Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 103 of 103
Found at i:39137958 original size:2 final size:2
Alignment explanation
Indices: 39137951--39137994 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
39137941 CAAAATGTAC
39137951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39137993 AT
1 AT
39137995 GGTAATACAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39165049 original size:20 final size:20
Alignment explanation
Indices: 39164996--39165063 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
39164986 GGATATTCAG
39164996 ATTTAAATCAAAATCCTAATCAA
1 ATTTAAA-C-AAATCC-AATCAA
*
39165019 ATCTAAACAAATCCAATCAA
1 ATTTAAACAAATCCAATCAA
** * *
39165039 ATTTATGCAAATCTATTCAA
1 ATTTAAACAAATCCAATCAA
39165059 ATTTA
1 ATTTA
39165064 CATTAAGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 26 0.67
21 6 0.15
22 1 0.03
23 6 0.15
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (20 bp):
ATTTAAACAAATCCAATCAA
Found at i:39166523 original size:16 final size:16
Alignment explanation
Indices: 39166499--39166553 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
39166489 ACATTCCCTT
*
39166499 TTTATTTTTTATTTTA
1 TTTAATTTTTATTTTA
*
39166515 TTTAATTTTTATTTTG
1 TTTAATTTTTATTTTA
*
39166531 TTTCATTTATTAGCTTTTA
1 TTTAATTT-TTA--TTTTA
39166550 TTTA
1 TTTA
39166554 TTTAACATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 21 0.68
17 3 0.10
19 7 0.23
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (16 bp):
TTTAATTTTTATTTTA
Found at i:39166721 original size:15 final size:15
Alignment explanation
Indices: 39166701--39166743 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
39166691 CATAATAAGA
39166701 AAAAAGAAAAAAAGG
1 AAAAAGAAAAAAAGG
*
39166716 AAAAAGAAAGAAA-G
1 AAAAAGAAAAAAAGG
39166730 -AAAAGAACAAAAAG
1 AAAAAGAA-AAAAAG
39166744 TTGTGGTGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 7 0.29
14 5 0.21
15 12 0.50
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAGG
Found at i:39167561 original size:34 final size:36
Alignment explanation
Indices: 39167494--39167561 Score: 88
Period size: 34 Copynumber: 1.9 Consensus size: 36
39167484 AAAAAAAAGG
**
39167494 AAAAAAAAGAATAGAGAAGCGAGAAAAGTAAGAAAA
1 AAAAAAAAGAATAGAGAAGCGAGAAAAACAAGAAAA
39167530 AAAAATAAAGAA-AGA-AAG-GAGAAAAACAAGAA
1 AAAAA-AAAGAATAGAGAAGCGAGAAAAACAAGAA
39167562 GAAAGAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 12 0.41
35 3 0.10
36 8 0.28
37 6 0.21
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.04
Consensus pattern (36 bp):
AAAAAAAAGAATAGAGAAGCGAGAAAAACAAGAAAA
Found at i:39168938 original size:53 final size:54
Alignment explanation
Indices: 39168843--39168962 Score: 158
Period size: 53 Copynumber: 2.2 Consensus size: 54
39168833 CTCTCTTTAA
*
39168843 ATTAAAATTTTAATATAAAATATAAAAATTAAATAACAATTTTAATTAT-AATT
1 ATTAAAATTTTAATATAAAATATAAAAATAAAATAACAATTTTAATTATAAATT
* *
39168896 -TTAAATATTTTTATATAAAGA-ATAATAATAATAATAAC-ATTTTAATTATAAATT
1 ATTAAA-ATTTTAATATAAA-ATATAAAAATAA-AATAACAATTTTAATTATAAATT
39168950 ATTAAAATTTTAA
1 ATTAAAATTTTAA
39168963 GTGAAATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
52 5 0.09
53 31 0.53
54 17 0.29
55 5 0.09
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (54 bp):
ATTAAAATTTTAATATAAAATATAAAAATAAAATAACAATTTTAATTATAAATT
Found at i:39169447 original size:20 final size:20
Alignment explanation
Indices: 39169394--39169461 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
39169384 GGATATTCAG
39169394 ATTTAAATCAAAATCCTAATCAA
1 ATTTAAA-C-AAATCC-AATCAA
*
39169417 ATCTAAACAAATCCAATCAA
1 ATTTAAACAAATCCAATCAA
** * *
39169437 ATTTATGCAAATCTATTCAA
1 ATTTAAACAAATCCAATCAA
39169457 ATTTA
1 ATTTA
39169462 CATTAAGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 26 0.67
21 6 0.15
22 1 0.03
23 6 0.15
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (20 bp):
ATTTAAACAAATCCAATCAA
Found at i:39170145 original size:1 final size:1
Alignment explanation
Indices: 39170141--39170242 Score: 195
Period size: 1 Copynumber: 102.0 Consensus size: 1
39170131 TTTTTAACTT
*
39170141 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39170206 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39170243 TTTCTTTGAN
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
1 99 1.00
ACGTcount: A:0.99, C:0.01, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39171834 original size:12 final size:12
Alignment explanation
Indices: 39171785--39171835 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
39171775 AAAATAAAAA
39171785 AAAAG-AAAGAG
1 AAAAGAAAAGAG
*
39171796 AAAAGAAAAGAA
1 AAAAGAAAAGAG
*
39171808 AAAAGGAAAAAAG
1 AAAA-GAAAAGAG
*
39171821 AAAACAAAAGAG
1 AAAAGAAAAGAG
39171833 AAA
1 AAA
39171836 TGGGAAAGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
11 5 0.15
12 18 0.55
13 10 0.30
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:39175123 original size:11 final size:10
Alignment explanation
Indices: 39175105--39175144 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
39175095 CTACCACAAC
39175105 TCTTTTTTCTT
1 TCTTTTTT-TT
*
39175116 TGTTTTTTTT
1 TCTTTTTTTT
39175126 TCTTTTTTTTT
1 TC-TTTTTTTT
39175137 TCTTTTTT
1 TCTTTTTT
39175145 GCTATTATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.88
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:39175126 original size:14 final size:13
Alignment explanation
Indices: 39175107--39175137 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
39175097 ACCACAACTC
39175107 TTTTTTCTTTGTTT
1 TTTTTTCTTT-TTT
39175121 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
39175134 TTTT
1 TTTT
39175138 CTTTTTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.90
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:39175131 original size:21 final size:21
Alignment explanation
Indices: 39175105--39175144 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39175095 CTACCACAAC
*
39175105 TCTTTTTTCTTTGTTTTTTTT
1 TCTTTTTTCTTTCTTTTTTTT
*
39175126 TCTTTTTTTTTTCTTTTTT
1 TCTTTTTTCTTTCTTTTTT
39175145 GCTATTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.88
Consensus pattern (21 bp):
TCTTTTTTCTTTCTTTTTTTT
Found at i:39176051 original size:22 final size:22
Alignment explanation
Indices: 39176015--39176059 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39176005 TGATGATGGT
* *
39176015 TACTCGGAGGTTTTGAAAATTG
1 TACTCGAAGGATTTGAAAATTG
39176037 TACTCGAAGGATTTGAAAATTG
1 TACTCGAAGGATTTGAAAATTG
39176059 T
1 T
39176060 TCCCAGAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (22 bp):
TACTCGAAGGATTTGAAAATTG
Found at i:39176069 original size:22 final size:21
Alignment explanation
Indices: 39176021--39176070 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
39176011 TGGTTACTCG
* *
39176021 GAGGTTTTGAAAATTGTACTC
1 GAGGATTTGAAAATTGTACCC
*
39176042 GAAGGATTTGAAAATTGTTCCC
1 G-AGGATTTGAAAATTGTACCC
39176064 AGAGGAT
1 -GAGGAT
39176071 ATCAAGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 22 0.92
23 1 0.04
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (21 bp):
GAGGATTTGAAAATTGTACCC
Found at i:39176127 original size:44 final size:45
Alignment explanation
Indices: 39176064--39176212 Score: 128
Period size: 44 Copynumber: 3.4 Consensus size: 45
39176054 AATTGTTCCC
* * *
39176064 AGAGGATATCAAGATTATACTTGAAA-TATTTAGAAA-TCTTACTT
1 AGAGGATTTCAAGATTATACTTCAAAGGATTT-GAAATTCTTACTT
* *
39176108 AGAGGATTTCAAGATTATAC-TCAAAGGATTTGAAATTGTTATTT
1 AGAGGATTTCAAGATTATACTTCAAAGGATTTGAAATTCTTACTT
* * ** * * * *
39176152 GGAGGATTTTAAGATTATAC-TCGGAGGATTTAAAATTATCACCT
1 AGAGGATTTCAAGATTATACTTCAAAGGATTTGAAATTCTTACTT
*
39176196 AGAGGATTTGAA-ATTAT
1 AGAGGATTTCAAGATTAT
39176213 CACCCAAAGG
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
43 13 0.15
44 74 0.85
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (45 bp):
AGAGGATTTCAAGATTATACTTCAAAGGATTTGAAATTCTTACTT
Found at i:39176128 original size:22 final size:21
Alignment explanation
Indices: 39176103--39176212 Score: 85
Period size: 22 Copynumber: 5.0 Consensus size: 21
39176093 TTAGAAATCT
*
39176103 TACTTAGAGGATTTCAAGATTA
1 TACTTAGAGGATTTGAA-ATTA
* * *
39176125 TACTCAAAGGATTTGAAATTGT
1 TACTTAGAGGATTTGAAATT-A
* * *
39176147 TATTTGGAGGATTTTAAGATTA
1 TACTTAGAGGATTTGAA-ATTA
** *
39176169 TACTCGGAGGATTTAAAATTA
1 TACTTAGAGGATTTGAAATTA
*
39176190 TCACCTAGAGGATTTGAAATTA
1 T-ACTTAGAGGATTTGAAATTA
39176212 T
1 T
39176213 CACCCAAAGG
Statistics
Matches: 68, Mismatches: 17, Indels: 6
0.75 0.19 0.07
Matches are distributed among these distances:
21 8 0.12
22 57 0.84
23 3 0.04
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.37
Consensus pattern (21 bp):
TACTTAGAGGATTTGAAATTA
Found at i:39176656 original size:15 final size:15
Alignment explanation
Indices: 39176634--39176666 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
39176624 ATAAAAAATT
39176634 AAAA-AGAAAAAAGA
1 AAAATAGAAAAAAGA
39176648 AAAATAGAAAAATAGA
1 AAAATAGAAAAA-AGA
39176664 AAA
1 AAA
39176667 GGGAAACACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAATAGAAAAAAGA
Found at i:39177260 original size:3 final size:3
Alignment explanation
Indices: 39177252--39177293 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
39177242 GATAAAAAGT
39177252 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39177294 TGGTATCTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39198562 original size:2 final size:2
Alignment explanation
Indices: 39198557--39198582 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39198547 ATATATGGTA
39198557 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
39198583 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:39204259 original size:2 final size:2
Alignment explanation
Indices: 39204252--39204288 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
39204242 CAATTATTCT
*
39204252 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39204289 TTCTTCTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39208951 original size:2 final size:2
Alignment explanation
Indices: 39208944--39208973 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39208934 GGCAGGAAGC
39208944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39208974 GTGTGTCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39221209 original size:45 final size:44
Alignment explanation
Indices: 39221160--39221306 Score: 170
Period size: 45 Copynumber: 3.3 Consensus size: 44
39221150 CATCATGTAT
*
39221160 AAAAACTTGTAACAAGTCATGATTAGCATGTTACACCTTACGTAC
1 AAAAACTTGTGACAAGTCATGATTAGCATGTTACACC-TACGTAC
* * *
39221205 AAAAACTTGTGACAAGTTATGGTTAGCGTGTTATACACC-ACGTAC
1 AAAAACTTGTGACAAGTCATGATTAGCATG-T-TACACCTACGTAC
* * * *
39221250 AAAAACCTATGACAAGTCATGATTAGCTTGTTACACGCTAGGTAC
1 AAAAACTTGTGACAAGTCATGATTAGCATGTTACAC-CTACGTAC
*
39221295 AAAAACCTGTGA
1 AAAAACTTGTGA
39221307 TAAGCTATGG
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
43 5 0.06
44 2 0.02
45 73 0.84
46 1 0.01
47 6 0.07
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (44 bp):
AAAAACTTGTGACAAGTCATGATTAGCATGTTACACCTACGTAC
Found at i:39221344 original size:45 final size:45
Alignment explanation
Indices: 39221171--39221334 Score: 152
Period size: 45 Copynumber: 3.6 Consensus size: 45
39221161 AAAACTTGTA
* * * *
39221171 ACAAGTCATGATTAGCATGTTACAC-CTTACGTACAAAAACTTGTG
1 ACAAGTCATGATTAGCTTGTTACACGC-TAGGTACAAAAACCTATG
* * * * * * *
39221216 ACAAGTTATGGTTAGCGTGTTATACACCACGTACAAAAACCTATG
1 ACAAGTCATGATTAGCTTGTTACACGCTAGGTACAAAAACCTATG
*
39221261 ACAAGTCATGATTAGCTTGTTACACGCTAGGTACAAAAACCTGTG
1 ACAAGTCATGATTAGCTTGTTACACGCTAGGTACAAAAACCTATG
* * * *
39221306 ATAAG-CTATGGTTAGGTTGTTACATGCTA
1 ACAAGTC-ATGATTAGCTTGTTACACGCTA
39221335 TGTTGAAAAA
Statistics
Matches: 98, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
44 1 0.01
45 96 0.98
46 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (45 bp):
ACAAGTCATGATTAGCTTGTTACACGCTAGGTACAAAAACCTATG
Found at i:39228817 original size:15 final size:15
Alignment explanation
Indices: 39228799--39228832 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
39228789 CATCTAAAAT
39228799 CTGATTGATTGATAA
1 CTGATTGATTGATAA
39228814 CTGATTGATTGATAA
1 CTGATTGATTGATAA
39228829 -TGAT
1 CTGAT
39228833 AGGAATACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (15 bp):
CTGATTGATTGATAA
Found at i:39233321 original size:2 final size:2
Alignment explanation
Indices: 39233316--39233343 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39233306 GTGTGTGTGT
39233316 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39233344 GAGGAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39237637 original size:25 final size:25
Alignment explanation
Indices: 39237609--39237662 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
39237599 AATATAATTA
39237609 ATAATTTAAATA-TCAATATTTTAAT
1 ATAATTTAAATACT-AATATTTTAAT
*
39237634 ATAATTTAATTACTAATATTTTAAT
1 ATAATTTAAATACTAATATTTTAAT
39237659 -TAAT
1 ATAAT
39237663 AATATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 22 0.81
26 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
ATAATTTAAATACTAATATTTTAAT
Found at i:39237654 original size:14 final size:14
Alignment explanation
Indices: 39237637--39237679 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
39237627 TTTTAATATA
*
39237637 ATTTAATTACTAAT
1 ATTTAATTAATAAT
39237651 ATTTTAATTAATAAT
1 A-TTTAATTAATAAT
* *
39237666 ATTTTATTTATAAT
1 ATTTAATTAATAAT
39237680 TTAATATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTAATTAATAAT
Found at i:39237657 original size:40 final size:41
Alignment explanation
Indices: 39237607--39237684 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
39237597 TTAATATAAT
39237607 TAATAATTTAAAT-ATCAATATTTTA-ATATAATTTAATTAC
1 TAATAATTTAAATAAT-AATATTTTATATATAATTTAATTAC
* * *
39237647 TAATATTTTAATTAATAATATTTTATTTATAATTTAAT
1 TAATAATTTAAATAATAATATTTTATATATAATTTAAT
39237685 ATTATTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 20 0.61
41 13 0.39
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (41 bp):
TAATAATTTAAATAATAATATTTTATATATAATTTAATTAC
Found at i:39237658 original size:15 final size:15
Alignment explanation
Indices: 39237629--39237671 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
39237619 TATCAATATT
*
39237629 TTAAT-ATAATTTAA
1 TTAATAATATTTTAA
*
39237643 TTACTAATATTTTAA
1 TTAATAATATTTTAA
39237658 TTAATAATATTTTA
1 TTAATAATATTTTA
39237672 TTTATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATAATATTTTAA
Found at i:39238237 original size:17 final size:16
Alignment explanation
Indices: 39238196--39238238 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
39238186 GGTGCCACTT
39238196 AGAGAGAAAATGAGAG
1 AGAGAGAAAATGAGAG
* *
39238212 AGGAAAGAACATGAGAAG
1 A-GAGAGAAAATGAG-AG
39238230 AGAGAGAAA
1 AGAGAGAAA
39238239 GAAGAAGGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
16 1 0.05
17 17 0.81
18 3 0.14
ACGTcount: A:0.58, C:0.02, G:0.35, T:0.05
Consensus pattern (16 bp):
AGAGAGAAAATGAGAG
Found at i:39252090 original size:16 final size:16
Alignment explanation
Indices: 39252069--39252101 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39252059 GAGCTCATAA
39252069 TTTCTCCTCTAGTGTT
1 TTTCTCCTCTAGTGTT
39252085 TTTCTCCTCTAGTGTT
1 TTTCTCCTCTAGTGTT
39252101 T
1 T
39252102 CAGGATCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.12, T:0.58
Consensus pattern (16 bp):
TTTCTCCTCTAGTGTT
Found at i:39263510 original size:16 final size:16
Alignment explanation
Indices: 39263489--39263526 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
39263479 TTTATAGCTA
39263489 CCATCCTTAAATTATT
1 CCATCCTTAAATTATT
39263505 CCATCCTTAAATTATT
1 CCATCCTTAAATTATT
39263521 CCATCC
1 CCATCC
39263527 ATAAGGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (16 bp):
CCATCCTTAAATTATT
Found at i:39267804 original size:16 final size:16
Alignment explanation
Indices: 39267783--39267814 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39267773 ATTATTAACT
39267783 TATCGATTAAATAATA
1 TATCGATTAAATAATA
*
39267799 TATCGATTAATTAATA
1 TATCGATTAAATAATA
39267815 ATTTTCATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
TATCGATTAAATAATA
Found at i:39273937 original size:2 final size:2
Alignment explanation
Indices: 39273930--39273978 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
39273920 GATCCCCCTT
39273930 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
39273972 TA TA TA T
1 TA TA TA T
39273979 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39274112 original size:2 final size:2
Alignment explanation
Indices: 39274105--39274143 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
39274095 NNNNNNNNNN
39274105 TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC T
39274144 TTGGTTTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:39277224 original size:19 final size:17
Alignment explanation
Indices: 39277183--39277226 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
39277173 AAAAAAGATA
39277183 AAAAATAAAACAAAAAG
1 AAAAATAAAACAAAAAG
* *
39277200 CAAAATAGAAAGAAAAAG
1 AAAAATA-AAACAAAAAG
39277218 AAGAAATAA
1 AA-AAATAA
39277227 TACCTGAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 6 0.27
18 11 0.50
19 5 0.23
ACGTcount: A:0.77, C:0.05, G:0.11, T:0.07
Consensus pattern (17 bp):
AAAAATAAAACAAAAAG
Found at i:39277791 original size:56 final size:57
Alignment explanation
Indices: 39277729--39277845 Score: 141
Period size: 56 Copynumber: 2.1 Consensus size: 57
39277719 CGTTGTCAGT
* * *
39277729 AGTGGGGCGA-AAATACCATTGGCGTTTGGGTCAGAGTACTCTATG-TGCATTGCCT-C
1 AGTGGGG-GATAAATACCACTGGCGTGTGGGTCAGAGTACCCT-TGATGCATTGCCTAC
* * *
39277785 AGTGGGGTATAAATACCACTGGTGTGTGGGTCAGAGTACCCTTGATGCGTTGCCTAC
1 AGTGGGGGATAAATACCACTGGCGTGTGGGTCAGAGTACCCTTGATGCATTGCCTAC
39277842 AGTG
1 AGTG
39277846 AGGAGGAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
55 3 0.06
56 44 0.85
57 5 0.10
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (57 bp):
AGTGGGGGATAAATACCACTGGCGTGTGGGTCAGAGTACCCTTGATGCATTGCCTAC
Found at i:39277919 original size:57 final size:55
Alignment explanation
Indices: 39277740--39277919 Score: 150
Period size: 57 Copynumber: 3.2 Consensus size: 55
39277730 GTGGGGCGAA
* * * **
39277740 AATACCATTGGCGTTTGGGTCAGAGTA-CTCTATGTGCATTGCCTCAGTGGGGTATA
1 AATACCACTGGTG-TTGGGTCAGAGTACCT-TATGTGCATTGCTTCAGTGGGGTAGG
* * * *
39277796 AATACCACTGGTGTGTGGGTCAGAGTACCCT-TGATGCGTTGCCTACAGTGAGG-AGG
1 AATACCACTGGTGT-TGGGTCAGAGTACCTTATG-TGCATTG-CTTCAGTGGGGTAGG
** * *
39277852 AAATGGCACTGGTGCTTGCGTCAGAGTACCTTATGTGCATTGTCTTTAGTGGGGTAGG
1 -AATACCACTGGTG-TTGGGTCAGAGTACCTTATGTGCATTG-CTTCAGTGGGGTAGG
39277910 AATACCACTG
1 AATACCACTG
39277920 ATTGTCATGT
Statistics
Matches: 96, Mismatches: 20, Indels: 15
0.73 0.15 0.11
Matches are distributed among these distances:
55 3 0.03
56 31 0.32
57 56 0.58
58 6 0.06
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (55 bp):
AATACCACTGGTGTTGGGTCAGAGTACCTTATGTGCATTGCTTCAGTGGGGTAGG
Found at i:39279287 original size:21 final size:21
Alignment explanation
Indices: 39279263--39279303 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39279253 CTATGAAAAC
* * *
39279263 AATAAATATATGAACAAATAG
1 AATAAAAATATAAAAAAATAG
39279284 AATAAAAATATAAAAAAATA
1 AATAAAAATATAAAAAAATA
39279304 TATAATAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (21 bp):
AATAAAAATATAAAAAAATAG
Found at i:39281255 original size:2 final size:2
Alignment explanation
Indices: 39281248--39281418 Score: 115
Period size: 2 Copynumber: 86.0 Consensus size: 2
39281238 TTTATTATGA
39281248 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
39281289 AT AT AT AT AT AT AT AT AA AT GT CAT NAT GCT ACC AC A- AT TT CAT
1 AT AT AT AT AT AT AT AT AT AT AT -AT -AT -AT A-T AT AT AT AT -AT
* ** * *
39281333 A- AG CC AT CA- AT -T CAA AT A- AA AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
39281372 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39281413 AT AT AT
1 AT AT AT
39281419 TCCTATAATC
Statistics
Matches: 136, Mismatches: 20, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
1 8 0.06
2 121 0.89
3 7 0.05
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:39285548 original size:14 final size:13
Alignment explanation
Indices: 39285515--39285552 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
39285505 TATCATGAAC
39285515 TATATTTTTTATG
1 TATATTTTTTATG
39285528 T-TATTTTATTATG
1 TATATTTT-TTATG
39285541 TATATTTTTTAT
1 TATATTTTTTAT
39285553 TTAAGCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.26
13 11 0.48
14 6 0.26
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (13 bp):
TATATTTTTTATG
Found at i:39286224 original size:2 final size:2
Alignment explanation
Indices: 39286217--39286304 Score: 167
Period size: 2 Copynumber: 43.5 Consensus size: 2
39286207 TATTATAATG
39286217 TA TA TA TA TA TA TA TA TA TA TA TA NTA 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
39286260 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
39286302 TA T
1 TA T
39286305 TTAAACCATA
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 83 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39286349 original size:2 final size:2
Alignment explanation
Indices: 39286342--39286369 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39286332 ATTGATCCTA
39286342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39286370 TACTATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39286865 original size:23 final size:23
Alignment explanation
Indices: 39286839--39286890 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
39286829 TCTTTGAAAC
39286839 TATATATTTATTTACTTTCT-ATT
1 TATATATTT-TTTACTTTCTCATT
* *
39286862 TATA-ATTTTTTGCTTTTTCATT
1 TATATATTTTTTACTTTCTCATT
39286884 TA-ATATT
1 TATATATT
39286891 CCTACCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 9 0.36
22 12 0.48
23 4 0.16
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (23 bp):
TATATATTTTTTACTTTCTCATT
Found at i:39289486 original size:17 final size:16
Alignment explanation
Indices: 39289456--39289488 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
39289446 TACAAAATGA
39289456 TTAAATAAATAAATAG
1 TTAAATAAATAAATAG
39289472 TTAAATAATATAAATAG
1 TTAAATAA-ATAAATAG
39289489 AAAGAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TTAAATAAATAAATAG
Found at i:39290613 original size:16 final size:17
Alignment explanation
Indices: 39290592--39290632 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
39290582 GAATTGAACA
*
39290592 TATGATATTAG-TTTTG
1 TATGATATTAGACTTTG
*
39290608 TATGATATTTGACTTTG
1 TATGATATTAGACTTTG
39290625 TATGATAT
1 TATGATAT
39290633 ATATATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (17 bp):
TATGATATTAGACTTTG
Found at i:39298693 original size:18 final size:17
Alignment explanation
Indices: 39298661--39298706 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
39298651 AACAAACAGA
39298661 AAAT-ATAA-AAAATAG
1 AAATAATAATAAAATAG
39298676 AAATAATAATAAAGATAG
1 AAATAATAATAAA-ATAG
*
39298694 CAA-AATAATAAAA
1 AAATAATAATAAAA
39298707 ATGTTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 12 0.44
18 6 0.22
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (17 bp):
AAATAATAATAAAATAG
Found at i:39307551 original size:2 final size:2
Alignment explanation
Indices: 39307544--39307578 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
39307534 TCGATCCCTC
**
39307544 TG TG TG TG TG AA TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
39307579 AATATTGGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.06, C:0.00, G:0.46, T:0.49
Consensus pattern (2 bp):
TG
Found at i:39317931 original size:20 final size:18
Alignment explanation
Indices: 39317885--39317946 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
39317875 AAAAGTTATT
*
39317885 ATAAAATTTTTATATAAA
1 ATAAAATTTTTAAATAAA
39317903 ATAATAATTTTTAAAATTAAA
1 ATAA-AATTTTT-AAA-TAAA
* *
39317924 TTAAAATTATTT-GATAAA
1 ATAAAATT-TTTAAATAAA
39317942 ATAAA
1 ATAAA
39317947 TTATATAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 12 0.33
19 8 0.22
20 6 0.17
21 10 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
ATAAAATTTTTAAATAAA
Found at i:39324524 original size:10 final size:11
Alignment explanation
Indices: 39324509--39324552 Score: 56
Period size: 10 Copynumber: 4.0 Consensus size: 11
39324499 TGGAAAACTA
39324509 ATTTTC-TTTC
1 ATTTTCTTTTC
39324519 ATTTTCTTTTC
1 ATTTTCTTTTC
39324530 TTATTTTCTTTTC
1 --ATTTTCTTTTC
39324543 A-TTTCTTTTC
1 ATTTTCTTTTC
39324553 TCTTCTTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 15 0.48
11 5 0.16
13 11 0.35
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTCTTTTC
Found at i:39324535 original size:23 final size:23
Alignment explanation
Indices: 39324509--39324553 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
39324499 TGGAAAACTA
39324509 ATTTTC-TTTCATTTTCTTTTCTT
1 ATTTTCTTTTCA-TTTCTTTTCTT
39324532 ATTTTCTTTTCATTTCTTTTCT
1 ATTTTCTTTTCATTTCTTTTCT
39324554 CTTCTTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTTCTTTTCATTTCTTTTCTT
Found at i:39325776 original size:42 final size:42
Alignment explanation
Indices: 39325713--39325827 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 42
39325703 GTGATAGTTA
* *
39325713 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGTTGTGC
1 TGACCCAGCCATGTGCAGTGTAGGAGTGCACATGAGCTGTGC
* *
39325755 TGACCCAGCCATGTGTAGTGTATGAGTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGCAGTGTAGGAGTGCACATGAGCTGTGC
* * *
39325797 CGACCCTGCTATGTGCAGTGT-GGTAGTGCAC
1 TGACCCAGCCATGTGCAGTGTAGG-AGTGCAC
39325828 GTAAGTTGAG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.02
42 62 0.98
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.25
Consensus pattern (42 bp):
TGACCCAGCCATGTGCAGTGTAGGAGTGCACATGAGCTGTGC
Found at i:39325871 original size:2 final size:2
Alignment explanation
Indices: 39325864--39325928 Score: 103
Period size: 2 Copynumber: 32.0 Consensus size: 2
39325854 GGCCGTTGGT
* *
39325864 TA TA TA TA TG TT TA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
39325907 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
39325929 GAGGTTTTGA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 57 0.97
3 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39328041 original size:9 final size:10
Alignment explanation
Indices: 39327999--39328062 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
39327989 ATTTGAAGAT
*
39327999 TTTTTTATG-
1 TTTTTAATGA
*
39328008 TTTTTAAGGGA
1 TTTTTAA-TGA
*
39328019 TTTTTAA-AA
1 TTTTTAATGA
39328028 TTTTTAATGA
1 TTTTTAATGA
*
39328038 TTTTTTATGA
1 TTTTTAATGA
*
39328048 TTTTTAAGGA
1 TTTTTAATGA
39328058 TTTTT
1 TTTTT
39328063 TTTTGTTTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
9 14 0.31
10 24 0.53
11 7 0.16
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (10 bp):
TTTTTAATGA
Found at i:39328063 original size:20 final size:20
Alignment explanation
Indices: 39327999--39328063 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
39327989 ATTTGAAGAT
39327999 TTTTTTATG-TTTTTAAGGGA
1 TTTTTTATGATTTTTAA-GGA
** *
39328019 -TTTTTAAAATTTTTAATGA
1 TTTTTTATGATTTTTAAGGA
39328038 TTTTTTATGATTTTTAAGGA
1 TTTTTTATGATTTTTAAGGA
39328058 TTTTTT
1 TTTTTT
39328064 TTTGTTTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 8 0.22
20 29 0.78
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.63
Consensus pattern (20 bp):
TTTTTTATGATTTTTAAGGA
Found at i:39328063 original size:40 final size:39
Alignment explanation
Indices: 39327999--39328144 Score: 115
Period size: 40 Copynumber: 3.7 Consensus size: 39
39327989 ATTTGAAGAT
39327999 TTTTTTATG-TTTTTAAGGGA-TTTTTAAAATTTTTAATGA
1 TTTTTTATGATTTTTAA-GGATTTTTTAAAATTTTT-ATGA
****
39328038 TTTTTTATGATTTTTAAGGATTTTTTTTTGTTTTGTATGA
1 TTTTTTATGATTTTTAAGGATTTTTTAAAATTTT-TATGA
* *
39328078 TTTTTTAAAGGATTTTT-AGGATTTTTTAAATATATTTAT-A
1 TTTTTT--ATGATTTTTAAGGATTTTTTAAA-ATTTTTATGA
39328118 TTTATTCTATGCATTTTTAA--ATTTTTT
1 TTT-TT-TATG-ATTTTTAAGGATTTTTT
39328145 TATGGATTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
39 12 0.14
40 39 0.45
41 22 0.26
42 13 0.15
ACGTcount: A:0.25, C:0.01, G:0.11, T:0.62
Consensus pattern (39 bp):
TTTTTTATGATTTTTAAGGATTTTTTAAAATTTTTATGA
Found at i:39328513 original size:21 final size:20
Alignment explanation
Indices: 39328489--39328533 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
39328479 TTTTTATGGA
* *
39328489 TTTTTAAGCATTTTTAAGGT
1 TTTTTAAACATATTTAAGGT
*
39328509 CTTTTTAAATATATTTAAGGT
1 -TTTTTAAACATATTTAAGGT
39328530 TTTT
1 TTTT
39328534 AGAGATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.04, G:0.11, T:0.58
Consensus pattern (20 bp):
TTTTTAAACATATTTAAGGT
Found at i:39328526 original size:31 final size:28
Alignment explanation
Indices: 39328491--39328566 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 28
39328481 TTTATGGATT
* *
39328491 TTTAAGCATTTTTAAGGTCTTTTTAAATATA
1 TTTAAG-ATTTTTAAGAT-TTTTTAAAGA-A
*
39328522 TTTAAGGTTTTTAGAGATTTTTTAAAGAA
1 TTTAAGATTTTTA-AGATTTTTTAAAGAA
39328551 TTTGAAGAATTTTTAA
1 TTT-AAG-ATTTTTAA
39328567 CGTATTTGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 4 0.11
30 19 0.50
31 15 0.39
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (28 bp):
TTTAAGATTTTTAAGATTTTTTAAAGAA
Found at i:39328938 original size:10 final size:10
Alignment explanation
Indices: 39328925--39329171 Score: 73
Period size: 10 Copynumber: 23.9 Consensus size: 10
39328915 ATTTTTGACT
39328925 ATTTTTAAGG
1 ATTTTTAAGG
39328935 ATTTTT-A-G
1 ATTTTTAAGG
*
39328943 CTTTTATATA-G
1 ATTTT-TA-AGG
* *
39328954 TTTTTTAAAAG
1 ATTTTT-AAGG
*
39328965 ATTTTTAGGG
1 ATTTTTAAGG
39328975 TATTTTTAAGG
1 -ATTTTTAAGG
*
39328986 ATGTTTAAGG
1 ATTTTTAAGG
**
39328996 -TCATTTTAAAC
1 AT--TTTTAAGG
* *
39329007 ATTTTAAAGTT
1 ATTTTTAAG-G
*
39329018 TTTTTTATA-G
1 ATTTTTA-AGG
*
39329028 ATTTTTAAAG
1 ATTTTTAAGG
39329038 ATTTTTAA-G
1 ATTTTTAAGG
39329047 ATCTTTTCAAGG
1 AT-TTTT-AAGG
* *
39329059 ACTTTCAATGG
1 ATTTTTAA-GG
*
39329070 -TTTTTATGG
1 ATTTTTAAGG
*
39329079 ATTTTTAA-A
1 ATTTTTAAGG
39329088 ATTTTGTAA-G
1 ATTTT-TAAGG
* *
39329098 TTTTTTAAAAAG
1 ATTTTT--AAGG
*
39329110 ATTTTTAAAG
1 ATTTTTAAGG
39329120 -TCTTTTAAGG
1 AT-TTTTAAGG
39329130 CATTTTTAAGG
1 -ATTTTTAAGG
* *
39329141 TTTTCTTAAAGA
1 ATTT-TT-AAGG
*
39329153 ATTTTTAAGC
1 ATTTTTAAGG
39329163 ATTTTTAAG
1 ATTTTTAAG
39329172 TTCCTTTTAA
Statistics
Matches: 179, Mismatches: 32, Indels: 52
0.68 0.12 0.20
Matches are distributed among these distances:
8 5 0.03
9 16 0.09
10 88 0.49
11 53 0.30
12 17 0.09
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.51
Consensus pattern (10 bp):
ATTTTTAAGG
Found at i:39329020 original size:9 final size:10
Alignment explanation
Indices: 39329019--39329214 Score: 73
Period size: 10 Copynumber: 19.0 Consensus size: 10
39329009 TTTAAAGTTT
*
39329019 TTTTTATAGA
1 TTTTTAAAGA
39329029 TTTTTAAAGA
1 TTTTTAAAGA
39329039 TTTTT-AAGA
1 TTTTTAAAGA
*
39329048 TCTTTTCAAGGA
1 T-TTTT-AAAGA
* * * *
39329060 CTTTCAATGG
1 TTTTTAAAGA
**
39329070 TTTTTATGGA
1 TTTTTAAAGA
39329080 TTTTTAAA-A
1 TTTTTAAAGA
*
39329089 TTTTGT-AAGT
1 TTTT-TAAAGA
39329099 TTTTTAAAAAGA
1 TTTTT--AAAGA
39329111 TTTTTAAAG-
1 TTTTTAAAGA
*
39329120 TCTTTTAAGGCA
1 T-TTTTAAAG-A
* *
39329132 TTTTTAAGGT
1 TTTTTAAAGA
39329142 TTTCTTAAAGAA
1 TTT-TTAAAG-A
39329154 TTTTT-AAGCA
1 TTTTTAAAG-A
*
39329164 TTTTT-AAGT
1 TTTTTAAAGA
39329173 TCCTTTTAAAGA
1 T--TTTTAAAGA
* *
39329185 TATTT-CAGA
1 TTTTTAAAGA
*
39329194 TTTTTTAGAGA
1 -TTTTTAAAGA
*
39329205 TTTTTCAAGA
1 TTTTTAAAGA
39329215 AATTTGAAAT
Statistics
Matches: 140, Mismatches: 28, Indels: 36
0.69 0.14 0.18
Matches are distributed among these distances:
9 18 0.13
10 78 0.56
11 25 0.18
12 19 0.14
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.51
Consensus pattern (10 bp):
TTTTTAAAGA
Found at i:39329136 original size:11 final size:11
Alignment explanation
Indices: 39329122--39329171 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
39329112 TTTTAAAGTC
39329122 TTTTAAGGCAT
1 TTTTAAGGCAT
*
39329133 TTTTAAGG-TT
1 TTTTAAGGCAT
* *
39329143 TTCTTAAAGAAT
1 TT-TTAAGGCAT
39329155 TTTTAA-GCAT
1 TTTTAAGGCAT
39329165 TTTTAAG
1 TTTTAAG
39329172 TTCCTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 12 0.38
11 17 0.53
12 3 0.09
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.50
Consensus pattern (11 bp):
TTTTAAGGCAT
Found at i:39329161 original size:22 final size:21
Alignment explanation
Indices: 39329070--39329170 Score: 73
Period size: 22 Copynumber: 4.8 Consensus size: 21
39329060 CTTTCAATGG
* *
39329070 TTTTTATGGATTTTT-AA-AA
1 TTTTTAAGGTTTTTTAAAGAA
*
39329089 TTTTGTAA-GTTTTTTAAAAAGA
1 TTTT-TAAGGTTTTTTAAAGA-A
* * * *
39329111 TTTTTAAAGTCTTTTAAGGCA
1 TTTTTAAGGTTTTTTAAAGAA
39329132 TTTTTAAGGTTTTCTTAAAGAA
1 TTTTTAAGGTTTT-TTAAAGAA
**
39329154 TTTTTAAGCATTTTTAA
1 TTTTTAAGGTTTTTTAA
39329171 GTTCCTTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
19 10 0.16
20 4 0.06
21 20 0.31
22 30 0.47
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (21 bp):
TTTTTAAGGTTTTTTAAAGAA
Found at i:39329182 original size:32 final size:34
Alignment explanation
Indices: 39329122--39329189 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
39329112 TTTTAAAGTC
39329122 TTTTAAGGCATTTTTAAGGTTTTCTTAAAGA-AT
1 TTTTAAGGCATTTTTAAGGTTTTCTTAAAGATAT
39329155 TTTTAA-GCATTTTTAA-GTTCCTT-TTAAAGATAT
1 TTTTAAGGCATTTTTAAGGTT--TTCTTAAAGATAT
39329188 TT
1 TT
39329190 CAGATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
31 3 0.09
32 17 0.53
33 12 0.38
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.51
Consensus pattern (34 bp):
TTTTAAGGCATTTTTAAGGTTTTCTTAAAGATAT
Found at i:39329374 original size:20 final size:20
Alignment explanation
Indices: 39329338--39329382 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
39329328 TTTAAAGATG
*
39329338 TTTAAGGTCATTTTATGCAT
1 TTTAAGGTCATTTTATGAAT
*
39329358 TTTAAGGT-TTTTATATGAAT
1 TTTAAGGTCATTT-TATGAAT
39329378 TTTAA
1 TTTAA
39329383 AGTATTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTAAGGTCATTTTATGAAT
Found at i:39329420 original size:30 final size:29
Alignment explanation
Indices: 39329347--39329420 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
39329337 GTTTAAGGTC
*
39329347 ATTTTATGCATTTTAAGGTTTTTATATGA
1 ATTTTATGCATTTTAAGGGTTTTATATGA
* *
39329376 ATTTTAAAGTATTTTCAAGGGTTTT-TATGAA
1 ATTTT-ATGCATTTT-AAGGGTTTTATATG-A
*
39329407 ATTTTATGGATTTT
1 ATTTTATGCATTTT
39329421 TGAGGTTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
29 5 0.14
30 18 0.49
31 14 0.38
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (29 bp):
ATTTTATGCATTTTAAGGGTTTTATATGA
Found at i:39329538 original size:10 final size:10
Alignment explanation
Indices: 39329491--39329590 Score: 76
Period size: 10 Copynumber: 9.8 Consensus size: 10
39329481 TTTTCCATGA
* *
39329491 ATTTTTATAC
1 ATTTTTAAAG
39329501 ATTTTTAAAG
1 ATTTTTAAAG
* *
39329511 TCTTTTTAAGG
1 -ATTTTTAAAG
*
39329522 ATATTTAAAG
1 ATTTTTAAAG
* *
39329532 TTTTTTAGAG
1 ATTTTTAAAG
*
39329542 ATTTTTTAAG
1 ATTTTTAAAG
* *
39329552 AAATTTGAAAG
1 -ATTTTTAAAG
39329563 ATTTTTAAAG
1 ATTTTTAAAG
39329573 -TTTTTAAGAG
1 ATTTTTAA-AG
39329583 ATTTTTAA
1 ATTTTTAA
39329591 TTTGTTTAAT
Statistics
Matches: 68, Mismatches: 18, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
9 7 0.10
10 39 0.57
11 22 0.32
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (10 bp):
ATTTTTAAAG
Found at i:39329599 original size:20 final size:20
Alignment explanation
Indices: 39329501--39329590 Score: 85
Period size: 20 Copynumber: 4.4 Consensus size: 20
39329491 ATTTTTATAC
39329501 ATTTTTAAAGTCTTTTTAAG-G
1 ATTTTTAAAG--TTTTTAAGAG
* *
39329522 ATATTTAAAGTTTTTTAGAG
1 ATTTTTAAAGTTTTTAAGAG
** *
39329542 ATTTTTTAAGAAATTTGAA-AG
1 A-TTTTTAA-AGTTTTTAAGAG
39329563 ATTTTTAAAGTTTTTAAGAG
1 ATTTTTAAAGTTTTTAAGAG
39329583 ATTTTTAA
1 ATTTTTAA
39329591 TTTGTTTAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
19 13 0.24
20 19 0.35
21 18 0.33
22 5 0.09
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (20 bp):
ATTTTTAAAGTTTTTAAGAG
Found at i:39330535 original size:35 final size:33
Alignment explanation
Indices: 39330412--39330537 Score: 103
Period size: 35 Copynumber: 3.7 Consensus size: 33
39330402 TTAGGTGTTG
* * * *
39330412 GGTTTTAGTTGATCTTGTGAAAAATCATTGTTGTA
1 GGTTTTGGTTGAGCTTTTGAAAAACCATTG-TG-A
* *
39330447 GGTTGTGGTTGAGCCTTTGAAAAACCACTT-TGA
1 GGTTTTGGTTGAGCTTTTGAAAAACCA-TTGTGA
* **
39330480 -GTCTTGGTTGAGCTCGTGAAAAACCATTGTGAAA
1 GGTTTTGGTTGAGCTTTTGAAAAACCATTGTG--A
*
39330514 GGTTTTGGTTCAGCTTTTGAAAAA
1 GGTTTTGGTTGAGCTTTTGAAAAA
39330538 TCACTTTGGG
Statistics
Matches: 71, Mismatches: 15, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
31 2 0.03
32 23 0.32
33 1 0.01
34 3 0.04
35 40 0.56
36 2 0.03
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.37
Consensus pattern (33 bp):
GGTTTTGGTTGAGCTTTTGAAAAACCATTGTGA
Found at i:39330585 original size:67 final size:67
Alignment explanation
Indices: 39330409--39330596 Score: 209
Period size: 67 Copynumber: 2.8 Consensus size: 67
39330399 AAGTTAGGTG
** * * * *
39330409 TTGGGTTTTAGTTGATCTTGTGAAAAATCATTGTTG-TAGGTTGTGGTTGAGCCTTTGAAAAACC
1 TTGGGTTTTAGTTGATCCCGTGAAAAACCATTG-TGAAAGGTTTTGGTTCAGCCTTTGAAAAACC
39330473 ACT
65 ACT
* * * * * * *
39330476 TTGAGTCTTGGTTGAGCTCGTGAAAAACCATTGTGAAAGGTTTTGGTTCAGCTTTTGAAAAATCA
1 TTGGGTTTTAGTTGATCCCGTGAAAAACCATTGTGAAAGGTTTTGGTTCAGCCTTTGAAAAACCA
39330541 CT
66 CT
* *
39330543 TTGGGTTTTAGTTGATCCCG-GTAAAAACCATTGTGAAAGGTTTTGTTTAAGCCT
1 TTGGGTTTTAGTTGATCCCGTG-AAAAACCATTGTGAAAGGTTTTGGTTCAGCCT
39330597 GGTAAAAGCC
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
66 3 0.03
67 97 0.97
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.38
Consensus pattern (67 bp):
TTGGGTTTTAGTTGATCCCGTGAAAAACCATTGTGAAAGGTTTTGGTTCAGCCTTTGAAAAACCA
CT
Found at i:39340601 original size:7 final size:7
Alignment explanation
Indices: 39340589--39340686 Score: 99
Period size: 7 Copynumber: 13.7 Consensus size: 7
39340579 GTTTTGGTTT
39340589 GGTTTAG
1 GGTTTAG
39340596 GGTTTAG
1 GGTTTAG
*
39340603 GGTTAAG
1 GGTTTAG
*
39340610 GGCTTAG
1 GGTTTAG
39340617 GGTTTTAG
1 GG-TTTAG
* *
39340625 GGGTTGG
1 GGTTTAG
39340632 GGTTTAG
1 GGTTTAG
*
39340639 GGGTTAGG
1 GGTTTA-G
39340647 GGTTTAG
1 GGTTTAG
39340654 AGG-TTAG
1 -GGTTTAG
39340661 GGTTTAG
1 GGTTTAG
*
39340668 GGTTCAG
1 GGTTTAG
*
39340675 GATTTAG
1 GGTTTAG
39340682 GGTTT
1 GGTTT
39340687 TTTTTTATGC
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
6 2 0.03
7 57 0.78
8 14 0.19
ACGTcount: A:0.15, C:0.02, G:0.45, T:0.38
Consensus pattern (7 bp):
GGTTTAG
Found at i:39340634 original size:29 final size:29
Alignment explanation
Indices: 39340589--39340669 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
39340579 GTTTTGGTTT
* *
39340589 GGTTTAGGGTTTAGGGTTAAGGGCTTAGG
1 GGTTTAGGGGTTAGGGTTTAGGGCTTAGG
* * *
39340618 GTTTTAGGGGTTGGGGTTTAGGGGTTAGG
1 GGTTTAGGGGTTAGGGTTTAGGGCTTAGG
*
39340647 GGTTTAGAGGTTAGGGTTTAGGG
1 GGTTTAGGGGTTAGGGTTTAGGG
39340670 TTCAGGATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.15, C:0.01, G:0.48, T:0.36
Consensus pattern (29 bp):
GGTTTAGGGGTTAGGGTTTAGGGCTTAGG
Found at i:39342655 original size:7 final size:7
Alignment explanation
Indices: 39342638--39342885 Score: 200
Period size: 7 Copynumber: 35.9 Consensus size: 7
39342628 CCGAGGCTTG
*
39342638 GGGTTTG
1 GGGTTTA
*
39342645 GGGTTCA
1 GGGTTTA
*
39342652 GGG-TTC
1 GGGTTTA
39342658 GGGTTTA
1 GGGTTTA
39342665 GGAG-TTA
1 GG-GTTTA
39342672 GGGTTTA
1 GGGTTTA
39342679 GGGTTTA
1 GGGTTTA
39342686 GGGTTTA
1 GGGTTTA
**
39342693 GGGGCTA
1 GGGTTTA
* *
39342700 AGATTTA
1 GGGTTTA
*
39342707 GGGGTTA
1 GGGTTTA
*
39342714 GGGGTTA
1 GGGTTTA
*
39342721 GGGTTAA
1 GGGTTTA
39342728 GGG-TTA
1 GGGTTTA
*
39342734 AGGTTTA
1 GGGTTTA
*
39342741 GGGGTTA
1 GGGTTTA
*
39342748 GGGGTTA
1 GGGTTTA
*
39342755 GGGGTTA
1 GGGTTTA
39342762 GGG-TTA
1 GGGTTTA
39342768 GGGTTTA
1 GGGTTTA
*
39342775 GGGATTA
1 GGGTTTA
*
39342782 GGGGTTA
1 GGGTTTA
39342789 GGG-TTA
1 GGGTTTA
*
39342795 GGGGTTA
1 GGGTTTA
*
39342802 GGGTGTA
1 GGGTTTA
* *
39342809 GAGTGTA
1 GGGTTTA
*
39342816 GGGTTGA
1 GGGTTTA
*
39342823 GGGTTGA
1 GGGTTTA
*
39342830 GGGTTAA
1 GGGTTTA
39342837 GGGTTTA
1 GGGTTTA
*
39342844 GGGGTTA
1 GGGTTTA
*
39342851 GGGGTTA
1 GGGTTTA
*
39342858 GGGGTTA
1 GGGTTTA
39342865 GGGGTTTA
1 -GGGTTTA
*
39342873 GGGTTAA
1 GGGTTTA
39342880 GGGTTT
1 GGGTTT
39342886 TTTTTTATAC
Statistics
Matches: 200, Mismatches: 34, Indels: 14
0.81 0.14 0.06
Matches are distributed among these distances:
6 21 0.10
7 172 0.86
8 7 0.04
ACGTcount: A:0.17, C:0.01, G:0.49, T:0.33
Consensus pattern (7 bp):
GGGTTTA
Found at i:39342683 original size:34 final size:33
Alignment explanation
Indices: 39342645--39342882 Score: 174
Period size: 34 Copynumber: 6.7 Consensus size: 33
39342635 TTGGGGTTTG
* * *
39342645 GGGTTCAGGGTTCGGGTTTAGGAGTTAGGGTTTA
1 GGGTT-AGGGTTAGGGTTTAGGGGTTAGGGGTTA
** * **
39342679 GGGTTTAGGGTTTAGGGGCTAAGATTTAGGGGTTA
1 GGG-TTAGGG-TTAGGGTTTAGGGGTTAGGGGTTA
39342714 GGGGTTAGGGTTAAGGGTTAAGGTTTAGGGGTTAGGGGTTA
1 -GGGTTAGGGTT-A--G----GGTTTAGGGGTTAGGGGTTA
*
39342755 GGGGTTAGGGTTAGGGTTTAGGGATTAGGGGTTA
1 -GGGTTAGGGTTAGGGTTTAGGGGTTAGGGGTTA
* *
39342789 GGGTTAGGGGTTAGGGTGTA-GAGTGTA-GGGTTGA
1 GGGTTA-GGGTTAGGGTTTAGGGGT-TAGGGGTT-A
39342823 GGGTTGAGGGTTAAGGGTTTAGGGGTTAGGGGTTA
1 GGGTT-AGGGTT-AGGGTTTAGGGGTTAGGGGTTA
*
39342858 GGGGTTAGGGGTTTAGGGTTAAGGG
1 -GGGTTA-GGG-TTAGGGTTTAGGG
39342883 TTTTTTTTTA
Statistics
Matches: 166, Mismatches: 18, Indels: 38
0.75 0.08 0.17
Matches are distributed among these distances:
33 13 0.08
34 53 0.32
35 39 0.23
36 29 0.17
37 3 0.02
38 1 0.01
40 1 0.01
41 27 0.16
ACGTcount: A:0.18, C:0.01, G:0.49, T:0.32
Consensus pattern (33 bp):
GGGTTAGGGTTAGGGTTTAGGGGTTAGGGGTTA
Found at i:39349374 original size:7 final size:7
Alignment explanation
Indices: 39349356--39349632 Score: 260
Period size: 7 Copynumber: 39.7 Consensus size: 7
39349346 TTTTTTGTTT
39349356 GGTTTA-
1 GGTTTAG
39349362 GGTTTAG
1 GGTTTAG
*
39349369 GGTTTAA
1 GGTTTAG
39349376 GGTTTAGG
1 GGTTTA-G
**
39349384 GGTTCGG
1 GGTTTAG
39349391 GGTTT-G
1 GGTTTAG
*
39349397 GGGTTAG
1 GGTTTAG
39349404 GGTTTAG
1 GGTTTAG
39349411 GGTTTAG
1 GGTTTAG
39349418 GGATTTAAG
1 GG-TTT-AG
* *
39349427 GTTTTAA
1 GGTTTAG
39349434 GGTTTAG
1 GGTTTAG
*
39349441 GTTTTAG
1 GGTTTAG
*
39349448 GGTTTGG
1 GGTTTAG
39349455 GGTTTAG
1 GGTTTAG
39349462 GGTTTAG
1 GGTTTAG
39349469 GGTTTA-
1 GGTTTAG
*
39349475 GGTTTAA
1 GGTTTAG
*
39349482 GGTTTTG
1 GGTTTAG
39349489 GGTTTAG
1 GGTTTAG
*
39349496 GGTTTTG
1 GGTTTAG
*
39349503 GGTTTTG
1 GGTTTAG
39349510 GGTTTAG
1 GGTTTAG
*
39349517 GGTTTGG
1 GGTTTAG
39349524 GGTTTAG
1 GGTTTAG
39349531 GGTTTAG
1 GGTTTAG
39349538 GGTTTAG
1 GGTTTAG
39349545 GG-TTAG
1 GGTTTAG
* *
39349551 GGGTTGG
1 GGTTTAG
39349558 GGTTTAG
1 GGTTTAG
*
39349565 AGTTT-G
1 GGTTTAG
*
39349571 GAGTTTGG
1 G-GTTTAG
*
39349579 GGTTTGG
1 GGTTTAG
*
39349586 GGGTT-G
1 GGTTTAG
*
39349592 AGGTTGAG
1 -GGTTTAG
*
39349600 GGTTGAG
1 GGTTTAG
*
39349607 GGTTGAG
1 GGTTTAG
*
39349614 GGGTTAG
1 GGTTTAG
39349621 GGTTTAG
1 GGTTTAG
39349628 GGTTT
1 GGTTT
39349633 TTTTTTTTAA
Statistics
Matches: 227, Mismatches: 33, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
6 25 0.11
7 186 0.82
8 13 0.06
9 3 0.01
ACGTcount: A:0.13, C:0.00, G:0.45, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:39356417 original size:6 final size:7
Alignment explanation
Indices: 39356395--39356740 Score: 329
Period size: 7 Copynumber: 49.7 Consensus size: 7
39356385 TTTTTTTTTT
39356395 GGGTTTA
1 GGGTTTA
39356402 GGGTTTA
1 GGGTTTA
39356409 GGG-TTA
1 GGGTTTA
*
39356415 GGGGTTTG
1 -GGGTTTA
39356423 GGGTTT-
1 GGGTTTA
*
39356429 GGGTTTTG
1 GGG-TTTA
*
39356437 GGGTTTG
1 GGGTTTA
*
39356444 GGGTTTTT
1 GGG-TTTA
*
39356452 GGGTTTG
1 GGGTTTA
*
39356459 GGGTTTTT
1 GGG-TTTA
*
39356467 GGGTTTG
1 GGGTTTA
*
39356474 GGGTTTT
1 GGGTTTA
* *
39356481 TGGTTTT
1 GGGTTTA
*
39356488 GGGTTTT
1 GGGTTTA
*
39356495 GGGTTTTG
1 GGG-TTTA
39356503 GGGTTTA
1 GGGTTTA
39356510 GGGTTTA
1 GGGTTTA
39356517 GGGTTT-
1 GGGTTTA
*
39356523 --TTTTA
1 GGGTTTA
39356528 GGGTTTTTTA
1 GGG---TTTA
39356538 GGGTTTA
1 GGGTTTA
39356545 GGGTTTA
1 GGGTTTA
39356552 GGGTTTA
1 GGGTTTA
* *
39356559 TGTTTTA
1 GGGTTTA
39356566 GGGTTTA
1 GGGTTTA
39356573 GGGTTTA
1 GGGTTTA
39356580 -GG-TTA
1 GGGTTTA
39356585 GGGTTTA
1 GGGTTTA
39356592 GGG-TTA
1 GGGTTTA
39356598 GGGTTTA
1 GGGTTTA
39356605 GGGGTTT-
1 -GGGTTTA
*
39356612 -GGTTTT
1 GGGTTTA
*
39356618 GGGTTTG
1 GGGTTTA
*
39356625 GGGTTTG
1 GGGTTTA
*
39356632 GGGTTTTG
1 GGG-TTTA
*
39356640 GGGTTTG
1 GGGTTTA
39356647 GGGTTT-
1 GGGTTTA
39356653 GGGTTTA
1 GGGTTTA
39356660 GGGTTTA
1 GGGTTTA
39356667 GGG-TTA
1 GGGTTTA
*
39356673 GGGGTTA
1 GGGTTTA
39356680 GGGTTTA
1 GGGTTTA
39356687 GGGTTTA
1 GGGTTTA
39356694 GGGTTTA
1 GGGTTTA
39356701 GGGTTTA
1 GGGTTTA
39356708 GGGTTTA
1 GGGTTTA
39356715 GGGTTTA
1 GGGTTTA
39356722 GGGTTTA
1 GGGTTTA
39356729 GGGTTTA
1 GGGTTTA
39356736 GGGTT
1 GGGTT
39356741 NNNNNNNNNN
Statistics
Matches: 299, Mismatches: 18, Indels: 44
0.83 0.05 0.12
Matches are distributed among these distances:
4 3 0.01
5 8 0.03
6 28 0.09
7 217 0.73
8 36 0.12
10 7 0.02
ACGTcount: A:0.08, C:0.00, G:0.45, T:0.47
Consensus pattern (7 bp):
GGGTTTA
Found at i:39356529 original size:11 final size:11
Alignment explanation
Indices: 39356513--39356543 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
39356503 GGGTTTAGGG
39356513 TTTAGGGTTTT
1 TTTAGGGTTTT
39356524 TTTAGGG-TTT
1 TTTAGGGTTTT
39356534 TTTAGGGTTT
1 TTTAGGGTTT
39356544 AGGGTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.10, C:0.00, G:0.29, T:0.61
Consensus pattern (11 bp):
TTTAGGGTTTT
Found at i:39357268 original size:7 final size:7
Alignment explanation
Indices: 39357250--39357404 Score: 98
Period size: 7 Copynumber: 23.3 Consensus size: 7
39357240 NNNNNNNGTG
39357250 TTAGGG-
1 TTAGGGT
39357256 TTAGGGT
1 TTAGGGT
*
39357263 TTAGGGG
1 TTAGGGT
39357270 TTAGGGT
1 TTAGGGT
* * *
39357277 ATA-AGA
1 TTAGGGT
*
39357283 TTA-AGT
1 TTAGGGT
39357289 TTA-GGT
1 TTAGGGT
39357295 TTAGGGT
1 TTAGGGT
39357302 TTAGGGGT
1 TTA-GGGT
***
39357310 CGGGGGT
1 TTAGGGT
*
39357317 TTGGGGT
1 TTAGGGT
39357324 TGT-GGGT
1 T-TAGGGT
* *
39357331 TTGGGGG
1 TTAGGGT
39357338 TTAGGAG-
1 TTAGG-GT
39357345 TTA-GGT
1 TTAGGGT
*
39357351 TGAGGGT
1 TTAGGGT
39357358 TTAGGGT
1 TTAGGGT
39357365 TTAGGGT
1 TTAGGGT
39357372 TTAGGGT
1 TTAGGGT
39357379 TTA-GGT
1 TTAGGGT
39357385 TTA-GGT
1 TTAGGGT
39357391 TTA-GGT
1 TTAGGGT
39357397 TT-GGGT
1 TTAGGGT
39357403 TT
1 TT
39357405 TTTTTTTTTT
Statistics
Matches: 123, Mismatches: 17, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
5 1 0.01
6 45 0.37
7 71 0.58
8 6 0.05
ACGTcount: A:0.15, C:0.01, G:0.45, T:0.40
Consensus pattern (7 bp):
TTAGGGT
Found at i:39365160 original size:11 final size:11
Alignment explanation
Indices: 39365144--39365168 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39365134 TGCCACTTTT
39365144 TTTTTTTTTGG
1 TTTTTTTTTGG
39365155 TTTTTTTTTGG
1 TTTTTTTTTGG
39365166 TTT
1 TTT
39365169 GGTTTTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTGG
Found at i:39365161 original size:16 final size:16
Alignment explanation
Indices: 39365140--39365175 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
39365130 CGTTTGCCAC
*
39365140 TTTTTTTTT-TTTTGG
1 TTTTTTTTTGGTTTGG
39365155 TTTTTTTTTGGTTTGG
1 TTTTTTTTTGGTTTGG
39365171 TTTTT
1 TTTTT
39365176 CAGGTTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTGGTTTGG
Found at i:39365196 original size:7 final size:7
Alignment explanation
Indices: 39365184--39365286 Score: 134
Period size: 7 Copynumber: 14.7 Consensus size: 7
39365174 TTCAGGTTTT
39365184 GGTTTAG
1 GGTTTAG
39365191 GGTTTAG
1 GGTTTAG
39365198 GGTTTAG
1 GGTTTAG
39365205 GGTTTAG
1 GGTTTAG
*
39365212 GGGTTAG
1 GGTTTAG
*
39365219 GGGTTAG
1 GGTTTAG
*
39365226 GGGTTAG
1 GGTTTAG
*
39365233 GGGTTAG
1 GGTTTAG
*
39365240 GGTTTGG
1 GGTTTAG
*
39365247 GGTTTGG
1 GGTTTAG
*
39365254 GGTTTGG
1 GGTTTAG
*
39365261 GGTTTGG
1 GGTTTAG
39365268 GGTTTAG
1 GGTTTAG
39365275 GGTTTAG
1 GGTTTAG
39365282 GGTTT
1 GGTTT
39365287 TTTTTTTTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 92 1.00
ACGTcount: A:0.10, C:0.00, G:0.50, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Done.