Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 15 of 59
Found at i:5390740 original size:43 final size:38
Alignment explanation
Indices: 5390663--5390753 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 38
5390653 CTATTCATTC
*
5390663 TTATTTTTTTTTCTATTTTTTAATTTATTTTTTATTTT
1 TTATTTTTTTTTATATTTTTTAATTTATTTTTTATTTT
5390701 TTAGTTTTTTTATTATATTTTATTATATTTTATTTTTTATTTT
1 TTA-TTTTTTT-TTATATTTT-TTA-A-TTTATTTTTTATTTT
5390744 TTATTTTTTT
1 TTATTTTTTT
5390754 GAAATAGGTG
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
38 3 0.06
39 7 0.15
40 8 0.17
41 3 0.06
42 8 0.17
43 18 0.38
ACGTcount: A:0.18, C:0.01, G:0.01, T:0.80
Consensus pattern (38 bp):
TTATTTTTTTTTATATTTTTTAATTTATTTTTTATTTT
Found at i:5391173 original size:59 final size:59
Alignment explanation
Indices: 5391009--5391837 Score: 851
Period size: 59 Copynumber: 13.9 Consensus size: 59
5390999 AAAAAAAAGA
* * * * *
5391009 GAAATTTCTAGACTTGATTTAGGCTCGACCTATCTCAAAATAGGTTCGACTCAAAAATT
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATT
* * * * * *
5391068 GAAATTCCTA-ACTTGATCTAGGTTCAACCTATCTCACAATAGGTTCGATTGACAAATT
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATT
* * *
5391126 AAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAAGTTCGATTAAAAAATT
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATT
*
5391185 GAAATTCCTAGACTTGACCTAGGCTCGACCTATCTCACAAAACAGGTTCGATTTAAAAAATT
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCT--CAAAACAGGTTCGATTT-AAAAATT
* * *
5391247 GAAATTCCTAGACTTGA-CTTAGGTTCGACCTATCTCACAACAGGTTCGATTTAAAAGTT
1 GAAATTCCTAGACTTGATC-TAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATT
* * * *
5391306 GAAACTT-CTAGACTTGATCTAGACTCGACTTATC-CGACAACATGTTCGATTTAAAAAAAATT
1 GAAA-TTCCTAGACTTGATCTAGGCTCGACCTATCTC-AAAACAGGTTCGATTT---AAAAATT
* * * ** * * *
5391368 GCAACTCCTAGACTTGATCTAGGCTTGACCTATCTCACGACAAGTTTGATTTAAAAGTT
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATT
* * * * *
5391427 GAAACTCCTAGACTTGATCTAGACTCGACCTGTC-CAACAACAAGTTTGATTTAAAAAATT
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAA-AACAGGTTCGATTT-AAAAATT
* * * * *
5391487 -ACAACTCCTAGACTTGATTTAGGCTCGACCTATCTTAAAACATGTTCGATTTTGAAAATT
1 GA-AATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGA-TTTAAAAATT
* * * * ** * *
5391547 GAAATTCCTAAACTTGATCTAGGTTCGACCTCTCTTAGGACGGGTTCGACTTAAAAATT
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATT
* * * * *
5391606 AAAATTTCTAGATTTGATCTAGGCTCGACCTATCTTAGAACAGGTTCGATTTAAAAATT
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATT
* * * * * * ** *
5391665 AAAATTCCTAAACTTGATTTAAGCTCGATCTATCTTAGGACAGGTTTGATTTTAAAAATT
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGA-TTTAAAAATT
* * * *
5391725 GAAATTCTTAGACTTGATTTAGGCTCGACCTATCTTAGAACAGGTTCGATTTAAAAATT
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATT
* * * * *
5391784 AAAATTCTTGGACTTGATTTAGGCTCGACCTATCTCAAAACAAGTTCGATTTAA
1 GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAA
5391838 TTCACCGATG
Statistics
Matches: 659, Mismatches: 91, Indels: 40
0.83 0.12 0.05
Matches are distributed among these distances:
58 53 0.08
59 338 0.51
60 159 0.24
61 23 0.03
62 85 0.13
63 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (59 bp):
GAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATT
Found at i:5391603 original size:119 final size:118
Alignment explanation
Indices: 5391010--5391837 Score: 858
Period size: 119 Copynumber: 6.9 Consensus size: 118
5391000 AAAAAAAGAG
* * * *
5391010 AAATTTCTAGACTTGATTTAGGCTCGACCTATCTCAAAATAGGTTCGACTCAAAAATTGAAATTC
1 AAATTCCTAGACTTGATTTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTC
* * * * *
5391075 CTA-ACTTGATCTAGGTTCAACCTATCTCACAATAGGTTCGA-TTGACAAATT
66 CTAGACTTGATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAATT
* * *
5391126 AAAATTCCTAGACTTGATCTAGGCTCGACCTATCTCAAAACAAGTTCGATTAAAAAATTGAAATT
1 -AAATTCCTAGACTTGATTTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATT
*
5391191 CCTAGACTTGACCTAGGCTCGACCTATCTCACAAAACAGGTTCGATTTAAAAAATT
65 CCTAGACTTGATCTAGGCTCGACCTATCTCAC--AACAGGTTCGATTTAAAAAATT
* * * *
5391247 GAAATTCCTAGACTTGACTTAGGTTCGACCTATCTCACAACAGGTTCGATTTAAAAGTTGAAACT
1 -AAATTCCTAGACTTGATTTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAA-T
* * *
5391312 T-CTAGACTTGATCTAGACTCGACTTATC-CGACAACATGTTCGATTTAAAAAAAATT
64 TCCTAGACTTGATCTAGGCTCGACCTATCTC-ACAACAGGTTCGATTT--AAAAAATT
* * * * ** * * * *
5391368 GCAACTCCTAGACTTGATCTAGGCTTGACCTATCTCACGACAAGTTTGATTTAAAAGTTGAAACT
1 -AAATTCCTAGACTTGATTTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATT
* * * *
5391433 CCTAGACTTGATCTAGACTCGACCTGTC-CAACAACAAGTTTGATTTAAAAAATT
65 CCTAGACTTGATCTAGGCTCGACCTATCTC-ACAACAGGTTCGATTTAAAAAATT
* * * *
5391487 ACAACTCCTAGACTTGATTTAGGCTCGACCTATCTTAAAACATGTTCGATTTTGAAAATTGAAAT
1 A-AATTCCTAGACTTGATTTAGGCTCGACCTATCTCAAAACAGGTTCGA-TTTAAAAATTGAAAT
* * * * ** * *
5391552 TCCTAAACTTGATCTAGGTTCGACCTCTCTTAGGACGGGTTCGACTT-AAAAATT
64 TCCTAGACTTGATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAATT
* * * * * *
5391606 AAAATTTCTAGATTTGATCTAGGCTCGACCTATCTTAGAACAGGTTCGATTTAAAAATTAAAATT
1 -AAATTCCTAGACTTGATTTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATT
* * * * * ** * *
5391671 CCTAAACTTGATTTAAGCTCGATCTATCTTAGGACAGGTTTGATTTTAAAAATT
65 CCTAGACTTGATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAATT
* * * *
5391725 GAAATTCTTAGACTTGATTTAGGCTCGACCTATCTTAGAACAGGTTCGATTTAAAAATTAAAATT
1 -AAATTCCTAGACTTGATTTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATT
* * * * *
5391790 CTTGGACTTGATTTAGGCTCGACCTATCTCAAAACAAGTTCGATTTAA
65 CCTAGACTTGATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAA
5391838 TTCACCGATG
Statistics
Matches: 604, Mismatches: 93, Indels: 26
0.84 0.13 0.04
Matches are distributed among these distances:
117 62 0.10
118 76 0.13
119 213 0.35
120 60 0.10
121 191 0.32
122 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (118 bp):
AAATTCCTAGACTTGATTTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTC
CTAGACTTGATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAATT
Found at i:5406763 original size:2 final size:2
Alignment explanation
Indices: 5406758--5406788 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5406748 GATTTTTTTA
5406758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5406789 ACCAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5407659 original size:26 final size:26
Alignment explanation
Indices: 5407615--5407666 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5407605 TAATTTTAAG
5407615 AATAATTTTACCATCAAAAGTAGATA
1 AATAATTTTACCATCAAAAGTAGATA
* * *
5407641 AATAATTTTATCATTAAAAGTGGATA
1 AATAATTTTACCATCAAAAGTAGATA
5407667 GATATCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.35
Consensus pattern (26 bp):
AATAATTTTACCATCAAAAGTAGATA
Found at i:5422850 original size:15 final size:15
Alignment explanation
Indices: 5422830--5422865 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
5422820 ATTTCTTTGA
5422830 TAATAATTAT-ATTTT
1 TAATAATT-TCATTTT
5422845 TAATAATTTCATTTT
1 TAATAATTTCATTTT
5422860 TAATAA
1 TAATAA
5422866 AATATCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 1 0.05
15 19 0.95
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATAATTTCATTTT
Found at i:5422990 original size:22 final size:23
Alignment explanation
Indices: 5422965--5423012 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
5422955 TCGATTATCG
5422965 AACTGAATCC-AATTTG-TGAATT
1 AACT-AATCCAAATTTGCTGAATT
*
5422987 AACTTATCCAAATTTGCTTGAATT
1 AACTAATCCAAATTTGC-TGAATT
5423011 AA
1 AA
5423013 TTGCAGTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.18
22 10 0.45
24 8 0.36
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (23 bp):
AACTAATCCAAATTTGCTGAATT
Found at i:5425101 original size:25 final size:23
Alignment explanation
Indices: 5425068--5425114 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 23
5425058 ATTAAATCAT
5425068 CAATTATTAATATTTTAAATAATAC
1 CAATTATTAATA-TTTAAA-AATAC
5425093 CAATTATTAATATTTAAAAATA
1 CAATTATTAATATTTAAAAATA
5425115 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.18
24 6 0.27
25 12 0.55
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (23 bp):
CAATTATTAATATTTAAAAATAC
Found at i:5425178 original size:104 final size:103
Alignment explanation
Indices: 5424933--5425294 Score: 374
Period size: 104 Copynumber: 3.3 Consensus size: 103
5424923 TCCAACTTTT
** * **
5424933 AATAAAATATTAATATTTAAATATCAATTATTAATA-AATAAATTATA-AATTATTCCTATTTAA
1 AATAAAATATTAATATTTAAATATCAATTATTAATATTTTAAATAATACAATTATTAATATTT--
*
5424996 AACAAAATAAATTAAAAATAAATAAACATAAT-ATCATTTAAATTA
64 -A-AAAATAAAATAAAAATAAAT---CATAATAAT-ATTTAAATTA
* *
5425041 TATAAACAATATTAATAATTAAATCATCAATTATTAATATTTTAAATAATACCAATTATTAATAT
1 AAT-AA-AATATTAATATTTAAAT-ATCAATTATTAATATTTTAAATAATA-CAATTATTAATAT
5425106 TTAAAAATAAAATAAAAATAAATCATAATAATA-TTAAATTA
62 TTAAAAATAAAATAAAAATAAATCATAATAATATTTAAATTA
*
5425147 AATAAAATATTAATATTTAAACTATCAATTATTAATATTTTAAATATATTAATCAATTATTAATT
1 AATAAAATATTAATATTTAAA-TATCAATTATTAATATTTTAAATA-A-T-A-CAATTATTAATA
*
5425212 TTTAAAAATAAAATAAAATAAAAATTGATCATAATAATATTTAAATTA
61 TTTAAAAATAAAAT-AAA-AATAA---ATCATAATAATATTTAAATTA
*
5425260 AATTAAAATATTAATATTTTAAATAT-AATAATTAA
1 AA-TAAAATATTAATA-TTTAAATATCAATTATTAA
5425295 ATATAAATAA
Statistics
Matches: 221, Mismatches: 14, Indels: 33
0.82 0.05 0.12
Matches are distributed among these distances:
104 38 0.17
105 4 0.02
106 11 0.05
107 33 0.15
108 7 0.03
109 6 0.03
110 35 0.16
111 15 0.07
112 20 0.09
113 18 0.08
114 28 0.13
115 6 0.03
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.39
Consensus pattern (103 bp):
AATAAAATATTAATATTTAAATATCAATTATTAATATTTTAAATAATACAATTATTAATATTTAA
AAATAAAATAAAAATAAATCATAATAATATTTAAATTA
Found at i:5425255 original size:39 final size:38
Alignment explanation
Indices: 5425207--5425396 Score: 102
Period size: 39 Copynumber: 4.7 Consensus size: 38
5425197 AATCAATTAT
*
5425207 TAATTTTTAAAAATAAAATAAAATAAAAATTGATCATAA
1 TAATATTTAAAAATAAAATAAAATAAAAATT-ATCATAA
* * * * *
5425246 TAATATTT-AAATTAAATTAAAATATTAATATT-TTAAATA
1 TAATATTTAAAAATAAAATAAAATA--AAAATTATCATA-A
* * *
5425285 TAATAATTAAATAT-AAATAAAATATTAATATTTAATTATCAATTAT
1 TAATATTTAAAAATAAAAT-AAA-A-TAA-A---AATTATC-A-TAA
5425331 TAATATTTTTAAAAAATAAAATAAAATAAAAATTACTCATAA
1 TAATA--TTT-AAAAATAAAATAAAATAAAAATTA-TCATAA
*
5425373 TAATATTT--AAATTAAATAAAATAA
1 TAATATTTAAAAATAAAATAAAATAA
5425397 TTTTTTAAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 40
0.66 0.10 0.23
Matches are distributed among these distances:
37 15 0.13
38 17 0.15
39 18 0.16
40 15 0.13
41 2 0.02
42 9 0.08
43 6 0.05
44 5 0.04
45 1 0.01
46 7 0.06
47 4 0.04
48 3 0.03
49 8 0.07
50 4 0.04
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (38 bp):
TAATATTTAAAAATAAAATAAAATAAAAATTATCATAA
Found at i:5425283 original size:21 final size:19
Alignment explanation
Indices: 5425257--5425338 Score: 76
Period size: 21 Copynumber: 4.1 Consensus size: 19
5425247 AATATTTAAA
5425257 TTAAATTAAAATATTAATATT
1 TTAAA-TAAAATATTAATA-T
*
5425278 TTAAATATAATAATTAA-AT
1 TTAAATAAAAT-ATTAATAT
*
5425297 ATAAATAAAATATTAATAT
1 TTAAATAAAATATTAATAT
* *
5425316 TTAATTATCAATTATTAATAT
1 TTAA--ATAAAATATTAATAT
5425337 TT
1 TT
5425339 TTAAAAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
18 5 0.10
19 15 0.29
20 6 0.12
21 25 0.49
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATAAAATATTAATAT
Found at i:5433743 original size:15 final size:15
Alignment explanation
Indices: 5433725--5433762 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
5433715 ATTTGTTAAA
*
5433725 AATAAATTTAAAAGT
1 AATAAATTTAAAAAT
*
5433740 AAT-ATTTTAAAAAT
1 AATAAATTTAAAAAT
5433754 AATAAATTT
1 AATAAATTT
5433763 TAATAAGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AATAAATTTAAAAAT
Found at i:5433750 original size:14 final size:14
Alignment explanation
Indices: 5433720--5433757 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5433710 ACTTAATTTG
5433720 TTAAAAATAA-A-T
1 TTAAAAATAATATT
*
5433732 TTAAAAGTAATATT
1 TTAAAAATAATATT
5433746 TTAAAAATAATA
1 TTAAAAATAATA
5433758 AATTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 9 0.41
13 1 0.05
14 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
TTAAAAATAATATT
Found at i:5441695 original size:2 final size:2
Alignment explanation
Indices: 5441682--5441714 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5441672 TTCATATCTT
*
5441682 TA TA TA TT 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 T
5441715 TTGATTAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5443428 original size:36 final size:35
Alignment explanation
Indices: 5443384--5443451 Score: 118
Period size: 36 Copynumber: 1.9 Consensus size: 35
5443374 TTAAACTTAT
5443384 AATATTAAATATAAAAATATAATGCATAAAATATA
1 AATATTAAATATAAAAATATAATGCATAAAATATA
*
5443419 AATAGTTAAATATAAAACTATAATGCATAAAAT
1 AATA-TTAAATATAAAAATATAATGCATAAAAT
5443452 TTAGATTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.13
36 27 0.87
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (35 bp):
AATATTAAATATAAAAATATAATGCATAAAATATA
Found at i:5443492 original size:16 final size:17
Alignment explanation
Indices: 5443451--5443492 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
5443441 ATGCATAAAA
5443451 TTTAGAT-TTTGATTCT
1 TTTAGATATTTGATTCT
*
5443467 TTTAGA-ATTTGA-TGT
1 TTTAGATATTTGATTCT
5443482 TTTAGATATTT
1 TTTAGATATTT
5443493 TTATTGAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (17 bp):
TTTAGATATTTGATTCT
Found at i:5445052 original size:28 final size:29
Alignment explanation
Indices: 5445011--5445070 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
5445001 GTCTATGGGC
*
5445011 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
5445039 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
5445069 AA
1 AA
5445071 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:5467031 original size:21 final size:21
Alignment explanation
Indices: 5466990--5467033 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5466980 AATAAAACAA
* *
5466990 AATAAATATATAATAGTAATG
1 AATAAATAAATAATAGGAATG
5467011 AATAAATAAAATAAT-GGAATG
1 AATAAAT-AAATAATAGGAATG
5467032 AA
1 AA
5467034 GGAAGAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.27
Consensus pattern (21 bp):
AATAAATAAATAATAGGAATG
Found at i:5467433 original size:35 final size:35
Alignment explanation
Indices: 5467393--5467479 Score: 120
Period size: 35 Copynumber: 2.5 Consensus size: 35
5467383 TTGCTGCTGA
*
5467393 TTTTGAGAGGGAGAAAGGAGGAAACTTGTTACTAG
1 TTTTGAGAGGGAGAAAGGAGGAAACTTGCTACTAG
* * *
5467428 TTTTGAGAGGGAGAAATGAGGGAACTTGCTGCTAG
1 TTTTGAGAGGGAGAAAGGAGGAAACTTGCTACTAG
* *
5467463 TTTTAAGAGGGAAAAAG
1 TTTTGAGAGGGAGAAAG
5467480 AGAGAGTCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.34, C:0.06, G:0.34, T:0.25
Consensus pattern (35 bp):
TTTTGAGAGGGAGAAAGGAGGAAACTTGCTACTAG
Found at i:5467491 original size:35 final size:35
Alignment explanation
Indices: 5467366--5467516 Score: 109
Period size: 35 Copynumber: 4.4 Consensus size: 35
5467356 TGCTGGTTGT
* *
5467366 GAGGGAAAAA-A-AAAGTCTTGCTGCT-GATTTTGA
1 GAGGGAAAAAGAGAGAGACTTGCTGCTAG-TTTTGA
* * * *
5467399 GAGGGAGAAAG-GAGGAAACTTGTTACTAGTTTTGA
1 GAGGGAAAAAGAGA-GAGACTTGCTGCTAGTTTTGA
* * *
5467434 GAGGGAGAAATGAGGGA-ACTTGCTGCTAGTTTTAA
1 GAGGGA-AAAAGAGAGAGACTTGCTGCTAGTTTTGA
* * *
5467469 GAGGGAAAAAGAGAGAGTCTTGCTACT-G-GTTGA
1 GAGGGAAAAAGAGAGAGACTTGCTGCTAGTTTTGA
*
5467502 GAAGGAAAAAGAGAG
1 GAGGGAAAAAGAGAG
5467517 GCTTTGTGCT
Statistics
Matches: 92, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
33 26 0.28
34 10 0.11
35 49 0.53
36 6 0.07
37 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.34, T:0.23
Consensus pattern (35 bp):
GAGGGAAAAAGAGAGAGACTTGCTGCTAGTTTTGA
Found at i:5470932 original size:15 final size:15
Alignment explanation
Indices: 5470912--5470944 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5470902 GGGTATTAAA
5470912 TTAAATTCTGCACAC
1 TTAAATTCTGCACAC
5470927 TTAAATTCTGCACAC
1 TTAAATTCTGCACAC
5470942 TTA
1 TTA
5470945 GATAGTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (15 bp):
TTAAATTCTGCACAC
Found at i:5471817 original size:41 final size:41
Alignment explanation
Indices: 5471754--5471833 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
5471744 AAAATTTTCA
5471754 AAGTCCACTTCCCAAGCATAATCAAATTTCCAATATTTCTT
1 AAGTCCACTTCCCAAGCATAATCAAATTTCCAATATTTCTT
* * ** *
5471795 AAGTCCGCTTCTCAAGGGTAATCAAATTTCTAATATTTC
1 AAGTCCACTTCCCAAGCATAATCAAATTTCCAATATTTC
5471834 CAAAGTTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35
Consensus pattern (41 bp):
AAGTCCACTTCCCAAGCATAATCAAATTTCCAATATTTCTT
Found at i:5471859 original size:42 final size:41
Alignment explanation
Indices: 5471747--5471839 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 41
5471737 TTTCTAAAAA
* * * **
5471747 ATTTTCAAAGTCCACTTCCCAAGCATAATCAAATTTCCAAT
1 ATTTCCAAAGTCCGCTTCTCAAGGGTAATCAAATTTCCAAT
** *
5471788 ATTTCTTAAGTCCGCTTCTCAAGGGTAATCAAATTTCTAAT
1 ATTTCCAAAGTCCGCTTCTCAAGGGTAATCAAATTTCCAAT
5471829 ATTTCCAAAGT
1 ATTTCCAAAGT
5471840 TTCGCTTCCA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (41 bp):
ATTTCCAAAGTCCGCTTCTCAAGGGTAATCAAATTTCCAAT
Found at i:5476391 original size:22 final size:23
Alignment explanation
Indices: 5476329--5476391 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
5476319 ACTCATGTTC
* *
5476329 CCAATCATG-TAAGGTATATAAA
1 CCAAACATGTTAAGGCATATAAA
* * **
5476351 CGAAATATGTTAATACATAT-AA
1 CCAAACATGTTAAGGCATATAAA
5476373 CCAAACATGTTAAGGCATA
1 CCAAACATGTTAAGGCATA
5476392 CAAATGAAAT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (23 bp):
CCAAACATGTTAAGGCATATAAA
Found at i:5477561 original size:36 final size:36
Alignment explanation
Indices: 5477521--5477589 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
5477511 CATCAGCTCA
* * *
5477521 TGTGCACGCCTACATCGCACATAGTTGGAATCATCC
1 TGTGCACGCCCACACCGCACATAGCTGGAATCATCC
*
5477557 TGTGCACTCCCACACCGCACATAGCTGGAATCA
1 TGTGCACGCCCACACCGCACATAGCTGGAATCA
5477590 CACCACGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (36 bp):
TGTGCACGCCCACACCGCACATAGCTGGAATCATCC
Found at i:5478078 original size:2 final size:2
Alignment explanation
Indices: 5478073--5478117 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5478063 TAATCACACA
5478073 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
5478115 AT A
1 AT A
5478118 AACAACCTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5479887 original size:19 final size:19
Alignment explanation
Indices: 5479863--5479901 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5479853 TAGAGGAATT
*
5479863 AAGAGAAAAAATGAGTGAA
1 AAGAGAAAAAATGAGAGAA
* *
5479882 AAGAGAGAAATTGAGAGAA
1 AAGAGAAAAAATGAGAGAA
5479901 A
1 A
5479902 TTTTGTGTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (19 bp):
AAGAGAAAAAATGAGAGAA
Found at i:5481645 original size:2 final size:2
Alignment explanation
Indices: 5481638--5481671 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5481628 CTGGACATGT
5481638 AG AG AG AG 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 AG AG AG AG
5481672 TGTGTGAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5482341 original size:43 final size:43
Alignment explanation
Indices: 5482293--5482413 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
5482283 ATTATGTGAT
*
5482293 GATGATGACCCGACTTTGTGCGAGTAGGGAGTGCACATAAGCC
1 GATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATAAGCC
* * *
5482336 GATGATGACCCGGCTATGTGCGAGTAGGGAGTGCACATGAGCT
1 GATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATAAGCC
** *
5482379 GATGATG--TTGA-AATGTGCGAGTAGGGAGTGCACAT
1 GATGATGACCCGACTATGTGCGAGTAGGGAGTGCACAT
5482414 GGCAGTGAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 23 0.33
41 1 0.01
43 46 0.66
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.22
Consensus pattern (43 bp):
GATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATAAGCC
Found at i:5485416 original size:14 final size:14
Alignment explanation
Indices: 5485397--5485423 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5485387 ACTTTTACTT
5485397 AAAAGTTAAGTTAG
1 AAAAGTTAAGTTAG
5485411 AAAAGTTAAGTTA
1 AAAAGTTAAGTTA
5485424 AAGTTAAAGT
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:0.52, C:0.00, G:0.19, T:0.30
Consensus pattern (14 bp):
AAAAGTTAAGTTAG
Found at i:5486391 original size:2 final size:2
Alignment explanation
Indices: 5486384--5486411 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5486374 TTATGAAGAA
5486384 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
5486412 TCTTCAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5490378 original size:20 final size:20
Alignment explanation
Indices: 5490353--5490398 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
5490343 CTTCTAAACC
5490353 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
5490373 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
5490393 TCAAAT
1 TCAAAT
5490399 GGGGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:5492296 original size:19 final size:19
Alignment explanation
Indices: 5492259--5492342 Score: 147
Period size: 19 Copynumber: 4.6 Consensus size: 19
5492249 ATAACGAATG
5492259 AAAA-AATATTTTA--AAT
1 AAAATAATATTTTATTAAT
5492275 AAAATAATATTTTATTAAT
1 AAAATAATATTTTATTAAT
5492294 AAAATAATATTTTATTAAT
1 AAAATAATATTTTATTAAT
5492313 AAAATAATATTTTATTAAT
1 AAAATAATATTTTATTAAT
5492332 AAAATAATATT
1 AAAATAATATT
5492343 AAAAATTAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.06
17 9 0.14
19 52 0.80
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATAATATTTTATTAAT
Found at i:5497754 original size:24 final size:24
Alignment explanation
Indices: 5497726--5497772 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5497716 GAGTTTTTCA
*
5497726 ATTTCTTTTCCTTGTTTT-CTTCTC
1 ATTTCCTTT-CTTGTTTTACTTCTC
*
5497750 ATTTCCTTTCTTTTTTTACTTCT
1 ATTTCCTTTCTTGTTTTACTTCT
5497773 TTCTTGTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.06, C:0.23, G:0.02, T:0.68
Consensus pattern (24 bp):
ATTTCCTTTCTTGTTTTACTTCTC
Found at i:5501580 original size:40 final size:38
Alignment explanation
Indices: 5501492--5501596 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 38
5501482 ATAGTGCCCG
* *
5501492 TGTGCACGATGT-GGGGGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACGGAT
* * *
5501529 TGTGCATGATGTGGGGGGATGCACATGATAGCGC-CGGCT
1 TGTGCACGATGTGGGGGGATGTACATGAT-G-GCACGGAT
5501568 ATGTGCACGATGTGGGGGGATGTACATGA
1 -TGTGCACGATGTGGGGGGATGTACATGA
5501597 GCCGGGTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
37 11 0.19
38 14 0.25
39 4 0.07
40 28 0.49
ACGTcount: A:0.21, C:0.15, G:0.40, T:0.24
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACGGAT
Found at i:5512482 original size:38 final size:40
Alignment explanation
Indices: 5512421--5512519 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
5512411 CCGTGTGCAT
** * *
5512421 GATGTGGGAAGATGTACACGATGGC-ACTAAT-TGTGAAC
1 GATGTGGGGGGATGTACATGATGGCGACGAATATGTGAAC
* * ** *
5512459 GATGTGGGGGGATGCACATGATGGCGCCGGGTATGTGCAC
1 GATGTGGGGGGATGTACATGATGGCGACGAATATGTGAAC
5512499 GATGTGGGGGGATGTACATGA
1 GATGTGGGGGGATGTACATGA
5512520 GCCAGGTGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
38 21 0.43
39 2 0.04
40 26 0.53
ACGTcount: A:0.24, C:0.13, G:0.40, T:0.22
Consensus pattern (40 bp):
GATGTGGGGGGATGTACATGATGGCGACGAATATGTGAAC
Found at i:5525094 original size:41 final size:41
Alignment explanation
Indices: 5525031--5525110 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
5525021 AAAATTTTAG
5525031 AAGTCCACTTCTCAAGCATAATCAAATTTCCAATATTTCTT
1 AAGTCCACTTCTCAAGCATAATCAAATTTCCAATATTTCTT
**
5525072 AAGTCCACTTCTCAAGTGTAATCAAATTTCCAATATTTC
1 AAGTCCACTTCTCAAGCATAATCAAATTTCCAATATTTC
5525111 CAAAGTTTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (41 bp):
AAGTCCACTTCTCAAGCATAATCAAATTTCCAATATTTCTT
Found at i:5532181 original size:23 final size:23
Alignment explanation
Indices: 5532155--5532206 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
5532145 CGTGTAAGTT
* * *
5532155 ATATAAACCAAATATGTTAATAC
1 ATATAAACCAAACATGCTAAGAC
*
5532178 ATAT-AACCAAACATGCTAAGGC
1 ATATAAACCAAACATGCTAAGAC
5532200 ATATAAA
1 ATATAAA
5532207 TGAAATTCGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (23 bp):
ATATAAACCAAACATGCTAAGAC
Found at i:5532202 original size:22 final size:22
Alignment explanation
Indices: 5532177--5532297 Score: 75
Period size: 22 Copynumber: 5.5 Consensus size: 22
5532167 TATGTTAATA
5532177 CATATAACCAAACATGCTAAGG
1 CATATAACCAAACATGCTAAGG
** * *
5532199 CATATAAATGAAA-TTCGCTAAAG
1 CATAT-AACCAAACAT-GCTAAGG
** * *
5532222 TGTATAATCACACATGCTAAGG
1 CATATAACCAAACATGCTAAGG
* * *
5532244 CATATAATC-AATATGTTAAGG
1 CATATAACCAAACATGCTAAGG
* * *
5532265 CATATAAACCAAATATTCTAAAG
1 CATAT-AACCAAACATGCTAAGG
5532288 CATATAACCA
1 CATATAACCA
5532298 TTCATCTTAT
Statistics
Matches: 75, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
21 14 0.19
22 32 0.43
23 29 0.39
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (22 bp):
CATATAACCAAACATGCTAAGG
Found at i:5532265 original size:21 final size:22
Alignment explanation
Indices: 5532224--5532271 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
5532214 CGCTAAAGTG
5532224 TATAATCACACATGCTAAGGCA
1 TATAATCACACATGCTAAGGCA
* *
5532246 TATAATCA-ATATGTTAAGGCA
1 TATAATCACACATGCTAAGGCA
5532267 TATAA
1 TATAA
5532272 ACCAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (22 bp):
TATAATCACACATGCTAAGGCA
Found at i:5533228 original size:19 final size:19
Alignment explanation
Indices: 5533196--5533233 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5533186 AGAGGAATTG
*
5533196 AGAGAAGAAATGAGTGAAA
1 AGAGAAGAAATGAGAGAAA
5533215 AGAG-AGAAATTGAGAGAAA
1 AGAGAAGAAA-TGAGAGAAA
5533234 TTTCATGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.11
Consensus pattern (19 bp):
AGAGAAGAAATGAGAGAAA
Found at i:5539784 original size:17 final size:17
Alignment explanation
Indices: 5539762--5539796 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5539752 GGAGGTTTTC
5539762 CTCCCCCTAAGTGTGTG
1 CTCCCCCTAAGTGTGTG
*
5539779 CTCCCCCTTAGTGTGTG
1 CTCCCCCTAAGTGTGTG
5539796 C
1 C
5539797 ATAGTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.09, C:0.37, G:0.23, T:0.31
Consensus pattern (17 bp):
CTCCCCCTAAGTGTGTG
Found at i:5540878 original size:60 final size:61
Alignment explanation
Indices: 5540785--5540904 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 61
5540775 AGTTTTTCGC
* *** * * *
5540785 TGAATCTCGCTGCAGTGAAATTTTTACCTAG-AAACAGAAA-GTTTCTCCTTGCAGCGAGAT
1 TGAATCTCGCTGCAGCGAAATTGCAACCCAGAAAACA-AAATGTTTCTCCCTACAGCGAGAT
5540845 TGAATCTCGCTGCAGCGAAATTGCAACCCAGAAAACAAAATGTTTCTCCCTACAGCGAGA
1 TGAATCTCGCTGCAGCGAAATTGCAACCCAGAAAACAAAATGTTTCTCCCTACAGCGAGA
5540905 ATGTATTTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 29 0.57
61 22 0.43
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (61 bp):
TGAATCTCGCTGCAGCGAAATTGCAACCCAGAAAACAAAATGTTTCTCCCTACAGCGAGAT
Found at i:5543484 original size:37 final size:37
Alignment explanation
Indices: 5543432--5543505 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
5543422 CTTTAGCTGC
* * *
5543432 TTCTTTCTCTGTCTGCTCTTCTCTAACTATTTGATGG
1 TTCTTTCTCTATCTGCTATTCCCTAACTATTTGATGG
*
5543469 TTCTTTCTCTATCTGCTATTCCCTGACTATTTGATGG
1 TTCTTTCTCTATCTGCTATTCCCTAACTATTTGATGG
5543506 AAGACATCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.12, C:0.24, G:0.14, T:0.50
Consensus pattern (37 bp):
TTCTTTCTCTATCTGCTATTCCCTAACTATTTGATGG
Found at i:5555958 original size:15 final size:15
Alignment explanation
Indices: 5555940--5555968 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5555930 ATGGCTTGAT
5555940 TCAACCTTTCAATGA
1 TCAACCTTTCAATGA
5555955 TCAACCTTTCAATG
1 TCAACCTTTCAATG
5555969 TAATTCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (15 bp):
TCAACCTTTCAATGA
Found at i:5563910 original size:42 final size:42
Alignment explanation
Indices: 5563829--5563910 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
5563819 CACATGGTTG
* * * *
5563829 GGTCAGCATTGGCTTATGCACACTTCTACTCGTACATAGCTA
1 GGTCAGCATCGGCGTATGCACACTCCTACTCGCACATAGCTA
* * *
5563871 GGTCATCATCGGCGTATGCGCACTCCTACTCGCATATAGC
1 GGTCAGCATCGGCGTATGCACACTCCTACTCGCACATAGC
5563911 CGGGTCCACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (42 bp):
GGTCAGCATCGGCGTATGCACACTCCTACTCGCACATAGCTA
Found at i:5571442 original size:42 final size:42
Alignment explanation
Indices: 5571391--5571477 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
5571381 ACATGGTTGG
* *
5571391 GTCAGCATCGACTTATACGCACTCCTACTCGCACATAGCTGA
1 GTCAGCATCGACGTATACGCACTCCTACTCGCACATAGCCGA
* *
5571433 GTCATCATCGACGTATGCGCACTCCTACTCGCACATAGCCGA
1 GTCAGCATCGACGTATACGCACTCCTACTCGCACATAGCCGA
5571475 GTC
1 GTC
5571478 CACATCAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.23
Consensus pattern (42 bp):
GTCAGCATCGACGTATACGCACTCCTACTCGCACATAGCCGA
Found at i:5576488 original size:23 final size:22
Alignment explanation
Indices: 5576462--5576542 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 22
5576452 ACCAAACATG
*
5576462 CTAAGGCATATAAATCAAAATC
1 CTAAAGCATATAAATCAAAATC
** * *
5576484 ACTAAAGTGTAT-AATCACACATG
1 -CTAAAGCATATAAATCA-AAATC
* *
5576507 CTAAGGCATATAAACCAAATATC
1 CTAAAGCATATAAATCAAA-ATC
5576530 CTAAAGCATATAA
1 CTAAAGCATATAA
5576543 CCATTCATCT
Statistics
Matches: 43, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
22 14 0.33
23 29 0.67
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (22 bp):
CTAAAGCATATAAATCAAAATC
Found at i:5576542 original size:45 final size:45
Alignment explanation
Indices: 5576457--5576542 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
5576447 GCATAACCAA
* **
5576457 ACATGCTAAGGCATATAAATCAAAATCACTAAAGTGTATAATCAC
1 ACATGCTAAGGCATATAAACCAAAATCACTAAAGCATATAATCAC
5576502 ACATGCTAAGGCATATAAACCAAATATC-CTAAAGCATATAA
1 ACATGCTAAGGCATATAAACCAAA-ATCACTAAAGCATATAA
5576543 CCATTCATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 34 0.92
46 3 0.08
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (45 bp):
ACATGCTAAGGCATATAAACCAAAATCACTAAAGCATATAATCAC
Found at i:5577474 original size:19 final size:19
Alignment explanation
Indices: 5577442--5577479 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5577432 AGAGGAATTG
*
5577442 AGAGAAGAAATGAGTGAAA
1 AGAGAAGAAATGAGAGAAA
5577461 AGAG-AGAAATTGAGAGAAA
1 AGAGAAGAAA-TGAGAGAAA
5577480 TTTCATGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.11
Consensus pattern (19 bp):
AGAGAAGAAATGAGAGAAA
Found at i:5581598 original size:2 final size:2
Alignment explanation
Indices: 5581591--5581719 Score: 172
Period size: 2 Copynumber: 65.0 Consensus size: 2
5581581 CTATGAATAA
* * *
5581591 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AC AC 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
* *
5581633 AT AT AT AT AT AT AT AT AT NA- AT AA AT A- AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
* *
5581674 AT AT AT AT AT AT AT AT AC AC 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
5581716 AT AT
1 AT AT
5581720 TCTTCAACAA
Statistics
Matches: 114, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
1 2 0.02
2 111 0.97
3 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5583246 original size:21 final size:21
Alignment explanation
Indices: 5583196--5583257 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
5583186 TATAAATACT
* *
5583196 TTCTTTTCTTCTCATTTCCCT
1 TTCTTTTTTTCTCATTTCCCC
5583217 TTCCTTTTTTTCTCATTTCCCC
1 TT-CTTTTTTTCTCATTTCCCC
*
5583239 TTCTTTTTTCTCTCTTTTC
1 TTCTTTTTT-TCTCATTTC
5583258 TCACATTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.25
22 27 0.75
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (21 bp):
TTCTTTTTTTCTCATTTCCCC
Found at i:5583701 original size:23 final size:23
Alignment explanation
Indices: 5583656--5583701 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5583646 AAAAAAAGTG
* *
5583656 AAAAATTTATTTATAAATTATAA
1 AAAAATTTATATATAAATCATAA
* *
5583679 AAAAATTTATATCTTAATCATAA
1 AAAAATTTATATATAAATCATAA
5583702 TAATGTTTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAAATTTATATATAAATCATAA
Found at i:5584154 original size:25 final size:25
Alignment explanation
Indices: 5584122--5584216 Score: 92
Period size: 25 Copynumber: 3.8 Consensus size: 25
5584112 AATATTAGTC
5584122 TTTAAAATATTAATGA-TTAAATTAT
1 TTTAAAATATTAAT-ATTTAAATTAT
5584147 TTTAAAATATTAATATTTAAATTA-
1 TTTAAAATATTAATATTTAAATTAT
*
5584171 -TT-AATTATTAATAGTTT-AATTAAAT
1 TTTAAAATATTAATA-TTTAAATT--AT
* *
5584196 TATAAATTATTAATATTTAAA
1 TTTAAAATATTAATATTTAAA
5584217 AATAAAATAA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
22 14 0.23
23 5 0.08
24 2 0.03
25 22 0.37
26 4 0.07
27 13 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTAAAATATTAATATTTAAATTAT
Found at i:5584165 original size:15 final size:15
Alignment explanation
Indices: 5584109--5584175 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 15
5584099 AAATTATAAA
* *
5584109 TAAAATATTAGTCTT
1 TAAAATATTAATATT
5584124 TAAAATATTAATGA-T
1 TAAAATATTAAT-ATT
5584139 T--AA-ATT-AT-TT
1 TAAAATATTAATATT
5584149 TAAAATATTAATATT
1 TAAAATATTAATATT
*
5584164 TAAATTATTAAT
1 TAAAATATTAAT
5584176 TATTAATAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
10 2 0.05
11 2 0.05
12 5 0.12
13 5 0.12
14 2 0.05
15 26 0.62
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (15 bp):
TAAAATATTAATATT
Found at i:5584166 original size:40 final size:40
Alignment explanation
Indices: 5584062--5584194 Score: 126
Period size: 40 Copynumber: 3.2 Consensus size: 40
5584052 ATTTGGAAAT
* *
5584062 TAATTAAAATTATTAATATTTTAATCATAATAATATTAAATTA
1 TAATTAAAA-TATTAATA-TTTAA-AATATTAATATTAAATTA
* * *
5584105 TAAATAAAATATTAGTCTTTAAAATATTAATGATTAAATTA
1 TAATTAAAATATTAATATTTAAAATATTAAT-ATTAAATTA
* *
5584146 T-TTTAAAATATTAATATTTAAATTATTAATTATTAATAGTT-
1 TAATTAAAATATTAATATTTAAAATATTAA-TATTAA-A-TTA
5584187 TAATTAAA
1 TAATTAAA
5584195 TTATAAATTA
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
40 35 0.47
41 18 0.24
42 13 0.18
43 8 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (40 bp):
TAATTAAAATATTAATATTTAAAATATTAATATTAAATTA
Found at i:5584181 original size:15 final size:15
Alignment explanation
Indices: 5584123--5584209 Score: 53
Period size: 15 Copynumber: 5.9 Consensus size: 15
5584113 ATATTAGTCT
* *
5584123 TTAAAATATTAATGA
1 TTAAATTATTAATTA
5584138 TTAAATTATT--TTA
1 TTAAATTATTAATTA
5584151 --AAA-TATTAA-TA
1 TTAAATTATTAATTA
5584162 TTTAAATTATTAATTA
1 -TTAAATTATTAATTA
5584178 TTAATAGTTTAATTAAATTA
1 TTAA-A--TT-ATT-AATTA
5584198 -TAAATTATTAAT
1 TTAAATTATTAAT
5584210 ATTTAAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 25
0.68 0.02 0.29
Matches are distributed among these distances:
10 4 0.07
11 5 0.09
13 2 0.03
14 6 0.10
15 22 0.38
16 5 0.09
18 3 0.05
19 6 0.10
20 5 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TTAAATTATTAATTA
Found at i:5584197 original size:27 final size:26
Alignment explanation
Indices: 5584163--5584215 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
5584153 ATATTAATAT
*
5584163 TTAAATTATTAATTATTAATAGTTTAA
1 TTAAATTATAAATTATTAATA-TTTAA
5584190 TTAAATTATAAATTATTAATATTTAA
1 TTAAATTATAAATTATTAATATTTAA
5584216 AAATAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TTAAATTATAAATTATTAATATTTAA
Found at i:5584216 original size:15 final size:15
Alignment explanation
Indices: 5584147--5584216 Score: 63
Period size: 15 Copynumber: 4.4 Consensus size: 15
5584137 ATTAAATTAT
*
5584147 TTTAAAATATTAATA
1 TTTAAATTATTAATA
5584162 TTTAAATTATTAAT-
1 TTTAAATTATTAATA
5584176 TATTAATAGTTTAATTAA-A
1 T-TTAA-A--TT-ATTAATA
5584195 TTATAAATTATTAATA
1 TT-TAAATTATTAATA
5584211 TTTAAA
1 TTTAAA
5584217 AATAAAATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.02
15 26 0.57
16 6 0.13
18 4 0.09
19 9 0.20
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
TTTAAATTATTAATA
Found at i:5586618 original size:49 final size:49
Alignment explanation
Indices: 5586565--5586675 Score: 204
Period size: 49 Copynumber: 2.3 Consensus size: 49
5586555 GTGATAATAT
*
5586565 TGACCCGGCTATGTGCGAGTACGGAGTGCGCATAAGCCGATGATGATGA
1 TGACCCGGCTATGTGCGAGTACGGAGTGCACATAAGCCGATGATGATGA
*
5586614 TGACCCGGCTATGTGCGAGTAGGGAGTGCACATAAGCCGATGATGATGA
1 TGACCCGGCTATGTGCGAGTACGGAGTGCACATAAGCCGATGATGATGA
5586663 TGACCCGGCTATG
1 TGACCCGGCTATG
5586676 ACGATGAATG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (49 bp):
TGACCCGGCTATGTGCGAGTACGGAGTGCACATAAGCCGATGATGATGA
Found at i:5586951 original size:21 final size:21
Alignment explanation
Indices: 5586925--5586983 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
5586915 CAACCCTGTT
* *
5586925 TCTCGCTGCAGCGAGATTGAA
1 TCTCGCTGCAGCGAGAATAAA
* * *
5586946 TCTCGCTACAACGAAAATAAA
1 TCTCGCTGCAGCGAGAATAAA
*
5586967 TCTTGCTGCAGCGAGAA
1 TCTCGCTGCAGCGAGAA
5586984 ACTCTCAGGC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
TCTCGCTGCAGCGAGAATAAA
Found at i:5589002 original size:44 final size:44
Alignment explanation
Indices: 5588952--5589066 Score: 203
Period size: 44 Copynumber: 2.6 Consensus size: 44
5588942 GGTTTATGCC
* *
5588952 ATGTGCGGTGTGGGAGAGCACATGATGTTGATGATGATATTGTA
1 ATGTGCGGTGTGGGAGAGCACATGATGCTGATGATGATATTGAA
5588996 ATGTGCGGTGTGGGAGAGCACATGATGCTGATGATGATATTGAA
1 ATGTGCGGTGTGGGAGAGCACATGATGCTGATGATGATATTGAA
*
5589040 ATGTGCGGTGTGGGAGTGCACATGATG
1 ATGTGCGGTGTGGGAGAGCACATGATG
5589067 ACCTAGGTAT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (44 bp):
ATGTGCGGTGTGGGAGAGCACATGATGCTGATGATGATATTGAA
Found at i:5592596 original size:62 final size:62
Alignment explanation
Indices: 5592439--5592652 Score: 182
Period size: 62 Copynumber: 3.5 Consensus size: 62
5592429 ATACATAGCC
* * * * * * *
5592439 ATGAGTTGGGGTGGAATCCCACTCATAGCAATCCAAGATAGTGGAGATTTGTACCCTATCCACT
1 ATGAGTTGGGATGGACTACCACTCACAGAAATCCAAGATAG-GGGGA-TTGTACCCTATCTACT
* * * * * *
5592503 ATGAGTCGAGG-TAGACTACCAGT--TAGAAATCCAAGATAGGGGGATTGTACCCTATTTGCT
1 ATGAGTTG-GGATGGACTACCACTCACAGAAATCCAAGATAGGGGGATTGTACCCTATCTACT
* ** *
5592563 ATGAGTTGGGATGGACTACCACTCACAGAAATCCAATATAAAGGGATCGTACCCTATCTACT
1 ATGAGTTGGGATGGACTACCACTCACAGAAATCCAAGATAGGGGGATTGTACCCTATCTACT
* * ** *
5592625 TTAAGTTGAAAGGGACTACCACTCACAG
1 ATGAGTTGGGATGGACTACCACTCACAG
5592653 TTATCGAAGT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
59 2 0.02
60 30 0.25
61 4 0.03
62 68 0.56
64 15 0.12
65 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (62 bp):
ATGAGTTGGGATGGACTACCACTCACAGAAATCCAAGATAGGGGGATTGTACCCTATCTACT
Found at i:5595940 original size:15 final size:15
Alignment explanation
Indices: 5595915--5595947 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
5595905 AATAAAAAAC
5595915 AAAATAAGAGC-AGA
1 AAAATAAGAGCAAGA
5595929 AAAATCAAGAGCAAGA
1 AAAAT-AAGAGCAAGA
5595945 AAA
1 AAA
5595948 GTGTTGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.67, C:0.09, G:0.18, T:0.06
Consensus pattern (15 bp):
AAAATAAGAGCAAGA
Found at i:5601532 original size:46 final size:46
Alignment explanation
Indices: 5601465--5601552 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
5601455 AGGAAAATTC
5601465 TTAACTCTAACTATCTGAGAGATTCAAATTATTATTGATAGAAGTA
1 TTAACTCTAACTATCTGAGAGATTCAAATTATTATTGATAGAAGTA
*
5601511 TTAACTCTAACTGTCTGAGAGATTCAAATTATTATTGATAGA
1 TTAACTCTAACTATCTGAGAGATTCAAATTATTATTGATAGA
5601553 TGTACTTGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (46 bp):
TTAACTCTAACTATCTGAGAGATTCAAATTATTATTGATAGAAGTA
Found at i:5609094 original size:24 final size:25
Alignment explanation
Indices: 5609028--5609094 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 25
5609018 CATAGTTTTT
*
5609028 TTTTTAAATATTATCCAAAAATAATGC
1 TTTTTAAATA--ATCAAAAAATAATGC
5609055 TTTTTTTAAA-AA--AAAAAATAATGC
1 --TTTTTAAATAATCAAAAAATAATGC
5609079 -TTTTAAATAATCAAAA
1 TTTTTAAATAATCAAAA
5609095 CTTCATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
21 7 0.21
22 2 0.06
24 15 0.44
26 1 0.03
28 1 0.03
29 8 0.24
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (25 bp):
TTTTTAAATAATCAAAAAATAATGC
Found at i:5613885 original size:20 final size:21
Alignment explanation
Indices: 5613856--5613900 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
5613846 AAAATAAGAA
5613856 AAAAATTATAAATTAA-ATAAC
1 AAAAATTATAAATTAATAT-AC
*
5613877 AAAAA-TATATATTAATATAC
1 AAAAATTATAAATTAATATAC
5613897 AAAA
1 AAAA
5613901 TTTAATCTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATTATAAATTAATATAC
Found at i:5615482 original size:24 final size:24
Alignment explanation
Indices: 5615455--5615500 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5615445 TGTTAATTTC
*
5615455 TTGATTTTAG-GATTTCTTGTTTGT
1 TTGA-TTTAGAGATTTCTGGTTTGT
5615479 TTGATTTAGAGATTTCTGGTTT
1 TTGATTTAGAGATTTCTGGTTT
5615501 ATGGAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.15, C:0.04, G:0.22, T:0.59
Consensus pattern (24 bp):
TTGATTTAGAGATTTCTGGTTTGT
Found at i:5618049 original size:3 final size:3
Alignment explanation
Indices: 5618041--5618084 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
5618031 ATGATAAAAA
* *
5618041 ATT ATT ATT ATT ATT A-T ATT ATT ATT GTT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5618085 TAAATCGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5622429 original size:2 final size:2
Alignment explanation
Indices: 5622422--5622493 Score: 96
Period size: 2 Copynumber: 37.0 Consensus size: 2
5622412 TAGAAAAGAA
*
5622422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT -T GNT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
5622462 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5622494 TGAAATTAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
1 3 0.05
2 59 0.94
3 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5630104 original size:2 final size:2
Alignment explanation
Indices: 5630097--5630133 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5630087 TCTATTGCGC
5630097 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5630134 CATACATAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5635529 original size:15 final size:15
Alignment explanation
Indices: 5635509--5635538 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5635499 TTGATGAATA
5635509 ATAATAACTTTTGAT
1 ATAATAACTTTTGAT
5635524 ATAATAACTTTTGAT
1 ATAATAACTTTTGAT
5635539 CAAATCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
ATAATAACTTTTGAT
Found at i:5639008 original size:20 final size:20
Alignment explanation
Indices: 5638984--5639027 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
5638974 TATATAAATG
5638984 AAAAATATACATTT-CATATCT
1 AAAAATA-A-ATTTACATATCT
*
5639005 AAAAATAAATTTAGATATCT
1 AAAAATAAATTTACATATCT
5639025 AAA
1 AAA
5639028 TCATCCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 10 0.48
21 7 0.33
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAATAAATTTACATATCT
Found at i:5647995 original size:17 final size:17
Alignment explanation
Indices: 5647973--5648009 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5647963 AGCAAAATAT
5647973 GCACACACTAAGGGGGA
1 GCACACACTAAGGGGGA
* *
5647990 GCACACATTTAGGGGGA
1 GCACACACTAAGGGGGA
5648007 GCA
1 GCA
5648010 ATCCCCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.35, T:0.11
Consensus pattern (17 bp):
GCACACACTAAGGGGGA
Found at i:5658588 original size:14 final size:14
Alignment explanation
Indices: 5658571--5658600 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5658561 ATATTCTCTT
*
5658571 TTTTTTTCTTTTCA
1 TTTTTGTCTTTTCA
5658585 TTTTTGTCTTTTCA
1 TTTTTGTCTTTTCA
5658599 TT
1 TT
5658601 ATTCATCCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTGTCTTTTCA
Found at i:5658739 original size:26 final size:26
Alignment explanation
Indices: 5658689--5658739 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5658679 TTACAACATT
*
5658689 CATCCACTTCTGGTGGTAACATTATC
1 CATCCACTTCTGGTGGAAACATTATC
5658715 CATCCACTTCTGGTGGCAAAC-TTAT
1 CATCCACTTCTGGTGG-AAACATTAT
5658740 TCTTAGATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (26 bp):
CATCCACTTCTGGTGGAAACATTATC
Found at i:5660724 original size:15 final size:15
Alignment explanation
Indices: 5660701--5660732 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5660691 GGATGTGGGA
*
5660701 CAAATGTTGACATGG
1 CAAAGGTTGACATGG
5660716 CAAAGGTTGACATGG
1 CAAAGGTTGACATGG
5660731 CA
1 CA
5660733 TAAAGCTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (15 bp):
CAAAGGTTGACATGG
Found at i:5667682 original size:20 final size:19
Alignment explanation
Indices: 5667657--5667706 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
5667647 TTACTTTCGC
5667657 CATTTTTTTCAT-CTTTTTGT
1 CATTTTTTT-ATACTTTTT-T
5667677 CATTTTTTTATAGCTTTTTT
1 CATTTTTTTATA-CTTTTTT
5667697 CATTTTTTTA
1 CATTTTTTTA
5667707 CTTTTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.07
20 20 0.71
21 6 0.21
ACGTcount: A:0.14, C:0.12, G:0.04, T:0.70
Consensus pattern (19 bp):
CATTTTTTTATACTTTTTT
Found at i:5667703 original size:9 final size:9
Alignment explanation
Indices: 5667657--5667715 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 9
5667647 TTACTTTCGC
5667657 CATTTTTTT
1 CATTTTTTT
5667666 CATCTTTTTGT
1 CAT-TTTTT-T
5667677 CATTTTTTT
1 CATTTTTTT
5667686 -ATAGCTTTTTT
1 CAT---TTTTTT
5667697 CATTTTTTT
1 CATTTTTTT
5667706 -ACTTTTTTT
1 CA-TTTTTTT
5667715 C
1 C
5667716 TTTGGCTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
8 3 0.07
9 17 0.40
10 10 0.24
11 10 0.24
12 2 0.05
ACGTcount: A:0.12, C:0.14, G:0.03, T:0.71
Consensus pattern (9 bp):
CATTTTTTT
Found at i:5668899 original size:129 final size:128
Alignment explanation
Indices: 5668657--5668899 Score: 305
Period size: 129 Copynumber: 1.9 Consensus size: 128
5668647 TGATTATCCG
* * * *
5668657 GTTTTTATTATTTAGATTTTTATTATATGTTTTTATAATGTTATTGCTTCTAAATAGAAACCAGA
1 GTTTTTATTATTTAGATTTTTATTATATATTTTTATAATGTTATTGCTTCCAAACAGAAACCAAA
*
5668722 AACCTTTGGTATATATAAGTTTCTAATTTCCGTTCTTCTTATCTCATTTTATTTGTTTATTCCA
66 AACCTTT-GTATAGATAAGTTTCTAATTTCCGTTCTTCTTATCTCATTTTATTTGTTTATTCCA
* * *
5668786 GTTTTTATTATTTAGATTCTTTATTACTTTTATTTTTATAATGTTATTG-TCTCCATACAGAAAT
1 GTTTTTATTATTTAGATT-TTTATTA--TATATTTTTATAATGTTATTGCT-TCCAAACAGAAAC
* * *
5668850 CAAAAACC-TT-T-TAGATAGGTTTCTAAATTTTCTTTCTTCTTATCTCATTT
62 CAAAAACCTTTGTATAGATAAGTTTCT-AATTTCCGTTCTTCTTATCTCATTT
5668900 AATTAAATGT
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
128 11 0.11
129 42 0.43
130 7 0.07
131 3 0.03
132 35 0.36
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.53
Consensus pattern (128 bp):
GTTTTTATTATTTAGATTTTTATTATATATTTTTATAATGTTATTGCTTCCAAACAGAAACCAAA
AACCTTTGTATAGATAAGTTTCTAATTTCCGTTCTTCTTATCTCATTTTATTTGTTTATTCCA
Found at i:5670974 original size:17 final size:17
Alignment explanation
Indices: 5670949--5670981 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
5670939 TTGCTGATTG
5670949 GTTTTGTTTG-TTATTT
1 GTTTTGTTTGATTATTT
5670965 GTTTTGGTTTGATTATT
1 GTTTT-GTTTGATTATT
5670982 CACTTGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.09, C:0.00, G:0.21, T:0.70
Consensus pattern (17 bp):
GTTTTGTTTGATTATTT
Found at i:5674440 original size:2 final size:2
Alignment explanation
Indices: 5674433--5674466 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5674423 ACACTTTTTA
*
5674433 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5674467 CAAATATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5677741 original size:18 final size:18
Alignment explanation
Indices: 5677706--5677743 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5677696 TCACGTGTCT
*
5677706 AATAAAAACTATTTTTTA
1 AATAAAAACTATATTTTA
5677724 AATAAAATACT-TATTTTA
1 AATAAAA-ACTATATTTTA
5677742 AA
1 AA
5677744 AATTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAAAAACTATATTTTA
Found at i:5679582 original size:31 final size:29
Alignment explanation
Indices: 5679512--5679582 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 29
5679502 TTAAAAAAAT
* *
5679512 TTAAATAA-TTTTTTATTTTTTTATTACA
1 TTAAATAAGTTTTGTATTTTTTTATTAAA
* *
5679540 TTCAATCAAGTTTATGTATTTTTTATTTTAAA
1 TTAAAT-AAGTTT-TGTATTTTTT-TATTAAA
5679572 TTAAATAAGTT
1 TTAAATAAGTT
5679583 CTTATAACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
28 5 0.15
29 2 0.06
30 3 0.09
31 14 0.41
32 10 0.29
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (29 bp):
TTAAATAAGTTTTGTATTTTTTTATTAAA
Found at i:5682375 original size:10 final size:10
Alignment explanation
Indices: 5682358--5682398 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
5682348 TGGACCATTC
5682358 CACTTTCTCT
1 CACTTTCTCT
*
5682368 CTCTTTCTTCTT
1 CACTTTC-TC-T
5682380 CACTTTCTCT
1 CACTTTCTCT
5682390 CACTTTCTC
1 CACTTTCTC
5682399 GAGGAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 16 0.59
11 4 0.15
12 7 0.26
ACGTcount: A:0.07, C:0.39, G:0.00, T:0.54
Consensus pattern (10 bp):
CACTTTCTCT
Found at i:5686579 original size:7 final size:7
Alignment explanation
Indices: 5686567--5686595 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5686557 TGATACTATG
5686567 ATCAGAT
1 ATCAGAT
5686574 ATCAGAT
1 ATCAGAT
5686581 ATCAGAT
1 ATCAGAT
5686588 ATCAGAT
1 ATCAGAT
5686595 A
1 A
5686596 AGAAGAGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (7 bp):
ATCAGAT
Found at i:5687360 original size:23 final size:23
Alignment explanation
Indices: 5687334--5687422 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
5687324 AAAGGTATGT
5687334 TGGGAATGTGTGACACGACATGG
1 TGGGAATGTGTGACACGACATGG
** *
5687357 TGGGAATGTGTGACACGGTAGGG
1 TGGGAATGTGTGACACGACATGG
** * * *
5687380 TTTAGAGTTTGTGACATGACATGG
1 -TGGGAATGTGTGACACGACATGG
*
5687404 TTGGAATGTGTGACACGAC
1 TGGGAATGTGTGACACGAC
5687423 TGTGACACGG
Statistics
Matches: 50, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
23 35 0.70
24 15 0.30
ACGTcount: A:0.25, C:0.11, G:0.37, T:0.27
Consensus pattern (23 bp):
TGGGAATGTGTGACACGACATGG
Found at i:5687455 original size:58 final size:58
Alignment explanation
Indices: 5687365--5687535 Score: 243
Period size: 58 Copynumber: 2.9 Consensus size: 58
5687355 GGTGGGAATG
* * *
5687365 TGTGACACGGTAGGGTTTAGAGTTTGTGACATGACATGGTTGGAATGTGTGACACGAC
1 TGTGACACGGTAAGGTTTAGAGTTTGTGACATGCCATGGTGGGAATGTGTGACACGAC
* * *
5687423 TGTGACACGGCAAGGTTTAGAGTTTGTAACATGCCATGGTGGGAATGTGTGACATGAC
1 TGTGACACGGTAAGGTTTAGAGTTTGTGACATGCCATGGTGGGAATGTGTGACACGAC
* * * * *
5687481 TGTGACACGTTAACGTTTAGAGTTTGTGACATGCCATGGAGGGAATCTGTAACAC
1 TGTGACACGGTAAGGTTTAGAGTTTGTGACATGCCATGGTGGGAATGTGTGACAC
5687536 TCCATTTCCC
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 99 1.00
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.29
Consensus pattern (58 bp):
TGTGACACGGTAAGGTTTAGAGTTTGTGACATGCCATGGTGGGAATGTGTGACACGAC
Found at i:5687786 original size:31 final size:31
Alignment explanation
Indices: 5687743--5687950 Score: 299
Period size: 31 Copynumber: 6.7 Consensus size: 31
5687733 TCAGCGTTGG
* *
5687743 CGTGATACAACATTTTAAGTTATATGCATGA
1 CGTGTTACAACATTTTACGTTATATGCATGA
*
5687774 CGTGTTACAACATTTTACGTTATATGCATGG
1 CGTGTTACAACATTTTACGTTATATGCATGA
* *
5687805 CGTGTTACCACATTTTACGTTATATGCATGG
1 CGTGTTACAACATTTTACGTTATATGCATGA
*
5687836 CGTGTTACCACATTTTACGTTATATGCATGA
1 CGTGTTACAACATTTTACGTTATATGCATGA
* * * *
5687867 CGTGTTATAATATTTTACATTATATGCATGG
1 CGTGTTACAACATTTTACGTTATATGCATGA
* * *
5687898 CATGTTCCCACATTTTACGTTATATGCATGA
1 CGTGTTACAACATTTTACGTTATATGCATGA
5687929 CGTGTTACAACATTTTACGTTA
1 CGTGTTACAACATTTTACGTTA
5687951 CAACATTTTA
Statistics
Matches: 157, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 157 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (31 bp):
CGTGTTACAACATTTTACGTTATATGCATGA
Found at i:5687909 original size:93 final size:93
Alignment explanation
Indices: 5687740--5687950 Score: 341
Period size: 93 Copynumber: 2.3 Consensus size: 93
5687730 GTGTCAGCGT
* *
5687740 TGGCGTGATACAACATTTTAAGTTATATGCATGACGTGTTACAACATTTTACGTTATATGCATGG
1 TGGCGTGTTACAACATTTTACGTTATATGCATGACGTGTTACAACATTTTACGTTATATGCATGG
5687805 CGTGTTACCACATTTTACGTTATATGCA
66 CGTGTTACCACATTTTACGTTATATGCA
* * * *
5687833 TGGCGTGTTACCACATTTTACGTTATATGCATGACGTGTTATAATATTTTACATTATATGCATGG
1 TGGCGTGTTACAACATTTTACGTTATATGCATGACGTGTTACAACATTTTACGTTATATGCATGG
* *
5687898 CATGTTCCCACATTTTACGTTATATGCA
66 CGTGTTACCACATTTTACGTTATATGCA
*
5687926 TGACGTGTTACAACATTTTACGTTA
1 TGGCGTGTTACAACATTTTACGTTA
5687951 CAACATTTTA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 108 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (93 bp):
TGGCGTGTTACAACATTTTACGTTATATGCATGACGTGTTACAACATTTTACGTTATATGCATGG
CGTGTTACCACATTTTACGTTATATGCA
Found at i:5687952 original size:15 final size:15
Alignment explanation
Indices: 5687932--5687960 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5687922 TGCATGACGT
5687932 GTTACAACATTTTAC
1 GTTACAACATTTTAC
5687947 GTTACAACATTTTA
1 GTTACAACATTTTA
5687961 TGGTATATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (15 bp):
GTTACAACATTTTAC
Found at i:5687959 original size:46 final size:46
Alignment explanation
Indices: 5687907--5687996 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
5687897 GCATGTTCCC
*
5687907 ACATTTTACGTTATATGCA-TGACGTGTTACAACATTTTACGTTACA
1 ACATTTTACGGTATATGCATTG-CGTGTTACAACATTTTACGTTACA
* *
5687953 ACATTTTATGGTATATGCATTGTGTGTTACAACATTTTACGTTA
1 ACATTTTACGGTATATGCATTGCGTGTTACAACATTTTACGTTA
5687997 TATGCATGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 38 0.95
47 2 0.05
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (46 bp):
ACATTTTACGGTATATGCATTGCGTGTTACAACATTTTACGTTACA
Found at i:5687985 original size:31 final size:31
Alignment explanation
Indices: 5687947--5688112 Score: 242
Period size: 31 Copynumber: 5.4 Consensus size: 31
5687937 AACATTTTAC
* * * *
5687947 GTTACAACATTTTATGGTATATGCATTGTGT
1 GTTACAACATTTTACGTTATATGCATGGCGT
*
5687978 GTTACAACATTTTACGTTATATGCATGACGT
1 GTTACAACATTTTACGTTATATGCATGGCGT
* *
5688009 GTTACCACATATTACGTTATATGCATGGCGT
1 GTTACAACATTTTACGTTATATGCATGGCGT
*
5688040 GTTACAACAATTTACGTTATATGCATGGCGT
1 GTTACAACATTTTACGTTATATGCATGGCGT
*
5688071 GTTACCACATTTTACGTTATATGCATGGCGT
1 GTTACAACATTTTACGTTATATGCATGGCGT
*
5688102 GTTACCACATT
1 GTTACAACATT
5688113 ATGGGTTAAC
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 122 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (31 bp):
GTTACAACATTTTACGTTATATGCATGGCGT
Found at i:5687997 original size:139 final size:139
Alignment explanation
Indices: 5687808--5688089 Score: 411
Period size: 139 Copynumber: 2.0 Consensus size: 139
5687798 TGCATGGCGT
* * *
5687808 GTTACCACATTTTACGTTATATGCATGGCGTGTTACCACATTTTACGTTATATGCATGACGTGTT
1 GTTACAACATTTTACGGTATATGCATGGCGTGTTACAACATTTTACGTTATATGCATGACGTGTT
* * * * * *
5687873 ATAATATTTTACATTATATGCATGGCATGTTCCCACATTTTACGTTATATGCATGACGTGTTACA
66 ACAACATATTACATTATATGCATGGCATGTTACAACAATTTACGTTATATGCATGACGTGTTACA
5687938 ACATTTTAC
131 ACATTTTAC
* * *
5687947 GTTACAACATTTTATGGTATATGCATTGTGTGTTACAACATTTTACGTTATATGCATGACGTGTT
1 GTTACAACATTTTACGGTATATGCATGGCGTGTTACAACATTTTACGTTATATGCATGACGTGTT
* * * * *
5688012 ACCACATATTACGTTATATGCATGGCGTGTTACAACAATTTACGTTATATGCATGGCGTGTTACC
66 ACAACATATTACATTATATGCATGGCATGTTACAACAATTTACGTTATATGCATGACGTGTTACA
5688077 ACATTTTAC
131 ACATTTTAC
5688086 GTTA
1 GTTA
5688090 TATGCATGGC
Statistics
Matches: 126, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
139 126 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (139 bp):
GTTACAACATTTTACGGTATATGCATGGCGTGTTACAACATTTTACGTTATATGCATGACGTGTT
ACAACATATTACATTATATGCATGGCATGTTACAACAATTTACGTTATATGCATGACGTGTTACA
ACATTTTAC
Found at i:5688028 original size:108 final size:108
Alignment explanation
Indices: 5687839--5688058 Score: 307
Period size: 108 Copynumber: 2.0 Consensus size: 108
5687829 TGCATGGCGT
* * * * *
5687839 GTTACCACATTTTACGTTATATGCATGACGTGTTATAATATTTTACATTATATGCATGGCATGTT
1 GTTACAACATTTTACGGTATATGCATGACGTGTTACAACATTTTACATTATATGCATGACATGTT
* * *
5687904 CCCACATTTTACGTTATATGCATGACGTGTTACAACATTTTAC
66 ACCACATATTACGTTATATGCATGACGTGTTACAACAATTTAC
* * * *
5687947 GTTACAACATTTTATGGTATATGCATTG-TGTGTTACAACATTTTACGTTATATGCATGACGTGT
1 GTTACAACATTTTACGGTATATGCA-TGACGTGTTACAACATTTTACATTATATGCATGACATGT
*
5688011 TACCACATATTACGTTATATGCATGGCGTGTTACAACAATTTAC
65 TACCACATATTACGTTATATGCATGACGTGTTACAACAATTTAC
5688055 GTTA
1 GTTA
5688059 TATGCATGGC
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
108 96 0.98
109 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (108 bp):
GTTACAACATTTTACGGTATATGCATGACGTGTTACAACATTTTACATTATATGCATGACATGTT
ACCACATATTACGTTATATGCATGACGTGTTACAACAATTTAC
Found at i:5688062 original size:170 final size:170
Alignment explanation
Indices: 5687777--5688112 Score: 528
Period size: 170 Copynumber: 2.0 Consensus size: 170
5687767 TGCATGACGT
* * *
5687777 GTTACAACATTTTACGTTATATGCATGGCGTGTTACCACATTTTACGTTATATGCATGGCGTGTT
1 GTTACAACATTTTACGGTATATGCATGGCGTGTTACAACATTTTACGTTATATGCATGACGTGTT
* * * * *
5687842 ACCACATTTTACGTTATATGCATGACGTGTTATAATATTTTACATTATATGCATGGCATGTTCCC
66 ACCACATATTACGTTATATGCATGACGTGTTACAACAATTTACATTATATGCATGGCATGTTACC
5687907 ACATTTTACGTTATATGCATGACGTGTTACAACATTTTAC
131 ACATTTTACGTTATATGCATGACGTGTTACAACATTTTAC
* * *
5687947 GTTACAACATTTTATGGTATATGCATTGTGTGTTACAACATTTTACGTTATATGCATGACGTGTT
1 GTTACAACATTTTACGGTATATGCATGGCGTGTTACAACATTTTACGTTATATGCATGACGTGTT
* * *
5688012 ACCACATATTACGTTATATGCATGGCGTGTTACAACAATTTACGTTATATGCATGGCGTGTTACC
66 ACCACATATTACGTTATATGCATGACGTGTTACAACAATTTACATTATATGCATGGCATGTTACC
* *
5688077 ACATTTTACGTTATATGCATGGCGTGTTACCACATT
131 ACATTTTACGTTATATGCATGACGTGTTACAACATT
5688113 ATGGGTTAAC
Statistics
Matches: 150, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
170 150 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (170 bp):
GTTACAACATTTTACGGTATATGCATGGCGTGTTACAACATTTTACGTTATATGCATGACGTGTT
ACCACATATTACGTTATATGCATGACGTGTTACAACAATTTACATTATATGCATGGCATGTTACC
ACATTTTACGTTATATGCATGACGTGTTACAACATTTTAC
Found at i:5689802 original size:145 final size:145
Alignment explanation
Indices: 5689509--5689855 Score: 412
Period size: 145 Copynumber: 2.4 Consensus size: 145
5689499 GAAGAGCCGA
* *
5689509 TAAGGACGATTCTAAAGGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATATCTGTG
1 TAAGGACGGTTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATATCTGTG
* * * *
5689574 TTTGCAGTTAGACCATGCAACGACAATTCCACAACCATCGATAGGTTCTCCTTAGACTCACAATG
66 TTTACAGTTAGACCATGCAACGACAACTCCACAACCATCGAGAGGTCCTCCTTAGACTCACAATG
**
5689639 CTAACGAGGAGTCAG
131 CTAACGACCAGTCAG
* *
5689654 TAAGGACGGTTATAACGGTTTGTGTTCAACAATTCCATATGTGATTATTGAATAACATATCTGTG
1 TAAGGACGGTTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATATCTGTG
* * * * * *
5689719 TTTACAGTTGGACCATGCAACGATAGCTCCTCAACCA-CTGAGAGGTCCTCCTTAGACGT-ATAG
66 TTTACAGTTAGACCATGCAACGACAACTCCACAACCATC-GAGAGGTCCTCCTTAGAC-TCACAA
* **
5689782 TGCTAACGACCTGTTGG
129 TGCTAACGACCAGTCAG
* * * * * * *
5689799 TAA-GATCGGTTCTAACAGTTTATGTTCAACATTTCCACATTTGTTTATCGAGTAACA
1 TAAGGA-CGGTTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACA
5689856 CATTAATTTT
Statistics
Matches: 171, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
144 3 0.02
145 167 0.98
146 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (145 bp):
TAAGGACGGTTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATATCTGTG
TTTACAGTTAGACCATGCAACGACAACTCCACAACCATCGAGAGGTCCTCCTTAGACTCACAATG
CTAACGACCAGTCAG
Found at i:5692032 original size:31 final size:29
Alignment explanation
Indices: 5691997--5692068 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 29
5691987 AAGAAGTCAA
*
5691997 CGTGTCACCACAGAAATCTGCATGCACTCAG
1 CGTGTCACCA-A-AAATCTGCATCCACTCAG
** *
5692028 CGTGTCAAGCCAACTATCTGCTTCCACTCAG
1 CGTGTC-A-CCAAAAATCTGCATCCACTCAG
5692059 CGTGTCACCA
1 CGTGTCACCA
5692069 TAAGATAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 3 0.09
30 1 0.03
31 26 0.74
32 2 0.06
33 3 0.09
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (29 bp):
CGTGTCACCAAAAATCTGCATCCACTCAG
Found at i:5692122 original size:118 final size:118
Alignment explanation
Indices: 5691907--5692500 Score: 834
Period size: 118 Copynumber: 5.0 Consensus size: 118
5691897 TTGGAACAAG
* * * *
5691907 TCAGCGTGTCACA-CCAAGTATCTGGTTCCACT-TAGGATGTCACCACAAG-TGGGGCGTGTCGT
1 TCAGCGTGTCA-AGCCAAGTATCTGCTTCCACTCAAAG-TGTCACCACAAGATGGGGCGTGCCGT
* * * *
5691969 GTCACCTCACAATACAGCAAGAAGTCAACGTGTCACCACAGAAATCTGCATGCAC
64 GTCACCCCACAATACTGCAAGAAGTCAGCGTGTCACCACAAAAATCTGCATGCAC
* ** * * * *
5692024 TCAGCGTGTCAAGCCAACTATCTGCTTCCACTCAGCGTGTCACCATAAGATAGGACGTGCTGTGT
1 TCAGCGTGTCAAGCCAAGTATCTGCTTCCACTCAAAGTGTCACCACAAGATGGGGCGTGCCGTGT
*
5692089 CACCCCATAATACTGCAAGAAGTCAGCGTGTCACCACAAAAATCTGCATGCAC
66 CACCCCACAATACTGCAAGAAGTCAGCGTGTCACCACAAAAATCTGCATGCAC
* * * * *
5692142 TCAGCATGTCATGCCAAGTATCTACTTTCACTCAAAGTGTCACCACAAGATGAGGCGTGCCGTGT
1 TCAGCGTGTCAAGCCAAGTATCTGCTTCCACTCAAAGTGTCACCACAAGATGGGGCGTGCCGTGT
* *
5692207 CACCCCACAATACTGTAAGAAGTCAGTGTGTCACCACAAAAATCTGCATGCAC
66 CACCCCACAATACTGCAAGAAGTCAGCGTGTCACCACAAAAATCTGCATGCAC
* * *
5692260 TCAGCGTGTCACGCCAACTATCTGCTTCCACTCAACGTGTCACCACAAGATGGGGCGTGCCGTGT
1 TCAGCGTGTCAAGCCAAGTATCTGCTTCCACTCAAAGTGTCACCACAAGATGGGGCGTGCCGTGT
*
5692325 CACCCCACAATACTGCAAGAAGTCAGCGTGTCACCACAAAAATCTGCATGCAG
66 CACCCCACAATACTGCAAGAAGTCAGCGTGTCACCACAAAAATCTGCATGCAC
* *
5692378 TCAGCGTGTCAAGCCAAGTATCTACTTCCACTCAAAGTGTCACCATAAGATGGGGCGTGCCGTGT
1 TCAGCGTGTCAAGCCAAGTATCTGCTTCCACTCAAAGTGTCACCACAAGATGGGGCGTGCCGTGT
** * * * *
5692443 CACCCCATGATAATGCAAAAAGTCAGCGTATCACCACAGAAATCTGCATGCAC
66 CACCCCACAATACTGCAAGAAGTCAGCGTGTCACCACAAAAATCTGCATGCAC
5692496 TCAGC
1 TCAGC
5692501 ATGTTAGCTT
Statistics
Matches: 422, Mismatches: 52, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
116 1 0.00
117 39 0.09
118 382 0.91
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (118 bp):
TCAGCGTGTCAAGCCAAGTATCTGCTTCCACTCAAAGTGTCACCACAAGATGGGGCGTGCCGTGT
CACCCCACAATACTGCAAGAAGTCAGCGTGTCACCACAAAAATCTGCATGCAC
Found at i:5692240 original size:56 final size:56
Alignment explanation
Indices: 5692178--5692363 Score: 153
Period size: 56 Copynumber: 3.2 Consensus size: 56
5692168 TTCACTCAAA
*
5692178 GTGTCACCACAAGATGAGGCGTGCCGTGTCACCCCACAATACTGTAAGAAGTCAGT
1 GTGTCACCACAAGATGAGGCGTGCCGTGTCACCCCACAATACTGTAAGAAGTCAGC
* * * * * *** * *
5692234 GTGTCACCACAAAAATCTGCATGCACT-CAGCGTGTCACGCCA-ACTATCTGCT-TCCACTCAAC
1 GTGTCACCAC-AAGA--TG-AGGC-GTGC--CGTGTCACCCCACAATA-CTG-TAAGAAGTCAGC
* *
5692296 GTGTCACCACAAGATGGGGCGTGCCGTGTCACCCCACAATACTGCAAGAAGTCAGC
1 GTGTCACCACAAGATGAGGCGTGCCGTGTCACCCCACAATACTGTAAGAAGTCAGC
5692352 GTGTCACCACAA
1 GTGTCACCACAA
5692364 AAATCTGCAT
Statistics
Matches: 95, Mismatches: 23, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
56 41 0.43
57 7 0.07
58 3 0.03
59 4 0.04
60 4 0.04
61 7 0.07
62 28 0.29
63 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (56 bp):
GTGTCACCACAAGATGAGGCGTGCCGTGTCACCCCACAATACTGTAAGAAGTCAGC
Found at i:5692269 original size:31 final size:31
Alignment explanation
Indices: 5692229--5692307 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
5692219 CTGTAAGAAG
* *
5692229 TCAGTGTGTCACCACAAAAATCTGCATGCAC
1 TCAGCGTGTCACCACAAAAATCTGCATCCAC
** *
5692260 TCAGCGTGTCACGC-CAACTATCTGCTTCCAC
1 TCAGCGTGTCAC-CACAAAAATCTGCATCCAC
*
5692291 TCAACGTGTCACCACAA
1 TCAGCGTGTCACCACAA
5692308 GATGGGGCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.03
31 38 0.95
32 1 0.03
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (31 bp):
TCAGCGTGTCACCACAAAAATCTGCATCCAC
Found at i:5692356 original size:31 final size:31
Alignment explanation
Indices: 5692320--5692388 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
5692310 TGGGGCGTGC
* *
5692320 CGTGTCACC-CCACAATACTGCAAGAAGTCAG
1 CGTGTCACCACAAAAAT-CTGCAAGAAGTCAG
* *
5692351 CGTGTCACCACAAAAATCTGCATGCAGTCAG
1 CGTGTCACCACAAAAATCTGCAAGAAGTCAG
5692382 CGTGTCA
1 CGTGTCA
5692389 AGCCAAGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (31 bp):
CGTGTCACCACAAAAATCTGCAAGAAGTCAG
Found at i:5699524 original size:31 final size:31
Alignment explanation
Indices: 5699292--5699513 Score: 318
Period size: 31 Copynumber: 7.2 Consensus size: 31
5699282 TTTGTCAGTC
*
5699292 ATGTTGTAACACGCCATGCATATAACATAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
5699323 ATGTTGTAACACGCCATGCATTTAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* * *
5699354 ATATTGTAACACGACATGCATATAACGTTAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
** *
5699385 ATGTTGTAACACATCATGCATATAACGTTAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
5699416 ATGTTGTAACACACCATGCAGATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
**
5699447 ATGTTGTAACACGCCATGGGTATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
5699478 ATTTTGTAACACGCCATGCATATAACATAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
5699509 ATGTT
1 ATGTT
5699514 ACAATACGCC
Statistics
Matches: 170, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 170 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (31 bp):
ATGTTGTAACACGCCATGCATATAACGTAAA
Found at i:5699904 original size:9 final size:9
Alignment explanation
Indices: 5699890--5699929 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
5699880 TGCTCAACAT
*
5699890 AGAGTTGAC
1 AGAGTTGAG
5699899 AGAGTTGAG
1 AGAGTTGAG
* *
5699908 ACAGTTCAG
1 AGAGTTGAG
5699917 AGAGTTGAG
1 AGAGTTGAG
5699926 AGAG
1 AGAG
5699930 AAAGATGAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.38, T:0.20
Consensus pattern (9 bp):
AGAGTTGAG
Found at i:5701036 original size:16 final size:17
Alignment explanation
Indices: 5701017--5701051 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5701007 TTTAAAAGTA
5701017 TTTAAAA-ATAAATATT
1 TTTAAAATATAAATATT
5701033 TTTAAAATTATAAATATT
1 TTTAAAA-TATAAATATT
5701051 T
1 T
5701052 ATTTGTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAAATATAAATATT
Found at i:5701176 original size:2 final size:2
Alignment explanation
Indices: 5701171--5701208 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5701161 TATATATATA
*
5701171 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5701209 AACAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5701303 original size:16 final size:17
Alignment explanation
Indices: 5701278--5701316 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5701268 TATATATCAT
*
5701278 ATAAACTAATA-AAACC
1 ATAAAATAATATAAACC
*
5701294 TTAAAATAATATAAACC
1 ATAAAATAATATAAACC
5701311 ATAAAA
1 ATAAAA
5701317 AAGGAATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAAAATAATATAAACC
Found at i:5702064 original size:2 final size:2
Alignment explanation
Indices: 5702057--5702104 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5702047 TCGATTAAAC
5702057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5702099 TA TA TA
1 TA TA TA
5702105 GCTATACAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5711198 original size:132 final size:133
Alignment explanation
Indices: 5711011--5711274 Score: 359
Period size: 132 Copynumber: 2.0 Consensus size: 133
5711001 TGCTTTCTTA
* * * *
5711011 ACCCATTCCCATCCGGCCATCCCATTGCTGATCGGCTTTCAGGCTTCAGTAGTTCGATTCGACCC
1 ACCCATTCCCATCCGGCCATCCCATAGCCGATCGGCTTTCAGACTTCAGCAGTTCGATTCGACCC
* ** * *
5711076 TTCCCCCTTCTGCCGTTCTTTCAGCCTATAAAGCAGTCAAGTTTTGCTTCCTCAACCCATACCCA
66 TTCCCCCTTCTACAATTCTTTCAGCCTACAAAGCAGTCAACTTTTGCTTCCTCAACCCATACCCA
5711141 TCC
131 TCC
* * * *
5711144 ACCCA-TCCCTTCTGGCCATCCCATAGCCGATCGGCTTTCAGACTTCAGCAGTTCGGTTCGGCCC
1 ACCCATTCCCATCCGGCCATCCCATAGCCGATCGGCTTTCAGACTTCAGCAGTTCGATTCGACCC
* * * * *
5711208 TTCCCCCTTCTACAATTCTTTCAGCCTACAGAGCAGTCGACTTTTTCTTTCTCAACCCATCCCCA
66 TTCCCCCTTCTACAATTCTTTCAGCCTACAAAGCAGTCAACTTTTGCTTCCTCAACCCATACCCA
5711273 TC
131 TC
5711275 TGGCCATCCC
Statistics
Matches: 113, Mismatches: 18, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
132 108 0.96
133 5 0.04
ACGTcount: A:0.18, C:0.38, G:0.14, T:0.30
Consensus pattern (133 bp):
ACCCATTCCCATCCGGCCATCCCATAGCCGATCGGCTTTCAGACTTCAGCAGTTCGATTCGACCC
TTCCCCCTTCTACAATTCTTTCAGCCTACAAAGCAGTCAACTTTTGCTTCCTCAACCCATACCCA
TCC
Found at i:5711296 original size:119 final size:120
Alignment explanation
Indices: 5711144--5711366 Score: 297
Period size: 119 Copynumber: 1.9 Consensus size: 120
5711134 ATACCCATCC
* * **
5711144 ACCCATCCCTTCTGGCCATCCCATAGCCGATCGGCTTTCAGACTTCAGCAGTTCGGTTC-G-GCC
1 ACCCATCCCATCTGGCCATCCCATAGCCGATCGGCTTTCAGACTTCAGCAATTCAATTCGGTGCC
* * *
5711207 CTTCCCCCTTCTACAATTCTTTCAGCCTACAGAGCAGTCGACTTTTTCTTTCTCA
66 CTTCCCCCTTCTACAATTCTTTCAACCTAAAAAGCAGTCGACTTTTTCTTTCTCA
* * * *
5711262 ACCCATCCCCATCTGGCCATCCCATCGCCTATCGGCTTTTAGACTTTAGCAATTCAATTCGGTGC
1 ACCCAT-CCCATCTGGCCATCCCATAGCCGATCGGCTTTCAGACTTCAGCAATTCAATTCGGTGC
* **
5711327 CCTTCCCCCTTCTGCTGTTCTTTCAACCTAAAAAGCAGTC
65 CCTTCCCCCTTCTACAATTCTTTCAACCTAAAAAGCAGTC
5711367 AAAAATTCTT
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
118 6 0.07
119 45 0.51
120 1 0.01
121 36 0.41
ACGTcount: A:0.18, C:0.36, G:0.14, T:0.31
Consensus pattern (120 bp):
ACCCATCCCATCTGGCCATCCCATAGCCGATCGGCTTTCAGACTTCAGCAATTCAATTCGGTGCC
CTTCCCCCTTCTACAATTCTTTCAACCTAAAAAGCAGTCGACTTTTTCTTTCTCA
Found at i:5717206 original size:25 final size:24
Alignment explanation
Indices: 5717166--5717220 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 24
5717156 ATATCTTTAA
5717166 ATTATTTAAAAA-TTTTAAAAAAT
1 ATTATTTAAAAATTTTTAAAAAAT
*
5717189 ATTATNTTAAAAAATTTTTAAAAATT
1 ATTAT-TT-AAAAATTTTTAAAAAAT
5717215 ATTATT
1 ATTATT
5717221 ATTTTATTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 5 0.18
24 2 0.07
25 6 0.21
26 15 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTATTTAAAAATTTTTAAAAAAT
Found at i:5717286 original size:17 final size:17
Alignment explanation
Indices: 5717256--5717290 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5717246 TATATTTTTA
5717256 TTTTAAATTAAATAATT
1 TTTTAAATTAAATAATT
5717273 TTTTATAATT-AATAATT
1 TTTTA-AATTAAATAATT
5717290 T
1 T
5717291 ACTATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAAATTAAATAATT
Found at i:5729023 original size:2 final size:2
Alignment explanation
Indices: 5729016--5729086 Score: 72
Period size: 2 Copynumber: 34.5 Consensus size: 2
5729006 TGCTTCACAA
* * * *
5729016 AT AT AT AT AT AT AT AT AT AT ACT A- ACT TT GT AA AT CAN AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT -AT AT AT
5729058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5729087 ATAAAAGAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
1 1 0.02
2 54 0.93
3 3 0.05
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5734533 original size:24 final size:24
Alignment explanation
Indices: 5734506--5734558 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5734496 TATCTGCATA
** *
5734506 TGCATCGCCTGCTGGATCTCCAAT
1 TGCATCGCCCACTGGATCTCCAAC
* *
5734530 TGCATTGCCCATTGGATCTCCAAC
1 TGCATCGCCCACTGGATCTCCAAC
5734554 TGCAT
1 TGCAT
5734559 TGCATGCATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30
Consensus pattern (24 bp):
TGCATCGCCCACTGGATCTCCAAC
Found at i:5736512 original size:27 final size:27
Alignment explanation
Indices: 5736482--5736546 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
5736472 CATACATATA
5736482 AATTTCATACAGTTATGACTTGCGTGC
1 AATTTCATACAGTTATGACTTGCGTGC
5736509 AATTTCATACAGTTATGACTTGCGTGC
1 AATTTCATACAGTTATGACTTGCGTGC
5736536 AATTTCATACA
1 AATTTCATACA
5736547 AAAACAGTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (27 bp):
AATTTCATACAGTTATGACTTGCGTGC
Found at i:5736803 original size:113 final size:113
Alignment explanation
Indices: 5736656--5736905 Score: 455
Period size: 113 Copynumber: 2.2 Consensus size: 113
5736646 ACCAGTCGCG
* *
5736656 CAATGTTAAACCCTAATGCAATCACGCACACCCTAACCCCATGCCAAAATCTAGTAATGCTGTCA
1 CAATGTTAAACCCTAATGCAATCACGCAAACCCTAACCCCATGCCAAAATCCAGTAATGCTGTCA
*
5736721 CGCAATGACCTACCAATATGTCACGCAATCACATATCAAACATTCACA
66 CGCAATGACCTACCAATATGTCACGCAATCACATATCAAACACTCACA
*
5736769 CAATGTTAAACCCTAATGCAATCACGTAAACCCTAACCCCATGCCAAAATCCAGTAATGCTGTCA
1 CAATGTTAAACCCTAATGCAATCACGCAAACCCTAACCCCATGCCAAAATCCAGTAATGCTGTCA
*
5736834 CGCAATGACCTACCAATATGTCACGCAATCACATATCAAACACTCACG
66 CGCAATGACCTACCAATATGTCACGCAATCACATATCAAACACTCACA
5736882 CAATGTTAAACCCTAATGCAATCA
1 CAATGTTAAACCCTAATGCAATCA
5736906 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 132 1.00
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (113 bp):
CAATGTTAAACCCTAATGCAATCACGCAAACCCTAACCCCATGCCAAAATCCAGTAATGCTGTCA
CGCAATGACCTACCAATATGTCACGCAATCACATATCAAACACTCACA
Found at i:5741189 original size:12 final size:12
Alignment explanation
Indices: 5741123--5741198 Score: 62
Period size: 12 Copynumber: 6.0 Consensus size: 12
5741113 TTTTATACAG
5741123 AATTAAATTAGTT
1 AATT-AATTAGTT
*
5741136 AATTTAAATTATTT
1 AA-TT-AATTAGTT
* *
5741150 TATAAATTAGTT
1 AATTAATTAGTT
**
5741162 AATTTAATTAACT
1 AA-TTAATTAGTT
5741175 AATTAATTAGTT
1 AATTAATTAGTT
*
5741187 AATCAATTAGTT
1 AATTAATTAGTT
5741199 TAAAATTATT
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
12 27 0.54
13 12 0.24
14 11 0.22
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (12 bp):
AATTAATTAGTT
Found at i:5745042 original size:34 final size:34
Alignment explanation
Indices: 5745004--5745071 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
5744994 ATTAAAACAA
*
5745004 ATTAAGAAG-AAAGAAGCCCACAAAATAAAGGAAG
1 ATTAA-AAGTAAAGAAGCCCAAAAAATAAAGGAAG
* *
5745038 ATTAAAAGTATAGAAGCCCAAAAAATAAGGGAAG
1 ATTAAAAGTAAAGAAGCCCAAAAAATAAAGGAAG
5745072 CTATGACCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 3 0.10
34 27 0.90
ACGTcount: A:0.57, C:0.10, G:0.21, T:0.12
Consensus pattern (34 bp):
ATTAAAAGTAAAGAAGCCCAAAAAATAAAGGAAG
Found at i:5751634 original size:91 final size:89
Alignment explanation
Indices: 5751524--5751825 Score: 233
Period size: 91 Copynumber: 3.3 Consensus size: 89
5751514 CCGTAAGAGA
5751524 ACCAGTCGCGCCACCAGATCTGTCGCCGGTTGGGGAGAGCCGACTTGACCCACGCCGCAAGGAAG
1 ACCA-TCGCGCCACCAGATCTGTCGCCGGTTGGGGAGAGCCGACTTGACCCACGCCGCAAGGAAG
5751589 AGTTCGCCGATACCAGAAGGAGCCCG
65 AGTTCGCCGA-ACCAGAAGGAGCCCG
* *** * ** * ** *
5751615 ACCATCGACGCCGCCAGATCTGTCGCC-GCAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCTAC
1 ACCATCG-CGCCACCAGATCTGTCGCCGGTTGGGGAGAGCCGA-CTTGAC--CCA-CGCCGC-A-
* ** * *** *
5751679 CGGTTGGGGAAGCCG-ACC-GTAAGAGAACCCG
59 AGGAAGAGTTCGCCGAACCAG-AAG-GAGCCCG
5751710 ----TCGCGCCACCAGATCTGTCGCCGGTTGGGGAGAGCCGACTTGACCCACGCCGCAAGGAAGA
1 ACCATCGCGCCACCAGATCTGTCGCCGGTTGGGGAGAGCCGACTTGACCCACGCCGCAAGGAAGA
*
5751771 GTTCGCCG-ACGCGAGAAGGGGCCCCG
66 GTTCGCCGAAC-C-AGAAGGAG-CCCG
5751797 ACCATCGACGCCACCAGATCTGTCGCCGG
1 ACCATCG-CGCCACCAGATCTGTCGCCGG
5751826 AAAGAAGAGT
Statistics
Matches: 153, Mismatches: 39, Indels: 37
0.67 0.17 0.16
Matches are distributed among these distances:
85 10 0.07
86 3 0.02
87 12 0.08
88 2 0.01
90 35 0.23
91 42 0.27
92 21 0.14
93 2 0.01
94 11 0.07
95 7 0.05
96 8 0.05
ACGTcount: A:0.23, C:0.34, G:0.33, T:0.11
Consensus pattern (89 bp):
ACCATCGCGCCACCAGATCTGTCGCCGGTTGGGGAGAGCCGACTTGACCCACGCCGCAAGGAAGA
GTTCGCCGAACCAGAAGGAGCCCG
Found at i:5751741 original size:181 final size:182
Alignment explanation
Indices: 5751432--5751834 Score: 693
Period size: 181 Copynumber: 2.2 Consensus size: 182
5751422 GGCCAGAGAA
5751432 GACCGATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCCA
1 GACC-ATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCCA
5751497 CCGGTTGGGGAGACCGACCGTAAGAGAACCAGTCGCGCCACCAGATCTGTCGCCGGTTGGGGAGA
65 CCGGTTGGGGAGACCGACCGTAAGAGAACCAGTCGCGCCACCAGATCTGTCGCCGGTTGGGGAGA
*
5751562 GCCGACTTGACCCACGCCGCAAGGAAGAGTTCGCCGATACCAGAAGGAG-CCC
130 GCCGACTTGACCCACGCCGCAAGGAAGAGTTCGCCGACACCAGAAGGAGCCCC
* *
5751614 GACCATCGACGCCGCCAGATCTGTCGCCGCAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCTAC
1 GACCATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCCAC
*
5751679 CGGTTGGGGA-AGCCGACCGTAAGAGAACCCGTCGCGCCACCAGATCTGTCGCCGGTTGGGGAGA
66 CGGTTGGGGAGA-CCGACCGTAAGAGAACCAGTCGCGCCACCAGATCTGTCGCCGGTTGGGGAGA
* * *
5751743 GCCGACTTGACCCACGCCGCAAGGAAGAGTTCGCCGACGCGAGAAGGGGCCCC
130 GCCGACTTGACCCACGCCGCAAGGAAGAGTTCGCCGACACCAGAAGGAGCCCC
* *
5751796 GACCATCGACGCCACCAGATCTGTCGCCGGAAAGAAGAG
1 GACCATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAG
5751835 TGTAGAGAGA
Statistics
Matches: 209, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
180 1 0.00
181 165 0.79
182 43 0.21
ACGTcount: A:0.24, C:0.32, G:0.34, T:0.10
Consensus pattern (182 bp):
GACCATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCCAC
CGGTTGGGGAGACCGACCGTAAGAGAACCAGTCGCGCCACCAGATCTGTCGCCGGTTGGGGAGAG
CCGACTTGACCCACGCCGCAAGGAAGAGTTCGCCGACACCAGAAGGAGCCCC
Done.