Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 53 of 356
Found at i:17356066 original size:25 final size:23
Alignment explanation
Indices: 17356038--17356093 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
17356028 TAAATTATAA
* *
17356038 GTAATTATATATTTATTTTACATTT
1 GTAATTATA-ATTT-TATTACAATT
*
17356063 GTAATAATAATTTTATTACAATT
1 GTAATTATAATTTTATTACAATT
*
17356086 GTCATTAT
1 GTAATTAT
17356094 TTAATTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 14 0.54
24 4 0.15
25 8 0.31
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (23 bp):
GTAATTATAATTTTATTACAATT
Found at i:17356302 original size:16 final size:16
Alignment explanation
Indices: 17356283--17356324 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
17356273 AATCTCATAA
17356283 TATAATTAATATAAAT
1 TATAATTAATATAAAT
*
17356299 TATAATTTA-ATAAAT
1 TATAATTAATATAAAT
17356314 TAATAA-TAATA
1 T-ATAATTAATA
17356325 ATACACTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATTAATATAAAT
Found at i:17358368 original size:28 final size:28
Alignment explanation
Indices: 17358299--17358375 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
17358289 ATTATGGAAT
17358299 TGAAAAG-GAAATTGAATTGATGATGGA
1 TGAAAAGTGAAATTGAATTGATGATGGA
* * * *
17358326 T-AAGTATTGATATTGAATTGTAT-ATTGA
1 TGAA-AAGTGAAATTGAATTG-ATGATGGA
17358354 TGAAAAGTGAAATTGAATTGAT
1 TGAAAAGTGAAATTGAATTGAT
17358376 TCGTAAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 29 0.74
29 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (28 bp):
TGAAAAGTGAAATTGAATTGATGATGGA
Found at i:17358599 original size:39 final size:39
Alignment explanation
Indices: 17358556--17358630 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
17358546 GGTACCAACT
* *
17358556 TTACTTCG-GCTAGGCCAATGAGACATTGGGTGTCAAATA
1 TTACTTCGAACTA-GCCAATGAGACACTGGGTGTCAAATA
* *
17358595 TTACTTCGAACTATCCAATGAGGCACTGGGTGTCAA
1 TTACTTCGAACTAGCCAATGAGACACTGGGTGTCAA
17358631 TTTGGTGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 28 0.90
40 3 0.10
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (39 bp):
TTACTTCGAACTAGCCAATGAGACACTGGGTGTCAAATA
Found at i:17362237 original size:20 final size:19
Alignment explanation
Indices: 17362203--17362244 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
17362193 AATTCAAAAA
*
17362203 AAATTATTAACATAATATT
1 AAATTATTAACATAACATT
*
17362222 AAATTATATTACATAACATT
1 AAATTAT-TAACATAACATT
17362242 AAA
1 AAA
17362245 AAAAAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTATTAACATAACATT
Found at i:17373397 original size:9 final size:9
Alignment explanation
Indices: 17373383--17373451 Score: 113
Period size: 9 Copynumber: 7.8 Consensus size: 9
17373373 TTTGGTTAAA
17373383 AATTACCCG
1 AATTACCCG
17373392 AATTA-CCG
1 AATTACCCG
17373400 AATTACCCG
1 AATTACCCG
17373409 AATTACCCG
1 AATTACCCG
17373418 AATTACCCG
1 AATTACCCG
*
17373427 AATTAACCG
1 AATTACCCG
*
17373436 AATTAACCG
1 AATTACCCG
17373445 AATTACC
1 AATTACC
17373452 GAAAAATACC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
8 8 0.14
9 49 0.86
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:17374997 original size:16 final size:17
Alignment explanation
Indices: 17374978--17375015 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 17
17374968 AATATTTAAA
17374978 TAAATATTTTT-ATTTT
1 TAAATATTTTTAATTTT
17374994 TAAATATTTTTGAATTTT
1 TAAATATTTTT-AATTTT
17375012 TAAA
1 TAAA
17375016 AAGTAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
18 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TAAATATTTTTAATTTT
Found at i:17375933 original size:14 final size:14
Alignment explanation
Indices: 17375914--17375960 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
17375904 GAGTTTTAAA
17375914 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
17375928 TTTAATTTGATTATTT
1 TTTAATTT--TTATAT
*
17375944 TTTTATTTTTATAT
1 TTTAATTTTTATAT
17375958 TTT
1 TTT
17375961 TAAAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 16 0.57
16 12 0.43
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:17387156 original size:54 final size:55
Alignment explanation
Indices: 17387089--17387209 Score: 133
Period size: 54 Copynumber: 2.2 Consensus size: 55
17387079 GGCAACAACG
* * *
17387089 AAATTCTTTAAAAAAAAAT-TTTGGGTG-CTATTAGTATGTCAAATGATATCGG-TA
1 AAATT-TTTAAAAAAAAATCTTTGGGTGCCT-CTAGTATGTCAAACGACATCGGTTA
* * *
17387143 AATATTTTT-AAAAAATATCTTTTGGTGCCTCTAGTATGTCAAGCGACATCGGTTA
1 AA-ATTTTTAAAAAAAAATCTTTGGGTGCCTCTAGTATGTCAAACGACATCGGTTA
17387198 AAATTTTTAAAA
1 AAATTTTTAAAA
17387210 TATATATTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
53 8 0.14
54 36 0.64
55 12 0.21
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (55 bp):
AAATTTTTAAAAAAAAATCTTTGGGTGCCTCTAGTATGTCAAACGACATCGGTTA
Found at i:17389303 original size:20 final size:21
Alignment explanation
Indices: 17389255--17389304 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
17389245 AGAAAAGATG
17389255 ATAAT-ATAACAAAATTGATA
1 ATAATAATAACAAAATTGATA
*
17389275 ATACA-AATAACACAA-TGATA
1 ATA-ATAATAACAAAATTGATA
17389295 ATAATAATAA
1 ATAATAATAA
17389305 TAGTCAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.04
20 16 0.62
21 9 0.35
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (21 bp):
ATAATAATAACAAAATTGATA
Found at i:17393768 original size:40 final size:40
Alignment explanation
Indices: 17393713--17393794 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
17393703 ACTAAATTGA
17393713 CATAATTTATAAGCTTTGAGGGTTAAAGTTGTTATTATGC
1 CATAATTTATAAGCTTTGAGGGTTAAAGTTGTTATTATGC
17393753 CATAATTTATAAGCTTTGAGGGTTAAAGTTGTTATTATGC
1 CATAATTTATAAGCTTTGAGGGTTAAAGTTGTTATTATGC
17393793 CA
1 CA
17393795 ATTTTAAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (40 bp):
CATAATTTATAAGCTTTGAGGGTTAAAGTTGTTATTATGC
Found at i:17397173 original size:20 final size:20
Alignment explanation
Indices: 17397148--17397190 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
17397138 CTCAAACCCG
17397148 CATATTTCTGTATTGAAAAC
1 CATATTTCTGTATTGAAAAC
17397168 CATATTTCTGTATTGAAAAC
1 CATATTTCTGTATTGAAAAC
17397188 CAT
1 CAT
17397191 GTCAATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (20 bp):
CATATTTCTGTATTGAAAAC
Found at i:17411601 original size:11 final size:11
Alignment explanation
Indices: 17411585--17411609 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17411575 TGCTGTGACG
17411585 TGTGTATTTAC
1 TGTGTATTTAC
17411596 TGTGTATTTAC
1 TGTGTATTTAC
17411607 TGT
1 TGT
17411610 AAGAAAGTAG
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:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (11 bp):
TGTGTATTTAC
Found at i:17426407 original size:23 final size:22
Alignment explanation
Indices: 17426381--17426435 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
17426371 TCCTATTGAA
17426381 ATTTATTTCAAATATATAATATT
1 ATTTATTT-AAATATATAATATT
* *
17426404 ATTTATTTGAATTTATAATATT
1 ATTTATTTAAATATATAATATT
*
17426426 ATTTTTTTAA
1 ATTTATTTAA
17426436 TATTCAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTATTTAAATATATAATATT
Found at i:17434965 original size:6 final size:6
Alignment explanation
Indices: 17434949--17434993 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
17434939 CAACAACGAA
* * *
17434949 GAGAAG AAGAAG GAGAAG GAGAAG GAGAAG GAGAGG GAGAGG GAG
1 GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAG
17434994 GAGAGCATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
GAGAAG
Found at i:17435164 original size:5 final size:5
Alignment explanation
Indices: 17435154--17435179 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17435144 GGTTGTGCAC
17435154 TTGAG TTGAG TTGAG TTGAG TTGAG T
1 TTGAG TTGAG TTGAG TTGAG TTGAG T
17435180 GAATCTGTAA
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:0.19, C:0.00, G:0.38, T:0.42
Consensus pattern (5 bp):
TTGAG
Found at i:17441173 original size:19 final size:20
Alignment explanation
Indices: 17441136--17441173 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
17441126 TTTTTACTAA
*
17441136 TTAATTATTGTTTTATTTAT
1 TTAATTATTGTTATATTTAT
*
17441156 TTAATT-TTGTTATCTTTA
1 TTAATTATTGTTATATTTA
17441174 ATATTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (20 bp):
TTAATTATTGTTATATTTAT
Found at i:17448009 original size:19 final size:21
Alignment explanation
Indices: 17447985--17448023 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17447975 ATTAATACTT
17447985 AAATTA-TAT-TAATTTTTTC
1 AAATTAGTATCTAATTTTTTC
17448004 AAATTAGTATCTAATTTTTT
1 AAATTAGTATCTAATTTTTT
17448024 TTATCATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (21 bp):
AAATTAGTATCTAATTTTTTC
Found at i:17448842 original size:21 final size:21
Alignment explanation
Indices: 17448813--17448854 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17448803 ATAACAGTTG
* *
17448813 AATATAAATATTGAAATAAAA
1 AATAAAAATATAGAAATAAAA
17448834 AATAAAAATATAGAAATAAAA
1 AATAAAAATATAGAAATAAAA
17448855 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (21 bp):
AATAAAAATATAGAAATAAAA
Found at i:17450622 original size:72 final size:72
Alignment explanation
Indices: 17450504--17450694 Score: 328
Period size: 72 Copynumber: 2.6 Consensus size: 72
17450494 TATATATTAG
17450504 TGCTTTTTTGATAGGTTTCAGCTTAATAATGTCTTTTGATCTGAGTTTGATCTGAGTTCGGAAAA
1 TGCTTTTTT-ATAGGTTTCAGCTTAATAATGTCTTTTGATCTGAGTTTGATCTGAGTTCGGAAAA
17450569 CTCTTTAC
65 CTCTTTAC
* *
17450577 TGCTTTTTTATAGGTTTCAGCTCAATAATGTCTTTTGATCTGAGTTTGATCTGAGTTTGGAAAAC
1 TGCTTTTTTATAGGTTTCAGCTTAATAATGTCTTTTGATCTGAGTTTGATCTGAGTTCGGAAAAC
*
17450642 TCTTTAG
66 TCTTTAC
* *
17450649 TGTTTTTTTATAGGTTTCAGCTTAATAATTTCTTTTGATCTGAGTT
1 TGCTTTTTTATAGGTTTCAGCTTAATAATGTCTTTTGATCTGAGTT
17450695 CTGTGATAGA
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
72 103 0.92
73 9 0.08
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (72 bp):
TGCTTTTTTATAGGTTTCAGCTTAATAATGTCTTTTGATCTGAGTTTGATCTGAGTTCGGAAAAC
TCTTTAC
Found at i:17450626 original size:11 final size:11
Alignment explanation
Indices: 17450610--17450635 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17450600 AATAATGTCT
17450610 TTTGATCTGAG
1 TTTGATCTGAG
17450621 TTTGATCTGAG
1 TTTGATCTGAG
17450632 TTTG
1 TTTG
17450636 GAAAACTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.08, G:0.27, T:0.50
Consensus pattern (11 bp):
TTTGATCTGAG
Found at i:17450943 original size:18 final size:19
Alignment explanation
Indices: 17450920--17450955 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17450910 ATTGTTTTCA
17450920 TACCTT-TAGGTATATCAC
1 TACCTTGTAGGTATATCAC
17450938 TACCTTGTAGGTATATCA
1 TACCTTGTAGGTATATCA
17450956 TTAATATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (19 bp):
TACCTTGTAGGTATATCAC
Found at i:17453275 original size:32 final size:32
Alignment explanation
Indices: 17453239--17453396 Score: 199
Period size: 32 Copynumber: 4.9 Consensus size: 32
17453229 ACTATGCTAG
17453239 TTTTTTATATGTAAAACTAATGTATGATATAC
1 TTTTTTATATGTAAAACTAATGTATGATATAC
* * * *
17453271 TTTTTCATTTGCAAAACTAATGTATGATCTAC
1 TTTTTTATATGTAAAACTAATGTATGATATAC
* * * *
17453303 TTTTTTATATGTGAACCTAATGTATTATCTAC
1 TTTTTTATATGTAAAACTAATGTATGATATAC
* *
17453335 TTTTTTATATGCAAAACTAATGTATGATTTAC
1 TTTTTTATATGTAAAACTAATGTATGATATAC
* * *
17453367 TTTTTTATACGTAAACCTAATGTATCATAT
1 TTTTTTATATGTAAAACTAATGTATGATAT
17453397 TTTTTATAAT
Statistics
Matches: 106, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 106 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (32 bp):
TTTTTTATATGTAAAACTAATGTATGATATAC
Found at i:17453348 original size:64 final size:64
Alignment explanation
Indices: 17453239--17453396 Score: 235
Period size: 64 Copynumber: 2.5 Consensus size: 64
17453229 ACTATGCTAG
* *
17453239 TTTTTTATATGTAAAACTAATGTATGATATACTTTTTCATTTGCAAAACTAATGTATGATCTAC
1 TTTTTTATATGTAAACCTAATGTATGATATACTTTTTCATATGCAAAACTAATGTATGATCTAC
* * * * *
17453303 TTTTTTATATGTGAACCTAATGTATTATCTACTTTTTTATATGCAAAACTAATGTATGATTTAC
1 TTTTTTATATGTAAACCTAATGTATGATATACTTTTTCATATGCAAAACTAATGTATGATCTAC
* *
17453367 TTTTTTATACGTAAACCTAATGTATCATAT
1 TTTTTTATATGTAAACCTAATGTATGATAT
17453397 TTTTTATAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 83 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (64 bp):
TTTTTTATATGTAAACCTAATGTATGATATACTTTTTCATATGCAAAACTAATGTATGATCTAC
Found at i:17456956 original size:21 final size:21
Alignment explanation
Indices: 17456908--17456957 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
17456898 ACCGCTGTTT
*
17456908 CTAATCTCACCGCTACAGTAT
1 CTAATCTCACCGCTACAGTAA
17456929 C-AATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAGTAA
17456949 CTAATCTCA
1 CTAATCTCA
17456958 TCGCCACCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:17462236 original size:22 final size:22
Alignment explanation
Indices: 17462210--17462254 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
17462200 TCCACTTTGG
17462210 TAAGCATATTGTTTAATAATGA
1 TAAGCATATTGTTTAATAATGA
17462232 TAAGCATATTGTTTAATAATGA
1 TAAGCATATTGTTTAATAATGA
17462254 T
1 T
17462255 TTGCAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (22 bp):
TAAGCATATTGTTTAATAATGA
Found at i:17466752 original size:197 final size:197
Alignment explanation
Indices: 17466377--17466944 Score: 736
Period size: 197 Copynumber: 2.9 Consensus size: 197
17466367 GAAACGTTAG
* * * * * * * * *
17466377 ATTCACAGTAATTTCAACCTCAAAAATTCCTGTGAA-TGCTTTACATATGATCAACAATGCTTTA
1 ATTCAAAGTAGTTTCAACCTCTAAAATTCCAG-GAAGTCCTTTATATAAGATCAAGAATGCTTGA
* * * * *
17466441 A-GTCTCTTGAACAAGCTAATAAATTACTATAGATTGGAGCTA-CAATTTAGTTTCCA-TGCTAC
65 AGGT-TCTTGAACAAGCTAATAAAGTAC--TAGGTTGGAGATACCAA-TTAGTTTCCACTGATAT
* *
17466503 AGAAAGAAATACAATTTCAAAAAGGGCAAAGAGTGCAACAAAATCCCACAAAGCATACTAATCTA
126 AGAATGAAATTCAATTTCAAAAAGGGCAAAGAGTGCAACAAAATCCCACAAAGCATACTAATCTA
17466568 ACCACAA
191 ACCACAA
17466575 ATTCAAAGTAGTTTCAACCTCTAAAATTCC-GGACAGTCCTTTATATAAGATCAAGAATGCTTGA
1 ATTCAAAGTAGTTTCAACCTCTAAAATTCCAGGA-AGTCCTTTATATAAGATCAAGAATGCTTGA
* *
17466639 AGGTTCTTGAACGAA-CTAATAAAGAACTAGGTTGGAGATACCAATTAGTTTCCACGGATATAGA
65 AGGTTCTTGAAC-AAGCTAATAAAGTACTAGGTTGGAGATACCAATTAGTTTCCACTGATATAGA
* * *
17466703 ATGCAATTCAATTTCAAAAAGGGCAATGAGTGCAACAAAATCCCACAAAGCATACTAATCTAATC
129 ATGAAATTCAATTTCAAAAAGGGCAAAGAGTGCAACAAAATCCCACAAAGCATACTAATCTAACC
17466768 ACAA
194 ACAA
* * * *
17466772 ATTCAGAGTAGTTTCAACCTTTAAAATTCCAGGGAGTCCATTATATAAGATCAAGAATGC-TGTA
1 ATTCAAAGTAGTTTCAACCTCTAAAATTCCAGGAAGTCCTTTATATAAGATCAAGAATGCTTG-A
* * *
17466836 AGGTTCTTGAACAAGCTAACAAAGTACTAGGTTGGGGATACCAATTTGTTTCCACTGATATAGAA
65 AGGTTCTTGAACAAGCTAATAAAGTACTAGGTTGGAGATACCAATTAGTTTCCACTGATATAGAA
** *
17466901 TGGGATTCAATTTCACAAAGGGCAAAGAGTGCAACAAAATCCCA
130 TGAAATTCAATTTCAAAAAGGGCAAAGAGTGCAACAAAATCCCA
17466945 AACACATAAA
Statistics
Matches: 328, Mismatches: 33, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
196 27 0.08
197 226 0.69
198 71 0.22
199 4 0.01
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (197 bp):
ATTCAAAGTAGTTTCAACCTCTAAAATTCCAGGAAGTCCTTTATATAAGATCAAGAATGCTTGAA
GGTTCTTGAACAAGCTAATAAAGTACTAGGTTGGAGATACCAATTAGTTTCCACTGATATAGAAT
GAAATTCAATTTCAAAAAGGGCAAAGAGTGCAACAAAATCCCACAAAGCATACTAATCTAACCAC
AA
Found at i:17472051 original size:36 final size:36
Alignment explanation
Indices: 17472008--17472079 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
17471998 CATAAGAGTA
*
17472008 AGACTATTGATTTTGTTGCTTTCTTACAAAATTAAG
1 AGACTATTGATTTTATTGCTTTCTTACAAAATTAAG
17472044 AGACTATTGATTTTATTGCTTTCTTACAAAATTAAG
1 AGACTATTGATTTTATTGCTTTCTTACAAAATTAAG
17472080 GATGGATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (36 bp):
AGACTATTGATTTTATTGCTTTCTTACAAAATTAAG
Found at i:17474714 original size:17 final size:16
Alignment explanation
Indices: 17474686--17474738 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
17474676 TTTGGTTCGC
17474686 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
17474702 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
17474719 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
17474735 TGTA
1 TGTA
17474739 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:17474803 original size:44 final size:45
Alignment explanation
Indices: 17474719--17474809 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
17474709 GGATTAGAGG
* * *
17474719 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
17474764 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
17474808 TG
1 TG
17474810 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:17474995 original size:18 final size:17
Alignment explanation
Indices: 17474974--17475008 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17474964 TCATTATTAA
*
17474974 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
17474992 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
17475009 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17475122 original size:14 final size:15
Alignment explanation
Indices: 17475073--17475124 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
17475063 GTAAAATATA
17475073 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
17475088 TATTAAATATATTAT
1 AATTAAATATATTAT
17475103 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
17475116 AATTTAATA
1 AATTAAATA
17475125 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:17475175 original size:120 final size:120
Alignment explanation
Indices: 17474957--17475175 Score: 393
Period size: 120 Copynumber: 1.8 Consensus size: 120
17474947 ATCATATTTA
*
17474957 AACATAATCATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATCATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
17475022 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
17475077 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATCATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
17475142 TATTCTTATATGAATTTACTCAAATCATCATATA
66 TATTCTTATATGAATTTACTCAAATCATAATATA
17475176 AAATCGTGTT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 94 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATCATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:17484865 original size:21 final size:22
Alignment explanation
Indices: 17484839--17484885 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
17484829 CTCTGCTCAA
*
17484839 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
17484860 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
17484882 ACTC
1 ACTC
17484886 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:17489705 original size:25 final size:24
Alignment explanation
Indices: 17489677--17489739 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
17489667 TTTATTTATG
* *
17489677 ATTTTTAATTTTTTTATTCTCAATT
1 ATTTTTAATTTTTTAATACT-AATT
*
17489702 ATTTTCAATTTCTTTAATACTAATT
1 ATTTTTAATTT-TTTAATACTAATT
* *
17489727 TTTTTTTATTTTT
1 ATTTTTAATTTTT
17489740 CTTTTCAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 2 0.06
25 22 0.71
26 7 0.23
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTTAATTTTTTAATACTAATT
Found at i:17496826 original size:25 final size:25
Alignment explanation
Indices: 17496797--17496848 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
17496787 AAGAATAATT
**
17496797 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
17496822 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
17496847 TG
1 TG
17496849 TCAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:17501388 original size:19 final size:19
Alignment explanation
Indices: 17501364--17501403 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
17501354 TTAATTATTC
17501364 TTTAATTTATAATTCAACT
1 TTTAATTTATAATTCAACT
*
17501383 TTTAATTTTTAATTCAACT
1 TTTAATTTATAATTCAACT
17501402 TT
1 TT
17501404 CACCCTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATTTATAATTCAACT
Found at i:17502802 original size:76 final size:76
Alignment explanation
Indices: 17502664--17503085 Score: 361
Period size: 76 Copynumber: 5.6 Consensus size: 76
17502654 GTGACATTCA
* *
17502664 ATTTTCTAACAGTTCGCTTGATTTAATATCGCAACTGTCATTTTTACGATCCACTAAATTAAGAT
1 ATTTTCTAACAGTTCGCTTGATTTAATATCGCGACTGTCATTTTTACGATCCACTAATTTAAGAT
* *
17502729 CGCGACCTTTG
66 CGCAACCTTCG
* * * * * * * * *
17502740 ATTTTCTAACAGTTCACTTGATTTAATATTGTGACTGCCATTTTTATGGTTCATTGATTTAAGAT
1 ATTTTCTAACAGTTCGCTTGATTTAATATCGCGACTGTCATTTTTACGATCCACTAATTTAAGAT
17502805 CGCAACCTTCG
66 CGCAACCTTCG
* ** * * *
17502816 GTTTTCTAACAACTCGTTTGATTTAATATCGCGACTGTCAGTTTTACGATCCACTAATTTAATAT
1 ATTTTCTAACAGTTCGCTTGATTTAATATCGCGACTGTCATTTTTACGATCCACTAATTTAAGAT
*
17502881 CGTAACCTTCG
66 CGCAACCTTCG
* * * * * * * *
17502892 ATTTTCTAATAGTTTGCTTGATTTAATATCGTGATTGTCATTTTTATGGTCCATTGATTTAAGAT
1 ATTTTCTAACAGTTCGCTTGATTTAATATCGCGACTGTCATTTTTACGATCCACTAATTTAAGAT
* *
17502957 TGCGACCTTCG
66 CGCAACCTTCG
* * * * * * * * *
17502968 A-----T-ACAGTTTGTTTGATTTAATATCGAGGCTGTCATTTTTAAGGTCCGCTGATTTAATAT
1 ATTTTCTAACAGTTCGCTTGATTTAATATCGCGACTGTCATTTTTACGATCCACTAATTTAAGAT
**** *
17503027 TATGACCTTTG
66 CGCAACCTTCG
* * * * *
17503038 ATTTTTTAATAGTTCGCTTGAATTATTCTCGCGACTGTCATTTTTACG
1 ATTTTCTAACAGTTCGCTTGATTTAATATCGCGACTGTCATTTTTACG
17503086 GTCCGTTGAT
Statistics
Matches: 273, Mismatches: 67, Indels: 12
0.78 0.19 0.03
Matches are distributed among these distances:
70 57 0.21
71 1 0.00
75 1 0.00
76 214 0.78
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (76 bp):
ATTTTCTAACAGTTCGCTTGATTTAATATCGCGACTGTCATTTTTACGATCCACTAATTTAAGAT
CGCAACCTTCG
Found at i:17503034 original size:70 final size:70
Alignment explanation
Indices: 17502902--17503035 Score: 178
Period size: 70 Copynumber: 1.9 Consensus size: 70
17502892 ATTTTCTAAT
* * * * *
17502902 AGTTTGCTTGATTTAATATCGTGATTGTCATTTTTATGGTCCATTGATTTAAGATTGCGACCTTC
1 AGTTTGCTTGATTTAATATCGAGACTGTCATTTTTAAGGTCCACTGATTTAAGATTACGACCTTC
17502967 GATAC
66 GATAC
* * * * *
17502972 AGTTTGTTTGATTTAATATCGAGGCTGTCATTTTTAAGGTCCGCTGATTTAATATTATGACCTT
1 AGTTTGCTTGATTTAATATCGAGACTGTCATTTTTAAGGTCCACTGATTTAAGATTACGACCTT
17503036 TGATTTTTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
70 54 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (70 bp):
AGTTTGCTTGATTTAATATCGAGACTGTCATTTTTAAGGTCCACTGATTTAAGATTACGACCTTC
GATAC
Found at i:17503057 original size:146 final size:149
Alignment explanation
Indices: 17502681--17503108 Score: 450
Period size: 152 Copynumber: 2.9 Consensus size: 149
17502671 AACAGTTCGC
* * * * **
17502681 TTGATTTAATATCGCA-ACTGTCATTTTTACGATCCACTAAATTAAGATCGCGACCTTTGATTTT
1 TTGATTTAATATCG-AGACTGTCAGTTTTAAGATCCACTAATTTAATATCATGACCTTTGATTTT
* * * * * * *
17502745 CTAACAGTTCACTTGATTTAATATTGTGACTGCCATTTTTATGGTTCATTGATTTAAGATCGCAA
65 CTAATAGTTCGCTTGATTTAATATCGTGACTGTCATTTTTATGGTCCATTGATTTAAGATTGCGA
*
17502810 CCTTCGGTTTTCTAACAACTCGT
130 CCTTCGG---TATAACAACTCGT
* * * * *
17502833 TTGATTTAATATCGCGACTGTCAGTTTTACGATCCACTAATTTAATATCGTAACCTTCGATTTTC
1 TTGATTTAATATCGAGACTGTCAGTTTTAAGATCCACTAATTTAATATCATGACCTTTGATTTTC
* *
17502898 TAATAGTTTGCTTGATTTAATATCGTGATTGTCATTTTTATGGTCCATTGATTTAAGATTGCGAC
66 TAATAGTTCGCTTGATTTAATATCGTGACTGTCATTTTTATGGTCCATTGATTTAAGATTGCGAC
** *
17502963 CTTC-G-AT-ACAGTTTGT
131 CTTCGGTATAACAACTCGT
* * * * * * *
17502979 TTGATTTAATATCGAGGCTGTCATTTTTAAGGTCCGCTGATTTAATATTATGACCTTTGATTTTT
1 TTGATTTAATATCGAGACTGTCAGTTTTAAGATCCACTAATTTAATATCATGACCTTTGATTTTC
* * * * * * *
17503044 TAATAGTTCGCTTGAATTATTCTCGCGACTGTCATTTTTACGGTCCGTTGATTTAATATTGCGAC
66 TAATAGTTCGCTTGATTTAATATCGTGACTGTCATTTTTATGGTCCATTGATTTAAGATTGCGAC
17503109 ATTTGGTTTT
Statistics
Matches: 234, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
146 115 0.49
147 1 0.00
151 1 0.00
152 117 0.50
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.43
Consensus pattern (149 bp):
TTGATTTAATATCGAGACTGTCAGTTTTAAGATCCACTAATTTAATATCATGACCTTTGATTTTC
TAATAGTTCGCTTGATTTAATATCGTGACTGTCATTTTTATGGTCCATTGATTTAAGATTGCGAC
CTTCGGTATAACAACTCGT
Found at i:17504818 original size:31 final size:31
Alignment explanation
Indices: 17504779--17504845 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
17504769 ACATAATATT
*
17504779 TATA-GGAAATAAATATAATATATTCCTAAA
1 TATATGGAAAGAAATATAATATATTCCTAAA
*
17504809 TATATGGAAAGATATATAATATATTCCTAAA
1 TATATGGAAAGAAATATAATATATTCCTAAA
17504840 TATATG
1 TATATG
17504846 CCTAAAAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (31 bp):
TATATGGAAAGAAATATAATATATTCCTAAA
Found at i:17505987 original size:12 final size:13
Alignment explanation
Indices: 17505970--17506001 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
17505960 AACTAAGGGG
17505970 AGTTGGAATATC-
1 AGTTGGAATATCA
17505982 AGTTGGAATATCA
1 AGTTGGAATATCA
17505995 AGTTGGA
1 AGTTGGA
17506002 TTCAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (13 bp):
AGTTGGAATATCA
Found at i:17510688 original size:21 final size:21
Alignment explanation
Indices: 17510664--17510721 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
17510654 TAGACATCAA
17510664 GAGTATACATAATATTTATAG
1 GAGTATACATAATATTTATAG
*
17510685 GAGTACACATAATATTTATAG
1 GAGTATACATAATATTTATAG
*
17510706 GAAATATACATAATAT
1 G-AGTATACATAATAT
17510722 ATTCCTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (21 bp):
GAGTATACATAATATTTATAG
Found at i:17510750 original size:31 final size:31
Alignment explanation
Indices: 17510701--17510767 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
17510691 ACATAATATT
*
17510701 TATA-GGAAATATACATAATATATTCCTAAA
1 TATATGGAAAGATACATAATATATTCCTAAA
* **
17510731 TATATGGAAAGATATATAATATATTTTTAAA
1 TATATGGAAAGATACATAATATATTCCTAAA
17510762 TATATG
1 TATATG
17510768 CCTAAAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (31 bp):
TATATGGAAAGATACATAATATATTCCTAAA
Found at i:17510835 original size:31 final size:32
Alignment explanation
Indices: 17510760--17510839 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 32
17510750 TATATTTTTA
* *
17510760 AATATATGCCTAAAAGAT-ATTCAATATATTT
1 AATATATTCCTAAAAGATAATTCAATATATAT
* *
17510791 AA-ATATTCTTAAAAGATAATATC-TTATA-AT
1 AATATATTCCTAAAAGATAAT-TCAATATATAT
17510821 AATATATTCCTAAAAGATA
1 AATATATTCCTAAAAGATA
17510840 TCCCGTAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
30 16 0.39
31 23 0.56
32 2 0.05
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.38
Consensus pattern (32 bp):
AATATATTCCTAAAAGATAATTCAATATATAT
Found at i:17512440 original size:21 final size:23
Alignment explanation
Indices: 17512390--17512452 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 23
17512380 ATTGAATTTA
*
17512390 AATTATAAATTATGTTTGATATATT
1 AATTA-AAATTAT-TTAGATATATT
17512415 AATTAAAATTATTTAGA-ATA-T
1 AATTAAAATTATTTAGATATATT
17512436 AATT-AAATTATTT-GATA
1 AATTAAAATTATTTAGATA
17512453 AATATAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 2 0.06
20 10 0.28
21 5 0.14
22 3 0.08
23 4 0.11
24 7 0.19
25 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (23 bp):
AATTAAAATTATTTAGATATATT
Found at i:17512441 original size:25 final size:25
Alignment explanation
Indices: 17512390--17512440 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
17512380 ATTGAATTTA
*
17512390 AATTATAAATTATGTTTGATATATT
1 AATTATAAATTATGTTAGATATATT
17512415 AATTA-AAATTAT-TTAGA-ATA-T
1 AATTATAAATTATGTTAGATATATT
17512436 AATTA
1 AATTA
17512441 AATTATTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 6 0.24
22 3 0.12
23 4 0.16
24 7 0.28
25 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (25 bp):
AATTATAAATTATGTTAGATATATT
Found at i:17512456 original size:22 final size:22
Alignment explanation
Indices: 17512395--17512459 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 22
17512385 ATTTAAATTA
*
17512395 TAAATTATGTTTGATATAT-TAAT
1 TAAATTA--TTTGATAAATATAAT
*
17512418 TAAAATTATTT-A-GAATATAAT
1 T-AAATTATTTGATAAATATAAT
17512439 TAAATTATTTGATAAATATAA
1 TAAATTATTTGATAAATATAA
17512460 ATTTTAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
20 11 0.31
21 7 0.20
22 10 0.29
23 1 0.03
24 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (22 bp):
TAAATTATTTGATAAATATAAT
Found at i:17523863 original size:24 final size:24
Alignment explanation
Indices: 17523836--17523882 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
17523826 TATGGTAACT
*
17523836 AATATTATATTAATTATTTTTTAA
1 AATAATATATTAATTATTTTTTAA
* **
17523860 AATAATGTATTTTTTATTTTTTA
1 AATAATATATTAATTATTTTTTA
17523883 TTTATAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AATAATATATTAATTATTTTTTAA
Found at i:17525300 original size:6 final size:7
Alignment explanation
Indices: 17525283--17525309 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17525273 TAGCTTTATT
17525283 TTTTTTA
1 TTTTTTA
17525290 TTTTTTA
1 TTTTTTA
17525297 TTTTTTA
1 TTTTTTA
17525304 TTTTTT
1 TTTTTT
17525310 GAGTTTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:17527117 original size:41 final size:41
Alignment explanation
Indices: 17527020--17527263 Score: 328
Period size: 41 Copynumber: 6.0 Consensus size: 41
17527010 TAAAACACAT
* *
17527020 AGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAAAT-AG
1 AGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAG
* * * * *
17527060 AGAAATAGTGGCGCTTTAGGTAAAACACCGTTAAAAGTCAG
1 AGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAG
*
17527101 AGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTCAG
1 AGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAG
* * *
17527142 AGCATTAGCGGCACTTTTGGTAAAACGCCGCTAAAAGTCGG
1 AGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAG
* * **
17527183 AGCAATAGTGGCGCTTTTAGTAAAACGCCATTAAAAGTCAG
1 AGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAG
* *
17527224 AGCATTAGAGGCGCTTTTGGTAAAACGCCGCTAAAAGTCA
1 AGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCA
17527264 TATAACCCCT
Statistics
Matches: 175, Mismatches: 28, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 0.18
41 144 0.82
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (41 bp):
AGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAG
Found at i:17527225 original size:123 final size:122
Alignment explanation
Indices: 17527020--17527263 Score: 364
Period size: 123 Copynumber: 2.0 Consensus size: 122
17527010 TAAAACACAT
**
17527020 AGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAAATAGAGAAATAGTGGCGCTTTAGGTAAAA
1 AGCAATAGCGGCACTTTTGGTAAAACGCCGCTAAAAATAGAGAAATAGTGGCGCTTTAGGTAAAA
* *
17527085 CACCGTTAAAAGTCAGAGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTCAG
66 CACCATTAAAAGTCAGAGCAATAGAGGCGCTTTCGGTAAAACGCCGCTAAAAGTCAG
* * * *
17527142 AGCATTAGCGGCACTTTTGGTAAAACGCCGCTAAAAGTCGGAGCAATAGTGGCGCTTTTA-GTAA
1 AGCAATAGCGGCACTTTTGGTAAAACGCCGCTAAAAAT-AGAGAAATAGTGGCGC-TTTAGGTAA
* * *
17527206 AACGCCATTAAAAGTCAGAGCATTAGAGGCGCTTTTGGTAAAACGCCGCTAAAAGTCA
64 AACACCATTAAAAGTCAGAGCAATAGAGGCGCTTTCGGTAAAACGCCGCTAAAAGTCA
17527264 TATAACCCCT
Statistics
Matches: 109, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
122 34 0.31
123 71 0.65
124 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (122 bp):
AGCAATAGCGGCACTTTTGGTAAAACGCCGCTAAAAATAGAGAAATAGTGGCGCTTTAGGTAAAA
CACCATTAAAAGTCAGAGCAATAGAGGCGCTTTCGGTAAAACGCCGCTAAAAGTCAG
Found at i:17527485 original size:7 final size:7
Alignment explanation
Indices: 17527473--17527536 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
17527463 TTTATTTTTT
*
17527473 GGTTTAC
1 GGTTTAA
17527480 GGTTTAA
1 GGTTTAA
**
17527487 TATTTAA
1 GGTTTAA
17527494 GGTTTAA
1 GGTTTAA
* *
17527501 GGTCTAT
1 GGTTTAA
*
17527508 GGTTTAG
1 GGTTTAA
*
17527515 GGTTTTAT
1 GG-TTTAA
17527523 GGTTTAA
1 GGTTTAA
17527530 GGTTTAA
1 GGTTTAA
17527537 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:17527525 original size:15 final size:15
Alignment explanation
Indices: 17527489--17527539 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
17527479 CGGTTTAATA
*
17527489 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
17527503 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
17527518 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
17527533 TTAATGG
1 TTTATGG
17527540 CCATGGGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:17528153 original size:8 final size:8
Alignment explanation
Indices: 17528135--17528226 Score: 70
Period size: 7 Copynumber: 12.1 Consensus size: 8
17528125 AAATAAACTC
17528135 AAAAATT-
1 AAAAATTA
17528142 AAAAATTA
1 AAAAATTA
17528150 AAAAATT-
1 AAAAATTA
*
17528157 TAAAATT-
1 AAAAATTA
*
17528164 TAAAATT-
1 AAAAATTA
* *
17528171 TAAAATTT
1 AAAAATTA
17528179 AAAAA-TA
1 AAAAATTA
17528186 AAAAA-TA
1 AAAAATTA
*
17528193 AAAAATAA
1 AAAAATTA
17528201 AAAAACTTA
1 AAAAA-TTA
*
17528210 AAAAATTT
1 AAAAATTA
*
17528218 AAAATTTA
1 AAAAATTA
17528226 A
1 A
17528227 TATTTTAGTC
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
7 40 0.55
8 26 0.36
9 7 0.10
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAAATTA
Found at i:17533476 original size:21 final size:21
Alignment explanation
Indices: 17533452--17533493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17533442 ATTTAATCTA
*
17533452 ATTTTTA-TTATATATTTTAAT
1 ATTTTTAGTTA-AAATTTTAAT
17533473 ATTTTTAGTTAAAATTTTAAT
1 ATTTTTAGTTAAAATTTTAAT
17533494 CAAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTTTTAGTTAAAATTTTAAT
Found at i:17533684 original size:43 final size:43
Alignment explanation
Indices: 17533636--17533726 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
17533626 TTTTATTACC
* * * * *
17533636 TTTAGCTGCGTTTTTGGGTAAAGCGTCGCTAAAGGTCATGACA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGACA
* *
17533679 TTTAGCGGCGTTTGTGGGAAAAGCGCCATTAAAGGTCATGACC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGACA
17533722 TTTAG
1 TTTAG
17533727 TGGTGTTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGACA
Found at i:17535658 original size:20 final size:20
Alignment explanation
Indices: 17535633--17535718 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 20
17535623 ATTTTATAAT
17535633 ATATATTTTTTAAATTTTAA
1 ATATATTTTTTAAATTTTAA
17535653 ATATA-----T--ATTTTGAA
1 ATATATTTTTTAAATTTT-AA
*
17535667 AT-TATTTTTTTAATTTTAA
1 ATATATTTTTTAAATTTTAA
*
17535686 ATAT-TATTTTTAAATATTAA
1 ATATAT-TTTTTAAATTTTAA
*
17535706 ATATATATTTTAA
1 ATATATTTTTTAA
17535719 TAATATAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 22
0.68 0.04 0.29
Matches are distributed among these distances:
13 7 0.13
14 4 0.08
15 1 0.02
18 1 0.02
19 5 0.10
20 33 0.63
21 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
ATATATTTTTTAAATTTTAA
Found at i:17535673 original size:24 final size:23
Alignment explanation
Indices: 17535591--17535674 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
17535581 TTTATTATTA
* *
17535591 ATTTT-AAAAATTTTGAAATGTAT
1 ATTTTGAAATATTTT-AAATATAT
17535614 A-TTTGAAATATTTTATAATATAT
1 ATTTTGAAATATTTTA-AATATAT
**
17535637 ATTTTTTAA-ATTTTAAATATAT
1 ATTTTGAAATATTTTAAATATAT
17535659 ATTTTGAAATTATTTT
1 ATTTTGAAA-TATTTT
17535675 TTTAATTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
22 18 0.36
23 22 0.44
24 10 0.20
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
ATTTTGAAATATTTTAAATATAT
Found at i:17535682 original size:33 final size:32
Alignment explanation
Indices: 17535636--17535700 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
17535626 TTATAATATA
17535636 TATTTTTTAAATTTTAAATATATATTTTGAAAT
1 TATTTTTTAAATTTTAAATAT-TATTTTGAAAT
* *
17535669 TATTTTTTTAATTTTAAATATTATTTTTAAAT
1 TATTTTTTAAATTTTAAATATTATTTTGAAAT
17535701 ATTAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (32 bp):
TATTTTTTAAATTTTAAATATTATTTTGAAAT
Found at i:17535692 original size:21 final size:21
Alignment explanation
Indices: 17535659--17535716 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
17535649 TTAAATATAT
* *
17535659 ATTTTGAA-ATTATTTTTTTA
1 ATTTTAAATATTATTTTTTAA
17535679 ATTTTAAATATTA-TTTTTAA
1 ATTTTAAATATTATTTTTTAA
*
17535699 ATATTAAATATATATTTT
1 ATTTTAAATAT-TATTTT
17535717 AATAATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 23 0.72
21 6 0.19
22 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTTAAATATTATTTTTTAA
Found at i:17535703 original size:13 final size:13
Alignment explanation
Indices: 17535680--17535704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17535670 ATTTTTTTAA
17535680 TTTTAAATATTAT
1 TTTTAAATATTAT
17535693 TTTTAAATATTA
1 TTTTAAATATTA
17535705 AATATATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:17535711 original size:22 final size:22
Alignment explanation
Indices: 17535684--17535731 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
17535674 TTTTAATTTT
* *
17535684 AAATAT-TATTTTTA-AATATT
1 AAATATATATTTTAATAATATA
17535704 AAATATATATTTTAATAATATA
1 AAATATATATTTTAATAATATA
17535726 AAATAT
1 AAATAT
17535732 TTAAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 7 0.29
22 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATATATATTTTAATAATATA
Found at i:17535731 original size:20 final size:20
Alignment explanation
Indices: 17535684--17535731 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
17535674 TTTTAATTTT
*
17535684 AAATATTATTTTTAAATATTA
1 AAATA-TATTTTAAAATATTA
17535705 AATATATATTTTAATAATA-TA
1 AA-ATATATTTTAA-AATATTA
17535726 AAATAT
1 AAATAT
17535732 TTAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 13 0.54
22 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATATATTTTAAAATATTA
Found at i:17535824 original size:21 final size:21
Alignment explanation
Indices: 17535790--17535847 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 21
17535780 ATATTTTAAA
*
17535790 TTTTAAATATTTTTTAATTTG
1 TTTTAAATATTTTTAAATTTG
17535811 TTTTATAATA-TTTTAAATTATG
1 TTTTA-AATATTTTTAAATT-TG
17535833 ATTTTTAAATTATTT
1 --TTTTAAA-TATTT
17535848 AAAATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 13 0.43
22 6 0.20
23 2 0.07
24 7 0.23
25 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
TTTTAAATATTTTTAAATTTG
Found at i:17535846 original size:24 final size:24
Alignment explanation
Indices: 17535811--17535866 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
17535801 TTTTAATTTG
*
17535811 TTTTATAATATTTTAAAT-TATGAT
1 TTTTA-AATATTTAAAATATATGAT
*
17535835 TTTTAAATTATTTAAAATATATTAT
1 TTTTAAA-TATTTAAAATATATGAT
17535860 TTTTAAA
1 TTTTAAA
17535867 GATATGACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 14 0.50
25 12 0.43
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTAAATATTTAAAATATATGAT
Found at i:17537152 original size:3 final size:3
Alignment explanation
Indices: 17537144--17537170 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17537134 AAATGGTAAG
17537144 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
17537171 GGTATTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17537513 original size:6 final size:6
Alignment explanation
Indices: 17537502--17537534 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
17537492 TGTGTACCGC
*
17537502 TACTAT TACTAT TACTAT TACTAT TACTGT TAC
1 TACTAT TACTAT TACTAT TACTAT TACTAT TAC
17537535 CCTTACGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.48
Consensus pattern (6 bp):
TACTAT
Found at i:17537540 original size:18 final size:18
Alignment explanation
Indices: 17537502--17537540 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17537492 TGTGTACCGC
*
17537502 TACTATTACTATTACTAT
1 TACTATTACTATTACCAT
* *
17537520 TACTATTACTGTTACCCT
1 TACTATTACTATTACCAT
17537538 TAC
1 TAC
17537541 GGTGTATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.03, T:0.46
Consensus pattern (18 bp):
TACTATTACTATTACCAT
Found at i:17537723 original size:18 final size:18
Alignment explanation
Indices: 17537666--17537725 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
17537656 GATTGTCTGC
* *
17537666 TACTGAATAATTGACTGT
1 TACTGAATAAATGACTAT
* * *
17537684 TACAGAATAAACGACTAA
1 TACTGAATAAATGACTAT
*
17537702 TACTGAATAAATGAATAT
1 TACTGAATAAATGACTAT
17537720 TACTGA
1 TACTGA
17537726 TTAACCGATT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (18 bp):
TACTGAATAAATGACTAT
Found at i:17540928 original size:31 final size:31
Alignment explanation
Indices: 17540893--17541045 Score: 234
Period size: 31 Copynumber: 4.9 Consensus size: 31
17540883 TTGTCACTTT
* * *
17540893 TAGCCGAAGCTACCACTATTCACTGATCAAG
1 TAGCCGAAGCTACCATTTTTCACTGATCAGG
*
17540924 TAGCCGGAGCTACCATTTTTCACTGATCAGG
1 TAGCCGAAGCTACCATTTTTCACTGATCAGG
*
17540955 TAGCCGAGGCTACCATTTTTCACTGATCAGG
1 TAGCCGAAGCTACCATTTTTCACTGATCAGG
17540986 TAGCCGAAGCTACCATTTTTCACTGATCAGG
1 TAGCCGAAGCTACCATTTTTCACTGATCAGG
* * *
17541017 TTGCCGAAGCTACCACTTTTCACTTATCA
1 TAGCCGAAGCTACCATTTTTCACTGATCA
17541046 TTTGTCCTTG
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 112 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (31 bp):
TAGCCGAAGCTACCATTTTTCACTGATCAGG
Found at i:17541116 original size:50 final size:51
Alignment explanation
Indices: 17541023--17541142 Score: 170
Period size: 50 Copynumber: 2.4 Consensus size: 51
17541013 CAGGTTGCCG
* * * *
17541023 AAGCTACCACTTTTCACTTATCATTTGTCCTTGATCAGATAAGTGTAGCCA
1 AAGCTATCACTTATCACTTATCACTTATCCTTGATCAGATAAGTGTAGCCA
* * *
17541074 AAGCTGTCACTTATCACTT-TCACTTATCCTTGATCAGTTAAGTGTAGCCG
1 AAGCTATCACTTATCACTTATCACTTATCCTTGATCAGATAAGTGTAGCCA
17541124 AAGCTATCACTTATCACTT
1 AAGCTATCACTTATCACTT
17541143 GTTGCCATGG
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
50 45 0.74
51 16 0.26
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (51 bp):
AAGCTATCACTTATCACTTATCACTTATCCTTGATCAGATAAGTGTAGCCA
Found at i:17544981 original size:52 final size:48
Alignment explanation
Indices: 17544900--17545106 Score: 177
Period size: 47 Copynumber: 4.2 Consensus size: 48
17544890 CCATGACAGC
* * * * *
17544900 ATGTGAAATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCTTCGG
1 ATGTGATATGTG-CTTCCGTATAAGACCATATCTGGGATATGGCCTCGG
* *
17544949 ACAAATGTGATATGTGCTTCCGTATAATACCATATCCGGGATATGGCCTCGG
1 ----ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCCTCGG
* * * *
17545001 -TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAG
1 ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCCTCGG
* * * ** * *
17545048 -TGTGATACGTG-ATCCGTGTAAGACCATGGCTGGGCTATGGCCTCAGT
1 ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCCTC-GG
17545095 ATGTGATATGTG
1 ATGTGATATGTG
17545107 ACTATGTGCA
Statistics
Matches: 127, Mismatches: 25, Indels: 9
0.79 0.16 0.06
Matches are distributed among these distances:
46 25 0.20
47 51 0.40
48 10 0.08
52 30 0.24
53 11 0.09
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (48 bp):
ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCCTCGG
Found at i:17547605 original size:39 final size:39
Alignment explanation
Indices: 17547562--17547728 Score: 244
Period size: 39 Copynumber: 4.3 Consensus size: 39
17547552 ATGCAAGATA
*
17547562 CTGGAAATATATCCGAGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
17547601 CTGGAAATGTATCCGGGCTAAAGTCCCGTAGGCTTCGTG
1 CTGGAAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* * *
17547640 TTGGAAATATATCCGGGCTAAAGTCCCGTAGGGTTCGTG
1 CTGGAAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* * *
17547679 CAGGAAATATATCCGGGCTAAAGTCCCGCAAGCTTTGTG
1 CTGGAAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
17547718 CTGGTAATATA
1 CTGGAAATATA
17547729 ATTTCGGGTT
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 114 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CTGGAAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:17551896 original size:30 final size:30
Alignment explanation
Indices: 17551861--17551962 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 30
17551851 TGGTCGCTTT
* * *
17551861 GGGTGAAATGAACTCGAACCTCCTATGTCC
1 GGGTGATATGAACTCGAACCGCCAATGTCC
* * *
17551891 GGGTGATATGAACTCAAATCGCCGATGTCC
1 GGGTGATATGAACTCGAACCGCCAATGTCC
*
17551921 GGGTGATATGAACTTGAACCGCCAATGTCC
1 GGGTGATATGAACTCGAACCGCCAATGTCC
*
17551951 GAGTGATATGAA
1 GGGTGATATGAA
17551963 GTGCTCTGTG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (30 bp):
GGGTGATATGAACTCGAACCGCCAATGTCC
Found at i:17554197 original size:17 final size:17
Alignment explanation
Indices: 17554175--17554243 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
17554165 CAACATTTTC
17554175 TTTTAACATATTTAAAA
1 TTTTAACATATTTAAAA
* **
17554192 TTTTAATATATTTAATT
1 TTTTAACATATTTAAAA
* * *
17554209 TTTTTACGTTTTTTAAAA
1 TTTTAAC-ATATTTAAAA
17554227 TTTTAA-ATATATTAAAA
1 TTTTAACATAT-TTAAAA
17554244 AATCATTTTC
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
16 2 0.05
17 25 0.66
18 11 0.29
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (17 bp):
TTTTAACATATTTAAAA
Found at i:17554283 original size:9 final size:9
Alignment explanation
Indices: 17554269--17554331 Score: 53
Period size: 9 Copynumber: 7.3 Consensus size: 9
17554259 TCCTATTAAA
17554269 AAATATATT
1 AAATATATT
17554278 AAATATATT
1 AAATATATT
*
17554287 AAA-ATTTT
1 AAATATATT
17554295 AAAATATATT
1 -AAATATATT
* **
17554305 ---TTTAAA
1 AAATATATT
17554311 AAATATATT
1 AAATATATT
17554320 AAATATATT
1 AAATATATT
17554329 AAA
1 AAA
17554332 ATTTTAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
6 3 0.07
8 4 0.10
9 30 0.73
10 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATATATT
Found at i:17554378 original size:71 final size:72
Alignment explanation
Indices: 17554303--17554452 Score: 241
Period size: 70 Copynumber: 2.1 Consensus size: 72
17554293 TTAAAATATA
* *
17554303 TTTTTAAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAA-TTTTTTTAATAT
1 TTTTTAAAAAATATATTAAATATATTAAAATTTTAAAATTGGCTATACTTAACATTTTTTAATAT
17554367 ATTTAAT
66 ATTTAAT
* *
17554374 TTTTT-AAAAATATATTAAATATATTAAAATTTTGAAATTTGCTATACTTAACATTTTTTAATAT
1 TTTTTAAAAAATATATTAAATATATTAAAATTTTAAAATTGGCTATACTTAACATTTTTTAATAT
17554438 ATTTAAT
66 ATTTAAT
17554445 TTCTTTAA
1 TT-TTTAA
17554453 GTTTTTAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
70 43 0.60
71 25 0.35
72 3 0.04
73 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (72 bp):
TTTTTAAAAAATATATTAAATATATTAAAATTTTAAAATTGGCTATACTTAACATTTTTTAATAT
ATTTAAT
Found at i:17554386 original size:18 final size:19
Alignment explanation
Indices: 17554346--17554391 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
17554336 TAAAATTGGT
* *
17554346 TATACTTAATTTTTTTAATA
1 TATA-TTAATTTTTTAAAAA
17554366 TAT-TTAATTTTTTAAAAA
1 TATATTAATTTTTTAAAAA
17554384 TATATTAA
1 TATATTAA
17554392 ATATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 16 0.70
19 4 0.17
20 3 0.13
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTAATTTTTTAAAAA
Found at i:17554400 original size:20 final size:20
Alignment explanation
Indices: 17554362--17554402 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17554352 TAATTTTTTT
* * *
17554362 AATATATTTAATTTTTTAAA
1 AATATATTAAATATATTAAA
17554382 AATATATTAAATATATTAAA
1 AATATATTAAATATATTAAA
17554402 A
1 A
17554403 TTTTGAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATTAAATATATTAAA
Found at i:17554549 original size:20 final size:20
Alignment explanation
Indices: 17554521--17554592 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
17554511 TATATATTAA
*
17554521 GTACATAAATTTTATAAATGT
1 GTAC-TAAAATTTATAAATGT
* *
17554542 GTACTAAAATTAAAAAAT-T
1 GTACTAAAATTTATAAATGT
*
17554561 AATA-TATAAATTTATAAATGT
1 -GTACTA-AAATTTATAAATGT
17554582 GTACTAAAATT
1 GTACTAAAATT
17554593 AAAAAATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
19 3 0.08
20 30 0.75
21 7 0.17
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (20 bp):
GTACTAAAATTTATAAATGT
Found at i:17554551 original size:40 final size:39
Alignment explanation
Indices: 17554516--17554601 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 39
17554506 AAAAATATAT
17554516 ATTAAGTACATAAATTTTATAAATGTGTACTAAAATTAAAAA
1 ATTAA-TACATAAA-TTTATAAATGTGTACTAAAA-TAAAAA
*
17554558 ATTAATATATAAATTTATAAATGTGTACTAAAATTAAAAA
1 ATTAATACATAAATTTATAAATGTGTACTAAAA-TAAAAA
17554598 ATTA
1 ATTA
17554602 TAACCAACAC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 31 0.72
41 7 0.16
42 5 0.12
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.37
Consensus pattern (39 bp):
ATTAATACATAAATTTATAAATGTGTACTAAAATAAAAA
Found at i:17554599 original size:20 final size:20
Alignment explanation
Indices: 17554536--17554599 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
17554526 TAAATTTTAT
17554536 AAATGTGTACTAAAATTAAA
1 AAATGTGTACTAAAATTAAA
* * *
17554556 AAAT-TAATA-TATAAATTTAT
1 AAATGT-GTACTA-AAATTAAA
17554576 AAATGTGTACTAAAATTAAA
1 AAATGTGTACTAAAATTAAA
17554596 AAAT
1 AAAT
17554600 TATAACCAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (20 bp):
AAATGTGTACTAAAATTAAA
Found at i:17555002 original size:20 final size:20
Alignment explanation
Indices: 17554971--17555025 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
17554961 TGTAATCTTA
*
17554971 TAATATATATTTTTAATTTT
1 TAATATAAATTTTTAATTTT
* *
17554991 TAATTTAAATTTTTACTTTT
1 TAATATAAATTTTTAATTTT
17555011 TAATATAAATATTTT
1 TAATATAAAT-TTTT
17555026 TAAATAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATATAAATTTTTAATTTT
Found at i:17555039 original size:16 final size:17
Alignment explanation
Indices: 17554986--17555042 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 17
17554976 TATATTTTTA
*
17554986 ATTTTTAATTTAAATTTTT
1 ATTTTTAATATAAA--TTT
17555005 ACTTTTTAATATAAA--T
1 A-TTTTTAATATAAATTT
17555021 ATTTTTAA-ATAAATTT
1 ATTTTTAATATAAATTT
17555037 ATTTTT
1 ATTTTT
17555043 TTAACAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 9 0.26
19 1 0.03
20 12 0.35
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTAATATAAATTT
Found at i:17555075 original size:15 final size:15
Alignment explanation
Indices: 17555036--17555079 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 15
17555026 TAAATAAATT
17555036 TATTTTTTTAACAAA
1 TATTTTTTTAACAAA
17555051 TAAATCTTTTTTTAACAAA
1 T--A--TTTTTTTAACAAA
17555070 TATTTTTTTA
1 TATTTTTTTA
17555080 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 9 0.36
17 2 0.08
19 14 0.56
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTTTTTAACAAA
Found at i:17555489 original size:21 final size:21
Alignment explanation
Indices: 17555441--17555509 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
17555431 AAAATATTTA
* * *
17555441 AATATTTTATATTATTAAAATT
1 AATATTTAATATT-TAAAAAAT
17555463 ATATATTTAATATTTAAAAAAT
1 A-ATATTTAATATTTAAAAAAT
*
17555485 AATATTTAAAATTTTAAAAAAT
1 AATATTTAATA-TTTAAAAAAT
17555507 AAT
1 AAT
17555510 TAAAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.22
22 21 0.51
23 11 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATTTAATATTTAAAAAAT
Found at i:17555518 original size:22 final size:22
Alignment explanation
Indices: 17555475--17555516 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17555465 ATATTTAATA
**
17555475 TTTAAAAAATAATATTTAAAAT
1 TTTAAAAAATAATATAAAAAAT
17555497 TTTAAAAAATAAT-TAAAAAA
1 TTTAAAAAATAATATAAAAAA
17555517 ATATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTAAAAAATAATATAAAAAAT
Found at i:17555539 original size:23 final size:23
Alignment explanation
Indices: 17555507--17555554 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
17555497 TTTAAAAAAT
*
17555507 AATTAAAAAAATATATATT-TAA
1 AATTTAAAAAATATATATTATAA
17555529 AATTTAAAAAATATATATTATAA
1 AATTTAAAAAATATATATTATAA
17555552 AAT
1 AAT
17555555 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATTTAAAAAATATATATTATAA
Found at i:17556673 original size:15 final size:15
Alignment explanation
Indices: 17556653--17556683 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17556643 GACGGTTCCG
17556653 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
17556668 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
17556683 T
1 T
17556684 ACTGATACAG
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:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
TGTGCTCTGATTCAT
Found at i:17559920 original size:20 final size:19
Alignment explanation
Indices: 17559890--17559973 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
17559880 GATGTTAGAA
17559890 TATTAATTCTATTATATATT
1 TATT-ATTCTATTATATATT
17559910 TATCTATTCTATTATATA--
1 TAT-TATTCTATTATATATT
*
17559928 TA-TATTCTAATATATATT
1 TATTATTCTATTATATATT
17559946 AGTATTATT-T-TTATATTATT
1 --TATTATTCTATTATA-TATT
17559966 TATCTATT
1 TAT-TATT
17559974 TCTTATCTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
16 13 0.24
18 5 0.09
19 8 0.15
20 23 0.43
21 5 0.09
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (19 bp):
TATTATTCTATTATATATT
Found at i:17559935 original size:16 final size:17
Alignment explanation
Indices: 17559895--17559944 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 17
17559885 TAGAATATTA
17559895 ATTCTATTATATATTTATCT
1 ATTCTATTATATA--TA-CT
17559915 ATTCTATTATATATA-T
1 ATTCTATTATATATACT
*
17559931 ATTCTAATATATAT
1 ATTCTATTATATAT
17559945 TAGTATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.48
18 2 0.07
20 13 0.45
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTCTATTATATATACT
Found at i:17561699 original size:18 final size:18
Alignment explanation
Indices: 17561678--17561714 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17561668 AATTCGACGC
* *
17561678 AGTGGATAAATTAGATAA
1 AGTGGAAAAATGAGATAA
17561696 AGTGGAAAAATGAGATAA
1 AGTGGAAAAATGAGATAA
17561714 A
1 A
17561715 CCAGCTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (18 bp):
AGTGGAAAAATGAGATAA
Found at i:17564579 original size:17 final size:17
Alignment explanation
Indices: 17564557--17564590 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17564547 ATAGATTCGC
*
17564557 TTAGATATACTTAGTAT
1 TTAGATATAATTAGTAT
17564574 TTAGATATAATTAGTAT
1 TTAGATATAATTAGTAT
17564591 AATATACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAGATATAATTAGTAT
Found at i:17565879 original size:14 final size:14
Alignment explanation
Indices: 17565860--17565888 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17565850 CATGTTTGAT
17565860 TAGATTTCAGGTCA
1 TAGATTTCAGGTCA
17565874 TAGATTTCAGGTCA
1 TAGATTTCAGGTCA
17565888 T
1 T
17565889 TTTTTGTATT
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:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (14 bp):
TAGATTTCAGGTCA
Found at i:17571503 original size:26 final size:30
Alignment explanation
Indices: 17571461--17571522 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
17571451 CACCATTAAA
17571461 ATAATA-AAAATATAAATT-T-T-AATAAT
1 ATAATATAAAATATAAATTATATAAATAAT
*
17571487 ATAATATATAATA-AAATTATATAAATAAT
1 ATAATATAAAATATAAATTATATAAATAAT
*
17571516 TTAATAT
1 ATAATAT
17571523 TTGTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 11 0.37
27 6 0.20
28 1 0.03
29 12 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
ATAATATAAAATATAAATTATATAAATAAT
Found at i:17574345 original size:20 final size:19
Alignment explanation
Indices: 17574317--17574360 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
17574307 ATAATTTTTA
*
17574317 TATTATTAAACATACATATT
1 TATTATTAAACATA-ATAAT
* *
17574337 TATTTTTAAATATAATAAT
1 TATTATTAAACATAATAAT
17574356 TATTA
1 TATTA
17574361 ATATAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTATTAAACATAATAAT
Found at i:17577744 original size:133 final size:131
Alignment explanation
Indices: 17577579--17577824 Score: 388
Period size: 132 Copynumber: 1.9 Consensus size: 131
17577569 AGCAACTACT
* * *
17577579 GTAGAAATCTTCATCTAGGATGAGGAGGGCTAGCCAAAAGCTGTTTTTGGGATTCCAAATTGCCT
1 GTAGAAATCTACATCTAGGATGAGGAGGGCTAGCCAAAAGCTGTTTTT-GGATTCCAAATTACAT
*
17577644 TACATTGAACATGCATAT-TGAATAGGGCATA-TTGAGCTCATCACTCTCACTCATCACTTTCAT
65 TACATTAAACATGCATATGT-AAT-GGG-ATAGTTGAGCTCATCACTCTCACTCATCACTTTCAT
17577707 CCACC
127 CCACC
*
17577712 GTAGAAATCTACATCTAGGATGAGGAGGGCTAGCCAAAAGCTGTTTTTGGATTTCAAATTACATT
1 GTAGAAATCTACATCTAGGATGAGGAGGGCTAGCCAAAAGCTGTTTTTGGATTCCAAATTACATT
17577777 ACATTAAACATGCATATGTAATGGGATATGTTGAGCTCATCACTCTCA
66 ACATTAAACATGCATATGTAATGGGATA-GTTGAGCTCATCACTCTCA
17577825 GCCATTTCCA
Statistics
Matches: 105, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
130 3 0.03
131 3 0.03
132 51 0.49
133 48 0.46
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (131 bp):
GTAGAAATCTACATCTAGGATGAGGAGGGCTAGCCAAAAGCTGTTTTTGGATTCCAAATTACATT
ACATTAAACATGCATATGTAATGGGATAGTTGAGCTCATCACTCTCACTCATCACTTTCATCCAC
C
Found at i:17580012 original size:48 final size:48
Alignment explanation
Indices: 17579916--17580016 Score: 116
Period size: 48 Copynumber: 2.1 Consensus size: 48
17579906 GAGGCAACAA
* * *
17579916 AGGGAAAGAGAAGAGGAAGAGAGAGAGCAAAGGAGGCGTGAAGTAGAG
1 AGGGAAAGAGAAGAGGAAGAGAGAGAACAAAGAAGGCGTGAAGAAGAG
* * *
17579964 AGGGAAAGGGAGGA-GAAGGAGAGAGAACAAAGAAGGCTTG-AGAAAGAG
1 AGGGAAAGAGAAGAGGAA-GAGAGAGAACAAAGAAGGCGTGAAG-AAGAG
17580012 AGGGA
1 AGGGA
17580017 GCGAATTAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 5 0.11
48 40 0.89
ACGTcount: A:0.47, C:0.04, G:0.46, T:0.04
Consensus pattern (48 bp):
AGGGAAAGAGAAGAGGAAGAGAGAGAACAAAGAAGGCGTGAAGAAGAG
Found at i:17599358 original size:21 final size:21
Alignment explanation
Indices: 17599332--17599373 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
17599322 AATTAAAACC
17599332 CATCAATCAGATACAGAAATG
1 CATCAATCAGATACAGAAATG
17599353 CATCAATCAGATACAGAAATG
1 CATCAATCAGATACAGAAATG
17599374 GAAACAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (21 bp):
CATCAATCAGATACAGAAATG
Found at i:17599547 original size:3 final size:3
Alignment explanation
Indices: 17599539--17599573 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17599529 AACCTCCATT
17599539 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
17599574 TCACTAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:17608898 original size:30 final size:31
Alignment explanation
Indices: 17608862--17608922 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
17608852 AATTGCTTAA
*
17608862 AAAATATTTAA-AATTAA-TATTTTATATATT
1 AAAATA-TTAACAATAAATTATTTTATATATT
*
17608892 AAAATATTAACAATAAATTATTTTTTATATT
1 AAAATATTAACAATAAATTATTTTATATATT
17608923 TTTACTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 4 0.15
30 11 0.41
31 12 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (31 bp):
AAAATATTAACAATAAATTATTTTATATATT
Found at i:17608999 original size:22 final size:19
Alignment explanation
Indices: 17608958--17608999 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
17608948 TAATTTGAAC
17608958 ATTATTTAAATACATATTT
1 ATTATTTAAATACATATTT
17608977 ATTATTTTATAATACAATATTT
1 ATTA-TTTA-AATAC-ATATTT
17608999 A
1 A
17609000 AAATAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 5 0.25
22 7 0.35
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTATTTAAATACATATTT
Found at i:17611355 original size:18 final size:18
Alignment explanation
Indices: 17611329--17611399 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
17611319 AATTGATTGG
* *
17611329 TTATCCAGTAACAGTCAA
1 TTATTCAGTAAAAGTCAA
*
17611347 TTATTCAGTAAAAATCAA
1 TTATTCAGTAAAAGTCAA
* * * *
17611365 ATATACAGTAACAATTAAA
1 TTATTCAGTAA-AAGTCAA
17611384 TTATTCAGTAAAAGTC
1 TTATTCAGTAAAAGTC
17611400 GATCTTTCCA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 27 0.66
19 14 0.34
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.31
Consensus pattern (18 bp):
TTATTCAGTAAAAGTCAA
Found at i:17611572 original size:47 final size:47
Alignment explanation
Indices: 17611518--17611634 Score: 166
Period size: 47 Copynumber: 2.5 Consensus size: 47
17611508 CCGAAATAGT
* * *
17611518 AACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAA-TCTGG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCAGAACAAATTC-GA
*
17611565 AACAGTAACAGTACAGTACACAGAGTACCTCATCAGAACAAATTCGA
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCAGAACAAATTCGA
17611612 AACAGTAACAGTAACGGTA-ACAG
1 AACAGTAACAGT-ACGGTACACAG
17611635 TAACAATATC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
47 56 0.89
48 7 0.11
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCAGAACAAATTCGA
Found at i:17616083 original size:18 final size:17
Alignment explanation
Indices: 17616050--17616083 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17616040 ACTGGCGTTG
*
17616050 AATAGCTATTTTATGAA
1 AATAGCTATATTATGAA
17616067 AATAGCTAGTATTATGA
1 AATAGCTA-TATTATGA
17616084 TCTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
AATAGCTATATTATGAA
Found at i:17622401 original size:18 final size:19
Alignment explanation
Indices: 17622368--17622406 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
17622358 AAAATTTAAA
* *
17622368 TATATCTTTTTTATAACTT
1 TATATCTTTTTAATAAATT
17622387 TATAT-TTTTTAATAAATT
1 TATATCTTTTTAATAAATT
17622405 TA
1 TA
17622407 ATGATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATCTTTTTAATAAATT
Found at i:17626415 original size:36 final size:37
Alignment explanation
Indices: 17626375--17626451 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
17626365 TTATAAATTT
* * * *
17626375 ATTAAAATATTATAAAATTG-AAAGAAAATATTAAAA
1 ATTAAAAAAGTATAAAATTGCAAAGAAAAAATAAAAA
* *
17626411 ATTAAAAAAGTATAAAGTTGCAAATAAAAAATAAAAA
1 ATTAAAAAAGTATAAAATTGCAAAGAAAAAATAAAAA
17626448 ATTA
1 ATTA
17626452 TATAAAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 17 0.50
37 17 0.50
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.27
Consensus pattern (37 bp):
ATTAAAAAAGTATAAAATTGCAAAGAAAAAATAAAAA
Found at i:17626760 original size:37 final size:38
Alignment explanation
Indices: 17626705--17626786 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 38
17626695 TAACTCTTGA
* * * * *
17626705 AATTTTTTTTCAATTTTTCTAATTTTTAATGTTTTTGT
1 AATTTTTTATCAATTTTTCAAAATTCTAATGTTTTTAT
*
17626743 CAATTTTTTAT-AA-TTTTCAAAATTCTAATTTTTTTAT
1 -AATTTTTTATCAATTTTTCAAAATTCTAATGTTTTTAT
17626780 AATTTTT
1 AATTTTT
17626787 CCTTTTTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
36 7 0.19
37 19 0.51
38 2 0.05
39 9 0.24
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (38 bp):
AATTTTTTATCAATTTTTCAAAATTCTAATGTTTTTAT
Found at i:17627464 original size:11 final size:9
Alignment explanation
Indices: 17627429--17627464 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
17627419 CATTTTTATC
17627429 AATTCTCTA
1 AATTCTCTA
17627438 AATTCTCTA
1 AATTCTCTA
17627447 AATTCTCTCA
1 AATTCTCT-A
17627457 AATGTCTC
1 AAT-TCTC
17627465 AAGAATTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.68
10 4 0.16
11 4 0.16
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.42
Consensus pattern (9 bp):
AATTCTCTA
Found at i:17628884 original size:6 final size:6
Alignment explanation
Indices: 17628873--17628905 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
17628863 TGTCTATTTT
*
17628873 AAACAC AAACAC AAACAC AAACAT AAACAC AAA
1 AAACAC AAACAC AAACAC AAACAC AAACAC AAA
17628906 TAAATCGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.70, C:0.27, G:0.00, T:0.03
Consensus pattern (6 bp):
AAACAC
Found at i:17632658 original size:18 final size:18
Alignment explanation
Indices: 17632637--17632680 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
17632627 AATAAAAAGA
*
17632637 TATTTTTATAATAATAAT
1 TATTATTATAATAATAAT
* *
17632655 TATTATTGTTATAATAAT
1 TATTATTATAATAATAAT
17632673 TATTATTA
1 TATTATTA
17632681 ATTAGTATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TATTATTATAATAATAAT
Found at i:17632666 original size:21 final size:21
Alignment explanation
Indices: 17632637--17632680 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
17632627 AATAAAAAGA
*
17632637 TATTTTTATAATAATAATTAT
1 TATTGTTATAATAATAATTAT
*
17632658 TATTGTTATAATAATTATTAT
1 TATTGTTATAATAATAATTAT
17632679 TA
1 TA
17632681 ATTAGTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TATTGTTATAATAATAATTAT
Found at i:17633542 original size:18 final size:18
Alignment explanation
Indices: 17633519--17633554 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17633509 TTTGTGATTA
17633519 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
17633537 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
17633555 GTATGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:17633544 original size:12 final size:12
Alignment explanation
Indices: 17633519--17633554 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
17633509 TTTGTGATTA
17633519 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
17633531 AAAGTGAAATTG
1 AAATTGAAAGTG
17633543 AAATTGAAAGTG
1 AAATTGAAAGTG
17633555 GTATGAATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:17633780 original size:39 final size:38
Alignment explanation
Indices: 17633660--17633792 Score: 110
Period size: 39 Copynumber: 3.4 Consensus size: 38
17633650 ACCTCGAGTT
* * *
17633660 GATGATACACTGGGTGTCATTA-TATTACTTCGGATTGATTC
1 GATGAGACACTGGGTGTCA--ACTATTACTTC-GACT-ATCC
** * * *
17633701 GATGAGGTACTGGGTATCAAC--TTAATTCGACTAGGCC
1 GATGAGACACTGGGTGTCAACTATTACTTCGACTA-TCC
17633738 GATGAGACACTGGGTGTCAACTATTACTTCGAACTATCC
1 GATGAGACACTGGGTGTCAACTATTACTTCG-ACTATCC
*
17633777 GATGAGGCACTGGGTG
1 GATGAGACACTGGGTG
17633793 CCATACTGGA
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
36 1 0.01
37 22 0.30
38 6 0.08
39 25 0.34
40 4 0.05
41 15 0.21
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (38 bp):
GATGAGACACTGGGTGTCAACTATTACTTCGACTATCC
Found at i:17634946 original size:17 final size:17
Alignment explanation
Indices: 17634924--17634957 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17634914 ATTGAGAATA
17634924 TAATTAGCAATAAAAAT
1 TAATTAGCAATAAAAAT
17634941 TAATTAGCAATAAAAAT
1 TAATTAGCAATAAAAAT
17634958 AAGTTCTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATTAGCAATAAAAAT
Found at i:17638730 original size:35 final size:35
Alignment explanation
Indices: 17638684--17638753 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
17638674 TAGTGTATTT
17638684 TATTCTTACTAATTAAACTTAAAACAATTATAGAG
1 TATTCTTACTAATTAAACTTAAAACAATTATAGAG
17638719 TATTCTTACTAATTAAACTTAAAACAATTATAGAG
1 TATTCTTACTAATTAAACTTAAAACAATTATAGAG
17638754 CAATTGTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (35 bp):
TATTCTTACTAATTAAACTTAAAACAATTATAGAG
Found at i:17644588 original size:22 final size:23
Alignment explanation
Indices: 17644563--17644611 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
17644553 AATTTTGAAA
* *
17644563 TAAT-TTAAAATATATATAAATT
1 TAATGTTAAAATATATAAAAAAT
17644585 TAATGGTTAAAATATATAAAAAAT
1 TAAT-GTTAAAATATATAAAAAAT
17644609 TAA
1 TAA
17644612 ATAGAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
24 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
TAATGTTAAAATATATAAAAAAT
Found at i:17648432 original size:42 final size:42
Alignment explanation
Indices: 17648380--17648464 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
17648370 ATGAAGGCTC
17648380 GCTTGAAATGTAGGAGCTTTGAAATGTAGAAATGTTGAAGCA
1 GCTTGAAATGTAGGAGCTTTGAAATGTAGAAATGTTGAAGCA
17648422 GCTTGAAATGTAGGAGCTTTGAAATGTAGAAATGTTGAAGCA
1 GCTTGAAATGTAGGAGCTTTGAAATGTAGAAATGTTGAAGCA
17648464 G
1 G
17648465 AAATGTGTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.28
Consensus pattern (42 bp):
GCTTGAAATGTAGGAGCTTTGAAATGTAGAAATGTTGAAGCA
Done.