Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 61 of 204
Found at i:19468472 original size:27 final size:26
Alignment explanation
Indices: 19468441--19468728 Score: 308
Period size: 27 Copynumber: 10.7 Consensus size: 26
19468431 CTGTATTGAG
19468441 ACCCCCATAGGGTAAAATGATCGAAAT
1 ACCCCCA-AGGGTAAAATGATCGAAAT
*
19468468 ACCCCCATAGGATAAAATGA-CGAAAAT
1 ACCCCCA-AGGGTAAAATGATCG-AAAT
* *
19468495 ACCCCCATAGGATAAAATGACCGAAAT
1 ACCCCCA-AGGGTAAAATGATCGAAAT
*
19468522 ACCCCCTAAGGATAAAATGATCGAAAT
1 ACCCCC-AAGGGTAAAATGATCGAAAT
* * * *
19468549 ACCCTCGAAGGGTAAAATCACCAAAAT
1 ACCC-CCAAGGGTAAAATGATCGAAAT
* *
19468576 ACCCCTGAAGGGTAAAATGACCGAAAT
1 ACCCC-CAAGGGTAAAATGATCGAAAT
19468603 ACCCCCGAAGGGTAAAATGATCGAAAT
1 ACCCCC-AAGGGTAAAATGATCGAAAT
** *
19468630 ACTCCTGAAGGGTAAAATGACCGAAAT
1 AC-CCCCAAGGGTAAAATGATCGAAAT
*
19468657 ACCCTCAAAGGGTAAAATGATCGAAAT
1 ACCC-CCAAGGGTAAAATGATCGAAAT
* *
19468684 ACCCCTAATGGGTAAATTGATCGAAAT
1 ACCCCCAA-GGGTAAAATGATCGAAAT
*
19468711 ACCCCTGAAGGGTAAAAT
1 ACCCC-CAAGGGTAAAAT
19468729 AATTGTTATG
Statistics
Matches: 230, Mismatches: 21, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
26 8 0.03
27 214 0.93
28 8 0.03
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.17
Consensus pattern (26 bp):
ACCCCCAAGGGTAAAATGATCGAAAT
Found at i:19468576 original size:81 final size:79
Alignment explanation
Indices: 19468441--19468728 Score: 364
Period size: 81 Copynumber: 3.6 Consensus size: 79
19468431 CTGTATTGAG
* * *
19468441 ACCCCC-ATAGGGTAAAATGATCGAAATACCCCCATAGGATAAAATGACGAAAATACCCCCATAG
1 ACCCCCTA-AGGGTAAAATGATCGAAATACCCCGA-AGGGTAAAATGACCAAAATACCCCCA-AG
*
19468505 GATAAAATGACCGAAAT
63 GGTAAAATGACCGAAAT
* * *
19468522 ACCCCCTAAGGATAAAATGATCGAAATACCCTCGAAGGGTAAAATCACCAAAATACCCCTGAAGG
1 ACCCCCTAAGGGTAAAATGATCGAAATACCC-CGAAGGGTAAAATGACCAAAATACCCC-CAAGG
19468587 GTAAAATGACCGAAAT
64 GTAAAATGACCGAAAT
* * * *
19468603 ACCCCCGAAGGGTAAAATGATCGAAATACTCCTGAAGGGTAAAATGACCGAAATACCCTCAAAGG
1 ACCCCCTAAGGGTAAAATGATCGAAATAC-CCCGAAGGGTAAAATGACCAAAATACCC-CCAAGG
*
19468668 GTAAAATGATCGAAAT
64 GTAAAATGACCGAAAT
*
19468684 A-CCCCTAATGGGTAAATTGATCGAAATACCCCTGAAGGGTAAAAT
1 ACCCCCTAA-GGGTAAAATGATCGAAATACCCC-GAAGGGTAAAAT
19468729 AATTGTTATG
Statistics
Matches: 183, Mismatches: 17, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
80 8 0.04
81 168 0.92
82 7 0.04
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.17
Consensus pattern (79 bp):
ACCCCCTAAGGGTAAAATGATCGAAATACCCCGAAGGGTAAAATGACCAAAATACCCCCAAGGGT
AAAATGACCGAAAT
Found at i:19468977 original size:25 final size:26
Alignment explanation
Indices: 19468908--19468983 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
19468898 TTGCCACATA
* *
19468908 TACTGTTACTGGCAGCTTTGCTGCAT
1 TACTATTACTGGCAGCTTTGCTGCGT
*
19468934 TACTATTACTGGCAACTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
19468960 TACTATT-CTGGCAGCTTTGCTGCG
1 TACTATTACTGGCAGCTTTGCTGCG
19468984 ATATTGGTGC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 16 0.35
26 30 0.65
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCGT
Found at i:19469133 original size:28 final size:28
Alignment explanation
Indices: 19469093--19469173 Score: 135
Period size: 28 Copynumber: 2.9 Consensus size: 28
19469083 TATTTTGTTT
*
19469093 ACTGTATTGGGCTAAGGCCCACATTATC
1 ACTGTATTGGGCTAAGGCCCACACTATC
*
19469121 ACTGTATTGGGCTAAGGCCCACACTATT
1 ACTGTATTGGGCTAAGGCCCACACTATC
*
19469149 ACTGTAATGGGCTAAGGCCCACACT
1 ACTGTATTGGGCTAAGGCCCACACT
19469174 GTACCGATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (28 bp):
ACTGTATTGGGCTAAGGCCCACACTATC
Found at i:19474779 original size:41 final size:41
Alignment explanation
Indices: 19474722--19474853 Score: 176
Period size: 41 Copynumber: 3.2 Consensus size: 41
19474712 AGAATATTGT
* *
19474722 TGAATTGCATATACGTGACCTTATTTGTACTTTGGTACCCC
1 TGAATTGCACATACGTGACCTTGTTTGTACTTTGGTACCCC
* * * *
19474763 TGAATTGCACATACGTGTCCCTGTTTGTACTTCGATACCCC
1 TGAATTGCACATACGTGACCTTGTTTGTACTTTGGTACCCC
* * *
19474804 TGAATTGCACATACGTGCCCTTGTTTGTAATTTGGTGCCCC
1 TGAATTGCACATACGTGACCTTGTTTGTACTTTGGTACCCC
19474845 TGAA-TGCAC
1 TGAATTGCAC
19474854 TTTTGTACCT
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 5 0.06
41 74 0.94
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (41 bp):
TGAATTGCACATACGTGACCTTGTTTGTACTTTGGTACCCC
Found at i:19474824 original size:20 final size:20
Alignment explanation
Indices: 19474760--19474824 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
19474750 ACTTTGGTAC
19474760 CCCTGAATTGCACATACGTG
1 CCCTGAATTGCACATACGTG
* * * *
19474780 TCCCTG-TTTGTAC-TTCGATAC
1 -CCCTGAATTGCACATACG-T-G
19474801 CCCTGAATTGCACATACGTG
1 CCCTGAATTGCACATACGTG
19474821 CCCT
1 CCCT
19474825 TGTTTGTAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 9
0.65 0.16 0.18
Matches are distributed among these distances:
19 3 0.09
20 15 0.47
21 11 0.34
22 3 0.09
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.31
Consensus pattern (20 bp):
CCCTGAATTGCACATACGTG
Found at i:19482661 original size:21 final size:22
Alignment explanation
Indices: 19482615--19482665 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
19482605 TTAGATTATC
*
19482615 TCAAGACATAAGGTGCCAAGTC
1 TCAAGACATAAGGTGCCAAGTA
*
19482637 TCAAGACAT-AGGT-TCAATGTA
1 TCAAGACATAAGGTGCCAA-GTA
19482658 TCAAGACA
1 TCAAGACA
19482666 CTGTCCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 14 0.54
22 9 0.35
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (22 bp):
TCAAGACATAAGGTGCCAAGTA
Found at i:19484699 original size:2 final size:2
Alignment explanation
Indices: 19484692--19484735 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
19484682 ACACATTTTC
19484692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19484734 AT
1 AT
19484736 GAGCATATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19490668 original size:12 final size:11
Alignment explanation
Indices: 19490649--19490678 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
19490639 AATCTTTGGG
19490649 TTTTTTTTTGT
1 TTTTTTTTTGT
19490660 TTTTGTTTTTGT
1 TTTT-TTTTTGT
19490672 TTTTTTT
1 TTTTTTT
19490679 GGCCTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:19494447 original size:31 final size:31
Alignment explanation
Indices: 19494409--19494467 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
19494399 ATTTATTATC
19494409 AAATTTATCGTACGTAGTCAAAAACGACGTT
1 AAATTTATCGTACGTAGTCAAAAACGACGTT
*
19494440 AAATTTATCGTATGTAGTCAAAAACGAC
1 AAATTTATCGTACGTAGTCAAAAACGAC
19494468 ATTAGGTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (31 bp):
AAATTTATCGTACGTAGTCAAAAACGACGTT
Found at i:19498664 original size:21 final size:21
Alignment explanation
Indices: 19498638--19498684 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
19498628 CTAGGCTTCG
19498638 AGACAAGAATCCCTTCTCTCA
1 AGACAAGAATCCCTTCTCTCA
19498659 AGACAAGAATCCCTTCTCTCA
1 AGACAAGAATCCCTTCTCTCA
19498680 AGACA
1 AGACA
19498685 TTCAAACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.21
Consensus pattern (21 bp):
AGACAAGAATCCCTTCTCTCA
Found at i:19502099 original size:2 final size:2
Alignment explanation
Indices: 19502092--19502126 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19502082 TAAATTTTGT
19502092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19502127 TGTGAGATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19505616 original size:109 final size:109
Alignment explanation
Indices: 19505426--19505766 Score: 488
Period size: 112 Copynumber: 3.1 Consensus size: 109
19505416 TGGATTAAGA
* ** * * *
19505426 TTTAAGAGGATATTCAGCTATTTGGTCCAACGAG--AAATCGAAACCCAGCGCATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
*
19505489 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAGTT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
* *
19505533 TTTAAAAGGATATTTGGCCATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACAT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
* * **
19505598 TTTCTCGAATTTCTAAACGCAAAACATTGCCTCATTTTGATTTTT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGA-AATT
* * *
19505643 TTTAAAAGAGGATATTTGGCTATTTGGTTGAACGAGAAAAATTGAAACCCAACACATTTGGGCAC
1 TTT-AAA-AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCAC
19505708 GTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
64 GTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG-AAATT
19505755 TTTAAAAGGATA
1 TTTAAAAGGATA
19505767 ATTAGTATGC
Statistics
Matches: 207, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
107 29 0.14
109 64 0.31
110 11 0.05
111 6 0.03
112 96 0.46
113 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (109 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
Found at i:19506970 original size:24 final size:26
Alignment explanation
Indices: 19506942--19506989 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
19506932 TGTTTTAGTT
19506942 TTTGGGCCAT-TAGGGTT-TTGGGAA
1 TTTGGGCCATATAGGGTTATTGGGAA
*
19506966 TTTGGGCCATATTGGGTTATTGGG
1 TTTGGGCCATATAGGGTTATTGGG
19506990 CTGGTAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.40
Consensus pattern (26 bp):
TTTGGGCCATATAGGGTTATTGGGAA
Found at i:19510987 original size:29 final size:30
Alignment explanation
Indices: 19510955--19511031 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 30
19510945 AAATCAATAA
19510955 AAAATTTAT-AAAAATGATT-AAATTTTAAT
1 AAAATTTATAAAAAAT-ATTAAAATTTTAAT
* *
19510984 AAAA-CTATAAAAAATATTAAAATTTTATT
1 AAAATTTATAAAAAATATTAAAATTTTAAT
* *
19511013 AAAA-TTAGAAAAAAAATTA
1 AAAATTTATAAAAAATATTA
19511032 TAAAAATTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 6 0.15
29 35 0.85
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTTATAAAAAATATTAAAATTTTAAT
Found at i:19511026 original size:21 final size:21
Alignment explanation
Indices: 19511002--19511159 Score: 56
Period size: 20 Copynumber: 8.1 Consensus size: 21
19510992 AAAAAATATT
* *
19511002 AAAATTTTATTAAAATTAG-AA
1 AAAATATTATAAAAATT-GTAA
*
19511023 AAAAAATTATAAAAATTGTAA
1 AAAATATTATAAAAATTGTAA
* *
19511044 AAAATA-TA-AAATA-TAT-A
1 AAAATATTATAAAAATTGTAA
* * * *
19511061 GAAATA-TAGAAAAAGT-TAT
1 AAAATATTATAAAAATTGTAA
* * * *
19511080 AAGATTTTAT-AAAGTCGTAA
1 AAAATATTATAAAAATTGTAA
* *
19511100 GAAA-ATTATAAAAAATGTAA
1 AAAATATTATAAAAATTGTAA
19511120 AAAA-A-TAT-AAAATTCGT-A
1 AAAATATTATAAAAATT-GTAA
*
19511138 AAAA-ATTATAAAAATTATAA
1 AAAATATTATAAAAATTGTAA
19511158 AA
1 AA
19511160 TACTTCTTTT
Statistics
Matches: 100, Mismatches: 26, Indels: 23
0.67 0.17 0.15
Matches are distributed among these distances:
17 8 0.08
18 18 0.18
19 24 0.24
20 29 0.29
21 21 0.21
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAATATTATAAAAATTGTAA
Found at i:19511047 original size:19 final size:19
Alignment explanation
Indices: 19511023--19511159 Score: 86
Period size: 19 Copynumber: 7.2 Consensus size: 19
19511013 AAAATTAGAA
19511023 AAAAAATTATAAAAATTGT
1 AAAAAATTATAAAAATTGT
*
19511042 AAAAAA-TAT-AAAA-TAT
1 AAAAAATTATAAAAATTGT
* * *
19511058 ATAGAAATATAGAAAAAGT-T
1 A-AAAAAT-TATAAAAATTGT
* * * * *
19511078 ATAAGATTTTATAAAGTCGT
1 AAAAAATTATA-AAAATTGT
*
19511098 AAGAAAATTATAAAAAATGT
1 AA-AAAATTATAAAAATTGT
*
19511118 AAAAAAATAT-AAAATTCGT
1 AAAAAATTATAAAAATT-GT
*
19511137 AAAAAATTATAAAAATTAT
1 AAAAAATTATAAAAATTGT
19511156 AAAA
1 AAAA
19511160 TACTTCTTTT
Statistics
Matches: 87, Mismatches: 21, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
16 3 0.03
17 8 0.09
18 10 0.11
19 37 0.43
20 21 0.24
21 8 0.09
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.28
Consensus pattern (19 bp):
AAAAAATTATAAAAATTGT
Found at i:19511149 original size:10 final size:10
Alignment explanation
Indices: 19511101--19511159 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
19511091 AAGTCGTAAG
19511101 AAAATTATAA
1 AAAATTATAA
19511111 AAAATGTA-AA
1 AAAAT-TATAA
19511121 AAAA-TAT--
1 AAAATTATAA
*
19511128 AAAATTCGTAA
1 AAAATT-ATAA
19511139 AAAATTAT-A
1 AAAATTATAA
19511148 AAAATTATAA
1 AAAATTATAA
19511158 AA
1 AA
19511160 TACTTCTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
7 4 0.10
8 3 0.08
9 10 0.25
10 15 0.38
11 8 0.20
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (10 bp):
AAAATTATAA
Found at i:19511160 original size:8 final size:9
Alignment explanation
Indices: 19511024--19511159 Score: 57
Period size: 9 Copynumber: 14.4 Consensus size: 9
19511014 AAATTAGAAA
19511024 AAAAATTAT
1 AAAAATTAT
*
19511033 AAAAATTGT
1 AAAAATTAT
*
19511042 AAAAAATAT
1 AAAAATTAT
19511051 -AAAATATAT
1 AAAAAT-TAT
* *
19511060 AGAAATATAG
1 AAAAAT-TAT
19511070 AAAAAGTTAT
1 AAAAA-TTAT
* *
19511080 -AAGATTTT
1 AAAAATTAT
*
19511088 ATAAAGTCGTA-
1 A-AAAAT--TAT
19511099 AGAAAATTAT
1 A-AAAATTAT
19511109 AAAAAATGTA-
1 -AAAAAT-TAT
*
19511119 AAAAAATAT
1 AAAAATTAT
*
19511128 -AAAATTCGT
1 AAAAATT-AT
19511137 AAAAAATTAT
1 -AAAAATTAT
19511147 AAAAATTAT
1 AAAAATTAT
19511156 AAAA
1 AAAA
19511160 TACTTCTTTT
Statistics
Matches: 94, Mismatches: 19, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
8 14 0.15
9 42 0.45
10 22 0.23
11 15 0.16
12 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:19511322 original size:20 final size:20
Alignment explanation
Indices: 19511299--19511344 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
19511289 TTAAATGACC
19511299 TTTTTAATGTAT-TTTATAAT
1 TTTTTAAT-TATATTTATAAT
19511319 TTTTT-ATTATATTTATAAT
1 TTTTTAATTATATTTATAAT
19511338 TTATTTA
1 TT-TTTA
19511345 TAATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 3 0.13
19 12 0.52
20 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTAATTATATTTATAAT
Found at i:19511344 original size:11 final size:11
Alignment explanation
Indices: 19511311--19511350 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
19511301 TTTAATGTAT
19511311 TTTATAATTT-
1 TTTATAATTTA
*
19511321 TTTAT--TATA
1 TTTATAATTTA
19511330 TTTATAATTTA
1 TTTATAATTTA
19511341 TTTATAATTT
1 TTTATAATTT
19511351 TTAATAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
8 2 0.08
9 5 0.20
10 5 0.20
11 13 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATAATTTA
Found at i:19511352 original size:29 final size:27
Alignment explanation
Indices: 19511310--19511415 Score: 110
Period size: 29 Copynumber: 3.8 Consensus size: 27
19511300 TTTTAATGTA
*
19511310 TTTTATAATTTTTTATTATATTTATAATT
1 TTTTATAA-TTTTTATTAAATTTATAA-T
*
19511339 TATTTATAATTTTTAATAAGATTTA-AAT
1 T-TTTATAATTTTTATTAA-ATTTATAAT
*
19511367 TTTTGT-ATTTTTATTAAAATTTAATAAT
1 TTTTATAATTTTTATT-AAATTT-ATAAT
19511395 TTTTATAATTTTTA-TAAATTT
1 TTTTATAATTTTTATTAAATTT
19511416 TATTGATTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
26 12 0.18
27 13 0.20
28 11 0.17
29 18 0.27
30 12 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTATAATTTTTATTAAATTTATAAT
Found at i:19511388 original size:26 final size:27
Alignment explanation
Indices: 19511310--19511418 Score: 105
Period size: 28 Copynumber: 3.9 Consensus size: 27
19511300 TTTTAATGTA
* *
19511310 TTTTATAATTTTTTATTATATTTATAATT
1 TTTTATAA-TTTTTATAAAATTTATAA-T
*
19511339 TATTTATAATTTTTAATAAGATTTA-AAT
1 T-TTTATAATTTTT-ATAAAATTTATAAT
*
19511367 TTTTGT-ATTTTTATTAAAATTTAATAAT
1 TTTTATAATTTTTA-TAAAATTT-ATAAT
*
19511395 TTTTATAATTTTTATAAATTTTAT
1 TTTTATAATTTTTATAAAATTTAT
19511419 TGATTTTTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
25 1 0.01
26 13 0.19
27 7 0.10
28 17 0.25
29 15 0.22
30 15 0.22
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTATAATTTTTATAAAATTTATAAT
Found at i:19511399 original size:10 final size:9
Alignment explanation
Indices: 19511310--19511418 Score: 78
Period size: 9 Copynumber: 11.7 Consensus size: 9
19511300 TTTTAATGTA
19511310 TTTTATAATT
1 TTTTATAA-T
*
19511320 TTTTATTAT
1 TTTTATAAT
*
19511329 ATTTATAATT
1 TTTTATAA-T
19511339 TATTTATAAT
1 T-TTTATAAT
*
19511349 TTTTAATAAG
1 TTTT-ATAAT
*
19511359 ATTTA-AAT
1 TTTTATAAT
*
19511367 TTTTGT-AT
1 TTTTATAAT
*
19511375 TTTTATTAAAA
1 TTTTA-T-AAT
*
19511386 TTTAATAAT
1 TTTTATAAT
19511395 TTTTATAAT
1 TTTTATAAT
*
19511404 TTTTATAAA
1 TTTTATAAT
19511413 TTTTAT
1 TTTTAT
19511419 TGATTTTTTA
Statistics
Matches: 77, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
8 11 0.14
9 36 0.47
10 18 0.23
11 12 0.16
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:19511435 original size:28 final size:25
Alignment explanation
Indices: 19511359--19511435 Score: 66
Period size: 28 Copynumber: 2.9 Consensus size: 25
19511349 TTTTAATAAG
19511359 ATTTAA-ATTTTTGTATTTTTATTAAA
1 ATTTAATATTTTT-TATTTTT-TTAAA
*
19511385 ATTTAATAATTTTTATAATTTTTATAAA
1 ATTTAAT-ATTTTT-T-ATTTTTTTAAA
* *
19511413 TTTTATTGATTTTTTATTTTTTT
1 ATTTAAT-ATTTTTTATTTTTTT
19511436 GTTACATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 13 0.31
27 1 0.02
28 22 0.52
29 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (25 bp):
ATTTAATATTTTTTATTTTTTTAAA
Found at i:19522137 original size:27 final size:28
Alignment explanation
Indices: 19522088--19522148 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
19522078 AAAAGTTATT
19522088 AAATTTTAATAAAAATATAAAAATATAA
1 AAATTTTAATAAAAATATAAAAATATAA
* *
19522116 AAATTTTATTAAAAATAGAAAATATATATA
1 AAATTTTAATAAAAATATAAAA-ATATA-A
19522146 AAA
1 AAA
19522149 AATTGTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 20 0.69
29 5 0.17
30 4 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (28 bp):
AAATTTTAATAAAAATATAAAAATATAA
Found at i:19522149 original size:20 final size:18
Alignment explanation
Indices: 19522095--19522151 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 18
19522085 ATTAAATTTT
19522095 AATAAAAA-TATA-AAAA
1 AATAAAAATTATATAAAA
* * *
19522111 TATAAAAATTTTATTAAA
1 AATAAAAATTATATAAAA
19522129 AATAGAAAATATATATAAAA
1 AATA-AAAAT-TATATAAAA
19522149 AAT
1 AAT
19522152 TGTAAGATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 7 0.23
17 3 0.10
18 6 0.19
19 5 0.16
20 10 0.32
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAAAAATTATATAAAA
Found at i:19528418 original size:25 final size:25
Alignment explanation
Indices: 19528388--19528479 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
19528378 CTTATGAGAG
19528388 TCCCGA-TATATGGCTCTCCGGAGCT
1 TCCCGATTA-ATGGCTCTCCGGAGCT
* * ***
19528413 TTCCGATTAAAGGCTCTTTTATGAGCT
1 TCCCGATTAATGGCTC--TCCGGAGCT
19528440 TCCCGATTAATGGCTCTCCGGAGCT
1 TCCCGATTAATGGCTCTCCGGAGCT
*
19528465 TCCCGA-TATTGGCTC
1 TCCCGATTAATGGCTC
19528480 ACTTGAACTT
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
24 8 0.15
25 23 0.43
26 2 0.04
27 20 0.38
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (25 bp):
TCCCGATTAATGGCTCTCCGGAGCT
Found at i:19540710 original size:43 final size:43
Alignment explanation
Indices: 19540663--19540809 Score: 172
Period size: 43 Copynumber: 3.4 Consensus size: 43
19540653 ATCCAAAATT
19540663 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
** * * * * * *
19540706 TTATGTAAGTTATGAT-CCAAAGT-TTTTTTTTTATTCTTTAAATG
1 TTATGTAAGTTATGATATGATA-TATATTTATGTATTATGT-AA-G
19540750 TTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
1 -TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
19540794 TTATGTAAGTTATGAT
1 TTATGTAAGTTATGAT
19540810 CCAAAGATTT
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
42 13 0.16
43 35 0.43
44 2 0.02
45 19 0.23
46 13 0.16
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (43 bp):
TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
Found at i:19540789 original size:88 final size:90
Alignment explanation
Indices: 19540658--19540856 Score: 377
Period size: 88 Copynumber: 2.2 Consensus size: 90
19540648 TTCTGATCCA
19540658 AAAT-TTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
1 AAATGTTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
19540722 CCAAAG-TTTTTTT-TTTATTCTTT
66 CCAAAGATTTTTTTATTTATTCTTT
19540745 AAATGTTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
1 AAATGTTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
19540810 CCAAAGATTTTTTTATTTATTCTTT
66 CCAAAGATTTTTTTATTTATTCTTT
19540835 AAATGTTTATGTAAGTTATGAT
1 AAATGTTTATGTAAGTTATGAT
19540857 TATCATCTTT
Statistics
Matches: 109, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
87 4 0.04
88 66 0.61
89 7 0.06
90 32 0.29
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (90 bp):
AAATGTTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
CCAAAGATTTTTTTATTTATTCTTT
Found at i:19540881 original size:13 final size:13
Alignment explanation
Indices: 19540863--19540889 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19540853 TGATTATCAT
19540863 CTTTAAATTTTAA
1 CTTTAAATTTTAA
19540876 CTTTAAATTTTAA
1 CTTTAAATTTTAA
19540889 C
1 C
19540890 CTTTTAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:19540898 original size:14 final size:14
Alignment explanation
Indices: 19540863--19540914 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
19540853 TGATTATCAT
19540863 CTTTAAATTTTAA-
1 CTTTAAATTTTAAC
19540876 CTTTAAATTTTAAC
1 CTTTAAATTTTAAC
* * *
19540890 CTTTTAATTGTACC
1 CTTTAAATTTTAAC
*
19540904 CTTTTAATTTT
1 CTTTAAATTTT
19540915 TAAATTTGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 13 0.38
14 21 0.62
ACGTcount: A:0.29, C:0.13, G:0.02, T:0.56
Consensus pattern (14 bp):
CTTTAAATTTTAAC
Found at i:19541732 original size:14 final size:16
Alignment explanation
Indices: 19541713--19541752 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
19541703 TATTTTAGCT
19541713 AAAATTAAAAA-TA-A
1 AAAATTAAAAATTATA
19541727 AAAATTATAAAATTATA
1 AAAATTA-AAAATTATA
19541744 AAAA-TAAAA
1 AAAATTAAAA
19541753 TTTAACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.30
15 7 0.30
16 4 0.17
17 5 0.22
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATTAAAAATTATA
Found at i:19541899 original size:16 final size:16
Alignment explanation
Indices: 19541878--19541909 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19541868 AAATTAAAAT
19541878 GCATTCATATCACCAA
1 GCATTCATATCACCAA
19541894 GCATTCATATCACCAA
1 GCATTCATATCACCAA
19541910 TATTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (16 bp):
GCATTCATATCACCAA
Found at i:19552845 original size:8 final size:8
Alignment explanation
Indices: 19552832--19552860 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
19552822 CACTAGAGAC
19552832 CAGTGTTA
1 CAGTGTTA
19552840 CAGTGTTA
1 CAGTGTTA
19552848 CAGTGTTA
1 CAGTGTTA
19552856 CAGTG
1 CAGTG
19552861 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:19552974 original size:23 final size:23
Alignment explanation
Indices: 19552947--19553022 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
19552937 AGTGTTATTG
19552947 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
19552970 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
19552993 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
19553016 ATCAGTG
1 ATCAGTG
19553023 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:19558780 original size:35 final size:35
Alignment explanation
Indices: 19558741--19558829 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
19558731 TACATGTTTA
* *
19558741 ACCATCCAACACACCAGATGCTTATAAGAGCTAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
* * * *
19558776 ACCATCTAGCACACCAAATGCTCATAATAGCCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
* * *
19558811 ACAAACCATCACACCAGAT
1 ACCATCCAACACACCAGAT
19558830 AACACTGTAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.39, C:0.31, G:0.11, T:0.18
Consensus pattern (35 bp):
ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
Found at i:19559141 original size:164 final size:164
Alignment explanation
Indices: 19558870--19559198 Score: 604
Period size: 164 Copynumber: 2.0 Consensus size: 164
19558860 CAAATGCAAG
* *
19558870 ACCTCGGGATATCCAGTGAACAAAGAATATACAGAAATCATCTTCACTACTCAGATCAATCCCGT
1 ACCTCGGGATATCCAGTGAACAAAGAATATACAGAAATAATCTTAACTACTCAGATCAATCCCGT
*
19558935 ACCGCACGCATAATAACCTATTGACATGCCAGTCGTACTCTATCCTACGTTCATCGATTCAGAGC
66 ACCGCACGCATAATAACCTATTGACATGCCAATCGTACTCTATCCTACGTTCATCGATTCAGAGC
19559000 ATTCCATCACAGAAAAATATGTGAATATCTCACT
131 ATTCCATCACAGAAAAATATGTGAATATCTCACT
19559034 ACCTCGGGATATCCAGTGAACAAAGAATATACAGAAATAATCTTAACTACTCAGATCAATCCCGT
1 ACCTCGGGATATCCAGTGAACAAAGAATATACAGAAATAATCTTAACTACTCAGATCAATCCCGT
* *
19559099 ACCGCGCGCATAATAACCTATTGACATGCCAATCGTACTCTATCCTACGTTCATCGGTTCAGAGC
66 ACCGCACGCATAATAACCTATTGACATGCCAATCGTACTCTATCCTACGTTCATCGATTCAGAGC
*
19559164 ATTCCATCACAGAACAATATGTGAATATCTCACT
131 ATTCCATCACAGAAAAATATGTGAATATCTCACT
19559198 A
1 A
19559199 TCTCATATTC
Statistics
Matches: 159, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
164 159 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (164 bp):
ACCTCGGGATATCCAGTGAACAAAGAATATACAGAAATAATCTTAACTACTCAGATCAATCCCGT
ACCGCACGCATAATAACCTATTGACATGCCAATCGTACTCTATCCTACGTTCATCGATTCAGAGC
ATTCCATCACAGAAAAATATGTGAATATCTCACT
Found at i:19559499 original size:31 final size:31
Alignment explanation
Indices: 19559453--19559519 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
19559443 TCCATGGCTC
* *
19559453 AATTTTCAACGCATTCTTGATTTAGAATAAT
1 AATTTTCAACCCATTCTTGATCTAGAATAAT
*
19559484 AATTTTTAACCCATTCTTGATCTAGAATAAT
1 AATTTTCAACCCATTCTTGATCTAGAATAAT
19559515 AATTT
1 AATTT
19559520 CATTCAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.43
Consensus pattern (31 bp):
AATTTTCAACCCATTCTTGATCTAGAATAAT
Found at i:19564331 original size:39 final size:39
Alignment explanation
Indices: 19564252--19564415 Score: 172
Period size: 39 Copynumber: 4.1 Consensus size: 39
19564242 AATTGCCGGC
* * * *
19564252 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
*
19564290 TTACTGATTCGTCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
*
19564329 TTACCGATTCGGCACTTTGTGTGTCGAATACTGTTA-TCG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACT-G
*
19564368 TTACTG-TTACAGGTTCAACACTTTGTGTGTTGAATACTGTTACTG
1 TTACTGATT-C-GG-----CACTTTGTGTGTCGAATACTGTTACTG
19564413 TTA
1 TTA
19564416 TTGTTACTGC
Statistics
Matches: 107, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
38 16 0.15
39 61 0.57
40 2 0.02
45 27 0.25
46 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:19564371 original size:45 final size:45
Alignment explanation
Indices: 19564283--19564422 Score: 150
Period size: 45 Copynumber: 3.2 Consensus size: 45
19564273 GCCGACTACT
* *
19564283 GTTACTGTTACTGATTCGTCACTTTGTGTGTCGAATAC-----T-
1 GTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGTTATC
* *
19564322 GTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTATC
1 GTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGTTATC
* * *
19564367 GTTACTGTTACAGGTTCAACACTTTGTGTGTTGAATACTGTTA-C
1 GTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGTTATC
*
19564411 TGTTATTGTTAC
1 -GTTACTGTTAC
19564423 TGCTACCGTT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
39 36 0.42
44 2 0.02
45 48 0.56
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (45 bp):
GTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGTTATC
Found at i:19564413 original size:6 final size:6
Alignment explanation
Indices: 19564402--19564450 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
19564392 GTGTGTTGAA
* * *
19564402 TACTGT TACTGT TATTGT TACTGC TACCGT TACTGAT TACTGT ATACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT -TACTG
19564451 GTGTGTTTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
6 24 0.69
7 11 0.31
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:19565818 original size:49 final size:51
Alignment explanation
Indices: 19565743--19565838 Score: 128
Period size: 49 Copynumber: 1.9 Consensus size: 51
19565733 ATGTGAAAAT
*
19565743 GTGATTATGTGATTTCCGTGTAAGACCATA-TCTGGGA-TATGGCATCGGTAA
1 GTGATTATGTGATTTCCATGTAAGACCATAGT-T-GGACTATGGCATCGGTAA
*
19565794 GTGA-TATGTGA-TTCTATGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATTATGTGATTTCCATGTAAGACCATAGTTGGACTATGGCATCG
19565839 AGAAAACGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
48 3 0.07
49 26 0.63
50 8 0.20
51 4 0.10
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (51 bp):
GTGATTATGTGATTTCCATGTAAGACCATAGTTGGACTATGGCATCGGTAA
Found at i:19569752 original size:39 final size:39
Alignment explanation
Indices: 19569678--19569844 Score: 174
Period size: 39 Copynumber: 4.2 Consensus size: 39
19569668 AATTGCCGGC
* * * *
19569678 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
* *
19569716 TTACTGATTCGGCATTTTGTGTGTCGAATACTGTTACTA
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
*
19569755 TTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATAC---T---GTTACTG
* ** *
19569800 TTACAGATTCAACACTTTGTGTGTTGAATACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
19569839 TTACTG
1 TTACTG
19569845 TTACTGCTAC
Statistics
Matches: 108, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
38 13 0.12
39 60 0.56
42 2 0.02
45 33 0.31
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:19569809 original size:45 final size:45
Alignment explanation
Indices: 19569709--19569848 Score: 175
Period size: 45 Copynumber: 3.2 Consensus size: 45
19569699 GCCGACTACT
* *
19569709 GTTACTGTTACTGATTCGGCATTTTGTGTGTCGAATACTGTTA-C
1 GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACC
*
19569753 --TA---TTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACC
** * *
19569793 GTTACTGTTACAGATTCAACACTTTGTGTGTTGAATACTGTTACT
1 GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACC
19569838 GTTACTGTTAC
1 GTTACTGTTAC
19569849 TGCTACCGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
39 34 0.41
40 1 0.01
42 4 0.05
45 44 0.53
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (45 bp):
GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACC
Found at i:19569839 original size:6 final size:6
Alignment explanation
Indices: 19569828--19569876 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
19569818 GTGTGTTGAA
* *
19569828 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGAT TACTGT ATACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT -TACTG
19569877 GTGTGTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 26 0.70
7 11 0.30
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.43
Consensus pattern (6 bp):
TACTGT
Found at i:19571028 original size:44 final size:46
Alignment explanation
Indices: 19570938--19571029 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
19570928 TTTGGTTCGC
*
19570938 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
*
19570984 TGTAATGGAATAGAGTCGTAAT-GGT-ATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
19571028 TG
1 TG
19571030 GAATAGAGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 20 0.45
45 3 0.07
46 21 0.48
ACGTcount: A:0.26, C:0.04, G:0.29, T:0.40
Consensus pattern (46 bp):
TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
Found at i:19571030 original size:39 final size:44
Alignment explanation
Indices: 19570938--19571046 Score: 138
Period size: 46 Copynumber: 2.5 Consensus size: 44
19570928 TTTGGTTCGC
*
19570938 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--A
*
19570984 TGTAATGGAATAGAGTCGTAAT-GGT-ATTCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTA
*
19571024 TG-AATGGAATAGAGGTGTAATAG
1 TGTAATGGAATAGAGGCGTAATAG
19571047 CATAAGGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
39 17 0.29
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 21 0.36
ACGTcount: A:0.28, C:0.04, G:0.30, T:0.38
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTA
Found at i:19571204 original size:16 final size:16
Alignment explanation
Indices: 19571196--19571232 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
19571186 TAATTGTTAT
19571196 AAAATATAATTTAATAA
1 AAAATATAATTTAAT-A
19571213 AAATATATAATTTAATA
1 AAA-ATATAATTTAATA
19571230 AAA
1 AAA
19571233 TTGTTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATAATTTAATA
Found at i:19571245 original size:44 final size:44
Alignment explanation
Indices: 19571187--19571354 Score: 105
Period size: 44 Copynumber: 4.1 Consensus size: 44
19571177 ATTTTAACAT
19571187 AATTGTT-ATAAAATATAATTTAATAAAAATATATAATTTAATAA
1 AATTGTTAAT-AAATATAATTTAATAAAAATATATAATTTAATAA
**
19571231 AATTGTTAATAAATAT--TCTT-ATATGAAT-T-TAA--TAATAA
1 AATTGTTAATAAATATAAT-TTAATAAAAATATATAATTTAATAA
** ** *
19571269 AA-TCATAAT--ATATAA--TACCATAAA-ATATAATTTAA-AA
1 AATTGTTAATAAATATAATTTAATAAAAATATATAATTTAATAA
* * * *
19571306 TAATTATTATTAAATATAATTTAATAATAATATATAATTTAATTA
1 -AATTGTTAATAAATATAATTTAATAAAAATATATAATTTAATAA
19571351 AATT
1 AATT
19571355 CTTATTCTTA
Statistics
Matches: 92, Mismatches: 15, Indels: 34
0.65 0.11 0.24
Matches are distributed among these distances:
34 1 0.01
35 9 0.10
36 3 0.03
37 7 0.08
38 13 0.14
39 4 0.04
40 3 0.03
41 7 0.08
42 7 0.08
43 7 0.08
44 28 0.30
45 3 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (44 bp):
AATTGTTAATAAATATAATTTAATAAAAATATATAATTTAATAA
Found at i:19571307 original size:22 final size:23
Alignment explanation
Indices: 19571265--19571307 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
19571255 GAATTTAATA
*
19571265 ATAAAATCATAATATATAATACC
1 ATAAAATCATAATATAAAATACC
*
19571288 ATAAAAT-ATAATTTAAAATA
1 ATAAAATCATAATATAAAATA
19571308 ATTATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAAATCATAATATAAAATACC
Found at i:19571325 original size:120 final size:110
Alignment explanation
Indices: 19571179--19571438 Score: 333
Period size: 120 Copynumber: 2.3 Consensus size: 110
19571169 TTAATCATAT
* * *
19571179 TTTAACATAATTGTTATAAAATATAATTTAATAAAAATATATAATTTAATAAAATTGTTAATAAA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAA---TT-AT---
*
19571244 TATTCTTATATGAATTTAATAATAAAATCATAATATATAATACCATAAAATATAA
59 TATTCTTATATGAA-TT--TAATAAAATCATAATATATAATAACATAAAATATAA
* * *
19571299 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATTAAATTCTTATTCTT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTATTCTT
* *
19571364 ATATGAATTTACTAAAATCATAATATATAATAATATAAAATATAA
66 ATATGAATTTAATAAAATCATAATATATAATAACATAAAATATAA
19571409 TTT-AAATAATTATTATTAAATTATAATTTA
1 TTTAAAATAATTATTATTAAA-TATAATTTA
19571439 TAATCTACTT
Statistics
Matches: 130, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
109 17 0.13
110 45 0.35
112 2 0.02
113 14 0.11
116 1 0.01
117 2 0.02
120 49 0.38
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (110 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTATTCTT
ATATGAATTTAATAAAATCATAATATATAATAACATAAAATATAA
Found at i:19571333 original size:110 final size:107
Alignment explanation
Indices: 19571236--19571442 Score: 287
Period size: 110 Copynumber: 1.9 Consensus size: 107
19571226 AATAAAATTG
*
19571236 TTAA-TAAA-TATTCTTATATGAATTTAATAATAAAATCATAATATATAATACCATAAAATATAA
1 TTAATTAAATTATTCTTATATGAA-TT--TAATAAAATCATAATATATAATAACATAAAATATAA
19571299 TTTAAAATAATTATTATTAAA-TATAATTTAATAA-TAATATATAAT
63 TTT-AAATAATTATTATTAAATTATAATTT-ATAATTAATATATAAT
* *
19571344 TTAATTAAATTCTTATTCTTATATGAATTTACTAAAATCATAATATATAATAATATAAAATATAA
1 TTAATTAAA---TTATTCTTATATGAATTTAATAAAATCATAATATATAATAACATAAAATATAA
19571409 TTTAAATAATTATTATTAAATTATAATTTATAAT
63 TTTAAATAATTATTATTAAATTATAATTTATAAT
19571443 CTACTTTATT
Statistics
Matches: 89, Mismatches: 3, Indels: 12
0.86 0.03 0.12
Matches are distributed among these distances:
108 4 0.04
109 25 0.28
110 44 0.49
112 2 0.02
113 14 0.16
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (107 bp):
TTAATTAAATTATTCTTATATGAATTTAATAAAATCATAATATATAATAACATAAAATATAATTT
AAATAATTATTATTAAATTATAATTTATAATTAATATATAAT
Found at i:19571434 original size:33 final size:33
Alignment explanation
Indices: 19571397--19571461 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
19571387 TATATAATAA
*
19571397 TATAAAATATAATTTAAATAATTATTATTAAAT
1 TATAAAATATAATCTAAATAATTATTATTAAAT
** ** *
19571430 TATAATTTATAATCTACTTTATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
19571462 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (33 bp):
TATAAAATATAATCTAAATAATTATTATTAAAT
Found at i:19572921 original size:49 final size:49
Alignment explanation
Indices: 19572834--19572930 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 49
19572824 AAAAACAAAT
* * * *
19572834 TAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATAAAAC
1 TAAAATTAAGTTGAATATCATGAATCAAAAGCTCAACACTGTATAAAAC
*
19572883 TAAAATTGAGTTGAATATCATGAATCACAAA-CTCAACACTGTATAAAA
1 TAAAATTAAGTTGAATATCATGAATCA-AAAGCTCAACACTGTATAAAA
19572931 TTATAACACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 39 0.93
50 3 0.07
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.29
Consensus pattern (49 bp):
TAAAATTAAGTTGAATATCATGAATCAAAAGCTCAACACTGTATAAAAC
Found at i:19575073 original size:4 final size:4
Alignment explanation
Indices: 19575064--19575088 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19575054 GCATCATCTG
19575064 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
19575089 AAAGAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:19586341 original size:30 final size:30
Alignment explanation
Indices: 19586307--19586364 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19586297 AGGTGGGATG
*
19586307 GGAAGGGAATAAAAGTTTTAGGGGAAAAGT
1 GGAAGGGAATAAAAATTTTAGGGGAAAAGT
* *
19586337 GGAAGGGAGTAAAAATTTTGGGGGAAAA
1 GGAAGGGAATAAAAATTTTAGGGGAAAA
19586365 TAAAATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.19
Consensus pattern (30 bp):
GGAAGGGAATAAAAATTTTAGGGGAAAAGT
Found at i:19586590 original size:9 final size:9
Alignment explanation
Indices: 19586576--19586612 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
19586566 TATAGTTTGA
19586576 TATTCGAAT
1 TATTCGAAT
19586585 TATTCGAAT
1 TATTCGAAT
*
19586594 TATTCGAGT
1 TATTCGAAT
19586603 TATTCGAAT
1 TATTCGAAT
19586612 T
1 T
19586613 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19586681 original size:9 final size:9
Alignment explanation
Indices: 19586664--19586694 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19586654 TCGAGTTGAT
19586664 TCGAATAAC
1 TCGAATAAC
*
19586673 TCGATTAAC
1 TCGAATAAC
19586682 TCGAATAAC
1 TCGAATAAC
19586691 TCGA
1 TCGA
19586695 TTCTTTTAAC
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:19587658 original size:16 final size:16
Alignment explanation
Indices: 19587637--19587667 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19587627 AAATAAAGTA
19587637 TAATAAAACAAATAGG
1 TAATAAAACAAATAGG
*
19587653 TAATAAAAGAAATAG
1 TAATAAAACAAATAG
19587668 AAAGCCATGC
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:0.65, C:0.03, G:0.13, T:0.19
Consensus pattern (16 bp):
TAATAAAACAAATAGG
Found at i:19594802 original size:52 final size:52
Alignment explanation
Indices: 19594626--19594814 Score: 222
Period size: 52 Copynumber: 3.6 Consensus size: 52
19594616 TGTACCGGAA
* * * *
19594626 TAGCAGGCCTTGAGCC-A-GTATTTACTTAGCAAGCCTTAAGCCAGTGTTTATT
1 TAGCAGGCTTTGAGCCGATG-A-TTACTTAGCAGGCCTTGAGCCGGTGTTTATT
* * *
19594678 TAGCAGGCTTTGAGCTGATGTTTACTTAGCAGGCCTTGAGCCGATGTTTATT
1 TAGCAGGCTTTGAGCCGATGATTACTTAGCAGGCCTTGAGCCGGTGTTTATT
* *
19594730 TAGTAGGCTTTGAGCCGATGATTACTTAGTAGG-CTATGAGCCGGTGTTTATT
1 TAGCAGGCTTTGAGCCGATGATTACTTAGCAGGCCT-TGAGCCGGTGTTTATT
* * *
19594782 TAGCAGGCTTTGAACCGATGAATAGTTAGCAGG
1 TAGCAGGCTTTGAGCCGATGATTACTTAGCAGG
19594815 TATTATGTAC
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
51 2 0.02
52 113 0.97
53 1 0.01
54 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (52 bp):
TAGCAGGCTTTGAGCCGATGATTACTTAGCAGGCCTTGAGCCGGTGTTTATT
Found at i:19594814 original size:26 final size:26
Alignment explanation
Indices: 19594626--19594801 Score: 176
Period size: 26 Copynumber: 6.8 Consensus size: 26
19594616 TGTACCGGAA
* *
19594626 TAGCAGGCCTTGAGCC-AGTATTTACT
1 TAGCAGGCTTTGAGCCGA-TGTTTACT
* * * *
19594652 TAGCAAGCCTTAAGCC-AGTGTTTATT
1 TAGCAGGCTTTGAGCCGA-TGTTTACT
*
19594678 TAGCAGGCTTTGAGCTGATGTTTACT
1 TAGCAGGCTTTGAGCCGATGTTTACT
* *
19594704 TAGCAGGCCTTGAGCCGATGTTTATT
1 TAGCAGGCTTTGAGCCGATGTTTACT
* *
19594730 TAGTAGGCTTTGAGCCGATGATTACT
1 TAGCAGGCTTTGAGCCGATGTTTACT
* * * *
19594756 TAGTAGGCTATGAGCCGGTGTTTATT
1 TAGCAGGCTTTGAGCCGATGTTTACT
*
19594782 TAGCAGGCTTTGAACCGATG
1 TAGCAGGCTTTGAGCCGATG
19594802 AATAGTTAGC
Statistics
Matches: 125, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 124 0.99
27 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (26 bp):
TAGCAGGCTTTGAGCCGATGTTTACT
Found at i:19597476 original size:42 final size:43
Alignment explanation
Indices: 19597417--19597529 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 43
19597407 TGTGTTTTCG
* *
19597417 TGTAAGACCACGTCTGGGACGTTGGCATCAACTTGTGATT-CC
1 TGTAAGACCACGTCTGGGACGTTGGCATCAACATGTGATTACA
*
19597459 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGACATGTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCAACATGTGATTACA
*
19597502 TGTAAGACCACGTCTGTGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
19597530 TGTACGGACT
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
41 1 0.02
42 35 0.56
43 25 0.40
44 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCAACATGTGATTACA
Found at i:19602112 original size:30 final size:30
Alignment explanation
Indices: 19602050--19602112 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
19602040 ACTTTTCCCT
* *
19602050 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCCTCCCACTTCCCCCC
19602080 CAAAACTTTTACTCCCCTCCC-C-TCCCCTCC
1 CAAAACTTTTACT-CCCTCCCACTTCCCC-CC
19602110 CAA
1 CAA
19602113 CCCCCCAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 19 0.66
31 6 0.21
ACGTcount: A:0.21, C:0.51, G:0.00, T:0.29
Consensus pattern (30 bp):
CAAAACTTTTACTCCCTCCCACTTCCCCCC
Found at i:19602500 original size:19 final size:17
Alignment explanation
Indices: 19602477--19602557 Score: 51
Period size: 17 Copynumber: 4.6 Consensus size: 17
19602467 TTATATCTAC
19602477 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* *
19602494 TAAATTTCA-ATTTTTATAT
1 T--ATTT-ATATTATTAAAT
*
19602513 TATTTATATTATTGAAT
1 TATTTATATTATTAAAT
* *
19602530 TGTTTAGTCA-TATTGAA-
1 TATTTA-T-ATTATTAAAT
19602547 TATTTATATTA
1 TATTTATATTA
19602558 AAATTGAGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
15 1 0.02
16 4 0.08
17 22 0.44
18 8 0.16
19 14 0.28
20 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:19604368 original size:3 final size:3
Alignment explanation
Indices: 19604360--19604396 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
19604350 ACTGATATTG
19604360 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
19604397 TGTATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:19605454 original size:19 final size:19
Alignment explanation
Indices: 19605430--19605467 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19605420 CATTTGTTGG
19605430 GTCTAACTGTCACTGACAT
1 GTCTAACTGTCACTGACAT
19605449 GTCTAACTGTCACTGACAT
1 GTCTAACTGTCACTGACAT
19605468 TCTTTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (19 bp):
GTCTAACTGTCACTGACAT
Found at i:19606091 original size:22 final size:22
Alignment explanation
Indices: 19606063--19606115 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
19606053 TAGTGAAATG
* *
19606063 ACAACAATACAGTGGGAAAACA
1 ACAACAAAACAGTGAGAAAACA
* *
19606085 ACAACAAAATAGTGAGAAAGCA
1 ACAACAAAACAGTGAGAAAACA
*
19606107 ACAGCAAAA
1 ACAACAAAA
19606116 GATAGGGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.58, C:0.17, G:0.17, T:0.08
Consensus pattern (22 bp):
ACAACAAAACAGTGAGAAAACA
Found at i:19609439 original size:23 final size:23
Alignment explanation
Indices: 19609408--19609460 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
19609398 TGATTTAAAC
* *
19609408 AAATGTTCATA-TTTATATTATTA
1 AAATATTCATATTTTATACTA-TA
19609431 AAATATTCATATTTTATACTATA
1 AAATATTCATATTTTATACTATA
19609454 AAATATT
1 AAATATT
19609461 TTTACTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATATTCATATTTTATACTATA
Found at i:19609506 original size:22 final size:23
Alignment explanation
Indices: 19609481--19609536 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
19609471 TTATAAATTG
*
19609481 TAATATATTTTT-ATTAAAATAT
1 TAATATATTTTTCAATAAAATAT
19609503 TAATATGATTTTTCAATAAAATAT
1 TAATAT-ATTTTTCAATAAAATAT
19609527 TAATAATATT
1 TAAT-ATATT
19609537 ACTTCAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 6 0.20
23 6 0.20
24 16 0.53
25 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TAATATATTTTTCAATAAAATAT
Found at i:19610005 original size:6 final size:6
Alignment explanation
Indices: 19609994--19610025 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
19609984 AAAAATTGTG
19609994 ATAATT ATAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT ATAATT AT
19610026 CAGTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:19618265 original size:23 final size:23
Alignment explanation
Indices: 19618239--19618283 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
19618229 TAAATTTGAG
*
19618239 TGCAATTATTTTATAATTACCTA
1 TGCAATTATTCTATAATTACCTA
19618262 TGCAATTATTCTATAATTACCT
1 TGCAATTATTCTATAATTACCT
19618284 CCTCATTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (23 bp):
TGCAATTATTCTATAATTACCTA
Found at i:19623253 original size:77 final size:78
Alignment explanation
Indices: 19623114--19623283 Score: 306
Period size: 77 Copynumber: 2.2 Consensus size: 78
19623104 CAACAAAAAC
*
19623114 AAATAAAAAATAAAAAATCCAACAAACTTTAAAAAGAAAAAAATCTTCTCCTTCCTTTATTATTA
1 AAATATAAAATAAAAAATCCAACAAACTTTAAAAAGAAAAAAATCTTCTCCTTCCTTTATTATTA
19623179 TTCTTCTATCCAA
66 TTCTTCTATCCAA
*
19623192 AAATATAAAATAAAAAATCCAACAAACTTTAAAAAG-AAAAAATCTTCTCTTTCCTTTATTATTA
1 AAATATAAAATAAAAAATCCAACAAACTTTAAAAAGAAAAAAATCTTCTCCTTCCTTTATTATTA
19623256 TTCTTCTATCCAA
66 TTCTTCTATCCAA
*
19623269 AAATATAAAAGAAAA
1 AAATATAAAATAAAA
19623284 TAAATTCATT
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 54 0.61
78 35 0.39
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.32
Consensus pattern (78 bp):
AAATATAAAATAAAAAATCCAACAAACTTTAAAAAGAAAAAAATCTTCTCCTTCCTTTATTATTA
TTCTTCTATCCAA
Found at i:19623377 original size:19 final size:19
Alignment explanation
Indices: 19623342--19623379 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19623332 CAATCAATAA
*
19623342 TTTCTTCCATTAGTTTCCT
1 TTTCTTCCATTACTTTCCT
19623361 TTTC-TCCATTCACTTTCCT
1 TTTCTTCCATT-ACTTTCCT
19623380 AAGCTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.11, C:0.32, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTCTTCCATTACTTTCCT
Found at i:19623519 original size:27 final size:27
Alignment explanation
Indices: 19623481--19623535 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
19623471 CATTTTTACG
19623481 TACAATGCTTCATTTTAGGATAAATCC
1 TACAATGCTTCATTTTAGGATAAATCC
19623508 TACAATGCTTCATTTTAGGATAAATCC
1 TACAATGCTTCATTTTAGGATAAATCC
19623535 T
1 T
19623536 TACTTAACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (27 bp):
TACAATGCTTCATTTTAGGATAAATCC
Found at i:19623824 original size:5 final size:6
Alignment explanation
Indices: 19623809--19623833 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19623799 AATATTTTAA
19623809 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
19623834 TTTTTAAATT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:19623955 original size:30 final size:30
Alignment explanation
Indices: 19623919--19624011 Score: 177
Period size: 30 Copynumber: 3.1 Consensus size: 30
19623909 ACTTTTTTGG
19623919 CCAAGCCCATATTTCGGGCCTATATTTTTA
1 CCAAGCCCATATTTCGGGCCTATATTTTTA
19623949 CCAAGCCCATATTTCGGGCCTATATTTTTA
1 CCAAGCCCATATTTCGGGCCTATATTTTTA
19623979 CCCAAGCCCATATTTCGGGCCTATATTTTTA
1 -CCAAGCCCATATTTCGGGCCTATATTTTTA
19624010 CC
1 CC
19624012 CGAACCCTCC
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
30 32 0.52
31 30 0.48
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (30 bp):
CCAAGCCCATATTTCGGGCCTATATTTTTA
Found at i:19624012 original size:31 final size:31
Alignment explanation
Indices: 19623919--19624012 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
19623909 ACTTTTTTGG
19623919 CCAAGCCCATATTTCGGGCCTATATTTTTA-
1 CCAAGCCCATATTTCGGGCCTATATTTTTAC
19623949 CCAAGCCCATATTTCGGGCCTATATTTTTAC
1 CCAAGCCCATATTTCGGGCCTATATTTTTAC
19623980 CCAAGCCCATATTTCGGGCCTATATTTTTAC
1 CCAAGCCCATATTTCGGGCCTATATTTTTAC
19624011 CC
1 CC
19624013 GAACCCTCCT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 30 0.48
31 33 0.52
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (31 bp):
CCAAGCCCATATTTCGGGCCTATATTTTTAC
Found at i:19626254 original size:16 final size:15
Alignment explanation
Indices: 19626233--19626262 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19626223 AAGTTTTAAA
19626233 AAAACTTTAACAAAAT
1 AAAACTTTAA-AAAAT
19626249 AAAACTTTAAAAAA
1 AAAACTTTAAAAAA
19626263 GTTTAAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAACTTTAAAAAAT
Found at i:19629036 original size:9 final size:9
Alignment explanation
Indices: 19629022--19629048 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
19629012 GTGGGACACA
19629022 TGACTCCAT
1 TGACTCCAT
19629031 TGACTCCAT
1 TGACTCCAT
19629040 TGACTCCAT
1 TGACTCCAT
19629049 CATAACCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (9 bp):
TGACTCCAT
Found at i:19631357 original size:18 final size:18
Alignment explanation
Indices: 19631313--19631348 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19631303 TTTCTTATAG
* *
19631313 AATTTAGTTTTTTTAATA
1 AATTTAATTCTTTTAATA
19631331 AATTTAATTCTTTTAATA
1 AATTTAATTCTTTTAATA
19631349 TTTTTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
AATTTAATTCTTTTAATA
Found at i:19633642 original size:13 final size:14
Alignment explanation
Indices: 19633619--19633659 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
19633609 GAAAAAAATT
19633619 ATATATATTTAATA
1 ATATATATTTAATA
19633633 ATAT-TATTTAA-A
1 ATATATATTTAATA
*
19633645 TTATATATTTAATA
1 ATATATATTTAATA
19633659 A
1 A
19633660 AATTTATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.17
13 14 0.61
14 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATATTTAATA
Found at i:19634506 original size:14 final size:15
Alignment explanation
Indices: 19634489--19634518 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19634479 TTGATTAAAT
19634489 TAATAAAG-TTAAGA
1 TAATAAAGATTAAGA
19634503 TAATAAAGATTAAGA
1 TAATAAAGATTAAGA
19634518 T
1 T
19634519 GTTTTGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (15 bp):
TAATAAAGATTAAGA
Found at i:19639312 original size:25 final size:23
Alignment explanation
Indices: 19639283--19639328 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
19639273 AAGAAAAAAT
19639283 TGCAAACAACCCAACAACTTTTAAC
1 TGCAAACAA--CAACAACTTTTAAC
* *
19639308 TGCAATCAAGAACAACTTTTA
1 TGCAAACAACAACAACTTTTA
19639329 GGAACAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (23 bp):
TGCAAACAACAACAACTTTTAAC
Found at i:19641216 original size:2 final size:2
Alignment explanation
Indices: 19641203--19641233 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19641193 CTCCAAACTC
*
19641203 CT CT CT CG CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
19641234 GGTCCAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.03, T:0.45
Consensus pattern (2 bp):
CT
Found at i:19646871 original size:24 final size:23
Alignment explanation
Indices: 19646844--19646928 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 23
19646834 GGGCACAACA
19646844 CAGCTTGTACTAGCTTACCGATTT
1 CAGCTTGTA-TAGCTTACCGATTT
* * *
19646868 CAGCTCGTGAGAGCTTACCGATTCA
1 CAGCTTGT-ATAGCTTACCGATT-T
*
19646893 CAACTTGTATGAGCTTACCGATTT
1 CAGCTTGTAT-AGCTTACCGATTT
*
19646917 ACAGCTCGTATA
1 -CAGCTTGTATA
19646929 AGCATACATG
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
24 21 0.44
25 27 0.56
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (23 bp):
CAGCTTGTATAGCTTACCGATTT
Found at i:19646927 original size:25 final size:25
Alignment explanation
Indices: 19646855--19646927 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
19646845 AGCTTGTACT
19646855 AGCTTACCGATTT-CAGCTCGTGA-G
1 AGCTTACCGATTTACAGCTCGT-ATG
* * *
19646879 AGCTTACCGATTCACAACTTGTATG
1 AGCTTACCGATTTACAGCTCGTATG
19646904 AGCTTACCGATTTACAGCTCGTAT
1 AGCTTACCGATTTACAGCTCGTAT
19646928 AAGCATACAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 13 0.32
25 28 0.68
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (25 bp):
AGCTTACCGATTTACAGCTCGTATG
Found at i:19647685 original size:19 final size:18
Alignment explanation
Indices: 19647649--19647690 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
19647639 TACAAGTGTT
*
19647649 TTGTGAGTTGGTGAATTGG
1 TTGTGAATTGGTGAATT-G
19647668 TTGTGAATTGGT-ACATTG
1 TTGTGAATTGGTGA-ATTG
19647686 TTGTG
1 TTGTG
19647691 TAAGACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.17, C:0.02, G:0.36, T:0.45
Consensus pattern (18 bp):
TTGTGAATTGGTGAATTG
Found at i:19656370 original size:26 final size:26
Alignment explanation
Indices: 19656341--19656414 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
19656331 CCTATGATAG
19656341 ACACACTCTAGCAAACCCTATGGCAA
1 ACACACTCTAGCAAACCCTATGGCAA
** * **
19656367 ACACACTCTAGTGAACCCTATAGTGA
1 ACACACTCTAGCAAACCCTATGGCAA
* *
19656393 ACTCACTCTAACAAACCCTATG
1 ACACACTCTAGCAAACCCTATG
19656415 CCTGGAGAAC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.20
Consensus pattern (26 bp):
ACACACTCTAGCAAACCCTATGGCAA
Found at i:19658870 original size:21 final size:23
Alignment explanation
Indices: 19658833--19658874 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
19658823 TTCGTAACTC
19658833 AATATTTTAATTTTAATTATTTT
1 AATATTTTAATTTTAATTATTTT
19658856 AATATTTT-A-TTTAATTATT
1 AATATTTTAATTTTAATTATT
19658875 CCTAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
AATATTTTAATTTTAATTATTTT
Found at i:19658882 original size:10 final size:8
Alignment explanation
Indices: 19658862--19658895 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
19658852 TTTTAATATT
19658862 TTATTTAA
1 TTATTTAA
19658870 TTATTCCTAA
1 TTATT--TAA
19658880 TTATTTAA
1 TTATTTAA
19658888 TTATTTAA
1 TTATTTAA
19658896 CCTAATTACG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATTTAA
Found at i:19660128 original size:25 final size:26
Alignment explanation
Indices: 19660080--19660130 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
19660070 ATTTTTCAAA
* *
19660080 AGTATGAATTTTGGACTGAATTGAAT
1 AGTATGAATATTGAACTGAATTGAAT
*
19660106 AGTATGAATATT-AACTGGATTGAAT
1 AGTATGAATATTGAACTGAATTGAAT
19660131 TTACTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (26 bp):
AGTATGAATATTGAACTGAATTGAAT
Found at i:19664972 original size:59 final size:59
Alignment explanation
Indices: 19664904--19665057 Score: 290
Period size: 59 Copynumber: 2.6 Consensus size: 59
19664894 GCTTCAATAA
*
19664904 AAAAATATATATGTATTGTATTTTAAAAATAAAAAATATATGTAGTGTATTTTAAAAAT
1 AAAAATATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTATTTTAAAAAT
19664963 AAAAATATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTATTTTAAAAAT
1 AAAAATATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTATTTTAAAAAT
*
19665022 AAAAAAATATATGTAGTGTATTTTAAAAATAAAAAA
1 AAAAATATATATGTAGTGTATTTTAAAAATAAAAAA
19665058 ATTTAATCTG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 93 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (59 bp):
AAAAATATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTATTTTAAAAAT
Found at i:19665058 original size:30 final size:30
Alignment explanation
Indices: 19664903--19665059 Score: 273
Period size: 30 Copynumber: 5.3 Consensus size: 30
19664893 TGCTTCAATA
*
19664903 AAAAAATATATATGTATTGTATTTTAAAAAT
1 AAAAAA-ATATATGTAGTGTATTTTAAAAAT
19664934 -AAAAAATATATGTAGTGTATTTTAAAAAT
1 AAAAAAATATATGTAGTGTATTTTAAAAAT
*
19664963 AAAAATATATATGTAGTGTATTTTAAAAAT
1 AAAAAAATATATGTAGTGTATTTTAAAAAT
19664993 -AAAAAATATATGTAGTGTATTTTAAAAAT
1 AAAAAAATATATGTAGTGTATTTTAAAAAT
19665022 AAAAAAATATATGTAGTGTATTTTAAAAAT
1 AAAAAAATATATGTAGTGTATTTTAAAAAT
19665052 AAAAAAAT
1 AAAAAAAT
19665060 TTAATCTGAT
Statistics
Matches: 121, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
29 51 0.42
30 70 0.58
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.38
Consensus pattern (30 bp):
AAAAAAATATATGTAGTGTATTTTAAAAAT
Found at i:19668291 original size:24 final size:25
Alignment explanation
Indices: 19668250--19668311 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
19668240 ATATTAGTTA
19668250 AAAAAAAATTAGCGAGTGACTAAAATA-
1 AAAAAAAATT--C-AGTGACTAAAATAC
* * *
19668277 AAAATAAATTCAGTGCCTAAATTAC
1 AAAAAAAATTCAGTGACTAAAATAC
19668302 AAAAAAAATT
1 AAAAAAAATT
19668312 AAATTAATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 11 0.37
25 10 0.33
27 9 0.30
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.23
Consensus pattern (25 bp):
AAAAAAAATTCAGTGACTAAAATAC
Found at i:19672814 original size:17 final size:17
Alignment explanation
Indices: 19672778--19672831 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
19672768 ATTTACTTTG
*
19672778 AAATTTAAT-TAATTTAT
1 AAATTTAATGTTATTT-T
19672795 AAATTTAATGTTATTTT
1 AAATTTAATGTTATTTT
*
19672812 AAAATT-ATG-T-TTTT
1 AAATTTAATGTTATTTT
19672826 AAATTT
1 AAATTT
19672832 CTTTATAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 3 0.09
17 15 0.45
18 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
AAATTTAATGTTATTTT
Found at i:19675221 original size:46 final size:46
Alignment explanation
Indices: 19675154--19675249 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
19675144 TGAACAGAGA
19675154 GCATTGATGTTCTAATAATCAGAGAGCGCGCTAAGGTTCCTTAATG
1 GCATTGATGTTCTAATAATCAGAGAGCGCGCTAAGGTTCCTTAATG
*
19675200 GCATTGATGTTCTAATAATCAGGGAGCGCGCTAAGGTTCCTTAATG
1 GCATTGATGTTCTAATAATCAGAGAGCGCGCTAAGGTTCCTTAATG
19675246 GCAT
1 GCAT
19675250 GCCACTAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (46 bp):
GCATTGATGTTCTAATAATCAGAGAGCGCGCTAAGGTTCCTTAATG
Found at i:19675825 original size:49 final size:46
Alignment explanation
Indices: 19675772--19675876 Score: 122
Period size: 47 Copynumber: 2.2 Consensus size: 46
19675762 TAGTATAACT
*
19675772 ATGGTCTTGCACAT-AATCACATATCACAAACCAAAGCCATAGCCCAGCC
1 ATGGTCTT--ACATGAAGCACATATCAC--ACCAAAGCCATAGCCCAGCC
* * *
19675821 ATGGTCTTACATGGAAGCACATATCACACCGATGCCATAGCCCAGCT
1 ATGGTCTTACAT-GAAGCACATATCACACCAAAGCCATAGCCCAGCC
19675868 ATGGTCTTA
1 ATGGTCTTA
19675877 TACGGAAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
47 30 0.60
49 20 0.40
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (46 bp):
ATGGTCTTACATGAAGCACATATCACACCAAAGCCATAGCCCAGCC
Found at i:19685944 original size:33 final size:32
Alignment explanation
Indices: 19685906--19685991 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 32
19685896 CTTGGTCTAA
* **
19685906 CTATGGTCTTACGTTCAAGGTGCCATAACCCAG
1 CTATGGTCTTACATT-AAAATGCCATAACCCAG
* * *
19685939 TTATGGTCTTTTCATTAAAATGCCATAGCCCAG
1 CTATGGTC-TTACATTAAAATGCCATAACCCAG
19685972 CTATGGTCTTACATTTAAAA
1 CTATGGTCTTACA-TTAAAA
19685992 ATTGCCATGG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
32 4 0.09
33 34 0.79
34 5 0.12
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (32 bp):
CTATGGTCTTACATTAAAATGCCATAACCCAG
Found at i:19690309 original size:23 final size:23
Alignment explanation
Indices: 19690274--19690329 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
19690264 ATTATTTTAA
*
19690274 TAATATTTAATATTAAATTTAATC
1 TAATA-TTAATATTAAATTAAATC
* * *
19690298 TAATATTGATATTAGATTAAATT
1 TAATATTAATATTAAATTAAATC
19690321 TAATATTAA
1 TAATATTAA
19690330 AGTGATTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
TAATATTAATATTAAATTAAATC
Found at i:19698741 original size:43 final size:43
Alignment explanation
Indices: 19698693--19698994 Score: 372
Period size: 43 Copynumber: 7.0 Consensus size: 43
19698683 TCTTTTAAAG
* *
19698693 CGCCGCTATAGACTATGGTCTTTAGCGGCGCTTAGACAAAAAA
1 CGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAA
* * *
19698736 CGCCGCGATAGACCATGGTCTTTAGCGGCGCTTATACAAAAAA
1 CGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAA
*** *
19698779 CGCCACTATAGATTGTGGTCTTTAGCGGCGCTTATACAAAAAA
1 CGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAA
* * * *
19698822 CGCCACTATAGATCGTGGTCTTTAGCGGCGTTTGGACAAAAAA
1 CGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAA
* *
19698865 CGCCATTATAGACCATGGT-TTTCAGCGGCGCTTGGACAAAAAA
1 CGCCACTATAGACCATGGTCTTT-AGCGGCGCTTAGACAAAAAA
* *
19698908 CGCCACTATAGACGATGGTCTTTAGCGGCGCTTAGGCAAAAAAA
1 CGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGAC-AAAAAA
* * * * **
19698952 TGCCACTATAGGCCGTGTTCTTTAGCGGCGCTTACCCAAAAAA
1 CGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAA
19698995 TACCGCTAAT
Statistics
Matches: 229, Mismatches: 27, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
42 3 0.01
43 187 0.82
44 39 0.17
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (43 bp):
CGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAA
Found at i:19699336 original size:21 final size:21
Alignment explanation
Indices: 19699310--19699363 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
19699300 GCTGTTCTGC
*
19699310 TTCCCTCGTTGCAGCCTCTAA
1 TTCCCTCGCTGCAGCCTCTAA
**
19699331 TTCCCTCGCTGCAGCCTCTGC
1 TTCCCTCGCTGCAGCCTCTAA
*
19699352 TTCTCTCGCTGC
1 TTCCCTCGCTGC
19699364 TGCATCTGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.07, C:0.43, G:0.17, T:0.33
Consensus pattern (21 bp):
TTCCCTCGCTGCAGCCTCTAA
Found at i:19699371 original size:21 final size:21
Alignment explanation
Indices: 19699305--19699374 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
19699295 TTTAAGCTGT
* * *
19699305 TCTGCTTCCCTCGTTGCAGCC
1 TCTGCTTCTCTCGCTGCAGCA
** * *
19699326 TCTAATTCCCTCGCTGCAGCC
1 TCTGCTTCTCTCGCTGCAGCA
*
19699347 TCTGCTTCTCTCGCTGCTGCA
1 TCTGCTTCTCTCGCTGCAGCA
19699368 TCTGCTT
1 TCTGCTT
19699375 TAAGCTGCTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.07, C:0.40, G:0.17, T:0.36
Consensus pattern (21 bp):
TCTGCTTCTCTCGCTGCAGCA
Found at i:19699426 original size:87 final size:87
Alignment explanation
Indices: 19699335--19699512 Score: 270
Period size: 87 Copynumber: 2.0 Consensus size: 87
19699325 CTCTAATTCC
*
19699335 CTCGCTGCAGCCTCTGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCAT
1 CTCGCTGCAGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCAT
19699399 A-CTTTCGTTGAACCTCAGCTTCT
65 ATCTTT-GTTGAACCTCAGCTTCT
* * * *
19699422 CTCGCTGCTGCCTCTGCTTCTCTTGTTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATA
1 CTCGCTGCAGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATA
*
19699487 TCTTTTTTGAACCTCAGCTTCT
66 TCTTTGTTGAACCTCAGCTTCT
19699509 CTCG
1 CTCG
19699513 ATGTTGCCTC
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
86 1 0.01
87 78 0.94
88 4 0.05
ACGTcount: A:0.11, C:0.30, G:0.19, T:0.39
Consensus pattern (87 bp):
CTCGCTGCAGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATA
TCTTTGTTGAACCTCAGCTTCT
Found at i:19699458 original size:21 final size:21
Alignment explanation
Indices: 19699416--19699461 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
19699406 TTGAACCTCA
* *
19699416 GCTTCTCTCGCTGCTGCCTCT
1 GCTTCTCTCGCTGCCGCATCT
* *
19699437 GCTTCTCTTGTTGCCGCATCT
1 GCTTCTCTCGCTGCCGCATCT
19699458 GCTT
1 GCTT
19699462 TAAGTTGTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.37, G:0.20, T:0.41
Consensus pattern (21 bp):
GCTTCTCTCGCTGCCGCATCT
Found at i:19701202 original size:114 final size:114
Alignment explanation
Indices: 19701002--19701231 Score: 451
Period size: 114 Copynumber: 2.0 Consensus size: 114
19700992 GTTTGTTGTT
19701002 CAGTGCTGTTTGTTTCGGTCGAGTTTGGAGTACCTTGAACAATGCGGTGCGCTCGCACGGGTCTT
1 CAGTGCTGTTTGTTTCGGTCGAGTTTGGAGTACCTTGAACAATGCGGTGCGCTCGCACGGGTCTT
*
19701067 CTAGGCATTTTATCTGCAATACAAATAAATTAGTTGAAAACTTAATATA
66 CTAGGCATTTTATCTACAATACAAATAAATTAGTTGAAAACTTAATATA
19701116 CAGTGCTGTTTGTTTCGGTCGAGTTTGGAGTACCTTGAACAATGCGGTGCGCTCGCACGGGTCTT
1 CAGTGCTGTTTGTTTCGGTCGAGTTTGGAGTACCTTGAACAATGCGGTGCGCTCGCACGGGTCTT
19701181 CTAGGCATTTTATCTACAATACAAATAAATTAGTTGAAAACTTAATATA
66 CTAGGCATTTTATCTACAATACAAATAAATTAGTTGAAAACTTAATATA
19701230 CA
1 CA
19701232 ATTACAACAA
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (114 bp):
CAGTGCTGTTTGTTTCGGTCGAGTTTGGAGTACCTTGAACAATGCGGTGCGCTCGCACGGGTCTT
CTAGGCATTTTATCTACAATACAAATAAATTAGTTGAAAACTTAATATA
Found at i:19703404 original size:11 final size:11
Alignment explanation
Indices: 19703388--19703414 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
19703378 TTACTCAACC
19703388 AGTAATATGAA
1 AGTAATATGAA
19703399 AGTAATATGAA
1 AGTAATATGAA
19703410 AGTAA
1 AGTAA
19703415 ATTAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.26
Consensus pattern (11 bp):
AGTAATATGAA
Found at i:19704341 original size:27 final size:27
Alignment explanation
Indices: 19704293--19704344 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
19704283 TCTTACATTT
* *
19704293 AAATAATTAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
**
19704320 AAATAAATAATTACTTACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
19704345 TTTGTTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:19704429 original size:10 final size:10
Alignment explanation
Indices: 19704414--19704450 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
19704404 ATAACTATAT
19704414 ATATATATCC
1 ATATATATCC
*
19704424 ATATATAT-T
1 ATATATATCC
19704433 A-ATATATCC
1 ATATATATCC
19704442 ATATATATC
1 ATATATATC
19704451 AAAAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
10 15 0.65
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATCC
Found at i:19704965 original size:23 final size:23
Alignment explanation
Indices: 19704935--19704987 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
19704925 TGCATCGACC
*
19704935 AAAATATTCCCTAAATATTTTTT
1 AAAATATTCCCTAAATATTCTTT
19704958 AAAATATTCCCTAAATATTCTTT
1 AAAATATTCCCTAAATATTCTTT
19704981 AATAATA
1 AA-AATA
19704988 AAAAAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAATATTCCCTAAATATTCTTT
Found at i:19705771 original size:14 final size:14
Alignment explanation
Indices: 19705752--19705819 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
19705742 ATGATCGTTG
19705752 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
19705766 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
19705781 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
19705794 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
19705807 AAACCTTAAATCT
1 AAACCCTAAATCT
19705820 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:19705775 original size:15 final size:15
Alignment explanation
Indices: 19705755--19705792 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19705745 ATCGTTGAAA
19705755 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
19705770 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
19705785 CCCTAAAT
1 CCCTAAAT
19705793 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:19706364 original size:41 final size:41
Alignment explanation
Indices: 19706314--19706632 Score: 284
Period size: 41 Copynumber: 7.8 Consensus size: 41
19706304 GGTAAATGCG
* * *
19706314 TTAGCGGCGCTTAGATACAAACGCCGCTAAAGGCCGGAGAA
1 TTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGAA
* * * * *
19706355 TTAGTGGCGCTCAGATAAAAACGTCACTAAAGATCC-GAGCA
1 TTAGCGGCGCTCAGATAAAAACGCCGCTAAAG-GCCAGAGAA
* * * * *
19706396 TTAGCGGCGCTTAGACAAAAACGTCGCTAAATGCCAGAGTA
1 TTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGAA
* * ** *
19706437 TTAGTGGCGCTCAGATAAAAACGCCACTAAAGATCAGAGCA
1 TTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGAA
* * * **
19706478 TTAGCGGCGCTGAGAGAAAATCGCCGCTAAAGGCCAGAGGT
1 TTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGAA
* * ** *
19706519 TTAGCGGCGTTCATATAAAAA-GCCGCTAAAGATCGGAGAA
1 TTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGAA
* * * **
19706559 TTAGCGACGCTCAGATAAAAACGCCACTAAAGATCC-GATCA
1 TTAGCGGCGCTCAGATAAAAACGCCGCTAAAG-GCCAGAGAA
* *
19706600 TTAGCGGCGCACAAATAAAAACGCCGCTAAAGG
1 TTAGCGGCGCTCAGATAAAAACGCCGCTAAAGG
19706633 TTTAAAAATC
Statistics
Matches: 219, Mismatches: 55, Indels: 9
0.77 0.19 0.03
Matches are distributed among these distances:
40 34 0.16
41 182 0.83
42 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17
Consensus pattern (41 bp):
TTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGAA
Found at i:19706409 original size:82 final size:82
Alignment explanation
Indices: 19706314--19706631 Score: 352
Period size: 82 Copynumber: 3.9 Consensus size: 82
19706304 GGTAAATGCG
* * *
19706314 TTAGCGGCGCTTAGATACAAACGCCGCTAAAGGCCGGAGAATTAGTGGCGCTCAGATAAAAACGT
1 TTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAACGC
*
19706379 CACTAAAGATCCGAGCA
66 CACTAAAGATCAGAGCA
* * * *
19706396 TTAGCGGCGCTTAGACAAAAACGTCGCTAAATGCCAGAGTATTAGTGGCGCTCAGATAAAAACGC
1 TTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAACGC
19706461 CACTAAAGATCAGAGCA
66 CACTAAAGATCAGAGCA
* * * ** * * *
19706478 TTAGCGGCGCTGAGAGAAAATCGCCGCTAAAGGCCAGAGGTTTAGCGGCGTTCATATAAAAA-GC
1 TTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAACGC
* * *
19706542 CGCTAAAGATCGGAGAA
66 CACTAAAGATCAGAGCA
* * * * ** * * *
19706559 TTAGCGACGCTCAGATAAAAACGCCACTAAAGATCC-GATCATTAGCGGCGCACAAATAAAAACG
1 TTAGCGGCGCTTAGATAAAAACGCCGCTAAAG-GCCAGAGAATTAGTGGCGCTCAGATAAAAACG
*
19706623 CCGCTAAAG
65 CCACTAAAG
19706632 GTTTAAAAAT
Statistics
Matches: 201, Mismatches: 33, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
81 63 0.31
82 138 0.69
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17
Consensus pattern (82 bp):
TTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAACGC
CACTAAAGATCAGAGCA
Found at i:19706783 original size:40 final size:40
Alignment explanation
Indices: 19706709--19706784 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
19706699 AATTTCTATT
* *
19706709 TTTAGCGGCGCTTCTTCGAAATCGCCGCGGATGCTCTACC
1 TTTAGCGGCGCTTCTGCGAAATCGCCGCGAATGCTCTACC
* *
19706749 TTTAGCGGCGCTT-TGGCTAAATCGCCGCTAATGCTC
1 TTTAGCGGCGCTTCT-GCGAAATCGCCGCGAATGCTC
19706785 GATTTTTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 30 0.97
ACGTcount: A:0.16, C:0.30, G:0.25, T:0.29
Consensus pattern (40 bp):
TTTAGCGGCGCTTCTGCGAAATCGCCGCGAATGCTCTACC
Found at i:19707415 original size:21 final size:23
Alignment explanation
Indices: 19707382--19707429 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
19707372 TGATGAGAAT
*
19707382 AAAATCTCTTTTTC-CTTATTTA
1 AAAATATCTTTTTCTCTTATTTA
*
19707404 AAAATATC-TTTTCTTTTATTTA
1 AAAATATCTTTTTCTCTTATTTA
19707426 AAAA
1 AAAA
19707430 GGAATAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.52
Consensus pattern (23 bp):
AAAATATCTTTTTCTCTTATTTA
Found at i:19737542 original size:29 final size:30
Alignment explanation
Indices: 19737510--19737566 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19737500 CATCGACTCT
19737510 AACTTTT-CAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
19737539 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
19737567 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:19739031 original size:35 final size:35
Alignment explanation
Indices: 19738985--19739054 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
19738975 CTTAAAAAGT
19738985 TTAATCTTTTCAACTGTATACCAGCATCTACACCC
1 TTAATCTTTTCAACTGTATACCAGCATCTACACCC
19739020 TTAATCTTTTCAACTGTATACCAGCATCTACACCC
1 TTAATCTTTTCAACTGTATACCAGCATCTACACCC
19739055 ATGGATCCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (35 bp):
TTAATCTTTTCAACTGTATACCAGCATCTACACCC
Found at i:19741598 original size:3 final size:3
Alignment explanation
Indices: 19741590--19741666 Score: 72
Period size: 3 Copynumber: 25.7 Consensus size: 3
19741580 AAGTAATTAA
19741590 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AA- AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* *
19741634 GAT AAT ACATT AA- AAT AAT GAAG AA- AAT AAT AA
1 AAT AAT A-A-T AAT AAT AAT -AAT AAT AAT AAT AA
19741667 AAATGCTAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
2 8 0.12
3 47 0.73
4 7 0.11
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:19741638 original size:13 final size:14
Alignment explanation
Indices: 19741572--19741640 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 14
19741562 ATATATGCGT
19741572 ATATATATAAGTAATTA
1 ATATA-ATAA-TAA-TA
*
19741589 AAATAATAATAATA
1 ATATAATAATAATA
19741603 ATAATAATAATAATA
1 AT-ATAATAATAATA
19741618 A-ATAATAATAA-A
1 ATATAATAATAATA
*
19741630 ATATGATAATA
1 ATATAATAATA
19741641 CATTAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
12 2 0.04
13 18 0.38
14 3 0.06
15 16 0.34
16 4 0.09
17 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATAATAATAATA
Done.