Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 163 of 310
Found at i:53326361 original size:19 final size:18
Alignment explanation
Indices: 53326321--53326364 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
53326311 GTATTGTTTT
53326321 TGTTGTTTATTTGGACTCA
1 TGTTGTTTATTTGGA-TCA
53326340 TGTTGTTTATTTAGG-TCGA
1 TGTTGTTTATTT-GGATC-A
53326359 TGTTGT
1 TGTTGT
53326365 GTTGCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.14, C:0.07, G:0.25, T:0.55
Consensus pattern (18 bp):
TGTTGTTTATTTGGATCA
Found at i:53327763 original size:27 final size:27
Alignment explanation
Indices: 53327721--53327896 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
53327711 AACACTCCAG
*
53327721 GAAAGGAATGCGTTTGTGGCAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* *
53327748 GAAAGGAATACCTTTGTGGCAATATCT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* *
53327775 -AAGAGAAATGCCTTTGTGGCAATTTAT
1 GAA-AGGAATGCCTTTGTGGCAATATAT
* *
53327802 GAAATGAATGCCCTTGTGGCAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
** * *
53327829 GAAAAAAATGCCTTTGTGACAATATAC
1 GAAAGGAATGCCTTTGTGGCAATATAT
* * * *
53327856 GAAAAG-ATGTCTTTGTGGTAGA-ATTT
1 GAAAGGAATGCCTTTGTGGCA-ATATAT
*
53327882 GGAAGGAATGCCTTT
1 GAAAGGAATGCCTTT
53327897 ACGACATACT
Statistics
Matches: 120, Mismatches: 25, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
26 19 0.16
27 99 0.82
28 2 0.02
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (27 bp):
GAAAGGAATGCCTTTGTGGCAATATAT
Found at i:53329997 original size:27 final size:29
Alignment explanation
Indices: 53329967--53330024 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
53329957 TATAGCCATG
*
53329967 AAGG-CTTCCTGT-ATAGAGAATGCCACA
1 AAGGTCTTCCTGTGACAGAGAATGCCACA
* * *
53329994 AAGGTTTTCCTTTGACAGAGATTGCCACA
1 AAGGTCTTCCTGTGACAGAGAATGCCACA
53330023 AA
1 AA
53330025 TGCATTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 4 0.16
28 6 0.24
29 15 0.60
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (29 bp):
AAGGTCTTCCTGTGACAGAGAATGCCACA
Found at i:53332882 original size:61 final size:61
Alignment explanation
Indices: 53332807--53332953 Score: 163
Period size: 61 Copynumber: 2.4 Consensus size: 61
53332797 TCCAGTCTAG
* * * *
53332807 AGTTTTTCTACAAAGGCGTTCCTTTAGATTCAGAACTCTCCACAAAGGCTTT-TGTGTCCAA
1 AGTTTTTCCACAAAGGCATTCCTTTACATTCAGAACTCCCCACAAAGGCTTTCT-TGTCCAA
* * * * * *
53332868 AGTTTTGCCACAAAGGCATTTCTTTACATTTAGTACTCCCCACAATGGCTTTCTTGTCCAG
1 AGTTTTTCCACAAAGGCATTCCTTTACATTCAGAACTCCCCACAAAGGCTTTCTTGTCCAA
* *
53332929 ATTTTTTCCACAAAGG-TTTCCTTTA
1 AGTTTTTCCACAAAGGCATTCCTTTA
53332954 ATTGGTGTTT
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
60 7 0.10
61 63 0.89
62 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (61 bp):
AGTTTTTCCACAAAGGCATTCCTTTACATTCAGAACTCCCCACAAAGGCTTTCTTGTCCAA
Found at i:53335258 original size:21 final size:22
Alignment explanation
Indices: 53335232--53335272 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53335222 TGCACCTCCT
* *
53335232 TTTTAATTTACAAA-TATCAAA
1 TTTTAAATTAAAAACTATCAAA
53335253 TTTTAAATTAAAAACTATCA
1 TTTTAAATTAAAAACTATCA
53335273 TGGTAGATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAATTAAAAACTATCAAA
Found at i:53335664 original size:37 final size:37
Alignment explanation
Indices: 53335609--53335684 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
53335599 CCTTGTATTA
*
53335609 ATTTACTAATTTTGAACTAACTTATAAAACAAATCAT
1 ATTTACTAATTTTAAACTAACTTATAAAACAAATCAT
53335646 ATTTACTAATTTTAAACTAACTTATAAAACAAATCAT
1 ATTTACTAATTTTAAACTAACTTATAAAACAAATCAT
53335683 AT
1 AT
53335685 ATCTAATATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.38
Consensus pattern (37 bp):
ATTTACTAATTTTAAACTAACTTATAAAACAAATCAT
Found at i:53342490 original size:19 final size:20
Alignment explanation
Indices: 53342442--53342490 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
53342432 ACATTTGCGT
53342442 ACTTGCGTTTACTTTGTAAAA
1 ACTTG-GTTTACTTTGTAAAA
53342463 ACATT-GTTT-CTTT-TAAAA
1 AC-TTGGTTTACTTTGTAAAA
53342481 ACTTGAGTTT
1 ACTTG-GTTT
53342491 TCCTATCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 2 0.08
18 7 0.28
19 8 0.32
20 4 0.16
21 2 0.08
22 2 0.08
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
ACTTGGTTTACTTTGTAAAA
Found at i:53346031 original size:27 final size:26
Alignment explanation
Indices: 53345981--53346054 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
53345971 ATACATCACG
* *
53345981 CAAGGGTAAAACAGTCATCTTACCATA
1 CAAGGGCAAAATAGTCAT-TTACCATA
*
53346008 TAAGTGG-AAAATAGTCATTATACCATA
1 CAAG-GGCAAAATAGTCATT-TACCATA
53346035 CAAGGGCAAAATAGTCATTT
1 CAAGGGCAAAATAGTCATTT
53346055 TATAGATTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.10
27 35 0.85
28 2 0.05
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (26 bp):
CAAGGGCAAAATAGTCATTTACCATA
Found at i:53355294 original size:24 final size:24
Alignment explanation
Indices: 53355250--53355295 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
53355240 AATTGATTGA
*
53355250 GATTGAATAATGATCATAAGTAAT
1 GATTGAATAATGATCAAAAGTAAT
*
53355274 GATTGAATATATGA-GAAAAGTA
1 GATTGAATA-ATGATCAAAAGTA
53355296 TGTTTAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (24 bp):
GATTGAATAATGATCAAAAGTAAT
Found at i:53358786 original size:37 final size:37
Alignment explanation
Indices: 53358741--53358816 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
53358731 CATATTAGAT
*
53358741 ATATGATTTGTTTTATAAGTTAGTTTAAAATTAGTAA
1 ATATGATTTGTTTTATAAGTTAGTTCAAAATTAGTAA
53358778 ATATGATTTGTTTTATAAGTTAGTTCAAAATTAGTAA
1 ATATGATTTGTTTTATAAGTTAGTTCAAAATTAGTAA
53358815 AT
1 AT
53358817 TAATACAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.47
Consensus pattern (37 bp):
ATATGATTTGTTTTATAAGTTAGTTCAAAATTAGTAA
Found at i:53359193 original size:21 final size:22
Alignment explanation
Indices: 53359153--53359193 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53359143 AGATCTACCA
* *
53359153 TGATAGTTTTTAATTTAAAATT
1 TGATAGTTTGTAAATTAAAATT
53359175 TGATA-TTTGTAAATTAAAA
1 TGATAGTTTGTAAATTAAAA
53359194 AGGAGGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (22 bp):
TGATAGTTTGTAAATTAAAATT
Found at i:53361578 original size:61 final size:61
Alignment explanation
Indices: 53361481--53361620 Score: 165
Period size: 61 Copynumber: 2.3 Consensus size: 61
53361471 TTAAAGGAAA
* * * *
53361481 CCTTTGTGGAAAAAATCTGGACAAGAAAGCCATTGTGGGGAGTACTAAATGTAAAGAAATG
1 CCTTTGTGGAAAAACTCTGGACAAGAAAGCCATTGTGGAGAGTACTAAATCTAAAGAAACG
* * * * * *
53361542 CCTTTGTGGCAAAACTTTGGACACA-AAAGCCTTTGTGGAGAGTTCTGAATCTAAAGGAACG
1 CCTTTGTGGAAAAACTCTGGACA-AGAAAGCCATTGTGGAGAGTACTAAATCTAAAGAAACG
*
53361603 CCTTTGTAGAAAAACTCT
1 CCTTTGTGGAAAAACTCT
53361621 AGACTGGAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 64 0.98
62 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.26
Consensus pattern (61 bp):
CCTTTGTGGAAAAACTCTGGACAAGAAAGCCATTGTGGAGAGTACTAAATCTAAAGAAACG
Found at i:53366603 original size:27 final size:27
Alignment explanation
Indices: 53366552--53366704 Score: 166
Period size: 27 Copynumber: 5.7 Consensus size: 27
53366542 CCAAATTCTA
* *
53366552 CCACAAAGACA-TCTTTTCGTATATTG
1 CCACAAAGGCATTCTTTTCATATATTG
* *
53366578 TCACAAAGGCATTTTTTTCATATATTG
1 CCACAAAGGCATTCTTTTCATATATTG
* * *
53366605 CCACAAGGGCATTCATTTCATAAATTG
1 CCACAAAGGCATTCTTTTCATATATTG
* *
53366632 CCACAAAGGCATTTCTCTT-AGATATTG
1 CCACAAAGGCA-TTCTTTTCATATATTG
* *
53366659 CCACAAAGGTATTCCTTTCATATATTG
1 CCACAAAGGCATTCTTTTCATATATTG
* *
53366686 CCACAAACGCATTCCTTTC
1 CCACAAAGGCATTCTTTTC
53366705 CTGGAGTGTT
Statistics
Matches: 104, Mismatches: 20, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
26 14 0.13
27 85 0.82
28 5 0.05
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.35
Consensus pattern (27 bp):
CCACAAAGGCATTCTTTTCATATATTG
Found at i:53368085 original size:19 final size:18
Alignment explanation
Indices: 53368061--53368104 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
53368051 TAAAAGCAAC
53368061 ACAACATCGA-CCTAAATAA
1 ACAACAT-GAGCC-AAATAA
53368080 ACAACATGAGTCCAAATAA
1 ACAACATGAG-CCAAATAA
53368099 ACAACA
1 ACAACA
53368105 AAAACAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.55, C:0.25, G:0.07, T:0.14
Consensus pattern (18 bp):
ACAACATGAGCCAAATAA
Found at i:53372328 original size:93 final size:93
Alignment explanation
Indices: 53372169--53372339 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
53372159 GGATGGTTGA
* * *
53372169 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCGTTGAGT
53372234 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
53372262 GCATCCAAACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAA-CTCGTTGAG
53372326 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
53372340 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 4 0.06
93 68 0.94
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53372342 original size:46 final size:45
Alignment explanation
Indices: 53372176--53372344 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 45
53372166 TGAGCATCCG
* * *
53372176 AACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCC
* * *
53372222 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC--CC
*
53372268 AAACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 -AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
53372314 AAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 AA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
53372345 GGGGCGGGTT
Statistics
Matches: 101, Mismatches: 11, Indels: 22
0.75 0.08 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 4 0.04
46 55 0.54
47 24 0.24
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
Found at i:53380493 original size:25 final size:25
Alignment explanation
Indices: 53380404--53380495 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
53380394 ATCCCGACCC
*** *
53380404 ATAGCTTGTGTGAGCAAGCCCATTT
1 ATAGCTTGTGTGAGCAATTACAATT
* *
53380429 CATTGCTTGTGTGAGCATTTACAATT
1 -ATAGCTTGTGTGAGCAATTACAATT
* * *
53380455 ATAGCTCGGGTGAGCAATTACAGTT
1 ATAGCTTGTGTGAGCAATTACAATT
*
53380480 ATAGCTTGTATGAGCA
1 ATAGCTTGTGTGAGCA
53380496 TTATTCTTGT
Statistics
Matches: 52, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
25 33 0.63
26 19 0.37
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (25 bp):
ATAGCTTGTGTGAGCAATTACAATT
Found at i:53380567 original size:13 final size:13
Alignment explanation
Indices: 53380551--53380610 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 13
53380541 GAAAAACGAA
53380551 TATATAAAATGAT
1 TATATAAAATGAT
* *
53380564 TATAT-GAATAGGT
1 TATATAAAAT-GAT
*
53380577 TATATGGAAAAATGAA
1 TATAT---AAAATGAT
53380593 TATATAAAATGAT
1 TATATAAAATGAT
53380606 TATAT
1 TATAT
53380611 GAATCGGTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
12 3 0.08
13 24 0.67
16 6 0.17
17 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (13 bp):
TATATAAAATGAT
Found at i:53380586 original size:42 final size:41
Alignment explanation
Indices: 53380539--53380667 Score: 163
Period size: 42 Copynumber: 3.1 Consensus size: 41
53380529 GTTCATTGGG
53380539 TGGAAAAACGAATATATAAAATGATTATATGAATAGGTTATA
1 TGGAAAAA-GAATATATAAAATGATTATATGAATAGGTTATA
*
53380581 TGGAAAAATGAATATATAAAATGATTATATGAATCGGTTATA
1 TGGAAAAA-GAATATATAAAATGATTATATGAATAGGTTATA
* * * * *
53380623 TGGACATA-AATATACAGAATAATTATATGAATCA-GTTATA
1 TGGAAAAAGAATATATAAAATGATTATATGAAT-AGGTTATA
53380663 TGGAA
1 TGGAA
53380668 GTAGTTATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 31 0.40
42 46 0.60
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (41 bp):
TGGAAAAAGAATATATAAAATGATTATATGAATAGGTTATA
Found at i:53380612 original size:21 final size:21
Alignment explanation
Indices: 53380548--53380614 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
53380538 GTGGAAAAAC
53380548 GAATATATAAAATGATTATAT
1 GAATATATAAAATGATTATAT
** * * * *
53380569 GAATAGGTTATATGGA-AAAAT
1 GAATATATAAAAT-GATTATAT
53380590 GAATATATAAAATGATTATAT
1 GAATATATAAAATGATTATAT
53380611 GAAT
1 GAAT
53380615 CGGTTATATG
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (21 bp):
GAATATATAAAATGATTATAT
Found at i:53380635 original size:40 final size:40
Alignment explanation
Indices: 53380549--53380667 Score: 157
Period size: 40 Copynumber: 2.9 Consensus size: 40
53380539 TGGAAAAACG
* *
53380549 AATATATAAAATGATTATATGAATAGGTTATATGGAAAAATG
1 AATATATAAAATGATTATATGAATCGGTTATATGG--AAATA
*
53380591 AATATATAAAATGATTATATGAATCGGTTATATGGACATA
1 AATATATAAAATGATTATATGAATCGGTTATATGGAAATA
* * * *
53380631 AATATACAGAATAATTATATGAATCAGTTATATGGAA
1 AATATATAAAATGATTATATGAATCGGTTATATGGAA
53380668 GTAGTTATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 35 0.51
42 34 0.49
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.34
Consensus pattern (40 bp):
AATATATAAAATGATTATATGAATCGGTTATATGGAAATA
Found at i:53380661 original size:13 final size:12
Alignment explanation
Indices: 53380639--53380681 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 12
53380629 TAAATATACA
*
53380639 GAATAATTATAT
1 GAATAGTTATAT
53380651 GAATCAGTTATAT
1 GAAT-AGTTATAT
53380664 GGAAGTAGTTATAT
1 -GAA-TAGTTATAT
53380678 GAAT
1 GAAT
53380682 TGTGTATACG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.19
13 10 0.37
14 11 0.41
15 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (12 bp):
GAATAGTTATAT
Found at i:53384053 original size:17 final size:17
Alignment explanation
Indices: 53384031--53384073 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
53384021 TGTTTATTTC
53384031 TTGTTTTTCA-ATTTATT
1 TTGTTTTT-AGATTTATT
*
53384048 TTGTTTTTAGTTTTTATT
1 TTGTTTTTAG-ATTTATT
53384066 TTGTTTTT
1 TTGTTTTT
53384074 GTTTAGCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 8 0.35
18 14 0.61
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.77
Consensus pattern (17 bp):
TTGTTTTTAGATTTATT
Found at i:53384063 original size:18 final size:17
Alignment explanation
Indices: 53384042--53384077 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
53384032 TGTTTTTCAA
53384042 TTTATTTTGTTTTTAGTT
1 TTTATTTTGTTTTT-GTT
53384060 TTTATTTTGTTTTTGTT
1 TTTATTTTGTTTTTGTT
53384077 T
1 T
53384078 AGCTTGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81
Consensus pattern (17 bp):
TTTATTTTGTTTTTGTT
Found at i:53386352 original size:40 final size:40
Alignment explanation
Indices: 53386315--53386539 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
53386305 GCTACTCGTT
* *
53386315 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
53386355 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
53386395 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
53386435 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
53386474 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
53386515 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
53386540 CATCATTCGA
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 115 0.71
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:53386499 original size:119 final size:120
Alignment explanation
Indices: 53386317--53386539 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
53386307 TACTCGTTCA
* *
53386317 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
53386382 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACC
* * **
53386437 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
53386499 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
53386540 CATCATTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 65 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACC
Found at i:53387740 original size:56 final size:56
Alignment explanation
Indices: 53387673--53387789 Score: 225
Period size: 56 Copynumber: 2.1 Consensus size: 56
53387663 TAGTTTATTT
53387673 CCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTG
1 CCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTG
*
53387729 CCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTTTTG
1 CCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTG
53387785 CCCAT
1 CCCAT
53387790 CATCCCTTGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (56 bp):
CCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTG
Found at i:53395564 original size:34 final size:33
Alignment explanation
Indices: 53395512--53395583 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
53395502 TGTTACTGTC
* *
53395512 ACTGAAATAGGCTAAGG-CCTACACTGATACTGA
1 ACTGTAATAGGCTAAGGCCCTA-ACTGAAACTGA
* *
53395545 TACTGTAATGGGCTTAGGCCCTAACTGAAACTGA
1 -ACTGTAATAGGCTAAGGCCCTAACTGAAACTGA
53395579 ACTGT
1 ACTGT
53395584 TACTGAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 5 0.15
34 24 0.73
35 4 0.12
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (33 bp):
ACTGTAATAGGCTAAGGCCCTAACTGAAACTGA
Found at i:53398797 original size:41 final size:40
Alignment explanation
Indices: 53398739--53398820 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 40
53398729 AGTACTATAG
53398739 ATAAGGTAGTATTAAGGCTACAAAACTGAGACTGTAGGGA
1 ATAAGGTAGTATTAAGGCTACAAAACTGAGACTGTAGGGA
53398779 ANTAAGGTAGTATTAAGGCTACAAAACTGAGACTGTAGGGA
1 A-TAAGGTAGTATTAAGGCTACAAAACTGAGACTGTAGGGA
53398820 A
1 A
53398821 AACTAAACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 1 0.02
41 40 0.98
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.22
Consensus pattern (40 bp):
ATAAGGTAGTATTAAGGCTACAAAACTGAGACTGTAGGGA
Found at i:53399149 original size:23 final size:23
Alignment explanation
Indices: 53399123--53399169 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
53399113 GACGATGCTC
*
53399123 TGTCTCAGGCCATGTTGAGAGTT
1 TGTCCCAGGCCATGTTGAGAGTT
53399146 TGTCCCAGGCCATGTTGAGAGTT
1 TGTCCCAGGCCATGTTGAGAGTT
53399169 T
1 T
53399170 TCGAAAGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (23 bp):
TGTCCCAGGCCATGTTGAGAGTT
Found at i:53404109 original size:39 final size:40
Alignment explanation
Indices: 53403997--53404173 Score: 245
Period size: 40 Copynumber: 4.5 Consensus size: 40
53403987 CGGATGATAA
* *
53403997 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTGAT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAT
53404037 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
53404077 CCGGGCTAGGTCCC-AAGGAATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53404116 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
53404156 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53404174 TACTTGGTTT
Statistics
Matches: 124, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
39 55 0.44
40 69 0.56
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53404129 original size:79 final size:80
Alignment explanation
Indices: 53403997--53404173 Score: 245
Period size: 79 Copynumber: 2.2 Consensus size: 80
53403987 CGGATGATAA
* * *
53403997 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTGATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGAATTTGTGCGAGTGACTGATACCGGGCTAAGTCCCGAAGGCATTTG
*
53404062 TGCGAGTTA-CTATAT
66 AGCGAG-TAGCTATAT
* *
53404077 CCGGGCTAGGTCCC-AAGGAATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGAATTTGTGCGAGTGACTGAT-ACCGGGCTAAGTCCCGAAGGCATTT
53404140 GAGCGAGTAGCTATAT
65 GAGCGAGTAGCTATAT
*
53404156 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53404174 TACTTGGTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
78 13 0.15
79 60 0.70
80 13 0.15
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGAATTTGTGCGAGTGACTGATACCGGGCTAAGTCCCGAAGGCATTTG
AGCGAGTAGCTATAT
Found at i:53418162 original size:39 final size:39
Alignment explanation
Indices: 53418045--53418174 Score: 170
Period size: 40 Copynumber: 3.3 Consensus size: 39
53418035 GGACTAAGAT
* * *
53418045 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGAGTTACTAAATCCGGGTTATGTC
* **
53418085 CCGAAGGCATTCGTGCGAATTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTATGTC
* *
53418125 CCGAAGGCATTGTGTGAGTTACTAAATCCGGGCTATGTC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
53418164 CCGAAGGCATT
1 CCGAAGGCATT
53418175 TGAACGAGGA
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 37 0.47
40 41 0.53
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
Found at i:53418194 original size:79 final size:79
Alignment explanation
Indices: 53418045--53418209 Score: 179
Period size: 79 Copynumber: 2.1 Consensus size: 79
53418035 GGACTAAGAT
* * ** ** *
53418045 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAATTGTTA
1 CCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAAGAGCTA
**
53418110 AATCCGGGTTATGTC
66 AATCC-GGTTAAATC
* * * * *
53418125 CCGAAGG-CATTGTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAAGAGCTA
*
53418189 TATCCGGTTAAATC
66 AATCCGGTTAAATC
53418203 CCGAAGG
1 CCGAAGG
53418210 TACGTGATTT
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
78 14 0.20
79 49 0.70
80 7 0.10
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAAGAGCTA
AATCCGGTTAAATC
Found at i:53429933 original size:30 final size:28
Alignment explanation
Indices: 53429879--53429937 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
53429869 CACATGAGAG
*
53429879 AGAAAAAAGAAAATAAAAGTGAAAAAGAA
1 AGAAAAAAGAAAATAAAAGAG-AAAAGAA
**
53429908 AGAAAAGAAGAAAATATGAGAGAAAAGAA
1 AGAAAA-AAGAAAATAAAAGAGAAAAGAA
53429937 A
1 A
53429938 ACGAGTTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (28 bp):
AGAAAAAAGAAAATAAAAGAGAAAAGAA
Found at i:53441773 original size:22 final size:22
Alignment explanation
Indices: 53441745--53441866 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
53441735 TTCCACATCC
53441745 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
53441767 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
53441791 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
53441814 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
53441838 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
53441861 ATCACA
1 ATCACA
53441867 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:53441780 original size:47 final size:47
Alignment explanation
Indices: 53441738--53442759 Score: 1956
Period size: 47 Copynumber: 21.7 Consensus size: 47
53441728 TATACACTTC
* * *
53441738 CACATCCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-TGTT
* * **
53441785 CACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53441832 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53441879 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53441926 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53441973 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442020 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442067 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442114 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442161 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442208 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442255 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442302 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442349 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442396 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442443 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
*
53442490 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACTCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442537 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442584 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442631 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442678 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
53442725 CACATTCATCACATTGGCCATTCGGCCTTATCACA
1 CACATTCATCACATTGGCCATTCGGCCTTATCACA
53442760 TATATATATA
Statistics
Matches: 965, Mismatches: 9, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
46 1 0.00
47 964 1.00
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.30
Consensus pattern (47 bp):
CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
Found at i:53444228 original size:56 final size:56
Alignment explanation
Indices: 53444161--53444280 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
53444151 TATTAGTTTA
53444161 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
53444217 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
53444273 TTGCCCAT
1 TTGCCCAT
53444281 TATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:53458040 original size:96 final size:98
Alignment explanation
Indices: 53457873--53458105 Score: 310
Period size: 96 Copynumber: 2.4 Consensus size: 98
53457863 TACTAGGGTA
* ** * *
53457873 ATGAGAGCTAGTGTAAGACCATGTCTGGCACATGGCATTGGCCTCGATATGTGAGCCAGTGTAAG
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAACATGTGAGCCAGTGTAAG
* ** *
53457938 ATCATGTTTGGAACATGGCATTGGCATTC-ATA-
66 ACCATGTTTGGAACATGGCATCAGCA-CCAATAT
* *
53457970 A-GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAACATGTGGGCTAGTGTAAG
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAACATGTGAGCCAGTGTAAG
53458034 ACCATGTTTGGAACATGGCATCAGCACCAATAT
66 ACCATGTTTGGAACATGGCATCAGCACCAATAT
* **
53458067 ATGAGAGCCAGTGTAAGACCATGTCTAAGACATGGCATC
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC
53458106 GGCATCTTAC
Statistics
Matches: 119, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
95 1 0.01
96 82 0.69
97 2 0.02
98 34 0.29
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (98 bp):
ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAACATGTGAGCCAGTGTAAG
ACCATGTTTGGAACATGGCATCAGCACCAATAT
Found at i:53458055 original size:48 final size:49
Alignment explanation
Indices: 53457877--53458105 Score: 225
Period size: 48 Copynumber: 4.7 Consensus size: 49
53457867 AGGGTAATGA
* ** *
53457877 GAGCTAGTGTAAGACCATGTCTGGCACATGGCATTGGC-CTCGATATGT
1 GAGCTAGTGTAAGACCATGTCTGGAACATGGCATCAGCACTCAATATGT
* * * ** * * *
53457925 GAGCCAGTGTAAGATCATGTTTGGAACATGGCATTGGCATTC-ATAAGA
1 GAGCTAGTGTAAGACCATGTCTGGAACATGGCATCAGCACTCAATATGT
* *
53457973 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGC-CTCAACATGT
1 GAGCTAGTGTAAGACCATGTCTGGAACATGGCATCAGCACTCAATATGT
* * *
53458021 GGGCTAGTGTAAGACCATGTTTGGAACATGGCATCAGCAC-CAATATATGA
1 GAGCTAGTGTAAGACCATGTCTGGAACATGGCATCAGCACTC-A-ATATGT
* *
53458071 GAGCCAGTGTAAGACCATGTCT-AAGACATGGCATC
1 GAGCTAGTGTAAGACCATGTCTGGA-ACATGGCATC
53458106 GGCATCTTAC
Statistics
Matches: 149, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
47 2 0.01
48 109 0.73
49 5 0.03
50 33 0.22
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (49 bp):
GAGCTAGTGTAAGACCATGTCTGGAACATGGCATCAGCACTCAATATGT
Found at i:53460428 original size:39 final size:39
Alignment explanation
Indices: 53460311--53461274 Score: 1733
Period size: 39 Copynumber: 24.6 Consensus size: 39
53460301 GCTCCTCGTT
* *
53460311 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
53460351 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
53460391 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460430 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460469 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460508 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460547 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460586 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460625 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460664 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460703 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460742 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460781 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460820 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460859 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460898 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460937 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53460976 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53461015 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53461054 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53461093 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53461132 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53461171 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
53461210 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
53461251 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
53461275 CATCATTCAA
Statistics
Matches: 906, Mismatches: 11, Indels: 15
0.97 0.01 0.02
Matches are distributed among these distances:
39 834 0.92
40 61 0.07
41 11 0.01
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:53463481 original size:19 final size:19
Alignment explanation
Indices: 53463457--53463494 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
53463447 GTATACATGT
53463457 GTTTAAATCTAGTAACGCC
1 GTTTAAATCTAGTAACGCC
53463476 GTTTAAATCTAGTAACGCC
1 GTTTAAATCTAGTAACGCC
53463495 TCGTACACTG
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:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (19 bp):
GTTTAAATCTAGTAACGCC
Found at i:53468978 original size:43 final size:43
Alignment explanation
Indices: 53468885--53469043 Score: 135
Period size: 43 Copynumber: 3.7 Consensus size: 43
53468875 GGTTATCGAG
* *
53468885 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCTTTGCA
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGCA
* * *
53468928 TTGTGATTACATGTAAGACCATGTTTGGGACATTGGCATCGTTA
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG-CA
*** * * * * * *
53468972 AT-TGATTTTGTGCAAGACCCTATCTAGGACAGTGGCATTG-A
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGCA
*
53469013 TATGTG-TTAACATGTAAGACCATATCTGGGA
1 -ATGTGATT-ACATGTAAGACCATGTCTGGGA
53469044 TATGACATTG
Statistics
Matches: 90, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 83 0.92
44 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGCA
Found at i:53474013 original size:40 final size:40
Alignment explanation
Indices: 53473965--53474272 Score: 553
Period size: 40 Copynumber: 7.7 Consensus size: 40
53473955 GCAAACACAT
* * *
53473965 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
53474005 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
53474045 TTGCCTTCGGGTCGTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
53474085 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
53474125 TTGCCTTCGGGTCGTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
53474165 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
53474205 TTGCCTTCGGGTCCTAGCCCGGATATATCAATTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
53474245 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
53474273 TCCAATGCTC
Statistics
Matches: 258, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 258 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:53482770 original size:25 final size:25
Alignment explanation
Indices: 53482741--53482792 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
53482731 AAACAACTAA
*
53482741 ATCAAGCCTAATTCATGTTAGTTCT
1 ATCAAGCCTAATTCATGCTAGTTCT
53482766 ATCAAGCCTAATTCATGCTAGTTCT
1 ATCAAGCCTAATTCATGCTAGTTCT
53482791 AT
1 AT
53482793 ACCATCGTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (25 bp):
ATCAAGCCTAATTCATGCTAGTTCT
Found at i:53488126 original size:14 final size:14
Alignment explanation
Indices: 53488098--53488130 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53488088 TATTAATGAG
*
53488098 ATTTT-TTAGTATT
1 ATTTTATTAATATT
53488111 ATTTTATTAATATT
1 ATTTTATTAATATT
53488125 ATTTTA
1 ATTTTA
53488131 CATAAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
ATTTTATTAATATT
Found at i:53490662 original size:93 final size:93
Alignment explanation
Indices: 53490503--53490674 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
53490493 CGCCCATAAG
* * * * *
53490503 CGAACTTGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAGGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53490568 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
*
53490596 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53490661 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
53490675 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:53490671 original size:46 final size:46
Alignment explanation
Indices: 53490496--53490671 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
53490486 TGTAACCCGC
* * * * *
53490496 CCATAAGCGAACTTGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
53490542 CCATAGGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
53490592 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
53490635 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
53490672 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.57
47 29 0.28
48 1 0.01
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:53490690 original size:46 final size:44
Alignment explanation
Indices: 53490548--53490690 Score: 130
Period size: 46 Copynumber: 3.1 Consensus size: 44
53490538 GCATCCATAG
*
53490548 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATTTCA
1 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT-A
* * * *
53490596 -CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AA
1 GTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTA
53490641 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTA
1 GTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CTA
53490687 GTGA
1 GTGA
53490691 CATGTCACTT
Statistics
Matches: 79, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 33 0.42
47 31 0.39
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (44 bp):
GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTA
Found at i:53493105 original size:30 final size:30
Alignment explanation
Indices: 53493061--53493149 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
53493051 CAAAGATAAC
*
53493061 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
53493090 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
53493120 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
53493150 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:53493109 original size:15 final size:14
Alignment explanation
Indices: 53493061--53493143 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
53493051 CAAAGATAAC
*
53493061 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
53493075 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
53493090 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
53493105 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
53493120 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
53493135 AAGAAACCC
1 AAGAAACCC
53493144 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:53493149 original size:15 final size:15
Alignment explanation
Indices: 53493072--53493149 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
53493062 AGAAAACCGA
53493072 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
53493087 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
53493101 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
53493116 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
53493132 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
53493147 ATA
1 ATA
53493150 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:53496226 original size:46 final size:46
Alignment explanation
Indices: 53496064--53496239 Score: 155
Period size: 46 Copynumber: 3.8 Consensus size: 46
53496054 TGTAACCCGC
* *** *
53496064 CTATAAGCGAACTCGGACTCAACTCAATGAGCTT-GGGTGTTCGCGT
1 CTATAAGCGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCAT
* * * * *
53496110 CCATAGGTGAACTCGGACTCTACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CTATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
53496160 -T-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CTATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
53496203 CTATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CTATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
53496240 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 57 0.56
47 28 0.27
48 1 0.01
50 2 0.02
51 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (46 bp):
CTATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:53496230 original size:93 final size:93
Alignment explanation
Indices: 53496071--53496242 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 93
53496061 CGCCTATAAG
* *** * * *
53496071 CGAACTCGGACTCAACTCAATGAGCTTGGGTGTTCGCGTCCATAGGTGAACTCGGACTCTACTCA
1 CGAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53496136 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
*
53496164 CGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCTATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
53496228 AACGAGTTCGGATGC
65 AACGAGTTCGGATGC
53496243 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
92 2 0.03
93 68 0.97
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:53496258 original size:46 final size:45
Alignment explanation
Indices: 53496165--53496250 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
53496155 TACATTTCAC
* * *
53496165 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCTATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGA-ATGCGCAACCATAAGT
*
53496211 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
1 GAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAACCAT
53496251 CCTAGTGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 8 0.22
46 28 0.78
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAACCATAAGT
Found at i:53505397 original size:42 final size:42
Alignment explanation
Indices: 53505338--53505422 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
53505328 TACTAATTTG
* *
53505338 TACATAAATAGAAAATTTTGAAAATTAATCAAAATAAAAAGT
1 TACATAAATACAAAATTTTGAAAATTAATCAAAAGAAAAAGT
53505380 TACATAAATACAAAATTTTGAAAATTAATCAAAAGAAAAAGT
1 TACATAAATACAAAATTTTGAAAATTAATCAAAAGAAAAAGT
53505422 T
1 T
53505423 TAAAAAGACT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.59, C:0.06, G:0.07, T:0.28
Consensus pattern (42 bp):
TACATAAATACAAAATTTTGAAAATTAATCAAAAGAAAAAGT
Found at i:53505503 original size:17 final size:18
Alignment explanation
Indices: 53505468--53505506 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53505458 GCAAAAATTG
* *
53505468 AAAAGCAAAGTGAATGAA
1 AAAAGCAAAGTAAAAGAA
53505486 AAAAGCAAAG-AAAAGAA
1 AAAAGCAAAGTAAAAGAA
53505503 AAAA
1 AAAA
53505507 TCCTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.72, C:0.05, G:0.18, T:0.05
Consensus pattern (18 bp):
AAAAGCAAAGTAAAAGAA
Found at i:53512801 original size:15 final size:15
Alignment explanation
Indices: 53512781--53512836 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
53512771 GTATCTTGGG
53512781 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
53512796 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
53512811 TTTCTCTA-TCTTTGA
1 TTTCTTTATTC-TGGA
53512826 TTTCTTTATTC
1 TTTCTTTATTC
53512837 GGTTTCCTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 2 0.06
15 32 0.89
16 2 0.06
ACGTcount: A:0.12, C:0.16, G:0.09, T:0.62
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:53518078 original size:27 final size:27
Alignment explanation
Indices: 53518030--53518081 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
53518020 GTGAGGCTGC
*
53518030 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGACAAAGCCACCAGATA
* * *
53518057 CAGATATTGTGGCTAGGCCACCAGA
1 CAGATATTGTGACAAAGCCACCAGA
53518082 ACATCTATAT
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:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (27 bp):
CAGATATTGTGACAAAGCCACCAGATA
Found at i:53521514 original size:16 final size:17
Alignment explanation
Indices: 53521493--53521526 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
53521483 ATTAAATTAA
53521493 TTTTAATTAATT-ATTT
1 TTTTAATTAATTAATTT
53521509 TTTTAATTAATTAATTT
1 TTTTAATTAATTAATTT
53521526 T
1 T
53521527 CTCAATCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAATTAATTAATTT
Found at i:53527191 original size:40 final size:39
Alignment explanation
Indices: 53527126--53527211 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 39
53527116 TATATAAATA
**
53527126 TAGCCGAAGCTATCTCAAATTGCACACCAAGTGCCACTTT
1 TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCA-TTT
* * * *
53527166 TAGCCGAAGCTATTTCGAACCGCACACTAAGTGTCATTT
1 TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCATTT
53527205 TAGCCGA
1 TAGCCGA
53527212 TAAGTCGTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 10 0.25
40 30 0.75
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (39 bp):
TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCATTT
Found at i:53531796 original size:20 final size:20
Alignment explanation
Indices: 53531760--53531800 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
53531750 AAATATTTTA
*
53531760 TTTATTTAATTGCTCTATTT
1 TTTATTTAATTGATCTATTT
53531780 TTTATCTTAATT-ATCTATTT
1 TTTAT-TTAATTGATCTATTT
53531800 T
1 T
53531801 AATTGTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTATTTAATTGATCTATTT
Found at i:53534413 original size:39 final size:41
Alignment explanation
Indices: 53534318--53534501 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
53534308 TTGAATGATG
*
53534318 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
53534357 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
53534397 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
53534436 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
53534476 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53534502 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:53534453 original size:79 final size:81
Alignment explanation
Indices: 53534318--53534501 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
53534308 TTGAATGATG
53534318 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
53534381 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
53534396 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
53534457 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
53534476 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53534502 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:53534523 original size:79 final size:79
Alignment explanation
Indices: 53534370--53534534 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
53534360 GGACTAAGAT
* ** *
53534370 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
53534435 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
53534449 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
53534511 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
53534528 CCGAAGG
1 CCGAAGG
53534535 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:53541341 original size:30 final size:29
Alignment explanation
Indices: 53541305--53541364 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
53541295 ATAAGGTACT
53541305 ATTAAGGCTACAAAACTAAGACTGTAGGGA
1 ATTAAGGCTACAAAACTAA-ACTGTAGGGA
* *
53541335 ATTAAGGCTACAAAACTGAATTGTAGGGA
1 ATTAAGGCTACAAAACTAAACTGTAGGGA
53541364 A
1 A
53541365 AACTAAGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (29 bp):
ATTAAGGCTACAAAACTAAACTGTAGGGA
Found at i:53555095 original size:58 final size:58
Alignment explanation
Indices: 53555030--53555145 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
53555020 TATATGATAT
*
53555030 TATGTTTTAAATATGTGAATGAGAACTTTACAGAGTAAATTGTATAAATCTGCTAGGG
1 TATGTTTTAAATATGTGAATGAGAACTTTACAGAGTAAATTGGATAAATCTGCTAGGG
*
53555088 TATGTTTTAAATATGTGAATGAGAACTTTACAGAGTAAATTGGATAAATTTGCTAGGG
1 TATGTTTTAAATATGTGAATGAGAACTTTACAGAGTAAATTGGATAAATCTGCTAGGG
53555146 ACAGCTGTAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (58 bp):
TATGTTTTAAATATGTGAATGAGAACTTTACAGAGTAAATTGGATAAATCTGCTAGGG
Found at i:53556171 original size:22 final size:22
Alignment explanation
Indices: 53556146--53556268 Score: 56
Period size: 22 Copynumber: 5.3 Consensus size: 22
53556136 ACATGCATAT
53556146 ATGTGATAAGGCCGAATGGCAA
1 ATGTGATAAGGCCGAATGGCAA
* * *
53556168 ATGTGGTGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGCA-A
* *
53556192 TATGAGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCAA
*
53556215 ATGTGATGAAGG-TGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGCA-A
* *
53556239 TGTGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCAA
53556262 ATGTGAT
1 ATGTGAT
53556269 GAATGTGAAC
Statistics
Matches: 72, Mismatches: 15, Indels: 28
0.63 0.13 0.24
Matches are distributed among these distances:
22 20 0.28
23 20 0.28
24 19 0.26
25 13 0.18
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCAA
Found at i:53556265 original size:24 final size:24
Alignment explanation
Indices: 53556197--53556266 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
53556187 GCATATATGA
53556197 GATAAGGCCGAATGGCCAA--TGT
1 GATAAGGCCGAATGGCCAATGTGT
*
53556219 GATGAAGG-TGAACAT-G-CATATGTGT
1 GAT-AAGGCCG-A-ATGGCCA-ATGTGT
53556244 GATAAGGCCGAATGGCCAATGTG
1 GATAAGGCCGAATGGCCAATGTG
53556267 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
22 6 0.16
23 9 0.24
24 13 0.35
25 9 0.24
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.21
Consensus pattern (24 bp):
GATAAGGCCGAATGGCCAATGTGT
Found at i:53556430 original size:47 final size:47
Alignment explanation
Indices: 53556027--53556412 Score: 601
Period size: 47 Copynumber: 8.2 Consensus size: 47
53556017 TTAGGATTTT
** * * *
53556027 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGACCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
53556074 ATGTGATGAATGTGAACATGCATATGTGTGACAAGGACGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53556121 ATGTCATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53556168 ATGTGGTGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53556215 ATGTGATGAAGGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
53556262 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGACCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
53556309 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
53556356 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
53556403 ATGTGATGAA
1 ATGTGATGAA
53556413 CGTGGAAGTG
Statistics
Matches: 310, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 310 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.25
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:53556490 original size:46 final size:46
Alignment explanation
Indices: 53556426--53556562 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
53556416 GGAAGTGTAT
* * *
53556426 ATATGGGGAAAAGTCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
*
53556472 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * * *
53556518 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
53556563 TGTATATATA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.35, C:0.08, G:0.32, T:0.25
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:53562231 original size:40 final size:40
Alignment explanation
Indices: 53562179--53562534 Score: 514
Period size: 40 Copynumber: 8.9 Consensus size: 40
53562169 GTTATATATG
* *
53562179 ATCCGGGCTAAGTCCCAAAGAGCATACGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
*
53562219 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* * *
53562259 ATCCGGGCTAAGTCCCGAAGAGCATACGCGCTGGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* *
53562299 ATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGAGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* * *
53562339 ATCCGGGCTAAGTCCTGAAGAGCATACGTGCTGGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* * *
53562379 ATCCGGGCTAAGTCTCGAAGAGTATTCGTGCTGGAGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* *
53562419 ATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGAGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* * * **
53562459 ATCAGGGTTAAGTCCCAAAGAGCATTCGCACTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
*
53562499 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTG
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
53562535 ATGTGTATTC
Statistics
Matches: 283, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 283 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
Found at i:53563733 original size:32 final size:32
Alignment explanation
Indices: 53563687--53563750 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
53563677 GGTTTCGGGA
53563687 CCACGAAACCGAGTCATAAAAATAATTAACAG
1 CCACGAAACCGAGTCATAAAAATAATTAACAG
*
53563719 CCACGAAACTGAGTCATAAAAATAATTAACAG
1 CCACGAAACCGAGTCATAAAAATAATTAACAG
53563751 TCATATTCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.50, C:0.20, G:0.12, T:0.17
Consensus pattern (32 bp):
CCACGAAACCGAGTCATAAAAATAATTAACAG
Found at i:53566252 original size:46 final size:47
Alignment explanation
Indices: 53566118--53566263 Score: 204
Period size: 47 Copynumber: 3.1 Consensus size: 47
53566108 TTAGGATTTT
** * * *
53566118 ATGTGATGAATGTGAATGTGTATATTTGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
53566165 ATGTGATGAATGTGAACATGCATATGTGTGACAAGGACGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
53566212 ATGTGATGAATGTGAA-ATGCATATATGTGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
53566258 ATGTGA
1 ATGTGA
53566264 GTATTCGAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
46 32 0.36
47 56 0.64
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:53566491 original size:47 final size:46
Alignment explanation
Indices: 53566437--53566558 Score: 163
Period size: 47 Copynumber: 2.6 Consensus size: 46
53566427 TTAGGATTTT
*
53566437 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGACCA
1 ATGTGATGAATGTGAA-GTGTATATATGAGATAAGGCAGAATGACCA
* * * *
53566484 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAA-GTGTATATATGAGATAAGGCAGAATGACCA
*
53566531 ATGTGATGAACGTGGAAGTGTATATATG
1 ATGTGATGAATGT-GAAGTGTATATATG
53566559 GGGAAAAGTC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
47 62 0.95
48 3 0.05
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.28
Consensus pattern (46 bp):
ATGTGATGAATGTGAAGTGTATATATGAGATAAGGCAGAATGACCA
Found at i:53566528 original size:319 final size:320
Alignment explanation
Indices: 53565944--53566558 Score: 1144
Period size: 319 Copynumber: 1.9 Consensus size: 320
53565934 TAAGTTTATA
53565944 AGTATTCGAATATGAAATGATAGTATGGCTTGAAATTGAATTATTCATTGGAAAATGATAGATGT
1 AGTATTCGAATATGAAATGATAGTATGGCTTGAAATTGAATTATTCATTGGAAAATGATAGATGT
53566009 AGATTCAGCCAAGACAAAGTGTATACATGAAAGTATATATGGTATGTGAAGTATATTTGGATAAT
66 AGATTCAGCCAAGACAAAGTGTATACATGAAAGTATATATGGTATGTGAAGTATATTTGGATAAT
53566074 TGTGATGTGAATACATGAAAATTTATATTTTGATTTAGGATTTTATGTGATGAATGTGAATGTGT
131 TGTGATGTGAATACATGAAAATTTATATTTTGATTTAGGATTTTATGTGATGAATGTGAATGTGT
* * *
53566139 ATATTTGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGACAAGGACG
196 ATATATGAGATAAGGCCGAATGACCAATGTGATGAATGTGAACATGCATATATGTGACAAGGACG
*
53566204 AATGGCCAATGTGATGAATGT-GAAATGCATATATGTGATAAGGCCGAATGGCAAATGTG
261 AATGGCCAATGTGATGAACGTGGAAATGCATATATGTGATAAGGCCGAATGGCAAATGTG
53566263 AGTATTCGAATATGAAATGATAGTATGGCTTGAAATTGAATTATTCATTGGAAAATGATAGATGT
1 AGTATTCGAATATGAAATGATAGTATGGCTTGAAATTGAATTATTCATTGGAAAATGATAGATGT
53566328 AGATTCAGCCAAGACAAAGTGTATACATGAAAGTATATATGGTATGTGAAGTATATTTGGATAAT
66 AGATTCAGCCAAGACAAAGTGTATACATGAAAGTATATATGGTATGTGAAGTATATTTGGATAAT
53566393 TGTGATGTGAATACATGAAAATTTATATTTTGATTTAGGATTTTATGTGATGAATGTGAATGTGT
131 TGTGATGTGAATACATGAAAATTTATATTTTGATTTAGGATTTTATGTGATGAATGTGAATGTGT
*
53566458 ATATATGAGATAAGGCCGAATGACCAATGTGATGAATGTGAACATGCATATATGTGATAAGG-CA
196 ATATATGAGATAAGGCCGAATGACCAATGTGATGAATGTGAACATGCATATATGTGACAAGGAC-
* *
53566522 GAATGGCCAATGTGATGAACGTGGAAGTGTATATATG
260 GAATGGCCAATGTGATGAACGTGGAAATGCATATATG
53566559 GGGAAAAGTC
Statistics
Matches: 287, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
318 1 0.00
319 274 0.95
320 12 0.04
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (320 bp):
AGTATTCGAATATGAAATGATAGTATGGCTTGAAATTGAATTATTCATTGGAAAATGATAGATGT
AGATTCAGCCAAGACAAAGTGTATACATGAAAGTATATATGGTATGTGAAGTATATTTGGATAAT
TGTGATGTGAATACATGAAAATTTATATTTTGATTTAGGATTTTATGTGATGAATGTGAATGTGT
ATATATGAGATAAGGCCGAATGACCAATGTGATGAATGTGAACATGCATATATGTGACAAGGACG
AATGGCCAATGTGATGAACGTGGAAATGCATATATGTGATAAGGCCGAATGGCAAATGTG
Found at i:53566573 original size:47 final size:46
Alignment explanation
Indices: 53566437--53566580 Score: 137
Period size: 47 Copynumber: 3.1 Consensus size: 46
53566427 TTAGGATTTT
* * *
53566437 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGACCA
1 ATGTGATGAATGTGAACGTGTATATATGAGA-AAAGCCGAATGGCCA
* * * * *
53566484 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACGTGTATATATGAGA-AAAGCCGAATGGCCA
* * * *
53566531 ATGTGATGAACGTGGAA-GTGTATATATGGGGAAAAGTCGAATGGCTA
1 ATGTGATGAATGT-GAACGTGTATATAT-GAGAAAAGCCGAATGGCCA
53566578 ATG
1 ATG
53566581 CGAAATGTGT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
47 75 0.93
48 6 0.07
ACGTcount: A:0.35, C:0.08, G:0.30, T:0.26
Consensus pattern (46 bp):
ATGTGATGAATGTGAACGTGTATATATGAGAAAAGCCGAATGGCCA
Found at i:53574422 original size:11 final size:11
Alignment explanation
Indices: 53574406--53574431 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53574396 TTTTTTTCTC
53574406 ACATGTACATA
1 ACATGTACATA
53574417 ACATGTACATA
1 ACATGTACATA
53574428 ACAT
1 ACAT
53574432 CTCCATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (11 bp):
ACATGTACATA
Found at i:53580274 original size:30 final size:28
Alignment explanation
Indices: 53580220--53580278 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
53580210 CACATGAGAG
*
53580220 AGAAAAAAGAAAATAAAAGTGAAAAAGAA
1 AGAAAAAAGAAAATAAAAGAG-AAAAGAA
**
53580249 AGAAAAGAAGAAAATATGAGAGAAAAGAA
1 AGAAAA-AAGAAAATAAAAGAGAAAAGAA
53580278 A
1 A
53580279 ACGAGTTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (28 bp):
AGAAAAAAGAAAATAAAAGAGAAAAGAA
Found at i:53590281 original size:40 final size:40
Alignment explanation
Indices: 53590251--53590420 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
53590241 GGACTAAGAT
* *
53590251 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * *
53590291 CCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* ** *
53590331 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
53590371 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
53590410 CCGAAGGCATT
1 CCGAAGGCATT
53590421 TGAACGAGGA
Statistics
Matches: 116, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 33 0.28
40 83 0.72
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:53590347 original size:80 final size:79
Alignment explanation
Indices: 53590198--53590420 Score: 232
Period size: 80 Copynumber: 2.8 Consensus size: 79
53590188 TTGAATGCTG
* * * ** * * * * *
53590198 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGCGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
*
53590262 TGTGCGAGATACTAAA
64 CGTGCGAGATACTAAA
* * *
53590278 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* **
53590343 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * *
53590358 TCCGGGTTACGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
53590421 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
79 35 0.29
80 81 0.68
81 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAA
Found at i:53590440 original size:79 final size:80
Alignment explanation
Indices: 53590273--53590455 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
53590263 GTGCGAGATA
* * *
53590273 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
53590338 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
53590353 TTAAATCCGGGTTACGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
53590417 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
53590432 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
53590456 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:53610512 original size:48 final size:48
Alignment explanation
Indices: 53610426--53610646 Score: 237
Period size: 48 Copynumber: 4.6 Consensus size: 48
53610416 ATACTAGGAT
* * *
53610426 TATGAGAGCTAGTGTAAGACCATGTCTGGGACACGGCATTGGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATTGGCCTCAA
* * * * **
53610474 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATTGGCATTTA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATTGGCCTCAA
* * **
53610522 TAAGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATTGGCCTCAA
* * * * **
53610570 CATGTGGGCTAGTGTAAGACCATGTTTGGAACATGGCATCAGCAC-CAATA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATTGGC-CTC-A-A
53610620 TATGAGAGCTAGTGTAAGACCATGTCT
1 TATGAGAGCTAGTGTAAGACCATGTCT
53610647 AAGACATGGC
Statistics
Matches: 142, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
48 116 0.82
49 2 0.01
50 24 0.17
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (48 bp):
TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATTGGCCTCAA
Found at i:53610593 original size:96 final size:97
Alignment explanation
Indices: 53610429--53610659 Score: 320
Period size: 96 Copynumber: 2.4 Consensus size: 97
53610419 CTAGGATTAT
* ** * *
53610429 GAGAGCTAGTGTAAGACCATGTCTGGGACACGGCATTGGCCTCGATATGTGAGCCAGTGTAAGAC
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAACATGTGAGCCAGTGTAAGAC
** **
53610494 CATGTTTGGAACATGGCATTGGCA-TTTATAA
66 CATGTTTGGAACATGGCATCAGCACAATATAA
* *
53610525 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAACATGTGGGCTAGTGTAAGAC
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAACATGTGAGCCAGTGTAAGAC
*
53610590 CATGTTTGGAACATGGCATCAGCACCAATATAT
66 CATGTTTGGAACATGGCATCAGCA-CAATATAA
**
53610623 GAGAGCTAGTGTAAGACCATGTCTAAGACATGGCATC
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC
53610660 GGCATCTTAC
Statistics
Matches: 119, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
96 80 0.67
98 39 0.33
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (97 bp):
GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAACATGTGAGCCAGTGTAAGAC
CATGTTTGGAACATGGCATCAGCACAATATAA
Found at i:53612025 original size:21 final size:21
Alignment explanation
Indices: 53611970--53612025 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
53611960 TTTCTAGAAC
53611970 AGTTTGAGGCTT-TTGATTCA
1 AGTTTGAGGCTTATTGATTCA
* ** * * *
53611990 AGTTTAAATCATATTGGTTCG
1 AGTTTGAGGCTTATTGATTCA
53612011 AGTTTGAGGCTTATT
1 AGTTTGAGGCTTATT
53612026 TTTTTATATA
Statistics
Matches: 25, Mismatches: 10, Indels: 1
0.69 0.28 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (21 bp):
AGTTTGAGGCTTATTGATTCA
Found at i:53618467 original size:25 final size:25
Alignment explanation
Indices: 53618438--53618489 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
53618428 AAACAACTAA
*
53618438 ATCAAGCCTAATTCATGTTAGTTCT
1 ATCAAGCCTAATTCATGCTAGTTCT
*
53618463 ATCAAGCCTAATTCGTGCTAGTTCT
1 ATCAAGCCTAATTCATGCTAGTTCT
53618488 AT
1 AT
53618490 ACCATCGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (25 bp):
ATCAAGCCTAATTCATGCTAGTTCT
Found at i:53620319 original size:24 final size:24
Alignment explanation
Indices: 53620272--53620650 Score: 585
Period size: 24 Copynumber: 16.0 Consensus size: 24
53620262 GCTTTATCAT
*
53620272 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
53620297 ATAACTGGGGTA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
53620322 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53620346 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53620369 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53620392 ATAATTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53620416 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53620439 ATAATTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53620463 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53620486 ATAATTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53620510 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53620533 ATAATTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53620557 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53620580 ATAATTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53620604 ATAACTGGGGCATAAGCCCTTTAA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53620628 ATAATTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
53620651 GCACTTCCTC
Statistics
Matches: 329, Mismatches: 16, Indels: 19
0.90 0.04 0.05
Matches are distributed among these distances:
23 134 0.41
24 165 0.50
25 24 0.07
26 6 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:53620380 original size:47 final size:47
Alignment explanation
Indices: 53620293--53620650 Score: 639
Period size: 47 Copynumber: 7.6 Consensus size: 47
53620283 CCTAGCCTCT
* *
53620293 TTTAATAACTGGGGTA-AAGCCCTTTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAATTGGGGCATAAGCCC--TTTTAATAACTGGGGCATAAGCCC
*
53620341 TTTTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC
1 -TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
53620388 TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
53620435 TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
53620482 TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
53620529 TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
53620576 TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
53620623 TTTAAATAATTGGGGCATAAGCCCTTTT
1 TTT-AATAATTGGGGCATAAGCCCTTTT
53620651 GCACTTCCTC
Statistics
Matches: 304, Mismatches: 2, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
46 22 0.07
47 237 0.78
48 24 0.08
49 15 0.05
50 6 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (47 bp):
TTTAATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
Found at i:53620726 original size:20 final size:20
Alignment explanation
Indices: 53620703--53620745 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
53620693 GAACATCTCG
53620703 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
53620723 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
53620743 TGT
1 TGT
53620746 TTATCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:53620814 original size:25 final size:25
Alignment explanation
Indices: 53620782--53620829 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53620772 ATATTTAAAC
* * *
53620782 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGAAAAACGGTCATTTTTA
53620807 CCTAGGGGAAAAACGGTCATTTT
1 CCTAGGGGAAAAACGGTCATTTT
53620830 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGAAAAACGGTCATTTTTA
Found at i:53628387 original size:31 final size:31
Alignment explanation
Indices: 53628344--53628407 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
53628334 CCTTTTCATA
53628344 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
53628375 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
53628406 TT
1 TT
53628408 ACGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:53628647 original size:24 final size:24
Alignment explanation
Indices: 53628600--53628767 Score: 252
Period size: 24 Copynumber: 7.0 Consensus size: 24
53628590 GCTTTATCAT
*
53628600 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
53628625 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
53628650 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53628673 ATAATTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53628697 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53628721 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53628745 ATAATTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
53628768 GCACTTCCTC
Statistics
Matches: 134, Mismatches: 4, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
23 23 0.17
24 80 0.60
25 25 0.19
26 6 0.04
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:53628866 original size:40 final size:40
Alignment explanation
Indices: 53628822--53629620 Score: 1589
Period size: 40 Copynumber: 20.0 Consensus size: 40
53628812 ACATCTCGTG
53628822 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53628862 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53628902 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53628942 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53628982 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629022 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629062 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629102 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629142 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629182 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629222 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629262 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629302 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629342 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629382 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629422 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629462 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629502 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
53629542 TGCATATCATACATATCATGTGCATATCATACATGTCATC
1 TGCATATCATACATATCATGTGCATATCATACATGTCATC
*
53629582 TGCATATCATACATATCATGTGCATATCATACATATCAT
1 TGCATATCATACATATCATGTGCATATCATACATGTCAT
53629621 GTTTATCAAA
Statistics
Matches: 758, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 758 1.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (40 bp):
TGCATATCATACATATCATGTGCATATCATACATGTCATC
Found at i:53629687 original size:25 final size:25
Alignment explanation
Indices: 53629659--53629706 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53629649 ATATATAAAC
* * *
53629659 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
53629684 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
53629707 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:53641619 original size:24 final size:24
Alignment explanation
Indices: 53641587--53641633 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
53641577 CTATCAAGAG
**
53641587 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
53641611 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
53641634 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:53643087 original size:27 final size:27
Alignment explanation
Indices: 53643047--53643158 Score: 113
Period size: 27 Copynumber: 4.1 Consensus size: 27
53643037 AGGAAGCGTC
*
53643047 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
53643074 CTGGTGGCTCTGCCACATATT-TCT-AT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* *
53643100 CCTAGTGGCTCTGCCACGATTATCTGTAT
1 -CTGGTGGCTCTGCCACAATTATCTG-AT
** * *
53643129 CTGGTAACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
53643155 CTGG
1 CTGG
53643159 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
26 10 0.14
27 45 0.62
28 15 0.21
29 2 0.03
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:53653068 original size:46 final size:46
Alignment explanation
Indices: 53652915--53653185 Score: 185
Period size: 46 Copynumber: 5.8 Consensus size: 46
53652905 TCACTTGTGT
* * * *
53652915 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGA
* ** *
53652961 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGTATAGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGA
* * * *
53653009 GTGCTAGTGTAAGACATGTCTGGGACATGTATTGGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-A
* *
53653056 -AGCCAGTGTAAGACATGTCTAGGACATGCATCGG-CT-AAG-CGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
* ** * * *
53653098 TGTGTTAGTGTAAGACCCTGTCTGGGACATGGCATCAGCACT-GATATACGA
1 -GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTCG--AGACGA
* * *
53653149 GAGCTAGTATAAGACCATGTCTAGGACATGGCATCGG
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGG
53653186 TAGTTACCCC
Statistics
Matches: 176, Mismatches: 36, Indels: 22
0.75 0.15 0.09
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 12 0.07
45 14 0.08
46 59 0.34
47 29 0.16
48 23 0.13
49 1 0.01
50 32 0.18
51 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
Found at i:53666365 original size:43 final size:43
Alignment explanation
Indices: 53666281--53666362 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
53666271 ATATCGTACT
* * * *
53666281 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCA
1 ATGCCAATGTCCCAAACAAGGTCTTACACGCAATCACATATCA
*
53666324 ATGCCACTGTCCCAAACAAGGTCTTACACGC-A-CACATAT
1 ATGCCAATGTCCCAAACAAGGTCTTACACGCAATCACATAT
53666363 ATCGGAGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 7 0.21
42 1 0.03
43 26 0.76
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAAACAAGGTCTTACACGCAATCACATATCA
Found at i:53666464 original size:55 final size:56
Alignment explanation
Indices: 53666343--53666472 Score: 208
Period size: 55 Copynumber: 2.3 Consensus size: 56
53666333 TCCCAAACAA
*
53666343 GGTCTTACACGCACACATATATCGGAGTCACATATCGATGCCAACATATAAAACGT
1 GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACATATAAAACGT
* * **
53666399 GTTCTAACTCGCACACATATATCGGAGTCACA-ATCGATGCCAATGTATAAAACGT
1 GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACATATAAAACGT
53666454 GGTCTTACTCGCACACATA
1 GGTCTTACTCGCACACATA
53666473 AATTGATGCC
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
55 38 0.57
56 29 0.43
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACATATAAAACGT
Found at i:53670632 original size:40 final size:40
Alignment explanation
Indices: 53670581--53670861 Score: 472
Period size: 40 Copynumber: 7.0 Consensus size: 40
53670571 CATTTGAATG
53670581 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
53670621 ATATCCGGGCTAAGACCTGAAGGCATTTGTACGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
53670661 ATATCCAGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
53670701 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
53670741 ATATCCGGGATAAGACCCGAACGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
53670781 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* * *
53670821 ATATCCGGGATAAGACCCGAAGGCATTTGTCCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
53670861 A
1 A
53670862 NNNNNNNNNN
Statistics
Matches: 224, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 224 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:53672828 original size:37 final size:37
Alignment explanation
Indices: 53672778--53672852 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
53672768 AAGTATGCTA
53672778 TTACAACCATCTCGTGATTGATCTTTAGGCATACTCT
1 TTACAACCATCTCGTGATTGATCTTTAGGCATACTCT
53672815 TTACAACCATCTCGTGATTGATCTTTAGGCATACTCT
1 TTACAACCATCTCGTGATTGATCTTTAGGCATACTCT
53672852 T
1 T
53672853 ACACTAACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (37 bp):
TTACAACCATCTCGTGATTGATCTTTAGGCATACTCT
Found at i:53677702 original size:19 final size:19
Alignment explanation
Indices: 53677678--53677714 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
53677668 CTTGGGTTGT
53677678 GAATAGGCCAAATGGGCCG
1 GAATAGGCCAAATGGGCCG
*
53677697 GAATAGGCTAAATGGGCC
1 GAATAGGCCAAATGGGCC
53677715 CGAGGGGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.35, T:0.14
Consensus pattern (19 bp):
GAATAGGCCAAATGGGCCG
Found at i:53677833 original size:29 final size:28
Alignment explanation
Indices: 53677792--53677936 Score: 127
Period size: 28 Copynumber: 5.1 Consensus size: 28
53677782 GTGAGCATGA
*
53677792 ATAT-AATGTGATTTGGGCCGGATGGGCA
1 ATATAAATGTGA-TTGGGCCGGATGGGCC
* *
53677820 ATATAAATGAGATTGGG-CGTAATGGGCC
1 ATATAAATGTGATTGGGCCG-GATGGGCC
* * *
53677848 ACATGAATGTGAATTGGGCCAGATGGGCC
1 ATATAAATGTG-ATTGGGCCGGATGGGCC
* *
53677877 ATATGAACGTGAATT-GGCCGGATGGGCC
1 ATATAAATGTG-ATTGGGCCGGATGGGCC
* *
53677905 ATATAAATGAGATTGGGCC-TAGTGGGCC
1 ATATAAATGTGATTGGGCCGGA-TGGGCC
53677933 ATAT
1 ATAT
53677937 GTTGGTATGT
Statistics
Matches: 96, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
27 6 0.06
28 57 0.59
29 32 0.33
30 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.25
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCGGATGGGCC
Found at i:53677902 original size:57 final size:58
Alignment explanation
Indices: 53677796--53677937 Score: 150
Period size: 57 Copynumber: 2.5 Consensus size: 58
53677786 GCATGAATAT
* * * * *
53677796 AATGTGATTTGGGCCGGATGGGCAATAT-AAATGAGATTGGGCGTAATGGGCCACATG
1 AATGTGAATTGGGCCAGATGGGCCATATGAAATGAGATTGGCCGTAATGGGCCACATA
* * *
53677853 AATGTGAATTGGGCCAGATGGGCCATATGAACGTGA-ATTGGCCG-GATGGGCCATATA
1 AATGTGAATTGGGCCAGATGGGCCATATGAA-ATGAGATTGGCCGTAATGGGCCACATA
*
53677910 AATGAG-ATTGGGCCTAG-TGGGCCATATG
1 AATGTGAATTGGGCC-AGATGGGCCATATG
53677938 TTGGTATGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
56 19 0.26
57 42 0.58
58 9 0.12
59 3 0.04
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (58 bp):
AATGTGAATTGGGCCAGATGGGCCATATGAAATGAGATTGGCCGTAATGGGCCACATA
Found at i:53682064 original size:47 final size:47
Alignment explanation
Indices: 53681993--53682481 Score: 915
Period size: 47 Copynumber: 10.4 Consensus size: 47
53681983 CCCTTCGGGA
* * * * * *
53681993 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53682040 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53682087 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53682134 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53682181 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53682228 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53682275 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53682322 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53682369 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53682416 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53682463 CTTATCACATATATACACT
1 CTTATCACATATATACACT
53682482 GTCTTGGCTG
Statistics
Matches: 434, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 434 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53701776 original size:28 final size:28
Alignment explanation
Indices: 53701742--53701865 Score: 135
Period size: 28 Copynumber: 4.4 Consensus size: 28
53701732 TTCAGGCCGG
53701742 ATGGGCCATATAAATGAGATTGGGCCTA
1 ATGGGCCATATAAATGAGATTGGGCCTA
* * * *
53701770 ATGGGCCATATGAATGTGAATTGGGTC-G
1 ATGGGCCATATAAATGAG-ATTGGGCCTA
* **
53701798 ATGGGCCATATGAACGTGA-ATTGGGCCGG
1 ATGGGCCATAT-AA-ATGAGATTGGGCCTA
53701827 ATGGGCCATATAAATGAGATTGGGCCTA
1 ATGGGCCATATAAATGAGATTGGGCCTA
*
53701855 GTGGGCCATAT
1 ATGGGCCATAT
53701866 GTAGGTATGC
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.04
28 54 0.68
29 20 0.25
30 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (28 bp):
ATGGGCCATATAAATGAGATTGGGCCTA
Found at i:53701831 original size:57 final size:56
Alignment explanation
Indices: 53701736--53701866 Score: 149
Period size: 57 Copynumber: 2.3 Consensus size: 56
53701726 CACGCGTTCA
* * *
53701736 GGCCGGATGGGCCATAT-AAATGAGATTGGGCCTAATGGGCCATATGAATGTGAATTG
1 GGCC-GATGGGCCATATGAAATGAGATTGGGCCGAATGGGCCATATAAATGAG-ATTG
* * *
53701793 GGTCGATGGGCCATATGAACGTGA-ATTGGGCCGGATGGGCCATATAAATGAGATTG
1 GGCCGATGGGCCATATGAA-ATGAGATTGGGCCGAATGGGCCATATAAATGAGATTG
*
53701849 GGCCTAGTGGGCCATATG
1 GGCCGA-TGGGCCATATG
53701867 TAGGTATGCA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
56 20 0.32
57 40 0.63
58 3 0.05
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (56 bp):
GGCCGATGGGCCATATGAAATGAGATTGGGCCGAATGGGCCATATAAATGAGATTG
Found at i:53717859 original size:40 final size:40
Alignment explanation
Indices: 53717815--53718009 Score: 216
Period size: 40 Copynumber: 4.9 Consensus size: 40
53717805 GTTAGTGATT
*
53717815 AATTCCGGTCTAAGTCCCGAAGGCATTTGTGCGAGTTACA
1 AATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACA
* * * *
53717855 AATTCTGGGCTAAGTCTCGAAGGCATTGGTGCGAGTTACT
1 AATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACA
* *
53717895 AATTCCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTGC-
1 AATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACA
* * * * *
53717934 TATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACCA
1 AAT-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CA
* * *
53717976 TATT-CGGGCTAAGACCCGAAGGC-CTTGTGCGAGT
1 AATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
53718010 GGTTATATCC
Statistics
Matches: 134, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
39 10 0.07
40 119 0.89
41 2 0.01
42 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
AATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACA
Found at i:53734745 original size:14 final size:14
Alignment explanation
Indices: 53734728--53734758 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
53734718 GAAAAATCAC
53734728 TTAGTAAAAGTGGT
1 TTAGTAAAAGTGGT
53734742 TTAGTAAAAGTGGT
1 TTAGTAAAAGTGGT
53734756 TTA
1 TTA
53734759 CCATCCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (14 bp):
TTAGTAAAAGTGGT
Found at i:53737500 original size:49 final size:50
Alignment explanation
Indices: 53737369--53737504 Score: 159
Period size: 49 Copynumber: 2.7 Consensus size: 50
53737359 CACCATTTGC
* * * * *
53737369 GGACAAGCCACCACTGATTTGCAAATAAACTGCCAATGATAATACTTTGT
1 GGACAAGCCACCACTGATTTGCAGATAAACTACCACTGATAACACTCTGT
* * * *
53737419 AGACAAGCCACCACTAATATGC-GTATATACTACCACTGA-AACACTCTGT
1 GGACAAGCCACCACTGATTTGCAG-ATAAACTACCACTGATAACACTCTGT
*
53737468 GGACAAGCCACCATTGATTTGCAGATAAACTACCACT
1 GGACAAGCCACCACTGATTTGCAGATAAACTACCACT
53737505 TACTTTGTAA
Statistics
Matches: 70, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
49 38 0.54
50 32 0.46
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (50 bp):
GGACAAGCCACCACTGATTTGCAGATAAACTACCACTGATAACACTCTGT
Found at i:53737539 original size:16 final size:16
Alignment explanation
Indices: 53737518--53737549 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53737508 TTTGTAACGC
*
53737518 CCCAAAAATCTCAAAA
1 CCCAAAAATCCCAAAA
53737534 CCCAAAAATCCCAAAA
1 CCCAAAAATCCCAAAA
53737550 TCCTGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.34, G:0.00, T:0.09
Consensus pattern (16 bp):
CCCAAAAATCCCAAAA
Found at i:53739002 original size:29 final size:29
Alignment explanation
Indices: 53738960--53739046 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 29
53738950 TGAATGTTAC
* *
53738960 TGGGCCTAACAGGCTATATAAATGTGATT
1 TGGGCCTAATAGGCCATATAAATGTGATT
* * *
53738989 TGGGGCTAATAGGCCATATACAGGTGATT
1 TGGGCCTAATAGGCCATATAAATGTGATT
* * *
53739018 TGGGCCTAATGGGCCATATGAATATGATT
1 TGGGCCTAATAGGCCATATAAATGTGATT
53739047 AGGCTTAGTG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (29 bp):
TGGGCCTAATAGGCCATATAAATGTGATT
Found at i:53749828 original size:30 final size:29
Alignment explanation
Indices: 53749789--53749846 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
53749779 AACGGAAGTT
* *
53749789 TTGGGACTAAGTGTGTGATTTAAACTAGCC
1 TTGGCACTAAGTGTGCGATTT-AACTAGCC
53749819 TTGGCACTAAGTGTGCGATTTAACTAGC
1 TTGGCACTAAGTGTGCGATTTAACTAGC
53749847 TCCGGCTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (29 bp):
TTGGCACTAAGTGTGCGATTTAACTAGCC
Found at i:53750210 original size:14 final size:15
Alignment explanation
Indices: 53750191--53750220 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53750181 GTTTATTATA
53750191 TGTG-AAGTATCATG
1 TGTGAAAGTATCATG
53750205 TGTGAAAGTATCATG
1 TGTGAAAGTATCATG
53750220 T
1 T
53750221 CTAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (15 bp):
TGTGAAAGTATCATG
Found at i:53752243 original size:41 final size:43
Alignment explanation
Indices: 53752152--53752247 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 43
53752142 CCGGGCTTCG
* * * *
53752152 AGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTCA
1 AGCCTAGCAGGCGATAATGCCAGTGAAATGATATCGGACTTAA
53752195 AGCCTAGCAGGCGA-AATGCCAGTG-AATGAGT-TCGGACTTAA
1 AGCCTAGCAGGCGATAATGCCAGTGAAATGA-TATCGGACTTAA
*
53752236 AGTCTAGCAGGC
1 AGCCTAGCAGGC
53752248 TTCGTGCTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
41 24 0.51
42 10 0.21
43 13 0.28
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (43 bp):
AGCCTAGCAGGCGATAATGCCAGTGAAATGATATCGGACTTAA
Found at i:53752301 original size:40 final size:41
Alignment explanation
Indices: 53752098--53752300 Score: 151
Period size: 40 Copynumber: 4.9 Consensus size: 41
53752088 AAATGTGATA
* * * * *
53752098 TCGGGCTTCAAGCCTAGCAAGCTTTAA-GCTGGTGAATAATAT
1 TCGGGCTTAAAGCCTAGCAGGC-TAAATGCCGGTGAATGA-AT
**
53752140 TACCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATG-AT
1 T--CGGGCTTAAAGCCTAGCAGGCTA-AATGCCGGTG-AATGAAT
* * * *
53752184 ATCGGGCTTCAAGCCTAGCAGGCGAAATGCCAGTGAATGAGT
1 -TCGGGCTTAAAGCCTAGCAGGCTAAATGCCGGTGAATGAAT
* * *** *
53752226 TCGGACTTAAAGTCTAGCAGGCTTCGTGCTGGTG-ATGAAT
1 TCGGGCTTAAAGCCTAGCAGGCTAAATGCCGGTGAATGAAT
* *
53752266 TCGGGTTTAAAACCTAGCAGGCTAAATGCCGGTGA
1 TCGGGCTTAAAGCCTAGCAGGCTAAATGCCGGTGA
53752301 TTTGATAAAA
Statistics
Matches: 126, Mismatches: 27, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
40 31 0.25
41 29 0.23
42 11 0.09
43 22 0.17
44 23 0.18
45 7 0.06
46 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (41 bp):
TCGGGCTTAAAGCCTAGCAGGCTAAATGCCGGTGAATGAAT
Found at i:53753462 original size:180 final size:180
Alignment explanation
Indices: 53753255--53753611 Score: 660
Period size: 180 Copynumber: 2.0 Consensus size: 180
53753245 AAATCTGCTA
53753255 TTGATTGGCCAAACCAAAAATTCTGAAAATTTTATGGATAGAAGATATTTGAGTCTATTTCCAGA
1 TTGATTGGCCAAACCAAAAATTCTGAAAATTTTATGGATAGAAGATATTTGAGTCTATTTCCAGA
* *
53753320 TAAAATTAACAGAAATTTATTTGGAGTTTAGTATCTCCAGTTATAAACAATTTAGTGACTGTTGC
66 TAAAATTAACAGAAATTTATTTGGAGTTTAGTAGCTCCAATTATAAACAATTTAGTGACTGTTGC
*
53753385 TCAGGAAGACAACTTGTAGTGAATTTGTGATTATGTTATAAACATTGGTC
131 TCAGGAAGACAACTTGTAGTGAATTTGTGATTATATTATAAACATTGGTC
* *
53753435 TTGATTGGCCAAACCAAAAATTCTGAAAATTTTATGGATATAAGATATTTGAGTCTATTTTCAGA
1 TTGATTGGCCAAACCAAAAATTCTGAAAATTTTATGGATAGAAGATATTTGAGTCTATTTCCAGA
*
53753500 TAAAATTAACGGAAATTTATTTGGAGTTTAGTAGCTCCAATTATAAACAATTTAGTGACTGTTGC
66 TAAAATTAACAGAAATTTATTTGGAGTTTAGTAGCTCCAATTATAAACAATTTAGTGACTGTTGC
53753565 TCAGGAAGACAACTTGTAGTGAATTTGTGATTATATTATAAACATTG
131 TCAGGAAGACAACTTGTAGTGAATTTGTGATTATATTATAAACATTG
53753612 ATTAAACTTG
Statistics
Matches: 171, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 171 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (180 bp):
TTGATTGGCCAAACCAAAAATTCTGAAAATTTTATGGATAGAAGATATTTGAGTCTATTTCCAGA
TAAAATTAACAGAAATTTATTTGGAGTTTAGTAGCTCCAATTATAAACAATTTAGTGACTGTTGC
TCAGGAAGACAACTTGTAGTGAATTTGTGATTATATTATAAACATTGGTC
Found at i:53756868 original size:29 final size:29
Alignment explanation
Indices: 53756836--53756907 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
53756826 CTAACAGGCT
**
53756836 ATATAAATGTGATTTGGGGCTAATGGGCC
1 ATATAAATGTGATTTGGACCTAATGGGCC
* *
53756865 ATATACAGGTGATTTGGACCTAATGGGCC
1 ATATAAATGTGATTTGGACCTAATGGGCC
* *
53756894 ATATGAATATGATT
1 ATATAAATGTGATT
53756908 GAGCTTAATG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (29 bp):
ATATAAATGTGATTTGGACCTAATGGGCC
Found at i:53763495 original size:12 final size:12
Alignment explanation
Indices: 53763474--53763503 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53763464 GTCAGGTTTT
*
53763474 ACACGACCTAGC
1 ACACGGCCTAGC
53763486 ACACGGCCTAGC
1 ACACGGCCTAGC
53763498 ACACGG
1 ACACGG
53763504 GTGTGTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.40, G:0.23, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:53765264 original size:259 final size:259
Alignment explanation
Indices: 53764808--53767114 Score: 4548
Period size: 259 Copynumber: 8.9 Consensus size: 259
53764798 CCATGGGCCT
53764808 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTA---TAACAATTTA
1 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
*
53764870 GTCCCTCATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
66 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
* *
53764935 CAAATTCATCATTTAACACAAAAAAATCATTAGACTCATTAATGGAATCATTAAAAATCTTTAAA
131 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
* *
53765000 ACTTTCAAAATCGAAGGTACGGACTAGCTAGACCTAGTCGCAAGAGTGAGTATTCATGGCAGAC
196 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
53765064 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
1 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
53765129 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
66 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
53765194 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
131 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
53765259 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
196 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
53765323 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
1 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
53765388 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
66 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
53765453 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
131 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
53765518 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
196 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
53765582 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
1 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
53765647 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
66 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
53765712 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
131 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
53765777 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
196 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
53765841 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
1 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
53765906 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
66 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
53765971 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
131 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
53766036 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
196 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
53766100 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
1 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
53766165 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
66 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
53766230 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
131 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
53766295 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
196 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
53766359 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
1 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
53766424 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
66 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
53766489 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
131 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
53766554 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
196 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
53766618 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
1 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
53766683 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
66 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
53766748 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
131 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
53766813 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
196 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
53766877 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
1 AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
53766942 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
66 GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
53767007 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
131 CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
53767072 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAA
196 ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAA
53767115 CGATCTCAAA
Statistics
Matches: 2043, Mismatches: 5, Indels: 3
1.00 0.00 0.00
Matches are distributed among these distances:
256 52 0.03
259 1991 0.97
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.32
Consensus pattern (259 bp):
AAAACAACCCACATTTGTAATAATTTCATATCCAATCCTTGTATTTTTACTACTTTAACAATTTA
GTCCCTAATCGATAAATTTATCAAAAATTACTTAACAAAATACATTTAAATAACAAATAATATTA
CAAATTCATCATTTAACATAAAAAAATCATTAGATTCATTAATGGAATCATTAAAAATCTTTAAA
ACTTTCAAAATCGAAGGTACGGGCTAGCTAGACCTAGTTGCAAGAGTGAGTATTCATGGCAGAC
Done.