Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 173 of 207
Found at i:53433534 original size:23 final size:23
Alignment explanation
Indices: 53433508--53433606 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
53433498 ATAACTGCAA
53433508 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
53433531 CACTGAAATGTAGCCTAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
53433554 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
53433577 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53433600 CACTGAT
1 CACTGAT
53433607 CAATAACACT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:53433575 original size:46 final size:46
Alignment explanation
Indices: 53433508--53433606 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
53433498 ATAACTGCAA
* *
53433508 CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCTAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTAC
*
53433554 CACTGTTATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTAC
53433600 CACTGAT
1 CACTGAT
53433607 CAATAACACT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (46 bp):
CACTGATATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTAC
Found at i:53442218 original size:6 final size:6
Alignment explanation
Indices: 53442203--53442255 Score: 79
Period size: 6 Copynumber: 8.7 Consensus size: 6
53442193 AAGTTTCCAC
* *
53442203 AAATGG AAATGA AAATGG AAATGA AAATGA AAATGA AAATGA AAATGGA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAAT-GA
53442252 AAAT
1 AAAT
53442256 TGCAATCCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
6 37 0.86
7 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (6 bp):
AAATGA
Found at i:53445924 original size:6 final size:6
Alignment explanation
Indices: 53445915--53445939 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
53445905 GTAAAAGTGA
53445915 ATGTGT ATGTGT ATGTGT ATGTGT A
1 ATGTGT ATGTGT ATGTGT ATGTGT A
53445940 AATAAAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (6 bp):
ATGTGT
Found at i:53447541 original size:24 final size:24
Alignment explanation
Indices: 53447514--53447569 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
53447504 AATATTTTAA
*
53447514 TATATAAT-ATTAATTTTAAATATT
1 TATA-AATAATTAATATTAAATATT
* *
53447538 TATAAGTAATTAATATTAATTATT
1 TATAAATAATTAATATTAAATATT
53447562 TATTAAAT
1 TA-TAAAT
53447570 TTAATTAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 20 0.77
25 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATAAATAATTAATATTAAATATT
Found at i:53448539 original size:22 final size:22
Alignment explanation
Indices: 53448498--53448540 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
53448488 TATCCAAATA
*
53448498 ATAATAACAAAATAGTAGCAAT
1 ATAATAACAAAATAGCAGCAAT
53448520 ATAATAACAAAAT-GACAGCAA
1 ATAATAACAAAATAG-CAGCAA
53448541 AACAATGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAATAACAAAATAGCAGCAAT
Found at i:53451441 original size:6 final size:6
Alignment explanation
Indices: 53451425--53451468 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
53451415 ACGGTGGTGC
* * * *
53451425 TGGAGG GGGAGG TGGAGG TGGAGG AGGAGG CGGAGG AGGAGG TG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TG
53451469 CCTCTGGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.20, C:0.02, G:0.68, T:0.09
Consensus pattern (6 bp):
TGGAGG
Found at i:53451560 original size:9 final size:9
Alignment explanation
Indices: 53451546--53451575 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
53451536 GGGAGGAGGT
53451546 GGTGGTGGA
1 GGTGGTGGA
53451555 GGTGGTGGA
1 GGTGGTGGA
*
53451564 GGTGGTGAA
1 GGTGGTGGA
53451573 GGT
1 GGT
53451576 AGTGCTAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.63, T:0.23
Consensus pattern (9 bp):
GGTGGTGGA
Found at i:53451916 original size:6 final size:6
Alignment explanation
Indices: 53451907--53451938 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
53451897 TGGTGGTGGG
*
53451907 GGAGGA GGAGGT GGAGGT GGAGGT GGAGGT GG
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GG
53451939 GGCTAAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.69, T:0.12
Consensus pattern (6 bp):
GGAGGT
Found at i:53452009 original size:6 final size:6
Alignment explanation
Indices: 53451998--53452028 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
53451988 GTTGGGACTA
*
53451998 GTGGAG GTGGAG GTGGAG GTGAAG GTGGAG G
1 GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG G
53452029 AGGTGGCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.65, T:0.16
Consensus pattern (6 bp):
GTGGAG
Found at i:53452119 original size:3 final size:3
Alignment explanation
Indices: 53452111--53452154 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
53452101 AGAGGTGGGA
* * * *
53452111 GGT GGT GGT GGC GGT GGT GGT GGA GGT GGA GGT GGG GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
53452155 AAGCTCTAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.05, C:0.02, G:0.70, T:0.23
Consensus pattern (3 bp):
GGT
Found at i:53452126 original size:6 final size:6
Alignment explanation
Indices: 53452102--53452151 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
53452092 TGCAGGCATA
* * * *
53452102 GAGGTGG GAGGTG GTGGTG GCGGTG GTGGTG GAGGTG GAGGTG GGGGTG
1 GAGGT-G GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG
53452151 G
1 G
53452152 TGGAAGCTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.08, C:0.02, G:0.70, T:0.20
Consensus pattern (6 bp):
GAGGTG
Found at i:53452128 original size:12 final size:12
Alignment explanation
Indices: 53452108--53452154 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
53452098 CATAGAGGTG
53452108 GGAGGTGGTGGT
1 GGAGGTGGTGGT
*
53452120 GGCGGTGGTGGT
1 GGAGGTGGTGGT
*
53452132 GGAGGTGGAGGT
1 GGAGGTGGTGGT
*
53452144 GGGGGTGGTGG
1 GGAGGTGGTGG
53452155 AAGCTCTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.06, C:0.02, G:0.70, T:0.21
Consensus pattern (12 bp):
GGAGGTGGTGGT
Found at i:53452292 original size:18 final size:18
Alignment explanation
Indices: 53452271--53452306 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53452261 GGTGGTTCGA
* *
53452271 GTGGAGGTGGAGGCGGAG
1 GTGGAAGTGGAGGAGGAG
53452289 GTGGAAGTGGAGGAGGAG
1 GTGGAAGTGGAGGAGGAG
53452307 AAGGGATGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.64, T:0.11
Consensus pattern (18 bp):
GTGGAAGTGGAGGAGGAG
Found at i:53453944 original size:89 final size:89
Alignment explanation
Indices: 53453793--53453971 Score: 358
Period size: 89 Copynumber: 2.0 Consensus size: 89
53453783 CATAGTGAGA
53453793 AAGAATGTTTTCCTTCAGCAAAAATATAGGGTCGGTTTAGTTTTTTCATGTACTTGGAGGGCTCT
1 AAGAATGTTTTCCTTCAGCAAAAATATAGGGTCGGTTTAGTTTTTTCATGTACTTGGAGGGCTCT
53453858 TAGAGGATTATATCACAAACCAAT
66 TAGAGGATTATATCACAAACCAAT
53453882 AAGAATGTTTTCCTTCAGCAAAAATATAGGGTCGGTTTAGTTTTTTCATGTACTTGGAGGGCTCT
1 AAGAATGTTTTCCTTCAGCAAAAATATAGGGTCGGTTTAGTTTTTTCATGTACTTGGAGGGCTCT
53453947 TAGAGGATTATATCACAAACCAAT
66 TAGAGGATTATATCACAAACCAAT
53453971 A
1 A
53453972 TAAAAAAATG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (89 bp):
AAGAATGTTTTCCTTCAGCAAAAATATAGGGTCGGTTTAGTTTTTTCATGTACTTGGAGGGCTCT
TAGAGGATTATATCACAAACCAAT
Found at i:53473061 original size:17 final size:17
Alignment explanation
Indices: 53473039--53473077 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
53473029 TATAATCAAT
53473039 TTTAAAATTTTAATATA
1 TTTAAAATTTTAATATA
53473056 TTTAAAATTTTAATATA
1 TTTAAAATTTTAATATA
*
53473073 CTTAA
1 TTTAA
53473078 TATATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAAATTTTAATATA
Found at i:53473412 original size:14 final size:15
Alignment explanation
Indices: 53473382--53473413 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53473372 TCTCCAAATT
53473382 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
53473397 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
53473411 TTT
1 TTT
53473414 TTATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:53473542 original size:126 final size:126
Alignment explanation
Indices: 53473317--53473565 Score: 462
Period size: 126 Copynumber: 2.0 Consensus size: 126
53473307 TGAAAAACAT
*
53473317 GACTCGAAATACCCATTTCAGAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
1 GACTCGAAATACCCATTTCAAAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
*
53473382 TTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTTCAAATTACGATTACAG
66 TTTAAGTTTTCAAAATTTAAATTTTAAAATTTTTATTACAAATTTCAAATTACGATTACAG
* *
53473443 GACTCTAAATACCCATTTCAAAAATCAAAACTTGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
1 GACTCGAAATACCCATTTCAAAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
53473508 TTTAAGTTTTCAAAATTTAAATTTTAAAATTTTTATTACAAATTTCAAATTACGATTA
66 TTTAAGTTTTCAAAATTTAAATTTTAAAATTTTTATTACAAATTTCAAATTACGATTA
53473566 TCTCATTCCA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 119 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.39
Consensus pattern (126 bp):
GACTCGAAATACCCATTTCAAAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
TTTAAGTTTTCAAAATTTAAATTTTAAAATTTTTATTACAAATTTCAAATTACGATTACAG
Found at i:53481009 original size:14 final size:15
Alignment explanation
Indices: 53480979--53481010 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53480969 TCTCCAAATT
53480979 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
53480994 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
53481008 TTT
1 TTT
53481011 TTATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:53481139 original size:126 final size:126
Alignment explanation
Indices: 53480914--53481162 Score: 462
Period size: 126 Copynumber: 2.0 Consensus size: 126
53480904 TGAAAAACAT
*
53480914 GACTCGAAATACCCATTTCAGAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
1 GACTCGAAATACCCATTTCAAAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
*
53480979 TTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTTCAAATTACGATTACAG
66 TTTAAGTTTTCAAAATTTAAATTTTAAAATTTTTATTACAAATTTCAAATTACGATTACAG
* *
53481040 GACTCTAAATACCCATTTCAAAAATCAAAACTTGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
1 GACTCGAAATACCCATTTCAAAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
53481105 TTTAAGTTTTCAAAATTTAAATTTTAAAATTTTTATTACAAATTTCAAATTACGATTA
66 TTTAAGTTTTCAAAATTTAAATTTTAAAATTTTTATTACAAATTTCAAATTACGATTA
53481163 TCATATATTT
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 119 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.39
Consensus pattern (126 bp):
GACTCGAAATACCCATTTCAAAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
TTTAAGTTTTCAAAATTTAAATTTTAAAATTTTTATTACAAATTTCAAATTACGATTACAG
Found at i:53481255 original size:9 final size:8
Alignment explanation
Indices: 53481227--53481258 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
53481217 AAGTATAACC
53481227 AATTTTAA
1 AATTTTAA
53481235 AATTTTAA
1 AATTTTAA
53481243 AATTTTAA
1 AATTTTAA
*
53481251 AAATTTAA
1 AATTTTAA
53481259 TATATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AATTTTAA
Found at i:53481313 original size:8 final size:8
Alignment explanation
Indices: 53481300--53481357 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
53481290 TTTTTAATAT
53481300 ATTTAAAA
1 ATTTAAAA
53481308 ATTTAAAA
1 ATTTAAAA
53481316 ATTTTAAAA
1 A-TTTAAAA
*
53481325 ACTTAAAAAA
1 A-TT-TAAAA
*
53481335 ATTTAAAT
1 ATTTAAAA
53481343 ATATTAAAA
1 AT-TTAAAA
*
53481352 TTTTAA
1 ATTTAA
53481358 TATACTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
8 18 0.44
9 18 0.44
10 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
ATTTAAAA
Found at i:53481316 original size:9 final size:9
Alignment explanation
Indices: 53481300--53481341 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
53481290 TTTTTAATAT
53481300 ATTT-AAAA
1 ATTTAAAAA
53481308 ATTTAAAAA
1 ATTTAAAAA
*
53481317 TTTTAAAAA
1 ATTTAAAAA
* *
53481326 CTTAAAAAA
1 ATTTAAAAA
53481335 ATTTAAA
1 ATTTAAA
53481342 TATATTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
8 4 0.14
9 24 0.86
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:53481321 original size:17 final size:17
Alignment explanation
Indices: 53481301--53481357 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
53481291 TTTTAATATA
53481301 TTTAAAAATTTAAAAAT
1 TTTAAAAATTTAAAAAT
* *
53481318 TTTAAAAACTTAAAAAAA
1 TTTAAAAA-TTTAAAAAT
*
53481336 TTTAAATATATT-AAAAT
1 TTTAAAAAT-TTAAAAAT
53481353 TTTAA
1 TTTAA
53481358 TATACTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 18 0.55
18 15 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTAAAAATTTAAAAAT
Found at i:53481349 original size:9 final size:9
Alignment explanation
Indices: 53481337--53481386 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
53481327 TTAAAAAAAT
53481337 TTAAATATA
1 TTAAATATA
53481346 TTAAA-AT-
1 TTAAATATA
*
53481353 TTTAATATA
1 TTAAATATA
53481362 CTT-AATATA
1 -TTAAATATA
53481371 TTAAAATATA
1 TT-AAATATA
53481381 TTAAAT
1 TTAAAT
53481387 TGTAAACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
7 4 0.11
8 6 0.17
9 15 0.43
10 10 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAAATATA
Found at i:53481366 original size:17 final size:16
Alignment explanation
Indices: 53481332--53481403 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 16
53481322 AAAACTTAAA
53481332 AAAATTTAAATATATT
1 AAAATTTAAATATATT
*
53481348 AAAATTTTAATATACTT
1 AAAATTTAAATATA-TT
*
53481365 AATATATTAAAATATATT
1 AA-A-ATTTAAATATATT
*
53481383 -AAATTGTAAACATATTT
1 AAAATT-TAAATATA-TT
53481400 AAAA
1 AAAA
53481404 AAATTAAGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
15 3 0.07
16 20 0.44
17 7 0.16
18 6 0.13
19 9 0.20
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (16 bp):
AAAATTTAAATATATT
Found at i:53481378 original size:35 final size:34
Alignment explanation
Indices: 53481293--53481385 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 34
53481283 AAAAATATTT
53481293 TTAATATATTTAAAA-AT-TTAAAAATTTTAAAAAC
1 TTAATATA-TTAAAATATATT-AAAATTTTAAAAAC
* * * *
53481327 TTAAAAAAATTTAAATATATTAAAATTTTAATATAC
1 TT-AATATATTAAAATATATTAAAATTTTAA-AAAC
53481363 TTAATATATTAAAATATATTAAA
1 TTAATATATTAAAATATATTAAA
53481386 TTGTAAACAT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
34 7 0.15
35 34 0.71
36 7 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (34 bp):
TTAATATATTAAAATATATTAAAATTTTAAAAAC
Found at i:53486336 original size:14 final size:14
Alignment explanation
Indices: 53486319--53486349 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53486309 TTAATTTAGA
53486319 AAATTTAATTAATT
1 AAATTTAATTAATT
*
53486333 AAATTTAGTTAATT
1 AAATTTAATTAATT
53486347 AAA
1 AAA
53486350 AAATCAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:53487105 original size:25 final size:25
Alignment explanation
Indices: 53487071--53487119 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
53487061 CTTGGATATG
53487071 TTAGTTTTAATTTTT-TATTTAAAAT
1 TTAGTTTTAATTTTTCT-TTTAAAAT
53487096 TTAGTTTTAATTTTTCTTTTAAAA
1 TTAGTTTTAATTTTTCTTTTAAAA
53487120 ATTATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (25 bp):
TTAGTTTTAATTTTTCTTTTAAAAT
Found at i:53490093 original size:5 final size:6
Alignment explanation
Indices: 53490080--53490208 Score: 60
Period size: 6 Copynumber: 21.2 Consensus size: 6
53490070 ATAATTTAAT
* * * * * *
53490080 AAATAA AAATAA AATTCTAA AACTAA AACTAA AACTAA AACTAA AACTAA
1 AAATAA AAATAA AA--ATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * * * * * * * *
53490130 AACTAA AACTAA AACTAA GACTAA AACTAA AACTAA AACTAA AACTAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * * * *
53490178 AACTAA AACTAA AACTAA AACTAA AACTAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA A
53490209 GTCTAAAAGT
Statistics
Matches: 118, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
6 113 0.96
8 5 0.04
ACGTcount: A:0.67, C:0.15, G:0.01, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:53490105 original size:6 final size:6
Alignment explanation
Indices: 53490096--53490208 Score: 217
Period size: 6 Copynumber: 18.8 Consensus size: 6
53490086 AAATAAAATT
53490096 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA
*
53490144 CTAAGA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA
53490192 CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAA
53490209 GTCTAAAAGT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 105 1.00
ACGTcount: A:0.65, C:0.17, G:0.01, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:53490262 original size:9 final size:9
Alignment explanation
Indices: 53490248--53490304 Score: 82
Period size: 9 Copynumber: 6.4 Consensus size: 9
53490238 GTAGTGATTC
53490248 AATTCGGTT
1 AATTCGGTT
*
53490257 AATTCGGGT
1 AATTCGGTT
53490266 AATTCAGG-T
1 AATTC-GGTT
53490275 AATTCGGTT
1 AATTCGGTT
53490284 AATTCGG-T
1 AATTCGGTT
53490292 AATTCGGTT
1 AATTCGGTT
53490301 AATT
1 AATT
53490305 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
8 10 0.23
9 32 0.73
10 2 0.05
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:53497643 original size:28 final size:27
Alignment explanation
Indices: 53497578--53497643 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
53497568 TTTAACAGTA
*
53497578 ACAGTACAGTGTGGGCCTTAGCCCAAT
1 ACAGTACAGTGTGGGCCTAAGCCCAAT
*
53497605 ACA-TAAACAGTGTGGGCCTAAGCCCGAT
1 ACAGT--ACAGTGTGGGCCTAAGCCCAAT
*
53497633 TCAGTATCAGT
1 ACAGTA-CAGT
53497644 ATGGTGCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 1 0.03
27 4 0.12
28 26 0.81
29 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (27 bp):
ACAGTACAGTGTGGGCCTAAGCCCAAT
Found at i:53497894 original size:32 final size:32
Alignment explanation
Indices: 53497840--53498091 Score: 229
Period size: 32 Copynumber: 7.9 Consensus size: 32
53497830 AGTAGTACAA
* * *
53497840 TAATGTGATTGGCACAAAGCCATCAGTAGCAG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
** ** * *
53497872 CGATATGATCAACACACAGCCATGAGTAACAG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * * * *
53497904 TAACATGATCAGCACAAAGCCATTAGTAGCCG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * *
53497936 TAATATGATCGGCATACATCCATCAGTAACAG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * *
53497968 TGAA-ATGATCGGCACACAGCCATTAGTAACGG
1 T-AATATGATCGGCACAAAGCCATCAGTAACAG
53498000 TAATATGATCGGCACAAAGCCATCAGTAACAG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * *
53498032 TACTATGATCGACACAAAGCTATCAGTAAC-G
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * * *
53498063 ATACTATGATTGGCACAAAACCATTAGTA
1 -TAATATGATCGGCACAAAGCCATCAGTA
53498092 GCATCGCAGC
Statistics
Matches: 177, Mismatches: 40, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
31 3 0.02
32 172 0.97
33 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAACAG
Found at i:53498072 original size:96 final size:96
Alignment explanation
Indices: 53497852--53498091 Score: 259
Period size: 96 Copynumber: 2.5 Consensus size: 96
53497842 ATGTGATTGG
* * ** *
53497852 CACAAAGCCATCAGTAGCAGCGATATGATCAACACACAGCCATGAGTAACAGTAACATGATCAGC
1 CACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATTAGTAACAGTAACATGATCAGC
* * * *
53497917 ACAAAGCCATTAGTAGCCGTAATATGATCGG
66 ACAAAGCCATCAGTAACAGTAATATGATCGA
* * * * * * *
53497948 CATACATCCATCAGTAACAGTGAAATGATCGGCACACAGCCATTAGTAACGGTAATATGATCGGC
1 CACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATTAGTAACAGTAACATGATCAGC
*
53498013 ACAAAGCCATCAGTAACAGTACTATGATCGA
66 ACAAAGCCATCAGTAACAGTAATATGATCGA
* * * *
53498044 CACAAAGCTATCAGTAAC-GAT-ACTATGATTGGCACAAAACCATTAGTA
1 CACAAAGCCATCAGTAACAG-TGA-TATGATCGGCACACAGCCATTAGTA
53498092 GCATCGCAGC
Statistics
Matches: 117, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
95 2 0.02
96 115 0.98
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (96 bp):
CACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATTAGTAACAGTAACATGATCAGC
ACAAAGCCATCAGTAACAGTAATATGATCGA
Found at i:53498123 original size:26 final size:26
Alignment explanation
Indices: 53498094--53498147 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
53498084 CATTAGTAGC
*
53498094 ATCGCAGCAAAGCTGCCAGCAACAGT
1 ATCGCAGCAAAGCTACCAGCAACAGT
* *
53498120 ATCGCAGCAAAGCTACCAGTAATAGT
1 ATCGCAGCAAAGCTACCAGCAACAGT
53498146 AT
1 AT
53498148 ATGTGGTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (26 bp):
ATCGCAGCAAAGCTACCAGCAACAGT
Found at i:53498164 original size:27 final size:26
Alignment explanation
Indices: 53498129--53498194 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
53498119 TATCGCAGCA
* *
53498129 AAGCTACCAGTAATAGT-ATATGTGGTC
1 AAGCCACCAGTAACAGTGAT-TGTGG-C
53498156 AAGCCACCAGTAACAGTGATTGTGGC
1 AAGCCACCAGTAACAGTGATTGTGGC
53498182 AGAGCCACCAGTA
1 A-AGCCACCAGTA
53498195 CAATACTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 2 0.06
27 31 0.89
28 2 0.06
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (26 bp):
AAGCCACCAGTAACAGTGATTGTGGC
Found at i:53498441 original size:27 final size:27
Alignment explanation
Indices: 53498366--53498778 Score: 304
Period size: 27 Copynumber: 15.4 Consensus size: 27
53498356 GACAAAAATA
53498366 GTCA-TTTACCC-ACTA-GGGCATTACG
1 GTCATTTTACCCTAC-AGGGGCATTACG
* *
53498391 GTCATTTTA-CCTACAGGGGTATTAGG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
53498417 GTCATTTGACCCTACATGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
53498444 GTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
53498471 ATCATTTTACCCTATAGAGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * * *
53498498 ATCATTTTATCCTATAGAGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
53498525 GCCATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
53498552 GTCATTTTACCTTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * **
53498579 GTCATTTTACCCTACAAGGGTATTATA
1 GTCATTTTACCCTACAGGGGCATTACG
* **
53498606 GTCATTTTACCCTACAGGGGTATTTTG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * *
53498633 GT-ATTCTACCCTACGGGGGTATTTCG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * * *
53498659 ATTATTTTACCATA-TGGGAGCATTTCG
1 GTCATTTTACCCTACAGGG-GCATTACG
* * *
53498686 GT-TTTCTTACCC-ATC-GAGGGTATTTCG
1 GTCATT-TTACCCTA-CAG-GGGCATTACG
* * ** * *
53498713 ATTATTTTACCCTATGGGGGCATTTCA
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
53498740 GTCATTTTATCTTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
53498767 GTCATTTTACCC
1 GTCATTTTACCC
53498779 ATCGAGGGTA
Statistics
Matches: 319, Mismatches: 56, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
25 7 0.02
26 50 0.16
27 256 0.80
28 6 0.02
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:53498827 original size:27 final size:27
Alignment explanation
Indices: 53498528--53498849 Score: 153
Period size: 27 Copynumber: 12.0 Consensus size: 27
53498518 CATTACAGCC
* * *
53498528 ATTTTACCCTATAG-GGGTATTACGGTC
1 ATTTTACCCT-TCGAGGGTATTTCGGTT
* *
53498555 ATTTTA-CCTTAC-AGGGGTATTACGGTC
1 ATTTTACCCTT-CGA-GGGTATTTCGGTT
* * * *
53498582 ATTTTACCCTACAAGGGTATTAT-AGTC
1 ATTTTACCCTTCGAGGGTATT-TCGGTT
* *
53498609 ATTTTACCCTAC-AGGGGTATTTTGG-T
1 ATTTTACCCTTCGA-GGGTATTTCGGTT
* * * *
53498635 ATTCTACCCTACGGGGGTATTTCGATT
1 ATTTTACCCTTCGAGGGTATTTCGGTT
* *
53498662 ATTTTACCATAT-G-GGAGCATTTCGGTT
1 ATTTTACCCT-TCGAGG-GTATTTCGGTT
* *
53498689 -TTCTTACCCATCGAGGGTATTTCGATT
1 ATT-TTACCCTTCGAGGGTATTTCGGTT
* * * *
53498716 ATTTTACCCTAT-GGGGGCATTTCAGTC
1 ATTTTACCCT-TCGAGGGTATTTCGGTT
* ** * * *
53498743 ATTTTA-TCTTATAGGGGCATTACGGTC
1 ATTTTACCCTTCGA-GGGTATTTCGGTT
* * *
53498770 ATTTTACCCATCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGGTT
*
53498797 ATTTTACCCTTCGAGGGTATTTTGGTT
1 ATTTTACCCTTCGAGGGTATTTCGGTT
* * *
53498824 ATTTTACCTTTTGGGGGTATTTCGGT
1 ATTTTACCCTTCGAGGGTATTTCGGT
53498850 CCAGATATTA
Statistics
Matches: 230, Mismatches: 45, Indels: 40
0.73 0.14 0.13
Matches are distributed among these distances:
25 2 0.01
26 32 0.14
27 184 0.80
28 12 0.05
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGGTT
Found at i:53498828 original size:81 final size:81
Alignment explanation
Indices: 53498366--53498831 Score: 296
Period size: 81 Copynumber: 5.8 Consensus size: 81
53498356 GACAAAAATA
* * * * * ** *
53498366 GTCA-TTTACCCA-CTAGGGCATTACGGTCATTTTA-CCTAC-AGGGGTATTAGGGTCATTTGAC
1 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCTTCGA-GGGTATTTCGGTCATTTTAC
* *
53498427 CCTACATGGGCATTACG
65 CCTATAGGGGCATTACG
* * * * * * *
53498444 GTCATTTTACCC-TACAAGGGCATTACGATCATTTTACCCTATAGA-GGCATTACGATCATTTTA
1 GTCATTTTACCCAT-CGAGGGTATTTCGATCATTTTACCCT-TCGAGGGTATTTCGGTCATTTTA
* * *
53498507 TCCTATAGAGGCATTACA
64 CCCTATAGGGGCATTACG
* * * * *
53498525 GCCATTTTACCCTATAG-GGGTATTACGGTCATTTTA-CCTTAC-AGGGGTATTACGGTCATTTT
1 GTCATTTTACCC-ATCGAGGGTATTTCGATCATTTTACCCTT-CGA-GGGTATTTCGGTCATTTT
* * * **
53498587 ACCCTACAAGGGTATTATA
63 ACCCTATAGGGGCATTACG
* * * * * * *
53498606 GTCATTTTACCC-TAC-AGGGGTATTTTGGT-ATTCTACCCTACGGGGGTATTTCGATTATTTTA
1 GTCATTTTACCCAT-CGA-GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTA
* *
53498668 CCATAT-GGGAGCATTTCG
64 CCCTATAGGG-GCATTACG
* * * * *
53498686 GT-TTTCTTACCCATCGAGGGTATTTCGATTATTTTACCCTAT-GGGGGCATTTCAGTCATTTTA
1 GTCATT-TTACCCATCGAGGGTATTTCGATCATTTTACCCT-TCGAGGGTATTTCGGTCATTTTA
* *
53498749 TCTTATAGGGGCATTACG
64 CCCTATAGGGGCATTACG
* *
53498767 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTGGTTATTTTACC
1 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACC
53498832 TTTTGGGGGT
Statistics
Matches: 299, Mismatches: 64, Indels: 47
0.73 0.16 0.11
Matches are distributed among these distances:
78 4 0.01
79 14 0.05
80 73 0.24
81 201 0.67
82 5 0.02
83 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (81 bp):
GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACC
CTATAGGGGCATTACG
Found at i:53498842 original size:54 final size:54
Alignment explanation
Indices: 53498380--53498850 Score: 265
Period size: 54 Copynumber: 8.8 Consensus size: 54
53498370 TTTACCCACT
* * ** * *
53498380 AGGGCATTACGGTCATTTTA-CCTACAGGGGTATTAGGGTCATTTGACCCTAC-
1 AGGGTATTACGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACCCTTCG
* ** * * * *
53498432 ATGGGCATTACGGTCATTTTACCCTACAAGGGCATTACGATCATTTTACCCTATAG
1 A-GGGTATTACGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACCCT-TCG
* * * ** * * * * * *
53498488 A-GGCATTACGATCATTTTATCCTATAGAGGCATTACAGCCATTTTACCCTATAG
1 AGGGTATTACGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACCCT-TCG
* * * * *
53498542 -GGGTATTACGGTCATTTTACCTTACAGGGGTATTACGGTCATTTTACCCTACA
1 AGGGTATTACGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACCCTTCG
** * * * *
53498595 AGGGTATTATAGTCATTTTACCCTACAGGGGTATTTTGGT-ATTCTACCCTACG
1 AGGGTATTACGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACCCTTCG
* * * * * * * * * *
53498648 GGGGTATTTCGATTATTTTACCATATGGGAGCATTTCGGT-TTTCTTACCCATCG
1 AGGGTATTACGGTCATTTTACCCTACGGGGGTATTTCGGTCATT-TTACCCTTCG
* * * * * * * **
53498702 AGGGTATTTCGATTATTTTACCCTATGGGGGCATTTCAGTCATTTTA-TCTTAT
1 AGGGTATTACGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACCCTTCG
* * *
53498755 AGGGGCATTACGGTCATTTTACCC-ATCGAGGGTATTTCGATCATTTTACCCTTCG
1 A-GGGTATTACGGTCATTTTACCCTA-CGGGGGTATTTCGGTCATTTTACCCTTCG
** * * **
53498810 AGGGTATTTTGGTTATTTTACCTTTTGGGGGTATTTCGGTC
1 AGGGTATTACGGTCATTTTACCCTACGGGGGTATTTCGGTC
53498851 CAGATATTAA
Statistics
Matches: 327, Mismatches: 80, Indels: 22
0.76 0.19 0.05
Matches are distributed among these distances:
52 1 0.00
53 64 0.20
54 255 0.78
55 6 0.02
56 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (54 bp):
AGGGTATTACGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACCCTTCG
Found at i:53501931 original size:9 final size:9
Alignment explanation
Indices: 53501917--53501976 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
53501907 TTTGGTTAAA
53501917 AATTACCCG
1 AATTACCCG
*
53501926 AATTACCCAAA
1 AATTACCC--G
53501937 AATTACCCG
1 AATTACCCG
*
53501946 AATTACCTG
1 AATTACCCG
53501955 AATTACCCG
1 AATTACCCG
*
53501964 AATTACCTG
1 AATTACCCG
53501973 AATT
1 AATT
53501977 GTATCACTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
9 36 0.82
11 8 0.18
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (9 bp):
AATTACCCG
Found at i:53501939 original size:20 final size:20
Alignment explanation
Indices: 53501914--53501970 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
53501904 ATTTTTGGTT
53501914 AAAAATTACCCGAATTACCC
1 AAAAATTACCCGAATTACCC
53501934 AAAAATTACCCGAATTA-CC
1 AAAAATTACCCGAATTACCC
**
53501953 -TGAATTACCCGAATTACC
1 AAAAATTACCCGAATTACC
53501971 TGAATTGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 14 0.41
19 3 0.09
20 17 0.50
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAAATTACCCGAATTACCC
Found at i:53501960 original size:18 final size:18
Alignment explanation
Indices: 53501917--53501976 Score: 84
Period size: 18 Copynumber: 3.2 Consensus size: 18
53501907 TTTGGTTAAA
**
53501917 AATTACCCGAATTACCCAAA
1 AATTACCCGAATTA-CC-TG
53501937 AATTACCCGAATTACCTG
1 AATTACCCGAATTACCTG
53501955 AATTACCCGAATTACCTG
1 AATTACCCGAATTACCTG
53501973 AATT
1 AATT
53501977 GTATCACTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 22 0.58
19 2 0.05
20 14 0.37
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTACCCGAATTACCTG
Found at i:53502006 original size:17 final size:17
Alignment explanation
Indices: 53501984--53502044 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
53501974 ATTGTATCAC
53501984 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
53502001 TACATAAATCTTTGAATCAC
1 TACAT-AA--TTAAAAACAT
53502021 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
53502038 TACATAA
1 TACATAA
53502045 GTCTTGAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 18 0.55
18 2 0.06
19 2 0.06
20 11 0.33
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:53502025 original size:37 final size:37
Alignment explanation
Indices: 53501979--53502049 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
53501969 CCTGAATTGT
53501979 ATCACTACATAATTAAAAACATTACATAAATCTTTGA
1 ATCACTACATAATTAAAAACATTACATAAATCTTTGA
*
53502016 ATCACTACATAATTAAAAACATTACATAAGTCTT
1 ATCACTACATAATTAAAAACATTACATAAATCTT
53502050 GAAATTAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (37 bp):
ATCACTACATAATTAAAAACATTACATAAATCTTTGA
Found at i:53502063 original size:37 final size:37
Alignment explanation
Indices: 53501982--53502066 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
53501972 GAATTGTATC
*
53501982 ACTACATAATTAAAAACATTACATAAATCTTTGAATC
1 ACTACATAATTAAAAACATTACATAAATCTTTGAATA
*
53502019 ACTACATAATTAAAAACATTACATAAGTC-TTGAAATTA
1 ACTACATAATTAAAAACATTACATAAATCTTTG-AA-TA
53502057 AC-ACATAATT
1 ACTACATAATT
53502067 GAAATGTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 3 0.07
37 38 0.86
38 3 0.07
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (37 bp):
ACTACATAATTAAAAACATTACATAAATCTTTGAATA
Found at i:53504327 original size:234 final size:234
Alignment explanation
Indices: 53503918--53504380 Score: 847
Period size: 234 Copynumber: 2.0 Consensus size: 234
53503908 CATCTAAATG
53503918 CAATTGATAAACATCCCTAGTCATAGTAGTTCGTGAAGGAATATGAAACCTAGGACATGCCACAA
1 CAATTGATAAACATCCCTAGTCATAGTAGTTCGTGAAGGAATATGAAACCTAGGACATGCCACAA
*
53503983 ACATAAATTTTTTAAAACCTTCACTTTCAACAAACTTGAAAGGTAATTCATCAATCACAATCATT
66 ACATAAATTTCTTAAAACCTTCACTTTCAACAAACTTGAAAGGTAATTCATCAATCACAATCATT
*
53504048 TGTGCTAATTCTTTCCTACATGCTTCTCGATCAAATCTCCAAGTTGAAAGATTCCTTTCCCCCCT
131 TGTGCTAATTCTTTCCTACATGCTTCTCGATCAAATCTCCAAGTTGAAAGATTCCCTTCCCCCCT
*
53504113 TCAACTCCCTTTCTAGGTAAAACTAGTTGTCCTTTCCTA
196 TCAACTCCCTTTCTAGGTAAAACTAGTTGCCCTTTCCTA
* *
53504152 CAATTGATAAATATTCCTAGTCATAGTAGTTCGTGAAGGAATATGAAACCTAGGACATGCCACAA
1 CAATTGATAAACATCCCTAGTCATAGTAGTTCGTGAAGGAATATGAAACCTAGGACATGCCACAA
*
53504217 ACATAAGTTTCTTAAAACCTTCACTTTCAACAAACTTGAAAGGTAATTCATCAATCACAATCATT
66 ACATAAATTTCTTAAAACCTTCACTTTCAACAAACTTGAAAGGTAATTCATCAATCACAATCATT
*
53504282 TGTGCTAA-TCTTTTCCTACATGCTTCTTGATCAAATCTCCAAGTTGAAAGATTCCCTTCCCCCC
131 TGTGCTAATTC-TTTCCTACATGCTTCTCGATCAAATCTCCAAGTTGAAAGATTCCCTTCCCCCC
53504346 TTCAACTCCCTTTCTAGGTAAAACTAGTTGCCCTT
195 TTCAACTCCCTTTCTAGGTAAAACTAGTTGCCCTT
53504381 GACTAGTGTC
Statistics
Matches: 221, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
233 2 0.01
234 219 0.99
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (234 bp):
CAATTGATAAACATCCCTAGTCATAGTAGTTCGTGAAGGAATATGAAACCTAGGACATGCCACAA
ACATAAATTTCTTAAAACCTTCACTTTCAACAAACTTGAAAGGTAATTCATCAATCACAATCATT
TGTGCTAATTCTTTCCTACATGCTTCTCGATCAAATCTCCAAGTTGAAAGATTCCCTTCCCCCCT
TCAACTCCCTTTCTAGGTAAAACTAGTTGCCCTTTCCTA
Found at i:53507009 original size:43 final size:43
Alignment explanation
Indices: 53506903--53507084 Score: 179
Period size: 43 Copynumber: 4.3 Consensus size: 43
53506893 CACACCCCTA
* * * * *
53506903 ACGCCAGTGTGGCCAGGCTGTGTGTCTCACATGGCTAAGAGGC
1 ACGCCTGTGTGGCCAGGCCGTGAGTCTCACATGGCCAAGAGAC
* * ***
53506946 AC-CCTATCTGGCCAGGCCGTGAGTCTCACAAATCCAAGAGAC
1 ACGCCTGTGTGGCCAGGCCGTGAGTCTCACATGGCCAAGAGAC
53506988 ACGCCTGTGTGGCCAGGCCGTGCA-TCTCACATGGCCAAGAGAC
1 ACGCCTGTGTGGCCAGGCCGTG-AGTCTCACATGGCCAAGAGAC
* * * * * *
53507031 ATGCCGGTGTGGCCAGGCTGAGTGTCTCACACGGCCAAGAGAC
1 ACGCCTGTGTGGCCAGGCCGTGAGTCTCACATGGCCAAGAGAC
* *
53507074 ACCCCCGTGTG
1 ACGCCTGTGTG
53507085 TCTTACACAG
Statistics
Matches: 112, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
42 32 0.29
43 79 0.71
44 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.30, T:0.18
Consensus pattern (43 bp):
ACGCCTGTGTGGCCAGGCCGTGAGTCTCACATGGCCAAGAGAC
Found at i:53508393 original size:25 final size:25
Alignment explanation
Indices: 53508365--53508420 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
53508355 AAGCTCCGCT
*
53508365 GAGCTGAATAACGGTAAGGTCATAA
1 GAGCTGAATAACGGTAAGCTCATAA
* * *
53508390 GAGCTGAGTATCTGTAAGCTCATAA
1 GAGCTGAATAACGGTAAGCTCATAA
53508415 GAGCTG
1 GAGCTG
53508421 GAATCGGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (25 bp):
GAGCTGAATAACGGTAAGCTCATAA
Found at i:53515958 original size:25 final size:25
Alignment explanation
Indices: 53515930--53515985 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
53515920 AAGCTCCTCT
*
53515930 GAGCTGAATAACGGTAAGCTCATAC
1 GAGCTGAATAACGGTAAGCTCATAA
* **
53515955 GAGCTGAGTATTGGTAAGCTCATAA
1 GAGCTGAATAACGGTAAGCTCATAA
53515980 GAGCTG
1 GAGCTG
53515986 GAATTGGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (25 bp):
GAGCTGAATAACGGTAAGCTCATAA
Found at i:53516282 original size:5 final size:5
Alignment explanation
Indices: 53516272--53516297 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53516262 TTTAATCTTT
53516272 ATTCA ATTCA ATTCA ATTCA ATTCA A
1 ATTCA ATTCA ATTCA ATTCA ATTCA A
53516298 AAACCATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTCA
Found at i:53518197 original size:29 final size:28
Alignment explanation
Indices: 53518164--53518236 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 28
53518154 GACTATAGTA
* *
53518164 CTCACACAAGCTGACAGTGATTAGGGTTG
1 CTCACACAAGCTGACAGTGATGA-AGTTG
* * * *
53518193 CTCACACAAGTTGACATTTATGAATTTG
1 CTCACACAAGCTGACAGTGATGAAGTTG
53518221 CTCACACAAGCTGACA
1 CTCACACAAGCTGACA
53518237 TTTAGGAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 18 0.49
29 19 0.51
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (28 bp):
CTCACACAAGCTGACAGTGATGAAGTTG
Found at i:53518230 original size:28 final size:28
Alignment explanation
Indices: 53518190--53518273 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
53518180 GTGATTAGGG
*
53518190 TTGCTCACACAAGTTGACATTTATGAAT
1 TTGCTCACACAAGCTGACATTTATGAAT
*
53518218 TTGCTCACACAAGCTGACATTTAGGAAT
1 TTGCTCACACAAGCTGACATTTATGAAT
* * * *
53518246 TTTCTCACAAAAGCTAATATTTATGAAT
1 TTGCTCACACAAGCTGACATTTATGAAT
53518274 CGAGAATCCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (28 bp):
TTGCTCACACAAGCTGACATTTATGAAT
Found at i:53522368 original size:31 final size:33
Alignment explanation
Indices: 53522327--53522391 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
53522317 GTCATTGTAT
*
53522327 ACATGAAACTTGAATTGTGATTT-A-TATATAC
1 ACATAAAACTTGAATTGTGATTTAATTATATAC
** *
53522358 ACATAAAACTTTTATTTTGATTTAATTATATAC
1 ACATAAAACTTGAATTGTGATTTAATTATATAC
53522391 A
1 A
53522392 TTTAAAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 19 0.68
32 1 0.04
33 8 0.29
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (33 bp):
ACATAAAACTTGAATTGTGATTTAATTATATAC
Found at i:53529076 original size:90 final size:90
Alignment explanation
Indices: 53528852--53529081 Score: 298
Period size: 90 Copynumber: 2.5 Consensus size: 90
53528842 GAAGATTCTG
* *
53528852 GCGTGTTATCGGTTGGAAAACTCTTATGAGCAATCTAGCGTGTTATCAGGGGCGAATATTTAGCC
1 GCGTGTTATCGGTTGGAAAGCTCTTATGAGCAATCTAACGTGTTATC-GGGGCGAATATTTAGCC
*
53528917 TATAAGCTTAGCACTATATGCATCTA
65 TACAAGCTTAGCACTATATGCATCTA
* * * * *
53528943 GCATGTTATTGGTTGGAAAGCTCTTATGAGCAATCTGACGTGTTGTCGGGGGGAATATTTAGCCT
1 GCGTGTTATCGGTTGGAAAGCTCTTATGAGCAATCTAACGTGTTATCGGGGCGAATATTTAGCCT
** * * * *
53529008 ACGGGTTTAGCACTATGTGCATTTT
66 ACAAGCTTAGCACTATATGCATCTA
* * *
53529033 GCGTGTTATCAGTTGGAAAGCTCTTATGAGCAATTTAATGTGTTATCGG
1 GCGTGTTATCGGTTGGAAAGCTCTTATGAGCAATCTAACGTGTTATCGG
53529082 ATGGTCACCT
Statistics
Matches: 118, Mismatches: 21, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
90 77 0.65
91 41 0.35
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.34
Consensus pattern (90 bp):
GCGTGTTATCGGTTGGAAAGCTCTTATGAGCAATCTAACGTGTTATCGGGGCGAATATTTAGCCT
ACAAGCTTAGCACTATATGCATCTA
Found at i:53542030 original size:2 final size:2
Alignment explanation
Indices: 53542023--53542052 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53542013 AATAATTCAT
53542023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53542053 AACATCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53545027 original size:43 final size:43
Alignment explanation
Indices: 53544961--53545093 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 43
53544951 AAATACATAT
* * *
53544961 CGAAGCAATTGTACTGGCACACACAGTGCATCATATGACAAAC
1 CGAAACAATTATACTGGCACACACAGTGCATCATAGGACAAAC
* * * **
53545004 CGAAACAATTATACTGGCACACACAATACATCATCGGACAGGC
1 CGAAACAATTATACTGGCACACACAGTGCATCATAGGACAAAC
* * *
53545047 C-AAAGCAATTATACTGGCACACACGGTGCATCATCGGATAAAC
1 CGAAA-CAATTATACTGGCACACACAGTGCATCATAGGACAAAC
53545090 CGAA
1 CGAA
53545094 GTATAACCTA
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
42 3 0.04
43 69 0.93
44 2 0.03
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.17
Consensus pattern (43 bp):
CGAAACAATTATACTGGCACACACAGTGCATCATAGGACAAAC
Found at i:53547827 original size:27 final size:29
Alignment explanation
Indices: 53547768--53547828 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
53547758 TGTGCCTCCG
* *
53547768 CACGGTCTAGCACATGCCCGTGTGTCTTA
1 CACGGTCTAACACACGCCCGTGTGTCTTA
*
53547797 CACGGTCTAACACACG-CCG-GTGTGTTA
1 CACGGTCTAACACACGCCCGTGTGTCTTA
53547824 CACGG
1 CACGG
53547829 GCCTAATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 12 0.41
28 3 0.10
29 14 0.48
ACGTcount: A:0.20, C:0.31, G:0.26, T:0.23
Consensus pattern (29 bp):
CACGGTCTAACACACGCCCGTGTGTCTTA
Found at i:53554214 original size:6 final size:6
Alignment explanation
Indices: 53554205--53554239 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
53554195 AATGGAGAAT
*
53554205 ATATAC ATATAT ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
53554240 TATACACGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:53554216 original size:2 final size:2
Alignment explanation
Indices: 53554203--53554277 Score: 51
Period size: 2 Copynumber: 37.0 Consensus size: 2
53554193 GAAATGGAGA
* * * * *
53554203 AT AT AT AC AT AT AT AT AT AC AT AT AC AT AT AC AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
53554245 AC GT AA AT GAT AT AT AT AT GT AT GT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
53554278 CCATGGTTGG
Statistics
Matches: 54, Mismatches: 18, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
2 52 0.96
3 2 0.04
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (2 bp):
AT
Found at i:53554220 original size:12 final size:12
Alignment explanation
Indices: 53554203--53554243 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
53554193 GAAATGGAGA
53554203 ATATATACATAT
1 ATATATACATAT
53554215 ATATATACATAT
1 ATATATACATAT
*
53554227 ACATATACATAT
1 ATATATACATAT
53554239 ATATA
1 ATATA
53554244 CACGTAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATATACATAT
Found at i:53554428 original size:10 final size:10
Alignment explanation
Indices: 53554403--53554436 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
53554393 GAAGATACCT
53554403 TATAATATGTA
1 TATAATAT-TA
*
53554414 TATAATATAA
1 TATAATATTA
53554424 TATAATATTA
1 TATAATATTA
53554434 TAT
1 TAT
53554437 GTATATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (10 bp):
TATAATATTA
Found at i:53558640 original size:206 final size:198
Alignment explanation
Indices: 53558344--53558803 Score: 595
Period size: 206 Copynumber: 2.3 Consensus size: 198
53558334 ATGCATACCC
* * * *
53558344 GTGTGATAGGATTTTTAGTATTGATAATGTATTTGATTGAGTTGATGTCAAAAGTTAAACTATTT
1 GTGTGATAGGATTTTCAGTATTAATAATGTATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
*
53558409 TTCATTTTAATTTCATGCATATTGCACATGTGGTGCTGTTATTATTATTACCAGTTTCAAATCTT
66 TTCATTTTAATTT-ATGCATATTGCACATGT-GT--TGTTATTATTATT---AGTTTCAAACCTT
* * *
53558474 ACGTCTCATTATTTATTTTATGTTATTTTTAAACATACATTTTTATTCAAAATTTATGGCTTCAA
124 ACGTCTCATTATTTATTATATGTTA-TTTTAAACACACATTTTTATTCAAAATTTATAGCTTCAA
**
53558539 CACGA-ATAGGT
188 CAC-ACATACAT
53558550 GTGTGATAGGATTTTCAGTATTAATAATGTATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
1 GTGTGATAGGATTTTCAGTATTAATAATGTATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
* *
53558615 TTCATTTTAATTT-TGCACGTATTGCATATGTGTTGTTATTATTATTAGTTTCAAACCTTACGTT
66 TTCATTTTAATTTATGCA--TATTGCACATGTGTTGTTATTATTATTAGTTTCAAACCTTACGTC
* * * *
53558679 TCATTATTTATTATATGTTATTTTAAACACATATTTTTATTCAAAATTTGTAGTTTCCACACACA
129 TCATTATTTATTATATGTTATTTTAAACACACATTTTTATTCAAAATTTATAGCTTCAACACACA
53558744 TACAT
194 TACAT
* * * *
53558749 GTGTGATA-GAATTCCTAGTATTAATTATGT-TGTTAATTGAGTTGGTGTCACAAGT
1 GTGTGATAGGATTTTC-AGTATTAATAATGTAT-TTGATTGAGTTGGTGTCACAAGT
53558804 CAACTCGACA
Statistics
Matches: 229, Mismatches: 20, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
198 7 0.03
199 83 0.36
200 35 0.15
203 13 0.06
204 4 0.02
205 2 0.01
206 85 0.37
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (198 bp):
GTGTGATAGGATTTTCAGTATTAATAATGTATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
TTCATTTTAATTTATGCATATTGCACATGTGTTGTTATTATTATTAGTTTCAAACCTTACGTCTC
ATTATTTATTATATGTTATTTTAAACACACATTTTTATTCAAAATTTATAGCTTCAACACACATA
CAT
Found at i:53558799 original size:199 final size:201
Alignment explanation
Indices: 53558344--53558803 Score: 601
Period size: 199 Copynumber: 2.3 Consensus size: 201
53558334 ATGCATACCC
* * *
53558344 GTGTGATAGGATTTTTAGTATTGATAATGTATTTGATTGAGTTGATGTCAAAAGTTAAACTATTT
1 GTGTGATAGGA-TTTTAGTATTAATAATGTATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
*
53558409 TTCATTTTAATTTCATGCATATTGCACATGTGGTGCTGTTATTATTATTACCAGTTTCAAATCTT
65 TTCATTTTAATTT-ATGCATATTGCACATGTGGT-CTGTTATTATTATT--CAGTTTCAAACCTT
* * *
53558474 ACGTCTCATTATTTATTTTATGTTATTTTTAAACATACATTTTTATTCAAAATTTATGGCTTCAA
126 ACGTCTCATTATTTATTATATGTTATTTTTAAACACACATTTTTATTCAAAATTTATAGCTTCAA
**
53558539 CACGAATAGGT
191 CACGAATACAT
53558550 GTGTGATAGGATTTTCAGTATTAATAATGTATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
1 GTGTGATAGGATTTT-AGTATTAATAATGTATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
*
53558615 TTCATTTTAATTT-TGCACGTATTGCATATGT-GT-TGTTATTATTATT-AGTTTCAAACCTTAC
65 TTCATTTTAATTTATGCA--TATTGCACATGTGGTCTGTTATTATTATTCAGTTTCAAACCTTAC
* * * * *
53558676 GTTTCATTATTTATTATATGTTA-TTTTAAACACATATTTTTATTCAAAATTTGTAGTTTCCACA
128 GTCTCATTATTTATTATATGTTATTTTTAAACACACATTTTTATTCAAAATTTATAGCTTCAACA
53558740 C-ACATACAT
193 CGA-ATACAT
* * * *
53558749 GTGTGATAGAATTCCTAGTATTAATTATGT-TGTTAATTGAGTTGGTGTCACAAGT
1 GTGTGATAGGATT-TTAGTATTAATAATGTAT-TTGATTGAGTTGGTGTCACAAGT
53558804 CAACTCGACA
Statistics
Matches: 229, Mismatches: 19, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
198 2 0.01
199 87 0.38
200 36 0.16
203 13 0.06
204 4 0.02
205 6 0.03
206 81 0.35
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (201 bp):
GTGTGATAGGATTTTAGTATTAATAATGTATTTGATTGAGTTGGTGTCACAAGTTAAACTATTTT
TCATTTTAATTTATGCATATTGCACATGTGGTCTGTTATTATTATTCAGTTTCAAACCTTACGTC
TCATTATTTATTATATGTTATTTTTAAACACACATTTTTATTCAAAATTTATAGCTTCAACACGA
ATACAT
Found at i:53578939 original size:49 final size:49
Alignment explanation
Indices: 53578881--53578980 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
53578871 ACATAACTCA
*
53578881 TAAAATAAAACATATTTAGCAAATGGTAATAATAAGAGTAACATAGTAT
1 TAAAATAAAACATATTTAGCAAATGGTAATAACAAGAGTAACATAGTAT
53578930 TAAAATAAAACATATTTAGCAAATGGTAATAACAAGAGTAACATAGTAT
1 TAAAATAAAACATATTTAGCAAATGGTAATAACAAGAGTAACATAGTAT
53578979 TA
1 TA
53578981 GCAAAAGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (49 bp):
TAAAATAAAACATATTTAGCAAATGGTAATAACAAGAGTAACATAGTAT
Found at i:53580396 original size:16 final size:17
Alignment explanation
Indices: 53580374--53580411 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
53580364 AACTAAATAG
*
53580374 CTAAAATAAATAAACAA
1 CTAAAATAAACAAACAA
53580391 -TAAAATAAACAAACAA
1 CTAAAATAAACAAACAA
53580407 CTAAA
1 CTAAA
53580412 CAAATTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (17 bp):
CTAAAATAAACAAACAA
Found at i:53583633 original size:24 final size:24
Alignment explanation
Indices: 53583606--53583651 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53583596 ATGACTATAT
53583606 ATAAAATT-TTAATAAATAAAATAG
1 ATAAAATTATTAA-AAATAAAATAG
*
53583630 ATAAAATTATTAAATATAAAAT
1 ATAAAATTATTAAAAATAAAAT
53583652 TAAAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
ATAAAATTATTAAAAATAAAATAG
Found at i:53584990 original size:30 final size:30
Alignment explanation
Indices: 53584951--53585011 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
53584941 GGGGGTGGGA
*
53584951 TGGGAAGGGAGTAAAAGTTTTGAGGGGAAAG
1 TGGGAAGGGAGTAAAAGTATTG-GGGGAAAG
53584982 TGGG-AGGGAGTAAAAGTATTGGGGGAAAG
1 TGGGAAGGGAGTAAAAGTATTGGGGGAAAG
53585011 T
1 T
53585012 AAAAAGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 9 0.31
30 16 0.55
31 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.46, T:0.20
Consensus pattern (30 bp):
TGGGAAGGGAGTAAAAGTATTGGGGGAAAG
Found at i:53585042 original size:7 final size:8
Alignment explanation
Indices: 53585017--53585041 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53585007 AAAGTAAAAA
53585017 GGTTTGGG
1 GGTTTGGG
53585025 GGTTTGGG
1 GGTTTGGG
53585033 GGTTTGGG
1 GGTTTGGG
53585041 G
1 G
53585042 TAAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (8 bp):
GGTTTGGG
Found at i:53585390 original size:20 final size:20
Alignment explanation
Indices: 53585354--53585391 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53585344 TACATTTATT
*
53585354 TTTTATTTAATTTTTAATTA
1 TTTTATTTAATTATTAATTA
53585374 TTTTATTTTAA-TATTAAT
1 TTTTA-TTTAATTATTAAT
53585392 AAAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATTTAATTATTAATTA
Found at i:53585970 original size:26 final size:28
Alignment explanation
Indices: 53585918--53585972 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
53585908 TTATTTAAAT
*
53585918 TTTTAATATAATTAAAATATGTTAATAA
1 TTTTAATATAATTAAAATATGTCAATAA
53585946 TTTTAA-A-AATTAAAATAT-TACAATAA
1 TTTTAATATAATTAAAATATGT-CAATAA
53585972 T
1 T
53585973 AAAAAACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 1 0.04
26 17 0.68
27 1 0.04
28 6 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
TTTTAATATAATTAAAATATGTCAATAA
Found at i:53589058 original size:15 final size:15
Alignment explanation
Indices: 53589035--53589069 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53589025 TTATGTTAAA
*
53589035 TTTTGATTTGATAAT
1 TTTTAATTTGATAAT
53589050 TTTTAATTTGATAAT
1 TTTTAATTTGATAAT
*
53589065 CTTTA
1 TTTTA
53589070 CAGAGTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.60
Consensus pattern (15 bp):
TTTTAATTTGATAAT
Found at i:53590455 original size:25 final size:25
Alignment explanation
Indices: 53590415--53590473 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
53590405 TAGCTATTTG
* * * *
53590415 AGGCATGTATGCTTAATTCTAGTGA
1 AGGCATGAATGCTTAATGCTAATCA
*
53590440 AGGCATGAATGGTTAATGCTAATCA
1 AGGCATGAATGCTTAATGCTAATCA
53590465 A-GCATGAAT
1 AGGCATGAAT
53590474 TGGTAAGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (25 bp):
AGGCATGAATGCTTAATGCTAATCA
Found at i:53596344 original size:22 final size:22
Alignment explanation
Indices: 53596319--53596365 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
53596309 AGGAAGTGAT
*
53596319 ATGAAAAAATAAAAAAATGAAA
1 ATGAAAAAATAAAAAAATAAAA
* *
53596341 ATGAAAAAATGAAAAAGTAAAA
1 ATGAAAAAATAAAAAAATAAAA
53596363 ATG
1 ATG
53596366 GAGAGGCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (22 bp):
ATGAAAAAATAAAAAAATAAAA
Found at i:53596347 original size:14 final size:14
Alignment explanation
Indices: 53596324--53596365 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
53596314 GTGATATGAA
*
53596324 AAAATAAAAAAATG
1 AAAATGAAAAAATG
53596338 AAAATGAAAAAATG
1 AAAATGAAAAAATG
* *
53596352 AAAAAGTAAAAATG
1 AAAATGAAAAAATG
53596366 GAGAGGCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (14 bp):
AAAATGAAAAAATG
Found at i:53597889 original size:132 final size:132
Alignment explanation
Indices: 53597711--53598617 Score: 1318
Period size: 132 Copynumber: 6.9 Consensus size: 132
53597701 CATAGACAGC
* *
53597711 GGAGCAGATCAAAGATGG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCAGT
1 GGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
* * * * * *
53597775 AATTC-AATCTCCCTGGGCAGCAGTGGAATAGATTGAGGATTTCAGATCTTATCTCCCTAAGTAG
65 AATTCTACT-TCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAG
53597839 TAGT
129 TAGT
* * * * *
53597843 GGAGAAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTAAAGCCAGTA
1 GGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* ** * * * *
53597908 ATTCTA-TCTCCCTGGGCAGCAATGGAATAGACTGAAGATTTTAGATCTTGTCTTCCTACA-TAG
66 ATTCTACT-TCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTA-AGCAG
*
53597971 ATAGA
129 -TAGT
* * *
53597976 GAAGCAGATCGAAGACGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* * * **
53598041 ATTCTACTTCTCTAGATAGCAGTAGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
66 ATTCTACTTCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
53598106 GT
131 GT
* *
53598108 GGAGCAGATCAAAGATGGCAGATATTACCTCCCTGTAGTTACAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* * *
53598173 ATTCTACTTCCTTGGACAGCAGCGGAATAGATTGAAGATTTCAGATATTGTTTCCCTAAGCAGTA
66 ATTCTACTTCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
*
53598238 GC
131 GT
* *
53598240 GGAGTAGATCAAATATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* * * *
53598305 ATTCTACTTCCCTGGACAGCAACGGAATAGATTGAGGATTTCAAATCTTGTCTCCCTAAGTAGTA
66 ATTCTACTTCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
53598370 GT
131 GT
* * *
53598372 GGAGTAGATCAAAGATGGCAGATTTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGCA
1 GGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* *
53598437 ATTCTACTTCCTTGGACAGCAGCGAAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
66 ATTCTACTTCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
53598502 GT
131 GT
53598504 GGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
*
53598569 ATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTT
66 ATTCTACTTCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGATCTT
53598618 ACCTCCTTAG
Statistics
Matches: 697, Mismatches: 72, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
132 582 0.84
133 114 0.16
134 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
GGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
ATTCTACTTCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
GT
Found at i:53598788 original size:100 final size:100
Alignment explanation
Indices: 53598612--53599101 Score: 777
Period size: 100 Copynumber: 4.9 Consensus size: 100
53598602 GAAGATTTCA
*
53598612 GATCTTACCTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
* *
53598677 ATATTGTAATTAAAAAGATTGAAGCCACAACGGCG
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGACG
* * *
53598712 GATCTTACTTCCTTAGCTGTGTAGTGGAATAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
*
53598777 ATATTGGAATTAAAAAGATTGAAGCCACAACGACG
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGACG
53598812 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
*
53598877 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGACG
* * *
53598912 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACAACGGCAGATCTGGTTTCTCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
*
53598977 ATATTGCAATTAAAAAGATTGAAGCCACAACGACA
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGACG
* * * *
53599012 GATCTTACTTCCCT-GACGGTGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCC
1 GATCTTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCT
* * *
53599076 GACATTGCAGTTGAACAA-ATTGAAGC
65 GATATTGCAATT-AAAAAGATTGAAGC
53599102 TATAAGTCTT
Statistics
Matches: 362, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
99 1 0.00
100 357 0.99
101 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (100 bp):
GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
ATATTGCAATTAAAAAGATTGAAGCCACAACGACG
Found at i:53599092 original size:50 final size:50
Alignment explanation
Indices: 53598631--53599103 Score: 342
Period size: 50 Copynumber: 9.5 Consensus size: 50
53598621 TCCTTAGCAG
* *
53598631 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGACAT
* * ** * * *** *
53598681 TGTAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGC-T
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGA-CAT
* * * *
53598730 GTGTAGTGGAATAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 -TGCAGTGGAACAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGACAT
* * ** * * * *** * *
53598781 TGGAATTAAAAAGATTGAAGCCACAACGACGGATCTTACTT-CCTTAGCAG
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGA-CAT
* *
53598831 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGACAT
* ** * * *** * *
53598881 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAG
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGA-CAT
* * *
53598931 TGCAGTGGAACAGATTGAAGCTACAACGGCAGATCTGGTTTCTCTGATAT
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGACAT
* ** * * * * *** **
53598981 TGCAATTAAAAAGATTGAAGCCACAACGACAGATCTTACTTCCCTGACGG
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGACAT
* * *
53599031 TGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACAT
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGACAT
* *
53599081 TGCAGTTGAACAAATTGAAGCTA
1 TGCAGTGGAACAGATTGAAGCTA
53599104 TAAGTCTTAT
Statistics
Matches: 308, Mismatches: 107, Indels: 16
0.71 0.25 0.04
Matches are distributed among these distances:
49 13 0.04
50 283 0.92
51 12 0.04
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (50 bp):
TGCAGTGGAACAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGACAT
Found at i:53616254 original size:80 final size:77
Alignment explanation
Indices: 53616121--53616334 Score: 331
Period size: 76 Copynumber: 2.8 Consensus size: 77
53616111 AACCGTTATC
* *
53616121 GGTGGATTCAGCACTTAGCAACCACCAGTGATTCGAGGAATCAGCACTTAGCAACCCCCTTTTTT
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCC---TTT
*
53616186 TACATTCAAGGATAT
63 CACATTCAAGGATAT
53616201 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAA-CCCCTTTCAC
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCCTTTCAC
53616265 ATTCAAGGATAT
66 ATTCAAGGATAT
* ** *
53616277 GGTAGAATCAGCACTTAGCAACCACCAAAGAGTCGGGGAATCAGCACTTAGCAACCCC
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCC
53616335 TTGGGGAATC
Statistics
Matches: 126, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
76 67 0.53
77 3 0.02
79 4 0.03
80 52 0.41
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.22
Consensus pattern (77 bp):
GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCCTTTCAC
ATTCAAGGATAT
Found at i:53616323 original size:33 final size:32
Alignment explanation
Indices: 53616281--53616358 Score: 96
Period size: 26 Copynumber: 2.6 Consensus size: 32
53616271 GGATATGGTA
53616281 GAATCAGCACTTAGCAACCACCAAAGAGTCGGG
1 GAATCAGCACTTAGCAACCACCAAA-AGTCGGG
*
53616314 GAATCAGCACTTAGCAACC-CC-----TTGGG
1 GAATCAGCACTTAGCAACCACCAAAAGTCGGG
53616340 GAATCAGCACTTAGCAACC
1 GAATCAGCACTTAGCAACC
53616359 CCTTTCACAT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
26 23 0.52
32 2 0.05
33 19 0.43
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.15
Consensus pattern (32 bp):
GAATCAGCACTTAGCAACCACCAAAAGTCGGG
Found at i:53616340 original size:26 final size:26
Alignment explanation
Indices: 53616311--53616362 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
53616301 CCAAAGAGTC
53616311 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
53616337 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
53616363 TCACATTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (26 bp):
GGGGAATCAGCACTTAGCAACCCCTT
Found at i:53616392 original size:102 final size:103
Alignment explanation
Indices: 53616235--53616466 Score: 421
Period size: 102 Copynumber: 2.3 Consensus size: 103
53616225 CCAGTGATTC
53616235 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGGATATGGTAGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGGATATGGTAGAATCAGCACTTAGCAACC
*
53616300 ACCAAAGAGTCGGGGAATCAGCACTTAGCAACCCCTT-
66 ACCAAAGAGTCAGGGAATCAGCACTTAGCAACCCCTTG
* *
53616337 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGGATATGGTGGAATTAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGGATATGGTAGAATCAGCACTTAGCAACC
53616402 ACCAAAGAGTCAGGGAATCAGCACTTAGCAACCCCTTG
66 ACCAAAGAGTCAGGGAATCAGCACTTAGCAACCCCTTG
53616440 GGGGAATCAGCACTTAGCAACTCCCTT
1 GGGGAATCAGCACTTAGCAAC-CCCTT
53616467 GTTATTCAAT
Statistics
Matches: 125, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
102 99 0.79
103 21 0.17
104 5 0.04
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGGATATGGTAGAATCAGCACTTAGCAACC
ACCAAAGAGTCAGGGAATCAGCACTTAGCAACCCCTTG
Found at i:53616444 original size:27 final size:28
Alignment explanation
Indices: 53616414--53616467 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
53616404 CAAAGAGTCA
53616414 GGGAATCAGCACTTAGCAAC-CCCTTGG
1 GGGAATCAGCACTTAGCAACTCCCTTGG
53616441 GGGAATCAGCACTTAGCAACTCCCTTG
1 GGGAATCAGCACTTAGCAACTCCCTTG
53616468 TTATTCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (28 bp):
GGGAATCAGCACTTAGCAACTCCCTTGG
Found at i:53622383 original size:11 final size:11
Alignment explanation
Indices: 53622369--53622393 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53622359 CCCATAATTA
53622369 TTTTTTAAAAT
1 TTTTTTAAAAT
53622380 TTTTTTAAAAT
1 TTTTTTAAAAT
53622391 TTT
1 TTT
53622394 CTAAAGTCAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTTAAAAT
Found at i:53622739 original size:23 final size:22
Alignment explanation
Indices: 53622696--53622739 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
53622686 TTCTAAGTGA
53622696 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
53622719 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
53622740 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:53622908 original size:26 final size:25
Alignment explanation
Indices: 53622879--53622959 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
53622869 ATGTTCGGTT
53622879 CACATAGTAGCCTGCACATAGTACTA
1 CACATAGTAGCCT-CACATAGTACTA
* * *
53622905 CACAT-GTGGCCATTACCATCCG-A-TA
1 CACATAGTAGCC-TCA-CAT-AGTACTA
*
53622930 CACGTAGTAGCCTACACATAGTACTA
1 CACATAGTAGCCT-CACATAGTACTA
53622956 CACA
1 CACA
53622960 CGTGATCGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
24 1 0.03
25 17 0.43
26 21 0.52
27 1 0.03
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (25 bp):
CACATAGTAGCCTCACATAGTACTA
Found at i:53622941 original size:51 final size:50
Alignment explanation
Indices: 53622874--53623069 Score: 223
Period size: 51 Copynumber: 3.9 Consensus size: 50
53622864 CAATGATGTT
* * * *
53622874 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGGCCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * * *
53622925 CGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* * * * * *
53622976 CGGTACGCATAGTATCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
53623026 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
53623070 CACTTTCACT
Statistics
Matches: 117, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 73 0.62
52 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:53623058 original size:101 final size:101
Alignment explanation
Indices: 53622881--53623065 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
53622871 GTTCGGTTCA
* *
53622881 CATAGTAGCCTGCACATAGTACTACACATGTGGCCATTACCATCCGATACACGTAGTAGCCTACA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTACA
53622946 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * * *
53622983 CATAGTATCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTACA
53623047 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
53623066 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.53
102 32 0.42
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTACAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:53625287 original size:18 final size:19
Alignment explanation
Indices: 53625260--53625295 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
53625250 CAATATAGGG
53625260 TCATTAATTTC-ACTTAAA
1 TCATTAATTTCAACTTAAA
*
53625278 TCATTCATTTCAACTTAA
1 TCATTAATTTCAACTTAA
53625296 GCAAACAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.44
Consensus pattern (19 bp):
TCATTAATTTCAACTTAAA
Found at i:53628176 original size:14 final size:14
Alignment explanation
Indices: 53628159--53628211 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
53628149 TTCAATGTTT
*
53628159 ATATTGCAATGATC
1 ATATTGCAACGATC
*
53628173 ATATTCCAACGATC
1 ATATTGCAACGATC
*
53628187 ATATTGTAAC-AGTC
1 ATATTGCAACGA-TC
*
53628201 ATATTCCAACG
1 ATATTGCAACG
53628212 GCCATATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 1 0.03
14 30 0.97
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (14 bp):
ATATTGCAACGATC
Found at i:53628217 original size:14 final size:14
Alignment explanation
Indices: 53628171--53628219 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
53628161 ATTGCAATGA
*
53628171 TCATATTCCAACGA
1 TCATATTCCAACGG
** *
53628185 TCATATTGTAACAG
1 TCATATTCCAACGG
53628199 TCATATTCCAACGG
1 TCATATTCCAACGG
*
53628213 CCATATT
1 TCATATT
53628220 TTTGCATTAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (14 bp):
TCATATTCCAACGG
Found at i:53639570 original size:44 final size:44
Alignment explanation
Indices: 53639449--53639570 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 44
53639439 TGTCATTAGG
*
53639449 ATTTATATTCAA-AAGGTACTATGT-CCAGGTGTTGGCTACTTGCC
1 ATTTATATTCAACAA-GTACTATGTACC-GATGTTGGCTACTTGCC
* *
53639493 ATTTATATTCAGCAAGTACTATGTACC-AGTGTTGGCTA-TGTTCC
1 ATTTATATTCAACAAGTACTATGTACCGA-TGTTGGCTACT-TGCC
*
53639537 ATTTATATTCAACAAGTATTATGTACCGATGTTG
1 ATTTATATTCAACAAGTACTATGTACCGATGTTG
53639571 TAGTAGCAGA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
43 1 0.01
44 62 0.91
45 5 0.07
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (44 bp):
ATTTATATTCAACAAGTACTATGTACCGATGTTGGCTACTTGCC
Found at i:53649813 original size:15 final size:15
Alignment explanation
Indices: 53649793--53649822 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53649783 TGATTACGTG
53649793 ATTCAAAGTTCAAAC
1 ATTCAAAGTTCAAAC
53649808 ATTCAAAGTTCAAAC
1 ATTCAAAGTTCAAAC
53649823 TTTTTCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (15 bp):
ATTCAAAGTTCAAAC
Found at i:53652687 original size:175 final size:175
Alignment explanation
Indices: 53652396--53653251 Score: 1525
Period size: 175 Copynumber: 4.9 Consensus size: 175
53652386 AGACCACAGA
* * *
53652396 TCCACTGTAATCTCAAGGAAATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
* *
53652461 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGGGATAGGATTACTAGCTTCAATATGCT
66 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
*
53652526 CCGCTATAATCTCAGGGAGATAAGATCTGAAATTCTTCGATCTGT
131 CCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGATCTGT
53652571 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
* *
53652636 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGAGAAAT-GGAATTACTAGCTTCAATCTGC
66 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG-ATTACTAGCTTCAATCTGC
*
53652700 TCCGCTGTAATCTCAGAGAGATAAGATCTGAAATTCTTCGATCTGT
130 TCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGATCTGT
* * *
53652746 TCCACTGTAATCTTAGGGAAAAAAGACCTGGTGCGATCTACTCTGCTGTAACTTCAAAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
53652811 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
66 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
*
53652876 CCGCTGTAATCTCAGGAAGATAAGATCTGAAATTCTTCGATCTGT
131 CCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGATCTGT
*
53652921 TCCGCTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
* *
53652986 GATCCTTTATTTTAATCCGCTCTACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCT
66 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
53653051 CCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGATCTGT
131 CCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGATCTGT
53653096 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
* * *
53653161 GATCCTTTATTTTAATCCGTTCCATTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACT
66 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
53653226 CCGCTGTAATCTCAGGGAGATAAGAT
131 CCGCTGTAATCTCAGGGAGATAAGAT
53653252 TTCTAGCTTC
Statistics
Matches: 650, Mismatches: 29, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
174 2 0.00
175 646 0.99
176 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (175 bp):
TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
CCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGATCTGT
Found at i:53652877 original size:44 final size:44
Alignment explanation
Indices: 53652474--53653339 Score: 343
Period size: 44 Copynumber: 19.8 Consensus size: 44
53652464 CCTTTATTTT
* * *
53652474 AATCCGCTCCACTGTAATCTCAGGGGGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * *
53652518 AATATGCTCCGCTATAATCTCAGGGAGATAAGATCTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTC
* * * * * *
53652564 GATCTGTTCCACTGTAATCTCAGGGAAATAAGA--CCT-GGTGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * ** * * * *
53652605 GATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* * * *
53652649 AATCCGCTCCACTGTAATCTCAGAGAAAT-GGAATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAG-ATTACTAGCTTC
* * * *
53652693 AATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTC
* * * * * * * *
53652739 GATCTGTTCCACTGTAATCTTAGGGAAAAAAGA--CCT-GGTGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * ** ** * * *
53652780 GATCTACTCTGCTGTAA-CTTCAAAGAGATAAGATCCT-TTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* *
53652824 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * *
53652868 AATCTGCTCCGCTGTAATCTCAGGAAGATAAGATCTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTC
* * * * * * *
53652914 GATCTGTTCCGCTGTAATCTCAGGGAAATAAGA--CCT-GGTGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * ** * * * *
53652955 GATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* * * *
53652999 AATCCGCTCTACTGTAATCTTAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
53653043 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTC
* * * * * *
53653089 GATCTGTTCCACTGTAATCTCAGGGAAATAAGA--CCT-GGTGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * ** * * * *
53653130 GATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* * * *
53653174 AATCCGTTCCATTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
53653218 AATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * ** *
53653262 AATCTACTCCACTGTAACCTCAGGGAGATAAGATCTAAAATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-TACTA-GCTTC
* * *
53653308 -GTCTACTCCACTGTAACCTCAGGGAGATAAGA
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGA
53653340 CCTGATGCGA
Statistics
Matches: 599, Mismatches: 167, Indels: 111
0.68 0.19 0.13
Matches are distributed among these distances:
40 4 0.01
41 106 0.18
42 4 0.01
43 9 0.02
44 295 0.49
45 46 0.08
46 135 0.23
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:53653536 original size:87 final size:87
Alignment explanation
Indices: 53653388--53653680 Score: 397
Period size: 87 Copynumber: 3.4 Consensus size: 87
53653378 AGATCCTTTA
* * * * * *
53653388 TTCAACCAGCTTCACTGCAACCGATGAAGGCAAGGCTTTATTTTCGATCTGCTTCGTTGTTAACA
1 TTCAACCAGCTCCACTACAACCGATGGAGACAAGGCTTTATTTTCAATCTGCTTCGTTGTTAACG
* * * *
53653453 CCGAAAGGCAAGTTCTGCTATC
66 CAGGAAGGCCAGATCTGCTATC
* *
53653475 TTCAATCAGCTCCACTACAACCGATGGAGACAAGGCTTTATTTTCAATCTGCTTCGCTGTTAACG
1 TTCAACCAGCTCCACTACAACCGATGGAGACAAGGCTTTATTTTCAATCTGCTTCGTTGTTAACG
*
53653540 CAGGAAGGCCAGATCTGCTATA
66 CAGGAAGGCCAGATCTGCTATC
* * * *
53653562 TTCAACCAGTTCCACTACAACCAATGGAGACAAGGCTTTGTTTTCAATCTACTTCGTTGTTAACG
1 TTCAACCAGCTCCACTACAACCGATGGAGACAAGGCTTTATTTTCAATCTGCTTCGTTGTTAACG
53653627 CAGGAAGGCCAGATCTGCTATC
66 CAGGAAGGCCAGATCTGCTATC
* ** *
53653649 TTCAACCAGTTCCACCGCAATCGATGGAGACA
1 TTCAACCAGCTCCACTACAACCGATGGAGACA
53653681 TAGCTTGTAT
Statistics
Matches: 182, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 182 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (87 bp):
TTCAACCAGCTCCACTACAACCGATGGAGACAAGGCTTTATTTTCAATCTGCTTCGTTGTTAACG
CAGGAAGGCCAGATCTGCTATC
Found at i:53654849 original size:21 final size:21
Alignment explanation
Indices: 53654823--53654869 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
53654813 GGTATAGCAA
53654823 GATCACCGCATGCCCCAATCT
1 GATCACCGCATGCCCCAATCT
*** *
53654844 GATCACTTTATGCCCCATTCT
1 GATCACCGCATGCCCCAATCT
53654865 GATCA
1 GATCA
53654870 ATATTTGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.36, G:0.13, T:0.28
Consensus pattern (21 bp):
GATCACCGCATGCCCCAATCT
Found at i:53654971 original size:7 final size:7
Alignment explanation
Indices: 53654952--53654986 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
53654942 TTAGCCTCTC
53654952 CATTTTT
1 CATTTTT
53654959 -ACTTTTT
1 CA-TTTTT
53654966 CATTTTT
1 CATTTTT
53654973 CATTTTT
1 CATTTTT
53654980 CATTTTT
1 CATTTTT
53654987 TTGACTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 1 0.04
7 24 0.92
8 1 0.04
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:53655807 original size:7 final size:7
Alignment explanation
Indices: 53655795--53655847 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
53655785 TTTGACTTTG
53655795 ATTTTTT
1 ATTTTTT
53655802 A-TTTTT
1 ATTTTTT
53655808 ATTTTTT
1 ATTTTTT
53655815 GA-TTTTT
1 -ATTTTTT
*
53655822 -TTTTAT
1 ATTTTTT
53655828 -TTTTTT
1 ATTTTTT
*
53655834 ATTTTTG
1 ATTTTTT
53655841 ATTTTTT
1 ATTTTTT
53655848 TTTGAGTCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 15 0.39
7 22 0.58
8 1 0.03
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.83
Consensus pattern (7 bp):
ATTTTTT
Found at i:53655824 original size:25 final size:25
Alignment explanation
Indices: 53655781--53655850 Score: 97
Period size: 25 Copynumber: 2.7 Consensus size: 25
53655771 CTTTTTCTCC
53655781 TATTTTTGACTTTGATTTTTTATTTTTA
1 TATTTTTGA-TTT--TTTTTTATTTTTA
*
53655809 T-TTTTTGATTTTTTTTTATTTTTT
1 TATTTTTGATTTTTTTTTATTTTTA
53655833 TATTTTTGATTTTTTTTT
1 TATTTTTGATTTTTTTTT
53655851 GAGTCTGAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
24 13 0.32
25 16 0.40
26 3 0.08
27 7 0.17
28 1 0.03
ACGTcount: A:0.13, C:0.01, G:0.06, T:0.80
Consensus pattern (25 bp):
TATTTTTGATTTTTTTTTATTTTTA
Found at i:53655826 original size:18 final size:18
Alignment explanation
Indices: 53655798--53655852 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
53655788 GACTTTGATT
53655798 TTTTATTTTTATTTTTTGA
1 TTTT-TTTTTATTTTTTGA
*
53655817 TTTTTTTTTATTTTTTTA
1 TTTTTTTTTATTTTTTGA
*
53655835 TTTTTGATTT-TTTTTTGA
1 TTTTT-TTTTATTTTTTGA
53655853 GTCTGAACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 25 0.78
19 7 0.22
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTATTTTTTGA
Found at i:53657113 original size:19 final size:20
Alignment explanation
Indices: 53657084--53657135 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
53657074 CACTTCGAGA
* *
53657084 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
53657103 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
53657123 AAATG-AATGCAAA
1 AAATGTAATGCAAA
53657136 AAAGAGACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:53660541 original size:16 final size:17
Alignment explanation
Indices: 53660509--53660548 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
53660499 CTTACTGTAA
53660509 TGGGC-TTGTTTGGATT
1 TGGGCTTTGTTTGGATT
*
53660525 TGGGCTTTGTTT-TATT
1 TGGGCTTTGTTTGGATT
53660541 TGGG-TTTG
1 TGGGCTTTG
53660549 GCATTTGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 12 0.55
17 6 0.27
ACGTcount: A:0.05, C:0.05, G:0.35, T:0.55
Consensus pattern (17 bp):
TGGGCTTTGTTTGGATT
Found at i:53662503 original size:21 final size:21
Alignment explanation
Indices: 53662471--53662520 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
53662461 TGACATTTTT
53662471 AATTAA-ATAAAAATATTTAA
1 AATTAACATAAAAATATTTAA
53662491 AATTAACATAAAAATATTTAA
1 AATTAACATAAAAATATTTAA
53662512 AATTAACAT
1 AATTAACAT
53662521 TAAGTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTAACATAAAAATATTTAA
Found at i:53663393 original size:10 final size:10
Alignment explanation
Indices: 53663378--53663412 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
53663368 TATTTTTTAA
53663378 TTTTAATTTT
1 TTTTAATTTT
53663388 TTTTAA-TTT
1 TTTTAATTTT
*
53663397 TTTTAATTGT
1 TTTTAATTTT
53663407 TTTTAA
1 TTTTAA
53663413 AAAATATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:53668661 original size:42 final size:41
Alignment explanation
Indices: 53668566--53668705 Score: 147
Period size: 42 Copynumber: 3.4 Consensus size: 41
53668556 GCTAATCAAA
* * * *
53668566 AAACACTGCAAAAGGTTAGAGCTATAGTGGCGTTTCTTCAT
1 AAACACCGCAAAAGGTTAGAGCTATAGAGGCTTTTTTTCAT
** *
53668607 AAACGTCGCAAAAGGTTAGATCTATAGAGGCATTTTTTTCAT
1 AAACACCGCAAAAGGTTAGAGCTATAGAGGC-TTTTTTTCAT
* * *
53668649 AAATACCGCAAAATGTTAGAGCTATAGCGGCGTTTTTATT-AT
1 AAACACCGCAAAAGGTTAGAGCTATAGAGGC-TTTTT-TTCAT
*
53668691 AAACACTGCAAAAGG
1 AAACACCGCAAAAGG
53668706 AAGCAATAAC
Statistics
Matches: 80, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
41 26 0.32
42 52 0.65
43 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (41 bp):
AAACACCGCAAAAGGTTAGAGCTATAGAGGCTTTTTTTCAT
Found at i:53670581 original size:20 final size:19
Alignment explanation
Indices: 53670551--53670588 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
53670541 AATCCAAGGC
*
53670551 ATTTTTTTATTTATCTATT
1 ATTTTTTTATTTACCTATT
53670570 ATTTTATTTATTTACCTAT
1 ATTTT-TTTATTTACCTAT
53670589 ACTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTTTATTTACCTATT
Found at i:53670583 original size:24 final size:24
Alignment explanation
Indices: 53670550--53670619 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
53670540 TAATCCAAGG
*
53670550 CATTTTTTTATTTATCTATTATTTT
1 CATTTATTTATTTAT-TATTATTTT
**
53670575 -ATTTATTTACCTA-TACTTATTTT
1 CATTTATTTATTTATTA-TTATTTT
53670598 CATTTA-TTATTTATTTATTATT
1 CATTTATTTATTTA-TTATTATT
53670620 ATTCCTTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
22 2 0.06
23 12 0.33
24 20 0.56
25 2 0.06
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (24 bp):
CATTTATTTATTTATTATTATTTT
Found at i:53672742 original size:21 final size:22
Alignment explanation
Indices: 53672716--53672761 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
53672706 AATCTATATA
53672716 TATACATGT-ATATTTATTTTT
1 TATACATGTAATATTTATTTTT
53672737 TATACATGTACATATTTATTTTT
1 TATACATGTA-ATATTTATTTTT
53672760 TA
1 TA
53672762 ACTAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (22 bp):
TATACATGTAATATTTATTTTT
Found at i:53673238 original size:19 final size:20
Alignment explanation
Indices: 53673197--53673238 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
53673187 ATTTCTATGC
*
53673197 CATTGTAATATTTAATATTG
1 CATTGTAATATTTAATATAG
*
53673217 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
53673236 CAT
1 CAT
53673239 CACATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:53685059 original size:44 final size:44
Alignment explanation
Indices: 53684928--53685877 Score: 461
Period size: 44 Copynumber: 21.8 Consensus size: 44
53684918 CCAATGATCC
* *
53684928 TATCTCCCTGAAGTTGCAGTGGAGCGGACTAA--AACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCA-AG-TCT
* ** * * *
53684972 TATCTCTCTGAAGTTGCA-AAGAGCAGA-T-TGC-ATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCT
* * * *
53685012 TATCTCCCTAAAGTTGCAGTAGAGTAGACTAAGCAAGCATGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCT
* * *
53685056 TATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAG-ATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGCA-AGCAAGTCT
* * *
53685101 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGC-AG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTA-AGCAAGCA-AGTCT
*
53685145 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCT
* * * **
53685189 TATC-CTCCTGAAGTTACAGTGGGGCAGACTGAAG-ATGGCAAACCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGCA-AGCAAGTCT
* ** * * *
53685234 TATCTCCCTGAAGTTACAGTGGAGCAGGTTAAAGC-CG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAAGCA-AGTCT
* * * * **
53685278 TATCTCCCTAAAGTTGCAGTGGAGC-GAATTA--AATCTTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGC--AAG-TCT
* * * * *
53685322 TATC-CTTCTGAAGTTGCAG-AGAGCAGA-T-TGC-ATCTAGTCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCT
*
53685362 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCT
* * * **
53685406 TATC-CTCCTGAAGTTACAGTGGGGCAGACTGAAG-ATGGCAAACCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGCA-AGCAAGTCT
* * ** * * *
53685451 TA-CTTCCTGAAGTTACAGTGGAGCAGGTTAAAGC-CG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAAGCA-AGTCT
* * *
53685494 TATCTCCCTGAAGGTGCAGAGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCT
* ** * **
53685538 TATC-CTCCTGAAGTTGCAGTGGTGCAGACTAAATATGGCAAACCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACTAAGCA-AGCAAGTCT
* * ** * * *
53685583 TATCTCCCTGAGGATGCAGTGGAGCAGGTTAAAGC-CG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAAGCA-AGTCT
* * * ** **
53685627 TATCCCCCTGAAGTTGCAGTGGAGCGGATTAA--ATCCTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGC-AAG-TCT
* * * * *
53685671 TATCTCGCTGAAGTTGCAG-AGAGCAGA-TCA-C-ATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCT
* *
53685711 TGTCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCT
* * * * *
53685755 TATC-CTCTTGAAGTTGCAGTGGGGCAGATTGAAG-ATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGCA-AGCAAGTCT
* * * *
53685800 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AAGTTGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAG--CA-AGTCT
*
53685845 TATCTCCCTGAAGTTGCAATGGAGCAGACTAAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG
53685878 TAGAGCAGAT
Statistics
Matches: 698, Mismatches: 140, Indels: 134
0.72 0.14 0.14
Matches are distributed among these distances:
40 58 0.08
41 28 0.04
42 13 0.02
43 50 0.07
44 358 0.51
45 183 0.26
46 8 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCT
Found at i:53685162 original size:133 final size:133
Alignment explanation
Indices: 53685012--53685302 Score: 456
Period size: 133 Copynumber: 2.2 Consensus size: 133
53685002 CATCTAGTCT
* * *
53685012 TATCTCCCTAAAGTTGCAGTAGAGTAGACTAAGCAAGCATGTCTTATCCTCCTGAAGTTGCAGTG
1 TATCTCCCTAAAGTTGCAGTAGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTACAGTG
* * * *
53685077 AGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCAGATAA
66 AGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCAGATAA
53685142 TCC
131 TCC
* * *
53685145 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTG
1 TATCTCCCTAAAGTTGCAGTAGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTACAGTG
* * *
53685210 GGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTAAAGCCGATAA
66 AGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCAGATAA
53685275 TCC
131 TCC
*
53685278 TATCTCCCTAAAGTTGCAGTGGAGC
1 TATCTCCCTAAAGTTGCAGTAGAGC
53685303 GAATTAAATC
Statistics
Matches: 144, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
133 144 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (133 bp):
TATCTCCCTAAAGTTGCAGTAGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTACAGTG
AGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCAGATAA
TCC
Found at i:53685623 original size:349 final size:350
Alignment explanation
Indices: 53684914--53685884 Score: 1498
Period size: 349 Copynumber: 2.8 Consensus size: 350
53684904 GAACAGATCG
* * * * ***
53684914 AAAGCCAATGATCCTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAAACCACAGATCTTATCTCT
1 AAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAATCCTTGGATCTTATCTCT
* * * *
53684979 CTGAAGTTGCAAAGAGCAGATTGCATCTAGTCTTATCTCCCTAAAGTTGCAGTAGAGTAGACTAA
66 CTGAAGTTGCAGAGAGCAGATTGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
* * * *
53685044 GCAAGCATGTCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCC
131 GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCC
* *
53685109 TGAAGTTGCAGTGGAGCAGATTAGAGCAGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAC
196 TGAAGTTGCAGTGGAGCAGATTAAAGCAGATAATCCTATCTCCCTGAAGTTGCAGAGGAGCAGAC
*
53685174 TAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGGGGCAGACTGAAGATGGCAAACCTTATCT
261 TAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGGGGCAGACTAAAGATGGCAAACCTTATCT
*
53685239 CCCTGAAGTTACAGTGGAGCAGGTT
326 CCCTGAAGATACAGTGGAGCAGGTT
* * *
53685264 AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATTAAATCTTTGGATCTTATC-CT
1 AAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAATCCTTGGATCTTATCTC-
53685328 TCTGAAGTTGCAGAGAGCAGATTGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
65 TCTGAAGTTGCAGAGAGCAGATTGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
* * *
53685393 AGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGGGGCAGACTGAAGATGGCAAACCTTA-CTTC
130 AGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTTATCTCC
* * * *
53685457 CTGAAGTTACAGTGGAGCAGGTTAAAGCCGATAATCCTATCTCCCTGAAGGTGCAGAGGAGCAGA
195 CTGAAGTTGCAGTGGAGCAGATTAAAGCAGATAATCCTATCTCCCTGAAGTTGCAGAGGAGCAGA
* * *
53685522 CTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGTGCAGACTAAATATGGCAAACCTTATC
260 CTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGGGGCAGACTAAAGATGGCAAACCTTATC
* *
53685587 TCCCTGAGGATGCAGTGGAGCAGGTT
325 TCCCTGAAGATACAGTGGAGCAGGTT
* *
53685613 AAAGCCGATAATCCTATCCCCCTGAAGTTGCAGTGGAGCGGATTAAATCCTTGGATCTTATCTCG
1 AAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAATCCTTGGATCTTATCTCT
** *
53685678 CTGAAGTTGCAGAGAGCAGATCACATCTAGTCTTGTCTCCCTGAAGTTGCAGTGGAGCAGACTAA
66 CTGAAGTTGCAGAGAGCAGATTGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
* *
53685743 GTAAGCAAGTCTTATCCTCTTGAAGTTGCAGTGGGGCAGATTGAAGATGGCAAATCTTATCTCCC
131 GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCC
**
53685808 TGAAGTTGCAGTGGAGCAGATTAAAAGTTGATAATCCTATCTCCCTGAAGTTGCA-ATGGAGCAG
196 TGAAGTTGCAGTGGAGCAGATT-AAAGCAGATAATCCTATCTCCCTGAAGTTGCAGA-GGAGCAG
53685872 ACTAAGTAGAGCA
259 ACTAAGTA-AGCA
53685885 GATCGCATGA
Statistics
Matches: 563, Mismatches: 52, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
349 322 0.57
350 193 0.34
351 44 0.08
352 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (350 bp):
AAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAATCCTTGGATCTTATCTCT
CTGAAGTTGCAGAGAGCAGATTGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCC
TGAAGTTGCAGTGGAGCAGATTAAAGCAGATAATCCTATCTCCCTGAAGTTGCAGAGGAGCAGAC
TAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGGGGCAGACTAAAGATGGCAAACCTTATCT
CCCTGAAGATACAGTGGAGCAGGTT
Found at i:53686785 original size:19 final size:20
Alignment explanation
Indices: 53686744--53686785 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
53686734 ATTTCTATGC
* *
53686744 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
53686764 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
53686783 CAT
1 CAT
53686786 CACATCATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:53688157 original size:18 final size:18
Alignment explanation
Indices: 53688134--53688197 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
53688124 TATAGGTAAG
53688134 TATAATAATAATAAATAA
1 TATAATAATAATAAATAA
* * *
53688152 TATAATTATTATTAAT-A
1 TATAATAATAATAAATAA
*
53688169 -ATAATAATAACAAATAA
1 TATAATAATAATAAATAA
**
53688186 TGCAATAATAAT
1 TATAATAATAAT
53688198 GATGCAATAA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
16 11 0.32
17 2 0.06
18 21 0.62
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (18 bp):
TATAATAATAATAAATAA
Found at i:53689784 original size:50 final size:50
Alignment explanation
Indices: 53689730--53690203 Score: 319
Period size: 50 Copynumber: 9.5 Consensus size: 50
53689720 CAAGGAAGTA
* *
53689730 AGATCCGCCATTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
* * * ** * *** ***
53689780 AGATCCGCCATCGTAGCTTCAATCTGTTCCACTGCACCATCAGGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
* *
53689830 AGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
* * * * ** * ** * ***
53689880 AGATCCACCATCT-TAACTTCAATCTGTTCCACTGCACCGCCAGGGAAGTA
1 AGATCCGCCGT-TGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
* * * **
53689930 AGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTTGGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
* * * ** * ***
53689980 AGATCCGCCGTCGTAGCTTCAATCTGTTCT-AGTGCACCGCCAGGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCT-TTTTAATTGCAATGTCAGGGAAACC
* * *
53690030 AGATCCGTCATTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
* * ** * * ***
53690080 AGATCCACCGTTGTAGCTTCAATCTATTCCACTGC-ATCG-CTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAAT-GTC-AGGGAAACC
* * * * * *
53690130 AGATTCGTCGTTGTGGCTTTAATC-TTTAAATTGCAATGTCGGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
*
53690179 AGATCCGCCGTCGTAGCTTCAATCT
1 AGATCCGCCGTTGTAGCTTCAATCT
53690204 GTTCCACTAC
Statistics
Matches: 299, Mismatches: 116, Indels: 18
0.69 0.27 0.04
Matches are distributed among these distances:
49 37 0.12
50 258 0.86
51 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (50 bp):
AGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACC
Found at i:53689827 original size:100 final size:100
Alignment explanation
Indices: 53689646--53690252 Score: 788
Period size: 100 Copynumber: 6.1 Consensus size: 100
53689636 GGATTATTTT
* ** * * * * * *
53689646 CTTCAAT-TTGTTTAACTGCAATGTTGGGGAAACAAGATTCACCGTTGT-GACTTCAATCTATTT
1 CTTCAATCTT-TTTAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGTTC
* * *
53689709 CACTACACCGCCAAGGAAGTAAGATCCGCCATTGTGG
64 CACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
*
53689746 CTTCAATCTTTTTAATTGCAATGTCAGGGAAACCAGATCCGCCATCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
** *
53689811 CTGCACCATCAGGGAAGTAAGATCTGCCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
* * * *
53689846 CTTCAATCTTTTTAATTGCAATGTCAGGGAAACCAGATCCACCATCTTAACTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
*
53689911 CTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
* ** *
53689946 CTTCAATCTTTTTAATTGTAATGTTGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCTA
1 CTTCAATCTTTTTAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
53690011 GTGCACCGCCAGGGAAGTAAGATCCGTCATTGTGG
66 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
* * *
53690046 CTTCAATCTTTTTAATTGCAATGTCAGGGAAACCAGATCCACCGTTGTAGCTTCAATCTATTCCA
1 CTTCAATCTTTTTAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * * * *
53690111 CTGCATCGCTAAGGAAGTAAGATTCGTCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
* * *
53690146 CTTTAATC-TTTAAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * * *
53690210 CTACACCGCTAGGGAAGCAAGATTCGCCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
53690245 CTTCAATC
1 CTTCAATC
53690253 CGTTCCACTG
Statistics
Matches: 447, Mismatches: 58, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
99 88 0.20
100 356 0.80
101 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (100 bp):
CTTCAATCTTTTTAATTGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
Found at i:53690448 original size:50 final size:48
Alignment explanation
Indices: 53690342--53690448 Score: 106
Period size: 50 Copynumber: 2.1 Consensus size: 48
53690332 ACGCCAGGGA
* * * *
53690342 GATAAGATTCGCTGTCGTGGCTTCAATCTGCTCCGCTACAATGCTAGG
1 GATAAGATTCGCCGTCGTGGCTTCAATCTGCTCCACTACAACGCAAGG
** * *
53690390 GAAGTAAGATTCGCCGTCGTGGCTTCAATCTTTTCCATTGCAACGTCAAGG
1 G-A-TAAGATTCGCCGTCGTGGCTTCAATCTGCTCCACTACAACG-CAAGG
53690441 CGATAAGA
1 -GATAAGA
53690449 CTGATGTCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
48 1 0.02
49 1 0.02
50 39 0.83
51 5 0.11
52 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.28
Consensus pattern (48 bp):
GATAAGATTCGCCGTCGTGGCTTCAATCTGCTCCACTACAACGCAAGG
Found at i:53690529 original size:44 final size:44
Alignment explanation
Indices: 53690480--53690615 Score: 130
Period size: 44 Copynumber: 3.1 Consensus size: 44
53690470 GCTGCCAGTA
* *
53690480 CAGGAAGGCAAGATCTGCCATTTTCAACCTACTCCACTGCTGCT
1 CAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCT
* * ** * * * * ** *
53690524 CAGGAAGACAAG-GCTGGTATCCTCGATCTACTTCGCTGTCAACA
1 CAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTG-CTGCT
*
53690568 CAGGAAGACAATATCTGCTATTTTCAACCTACTCCACTGCTGCT
1 CAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCT
53690612 CAGG
1 CAGG
53690616 GAGATAAGGC
Statistics
Matches: 65, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
43 17 0.26
44 30 0.46
45 18 0.28
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (44 bp):
CAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCT
Done.