Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 74 of 378
Found at i:19644404 original size:11 final size:10
Alignment explanation
Indices: 19644388--19644449 Score: 56
Period size: 11 Copynumber: 5.9 Consensus size: 10
19644378 ATTTTTTAAA
19644388 TATTATTTTC
1 TATTATTTTC
19644398 TTATTATTTT-
1 -TATTATTTTC
19644408 TCA-TATTTTAC
1 T-ATTATTTT-C
19644419 TATTATTTTAC
1 TATTATTTT-C
*
19644430 TATTATATTAC
1 TATTAT-TTTC
19644441 TATTATTTT
1 TATTATTTT
19644450 ATTGGTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
9 7 0.16
10 4 0.09
11 31 0.70
12 2 0.05
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (10 bp):
TATTATTTTC
Found at i:19644443 original size:22 final size:20
Alignment explanation
Indices: 19644399--19644450 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
19644389 ATTATTTTCT
* *
19644399 TATTATTTTTCATATTTTAC
1 TATTATTTTACATATATTAC
19644419 TATTATTTTACTATTATATTAC
1 TATTATTTTAC-A-TATATTAC
19644441 TATTATTTTA
1 TATTATTTTA
19644451 TTGGTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.36
21 1 0.04
22 17 0.61
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTATTTTACATATATTAC
Found at i:19644529 original size:18 final size:20
Alignment explanation
Indices: 19644506--19644546 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
19644496 TTTATTGATA
*
19644506 TTTTGATGT-TTTTA-ATAT
1 TTTTGATGTATTATATATAT
19644524 TTTTGATGTATTATATATAT
1 TTTTGATGTATTATATATAT
19644544 TTT
1 TTT
19644547 ACAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 4 0.20
20 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTTGATGTATTATATATAT
Found at i:19664405 original size:2 final size:2
Alignment explanation
Indices: 19664398--19664438 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
19664388 CTTAGTTTGC
19664398 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19664439 ATTAAGATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19673855 original size:30 final size:32
Alignment explanation
Indices: 19673811--19673896 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 32
19673801 TGTGCCTTTG
*
19673811 TGAAATGATAACAAATATCAACTTTAATTTTT
1 TGAAATGATAACAAATACCAACTTTAATTTTT
* *
19673843 TGAAAT-A-AACAAATACCAACTTTAATTATG
1 TGAAATGATAACAAATACCAACTTTAATTTTT
* *
19673873 TAAAATGGTAA-AACATACCAACTT
1 TGAAATGATAACAA-ATACCAACTT
19673897 GGATGAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 25 0.54
31 3 0.07
32 18 0.39
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (32 bp):
TGAAATGATAACAAATACCAACTTTAATTTTT
Found at i:19674579 original size:11 final size:11
Alignment explanation
Indices: 19674563--19674596 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19674553 ATGTCAAATC
19674563 ATTAAGAATAA
1 ATTAAGAATAA
**
19674574 ATTAAGAGCAA
1 ATTAAGAATAA
19674585 ATTAAGAATAA
1 ATTAAGAATAA
19674596 A
1 A
19674597 ACTAGATGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.24
Consensus pattern (11 bp):
ATTAAGAATAA
Found at i:19681604 original size:25 final size:25
Alignment explanation
Indices: 19681576--19681637 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
19681566 TTTCTAACTA
*
19681576 ATCATTAAATTGATAAAATTTTCCT
1 ATCATTAAATTCATAAAATTTTCCT
* ** **
19681601 ATCAATATTTTCATACGATTTTCCT
1 ATCATTAAATTCATAAAATTTTCCT
19681626 ATCATATAAATT
1 ATCAT-TAAATT
19681638 TTCAAGCAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.45
Consensus pattern (25 bp):
ATCATTAAATTCATAAAATTTTCCT
Found at i:19687871 original size:3 final size:3
Alignment explanation
Indices: 19687858--19687896 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
19687848 AATTTCCACT
*
19687858 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19687897 GACATATCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:19689359 original size:39 final size:39
Alignment explanation
Indices: 19689305--19689379 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
19689295 CCCCACACCA
19689305 TTTATCATGTTGGATCATCAAGAACAAAAACTAGATGTG
1 TTTATCATGTTGGATCATCAAGAACAAAAACTAGATGTG
19689344 TTTATCATGTTGGATCATCAAGAACAAAAACTAGAT
1 TTTATCATGTTGGATCATCAAGAACAAAAACTAGAT
19689380 ATGGAAGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (39 bp):
TTTATCATGTTGGATCATCAAGAACAAAAACTAGATGTG
Found at i:19691664 original size:4 final size:4
Alignment explanation
Indices: 19691655--19691739 Score: 80
Period size: 4 Copynumber: 20.8 Consensus size: 4
19691645 GAGTAAGTTA
* *** * *
19691655 AAAG AAAG AAAG AAAG AAAG AAAG ATAG AAAG AGTT ACAG AGAG CAAACG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G
**
19691705 TGAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
19691740 TAGAAAAGGG
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
4 61 0.94
5 3 0.05
6 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.26, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:19698872 original size:4 final size:4
Alignment explanation
Indices: 19698863--19698951 Score: 88
Period size: 4 Copynumber: 21.8 Consensus size: 4
19698853 TGAGTAAGTT
* *** * *
19698863 AAAG AAAG AAAG AAAG AAAG AAAG ATAG AAAG AGTT ACAG AGAG CAAACG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G
**
19698913 TGAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
19698952 TAGAAAAGGG
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
4 65 0.94
5 3 0.04
6 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.26, T:0.04
Consensus pattern (4 bp):
AAAG
Found at i:19699777 original size:47 final size:47
Alignment explanation
Indices: 19699713--19699823 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
19699703 GACATTGAGT
*
19699713 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
19699760 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
19699807 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
19699824 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:19702300 original size:13 final size:13
Alignment explanation
Indices: 19702270--19702312 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
19702260 CTTAATTAGA
19702270 AAATTAATTAAGTT
1 AAATTAATTAA-TT
19702284 AAATTAATTAATT
1 AAATTAATTAATT
*
19702297 AAATTAATTGATT
1 AAATTAATTAATT
19702310 AAA
1 AAA
19702313 AAAATAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:19708098 original size:5 final size:5
Alignment explanation
Indices: 19708088--19708122 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
19708078 GCTTAGCTAT
19708088 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAA
19708123 AAGATGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:19708204 original size:12 final size:12
Alignment explanation
Indices: 19708189--19708216 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19708179 GTGGGGGGCA
19708189 AAGTGCATGTGC
1 AAGTGCATGTGC
19708201 AAGTGCATGTGC
1 AAGTGCATGTGC
19708213 AAGT
1 AAGT
19708217 TCAAGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (12 bp):
AAGTGCATGTGC
Found at i:19711968 original size:18 final size:18
Alignment explanation
Indices: 19711945--19712000 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
19711935 CCACCACCAA
19711945 CTCCACTAACCACACTTG
1 CTCCACTAACCACACTTG
*
19711963 CTCCAC-CACCA-A----
1 CTCCACTAACCACACTTG
*
19711975 CTCCACTAGCCACACTTG
1 CTCCACTAACCACACTTG
19711993 CTCCACTA
1 CTCCACTA
19712001 CCTACTCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 12
0.66 0.07 0.27
Matches are distributed among these distances:
12 6 0.21
13 3 0.10
14 1 0.03
16 1 0.03
17 4 0.14
18 14 0.48
ACGTcount: A:0.27, C:0.48, G:0.05, T:0.20
Consensus pattern (18 bp):
CTCCACTAACCACACTTG
Found at i:19711971 original size:30 final size:30
Alignment explanation
Indices: 19711935--19712033 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
19711925 CTAGCCTTTG
*
19711935 CCACCACCAACTCCACTAACCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
19711965 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
19711995 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
19712025 CCACCACCA
1 CCACCACCA
19712034 CTTGTACCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.27, C:0.51, G:0.05, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:19712028 original size:18 final size:18
Alignment explanation
Indices: 19711975--19712028 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
19711965 CCACCACCAA
19711975 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
19711993 CTCCACT----AC-C-TA
1 CTCCACTAGCCACACTTG
19712005 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
19712023 CTCCAC
1 CTCCAC
19712029 CACCACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 8 0.29
13 1 0.04
14 2 0.07
16 2 0.07
17 1 0.04
18 14 0.50
ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:19715455 original size:51 final size:51
Alignment explanation
Indices: 19715374--19715476 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
19715364 TACTGATTTC
* * *
19715374 AGAATGGAAATGAGAGCGAGTTATAATGGATTTTGTATTAGGATTACCGTT
1 AGAAGGGAAATGAGAGCGAGTTACAATGGATTTTATATTAGGATTACCGTT
*
19715425 AGAAGGGAAAT-AGGAGCGAGTTACAATGGATTTTATATTAGGATTGCCGTT
1 AGAAGGGAAATGA-GAGCGAGTTACAATGGATTTTATATTAGGATTACCGTT
19715476 A
1 A
19715477 ACTCCGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
50 1 0.02
51 46 0.98
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (51 bp):
AGAAGGGAAATGAGAGCGAGTTACAATGGATTTTATATTAGGATTACCGTT
Found at i:19719864 original size:2 final size:2
Alignment explanation
Indices: 19719857--19719897 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
19719847 TCATACATCG
19719857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19719898 CATACAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19721109 original size:27 final size:27
Alignment explanation
Indices: 19721037--19721109 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
19721027 TAGGTCTAGC
* *
19721037 GAGATGGTATACGCTAGCAAGCCTGGA
1 GAGATGGTGTACGCTAGTAAGCCTGGA
* * * *
19721064 GAGACGATGTATGCCAGTAAGCCTGGCA
1 GAGATGGTGTACGCTAGTAAGCCTGG-A
19721092 -AGATGGTGTACGCTAGTA
1 GAGATGGTGTACGCTAGTA
19721110 GGTCTGGCGA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.33, T:0.21
Consensus pattern (27 bp):
GAGATGGTGTACGCTAGTAAGCCTGGA
Found at i:19727425 original size:12 final size:12
Alignment explanation
Indices: 19727408--19727457 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
19727398 ATAATTATTA
19727408 TTTTATTAAAT-T
1 TTTTA-TAAATAT
*
19727420 TTTTATATAT-T
1 TTTTATAAATAT
*
19727431 TTTTAAAAATAT
1 TTTTATAAATAT
*
19727443 TTTTTTAAATAT
1 TTTTATAAATAT
19727455 TTT
1 TTT
19727458 GAATTATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 13 0.41
12 19 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTATAAATAT
Found at i:19729041 original size:14 final size:14
Alignment explanation
Indices: 19729022--19729056 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
19729012 ATAATGGTGT
19729022 TTAATTGAATAATA
1 TTAATTGAATAATA
19729036 TTAATTGAATAATA
1 TTAATTGAATAATA
19729050 TTAATTG
1 TTAATTG
19729057 TTTTTGAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (14 bp):
TTAATTGAATAATA
Found at i:19729762 original size:97 final size:98
Alignment explanation
Indices: 19729659--19729851 Score: 327
Period size: 97 Copynumber: 2.0 Consensus size: 98
19729649 TTAGAAACTC
* *
19729659 AAAAAAATATTTGGAAAATAACCAATAGTAAATTAGTAAATAA-TTAGATAAAATATGAATTTTA
1 AAAAAAATATTTGGAAAACAACCAATAGTAAATTAATAAA-AAGTTAGATAAAATATGAATTTTA
19729723 AGAAAATAAATTATAA-ATTAAATTGAAAAAAGT
65 AGAAAATAAATTATAATATTAAATTGAAAAAAGT
19729756 AAAAAAATATTTGGAAAACAACCAATAGTAAATTAATAAAAAGTTAGATAAAATATGAATTTTAA
1 AAAAAAATATTTGGAAAACAACCAATAGTAAATTAATAAAAAGTTAGATAAAATATGAATTTTAA
* *
19729821 GAAAGTAGATTATAATATTAAATTGAAAAAA
66 GAAAATAAATTATAATATTAAATTGAAAAAA
19729852 AAAGGTAAAG
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
96 2 0.02
97 73 0.81
98 15 0.17
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.29
Consensus pattern (98 bp):
AAAAAAATATTTGGAAAACAACCAATAGTAAATTAATAAAAAGTTAGATAAAATATGAATTTTAA
GAAAATAAATTATAATATTAAATTGAAAAAAGT
Found at i:19732147 original size:36 final size:36
Alignment explanation
Indices: 19732087--19732178 Score: 130
Period size: 36 Copynumber: 2.5 Consensus size: 36
19732077 AAAATAAAAT
*** *
19732087 AAATAATAAAAAAATTAAAAGTATAACTTTTAAATTG
1 AAATAAT-AAAAAATTATTTGTATAACTTCTAAATTG
*
19732124 AAATAATGAAAAATTATTTGTATAACTTCTAAATTG
1 AAATAATAAAAAATTATTTGTATAACTTCTAAATTG
19732160 AAATAATAAAAAATTATTT
1 AAATAATAAAAAATTATTT
19732179 TAAAAAATAG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 42 0.86
37 7 0.14
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (36 bp):
AAATAATAAAAAATTATTTGTATAACTTCTAAATTG
Found at i:19733035 original size:3 final size:3
Alignment explanation
Indices: 19733027--19733061 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19733017 TTCTGATTTT
19733027 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
19733062 TTTCCTTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:19735834 original size:10 final size:11
Alignment explanation
Indices: 19735808--19735833 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19735798 AAACGGTCCA
19735808 TTTTTGTTTTT
1 TTTTTGTTTTT
19735819 TTTTTGTTTTT
1 TTTTTGTTTTT
19735830 TTTT
1 TTTT
19735834 GGAAATAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:19736809 original size:21 final size:21
Alignment explanation
Indices: 19736783--19736822 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19736773 GGGTTTAAAA
19736783 TTTAAGTTCAGGGTTCAGGAT
1 TTTAAGTTCAGGGTTCAGGAT
19736804 TTTAAGTTCAGGGTTCAGG
1 TTTAAGTTCAGGGTTCAGG
19736823 GTAAAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.38
Consensus pattern (21 bp):
TTTAAGTTCAGGGTTCAGGAT
Found at i:19737009 original size:18 final size:18
Alignment explanation
Indices: 19736986--19737020 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19736976 TTGTTTATAA
19736986 TTTAAAAAAATTAATTAT
1 TTTAAAAAAATTAATTAT
* *
19737004 TTTAAATAATTTAATTA
1 TTTAAAAAAATTAATTA
19737021 AAGTTATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAAAAATTAATTAT
Found at i:19737681 original size:11 final size:11
Alignment explanation
Indices: 19737667--19737707 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
19737657 TATTTTCTCC
19737667 CTATTTTGCTA
1 CTATTTTGCTA
*
19737678 CTATTTTACTA
1 CTATTTTGCTA
* *
19737689 TTATATTGCTA
1 CTATTTTGCTA
19737700 CTATTTTG
1 CTATTTTG
19737708 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:19737790 original size:30 final size:30
Alignment explanation
Indices: 19737750--19737808 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
19737740 TTTATTGTTT
*
19737750 ATTTTTTTATTATTTTAAAGACATTTGCTA
1 ATTTTATTATTATTTTAAAGACATTTGCTA
* *
19737780 ATTTTATTATTATTTTAGAGGCATTTGCT
1 ATTTTATTATTATTTTAAAGACATTTGCT
19737809 TTCTAAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.56
Consensus pattern (30 bp):
ATTTTATTATTATTTTAAAGACATTTGCTA
Found at i:19737959 original size:12 final size:12
Alignment explanation
Indices: 19737929--19737961 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
19737919 TATATATTTT
19737929 AAAATT-ATATA
1 AAAATTAATATA
19737940 AAAA-TAATATA
1 AAAATTAATATA
19737951 AAAATTAATAT
1 AAAATTAATAT
19737962 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:19738544 original size:9 final size:9
Alignment explanation
Indices: 19738511--19738567 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
19738501 TTAACGTTAG
19738511 TTTTTCTTCT
1 TTTTTCTT-T
* *
19738521 TCTTTATTT
1 TTTTTCTTT
*
19738530 TCTTTCTTT
1 TTTTTCTTT
19738539 TTTTTCTTT
1 TTTTTCTTT
* *
19738548 TTTTTGGTTC
1 TTTTT-CTTT
19738558 TTTTTCTTT
1 TTTTTCTTT
19738567 T
1 T
19738568 CTTCTTTGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
9 25 0.66
10 13 0.34
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:19738552 original size:13 final size:13
Alignment explanation
Indices: 19738511--19738574 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
19738501 TTAACGTTAG
19738511 TTTTTCTTCTTCTTT
1 TTTTTCTT-TT-TTT
* *
19738526 ATTTTCTTTCTTT
1 TTTTTCTTTTTTT
19738539 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
**
19738552 TGGTTCTTTTTCTT
1 TTTTTCTTTTT-TT
*
19738566 TTCTTCTTT
1 TTTTTCTTT
19738575 GTTTGTCGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
13 23 0.57
14 10 0.25
15 7 0.17
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:19738552 original size:22 final size:22
Alignment explanation
Indices: 19738520--19738562 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19738510 GTTTTTCTTC
*
19738520 TTCTTTATTTTCTTTCTTTTTT
1 TTCTTTATTTTCGTTCTTTTTT
* *
19738542 TTCTTTTTTTTGGTTCTTTTT
1 TTCTTTATTTTCGTTCTTTTT
19738563 CTTTTCTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (22 bp):
TTCTTTATTTTCGTTCTTTTTT
Found at i:19746341 original size:2 final size:2
Alignment explanation
Indices: 19746334--19746366 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19746324 AATTTTAATG
19746334 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19746367 GTTAAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19749292 original size:50 final size:50
Alignment explanation
Indices: 19749207--19749422 Score: 211
Period size: 50 Copynumber: 4.3 Consensus size: 50
19749197 GCTAAATGAC
* * * * *
19749207 CTTGTATATTCGGCCACATAAGTATGTACATATGTGATGTTGTATTGGAT
1 CTTGTATATTCGGCCATATAGGTAAGCACATATGTGATGTTATATTGGAT
* * * * *
19749257 CTTGAATATTCGGCCATGA-AGGTATGCACAAATGTGATTTTATATTTGAAT
1 CTTGTATATTCGGCCAT-ATAGGTAAGCACATATGTGATGTTATA-TTGGAT
* * * *
19749308 -TTGTATATTCGGCCATATAAGTAAGTACATATGTGATGTTAAATTTGAT
1 CTTGTATATTCGGCCATATAGGTAAGCACATATGTGATGTTATATTGGAT
* * * * *
19749357 CTTGCATATTTGGCCATATAGGTAAGCACATATGTGCTCTTATATTTGAT
1 CTTGTATATTCGGCCATATAGGTAAGCACATATGTGATGTTATATTGGAT
* *
19749407 CTTGTACATTTGGCCA
1 CTTGTATATTCGGCCA
19749423 AATGAGTGAT
Statistics
Matches: 136, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
49 5 0.04
50 125 0.92
51 6 0.04
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.39
Consensus pattern (50 bp):
CTTGTATATTCGGCCATATAGGTAAGCACATATGTGATGTTATATTGGAT
Found at i:19749386 original size:100 final size:100
Alignment explanation
Indices: 19749207--19749422 Score: 283
Period size: 100 Copynumber: 2.2 Consensus size: 100
19749197 GCTAAATGAC
* **
19749207 CTTGTATATTCGGCCACATAAGTATGTACATATGTGATGTTGTATTGGATCTTGAATATTCGGCC
1 CTTGTATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCC
* *
19749272 ATGAAGGTATGCACAAATGTGATTTTATATTTGAAT
66 ATGAAGGTAAGCACAAATGTGATCTTATATTTG-AT
* * * *
19749308 -TTGTATATTCGGCCATATAAGTAAGTACATATGTGATGTTAAATTTGATCTTGCATATTTGGCC
1 CTTGTATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCC
* *
19749372 AT-ATAGGTAAGCACATATGTGCTCTTATATTTGAT
66 ATGA-AGGTAAGCACAAATGTGATCTTATATTTGAT
* *
19749407 CTTGTACATTTGGCCA
1 CTTGTATATTCGGCCA
19749423 AATGAGTGAT
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
99 3 0.03
100 97 0.97
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.39
Consensus pattern (100 bp):
CTTGTATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCC
ATGAAGGTAAGCACAAATGTGATCTTATATTTGAT
Found at i:19750251 original size:2 final size:2
Alignment explanation
Indices: 19750244--19750268 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19750234 CGTGGCAATG
19750244 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19750269 AATGCATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19764942 original size:41 final size:41
Alignment explanation
Indices: 19764881--19764961 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
19764871 AACTGAGTTG
* * *
19764881 TTATGGCGGTGTATTATATCGGGCCTT-AGGCCTAGCAGGCT
1 TTATGCCGATGTATTATATCGGGCCTTGA-GCCTAACAGGCT
*
19764922 TTATGCCGATGTATTGTATCGGGCCTTGAGCCTAACAGGC
1 TTATGCCGATGTATTATATCGGGCCTTGAGCCTAACAGGC
19764962 CTCATGTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 34 0.97
42 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.31
Consensus pattern (41 bp):
TTATGCCGATGTATTATATCGGGCCTTGAGCCTAACAGGCT
Found at i:19766386 original size:71 final size:71
Alignment explanation
Indices: 19766293--19766508 Score: 202
Period size: 71 Copynumber: 3.0 Consensus size: 71
19766283 AGACTACAGG
* * *
19766293 AACACATGATAGATCTCGACCATCAATAAAGT-ATAATGTGATACTGCTCACTCAAGCTGTCAAG
1 AACACATGATAGATCTCAACCATCAATAAA-TAATAATCTGATACTGCTCACTCAAGCAGTCAAG
19766357 AATCCAC
65 AATCCAC
* * ** * * *
19766364 AACACATGTTGGATCTCAACCATCGCTAAATAATTATCTGATGCTGCTCACTCAAGCAGTCTAGA
1 AACACATGATAGATCTCAACCATCAATAAATAATAATCTGATACTGCTCACTCAAGCAGTCAAGA
**
19766429 ATCTGC
66 ATCCAC
* ** * ** ** *
19766435 AACACATGCTAGATCTCAACCATCGCTAAATAATGATCCAATGTTGCTCACTCAAGCTA-TTAAG
1 AACACATGATAGATCTCAACCATCAATAAATAATAATCTGATACTGCTCACTCAAGC-AGTCAAG
*
19766499 AATCCCC
65 AATCCAC
19766506 AAC
1 AAC
19766509 TTAAGTTGGA
Statistics
Matches: 121, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
70 1 0.01
71 119 0.98
72 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.25
Consensus pattern (71 bp):
AACACATGATAGATCTCAACCATCAATAAATAATAATCTGATACTGCTCACTCAAGCAGTCAAGA
ATCCAC
Found at i:19766521 original size:71 final size:71
Alignment explanation
Indices: 19766336--19766508 Score: 215
Period size: 71 Copynumber: 2.4 Consensus size: 71
19766326 TAATGTGATA
* * *
19766336 CTGCTCACTCAAGCTGTCAAGAATCCACAACACATGTTGGATCTCAACCATCGCTAAATAATTAT
1 CTGCTCACTCAAGCTATTAAGAATCCACAACACATGTTGGATCTCAACCATCGCTAAATAATGAT
**
19766401 CTGATG
66 CCAATG
** * *
19766407 CTGCTCACTCAAGC-AGTCT-AGAATCTGCAACACATGCTAGATCTCAACCATCGCTAAATAATG
1 CTGCTCACTCAAGCTA-T-TAAGAATCCACAACACATGTTGGATCTCAACCATCGCTAAATAATG
19766470 ATCCAATG
64 ATCCAATG
* *
19766478 TTGCTCACTCAAGCTATTAAGAATCCCCAAC
1 CTGCTCACTCAAGCTATTAAGAATCCACAAC
19766509 TTAAGTTGGA
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
70 1 0.01
71 84 0.98
72 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.25
Consensus pattern (71 bp):
CTGCTCACTCAAGCTATTAAGAATCCACAACACATGTTGGATCTCAACCATCGCTAAATAATGAT
CCAATG
Found at i:19768904 original size:15 final size:17
Alignment explanation
Indices: 19768863--19768921 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
19768853 TTAATTTTTT
* *
19768863 AAATAAAAAATTTTAAA
1 AAATTAAAAATTATAAA
19768880 AAATTAAAAATTATAAA
1 AAATTAAAAATTATAAA
19768897 AAA-T-AAAATTA-AAA
1 AAATTAAAAATTATAAA
*
19768911 AGTATTAAAAA
1 A-AATTAAAAA
19768922 AATTTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 4 0.11
15 8 0.22
16 2 0.06
17 22 0.61
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAATTAAAAATTATAAA
Found at i:19768904 original size:22 final size:23
Alignment explanation
Indices: 19768879--19768922 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
19768869 AAAATTTTAA
*
19768879 AAAATTAAAAATTA-TAAAAAAT
1 AAAATTAAAAAGTATTAAAAAAT
19768901 AAAATTAAAAAGTATTAAAAAA
1 AAAATTAAAAAGTATTAAAAAA
19768923 ATTTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAATTAAAAAGTATTAAAAAAT
Found at i:19772535 original size:1 final size:1
Alignment explanation
Indices: 19772531--19772555 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
19772521 CCCCCCTCAG
19772531 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
19772556 GAGAGAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19775965 original size:20 final size:20
Alignment explanation
Indices: 19775940--19775977 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19775930 CAATTCAAAT
19775940 ATTATAATAAAAAAATTTAA
1 ATTATAATAAAAAAATTTAA
* *
19775960 ATTATAATGAAAACATTT
1 ATTATAATAAAAAAATTT
19775978 TTAACATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (20 bp):
ATTATAATAAAAAAATTTAA
Found at i:19776281 original size:16 final size:17
Alignment explanation
Indices: 19776252--19776283 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19776242 AGTTTATATT
19776252 ATATTATATTATAAAAA
1 ATATTATATTATAAAAA
19776269 ATATTAT-TTATAAAA
1 ATATTATATTATAAAA
19776284 TTTTATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATTATATTATAAAAA
Found at i:19776408 original size:15 final size:16
Alignment explanation
Indices: 19776379--19776412 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
19776369 ATGTAAACAT
19776379 AATAATTTAAATATAA
1 AATAATTTAAATATAA
19776395 AATAATTT-AATATAA
1 AATAATTTAAATATAA
19776410 AAT
1 AAT
19776413 TTGACTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAATTTAAATATAA
Found at i:19779570 original size:46 final size:45
Alignment explanation
Indices: 19779518--19779685 Score: 176
Period size: 46 Copynumber: 3.6 Consensus size: 45
19779508 TCTAGTAGCC
* * *
19779518 GATGCATGTCCTAGACATGTCTTACACCGGCTTACGTGTCGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTT-CGTATCGAGGCT
* * * * *
19779564 GATGCATGTCCCAGATATGTCTTACACTAGCATTCGTCTCGATGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-TTCGTATCGAGGCT
* * *
19779610 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAAT-GTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TCGT-ATCGAGGCT
19779658 GATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
19779686 AGCCCACAAT
Statistics
Matches: 101, Mismatches: 16, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
46 50 0.50
47 28 0.28
48 22 0.22
49 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.29
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTCGTATCGAGGCT
Found at i:19789483 original size:29 final size:29
Alignment explanation
Indices: 19789420--19789485 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
19789410 TGTTAAAATT
*
19789420 AATTATTAAAATAAAATTGTAGTATTAAA
1 AATTATTAAAATAAAAATGTAGTATTAAA
19789449 AATTATTAAAATAATAAAT-TA-TATTAATA
1 AATTATTAAAATAA-AAATGTAGTATTAA-A
*
19789478 ATTTATTA
1 AATTATTA
19789486 TATTATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 6 0.18
29 24 0.73
30 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (29 bp):
AATTATTAAAATAAAAATGTAGTATTAAA
Found at i:19791606 original size:20 final size:20
Alignment explanation
Indices: 19791581--19791619 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
19791571 ATGTACTTAG
19791581 TTTCTTGCACTCTTGTTCAA
1 TTTCTTGCACTCTTGTTCAA
19791601 TTTCTTGCACTCTTGTTCA
1 TTTCTTGCACTCTTGTTCA
19791620 TTCTATAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.13, C:0.26, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTCTTGCACTCTTGTTCAA
Found at i:19795598 original size:22 final size:22
Alignment explanation
Indices: 19795536--19795596 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
19795526 TTTCAATATT
*
19795536 CTCTC-AAATTCTTTTCAAA-T-
1 CTCTCAAAATTCTCTT-AAATTC
**
19795556 CTCTCAAGTTTCTCTTAAATTC
1 CTCTCAAAATTCTCTTAAATTC
19795578 CTCTCAAAATTCTCGTTAA
1 CTCTCAAAATTCTC-TTAA
19795597 TTTTTTTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.25
21 8 0.25
22 12 0.38
23 4 0.12
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.43
Consensus pattern (22 bp):
CTCTCAAAATTCTCTTAAATTC
Found at i:19796743 original size:7 final size:7
Alignment explanation
Indices: 19796731--19796757 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
19796721 TAGTGGATTC
19796731 GTATTTA
1 GTATTTA
19796738 GTATTTA
1 GTATTTA
19796745 GTATTTA
1 GTATTTA
19796752 GTATTT
1 GTATTT
19796758 TTTATTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (7 bp):
GTATTTA
Found at i:19797296 original size:30 final size:30
Alignment explanation
Indices: 19797255--19797320 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
19797245 CGACGACGCA
*
19797255 GGCCCATCAACAGCG-CCCACACAATCACCC
1 GGCCCAGCAACAG-GACCCACACAATCACCC
* * *
19797285 GGCCCAGCAACAGGACCTACACAGTCACCG
1 GGCCCAGCAACAGGACCCACACAATCACCC
19797315 GGCCCA
1 GGCCCA
19797321 ACAGTTCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.29, C:0.45, G:0.20, T:0.06
Consensus pattern (30 bp):
GGCCCAGCAACAGGACCCACACAATCACCC
Found at i:19797397 original size:18 final size:18
Alignment explanation
Indices: 19797374--19797416 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
19797364 TGCCAGGTAC
*
19797374 GTATCCTAGCCCTTTTAT
1 GTATCCTAGCCCTTATAT
19797392 GTATCCTAGCCCTTATAT
1 GTATCCTAGCCCTTATAT
*
19797410 GTTTCCT
1 GTATCCT
19797417 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (18 bp):
GTATCCTAGCCCTTATAT
Found at i:19797705 original size:22 final size:23
Alignment explanation
Indices: 19797680--19797725 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
19797670 CAACCAAATC
19797680 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
19797702 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
19797725 A
1 A
19797726 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:19797731 original size:23 final size:23
Alignment explanation
Indices: 19797687--19797731 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
19797677 ATCAATTCAA
*
19797687 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
19797710 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
19797732 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:19800996 original size:116 final size:116
Alignment explanation
Indices: 19800792--19801058 Score: 480
Period size: 116 Copynumber: 2.3 Consensus size: 116
19800782 TATTTGTACA
* *
19800792 AACATTTTGAATCTTTTTATATTATTTCATGTAATTAGATAAAATGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
* * *
19800857 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
66 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
19800908 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
19800973 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
66 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
*
19801024 AACATTTTGAATATTTTTATATTATTTTATGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAAT
19801059 AAAATATAAA
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 145 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (116 bp):
AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
Found at i:19801021 original size:54 final size:54
Alignment explanation
Indices: 19800841--19801022 Score: 172
Period size: 54 Copynumber: 3.2 Consensus size: 54
19800831 TAAAATGTTG
* *
19800841 TTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTA
1 TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
* * * * * *
19800895 TTTTAAATAAGGCAACATTTTGAATATT--TTTATATTATTTCATGTAATTAGAT-AAAAGGTTG
1 TTTTAAATAAAG-TA-ATTAT-AAT-TTACTTT-TA-TATTT--T-TAATAAAATGAAAA--TTA
19800957 TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
1 TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
19801011 TTTTAAATAAAG
1 TTTTAAATAAAG
19801023 CAACATTTTG
Statistics
Matches: 101, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
54 25 0.25
55 8 0.08
56 12 0.12
57 5 0.05
58 14 0.14
59 5 0.05
60 11 0.11
61 8 0.08
62 13 0.13
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (54 bp):
TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
Found at i:19804307 original size:126 final size:125
Alignment explanation
Indices: 19804077--19804740 Score: 1001
Period size: 126 Copynumber: 5.3 Consensus size: 125
19804067 GCCCAAGTTA
*
19804077 TTTCAGAAACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
1 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*
19804142 TGCATCTTGCTTGAAGCGTTTTTGACACTATTT-ATGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTT-ACACTATTTGA-GCAGACACGTCTTCTCAAAATTATTT
* *
19804203 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAA
1 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*
19804268 TGCATCCTGCTTGAAGCATTTTTACCACTATTTGAGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTA-CACTATTTGAGCAGACACGTCTTCTCAAAATTATTT
* * * * *
19804329 TTTCAAAGACCACTGTAGCAAAAGAGAATCCACGTGGGAGCTTCTTCCAGTAATTTTGTTGAAAA
1 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
19804394 TGCATCCTACTTGAAGCGTTTTTACCACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTA-CACTATTTGAGCAGACACGTCTTCTCAAAATTATTT
* * * *
19804455 TTTCAGAGACTACTGTAGTAAAAGAGCATCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*
19804520 TGCATCCTGCTTGAAGCGTTTTTTACACTATTTGCA-CAGACACGTCTTCTCAAATTTATTT
66 TGCATCCTGCTTGAAGCG-TTTTTACACTATTTG-AGCAGACACGTCTTCTCAAAATTATTT
* * * * *
19804581 TTTCAGATACTACTATAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* * *
19804646 TGCATCCTGCTTG-TGCGTTTTTAACACTATTTGCGCAGACACGTCTTCTCAAATTTATTT
66 TGCATCCTGCTTGAAGCGTTTTT-ACACTATTTGAGCAGACACGTCTTCTCAAAATTATTT
* *
19804706 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
1 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGT
19804741 AGAAGCTTTT
Statistics
Matches: 500, Mismatches: 32, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
124 5 0.01
125 72 0.14
126 416 0.83
127 7 0.01
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (125 bp):
TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTACACTATTTGAGCAGACACGTCTTCTCAAAATTATTT
Found at i:19805004 original size:96 final size:98
Alignment explanation
Indices: 19804837--19805035 Score: 242
Period size: 96 Copynumber: 2.0 Consensus size: 98
19804827 TTAAAACCCT
* * * * * **
19804837 AAACCCTAAACCCTAAAATCCTAATCTAATTTTTTTTTAAATTTATAATTAATTTACTCAAGTAA
1 AAACCATAAACACTAAAATCATAATCTAA--TTTTTTTAAAATTATAATTAATTTAATCAACAAA
* *
19804902 CCCTAAACCCTAATTTATTTGA-TTTTTTCCTTAA
64 CACTAAACCCTAATTTATTTAATTTTTTTCCTTAA
*
19804936 AAACCATAAACACT-AAATCATAATCTAA-TTTTTTAAAATTAGTAATTAATTTAATTAACAAAC
1 AAACCATAAACACTAAAATCATAATCTAATTTTTTTAAAATTA-TAATTAATTTAATCAACAAAC
*
19804999 ACTAAACCTTAATTTATTTAATTTTTTTTCCTTAA
65 ACTAAACCCTAATTTATTTAA-TTTTTTTCCTTAA
19805034 AA
1 AA
19805036 CCCTAAAATT
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
95 12 0.14
96 35 0.41
98 27 0.31
99 12 0.14
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.42
Consensus pattern (98 bp):
AAACCATAAACACTAAAATCATAATCTAATTTTTTTAAAATTATAATTAATTTAATCAACAAACA
CTAAACCCTAATTTATTTAATTTTTTTCCTTAA
Found at i:19805050 original size:15 final size:16
Alignment explanation
Indices: 19805032--19805073 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
19805022 TTTTTTCCTT
19805032 AAAACCCTAAAATTTA
1 AAAACCCTAAAATTTA
* *
19805048 AAAATCC-AAAATTCTC
1 AAAACCCTAAAATT-TA
19805064 AAAACCCTAA
1 AAAACCCTAA
19805074 CTCTAATTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 6 0.29
16 13 0.62
17 2 0.10
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAACCCTAAAATTTA
Found at i:19805428 original size:2 final size:2
Alignment explanation
Indices: 19805421--19805449 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19805411 TAAGTGAAAC
19805421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19805450 ATGTTCCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19808146 original size:46 final size:47
Alignment explanation
Indices: 19808086--19808313 Score: 313
Period size: 46 Copynumber: 5.0 Consensus size: 47
19808076 TTTGACGTGA
* * * * * *
19808086 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
** * *
19808132 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*
19808178 TGGCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
19808224 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*
19808270 TGTCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAG
19808314 AGAGCACACT
Statistics
Matches: 168, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 5 0.03
46 163 0.97
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
Found at i:19812685 original size:128 final size:128
Alignment explanation
Indices: 19812442--19812742 Score: 383
Period size: 128 Copynumber: 2.4 Consensus size: 128
19812432 ATACTCCATG
* * *
19812442 TTTAGAAGTTTGAGAGATCGTGCCCAATCGTGTTAGGTTTCGA-TTTTTTCATTCGACTGAAATA
1 TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGTTGGGTTTCGATTTTTTTCATTCGACTAAAATA
* ** ** * *
19812506 TAGAATATCCTTTTAAAATTTTGTCTATGTCCTCTTAAATTAAAAACAAGGCAATATTTCGTA
66 CAGAATATCCTCATAAAATTTCATCCATGTCCTCTTAAATTAAAAACAAGGCAATATTTCATA
**
19812569 TTTAGGAGTTTGAGAGATTATGCCCAATCGTGTTGGGTTTCGATTTTTTTCATTCGACTAAAATA
1 TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGTTGGGTTTCGATTTTTTTCATTCGACTAAAATA
* ** *
19812634 CGGAATATCCTCATAAAATTTCATCCATGTTTTCTTAGAATT-AAAATAAGGCAATATTTCATA
66 CAGAATATCCTCATAAAATTTCATCCATGTCCTCTTA-AATTAAAAACAAGGCAATATTTCATA
* * * *
19812697 TTT-GGAAGTTCGATAAATCGTGCCCAATCGTGATGGGTTTCGATTT
1 TTTAGG-AGTTTGAGAGATCGTGCCCAATCGTGTTGGGTTTCGATTT
19812743 ACCGTTTGAC
Statistics
Matches: 149, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
127 41 0.28
128 104 0.70
129 4 0.03
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (128 bp):
TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGTTGGGTTTCGATTTTTTTCATTCGACTAAAATA
CAGAATATCCTCATAAAATTTCATCCATGTCCTCTTAAATTAAAAACAAGGCAATATTTCATA
Found at i:19822226 original size:45 final size:45
Alignment explanation
Indices: 19822097--19822247 Score: 221
Period size: 45 Copynumber: 3.4 Consensus size: 45
19822087 AAATTACAGA
* ** * *
19822097 TCTTATCTCCATGTATCGGCTATGAAGCAGATCAAAAATTACAAA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAATGGCGAG
*
19822142 TCTTATCTTCATGTATCGGCTATGGAGCAGATCAAAAATGGCGAG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAATGGCGAG
* * *
19822187 TCTTATCTCTATGTATCGGCTATGGAGTAGATCGAAAATGGCGAG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAATGGCGAG
19822232 TCTTATCTCCATGTAT
1 TCTTATCTCCATGTAT
19822248 TGACTATAGA
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 95 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (45 bp):
TCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAATGGCGAG
Found at i:19822592 original size:177 final size:176
Alignment explanation
Indices: 19822187--19822903 Score: 839
Period size: 177 Copynumber: 4.0 Consensus size: 176
19822177 AAATGGCGAG
* * * * * *
19822187 TCTTATCTCTATGTATCGGCTATGGAGTAGATC-GAAAATGGCGAGTCTTATCTCCATGTATTGA
1 TCTTATCTCCATGTATCAGCTATGGAGCAGATCAG-AAATGGCGAGTCTTATCTCTATGTATCGG
* * * * * *
19822251 CTATAGAGCAAATTTTAGCCACCAGCCTTATCTCTTTGAGGCAGTAAGAGAGCAGGTTGAAGATA
65 CTATGGAGCAGATTTAAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATA
* * ** * * * * * *
19822316 CGAGTCTTATCTTCCTGAGGTAGCAAGG-AAGCAGACTAAAAATTACAAA
130 CGAGCCTTAACCCCCT-AAGCAGTAGGGTAA-CAGGCTGAAAATTAC-AA
* * * * *
19822365 TCTTATCTCCGTGTATCTGCTATGGAGCAGATCAAAAATGGAGAGTCTTATCTCTATGTATCAGC
1 TCTTATCTCCATGTATCAGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCTATGTATCGGC
* * * * * *
19822430 TATGGAGCAGATTTAAGTCACCAGTCATATGTCTCTGAGGTAGCAAGAGAGTAGGTTGAAAATAC
66 TATGGAGCAGATTTAAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATAC
* * * *
19822495 GAGCCGTAACCCTCTAAGCAGTAGGGTAACAGGCTGCAAATTATAGA
131 GAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACA-A
* *
19822542 TCTTATCTCCATGTATCAGTTATGGAGCAGATCAGAAATAGCGAGTCTTATCT-TCATGTATCGG
1 TCTTATCTCCATGTATCAGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCT-ATGTATCGG
*
19822606 CTATGGAGCAGATTTTAA-CCACCAGCCTTATCTCTCTGAGGAAGCAAGAGAGCAGGTTGAAGAT
65 CTATGGAGCAGA-TTTAAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAT
* * *
19822670 ATGAGCCTTAACCCCCTAAGCAGTAGGGTAAAAGGCTGTAAATTACCAA
129 ACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTA-CAA
* * * * *
19822719 TCTTATCTCCATGTATCAGCTACGAAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATTGGA
1 TCTTATCTCCATGTATCAGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCTATGTATCGGC
* *
19822784 TATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATAC
66 TATGGAGCAGATTTAAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATAC
* * * *
19822849 GAGCCTTAACCCCCTAGGCAGTAGGGTGACTGGCTGAAAATTGCAAA
131 GAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTAC-AA
19822896 TCTTATCT
1 TCTTATCT
19822904 TCCAGAAGTC
Statistics
Matches: 457, Mismatches: 73, Indels: 19
0.83 0.13 0.03
Matches are distributed among these distances:
176 7 0.02
177 326 0.71
178 124 0.27
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (176 bp):
TCTTATCTCCATGTATCAGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCTATGTATCGGC
TATGGAGCAGATTTAAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATAC
GAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAA
Found at i:19823786 original size:11 final size:11
Alignment explanation
Indices: 19823772--19823798 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
19823762 AAATAATATT
19823772 TTATTATTTTA
1 TTATTATTTTA
19823783 TTATTATTTTA
1 TTATTATTTTA
19823794 TTATT
1 TTATT
19823799 TTATTTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:19828075 original size:127 final size:128
Alignment explanation
Indices: 19827848--19828147 Score: 392
Period size: 127 Copynumber: 2.4 Consensus size: 128
19827838 ATACTCCGTG
* *
19827848 TTTAGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGA-TTTTTTCATTCGACTGAAATA
1 TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTTCATTCGACTAAAATA
* ** ** * *
19827912 TAGAATATCCTTTTAAAATTTTGTCTATGTTCTCTTA-AATTAAAAACAAGGCAATATTTCGTA
66 CAGAATATCCTCATAAAATTTCATCCATGTTCTCTTAGAATT-AAAACAAGGCAATATTTCATA
19827975 TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTTCATTCGACTAAAATA
1 TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTTCATTCGACTAAAATA
* * *
19828040 CGGAATATCCTCATAAAATTTCATCCAT-TTTTCTTAGAATTAAAATAAGGCAATATTTCATA
66 CAGAATATCCTCATAAAATTTCATCCATGTTCTCTTAGAATTAAAACAAGGCAATATTTCATA
* * * * * *
19828102 TTT-GGAAGTTCGATAAATCATGCCCAATCATGATGGGTTTCGATTT
1 TTTAGG-AGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTT
19828148 ACCGTTTGAC
Statistics
Matches: 152, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
126 2 0.01
127 105 0.69
128 45 0.30
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (128 bp):
TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTTCATTCGACTAAAATA
CAGAATATCCTCATAAAATTTCATCCATGTTCTCTTAGAATTAAAACAAGGCAATATTTCATA
Found at i:19833994 original size:29 final size:29
Alignment explanation
Indices: 19833962--19834093 Score: 237
Period size: 29 Copynumber: 4.5 Consensus size: 29
19833952 ATAGTGAATC
19833962 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
19833991 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
*
19834021 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
*
19834050 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
19834079 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
19834094 GTACAATTTT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 72 0.71
30 29 0.29
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:19834103 original size:59 final size:59
Alignment explanation
Indices: 19833962--19834093 Score: 239
Period size: 59 Copynumber: 2.3 Consensus size: 59
19833952 ATAGTGAATC
19833962 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
* *
19834021 CGCACACTTAGTGCTATATATTTTCAGTTCGCACACTTAGTGCTATAT-ATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
19834079 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
19834094 GTACAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 24 0.34
59 47 0.66
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (59 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:19835459 original size:19 final size:18
Alignment explanation
Indices: 19835435--19835470 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19835425 CCTCCTTTTT
*
19835435 CTTTTCTTATTTTATTCCC
1 CTTTTCTT-TTTAATTCCC
19835454 CTTTTCTTTTTAATTCC
1 CTTTTCTTTTTAATTCC
19835471 TTTCTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.11, C:0.25, G:0.00, T:0.64
Consensus pattern (18 bp):
CTTTTCTTTTTAATTCCC
Found at i:19836725 original size:30 final size:30
Alignment explanation
Indices: 19836691--19836747 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
19836681 TGGCCCAATA
*
19836691 GTAAATACTCAAAATTTGAGGGA-TTAAAGT
1 GTAAATA-TCAAAATTTGAAGGACTTAAAGT
*
19836721 GTAAATATGAAAATTTGAAGGACTTAA
1 GTAAATATCAAAATTTGAAGGACTTAA
19836748 GGGTGGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (30 bp):
GTAAATATCAAAATTTGAAGGACTTAAAGT
Found at i:19841327 original size:128 final size:126
Alignment explanation
Indices: 19841080--19841380 Score: 417
Period size: 128 Copynumber: 2.4 Consensus size: 126
19841070 ATACTCCGTG
* * *
19841080 TTTAGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTTATTCGACTGAAATAT
1 TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTTATTCGACTAAAATAC
** * * * *
19841145 AAAATATCCTTTTGAAATTTCGTCTATGTTCTCTTAAATTAAAAACGAGGCAATATTTCGTA
66 AAAATATCCTCATGAAATTTCATCCATGTTCTCTTAAATTAAAAAC-AGACAATATTTCATA
19841207 TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTTCATTCGACTAAAATA
1 TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTT-ATTCGACTAAAATA
*
19841272 CAAAATATCCTCATGAAATTTCATCCATGTTTTCTTAGAATTAAAATA-AGACAATATTTCATA
65 CAAAATATCCTCATGAAATTTCATCCATGTTCTCTTA-AATTAAAA-ACAGACAATATTTCATA
** * *
19841335 TTT-GGAAGTTCAATAAATCGTGCCCAATCGTGCTGGGTTTCGATTT
1 TTTAGG-AGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTT
19841381 ACCGTTTGAC
Statistics
Matches: 156, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
127 51 0.33
128 96 0.62
129 8 0.05
130 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (126 bp):
TTTAGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTTATTCGACTAAAATAC
AAAATATCCTCATGAAATTTCATCCATGTTCTCTTAAATTAAAAACAGACAATATTTCATA
Found at i:19844459 original size:23 final size:23
Alignment explanation
Indices: 19844429--19844472 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
19844419 AACACTTAAA
19844429 ACATGAACAGAACTTTTATTAGT
1 ACATGAACAGAACTTTTATTAGT
19844452 ACATGAACAGAACTTTTATTA
1 ACATGAACAGAACTTTTATTA
19844473 TTTTAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (23 bp):
ACATGAACAGAACTTTTATTAGT
Found at i:19856994 original size:2 final size:2
Alignment explanation
Indices: 19856989--19857078 Score: 173
Period size: 2 Copynumber: 45.5 Consensus size: 2
19856979 TTCAATCGTG
19856989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19857031 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19857073 TA -A TA T
1 TA TA TA T
19857079 GTTTATCATC
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 86 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19865115 original size:2 final size:2
Alignment explanation
Indices: 19865108--19865134 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19865098 TGATTGGTAT
19865108 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19865135 GTTCTATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19868682 original size:19 final size:19
Alignment explanation
Indices: 19868644--19868684 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
19868634 ACTCACTGAG
* *
19868644 AAGGCTAAGTACGGATTCT
1 AAGGCTAAGTACAGAATCT
*
19868663 AAGGCTAAGTGCAGAATCT
1 AAGGCTAAGTACAGAATCT
19868682 AAG
1 AAG
19868685 CCTCATGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.22
Consensus pattern (19 bp):
AAGGCTAAGTACAGAATCT
Found at i:19869034 original size:19 final size:19
Alignment explanation
Indices: 19868996--19869036 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
19868986 ACTCACTGAG
* *
19868996 AAGGCTAAGTACGGATTCT
1 AAGGCTAAGTACAGAATCT
*
19869015 AAGGCTAAGTGCAGAATCT
1 AAGGCTAAGTACAGAATCT
19869034 AAG
1 AAG
19869037 CCTCATGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.22
Consensus pattern (19 bp):
AAGGCTAAGTACAGAATCT
Found at i:19869199 original size:352 final size:352
Alignment explanation
Indices: 19868555--19869263 Score: 1418
Period size: 352 Copynumber: 2.0 Consensus size: 352
19868545 AAGTGGCTGC
19868555 CTTTGCATAAAATGAAAAGGCTACTTTTGGAAGGACATGAACGGAAGCGTCAATCCCGTAATGCG
1 CTTTGCATAAAATGAAAAGGCTACTTTTGGAAGGACATGAACGGAAGCGTCAATCCCGTAATGCG
19868620 AAGAAACGATGACTACTCACTGAGAAGGCTAAGTACGGATTCTAAGGCTAAGTGCAGAATCTAAG
66 AAGAAACGATGACTACTCACTGAGAAGGCTAAGTACGGATTCTAAGGCTAAGTGCAGAATCTAAG
19868685 CCTCATGAACCTTTTTTTGGGGAATCTCGACAACCTTTGGCTAGATGAGTTTAATGGCTCATGTT
131 CCTCATGAACCTTTTTTTGGGGAATCTCGACAACCTTTGGCTAGATGAGTTTAATGGCTCATGTT
19868750 TTTTTGGGAAAAAAGAAATAAATTTAATTAAATAGAATTTTATTGAATAATAAAAAGGAACAAAA
196 TTTTTGGGAAAAAAGAAATAAATTTAATTAAATAGAATTTTATTGAATAATAAAAAGGAACAAAA
19868815 ACTAAGAGCTTTAGGGAGATAGAGTTTTTATAGAAAAGATGAGTCCATATTTATGTTACTCCATC
261 ACTAAGAGCTTTAGGGAGATAGAGTTTTTATAGAAAAGATGAGTCCATATTTATGTTACTCCATC
19868880 CTCTATTTATAATACATAGATAACCTA
326 CTCTATTTATAATACATAGATAACCTA
19868907 CTTTGCATAAAATGAAAAGGCTACTTTTGGAAGGACATGAACGGAAGCGTCAATCCCGTAATGCG
1 CTTTGCATAAAATGAAAAGGCTACTTTTGGAAGGACATGAACGGAAGCGTCAATCCCGTAATGCG
19868972 AAGAAACGATGACTACTCACTGAGAAGGCTAAGTACGGATTCTAAGGCTAAGTGCAGAATCTAAG
66 AAGAAACGATGACTACTCACTGAGAAGGCTAAGTACGGATTCTAAGGCTAAGTGCAGAATCTAAG
19869037 CCTCATGAACCTTTTTTTGGGGAATCTCGACAACCTTTGGCTAGATGAGTTTAATGGCTCATGTT
131 CCTCATGAACCTTTTTTTGGGGAATCTCGACAACCTTTGGCTAGATGAGTTTAATGGCTCATGTT
19869102 TTTTTGGGAAAAAAGAAATAAATTTAATTAAATAGAATTTTATTGAATAATAAAAAGGAACAAAA
196 TTTTTGGGAAAAAAGAAATAAATTTAATTAAATAGAATTTTATTGAATAATAAAAAGGAACAAAA
19869167 ACTAAGAGCTTTAGGGAGATAGAGTTTTTATAGAAAAGATGAGTCCATATTTATGTTACTCCATC
261 ACTAAGAGCTTTAGGGAGATAGAGTTTTTATAGAAAAGATGAGTCCATATTTATGTTACTCCATC
19869232 CTCTATTTATAATACATAGATAACCTA
326 CTCTATTTATAATACATAGATAACCTA
19869259 CTTTG
1 CTTTG
19869264 TTCCTATTTA
Statistics
Matches: 357, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
352 357 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (352 bp):
CTTTGCATAAAATGAAAAGGCTACTTTTGGAAGGACATGAACGGAAGCGTCAATCCCGTAATGCG
AAGAAACGATGACTACTCACTGAGAAGGCTAAGTACGGATTCTAAGGCTAAGTGCAGAATCTAAG
CCTCATGAACCTTTTTTTGGGGAATCTCGACAACCTTTGGCTAGATGAGTTTAATGGCTCATGTT
TTTTTGGGAAAAAAGAAATAAATTTAATTAAATAGAATTTTATTGAATAATAAAAAGGAACAAAA
ACTAAGAGCTTTAGGGAGATAGAGTTTTTATAGAAAAGATGAGTCCATATTTATGTTACTCCATC
CTCTATTTATAATACATAGATAACCTA
Found at i:19869296 original size:10 final size:10
Alignment explanation
Indices: 19869281--19869309 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
19869271 TTAAACTCTA
19869281 AAAGATAAAT
1 AAAGATAAAT
19869291 AAAGATAAAT
1 AAAGATAAAT
19869301 AAAGATAAA
1 AAAGATAAA
19869310 GCTGAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:19870523 original size:2 final size:2
Alignment explanation
Indices: 19870510--19870543 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
19870500 TTATTGTTAT
*
19870510 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19870544 AAGTAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19872925 original size:23 final size:25
Alignment explanation
Indices: 19872899--19872945 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
19872889 TATCATTCAT
*
19872899 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
19872922 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
19872946 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:19873266 original size:46 final size:46
Alignment explanation
Indices: 19873206--19873555 Score: 421
Period size: 46 Copynumber: 8.0 Consensus size: 46
19873196 TTTGACGTGA
* * * * *
19873206 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT
* * * *
19873252 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* *
19873298 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
19873344 TGCCATGGTATCTTTCAACCATGGTCTTA-TACATTTCGTATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACT-CATTTCATATCAGGT
*
19873390 TGCCATGGTATCCTTCAACCATGGTCTTA--CA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
19873428 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
19873474 TGCCATGGTATCTTTCAACCATGGTCTTA--CA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
19873512 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
19873556 AGAGCACACT
Statistics
Matches: 269, Mismatches: 17, Indels: 36
0.84 0.05 0.11
Matches are distributed among these distances:
38 67 0.25
39 2 0.01
40 4 0.01
41 2 0.01
43 2 0.01
44 4 0.01
45 6 0.02
46 182 0.68
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
Found at i:19873322 original size:92 final size:84
Alignment explanation
Indices: 19873250--19873555 Score: 468
Period size: 84 Copynumber: 3.5 Consensus size: 84
19873240 TTTCTGTCAT
* * * *
19873250 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAGGTTGCCATGGTATCTTTCA
19873315 ACCATGGTCTTACACATCTCATATCAG
66 ACCATGGTCTT--ACA---C--A-CAG
* *
19873342 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCGTATCAGGTTGCCATGGTATCCTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAGGTTGCCATGGTATCTTTCA
19873407 ACCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
*
19873426 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAGGTTGCCATGGTATCTTTCA
19873491 ACCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
*
19873510 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAG
19873556 AGAGCACACT
Statistics
Matches: 205, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
84 130 0.63
85 1 0.00
87 1 0.00
90 3 0.01
92 70 0.34
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (84 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAGGTTGCCATGGTATCTTTCA
ACCATGGTCTTACACACAG
Found at i:19873436 original size:38 final size:38
Alignment explanation
Indices: 19873385--19873544 Score: 239
Period size: 38 Copynumber: 4.0 Consensus size: 38
19873375 CATTTCGTAT
*
19873385 CAGGTTGCCATGGTATCCTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
19873423 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A
19873468 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
19873507 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
19873545 TTTCATATCA
Statistics
Matches: 113, Mismatches: 1, Indels: 16
0.87 0.01 0.12
Matches are distributed among these distances:
38 70 0.62
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 1 0.01
46 33 0.29
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:19876370 original size:46 final size:46
Alignment explanation
Indices: 19876318--19876453 Score: 175
Period size: 46 Copynumber: 3.0 Consensus size: 46
19876308 AGTGTGCTCT
* *
19876318 CTGATATGAAATGTGTAAGACTATGATTGGAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGATTGAAAGATACCATGGCAAC
*
19876364 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGATTGAAAGATACCATGGCAAC
* * ** * *
19876410 ATGACAAAAAATGAGTAAGACCAT-AGTTGAAAGATACTATGGCA
1 CTGATATGAAATGTGTAAGACCATGA-TTGAAAGATACCATGGCA
19876454 TCATGTCAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGATTGAAAGATACCATGGCAAC
Found at i:19876715 original size:100 final size:100
Alignment explanation
Indices: 19876595--19876807 Score: 390
Period size: 100 Copynumber: 2.1 Consensus size: 100
19876585 GTCATATGGA
*
19876595 AATATATATACAAAATAGTTATATGAAATAATTATGAAGATAAACGAAATAAGTATAAGTACATG
1 AATAAATATAC-AAATAGTTATATGAAATAATTATGAAGATAAACGAAATAAGTATAAGTACATG
*
19876660 GAATATAATTTATGTTAAGATATAAGTTATTACCGG
65 GAATATAATTTATGTTAAGATATAAGCTATTACCGG
*
19876696 AATAAATATACAAATAGTTATATGAAATAATTATGAAGATAAACGAAATAAGTATAAGTATATGG
1 AATAAATATACAAATAGTTATATGAAATAATTATGAAGATAAACGAAATAAGTATAAGTACATGG
19876761 AATATAATTTATGTTAAGATATAAGCTATTACCGG
66 AATATAATTTATGTTAAGATATAAGCTATTACCGG
19876796 AATAAATATACA
1 AATAAATATACA
19876808 TAAAATATAT
Statistics
Matches: 109, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
100 99 0.91
101 10 0.09
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (100 bp):
AATAAATATACAAATAGTTATATGAAATAATTATGAAGATAAACGAAATAAGTATAAGTACATGG
AATATAATTTATGTTAAGATATAAGCTATTACCGG
Found at i:19878001 original size:3 final size:3
Alignment explanation
Indices: 19877993--19878064 Score: 135
Period size: 3 Copynumber: 23.7 Consensus size: 3
19877983 CTCGATGTGA
19877993 AAG AAG AAGG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
19878039 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
19878065 AACAAATAGG
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19884966 original size:15 final size:16
Alignment explanation
Indices: 19884946--19884978 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19884936 ATATATTTTT
19884946 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
19884961 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
19884978 T
1 T
19884979 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:19885060 original size:22 final size:21
Alignment explanation
Indices: 19885024--19885086 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
19885014 TGTTTTAAAA
*
19885024 TTGTTTTAGTATTATTTTTAT
1 TTGTTTTAATATTATTTTTAT
19885045 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATA-TTATTTTTAT
*
19885067 GT-TTTTAA-ATT-TTTTTAT
1 TTGTTTTAATATTATTTTTAT
19885085 TT
1 TT
19885087 AATGAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 8 0.21
19 2 0.05
20 1 0.03
21 16 0.42
22 11 0.29
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (21 bp):
TTGTTTTAATATTATTTTTAT
Found at i:19901626 original size:11 final size:11
Alignment explanation
Indices: 19901610--19901640 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
19901600 ACTCTTGCTC
19901610 AAAAAAAAGAA
1 AAAAAAAAGAA
19901621 AAAAAAAAGAA
1 AAAAAAAAGAA
19901632 AAAAGAAAA
1 AAAA-AAAA
19901641 AGAAGCAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:19903138 original size:12 final size:12
Alignment explanation
Indices: 19903123--19903151 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
19903113 AAAAAAAAAA
19903123 AAGAAAAAGAAG
1 AAGAAAAAGAAG
19903135 AAGAAAAAGAAG
1 AAGAAAAAGAAG
19903147 AAGAA
1 AAGAA
19903152 GAAAAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAG
Found at i:19907830 original size:15 final size:15
Alignment explanation
Indices: 19907810--19907845 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
19907800 TTATATGGCC
*
19907810 TGACACATAGGCATG
1 TGACACATAGACATG
19907825 TGACACATAGACATG
1 TGACACATAGACATG
19907840 TGACAC
1 TGACAC
19907846 GATCGTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (15 bp):
TGACACATAGACATG
Found at i:19912070 original size:16 final size:16
Alignment explanation
Indices: 19912051--19912103 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
19912041 GAAAAAAATA
* *
19912051 TTTCTATTCTTTTATT
1 TTTCTATTCTTTCAAT
*
19912067 TTTCTACTCTTTCAAT
1 TTTCTATTCTTTCAAT
19912083 TTTCTA-TCTTCTCAAT
1 TTTCTATTCTT-TCAAT
19912099 TTTCT
1 TTTCT
19912104 TTCCATTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 4 0.12
16 29 0.88
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTCTATTCTTTCAAT
Found at i:19915694 original size:27 final size:28
Alignment explanation
Indices: 19915637--19915694 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
19915627 ATATTCTATC
* * * * *
19915637 AAAATATGAATAGACATTGTTTTATATT
1 AAAATAAGAATACACATTGTGTTAAAAT
19915665 AAAATAAGAATACA-ATTGTGTTAAAAT
1 AAAATAAGAATACACATTGTGTTAAAAT
19915692 AAA
1 AAA
19915695 TTAAAAACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.34
Consensus pattern (28 bp):
AAAATAAGAATACACATTGTGTTAAAAT
Found at i:19920219 original size:44 final size:45
Alignment explanation
Indices: 19920129--19920257 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
19920119 GACAGAACGA
*
19920129 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
19920175 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
19920219 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
19920258 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:19921664 original size:31 final size:31
Alignment explanation
Indices: 19921621--19921684 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
19921611 CCTTTTCATA
19921621 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
19921652 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
19921683 TT
1 TT
19921685 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:19921941 original size:24 final size:24
Alignment explanation
Indices: 19921877--19921996 Score: 172
Period size: 24 Copynumber: 5.0 Consensus size: 24
19921867 GCTTTATCAT
* *
19921877 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
19921902 ATAACTGGGGCA-AAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
19921925 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
* *
19921949 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
19921973 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
19921997 CACTTCCTCC
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 17 0.20
24 62 0.71
25 8 0.09
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:19922071 original size:20 final size:20
Alignment explanation
Indices: 19922048--19922111 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
19922038 TGAACATCTT
*
19922048 ATGTGCATATCATACATATA
1 ATGTGCATATCATACATATC
*
19922068 ATGTGCATATCATACATGTC
1 ATGTGCATATCATACATATC
19922088 ATGTGCATATCATACATATC
1 ATGTGCATATCATACATATC
19922108 ATGT
1 ATGT
19922112 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGTGCATATCATACATATC
Found at i:19922176 original size:25 final size:25
Alignment explanation
Indices: 19922148--19922195 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
19922138 ATATATAAAC
* * *
19922148 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
19922173 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
19922196 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:19923349 original size:18 final size:17
Alignment explanation
Indices: 19923322--19923355 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
19923312 TAAGGAAGAA
19923322 AATAAGAAGAGAAAACT
1 AATAAGAAGAGAAAACT
19923339 AATACAGAAGAGAAAAC
1 AATA-AGAAGAGAAAAC
19923356 GGCACAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.65, C:0.09, G:0.18, T:0.09
Consensus pattern (17 bp):
AATAAGAAGAGAAAACT
Found at i:19930053 original size:16 final size:16
Alignment explanation
Indices: 19930032--19930065 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
19930022 ACTATTTAAT
*
19930032 AATATCAAAGGTTCTC
1 AATATCAAAGATTCTC
19930048 AATATCAAAGATTCTC
1 AATATCAAAGATTCTC
19930064 AA
1 AA
19930066 CACTCCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (16 bp):
AATATCAAAGATTCTC
Found at i:19932103 original size:21 final size:21
Alignment explanation
Indices: 19932070--19932109 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19932060 AATATTATTT
*
19932070 TTTATTATCTTTATATTTAAA
1 TTTATTATATTTATATTTAAA
* *
19932091 TTTATTTTATTTATTTTTA
1 TTTATTATATTTATATTTA
19932110 TAAAATATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATTATATTTATATTTAAA
Found at i:19932104 original size:27 final size:29
Alignment explanation
Indices: 19932057--19932111 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
19932047 TGGTCTATTG
*
19932057 TTAAATATTATTTTTTATTATCTTTATAT
1 TTAAATATTATTTTATATTATCTTTATAT
*
19932086 TTAAAT-TTATTTTAT-TTATTTTTATA
1 TTAAATATTATTTTATATTATCTTTATA
19932112 AAATATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.42
28 8 0.33
29 6 0.25
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (29 bp):
TTAAATATTATTTTATATTATCTTTATAT
Found at i:19933534 original size:12 final size:12
Alignment explanation
Indices: 19933519--19933544 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19933509 TATAAAGTAT
19933519 TATAACACTTTA
1 TATAACACTTTA
19933531 TATAACACTTTA
1 TATAACACTTTA
19933543 TA
1 TA
19933545 ACATAGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (12 bp):
TATAACACTTTA
Found at i:19939077 original size:30 final size:29
Alignment explanation
Indices: 19939038--19939112 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
19939028 GATGTTTAAT
*
19939038 AATAAATTTAAAATATAATATATAATAAAA
1 AATATATTTAAAATATAATA-ATAATAAAA
* *
19939068 AATATATTTATAAGA-ATAATAATTATATAA
1 AATATATTTA-AA-ATATAATAATAATAAAA
19939098 AATATA--TAAAATATA
1 AATATATTTAAAATATA
19939113 TTGGTTTAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
26 1 0.03
27 5 0.13
28 2 0.05
30 22 0.56
31 8 0.21
32 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (29 bp):
AATATATTTAAAATATAATAATAATAAAA
Found at i:19939642 original size:17 final size:18
Alignment explanation
Indices: 19939589--19939686 Score: 146
Period size: 18 Copynumber: 5.5 Consensus size: 18
19939579 AATCATATCT
*
19939589 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
19939608 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
19939626 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
19939643 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
19939661 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
19939678 TCTAAGATT
1 TCTAAGATT
19939687 ACATATCATT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
17 31 0.42
18 32 0.44
19 10 0.14
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:19939647 original size:35 final size:35
Alignment explanation
Indices: 19939589--19939695 Score: 178
Period size: 35 Copynumber: 3.0 Consensus size: 35
19939579 AATCATATCT
19939589 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
19939626 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
19939661 TCTAAGATTGTATCATATCTAAGATTACATATCAT
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCAT
19939696 TGAAGATTAT
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
35 53 0.78
36 5 0.07
37 10 0.15
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:19946901 original size:3 final size:3
Alignment explanation
Indices: 19946893--19946926 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
19946883 ACAAATAAAA
19946893 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19946927 GCAAGCAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19955958 original size:3 final size:3
Alignment explanation
Indices: 19955950--19955986 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
19955940 GCAAAGACGA
19955950 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19955987 TCAAAACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19956155 original size:3 final size:3
Alignment explanation
Indices: 19956147--19956182 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
19956137 GTGCAATTTG
19956147 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19956183 CGTATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19957000 original size:3 final size:3
Alignment explanation
Indices: 19956992--19957024 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
19956982 AAAACCCCTT
19956992 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
19957025 GCTTTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:19957792 original size:44 final size:44
Alignment explanation
Indices: 19957726--19957845 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 44
19957716 TGTTGCTTCC
* *
19957726 ATCTACTCCACTGCAACTTCAAGGAGATAAGATTAGTAGCTTTA
1 ATCTGCTCCACTGCAAATTCAAGGAGATAAGATTAGTAGCTTTA
* * * * * *
19957770 ATCTGTTCCATTGTAAATTCAAGGAGATAAGGTTTGTAGTTTTA
1 ATCTGCTCCACTGCAAATTCAAGGAGATAAGATTAGTAGCTTTA
* * *
19957814 GTCTGCTCCACTGCAACTTTAAGGAGATAAGA
1 ATCTGCTCCACTGCAAATTCAAGGAGATAAGA
19957846 CTCGTAACTT
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (44 bp):
ATCTGCTCCACTGCAAATTCAAGGAGATAAGATTAGTAGCTTTA
Found at i:19958845 original size:46 final size:44
Alignment explanation
Indices: 19958786--19958900 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
19958776 ACAGGACAGA
* *
19958786 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
19958832 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
19958876 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
19958901 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:19958881 original size:44 final size:45
Alignment explanation
Indices: 19958786--19958919 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
19958776 ACAGGACAGA
* *
19958786 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
19958832 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
19958876 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
19958920 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:19960233 original size:45 final size:45
Alignment explanation
Indices: 19960159--19960269 Score: 109
Period size: 45 Copynumber: 2.4 Consensus size: 45
19960149 CGTTACAACC
* * * *
19960159 CCACTGTAACTTCAG-GGTGATAAGGTTTAC-AGCTTTAATTCTGCT
1 CCACTGCAACTTCAGAGAT-ATAAGATTTACTAGCTTCAA-TCTGCT
* * *
19960204 CTACTGCAACTTCAGAGATATAAGATTTACTATCTTCAATCTGTT
1 CCACTGCAACTTCAGAGATATAAGATTTACTAGCTTCAATCTGCT
*
19960249 CCACTACAACTTCAGGAGATA
1 CCACTGCAACTTCA-GAGATA
19960270 GGACGCGTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
45 40 0.74
46 14 0.26
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (45 bp):
CCACTGCAACTTCAGAGATATAAGATTTACTAGCTTCAATCTGCT
Found at i:19963361 original size:46 final size:46
Alignment explanation
Indices: 19963294--19963508 Score: 209
Period size: 46 Copynumber: 4.8 Consensus size: 46
19963284 TGTAACCCGC
* *
19963294 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACAT
19963340 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCACAT
* * *
19963390 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGATGC---CACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG-GGCGTTCACAT
* * * * *
19963431 -C-TCA-CGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACAT
19963473 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
19963509 ATGCTCAACC
Statistics
Matches: 145, Mismatches: 10, Indels: 28
0.79 0.05 0.15
Matches are distributed among these distances:
39 1 0.01
40 20 0.14
41 15 0.10
42 4 0.03
43 1 0.01
44 2 0.01
45 7 0.05
46 57 0.39
47 27 0.19
48 3 0.02
49 2 0.01
50 3 0.02
51 3 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACAT
Found at i:19963457 original size:40 final size:42
Alignment explanation
Indices: 19963348--19963461 Score: 169
Period size: 47 Copynumber: 2.6 Consensus size: 42
19963338 ATCCATAAGT
19963348 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTC-GATGCC----TACATCTCAC
19963395 GAACTCGGACTCAACTCAACGAGTTCGATGCC-ACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGATGCCTACATCTCAC
19963436 GAACTC-GACTCAACTCAACGAGTTCG
1 GAACTCGGACTCAACTCAACGAGTTCG
19963462 GACATTCGCA
Statistics
Matches: 67, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
40 20 0.30
41 15 0.22
46 6 0.09
47 26 0.39
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (42 bp):
GAACTCGGACTCAACTCAACGAGTTCGATGCCTACATCTCAC
Found at i:19965925 original size:29 final size:29
Alignment explanation
Indices: 19965886--19965973 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
19965876 CAAAGATAAC
*
19965886 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
19965915 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
19965944 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
19965974 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Done.