Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 135 of 290
Found at i:42591810 original size:41 final size:41
Alignment explanation
Indices: 42591753--42591842 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
42591743 TTTAGTGGCT
* * * * *
42591753 TTAGCAGCGTTTTTTTGAAAATCGCCGCTATATATCGAGCA
1 TTAGCAGCGCTTTTTTGAAAAACACCGCAATAGATCGAGCA
* *
42591794 TTAGCGGCGCTTTTTTGAAAAACACCGCAATAGGTCGAGCA
1 TTAGCAGCGCTTTTTTGAAAAACACCGCAATAGATCGAGCA
42591835 TTAGCAGC
1 TTAGCAGC
42591843 ATTTTTCAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (41 bp):
TTAGCAGCGCTTTTTTGAAAAACACCGCAATAGATCGAGCA
Found at i:42592124 original size:7 final size:7
Alignment explanation
Indices: 42592109--42592146 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
42592099 TTAATTATCA
*
42592109 TTATAGT
1 TTATGGT
42592116 TTATGGT
1 TTATGGT
42592123 TTATGGT
1 TTATGGT
*
42592130 TTGTGGT
1 TTATGGT
42592137 TTATGGT
1 TTATGGT
42592144 TTA
1 TTA
42592147 ACAATTGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (7 bp):
TTATGGT
Found at i:42592197 original size:7 final size:7
Alignment explanation
Indices: 42592165--42592230 Score: 71
Period size: 7 Copynumber: 9.4 Consensus size: 7
42592155 GGTTTAAGAT
42592165 TTAAGGG
1 TTAAGGG
42592172 TT-AGGTG
1 TTAAGG-G
*
42592179 TTAGGGG
1 TTAAGGG
*
42592186 CTAAGGG
1 TTAAGGG
42592193 TTAAGGG
1 TTAAGGG
*
42592200 TTAGGGG
1 TTAAGGG
* *
42592207 TTAAAGA
1 TTAAGGG
42592214 TTAAGGG
1 TTAAGGG
42592221 TTAAGGG
1 TTAAGGG
42592228 TTA
1 TTA
42592231 GAGGTTTATA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
6 3 0.06
7 42 0.89
8 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.41, T:0.30
Consensus pattern (7 bp):
TTAAGGG
Found at i:42592300 original size:29 final size:28
Alignment explanation
Indices: 42592268--42592353 Score: 91
Period size: 29 Copynumber: 3.0 Consensus size: 28
42592258 TATGTTTTGT
*
42592268 GATTTAGGGCTTAAGGGTTTATGGTTTAG
1 GATTTAGGGCTTAA-GGTTTAGGGTTTAG
* * *
42592297 GATTCAGGGTTTAAAGTTTAGGGTTTAG
1 GATTTAGGGCTTAAGGTTTAGGGTTTAG
** *
42592325 GAGATAGGGGTTAAAGGTTTAGGGTTTAG
1 GATTTAGGGCTT-AAGGTTTAGGGTTTAG
42592354 ATTAATTAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 20 0.43
29 27 0.57
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.37
Consensus pattern (28 bp):
GATTTAGGGCTTAAGGTTTAGGGTTTAG
Found at i:42592322 original size:7 final size:7
Alignment explanation
Indices: 42592270--42592353 Score: 53
Period size: 7 Copynumber: 11.7 Consensus size: 7
42592260 TGTTTTGTGA
42592270 TTTAGGG
1 TTTAGGG
*
42592277 CTTAAGGG
1 -TTTAGGG
*
42592285 TTTATGG
1 TTTAGGG
*
42592292 TTTAGGA
1 TTTAGGG
*
42592299 TTCAGGG
1 TTTAGGG
**
42592306 TTTAAAG
1 TTTAGGG
42592313 TTTAGGG
1 TTTAGGG
42592320 TTTAGGAG
1 TTTAGG-G
*
42592328 -ATAGGGG
1 TTTA-GGG
* *
42592335 TTAAAGG
1 TTTAGGG
42592342 TTTAGGG
1 TTTAGGG
42592349 TTTAG
1 TTTAG
42592354 ATTAATTAGT
Statistics
Matches: 55, Mismatches: 18, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
7 45 0.82
8 10 0.18
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (7 bp):
TTTAGGG
Found at i:42592324 original size:28 final size:29
Alignment explanation
Indices: 42592272--42592353 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 29
42592262 TTTTGTGATT
* * * *
42592272 TAGGGCTTAAGGGTTTATGGTTTAGGA-T
1 TAGGGGTTAAAGGTTTAGGGTTTAGGAGA
*
42592300 TCAGGGTTTAAA-GTTTAGGGTTTAGGAGA
1 T-AGGGGTTAAAGGTTTAGGGTTTAGGAGA
42592329 TAGGGGTTAAAGGTTTAGGGTTTAG
1 TAGGGGTTAAAGGTTTAGGGTTTAG
42592354 ATTAATTAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 24 0.52
29 22 0.48
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (29 bp):
TAGGGGTTAAAGGTTTAGGGTTTAGGAGA
Found at i:42592524 original size:15 final size:15
Alignment explanation
Indices: 42592504--42592562 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 15
42592494 ATGGTTTAGG
42592504 ATTTAATCTAAAAAT
1 ATTTAATCTAAAAAT
*
42592519 ATTTAATCTAAACCAT
1 ATTTAATCTAAA-AAT
42592535 -TTGATATAT-TAAAAAT
1 ATT--TA-ATCTAAAAAT
42592551 ATTTAATCTAAA
1 ATTTAATCTAAA
42592563 CCATTCGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
14 2 0.06
15 20 0.56
16 4 0.11
17 8 0.22
18 2 0.06
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (15 bp):
ATTTAATCTAAAAAT
Found at i:42592548 original size:32 final size:32
Alignment explanation
Indices: 42592512--42592584 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
42592502 GGATTTAATC
*
42592512 TAAAAATATTTAATCTAAACCATTTGATATAT
1 TAAAAATATTTAATCTAAACCATTCGATATAT
42592544 TAAAAATATTTAATCTAAACCATTCGATATAT
1 TAAAAATATTTAATCTAAACCATTCGATATAT
*
42592576 T-TAAATATT
1 TAAAAATATT
42592585 AGGATTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 7 0.18
32 32 0.82
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.41
Consensus pattern (32 bp):
TAAAAATATTTAATCTAAACCATTCGATATAT
Found at i:42594204 original size:15 final size:16
Alignment explanation
Indices: 42594180--42594220 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42594170 ATTAAATTTT
42594180 AATA-AAAAATT--AA
1 AATATAAAAATTAGAA
42594193 AATATTAAAAATTAGAA
1 AATA-TAAAAATTAGAA
42594210 AATATAAAAAT
1 AATATAAAAAT
42594221 CGTAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
15 7 0.29
16 7 0.29
17 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
AATATAAAAATTAGAA
Found at i:42594211 original size:17 final size:17
Alignment explanation
Indices: 42594191--42594238 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
42594181 ATAAAAAATT
42594191 AAAATATTAAAAAT-TA
1 AAAATATTAAAAATCTA
42594207 GAAAATA-TAAAAATCGTA
1 -AAAATATTAAAAATC-TA
42594225 AAAATATATAAAAA
1 AAAATAT-TAAAAA
42594239 ATTGTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.26
17 12 0.44
18 2 0.07
19 6 0.22
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (17 bp):
AAAATATTAAAAATCTA
Found at i:42594240 original size:20 final size:19
Alignment explanation
Indices: 42594181--42594255 Score: 60
Period size: 16 Copynumber: 4.3 Consensus size: 19
42594171 TTAAATTTTA
42594181 ATAAAAAAT--TAAAATAT
1 ATAAAAAATCGTAAAATAT
42594198 -T-AAAAAT--TAGAAA-AT
1 ATAAAAAATCGTA-AAATAT
42594213 AT-AAAAATCGTAAAAATAT
1 ATAAAAAATCGT-AAAATAT
*
42594232 ATAAAAAATTGTAAAAT-T
1 ATAAAAAATCGTAAAATAT
42594250 ATAAAA
1 ATAAAA
42594256 TAAATAAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
15 10 0.20
16 11 0.22
18 11 0.22
19 10 0.20
20 8 0.16
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (19 bp):
ATAAAAAATCGTAAAATAT
Found at i:42594260 original size:20 final size:20
Alignment explanation
Indices: 42594211--42594255 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
42594201 AAATTAGAAA
42594211 ATAT-AAAAATCGTAAAAAT
1 ATATAAAAAATCGTAAAAAT
*
42594230 ATATAAAAAATTGT-AAAAT
1 ATATAAAAAATCGTAAAAAT
42594249 -TATAAAA
1 ATATAAAA
42594256 TAAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 9 0.38
20 8 0.33
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
ATATAAAAAATCGTAAAAAT
Found at i:42594271 original size:18 final size:19
Alignment explanation
Indices: 42594250--42594291 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
42594240 TTGTAAAATT
42594250 ATAAAATAAATA-AAATAC
1 ATAAAATAAATAGAAATAC
*
42594268 ATAAAATATATAGAAATAC
1 ATAAAATAAATAGAAATAC
42594287 A-AAAA
1 ATAAAA
42594292 AATTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (19 bp):
ATAAAATAAATAGAAATAC
Found at i:42594292 original size:19 final size:18
Alignment explanation
Indices: 42594252--42594292 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
42594242 GTAAAATTAT
*
42594252 AAAATAAATAAAATACAT
1 AAAATAAATAAAATACAA
*
42594270 AAAATATATAGAAATACAA
1 AAAATAAATA-AAATACAA
42594289 AAAA
1 AAAA
42594293 ATTATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAATAAATAAAATACAA
Found at i:42600595 original size:34 final size:34
Alignment explanation
Indices: 42600557--42600627 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
42600547 AAGCAAAATT
*
42600557 AGTACTCATGATAATCCTGTAGATATGATGACTA
1 AGTACTCATGATAATCCTGCAGATATGATGACTA
42600591 AGTACTCATGATAATCCTGCAGATATGATGACTA
1 AGTACTCATGATAATCCTGCAGATATGATGACTA
42600625 AGT
1 AGT
42600628 CACTTCCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (34 bp):
AGTACTCATGATAATCCTGCAGATATGATGACTA
Found at i:42600835 original size:38 final size:38
Alignment explanation
Indices: 42600792--42600871 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
42600782 AGATTGTTAG
*
42600792 AAGTTGTGTGACTCAAATTCCTATTAAACATAAAATAC
1 AAGTTGTGTGACCCAAATTCCTATTAAACATAAAATAC
*
42600830 AAGTTGTGTGACCCAAATTCTTATTAAACATAAAATAC
1 AAGTTGTGTGACCCAAATTCCTATTAAACATAAAATAC
42600868 AAGT
1 AAGT
42600872 CAAGCTGCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.31
Consensus pattern (38 bp):
AAGTTGTGTGACCCAAATTCCTATTAAACATAAAATAC
Found at i:42601311 original size:9 final size:9
Alignment explanation
Indices: 42601299--42601356 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
42601289 GACTTTTAGC
42601299 ATTTTTATA
1 ATTTTTATA
42601308 ATTTTTATA
1 ATTTTTATA
42601317 ATTTTTA-A
1 ATTTTTATA
** *
42601325 AAATTT-GA
1 ATTTTTATA
42601333 ATTTTTAATA
1 ATTTTT-ATA
42601343 ATTTTTATA
1 ATTTTTATA
42601352 ATTTT
1 ATTTT
42601357 AAAAATTCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
8 10 0.24
9 24 0.59
10 7 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:42601337 original size:16 final size:15
Alignment explanation
Indices: 42601315--42601376 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
42601305 ATAATTTTTA
42601315 TAATTTTTAAAAATT
1 TAATTTTTAAAAATT
*
42601330 TGAATTTTTAATAATTTT
1 T-AATTTTTAA-AA-ATT
*
42601348 TATAATTTTAAAAATT
1 TA-ATTTTTAAAAATT
42601364 CT-ATTTTTAAAAA
1 -TAATTTTTAAAAA
42601377 ATATTTTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
15 11 0.29
16 11 0.29
17 6 0.16
18 10 0.26
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
TAATTTTTAAAAATT
Found at i:42601339 original size:34 final size:34
Alignment explanation
Indices: 42601299--42601363 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
42601289 GACTTTTAGC
42601299 ATTTTT-ATAATTTTTATAATTTTTAAAAATTTGA
1 ATTTTTAATAATTTTTATAA-TTTTAAAAATTTGA
42601333 ATTTTTAATAATTTTTATAATTTTAAAAATT
1 ATTTTTAATAATTTTTATAATTTTAAAAATT
42601364 CTATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (34 bp):
ATTTTTAATAATTTTTATAATTTTAAAAATTTGA
Found at i:42601363 original size:9 final size:9
Alignment explanation
Indices: 42601299--42601363 Score: 53
Period size: 9 Copynumber: 7.3 Consensus size: 9
42601289 GACTTTTAGC
*
42601299 ATTTTTATA
1 ATTTTAATA
*
42601308 ATTTTTATA
1 ATTTTAATA
*
42601317 ATTTTTAAAA
1 A-TTTTAATA
*
42601327 ATTTGAAT-
1 ATTTTAATA
42601335 -TTTTAATA
1 ATTTTAATA
*
42601343 ATTTTTATA
1 ATTTTAATA
*
42601352 ATTTTAAAA
1 ATTTTAATA
42601361 ATT
1 ATT
42601364 CTATTTTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
7 6 0.13
9 32 0.71
10 7 0.16
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (9 bp):
ATTTTAATA
Found at i:42601384 original size:35 final size:34
Alignment explanation
Indices: 42601299--42601376 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 34
42601289 GACTTTTAGC
*
42601299 ATTTTT-ATAATTTTTATAATTTTTAAAAATTTGA
1 ATTTTTAAAAATTTTTATAATTTTTAAAAATTT-A
*
42601333 ATTTTTAATAATTTTTATAA-TTTTAAAAATTCT-
1 ATTTTTAAAAATTTTTATAATTTTTAAAAATT-TA
42601366 ATTTTTAAAAA
1 ATTTTTAAAAA
42601377 ATATTTTACA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
33 10 0.24
34 17 0.41
35 14 0.34
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (34 bp):
ATTTTTAAAAATTTTTATAATTTTTAAAAATTTA
Found at i:42601419 original size:14 final size:14
Alignment explanation
Indices: 42601400--42601428 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42601390 TTTTCTATTA
42601400 ATTTAAATATTTTT
1 ATTTAAATATTTTT
42601414 ATTTAAATATTTTT
1 ATTTAAATATTTTT
42601428 A
1 A
42601429 ATAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTAAATATTTTT
Found at i:42611647 original size:18 final size:17
Alignment explanation
Indices: 42611606--42611654 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
42611596 TCTATTAAAA
42611606 ATATTAAAATATTTTTT
1 ATATTAAAATATTTTTT
*
42611623 ATCTTAAAATATTATTTT
1 ATATTAAAATATT-TTTT
*
42611641 TTATTAAAATATTT
1 ATATTAAAATATTT
42611655 AAATTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTAAAATATTTTTT
Found at i:42612638 original size:18 final size:18
Alignment explanation
Indices: 42612598--42612641 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
42612588 TTACTAAAAC
*
42612598 TAAAAAATAATATTTTATT
1 TAAAAAAT-ATATTTTATA
42612617 TAAAAAAT-TATTTTAATA
1 TAAAAAATATATTTT-ATA
42612635 TAAAAAA
1 TAAAAAA
42612642 AGGAGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAAAATATATTTTATA
Found at i:42613160 original size:23 final size:23
Alignment explanation
Indices: 42613133--42613177 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
42613123 GTAATTATTG
42613133 TTGCAACTTGTAGTAGCCTCTAT
1 TTGCAACTTGTAGTAGCCTCTAT
42613156 TTGCAACTTGTAGTAGCCTCTA
1 TTGCAACTTGTAGTAGCCTCTA
42613178 CCTCATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (23 bp):
TTGCAACTTGTAGTAGCCTCTAT
Found at i:42615475 original size:40 final size:40
Alignment explanation
Indices: 42615443--42615674 Score: 328
Period size: 40 Copynumber: 5.8 Consensus size: 40
42615433 GGATATAGCT
* * *
42615443 ACTCGCTCGAATGCCTTCAGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
**
42615483 GTTCGCACAAATGCCTTCGGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
*
42615523 ACTCGCACAAATACCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
42615563 ACTCGCA-ACAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACA-AATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
42615603 ACTCGCAACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTC
1 ACTCGC-ACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
42615643 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
42615675 TTATCATCCG
Statistics
Matches: 176, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
39 6 0.03
40 164 0.93
41 5 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:42615569 original size:80 final size:80
Alignment explanation
Indices: 42615417--42615674 Score: 339
Period size: 80 Copynumber: 3.2 Consensus size: 80
42615407 AAACCAAGTA
* * * * *
42615417 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATGCCTTCAGGACTTAGCCCGG-ATAT
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-T
**
42615479 AGTAGTTCGCACAAATG
64 AGTAACTCGCACAAATG
*
42615496 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAGCCCGGAATTAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAG
42615561 TAACTCGCA-ACAATG
66 TAACTCGCACA-AATG
42615576 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCAACAAA-GCCTTCGGGACTTAGCCCGGAATT
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGC-ACAAATGCCTTCGGGACTTAGCCCGGAATT
* *
42615639 AGTCACTAGCACAAATG
64 AGTAACTCGCACAAATG
42615656 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
42615675 TTATCATCCG
Statistics
Matches: 161, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
79 15 0.09
80 138 0.86
81 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAG
TAACTCGCACAAATG
Found at i:42619933 original size:44 final size:44
Alignment explanation
Indices: 42619853--42619936 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
42619843 CATGTATCGT
* * *
42619853 ATCCATTATGAACTCGGACCAATTCAACAAGTTTAGATGCTCGC
1 ATCCATAATGAACTCGGACCAACTCAACAAGCTTAGATGCTCGC
**
42619897 ATCCATAATGAACTCGGACCAACTCAATGAGCTTAGATGC
1 ATCCATAATGAACTCGGACCAACTCAACAAGCTTAGATGC
42619937 CTCATATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (44 bp):
ATCCATAATGAACTCGGACCAACTCAACAAGCTTAGATGCTCGC
Found at i:42626039 original size:49 final size:48
Alignment explanation
Indices: 42625965--42626146 Score: 181
Period size: 49 Copynumber: 3.7 Consensus size: 48
42625955 TGATGTGTGT
*
42625965 GCTAGTGTAAGACTTGTCTAGGACATGGCATCGGCACCGATAGATGAGA
1 GCTAGTGTAAGACCTGTCTAGGACATGGCATCGGCACCGATA-ATGAGA
* * * *
42626014 GCTAGTGTAAAACCTGTCT-GAGACATGACATCGGCTTCAAGAT-ATGCA-A
1 GCTAGTGTAAGACCTGTCTAG-GACATGGCATCGGC-AC-CGATAATG-AGA
* * * * *
42626063 GCTAGTGTAAGACCTGTATAGGACTTGGCACCGACACAGATAAGTGAGA
1 GCTAGTGTAAGACCTGTCTAGGACATGGCATCGGCACCGATAA-TGAGA
* *
42626112 GCTAGTGTAAGACCTATCTGGGACATGGCATCGGC
1 GCTAGTGTAAGACCTGTCTAGGACATGGCATCGGC
42626147 TTAGATGTGA
Statistics
Matches: 107, Mismatches: 18, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
47 4 0.04
48 4 0.04
49 93 0.87
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (48 bp):
GCTAGTGTAAGACCTGTCTAGGACATGGCATCGGCACCGATAATGAGA
Found at i:42626137 original size:98 final size:98
Alignment explanation
Indices: 42625965--42626148 Score: 262
Period size: 98 Copynumber: 1.9 Consensus size: 98
42625955 TGATGTGTGT
* * * * * *
42625965 GCTAGTGTAAGACTTGTCTAGGACATGGCATCGGCACCGATAGATGAGAGCTAGTGTAAAACCTG
1 GCTAGTGTAAGACCTGTATAGGACATGGCACCGACACAGATAGATGAGAGCTAGTGTAAAACCTA
42626030 TCTGAGACATGACATCGGCTTCAAGATATGCAA
66 TCTGAGACATGACATCGGCTTCAAGATATGCAA
* *
42626063 GCTAGTGTAAGACCTGTATAGGACTTGGCACCGACACAGATA-AGTGAGAGCTAGTGTAAGACCT
1 GCTAGTGTAAGACCTGTATAGGACATGGCACCGACACAGATAGA-TGAGAGCTAGTGTAAAACCT
* *
42626127 ATCTGGGACATGGCATCGGCTT
65 ATCTGAGACATGACATCGGCTT
42626149 AGATGTGAGA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
97 1 0.01
98 74 0.99
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (98 bp):
GCTAGTGTAAGACCTGTATAGGACATGGCACCGACACAGATAGATGAGAGCTAGTGTAAAACCTA
TCTGAGACATGACATCGGCTTCAAGATATGCAA
Found at i:42633768 original size:49 final size:48
Alignment explanation
Indices: 42633614--42633780 Score: 171
Period size: 49 Copynumber: 3.4 Consensus size: 48
42633604 TGATGTGTGT
* *
42633614 GCTAGTGTAAGACCTATCTGAGACATGGCATCGGCAC-CGATAGAT-GAGA
1 GCTAGTGTAAGACCTATCTGGGACATGGCATCGGC-CTCGA-CGATGGA-A
* * ** *
42633663 GCTAGTGTAAGACCTGTTTGGGACACAGCATCGGCCTCAAGAC-ATGCAA
1 GCTAGTGTAAGACCTATCTGGGACATGGCATCGGCCTC--GACGATGGAA
42633712 GCTAGTGTAAGACCTATCTGGGACATGGCATCGGCCTCGACGTATGGAA
1 GCTAGTGTAAGACCTATCTGGGACATGGCATCGGCCTCGACG-ATGGAA
*
42633761 G-TCAGTGTAAGACCTTTCTG
1 GCT-AGTGTAAGACCTATCTG
42633781 AGACCTGCTA
Statistics
Matches: 98, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
47 3 0.03
48 2 0.02
49 90 0.92
50 1 0.01
51 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (48 bp):
GCTAGTGTAAGACCTATCTGGGACATGGCATCGGCCTCGACGATGGAA
Found at i:42634279 original size:22 final size:21
Alignment explanation
Indices: 42634254--42634299 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
42634244 TTTTATTATC
42634254 TTGAGTATGGCATGTATAGGGA
1 TTGAGTA-GGCATGTATAGGGA
42634276 TT--G-AGGCATGTATAGGGA
1 TTGAGTAGGCATGTATAGGGA
42634294 TTGAGT
1 TTGAGT
42634300 CTTTTTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
18 16 0.76
19 1 0.05
20 2 0.10
22 2 0.10
ACGTcount: A:0.26, C:0.04, G:0.37, T:0.33
Consensus pattern (21 bp):
TTGAGTAGGCATGTATAGGGA
Found at i:42634285 original size:18 final size:18
Alignment explanation
Indices: 42634262--42634298 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
42634252 TCTTGAGTAT
42634262 GGCATGTATAGGGATTGA
1 GGCATGTATAGGGATTGA
42634280 GGCATGTATAGGGATTGA
1 GGCATGTATAGGGATTGA
42634298 G
1 G
42634299 TCTTTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.41, T:0.27
Consensus pattern (18 bp):
GGCATGTATAGGGATTGA
Found at i:42639120 original size:30 final size:30
Alignment explanation
Indices: 42639084--42639145 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
42639074 TGTAGTGATA
*
42639084 ATTATGTATATGATCCTCAGAATTGAGATC
1 ATTATGTATACGATCCTCAGAATTGAGATC
*
42639114 ATTATGTATACGATCCTCAGACTTGAGATC
1 ATTATGTATACGATCCTCAGAATTGAGATC
42639144 AT
1 AT
42639146 CATTGCTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (30 bp):
ATTATGTATACGATCCTCAGAATTGAGATC
Found at i:42644146 original size:53 final size:53
Alignment explanation
Indices: 42644066--42644254 Score: 145
Period size: 47 Copynumber: 3.8 Consensus size: 53
42644056 CATGACAACA
* * *
42644066 TGTGATATGTGATTTCTGTATAAGACCATAGCTGGGCTATGGCATCGGAAAGT
1 TGTGATATGTGACTTCCGTATAAGACCATAGCTGGGATATGGCATCGGAAAGT
**
42644119 TGTGACTATGTG-CTTCCGTATAAGACCATATTTGGGATATGGCATC-G---G-
1 TGTGA-TATGTGACTTCCGTATAAGACCATAGCTGGGATATGGCATCGGAAAGT
* * * **
42644167 TATGATATGTG-CTACTGTATAAGACCATATTTGGGATATGGCATC----AG-
1 TGTGATATGTGACTTCCGTATAAGACCATAGCTGGGATATGGCATCGGAAAGT
* * * *
42644214 TGTGATATGTGA--TCTGTGTAAGACCATGGCTGGGCTATGGC
1 TGTGATATGTGACTTCCGTATAAGACCATAGCTGGGATATGGC
42644255 TTCGATGTGT
Statistics
Matches: 118, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
46 23 0.19
47 49 0.42
48 4 0.03
49 1 0.01
52 1 0.01
53 34 0.29
54 6 0.05
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (53 bp):
TGTGATATGTGACTTCCGTATAAGACCATAGCTGGGATATGGCATCGGAAAGT
Found at i:42644194 original size:47 final size:46
Alignment explanation
Indices: 42644080--42644240 Score: 169
Period size: 47 Copynumber: 3.3 Consensus size: 46
42644070 ATATGTGATT
** * *
42644080 TCTGTATAAGACCATAGCTGGGCTATGGCATCGGAAAGTTGTGACTATGTGC
1 TCTGTATAAGACCATATTTGGGATATGGCATC----AG-TATGA-TATGTGC
* *
42644132 TTCCGTATAAGACCATATTTGGGATATGGCATCGGTATGATATGTGC
1 -TCTGTATAAGACCATATTTGGGATATGGCATCAGTATGATATGTGC
* *
42644179 TACTGTATAAGACCATATTTGGGATATGGCATCAGTGTGATATGTGA
1 T-CTGTATAAGACCATATTTGGGATATGGCATCAGTATGATATGTGC
*
42644226 TCTGTGTAAGACCAT
1 TCTGTATAAGACCAT
42644241 GGCTGGGCTA
Statistics
Matches: 96, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
46 14 0.15
47 49 0.51
48 4 0.04
49 1 0.01
53 28 0.29
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (46 bp):
TCTGTATAAGACCATATTTGGGATATGGCATCAGTATGATATGTGC
Found at i:42653092 original size:20 final size:20
Alignment explanation
Indices: 42653067--42653114 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
42653057 CCAAATAGGA
*
42653067 TCTTCTTTCTTTTCTCTGTT
1 TCTTCTTTCTTTTCTCTGCT
*
42653087 TCTTCTTTCTTTTCTTTGCT
1 TCTTCTTTCTTTTCTCTGCT
42653107 T-TTCTTTC
1 TCTTCTTTC
42653115 CTCTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.00, C:0.25, G:0.04, T:0.71
Consensus pattern (20 bp):
TCTTCTTTCTTTTCTCTGCT
Found at i:42657509 original size:73 final size:73
Alignment explanation
Indices: 42657432--42657579 Score: 269
Period size: 73 Copynumber: 2.0 Consensus size: 73
42657422 TTCTAAGAAT
42657432 CAAAACAATCTTTTAATGCTTCATTTATAAAACTTATCTTCAAATTCTCTTTTATATTTCACCAT
1 CAAAACAATCTTTTAATGCTTCATTTATAAAACTTATCTTCAAATTCTCTTTTATATTTCACCAT
42657497 ATCAAGTC
66 ATCAAGTC
* * *
42657505 CAAAACAATCTTTTAATGCTTCATTTATAAAATTTATCTTCAATTTCTCTTTTATATTTCACTAT
1 CAAAACAATCTTTTAATGCTTCATTTATAAAACTTATCTTCAAATTCTCTTTTATATTTCACCAT
42657570 ATCAAGTC
66 ATCAAGTC
42657578 CA
1 CA
42657580 GGAATGTTAC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.44
Consensus pattern (73 bp):
CAAAACAATCTTTTAATGCTTCATTTATAAAACTTATCTTCAAATTCTCTTTTATATTTCACCAT
ATCAAGTC
Found at i:42666266 original size:13 final size:12
Alignment explanation
Indices: 42666244--42666277 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
42666234 TATATATTTT
42666244 AAAAAAAACAAA
1 AAAAAAAACAAA
42666256 AAAACAAAACAAA
1 AAAA-AAAACAAA
42666269 ATAAAAAAA
1 A-AAAAAAA
42666278 TTGCTCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 13 0.65
14 3 0.15
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:42671530 original size:17 final size:17
Alignment explanation
Indices: 42671508--42671543 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
42671498 GTCATGGCCC
42671508 TTTCTT-TTTTTCTTTTT
1 TTTCTTGTTTTT-TTTTT
42671525 TTTCTTGTTTTTTTTTT
1 TTTCTTGTTTTTTTTTT
42671542 TT
1 TT
42671544 GGGGGGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (17 bp):
TTTCTTGTTTTTTTTTT
Found at i:42677601 original size:18 final size:18
Alignment explanation
Indices: 42677575--42677609 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42677565 AAATAGTTAA
*
42677575 AATTGTTGAAAATTTTGT
1 AATTGTTGAAAACTTTGT
*
42677593 AATTTTTGAAAACTTTG
1 AATTGTTGAAAACTTTG
42677610 AAGCATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (18 bp):
AATTGTTGAAAACTTTGT
Found at i:42681105 original size:27 final size:27
Alignment explanation
Indices: 42681067--42681121 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
42681057 ATAAAATAAG
42681067 GGTGGAGAGTACCCCACAGGCGACACC
1 GGTGGAGAGTACCCCACAGGCGACACC
*
42681094 GGTGGAGGGTACCCCACAGGCGACACC
1 GGTGGAGAGTACCCCACAGGCGACACC
42681121 G
1 G
42681122 ATCACTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.33, G:0.36, T:0.07
Consensus pattern (27 bp):
GGTGGAGAGTACCCCACAGGCGACACC
Found at i:42681827 original size:14 final size:14
Alignment explanation
Indices: 42681808--42681836 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42681798 AGCTTAATAG
42681808 TATATTTTAAAAAA
1 TATATTTTAAAAAA
42681822 TATATTTTAAAAAA
1 TATATTTTAAAAAA
42681836 T
1 T
42681837 CCGAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATTTTAAAAAA
Found at i:42682173 original size:143 final size:143
Alignment explanation
Indices: 42681832--42683008 Score: 1673
Period size: 144 Copynumber: 8.1 Consensus size: 143
42681822 TATATTTTAA
* * *
42681832 AAAATCCGAAAATAAAAT--AAAAAAGGCCAAAATCAGAATTTTTTACTAAATTAATATAAATAT
1 AAAATCCGAAAATAAAATAAAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAA
* *
42681895 ACTAAAATAATACATATGAAACATTATGTACTAAAATAA-AAAATAAAATAAAATACGAAAATAG
66 ACTAAAATAATACATTTG-AACATTATGTACTAAAATAATATAA-AAAATAAAATACGAAAATAG
42681959 TATATTTTAAAAAAT
129 TATATTTTAAAAAAT
42681974 AAAATCCGAAAATAAAATAAAAAACAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATAT-AA
1 AAAATCCGAAAATAAAAT-AAAAA-AAA-GGCCAAAATCAGAGTTTTTTACTAAATTAATATAAA
* *
42682038 AAAACTAAAATAATACATTTG-A-ATCATGTACTAAAATAATATAAAAAAATAAAATACTAAAAT
63 AAAACTAAAATAATACATTTGAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAAT
*
42682101 ATTATATTTTAAAAAAT
127 AGTATATTTTAAAAAAT
* * * *
42682118 AAAATTCGGGAAAACAAAATAAAAAAAAGGCCAAAATCACAGATTTTTACTAAATTAATAT-AAA
1 AAAA-TC-CGAAAATAAAATAAAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAA
*
42682182 AAACTAAAATAATACA--TGAAACATTATGTACTAAAATAATATAAAAAACAAAATACGAAAATA
64 AAACTAAAATAATACATTTG-AACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATA
*
42682245 ATATATTTTAAAAAAT
128 GTATATTTTAAAAAAT
* * * *
42682261 AAAATCCAAAAATAAAA-ATAAAAAAGGGCCAAAATCATAGTTTTTTTCTAAATTAATATAAAAA
1 AAAATCCGAAAATAAAATA-AAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAA
* *
42682325 AATTAAAATAATACATTTAAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATA
65 AACTAAAATAATACATTT-GAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAATA
42682390 GTATATTTTAAAAAAT
128 GTATATTTTAAAAAAT
* * * *
42682406 AAAATCCGAAAACAAAAT-GAAAAAAGAGCCAAAATCACAGATTTTTACTAAATTAATATAAAAA
1 AAAATCCGAAAATAAAATAAAAAAAAG-GCCAAAATCAGAGTTTTTTACTAAATTAATAT-AAAA
*
42682470 AAACTAAAATAATACA--TGAAACATTATGTACTAAAATAATATAAAAAATAAAATCCGAAAATA
64 AAACTAAAATAATACATTTG-AACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATA
42682533 GTATATTTTAAAAAAT
128 GTATATTTTAAAAAAT
* * * *
42682549 AAAATCCAAAAATAAAA-ATAAAAAAGGGCTAAAATCAGAGTTTTTTTCTAAATTAATATAAAAA
1 AAAATCCGAAAATAAAATA-AAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAA
*
42682613 AACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAG
65 AACTAAAATAATACATTTG-AACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAG
42682678 TATATTTTAAAAAAT
129 TATATTTTAAAAAAT
* *
42682693 AAAATCCGAAAATAAAATAAAAAATAAACGGCCAGAATCAGAGTTTTTTATTAAATTAATATAAA
1 AAAATCCGAAAATAAAAT-AAAAA-AAA-GGCCAAAATCAGAGTTTTTTACTAAATTAATATAAA
42682758 AAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAAT
63 AAAACTAAAATAATACATTTG-AACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAAT
*
42682823 AGTATATTTTAAAAAGT
127 AGTATATTTTAAAAAAT
* *
42682840 AAAATCCGAAAATAAAATAAAAAAACAAATGGCCAAAATTAGAGTTTTTTATTAAATTAATATAA
1 AAAATCCGAAAATAAAAT--AAAAA-AAA-GGCCAAAATCAGAGTTTTTTACTAAATTAATATAA
*
42682905 AAAATACAAAAATAATACATTTGAAACATTATGTACTAAAATAATAT-AAAAATAAAATACGAAA
62 AAAA-ACTAAAATAATACATTTG-AACATTATGTACTAAAATAATATAAAAAATAAAATACGAAA
*
42682969 ATAATATATTTTAAAAAAT
125 ATAGTATATTTTAAAAAAT
42682988 AAAATCCGAAAATAAAATAAA
1 AAAATCCGAAAATAAAATAAA
42683009 TACCAAAATA
Statistics
Matches: 941, Mismatches: 62, Indels: 60
0.89 0.06 0.06
Matches are distributed among these distances:
140 1 0.00
141 46 0.05
142 58 0.06
143 184 0.20
144 198 0.21
145 95 0.10
146 58 0.06
147 162 0.17
148 98 0.10
149 41 0.04
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (143 bp):
AAAATCCGAAAATAAAATAAAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAA
ACTAAAATAATACATTTGAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTA
TATTTTAAAAAAT
Found at i:42682674 original size:25 final size:25
Alignment explanation
Indices: 42682646--42682720 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 25
42682636 ATTATGTACT
42682646 AAAATAATATAAAAAATAAAATACA
1 AAAATAATATAAAAAATAAAATACA
* *
42682671 AAAATAGTATATTTTAAAAAATAAAATCCG
1 AAAATA--ATA---TAAAAAATAAAATACA
*
42682701 AAAATAAAATAAAAAATAAA
1 AAAATAATATAAAAAATAAA
42682721 CGGCCAGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
25 17 0.40
27 3 0.07
28 2 0.05
30 20 0.48
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.23
Consensus pattern (25 bp):
AAAATAATATAAAAAATAAAATACA
Found at i:42683018 original size:30 final size:28
Alignment explanation
Indices: 42682941--42683010 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
42682931 CATTATGTAC
42682941 TAAAATAATATAAAAATAAAATACGAAAA
1 TAAAATAA-ATAAAAATAAAATACGAAAA
* ** *
42682970 TAATATATTTTAAAAAATAAAATCCGAAAA
1 TAAAATA-AAT-AAAAATAAAATACGAAAA
42683000 TAAAATAAATA
1 TAAAATAAATA
42683011 CCAAAATATA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
28 1 0.03
29 8 0.25
30 23 0.72
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (28 bp):
TAAAATAAATAAAAATAAAATACGAAAA
Found at i:42689348 original size:4 final size:4
Alignment explanation
Indices: 42689334--42689377 Score: 54
Period size: 4 Copynumber: 10.5 Consensus size: 4
42689324 AAAATTACCT
42689334 TTTC TTTTC TTTC -TTC TTCTCC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC -TTTC TTTC TTTC TT-T-C TTTC TTTC TTTC TTTC TTTC TT
42689378 CTTCCTCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
3 3 0.08
4 24 0.67
5 6 0.17
6 3 0.08
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:42689501 original size:27 final size:27
Alignment explanation
Indices: 42689469--42689528 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
42689459 GTGAGAAAGG
*
42689469 CACCACTGGTGCCACCTGTGGGGTACC
1 CACCACTGGTGCCACCTGTGGGATACC
* *
42689496 CTCCACTGGTGCCACTTGTGGGATACC
1 CACCACTGGTGCCACCTGTGGGATACC
42689523 CACCAC
1 CACCAC
42689529 CCTTATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.17, C:0.38, G:0.25, T:0.20
Consensus pattern (27 bp):
CACCACTGGTGCCACCTGTGGGATACC
Found at i:42698209 original size:12 final size:12
Alignment explanation
Indices: 42698194--42698220 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42698184 GTATCATGAC
42698194 ATGTATATATAT
1 ATGTATATATAT
42698206 ATGTATATATAT
1 ATGTATATATAT
42698218 ATG
1 ATG
42698221 ACTAGTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (12 bp):
ATGTATATATAT
Found at i:42706234 original size:27 final size:27
Alignment explanation
Indices: 42706176--42706496 Score: 225
Period size: 27 Copynumber: 11.8 Consensus size: 27
42706166 ATTTGGTTTA
*** *
42706176 TAAAATTACCAAAATACCCCCAATTAG
1 TAAAATTACCAAAATACCCTTGATTTG
* *
42706203 CAAAATTACCAAAATACCCTTGGTTTG
1 TAAAATTACCAAAATACCCTTGATTTG
* *
42706230 TAAAATTGCCAAAATACCATTGATTTG
1 TAAAATTACCAAAATACCCTTGATTTG
* *
42706257 TGAAATTACCGAAATAGCCC-TGATTTG
1 TAAAATTACCAAAATA-CCCTTGATTTG
* ** * * * *
42706284 TGAAATTACTGAAATATCATTGACTTA
1 TAAAATTACCAAAATACCCTTGATTTG
*
42706311 TAAAATTACCGAAATACCCTTGATTTG
1 TAAAATTACCAAAATACCCTTGATTTG
* *
42706338 GAAAATTACCAAAATACCATTGATTTG
1 TAAAATTACCAAAATACCCTTGATTTG
* * * * *
42706365 GAAAATTACAAAAATACCCCTAATTTA
1 TAAAATTACCAAAATACCCTTGATTTG
* * * *
42706392 CAAAATTA-TAGAAATACCATTGACTTTC
1 TAAAATTACCA-AAATACCCTTGA-TTTG
* * * *
42706420 AAAAATTA-TAGAAATACCATTGGTTTG
1 TAAAATTACCA-AAATACCCTTGATTTG
** *
42706447 TAAAATTACTGAAATAACCTTGATTTG
1 TAAAATTACCAAAATACCCTTGATTTG
* * *
42706474 TAGATTTACCAAAAACACCCTTG
1 TAAAATTACC-AAAATACCCTTG
42706497 TAGGGTGAAA
Statistics
Matches: 235, Mismatches: 53, Indels: 11
0.79 0.18 0.04
Matches are distributed among these distances:
26 2 0.01
27 197 0.84
28 36 0.15
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTTGATTTG
Found at i:42706326 original size:108 final size:108
Alignment explanation
Indices: 42706204--42706473 Score: 314
Period size: 108 Copynumber: 2.5 Consensus size: 108
42706194 CCCAATTAGC
* * **
42706204 AAAATTACCAAAATACCCTTGGTTTGTAAAATTGCCAAAATACCATTGATTTGTG-AAATTACCG
1 AAAATTACCGAAATACCCTTGGTTTGTAAAATTACCAAAATACCATTGATTTG-GAAAATTACAA
* * *** *
42706268 AAATAGCCCTGATTTGTGAAATTACT-GAAATATCATTGAC-TTA
65 AAATACCCCTAATTTACAAAATTA-TAGAAATACCATTGACTTTA
* *
42706311 TAAAATTACCGAAATACCCTTGATTTGGAAAATTACCAAAATACCATTGATTTGGAAAATTACAA
1 -AAAATTACCGAAATACCCTTGGTTTGTAAAATTACCAAAATACCATTGATTTGGAAAATTACAA
42706376 AAATACCCCTAATTTACAAAATTATAGAAATACCATTGACTTTCA
65 AAATACCCCTAATTTACAAAATTATAGAAATACCATTGACTTT-A
** * **
42706421 AAAATTATAGAAATACCATTGGTTTGTAAAATTACTGAAATAACC-TTGATTTG
1 AAAATTACCGAAATACCCTTGGTTTGTAAAATTACCAAAAT-ACCATTGATTTG
42706474 TAGATTTACC
Statistics
Matches: 138, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
107 2 0.01
108 88 0.64
109 44 0.32
110 4 0.03
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (108 bp):
AAAATTACCGAAATACCCTTGGTTTGTAAAATTACCAAAATACCATTGATTTGGAAAATTACAAA
AATACCCCTAATTTACAAAATTATAGAAATACCATTGACTTTA
Found at i:42707016 original size:22 final size:22
Alignment explanation
Indices: 42706956--42707020 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
42706946 GCCAATCATT
* *
42706956 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTCTGTGCCAAC
* *
42706978 CT-ACATATAGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
42707000 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
42707021 ACATATTTGC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:42708215 original size:32 final size:32
Alignment explanation
Indices: 42708179--42708242 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
42708169 ACTCAAGGAG
42708179 ATGAGATTCTGTCGTAAATCAGGTACATACCT
1 ATGAGATTCTGTCGTAAATCAGGTACATACCT
*
42708211 ATGAGATTCTTTCGTAAATCAGGTACATACCT
1 ATGAGATTCTGTCGTAAATCAGGTACATACCT
42708243 GACATCTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (32 bp):
ATGAGATTCTGTCGTAAATCAGGTACATACCT
Found at i:42712564 original size:33 final size:33
Alignment explanation
Indices: 42712522--42712587 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
42712512 CCAAATCTTG
42712522 TTTCCTTTTTATGGTGATTCCATATTGGAAGAT
1 TTTCCTTTTTATGGTGATTCCATATTGGAAGAT
42712555 TTTCCTTTTTATGGTGATTCCATATTGGAAGAT
1 TTTCCTTTTTATGGTGATTCCATATTGGAAGAT
42712588 CTGGTGGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCCTTTTTATGGTGATTCCATATTGGAAGAT
Found at i:42718323 original size:46 final size:47
Alignment explanation
Indices: 42718180--42718394 Score: 185
Period size: 46 Copynumber: 4.6 Consensus size: 47
42718170 ATTGTTGGCT
* * ** *
42718180 AGTGTAAGA-GATGTCTGGGAC-T-GCATCAACCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-ACCTCAAGACGAGAGCC
* * ** *
42718225 AGTATAAGACCATGTCTGGGACATGGCATCAGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCA-CCTCAAGACGAGAGCC
*
42718273 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCCAGACGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-ACCTCAAGACG-AGAGCC
* * * **
42718319 AGTGTAAGA-CATGTCTGGGACAT-GCATCAACTACAAGATGATAGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCACCT-CAAGACGAGAGCC
42718365 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
42718395 GACACCTTAC
Statistics
Matches: 140, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
45 12 0.09
46 70 0.50
47 32 0.23
48 26 0.19
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCACCTCAAGACGAGAGCC
Found at i:42718336 original size:93 final size:93
Alignment explanation
Indices: 42718177--42718397 Score: 245
Period size: 93 Copynumber: 2.4 Consensus size: 93
42718167 GTTATTGTTG
* * * *
42718177 GCTAGTGTAAGAGATGTCTGGGAC-TGCATCAACCACATTATGAGAGCCAGTATAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATGACGAGAGCCAGTATAAGACCATGTC
* **
42718241 TGGGACATGGCATCAGC-ATTGAGACGAGA
66 TGGGACAT-GCATCAACTA-CAAGACGAGA
* *
42718270 GCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCCA-GACGTA-AGCCAGTGTAAGA-CATG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACC-ACATGACG-AGAGCCAGTATAAGACCATG
* *
42718332 TCTGGGACATGCATCAACTACAAGATGATA
64 TCTGGGACATGCATCAACTACAAGACGAGA
*
42718362 GTTAGTGTAAGACCATGTCTGGGACATGGCATCGAC
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGAC
42718398 ACCTTACCTA
Statistics
Matches: 110, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
92 24 0.22
93 52 0.47
94 31 0.28
95 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATGACGAGAGCCAGTATAAGACCATGTC
TGGGACATGCATCAACTACAAGACGAGA
Found at i:42719558 original size:20 final size:21
Alignment explanation
Indices: 42719520--42719558 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42719510 TCGAGTTGGT
42719520 CACACGGACATGTTGCCCTCC
1 CACACGGACATGTTGCCCTCC
*
42719541 CACACGGGCATG-TGCCCT
1 CACACGGACATGTTGCCCT
42719559 ATCTTAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (21 bp):
CACACGGACATGTTGCCCTCC
Found at i:42725437 original size:30 final size:31
Alignment explanation
Indices: 42725403--42725462 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
42725393 TTTTTGAGCA
42725403 TAGGGGTAAAATGATCATTTTACC-AAGATC
1 TAGGGGTAAAATGATCATTTTACCGAAGATC
*
42725433 TAGGGGTAAAATGGTCATTTTACCGAAGAT
1 TAGGGGTAAAATGATCATTTTACCGAAGAT
42725463 GTGAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (31 bp):
TAGGGGTAAAATGATCATTTTACCGAAGATC
Found at i:42725944 original size:46 final size:46
Alignment explanation
Indices: 42725797--42726038 Score: 199
Period size: 46 Copynumber: 5.2 Consensus size: 46
42725787 CTTGTTGGCT
* * * *
42725797 AGTGTAAGAGATGTCTGAGACATGCATCAGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGA-GATGAGAGCC
* * ** * *
42725843 AGTGTAAGACCATGTCTAGGACATGGCATCGGTATTGAGATGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGATGAGAGCC
* *
42725891 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAAACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATG-AGAGCC
* * * * *
42725937 AGTGTAAGACATGTCTGGGACATGTAT-TGGCTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGATGAGAGCC
*
42725983 AGTGTAAGACCATGTCTGGGACATGGCATCTA--CTTGAGAT-ATGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC-AGCCTCGAGATGA-GAGCC
42726030 AGTGTAAGA
1 AGTGTAAGA
42726039 TCGTGTTTGG
Statistics
Matches: 156, Mismatches: 29, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
45 4 0.03
46 67 0.43
47 56 0.36
48 28 0.18
49 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATGAGAGCC
Found at i:42726022 original size:47 final size:47
Alignment explanation
Indices: 42725839--42726059 Score: 174
Period size: 47 Copynumber: 4.7 Consensus size: 47
42725829 ACATTATGAG
* *
42725839 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGTA-TTGAGATGA-G
1 AGCCAGTGTAAGA-CATGTCTGGGACATGGCATC--TACTTGAGATGATA
* * * *
42725887 AGCTAGTGTAAGACATGTCTGGGACAT-GCATC-AGCCTCGAAACG-TA
1 AGCCAGTGTAAGACATGTCTGGGACATGGCATCTA--CTTGAGATGATA
*
42725933 AGCCAGTGTAAGACATGTCTGGGACAT-GTATTGGCTAC--GAGATGAT-
1 AGCCAGTGTAAGACATGTCTGGGACATGGCA-T--CTACTTGAGATGATA
* *
42725979 AGTCAGTGTAAGACCATGTCTGGGACATGGCATCTACTTGAGAT-ATG
1 AGCCAGTGTAAGA-CATGTCTGGGACATGGCATCTACTTGAGATGATA
* * *
42726026 AGCCAGTGTAAGATCGTGTTTGGGATATGGCATC
1 AGCCAGTGTAAGA-CATGTCTGGGACATGGCATC
42726060 GGCACTTTAC
Statistics
Matches: 142, Mismatches: 17, Indels: 29
0.76 0.09 0.15
Matches are distributed among these distances:
43 1 0.01
45 4 0.03
46 56 0.39
47 64 0.45
48 15 0.11
49 1 0.01
50 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.25
Consensus pattern (47 bp):
AGCCAGTGTAAGACATGTCTGGGACATGGCATCTACTTGAGATGATA
Found at i:42726030 original size:93 final size:93
Alignment explanation
Indices: 42725794--42726061 Score: 226
Period size: 94 Copynumber: 2.9 Consensus size: 93
42725784 GTTCTTGTTG
* * * **
42725794 GCTAGTGTAAGAGATGTCTGAGACATGCATCAGC-C-ACATTATGAGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCACCTCGA-AACAT--GAGCCAGTGTAAGACCATG
*
42725857 TCTAGGACATGGCATCGGTATTGAGATGAGA
63 TCTAGGACATGGCATCGGTATCGAGATGAGA
* *
42725888 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAAACGTAAGCCAGTGTAAGA-CATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCA-CCTCGAAACATGAGCCAGTGTAAGACCATGTC
* * * *
42725952 TGGGACAT-GTATTGGCTA-CGAGATGATA
65 TAGGACATGGCATCGG-TATCGAGATGAGA
* * * * *
42725980 G-TCAGTGTAAGACCATGTCTGGGACATGGCATCTA-CTTGAGATATGAGCCAGTGTAAGATCGT
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATC-ACCTCGAAACATGAGCCAGTGTAAGACCAT
* * *
42726043 GTTTGGGATATGGCATCGG
62 GTCTAGGACATGGCATCGG
42726062 CACTTTACCC
Statistics
Matches: 142, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
91 1 0.01
92 23 0.16
93 48 0.34
94 59 0.42
95 7 0.05
96 3 0.02
97 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.25
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCACCTCGAAACATGAGCCAGTGTAAGACCATGTCT
AGGACATGGCATCGGTATCGAGATGAGA
Found at i:42729227 original size:15 final size:15
Alignment explanation
Indices: 42729207--42729237 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42729197 ATTCCAAGCC
42729207 TAGCCAATTTTTACA
1 TAGCCAATTTTTACA
42729222 TAGCCAATTTTTACA
1 TAGCCAATTTTTACA
42729237 T
1 T
42729238 GTAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (15 bp):
TAGCCAATTTTTACA
Found at i:42738451 original size:26 final size:26
Alignment explanation
Indices: 42738418--42738480 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
42738408 ACTCAACTCA
42738418 ACGAGCTCGGATGCCTTTTACATCTC
1 ACGAGCTCGGATGCCTTTTACATCTC
*
42738444 ACGAGCTCGGATGCCTTTTTCATCTC
1 ACGAGCTCGGATGCCTTTTACATCTC
*
42738470 ACGAACTCGGA
1 ACGAGCTCGGA
42738481 CTCAACTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.29
Consensus pattern (26 bp):
ACGAGCTCGGATGCCTTTTACATCTC
Found at i:42742332 original size:21 final size:21
Alignment explanation
Indices: 42742302--42742353 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
42742292 GCACCACTCG
*
42742302 AGTTGAAAGAATTAAAAGCAC
1 AGTTGCAAGAATTAAAAGCAC
42742323 AGTTGCAAGAATTAAAAGCAC
1 AGTTGCAAGAATTAAAAGCAC
42742344 AGTTGCAAGA
1 AGTTGCAAGA
42742354 GCTGAAGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (21 bp):
AGTTGCAAGAATTAAAAGCAC
Found at i:42742845 original size:21 final size:21
Alignment explanation
Indices: 42742821--42742864 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
42742811 CAGACCTTAC
42742821 AGGAAAAGCAATTGTATGCTA
1 AGGAAAAGCAATTGTATGCTA
*
42742842 AGGAAAAGCAATTGTGTGCTA
1 AGGAAAAGCAATTGTATGCTA
42742863 AG
1 AG
42742865 TTTAGCAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.27, T:0.23
Consensus pattern (21 bp):
AGGAAAAGCAATTGTATGCTA
Found at i:42750113 original size:18 final size:18
Alignment explanation
Indices: 42750085--42750119 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42750075 ACATGGCCAA
42750085 GGCCAACATGGGCCGTGTG
1 GGCCAACATGGG-CGTGTG
42750104 GGCC-ACATGGGCGTGT
1 GGCCAACATGGGCGTGT
42750120 AAGACCACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.14, C:0.26, G:0.43, T:0.17
Consensus pattern (18 bp):
GGCCAACATGGGCGTGTG
Found at i:42756990 original size:30 final size:30
Alignment explanation
Indices: 42756954--42757026 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
42756944 GACTTGGGAA
* *
42756954 ACATGCCTATGTGCGTTACTCGTGTGTGAC
1 ACATGCCCATGTGCGTTACCCGTGTGTGAC
* * *
42756984 ACATGCCCATGTGTGTTGCCCGTTTGTGAC
1 ACATGCCCATGTGCGTTACCCGTGTGTGAC
**
42757014 ACACACCCATGTG
1 ACATGCCCATGTG
42757027 GCCAAGCTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (30 bp):
ACATGCCCATGTGCGTTACCCGTGTGTGAC
Found at i:42757986 original size:15 final size:16
Alignment explanation
Indices: 42757956--42757991 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
42757946 AATTGTAATT
*
42757956 AAAATTAAATTAAAAC
1 AAAATTAAAGTAAAAC
42757972 AAAATT-AAGTAAAAC
1 AAAATTAAAGTAAAAC
42757987 AAAAT
1 AAAAT
42757992 GCTTTCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (16 bp):
AAAATTAAAGTAAAAC
Found at i:42758787 original size:38 final size:38
Alignment explanation
Indices: 42758745--42758935 Score: 220
Period size: 38 Copynumber: 5.0 Consensus size: 38
42758735 AAACGTAATA
* *
42758745 TTATTCGGGCTATGTGCTTAGCAAGCTTTGTGCCGGTG
1 TTATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
*
42758783 TTATTCGGGCTATGTGCCTAGCAGGCTTTGTACCGGTG
1 TTATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
* * * * * *
42758821 TTATTCGAGCTAGGTGCCTAGCAGGATTTGGGACAGTG
1 TTATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
* ** * *
42758859 TTATTCGGGATATGCACCTAGCAGGCTTTGTGCCAGTT
1 TTATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
* * * *
42758897 TTATTCAGGCTCTGTGCCTAGCAGGCTTAGTGCTGGTG
1 TTATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
42758935 T
1 T
42758936 ATTGAAAATT
Statistics
Matches: 125, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 125 1.00
ACGTcount: A:0.16, C:0.19, G:0.31, T:0.34
Consensus pattern (38 bp):
TTATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
Found at i:42760643 original size:12 final size:12
Alignment explanation
Indices: 42760626--42760666 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
42760616 TCTCAAGTCA
42760626 TCATTTCATATC
1 TCATTTCATATC
*
42760638 TCATTTCGTATC
1 TCATTTCATATC
*
42760650 TCATTATCATTTC
1 TCATT-TCATATC
42760663 TCAT
1 TCAT
42760667 CTTTTCCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.51
Consensus pattern (12 bp):
TCATTTCATATC
Found at i:42760877 original size:37 final size:33
Alignment explanation
Indices: 42760836--42760917 Score: 103
Period size: 32 Copynumber: 2.4 Consensus size: 33
42760826 AATTGGTATT
42760836 CAGTGCCTTATCGGATAAACTGAAGCAAATTGGCACA
1 CAGTGCCTTATCGGAT--A--GAAGCAAATTGGCACA
*
42760873 CAGTGCCTTATC-GATAGAAGCAAATTGGCACC
1 CAGTGCCTTATCGGATAGAAGCAAATTGGCACA
*
42760905 CAGTGCCTCATCG
1 CAGTGCCTTATCG
42760918 ACTCGAGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 26 0.62
34 1 0.02
36 3 0.07
37 12 0.29
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (33 bp):
CAGTGCCTTATCGGATAGAAGCAAATTGGCACA
Found at i:42760898 original size:32 final size:32
Alignment explanation
Indices: 42760857--42760918 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
42760847 CGGATAAACT
*
42760857 GAAGCAAATTGGCACACAGTGCCTTATCGATA
1 GAAGCAAATTGGCACACAGTGCCTCATCGATA
*
42760889 GAAGCAAATTGGCACCCAGTGCCTCATCGA
1 GAAGCAAATTGGCACACAGTGCCTCATCGA
42760919 CTCGAGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (32 bp):
GAAGCAAATTGGCACACAGTGCCTCATCGATA
Found at i:42771461 original size:37 final size:37
Alignment explanation
Indices: 42771406--42771502 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
42771396 GCACTATATA
* **
42771406 AAATTGGCACCCAATGCCTCATCTGATAAACAGAAGC
1 AAATTGGCACCCAGTGCCTCATCACATAAACAGAAGC
* * *
42771443 AAATTGGCAGCTAGTGCCTCATCACATAGACAGAAGC
1 AAATTGGCACCCAGTGCCTCATCACATAAACAGAAGC
42771480 AAATTGGCACCCAGTGCCTCATC
1 AAATTGGCACCCAGTGCCTCATC
42771503 GACTCGAGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.20
Consensus pattern (37 bp):
AAATTGGCACCCAGTGCCTCATCACATAAACAGAAGC
Found at i:42772516 original size:21 final size:23
Alignment explanation
Indices: 42772487--42772528 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
42772477 TAATAAACAT
*
42772487 ACATTTATACA-ATT-TATTATA
1 ACATATATACATATTATATTATA
42772508 ACATATATACATATTATATTA
1 ACATATATACATATTATATTA
42772529 ACATAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 3 0.17
23 5 0.28
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (23 bp):
ACATATATACATATTATATTATA
Found at i:42774106 original size:19 final size:19
Alignment explanation
Indices: 42774082--42774124 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
42774072 AGCTCTCACA
42774082 AGCTTCTGTTCAGCTTTCG
1 AGCTTCTGTTCAGCTTTCG
42774101 AGCTTCTGTTCAGCTTTCG
1 AGCTTCTGTTCAGCTTTCG
*
42774120 CGCTT
1 AGCTT
42774125 ATATTGGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.28, G:0.21, T:0.42
Consensus pattern (19 bp):
AGCTTCTGTTCAGCTTTCG
Found at i:42789585 original size:5 final size:5
Alignment explanation
Indices: 42789571--42789624 Score: 56
Period size: 5 Copynumber: 10.4 Consensus size: 5
42789561 AAGATATGAT
* *
42789571 TTTTA TTTTTA TTTTA -TTTA TTTAAA TATTA TTTTTA TTTTA TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTT-TA TTTTA -TTTTA TTTTA TTTTA
42789618 TTTTA TT
1 TTTTA TT
42789625 ATTAAATTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
4 4 0.10
5 25 0.61
6 12 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:42790161 original size:6 final size:6
Alignment explanation
Indices: 42790143--42790185 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
42790133 ATTATCACTA
42790143 TTATTAT TT-TTT TTATTT TTATTT TTATTT TTATTT TTATTT T
1 TTATT-T TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT T
42790186 GTTATTCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 3 0.09
6 30 0.86
7 2 0.06
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:42790221 original size:15 final size:15
Alignment explanation
Indices: 42790201--42790236 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
42790191 TCTAATACTA
42790201 TTATTATATTTCTAT
1 TTATTATATTTCTAT
*
42790216 TTATTATATTTTTAT
1 TTATTATATTTCTAT
42790231 TT-TTAT
1 TTATTAT
42790237 TTATATACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTATATTTCTAT
Found at i:42790245 original size:46 final size:46
Alignment explanation
Indices: 42790174--42790270 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 46
42790164 TTTTTATTTT
*
42790174 TATTTTTATTTTGTTATTCTAATACTATTATTATATTTCTATTTATTA
1 TATTTTTATTTTGTTATTCTAATACTAATATTATATTTC-A-TTATTA
*
42790222 TATTTTTA-TTT-TTATT-TATATACTAATATTATTTTTCATTATTA
1 TATTTTTATTTTGTTATTCTA-ATACTAATATTATATTTCATTATTA
42790266 T-TTTT
1 TATTTT
42790271 CTTATATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
43 4 0.09
44 7 0.15
45 3 0.07
46 21 0.46
47 3 0.07
48 8 0.17
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (46 bp):
TATTTTTATTTTGTTATTCTAATACTAATATTATATTTCATTATTA
Found at i:42790284 original size:15 final size:14
Alignment explanation
Indices: 42790247--42790285 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
42790237 TTATATACTA
42790247 ATATTATTTTTCAT
1 ATATTATTTTTCAT
*
42790261 -TATTATTTTTCTT
1 ATATTATTTTTCAT
42790274 ATATATATTTTT
1 ATAT-TATTTTT
42790286 TACTCTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.55
14 3 0.14
15 7 0.32
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (14 bp):
ATATTATTTTTCAT
Found at i:42790432 original size:25 final size:24
Alignment explanation
Indices: 42790371--42790432 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
42790361 TATAACACTC
* *
42790371 ATTTCAAATTTTTATACATTATTT
1 ATTTCAAATTTTCATACATTATGT
*
42790395 ACTTT-AATATTTTCATATATTATGT
1 A-TTTCAA-ATTTTCATACATTATGT
42790420 ATTTCAAACTTTT
1 ATTTCAAA-TTTT
42790433 TTTTACACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTCAAATTTTCATACATTATGT
Found at i:42790501 original size:15 final size:15
Alignment explanation
Indices: 42790481--42790515 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42790471 TGTAATAAGG
42790481 CCATTTCACCCGAGC
1 CCATTTCACCCGAGC
* *
42790496 CCATTTCGCCCGGGC
1 CCATTTCACCCGAGC
42790511 CCATT
1 CCATT
42790516 AGAATAAAAA
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:0.14, C:0.46, G:0.17, T:0.23
Consensus pattern (15 bp):
CCATTTCACCCGAGC
Found at i:42791878 original size:17 final size:17
Alignment explanation
Indices: 42791856--42791890 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42791846 ATATATATAT
* *
42791856 TTTTTTTTTATTTTTTA
1 TTTTTTTGTATTATTTA
42791873 TTTTTTTGTATTATTTA
1 TTTTTTTGTATTATTTA
42791890 T
1 T
42791891 ATTATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTTTTTGTATTATTTA
Found at i:42792411 original size:16 final size:16
Alignment explanation
Indices: 42792392--42792423 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42792382 TTCATATAAC
42792392 TTTATGTAAATATTTT
1 TTTATGTAAATATTTT
*
42792408 TTTATGTATATATTTT
1 TTTATGTAAATATTTT
42792424 CTTTTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTATGTAAATATTTT
Found at i:42798418 original size:21 final size:21
Alignment explanation
Indices: 42798392--42798432 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42798382 ATCTGCTCAA
* *
42798392 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
42798413 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
42798433 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:42808337 original size:31 final size:31
Alignment explanation
Indices: 42808301--42808433 Score: 105
Period size: 31 Copynumber: 4.3 Consensus size: 31
42808291 TAGAAATTTT
42808301 ATTAAACTTTCTAAAAGTTTTGAAAATTTCA
1 ATTAAACTTTCTAAAAGTTTTGAAAATTTCA
* * * *
42808332 ATTAAATCCTTC-AAAACTTTTGGAAA-TTCTT
1 ATTAAA-CTTTCTAAAAGTTTTGAAAATTTC-A
*
42808363 ATT-AA-TTCTCTCAAAAGTTTTAAAAATTTCA
1 ATTAAACTT-TCT-AAAAGTTTTGAAAATTTCA
* ** *
42808394 AGTAAACCATCTAAAA-TTGTTGAAAATTTTA
1 ATTAAACTTTCTAAAAGTT-TTGAAAATTTCA
42808425 ATTAAACTT
1 ATTAAACTT
42808434 CTCTTTTTTT
Statistics
Matches: 76, Mismatches: 17, Indels: 18
0.68 0.15 0.16
Matches are distributed among these distances:
28 1 0.01
29 2 0.03
30 7 0.09
31 54 0.71
32 12 0.16
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (31 bp):
ATTAAACTTTCTAAAAGTTTTGAAAATTTCA
Found at i:42808421 original size:62 final size:62
Alignment explanation
Indices: 42808313--42808429 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 62
42808303 TAAACTTTCT
* * * *
42808313 AAAAGTTTTGAAAATTTCAATTAAATCCTTCAAAACTTTTGGAAATTCTT-ATTAATTCTCTC
1 AAAAGTTTTAAAAATTTCAAGTAAATCCATCAAAACTTTTGAAAATT-TTAATTAATTCTCTC
42808375 AAAAGTTTTAAAAATTTCAAGTAAA-CCATCTAAAA-TTGTTGAAAATTTTAATTAA
1 AAAAGTTTTAAAAATTTCAAGTAAATCCATC-AAAACTT-TTGAAAATTTTAATTAA
42808430 ACTTCTCTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
61 8 0.17
62 40 0.83
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (62 bp):
AAAAGTTTTAAAAATTTCAAGTAAATCCATCAAAACTTTTGAAAATTTTAATTAATTCTCTC
Found at i:42811559 original size:20 final size:21
Alignment explanation
Indices: 42811536--42811574 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
42811526 AAGAAAACAT
42811536 TAATAAATAAAT-GAAATGAG
1 TAATAAATAAATGGAAATGAG
* *
42811556 TAATTAATAGATGGAAATG
1 TAATAAATAAATGGAAATG
42811575 GAAACGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.28
Consensus pattern (21 bp):
TAATAAATAAATGGAAATGAG
Found at i:42819423 original size:29 final size:29
Alignment explanation
Indices: 42819382--42819466 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
42819372 CTAAACTTTG
42819382 ATTAAAA-TTACATTTTAATCACTCAACTT
1 ATTAAAAGTTACATTTT-ATCACTCAACTT
* *
42819411 -TTAAAAGTTACATAATTATCACTAAACTT
1 ATTAAAAGTTACAT-TTTATCACTCAACTT
* *
42819440 ATCAAAATGTTACATTTTGTTCACTCA
1 ATTAAAA-GTTACATTTT-ATCACTCA
42819467 TTCGTTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
28 6 0.13
29 17 0.38
30 9 0.20
31 13 0.29
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (29 bp):
ATTAAAAGTTACATTTTATCACTCAACTT
Found at i:42820618 original size:17 final size:17
Alignment explanation
Indices: 42820586--42820626 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
42820576 TTGATTGACT
*
42820586 TTTTTTTGAATGTTTTA
1 TTTTTTTGAATATTTTA
42820603 TATTTTTT-AATATTTTA
1 T-TTTTTTGAATATTTTA
42820620 TTTTTTT
1 TTTTTTT
42820627 TTGAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 10 0.45
18 6 0.27
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTTTTGAATATTTTA
Found at i:42820627 original size:17 final size:18
Alignment explanation
Indices: 42820585--42820637 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
42820575 TTTGATTGAC
*
42820585 TTTTTTTTGAATGTTTTA
1 TTTTTTTTGAATATTTTA
*
42820603 TATTTTTT-AATATTTTA
1 TTTTTTTTGAATATTTTA
42820620 TTTTTTTTTGAAT-TTTTA
1 -TTTTTTTTGAATATTTTA
42820638 GAATTTGGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 8 0.27
18 19 0.63
19 3 0.10
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTTTTTTGAATATTTTA
Found at i:42833551 original size:19 final size:19
Alignment explanation
Indices: 42833523--42833581 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
42833513 TTAAAAAATT
*
42833523 AAAAATAAAAAGTTATAAA
1 AAAAAGAAAAAGTTATAAA
42833542 AAAAAGAAAAAGTTATAAA
1 AAAAAGAAAAAGTTATAAA
* *
42833561 ATATAAGAAAAA-TTACAAA
1 A-AAAAGAAAAAGTTATAAA
42833580 AA
1 AA
42833582 TATTAAAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.03
19 26 0.72
20 9 0.25
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.19
Consensus pattern (19 bp):
AAAAAGAAAAAGTTATAAA
Found at i:42833609 original size:28 final size:28
Alignment explanation
Indices: 42833569--42833695 Score: 87
Period size: 28 Copynumber: 4.5 Consensus size: 28
42833559 AAATATAAGA
**
42833569 AAAATTACAAAAATATTAAAACTGATAT
1 AAAATTATTAAAATATTAAAACTGATAT
* * *
42833597 AAACTTATTAAAATCATAAAAACTTATA-
1 AAAATTATTAAAAT-ATTAAAACTGATAT
* * *
42833625 AAAATTA-TAAAATTAATAAAACTTAATAG
1 AAAATTATTAAAA-TATTAAAAC-TGATAT
** * *
42833654 AAAAAAATTAAAAAATTAAAATTGATAT
1 AAAATTATTAAAATATTAAAACTGATAT
* *
42833682 AAACTTATAAAAAT
1 AAAATTATTAAAAT
42833696 TATAAAAAAT
Statistics
Matches: 73, Mismatches: 21, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
27 11 0.15
28 35 0.48
29 22 0.30
30 5 0.07
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATTATTAAAATATTAAAACTGATAT
Found at i:42833624 original size:85 final size:83
Alignment explanation
Indices: 42833520--42833713 Score: 209
Period size: 85 Copynumber: 2.3 Consensus size: 83
42833510 TCTTTAAAAA
* *
42833520 ATTAAAA-ATAAAAAGTTATAAAAAAAAGAAAAAGTT-ATAAAA-T-ATA-AGAAAAATTACAAA
1 ATTAAAATATAAAAAATTATAAAAAAAA-AAAAA-TTAATAAAACTAATAGAAAAAAATT--AAA
42833580 AATATTAAAACTGATATAAACTT
62 AA-ATTAAAACTGATATAAACTT
* ** *
42833603 ATTAAAATCATAAAAACTTATAAAAATTATAAAATTAATAAAACTTAATAGAAAAAAATTAAAAA
1 ATTAAAAT-ATAAAAAATTATAAAAAAAAAAAAATTAATAAAAC-TAATAGAAAAAAATTAAAAA
*
42833668 ATTAAAATTGATATAAACTT
64 ATTAAAACTGATATAAACTT
*
42833688 ATAAAAATTATAAAAAATTATAAAAA
1 ATTAAAA-TATAAAAAATTATAAAAA
42833714 CTTGAACTGA
Statistics
Matches: 95, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
83 9 0.09
84 10 0.11
85 58 0.61
86 7 0.07
87 3 0.03
88 8 0.08
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (83 bp):
ATTAAAATATAAAAAATTATAAAAAAAAAAAAATTAATAAAACTAATAGAAAAAAATTAAAAAAT
TAAAACTGATATAAACTT
Found at i:42833627 original size:10 final size:9
Alignment explanation
Indices: 42833527--42833713 Score: 85
Period size: 10 Copynumber: 19.8 Consensus size: 9
42833517 AAAATTAAAA
42833527 ATAAAAAGTT
1 ATAAAAA-TT
**
42833537 ATAAAAAAA
1 ATAAAAATT
*
42833546 AGAAAAAGTT
1 ATAAAAA-TT
*
42833556 ATAAAATATA
1 ATAAAA-ATT
*
42833566 AGAAAAATT
1 ATAAAAATT
*
42833575 ACAAAAA-T
1 ATAAAAATT
* *
42833583 ATTAAAACTG
1 A-TAAAAATT
*
42833593 ATATAAACTT
1 ATA-AAAATT
* *
42833603 ATTAAAATC
1 ATAAAAATT
42833612 ATAAAAACTT
1 ATAAAAA-TT
42833622 ATAAAAATT
1 ATAAAAATT
42833631 AT-AAAATT
1 ATAAAAATT
*
42833639 AATAAAACTT
1 -ATAAAAATT
**
42833649 AATAGAAAAAA
1 -ATA-AAAATT
42833660 ATTAAAAA--
1 A-TAAAAATT
*
42833668 ATTAAAATT
1 ATAAAAATT
*
42833677 GATATAAACTT
1 -ATA-AAAATT
42833688 ATAAAAATT
1 ATAAAAATT
42833697 ATAAAAAATT
1 AT-AAAAATT
42833707 ATAAAAA
1 ATAAAAA
42833714 CTTGAACTGA
Statistics
Matches: 135, Mismatches: 27, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
7 5 0.04
8 9 0.07
9 48 0.36
10 62 0.46
11 11 0.08
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (9 bp):
ATAAAAATT
Found at i:42833713 original size:19 final size:19
Alignment explanation
Indices: 42833527--42833713 Score: 70
Period size: 19 Copynumber: 9.9 Consensus size: 19
42833517 AAAATTAAAA
* **
42833527 ATAAAAAGTTATAAAAAAA
1 ATAAAAAATTATAAAAATT
* *
42833546 AGAAAAAGTTAT-AAAA-T
1 ATAAAAAATTATAAAAATT
*
42833563 ATAAGAAAAATTACAAAAA-T
1 AT-A-AAAAATTATAAAAATT
* * * *
42833583 ATTAAAACTGATATAAACTT
1 ATAAAAAATTATA-AAAATT
* *
42833603 AT-TAAAATCATAAAAACTT
1 ATAAAAAATTATAAAAA-TT
42833622 AT-AAAAATTAT-AAAATT
1 ATAAAAAATTATAAAAATT
* **
42833639 A-ATAAAACTTAATAGAAAAAA
1 ATA-AAAAATT-ATA-AAAATT
42833660 ATTAAAAAA-T-T-AAAATT
1 A-TAAAAAATTATAAAAATT
* *
42833677 GATATAAACTTATAAAAATT
1 -ATAAAAAATTATAAAAATT
42833697 ATAAAAAATTATAAAAA
1 ATAAAAAATTATAAAAA
42833714 CTTGAACTGA
Statistics
Matches: 125, Mismatches: 26, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
17 13 0.10
18 27 0.22
19 58 0.46
20 16 0.13
21 6 0.05
22 4 0.03
23 1 0.01
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (19 bp):
ATAAAAAATTATAAAAATT
Found at i:42834157 original size:49 final size:52
Alignment explanation
Indices: 42834101--42834217 Score: 138
Period size: 49 Copynumber: 2.3 Consensus size: 52
42834091 CCAGTTCAAA
42834101 TTTTTATGATTTTTTTATA-AATTTT-ATAAG-TTTATATAA-ATTTTAAAT-T-
1 TTTTTATGA--TTTTTATAGAATTTTAATAAGCTTT-TATAATATTTTAAATATG
*
42834150 TTTTTATGATTTTTATAGAATTTTAATAAGCTTTTATAATGTTTTAAATATG
1 TTTTTATGATTTTTATAGAATTTTAATAAGCTTTTATAATATTTTAAATATG
* *
42834202 TTTTTATTAATTTTAT
1 TTTTTATGATTTTTAT
42834218 GATTTTTTTA
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
47 8 0.14
48 6 0.10
49 19 0.32
50 11 0.19
51 1 0.02
52 14 0.24
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (52 bp):
TTTTTATGATTTTTATAGAATTTTAATAAGCTTTTATAATATTTTAAATATG
Found at i:42834258 original size:8 final size:8
Alignment explanation
Indices: 42834240--42834309 Score: 59
Period size: 8 Copynumber: 7.9 Consensus size: 8
42834230 ATTTATTAAA
42834240 ATTTATTAT
1 ATTT-TTAT
42834249 ATTTTTAT
1 ATTTTTAT
42834257 ATTTTTAT
1 ATTTTTAT
42834265 ATCAATTTTAAT
1 AT---TTTT-AT
*
42834277 ATTTTTTT
1 ATTTTTAT
*
42834285 AATATTTAAT
1 -AT-TTTTAT
42834295 ATTTTTAT
1 ATTTTTAT
42834303 ATTTTTA
1 ATTTTTA
42834310 ATAAATTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
8 27 0.53
9 12 0.24
10 4 0.08
11 4 0.08
12 4 0.08
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (8 bp):
ATTTTTAT
Found at i:42840920 original size:34 final size:32
Alignment explanation
Indices: 42840876--42840984 Score: 91
Period size: 34 Copynumber: 3.4 Consensus size: 32
42840866 CTCCCTGAAT
*
42840876 TTAATCTTTATACTTTTTATTTGTCATTTCTAAC
1 TTAATTTTTATACTTTTTA-TTGTCATTT-TAAC
** **
42840910 TTAATTTTTATAAATTTTA---AAATTTTAATC
1 TTAATTTTTATACTTTTTATTGTCATTTTAA-C
42840940 TTAA-TTTTATACTTTTTATATGTCATTTTTAAC
1 TTAATTTTTATACTTTTTAT-TGTCA-TTTTAAC
*
42840973 TTGATTTTTATA
1 TTAATTTTTATA
42840985 AAAATTTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
29 15 0.26
30 9 0.16
33 5 0.09
34 29 0.50
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (32 bp):
TTAATTTTTATACTTTTTATTGTCATTTTAAC
Found at i:42840973 original size:63 final size:65
Alignment explanation
Indices: 42840876--42841000 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 65
42840866 CTCCCTGAAT
* *
42840876 TTAATCTTTATACTTTTTATTTGTCATTTCTAACTTAATTTTTAT-AAATTTTAAAATTTTAATC
1 TTAATCTTTATACTTTTTATATGTCATTTCTAACTTAATTTTTATAAAAATTTAAAATTTTAATC
* *
42840940 TTAAT-TTTATACTTTTTATATGTCATTTTTAACTTGATTTTTATAAAAATTTAAAATTTTA
1 TTAATCTTTATACTTTTTATATGTCATTTCTAACTTAATTTTTATAAAAATTTAAAATTTTA
42841001 GTCCAGATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
63 36 0.64
64 20 0.36
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (65 bp):
TTAATCTTTATACTTTTTATATGTCATTTCTAACTTAATTTTTATAAAAATTTAAAATTTTAATC
Found at i:42848395 original size:20 final size:20
Alignment explanation
Indices: 42848357--42848404 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
42848347 TAAATTCTAA
* **
42848357 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
42848377 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
42848397 AAA-ATAAA
1 AAAGATAAA
42848405 ATCCTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:42848448 original size:15 final size:15
Alignment explanation
Indices: 42848428--42848457 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42848418 ATAATCCTAA
*
42848428 TAATTATCTTAATAT
1 TAATTATCCTAATAT
42848443 TAATTATCCTAATAT
1 TAATTATCCTAATAT
42848458 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:42850020 original size:6 final size:6
Alignment explanation
Indices: 42850009--42850065 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
42849999 ATCTGAAAAT
42850009 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
42850057 AATAAA AAT
1 AATAAA AAT
42850066 TGGGTTGCCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:42856421 original size:20 final size:20
Alignment explanation
Indices: 42856383--42856430 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
42856373 TAAATTCTAA
* **
42856383 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
42856403 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
42856423 AAA-ATAAA
1 AAAGATAAA
42856431 ATCCTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:42856474 original size:15 final size:15
Alignment explanation
Indices: 42856454--42856483 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42856444 ATAATCCTAA
*
42856454 TAATTATCTTAATAT
1 TAATTATCCTAATAT
42856469 TAATTATCCTAATAT
1 TAATTATCCTAATAT
42856484 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:42858346 original size:26 final size:26
Alignment explanation
Indices: 42858310--42858396 Score: 83
Period size: 26 Copynumber: 3.5 Consensus size: 26
42858300 AAGTGGTTGT
*
42858310 TTTGGTATGTTTAGGTTTATATGCAA
1 TTTGGAATGTTTAGGTTTATATGCAA
* ** *
42858336 TTTGGAATGTTTGAAG-TGGT-TG--T
1 TTTGGAATGTTT-AGGTTTATATGCAA
*
42858359 TTTGGTATGTTTAGGTTTATATGCAA
1 TTTGGAATGTTTAGGTTTATATGCAA
42858385 TTTGGAATGTTT
1 TTTGGAATGTTT
42858397 GAAGCTTGAT
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
22 2 0.04
23 13 0.29
24 2 0.04
25 2 0.04
26 24 0.53
27 2 0.04
ACGTcount: A:0.21, C:0.02, G:0.26, T:0.51
Consensus pattern (26 bp):
TTTGGAATGTTTAGGTTTATATGCAA
Found at i:42858357 original size:49 final size:49
Alignment explanation
Indices: 42858300--42858400 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
42858290 AGATGCATAC
42858300 AAGTGGTTGTTTTGGTATGTTTAGGTTTATATGCAATTTGGAATGTTTG
1 AAGTGGTTGTTTTGGTATGTTTAGGTTTATATGCAATTTGGAATGTTTG
42858349 AAGTGGTTGTTTTGGTATGTTTAGGTTTATATGCAATTTGGAATGTTTG
1 AAGTGGTTGTTTTGGTATGTTTAGGTTTATATGCAATTTGGAATGTTTG
42858398 AAG
1 AAG
42858401 CTTGATGAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.48
Consensus pattern (49 bp):
AAGTGGTTGTTTTGGTATGTTTAGGTTTATATGCAATTTGGAATGTTTG
Found at i:42872723 original size:43 final size:42
Alignment explanation
Indices: 42872665--42872815 Score: 162
Period size: 43 Copynumber: 3.5 Consensus size: 42
42872655 GATTGCCAAG
* *
42872665 ATGTGATTACATGTAAGACCATGTATGGGACATTGGCATTG-T
1 ATGTGATTACGTGTAAGACCATGT-TGGGACATTGGCATCGTT
*
42872707 ATTGTGAATACGTGTAAGACCATGTTTGGGACATTGGCATCGTT
1 A-TGTGATTACGTGTAAGACCATG-TTGGGACATTGGCATCGTT
* * *
42872751 ATGTGATTTCGTGTAAGATCATAGTTGGG-CTATTGGCATCGAT
1 ATGTGATTACGTGTAAGACCAT-GTTGGGAC-ATTGGCATCGTT
* * *
42872794 ATGAGATAACATGTAAGACCAT
1 ATGTGATTACGTGTAAGACCAT
42872816 ATTTGGGATA
Statistics
Matches: 92, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
42 2 0.02
43 86 0.93
44 4 0.04
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (42 bp):
ATGTGATTACGTGTAAGACCATGTTGGGACATTGGCATCGTT
Found at i:42872822 original size:43 final size:43
Alignment explanation
Indices: 42872719--42872831 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
42872709 TGTGAATACG
* * * ** *
42872719 TGTAAGACCATGTTTGGGAC-ATTGGCATCGTTATGTGATTTCG
1 TGTAAGACCATATTTGGG-CTATTGGCATCGATATGAGATAACA
* *
42872762 TGTAAGATCATAGTTGGGCTATTGGCATCGATATGAGATAACA
1 TGTAAGACCATATTTGGGCTATTGGCATCGATATGAGATAACA
*
42872805 TGTAAGACCATATTTGGGATA-TGGCAT
1 TGTAAGACCATATTTGGGCTATTGGCAT
42872832 TGTACGAGCT
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 7 0.12
43 51 0.88
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATATTTGGGCTATTGGCATCGATATGAGATAACA
Found at i:42874226 original size:41 final size:41
Alignment explanation
Indices: 42874179--42874258 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
42874169 TAAAGTCTCG
*
42874179 TAGAGCCTTATAAGGGACAATATGGTTATGTTTGATTAACA
1 TAGAGCCTTATAAGGGACAATATGATTATGTTTGATTAACA
*
42874220 TAGAGCCTTATAAGGGACAATTTGATTATGTTTGATTAA
1 TAGAGCCTTATAAGGGACAATATGATTATGTTTGATTAA
42874259 TATTTATGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (41 bp):
TAGAGCCTTATAAGGGACAATATGATTATGTTTGATTAACA
Found at i:42876443 original size:43 final size:43
Alignment explanation
Indices: 42876346--42876447 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
42876336 ATCAATATGT
* * * *
42876346 GATTACATGTAAGACCATGTCTGGGACATTGACATTGTATTGA
1 GATTATATGTAAGACCATGTCTGGGACATTGACATGGTAATCA
* *
42876389 GATTATGTGTAAGACCATGTCTGGGACATTGTCATCGGTAATCA
1 GATTATATGTAAGACCATGTCTGGGACATTGACAT-GGTAATCA
*
42876433 -ATTTTATGTAAGACC
1 GATTATATGTAAGACC
42876448 CTGTTTAGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
43 45 0.90
44 5 0.10
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (43 bp):
GATTATATGTAAGACCATGTCTGGGACATTGACATGGTAATCA
Found at i:42879004 original size:16 final size:16
Alignment explanation
Indices: 42878985--42879016 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42878975 ATGTACACAA
42878985 ATATATATGTGTTTAT
1 ATATATATGTGTTTAT
*
42879001 ATATATGTGTGTTTAT
1 ATATATATGTGTTTAT
42879017 TTGAAGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (16 bp):
ATATATATGTGTTTAT
Found at i:42879470 original size:24 final size:24
Alignment explanation
Indices: 42879443--42879775 Score: 252
Period size: 24 Copynumber: 13.9 Consensus size: 24
42879433 GAAATGATTT
*
42879443 TGGCACTATGTGTGCTAATTTGAA
1 TGGCACTATGTGTGCGAATTTGAA
*
42879467 TGGCACTATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGAA
* *
42879491 TGGCACTATGTGTGCGGATTTGGA
1 TGGCACTATGTGTGCGAATTTGAA
* * * *
42879515 TGTCAATATGTATGTGAATTACT-AA
1 TGGCACTATGTGTGCGAATT--TGAA
*
42879540 -GGCACTATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGAA
* * *
42879563 TGGCACTATATCTGCGGATTT-ATA
1 TGGCACTATGTGTGCGAATTTGA-A
*
42879587 TGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGAATTTGAA
* * * *
42879611 TGTCAATATGTATGTGAATTACT-AA
1 TGGCACTATGTGTGCGAATT--TGAA
* *
42879636 -GGCATTATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGAA
* *
42879659 TGGCACTATATGTGCGGATTT-ATA
1 TGGCACTATGTGTGCGAATTTGA-A
*
42879683 TGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGAATTTGAA
* * * *
42879707 TGTCAATATGTATGTGAATTACT-AA
1 TGGCACTATGTGTGCGAATT--TGAA
** *
42879732 T-GCACTATGTGTGCG-GGTTAACA
1 TGGCACTATGTGTGCGAATTTGA-A
*
42879755 TGGCACTATGGGTGCGAATTT
1 TGGCACTATGTGTGCGAATTT
42879776 CCTTGCTTGA
Statistics
Matches: 241, Mismatches: 50, Indels: 35
0.74 0.15 0.11
Matches are distributed among these distances:
21 1 0.00
22 3 0.01
23 5 0.02
24 219 0.91
25 10 0.04
26 3 0.01
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (24 bp):
TGGCACTATGTGTGCGAATTTGAA
Found at i:42879495 original size:48 final size:48
Alignment explanation
Indices: 42879443--42879746 Score: 308
Period size: 48 Copynumber: 6.3 Consensus size: 48
42879433 GAAATGATTT
* * * **
42879443 TGGCACTATGTGTGCTAATTTGAATGGCACTATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGAATGGCAATATGTATGCGAATTACTA
* * * *
42879491 TGGCACTATGTGTGCGGATTTGGATGTCAATATGTATGTGAATTACTA
1 TGGCACTATGTGTGCGAATTTGAATGGCAATATGTATGCGAATTACTA
* * * * * *
42879539 AGGCACTATGTGTGCGAATTTGTATGGCACTATATCTGCGGATTTA-TA
1 TGGCACTATGTGTGCGAATTTGAATGGCAATATGTATGC-GAATTACTA
* * *
42879587 TGGCACTATGTGTGCGGATTTGAATGTCAATATGTATGTGAATTACTA
1 TGGCACTATGTGTGCGAATTTGAATGGCAATATGTATGCGAATTACTA
* * * * * * *
42879635 AGGCATTATGTGTGCGAATTTGTATGGCACTATATGTGCGGATTTA-TA
1 TGGCACTATGTGTGCGAATTTGAATGGCAATATGTATGC-GAATTACTA
* * *
42879683 TGGCACTATGTGTGCGGATTTGAATGTCAATATGTATGTGAATTACTAA
1 TGGCACTATGTGTGCGAATTTGAATGGCAATATGTATGCGAATTACT-A
42879732 T-GCACTATGTGTGCG
1 TGGCACTATGTGTGCG
42879747 GGTTAACATG
Statistics
Matches: 204, Mismatches: 47, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
47 10 0.05
48 182 0.89
49 12 0.06
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (48 bp):
TGGCACTATGTGTGCGAATTTGAATGGCAATATGTATGCGAATTACTA
Found at i:42879763 original size:96 final size:96
Alignment explanation
Indices: 42879444--42879746 Score: 525
Period size: 96 Copynumber: 3.2 Consensus size: 96
42879434 AAATGATTTT
* * * * *
42879444 GGCACTATGTGTGCTAATTTGAATGGCACTATGTGTGCGAATTTGTATGGCACTATGTGTGCGGA
1 GGCACTATGTGTGCGAATTTGTATGGCACTATATGTGCGGATTTATATGGCACTATGTGTGCGGA
*
42879509 TTTGGATGTCAATATGTATGTGAATTACTAA
66 TTTGAATGTCAATATGTATGTGAATTACTAA
*
42879540 GGCACTATGTGTGCGAATTTGTATGGCACTATATCTGCGGATTTATATGGCACTATGTGTGCGGA
1 GGCACTATGTGTGCGAATTTGTATGGCACTATATGTGCGGATTTATATGGCACTATGTGTGCGGA
42879605 TTTGAATGTCAATATGTATGTGAATTACTAA
66 TTTGAATGTCAATATGTATGTGAATTACTAA
*
42879636 GGCATTATGTGTGCGAATTTGTATGGCACTATATGTGCGGATTTATATGGCACTATGTGTGCGGA
1 GGCACTATGTGTGCGAATTTGTATGGCACTATATGTGCGGATTTATATGGCACTATGTGTGCGGA
42879701 TTTGAATGTCAATATGTATGTGAATTACTAA
66 TTTGAATGTCAATATGTATGTGAATTACTAA
*
42879732 TGCACTATGTGTGCG
1 GGCACTATGTGTGCG
42879747 GGTTAACATG
Statistics
Matches: 196, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 196 1.00
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (96 bp):
GGCACTATGTGTGCGAATTTGTATGGCACTATATGTGCGGATTTATATGGCACTATGTGTGCGGA
TTTGAATGTCAATATGTATGTGAATTACTAA
Found at i:42884864 original size:40 final size:40
Alignment explanation
Indices: 42884774--42884996 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
42884764 TTGAATGCTG
* * * * * *
42884774 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * * * *
42884814 TCTGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
42884854 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* **
42884894 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
42884934 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
42884973 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
42884997 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 35 0.22
40 114 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:42885016 original size:79 final size:80
Alignment explanation
Indices: 42884849--42885031 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
42884839 GTGCGAGATA
* * *
42884849 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
42884914 CAGTCGTGCGAGTTG
66 CAGTCGAACGAGGAG
* * * *
42884929 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
42884993 CATTTGAACGAGGAG
66 CAGTCGAACGAGGAG
* *
42885008 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
42885032 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGGAG
Found at i:42889774 original size:43 final size:43
Alignment explanation
Indices: 42889727--42889830 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
42889717 GATTACATAT
* *
42889727 AAGACCATGTCTGGGACATTGGCAT-TTTATTGAGATTATGTGC
1 AAGACCATGTCTGGGACATTGGCATCGTTAAT-AGATTATGTGC
* * * * *
42889770 AAGACCATTTCTGGAACATTGGCATCGTTAATCGATTTTGTGT
1 AAGACCATGTCTGGGACATTGGCATCGTTAATAGATTATGTGC
*
42889813 AAGACCTTGTCTGGGACA
1 AAGACCATGTCTGGGACA
42889831 GTGGAATTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 46 0.92
44 4 0.08
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (43 bp):
AAGACCATGTCTGGGACATTGGCATCGTTAATAGATTATGTGC
Found at i:42892283 original size:45 final size:45
Alignment explanation
Indices: 42892219--42892380 Score: 240
Period size: 45 Copynumber: 3.6 Consensus size: 45
42892209 TATTGTACGG
* *
42892219 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATGATGCCCGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
42892264 TACTATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
42892309 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
42892354 TGA-TA-TCGGG-CTTCGAGGCTAGCAGGC
1 T-ACTATTCGGGCCTTTGAGCCTAGCAGGC
42892381 GAAATGCTGG
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
43 15 0.14
44 5 0.05
45 88 0.81
46 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:42892427 original size:41 final size:41
Alignment explanation
Indices: 42892372--42892474 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
42892362 GGCTTCGAGG
* *
42892372 CTAGCAGGCGAAATGCTGGTGGATGAATTCAGGTTTAAAAC
1 CTAGCAGGCAAAATGCCGGTGGATGAATTCAGGTTTAAAAC
* *
42892413 CTAGTAGGCAAAATGCCAGTGGATGAATTCAGGTTTAAAAC
1 CTAGCAGGCAAAATGCCGGTGGATGAATTCAGGTTTAAAAC
*
42892454 CTAGCAGGCTAAATGCCGGTG
1 CTAGCAGGCAAAATGCCGGTG
42892475 ATTTGATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCAAAATGCCGGTGGATGAATTCAGGTTTAAAAC
Done.