Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold298
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: 1060864
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.35
Warning! 20344 characters in sequence are not A, C, G, or T
File 3 of 7
Found at i:280967 original size:17 final size:18
Alignment explanation
Indices: 280947--280984 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
280937 TTTTGATATC
280947 TTTGTTATTTAAGTT-TT
1 TTTGTTATTTAAGTTATT
280964 TTTGTTATTTAAGTTATT
1 TTTGTTATTTAAGTTATT
280982 TTT
1 TTT
280985 ATAAGATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71
Consensus pattern (18 bp):
TTTGTTATTTAAGTTATT
Found at i:281610 original size:31 final size:32
Alignment explanation
Indices: 281575--281645 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
281565 TTTGAAGTCC
* *
281575 TTATTAAT-CTAAATTTTTCTTAA-CTGATTTT
1 TTATTAATACTAAATATTT-TTAATCTAATTTT
* *
281606 TTATTAATATTAACTATTTTTAATCTAATTTT
1 TTATTAATACTAAATATTTTTAATCTAATTTT
281638 TTATTAAT
1 TTATTAAT
281646 TATTCCCCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.59
Consensus pattern (32 bp):
TTATTAATACTAAATATTTTTAATCTAATTTT
Found at i:281634 original size:21 final size:21
Alignment explanation
Indices: 281594--281634 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
281584 TAAATTTTTC
*
281594 TTAACTGATTTTTTATTAATA
1 TTAACTGATTTTTAATTAATA
281615 TTAACT-ATTTTTAATCTAAT
1 TTAACTGATTTTTAAT-TAAT
281635 TTTTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TTAACTGATTTTTAATTAATA
Found at i:282515 original size:19 final size:19
Alignment explanation
Indices: 282488--282530 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
282478 TAATTATATG
*
282488 ATTTTATTTA-AAATAAAAT
1 ATTTAATTTATAAA-AAAAT
*
282507 ATTTAATTTATAAAAATAT
1 ATTTAATTTATAAAAAAAT
282526 ATTTA
1 ATTTA
282531 TAATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAATTTATAAAAAAAT
Found at i:283037 original size:15 final size:15
Alignment explanation
Indices: 283019--283048 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
283009 TAAATACATC
*
283019 TAAACAAAATATATT
1 TAAACAAAAGATATT
283034 TAAACAAAAGATATT
1 TAAACAAAAGATATT
283049 CTTCAATTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (15 bp):
TAAACAAAAGATATT
Found at i:283613 original size:16 final size:16
Alignment explanation
Indices: 283592--283647 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
283582 ATATGGAGTA
283592 AATTTATTAATAATAT
1 AATTTATTAATAATAT
*
283608 AATTTACTAATAATAATT
1 AATTTATTAATAAT-A-T
283626 AATATTTATATAATAATAT
1 -A-ATTTAT-TAATAATAT
283645 AAT
1 AAT
283648 AACACAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
16 13 0.39
17 3 0.09
18 2 0.06
19 2 0.06
20 6 0.18
21 7 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTTATTAATAATAT
Found at i:283792 original size:131 final size:131
Alignment explanation
Indices: 283588--283825 Score: 307
Period size: 131 Copynumber: 1.8 Consensus size: 131
283578 CTAAATATGG
* * * * * *
283588 AGTAAATTTATTAATAATATAATTTACTAATAATAATTAATATTTATATAATAATATAATAACAC
1 AGTAAATGTACTAATAATATAATTTAATAATAATAATCAATATTTATATAACAATACAATAACAC
* * * *
283653 AAATTATAT-GATAACTTTATAAACTTAAATAGTAATAATATATAGTATGACATGTACTAAATAA
66 AAAGTATATAG-TAACTATATAAAATTAAATACTAATAATATATAGTATGACATGTACTAAATAA
283717 AA
130 AA
* * * * *
283719 AGTAAATGTACTAATAATATAATTTAATAATATTAATCAATATTTATATAGCAATACAGTAGCAT
1 AGTAAATGTACTAATAATATAATTTAATAATAATAATCAATATTTATATAACAATACAATAACAC
* *
283784 GACGTATATAGTAACTATATAAAATTAAATACTAATAATATA
66 AAAGTATATAGTAACTATATAAAATTAAATACTAATAATATA
283826 CATCAATAAT
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
131 88 0.99
132 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (131 bp):
AGTAAATGTACTAATAATATAATTTAATAATAATAATCAATATTTATATAACAATACAATAACAC
AAAGTATATAGTAACTATATAAAATTAAATACTAATAATATATAGTATGACATGTACTAAATAAA
A
Found at i:284306 original size:29 final size:29
Alignment explanation
Indices: 284269--284325 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
284259 TTTGAAAAAC
284269 CGTAATAAGTTTTATTC-TTTCAAAAATAT
1 CGTAATAAGTTTTATTCATTT-AAAAATAT
284298 CGTAATAAGTTTTATTCATTTAAAAATA
1 CGTAATAAGTTTTATTCATTTAAAAATA
284326 CTCTAAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (29 bp):
CGTAATAAGTTTTATTCATTTAAAAATAT
Found at i:284561 original size:13 final size:13
Alignment explanation
Indices: 284543--284567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
284533 CAGTATGCTT
284543 TGTATCGATACAA
1 TGTATCGATACAA
284556 TGTATCGATACA
1 TGTATCGATACA
284568 TGCTCAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:284600 original size:20 final size:19
Alignment explanation
Indices: 284553--284607 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
284543 TGTATCGATA
* *
284553 CAATGTATCGATACATGCT
1 CAATGTATCGATATATACT
284572 CAATGTATCGATATATACT
1 CAATGTATCGATATATACT
284591 CAATTGTATCGATATAT
1 CAA-TGTATCGATATAT
284608 GAAATTGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (19 bp):
CAATGTATCGATATATACT
Found at i:286266 original size:3 final size:3
Alignment explanation
Indices: 286253--286307 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
286243 ATCAAAGATA
*
286253 ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
*
286301 GTG ATG A
1 ATG ATG A
286308 AGTTGACTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:286753 original size:16 final size:15
Alignment explanation
Indices: 286732--286772 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
286722 AAATAAATCA
286732 AAATTTGTTGAGAATG
1 AAATTTGTTGAGAA-G
*
286748 AAATTTCTTGAGAAG
1 AAATTTGTTGAGAAG
286763 AAA-TTGTTGA
1 AAATTTGTTGA
286773 ACTAGAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 13 0.57
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (15 bp):
AAATTTGTTGAGAAG
Found at i:290868 original size:13 final size:13
Alignment explanation
Indices: 290833--290869 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
290823 AATGTTTTAA
290833 GTATCGATACATT
1 GTATCGATACATT
*
290846 GTCTCGATACATT
1 GTATCGATACATT
*
290859 GTATCAATACA
1 GTATCGATACA
290870 GGGTTACTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:291016 original size:20 final size:20
Alignment explanation
Indices: 290993--291030 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
290983 AAAAAAAATT
290993 ATCT-TTTTCACATCAAAACA
1 ATCTATTTT-ACATCAAAACA
*
291013 ATCTATTTTTCATCAAAA
1 ATCTATTTTACATCAAAA
291031 TCATCAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (20 bp):
ATCTATTTTACATCAAAACA
Found at i:291667 original size:13 final size:13
Alignment explanation
Indices: 291649--291674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
291639 GATAAAGTGT
291649 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
291662 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
291675 AAAAACAATT
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:291713 original size:21 final size:21
Alignment explanation
Indices: 291689--291745 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
291679 ACAATTTCCA
291689 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
291710 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
291731 AATGTATCGATACAT
1 AATGTATCGATACAT
291746 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:291825 original size:19 final size:19
Alignment explanation
Indices: 291801--291868 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
291791 AATTCAACAA
291801 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
291820 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
291835 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
291852 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
291869 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:291840 original size:13 final size:13
Alignment explanation
Indices: 291822--291846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291812 ACATAAGTTT
291822 TGTATCGATACAA
1 TGTATCGATACAA
291835 TGTATCGATACA
1 TGTATCGATACA
291847 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:291844 original size:32 final size:32
Alignment explanation
Indices: 291803--291865 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
291793 TTCAACAATT
*
291803 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
291835 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
291866 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:291922 original size:13 final size:13
Alignment explanation
Indices: 291904--291929 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
291894 GATTTTTCTG
291904 TGTATCGATACAT
1 TGTATCGATACAT
291917 TGTATCGATACAT
1 TGTATCGATACAT
291930 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:312799 original size:52 final size:53
Alignment explanation
Indices: 312721--312840 Score: 147
Period size: 52 Copynumber: 2.3 Consensus size: 53
312711 NNNNNNNNNN
* * * *
312721 TCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATTTTCCTTTAA
1 TCGGGGATACTCCAACTCCTGATTTTATTTCCAAAAACACCAATTTTCC-ATAA
* *
312773 TCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAATACCAATTTTTCATAA
1 TCGGGGATACTCCAACTCCTGATTTTATTTCCAAAAACACCAATTTTCCATAA
*
312825 TCGAGGATACTCCAAC
1 TCGGGGATACTCCAAC
312841 CTCGTTATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
52 43 0.73
53 16 0.27
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (53 bp):
TCGGGGATACTCCAACTCCTGATTTTATTTCCAAAAACACCAATTTTCCATAA
Found at i:312860 original size:28 final size:28
Alignment explanation
Indices: 312824--312900 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
312814 ATTTTTCATA
* * *
312824 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
312852 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
312880 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
312901 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:312966 original size:107 final size:107
Alignment explanation
Indices: 312775--312979 Score: 261
Period size: 107 Copynumber: 1.9 Consensus size: 107
312765 TCCTTTAATC
* * *
312775 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCATAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCATAATCGAGGATACTCCAA
*
312840 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTTCA-CGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * *
312883 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCATAATCGAGGATACTCCAA
*
312947 CCCCGTTATTTTCGA-GGGGATACTCCAATCCCG
66 CCCCGTTA-TTTC-ACGGGGATACTCCAACCCCG
312980 ATTTTTTTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
107 57 0.69
108 25 0.30
109 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCATAATCGAGGATACTCCAA
CCCCGTTATTTCACGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:313003 original size:79 final size:79
Alignment explanation
Indices: 312854--313056 Score: 237
Period size: 79 Copynumber: 2.6 Consensus size: 79
312844 GTTATTTCAT
* * *
312854 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
312919 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
312933 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
312997 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * *
313012 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC
313057 TGTTATTATC
Statistics
Matches: 104, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 3 0.03
79 101 0.97
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:315907 original size:62 final size:61
Alignment explanation
Indices: 315810--315933 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 61
315800 GTGGATATCA
315810 GATTACAGGTTAGAATTTTGTTGATACAAAAAGAATGATTGTACACAAGCTTAAACTATTC
1 GATTACAGGTTAGAATTTTGTTGATACAAAAAGAATGATTGTACACAAGCTTAAACTATTC
**
315871 GATTACAGGTTACGAATTTTGTTGATACAAGGAGAATGATTGTACACAAGCTTAAACTATTC
1 GATTACAGGTTA-GAATTTTGTTGATACAAAAAGAATGATTGTACACAAGCTTAAACTATTC
315933 G
1 G
315934 GTAAGGTCAT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 12 0.20
62 48 0.80
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (61 bp):
GATTACAGGTTAGAATTTTGTTGATACAAAAAGAATGATTGTACACAAGCTTAAACTATTC
Found at i:316396 original size:19 final size:20
Alignment explanation
Indices: 316367--316419 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
316357 ATTGATGCAA
316367 TGTATCGATACATGCTC-AT
1 TGTATCGATACATGCTCAAT
* * *
316386 TTTATCAATACATACTCAAT
1 TGTATCGATACATGCTCAAT
316406 TGTATCGATACATG
1 TGTATCGATACATG
316420 AAACTGACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGCTCAAT
Found at i:316472 original size:20 final size:20
Alignment explanation
Indices: 316447--316499 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
316437 CTAAGTGAAA
*
316447 TGTATCGATACATG-GGACAT
1 TGTATCGATACATGAAGA-AT
316467 TGTATCGATACATGAAGAAT
1 TGTATCGATACATGAAGAAT
316487 TGTATCGATACAT
1 TGTATCGATACAT
316500 TATGCCTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:317310 original size:18 final size:17
Alignment explanation
Indices: 317282--317319 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
317272 TGTATATTAT
317282 TATAATTATATATAGTA
1 TATAATTATATATAGTA
*
317299 TATAATTAATATATATTA
1 TATAATT-ATATATAGTA
317317 TAT
1 TAT
317320 CATGTACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATAATTATATATAGTA
Found at i:317319 original size:9 final size:9
Alignment explanation
Indices: 317274--317319 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
317264 TTATGCAATG
317274 TATATTAT-
1 TATATTATA
317282 TATAATTATA
1 TAT-ATTATA
*
317292 TATAGTATA
1 TATATTATA
317301 TA-ATTAATA
1 TATATT-ATA
317310 TATATTATA
1 TATATTATA
317319 T
1 T
317320 CATGTACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 5 0.16
9 21 0.66
10 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (9 bp):
TATATTATA
Found at i:318518 original size:21 final size:22
Alignment explanation
Indices: 318475--318521 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
318465 AATAATAAAA
*
318475 AAAATTATTTAAATTTAATTAT
1 AAAATTATATAAATTTAATTAT
318497 AAAA-TATATAAATATTAA-TAT
1 AAAATTATATAAAT-TTAATTAT
318518 AAAA
1 AAAA
318522 ATAACTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATTATATAAATTTAATTAT
Found at i:318522 original size:22 final size:20
Alignment explanation
Indices: 318474--318524 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
318464 TAATAATAAA
*
318474 AAAAATTATTTAAATTTAATT
1 AAAAA-TATATAAATTTAATT
318495 ATAAAATATATAAATATTAATAT
1 A-AAAATATATAAAT-TTAAT-T
318518 AAAAATA
1 AAAAATA
318525 ACTTTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.35
22 15 0.58
23 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATATATAAATTTAATT
Found at i:318919 original size:2 final size:2
Alignment explanation
Indices: 318914--318940 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
318904 ATTCGACTAC
318914 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
318941 ATCGTATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:320345 original size:2 final size:2
Alignment explanation
Indices: 320338--320371 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
320328 AGGTTGCTAT
*
320338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
320372 CATTTTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:320624 original size:21 final size:21
Alignment explanation
Indices: 320591--320643 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
320581 TTTTATTTAT
* *
320591 TTTTAAATA-ATAATTATAT-
1 TTTTAAAAATATAAATATATG
*
320610 TTATTAAAAATATAAATGTATG
1 TT-TTAAAAATATAAATATATG
320632 TTTTAAAAATAT
1 TTTTAAAAATAT
320644 TTAAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.07
20 6 0.21
21 18 0.64
22 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTTAAAAATATAAATATATG
Found at i:321927 original size:16 final size:16
Alignment explanation
Indices: 321906--321937 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
321896 AATTAAAATA
321906 TAATTTAATAATAATT
1 TAATTTAATAATAATT
321922 TAATTTAATAATAATT
1 TAATTTAATAATAATT
321938 AAAGATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTTAATAATAATT
Found at i:325183 original size:82 final size:81
Alignment explanation
Indices: 325042--325287 Score: 332
Period size: 82 Copynumber: 3.0 Consensus size: 81
325032 ATCATTACCT
* * * *
325042 ACCTTTGAGTTAAATAGTTTATAGAGAAAAGGTTATGACCTGGTATCAAATATCTTATCCTTGAG
1 ACCTTTGAGTTAAATAGTATATAGAGAAATGTTTATGACCTGGTATCAAATATCATATCCTTGAG
*
325107 TAATTCTTTATCGAAGG
66 TAA-TCTTTATTGAAGG
* * * *
325124 ACCTTTGAATTAAATAGTATATTGAGGAATGTTTATGACCTTGTATCAAATATCATATCCTTGAG
1 ACCTTTGAGTTAAATAGTATATAGAGAAATGTTTATGACCTGGTATCAAATATCATATCCTTGAG
*
325189 TAAT-TTTATTGAAGC
66 TAATCTTTATTGAAGG
* * * *
325204 ACCTTTGAGTTAAATGGTATATAGAGAAATATTTATGACCTGGTATCAACTATCATATCCTAGAG
1 ACCTTTGAGTTAAATAGTATATAGAGAAATGTTTATGACCTGGTATCAAATATCATATCCTTGAG
*
325269 TAAATCTTCATTGAAGG
66 T-AATCTTTATTGAAGG
325286 AC
1 AC
325288 TTTTAAGCTC
Statistics
Matches: 142, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
80 67 0.47
81 4 0.03
82 71 0.50
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (81 bp):
ACCTTTGAGTTAAATAGTATATAGAGAAATGTTTATGACCTGGTATCAAATATCATATCCTTGAG
TAATCTTTATTGAAGG
Found at i:325250 original size:80 final size:82
Alignment explanation
Indices: 325042--325276 Score: 314
Period size: 80 Copynumber: 2.9 Consensus size: 82
325032 ATCATTACCT
* * *
325042 ACCTTTGAGTTAAATAGTTTATAGAGAAA-AGGTTATGACCTGGTATCAAATATCTTATCCTTGA
1 ACCTTTGAGTTAAATAGTATATAGAGAAATA-TTTATGACCTGGTATCAAATATCATATCCTTGA
*
325106 GTAATTCTTTATCGAAGG
65 GTAATTCTTTATCGAAGC
* * * * *
325124 ACCTTTGAATTAAATAGTATATTGAGGAATGTTTATGACCTTGTATCAAATATCATATCCTTGAG
1 ACCTTTGAGTTAAATAGTATATAGAGAAATATTTATGACCTGGTATCAAATATCATATCCTTGAG
*
325189 TAA-T-TTTATTGAAGC
66 TAATTCTTTATCGAAGC
* * *
325204 ACCTTTGAGTTAAATGGTATATAGAGAAATATTTATGACCTGGTATCAACTATCATATCCTAGAG
1 ACCTTTGAGTTAAATAGTATATAGAGAAATATTTATGACCTGGTATCAAATATCATATCCTTGAG
*
325269 TAAATCTT
66 TAATTCTT
325277 CATTGAAGGA
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
80 69 0.52
81 2 0.02
82 61 0.46
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (82 bp):
ACCTTTGAGTTAAATAGTATATAGAGAAATATTTATGACCTGGTATCAAATATCATATCCTTGAG
TAATTCTTTATCGAAGC
Found at i:326738 original size:13 final size:13
Alignment explanation
Indices: 326720--326747 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
326710 ATAAAATGAT
326720 ATATTTTTAAAAA
1 ATATTTTTAAAAA
326733 ATATTTTTAAAAA
1 ATATTTTTAAAAA
326746 AT
1 AT
326748 TATAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTTTTAAAAA
Found at i:327849 original size:5 final size:5
Alignment explanation
Indices: 327839--327882 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
327829 ACTATTATAA
* *
327839 TTATT TTATT TTATT TTAATG ATATT TTAATT TTATT TTATT TT
1 TTATT TTATT TTATT TT-ATT TTATT TT-ATT TTATT TTATT TT
327883 TATAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 25 0.76
6 8 0.24
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:327875 original size:11 final size:11
Alignment explanation
Indices: 327839--327885 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
327829 ACTATTATAA
327839 TTATTTT-ATT
1 TTATTTTAATT
*
327849 TTATTTTAATG
1 TTATTTTAATT
*
327860 ATATTTTAATT
1 TTATTTTAATT
*
327871 TTATTTTATTT
1 TTATTTTAATT
327882 TTAT
1 TTAT
327886 AAAATAACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (11 bp):
TTATTTTAATT
Found at i:329087 original size:22 final size:22
Alignment explanation
Indices: 329072--329113 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
329062 TATTTTATTT
329072 TTACTGTAATATTATTGTAATA
1 TTACTGTAATATTATTGTAATA
329094 TTACTGTAATATTATTGTAA
1 TTACTGTAATATTATTGTAA
329114 ACTGCCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (22 bp):
TTACTGTAATATTATTGTAATA
Found at i:329092 original size:11 final size:11
Alignment explanation
Indices: 329076--329113 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
329066 TTATTTTTAC
329076 TGTAATATTAT
1 TGTAATATTAT
*
329087 TGTAATATTAC
1 TGTAATATTAT
329098 TGTAATATTAT
1 TGTAATATTAT
329109 TGTAA
1 TGTAA
329114 ACTGCCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (11 bp):
TGTAATATTAT
Found at i:330086 original size:14 final size:15
Alignment explanation
Indices: 330067--330104 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 15
330057 ATAAAAAATA
330067 TTATTTTTTAAT-TT
1 TTATTTTTTAATATT
330081 TTA--TTTTAATATT
1 TTATTTTTTAATATT
330094 TTATTTTTTAA
1 TTATTTTTTAA
330105 ACATAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.33
13 5 0.24
14 3 0.14
15 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTTTAATATT
Found at i:330095 original size:13 final size:13
Alignment explanation
Indices: 330063--330100 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
330053 AAAAATAAAA
330063 AATATTATT-TTTT
1 AATATT-TTATTTT
330076 AAT-TTTTATTTT
1 AATATTTTATTTT
330088 AATATTTTATTTT
1 AATATTTTATTTT
330101 TTAAACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 9 0.39
13 12 0.52
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
AATATTTTATTTT
Found at i:330177 original size:16 final size:16
Alignment explanation
Indices: 330151--330189 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
330141 AATAACATTT
*
330151 TAATATTTTATAATAA
1 TAATTTTTTATAATAA
*
330167 TTATTTTTTATAATAA
1 TAATTTTTTATAATAA
330183 TAATTTT
1 TAATTTT
330190 ATTAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTTTTATAATAA
Found at i:335038 original size:14 final size:14
Alignment explanation
Indices: 335019--335045 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
335009 TATGAATATG
335019 TAAAAGAATTTATA
1 TAAAAGAATTTATA
335033 TAAAAGAATTTAT
1 TAAAAGAATTTAT
335046 TAATATATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
TAAAAGAATTTATA
Found at i:335197 original size:3 final size:3
Alignment explanation
Indices: 335191--335227 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
335181 AAAATAATAA
335191 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
335228 GATAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:336125 original size:30 final size:29
Alignment explanation
Indices: 336068--336125 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
336058 TTCTTAAATA
* *
336068 AATAAGGGTAAAATAAGTATGTCAAATTG
1 AATAAGGATAAAATAAGCATGTCAAATTG
* *
336097 AATAAGAGATAAAATAGGCATGTTAAATT
1 AATAAG-GATAAAATAAGCATGTCAAATT
336126 CATGCAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.50, C:0.03, G:0.19, T:0.28
Consensus pattern (29 bp):
AATAAGGATAAAATAAGCATGTCAAATTG
Found at i:337166 original size:2 final size:2
Alignment explanation
Indices: 337098--337151 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
337088 TATATTGTTT
337098 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
337140 TA TA TA TA TA TA
1 TA TA TA TA TA TA
337152 CACACACACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:337788 original size:15 final size:14
Alignment explanation
Indices: 337772--337806 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
337762 CTTAATATTA
337772 AAAATATAAAAATT
1 AAAATATAAAAATT
*
337786 AAATTATAAAAATTT
1 AAAATATAAAAA-TT
337801 AAAATA
1 AAAATA
337807 CGGAAACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:338440 original size:2 final size:2
Alignment explanation
Indices: 338433--338466 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
338423 CCGCCTGTAA
338433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
338467 TCTTCTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:338512 original size:18 final size:18
Alignment explanation
Indices: 338485--338520 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
338475 TTATTGTTAA
338485 TTTTATTTTTCAGTTTTTT
1 TTTTATTTTTCA-TTTTTT
338504 TTTTA-TTTTCATTTTTT
1 TTTTATTTTTCATTTTTT
338521 ATTGTTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.11, C:0.06, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTATTTTTCATTTTTT
Found at i:339230 original size:15 final size:15
Alignment explanation
Indices: 339210--339238 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
339200 AATTCTAATT
339210 AATTTTAATTAAATC
1 AATTTTAATTAAATC
339225 AATTTTAATTAAAT
1 AATTTTAATTAAAT
339239 TTCAATTGAT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTTAATTAAATC
Found at i:343123 original size:30 final size:32
Alignment explanation
Indices: 343089--343164 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
343079 GATATTAATT
* *
343089 ATAAATTTGAT-A-AATTAAATATAATTATTC
1 ATAAATTTGATGATAATTAAATAAAATTACTC
* * *
343119 ATAAAATTGATGATCATTTAATAAAATTACTC
1 ATAAATTTGATGATAATTAAATAAAATTACTC
343151 ATAAAATTTGATGA
1 AT-AAATTTGATGA
343165 ATGTTAGACT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 10 0.27
31 1 0.03
32 16 0.43
33 10 0.27
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (32 bp):
ATAAATTTGATGATAATTAAATAAAATTACTC
Found at i:343338 original size:21 final size:21
Alignment explanation
Indices: 343295--343341 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
343285 ATATGAAATT
* *
343295 TATTTAAATATATTTATTTTA
1 TATTTAAAAATATTTATTATA
343316 TATTTAAAAATATTATATATATA
1 TATTTAAAAATATT-TAT-TATA
343339 TAT
1 TAT
343342 ATAATACTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 3 0.14
23 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTAAAAATATTTATTATA
Found at i:348754 original size:27 final size:27
Alignment explanation
Indices: 348716--348771 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
348706 AAACCTTCAC
348716 TGGCTTCAAAGATATGTGATTAGGTGA
1 TGGCTTCAAAGATATGTGATTAGGTGA
*
348743 TGGCTTCAAAGATATGTGATTGGGTGA
1 TGGCTTCAAAGATATGTGATTAGGTGA
348770 TG
1 TG
348772 TAAGGAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.07, G:0.32, T:0.34
Consensus pattern (27 bp):
TGGCTTCAAAGATATGTGATTAGGTGA
Found at i:355888 original size:26 final size:26
Alignment explanation
Indices: 355859--355912 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
355849 CAACATATAG
355859 TTAACCTCATGAATTTAAAAAAATAA
1 TTAACCTCATGAATTTAAAAAAATAA
* * *
355885 TTAATCTCATGAATTTAGAGAAATAA
1 TTAACCTCATGAATTTAAAAAAATAA
355911 TT
1 TT
355913 TGTCCTCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (26 bp):
TTAACCTCATGAATTTAAAAAAATAA
Found at i:357172 original size:78 final size:78
Alignment explanation
Indices: 357038--357267 Score: 196
Period size: 78 Copynumber: 2.9 Consensus size: 78
357028 TTCCTTTAAG
* * *
357038 GACTAGGATTTCTCATGAAACTCAGTAAAATAGGCTTAATGTAGATGTCTCGATATGTAAATACC
1 GACTAGGATTTCTCATGAAACTCAGTAAAATAGGCTTAATGCACATGTCTCGATATGAAAATACC
357103 AACATGCTTCAAA
66 AACATGCTTCAAA
* ** * * * *
357116 GACTTGGATTTCTCATGAAACTCCTTACAGT-GGCTTTAATGCACATGTCTTGATATGAAAATAT
1 GACTAGGATTTCTCATGAAACTCAGTAAAATAGGC-TTAATGCACATGTCTCGATATGAAAATAC
* *
357180 CAACAT-ATTCCTAAG
65 CAACATGCTT-C-AAA
* * * * * * * * * *
357195 GAATCGAACTTCTTATGAAATTTACTAAAAT-GACTTTAATGCATATGTCTCGATATGAAAATAC
1 GACTAGGATTTCTCATGAAACTCAGTAAAATAGGC-TTAATGCACATGTCTCGATATGAAAATAC
*
357259 CAATATGCT
65 CAACATGCT
357268 CTTATGGTGA
Statistics
Matches: 119, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
77 5 0.04
78 57 0.48
79 56 0.47
80 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (78 bp):
GACTAGGATTTCTCATGAAACTCAGTAAAATAGGCTTAATGCACATGTCTCGATATGAAAATACC
AACATGCTTCAAA
Found at i:357339 original size:58 final size:57
Alignment explanation
Indices: 357275--357466 Score: 138
Period size: 58 Copynumber: 3.3 Consensus size: 57
357265 GCTCTTATGG
* * * *
357275 TGATGAAAATTGTTAAAATGATCTTAGATTATATAAAATAACCTAAATGACCCTAAAA
1 TGATAAAAATTATTAAAAT-ACCTTAGATTATATAAAATAACCTAAATGAACCTAAAA
** * * * * **
357333 TGATGAAAAA-TGGTAAGACA-ACCCTAAATTATGTAAAATAATCTAAACAAACCTAAAA
1 TGAT-AAAAATTATTAA-A-ATACCTTAGATTATATAAAATAACCTAAATGAACCTAAAA
* * * * ** *
357391 TGCATAAAAATTACT-AAATAGCTTTCGATTATATAAAGTAACCTAAATGGTCTTAAAA
1 TG-ATAAAAATTATTAAAATA-CCTTAGATTATATAAAATAACCTAAATGAACCTAAAA
357449 TGATAAAAATTATTAAAA
1 TGATAAAAATTATTAAAA
357467 CAACACTAAC
Statistics
Matches: 101, Mismatches: 25, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
56 1 0.01
57 13 0.13
58 77 0.76
59 9 0.09
60 1 0.01
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (57 bp):
TGATAAAAATTATTAAAATACCTTAGATTATATAAAATAACCTAAATGAACCTAAAA
Found at i:358357 original size:20 final size:20
Alignment explanation
Indices: 358332--358387 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
358322 CTTGCTTCTT
358332 TTTTTTTTCTATTTTCTCTA
1 TTTTTTTTCTATTTTCTCTA
* *
358352 TTTTTTTCCCT-TTATCTCTA
1 TTTTTTT-TCTATTTTCTCTA
*
358372 TTTTTTCTCTCATTTT
1 TTTTTTTTCT-ATTTT
358388 TGCTACTACC
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 2 0.07
20 21 0.75
21 5 0.18
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTTTCTATTTTCTCTA
Found at i:358798 original size:15 final size:17
Alignment explanation
Indices: 358766--358803 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
358756 TTGCTTTTTT
358766 TTTTTGTTTTATCTTTC
1 TTTTTGTTTTATCTTTC
*
358783 TTTTT-TTTTCTC-TTC
1 TTTTTGTTTTATCTTTC
358798 TTTTTG
1 TTTTTG
358804 CTACTACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTTGTTTTATCTTTC
Found at i:361031 original size:67 final size:69
Alignment explanation
Indices: 360855--361107 Score: 282
Period size: 68 Copynumber: 3.7 Consensus size: 69
360845 ACCTTAACAA
* * * *
360855 ACTTTAAAAATAACCAATATACCCTTAAAGTACACCTTTGACATAAAAATCTCTCGATG-GCCGT
1 ACTTTAAAAATGACCAACATATCCTT-AAGTACACCTTTGACATAAAAATATCTCGATGAGCCGT
*
360919 AAAAA
65 AAAAG
* *
360924 ATTTTAAAAAAATGACCAACCTAT-CTCTAAGTACACCTTTGACAT-AAAATATCTCGATGAGCC
1 ACTTT--AAAAATGACCAACATATCCT-TAAGTACACCTTTGACATAAAAATATCTCGATGAGCC
360987 -TAAAAG
63 GTAAAAG
* * * * *
360993 ACTTTAAAAATGACCAACATATCCTTAAGTACATCTTTGACATGAAAATATCTCGGT-AACCTTA
1 ACTTTAAAAATGACCAACATATCCTTAAGTACACCTTTGACATAAAAATATCTCGATGAGCCGTA
361057 AAAG
66 AAAG
* * * * *
361061 ACTCTAAAAATGACCAACAGATCCCTAAGTACACTTTTGGCATAAAA
1 ACTTTAAAAATGACCAACATATCCTTAAGTACACCTTTGACATAAAA
361108 GTATTTTAGT
Statistics
Matches: 158, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
67 36 0.23
68 60 0.38
69 26 0.16
70 22 0.14
71 14 0.09
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (69 bp):
ACTTTAAAAATGACCAACATATCCTTAAGTACACCTTTGACATAAAAATATCTCGATGAGCCGTA
AAAG
Found at i:361125 original size:68 final size:67
Alignment explanation
Indices: 360931--361132 Score: 203
Period size: 68 Copynumber: 3.0 Consensus size: 67
360921 AAAATTTTAA
* * * * *
360931 AAAAATGACCAACCTATCTCTAAGTACACCTTTGACATAAAATA-TCTCGATGAGCC-TAAAAGA
1 AAAAATGACCAACATATCCCTAAGTACACTTTTGACATAAAATATTTTAG-TGA-CCTTAAAAGA
*
360994 CTTT
64 CTCT
* * ** *
360998 AAAAATGACCAACATATCCTTAAGTACA-TCTTTGACATGAAAATATCTCGGTAACCTTAAAAGA
1 AAAAATGACCAACATATCCCTAAGTACACT-TTTGACAT-AAAATATTTTAGTGACCTTAAAAGA
361062 CTCT
64 CTCT
* * * *
361066 AAAAATGACCAACAGATCCCTAAGTACACTTTTGGCATAAAAGTATTTTAGTGATCTTAAAGGAC
1 AAAAATGACCAACATATCCCTAAGTACACTTTTGACATAAAA-TATTTTAGTGACCTTAAAAGAC
361131 TC
65 TC
361133 GATAATAACA
Statistics
Matches: 110, Mismatches: 19, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
67 39 0.35
68 69 0.63
69 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (67 bp):
AAAAATGACCAACATATCCCTAAGTACACTTTTGACATAAAATATTTTAGTGACCTTAAAAGACT
CT
Found at i:363207 original size:28 final size:28
Alignment explanation
Indices: 363175--363242 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
363165 TCAAATGGTT
363175 TAATTAAAATTTTATAT-ATGATAAAATTC
1 TAATTAAAATTTTA-ATCAT-ATAAAATTC
* *
363204 -AATTAAGAA-TCTAATCATATAGAATTC
1 TAATTAA-AATTTTAATCATATAAAATTC
363231 TAATTAAAATTT
1 TAATTAAAATTT
363243 CATAAGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
27 12 0.38
28 18 0.56
29 2 0.06
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (28 bp):
TAATTAAAATTTTAATCATATAAAATTC
Found at i:364943 original size:13 final size:13
Alignment explanation
Indices: 364894--364943 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
364884 TTTTATTATA
*
364894 ATTTAATTAATTT
1 ATTTAATTAAATT
* * *
364907 AATTAATTGAATC
1 ATTTAATTAAATT
*
364920 ATTAAATTAAATT
1 ATTTAATTAAATT
364933 ATTTAATTAAA
1 ATTTAATTAAA
364944 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (13 bp):
ATTTAATTAAATT
Found at i:364985 original size:34 final size:34
Alignment explanation
Indices: 364911--364988 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
364901 TAATTTAATT
* *
364911 AATTGAATCATTAAATTAAATTATTTAATTAAAAA
1 AATTAAAT-ATTAAATTAAATAATTTAATTAAAAA
* *
364946 AATTAAATATTAAA-TAAATAATTTTATTATTAAA
1 AATTAAATATTAAATTAAATAATTTAATTA-AAAA
*
364980 TATTAAATA
1 AATTAAATA
364989 CAATAAATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 13 0.35
34 17 0.46
35 7 0.19
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (34 bp):
AATTAAATATTAAATTAAATAATTTAATTAAAAA
Found at i:366003 original size:18 final size:17
Alignment explanation
Indices: 365937--366006 Score: 58
Period size: 17 Copynumber: 4.1 Consensus size: 17
365927 ATAGTGAATA
365937 TAAAATATTTAATATATT
1 TAAAAT-TTTAATATATT
* *
365955 TATAAA--AT-ATGTATT
1 TA-AAATTTTAATATATT
365970 TAAAATTTTAATATATT
1 TAAAATTTTAATATATT
365987 TAATAA-TTTAATAATATT
1 TAA-AATTTTAAT-ATATT
366005 TA
1 TA
366007 TATCTACATA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
14 3 0.07
15 8 0.19
16 2 0.05
17 15 0.36
18 11 0.26
19 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (17 bp):
TAAAATTTTAATATATT
Found at i:366672 original size:34 final size:34
Alignment explanation
Indices: 366625--366721 Score: 88
Period size: 34 Copynumber: 2.8 Consensus size: 34
366615 CTTGAATTCA
* * *
366625 ATAAATAATATTTTATTTATATTAT-TCTTAATAT
1 ATAAATAAAATTTTA-ATAAATTATATCTTAATAT
* *
366659 ATAATTAAAATTTTAATAAATTATATTTTAATAT
1 ATAAATAAAATTTTAATAAATTATATCTTAATAT
* *
366693 ATATTACTAAAATTTAAATAAAATTATAT
1 ATA--AATAAAATTTTAAT-AAATTATAT
366722 TCACTAATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
33 7 0.13
34 24 0.46
36 12 0.23
37 9 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (34 bp):
ATAAATAAAATTTTAATAAATTATATCTTAATAT
Found at i:366704 original size:36 final size:36
Alignment explanation
Indices: 366647--366723 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 36
366637 TTATTTATAT
* *
366647 TATTCTTAATATATAATTAAAATTTTAAT-AAATTA
1 TATTCTTAATATATAACTAAAATTTAAATAAAATTA
366682 TATT-TTAATATATATTACTAAAATTTAAATAAAATTA
1 TATTCTTAATATATA--ACTAAAATTTAAATAAAATTA
366719 TATTC
1 TATTC
366724 ACTAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
34 10 0.28
35 4 0.11
36 12 0.33
37 10 0.28
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (36 bp):
TATTCTTAATATATAACTAAAATTTAAATAAAATTA
Found at i:366792 original size:20 final size:20
Alignment explanation
Indices: 366763--366800 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
366753 AATGTTTTAA
*
366763 AAAAACATTTTGATAAATCT
1 AAAAACATTTTAATAAATCT
*
366783 AAAAATATTTTAATAAAT
1 AAAAACATTTTAATAAAT
366801 TATAATTTTA
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:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAAACATTTTAATAAATCT
Found at i:371842 original size:19 final size:19
Alignment explanation
Indices: 371818--371854 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
371808 ATTCAAAATT
371818 AAAAAATTAAAAAATAAAA
1 AAAAAATTAAAAAATAAAA
371837 AAAAAATTAAAAAATAAA
1 AAAAAATTAAAAAATAAA
371855 TTTCTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAATTAAAAAATAAAA
Found at i:372111 original size:28 final size:28
Alignment explanation
Indices: 372065--372136 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
372055 TAAATATACA
*
372065 AATATATTTAAAATATATAAT-AAATTATT
1 AATATA-TAAAAATATATAATCAAATTA-T
* * *
372094 AATATATAAAAATTTATATTCAACTTAT
1 AATATATAAAAATATATAATCAAATTAT
*
372122 AATATAT-TAAATATA
1 AATATATAAAAATATA
372137 AATATAAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 6 0.17
28 19 0.53
29 11 0.31
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (28 bp):
AATATATAAAAATATATAATCAAATTAT
Found at i:373754 original size:15 final size:16
Alignment explanation
Indices: 373723--373755 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
373713 ATTTAAAAGT
*
373723 TACTTGAATATTGTCA
1 TACTTGAATAGTGTCA
373739 TACTTGAA-AGTGTCA
1 TACTTGAATAGTGTCA
373754 TA
1 TA
373756 TATGAATACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (16 bp):
TACTTGAATAGTGTCA
Found at i:373981 original size:22 final size:24
Alignment explanation
Indices: 373933--373984 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
373923 ACACGACATA
373933 AATAT-AAATAAATAATTAAAATT
1 AATATAAAATAAATAATTAAAATT
*
373956 AATATAAAATAAA-AA-TAATATT
1 AATATAAAATAAATAATTAAAATT
373978 AATATAA
1 AATATAA
373985 CACGAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 13 0.48
23 7 0.26
24 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATATAAAATAAATAATTAAAATT
Found at i:374022 original size:21 final size:23
Alignment explanation
Indices: 373993--374041 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
373983 AACACGAAAG
373993 TATA-AATGTGT-AAAAATT-TA
1 TATATAATGTGTCAAAAATTATA
*
374013 TATATAATGTGTCAACAATTATA
1 TATATAATGTGTCAAAAATTATA
374036 TATATA
1 TATATA
374042 TAATACACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 7 0.28
22 6 0.24
23 8 0.32
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (23 bp):
TATATAATGTGTCAAAAATTATA
Found at i:375616 original size:2 final size:2
Alignment explanation
Indices: 375609--375638 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
375599 AGCTATACAA
375609 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
375639 TCTAAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:376381 original size:16 final size:15
Alignment explanation
Indices: 376352--376389 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
376342 AATAATTAAA
*
376352 ATTAATAAATTTTTT
1 ATTAATAAAATTTTT
376367 ATTAACTAAAATTTTT
1 ATTAA-TAAAATTTTT
376383 ATTAATA
1 ATTAATA
376390 TATAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTAATAAAATTTTT
Found at i:377772 original size:21 final size:20
Alignment explanation
Indices: 377748--377790 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
377738 TATATATAAG
*
377748 TTATATATTATAAAATATTTT
1 TTATATATTA-AAAATATATT
* *
377769 TTATCTTTTAAAAATATATT
1 TTATATATTAAAAATATATT
377789 TT
1 TT
377791 CAAAAAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATATATTAAAAATATATT
Found at i:377852 original size:24 final size:24
Alignment explanation
Indices: 377807--377853 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
377797 GAGTTTTTAA
* *
377807 AAAATTATATGATTTAATATTTTT
1 AAAATTAAATGATTTAAAATTTTT
377831 AAAATTAAAT-ATTTCAAAATTTT
1 AAAATTAAATGATTT-AAAATTTT
377854 AAATTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
AAAATTAAATGATTTAAAATTTTT
Found at i:378132 original size:18 final size:17
Alignment explanation
Indices: 378107--378153 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
378097 TAAAAAATTT
*
378107 TAAATAAAAATAAAATA
1 TAAATAAAAATAAAAAA
*
378124 TAAATTAAAAGTAAAAAA
1 TAAA-TAAAAATAAAAAA
*
378142 T-AATAAATATAA
1 TAAATAAAAATAA
378154 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 7 0.28
17 6 0.24
18 12 0.48
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
TAAATAAAAATAAAAAA
Found at i:378265 original size:31 final size:31
Alignment explanation
Indices: 378230--378290 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
378220 AAAGTGTAAA
* *
378230 TAAAAAATTATGAAT-AATTAAAAAGTTTTAT
1 TAAAAAAATATAAATAAATTAAAAA-TTTTAT
*
378261 TAAAAAAATATAAATAAATTTAAAATTTTA
1 TAAAAAAATATAAATAAATTAAAAATTTTA
378291 ATTTACTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (31 bp):
TAAAAAAATATAAATAAATTAAAAATTTTAT
Found at i:381780 original size:3 final size:3
Alignment explanation
Indices: 381772--381807 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
381762 TTTAAAAATG
381772 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
381808 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:382311 original size:26 final size:26
Alignment explanation
Indices: 382235--382300 Score: 98
Period size: 26 Copynumber: 2.5 Consensus size: 26
382225 ATATATATTA
382235 TTTTTAATCTTTAATAATTTAATA-AT
1 TTTTTAAT-TTTAATAATTTAATATAT
382261 TTTTTAATTTTAAATAATTTAATATAT
1 TTTTTAATTTT-AATAATTTAATATAT
382288 TTTTTAATATTTA
1 TTTTTAAT-TTTA
382301 TATTATAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.08
26 20 0.54
27 11 0.30
28 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTTAATTTTAATAATTTAATATAT
Found at i:383072 original size:19 final size:19
Alignment explanation
Indices: 383048--383107 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
383038 AGCTATGTCA
383048 ATTATAAATATATATTTAT
1 ATTATAAATATATATTTAT
* *
383067 ATTAT-ATTATGTTATTT-T
1 ATTATAAATAT-ATATTTAT
* *
383085 ATTAAAAATAAATTATTTAT
1 ATTATAAATATA-TATTTAT
383105 ATT
1 ATT
383108 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 9 0.29
19 18 0.58
20 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
ATTATAAATATATATTTAT
Found at i:383870 original size:19 final size:19
Alignment explanation
Indices: 383846--383887 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
383836 TTATAATTAA
383846 ATTTAAA-TAAAAATATATT
1 ATTTAAATTAAAAAT-TATT
383865 ATTTAAATTAAAAATTATT
1 ATTTAAATTAAAAATTATT
383884 ATTT
1 ATTT
383888 CTGACTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTAAATTAAAAATTATT
Found at i:386280 original size:23 final size:23
Alignment explanation
Indices: 386242--386285 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
386232 CATTAATCTT
386242 ATTTTAGTTTTATATAAAATAAA
1 ATTTTAGTTTTATATAAAATAAA
386265 ATTTTA-TTTTATTATAAAATA
1 ATTTTAGTTTTA-TATAAAATA
386286 TTATATGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTTAGTTTTATATAAAATAAA
Found at i:391854 original size:25 final size:25
Alignment explanation
Indices: 391796--391854 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
391786 ACAACAAGCT
* **
391796 ATCA-ATTTTGACAAATAATAAATC
1 ATCATATTTTGACAAACAATAAAAA
*
391820 ATCATTTTTTGACAAACAA-AAAAA
1 ATCATATTTTGACAAACAATAAAAA
391844 ATCACTATTTT
1 ATCA-TATTTT
391855 TTATAAACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (25 bp):
ATCATATTTTGACAAACAATAAAAA
Found at i:391868 original size:26 final size:27
Alignment explanation
Indices: 391801--391868 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
391791 AAGCTATCAA
*
391801 TTTTGAC-AA-ATAATAAATCATCATT
1 TTTTGACAAACATAAAAAATCATCATT
*
391826 TTTTGACAAACAAAAAAAATCA-CTATT
1 TTTTGACAAACATAAAAAATCATC-ATT
*
391853 TTTT-ATAAACATAAAA
1 TTTTGACAAACATAAAA
391869 TCGTCATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.19
26 13 0.36
27 16 0.44
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (27 bp):
TTTTGACAAACATAAAAAATCATCATT
Found at i:393067 original size:2 final size:2
Alignment explanation
Indices: 393060--393089 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
393050 TACTTGGATT
393060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
393090 AAATTATTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:394241 original size:89 final size:90
Alignment explanation
Indices: 394072--394242 Score: 220
Period size: 89 Copynumber: 1.9 Consensus size: 90
394062 CGTAATAGAT
* * * * *
394072 AATTAAAATTTTGAATCAAAAATTTTTACTTTAATTTTCATTAAACAAGTCGATCCTTTACATTA
1 AATTAAAATTTTGAATCAAAAACTTCTACTTTAATTCTCATTAAACAAGTCAAACCTTTACATTA
394137 AAACTCATAATTAAATGTAGTAAAG
66 AAACTCATAATTAAATGTAGTAAAG
* * * *
394162 AATTAAAATTTCT-AATCAAGAACTTCTACTTTAATTCT-ATTAAACAAGTTAAACTTTTTCATT
1 AATTAAAATTT-TGAATCAAAAACTTCTACTTTAATTCTCATTAAACAAGTCAAACCTTTACATT
* *
394225 AACACTTATAATTAAATG
65 AAAACTCATAATTAAATG
394243 GTTAATATGG
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
89 36 0.52
90 32 0.46
91 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (90 bp):
AATTAAAATTTTGAATCAAAAACTTCTACTTTAATTCTCATTAAACAAGTCAAACCTTTACATTA
AAACTCATAATTAAATGTAGTAAAG
Found at i:394554 original size:2 final size:2
Alignment explanation
Indices: 394549--394573 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
394539 AAAAATAAAT
394549 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
394574 GGAATGGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:402773 original size:27 final size:28
Alignment explanation
Indices: 402699--402773 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 28
402689 AATATGATAC
*
402699 AAATAAATAAATATATTTAAAATTTATAA
1 AAATATAT-AATATATTTAAAATTTATAA
* * *** *
402728 AAAAAT-TATTATGGATAAAATTTATAT
1 AAATATATAATATATTTAAAATTTATAA
402755 AAATATATAATAT-TTTAAA
1 AAATATATAATATATTTAAA
402774 TATGATTACG
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
27 24 0.71
28 6 0.18
29 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
AAATATATAATATATTTAAAATTTATAA
Found at i:403097 original size:17 final size:18
Alignment explanation
Indices: 403075--403110 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
403065 AAAATAATTA
403075 AAAAATAATAT-AATACG
1 AAAAATAATATAAATACG
403092 AAAAATAATATAAATACG
1 AAAAATAATATAAATACG
403110 A
1 A
403111 TATATATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (18 bp):
AAAAATAATATAAATACG
Found at i:404115 original size:27 final size:27
Alignment explanation
Indices: 404055--404117 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
404045 TTTACATATG
404055 AAATTTTA-TTATGAAATTTTCAATTA
1 AAATTTTATTTATGAAATTTTCAATTA
* *
404081 AACCTTTTATTTAT-AAATTTTTGAATTA
1 AA-ATTTTATTTATGAAA-TTTTCAATTA
404109 AAATTTTAT
1 AAATTTTAT
404118 ATGTGAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.06
27 14 0.45
28 15 0.48
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (27 bp):
AAATTTTATTTATGAAATTTTCAATTA
Found at i:404282 original size:39 final size:39
Alignment explanation
Indices: 404230--404318 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 39
404220 CAAAATTGAA
*
404230 TTTTGAACCATGTTCTCAACCAATTAAATTAA-TGTTAAAT
1 TTTTGAA-TATGTTCTCAACC-ATTAAATTAATTGTTAAAT
* * * * *
404270 TTTTGAATATGTTTTCAATCATTAGATTAATTTTTAACT
1 TTTTGAATATGTTCTCAACCATTAAATTAATTGTTAAAT
*
404309 TTTTTAATAT
1 TTTTGAATAT
404319 ATTGATGACC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
38 9 0.22
39 25 0.61
40 7 0.17
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (39 bp):
TTTTGAATATGTTCTCAACCATTAAATTAATTGTTAAAT
Found at i:404754 original size:2 final size:2
Alignment explanation
Indices: 404747--404779 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
404737 ACCGAAGATT
404747 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
404780 TAAAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:409144 original size:17 final size:17
Alignment explanation
Indices: 409111--409159 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
409101 TTAATAAATT
*
409111 TTTATCATATA-ATTTA
1 TTTATAATATATATTTA
409127 -TTATTAATATATATTTA
1 TTTA-TAATATATATTTA
*
409144 TTTATAATCTATATTT
1 TTTATAATATATATTT
409160 CAAATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 3 0.11
16 6 0.21
17 16 0.57
18 3 0.11
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATAATATATATTTA
Found at i:413194 original size:18 final size:19
Alignment explanation
Indices: 413163--413198 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
413153 TAATTTCAGA
*
413163 ACTCATAATAATTTTTAAG
1 ACTCAAAATAATTTTTAAG
413182 ACTCAAAAT-ATTTTTAA
1 ACTCAAAATAATTTTTAA
413199 TTAGACAACG
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:0.11, G:0.03, T:0.42
Consensus pattern (19 bp):
ACTCAAAATAATTTTTAAG
Found at i:413764 original size:20 final size:20
Alignment explanation
Indices: 413711--413764 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
413701 GAAATTAGGG
413711 TATATTTAATTATTATACATT
1 TATATTTAATT-TTATACATT
413732 TAT-TTTATTATTTTATA-ATT
1 TATATTTA--ATTTTATACATT
413752 TATATTTGAATTT
1 TATATTT-AATTT
413765 CGTAATGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
20 14 0.48
21 11 0.38
22 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TATATTTAATTTTATACATT
Found at i:414107 original size:20 final size:21
Alignment explanation
Indices: 414084--414141 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
414074 TTTTATGAAT
414084 TTTTTTA-TATTA-TATTAGA
1 TTTTTTATTATTATTATTAGA
414103 TTTTTTATTATTATTATT--A
1 TTTTTTATTATTATTATTAGA
414122 TTATTATTATTATTATTATT
1 TT-TT-TTATTATTATTATT
414142 GTATACATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.29
20 7 0.20
21 18 0.51
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTTATTATTATTATTAGA
Found at i:414115 original size:3 final size:3
Alignment explanation
Indices: 414107--414141 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
414097 ATTAGATTTT
414107 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
414142 GTATACATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:416529 original size:21 final size:21
Alignment explanation
Indices: 416505--416547 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
416495 CTCATCTTTG
416505 CTTTTCTTGAGTT-TTTTTCTT
1 CTTTTCTTG-GTTATTTTTCTT
* *
416526 CTTTTTTTGTTTATTTTTCTT
1 CTTTTCTTGGTTATTTTTCTT
416547 C
1 C
416548 CTCATCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.74
Consensus pattern (21 bp):
CTTTTCTTGGTTATTTTTCTT
Found at i:420513 original size:2 final size:2
Alignment explanation
Indices: 420506--420538 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
420496 AGAGACACAA
*
420506 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
420539 CCAAAAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:420690 original size:41 final size:41
Alignment explanation
Indices: 420630--420725 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
420620 TAGTGGAGAT
* * * * *
420630 ATTTAGCAGCATTTTTTAGTAAAACGCCATTATATTGACAG
1 ATTTAGCGGCATTTGTTAGTAAAACACCACTATATTGACAA
*
420671 ATTTAGCGGCGTTTGTTAGTAAAACACCACTATATTGACAA
1 ATTTAGCGGCATTTGTTAGTAAAACACCACTATATTGACAA
420712 ATTTAGCGGCATTT
1 ATTTAGCGGCATTT
420726 TTATGACAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (41 bp):
ATTTAGCGGCATTTGTTAGTAAAACACCACTATATTGACAA
Found at i:420791 original size:26 final size:26
Alignment explanation
Indices: 420743--420792 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
420733 AACGTTGCTA
* **
420743 TATGTATAGATTTAGCGGTGTTTTAC
1 TATGGATAGATTTAGCGACGTTTTAC
420769 TATGGATAGATTTAGCGACGTTTT
1 TATGGATAGATTTAGCGACGTTTT
420793 TGGTGACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (26 bp):
TATGGATAGATTTAGCGACGTTTTAC
Found at i:425451 original size:22 final size:21
Alignment explanation
Indices: 425418--425458 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
425408 ATGTTAAAAT
*
425418 TATTTAAGATTATAATATTAA
1 TATTTAAGATTAAAATATTAA
*
425439 TATTTTAGTATTAAAATATT
1 TATTTAAG-ATTAAAATATT
425459 TAAAAAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TATTTAAGATTAAAATATTAA
Found at i:429440 original size:27 final size:28
Alignment explanation
Indices: 429393--429446 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
429383 ACATGTAATA
*
429393 AAAAATTCCATATGAATAAA-TTAACTT
1 AAAAATTCCATATGAAAAAATTTAACTT
*
429420 AAAAATTCTATAT-ACAAAAATTTAACT
1 AAAAATTCCATATGA-AAAAATTTAACT
429447 AAAGGATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.04
27 16 0.70
28 6 0.26
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAAATTCCATATGAAAAAATTTAACTT
Found at i:430441 original size:22 final size:22
Alignment explanation
Indices: 430407--430463 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
430397 TTTTAATATA
430407 TATATATATATATTAGAT-CAT
1 TATATATATATATTAGATACAT
*
430428 GTATATACTA-ATATTATATACAT
1 -TATATA-TATATATTAGATACAT
430451 TATATATATATAT
1 TATATATATATAT
430464 ATATGTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 2 0.06
22 24 0.77
23 5 0.16
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (22 bp):
TATATATATATATTAGATACAT
Found at i:430484 original size:2 final size:2
Alignment explanation
Indices: 430402--430467 Score: 59
Period size: 2 Copynumber: 34.0 Consensus size: 2
430392 CACATTTTTA
* *
430402 AT AT AT AT AT AT AT AT AT -T AG AT CAT GT AT AT ACT A- AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A-T AT AT AT AT
*
430443 AT AT AC AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
430468 GTAATTTACA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
1 4 0.08
2 44 0.85
3 4 0.08
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:434095 original size:33 final size:32
Alignment explanation
Indices: 434058--434134 Score: 91
Period size: 33 Copynumber: 2.4 Consensus size: 32
434048 TAAAAAATTT
434058 GATCAAAGTTAACCAAAAGTATATAATATCTAA
1 GATCAAAGTTAACCAAAAGTATATAA-ATCTAA
* * * * **
434091 GATCAAAGTAAATCAAAAGTGTATAAATTTGT
1 GATCAAAGTTAACCAAAAGTATATAAATCTAA
434123 GATCAAAGTTAA
1 GATCAAAGTTAA
434135 TAACTTCAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 14 0.38
33 23 0.62
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (32 bp):
GATCAAAGTTAACCAAAAGTATATAAATCTAA
Found at i:439443 original size:20 final size:20
Alignment explanation
Indices: 439418--439472 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
439408 TTTTAACTAG
*
439418 ATGTATCGATACATTCATA-C
1 ATGTATCGATACATTCA-AGA
* *
439438 ATGTATCAATACATTGAAGA
1 ATGTATCGATACATTCAAGA
439458 ATGTATCGATACATT
1 ATGTATCGATACATT
439473 TAGGTAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTCAAGA
Found at i:441616 original size:64 final size:64
Alignment explanation
Indices: 441515--441648 Score: 250
Period size: 64 Copynumber: 2.1 Consensus size: 64
441505 TTGCTTTTCT
* *
441515 CTTATACTTTTCTCAAATTCTCTATATATAACTTAATTAAGTTAGCCACACTTTAATTAAAAAC
1 CTTATACTTTTCTCAAATTCTCTATATATAACTTAATTAAGTCAACCACACTTTAATTAAAAAC
441579 CTTATACTTTTCTCAAATTCTCTATATATAACTTAATTAAGTCAACCACACTTTAATTAAAAAC
1 CTTATACTTTTCTCAAATTCTCTATATATAACTTAATTAAGTCAACCACACTTTAATTAAAAAC
441643 CTTATA
1 CTTATA
441649 ATAAAAAAGC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.40
Consensus pattern (64 bp):
CTTATACTTTTCTCAAATTCTCTATATATAACTTAATTAAGTCAACCACACTTTAATTAAAAAC
Found at i:447598 original size:13 final size:13
Alignment explanation
Indices: 447580--447604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
447570 TATTAGCTGA
447580 AAAAAATAAAAAT
1 AAAAAATAAAAAT
447593 AAAAAATAAAAA
1 AAAAAATAAAAA
447605 AGCTGACATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:449283 original size:14 final size:14
Alignment explanation
Indices: 449264--449290 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
449254 TATTTTATAT
449264 AAATTATATTTAAA
1 AAATTATATTTAAA
449278 AAATTATATTTAA
1 AAATTATATTTAA
449291 TATTTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTATATTTAAA
Found at i:449315 original size:28 final size:30
Alignment explanation
Indices: 449215--449344 Score: 96
Period size: 30 Copynumber: 4.5 Consensus size: 30
449205 TTGTTATATA
* *
449215 AATTTTAAAATATATTTTTATATTTTATTAT
1 AATTTTAATAT-TATATTTATATTTTATTAT
* * * * *
449246 ATTTTTAATATTTTATATAAATTATATT-T
1 AATTTTAATATTATATTTATATTTTATTAT
*
449275 AA----AAAATTATATTTAATATTTT-TTA-
1 AATTTTAATATTATATTT-ATATTTTATTAT
*
449300 AATTTTAATA-TATATTTTTATTTTATTAT
1 AATTTTAATATTATATTTATATTTTATTAT
*
449329 ATTTTTAATATTATAT
1 AATTTTAATATTATAT
449345 ACGTATTATA
Statistics
Matches: 74, Mismatches: 16, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
25 13 0.18
26 5 0.07
27 6 0.08
28 10 0.14
29 14 0.19
30 17 0.23
31 9 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
AATTTTAATATTATATTTATATTTTATTAT
Found at i:449342 original size:14 final size:14
Alignment explanation
Indices: 449302--449344 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 14
449292 ATTTTTTAAA
449302 TTTTAATA-TATAT
1 TTTTAATATTATAT
*
449315 TTTTATTTTATTATAT
1 TTTTA--ATATTATAT
449331 TTTTAATATTATAT
1 TTTTAATATTATAT
449345 ACGTATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 2 0.08
16 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTAATATTATAT
Found at i:450139 original size:16 final size:15
Alignment explanation
Indices: 450120--450153 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
450110 TTGGTTTTCC
*
450120 TTTTTTTTTTTTTGAA
1 TTTTTTTATTTTT-AA
450136 TTTTTTTATTTTTAA
1 TTTTTTTATTTTTAA
450151 TTT
1 TTT
450154 CACATTTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTTTATTTTTAA
Found at i:451019 original size:33 final size:33
Alignment explanation
Indices: 450957--451020 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
450947 AATTTTTTTA
* * *
450957 TTTTAAATTTAATAATATGTGAGATGAATATCG
1 TTTTAAATTTAACAATATGTGAAACGAATATCG
450990 TTTTAAATTTAACAATAT-TGAAAACGAATAT
1 TTTTAAATTTAACAATATGTG-AAACGAATAT
451021 TTTTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (33 bp):
TTTTAAATTTAACAATATGTGAAACGAATATCG
Found at i:451085 original size:29 final size:30
Alignment explanation
Indices: 451048--451108 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
451038 TTTATAAGAT
**
451048 AATTGTTAAGGATAA-ATTTTAATTTTTAA
1 AATTGTTAAAAATAATATTTTAATTTTTAA
* * *
451077 AATTTTTAAAAATAATTTTTTATTTTTTAA
1 AATTGTTAAAAATAATATTTTAATTTTTAA
451107 AA
1 AA
451109 ATATTAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (30 bp):
AATTGTTAAAAATAATATTTTAATTTTTAA
Found at i:451092 original size:22 final size:21
Alignment explanation
Indices: 451067--451111 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
451057 GGATAAATTT
451067 TAATTTTTAAAATTTTTAAAAA
1 TAATTTTT-AAATTTTTAAAAA
* *
451089 TAATTTTTTATTTTTTAAAAA
1 TAATTTTTAAATTTTTAAAAA
451110 TA
1 TA
451112 TTAATAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATTTTTAAATTTTTAAAAA
Done.