTTTAGGGTTT
1 AGGTTTAAGGTTTAGGGTTT
62133009 ATGTTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (21 bp):
AGGTTTAAGGTTTAGGGTTTG
Found at i:62133007 original size:14 final size:14
Alignment explanation
Indices: 62132968--62133009 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
62132958 TTTATAGTGT
*
62132968 AGGTTTAGGGTTTG
1 AGGTTTAGGGTTTA
*
62132982 GGGTTT-GAGGTTTA
1 AGGTTTAG-GGTTTA
62132996 AGGTTTAGGGTTTA
1 AGGTTTAGGGTTTA
62133010 TGTTTTAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (14 bp):
AGGTTTAGGGTTTA
Found at i:62133159 original size:20 final size:21
Alignment explanation
Indices: 62133130--62133177 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
62133120 TACAATGCAT
* *
62133130 GGTTTTGGGTTTTGGA-TTAG
1 GGTTTAGGGTTTAGGATTTAG
62133150 GGTTTAGGGTTTAGGATTTAG
1 GGTTTAGGGTTTAGGATTTAG
*
62133171 GATTTAG
1 GGTTTAG
62133178 TGTTACAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.46
Consensus pattern (21 bp):
GGTTTAGGGTTTAGGATTTAG
Found at i:62133169 original size:14 final size:14
Alignment explanation
Indices: 62133136--62133177 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
62133126 GCATGGTTTT
*
62133136 GGGTTTTGGA-TTA
1 GGGTTTAGGATTTA
*
62133149 GGGTTTAGGGTTTA
1 GGGTTTAGGATTTA
*
62133163 GGATTTAGGATTTA
1 GGGTTTAGGATTTA
62133177 G
1 G
62133178 TGTTACAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (14 bp):
GGGTTTAGGATTTA
Found at i:62133731 original size:83 final size:83
Alignment explanation
Indices: 62133634--62134062 Score: 687
Period size: 83 Copynumber: 5.2 Consensus size: 83
62133624 AAAGTGAATA
* * * * *
62133634 ATTAGTGGCGTTTTGTCAATAAACGCCGTAAAGAAAATAATAAAAATTGAATAAAACAGCGCTGT
1 ATTAGTGGCGTTTTGTCAATAAACGCCGCAAAGAATATAATAAAAATTGAACAAAACGGCGCCGT
*
62133699 TTCATTGATGAATTAAAT
66 TTCATTGACGAATTAAAT
* * * *
62133717 ATTAGTGGCATTTTGTCAATAAACACCGCAAATAATATAATAAAAATTGAACAAAACGGTGCCGT
1 ATTAGTGGCGTTTTGTCAATAAACGCCGCAAAGAATATAATAAAAATTGAACAAAACGGCGCCGT
*
62133782 TTCATTGACAAATTAAAT
66 TTCATTGACGAATTAAAT
* *
62133800 ATTAGTGGCGTTTTGTCAATAAACGCCGCAAAGAAAATAATAAAAATTGAACAAAACGGCGCCAT
1 ATTAGTGGCGTTTTGTCAATAAACGCCGCAAAGAATATAATAAAAATTGAACAAAACGGCGCCGT
*
62133865 TTCATTGAAGAATTAAAT
66 TTCATTGACGAATTAAAT
* *
62133883 ATTAGTGGCGTTTTGTCAATAAACGCTGCAAAGAATATAATAAAAATTGAACAAAACGACGCCGT
1 ATTAGTGGCGTTTTGTCAATAAACGCCGCAAAGAATATAATAAAAATTGAACAAAACGGCGCCGT
62133948 TTCATTGACGAATTAAAT
66 TTCATTGACGAATTAAAT
* * *
62133966 ATTAGTGGCATTTTGTCAATAAACGCCACAAAGAATACAATAAAAATTGAACAAAACGGCGCCGT
1 ATTAGTGGCGTTTTGTCAATAAACGCCGCAAAGAATATAATAAAAATTGAACAAAACGGCGCCGT
62134031 TTCATTGACGAATTAAAT
66 TTCATTGACGAATTAAAT
62134049 ATTAGTGGCGTTTT
1 ATTAGTGGCGTTTT
62134063 ATCTCCAAAT
Statistics
Matches: 316, Mismatches: 30, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 316 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (83 bp):
ATTAGTGGCGTTTTGTCAATAAACGCCGCAAAGAATATAATAAAAATTGAACAAAACGGCGCCGT
TTCATTGACGAATTAAAT
Found at i:62135002 original size:31 final size:31
Alignment explanation
Indices: 62134964--62135043 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
62134954 TTGGATTTTA
*
62134964 ATTGGTTTTTGCAGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
62134995 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
*
62135026 ATTGATTTTTGCTGCTAA
1 ATTGGTTTTTGCTGCTAA
62135044 ATCAACCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (31 bp):
ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
Found at i:62135889 original size:12 final size:12
Alignment explanation
Indices: 62135872--62135899 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
62135862 GCTAGCCATG
62135872 ATGTTACTATTA
1 ATGTTACTATTA
62135884 ATGTTACTATTA
1 ATGTTACTATTA
62135896 ATGT
1 ATGT
62135900 CCTTAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (12 bp):
ATGTTACTATTA
Found at i:62140144 original size:18 final size:17
Alignment explanation
Indices: 62140116--62140150 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62140106 ATTATTAAGA
*
62140116 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
62140133 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
62140151 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:62140288 original size:18 final size:17
Alignment explanation
Indices: 62140260--62140294 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62140250 ATTATTAAGA
*
62140260 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
62140277 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
62140295 TAAATAATAA
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:62140505 original size:44 final size:45
Alignment explanation
Indices: 62140456--62140550 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
62140446 TTACACCTCT
* *
62140456 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
62140500 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
62140545 ATTACA
1 ATTACA
62140551 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:62140550 original size:16 final size:16
Alignment explanation
Indices: 62140529--62140561 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
62140519 TTGATTTGCT
*
62140529 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
62140545 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
62140561 A
1 A
62140562 ATCCAATACA
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:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:62140571 original size:21 final size:21
Alignment explanation
Indices: 62140542--62140584 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
62140532 ACACCTCTAT
*
62140542 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
62140563 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
62140584 T
1 T
62140585 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:62143865 original size:45 final size:45
Alignment explanation
Indices: 62143756--62143851 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
62143746 CTGCAAACTT
* * * * *
62143756 TTTATCTGAAAATAATGATGGTTTACCCACAATTTTTACTGGTAG
1 TTTATCTAAAAATAATGGTGGTTTACCCACAATTTTTACGGGCAA
62143801 TTTATCTAAAAATAATGGTGGTTTACCCACAATTTTTACGGGCAA
1 TTTATCTAAAAATAATGGTGGTTTACCCACAATTTTTACGGGCAA
62143846 TTTATC
1 TTTATC
62143852 ACAAATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (45 bp):
TTTATCTAAAAATAATGGTGGTTTACCCACAATTTTTACGGGCAA
Found at i:62147756 original size:54 final size:54
Alignment explanation
Indices: 62147697--62147802 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 54
62147687 CTTTACCAAA
62147697 TTATAAAAATATAAAATTTTTATAAATTCATT-AAAAT-TCATTTTTTAAATTTTT
1 TTAT-AAAATATAAAATTTTTATAAATTCATTAAAAATAT-ATTTTTTAAATTTTT
** ***
62147751 TTATAAGTTATATTTTTTTTATAAATTCATTAAAAATATATTTTTTAAATTT
1 TTATAAAATATAAAATTTTTATAAATTCATTAAAAATATATTTTTTAAATTT
62147803 ATCGTAATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
53 22 0.49
54 22 0.49
55 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (54 bp):
TTATAAAATATAAAATTTTTATAAATTCATTAAAAATATATTTTTTAAATTTTT
Found at i:62154845 original size:273 final size:273
Alignment explanation
Indices: 62154358--62154906 Score: 1098
Period size: 273 Copynumber: 2.0 Consensus size: 273
62154348 TAGAATGATT
62154358 TAGGGTTCCCCTGTTCTGACTTTGGAAAATCATTTAAAATTTAATAAAAATAATAATGAGTTATA
1 TAGGGTTCCCCTGTTCTGACTTTGGAAAATCATTTAAAATTTAATAAAAATAATAATGAGTTATA
62154423 ATTTATATTTTTAGAATCCTCGATGAGTCTATTTTCAAATAAAGTAAAAGGAAACATCATCCGAA
66 ATTTATATTTTTAGAATCCTCGATGAGTCTATTTTCAAATAAAGTAAAAGGAAACATCATCCGAA
62154488 TTCTGTACAATTAGATAATTCATTTTTAGTGAAGAGTGGTCGGAACTGTTAGACAGCAAAACAGG
131 TTCTGTACAATTAGATAATTCATTTTTAGTGAAGAGTGGTCGGAACTGTTAGACAGCAAAACAGG
62154553 GGAACGTTAAAGAATAAACTTTATTAATTGGCTGAACCAAAAATTCTGAAAATTTTATGGTAAGA
196 GGAACGTTAAAGAATAAACTTTATTAATTGGCTGAACCAAAAATTCTGAAAATTTTATGGTAAGA
62154618 ATATATTTGAGTC
261 ATATATTTGAGTC
62154631 TAGGGTTCCCCTGTTCTGACTTTGGAAAATCATTTAAAATTTAATAAAAATAATAATGAGTTATA
1 TAGGGTTCCCCTGTTCTGACTTTGGAAAATCATTTAAAATTTAATAAAAATAATAATGAGTTATA
62154696 ATTTATATTTTTAGAATCCTCGATGAGTCTATTTTCAAATAAAGTAAAAGGAAACATCATCCGAA
66 ATTTATATTTTTAGAATCCTCGATGAGTCTATTTTCAAATAAAGTAAAAGGAAACATCATCCGAA
62154761 TTCTGTACAATTAGATAATTCATTTTTAGTGAAGAGTGGTCGGAACTGTTAGACAGCAAAACAGG
131 TTCTGTACAATTAGATAATTCATTTTTAGTGAAGAGTGGTCGGAACTGTTAGACAGCAAAACAGG
62154826 GGAACGTTAAAGAATAAACTTTATTAATTGGCTGAACCAAAAATTCTGAAAATTTTATGGTAAGA
196 GGAACGTTAAAGAATAAACTTTATTAATTGGCTGAACCAAAAATTCTGAAAATTTTATGGTAAGA
62154891 ATATATTTGAGTC
261 ATATATTTGAGTC
62154904 TAG
1 TAG
62154907 TTTCATGTAA
Statistics
Matches: 276, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
273 276 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (273 bp):
TAGGGTTCCCCTGTTCTGACTTTGGAAAATCATTTAAAATTTAATAAAAATAATAATGAGTTATA
ATTTATATTTTTAGAATCCTCGATGAGTCTATTTTCAAATAAAGTAAAAGGAAACATCATCCGAA
TTCTGTACAATTAGATAATTCATTTTTAGTGAAGAGTGGTCGGAACTGTTAGACAGCAAAACAGG
GGAACGTTAAAGAATAAACTTTATTAATTGGCTGAACCAAAAATTCTGAAAATTTTATGGTAAGA
ATATATTTGAGTC
Found at i:62155708 original size:39 final size:39
Alignment explanation
Indices: 62155664--62155762 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 39
62155654 CGACTACTGT
* *
62155664 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGACTAGGCACTTTGTGTGTCGAA
*
62155703 TACTGTTACGTTACTGTTACCGACTAGGCACTTTGTGTGTCGAA
1 TAC---T--GTTACTGTTACTGACTAGGCACTTTGTGTGTCGAA
* *
62155747 TATTGTTACCGTTACT
1 TACTGTTACTGTTACT
62155763 ATTACAGGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
39 13 0.27
41 1 0.02
42 1 0.02
44 34 0.69
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (39 bp):
TACTGTTACTGTTACTGACTAGGCACTTTGTGTGTCGAA
Found at i:62155716 original size:44 final size:45
Alignment explanation
Indices: 62155631--62155814 Score: 212
Period size: 45 Copynumber: 4.1 Consensus size: 45
62155621 ATTTGCCGGC
* *
62155631 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGTCGAATACTGTTACTGTTACTG
* *
62155675 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTAC-GTTACTG
1 TTACTGATTAGGCACTTTATGTGTCGAATACTGTTACTGTTACTG
* * * * * *
62155719 TTACCGACTAGGCACTTTGTGTGTCGAATATTGTTACCGTTACTA
1 TTACTGATTAGGCACTTTATGTGTCGAATACTGTTACTGTTACTG
* * * *
62155764 TTACAGGTTCA-GCACTTTATGTGTTGAATATTGTTACTGTTACTG
1 TTACTGATT-AGGCACTTTATGTGTCGAATACTGTTACTGTTACTG
62155809 TTACTG
1 TTACTG
62155815 CTACCGTTAC
Statistics
Matches: 120, Mismatches: 17, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
44 54 0.45
45 65 0.54
46 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (45 bp):
TTACTGATTAGGCACTTTATGTGTCGAATACTGTTACTGTTACTG
Found at i:62155839 original size:7 final size:6
Alignment explanation
Indices: 62155795--62155835 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
62155785 TGTTGAATAT
* *
62155795 TGTTAC TGTTAC TGTTAC TGCTAC CGTTAC TGATTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TG-TTAC TGTT
62155836 TACTAGTGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (6 bp):
TGTTAC
Found at i:62156345 original size:13 final size:15
Alignment explanation
Indices: 62156327--62156358 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
62156317 TATATGAAAT
62156327 AATGATT-TT-ATGA
1 AATGATTATTGATGA
62156340 AATGATTATTGATGA
1 AATGATTATTGATGA
62156355 AATG
1 AATG
62156359 CATGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (15 bp):
AATGATTATTGATGA
Found at i:62161255 original size:25 final size:27
Alignment explanation
Indices: 62161226--62161278 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
62161216 ACAGTTATAC
*
62161226 ATAACATA-GAGCAT-ATAGTCATTTT
1 ATAACATAGGAGCATCACAGTCATTTT
*
62161251 ATAACATAGGGGCATCACAGTCATTTT
1 ATAACATAGGAGCATCACAGTCATTTT
62161278 A
1 A
62161279 CCACGTGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 5 0.21
27 11 0.46
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (27 bp):
ATAACATAGGAGCATCACAGTCATTTT
Found at i:62165211 original size:19 final size:18
Alignment explanation
Indices: 62165189--62165245 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
62165179 TTTTACAAAA
* *
62165189 TTTATAAATTTTTAGTTTT
1 TTTATAAATTTATA-TATT
*
62165208 TTTATATATTTATATATT
1 TTTATAAATTTATATATT
* *
62165226 TTCATAAATTTATAAATT
1 TTTATAAATTTATATATT
62165244 TT
1 TT
62165246 AACTTTTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 20 0.62
19 12 0.38
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTATAAATTTATATATT
Found at i:62165217 original size:46 final size:46
Alignment explanation
Indices: 62165150--62165271 Score: 151
Period size: 46 Copynumber: 2.6 Consensus size: 46
62165140 TATATATGAG
* *
62165150 ATTTTTAATTCTTTTATATATTTATATTTTTTTACA-AAATTTATAA
1 ATTTTTAATTTTTTTATATATTTATATTATTTT-CATAAATTTATAA
*
62165196 ATTTTTAGTTTTTTTATATATTTATA-TATTTTCATAAATTTATAA
1 ATTTTTAATTTTTTTATATATTTATATTATTTTCATAAATTTATAA
62165241 A-TTTTAACTTTTTATTTATATATTATATATT
1 ATTTTTAA--TTTT-TTTATATATT-TATATT
62165272 GTAATTTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
44 7 0.11
45 16 0.24
46 28 0.42
47 10 0.15
48 4 0.06
49 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (46 bp):
ATTTTTAATTTTTTTATATATTTATATTATTTTCATAAATTTATAA
Found at i:62165227 original size:27 final size:27
Alignment explanation
Indices: 62165162--62165227 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
62165152 TTTTAATTCT
*
62165162 TTTATATATTTATATTTTTTTACAAAA
1 TTTATATATTTTTATTTTTTTACAAAA
* * *
62165189 TTTATAAATTTTTAGTTTTTTTA-TATA
1 TTTATATATTTTTA-TTTTTTTACAAAA
62165216 TTTATATATTTT
1 TTTATATATTTT
62165228 CATAAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 25 0.76
28 8 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTATATATTTTTATTTTTTTACAAAA
Found at i:62166385 original size:14 final size:14
Alignment explanation
Indices: 62166366--62166392 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62166356 TTCTGCTTGT
62166366 TTATTTTATTTTAC
1 TTATTTTATTTTAC
62166380 TTATTTTATTTTA
1 TTATTTTATTTTA
62166393 TCTTTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTTATTTTAC
Found at i:62167198 original size:3 final size:3
Alignment explanation
Indices: 62167155--62167235 Score: 67
Period size: 3 Copynumber: 26.0 Consensus size: 3
62167145 TTTAGCAGTC
* *
62167155 TTA TTA TT- TTG TTAA TTA TT- TTAA TGTA TTA TCA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TT-A T-TA TTA TTA -TTA TTA TTA TTA
* *
62167202 TTA TTA CTA TTA TTA TCA TTA TTAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
62167236 GTTTTATTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
2 4 0.06
3 49 0.77
4 10 0.16
5 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:62172865 original size:11 final size:11
Alignment explanation
Indices: 62172851--62172976 Score: 100
Period size: 11 Copynumber: 11.5 Consensus size: 11
62172841 ATTATTTTAA
62172851 TTTTAAAATAT
1 TTTTAAAATAT
62172862 TTTTAAAATACT
1 TTTTAAAATA-T
***
62172874 TTTTTTTAT-T
1 TTTTAAAATAT
*
62172884 TTTTTAAA-A-
1 TTTTAAAATAT
62172893 TTTTAAAATAT
1 TTTTAAAATAT
62172904 TTTTAAAATACT
1 TTTTAAAATA-T
*** *
62172916 TTTT-TTTTAA
1 TTTTAAAATAT
62172926 TTTTAAAATAT
1 TTTTAAAATAT
62172937 TTTTAAAATAT
1 TTTTAAAATAT
62172948 TTTTAAAATACTT
1 TTTTAAAATA--T
*
62172961 TTTTTAAAT-T
1 TTTTAAAATAT
62172971 TTTTAA
1 TTTTAA
62172977 TTTTTAAAAT
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
9 7 0.08
10 18 0.20
11 45 0.49
12 12 0.13
13 9 0.10
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:62172896 original size:42 final size:42
Alignment explanation
Indices: 62172849--62172987 Score: 192
Period size: 42 Copynumber: 3.3 Consensus size: 42
62172839 TAATTATTTT
62172849 AATTTTAAAATATTTTTAAAATACTTTTTTTTATTTTTTTAA
1 AATTTTAAAATATTTTTAAAATACTTTTTTTTATTTTTTTAA
* *
62172891 AATTTTAAAATATTTTTAAAATACTTTTTTTT-TAATTTTAAA
1 AATTTTAAAATATTTTTAAAATACTTTTTTTTAT-TTTTTTAA
* *
62172933 ATATTTTTAAAATATTTTTAAAATACTTTTTTTAAATTTTTT-A
1 A-A-TTTTAAAATATTTTTAAAATACTTTTTTTTATTTTTTTAA
*
62172976 ATTTTTAAAATA
1 AATTTTAAAATA
62172988 AATTTTTGGT
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
41 11 0.13
42 39 0.45
43 3 0.03
44 33 0.38
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (42 bp):
AATTTTAAAATATTTTTAAAATACTTTTTTTTATTTTTTTAA
Found at i:62172928 original size:33 final size:32
Alignment explanation
Indices: 62172880--62172951 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 32
62172870 TACTTTTTTT
62172880 TATTTTTTTAAAATTTTAAAATATTTTTAAAA
1 TATTTTTTTAAAATTTTAAAATATTTTTAAAA
**
62172912 TACTTTTTTTTTAATTTTAAAATATTTTTAAAA
1 TA-TTTTTTTAAAATTTTAAAATATTTTTAAAA
62172945 TATTTTT
1 TATTTTT
62172952 AAAATACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 7 0.19
33 30 0.81
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (32 bp):
TATTTTTTTAAAATTTTAAAATATTTTTAAAA
Found at i:62176082 original size:16 final size:16
Alignment explanation
Indices: 62176057--62176087 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62176047 AATTATTTAT
62176057 ATTTAGTAATATAATA
1 ATTTAGTAATATAATA
*
62176073 ATTTATTAATATAAT
1 ATTTAGTAATATAAT
62176088 TAATATAAAT
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
ATTTAGTAATATAATA
Found at i:62176211 original size:24 final size:25
Alignment explanation
Indices: 62176170--62176217 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
62176160 ATTTTGAATT
*
62176170 TTGAATAATATTCTTAAT-ATATTA
1 TTGAAAAATATTCTTAATAATATTA
62176194 TTGAAAAATATT-TATAATAATATT
1 TTGAAAAATATTCT-TAATAATATT
62176218 TTAATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 15 0.71
25 5 0.24
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (25 bp):
TTGAAAAATATTCTTAATAATATTA
Found at i:62176323 original size:17 final size:17
Alignment explanation
Indices: 62176289--62176340 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
62176279 ATTATTAAGT
* **
62176289 TTAAATATTATATTATA
1 TTAATTATTATAAAATA
62176306 TTAATTATTATAAAATA
1 TTAATTATTATAAAATA
* *
62176323 TTATCTTATCATAAAATA
1 TTA-ATTATTATAAAATA
62176341 AATTTTGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATTATTATAAAATA
Found at i:62176539 original size:14 final size:14
Alignment explanation
Indices: 62176520--62176546 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62176510 CCATAAAATC
62176520 AATTCATTTTCCAA
1 AATTCATTTTCCAA
62176534 AATTCATTTTCCA
1 AATTCATTTTCCA
62176547 GAAGTTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTCATTTTCCAA
Found at i:62176863 original size:31 final size:31
Alignment explanation
Indices: 62176828--62176893 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
62176818 ATTTTCGTTA
* * *
62176828 AATTCAACT-TTTTATAAAATGTTGATGGTCG
1 AATTCAACTCCTTT-TAAAATGTTAAGGGTCG
*
62176859 AATTCGACTCCTTTTAAAATGTTAAGGGTCG
1 AATTCAACTCCTTTTAAAATGTTAAGGGTCG
62176890 AATT
1 AATT
62176894 TAGTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (31 bp):
AATTCAACTCCTTTTAAAATGTTAAGGGTCG
Found at i:62176972 original size:3 final size:3
Alignment explanation
Indices: 62176964--62177003 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
62176954 TTATGTGAGT
62176964 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
62177004 GAAAAGGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:62185372 original size:44 final size:44
Alignment explanation
Indices: 62185315--62185676 Score: 207
Period size: 44 Copynumber: 7.9 Consensus size: 44
62185305 GTTGCAGCAT
* * * *
62185315 AGATTAAAACTACAAATCTTATCTCTTTGAAGTTACAGTGAAGC
1 AGATTAAAGCTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGC
* * *
62185359 AGATTGAAGCTACAAATCTTATAT-TCCTGAAGTTGCAGTGGAGT
1 AGATTAAAGCTACAAATCTTATCTCT-CTGAAGTTGCAGTGGAGC
* * *
62185403 AGATTAAAGCTACAAATCTTATCTCACTAAAGTTGTAGTGGAGC
1 AGATTAAAGCTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGC
* * *
62185447 AGATTGAAA--TGACAAATCCTATAC-CTCTTAAGTTGTAGTGG-GTC
1 AGATT-AAAGCT-ACAAATCTTAT-CTCTCTGAAGTTGCAGTGGAG-C
* * * * *
62185491 GGATTAAATCTACCATAGCGAGTCTTATTTCCCTGAAGTTGCAGTGGAAC
1 AGATTAAAGCTA-CA-A---A-TCTTATCTCTCTGAAGTTGCAGTGGAGC
* * *
62185541 AAATTAAAGCTACAAGCTACAAATCTTATCTCACTGAAGTTGTAGTGGAGC
1 AGA-T-----TA-AAGCTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGC
* * * * * * *
62185592 AGATTGAAGCTACGAATCTCATCTCCCTGAAATTGCAGCGGAGT
1 AGATTAAAGCTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGC
* * * *
62185636 AGATTGAAA-CTACAATTCCTATAC-CCCTTAAGTTGCAGTGG
1 AGATT-AAAGCTACAAATCTTAT-CTCTCTGAAGTTGCAGTGG
62185677 GTTAGAATGA
Statistics
Matches: 246, Mismatches: 47, Indels: 50
0.72 0.14 0.15
Matches are distributed among these distances:
43 6 0.02
44 167 0.68
45 11 0.04
46 1 0.00
49 1 0.00
50 22 0.09
51 27 0.11
52 1 0.00
55 1 0.00
56 4 0.02
57 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (44 bp):
AGATTAAAGCTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGC
Found at i:62188126 original size:16 final size:16
Alignment explanation
Indices: 62188095--62188131 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
62188085 TTCAAAAGAA
62188095 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
62188111 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
62188127 TATTA
1 TATTA
62188132 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:62188164 original size:20 final size:20
Alignment explanation
Indices: 62188139--62188199 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
62188129 TTAAAATAAA
62188139 ATTAAAATATTAAATAATTT
1 ATTAAAATATTAAATAATTT
*
62188159 ATTAAAATAATAAAT-A--T
1 ATTAAAATATTAAATAATTT
*
62188176 ATTAATTATATT-AATAATTT
1 ATTAA-AATATTAAATAATTT
62188196 ATTA
1 ATTA
62188200 TATGACTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 9 0.26
18 5 0.15
19 1 0.03
20 19 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTAAAATATTAAATAATTT
Found at i:62188171 original size:34 final size:37
Alignment explanation
Indices: 62188116--62188201 Score: 94
Period size: 37 Copynumber: 2.4 Consensus size: 37
62188106 ATTATTATTT
*
62188116 TTAA-AATTTATTATTAAAAT-AA-A-ATTAA-AATA
1 TTAATAATTTATTATAAAAATAAATATATTAATAATA
*
62188148 TTAAATAATTTATTA-AAATAATAAATATATTAATTATA
1 TT-AATAATTTATTATAAA-AATAAATATATTAATAATA
62188186 TTAATAATTTATTATA
1 TTAATAATTTATTATA
62188202 TGACTAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
32 2 0.05
33 4 0.09
34 12 0.27
35 2 0.05
36 1 0.02
37 17 0.39
38 6 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (37 bp):
TTAATAATTTATTATAAAAATAAATATATTAATAATA
Found at i:62189295 original size:14 final size:14
Alignment explanation
Indices: 62189262--62189289 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
62189252 ACAATTTTTG
62189262 GCATTTTAGTTCTA
1 GCATTTTAGTTCTA
62189276 GCATTTTAGTTCTA
1 GCATTTTAGTTCTA
62189290 CAATTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
GCATTTTAGTTCTA
Found at i:62190194 original size:29 final size:29
Alignment explanation
Indices: 62190162--62190220 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
62190152 AACCAACATA
62190162 TATCATTTAACCAACCTAATAGCTAATTT
1 TATCATTTAACCAACCTAATAGCTAATTT
62190191 TATCATTTAACCAACCTAATAGCTAATTT
1 TATCATTTAACCAACCTAATAGCTAATTT
62190220 T
1 T
62190221 CTATTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.39
Consensus pattern (29 bp):
TATCATTTAACCAACCTAATAGCTAATTT
Found at i:62197242 original size:24 final size:24
Alignment explanation
Indices: 62197114--62197232 Score: 175
Period size: 24 Copynumber: 5.0 Consensus size: 24
62197104 AGTAGTTGGT
62197114 GGACTGCCACCTCCATATGATGGG
1 GGACTGCCACCTCCATATGATGGG
*
62197138 GGACTGCCACCTCCGTATGATGGG
1 GGACTGCCACCTCCATATGATGGG
* *
62197162 GGACTGCCTCCTCCATACGATGGG
1 GGACTGCCACCTCCATATGATGGG
* *
62197186 GGACTGCCTCCTCCATACGATGGG
1 GGACTGCCACCTCCATATGATGGG
* *
62197210 GGACTACCACCTCCAGATGATGG
1 GGACTGCCACCTCCATATGATGG
62197233 TGGAGTACCA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 87 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.20
Consensus pattern (24 bp):
GGACTGCCACCTCCATATGATGGG
Found at i:62200952 original size:3 final size:3
Alignment explanation
Indices: 62200944--62200973 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
62200934 GTAAATGTGA
62200944 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
62200974 CCTAAATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:62223111 original size:22 final size:22
Alignment explanation
Indices: 62223086--62223129 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
62223076 TGGCTGATTG
*
62223086 TTTGGCAAAATTAAGTTTAGAT
1 TTTGACAAAATTAAGTTTAGAT
* *
62223108 TTTGACAAAGTTTAGTTTAGAT
1 TTTGACAAAATTAAGTTTAGAT
62223130 CTTCGAGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (22 bp):
TTTGACAAAATTAAGTTTAGAT
Found at i:62227960 original size:18 final size:18
Alignment explanation
Indices: 62227937--62227976 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
62227927 ACCCAATCCA
62227937 AACCCAAGTATCCAACCC
1 AACCCAAGTATCCAACCC
* *
62227955 AACCCAATTATCGAACCC
1 AACCCAAGTATCCAACCC
62227973 AACC
1 AACC
62227977 TAATCATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.42, G:0.05, T:0.12
Consensus pattern (18 bp):
AACCCAAGTATCCAACCC
Found at i:62228144 original size:9 final size:9
Alignment explanation
Indices: 62228126--62228192 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
62228116 GTAGTGATTC
62228126 AATTCGGGT
1 AATTCGGGT
*
62228135 AATTCAGGT
1 AATTCGGGT
62228144 AATTCGGGT
1 AATTCGGGT
* *
62228153 AATTTGGTT
1 AATTCGGGT
* *
62228162 AATTCAGTT
1 AATTCGGGT
62228171 AATTCGGGT
1 AATTCGGGT
*
62228180 AATTCGGTT
1 AATTCGGGT
62228189 AATT
1 AATT
62228193 TTTAACCAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:62228164 original size:27 final size:27
Alignment explanation
Indices: 62228126--62228192 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
62228116 GTAGTGATTC
*
62228126 AATTCGGGTAATTCAGGTAATTCGGGT
1 AATTCGGTTAATTCAGGTAATTCGGGT
* *
62228153 AATTTGGTTAATTCAGTTAATTCGGGT
1 AATTCGGTTAATTCAGGTAATTCGGGT
62228180 AATTCGGTTAATT
1 AATTCGGTTAATT
62228193 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (27 bp):
AATTCGGTTAATTCAGGTAATTCGGGT
Found at i:62233295 original size:21 final size:21
Alignment explanation
Indices: 62233247--62233295 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
62233237 CTCTACTATT
* * *
62233247 TCCGCATTGGTTTTGTCCAAC
1 TCCGCCTTGGTTCTGGCCAAC
* *
62233268 TCAGCCTTGGTTCTGGCCACC
1 TCCGCCTTGGTTCTGGCCAAC
62233289 TCCGCCT
1 TCCGCCT
62233296 GGAGTGCATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.10, C:0.37, G:0.20, T:0.33
Consensus pattern (21 bp):
TCCGCCTTGGTTCTGGCCAAC
Found at i:62240670 original size:3 final size:3
Alignment explanation
Indices: 62240662--62240709 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
62240652 ATACACTCTG
* *
62240662 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTC CTT CTT CTT CTC CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
62240710 TTACAACAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:62244001 original size:421 final size:419
Alignment explanation
Indices: 62243103--62244143 Score: 1597
Period size: 421 Copynumber: 2.5 Consensus size: 419
62243093 GTAAACACCT
* *
62243103 ACATTTTAGAGGATTTTCATTTTTTTACACAAATCACCAATTTGTATATTCAGAGGATTACTAAT
1 ACATTTTAGAGGTTTTTCA-TTTTTTACACAAATCACCAATTTGTATATTCGGAGGATTACTAAT
* *
62243168 TGAACCATAAAAACTAGAG-AGATTTTTAGTTGGGCCTTCGAAAAGTTACAAGGTTCTAGTTAAG
65 TGAGCCATAAAAACTAGAGAAG-TTTTTAGTTGGGCCTTCGAAAAGTTAGAAGGTTCTAGTTAAG
* * * *
62243232 CTACAAAAATTATGAAATGGTTCTACCTTAACCCAAGTAAATAATAGATAGTTGTGAATG-T-TA
129 CTACAAAAACTATGAAATGGTTCTATCTTAACCCAAGTAAATAATAGAGAGTTGTGAAAGTTATA
** * *
62243295 CCTTGTCCTTGAAAGATGCCAATTAGTGAACTGAGAAAACCTTTAGGCTATGTTTGAAAAGCAAC
194 CCTTGTTATTGAAAGATACCAATTACTGAACTGAGAAAACCTTTAGGCTATGTTTGAAAAGCAAC
62243360 TTAGTAATTGAATTTGGGTGTAACTGGTGGATCACATTAAAATGGGTATAATTGAAGCACCCAAT
259 TTAGTAATTGAATTTGGGTGTAACTGGTGGATCACATTAAAATGGGTATAATTGAAGCACCCAAT
*
62243425 TACACTTTCCAACTCTTCGACGAGGGTGAGAATTGGAGTAATTACACAAGTAATTACACCAAAAT
324 TACACTTTCCAACTCTTAGACGAGGGTGAGAATTGGAGTAATTACACAAGTAATTACACCAAAAT
* *
62243490 CCAATTACTATATGGCTTTCCAAACACTCAT
389 CCAATTACTATATGACTTTCCAAACACTCAA
* *
62243521 ACATTTTAGAGGTTTTTCATTTTCTTACACATATCACCAATTTGTATATTCGAAGGATTACTAAT
1 ACATTTTAGAGGTTTTTCATTTT-TTACACAAATCACCAATTTGTATATTCGGAGGATTACTAAT
62243586 TGAGCCATAAAAACTAGAGAAGTTTTTAGTTGGGCCTTCGAAAAGTTAGAAGGTTCTAGTTAAGC
65 TGAGCCATAAAAACTAGAGAAGTTTTTAGTTGGGCCTTCGAAAAGTTAGAAGGTTCTAGTTAAGC
*
62243651 TACAAAAACTATGAAATGGTTCTATCTTAACCCAAGTAAATAATAAAGAGTTGTGAAAGTTATAC
130 TACAAAAACTATGAAATGGTTCTATCTTAACCCAAGTAAATAATAGAGAGTTGTGAAAGTTATAC
* *
62243716 CTTGTTATTGAAAGATACCAATTACTGAACTGGGAAAACCTTTTGGCTATGTTTGGAAAA-CAAC
195 CTTGTTATTGAAAGATACCAATTACTGAACTGAGAAAACCTTTAGGCTATGTTT-GAAAAGCAAC
* * * *
62243780 TTAGTAATTGAATTTGGGTGTAATTGGTGGATCCCATTAAATTGTGTATAATTGAAGCACCCCAA
259 TTAGTAATTGAATTTGGGTGTAACTGGTGGATCACATTAAAATGGGTATAATTGAAGCA-CCCAA
* * **
62243845 TTACACTTTCCAACTCTTAGGCGAGGTTGAGAATTGGAGTAATTATGCAAGTAATTACACCAAAA
323 TTACACTTTCCAACTCTTAGACGAGGGTGAGAATTGGAGTAATTACACAAGTAATTACACCAAAA
*
62243910 TCCAATTACTATATGACTTTGCAAACACTCAA
388 TCCAATTACTATATGACTTTCCAAACACTCAA
* * *
62243942 ACATTTTTGAGGTTTTTCATTTGTTTATACAAATCACCAATTTGCATATTCGGAGGATTACTAAT
1 ACATTTTAGAGGTTTTTCATTT-TTTACACAAATCACCAATTTGTATATTCGGAGGATTACTAAT
* * * ** * *
62244007 TGAGCCATAAAAATTAAATAAGTTTTTAGTTAAGCCTTCGAAAAGTTAGAAGGTTTTAGTTAGGC
65 TGAGCCATAAAAACTAGAGAAGTTTTTAGTTGGGCCTTCGAAAAGTTAGAAGGTTCTAGTTAAGC
* * * *
62244072 TACAAAACCTATGAAATGGTTCTATCTTAGCCCCAAGTAAATAATAGAGTGTTGTGAAGGTTATA
130 TACAAAAACTATGAAATGGTTCTATCTTA-ACCCAAGTAAATAATAGAGAGTTGTGAAAGTTATA
62244137 CC-TGTTA
194 CCTTGTTA
62244144 GAATTGTAAA
Statistics
Matches: 569, Mismatches: 46, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
417 4 0.01
418 170 0.30
419 3 0.01
420 110 0.19
421 248 0.44
422 34 0.06
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (419 bp):
ACATTTTAGAGGTTTTTCATTTTTTACACAAATCACCAATTTGTATATTCGGAGGATTACTAATT
GAGCCATAAAAACTAGAGAAGTTTTTAGTTGGGCCTTCGAAAAGTTAGAAGGTTCTAGTTAAGCT
ACAAAAACTATGAAATGGTTCTATCTTAACCCAAGTAAATAATAGAGAGTTGTGAAAGTTATACC
TTGTTATTGAAAGATACCAATTACTGAACTGAGAAAACCTTTAGGCTATGTTTGAAAAGCAACTT
AGTAATTGAATTTGGGTGTAACTGGTGGATCACATTAAAATGGGTATAATTGAAGCACCCAATTA
CACTTTCCAACTCTTAGACGAGGGTGAGAATTGGAGTAATTACACAAGTAATTACACCAAAATCC
AATTACTATATGACTTTCCAAACACTCAA
Found at i:62256520 original size:24 final size:23
Alignment explanation
Indices: 62256489--62256534 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
62256479 TATTCACACG
62256489 TATTCTTA-CTTAATTTCAAATGC
1 TATTCTTACCTTAATTT-AAATGC
*
62256512 TATTACTTACCTTACTTTAAATG
1 TATT-CTTACCTTAATTTAAATG
62256535 TCCCATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 9 0.45
25 7 0.35
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.48
Consensus pattern (23 bp):
TATTCTTACCTTAATTTAAATGC
Found at i:62257320 original size:16 final size:16
Alignment explanation
Indices: 62257295--62257336 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
62257285 CTTGTTTTAT
62257295 TATTACAATAATATAA
1 TATTACAATAATATAA
*
62257311 TATTATAATAATATAA
1 TATTACAATAATATAA
*
62257327 TATAACAATA
1 TATTACAATA
62257337 TATTTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
TATTACAATAATATAA
Found at i:62261315 original size:44 final size:43
Alignment explanation
Indices: 62261251--62261391 Score: 174
Period size: 44 Copynumber: 3.2 Consensus size: 43
62261241 ACCATTGAAA
* * *
62261251 TTCTTACCTAAACAATCAACCAAGACAATTATATTACATGTCCAT
1 TTCTTACC-AAACAATCAACCAA-ACAATTATAATGCATGTTCAT
* * *
62261296 TTCTTGCCAAACAATCAACCAAACATTTATAATGCGTGTTCAT
1 TTCTTACCAAACAATCAACCAAACAATTATAATGCATGTTCAT
* * *
62261339 TTATTACCAAGACAACCAATCAAACAATTATAATGCATGTTCAT
1 TTCTTACCAA-ACAATCAACCAAACAATTATAATGCATGTTCAT
62261383 TTCTTACCA
1 TTCTTACCA
62261392 TTTAACAACT
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
43 24 0.29
44 51 0.62
45 7 0.09
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (43 bp):
TTCTTACCAAACAATCAACCAAACAATTATAATGCATGTTCAT
Found at i:62265634 original size:22 final size:22
Alignment explanation
Indices: 62265606--62265649 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
62265596 ATTAGATAAA
62265606 ATTGCATATGATGTTTATTCTT
1 ATTGCATATGATGTTTATTCTT
62265628 ATTGCATATGATGTTTATTCTT
1 ATTGCATATGATGTTTATTCTT
62265650 CTTCTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (22 bp):
ATTGCATATGATGTTTATTCTT
Found at i:62270119 original size:16 final size:16
Alignment explanation
Indices: 62270050--62270117 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
62270040 TTTGGTTCGC
*
62270050 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
62270066 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
62270082 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
62270098 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
62270114 TGTA
1 TGTA
62270118 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Done.