Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 140 of 173
Found at i:42597715 original size:17 final size:17
Alignment explanation
Indices: 42597693--42597745 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
42597683 TAATATTAGT
42597693 TTATTAATATTTTATTA
1 TTATTAATATTTTATTA
***
42597710 TTATTAGCCTTTTATTA
1 TTATTAATATTTTATTA
* *
42597727 TTATTACTA-TATATTA
1 TTATTAATATTTTATTA
42597743 TTA
1 TTA
42597746 CTCTTATTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (17 bp):
TTATTAATATTTTATTA
Found at i:42597743 original size:13 final size:12
Alignment explanation
Indices: 42597722--42597756 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
42597712 ATTAGCCTTT
42597722 TATTATTATTAC
1 TATTATTATTAC
42597734 TATATATTATTAC
1 TAT-TATTATTAC
*
42597747 TCTTATTATT
1 TATTATTATT
42597757 GTAGATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:42601202 original size:44 final size:44
Alignment explanation
Indices: 42601152--42601405 Score: 183
Period size: 44 Copynumber: 5.6 Consensus size: 44
42601142 CTCTCTGAAA
* * *
42601152 CTACAAGTCTTATCCCCCTAAAGTTGCAGTGGAGCTGATTAAAG
1 CTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * * *
42601196 CTACAAGTTTTATCTCCCTGAAGTTACAATGGAGCAGATTGAAG
1 CTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * * * * * *
42601240 CGACAAATCCTATGC-CTCTGAATTTGTAGTGG-GTCAGATTAAAT
1 CTACAAGTCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTAAAG
* *
42601284 CTACCATAGCCAGTCTTATTTCCCTGAAGTAGCAGTGGAGCAGATTAAAG
1 CTA-C--A---AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * * *
42601334 CTACAAATCATATCTCCCTGAAGTTGCAGCGGAGTAGATTGAAA-
1 CTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAG
* * *
42601378 CTACGATTCCTATAC-CCCTGAAGTTGCA
1 CTACAAGTCTTAT-CTCCCTGAAGTTGCA
42601406 ATGGGTTAGA
Statistics
Matches: 162, Mismatches: 36, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
43 1 0.01
44 120 0.74
45 6 0.04
47 2 0.01
49 1 0.01
50 31 0.19
51 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
CTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
Found at i:42601373 original size:94 final size:94
Alignment explanation
Indices: 42601205--42601381 Score: 209
Period size: 94 Copynumber: 1.9 Consensus size: 94
42601195 GCTACAAGTT
* * * * * *
42601205 TTATCTCCCTGAAGTTACAATGGAGCAGATTGAAGCGACAAATCCTATGCCTCTGAATTTGTAGT
1 TTATCTCCCTGAAGTTACAATGGAGCAGATTAAAGCGACAAATCATATGCCCCTGAAGTTGCAGC
42601270 GGGTCAGATT-AAATCTACCATAGCCAGTC
66 GGGTCAGATTGAAA-CTACCATAGCCAGTC
* * *
42601299 TTATTTCCCTGAAG-TAGCAGTGGAGCAGATTAAAGCTACAAATCATAT-CTCCCTGAAGTTGCA
1 TTATCTCCCTGAAGTTA-CAATGGAGCAGATTAAAGCGACAAATCATATGC-CCCTGAAGTTGCA
42601362 GCGGAGT-AGATTGAAACTAC
64 GCGG-GTCAGATTGAAACTAC
42601382 GATTCCTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
93 3 0.04
94 62 0.89
95 5 0.07
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (94 bp):
TTATCTCCCTGAAGTTACAATGGAGCAGATTAAAGCGACAAATCATATGCCCCTGAAGTTGCAGC
GGGTCAGATTGAAACTACCATAGCCAGTC
Found at i:42601411 original size:138 final size:138
Alignment explanation
Indices: 42601157--42601411 Score: 321
Period size: 138 Copynumber: 1.8 Consensus size: 138
42601147 TGAAACTACA
* * * **
42601157 AGTCTTATCCCCCTAAAGTTGCAGTGGAGCTGATTAAAGCTACAAGTTTTATCTCCCTGAAGTTA
1 AGTCTTATCCCCCTAAAGTAGCAGTGGAGCAGATTAAAGCTACAAATCATATCTCCCTGAAGTTA
* * * * * * *
42601222 CAATGGAGCAGATTGAAGCGACAAATCCTATGCCTCTGAATTTGTAGTGGGTCAGATTAAATCTA
66 CAACGGAGCAGATTGAAACGACAAATCCTATACCCCTGAAGTTGCAATGGGTCAGATTAAATCTA
42601287 CCATAGCC
131 CCATAGCC
** * *
42601295 AGTCTTATTTCCCTGAAGTAGCAGTGGAGCAGATTAAAGCTACAAATCATATCTCCCTGAAGTTG
1 AGTCTTATCCCCCTAAAGTAGCAGTGGAGCAGATTAAAGCTACAAATCATATCTCCCTGAAGTTA
* * * * *
42601360 CAGCGGAGTAGATTGAAACTACGATTCCTATACCCCTGAAGTTGCAATGGGT
66 CAACGGAGCAGATTGAAACGACAAATCCTATACCCCTGAAGTTGCAATGGGT
42601412 TAGAATGAGA
Statistics
Matches: 96, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
138 96 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (138 bp):
AGTCTTATCCCCCTAAAGTAGCAGTGGAGCAGATTAAAGCTACAAATCATATCTCCCTGAAGTTA
CAACGGAGCAGATTGAAACGACAAATCCTATACCCCTGAAGTTGCAATGGGTCAGATTAAATCTA
CCATAGCC
Found at i:42601604 original size:15 final size:14
Alignment explanation
Indices: 42601566--42601611 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
42601556 CATTCGGCCC
42601566 AAAACCAAAAATAA
1 AAAACCAAAAATAA
*
42601580 ATAAA--TAAAATATA
1 A-AAACCAAAAATA-A
42601594 AAAACCAAAAATAA
1 AAAACCAAAAATAA
42601608 AAAA
1 AAAA
42601612 ATCCAAGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 9 0.35
14 8 0.31
15 9 0.35
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAACCAAAAATAA
Found at i:42601607 original size:13 final size:13
Alignment explanation
Indices: 42601566--42601610 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
42601556 CATTCGGCCC
42601566 AAAACCAAAAATA
1 AAAACCAAAAATA
**
42601579 AATAAATAAAATATA
1 AA-AACCAAAA-ATA
42601594 AAAACCAAAAATA
1 AAAACCAAAAATA
42601607 AAAA
1 AAAA
42601611 AATCCAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 9 0.35
14 12 0.46
15 5 0.19
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAACCAAAAATA
Found at i:42601612 original size:15 final size:15
Alignment explanation
Indices: 42601566--42601617 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
42601556 CATTCGGCCC
42601566 AAAACCAAAAATAAA
1 AAAACCAAAAATAAA
* * *
42601581 TAAA--TAAAATATA
1 AAAACCAAAAATAAA
42601594 AAAACCAAAAATAAA
1 AAAACCAAAAATAAA
42601609 AAAATCCAA
1 AAAA-CCAA
42601618 GTTCATTTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
13 10 0.36
15 14 0.50
16 4 0.14
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAACCAAAAATAAA
Found at i:42602943 original size:17 final size:20
Alignment explanation
Indices: 42602921--42602958 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42602911 CTTTATTTAC
42602921 TAAAT-CTT-TTA-TTATTT
1 TAAATCCTTGTTATTTATTT
42602938 TAAATCCTTGTTATTTATTT
1 TAAATCCTTGTTATTTATTT
42602958 T
1 T
42602959 CTTTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 3 0.17
20 7 0.39
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TAAATCCTTGTTATTTATTT
Found at i:42602992 original size:15 final size:16
Alignment explanation
Indices: 42602960--42603000 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
42602950 ATTTATTTTC
*
42602960 TTTATTATTATGCATT
1 TTTATTATTATCCATT
*
42602976 TTTATT-TTATCC-CT
1 TTTATTATTATCCATT
42602990 TTTATTATTAT
1 TTTATTATTAT
42603001 TATTTCTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 7 0.32
15 9 0.41
16 6 0.27
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTATTATTATCCATT
Found at i:42603153 original size:12 final size:12
Alignment explanation
Indices: 42603136--42603160 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42603126 CCTTTTTTAT
42603136 TTTATTTATTCA
1 TTTATTTATTCA
42603148 TTTATTTATTCA
1 TTTATTTATTCA
42603160 T
1 T
42603161 CTATCATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTATTCA
Found at i:42603929 original size:16 final size:16
Alignment explanation
Indices: 42603893--42603956 Score: 69
Period size: 17 Copynumber: 4.1 Consensus size: 16
42603883 TAACTGCTTA
* *
42603893 TATTTTTCTCTATTGTG
1 TATTTTTCTTTATT-TT
42603910 TATTTTTCTTTATTTT
1 TATTTTTCTTTATTTT
42603926 TA-TTTT-TTTATTTT
1 TATTTTTCTTTATTTT
* *
42603940 TATGTTTGTTTATTTT
1 TATTTTTCTTTATTTT
42603956 T
1 T
42603957 TTTACTACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
14 10 0.24
15 7 0.17
16 12 0.29
17 13 0.31
ACGTcount: A:0.12, C:0.05, G:0.06, T:0.77
Consensus pattern (16 bp):
TATTTTTCTTTATTTT
Found at i:42603937 original size:14 final size:15
Alignment explanation
Indices: 42603913--42603956 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
42603903 TATTGTGTAT
42603913 TTTTCTTTATTTTTA
1 TTTTCTTTATTTTTA
42603928 TTTT-TTTATTTTTA
1 TTTTCTTTATTTTTA
*
42603942 TGTTTGTTTATTTTT
1 T-TTTCTTTATTTTT
42603957 TTTACTACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.41
15 7 0.26
16 9 0.33
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.82
Consensus pattern (15 bp):
TTTTCTTTATTTTTA
Found at i:42607295 original size:19 final size:19
Alignment explanation
Indices: 42607259--42607358 Score: 78
Period size: 19 Copynumber: 5.3 Consensus size: 19
42607249 AATAGGGGAA
42607259 ACTGGCACACATAA-TGCAT
1 ACTGGCACACA-AAGTGCAT
*
42607278 ACTGGCACACGAAGTGCAT
1 ACTGGCACACAAAGTGCAT
* * *
42607297 CCTGACATACAAAGTGCAT
1 ACTGGCACACAAAGTGCAT
* * * * * *
42607316 ATTGACGCACGAAGCGTAT
1 ACTGGCACACAAAGTGCAT
42607335 -CTTGGCACACAAAGTGCAT
1 AC-TGGCACACAAAGTGCAT
42607354 ACTGG
1 ACTGG
42607359 GAAAATTAGT
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
18 2 0.03
19 57 0.95
20 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (19 bp):
ACTGGCACACAAAGTGCAT
Found at i:42607315 original size:38 final size:38
Alignment explanation
Indices: 42607264--42607358 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
42607254 GGGAAACTGG
*
42607264 CACACATAA-TGCATACTGGCACACGAAGTGCATCCTGA
1 CACACA-AAGTGCATACTGGCACACGAAGCGCATCCTGA
* * * * * * *
42607302 CATACAAAGTGCATATTGACGCACGAAGCGTATCTTGG
1 CACACAAAGTGCATACTGGCACACGAAGCGCATCCTGA
42607340 CACACAAAGTGCATACTGG
1 CACACAAAGTGCATACTGG
42607359 GAAAATTAGT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
37 2 0.04
38 43 0.96
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (38 bp):
CACACAAAGTGCATACTGGCACACGAAGCGCATCCTGA
Found at i:42613138 original size:36 final size:34
Alignment explanation
Indices: 42613098--42613178 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 34
42613088 AATTTAATTT
42613098 ATATTTTATTATTTGATTCA-AATATAATCTGTAAAA
1 ATATTTTATTATTTGATT-AGAATATAAT-T-TAAAA
*
42613134 ATATTTTGA-TATTTTATTATGAATATAATTTAAAA
1 ATATTTT-ATTATTTGATTA-GAATATAATTTAAAA
42613169 ATATTTTATT
1 ATATTTTATT
42613179 GTATATTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
34 1 0.03
35 14 0.35
36 16 0.40
37 9 0.22
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (34 bp):
ATATTTTATTATTTGATTAGAATATAATTTAAAA
Found at i:42613345 original size:19 final size:18
Alignment explanation
Indices: 42613303--42613348 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
42613293 ATATAATTGT
*
42613303 AATAATTTTTAATTATTT
1 AATAATTTTTAATTATTA
* *
42613321 ATTAATTTTGTAATTGTTA
1 AATAATTTT-TAATTATTA
42613340 AATAATTTT
1 AATAATTTT
42613349 AAAAACTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (18 bp):
AATAATTTTTAATTATTA
Found at i:42613488 original size:21 final size:21
Alignment explanation
Indices: 42613460--42613514 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
42613450 ACCGCTGTTT
42613460 CTAATCTCACCGCTACAGTATC
1 CTAATCTCACCGCTACAGTA-C
42613482 C-AATCTCACCGCTACAGTAC
1 CTAATCTCACCGCTACAGTAC
42613502 CTAATCTCACCGC
1 CTAATCTCACCGC
42613515 CACCGCTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.27, C:0.40, G:0.09, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAC
Found at i:42618500 original size:9 final size:9
Alignment explanation
Indices: 42618469--42618540 Score: 63
Period size: 9 Copynumber: 7.8 Consensus size: 9
42618459 TTTTTCCTAT
*
42618469 ATTTCTATA
1 ATTTTTATA
*
42618478 ATTTTTATG
1 ATTTTTATA
42618487 ATTTTTATA
1 ATTTTTATA
*
42618496 ATTTTTTTTA
1 A-TTTTTATA
* * *
42618506 AATTTAATT
1 ATTTTTATA
42618515 ATTTTTATA
1 ATTTTTATA
*
42618524 AATTTTATTA
1 ATTTTTA-TA
42618534 ATTTTTA
1 ATTTTTA
42618541 CTTTTTATCC
Statistics
Matches: 48, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
9 32 0.67
10 16 0.33
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:42618511 original size:18 final size:20
Alignment explanation
Indices: 42618443--42618539 Score: 59
Period size: 18 Copynumber: 5.0 Consensus size: 20
42618433 TTCTTACGAA
42618443 TTTATAAAATTTTAT-ATTTT
1 TTTAT-AAATTTTATAATTTT
*
42618463 TCCTAT--ATTTCTATAA--TT
1 T-TTATAAATTT-TATAATTTT
* *
42618481 TTTATGATTTTTATAATTTT
1 TTTATAAATTTTATAATTTT
42618501 TTT-TAAA--TT-TAATTATT
1 TTTATAAATTTTATAATT-TT
42618518 TTTATAAATTTTATTAATTTT
1 TTTATAAATTTTA-TAATTTT
42618539 T
1 T
42618540 ACTTTTTATC
Statistics
Matches: 59, Mismatches: 5, Indels: 25
0.66 0.06 0.28
Matches are distributed among these distances:
16 5 0.08
17 10 0.17
18 16 0.27
19 8 0.14
20 9 0.15
21 6 0.10
22 5 0.08
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (20 bp):
TTTATAAATTTTATAATTTT
Found at i:42625283 original size:14 final size:14
Alignment explanation
Indices: 42625260--42625293 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
42625250 TGGTATGAGT
42625260 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
42625273 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
42625287 TTATAGG
1 TTATAGG
42625294 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:42625859 original size:29 final size:29
Alignment explanation
Indices: 42625817--42625877 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
42625807 AATTAATAAG
42625817 ATAAAATTATATTTTAATTTTTA-AAAATA
1 ATAAAATTATATTTTAATTTTTAGAAAA-A
* * *
42625846 ATAACATTTTATTTTATTTTTTAGAAAAA
1 ATAAAATTATATTTTAATTTTTAGAAAAA
42625875 ATA
1 ATA
42625878 TAAAGATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (29 bp):
ATAAAATTATATTTTAATTTTTAGAAAAA
Found at i:42625932 original size:14 final size:14
Alignment explanation
Indices: 42625913--42625940 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42625903 AAAATTATAG
42625913 TCTAAAATGATGAA
1 TCTAAAATGATGAA
42625927 TCTAAAATGATGAA
1 TCTAAAATGATGAA
42625941 AAAAAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
TCTAAAATGATGAA
Found at i:42627601 original size:54 final size:55
Alignment explanation
Indices: 42627534--42627648 Score: 205
Period size: 56 Copynumber: 2.1 Consensus size: 55
42627524 AAAGCAAAGT
*
42627534 AAAATAGTTGGTG-TACCATCAGAAAATATAGGCTCTGTCGAAACCATTTTTTTG
1 AAAAAAGTTGGTGTTACCATCAGAAAATATAGGCTCTGTCGAAACCATTTTTTTG
42627588 AAAAAAGTTGGTGTTTACCATCAGAAAATATAGGCTCTGTCGAAACCATTTTTTTG
1 AAAAAAGTTGGTG-TTACCATCAGAAAATATAGGCTCTGTCGAAACCATTTTTTTG
42627644 AAAAA
1 AAAAA
42627649 CAAAAAAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
54 12 0.21
56 46 0.79
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (55 bp):
AAAAAAGTTGGTGTTACCATCAGAAAATATAGGCTCTGTCGAAACCATTTTTTTG
Found at i:42630474 original size:44 final size:44
Alignment explanation
Indices: 42630426--42630957 Score: 293
Period size: 44 Copynumber: 12.3 Consensus size: 44
42630416 ACTACTGCTT
*
42630426 AGGGAGATAAGATCTGCTTACTTAGTCTGCTCCACTACAACTTC
1 AGGGAGATAAGATCTGCTTACTTAGTCTGCTCCACTGCAACTTC
* * *
42630470 AGGGAGATAAGA-CTAG-ATAC-GA-TCTGCT-CTCTGCAACTTC
1 AGGGAGATAAGATCT-GCTTACTTAGTCTGCTCCACTGCAACTTC
* ** *
42630510 AGGGAGA-CAGAAT-TG-TCGGCTTTAATCTGCTCCACTGCAACTTC
1 AGGGAGATAAG-ATCTGCT-TAC-TTAGTCTGCTCCACTGCAACTTC
* *
42630554 AGGGAGATAAGATTTGC-CATCTTCAGTCTGC-CTCACTGCAACTTC
1 AGGGAGATAAGATCTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTC
42630599 -GGGAGGATAAGA-CTTGCTTACTTAGTCTGCTCCACTGCAACTTC
1 AGGGA-GATAAGATC-TGCTTACTTAGTCTGCTCCACTGCAACTTC
* * * *
42630643 AGGGAGATAAGA-CTAG-ATAC-GA-TCTACT-CTCTGCAACTTC
1 AGGGAGATAAGATCT-GCTTACTTAGTCTGCTCCACTGCAACTTC
** * * * * * *
42630683 AGAAAGATAAGATCTGAGATT--TTAATCCGCTTCACCGCAACTTT
1 AGGGAGATAAGATCT--GCTTACTTAGTCTGCTCCACTGCAACTTC
* * *
42630727 AGGGAGATAGGAT-TGTCAGTT--TTAATCTGCTCTACTGCAACTTC
1 AGGGAGATAAGATCTG-C--TTACTTAGTCTGCTCCACTGCAACTTC
* *
42630771 AGGGAGATAAGATTTG-TCATCTTCAGTCTGC-CTCACTGCAACTTC
1 AGGGAGATAAGATCTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTC
42630816 A-GGAGGATAAGA-CTTGCTTACTTAGTCTGCTCCACTGCAACTTC
1 AGGGA-GATAAGATC-TGCTTACTTAGTCTGCTCCACTGCAACTTC
* * * * *
42630860 AGGGAGATAAGA-CTAG-AT-GTGA-TCCGCT-CTCTGCAACTTC
1 AGGGAGATAAGATCT-GCTTACTTAGTCTGCTCCACTGCAACTTC
* * * *
42630900 AGAGAGATAAGATCTGAGATT--TTAATCCGCTCCACTGCAACTTC
1 AGGGAGATAAGATCT--GCTTACTTAGTCTGCTCCACTGCAACTTC
*
42630944 AGGGAGATAGGATC
1 AGGGAGATAAGATC
42630958 CCGGCCACTA
Statistics
Matches: 387, Mismatches: 55, Indels: 92
0.72 0.10 0.17
Matches are distributed among these distances:
39 3 0.01
40 63 0.16
41 22 0.06
42 12 0.03
43 30 0.08
44 177 0.46
45 77 0.20
46 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (44 bp):
AGGGAGATAAGATCTGCTTACTTAGTCTGCTCCACTGCAACTTC
Found at i:42630632 original size:89 final size:83
Alignment explanation
Indices: 42630426--42630871 Score: 316
Period size: 89 Copynumber: 5.1 Consensus size: 83
42630416 ACTACTGCTT
*
42630426 AGGGAGATAAGATCTGCTTACTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAGATACG
1 AGGGAGATAAGAT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACG
*
42630491 ATCTGCTCTCTGCAACTTC
65 ATCTGCTCACTGCAACTTC
* ** * * *
42630510 AGGGAGA-CAGAATTG-TCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCA
1 AGGGAGATAAG-ATTGCT-TAC-TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG--A
*
42630573 T-CTTCAGTCTGCCTCACTGCAACTTC
61 TAC--GA-TCTG-CTCACTGCAACTTC
42630599 -GGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATAC
1 AGGGA-GATAAGA-TTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATAC
* *
42630663 GATCTACTCTCTGCAACTTC
64 GATCTGCTCACTGCAACTTC
** * * * * * * * *
42630683 AGAAAGATAAGATCTGAGATT--TTAATCCGCTTCACCGCAACTTTAGGGAGATAGGATTGTCAG
1 AGGGAGATAAGAT-T--GCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA--CT-AG
* ***
42630746 TTTTAATCTGCTCTACTGCAACTTC
60 ATACGATCTGCTC-ACTGCAACTTC
* *
42630771 AGGGAGATAAGATTTG-TCATCTTCAGTCTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTGC
1 AGGGAGATAAGA-TTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTAG-
* *
42630833 TTACTTAGTCTGCTCCACTGCAACTTC
60 ATAC-GA-TCTGCT-CACTGCAACTTC
42630860 AGGGAGATAAGA
1 AGGGAGATAAGA
42630872 CTAGATGTGA
Statistics
Matches: 281, Mismatches: 48, Indels: 61
0.72 0.12 0.16
Matches are distributed among these distances:
82 1 0.00
83 6 0.02
84 94 0.33
85 7 0.02
86 9 0.03
87 16 0.06
88 36 0.13
89 104 0.37
90 7 0.02
91 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (83 bp):
AGGGAGATAAGATTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGA
TCTGCTCACTGCAACTTC
Found at i:42630725 original size:173 final size:171
Alignment explanation
Indices: 42630426--42630829 Score: 482
Period size: 173 Copynumber: 2.3 Consensus size: 171
42630416 ACTACTGCTT
*
42630426 AGGGAGATAAGATCTGCTTACTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAGATACG
1 AGGGAGATAAGAT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACG
* ** * * * * *
42630491 ATCTGCTCTCTGCAACTTCAGGGAGACAGAATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAG
65 ATCTACTCTCTGCAACTTCAGAAAGAAAGAATTGTAGACTTTAATCCGCTCCACCGCAACTTCAG
*
42630556 GGAGATAAGATTTGCCA-TCTTCAGTCTGC-CTCACTGCAACTTC
130 GGAGATAAGA-TTGCCAGT-TTCAATCTGCTCT-ACTGCAACTTC
42630599 -GGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATAC
1 AGGGA-GATAAGA-TTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATAC
* *
42630663 GATCTACTCTCTGCAACTTCAGAAAGATAAG-ATCTG-AGATTTTAATCCGCTTCACCGCAACTT
64 GATCTACTCTCTGCAACTTCAGAAAGA-AAGAAT-TGTAGACTTTAATCCGCTCCACCGCAACTT
* * * *
42630726 TAGGGAGATAGGATTGTCAGTTTTAATCTGCTCTACTGCAACTTC
127 CAGGGAGATAAGATTGCCAGTTTCAATCTGCTCTACTGCAACTTC
*
42630771 AGGGAGATAAGATTTG-TCATCTTCAGTCTGC-CTCACTGCAACTTCA-GGAGGATAAGACT
1 AGGGAGATAAGA-TTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACT
42630830 TGCTTACTTA
Statistics
Matches: 202, Mismatches: 18, Indels: 22
0.83 0.07 0.09
Matches are distributed among these distances:
171 2 0.01
172 45 0.22
173 150 0.74
174 5 0.02
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (171 bp):
AGGGAGATAAGATTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGA
TCTACTCTCTGCAACTTCAGAAAGAAAGAATTGTAGACTTTAATCCGCTCCACCGCAACTTCAGG
GAGATAAGATTGCCAGTTTCAATCTGCTCTACTGCAACTTC
Found at i:42630801 original size:217 final size:217
Alignment explanation
Indices: 42630502--42630956 Score: 775
Period size: 217 Copynumber: 2.1 Consensus size: 217
42630492 TCTGCTCTCT
* * *
42630502 GCAACTTCAGGGAGACAGAATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
1 GCAACTTCAGGGAGATAGGATTGTCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
42630567 TTGCCATCTTCAGTCTGCCTCACTGCAACTTCGGGAGGATAAGACTTGCTTACTTAGTCTGCTCC
66 TTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCC
*
42630632 ACTGCAACTTCAGGGAGATAAGACTAGATACGATCTACTCTCTGCAACTTCAGAAAGATAAGATC
131 ACTGCAACTTCAGGGAGATAAGACTAGATACGATCCACTCTCTGCAACTTCAGAAAGATAAGATC
*
42630697 TGAGATTTTAATCCGCTTCACC
196 TGAGATTTTAATCCGCTCCACC
* * *
42630719 GCAACTTTAGGGAGATAGGATTGTCAGTTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGAT
1 GCAACTTCAGGGAGATAGGATTGTCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
42630784 TTGTCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCC
66 TTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCC
** * *
42630849 ACTGCAACTTCAGGGAGATAAGACTAGATGTGATCCGCTCTCTGCAACTTCAGAGAGATAAGATC
131 ACTGCAACTTCAGGGAGATAAGACTAGATACGATCCACTCTCTGCAACTTCAGAAAGATAAGATC
*
42630914 TGAGATTTTAATCCGCTCCACT
196 TGAGATTTTAATCCGCTCCACC
42630936 GCAACTTCAGGGAGATAGGAT
1 GCAACTTCAGGGAGATAGGAT
42630957 CCCGGCCACT
Statistics
Matches: 222, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 222 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (217 bp):
GCAACTTCAGGGAGATAGGATTGTCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
TTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCC
ACTGCAACTTCAGGGAGATAAGACTAGATACGATCCACTCTCTGCAACTTCAGAAAGATAAGATC
TGAGATTTTAATCCGCTCCACC
Found at i:42646819 original size:7 final size:7
Alignment explanation
Indices: 42646807--42646902 Score: 86
Period size: 7 Copynumber: 13.4 Consensus size: 7
42646797 AATGCACCAC
42646807 AAACCCT
1 AAACCCT
42646814 AAACCCT
1 AAACCCT
*
42646821 AAAACCTT
1 -AAACCCT
42646829 AAACCCT
1 AAACCCT
42646836 -AACCCT
1 AAACCCT
42646842 AAAACCCT
1 -AAACCCT
* *
42646850 AAGCACT
1 AAACCCT
**
42646857 AAACATT
1 AAACCCT
42646864 AAACCCT
1 AAACCCT
**
42646871 AGAATTCT
1 A-AACCCT
42646879 AAACCCT
1 AAACCCT
*
42646886 AAACTCT
1 AAACCCT
42646893 AAACCCT
1 AAACCCT
42646900 AAA
1 AAA
42646903 ATTAATAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
6 6 0.08
7 48 0.68
8 17 0.24
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:42646831 original size:8 final size:8
Alignment explanation
Indices: 42646807--42646851 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
42646797 AATGCACCAC
42646807 AAACCCT-
1 AAACCCTA
42646814 AAACCCTA
1 AAACCCTA
*
42646822 AAA-CCTT
1 AAACCCTA
42646829 AAACCCT-
1 AAACCCTA
42646836 -AACCCTA
1 AAACCCTA
42646843 AAACCCTA
1 AAACCCTA
42646851 A
1 A
42646852 GCACTAAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
6 6 0.18
7 13 0.39
8 14 0.42
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.16
Consensus pattern (8 bp):
AAACCCTA
Found at i:42646868 original size:29 final size:29
Alignment explanation
Indices: 42646807--42646903 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
42646797 AATGCACCAC
*
42646807 AAACCCT-AAACCCTAAA-ACCTTAAACCCT
1 AAACCCTAAAACCCTAAACA-C-TAAACTCT
*
42646836 -AACCCTAAAACCCTAAGCACTAAACAT-T
1 AAACCCTAAAACCCTAAACACTAAAC-TCT
* ** *
42646864 AAACCCTAGAATTCTAAACCCTAAACTCT
1 AAACCCTAAAACCCTAAACACTAAACTCT
42646893 AAACCCTAAAA
1 AAACCCTAAAA
42646904 TTAATAAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 13 0.24
29 41 0.75
30 1 0.02
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (29 bp):
AAACCCTAAAACCCTAAACACTAAACTCT
Found at i:42654983 original size:20 final size:19
Alignment explanation
Indices: 42654942--42654994 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
42654932 TTGAGAACTT
42654942 TTTGAG-AATTGTGAGAAA
1 TTTGAGAAATTGTGAGAAA
42654960 TTTGAGAAATTAG-GAGAGAA
1 TTTGAGAAATT-GTGAGA-AA
*
42654980 TTTGTGAAAATTGTG
1 TTTGAG-AAATTGTG
42654995 TGTGTGTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 8 0.28
20 9 0.31
21 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (19 bp):
TTTGAGAAATTGTGAGAAA
Found at i:42660315 original size:72 final size:71
Alignment explanation
Indices: 42660238--42660443 Score: 211
Period size: 72 Copynumber: 2.9 Consensus size: 71
42660228 GCATTGGCTA
* *
42660238 GTAAAATCGACAAATGAGTGTGCCTAGCACTGGTCAGTATAATTGACAAATAAGTGCGCCCTGA-
1 GTAAAATCGAAAAATGAGTGTGCCTAGCACTGGTC-GTATAAATGACAAATAAGTGCGCCCT-AC
*
42660302 GCTGGTCG
64 GCTAGTCG
** * * *
42660310 GTAAAATAAAAAAATGAGTGTG-ATCAGCACTGGTCGGTATAAACGACAAATAAGTGCGCACTAC
1 GTAAAATCGAAAAATGAGTGTGCCT-AGCACTGGTC-GTATAAATGACAAATAAGTGCGCCCTAC
42660374 GCTAGTCG
64 GCTAGTCG
* * * * * *
42660382 ATAAAA-CTGAAAAATGATTGTGCCCAGCACTGGTCGATATAACTAACAAATAAGTACGCCCT
1 GTAAAATC-GAAAAATGAGTGTGCCTAGCACTGGTCG-TATAAATGACAAATAAGTGCGCCCT
42660444 CCTTGGTCAG
Statistics
Matches: 109, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
71 3 0.03
72 106 0.97
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (71 bp):
GTAAAATCGAAAAATGAGTGTGCCTAGCACTGGTCGTATAAATGACAAATAAGTGCGCCCTACGC
TAGTCG
Found at i:42663553 original size:23 final size:24
Alignment explanation
Indices: 42663512--42663558 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
42663502 AAGTTAATTC
*
42663512 AATGATATATATATATATGGAAAAA
1 AATGAGATATATATATAT-GAAAAA
42663537 AATGAGATAT-TAT-TATGAAAAA
1 AATGAGATATATATATATGAAAAA
42663559 TTTGAAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 3 0.14
24 3 0.14
25 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (24 bp):
AATGAGATATATATATATGAAAAA
Found at i:42675997 original size:45 final size:46
Alignment explanation
Indices: 42675931--42676050 Score: 161
Period size: 45 Copynumber: 2.6 Consensus size: 46
42675921 AAGGAGAAGG
**
42675931 GACCAAGGTGAAAACTTGCAAAGGGCACTTTGAGTCCT-AAAAAGA
1 GACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCTAAAAAAGA
*
42675976 GACCAAGGTGAAAACCCGCAAATGGCACTTTGAGTCCTAAAAAAAAAGA
1 GACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCT---AAAAAAGA
* *
42676025 GGCCAAGGTGAAAACCCTCAAAGGGC
1 GACCAAGGTGAAAACCCGCAAAGGGC
42676051 GCCTTGAGAC
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
45 35 0.54
49 30 0.46
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (46 bp):
GACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCTAAAAAAGA
Found at i:42676913 original size:24 final size:24
Alignment explanation
Indices: 42676877--42676928 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
42676867 ATGTCCCAAA
* *
42676877 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTAGATTGAACCTTAAAG
42676901 ATTACAGTAGATTGAACCTTAAAG
1 ATTACAGTAGATTGAACCTTAAAG
42676925 ATTA
1 ATTA
42676929 TAGTGGGGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (24 bp):
ATTACAGTAGATTGAACCTTAAAG
Found at i:42677278 original size:51 final size:51
Alignment explanation
Indices: 42677223--42677390 Score: 213
Period size: 51 Copynumber: 3.4 Consensus size: 51
42677213 CCCTGACATG
*
42677223 GCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTGGCGTT
1 GCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTT
* *
42677274 GCAGT-----AGATTAAAGCTGAAGGCAGCAAATCTTATTTCCTTGGCGTT
1 GCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTT
* * *
42677320 GCACTGGAACAGATTAAAGCTGAAAGCAGCGAACCTTATTTCCC-GAGCGTT
1 GCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTG-GCGTT
* *
42677371 GCAGTGAAATAGATTAAAGC
1 GCAGTGGAACAGATTAAAGC
42677391 CACAAATTAT
Statistics
Matches: 100, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
46 42 0.42
50 1 0.01
51 57 0.57
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (51 bp):
GCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTT
Found at i:42677304 original size:46 final size:46
Alignment explanation
Indices: 42677233--42677375 Score: 171
Period size: 46 Copynumber: 3.0 Consensus size: 46
42677223 GCAGTGGAAC
*
42677233 AGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTGGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGT
* * *
42677279 AGATTAAAGCTGAAGGCAGCAAATCTTATTTCCTTGGCGTTGCACTGGAAC
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCA---G--T
* *
42677330 AGATTAAAGCTGAAAGCAGCGAACCTTATTTCCC-GAGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTG-GCGTTGCAGT
42677376 GAAATAGATT
Statistics
Matches: 82, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
46 41 0.50
48 1 0.01
49 1 0.01
50 1 0.01
51 38 0.46
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (46 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGT
Found at i:42680326 original size:23 final size:22
Alignment explanation
Indices: 42680269--42680381 Score: 73
Period size: 23 Copynumber: 5.0 Consensus size: 22
42680259 AAATGTCTAG
* *
42680269 TTTTGACAACACTTAAAACATGC
1 TTTTGACAACATTTAAAACAT-A
* **
42680292 TTTGGATGACATTTAAAACATA
1 TTTTGACAACATTTAAAACATA
* * *
42680314 TTTTGGACAACATTCAAACCTTA
1 TTTT-GACAACATTTAAAACATA
* * *
42680337 CTTTGACAGCATTTGAAACATA
1 TTTTGACAACATTTAAAACATA
* * *
42680359 CTTTTGCCAGCATTTAAAGCATA
1 -TTTTGACAACATTTAAAACATA
42680382 CCAAATGTTA
Statistics
Matches: 67, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
22 16 0.24
23 51 0.76
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (22 bp):
TTTTGACAACATTTAAAACATA
Found at i:42681803 original size:23 final size:24
Alignment explanation
Indices: 42681772--42681819 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
42681762 TAGTGGATAA
*
42681772 TTGCTCATTT-GGTCCCTCCTATT
1 TTGCCCATTTAGGTCCCTCCTATT
42681795 TTGCCCATTTAGGTCCCTCCTATT
1 TTGCCCATTTAGGTCCCTCCTATT
42681819 T
1 T
42681820 ATTTCTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.10, C:0.31, G:0.12, T:0.46
Consensus pattern (24 bp):
TTGCCCATTTAGGTCCCTCCTATT
Found at i:42687905 original size:111 final size:111
Alignment explanation
Indices: 42687710--42687930 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
42687700 ATATAATCAA
* *
42687710 AATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATTATTTTTCATTACTGTAGGAGCCAT
1 AATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATCACTTTTCATTACTGTAGGAGCCAT
*
42687775 TATTAATATTCAATACAGAACCATCTAATTAAGCAATGAATATCCAT
66 TATTAATATTCAATACAGAACCATCT-ATTAAGCAATGAACATCCAT
* *
42687822 AATATCTTAAAAGCTTGAAGAAG-AAAAAAGAACAATAGTCACTTTTCATTACTGTAGGAGCCAT
1 AATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATCACTTTTCATTACTGTAGGAGCCAT
42687886 TATTAATATTCAATACAGAACCATCTATTAAGCAATGAACATCCA
66 TATTAATATTCAATACAGAACCATCTATTAAGCAATGAACATCCA
42687931 ATAAACACCA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
110 18 0.17
111 63 0.61
112 23 0.22
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (111 bp):
AATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATCACTTTTCATTACTGTAGGAGCCAT
TATTAATATTCAATACAGAACCATCTATTAAGCAATGAACATCCAT
Found at i:42691004 original size:19 final size:20
Alignment explanation
Indices: 42690982--42691077 Score: 67
Period size: 19 Copynumber: 4.8 Consensus size: 20
42690972 AAACAATTCA
*
42690982 AAAATAATTTTCAAAAA-TT
1 AAAATAATTTTAAAAAATTT
*
42691001 AAAATTA-TTTATAAAAATTT
1 AAAATAATTTTA-AAAAATTT
42691021 CAAAATTTATATTTTAAAAAA-TT
1 -AAAA--TA-ATTTTAAAAAATTT
*
42691044 ATAAA-AATTCTAAAAAATTT
1 A-AAATAATTTTAAAAAATTT
*
42691064 AAAA-AAATTTAAAA
1 AAAATAATTTTAAAA
42691078 TTTTAAGAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
18 3 0.05
19 32 0.52
20 6 0.10
21 4 0.06
22 1 0.02
23 6 0.10
24 6 0.10
25 4 0.06
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATTTTAAAAAATTT
Found at i:42691050 original size:10 final size:9
Alignment explanation
Indices: 42691033--42691077 Score: 56
Period size: 10 Copynumber: 4.8 Consensus size: 9
42691023 AAATTTATAT
42691033 TTTAAAAAA
1 TTTAAAAAA
42691042 -TTATAAAAA
1 TTTA-AAAAA
42691051 TTCTAAAAAA
1 TT-TAAAAAA
42691061 TTTAAAAAAA
1 TTT-AAAAAA
42691071 TTTAAAA
1 TTTAAAA
42691078 TTTTAAGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 3 0.09
9 10 0.31
10 17 0.53
11 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:42693731 original size:105 final size:106
Alignment explanation
Indices: 42693611--42693821 Score: 352
Period size: 105 Copynumber: 2.0 Consensus size: 106
42693601 CCTAGAAAAT
* ** *
42693611 ATTTTGGCTTTGCCCCTCATGATGTCCTAAACTATTTCACAAAGAAAATTGAAATGTAGAAGAGA
1 ATTTTGGCTTTGCCCCTCATGACGTCAAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
*
42693676 A-GGGGAAAAGAGTTTTTAATTAGTGCAAGTAGAGTGATAA
66 AGGGGGAAAAGAGTTTTTAATTAGTGCAAGCAGAGTGATAA
42693716 ATTTTGGCTTTGCCCCTCATGACGTCAAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
1 ATTTTGGCTTTGCCCCTCATGACGTCAAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
* *
42693781 AGGGGGAAAAGAGTTTTTGATTGGTGCAAGCAGAGTGATAA
66 AGGGGGAAAAGAGTTTTTAATTAGTGCAAGCAGAGTGATAA
42693822 GAGAAAGCCA
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
105 62 0.63
106 36 0.37
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (106 bp):
ATTTTGGCTTTGCCCCTCATGACGTCAAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
AGGGGGAAAAGAGTTTTTAATTAGTGCAAGCAGAGTGATAA
Found at i:42694405 original size:10 final size:9
Alignment explanation
Indices: 42694378--42694409 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
42694368 TTTTACAGGG
42694378 TAGGATTTT
1 TAGGATTTT
42694387 TAGGATTTT
1 TAGGATTTT
*
42694396 TAGGGTTTT
1 TAGGATTTT
42694405 TAGGA
1 TAGGA
42694410 AAAAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (9 bp):
TAGGATTTT
Found at i:42694759 original size:126 final size:125
Alignment explanation
Indices: 42694518--42695086 Score: 793
Period size: 126 Copynumber: 4.5 Consensus size: 125
42694508 GATAAAATTA
* * * * * *
42694518 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
42694583 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAGCGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * * * *
42694643 AACCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGTCCTCGTAGACGCTCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
42694708 TGGTCTTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAAACGCTTC
*
42694770 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
42694835 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTGCTGAGCAAATAATATAAAATAACGCTGC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAA-AACGCTTC
* *
42694896 AAGCAGGATGCTATT-TGAGAA-AATTTTGTGAAATCGCGCCCCCGTGGACGCGCTTTTGCTATA
1 AAGCAGGATGCT-TTATGAGAAGAA-TTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACA
* * * *
42694959 GTAGGTCTTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTAT-AAAATCGTTTC
64 GTAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * *
42695020 TAGCAGGATGCTATATGAGAAGAATTTGTGAAATCGCGCCCATGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
42695085 AG
66 AG
42695087 CATGTTTGGG
Statistics
Matches: 392, Mismatches: 45, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
123 1 0.00
124 62 0.16
125 74 0.19
126 175 0.45
127 80 0.20
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:42698331 original size:22 final size:22
Alignment explanation
Indices: 42698236--42698896 Score: 611
Period size: 22 Copynumber: 31.0 Consensus size: 22
42698226 TCAAATTATA
42698236 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42698257 TTTAAGTTAAGTG-TTAGGGCTT
1 TTTAAGTTAAGGGTTTAGGG-TT
* ** *
42698279 TTT-ATTTAAGGG-TTACAGCT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
42698299 TTAAAGTTAAGGTTTTAGGGTA
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42698321 TTTAATTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42698343 TTTAAGTTAAGGG-TTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42698364 TTTAAGTTAAGGGTTTAGGGTA
1 TTTAAGTTAAGGGTTTAGGGTT
* * * *
42698386 TTTAATTTAAGGGTCTACGATT
1 TTTAAGTTAAGGGTTTAGGGTT
42698408 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42698430 TTAAAGTTAA-GGATTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
42698451 TTTAATTTAAGGG-TT-GCAATT
1 TTTAAGTTAAGGGTTTAG-GGTT
42698472 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42698494 TTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
42698515 TTTAGGTTTAGGGTTTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42698537 TTTAAGTTAAGGG-TTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42698557 TTTATGGTTTAA-GGTTTAAGGTT
1 TTTA-AG-TTAAGGGTTTAGGGTT
* * *
42698580 TTTAATTTAAGGGTTTACGATT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42698602 TTTAAGTTAAGGTTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42698624 TTAAAGTTAAAGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42698645 TTTAATTTAAGGGTTATA--GTT
1 TTTAAGTTAAGGGTT-TAGGGTT
*
42698666 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* ***
42698688 TTAAAGTTAA-AAATTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
42698708 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42698730 TTTAAGTCAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42698752 TTTAAGTTAAGGG-TTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42698773 TTTAAATTAAGGGTTTATGG--
1 TTTAAGTTAAGGGTTTAGGGTT
**
42698793 -TT---TTAA-GGTTTAAAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
42698810 TTTAATTTAAGGGGTTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42698832 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42698853 TTTAAGTTTAGGG-TTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
42698874 TTTAGGTTAAGGGATTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42698896 T
1 T
42698897 GTCAATTAAA
Statistics
Matches: 519, Mismatches: 92, Indels: 57
0.78 0.14 0.09
Matches are distributed among these distances:
15 7 0.01
16 4 0.01
18 2 0.00
19 2 0.00
20 21 0.04
21 226 0.44
22 249 0.48
23 8 0.02
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.45
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:42698331 original size:43 final size:42
Alignment explanation
Indices: 42698236--42698896 Score: 570
Period size: 43 Copynumber: 15.5 Consensus size: 42
42698226 TCAAATTATA
42698236 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GTGTTAGGGCTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGT-TTAGGG-TT
* ** * * *
42698279 TTT-ATTTAAGGGTTACAGCTTTAAAGTTAAGGTTTTAGGGTA
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG-TTTAGGGTT
* * * *
42698321 TTTAATTTAAGGGTTTAGTGTTTTTAAGTTAAGGGTTAGAGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGTTTAGGGTT
* * * * *
42698364 TTTAAGTTAAGGGTTTAGGGTATTTAATTTAAGGGTCTACGATT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAA-GGTTTAGGGTT
* *
42698408 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGATTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGTTTAGGGTT
* **
42698451 TTTAATTTAAGGGTT-GCAATTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAG-GGTTTTTAAGTTAA-GGTTTAGGGTT
* * * *
42698494 TTAAAGTTAAGGGTTAGGGTTTTTAGGTTTAGGGTTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAG-TTAAGGTTTAGGGTT
* *
42698537 TTTAAGTTAAGGGTTAGGG-TTTTATGGTTTAAGGTTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTA-AG-TTAAGGTTTAGGGTT
* * *
42698580 TTTAATTTAAGGGTTTACGATTTTTAAGTTAAGGTTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGG-TTTAGGGTT
* * * * **
42698624 TTAAAGTTAAAGGTTAGGGTTTTTAATTTAAGGGTTATAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGTTTAGGGTT
* * ***
42698666 TTTAAGTTAAGGGTTTAAGGTTTTAAAGTTAAAAATTAGGG-T
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGTTTAGGGTT
*
42698708 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTCAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAA-GGTTTAGGGTT
* * *
42698752 TTTAAGTTAAGGGTTAGGATTTTTAAATTAAGGGTTTATGG--
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GGTTTAGGGTT
* ** * * *
42698793 -TT---TTAAGGTTTAAAGTTTTTAATTTAAGGGGTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GGTTTAGGGTT
* * *
42698832 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTTAGGGTTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGTTTAGGGTT
* *
42698874 TTTAGGTTAAGGGATTAAGGTTT
1 TTTAAGTTAAGGG-TTAGGGTTT
42698897 GTCAATTAAA
Statistics
Matches: 500, Mismatches: 95, Indels: 46
0.78 0.15 0.07
Matches are distributed among these distances:
37 27 0.05
40 4 0.01
41 1 0.00
42 113 0.23
43 257 0.51
44 93 0.19
45 5 0.01
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.45
Consensus pattern (42 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGTTTAGGGTT
Found at i:42698586 original size:194 final size:191
Alignment explanation
Indices: 42698239--42698786 Score: 674
Period size: 194 Copynumber: 2.8 Consensus size: 191
42698229 AATTATATTT
* * *** * *
42698239 AAGTTAAGGGTTAGGGTTTTTAAGTTAAGTGTTAGGGCTTTTT-ATTTAAGGG-TTACA-GCTTT
1 AAGTTAA-GGTTAGGGTTTTTAATTTAAGGGTT-GCAATTTTTAAGTTAAGGGTTTA-AGGTTTT
* * * * *
42698301 AAAGTTAAGGTTTTAGGGTATTTAATTTAAGGGTTTAGTGTTTTTAAGTTAAGGGTTAGAGTTTT
63 AAAGTTAAGG-ATTAGGGTTTTTAGTTT-AGGGTTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTT
* *
42698366 TAAGTTAAGGGTTTAGGGTATTTAATTTAAGGGTCTACGATTTTTAAGTTAAGGGTTTAGGGTTT
126 TAAGTTAA-GGTTTAAGGTTTTTAATTTAAGGGTCTACGATTTTTAAGTTAAGGGTTTAGGGTTT
42698431 TA
190 TA
*
42698433 AAGTTAAGGATTAGGGTTTTTAATTTAAGGGTTGCAATTTTTAAGTTAAGGGTTTAGGGTTTTAA
1 AAGTTAAGG-TTAGGGTTTTTAATTTAAGGGTTGCAATTTTTAAGTTAAGGGTTTAAGGTTTTAA
*
42698498 AGTTAAGGGTTAGGGTTTTTAGGTTTAGGGTTTAGAGTTTTTAAGTTAAGGGTTAGGG-TTTTAT
65 AGTTAAGGATTAGGGTTTTTA-GTTTAGGGTTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTA-
* * *
42698562 GGTTTAAGGTTTAAGGTTTTTAATTTAAGGGTTTACGATTTTTAAGTTAAGGTTTTAGGGTTTTA
128 AG-TTAAGGTTTAAGGTTTTTAATTTAAGGGTCTACGATTTTTAAGTTAAGGGTTTAGGGTTTTA
** *
42698627 AAGTTAAAGGTTAGGGTTTTTAATTTAAGGGTTATAGTTTTTAAGTTAAGGGTTTAAGGTTTTAA
1 AAGTT-AAGGTTAGGGTTTTTAATTTAAGGGTTGCAATTTTTAAGTTAAGGGTTTAAGGTTTTAA
** * * * *
42698692 AGTTAAAAATTAGGGTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTCAAGGGTTTAGGGTTTTTAA
65 AGTTAAGGATTAGGGTTTTTAGTTTAGGGTTTAGAGTTTTTAAGTTAAGGG-TTAGGGTTTTTAA
* *
42698757 GTTAAGGGTT-AGGATTTTTAAATTAAGGGT
129 GTTAAGGTTTAAGG-TTTTTAATTTAAGGGT
42698787 TTATGGTTTT
Statistics
Matches: 311, Mismatches: 32, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
192 3 0.01
193 63 0.20
194 212 0.68
195 33 0.11
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.44
Consensus pattern (191 bp):
AAGTTAAGGTTAGGGTTTTTAATTTAAGGGTTGCAATTTTTAAGTTAAGGGTTTAAGGTTTTAAA
GTTAAGGATTAGGGTTTTTAGTTTAGGGTTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGT
TAAGGTTTAAGGTTTTTAATTTAAGGGTCTACGATTTTTAAGTTAAGGGTTTAGGGTTTTA
Found at i:42698803 original size:58 final size:59
Alignment explanation
Indices: 42698608--42698867 Score: 165
Period size: 64 Copynumber: 4.3 Consensus size: 59
42698598 GATTTTTAAG
* * * * **
42698608 TTAAGGTTTTAGGGTTTTAAAGTTAA-AGGTTAGGGTTTTTAATTTAAGGGTTATAGTTTTT
1 TTAAGG-TTTAGGGTTTTTAAGTTAAGGGGTTAGAGTTTTTAAATTAAGGG-T-TAGGGTTT
* * *** * *
42698669 AAGTTAAGGGTTTAAGGTTTTAAAGTTAA-AAATTAG-GGTTTTAAGTTAAGGGTTTAGGGTTTT
1 ---TTAA-GGTTTAGGGTTTTTAAGTTAAGGGGTTAGAGTTTTTAAATTAAGGG-TTAGGG-TTT
*
42698732 TAAGTCAAGGGTTTAGGGTTTTTAAGTTAA-GGGTTAG-GATTTTTAAATTAAGGGTTTATGG-T
1 T---T-AA-GGTTTAGGGTTTTTAAGTTAAGGGGTTAGAG-TTTTTAAATTAAGGG-TTAGGGTT
42698794 T
59 T
** * *
42698795 TTAAGGTTTAAAGTTTTTAATTTAAGGGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTT
1 TTAAGGTTTAGGGTTTTTAAGTTAAGGGGTTAGAGTTTTTAAATTAAGGGTTAGGGTTT
42698854 TTAA-GTTTAGGGTT
1 TTAAGGTTTAGGGTT
42698868 AGTGTTTTTA
Statistics
Matches: 164, Mismatches: 22, Indels: 26
0.77 0.10 0.12
Matches are distributed among these distances:
58 31 0.19
59 29 0.18
60 3 0.02
62 3 0.02
63 23 0.14
64 54 0.33
65 21 0.13
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (59 bp):
TTAAGGTTTAGGGTTTTTAAGTTAAGGGGTTAGAGTTTTTAAATTAAGGGTTAGGGTTT
Found at i:42698825 original size:23 final size:22
Alignment explanation
Indices: 42698802--42698896 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 22
42698792 GTTTTAAGGT
*
42698802 TTAAAGTTTTTAATTTAAGGGG
1 TTAAAGTTTTTAAGTTAAGGGG
*
42698824 TTAGAGTTTTTAAGTTAA-GGG
1 TTAAAGTTTTTAAGTTAAGGGG
** *
42698845 TTAGGGTTTTTAAGTTTA-GGG
1 TTAAAGTTTTTAAGTTAAGGGG
** * *
42698866 TTAGTGTTTTTAGGTTAAGGGA
1 TTAAAGTTTTTAAGTTAAGGGG
*
42698888 TTAAGGTTT
1 TTAAAGTTT
42698897 GTCAATTAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
21 37 0.60
22 25 0.40
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.46
Consensus pattern (22 bp):
TTAAAGTTTTTAAGTTAAGGGG
Found at i:42701180 original size:59 final size:58
Alignment explanation
Indices: 42701027--42701182 Score: 194
Period size: 59 Copynumber: 2.7 Consensus size: 58
42701017 ATATTATGAT
* *
42701027 TTTTATT-AATTCATATTTTAAAAATAAT-TATATTAAGAATGTTATTAAATTATATATTA
1 TTTTATTAAATT-ATA-TTTAATAATAATCTATATTAA-AATATTATTAAATTATATATTA
* *
42701086 TTTTATTAAATTGTATTTAATAATAA-CTATTTTAAAATATTATTAAATTATATCATTA
1 TTTTATTAAATTATATTTAATAATAATCTATATTAAAATATTATTAAATTATAT-ATTA
*
42701144 CTTTTATTAAATTATATTTAGTAATAATCT-TATTAAAAT
1 -TTTTATTAAATTATATTTAATAATAATCTATATTAAAAT
42701183 TTAATAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
57 17 0.20
58 21 0.25
59 41 0.48
60 6 0.07
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (58 bp):
TTTTATTAAATTATATTTAATAATAATCTATATTAAAATATTATTAAATTATATATTA
Found at i:42702688 original size:21 final size:21
Alignment explanation
Indices: 42702640--42702693 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
42702630 TTGCTCTGTT
* * *
42702640 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCCCTCGCTGCAACCG
**
42702661 CCACTTCCCTCGCTGCAACCG
1 CTGCTTCCCTCGCTGCAACCG
42702682 CTGCTTCCCTCG
1 CTGCTTCCCTCG
42702694 TTGCCGCCTC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.07, C:0.48, G:0.17, T:0.28
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAACCG
Found at i:42705350 original size:63 final size:63
Alignment explanation
Indices: 42705275--42705874 Score: 787
Period size: 63 Copynumber: 9.6 Consensus size: 63
42705265 ATGTAAGTAC
* * *
42705275 TGTAAGTAATGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGATATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * * * * *
42705338 TGTAAGTTATGTAAGTTACT-TAATTTCTGTAAGTTATGTAAGTTATGTAAGATATTTAGTTTA
1 TGTAAGTTATGTAAGTTA-TGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * *
42705401 TGTAATTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTACTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* *
42705464 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATATTTAGTTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * *
42705527 TGTAA--AATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTACTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * * * * *
42705588 TGTAAGTTATGTAAGTTATGTAAGATATTTAGTTTATATAAGTTATGTAAGATATTTAGTTAA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * * * * * * *
42705651 TGTAATTTATGTAAGTTACGTAAGATATTTAGTTAATGTAATTTATGTAAGTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * * *
42705714 TTTAATTTTTGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * * *
42705777 TGTAAGTTATGTAAGATAT-TTAGTTTATGTAATTTATGTAAGTTATGTAAGTTATTTAATTTT
1 TGTAAGTTATGTAAGTTATGTAAG-TTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
42705840 TGTAAGTTATGTAA-TTAATGTAAGTTATTTAATTT
1 TGTAAGTTATGTAAGTT-ATGTAAGTTATTTAATTT
42705875 GTGAACCCTA
Statistics
Matches: 464, Mismatches: 66, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
61 56 0.12
62 5 0.01
63 399 0.86
64 4 0.01
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (63 bp):
TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
Found at i:42705829 original size:9 final size:9
Alignment explanation
Indices: 42705263--42705867 Score: 583
Period size: 9 Copynumber: 67.4 Consensus size: 9
42705253 GTATTATGTA
42705263 TTATGTAAG
1 TTATGTAAG
42705272 -TACTGTAAG
1 TTA-TGTAAG
*
42705281 TAATGTAAG
1 TTATGTAAG
42705290 TTATGTAAG
1 TTATGTAAG
*
42705299 TTACT-TAAT
1 TTA-TGTAAG
42705308 TTATGTAAG
1 TTATGTAAG
42705317 TTATGTAAG
1 TTATGTAAG
* * *
42705326 ATATTTAAT
1 TTATGTAAG
42705335 TTATGTAAG
1 TTATGTAAG
42705344 TTATGTAAG
1 TTATGTAAG
*
42705353 TTACT-TAAT
1 TTA-TGTAAG
*
42705362 TTCTGTAAG
1 TTATGTAAG
42705371 TTATGTAAG
1 TTATGTAAG
42705380 TTATGTAAG
1 TTATGTAAG
* *
42705389 ATAT-TTAG
1 TTATGTAAG
*
42705397 TTTATGTAAT
1 -TTATGTAAG
42705407 TTATGTAAG
1 TTATGTAAG
42705416 TTATGTAAG
1 TTATGTAAG
* *
42705425 TTATTTAAT
1 TTATGTAAG
*
42705434 TTTTGTAAG
1 TTATGTAAG
42705443 TTATGTAAG
1 TTATGTAAG
*
42705452 TTACT-TAAT
1 TTA-TGTAAG
42705461 TTATGTAAG
1 TTATGTAAG
42705470 TTATGTAAG
1 TTATGTAAG
42705479 TTATGTAAG
1 TTATGTAAG
* *
42705488 TTATTTAAT
1 TTATGTAAG
42705497 TTATGTAAG
1 TTATGTAAG
42705506 TTATGTAAG
1 TTATGTAAG
* *
42705515 ATAT-TTAG
1 TTATGTAAG
42705523 TTTATGTAA-
1 -TTATGTAAG
*
42705532 -AATGTAAG
1 TTATGTAAG
42705540 TTATGTAAG
1 TTATGTAAG
* *
42705549 TTATTTAAT
1 TTATGTAAG
*
42705558 TTTTGTAAG
1 TTATGTAAG
42705567 TTATGTAAG
1 TTATGTAAG
*
42705576 TTACT-TAAT
1 TTA-TGTAAG
42705585 TTATGTAAG
1 TTATGTAAG
42705594 TTATGTAAG
1 TTATGTAAG
42705603 TTATGTAAG
1 TTATGTAAG
* *
42705612 ATAT-TTAG
1 TTATGTAAG
*
42705620 TTTATATAAG
1 -TTATGTAAG
42705630 TTATGTAAG
1 TTATGTAAG
* *
42705639 ATAT-TTAG
1 TTATGTAAG
*
42705647 TTAATGTAAT
1 TT-ATGTAAG
42705657 TTATGTAAG
1 TTATGTAAG
*
42705666 TTACGTAAG
1 TTATGTAAG
* *
42705675 ATAT-TTAG
1 TTATGTAAG
*
42705683 TTAATGTAAT
1 TT-ATGTAAG
42705693 TTATGTAAG
1 TTATGTAAG
42705702 TTATGTAAG
1 TTATGTAAG
* *
42705711 TTATTTAAT
1 TTATGTAAG
*
42705720 TTTTGTAAG
1 TTATGTAAG
42705729 TTATGTAAG
1 TTATGTAAG
*
42705738 TTACT-TAAT
1 TTA-TGTAAG
42705747 TTATGTAAG
1 TTATGTAAG
42705756 TTATGTAAG
1 TTATGTAAG
* *
42705765 TTATTTAAT
1 TTATGTAAG
42705774 TTATGTAAG
1 TTATGTAAG
42705783 TTATGTAAG
1 TTATGTAAG
* *
42705792 ATAT-TTAG
1 TTATGTAAG
*
42705800 TTTATGTAAT
1 -TTATGTAAG
42705810 TTATGTAAG
1 TTATGTAAG
42705819 TTATGTAAG
1 TTATGTAAG
* *
42705828 TTATTTAAT
1 TTATGTAAG
*
42705837 TTTTGTAAG
1 TTATGTAAG
42705846 TTATGTAA-
1 TTATGTAAG
42705854 TTAATGTAAG
1 TT-ATGTAAG
42705864 TTAT
1 TTAT
42705868 TTAATTTGTG
Statistics
Matches: 479, Mismatches: 89, Indels: 56
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.01
8 29 0.06
9 419 0.87
10 25 0.05
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:42710135 original size:21 final size:20
Alignment explanation
Indices: 42710107--42710145 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42710097 CTTAACACAT
42710107 AACCTTAAA-CATTAAACCCC
1 AACCTTAAACCA-TAAACCCC
42710127 AACCTTTAAACCATAAACC
1 AACC-TTAAACCATAAACC
42710146 ATAGACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (20 bp):
AACCTTAAACCATAAACCCC
Found at i:42710416 original size:115 final size:115
Alignment explanation
Indices: 42710218--42710744 Score: 408
Period size: 115 Copynumber: 4.6 Consensus size: 115
42710208 ACCAAAACTT
* * * * *
42710218 TGCGTTTTGGTTAAGATATTTTTCGGCGCTTTTCAAAAAGCGCCGCTGATACTATACTTTAGCGG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
* **
42710283 CGATTTCTCG--T-GGACGCCACTAATTCCATTATACATCAAGACTTAAACGC
66 CG--TTCTCGCATATG-CGCCACTAATTCCATTATACATCAAGACAAAAACGC
* * *
42710333 TGCGTTTTTGTTAATATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAATATGCTTTAGCGG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
* * * * * * * *
42710398 CGTTCCCGCATAAGCGCCACTAAGTCTAATATACCTCATGA-AAAAACTC
66 CGTTCTCGCATATGCGCCACTAATTCCATTATACATCAAGACAAAAACGC
** * * * **** * *
42710447 TATGTTTTGGTGAGCATATTTTGCGGCGCTTTTTTCCAAGCGCCGCTAATACTATGATGTAGCGG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
* *** * * * *
42710512 CGTTTTTTTAATATGCGCCACTAATTAC-TGTATACATCGAGACAAAAATGT
66 CG-TTCTCGCATATGCGCCACTAATTCCAT-TATACATCAAGACAAAAACGC
* * * * *
42710563 TGCGTTTTGGTTACCAAATTTTGCGGCGCTTCTCTGAAAA-CGCCGCTAATAGTATGCCTTAGCG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTC-AAAAAGCGCCGCTAATACTATGCTTTAGCG
* * * * * * *
42710627 GCGTGT-TC-CTTTTGCGCCACTAATTCTAGTATACCTCAAGAC-CAAACTC
65 GCGT-TCTCGCATATGCGCCACTAATTCCATTATACATCAAGACAAAAACGC
* * * * * *
42710676 TACATTTTGGTTCAGATATTTTGCGGCGCTTCTCACAAAA-CGCCGTTAATATTATGCTTTAGCG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCA-AAAAGCGCCGCTAATACTATGCTTTAGCG
42710740 GCGTT
65 GCGTT
42710745 TTCCATTAAA
Statistics
Matches: 318, Mismatches: 84, Indels: 23
0.75 0.20 0.05
Matches are distributed among these distances:
112 1 0.00
113 65 0.20
114 83 0.26
115 110 0.35
116 57 0.18
117 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (115 bp):
TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
CGTTCTCGCATATGCGCCACTAATTCCATTATACATCAAGACAAAAACGC
Found at i:42710741 original size:229 final size:230
Alignment explanation
Indices: 42710222--42710746 Score: 553
Period size: 229 Copynumber: 2.3 Consensus size: 230
42710212 AAACTTTGCG
* * *
42710222 TTTTGGTTAAGATATTTTTCGGCGCTTTTCA-AAAAGCGCCGCTGATACTATACTTTAGCGGCG-
1 TTTTGGTTAAGATATTTTGCGGCGCTTTTCACAAAA-CGCCGCTAATACTATGCTTTAGCGGCGT
* ** * ** * * *
42710285 ATTTCTCGTGGACGCCACTAATTCCATTATACATCAAGACTTAAACGCTGCGTTTTTGTTAATAT
65 TTTTCTAATGGACGCCACTAATTACATTATACATCAAGACAAAAACGCTGCGTTTTGGTTAACAA
*
42710350 ATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAATATGCTTTAGCGGCGTTCCCGCATAAGCGC
130 ATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAATATGCCTTAGCGGCGTTCCCGCATAAGCGC
* **
42710415 CACTAAGTCTAATATACCTCATGAAAAAACTCTATG
195 CACTAAGTCTAATATACCTCAAGAAAAAACTCTACA
* ** * * * *
42710451 TTTTGG-TGAGCATATTTTGCGGCGCTTTTTTCCAAGCGCCGCTAATACTATGATGTAGCGGCGT
1 TTTTGGTTAAG-ATATTTTGCGGCGCTTTTCACAAAACGCCGCTAATACTATGCTTTAGCGGCGT
* * * * * *
42710515 TTTTTTAATATG-CGCCACTAATTAC-TGTATACATCGAGACAAAAATGTTGCGTTTTGGTTACC
65 TTTTCTAAT-GGACGCCACTAATTACAT-TATACATCAAGACAAAAACGCTGCGTTTTGGTTAAC
* * * * **
42710578 AAATTTTGCGGCGCTTCTCTGAAAA-CGCCGCTAATAGTATGCCTTAGCGGCGTGT-TC-CTTTT
128 AAATTTTGCGGCGCTTCTC-AAAAAGCGCCGCTAATAATATGCCTTAGCGGCGT-TCCCGCATAA
* * **
42710640 GCGCCACTAATTCTAGTATACCTCAAGACCAAACTCTACA
191 GCGCCACTAAGTCTAATATACCTCAAGAAAAAACTCTACA
* * * *
42710680 TTTTGGTTCAGATATTTTGCGGCGCTTCTCACAAAACGCCGTTAATATTATGCTTTAGCGGCGTT
1 TTTTGGTTAAGATATTTTGCGGCGCTTTTCACAAAACGCCGCTAATACTATGCTTTAGCGGCGTT
42710745 TT
66 TT
42710747 CCATTAAACG
Statistics
Matches: 239, Mismatches: 49, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
228 3 0.01
229 135 0.56
230 95 0.40
231 6 0.03
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (230 bp):
TTTTGGTTAAGATATTTTGCGGCGCTTTTCACAAAACGCCGCTAATACTATGCTTTAGCGGCGTT
TTTCTAATGGACGCCACTAATTACATTATACATCAAGACAAAAACGCTGCGTTTTGGTTAACAAA
TTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAATATGCCTTAGCGGCGTTCCCGCATAAGCGCC
ACTAAGTCTAATATACCTCAAGAAAAAACTCTACA
Found at i:42711020 original size:112 final size:113
Alignment explanation
Indices: 42710867--42711098 Score: 279
Period size: 112 Copynumber: 2.1 Consensus size: 113
42710857 ACCAAACTCT
* * *
42710867 GCGTTTTGGTTAACATATGTTGCGGCGCTTTTGATAAGCGCCGCTAATACTTCCTTTAGCGGCGG
1 GCGTTTTCGTTAACATATGTTGCGGCGCTTTGGATAAGCGCCGCTAATACTTCCTTTAACGGCGG
* * * *
42710932 GTTTTCGTCAGCGCCACTAACGCTAATATACAACGAGA-CAAAACGAA
66 GTTTTCATAAACGCCACTAACGCTAATATACAACAAGACCAAAACGAA
* * * *
42710979 GCGTTTTCGTTAAGAT-TTTTGCGGCGCATTTGGCTATGCGCCGCTAATACTTCCTTTAACGGCG
1 GCGTTTTCGTTAACATATGTTGCGGCGC-TTTGGATAAGCGCCGCTAATACTTCCTTTAACGGCG
** ** * * *
42711043 TTTTTTCATAAACGCCACTAATTCTAGTATACATCAAGACCAAAACGAT
65 GGTTTTCATAAACGCCACTAACGCTAATATACAACAAGACCAAAACGAA
42711092 GCGTTTT
1 GCGTTTT
42711099 GATCTTCAGA
Statistics
Matches: 100, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
111 10 0.10
112 75 0.75
113 15 0.15
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (113 bp):
GCGTTTTCGTTAACATATGTTGCGGCGCTTTGGATAAGCGCCGCTAATACTTCCTTTAACGGCGG
GTTTTCATAAACGCCACTAACGCTAATATACAACAAGACCAAAACGAA
Found at i:42713766 original size:18 final size:18
Alignment explanation
Indices: 42713706--42713771 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
42713696 TTTTAAATTT
42713706 TTTTAATATATTTTT-TAA
1 TTTTAA-ATATTTTTATAA
**
42713724 TTTTAAA-ATTTTTATTC
1 TTTTAAATATTTTTATAA
* * *
42713741 GTTAAAATATTTTTAGAA
1 TTTTAAATATTTTTATAA
42713759 TTTTAAATTATTT
1 TTTTAAA-TATTT
42713772 GTTAATGTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
16 6 0.17
17 7 0.19
18 18 0.50
19 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTAAATATTTTTATAA
Found at i:42718229 original size:3 final size:3
Alignment explanation
Indices: 42718221--42718259 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
42718211 GAATCTGCAA
42718221 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
42718260 TAGCATGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:42719356 original size:12 final size:13
Alignment explanation
Indices: 42719330--42719363 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
42719320 AGGGAGAAGC
*
42719330 AAAATAGAATGAA
1 AAAATAAAATGAA
42719343 AAAATAAAAT-AA
1 AAAATAAAATGAA
42719355 AAAATAAAA
1 AAAATAAAA
42719364 GTTAAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAATAAAATGAA
Found at i:42720477 original size:4 final size:4
Alignment explanation
Indices: 42720468--42720494 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
42720458 TATTGATGGT
42720468 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
42720495 TTGACTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:42724547 original size:6 final size:6
Alignment explanation
Indices: 42724538--42724597 Score: 50
Period size: 6 Copynumber: 10.2 Consensus size: 6
42724528 TTAGGGTTAG
* * * * **
42724538 AGAAAA AGAAAA AGAACA AGAAGA AG-AGA AGAAAA AGAAGA AGAAGG
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
*
42724585 AGAAAA GGAAAA A
1 AGAAAA AGAAAA A
42724598 TAGAGATGCC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.72, C:0.02, G:0.27, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:42724563 original size:3 final size:3
Alignment explanation
Indices: 42724538--42724588 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
42724528 TTAGGGTTAG
* * * * *
42724538 AGA AAA AGA AAA AGA ACA AGA AGA AG- AGA AGA AAA AGA AGA AGA AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
42724585 AGA A
1 AGA A
42724589 AAGGAAAAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:42724571 original size:23 final size:23
Alignment explanation
Indices: 42724541--42724597 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
42724531 GGGTTAGAGA
42724541 AAAAGAAAAAGAACAAGAAGAAG
1 AAAAGAAAAAGAACAAGAAGAAG
* * *
42724564 AGAAGAAAAAGAAGAAGAAGGAG
1 AAAAGAAAAAGAACAAGAAGAAG
42724587 AAAAGGAAAAA
1 AAAA-GAAAAA
42724598 TAGAGATGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (23 bp):
AAAAGAAAAAGAACAAGAAGAAG
Found at i:42724575 original size:17 final size:17
Alignment explanation
Indices: 42724549--42724581 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42724539 GAAAAAGAAA
*
42724549 AAGAACAAGAAGAAGAG
1 AAGAAAAAGAAGAAGAG
42724566 AAGAAAAAGAAGAAGA
1 AAGAAAAAGAAGAAGA
42724582 AGGAGAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.27, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAGAAGAG
Found at i:42724590 original size:17 final size:16
Alignment explanation
Indices: 42724549--42724591 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
42724539 GAAAAAGAAA
42724549 AAGAACAAGAAGAAGAG
1 AAGAA-AAGAAGAAGAG
42724566 AAGAAAAAGAAGAAGAAG
1 AAG-AAAAGAAGAAG-AG
*
42724584 GAGAAAAG
1 AAGAAAAG
42724592 GAAAAATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAGAAGAG
Found at i:42725167 original size:17 final size:18
Alignment explanation
Indices: 42725145--42725181 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
42725135 TATATTTTTT
42725145 TATTTTTTA-TTTTAAAA
1 TATTTTTTATTTTTAAAA
42725162 TATTTTTTATTTTTAAAA
1 TATTTTTTATTTTTAAAA
42725180 TA
1 TA
42725182 AATTTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTTTTATTTTTAAAA
Found at i:42725187 original size:18 final size:17
Alignment explanation
Indices: 42725149--42725187 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
42725139 TTTTTTTATT
**
42725149 TTTTATTTTAAAATATT
1 TTTTATTTTAAAATAAA
42725166 TTTTATTTTTAAAATAAA
1 TTTTA-TTTTAAAATAAA
42725184 TTTT
1 TTTT
42725188 TGGTGTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATTTTAAAATAAA
Found at i:42725612 original size:19 final size:20
Alignment explanation
Indices: 42725588--42725636 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
42725578 TTGTTTCACA
*
42725588 GAAAATAACTT-GGTCAATG
1 GAAAATAACTTAGGTCAACG
*
42725607 GAAAATGACTTACAGGTCAACG
1 GAAAATAACTT--AGGTCAACG
42725629 GAAAATAA
1 GAAAATAA
42725637 GCTTTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
22 14 0.58
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.20
Consensus pattern (20 bp):
GAAAATAACTTAGGTCAACG
Found at i:42725917 original size:13 final size:14
Alignment explanation
Indices: 42725901--42725942 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
42725891 TTTAAATTTT
42725901 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
42725914 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
42725929 ATTTTAAATAATAT
1 ATTTT-AATAATAT
42725943 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:42725927 original size:16 final size:16
Alignment explanation
Indices: 42725905--42725941 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
42725895 AATTTTATTT
42725905 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
42725922 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
42725937 TAATA
1 TAATA
42725942 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:42727845 original size:28 final size:28
Alignment explanation
Indices: 42727796--42727849 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
42727786 CACACACCTA
* *
42727796 AAAAAATAGTCACTATATGCATATTATT
1 AAAAAATACTCACTATAAGCATATTATT
42727824 AAAAAATACTCACTGA-AAGCATATTA
1 AAAAAATACTCACT-ATAAGCATATTA
42727850 AAAAATAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (28 bp):
AAAAAATACTCACTATAAGCATATTATT
Found at i:42729599 original size:15 final size:15
Alignment explanation
Indices: 42729567--42729616 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
42729557 TTATCCTATT
**
42729567 AGACACATCACTTTC
1 AGACACATCACTACC
**
42729582 AGATGCATCACTACC
1 AGACACATCACTACC
42729597 AGACACATCACTACC
1 AGACACATCACTACC
42729612 AGACA
1 AGACA
42729617 TTTCTTCTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.18
Consensus pattern (15 bp):
AGACACATCACTACC
Found at i:42730114 original size:18 final size:18
Alignment explanation
Indices: 42730068--42730168 Score: 91
Period size: 18 Copynumber: 5.6 Consensus size: 18
42730058 TAACCAAACT
*
42730068 GAAATCCAAATCTAAATC
1 GAAATCAAAATCTAAATC
* *
42730086 TAAATCTAAATCTAAATC
1 GAAATCAAAATCTAAATC
*
42730104 GAGATCAAAAT-TGAAAT-
1 GAAATCAAAATCT-AAATC
* *
42730121 GAAAATAAAAATCAAAATC
1 G-AAATCAAAATCTAAATC
*
42730140 AAAATCAAAAT-TAGAATC
1 GAAATCAAAATCTA-AATC
42730158 GAAATCAAAAT
1 GAAATCAAAAT
42730169 TGAAATTGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.05
18 63 0.95
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (18 bp):
GAAATCAAAATCTAAATC
Found at i:42730126 original size:6 final size:6
Alignment explanation
Indices: 42730069--42730168 Score: 74
Period size: 6 Copynumber: 16.7 Consensus size: 6
42730059 AACCAAACTG
* * * * * * * **
42730069 AAATCC AAATCT AAATCT AAATCT AAATCT AAATCG AGATCA AAATTG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* * * * *
42730117 AAATGA AAATAA AAATCA AAATCA AAATCA AAATTA GAATCG AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
42730165 AAAT
1 AAAT
42730169 TGAAATTGAA
Statistics
Matches: 77, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (6 bp):
AAATCA
Found at i:42730169 original size:18 final size:17
Alignment explanation
Indices: 42730068--42730180 Score: 84
Period size: 18 Copynumber: 6.3 Consensus size: 17
42730058 TAACCAAACT
*
42730068 GAAATCCAAATCTAAATC
1 GAAATCAAAAT-TAAATC
* *
42730086 TAAATCTAAATCTAAATC
1 GAAATCAAAAT-TAAATC
*
42730104 GAGATCAAAATTGAAAT-
1 GAAATCAAAATT-AAATC
* *
42730121 GAAAATAAAAATCAAAATC
1 G-AAATCAAAAT-TAAATC
*
42730140 AAAATCAAAATTAGAATC
1 GAAATCAAAATTA-AATC
*
42730158 GAAATCAAAATTGAAATT
1 GAAATCAAAATT-AAATC
42730176 GAAAT
1 GAAAT
42730181 AACCCTAAAT
Statistics
Matches: 76, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
17 3 0.04
18 72 0.95
19 1 0.01
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.24
Consensus pattern (17 bp):
GAAATCAAAATTAAATC
Found at i:42731286 original size:18 final size:19
Alignment explanation
Indices: 42731249--42731285 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
42731239 TTTTTAAAAA
*
42731249 TATAAA-ATTTGAAATTTT
1 TATAAATATTTTAAATTTT
42731267 TATAAATATTTTAAATTTT
1 TATAAATATTTTAAATTTT
42731286 AAAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:42733353 original size:4 final size:4
Alignment explanation
Indices: 42733344--42733368 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
42733334 ACAAGTAAGG
42733344 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
42733369 GAAATCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:42734029 original size:44 final size:44
Alignment explanation
Indices: 42733947--42734184 Score: 143
Period size: 44 Copynumber: 5.2 Consensus size: 44
42733937 ACCCGCTGTT
* * * * * * *
42733947 ACTTCAGGGAGATGAGACTTGTGGTTTTAGTCTACTCCACTGCA
1 ACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCA
42733991 ACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCA
1 ACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCA
* * * * *
42734035 ACTTCATGAAGATAAAATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTACA
1 ACTTCAGGGAGATAAAA-CTG--G-----TG--GCTTCAATCTGCTCCACTGCA
** * * * * * * *
42734089 ACACCAGGGAAATAAGATCTGCTGTCTTCAGTCTGCTTCGCTGCA
1 ACTTCAGGGAGATAA-AACTGGTGGCTTCAATCTGCTCCACTGCA
* ** * *
42734134 ACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGTA
1 ACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCA
42734178 ACTTCAG
1 ACTTCAG
42734185 AAAGATAAGA
Statistics
Matches: 143, Mismatches: 40, Indels: 22
0.70 0.20 0.11
Matches are distributed among these distances:
44 78 0.55
45 28 0.20
47 3 0.02
52 2 0.01
54 31 0.22
55 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
ACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCA
Found at i:42734234 original size:143 final size:142
Alignment explanation
Indices: 42733975--42734394 Score: 540
Period size: 143 Copynumber: 2.9 Consensus size: 142
42733965 TTGTGGTTTT
* * **
42733975 AGTCTACTCCACTGCAACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCAACTTC
1 AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTC
* *
42734040 ATG-AAGATAAAATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTACAACACCAGGGAAATAA
66 A-GAAAGATAAGATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAA
42734104 GATCTGC-TGTCTTC
130 GAT-T-CATGTCTTC
* * * *
42734118 AGTCTGCTTCGCTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGTAACTTC
1 AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTC
* * **
42734183 AGAAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACACTGGGGAAATAAG
66 AGAAAGATAAGATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAG
42734248 ATTCATTGTCTTC
131 ATTCA-TGTCTTC
* * * * * *
42734261 AGTCTGCTCCGCTGCAACTTTAGGGAGATAAGGTTGGTGGCTTCAATCTGCTTCGCTACAACCTC
1 AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTC
* * * * **
42734326 AAGAAA-ATAAGATTTACCGTAACTTGTAACTTTAATCTATTCCACTGCAATGCCAGGGAAATAA
66 -AGAAAGATAAGATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAA
42734390 GATTC
130 GATTC
42734395 TCCATAATGA
Statistics
Matches: 239, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
141 1 0.00
142 2 0.01
143 231 0.97
144 5 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (142 bp):
AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTC
AGAAAGATAAGATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAG
ATTCATGTCTTC
Found at i:42741557 original size:19 final size:19
Alignment explanation
Indices: 42741533--42741576 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
42741523 AAACGACATG
42741533 TACAACGAATAAACTCTGA
1 TACAACGAATAAACTCTGA
42741552 TACAACGAATAAACTCTGA
1 TACAACGAATAAACTCTGA
42741571 TACAAC
1 TACAAC
42741577 TTTCTATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.20
Consensus pattern (19 bp):
TACAACGAATAAACTCTGA
Found at i:42748671 original size:14 final size:14
Alignment explanation
Indices: 42748654--42748692 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
42748644 TTAATATTTT
* *
42748654 TAATTTAATTCGAA
1 TAATTTAACTCAAA
42748668 TAATTTAACTCAAA
1 TAATTTAACTCAAA
*
42748682 TAATTTCACTC
1 TAATTTAACTC
42748693 GGTTCGATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (14 bp):
TAATTTAACTCAAA
Found at i:42751767 original size:41 final size:41
Alignment explanation
Indices: 42751722--42751802 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
42751712 AAAGAATATC
* **
42751722 TAAAATTAAAATGTGGTATATATAATTGTTTAAAATTAAAG
1 TAAAATTAAAATGTGATATATATAATTGCATAAAATTAAAG
* *
42751763 TAAAATTTAAATGTTATATATATAATTGCATAAAATTAAA
1 TAAAATTAAAATGTGATATATATAATTGCATAAAATTAAA
42751803 ATTTACGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.40
Consensus pattern (41 bp):
TAAAATTAAAATGTGATATATATAATTGCATAAAATTAAAG
Found at i:42753575 original size:23 final size:23
Alignment explanation
Indices: 42753536--42753601 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
42753526 TAATTTACAC
* *
42753536 CGAAGTGCTACTGTCACTTGCAT
1 CGAAGTGCCACTATCACTTGCAT
* *
42753559 GGGAGTGCCACTATCACTTGCAT
1 CGAAGTGCCACTATCACTTGCAT
*
42753582 CGAAGTGCCACCATCACTTG
1 CGAAGTGCCACTATCACTTG
42753602 TTCGCGTGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (23 bp):
CGAAGTGCCACTATCACTTGCAT
Found at i:42757630 original size:51 final size:50
Alignment explanation
Indices: 42757561--42757660 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 50
42757551 TTGTTTTTTC
* * *
42757561 CTTTCTTTTGCCTTTTTCCATCTTTTCTTGATTTCTTGCTAGCCACCGTT
1 CTTTCTTTTGCCTTTTTCCAGCTCTTCTTGATTTCTTGCAAGCCACCGTT
* *
42757611 CTTTCTTTTTTCCTTTTTCCAGCTCTTCTTGCTTTCTTGCAAGCCACCGT
1 CTTTC-TTTTGCCTTTTTCCAGCTCTTCTTGATTTCTTGCAAGCCACCGT
42757661 CATCGTCCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 5 0.11
51 39 0.89
ACGTcount: A:0.08, C:0.30, G:0.10, T:0.52
Consensus pattern (50 bp):
CTTTCTTTTGCCTTTTTCCAGCTCTTCTTGATTTCTTGCAAGCCACCGTT
Found at i:42761686 original size:27 final size:27
Alignment explanation
Indices: 42761646--42761708 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
42761636 GGTAATGGAA
*
42761646 TGGCGGCACCGGTGGTGCCATTCTCAT
1 TGGCGGCACCGGTGGTGCCATTCCCAT
*
42761673 TGGCGGCACTGGTGGTGCCATTCCCAT
1 TGGCGGCACCGGTGGTGCCATTCCCAT
*
42761700 TGGTGGCAC
1 TGGCGGCAC
42761709 AGGACTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.11, C:0.29, G:0.35, T:0.25
Consensus pattern (27 bp):
TGGCGGCACCGGTGGTGCCATTCCCAT
Found at i:42762995 original size:15 final size:15
Alignment explanation
Indices: 42762975--42763011 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
42762965 TTTTTCGGCT
42762975 GATTTGCTCTCTATC
1 GATTTGCTCTCTATC
*
42762990 GATTTGCTCTCTGTC
1 GATTTGCTCTCTATC
42763005 GATTTGC
1 GATTTGC
42763012 GTCATCGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (15 bp):
GATTTGCTCTCTATC
Found at i:42765556 original size:47 final size:48
Alignment explanation
Indices: 42765486--42765661 Score: 309
Period size: 48 Copynumber: 3.7 Consensus size: 48
42765476 TAAAAATTAC
42765486 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
*** *
42765534 ATCAATAATT-AAATAAGGACTTTAATATTTTATTGCTATAATGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
42765581 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
42765629 ATCAATAATTAAAATAAGGACTTTAATATTTTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTA
42765662 ATAACTTCAA
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
47 43 0.36
48 76 0.64
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.38
Consensus pattern (48 bp):
ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
Found at i:42765588 original size:95 final size:96
Alignment explanation
Indices: 42765486--42765661 Score: 345
Period size: 95 Copynumber: 1.8 Consensus size: 96
42765476 TAAAAATTAC
42765486 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTAATCAATAATT-AAATAA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTAATCAATAATTAAAATAA
42765550 GGACTTTAATATTTTATTGCTATAATGACTA
66 GGACTTTAATATTTTATTGCTATAATGACTA
42765581 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTAATCAATAATTAAAATAA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTAATCAATAATTAAAATAA
42765646 GGACTTTAATATTTTA
66 GGACTTTAATATTTTA
42765662 ATAACTTCAA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 58 0.73
96 22 0.28
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.38
Consensus pattern (96 bp):
ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTAATCAATAATTAAAATAA
GGACTTTAATATTTTATTGCTATAATGACTA
Found at i:42769005 original size:92 final size:91
Alignment explanation
Indices: 42768848--42769056 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 91
42768838 TTGATTTTAG
* * * *
42768848 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTGTTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
42768913 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
42768940 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
42769004 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
42769032 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
42769057 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 70 0.68
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:42769019 original size:24 final size:25
Alignment explanation
Indices: 42768984--42769031 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
42768974 TTATGAAATT
42768984 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
42769008 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
42769032 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:42769185 original size:66 final size:63
Alignment explanation
Indices: 42769110--42769440 Score: 238
Period size: 66 Copynumber: 5.4 Consensus size: 63
42769100 AAATATATTT
42769110 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
42769175 G
63 G
* * * * **
42769176 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
42769230 AATAATAATTATGTT-AATTTATATTTTACAGTAACATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
42769294 AG
62 AG
* * * * **
42769296 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
*
42769350 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
42769414 AG
62 AG
*
42769416 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
42769441 AAATTATATA
Statistics
Matches: 201, Mismatches: 31, Indels: 67
0.67 0.10 0.22
Matches are distributed among these distances:
53 10 0.05
54 26 0.13
55 10 0.05
56 8 0.04
57 6 0.03
58 2 0.01
59 19 0.09
60 16 0.08
61 19 0.09
62 2 0.01
63 6 0.03
64 8 0.04
65 14 0.07
66 45 0.22
67 10 0.05
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:42769210 original size:120 final size:120
Alignment explanation
Indices: 42769072--42769484 Score: 724
Period size: 120 Copynumber: 3.4 Consensus size: 120
42769062 AATTATTTTA
* * * *
42769072 AATTTTATTAAATCATATATTTTAAATAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
*
42769134 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
42769192 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
42769257 ACAGTAACATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
42769312 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
42769377 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
42769432 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
42769485 TAAATATGAT
Statistics
Matches: 283, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
119 6 0.02
120 275 0.97
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:42769232 original size:15 final size:15
Alignment explanation
Indices: 42769197--42769248 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
42769187 TTAAGAATTT
*
42769197 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42769211 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42769225 TATTTAATAATAAT-
1 TATTTAATTATAATA
42769239 TATGTTAATT
1 TAT-TTAATT
42769249 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42769352 original size:15 final size:15
Alignment explanation
Indices: 42769317--42769368 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
42769307 TTAAGAATTT
*
42769317 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42769331 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42769345 TATTTAATAATAAT-
1 TATTTAATTATAATA
42769359 TATGTTAATT
1 TAT-TTAATT
42769369 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42769467 original size:16 final size:16
Alignment explanation
Indices: 42769446--42769487 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42769436 TTATTAAATT
*
42769446 ATATATTTTAATTATA
1 ATATATTTTAATAATA
42769462 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
42769477 AT-TATGTTTAA
1 ATATAT-TTTAA
42769488 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:42769472 original size:15 final size:15
Alignment explanation
Indices: 42769437--42769478 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42769427 TTAAGAATTT
*
42769437 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42769451 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42769465 TATTTAATAATAAT
1 TATTTAATTATAAT
42769479 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42769599 original size:153 final size:156
Alignment explanation
Indices: 42769421--42769733 Score: 515
Period size: 153 Copynumber: 2.0 Consensus size: 156
42769411 ATAAGAATAT
* * *
42769421 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
* *
42769486 AAATATGATTAAATTATTTATTATTGATATTAACAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAACAATCTTATTAAAATTTAAATAACAATAACAA
*
42769551 T-A-A-TTACCAAAACAAATTTCTGC
131 TAACATTTACCAAAACAAATTTATGC
* *
42769574 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATGGGTTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
*
42769639 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAACAATCTTATTAAAATTTAAATAACAATAACAA
42769704 TAATCATTTACCAAAACAAATTTATGC
131 TAA-CATTTACCAAAACAAATTTATGC
42769731 TAA
1 TAA
42769734 GGGTATTCTA
Statistics
Matches: 147, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
153 123 0.84
154 1 0.01
156 1 0.01
157 22 0.15
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (156 bp):
TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAACAATCTTATTAAAATTTAAATAACAATAACAA
TAACATTTACCAAAACAAATTTATGC
Found at i:42769877 original size:16 final size:16
Alignment explanation
Indices: 42769856--42769891 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
42769846 GATTTGCTAT
42769856 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42769872 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42769888 TACA
1 TACA
42769892 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:42770999 original size:19 final size:19
Alignment explanation
Indices: 42770975--42771068 Score: 125
Period size: 19 Copynumber: 4.8 Consensus size: 19
42770965 AATCATATCT
42770975 TCCAAGATTACATATCATA
1 TCCAAGATTACATATCATA
42770994 TCCAAGATTACATATCATA
1 TCCAAGATTACATATCATA
*
42771013 TCCAAGATTGCATATATCATA
1 TCCAAGATT--ACATATCATA
* *
42771034 TCTAAGATTGCATATCATA
1 TCCAAGATTACATATCATA
* *
42771053 TCTAAGATTGCATATC
1 TCCAAGATTACATATC
42771069 CTTGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 52 0.75
21 17 0.25
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (19 bp):
TCCAAGATTACATATCATA
Found at i:42771041 original size:40 final size:40
Alignment explanation
Indices: 42770952--42771067 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
42770942 AAATTAAATC
* *
42770952 TCTAAGATTACAAAATCATATCTTCCAAGATT--ACATATCATA
1 TCTAAGATTAC-ATATCATA---TCCAAGATTGCATATATCATA
*
42770994 TCCAAGATTACATATCATATCCAAGATTGCATATATCATA
1 TCTAAGATTACATATCATATCCAAGATTGCATATATCATA
* *
42771034 TCTAAGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTACATATCATATCCAAGATTGCATAT
42771068 CCTTGAAGAT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
38 9 0.14
40 40 0.61
41 7 0.11
42 10 0.15
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (40 bp):
TCTAAGATTACATATCATATCCAAGATTGCATATATCATA
Found at i:42771644 original size:89 final size:89
Alignment explanation
Indices: 42771412--42771690 Score: 411
Period size: 89 Copynumber: 3.2 Consensus size: 89
42771402 AAGACTTGTA
* * * *
42771412 TCTTCGATCTACTTCGCCACCAGTATGGGAAAACAAGATCTGCTACCTTTGATCTATTTCATGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
* * *
42771477 GATACATGAAGACAATATCTACTT
66 AATACATGAAGACAAGATCTGCTT
* * ***
42771501 TCTTCGATCTATTTCGCTA--A-TACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
42771563 AATACATGAAGACAAGATCTGCTT
66 AATACATGAAGACAAGATCTGCTT
*
42771587 TCTTCGATATACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
*
42771652 AATACATGAAGATAAGATCTGCTT
66 AATACATGAAGACAAGATCTGCTT
42771676 TCTTCGATCTACTTC
1 TCTTCGATCTACTTC
42771691 ACGATAACCC
Statistics
Matches: 167, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
86 72 0.43
87 1 0.01
88 1 0.01
89 93 0.56
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (89 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
AATACATGAAGACAAGATCTGCTT
Found at i:42771692 original size:44 final size:44
Alignment explanation
Indices: 42771444--42771693 Score: 279
Period size: 44 Copynumber: 5.7 Consensus size: 44
42771434 GTATGGGAAA
* * * * *
42771444 ACAAGATCTGCTACCTTTGATCTATTTCATGCCGATACATGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
* * * * *
42771488 ACAATATCTACTTTCTTCGATCTA-TT-TCGCTAATACATGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
*
42771530 ACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
* * * * * ***
42771574 ACAAGATCTGCTTTCTTCGATATACTTCGCCACCAGTATGGGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAG
*
42771619 ACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
* *
42771663 ATAAGATCTGCTTTCTTCGATCTACTTCACG
1 ACAAGATCTGCTATCTTCGATCTACTTCACG
42771694 ATAACCCAGG
Statistics
Matches: 167, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
42 32 0.19
43 4 0.02
44 96 0.57
45 35 0.21
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (44 bp):
ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
Found at i:42771788 original size:88 final size:88
Alignment explanation
Indices: 42771696--42772066 Score: 553
Period size: 88 Copynumber: 4.2 Consensus size: 88
42771686 ACTTCACGAT
* * * * *
42771696 AACCCAGGGAGGGAAGGCTGATATTTTTGATCTGCTTCACTGTGGGTACAGGAAGGCAAGATCTG
1 AACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTG
42771761 CTATCTTCAACCTGCTCCACTAC
66 CTATCTTCAACCTGCTCCACTAC
*
42771784 AACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTG
1 AACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTG
42771849 CTATCTTCAACCTGCTCCACTAC
66 CTATCTTCAACCTGCTCCACTAC
* * * * * *
42771872 AACCCAGGGAGGAAAGGCTGGTATCTTCGATCTGCTTTATTGTCGATGCAGGAAGGCAAGATTTG
1 AACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTG
42771937 CTATCTTCAACCTGCTCCACTAC
66 CTATCTTCAACCTGCTCCACTAC
* * *
42771960 AACCCAGAGAGGCAAGGCTGGTATCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTG
1 AACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTG
* * * *
42772025 TTATTTTCAACCTGCTCCGCTGC
66 CTATCTTCAACCTGCTCCACTAC
* *
42772048 AAACCAGGAAGGCAAGGCT
1 AACCCAGGGAGGCAAGGCT
42772067 TTGTGATTTC
Statistics
Matches: 256, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 256 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (88 bp):
AACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTG
CTATCTTCAACCTGCTCCACTAC
Found at i:42771799 original size:44 final size:44
Alignment explanation
Indices: 42771744--42772063 Score: 218
Period size: 44 Copynumber: 7.3 Consensus size: 44
42771734 ACTGTGGGTA
42771744 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
* * * * * * * ****
42771788 CAGGGAGGCAAG-GCTGGTATCTTCGATCTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT-ACAACC
42771832 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
* * * * * * ** * * * **
42771876 CAGGGAGGAAAG-GCTGGTATCTTCGATCTGCTTTATTGTCGATG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT-ACAACC
*
42771920 CAGGAAGGCAAGATTTGCTATCTTCAACCTGCTCCACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
* * * * * ***
42771964 CA-GAGAGGCAAG-GCTGGTATCTTCGATCTGCTTCACCGT-CAGTA
1 CAGGA-AGGCAAGATCTGCTATCTTCAACCTGCTCCA-C-TACAACC
* * * * *
42772008 CAGGAAGGCAAGATCTGTTATTTTCAACCTGCTCCGCTGCAAAC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
42772052 CAGGAAGGCAAG
1 CAGGAAGGCAAG
42772064 GCTTTGTGAT
Statistics
Matches: 198, Mismatches: 68, Indels: 20
0.69 0.24 0.07
Matches are distributed among these distances:
43 58 0.29
44 84 0.42
45 56 0.28
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
Found at i:42771995 original size:43 final size:42
Alignment explanation
Indices: 42771744--42771987 Score: 164
Period size: 43 Copynumber: 5.5 Consensus size: 42
42771734 ACTGTGGGTA
* *
42771744 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
1 CAGG-AGGCAAG-GCTGGTATCTTCAACCTGCTCCACTACAACC
* * * * ****
42771788 CAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTG
1 CA-GGAGGCAAGGCTGGTATCTTCAACCTGCTCCACT-ACAACC
* *
42771832 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
1 CAGG-AGGCAAG-GCTGGTATCTTCAACCTGCTCCACTACAACC
* * * ** * * * **
42771876 CAGGGAGGAAAGGCTGGTATCTTCGATCTGCTTTATTGTCGATG
1 CA-GGAGGCAAGGCTGGTATCTTCAACCTGCTCCACT-ACAACC
** *
42771920 CAGGAAGGCAAGATTTGCTATCTTCAACCTGCTCCACTACAACC
1 CAGG-AGGCAAG-GCTGGTATCTTCAACCTGCTCCACTACAACC
42771964 CAGAGAGGCAAGGCTGGTATCTTC
1 CAG-GAGGCAAGGCTGGTATCTTC
42771988 GATCTGCTTC
Statistics
Matches: 143, Mismatches: 48, Indels: 19
0.68 0.23 0.09
Matches are distributed among these distances:
43 51 0.36
44 50 0.35
45 42 0.29
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (42 bp):
CAGGAGGCAAGGCTGGTATCTTCAACCTGCTCCACTACAACC
Found at i:42779006 original size:19 final size:19
Alignment explanation
Indices: 42778978--42779052 Score: 96
Period size: 19 Copynumber: 3.8 Consensus size: 19
42778968 AATTATATCT
*
42778978 TCCAAAATTGCATATCATA
1 TCCAAGATTGCATATCATA
*
42778997 TCCAAGATTGCATATATAATA
1 TCCAAGATTGC--ATATCATA
*
42779018 TCTAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
*
42779037 TCTAAGATTGCATATC
1 TCCAAGATTGCATATC
42779053 CTTGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 33 0.66
21 17 0.34
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:42779018 original size:21 final size:21
Alignment explanation
Indices: 42778989--42779051 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
42778979 CCAAAATTGC
*
42778989 ATATCATATCCAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
*
42779010 ATATAATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
42779029 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
42779050 AT
1 AT
42779052 CCTTGAAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 18 0.49
21 19 0.51
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:42780311 original size:27 final size:27
Alignment explanation
Indices: 42780273--42780335 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
42780263 TTTTAGTCTT
*
42780273 GTGCCGCCAATGGGAATGGCACCACCG
1 GTGCCGCCAATGAGAATGGCACCACCG
42780300 GTGCCGCCAATGAGAATGGCACCACCG
1 GTGCCGCCAATGAGAATGGCACCACCG
42780327 GTGCCGCCA
1 GTGCCGCCA
42780336 TTCCATTACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.22, C:0.35, G:0.32, T:0.11
Consensus pattern (27 bp):
GTGCCGCCAATGAGAATGGCACCACCG
Found at i:42780404 original size:11 final size:11
Alignment explanation
Indices: 42780385--42780432 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 11
42780375 ATAAATAATT
42780385 TTTTA-TATTA
1 TTTTAGTATTA
*
42780395 TTTTAGTATTT
1 TTTTAGTATTA
*
42780406 TTTTA-T-TTC
1 TTTTAGTATTA
42780415 TTTT-GTATTA
1 TTTTAGTATTA
42780425 TTTTAGTA
1 TTTTAGTA
42780433 AAAAACCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
9 7 0.23
10 12 0.39
11 12 0.39
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.71
Consensus pattern (11 bp):
TTTTAGTATTA
Found at i:42780422 original size:19 final size:21
Alignment explanation
Indices: 42780383--42780429 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
42780373 TAATAAATAA
42780383 TTTTTTATATTATTTTAGTAT
1 TTTTTTATATTATTTTAGTAT
*
42780404 TTTTTTAT-TTCTTTT-GTAT
1 TTTTTTATATTATTTTAGTAT
*
42780423 TATTTTA
1 TTTTTTA
42780430 GTAAAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.42
20 6 0.25
21 8 0.33
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTTTATATTATTTTAGTAT
Found at i:42785770 original size:24 final size:24
Alignment explanation
Indices: 42785725--42785770 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42785715 ATTTAAATAT
*
42785725 AAAATTTAATCCACAACTTAACCG
1 AAAATTTAATCCACAACATAACCG
42785749 AAAATTTAATCC-CTAACATAAC
1 AAAATTTAATCCAC-AACATAAC
42785771 TTCCCCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATTTAATCCACAACATAACCG
Found at i:42786427 original size:71 final size:71
Alignment explanation
Indices: 42786345--42786478 Score: 232
Period size: 71 Copynumber: 1.9 Consensus size: 71
42786335 AACCGCCACA
42786345 AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTCGTGTTAAGTG
1 AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTCGTGTTAAGTG
42786410 ATTAAG
66 ATTAAG
* * * *
42786416 AGAGTAAGTAAGACTTTGATTTTCTGATATTCTGTCATGTATTAAGGAGAAGTTTGTGTTAAG
1 AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTCGTGTTAAG
42786479 AAATTAACGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (71 bp):
AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTCGTGTTAAGTG
ATTAAG
Found at i:42791460 original size:20 final size:19
Alignment explanation
Indices: 42791430--42791490 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
42791420 TTTACATCTC
42791430 AAAAAAT-TATAAAAAAACT
1 AAAAAATATAT-AAAAAACT
*
42791449 AAAAAATATATAATAAACT
1 AAAAAATATATAAAAAACT
*
42791468 TAAAAA-ATATAAAAAACT
1 AAAAAATATATAAAAAACT
42791486 AAAAA
1 AAAAA
42791491 CCTTAAACCC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 15 0.41
19 19 0.51
20 3 0.08
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAAATATATAAAAAACT
Found at i:42791680 original size:29 final size:28
Alignment explanation
Indices: 42791634--42791690 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
42791624 ATTTTTTTTC
*
42791634 TTTAAAAAAGGGCCTAATTAAGTAAATTT
1 TTTAAAAAAGGGCATAATTAA-TAAATTT
* * *
42791663 TTTAAAAATGGGTATAATTTATAAATTT
1 TTTAAAAAAGGGCATAATTAATAAATTT
42791691 AGTCAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (28 bp):
TTTAAAAAAGGGCATAATTAATAAATTT
Found at i:42794610 original size:42 final size:41
Alignment explanation
Indices: 42794549--42794757 Score: 196
Period size: 42 Copynumber: 5.0 Consensus size: 41
42794539 AACTTGCACA
* *
42794549 ATGCCATAT-CCCAGATATGGTCTTACATGCTATCAT-ATATCG
1 ATGCCA-ATGCCCAGCTATGGTCTTACATG-AATC-TCATATCG
42794591 ATGCCAATAG-CCAGCTATGGTCTTACATGAATCTCATATCG
1 ATGCCAAT-GCCCAGCTATGGTCTTACATGAATCTCATATCG
* *
42794632 ATGCCAATGTCCCAGAC-ATGGTCTTACATGAATCTCGTATTG
1 ATGCCAATG-CCCAG-CTATGGTCTTACATGAATCTCATATCG
* * *
42794674 ATGCCAATGTCCCAGAC-ATGGTCTTAGATGAATCACATAACG
1 ATGCCAATG-CCCAG-CTATGGTCTTACATGAATCTCATATCG
* *
42794716 ATGCCAATGTCCCAGAC-ATGGTCTTACACGTAATCACATATC
1 ATGCCAATG-CCCAG-CTATGGTCTTACATG-AATCTCATATC
42794758 AGTATCCTAA
Statistics
Matches: 148, Mismatches: 12, Indels: 13
0.86 0.07 0.08
Matches are distributed among these distances:
40 2 0.01
41 19 0.13
42 116 0.78
43 11 0.07
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (41 bp):
ATGCCAATGCCCAGCTATGGTCTTACATGAATCTCATATCG
Found at i:42794656 original size:84 final size:83
Alignment explanation
Indices: 42794549--42794757 Score: 246
Period size: 84 Copynumber: 2.5 Consensus size: 83
42794539 AACTTGCACA
* * *
42794549 ATGCC-ATATCCCAGATATGGTCTTACATGCTATCAT-ATATCGATGCCAATAG-CCAG-CTATG
1 ATGCCAATGTCCCAGACATGGTCTTACATG-AATC-TCATATCGATGCCAAT-GCCCAGAC-ATG
* *
42794610 GTCTTACATGAATCTCATATCG
62 GTCTTACATGAATCACATAACG
* *
42794632 ATGCCAATGTCCCAGACATGGTCTTACATGAATCTCGTATTGATGCCAATGTCCCAGACATGGTC
1 ATGCCAATGTCCCAGACATGGTCTTACATGAATCTCATATCGATGCCAATG-CCCAGACATGGTC
*
42794697 TTAGATGAATCACATAACG
65 TTACATGAATCACATAACG
* *
42794716 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATC
1 ATGCCAATGTCCCAGACATGGTCTTACATG-AATCTCATATC
42794758 AGTATCCTAA
Statistics
Matches: 108, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
82 2 0.02
83 20 0.19
84 77 0.71
85 9 0.08
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (83 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGAATCTCATATCGATGCCAATGCCCAGACATGGTCT
TACATGAATCACATAACG
Found at i:42795041 original size:20 final size:19
Alignment explanation
Indices: 42795010--42795061 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
42795000 ATCTATATAA
* *
42795010 TAACAAAATTTACT-TATT
1 TAACACAATTTACTCAATT
42795028 TAATCACTAATTTACTCAATT
1 TAA-CAC-AATTTACTCAATT
42795049 TAACACAATTTAC
1 TAACACAATTTAC
42795062 ACATTAGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 3 0.10
19 9 0.31
20 11 0.38
21 6 0.21
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
TAACACAATTTACTCAATT
Done.