Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 23 of 171
Found at i:10729111 original size:20 final size:19
Alignment explanation
Indices: 10729057--10729111 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
10729047 GCTGTCTACG
*
10729057 TAAAATTCTAAAAAATTAA
1 TAAAATTTTAAAAAATTAA
*
10729076 TAAAAATATTT-TAAAATTCAA
1 T-AAAAT-TTTAAAAAATT-AA
10729097 TAAAATTTTAAAAAA
1 TAAAATTTTAAAAAA
10729112 AATTCAGTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 4 0.14
20 20 0.69
21 5 0.17
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAATTTTAAAAAATTAA
Found at i:10738437 original size:5 final size:5
Alignment explanation
Indices: 10738427--10738465 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
10738417 TTCATCACCC
10738427 TGTTG TGTTG TGTTG TGTTG TGTTG TGTTG TGTTG TGTT
1 TGTTG TGTTG TGTTG TGTTG TGTTG TGTTG TGTTG TGTT
10738466 CTTTTTCTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (5 bp):
TGTTG
Found at i:10753983 original size:25 final size:26
Alignment explanation
Indices: 10753948--10754006 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
10753938 AAACAAATAT
* * *
10753948 TAAAAAATAAACAAATTTAATATTCA
1 TAAAAAATAAAAAAATTTAAAATACA
10753974 -AAAAAATAAAAAAATTTAAAATACA
1 TAAAAAATAAAAAAATTTAAAATACA
10753999 TAAAAAAT
1 TAAAAAAT
10754007 TCTTTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (26 bp):
TAAAAAATAAAAAAATTTAAAATACA
Found at i:10754917 original size:3 final size:3
Alignment explanation
Indices: 10754909--10754956 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
10754899 GAATCACAAG
* * *
10754909 AGA AGA AGA TA-A AGA TGA AGA AGA AGA AGA AAA AAA AGA AGA AGA
1 AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
10754954 AGA
1 AGA
10754957 GAGGTGCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:10755329 original size:9 final size:9
Alignment explanation
Indices: 10755317--10755359 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
10755307 AAAACAGCAA
10755317 AAAAATAAC
1 AAAAATAAC
10755326 AAAAA-AAC
1 AAAAATAAC
10755334 AAAAATAGCAGC
1 AAAAATA--A-C
10755346 AAAAATAAC
1 AAAAATAAC
10755355 AAAAA
1 AAAAA
10755360 AATAACAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.27
9 12 0.40
10 1 0.03
11 1 0.03
12 8 0.27
ACGTcount: A:0.77, C:0.12, G:0.05, T:0.07
Consensus pattern (9 bp):
AAAAATAAC
Found at i:10755332 original size:28 final size:29
Alignment explanation
Indices: 10755300--10755364 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
10755290 TCAAAACAGC
10755300 AAAAATAAAAACAGCA-AAAAAATAACAA
1 AAAAATAAAAACAGCAGAAAAAATAACAA
* * *
10755328 AAAAACAAAAATAGCAGCAAAAATAACAA
1 AAAAATAAAAACAGCAGAAAAAATAACAA
10755357 AAAAATAA
1 AAAAATAA
10755365 CAGCAAAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.77, C:0.11, G:0.05, T:0.08
Consensus pattern (29 bp):
AAAAATAAAAACAGCAGAAAAAATAACAA
Found at i:10755348 original size:12 final size:12
Alignment explanation
Indices: 10755333--10755372 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
10755323 AACAAAAAAA
*
10755333 CAAAAATAGCAG
1 CAAAAATAACAG
10755345 CAAAAATAACA-
1 CAAAAATAACAG
*
10755356 AAAAAATAACAG
1 CAAAAATAACAG
10755368 CAAAA
1 CAAAA
10755373 GCAGTACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.07
Consensus pattern (12 bp):
CAAAAATAACAG
Found at i:10755420 original size:34 final size:34
Alignment explanation
Indices: 10755347--10755429 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
10755337 AATAGCAGCA
* * * *
10755347 AAAATAACAAAAAAATAACAGCAAAAGCAGTACT
1 AAAACAACAAAAAAACAACACCAAAAGCAATACT
* *
10755381 GAAACAATAAAAAAACAACACCAAAA-CAATAACT
1 AAAACAACAAAAAAACAACACCAAAAGCAAT-ACT
*
10755415 AAAACAGCAAAAAAA
1 AAAACAACAAAAAAA
10755430 AACCTAAAAC
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
33 3 0.08
34 36 0.92
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.08
Consensus pattern (34 bp):
AAAACAACAAAAAAACAACACCAAAAGCAATACT
Found at i:10758706 original size:27 final size:25
Alignment explanation
Indices: 10758672--10758727 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
10758662 TATAAATTAC
*
10758672 ATTAAAAAAAAACTAAATATATATCAAA
1 ATTAAAATAAAAC-AAATATAT-T-AAA
*
10758700 ATTAAAATAATACAAATATATTAAA
1 ATTAAAATAAAACAAATATATTAAA
10758725 ATT
1 ATT
10758728 TATATAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 6 0.23
26 1 0.04
27 8 0.31
28 11 0.42
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (25 bp):
ATTAAAATAAAACAAATATATTAAA
Found at i:10758718 original size:25 final size:25
Alignment explanation
Indices: 10758685--10758741 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
10758675 AAAAAAAAAC
*
10758685 TAAATATATATCAAAATTAAAATAA
1 TAAAAATATATCAAAATTAAAATAA
* * * *
10758710 TACAAATATATTAAAATTTATATAA
1 TAAAAATATATCAAAATTAAAATAA
10758735 TAAAAAT
1 TAAAAAT
10758742 TATTACAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAAAATATATCAAAATTAAAATAA
Found at i:10760156 original size:2 final size:2
Alignment explanation
Indices: 10760149--10760212 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
10760139 ACGGAAAATG
10760149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10760191 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
10760213 GTATGTTTGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10760379 original size:2 final size:2
Alignment explanation
Indices: 10760372--10760403 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10760362 CCCATGCAAC
10760372 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10760404 TTGCTCAACA
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10769485 original size:18 final size:17
Alignment explanation
Indices: 10769446--10769496 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 17
10769436 CAGAAAATTG
*
10769446 ATATTATAA-ATTTTTT
1 ATATTTTAATATTTTTT
10769462 -TATTTTAATATTTTATT
1 ATATTTTAATATTTT-TT
*
10769479 ATATTTTAGTATTTTTT
1 ATATTTTAATATTTTTT
10769496 A
1 A
10769497 AATTATATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 5 0.17
18 13 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATATTTTAATATTTTTT
Found at i:10769737 original size:20 final size:20
Alignment explanation
Indices: 10769709--10769756 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
10769699 CAAAATTTTT
*
10769709 ACGAGTTTGTTAAAATATCTA
1 ACGA-TTTGTCAAAATATCTA
* *
10769730 ATGATTTGTCAATATATCTA
1 ACGATTTGTCAAAATATCTA
10769750 ACGATTT
1 ACGATTT
10769757 ACCTAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (20 bp):
ACGATTTGTCAAAATATCTA
Found at i:10769769 original size:20 final size:19
Alignment explanation
Indices: 10769746--10769866 Score: 77
Period size: 20 Copynumber: 6.1 Consensus size: 19
10769736 TGTCAATATA
10769746 TCTAACGATTTACCTAAATT
1 TCTAACGATTTACC-AAATT
* *
10769766 TCTAAGGATTTA--ATATT
1 TCTAACGATTTACCAAATT
10769783 ATACCTAACGATTTACCAATATT
1 -T--CTAACGATTTACCAA-ATT
* *
10769806 TTTAAAGATTTATCCAAATAT
1 TCTAACGATTTA-CCAAAT-T
*
10769827 T-TAACGATTTATCAAAATT
1 TCTAACGATTTA-CCAAATT
* *
10769846 TCTATCAATTTACCAATATT
1 TCTAACGATTTACCAA-ATT
10769866 T
1 T
10769867 ATGAGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
17 4 0.05
18 1 0.01
19 5 0.06
20 59 0.74
21 6 0.08
22 2 0.03
23 3 0.04
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (19 bp):
TCTAACGATTTACCAAATT
Found at i:10769791 original size:40 final size:40
Alignment explanation
Indices: 10769742--10769817 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
10769732 GATTTGTCAA
* *
10769742 TATATCTAACGATTTACCTAA-ATTTCTAAGGATTTAATAT
1 TATACCTAACGATTTACC-AATATTTCTAAAGATTTAATAT
*
10769782 TATACCTAACGATTTACCAATATTTTTAAAGATTTA
1 TATACCTAACGATTTACCAATATTTCTAAAGATTTA
10769818 TCCAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (40 bp):
TATACCTAACGATTTACCAATATTTCTAAAGATTTAATAT
Found at i:10770008 original size:40 final size:41
Alignment explanation
Indices: 10769932--10770038 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 41
10769922 CTATACTTAG
* * *
10769932 TTTTAACA-TTTACCAAAAATTC-AATGAATTTTTCAAAAA
1 TTTTAACATTTTACCAATATTTCTAATGAATTTATCAAAAA
** * *
10769971 TTTTGTCATTTTACCTATATTTCTAATG-ATTTATCAAAAT
1 TTTTAACATTTTACCAATATTTCTAATGAATTTATCAAAAA
* *
10770011 TTTTAAGATTTTACCAATTTTTCTAATG
1 TTTTAACATTTTACCAATATTTCTAATG
10770039 TTTCACCAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
39 6 0.11
40 44 0.81
41 4 0.07
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (41 bp):
TTTTAACATTTTACCAATATTTCTAATGAATTTATCAAAAA
Found at i:10770012 original size:20 final size:20
Alignment explanation
Indices: 10769989--10770052 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
10769979 TTTTACCTAT
*
10769989 ATTTCTAATGATTTATCAAA
1 ATTTCTAATGATTTACCAAA
* *
10770009 ATTTTTAA-GATTTTACCAAT
1 ATTTCTAATGA-TTTACCAAA
*
10770029 TTTTCTAATG-TTTCACCAAA
1 ATTTCTAATGATTT-ACCAAA
10770049 ATTT
1 ATTT
10770053 ATAAGAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 5 0.15
20 28 0.82
21 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTTCTAATGATTTACCAAA
Found at i:10770049 original size:40 final size:41
Alignment explanation
Indices: 10769978--10770065 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 41
10769968 AAATTTTGTC
* * *
10769978 ATTTTACCTATATTTCTAATGATTTATCAAAATTTTTAAG-
1 ATTTTACCAATATTTCTAATGATTTACCAAAATTTATAAGA
*
10770018 ATTTTACCAATTTTTCTAATG-TTTCACCAAAATTTATAAGA
1 ATTTTACCAATATTTCTAATGATTT-ACCAAAATTTATAAGA
10770059 ATTTTAC
1 ATTTTAC
10770066 AAAAATTCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 3 0.07
40 32 0.76
41 7 0.17
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.48
Consensus pattern (41 bp):
ATTTTACCAATATTTCTAATGATTTACCAAAATTTATAAGA
Found at i:10770178 original size:20 final size:21
Alignment explanation
Indices: 10770159--10770197 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
10770149 TGTCACTTTA
10770159 ACTA-AATCTTTAA-AATTTT
1 ACTAGAATCTTTAATAATTTT
*
10770178 ACTAGAATTTTTAATAATTT
1 ACTAGAATCTTTAATAATTT
10770198 ATCAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (21 bp):
ACTAGAATCTTTAATAATTTT
Found at i:10770276 original size:40 final size:39
Alignment explanation
Indices: 10770193--10770278 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 39
10770183 AATTTTTAAT
*
10770193 AATTTATCAAAATATCTAACAATTTATCAAAACTTTTGGC
1 AATTTATCAAAATATCTAACAATTTA-CAAAAATTTTGGC
* * **
10770233 AATTTATCAATATTTCTAATGATTTA-AAAAATTTTGTGAC
1 AATTTATCAAAATATCTAACAATTTACAAAAATTTTG-G-C
10770273 AATTTA
1 AATTTA
10770279 CTTTTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
38 9 0.23
39 1 0.03
40 29 0.74
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (39 bp):
AATTTATCAAAATATCTAACAATTTACAAAAATTTTGGC
Found at i:10770351 original size:21 final size:20
Alignment explanation
Indices: 10770327--10770375 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
10770317 TACCAATGTT
* * *
10770327 TTTACCTATATTTTTTATGGA
1 TTTACCAATATCTTTT-TGAA
*
10770348 TTTATCAATATCTTTTTGAA
1 TTTACCAATATCTTTTTGAA
10770368 TTTACCAA
1 TTTACCAA
10770376 AATATCTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (20 bp):
TTTACCAATATCTTTTTGAA
Found at i:10770398 original size:40 final size:39
Alignment explanation
Indices: 10770348--10770475 Score: 157
Period size: 40 Copynumber: 3.2 Consensus size: 39
10770338 TTTTTATGGA
* * *
10770348 TTTATCAATATCTTTTTGAATTTACCAAAATATCTAAAAT
1 TTTACCAATAT-TTTATGAATTTATCAAAATATCTAAAAT
*
10770388 TTTACCAATATTTTCATGGATTTATCAAAATATCTAAAAT
1 TTTACCAATATTTT-ATGAATTTATCAAAATATCTAAAAT
* * * *
10770428 TTTCCCAATATTTATATGAATTTATAAAAATATTTAACAT
1 TTTACCAATATTT-TATGAATTTATCAAAATATCTAAAAT
10770468 TTTACCAA
1 TTTACCAA
10770476 AAATTTTAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
39 3 0.04
40 72 0.95
41 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (39 bp):
TTTACCAATATTTTATGAATTTATCAAAATATCTAAAAT
Found at i:10770719 original size:18 final size:18
Alignment explanation
Indices: 10770685--10770722 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
10770675 TTAATTTTCG
*
10770685 AATTCGAATTACTCGAAT
1 AATTCGAATAACTCGAAT
10770703 AATTCGAATAAAC-CGAAT
1 AATTCGAAT-AACTCGAAT
10770721 AA
1 AA
10770723 AAAATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:10770920 original size:58 final size:58
Alignment explanation
Indices: 10770855--10770976 Score: 192
Period size: 58 Copynumber: 2.1 Consensus size: 58
10770845 AAACCCATCA
*
10770855 ATAAACTAAACCCAAATATTTTTAAA-CTCAAATATAATTTCATTATTAAAAAACACTC
1 ATAAACTAAACCCAAATATTTTTAAATC-CAAATATAATTTCATTACTAAAAAACACTC
* * *
10770913 ATAAACTAAACCCAAATATTTTTAAATCCAAATATAATTTTATTCCTAAATAACACTC
1 ATAAACTAAACCCAAATATTTTTAAATCCAAATATAATTTCATTACTAAAAAACACTC
10770971 ATAAAC
1 ATAAAC
10770977 AACTCTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
58 58 0.98
59 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (58 bp):
ATAAACTAAACCCAAATATTTTTAAATCCAAATATAATTTCATTACTAAAAAACACTC
Found at i:10775197 original size:2 final size:2
Alignment explanation
Indices: 10775190--10775219 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10775180 GTATAGTTGG
10775190 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
10775220 TAAAATAACT
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:10778873 original size:57 final size:54
Alignment explanation
Indices: 10778812--10778926 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
10778802 GAAACTATTT
10778812 AAAATTATATAAAATATTATGTTAATAATATTAAAATTACAAAATAAATAATTTTAA
1 AAAATTA-A-AAAATATTATGTTAATAATATTAAAATTACAAAATAAATAA-TTTAA
* * * * *
10778869 AAAA-TAAGATATATTATGTTATTAATATTAAAATTACAACATAAGTAATTTAA
1 AAAATTAAAAAATATTATGTTAATAATATTAAAATTACAAAATAAATAATTTAA
10778922 AAAAT
1 AAAAT
10778927 CAAGATTTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
53 9 0.17
54 36 0.69
55 1 0.02
56 2 0.04
57 4 0.08
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (54 bp):
AAAATTAAAAAATATTATGTTAATAATATTAAAATTACAAAATAAATAATTTAA
Found at i:10778889 original size:54 final size:54
Alignment explanation
Indices: 10778825--10778932 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
10778815 ATTATATAAA
10778825 ATATTATGTTAATAATATTAAAATTACAAAATAAATAATTTTAAAAAAT-AAGAT
1 ATATTATGTTAATAATATTAAAATTACAAAATAAATAA-TTTAAAAAATCAAGAT
* * *
10778879 ATATTATGTTATTAATATTAAAATTACAACATAAGTAATTTAAAAAATCAAGAT
1 ATATTATGTTAATAATATTAAAATTACAAAATAAATAATTTAAAAAATCAAGAT
10778933 TTACTTTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 10 0.20
54 40 0.80
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.37
Consensus pattern (54 bp):
ATATTATGTTAATAATATTAAAATTACAAAATAAATAATTTAAAAAATCAAGAT
Found at i:10778950 original size:53 final size:54
Alignment explanation
Indices: 10778829--10778950 Score: 160
Period size: 54 Copynumber: 2.3 Consensus size: 54
10778819 TATAAAATAT
* *
10778829 TATGTTAATAATATTAAAATTACAAAATAAATAATTTTAAAAAATAAGATATAT
1 TATGTTATTAATATTAAAATTACAAAATAAATAATTTTAAAAAATAAGATATAC
* * *
10778883 TATGTTATTAATATTAAAATTACAACATAAGTAA-TTTAAAAAATCAAGATTTAC
1 TATGTTATTAATATTAAAATTACAAAATAAATAATTTTAAAAAAT-AAGATATAC
10778937 T-T-TTATTAAATATT
1 TATGTTATT-AATATT
10778951 GAGTATTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
52 5 0.08
53 17 0.28
54 39 0.64
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (54 bp):
TATGTTATTAATATTAAAATTACAAAATAAATAATTTTAAAAAATAAGATATAC
Found at i:10779060 original size:19 final size:19
Alignment explanation
Indices: 10779016--10779051 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
10779006 CGTCAAATAT
10779016 TTTTAAATTATGATTTTCA
1 TTTTAAATTATGATTTTCA
10779035 TTTTAAA-T-TGATTTTCA
1 TTTTAAATTATGATTTTCA
10779052 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTTAAATTATGATTTTCA
Found at i:10779216 original size:15 final size:15
Alignment explanation
Indices: 10779198--10779226 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10779188 AAGAAAAATA
10779198 TTGTAAAAATATTTG
1 TTGTAAAAATATTTG
10779213 TTGTAAAAATATTT
1 TTGTAAAAATATTT
10779227 ATTTTGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
TTGTAAAAATATTTG
Found at i:10783044 original size:3 final size:3
Alignment explanation
Indices: 10783036--10783097 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
10783026 TGTTGAGTCT
* * *
10783036 TTA TTA TTA TTA TTA TTG TTA TTG TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
10783084 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
10783098 TCTTGATGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10786646 original size:1 final size:1
Alignment explanation
Indices: 10786640--10786674 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
10786630 TGCCAGCTCT
10786640 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
10786675 GGTTTCGCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:10797041 original size:8 final size:9
Alignment explanation
Indices: 10797001--10797050 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
10796991 TTAATTTTTT
10797001 AAAATTA-A
1 AAAATTATA
10797009 AAAAGTTATA
1 AAAA-TTATA
*
10797019 AAAGTATTTTA
1 AAA--ATTATA
10797030 AAAA-TATA
1 AAAATTATA
10797038 AAAATTATA
1 AAAATTATA
10797047 AAAA
1 AAAA
10797051 AAATATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 11 0.31
9 12 0.34
10 4 0.11
11 7 0.20
12 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:10800152 original size:24 final size:25
Alignment explanation
Indices: 10800100--10800171 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 25
10800090 CCGCTGAAAT
*
10800100 TAAATTATATATTTTTATAA---TAA
1 TAAA-TATATAATTTTATAATTTTAA
*
10800123 TAAATATATAATTTTATTATTTTAA
1 TAAATATATAATTTTATAATTTTAA
*
10800148 T-AATATATATTTTTATAATTTTAA
1 TAAATATATAATTTTATAATTTTAA
10800172 AGGATTAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 13 0.31
23 4 0.10
24 21 0.50
25 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAAATATATAATTTTATAATTTTAA
Found at i:10802630 original size:143 final size:143
Alignment explanation
Indices: 10802372--10802657 Score: 545
Period size: 143 Copynumber: 2.0 Consensus size: 143
10802362 TAAAAAAAAA
10802372 ATTATTTCAAGAATGACTCTTAAAGATTAAGATAAAATTGAGACTTAGGAATACATGTAACTCAT
1 ATTATTTCAAGAATGACTCTTAAAGATTAAGATAAAATTGAGACTTAGGAATACATGTAACTCAT
10802437 TTTTGAAGAGTCCAAGATCAATTAGTGACTTGGTGATAAGATATTGATACGTGTTGATAATCTAT
66 TTTTGAAGAGTCCAAGATCAATTAGTGACTTGGTGATAAGATATTGATACGTGTTGATAATCTAT
10802502 TTATCTAACTAAT
131 TTATCTAACTAAT
* *
10802515 ATTATTTCAAGAATGACTCTTAAAGATTAAGATAAAATTGGGACTTAGGAATATATGTAACTCAT
1 ATTATTTCAAGAATGACTCTTAAAGATTAAGATAAAATTGAGACTTAGGAATACATGTAACTCAT
*
10802580 TTTTGAAGAGTCCAAGATCGATTAGTGACTTGGTGATAAGATATTGATACGTGTTGATAATCTAT
66 TTTTGAAGAGTCCAAGATCAATTAGTGACTTGGTGATAAGATATTGATACGTGTTGATAATCTAT
10802645 TTATCTAACTAAT
131 TTATCTAACTAAT
10802658 CCCACAATAC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
143 140 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (143 bp):
ATTATTTCAAGAATGACTCTTAAAGATTAAGATAAAATTGAGACTTAGGAATACATGTAACTCAT
TTTTGAAGAGTCCAAGATCAATTAGTGACTTGGTGATAAGATATTGATACGTGTTGATAATCTAT
TTATCTAACTAAT
Found at i:10813961 original size:27 final size:27
Alignment explanation
Indices: 10813931--10813986 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
10813921 TAATCTTTCT
10813931 AAAAAATAT-TATTTTAACTCTTTTTTA
1 AAAAAATATCTA-TTTAACTCTTTTTTA
* *
10813958 AAAAATTATCGTATTTAACTTTTTTTTA
1 AAAAAATATC-TATTTAACTCTTTTTTA
10813986 A
1 A
10813987 TATAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.32
28 15 0.60
29 2 0.08
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (27 bp):
AAAAAATATCTATTTAACTCTTTTTTA
Found at i:10822630 original size:27 final size:29
Alignment explanation
Indices: 10822573--10822630 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
10822563 AAGTTAATTG
* *
10822573 TATAAAAAAATTTAATAAATAAAAGATTA
1 TATAAAAAAATTAAATAAATAAAAGAATA
* *
10822602 TATAAAAATATTAAAT-ATTAAAA-AATA
1 TATAAAAAAATTAAATAAATAAAAGAATA
10822629 TA
1 TA
10822631 ATATAAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 5 0.20
28 6 0.24
29 14 0.56
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
TATAAAAAAATTAAATAAATAAAAGAATA
Found at i:10823248 original size:17 final size:18
Alignment explanation
Indices: 10823216--10823250 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10823206 ATAAATATAT
10823216 TTAAATATTTTAATAACA
1 TTAAATATTTTAATAACA
*
10823234 TTAAA-ATTTTTATAACA
1 TTAAATATTTTAATAACA
10823251 ATTTTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAATATTTTAATAACA
Found at i:10823340 original size:32 final size:30
Alignment explanation
Indices: 10823282--10823340 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
10823272 AAAAATATTT
10823282 AAATAATATAATTTTTGTTACAAATTTATA
1 AAATAATATAATTTTTGTTACAAATTTATA
*
10823312 AAATACATATAAATTATTTTTTA-AAATTT
1 AAATA-ATAT-AATT-TTTGTTACAAATTT
10823341 TTCATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 5 0.20
31 4 0.16
32 10 0.40
33 6 0.24
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (30 bp):
AAATAATATAATTTTTGTTACAAATTTATA
Found at i:10831188 original size:30 final size:30
Alignment explanation
Indices: 10831152--10831211 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
10831142 GCTTGCTTTC
10831152 CCACCAAAAGGATCTAATTTTGGCTTCCAA
1 CCACCAAAAGGATCTAATTTTGGCTTCCAA
10831182 CCACCAAAAGGATCTAATTTTGGCTTCCAA
1 CCACCAAAAGGATCTAATTTTGGCTTCCAA
10831212 GTTATCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (30 bp):
CCACCAAAAGGATCTAATTTTGGCTTCCAA
Found at i:10835660 original size:15 final size:15
Alignment explanation
Indices: 10835640--10835675 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
10835630 AATGTTCTCT
10835640 GCACGTTCTCAAAGG
1 GCACGTTCTCAAAGG
10835655 GCACGTTCTCAAAGG
1 GCACGTTCTCAAAGG
10835670 GCACGT
1 GCACGT
10835676 CCCATCCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (15 bp):
GCACGTTCTCAAAGG
Found at i:10840463 original size:18 final size:20
Alignment explanation
Indices: 10840435--10840478 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 20
10840425 ATACAACATT
10840435 ACAAGAAAAATTAAA-T-AAA
1 ACAA-AAAAATTAAATTAAAA
10840454 ACAAAAAAATTAAATTAAAA
1 ACAAAAAAATTAAATTAAAA
10840474 ACAAA
1 ACAAA
10840479 TAATTGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 5 0.22
20 8 0.35
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (20 bp):
ACAAAAAAATTAAATTAAAA
Found at i:10841366 original size:14 final size:15
Alignment explanation
Indices: 10841339--10841372 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
10841329 GATTCAAATT
10841339 TTAAAAATAATATTA
1 TTAAAAATAATATTA
*
10841354 TTAAAAA-AGTATTA
1 TTAAAAATAATATTA
10841368 TTAAA
1 TTAAA
10841373 TTTTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TTAAAAATAATATTA
Found at i:10851608 original size:28 final size:27
Alignment explanation
Indices: 10851538--10851609 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
10851528 AGTATCAAAA
10851538 TTAATT-AATAATTATATTCAATAACT
1 TTAATTAAATAATTATATTCAATAACT
** *
10851564 TTTTTTAAAATAATTATGTTCAATAA-T
1 TTAATT-AAATAATTATATTCAATAACT
10851591 TTAATTAAACTAATT-TATT
1 TTAATTAAA-TAATTATATT
10851610 TTTTAATAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 10 0.27
27 10 0.27
28 17 0.46
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (27 bp):
TTAATTAAATAATTATATTCAATAACT
Found at i:10856359 original size:403 final size:403
Alignment explanation
Indices: 10855564--10856370 Score: 1589
Period size: 402 Copynumber: 2.0 Consensus size: 403
10855554 GTATCGATCG
10855564 TCGCTTAGAGCTCACTAGTTAGACTTTAAAGAAAAAAAGCTTAACAATCCAATAATTTAAATAAA
1 TCGCTTAGAGCTCACTAGTTAGACTTTAAAGAAAAAAAGCTTAACAATCCAATAATTTAAATAAA
10855629 TTTTTTTATATTTTTGAATAGTTTAATGATATTTTATAATTTTTTAAAATTAAATTATCAAAATA
66 TTTTTTTATATTTTTGAATAGTTTAATGATATTTTATAATTTTTTAAAATTAAATTATCAAAATA
10855694 TGAATTTATTAATAATCTAATAATAAGTGTAGTTTAACCTAAAAGCAATGGTACATACAAGTTAC
131 TGAATTTATTAATAATCTAATAATAAGTGTAGTTTAACCTAAAAGCAATGGTACATACAAGTTAC
10855759 AGACTCGTTAAATATATATTTTAATTTCTTTTAGCAGAATTTAGTCCAATCCAAGATGATCCATC
196 AGACTCGTTAAATATATATTTTAATTTCTTTTAGCAGAATTTAGTCCAATCCAAGATGATCCATC
10855824 TCTTGAAAACTCAATTTGTAAGTTTTAAATCCAAAAGCCCACAATTGAAATCCAGGAAGCTGCTT
261 TCTTGAAAACTCAATTTGTAAGTTTTAAATCCAAAAGCCCACAATTGAAATCCAGGAAGCTGCTT
10855889 TCACATTTTTTACATTTTTTAATCACTTGAATGAGTTTGTAATATTTAACTTGATACGCTGGCTT
326 TCACATTTTTTACATTTTTTAATCACTTGAATGAGTTTGTAATATTTAACTTGATACGCTGGCTT
10855954 AAGTCGATTGTAT
391 AAGTCGATTGTAT
10855967 TCGCTTAGAGCTCACTAGTTAGACTTTAAAG-AAAAAAGCTTAACAATCCAATAATTTAAATAAA
1 TCGCTTAGAGCTCACTAGTTAGACTTTAAAGAAAAAAAGCTTAACAATCCAATAATTTAAATAAA
10856031 TTTTTTTATATTTTTGAATAGTTTAATGATATTTTATAATTTTTTAAAATTAAATTATCAAAATA
66 TTTTTTTATATTTTTGAATAGTTTAATGATATTTTATAATTTTTTAAAATTAAATTATCAAAATA
10856096 TGAATTTATTAATAATCTAATAATAAGTGTAGTTTAACCTAAAAGCAATGGTACATACAAGTTAC
131 TGAATTTATTAATAATCTAATAATAAGTGTAGTTTAACCTAAAAGCAATGGTACATACAAGTTAC
*
10856161 AGACTCGTTAAATATATATTTTAATTTCTTTTAGCAGAATTTATTCCAATCCAAGATGATCCATC
196 AGACTCGTTAAATATATATTTTAATTTCTTTTAGCAGAATTTAGTCCAATCCAAGATGATCCATC
10856226 TCTTGAAAACTCAATTTGTAAGTTTTAAATCCAAAAAGCCCACAATTGAAATCCAGGAAGCTGCT
261 TCTTGAAAACTCAATTTGTAAGTTTTAAATCC-AAAAGCCCACAATTGAAATCCAGGAAGCTGCT
10856291 TTCACATTTTTTACATTTTTTAATCACTTGAATGAGTTTGTAATATTTAACTTGATACGCTGGCT
325 TTCACATTTTTTACATTTTTTAATCACTTGAATGAGTTTGTAATATTTAACTTGATACGCTGGCT
10856356 TAAGTCGATTGTAT
390 TAAGTCGATTGTAT
10856370 T
1 T
10856371 TCCATAAGGA
Statistics
Matches: 402, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
402 259 0.64
403 143 0.36
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (403 bp):
TCGCTTAGAGCTCACTAGTTAGACTTTAAAGAAAAAAAGCTTAACAATCCAATAATTTAAATAAA
TTTTTTTATATTTTTGAATAGTTTAATGATATTTTATAATTTTTTAAAATTAAATTATCAAAATA
TGAATTTATTAATAATCTAATAATAAGTGTAGTTTAACCTAAAAGCAATGGTACATACAAGTTAC
AGACTCGTTAAATATATATTTTAATTTCTTTTAGCAGAATTTAGTCCAATCCAAGATGATCCATC
TCTTGAAAACTCAATTTGTAAGTTTTAAATCCAAAAGCCCACAATTGAAATCCAGGAAGCTGCTT
TCACATTTTTTACATTTTTTAATCACTTGAATGAGTTTGTAATATTTAACTTGATACGCTGGCTT
AAGTCGATTGTAT
Found at i:10857440 original size:20 final size:21
Alignment explanation
Indices: 10857400--10857441 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
10857390 TGTGATTATT
10857400 TATTTTAATAATATCAATTTTAA
1 TATTTTAATAATAT--ATTTTAA
*
10857423 TATTTTAATAATATTTTTT
1 TATTTTAATAATATATTTT
10857442 TATTTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
23 14 0.78
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTAATAATATATTTTAA
Found at i:10872206 original size:22 final size:20
Alignment explanation
Indices: 10872174--10872217 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
10872164 GTTTTAAAAA
*
10872174 AATAATTTTTAACTTTTTTT
1 AATAATTTTTAACATTTTTT
*
10872194 AATATATTCTTTAAGATTTTTT
1 AATA-ATT-TTTAACATTTTTT
10872216 AA
1 AA
10872218 GATCTTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 3 0.15
22 13 0.65
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
AATAATTTTTAACATTTTTT
Found at i:10872261 original size:17 final size:16
Alignment explanation
Indices: 10872241--10872283 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
10872231 TTTTAAAATA
10872241 TATAAATTTTGAAATTT
1 TATAAATTTTG-AATTT
10872258 TATAAATACTTTGAATTT
1 TATAAAT--TTTGAATTT
10872276 TA-AAATTT
1 TATAAATTT
10872284 ATTTTGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 2 0.08
17 11 0.46
18 7 0.29
19 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (16 bp):
TATAAATTTTGAATTT
Found at i:10872289 original size:19 final size:18
Alignment explanation
Indices: 10872246--10872296 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
10872236 AAATATATAA
10872246 ATTTTGAAATTTTATAAAT
1 ATTTTG-AATTTTATAAAT
*
10872265 ACTTTGAATTTTA-AAATTT
1 ATTTTGAATTTTATAAA--T
10872284 ATTTTGAACTTTT
1 ATTTTGAA-TTTT
10872297 TTTAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.11
18 7 0.26
19 13 0.48
20 4 0.15
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (18 bp):
ATTTTGAATTTTATAAAT
Found at i:10877381 original size:35 final size:35
Alignment explanation
Indices: 10877342--10877410 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 35
10877332 AAAAAGTTGT
**
10877342 TAATTA-AAAATATGAATTAAAAAAATTGAAAACAA
1 TAATTATAAAATAAAAATTAAAAAAATT-AAAACAA
* *
10877377 TAATTATTAATTAAAAATTAAAAAAATTAAAACA
1 TAATTATAAAATAAAAATTAAAAAAATTAAAACA
10877411 TCATGAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 12 0.41
36 17 0.59
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (35 bp):
TAATTATAAAATAAAAATTAAAAAAATTAAAACAA
Found at i:10879761 original size:22 final size:22
Alignment explanation
Indices: 10879719--10879761 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10879709 TCATTTTTTT
*
10879719 TTATATATTTTTAAATTTATTA
1 TTATATATTTTTAAATATATTA
10879741 TTATATATTTTTGAAA-ATATT
1 TTATATATTTTT-AAATATATT
10879762 TATGTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATATATTTTTAAATATATTA
Found at i:10887253 original size:2 final size:2
Alignment explanation
Indices: 10887248--10887283 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
10887238 ATATATATAT
*
10887248 AG AG AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10887284 TATTGAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10889160 original size:252 final size:252
Alignment explanation
Indices: 10888743--10889397 Score: 1044
Period size: 252 Copynumber: 2.6 Consensus size: 252
10888733 TGTTATTCCG
* * * *
10888743 AAAAATTAGAGGCTCGCCTTGGAACAACTGATAGAATATTCAAAAAAGGAAAGACTTCTAAATAA
1 AAAAATTAGAGGCTCACCTTGAAACAACAGATAGAATATTCAAAAAAGGAAAAACTTCTAAATAA
*
10888808 GTCAAGAAAAAAAAGCTCCAAAAGCATATAAGGAAATAATAGATATCAAATCTATTGCATTGCAA
66 GTCAAGAAAAAAAA-CTCCAAAAGCATATAA-AAAATAATAGATATCAAATCTATTGCATTGCAA
* * *
10888873 ATTATGGTAAATTCTAGAACAAGATGTACTACCAAAGAATGAAAAAATATCCATAATATTATGGT
129 ATTATGGTAAATTTTAGAAAAAGATGTACTACCAAAGAATGAAAAAATATCCATAATATTATAGT
*
10888938 ACATTCTAAGTAAATTATACGATAAAAAGTATCGAAAATCGATAGTGTTATTTC-AAAA
194 ACATTCTAAGTAAATTATACGATAAAAAATATCGAAAATCGATAGTGTTATTTCAAAAA
*
10888996 AAAAATTAGAGGCTCATCC-CGAAACAACAGATAGAATATTCAAAAAAGGAAAAACTTCTAAATA
1 AAAAATTAGAGGCTCA-CCTTGAAACAACAGATAGAATATTCAAAAAAGGAAAAACTTCTAAATA
* *
10889060 AGTCAAGAAAAAAAACTCCAAAAGCATATAAAAAATATATATATATCAAATATATTGCATTGCAA
65 AGTCAAGAAAAAAAACTCCAAAAGCATATAAAAAATA-ATAGATATCAAATCTATTGCATTGCAA
* *
10889125 ATTATGTTAAATTTTAGAAAAATATGTACTACCAAAGAATGAAAAAATATCCATAATATTATAGT
129 ATTATGGTAAATTTTAGAAAAAGATGTACTACCAAAGAATGAAAAAATATCCATAATATTATAGT
10889190 ACATTCTAAGTAAATTATACGATAAAAAATATCGAAAATCGATAGTGTTATTTCAAAAAA
194 ACATTCTAAGTAAATTATACGATAAAAAATATCGAAAATCGATAGTGTTATTTC-AAAAA
* * *
10889250 AAAAAATAGAGGCTCACCTTGAAACAACAAATAGAATATTCAAAAAAGGAAATACTTCTAAATAA
1 AAAAATTAGAGGCTCACCTTGAAACAACAGATAGAATATTCAAAAAAGGAAAAACTTCTAAATAA
* * ** *
10889315 GTCAAGAAAAAAAGCTCCAAAAGCATATAAAGAAATAATGGATATCAAATCTATTATATTGCAAT
66 GTCAAGAAAAAAAACTCCAAAAGCATATAAA-AAATAATAGATATCAAATCTATTGCATTGCAAA
10889380 TTATGGTAAATTTTAGAA
130 TTATGGTAAATTTTAGAA
10889398 CAGGTTAAGC
Statistics
Matches: 370, Mismatches: 26, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
251 5 0.01
252 154 0.42
253 73 0.20
254 133 0.36
255 5 0.01
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (252 bp):
AAAAATTAGAGGCTCACCTTGAAACAACAGATAGAATATTCAAAAAAGGAAAAACTTCTAAATAA
GTCAAGAAAAAAAACTCCAAAAGCATATAAAAAATAATAGATATCAAATCTATTGCATTGCAAAT
TATGGTAAATTTTAGAAAAAGATGTACTACCAAAGAATGAAAAAATATCCATAATATTATAGTAC
ATTCTAAGTAAATTATACGATAAAAAATATCGAAAATCGATAGTGTTATTTCAAAAA
Found at i:10895905 original size:32 final size:31
Alignment explanation
Indices: 10895830--10895910 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 31
10895820 ACTTGAAAAC
10895830 TTTTAAAAATATATAAAAACCTTAAAATTCTTT
1 TTTTAAAAA-A-ATAAAAACCTTAAAATTCTTT
* *
10895863 TTTT-AGAAAATAAAAACCTT-AAATTTTAATT
1 TTTTAAAAAAATAAAAACCTTAAAATTCT--TT
*
10895894 TTTTAAAAAAATCAAAA
1 TTTTAAAAAAATAAAAA
10895911 GGATAAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 6 0.15
30 11 0.27
31 7 0.17
32 13 0.32
33 4 0.10
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (31 bp):
TTTTAAAAAAATAAAAACCTTAAAATTCTTT
Found at i:10905056 original size:102 final size:104
Alignment explanation
Indices: 10904853--10905057 Score: 308
Period size: 102 Copynumber: 2.0 Consensus size: 104
10904843 TACAATATTT
10904853 AAATTTTATTTTACTCACAATTTAAACTATTTTTTTATTTAAAATTAATACATACGGCATGTCTG
1 AAATTTTATTTTACTCACAATTTAAACTA-TTTTTTATTTAAAATTAATACATACGG-ATGTCTG
10904918 TAATTATTAATTTTAAACGTTGCACTTCATTATTTGTTTAA
64 TAATTATTAATTTTAAACGTTGCACTTCATTATTTGTTTAA
* * **
10904959 AAATTTTATTTTACTCACAATTTAAACTA-TTTTTATTTTAATTTAATACATATTG-TGTGC-GT
1 AAATTTTATTTTACTCACAATTTAAACTATTTTTTATTTAAAATTAATACATACGGATGT-CTGT
* *
10905021 AATTATTAATTTTAAATGTTGCACTTCATTGTTTGTT
65 AATTATTAATTTTAAACGTTGCACTTCATTATTTGTT
10905058 ATATGTTACT
Statistics
Matches: 92, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
102 40 0.43
103 1 0.01
104 22 0.24
106 29 0.32
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.50
Consensus pattern (104 bp):
AAATTTTATTTTACTCACAATTTAAACTATTTTTTATTTAAAATTAATACATACGGATGTCTGTA
ATTATTAATTTTAAACGTTGCACTTCATTATTTGTTTAA
Found at i:10906052 original size:18 final size:19
Alignment explanation
Indices: 10906031--10906071 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
10906021 TTATCAAAAG
* *
10906031 ATATAT-TAATTAATAGTA
1 ATATATATAATAAATAATA
10906049 ATAT-TATAATAAATAATA
1 ATATATATAATAAATAATA
10906067 ATATA
1 ATATA
10906072 AAATATAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATATATAATAAATAATA
Found at i:10909298 original size:15 final size:14
Alignment explanation
Indices: 10909261--10909288 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10909251 GTATATTTCA
10909261 GGTATATTTTAGTT
1 GGTATATTTTAGTT
10909275 GGTATATTTTAGTT
1 GGTATATTTTAGTT
10909289 ATTTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (14 bp):
GGTATATTTTAGTT
Found at i:10910869 original size:18 final size:17
Alignment explanation
Indices: 10910829--10910870 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
10910819 TATATAAAAA
10910829 ATTAA-ATT-GTTTAAT
1 ATTAATATTAGTTTAAT
10910844 ATTAATATTAGTTTAATT
1 ATTAATATTAGTTTAA-T
*
10910862 ATTTATATT
1 ATTAATATT
10910871 TTAATGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 3 0.13
17 6 0.26
18 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTAATATTAGTTTAAT
Found at i:10911142 original size:28 final size:31
Alignment explanation
Indices: 10911102--10911169 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
10911092 ATTTGACCCG
*
10911102 TTGTCATAATTT-AA-G-AAAAACGACAACT
1 TTGTCACAATTTAAAGGAAAAAACGACAACT
*
10911130 TTGTCACAATTTAGAAGGAAAAAAAGGACAACT
1 TTGTCACAATTTA-AAGG-AAAAAACGACAACT
10911163 TTGTCAC
1 TTGTCAC
10911170 GATCTGTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 11 0.33
30 2 0.06
31 1 0.03
33 19 0.58
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (31 bp):
TTGTCACAATTTAAAGGAAAAAACGACAACT
Found at i:10919597 original size:13 final size:13
Alignment explanation
Indices: 10919579--10919604 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10919569 AATTCTAAAC
10919579 TCTAATGAGTGTA
1 TCTAATGAGTGTA
10919592 TCTAATGAGTGTA
1 TCTAATGAGTGTA
10919605 GACAATTTGA
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:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TCTAATGAGTGTA
Found at i:10920599 original size:19 final size:19
Alignment explanation
Indices: 10920563--10920600 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
10920553 AAGAAATTAC
*
10920563 TAAATAACTTTATATATTT
1 TAAATAAATTTATATATTT
10920582 TAAATAAA-TTATATTATTT
1 TAAATAAATTTATA-TATTT
10920601 ATCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATAAATTTATATATTT
Found at i:10921906 original size:20 final size:20
Alignment explanation
Indices: 10921872--10921942 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
10921862 ATGAAATGAC
10921872 AACAAAACAGTTGAAAAAAAT
1 AACAAAACAG-TGAAAAAAAT
*
10921893 AACAAAACAGTGAAAAAAGT
1 AACAAAACAGTGAAAAAAAT
* *
10921913 AACAAAACAGTAAAAAATAAC
1 AACAAAACAGTGAAAAA-AAT
10921934 AACAAAACA
1 AACAAAACA
10921943 TTATTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 25 0.56
21 20 0.44
ACGTcount: A:0.69, C:0.13, G:0.08, T:0.10
Consensus pattern (20 bp):
AACAAAACAGTGAAAAAAAT
Found at i:10924282 original size:116 final size:116
Alignment explanation
Indices: 10924156--10924366 Score: 280
Period size: 116 Copynumber: 1.8 Consensus size: 116
10924146 AATAATTTAA
* ** * ** *
10924156 TTTTTTTAAGTAATAAAAAGGAAAGGGTATAACGAATTGTGCCGCAAAAATAATATAAATATTAT
1 TTTTTTTAAGTAATAAAAAAGAAAGGACATAACAAATTCCGCCACAAAAATAATATAAATATTAT
*
10924221 GTTT-GAATATATTTTACATGTAAGAAGTTTTTAATTTTGCTTTAACAATAT
66 ATTTAG-ATATATTTTACATGTAAGAAGTTTTTAATTTTGCTTTAACAATAT
* * * *
10924272 TTTTTTTAAGTAATAAAAAAGAAAGGACATAACAAATTCCGTCACAAAAATAATCTTAATGTTAT
1 TTTTTTTAAGTAATAAAAAAGAAAGGACATAACAAATTCCGCCACAAAAATAATATAAATATTAT
* *
10924337 ATTTAGATATATTTTATATGTAAGGAGTTT
66 ATTTAGATATATTTTACATGTAAGAAGTTT
10924367 AAAAAAAAAC
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
116 79 0.99
117 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.39
Consensus pattern (116 bp):
TTTTTTTAAGTAATAAAAAAGAAAGGACATAACAAATTCCGCCACAAAAATAATATAAATATTAT
ATTTAGATATATTTTACATGTAAGAAGTTTTTAATTTTGCTTTAACAATAT
Found at i:10931768 original size:15 final size:15
Alignment explanation
Indices: 10931748--10931781 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
10931738 AGGTTTACTG
10931748 ATATGCATAAAGTGT
1 ATATGCATAAAGTGT
10931763 ATATGCATAAAGTGT
1 ATATGCATAAAGTGT
10931778 ATAT
1 ATAT
10931782 ATAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (15 bp):
ATATGCATAAAGTGT
Found at i:10944717 original size:6 final size:6
Alignment explanation
Indices: 10944706--10944738 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
10944696 TGATCAAAAT
*
10944706 TGAAAG TGAAAG TGAAAG TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
10944739 TATGAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.21
Consensus pattern (6 bp):
TGAAAG
Found at i:10944888 original size:41 final size:40
Alignment explanation
Indices: 10944841--10944940 Score: 116
Period size: 38 Copynumber: 2.5 Consensus size: 40
10944831 CGACCTCGAG
** *
10944841 TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGA
1 TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGA
** *
10944881 TTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAGA
1 -TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGA
10944919 TCGATGAGACACTGGGTGTCAC
1 TCGATGAGACACTGGGTGTCAC
10944941 TTTATTGCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
37 11 0.23
38 18 0.38
39 4 0.08
40 4 0.08
41 11 0.23
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGA
Found at i:10944933 original size:37 final size:38
Alignment explanation
Indices: 10944866--10944944 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
10944856 GTGTCATTAT
**
10944866 TTTACTTCGGATAGATTCGATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGATTCGATGAGACACTGGGTACCAC
* **
10944904 TTTACTTCGGCTAGA-TCGATGAGACACTGGGTGTCAC
1 TTTACTTCGGATAGATTCGATGAGACACTGGGTACCAC
10944941 TTTA
1 TTTA
10944945 TTGCTTCGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 22 0.61
38 14 0.39
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (38 bp):
TTTACTTCGGATAGATTCGATGAGACACTGGGTACCAC
Found at i:10945882 original size:20 final size:21
Alignment explanation
Indices: 10945857--10945903 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
10945847 AGCGTTAATA
10945857 TAAAATAATTTATAAAA-GTT
1 TAAAATAATTTATAAAATGTT
* * *
10945877 TAAAATCATTTTTAAAATTTT
1 TAAAATAATTTATAAAATGTT
10945898 TAAAAT
1 TAAAAT
10945904 GTATACTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TAAAATAATTTATAAAATGTT
Found at i:10947624 original size:20 final size:20
Alignment explanation
Indices: 10947596--10947674 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
10947586 CCAGGTCAAC
*
10947596 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
10947616 AAATTATTTTTTAAAATATAAAATTATTA
1 AAATTA--TTTTAAAAT-T---A---TTA
10947645 AAATTATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
10947665 AAATTATTTT
1 AAATTATTTT
10947675 TTTTGAAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
20 18 0.37
22 9 0.18
23 2 0.04
26 2 0.04
27 9 0.18
29 9 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:10947647 original size:29 final size:29
Alignment explanation
Indices: 10947600--10947672 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
10947590 GTCAACAAAT
10947600 AATT-TTAAAATTATTAAAATTATTTTTTAA
1 AATTATTAAAATTATTAAAATTA--TTTTAA
10947630 AA-TA-TAAAATTATTAAAATTATTTTAA
1 AATTATTAAAATTATTAAAATTATTTTAA
10947657 AATTATTAAAATTATT
1 AATTATTAAAATTATT
10947673 TTTTTTGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
27 8 0.20
28 2 0.05
29 28 0.70
30 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATTATTAAAATTATTAAAATTATTTTAA
Found at i:10947673 original size:49 final size:50
Alignment explanation
Indices: 10947596--10947707 Score: 174
Period size: 49 Copynumber: 2.2 Consensus size: 50
10947586 CCAGGTCAAC
10947596 AAATAATTTTAAAATTATTAAAATTA-TTTTTTAAAAT-ATAAAATTATT
1 AAATAATTTTAAAATTATTAAAATTATTTTTTTAAAATAATAAAATTATT
* *
10947644 AAAATTATTTTAAAATTATTAAAATTATTTTTTTTGAAATAATAAAATTATT
1 -AAATAATTTTAAAATTATTAAAATTA-TTTTTTTAAAATAATAAAATTATT
10947696 AAATAATTTTAA
1 AAATAATTTTAA
10947708 TTTCTAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
49 25 0.44
51 21 0.37
52 11 0.19
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (50 bp):
AAATAATTTTAAAATTATTAAAATTATTTTTTTAAAATAATAAAATTATT
Found at i:10948355 original size:9 final size:9
Alignment explanation
Indices: 10948341--10948411 Score: 74
Period size: 9 Copynumber: 7.6 Consensus size: 9
10948331 ATTAAAATTA
10948341 TTTAATAAT
1 TTTAATAAT
10948350 TTTAATAAT
1 TTTAATAAT
*
10948359 TTTAAATTAAG
1 TTT-AA-TAAT
10948370 TTTAATAAT
1 TTTAATAAT
10948379 TTT-AT-AT
1 TTTAATAAT
10948386 TTTAAAAATAAT
1 TTT---AATAAT
10948398 TTTAATAAT
1 TTTAATAAT
10948407 TTTAA
1 TTTAA
10948412 AATCATTTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
7 5 0.09
8 2 0.04
9 29 0.55
10 4 0.08
11 8 0.15
12 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (9 bp):
TTTAATAAT
Found at i:10948397 original size:19 final size:21
Alignment explanation
Indices: 10948373--10948413 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
10948363 AATTAAGTTT
10948373 AATAATTTT-AT-ATTTTAAA
1 AATAATTTTAATAATTTTAAA
10948392 AATAATTTTAATAATTTTAAA
1 AATAATTTTAATAATTTTAAA
10948413 A
1 A
10948414 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATAATTTTAATAATTTTAAA
Found at i:10948410 original size:28 final size:28
Alignment explanation
Indices: 10948332--10948410 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 28
10948322 AAATTGGAAA
*
10948332 TTAAAATTA-TTTAATAATTTTAATAATT
1 TTAAAATAAGTTTAATAATTTT-ATAATT
*
10948360 TTAAATTAAGTTTAATAATTTTAT-ATT
1 TTAAAATAAGTTTAATAATTTTATAATT
*
10948387 TTAAAAATAATTTTAATAATTTTA
1 TT-AAAATAAGTTTAATAATTTTA
10948411 AAATCATTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 5 0.11
28 28 0.62
29 12 0.27
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
TTAAAATAAGTTTAATAATTTTATAATT
Found at i:10948419 original size:20 final size:20
Alignment explanation
Indices: 10948332--10948419 Score: 73
Period size: 20 Copynumber: 4.6 Consensus size: 20
10948322 AAATTGGAAA
*
10948332 TTAAAATTA-TTTAATAATT
1 TTAAAATAATTTTAATAATT
*
10948351 TT--AATAATTTTAAATTAAGT
1 TTAAAATAATTTT-AA-TAATT
10948371 TT--AATAATTTT-AT-ATT
1 TTAAAATAATTTTAATAATT
10948387 TTAAAAATAATTTTAATAATT
1 TT-AAAATAATTTTAATAATT
*
10948408 TTAAAATCATTT
1 TTAAAATAATTT
10948420 GCTGATGTGG
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
16 4 0.07
17 5 0.09
18 4 0.07
19 13 0.23
20 26 0.46
21 5 0.09
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (20 bp):
TTAAAATAATTTTAATAATT
Found at i:10979057 original size:21 final size:21
Alignment explanation
Indices: 10979037--10979094 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
10979027 ACCCGATCAC
10979037 CAAC-CCGACAGCCCCAGTCA
1 CAACTCCGACAGCCCCAGTCA
* * *
10979057 CAACTCCAACAGCACCAGTTA
1 CAACTCCGACAGCCCCAGTCA
*
10979078 CAACTCCGACAACCCCA
1 CAACTCCGACAGCCCCA
10979095 ACCCCGACTC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.34, C:0.47, G:0.10, T:0.09
Consensus pattern (21 bp):
CAACTCCGACAGCCCCAGTCA
Found at i:10980828 original size:32 final size:32
Alignment explanation
Indices: 10980758--10980828 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
10980748 TTTTTAGAGG
* *
10980758 ATGATTAATACAAATCCTTAAAGAGATCAGGA
1 ATGATTAATACAAATCCTTAAACAAATCAGGA
** * * *
10980790 CCGATTAATACAAATCTTTGAACAAATTAGGA
1 ATGATTAATACAAATCCTTAAACAAATCAGGA
10980822 ATGATTA
1 ATGATTA
10980829 GAAATTTAAC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (32 bp):
ATGATTAATACAAATCCTTAAACAAATCAGGA
Found at i:10999101 original size:2 final size:2
Alignment explanation
Indices: 10999094--10999118 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10999084 GAATGATTGT
10999094 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
10999119 GAACTGTGTT
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:10999658 original size:12 final size:12
Alignment explanation
Indices: 10999643--10999691 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
10999633 GTTTAATTAT
10999643 ATGTTCATGAAC
1 ATGTTCATGAAC
**
10999655 ATGTTCATTTA-
1 ATGTTCATGAAC
*
10999666 ATATTCATGAAC
1 ATGTTCATGAAC
*
10999678 ATGTTCGTGAAC
1 ATGTTCATGAAC
10999690 AT
1 AT
10999692 TAAACAAGCA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (12 bp):
ATGTTCATGAAC
Found at i:11001249 original size:17 final size:17
Alignment explanation
Indices: 11001223--11001256 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11001213 TCATTATTTA
*
11001223 ATTATTTTTTATTTAAT
1 ATTATATTTTATTTAAT
11001240 ATTATATTTTATTTAAT
1 ATTATATTTTATTTAAT
11001257 GTCACCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTATATTTTATTTAAT
Found at i:11004256 original size:21 final size:23
Alignment explanation
Indices: 11004232--11004277 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
11004222 ACAAGCCAGA
11004232 CTCCAACTC-CTC-CATCTTCTC
1 CTCCAACTCGCTCGCATCTTCTC
*
11004253 CTCCATCTCGCTCGTCATCTTCTC
1 CTCCAACTCGCTCG-CATCTTCTC
11004277 C
1 C
11004278 GACCCTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
24 10 0.48
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (23 bp):
CTCCAACTCGCTCGCATCTTCTC
Found at i:11005997 original size:10 final size:10
Alignment explanation
Indices: 11005967--11005998 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
11005957 TTATATTAAA
11005967 TTATATATAT
1 TTATATATAT
*
11005977 ATATATATAT
1 TTATATATAT
11005987 TTATATATAT
1 TTATATATAT
11005997 TT
1 TT
11005999 TGCTTTTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATATATAT
Found at i:11007745 original size:61 final size:61
Alignment explanation
Indices: 11007621--11007746 Score: 157
Period size: 61 Copynumber: 2.1 Consensus size: 61
11007611 TTTTTGAAAA
* * * * **
11007621 TTTTAAAGTTAGAATTAAATTGATAAATTTTGTAAATGTTGAAGGTTATGTTTATTAAATT
1 TTTTAAAGTTAGAATTAAAATAATAAATTTTGTAAATATTGAAAGTTAAATTTATTAAATT
* *
11007682 TTTTAGAA-TTAGAATTAAAATAATAAATTTTGTAAATATT-AAAGTTAAATTTGTTGAATT
1 TTTTA-AAGTTAGAATTAAAATAATAAATTTTGTAAATATTGAAAGTTAAATTTATTAAATT
11007742 TTTTA
1 TTTTA
11007747 GATTAAGACA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 20 0.36
61 34 0.61
62 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (61 bp):
TTTTAAAGTTAGAATTAAAATAATAAATTTTGTAAATATTGAAAGTTAAATTTATTAAATT
Found at i:11007762 original size:61 final size:61
Alignment explanation
Indices: 11007621--11007762 Score: 146
Period size: 61 Copynumber: 2.3 Consensus size: 61
11007611 TTTTTGAAAA
* * * * * **
11007621 TTTTA-AAGTTAGAATTAAATTGATAAATTTTGTAAATGTTGAAGGTTATGTTTATTAAATT
1 TTTTAGAA-TTAGAAATAAAATAATAAATTTTGTAAATATTGAAAGTTAAATTTATTAAATT
* * *
11007682 TTTTAGAATTAGAATTAAAATAATAAATTTTGTAAATATT-AAAGTTAAATTTGTTGAATT
1 TTTTAGAATTAGAAATAAAATAATAAATTTTGTAAATATTGAAAGTTAAATTTATTAAATT
11007742 TTTTAG-ATTAAGACAATAAAA
1 TTTTAGAATT-AGA-AATAAAA
11007763 AGGGCTTACA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 3 0.04
60 24 0.35
61 40 0.58
62 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.12, T:0.44
Consensus pattern (61 bp):
TTTTAGAATTAGAAATAAAATAATAAATTTTGTAAATATTGAAAGTTAAATTTATTAAATT
Found at i:11014456 original size:15 final size:16
Alignment explanation
Indices: 11014425--11014459 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
11014415 ATTTAAAATT
11014425 TTATAAATTACAAAAA
1 TTATAAATTACAAAAA
11014441 TTATAAATTA-AAAAA
1 TTATAAATTACAAAAA
11014456 TTAT
1 TTAT
11014460 CAAGATTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TTATAAATTACAAAAA
Found at i:11015065 original size:30 final size:31
Alignment explanation
Indices: 11015006--11015068 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
11014996 ATAATTTAAT
11015006 TTGATCAATTTTAATTTTTATATTTTTTGAA
1 TTGATCAATTTTAATTTTTATATTTTTTGAA
*
11015037 TTGATCAGTTTTAATTTTTATA-TTTTTGAA
1 TTGATCAATTTTAATTTTTATATTTTTTGAA
11015067 TT
1 TT
11015069 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (31 bp):
TTGATCAATTTTAATTTTTATATTTTTTGAA
Found at i:11015070 original size:16 final size:15
Alignment explanation
Indices: 11015014--11015082 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 15
11015004 ATTTGATCAA
11015014 TTTTAATTTTTATATT
1 TTTTAATTTTTATA-T
* *
11015030 TTTTGAA--TTGATCAG
1 TTTT-AATTTTTAT-AT
11015045 TTTTAATTTTTATAT
1 TTTTAATTTTTATAT
* *
11015060 TTTTGAATTTTTAAAA
1 TTTT-AATTTTTATAT
11015076 TTTTAAT
1 TTTTAAT
11015083 CTTGACTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 2 0.05
15 16 0.38
16 22 0.52
17 2 0.05
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTAATTTTTATAT
Found at i:11015080 original size:31 final size:31
Alignment explanation
Indices: 11015006--11015082 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
11014996 ATAATTTAAT
*
11015006 TTGATCAATTTTAATTTTTATATTTTTTGAA
1 TTGATAAATTTTAATTTTTATATTTTTTGAA
* *
11015037 TTGATCAGTTTTAATTTTTATA-TTTTTGAA
1 TTGATAAATTTTAATTTTTATATTTTTTGAA
**
11015067 TTTTTAAAATTTTAAT
1 TTGAT-AAATTTTAAT
11015083 CTTGACTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 11 0.28
31 29 0.73
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (31 bp):
TTGATAAATTTTAATTTTTATATTTTTTGAA
Found at i:11028449 original size:80 final size:80
Alignment explanation
Indices: 11028316--11028475 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
11028306 GTCCGGATGC
*
11028316 CATCAGATAAGGATGCTATCACTTCATGTTCTTGGAGTGAAACACCTGGCAAATGCTTTTCCTTG
1 CATCAGAAAAGGATGCTATCACTTCATGTTCTTGGAGTGAAACACCTGGCAAATGCTTTTCCTTG
11028381 TTGATAAGCATTAGT
66 TTGATAAGCATTAGT
11028396 CATCAGAAAAGGATGCTATCACTTCATGTTCTTGGAGTGAAACACCTGGCAAATGCTTTTCCTTG
1 CATCAGAAAAGGATGCTATCACTTCATGTTCTTGGAGTGAAACACCTGGCAAATGCTTTTCCTTG
11028461 TTGATAAGCATTAGT
66 TTGATAAGCATTAGT
11028476 TCTTCCGGAT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (80 bp):
CATCAGAAAAGGATGCTATCACTTCATGTTCTTGGAGTGAAACACCTGGCAAATGCTTTTCCTTG
TTGATAAGCATTAGT
Found at i:11048777 original size:30 final size:30
Alignment explanation
Indices: 11048741--11048800 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
11048731 TATTTGTAAG
11048741 ATAATTTTTTATCATACTAATTAAAACAAT
1 ATAATTTTTTATCATACTAATTAAAACAAT
11048771 ATAATTTTTTATCATACTAATTAAAACAAT
1 ATAATTTTTTATCATACTAATTAAAACAAT
11048801 TTTAAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (30 bp):
ATAATTTTTTATCATACTAATTAAAACAAT
Found at i:11050386 original size:13 final size:13
Alignment explanation
Indices: 11050363--11050402 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
11050353 CTTTAAATTC
11050363 AATACTTATTTTT
1 AATACTTATTTTT
**
11050376 AATGTTTATTTTTT
1 AATACTTA-TTTTT
11050390 AATACTTATTTTT
1 AATACTTATTTTT
11050403 TTAATTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (13 bp):
AATACTTATTTTT
Found at i:11050388 original size:14 final size:14
Alignment explanation
Indices: 11050363--11050403 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
11050353 CTTTAAATTC
11050363 AATACTTA-TTTTT
1 AATACTTATTTTTT
**
11050376 AATGTTTATTTTTT
1 AATACTTATTTTTT
11050390 AATACTTATTTTTT
1 AATACTTATTTTTT
11050404 TAATTTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (14 bp):
AATACTTATTTTTT
Found at i:11051527 original size:2 final size:2
Alignment explanation
Indices: 11051522--11051548 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11051512 GTTTTTTTGT
11051522 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 T
11051549 CAAGTCAACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11062250 original size:16 final size:16
Alignment explanation
Indices: 11062229--11062259 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11062219 AAATTCAATA
*
11062229 TTTTTCTTTTTTCTTT
1 TTTTTCTATTTTCTTT
11062245 TTTTTCTATTTTCTT
1 TTTTTCTATTTTCTT
11062260 ACCGGACCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTATTTTCTTT
Found at i:11088567 original size:27 final size:26
Alignment explanation
Indices: 11088533--11088641 Score: 91
Period size: 27 Copynumber: 4.2 Consensus size: 26
11088523 AAAATAATTT
11088533 TAAA-ATCTCAAATTT-TATATTTTTA
1 TAAATATCT-AAATTTATATATTTTTA
*
11088558 TAAATGATCTAAGTTTATAATATTTTTGA
1 TAAAT-ATCTAAATTTAT-ATATTTTT-A
* * * *
11088587 -AAATTTTTAAGGTTTTTATATTTTTA
1 TAAATATCTAA-ATTTATATATTTTTA
*
11088613 TAAATTTCTAAATTTATATATTTTT-
1 TAAATATCTAAATTTATATATTTTTA
11088638 TAAA
1 TAAA
11088642 ATTTTTAAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
25 8 0.11
26 18 0.26
27 26 0.37
28 17 0.24
29 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (26 bp):
TAAATATCTAAATTTATATATTTTTA
Found at i:11088654 original size:18 final size:18
Alignment explanation
Indices: 11088587--11088656 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 18
11088577 ATATTTTTGA
*
11088587 AAATTTTTA-AGGTTTTT
1 AAATTTTTATAGTTTTTT
* ** *
11088604 ATATTTTTATAAATTTCT
1 AAATTTTTATAGTTTTTT
*
11088622 AAATTTATATA-TTTTTT
1 AAATTTTTATAGTTTTTT
11088639 AAAATTTTTA-AGTTTTTT
1 -AAATTTTTATAGTTTTTT
11088657 TTATAAATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
17 13 0.32
18 28 0.68
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (18 bp):
AAATTTTTATAGTTTTTT
Found at i:11088661 original size:55 final size:55
Alignment explanation
Indices: 11088545--11088656 Score: 174
Period size: 53 Copynumber: 2.1 Consensus size: 55
11088535 AAATCTCAAA
*
11088545 TTTTATATTTTTATAAATGATCTAAGTTTATAATATTTTTGAAAATTTTTAAGGT
1 TTTTATATTTTTATAAATGATCTAAATTTATAATATTTTTGAAAATTTTTAAGGT
* * *
11088600 TTTTATATTTTTATAAAT-TTCTAAATTTAT-ATATTTTTTAAAATTTTTAAGTT
1 TTTTATATTTTTATAAATGATCTAAATTTATAATATTTTTGAAAATTTTTAAGGT
11088653 TTTT
1 TTTT
11088657 TTATAAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 25 0.47
54 10 0.19
55 18 0.34
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (55 bp):
TTTTATATTTTTATAAATGATCTAAATTTATAATATTTTTGAAAATTTTTAAGGT
Found at i:11089503 original size:21 final size:21
Alignment explanation
Indices: 11089476--11089526 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
11089466 AGATTATGTA
11089476 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* * *
11089497 GTTTGGATTTCTAAATTTTAT
1 ATTTGGATTTATAAACTTTAT
11089518 ATTTGGATT
1 ATTTGGATT
11089527 ATGTTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:11097284 original size:38 final size:38
Alignment explanation
Indices: 11097233--11097311 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
11097223 CATATTATAT
11097233 AATCACTTAGATGATTAGTTGGGATAAATTTGCATTTG
1 AATCACTTAGATGATTAGTTGGGATAAATTTGCATTTG
*
11097271 AATCACTTTGATGATTAGTTGGGATAAATTTGCATTTG
1 AATCACTTAGATGATTAGTTGGGATAAATTTGCATTTG
11097309 AAT
1 AAT
11097312 TTGAAGCCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (38 bp):
AATCACTTAGATGATTAGTTGGGATAAATTTGCATTTG
Found at i:11101820 original size:43 final size:43
Alignment explanation
Indices: 11101772--11101857 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
11101762 CATTTGGACT
*
11101772 AATATTTTCCATATATAAC-TTTATTAATGTTATTTACAAATTA
1 AATATTTTCCATATAT-ACGTTTATTAATGATATTTACAAATTA
11101815 AATATTTTCCATATATACGTTTATTAATGATATTTACAAATTA
1 AATATTTTCCATATATACGTTTATTAATGATATTTACAAATTA
11101858 TAACTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 2 0.05
43 39 0.95
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (43 bp):
AATATTTTCCATATATACGTTTATTAATGATATTTACAAATTA
Found at i:11105005 original size:2 final size:2
Alignment explanation
Indices: 11104998--11105024 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11104988 GCTTGCAGAT
11104998 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 T
11105025 GTGTGAACTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11110021 original size:14 final size:14
Alignment explanation
Indices: 11109977--11110028 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
11109967 AAATTATATT
11109977 TATATTTT-T-AAA
1 TATATTTTATAAAA
11109989 TATATTTTA-AAAA
1 TATATTTTATAAAA
* *
11110002 CAATATTATATAAAA
1 -TATATTTTATAAAA
11110017 TATATTTTATAA
1 TATATTTTATAA
11110029 GTATTGGGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
12 8 0.25
13 3 0.09
14 17 0.53
15 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TATATTTTATAAAA
Found at i:11111416 original size:3 final size:3
Alignment explanation
Indices: 11111408--11111434 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11111398 GAATATTCAA
11111408 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
11111435 TTCCCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11114023 original size:24 final size:22
Alignment explanation
Indices: 11113996--11114046 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
11113986 TTTGGATCAA
*
11113996 AAATTAAATCCAATTTTAGATTTT
1 AAATTAAATCC-ATTTTA-AGTTT
* *
11114020 AAATTTAATTCATTTTAAGTTT
1 AAATTAAATCCATTTTAAGTTT
11114042 AAATT
1 AAATT
11114047 TATTATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.38
23 6 0.25
24 9 0.38
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (22 bp):
AAATTAAATCCATTTTAAGTTT
Found at i:11114036 original size:16 final size:16
Alignment explanation
Indices: 11114015--11114060 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
11114005 CCAATTTTAG
11114015 ATTTTAAATTTAATTC
1 ATTTTAAATTTAATTC
* *
11114031 ATTTTAAGTTTAAATTT
1 ATTTTAAATTT-AATTC
*
11114048 ATTATAAATTTAA
1 ATTTTAAATTTAA
11114061 GCTTATTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTTTAAATTTAATTC
Found at i:11115083 original size:29 final size:29
Alignment explanation
Indices: 11115023--11116034 Score: 334
Period size: 29 Copynumber: 34.4 Consensus size: 29
11115013 AACCACTAAT
* * *
11115023 CTTTTCAAAAATTATATTTTAACCCCTAAA
1 CTTTCCAAAAATTACATTTTGACCCC-AAA
*
11115053 CTATCCAAAAATTACATTTTGACCCCAAA
1 CTTTCCAAAAATTACATTTTGACCCCAAA
* *
11115082 CTTTCTAAAAATTACCTTTT-ACCCCTCAAA
1 CTTTCCAAAAATTACATTTTGA-CCC-CAAA
* * * **
11115112 CTATCCAAATATTACAATTTTTACCTTAAA
1 CTTTCCAAAAATTAC-ATTTTGACCCCAAA
* *
11115142 CTTCCCAAAAATTACACTTTGACCCTCAAA
1 CTTTCCAAAAATTACATTTTGACCC-CAAA
* * *
11115172 CTTTCCAAAAACTACATTTTGATCTCAAA
1 CTTTCCAAAAATTACATTTTGACCCCAAA
* * *
11115201 C-TTCTCAAAAATTATATTTTTACCCACGAA
1 CTTTC-CAAAAATTACATTTTGACCC-CAAA
** *
11115231 -TTTCC-AAAATT-CTATTTTTGATTCCGAA
1 CTTTCCAAAAATTAC-A-TTTTGACCCCAAA
* * * *
11115259 TTTTCTAAAAATTACCA-TTTCACCCCCAGA
1 CTTTCCAAAAATTA-CATTTTGA-CCCCAAA
* * **
11115289 -TGTCCAAAAATTACATTTCTGATCCTGAA
1 CTTTCCAAAAATTACATTT-TGACCCCAAA
* * *
11115318 TTTTCC-AAAATTATCATTTTAACCCCGAA
1 CTTTCCAAAAATTA-CATTTTGACCCCAAA
* * * * *
11115347 -TCTTCGAAAAGTATA-TTTTTGATCCCGAA
1 CT-TTCCAAAAAT-TACATTTTGACCCCAAA
* *
11115376 TTTTCCTAAAATTACCATTTT-ACCCCCAAA
1 CTTTCCAAAAATTA-CATTTTGA-CCCCAAA
* * * *
11115406 C-TTCCTAAAATTGCATTTTTGACCTCGAA
1 CTTTCCAAAAATTACA-TTTTGACCCCAAA
*
11115435 C-TTCCAAAAATTACATTTTTACCCCCAAA
1 CTTTCCAAAAATTACATTTTGA-CCCCAAA
* *
11115464 C-ATCCAAAAATTACCATTTT-ACCCTCGAA
1 CTTTCCAAAAATTA-CATTTTGACCC-CAAA
* *
11115493 -TGTCCAAAAATTACATTTT--CCCCCAA
1 CTTTCCAAAAATTACATTTTGACCCCAAA
* * * * *
11115519 GTTTCCAAAAA--A-A-ATTAACACCTAAT
1 CTTTCCAAAAATTACATTTTGAC-CCCAAA
* * *
11115545 CTTT-TACAAAATTATATTTTAACCCCTAAA
1 CTTTCCA-AAAATTACATTTTGACCCC-AAA
11115575 CTTTCCAAAAATTACATTTTGACCCCTAAA
1 CTTTCCAAAAATTACATTTTGACCCC-AAA
** * * **
11115605 CTTTTTAGAAATTACATTTTAACCATATTTTGACCCCA
1 CTTTCCAAAAATTACATTTTGACC---------CCAAA
** * * *
11115643 AACTTTCTAAAAATTACCTTTTAACCCCTCAAA
1 CT--TTCCAAAAATTACATTTTGACCC--CAAA
* * *
11115676 CTATCCAAAAATTACATTTTTACCCTAAA
1 CTTTCCAAAAATTACATTTTGACCCCAAA
* * *
11115705 CTTCCCAAAAATTACACTTTAACCCTCAAA
1 CTTTCCAAAAATTACATTTTGACCC-CAAA
* *
11115735 CTTTCCAAAAACTACATTTTGACCTCAAA
1 CTTTCCAAAAATTACATTTTGACCCCAAA
* * * *
11115764 C-TTCTCGAAAATTATATTTTTACCCACGAA
1 CTTTC-CAAAAATTACATTTTGACCC-CAAA
** *
11115794 -TTTCC-AAAATT-CTATTTTCGATTCCGAA
1 CTTTCCAAAAATTAC-ATTTT-GACCCCAAA
* * ** **
11115822 TTTTCTAAAAATTACCATTTCAACCCCGGA
1 CTTTCCAAAAATTA-CATTTTGACCCCAAA
* * *
11115852 -TGTCCAAAAATTACATTTCTGATCCCGAA
1 CTTTCCAAAAATTACATTT-TGACCCCAAA
* * *
11115881 TTTTCC-AAAATTATCATTTTAACCCCGAA
1 CTTTCCAAAAATTA-CATTTTGACCCCAAA
* * * * *
11115910 -TGTTCGAAAAGTATA-TTTTTGATCCCGAA
1 CT-TTCCAAAAAT-TACATTTTGACCCCAAA
* **
11115939 TTTTCCTGAAATTACCATTTT-ACCCCCAAA
1 CTTTCCAAAAATTA-CATTTTGA-CCCCAAA
*
11115969 C-ATCCAAAAATTACCATTTT-ACCCCCAAA
1 CTTTCCAAAAATTA-CATTTTGA-CCCCAAA
* *
11115998 -TGTCCAAAAATTACATTTT--CCCCCAA
1 CTTTCCAAAAATTACATTTTGACCCCAAA
*
11116024 GTTTCCAAAAA
1 CTTTCCAAAAA
11116035 AATTTACCAT
Statistics
Matches: 741, Mismatches: 163, Indels: 159
0.70 0.15 0.15
Matches are distributed among these distances:
23 2 0.00
24 1 0.00
25 3 0.00
26 19 0.03
27 21 0.03
28 69 0.09
29 325 0.44
30 238 0.32
31 36 0.05
32 3 0.00
33 2 0.00
38 1 0.00
39 2 0.00
40 19 0.03
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
CTTTCCAAAAATTACATTTTGACCCCAAA
Found at i:11115368 original size:117 final size:116
Alignment explanation
Indices: 11115149--11115459 Score: 341
Period size: 117 Copynumber: 2.7 Consensus size: 116
11115139 AAACTTCCCA
* * * * *
11115149 AAAATTA-CACTTTGACCCTCAAACTTTCCAAAAACTACATTT-TGATCTCAAACTTCTCAAAAA
1 AAAATTACCA-TTTCACCCCCAAAC-TTCCAAAAATTACATTTCTGACCTCGAACTTC-CAAAAA
* * *
11115212 TTAT-ATTTTTACCCACGAATTTCCAAAATTCTATTTTTGATTCCGAATTTT-CT
63 TTATCATTTTTACCC-CGAATTTCCAAAAGTATATTTTTGATCCCGAATTTTCCT
* *
11115265 AAAAATTACCATTTCACCCCCAGA-TGTCCAAAAATTACATTTCTGATCCT-GAATTTTCC-AAA
1 -AAAATTACCATTTCACCCCCAAACT-TCCAAAAATTACATTTCTGA-CCTCGAA-CTTCCAAAA
* *
11115327 ATTATCATTTTAACCCCGAATCTTCGAAAAGTATATTTTTGATCCCGAATTTTCCT
62 ATTATCATTTTTACCCCGAAT-TTCCAAAAGTATATTTTTGATCCCGAATTTTCCT
* * * *
11115383 AAAATTACCATTTTACCCCCAAACTTCCTAAAATTGCATTTTTGACCTCGAACTTCCAAAAATTA
1 AAAATTACCATTTCACCCCCAAACTTCCAAAAATTACATTTCTGACCTCGAACTTCCAAAAATTA
11115448 -CATTTTTACCCC
66 TCATTTTTACCCC
11115460 CAAACATCCA
Statistics
Matches: 164, Mismatches: 19, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
115 1 0.01
116 46 0.28
117 107 0.65
118 10 0.06
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.36
Consensus pattern (116 bp):
AAAATTACCATTTCACCCCCAAACTTCCAAAAATTACATTTCTGACCTCGAACTTCCAAAAATTA
TCATTTTTACCCCGAATTTCCAAAAGTATATTTTTGATCCCGAATTTTCCT
Found at i:11115657 original size:40 final size:41
Alignment explanation
Indices: 11115590--11115668 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 41
11115580 CAAAAATTAC
* *
11115590 ATTTTGACCCCTAAACTTTTTAGAAATTACATTTTAACCAT
1 ATTTTGACCCCTAAACTTTCTAAAAATTACATTTTAACCAT
*
11115631 ATTTTGACCCC-AAACTTTCTAAAAATTACCTTTTAACC
1 ATTTTGACCCCTAAACTTTCTAAAAATTACATTTTAACC
11115669 CCTCAAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 24 0.69
41 11 0.31
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (41 bp):
ATTTTGACCCCTAAACTTTCTAAAAATTACATTTTAACCAT
Found at i:11115659 original size:70 final size:72
Alignment explanation
Indices: 11115558--11115695 Score: 190
Period size: 71 Copynumber: 1.9 Consensus size: 72
11115548 TTACAAAATT
* * ** *
11115558 ATATTTTAACCCCTAAACTTTCCAAAAATTACATTTTGACCCCT-AAACTTTTTAGAAATTACAT
1 ATATTTTAACCCCTAAACTTTCCAAAAATTACATTTTAACCCCTCAAACTATCCAAAAATTACAT
11115622 TTTAACC
66 TTTAACC
* * *
11115629 ATATTTTGACCCC-AAACTTTCTAAAAATTACCTTTTAACCCCTCAAACTATCCAAAAATTACAT
1 ATATTTTAACCCCTAAACTTTCCAAAAATTACATTTTAACCCCTCAAACTATCCAAAAATTACAT
11115693 TTT
66 TTT
11115696 TACCCTAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 27 0.47
71 31 0.53
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (72 bp):
ATATTTTAACCCCTAAACTTTCCAAAAATTACATTTTAACCCCTCAAACTATCCAAAAATTACAT
TTTAACC
Found at i:11115765 original size:59 final size:59
Alignment explanation
Indices: 11115631--11115777 Score: 181
Period size: 59 Copynumber: 2.5 Consensus size: 59
11115621 TTTTAACCAT
* * *
11115631 ATTTTGACCCCAAACTTTCTAAAAATTACCTTTTAACCCCTCAAACTATCCAAAAATTAC
1 ATTTTGA-CCCAAACTTCCCAAAAATTACCTTTTAACCCCTCAAACTATCCAAAAACTAC
* *
11115691 ATTTTTACCCTAAACTTCCCAAAAATTACAC-TTTAA-CCCTCAAACTTTCCAAAAACTAC
1 ATTTTGACCC-AAACTTCCCAAAAATTAC-CTTTTAACCCCTCAAACTATCCAAAAACTAC
* *
11115750 ATTTTGACCTCAAACTTCTCGAAAATTA
1 ATTTTGACC-CAAACTTCCCAAAAATTA
11115778 TATTTTTACC
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
59 47 0.62
60 28 0.37
61 1 0.01
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (59 bp):
ATTTTGACCCAAACTTCCCAAAAATTACCTTTTAACCCCTCAAACTATCCAAAAACTAC
Found at i:11116008 original size:117 final size:117
Alignment explanation
Indices: 11115711--11116016 Score: 265
Period size: 117 Copynumber: 2.6 Consensus size: 117
11115701 TAAACTTCCC
* * *
11115711 AAAAATTA-CACTTT-AACCCTCAAACTTTCCAAAAACTACATTT-TGA-CCTCAAACT-TCTCG
1 AAAAATTACCA-TTTCAACCC-CAAAC-ATCCAAAAATTACATTTCTGACCCCCAAA-TGTC-C-
* * * *
11115771 AAAATTAT-ATTTTTACCCACGAATTTCCAAAATTCTATTTTCGATTCCGAATTTTCT
60 AAAATTATCATTTTAACCCACGAATTTCCAAAAGTATATTTTCGATCCCGAATTTTCT
** ** * * * *
11115828 AAAAATTACCATTTCAACCCCGGATGTCCAAAAATTACATTTCTGATCCCGAATTTTCCAAAATT
1 AAAAATTACCATTTCAACCCCAAACATCCAAAAATTACATTTCTGACCCCCAAATGTCCAAAATT
* *
11115893 ATCATTTTAACCC-CGAATGTTCGAAAAGTATATTTTTGATCCCGAATTTTCCT
66 ATCATTTTAACCCACGAAT-TTCCAAAAGTATATTTTCGATCCCGAATTTT-CT
* * *
11115946 -GAAATTACCATTTTACCCCCAAACATCCAAAAATTACCATTT-T-ACCCCCAAATGTCCAAAAA
1 AAAAATTACCATTTCAACCCCAAACATCCAAAAATTA-CATTTCTGACCCCCAAATGTCC-AAAA
11116008 TTA-CATTTT
64 TTATCATTTT
11116017 CCCCCAAGTT
Statistics
Matches: 154, Mismatches: 25, Indels: 21
0.77 0.12 0.10
Matches are distributed among these distances:
116 44 0.29
117 90 0.58
118 20 0.13
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (117 bp):
AAAAATTACCATTTCAACCCCAAACATCCAAAAATTACATTTCTGACCCCCAAATGTCCAAAATT
ATCATTTTAACCCACGAATTTCCAAAAGTATATTTTCGATCCCGAATTTTCT
Found at i:11116140 original size:29 final size:29
Alignment explanation
Indices: 11115828--11116141 Score: 182
Period size: 29 Copynumber: 10.8 Consensus size: 29
11115818 CGAATTTTCT
* * *
11115828 AAAAATTACCATTTCAACCCCGGATGTCC
1 AAAAATTACCATTTTACCCCCGAATGTCC
* *
11115857 AAAAATTA-CATTTCTGA-TCCCGAATTTTCC
1 AAAAATTACCATTT-T-ACCCCCGAA-TGTCC
* * *
11115887 -AAAATTATCATTTTAACCCCGAATGTTC
1 AAAAATTACCATTTTACCCCCGAATGTCC
* * * * *
11115915 GAAAAGTA-TATTTTTGA-TCCCGAATTTTCC
1 AAAAATTACCA-TTTT-ACCCCCGAA-TGTCC
** * **
11115945 TGAAATTACCATTTTACCCCCAAACATCC
1 AAAAATTACCATTTTACCCCCGAATGTCC
*
11115974 AAAAATTACCATTTTACCCCCAAATGTCC
1 AAAAATTACCATTTTACCCCCGAATGTCC
*
11116003 AAAAATTA-CATTTT-CCCCC-AAGTTTCC
1 AAAAATTACCATTTTACCCCCGAA-TGTCC
*
11116030 AAAAAAATTTACCA-TTTACCCCTGAATGTCC
1 --AAAAA-TTACCATTTTACCCCCGAATGTCC
** * *
11116061 AAAAATTA-CATTTTTGTCCTCGAGTGTCC
1 AAAAATTACCA-TTTTACCCCCGAATGTCC
** *
11116090 AAAAATTACTGTTTTGCCCCCGAA-GTCTC
1 AAAAATTACCATTTTACCCCCGAATGTC-C
*
11116119 TAAAATTACCATTTTACCCCCGA
1 AAAAATTACCATTTTACCCCCGA
11116142 GCATCCAAAA
Statistics
Matches: 222, Mismatches: 41, Indels: 44
0.72 0.13 0.14
Matches are distributed among these distances:
26 2 0.01
27 11 0.05
28 22 0.10
29 140 0.63
30 34 0.15
31 11 0.05
32 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.32
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGAATGTCC
Found at i:11116149 original size:87 final size:86
Alignment explanation
Indices: 11115947--11116164 Score: 219
Period size: 87 Copynumber: 2.5 Consensus size: 86
11115937 AATTTTCCTG
*
11115947 AAATTACCATTTTACCCCCAAACATCCAAAAATTACCA-TTTTACCCCCAAATGTCCAAAAATTA
1 AAATTACCATTTTACCCCCGAACATCCAAAAATTA-CATTTTTACCCCCAAATGTCCAAAAATTA
*
11116011 CATTTTCCCCCAAGTTTCCAAAA
65 CATTTTCCCCCAAGTCTCC-AAA
* ** ** * * *
11116034 AAATTTACCA-TTTACCCCTGAATGTCCAAAAATTACATTTTTGTCCTCGAGTGTCCAAAAATTA
1 AAA-TTACCATTTTACCCCCGAACATCCAAAAATTACATTTTTACCCCCAAATGTCCAAAAATTA
* *
11116098 CTGTTTTGCCCCCGAAGTCT-C-TA
65 C-ATTTT-CCCCC-AAGTCTCCAAA
* **
11116121 AAATTACCATTTTACCCCCGAGCATCCAAAAATCGCATTTTTAC
1 AAATTACCATTTTACCCCCGAACATCCAAAAATTACATTTTTAC
11116165 TCCATTTTTT
Statistics
Matches: 105, Mismatches: 20, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
86 8 0.08
87 76 0.72
88 10 0.10
89 6 0.06
90 5 0.05
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (86 bp):
AAATTACCATTTTACCCCCGAACATCCAAAAATTACATTTTTACCCCCAAATGTCCAAAAATTAC
ATTTTCCCCCAAGTCTCCAAA
Found at i:11122223 original size:21 final size:22
Alignment explanation
Indices: 11122182--11122226 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
11122172 ACTGATAAAA
11122182 TGAAAATTCAATTAAAAATATTT
1 TGAAAATTCAATT-AAAATATTT
11122205 TGAAAATTCAATT-AAATATTT
1 TGAAAATTCAATTAAAATATTT
11122226 T
1 T
11122227 AAAGTTGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.41
23 13 0.59
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (22 bp):
TGAAAATTCAATTAAAATATTT
Found at i:11132919 original size:23 final size:23
Alignment explanation
Indices: 11132865--11132919 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
11132855 CTCAAGAGTG
* * *
11132865 AAAATATTTCTATAAAAAAATTA
1 AAAATAATTCGATAAAAAAACTA
* *
11132888 AAAAAAATTCGATATAAAAACTA
1 AAAATAATTCGATAAAAAAACTA
*
11132911 TAAATAATT
1 AAAATAATT
11132920 TTAGCTGAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATAATTCGATAAAAAAACTA
Found at i:11133759 original size:29 final size:31
Alignment explanation
Indices: 11133707--11133777 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
11133697 TTAAATTAGT
* * *
11133707 AATGAT-AAAATTATACTTTGACCC-CTCAA
1 AATGATAAAAATTATAATTTAACCCTCTAAA
*
11133736 AATGATAAAAATT-TAATTTAACCCTTTAAA
1 AATGATAAAAATTATAATTTAACCCTCTAAA
11133766 AATGATAAAAAT
1 AATGATAAAAAT
11133778 GTAAACTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 15 0.42
30 21 0.58
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (31 bp):
AATGATAAAAATTATAATTTAACCCTCTAAA
Found at i:11134283 original size:19 final size:19
Alignment explanation
Indices: 11134249--11134288 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
11134239 CCGTTGAGTG
*
11134249 TAATTATTATGCCTTTCAA
1 TAATTATTATGCCTTTAAA
11134268 TAATTATTATTG-CTTTAAA
1 TAATTATTA-TGCCTTTAAA
11134287 TA
1 TA
11134289 TCCATCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (19 bp):
TAATTATTATGCCTTTAAA
Found at i:11136508 original size:2 final size:2
Alignment explanation
Indices: 11136501--11136537 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11136491 TCAATCAATT
11136501 TA TA 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 TA TA T
11136538 TTTTTCTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11146195 original size:16 final size:16
Alignment explanation
Indices: 11146176--11146214 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
11146166 TGAATAGTAT
11146176 TGTAATAGAATAAAAC
1 TGTAATAGAATAAAAC
* *
11146192 TGTAATGGAATAAAAT
1 TGTAATAGAATAAAAC
11146208 TGTAATA
1 TGTAATA
11146215 AGTAATTCAA
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:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (16 bp):
TGTAATAGAATAAAAC
Done.