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 5 of 208
Found at i:1537800 original size:28 final size:27
Alignment explanation
Indices: 1537745--1537801 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1537735 AATATAAAAT
*
1537745 AAAAATTAATTAAAATTACATAAATAA
1 AAAAATTAATTAAAATTACAAAAATAA
* *
1537772 AAAAGATTAATTAATATT-CAAAAATTA
1 AAAA-ATTAATTAAAATTACAAAAATAA
1537799 AAA
1 AAA
1537802 TTAACCCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAAATTAATTAAAATTACAAAAATAA
Found at i:1541496 original size:18 final size:18
Alignment explanation
Indices: 1541473--1541547 Score: 132
Period size: 18 Copynumber: 4.2 Consensus size: 18
1541463 TACGACCGTT
1541473 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
1541491 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
1541509 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
1541527 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
1541545 TAC
1 TAC
1541548 AGTAGTTGGG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:1545976 original size:50 final size:50
Alignment explanation
Indices: 1545853--1546101 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
1545843 GATAATAACA
* * ** * **
1545853 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGACGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
1545904 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
1545954 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
1546004 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
1546059 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
1546102 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
50 93 0.55
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:1546030 original size:100 final size:104
Alignment explanation
Indices: 1545852--1546101 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 104
1545842 TGATAATAAC
** *
1545852 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGACGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTCACGGTGCCCATGCCATG
* *
1545917 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
1545954 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCACGGTGCCCATGCCATGT
1546018 CCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
1546059 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1546102 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
100 51 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCACGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:1546217 original size:13 final size:13
Alignment explanation
Indices: 1546196--1546227 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1546186 GCTTGGATCA
*
1546196 TCATCAAATAAAT
1 TCATAAAATAAAT
1546209 TCATAAAATAAAT
1 TCATAAAATAAAT
1546222 TCATAA
1 TCATAA
1546228 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1546475 original size:30 final size:30
Alignment explanation
Indices: 1546439--1546496 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1546429 CCTCGACTCT
*
1546439 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1546469 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1546497 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:1547261 original size:40 final size:40
Alignment explanation
Indices: 1547199--1547293 Score: 145
Period size: 40 Copynumber: 2.3 Consensus size: 40
1547189 CTTTTCTTTT
* *
1547199 TTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTT-CTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
*
1547240 TTTCTTTCTTTCTCCCTTCTCTGTTTTGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
1547280 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
1547294 TTCTTTGTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 34 0.68
41 16 0.32
ACGTcount: A:0.00, C:0.28, G:0.08, T:0.63
Consensus pattern (40 bp):
TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:1547324 original size:5 final size:5
Alignment explanation
Indices: 1547314--1547366 Score: 83
Period size: 5 Copynumber: 10.8 Consensus size: 5
1547304 TATATATATA
1547314 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT -TAAT AATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT
1547363 ATAA
1 ATAA
1547367 AAACATAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
3 1 0.02
4 4 0.09
5 36 0.80
6 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:1547375 original size:24 final size:23
Alignment explanation
Indices: 1547305--1547366 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 23
1547295 TCTTTGTCAT
1547305 ATATATATAATAATATAATATAATATA
1 ATATA-AT-ATAATATAATA-AA-ATA
*
1547332 ATATAATATAATATATTAATAATA
1 ATATAATATAATATAATAA-AATA
1547356 ATATAATATAA
1 ATATAATATAA
1547367 AAACATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 15 0.45
25 11 0.33
26 2 0.06
27 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATAATATAATATAATAAAATA
Found at i:1558128 original size:11 final size:10
Alignment explanation
Indices: 1558115--1558229 Score: 63
Period size: 11 Copynumber: 12.0 Consensus size: 10
1558105 TAAAAAAAGT
1558115 ATTTTAAAAA
1 ATTTTAAAAA
1558125 TATTTT--AAA
1 -ATTTTAAAAA
1558134 A--TTAAAAA
1 ATTTTAAAAA
*
1558142 AATTTAAAAA
1 ATTTTAAAAA
*
1558152 GTATTTAAAAA
1 AT-TTTAAAAA
1558163 ATTTT--AAA
1 ATTTTAAAAA
1558171 A-TTTAAAAA
1 ATTTTAAAAA
*
1558180 ATTTAAAAAAA
1 ATTT-TAAAAA
*
1558191 GTATTTTAAAAGT
1 --ATTTTAAAA-A
1558204 ATTTT--AAA
1 ATTTTAAAAA
1558212 A-TTTAAAAA
1 ATTTTAAAAA
1558221 A-TTTAAAAA
1 ATTTTAAAAA
1558230 TAAAAATATT
Statistics
Matches: 83, Mismatches: 7, Indels: 30
0.69 0.06 0.25
Matches are distributed among these distances:
6 2 0.02
7 6 0.07
8 10 0.12
9 21 0.25
10 12 0.14
11 24 0.29
12 4 0.05
13 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:1558140 original size:17 final size:17
Alignment explanation
Indices: 1558117--1558230 Score: 84
Period size: 17 Copynumber: 6.1 Consensus size: 17
1558107 AAAAAAGTAT
1558117 TTTAAAAATATTTTAAAA
1 TTTAAAAA-ATTTTAAAA
* *
1558135 TTAAAAAAATTTAAAAAGTA
1 TTTAAAAAATTT-TAAA--A
1558155 TTTAAAAAATTTTAAAA
1 TTTAAAAAATTTTAAAA
*
1558172 TTTAAAAAATTTAAAAAAAGTA
1 TTTAAAAAATTT---TAAA--A
*
1558194 TTTTAAAAGTATTTTAAAA
1 -TTTAAAA-AATTTTAAAA
*
1558213 TTTAAAAAATTTAAAAA
1 TTTAAAAAATTTTAAAA
1558230 T
1 T
1558231 AAAAATATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
17 26 0.34
18 17 0.22
19 4 0.05
20 15 0.19
21 3 0.04
22 1 0.01
23 7 0.09
24 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TTTAAAAAATTTTAAAA
Found at i:1558230 original size:8 final size:9
Alignment explanation
Indices: 1558117--1558229 Score: 79
Period size: 9 Copynumber: 11.9 Consensus size: 9
1558107 AAAAAAGTAT
1558117 TTTAAAAATA
1 TTTAAAAA-A
*
1558127 TTT-TAAAA
1 TTTAAAAAA
*
1558135 TTAAAAAAA
1 TTTAAAAAA
1558144 TTTAAAAAGTA
1 TTTAAAAA--A
1558155 TTTAAAAAA
1 TTTAAAAAA
*
1558164 TTT-TAAAA
1 TTTAAAAAA
1558172 TTTAAAAAA
1 TTTAAAAAA
1558181 TTTAAAAAAAGTA
1 TTT--AAAAA--A
*
1558194 TTTTAAAAGTA
1 -TTTAAAA-AA
*
1558205 TTT-TAAAA
1 TTTAAAAAA
1558213 TTTAAAAAA
1 TTTAAAAAA
1558222 TTTAAAAA
1 TTTAAAAA
1558230 TAAAAATATT
Statistics
Matches: 82, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
8 14 0.17
9 39 0.48
10 6 0.07
11 15 0.18
12 4 0.05
13 1 0.01
14 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:1570375 original size:4 final size:4
Alignment explanation
Indices: 1570368--1570393 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1570358 TATATGTATC
1570368 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
1570394 TTTCAGCCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1579496 original size:3 final size:3
Alignment explanation
Indices: 1579488--1579512 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1579478 TTTTCCCTCA
1579488 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1579513 AGCATCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1581425 original size:15 final size:16
Alignment explanation
Indices: 1581407--1581440 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1581397 GAAAACTTTG
1581407 AATTTTAAA-ATATTT
1 AATTTTAAATATATTT
1581422 AATTTTAAATTATATTT
1 AATTTTAAA-TATATTT
1581439 AA
1 AA
1581441 AGTGAATCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTTAAATATATTT
Found at i:1581483 original size:29 final size:29
Alignment explanation
Indices: 1581419--1581483 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
1581409 TTTTAAAATA
* * *
1581419 TTTAATTTTAAATTATATTTAAAGTGAAT
1 TTTATTTTTAAATTAAATTTAAAATGAAT
* *
1581448 CTCATTTTTAAATTAAATTTAAATATG-AT
1 TTTATTTTTAAATTAAATTTAAA-ATGAAT
1581477 TTTATTT
1 TTTATTT
1581484 CCATTAATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (29 bp):
TTTATTTTTAAATTAAATTTAAAATGAAT
Found at i:1586529 original size:21 final size:21
Alignment explanation
Indices: 1586505--1586547 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1586495 ACCATATCCC
1586505 AAAGGATTAATTTATGTAAGG
1 AAAGGATTAATTTATGTAAGG
1586526 AAAGGATTAATTTATGTAAGG
1 AAAGGATTAATTTATGTAAGG
1586547 A
1 A
1586548 CTTTGTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (21 bp):
AAAGGATTAATTTATGTAAGG
Found at i:1597568 original size:23 final size:23
Alignment explanation
Indices: 1597542--1597594 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1597532 TAGGATTTAA
*
1597542 AGTAAGATACGTAAAACAATTTG
1 AGTAAGATACGTAAAACAAATTG
1597565 AGTAAGATACGTAAAACAAATTG
1 AGTAAGATACGTAAAACAAATTG
*
1597588 AATAAGA
1 AGTAAGA
1597595 GGTAAAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.23
Consensus pattern (23 bp):
AGTAAGATACGTAAAACAAATTG
Found at i:1597738 original size:26 final size:28
Alignment explanation
Indices: 1597683--1597740 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
1597673 AGAATAAATT
*
1597683 TAAAATTTATGTATAAAGCAACTAAAAA
1 TAAAATTTATATATAAAGCAACTAAAAA
* *
1597711 TAAAA-TTATATATAAA-TAACTTAAAA
1 TAAAATTTATATATAAAGCAACTAAAAA
1597737 TAAA
1 TAAA
1597741 TCATTTGCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 12 0.44
27 10 0.37
28 5 0.19
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.31
Consensus pattern (28 bp):
TAAAATTTATATATAAAGCAACTAAAAA
Found at i:1597896 original size:39 final size:37
Alignment explanation
Indices: 1597835--1597920 Score: 120
Period size: 39 Copynumber: 2.2 Consensus size: 37
1597825 TTGAAATAAC
1597835 ATATAAAAAAAATTAAACTAAATAATATAT-ATACAT
1 ATATAAAAAAAATTAAACTAAATAATATATAATACAT
1597871 ATATAAAAAAACAATTTAAACTAAATAATATATACATACAT
1 ATAT-AAAAAA-AA-TTAAACTAAATAATATATA-ATACAT
*
1597912 ATATTAAAA
1 ATATAAAAA
1597921 TAGGTGCTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
36 4 0.09
37 6 0.14
38 2 0.05
39 18 0.41
40 4 0.09
41 10 0.23
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (37 bp):
ATATAAAAAAAATTAAACTAAATAATATATAATACAT
Found at i:1633454 original size:24 final size:24
Alignment explanation
Indices: 1633406--1633455 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1633396 AGAGTCCCAT
*
1633406 TATTAGCTCTCATGAGCATCTCGA
1 TATTAGCTCTCATGAGCATCCCGA
1633430 TATTAGCTCT-ATTGAGC-TACCCGA
1 TATTAGCTCTCA-TGAGCAT-CCCGA
1633454 TA
1 TA
1633456 CATGGCTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (24 bp):
TATTAGCTCTCATGAGCATCCCGA
Found at i:1634201 original size:21 final size:21
Alignment explanation
Indices: 1634168--1634207 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1634158 AGGAAATGAA
*
1634168 AAAAAGGAAAGAAA-CAAAAC
1 AAAAAGAAAAGAAAGCAAAAC
1634188 AAAAAGAAATAGAAAGCAAA
1 AAAAAGAAA-AGAAAGCAAA
1634208 GGAAAATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.75, C:0.07, G:0.15, T:0.03
Consensus pattern (21 bp):
AAAAAGAAAAGAAAGCAAAAC
Found at i:1636237 original size:33 final size:33
Alignment explanation
Indices: 1636195--1636331 Score: 105
Period size: 33 Copynumber: 4.1 Consensus size: 33
1636185 AATTGATGGA
*
1636195 TAAGACCATAACTGGGTTATGGCACTATGAACG
1 TAAGACCATAACTGGGTTATGGCACTATGAATG
** * * * * *
1636228 TAAGACCATAGTTGGATCATGGCAGTTTTTACATG
1 TAAGACCATAACTGGGTTATGGCA-CTATGA-ATG
** * * *
1636263 TAAGACCATAGTTGGGCTATGGCATTCTG-ATG
1 TAAGACCATAACTGGGTTATGGCACTATGAATG
* *
1636295 ATAAAACCATAACTGGGTTATGGCACTACGAATG
1 -TAAGACCATAACTGGGTTATGGCACTATGAATG
1636329 TAA
1 TAA
1636332 AGGATGAATA
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
32 3 0.04
33 45 0.56
34 9 0.11
35 23 0.29
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (33 bp):
TAAGACCATAACTGGGTTATGGCACTATGAATG
Found at i:1642886 original size:61 final size:61
Alignment explanation
Indices: 1642820--1642943 Score: 230
Period size: 61 Copynumber: 2.0 Consensus size: 61
1642810 AACAACAAAA
*
1642820 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAACAATAAGAAAATAATAT
1 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAAAAATAAGAAAATAATAT
*
1642881 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGTGAGAAAAAAATAAGAAAATAATAT
1 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAAAAATAAGAAAATAATAT
1642942 TA
1 TA
1642944 AAAACAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (61 bp):
TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAAAAATAAGAAAATAATAT
Found at i:1647430 original size:17 final size:17
Alignment explanation
Indices: 1647408--1647444 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1647398 TTTTAACCGT
1647408 AAGTTTGTAATTTTGAA
1 AAGTTTGTAATTTTGAA
1647425 AAGTTTGTAATTTTGAA
1 AAGTTTGTAATTTTGAA
1647442 AAG
1 AAG
1647445 GAACAAGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (17 bp):
AAGTTTGTAATTTTGAA
Found at i:1656242 original size:22 final size:22
Alignment explanation
Indices: 1656217--1656259 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1656207 TCTCTCTATT
1656217 TTGCTACCATTTTACTGTTATG
1 TTGCTACCATTTTACTGTTATG
**
1656239 TTGCTATTATTTTACTGTTAT
1 TTGCTACCATTTTACTGTTAT
1656260 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTTACTGTTATG
Found at i:1659582 original size:15 final size:13
Alignment explanation
Indices: 1659547--1659579 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1659537 GAGGATGCTC
1659547 TCTTTTTTCTTCT
1 TCTTTTTTCTTCT
1659560 TCTTTTTTC-TCT
1 TCTTTTTTCTTCT
*
1659572 CCTTTTTT
1 TCTTTTTT
1659580 TTTGATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTTTTTTCTTCT
Found at i:1671066 original size:19 final size:20
Alignment explanation
Indices: 1671027--1671066 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1671017 ATTTCTTTTG
*
1671027 TTTTTAAAATATTTTTATAA
1 TTTTTAAAATATTTATATAA
*
1671047 TTTTTAAATTATTTAT-TAA
1 TTTTTAAAATATTTATATAA
1671066 T
1 T
1671067 ATAGCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAAAATATTTATATAA
Found at i:1682706 original size:15 final size:16
Alignment explanation
Indices: 1682681--1682714 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1682671 AAATTGTAAT
1682681 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
1682697 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
1682712 TTT
1 TTT
1682715 TAAAAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:1686169 original size:21 final size:22
Alignment explanation
Indices: 1686159--1686201 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
1686149 TCTTTAATTA
1686159 TAAAAT-ATTATTTTATACATT
1 TAAAATAATTATTTTATACATT
1686180 TAAAATAATTATATTTAATACA
1 TAAAATAATTAT-TTT-ATACA
1686202 AATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 3 0.16
24 5 0.26
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAATAATTATTTTATACATT
Found at i:1686239 original size:22 final size:23
Alignment explanation
Indices: 1686194--1686240 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1686184 ATAATTATAT
* *
1686194 TTAATACAAATATATAAATTAAA
1 TTAATAAAAATATATAAATAAAA
*
1686217 TTAATAAAAAT-TATATATAAAA
1 TTAATAAAAATATATAAATAAAA
1686239 TT
1 TT
1686241 TGATGATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAATAAAAATATATAAATAAAA
Found at i:1687047 original size:24 final size:24
Alignment explanation
Indices: 1686996--1687050 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1686986 ACTCAAAAAA
* **
1686996 TAAATAAACTATACTAATAAATGT
1 TAAATATACTATACTAATAAATAC
*
1687020 TAAATATATTATACTAATAAATAC
1 TAAATATACTATACTAATAAATAC
1687044 TAAATAT
1 TAAATAT
1687051 TCTAGGAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (24 bp):
TAAATATACTATACTAATAAATAC
Found at i:1690188 original size:23 final size:23
Alignment explanation
Indices: 1690162--1690237 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
1690152 ATAAGCGCAA
*
1690162 CACTGATATGTAGCCGAAGCTAT
1 CACTGATATGTAGCCGAAGCTAC
*
1690185 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1690208 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1690231 CACTGAT
1 CACTGAT
1690238 CAATAACACT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1691610 original size:24 final size:24
Alignment explanation
Indices: 1691583--1691635 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1691573 TTAGTAAGTC
*
1691583 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1691607 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1691631 AAATA
1 AAATA
1691636 TTCTAGAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1691636 original size:24 final size:24
Alignment explanation
Indices: 1691591--1691636 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1691581 TCAAATAAAC
*
1691591 TATACTAATAAATGCTAAATATAT
1 TATACTAATAAATACTAAATATAT
1691615 TATACTAATAAATACTAAATAT
1 TATACTAATAAATACTAAATAT
1691637 TCTAGAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (24 bp):
TATACTAATAAATACTAAATATAT
Found at i:1692252 original size:11 final size:11
Alignment explanation
Indices: 1692217--1692256 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
1692207 GATTGAATCG
*
1692217 ATTTTTTTAT-
1 ATTTTTTAATA
1692227 ATTTTTTAA-A
1 ATTTTTTAATA
1692237 A-TTTTTAATA
1 ATTTTTTAATA
1692247 ATTTTTTAAT
1 ATTTTTTAAT
1692257 CGAACTGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
9 7 0.27
10 11 0.42
11 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTTTTAATA
Found at i:1699386 original size:13 final size:12
Alignment explanation
Indices: 1699364--1699394 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
1699354 TGCAATTCTC
1699364 AAAAAAAAAAGA
1 AAAAAAAAAAGA
1699376 AAAAGAAAAAAGA
1 AAAA-AAAAAAGA
1699389 AAAAAA
1 AAAAAA
1699395 CAGTAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:1720265 original size:51 final size:50
Alignment explanation
Indices: 1720096--1720320 Score: 164
Period size: 51 Copynumber: 4.4 Consensus size: 50
1720086 TTCAGTGGTT
* * * * * * **
1720096 TGCACATAGTACCACCCACGTGACCATTGTCATCCGATACATGTAGTAGCC
1 TGCACATAGTACTACACACGTGAACA-AGCCATCCGGTACACATAGTAGCC
* * ** * * * *
1720147 TACACATAGTACTACACACGTGATCAAGCTTTCCGGTTCACGTAGTAACT
1 TGCACATAGTACTACACACGTGAACAAGCCATCCGGTACACATAGTAGCC
*
1720197 TGCACATAGTACTACACACGTGAACAAGGCCATCTGGTACACATAGTAGCC
1 TGCACATAGTACTACACACGTGAACAA-GCCATCCGGTACACATAGTAGCC
* * * * * * *
1720248 TGCATATAGTACTACACATGTGACCATTATCTAT-CGATACACGTAGTAGCC
1 TGCACATAGTACTACACACGTGAACA--AGCCATCCGGTACACATAGTAGCC
* * *
1720299 TGCACTTTGTACTACATACGTG
1 TGCACATAGTACTACACACGTG
1720321 CTCATAGGTA
Statistics
Matches: 136, Mismatches: 35, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
50 40 0.29
51 92 0.68
52 3 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (50 bp):
TGCACATAGTACTACACACGTGAACAAGCCATCCGGTACACATAGTAGCC
Found at i:1722161 original size:101 final size:101
Alignment explanation
Indices: 1721982--1722298 Score: 429
Period size: 101 Copynumber: 3.1 Consensus size: 101
1721972 AATTATTAAA
* * * * *
1721982 ACGTAAGACTATGGTTGGACCATGATAGTGTTTATATGTAAGACCATAACTAGACTATGGCATTC
1 ACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
* * *
1722047 TGATGATATGACCATAGCTGGGTTATAACACTATGG
66 TGATGATAAGACCATAACTGGGTTATAGCACTATGG
* ** *
1722083 ACGTAAGACCATGGTTAGACCACAACAGTGTTTATATGTAAGACCATAGTTGGGCTATGGCATTC
1 ACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
* * *
1722148 TGATGACAAGACCATAACTGAGTTATGGCACTATGG
66 TGATGATAAGACCATAACTGGGTTATAGCACTATGG
*
1722184 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
1 ACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
* * * *
1722249 TTATGATAAGACCACAATTGGGTTATAGCACTA-CG
66 TGATGATAAGACCATAACTGGGTTATAGCACTATGG
*
1722284 ACTGTAAGACTATGG
1 AC-GTAAGACCATGG
1722299 CAGGGCAATG
Statistics
Matches: 187, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
100 3 0.02
101 184 0.98
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (101 bp):
ACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
TGATGATAAGACCATAACTGGGTTATAGCACTATGG
Found at i:1727599 original size:42 final size:42
Alignment explanation
Indices: 1727538--1727667 Score: 152
Period size: 42 Copynumber: 3.1 Consensus size: 42
1727528 CATGGAAGTA
* * * * *
1727538 CATAAGTGCTAAATGGAAACCTATAAGGGTTAAACGGAAGCT
1 CATAAGAGCTAAACGGAAACCCATAAGGGTTAAACTGAAACT
* * * *
1727580 CATAGGAGCTGAACGGAAACCCATAATGGTTAATCTGAAACT
1 CATAAGAGCTAAACGGAAACCCATAAGGGTTAAACTGAAACT
* * *
1727622 CAGAAGAGCTAAACTGAAACCCATTAGGGTTAAACTGAAACT
1 CATAAGAGCTAAACGGAAACCCATAAGGGTTAAACTGAAACT
1727664 CATA
1 CATA
1727668 TGAGTTGACT
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (42 bp):
CATAAGAGCTAAACGGAAACCCATAAGGGTTAAACTGAAACT
Found at i:1727619 original size:21 final size:20
Alignment explanation
Indices: 1727595--1727667 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
1727585 GAGCTGAACG
*
1727595 GAAACCCATAATGGTTAATCT
1 GAAACCCATAA-GGTTAAACT
* * *
1727616 GAAACTCAGAAGAGCTAAACT
1 GAAACCCATAAG-GTTAAACT
*
1727637 GAAACCCATTAGGGTTAAACT
1 GAAACCCA-TAAGGTTAAACT
*
1727658 GAAACTCATA
1 GAAACCCATA
1727668 TGAGTTGACT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 3 0.07
21 36 0.88
22 2 0.05
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.22
Consensus pattern (20 bp):
GAAACCCATAAGGTTAAACT
Found at i:1728645 original size:54 final size:54
Alignment explanation
Indices: 1728543--1728646 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 54
1728533 TCATCGAATT
* * **
1728543 TAGTGGTCTTGAACCATTATTTCTGACACTACTAAAAATTGGGTTGTTACTTAC
1 TAGTGGTCTTGAACCACTATTTCTGACACTACTAAAAATTAGACTGTTACTTAC
* * *
1728597 TAGTGGTCTTGAACCACTGTTTTTGACA-TCACTGAAAATTAGACTGTTAC
1 TAGTGGTCTTGAACCACTATTTCTGACACT-ACTAAAAATTAGACTGTTAC
1728647 AGTAAGTGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 1 0.02
54 41 0.98
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (54 bp):
TAGTGGTCTTGAACCACTATTTCTGACACTACTAAAAATTAGACTGTTACTTAC
Found at i:1729998 original size:9 final size:9
Alignment explanation
Indices: 1729984--1730009 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1729974 TCTCCTCCCT
1729984 AATTTCACA
1 AATTTCACA
1729993 AATTTCACA
1 AATTTCACA
1730002 AATTTCAC
1 AATTTCAC
1730010 TTTTACACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
AATTTCACA
Found at i:1733825 original size:24 final size:24
Alignment explanation
Indices: 1733798--1733848 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1733788 GCAAATGGAG
*
1733798 ATATTTTGGAGAGATGAAATGAAT
1 ATATTTTGGAAAGATGAAATGAAT
*
1733822 ATATTTTGGAAAGATGAAATGGAT
1 ATATTTTGGAAAGATGAAATGAAT
1733846 ATA
1 ATA
1733849 AATGGAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (24 bp):
ATATTTTGGAAAGATGAAATGAAT
Found at i:1733940 original size:20 final size:19
Alignment explanation
Indices: 1733914--1733978 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
1733904 AATATTTTTA
1733914 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
* ***
1733933 ACTTATGTAAT-ATTTTTA-
1 A-TTATGTAGTGATTCAAAG
1733951 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
1733970 ATTTATGTA
1 A-TTATGTA
1733979 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 6 0.18
20 15 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (19 bp):
ATTATGTAGTGATTCAAAG
Found at i:1733943 original size:37 final size:37
Alignment explanation
Indices: 1733889--1734001 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
1733879 TTATGTTTTA
*
1733889 ATTC-AAGACTTGTGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1733925 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* *
1733962 ATTCAAAGATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1733999 ATT
1 ATT
1734002 TAATTCGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:1733957 original size:17 final size:17
Alignment explanation
Indices: 1733901--1733995 Score: 55
Period size: 17 Copynumber: 5.2 Consensus size: 17
1733891 TCAAGACTTG
1733901 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
1733918 TGTAGTGATTCAAAGACTTA
1 TGTAAT-ATTTTTA-A-TTA
1733938 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
1733955 TGTAGTGATTCAAAGATTTA
1 TGTAAT-ATTTTTA-A-TTA
*
1733975 TGTAATGTTTTTAATTA
1 TGTAATATTTTTAATTA
1733992 TGTA
1 TGTA
1733996 GTGATTTAAT
Statistics
Matches: 55, Mismatches: 17, Indels: 12
0.65 0.20 0.14
Matches are distributed among these distances:
17 20 0.36
18 10 0.18
19 9 0.16
20 16 0.29
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (17 bp):
TGTAATATTTTTAATTA
Found at i:1734016 original size:9 final size:9
Alignment explanation
Indices: 1734002--1734138 Score: 184
Period size: 9 Copynumber: 14.6 Consensus size: 9
1733992 TGTAGTGATT
1734002 TAATTCGGG
1 TAATTCGGG
1734011 TAATTCGGG
1 TAATTCGGG
1734020 TAATTTTCGGG
1 TAA--TTCGGG
1734031 TAATTTTCGGG
1 TAA--TTCGGG
1734042 TAATTCGGG
1 TAATTCGGG
*
1734051 TAATTTGGG
1 TAATTCGGG
1734060 TAATTTTCGGG
1 TAA--TTCGGG
1734071 TAATTCGGG
1 TAATTCGGG
1734080 TAATTCGGG
1 TAATTCGGG
*
1734089 TAAGTCGGG
1 TAATTCGGG
1734098 TAATTCGGG
1 TAATTCGGG
*
1734107 TAAGTCGGG
1 TAATTCGGG
*
1734116 TAATTCAGG
1 TAATTCGGG
1734125 TAATTCGGG
1 TAATTCGGG
1734134 TAATT
1 TAATT
1734139 TTTAACCAAA
Statistics
Matches: 116, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
9 88 0.76
11 28 0.24
ACGTcount: A:0.23, C:0.09, G:0.31, T:0.36
Consensus pattern (9 bp):
TAATTCGGG
Found at i:1734275 original size:28 final size:27
Alignment explanation
Indices: 1734243--1734308 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
1734233 AAAATTCAGT
1734243 TCGGTTAACGGTTA-AAAAATTTGAGAGG
1 TCGGTTAACGGTTACAAAAATTT-AG-GG
* *
1734271 TCGGTTAATTCGGTTACAAGAATTTCGGG
1 TCGGTTAA--CGGTTACAAAAATTTAGGG
1734300 TCGGTTAAC
1 TCGGTTAAC
1734309 CGGTCGGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 8 0.24
29 10 0.30
30 7 0.21
31 7 0.21
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (27 bp):
TCGGTTAACGGTTACAAAAATTTAGGG
Found at i:1734315 original size:12 final size:12
Alignment explanation
Indices: 1734298--1734322 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1734288 AAGAATTTCG
1734298 GGTCGGTTAACC
1 GGTCGGTTAACC
1734310 GGTCGGTTAACC
1 GGTCGGTTAACC
1734322 G
1 G
1734323 ACTGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:1736786 original size:35 final size:35
Alignment explanation
Indices: 1736740--1736809 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
1736730 TTAGTTTTGA
1736740 GGGCCAATAAATAAGAAGGTTCCATCCCCAGTTGT
1 GGGCCAATAAATAAGAAGGTTCCATCCCCAGTTGT
*
1736775 GGGCCAATAAATAGGAAGGTTCCATCCCCAGTTGT
1 GGGCCAATAAATAAGAAGGTTCCATCCCCAGTTGT
1736810 ACATACTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (35 bp):
GGGCCAATAAATAAGAAGGTTCCATCCCCAGTTGT
Found at i:1738111 original size:34 final size:33
Alignment explanation
Indices: 1738047--1738113 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
1738037 TAATAATTTT
*
1738047 TATTTTTTAAAATTTTAAAATTATAATTTTTTAG
1 TATTTTTTAAAAATTTAAAATTAT-ATTTTTTAG
*
1738081 TATTTTTTAATAAATTTATAAGTTAT-TTTTTTA
1 TATTTTTTAA-AAATTTA-AAATTATATTTTTTA
1738114 TAAAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 17 0.59
35 6 0.21
36 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (33 bp):
TATTTTTTAAAAATTTAAAATTATATTTTTTAG
Found at i:1738307 original size:16 final size:15
Alignment explanation
Indices: 1738281--1738310 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1738271 ATAATAATAT
1738281 TTAATTTAAATTTAG
1 TTAATTTAAATTTAG
1738296 TTAATATTAAATTTA
1 TTAAT-TTAAATTTA
1738311 AAAATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTAATTTAAATTTAG
Found at i:1754738 original size:39 final size:37
Alignment explanation
Indices: 1754671--1754763 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
1754661 ACCAGAATGG
* *
1754671 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
1754710 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
1754747 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
1754764 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:1755126 original size:3 final size:3
Alignment explanation
Indices: 1755118--1755161 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
1755108 ATTCCCACCC
* * *
1755118 ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA A-A TTA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1755162 TTATACTTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1755892 original size:17 final size:16
Alignment explanation
Indices: 1755860--1755893 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1755850 TTGGCTATTC
*
1755860 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
1755876 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
1755893 T
1 T
1755894 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:1755941 original size:14 final size:14
Alignment explanation
Indices: 1755882--1755932 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1755872 CTTTTGTTTC
*
1755882 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
1755895 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
1755910 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
1755924 TTTTATTTC
1 TTTTATTTC
1755933 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:1756101 original size:14 final size:17
Alignment explanation
Indices: 1756082--1756118 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
1756072 ATTTATTTCT
1756082 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
1756096 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
1756113 TAATAT
1 TAATAT
1756119 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:1761097 original size:21 final size:21
Alignment explanation
Indices: 1761055--1761097 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1761045 TTCAGTATAC
*
1761055 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
1761076 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
1761097 A
1 A
1761098 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:1762699 original size:37 final size:37
Alignment explanation
Indices: 1762649--1762727 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
1762639 TTATTACGAA
* *
1762649 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
1762686 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
1762723 GTCTT
1 GTCTT
1762728 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:1762924 original size:47 final size:47
Alignment explanation
Indices: 1762846--1763528 Score: 1096
Period size: 47 Copynumber: 14.4 Consensus size: 47
1762836 CCCTTCGGGA
* * * * * * *
1762846 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1762893 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1762940 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1762987 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1763034 CTTATCACATATATACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1763081 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1763130 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1763177 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1763224 CTTATCATACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1763271 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1763320 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1763367 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1763414 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1763461 CTTATATCATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 C-T-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1763510 CTTATCACATATATACACT
1 CTTATCACATATATACACT
1763529 GTCTTGGCTG
Statistics
Matches: 601, Mismatches: 29, Indels: 12
0.94 0.05 0.02
Matches are distributed among these distances:
47 464 0.77
48 2 0.00
49 135 0.22
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:1763167 original size:190 final size:190
Alignment explanation
Indices: 1762846--1763528 Score: 1174
Period size: 190 Copynumber: 3.6 Consensus size: 190
1762836 CCCTTCGGGA
** * * * * * * * *
1762846 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1762909 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
* * *
1762974 TCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
1763034 CTTATCACATATATACACTTTCTCATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1763099 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
1763164 TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
1763224 CTTATCATACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
1763289 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
1763354 TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1763414 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-ATCATATATATA
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA-CATATATATA
1763478 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
65 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
1763529 GTCTTGGCTG
Statistics
Matches: 471, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
188 45 0.10
189 1 0.00
190 425 0.90
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (190 bp):
CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:1763525 original size:143 final size:141
Alignment explanation
Indices: 1762846--1763528 Score: 1105
Period size: 143 Copynumber: 4.8 Consensus size: 141
1762836 CCCTTCGGGA
* * * * * * * * * *
1762846 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1762911 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
1762976 GGCCATTAGGC
131 GGCCATTAGGC
*
1762987 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
1763052 TTTCTCATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
1763117 TCGGCCATTAGGC
129 TCGGCCATTAGGC
*
1763130 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
* * *
1763195 TTTCACATTCATCACATCGGCTATTAGGCCTTATCATACATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
1763260 GGCCATTAGGC
131 GGCCATTAGGC
*
1763271 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATAC
* *
1763336 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
1763401 TCGGCTATTAGGC
129 TCGGCCATTAGGC
* * *
1763414 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATATCATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCC-T-TATCACATATATAC
1763479 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
1763529 GTCTTGGCTG
Statistics
Matches: 510, Mismatches: 26, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
141 174 0.34
142 1 0.00
143 335 0.66
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:1766879 original size:39 final size:37
Alignment explanation
Indices: 1766812--1766904 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
1766802 ACCAGAATGG
* *
1766812 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
1766851 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
1766888 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
1766905 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:1768027 original size:17 final size:16
Alignment explanation
Indices: 1767995--1768028 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1767985 TTGGCTATTC
*
1767995 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
1768011 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
1768028 T
1 T
1768029 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:1768076 original size:14 final size:14
Alignment explanation
Indices: 1768017--1768067 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1768007 CTTTTGTTTC
*
1768017 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
1768030 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
1768045 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
1768059 TTTTATTTC
1 TTTTATTTC
1768068 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:1768236 original size:14 final size:17
Alignment explanation
Indices: 1768217--1768253 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
1768207 ATTTATTTCT
1768217 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
1768231 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
1768248 TAATAT
1 TAATAT
1768254 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:1782490 original size:41 final size:41
Alignment explanation
Indices: 1782445--1782530 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
1782435 AAATGGGGTA
1782445 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
*
1782486 TGGGAGTGGCTTAGATACAAAAGGGTCTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
1782527 TGGG
1 TGGG
1782531 GATGGAGAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.26
Consensus pattern (41 bp):
TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
Found at i:1788951 original size:20 final size:20
Alignment explanation
Indices: 1788926--1788963 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1788916 GATAGTAATG
* *
1788926 AGATATCTATATCTATATCT
1 AGATATATATATATATATCT
1788946 AGATATATATATATATAT
1 AGATATATATATATATAT
1788964 GAGAAGCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
AGATATATATATATATATCT
Found at i:1791533 original size:29 final size:30
Alignment explanation
Indices: 1791501--1791571 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
1791491 CAAATAGAGT
* *
1791501 TTCATGTGTATAATTGCAC-CAAATTAAAG
1 TTCATGTATATAATTGCACACAAATCAAAG
* *
1791530 TTCATGTATATAATTTCACATTAAATCAAAG
1 TTCATGTATATAATTGCACA-CAAATCAAAG
1791561 TTCATGTATAT
1 TTCATGTATAT
1791572 TTTTTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 17 0.47
31 19 0.53
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (30 bp):
TTCATGTATATAATTGCACACAAATCAAAG
Found at i:1792007 original size:20 final size:22
Alignment explanation
Indices: 1791974--1792017 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1791964 GTTTTTAATG
1791974 TTTTAATGTGTTTG-ATAATCA
1 TTTTAATGTGTTTGCATAATCA
* *
1791995 TTTTAA-GTTTTTGCCTAATCA
1 TTTTAATGTGTTTGCATAATCA
1792016 TT
1 TT
1792018 ATTCCATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (22 bp):
TTTTAATGTGTTTGCATAATCA
Found at i:1793684 original size:12 final size:12
Alignment explanation
Indices: 1793667--1793705 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1793657 ATTTAGACTG
1793667 ATTTTTTTAAAT
1 ATTTTTTTAAAT
1793679 ATTTTTTT-AAT
1 ATTTTTTTAAAT
*
1793690 -TTTTTTTAAAA
1 ATTTTTTTAAAT
1793701 ATTTT
1 ATTTT
1793706 AATGATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 7 0.29
11 5 0.21
12 12 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTTTTTTAAAT
Found at i:1793713 original size:22 final size:22
Alignment explanation
Indices: 1793668--1793713 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1793658 TTTAGACTGA
* **
1793668 TTTTTTTAAATATTTTTTTAAT
1 TTTTTTTAAAAATTTTAATAAT
*
1793690 TTTTTTTAAAAATTTTAATGAT
1 TTTTTTTAAAAATTTTAATAAT
1793712 TT
1 TT
1793714 ATTTAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTTTAAAAATTTTAATAAT
Found at i:1813587 original size:20 final size:21
Alignment explanation
Indices: 1813564--1813606 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1813554 TAGTTGGCAT
*
1813564 TTTATATTTTTA-TAATTAAA
1 TTTAAATTTTTATTAATTAAA
*
1813584 TTTAAATTTTTATTATTTAAA
1 TTTAAATTTTTATTAATTAAA
1813605 TT
1 TT
1813607 GAATTCTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTAAATTTTTATTAATTAAA
Found at i:1813909 original size:74 final size:74
Alignment explanation
Indices: 1813752--1813902 Score: 272
Period size: 73 Copynumber: 2.1 Consensus size: 74
1813742 AGCTTTAAAT
1813752 TTTTATAAAATTGTTGATATATTACTTAAAATAAATTAATTACGAAACATAATCAGTTTTTTGAT
1 TTTTATAAAATTGTTGATATATTACTTAAAATAAATTAATTACGAAACATAATCAGTTTTTTGAT
1813817 AAATAAAGA
66 AAATAAAGA
1813826 TTTTATAAAATTGTTTGATATATTACTTAAAA-AAATT-ATTACGAAACATAATCAGTTTTTTGA
1 TTTTATAAAATTG-TTGATATATTACTTAAAATAAATTAATTACGAAACATAATCAGTTTTTTGA
1813889 T-AATAAAGA
65 TAAATAAAGA
1813898 TTTTA
1 TTTTA
1813903 ATTAAAAATA
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
72 13 0.17
73 27 0.36
74 18 0.24
75 18 0.24
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (74 bp):
TTTTATAAAATTGTTGATATATTACTTAAAATAAATTAATTACGAAACATAATCAGTTTTTTGAT
AAATAAAGA
Found at i:1814430 original size:68 final size:71
Alignment explanation
Indices: 1814309--1814453 Score: 228
Period size: 68 Copynumber: 2.1 Consensus size: 71
1814299 TATTTTTAAT
*
1814309 TAAAATCTTTATTTATCAAAAAACGATATGTTTCGTAATTAATTTTTTTAAGTAATATATCAAAC
1 TAAAATCTTTATTTATCAAAAAACGATATGTTTCGTAATTAATTTATTTAAGTAATATATC-AAC
1814374 AATTTTA
65 AATTTTA
1814381 TAAAATCTTTA-TTATC-AAAAACTGATA-G-TTCGTAATTAA-TTATTTAAGTAATATATCAAC
1 TAAAATCTTTATTTATCAAAAAAC-GATATGTTTCGTAATTAATTTATTTAAGTAATATATCAAC
1814441 AATTTTA
65 AATTTTA
1814448 TAAAAT
1 TAAAAT
1814454 TAAAGCTAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
67 16 0.23
68 17 0.24
69 11 0.15
70 7 0.10
71 9 0.13
72 11 0.15
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (71 bp):
TAAAATCTTTATTTATCAAAAAACGATATGTTTCGTAATTAATTTATTTAAGTAATATATCAACA
ATTTTA
Found at i:1814638 original size:21 final size:21
Alignment explanation
Indices: 1814596--1814638 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1814586 CCAAGAATTC
*
1814596 ATTTAAATAATAAAAATTTAA
1 ATTTAAATAATAAAAATGTAA
*
1814617 ATTT-AATTATAAAATATGTAA
1 ATTTAAATAATAAAA-ATGTAA
1814638 A
1 A
1814639 ATTCAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTAAATAATAAAAATGTAA
Found at i:1829049 original size:123 final size:124
Alignment explanation
Indices: 1828529--1829251 Score: 849
Period size: 125 Copynumber: 5.9 Consensus size: 124
1828519 TTAATACAGT
* * * * *
1828529 AATTTTTTCTAAAA-GC-TTTT-TTTTTTTAGAAATTTCCATATTGGATCTAATTAATACAATTA
1 AATTTTTT-TAAAAGGCATTTTCTTTTTTAAGTAA-TTACATATCGGATCTGATTAATACAATTA
* * * * * * *
1828591 A--C--T-AA-TTTTTTATTCTTCATATTTATTTTAAAGTT-ATTTTTAAAGTTTTTAAGTC
64 ACTCATTCAATTTTTTTATTCTTCATGTCTATTTTATAGTTCA-TATTCAAGGTTTCAAGTC
* *
1828646 AATTTTTTTAAAAGACATTTTC-TTTTTAAGTAATTACATATCGGATTTGATTAATACAATTAAC
1 AATTTTTTTAAAAGGCATTTTCTTTTTTAAGTAATTACATATCGGATCTGATTAATACAATTAAC
* * * *
1828710 TCATTCAATTTTTTTTATTCTTCATGTCTGTTTTATAGTTTATGTTCAAGGTTTCAAGCC
66 TCATTCAA-TTTTTTTATTCTTCATGTCTATTTTATAGTTCATATTCAAGGTTTCAAGTC
* *
1828770 AA--CTTTTAAAAGGCATTTTC-TTTTTAAGTAATTACATATCGGATCCGATTAATACAATTAAC
1 AATTTTTTTAAAAGGCATTTTCTTTTTTAAGTAATTACATATCGGATCTGATTAATACAATTAAC
* *
1828832 TCATTCAATTTTTTTATTATTCATGTCTATTTTATAGTTCTAGTTCATATTCAAGGTTTCAATTC
66 TCATTCAATTTTTTTATTCTTCATGTCTA-TTT-TA----TAGTTCATATTCAAGGTTTCAAGTC
* *
1828897 AATTTTTTTAAAAGGCATCTTCTTTTTTAAGTAATTACATATCGGATATGATTAATACAATTAAC
1 AATTTTTTTAAAAGGCATTTTCTTTTTTAAGTAATTACATATCGGATCTGATTAATACAATTAAC
** * * *
1828962 TCATTCAATTTTTACATTCTTCA-GCCTATTTTATAGTTCATATTCAATGTTTCAATTC
66 TCATTCAATTTTTTTATTCTTCATGTCTATTTTATAGTTCATATTCAAGGTTTCAAGTC
* * * *
1829020 AATTTTTTTAAAAGGCATTTTCTTTTTTAAGTAATTACATATTGGATCCGATTAATAGAATTATC
1 AATTTTTTTAAAAGGCATTTTCTTTTTTAAGTAATTACATATCGGATCTGATTAATACAATTAAC
* *
1829085 TCATTCAATTTTTTTTATTCTTCAGGTCTATTTTATAGTTCATATTCAAGGTTTTAAGTC
66 TCATTCAA-TTTTTTTATTCTTCATGTCTATTTTATAGTTCATATTCAAGGTTTCAAGTC
* *
1829145 AATTTTTTTAAAAGGCATTTTCTTTTTTAAGTAATTACATATTGGAT-TAGATTAATACAATTAT
1 AATTTTTTTAAAAGGCATTTTCTTTTTTAAGTAATTACATATCGGATCT-GATTAATACAATTAA
*
1829209 CTCATTCAA---TTTT-TT-TTCATGTCTATTTTATAGTTCATGTTCA
65 CTCATTCAATTTTTTTATTCTTCATGTCTATTTTATAGTTCATATTCA
1829252 GGATTTGAAA
Statistics
Matches: 532, Mismatches: 51, Indels: 44
0.85 0.08 0.07
Matches are distributed among these distances:
116 5 0.01
117 35 0.07
118 13 0.02
119 27 0.05
120 2 0.00
121 24 0.05
122 69 0.13
123 93 0.17
124 54 0.10
125 102 0.19
127 25 0.05
128 3 0.01
129 20 0.04
130 60 0.11
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.49
Consensus pattern (124 bp):
AATTTTTTTAAAAGGCATTTTCTTTTTTAAGTAATTACATATCGGATCTGATTAATACAATTAAC
TCATTCAATTTTTTTATTCTTCATGTCTATTTTATAGTTCATATTCAAGGTTTCAAGTC
Found at i:1829200 original size:248 final size:245
Alignment explanation
Indices: 1828596--1829251 Score: 862
Period size: 248 Copynumber: 2.7 Consensus size: 245
1828586 AATTAACTAA
* * * * * *
1828596 TTTTTTATTCTTCATATTTATTTTAAAGTT-ATTTTTAAAGTTTTTAAGTCAATTTTTTTAAAAG
1 TTTTTTATTCTTCATGTCTATTTTATAGTTCA-TATTCAAGGTTTTAAGTCAATTTTTTTAAAAG
* *
1828660 ACATTTTC-TTTTTAAGTAATTACATATCGGATTTGATTAATACAATTAACTCATTCAATTTTTT
65 GCATTTTCTTTTTTAAGTAATTACATATCGGATTAGATTAATACAATTAACTCATTCAA-TTTTT
** * * * *
1828724 TTATTCTTCATGTCTGTTTTATAGTTTATGTTCAAGGTTTCAAGCCAACTTTTAAAAGGCATTTT
129 ACATTCTTCATGCCTATTTTATAGTTCATATTCAAGGTTTCAAGCCAACTTTTAAAAGGCATTTT
1828789 CTTTTTAAGTAATTACATATCGGATCCGATTAATACAATTAACTCATTCAAT
194 CTTTTTAAGTAATTACATATCGGATCCGATTAATACAATTAACTCATTCAAT
* * *
1828841 TTTTTTATTATTCATGTCTATTTTATAGTTCTAGTTCATATTCAAGGTTTCAATTCAATTTTTTT
1 TTTTTTATTCTTCATGTCTA-TTT-TA----TAGTTCATATTCAAGGTTTTAAGTCAATTTTTTT
*
1828906 AAAAGGCATCTTCTTTTTTAAGTAATTACATATCGGA-TATGATTAATACAATTAACTCATTCAA
60 AAAAGGCATTTTCTTTTTTAAGTAATTACATATCGGATTA-GATTAATACAATTAACTCATTCAA
* ** *
1828970 TTTTTACATTCTTCA-GCCTATTTTATAGTTCATATTCAATGTTTCAATTCAATTTTTTTAAAAG
124 TTTTTACATTCTTCATGCCTATTTTATAGTTCATATTCAAGGTTTCAAGCCAA--CTTTTAAAAG
* * *
1829034 GCATTTTCTTTTTTAAGTAATTACATATTGGATCCGATTAATAGAATTATCTCATTCAATT
187 GCATTTTC-TTTTTAAGTAATTACATATCGGATCCGATTAATACAATTAACTCATTCAA-T
*
1829095 TTTTTTATTCTTCAGGTCTATTTTATAGTTCATATTCAAGGTTTTAAGTCAATTTTTTTAAAAGG
1 TTTTTTATTCTTCATGTCTATTTTATAGTTCATATTCAAGGTTTTAAGTCAATTTTTTTAAAAGG
* *
1829160 CATTTTCTTTTTTAAGTAATTACATATTGGATTAGATTAATACAATTATCTCATTCAA-TTTT--
66 CATTTTCTTTTTTAAGTAATTACATATCGGATTAGATTAATACAATTAACTCATTCAATTTTTAC
* *
1829222 -TT-TTCATGTCTATTTTATAGTTCATGTTCA
131 ATTCTTCATGCCTATTTTATAGTTCATATTCA
1829252 GGATTTGAAA
Statistics
Matches: 362, Mismatches: 34, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
243 4 0.01
244 23 0.06
245 17 0.05
246 3 0.01
247 6 0.02
248 90 0.25
249 2 0.01
250 30 0.08
251 51 0.14
252 67 0.19
253 50 0.14
254 19 0.05
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.50
Consensus pattern (245 bp):
TTTTTTATTCTTCATGTCTATTTTATAGTTCATATTCAAGGTTTTAAGTCAATTTTTTTAAAAGG
CATTTTCTTTTTTAAGTAATTACATATCGGATTAGATTAATACAATTAACTCATTCAATTTTTAC
ATTCTTCATGCCTATTTTATAGTTCATATTCAAGGTTTCAAGCCAACTTTTAAAAGGCATTTTCT
TTTTAAGTAATTACATATCGGATCCGATTAATACAATTAACTCATTCAAT
Found at i:1829449 original size:150 final size:150
Alignment explanation
Indices: 1829178--1829476 Score: 598
Period size: 150 Copynumber: 2.0 Consensus size: 150
1829168 TTTTTAAGTA
1829178 ATTACATATTGGATTAGATTAATACAATTATCTCATTCAATTTTTTTTCATGTCTATTTTATAGT
1 ATTACATATTGGATTAGATTAATACAATTATCTCATTCAATTTTTTTTCATGTCTATTTTATAGT
1829243 TCATGTTCAGGATTTGAAATTGTCCTTTTCAATAACATAATCTCTAATATTCAAACATACATTTT
66 TCATGTTCAGGATTTGAAATTGTCCTTTTCAATAACATAATCTCTAATATTCAAACATACATTTT
1829308 CTCTTAAAAGGTGTATTACC
131 CTCTTAAAAGGTGTATTACC
1829328 ATTACATATTGGATTAGATTAATACAATTATCTCATTCAATTTTTTTTCATGTCTATTTTATAGT
1 ATTACATATTGGATTAGATTAATACAATTATCTCATTCAATTTTTTTTCATGTCTATTTTATAGT
1829393 TCATGTTCAGGATTTGAAATTGTCCTTTTCAATAACATAATCTCTAATATTCAAACATACATTTT
66 TCATGTTCAGGATTTGAAATTGTCCTTTTCAATAACATAATCTCTAATATTCAAACATACATTTT
1829458 CTCTTAAAAGGTGTATTAC
131 CTCTTAAAAGGTGTATTAC
1829477 TATTCCACTC
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (150 bp):
ATTACATATTGGATTAGATTAATACAATTATCTCATTCAATTTTTTTTCATGTCTATTTTATAGT
TCATGTTCAGGATTTGAAATTGTCCTTTTCAATAACATAATCTCTAATATTCAAACATACATTTT
CTCTTAAAAGGTGTATTACC
Found at i:1833905 original size:19 final size:19
Alignment explanation
Indices: 1833866--1833904 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1833856 TATGTTATTT
1833866 TATTATATAATATAATATA
1 TATTATATAATATAATATA
*
1833885 TATTATAT--TATTATATA
1 TATTATATAATATAATATA
1833902 TAT
1 TAT
1833905 AAAACAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
19 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATATAATATAATATA
Found at i:1833989 original size:15 final size:14
Alignment explanation
Indices: 1833967--1833996 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1833957 AACAGGGGAG
1833967 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
1833981 AAAGTAAAGAAAGAA
1 AAAG-AAAGAAAGAA
1833996 A
1 A
1833997 TTTAGGGTTT
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:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:1834987 original size:22 final size:22
Alignment explanation
Indices: 1834936--1834988 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 22
1834926 TCTCTGATTA
*
1834936 TTAGCACGTTGGTGCTTTTGATAT
1 TTAGCACGTTAGTGCTTTTG--AT
1834960 TTAGCACGTTAGTGCTCTTTG-T
1 TTAGCACGTTAGTGCT-TTTGAT
1834982 TTAGCAC
1 TTAGCAC
1834989 ATCTGTGCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 8 0.30
24 15 0.56
25 4 0.15
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (22 bp):
TTAGCACGTTAGTGCTTTTGAT
Found at i:1852752 original size:21 final size:21
Alignment explanation
Indices: 1852728--1852779 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1852718 AGCTCGTTTG
1852728 AGCTTCTGTTCAGCTCTTACA
1 AGCTTCTGTTCAGCTCTTACA
* * **
1852749 AGCTTCTGCTCAGCTTTTATG
1 AGCTTCTGTTCAGCTCTTACA
1852770 AGCTTCTGTT
1 AGCTTCTGTT
1852780 AACGATGTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.42
Consensus pattern (21 bp):
AGCTTCTGTTCAGCTCTTACA
Found at i:1854373 original size:51 final size:51
Alignment explanation
Indices: 1854297--1854401 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
1854287 TTTTTAAGAA
1854297 TGTAAGTAAGTATGTTCATAAGGCCTAGCACACGGGCGTGTGACTTGGCCG
1 TGTAAGTAAGTATGTTCATAAGGCCTAGCACACGGGCGTGTGACTTGGCCG
1854348 TGTAAGTAAGTATGTTCATAAGGCCTAGCACACGGGCGTGTGACTTGGCCG
1 TGTAAGTAAGTATGTTCATAAGGCCTAGCACACGGGCGTGTGACTTGGCCG
1854399 TGT
1 TGT
1854402 GACCCAAGTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (51 bp):
TGTAAGTAAGTATGTTCATAAGGCCTAGCACACGGGCGTGTGACTTGGCCG
Found at i:1854483 original size:31 final size:31
Alignment explanation
Indices: 1854445--1854510 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1854435 ACAGGCTGAG
* *
1854445 ACACGGCCGTGTGTTCTTATTTCCAATGTCC
1 ACACGGCCGTGTGTTCCTATTTCAAATGTCC
1854476 ACACGGCCGTGTGTTCCTATTTCAAATGTCC
1 ACACGGCCGTGTGTTCCTATTTCAAATGTCC
1854507 ACAC
1 ACAC
1854511 CGCCTAAGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (31 bp):
ACACGGCCGTGTGTTCCTATTTCAAATGTCC
Found at i:1855613 original size:2 final size:2
Alignment explanation
Indices: 1855602--1855632 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1855592 TTTTTTTTCT
*
1855602 TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1855633 ATTAATAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1856800 original size:2 final size:2
Alignment explanation
Indices: 1856793--1856824 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1856783 TCTGTTCATA
1856793 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1856825 CTCGCATTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1871548 original size:32 final size:32
Alignment explanation
Indices: 1871490--1871554 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1871480 CACTTTTCAC
**
1871490 GCTTCTGGTTTAGTCCTGGACCATCTTTTTAG
1 GCTTCTGGTTTAGTCCTAAACCATCTTTTTAG
*
1871522 GCTTCTGGTTTAGAT-CTAAACGATCTTTTTAG
1 GCTTCTGGTTTAG-TCCTAAACCATCTTTTTAG
1871554 G
1 G
1871555 TTTGAAGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (32 bp):
GCTTCTGGTTTAGTCCTAAACCATCTTTTTAG
Found at i:1886845 original size:35 final size:35
Alignment explanation
Indices: 1886806--1886915 Score: 102
Period size: 36 Copynumber: 3.1 Consensus size: 35
1886796 AAGAACAAAC
1886806 AAAAACATATGAAAAGGAATATTTGTTAAACAACAA
1 AAAAACATAT-AAAAGGAATATTTGTTAAACAACAA
** *
1886842 AAAAACATA-AAAA--AA-AAGTGTTAGAAGAACAA
1 AAAAACATATAAAAGGAATATTTGTTA-AACAACAA
* *
1886874 ACAAAAAATTATAAAAAGGAATATTTGTTAAACAACGA
1 A-AAAACA-TAT-AAAAGGAATATTTGTTAAACAACAA
1886912 AAAA
1 AAAA
1886916 CAAACAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
31 6 0.10
32 10 0.17
33 5 0.09
34 6 0.10
36 13 0.22
37 3 0.05
38 9 0.16
39 6 0.10
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.19
Consensus pattern (35 bp):
AAAAACATATAAAAGGAATATTTGTTAAACAACAA
Found at i:1886893 original size:70 final size:70
Alignment explanation
Indices: 1886783--1886915 Score: 223
Period size: 70 Copynumber: 1.9 Consensus size: 70
1886773 AAGCAATACT
* *
1886783 AAAAAAGTGTTGGAAGAACAAACAAAAACATATGAAAAGGAATATTTGTTAAACAACAAAAAAAC
1 AAAAAAGTGTTAGAAGAACAAACAAAAACATATAAAAAGGAATATTTGTTAAACAACAAAAAAAC
1886848 ATAAA
66 ATAAA
*
1886853 AAAAAAGTGTTAGAAGAACAAACAAAAA-ATTATAAAAAGGAATATTTGTTAAACAACGAAAAA
1 AAAAAAGTGTTAGAAGAACAAACAAAAACA-TATAAAAAGGAATATTTGTTAAACAACAAAAAA
1886916 CAAACAAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 1 0.02
70 58 0.98
ACGTcount: A:0.62, C:0.08, G:0.13, T:0.18
Consensus pattern (70 bp):
AAAAAAGTGTTAGAAGAACAAACAAAAACATATAAAAAGGAATATTTGTTAAACAACAAAAAAAC
ATAAA
Found at i:1905020 original size:18 final size:19
Alignment explanation
Indices: 1904994--1905029 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1904984 AACTAAAATG
*
1904994 TACCTTAAA-TTAATAATT
1 TACCCTAAATTTAATAATT
1905012 TACCCTAAATTTAATAAT
1 TACCCTAAATTTAATAAT
1905030 AGTTTAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (19 bp):
TACCCTAAATTTAATAATT
Found at i:1906653 original size:14 final size:15
Alignment explanation
Indices: 1906634--1906666 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1906624 TTAATCTATC
*
1906634 AAATTAAAA-ATTAA
1 AAATTAAAAGAATAA
1906648 AAATTAAAAGAATAA
1 AAATTAAAAGAATAA
1906663 AAAT
1 AAAT
1906667 AAACCCATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAATTAAAAGAATAA
Found at i:1907130 original size:15 final size:16
Alignment explanation
Indices: 1907101--1907134 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1907091 AATATCTTAT
*
1907101 AAAGAATTTTATATTA
1 AAAGAACTTTATATTA
1907117 AAAGAACTTT-TATTA
1 AAAGAACTTTATATTA
1907132 AAA
1 AAA
1907135 ATAAATTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (16 bp):
AAAGAACTTTATATTA
Found at i:1909228 original size:6 final size:6
Alignment explanation
Indices: 1909219--1909258 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1909209 ATTGTTTTAA
* *
1909219 AAAAAT AAAAAT AAAAAT GAAAAT AAAAAAT GAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT AAA
1909259 TTATTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:1909241 original size:13 final size:12
Alignment explanation
Indices: 1909219--1909258 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
1909209 ATTGTTTTAA
*
1909219 AAAAATAAAAAT
1 AAAAATGAAAAT
1909231 AAAAATGAAAAT
1 AAAAATGAAAAT
1909243 AAAAAATGAAAAT
1 -AAAAATGAAAAT
1909256 AAA
1 AAA
1909259 TTATTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 14 0.54
13 12 0.46
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAAATGAAAAT
Found at i:1918614 original size:23 final size:25
Alignment explanation
Indices: 1918590--1918639 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
1918580 CTAAAATGTT
*
1918590 ATTTTTTTATTTATCAAAATATTATA
1 ATTTTTTTATTTACCAAAATA-TATA
1918616 ATTTTTTTATTTACCAAAATATAT
1 ATTTTTTTATTTACCAAAATATAT
1918640 CAAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTTTTTATTTACCAAAATATATA
Found at i:1919161 original size:19 final size:19
Alignment explanation
Indices: 1919137--1919199 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1919127 TCTAATTAAG
1919137 TAATAATTCTATTTTACTT
1 TAATAATTCTATTTTACTT
** ***
1919156 TAATAAGTT-TATTAAAAAG
1 TAATAA-TTCTATTTTACTT
*
1919175 TAATAACTCTATTTTACTT
1 TAATAATTCTATTTTACTT
1919194 TAATAA
1 TAATAA
1919200 ACTATTGCTT
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
18 1 0.03
19 28 0.90
20 2 0.06
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (19 bp):
TAATAATTCTATTTTACTT
Found at i:1920692 original size:28 final size:27
Alignment explanation
Indices: 1920637--1920699 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 27
1920627 TTTTTTTTGT
**
1920637 ATATTTTGATAAATAAAAAAAATTATA
1 ATATTTTGATAAATAAAAAAAAGGATA
1920664 ATATTTTGATAAATAAAAAAAAAGGATA
1 ATATTTTGATAAAT-AAAAAAAAGGATA
*
1920692 ACATTTTG
1 ATATTTTG
1920700 GTTATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 14 0.44
28 18 0.56
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.35
Consensus pattern (27 bp):
ATATTTTGATAAATAAAAAAAAGGATA
Found at i:1923347 original size:22 final size:23
Alignment explanation
Indices: 1923322--1923364 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1923312 AATAAGTAGG
* *
1923322 CTTTCAA-AGGTGAAGTTTATCC
1 CTTTCAAGAGATGAACTTTATCC
1923344 CTTTCAAGAGATGAACTTTAT
1 CTTTCAAGAGATGAACTTTAT
1923365 GGCTAGTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (23 bp):
CTTTCAAGAGATGAACTTTATCC
Found at i:1929782 original size:21 final size:22
Alignment explanation
Indices: 1929758--1929802 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1929748 AAATTTAGTG
1929758 TTAAGATAAAATAT-TGTTTAA
1 TTAAGATAAAATATGTGTTTAA
* * *
1929779 TTAATATAAATTTTGTGTTTAA
1 TTAAGATAAAATATGTGTTTAA
1929801 TT
1 TT
1929803 TTAAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TTAAGATAAAATATGTGTTTAA
Found at i:1933342 original size:12 final size:13
Alignment explanation
Indices: 1933315--1933341 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1933305 TTTACCGAGT
1933315 AAGATTTTTATAA
1 AAGATTTTTATAA
1933328 AAGATTTTTATAA
1 AAGATTTTTATAA
1933341 A
1 A
1933342 GGAGTTGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
AAGATTTTTATAA
Found at i:1940373 original size:33 final size:33
Alignment explanation
Indices: 1940331--1940453 Score: 158
Period size: 33 Copynumber: 3.7 Consensus size: 33
1940321 GATACATGTG
*
1940331 TAAGACCATAACTGGGCTATGGCATTCTGATGA
1 TAAGACCATAACTGGGCTATGACATTCTGATGA
* * * **
1940364 TAAGACCATAATTGGGTTATGACACTACAAATG-
1 TAAGACCATAACTGGGCTATGACA-TTCTGATGA
*
1940397 TAAGACCATAGCTGGGCTATGACATTCTGATGA
1 TAAGACCATAACTGGGCTATGACATTCTGATGA
*
1940430 TAAGACCATAACTGGGTTATGACA
1 TAAGACCATAACTGGGCTATGACA
1940454 CTACAAATGT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
32 5 0.07
33 64 0.86
34 5 0.07
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (33 bp):
TAAGACCATAACTGGGCTATGACATTCTGATGA
Found at i:1940412 original size:66 final size:66
Alignment explanation
Indices: 1940329--1940510 Score: 253
Period size: 66 Copynumber: 2.8 Consensus size: 66
1940319 TAGATACATG
*
1940329 TGTAAGACCATAACTGGGCTATGGCATTCTGATGATAAGACCATAATTGGGTTATGACACTACAA
1 TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAATTGGGTTATGACACTACAA
1940394 A
66 A
* *
1940395 TGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGACACTACAA
1 TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAATTGGGTTATGACACTACAA
1940460 A
66 A
* * * *
1940461 TGTAAGATCATGGCAGGGAC-ATGGCAATGTATG-TG-TAAGACCATAATTGG
1 TGTAAGACCATAGCTGGG-CTATGGC-AT-TCTGATGATAAGACCATAATTGG
1940511 ACTATAGCAC
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
66 96 0.92
67 5 0.05
68 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (66 bp):
TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAATTGGGTTATGACACTACAA
A
Found at i:1940467 original size:33 final size:32
Alignment explanation
Indices: 1940329--1940467 Score: 143
Period size: 33 Copynumber: 4.2 Consensus size: 32
1940319 TAGATACATG
* * **
1940329 TGTAAGACCATAACTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTGGGCTATGACATACAAA
* *
1940361 TGATAAGACCATAATTGGGTTATGACACTACAAA
1 TG-TAAGACCATAACTGGGCTATGACA-TACAAA
* * **
1940395 TGTAAGACCATAGCTGGGCTATGACATTCTGA
1 TGTAAGACCATAACTGGGCTATGACATACAAA
*
1940427 TGATAAGACCATAACTGGGTTATGACACTACAAA
1 TG-TAAGACCATAACTGGGCTATGACA-TACAAA
1940461 TGTAAGA
1 TGTAAGA
1940468 TCATGGCAGG
Statistics
Matches: 86, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
32 7 0.08
33 69 0.80
34 10 0.12
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGACATACAAA
Found at i:1942324 original size:178 final size:178
Alignment explanation
Indices: 1942025--1942381 Score: 705
Period size: 178 Copynumber: 2.0 Consensus size: 178
1942015 TTTCATTTAC
1942025 TTATACCTACCTATTTAACTCATTTCATTGATTTATCGAATTCTACTACTAATTACATAAACATA
1 TTATACCTACCTATTTAACTCATTTCATTGATTTATCGAATTCTACTACTAATTACATAAACATA
1942090 CATACAATATATATATTATTTACAACCACATTTCAAATTATATAATTGCCAATTCAACCTTATAC
66 CATACAATATATATATTATTTACAACCACATTTCAAATTATATAATTGCCAATTCAACCTTATAC
1942155 ATGTCATATAAACCAAAATTTACATTGTAAAAACTGGATTAAACTGGA
131 ATGTCATATAAACCAAAATTTACATTGTAAAAACTGGATTAAACTGGA
1942203 TTATACCTACCTATTTAACTCATTTCATTGATTTATCGAATTCTACTACTAATTACATAAACATA
1 TTATACCTACCTATTTAACTCATTTCATTGATTTATCGAATTCTACTACTAATTACATAAACATA
*
1942268 CATACAATATATATATTATTTACAACCACATTTCAAATTATATCATTGCCAATTCAACCTTATAC
66 CATACAATATATATATTATTTACAACCACATTTCAAATTATATAATTGCCAATTCAACCTTATAC
1942333 ATGTCATATAAACCAAAATTTACATTGTAAAAACTGGATTAAACTGGA
131 ATGTCATATAAACCAAAATTTACATTGTAAAAACTGGATTAAACTGGA
1942381 T
1 T
1942382 AGTGTAGCTT
Statistics
Matches: 178, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
178 178 1.00
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (178 bp):
TTATACCTACCTATTTAACTCATTTCATTGATTTATCGAATTCTACTACTAATTACATAAACATA
CATACAATATATATATTATTTACAACCACATTTCAAATTATATAATTGCCAATTCAACCTTATAC
ATGTCATATAAACCAAAATTTACATTGTAAAAACTGGATTAAACTGGA
Found at i:1950202 original size:42 final size:41
Alignment explanation
Indices: 1950127--1950207 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 41
1950117 TAATAATATA
* *
1950127 TAATATAAACATTAAAAAATTAAGATAACTATATATTAAAT
1 TAATATAAACATTAAAAAATTAAAATAAATATATATTAAAT
* *
1950168 TAATATAAA-ATTATTAAATATTAAAATAAATATATTTTAA
1 TAATATAAACATTA--AAAAATTAAAATAAATATATATTAA
1950208 TAAATAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 4 0.12
41 9 0.26
42 21 0.62
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (41 bp):
TAATATAAACATTAAAAAATTAAAATAAATATATATTAAAT
Found at i:1950203 original size:21 final size:19
Alignment explanation
Indices: 1950143--1950203 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 19
1950133 AAACATTAAA
*
1950143 AAATTAAGATAACTATATATT
1 AAATTAAAATAA--ATATATT
*
1950164 AAATTAATATAAA-ATTATT
1 AAATTAAAATAAATA-TATT
1950183 AAATATTAAAATAAATATATT
1 -AA-ATTAAAATAAATATATT
1950204 TTAATAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 1 0.03
19 5 0.15
20 2 0.06
21 25 0.74
22 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
AAATTAAAATAAATATATT
Found at i:1954160 original size:11 final size:11
Alignment explanation
Indices: 1954133--1954178 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
1954123 ATTAATCATT
*
1954133 TCTCAATTATTC
1 TCTCAATT-TCC
1954145 TCTCAATTTCC
1 TCTCAATTTCC
*
1954156 TCTCAATTTGC
1 TCTCAATTTCC
1954167 TCTCAATTTCC
1 TCTCAATTTCC
1954178 T
1 T
1954179 TCCAAATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 23 0.74
12 8 0.26
ACGTcount: A:0.20, C:0.30, G:0.02, T:0.48
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:1954172 original size:22 final size:21
Alignment explanation
Indices: 1954133--1954194 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 21
1954123 ATTAATCATT
1954133 TCTCAATTATTCTCTCAATTTCC
1 TCTCAA-T-TTCTCTCAATTTCC
1954156 TCTCAATTTGCTCTCAATTTCC
1 TCTCAATTT-CTCTCAATTTCC
1954178 T-TCCAAATTTCTCTCAA
1 TCT-C-AATTTCTCTCAA
1954195 ATCCATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 3 0.08
22 22 0.61
23 11 0.31
ACGTcount: A:0.23, C:0.31, G:0.02, T:0.45
Consensus pattern (21 bp):
TCTCAATTTCTCTCAATTTCC
Found at i:1954252 original size:16 final size:16
Alignment explanation
Indices: 1954231--1954266 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1954221 AAATCCCTAT
*
1954231 TTTTAATTTTTTTTAA
1 TTTTAATTTTTTTAAA
1954247 TTTTAATTTTTTTAAA
1 TTTTAATTTTTTTAAA
1954263 TTTT
1 TTTT
1954267 TTTAAATCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTAATTTTTTTAAA
Found at i:1956051 original size:18 final size:18
Alignment explanation
Indices: 1956028--1956070 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1956018 TGCCAGGTGC
* *
1956028 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
1956046 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
1956064 GTTTCCT
1 GTATCCT
1956071 TTTCTGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:1957584 original size:26 final size:26
Alignment explanation
Indices: 1957543--1957607 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 26
1957533 TATAATAAAT
1957543 AAATATTTTTTATTC-TTTAATTTTA
1 AAATATTTTTTATTCTTTTAATTTTA
*
1957568 AAATATTTTTTTATTCTTTTTATTTTTA
1 AAATA-TTTTTTATTC-TTTTAATTTTA
1957596 AAATAATTTTTT
1 AAAT-ATTTTTT
1957608 CGATGTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 5 0.14
26 10 0.29
28 19 0.54
29 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (26 bp):
AAATATTTTTTATTCTTTTAATTTTA
Found at i:1957853 original size:14 final size:15
Alignment explanation
Indices: 1957827--1957857 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1957817 TTTAATTTTT
1957827 AACCTTAAAACCCTA
1 AACCTTAAAACCCTA
1957842 AACCTT-AAACCCTA
1 AACCTTAAAACCCTA
1957856 AA
1 AA
1957858 AGCAGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCTTAAAACCCTA
Found at i:1962892 original size:18 final size:18
Alignment explanation
Indices: 1962869--1962904 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1962859 CAAAGTTTGA
1962869 ATAATCAGTTAACGGTTG
1 ATAATCAGTTAACGGTTG
1962887 ATAATCAGTTAACGGTTG
1 ATAATCAGTTAACGGTTG
1962905 TAACAGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (18 bp):
ATAATCAGTTAACGGTTG
Found at i:1987066 original size:22 final size:23
Alignment explanation
Indices: 1987040--1987091 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1987030 TTTTATGTTG
*
1987040 ATATATTATAATAT-AAATAATT
1 ATATATTATAATATAAAATAAAT
* *
1987062 ATATAATCTAATATGAAAATAAAT
1 ATATATTATAATAT-AAAATAAAT
1987086 ATATAT
1 ATATAT
1987092 GATTGAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 12 0.50
24 12 0.50
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
ATATATTATAATATAAAATAAAT
Found at i:1998173 original size:22 final size:24
Alignment explanation
Indices: 1998125--1998173 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
1998115 GAGCTTCTTA
* *
1998125 TATATTTTTCTTGAATTTTTCATT
1 TATATTTTTCTTGAATTTTTAAAT
1998149 TATATTTTT-TTGAA-TTTTAAAT
1 TATATTTTTCTTGAATTTTTAAAT
1998171 TAT
1 TAT
1998174 TTGTTAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 5 0.22
24 9 0.39
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TATATTTTTCTTGAATTTTTAAAT
Found at i:2000191 original size:3 final size:3
Alignment explanation
Indices: 2000185--2000210 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2000175 CTCTTTTTTT
2000185 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
2000211 TCATGTATAT
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:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2018659 original size:36 final size:36
Alignment explanation
Indices: 2018590--2018662 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
2018580 AGAAAGTTGC
** * * *
2018590 AACTTAACAAGCAAATGTTTTTAAGATAGTAACAAA
1 AACTTAACAAGCAAATGACTCTAAAATAATAACAAA
*
2018626 AACTTAGCAAGCAAATGACTCTAAAATAATAACAAA
1 AACTTAACAAGCAAATGACTCTAAAATAATAACAAA
2018662 A
1 A
2018663 TTAATAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.23
Consensus pattern (36 bp):
AACTTAACAAGCAAATGACTCTAAAATAATAACAAA
Found at i:2023736 original size:21 final size:21
Alignment explanation
Indices: 2023710--2023750 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2023700 ATATGCTCAA
* *
2023710 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2023731 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2023751 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Done.