Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 109 of 141
Found at i:35323552 original size:21 final size:21
Alignment explanation
Indices: 35323528--35323603 Score: 54
Period size: 21 Copynumber: 3.7 Consensus size: 21
35323518 TACAACTGTG
35323528 TTAATATATAATTACAAATAT
1 TTAATATATAATTACAAATAT
*
35323549 TTAAT-TATTA-TACTTAAATAT
1 TTAATATATAATTAC--AAATAT
* *
35323570 TTAAAATA-AAGTTA-ATATAT
1 TTAATATATAA-TTACAAATAT
35323590 TATAATAT-TAATTA
1 T-TAATATATAATTA
35323604 ATTTGAACAT
Statistics
Matches: 43, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
19 3 0.07
20 13 0.30
21 23 0.53
22 2 0.05
23 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (21 bp):
TTAATATATAATTACAAATAT
Found at i:35330687 original size:27 final size:26
Alignment explanation
Indices: 35330656--35330797 Score: 135
Period size: 27 Copynumber: 5.3 Consensus size: 26
35330646 ACCCCAAAAT
**
35330656 AGGTAAAATGACCAAAATAGCCCCATA
1 AGGTAAAATGACTGAAATA-CCCCATA
**
35330683 AGGTAAAATGACTGAAATACCCCCGA
1 AGGTAAAATGACTGAAATACCCCATA
* *
35330709 AGGGTAAAATGACCGAAATACCTC-TGA
1 A-GGTAAAATGACTGAAATACCCCAT-A
*
35330736 AGGGTAAAATGATTGAAATACCCC-TAA
1 A-GGTAAAATGACTGAAATACCCCAT-A
35330763 AGGGTAAAATGACTGAAATACCCCCATA
1 A-GGTAAAATGACTGAAATA-CCCCATA
*
35330791 GGGTAAA
1 AGGTAAA
35330798 CTAATTTTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
26 6 0.06
27 86 0.88
28 5 0.05
29 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.18
Consensus pattern (26 bp):
AGGTAAAATGACTGAAATACCCCATA
Found at i:35330742 original size:54 final size:53
Alignment explanation
Indices: 35330657--35330797 Score: 176
Period size: 54 Copynumber: 2.6 Consensus size: 53
35330647 CCCCAAAATA
* *
35330657 GGTAAAATGACCAAAATAGCCCCATAAGGTAAAATGACTGAAATACCCCCGAAG
1 GGTAAAATGACCGAAATA-CCCCATAAGGTAAAATGACTGAAATACCCCCAAAG
* * *
35330711 GGTAAAATGACCGAAATACCTC-TGAAGGGTAAAATGATTGAAATACCCCTAAAG
1 GGTAAAATGACCGAAATACCCCAT-AA-GGTAAAATGACTGAAATACCCCCAAAG
* *
35330765 GGTAAAATGACTGAAATACCCCCATAGGGTAAA
1 GGTAAAATGACCGAAATA-CCCCATAAGGTAAA
35330798 CTAATTTTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
52 1 0.01
53 5 0.07
54 64 0.85
55 4 0.05
56 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (53 bp):
GGTAAAATGACCGAAATACCCCATAAGGTAAAATGACTGAAATACCCCCAAAG
Found at i:35332458 original size:53 final size:53
Alignment explanation
Indices: 35332400--35332502 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
35332390 GTAAACAAAG
* *
35332400 TAAGCTTTTATAGCTTAGTAATTTTATAGCATAACCACAAATATATATATTTA
1 TAAGCTTTTATAGCTTAGTAAGTCTATAGCATAACCACAAATATATATATTTA
35332453 TAAGCTTTTATAGCTTAGTAAGTCTATAGCATAACCACAAATATATATAT
1 TAAGCTTTTATAGCTTAGTAAGTCTATAGCATAACCACAAATATATATAT
35332503 AAATATATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (53 bp):
TAAGCTTTTATAGCTTAGTAAGTCTATAGCATAACCACAAATATATATATTTA
Found at i:35333484 original size:41 final size:41
Alignment explanation
Indices: 35333408--35333485 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
35333398 CCGAAATGTA
** *
35333408 TCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATT
1 TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTATT
* *
35333449 TCACCGGCATTAAGCCTGCTAGGCACATAGCCTGAAT
1 TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAAT
35333486 AACTGAGATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTATT
Found at i:35336569 original size:21 final size:21
Alignment explanation
Indices: 35336545--35336586 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35336535 TGGTTTGTCC
*
35336545 ATGAGTGCTTCGTCCACAATG
1 ATGAGTGCTTCATCCACAATG
* *
35336566 ATGAGTGGTTTATCCACAATG
1 ATGAGTGCTTCATCCACAATG
35336587 TGGTGTAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (21 bp):
ATGAGTGCTTCATCCACAATG
Found at i:35340852 original size:13 final size:13
Alignment explanation
Indices: 35340834--35340858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35340824 GAATATATTT
35340834 ATTAATTAAAAAC
1 ATTAATTAAAAAC
35340847 ATTAATTAAAAA
1 ATTAATTAAAAA
35340859 TAAAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:35344095 original size:18 final size:18
Alignment explanation
Indices: 35344068--35344111 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
35344058 GTTCGTTTTT
35344068 AAAACATTATTC-ATTTAC
1 AAAACATTATTCAATTT-C
*
35344086 AAATCATTATTCAATTTC
1 AAAACATTATTCAATTTC
35344104 AAAACATT
1 AAAACATT
35344112 TTCTTATTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAACATTATTCAATTTC
Found at i:35344835 original size:131 final size:132
Alignment explanation
Indices: 35344667--35344930 Score: 503
Period size: 131 Copynumber: 2.0 Consensus size: 132
35344657 CAAATAACCT
35344667 GTAGCCTTAATCATAAAAACTTATATAAACTTAATTTGGAGAAAGAATTATGCTAGACTATAACC
1 GTAGCCTTAA-CATAAAAACTTATATAAACTTAATTTGGAGAAAGAATTATGCTAGACTATAACC
*
35344732 CTTTTTATAATATGTAAATTAAGTAAAAAATAATATAATATTTATAATATTTAACCTTTATAAAA
65 CTTTTTATAATATGTAAATTAAGTAAAAAAAAATATAATATTTATAATATTTAACCTTTATAAAA
35344797 AAG
130 AAG
35344800 GTAGCCTTAA-ATAAAAACTTATATAAACTTAATTTGGAGAAAGAATTATGCTAGACTATAACCC
1 GTAGCCTTAACATAAAAACTTATATAAACTTAATTTGGAGAAAGAATTATGCTAGACTATAACCC
35344864 TTTTTATAATATGTAAATTAAGTAAAAAAAAATATAATATTTATAATATTTAACCTTTATAAAAA
66 TTTTTATAATATGTAAATTAAGTAAAAAAAAATATAATATTTATAATATTTAACCTTTATAAAAA
35344929 AG
131 AG
35344931 TGTTTTTTTA
Statistics
Matches: 130, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
131 120 0.92
133 10 0.08
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (132 bp):
GTAGCCTTAACATAAAAACTTATATAAACTTAATTTGGAGAAAGAATTATGCTAGACTATAACCC
TTTTTATAATATGTAAATTAAGTAAAAAAAAATATAATATTTATAATATTTAACCTTTATAAAAA
AG
Found at i:35345095 original size:26 final size:28
Alignment explanation
Indices: 35345036--35345096 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
35345026 GTTATTAAAA
* *
35345036 AAATTATAACATTTTTTTATGAATAAAT
1 AAATTATAACATCTTTTTATGAACAAAT
* *
35345064 ATATTATAACA-CTTTTTAT-AACATAT
1 AAATTATAACATCTTTTTATGAACAAAT
35345090 AAATTAT
1 AAATTAT
35345097 TTTTATAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 11 0.39
27 7 0.25
28 10 0.36
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (28 bp):
AAATTATAACATCTTTTTATGAACAAAT
Found at i:35346319 original size:26 final size:28
Alignment explanation
Indices: 35346260--35346320 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
35346250 GTTATTAAAA
* *
35346260 AAATTATAACATTTTTTTATGAATAAAT
1 AAATTATAACATCTTTTTATGAACAAAT
* *
35346288 ATATTATAACA-CTTTTTAT-AACATAT
1 AAATTATAACATCTTTTTATGAACAAAT
35346314 AAATTAT
1 AAATTAT
35346321 TTTTATAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 11 0.39
27 7 0.25
28 10 0.36
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (28 bp):
AAATTATAACATCTTTTTATGAACAAAT
Found at i:35347171 original size:18 final size:18
Alignment explanation
Indices: 35347144--35347187 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
35347134 GTTCGTTTTT
35347144 AAAACATTATTC-ATTTAC
1 AAAACATTATTCAATTT-C
*
35347162 AAATCATTATTCAATTTC
1 AAAACATTATTCAATTTC
35347180 AAAACATT
1 AAAACATT
35347188 TTCTTATTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAACATTATTCAATTTC
Found at i:35352311 original size:32 final size:32
Alignment explanation
Indices: 35352272--35352332 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
35352262 AAATACGAGA
* * * *
35352272 ATTTTTTTAACATGAAGATTTTTGAAACAATT
1 ATTTTTTTAAAACGAAAATTTATGAAACAATT
35352304 ATTTTTTTAAAACGAAAATTTATGAAACA
1 ATTTTTTTAAAACGAAAATTTATGAAACA
35352333 CGAGATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (32 bp):
ATTTTTTTAAAACGAAAATTTATGAAACAATT
Found at i:35352335 original size:17 final size:17
Alignment explanation
Indices: 35352306--35352662 Score: 242
Period size: 17 Copynumber: 20.5 Consensus size: 17
35352296 AAACAATTAT
*
35352306 TTTTTTAAA-ACGAAAA
1 TTTTTGAAACACGAAAA
* **
35352322 TTTATGAAACACGAGATT
1 TTTTTGAAACACGA-AAA
*
35352340 TTCTTTGAAAACACAAAAA
1 TT-TTTG-AAACACGAAAA
**
35352359 TTTTCAAAACACCG-AAA
1 TTTTTGAAACA-CGAAAA
* **
35352376 TTTTTGAAAATACGAGGA
1 TTTTTG-AAACACGAAAA
** *
35352394 TTTTTGAAACAATAGAAT
1 TTTTTGAAACACGA-AAA
35352412 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* *
35352430 ATTTTGAAAACCCGAAAA
1 TTTTTG-AAACACGAAAA
* ** *
35352448 TTTTTAAAACGGGAAAT
1 TTTTTGAAACACGAAAA
35352465 TTTTTGAAACAACG-AAA
1 TTTTTGAAAC-ACGAAAA
35352482 TTTTTGAAAACAC-AAAGA
1 TTTTTG-AAACACGAAA-A
35352500 TTTTTGAAACACGCAAAA
1 TTTTTGAAACACG-AAAA
35352518 -TTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
*
35352535 TTTTTGAAATACGAAAA
1 TTTTTGAAACACGAAAA
*
35352552 -TTTAGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* *
35352568 TTTTTAAAACACGACAA
1 TTTTTGAAACACGAAAA
* *
35352585 TTTTTTAAACACGAGAATTT
1 TTTTTGAAACACGA-AA--A
* *
35352605 TTTTTAAAACATGAAAA
1 TTTTTGAAACACGAAAA
*
35352622 TTTTAGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* * *
35352639 TTCTTAAAACAC-AAAT
1 TTTTTGAAACACGAAAA
35352655 TTTTTGAA
1 TTTTTGAA
35352663 TATTTTCGAT
Statistics
Matches: 263, Mismatches: 57, Indels: 42
0.73 0.16 0.12
Matches are distributed among these distances:
16 30 0.11
17 126 0.48
18 71 0.27
19 17 0.06
20 19 0.07
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:35352382 original size:35 final size:34
Alignment explanation
Indices: 35352315--35352658 Score: 259
Period size: 35 Copynumber: 9.8 Consensus size: 34
35352305 TTTTTTTAAA
* *
35352315 ACGAAAATTTATGAAACACGAGATTTTCTTTGAAAAC
1 ACGAAAATTTTTGAAACACGA-A-ATT-TTTGAAAAC
* ** *
35352352 ACAAAAATTTTCAAAACACCGAAATTTTTGAAAAT
1 ACGAAAATTTTTGAAACA-CGAAATTTTTGAAAAC
** * *
35352387 ACGAGGATTTTTGAAACAATAGAATTTTTTGAAAAC
1 ACGAAAATTTTTGAAAC-A-CGAAATTTTTGAAAAC
* *
35352423 ACGAAAAATTTTGAAAACCCGAAAATTTTT-AAAAC
1 ACGAAAATTTTTG-AAACACG-AAATTTTTGAAAAC
** *
35352458 GGGAAATTTTTTGAAACAACGAAATTTTTGAAAAC
1 ACGAAAATTTTTGAAAC-ACGAAATTTTTGAAAAC
*
35352493 AC-AAAGATTTTTGAAACACGCAAAATTTTGAAAAC
1 ACGAAA-ATTTTTGAAACACG-AAATTTTTGAAAAC
* * *
35352528 ACGAAAATTTTTGAAATACGAAAATTTAG-AAAC
1 ACGAAAATTTTTGAAACACGAAATTTTTGAAAAC
* *
35352561 ACGAAAATTTTTAAAACACGACAATTTTT-TAAAC
1 ACGAAAATTTTTGAAACACGA-AATTTTTGAAAAC
* * * *
35352595 ACGAGAATTTTTTTTAAAACATGAAAATTTT-AGAAAC
1 ACGA-AA--ATTTTTGAAACACGAAATTTTTGA-AAAC
* *
35352632 ACGAAAATTCTTAAAACAC-AAATTTTT
1 ACGAAAATTTTTGAAACACGAAATTTTT
35352659 TGAATATTTT
Statistics
Matches: 248, Mismatches: 44, Indels: 34
0.76 0.13 0.10
Matches are distributed among these distances:
33 30 0.12
34 49 0.20
35 82 0.33
36 44 0.18
37 40 0.16
38 3 0.01
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (34 bp):
ACGAAAATTTTTGAAACACGAAATTTTTGAAAAC
Found at i:35352624 original size:37 final size:37
Alignment explanation
Indices: 35352500--35352640 Score: 136
Period size: 37 Copynumber: 4.0 Consensus size: 37
35352490 AACACAAAGA
*
35352500 TTTTTGAAACACGCAAAATTTT-GAAAACACGAAAA---
1 TTTTTAAAACACG-AAAATTTTAG-AAACACGAAAATTT
* *
35352535 TTTTTGAAATACGAAAA-TTTAGAAACACGAAAA---
1 TTTTTAAAACACGAAAATTTTAGAAACACGAAAATTT
* ** *
35352568 TTTTTAAAACACGACAATTTTTTAAACACGAGAATTT
1 TTTTTAAAACACGAAAATTTTAGAAACACGAAAATTT
*
35352605 TTTTTAAAACATGAAAATTTTAGAAACACGAAAATT
1 TTTTTAAAACACGAAAATTTTAGAAACACGAAAATT
35352641 CTTAAAACAC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
33 28 0.31
34 18 0.20
35 12 0.13
37 31 0.35
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (37 bp):
TTTTTAAAACACGAAAATTTTAGAAACACGAAAATTT
Found at i:35352632 original size:54 final size:53
Alignment explanation
Indices: 35352460--35352659 Score: 148
Period size: 50 Copynumber: 3.8 Consensus size: 53
35352450 TTTAAAACGG
* * * **
35352460 GAAATTTTTTGAAACAACG-AAATTTTTGAAAACACAAA-GATTTTT-GAAACAC
1 GAAAATTTTTAAAAC-ACGAAAATTCTT-AAAACACAAATTTTTTTTAGAAACAC
* * * * *
35352512 GCAAAATTTTGAAAACACGAAAATTTTTGAAATACGAAA----ATTTAGAAACAC
1 G-AAAATTTTTAAAACACGAAAATTCTTAAAACAC-AAATTTTTTTTAGAAACAC
* * * *
35352563 GAAAATTTTTAAAACACGACAATTTTTTAAACACGAGAATTTTTTTTA-AAACAT
1 GAAAATTTTTAAAACACGAAAATTCTTAAAACAC-A-AATTTTTTTTAGAAACAC
35352617 GAAAA-TTTTAGAAACACGAAAATTCTTAAAACACAAATTTTTT
1 GAAAATTTTTA-AAACACGAAAATTCTTAAAACACAAATTTTTT
35352660 GAATATTTTC
Statistics
Matches: 123, Mismatches: 15, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
50 34 0.28
51 10 0.08
52 17 0.14
53 28 0.23
54 30 0.24
55 4 0.03
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.32
Consensus pattern (53 bp):
GAAAATTTTTAAAACACGAAAATTCTTAAAACACAAATTTTTTTTAGAAACAC
Found at i:35352923 original size:7 final size:7
Alignment explanation
Indices: 35352911--35352951 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
35352901 ATTGAACCTT
35352911 TTTTTTC
1 TTTTTTC
35352918 TTTTTTTC
1 -TTTTTTC
35352926 TTTTTTC
1 TTTTTTC
35352933 -TTTTTC
1 TTTTTTC
35352939 TTTTTTC
1 TTTTTTC
35352946 TTTTTT
1 TTTTTT
35352952 TTCTCTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 7 0.22
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:35352923 original size:8 final size:8
Alignment explanation
Indices: 35352910--35352971 Score: 69
Period size: 9 Copynumber: 7.9 Consensus size: 8
35352900 AATTGAACCT
35352910 TTTTTTTC
1 TTTTTTTC
35352918 TTTTTTTC
1 TTTTTTTC
35352926 -TTTTTTC
1 TTTTTTTC
35352933 --TTTTTC
1 TTTTTTTC
35352939 -TTTTTTC
1 TTTTTTTC
35352946 TTTTTTTTC
1 -TTTTTTTC
35352955 TCTTTTTCTC
1 T-TTTTT-TC
35352965 TTTTTTT
1 TTTTTTT
35352972 TCTGCTGGGC
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
6 6 0.12
7 13 0.27
8 10 0.20
9 17 0.35
10 3 0.06
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTC
Found at i:35353276 original size:20 final size:20
Alignment explanation
Indices: 35353251--35353323 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
35353241 TCAATTATTT
35353251 TTTTCTTTTTTTCCTTTTTC
1 TTTTCTTTTTTTCCTTTTTC
* *
35353271 TTTTCTGTTTTTCTTTCTTTC
1 TTTTCTTTTTTTCCTT-TTTC
* * *
35353292 TTCTTCGTCTTCTTCCTTCTTC
1 TT-TTC-TTTTTTTCCTTTTTC
35353314 -TTTCTTTTTT
1 TTTTCTTTTTT
35353324 CTTCTCCGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.10
20 17 0.40
21 7 0.17
22 6 0.14
23 8 0.19
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTCTTTTTTTCCTTTTTC
Found at i:35353764 original size:58 final size:60
Alignment explanation
Indices: 35353688--35353803 Score: 173
Period size: 58 Copynumber: 2.0 Consensus size: 60
35353678 TTATGGGTCA
** *
35353688 AAATGTAATTTTGTGAAAGTTTAGGGGTCAAAATGTAA-TTTA-AAAATTTTAGGGGTTG
1 AAATGTAATTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAATTTTAGGGGTTG
* *
35353746 AAATGTAGTTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAACATTTTAGGGGT
1 AAATGTAATTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAATTTTAGGGGT
35353804 CAAAATGCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 34 0.67
59 4 0.08
60 13 0.25
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (60 bp):
AAATGTAATTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAATTTTAGGGGTTG
Found at i:35353813 original size:30 final size:30
Alignment explanation
Indices: 35353663--35353810 Score: 176
Period size: 30 Copynumber: 5.0 Consensus size: 30
35353653 GGCCAAAACA
*
35353663 TAATTTTGAGAAAGTTTATGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
*
35353693 TAATTTTGTGAAAGTTTAGGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
* * **
35353723 TAA-TTT-AAAAATTTTAGGGGTTGAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
* *
35353751 TAGTTTTAAGAAAGTTTAGGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
* *
35353781 CAATTTT-AGAACATTTTAGGGGTCAAAATG
1 TAATTTTGAGAA-AGTTTAGGGGTCAAAATG
35353811 CAAAAAAATT
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
28 19 0.19
29 10 0.10
30 71 0.71
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (30 bp):
TAATTTTGAGAAAGTTTAGGGGTCAAAATG
Found at i:35354427 original size:76 final size:76
Alignment explanation
Indices: 35354301--35355339 Score: 1267
Period size: 76 Copynumber: 13.7 Consensus size: 76
35354291 NNNNNNNNNN
35354301 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
35354366 AGTACCTCGGT
66 AGTACCTCGGT
35354377 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
35354442 AGTACCTCGGT
66 AGTACCTCGGT
35354453 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
35354518 AGTACCTCGGT
66 AGTACCTCGGT
35354529 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
35354594 AGTACCTCGGT
66 AGTACCTCGGT
35354605 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
35354670 AGTACCTCGGT
66 AGTACCTCGGT
35354681 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
35354746 AGTACCTCGGT
66 AGTACCTCGGT
35354757 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
35354822 AGTACCTCGGT
66 AGTACCTCGGT
35354833 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGATAAA-TT-
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTG-AAAAA-C-GA-AAATTTG
* *
35354896 AAA-AA-TACCTCAGC
61 AAAGAAGTACCTCGGT
* * * * *
35354910 GTGACCTGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAAGACATAAATT-A
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT--GAAAAACGA-A-AATTTGA
* *
35354974 AA-AA-TACCTCAGC
62 AAGAAGTACCTCGGT
* * * * * * * * *
35354987 GTGACCCAACGCTCGACTTACCTCTGTTTTATGAGTTGATTTTTTTAAAAAAAGACATAAATT-A
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA--TTTTTGAAAAACGA-A-AATTTGA
* *
35355051 AA-AA-TACCTCAGC
62 AAGAAGTACCTCGGT
* * * * * * ** * *
35355064 GTGACCCAACGCTCGACTTACCTCTGTTTTATGAGTT-A-TTTAAAAAAAAGAGATAAATT-AAA
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGA-A-AATTTGAAA
* *
35355126 -AA-TACCTCAGC
64 GAAGTACCTCGGT
* * ** * *
35355137 GTGACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTTAAAAAAAAAGACATAAATT-AA
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT-TGAAAAACGA-A-AATTTGAA
* *
35355201 A-AA-TACCTCAGC
63 AGAAGTACCTCGGT
* ** *
35355213 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATATTTAAAAAAAAAGATCGAAA-TT-
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAT-TTT-TGAAAAACGA---AAATTTG
* *
35355276 AAA-AA-TACCTCAGC
61 AAAGAAGTACCTCGGT
* * * *
35355290 GTGACCCGAGGCTCAACTTACATCTGTATTATGAGTTGATATTTGAAAAA
1 ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAA
35355340 AACAGAAAGT
Statistics
Matches: 917, Mismatches: 29, Indels: 35
0.93 0.03 0.04
Matches are distributed among these distances:
73 64 0.07
74 1 0.00
75 11 0.01
76 575 0.63
77 240 0.26
78 9 0.01
79 10 0.01
80 4 0.00
81 3 0.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (76 bp):
ATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTGAAAGA
AGTACCTCGGT
Found at i:35356259 original size:20 final size:19
Alignment explanation
Indices: 35356231--35356296 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 19
35356221 TTCATTTTGA
35356231 TTTTTCTTTCTTTT-TTTCT
1 TTTTTCTTTCTTTTGTTT-T
35356250 TTTTTCCTTTCTTTTGTTTT
1 TTTTT-CTTTCTTTTGTTTT
35356270 TTTTGTCTGTT-TTTTGTCTGTT
1 TTTT-TCT-TTCTTTTGT-T-TT
35356292 TTTTT
1 TTTTT
35356297 TGTTTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
19 5 0.12
20 22 0.54
21 8 0.20
22 6 0.15
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTCTTTTGTTTT
Found at i:35356282 original size:11 final size:10
Alignment explanation
Indices: 35356268--35356325 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 10
35356258 TTCTTTTGTT
35356268 TTTTTTGTCTG
1 TTTTTT-TCTG
35356279 TTTTTTGTCTG
1 TTTTTT-TCTG
35356290 TTTTTTT-TG
1 TTTTTTTCTG
*
35356299 TTTTTTTTCTA
1 -TTTTTTTCTG
35356310 TTTTTTT-TG
1 TTTTTTTCTG
35356319 TTTTTTT
1 TTTTTTT
35356326 AAGCATAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
9 10 0.23
10 15 0.35
11 18 0.42
ACGTcount: A:0.02, C:0.05, G:0.10, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTG
Found at i:35356282 original size:13 final size:13
Alignment explanation
Indices: 35356264--35356299 Score: 58
Period size: 11 Copynumber: 2.9 Consensus size: 13
35356254 TCCTTTCTTT
35356264 TGTTTTTTTTGTC
1 TGTTTTTTTTGTC
35356277 TG--TTTTTTGTC
1 TGTTTTTTTTGTC
35356288 TGTTTTTTTTGT
1 TGTTTTTTTTGT
35356300 TTTTTTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.00, C:0.06, G:0.17, T:0.78
Consensus pattern (13 bp):
TGTTTTTTTTGTC
Found at i:35356325 original size:20 final size:20
Alignment explanation
Indices: 35356277--35356325 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
35356267 TTTTTTTGTC
* *
35356277 TGTTTTTTGTCTGTTTTTTT
1 TGTTTTTTTTCTATTTTTTT
35356297 TGTTTTTTTTCTATTTTTTT
1 TGTTTTTTTTCTATTTTTTT
35356317 TGTTTTTTT
1 TGTTTTTTT
35356326 AAGCATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.84
Consensus pattern (20 bp):
TGTTTTTTTTCTATTTTTTT
Found at i:35363484 original size:32 final size:32
Alignment explanation
Indices: 35363445--35363567 Score: 149
Period size: 32 Copynumber: 3.7 Consensus size: 32
35363435 AATACGAGAA
*
35363445 ATTTTTTTAACACGAAAATTTTTGAAACAATT
1 ATTTTTTTAAAACGAAAATTTTTGAAACAATT
*
35363477 ATTTTTTTAAAACGAAAATTTATGAAACACGAGATT
1 ATTTTTTTAAAACGAAAATTTTTG-AA-AC-A-ATT
*
35363513 -TTTTTTGAAAACACGAAAATTTTTGAAACAATT
1 ATTTTTT-TAAA-ACGAAAATTTTTGAAACAATT
35363546 ATTTTTTTTAAAACGAAAATTT
1 A-TTTTTTTAAAACGAAAATTT
35363568 ATAAAACACG
Statistics
Matches: 78, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
32 22 0.28
33 15 0.19
34 6 0.08
35 15 0.19
36 8 0.10
37 12 0.15
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (32 bp):
ATTTTTTTAAAACGAAAATTTTTGAAACAATT
Found at i:35363541 original size:17 final size:17
Alignment explanation
Indices: 35363438--35363870 Score: 243
Period size: 17 Copynumber: 24.9 Consensus size: 17
35363428 CGATCAAAAT
**
35363438 ACGAGAAATTTTTTTAAC
1 ACGA-AAATTTTTGAAAC
35363456 ACGAAAATTTTTGAAAC
1 ACGAAAATTTTTGAAAC
* * *
35363473 A--ATTATTTTTTTAAA-
1 ACGA-AAATTTTTGAAAC
*
35363488 ACGAAAATTTATGAAAC
1 ACGAAAATTTTTGAAAC
**
35363505 ACGAGATTTTTTTTGAAAAC
1 ACGA-A-AATTTTTG-AAAC
35363525 ACGAAAATTTTTGAAAC
1 ACGAAAATTTTTGAAAC
*** ** *
35363542 AATTATTTTTTTTAAA-
1 ACGAAAATTTTTGAAAC
* *
35363558 ACGAAAATTTATAAAAC
1 ACGAAAATTTTTGAAAC
**
35363575 ACGAGATTTTTTTTGAAAAC
1 ACGA-A-AATTTTTG-AAAC
**
35363595 ACGAAAATTTTCAAAAC
1 ACGAAAATTTTTGAAAC
35363612 ACCG-AAATTTTTGAAAAC
1 A-CGAAAATTTTTG-AAAC
**
35363630 ACGAGGATTTTTGAAAC
1 ACGAAAATTTTTGAAAC
* *
35363647 AAGAGAATTTTTTGAAAAC
1 ACGA-AAATTTTTG-AAAC
*
35363666 ACGAAAAATTTTGAAAAC
1 ACGAAAATTTTTG-AAAC
* *
35363684 CCGAAAATTTTTAAAAC
1 ACGAAAATTTTTGAAAC
** ** *
35363701 GGGAATTTTTTTGAAAT
1 ACGAAAATTTTTGAAAC
35363718 ACCG-AAATTTTTGAAAAC
1 A-CGAAAATTTTTG-AAAC
* *
35363736 ACGAAAATTTTTAAAAT
1 ACGAAAATTTTTGAAAC
*
35363753 ACGAAAA-TTTAGAAAC
1 ACGAAAATTTTTGAAAC
* *
35363769 ACGAGAATTTTTAAAAC
1 ACGAAAATTTTTGAAAC
*
35363786 ACGACAATTTTTGAAAC
1 ACGAAAATTTTTGAAAC
* *
35363803 ACGAGAATTTTTTTTAAAAC
1 ACGA-AA--ATTTTTGAAAC
* *
35363823 ATGAAAATTTTAGAAAC
1 ACGAAAATTTTTGAAAC
* *
35363840 ACGAAAATTCTTAAAAC
1 ACGAAAATTTTTGAAAC
*
35363857 AC-AAATTTTTTGAA
1 ACGAAAATTTTTGAA
35363871 TATTTTCGAT
Statistics
Matches: 308, Mismatches: 84, Indels: 48
0.70 0.19 0.11
Matches are distributed among these distances:
15 2 0.01
16 47 0.15
17 139 0.45
18 72 0.23
19 20 0.06
20 28 0.09
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (17 bp):
ACGAAAATTTTTGAAAC
Found at i:35363612 original size:70 final size:69
Alignment explanation
Indices: 35363453--35363605 Score: 288
Period size: 70 Copynumber: 2.2 Consensus size: 69
35363443 AAATTTTTTT
*
35363453 AACACGAAAATTTTTGAAACAATTATTTTTTTAAAACGAAAATTTATGAAACACGAGATTTTTTT
1 AACACGAAAATTTTTGAAACAATTATTTTTTTAAAACGAAAATTTATAAAACACGAGATTTTTTT
35363518 TGAA
66 TGAA
35363522 AACACGAAAATTTTTGAAACAATTATTTTTTTTAAAACGAAAATTTATAAAACACGAGATTTTTT
1 AACACGAAAATTTTTGAAACAATTA-TTTTTTTAAAACGAAAATTTATAAAACACGAGATTTTTT
35363587 TTGAA
65 TTGAA
35363592 AACACGAAAATTTT
1 AACACGAAAATTTT
35363606 CAAAACACCG
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
69 25 0.30
70 57 0.70
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (69 bp):
AACACGAAAATTTTTGAAACAATTATTTTTTTAAAACGAAAATTTATAAAACACGAGATTTTTTT
TGAA
Found at i:35363623 original size:35 final size:34
Alignment explanation
Indices: 35363453--35363866 Score: 272
Period size: 37 Copynumber: 11.9 Consensus size: 34
35363443 AAATTTTTTT
* * **
35363453 AACACGAAAATTTTTGAAACA--ATTATTTTTTTA
1 AACACGAAAATTTTTAAAACACGA-AATTTTTGAA
* * *
35363486 AA-ACGAAAATTTATGAAACACGAGATTTTTTTTGAA
1 AACACGAAAATTTTTAAAACACGA-A--ATTTTTGAA
* *** * **
35363522 AACACGAAAATTTTTGAAACAATTATTTTTTTTA
1 AACACGAAAATTTTTAAAACACGAAATTTTTGAA
* *
35363556 AA-ACGAAAATTTATAAAACACGAGATTTTTTTTGAA
1 AACACGAAAATTTTTAAAACACGA-A--ATTTTTGAA
*
35363592 AACACGAAAATTTTCAAAACACCGAAATTTTTGAA
1 AACACGAAAATTTTTAAAACA-CGAAATTTTTGAA
** * *
35363627 AACACGAGGATTTTTGAAACAAGAGAATTTTTTGAA
1 AACACGAAAATTTTTAAAACACGA-AA-TTTTTGAA
* *
35363663 AACACGAAAAATTTTGAAAACCCGAAAATTTTT-AA
1 AACACG-AAAATTTTTAAAACACG-AAATTTTTGAA
** **
35363698 AACGGGAATTTTTTTGAAATAC-CGAAATTTTTGAA
1 AACACGAAAATTTTT-AAA-ACACGAAATTTTTGAA
* * *
35363733 AACACGAAAATTTTTAAAATACGAAAATTTAG-A
1 AACACGAAAATTTTTAAAACACGAAATTTTTGAA
*
35363766 AACACGAGAATTTTTAAAACACGACAATTTTTG-A
1 AACACGAAAATTTTTAAAACACGA-AATTTTTGAA
* * *
35363800 AACACGAGAATTTTTTTTAAAACATGAAAATTTT-AGA
1 AACACGA-AA--ATTTTTAAAACACGAAATTTTTGA-A
*
35363837 AACACGAAAATTCTTAAAACAC-AAATTTTT
1 AACACGAAAATTTTTAAAACACGAAATTTTT
35363867 TGAATATTTT
Statistics
Matches: 300, Mismatches: 57, Indels: 48
0.74 0.14 0.12
Matches are distributed among these distances:
32 17 0.06
33 49 0.16
34 63 0.21
35 52 0.17
36 47 0.16
37 68 0.23
38 4 0.01
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (34 bp):
AACACGAAAATTTTTAAAACACGAAATTTTTGAA
Found at i:35363623 original size:70 final size:70
Alignment explanation
Indices: 35363479--35363701 Score: 261
Period size: 70 Copynumber: 3.2 Consensus size: 70
35363469 AAACAATTAT
** *
35363479 TTTTTTAAAACGAAAATTTATGAAACACGAGATTTTTTTTGAAAACACGAAAATTTTTGAAACAA
1 TTTTTTAAAACGAAAATTTATGAAACACGAGATTTTTTTTGAAAACACGAAAATTTTCAAAACAC
** **
35363544 TTATT
66 CGAAA
*
35363549 TTTTTTAAAACGAAAATTTATAAAACACGAGATTTTTTTTGAAAACACGAAAATTTTCAAAACAC
1 TTTTTTAAAACGAAAATTTATGAAACACGAGATTTTTTTTGAAAACACGAAAATTTTCAAAACAC
35363614 CGAAA
66 CGAAA
* ** * * * *
35363619 TTTTTGAAAACACGAGGATTTTTGAAACAAGAGA-ATTTTTTGAAAACACGAAAAATTTTGAAAA
1 TTTTT-TAAA-ACGAAAATTTATGAAACACGAGATTTTTTTTGAAAACACG-AAAATTTTCAAAA
35363683 C-CCGAAA
63 CACCGAAA
*
35363690 ATTTTTAAAACG
1 TTTTTTAAAACG
35363702 GGAATTTTTT
Statistics
Matches: 132, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
69 3 0.02
70 70 0.53
71 28 0.21
72 31 0.23
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (70 bp):
TTTTTTAAAACGAAAATTTATGAAACACGAGATTTTTTTTGAAAACACGAAAATTTTCAAAACAC
CGAAA
Found at i:35364200 original size:8 final size:8
Alignment explanation
Indices: 35364187--35364241 Score: 60
Period size: 8 Copynumber: 6.8 Consensus size: 8
35364177 ATTGAACCTG
35364187 TTTTTTCT
1 TTTTTTCT
35364195 TTTTTT-T
1 TTTTTTCT
35364202 TTTCTTT-T
1 TTT-TTTCT
35364210 TTTTTTCT
1 TTTTTTCT
*
35364218 CTTTTTCT
1 TTTTTTCT
35364226 TCTTTTTCT
1 T-TTTTTCT
35364235 CTTTTTT
1 -TTTTTT
35364242 TTCTGCTGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
7 7 0.17
8 21 0.51
9 12 0.29
10 1 0.02
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTCT
Found at i:35364201 original size:9 final size:9
Alignment explanation
Indices: 35364187--35364245 Score: 61
Period size: 9 Copynumber: 6.9 Consensus size: 9
35364177 ATTGAACCTG
35364187 TTTTTTCTT
1 TTTTTTCTT
35364196 TTTTTT-TT
1 TTTTTTCTT
*
35364204 TCTTTT-TT
1 TTTTTTCTT
*
35364212 TTTTCTCTT
1 TTTTTTCTT
*
35364221 TTTCTTC-T
1 TTTTTTCTT
*
35364229 TTTTCTCTT
1 TTTTTTCTT
35364238 TTTTTTCT
1 TTTTTTCT
35364246 GCTGGGCTGC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 19 0.47
9 21 0.52
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:35364203 original size:11 final size:11
Alignment explanation
Indices: 35364187--35364232 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
35364177 ATTGAACCTG
35364187 TTTTTTCTTTTT
1 TTTTTTC-TTTT
35364199 TTTTTTCTTTT
1 TTTTTTCTTTT
*
35364210 TTTTTTCTCTT
1 TTTTTTCTTTT
*
35364221 TTTCTTCTTTT
1 TTTTTTCTTTT
35364232 T
1 T
35364233 CTCTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 24 0.77
12 7 0.23
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:35364211 original size:19 final size:20
Alignment explanation
Indices: 35364187--35364243 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
35364177 ATTGAACCTG
35364187 TTTTTTCTTTTTTTTT-TTC
1 TTTTTTCTTTTTTTTTCTTC
*
35364206 TTTTTTTTTTCTCTTTTTCTTC
1 TTTTTTCTTT-T-TTTTTCTTC
35364228 TTTTTCTCTTTTTTTT
1 TTTTT-TCTTTTTTTT
35364244 CTGCTGGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 9 0.28
20 1 0.03
21 9 0.28
22 9 0.28
23 4 0.12
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTTTCTTTTTTTTTCTTC
Found at i:35364214 original size:17 final size:17
Alignment explanation
Indices: 35364188--35364245 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 17
35364178 TTGAACCTGT
35364188 TTTTTCTTTTTTTTTTTC
1 TTTTT-TTTTTTTTTTTC
35364206 TTTTTTTTTTCTCTTTTTC
1 TTTTTTTTTT-T-TTTTTC
35364225 TTCTTTTTCTCTTTTTTTTC
1 TT-TTTTT-T-TTTTTTTTC
35364245 T
1 T
35364246 GCTGGGCTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.14
18 6 0.17
19 8 0.23
20 12 0.34
21 2 0.06
22 2 0.06
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTTTTTTTTTTC
Found at i:35364237 original size:11 final size:10
Alignment explanation
Indices: 35364187--35364245 Score: 59
Period size: 11 Copynumber: 5.8 Consensus size: 10
35364177 ATTGAACCTG
35364187 TTTTTTCTT-
1 TTTTTTCTTC
*
35364196 TTTTTTTTTC
1 TTTTTTCTTC
*
35364206 TTTTTTTTTTC
1 -TTTTTTCTTC
35364217 TCTTTTTCTTC
1 T-TTTTTCTTC
35364228 TTTTTCTCTT-
1 TTTTT-TCTTC
35364238 TTTTTTCT
1 TTTTTTCT
35364246 GCTGGGCTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 11 0.25
10 10 0.23
11 23 0.52
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:35364545 original size:16 final size:16
Alignment explanation
Indices: 35364524--35364558 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35364514 CTATCAATTA
* *
35364524 TTTTTTTCTTTTTTCT
1 TTTTTTTCCTTTTCCT
35364540 TTTTTTTCCTTTTCCT
1 TTTTTTTCCTTTTCCT
35364556 TTT
1 TTT
35364559 CTCTTTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTCCTTTTCCT
Found at i:35364557 original size:23 final size:24
Alignment explanation
Indices: 35364526--35364571 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
35364516 ATCAATTATT
* *
35364526 TTTTTCTTTTTTCTTTTT-TTTCC
1 TTTTCCTTTTCTCTTTTTCTTTCC
35364549 TTTTCCTTTTCTCTTTTTCTTTC
1 TTTTCCTTTTCTCTTTTTCTTTC
35364572 TTTCTTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTCCTTTTCTCTTTTTCTTTCC
Found at i:35364980 original size:30 final size:30
Alignment explanation
Indices: 35364946--35365093 Score: 160
Period size: 30 Copynumber: 5.0 Consensus size: 30
35364936 GGCCAAAACA
* *
35364946 TAATTTTGAGAAAGTTTATGGGTCAAAATG
1 TAATTTTAAGAAAGTTTAGGGGTCAAAATG
**
35364976 TAATTTCGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTTAAGAAAGTTTAGGGGTCAAAATG
* * **
35365006 TAA-TTTAAAAAATTTTAGGGGTTGAAATG
1 TAATTTTAAGAAAGTTTAGGGGTCAAAATG
*
35365035 TAGTTTTAAGAAAGTTTAGGGGTC-AAATG
1 TAATTTTAAGAAAGTTTAGGGGTCAAAATG
*
35365064 CAATTTT-AGAACA-TTTCAGGGGTCAAAATG
1 TAATTTTAAGAA-AGTTT-AGGGGTCAAAATG
35365094 CAAAAAAAAT
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
28 7 0.07
29 40 0.40
30 53 0.53
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (30 bp):
TAATTTTAAGAAAGTTTAGGGGTCAAAATG
Found at i:35365093 original size:59 final size:59
Alignment explanation
Indices: 35364965--35365093 Score: 161
Period size: 59 Copynumber: 2.2 Consensus size: 59
35364955 GAAAGTTTAT
* * *
35364965 GGGTCAAAATGTAATTTCGAGAAAGTTTAGGGGTCAAAATGTAATTTAAAAAATTTTAG
1 GGGTCAAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAATGCAATTTAAAAAATTTCAG
** * * * *
35365024 GGGTTGAAATGTAGTTTTAAGAAAGTTTAGGGGTC-AAATGCAATTTTAGAACATTTCAG
1 GGGTCAAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAATGCAA-TTTAAAAAATTTCAG
35365083 GGGTCAAAATG
1 GGGTCAAAATG
35365094 CAAAAAAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 7 0.12
59 51 0.88
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (59 bp):
GGGTCAAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAATGCAATTTAAAAAATTTCAG
Found at i:35370413 original size:21 final size:21
Alignment explanation
Indices: 35370384--35370438 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
35370374 CATGGTCATA
35370384 TGGCTACTCCACACGTTCGTG
1 TGGCTACTCCACACGTTCGTG
* *
35370405 TGTCTACTCCACACGTTTGTG
1 TGGCTACTCCACACGTTCGTG
*
35370426 TGGCTATTCCACA
1 TGGCTACTCCACA
35370439 TGCCCATGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.33
Consensus pattern (21 bp):
TGGCTACTCCACACGTTCGTG
Found at i:35392903 original size:45 final size:45
Alignment explanation
Indices: 35392834--35393321 Score: 492
Period size: 45 Copynumber: 11.0 Consensus size: 45
35392824 AACAAATCAG
* * * * *
35392834 TGAAGATTGCAAATCCTATATCCCTGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* *
35392879 TGAAGATAACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * * *
35392924 TAAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * ** * *
35392969 TGAAGATAGCAAGTCGTATCTCCTTGAAGTTGCAACGGAGCAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * *
35393014 TGAAGATAGCAAATCCTATCTCCCTGAAGTTACAGTGGAGTAGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * *
35393059 TGAAGATAGTAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * * *
35393104 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGTAGCAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * * *
35393149 TGAAGATAGCAAATCTTATCTCCCTGAA-ATGACAGTAGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTG-CAGTGGAGTAGAT
* * * * *
35393194 TAAAAATA--ATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TGAAGATAGCA-AG-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * * * *
35393239 CG--CAT--CAAGTCTTATCTCCCTG-A-TTGCAGTGGAGAAAAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* *
35393278 TGAAGATAGCAAGTCTTATCTCTCTGAAGTTGCAG-AGAGTAGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
35393322 CACATTTAGT
Statistics
Matches: 359, Mismatches: 73, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
39 13 0.04
40 1 0.00
41 14 0.04
42 2 0.01
43 20 0.06
44 9 0.03
45 298 0.83
46 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (45 bp):
TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
Found at i:35392989 original size:90 final size:90
Alignment explanation
Indices: 35392834--35393437 Score: 518
Period size: 90 Copynumber: 6.9 Consensus size: 90
35392824 AACAAATCAG
* * * *
35392834 TGAAGATTGCAAATCCTATATCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAACAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCAAGTCTTATC
35392899 TCCCTGAAGTTGCAGTGGAGTAGAC
66 TCCCTGAAGTTGCAGTGGAGTAGAC
* * *
35392924 TAAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCGTATC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCAAGTCTTATC
* ** *
35392989 TCCTTGAAGTTGCAACGGAGCAGAC
66 TCCCTGAAGTTGCAGTGGAGTAGAC
* *
35393014 TGAAGATAGCAAATCCTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGATAGTAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCAAGTCTTATC
* * *
35393079 TCCCTAAAGTTGCAGTGGAGTGGAT
66 TCCCTGAAGTTGCAGTGGAGTAGAC
* * * * * * *
35393104 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGTAGCAGACTGAAGATAGCAAATCTTATC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCAAGTCTTATC
* * * *
35393169 TCCCTGAA-ATGACAGTAGAGTGGAT
66 TCCCTGAAGTTG-CAGTGGAGTAGAC
* * ** * * * * * * *
35393194 TAAAAATAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCG--CAT--CAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCAAGTCTTATC
* *
35393255 TCCCTG-A-TTGCAGTGGAGAAAAC
66 TCCCTGAAGTTGCAGTGGAGTAGAC
* * * * * * ** *
35393278 TGAAGATAGCAAGTCTTATCTCTCTGAAGTTGCAG-AGAGTAGA-T-CACAT--TTAGTCTTATT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCAAGTCTTATC
* *
35393338 TCCCTGAAGTTGTAGTGGAGCAGAC
66 TCCCTGAAGTTGCAGTGGAGTAGAC
* * * * * * ** * ** *
35393363 TGAATAAACCAAA--CTGATTTCCTTGAAGTTGCAGTGAAACAGATTGAAGAAAATAA-TCCTAT
1 TGAAGATAGCAAATCCT-ATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCAAGTCTTAT
35393425 CTCCCTGAAGTTG
65 CTCCCTGAAGTTG
35393438 TAGTAGAGCC
Statistics
Matches: 418, Mismatches: 85, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
83 25 0.06
84 53 0.13
85 29 0.07
86 17 0.04
87 2 0.00
88 19 0.05
89 4 0.01
90 269 0.64
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (90 bp):
TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCAAGTCTTATC
TCCCTGAAGTTGCAGTGGAGTAGAC
Found at i:35394636 original size:24 final size:22
Alignment explanation
Indices: 35394601--35394644 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
35394591 CAAGTAAAAT
35394601 GGGGTTTCATTTAGGGTTTGAATA
1 GGGGTTTCATTT--GGTTTGAATA
*
35394625 GGGGTTTTATTTGGTTTGAA
1 GGGGTTTCATTTGGTTTGAA
35394645 AAACGAGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.18, C:0.02, G:0.34, T:0.45
Consensus pattern (22 bp):
GGGGTTTCATTTGGTTTGAATA
Found at i:35395334 original size:26 final size:27
Alignment explanation
Indices: 35395284--35395335 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
35395274 TTATTAAACA
* *
35395284 TTTTTTTTAAAAATATTTGTATATTTG
1 TTTTTTCTAAAAATATGTGTATATTTG
*
35395311 TTTTTTCTAAAAA-ATGTGTGTATTT
1 TTTTTTCTAAAAATATGTGTATATTT
35395336 TATTGAAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (27 bp):
TTTTTTCTAAAAATATGTGTATATTTG
Found at i:35398506 original size:12 final size:12
Alignment explanation
Indices: 35398491--35398523 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35398481 TCAGTAGCAA
35398491 TGGCAGTGGTAG
1 TGGCAGTGGTAG
35398503 TGGCA-TCGGTAG
1 TGGCAGT-GGTAG
35398515 TGGCAGTGG
1 TGGCAGTGG
35398524 CTTGCTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 17 0.89
13 1 0.05
ACGTcount: A:0.15, C:0.12, G:0.48, T:0.24
Consensus pattern (12 bp):
TGGCAGTGGTAG
Found at i:35412077 original size:21 final size:21
Alignment explanation
Indices: 35412051--35412124 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
35412041 AATTAGTCTA
35412051 CAACACCTAGCCACTCACATG
1 CAACACCTAGCCACTCACATG
* * *
35412072 CAACACCTGCGCCACATCCCACTA
1 CAACACCT-AGCCAC-TCACA-TG
35412096 CAACACCTAGTCC-CTCACATG
1 CAACACCTAG-CCACTCACATG
35412117 CAACACCT
1 CAACACCT
35412125 GTGTTACATT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 17 0.40
22 9 0.21
23 6 0.14
24 11 0.26
ACGTcount: A:0.31, C:0.46, G:0.08, T:0.15
Consensus pattern (21 bp):
CAACACCTAGCCACTCACATG
Found at i:35415244 original size:98 final size:97
Alignment explanation
Indices: 35415073--35415255 Score: 312
Period size: 98 Copynumber: 1.9 Consensus size: 97
35415063 TTGTGCGAAG
* *
35415073 AAAACTCTTAGTTGTGCCCAAATCTCCCGTAATGAAACAAACCATAGGTAAGGATTCATACTCGA
1 AAAACTCTCAGTTGTGCCCAAATCTCCCGCAATGAAACAAACCATAGGTAAGGATTCATACTCGA
35415138 CACATTGAGTTTTCCCATCGATTTGTGTGGAC
66 CACATTGAGTTTTCCCATCGATTTGTGTGGAC
* *
35415170 AAAACTCTCGGTTGTGCCCAAATCTCCCGCAATCGAAGCAAACCATAGGTAAGGATTCATACTCG
1 AAAACTCTCAGTTGTGCCCAAATCTCCCGCAAT-GAAACAAACCATAGGTAAGGATTCATACTCG
*
35415235 ACACGTTGAGTTTTCCCATCG
65 ACACATTGAGTTTTCCCATCG
35415256 TTTTTAACTT
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
97 30 0.38
98 50 0.62
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (97 bp):
AAAACTCTCAGTTGTGCCCAAATCTCCCGCAATGAAACAAACCATAGGTAAGGATTCATACTCGA
CACATTGAGTTTTCCCATCGATTTGTGTGGAC
Found at i:35416643 original size:3 final size:3
Alignment explanation
Indices: 35416635--35416697 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
35416625 CTTATTTTCC
35416635 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
35416683 ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
35416698 TCCATGGACA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35416804 original size:5 final size:5
Alignment explanation
Indices: 35416785--35416824 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
35416775 TACATGTACA
35416785 TATTT TATTT ATATTT TATTT TATTAT TATTT TATCTT TA
1 TATTT TATTT -TATTT TATTT TATT-T TATTT TAT-TT TA
35416825 CAATTCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 18 0.56
6 14 0.44
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:35416806 original size:16 final size:16
Alignment explanation
Indices: 35416785--35416824 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
35416775 TACATGTACA
35416785 TATTTTATT-TATATTT
1 TATTTTATTAT-TATTT
35416801 TATTTTATTATTATTT
1 TATTTTATTATTATTT
35416817 TATCTTTA
1 TAT-TTTA
35416825 CAATTCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTTATTATTATTT
Found at i:35416817 original size:11 final size:10
Alignment explanation
Indices: 35416785--35416824 Score: 53
Period size: 11 Copynumber: 3.7 Consensus size: 10
35416775 TACATGTACA
35416785 TATTTTATTT
1 TATTTTATTT
35416795 ATATTTTATTT
1 -TATTTTATTT
35416806 TATTATTATTT
1 TATT-TTATTT
35416817 TATCTTTA
1 TAT-TTTA
35416825 CAATTCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 22 0.81
12 1 0.04
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTATTT
Found at i:35416957 original size:23 final size:22
Alignment explanation
Indices: 35416906--35416950 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 22
35416896 ATCCATGCAC
*
35416906 ATATACATGTATTTTTTATAATAT
1 ATATACA--TATTTTTTAAAATAT
35416930 ATATACATATTTTTTAGAAAT
1 ATATACATATTTTTTA-AAAT
35416951 TATTATAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 3 0.16
24 7 0.37
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
ATATACATATTTTTTAAAATAT
Found at i:35416984 original size:21 final size:23
Alignment explanation
Indices: 35416951--35416997 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
35416941 TTTTAGAAAT
35416951 TATTATAAGTTTT-TTGTTTTATA
1 TATTATAAGTTTTGTT-TTTTATA
35416974 TATT-TAA-TTTTGTTTTTTATA
1 TATTATAAGTTTTGTTTTTTATA
35416995 TAT
1 TAT
35416998 ATACTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 14 0.61
22 5 0.22
23 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (23 bp):
TATTATAAGTTTTGTTTTTTATA
Found at i:35418897 original size:19 final size:19
Alignment explanation
Indices: 35418873--35418917 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
35418863 AACGTCTCTT
*
35418873 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
35418892 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
35418911 TATGCAT
1 TTTGCAT
35418918 CAAAGACTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:35421657 original size:6 final size:6
Alignment explanation
Indices: 35421646--35421670 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35421636 AGTTTCAAAA
35421646 AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG A
35421671 TGGAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:35421692 original size:17 final size:17
Alignment explanation
Indices: 35421672--35421711 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
35421662 TGAAAATGAT
*
35421672 GGAAAAAGAAAAGGAAA
1 GGAAAAAGAAAAAGAAA
*
35421689 GGAAAAATAAAAAGAAA
1 GGAAAAAGAAAAAGAAA
*
35421706 AGAAAA
1 GGAAAA
35421712 GGAGAGGCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (17 bp):
GGAAAAAGAAAAAGAAA
Found at i:35423070 original size:45 final size:45
Alignment explanation
Indices: 35423007--35423673 Score: 879
Period size: 45 Copynumber: 14.8 Consensus size: 45
35422997 GAGCAGGTTG
* * * *
35423007 AAGATAGCAGATCTTGTCTTCCTATATTAGTAGCGAAGTAGATCG
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* * *
35423052 AAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
**
35423097 AAGATAGTAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* * * * **
35423142 AAGATAACATATCTTGCCTTCTTGTATTGACAGCT-AAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAG-TGAAGTAGATCA
* * *
35423187 AAGATAGCAGATCTTGTATTCCTATATTGGTAGTGAAGTAGATCG
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* * *
35423232 AAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* * *
35423277 AAGATAGCAGATCTTGTATTCCTATATTGGTAGTGAAGTAGATCG
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
35423322 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGACA-TAGATCA
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGA-AGTAGATCA
* * * * ** **
35423367 AAGATAATAGATATTGTCTTCCTGTATTGGCAGCAAAGTAGATTT
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* * * *
35423412 AAGATAGCAGATCTGGTCTTCCTATATTGGTAGTGAAGTAAATCG
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* **
35423457 AAGATAATAGATCTTGTCTTTTTATATTGGTAGTGAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* * * *
35423502 AAGATAATAGATATTGTCTTCTTATATTGGTAGTGAAGTAGATCG
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* *
35423547 AAGATAACAGATCTTGTCTTCCTGTATTGGTAGTGAAATAGATCA
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
*
35423592 AAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
*
35423637 AAGATAACAGATCTTGTCTTCCTATATTGGCAGTGAA
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAA
35423674 ACAAATCTTG
Statistics
Matches: 536, Mismatches: 82, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
44 2 0.00
45 532 0.99
46 2 0.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.33
Consensus pattern (45 bp):
AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
Found at i:35423249 original size:135 final size:135
Alignment explanation
Indices: 35423007--35423877 Score: 1063
Period size: 135 Copynumber: 6.6 Consensus size: 135
35422997 GAGCAGGTTG
* * * *
35423007 AAGATAGCAGATCTTGTCTTCCTATATTAGTAGCGAAGTAGATCGAAGATAACAGATCTTGTCTT
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTGTCTT
* * * ** *
35423072 CCTGTATTGGCAGCGAAGTAGATCAAAGATAGTAGATCTTGTCTTCCTATATTGGTAGTGAAGTA
66 CCTATATTGGTAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGTGAAGTA
35423137 GATCA
131 GATCA
* * * * ** * *
35423142 AAGATAACATATCTTGCCTTCTTGTATTGACAGCT-AAGTAGATCAAAGATAGCAGATCTTGTAT
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAG-TGAAGTAGATCGAAGATAGCAGATCTTGTCT
* * *
35423206 TCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
65 TCCTATATTGGTAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGTGAAGT
35423271 AGATCA
130 AGATCA
* * *
35423277 AAGATAGCAGATCTTGTATTCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGATCTTGTCTT
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTGTCTT
* * * **
35423342 CCTATATTGGTAGTGACA-TAGATCAAAGATAATAGATATTGTCTTCCTGTATTGGCAGCAAAGT
66 CCTATATTGGTAGTGA-AGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGTGAAGT
**
35423406 AGATTT
130 AGATCA
* * * **
35423412 AAGATAGCAGATCTGGTCTTCCTATATTGGTAGTGAAGTAAATCGAAGATAATAGATCTTGTCTT
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTGTCTT
** * * * *
35423477 TTTATATTGGTAGTGAAGTAGATCAAAGATAATAGATATTGTCTTCTTATATTGGTAGTGAAGTA
66 CCTATATTGGTAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGTGAAGTA
*
35423542 GATCG
131 GATCA
* * *
35423547 AAGATAACAGATCTTGTCTTCCTGTATTGGTAGTGAAATAGATCAAAGATAGCAGATCTTGTCTT
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTGTCTT
35423612 CCTATATTGGTAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGTG-A--A
66 CCTATATTGGTAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGTGAAGTA
35423674 -A-C-
131 GATCA
* * *
35423676 ------A-A-ATCTTGTCTTCCTATATTGGTAGCGAAATAGATTGAAGATAGCAGATCTTGTCTT
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTGTCTT
* * * *
35423733 CCTGTATTGGCAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTGTATTGGCAATGAAGTA
66 CCTATATTGGTAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGTGAAGTA
35423798 GATCA
131 GATCA
* * * * * ** *
35423803 AGGATAGCAGATCTTATCTTTCTATATTGGCAGCAAAGTAGATCAAAGATAGCAGATCTTGTCTT
1 AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTGTCTT
35423868 CCTATATTGG
66 CCTATATTGG
35423878 CAACGAAGAA
Statistics
Matches: 636, Mismatches: 82, Indels: 36
0.84 0.11 0.05
Matches are distributed among these distances:
121 107 0.17
122 2 0.00
123 1 0.00
124 1 0.00
125 1 0.00
126 1 0.00
130 1 0.00
131 1 0.00
132 1 0.00
134 4 0.01
135 515 0.81
136 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (135 bp):
AAGATAACAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTGTCTT
CCTATATTGGTAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGTGAAGTA
GATCA
Found at i:35423699 original size:76 final size:76
Alignment explanation
Indices: 35423602--35423749 Score: 242
Period size: 76 Copynumber: 1.9 Consensus size: 76
35423592 AAGATAGCAG
* *
35423602 ATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGG
1 ATCTTGTCTTCCTATATTGGTAGCGAAATAGATCAAAGATAACAGATCTTGTCTTCCTATATTGG
35423667 CAGTGAAACAA
66 CAGTGAAACAA
** * *
35423678 ATCTTGTCTTCCTATATTGGTAGCGAAATAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGG
1 ATCTTGTCTTCCTATATTGGTAGCGAAATAGATCAAAGATAACAGATCTTGTCTTCCTATATTGG
35423743 CAGTGAA
66 CAGTGAA
35423750 GTAGATCAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (76 bp):
ATCTTGTCTTCCTATATTGGTAGCGAAATAGATCAAAGATAACAGATCTTGTCTTCCTATATTGG
CAGTGAAACAA
Found at i:35423710 original size:121 final size:121
Alignment explanation
Indices: 35423552--35423897 Score: 406
Period size: 121 Copynumber: 2.7 Consensus size: 121
35423542 GATCGAAGAT
* * *
35423552 AACAGATCTTGTCTTCCTGTATTGGTAGTGAAATAGATCAAAGATAGCAGATCTTGTCTTCCTAT
1 AACAAATCTTGTCTTCCTATATTGGTAGCGAAATAGATCAAAGATAGCAGATCTTGTCTTCCTAT
* *
35423617 ATTGGTAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGTGA
66 ATTGGCAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAATGA
** *
35423673 AACAAATCTTGTCTTCCTATATTGGTAGCGAAATAGATTGAAGATAGCAGATCTTGTCTTCCTGT
1 AACAAATCTTGTCTTCCTATATTGGTAGCGAAATAGATCAAAGATAGCAGATCTTGTCTTCCTAT
*
35423738 ATTGGCAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTGTATTGGCAATGAA
66 ATTGGCAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAATG-A
* * *
35423795 GTAGATCAAGGATAGCAGATCTTATCTTTCTATATTGGCAGC-AAAGTAGATCAAAGATAGCAGA
1 --A-A-C------A--A-ATCTTGTCTTCCTATATTGGTAGCGAAA-TAGATCAAAGATAGCAGA
** * *
35423859 TCTTGTCTTCCTATATTGGCAACGAAGAAGATCGAAGAT
52 TCTTGTCTTCCTATATTGGCAGTGAAGTAGATCAAAGAT
35423898 CGCATCCAGT
Statistics
Matches: 191, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
121 111 0.58
122 1 0.01
124 1 0.01
125 1 0.01
126 1 0.01
132 1 0.01
134 4 0.02
135 71 0.37
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (121 bp):
AACAAATCTTGTCTTCCTATATTGGTAGCGAAATAGATCAAAGATAGCAGATCTTGTCTTCCTAT
ATTGGCAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAATGA
Found at i:35423742 original size:45 final size:45
Alignment explanation
Indices: 35423678--35423897 Score: 264
Period size: 45 Copynumber: 4.9 Consensus size: 45
35423668 AGTGAAACAA
* **
35423678 ATCTTGTCTTCCTATATTGGTAGCGAAATAGATTGAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGCAGCGAAATAGATCAAAGATAGCAG
* * * *
35423723 ATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAACAG
1 ATCTTGTCTTCCTATATTGGCAGCGAAATAGATCAAAGATAGCAG
* ** * *
35423768 ATCTTGTCTTCCTGTATTGGCAATGAAGTAGATCAAGGATAGCAG
1 ATCTTGTCTTCCTATATTGGCAGCGAAATAGATCAAAGATAGCAG
* *
35423813 ATCTTATCTTTCTATATTGGCAGC-AAAGTAGATCAAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGCAGCGAAA-TAGATCAAAGATAGCAG
* *
35423858 ATCTTGTCTTCCTATATTGGCAACGAAGA-AGATCGAAGAT
1 ATCTTGTCTTCCTATATTGGCAGCGAA-ATAGATCAAAGAT
35423898 CGCATCCAGT
Statistics
Matches: 151, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
44 2 0.01
45 146 0.97
46 2 0.01
47 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (45 bp):
ATCTTGTCTTCCTATATTGGCAGCGAAATAGATCAAAGATAGCAG
Found at i:35423770 original size:211 final size:211
Alignment explanation
Indices: 35423467--35423879 Score: 619
Period size: 211 Copynumber: 2.0 Consensus size: 211
35423457 AAGATAATAG
** * * * *
35423467 ATCTTGTCTTTTTATATTGGTAGTGAAGTAGATCAAAGATAATAGATATTGTCTTCTTATATTGG
1 ATCTTGTCTTCCTATATTGGTAGCGAAATAGATCAAAGATAACAGATATTGTCTTCCTATATTGG
* * * *
35423532 TAGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTGGTAGTGAAATAGATCAAAGAT
66 CAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTGTATTGGCAATGAAATAGATCAAAGAT
* * **
35423597 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTAT
131 AGCAGATCTTATCTTCCTATATTGGCAGCAAAGTAGATCAAAGATAACAGATCTTGTCTTCCTAT
35423662 ATTGGCAGTGAAACAA
196 ATTGGCAGTGAAACAA
** * * *
35423678 ATCTTGTCTTCCTATATTGGTAGCGAAATAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGG
1 ATCTTGTCTTCCTATATTGGTAGCGAAATAGATCAAAGATAACAGATATTGTCTTCCTATATTGG
* *
35423743 CAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTGTATTGGCAATGAAGTAGATCAAGGAT
66 CAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTGTATTGGCAATGAAATAGATCAAAGAT
* *
35423808 AGCAGATCTTATCTTTCTATATTGGCAGCAAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTAT
131 AGCAGATCTTATCTTCCTATATTGGCAGCAAAGTAGATCAAAGATAACAGATCTTGTCTTCCTAT
35423873 ATTGGCA
196 ATTGGCA
35423880 ACGAAGAAGA
Statistics
Matches: 179, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
211 179 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (211 bp):
ATCTTGTCTTCCTATATTGGTAGCGAAATAGATCAAAGATAACAGATATTGTCTTCCTATATTGG
CAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTGTATTGGCAATGAAATAGATCAAAGAT
AGCAGATCTTATCTTCCTATATTGGCAGCAAAGTAGATCAAAGATAACAGATCTTGTCTTCCTAT
ATTGGCAGTGAAACAA
Found at i:35423797 original size:166 final size:166
Alignment explanation
Indices: 35423327--35423835 Score: 552
Period size: 166 Copynumber: 3.0 Consensus size: 166
35423317 GATCGAAGAT
* * * * * *
35423327 AACAGATCTTGTCTTCCTATATTGGTAGTGACATAGATCAAAGATAATAGATATTGTCTTCCTGT
1 AACAAATCTTGTCTTCCTATATTGGTAGCGAAATAGATCGAAGATAACAGATCTTGTCTTCCTGT
* ** * * * * *
35423392 ATTGGCAG-CAAAGTAGATTTAAGATAGCAGATCTGGTCTTCCTATATTGGTAGTGAAGTAAATC
66 ATTGGCAGTGAAA-TAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAATGAAGTAGATC
* * * ** *
35423456 GAAGATAATAGATCTTGTCTTTTTATATTGGTAGTGAA
130 AAAGATAACAGATCTTATCTTCCTATATTGGCAGTG-A
* * * *
35423494 GTAGATCAAAGATAATAGATATTGTCTTCTTATATTGGTAGTGAAGTAGATCGAAGATAACAGAT
1 --A-A-C-------A-A-ATCTTGTCTTCCTATATTGGTAGCGAAATAGATCGAAGATAACAGAT
* * *
35423559 CTTGTCTTCCTGTATTGGTAGTGAAATAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTA
53 CTTGTCTTCCTGTATTGGCAGTGAAATAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCA
* *
35423624 GTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGTGA
118 ATGAAGTAGATCAAAGATAACAGATCTTATCTTCCTATATTGGCAGTGA
* *
35423673 AACAAATCTTGTCTTCCTATATTGGTAGCGAAATAGATTGAAGATAGCAGATCTTGTCTTCCTGT
1 AACAAATCTTGTCTTCCTATATTGGTAGCGAAATAGATCGAAGATAACAGATCTTGTCTTCCTGT
* *
35423738 ATTGGCAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTGTATTGGCAATGAAGTAGATCA
66 ATTGGCAGTGAAATAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAATGAAGTAGATCA
* * *
35423803 AGGATAGCAGATCTTATCTTTCTATATTGGCAG
131 AAGATAACAGATCTTATCTTCCTATATTGGCAG
35423836 CAAAGTAGAT
Statistics
Matches: 293, Mismatches: 35, Indels: 27
0.83 0.10 0.08
Matches are distributed among these distances:
166 142 0.48
167 1 0.00
168 1 0.00
169 1 0.00
170 1 0.00
171 1 0.00
175 1 0.00
176 1 0.00
177 1 0.00
178 1 0.00
179 1 0.00
180 138 0.47
181 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (166 bp):
AACAAATCTTGTCTTCCTATATTGGTAGCGAAATAGATCGAAGATAACAGATCTTGTCTTCCTGT
ATTGGCAGTGAAATAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAATGAAGTAGATCA
AAGATAACAGATCTTATCTTCCTATATTGGCAGTGA
Found at i:35423800 original size:90 final size:90
Alignment explanation
Indices: 35423673--35423897 Score: 299
Period size: 90 Copynumber: 2.5 Consensus size: 90
35423663 TTGGCAGTGA
* * * * * *
35423673 AACAAATCTTGTCTTCCTATATTGGTAGCGAAATAGATTGAAGATAGCAGATCTTGTCTTCCTGT
1 AACAGATCTTGTCTTCCTATATTGGCAACGAAGTAGATTGAAGATAGCAGATCTTATCTTCCTAT
**
35423738 ATTGGCAGTGAAGTAGATCAAAGAT
66 ATTGGCAGCAAAGTAGATCAAAGAT
* * * *
35423763 AACAGATCTTGTCTTCCTGTATTGGCAATGAAGTAGA-TCAAGGATAGCAGATCTTATCTTTCTA
1 AACAGATCTTGTCTTCCTATATTGGCAACGAAGTAGATTGAA-GATAGCAGATCTTATCTTCCTA
35423827 TATTGGCAGCAAAGTAGATCAAAGAT
65 TATTGGCAGCAAAGTAGATCAAAGAT
* * *
35423853 AGCAGATCTTGTCTTCCTATATTGGCAACGAAGAAGATCGAAGAT
1 AACAGATCTTGTCTTCCTATATTGGCAACGAAGTAGATTGAAGAT
35423898 CGCATCCAGT
Statistics
Matches: 115, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
89 3 0.03
90 110 0.96
91 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (90 bp):
AACAGATCTTGTCTTCCTATATTGGCAACGAAGTAGATTGAAGATAGCAGATCTTATCTTCCTAT
ATTGGCAGCAAAGTAGATCAAAGAT
Found at i:35424074 original size:44 final size:44
Alignment explanation
Indices: 35424002--35424102 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
35423992 GCAAATATTG
* * * *
35424002 TCTCCCTGAATTTGCAGTGGAGTAGATTAAAGCCAATA-ATCCTA
1 TCTCTCTGAAGTTACAGTGGAGCAGATTAAAG-CAATACATCCTA
* ** *
35424046 TCTCTCTGAAGTTACAGTGGAGCGGATTAAAGGGATACATCTTA
1 TCTCTCTGAAGTTACAGTGGAGCAGATTAAAGCAATACATCCTA
35424090 TCTCTCTGAAGTT
1 TCTCTCTGAAGTT
35424103 GTAGTAGAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 3 0.06
44 45 0.94
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (44 bp):
TCTCTCTGAAGTTACAGTGGAGCAGATTAAAGCAATACATCCTA
Found at i:35425525 original size:3 final size:3
Alignment explanation
Indices: 35425517--35425564 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
35425507 CTTATGTTCC
35425517 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35425565 TCCATGGACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:35425670 original size:5 final size:5
Alignment explanation
Indices: 35425651--35425685 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
35425641 TACATGTATA
35425651 TATTT TATTT ATATTT TATTT TATTAT TATTT TAT
1 TATTT TATTT -TATTT TATTT TATT-T TATTT TAT
35425686 CTTCACAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:35425672 original size:16 final size:16
Alignment explanation
Indices: 35425651--35425685 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
35425641 TACATGTATA
35425651 TATTTTATT-TATATTT
1 TATTTTATTAT-TATTT
35425667 TATTTTATTATTATTT
1 TATTTTATTATTATTT
35425683 TAT
1 TAT
35425686 CTTCACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.94
17 1 0.06
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTATTATTATTT
Found at i:35425683 original size:11 final size:10
Alignment explanation
Indices: 35425651--35425685 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
35425641 TACATGTATA
35425651 TATTTTATTT
1 TATTTTATTT
35425661 ATATTTTATTT
1 -TATTTTATTT
35425672 TATTATTATTT
1 TATT-TTATTT
35425683 TAT
1 TAT
35425686 CTTCACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TATTTTATTT
Found at i:35427378 original size:34 final size:34
Alignment explanation
Indices: 35427339--35427404 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
35427329 ATTGTTGCAA
35427339 ATTAATATTATT-AAAAATAATTAAAAAAATAATT
1 ATTAAT-TTATTGAAAAATAATTAAAAAAATAATT
** *
35427373 ATTAATTTATTGATGAATTATTAAAAAAATAA
1 ATTAATTTATTGAAAAATAATTAAAAAAATAA
35427405 ATTTCAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 23 0.82
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (34 bp):
ATTAATTTATTGAAAAATAATTAAAAAAATAATT
Found at i:35431226 original size:178 final size:179
Alignment explanation
Indices: 35430919--35431275 Score: 707
Period size: 178 Copynumber: 2.0 Consensus size: 179
35430909 TTAAAAATTT
35430919 TGCTAAATTTTTTAATATATAAAATATTATATTATATCAGTTCTATACCACATTTATAATATAAC
1 TGCTAAATTTTTTAATATATAAAATATTATATTATATCAGTTCTATACCACATTTATAATATAAC
35430984 ATACAAGTAGTTATTCTATATCATAATCTAATATGTAACTATTCTACGTAACTTTTGAATTACTA
66 ATACAAGTAGTTATTCTATATCATAATCTAATATGTAACTATTCTACGTAACTTTTGAATTACTA
35431049 AAAATAGATAAAAGTATTAAAGAAGTCTTTGGATTTAGAAGCAGATCCC
131 AAAATAGATAAAAGTATTAAAGAAGTCTTTGGATTTAGAAGCAGATCCC
35431098 TGCTAAA-TTTTTAATATATAAAATATTATATTATATCAGTTCTATACCACATTTATAATATAAC
1 TGCTAAATTTTTTAATATATAAAATATTATATTATATCAGTTCTATACCACATTTATAATATAAC
35431162 ATACAAGTAGTTATTCTATATCATAATCTAATATGTAACTATTCTACGTAACTTTTGAATTACTA
66 ATACAAGTAGTTATTCTATATCATAATCTAATATGTAACTATTCTACGTAACTTTTGAATTACTA
35431227 AAAATAGATAAAAGTATTAAAGAAGTCTTTGGATTTAGAAGCAGATCCC
131 AAAATAGATAAAAGTATTAAAGAAGTCTTTGGATTTAGAAGCAGATCCC
35431276 ATCTCGGCTA
Statistics
Matches: 178, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
178 171 0.96
179 7 0.04
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (179 bp):
TGCTAAATTTTTTAATATATAAAATATTATATTATATCAGTTCTATACCACATTTATAATATAAC
ATACAAGTAGTTATTCTATATCATAATCTAATATGTAACTATTCTACGTAACTTTTGAATTACTA
AAAATAGATAAAAGTATTAAAGAAGTCTTTGGATTTAGAAGCAGATCCC
Found at i:35431464 original size:10 final size:10
Alignment explanation
Indices: 35431437--35431496 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
35431427 TTTTTAAATC
*
35431437 TTAAAAATAA
1 TTAAAAATTA
* *
35431447 ATATAAATTA
1 TTAAAAATTA
35431457 TTAAAAA-TA
1 TTAAAAATTA
35431466 TTAAAAATTA
1 TTAAAAATTA
*
35431476 TGTTAAAATATTT
1 --TTAAAA-ATTA
35431489 TTAAAAAT
1 TTAAAAAT
35431497 AAACATTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 9 0.22
10 16 0.40
11 6 0.15
12 6 0.15
13 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:35432210 original size:25 final size:25
Alignment explanation
Indices: 35432178--35432234 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
35432168 NNNNNNNNNN
35432178 AAAATATAAATTTGATTAAAAATAA
1 AAAATATAAATTTGATTAAAAATAA
*
35432203 AAAATATATATTTGATTAAAAATAA
1 AAAATATAAATTTGATTAAAAATAA
35432228 AAAATAT
1 AAAATAT
35432235 TTAATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (25 bp):
AAAATATAAATTTGATTAAAAATAA
Found at i:35433930 original size:11 final size:11
Alignment explanation
Indices: 35433899--35433949 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
35433889 ATTTTTTTGA
*
35433899 ATTTTTAACAT
1 ATTTTTAATAT
35433910 AATTTTTAATAT
1 -ATTTTTAATAT
35433922 ATTTTTAATA-
1 ATTTTTAATAT
*
35433932 ATTTAT-ATAT
1 ATTTTTAATAT
35433942 -TTTTTAAT
1 ATTTTTAAT
35433950 TTTTTTAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.21
10 7 0.21
11 10 0.29
12 10 0.29
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:35433949 original size:16 final size:17
Alignment explanation
Indices: 35433918--35433951 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35433908 ATAATTTTTA
35433918 ATATATTTTTAATAATTT
1 ATATATTTTT-ATAATTT
35433936 ATATATTTTT-TAATTT
1 ATATATTTTTATAATTT
35433952 TTTTAGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATATTTTTATAATTT
Found at i:35436126 original size:18 final size:18
Alignment explanation
Indices: 35436098--35436156 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
35436088 ATTTGTATAA
*
35436098 TATATATTTTTATAAATT
1 TATATAATTTTATAAATT
*
35436116 TATA-AAGTTTTATATATT
1 TATATAA-TTTTATAAATT
*
35436134 TATATAATTTTATAATTT
1 TATATAATTTTATAAATT
35436152 TATAT
1 TATAT
35436157 TTTATATGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.03
18 32 0.91
19 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TATATAATTTTATAAATT
Found at i:35436139 original size:28 final size:26
Alignment explanation
Indices: 35436098--35436163 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 26
35436088 ATTTGTATAA
*
35436098 TATATATTTTTATAAATTTATAAAGTTT
1 TATATATTTATATAAATTTAT-AA-TTT
*
35436126 TATATATTTATATAATTTTATAATTT
1 TATATATTTATATAAATTTATAATTT
35436152 TATAT-TTTATAT
1 TATATATTTATAT
35436164 GCTTTTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 7 0.19
26 8 0.22
27 2 0.06
28 19 0.53
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
TATATATTTATATAAATTTATAATTT
Found at i:35441480 original size:28 final size:28
Alignment explanation
Indices: 35441440--35441493 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
35441430 ATATTACTGT
35441440 TGCCTCTGCTGTAAATCAAGCCATTTTC
1 TGCCTCTGCTGTAAATCAAGCCATTTTC
35441468 TGCCTCTGCTGTAAATCAAGCCATTT
1 TGCCTCTGCTGTAAATCAAGCCATTT
35441494 GGCTTAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (28 bp):
TGCCTCTGCTGTAAATCAAGCCATTTTC
Found at i:35442948 original size:21 final size:21
Alignment explanation
Indices: 35442922--35442977 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
35442912 AACAGCGGTG
*
35442922 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
35442943 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
35442964 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
35442978 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:35448492 original size:18 final size:18
Alignment explanation
Indices: 35448445--35448493 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
35448435 TTCTTACGAC
35448445 TTTATAAAATTTTACAATT
1 TTTAT-AAATTTTACAATT
* *
35448464 TTT-TATTATTTTACGATT
1 TTTATA-AATTTTACAATT
35448482 TTTATAAATTTT
1 TTTATAAATTTT
35448494 TTTCTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.04
18 19 0.76
19 5 0.20
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTATAAATTTTACAATT
Found at i:35449706 original size:106 final size:106
Alignment explanation
Indices: 35449521--35449735 Score: 360
Period size: 106 Copynumber: 2.0 Consensus size: 106
35449511 TGGATTGGAA
* * *
35449521 TTTAAGAGGATATTTGGCTATTTGGTCGGACGAGAAATCGAAACCCAGCATGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
35449586 TCTCGAATTTCCAAACACAAAATATT-TCCTTACTTTGAAAT
66 TCTCGAATTTCCAAACACAAAATATTGT-CTTACTTTGAAAT
35449627 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
* * *
35449692 TCTCGATTTTCCAAACGCAAAATATTGTCTTACTTTGAATT
66 TCTCGAATTTCCAAACACAAAATATTGTCTTACTTTGAAAT
35449733 TTT
1 TTT
35449736 TATTTTTGTA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
106 101 0.99
107 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
TCTCGAATTTCCAAACACAAAATATTGTCTTACTTTGAAAT
Found at i:35455445 original size:14 final size:15
Alignment explanation
Indices: 35455426--35455466 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
35455416 AAACATCTTA
35455426 AATTAATTTT-AATT
1 AATTAATTTTCAATT
35455440 AATTAATTTTTCAATT
1 AATTAA-TTTTCAATT
*
35455456 AAATAATTTTC
1 AATTAATTTTC
35455467 TCAACTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 9 0.38
16 9 0.38
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTAATTTTCAATT
Found at i:35457349 original size:20 final size:22
Alignment explanation
Indices: 35457326--35457376 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
35457316 GGGTCAACAT
*
35457326 GCCCATGTGG-AGG-GACACAC
1 GCCCGTGTGGAAGGAGACACAC
*
35457346 GCCCGTGTGGAAGGAGGCACAC
1 GCCCGTGTGGAAGGAGACACAC
35457368 GCCCGTGTG
1 GCCCGTGTG
35457377 ACCTAGGGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 9 0.33
21 3 0.11
22 15 0.56
ACGTcount: A:0.20, C:0.29, G:0.39, T:0.12
Consensus pattern (22 bp):
GCCCGTGTGGAAGGAGACACAC
Found at i:35463001 original size:28 final size:28
Alignment explanation
Indices: 35462952--35463006 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
35462942 TGAGCAGCCT
*
35462952 AAATATCACAACTTAAGAGAGAAAATTC
1 AAATATCACAACTCAAGAGAGAAAATTC
* * *
35462980 AAATATCACAGCTCAGGTGAGAAAATT
1 AAATATCACAACTCAAGAGAGAAAATT
35463007 GAATTATTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (28 bp):
AAATATCACAACTCAAGAGAGAAAATTC
Found at i:35466119 original size:6 final size:6
Alignment explanation
Indices: 35466108--35466153 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
35466098 CTTAAGCTCT
* *
35466108 ACAACC ACAACC ACAACT GCAACC ACAACC ACAACC ACAACC ACAA
1 ACAACC ACAACC ACAACC ACAACC ACAACC ACAACC ACAACC ACAA
35466154 ATGCCTTGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.46, G:0.02, T:0.02
Consensus pattern (6 bp):
ACAACC
Found at i:35469716 original size:14 final size:14
Alignment explanation
Indices: 35469697--35469729 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
35469687 GTTGATAAAT
35469697 GATATAATGTCAAC
1 GATATAATGTCAAC
35469711 GATATAATGTCAAC
1 GATATAATGTCAAC
35469725 GATAT
1 GATAT
35469730 TATTTGGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (14 bp):
GATATAATGTCAAC
Found at i:35471185 original size:18 final size:17
Alignment explanation
Indices: 35471162--35471214 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
35471152 AATTGTGTCG
35471162 TTCATTTCTAAAACATTA
1 TTCATTTC-AAAACATTA
* *
35471180 TTCATTTACAAATCGTTA
1 TTCATTT-CAAAACATTA
35471198 TTCAATTTCAAAACATT
1 TTC-ATTTCAAAACATT
35471215 TTCTTATTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (17 bp):
TTCATTTCAAAACATTA
Found at i:35475874 original size:16 final size:17
Alignment explanation
Indices: 35475843--35475890 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
35475833 ATATGGTATA
* *
35475843 TATGTATTTAAGTTGT-
1 TATGTATTTGATTTGTG
35475859 TATGTATTTGATTTGTG
1 TATGTATTTGATTTGTG
35475876 TATGTCTATTTGATT
1 TATG--TATTTGATT
35475891 GTGGGTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 14 0.52
17 4 0.15
19 9 0.33
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.58
Consensus pattern (17 bp):
TATGTATTTGATTTGTG
Found at i:35478163 original size:16 final size:17
Alignment explanation
Indices: 35478132--35478166 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
35478122 ATTAATCAAA
35478132 CTAACTAAATTAATTTT
1 CTAACTAAATTAATTTT
*
35478149 CTAATTAAA-TAATTTT
1 CTAACTAAATTAATTTT
35478165 CT
1 CT
35478167 CAATCCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
CTAACTAAATTAATTTT
Found at i:35481505 original size:39 final size:40
Alignment explanation
Indices: 35481431--35481506 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
35481421 TATCTGCATT
* *
35481431 CTGTATCTGATATGGGCCAAGGCCCTAATGTATTCTGAGA
1 CTGTATCTGATATAGGCCAAGGCCCAAATGTATTCTGAGA
*
35481471 CTGTATCTGA-ATAGGCTAAGGCCCAAACTG-ATTCTG
1 CTGTATCTGATATAGGCCAAGGCCCAAA-TGTATTCTG
35481507 TGATGGGTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 20 0.62
40 12 0.38
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (40 bp):
CTGTATCTGATATAGGCCAAGGCCCAAATGTATTCTGAGA
Found at i:35488524 original size:44 final size:44
Alignment explanation
Indices: 35488470--35488563 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
35488460 TTAATAGGTC
* *
35488470 AAAC-AATATTAAAATAACCTAAACTAATTAGAGTTTAAGTGGG
1 AAACTAATATTAAAATAACCTAAACTAATCAGAGTTTAAGTGAG
35488513 AAACTAATATTAAAATAACCTAAACTAATCAGAGTTTAAGTGAG
1 AAACTAATATTAAAATAACCTAAACTAATCAGAGTTTAAGTGAG
35488557 AAACTAA
1 AAACTAA
35488564 AAACATAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
43 4 0.08
44 44 0.92
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.27
Consensus pattern (44 bp):
AAACTAATATTAAAATAACCTAAACTAATCAGAGTTTAAGTGAG
Found at i:35494858 original size:63 final size:63
Alignment explanation
Indices: 35494779--35494968 Score: 299
Period size: 63 Copynumber: 3.0 Consensus size: 63
35494769 AATAAGAAGA
* *
35494779 AAATGGGCAGATTTGGTCAAATGATCCACGATGACCTAAACAGAATCTTACTTAGTGGGTGTT
1 AAATGGGCAGATTTGGTCAAATGATCTACGATGACCTAAACAGAATCTTTCTTAGTGGGTGTT
* *
35494842 AAATGGGCAAATTTGGTCAAATGATCTACAATGACCTAAACAGAATCTTTCTTAGTGGGTGTT
1 AAATGGGCAGATTTGGTCAAATGATCTACGATGACCTAAACAGAATCTTTCTTAGTGGGTGTT
* * * * *
35494905 AAATGGACAGATTTCGTCAAATAATCTATGATGACCTAAGCAGAATCTTTCTTAGTGGGTGTT
1 AAATGGGCAGATTTGGTCAAATGATCTACGATGACCTAAACAGAATCTTTCTTAGTGGGTGTT
35494968 A
1 A
35494969 GGGGCAACCC
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 116 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (63 bp):
AAATGGGCAGATTTGGTCAAATGATCTACGATGACCTAAACAGAATCTTTCTTAGTGGGTGTT
Found at i:35499625 original size:31 final size:32
Alignment explanation
Indices: 35499579--35499639 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
35499569 CTCATGTGAC
** * *
35499579 CCACACGGCTTAAATGGCC-AGCCCGTGTGGT
1 CCACACGGCCAAAATGACCTAGACCGTGTGGT
35499610 CCACACGGCCAAAATGACCTAGACCGTGTG
1 CCACACGGCCAAAATGACCTAGACCGTGTG
35499640 TCTCACATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (32 bp):
CCACACGGCCAAAATGACCTAGACCGTGTGGT
Found at i:35501527 original size:31 final size:30
Alignment explanation
Indices: 35501507--35501565 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
35501497 CAATCCTCAG
*
35501507 CCATTGAACCAAATTAAATTACTTAACACAA
1 CCATTAAACCAAATTAAATTAC-TAACACAA
35501538 CCATTAAACCAAATTAAATTACTTAACA
1 CCATTAAACCAAATTAAATTAC-TAACA
35501566 TACTTTAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (30 bp):
CCATTAAACCAAATTAAATTACTAACACAA
Found at i:35522465 original size:26 final size:25
Alignment explanation
Indices: 35522409--35522477 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
35522399 GAACCAAATT
*
35522409 GGGAAGCTCACAAAGAGCCAATTAAC
1 GGGAAGCTCA-TAAGAGCCAATTAAC
* *
35522435 AGGAAGCTCATGAAGAGCCTA-TAATC
1 GGGAAGCTCAT-AAGAGCCAATTAA-C
*
35522461 GGGAAGTTCATAAGAGC
1 GGGAAGCTCATAAGAGC
35522478 TAAGGTGTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 9 0.25
26 27 0.75
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (25 bp):
GGGAAGCTCATAAGAGCCAATTAAC
Found at i:35528130 original size:2 final size:2
Alignment explanation
Indices: 35528123--35528158 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
35528113 TGCTAAATAC
*
35528123 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35528159 GAAGAAATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35529853 original size:9 final size:9
Alignment explanation
Indices: 35529760--35529903 Score: 51
Period size: 10 Copynumber: 15.0 Consensus size: 9
35529750 TGATATAAAC
*
35529760 TTATTAAAA
1 TTATAAAAA
35529769 TTATAAAAAA
1 TTAT-AAAAA
**
35529779 TT-GGAAAA
1 TTATAAAAA
*
35529787 TTATTTAAAA
1 TTA-TAAAAA
35529797 TTA-AAAAA
1 TTATAAAAA
* *
35529805 TATATTAGAAT
1 T-TA-TAAAAA
*
35529816 TTTTAAGAAA
1 TTATAA-AAA
*
35529826 TAATAAAACA
1 TTATAAAA-A
*
35529836 TTGTAAAAA
1 TTATAAAAA
35529845 TTATAAAAAAAA
1 TTAT---AAAAA
*
35529857 CTATTAAAAA
1 TTA-TAAAAA
*
35529867 -TATTAAAA
1 TTATAAAAA
35529875 TTGATATAAAA
1 TT-ATA-AAAA
*
35529886 TTATAAATA
1 TTATAAAAA
35529895 TTATAAAAA
1 TTATAAAAA
35529904 AAAGAGTCAT
Statistics
Matches: 99, Mismatches: 21, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
8 16 0.16
9 28 0.28
10 37 0.37
11 10 0.10
12 7 0.07
13 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:35530203 original size:5 final size:6
Alignment explanation
Indices: 35530176--35530210 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
35530166 CAGCTCAAGT
35530176 AAATAA AACATTAA AAATAA AAATAA AAATAA AAA
1 AAATAA AA-A-TAA AAATAA AAATAA AAATAA AAA
35530211 ATTTAGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.74
7 2 0.07
8 5 0.19
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:35530357 original size:21 final size:21
Alignment explanation
Indices: 35530317--35530358 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35530307 ATCCAGTTCA
* * *
35530317 AATTTTTATGATTTTTTAAAT
1 AATTTTTATAACTTTATAAAT
35530338 AATTTTTATAACTTTATAAAT
1 AATTTTTATAACTTTATAAAT
35530359 TTTAATACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
AATTTTTATAACTTTATAAAT
Found at i:35530361 original size:18 final size:18
Alignment explanation
Indices: 35530335--35530382 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
35530325 TGATTTTTTA
35530335 AATAATTTTTATAACTT-T
1 AATAATTTTTAT-ACTTCT
*
35530353 -ATAAATTTTAATACTTCT
1 AAT-AATTTTTATACTTCT
35530371 AATAATTTTTAT
1 AATAATTTTTAT
35530383 GATTTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.24
18 17 0.68
19 2 0.08
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAATTTTTATACTTCT
Found at i:35530433 original size:21 final size:22
Alignment explanation
Indices: 35530380--35530431 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
35530370 TAATAATTTT
*
35530380 TATGATTTTTATAGAATTTT-AA
1 TATG-TTTTTATAAAATTTTAAA
35530402 TATGTTTTTATAAAATTTTAAA
1 TATGTTTTTATAAAATTTTAAA
35530424 TATGTTTT
1 TATGTTTT
35530432 ATTAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (22 bp):
TATGTTTTTATAAAATTTTAAA
Found at i:35530795 original size:21 final size:21
Alignment explanation
Indices: 35530755--35530795 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35530745 ATCCAGTTCA
* * *
35530755 AATTTTTATGATTTTTTAAAT
1 AATTTTTATAACTTTATAAAT
35530776 AATTTTTATAACTTTATAAA
1 AATTTTTATAACTTTATAAA
35530796 ATTTTCTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
AATTTTTATAACTTTATAAAT
Found at i:35531741 original size:306 final size:300
Alignment explanation
Indices: 35531127--35531677 Score: 796
Period size: 306 Copynumber: 1.8 Consensus size: 300
35531117 TGTGAGTTTA
* * * *
35531127 AAAATAACATACAATAATTAATGAAATGTATAGTTTGAAACTAATTAATCATAATAACACATGAA
1 AAAATAACACACAATAAATAATGAAACGTATAGCTTGAAACTAATTAATCATAATAACACATGAA
* * *
35531192 ATATGTACGATCTTAAAATTAAAAAAATTAAATTGTGAGTAAAACGAAATTTAAGCACATAAATA
66 ATATGTACGATATTAAAATAAAAAAAATTAAATTGTGAGTAAAACGAAATTTAAACACATAAATA
* *
35531257 CATCAGATAAATAATACTAAATGCACTACAATTATTTATCATGATTTTTCAACAATTGTGAGTTA
131 CATAAGATAAACAATACTAAATGCACTACAATTATTTATCATGATTTTTCAACAATTGTGAGTTA
* * * *
35531322 GTGTCGAGTTGACTTGTGACACCAACTCAATTAACAACATTATTAATATTCTAAATCTTATCACA
196 GTATCGAATTGACTTGTGACACCAACTCAATTAACAACATTATTAATATTATAAATCTAAT-ACA
* * * * * * *
35531387 AGCGTACGCGTACGGAGACTGTATTTAGAACACATGTGTGCTTT
260 AGCATA--CATACGGAGA-TGTATTTAAAAAAAATGTATGCATT
* * *
35531431 AAAATGACACACAATAAATAATGAAACGTATGGCTTGAAATTAATTAATCATAATAACACATGAA
1 AAAATAACACACAATAAATAATGAAACGTATAGCTTGAAACTAATTAATCATAATAACACATGAA
* *
35531496 ATATGTATGATATTAAAATAAAAAATAGATTAAATTGTGAGTAAAACTAAATTTAAACACATAAA
66 ATATGTACGATATTAAAATAAAAAA-A-ATTAAATTGTGAGTAAAACGAAATTTAAACACATAAA
35531561 TACATAAGATAAACAATACTAAATGCACTACAATTATTTATCATGATTTTGTCAACAATTGTGAG
129 TACATAAGATAAACAATACTAAATGCACTACAATTATTTATCATGATTTT-TCAACAATTGTGAG
* *
35531626 TTAGTATTGAATTGACTTGTGACACCTACTCAATTAACAACATTATTAATAT
193 TTAGTATCGAATTGACTTGTGACACCAACTCAATTAACAACATTATTAATAT
35531678 ATACAATTAA
Statistics
Matches: 226, Mismatches: 18, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
304 80 0.35
305 1 0.00
306 83 0.37
307 62 0.27
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (300 bp):
AAAATAACACACAATAAATAATGAAACGTATAGCTTGAAACTAATTAATCATAATAACACATGAA
ATATGTACGATATTAAAATAAAAAAAATTAAATTGTGAGTAAAACGAAATTTAAACACATAAATA
CATAAGATAAACAATACTAAATGCACTACAATTATTTATCATGATTTTTCAACAATTGTGAGTTA
GTATCGAATTGACTTGTGACACCAACTCAATTAACAACATTATTAATATTATAAATCTAATACAA
GCATACATACGGAGATGTATTTAAAAAAAATGTATGCATT
Found at i:35532465 original size:294 final size:292
Alignment explanation
Indices: 35531680--35532571 Score: 956
Period size: 297 Copynumber: 3.0 Consensus size: 292
35531670 ATTAATATAT
* ** *
35531680 ACAATTAATGGAGATAATAACTTGTGTATATTAAAATAAAAATGTATAAAATGCATTAAAATAAA
1 ACAATTAATGGAGATAATAACTTGTGTATATTAAAATAAAAATGTATAAAATACA-CCAAATGAA
* ** * * ** ***
35531745 GCTTTAGTTGAATGACAAATTTAAG-GTTTTACTAATCCAATTGGCGTGGGTGCAAATCCCATTA
65 GCTTTAGTTGAGTGGTAAATTTAAGTG-TTTACTAATCCAATTGG-ATGAGTTTAAATATTATTA
* * *
35531809 TATGCATATTTTAATTGGTTTTTGTTAAAATGAAAATG-CTAAAATACCCTCAAACAGTACAACT
128 TATGCATATTTTAATTGGTTTTTGTTAAAATGAAAA-GACTAAAATACCATCAAATAGTATAACT
* * * *
35531873 TATTTTAGTTATGGAAAGACA-TTTCTATAACTTTCTAA-CATAGTTGGTGACCCGATTGA--G-
192 TATTTTAATTATGGAAGGACATTTTC-GTAA-TTTCTAACCA-A-TTGGTGACCCAATTGAGGGT
* ** * *
35531933 GAAGACTCTCAGTAAAATACTTAATAAGTAGTACGTATAAATAT
253 GAACAAACTCAGTAAAATACTTAATAA--A-TA-GTATAGATAA
* * * * * *
35531977 ACAACTAATGGAGATAACAACTTATGCATATTAAAATAAAAATGTATTAAATATACCAATATGAA
1 ACAATTAATGGAGATAATAACTTGTGTATATTAAAATAAAAATGTATAAAATACACCAA-ATGAA
* ** *
35532042 GCTTT-GATTGAGTGGTAAATTTAAGAT-TTTACTAATCCAATTAGCACAAGCTTAAATATTATT
65 GCTTTAG-TTGAGTGGTAAATTTAAG-TGTTTACTAATCCAATT-GGATGAGTTTAAATATTATT
* * ** *
35532105 TTATGCATATTTTAATTGGTTTTTGTTAAAATGAAAAGATTAAAATGTCATCAAATAATATAACT
127 ATATGCATATTTTAATTGGTTTTTGTTAAAATGAAAAGACTAAAATACCATCAAATAGTATAACT
* *
35532170 TATTTTACTTATGGAAGGGCATTTTCGTAATTTTCTAACCGAATTGGTGACCCAATTGAGGGTGA
192 TATTTTAATTATGGAAGGACATTTTCGTAA-TTTCTAACC-AATTGGTGACCCAATTGAGGGTGA
* * *
35532235 ACAAACTTAGTAAAACACTTAATAAATATTATAGATAA
255 ACAAACTCAGTAAAATACTTAATAAATAGTATAGATAA
*
35532273 ACAATTAATAGAGATAATAACTTGTGTATATTAAAATAAAAATGTATAAAATACACCAAATGAAG
1 ACAATTAATGGAGATAATAACTTGTGTATATTAAAATAAAAATGTATAAAATACACCAAATGAAG
* * * * * *
35532338 CTTTAGTTGAGTGGTAAAATTAAGTGATTATTAATCTAATTGGTTGAGTTTAAATTTTATTATAT
66 CTTTAGTTGAGTGGTAAATTTAAGTGTTTACTAATCCAATTGGATGAGTTTAAATATTATTATAT
* * **
35532403 GAATATTTTAATTGATTTTCATTAAAATGAAAAGACTAAAATACCATCAAATAGTATAACTTATT
131 GCATATTTTAATTGGTTTTTGTTAAAATGAAAAGACTAAAATACCATCAAATAGTATAACTTATT
* * * * *
35532468 TTAATAATGAAAGGATATTTTCGTAATTTCTTAATTCAATTGGTGACCCAATTGAGGGTGACACC
196 TTAATTATGGAAGGACATTTTCGTAATTTC-TAA-CCAATTGGTGACCCAATTGAGGGTGA-ACA
*
35532533 AACTCAATAAAATACTTAATAAATAGTATAGATATA
258 AACTCAGTAAAATACTTAATAAATAGTATAGATA-A
35532569 ACA
1 ACA
35532572 TAATTTCTTT
Statistics
Matches: 494, Mismatches: 83, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
293 4 0.01
294 123 0.25
295 72 0.15
296 68 0.14
297 195 0.39
298 8 0.02
299 2 0.00
300 22 0.04
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (292 bp):
ACAATTAATGGAGATAATAACTTGTGTATATTAAAATAAAAATGTATAAAATACACCAAATGAAG
CTTTAGTTGAGTGGTAAATTTAAGTGTTTACTAATCCAATTGGATGAGTTTAAATATTATTATAT
GCATATTTTAATTGGTTTTTGTTAAAATGAAAAGACTAAAATACCATCAAATAGTATAACTTATT
TTAATTATGGAAGGACATTTTCGTAATTTCTAACCAATTGGTGACCCAATTGAGGGTGAACAAAC
TCAGTAAAATACTTAATAAATAGTATAGATAA
Found at i:35536676 original size:29 final size:28
Alignment explanation
Indices: 35536639--35536736 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 28
35536629 ACCTAGCCCA
* *
35536639 TGTGGCCCACATGGCCTACCACACGCTCG
1 TGTGACCCACATGGCCTACCACAAGC-CG
* *
35536668 TGTGACCCACACGGCCAACCACAAGACCG
1 TGTGACCCACATGGCCTACCACAAG-CCG
* * * *
35536697 TGTAACCCACATGGTCTGCCACATGGCCG
1 TGTGACCCACATGGCCTACCACA-AGCCG
35536726 TGTGACCCACA
1 TGTGACCCACA
35536737 CGGTTTGCCA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 54 0.96
30 2 0.04
ACGTcount: A:0.23, C:0.39, G:0.22, T:0.15
Consensus pattern (28 bp):
TGTGACCCACATGGCCTACCACAAGCCG
Found at i:35536745 original size:29 final size:29
Alignment explanation
Indices: 35536666--35536760 Score: 100
Period size: 29 Copynumber: 3.3 Consensus size: 29
35536656 ACCACACGCT
* **
35536666 CGTGTGACCCACACGGCCAACCACAAGAC
1 CGTGTGACCCACACGGTCTGCCACAAGAC
* * * *
35536695 CGTGTAACCCACATGGTCTGCCACATGGC
1 CGTGTGACCCACACGGTCTGCCACAAGAC
* *
35536724 CGTGTGACCCACACGGTTTGCCACACGAC
1 CGTGTGACCCACACGGTCTGCCACAAGAC
*
35536753 CATGTGAC
1 CGTGTGAC
35536761 GTCGACAGAA
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.24, C:0.37, G:0.23, T:0.16
Consensus pattern (29 bp):
CGTGTGACCCACACGGTCTGCCACAAGAC
Found at i:35538297 original size:23 final size:23
Alignment explanation
Indices: 35538236--35538349 Score: 158
Period size: 23 Copynumber: 5.0 Consensus size: 23
35538226 TCTATCATCC
* * *
35538236 ACCAAACATAGCCTCCAAGCACA
1 ACCAAATATACCCTCCAAACACA
*
35538259 ACC-AATTTACCCTCCAAACACA
1 ACCAAATATACCCTCCAAACACA
* * *
35538281 ACCATATGTACCTTCCAAACACA
1 ACCAAATATACCCTCCAAACACA
35538304 ACCAAATATACCCTCCAAACACA
1 ACCAAATATACCCTCCAAACACA
35538327 ACCAAATATACCCTCCAAACACA
1 ACCAAATATACCCTCCAAACACA
35538350 TCCACTTAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
22 18 0.22
23 62 0.77
ACGTcount: A:0.44, C:0.39, G:0.03, T:0.15
Consensus pattern (23 bp):
ACCAAATATACCCTCCAAACACA
Found at i:35546566 original size:2 final size:2
Alignment explanation
Indices: 35546554--35546589 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
35546544 ATTCTATCAA
* *
35546554 CT CT CT TT CT CT CT TT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
35546590 ATTTCTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
CT
Found at i:35546567 original size:8 final size:8
Alignment explanation
Indices: 35546554--35546595 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
35546544 ATTCTATCAA
35546554 CTCTCTTT
1 CTCTCTTT
35546562 CTCTCTTT
1 CTCTCTTT
*
35546570 CTCTCTCT
1 CTCTCTTT
*
35546578 CTCTCTCT
1 CTCTCTTT
*
35546586 CTCTATTT
1 CTCTCTTT
35546594 CT
1 CT
35546596 TTTGCAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (8 bp):
CTCTCTTT
Found at i:35550081 original size:19 final size:19
Alignment explanation
Indices: 35550052--35550118 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
35550042 ATTTAATTGG
35550052 CACGTAAGTGCATACTGGCA
1 CACG-AAGTGCATACTGGCA
* *
35550072 CTCGAAGTGCGTACTGGCA
1 CACGAAGTGCATACTGGCA
*
35550091 CAC-ATAGTGCATTCTGGCA
1 CACGA-AGTGCATACTGGCA
35550110 CACGAAGTG
1 CACGAAGTG
35550119 AATCTTGGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 35 0.88
20 4 0.10
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (19 bp):
CACGAAGTGCATACTGGCA
Found at i:35551052 original size:3 final size:3
Alignment explanation
Indices: 35551044--35551080 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
35551034 ACCCTTCAAT
*
35551044 GAA GAA GAA GAA TAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
35551081 TTTCCATCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:35551796 original size:29 final size:28
Alignment explanation
Indices: 35551750--35551811 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
35551740 ATACAAAATT
* *
35551750 TTTATAAAAATATAGAAAATATTTAAAA
1 TTTATAAAAATATAGAAAAAATATAAAA
*
35551778 TTTACTAAAAATTTAGAAAAAATATAAAA
1 TTTA-TAAAAATATAGAAAAAATATAAAA
*
35551807 ATTAT
1 TTTAT
35551812 TACACAACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (28 bp):
TTTATAAAAATATAGAAAAAATATAAAA
Found at i:35551987 original size:26 final size:27
Alignment explanation
Indices: 35551951--35552011 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
35551941 TGAAAAAATC
35551951 AAAAAT-TAAAATCAA-TAAA-AATGAT
1 AAAAATATAAAAT-AATTAAAGAATGAT
*
35551976 AAAAATATAAAATAATTAAAGTAATTAT
1 AAAAATATAAAATAATTAAAG-AATGAT
35552004 AAAAATAT
1 AAAAATAT
35552012 GTAAAAGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 8 0.26
26 10 0.32
28 13 0.42
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAATATAAAATAATTAAAGAATGAT
Found at i:35552016 original size:21 final size:22
Alignment explanation
Indices: 35551984--35552034 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
35551974 ATAAAAATAT
*
35551984 AAAATAATT-AAAGTAATT-ATA
1 AAAAT-ATTAAAAGTAATTGAAA
*
35552005 AAAATATGTAAAAGTTATTGAAA
1 AAAATAT-TAAAAGTAATTGAAA
35552028 AAAATAT
1 AAAATAT
35552035 ATAATTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.08
21 6 0.24
22 8 0.32
23 9 0.36
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (22 bp):
AAAATATTAAAAGTAATTGAAA
Found at i:35552573 original size:23 final size:23
Alignment explanation
Indices: 35552511--35552574 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 23
35552501 ATTTATAAGG
* * *
35552511 AAAATA-TTTTATGATTTTTTAT
1 AAAATATTTTTTTTATTTTTAAT
*
35552533 -AAATATTTTCTATATATTTTTAAT
1 AAAATATTTT-T-TTTATTTTTAAT
35552557 AAAATATTTTTTTTATTT
1 AAAATATTTTTTTTATTT
35552575 GTTTCAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
21 5 0.15
22 3 0.09
23 7 0.21
24 9 0.27
25 9 0.27
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
AAAATATTTTTTTTATTTTTAAT
Found at i:35574428 original size:20 final size:20
Alignment explanation
Indices: 35574387--35574428 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
35574377 TTCAAAAAAG
*
35574387 TAGAAAAAATATCAAATTAA
1 TAGAAAAAATATCAAATCAA
*
35574407 TAGAAAACATATCTAAA-CAA
1 TAGAAAAAATATC-AAATCAA
35574427 TA
1 TA
35574429 ATTATGTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (20 bp):
TAGAAAAAATATCAAATCAA
Found at i:35579866 original size:15 final size:16
Alignment explanation
Indices: 35579841--35579877 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
35579831 TGGGTAGGAC
35579841 CTGTATACTGT-ATAAT
1 CTGT-TACTGTAATAAT
35579857 CTGTTACTGTAATAAT
1 CTGTTACTGTAATAAT
35579873 -TGTTA
1 CTGTTA
35579878 TTACTGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (16 bp):
CTGTTACTGTAATAAT
Done.