Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 200 of 208
Found at i:61810626 original size:22 final size:22
Alignment explanation
Indices: 61810598--61810639 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
61810588 TTTATTTTGA
*
61810598 TATTATAAATGTATTGATTATT
1 TATTATAAATGTATTAATTATT
61810620 TATTATAAATGTATTAATTA
1 TATTATAAATGTATTAATTA
61810640 ATTCAGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
TATTATAAATGTATTAATTATT
Found at i:61810844 original size:233 final size:233
Alignment explanation
Indices: 61810437--61810867 Score: 731
Period size: 233 Copynumber: 1.8 Consensus size: 233
61810427 CATACAAGTT
* *
61810437 TTTGTGTTTTAATGCCATAAGTTAGCAATAATTTAATTTTATTCAATGGATTTGAGTTATATACA
1 TTTGTGTTTTAATGCCATAACTTAGCAATAAATTAATTTTATTCAATGGATTTGAGTTATATACA
* * * *
61810502 TTATTTTTTAGTTAAAGACTAGAATTTATTACTTATTTTTTATTTTTTTATTTTAAGTTTAGATT
66 TTATTTTTTAGTTAAAGACTAGAATTTATTACTTATTTTTAATTTTTTAAGTTTAAGTTTAAATT
* *
61810567 TGTATTAATTATTTTATTTTTTTTATTTTGATATTATAAATGTATTGATTATTTATTATAA-ATG
131 TATATTAATTATTTTA-TTTTTTTATTTTGATATTATAAATGTATTGATTATTTATTAAAATATG
61810631 TATTAATTAATTCAGTAATTATGACTATTTAATTGTGTA
195 TATTAATTAATTCAGTAATTATGACTATTTAATTGTGTA
61810670 TTTGTGTTTTAATGCCATAACTTAGCAATAAATTAATTTTATTCAATGGATTTGAGTTATATACA
1 TTTGTGTTTTAATGCCATAACTTAGCAATAAATTAATTTTATTCAATGGATTTGAGTTATATACA
* *
61810735 TTATTTTTTTGTTCAAGACTAGAATTTATTACTTATTTATTAATATTTTTAAGTTTAAGTTTAAA
66 TTATTTTTTAGTTAAAGACTAGAATTTATTACTTATTT-TTAAT-TTTTTAAGTTTAAGTTTAAA
61810800 TTTATATTAATTATTTTA-TTTTTTATTTTGATATTATAAATGTATTGATTATTTATTAAAATAT
129 TTTATATTAATTATTTTATTTTTTTATTTTGATATTATAAATGTATTGATTATTTATTAAAATAT
61810864 GTAT
194 GTAT
61810868 CTTCAAAATT
Statistics
Matches: 185, Mismatches: 10, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
233 141 0.76
234 10 0.05
235 34 0.18
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.54
Consensus pattern (233 bp):
TTTGTGTTTTAATGCCATAACTTAGCAATAAATTAATTTTATTCAATGGATTTGAGTTATATACA
TTATTTTTTAGTTAAAGACTAGAATTTATTACTTATTTTTAATTTTTTAAGTTTAAGTTTAAATT
TATATTAATTATTTTATTTTTTTATTTTGATATTATAAATGTATTGATTATTTATTAAAATATGT
ATTAATTAATTCAGTAATTATGACTATTTAATTGTGTA
Found at i:61812115 original size:14 final size:14
Alignment explanation
Indices: 61812092--61812138 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
61812082 TTTTCTAAAT
61812092 ATTT-ATATTTTTA
1 ATTTAATATTTTTA
*
61812105 ATTTAATATTTATA
1 ATTTAATATTTTTA
*
61812119 ATTTTATATATTTTTT
1 A-TTTA-ATATTTTTA
61812135 ATTT
1 ATTT
61812139 CTTGAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 4 0.14
14 9 0.32
15 7 0.25
16 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTAATATTTTTA
Found at i:61812447 original size:8 final size:8
Alignment explanation
Indices: 61812434--61812464 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
61812424 TATATTTTTT
61812434 AAAATTTC
1 AAAATTTC
*
61812442 AAAATTTT
1 AAAATTTC
61812450 AAAATTTC
1 AAAATTTC
61812458 AAAATTT
1 AAAATTT
61812465 TAAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (8 bp):
AAAATTTC
Found at i:61812451 original size:16 final size:16
Alignment explanation
Indices: 61812430--61812468 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
61812420 ATTATATATT
61812430 TTTTAAAATTTCAAAA
1 TTTTAAAATTTCAAAA
61812446 TTTTAAAATTTCAAAA
1 TTTTAAAATTTCAAAA
61812462 TTTTAAA
1 TTTTAAA
61812469 TTAATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTTAAAATTTCAAAA
Found at i:61814648 original size:50 final size:50
Alignment explanation
Indices: 61814467--61814704 Score: 196
Period size: 49 Copynumber: 4.7 Consensus size: 50
61814457 AAAGAGATCT
* * *
61814467 CATGTAAGACCATGTCTGAGACATGACATTGGCATCATTGAGATTATGAGAAGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C---CA-A-TATGAGAAGTCC
* * * *
61814523 TATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAAGTCC
* * * *
61814573 C-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAAGTCC
* * * ** *
61814622 CATATAAGACCATATCTGGGATATGGCATTGGCAGTACA-A-GA-AACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-ATATGAGAA-GTCC
* * *
61814671 TATGTAAGACCATGTCTGGGGCATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
61814705 TGTTATTATC
Statistics
Matches: 149, Mismatches: 30, Indels: 13
0.78 0.16 0.07
Matches are distributed among these distances:
48 2 0.01
49 75 0.50
50 38 0.26
51 2 0.01
52 1 0.01
55 1 0.01
56 30 0.20
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAAGTCC
Found at i:61825266 original size:212 final size:212
Alignment explanation
Indices: 61824899--61825285 Score: 641
Period size: 212 Copynumber: 1.8 Consensus size: 212
61824889 TTGAAATAAT
* *
61824899 TAAATATATTGATATCTATGCTTGAGTATCGATAAAATGTTTAGATTCAAAATTTGACAAAATGT
1 TAAATATATTGATATCTATGCTTGAGTATCGATAAAATGTTCAGATTCAAAATATGACAAAATGT
*
61824964 TGATAATCATAACCTATTTATATGGTTTATTTTTTGAGAAATTGATTACCTTTGAGATATGAAAC
66 TGATAATCATAACCTATTTATATGGTTTATTTTTTGAGAAATTGATTACATTTGAGATATGAAAC
* *
61825029 TAAAAAATTTATAATTATATAATTTAATATTTTGAAAATGGAGTGTGTCGAAATCACTTTTTACA
131 TAAAAAATTTACAATTATATAATTTAATATTTCGAAAATGGAGTGTGTCGAAATCACTTTTTACA
61825094 ATTATCGATACTCGGGA
196 ATTATCGATACTCGGGA
* * * *
61825111 TAAATATATTGATA-CTTATGCTTGAGTATCGGTAAAATGTTCGGATTTAAGATATGACAAAATG
1 TAAATATATTGATATC-TATGCTTGAGTATCGATAAAATGTTCAGATTCAAAATATGACAAAATG
* * *
61825175 TTGATAATCATAACCTATTTATATGGTTTATTTTTTTAGGAATTGATTACATTTGAGATCTGAAA
65 TTGATAATCATAACCTATTTATATGGTTTATTTTTTGAGAAATTGATTACATTTGAGATATGAAA
*
61825240 CTAAAAATTTTACAATTATATAATTTAATATTTCGAAAATGGAGTG
130 CTAAAAAATTTACAATTATATAATTTAATATTTCGAAAATGGAGTG
61825286 ATAATCATAA
Statistics
Matches: 161, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
211 1 0.01
212 160 0.99
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.40
Consensus pattern (212 bp):
TAAATATATTGATATCTATGCTTGAGTATCGATAAAATGTTCAGATTCAAAATATGACAAAATGT
TGATAATCATAACCTATTTATATGGTTTATTTTTTGAGAAATTGATTACATTTGAGATATGAAAC
TAAAAAATTTACAATTATATAATTTAATATTTCGAAAATGGAGTGTGTCGAAATCACTTTTTACA
ATTATCGATACTCGGGA
Found at i:61826059 original size:20 final size:21
Alignment explanation
Indices: 61826022--61826061 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61826012 GTTGACCTAC
61826022 TAAATTAAATAGTATTTATTA
1 TAAATTAAATAGTATTTATTA
*
61826043 TAAATTAATTA-TATTTATT
1 TAAATTAAATAGTATTTATT
61826062 TTATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TAAATTAAATAGTATTTATTA
Found at i:61829442 original size:23 final size:23
Alignment explanation
Indices: 61829412--61829457 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
61829402 AATGCAAGAA
* *
61829412 GAGACCAGCAGCAGTTCAGCATG
1 GAGACCAGCAGCAGCTCAACATG
61829435 GAGACCAGCAGCAGCTCAACATG
1 GAGACCAGCAGCAGCTCAACATG
61829458 AAGATAAGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.11
Consensus pattern (23 bp):
GAGACCAGCAGCAGCTCAACATG
Found at i:61829656 original size:15 final size:15
Alignment explanation
Indices: 61829632--61829662 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
61829622 CTATCATCTT
*
61829632 TAACTGCTAACAGAC
1 TAACTACTAACAGAC
61829647 TAACTACTAACAGAC
1 TAACTACTAACAGAC
61829662 T
1 T
61829663 TGCAACGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.23
Consensus pattern (15 bp):
TAACTACTAACAGAC
Found at i:61829696 original size:20 final size:20
Alignment explanation
Indices: 61829671--61829712 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
61829661 CTTGCAACGG
*
61829671 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
*
61829691 TACAACTGCTTTGACTATAT
1 TACAACGGCTTTGACTATAT
61829711 TA
1 TA
61829713 ACTCTAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Found at i:61834865 original size:21 final size:21
Alignment explanation
Indices: 61834839--61834882 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
61834829 GTGACAAAGA
61834839 ATGGATGAATCTGTAGAAGCC
1 ATGGATGAATCTGTAGAAGCC
61834860 ATGGATGAATCTGTAGAAGCC
1 ATGGATGAATCTGTAGAAGCC
61834881 AT
1 AT
61834883 TGTAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (21 bp):
ATGGATGAATCTGTAGAAGCC
Found at i:61837833 original size:18 final size:18
Alignment explanation
Indices: 61837800--61837834 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61837790 ACCAGCAGAT
* *
61837800 GGCATACTGACTTGTTGG
1 GGCATACTAACCTGTTGG
61837818 GGCATACTAACCTGTTG
1 GGCATACTAACCTGTTG
61837835 TGGAGAGCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (18 bp):
GGCATACTAACCTGTTGG
Found at i:61843878 original size:15 final size:15
Alignment explanation
Indices: 61843854--61843884 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
61843844 CTATCATCTT
*
61843854 TAACTGCTAACAGAC
1 TAACTACTAACAGAC
61843869 TAACTACTAACAGAC
1 TAACTACTAACAGAC
61843884 T
1 T
61843885 TGCAACGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.23
Consensus pattern (15 bp):
TAACTACTAACAGAC
Found at i:61846770 original size:23 final size:23
Alignment explanation
Indices: 61846744--61846787 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
61846734 AAGAATAGTG
*
61846744 AAGATACTTGAAGATGAAAGGTT
1 AAGAGACTTGAAGATGAAAGGTT
* *
61846767 AAGAGGCTTGAATATGAAAGG
1 AAGAGACTTGAAGATGAAAGG
61846788 ATACACACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.30, T:0.23
Consensus pattern (23 bp):
AAGAGACTTGAAGATGAAAGGTT
Found at i:61850446 original size:23 final size:23
Alignment explanation
Indices: 61850418--61850481 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
61850408 AAGTTAGAAA
61850418 AGACTTGAATATGAATA-GTGAAG
1 AGACTTGAATATGAA-AGGTGAAG
* *
61850441 AGACTTGAAAATGAAAGGTTAAG
1 AGACTTGAATATGAAAGGTGAAG
*
61850464 AGGCTTGAATATGAAAGG
1 AGACTTGAATATGAAAGG
61850482 ATACACACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.44, C:0.05, G:0.28, T:0.23
Consensus pattern (23 bp):
AGACTTGAATATGAAAGGTGAAG
Found at i:61850876 original size:31 final size:31
Alignment explanation
Indices: 61850841--61850904 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
61850831 TCGGCATCTA
61850841 GGCATTTTTTGTATCAATTCTTTTCCAAAAT
1 GGCATTTTTTGTATCAATTCTTTTCCAAAAT
61850872 GGCATTTTTTGTATCAATTCTTTTCCAAAAT
1 GGCATTTTTTGTATCAATTCTTTTCCAAAAT
61850903 GG
1 GG
61850905 TTGAATGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (31 bp):
GGCATTTTTTGTATCAATTCTTTTCCAAAAT
Found at i:61851452 original size:76 final size:76
Alignment explanation
Indices: 61851363--61851515 Score: 261
Period size: 76 Copynumber: 2.0 Consensus size: 76
61851353 ATCCACCACA
* * * *
61851363 ATCAATTGTTTTATGGCTTTGAACCATTAGCTCTTGTGATAATTTAATGTTCATATCATGGGCAA
1 ATCAATTGCTTTATGGCTTTGAACCATTAGCTCTTGCGATAACTTAATGTTCATATCAGGGGCAA
61851428 AAATTATCCAT
66 AAATTATCCAT
*
61851439 ATCAATTGCTTTATGGCTTTTAACCATTAGCTCTTGCGATAACTTAATGTTCATATCAGGGGCAA
1 ATCAATTGCTTTATGGCTTTGAACCATTAGCTCTTGCGATAACTTAATGTTCATATCAGGGGCAA
61851504 AAATTATCCAT
66 AAATTATCCAT
61851515 A
1 A
61851516 ATGGTCTCTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (76 bp):
ATCAATTGCTTTATGGCTTTGAACCATTAGCTCTTGCGATAACTTAATGTTCATATCAGGGGCAA
AAATTATCCAT
Found at i:61856746 original size:18 final size:19
Alignment explanation
Indices: 61856713--61856750 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
61856703 AGACTCCAGG
*
61856713 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
61856732 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
61856750 T
1 T
61856751 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:61867858 original size:14 final size:13
Alignment explanation
Indices: 61867835--61867883 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 13
61867825 TTTTTTAAAT
*
61867835 ATTTATATTTTTA
1 ATTTATATTTATA
61867848 ATTTAATATTTATA
1 ATTT-ATATTTATA
61867862 ATTT-TA--TATA
1 ATTTATATTTATA
*
61867872 ATTTTTATTTAT
1 ATTTATATTTAT
61867884 TGAAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
10 8 0.26
11 2 0.06
12 2 0.06
13 7 0.23
14 12 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTATATTTATA
Found at i:61867878 original size:19 final size:20
Alignment explanation
Indices: 61867832--61867879 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
61867822 CTTTTTTTTA
* *
61867832 AATATTTATATTTTTAATTT
1 AATATTTATAATTTTAATAT
61867852 AATATTTATAATTTT-ATAT
1 AATATTTATAATTTTAATAT
*
61867871 AATTTTTAT
1 AATATTTAT
61867880 TTATTGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATATTTATAATTTTAATAT
Found at i:61868682 original size:40 final size:40
Alignment explanation
Indices: 61868638--61868719 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
61868628 GAAGCAAGAT
61868638 AACCAATTATCATATATGCTCTATATTCAATATTTAAAAA
1 AACCAATTATCATATATGCTCTATATTCAATATTTAAAAA
61868678 AACCAATTATCATATATGCTCTATATTCAATATTTAAAAA
1 AACCAATTATCATATATGCTCTATATTCAATATTTAAAAA
61868718 AA
1 AA
61868720 TCCGCTCTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (40 bp):
AACCAATTATCATATATGCTCTATATTCAATATTTAAAAA
Found at i:61870098 original size:25 final size:26
Alignment explanation
Indices: 61870049--61870098 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
61870039 AATAGGAAGA
*
61870049 AAAGAAAGAAATAAAATTGAAATAGG
1 AAAGAAAGAAATAAAAGTGAAATAGG
61870075 AAAGAAA-AAA-AGAAAGTGAAATAG
1 AAAGAAAGAAATA-AAAGTGAAATAG
61870099 AAAAATAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 14 0.64
26 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (26 bp):
AAAGAAAGAAATAAAAGTGAAATAGG
Found at i:61870112 original size:31 final size:30
Alignment explanation
Indices: 61870039--61870101 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
61870029 AGAGGAAAAG
*
61870039 AATAGGAAGAAAAGAAAGAAATAAAATTGA
1 AATAGGAAGAAAAGAAAGAAATAAAATAGA
*
61870069 AATAGGAAAGAAAA-AAAGAAAGTGAAATAGA
1 AATAGG-AAGAAAAGAAAGAAA-TAAAATAGA
61870100 AA
1 AA
61870102 AATAGGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (30 bp):
AATAGGAAGAAAAGAAAGAAATAAAATAGA
Found at i:61877445 original size:28 final size:28
Alignment explanation
Indices: 61877412--61877471 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 28
61877402 CGTATAGATC
61877412 ATAAAAAATAATTACA-TATATAAAAAA
1 ATAAAAAATAATTACATTATATAAAAAA
*
61877439 ATAAAAAATAATTACATTATATTAAAAA
1 ATAAAAAATAATTACATTATATAAAAAA
61877467 ATAAA
1 ATAAA
61877472 TATGCGTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (28 bp):
ATAAAAAATAATTACATTATATAAAAAA
Found at i:61882637 original size:18 final size:20
Alignment explanation
Indices: 61882593--61882637 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
61882583 TAGTAATAAA
61882593 TTAATTTTATTCAATATTAC
1 TTAATTTTATTCAATATTAC
*
61882613 TT-A-TTTATT-AATATT-T
1 TTAATTTTATTCAATATTAC
61882629 TTAATTTTA
1 TTAATTTTA
61882638 AGTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 2 0.09
17 7 0.32
18 10 0.45
19 1 0.05
20 2 0.09
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATTTTATTCAATATTAC
Found at i:61891932 original size:103 final size:104
Alignment explanation
Indices: 61891752--61892016 Score: 408
Period size: 103 Copynumber: 2.6 Consensus size: 104
61891742 AACCGTTATT
* * * *
61891752 AGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 AGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
61891817 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
61891855 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 AGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
61891919 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
61891959 AGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 AGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
61892017 TTATGTACAA
Statistics
Matches: 147, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
102 1 0.01
103 81 0.55
104 64 0.44
105 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (104 bp):
AGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:61897572 original size:12 final size:12
Alignment explanation
Indices: 61897555--61897580 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61897545 GAAGAAAACT
61897555 ATTTGGATTTTG
1 ATTTGGATTTTG
61897567 ATTTGGATTTTG
1 ATTTGGATTTTG
61897579 AT
1 AT
61897581 CTGTTGATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (12 bp):
ATTTGGATTTTG
Found at i:61897818 original size:383 final size:385
Alignment explanation
Indices: 61897109--61897860 Score: 1355
Period size: 383 Copynumber: 2.0 Consensus size: 385
61897099 AGAAGAACAT
* * * *
61897109 AGCTTAGATTCAAGTTGATTTGACAGTCAATGTCGGAGCTCAGATATCTAAGAAGAAAACTATTT
1 AGCTTAGATCCAAGTTGATTTGACAGTCAATGTCGAAGCTCAAATATCGAAGAAGAAAACTATTT
* **
61897174 GGATTTTGATTTAGATTTTGATCTGTTGATTCGTGATGTTTCAAGCTACTTAATGGAAAAAAATT
66 GGATTTTGATTTAGATTTTGATCTGTTGATTCGTGATGTTTAAAGCTACTTAATGGAAAAAAAAA
* *
61897239 TTGAACTGTAGAAGAGTAATTTAATGATTTTTTATGTAAATTGTTTATTTTTATTTATTTATTGT
131 TTGAACTGTAGAAGAGTAATTTAATGATTTTATATGTAAATTGTTTATTTTTAGTTATTTATTGT
61897304 GAAATTATATATTTCTATAATCAAGCAATTTGTGCATATTAGTATTTATAATTAATTATTATAGT
196 GAAATTATATATTTCTATAATCAAGCAATTTGTGCATATTAGTATTTATAATTAATTATTATAGT
61897369 TGGTCAATAAATTTTGAATGAATCCTATATATCATAAACATCAATCAAATTATTATTTTTGCATG
261 TGGTCAATAAATTTTGAATGAATCCTATATATCATAAACATCAATCAAATTATTATTTTTGCATG
61897434 TATCATTATGATATATCAAAATTTTTATTTCAAATTAATTATTTACAAGCCCATTTTGAC
326 TATCATTATGATATATCAAAATTTTTATTTCAAATTAATTATTTACAAGCCCATTTTGAC
*
61897494 AGCTTAGATCCAAGTTGATTTGACAGTCAATGTTGAAGCTCAAATATCGAAGAAGAAAACTATTT
1 AGCTTAGATCCAAGTTGATTTGACAGTCAATGTCGAAGCTCAAATATCGAAGAAGAAAACTATTT
*
61897559 GGATTTTGATTTGGATTTTGATCTGTTGATTCGTGATGTTTAAAGCTACTTAAT-GAAAAAAAAA
66 GGATTTTGATTTAGATTTTGATCTGTTGATTCGTGATGTTTAAAGCTACTTAATGGAAAAAAAAA
*
61897623 TTGAATTGTAGAAGAGTAATTTAATGATTTTATATGTAAATTGTTTATTTTT-GTTATTTATTGT
131 TTGAACTGTAGAAGAGTAATTTAATGATTTTATATGTAAATTGTTTATTTTTAGTTATTTATTGT
*
61897687 GAAATTATATATTTCTATAATCAAGCAATTTGTGCATATTATTATTTATAATTAATTATTATAGT
196 GAAATTATATATTTCTATAATCAAGCAATTTGTGCATATTAGTATTTATAATTAATTATTATAGT
*
61897752 TGGTCAATAAATTTTGAATGAATCCTTTATATCATAAACATCAATCAAATTATTATTTTTGCATG
261 TGGTCAATAAATTTTGAATGAATCCTATATATCATAAACATCAATCAAATTATTATTTTTGCATG
*
61897817 TATCATTATGATATATCAATATTTTTATTTCAAATTAATTATTT
326 TATCATTATGATATATCAAAATTTTTATTTCAAATTAATTATTT
61897861 GAATATAAAA
Statistics
Matches: 352, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
383 182 0.52
384 58 0.16
385 112 0.32
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (385 bp):
AGCTTAGATCCAAGTTGATTTGACAGTCAATGTCGAAGCTCAAATATCGAAGAAGAAAACTATTT
GGATTTTGATTTAGATTTTGATCTGTTGATTCGTGATGTTTAAAGCTACTTAATGGAAAAAAAAA
TTGAACTGTAGAAGAGTAATTTAATGATTTTATATGTAAATTGTTTATTTTTAGTTATTTATTGT
GAAATTATATATTTCTATAATCAAGCAATTTGTGCATATTAGTATTTATAATTAATTATTATAGT
TGGTCAATAAATTTTGAATGAATCCTATATATCATAAACATCAATCAAATTATTATTTTTGCATG
TATCATTATGATATATCAAAATTTTTATTTCAAATTAATTATTTACAAGCCCATTTTGAC
Found at i:61898756 original size:8 final size:8
Alignment explanation
Indices: 61898743--61898767 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
61898733 ATTATATATT
61898743 TTTTAAAA
1 TTTTAAAA
61898751 TTTTAAAA
1 TTTTAAAA
61898759 TTTTAAAA
1 TTTTAAAA
61898767 T
1 T
61898768 AATTAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:61909911 original size:12 final size:12
Alignment explanation
Indices: 61909894--61909919 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61909884 CAAAACAGGC
61909894 TTTTAGCGGCGT
1 TTTTAGCGGCGT
61909906 TTTTAGCGGCGT
1 TTTTAGCGGCGT
61909918 TT
1 TT
61909920 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:61910289 original size:114 final size:114
Alignment explanation
Indices: 61909988--61910354 Score: 533
Period size: 114 Copynumber: 3.2 Consensus size: 114
61909978 AAAAGAAGCA
* * * * *
61909988 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGTCGTTTCTCGAGCTT
1 TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTT
* *
61910052 TCGGGGATTTAGAGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * *
61910101 TTAACGGCATTTTTGGG-AAGCGCCGCAAAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCTT
1 TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTT
* *
61910165 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCGGGGTT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
61910214 TTAGCGGCATTTTGGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTAAGCTT
1 TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTT
* *
61910279 TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGC-CTAGGACT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTC-AGGGCT
* * *
61910328 TTAGTGGCGTTTTTGGTAAAGCGCCGC
1 TTAGCGGCATTTTTGGGAAAGCGCCGC
61910355 TAATGCCCAG
Statistics
Matches: 226, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
112 9 0.04
113 107 0.47
114 110 0.49
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (114 bp):
TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:61910350 original size:41 final size:41
Alignment explanation
Indices: 61910305--61910395 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
61910295 GTTTTTAAGG
* * * *
61910305 AAGCGCCGCTAATGCCTAGGACTTTAGTGGCGTTTTTGGTA
1 AAGCGCCGCTAATGCCCAGGACTTTAGCGGCATTTTTGGAA
*
61910346 AAGCGCCGCTAATGCCCAGGGCTTTAGCGGCATTTTTGGAA
1 AAGCGCCGCTAATGCCCAGGACTTTAGCGGCATTTTTGGAA
61910387 AAGCGCCGC
1 AAGCGCCGC
61910396 AAAAAAACCT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.25
Consensus pattern (41 bp):
AAGCGCCGCTAATGCCCAGGACTTTAGCGGCATTTTTGGAA
Found at i:61910454 original size:155 final size:155
Alignment explanation
Indices: 61910172--61910471 Score: 453
Period size: 155 Copynumber: 1.9 Consensus size: 155
61910162 CTTTCGGGGA
* * * *
61910172 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCATTTTGGGGAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCATTTTGGGAAAAGCG
*
61910237 CCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTAAGCTTTCGGGGATTTAGCGGCG-TTTTT
66 CCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTT
61910301 -AAGGAAGCGCCGCTAATGCCTAGGAC
131 GAA--AAGCGCCGCTAATGCCTAGGAC
* * *
61910327 TTTAGTGGCGTTTTT-GGTAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCATTTTTGGAAAAGC
1 TTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCATTTTGGGAAAAGC
* * *
61910391 GCCGCAAAAAAACCTAAGCTCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTTGCGGCGTTTTT
65 GCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTT
61910456 TGAAAAGCGCCGCTAA
130 TGAAAAGCGCCGCTAA
61910472 ATTTTTTTTA
Statistics
Matches: 131, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
154 1 0.01
155 123 0.94
156 5 0.04
157 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (155 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCATTTTGGGAAAAGCG
CCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTT
GAAAAGCGCCGCTAATGCCTAGGAC
Found at i:61910755 original size:14 final size:14
Alignment explanation
Indices: 61910714--61910755 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
61910704 AGTTCATATT
61910714 TTATGGTTTAGGGA
1 TTATGGTTTAGGGA
*
61910728 GTATGGGTTTAGGGA
1 TTAT-GGTTTAGGGA
*
61910743 TTATGGATTAGGG
1 TTATGGTTTAGGG
61910756 GTTAGAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.38
Consensus pattern (14 bp):
TTATGGTTTAGGGA
Found at i:61911042 original size:7 final size:7
Alignment explanation
Indices: 61911032--61911080 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
61911022 GATTTAAGGT
61911032 TTAGGGG
1 TTAGGGG
61911039 TTAGGGG
1 TTAGGGG
61911046 TTTAGGGG
1 -TTAGGGG
**
61911054 TTAGATG
1 TTAGGGG
61911061 TTAGGGG
1 TTAGGGG
* *
61911068 TTAAGAG
1 TTAGGGG
61911075 TTAGGG
1 TTAGGG
61911081 ATTTAAGGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:61911049 original size:15 final size:15
Alignment explanation
Indices: 61911028--61911095 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
61911018 TTGAGATTTA
61911028 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
61911043 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
61911058 ATG-TTAGGGGTTA-
1 AGGTTTAGGGGTTAG
*
61911071 AGAG-TTAGGGATTTA-
1 AG-GTTTAGGG-GTTAG
61911086 AGGTTTAGGG
1 AGGTTTAGGG
61911096 ATTCAGGGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.02
14 18 0.40
15 26 0.58
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:61911049 original size:36 final size:36
Alignment explanation
Indices: 61911008--61911093 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
61910998 TAGGGATTAT
* * *
61911008 GGTTTAAGGGTTGAGAT-TTAAGGTTTAGGGGTTAGG
1 GGTTTAAGGGTT-AGATGTTAAGGGTTAAGAGTTAGG
* *
61911044 GGTTTAGGGGTTAGATGTTAGGGGTTAAGAGTTAGG
1 GGTTTAAGGGTTAGATGTTAAGGGTTAAGAGTTAGG
* *
61911080 GATTTAAGGTTTAG
1 GGTTTAAGGGTTAG
61911094 GGATTCAGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 4 0.10
36 37 0.90
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (36 bp):
GGTTTAAGGGTTAGATGTTAAGGGTTAAGAGTTAGG
Found at i:61911857 original size:145 final size:146
Alignment explanation
Indices: 61911581--61912195 Score: 1048
Period size: 146 Copynumber: 4.2 Consensus size: 146
61911571 TGAAATAGCT
* *
61911581 TAAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAATTTTATAATAGCAAAACGG
1 TAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTATAATAGCAAAACGG
* * *
61911646 CGCCGTTTTGTTCAAAATGAAAAAAAATTGCGGCGCATTATAAGAAGCGCCGCTAAAGGTAAGCA
66 CGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCA
61911711 ATAGCGGCGTTTT-TA
131 ATAGCGGCGTTTTCTA
61911726 TAGAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTATAATAGCAAAACG
1 TA-AAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTATAATAGCAAAACG
61911791 GCGTCGTTTTGTTCAAAATG-AAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGC
65 GCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGC
61911855 AATAGCGGCGTTTT-TA
130 AATAGCGGCGTTTTCTA
* *
61911871 TAGAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAAC
1 TA-AAAACGCCGCAAAAAATAAATCAATTTAT-AAAAAAATAAAAAAAATTTATAATAGCAAAAC
*
61911936 GGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAG
64 GGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAG
61912001 CAATAGCGGCGTTTTCTA
129 CAATAGCGGCGTTTTCTA
*
61912019 TAAAAACGCCGCAAAAAATAAATCAATTTAT-AAAAAATAAAAAAAA-TTATAATAGCAAAACAG
1 TAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTATAATAGCAAAACGG
* *
61912082 CGTCGTTTTGTTCAAAATGAAAAAAATTTACGACGC-TTAT-A-AAGCGCCGCTAAAGGTAAGCA
66 CGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCA
61912144 ATAGCGGCGTTTTCTA
131 ATAGCGGCGTTTTCTA
61912160 TAAAAACGCCGCAAAAAATAAATCAATTTATAAAAA
1 TAAAAACGCCGCAAAAAATAAATCAATTTATAAAAA
61912196 TTTCCCAAAA
Statistics
Matches: 451, Mismatches: 14, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
141 68 0.15
142 5 0.01
143 4 0.01
144 48 0.11
145 106 0.24
146 130 0.29
147 86 0.19
148 4 0.01
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (146 bp):
TAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTATAATAGCAAAACGG
CGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCA
ATAGCGGCGTTTTCTA
Found at i:61912068 original size:19 final size:19
Alignment explanation
Indices: 61912031--61912070 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
61912021 AAAACGCCGC
** *
61912031 AAAAAATAAATCAATTTAT
1 AAAAAATAAAAAAAATTAT
61912050 AAAAAATAAAAAAAATTAT
1 AAAAAATAAAAAAAATTAT
61912069 AA
1 AA
61912071 TAGCAAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAAATAAAAAAAATTAT
Found at i:61914314 original size:25 final size:26
Alignment explanation
Indices: 61914266--61914314 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
61914256 TTTCAGTTTG
*
61914266 ATTATTTTTAGTTTTATATTTTTAGT
1 ATTATTTTTAGTTTTATATATTTAGT
61914292 ATTA-TTTTAGTTTCTATA-ATTTA
1 ATTATTTTTAGTTT-TATATATTTA
61914315 ACATATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (26 bp):
ATTATTTTTAGTTTTATATATTTAGT
Found at i:61916003 original size:43 final size:42
Alignment explanation
Indices: 61915954--61916092 Score: 154
Period size: 43 Copynumber: 3.2 Consensus size: 42
61915944 CATAAATGCT
*
61915954 GCTAAAGAATCGTACTTTTAGTGGCGTTTGTAATAAAAGCGCC
1 GCTAAAG-ATCGTACTTTTAGTGGCGTTTGTGATAAAAGCGCC
* * * * *
61915997 GCTAAAGATCATGCTCTTTAGCGGTGTTTGTGATGAAAGCGCC
1 GCTAAAGATCGTACT-TTTAGTGGCGTTTGTGATAAAAGCGCC
* * *
61916040 ACTAAAGATCATGTTC-TTTAGTGGCGTTTGTGATAAAAGCGCT
1 GCTAAAGATC--GTACTTTTAGTGGCGTTTGTGATAAAAGCGCC
61916083 GCTAAAGATC
1 GCTAAAGATC
61916093 ATGTTCTTTA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
42 6 0.08
43 71 0.90
45 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (42 bp):
GCTAAAGATCGTACTTTTAGTGGCGTTTGTGATAAAAGCGCC
Found at i:61916093 original size:43 final size:43
Alignment explanation
Indices: 61915970--61916151 Score: 222
Period size: 43 Copynumber: 4.2 Consensus size: 43
61915960 GAATCGTACT
* * *
61915970 TTTAGTGGCGTTTGTAATAAAAGCGCCGCTAAAGATCATGCTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
* * *
61916013 TTTAGCGGTGTTTGTGATGAAAGCGCCACTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
* *
61916056 TTTAGTGGCGTTTGTGATAAAAGCGCTGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
* ** * **
61916099 TTTAGCGGCGTTT-TGTTTTTAAGCGCCGCTAAAGAACATGACC
1 TTTAGCGGCGTTTGTG-ATAAAAGCGCCGCTAAAGATCATGTTC
61916142 TTTAGCGGCG
1 TTTAGCGGCG
61916152 CTTATTTCTG
Statistics
Matches: 119, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
42 2 0.02
43 117 0.98
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
Found at i:61936599 original size:13 final size:13
Alignment explanation
Indices: 61936566--61936607 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
61936556 TATTTTTCTA
61936566 AATATATTTATTTT
1 AATAT-TTTATTTT
*
61936580 -TTATTTTATTTT
1 AATATTTTATTTT
61936592 AATATTTTATATTT
1 AATATTTTAT-TTT
61936606 AA
1 AA
61936608 AAATTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 8 0.33
13 11 0.46
14 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
AATATTTTATTTT
Found at i:61936709 original size:15 final size:15
Alignment explanation
Indices: 61936689--61936717 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
61936679 AAGTAGTATT
61936689 ATATATTTAGTATAG
1 ATATATTTAGTATAG
61936704 ATATATTTAGTATA
1 ATATATTTAGTATA
61936718 TCTCATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
ATATATTTAGTATAG
Found at i:61941821 original size:15 final size:15
Alignment explanation
Indices: 61941803--61941852 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
61941793 CTACAAAACT
61941803 TTTATTATTAATATA
1 TTTATTATTAATATA
*
61941818 TTTATAATTGAATAAATA
1 TTTATTATT-AAT--ATA
*
61941836 TTTATTATTAAAATA
1 TTTATTATTAATATA
61941851 TT
1 TT
61941853 AGTATTGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 13 0.45
16 3 0.10
17 2 0.07
18 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTATTATTAATATA
Found at i:61941910 original size:15 final size:16
Alignment explanation
Indices: 61941890--61941920 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61941880 AAGAATACAA
61941890 TTTAAAA-TTATTATT
1 TTTAAAATTTATTATT
61941905 TTTAAAATTTATTATT
1 TTTAAAATTTATTATT
61941921 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTTATTATT
Found at i:61946521 original size:16 final size:17
Alignment explanation
Indices: 61946483--61946524 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
61946473 ACAAACTTGA
61946483 TTATTATA-ATGAAATG
1 TTATTATAGATGAAATG
* *
61946499 TTGTTATAGATGATA-G
1 TTATTATAGATGAAATG
61946515 TTATTATAGA
1 TTATTATAGA
61946525 GATGGCTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (17 bp):
TTATTATAGATGAAATG
Found at i:61947847 original size:6 final size:6
Alignment explanation
Indices: 61947832--61947889 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
61947822 GAGTAGGATC
* * * * * *
61947832 TGTATA TGTATT TGTATC TGTATC TATATC TGCATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
61947880 TGTATA TGTA
1 TGTATA TGTA
61947890 ATTGCACCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:61950455 original size:29 final size:29
Alignment explanation
Indices: 61950419--61950495 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
61950409 TAAAAAATGA
61950419 ATAGTTGGGTGACCATTTTTCAACTTTTC
1 ATAGTTGGGTGACCATTTTTCAACTTTTC
* *
61950448 ATAGTTGGGCGACCAATTTTCAACTTTTC
1 ATAGTTGGGTGACCATTTTTCAACTTTTC
*
61950477 ATAGTTGGATGACCATTTT
1 ATAGTTGGGTGACCATTTT
61950496 GTAGTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (29 bp):
ATAGTTGGGTGACCATTTTTCAACTTTTC
Found at i:61951591 original size:274 final size:273
Alignment explanation
Indices: 61950956--61951581 Score: 769
Period size: 274 Copynumber: 2.3 Consensus size: 273
61950946 CCACTAAACC
** *
61950956 AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATAT-TCACAATTCGTTATATTCATC
1 AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATATGT-ACAATTTATTATCTTCATC
* * * ** *
61951020 AGTTGTATATCTATACTTACTATTTATTAAGCCCCTGACTGAGTTGGTGTCACCCTCAACCGGGT
65 AATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTGTCACCCTCAACCGAGT
* * * *
61951085 CACCAACTTGATCAAGAAATTATAAAAATGTTCTTTCATAATTAAAAAAAGGTTATATTATTCAA
130 CACCAACTTGATCAAAAAATTACAAAAATGTCCTTTCATAATTAAAAAAAGGTTATATAATTCAA
* * *
61951150 GGGTATTTTAGTCTTTTCATTTTAACAAAAACCAACTAAAAAATATACATACGGTGAGATTTGAA
195 GGGTATTTTAGTCTTTTCATTTTAACAAAAACCAACTAAAAAATATACATAAGATGAGACTTGAA
*
61951215 CCTATGCCAATTCT
260 CCCATGCCAATTCT
* * * *
61951229 AAACCTTTATTTTAATGTATTTTTATACATTTTGGTTTTAATATGCACAATATATTATCTTCATC
1 AAAACTTTATTTTAATATA-TTTTATACATTTTGGTTTTAATATGTACAATTTATTATCTTCATC
* * * *
61951294 AATTGTATATATATACTTAATATTTATTAAGCCCCTGGCTGAGTCAGTTTCACTCTCAATCGAGT
65 AATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTGTCACCCTCAACCGAGT
* * *
61951359 CACCAACTT-AGTCAAAAAATTACGAAAATGTCCTTTCGTAATT-AGAAAA-GTTATATAATTCA
130 CACCAACTTGA-TCAAAAAATTACAAAAATGTCCTTTCATAATTAAAAAAAGGTTATATAATTCA
** * *
61951421 AGGGTATTTTAGGT-TTTTCATTTT-AGGAAAACCAATTAAAAAATATACATAAGATGGGACTTG
194 AGGGTATTTTA-GTCTTTTCATTTTAACAAAAACCAACTAAAAAATATACATAAGATGAGACTTG
* *
61951484 AACCCGTGCCAATTAAATTATT
258 AACCCATGCC-----AATT-CT
* * * *
61951506 AAAACTTTATCTTAATATATTTTATACATTTTGATTTTAATATGTATAATTTATTATCTCCATCA
1 AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATATGTACAATTTATTATCTTCATCA
*
61951571 CTTGTATATAT
66 ATTGTATATAT
61951582 TAATAATATT
Statistics
Matches: 300, Mismatches: 43, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
271 40 0.13
272 33 0.11
273 25 0.08
274 130 0.43
276 55 0.18
277 17 0.06
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (273 bp):
AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATATGTACAATTTATTATCTTCATCA
ATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTGTCACCCTCAACCGAGTC
ACCAACTTGATCAAAAAATTACAAAAATGTCCTTTCATAATTAAAAAAAGGTTATATAATTCAAG
GGTATTTTAGTCTTTTCATTTTAACAAAAACCAACTAAAAAATATACATAAGATGAGACTTGAAC
CCATGCCAATTCT
Found at i:61955089 original size:28 final size:29
Alignment explanation
Indices: 61955035--61955099 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
61955025 TTCACTATTT
* *
61955035 TAAAAATAATATATGTATTTTACATTATAA
1 TAAAAATTATATATGTATTTTAAATTA-AA
61955065 -AAAAATTATA-AT-TATTTATAAATTAAA
1 TAAAAATTATATATGTATTT-TAAATTAAA
61955092 TAAAAATT
1 TAAAAATT
61955100 GAGAGTTCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 7 0.23
28 15 0.48
29 9 0.29
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (29 bp):
TAAAAATTATATATGTATTTTAAATTAAA
Found at i:61955509 original size:29 final size:29
Alignment explanation
Indices: 61955473--61955543 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
61955463 AAAAAAATGA
*
61955473 ATAGTTGGGTGACCATTTTTTAACATTTC
1 ATAGTTGGGTGACCATTTTGTAACATTTC
* ** *
61955502 ATAGTTGGATGACCATTTTGTAATTTTTT
1 ATAGTTGGGTGACCATTTTGTAACATTTC
*
61955531 ATAGTTGAGTGAC
1 ATAGTTGGGTGAC
61955544 AAAAAAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (29 bp):
ATAGTTGGGTGACCATTTTGTAACATTTC
Found at i:61956376 original size:274 final size:260
Alignment explanation
Indices: 61955764--61956459 Score: 873
Period size: 274 Copynumber: 2.6 Consensus size: 260
61955754 TCAACATCTA
* ** * ** * *
61955764 TACTATTAATTAAGCCATTGACTAAGTTGGTATCACCCTTGACCGGGTCATCAACTCGATCAAAA
1 TACTATTTATTAAGCCCCTGACTAAGTTGGTGTCACCCTCAACCGGGTCACCAACTTGATCAAAA
* *
61955829 AATTACAAAAATG-TCATTTCGTAATTAAAAAAGTTATATTATTTAAGGTTATTTGAGTC-TTTT
66 AATTACAAAAATGTTC-TTTCGTAATTAAAAAAGTTATATTATTCAAGG-TATTTTAGTCTTTTT
* * *
61955892 CATTTTAACAAAAACTAACTAAAAAATATACATATGGTGAGATTTGAACCCATGTCTTTATTTTA
129 CATTTTAACAAAAACCAATTAAAAAATATACATATGGTGAGATTTGAACCCATCTCTTTATTTTA
* * *
61955957 ATATATTTTATACATTTTGATTTTAATATGCTCAATTCCTTATATTCATCAGATGTATATCTATA
194 ATATATTTTATACATTTTGATTTTAATATGCACAATTCATTATATTCATCAGATGTATATATATA
61956022 CT
259 CT
* *
61956024 TACTATTTATTAAGCCCCTGACTAAATTGGTGTCACCCTCAACCGGGTCACCAACTTGATCAAGA
1 TACTATTTATTAAGCCCCTGACTAAGTTGGTGTCACCCTCAACCGGGTCACCAACTTGATCAAAA
* *
61956089 AATTATAAAAATGTTCTTTCATAATTAAAAAAGGTTATATTATTCAAGGTAATTTTAGTCTTTTT
66 AATTACAAAAATGTTCTTTCGTAATTAAAAAA-GTTATATTATTCAAGGT-ATTTTAGTCTTTTT
*
61956154 CATTTTAACAAAAACCAATTAAAAAATATGCATATGGTGAGATTTGAACCTATGCCAATTCTAAA
129 CATTTTAACAAAAACCAATTAAAAAATATACATATGGTGAGATTTGAA-C----CC-A-TCT---
* * *
61956219 CCTTTATTTTAATGTATTTTTATACATTTTGGTTTTAATATGCACAATAT-ATTATTTTCATCAG
184 -CTTTATTTTAATATA-TTTTATACATTTTGATTTTAATATGCACAAT-TCATTATATTCATCAG
*
61956283 TTGTATATATATACT
246 ATGTATATATATACT
* * *
61956298 TACTATTTATTAAGCCCCTGACTGAGTCGGTGTCACCCTCAACCGAGTCACCAACTT-AGTCAAA
1 TACTATTTATTAAGCCCCTGACTAAGTTGGTGTCACCCTCAACCGGGTCACCAACTTGA-TCAAA
* * *
61956362 AAATTACGAAAATGTCCTTTCGTAATTAAAAAAGTTATATAATTCAAGGGTATTTTAGGT-TTTT
65 AAATTACAAAAATGTTCTTTCGTAATTAAAAAAGTTATATTATTCAA-GGTATTTTA-GTCTTTT
**
61956426 TCATTTT-AGGAAAACCAATTAAAAAATATACATA
128 TCATTTTAACAAAAACCAATTAAAAAATATACATA
61956460 AGATGGGACT
Statistics
Matches: 378, Mismatches: 38, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
260 83 0.22
261 25 0.07
262 49 0.13
263 1 0.00
267 2 0.01
268 1 0.00
269 2 0.01
272 24 0.06
273 45 0.12
274 145 0.38
275 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (260 bp):
TACTATTTATTAAGCCCCTGACTAAGTTGGTGTCACCCTCAACCGGGTCACCAACTTGATCAAAA
AATTACAAAAATGTTCTTTCGTAATTAAAAAAGTTATATTATTCAAGGTATTTTAGTCTTTTTCA
TTTTAACAAAAACCAATTAAAAAATATACATATGGTGAGATTTGAACCCATCTCTTTATTTTAAT
ATATTTTATACATTTTGATTTTAATATGCACAATTCATTATATTCATCAGATGTATATATATACT
Found at i:61962927 original size:8 final size:7
Alignment explanation
Indices: 61962897--61962960 Score: 55
Period size: 7 Copynumber: 9.3 Consensus size: 7
61962887 TTAATATCCA
*
61962897 AATAAGT
1 AATAAAT
61962904 AATAAAT
1 AATAAAT
61962911 AAT-AA-
1 AATAAAT
61962916 AATAAAGT
1 AATAAA-T
61962924 AATAAAT
1 AATAAAT
*
61962931 AAAGTAAAG
1 -AA-TAAAT
61962940 AA-AAAT
1 AATAAAT
61962946 AATAAAT
1 AATAAAT
61962953 AA-AAAT
1 AATAAAT
61962959 AA
1 AA
61962961 AATTTGGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
5 3 0.06
6 15 0.31
7 16 0.33
8 10 0.21
9 4 0.08
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (7 bp):
AATAAAT
Found at i:61962928 original size:13 final size:12
Alignment explanation
Indices: 61962904--61962963 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
61962894 CCAAATAAGT
61962904 AATAAATAATAA
1 AATAAATAATAA
61962916 AATAAAGTAAT-A
1 AATAAA-TAATAA
*
61962928 AATAAAGTAA-AG
1 AATAAA-TAATAA
61962940 AA-AAATAAT-A
1 AATAAATAATAA
61962950 AATAAA-AATAA
1 AATAAATAATAA
61962961 AAT
1 AAT
61962964 TTGGGTTGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 8 0.20
11 10 0.24
12 19 0.46
13 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:61970527 original size:3 final size:3
Alignment explanation
Indices: 61970521--61970558 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
61970511 TTTAATAATT
*
61970521 ATG ATG ATG ATG ACG ATG ATG ATG ATG ATG AT- ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
61970559 TTGCATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:61976641 original size:16 final size:17
Alignment explanation
Indices: 61976620--61976653 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
61976610 TTTGTATTTT
*
61976620 TATTTTT-ATATTTTAA
1 TATTTTTGAAATTTTAA
61976636 TATTTTTGAAATTTTAA
1 TATTTTTGAAATTTTAA
61976653 T
1 T
61976654 CTTAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TATTTTTGAAATTTTAA
Found at i:61992000 original size:19 final size:18
Alignment explanation
Indices: 61991967--61992008 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
61991957 AAGAGAATGA
61991967 GACAGAGACGGAGACAGT
1 GACAGAGACGGAGACAGT
*
61991985 GACAGTGACAGGAGACAGT
1 GACAGAGAC-GGAGACAGT
61992004 GACAG
1 GACAG
61992009 CTAAAGGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.38, C:0.17, G:0.38, T:0.07
Consensus pattern (18 bp):
GACAGAGACGGAGACAGT
Found at i:61992016 original size:19 final size:19
Alignment explanation
Indices: 61991976--61992020 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
61991966 AGACAGAGAC
*
61991976 GGAGACAGTGACAGTGACA
1 GGAGACAGTGACAGTGAAA
61991995 GGAGACAGTGACAGCT-AAA
1 GGAGACAGTGACAG-TGAAA
61992014 GGAGACA
1 GGAGACA
61992021 ATATAGGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.40, C:0.16, G:0.36, T:0.09
Consensus pattern (19 bp):
GGAGACAGTGACAGTGAAA
Found at i:61992384 original size:3 final size:3
Alignment explanation
Indices: 61992378--61992403 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61992368 AACTTGTCGG
61992378 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
61992404 AACTCCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:61992694 original size:15 final size:12
Alignment explanation
Indices: 61992658--61992686 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
61992648 TTCTCTCTCC
61992658 TCCTC-TCTTCT
1 TCCTCGTCTTCT
61992669 TCCTCGTCTTCT
1 TCCTCGTCTTCT
61992681 TCCTCG
1 TCCTCG
61992687 AAGTCTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.00, C:0.45, G:0.07, T:0.48
Consensus pattern (12 bp):
TCCTCGTCTTCT
Found at i:61992946 original size:6 final size:6
Alignment explanation
Indices: 61992937--61992963 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
61992927 TCTTCTGTTG
61992937 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
61992964 CCACTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:61993730 original size:16 final size:16
Alignment explanation
Indices: 61993707--61993739 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
61993697 TATGCTTATA
61993707 AAATTAA-TTAAAAAT
1 AAATTAATTTAAAAAT
61993722 AAATATAATTTAAAAAT
1 AAAT-TAATTTAAAAAT
61993739 A
1 A
61993740 TCATCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 3 0.19
17 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTAATTTAAAAAT
Found at i:61998313 original size:26 final size:25
Alignment explanation
Indices: 61998273--61998340 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
61998263 ATAAACAAAC
* *
61998273 ATATTTTCTTCTTTTGCAAATTTTA
1 ATATTTTCTTTTTTTGCAAATGTTA
* * *
61998298 ATCATTTTGTTTTTTTCCATATGTTA
1 AT-ATTTTCTTTTTTTGCAAATGTTA
*
61998324 ATATTTTTTTATTTTTG
1 ATATTTTCTT-TTTTTG
61998341 TGCAACCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 9 0.26
26 25 0.74
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (25 bp):
ATATTTTCTTTTTTTGCAAATGTTA
Found at i:61999863 original size:23 final size:23
Alignment explanation
Indices: 61999820--61999863 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
61999810 TAAGGGTTTG
* *
61999820 ATATAATTTTTGAATGGAATTTT
1 ATATAATTTTTAAATGAAATTTT
61999843 ATATAATCTTTTAAAT-AAATT
1 ATATAAT-TTTTAAATGAAATT
61999864 AAATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (23 bp):
ATATAATTTTTAAATGAAATTTT
Found at i:62006459 original size:57 final size:57
Alignment explanation
Indices: 62006348--62006464 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 57
62006338 TTTTTTTTAC
* *
62006348 ATTATATAAAAATGGTCAAATTTCAATTTTAGTCTCTATCCTAAACTCAAATTTAAG
1 ATTATATAAAAATGGTCAAATTTCAATTTTAGTCCCTATCCTAAACACAAATTTAAG
* * * * *
62006405 ATTATATAATAATGGTCAAATTTCAATTTT-GATCCCTTTGCTACACACATATTTAAG
1 ATTATATAAAAATGGTCAAATTTCAATTTTAG-TCCCTATCCTAAACACAAATTTAAG
62006462 ATT
1 ATT
62006465 CAATCTTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
56 1 0.02
57 51 0.98
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (57 bp):
ATTATATAAAAATGGTCAAATTTCAATTTTAGTCCCTATCCTAAACACAAATTTAAG
Found at i:62006872 original size:17 final size:17
Alignment explanation
Indices: 62006836--62006907 Score: 57
Period size: 17 Copynumber: 4.5 Consensus size: 17
62006826 CCAATATAAT
* *
62006836 AAATATATTT-ATTTTT
1 AAATATTTTTAATTTTA
*
62006852 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
62006869 AAATATTTTTAA----A
1 AAATATTTTTAATTTTA
*
62006882 ATACT-TTTTTAATTTTA
1 A-AATATTTTTAATTTTA
62006899 AAATATTTT
1 AAATATTTT
62006908 AAAAATACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
13 9 0.21
14 2 0.05
16 10 0.23
17 22 0.51
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:62006878 original size:11 final size:11
Alignment explanation
Indices: 62006864--62006925 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
62006854 ATTTTTTTAA
62006864 TTTTAAAATAT
1 TTTTAAAATAT
62006875 TTTTAAAATACT
1 TTTTAAAATA-T
*
62006887 TTTT----TAA
1 TTTTAAAATAT
62006894 TTTTAAAATAT
1 TTTTAAAATAT
*
62006905 TTTAAAAATACTT
1 TTTTAAAATA--T
62006918 TTTTAAAA
1 TTTTAAAA
62006926 AAATTTTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
7 4 0.10
8 2 0.05
11 21 0.52
12 5 0.12
13 8 0.20
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:62006913 original size:30 final size:30
Alignment explanation
Indices: 62006856--62006923 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
62006846 ATTTTTAAAT
*
62006856 TTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTAAAATATTTTAAAAATAC
62006886 TTTTTTAATTTTAAAATATTTTAAAAATAC
1 TTTTTTAATTTTAAAATATTTTAAAAATAC
62006916 TTTTTTAA
1 TTTTTTAA
62006924 AAAAATTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTTTTAATTTTAAAATATTTTAAAAATAC
Found at i:62006923 original size:14 final size:14
Alignment explanation
Indices: 62006904--62006954 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
62006894 TTTTAAAATA
62006904 TTTTAAAAATACTT
1 TTTTAAAAATACTT
* *
62006918 TTTTAAAAAAATTT
1 TTTTAAAAATACTT
*
62006932 TAATTTTAAAATACTT
1 T--TTTAAAAATACTT
62006948 TTTTAAA
1 TTTTAAA
62006955 TTTTTTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 18 0.62
16 11 0.38
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTTAAAAATACTT
Found at i:62006980 original size:30 final size:29
Alignment explanation
Indices: 62006873--62006973 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 29
62006863 ATTTTAAAAT
**
62006873 ATTTTTAAAATACTTTTTT-AATTTTAAA
1 ATTTTTAAAATACTTTTTTAAATTTTTTA
**
62006901 ATATTTTAAAAATACTTTTTTAAAAAAATTTTA
1 AT-TTTT-AAAATACTTTTTT--AAATTTTTTA
62006934 A-TTTTAAAATACTTTTTTAAATTTTTTA
1 ATTTTTAAAATACTTTTTTAAATTTTTTA
62006962 ATTTTTAAAATA
1 ATTTTTAAAATA
62006974 AATTTTTGGT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
28 11 0.18
29 14 0.23
30 26 0.43
31 4 0.07
33 6 0.10
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTTTTAAAATACTTTTTTAAATTTTTTA
Found at i:62012089 original size:64 final size:62
Alignment explanation
Indices: 62012000--62012120 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 62
62011990 TAAAAAAAGT
* * *
62012000 AATCTGTCACCCATGAGACCCTCTATAAAAGCACAAAATCATTCATTTCAGTCCTCACCTAAAA
1 AATCTATCACCCATGAAACCCTCTATAAAAGCAC--AATCATTCATTTCACTCCTCACCTAAAA
* *
62012064 AATCTATCACCCTTGAAACCTTCTATAAAAGCACAATCATTCATTTCACTCCTCACC
1 AATCTATCACCCATGAAACCCTCTATAAAAGCACAATCATTCATTTCACTCCTCACC
62012121 CATCAAACCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
62 22 0.42
64 30 0.58
ACGTcount: A:0.36, C:0.31, G:0.06, T:0.27
Consensus pattern (62 bp):
AATCTATCACCCATGAAACCCTCTATAAAAGCACAATCATTCATTTCACTCCTCACCTAAAA
Found at i:62018672 original size:35 final size:35
Alignment explanation
Indices: 62018633--62018702 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
62018623 ACGATCTTCA
*
62018633 ATTAGTACTTTTAACAAATTTACTATGACATACTT
1 ATTAGTACTTTTAACAAATTTACTATCACATACTT
*
62018668 ATTAGTACTTTTAACAAATTTTCTATCACATACTT
1 ATTAGTACTTTTAACAAATTTACTATCACATACTT
62018703 TAACCATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (35 bp):
ATTAGTACTTTTAACAAATTTACTATCACATACTT
Found at i:62021352 original size:52 final size:48
Alignment explanation
Indices: 62021333--62021535 Score: 240
Period size: 46 Copynumber: 4.3 Consensus size: 48
62021323 TGACAAGTGG
* * *
62021333 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTTGGCTACACTTATCTGATCAAGTGACAA
62021379 AAAGTGATAAGTGATAG-TTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTT-GGCTACACTTATCTGATCAAGTGAC-A---A
* * *
62021431 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTTGGCTACACTTATCTGATCAAGTGACAA
* *
62021477 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTTGGCTACACTTATCTGATCAAGTGACAA
62021523 AAAGTGATAAGTG
1 AAAGTGATAAGTG
62021536 GCTACACTTA
Statistics
Matches: 140, Mismatches: 9, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
45 2 0.01
46 96 0.69
52 40 0.29
53 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTTGGCTACACTTATCTGATCAAGTGACAA
Found at i:62021387 original size:98 final size:98
Alignment explanation
Indices: 62021267--62021535 Score: 450
Period size: 98 Copynumber: 2.7 Consensus size: 98
62021257 TTTGAGTACT
*
62021267 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
62021332 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
62021365 TCTGATCAAGTGACAAAGTGATAAGTGATAG-TTTCGGCTACACTTATCTGATCAAGTGACAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTT-AGCTACACTTATCTGATCAAGTGACAAGT
*
62021429 GAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
65 GAAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
62021463 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
62021528 GATAAGTG
65 GAAAAGTG
62021536 GCTACACTTA
Statistics
Matches: 160, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
97 3 0.02
98 143 0.89
99 14 0.09
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:62021543 original size:37 final size:37
Alignment explanation
Indices: 62021499--62021607 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
62021489 GATAGCTTTA
62021499 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
62021536 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
62021573 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
62021608 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:62022355 original size:21 final size:19
Alignment explanation
Indices: 62022301--62022358 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
62022291 ATTTATTTTG
62022301 TAATTTTTATATATTTTTAA
1 TAATTTTTATA-ATTTTTAA
* * *
62022321 TAATGTTAAAAATTAATTTAA
1 TAATTTTTATAATT--TTTAA
62022342 TAATTTTTATAATTTTT
1 TAATTTTTATAATTTTT
62022359 GAATTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 6 0.20
20 8 0.27
21 16 0.53
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TAATTTTTATAATTTTTAA
Found at i:62023435 original size:31 final size:31
Alignment explanation
Indices: 62023374--62023439 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
62023364 TTATTATACC
* **
62023374 ATTTGGTACATGAGTTTGGCTTTGAGGTTCA
1 ATTTGGTACATGAATTTGGCTTCAAGGTTCA
*
62023405 ATTTGGTACATGAATTTGGCTTCAATGTTCA
1 ATTTGGTACATGAATTTGGCTTCAAGGTTCA
62023436 ATTT
1 ATTT
62023440 AATACCTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.44
Consensus pattern (31 bp):
ATTTGGTACATGAATTTGGCTTCAAGGTTCA
Found at i:62025590 original size:15 final size:15
Alignment explanation
Indices: 62025552--62025592 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
62025542 TAAATAACTG
62025552 AATTTAATAAGT-CAA
1 AATTTAA-AAGTACAA
62025567 AATTT-AAAGTACAA
1 AATTTAAAAGTACAA
*
62025581 ATTTTAAAAGTA
1 AATTTAAAAGTA
62025593 AAGCGAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
15 11 0.48
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (15 bp):
AATTTAAAAGTACAA
Found at i:62029370 original size:117 final size:116
Alignment explanation
Indices: 62029189--62029401 Score: 302
Period size: 117 Copynumber: 1.8 Consensus size: 116
62029179 TTTCAGGACA
* **
62029189 AAATTAAACCACTAACTGAAATGACTCCTGAAACCGAGAACAATTTGCTCCATGTTTTTCCATAC
1 AAATTAAACCACTAACTGAAATGACTCCGGAAACCGAGAACAATTTGCTCCACATTTTTCCATAC
*
62029254 AGTTCATGTTTCTCAAACTCAAATGCTGTATGCAGCCACATTTCTCAAATTC
66 AGTT-ATGTTTCTCAAACTCAAAAGCTGTATGCAGCCACATTTCTCAAATTC
* * ** *
62029306 AAATTGAATCACTAACTGAAATGACTCCGGAAATTGAGAACCATTTGCTCCACATTTCTT-CATA
1 AAATTAAACCACTAACTGAAATGACTCCGGAAACCGAGAACAATTTGCTCCACATTT-TTCCATA
* *
62029370 CGGTTATGTTTCTCAAACTCAAAAGTTGTATG
65 CAGTTATGTTTCTCAAACTCAAAAGCTGTATG
62029402 TAGCTAAGGA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
116 25 0.30
117 57 0.68
118 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (116 bp):
AAATTAAACCACTAACTGAAATGACTCCGGAAACCGAGAACAATTTGCTCCACATTTTTCCATAC
AGTTATGTTTCTCAAACTCAAAAGCTGTATGCAGCCACATTTCTCAAATTC
Found at i:62039213 original size:25 final size:24
Alignment explanation
Indices: 62039172--62039222 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
62039162 CTTTTAAATA
**
62039172 TATTATAATTATTATATTTAATTT
1 TATTATAATTAAAATATTTAATTT
62039196 TATTATTAATTAAAATATTTAATTT
1 TATTA-TAATTAAAATATTTAATTT
62039221 TA
1 TA
62039223 AAAAACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTATAATTAAAATATTTAATTT
Found at i:62039780 original size:17 final size:16
Alignment explanation
Indices: 62039758--62039791 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
62039748 TACTGGATAT
62039758 ATAATAAAATATTAAAA
1 ATAAT-AAATATTAAAA
*
62039775 ATAATAGATATTAAAA
1 ATAATAAATATTAAAA
62039791 A
1 A
62039792 AAAAGCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
ATAATAAATATTAAAA
Found at i:62053488 original size:39 final size:39
Alignment explanation
Indices: 62053392--62053503 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 39
62053382 AAAAACGCCG
* * * *
62053392 CTAAAAATTAAGCATTAGTGGCCCCTTTCAAAAAATGCCA
1 CTAAAAA-TAAGCATTAGTGGCGCTTTTTAAAAAATACCA
* *
62053432 CTAAAGATCAAGTATTAGTGGCGCTTTTTAAAAAATACCA
1 CTAAAAAT-AAGCATTAGTGGCGCTTTTTAAAAAATACCA
* * *
62053472 CTAAAAATGAGCATTAGCGGCG-TTTTTGAAAA
1 CTAAAAATAAGCATTAGTGGCGCTTTTTAAAAA
62053504 TGCGCCGCTA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 9 0.15
39 12 0.20
40 39 0.65
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (39 bp):
CTAAAAATAAGCATTAGTGGCGCTTTTTAAAAAATACCA
Found at i:62057203 original size:30 final size:30
Alignment explanation
Indices: 62057162--62057221 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
62057152 GGACTTGGGG
* * *
62057162 TGGTGGTGGAGCTGGTGCCGGTGGTGGGTT
1 TGGTGGAGGAGCTGGCGCAGGTGGTGGGTT
*
62057192 TGGTGGAGGAGCTGGCGGAGGTGGTGGGTT
1 TGGTGGAGGAGCTGGCGCAGGTGGTGGGTT
62057222 AGGAGGTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.07, C:0.08, G:0.58, T:0.27
Consensus pattern (30 bp):
TGGTGGAGGAGCTGGCGCAGGTGGTGGGTT
Found at i:62058936 original size:20 final size:20
Alignment explanation
Indices: 62058913--62058950 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
62058903 TATATTTTTT
62058913 ATTTTTAAAATACATTTCCC
1 ATTTTTAAAATACATTTCCC
*
62058933 ATTTTTAAAATATATTTC
1 ATTTTTAAAATACATTTC
62058951 ATATGTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTTAAAATACATTTCCC
Found at i:62059929 original size:19 final size:20
Alignment explanation
Indices: 62059887--62059941 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
62059877 AATATAAAAT
* *
62059887 AAAATTCAAAATAATTTTTG
1 AAAATTCAAAATAATTTATA
62059907 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTTATA
* *
62059926 AAAATTTAAAAAAATT
1 AAAATTCAAAATAATT
62059942 CTAAAACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAATTCAAAATAATTTATA
Found at i:62068528 original size:25 final size:25
Alignment explanation
Indices: 62068482--62068529 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
62068472 TATTTGATTT
* *
62068482 GTCTACTTCTAATAGTATGTTTTTA
1 GTCTACTTCTAATAGCAGGTTTTTA
*
62068507 GTCTGCTTCTAATAGCAGGTTTT
1 GTCTACTTCTAATAGCAGGTTTT
62068530 CTATTCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (25 bp):
GTCTACTTCTAATAGCAGGTTTTTA
Found at i:62077597 original size:22 final size:22
Alignment explanation
Indices: 62077569--62077621 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
62077559 ATTTTTTTGC
62077569 TAAAATAGGAAATGAAAAATAA
1 TAAAATAGGAAATGAAAAATAA
*
62077591 TAAAATAGGAAATGAGAAATAA
1 TAAAATAGGAAATGAAAAATAA
*
62077613 TATAATAGG
1 TAAAATAGG
62077622 TAAAAAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (22 bp):
TAAAATAGGAAATGAAAAATAA
Found at i:62077629 original size:19 final size:19
Alignment explanation
Indices: 62077569--62077630 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 19
62077559 ATTTTTTTGC
62077569 TAAAATAGGAAATGAAAAATAA
1 TAAAATAGG-AA--AAAAATAA
62077591 TAAAATAGGAAATGAGAAATAA
1 TAAAATAGGAAA--A-AAATAA
* *
62077613 TATAATAGGTAAAAAATA
1 TAAAATAGGAAAAAAATA
62077631 CTATGAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 6 0.17
20 1 0.03
21 3 0.09
22 25 0.71
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (19 bp):
TAAAATAGGAAAAAAATAA
Found at i:62078335 original size:51 final size:51
Alignment explanation
Indices: 62078259--62078377 Score: 143
Period size: 51 Copynumber: 2.3 Consensus size: 51
62078249 GATGATTATA
* * * * *
62078259 CTCATCATCAGAAGACCTATGATGCTTGTGCCGATGTCT-AGAGCG-TCGATG
1 CTCATCCTCAGAGGAGCTATCATGCTTGTGACGATGT-TGAGAGCGAT-GATG
* *
62078310 CTCATTCTCAGAGGAGCTATCATGCTTGTGACGATGTTGAGAGGGATGATG
1 CTCATCCTCAGAGGAGCTATCATGCTTGTGACGATGTTGAGAGCGATGATG
62078361 CTCATCCTCAGAGGAGC
1 CTCATCCTCAGAGGAGC
62078378 CACGACATCT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 1 0.02
51 56 0.97
52 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (51 bp):
CTCATCCTCAGAGGAGCTATCATGCTTGTGACGATGTTGAGAGCGATGATG
Found at i:62090486 original size:29 final size:29
Alignment explanation
Indices: 62090426--62090487 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
62090416 TATATTTCAG
* *
62090426 TAAATAATATTTTAAATGACCTATTTTCA
1 TAAATAATATTTCAAATGACCTATTTTAA
62090455 TAAATAATATTTCAAATAGA-CT-TTTCTAA
1 TAAATAATATTTCAAAT-GACCTATTT-TAA
62090484 TAAA
1 TAAA
62090488 ATACCCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.10
29 24 0.83
30 2 0.07
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (29 bp):
TAAATAATATTTCAAATGACCTATTTTAA
Found at i:62106074 original size:21 final size:23
Alignment explanation
Indices: 62106048--62106089 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
62106038 TATGACTAAA
62106048 AATTTAT-TATA-TTATAAAAAT
1 AATTTATGTATATTTATAAAAAT
*
62106069 AATTTATGTGTATTTATAAAA
1 AATTTATGTATATTTATAAAA
62106090 TTACGACGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
AATTTATGTATATTTATAAAAAT
Found at i:62121143 original size:30 final size:30
Alignment explanation
Indices: 62121114--62121250 Score: 131
Period size: 29 Copynumber: 4.7 Consensus size: 30
62121104 ATTTCTTTAA
* *
62121114 TTTTAAAATATTTTTTACATACTTTTTTAAA
1 TTTTAAAATATTTT-AAAATACTTTTTTAAA
***
62121145 TTTTTTTA-ATTTTAAAATACTTTTTTAAA
1 TTTTAAAATATTTTAAAATACTTTTTTAAA
62121174 TTTTAAAATATTTTAAAATACTTTTTT-AA
1 TTTTAAAATATTTTAAAATACTTTTTTAAA
*** *
62121203 TTTTTTTA-ATTTTAAAATA-TTTTTAAATA
1 TTTTAAAATATTTTAAAATACTTTTTTAA-A
*
62121232 TTTTATAAT-TTTTAAAATA
1 TTTTAAAATATTTTAAAATA
62121251 AAATGGGTCG
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
27 5 0.06
28 12 0.14
29 43 0.49
30 23 0.26
31 5 0.06
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTTAAAATATTTTAAAATACTTTTTTAAA
Found at i:62121166 original size:29 final size:29
Alignment explanation
Indices: 62121132--62121250 Score: 154
Period size: 29 Copynumber: 4.1 Consensus size: 29
62121122 TATTTTTTAC
*
62121132 ATACTTTTTTAAATTTTTTTAATTTTAAA
1 ATACTTTTTTAAATTTTTATAATTTTAAA
* *
62121161 ATACTTTTTTAAATTTTAAAATATTTTAAA
1 ATACTTTTTTAAATTTTTATA-ATTTTAAA
*
62121191 ATACTTTTTT-AATTTTTTTAATTTTAAA
1 ATACTTTTTTAAATTTTTATAATTTTAAA
62121219 ATA--TTTTTAAATATTTTATAATTTTTAAA
1 ATACTTTTTTAAAT-TTTTATAA-TTTTAAA
62121248 ATA
1 ATA
62121251 AAATGGGTCG
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
26 5 0.06
27 3 0.04
28 18 0.23
29 35 0.44
30 18 0.23
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (29 bp):
ATACTTTTTTAAATTTTTATAATTTTAAA
Found at i:62121170 original size:19 final size:19
Alignment explanation
Indices: 62121103--62121236 Score: 98
Period size: 20 Copynumber: 6.8 Consensus size: 19
62121093 TAAATATATT
62121103 TATTTCTTT-AATTTTAAAA
1 TATTT-TTTAAATTTTAAAA
*
62121122 TATTTTTTACATACTTTTTTAAA
1 TATTTTTTA-A-A--TTTTAAAA
62121145 T-TTTTTT-AATTTTAAAA
1 TATTTTTTAAATTTTAAAA
62121162 TACTTTTTTAAATTTTAAAA
1 TA-TTTTTTAAATTTTAAAA
** **
62121182 TATTTTAAAATACTTTTTTAA
1 TATTTTTTAA-A-TTTTAAAA
62121203 T-TTTTTT-AATTTTAAAA
1 TATTTTTTAAATTTTAAAA
*
62121220 TATTTTTAAATATTTTA
1 TATTTTTTAA-ATTTTA
62121237 TAATTTTTAA
Statistics
Matches: 91, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
17 15 0.16
18 9 0.10
19 20 0.22
20 25 0.27
21 8 0.09
22 6 0.07
23 8 0.09
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTTTAAATTTTAAAA
Found at i:62121216 original size:38 final size:37
Alignment explanation
Indices: 62121165--62121249 Score: 125
Period size: 38 Copynumber: 2.3 Consensus size: 37
62121155 TTTAAAATAC
*
62121165 TTTTTTAAATTTTAAAATATTTTAAAATACTTTTTTAA
1 TTTTTTAAATTTTAAAATATTTTAAAATA-TTTTATAA
* *
62121203 TTTTTTTAATTTTAAAATATTTTTAAATATTTTATAA
1 TTTTTTAAATTTTAAAATATTTTAAAATATTTTATAA
*
62121240 TTTTTAAAAT
1 TTTTTTAAAT
62121250 AAAATGGGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 15 0.36
38 27 0.64
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (37 bp):
TTTTTTAAATTTTAAAATATTTTAAAATATTTTATAA
Found at i:62121216 original size:58 final size:58
Alignment explanation
Indices: 62121112--62121250 Score: 201
Period size: 58 Copynumber: 2.4 Consensus size: 58
62121102 TTATTTCTTT
* * *
62121112 AATTTTAAAATATTTTTTACATACTTTTTTAAATTTTTTTAATTTTAAAATACTTTTTTA
1 AATTTTAAAATA-TTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATA-TTTTTAA
62121172 AATTTTAAAATATTTTAAAATACTTTTTT-AATTTTTTTAATTTTAAAATATTTTTAA
1 AATTTTAAAATATTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAA
*
62121229 ATATTTTATAAT-TTTTAAAATA
1 A-ATTTTAAAATATTTTAAAATA
62121251 AAATGGGTCG
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
57 17 0.23
58 30 0.41
59 15 0.20
60 12 0.16
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (58 bp):
AATTTTAAAATATTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAA
Found at i:62121226 original size:11 final size:10
Alignment explanation
Indices: 62121113--62121247 Score: 63
Period size: 9 Copynumber: 13.9 Consensus size: 10
62121103 TATTTCTTTA
*
62121113 ATTTTAAAAT
1 ATTTTTAAAT
*
62121123 ATTTTTTACAT
1 A-TTTTTAAAT
62121134 ACTTTTTTAAAT
1 A--TTTTTAAAT
*
62121146 -TTTTT-TA-
1 ATTTTTAAAT
*
62121153 ATTTTAAAAT
1 ATTTTTAAAT
*
62121163 ACTTTTTTAA-
1 A-TTTTTAAAT
*
62121173 ATTTTAAAAT
1 ATTTTTAAAT
*
62121183 ATTTTAAAAT
1 ATTTTTAAAT
*
62121193 ACTTTTTTAAT
1 A-TTTTTAAAT
*
62121204 -TTTTT-TA-
1 ATTTTTAAAT
*
62121211 ATTTTAAAAT
1 ATTTTTAAAT
62121221 ATTTTTAAAT
1 ATTTTTAAAT
*
62121231 A-TTTTATA-
1 ATTTTTAAAT
62121239 ATTTTTAAA
1 ATTTTTAAA
62121248 ATAAAATGGG
Statistics
Matches: 95, Mismatches: 18, Indels: 25
0.69 0.13 0.18
Matches are distributed among these distances:
8 11 0.12
9 30 0.32
10 24 0.25
11 21 0.22
12 9 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTTTAAAT
Found at i:62126754 original size:24 final size:24
Alignment explanation
Indices: 62126704--62126752 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
62126694 GATATTTTTT
** *
62126704 AATATAAAGAAATACTAAAATGAA
1 AATATAAAGAAATAAGAAAAAGAA
62126728 AATATAAAGAAA-AAGAAAAAGAA
1 AATATAAAGAAATAAGAAAAAGAA
62126751 AA
1 AA
62126753 ATCATTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.14
Consensus pattern (24 bp):
AATATAAAGAAATAAGAAAAAGAA
Found at i:62129013 original size:35 final size:36
Alignment explanation
Indices: 62128950--62129024 Score: 143
Period size: 35 Copynumber: 2.1 Consensus size: 36
62128940 GAGAGCATGG
62128950 AAAATGTGGCAACATGTTTTTTTTTACTTAATCATC
1 AAAATGTGGCAACATGTTTTTTTTTACTTAATCATC
62128986 AAAATGTGGCAACATG-TTTTTTTTACTTAATCATC
1 AAAATGTGGCAACATGTTTTTTTTTACTTAATCATC
62129021 AAAA
1 AAAA
62129025 CATCATTACA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
35 23 0.59
36 16 0.41
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (36 bp):
AAAATGTGGCAACATGTTTTTTTTTACTTAATCATC
Found at i:62130245 original size:35 final size:35
Alignment explanation
Indices: 62130200--62130281 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
62130190 ATTTATTTAA
*
62130200 TAATATAATAT-CATTATAACTT-AATTATCATAAAT
1 TAATATAATATAAATTATAA-TTCAA-TATCATAAAT
*
62130235 TAATATAATATAAATTATAATTCAATATCATTAAT
1 TAATATAATATAAATTATAATTCAATATCATAAAT
62130270 T-ATATAAT-TAAA
1 TAATATAATATAAA
62130282 AAAAATAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 4 0.09
34 7 0.16
35 23 0.53
36 9 0.21
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (35 bp):
TAATATAATATAAATTATAATTCAATATCATAAAT
Found at i:62130275 original size:22 final size:22
Alignment explanation
Indices: 62130196--62130278 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 22
62130186 TTTGATTTAT
* *
62130196 TTAATAATATAATATCATTATAA
1 TTAATTATATAAT-TCAATATAA
62130219 CTTAATTATCATAAATT-AATATAA
1 -TTAATTAT-AT-AATTCAATATAA
* *
62130243 TATAAAT-TATAATTCAATATCA
1 T-TAATTATATAATTCAATATAA
62130265 TTAATTATATAATT
1 TTAATTATATAATT
62130279 AAAAAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
21 8 0.16
22 16 0.33
23 2 0.04
24 17 0.35
25 3 0.06
26 3 0.06
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAATTATATAATTCAATATAA
Found at i:62132574 original size:25 final size:26
Alignment explanation
Indices: 62132519--62132673 Score: 93
Period size: 25 Copynumber: 5.9 Consensus size: 26
62132509 TTTTAAACTT
* *
62132519 TATATTATTTATTCTAAATTGTTCTA
1 TATATTATTTATTTTAAATTGTTATA
*
62132545 T-TATTATTTATTTTAAGTT-TTATA
1 TATATTATTTATTTTAAATTGTTATA
**
62132569 TATATTATGCATTTTAAACTATGTTA-A
1 TATATTATTTATTTTAAA-T-TGTTATA
* * *
62132596 TCTATAATTCATTTTAAATT-TATATA
1 TATATTATTTATTTTAAATTGT-TATA
* *** *
62132622 TGTATATTATTTATGTTAAACTACATATG
1 --TATATTATTTATTTTAAA-TTGTTATA
**
62132651 TATATTATTTATTTGGAATTGTT
1 TATATTATTTATTTTAAATTGTT
62132674 TTTATGCACA
Statistics
Matches: 97, Mismatches: 22, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
24 6 0.06
25 32 0.33
26 6 0.06
27 32 0.33
28 17 0.18
29 4 0.04
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.55
Consensus pattern (26 bp):
TATATTATTTATTTTAAATTGTTATA
Found at i:62132782 original size:21 final size:22
Alignment explanation
Indices: 62132757--62132805 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
62132747 GACATATTAT
62132757 TTATTTTAAACT-TTTTACATA
1 TTATTTTAAACTGTTTTACATA
* * *
62132778 TTATTTTAAATTGTTTTATATG
1 TTATTTTAAACTGTTTTACATA
62132800 TTATTT
1 TTATTT
62132806 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (22 bp):
TTATTTTAAACTGTTTTACATA
Found at i:62132853 original size:26 final size:26
Alignment explanation
Indices: 62132714--62132874 Score: 113
Period size: 26 Copynumber: 6.3 Consensus size: 26
62132704 AAAATAAAAT
62132714 TTGTTTT-CATATTATTCA-TTTAAGA
1 TTGTTTTACATATTATTCATTTTAA-A
* *
62132739 TTCCTTTTGACATATTATTTATTTTAAA
1 TT-GTTTT-ACATATTATTCATTTTAAA
*
62132767 CT-TTTTAC--A-TATT-ATTTTAAA
1 TTGTTTTACATATTATTCATTTTAAA
* * *
62132788 TTGTTTTATATGTTATTTAATTTTAAA
1 TTGTTTTACATATTA-TTCATTTTAAA
* * *
62132815 TTGCTTTGA-ATATTATTCCTTTTAAT
1 TTG-TTTTACATATTATTCATTTTAAA
***
62132841 TTGTTTTACATATTATTTGCTTTAAA
1 TTGTTTTACATATTATTCATTTTAAA
62132867 TTGTTTTA
1 TTGTTTTA
62132875 TGCTATCACT
Statistics
Matches: 108, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
21 9 0.08
22 9 0.08
23 1 0.01
25 10 0.09
26 42 0.39
27 16 0.15
28 16 0.15
29 5 0.05
ACGTcount: A:0.27, C:0.07, G:0.06, T:0.59
Consensus pattern (26 bp):
TTGTTTTACATATTATTCATTTTAAA
Found at i:62148898 original size:26 final size:26
Alignment explanation
Indices: 62148862--62148917 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
62148852 TTTGAATATT
62148862 AAAGTAAAACTGAGGTACCACATTCA
1 AAAGTAAAACTGAGGTACCACATTCA
62148888 AAAGTAAAACTGAGGTACCACATTCA
1 AAAGTAAAACTGAGGTACCACATTCA
62148914 AAAG
1 AAAG
62148918 CCCTATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (26 bp):
AAAGTAAAACTGAGGTACCACATTCA
Found at i:62153915 original size:28 final size:28
Alignment explanation
Indices: 62153875--62153931 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
62153865 TTTCCTGTGC
62153875 TCTAGAAGGAATTATTTGATTATATATG
1 TCTAGAAGGAATTATTTGATTATATATG
*
62153903 TCTAGAAGGAATTATTTGATTATTTATG
1 TCTAGAAGGAATTATTTGATTATATATG
62153931 T
1 T
62153932 GCTTTATTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.46
Consensus pattern (28 bp):
TCTAGAAGGAATTATTTGATTATATATG
Found at i:62155528 original size:35 final size:35
Alignment explanation
Indices: 62155482--62155552 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
62155472 GGCATCCAAA
*
62155482 AGTGAGGATGATTTTTCTTGTACTTTTCCTAGAAG
1 AGTGAGGATGATTTTCCTTGTACTTTTCCTAGAAG
*
62155517 AGTGAGGATGATTTTCCTTTTACTTTTCCTAGAAG
1 AGTGAGGATGATTTTCCTTGTACTTTTCCTAGAAG
62155552 A
1 A
62155553 CTTTGTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (35 bp):
AGTGAGGATGATTTTCCTTGTACTTTTCCTAGAAG
Found at i:62158402 original size:14 final size:15
Alignment explanation
Indices: 62158376--62158404 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
62158366 TTTAATGTTT
62158376 TATATTATAGTATGA
1 TATATTATAGTATGA
62158391 TATATT-TAGTATGA
1 TATATTATAGTATGA
62158405 GTTTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (15 bp):
TATATTATAGTATGA
Found at i:62160612 original size:16 final size:16
Alignment explanation
Indices: 62160591--62160637 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
62160581 AATTAATGTC
62160591 TTTC-TTAAAATATTAT
1 TTTCTTTAAAA-ATTAT
*
62160607 TTTCTTTAAAAATTAG
1 TTTCTTTAAAAATTAT
* *
62160623 TATCTTTTAAAATTA
1 TTTCTTTAAAAATTA
62160638 AAACACTTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTCTTTAAAAATTAT
Found at i:62163845 original size:234 final size:233
Alignment explanation
Indices: 62163427--62164170 Score: 1109
Period size: 234 Copynumber: 3.1 Consensus size: 233
62163417 TTTAGGACAA
* * *
62163427 ATCCAGGTTCGGAGTCTCGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
1 ATCCGGGTTCGGAGTTTAGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
** *
62163492 AAATATGTGACATGATGCAGAGTTTTGAAGGACAAATCCTGGTTGCGAGTTCAGATTCCGTTCTC
66 AAATATGTGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCC-TTCTC
* * *
62163557 GATACATATGTTCATGCTTTGCTTATCTTAAAATGTCTTCTGTTGTCGTTCTCAATACATATGTT
130 GATACATATTTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCGTTCTCAATGCATATGTT
62163622 CGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
195 CGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
62163661 ATCCGGGTTCGGAGTTTAGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
1 ATCCGGGTTCGGAGTTTAGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
62163726 AAATATGTGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCCATTCTC
66 AAATATGTGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCC-TTCTC
*
62163791 GATACATATTTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCATTCTCAATGCATATGTT
130 GATACATATTTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCGTTCTCAATGCATATGTT
62163856 CGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
195 CGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
* *
62163895 ATCCGGGTTCGGAGTTTAGATACCGTTCTTGACGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
1 ATCCGGGTTCGGAGTTTAGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
62163960 AAATATCGAGTCTTTTTTTTTGACATGATGC--AGTTTCAAAGGACAAATCCAGGTTGCGAGTTC
66 AAATAT---G----------TGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTC
* * *
62164023 AGATT--TTCTCGATCCATATGTTCATTTGATGCTTTGCTTATCTTAAAATGTCTTGTATTGTCG
118 AGATTCCTTCTCGATACATA---T--TTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCG
* * * *
62164086 TTCTCGATGCATATGTTCGTTCCTTGTCTCTCCTATGTTAAAATATTGAAGGACGA
178 TTCTCAATGCATATGTTCGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
62164142 ATCCGGGTTCGGAGTTTAGATACCGTTCT
1 ATCCGGGTTCGGAGTTTAGATACCGTTCT
62164171 TGATACATAT
Statistics
Matches: 471, Mismatches: 21, Indels: 23
0.91 0.04 0.04
Matches are distributed among these distances:
234 292 0.62
237 1 0.00
242 12 0.03
245 38 0.08
247 128 0.27
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (233 bp):
ATCCGGGTTCGGAGTTTAGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
AAATATGTGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCCTTCTCG
ATACATATTTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCGTTCTCAATGCATATGTTC
GTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
Found at i:62167039 original size:13 final size:13
Alignment explanation
Indices: 62167021--62167046 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62167011 TTTCAAGCTT
62167021 TTTTTAATTAATA
1 TTTTTAATTAATA
62167034 TTTTTAATTAATA
1 TTTTTAATTAATA
62167047 AATATATTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAATTAATA
Found at i:62167145 original size:16 final size:16
Alignment explanation
Indices: 62167098--62167148 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
62167088 TTTTTAATTA
62167098 ATAAATATT-TTATTT
1 ATAAATATTATTATTT
*
62167113 ATTAAATTAAATAATTATTT
1 A-TAAA-T--ATTATTATTT
62167133 ATAAATATTATTATTT
1 ATAAATATTATTATTT
62167149 TTAGTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 1 0.03
16 13 0.45
17 1 0.03
18 1 0.03
19 6 0.21
20 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAAATATTATTATTT
Found at i:62167162 original size:35 final size:34
Alignment explanation
Indices: 62167098--62167169 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
62167088 TTTTTAATTA
*
62167098 ATAAATATTTTATTTATTAAATTAAATAATTATTT
1 ATAAATATTTTATTTATTAAATAAAATAATT-TTT
*
62167133 ATAAATATTATTATTT-TT-AGTAAATATAATTTTT
1 ATAAATATT-TTATTTATTAAATAAA-ATAATTTTT
62167167 ATA
1 ATA
62167170 TGTGTAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
34 10 0.30
35 17 0.52
36 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (34 bp):
ATAAATATTTTATTTATTAAATAAAATAATTTTT
Found at i:62168569 original size:20 final size:22
Alignment explanation
Indices: 62168544--62168602 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
62168534 ATTTAATATT
62168544 TTTGTAACTG-TAAAA-AACGG
1 TTTGTAACTGCTAAAATAACGG
* *
62168564 TTTGTAACTGTTGAAAATAATGG
1 TTTGTAACTGCT-AAAATAACGG
62168587 TTTGTAACTGCTAAAA
1 TTTGTAACTGCTAAAA
62168603 CAAATTTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.29
21 1 0.03
22 8 0.24
23 15 0.44
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (22 bp):
TTTGTAACTGCTAAAATAACGG
Found at i:62169906 original size:39 final size:39
Alignment explanation
Indices: 62169661--62169905 Score: 251
Period size: 39 Copynumber: 6.3 Consensus size: 39
62169651 AGAAAATCTT
* * * *
62169661 ATTCAGTAGAATCAGTAGATAATGCTCGTTTGTGTAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* *
62169700 ATTCAGTATAATCAGTGGATAATGTTCG-TTGAACAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * * *
62169738 ATTCGGTATAATCAGTGAATATTGCTCTTTTGAGCAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * * *
62169777 ATTCAGTATAATCAATGAATAATGCTTGTTTGAACAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * * * *
62169816 ATTTAGTATGATTAATGGATATTGCTCGTTTGAGCAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * * *
62169855 AATT-AATATAATTAGTGGATAATGCTCGTATGAGCAAAC
1 -ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
*
62169894 ATTTAGTATAAT
1 ATTCAGTATAAT
62169906 TGGTATTCCA
Statistics
Matches: 171, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
38 33 0.19
39 135 0.79
40 3 0.02
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.35
Consensus pattern (39 bp):
ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
Found at i:62172017 original size:26 final size:26
Alignment explanation
Indices: 62171968--62172025 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
62171958 ATATACTTAC
* * *
62171968 ACTTTATTTTATTGTTTTCTATAGGA
1 ACTTTATTTTATTCTTTACAATAGGA
*
62171994 ACTTTCTTTTATTCTTTACAATAGG-
1 ACTTTATTTTATTCTTTACAATAGGA
62172019 -CTTTATT
1 ACTTTATT
62172026 AATGAAATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 6 0.22
26 21 0.78
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (26 bp):
ACTTTATTTTATTCTTTACAATAGGA
Found at i:62173647 original size:19 final size:20
Alignment explanation
Indices: 62173611--62173649 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
62173601 ACCCAACAAG
* *
62173611 AAAATCAATTTTATTATTTA
1 AAAATCAATATTACTATTTA
62173631 AAAATC-ATATTACTATTTA
1 AAAATCAATATTACTATTTA
62173650 CATATTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATCAATATTACTATTTA
Found at i:62181420 original size:12 final size:12
Alignment explanation
Indices: 62181403--62181433 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
62181393 GATCAATTGA
62181403 CTTGTTCTTCAT
1 CTTGTTCTTCAT
62181415 CTTGTTCTTCAT
1 CTTGTTCTTCAT
62181427 CTTGTTC
1 CTTGTTC
62181434 ATGTTCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.26, G:0.10, T:0.58
Consensus pattern (12 bp):
CTTGTTCTTCAT
Done.