Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 176 of 207
Found at i:54225225 original size:18 final size:18
Alignment explanation
Indices: 54225202--54225236 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
54225192 TTTACTAAAT
54225202 TTTTTTATCTAA-ATTTTA
1 TTTTTTAT-TAATATTTTA
54225220 TTTTTTATTAATATTTT
1 TTTTTTATTAATATTTT
54225237 CAAGAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTATTAATATTTTA
Found at i:54231209 original size:12 final size:11
Alignment explanation
Indices: 54231194--54231234 Score: 57
Period size: 10 Copynumber: 3.7 Consensus size: 11
54231184 CTTAACTTAA
*
54231194 ATTATATTTCAT
1 ATTATATAT-AT
54231206 ATTATATATAT
1 ATTATATATAT
54231217 A-TATATATAT
1 ATTATATATAT
54231227 ATTATATA
1 ATTATATA
54231235 AAAGAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.37
11 9 0.33
12 8 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTATATATAT
Found at i:54231955 original size:21 final size:21
Alignment explanation
Indices: 54231904--54231957 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
54231894 TAATTATTTA
54231904 AAATTTAA-AATTACAATATT
1 AAATTTAATAATTACAATATT
*
54231924 AAATATAAATAATTA-AATATGT
1 AAAT-TTAATAATTACAATAT-T
*
54231946 ACATTTAATAAT
1 AAATTTAATAAT
54231958 GTCGAACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 15 0.54
22 9 0.32
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTTAATAATTACAATATT
Found at i:54246355 original size:22 final size:22
Alignment explanation
Indices: 54246330--54246405 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
54246320 TTACACTACA
* * *
54246330 GTGCCTTCTAATTTGCACTTTG
1 GTGCCTACTAATTCGCACTTCG
*
54246352 GTGCCTACTGATTCGCACTTCG
1 GTGCCTACTAATTCGCACTTCG
** *
54246374 GTGCCTACT-GCTCAGCACTTCA
1 GTGCCTACTAATTC-GCACTTCG
54246396 GTGCCTACTA
1 GTGCCTACTA
54246406 TTAAAGCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 2 0.04
22 43 0.96
ACGTcount: A:0.16, C:0.30, G:0.20, T:0.34
Consensus pattern (22 bp):
GTGCCTACTAATTCGCACTTCG
Found at i:54250857 original size:22 final size:22
Alignment explanation
Indices: 54250829--54250874 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
54250819 TAAATGTGTT
54250829 AAAATAATTA-TACATAAAATAA
1 AAAATAATTAGTACA-AAAATAA
*
54250851 AAAATAATTAGTATAAAAATAA
1 AAAATAATTAGTACAAAAATAA
54250873 AA
1 AA
54250875 CCTCTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAATAATTAGTACAAAAATAA
Found at i:54255801 original size:52 final size:51
Alignment explanation
Indices: 54255740--54255845 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 51
54255730 ATAATATGTA
* *
54255740 ATTGCAACTAACGATATAATTTTA-AATTTATTATTGAGCTTTTGATTCATGAT
1 ATTGCAACTAACGATATAATTTTATAA---ATTATTCACCTTTTGATTCATGAT
*
54255793 ATTG-AACTAACGATATAATTTTATAAATTGTTCACCTTTTGATTCATGAT
1 ATTGCAACTAACGATATAATTTTATAAATTATTCACCTTTTGATTCATGAT
54255843 ATT
1 ATT
54255846 AAAAAAGAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
50 24 0.49
52 19 0.39
53 6 0.12
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (51 bp):
ATTGCAACTAACGATATAATTTTATAAATTATTCACCTTTTGATTCATGAT
Found at i:54256551 original size:91 final size:91
Alignment explanation
Indices: 54256404--54256612 Score: 319
Period size: 91 Copynumber: 2.3 Consensus size: 91
54256394 TTGATTTTAG
* *
54256404 TAAATTCATATAAGAACATTTTATTATTAAGAAATTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAAATTTATGAAATTATATATCATTATTAAATTAT
* * *
54256469 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* * *
54256496 TAAATTCATATAAGAAAATTTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAAATTTATGAAATTATATATCATTATTAAATTATA
54256561 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
54256587 CAAATTCATATAAGATAATTTATTAT
1 TAAATTCATATAAGAAAATTTATTAT
54256613 TTATAATTAT
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 91 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAAATTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:54256578 original size:47 final size:46
Alignment explanation
Indices: 54256438--54256579 Score: 118
Period size: 47 Copynumber: 3.1 Consensus size: 46
54256428 TATTAAGAAA
* *
54256438 TTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTAT
1 TTTATGAAATTATATATTATTATTAAATTATA-TTAATAATAATTAT
* * **
54256485 TTTA--AATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAT-A--AT
1 TTTATGAAAT-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTAT
54256529 TTTATGAAATTATATATTATTATTAAATTATATGTAATAATAATTAT
1 TTTATGAAATTATATATTATTATTAAATTATAT-TAATAATAATTAT
54256576 TTTA
1 TTTA
54256580 AATTATACAA
Statistics
Matches: 72, Mismatches: 10, Indels: 26
0.67 0.09 0.24
Matches are distributed among these distances:
42 6 0.08
43 4 0.06
44 12 0.17
45 13 0.18
46 12 0.17
47 16 0.22
48 3 0.04
49 6 0.08
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (46 bp):
TTTATGAAATTATATATTATTATTAAATTATATTAATAATAATTAT
Found at i:54256580 original size:26 final size:28
Alignment explanation
Indices: 54256526--54256586 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
54256516 TATTATCAAT
* *
54256526 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
54256554 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
54256580 AATTATA
1 AATTATA
54256587 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:54256751 original size:120 final size:120
Alignment explanation
Indices: 54256627--54257404 Score: 1375
Period size: 120 Copynumber: 6.5 Consensus size: 120
54256617 AATTATTTTA
* * *
54256627 AATTTTATTAAATCATATATTTTAAATAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAAATATAATATATTTAATAATAATTATGTT-AAATTATATTT
54256691 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
54256747 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAAATATAATATATTTAATAATAATTATGTTAAATTATATTTT
54256812 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
54256867 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAAATATAATATATTTAATAATAATTATGTTAAATTATATTTT
54256932 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
54256987 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAAATATAATATATTTAATAATAATTATGTTAAATTATATTTT
54257052 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
54257107 AATTTTATTAAATTATATA-TTTAAATTATAATATATTTAATAATAATTATGTTAAATTATATTT
1 AATTTTATTAAATTATATATTTTAAA-TATAATATATTTAATAATAATTATGTTAAATTATATTT
*
54257171 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
54257227 AATTTTATTAAATTATATA-TTTAAATTATAATATATTTAATAATAATTATGTTAAATTATATTT
1 AATTTTATTAAATTATATATTTTAAA-TATAATATATTTAATAATAATTATGTTAAATTATATTT
* *
54257291 TATAGTATCATATATTATGATTTGAGTTAATTCATATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
54257347 AATTTTATTAAATTATATA-TTTAAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAAA-TATAATATATTTAATAATAATTATG-TTAAAT
54257405 ATGATTAAAT
Statistics
Matches: 646, Mismatches: 9, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
119 5 0.01
120 633 0.98
121 8 0.01
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAAATATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:54256787 original size:15 final size:15
Alignment explanation
Indices: 54256752--54256803 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
54256742 TTAAGAATTT
*
54256752 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54256766 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54256780 TATTTAATAATAAT-
1 TATTTAATTATAATA
54256794 TATGTTAATT
1 TAT-TTAATT
54256804 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54256907 original size:15 final size:15
Alignment explanation
Indices: 54256872--54256923 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
54256862 TTAAGAATTT
*
54256872 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54256886 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54256900 TATTTAATAATAAT-
1 TATTTAATTATAATA
54256914 TATGTTAATT
1 TAT-TTAATT
54256924 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54257027 original size:15 final size:15
Alignment explanation
Indices: 54256992--54257043 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
54256982 TTAAGAATTT
*
54256992 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54257006 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54257020 TATTTAATAATAAT-
1 TATTTAATTATAATA
54257034 TATGTTAATT
1 TAT-TTAATT
54257044 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54257140 original size:16 final size:16
Alignment explanation
Indices: 54257121--54257167 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
54257111 TTATTAAATT
54257121 ATATATTTAAATTATA
1 ATATATTTAAATTATA
*
54257137 ATATATTT-AATAATA
1 ATATATTTAAATTATA
54257152 AT-TATGTTAAATTATA
1 ATATAT-TTAAATTATA
54257168 TTTTATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
16 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATATTTAAATTATA
Found at i:54257260 original size:16 final size:16
Alignment explanation
Indices: 54257241--54257287 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
54257231 TTATTAAATT
54257241 ATATATTTAAATTATA
1 ATATATTTAAATTATA
*
54257257 ATATATTT-AATAATA
1 ATATATTTAAATTATA
54257272 AT-TATGTTAAATTATA
1 ATATAT-TTAAATTATA
54257288 TTTTATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
16 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATATTTAAATTATA
Found at i:54257380 original size:16 final size:16
Alignment explanation
Indices: 54257361--54257405 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
54257351 TTATTAAATT
*
54257361 ATATATTTAAATTATA
1 ATATATTTAAATAATA
54257377 ATATATTT-AATAATA
1 ATATATTTAAATAATA
*
54257392 ATTATGTTTAAATA
1 A-TATATTTAAATA
54257406 TGATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 14 0.56
17 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATATTTAAATAATA
Found at i:54257641 original size:16 final size:16
Alignment explanation
Indices: 54257616--54257648 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54257606 TTGATTTGCT
54257616 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
54257632 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
54257648 A
1 A
54257649 ATATAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.36, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:54261444 original size:10 final size:10
Alignment explanation
Indices: 54261425--54261455 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
54261415 AATAAAAGCT
*
54261425 ATAAATATTA
1 ATAAAAATTA
54261435 ATAAAAATTA
1 ATAAAAATTA
54261445 ATAAAAATTA
1 ATAAAAATTA
54261455 A
1 A
54261456 AAATTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAAAAATTA
Found at i:54261458 original size:17 final size:18
Alignment explanation
Indices: 54261435--54261476 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
54261425 ATAAATATTA
54261435 ATAAAAATTA-ATAAAAAT
1 ATAAAAATTAGA-AAAAAT
54261453 -TAAAAATTAGAAAAAAT
1 ATAAAAATTAGAAAAAAT
54261470 ATAAAAA
1 ATAAAAA
54261477 ATGTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
ATAAAAATTAGAAAAAAT
Found at i:54261873 original size:18 final size:19
Alignment explanation
Indices: 54261824--54261865 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
54261814 TTCAAGTTTT
*
54261824 TTTAA-AATTTTTATTAAAA
1 TTTAATAATTTTT-CTAAAA
54261843 TTTAATAATTTTTCTAAAA
1 TTTAATAATTTTTCTAAAA
54261862 TTTA
1 TTTA
54261866 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAATAATTTTTCTAAAA
Found at i:54261881 original size:18 final size:19
Alignment explanation
Indices: 54261824--54261882 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
54261814 TTCAAGTTTT
54261824 TTTAA-AATTTTTATTAAAA
1 TTTAATAATTTTT-TTAAAA
*
54261843 TTTAATAATTTTTCTAAAA
1 TTTAATAATTTTTTTAAAA
* *
54261862 TTT-ATTATTTTTTTATAA
1 TTTAATAATTTTTTTAAAA
54261880 TTT
1 TTT
54261883 TTTCTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.43
19 13 0.37
20 7 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAATAATTTTTTTAAAA
Found at i:54262062 original size:85 final size:86
Alignment explanation
Indices: 54261917--54262074 Score: 201
Period size: 85 Copynumber: 1.8 Consensus size: 86
54261907 GGCATAATTG
* ** * *
54261917 TTTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTATGAAAGTTCAAGTACCCAATTGAGTG
1 TTTTTTTTGAAAAAGTTTGAGGACCTTTTTGATGCATTATAAAAATTCAAGTACCCAATTGAGTG
54261982 -AAAAAAAGGGTCTTAATAAC
66 CAAAAAAAGGGTCTTAATAAC
* * * ****
54262002 TTTTTTTTGAAGAAGTTTGAGGACCTTTTTGATGCATTTTAAAAATTTAAGTGTTTAATTGAGTG
1 TTTTTTTTGAAAAAGTTTGAGGACCTTTTTGATGCATTATAAAAATTCAAGTACCCAATTGAGTG
54262067 CAAAAAAA
66 CAAAAAAA
54262075 AAAAGAGAGG
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
85 53 0.88
86 7 0.12
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (86 bp):
TTTTTTTTGAAAAAGTTTGAGGACCTTTTTGATGCATTATAAAAATTCAAGTACCCAATTGAGTG
CAAAAAAAGGGTCTTAATAAC
Found at i:54278537 original size:30 final size:29
Alignment explanation
Indices: 54278480--54278542 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
54278470 TGCGAAAAAT
54278480 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCGGTAAATAATTAAAAAACC
* *
54278509 GGCCCATTTCGGTAAAT-TTTGAAAAAAACC
1 GGCCCATTCCGGTAAATAATT--AAAAAACC
54278539 GGCC
1 GGCC
54278543 TTTTTTGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 16 0.53
30 12 0.40
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATAATTAAAAAACC
Found at i:54281120 original size:18 final size:18
Alignment explanation
Indices: 54281099--54281135 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
54281089 GAGTAATAAG
*
54281099 AGCAGTTAGAAGTCAGTT
1 AGCAATTAGAAGTCAGTT
54281117 AGCAATTAGAAGTCAGTT
1 AGCAATTAGAAGTCAGTT
54281135 A
1 A
54281136 ACACAAACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (18 bp):
AGCAATTAGAAGTCAGTT
Found at i:54285680 original size:18 final size:18
Alignment explanation
Indices: 54285659--54285695 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
54285649 GAGTAATAAG
54285659 AGCAGTTAGAAGTCAGTT
1 AGCAGTTAGAAGTCAGTT
54285677 AGCAGTTAGAAGTCAGTT
1 AGCAGTTAGAAGTCAGTT
54285695 A
1 A
54285696 ACACAAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (18 bp):
AGCAGTTAGAAGTCAGTT
Found at i:54288435 original size:11 final size:11
Alignment explanation
Indices: 54288419--54288448 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
54288409 TCAGACTTGT
54288419 AAATATTTTTA
1 AAATATTTTTA
54288430 AAATATTTTTA
1 AAATATTTTTA
54288441 AAATATTT
1 AAATATTT
54288449 ACAAAGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AAATATTTTTA
Found at i:54288718 original size:7 final size:7
Alignment explanation
Indices: 54288706--54288731 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54288696 ATATATGTAT
54288706 TATATAA
1 TATATAA
54288713 TATATAA
1 TATATAA
54288720 TATATAA
1 TATATAA
54288727 TATAT
1 TATAT
54288732 GATAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TATATAA
Found at i:54288800 original size:9 final size:9
Alignment explanation
Indices: 54288785--54288845 Score: 61
Period size: 9 Copynumber: 6.3 Consensus size: 9
54288775 ATGCAAATTG
54288785 AAAGAAA-A
1 AAAGAAATA
54288793 AGAAGAAATA
1 A-AAGAAATA
54288803 AAAGAAATAA
1 AAAGAAAT-A
*
54288813 AATAGAAAGAA
1 AA-AGAAA-TA
54288824 AGAAGAAATA
1 A-AAGAAATA
54288834 AAAGAAATA
1 AAAGAAATA
54288843 AAA
1 AAA
54288846 TAGAAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
8 1 0.02
9 24 0.53
10 7 0.16
11 12 0.27
12 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (9 bp):
AAAGAAATA
Found at i:54288826 original size:31 final size:31
Alignment explanation
Indices: 54288791--54288861 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
54288781 ATTGAAAGAA
54288791 AAAGAAGAAATAAAAGAAATAAAATAGAAAG
1 AAAGAAGAAATAAAAGAAATAAAATAGAAAG
54288822 AAAGAAGAAATAAAAGAAATAAAATAGAAAG
1 AAAGAAGAAATAAAAGAAATAAAATAGAAAG
54288853 AAAGAAGAA
1 AAAGAAGAA
54288862 GGGTGACCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (31 bp):
AAAGAAGAAATAAAAGAAATAAAATAGAAAG
Found at i:54290467 original size:24 final size:24
Alignment explanation
Indices: 54290421--54290468 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
54290411 GGATTGTAAA
*
54290421 TTGAGTTATAAATATAATGTTGGT
1 TTGAGTTATAAATATAATATTGGT
54290445 TTGAGTATATAAATAT-ATATTGGT
1 TTGAGT-TATAAATATAATATTGGT
54290469 GTTTGAAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (24 bp):
TTGAGTTATAAATATAATATTGGT
Found at i:54297221 original size:43 final size:43
Alignment explanation
Indices: 54297160--54297297 Score: 179
Period size: 43 Copynumber: 3.2 Consensus size: 43
54297150 AGTTTTGTAT
* **
54297160 TTCACCAATGGGCGAATTGTATAAAGTCTGCTTGTGTATAGTA
1 TTCACCAATTGGAAAATTGTATAAAGTCTGCTTGTGTATAGTA
54297203 TTCACCAATTGGAAAATTGTATAAAGTCTGCTTGTGTATAGTA
1 TTCACCAATTGGAAAATTGTATAAAGTCTGCTTGTGTATAGTA
** * * *
54297246 TTTGCCAA-TAGACAAATTTTATAAAGCCTGCTTGTGTATAGTA
1 TTCACCAATTGGA-AAATTGTATAAAGTCTGCTTGTGTATAGTA
*
54297289 TTCGCCAAT
1 TTCACCAAT
54297298 AGGTGAACTA
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
42 3 0.04
43 81 0.96
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (43 bp):
TTCACCAATTGGAAAATTGTATAAAGTCTGCTTGTGTATAGTA
Found at i:54297298 original size:43 final size:42
Alignment explanation
Indices: 54297174--54297299 Score: 189
Period size: 43 Copynumber: 3.0 Consensus size: 42
54297164 CCAATGGGCG
* *
54297174 AATTGTATAAAGTCTGCTTGTGTATAGTATTCACCAATTGGAA
1 AATTGTATAAAGTCTGCTTGTGTATAGTATTCGCCAA-TAGAA
*
54297217 AATTGTATAAAGTCTGCTTGTGTATAGTATTTGCCAATAGACA
1 AATTGTATAAAGTCTGCTTGTGTATAGTATTCGCCAATAGA-A
* *
54297260 AATTTTATAAAGCCTGCTTGTGTATAGTATTCGCCAATAG
1 AATTGTATAAAGTCTGCTTGTGTATAGTATTCGCCAATAG
54297300 GTGAACTATG
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
42 3 0.04
43 73 0.96
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (42 bp):
AATTGTATAAAGTCTGCTTGTGTATAGTATTCGCCAATAGAA
Found at i:54301535 original size:22 final size:20
Alignment explanation
Indices: 54301505--54301544 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
54301495 TACATAACCA
54301505 AATCAAATATGATAATATATGC
1 AATCAAATA-GA-AATATATGC
*
54301527 AATCTAATAGAAATATAT
1 AATCAAATAGAAATATAT
54301545 ATTCGAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 2 0.12
22 8 0.47
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (20 bp):
AATCAAATAGAAATATATGC
Found at i:54303219 original size:18 final size:17
Alignment explanation
Indices: 54303179--54303222 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
54303169 TTTTTATTGA
* *
54303179 TTTTATTTTATTTTATT
1 TTTTATTTTATCTTACT
54303196 TATTTATTTTATCTTACCT
1 T-TTTATTTTATCTTA-CT
54303215 TTTTATTT
1 TTTTATTT
54303223 ATTACCCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 20 0.87
19 2 0.09
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATTTTATCTTACT
Found at i:54303919 original size:62 final size:60
Alignment explanation
Indices: 54303838--54303953 Score: 169
Period size: 62 Copynumber: 1.9 Consensus size: 60
54303828 AAAGATCGGC
* *
54303838 GGCGACTCCATTTTTATTTTTTAAAATAAAAGTCGATTTCAAAAAAAAGGTTTCGACAGCTT
1 GGCGACTCCATTTTCATTTTTTAAAATAAAAATCGA-TT-AAAAAAAAGGTTTCGACAGCTT
* **
54303900 GGCGACTCCGTTTTCATTTTTTAAAATAAAAATTTATTAAAAAAAAGGTTTCGA
1 GGCGACTCCATTTTCATTTTTTAAAATAAAAATCGATTAAAAAAAAGGTTTCGA
54303954 AAATCTCCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 16 0.33
61 2 0.04
62 31 0.63
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (60 bp):
GGCGACTCCATTTTCATTTTTTAAAATAAAAATCGATTAAAAAAAAGGTTTCGACAGCTT
Found at i:54319863 original size:15 final size:15
Alignment explanation
Indices: 54319843--54319873 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54319833 GCCCATATGG
54319843 ATCATCTTCATCTTC
1 ATCATCTTCATCTTC
*
54319858 ATCATCTTCTTCTTC
1 ATCATCTTCATCTTC
54319873 A
1 A
54319874 CTTTTAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.48
Consensus pattern (15 bp):
ATCATCTTCATCTTC
Found at i:54324637 original size:24 final size:24
Alignment explanation
Indices: 54324609--54324660 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54324599 TTAGTAAGTC
* *
54324609 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54324633 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54324657 AAAT
1 AAAT
54324661 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54331073 original size:106 final size:106
Alignment explanation
Indices: 54330941--54331137 Score: 367
Period size: 106 Copynumber: 1.9 Consensus size: 106
54330931 TTTTTCTAAG
54330941 TAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
1 TAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
*
54331006 CGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTGAA
66 CGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTTTGAA
*
54331047 TAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
1 TAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
*
54331112 CGTTCGACTAAACAGCCAAATATCCT
66 CGTTCGACCAAACAGCCAAATATCCT
54331138 CTTAAAGCTT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 88 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (106 bp):
TAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
CGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTTTGAA
Found at i:54335711 original size:12 final size:12
Alignment explanation
Indices: 54335694--54335726 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
54335684 GAGGCAGGAA
54335694 CCCAACACAAGG
1 CCCAACACAAGG
54335706 CCCAACACAAGG
1 CCCAACACAAGG
*
54335718 GCCAACACA
1 CCCAACACA
54335727 GAGAGACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.42, G:0.15, T:0.00
Consensus pattern (12 bp):
CCCAACACAAGG
Found at i:54342498 original size:44 final size:45
Alignment explanation
Indices: 54342387--54343300 Score: 709
Period size: 44 Copynumber: 20.7 Consensus size: 45
54342377 ATAGGTCCTA
* * *
54342387 TCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * * *
54342430 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * ** * *
54342475 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAGCAGATCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * *
54342519 TCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGGA--TTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCA-GATCTTG
* ** * * *
54342561 TCGAAGATGCAGATCTTGGTGGCGAAGTAGATCGCAA-AAAGCAGATCTTG
1 TC-----TTCCTATATTGGTCGTGAAGTAGATCG-AAGAAAGCAGATCTTG
* * * *
54342611 TCTTCATGTATTGG-CGTGAAGTAGATCGAA-AATAG--G-TCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAA-AGCAGATCTTG
* * *
54342652 TCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * * *
54342695 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * ** * *
54342740 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAGCAGATCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * *
54342784 TCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * *
54342827 TCTTCCCATATTGGTGGCGAAGTAGATCGCAA-AAAGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCG-AAGAAAGCAGATCTTG
* * ** * *
54342872 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAGCAGATCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * *
54342916 TCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * * *
54342959 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * ** * *
54343004 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAGCAGATCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * *
54343048 TCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * * *
54343091 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * * ** * *
54343136 TCTTCATGTATTAG-CGTGAAGTAGATCGAAGGTAGCAGATCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * *
54343180 TCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * ** *
54343223 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGATTGTAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
* * * *
54343267 CCTTCCTGTAGTT-GACAGTGAAGCAGATCGAAGA
1 TCTTCCTATA-TTGGTC-GTGAAGTAGATCGAAGA
54343301 TGGCAGATTT
Statistics
Matches: 686, Mismatches: 146, Indels: 75
0.76 0.16 0.08
Matches are distributed among these distances:
40 1 0.00
41 28 0.04
42 7 0.01
43 144 0.21
44 330 0.48
45 127 0.19
46 16 0.02
47 10 0.01
48 12 0.02
49 6 0.01
50 5 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (45 bp):
TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTG
Found at i:54342842 original size:132 final size:132
Alignment explanation
Indices: 54342382--54343308 Score: 1524
Period size: 132 Copynumber: 7.0 Consensus size: 132
54342372 CGTAAATAGG
54342382 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
54342447 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
54342512 GA
131 GA
* ** *
54342514 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGGA--TTGTCGAAGATGCAGATCT
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCA-GATCTTGTC-----TTCCCATAT
* *
54342577 TGGTGGCGAAGTAGATCGCAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAA
60 TGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
*
54342642 ATAG--G-
125 GTAGCAGA
54342647 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
54342712 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
54342777 GA
131 GA
54342779 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
*
54342844 CGAAGTAGATCGCAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
54342909 GA
131 GA
54342911 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
54342976 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
54343041 GA
131 GA
54343043 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
*
54343108 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGGTAGCA
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
54343173 GA
131 GA
*** *
54343175 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCATGTATTGG-CG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
* * ** * * * * * * *
54343239 TGAAGTAGATCGAAGATTGTAGATCTTGCCTTCCTGTAGTTGACAGTGAAGCAGATCGAAGATGG
66 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTA-TTGGC-GTGAAGTAGATCGAAGGTAG
54343304 CAGA
129 CAGA
54343308 T
1 T
54343309 TTTACCTCCC
Statistics
Matches: 749, Mismatches: 33, Indels: 25
0.93 0.04 0.03
Matches are distributed among these distances:
129 71 0.09
131 38 0.05
132 498 0.66
133 65 0.09
134 6 0.01
136 71 0.09
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (132 bp):
TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
GA
Found at i:54343434 original size:95 final size:95
Alignment explanation
Indices: 54343291--54343483 Score: 314
Period size: 95 Copynumber: 2.0 Consensus size: 95
54343281 ACAGTGAAGC
* * *
54343291 AGATCGAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTCTACCTCCCTGACTACAGTGGAGTACATTGAAGCCAATAACTCTAT
* * ** *
54343356 CTCCCTGCATTTGACAGTGGAATAGATTGA
66 CTCCATACATTCAACAGTGGAATAGAGTGA
54343386 AGATCAAAGATGGCAGATTCTACCTCCCTGACTACAGTGGAGTACATTGAAGCCAATAACTCTAT
1 AGATCAAAGATGGCAGATTCTACCTCCCTGACTACAGTGGAGTACATTGAAGCCAATAACTCTAT
54343451 CTCCATACATTCAACAGTGGAATAGAGTGA
66 CTCCATACATTCAACAGTGGAATAGAGTGA
54343481 AGA
1 AGA
54343484 GCACAAATCT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (95 bp):
AGATCAAAGATGGCAGATTCTACCTCCCTGACTACAGTGGAGTACATTGAAGCCAATAACTCTAT
CTCCATACATTCAACAGTGGAATAGAGTGA
Found at i:54346165 original size:106 final size:106
Alignment explanation
Indices: 54346033--54346229 Score: 367
Period size: 106 Copynumber: 1.9 Consensus size: 106
54346023 TTTTTCTAAG
54346033 TAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
1 TAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
*
54346098 CGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTGAA
66 CGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTTTGAA
*
54346139 TAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
1 TAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
*
54346204 CGTTCGACTAAACAGCCAAATATCCT
66 CGTTCGACCAAACAGCCAAATATCCT
54346230 CTTAAAGCTT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 88 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (106 bp):
TAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
CGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTTTGAA
Found at i:54349766 original size:4 final size:4
Alignment explanation
Indices: 54349751--54349780 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
54349741 TTTTGAAGTG
*
54349751 GTAT GGAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
54349781 GTATGTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:54350170 original size:124 final size:122
Alignment explanation
Indices: 54349947--54350194 Score: 460
Period size: 124 Copynumber: 2.0 Consensus size: 122
54349937 CCTGTCTCCA
54349947 AGTACTACTTCTTTCCTCGGTGTTCTTATTTTAAATCTCTTCAATCTTTTTTTTGTTAAAATTAT
1 AGTACTACTTCTTTCCTCGGTGTTCTTATTTTAAATCTCTTCAATCTTTTTTTTGTTAAAATTAT
*
54350012 CAAGTTCTTCTCTCCAAGGACCCCGGCTAGGTAGATGGTGGCGATTGAGGACTAGTT
66 CAAGTTCTTCTCTCCAAGCACCCCGGCTAGGTAGATGGTGGCGATTGAGGACTAGTT
*
54350069 AGTATTACTTCTTTCCTCGGTGTTCTTATTTTAAATCTCTTCAATCTTTTTTTTTGGTTAAAATT
1 AGTACTACTTCTTTCCTCGGTGTTCTTATTTTAAATCTCTTCAATC-TTTTTTTT-GTTAAAATT
54350134 ATCAAGTTCTTCTCTCCAAGCACCCCGGCTAGGTAGATGGTGGCGATTGAGGACTAGTT
64 ATCAAGTTCTTCTCTCCAAGCACCCCGGCTAGGTAGATGGTGGCGATTGAGGACTAGTT
54350193 AG
1 AG
54350195 CTGATGGTTC
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
122 45 0.37
123 8 0.07
124 69 0.57
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41
Consensus pattern (122 bp):
AGTACTACTTCTTTCCTCGGTGTTCTTATTTTAAATCTCTTCAATCTTTTTTTTGTTAAAATTAT
CAAGTTCTTCTCTCCAAGCACCCCGGCTAGGTAGATGGTGGCGATTGAGGACTAGTT
Found at i:54359221 original size:16 final size:16
Alignment explanation
Indices: 54359171--54359224 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
54359161 TTTGGTTCGC
*
54359171 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
* *
54359187 TGCATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
54359203 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
54359219 TGTAAT
1 TGTAAT
54359225 AGCAAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.30, C:0.02, G:0.35, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:54359269 original size:45 final size:44
Alignment explanation
Indices: 54359203--54359297 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
54359193 GGATTAGAGG
* *
54359203 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
54359248 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
54359292 TGTAAT
1 TGTAAT
54359298 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:54359461 original size:25 final size:25
Alignment explanation
Indices: 54359429--54359483 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
54359419 TAATTTAATC
*
54359429 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
54359453 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
54359478 ATATAT
1 ATATAT
54359484 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:54359665 original size:47 final size:46
Alignment explanation
Indices: 54359614--54359774 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
54359604 GATTTAATAA
54359614 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
54359661 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
54359702 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
54359749 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
54359775 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:54363978 original size:16 final size:16
Alignment explanation
Indices: 54363957--54363992 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
54363947 TTTGGTTCGC
*
54363957 TGTATTGGATTAGAGG
1 TGTATTGGAATAGAGG
54363973 TGTATTGGAATAGAGG
1 TGTATTGGAATAGAGG
54363989 TGTA
1 TGTA
54363993 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.36, T:0.36
Consensus pattern (16 bp):
TGTATTGGAATAGAGG
Found at i:54364237 original size:25 final size:25
Alignment explanation
Indices: 54364205--54364259 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
54364195 TAATTTAATC
*
54364205 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
54364229 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
54364254 ATATAT
1 ATATAT
54364260 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:54364441 original size:47 final size:46
Alignment explanation
Indices: 54364390--54364538 Score: 132
Period size: 47 Copynumber: 3.3 Consensus size: 46
54364380 GATTTAATAA
54364390 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
54364437 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
54364478 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
54364525 AATTTAAAATAATT
1 AATTTAAAATAATT
54364539 TAGGAAATGG
Statistics
Matches: 78, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.17
42 11 0.14
43 5 0.06
44 4 0.05
45 5 0.06
46 10 0.13
47 29 0.37
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:54368671 original size:73 final size:73
Alignment explanation
Indices: 54368578--54368722 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 73
54368568 ATAACCTTTT
* * *
54368578 CATGTTATAAAACATATACAAGTAAACACATTAGACATATCATTTATTCAACATCTATTCATTTA
1 CATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATCTATTAATTTA
54368643 ACATTTCA
66 ACATTTCA
* * *
54368651 CATGTTATAAAACGTGTACAAGTAAACACATTAGATATACCATTCATTCAACATCTATTAATTTA
1 CATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATCTATTAATTTA
54368716 ACATTTC
66 ACATTTC
54368723 CCATTTCCCA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (73 bp):
CATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATCTATTAATTTA
ACATTTCA
Found at i:54368806 original size:13 final size:13
Alignment explanation
Indices: 54368775--54368846 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
54368765 TATATCTATC
54368775 CATATAAACATTT
1 CATATAAACATTT
*
54368788 CGTATAAACACTTT
1 CATATAAACA-TTT
**
54368802 -ATATAATTATTT
1 CATATAAACATTT
*
54368814 CCATATAACCGA-TT
1 -CATATAAAC-ATTT
*
54368828 CATATAATCATTT
1 CATATAAACATTT
54368841 CATATA
1 CATATA
54368847 TTCTTTTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.09
13 31 0.66
14 11 0.23
15 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (13 bp):
CATATAAACATTT
Found at i:54368933 original size:12 final size:12
Alignment explanation
Indices: 54368916--54368944 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
54368906 TTTAACACAT
54368916 AATCATTTTGTA
1 AATCATTTTGTA
54368928 AATCATTTTGTA
1 AATCATTTTGTA
54368940 AATCA
1 AATCA
54368945 CATTTCGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (12 bp):
AATCATTTTGTA
Found at i:54369220 original size:45 final size:45
Alignment explanation
Indices: 54369161--54369434 Score: 167
Period size: 45 Copynumber: 6.1 Consensus size: 45
54369151 ACAGTTACGG
* *
54369161 TCTTACACACTTCCGAT-ATGATGTCATAGTGTCTTTCAACTATGA
1 TCTTAC-CATTTCCGATCATGATGCCATAGTGTCTTTCAACTATGA
* * * *
54369206 TCTTATCCATTTCCG-TCATGTTACCATAATGTCTTTCAACTATGG
1 TCTTA-CCATTTCCGATCATGATGCCATAGTGTCTTTCAACTATGA
* * ** * * *
54369251 TCTTA-CACGTT--GAATCGTGATGCCATAGCATCTTTTAGCTATGG
1 TCTTACCA-TTTCCG-ATCATGATGCCATAGTGTCTTTCAACTATGA
* * *
54369295 TCTTACTCGTTT--GAATCATGATGCCATAGCGTCTTTCAGCTATGA
1 TCTTAC-CATTTCCG-ATCATGATGCCATAGTGTCTTTCAACTATGA
* *
54369340 TCTTACTCATTTCC-AGT-AT-AGTGCCATAGTATCTTTCAACTATGG
1 TCTTAC-CATTTCCGA-TCATGA-TGCCATAGTGTCTTTCAACTATGA
* * * *
54369385 TCTTATTCACTCCCGAT-AT-AGTACCATAGTGTCTTTCAACTATGA
1 TCTTA-CCATTTCCGATCATGA-TGCCATAGTGTCTTTCAACTATGA
54369430 TCTTA
1 TCTTA
54369435 TTCATTTTTC
Statistics
Matches: 184, Mismatches: 32, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 31 0.17
45 146 0.79
46 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (45 bp):
TCTTACCATTTCCGATCATGATGCCATAGTGTCTTTCAACTATGA
Found at i:54370982 original size:24 final size:27
Alignment explanation
Indices: 54370955--54371004 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
54370945 CAAATACTCA
54370955 TTTATA-TA-ATTAAAATAT-TCATAT
1 TTTATACTAGATTAAAATATGTCATAT
54370979 TTTATACTAGATTAAAATATGTCATA
1 TTTATACTAGATTAAAATATGTCATA
54371005 AGTCCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
26 10 0.43
27 5 0.22
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (27 bp):
TTTATACTAGATTAAAATATGTCATAT
Found at i:54371390 original size:23 final size:23
Alignment explanation
Indices: 54371347--54371392 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
54371337 TACTATAAAA
*
54371347 ATTTATTATTAATATTGTAATAT
1 ATTTATTATTAAAATTGTAATAT
54371370 ATTTATTATTAAAATAT-TAATAT
1 ATTTATTATTAAAAT-TGTAATAT
54371393 TAATATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTTATTATTAAAATTGTAATAT
Found at i:54371594 original size:39 final size:38
Alignment explanation
Indices: 54371538--54371613 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
54371528 AATATGTATG
54371538 TTTAATAATATTGAAAATTATAATATTTTATT-TTAATAT
1 TTTAATAATATTGAAAATTA-AA-ATTTTATTATTAATAT
*
54371577 TTTAAT-ATATTTTAAAATTAAAATTTTATTATTAATA
1 TTTAATAATA-TTGAAAATTAAAATTTTATTATTAATA
54371614 GAATAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
37 8 0.24
38 11 0.32
39 15 0.44
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (38 bp):
TTTAATAATATTGAAAATTAAAATTTTATTATTAATAT
Found at i:54371764 original size:22 final size:19
Alignment explanation
Indices: 54371739--54371786 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 19
54371729 AAAAAAAAAC
54371739 TTATTTTCCATTGACTCATAAT
1 TTATTTTCCATTGAC-C--AAT
*
54371761 TTATTTTTCATTGACCAAT
1 TTATTTTCCATTGACCAAT
54371780 TTATTTT
1 TTATTTT
54371787 TCATGAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
21 1 0.04
22 14 0.56
ACGTcount: A:0.25, C:0.15, G:0.04, T:0.56
Consensus pattern (19 bp):
TTATTTTCCATTGACCAAT
Found at i:54371782 original size:19 final size:21
Alignment explanation
Indices: 54371739--54371790 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
54371729 AAAAAAAAAC
*
54371739 TTATTTTCCATTGACTCATAAT
1 TTATTTTTCATTGACTCA-AAT
54371761 TTATTTTTCATTGAC-C-AAT
1 TTATTTTTCATTGACTCAAAT
54371780 TTATTTTTCAT
1 TTATTTTTCAT
54371791 GAAACAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.48
21 1 0.03
22 14 0.48
ACGTcount: A:0.25, C:0.15, G:0.04, T:0.56
Consensus pattern (21 bp):
TTATTTTTCATTGACTCAAAT
Found at i:54390471 original size:16 final size:17
Alignment explanation
Indices: 54390431--54390473 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
54390421 TTCTCCACAT
54390431 AGTTATTCTCAATATAG
1 AGTTATTCTCAATATAG
54390448 AGGTTATTC-CGAATA-AG
1 A-GTTATTCTC-AATATAG
54390465 AGTTATTCT
1 AGTTATTCT
54390474 GTGATAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 7 0.30
17 5 0.22
18 11 0.48
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (17 bp):
AGTTATTCTCAATATAG
Found at i:54390536 original size:15 final size:16
Alignment explanation
Indices: 54390516--54390554 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
54390506 AAATAATGGC
*
54390516 TCTAAATAC-ATTTGT
1 TCTAAATACAAGTTGT
54390531 TCTAAATACAAGTTGT
1 TCTAAATACAAGTTGT
*
54390547 TCCAAATA
1 TCTAAATA
54390555 ATGGTTGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (16 bp):
TCTAAATACAAGTTGT
Found at i:54395008 original size:21 final size:21
Alignment explanation
Indices: 54394978--54395019 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
54394968 ATGGTGCAAA
*
54394978 TGAAGTATTTTAACTCGATTG
1 TGAAGCATTTTAACTCGATTG
54394999 TGAAGCATTTTAACTCGATTG
1 TGAAGCATTTTAACTCGATTG
54395020 GCGGTGACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (21 bp):
TGAAGCATTTTAACTCGATTG
Found at i:54399314 original size:17 final size:17
Alignment explanation
Indices: 54399285--54399327 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
54399275 AATTAGTTAT
*
54399285 TTAAAAAATTTATAATA
1 TTAAAAAATTTATAAAA
54399302 TTAAACAAA-TTATAAAA
1 TTAAA-AAATTTATAAAA
54399319 TTACAAAAA
1 TTA-AAAAA
54399328 AGAATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAAAATTTATAAAA
Found at i:54399394 original size:17 final size:18
Alignment explanation
Indices: 54399363--54399398 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
54399353 TTACTATTTT
54399363 TTTTAAATATATTATAAA
1 TTTTAAATATATTATAAA
*
54399381 TTTT-AATATTTTATAAA
1 TTTTAAATATATTATAAA
54399398 T
1 T
54399399 CACATTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAATATATTATAAA
Found at i:54399690 original size:22 final size:22
Alignment explanation
Indices: 54399664--54399720 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
54399654 TTTTCAGTAA
*
54399664 ATTTTTT-T-ATTTTTATATAT
1 ATTTTTTGTAATTTTTAAATAT
54399684 ATTTTTTGTAATTTTTAAATAT
1 ATTTTTTGTAATTTTTAAATAT
* *
54399706 -GTTTTTGGAATTTTT
1 ATTTTTTGTAATTTTT
54399721 TTGTAACTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.22
21 14 0.44
22 11 0.34
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (22 bp):
ATTTTTTGTAATTTTTAAATAT
Found at i:54399712 original size:21 final size:22
Alignment explanation
Indices: 54399672--54399742 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
54399662 AAATTTTTTT
*
54399672 ATTTTTATATATATTTTTTGTA
1 ATTTTTATATATATTTTTTGGA
54399694 ATTTTTA-A-ATATGTTTTTGGA
1 ATTTTTATATATAT-TTTTTGGA
* *
54399715 ATTTTTTTGTA-ACTTTTTTGGA
1 ATTTTTATATATA-TTTTTTGGA
*
54399737 TTTTTT
1 ATTTTT
54399743 TCATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.10
21 14 0.34
22 21 0.51
23 2 0.05
ACGTcount: A:0.23, C:0.01, G:0.10, T:0.66
Consensus pattern (22 bp):
ATTTTTATATATATTTTTTGGA
Found at i:54407014 original size:92 final size:91
Alignment explanation
Indices: 54406767--54407035 Score: 376
Period size: 91 Copynumber: 2.9 Consensus size: 91
54406757 AATATGCCAG
* * *
54406767 ATGCACATAGTGCAAACCCGTAGGCTAAATATTCTCCCTCGATAACACGCCAGATTTCTCATAAG
1 ATGCACATAGTGCAAAACCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTACTCATAAG
* * * * *
54406832 AGGTATTCTAATCAATAACATGCTAG
66 AGCTATTCTAATCGAGAACACGCTAA
* *
54406858 ATGCACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACATGCCAGATTACTCATAAG
1 ATGCACATAGTGCAAAACCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTACTCATAAG
*
54406923 AGCTATTCTAATCGAGAACACGTTAA
66 AGCTATTCTAATCGAGAACACGCTAA
* * * * *
54406949 ATGCACATAGTGCAAATACTGTAGGCTAAATATTCTCCCCCGATAAAACGCTAGATTGCTTATAA
1 ATGCACATAGTGCAAA-ACCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTACTCATAA
*
54407014 GAGCTATTCCAATCGAGAACAC
65 GAGCTATTCTAATCGAGAACAC
54407036 ACTAGAATCT
Statistics
Matches: 159, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 97 0.61
92 62 0.39
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (91 bp):
ATGCACATAGTGCAAAACCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTACTCATAAG
AGCTATTCTAATCGAGAACACGCTAA
Found at i:54411754 original size:22 final size:24
Alignment explanation
Indices: 54411729--54411777 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
54411719 CTCTTGAAAG
* *
54411729 AATACCTAAAAGAGAGT-CA-CAA
1 AATAACTAAAAGAAAGTACACCAA
*
54411751 AATAACTACAAGAAAGTACACCAA
1 AATAACTAAAAGAAAGTACACCAA
54411775 AAT
1 AAT
54411778 TGTGAACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 14 0.64
23 2 0.09
24 6 0.27
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (24 bp):
AATAACTAAAAGAAAGTACACCAA
Found at i:54417573 original size:51 final size:51
Alignment explanation
Indices: 54417504--54417798 Score: 321
Period size: 51 Copynumber: 5.8 Consensus size: 51
54417494 TAAGGTATCG
* * * *
54417504 ATGAACACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATA
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA
* * * *
54417555 ATGCTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAATTT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-TA
* * * * *
54417606 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACATGTACCGATAAATA
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA
* * *
54417657 ATGAACACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TA
* * * *
54417708 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACC-ATAAA-A
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA
* *
54417757 CTTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 -ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTA
54417799 TCGAATGATA
Statistics
Matches: 204, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
50 46 0.23
51 154 0.75
52 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (51 bp):
ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA
Found at i:54417593 original size:26 final size:26
Alignment explanation
Indices: 54417513--54417595 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
54417503 GATGAACACG
**
54417513 TGTGTAGTACTGTGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* * *
54417539 CGTGTA-T-CGATAAAT-AATGCTCAC-A
1 TGTGTAGTAC--TAAGTGAAGGCT-ACTA
54417564 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
54417590 TGTGTA
1 TGTGTA
54417596 CCGAAAATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:54417685 original size:102 final size:102
Alignment explanation
Indices: 54417509--54417803 Score: 450
Period size: 102 Copynumber: 2.9 Consensus size: 102
54417499 TATCGATGAA
* *
54417509 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGCTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTAC
**
54417574 TAAGTGAAGGCTACTATGTGTACCGAAAATTTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* *
54417611 CACGTGTGTAGTACTGTGTGAAGGCTACTACATGTACCGATAAATAATGAACACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTAC
54417676 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * * *
54417713 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACC-ATAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATA-ATGATCACATGTGTAGTA
* * *
54417776 CTATGTGAAGGCTACTACGTGTATCGAA
65 CTAAGTGAAGGCTACTATGTGTACCGAA
54417804 TGATAAAAGT
Statistics
Matches: 177, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
100 1 0.01
101 45 0.25
102 131 0.74
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
Found at i:54418978 original size:13 final size:11
Alignment explanation
Indices: 54418940--54418978 Score: 60
Period size: 12 Copynumber: 3.4 Consensus size: 11
54418930 ATAATTTTAA
54418940 TTTTTTATAAT
1 TTTTTTATAAT
54418951 TTTTTTATAAAT
1 TTTTTTAT-AAT
54418963 TTTGTTTATAAT
1 TTT-TTTATAAT
54418975 TTTT
1 TTTT
54418979 ATGATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.35
12 12 0.46
13 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:54420368 original size:47 final size:47
Alignment explanation
Indices: 54420314--54420420 Score: 198
Period size: 47 Copynumber: 2.3 Consensus size: 47
54420304 TATTCCCACA
54420314 TGTTAATTTTGGTTTTGTTCTTCTTTTCTTCTTTCTTTGTTTTCTTT
1 TGTTAATTTTGGTTTTGTTCTTCTTTTCTTCTTTCTTTGTTTTCTTT
54420361 TGTTAATTTTGGTTTTGTTCTTCTTTTCTTCTTTCTTTGTTTTCTTT
1 TGTTAATTTTGGTTTTGTTCTTCTTTTCTTCTTTCTTTGTTTTCTTT
*
54420408 TGTT-CTTTTGGTT
1 TGTTAATTTTGGTT
54420421 CTCTTGAGAT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
46 8 0.14
47 51 0.86
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.72
Consensus pattern (47 bp):
TGTTAATTTTGGTTTTGTTCTTCTTTTCTTCTTTCTTTGTTTTCTTT
Found at i:54420407 original size:21 final size:22
Alignment explanation
Indices: 54420327--54420415 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 22
54420317 TAATTTTGGT
54420327 TTTGTTCTTCTTTTCTTCTTTC
1 TTTGTTCTTCTTTTCTTCTTTC
* * *
54420349 TTTGTT-TTCTTTTGTTAATTTTGGT
1 TTTGTTCTTCTTTTCTT--CTTT--C
54420374 TTTGTTCTTCTTTTCTTCTTTC
1 TTTGTTCTTCTTTTCTTCTTTC
*
54420396 TTTGTT-TTCTTTTGTTCTTT
1 TTTGTTCTTCTTTTCTTCTTT
54420416 TGGTTCTCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
21 22 0.40
22 12 0.22
23 3 0.05
24 3 0.05
25 6 0.11
26 9 0.16
ACGTcount: A:0.02, C:0.15, G:0.09, T:0.74
Consensus pattern (22 bp):
TTTGTTCTTCTTTTCTTCTTTC
Found at i:54424380 original size:8 final size:8
Alignment explanation
Indices: 54424367--54424391 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54424357 TTAAAAATAA
54424367 TTTTAATT
1 TTTTAATT
54424375 TTTTAATT
1 TTTTAATT
54424383 TTTTAATT
1 TTTTAATT
54424391 T
1 T
54424392 AAAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTAATT
Found at i:54424890 original size:14 final size:14
Alignment explanation
Indices: 54424873--54424922 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
54424863 AGTCATCATC
54424873 TAAAAATTATAAAT
1 TAAAAATTATAAAT
54424887 TAAAAATTATAAAAAACT
1 TAAAAATTAT---AAA-T
54424905 TAAAAATTA-AAAT
1 TAAAAATTATAAAT
54424918 TAAAA
1 TAAAA
54424923 TATATATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 6 0.19
14 13 0.41
17 3 0.09
18 10 0.31
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAAATTATAAAT
Found at i:54427630 original size:22 final size:24
Alignment explanation
Indices: 54427603--54427646 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54427593 TTTTTTAACA
*
54427603 ATGAAAAT-A-AAAATAAAAATAT
1 ATGAAAATGAGAAAAAAAAAATAT
54427625 ATGAAAATGAGAAAAAAAAAAT
1 ATGAAAATGAGAAAAAAAAAAT
54427647 TAAATTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 1 0.05
24 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (24 bp):
ATGAAAATGAGAAAAAAAAAATAT
Found at i:54439565 original size:115 final size:112
Alignment explanation
Indices: 54439423--54439635 Score: 300
Period size: 112 Copynumber: 1.9 Consensus size: 112
54439413 GAGAAAATAA
* * *
54439423 TATTTTTTTTGTATACTGATATTTGATTCTGACATGAAAAAAAAAGAAAAAAAAATTTTAAATTG
1 TATTTTTTTCGTATACTGATATCTGATTCTGACACG-AAAAAAAAG--AAAAAAATTTTAAATTG
* *
54439488 TATTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTTAT
63 TACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTTAT
*****
54439538 TATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAGAATTTTTTTTTAAATTGTAC
1 TATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAGAAAAAAATTTTAAATTGTAC
*
54439603 TAGGTGTCGGCCATTGACAGGCCAGCACCCAAA
66 TAGGTGCCGGCCATTGACAGGCCAGCACCCAAA
54439636 TTTTTTTTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
112 45 0.52
114 9 0.10
115 33 0.38
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (112 bp):
TATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAGAAAAAAATTTTAAATTGTAC
TAGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTTAT
Found at i:54444857 original size:26 final size:26
Alignment explanation
Indices: 54444828--54444877 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
54444818 CAAATAAACC
54444828 TAGCCCAATACACCACAACCCAAAAA
1 TAGCCCAATACACCACAACCCAAAAA
*
54444854 TAGCCCAATACACTACAACCCAAA
1 TAGCCCAATACACCACAACCCAAA
54444878 TCAGAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.38, G:0.04, T:0.10
Consensus pattern (26 bp):
TAGCCCAATACACCACAACCCAAAAA
Found at i:54447914 original size:14 final size:14
Alignment explanation
Indices: 54447895--54447924 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54447885 TGAAGTATAT
*
54447895 TATATATATATTTA
1 TATATATATACTTA
54447909 TATATATATACTTA
1 TATATATATACTTA
54447923 TA
1 TA
54447925 AACAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATATATACTTA
Found at i:54449992 original size:30 final size:31
Alignment explanation
Indices: 54449956--54450022 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
54449946 ATACATGAAT
*
54449956 TTTAATT-TGATGCAACTATACATATGAAAC
1 TTTAATTGTGATGCAAATATACATATGAAAC
* * * *
54449986 TTTAATTGTGGTTCAAATTTATATATGAAAC
1 TTTAATTGTGATGCAAATATACATATGAAAC
54450017 TTTAAT
1 TTTAAT
54450023 CTTAAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.43
Consensus pattern (31 bp):
TTTAATTGTGATGCAAATATACATATGAAAC
Found at i:54451039 original size:97 final size:97
Alignment explanation
Indices: 54450909--54451226 Score: 377
Period size: 97 Copynumber: 3.1 Consensus size: 97
54450899 ATAATACTGA
*
54450909 TATACGAAAAAAGAAAAAGAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA
1 TATACGAAAAAAGTAAAA-AAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA
* *
54450974 -TTAAAAAAAATTCGTGTTAAAATAAGATATCAG
65 TTTAAAAAAAATT-GTGTCAAAATCAGATATCAG
* * *
54451007 TATATGAAAAAAGTAAAAAAAAAAATTTGGGTGCTGGCCTGTTAATGGCCGGCACCGAGTACAAT
1 TATACGAAAAAAGTAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAT
54451072 TTAGAAAAAAAAATTTTAATTTTTTTGTGTCAAAATCAGATATCAG
66 TT-----AAAAAA----AA-----TTGTGTCAAAATCAGATATCAG
* *
54451118 TATACGAAAAAAATAAAAAAAATAAAAATTTTGGGTGCTGGCCTATCAATGGCCGGCACCCAGTA
1 TATACGAAAAAAGT--AAAAAA-AAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTA
54451183 CAATTTAAAAAAAATTGTGTCAAAATCAGATATCAG
62 CAATTTAAAAAAAATTGTGTCAAAATCAGATATCAG
54451219 TATACGAA
1 TATACGAA
54451227 TTTTTTTTTT
Statistics
Matches: 190, Mismatches: 11, Indels: 35
0.81 0.05 0.15
Matches are distributed among these distances:
97 44 0.23
98 18 0.09
101 30 0.16
103 6 0.03
106 2 0.01
107 2 0.01
110 6 0.03
111 30 0.16
112 2 0.01
113 6 0.03
114 5 0.03
115 39 0.21
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (97 bp):
TATACGAAAAAAGTAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAT
TTAAAAAAAATTGTGTCAAAATCAGATATCAG
Found at i:54451107 original size:111 final size:113
Alignment explanation
Indices: 54450987--54451196 Score: 318
Period size: 115 Copynumber: 1.9 Consensus size: 113
54450977 AAAAAAATTC
* * * *
54450987 GTGTTAAAATAAGATATCAGTATATGAAAAAAGT-AAAAAA-AAAAA-TTTGGGTGCTGGCCTGT
1 GTGTCAAAATAAGATATCAGTATACGAAAAAAATAAAAAAATAAAAATTTTGGGTGCTGGCCTAT
* *
54451049 TAATGGCCGGCACCGAGTACAATTTAGAAAAAAAAATTTTAATTTTTTT
66 CAATGGCCGGCACCCAGTACAATTTA-AAAAAAAAATTTTAATTTTTTT
*
54451098 GTGTCAAAATCAGATATCAGTATACGAAAAAAATAAAAAAAATAAAAATTTTGGGTGCTGGCCTA
1 GTGTCAAAATAAGATATCAGTATACGAAAAAAAT-AAAAAAATAAAAATTTTGGGTGCTGGCCTA
54451163 TCAATGGCCGGCACCCAGTACAATTTAAAAAAAA
65 TCAATGGCCGGCACCCAGTACAATTTAAAAAAAA
54451197 TTGTGTCAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
111 30 0.34
113 6 0.07
114 12 0.14
115 40 0.45
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (113 bp):
GTGTCAAAATAAGATATCAGTATACGAAAAAAATAAAAAAATAAAAATTTTGGGTGCTGGCCTAT
CAATGGCCGGCACCCAGTACAATTTAAAAAAAAAATTTTAATTTTTTT
Found at i:54451309 original size:55 final size:54
Alignment explanation
Indices: 54451228--54451341 Score: 210
Period size: 55 Copynumber: 2.1 Consensus size: 54
54451218 GTATACGAAT
*
54451228 TTTTTTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAGAA
1 TTTTTTTTTATTTTTTTCGTATACTGATATCTAATTCTGACACGAAAAAAAA-AA
54451283 TTTTTTTTTATTTTTTTCGTATACTGATATCTAATTCTGACACGAAAAAAAAAA
1 TTTTTTTTTATTTTTTTCGTATACTGATATCTAATTCTGACACGAAAAAAAAAA
54451337 TTTTT
1 TTTTT
54451342 AAATTATACT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
54 7 0.12
55 51 0.88
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (54 bp):
TTTTTTTTTATTTTTTTCGTATACTGATATCTAATTCTGACACGAAAAAAAAAA
Found at i:54452093 original size:19 final size:19
Alignment explanation
Indices: 54452066--54452107 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54452056 CATACAAATT
*
54452066 TATTACCAAAAATAAAACG
1 TATTACCAAAAAGAAAACG
* *
54452085 TATTTCCAAAAAGAAAACT
1 TATTACCAAAAAGAAAACG
54452104 TATT
1 TATT
54452108 GCCATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (19 bp):
TATTACCAAAAAGAAAACG
Found at i:54453306 original size:108 final size:106
Alignment explanation
Indices: 54453119--54453318 Score: 301
Period size: 108 Copynumber: 1.9 Consensus size: 106
54453109 TGGATTGAGA
* * *
54453119 TTTAAGAGGATATTTGACTATTTGGTCAAACGAAAAATCGAAACCCAACACATTAGGGCGCGTTT
1 TTTAAAAGGATATTTGACTATTTGATCAAACGAAAAATCGAAACCCAACACATTAGGGCACGTTT
* *
54453184 CCTCGAATTTCCAAACGCAAAATATTATCTTACTTCGAAAT
66 CCTCAAATCTCCAAACGCAAAATATTATCTTACTTCGAAAT
* *
54453225 TTTAAAAGGATATTTGGCTATTTGATCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
1 TTTAAAAGGATATTTGACTATTTGATCAAAC--GAAAAATCGAAACCCAACACATTAGGGCACGT
* *
54453290 TTTCTCAAATCTCCAAACGTAAAATATTA
64 TTCCTCAAATCTCCAAACGCAAAATATTA
54453319 CCTTTATTAT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
106 27 0.33
108 56 0.67
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (106 bp):
TTTAAAAGGATATTTGACTATTTGATCAAACGAAAAATCGAAACCCAACACATTAGGGCACGTTT
CCTCAAATCTCCAAACGCAAAATATTATCTTACTTCGAAAT
Found at i:54454007 original size:17 final size:18
Alignment explanation
Indices: 54453985--54454021 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
54453975 ATGAAGTGTA
54453985 AAGTATATATATC-ATAT
1 AAGTATATATATCTATAT
*
54454002 AAGTATTTATATCTATAT
1 AAGTATATATATCTATAT
54454020 AA
1 AA
54454022 ATTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
AAGTATATATATCTATAT
Found at i:54460870 original size:108 final size:106
Alignment explanation
Indices: 54460683--54460886 Score: 311
Period size: 108 Copynumber: 1.9 Consensus size: 106
54460673 TGGATTAAGA
* * * *
54460683 TTTAAGAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACATTAGGGCACATTT
1 TTTAAAAGGATATTTGACTATTTGATCAAACGAGAAAACGAAACCCAGCACATTAGGGCACATTT
*
54460748 TCTCGAATTTCCAAACGCAAAACATTGCCTTACTTCGAAAT
66 TCTCGAATCTCCAAACGCAAAACATTGCCTTACTTCGAAAT
*
54460789 TTTAAAAGGATATTTGACTATTTGAT-AGAACGAGAAAAAACGAAACCCAGCACATTAGGGCACG
1 TTTAAAAGGATATTTGACTATTTGATCA-AACGAG--AAAACGAAACCCAGCACATTAGGGCACA
*
54460853 TTTTCTCGAATCTCCAAACGCAAAATATTGCCTT
63 TTTTCTCGAATCTCCAAACGCAAAACATTGCCTT
54460887 TATTATTCTT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
105 1 0.01
106 29 0.33
108 58 0.66
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (106 bp):
TTTAAAAGGATATTTGACTATTTGATCAAACGAGAAAACGAAACCCAGCACATTAGGGCACATTT
TCTCGAATCTCCAAACGCAAAACATTGCCTTACTTCGAAAT
Found at i:54461451 original size:12 final size:13
Alignment explanation
Indices: 54461416--54461452 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
54461406 ATAGACATGT
*
54461416 AAATAAATAAA-T
1 AAATAAATAAAGA
54461428 AAATAAATAAAGA
1 AAATAAATAAAGA
54461441 AAATAAA-AAAGA
1 AAATAAATAAAGA
54461453 TATATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (13 bp):
AAATAAATAAAGA
Found at i:54461585 original size:14 final size:12
Alignment explanation
Indices: 54461554--54461596 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
54461544 ACGTGTATGC
* *
54461554 ATATATATATAA
1 ATATACATATAT
54461566 ATATACATAGGTAT
1 ATATACATA--TAT
54461580 ATATACATATAT
1 ATATACATATAT
54461592 ATATA
1 ATATA
54461597 TTATGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (12 bp):
ATATACATATAT
Found at i:54461597 original size:14 final size:14
Alignment explanation
Indices: 54461558--54461597 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54461548 GTATGCATAT
*
54461558 ATATATAAATATAC
1 ATATATATATATAC
**
54461572 ATAGGTATATATAC
1 ATATATATATATAC
54461586 ATATATATATAT
1 ATATATATATAT
54461598 TATGAAAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (14 bp):
ATATATATATATAC
Found at i:54461685 original size:3 final size:3
Alignment explanation
Indices: 54461677--54461728 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
54461667 AAAATGAAAC
** * * *
54461677 TAA TAA TAA TTAA TGG TAA TAA TAA AAA TAA AAA TAA TAA TGA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54461723 TAA TAA
1 TAA TAA
54461729 AAATGATCAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:54461740 original size:15 final size:15
Alignment explanation
Indices: 54461677--54461740 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
54461667 AAAATGAAAC
* *
54461677 TAATAATAATTAATGG
1 TAATAATAA-AAATGA
54461693 TAATAATAAAAAT-A
1 TAATAATAAAAATGA
*
54461707 -AA-AATAATAATGA
1 TAATAATAAAAATGA
54461720 TAATAATAAAAATGA
1 TAATAATAAAAATGA
*
54461735 TCATAA
1 TAATAA
54461741 CACTAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
12 8 0.20
13 3 0.08
14 2 0.05
15 18 0.45
16 9 0.22
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (15 bp):
TAATAATAAAAATGA
Found at i:54464974 original size:15 final size:14
Alignment explanation
Indices: 54464956--54465011 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
54464946 ATTAATTTAA
54464956 TATTATTATTACCAT
1 TATTATTATTACC-T
54464971 TATTATT-TTACCCT
1 TATTATTATTA-CCT
54464985 TATTATTTATATA-CT
1 TATTA-TTAT-TACCT
54465000 TATTATTATTAC
1 TATTATTATTAC
54465012 TATATTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.06
14 13 0.36
15 18 0.50
16 1 0.03
17 2 0.06
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTATTATTACCT
Found at i:54464981 original size:14 final size:14
Alignment explanation
Indices: 54464956--54464992 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
54464946 ATTAATTTAA
54464956 TATTATTATTACCAT
1 TATTATT-TTACCAT
*
54464971 TATTATTTTACCCT
1 TATTATTTTACCAT
54464985 TATTATTT
1 TATTATTT
54464993 ATATACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.27, C:0.14, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATTTTACCAT
Found at i:54465174 original size:15 final size:16
Alignment explanation
Indices: 54465151--54465180 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54465141 AGACTATTTA
54465151 TTTATTTTTTATTATT
1 TTTATTTTTTATTATT
54465167 TTTA-TTTTTATTAT
1 TTTATTTTTTATTAT
54465181 AACTCTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTTTTTATTATT
Found at i:54465250 original size:3 final size:3
Alignment explanation
Indices: 54465242--54465269 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54465232 TGTTACTACC
54465242 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
54465270 CAATCTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:54465411 original size:21 final size:22
Alignment explanation
Indices: 54465387--54465431 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
54465377 TAGTATGGCT
* *
54465387 TTGTTTTTTTTAATTGTT-TTA
1 TTGTTGTTATTAATTGTTATTA
*
54465408 TTGTTGTTATTCATTGTTATTA
1 TTGTTGTTATTAATTGTTATTA
54465430 TT
1 TT
54465432 TATTTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.16, C:0.02, G:0.11, T:0.71
Consensus pattern (22 bp):
TTGTTGTTATTAATTGTTATTA
Found at i:54483674 original size:22 final size:22
Alignment explanation
Indices: 54483619--54483689 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 22
54483609 AAAGAATAAC
* * *
54483619 ATTTTCTATCAAAATA-ATAAT
1 ATTTTATATTAAAATATAAAAT
*
54483640 A-TTTAAATATAAAATATAAAAT
1 ATTTTATAT-TAAAATATAAAAT
54483662 ATTTTATATTAAATTATATTAAAAT
1 ATTTTATATTAAA--ATA-TAAAAT
54483687 ATT
1 ATT
54483690 CAAAATATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
20 5 0.13
21 7 0.18
22 9 0.23
23 6 0.15
24 3 0.08
25 9 0.23
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTATATTAAAATATAAAAT
Found at i:54483680 original size:10 final size:10
Alignment explanation
Indices: 54483665--54483723 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
54483655 ATAAAATATT
54483665 TTATATTAAA
1 TTATATTAAA
54483675 TTATATTAAA
1 TTATATTAAA
54483685 --ATATTCAAA
1 TTATATT-AAA
*
54483694 ATATTATTAAA
1 TTA-TATTAAA
*
54483705 TCATATTAAA
1 TTATATTAAA
*
54483715 CTAT-TTAAA
1 TTATATTAAA
54483724 AATATTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
8 5 0.12
9 8 0.20
10 19 0.46
11 5 0.12
12 4 0.10
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (10 bp):
TTATATTAAA
Found at i:54483696 original size:9 final size:8
Alignment explanation
Indices: 54483637--54483699 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 8
54483627 TCAAAATAAT
*
54483637 AATATTTA
1 AATATTAA
54483645 AATA-TAA
1 AATATTAA
54483652 AATA-TAA
1 AATATTAA
*
54483659 AATATT-T
1 AATATTAA
*
54483666 TATATTAA
1 AATATTAA
54483674 ATTATATTAA
1 A--ATATTAA
54483684 AATATTCAA
1 AATATT-AA
54483693 AATATTA
1 AATATTA
54483700 TTAAATCATA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
7 18 0.40
8 11 0.24
9 8 0.18
10 8 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
AATATTAA
Found at i:54483704 original size:30 final size:31
Alignment explanation
Indices: 54483668--54483729 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
54483658 AAATATTTTA
* *
54483668 TATTAAATTATATTAAAATA-TTCAAAATAT
1 TATTAAATCATATTAAAATATTTAAAAATAT
*
54483698 TATTAAATCATATTAAACTATTTAAAAATAT
1 TATTAAATCATATTAAAATATTTAAAAATAT
54483729 T
1 T
54483730 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTAAATCATATTAAAATATTTAAAAATAT
Found at i:54483800 original size:25 final size:25
Alignment explanation
Indices: 54483761--54483842 Score: 105
Period size: 25 Copynumber: 3.4 Consensus size: 25
54483751 ATTAGAAATG
*
54483761 ATATTTTATTTTAAATTATATTAAA
1 ATATTTTATATTAAATTATATTAAA
* * *
54483786 ATATTTTATAATAAA-TAAATT-TA
1 ATATTTTATATTAAATTATATTAAA
54483809 ATATTTTATATTAAATTATATTAAA
1 ATATTTTATATTAAATTATATTAAA
*
54483834 ATTTTTTAT
1 ATATTTTAT
54483843 TTTTTAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
23 15 0.32
24 10 0.21
25 22 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATTTTATATTAAATTATATTAAA
Found at i:54485725 original size:23 final size:23
Alignment explanation
Indices: 54485691--54485741 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
54485681 AACCCATTTA
*
54485691 TGTAATATCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
54485714 TGTAATACCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
54485737 AGTAA
1 TGTAA
54485742 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACTAC
Found at i:54488153 original size:50 final size:50
Alignment explanation
Indices: 54488006--54488337 Score: 289
Period size: 49 Copynumber: 6.6 Consensus size: 50
54487996 CGATCTCGTA
*** * * *
54488006 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGA-G--CCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA-TG
* *
54488054 TAAGACCATGTCTGAGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCCCATG
* *
54488110 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCACATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* * *
54488160 TAAGA-CATGTCTGGGACATGACGTTGGCACTGAGATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* * * **
54488209 TAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* * * * * * ** *
54488259 TAAGACCATATCTGGGATATGACATTGGCA--GTATAAGAAACATCTCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTCCCATG
* *
54488308 TAAGACCATGTCTGGGATATGGCTTTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
54488338 TGTTATTATC
Statistics
Matches: 237, Mismatches: 36, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
48 27 0.11
49 85 0.36
50 80 0.34
51 2 0.01
53 3 0.01
54 5 0.02
55 2 0.01
56 30 0.13
57 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
Found at i:54488185 original size:49 final size:50
Alignment explanation
Indices: 54488052--54488288 Score: 269
Period size: 50 Copynumber: 4.6 Consensus size: 50
54488042 TGTGAGCCAG
* * *
54488052 TGTAAGACCATGTCTGAGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGACATTGGCA-C--CGAG---ATGAGAGGTCCCA
* * *
54488108 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCACA
1 TGTAAGACCATGTCTGGGACATGACATTGGCACCGAGATGAGAGGTCCCA
* *
54488158 TGTAAGA-CATGTCTGGGACATGACGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGACATTGGCACCGAGATGAGAGGTCCCA
* * * * **
54488207 TGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATGACATTGGCACCGAGATGAGAGGTCCCA
* *
54488257 TGTAAGACCATATCTGGGATATGACATTGGCA
1 TGTAAGACCATGTCTGGGACATGACATTGGCA
54488289 GTATAAGAAA
Statistics
Matches: 160, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
49 46 0.29
50 80 0.50
53 3 0.02
55 1 0.01
56 30 0.19
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGACATTGGCACCGAGATGAGAGGTCCCA
Found at i:54488216 original size:99 final size:99
Alignment explanation
Indices: 54488006--54488337 Score: 301
Period size: 99 Copynumber: 3.3 Consensus size: 99
54487996 CGATCTCGTA
*** * * * * * * *
54488006 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGAGC-CA-GTGTAAGACCATGTCTGA
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCACATGTAAGACCATATCTGG
*
54488069 GACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
66 GACATGACATTGGCA-C--T-AG---ATGAGAGGTCCCATG
* ** *
54488110 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCACATGTAAGA-CATGTCTGG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCACATGTAAGACCATATCTGG
*
54488174 GACATGACGTTGGCACTGAGATGAGAGGTCCCATG
66 GACATGACATTGGCACT-AGATGAGAGGTCCCATG
* * * *
54488209 TAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCACATGTAAGACCATATCTGG
* * * * * ** *
54488274 GATATGACATTGGCAGTATAAGAAACATCTCATG
66 GACATGACATTGGCACTAGATGAGAGGTCCCATG
* *
54488308 TAAGACCATGTCTGGGATATGGCTTTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
54488338 TGTTATTATC
Statistics
Matches: 192, Mismatches: 33, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
99 100 0.52
100 22 0.11
102 4 0.02
104 36 0.19
105 23 0.12
106 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (99 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCACATGTAAGACCATATCTGG
GACATGACATTGGCACTAGATGAGAGGTCCCATG
Found at i:54489867 original size:23 final size:23
Alignment explanation
Indices: 54489817--54489861 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
54489807 GGGAGAGAAA
* *
54489817 TGTAATATCCTGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
54489840 TGTAATACCCCGAAAATTACTA
1 TGTAATACCCCGAAAATTACTA
54489862 TAGTAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:54492178 original size:16 final size:16
Alignment explanation
Indices: 54492157--54492196 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
54492147 TAATTTGATG
*
54492157 ATTTTACTAACAATTA
1 ATTTTAATAACAATTA
*
54492173 ATTTTAATAATAATTA
1 ATTTTAATAACAATTA
*
54492189 GTTTTAAT
1 ATTTTAAT
54492197 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTTAATAACAATTA
Found at i:54492197 original size:22 final size:23
Alignment explanation
Indices: 54492170--54492231 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
54492160 TTACTAACAA
* *
54492170 TTAATTTTAATAATAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
*
54492192 TTAATTTTATTAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
54492215 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
54492232 CGGGCCGGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 15 0.44
23 13 0.38
24 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:54494742 original size:37 final size:37
Alignment explanation
Indices: 54494645--54494775 Score: 154
Period size: 37 Copynumber: 3.5 Consensus size: 37
54494635 ACTAGTTTGG
* ** * *
54494645 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAAATAA
1 CACCCAGTGCCTCATCGGCTAAACCGAAG---TAAATTGA
* * *
54494685 CACCTAGTGTCTCATCGGCTAAACCGAAGTAAATTGG
1 CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
*
54494722 CACCCAGTGCCTCATCGGCTAAACTGAAGTAAATTGA
1 CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
54494759 CACCCAGTGCCTCATCG
1 CACCCAGTGCCTCATCG
54494776 AATTAATTCG
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
37 55 0.70
40 24 0.30
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.22
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
Found at i:54502929 original size:17 final size:16
Alignment explanation
Indices: 54502892--54502930 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
54502882 AATAAATAAT
54502892 TAAA-TAAATTGAAAA
1 TAAATTAAATTGAAAA
54502907 TAAAATTAAATTGAGAAA
1 T-AAATTAAATTGA-AAA
54502925 TAAATT
1 TAAATT
54502931 TAGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 13 0.62
18 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGAAAA
Found at i:54506547 original size:141 final size:141
Alignment explanation
Indices: 54506307--54506562 Score: 381
Period size: 141 Copynumber: 1.8 Consensus size: 141
54506297 AGAAGCAGCT
* *
54506307 CTCTTCTTGCCTTTCTCTATGGCATGCTCGAGAAGAATTTAGGGCTAGTGGCCGAAGGCGAAGCA
1 CTCTTCTTGCCTTTCTATATGGCATGCCCGAGAAGAATTTAGGGCTAGTGGCCGAAGGCGAAGCA
*
54506372 AGCAATAAAGGCTGAGTGAGAAGGACTGTAGGGTTGAGTGAGGAAAGTTTTAGAACGGAGAAAAA
66 AGCAATAAAGGCTGAGTGAGAAGGACTGTAGGGTTGAGTGAAGAAAGTTTTAGAACGGAGAAAAA
54506437 CAAAGGTGACC
131 CAAAGGTGACC
* * *
54506448 CTCTTCTTGCCTTTCTATATGGCATGCCCGAGAAGAGTTTAGGGCTAGTGGCCGGAGGTGAAGCA
1 CTCTTCTTGCCTTTCTATATGGCATGCCCGAGAAGAATTTAGGGCTAGTGGCCGAAGGCGAAGCA
** * * *
54506513 AGCAATGGAGGCTG-GATGAG-AGGAGTTGTCGGGTTGAGTGAAGAAGGTTT
66 AGCAATAAAGGCTGAG-TGAGAAGGA-CTGTAGGGTTGAGTGAAGAAAGTTT
54506563 CAAAATGATA
Statistics
Matches: 102, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
140 5 0.05
141 97 0.95
ACGTcount: A:0.27, C:0.15, G:0.34, T:0.24
Consensus pattern (141 bp):
CTCTTCTTGCCTTTCTATATGGCATGCCCGAGAAGAATTTAGGGCTAGTGGCCGAAGGCGAAGCA
AGCAATAAAGGCTGAGTGAGAAGGACTGTAGGGTTGAGTGAAGAAAGTTTTAGAACGGAGAAAAA
CAAAGGTGACC
Found at i:54512133 original size:26 final size:28
Alignment explanation
Indices: 54512101--54512159 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
54512091 TGGGTTAATG
54512101 ATTTAATATAAATAA-AAATAT-ATATT
1 ATTTAATATAAATAATAAATATGATATT
* *
54512127 ATTTAATATATATAATTAATATGATATT
1 ATTTAATATAAATAATAAATATGATATT
*
54512155 TTTTA
1 ATTTA
54512160 TAAGATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 14 0.50
27 5 0.18
28 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
ATTTAATATAAATAATAAATATGATATT
Found at i:54512134 original size:14 final size:14
Alignment explanation
Indices: 54512117--54512159 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54512107 TATAAATAAA
54512117 AATATATATTATTT
1 AATATATATTATTT
*
54512131 AATATATA-TAATT
1 AATATATATTATTT
*
54512144 AATATGATATTTTTT
1 AATAT-ATATTATTT
54512159 A
1 A
54512160 TAAGATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.38
14 11 0.46
15 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
AATATATATTATTT
Found at i:54518568 original size:24 final size:24
Alignment explanation
Indices: 54518518--54518569 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54518508 AATTAAAGTC
* *
54518518 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
54518542 AAATATATTATACTCATAAATATT
1 AAATATATTATACTAATAAATACT
54518566 AAAT
1 AAAT
54518570 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:54522934 original size:24 final size:24
Alignment explanation
Indices: 54522907--54522958 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
54522897 AATCAAAGTC
* *
54522907 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
54522931 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
54522955 AAAT
1 AAAT
54522959 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:54524140 original size:16 final size:15
Alignment explanation
Indices: 54524119--54524149 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
54524109 CGGGGGGAGG
54524119 ATTTTCTTTTTATTTT
1 ATTTTC-TTTTATTTT
54524135 ATTTTCTTTTATTTT
1 ATTTTCTTTTATTTT
54524150 CTTTGTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (15 bp):
ATTTTCTTTTATTTT
Done.