Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 46 of 132
Found at i:12554755 original size:58 final size:57
Alignment explanation
Indices: 12554594--12555109 Score: 314
Period size: 58 Copynumber: 9.0 Consensus size: 57
12554584 GCCCAAAGGT
* * *
12554594 CCCTAAACTATCCAAAAAAT-CATATTTTGACCCCCAAACTTTCCAAAAGTTA-CATTTTAA
1 CCCTAAACT-TCCAAAAATTCCAT-TTTTGA-CCCTAAAC-TTCCAAAAATTACCATTTT-A
* * * * * *
12554654 CCCCAAACTTTCCAAAATTTACA-TTAT--CAC-GAACTTCACAAAAATTACCATTTTA
1 CCCTAAAC-TTCCAAAAATTCCATTTTTGACCCTAAACTTC-CAAAAATTACCATTTTA
* *
12554709 CCCTAAATTTCCAAAAATTCCATTTTTGACCCTAAACTTCCTAAAAACTACCATTTTA
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCTAAACTTCC-AAAAATTACCATTTTA
* * * * * * *
12554767 CCTTAGACTTCAAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTTCA
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCTAAAC-TTCCAAAAATTACCATTTTA
* *
12554825 -CCTCGAA-TGTCCAAAAATTCCATTTTTGACTCTAAACTTCCCAAAAATTACCA-TTTA
1 CCCT-AAACT-TCCAAAAATTCCATTTTTGACCCTAAACTT-CCAAAAATTACCATTTTA
* * * * * *
12554882 CCCTTAAACTT-CAAAAATTCC----TTAACCTTGAACTTTCCCAAAATCACTATTTTA
1 CCC-TAAACTTCCAAAAATTCCATTTTTGACCCTAAAC-TTCCAAAAATTACCATTTTA
* * * * *
12554936 CCCCCAAACATCCAAAAATTCCATTTTT-ATCCCAAAATTTTCCTAAAATTACCATTTTA
1 -CCCTAAACTTCCAAAAATTCCATTTTTGA-CCCTAAA-CTTCCAAAAATTACCATTTTA
* * * * *
12554995 CCCTCAGACTTCCAAAAATT-CGTTTTT-AACCTCGAACTTTCCCAAAATTACCATTTTA
1 CCCT-AAACTTCCAAAAATTCCATTTTTGACCCT-AAAC-TTCCAAAAATTACCATTTTA
*** * * *
12555053 CCCCCGA-TGTCCAAAAATTCAATTTTTGA-CCTCGAACTTCCTAAAGATTACCATTTT
1 CCCTAAACT-TCCAAAAATTCCATTTTTGACCCT-AAACTTCC-AAAAATTACCATTTT
12555110 TCCTGGGCAT
Statistics
Matches: 358, Mismatches: 65, Indels: 68
0.73 0.13 0.14
Matches are distributed among these distances:
53 18 0.05
54 26 0.07
55 34 0.09
56 9 0.03
57 39 0.11
58 168 0.47
59 46 0.13
60 15 0.04
61 3 0.01
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (57 bp):
CCCTAAACTTCCAAAAATTCCATTTTTGACCCTAAACTTCCAAAAATTACCATTTTA
Found at i:12563558 original size:11 final size:11
Alignment explanation
Indices: 12563544--12563568 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12563534 TTAAATTGAG
12563544 ATAAAATAAAA
1 ATAAAATAAAA
12563555 ATAAAATAAAA
1 ATAAAATAAAA
12563566 ATA
1 ATA
12563569 GTAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:12577645 original size:24 final size:24
Alignment explanation
Indices: 12577612--12577674 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
12577602 AGAAATAATC
*
12577612 TTTCAGTTAAACTCTGTGTATTTG
1 TTTCAATTAAACTCTGTGTATTTG
* *
12577636 TTTCAATTAAACTCCGTTTATTTG
1 TTTCAATTAAACTCTGTGTATTTG
* *
12577660 TTTGAATCAAACTCT
1 TTTCAATTAAACTCT
12577675 TATTACTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTGTATTTG
Found at i:12622575 original size:24 final size:24
Alignment explanation
Indices: 12622546--12622602 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
12622536 TAGAGTAATA
*
12622546 AGAGTTTGATTCAAACAAATAAAC
1 AGAGTTTAATTCAAACAAATAAAC
* * *
12622570 GGAGTTTAATTGAAACAAATACAC
1 AGAGTTTAATTCAAACAAATAAAC
12622594 AGAGTTTAA
1 AGAGTTTAA
12622603 CTGAAAGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (24 bp):
AGAGTTTAATTCAAACAAATAAAC
Found at i:12622607 original size:24 final size:24
Alignment explanation
Indices: 12622558--12622608 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
12622548 AGTTTGATTC
* *
12622558 AAACAAATAAACGGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
*
12622582 AAACAAATACACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
12622606 AAA
1 AAA
12622609 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:12632188 original size:22 final size:18
Alignment explanation
Indices: 12632163--12632207 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
12632153 CTCATTTTCC
12632163 TAAAATAGCCCAACACCCAAAA
1 TAAAATA-CCCAA-A-CC-AAA
12632185 TAAAATACCCAAACCAAA
1 TAAAATACCCAAACCAAA
12632203 TAAAA
1 TAAAA
12632208 CCCATACCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 1 0.04
21 5 0.22
22 7 0.30
ACGTcount: A:0.60, C:0.27, G:0.02, T:0.11
Consensus pattern (18 bp):
TAAAATACCCAAACCAAA
Found at i:12636730 original size:11 final size:11
Alignment explanation
Indices: 12636714--12636738 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12636704 TTTATTTTAC
12636714 TATTTTTATTT
1 TATTTTTATTT
12636725 TATTTTTATTT
1 TATTTTTATTT
12636736 TAT
1 TAT
12636739 CTCAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:12644967 original size:590 final size:591
Alignment explanation
Indices: 12643842--12644941 Score: 1925
Period size: 590 Copynumber: 1.9 Consensus size: 591
12643832 GGAAAATAAT
12643842 TGTGAAACTAAAGTGGGTTGGCCCTGTCTTCAAGAAACTTTCACGAGTATTTTCGAGACAGGTAG
1 TGTGAAACTAAAGTGGGTTGGCCCTGTCTTCAAGAAACTTTCACGAGTATTTTCGAGACAGGTAG
12643907 TATTTCTAACAAGTGTTGCAGCGAACTTGTTACGTTGGGAAAAGTTTGCCACGCAGCATTAAGAA
66 TATTTCTAACAAGTGTTGCAGCGAACTTGTTACGTTGGGAAAAGTTTGCCACGCAGCATTAAGAA
* * *
12643972 AGAGGACTCTCGAGAATCCTCTATTCAAAGAACTAAACCCAACTACAATTATAGCGAAGAGCATC
131 AGAGGACTCTCGAGAATCCTCTATTCAAAGAAATAAACCCAACTAAAATTATAGCAAAGAGCATC
*
12644037 GAAACATGGAACAACTGCATGGCATTGATCGATTCACCATATCCGTCTGCTTAACGATATAGGAT
196 GAAACATGGAACAACTGCATGGCATTGATCGATTCACCATATCCGTCTGCTTAACGATATAAGAT
* *
12644102 TGCTTCAACTAACAATAAGTTACAGGACGTGATGTGCTCAAAATTGTTCTTTTGTCTTTATTTTC
261 TGCTTCAACTAACAACAAGTTACAAGACGTGATGTGCTCAAAATTGTTCTTTTGTCTTTATTTTC
* ** *
12644167 AATATTGTTCCTTAAGCGTCATTATTGTGTGTCGTTAAATTTAAGTCGAGTTAAATTATTTTAGT
326 AACATTGTTCCGGAAGCGTCATTATTGTCTGTCGTTAAATTTAAGTCGAGTTAAATTATTTTAGT
*
12644232 TGTACGAAAATTAAATGGTTCTAGAGAAGCCATTACGTAATACACTATGATTTTATAAGGCCCTT
391 TGTACGAAAATTAAATGGTTCTAGAGAAGCCATTACGTAATACACTATGATTTTATAAGGCCATT
* *
12644297 TTTTGTAATTTTATTGCATTAGAACTTGATAACCATCTCAAAACGAGTACTATATATTGTTTCAC
456 TTTTGTAATTTTATAGCATTAGAACTTGATAACCATCTCAAAACGAGTACTAGATATTGTTTCAC
* **
12644362 ATTGTTTAAATTGAAAAAAATTGCAATGTTATAAACGTTATGTTCATTGCAATAATGTGGAACAT
521 ATGGTAGAAATTGAAAAAAATTGCAATGTTATAAACGTTATGTTCATTGCAATAATGTGGAACAT
12644427 GGAACA
586 GGAACA
*
12644433 TGTGAAACTAAAGT-TGTTGGCCCTGTCTTCAAGAAACTTTCACGAGTATTTTCGAGACAGGTAG
1 TGTGAAACTAAAGTGGGTTGGCCCTGTCTTCAAGAAACTTTCACGAGTATTTTCGAGACAGGTAG
12644497 TATTTCTAACAAGTGTTGCAGCGAACTTGTTACGTTGGGAAAAGTTTGCCACGCAGCATTAAGAA
66 TATTTCTAACAAGTGTTGCAGCGAACTTGTTACGTTGGGAAAAGTTTGCCACGCAGCATTAAGAA
12644562 AGAGGACTCTCGAGAATCCTCTATTCAAAGAAATAAACCCAACTAAAATTATAGCAAAGAGCATC
131 AGAGGACTCTCGAGAATCCTCTATTCAAAGAAATAAACCCAACTAAAATTATAGCAAAGAGCATC
* * * *
12644627 GAAACATGGAACAACTGCATGGCATTGATCGATTTACCGTCTCCGTCTGCTTAATGATATAAGAT
196 GAAACATGGAACAACTGCATGGCATTGATCGATTCACCATATCCGTCTGCTTAACGATATAAGAT
* *
12644692 TGCTTCAACTAACAACAGGTTACAAGACGTGATGTGCTCAATATTGTTCTTTTGTCTTTATTTTC
261 TGCTTCAACTAACAACAAGTTACAAGACGTGATGTGCTCAAAATTGTTCTTTTGTCTTTATTTTC
*
12644757 AACATTGTTCCGGAAGCTTCATTATTGTCTGTCGTTAAATTTAAGTCGAGTTAAATTAATTTTAG
326 AACATTGTTCCGGAAGCGTCATTATTGTCTGTCGTTAAATTTAAGTCGAGTTAAATT-ATTTTAG
*
12644822 TTGTACGAAAATTAAATGGTTCTAGAGAAGCCATTACTTAATACACTATGATTTTATAAGGCCAT
390 TTGTACGAAAATTAAATGGTTCTAGAGAAGCCATTACGTAATACACTATGATTTTATAAGGCCAT
* *
12644887 TATTTT-TAATTTTATAGCATTGGAACTTGATAACCATCTCAAATCGAGTACTAGA
455 T-TTTTGTAATTTTATAGCATTAGAACTTGATAACCATCTCAAAACGAGTACTAGA
12644942 ATTTTTGGTG
Statistics
Matches: 483, Mismatches: 24, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
590 349 0.72
591 130 0.27
592 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (591 bp):
TGTGAAACTAAAGTGGGTTGGCCCTGTCTTCAAGAAACTTTCACGAGTATTTTCGAGACAGGTAG
TATTTCTAACAAGTGTTGCAGCGAACTTGTTACGTTGGGAAAAGTTTGCCACGCAGCATTAAGAA
AGAGGACTCTCGAGAATCCTCTATTCAAAGAAATAAACCCAACTAAAATTATAGCAAAGAGCATC
GAAACATGGAACAACTGCATGGCATTGATCGATTCACCATATCCGTCTGCTTAACGATATAAGAT
TGCTTCAACTAACAACAAGTTACAAGACGTGATGTGCTCAAAATTGTTCTTTTGTCTTTATTTTC
AACATTGTTCCGGAAGCGTCATTATTGTCTGTCGTTAAATTTAAGTCGAGTTAAATTATTTTAGT
TGTACGAAAATTAAATGGTTCTAGAGAAGCCATTACGTAATACACTATGATTTTATAAGGCCATT
TTTTGTAATTTTATAGCATTAGAACTTGATAACCATCTCAAAACGAGTACTAGATATTGTTTCAC
ATGGTAGAAATTGAAAAAAATTGCAATGTTATAAACGTTATGTTCATTGCAATAATGTGGAACAT
GGAACA
Found at i:12647394 original size:29 final size:27
Alignment explanation
Indices: 12647274--12647704 Score: 203
Period size: 29 Copynumber: 14.8 Consensus size: 27
12647264 TGCCCAAGGA
*
12647274 AAAATGGTAATCTTTAGGAAGTTCGA-GGT
1 AAAATGG-AAT-TTTTGGAAGTT-GAGGGT
* *
12647303 CAAAAATTGAATTTTTGGACA-TTCGGGGGT
1 --AAAATGGAATTTTTGGA-AGTT-GAGGGT
* *
12647333 AAAATGGTAATTTTGGGAAAGTTCGAGGTT
1 AAAATGG-AATTTTTGG-AAGTT-GAGGGT
*
12647363 AAAAATAGAATTTTTGGAAGTCTGAGGGT
1 -AAAATGGAATTTTTGGAAGT-TGAGGGT
* * *
12647392 AAAATGGTAATTTTAGGAAAATTTG-GGAT
1 AAAATGG-AATTTTTGG--AAGTTGAGGGT
* *
12647421 AAAAATGGAATTTTTGGATGTTTGGGGGT
1 -AAAATGGAATTTTTGGAAG-TTGAGGGT
* * *
12647450 AAAATAGTG-ATTTTGGGAAAGTTCAAGGT
1 AAAAT-G-GAATTTTTGG-AAGTTGAGGGT
* * *
12647479 TAAA-GGAATTTTTTGAAGTTTAAGGGT
1 AAAATGGAATTTTTGGAAG-TTGAGGGT
* *
12647506 AAAATGGTAATTTTTGGGAAGTTTAGAGT
1 AAAATGG-AATTTTT-GGAAGTTGAGGGT
12647535 CAAAAATGGAATTTTTGGACA-TTCGAGGGT
1 --AAAATGGAATTTTTGGA-AGTT-GAGGGT
* *
12647565 GAAATGGTAATTTTGGGAAAGTTTG-GGGTT
1 AAAATGG-AATTTTTGG-AAG-TTGAGGG-T
* *
12647595 AAAAATGGAATTTTTTGAAGTCT-AAGGT
1 -AAAATGGAATTTTTGGAAGT-TGAGGGT
* *
12647623 AAAATGGTAGTTTTTAGGAAGTTTAGGGT
1 AAAATGG-AATTTTT-GGAAGTTGAGGGT
* *
12647652 CAAAAATGGAATTTTTGGAAATTTAGGGGT
1 --AAAATGGAATTTTTGGAAGTTGA-GGGT
12647682 AAAATGGTAATTTTTGTGAAGTT
1 AAAATGG-AATTTTTG-GAAGTT
12647705 CGTGATAATG
Statistics
Matches: 313, Mismatches: 46, Indels: 83
0.71 0.10 0.19
Matches are distributed among these distances:
26 4 0.01
27 24 0.08
28 44 0.14
29 127 0.41
30 77 0.25
31 37 0.12
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (27 bp):
AAAATGGAATTTTTGGAAGTTGAGGGT
Found at i:12647683 original size:232 final size:232
Alignment explanation
Indices: 12647274--12647695 Score: 618
Period size: 232 Copynumber: 1.8 Consensus size: 232
12647264 TGCCCAAGGA
* * *
12647274 AAAATGGTAATCTTTAGGAAGTTCGAGGTCAAAAATTGAATTTTTGGACATTCGGGGGTAAAATG
1 AAAATGGTAATCTTTAGGAAGTTAGAGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAATG
*
12647339 GTAATTTTGGGAAAGTTCGAGGTTAAAAATAGAATTTTTGGAAGTCTGAGGGTAAAATGGTAATT
66 GTAATTTTGGGAAAGTTCGAGGTTAAAAATAGAATTTTTGGAAGTCTGAAGGTAAAATGGTAATT
** * *
12647404 TTAGGAAAATTTGGGATAAAAATGGAATTTTTGGATGTTTGGGGGTAAAATAGTGATTTTGGGAA
131 TTAGGAAAATTTGGGATAAAAATGGAATTTTTGGAAATTTAGGGGTAAAATAGTAATTTTGGGAA
12647469 AGTTCAAGGTTAAAGGAATTTTTTGAAGTTTAAGGGT
196 AGTTCAAGGTTAAAGGAATTTTTTGAAGTTTAAGGGT
* * *
12647506 AAAATGGTAATTTTTGGGAAGTTTAGA-GTCAAAAATGGAATTTTTGGACATTCGAGGGTGAAAT
1 AAAATGGTAATCTTTAGGAAG-TTAGAGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAAT
* * * * *
12647570 GGTAATTTTGGGAAAGTTTGGGGTTAAAAATGGAATTTTTTGAAGTCT-AAGGTAAAATGGTAGT
65 GGTAATTTTGGGAAAGTTCGAGGTTAAAAATAGAATTTTTGGAAGTCTGAAGGTAAAATGGTA-A
* *
12647634 TTTTAGG-AAGTTTAGGG-TCAAAAATGGAATTTTTGGAAATTTAGGGGTAAAATGGTAATTTT
129 TTTTAGGAAAATTT-GGGAT-AAAAATGGAATTTTTGGAAATTTAGGGGTAAAATAGTAATTTT
12647696 TGTGAAGTTC
Statistics
Matches: 168, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
231 19 0.11
232 145 0.86
233 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (232 bp):
AAAATGGTAATCTTTAGGAAGTTAGAGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAATG
GTAATTTTGGGAAAGTTCGAGGTTAAAAATAGAATTTTTGGAAGTCTGAAGGTAAAATGGTAATT
TTAGGAAAATTTGGGATAAAAATGGAATTTTTGGAAATTTAGGGGTAAAATAGTAATTTTGGGAA
AGTTCAAGGTTAAAGGAATTTTTTGAAGTTTAAGGGT
Found at i:12647703 original size:59 final size:60
Alignment explanation
Indices: 12647274--12647795 Score: 371
Period size: 59 Copynumber: 9.0 Consensus size: 60
12647264 TGCCCAAGGA
* * * * **
12647274 AAAATGGTAATCTTTAGG-AAG-TTCGAGGTCAAAAATTGAATTTTTGGACA-TTCGGGGGT
1 AAAATGGTAATTTTTGGGAAAGTTTAG-GGTCAAAAATGGAATTTTTGGA-AGTTTAGGGGT
* * * *
12647333 AAAATGGTAA-TTTTGGGAAAG-TTCGAGGTTAAAAATAGAATTTTTGGAAGTCT-GAGGGT
1 AAAATGGTAATTTTTGGGAAAGTTTAG-GGTCAAAAATGGAATTTTTGGAAGTTTAG-GGGT
* * * *
12647392 AAAATGGTAA-TTTTAGGAAAATTT-GGGAT-AAAAATGGAATTTTTGGATGTTTGGGGGT
1 AAAATGGTAATTTTTGGGAAAGTTTAGGG-TCAAAAATGGAATTTTTGGAAGTTTAGGGGT
* * * * * * *
12647450 AAAATAGTGA-TTTTGGGAAAGTTCAAGGT--TAAA-GGAATTTTTTGAAGTTTAAGGGT
1 AAAATGGTAATTTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGT
* *
12647506 AAAATGGTAATTTTTGGG-AAGTTTAGAGTCAAAAATGGAATTTTTGGACA--TTCGAGGGT
1 AAAATGGTAATTTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGA-AGTTTAG-GGGT
* * * * * *
12647565 GAAATGGTAA-TTTTGGGAAAGTTTGGGGTTAAAAATGGAATTTTTTGAAGTCTA-AGGT
1 AAAATGGTAATTTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGT
* * *
12647623 AAAATGGTAGTTTTTAGG-AAGTTTAGGGTCAAAAATGGAATTTTTGGAAATTTAGGGGT
1 AAAATGGTAATTTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGT
* * * * * * *
12647682 AAAATGGTAATTTTTGTG-AAG-TT--CGT-GATAATGTAAATTTTGGAAAGTTTGGGGGTT
1 AAAATGGTAATTTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGG-AAGTTTAGGGG-T
* *
12647739 AAAAT-GTAACTTTT-GGAAAGTTTGGGGGTCAAAATAT-G-ATTTTTGGATAGTTTAGGG
1 AAAATGGTAATTTTTGGGAAAGTTT-AGGGTCAAAA-ATGGAATTTTTGGA-AGTTTAGGG
12647796 ACCTTTTGGG
Statistics
Matches: 369, Mismatches: 66, Indels: 55
0.75 0.13 0.11
Matches are distributed among these distances:
55 14 0.04
56 57 0.15
57 18 0.05
58 110 0.30
59 145 0.39
60 21 0.06
61 2 0.01
62 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (60 bp):
AAAATGGTAATTTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGT
Found at i:12647746 original size:30 final size:30
Alignment explanation
Indices: 12647711--12647791 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
12647701 AGTTCGTGAT
*
12647711 AATGTAAATTTTGGAAAGTTTGGGGGTTAA
1 AATGTAAATTTTGGAAAGTTTGGGGGTCAA
*
12647741 AATGTAACTTTTGGAAAGTTTGGGGGTCAA
1 AATGTAAATTTTGGAAAGTTTGGGGGTCAA
* * * *
12647771 AATATGATTTTTGGATAGTTT
1 AATGTAAATTTTGGAAAGTTT
12647792 AGGGACCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.40
Consensus pattern (30 bp):
AATGTAAATTTTGGAAAGTTTGGGGGTCAA
Found at i:12647783 original size:232 final size:230
Alignment explanation
Indices: 12647274--12647785 Score: 583
Period size: 232 Copynumber: 2.2 Consensus size: 230
12647264 TGCCCAAGGA
* * *
12647274 AAAATGGTAATCTTTAGG-AAG-TTCGAGGTCAAAAATTGAATTTTTGGACATTCGGGGGTAAAA
1 AAAATGGTAA-CTTTTGGAAAGTTTAG-GGTCAAAAA-TGAATTTTTGGACATTCGAGGGTAAAA
*
12647337 TGGTAATTTTGGGAAAGTTCGAGGTTAAAAATAGAATTTTTGGAAGTCTGAGGGTAAAATGGTAA
63 TGGTAATTTTGGGAAAGTTCGAGGTTAAAAATAGAATTTTTGGAAGTCTGAAGGTAAAATGGTAA
** * *
12647402 TTTTAGGAAAATTTGGGATAAAAATGGAATTTTTGGATGTTTGGGGGTAAAATAGTGATTTTGGG
128 TTTTAGGAAAATTTGGGATAAAAATGGAATTTTTGGAAATTTAGGGGTAAAATAGTAATTTTGGG
* * *
12647467 AAAGTTCAAGGTTAAAGGAATTTTTTGAAGTTTAAGGGT
193 AAAGTTC-AGGATAAAGGAAATTTTGGAAGTTTAAGGGT
* * * *
12647506 AAAATGGTAATTTTTGGGAAGTTTAGAGTCAAAAATGGAATTTTTGGACATTCGAGGGTGAAATG
1 AAAATGGTAACTTTTGGAAAGTTTAGGGTCAAAAAT-GAATTTTTGGACATTCGAGGGTAAAATG
* * * * *
12647571 GTAATTTTGGGAAAGTTTGGGGTTAAAAATGGAATTTTTTGAAGTCT-AAGGTAAAATGGTAGTT
65 GTAATTTTGGGAAAGTTCGAGGTTAAAAATAGAATTTTTGGAAGTCTGAAGGTAAAATGGTA-AT
* *
12647635 TTTAGG-AAGTTTAGGG-TCAAAAATGGAATTTTTGGAAATTTAGGGGTAAAATGGTAATTTTTG
129 TTTAGGAAAATTT-GGGAT-AAAAATGGAATTTTTGGAAATTTAGGGGTAAAATAGTAA-TTTTG
* * * **
12647698 TG-AAGTTC-GTGATAATGTAAATTTTGGAAAGTTTGGGGGTT
191 GGAAAGTTCAG-GATAAAGGAAATTTTGG-AAGTTTAAGGG-T
*
12647739 AAAAT-GTAACTTTTGGAAAGTTTGGGGGTCAAAATATG-ATTTTTGGA
1 AAAATGGTAACTTTTGGAAAGTTT-AGGGTCAAAA-ATGAATTTTTGGA
12647786 TAGTTTAGGG
Statistics
Matches: 238, Mismatches: 30, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
230 1 0.00
231 37 0.16
232 174 0.73
233 24 0.10
234 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (230 bp):
AAAATGGTAACTTTTGGAAAGTTTAGGGTCAAAAATGAATTTTTGGACATTCGAGGGTAAAATGG
TAATTTTGGGAAAGTTCGAGGTTAAAAATAGAATTTTTGGAAGTCTGAAGGTAAAATGGTAATTT
TAGGAAAATTTGGGATAAAAATGGAATTTTTGGAAATTTAGGGGTAAAATAGTAATTTTGGGAAA
GTTCAGGATAAAGGAAATTTTGGAAGTTTAAGGGT
Found at i:12649732 original size:6 final size:6
Alignment explanation
Indices: 12649723--12649824 Score: 82
Period size: 6 Copynumber: 17.0 Consensus size: 6
12649713 TTAGAATATT
** *
12649723 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTTAAA -ACATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA
** ** * **
12649771 TTTAAA AATAAA TTTAAA TTTTAAA -ACATA TTTAAA TTTAAA AATAAA
1 TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12649819 TTTAAA
1 TTTAAA
12649825 ATGGGTTTAG
Statistics
Matches: 72, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 12 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:12649746 original size:18 final size:17
Alignment explanation
Indices: 12649725--12649824 Score: 110
Period size: 18 Copynumber: 5.6 Consensus size: 17
12649715 AGAATATTTT
*
12649725 TAAATTTAAATTTAAATT
1 TAAATTTAAATTTAAA-A
12649743 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
* *
12649761 CATATTTAAATTTAAAAA
1 TAAATTTAAATTT-AAAA
12649779 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
* *
12649797 CATATTTAAATTTAAAAA
1 TAAATTTAAATTT-AAAA
12649815 TAAATTTAAA
1 TAAATTTAAA
12649825 ATGGGTTTAG
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
17 6 0.09
18 54 0.78
19 9 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:12649774 original size:36 final size:36
Alignment explanation
Indices: 12649728--12649824 Score: 176
Period size: 36 Copynumber: 2.7 Consensus size: 36
12649718 ATATTTTTAA
**
12649728 ATTTAAATTTAAATTTAAATTTAAATTTTAAAACAT
1 ATTTAAATTTAAAAATAAATTTAAATTTTAAAACAT
12649764 ATTTAAATTTAAAAATAAATTTAAATTTTAAAACAT
1 ATTTAAATTTAAAAATAAATTTAAATTTTAAAACAT
12649800 ATTTAAATTTAAAAATAAATTTAAA
1 ATTTAAATTTAAAAATAAATTTAAA
12649825 ATGGGTTTAG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (36 bp):
ATTTAAATTTAAAAATAAATTTAAATTTTAAAACAT
Found at i:12650609 original size:209 final size:208
Alignment explanation
Indices: 12650187--12650841 Score: 900
Period size: 209 Copynumber: 3.1 Consensus size: 208
12650177 TTTCAATCCG
* *
12650187 CTTCTCAGTATCTCATCAGGAAGATAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGGTAACCGTTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
* *
12650252 AGGAAGCTGGGGTTCGAAGATTCGCTTACTTTGAGCTTGGCTTCATTGATTTGGCCTTCTTCTCA
66 AGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCTTGGCTTCATTGATTTGGCCTTCTTCTCA
* ** * *
12650317 GTATCTCATCAGGAAGATGACAGCATCACTTGTTTCAATCTGCTTCTCCGTATCTCATCAGAAAG
131 GTATCTCATCAGGAAGATGACAGCATCGCTTGTTT-AATCCACTTCTCTGTGTCTCATCAGAAAG
* * * *
12650382 GCGAATTTGGTCCA
195 ACGGATCTGGTTCA
* *
12650396 CTTCTCAGTATCTCATCTGGAAGCTAACCGTTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGGTAACCGTTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
* * * *
12650461 AAGAAGTTGGGGTTCGAAGATTTGCTCATTTTGAGCTTGGCTTCATTGATTTGGCCTTCTTCTTA
66 AGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCTTGGCTTCATTGATTTGGCCTTCTTCTCA
* * * * *
12650526 GTATCTTATCAGGAAGATGACCGCTTCGCTTAGTTTGATCCACTTCTCTGTGTCTCATTAGAAAG
131 GTATCTCATCAGGAAGATGACAGCATCGCTT-GTTTAATCCACTTCTCTGTGTCTCATCAGAAAG
12650591 ACGGATCTGGTTCA
195 ACGGATCTGGTTCA
* * * *
12650605 CTTCTCTGTATCTCATCAGGAAGGTAACTGCTTTATTGCTTCGACCTGCTTCTCAATATCTCATT
1 CTTCTCAGTATCTCATCAGGAAGGTAACCGTTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
* ** * *
12650670 AGGAAGCTGGGGTTCGAAGATTCT-CTCACTTTGAGCCTGATTTTATTGATTTGGTCTTCTTCTC
66 AGGAAGCTGGGGTTCGAAGATT-TGCTCACTTTGAGCTTGGCTTCATTGATTTGGCCTTCTTCTC
* * * *
12650734 AGTATCTCATCAAGAAGATGACTGAATCGCTTGTTTTAATCCACTTCTCTGTGTCTCATCAGGAA
130 AGTATCTCATCAGGAAGATGACAGCATCGCTTG-TTTAATCCACTTCTCTGTGTCTCATCAGAAA
* *
12650799 GACAGATCTGCTTCA
194 GACGGATCTGGTTCA
12650814 CTTCTCTA-TATCTCATCAGGAAGGTAAC
1 CTTCTC-AGTATCTCATCAGGAAGGTAAC
12650842 TGCTTTATAT
Statistics
Matches: 393, Mismatches: 49, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
208 1 0.00
209 387 0.98
210 5 0.01
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (208 bp):
CTTCTCAGTATCTCATCAGGAAGGTAACCGTTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
AGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCTTGGCTTCATTGATTTGGCCTTCTTCTCA
GTATCTCATCAGGAAGATGACAGCATCGCTTGTTTAATCCACTTCTCTGTGTCTCATCAGAAAGA
CGGATCTGGTTCA
Found at i:12706537 original size:59 final size:59
Alignment explanation
Indices: 12706433--12706550 Score: 141
Period size: 59 Copynumber: 2.0 Consensus size: 59
12706423 TGACATTTAA
* * *
12706433 GACATCCGAGGGTAAAATGGTAATTTTTGGAAAAATCGGGATCAAAAACGGAATTTTTG
1 GACATCCGAGGGTAAAACGGTAATTATTGGAAAAATCGGGATCAAAAACGGAATATTTG
*** *
12706492 GACATCCG-GGAGTAAAACGGTAATTATTGGAAGTTTCAGGG-TCAAAAATGGAATATTTG
1 GACATCCGAGG-GTAAAACGGTAATTATTGGAAAAATC-GGGATCAAAAACGGAATATTTG
12706551 AAATTTTGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 2 0.04
59 45 0.90
60 3 0.06
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.27
Consensus pattern (59 bp):
GACATCCGAGGGTAAAACGGTAATTATTGGAAAAATCGGGATCAAAAACGGAATATTTG
Found at i:12706592 original size:29 final size:29
Alignment explanation
Indices: 12706511--12706607 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
12706501 GAGTAAAACG
*
12706511 GTAATTATTGGAAGTTTC-AGGGTCAAAAAT
1 GTAATTTTTGGAAG-TTCGAGGGT-AAAAAT
* * * * * *
12706541 GGAATATTTGAAATTTTGGGGGTAAAAAT
1 GTAATTTTTGGAAGTTCGAGGGTAAAAAT
*
12706570 GTAATTTTTGGAAGTTCGAGGGTACAAAT
1 GTAATTTTTGGAAGTTCGAGGGTAAAAAT
12706599 GTAATTTTT
1 GTAATTTTT
12706608 AAAAGTTTCA
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
29 39 0.75
30 13 0.25
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
GTAATTTTTGGAAGTTCGAGGGTAAAAAT
Found at i:12708337 original size:17 final size:18
Alignment explanation
Indices: 12708317--12708359 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12708307 AAATTAATTC
12708317 AAATTC-AAATTTAAAAT
1 AAATTCTAAATTTAAAAT
12708334 AAA-TCTAAATTTAAAAT
1 AAATTCTAAATTTAAAAT
12708351 AAATT-TAAA
1 AAATTCTAAA
12708360 AGGGGTCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 21 0.88
18 1 0.04
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTCTAAATTTAAAAT
Found at i:12709127 original size:205 final size:206
Alignment explanation
Indices: 12708658--12709669 Score: 1394
Period size: 204 Copynumber: 4.9 Consensus size: 206
12708648 TCTGGTTTCA
* * ** * * ** *
12708658 TTGACTTGGCCTTCTTCTCTCTATCTCATCAGGAAGATGACCACATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
* * ** * * *
12708723 CTCTGTGTTTCATCAGGAAGACGGGTTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCAC
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* **
12708788 TTTATTGCTTAGACCTGCTTCTCAGTATCTCATCAAAAAGCTAGGGGTTCGAAGATTTGCTCACA
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTA-GGGTTCGAAGATTTGCTCACA
*
12708853 TCGAGCGTTGGT
195 TCGAGCGTGGGT
* *
12708865 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
* *
12708930 CTTTGTATCTCATCAGGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
12708995 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
*
12709059 GGAGCGTGGGT
196 CGAGCGTGGGT
* *
12709070 TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATTGCTTGTTTCAAT-CGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
* * * * *
12709134 CTTTGTACCTCATCAAGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
12709199 TTTATTGCTTCGGCCTGCTTCTCAATATCTCATCAGGAAGCT-GGGTTCGAAGACTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
12709263 CGAGCGTGGGT
196 CGAGCGTGGGT
*
12709274 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
* * *
12709339 CTCTATACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
12709404 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTAGGGTTCGAAGATTTGCTCACTT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
* *
12709469 TGAGC-----C
196 CGAGCGTGGGT
* * * * * * * * *
12709475 TTAAGTTGGTATACTTCTCTGTATCTCATCAGGAAGGTGACCGCCTCACTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
*
12709540 CTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * * * * * *
12709605 TTTATTACTTCGCCCTGCCTCAT-AGTATGTCATCAGGAAGCTGGGGTTCAAAGATCTGTTCACA
131 TTTATTGCTTCGACCTGCTTC-TCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACA
12709669 T
195 T
12709670 TGAGTTGGTA
Statistics
Matches: 724, Mismatches: 78, Indels: 12
0.89 0.10 0.01
Matches are distributed among these distances:
201 169 0.23
202 1 0.00
204 191 0.26
205 190 0.26
206 24 0.03
207 149 0.21
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
CGAGCGTGGGT
Found at i:12710201 original size:49 final size:49
Alignment explanation
Indices: 12710060--12710214 Score: 157
Period size: 49 Copynumber: 3.1 Consensus size: 49
12710050 CGACTTAAAC
* * * * *
12710060 CTTTCCTTTCAAATCTTCGTGGTACTGGATCTACTATCGCAGCTTAGAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATCCACCATCGCGGCTTAGAT
** * * * * **
12710109 CTTTCTGTTCCTGTCTTCGTAGTACTGGGTCCGTCATCGCGGCTTAGAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATCCACCATCGCGGCTTAGAT
* **
12710158 CTTTCCCTTCATATCTTCGTGGTACTGGATCCACCGTTACGGCTTTAGAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATCCACCATCGCGGC-TTAGAT
12710208 CTTTCCC
1 CTTTCCC
12710215 GTCGTGTCTC
Statistics
Matches: 82, Mismatches: 23, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
49 69 0.84
50 13 0.16
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.39
Consensus pattern (49 bp):
CTTTCCCTTCATATCTTCGTGGTACTGGATCCACCATCGCGGCTTAGAT
Found at i:12716449 original size:29 final size:29
Alignment explanation
Indices: 12716398--12716480 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
12716388 CTTTTGAAAG
**
12716398 TTTC-GGGGTCAAAAATGGGATTTTTAG-A
1 TTTCAGGGGT-AAAAATGTAATTTTTAGAA
*
12716426 TTCTCAGGGGTAAAAATGTAATTTTTGGAA
1 TT-TCAGGGGTAAAAATGTAATTTTTAGAA
* *
12716456 TTTTAGGGG-AAAAATGTAAATTTTA
1 TTTCAGGGGTAAAAATGTAATTTTTA
12716481 AAAGTTTCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
28 16 0.35
29 22 0.48
30 8 0.17
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (29 bp):
TTTCAGGGGTAAAAATGTAATTTTTAGAA
Found at i:12718381 original size:6 final size:6
Alignment explanation
Indices: 12718356--12718408 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
12718346 GCTTTTTTTT
* * *
12718356 TTTAAA TTTGAAA -ATAAA TTTAAA TTTAAA TTCAAA TTTAAA -ATAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12718403 TTTAAA
1 TTTAAA
12718409 AGGGCCCGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 7 0.18
6 28 0.74
7 3 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:12718405 original size:11 final size:11
Alignment explanation
Indices: 12718376--12718409 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
12718366 AAAATAAATT
*
12718376 TAAATTTAAAT
1 TAAATTTAAAA
12718387 TCAAATTTAAAA
1 T-AAATTTAAAA
12718399 TAAATTTAAAA
1 TAAATTTAAAA
12718410 GGGCCCGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:12724873 original size:59 final size:59
Alignment explanation
Indices: 12724805--12724944 Score: 142
Period size: 59 Copynumber: 2.4 Consensus size: 59
12724795 AAAAATGACA
* * *
12724805 TTTTAGACATCCGGGGATAAAATGGTAAATTTTAGAAA-ATTCGGGATCAAAAATGGATT
1 TTTTGGACATCCGGGGATAAAACGGT-AATTTTAGAAAGATTCGGGATCAAAAATGGAGT
** * * * *
12724864 TTTTGGACAT-TAGGGAGTAAAACGGTAATTTTTGAAAGTTTCGGGGTCCAAAATGGAGT
1 TTTTGGACATCCGGGGA-TAAAACGGTAATTTTAGAAAGATTCGGGATCAAAAATGGAGT
*
12724923 TTTTGGATATCCAGGGG-TAAAA
1 TTTTGGACATCC-GGGGATAAAA
12724945 ATGTATGGAA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
58 14 0.22
59 48 0.74
61 3 0.05
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (59 bp):
TTTTGGACATCCGGGGATAAAACGGTAATTTTAGAAAGATTCGGGATCAAAAATGGAGT
Found at i:12725006 original size:29 final size:29
Alignment explanation
Indices: 12724974--12725104 Score: 90
Period size: 29 Copynumber: 4.5 Consensus size: 29
12724964 TTCGAGGGTA
*
12724974 AAAATGTAATTTTTGGAAGTTTTG-GGTTC
1 AAAATGTAATTTTTAGAAGTTTTGAGG-TC
** * *
12725003 AAAAATGGGATTTTTAG-ATTTTTGAGTGTA
1 -AAAATGTAATTTTTAGAAGTTTTGAG-GTC
* *
12725033 AAAATGTAATTTTTTGAA-TTTT-AGCGGC
1 AAAATGTAATTTTTAGAAGTTTTGAG-GTC
* * *
12725061 AAGAATGTAATTTTAAGAAGTTTCGAGGCC
1 AA-AATGTAATTTTTAGAAGTTTTGAGGTC
*
12725091 AAAATATAATTTTT
1 AAAATGTAATTTTT
12725105 GAACAGTTTA
Statistics
Matches: 78, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
28 5 0.06
29 47 0.60
30 23 0.29
31 3 0.04
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (29 bp):
AAAATGTAATTTTTAGAAGTTTTGAGGTC
Found at i:12726923 original size:6 final size:6
Alignment explanation
Indices: 12726912--12726967 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
12726902 AATTTGAAAA
* * * *
12726912 TAAATT TAAATT TAAATT CAAATT TAAA-A TAAATC TAAATT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
12726958 TAAATT TAAA
1 TAAATT TAAA
12726968 AGGGCCCGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 8 0.20
6 33 0.80
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:12726951 original size:17 final size:17
Alignment explanation
Indices: 12726901--12726967 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
12726891 TTTTTTTTTA
*
12726901 AAATTTGAAAATAAATTT
1 AAATTT-AAAATAAATCT
12726919 AAATTT-AAAT---TC-
1 AAATTTAAAATAAATCT
12726931 AAATTTAAAATAAATCT
1 AAATTTAAAATAAATCT
*
12726948 AAATTTAAAATAAATTT
1 AAATTTAAAATAAATCT
12726965 AAA
1 AAA
12726968 AGGGCCCGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 6 0.14
13 5 0.12
16 6 0.14
17 19 0.45
18 6 0.14
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (17 bp):
AAATTTAAAATAAATCT
Found at i:12728094 original size:13 final size:12
Alignment explanation
Indices: 12728071--12728102 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
12728061 TATTTTAAGA
12728071 TTAAATTTAT-T
1 TTAAATTTATAT
12728082 TTAAATTTATAT
1 TTAAATTTATAT
12728094 TTAAATTTA
1 TTAAATTTA
12728103 AAATTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAAATTTATAT
Found at i:12728095 original size:17 final size:18
Alignment explanation
Indices: 12728053--12728096 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12728043 CTAAATCCAT
12728053 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
12728071 -TTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
*
12728087 TTTATATTTA
1 TTTAAATTTA
12728097 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:12728109 original size:29 final size:28
Alignment explanation
Indices: 12728051--12728119 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
12728041 AACTAAATCC
*
12728051 ATTTTAAATTTATTTTAAGATTAAATTT
1 ATTTTAAATTTATTTTAAGATTAAAATT
12728079 ATTTTAAATTTATATTTAA-ATTTAAAATT
1 ATTTTAAATTTAT-TTTAAGA-TTAAAATT
* *
12728108 ATTCTATATTTA
1 ATTTTAAATTTA
12728120 AATAAACAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTTTAAATTTATTTTAAGATTAAAATT
Found at i:12728298 original size:3 final size:3
Alignment explanation
Indices: 12728290--12728342 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
12728280 AAATAGTATC
* * ** *
12728290 AAT AAT AAT AAT AAT ACT ATT CTT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12728338 AAT AA
1 AAT AA
12728343 GGCAGTCGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:12729646 original size:29 final size:29
Alignment explanation
Indices: 12729614--12729685 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
12729604 TTTACCTTGG
* *
12729614 ACTTCCAAAAATTTTGTTTTTAACCCCAA
1 ACTTCCAAAAATTATGATTTTAACCCCAA
* *
12729643 ACTTTCCCAAAATTATGATTTTAACCCCGA
1 AC-TTCCAAAAATTATGATTTTAACCCCAA
12729673 A-TATCCAAAAATT
1 ACT-TCCAAAAATT
12729686 CCATTTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.03
29 11 0.31
30 24 0.67
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.35
Consensus pattern (29 bp):
ACTTCCAAAAATTATGATTTTAACCCCAA
Found at i:12729768 original size:29 final size:28
Alignment explanation
Indices: 12729708--12729882 Score: 131
Period size: 29 Copynumber: 6.0 Consensus size: 28
12729698 TTGAACTTCC
*
12729708 CCCTAAACTTCAAAAAATTCCATTTTTGA
1 CCCTAAACTTCCAAAAATTCCATTTTT-A
*
12729737 CCCTAAACTTTCCCAAAATTACCA-TTTTA
1 CCCTAAAC-TTCCAAAAATT-CCATTTTTA
* *
12729766 CCCCCAAACATCCAAAAATTCCATTTTTTA
1 -CCCTAAACTTCCAAAAATTCCA-TTTTTA
* * *
12729796 CCCCAAATTTTCCCAAAATTACCA-TTTTA
1 CCCTAAA-CTTCCAAAAATT-CCATTTTTA
* *
12729825 CCCTCATACTTCTAAAAATTCC-TTTTTAA
1 CCCT-AAACTTCCAAAAATTCCATTTTT-A
**
12729854 CCCCGAACTTCCTAAAAATTACCATTTTT
1 CCCTAAACTTCC-AAAAATT-CCATTTTT
12729883 CCTCGGGCAT
Statistics
Matches: 116, Mismatches: 17, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
28 14 0.12
29 53 0.46
30 38 0.33
31 11 0.09
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.35
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTCCATTTTTA
Found at i:12729797 original size:30 final size:30
Alignment explanation
Indices: 12729706--12729882 Score: 145
Period size: 30 Copynumber: 6.0 Consensus size: 30
12729696 CTTTGAACTT
*
12729706 CCCCCTAAACTTCAAAAAATT-CCATTTTTGA
1 CCCCC-AAACTTCCAAAAATTACCATTTTT-A
* *
12729737 -CCCTAAACTTTCCCAAAATTACCA-TTTTA
1 CCCCCAAAC-TTCCAAAAATTACCATTTTTA
*
12729766 CCCCCAAACATCCAAAAATT-CCATTTTTTA
1 CCCCCAAACTTCCAAAAATTACCA-TTTTTA
* *
12729796 -CCCCAAATTTTCCCAAAATTACCA-TTTTA
1 CCCCCAAA-CTTCCAAAAATTACCATTTTTA
* * *
12729825 CCCTCATACTTCTAAAAATT-CC-TTTTTA
1 CCCCCAAACTTCCAAAAATTACCATTTTTA
* *
12729853 ACCCCGAACTTCCTAAAAATTACCATTTTT
1 CCCCCAAACTTCC-AAAAATTACCATTTTT
12729883 CCTCGGGCAT
Statistics
Matches: 115, Mismatches: 19, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
28 18 0.16
29 42 0.37
30 44 0.38
31 11 0.10
ACGTcount: A:0.34, C:0.31, G:0.01, T:0.34
Consensus pattern (30 bp):
CCCCCAAACTTCCAAAAATTACCATTTTTA
Found at i:12729808 original size:59 final size:58
Alignment explanation
Indices: 12729706--12729881 Score: 210
Period size: 59 Copynumber: 3.0 Consensus size: 58
12729696 CTTTGAACTT
* *
12729706 CCCCCTAAACTTCAAAAAATTCCATTTTTGACCCTAAACTTTCCCAAAATTACCATTTTA
1 CCCCC-AAACTTCAAAAAATTCCATTTTTAACCCCAAA-TTTCCCAAAATTACCATTTTA
* * *
12729766 CCCCCAAACATCCAAAAATTCCATTTTTTACCCCAAATTTTCCCAAAATTACCATTTTA
1 CCCCCAAACTTCAAAAAATTCCATTTTTAACCCCAAA-TTTCCCAAAATTACCATTTTA
* * * * * *
12729825 CCCTCATACTTCTAAAAATTCC-TTTTTAACCCCGAACTTCCTAAAAATTACCATTTT
1 CCCCCAAACTTCAAAAAATTCCATTTTTAACCCCAAATTTCC-CAAAATTACCATTTT
12729882 TCCTCGGGCA
Statistics
Matches: 102, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
57 4 0.04
58 26 0.25
59 67 0.66
60 5 0.05
ACGTcount: A:0.34, C:0.31, G:0.01, T:0.34
Consensus pattern (58 bp):
CCCCCAAACTTCAAAAAATTCCATTTTTAACCCCAAATTTCCCAAAATTACCATTTTA
Found at i:12734547 original size:29 final size:29
Alignment explanation
Indices: 12734513--12734674 Score: 91
Period size: 29 Copynumber: 5.6 Consensus size: 29
12734503 TAATTTTTGA
* *
12734513 AAGTTTCGGGGTCTAAAATGAGTTTTTGG
1 AAGTTTCGGGGTCAAAAATGAGTTTTTAG
* * ** *
12734542 ATGTTTAGGGGT-GGAAATGTAATTTTTAG
1 AAGTTTCGGGGTCAAAAATG-AGTTTTTAG
* *
12734571 AAGTTTCAGGGTCAAAAATGGGATTTTTAG
1 AAGTTTCGGGGTCAAAAATGAG-TTTTTAG
* * *
12734601 ATGTTTGGGGGT-AAAAATGTA-TTGTTTGG
1 AAGTTTCGGGGTCAAAAATG-AGTT-TTTAG
* * *
12734630 AATTTTAGGGG-C-AAAATGTAATTTTTAG
1 AAGTTTCGGGGTCAAAAATG-AGTTTTTAG
* *
12734658 AAGTTTCGAGGACAAAA
1 AAGTTTCGGGGTCAAAA
12734675 TATAATTTCT
Statistics
Matches: 99, Mismatches: 25, Indels: 17
0.70 0.18 0.12
Matches are distributed among these distances:
28 27 0.27
29 48 0.48
30 24 0.24
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.36
Consensus pattern (29 bp):
AAGTTTCGGGGTCAAAAATGAGTTTTTAG
Found at i:12734564 original size:58 final size:59
Alignment explanation
Indices: 12734494--12734663 Score: 156
Period size: 58 Copynumber: 2.9 Consensus size: 59
12734484 ACATCCGAGA
* * *
12734494 GTAAAACA-GTAATTTTT-GAAAGTTTCGGGGTCTAAAATGAG-TTTTTGGATGTTTAGGG
1 GTAAAA-ATGTAATTTTTAG-AAGTTTCAGGGTCAAAAATGAGATTTTTAGATGTTTAGGG
** * *
12734552 GTGGAAATGTAATTTTTAGAAGTTTCAGGGTCAAAAATGGGATTTTTAGATGTTTGGGG
1 GTAAAAATGTAATTTTTAGAAGTTTCAGGGTCAAAAATGAGATTTTTAGATGTTTAGGG
* * * *
12734611 GTAAAAATGT-ATTGTTTGGAA-TTTTAGGGGC-AAAATGTA-ATTTTTAGAAGTTT
1 GTAAAAATGTAATT-TTTAGAAGTTTCAGGGTCAAAAATG-AGATTTTTAGATGTTT
12734664 CGAGGACAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
57 20 0.22
58 43 0.46
59 30 0.32
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.39
Consensus pattern (59 bp):
GTAAAAATGTAATTTTTAGAAGTTTCAGGGTCAAAAATGAGATTTTTAGATGTTTAGGG
Found at i:12734597 original size:30 final size:30
Alignment explanation
Indices: 12734556--12734664 Score: 91
Period size: 30 Copynumber: 3.7 Consensus size: 30
12734546 TTAGGGGTGG
*
12734556 AAATGTAATTTTTAGAAGTTTCAGGGTCAA
1 AAATGGAATTTTTAGAAGTTTCAGGGTCAA
* * **
12734586 AAATGGGATTTTTAGATGTTTGGGGGT-AA
1 AAATGGAATTTTTAGAAGTTTCAGGGTCAA
* * * *
12734615 AAAT-GTATTGTTTGGAA-TTTTAGGGGC-A
1 AAATGGAATT-TTTAGAAGTTTCAGGGTCAA
*
12734643 AAATGTAATTTTTAGAAGTTTC
1 AAATGGAATTTTTAGAAGTTTC
12734665 GAGGACAAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
28 21 0.35
29 17 0.28
30 22 0.37
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.39
Consensus pattern (30 bp):
AAATGGAATTTTTAGAAGTTTCAGGGTCAA
Found at i:12736549 original size:18 final size:17
Alignment explanation
Indices: 12736528--12736586 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
12736518 GCTTTTTTTT
12736528 TTTAAATATGAAAATAAA
1 TTTAAATAT-AAAATAAA
*
12736546 TTTAAAT-TCAAATTCAAA
1 TTTAAATAT-AAAAT-AAA
*
12736564 TTTAAA-ATAAATCTAAA
1 TTTAAATATAAA-ATAAA
12736581 TTTAAA
1 TTTAAA
12736587 ACAAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 17 0.49
18 18 0.51
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (17 bp):
TTTAAATATAAAATAAA
Found at i:12736571 original size:29 final size:28
Alignment explanation
Indices: 12736538--12736598 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
12736528 TTTAAATATG
* *
12736538 AAAATAAATTTAAATTCAAATTCAAATTT
1 AAAATAAATCTAAATTCAAA-ACAAATTT
*
12736567 AAAATAAATCTAAATTTAAAACAAATTT
1 AAAATAAATCTAAATTCAAAACAAATTT
12736595 AAAA
1 AAAA
12736599 GGGCTCGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (28 bp):
AAAATAAATCTAAATTCAAAACAAATTT
Found at i:12736581 original size:17 final size:16
Alignment explanation
Indices: 12736528--12736593 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
12736518 GCTTTTTTTT
*
12736528 TTTAAATATGAAAATAAA
1 TTTAAA-AT-AAATTAAA
*
12736546 TTTAAATTCAAATTCAAA
1 TTTAAAAT-AAATT-AAA
12736564 TTTAAAATAAATCTAAA
1 TTTAAAATAAAT-TAAA
*
12736581 TTTAAAACAAATT
1 TTTAAAATAAATT
12736594 TAAAAGGGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
16 1 0.02
17 23 0.56
18 17 0.41
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (16 bp):
TTTAAAATAAATTAAA
Found at i:12736597 original size:17 final size:17
Alignment explanation
Indices: 12736542--12736597 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
12736532 AATATGAAAA
*
12736542 TAAATTTAAATTCAAATT
1 TAAATTTAAA-ACAAATT
* * *
12736560 CAAATTTAAAATAAATC
1 TAAATTTAAAACAAATT
12736577 TAAATTTAAAACAAATT
1 TAAATTTAAAACAAATT
12736594 TAAA
1 TAAA
12736598 AGGGCTCGGT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATTTAAAACAAATT
Found at i:12744124 original size:6 final size:6
Alignment explanation
Indices: 12744087--12744156 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
12744077 CTAAATTCAT
* * *
12744087 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTATA TTTAAA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
12744133 TTTAAA ATT--A TTCTAAA TTTAAA T
1 TTTAAA TTTAAA TT-TAAA TTTAAA T
12744157 AAACAAAGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 34 0.69
7 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:12744128 original size:13 final size:12
Alignment explanation
Indices: 12744105--12744136 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
12744095 TATTTTAAGA
12744105 TTAAATTTAT-T
1 TTAAATTTATAT
12744116 TTAAATTTATAT
1 TTAAATTTATAT
12744128 TTAAATTTA
1 TTAAATTTA
12744137 AAATTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAAATTTATAT
Found at i:12744129 original size:17 final size:18
Alignment explanation
Indices: 12744087--12744130 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12744077 CTAAATTCAT
12744087 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
12744105 -TTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
*
12744121 TTTATATTTA
1 TTTAAATTTA
12744131 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:12744130 original size:12 final size:11
Alignment explanation
Indices: 12744078--12744136 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
12744068 GAGGCCAAAC
*
12744078 TAAATTCATTT
1 TAAATTTATTT
12744089 TAAATTTATTT
1 TAAATTTATTT
*
12744100 T-AA--GA--T
1 TAAATTTATTT
12744106 TAAATTTATTT
1 TAAATTTATTT
12744117 TAAATTTATATT
1 TAAATTTAT-TT
12744129 TAAATTTA
1 TAAATTTA
12744137 AAATTATTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
6 2 0.05
7 2 0.05
8 1 0.03
9 1 0.03
10 2 0.05
11 21 0.54
12 10 0.26
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TAAATTTATTT
Found at i:12744138 original size:18 final size:17
Alignment explanation
Indices: 12744087--12744156 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
12744077 CTAAATTCAT
*
12744087 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTCTAA-A
*
12744105 -TTAAATTTATTTTAAA
1 TTTAAATTTATTCTAAA
12744121 TTT--A--TATT-TAAA
1 TTTAAATTTATTCTAAA
*
12744133 TTTAAAATTATTCTAAA
1 TTTAAATTTATTCTAAA
12744150 TTTAAAT
1 TTTAAAT
12744157 AAACAAAGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
12 7 0.16
13 4 0.09
14 1 0.02
15 1 0.02
16 5 0.11
17 27 0.60
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTCTAAA
Found at i:12744143 original size:29 final size:28
Alignment explanation
Indices: 12744079--12744153 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
12744069 AGGCCAAACT
12744079 AAATTCATTTTAAATTTATTTTAAGATTA
1 AAATT-ATTTTAAATTTATTTTAAGATTA
*
12744108 AATTTATTTTAAATTTATATTTAA-ATTTA
1 AAATTATTTTAAATTTAT-TTTAAGA-TTA
*
12744137 AAATTATTCTAAATTTA
1 AAATTATTTTAAATTTA
12744154 AATAAACAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 14 0.34
29 27 0.66
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (28 bp):
AAATTATTTTAAATTTATTTTAAGATTA
Found at i:12744334 original size:3 final size:3
Alignment explanation
Indices: 12744326--12744397 Score: 81
Period size: 3 Copynumber: 23.7 Consensus size: 3
12744316 AAATAGTATC
* * ** *
12744326 AAT AAT AAT CAAT AAT AAT AAT ACT ATT CTT AAT AGT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
12744372 AAT AAT GAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
12744398 GGCAGTCGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:12745545 original size:30 final size:30
Alignment explanation
Indices: 12745510--12745657 Score: 89
Period size: 30 Copynumber: 5.0 Consensus size: 30
12745500 TGAACTGTCA
*
12745510 AAAAATCATATTTTGACC-CTTAAACTTTCC
1 AAAAATCACATTTTGACCTC-TAAACTTTCC
* *
12745540 AAAAATTACATTTTGACCTCTGAACTTTCC
1 AAAAATCACATTTTGACCTCTAAACTTTCC
* * *
12745570 AAAATTTACATTATTG-CACTC-GAAC-TTCAC
1 AAAAATCACATT-TTGAC-CTCTAAACTTTC-C
* *
12745600 AAAAATTACCATTTT-ACCTC-GAA-TTTCC
1 AAAAATCA-CATTTTGACCTCTAAACTTTCC
*
12745628 AAAAATTC-CATTTTTGACC-CCAAACTTTCC
1 AAAAA-TCACA-TTTTGACCTCTAAACTTTCC
12745658 CATAATTACC
Statistics
Matches: 99, Mismatches: 7, Indels: 24
0.76 0.05 0.18
Matches are distributed among these distances:
27 2 0.02
28 11 0.11
29 18 0.18
30 57 0.58
31 11 0.11
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (30 bp):
AAAAATCACATTTTGACCTCTAAACTTTCC
Found at i:12745632 original size:29 final size:27
Alignment explanation
Indices: 12745535--12745920 Score: 116
Period size: 29 Copynumber: 13.7 Consensus size: 27
12745525 ACCCTTAAAC
12745535 TTTCCAAAAATTACATTTTGACCTCTGAA
1 TTTCCAAAAATTACATTTT-ACCTC-GAA
* *
12745564 CTTTCCAAAATTTACATTATTGCACTCGAA
1 -TTTCCAAAAATTACATT-TTAC-CTCGAA
*
12745594 CTTCACAAAAATTACCATTTTACCTCGAA
1 TTTC-CAAAAATTA-CATTTTACCTCGAA
* * *
12745623 TTTCCAAAAATTCCATTTTTGACCCCAAA
1 TTTCCAAAAATTACA-TTTT-ACCTCGAA
* * * * *
12745652 CTTTCCCATAATTACCATTCTACCCCCAAA
1 -TTTCCAAAAATTA-CATTTTA-CCTCGAA
* *
12745682 TGTCCAAAAATTCCATTTTTCACC-CTGAA
1 TTTCCAAAAATTACA-TTTT-ACCTC-GAA
* * *
12745711 CTTGCCAAAAATTACCATTTTACCCCCAGA
1 -TTTCCAAAAATTA-CATTTTACCTCGA-A
*
12745741 CTTCCAAAAATT-CTATTTTGA-C-C---
1 TTTCCAAAAATTAC-ATTTT-ACCTCGAA
*
12745764 --T-C-AAAATTACCATTTTACCCCCGAA
1 TTTCCAAAAATTA-CATTTTA-CCTCGAA
* * * *
12745789 TGTCTAAAAATTCCATTTTTGACCCCGAA
1 TTTCCAAAAATTACA-TTTT-ACCTCGAA
* *
12745818 CTTTCCCAAAATTACCATTTTACCCTCAAA
1 -TTTCCAAAAATTA-CATTTTA-CCTCGAA
** * *
12745848 CATCCAAAAATTGCA-TTT-CCT-AAA
1 TTTCCAAAAATTACATTTTACCTCGAA
* *
12745872 CTTTCCCAAAATTACCATTTTAACCCCGAA
1 -TTTCCAAAAATTA-CATTTT-ACCTCGAA
* *
12745902 TGTCCAAAAATTCCATTTT
1 TTTCCAAAAATTACATTTT
12745921 TAACCTCAAA
Statistics
Matches: 269, Mismatches: 46, Indels: 84
0.67 0.12 0.21
Matches are distributed among these distances:
19 7 0.03
20 6 0.02
21 3 0.01
22 1 0.00
24 3 0.01
25 12 0.04
26 2 0.01
27 11 0.04
28 31 0.12
29 89 0.33
30 89 0.33
31 15 0.06
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (27 bp):
TTTCCAAAAATTACATTTTACCTCGAA
Found at i:12745692 original size:59 final size:59
Alignment explanation
Indices: 12745601--12745933 Score: 315
Period size: 59 Copynumber: 5.9 Consensus size: 59
12745591 GAACTTCACA
* * *
12745601 AAAATTACCATTTTA-CCTCGAATTTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
* * * ** * *
12745659 ATAATTACCATTCTACCCCCAAATGTCCAAAAATTCCATTTTTCACCCTGAACTTGCCA
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
* *
12745718 AAAATTACCATTTTACCCCCAGACT-TCCAAAAATTCTA-TTTTGA---C---C--T--C
1 AAAATTACCATTTTACCCCCA-AATGTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
* * *
12745766 AAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACCCCGAACTTTCCC
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
* ** * *
12745825 AAAATTACCATTTTACCCTCAAACATCCAAAAATTGCA--TTT---CCTAAACTTTCCC
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
* * * *
12745879 AAAATTACCATTTTAACCCCGAATGTCCAAAAATTCCATTTTTAACCTCAAACTT
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCCAAACTT
12745934 CATAAAAATT
Statistics
Matches: 218, Mismatches: 38, Indels: 37
0.74 0.13 0.13
Matches are distributed among these distances:
47 2 0.01
48 31 0.14
49 6 0.03
52 2 0.01
54 43 0.20
55 1 0.00
56 3 0.01
57 4 0.02
58 18 0.08
59 106 0.49
60 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
Found at i:12745721 original size:30 final size:30
Alignment explanation
Indices: 12745532--12745759 Score: 127
Period size: 30 Copynumber: 7.7 Consensus size: 30
12745522 TTGACCCTTA
* *
12745532 AACTTTCCAAAAATTACA-TTTTGACCTCTG
1 AACTTTCCAAAAATTCCATTTTTCACC-CTG
* * * *
12745562 AACTTTCCAAAATTTACATTATTGCACTC-G
1 AACTTTCCAAAAATTCCATT-TTTCACCCTG
12745592 AAC-TTCACAAAAATTACCA-TTTT-A-CCTCG
1 AACTTTC-CAAAAATT-CCATTTTTCACCCT-G
* **
12745621 AA-TTTCCAAAAATTCCATTTTTGACCCCA
1 AACTTTCCAAAAATTCCATTTTTCACCCTG
* * * **
12745650 AACTTTCCCATAATTACCA-TTCT-ACCCCC
1 AACTTTCCAAAAATT-CCATTTTTCACCCTG
* *
12745679 AAATGTCCAAAAATTCCATTTTTCACCCTG
1 AACTTTCCAAAAATTCCATTTTTCACCCTG
* * * *
12745709 AACTTGCCAAAAATTACCATTTTACCCCCAG
1 AACTTTCCAAAAATT-CCATTTTTCACCCTG
*
12745740 -AC-TTCCAAAAATTCTATTTT
1 AACTTTCCAAAAATTCCATTTT
12745760 GACCTCAAAA
Statistics
Matches: 154, Mismatches: 29, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
27 4 0.03
28 22 0.14
29 43 0.28
30 62 0.40
31 19 0.12
32 4 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (30 bp):
AACTTTCCAAAAATTCCATTTTTCACCCTG
Found at i:12745770 original size:48 final size:49
Alignment explanation
Indices: 12745718--12745930 Score: 151
Period size: 54 Copynumber: 4.1 Consensus size: 49
12745708 GAACTTGCCA
* *
12745718 AAAATTACCATTTTACCCCCAGACT-TCCAAAAATTCTA-TTTTGACCTC
1 AAAATTACCATTTTACCCCC-GAATGTCCAAAAATTCCATTTTTGACCTC
*
12745766 AAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACCCCGAACTTTCCC
1 AAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGA---C---C--T--C
* * ** * ** *
12745825 AAAATTACCATTTTACCCTCAAACATCCAAAAATTGCATTTCCTAAACTTTCCC
1 AAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTT--TTGAC---CTC
* *
12745879 AAAATTACCATTTTAACCCCGAATGTCCAAAAATTCCATTTTTAACCTC
1 AAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGACCTC
12745928 AAA
1 AAA
12745931 CTTCATAAAA
Statistics
Matches: 128, Mismatches: 23, Indels: 27
0.72 0.13 0.15
Matches are distributed among these distances:
47 3 0.02
48 31 0.24
49 11 0.09
52 5 0.04
54 36 0.28
55 1 0.01
57 1 0.01
58 2 0.02
59 36 0.28
61 2 0.02
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (49 bp):
AAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGACCTC
Found at i:12745801 original size:107 final size:110
Alignment explanation
Indices: 12745655--12745956 Score: 344
Period size: 107 Copynumber: 2.7 Consensus size: 110
12745645 CCCCAAACTT
* * * *
12745655 TCCCATAATTACCATTCTACCCCCAAATGTCCAAAAATTCCATTTTTCACCCTGAACTTGCCAAA
1 TCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTCACCCCGAACTTGCCAAA
* * *
12745720 AATTACCATTTTACCCCCAGACTTCCAAAAATT-CTATTT-T-GAC
66 AATTACCATTTTACCCCCAAACATCCAAAAATTGC-ATTTCTAAAC
* * * * *
12745763 -CTCAAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACCCCGAACTTTCCCAA
1 TCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTCACCCCGAACTTGCCAAA
*
12745827 AATTACCATTTTACCCTCAAACATCCAAAAATTGCATTTCCTAAAC
66 AATTACCATTTTACCCCCAAACATCCAAAAATTGCATTT-CTAAAC
* * * * *
12745873 TTTCCCAAAATTACCATTTTAACCCCGAATGTCCAAAAATTCCATTTTTAACCTCAAACTT-CAT
1 --TCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTCACCCCGAACTTGC-C
* *
12745937 AAAAATTACTATTTTGCCCC
63 AAAAATTACCATTTTACCCC
12745957 TGGCATCGAA
Statistics
Matches: 162, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
107 89 0.55
108 1 0.01
109 1 0.01
110 2 0.01
112 1 0.01
113 68 0.42
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (110 bp):
TCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTCACCCCGAACTTGCCAAA
AATTACCATTTTACCCCCAAACATCCAAAAATTGCATTTCTAAAC
Found at i:12745951 original size:59 final size:58
Alignment explanation
Indices: 12745765--12745933 Score: 204
Period size: 54 Copynumber: 2.9 Consensus size: 58
12745755 ATTTTGACCT
* * * *
12745765 CAAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACCCCGAACTTTCC
1 CAAAATTACCATTTTAACCCCGAATGTCCAAAAATTCCATTTTT-ACCTCAAACTTTCC
* ** *
12745824 CAAAATTACCATTTT-ACCCTCAAACATCCAAAAATTGCA--TTT-CCT-AAACTTTCC
1 CAAAATTACCATTTTAACCC-CGAATGTCCAAAAATTCCATTTTTACCTCAAACTTTCC
12745878 CAAAATTACCATTTTAACCCCGAATGTCCAAAAATTCCATTTTTAACCTCAAACTT
1 CAAAATTACCATTTTAACCCCGAATGTCCAAAAATTCCATTTTT-ACCTCAAACTT
12745934 CATAAAAATT
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
54 38 0.42
55 6 0.07
56 3 0.03
57 3 0.03
58 6 0.07
59 35 0.38
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (58 bp):
CAAAATTACCATTTTAACCCCGAATGTCCAAAAATTCCATTTTTACCTCAAACTTTCC
Found at i:12749905 original size:23 final size:23
Alignment explanation
Indices: 12749879--12749950 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
12749869 CCTTTTCTTA
** *
12749879 CATTACATACATGCATTTTTTCG
1 CATTACATATTTGCATATTTTCG
*
12749902 CATTGCATATTTGCATATTTTCG
1 CATTACATATTTGCATATTTTCG
12749925 CA-TAGCATATTTGCATATTTTCG
1 CATTA-CATATTTGCATATTTTCG
12749948 CAT
1 CAT
12749951 AATAATTCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.02
23 41 0.98
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (23 bp):
CATTACATATTTGCATATTTTCG
Found at i:12749951 original size:23 final size:23
Alignment explanation
Indices: 12749890--12749951 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
12749880 ATTACATACA
* *
12749890 TGCATTTTTTCGCATTGCATATT
1 TGCATATTTTCGCATAGCATATT
12749913 TGCATATTTTCGCATAGCATATT
1 TGCATATTTTCGCATAGCATATT
12749936 TGCATATTTTCGCATA
1 TGCATATTTTCGCATA
12749952 ATAATTCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.47
Consensus pattern (23 bp):
TGCATATTTTCGCATAGCATATT
Found at i:12756869 original size:23 final size:23
Alignment explanation
Indices: 12756839--12756934 Score: 113
Period size: 23 Copynumber: 4.2 Consensus size: 23
12756829 ACTTGTGATA
* *
12756839 GCATTACATACATGCATTTTTTC
1 GCATTACATACTTGCATATTTTC
*
12756862 GCATTACATACTTGCATTTTTTC
1 GCATTACATACTTGCATATTTTC
* * *
12756885 GCATTGCATATTTGAATATTTTC
1 GCATTACATACTTGCATATTTTC
*
12756908 GCA-TAGCATATTTGCATATTTTC
1 GCATTA-CATACTTGCATATTTTC
12756931 GCAT
1 GCAT
12756935 AATAATTCTA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
22 1 0.02
23 63 0.98
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (23 bp):
GCATTACATACTTGCATATTTTC
Found at i:12763346 original size:209 final size:209
Alignment explanation
Indices: 12762973--12763419 Score: 601
Period size: 209 Copynumber: 2.1 Consensus size: 209
12762963 AATATAAAGC
* *
12762973 GGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCTGTCTTCCTGATGAGACACAGAGAA
1 GGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCTGCCTTCCTGATGAGACACAGAGAA
** *
12763038 GTGGATCAAAACAAGTGAAGCGGTCATCTTCCTAATAAGATGCTAAGAAGAAGGCCAAATCAATG
66 GCAGATCAAAACAAGTGAAGCGGTCATCTTCCTAATAAGATACTAAGAAGAAGGCCAAATCAATG
* * *
12763103 AAGCCAAGCTCAAAATGAGCAAATCTTTGAACCCTAACTTCTTGATGAGATATTGAGAAGCAGGT
131 AAGCCAAGCTCAAAATAAGCAAATCTTCGAACCCTAACTTCCTGATGAGATATTGAGAAGCAGGT
*
12763168 CGAAGCAATAAAAT
196 CAAAGCAATAAAAT
* * * * * *
12763182 GGTTAGCTTCCTGATGAGATAGTA-AGAAGTGGACCAAAT-TCGCCTTTCTGATGAGATACGGAG
1 GGTTACCTTCCTGATGAGATA-CAGAGAAGTGAACCAAATCT-GCCTTCCTGATGAGACACAGAG
** * * * * * *
12763245 AAGCAGATTGAAACAAGTGATGCTGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAATCAG
64 AAGCAGATCAAAACAAGTGAAGCGGTCATCTTCCTAATAAGATACTAAGAAGAAGGCCAAATCAA
* * * *
12763310 TGAAGCCAAGCTCAAAGTAAGCGAATCTTCGAACCCTAGCTTCCTGATGAGATATTGAGAAGTAG
129 TGAAGCCAAGCTCAAAATAAGCAAATCTTCGAACCCTAACTTCCTGATGAGATATTGAGAAGCAG
12763375 GTCAAAGCAATAAAAT
194 GTCAAAGCAATAAAAT
* *
12763391 GGTTATCTTCCTGATGAGATACTGAGAAG
1 GGTTACCTTCCTGATGAGATACAGAGAAG
12763420 CGGATTGAAA
Statistics
Matches: 205, Mismatches: 30, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
208 1 0.00
209 203 0.99
210 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (209 bp):
GGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCTGCCTTCCTGATGAGACACAGAGAA
GCAGATCAAAACAAGTGAAGCGGTCATCTTCCTAATAAGATACTAAGAAGAAGGCCAAATCAATG
AAGCCAAGCTCAAAATAAGCAAATCTTCGAACCCTAACTTCCTGATGAGATATTGAGAAGCAGGT
CAAAGCAATAAAAT
Found at i:12763807 original size:18 final size:18
Alignment explanation
Indices: 12763784--12763829 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
12763774 CGAAACCCAT
*
12763784 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTAAAA
* *
12763802 TTTAAATATGTTTTAAAA
1 TTTAAATTTATTTTAAAA
12763820 TTTAAATTTA
1 TTTAAATTTA
12763830 AATTTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:12765806 original size:30 final size:30
Alignment explanation
Indices: 12765766--12766245 Score: 150
Period size: 29 Copynumber: 16.5 Consensus size: 30
12765756 AAAGGTCCTT
* * *
12765766 AAACTATCCAAAAATCATATTTTGACCCCC
1 AAACTTTCCAAAAATAACATTTTGACCCCC
*
12765796 AAACTTTCCAAAAGTAACATTTTGACCCCC
1 AAACTTTCCAAAAATAACATTTTGACCCCC
* * * *
12765826 AAACTTTCCAAAATTTACA--TT-A-TCAC
1 AAACTTTCCAAAAATAACATTTTGACCCCC
* * **
12765852 GAAC-TTCACAAAAATTACCATTTT-ACCCTT
1 AAACTTTC-CAAAAA-TAACATTTTGACCCCC
** *
12765882 AAA-TTTCCAAAAATTCCATTTTTGA-CCCT
1 AAACTTTCCAAAAATAACA-TTTTGACCCCC
* * * * *
12765911 GAACTTTCCCAAAATTACCATTTT-ATCCTC
1 AAACTTT-CCAAAAATAACATTTTGACCCCC
* ** *
12765941 AAA-TGTCCAAAAATTCCATTTTGGA-CCCT
1 AAACTTTCCAAAAATAACATTTT-GACCCCC
* *
12765970 AAAC-TTCCTAAAAACTACCATTTT-A-CCTC
1 AAACTTTCC-AAAAA-TAACATTTTGACCCCC
** * *
12765999 AAAC-TTCCAAAAATTTCATTTTTAACCCC
1 AAACTTTCCAAAAATAACATTTTGACCCCC
* * *
12766028 AAACTTTCCCAAAATTACTATTTT-ACCCCT
1 AAACTTTCCAAAAATAAC-ATTTTGACCCCC
** * * **
12766058 AAAC-TTCCAAAAATTCCATTTTTAACCAT
1 AAACTTTCCAAAAATAACATTTTGACCCCC
* *
12766087 AAACTTTCCCAAAATTACCATTTT-A-CCCC
1 AAACTTT-CCAAAAATAACATTTTGACCCCC
* ** * *
12766116 AAAC-ATCCAAAAATTCCATTTTTA-CCCT
1 AAACTTTCCAAAAATAACATTTTGACCCCC
* * * *
12766144 AAATTTTCCTAAAATTAC-TATTT-ACCCTC
1 AAACTTTCCAAAAATAACAT-TTTGACCCCC
* * * *
12766173 AAAC-TTCCAAAAAT-TCTATTTTTAACCTC
1 AAACTTTCCAAAAATAAC-ATTTTGACCCCC
* *
12766202 AAACTTTCCTAAAATTACCATTTT-ACCCCC
1 AAACTTTCC-AAAAATAACATTTTGACCCCC
*
12766232 AAA-TATCCAAAAAT
1 AAACTTTCCAAAAAT
12766246 TCAATTTTTG
Statistics
Matches: 349, Mismatches: 68, Indels: 68
0.72 0.14 0.14
Matches are distributed among these distances:
25 3 0.01
26 10 0.03
27 26 0.07
28 58 0.17
29 104 0.30
30 100 0.29
31 47 0.13
32 1 0.00
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (30 bp):
AAACTTTCCAAAAATAACATTTTGACCCCC
Found at i:12765894 original size:29 final size:29
Alignment explanation
Indices: 12765860--12766284 Score: 315
Period size: 29 Copynumber: 14.6 Consensus size: 29
12765850 ACGAACTTCA
*
12765860 CAAAAATTACCATTTTACCCTTAAATTTC
1 CAAAAATTACCATTTTACCCTCAAATTTC
* *
12765889 CAAAAATT-CCATTTTTGACCCTGAACTTTC
1 CAAAAATTACCA-TTTT-ACCCTCAAATTTC
* * *
12765919 CCAAAATTACCATTTTATCCTCAAATGTC
1 CAAAAATTACCATTTTACCCTCAAATTTC
*
12765948 CAAAAATT-CCATTTTGGACCCT-AAACTTC
1 CAAAAATTACCATTTT--ACCCTCAAATTTC
* *
12765977 CTAAAAACTACCATTTTA-CCTCAAACTTC
1 C-AAAAATTACCATTTTACCCTCAAATTTC
*
12766006 CAAAAATT-TCATTTTTAACCC-CAAACTTTC
1 CAAAAATTACCA-TTTT-ACCCTCAAA-TTTC
* * *
12766036 CCAAAATTACTATTTTACCC-CTAAACTTC
1 CAAAAATTACCATTTTACCCTC-AAATTTC
*
12766065 CAAAAATT-CCATTTTTAACCAT-AAACTTTC
1 CAAAAATTACCA-TTTT-ACCCTCAAA-TTTC
* **
12766095 CCAAAATTACCATTTTACCC-CAAACATC
1 CAAAAATTACCATTTTACCCTCAAATTTC
12766123 CAAAAATT-CCATTTTTACCCT-AAATTTTC
1 CAAAAATTACCA-TTTTACCCTCAAA-TTTC
* * *
12766152 CTAAAATTACTA-TTTACCCTCAAACTTC
1 CAAAAATTACCATTTTACCCTCAAATTTC
* *
12766180 CAAAAATT-CTATTTTTAACCTCAAACTTTC
1 CAAAAATTACCA-TTTTACCCTCAAA-TTTC
* * *
12766210 CTAAAATTACCATTTTACCCCCAAATATC
1 CAAAAATTACCATTTTACCCTCAAATTTC
* * *
12766239 CAAAAATT-CAATTTTTGA-CCTCGAACTTC
1 CAAAAATTACCA-TTTT-ACCCTCAAATTTC
12766268 CTAAAAATTACCATTTT
1 C-AAAAATTACCATTTT
12766285 TCCTCGGGCA
Statistics
Matches: 315, Mismatches: 48, Indels: 65
0.74 0.11 0.15
Matches are distributed among these distances:
27 8 0.03
28 65 0.21
29 121 0.38
30 103 0.33
31 18 0.06
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCAAATTTC
Found at i:12765925 original size:59 final size:59
Alignment explanation
Indices: 12765862--12766284 Score: 490
Period size: 59 Copynumber: 7.2 Consensus size: 59
12765852 GAACTTCACA
* * *
12765862 AAAATTACCATTTTACCCTTAAATTTCCAAAAATTCCATTTTTGACCCTGAACTTTCCC
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCTAAACTTTCCC
* * *
12765921 AAAATTACCATTTTATCCTCAAA-TGTCCAAAAATTCCATTTTGGACCCTAAAC-TTCCTA
1 AAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCCATTTTTGACCCTAAACTTTCC-C
* * * *
12765980 AAAACTACCATTTTA-CCTCAAACTTCCAAAAATTTCATTTTTAACCCCAAACTTTCCC
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCTAAACTTTCCC
* * *
12766038 AAAATTACTATTTTACCC-CTAAACTTCCAAAAATTCCATTTTTAACCATAAACTTTCCC
1 AAAATTACCATTTTACCCTC-AAACTTCCAAAAATTCCATTTTTGACCCTAAACTTTCCC
* * *
12766097 AAAATTACCATTTTACCC-CAAACATCCAAAAATTCCATTTTT-ACCCTAAATTTTCCT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCTAAACTTTCCC
* * * *
12766154 AAAATTACTA-TTTACCCTCAAACTTCCAAAAATTCTATTTTT-AACCTCAAACTTTCCT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCT-AAACTTTCCC
* * * *
12766212 AAAATTACCATTTTACCCCCAAA-TATCCAAAAATTCAATTTTTGA-CCTCGAAC-TTCCTA
1 AAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCCATTTTTGACCCT-AAACTTTCC-C
12766271 AAAATTACCATTTT
1 AAAATTACCATTTT
12766285 TCCTCGGGCA
Statistics
Matches: 321, Mismatches: 31, Indels: 24
0.85 0.08 0.06
Matches are distributed among these distances:
56 7 0.02
57 47 0.15
58 95 0.30
59 171 0.53
60 1 0.00
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCTAAACTTTCCC
Found at i:12766033 original size:117 final size:117
Alignment explanation
Indices: 12765766--12766289 Score: 472
Period size: 117 Copynumber: 4.5 Consensus size: 117
12765756 AAAGGTCCTT
* * * *
12765766 AAACTATCCAAAAA-T-CATATTTTGACCCCCAAACTTT-CCAAAAGTAACATTTTGACCCCCAA
1 AAACT-TCCAAAAATTCCAT-TTTTGA-CCCCAAACTTTCCCAAAATTACCATTTT-ATCCTCAA
* * * * * **
12765828 ACTTTCCAAAATTTACA--TTATCAC-GAAC-TTCACAAAAATTACCATTTTACCCTT
62 AC-TTCCAAAAATTCCATTTTAACCCTAAACTTTC-CAAAAATTACCATTTTACCCCC
* **
12765882 AAATTTCCAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTACCATTTTATCCTCAAA-TG
1 AAACTTCCAAAAATTCCATTTTTGACCCCAAACTTTCCCAAAATTACCATTTTATCCTCAAACT-
* * *
12765946 TCCAAAAATTCCATTTTGGACCCTAAAC-TTCCTAAAAACTACCATTTTA-CCTC
65 TCCAAAAATTCCATTTT-AACCCTAAACTTTCC-AAAAATTACCATTTTACCCCC
* * * *
12765999 AAACTTCCAAAAATTTCATTTTTAACCCCAAACTTTCCCAAAATTACTATTTTA-CCCCTAAACT
1 AAACTTCCAAAAATTCCATTTTTGACCCCAAACTTTCCCAAAATTACCATTTTATCCTC-AAACT
* *
12766063 TCCAAAAATTCCATTTTTAACCATAAACTTTCCCAAAATTACCATTTTA-CCCC
65 TCCAAAAATTCCA-TTTTAACCCTAAACTTTCCAAAAATTACCATTTTACCCCC
* * * * * *
12766116 AAACATCCAAAAATTCCATTTTT-ACCCTAAATTTTCCTAAAATTACTA-TTTACCCTCAAACTT
1 AAACTTCCAAAAATTCCATTTTTGACCCCAAACTTTCCCAAAATTACCATTTTATCCTCAAACTT
* *
12766179 CCAAAAATTCTATTTTTAA-CCTCAAACTTTCCTAAAATTACCATTTTACCCCC
66 CCAAAAATTCCA-TTTTAACCCT-AAACTTTCCAAAAATTACCATTTTACCCCC
* * * *
12766232 AAA-TATCCAAAAATTCAATTTTTGACCTCGAAC-TTCCTAAAAATTACCATTTT-TCCTC
1 AAACT-TCCAAAAATTCCATTTTTGACCCCAAACTTTCC-CAAAATTACCATTTTATCCTC
12766290 GGGCATCCAA
Statistics
Matches: 343, Mismatches: 45, Indels: 39
0.80 0.11 0.09
Matches are distributed among these distances:
113 1 0.00
114 13 0.04
115 76 0.22
116 83 0.24
117 137 0.40
118 33 0.10
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (117 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCAAACTTTCCCAAAATTACCATTTTATCCTCAAACTT
CCAAAAATTCCATTTTAACCCTAAACTTTCCAAAAATTACCATTTTACCCCC
Found at i:12797773 original size:20 final size:20
Alignment explanation
Indices: 12797718--12797775 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
12797708 TAATTTAGTC
**
12797718 AAAAAGAAAATAACAACTTAT
1 AAAAAGAAAATAACAA-AAAT
*
12797739 AAAAA-AATATAAACAAAAAT
1 AAAAAGAAAAT-AACAAAAAT
12797759 AAAAAGAAAATAACAAA
1 AAAAAGAAAATAACAAA
12797776 TTGACTAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.14
Consensus pattern (20 bp):
AAAAAGAAAATAACAAAAAT
Found at i:12824150 original size:29 final size:29
Alignment explanation
Indices: 12824118--12824212 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
12824108 AAACGGTAAT
*
12824118 TTTTGAAAGTTTTGGGGTCAAAAATGAAA
1 TTTTGGAAGTTTTGGGGTCAAAAATGAAA
* *
12824147 TTTTGGAAGTTTGGGGGTC-AAAATGTAAT
1 TTTTGGAAGTTTTGGGGTCAAAAATG-AAA
* *
12824176 TTTTGGAAG-TTTCGGGTCAAAAATGGAA
1 TTTTGGAAGTTTTGGGGTCAAAAATGAAA
12824204 TATTTGGAA
1 T-TTTGGAA
12824213 TATTTGGAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
28 15 0.27
29 41 0.73
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
TTTTGGAAGTTTTGGGGTCAAAAATGAAA
Found at i:12824213 original size:9 final size:9
Alignment explanation
Indices: 12824199--12824227 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
12824189 GGGTCAAAAA
12824199 TGGAATATT
1 TGGAATATT
12824208 TGGAATATT
1 TGGAATATT
12824217 TGGAAT-TT
1 TGGAATATT
12824225 TGG
1 TGG
12824228 GGGCAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (9 bp):
TGGAATATT
Found at i:12824248 original size:38 final size:38
Alignment explanation
Indices: 12824177--12824250 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
12824167 AAATGTAATT
*
12824177 TTTGGAAGTTTCGGGTCAAAAATGGAATATTTGGAATA
1 TTTGGAAGTTTCGGGGCAAAAATGGAATATTTGGAATA
* * * * *
12824215 TTTGGAATTTTGGGGGCAATAATGTAATTTTTGGAA
1 TTTGGAAGTTTCGGGGCAAAAATGGAATATTTGGAA
12824251 GTTCGAGGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (38 bp):
TTTGGAAGTTTCGGGGCAAAAATGGAATATTTGGAATA
Found at i:12824295 original size:29 final size:30
Alignment explanation
Indices: 12824235--12824313 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
12824225 TGGGGGCAAT
* *
12824235 AATGTAATTTTTGGAAG-TTCGAGGGTACA
1 AATGTAATTTTTAGAAGTTTCGAGGGCACA
12824264 AATGTAATTTTTAGAAGTTTC-AGGGC-CAA
1 AATGTAATTTTTAGAAGTTTCGAGGGCAC-A
* *
12824293 AATATAATTTTTTGACAGTTT
1 AATGTAATTTTTAGA-AGTTT
12824314 AAGGACCCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
28 1 0.02
29 34 0.79
30 8 0.19
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (30 bp):
AATGTAATTTTTAGAAGTTTCGAGGGCACA
Found at i:12826150 original size:17 final size:18
Alignment explanation
Indices: 12826130--12826173 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
12826120 AAAATTAATT
12826130 TAAATTC-AAATTTAAAA
1 TAAATTCTAAATTTAAAA
12826147 TAAA-TCTAAATTTAAAA
1 TAAATTCTAAATTTAAAA
12826164 TAAATT-TAAA
1 TAAATTCTAAA
12826174 AGGGCTCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 22 0.88
18 1 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATTCTAAATTTAAAA
Found at i:12826780 original size:48 final size:49
Alignment explanation
Indices: 12826662--12826784 Score: 153
Period size: 48 Copynumber: 2.5 Consensus size: 49
12826652 ATTTGGTCTT
* * *
12826662 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
1 CTTCTCAGTATCTCATCAGGAAGCTGAACGCATCGTTTGCTTCAATCCG
** *
12826711 CTTCTCAGTATCTCATCAGGAAGCT-AAC-CATTTTATTGCTTCGA-CCTG
1 CTTCTCAGTATCTCATCAGGAAGCTGAACGCATCGT-TTGCTTCAATCC-G
12826759 CTTCTCAGTATCTCATCAGGAAGCTG
1 CTTCTCAGTATCTCATCAGGAAGCTG
12826785 GGTTCGAAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
47 6 0.09
48 35 0.54
49 24 0.37
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (49 bp):
CTTCTCAGTATCTCATCAGGAAGCTGAACGCATCGTTTGCTTCAATCCG
Found at i:12826847 original size:168 final size:168
Alignment explanation
Indices: 12826542--12826896 Score: 604
Period size: 168 Copynumber: 2.1 Consensus size: 168
12826532 ATTTGGTTCA
*
12826542 CTTCTCCGTATCTCATCAGGAAGCTAACCACTTTATTGCTTAGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTTAGACCTGCTTCTCAGTATCTCATC
* *
12826607 AAAAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTTGGTTTGATTTGGTCTTCTTCTCAGTA
66 AAAAAGCTAGGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
*
12826672 TCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
131 TCTCATCAGGAAGATGACCGCATCGCTTGTTTCAAT-CG
* *
12826711 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTTAGACCTGCTTCTCAGTATCTCATC
**
12826776 AGGAAGCT-GGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
66 AAAAAGCTAGGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
12826840 TCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCG
131 TCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCG
* *
12826878 CTTCTCTGTACCTCATCAG
1 CTTCTCAGTATCTCATCAG
12826897 AAGACGAATT
Statistics
Matches: 176, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
167 19 0.11
168 89 0.51
169 68 0.39
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (168 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTTAGACCTGCTTCTCAGTATCTCATC
AAAAAGCTAGGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
TCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCG
Found at i:12827060 original size:203 final size:205
Alignment explanation
Indices: 12826711--12827415 Score: 1093
Period size: 201 Copynumber: 3.5 Consensus size: 205
12826701 TTTCAATCCG
12826711 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
*
12826776 AGGAAGCT-GGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
66 AGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
12826840 TCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTCTCTGTACCTCATCA-GAAGACGA
131 TCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTCTCTGTACCTCATCAGGAAGACGA
12826904 ATTTGGTCCA
196 ATTTGGTCCA
* *
12826914 CTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATT
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
12826979 AGGAAGCT-GGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
66 AGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
*
12827043 TCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTATACCTCATCAGGAAGACG
131 TCTCATCAGGAAGATGACCGCATCGCTTGTTTCAAT-CGCTTCTCTGTACCTCATCAGGAAGACG
12827108 AATTTGGTCCA
195 AATTTGGTCCA
* *
12827119 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGATCTGCTTCTCTGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* * * * * * * *
12827184 AGGAAGTTAGGGTTCGAAGATTTGCTCACTTTGAGC-----CTTGAGTTGGTATACTTCTCTGTA
66 AGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
* * * * *
12827244 TCTCATCAGGAAGGTGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGATG
131 TCTCATCAGGAAGATGACCGCATCGCTTGTTTCAA-TCGCTTCTCTGTACCTCATCAGGAAGACG
12827309 AATTTGGTCCA
195 AATTTGGTCCA
* * * *
12827320 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGCCCTGCCTCTCAGTATGTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* * * *
12827385 AGGAAGCTGGGGTTCAAAGATCTGTTCACAT
66 AGGAAGCTAGGGTTCGAAGATTTGCTCACAT
12827416 TGAGTTGGTA
Statistics
Matches: 464, Mismatches: 34, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
201 171 0.37
202 1 0.00
203 162 0.35
204 19 0.04
205 86 0.19
206 25 0.05
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.34
Consensus pattern (205 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
AGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
TCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTCTCTGTACCTCATCAGGAAGACGA
ATTTGGTCCA
Found at i:12827947 original size:49 final size:49
Alignment explanation
Indices: 12827806--12828013 Score: 200
Period size: 49 Copynumber: 4.2 Consensus size: 49
12827796 CGACTTAAAC
** * * *
12827806 CTTTCCCTTCAAATCTTCGTGGTACTGGATCTGCTGTCGCAGCTTAGAT
1 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTCGCGGCTTAGAT
* * * * * *
12827855 CTTTCTCTTCCTGTCTTCGTAGTACTGGGTCCGTCATCGCGGCTTAGAT
1 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTCGCGGCTTAGAT
**
12827904 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTACGGCTTTAGAT
1 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTCGCGGC-TTAGAT
* ** *** *
12827954 CTTTCCTTTTTTGTATCTTTACGGTACTGGATCCGCCGTTGCGGTCTTAGAT
1 CTTTCCCTTCATG--TCTTCGTGGTACTGGATCCGCCGTCGCGG-CTTAGAT
12828006 CTTTCCCT
1 CTTTCCCT
12828014 GTCAAATCTG
Statistics
Matches: 128, Mismatches: 27, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
49 73 0.57
50 16 0.12
52 38 0.30
53 1 0.01
ACGTcount: A:0.12, C:0.27, G:0.21, T:0.40
Consensus pattern (49 bp):
CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTCGCGGCTTAGAT
Found at i:12841083 original size:22 final size:18
Alignment explanation
Indices: 12841058--12841102 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
12841048 CTCATTTTCC
12841058 TAAAATAGCCCAACACCCAAAA
1 TAAAATA-CCCAA-A-CC-AAA
12841080 TAAAATACCCAAACCAAA
1 TAAAATACCCAAACCAAA
12841098 TAAAA
1 TAAAA
12841103 CCCATACCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 1 0.04
21 5 0.22
22 7 0.30
ACGTcount: A:0.60, C:0.27, G:0.02, T:0.11
Consensus pattern (18 bp):
TAAAATACCCAAACCAAA
Found at i:12844578 original size:21 final size:20
Alignment explanation
Indices: 12844542--12844600 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
12844532 ACTTAGTCAA
12844542 TTTGTTATTTTCTTTTTATT
1 TTTGTTATTTTCTTTTTATT
*
12844562 TTTGTTTATATTT-TTTTTATAA
1 TTTG-TTAT-TTTCTTTTTAT-T
*
12844584 GTTGTTATTTTCTTTTT
1 TTTGTTATTTTCTTTTT
12844601 GACTAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 7 0.21
21 20 0.61
22 6 0.18
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (20 bp):
TTTGTTATTTTCTTTTTATT
Found at i:12865459 original size:29 final size:29
Alignment explanation
Indices: 12865427--12865492 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
12865417 AAAATGAGAC
12865427 TTTTTGGA-TACCCGAGGACAAAATGGTAA
1 TTTTTGGACT-CCCGAGGACAAAATGGTAA
* * * **
12865456 TTTTGGGACTCTCGGGGGTAAAATGGTAA
1 TTTTTGGACTCCCGAGGACAAAATGGTAA
12865485 TTTTTGGA
1 TTTTTGGA
12865493 AAAATCGGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (29 bp):
TTTTTGGACTCCCGAGGACAAAATGGTAA
Found at i:12865545 original size:29 final size:29
Alignment explanation
Indices: 12865446--12865549 Score: 88
Period size: 29 Copynumber: 3.6 Consensus size: 29
12865436 ACCCGAGGAC
* *
12865446 AAAATGGTAATTTTGGGAC-TCTCGGGGGT
1 AAAATGGTAATTTTTGGACATC-CGGGAGT
*
12865475 AAAATGGTAATTTTTGGAAAAAT-CGGGA-T
1 AAAATGGTAATTTTTGG--ACATCCGGGAGT
** * *
12865504 CAAAAACGAAATTTTTGGACATCCAGGAGT
1 -AAAATGGTAATTTTTGGACATCCGGGAGT
12865534 AAAATGGTAATTTTTG
1 AAAATGGTAATTTTTG
12865550 AAAGTTTCGA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
28 3 0.05
29 34 0.59
30 19 0.33
31 1 0.02
32 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.31
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGACATCCGGGAGT
Found at i:12865591 original size:28 final size:28
Alignment explanation
Indices: 12865534--12865699 Score: 145
Period size: 29 Copynumber: 5.8 Consensus size: 28
12865524 ATCCAGGAGT
* *
12865534 AAAATGGTAATTTTTGAAAGTTTCGAGGTA
1 AAAATGG-AATTTTTGGAAGTTT-GGGGTA
12865564 AAAATGGAA-TTTTGGAAGTTTGGTGGTA
1 AAAATGGAATTTTTGGAAGTTTGG-GGTA
* * *
12865592 AAAATGTAATTTTTGGAAGTTTCAGGGTC
1 AAAATGGAATTTTTGGAAGTTT-GGGGTA
* * * **
12865621 AAAATGGAATATTTGAAATTTTGGGGGC
1 AAAATGGAATTTTTGGAAGTTTGGGGTA
* *
12865649 AAAATGTAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTG-GGGTA
* * *
12865678 CAAATGTAATTTTTAGAAGTTT
1 AAAATGGAATTTTTGGAAGTTT
12865700 CAGGGCCAAA
Statistics
Matches: 111, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.01
28 45 0.41
29 57 0.51
30 8 0.07
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTGGGGTA
Found at i:12865601 original size:57 final size:57
Alignment explanation
Indices: 12865534--12865699 Score: 194
Period size: 57 Copynumber: 2.9 Consensus size: 57
12865524 ATCCAGGAGT
* *
12865534 AAAATGGTAATTTTTGAAAGTTTCGA-GGTAAAAATGGAATTTTGGAAGTTTGGTGGTA
1 AAAAT-GTAATTTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTGGAAGTTTGG-GGGA
* * * *
12865592 AAAATGTAATTTTTGGAAGTTTC-AGGGTCAAAATGGAATATTTGAAATTTTGGGGGC
1 AAAATGTAATTTTTGGAAGTTTCGAGGGTAAAAATGGAAT-TTTGGAAGTTTGGGGGA
* * *
12865649 AAAATGTAATTTTTGGAAG-TTCGAGGGTACAAATGTAATTTTTAGAAGTTT
1 AAAATGTAATTTTTGGAAGTTTCGAGGGTAAAAATGGAA-TTTTGGAAGTTT
12865700 CAGGGCCAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
56 4 0.04
57 71 0.77
58 17 0.18
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTGGAAGTTTGGGGGA
Found at i:12865636 original size:86 final size:87
Alignment explanation
Indices: 12865534--12865711 Score: 227
Period size: 86 Copynumber: 2.1 Consensus size: 87
12865524 ATCCAGGAGT
* * *
12865534 AAAATGGTAATTTTTGAAAGTTTCGAGGTAAAAATGGAA-TTTTGGAAGTTTG-GTGGTAAAAAT
1 AAAATGGTAATATTTGAAA-TTTCGAGGGAAAAATGGAATTTTTGGAAGTTCGAG-GGTAAAAAT
* *
12865597 GTAATTTTTGGAAGTTTCAGGGTC
64 GTAATTTTTAGAAGTTTCAGGGCC
* * * * *
12865621 AAAATGG-AATATTTGAAATTTTGGGGGCAAAATGTAATTTTTGGAAGTTCGAGGGTACAAATGT
1 AAAATGGTAATATTTGAAATTTCGAGGGAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGT
12865685 AATTTTTAGAAGTTTCAGGGCC
66 AATTTTTAGAAGTTTCAGGGCC
12865707 AAAAT
1 AAAAT
12865712 ATAATTTCTT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
85 14 0.18
86 57 0.72
87 8 0.10
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (87 bp):
AAAATGGTAATATTTGAAATTTCGAGGGAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGT
AATTTTTAGAAGTTTCAGGGCC
Found at i:12865711 original size:29 final size:28
Alignment explanation
Indices: 12865534--12865718 Score: 142
Period size: 29 Copynumber: 6.4 Consensus size: 28
12865524 ATCCAGGAGT
* **
12865534 AAAATGGTAATTTTTGAAAGTTTCGAGGTA
1 AAAAT-GTAATTTTTGGAAGTTTC-AGGGC
* * *
12865564 AAAATGGAA-TTTTGGAAGTTT-GGTGGTA
1 AAAATGTAATTTTTGGAAGTTTCAG-GG-C
12865592 AAAATGTAATTTTTGGAAGTTTCAGGGTC
1 AAAATGTAATTTTTGGAAGTTTCAGGG-C
* * * * **
12865621 AAAATGGAATATTTGAAATTTTGGGGGC
1 AAAATGTAATTTTTGGAAGTTTCAGGGC
*
12865649 AAAATGTAATTTTTGGAAG-TTCGAGGGT
1 AAAATGTAATTTTTGGAAGTTTC-AGGGC
*
12865677 ACAAATGTAATTTTTAGAAGTTTCAGGGCC
1 A-AAATGTAATTTTTGGAAGTTTCAGGG-C
*
12865707 AAAATATAATTT
1 AAAATGTAATTT
12865719 CTTGACAGTT
Statistics
Matches: 124, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 3 0.02
28 40 0.32
29 70 0.56
30 10 0.08
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTCAGGGC
Found at i:12866583 original size:20 final size:20
Alignment explanation
Indices: 12866544--12866585 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12866534 GTCTTTTCAA
*
12866544 ATTTATTTTATTATTTAAAT
1 ATTTATTTTATTATTCAAAT
12866564 ATTTATTATTATTA-TCAAAT
1 ATTTATT-TTATTATTCAAAT
12866584 AT
1 AT
12866586 ATTTAGTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATTTTATTATTCAAAT
Found at i:12866588 original size:18 final size:18
Alignment explanation
Indices: 12866539--12866589 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
12866529 GATAAGTCTT
*
12866539 TTCAAATTTATTTTATTA
1 TTCAAATATATTTTATTA
*
12866557 TTTAAATAT-TTATTATTA
1 TTCAAATATATT-TTATTA
12866575 TTATCAAATATATTT
1 -T-TCAAATATATTT
12866590 AGTGTACTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 2 0.08
18 13 0.50
19 1 0.04
20 8 0.31
21 2 0.08
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCAAATATATTTTATTA
Found at i:12867421 original size:17 final size:18
Alignment explanation
Indices: 12867401--12867444 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
12867391 AAAATTAATT
12867401 TAAATTC-AAATTTAAAA
1 TAAATTCTAAATTTAAAA
12867418 TAAA-TCTAAATTTAAAA
1 TAAATTCTAAATTTAAAA
12867435 TAAATT-TAAA
1 TAAATTCTAAA
12867445 AGGGCTCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 22 0.88
18 1 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATTCTAAATTTAAAA
Found at i:12867427 original size:23 final size:24
Alignment explanation
Indices: 12867384--12867429 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
12867374 TCTTTTTTTT
* *
12867384 AAATTTGAAAATTAATTTAAATTC
1 AAATTTGAAAATAAATCTAAATTC
12867408 AAATTT-AAAATAAATCTAAATT
1 AAATTTGAAAATAAATCTAAATT
12867430 TAAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (24 bp):
AAATTTGAAAATAAATCTAAATTC
Found at i:12867444 original size:6 final size:6
Alignment explanation
Indices: 12867381--12867444 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
12867371 AATTCTTTTT
* * * *
12867381 TTTAAA TTTGAAA ATT-AA TTTAAA TTCAAA TTTAAA -ATAAA TCTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
12867428 TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
12867445 AGGGCTCGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
5 12 0.27
6 28 0.62
7 5 0.11
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:12868523 original size:205 final size:206
Alignment explanation
Indices: 12867744--12868755 Score: 1421
Period size: 204 Copynumber: 4.9 Consensus size: 206
12867734 TCTGGTTTCA
* * * * ** *
12867744 TTGACTTGGCCTTCTTCTCTGTATCTCATCAGGAAGATGACCACATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* * * * * *
12867809 CTCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCAC
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* **
12867874 TTTATTGCTTAGACCTGCTTCTCAGTATCTCATCAAAAAGCTAGGGGTTCGAAGATTTGCTCACA
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTA-GGGTTCGAAGATTTGCTCACA
*
12867939 TCGAGCGTCGGT
195 TCGAGCGTGGGT
* *
12867951 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTTGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
12868016 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
*
12868081 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCT-GGGTTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
*
12868145 GGAGCGTGGGT
196 CGAGCGTGGGT
* *
12868156 TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAAT-CGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* * * *
12868220 CTTTGTACCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
*
12868285 TTTATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTA-GGTTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
12868349 CGAGCGTGGGT
196 CGAGCGTGGGT
*
12868360 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* * * *
12868425 CTCTATACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
12868490 TTCATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTAGGGTTCGAAGATTTGCTCACTT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
* *
12868555 TGAGC-----C
196 CGAGCGTGGGT
* * * * * * * *
12868561 TTGAGTTGGTATACTTCTCTGTATCTCATCAGGATGGTGACCGTC-TTACTTGTTTCAATTCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCG-CATCACTTGTTTCAATCCGCT
* * *
12868625 TCTCTATATCTCATAAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * * * * * * *
12868690 TTTTATTACTTTGCCCTGCCTCTTAGTATGTCATCAGGAAGCTAGGGTTCAAAGATCTGTTCACA
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACA
12868755 T
195 T
12868756 TGAGTTGGTA
Statistics
Matches: 734, Mismatches: 67, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
201 167 0.23
202 1 0.00
204 194 0.26
205 193 0.26
206 24 0.03
207 155 0.21
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
CGAGCGTGGGT
Found at i:12869212 original size:49 final size:48
Alignment explanation
Indices: 12869146--12869275 Score: 138
Period size: 49 Copynumber: 2.7 Consensus size: 48
12869136 CGACTTAAAC
*
12869146 CTTTCCCTTCAAATCTTCGTGGTACTGGATCTACTGTC-GCA-GCTTAGAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATC--C-GTCAGCACGCTTAGAT
* * * * * *
12869195 CTTTCTCTTCCTGTCTTCGTAGTACTGGGTCCGTCATCACGGCTTAGAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATCCGTCAGCAC-GCTTAGAT
*
12869244 CTTTCCCTTCATATCTTCGTGATACTGGATCC
1 CTTTCCCTTCATATCTTCGTGGTACTGGATCC
12869276 ACCGTTACAG
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
46 3 0.05
47 3 0.05
49 59 0.91
ACGTcount: A:0.15, C:0.28, G:0.18, T:0.38
Consensus pattern (48 bp):
CTTTCCCTTCATATCTTCGTGGTACTGGATCCGTCAGCACGCTTAGAT
Found at i:12870869 original size:29 final size:29
Alignment explanation
Indices: 12870837--12870902 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
12870827 AAAATGAGAC
*
12870837 TTTTTGGA-TACTC-GAGGGCAAAATGGTAA
1 TTTTTGGACT-CTCGGA-GGCAAAATGGAAA
* *
12870866 TTTTGGGACTCTCGGAGGTAAAATGGAAA
1 TTTTTGGACTCTCGGAGGCAAAATGGAAA
12870895 TTTTTGGA
1 TTTTTGGA
12870903 AAAATCGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.33
Consensus pattern (29 bp):
TTTTTGGACTCTCGGAGGCAAAATGGAAA
Found at i:12873400 original size:30 final size:30
Alignment explanation
Indices: 12873366--12873459 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
12873356 CCCGGGGGGC
12873366 AAAATGGTAATTTTAGTGAAATCGGGGTTA
1 AAAATGGTAATTTTAGTGAAATCGGGGTTA
* *
12873396 AAAATGG-AATTTTA--GAAGCTTCGGGGGT-
1 AAAATGGTAATTTTAGTGAA--ATCGGGGTTA
* * *
12873424 AAAACGATAAATTTTGGTGAAATCGGGGTTA
1 AAAATGGT-AATTTTAGTGAAATCGGGGTTA
12873455 AAAAT
1 AAAAT
12873460 CAGATTCAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
27 3 0.06
28 5 0.10
29 14 0.29
30 20 0.41
31 4 0.08
32 3 0.06
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30
Consensus pattern (30 bp):
AAAATGGTAATTTTAGTGAAATCGGGGTTA
Found at i:12873504 original size:30 final size:30
Alignment explanation
Indices: 12873470--12873735 Score: 417
Period size: 30 Copynumber: 8.9 Consensus size: 30
12873460 CAGATTCAAG
*
12873470 AAAGTTTTGGGGTCAAAATGTAATTTGGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
12873500 AAAGTTTTGAGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
12873530 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
12873560 AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
12873590 AAAGTTTTGGGGTCAAAATGTAATTTTAGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
12873620 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
* * *
12873650 AAAGTTTTGGGGTTAAAATATAATTTTAGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
* *
12873680 AAA-TATTTGGGGTTAAAATGTAATTTTAGA
1 AAAGT-TTTGGGGTCAAAATGTAATTTTGGA
*
12873710 AAAGTTTTGGGGTTAAAATGTAATTT
1 AAAGTTTTGGGGTCAAAATGTAATTT
12873736 CTGAACAAGT
Statistics
Matches: 221, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
29 1 0.00
30 219 0.99
31 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGGA
Found at i:12875682 original size:6 final size:6
Alignment explanation
Indices: 12875658--12875762 Score: 79
Period size: 6 Copynumber: 17.0 Consensus size: 6
12875648 ACATTGGACT
* * **
12875658 TTTAAA TTTTTAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA
1 TTTAAA -TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
12875709 TTCAAA -TTAAA TTTAAATA TTTAAT TTTAAA TTTAAA -ATAAA TCTAAA
1 TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12875757 TTTAAA
1 TTTAAA
12875763 ATCAATTTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
5 8 0.10
6 48 0.61
7 19 0.24
8 4 0.05
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:12875708 original size:31 final size:30
Alignment explanation
Indices: 12875673--12875762 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 30
12875663 ATTTTTAATG
* *
12875673 TTAAATTTAATATTTTAATTT-TTATTTAAAT
1 TTAAATTTAA-A-TTAAATTTAATATTTAAAT
* *
12875704 TTAAATTCAAATTAAATTTAAATATTTAATT
1 TTAAATTTAAATTAAATTT-AATATTTAAAT
* *
12875735 TTAAATTTAAAATAAATCTAA-ATTTAAA
1 TTAAATTTAAATTAAATTTAATATTTAAA
12875763 ATCAATTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
29 13 0.27
30 3 0.06
31 33 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
TTAAATTTAAATTAAATTTAATATTTAAAT
Found at i:12875718 original size:17 final size:17
Alignment explanation
Indices: 12875698--12875772 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
12875688 TAATTTTTAT
*
12875698 TTAAATTTAAATTCAAA
1 TTAAATTTAAAATCAAA
* *
12875715 TTAAATTTAAATATTTAATT
1 TTAAATTTAAA-A-TCAA-A
12875735 TTAAATTTAAAAT-AAA
1 TTAAATTTAAAATCAAA
*
12875751 TCTAAATTTAAAATCAAT
1 T-TAAATTTAAAATCAAA
12875769 TTAA
1 TTAA
12875773 CTCAAAAGTC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.02
17 28 0.58
18 4 0.08
19 4 0.08
20 11 0.23
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATTTAAAATCAAA
Found at i:12876202 original size:69 final size:69
Alignment explanation
Indices: 12876090--12876713 Score: 705
Period size: 69 Copynumber: 8.9 Consensus size: 69
12876080 GGAAATGATC
* * *
12876090 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGAT
12876155 GACG
66 GACG
* * * *
12876159 TTGCTCTTTCTTCAATTTCAGAGATAAAGACTTGACATTCAACTTTACTTCAATTTCAAGCAGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTC-A--AG--
*
12876224 AGGAAATGATG
61 AGG--ATGACG
* * *
12876235 TTG-TCCTTACTTTAATTTC-GAAGATAAAGACGTGCTATCCAACTCTACTTCAATTTCAAGAGG
1 TTGCT-CTTACTTCAATTTCAG-AGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
*
12876298 ATGACA
64 ATGACG
* * * * **
12876304 TTGCTCTTACTTCAATTTCAGAGATGATGAC--G-T-TGC-TCT-TACTTCAATTTCAGAGATAA
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCA-AGAGGA
*
12876363 AGACG
65 TGACG
* * * * * * * * *
12876368 TATTATCCACTCTACTTTAATTTCAAAGGGATGACG-TTGTGTTATCC-ACTCTTCTTCAATTTC
1 ---T-TGCTCT-TACTTCAATTTC--AGAGATAAAGACT-TGATATCCAACTCTACTTCAATTTC
*
12876431 AAGGGGATGACG
58 AAGAGGATGACG
12876443 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGAT
12876508 GACG
66 GACG
*
12876512 TTGCTCTTACTTCAATTTCAGAGATAAAGAATTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGAT
12876577 GACG
66 GACG
12876581 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGAT
12876646 GACG
66 GACG
* *
12876650 TTGCTCTTACTTCAATTTCAGAGATAAAGACGT-ATTATCC-ACTCTACTTCAATTTCAAGGGGA
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGA-TATCCAACTCTACTTCAATTTCAAGAGGA
12876713 T
65 T
12876714 AGGAAAAGGT
Statistics
Matches: 474, Mismatches: 53, Indels: 57
0.81 0.09 0.10
Matches are distributed among these distances:
63 13 0.03
64 9 0.02
65 2 0.00
66 1 0.00
67 2 0.00
68 42 0.09
69 289 0.61
70 14 0.03
71 15 0.03
72 3 0.01
73 3 0.01
74 4 0.01
75 14 0.03
76 63 0.13
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (69 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGAT
GACG
Found at i:12876429 original size:39 final size:39
Alignment explanation
Indices: 12876370--12876445 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
12876360 TAAAGACGTA
*
12876370 TTATCCACTCTACTTTAATTTCAAAGGGATGACGTTGTG
1 TTATCCACTCTACTTCAATTTCAAAGGGATGACGTTGTG
* *
12876409 TTATCCACTCTTCTTCAATTTCAAGGGGATGACGTTG
1 TTATCCACTCTACTTCAATTTCAAAGGGATGACGTTG
12876446 CTCTTACTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (39 bp):
TTATCCACTCTACTTCAATTTCAAAGGGATGACGTTGTG
Found at i:12888938 original size:59 final size:58
Alignment explanation
Indices: 12888815--12888927 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 58
12888805 TATGGATACC
* * * *
12888815 CGGGGGTAAAATGGTAATTTTAGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
1 CGGGGGTAAAACGATAATTTTAGTGAAATCGAGGTTAAAAACGGAATTTAAGAAGCTT
*
12888873 CGGGGGTAAAACGATAAATTTTGGTGAAATCGAGGTTAAAAATC-GAATTTAAGAA
1 CGGGGGTAAAACGAT-AATTTTAGTGAAATCGAGGTTAAAAA-CGGAATTTAAGAA
12888928 AGTTTTGGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 13 0.27
59 34 0.71
60 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.27
Consensus pattern (58 bp):
CGGGGGTAAAACGATAATTTTAGTGAAATCGAGGTTAAAAACGGAATTTAAGAAGCTT
Found at i:12888962 original size:30 final size:30
Alignment explanation
Indices: 12888926--12889202 Score: 428
Period size: 30 Copynumber: 9.2 Consensus size: 30
12888916 CGAATTTAAG
12888926 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
12888956 AAAGTTTTGAGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
12888986 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
* *
12889016 AAAGTTTTGGGGTTAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
12889046 AAAGTTTTGGGGTCAAAATGTAATTTTAGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
12889076 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
** **
12889106 AAAGTTTTAAGGTCAAAACATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
12889136 AAAGTTTTGGGGTCAAAATGTAATTTTAGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
* *
12889166 AAATTTTTGGGGTTAAAATGTAATTTCTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTT-TGGA
*
12889197 CAAGTT
1 AAAGTT
12889203 AGGGGCTTAC
Statistics
Matches: 222, Mismatches: 24, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
30 215 0.97
31 7 0.03
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGGA
Found at i:12895043 original size:59 final size:59
Alignment explanation
Indices: 12894975--12895114 Score: 176
Period size: 59 Copynumber: 2.4 Consensus size: 59
12894965 AAAAATAACA
* * *
12894975 TTTTAGACATCCGAGGATAAAATGGTAATTTTTGGAA-AATTCGGGATCAAAAATGGATT
1 TTTTGGACATCCGAGGATAAAACGGTAATTTTT-GAAGAATTCGGGATCAAAAATGGAGT
** * *
12895034 TTTTGGACATCCGA-GAGTAAAACGGTAATTTTTGAAGGTTTCGGGGTCCAAAATGGAGT
1 TTTTGGACATCCGAGGA-TAAAACGGTAATTTTTGAAGAATTCGGGATCAAAAATGGAGT
*
12895093 TTTTGGACATCCGAGGGTAAAA
1 TTTTGGACATCCGAGGATAAAA
12895115 ATGTATGGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
58 5 0.07
59 64 0.91
60 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.31
Consensus pattern (59 bp):
TTTTGGACATCCGAGGATAAAACGGTAATTTTTGAAGAATTCGGGATCAAAAATGGAGT
Found at i:12895176 original size:29 final size:29
Alignment explanation
Indices: 12895123--12895274 Score: 98
Period size: 29 Copynumber: 5.2 Consensus size: 29
12895113 AAATGTATGG
*
12895123 AATTTTT-GAAG-TTCGAGGGTAAAAATGT
1 AATTTTTAGAAGTTTCGA-GGTCAAAATGT
*
12895151 AATTTTTAGAAGTTTCG-GGTTCAAAAATGG
1 AATTTTTAGAAGTTTCGAGG-TC-AAAATGT
* * * * *
12895181 GATTTTTAG-ATTTTTGTGTGTAAAAATGT
1 AATTTTTAGAAGTTTCGAG-GTCAAAATGT
* * * *
12895210 AATTTTTTGAATTTTAGCGG-CAAAAATGT
1 AATTTTTAGAAGTTTCGAGGTC-AAAATGT
* * *
12895239 AATTTTTAGAAGATTCGAGGCCAAAATAT
1 AATTTTTAGAAGTTTCGAGGTCAAAATGT
12895268 AATTTTT
1 AATTTTT
12895275 GAACAGTTTA
Statistics
Matches: 97, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
28 9 0.09
29 59 0.61
30 28 0.29
31 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (29 bp):
AATTTTTAGAAGTTTCGAGGTCAAAATGT
Found at i:12895179 original size:30 final size:30
Alignment explanation
Indices: 12895123--12895258 Score: 104
Period size: 29 Copynumber: 4.7 Consensus size: 30
12895113 AAATGTATGG
*
12895123 AATTTTT-GAAG-TTCGAGGGTAAAAATGT
1 AATTTTTAGAAGTTTCGAGGTTAAAAATGT
*
12895151 AATTTTTAGAAGTTTCG-GGTTCAAAAATGG
1 AATTTTTAGAAGTTTCGAGGTT-AAAAATGT
* * * *
12895181 GATTTTTAG-ATTTTTG-TGTGTAAAAATGT
1 AATTTTTAGAAGTTTCGAGGT-TAAAAATGT
* * * * *
12895210 AATTTTTTGAATTTTAGCGG-CAAAAATGT
1 AATTTTTAGAAGTTTCGAGGTTAAAAATGT
*
12895239 AATTTTTAGAAGATTCGAGG
1 AATTTTTAGAAGTTTCGAGG
12895259 CCAAAATATA
Statistics
Matches: 85, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
28 7 0.08
29 51 0.60
30 26 0.31
31 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.40
Consensus pattern (30 bp):
AATTTTTAGAAGTTTCGAGGTTAAAAATGT
Found at i:12897128 original size:6 final size:6
Alignment explanation
Indices: 12897103--12897172 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
12897093 TTTTTTTTTT
* * *
12897103 TTTAAA TTTGAAA -ATAAA TTTAAA TTTAAA TTCAAA TTTAAA -ATAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
12897150 TCTAAA GTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
12897173 AGGGCCCGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
5 11 0.22
6 36 0.72
7 3 0.06
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (6 bp):
TTTAAA
Found at i:12897160 original size:17 final size:17
Alignment explanation
Indices: 12897140--12897172 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12897130 AAATTCAAAT
12897140 TTAAAATAAATCTAAAG
1 TTAAAATAAATCTAAAG
*
12897157 TTAAAATAAATTTAAA
1 TTAAAATAAATCTAAA
12897173 AGGGCCCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAAAATAAATCTAAAG
Found at i:12900065 original size:13 final size:12
Alignment explanation
Indices: 12900042--12900073 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
12900032 TATTTTAAGA
12900042 TTAAATTTAT-T
1 TTAAATTTATAT
12900053 TTAAATTTATAT
1 TTAAATTTATAT
12900065 TTAAATTTA
1 TTAAATTTA
12900074 AAATTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAAATTTATAT
Found at i:12900066 original size:17 final size:18
Alignment explanation
Indices: 12900024--12900067 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12900014 CTAAATCCAT
12900024 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
12900042 -TTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
*
12900058 TTTATATTTA
1 TTTAAATTTA
12900068 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:12900271 original size:3 final size:3
Alignment explanation
Indices: 12900263--12900315 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
12900253 AAATAGTATC
* * ** * *
12900263 AAT AAT AAT AAT ACT ATT CTT AAT AGT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12900311 AAT AA
1 AAT AA
12900316 GGCAGTCGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:12901537 original size:29 final size:29
Alignment explanation
Indices: 12901407--12901930 Score: 210
Period size: 30 Copynumber: 17.9 Consensus size: 29
12901397 CCCAAAAGGT
* * *
12901407 CCCTAAACTATCCAAAAATCA-TATTTTGAC
1 CCCTAAA-TTTCCAAAAATTACCATTTT-AC
* *
12901437 CCCCAAACTTTCCAAAAGTTA-CATTTTGAC
1 CCCTAAA-TTTCCAAAAATTACCATTTT-AC
* * *
12901467 CCCCAAACTTTCCAAAATTTA-CA--TTAT
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
* * * *
12901494 CAC-GAACTTCAAAAAATTACCATTTTAC
1 CCCTAAATTTCCAAAAATTACCATTTTAC
12901522 CCCTAAATTTCCAAAAATTTA--ATTTTTGA-
1 CCCTAAATTTCCAAAAA-TTACCA-TTTT-AC
** * * *
12901551 CCCTGGACTTCTTAAAAACTACCATTTTA-
1 CCCTAAATTTC-CAAAAATTACCATTTTAC
* ** * ****
12901580 CCTTGGACTTCCAAAAATTTTGTTTTTAAC
1 CCCTAAATTTCCAAAAATTACCATTTT-AC
*
12901610 CCC-AAACTTTCCCAAAATTACCATTTTAC
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
** *
12901639 CCCCGAATGTCCAAAAATT-CCATTTTTTA-
1 CCCTAAATTTCCAAAAATTACCA--TTTTAC
** * *
12901668 CTTTGAACTTCCCAAAAATTACCATTTTAC
1 CCCT-AAATTTCCAAAAATTACCATTTTAC
* *
12901698 CCCTAAACTTCTAAAAATT-CCATTTTTGA-
1 CCCTAAATTTCCAAAAATTACCA-TTTT-AC
* *
12901727 CCTTAAACTTTCCCAAAATTACCATTTTAC
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
* **
12901757 CCCCAAACATCCAAAAATT-CCAATTTTTAC
1 CCCTAAATTTCCAAAAATTACC-A-TTTTAC
12901787 CCC-AAATTTTCCAAAAATTACCATTTTAC
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
* * * * *
12901816 CCTTAGACTTCTAAAAATT-CCTTTTTAAC
1 CCCTAAATTTCCAAAAATTACCATTTT-AC
*
12901845 CCC-AAACTTTCCCAAAATTACCATTTTAC
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
*
12901874 CCTCT-AATGTCCAAAAATT-CCATTTTTGAC
1 CC-CTAAATTTCCAAAAATTACCA-TTTT-AC
* * *
12901904 CTC-GAACTTCCTAAAAATTACCATTTT
1 CCCTAAATTTCC-AAAAATTACCATTTT
12901931 TCCCTGGGCA
Statistics
Matches: 374, Mismatches: 81, Indels: 78
0.70 0.15 0.15
Matches are distributed among these distances:
25 10 0.03
26 4 0.01
27 3 0.01
28 37 0.10
29 148 0.40
30 160 0.43
31 12 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCTAAATTTCCAAAAATTACCATTTTAC
Found at i:12901577 original size:59 final size:59
Alignment explanation
Indices: 12901497--12901930 Score: 336
Period size: 59 Copynumber: 7.4 Consensus size: 59
12901487 ACATTATCAC
* * **
12901497 GAACTTC-AAAAAATTACCATTTTACCCCTAAATTTCCAAAAATTTAATTTTTGACCCT
1 GAACTTCTCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCT
* * * * ** *** * *
12901555 GGACTTCTTAAAAACTACCATTTTA-CCTTGGACTTCCAAAAATTTTGTTTTTAACCCC
1 GAACTTCTCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCT
* * ** * **
12901613 AAACTT-TCCCAAAATTACCATTTTACCCCCGAA-TGTCCAAAAATTCCATTTTTTACTTT
1 GAACTTCT-CAAAAATTACCATTTTACCCCTAAACT-TCCAAAAATTCCATTTTTGACCCT
* * *
12901672 GAACTTCCCAAAAATTACCATTTTACCCCTAAACTTCTAAAAATTCCATTTTTGACCTT
1 GAACTTCTCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCT
* * * *
12901731 AAACTT-TCCCAAAATTACCATTTTACCCCCAAACATCCAAAAATTCCAATTTTT-ACCC-
1 GAACTTCT-CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCC-ATTTTTGACCCT
* * * * * * * *
12901789 CAAATTTTCCAAAAATTACCATTTTACCCTTAGACTTCTAAAAATTCC-TTTTTAACCCC
1 GAACTTCT-CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCT
* *
12901848 AAACTT-TCCCAAAATTACCATTTTACCCTCT-AA-TGTCCAAAAATTCCATTTTTGA-CCT
1 GAACTTCT-CAAAAATTACCATTTTACCC-CTAAACT-TCCAAAAATTCCATTTTTGACCCT
12901906 CGAACTTC-CTAAAAATTACCATTTT
1 -GAACTTCTC-AAAAATTACCATTTT
12901931 TCCCTGGGCA
Statistics
Matches: 300, Mismatches: 59, Indels: 33
0.77 0.15 0.08
Matches are distributed among these distances:
57 7 0.02
58 94 0.31
59 192 0.64
60 7 0.02
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (59 bp):
GAACTTCTCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCT
Found at i:12901652 original size:117 final size:118
Alignment explanation
Indices: 12901506--12901956 Score: 491
Period size: 117 Copynumber: 3.8 Consensus size: 118
12901496 CGAACTTCAA
* * * * * *
12901506 AAAATTACCATTTTACCCCTAAATTTCCAAAAATTTAATTTTTGACCCTGGACTTCTTAAAAACT
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCAATTTTTGACCCTGAACTTCCTAAAAATT
* * **
12901571 ACCATTTTA-CCTTGGACTTCCAAAAATTTTGTTTTTAACCCCAAACTTTCCC
66 ACCATTTTACCCCTAGACTTCCAAAAATTTCATTTTTAACCCCAAACTTTCCC
* * * ** *
12901623 AAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTTACTTTGAACTTCCCAAAAATT
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCAATTTTTGACCCTGAACTTCCTAAAAATT
* * * * **
12901688 ACCATTTTACCCCTAAACTTCTAAAAATTCCATTTTTGACCTTAAACTTTCCC
66 ACCATTTTACCCCTAGACTTCCAAAAATTTCATTTTTAACCCCAAACTTTCCC
** ** *
12901741 AAAATTACCATTTTACCCCCAAACATCCAAAAATTCCAATTTTT-ACCCCAAATTTTCC-AAAAA
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATT-CAATTTTTGACCCTGAA-CTTCCTAAAAA
* * *
12901804 TTACCATTTTACCCTTAGACTTCTAAAAA-TTCCTTTTTAACCCCAAACTTTCCC
64 TTACCATTTTACCCCTAGACTTCCAAAAATTTCATTTTTAACCCCAAACTTTCCC
* * *
12901858 AAAATTACCATTTTACCCTCTAATGTCCAAAAATTCCATTTTTGA-CCTCGAACTTCCTAAAAAT
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCAATTTTTGACCCT-GAACTTCCTAAAAAT
* * * * *
12901922 TACCATTTT-TCCCTGGGCATCCAAAAATTGCATTT
65 TACCATTTTACCCCTAGACTTCCAAAAATTTCATTT
12901957 AATCCCGATT
Statistics
Matches: 273, Mismatches: 54, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
116 25 0.09
117 136 0.50
118 101 0.37
119 11 0.04
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (118 bp):
AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCAATTTTTGACCCTGAACTTCCTAAAAATT
ACCATTTTACCCCTAGACTTCCAAAAATTTCATTTTTAACCCCAAACTTTCCC
Found at i:12911296 original size:209 final size:208
Alignment explanation
Indices: 12910779--12911436 Score: 773
Period size: 209 Copynumber: 3.2 Consensus size: 208
12910769 TATCCAAAAT
* * * * * * * *
12910779 ATAAAGTGGTTACCTTCCTAATGAGATACAGAGAAGTGAACCAGATCTGTCTTCCTAATGAGACA
1 ATAAAATGGTTAACTTCCTGATGAGATACTGAGAAATGAACCAAATCCGCCTTCCTAATGAGACA
** * ** *
12910844 CAGAA-AAGTGGATCAAAACAAGCGATACGGTCATCTTCTTGATGAGATACTGTGAAGAAGACCA
66 CA-AAGAAGCAGATC-AAACAAGCGATGCGGTCATCTTCTTGATGAGATACTAAGAAGAAGGCCA
*** * *
12910908 AATCAAT-AAAATAGGCTCAAAGTGAG-AGAATCTTCGAACCCCAGCTTCCTAATGAGATATTGA
129 AATCAATGAAGCCAAGCTCAAAGTGAGCA-AATCTTCGAACCCCAGCTTCCTGATGAGATATTGA
12910971 GAAGCAGGTCGAAGCA
193 GAAGCAGGTCGAAGCA
*** * * * *
12910987 ATAAAGCAGTTAACTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTAATGAGACA
1 ATAAAATGGTTAACTTCCTGATGAGATACTGAGAAATGAACCAAATCCGCCTTCCTAATGAGACA
** * * * *
12911052 CAAAGAAGTGGATCAAACTAAGCGAAGCGGTCATCTTCCTGGTAAGATACTAAGAAGAAGGCCAA
66 CAAAGAAGCAGATCAAAC-AAGCGATGCGGTCATCTTCTTGATGAGATACTAAGAAGAAGGCCAA
* * * *
12911117 ATCAATGAAGCCAAGCTCAAAATGAGCAAATCTTCGAACTCCAACTTCTTGATGAGATATTGAGA
130 ATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGA
12911182 AGCAGGTCGAAGCA
195 AGCAGGTCGAAGCA
* * * * * *
12911196 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGCCTTTCTGATGAGATA
1 ATAAAATGGTTAACTTCCTGATGAGATACTGAGAAATGAACCAAATCCGCCTTCCTAATGAGACA
** * * * *
12911261 CGGAGAAGCAGATTGAAACAAGTGATGCTGTCATCTTCTTGATGAGATACTTAGAAGAAGGCCAA
66 CAAAGAAGCAGA-TCAAACAAGCGATGCGGTCATCTTCTTGATGAGATACTAAGAAGAAGGCCAA
* *
12911326 ATCAATGAAGCCAAGCTCAAAGTAAGCGAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGA
130 ATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGA
*
12911391 AGCAGGTCAAAGCA
195 AGCAGGTCGAAGCA
* *
12911405 ATAAAATGGTTATCATCCTGATGAGATACTGA
1 ATAAAATGGTTAACTTCCTGATGAGATACTGA
12911437 AAAGCGGATT
Statistics
Matches: 389, Mismatches: 56, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
207 6 0.02
208 115 0.30
209 262 0.67
210 6 0.02
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (208 bp):
ATAAAATGGTTAACTTCCTGATGAGATACTGAGAAATGAACCAAATCCGCCTTCCTAATGAGACA
CAAAGAAGCAGATCAAACAAGCGATGCGGTCATCTTCTTGATGAGATACTAAGAAGAAGGCCAAA
TCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAA
GCAGGTCGAAGCA
Found at i:12911828 original size:18 final size:17
Alignment explanation
Indices: 12911805--12911868 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 17
12911795 CTAAACCAAT
12911805 TTTAAATTTATTTTGAAA
1 TTTAAATTTATTTT-AAA
* *
12911823 TTTAAATATGTTTTAAAA
1 TTTAAATTTATTTT-AAA
*
12911841 TTTAAATTTAATTTAATA
1 TTTAAATTTATTTTAA-A
12911859 TTTAAATTTA
1 TTTAAATTTA
12911869 AAAATATTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 2 0.05
18 37 0.95
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:12911869 original size:18 final size:18
Alignment explanation
Indices: 12911805--12911886 Score: 71
Period size: 18 Copynumber: 4.6 Consensus size: 18
12911795 CTAAACCAAT
*
12911805 TTTAAATTTATTTTGAA-A
1 TTTAAATTTAATTT-AATA
* ** *
12911823 TTTAAATATGTTTTAAAA
1 TTTAAATTTAATTTAATA
12911841 TTTAAATTTAATTTAATA
1 TTTAAATTTAATTTAATA
*
12911859 TTTAAATTTAA--AAATA
1 TTTAAATTTAATTTAATA
12911875 TTCTAAATTTAA
1 TT-TAAATTTAA
12911887 ATAAACAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
16 6 0.11
17 11 0.20
18 38 0.69
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTAAATTTAATTTAATA
Found at i:12911888 original size:6 final size:6
Alignment explanation
Indices: 12911838--12911870 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
12911828 ATATGTTTTA
12911838 AAATTT AAATTT -AATTT AATATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AA-ATTT AAATTT AAA
12911871 AATATTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:12913834 original size:30 final size:30
Alignment explanation
Indices: 12913796--12913864 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
12913786 CCCAAAAGGT
* *
12913796 CCCT-AAACTGCCCAAAAATCATATTTTGA
1 CCCTCAAACTGACCAAAAATCACATTTTGA
* * *
12913825 CCCTCAAACTTACCAAAAGTTACATTTTGA
1 CCCTCAAACTGACCAAAAATCACATTTTGA
12913855 CCCTCAAACT
1 CCCTCAAACT
12913865 TTCCAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.36, C:0.30, G:0.06, T:0.28
Consensus pattern (30 bp):
CCCTCAAACTGACCAAAAATCACATTTTGA
Found at i:12913865 original size:30 final size:30
Alignment explanation
Indices: 12913818--12913880 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
12913808 CAAAAATCAT
12913818 ATTTTGACCCTCAAACTTACCAAAAGTTAC
1 ATTTTGACCCTCAAACTTACCAAAAGTTAC
* *
12913848 ATTTTGACCCTCAAACTTTCCAAAATTTAC
1 ATTTTGACCCTCAAACTTACCAAAAGTTAC
12913878 ATT
1 ATT
12913881 ATCACGAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (30 bp):
ATTTTGACCCTCAAACTTACCAAAAGTTAC
Found at i:12913928 original size:29 final size:29
Alignment explanation
Indices: 12913894--12914380 Score: 277
Period size: 29 Copynumber: 16.6 Consensus size: 29
12913884 ACGAACTTCA
12913894 CAAAAATTACCA-TTTTACCCCTAAATTTC
1 CAAAAATTACCATTTTTA-CCCTAAATTTC
* * *
12913923 CAAAAATT-CCATTTTTGACCTTGAACTGTCC
1 CAAAAATTACCATTTTT-ACCCT-AAAT-TTC
* *
12913954 CAAAAATTACCA-TTTTATCCTCAAATGTC
1 CAAAAATTACCATTTTTACCCT-AAATTTC
*
12913983 CAAAAATT-CCATTTTTGACCCTAAACTTC
1 CAAAAATTACCATTTTT-ACCCTAAATTTC
* * ** *
12914012 CTAAAAACTACCA-TTTTACCTTCGACTTC
1 C-AAAAATTACCATTTTTACCCTAAATTTC
*
12914041 CAAAAATT-CCATTTTTAACCCCAAACTTTC
1 CAAAAATTACCATTTTT-ACCCTAAA-TTTC
* * * *
12914071 CCAAAATTACCA-TTTTATCCTCGAATGTC
1 CAAAAATTACCATTTTTACCCT-AAATTTC
* * *
12914100 CAAAAATT-CCATTTTTGACTCTGAACTTC
1 CAAAAATTACCATTTTT-ACCCTAAATTTC
*
12914129 CAAAAAATTACCATTTTTACCCCTAAACTTC
1 C-AAAAATTACCATTTTTA-CCCTAAATTTC
*
12914160 CAAAAATT-CCATTTTTAACCCTGAACTTTC
1 CAAAAATTACCATTTTT-ACCCT-AAATTTC
* * * * **
12914190 C-CAAATCACCATTTTAACCCCAAACATC
1 CAAAAATTACCATTTTTACCCTAAATTTC
* * *
12914218 C-AAAATTTCCATTTTTACCCCAATTTTC
1 CAAAAATTACCATTTTTACCCTAAATTTC
* *
12914246 CTAAAATTACCA-TTTTACCCTCAAACTTC
1 CAAAAATTACCATTTTTACCCT-AAATTTC
* * *
12914275 CAATAATT-CTATTTTTAACCTCAAACTTTC
1 CAAAAATTACCATTTTTACCCT-AAA-TTTC
* * ** *
12914305 CCAAAATTATCA-TTTTACCCCCGAATGTC
1 CAAAAATTACCATTTTTA-CCCTAAATTTC
* * *
12914334 CAAAAATT-CAATTTTTGA-CCTCCAACTTC
1 CAAAAATTACCATTTTT-ACCCT-AAATTTC
12914363 CTAAAAATTACCATTTTT
1 C-AAAAATTACCATTTTT
12914381 CCTGGGCATC
Statistics
Matches: 350, Mismatches: 75, Indels: 64
0.72 0.15 0.13
Matches are distributed among these distances:
27 3 0.01
28 58 0.17
29 142 0.41
30 96 0.27
31 48 0.14
32 3 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (29 bp):
CAAAAATTACCATTTTTACCCTAAATTTC
Done.