Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 71 of 218
Found at i:21202370 original size:10 final size:10
Alignment explanation
Indices: 21202304--21202372 Score: 68
Period size: 10 Copynumber: 6.5 Consensus size: 10
21202294 TAAAGGAAGG
*
21202304 AAAAAAAGGA
1 AAAAAAAAGA
21202314 AAAAAGAAAGA
1 AAAAA-AAAGA
21202325 AAAAAAGAA-A
1 AAAAAA-AAGA
*
21202335 AAAAAAGAGA
1 AAAAAAAAGA
21202345 AAAGAGAAAAGA
1 AAA-A-AAAAGA
21202357 AAAAAAAAGCA
1 AAAAAAAAG-A
21202368 AAAAA
1 AAAAA
21202373 GGTCGTGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
9 1 0.02
10 22 0.44
11 19 0.38
12 8 0.16
ACGTcount: A:0.83, C:0.01, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:21202372 original size:12 final size:11
Alignment explanation
Indices: 21202313--21202364 Score: 68
Period size: 12 Copynumber: 4.5 Consensus size: 11
21202303 GAAAAAAAGG
21202313 AAAAAAGAAAGA
1 AAAAAAGAAA-A
21202325 AAAAAAGAAAA
1 AAAAAAGAAAA
21202336 AAAAAGAGAAAA
1 AAAAA-AGAAAA
*
21202348 GAGAAAAGAAAA
1 -AAAAAAGAAAA
21202360 AAAAA
1 AAAAA
21202365 GCAAAAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
11 10 0.28
12 22 0.61
13 4 0.11
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:21203297 original size:20 final size:19
Alignment explanation
Indices: 21203272--21203397 Score: 68
Period size: 20 Copynumber: 6.6 Consensus size: 19
21203262 CGTTCGAAAC
*
21203272 AATACAAAAAATTATGATA
1 AATACAAAAAATTATGAGA
21203291 GAATACAAATAAA-TATGAGA
1 -AATACAAA-AAATTATGAGA
*
21203311 AAGTACAAAAAA-TATAAGGA
1 AA-TACAAAAAATTATGA-GA
* *
21203331 AGTAC-CAAAATTATGAGA
1 AATACAAAAAATTATGAGA
* *
21203349 AAGTACCAAAACTTA-GATG-
1 AA-TACAAAAAATTATGA-GA
*
21203368 --TATAAAAAATTATGAGA
1 AATACAAAAAATTATGAGA
21203385 GAATACCAAAAAA
1 -AATA-CAAAAAA
21203398 AAAATGAGGA
Statistics
Matches: 81, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
16 10 0.12
17 2 0.02
18 7 0.09
19 21 0.26
20 32 0.40
21 9 0.11
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21
Consensus pattern (19 bp):
AATACAAAAAATTATGAGA
Found at i:21203325 original size:19 final size:19
Alignment explanation
Indices: 21203274--21203359 Score: 84
Period size: 19 Copynumber: 4.4 Consensus size: 19
21203264 TTCGAAACAA
*
21203274 TACAAAAAATTATGATAGAA-
1 TACAAAAAA-TATGAGA-AAG
21203294 TACAAATAAATATGAGAAAG
1 TACAAA-AAATATGAGAAAG
* *
21203314 TACAAAAAATATAAGGAAG
1 TACAAAAAATATGAGAAAG
* *
21203333 TACCAAAATTATGAGAAAG
1 TACAAAAAATATGAGAAAG
21203352 TACCAAAA
1 TA-CAAAA
21203360 CTTAGATGTA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
19 30 0.55
20 22 0.40
21 3 0.05
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.20
Consensus pattern (19 bp):
TACAAAAAATATGAGAAAG
Found at i:21203424 original size:20 final size:18
Alignment explanation
Indices: 21203272--21203466 Score: 81
Period size: 19 Copynumber: 10.1 Consensus size: 18
21203262 CGTTCGAAAC
*
21203272 AATACAAAAAATTATGATAG
1 AATAC-AAAAATTATGA-GG
* *
21203292 AATACAAATAAATATGAGA
1 AATACAAA-AATTATGAGG
* *
21203311 AAGTACAAAAAATATAAGG
1 AA-TACAAAAATTATGAGG
* *
21203330 AAGTACCAAAATTATGAGA
1 AA-TACAAAAATTATGAGG
* *
21203349 AAGTACCAAAACTTA-GATG
1 AA-TA-CAAAAATTATGAGG
*
21203368 TATA-AAAAATTATGAGAG
1 AATACAAAAATTATGAG-G
**
21203386 AATACCAAAAAAAAAATGAGG
1 AATA-C--AAAAATTATGAGG
21203407 AAGTAGCAAAAATTATGATCGG
1 AA-TA-CAAAAATTATGA--GG
*
21203429 -ATACCAAAAGTTATGAGG
1 AATA-CAAAAATTATGAGG
* *
21203447 GATAGCAAAAAATATGAGG
1 AATA-CAAAAATTATGAGG
21203466 A
1 A
21203467 TGTAAATGTA
Statistics
Matches: 134, Mismatches: 28, Indels: 27
0.71 0.15 0.14
Matches are distributed among these distances:
16 7 0.05
17 2 0.01
18 8 0.06
19 51 0.38
20 47 0.35
21 4 0.03
22 15 0.11
ACGTcount: A:0.55, C:0.08, G:0.17, T:0.20
Consensus pattern (18 bp):
AATACAAAAATTATGAGG
Found at i:21203464 original size:19 final size:19
Alignment explanation
Indices: 21203394--21203465 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 19
21203384 AGAATACCAA
* *
21203394 AAAAAAAATGAGGAAGTAGC
1 AAAAAATATGAGGGA-TAGC
* * *
21203414 AAAAATTATGATCGGATACC
1 AAAAAATATGA-GGGATAGC
**
21203434 AAAAGTTATGAGGGATAGC
1 AAAAAATATGAGGGATAGC
21203453 AAAAAATATGAGG
1 AAAAAATATGAGG
21203466 ATGTAAATGT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
19 17 0.41
20 22 0.54
21 2 0.05
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (19 bp):
AAAAAATATGAGGGATAGC
Found at i:21203500 original size:20 final size:22
Alignment explanation
Indices: 21203470--21203515 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
21203460 ATGAGGATGT
21203470 AAATGTATGA-GG-ATACATAAA
1 AAATGTATGAGGGAATAC-TAAA
21203491 AAAT-TATGAGGGAATACTAAA
1 AAATGTATGAGGGAATACTAAA
21203512 AAAT
1 AAAT
21203516 ATTAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.17, T:0.24
Consensus pattern (22 bp):
AAATGTATGAGGGAATACTAAA
Found at i:21203641 original size:19 final size:16
Alignment explanation
Indices: 21203597--21203629 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21203587 AAAGTACAAA
21203597 AAAAATATGAGGATGT
1 AAAAATATGAGGATGT
*
21203613 AAAAATATGATGATGT
1 AAAAATATGAGGATGT
21203629 A
1 A
21203630 CCAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (16 bp):
AAAAATATGAGGATGT
Found at i:21203658 original size:57 final size:59
Alignment explanation
Indices: 21203539--21203657 Score: 147
Period size: 56 Copynumber: 2.1 Consensus size: 59
21203529 AGAATTCCAT
* *
21203539 AAAACATGAGGAAGTATAAAACAATGAGGATGTACCAATAAATTTGGGAAAGTACAAAA
1 AAAACATGAGGAAGTATAAAACAATGAGGATGTACCAATAAATATGAGAAAGTACAAAA
* * * *
21203598 AAAATATGAGGATGTA-AAAA-TATGATGATGTACCAA-AAATATGAGAGAA-TACAAAA
1 AAAACATGAGGAAGTATAAAACAATGAGGATGTACCAATAAATATGAGA-AAGTACAAAA
21203654 AAAA
1 AAAA
21203658 AAAAAACAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
56 19 0.36
57 16 0.30
58 4 0.08
59 14 0.26
ACGTcount: A:0.55, C:0.07, G:0.18, T:0.19
Consensus pattern (59 bp):
AAAACATGAGGAAGTATAAAACAATGAGGATGTACCAATAAATATGAGAAAGTACAAAA
Found at i:21203758 original size:17 final size:18
Alignment explanation
Indices: 21203725--21203760 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21203715 TCATAAAACC
*
21203725 TGAGGAAGTACCAAAAAA
1 TGAGAAAGTACCAAAAAA
21203743 TGAGAAAGTA-CAAAAAA
1 TGAGAAAGTACCAAAAAA
21203760 T
1 T
21203761 TATGAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.58, C:0.08, G:0.19, T:0.14
Consensus pattern (18 bp):
TGAGAAAGTACCAAAAAA
Found at i:21203767 original size:20 final size:20
Alignment explanation
Indices: 21203725--21203830 Score: 94
Period size: 20 Copynumber: 5.2 Consensus size: 20
21203715 TCATAAAACC
* *
21203725 TGAGGAAGTACCAAAAA--A
1 TGAGAAAGTACAAAAAATTA
21203743 TGAGAAAGTACAAAAAATTA
1 TGAGAAAGTACAAAAAATTA
21203763 TGAGAGAA-TACACAAAAAATATA
1 TGAGA-AAGT--ACAAAAAAT-TA
21203786 TGA-AAATGTACAAAAAATTA
1 TGAGAAA-GTACAAAAAATTA
* **
21203806 TGAGGAAGTGTAAAAAATTA
1 TGAGAAAGTACAAAAAATTA
21203826 TGAGA
1 TGAGA
21203831 GAATACCAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
18 15 0.21
20 27 0.37
21 15 0.21
22 10 0.14
23 6 0.08
ACGTcount: A:0.57, C:0.06, G:0.18, T:0.20
Consensus pattern (20 bp):
TGAGAAAGTACAAAAAATTA
Found at i:21214568 original size:21 final size:21
Alignment explanation
Indices: 21214544--21214599 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
21214534 CACCATTGTT
*
21214544 TCTAATCTCACTGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
21214565 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
21214586 ACTAATCTCACCGC
1 TCTAATCTCACCGC
21214600 CACCGCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:21217058 original size:49 final size:48
Alignment explanation
Indices: 21216986--21217144 Score: 212
Period size: 49 Copynumber: 3.2 Consensus size: 48
21216976 GAACTTGTAC
*
21216986 ATTCTACCATCCTGGTTGGCCCGACAACGATTGCTTTCACTATCTGCAT
1 ATTCTACCATCCTGG-TGGCCCGACAACGATTGCTTTCACTATTTGCAT
* *
21217035 ATTCTACCATCCCAGGTGGCCCGACAACGATAGCTTTCACTATTTGCAT
1 ATTCTACCAT-CCTGGTGGCCCGACAACGATTGCTTTCACTATTTGCAT
* * * *
21217084 ATTCTACCATCCTGAATGGCTCGACAATGA-TGATTTCCACTATTTGCAT
1 ATTCTACCATCCTG-GTGGCCCGACAACGATTGCTTT-CACTATTTGCAT
21217133 ATTCTACCATCC
1 ATTCTACCATCC
21217145 CGAGTGACCC
Statistics
Matches: 98, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
48 7 0.07
49 87 0.89
50 4 0.04
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (48 bp):
ATTCTACCATCCTGGTGGCCCGACAACGATTGCTTTCACTATTTGCAT
Found at i:21219307 original size:41 final size:41
Alignment explanation
Indices: 21219270--21219415 Score: 213
Period size: 41 Copynumber: 3.6 Consensus size: 41
21219260 GACTATACGT
21219270 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAGGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAGGC
21219311 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAGGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAGGC
* * ** *
21219352 CTAGCAGGCTAAGTGCCGGTGAACGGAATTAAACTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAGGC
* *
21219393 CTATCAGG-TGAAGTGCCAGTGAA
1 CTAGCAGGCT-AAGTGCCGGTGAA
21219416 TCTGTTTAAA
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
40 1 0.01
41 96 0.99
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAGGC
Found at i:21220377 original size:49 final size:49
Alignment explanation
Indices: 21220312--21220526 Score: 277
Period size: 49 Copynumber: 4.4 Consensus size: 49
21220302 GGGTGTTACA
* * * *
21220312 CCGACAATGATGGTTTTCACTATTTGCATATTTTACCATCTTGGGTGGC
1 CCGACAACGATGGTTTTCACTATTTACATATTCTACCATCCTGGGTGGC
* **
21220361 CCGACAACGATGGTTTTCACTATTTGCATATTCTACCATCCCAGGTGGC
1 CCGACAACGATGGTTTTCACTATTTACATATTCTACCATCCTGGGTGGC
* * * * *
21220410 TCGATAACGATAGTTTTCAGTATTTACATATTCTACCATCTTGGGTGGC
1 CCGACAACGATGGTTTTCACTATTTACATATTCTACCATCCTGGGTGGC
* * *
21220459 CCGACAACAATGGCTTTCACTATTTACATATTCTACCATCCTGAGTGGC
1 CCGACAACGATGGTTTTCACTATTTACATATTCTACCATCCTGGGTGGC
**
21220508 CTAACAACGATGGTTTTCA
1 CCGACAACGATGGTTTTCA
21220527 ATCACTATAT
Statistics
Matches: 141, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 141 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (49 bp):
CCGACAACGATGGTTTTCACTATTTACATATTCTACCATCCTGGGTGGC
Found at i:21224369 original size:12 final size:12
Alignment explanation
Indices: 21224341--21224384 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
21224331 ATGTTATTTT
*
21224341 ATAATAAAA-AC
1 ATAATAAAAGAA
21224352 ATAATAAAAGAA
1 ATAATAAAAGAA
**
21224364 ATAATAAAAGTT
1 ATAATAAAAGAA
21224376 ATAATAAAA
1 ATAATAAAA
21224385 AAAGGAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (12 bp):
ATAATAAAAGAA
Found at i:21232609 original size:15 final size:17
Alignment explanation
Indices: 21232569--21232610 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
21232559 GAAAGTGTTT
*
21232569 TGAGACTCACATGGCCG
1 TGAGACTCACACGGCCG
*
21232586 TGTGACTCACACGG-C-
1 TGAGACTCACACGGCCG
21232601 TGAGACTCAC
1 TGAGACTCAC
21232611 GCCCGTGTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 1 0.05
17 12 0.55
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (17 bp):
TGAGACTCACACGGCCG
Found at i:21236068 original size:27 final size:27
Alignment explanation
Indices: 21236027--21236114 Score: 113
Period size: 27 Copynumber: 3.3 Consensus size: 27
21236017 TTGTTACAAC
* **
21236027 TATTCTTTTAGAGTTCGCCATGAAGGT
1 TATTCTTTTATAGTTCGCCACAAAGGT
* *
21236054 TATTCTTTTTTAGTTCGCCACAAAGGC
1 TATTCTTTTATAGTTCGCCACAAAGGT
* *
21236081 TATTCTTTCATAGTTCGCAACAAAGGT
1 TATTCTTTTATAGTTCGCCACAAAGGT
21236108 TATTCTT
1 TATTCTT
21236115 CATGTCATGT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (27 bp):
TATTCTTTTATAGTTCGCCACAAAGGT
Found at i:21236865 original size:49 final size:50
Alignment explanation
Indices: 21236786--21236886 Score: 161
Period size: 49 Copynumber: 2.0 Consensus size: 50
21236776 CAATAGCAAC
* *
21236786 CACTGATTTGCATATTCTACCATCCTGGGTGGCCTGACAATGATGGTTTT
1 CACTGATTTGCATATTCTACCATCCTGGGTGGCCTGACAACGATGATTTT
21236836 CACT-ATTTGCATATTCTACCATTCC-GGGTGGCCTGACAACGATGATTTT
1 CACTGATTTGCATATTCTACCA-TCCTGGGTGGCCTGACAACGATGATTTT
21236885 CA
1 CA
21236887 ATCACTATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
49 41 0.85
50 7 0.15
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (50 bp):
CACTGATTTGCATATTCTACCATCCTGGGTGGCCTGACAACGATGATTTT
Found at i:21251033 original size:17 final size:17
Alignment explanation
Indices: 21251011--21251045 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21251001 CTAACTTTAT
21251011 GAAAAAAAAATATTGTA
1 GAAAAAAAAATATTGTA
**
21251028 GAAAAAAATTTATTGTA
1 GAAAAAAAAATATTGTA
21251045 G
1 G
21251046 CCATTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (17 bp):
GAAAAAAAAATATTGTA
Found at i:21251247 original size:23 final size:22
Alignment explanation
Indices: 21251202--21251247 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
21251192 ACTTATTAAA
*
21251202 ATTTTTAAAAATTAAAAGTATT
1 ATTTTTAAAAATTAAAAATATT
21251224 ATTTTTAAAAATTAAAAATCATT
1 ATTTTTAAAAATTAAAAAT-ATT
21251247 A
1 A
21251248 AAATTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTTTAAAAATTAAAAATATT
Found at i:21253815 original size:13 final size:13
Alignment explanation
Indices: 21253799--21253847 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
21253789 TTTAAACCAA
* *
21253799 ACTTTTTAAAAGT
1 ACTTTTCAAAAGC
*
21253812 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
21253825 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
21253838 ACTTTTCAAA
1 ACTTTTCAAA
21253848 GGCAATGAAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:21254406 original size:20 final size:19
Alignment explanation
Indices: 21254381--21254428 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
21254371 AGGATAAATT
21254381 AAAAAAAATGA-AGAAATACC
1 AAAAAAAATGAGAG-AATA-C
*
21254401 AAAAAAATTGAGAGAATAC
1 AAAAAAAATGAGAGAATAC
21254420 AAAAAAAAT
1 AAAAAAAAT
21254429 AAAAGAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 14 0.56
21 2 0.08
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.12
Consensus pattern (19 bp):
AAAAAAAATGAGAGAATAC
Found at i:21255087 original size:39 final size:37
Alignment explanation
Indices: 21255044--21255155 Score: 111
Period size: 36 Copynumber: 3.0 Consensus size: 37
21255034 ATTTATAAGA
*
21255044 AAGTACCAAAATTTATGAGCGAATACAAAAAGGATGAGG
1 AAGTACCAAAAATTATGAG-GAATACAAAAA-GATGAGG
* ** * *
21255083 AAGTACCAAAAGTTATGAGG-ATGTAAATATATGAGG
1 AAGTACCAAAAATTATGAGGAATACAAAAAGATGAGG
* *
21255119 ATGCACCAAAAATTATGAGGGAATACAAAAA-ATGAGG
1 AAGTACCAAAAATTATGA-GGAATACAAAAAGATGAGG
21255156 GGATACTAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
36 21 0.35
37 14 0.23
38 7 0.12
39 18 0.30
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.20
Consensus pattern (37 bp):
AAGTACCAAAAATTATGAGGAATACAAAAAGATGAGG
Found at i:21255100 original size:20 final size:20
Alignment explanation
Indices: 21255024--21255103 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
21255014 AAATACAAGT
* * * *
21255024 AAGTACCCAAATTTATAAGA
1 AAGTACCAAAAGTTATGAGG
*
21255044 AAGTACCAAAATTTATGAGCG
1 AAGTACCAAAAGTTATGAG-G
* *
21255065 AA-TACAAAAAG-GATGAGG
1 AAGTACCAAAAGTTATGAGG
21255083 AAGTACCAAAAGTTATGAGG
1 AAGTACCAAAAGTTATGAGG
21255103 A
1 A
21255104 TGTAAATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
18 3 0.06
19 13 0.27
20 31 0.63
21 2 0.04
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGTACCAAAAGTTATGAGG
Found at i:21255149 original size:20 final size:18
Alignment explanation
Indices: 21255125--21255201 Score: 57
Period size: 19 Copynumber: 4.1 Consensus size: 18
21255115 GAGGATGCAC
*
21255125 CAAAAATTATGAGGGAATA
1 CAAAAA-TATGAGAGAATA
* *
21255144 CAAAAA-ATGAGGGGATA
1 CAAAAATATGAGAGAATA
* *
21255161 CTAAAAAATATTAGAAAATA
1 C--AAAAATATGAGAGAATA
21255181 CCAAAAATTATGAGAGAATA
1 -CAAAAA-TATGAGAGAATA
21255201 C
1 C
21255202 CATAAAACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
17 11 0.24
19 17 0.37
20 17 0.37
21 1 0.02
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.19
Consensus pattern (18 bp):
CAAAAATATGAGAGAATA
Found at i:21255155 original size:17 final size:18
Alignment explanation
Indices: 21255133--21255169 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
21255123 ACCAAAAATT
21255133 ATGAGGGAATAC-AAAAA
1 ATGAGGGAATACTAAAAA
*
21255150 ATGAGGGGATACTAAAAA
1 ATGAGGGAATACTAAAAA
21255168 AT
1 AT
21255170 ATTAGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.54, C:0.05, G:0.24, T:0.16
Consensus pattern (18 bp):
ATGAGGGAATACTAAAAA
Found at i:21255202 original size:20 final size:20
Alignment explanation
Indices: 21255123--21255208 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 20
21255113 ATGAGGATGC
*
21255123 ACCAAAAATTATGAGGGAAT
1 ACCAAAAATTATGAGAGAAT
* *
21255143 A-CAAAAA--ATGAGGGGAT
1 ACCAAAAATTATGAGAGAAT
* * * *
21255160 ACTAAAAAATATTAGAAAAT
1 ACCAAAAATTATGAGAGAAT
21255180 ACCAAAAATTATGAGAGAAT
1 ACCAAAAATTATGAGAGAAT
21255200 ACCATAAAA
1 ACCA-AAAA
21255209 CTTGAGGAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
17 10 0.19
18 5 0.10
19 6 0.12
20 27 0.52
21 4 0.08
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (20 bp):
ACCAAAAATTATGAGAGAAT
Found at i:21255355 original size:154 final size:151
Alignment explanation
Indices: 21255098--21255387 Score: 379
Period size: 154 Copynumber: 1.9 Consensus size: 151
21255088 CCAAAAGTTA
* * * * *
21255098 TGAGGATGTAAATATATGAGGATGCACCAAAAATTATGAGGGAATACAAAAAATGAGGGGATACT
1 TGAGGACGTAAAAATATGAGGATGCACCAAAAATTATGAGAGAATAAAAAAAACGAGGGGATACT
*
21255163 AAAAAATATTAGAAAATACCAAAAATTATGAGAGAATACCATAAAACTTGAGGAAGTATAAAAAA
66 AAAAAATATGAGAAAATACCAAAAATTATGAGAGAATACCATAAAACTTGAGGAAGTA-AAAAAA
21255228 AAATGAGGATGTACCGATAATT
130 AAATGAGGATGTACCGATAATT
* *
21255250 TGAGGACGTAAAAATATGATGATGTACCAAAAA-TATGAGAGAATGCCAAAAAAACACGAGGGGA
1 TGAGGACGTAAAAATATGAGGATGCACCAAAAATTATGAGAGAAT---AAAAAAA-ACGAGGGGA
* * * * **
21255314 TA-TTAAAAATATGATG-AAGTACTAAATATTATGAGAGAATACCATAAAACTTGAGGAAGTACC
62 TACTAAAAAATATGA-GAAAATACCAAAAATTATGAGAGAATACCATAAAACTTGAGGAAGTAAA
21255377 AAAAAAATGAG
126 AAAAAAATGAG
21255388 AAAGTACAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
151 10 0.08
152 29 0.24
153 11 0.09
154 58 0.49
155 11 0.09
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.21
Consensus pattern (151 bp):
TGAGGACGTAAAAATATGAGGATGCACCAAAAATTATGAGAGAATAAAAAAAACGAGGGGATACT
AAAAAATATGAGAAAATACCAAAAATTATGAGAGAATACCATAAAACTTGAGGAAGTAAAAAAAA
AATGAGGATGTACCGATAATT
Found at i:21255397 original size:18 final size:19
Alignment explanation
Indices: 21255365--21255400 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21255355 CCATAAAACT
*
21255365 TGAGGAAGTACCAAAAAAA
1 TGAGAAAGTACCAAAAAAA
21255384 TGAGAAAGTA-CAAAAAA
1 TGAGAAAGTACCAAAAAA
21255401 TTATGAGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.08, G:0.19, T:0.11
Consensus pattern (19 bp):
TGAGAAAGTACCAAAAAAA
Found at i:21255406 original size:20 final size:20
Alignment explanation
Indices: 21255318--21255408 Score: 66
Period size: 20 Copynumber: 4.6 Consensus size: 20
21255308 AGGGGATATT
*
21255318 AAAAATATGATG-AAGTACTA
1 AAAAATATGA-GAAAGTACCA
* *
21255338 AATATTATGAGAGAA-TACCA
1 AAAAATATGAGA-AAGTACCA
* *
21255358 TAAAACT-TGAGGAAGTACCA
1 -AAAAATATGAGAAAGTACCA
21255378 AAAAA-ATGAGAAAGTA-CA
1 AAAAATATGAGAAAGTACCA
21255396 AAAAATTATGAGA
1 AAAAA-TATGAGA
21255409 GTGTAACACC
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
18 7 0.12
19 16 0.29
20 27 0.48
21 6 0.11
ACGTcount: A:0.55, C:0.08, G:0.16, T:0.21
Consensus pattern (20 bp):
AAAAATATGAGAAAGTACCA
Found at i:21263846 original size:20 final size:19
Alignment explanation
Indices: 21263805--21263846 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
21263795 GGGAATTTAA
* *
21263805 AAAAATTATGAGAAAGTAT
1 AAAAACTATGAGAAAATAT
21263824 AAAAACTATGAGAAAATACT
1 AAAAACTATGAGAAAATA-T
21263844 AAA
1 AAA
21263847 TAACATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (19 bp):
AAAAACTATGAGAAAATAT
Found at i:21265313 original size:20 final size:19
Alignment explanation
Indices: 21265288--21265368 Score: 83
Period size: 20 Copynumber: 4.2 Consensus size: 19
21265278 TTTTTTTATA
21265288 TTTTTAATTTTAAAATACTT
1 TTTTTAATTTTAAAATA-TT
21265308 TTTTTAATTTTAAAATATT
1 TTTTTAATTTTAAAATATT
** ***
21265327 TTTAAAATACTTTTTTA-ATT
1 TTTTTAAT--TTTAAAATATT
21265347 TTTTTAATTTTAAAATATT
1 TTTTTAATTTTAAAATATT
21265366 TTT
1 TTT
21265369 AAAATAAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
18 4 0.08
19 14 0.29
20 26 0.54
21 4 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTAATTTTAAAATATT
Found at i:21265331 original size:11 final size:11
Alignment explanation
Indices: 21265315--21265374 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
21265305 CTTTTTTTAA
21265315 TTTTAAAATAT
1 TTTTAAAATAT
21265326 TTTTAAAATACT
1 TTTTAAAATA-T
*
21265338 TTTT-TAAT-T
1 TTTTAAAATAT
*
21265347 TTTT----TAA
1 TTTTAAAATAT
21265354 TTTTAAAATAT
1 TTTTAAAATAT
21265365 TTTTAAAATA
1 TTTTAAAATA
21265375 AATTTTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
6 1 0.03
7 4 0.10
9 5 0.12
11 25 0.62
12 5 0.12
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:21265359 original size:39 final size:40
Alignment explanation
Indices: 21265306--21265390 Score: 145
Period size: 39 Copynumber: 2.1 Consensus size: 40
21265296 TTTAAAATAC
21265306 TTTTTTTAATTTTAAAATATTTTTAAAAT-ACTTTTTTAA
1 TTTTTTTAATTTTAAAATATTTTTAAAATAACTTTTTTAA
*
21265345 TTTTTTTAATTTTAAAATATTTTTAAAATAAATTTTTTTAA
1 TTTTTTTAATTTTAAAATATTTTTAAAAT-AACTTTTTTAA
21265386 TTTTT
1 TTTTT
21265391 AAAATAAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
39 29 0.67
41 14 0.33
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATAACTTTTTTAA
Found at i:21265410 original size:22 final size:21
Alignment explanation
Indices: 21265362--21265410 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
21265352 AATTTTAAAA
*
21265362 TATTTTTAAAATAAATTTTTT
1 TATTTTTAAAATAAATTTTTG
21265383 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
21265406 TATTT
1 TATTT
21265411 ATTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:21266071 original size:15 final size:15
Alignment explanation
Indices: 21266053--21266087 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21266043 TGGTTTAAAT
21266053 TTATATATTATCATC
1 TTATATATTATCATC
*
21266068 TTATATATTATTATC
1 TTATATATTATCATC
21266083 -TATAT
1 TTATAT
21266088 TAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATATTATCATC
Found at i:21266359 original size:4 final size:4
Alignment explanation
Indices: 21266350--21266374 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
21266340 AAATATATAC
21266350 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
21266375 TATTCTATTC
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:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:21266915 original size:107 final size:107
Alignment explanation
Indices: 21266729--21266934 Score: 331
Period size: 107 Copynumber: 1.9 Consensus size: 107
21266719 AGGAAAATTT
* ** * **
21266729 TTTCAAAACGAGGCAATGTTTTGTTTTTAGAAAATCGAGAAAATGTGCCCTAACGTGTTGGGTTT
1 TTTCAAAAAGAGGCAATGTTTTGCGTTTAGAAAATCGAGAAAACGTGCCCTAACGTACTGGGTTT
21266794 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAATAA
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAATAA
* *
21266836 TTTCAAAAAGAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTT
1 TTTCAAAAAGAGGCAATGTTTTGCGTTTAGAAAATCGAGAAAACGTGCCCTAACGTACTGGGTTT
*
21266901 CGATTTCTCGTTCGACTAAATAGCCAAATATCCT
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCT
21266935 CTTAAAACTT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 90 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (107 bp):
TTTCAAAAAGAGGCAATGTTTTGCGTTTAGAAAATCGAGAAAACGTGCCCTAACGTACTGGGTTT
CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAATAA
Found at i:21268249 original size:76 final size:76
Alignment explanation
Indices: 21268123--21268272 Score: 282
Period size: 76 Copynumber: 2.0 Consensus size: 76
21268113 TATAAATTCG
*
21268123 ATATTATTTTGACTTAATTTAAGCGTTATAAAAAGGGAGATAACCTAGCATAAGTCTTTCTCCAA
1 ATATTATTTTGACTTAATTTAAGCATTATAAAAAGGGAGATAACCTAGCATAAGTCTTTCTCCAA
*
21268188 ATTAAGTTTCA
66 AGTAAGTTTCA
21268199 ATATTATTTTGACTTAATTTAAGCATTATAAAAAGGGAGATAACCTAGCATAAGTCTTTCTCCAA
1 ATATTATTTTGACTTAATTTAAGCATTATAAAAAGGGAGATAACCTAGCATAAGTCTTTCTCCAA
21268264 AGTAAGTTT
66 AGTAAGTTT
21268273 ATATAAGTTC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (76 bp):
ATATTATTTTGACTTAATTTAAGCATTATAAAAAGGGAGATAACCTAGCATAAGTCTTTCTCCAA
AGTAAGTTTCA
Found at i:21295254 original size:12 final size:12
Alignment explanation
Indices: 21295237--21295266 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
21295227 GAGGATGACC
21295237 AAAAGAAGAAAA
1 AAAAGAAGAAAA
21295249 AAAAGAAGAAAA
1 AAAAGAAGAAAA
21295261 ACAAAG
1 A-AAAG
21295267 CTGTTACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAAA
Found at i:21307938 original size:33 final size:33
Alignment explanation
Indices: 21307901--21307965 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
21307891 CCTTCCCTTT
*
21307901 TCCATA-AGGTAGAAAGCTGGTTTTTGTCATTTC
1 TCCATAGA-GTAGAAAGCTGGATTTTGTCATTTC
*
21307934 TCCATAGAGTAGAAAGTTGGATTTTGTCATTT
1 TCCATAGAGTAGAAAGCTGGATTTTGTCATTT
21307966 TAGATTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (33 bp):
TCCATAGAGTAGAAAGCTGGATTTTGTCATTTC
Found at i:21311276 original size:17 final size:17
Alignment explanation
Indices: 21311254--21311287 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21311244 ATCAAACTCA
21311254 TCTGTCATAATTCTAAG
1 TCTGTCATAATTCTAAG
21311271 TCTGTCATAATTCTAAG
1 TCTGTCATAATTCTAAG
21311288 GCAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (17 bp):
TCTGTCATAATTCTAAG
Found at i:21321665 original size:21 final size:22
Alignment explanation
Indices: 21321639--21321685 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
21321629 CTCTGCTCAA
*
21321639 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
21321660 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
21321682 ACTC
1 ACTC
21321686 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:21326580 original size:72 final size:72
Alignment explanation
Indices: 21326463--21326599 Score: 213
Period size: 72 Copynumber: 1.9 Consensus size: 72
21326453 GGCTCACGGG
* * *
21326463 TCAACGAGTCTAATGCCTCTATCTAAATTGATACCTAAATCAATTCTCGATCCAA-TCAATTTAA
1 TCAACAAGTCTAATACCTCTATCTAAATTGATACCTAAACCAATTCTCGATCCAACT-AATTTAA
21326527 CTAGCTGA
65 CTAGCTGA
* *
21326535 TCAACAAGTCTAATATCTCTCTCTAAATTGATACCTAAACCAATTCTCGATCCAACTAATTTAAC
1 TCAACAAGTCTAATACCTCTATCTAAATTGATACCTAAACCAATTCTCGATCCAACTAATTTAAC
21326600 AATTCGAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 58 0.98
73 1 0.02
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (72 bp):
TCAACAAGTCTAATACCTCTATCTAAATTGATACCTAAACCAATTCTCGATCCAACTAATTTAAC
TAGCTGA
Found at i:21335422 original size:35 final size:35
Alignment explanation
Indices: 21335299--21335463 Score: 165
Period size: 34 Copynumber: 4.8 Consensus size: 35
21335289 TGTTCGCGTT
* **
21335299 TTTCGGGTGGATTAGCTCTTATGAGCACTGGCGTG
1 TTTCGGGTGGATTAGTTCTTATGAGCACTGGTATG
* * *
21335334 TTTCGAG-GGATTAGTTTTTATGAGCAATGG-AGTG
1 TTTCGGGTGGATTAGTTCTTATGAGCACTGGTA-TG
* *
21335368 TTTCAGG-GGATTAGTTCTTATGAGCATTGGTATG
1 TTTCGGGTGGATTAGTTCTTATGAGCACTGGTATG
* * *
21335402 TTTCGGGTGGATTAGCTCTTATGAACACTGGTGTG
1 TTTCGGGTGGATTAGTTCTTATGAGCACTGGTATG
** * *
21335437 TTTTAGGTAGATTAGTTCCTATGAGCA
1 TTTCGGGTGGATTAGTTCTTATGAGCA
21335464 TCAGCGTGCT
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
34 56 0.52
35 51 0.48
ACGTcount: A:0.20, C:0.12, G:0.30, T:0.38
Consensus pattern (35 bp):
TTTCGGGTGGATTAGTTCTTATGAGCACTGGTATG
Found at i:21346000 original size:22 final size:22
Alignment explanation
Indices: 21345961--21346004 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
21345951 GTTTGAGGAA
*
21345961 TATTAACACAATTGCAATAAAT
1 TATTAACACAATTCCAATAAAT
**
21345983 TATTAACACCGTTCCAATAAAT
1 TATTAACACAATTCCAATAAAT
21346005 ACGACAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (22 bp):
TATTAACACAATTCCAATAAAT
Found at i:21350244 original size:45 final size:42
Alignment explanation
Indices: 21350193--21350300 Score: 108
Period size: 45 Copynumber: 2.4 Consensus size: 42
21350183 AATATTGAAT
* *
21350193 ATATATAATATAATATTATTATTAGATATATATTAAAGTTTATAA
1 ATATATAATATAATA--ATT-TTAGACATATATTAAAGTATATAA
* *
21350238 ATATATAGATTCGTAATAATTTTAGACATATATTATAGTATATAA
1 ATATATA-A-T-ATAATAATTTTAGACATATATTAAAGTATATAA
*
21350283 AAATAATAATATAATAAT
1 ATAT-ATAATATAATAAT
21350301 AAATAAATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
43 7 0.13
44 1 0.02
45 32 0.60
46 7 0.13
47 1 0.02
48 5 0.09
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (42 bp):
ATATATAATATAATAATTTTAGACATATATTAAAGTATATAA
Found at i:21354592 original size:24 final size:24
Alignment explanation
Indices: 21354565--21354616 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
21354555 AATCAAAGTC
* *
21354565 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
21354589 AAATATATTGTACTCATAAATACT
1 AAATATATTATACTAATAAATACT
21354613 AAAT
1 AAAT
21354617 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:21360375 original size:13 final size:13
Alignment explanation
Indices: 21360357--21360400 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
21360347 AATAAACAAA
21360357 AAATAAAAAAATC
1 AAATAAAAAAATC
21360370 AAATAAAAAAA-C
1 AAATAAAAAAATC
* *
21360382 AAAGAAAATAAT-
1 AAATAAAAAAATC
21360394 AAATAAA
1 AAATAAA
21360401 TTCAGTCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (13 bp):
AAATAAAAAAATC
Found at i:21366360 original size:49 final size:48
Alignment explanation
Indices: 21366166--21366746 Score: 299
Period size: 44 Copynumber: 12.5 Consensus size: 48
21366156 GTCATCATGG
** * * *
21366166 CAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTT----GAAGCCA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAAAAGCTA
* * * * * *
21366210 TAAATCTTATCTACTTGAATTTACAGT--AG-AG--TAAATTAAAGATA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-AAAAGCTA
** * * *
21366254 CAAATCTTATCTCCCTGAAGTTGTAATGGAGCAGATT---GAAA-CTT
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAAAAGCTA
*
21366298 CAAATCTTATCTCCCTGAATTTACAGTGGAGCAGATTAAAAAATAGCTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAAA-AGCTA
* * *
21366347 CAAATCTTATCTCCCTGAAGTTACAATGGAGCAGATT---GAAA-CTT
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAAAAGCTA
*
21366391 CAAATCTTATCTCCCTGAATTTACAGTGGAGCAGATTAAAAAATAGCTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAAA-AGCTA
* * * * * * *
21366440 CAAATCTTATTTTCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA---AAAAGCTA
*
21366491 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT----GAAGCTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAAAAGCTA
* * ** * * * *
21366535 CAAATTTTAT-TCCATTGAAGTTGTAGTGAAACAGATTAAATCTACAAGTTA
1 CAAATCTTATCTCC-CTGAAGTTACAGTGGAGCAGATTAAA---AAAAGCTA
* * * * * *
21366586 CAAATCTTATCTCCTTGGAGTTGCAGTAGAGTAGATT---GAAA-CTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAAAAGCTA
* * * * * *
21366630 CAAATCTTATTTACCTGAGGTTGCAGTGG-GACAAATTAAAGCTACAAA-TTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAG-CAGATTAAA---A-AAAGCTA
* * * * *
21366681 CAAATATTATCTCTCTGAACTTGCAGTGGAGCAAATT----AAAGCTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAAAAGCTA
* *
21366725 CAAGTTTTATCTCCCTGAAGTT
1 CAAATCTTATCTCCCTGAAGTT
21366747 GAAGTGGGGT
Statistics
Matches: 408, Mismatches: 87, Indels: 84
0.70 0.15 0.15
Matches are distributed among these distances:
39 1 0.00
41 2 0.00
42 2 0.00
43 7 0.02
44 197 0.48
45 6 0.01
46 4 0.01
47 6 0.01
48 2 0.00
49 74 0.18
51 101 0.25
52 6 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (48 bp):
CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAAAAGCTA
Found at i:21366380 original size:93 final size:93
Alignment explanation
Indices: 21366166--21366527 Score: 432
Period size: 93 Copynumber: 3.9 Consensus size: 93
21366156 GTCATCATGG
* * * * * * *
21366166 CAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGCCAT-AAATCTTATCTACTTGAAT
1 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAA-ACTTCAAATCTTATCTCCCTGAAT
* *
21366230 TTACAGT--AG-AG--TAAATTAA-AGATA
65 TTACAGTGGAGCAGATTAAA-AAATAGCTA
*
21366254 CAAATCTTATCTCCCTGAAGTTGTAATGGAGCAGATTGAAACTTCAAATCTTATCTCCCTGAATT
1 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAACTTCAAATCTTATCTCCCTGAATT
21366319 TACAGTGGAGCAGATTAAAAAATAGCTA
66 TACAGTGGAGCAGATTAAAAAATAGCTA
*
21366347 CAAATCTTATCTCCCTGAAGTTACAATGGAGCAGATTGAAACTTCAAATCTTATCTCCCTGAATT
1 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAACTTCAAATCTTATCTCCCTGAATT
21366412 TACAGTGGAGCAGATTAAAAAATAGCTA
66 TACAGTGGAGCAGATTAAAAAATAGCTA
* * * * * *
21366440 CAAATCTTATTTTCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACAAATCTTATCTCC
1 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATT---G--A-AACTT-CAAATCTTATCTCC
*
21366505 CTGAAGTTACAGTGGAGCAGATT
59 CTGAATTTACAGTGGAGCAGATT
21366528 GAAGCTACAA
Statistics
Matches: 242, Mismatches: 18, Indels: 16
0.88 0.07 0.06
Matches are distributed among these distances:
87 2 0.01
88 62 0.26
90 2 0.01
91 2 0.01
92 2 0.01
93 130 0.54
96 1 0.00
98 1 0.00
99 4 0.02
100 36 0.15
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (93 bp):
CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAACTTCAAATCTTATCTCCCTGAATT
TACAGTGGAGCAGATTAAAAAATAGCTA
Found at i:21366508 original size:51 final size:51
Alignment explanation
Indices: 21366391--21366730 Score: 250
Period size: 51 Copynumber: 7.0 Consensus size: 51
21366381 ATTGAAACTT
* * * *
21366391 CAAATCTTATCTCCCTGAATTTACAGTGGAGCAGATTAAA---AAATAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA-AGTTA
* * * *
21366440 CAAATCTTATTTTCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTTA
* *
21366491 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT---G----AAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTTA
* * * * * *
21366535 CAAATTTTAT-TCCATTGAAGTTGTAGTGAAACAGATTAAATCTACAAGTTA
1 CAAATCTTATCTCC-CTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTTA
* * * * *
21366586 CAAATCTTATCTCCTTGGAGTTGCAGTAGAGTAGATT---G--A-AA-CTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTTA
* * * * *
21366630 CAAATCTTATTTACCTGAGGTTGCAGTGG-GACAAATTAAAGCTACAAATTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTAAAGCTACAAGTTA
* * * *
21366681 CAAATATTATCTCTCTGAACTTGCAGTGGAGCAAATTAAAGCTACAAGTT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTT
21366731 TTATCTCCCT
Statistics
Matches: 223, Mismatches: 47, Indels: 40
0.72 0.15 0.13
Matches are distributed among these distances:
43 4 0.02
44 61 0.27
45 2 0.01
46 1 0.00
47 1 0.00
48 1 0.00
49 35 0.16
50 2 0.01
51 110 0.49
52 6 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (51 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTTA
Found at i:21366754 original size:95 final size:94
Alignment explanation
Indices: 21366298--21366753 Score: 399
Period size: 95 Copynumber: 4.8 Consensus size: 94
21366288 ATTGAAACTT
* * *
21366298 CAAATCTTATCTCCCTGAATTTACAGTGGAGCAGATTAAAAAATAGCTACAAATCTTATCTCCCT
1 CAAATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATT----AA-AGCTACAAATCTTATTTCCCT
* * * * *
21366363 GAAGTTACAATGGAGCAGATT---G--A-AACTT-
60 GAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTA
* * *
21366391 CAAATCTTATCTCCCTGAATTTACAGTGGAGCAGATTAAAAAATAGCTACAAATCTTATTTTCCT
1 CAAATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATT----AA-AGCTACAAATCTTATTTCCCT
21366456 GAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTA
60 GAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTA
* * * *
21366491 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTACAAATTTTA-TTCCATTGAAG
1 CAAATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATTTCC-CTGAAG
* * * *
21366555 TTGTAGTGAAACAGATTAAATCTACAAGTTA
64 TTGCAGTGGAACAAATTAAAGCTACAAGTTA
* * * * *
21366586 CAAATCTTATCTCCTTGGAGTTGCAGTAGAGTAGATTGAAA-CTACAAATCTTATTTACCTGAGG
1 CAAATCTTATCTCC-TGAAGTTGCAGTGGAGCAGATT-AAAGCTACAAATCTTATTTCCCTGAAG
* *
21366650 TTGCAGTGGGACAAATTAAAGCTACAAATTA
64 TTGCAGTGGAACAAATTAAAGCTACAAGTTA
* * * * * *
21366681 CAAATATTATCTCTCTGAACTTGCAGTGGAGCAAATTAAAGCTACAAGTTTTATCTCCCTGAAGT
1 CAAATCTTATCTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATTTCCCTGAAGT
*
21366746 TGAAGTGG
65 TGCAGTGG
21366754 GGTAGCTTGA
Statistics
Matches: 307, Mismatches: 43, Indels: 24
0.82 0.11 0.06
Matches are distributed among these distances:
93 80 0.26
94 8 0.03
95 170 0.55
96 8 0.03
98 1 0.00
99 4 0.01
100 36 0.12
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (94 bp):
CAAATCTTATCTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATTTCCCTGAAGTT
GCAGTGGAACAAATTAAAGCTACAAGTTA
Found at i:21368120 original size:12 final size:12
Alignment explanation
Indices: 21368103--21368133 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21368093 GTTGTTATTG
21368103 TATTATTGTTAT
1 TATTATTGTTAT
*
21368115 TATTATCGTTAT
1 TATTATTGTTAT
21368127 TATTATT
1 TATTATT
21368134 ATTTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (12 bp):
TATTATTGTTAT
Found at i:21369301 original size:26 final size:25
Alignment explanation
Indices: 21369245--21369301 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
21369235 GAGAATAAAA
** *
21369245 TATCTTTTATTTTTCCTTTTCTTCT
1 TATCTTTTATTTTTCCTTAGCTTCC
*
21369270 TTTCTTTTCATTTTTCCTTAGCTTCC
1 TATCTTTT-ATTTTTCCTTAGCTTCC
21369296 TATCTT
1 TATCTT
21369302 CCTCTCTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.67
Consensus pattern (25 bp):
TATCTTTTATTTTTCCTTAGCTTCC
Found at i:21382055 original size:27 final size:27
Alignment explanation
Indices: 21382017--21382070 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
21382007 CTGCCAAGAG
* *
21382017 AGTACTCAGATATATCAAGGGAACTTT
1 AGTACTCAGATACATCAAGGAAACTTT
*
21382044 AGTACTTAGATACATCAAGGAAACTTT
1 AGTACTCAGATACATCAAGGAAACTTT
21382071 GATCCATGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (27 bp):
AGTACTCAGATACATCAAGGAAACTTT
Found at i:21383918 original size:24 final size:24
Alignment explanation
Indices: 21383891--21383942 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
21383881 AATCAAAGTC
* *
21383891 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
21383915 AAATATATTGTACTTATAAATACT
1 AAATATATTATACTAATAAATACT
21383939 AAAT
1 AAAT
21383943 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:21390406 original size:12 final size:12
Alignment explanation
Indices: 21390389--21390431 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
21390379 ATTCCTGAAC
21390389 ATGTTCAATTAT
1 ATGTTCAATTAT
* *
21390401 ATGTTC-ATGAAC
1 ATGTTCAAT-TAT
21390413 ATGTTCAATTAT
1 ATGTTCAATTAT
21390425 ATGTTCA
1 ATGTTCA
21390432 TGAACATGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (12 bp):
ATGTTCAATTAT
Found at i:21390411 original size:24 final size:24
Alignment explanation
Indices: 21390384--21390447 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
21390374 ACATTATTCC
21390384 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCAATTATATGTTCA
21390408 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCAATTATATGTTCA
*
21390432 TGAACATGTTCGATTA
1 TGAACATGTTCAATTA
21390448 AAATGAACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (24 bp):
TGAACATGTTCAATTATATGTTCA
Found at i:21390440 original size:12 final size:12
Alignment explanation
Indices: 21390401--21390442 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
21390391 GTTCAATTAT
21390401 ATGTTCATGAAC
1 ATGTTCATGAAC
* *
21390413 ATGTTCAAT-TAT
1 ATGTTC-ATGAAC
21390425 ATGTTCATGAAC
1 ATGTTCATGAAC
21390437 ATGTTC
1 ATGTTC
21390443 GATTAAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (12 bp):
ATGTTCATGAAC
Found at i:21391337 original size:18 final size:19
Alignment explanation
Indices: 21391297--21391339 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
21391287 AAGGTTTTTA
**
21391297 TTTTATTAGGGTTCGAGTT
1 TTTTATTAGGGTTCGAGGG
*
21391316 TTTTATTAGGGTT-TAGGG
1 TTTTATTAGGGTTCGAGGG
21391334 TTTTAT
1 TTTTAT
21391340 GGAAGTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.16, C:0.02, G:0.26, T:0.56
Consensus pattern (19 bp):
TTTTATTAGGGTTCGAGGG
Found at i:21393606 original size:11 final size:11
Alignment explanation
Indices: 21393590--21393616 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
21393580 AGATAAATGT
21393590 TATTTAATTAA
1 TATTTAATTAA
21393601 TATTTAATTAA
1 TATTTAATTAA
21393612 TATTT
1 TATTT
21393617 TTAGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTAATTAA
Found at i:21394167 original size:21 final size:21
Alignment explanation
Indices: 21394141--21394192 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
21394131 GCGGTGGCGG
*
21394141 TGAGATTAGTTACTGTAGCAA
1 TGAGATTAGATACTGTAGCAA
**
21394162 TGAGATTAGATACTGTAGCGG
1 TGAGATTAGATACTGTAGCAA
21394183 TGAGATTAGA
1 TGAGATTAGA
21394193 AACAATGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.31
Consensus pattern (21 bp):
TGAGATTAGATACTGTAGCAA
Found at i:21395725 original size:3 final size:3
Alignment explanation
Indices: 21395703--21395749 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
21395693 ATATAATGAG
* *
21395703 AAT AAC AAT GAT ATAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21395748 AA
1 AA
21395750 CATAAAATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21395737 original size:17 final size:17
Alignment explanation
Indices: 21395715--21395754 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
21395705 TAACAATGAT
21395715 ATATAATAATAATAATA
1 ATATAATAATAATAATA
21395732 ATATAATAATAATAATA
1 ATATAATAATAATAATA
*
21395749 ACATAA
1 ATATAA
21395755 AATTGCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAATAATAATAATA
Found at i:21395754 original size:14 final size:14
Alignment explanation
Indices: 21395720--21395748 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21395710 ATGATATATA
21395720 ATAATAATAATAAT
1 ATAATAATAATAAT
21395734 ATAATAATAATAAT
1 ATAATAATAATAAT
21395748 A
1 A
21395749 ACATAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:21399610 original size:19 final size:19
Alignment explanation
Indices: 21399586--21399625 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
21399576 GATATATATG
21399586 TTTGACTATTGCCCAGAGA
1 TTTGACTATTGCCCAGAGA
21399605 TTTGACTATTGCCCAGAGA
1 TTTGACTATTGCCCAGAGA
21399624 TT
1 TT
21399626 CTTTTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (19 bp):
TTTGACTATTGCCCAGAGA
Found at i:21400038 original size:44 final size:45
Alignment explanation
Indices: 21399947--21400039 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 45
21399937 TTCGCTGTAT
*
21399947 TGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGTAA
1 TGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGGAA
* *
21399992 TGGAATAGAGGCGTAATAG-TATTC-TTGTGTTTGGTTGAATGGAA
1 TGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAATGGAA
21400036 TGGA
1 TGGA
21400040 GGTGTAATAG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.55
45 19 0.43
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.34
Consensus pattern (45 bp):
TGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGGAA
Found at i:21400218 original size:18 final size:17
Alignment explanation
Indices: 21400197--21400231 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21400187 TTATTATTAA
*
21400197 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
21400215 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
21400232 TCTTAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:21400278 original size:61 final size:60
Alignment explanation
Indices: 21400212--21400402 Score: 182
Period size: 61 Copynumber: 3.2 Consensus size: 60
21400202 TTTTAATTAA
*
21400212 AATATATAATTTAATAAAATTCTTAACAATCAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATGATTTAATAAAATTCTTAA-AATCAATATTCTTATATGAATTTACTAAAATCAT
* * * * *
21400273 AATATATGATACTAGA-AAATATAAT-TTGAAAT-AATTATTATTAAAT-ATATTT--T--AATT
1 AATATATGAT-TTA-ATAAA-AT--TCTTAAAATCAA-TATTCTTATATGA-ATTTACTAAAATC
*
21400330 AA
59 AT
21400332 AATATATGATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATGATTTAATAAAATTCTTAA-AATCAATATTCTTATATGAATTTACTAAAATCAT
21400393 AATATATGAT
1 AATATATGAT
21400403 ACTTTATAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 32
0.69 0.09 0.22
Matches are distributed among these distances:
55 1 0.01
56 3 0.03
57 19 0.19
58 8 0.08
59 15 0.15
61 24 0.24
62 8 0.08
63 19 0.19
64 3 0.03
65 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (60 bp):
AATATATGATTTAATAAAATTCTTAAAATCAATATTCTTATATGAATTTACTAAAATCAT
Found at i:21400338 original size:18 final size:17
Alignment explanation
Indices: 21400315--21400351 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
21400305 AATTATTATT
21400315 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
21400331 AAATATATGATTTAATA
1 AAATATATGATTTAATA
21400348 AAAT
1 AAAT
21400352 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:21400396 original size:120 final size:120
Alignment explanation
Indices: 21400183--21400405 Score: 428
Period size: 120 Copynumber: 1.9 Consensus size: 120
21400173 ATATTTTAAC
21400183 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAACAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAACAATCAATAT
21400248 TCTTATATGAATTTACTAAAATCATAATATATGATACTAGAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTAGAAAATATAATTTGAA
* *
21400303 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAACAATCAATAT
21400368 TCTTATATGAATTTACTAAAATCATAATATATGATACT
66 TCTTATATGAATTTACTAAAATCATAATATATGATACT
21400406 TTATAAAATT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 101 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAACAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTAGAAAATATAATTTGAA
Found at i:21403556 original size:33 final size:33
Alignment explanation
Indices: 21403504--21403571 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
21403494 GTGTGTGGAG
21403504 AACTATGAGAAACAAAGGGAACAAATCGACAGA
1 AACTATGAGAAACAAAGGGAACAAATCGACAGA
* * * *
21403537 AACTGTGAGAAACAGAGGGAGCAAATCGGCAGA
1 AACTATGAGAAACAAAGGGAACAAATCGACAGA
21403570 AA
1 AA
21403572 AGAAAAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.50, C:0.15, G:0.26, T:0.09
Consensus pattern (33 bp):
AACTATGAGAAACAAAGGGAACAAATCGACAGA
Found at i:21403667 original size:19 final size:19
Alignment explanation
Indices: 21403643--21403681 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21403633 CTAGAAGGAA
21403643 GGAACAGAAGAGGCAAAGG
1 GGAACAGAAGAGGCAAAGG
*
21403662 GGAACAGAAGAGGCAGAGG
1 GGAACAGAAGAGGCAAAGG
21403681 G
1 G
21403682 TAAAATAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.46, T:0.00
Consensus pattern (19 bp):
GGAACAGAAGAGGCAAAGG
Found at i:21404524 original size:45 final size:45
Alignment explanation
Indices: 21404430--21404522 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 45
21404420 TGACGATGAA
*
21404430 TTTTACTACAATAACTTATCATCCAAGTTACCTGATTTTGATGGC
1 TTTTACTACAATAACTTATCATCCAAGTTACCAGATTTTGATGGC
* * *
21404475 TTTTATTACAATAAC-TATCATCCCAGTTGACCAGA-TTTGGTGGC
1 TTTTACTACAATAACTTATCATCCAAGTT-ACCAGATTTTGATGGC
21404519 TTTT
1 TTTT
21404523 TAACCTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 24 0.56
45 19 0.44
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (45 bp):
TTTTACTACAATAACTTATCATCCAAGTTACCAGATTTTGATGGC
Found at i:21405558 original size:12 final size:12
Alignment explanation
Indices: 21405543--21405572 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21405533 AATAATTTAA
21405543 TAAATTAGAAAT
1 TAAATTAGAAAT
*
21405555 TAAATTGGAAAT
1 TAAATTAGAAAT
21405567 TAAATT
1 TAAATT
21405573 CAGATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (12 bp):
TAAATTAGAAAT
Found at i:21415991 original size:44 final size:44
Alignment explanation
Indices: 21415928--21416015 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
21415918 TAACTGAGAT
21415928 ACACGTGTTCCCTATTCAAGATTCCAACAGCCTTGTGCTCTGAA
1 ACACGTGTTCCCTATTCAAGATTCCAACAGCCTTGTGCTCTGAA
21415972 ACACGTGTTCCCTATTCAAGATTCCAACAGCCTTGTGCTCTGAA
1 ACACGTGTTCCCTATTCAAGATTCCAACAGCCTTGTGCTCTGAA
21416016 GAACCCAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.30
Consensus pattern (44 bp):
ACACGTGTTCCCTATTCAAGATTCCAACAGCCTTGTGCTCTGAA
Found at i:21417275 original size:30 final size:30
Alignment explanation
Indices: 21417210--21417278 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
21417200 AGAGAAACGC
*
21417210 CTTTGTGGTGAGATTCAACTGAAAGGAAAC
1 CTTTGTGGTGAGATTCAACTGAAAGGAAAA
*
21417240 CTTTGTGGTGAGA-TCTGACTGAAA-GAAATA
1 CTTTGTGGTGAGATTC-AACTGAAAGGAAA-A
*
21417270 TTTTGTGGT
1 CTTTGTGGT
21417279 AATCTCTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.18
30 28 0.82
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.33
Consensus pattern (30 bp):
CTTTGTGGTGAGATTCAACTGAAAGGAAAA
Found at i:21417305 original size:28 final size:28
Alignment explanation
Indices: 21417274--21417329 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
21417264 GAAATATTTT
* *
21417274 GTGGTAAT-CTCTGTTAAAGGAAGCCTTC
1 GTGGTAATGC-CTGTTAAAAGAAACCTTC
*
21417302 GTGGTGATGCCTGTTAAAAGAAACCTTC
1 GTGGTAATGCCTGTTAAAAGAAACCTTC
21417330 ATGATTATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (28 bp):
GTGGTAATGCCTGTTAAAAGAAACCTTC
Found at i:21421127 original size:21 final size:21
Alignment explanation
Indices: 21421098--21421171 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 21
21421088 AAGGGAGGAA
*
21421098 GATTATTTTTTGATGAAGTTTG
1 GATT-TTTTTTAATGAAGTTTG
**
21421120 GA-TTTTTTTAATGGAA--TAA
1 GATTTTTTTTAAT-GAAGTTTG
*
21421139 GATTTTTTTTTATGAAGTTTG
1 GATTTTTTTTAATGAAGTTTG
*
21421160 GATATTTTTTAA
1 GATTTTTTTTAA
21421172 AATTTTATTC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
19 6 0.15
20 17 0.43
21 15 0.38
22 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (21 bp):
GATTTTTTTTAATGAAGTTTG
Found at i:21428389 original size:29 final size:28
Alignment explanation
Indices: 21428357--21428419 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
21428347 TTAATATTTA
*
21428357 AAAAATTCAAAAAATTATTTTTAAAAATT
1 AAAAATTCAAAAAATT-TATTTAAAAATT
**
21428386 AAAAA-TCATTAAATTTATTTAAAAATT
1 AAAAATTCAAAAAATTTATTTAAAAATT
21428413 ATAAAAT
1 A-AAAAT
21428420 ATATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 12 0.41
28 12 0.41
29 5 0.17
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (28 bp):
AAAAATTCAAAAAATTTATTTAAAAATT
Found at i:21428427 original size:21 final size:20
Alignment explanation
Indices: 21428384--21428438 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
21428374 TTTTTAAAAA
* * *
21428384 TTAAAAATCATTAAATTTAT
1 TTAAAAATTATAAAATATAT
21428404 TTAAAAATTATAAAATATATT
1 TTAAAAATTATAAAATATA-T
*
21428425 TTAAATATTA-AAAA
1 TTAAAAATTATAAAA
21428439 AGTAATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAAATTATAAAATATAT
Found at i:21428447 original size:50 final size:50
Alignment explanation
Indices: 21428351--21428448 Score: 121
Period size: 48 Copynumber: 2.0 Consensus size: 50
21428341 AATATTTTAA
*
21428351 TATTTAAAAAATTCAAAAAATTATTTTTAAAAATTAAAAATCATTAAATT
1 TATTTAAAAAATTCAAAAAATTATTTTTAAAAATTAAAAATAATTAAATT
* *
21428401 TATTT-AAAAATT-ATAAAA-TATATTTTAAATATTAAAAAAGTAATTAAA
1 TATTTAAAAAATTCAAAAAATTAT-TTTTAAAAATT-AAAAA-TAATTAAA
21428449 CCTTGACATG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
47 3 0.07
48 15 0.36
49 12 0.29
50 12 0.29
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (50 bp):
TATTTAAAAAATTCAAAAAATTATTTTTAAAAATTAAAAATAATTAAATT
Found at i:21430131 original size:24 final size:25
Alignment explanation
Indices: 21430097--21430163 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
21430087 TTTTTGCAAT
21430097 TTATTTA-TTTAAAATTTTTTA-TA
1 TTATTTATTTTAAAATTTTTTATTA
*
21430120 TTATTTGTTTT-AAATTATTTTATTA
1 TTATTTATTTTAAAATT-TTTTATTA
21430145 TTATTTATTTTAAAATTTT
1 TTATTTATTTTAAAATTTT
21430164 CACATATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.29
24 8 0.21
25 14 0.37
26 5 0.13
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (25 bp):
TTATTTATTTTAAAATTTTTTATTA
Found at i:21430171 original size:25 final size:23
Alignment explanation
Indices: 21430097--21430183 Score: 77
Period size: 25 Copynumber: 3.6 Consensus size: 23
21430087 TTTTTGCAAT
*
21430097 TTATTTA-TTTAAAATTTTTTATA
1 TTATTTATTTTAAAA-TTTTAATA
* *
21430120 TTATTTGTTTTAAATTATTTTATTA
1 TTATTTATTTTAAA--ATTTTAATA
21430145 TTATTTATTTTAAAATTTTCACATA
1 TTATTTATTTTAAAATTTT-A-ATA
**
21430170 TTATACATTTTAAA
1 TTATTTATTTTAAA
21430184 CTATATTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
23 11 0.21
24 7 0.13
25 33 0.63
26 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (23 bp):
TTATTTATTTTAAAATTTTAATA
Found at i:21430441 original size:23 final size:23
Alignment explanation
Indices: 21430409--21430456 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
21430399 TGGTTATTTA
* * *
21430409 TTTTAATTTGCTTTGTATGTTAT
1 TTTTAATTTGCGTTGCATATTAT
*
21430432 TTTTATTTTGCGTTGCATATTAT
1 TTTTAATTTGCGTTGCATATTAT
21430455 TT
1 TT
21430457 ACTTTGAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.12, T:0.65
Consensus pattern (23 bp):
TTTTAATTTGCGTTGCATATTAT
Found at i:21430490 original size:24 final size:25
Alignment explanation
Indices: 21430448--21430506 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
21430438 TTTGCGTTGC
* ** *
21430448 ATATTATTTACTTTGAATTG-CTTT
1 ATATTATTTACCTCAAATTGTCTAT
21430472 ATATTATTTACCTCAAATTGTTCTAT
1 ATATTATTTACCTCAAATTG-TCTAT
21430498 ATATTATTT
1 ATATTATTT
21430507 CGTTTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 17 0.59
26 12 0.41
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (25 bp):
ATATTATTTACCTCAAATTGTCTAT
Found at i:21434577 original size:13 final size:12
Alignment explanation
Indices: 21434549--21434595 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
21434539 CTATGGTTTT
21434549 CAAAA-AAATAAA
1 CAAAATAAA-AAA
21434561 -AAAATAAAAAA
1 CAAAATAAAAAA
21434572 TCAAAATAAAAAA
1 -CAAAATAAAAAA
21434585 CAAAATCAAAA
1 CAAAAT-AAAA
21434596 TAATATTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.23
12 9 0.29
13 15 0.48
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.11
Consensus pattern (12 bp):
CAAAATAAAAAA
Found at i:21434600 original size:21 final size:22
Alignment explanation
Indices: 21434553--21434600 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 22
21434543 GGTTTTCAAA
21434553 AAAATAA-AAAAATAAAAAATC
1 AAAATAATAAAAATAAAAAATC
*
21434574 --AA-AATAAAAA-ACAAAATC
1 AAAATAATAAAAATAAAAAATC
21434592 AAAATAATA
1 AAAATAATA
21434601 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 8
0.71 0.03 0.26
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 2 0.09
21 4 0.18
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (22 bp):
AAAATAATAAAAATAAAAAATC
Found at i:21434644 original size:6 final size:5
Alignment explanation
Indices: 21434633--21434695 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 5
21434623 ATATTTCAAA
* *
21434633 AAAATG AAAATG AAAAT A-AAG AAAAG AAAAG AAAAAG AGAATG AAAAG
1 AAAA-G AAAA-G AAAAG AAAAG AAAAG AAAAG -AAAAG A-AAAG AAAAG
21434681 AAAAGG AAAAG AAAA
1 AAAA-G AAAAG AAAA
21434696 AGGCGAAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
4 3 0.06
5 22 0.45
6 24 0.49
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (5 bp):
AAAAG
Found at i:21434656 original size:9 final size:10
Alignment explanation
Indices: 21434650--21434695 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
21434640 AAATGAAAAT
21434650 AAAGAAAAGA
1 AAAGAAAAGA
21434660 AAAGAAAAAGA
1 AAAG-AAAAGA
*
21434671 GAATGAAAAGA
1 -AAAGAAAAGA
21434682 AAAGGAAAAGA
1 AAA-GAAAAGA
21434693 AAA
1 AAA
21434696 AGGCGAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 6 0.19
11 22 0.71
12 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:21434697 original size:6 final size:5
Alignment explanation
Indices: 21434650--21434695 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
21434640 AAATGAAAAT
*
21434650 AAAGA AAAGA AAAGAA AAAGA GAATGA AAAGA AAAGGA AAAGA AAA
1 AAAGA AAAGA AAAG-A AAAGA -AAAGA AAAGA AAA-GA AAAGA AAA
21434696 AGGCGAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 22 0.61
6 14 0.39
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:21435717 original size:45 final size:45
Alignment explanation
Indices: 21435631--21435718 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
21435621 AAGAAGAAGG
* * *
21435631 GACCAAGGTGAAAACTCACAAAGGGCGCCTTGAGTCCTAAAAAAA
1 GACCAAGGTGAAAACCCACAAAAGGCGCCTTGAGTCATAAAAAAA
* * *
21435676 GACCAAGGTGAAAACCCGCAAAAGGCGCTTTGAGTTATAAAAA
1 GACCAAGGTGAAAACCCACAAAAGGCGCCTTGAGTCATAAAAA
21435719 TACAGTAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (45 bp):
GACCAAGGTGAAAACCCACAAAAGGCGCCTTGAGTCATAAAAAAA
Found at i:21437263 original size:44 final size:45
Alignment explanation
Indices: 21437195--21437708 Score: 223
Period size: 44 Copynumber: 10.9 Consensus size: 45
21437185 TATGGTGAAT
* * * *
21437195 CTTATCTTCCTGAAGTTGCGGTGGAGTAGATTGAAGCCA-CCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAGCTAGC
** * * **
21437239 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACCGAAGACAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAGCTAGC
* * * * * * * *
21437284 CTTATTTCCCGGATGTTGTAGTGGAACAAATTAAAGCTACAAGTTATGAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC--C-AGCTA-G-C
* *
21437334 GAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCA-CTAGC
1 ----CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAGCTAGC
** * * **
21437382 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACCGAAGACAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAGCTAGC
* * * * * *
21437427 CTTATTTCCC-GAATGTTGTAGTGGAACAAATTAAAGCTACAAGTTATGAC
1 CTTATCTCCCTGAA-GTTGCAGTGGAGCAGATTGAAGC--C-AGCTA-G-C
* *
21437477 GAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCA-CTAGC
1 ----CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAGCTAGC
* * * * * **
21437525 CTTATCTCCTTGAAGTTGCAGTGGAGCAAATTGAAGACAACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAGCTAGC
* * * * **
21437570 CTTATTTCCCTGGCA-TTGCAGTGGAACAGATT-AGAGTTACAAATTATGGC
1 CTTATCTCCCT-GAAGTTGCAGTGGAGCAGATTGA-AG---CCAGCTA--GC
* * * *
21437620 GAATCTTATCTTCATGAAGTTGCAGTGGAGCAGATTGAAGCTA-CCAGC
1 ----CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAGCTAGC
* * *
21437668 CTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGACAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAGC
21437709 GAATCTTATT
Statistics
Matches: 339, Mismatches: 94, Indels: 73
0.67 0.19 0.14
Matches are distributed among these distances:
44 138 0.41
45 85 0.25
46 2 0.01
47 2 0.01
48 13 0.04
49 2 0.01
50 5 0.01
51 4 0.01
52 2 0.01
53 2 0.01
54 80 0.24
55 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAGCTAGC
Found at i:21437307 original size:143 final size:143
Alignment explanation
Indices: 21437041--21438306 Score: 1596
Period size: 143 Copynumber: 8.9 Consensus size: 143
21437031 ATTACAGTAA
* * *
21437041 TTATGGCGAATCTTATCTTCTTGGAGTTGCAGTGGAGCAGATTGAAGCCATCAGCCTTATCTCCC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * * * * * *
21437106 TGAAGTTACAATAGAGTAGACTGAAGACAGTGAATCTTATTTCTCGGACT-TTACAGTGGAACAA
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGA-TGTTGCAGTGGAACAG
21437170 ATTAAAGCTACAAG
130 ATTAAAGCTACAAG
* * *
21437184 TTATGGTGAATCTTATCTTCCTGAAGTTGCGGTGGAGTAGATTGAAGCCACCAGCCTTATCTCCC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * *
21437249 TGAAGTTGCAGTGGAGCAGACCGAAGACAGCGAATCTTATTTCCCGGATGTTGTAGTGGAACAAA
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGATGTTGCAGTGGAACAGA
21437314 TTAAAGCTACAAG
131 TTAAAGCTACAAG
* * *
21437327 TTATGACGAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACTAGCCTTATCTCCC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * *
21437392 TGAAGTTGCAGTGGAGCAGACCGAAGACAGCGAATCTTATTTCCCGAATGTTGTAGTGGAACAAA
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGATGTTGCAGTGGAACAGA
21437457 TTAAAGCTACAAG
131 TTAAAGCTACAAG
* * * *
21437470 TTATGACGAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACTAGCCTTATCTCCT
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * *
21437535 TGAAGTTGCAGTGGAGCAAATTGAAGACAACAAATCTTATTTCCCTGGCA--TTGCAGTGGAACA
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCC-GG-ATGTTGCAGTGGAACA
* * *
21437598 GATTAGAGTTACAAA
129 GATTAAAGCTACAAG
* *
21437613 TTATGGCGAATCTTATCTTCATGAAGTTGCAGTGGAGCAGATTGAAGCTACCAGCCTTATCTCCC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * * *
21437678 TGAAGTTGTAGTGGAGCAGACTGAAGACAGCGAATCTTATTTTCC-TAGCGTTGCACTGGAACAG
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGA-TGTTGCAGTGGAACAG
* *
21437742 ATTAGAGCTACAAA
130 ATTAAAGCTACAAG
* * ** * * * * * *
21437756 TTATGGC-AGATATTATCTTCCTGAAGTTGTAGTGTTGCATAATAAAACCATCATCCTTATCTCC
1 TTATGGCGA-ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * *
21437820 ATGAAGTTGCAGTGGAGCAGACTGAAGACAACGAATCTTATTTCCTTGG-CGTTACAATGGAACA
65 CTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCC-CGGATGTTGCAGTGGAACA
* *
21437884 GATTAAAACTACAGG
129 GATTAAAGCTACAAG
* * * * * * *
21437899 TTATGGCAAATCTTATCTTCCTAAAGTTGCAGTCGAGCAGATTGAAACCACCAGCCTTGTATCTC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * * * * *
21437964 TGAAGTTACAGCGGAGCAAACTGAAGACAGTGAATCTTATTTCCCTGAAGTTGCAGTGGAACATA
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGATGTTGCAGTGGAACAGA
21438029 TTAAAGCTACAAG
131 TTAAAGCTACAAG
* * * *
21438042 TTATGGCAAATCTTATCTT-CTCGAAGTTGTAGTGGAGCAGATTGAAGCCACCAGACTTATCTCT
1 TTATGGCGAATCTTATCTTCCT-GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * *
21438106 CTGAAGTTACAGCGGAGCAGAATGAAGACAACGAATCTTATTTCCCTG-TGTTGCAGTGGAACAG
65 CTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGATGTTGCAGTGGAACAG
21438170 ATTAAAGCTACAAG
130 ATTAAAGCTACAAG
21438184 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * *
21438249 TAAAGTTGTAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGG-CGTTGCAGTG
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCC-GGATGTTGCAGTG
21438307 TAGTAGATTG
Statistics
Matches: 986, Mismatches: 123, Indels: 28
0.87 0.11 0.02
Matches are distributed among these distances:
140 1 0.00
142 131 0.13
143 851 0.86
144 2 0.00
145 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (143 bp):
TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGATGTTGCAGTGGAACAGA
TTAAAGCTACAAG
Found at i:21439781 original size:25 final size:23
Alignment explanation
Indices: 21439763--21439849 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 23
21439753 TTTTTGCAAT
*
21439763 TTATTTATTTTAAACTTTTTTATA
1 TTATTTATTTTAAA-TTTTTAATA
*
21439787 TTATTTATTTTAAATTATTTTATTA
1 TTATTTATTTTAAA-T-TTTTAATA
*
21439812 TTATTTATTTTAAATTTTCACATA
1 TTATTTATTTTAAATTTTTA-ATA
**
21439836 TTATGCATTTTAAA
1 TTATTTATTTTAAA
21439850 CTATATTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 4 0.07
24 30 0.56
25 20 0.37
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (23 bp):
TTATTTATTTTAAATTTTTAATA
Found at i:21439803 original size:14 final size:14
Alignment explanation
Indices: 21439780--21439827 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
21439770 TTTTAAACTT
*
21439780 TTTTATATTATTTA
1 TTTTAAATTATTTA
21439794 TTTTAAATTATTT-
1 TTTTAAATTATTTA
*
21439807 TATT--ATTATTTA
1 TTTTAAATTATTTA
21439819 TTTTAAATT
1 TTTTAAATT
21439828 TTCACATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 7 0.25
12 3 0.11
13 3 0.11
14 15 0.54
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTAAATTATTTA
Found at i:21440103 original size:23 final size:23
Alignment explanation
Indices: 21440071--21440118 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
21440061 TGGTTATTTA
* *
21440071 TTTTAATTTGCTTTGCATGTTAT
1 TTTTAATTTGCGTTGCATATTAT
*
21440094 TTTTATTTTGCGTTGCATATTAT
1 TTTTAATTTGCGTTGCATATTAT
21440117 TT
1 TT
21440119 ACTTTGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.08, G:0.12, T:0.62
Consensus pattern (23 bp):
TTTTAATTTGCGTTGCATATTAT
Found at i:21446224 original size:14 final size:14
Alignment explanation
Indices: 21446205--21446247 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
21446195 TGCAGCAGGC
*
21446205 AAGGTGACCATGCA
1 AAGGTGGCCATGCA
21446219 AAGGTGGCCATGCA
1 AAGGTGGCCATGCA
21446233 AAGGTGGCCATGCA
1 AAGGTGGCCATGCA
21446247 A
1 A
21446248 GAAGAAAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.33, C:0.21, G:0.33, T:0.14
Consensus pattern (14 bp):
AAGGTGGCCATGCA
Found at i:21448199 original size:5 final size:6
Alignment explanation
Indices: 21448183--21448208 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21448173 GCTTTAGCCC
21448183 ATTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT
21448209 AATAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:21448306 original size:30 final size:31
Alignment explanation
Indices: 21448266--21448411 Score: 115
Period size: 30 Copynumber: 4.9 Consensus size: 31
21448256 AAGGAAAAAA
* **
21448266 TAAATTTTACATTTTAACCCCTGTACTTTT-
1 TAAAATTTACATTTTAACCCCTAAACTTTTC
* *
21448296 TGAAATTTACATTTTGA-CCCTAAACTTTTC
1 TAAAATTTACATTTTAACCCCTAAACTTTTC
**
21448326 TAAAATTTACATTTTAACCCC-AAAAATTTC
1 TAAAATTTACATTTTAACCCCTAAACTTTTC
* * ** *
21448356 TATAA-TTACATTTCAACCTTTAGAC-TTTC
1 TAAAATTTACATTTTAACCCCTAAACTTTTC
* *
21448385 TCAAAATTT-CACTTTGACCCCTAAACT
1 T-AAAATTTACATTTTAACCCCTAAACT
21448412 CTCAAGAAAT
Statistics
Matches: 88, Mismatches: 22, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
29 27 0.31
30 56 0.64
31 5 0.06
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (31 bp):
TAAAATTTACATTTTAACCCCTAAACTTTTC
Found at i:21448911 original size:14 final size:15
Alignment explanation
Indices: 21448876--21448904 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21448866 AACCCAAAGG
21448876 AAAAAG-AGAGAAAA
1 AAAAAGAAGAGAAAA
21448890 AAAAAGAAGAGAAAA
1 AAAAAGAAGAGAAAA
21448905 GAAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAGAAAA
Found at i:21448920 original size:22 final size:20
Alignment explanation
Indices: 21448884--21448924 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
21448874 GGAAAAAGAG
21448884 AGAAAAAAAAAGAAGAGAAA
1 AGAAAAAAAAAGAAGAGAAA
21448904 AGAAAGAAAAAAGGAAGAGAA
1 AGAAA-AAAAAA-GAAGAGAA
21448925 GGGGAGGCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AGAAAAAAAAAGAAGAGAAA
Found at i:21449371 original size:18 final size:18
Alignment explanation
Indices: 21449333--21449370 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
21449323 CTTTTGGGTA
21449333 TTATTTTTTAAATATATT
1 TTATTTTTTAAATATATT
*
21449351 TTATTTTATTTAATATATT
1 TTATTTT-TTAAATATATT
21449370 T
1 T
21449371 AAATGGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTTTTAAATATATT
Found at i:21449645 original size:16 final size:16
Alignment explanation
Indices: 21449617--21449722 Score: 95
Period size: 16 Copynumber: 6.2 Consensus size: 16
21449607 TCATATTTAA
21449617 AAAATTTCTCGTGTTTT
1 AAAA-TTCTCGTGTTTT
* *
21449634 AAAATCCTCGTGTTTC
1 AAAATTCTCGTGTTTT
*
21449650 AAAATTGTCGTGTTTT
1 AAAATTCTCGTGTTTT
* *
21449666 CAAAAATTTTAGTGTTTTT
1 --AAAATTCTCGTG-TTTT
* *
21449685 AAGAATTTTCGTGTCTCT
1 AA-AATTCTCGTGT-TTT
21449703 AAAATTCTCGTGTTTT
1 AAAATTCTCGTGTTTT
21449719 AAAA
1 AAAA
21449723 AATTTTCGTG
Statistics
Matches: 73, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
16 29 0.40
17 17 0.23
18 23 0.32
19 4 0.05
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (16 bp):
AAAATTCTCGTGTTTT
Found at i:21449672 original size:34 final size:36
Alignment explanation
Indices: 21449596--21449743 Score: 128
Period size: 35 Copynumber: 4.2 Consensus size: 36
21449586 AAATAAAAAA
* *
21449596 TTCAAAAATCCTCAT-ATTTAAAAAATTTCTCGTGTT
1 TTCAAAAATCCTCGTGTTTTAAAAAATTT-TCGTGTT
* *
21449632 TT--AAAATCCTCGTG-TTT-CAAAATTGTCGTGTT
1 TTCAAAAATCCTCGTGTTTTAAAAAATTTTCGTGTT
** * * *
21449664 TTCAAAAATTTTAGTGTTTTTAAGAATTTTCGTG-T
1 TTCAAAAATCCTCGTGTTTTAAAAAATTTTCGTGTT
* * *
21449699 CTCTAAAATTCTCGTGTTTTAAAAAATTTTCGTGTT
1 TTCAAAAATCCTCGTGTTTTAAAAAATTTTCGTGTT
*
21449735 CTCAAAAAT
1 TTCAAAAAT
21449744 AAAAAATGTT
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
32 9 0.10
33 6 0.07
34 22 0.24
35 32 0.36
36 21 0.23
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (36 bp):
TTCAAAAATCCTCGTGTTTTAAAAAATTTTCGTGTT
Found at i:21449717 original size:53 final size:51
Alignment explanation
Indices: 21449612--21449734 Score: 158
Period size: 53 Copynumber: 2.4 Consensus size: 51
21449602 AATCCTCATA
* *
21449612 TTTAAAAAATTTCTCGTG-TTTTAAAATCCTCGTGTTTCAAAATTGTCGTGT
1 TTTAAAAAATTT-TCGTGTTTTTAAAATCCTCGTGTCTCAAAATTCTCGTGT
* * **
21449663 TTTCAAAAATTTTAGTGTTTTTAAGAATTTTCGTGTCTCTAAAATTCTCGTGT
1 TTTAAAAAATTTTCGTGTTTTTAA-AATCCTCGTGTCTC-AAAATTCTCGTGT
21449716 TTTAAAAAATTTTCGTGTT
1 TTTAAAAAATTTTCGTGTT
21449735 CTCAAAAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 4 0.07
51 17 0.28
52 11 0.18
53 29 0.48
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (51 bp):
TTTAAAAAATTTTCGTGTTTTTAAAATCCTCGTGTCTCAAAATTCTCGTGT
Found at i:21449741 original size:18 final size:18
Alignment explanation
Indices: 21449616--21449743 Score: 113
Period size: 18 Copynumber: 7.3 Consensus size: 18
21449606 CTCATATTTA
21449616 AAAAATTTCTCGTGTTTT-
1 AAAAATTT-TCGTGTTTTC
**
21449634 -AAAATCCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
21449650 -AAAATTGTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
21449667 AAAAATTTTAGTGTTTTT
1 AAAAATTTTCGTGTTTTC
* *
21449685 AAGAATTTTCGTG-TCTC
1 AAAAATTTTCGTGTTTTC
* * *
21449702 TAAAATTCTCGTGTTTTA
1 AAAAATTTTCGTGTTTTC
*
21449720 AAAAATTTTCGTGTTCTC
1 AAAAATTTTCGTGTTTTC
21449738 AAAAAT
1 AAAAAT
21449744 AAAAAATGTT
Statistics
Matches: 86, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
15 3 0.03
16 15 0.17
17 21 0.24
18 47 0.55
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:21464383 original size:8 final size:8
Alignment explanation
Indices: 21464380--21464436 Score: 87
Period size: 8 Copynumber: 6.9 Consensus size: 8
21464370 AAAAAAAGAA
21464380 AAAAATAAC
1 AAAAA-AAC
21464389 AAAAAAAC
1 AAAAAAAC
21464397 AAAAAAAC
1 AAAAAAAC
21464405 AAAAAAAC
1 AAAAAAAC
21464413 AAAAAAAAC
1 -AAAAAAAC
*
21464422 AAAAAAGC
1 AAAAAAAC
21464430 AAAAAAA
1 AAAAAAA
21464437 GTAAAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
8 32 0.71
9 13 0.29
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:21464444 original size:17 final size:16
Alignment explanation
Indices: 21464380--21464436 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 16
21464370 AAAAAAAGAA
21464380 AAAAATAACAAAAAAAC
1 AAAAA-AACAAAAAAAC
21464397 AAAAAAACAAAAAAAC
1 AAAAAAACAAAAAAAC
*
21464413 AAAAAAAACAAAAAAGC
1 -AAAAAAACAAAAAAAC
21464430 AAAAAAA
1 AAAAAAA
21464437 GTAAAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
16 18 0.47
17 20 0.53
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.02
Consensus pattern (16 bp):
AAAAAAACAAAAAAAC
Found at i:21464457 original size:1 final size:1
Alignment explanation
Indices: 21464369--21464448 Score: 61
Period size: 1 Copynumber: 80.0 Consensus size: 1
21464359 TATTATGCCT
* * * * * * * **
21464369 AAAAAAAAGAAAAAAATAACAAAAAAACAAAAAAACAAAAAAACAAAAAAAACAAAAAAGCAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
**
21464434 AAAGTAAAAAAAAAA
1 AAAAAAAAAAAAAAA
21464449 GAAGAAAAAT
Statistics
Matches: 59, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.86, C:0.07, G:0.04, T:0.03
Consensus pattern (1 bp):
A
Found at i:21465546 original size:78 final size:77
Alignment explanation
Indices: 21465319--21465889 Score: 527
Period size: 79 Copynumber: 7.4 Consensus size: 77
21465309 TCAAGAATTA
* *
21465319 TATTTTTCAATTTTTGTTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
21465382 TCACG-CTGAGG
66 TCACGTCTGAGG
* * *
21465393 TATTTTTAAATTGCTGCTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
21465457 TCA--TCTTGAGG
66 TCACGTC-TGAGG
* * * *
21465468 T-CTTTTCAATTTCTTTTTTTTCAAAAAAAAATCAACTCATAATGCTAGAAGTGAGTTGAGCCTC
1 TATTTTTCAATTTC-TGTTTTTC--AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
*
21465532 GAGTCACGTC-GAGG
63 GGGTCACGTCTGAGG
* * * * * ***
21465546 TATTTTTCAATTTTTGGTTTTCACAAAAATGAACTCATATTGCGAGAGGTGAGTTGAGCCTTAAG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
**
21465611 TCATATCCTGAGG
66 TCACGT-CTGAGG
* * * * *
21465624 TATTTTTCAATTTCTATTTTTCAAAAAAATTCGACTCATATTGCGAGAGGTGAGTTAAGTCTCGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAA-TCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
* * *
21465689 GTCACATACCGATG
65 GTCACGT-CTGAGG
* * * * *
21465703 TATTTCTTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCCAGAGGTGAGTTGAACCTC
1 TA--T-TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
* *
21465768 GGGTCACATATCGAGG
63 GGGTCACGTCT-GAGG
* * * * * *
21465784 TATTTCTTTTAAATTTCCGTTTCTC--CAAAATCAACTCATAATGCGAGAGGCGAGTTGAGACTC
1 TA--T-TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
* *
21465847 GGATCATG-CTGAGG
63 GGGTCACGTCTGAGG
*
21465861 TA-TTTTCAATTTCTATTTTTCAAGAAAAA
1 TATTTTTCAATTTCTGTTTTTCAA-AAAAA
21465890 ACGATAATAG
Statistics
Matches: 407, Mismatches: 70, Indels: 38
0.79 0.14 0.07
Matches are distributed among these distances:
73 15 0.04
74 28 0.07
75 55 0.14
76 44 0.11
77 7 0.02
78 83 0.20
79 87 0.21
80 2 0.00
81 63 0.15
82 23 0.06
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (77 bp):
TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
TCACGTCTGAGG
Found at i:21465786 original size:160 final size:154
Alignment explanation
Indices: 21465319--21465889 Score: 531
Period size: 160 Copynumber: 3.7 Consensus size: 154
21465309 TCAAGAATTA
* * *
21465319 TATTTTTCAATTTTTGTTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* * * *
21465382 TCACGCTGAGGTATTTTTAAATTGCTGCTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGT
66 TCACTCCGAGGTATTTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
21465446 TGAGCCTCGGGTCATC-T-T-GAGG
131 TGAGCCTCGGGTCA-CATATCGAGG
* * * *
21465468 T-CTTTTCAATTTCTTTTTTTTCAAAAAAAAATCAACTCATAATGCTAGAAGTGAGTTGAGCCTC
1 TATTTTTCAATTTC-TATTTTTC--AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
* * * * * *
21465532 GAGTCACGT-CGAGGTATTTTTCAATTTTTGGTTTTCACAAAAATGAACTCATATTGCGAGAGGT
63 GGGTCAC-TCCGAGGTATTTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGT
***
21465596 GAGTTGAGCCTTAAGT--CATATCCTGAGG
127 GAGTTGAGCCTCGGGTCACATAT-C-GAGG
* * * *
21465624 TATTTTTCAATTTCTATTTTTCAAAAAAATTCGACTCATATTGCGAGAGGTGAGTTAAGTCTCGG
1 TATTTTTCAATTTCTATTTTTCAAAAAAA-TCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
* *
21465689 GTCACATACCGATGTATTTCTTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCCAGAG
65 GTCAC-T-CCGAGGTA--T-TTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAG
*
21465754 GTGAGTTGAACCTCGGGTCACATATCGAGG
125 GTGAGTTGAGCCTCGGGTCACATATCGAGG
* ** * * * *
21465784 TATTTCTTTTAAATTTCCGTTTCTC--CAAAATCAACTCATAATGCGAGAGGCGAGTTGAGACTC
1 TA--T-TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
* * * **
21465847 GGATCA-TGCTGAGGTA-TTTTCAATTTCTATTTTTCAAGAAAAA
63 GGGTCACT-CCGAGGTATTTTTAAATTTCTGCTTTTCAA-AAAAA
21465890 ACGATAATAG
Statistics
Matches: 340, Mismatches: 57, Indels: 44
0.77 0.13 0.10
Matches are distributed among these distances:
148 10 0.03
149 8 0.02
151 1 0.00
152 1 0.00
153 64 0.19
154 62 0.18
155 39 0.11
156 12 0.04
157 17 0.05
158 7 0.02
159 1 0.00
160 92 0.27
161 5 0.01
162 6 0.02
163 15 0.04
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (154 bp):
TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
TCACTCCGAGGTATTTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
TGAGCCTCGGGTCACATATCGAGG
Found at i:21466192 original size:6 final size:6
Alignment explanation
Indices: 21466181--21466210 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
21466171 CTTTAGCCCA
21466181 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
21466211 AATAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:21466218 original size:18 final size:18
Alignment explanation
Indices: 21466181--21466219 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21466171 CTTTAGCCCA
** *
21466181 TTTTATTTTTATTTTTAT
1 TTTTATTTTTATAATAAT
21466199 TTTTATTTTTATAATAAT
1 TTTTATTTTTATAATAAT
21466217 TTT
1 TTT
21466220 AAATATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATTTTTATAATAAT
Found at i:21466306 original size:30 final size:31
Alignment explanation
Indices: 21466268--21466413 Score: 133
Period size: 30 Copynumber: 4.9 Consensus size: 31
21466258 AGGCAAAAAA
* **
21466268 TAAAATTTACATTTTAACCCCTGTACTTTT-
1 TAAAATTTACATTTTGACCCCTAAACTTTTC
*
21466298 TGAAATTTACATTTTGA-CCCTAAACTTTTC
1 TAAAATTTACATTTTGACCCCTAAACTTTTC
*
21466328 TAAAATTTACATTTTGACCCC-AAAATTTTC
1 TAAAATTTACATTTTGACCCCTAAACTTTTC
* ** ** *
21466358 TATAA-TTACATTTCAACCTTTAGAC-TTTC
1 TAAAATTTACATTTTGACCCCTAAACTTTTC
*
21466387 TCAAAATTT-CACTTTGACCCCTAAACT
1 T-AAAATTTACATTTTGACCCCTAAACT
21466414 CTCAAGAAAT
Statistics
Matches: 90, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
29 26 0.29
30 59 0.66
31 5 0.06
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (31 bp):
TAAAATTTACATTTTGACCCCTAAACTTTTC
Found at i:21466901 original size:14 final size:14
Alignment explanation
Indices: 21466882--21466911 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21466872 CCAAAGGAAA
21466882 AAGAGAAAAAAAAG
1 AAGAGAAAAAAAAG
*
21466896 AAGAGAAAAGAAAG
1 AAGAGAAAAAAAAG
21466910 AA
1 AA
21466912 AAAAGGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAGAGAAAAAAAAG
Found at i:21466913 original size:21 final size:22
Alignment explanation
Indices: 21466880--21466924 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
21466870 ACCCAAAGGA
21466880 AAAAGAGAAAAAAAA-GAAGAG
1 AAAAGAGAAAAAAAAGGAAGAG
21466901 AAAAGA-AAGAAAAAAGGAAGAG
1 AAAAGAGAA-AAAAAAGGAAGAG
21466923 AA
1 AA
21466925 GGGGAGGCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.09
21 12 0.55
22 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (22 bp):
AAAAGAGAAAAAAAAGGAAGAG
Found at i:21467059 original size:12 final size:12
Alignment explanation
Indices: 21467032--21467074 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
21467022 AAAAAGAGAG
*
21467032 AAAAAGAAAGAGA
1 AAAAAGAAA-ATA
21467045 AAAAAGAAAATA
1 AAAAAGAAAATA
*
21467057 AAAAAGGAAATA
1 AAAAAGAAAATA
21467069 ATAAAA
1 A-AAAA
21467075 AATAAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 14 0.52
13 13 0.48
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAAGAAAATA
Done.