Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 17 of 325
Found at i:5356520 original size:21 final size:21
Alignment explanation
Indices: 5356496--5356546 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
5356486 TAAAATTTTG
*
5356496 ATTTAATCATTTAAAAATTACA
1 ATTTAATCA-TAAAAAATTACA
* *
5356518 TTTTTTATCATAAAAAATTACA
1 -ATTTAATCATAAAAAATTACA
5356540 ATTTAAT
1 ATTTAAT
5356547 TTTGGCCCCC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 5 0.22
22 11 0.48
23 7 0.30
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTAATCATAAAAAATTACA
Found at i:5358351 original size:21 final size:22
Alignment explanation
Indices: 5358317--5358357 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5358307 TATTCAACTT
*
5358317 TAAAAAATTACAAAATAATTAC
1 TAAAAAATTACAAAAAAATTAC
*
5358339 TAAAATATT-CAAAAAAATT
1 TAAAAAATTACAAAAAAATT
5358358 CATTTAAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAATTACAAAAAAATTAC
Found at i:5361952 original size:24 final size:25
Alignment explanation
Indices: 5361925--5361976 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
5361915 ATTTATATTT
5361925 TTAAAAAAATTT-TAAAACTTTAAA
1 TTAAAAAAATTTATAAAACTTTAAA
* * *
5361949 TT-AATAAATTTATAAAATTTTAAT
1 TTAAAAAAATTTATAAAACTTTAAA
5361973 TTAA
1 TTAA
5361977 TTTTTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 8 0.35
24 14 0.61
25 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TTAAAAAAATTTATAAAACTTTAAA
Found at i:5361959 original size:23 final size:24
Alignment explanation
Indices: 5361931--5361977 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5361921 ATTTTTAAAA
5361931 AAATTT-TAAAACTTTAAATTAAT
1 AAATTTATAAAACTTTAAATTAAT
* *
5361954 AAATTTATAAAATTTTAATTTAAT
1 AAATTTATAAAACTTTAAATTAAT
5361978 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATTTATAAAACTTTAAATTAAT
Found at i:5366729 original size:17 final size:17
Alignment explanation
Indices: 5366691--5366722 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5366681 AGTCGTTTTC
5366691 TCTTTGTAAGTCTCAAG
1 TCTTTGTAAGTCTCAAG
5366708 TCTTTG-AAGT-TCAAG
1 TCTTTGTAAGTCTCAAG
5366723 CTTCTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (17 bp):
TCTTTGTAAGTCTCAAG
Found at i:5370322 original size:13 final size:12
Alignment explanation
Indices: 5370289--5370345 Score: 57
Period size: 13 Copynumber: 4.8 Consensus size: 12
5370279 TATCCTATTC
5370289 TAAATTAATAAAA
1 TAAA-TAATAAAA
5370302 TAAA-AATAATAA
1 TAAATAATAA-AA
5370314 TAAATAATAAAA
1 TAAATAATAAAA
*
5370326 CTAAATAA-AACA
1 -TAAATAATAAAA
5370338 -AAATAATA
1 TAAATAATA
5370346 TCTTCTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
10 6 0.15
11 6 0.15
12 11 0.28
13 16 0.41
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAATAATAAAA
Found at i:5373806 original size:18 final size:18
Alignment explanation
Indices: 5373763--5373812 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
5373753 GATTGTGGCA
* *
5373763 TTGGGTTTTTGG-TATTT
1 TTGGGTTTTGGGTTAATT
5373780 TATGTGGTTTTGGGTTAATT
1 T-TG-GGTTTTGGGTTAATT
5373800 TTGGG-TTTGGGTT
1 TTGGGTTTTGGGTT
5373813 CATATGGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 4 0.14
19 10 0.36
20 5 0.18
ACGTcount: A:0.08, C:0.00, G:0.34, T:0.58
Consensus pattern (18 bp):
TTGGGTTTTGGGTTAATT
Found at i:5373826 original size:17 final size:16
Alignment explanation
Indices: 5373801--5373845 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
5373791 GGGTTAATTT
5373801 TGGGTTTGGGTTCATA
1 TGGGTTTGGGTTCATA
* *
5373817 TGGGTATTGGGTTTATG
1 TGGGT-TTGGGTTCATA
5373834 TGGGTGTTGGGT
1 TGGGT-TTGGGT
5373846 GTGGTTGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.09, C:0.02, G:0.44, T:0.44
Consensus pattern (16 bp):
TGGGTTTGGGTTCATA
Found at i:5379929 original size:10 final size:10
Alignment explanation
Indices: 5379891--5379928 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5379881 TAAATTAATA
5379891 AAATAAAAAT
1 AAATAAAAAT
5379901 AAATAATAAAT
1 AAATAA-AAAT
*
5379912 -AATAAAACT
1 AAATAAAAAT
5379921 AAATAAAA
1 AAATAAAA
5379929 CAAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:5379935 original size:20 final size:20
Alignment explanation
Indices: 5379890--5379936 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5379880 CTAAATTAAT
5379890 AAAATAAAAATAAATAATAA
1 AAAATAAAAATAAATAATAA
* *
5379910 ATAATAAAACTAAATAA-AA
1 AAAATAAAAATAAATAATAA
5379929 CAAAATAA
1 -AAAATAA
5379937 TATCTTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAATAAAAATAAATAATAA
Found at i:5380371 original size:102 final size:102
Alignment explanation
Indices: 5380195--5380386 Score: 375
Period size: 102 Copynumber: 1.9 Consensus size: 102
5380185 TGTTGAAAGT
5380195 AAAATGGAGTATGTGAGAGGAAGAATCGAACAGTACTTGATATGGCTAGATGCTTATTGTTTGAA
1 AAAATGGAGTATGTGAGAGGAAGAATCGAACAGTACTTGATATGGCTAGATGCTTATTGTTTGAA
5380260 AGTAAGCTGCCAAGCAAATTTTGGGATACTCCTCAGC
66 AGTAAGCTGCCAAGCAAATTTTGGGATACTCCTCAGC
*
5380297 AAAATGGAGTATGTGAGAGGAAGAATCGAACAGTGCTTGATATGGCTAGATGCTTATTGTTTGAA
1 AAAATGGAGTATGTGAGAGGAAGAATCGAACAGTACTTGATATGGCTAGATGCTTATTGTTTGAA
5380362 AGTAAGCTGCCAAGCAAATTTTGGG
66 AGTAAGCTGCCAAGCAAATTTTGGG
5380387 CTGAGGCTGT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 89 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (102 bp):
AAAATGGAGTATGTGAGAGGAAGAATCGAACAGTACTTGATATGGCTAGATGCTTATTGTTTGAA
AGTAAGCTGCCAAGCAAATTTTGGGATACTCCTCAGC
Found at i:5390691 original size:35 final size:35
Alignment explanation
Indices: 5390642--5390711 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
5390632 ACGGGGCTGT
5390642 TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
1 TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
* **
5390677 TTCTAAAATGCCGTATGAATTGTTTTGTTATGCCA
1 TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
5390712 AATATCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (35 bp):
TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
Found at i:5404689 original size:2 final size:2
Alignment explanation
Indices: 5404684--5404708 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5404674 TTAAAAAAGG
5404684 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
5404709 AAAAAAGAGA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5405706 original size:18 final size:18
Alignment explanation
Indices: 5405666--5405708 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5405656 ATTTATGTTA
5405666 TTTTATATTAACAATAAT
1 TTTTATATTAACAATAAT
* *
5405684 ATTTATATTAATTAAT-AT
1 TTTTATATTAA-CAATAAT
5405702 TTTTATA
1 TTTTATA
5405709 ACAGTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTATATTAACAATAAT
Found at i:5406604 original size:6 final size:7
Alignment explanation
Indices: 5406585--5406612 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
5406575 AAAAAATGAA
5406585 TATTTTT
1 TATTTTT
5406592 TATTTTT
1 TATTTTT
5406599 TATTTTT
1 TATTTTT
5406606 TATTTTT
1 TATTTTT
5406613 CGTTTCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TATTTTT
Found at i:5411185 original size:16 final size:16
Alignment explanation
Indices: 5411165--5411202 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5411155 AAATTGGTTG
5411165 AAATTTAAGA-TATTTT
1 AAATTTAA-ATTATTTT
*
5411181 GAATTTAAATTATTTT
1 AAATTTAAATTATTTT
5411197 AAATTT
1 AAATTT
5411203 TGAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
AAATTTAAATTATTTT
Found at i:5417817 original size:15 final size:16
Alignment explanation
Indices: 5417797--5417826 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5417787 CAACAAGAAC
5417797 AATTTACA-TAAAATG
1 AATTTACATTAAAATG
5417812 AATTTACATTAAAAT
1 AATTTACATTAAAAT
5417827 AGGTTCCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (16 bp):
AATTTACATTAAAATG
Found at i:5422845 original size:17 final size:17
Alignment explanation
Indices: 5422823--5422855 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5422813 TTTTCTGACG
5422823 AATAAAATTAAGCTAAC
1 AATAAAATTAAGCTAAC
*
5422840 AATAAAATTAATCTAA
1 AATAAAATTAAGCTAA
5422856 AGCTTCTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (17 bp):
AATAAAATTAAGCTAAC
Found at i:5423410 original size:10 final size:10
Alignment explanation
Indices: 5423392--5423452 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
5423382 GAGGAAGAGC
*
5423392 AGAAGAAAAT
1 AGAAAAAAAT
*
5423402 AGAAAAAAAA
1 AGAAAAAAAT
*
5423412 AGATAAAAAT
1 AGAAAAAAAT
* *
5423422 ATAAAAATAT
1 AGAAAAAAAT
* *
5423432 AAAAAAATAAA
1 AGAAAAA-AAT
5423443 AGAAAAAAAT
1 AGAAAAAAAT
5423453 TAAATTGTTC
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
10 31 0.82
11 7 0.18
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (10 bp):
AGAAAAAAAT
Found at i:5423427 original size:7 final size:8
Alignment explanation
Indices: 5423408--5423443 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
5423398 AAATAGAAAA
*
5423408 AAAAAGAT
1 AAAAATAT
5423416 AAAAATAT
1 AAAAATAT
5423424 AAAAATAT
1 AAAAATAT
*
5423432 AAAAAAAT
1 AAAAATAT
5423440 AAAA
1 AAAA
5423444 GAAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (8 bp):
AAAAATAT
Found at i:5423433 original size:16 final size:16
Alignment explanation
Indices: 5423404--5423456 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
5423394 AAGAAAATAG
5423404 AAAA-AAAAAGATAAA
1 AAAATAAAAAGATAAA
* *
5423419 AATATAAAAATATAAA
1 AAAATAAAAAGATAAA
5423435 AAAAT-AAAAGA-AAA
1 AAAATAAAAAGATAAA
*
5423449 AAATTAAA
1 AAAATAAA
5423457 TTGTTCAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 7 0.23
15 10 0.32
16 14 0.45
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (16 bp):
AAAATAAAAAGATAAA
Found at i:5424096 original size:50 final size:50
Alignment explanation
Indices: 5424036--5424133 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
5424026 GATTACTTGT
*
5424036 AAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAGATTTAGTATTTGC
1 AAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAGATTTAATATTTGC
5424086 AAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAGATTTAATATTT
1 AAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAGATTTAATATTT
5424134 ATTAGTTTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (50 bp):
AAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAGATTTAATATTTGC
Found at i:5428981 original size:23 final size:23
Alignment explanation
Indices: 5428938--5428981 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5428928 TTAAAAGGTT
* *
5428938 AAGGGTCAAACTTAGTTAAAAAA
1 AAGGGTCAAACTTAATAAAAAAA
5428961 AAGGGTCAAA-TTAATAAAAAA
1 AAGGGTCAAACTTAATAAAAAA
5428982 TATAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.57, C:0.07, G:0.16, T:0.20
Consensus pattern (23 bp):
AAGGGTCAAACTTAATAAAAAAA
Found at i:5437268 original size:19 final size:20
Alignment explanation
Indices: 5437237--5437291 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 20
5437227 TTAATTTAAG
5437237 AATTTAGTTTTTTATAATT-T
1 AATTTA-TTTTTTATAATTAT
*
5437257 AATTTATTTTTTATCATTACT
1 AATTTATTTTTTATAATTA-T
5437278 AATGTTATTTTTTA
1 AAT-TTATTTTTTA
5437292 GTTTAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 11 0.35
20 6 0.19
21 4 0.13
22 10 0.32
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (20 bp):
AATTTATTTTTTATAATTAT
Found at i:5437880 original size:29 final size:30
Alignment explanation
Indices: 5437847--5437904 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
5437837 AAAGAACCCT
*
5437847 AATTTAAACTAAATTAACA-ATAAAAATTC
1 AATTTAAACTAAATTAAAATATAAAAATTC
***
5437876 AATTTATTTTAAATTAAAATATAAAAATT
1 AATTTAAACTAAATTAAAATATAAAAATT
5437905 AAATCATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (30 bp):
AATTTAAACTAAATTAAAATATAAAAATTC
Found at i:5438920 original size:24 final size:24
Alignment explanation
Indices: 5438888--5438935 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5438878 AGAGAAGAAA
5438888 CGATGCATTAATCTTAAAGGAATG
1 CGATGCATTAATCTTAAAGGAATG
5438912 CGATGCATTAATCTTAAAGGAATG
1 CGATGCATTAATCTTAAAGGAATG
5438936 ACTTGTTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (24 bp):
CGATGCATTAATCTTAAAGGAATG
Found at i:5439957 original size:19 final size:18
Alignment explanation
Indices: 5439935--5440031 Score: 58
Period size: 19 Copynumber: 5.3 Consensus size: 18
5439925 CTAAAAATAT
5439935 TAAAAATATATAAACTTTA
1 TAAAAATATATAAAC-TTA
5439954 TAAAAA-ATAATAAAACTTA
1 TAAAAATAT-AT-AAACTTA
* **
5439973 TAAATAT-TATAAAAATA
1 TAAAAATATATAAACTTA
* *
5439990 TAAAAATCTAGTAAA-TTC
1 TAAAAATATA-TAAACTTA
*
5440008 TAATAAAT-TATAAAATTAA
1 TAA-AAATATATAAACTT-A
5440027 TAAAA
1 TAAAA
5440032 CATGTTTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
17 15 0.24
18 16 0.25
19 28 0.44
20 4 0.06
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (18 bp):
TAAAAATATATAAACTTA
Found at i:5439961 original size:20 final size:19
Alignment explanation
Indices: 5439936--5439976 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
5439926 TAAAAATATT
5439936 AAAAAT-ATATAAACTTTATA
1 AAAAATAATA-AAAC-TTATA
5439956 AAAAATAATAAAACTTATA
1 AAAAATAATAAAACTTATA
5439975 AA
1 AA
5439977 TATTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 10 0.50
21 3 0.15
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATAATAAAACTTATA
Found at i:5440004 original size:28 final size:26
Alignment explanation
Indices: 5439926--5440006 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 26
5439916 TATTAAATTC
*
5439926 TAAAAATATTAAAAATATATAAACTTTA
1 TAAAAATA-TAAAAATCTATAAA-TTTA
*
5439954 TAAAAA-ATAATAAAACTTATAAATATTA
1 TAAAAATATAA-AAATC-TATAAAT-TTA
5439982 TAAAAATATAAAAATCTAGTAAATT
1 TAAAAATATAAAAATCTA-TAAATT
5440007 CTAATAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
26 3 0.07
27 8 0.18
28 30 0.67
29 4 0.09
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (26 bp):
TAAAAATATAAAAATCTATAAATTTA
Found at i:5440068 original size:47 final size:45
Alignment explanation
Indices: 5440017--5440108 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 45
5440007 CTAATAAATT
* *
5440017 ATAAAATTAATA-AAACATGTTTAAAATTTTATAAAAACAT-ATAAAAA
1 ATAAAATTAATATAAAC-T-TTGAAAA-ATTATAAAAA-ATCATAAAAA
*
5440064 ATAAATTTAATATAAACTTTGAAAAATTATAAAAAATCATAAAAA
1 ATAAAATTAATATAAACTTTGAAAAATTATAAAAAATCATAAAAA
5440109 CTTGAATTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
44 2 0.05
45 16 0.40
46 6 0.15
47 12 0.30
48 4 0.10
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (45 bp):
ATAAAATTAATATAAACTTTGAAAAATTATAAAAAATCATAAAAA
Found at i:5440764 original size:20 final size:19
Alignment explanation
Indices: 5440706--5440764 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
5440696 TAAAAAATTT
5440706 TAACTTTT--AATTTTTTA
1 TAACTTTTAGAATTTTTTA
* *
5440723 TAACTTTTATAATTTGTATA
1 TAACTTTTAGAATTT-TTTA
5440743 TAACTTATTAGAATTTTTTA
1 TAACTT-TTAGAATTTTTTA
5440763 TA
1 TA
5440765 TTATTTATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 8 0.23
19 5 0.14
20 14 0.40
21 8 0.23
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (19 bp):
TAACTTTTAGAATTTTTTA
Found at i:5440811 original size:31 final size:29
Alignment explanation
Indices: 5440727--5440811 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 29
5440717 TTTTTATAAC
* *
5440727 TTTTATAATTTGTATATAACTTATTAGAATT
1 TTTTATAATTTTTATA-AAATT-TTAGAATT
5440758 TTTTAT-ATTATTTAT-AAATTTTAGGAATT
1 TTTTATAATT-TTTATAAAATTTTA-GAATT
5440787 TTTTATAAGTTTTTATAAAATTTTA
1 TTTTATAA-TTTTTATAAAATTTTA
5440812 AATACATTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
28 3 0.06
29 15 0.32
30 9 0.19
31 20 0.43
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (29 bp):
TTTTATAATTTTTATAAAATTTTAGAATT
Found at i:5442608 original size:15 final size:16
Alignment explanation
Indices: 5442588--5442632 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
5442578 ATAACAATCC
5442588 ATAATTTAAAATT-AA
1 ATAATTTAAAATTAAA
*
5442603 ATAATTTAAATTTAAA
1 ATAATTTAAAATTAAA
5442619 ATATATTTTAAAAT
1 ATA-A-TTTAAAAT
5442633 AGTAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 12 0.48
16 5 0.20
17 1 0.04
18 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTTAAAATTAAA
Found at i:5445461 original size:24 final size:24
Alignment explanation
Indices: 5445423--5445471 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5445413 GGTTCCCTCG
* *
5445423 GCCTCTTAGGAGAATCTGTTGGAA
1 GCCTCTCAGGAGAATCAGTTGGAA
*
5445447 GCCTCTCAGGCGAATCAGTTGGAA
1 GCCTCTCAGGAGAATCAGTTGGAA
5445471 G
1 G
5445472 TCTTTGCTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (24 bp):
GCCTCTCAGGAGAATCAGTTGGAA
Found at i:5451648 original size:26 final size:26
Alignment explanation
Indices: 5451612--5451693 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
5451602 AACACACCAA
5451612 TATCGCAGCAAGGCTGCCAGTAACAG
1 TATCGCAGCAAGGCTGCCAGTAACAG
* * **
5451638 TATCGCAGCAAAGCTGTCAGTATTAG
1 TATCGCAGCAAGGCTGCCAGTAACAG
* * **
5451664 TATATGTAGCAAGGCCACCAGTAACAG
1 TAT-CGCAGCAAGGCTGCCAGTAACAG
5451691 TAT
1 TAT
5451694 ATGTGGCGAA
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
26 25 0.58
27 18 0.42
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (26 bp):
TATCGCAGCAAGGCTGCCAGTAACAG
Found at i:5463462 original size:18 final size:16
Alignment explanation
Indices: 5463432--5463481 Score: 73
Period size: 16 Copynumber: 3.0 Consensus size: 16
5463422 CAGTTAGGGT
5463432 GGGAAAAAGAAAAAGA
1 GGGAAAAAGAAAAAGA
*
5463448 GGGAAAATGAGAAAAAAA
1 GGGAAAA--AGAAAAAGA
5463466 GGGAAAAAGAAAAAGA
1 GGGAAAAAGAAAAAGA
5463482 AAAAGGAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 15 0.50
18 15 0.50
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (16 bp):
GGGAAAAAGAAAAAGA
Found at i:5468765 original size:24 final size:24
Alignment explanation
Indices: 5468738--5468804 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
5468728 TTTTTCTCAC
*
5468738 ATTTTTATTTCTT-GTTTTCTTTTT
1 ATTTTTA-TTCTTCCTTTTCTTTTT
*
5468762 ATTTTCTATTCTTCCTTTTTTTTTT
1 ATTTT-TATTCTTCCTTTTCTTTTT
*
5468787 ATTTTT-TTATT-CTTTTCT
1 ATTTTTATTCTTCCTTTTCT
5468805 GCAATCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
22 6 0.16
23 4 0.11
24 11 0.30
25 16 0.43
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.78
Consensus pattern (24 bp):
ATTTTTATTCTTCCTTTTCTTTTT
Found at i:5468780 original size:25 final size:26
Alignment explanation
Indices: 5468752--5468800 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5468742 TTATTTCTTG
5468752 TTTTCTTTTTA-TTTTCTATTCTTCC
1 TTTTCTTTTTATTTTTCTATTCTTCC
* *
5468777 TTTTTTTTTTATTTTTTTATTCTT
1 TTTTCTTTTTATTTTTCTATTCTT
5468801 TTCTGCAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTCTTTTTATTTTTCTATTCTTCC
Found at i:5475826 original size:20 final size:21
Alignment explanation
Indices: 5475801--5475851 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
5475791 AGGGGCACAT
*
5475801 GCCCGTGTGGCT-TGGGACAC
1 GCCCGTGTGGCTCTGGAACAC
*
5475821 GCCCGTGTGG-TCTGGAACAT
1 GCCCGTGTGGCTCTGGAACAC
5475841 GCCCGTGTGGC
1 GCCCGTGTGGC
5475852 CTGCCCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.10, C:0.29, G:0.39, T:0.22
Consensus pattern (21 bp):
GCCCGTGTGGCTCTGGAACAC
Found at i:5476724 original size:53 final size:52
Alignment explanation
Indices: 5476592--5476801 Score: 193
Period size: 52 Copynumber: 4.1 Consensus size: 52
5476582 TTCATTATCA
* * * *
5476592 CACATCACACACTGAAGCCATAGCCCTGCCATGGTCTTATACAG-ATCACATAT
1 CACATCACAC-C-GATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATAT
* * * *
5476645 --CAT---ACCGATGCAATATCCTAGATATGGTCTTATACGGAATCACATTAT
1 CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACA-TAT
* *
5476693 CACATCACACCGATGCCATAGCTCAGCTATGGTCTTATACGGGAA-CACAAAT
1 CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATAC-GGAATCACATAT
*** *
5476745 CACATTGTACCGATGCCATAGCCCGGCTATGGTCTTATACGG-ATCACATAT
1 CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATAT
*
5476796 CTCATC
1 CACATC
5476802 TTTTTCGTCA
Statistics
Matches: 126, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
46 23 0.18
47 7 0.06
48 5 0.04
50 4 0.03
51 15 0.12
52 37 0.29
53 31 0.25
54 4 0.03
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (52 bp):
CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATAT
Found at i:5479028 original size:13 final size:13
Alignment explanation
Indices: 5479012--5479044 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5479002 TTTAATTTAA
*
5479012 TTAGTTAATTAGT
1 TTAGATAATTAGT
5479025 TTAGATAATTAGT
1 TTAGATAATTAGT
5479038 TTA-ATAA
1 TTAGATAA
5479045 ACAAACCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:5487436 original size:3 final size:3
Alignment explanation
Indices: 5487423--5487468 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
5487413 TCTTATCTTT
5487423 TTA TTA TTTA TTA TTA TTA TTA TTA TT- TTA TTA TT- TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5487467 TT
1 TT
5487469 TTTCTTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:5487470 original size:19 final size:20
Alignment explanation
Indices: 5487423--5487470 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
5487413 TCTTATCTTT
5487423 TTATTA-TTTATTATTATTA
1 TTATTATTTTATTATTATTA
5487442 TTATTATTTTATTATT-TTA
1 TTATTATTTTATTATTATTA
5487461 TTATTATTTT
1 TTATTATTTT
5487471 TCTTTTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTATTATTTTATTATTATTA
Found at i:5487476 original size:6 final size:6
Alignment explanation
Indices: 5487467--5487495 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5487457 TTTATTATTA
5487467 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
5487496 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:5487501 original size:6 final size:6
Alignment explanation
Indices: 5487420--5487503 Score: 55
Period size: 6 Copynumber: 14.0 Consensus size: 6
5487410 TCCTCTTATC
* * * * *
5487420 TTTTTA TTATTTA TTATTA TTATTA TTATT- TTATTA -TTTTA TTATTA
1 TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * *
5487467 TTTTTC TTTTTC TTTTTC TTTTTCT TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTT-A TTTTTA TTTTTA
5487504 AAGACATGTC
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
5 9 0.13
6 47 0.70
7 11 0.16
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:5493916 original size:20 final size:19
Alignment explanation
Indices: 5493867--5493914 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
5493857 TAAACCTTAA
5493867 AAATAAAAATAATATAATT
1 AAATAAAAATAATATAATT
5493886 AGAATAAAAATAA-ACTAATT
1 A-AATAAAAATAATA-TAATT
5493906 AAATAAAAA
1 AAATAAAAA
5493915 ATTGGACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
AAATAAAAATAATATAATT
Found at i:5495706 original size:26 final size:25
Alignment explanation
Indices: 5495666--5495726 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
5495656 TATAATTTAT
5495666 TTATT-TT-AAAAACTATACATATA
1 TTATTATTAAAAAACTATACATATA
**
5495689 TTATTATTAAAAATACTATTTATATA
1 TTATTATTAAAAA-ACTATACATATA
5495715 TT-TATATTAAAA
1 TTAT-TATTAAAA
5495727 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 5 0.16
24 2 0.06
25 5 0.16
26 20 0.62
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (25 bp):
TTATTATTAAAAAACTATACATATA
Found at i:5495712 original size:24 final size:23
Alignment explanation
Indices: 5495660--5495717 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
5495650 TTTTTATATA
5495660 ATTTAT-TTATTTTAAAAACTAT
1 ATTTATATTATTTTAAAAACTAT
**
5495682 ACATATATTATTATTAAAAA-TACT
1 ATTTATATTATT-TTAAAAACTA-T
5495706 ATTTATA-TATTT
1 ATTTATATTATTT
5495718 ATATTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
22 5 0.17
23 11 0.38
24 13 0.45
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTATATTATTTTAAAAACTAT
Found at i:5495812 original size:32 final size:32
Alignment explanation
Indices: 5495763--5495833 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
5495753 CTATATATTT
*
5495763 TTATTTTATTTTATTATATAACATTTATTATA
1 TTATTTTATTTTATTATATAACACTTATTATA
**
5495795 TT-TTTTATTTTTATTATATATTACTTATTATA
1 TTATTTTA-TTTTATTATATAACACTTATTATA
5495827 TTATTTT
1 TTATTTT
5495834 TTATTCTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 5 0.15
32 25 0.74
33 4 0.12
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (32 bp):
TTATTTTATTTTATTATATAACACTTATTATA
Found at i:5495832 original size:35 final size:32
Alignment explanation
Indices: 5495756--5495847 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 32
5495746 TATTTTCCTA
*
5495756 TATATTTTTATTTTA-TTTTATTATATAACATT
1 TATATTATT-TTTTATTTTTATTATATAACATT
*
5495788 TAT-TATATTTTTTATTTTTATTATATATTACTTAT
1 TATAT-TATTTTTTATTTTTATTATATA--ACAT-T
*
5495823 TATATTATTTTTTATTCTATATTAT
1 TATATTATTTTTTATT-TTTATTAT
5495848 GTATATCATA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
31 6 0.12
32 18 0.36
34 3 0.06
35 15 0.30
36 8 0.16
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (32 bp):
TATATTATTTTTTATTTTTATTATATAACATT
Found at i:5499143 original size:30 final size:30
Alignment explanation
Indices: 5499109--5499271 Score: 114
Period size: 30 Copynumber: 5.5 Consensus size: 30
5499099 TAACCAAAGT
*
5499109 TATCCCTTTTCATAGTTCGACAGTCGAAAC
1 TATCCCTTTTCATAGTTCGATAGTCGAAAC
* * * **
5499139 TAT-CCATTTCATTGTTCGATGGTCGTCAC
1 TATCCCTTTTCATAGTTCGATAGTCGAAAC
* * * *
5499168 CATCCCTTTTCATAATTTGATAGTCG-AAG
1 TATCCCTTTTCATAGTTCGATAGTCGAAAC
* ** *
5499197 TCATCCCTTTTCATAGTGCGATAACCGAAGC
1 T-ATCCCTTTTCATAGTTCGATAGTCGAAAC
* * ** **
5499228 CATCCCTTTTCATAATTTAATAGTCGTCAC
1 TATCCCTTTTCATAGTTCGATAGTCGAAAC
*
5499258 CATCCCTTTTCATA
1 TATCCCTTTTCATA
5499272 ATATGATGGT
Statistics
Matches: 98, Mismatches: 32, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
29 23 0.23
30 74 0.76
31 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (30 bp):
TATCCCTTTTCATAGTTCGATAGTCGAAAC
Found at i:5499272 original size:30 final size:30
Alignment explanation
Indices: 5499160--5499309 Score: 135
Period size: 30 Copynumber: 5.0 Consensus size: 30
5499150 TTGTTCGATG
5499160 GTCGTCACCATCCCTTTTCATAATTTGATA
1 GTCGTCACCATCCCTTTTCATAATTTGATA
* * * **
5499190 GTCG-AAGTCATCCCTTTTCATAGTGCGATA
1 GTCGTCA-CCATCCCTTTTCATAATTTGATA
** * *
5499220 ACCG-AAGCCATCCCTTTTCATAATTTAATA
1 GTCGTCA-CCATCCCTTTTCATAATTTGATA
* *
5499250 GTCGTCACCATCCCTTTTCATAATATGATG
1 GTCGTCACCATCCCTTTTCATAATTTGATA
* * *
5499280 GTCATCACCATCTCTTTTCATGA-TTGATA
1 GTCGTCACCATCCCTTTTCATAATTTGATA
5499309 G
1 G
5499310 CGGAAGTTAT
Statistics
Matches: 95, Mismatches: 23, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
29 6 0.06
30 88 0.93
31 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (30 bp):
GTCGTCACCATCCCTTTTCATAATTTGATA
Found at i:5506087 original size:33 final size:33
Alignment explanation
Indices: 5506050--5506116 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
5506040 AGTGACTATG
5506050 ACTCAAGTAGACATCTTTGAATGAACTATAAAT
1 ACTCAAGTAGACATCTTTGAATGAACTATAAAT
5506083 ACTCAAGTAGACATCTTTGAATGAACTATAAAT
1 ACTCAAGTAGACATCTTTGAATGAACTATAAAT
5506116 A
1 A
5506117 ATAGTGGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (33 bp):
ACTCAAGTAGACATCTTTGAATGAACTATAAAT
Found at i:5512838 original size:29 final size:29
Alignment explanation
Indices: 5512787--5512844 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
5512777 AAAGGGGTTT
5512787 AAAATTAAAAAGAAAAAGTAAAAGTAAAAC
1 AAAATTAAAAAGAAAAAGTAAAAG-AAAAC
5512817 AAAA-TAAAAAGAAATAAG-AAAAGAAAAC
1 AAAATTAAAAAGAAA-AAGTAAAAGAAAAC
5512845 CAGTGAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 5 0.19
29 15 0.56
30 7 0.26
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (29 bp):
AAAATTAAAAAGAAAAAGTAAAAGAAAAC
Found at i:5514453 original size:40 final size:40
Alignment explanation
Indices: 5514392--5514467 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
5514382 CGGTACTTTA
* *
5514392 TGGTGCGTAGGGTTAGATGGGTTGATTTTATCCCCATATT
1 TGGTGCGTAGGGATAGATGGGTCGATTTTATCCCCATATT
* *
5514432 TGGTGTGTAGGGATAGGTGGGTCGATTTTATCCCCA
1 TGGTGCGTAGGGATAGATGGGTCGATTTTATCCCCA
5514468 CATGGTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.17, C:0.13, G:0.33, T:0.37
Consensus pattern (40 bp):
TGGTGCGTAGGGATAGATGGGTCGATTTTATCCCCATATT
Found at i:5520459 original size:17 final size:19
Alignment explanation
Indices: 5520437--5520471 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
5520427 CTAAAATATT
5520437 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
5520454 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
5520472 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:5520542 original size:19 final size:19
Alignment explanation
Indices: 5520520--5520573 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
5520510 AAATGATAGC
5520520 AAAATAGTAAAAAAAAAAG
1 AAAATAGTAAAAAAAAAAG
5520539 AAAATAG-AAAAAACAGAAAG
1 AAAATAGTAAAAAA-A-AAAG
5520559 --AATAGTAAAAAAAAA
1 AAAATAGTAAAAAAAAA
5520574 CAACAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 2 0.06
18 12 0.38
19 14 0.44
20 4 0.12
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (19 bp):
AAAATAGTAAAAAAAAAAG
Found at i:5520551 original size:20 final size:19
Alignment explanation
Indices: 5520522--5520573 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
5520512 ATGATAGCAA
5520522 AATAGTAAAAAAAAAAGAA-
1 AATAGTAAAAAAAAAA-AAG
* *
5520541 AATAG-AAAAAACAGAAAG
1 AATAGTAAAAAAAAAAAAG
5520559 AATAGTAAAAAAAAA
1 AATAGTAAAAAAAAA
5520574 CAACAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 13 0.48
19 12 0.44
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.10
Consensus pattern (19 bp):
AATAGTAAAAAAAAAAAAG
Found at i:5524507 original size:24 final size:23
Alignment explanation
Indices: 5524452--5524517 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
5524442 TATATTACAT
5524452 TTAAAAATATATATAATTTTTAA
1 TTAAAAATATATATAATTTTTAA
* * * *
5524475 TGATCAAATATATAGAATTTTTAC
1 TTA-AAAATATATATAATTTTTAA
5524499 TCTAAAAATATATATAATT
1 T-TAAAAATATATATAATT
5524518 CTCGACTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 2 0.06
24 31 0.91
25 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (23 bp):
TTAAAAATATATATAATTTTTAA
Found at i:5528992 original size:10 final size:10
Alignment explanation
Indices: 5528979--5529004 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5528969 TAACAAACTC
5528979 TTTTAATTTA
1 TTTTAATTTA
5528989 TTTTAATTTA
1 TTTTAATTTA
5528999 TTTTAA
1 TTTTAA
5529005 AATTTTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:5543125 original size:29 final size:31
Alignment explanation
Indices: 5543083--5543148 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 31
5543073 ATTATATGTT
* *
5543083 AATTAATTAATTGAACTTAATAACT-TAT-A
1 AATTGATTAATTGAACTTAATAAATCTATCA
5543112 AATTGATTAATTGAACTTAATAAATCTATCA
1 AATTGATTAATTGAACTTAATAAATCTATCA
5543143 AATTGA
1 AATTGA
5543149 AACATGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 23 0.70
30 3 0.09
31 7 0.21
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (31 bp):
AATTGATTAATTGAACTTAATAAATCTATCA
Found at i:5547870 original size:40 final size:40
Alignment explanation
Indices: 5547819--5547933 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
5547809 GCTATCTCGG
5547819 TTCGTACACTTAGTGCCTCA-TACAGCCGAAACTATACCAT
1 TTCGTACACTTAGTGCCT-ATTACAGCCGAAACTATACCAT
* *
5547859 TTCGTACACTTAGTG-CTATTTATAGCCGAAGCTATACCAT
1 TTCGTACACTTAGTGCCTA-TTACAGCCGAAACTATACCAT
* * *
5547899 TTTGCACACTTAGTG-CTATTTACAGCCGAAGCTAT
1 TTCGTACACTTAGTGCCTA-TTACAGCCGAAACTAT
5547934 TTTGAACCGC
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
38 1 0.01
39 2 0.03
40 65 0.96
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (40 bp):
TTCGTACACTTAGTGCCTATTACAGCCGAAACTATACCAT
Found at i:5550979 original size:38 final size:38
Alignment explanation
Indices: 5550922--5550998 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
5550912 TATTGCATCA
5550922 AAACACATCCCAAACCGATCAACGATGCATCACTGTAG
1 AAACACATCCCAAACCGATCAACGATGCATCACTGTAG
* * *
5550960 AAACACATCCCAGATCGATCAACGATGCATTACTGTAG
1 AAACACATCCCAAACCGATCAACGATGCATCACTGTAG
5550998 A
1 A
5550999 TCAAAAATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (38 bp):
AAACACATCCCAAACCGATCAACGATGCATCACTGTAG
Found at i:5555981 original size:52 final size:52
Alignment explanation
Indices: 5555869--5556017 Score: 190
Period size: 52 Copynumber: 2.8 Consensus size: 52
5555859 TTCATTTATT
* * * * *
5555869 TGCCATATCCCAGATATAGTCTCATACGGAAGCACATAATCACATCTCACCGA
1 TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACAT-ATCACATCACACCGA
*
5555922 TGCCATAGCCCAGCTATGGTCTTATACAGAAGCACATATCACATCACACCGA
1 TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATCACACCGA
* * * * *
5555974 TTCCATAGTCTAGCTATGGTCTTATACGGAAACACATGTCACAT
1 TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACAT
5556018 ATTGCCAAGG
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 52 0.62
53 32 0.38
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (52 bp):
TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATCACACCGA
Found at i:5558775 original size:3 final size:3
Alignment explanation
Indices: 5558769--5558800 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5558759 GTTGTTTATA
5558769 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5558801 TTGCAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:5561554 original size:17 final size:17
Alignment explanation
Indices: 5561544--5561579 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5561534 TTTTGTTTCT
5561544 TTTTATGTTTTATTTTA
1 TTTTATGTTTTATTTTA
*
5561561 TTTTATGTTTTATTATA
1 TTTTATGTTTTATTTTA
5561578 TT
1 TT
5561580 AATATTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTATGTTTTATTTTA
Found at i:5564525 original size:17 final size:17
Alignment explanation
Indices: 5564486--5564526 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5564476 ATGAAATGTT
* *
5564486 AATAATTTAAATTTTAA
1 AATATTTTAAATTTGAA
5564503 AATATTTTAAATTTGAA
1 AATATTTTAAATTTGAA
*
5564520 ATTATTT
1 AATATTT
5564527 AATTAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AATATTTTAAATTTGAA
Found at i:5564661 original size:16 final size:16
Alignment explanation
Indices: 5564611--5564667 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
5564601 AAATTAAATC
* *
5564611 AAATTTAAAATAATTT
1 AAATCTAAAATAATTA
**
5564627 AAA-CTTAAAATAACCA
1 AAATC-TAAAATAATTA
5564643 AAATCTAAAATAATTA
1 AAATCTAAAATAATTA
*
5564659 AAATTTAAA
1 AAATCTAAA
5564668 GCTAACACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 31 0.97
17 1 0.03
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATCTAAAATAATTA
Found at i:5566967 original size:59 final size:59
Alignment explanation
Indices: 5566901--5567019 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
5566891 TAAAAAATTG
5566901 ATAATATTAATTTAAAAATAACTTTTATTCGAAATCATTCAAATGAATAATTTTAAATA
1 ATAATATTAATTTAAAAATAACTTTTATTCGAAATCATTCAAATGAATAATTTTAAATA
5566960 ATAATATTAATTTAAAAATAACTTTTATTCGAAATCATTCAAATGAATAATTTTAAATA
1 ATAATATTAATTTAAAAATAACTTTTATTCGAAATCATTCAAATGAATAATTTTAAATA
5567019 A
1 A
5567020 CTTAAATTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (59 bp):
ATAATATTAATTTAAAAATAACTTTTATTCGAAATCATTCAAATGAATAATTTTAAATA
Found at i:5580566 original size:16 final size:17
Alignment explanation
Indices: 5580545--5580593 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 17
5580535 TTCTAATAAT
5580545 TTTTTAATAATTTTA-A
1 TTTTTAATAATTTTAGA
5580561 TTTTTAATAATATTTTATGA
1 TTTTTAAT-A-ATTTTA-GA
5580581 TTTTT-ATAATTTT
1 TTTTTAATAATTTT
5580594 TTTCTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 7 0.24
19 2 0.07
20 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTAATAATTTTAGA
Found at i:5580594 original size:9 final size:9
Alignment explanation
Indices: 5580540--5580594 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
5580530 ATCAATTCTA
5580540 ATAATTTTT
1 ATAATTTTT
*
5580549 -TAATAATTT
1 ATAAT-TTTT
5580558 -TAATTTTT
1 ATAATTTTT
5580566 AATAATATTTT
1 -ATAAT-TTTT
*
5580577 ATGATTTTT
1 ATAATTTTT
5580586 ATAATTTTT
1 ATAATTTTT
5580595 TTCTAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 7 0.18
9 19 0.50
10 8 0.21
11 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5580604 original size:20 final size:20
Alignment explanation
Indices: 5580540--5580594 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
5580530 ATCAATTCTA
*
5580540 ATAATTTTT--TAATAATTT
1 ATAATTTTTAATAATATTTT
5580558 -TAATTTTTAATAATATTTT
1 ATAATTTTTAATAATATTTT
*
5580577 ATGATTTTT-ATAAT-TTTT
1 ATAATTTTTAATAATATTTT
5580595 TTCTAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 8 0.25
18 4 0.12
19 13 0.41
20 7 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATAATTTTTAATAATATTTT
Found at i:5584608 original size:20 final size:21
Alignment explanation
Indices: 5584571--5584610 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
5584561 TAGAAAAAAA
5584571 AACTTAAATCAATTAATCAATC
1 AACTTAAATC-ATTAATCAATC
5584593 AACTTAAATC-TTAATCAA
1 AACTTAAATCATTAATCAA
5584611 ACTTAAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (21 bp):
AACTTAAATCATTAATCAATC
Found at i:5584615 original size:17 final size:18
Alignment explanation
Indices: 5584569--5584623 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
5584559 AATAGAAAAA
5584569 AAAACTTAAATCAATTAATC
1 AAAACTTAAATC--TTAATC
5584589 AATCAACTTAAATCTTAATC
1 AA--AACTTAAATCTTAATC
*
5584609 -AAACTTAAACCTTAA
1 AAAACTTAAATCTTAA
5584624 CTGATTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 13 0.41
19 1 0.03
20 8 0.25
22 10 0.31
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAACTTAAATCTTAATC
Found at i:5594345 original size:13 final size:13
Alignment explanation
Indices: 5594327--5594351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5594317 AATTTTTTTA
5594327 TTTTTAATTAATC
1 TTTTTAATTAATC
5594340 TTTTTAATTAAT
1 TTTTTAATTAAT
5594352 AACTCTTTTA
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATC
Found at i:5599554 original size:17 final size:18
Alignment explanation
Indices: 5599517--5599555 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5599507 AAAATTTTAA
* *
5599517 ATTAATTTATATTGTTGC
1 ATTAAATTATATTGGTGC
5599535 ATTAAATTAT-TTGGTGC
1 ATTAAATTATATTGGTGC
5599552 ATTA
1 ATTA
5599556 CCATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (18 bp):
ATTAAATTATATTGGTGC
Found at i:5599598 original size:18 final size:18
Alignment explanation
Indices: 5599577--5599619 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
5599567 AAAAATAATT
5599577 TATATTTATTATTTA-CAA
1 TATATTT-TTATTTATCAA
*
5599595 TATATATTTTATTTATCAT
1 TATAT-TTTTATTTATCAA
5599614 TATATT
1 TATATT
5599620 AAATAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATTTTTATTTATCAA
Found at i:5599628 original size:25 final size:24
Alignment explanation
Indices: 5599564--5599629 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 24
5599554 TACCATTTAT
* *
5599564 TTTAAAAATAATTTATATTTATTA
1 TTTACAAATAATTTATATTTATCA
5599588 TTTACAATATATATTT-TATTTATCA
1 TTTACAA-ATA-ATTTATATTTATCA
*
5599613 TTATATTAAATAATTTA
1 TT-TA-CAAATAATTTA
5599630 AAATTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
24 6 0.18
25 17 0.50
26 9 0.26
27 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTACAAATAATTTATATTTATCA
Found at i:5599999 original size:32 final size:32
Alignment explanation
Indices: 5599963--5600025 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
5599953 AATTCAGACA
*
5599963 AATTTAAACACAAAACAATATAAACCTAAATT
1 AATTTAAACACAAAACAATATAAACCCAAATT
* * *
5599995 AATTTGAACTCAAAACAATTTAAACCCAAAT
1 AATTTAAACACAAAACAATATAAACCCAAAT
5600026 CATCAAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.25
Consensus pattern (32 bp):
AATTTAAACACAAAACAATATAAACCCAAATT
Found at i:5600024 original size:16 final size:16
Alignment explanation
Indices: 5599963--5600024 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
5599953 AATTCAGACA
*
5599963 AATTTAAACACAAAAC
1 AATTTAAACCCAAAAC
* * **
5599979 AATATAAACCTAAATT
1 AATTTAAACCCAAAAC
* *
5599995 AATTTGAACTCAAAAC
1 AATTTAAACCCAAAAC
5600011 AATTTAAACCCAAA
1 AATTTAAACCCAAA
5600025 TCATCAAACT
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.56, C:0.18, G:0.02, T:0.24
Consensus pattern (16 bp):
AATTTAAACCCAAAAC
Found at i:5607938 original size:2 final size:2
Alignment explanation
Indices: 5607931--5607955 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5607921 TAATATACAT
5607931 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
5607956 AAAGTACAGC
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5610930 original size:41 final size:42
Alignment explanation
Indices: 5610885--5610964 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
5610875 ATATTGGGGA
* *
5610885 CACACGGTCT-ATCAACATGCCTGTGTG-CAAGCCGTGTGTCT
1 CACACGGTCTGATC-ACACGCCCGTGTGACAAGCCGTGTGTCT
*
5610926 CACACGGTCTGATCACACGCCCGTGTGACATGCCGTGTG
1 CACACGGTCTGATCACACGCCCGTGTGACAAGCCGTGTG
5610965 GACTCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 21 0.62
42 13 0.38
ACGTcount: A:0.19, C:0.31, G:0.26, T:0.24
Consensus pattern (42 bp):
CACACGGTCTGATCACACGCCCGTGTGACAAGCCGTGTGTCT
Found at i:5611696 original size:6 final size:6
Alignment explanation
Indices: 5611685--5611719 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5611675 GGAATACACC
*
5611685 GTAACA GTAACA ATAACA GTAACA GTAACA GTAAC
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAAC
5611720 GATACACAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (6 bp):
GTAACA
Found at i:5613430 original size:16 final size:15
Alignment explanation
Indices: 5613409--5613456 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
5613399 GATGGGAATA
5613409 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
5613425 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
5613440 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
5613456 A
1 A
5613457 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:5613439 original size:8 final size:8
Alignment explanation
Indices: 5613405--5613456 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
5613395 CAATGATGGG
*
5613405 AATAATAA
1 AATATTAA
5613413 AATATATAA
1 AATAT-TAA
5613422 AATA-TAA
1 AATATTAA
5613429 AATATTAA
1 AATATTAA
*
5613437 AATATCAA
1 AATATTAA
*
5613445 AATATTAG
1 AATATTAA
5613453 AATA
1 AATA
5613457 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:5613456 original size:24 final size:24
Alignment explanation
Indices: 5613404--5613460 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
5613394 ACAATGATGG
*
5613404 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
5613428 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
5613452 GAATAATAA
1 GAATAATAA
5613461 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:5613620 original size:23 final size:22
Alignment explanation
Indices: 5613569--5613622 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
5613559 ATACTACATC
5613569 AATATGTACATAT-ATA--AAA
1 AATATGTACATATAATATTAAA
**
5613588 AATAAATACATGATAATATTAAA
1 AATATGTACAT-ATAATATTAAA
5613611 AATATGTACATA
1 AATATGTACATA
5613623 ATATAGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 3 0.11
22 1 0.04
23 12 0.44
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
AATATGTACATATAATATTAAA
Found at i:5613669 original size:22 final size:24
Alignment explanation
Indices: 5613585--5613670 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 24
5613575 TACATATATA
* *
5613585 AAAAATAAATACATGATAATA--TT
1 AAAAATATATACATAAT-ATAGGTT
*
5613608 AAAAATATGTACATAATATAGTGTT
1 AAAAATATATACATAATATAG-GTT
*
5613633 AAAAATACATACATAATATA-GTT
1 AAAAATATATACATAATATAGGTT
*
5613656 -AAGATATATACATAA
1 AAAAATATATACATAA
5613671 GATAACATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
22 16 0.30
23 17 0.32
25 20 0.38
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAAATATATACATAATATAGGTT
Found at i:5613720 original size:25 final size:24
Alignment explanation
Indices: 5613692--5613821 Score: 92
Period size: 23 Copynumber: 5.6 Consensus size: 24
5613682 AAAAAAATAT
5613692 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAATATAATATT-AAG
* * *
5613717 ATATATAAATAAAATAGTA-TAAT
1 ATATATAAATAATATAATATTAAG
** *
5613740 ATATATACGTAATATAAATTTTAA-
1 ATATATAAATAATAT-AATATTAAG
** * *
5613764 A-ATATACCTAATATATTA-AAAG
1 ATATATAAATAATATAATATTAAG
*
5613786 A-ATATATATAATATAATATTAAG
1 ATATATAAATAATATAATATTAAG
*
5613809 AAATAT-AATAATA
1 ATATATAAATAATA
5613822 ACAAAAAAAT
Statistics
Matches: 83, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
21 2 0.02
22 17 0.20
23 36 0.43
24 8 0.10
25 20 0.24
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
ATATATAAATAATATAATATTAAG
Found at i:5613722 original size:16 final size:15
Alignment explanation
Indices: 5613685--5613741 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 15
5613675 ACATGTAAAA
5613685 AAAATATAT-ATA-T
1 AAAATATATAATATT
5613698 -AAATAATATAATATT
1 AAAAT-ATATAATATT
5613713 AAAGATATATAA-A-T
1 AAA-ATATATAATATT
5613727 AAAATAGTATAATAT
1 AAAATA-TATAATAT
5613742 ATATACGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
12 4 0.11
13 7 0.19
14 12 0.33
15 3 0.08
16 8 0.22
17 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (15 bp):
AAAATATATAATATT
Found at i:5614337 original size:30 final size:30
Alignment explanation
Indices: 5614301--5614445 Score: 227
Period size: 30 Copynumber: 4.8 Consensus size: 30
5614291 TAGGTACAAG
*
5614301 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
5614331 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
5614361 TGGTGGTGGAAAATGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
5614391 TGGTGGTGGAAAAGGTGTGCCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
5614421 TGGTGGTGGAAAAGGAGTAGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
5614446 TGAGAAAAGT
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 105 1.00
ACGTcount: A:0.22, C:0.04, G:0.48, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:5620718 original size:16 final size:15
Alignment explanation
Indices: 5620697--5620744 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
5620687 TGATGGAATA
5620697 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
5620713 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
5620728 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
5620744 A
1 A
5620745 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:5620727 original size:8 final size:8
Alignment explanation
Indices: 5620693--5620744 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
5620683 ACAATGATGG
*
5620693 AATAATAA
1 AATATTAA
5620701 AATATATAA
1 AATAT-TAA
5620710 AATA-TAA
1 AATATTAA
5620717 AATATTAA
1 AATATTAA
*
5620725 AATATCAA
1 AATATTAA
*
5620733 AATATTAG
1 AATATTAA
5620741 AATA
1 AATA
5620745 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:5620744 original size:24 final size:24
Alignment explanation
Indices: 5620692--5620748 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
5620682 AACAATGATG
*
5620692 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
5620716 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
5620740 GAATAATAA
1 GAATAATAA
5620749 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:5620906 original size:23 final size:22
Alignment explanation
Indices: 5620855--5620908 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
5620845 ATACTACATC
5620855 AATATGTACATAT-ATA--AAA
1 AATATGTACATATAATATTAAA
**
5620874 AATAAATACATGATAATATTAAA
1 AATATGTACAT-ATAATATTAAA
5620897 AATATGTACATA
1 AATATGTACATA
5620909 ATATAGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 3 0.11
22 1 0.04
23 12 0.44
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
AATATGTACATATAATATTAAA
Found at i:5620955 original size:22 final size:24
Alignment explanation
Indices: 5620871--5620956 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 24
5620861 TACATATATA
* *
5620871 AAAAATAAATACATGATAATA--TT
1 AAAAATATATACATAAT-ATAGGTT
*
5620894 AAAAATATGTACATAATATAGTGTT
1 AAAAATATATACATAATATAG-GTT
*
5620919 AAAAATACATACATAATATA-GTT
1 AAAAATATATACATAATATAGGTT
*
5620942 -AAGATATATACATAA
1 AAAAATATATACATAA
5620957 GATAACATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
22 16 0.30
23 17 0.32
25 20 0.38
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAAATATATACATAATATAGGTT
Found at i:5621002 original size:25 final size:25
Alignment explanation
Indices: 5620886--5621104 Score: 120
Period size: 25 Copynumber: 9.0 Consensus size: 25
5620876 TAAATACATG
* *
5620886 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* * * *
5620911 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
5620936 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
5620958 ATAACATGTAAAAAATATATATAAATAAT
1 ATAATAT-T---AAAGATATATACATAAT
* *
5620987 ATAATATTAAAGATATATAAATAAA
1 ATAATATTAAAGATATATACATAAT
* * *
5621012 ATAGTA-TAATATATATATACGTAAT
1 ATAATATTAA-AGATATATACATAAT
* *
5621037 ATAA-ATTTAA-A-ATATACCTAAT
1 ATAATATTAAAGATATATACATAAT
* *
5621059 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
5621081 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
5621104 A
1 A
5621105 ACAAAAAAAA
Statistics
Matches: 152, Mismatches: 28, Indels: 30
0.72 0.13 0.14
Matches are distributed among these distances:
21 4 0.03
22 39 0.26
23 17 0.11
24 12 0.08
25 60 0.39
28 1 0.01
29 19 0.12
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:5621004 original size:29 final size:29
Alignment explanation
Indices: 5620945--5621023 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
5620935 TATAGTTAAG
* * *
5620945 ATATATACATAAGATAACATGTAAAAAAT
1 ATATATAAATAATATAATATGTAAAAAAT
*
5620974 ATATATAAATAATATAATAT-TAAAGATAT
1 ATATATAAATAATATAATATGTAAA-AAAT
* *
5621003 ATAAATAAAATAGTATAATAT
1 ATATAT-AAATAATATAATAT
5621024 ATATATACGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.10
29 25 0.60
30 13 0.31
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (29 bp):
ATATATAAATAATATAATATGTAAAAAAT
Found at i:5621618 original size:30 final size:30
Alignment explanation
Indices: 5621582--5621786 Score: 329
Period size: 30 Copynumber: 6.8 Consensus size: 30
5621572 TAGGTACAAG
*
5621582 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
5621612 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
5621642 TGGTGGTGGAAAAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
5621672 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
5621702 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
5621732 TGGTGGTGGAAAAGGTGTGCCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
5621762 TAGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
5621787 TGAGAAAAGT
Statistics
Matches: 164, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 164 1.00
ACGTcount: A:0.23, C:0.04, G:0.48, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:5640103 original size:30 final size:30
Alignment explanation
Indices: 5640069--5640126 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5640059 CAGCAAGTAC
*
5640069 TAGAAGTGGAAGAGGAAATCGAAGAAGAAG
1 TAGAAGTAGAAGAGGAAATCGAAGAAGAAG
* *
5640099 TAGAAGTAGAAGAGGAATTTGAAGAAGA
1 TAGAAGTAGAAGAGGAAATCGAAGAAGA
5640127 GGAGGAGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.34, T:0.14
Consensus pattern (30 bp):
TAGAAGTAGAAGAGGAAATCGAAGAAGAAG
Found at i:5658580 original size:40 final size:40
Alignment explanation
Indices: 5658518--5658612 Score: 136
Period size: 40 Copynumber: 2.3 Consensus size: 40
5658508 CTTTTCTTTC
* *
5658518 TTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTT-CTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
* *
5658559 TTTCTTTCTTTCTCCCTTCTCTGTTTTGTTTTGCTCTTTG
1 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
5658599 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
5658613 TTCTTTGTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.67
41 16 0.33
ACGTcount: A:0.00, C:0.27, G:0.08, T:0.64
Consensus pattern (40 bp):
TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:5658589 original size:45 final size:44
Alignment explanation
Indices: 5658514--5658616 Score: 104
Period size: 45 Copynumber: 2.3 Consensus size: 44
5658504 TTTTCTTTTC
*
5658514 TTTCTTTCTTTCCTTCCTTCCTTCTCTGTTTCG-T-TTTGCTCTCT
1 TTTCTTTCTTT-CTCCCTTCCTTCTCTGTTTCGCTCTTTG-TCTCT
* * *
5658558 GTTTCTTTCTTTCTCCCTTCTCTGT-TTTGTTTTGCTCTTTGTTTCT
1 -TTTCTTTCTTTCTCCCTTC-CT-TCTCTGTTTCGCTCTTTGTCTCT
5658604 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
5658617 TTGTCATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
44 7 0.14
45 33 0.66
46 6 0.12
47 4 0.08
ACGTcount: A:0.00, C:0.27, G:0.08, T:0.65
Consensus pattern (44 bp):
TTTCTTTCTTTCTCCCTTCCTTCTCTGTTTCGCTCTTTGTCTCT
Found at i:5658629 original size:2 final size:2
Alignment explanation
Indices: 5658622--5658696 Score: 51
Period size: 2 Copynumber: 41.0 Consensus size: 2
5658612 TTTCTTTGTC
*
5658622 AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AA AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5658659 AT A- AT A- AT CAT -T ACT -T AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
5658697 TAACTAGAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 22
0.70 0.04 0.26
Matches are distributed among these distances:
1 9 0.15
2 47 0.80
3 3 0.05
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5659720 original size:30 final size:30
Alignment explanation
Indices: 5659663--5659721 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
5659653 ATAAATTTCA
* *
5659663 AATTTAATCTCCCTACTTTTATTTTTTAAG
1 AATTTAATCACCCTACTTTTATATTTTAAG
*
5659693 AATTTAATCACTCTACTTTTCA-ATTTTAA
1 AATTTAATCACCCTACTTTT-ATATTTTAA
5659722 AAATCCAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.51
Consensus pattern (30 bp):
AATTTAATCACCCTACTTTTATATTTTAAG
Found at i:5660254 original size:14 final size:14
Alignment explanation
Indices: 5660235--5660266 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5660225 CAATTTATTT
5660235 TAAAAATTAAATTA
1 TAAAAATTAAATTA
*
5660249 TAAAAATTAAATTT
1 TAAAAATTAAATTA
5660263 TAAA
1 TAAA
5660267 TTTAAGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAATTAAATTA
Found at i:5664778 original size:35 final size:35
Alignment explanation
Indices: 5664732--5664802 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
5664722 TTTAGGATCA
* * *
5664732 CATATCTTTGAAGATCCCCTTCCATATTTGCCAAG
1 CATATATTTGAAGATCACCTTCCATATTTACCAAG
* *
5664767 CATATATTTGAAGATCACTTTTCATATTTACCAAG
1 CATATATTTGAAGATCACCTTCCATATTTACCAAG
5664802 C
1 C
5664803 TCTAGAGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.37
Consensus pattern (35 bp):
CATATATTTGAAGATCACCTTCCATATTTACCAAG
Found at i:5669381 original size:48 final size:48
Alignment explanation
Indices: 5669257--5669381 Score: 146
Period size: 48 Copynumber: 2.6 Consensus size: 48
5669247 TTAGGGAATT
* * * *
5669257 CATTGATTTTGCTCCGGGCCATGATATCAGCACTTCAGGTGCTAGTTA
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGTTA
5669305 CATTGATTTGGCTTCGGAG-CATGATATCGGCACTTC-GGATGCGAGTTA
1 CATTGATTTGGCTTCGG-GCCATGATATCGGCACTTCAGG-TGCGAGTTA
* * * *
5669353 TATTGATTTGGTTTTGGGCCATGTTATCG
1 CATTGATTTGGCTTCGGGCCATGATATCG
5669382 AAACTTAAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
47 3 0.05
48 62 0.94
49 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (48 bp):
CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGTTA
Found at i:5679550 original size:58 final size:55
Alignment explanation
Indices: 5679445--5679587 Score: 146
Period size: 57 Copynumber: 2.5 Consensus size: 55
5679435 AACTTCACAC
* ** * *
5679445 TTTTCTTAATTTGGTAT-TTAGTTTTTTTTTTAATTTAGTACTTGAATTTGATACTT
1 TTTTC-TAATTTGGTATCTAAGTTTTTTTTCCAATTTAATACTTGAATTTGACA-TT
5679501 TTTTCTAATTTGGTATCTAAGTTTTCTTTGTCCAATTTAATA-TATGAATTTGACATT
1 TTTTCTAATTTGGTATCTAAGTTTT-TTT-TCCAATTTAATACT-TGAATTTGACATT
* * *
5679558 TTTCCTAATTTGATACCTAAGGTTTTTTTT
1 TTTTCTAATTTGGTATCTAA-GTTTTTTTT
5679588 TTTTGTGTGT
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
55 11 0.15
56 13 0.18
57 26 0.35
58 24 0.32
ACGTcount: A:0.23, C:0.09, G:0.10, T:0.57
Consensus pattern (55 bp):
TTTTCTAATTTGGTATCTAAGTTTTTTTTCCAATTTAATACTTGAATTTGACATT
Found at i:5682401 original size:19 final size:19
Alignment explanation
Indices: 5682361--5682407 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5682351 ATTTTATTTT
* *
5682361 ATTTTTTAAATTTTTATGA
1 ATTTTTTTAATTTTTATAA
5682380 ATTTTTTTAATATTTTA-AA
1 ATTTTTTTAAT-TTTTATAA
*
5682399 ATTTATTTA
1 ATTTTTTTA
5682408 TTTATTGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTTTAATTTTTATAA
Found at i:5683294 original size:17 final size:19
Alignment explanation
Indices: 5683260--5683308 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5683250 GTCCACGTGT
*
5683260 ATATTATAAAAATTTTAAA
1 ATATTATAAAAATCTTAAA
5683279 ATATTA-AAAAA-CTTAAA
1 ATATTATAAAAATCTTAAA
*
5683296 AAATTCATAAAAA
1 ATATT-ATAAAAA
5683309 AAAAGTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 9 0.35
18 6 0.23
19 11 0.42
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATTATAAAAATCTTAAA
Found at i:5683484 original size:24 final size:22
Alignment explanation
Indices: 5683432--5683484 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
5683422 GGATAAACAT
*
5683432 TAAAAAGCTAAAATTTTTAAAT
1 TAAAAAGCTAAAATTTTTAAAA
5683454 TAGAAAAGGACTAAAA-TTTTAGAAA
1 TA-AAAA-G-CTAAAATTTTTA-AAA
5683479 TAAAAA
1 TAAAAA
5683485 CAGAAAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 2 0.08
23 4 0.15
24 10 0.38
25 10 0.38
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.28
Consensus pattern (22 bp):
TAAAAAGCTAAAATTTTTAAAA
Found at i:5683698 original size:2 final size:2
Alignment explanation
Indices: 5683691--5683725 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5683681 TAAACAATAA
*
5683691 CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5683726 CTACACTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:5683784 original size:2 final size:2
Alignment explanation
Indices: 5683777--5683801 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5683767 GGGATAATAT
5683777 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5683802 GAAATTCTTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5688425 original size:32 final size:31
Alignment explanation
Indices: 5688347--5688425 Score: 74
Period size: 32 Copynumber: 2.5 Consensus size: 31
5688337 TTATTTAGAA
*
5688347 ATAATAAAAATATAAA-ATATTTTTATATTTT
1 ATAATAAAAA-ATAAATAAATTTTTATATTTT
**
5688378 ATAACT-AAATTTAAATACAATTTTTATTATTTT
1 ATAA-TAAAAAATAAATA-AATTTTTA-TATTTT
5688411 -TAATAAAAAATAAAT
1 ATAATAAAAAATAAAT
5688426 CATTTAACTG
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
30 4 0.11
31 9 0.24
32 19 0.50
33 6 0.16
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
ATAATAAAAAATAAATAAATTTTTATATTTT
Found at i:5691414 original size:23 final size:23
Alignment explanation
Indices: 5691387--5691443 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 23
5691377 ATTTTTAAAA
5691387 ATATTTAAAATTATTAAA-ATATC
1 ATATTTAAAATTATTAAATATA-C
*
5691410 ATATTTTTCAATATTATTAAATATAC
1 ATA--TTT-AAAATTATTAAATATAC
5691436 ATATTTAA
1 ATATTTAA
5691444 TTATTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
23 5 0.17
24 3 0.10
25 3 0.10
26 15 0.52
27 3 0.10
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTTAAAATTATTAAATATAC
Found at i:5691548 original size:15 final size:16
Alignment explanation
Indices: 5691521--5691555 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5691511 ATATTATTTT
5691521 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
*
5691537 AATAAT-AATTTTAAT
1 AATAATAAATTTTAAA
5691552 AATA
1 AATA
5691556 TTTCAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:5691577 original size:38 final size:38
Alignment explanation
Indices: 5691501--5691578 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
5691491 TTTATTATTT
* * *
5691501 TAATATTTTAATATTATTTTAATAATAAATTTTAAAAA
1 TAATATTTTAATAATATTTCAATAATAAATATTAAAAA
* *
5691539 TAATAATTTTAATAATATTTCAAT-ATTAATATTCAAAA
1 TAAT-ATTTTAATAATATTTCAATAATAAATATTAAAAA
5691577 TA
1 TA
5691579 TTCAAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 17 0.50
39 17 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (38 bp):
TAATATTTTAATAATATTTCAATAATAAATATTAAAAA
Found at i:5691580 original size:9 final size:9
Alignment explanation
Indices: 5691566--5691591 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5691556 TTTCAATATT
5691566 AATATTCAA
1 AATATTCAA
5691575 AATATTCAA
1 AATATTCAA
5691584 AATATTCA
1 AATATTCA
5691592 CATATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (9 bp):
AATATTCAA
Found at i:5693342 original size:22 final size:21
Alignment explanation
Indices: 5693314--5693358 Score: 81
Period size: 22 Copynumber: 2.1 Consensus size: 21
5693304 ACACCAAAAC
5693314 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCTTTTAGCGGCG-TTTTTT
5693336 AGGCTTTTAGCGGCGTTTTTT
1 AGGCTTTTAGCGGCGTTTTTT
5693357 AG
1 AG
5693359 CGCCACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.11, C:0.16, G:0.29, T:0.44
Consensus pattern (21 bp):
AGGCTTTTAGCGGCGTTTTTT
Found at i:5693532 original size:43 final size:43
Alignment explanation
Indices: 5693376--5693617 Score: 244
Period size: 42 Copynumber: 5.7 Consensus size: 43
5693366 AAAAGTATTT
* * *
5693376 GCGGCGCTTTTCCCACAAATGCCGCTAAAGACTATGACCTTTA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTA
* * *
5693419 GCGTCAC--TTCCCTACAAACGCCACTAAAGACCAAGACCTTTA
1 GCGGCGCTTTTCCC-ACAAACGCCGCTAAAGACCAAGACCTTTA
*
5693461 GCGGCGC-TTCCCCACAAACGCCGCTAAAGACCAAGACCTTTA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTA
* * * * *
5693503 GCGACGCTTTTCCCACAAACGCCACTAAAGA-TATTGAGCTTTA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-AGACCTTTA
* * *
5693546 GCGGCACTTTTTCCCACAAACGCTGCTATAGA--ATAGACCTTTA
1 GCGGCGC-TTTTCCCACAAACGCCGCTAAAGACCA-AGACCTTTA
* **
5693589 GCGGCGTTTTTAACACAAACGCCGCTAAA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAA
5693618 AATATATCTT
Statistics
Matches: 165, Mismatches: 29, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
41 5 0.03
42 83 0.50
43 56 0.34
44 21 0.13
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (43 bp):
GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTA
Done.