Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 179 of 182
Found at i:54534755 original size:15 final size:15
Alignment explanation
Indices: 54534735--54534764 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54534725 CCAAGAAACT
54534735 CCCTGCCATTGCCCA
1 CCCTGCCATTGCCCA
54534750 CCCTGCCATTGCCCA
1 CCCTGCCATTGCCCA
54534765 TGTTTTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.53, G:0.13, T:0.20
Consensus pattern (15 bp):
CCCTGCCATTGCCCA
Found at i:54543134 original size:30 final size:31
Alignment explanation
Indices: 54543095--54543161 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
54543085 ATATTATTAG
*
54543095 GGTTAAATAT-CAAATTTATACATGAACTTT
1 GGTTTAATATACAAATTTATACATGAACTTT
* * *
54543125 GGTTTAATATACAATTTTATATATGAATTTT
1 GGTTTAATATACAAATTTATACATGAACTTT
*
54543156 GATTTA
1 GGTTTA
54543162 GTGCAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.46
Consensus pattern (31 bp):
GGTTTAATATACAAATTTATACATGAACTTT
Found at i:54545482 original size:11 final size:11
Alignment explanation
Indices: 54545448--54545522 Score: 71
Period size: 11 Copynumber: 6.8 Consensus size: 11
54545438 AACCATTTGA
*
54545448 AAATTAAATTT
1 AAATTTAATTT
*
54545459 -ATTTTAATCTT
1 AAATTTAAT-TT
*
54545470 AAATTTATTTT
1 AAATTTAATTT
*
54545481 AAATTCAATTT
1 AAATTTAATTT
* *
54545492 TAATTAAATTT
1 AAATTTAATTT
*
54545503 GAATTTAATTT
1 AAATTTAATTT
54545514 AAATTTAAT
1 AAATTTAAT
54545523 ATTATTATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
10 6 0.12
11 39 0.76
12 6 0.12
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:54545485 original size:33 final size:32
Alignment explanation
Indices: 54545448--54545539 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 32
54545438 AACCATTTGA
* *
54545448 AAATTAAATTTATTTTAATCTTAAATTTATTTT
1 AAATTAAATTTATTTAAAT-TTAAATTTAATTT
* * *
54545481 AAATTCAATTTTAATTAAATTTGAATTTAATTT
1 AAATT-AAATTTATTTAAATTTAAATTTAATTT
*
54545514 AAATTTAATATTATTATAAATTTAAA
1 AAATTAAAT-TTATT-TAAATTTAAA
54545540 AAGAAAAGTC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
32 2 0.04
33 25 0.53
34 20 0.43
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (32 bp):
AAATTAAATTTATTTAAATTTAAATTTAATTT
Found at i:54545536 original size:17 final size:15
Alignment explanation
Indices: 54545448--54545538 Score: 74
Period size: 17 Copynumber: 5.5 Consensus size: 15
54545438 AACCATTTGA
*
54545448 AAATTAAATTTATTT
1 AAATTTAATTTATTT
*
54545463 TAATCTTAAATTTATTTT
1 AAAT-TT-AATTTA-TTT
* *
54545481 AAATTCAATTTTAATT
1 AAATTTAA-TTTATTT
54545497 AAATTTGAATTTAATTT
1 AAATTT-AATTT-ATTT
54545514 AAATTTAATATTATTAT
1 AAATTTAAT-TTATT-T
54545531 AAATTTAA
1 AAATTTAA
54545539 AAAGAAAAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
15 3 0.05
16 19 0.31
17 33 0.54
18 6 0.10
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (15 bp):
AAATTTAATTTATTT
Found at i:54546346 original size:14 final size:13
Alignment explanation
Indices: 54546312--54546338 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54546302 AATAAAAATG
54546312 AATAAATATTTTT
1 AATAAATATTTTT
54546325 AATAAATATTTTT
1 AATAAATATTTTT
54546338 A
1 A
54546339 CAATAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATAAATATTTTT
Found at i:54547260 original size:152 final size:153
Alignment explanation
Indices: 54547018--54547311 Score: 473
Period size: 152 Copynumber: 1.9 Consensus size: 153
54547008 CCAGAGGCTG
* * * *
54547018 CCACGTGTCTTTTTTTGGCTTATTTATGCATTTAGTCCCTGACATTTTTTATTAGTTTTAATTTA
1 CCACATGTCATTTTTTGGCTTATTTATGCATTTAATCCCTGACATTTTTAATTAGTTTTAATTTA
* * * * *
54547083 ATCCCTAAATCAACTTTTATTTAATTATAAAATTGGCTCAAGAATTTTTCAAGGTTTATAAATTA
66 ATCCCTAAATCAACTTTTACTTAATTACAAAATTGGCCCAAGAATTTTTCAAGATTTACAAATTA
*
54547148 GTCCTTTGACTGTTTGACTGCAC
131 ATCCTTTGACTGTTTGACTGCAC
*
54547171 CCACATGTCATTTTTTGGCTTATTTATGCATTTAATCCCTGACATTTTTAATTTG-TTTAATTTA
1 CCACATGTCATTTTTTGGCTTATTTATGCATTTAATCCCTGACATTTTTAATTAGTTTTAATTTA
*
54547235 ATCCCTAAATCAACTTTTACTTAATTACAAAATTGGCCCAAGAATTTTTCAAGATTTACAATTTA
66 ATCCCTAAATCAACTTTTACTTAATTACAAAATTGGCCCAAGAATTTTTCAAGATTTACAAATTA
54547300 ATCCTTTGACTG
131 ATCCTTTGACTG
54547312 GTGGATGCCT
Statistics
Matches: 129, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
152 79 0.61
153 50 0.39
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (153 bp):
CCACATGTCATTTTTTGGCTTATTTATGCATTTAATCCCTGACATTTTTAATTAGTTTTAATTTA
ATCCCTAAATCAACTTTTACTTAATTACAAAATTGGCCCAAGAATTTTTCAAGATTTACAAATTA
ATCCTTTGACTGTTTGACTGCAC
Found at i:54547449 original size:29 final size:30
Alignment explanation
Indices: 54547385--54547454 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
54547375 AACAATCTAG
* * *
54547385 AAATTGCATTTTGACCCCAAAATTTCAAGA
1 AAATTACATTCTGACCCCAAAACTTCAAGA
* *
54547415 AAATTACATTCTGACCCCGAAACTTCCA-A
1 AAATTACATTCTGACCCCAAAACTTCAAGA
54547444 AAATTATCATT
1 AAATTA-CATT
54547455 TTACTCTCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 7 0.21
30 27 0.79
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (30 bp):
AAATTACATTCTGACCCCAAAACTTCAAGA
Found at i:54547503 original size:59 final size:59
Alignment explanation
Indices: 54547440--54547696 Score: 354
Period size: 59 Copynumber: 4.4 Consensus size: 59
54547430 CCCGAAACTT
* * * * *
54547440 CCAAAAATTATCATTTTACTCTCGAACCTTCTAAAACTCCATTTTTAACCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCA
* * * * * * *
54547499 CCAAAAATTATCGTTTTACTCCCGAACTTTCTAAAATTCCATTTTTAACCTCAATTTTA
1 CCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCA
* * *
54547558 CCAAAAATTACCGTTTTACCCCCGGACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCA
*
54547617 CCAAAAATTACCATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCA
*
54547676 CC-AAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
54547697 TGGGTGTCCA
Statistics
Matches: 178, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 17 0.10
59 161 0.90
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCA
Found at i:54547544 original size:29 final size:28
Alignment explanation
Indices: 54547512--54547670 Score: 103
Period size: 29 Copynumber: 5.4 Consensus size: 28
54547502 AAAATTATCG
54547512 TTTTACTCCCGAACTTTCTAAAATTCCAT
1 TTTTAC-CCCGAACTTTCTAAAATTCCAT
* * * *
54547541 TTTTAACCTC-AATTTTACCAAAAATTACC-G
1 TTTT-ACCCCGAACTTT--CTAAAATT-CCAT
*
54547571 TTTTACCCCCGGACTTTCTAAAATTCCAT
1 TTTTA-CCCCGAACTTTCTAAAATTCCAT
*
54547600 TTTTAACCCCG-A-TTTCACCAAAAATTACCA-
1 TTTT-ACCCCGAACTTT---CTAAAATT-CCAT
*
54547630 TTTTACCCTCGAACCTTCTAAAATTCCAT
1 TTTTACCC-CGAACTTTCTAAAATTCCAT
54547659 TTTTAACCCCGA
1 TTTT-ACCCCGA
54547671 TTTCACCAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
27 3 0.03
28 11 0.11
29 41 0.41
30 34 0.34
31 10 0.10
32 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.36
Consensus pattern (28 bp):
TTTTACCCCGAACTTTCTAAAATTCCAT
Found at i:54547681 original size:29 final size:28
Alignment explanation
Indices: 54547472--54547691 Score: 107
Period size: 30 Copynumber: 7.5 Consensus size: 28
54547462 CGAACCTTCT
* *
54547472 AAAACTCCATTTTTAACCCCGGTTTCACC
1 AAAATTCCATTTTTAACCCCGATTT-ACC
*
54547501 AAAAATT--ATCGTTTT-ACTCCCGAACTTT-CT
1 -AAAATTCCAT--TTTTAAC-CCCG-A-TTTACC
* *
54547531 AAAATTCCATTTTTAACCTCAATTTTACC
1 AAAATTCCATTTTTAACCCCGA-TTTACC
* * *
54547560 AAAAATTACC-GTTTTACCCCCGGACTTT-CT
1 -AAAATT-CCATTTTTAACCCC-GA-TTTACC
54547590 AAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATTCCATTTTTAACCCCGATTT-ACC
* *
54547619 AAAAATTACCA-TTTT-ACCCTCGAACCTT-CT
1 -AAAATT-CCATTTTTAACCC-CG-A-TTTACC
54547649 AAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATTCCATTTTTAACCCCGATTT-ACC
54547678 AAAATTACCATTTT
1 AAAATT-CCATTTT
54547692 GCCCCTGGGT
Statistics
Matches: 145, Mismatches: 20, Indels: 50
0.67 0.09 0.23
Matches are distributed among these distances:
27 5 0.03
28 14 0.10
29 54 0.37
30 55 0.38
31 12 0.08
32 5 0.03
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTTAACCCCGATTTACC
Found at i:54554518 original size:174 final size:173
Alignment explanation
Indices: 54554217--54554593 Score: 445
Period size: 174 Copynumber: 2.2 Consensus size: 173
54554207 TAGGGATTGA
* * * * * *
54554217 TTTTTTT-TCTAAGTTAATCTCTGAACTTCGCACTTGTTTTCATATTGAGGCTTGGATTAGGCAA
1 TTTTTTTGTCTAAGTTAATCT-TAAACTTCGCACTTGTTCTCACATTGAGGCTCGGACTAGACAA
* * *
54554281 CTGGTCTCACTTTGGAGCTTAGACGTTTCTTTGTCTAAGTTAATCTCTCAACTTAAAAATTGTTC
65 CTGCTCTCACTTTGGAGCTTAGACGTTTCTTTGTCTAAATTAATCTCTAAACTTAAAAATTGTTC
*
54554346 CCACATTAGGGTCTAGACTAGAG-AACTATTCCCATGGCTTAGAC
130 CCACATTAAGGTCTAGACTAG-GCAACTATTCCCATGGCTTAGAC
* * *
54554390 TTTTTTTGTCCAAGTTAATCCTTAAACTTGGCACTTGTTCTCACATTGGGGCTCGGACTAGACAA
1 TTTTTTTGTCTAAGTTAAT-CTTAAACTTCGCACTTGTTCTCACATTGAGGCTCGGACTAGACAA
* * * * * *
54554455 TTGCTCTCATTTTAGG-GTTTAGACTTTTTTTTGTCTAAATTAATCTCTAAACTTAATAATTGTT
65 CTGCTCTCACTTT-GGAGCTTAGACGTTTCTTTGTCTAAATTAATCTCTAAACTTAAAAATTGTT
* * * * * * *
54554519 CCCACATTAAGTTCTGGATTAGGCAATTGTTCTCGTGGCTTAGAC
129 CCCACATTAAGGTCTAGACTAGGCAACTATTCCCATGGCTTAGAC
54554564 TTTCTTTTGTCTAAGTTAATTCTTAAACTT
1 TTT-TTTTGTCTAAGTTAA-TCTTAAACTT
54554594 TATAATTATT
Statistics
Matches: 171, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
173 8 0.05
174 135 0.79
175 27 0.16
176 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (173 bp):
TTTTTTTGTCTAAGTTAATCTTAAACTTCGCACTTGTTCTCACATTGAGGCTCGGACTAGACAAC
TGCTCTCACTTTGGAGCTTAGACGTTTCTTTGTCTAAATTAATCTCTAAACTTAAAAATTGTTCC
CACATTAAGGTCTAGACTAGGCAACTATTCCCATGGCTTAGAC
Found at i:54554591 original size:85 final size:85
Alignment explanation
Indices: 54554297--54554600 Score: 269
Period size: 84 Copynumber: 3.5 Consensus size: 85
54554287 TCACTTTGGA
* * *
54554297 GCTTAGACGTTTC-TTTGTCTAAGTTAATCTCTCAACTTAAAAATTGTTCCCACATTAGGGTCTA
1 GCTTAGAC-TTTCTTTTGTCTAAGTTAATCTCTAAACTTAATAATTGTTCCCACATTAGGGTCTG
* * *
54554361 GACTAGAG-AACTATTCCCATG
65 GACTAG-GCAATTGTTCTCATG
* *** * * *
54554382 GCTTAGACTTT-TTTTGTCCAAGTTAATC-CTTAAACTTGGCACTTGTTCTCACATT-GGGGCTC
1 GCTTAGACTTTCTTTTGTCTAAGTTAATCTC-TAAACTTAATAATTGTTCCCACATTAGGGTCT-
* *
54554444 GGACTAGACAATTGCTCTCATTTTAGG
64 GGACTAGGCAATTGTTCTCA---T--G
* * * * *
54554471 GTTTAGACTTTTTTTTGTCTAAATTAATCTCTAAACTTAATAATTGTTCCCACATTAAGTTCTGG
1 GCTTAGACTTTCTTTTGTCTAAGTTAATCTCTAAACTTAATAATTGTTCCCACATTAGGGTCTGG
* *
54554536 ATTAGGCAATTGTTCTCGTG
66 ACTAGGCAATTGTTCTCATG
*
54554556 GCTTAGACTTTCTTTTGTCTAAGTTAAT-TCTTAAACTTTATAATT
1 GCTTAGACTTTCTTTTGTCTAAGTTAATCTC-TAAACTTAATAATT
54554601 ATTTCCATAT
Statistics
Matches: 173, Mismatches: 33, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
83 6 0.03
84 52 0.30
85 47 0.27
87 2 0.01
89 11 0.06
90 51 0.29
91 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (85 bp):
GCTTAGACTTTCTTTTGTCTAAGTTAATCTCTAAACTTAATAATTGTTCCCACATTAGGGTCTGG
ACTAGGCAATTGTTCTCATG
Found at i:54555064 original size:22 final size:21
Alignment explanation
Indices: 54555035--54555076 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
54555025 TTGGATTTCA
*
54555035 AATTTTAAAATATTTTAATTG
1 AATTTTAAAATATTATAATTG
*
54555056 AATTCTTAAGATATTATAATT
1 AATT-TTAAAATATTATAATT
54555077 ATATCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
AATTTTAAAATATTATAATTG
Found at i:54559548 original size:2 final size:2
Alignment explanation
Indices: 54559541--54559574 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54559531 TTATGTTTCT
54559541 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
54559575 GAGTCGATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54560020 original size:21 final size:22
Alignment explanation
Indices: 54559996--54560055 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
54559986 TGATCAAAGG
54559996 AAAAATAAAAG-AAATAGAA-T
1 AAAAATAAAAGAAAATAGAACT
*
54560016 TAAAATAAAAGAAAATAGAACT
1 AAAAATAAAAGAAAATAGAACT
*
54560038 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
54560056 GGAAGTCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 15 0.44
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAACT
Found at i:54560048 original size:15 final size:16
Alignment explanation
Indices: 54560021--54560050 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54560011 AGAATTAAAA
54560021 TAAAAGAAAATAGAAC
1 TAAAAGAAAATAGAAC
54560037 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
54560051 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (16 bp):
TAAAAGAAAATAGAAC
Found at i:54560879 original size:19 final size:19
Alignment explanation
Indices: 54560855--54560897 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54560845 AAATATAAAT
54560855 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
54560874 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
54560893 TAAAT
1 TAAAT
54560898 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:54561610 original size:106 final size:105
Alignment explanation
Indices: 54561465--54561656 Score: 260
Period size: 106 Copynumber: 1.8 Consensus size: 105
54561455 ATTTTGTGAA
* * * *
54561465 TTTTTTCTTTTTTTTTCTTTAAGAATACATTGGATCTTTTGATGCGAAATGAAATGACACCCAAG
1 TTTTTTCTTTTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAG
* *
54561530 CACTCCATCCTAGTTACTCAGCCCAACATGCTCTCAATTT
66 CACTCCACCCCAGTTACTCAGCCCAACATGCTCTCAATTT
* * * *
54561570 TTTTCTTCTTTTTTTTT-TTTGTAGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACAACCA
1 TTTT-TTCTTTTTTTTTCTTT-AAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCA
*
54561634 AGCACTCCACCCCGGTTACTCAG
64 AGCACTCCACCCCAGTTACTCAG
54561657 TCTAACACAT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
105 7 0.09
106 67 0.91
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (105 bp):
TTTTTTCTTTTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAG
CACTCCACCCCAGTTACTCAGCCCAACATGCTCTCAATTT
Found at i:54561693 original size:106 final size:105
Alignment explanation
Indices: 54561500--54561695 Score: 241
Period size: 106 Copynumber: 1.8 Consensus size: 105
54561490 TACATTGGAT
* * * *
54561500 CTTTTGATGCGAAATGAAATGACACCCAAGCACTCCATCCTAGTTACTCAGCCCAACATGCTCTC
1 CTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCAGTTACTCAGCCCAACA-GCTCTC
* * * *
54561565 AATTTTTTTCTTCTTTTTTTTTTTTGTAGAATGCATTAGCC
65 AATTTATTTATTATTTTCTTTTTTTGTAGAATGCATTAGCC
* * * * *
54561606 CTTTTGACGCGAAGTGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGTCTAACA-CATTTC
1 CTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCAGTTACTCAGCCCAACAGC-TCTC
54561670 GAATTTATTTATTATTTTCTTTTTTT
65 -AATTTATTTATTATTTTCTTTTTTT
54561696 TATTCGGGTT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
104 1 0.01
105 3 0.04
106 71 0.95
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (105 bp):
CTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCAGTTACTCAGCCCAACAGCTCTCA
ATTTATTTATTATTTTCTTTTTTTGTAGAATGCATTAGCC
Found at i:54564359 original size:21 final size:21
Alignment explanation
Indices: 54564329--54564388 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
54564319 TAGATGCCTC
*
54564329 AGTTTTCTTTTGAAAATCCAT
1 AGTTTGCTTTTGAAAATCCAT
* *
54564350 AGTTTGCTTTTGGAAATCTAT
1 AGTTTGCTTTTGAAAATCCAT
* **
54564371 AGATTGCCGTTGAAAATC
1 AGTTTGCTTTTGAAAATC
54564389 AAGAACTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (21 bp):
AGTTTGCTTTTGAAAATCCAT
Found at i:54565964 original size:21 final size:22
Alignment explanation
Indices: 54565918--54565978 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
54565908 TGATCTAAGG
*
54565918 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAACT
54565939 AAAAATAAAAGAAAATCA-AACT
1 AAAAATAAAAGAAAAT-AGAACT
*
54565961 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
54565979 GGAAGTCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 12 0.35
22 20 0.59
23 2 0.06
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAACT
Found at i:54566802 original size:19 final size:19
Alignment explanation
Indices: 54566778--54566820 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54566768 AAACATAAAT
54566778 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
54566797 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
54566816 TAAAT
1 TAAAT
54566821 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:54568804 original size:18 final size:17
Alignment explanation
Indices: 54568762--54568804 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
54568752 TTTTTTAGTT
*
54568762 TGTAATGTTTTATATTA
1 TGTAATTTTTTATATTA
54568779 TGCT-ATTTTTATATATTA
1 TG-TAATTTTT-TATATTA
54568797 TGTAATTT
1 TGTAATTT
54568805 ATAACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.60
Consensus pattern (17 bp):
TGTAATTTTTTATATTA
Found at i:54582810 original size:104 final size:104
Alignment explanation
Indices: 54582676--54582883 Score: 389
Period size: 104 Copynumber: 2.0 Consensus size: 104
54582666 GTGCATGTTT
* *
54582676 CACAATGCAAGTATGCTAGGGAGTTGCTTGAAAAGGCTCAGATGGCTAATGCAAATCCTGTGTCC
1 CACAATGCAAGTATGCTAGGGAGTTGCTTGAAAAGGCTCAGATGACTAATACAAATCCTGTGTCC
54582741 ACACTTATGGTTAGTTCTCCTACTCTCACCTCTTTGGTA
66 ACACTTATGGTTAGTTCTCCTACTCTCACCTCTTTGGTA
54582780 CACAATGCAAGTATGCTAGGGAGTTGCTTGAAAAGGCTCAGATGACTAATACAAATCCTGTGTCC
1 CACAATGCAAGTATGCTAGGGAGTTGCTTGAAAAGGCTCAGATGACTAATACAAATCCTGTGTCC
*
54582845 ACACTTATGGTTAGTTCTCCTACTCTCTCCTCTTTGGTA
66 ACACTTATGGTTAGTTCTCCTACTCTCACCTCTTTGGTA
54582884 GGAGCTAAGC
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (104 bp):
CACAATGCAAGTATGCTAGGGAGTTGCTTGAAAAGGCTCAGATGACTAATACAAATCCTGTGTCC
ACACTTATGGTTAGTTCTCCTACTCTCACCTCTTTGGTA
Found at i:54584169 original size:25 final size:25
Alignment explanation
Indices: 54584138--54584189 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
54584128 AGTTTGACTC
*
54584138 AAACAAATAAACAGAGTTTAATTGA
1 AAACAAATAAACAAAGTTTAATTGA
54584163 AAACAAATAAACAAAGTTTAATTGA
1 AAACAAATAAACAAAGTTTAATTGA
54584188 AA
1 AA
54584190 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.23
Consensus pattern (25 bp):
AAACAAATAAACAAAGTTTAATTGA
Found at i:54586067 original size:24 final size:24
Alignment explanation
Indices: 54586039--54586102 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
54586029 TAGAGTAATA
*
54586039 AGAATTTGACTAAAACAAATAAAC
1 AGAATTTAACTAAAACAAATAAAC
* *
54586063 AGAATTTAATTAAAAATAAATAAAC
1 AGAATTTAACT-AAAACAAATAAAC
*
54586088 AAAATTTAACTAAAA
1 AGAATTTAACTAAAA
54586103 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 13 0.38
25 21 0.62
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (24 bp):
AGAATTTAACTAAAACAAATAAAC
Found at i:54587578 original size:15 final size:16
Alignment explanation
Indices: 54587553--54587590 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
54587543 ATTTTTCTGG
54587553 GTAAGGCTCGACAAAT
1 GTAAGGCTCGACAAAT
*
54587569 GTAA-GCTCGACAGAT
1 GTAAGGCTCGACAAAT
54587584 GTGAAGG
1 GT-AAGG
54587591 ATAGATCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 12 0.63
16 6 0.32
17 1 0.05
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (16 bp):
GTAAGGCTCGACAAAT
Found at i:54591405 original size:20 final size:21
Alignment explanation
Indices: 54591377--54591416 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
54591367 TTTTCAAGAA
**
54591377 TTATCTTTTATTATTTTTAGG
1 TTATCTTTTAGGATTTTTAGG
54591398 TTAT-TTTTAGGATTTTTAG
1 TTATCTTTTAGGATTTTTAG
54591417 AACTATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (21 bp):
TTATCTTTTAGGATTTTTAGG
Found at i:54600534 original size:24 final size:24
Alignment explanation
Indices: 54600506--54600556 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
54600496 GTGCTGCACC
* *
54600506 TGATTTATCTGCAGATGTTGCTGG
1 TGATTTATCTACAGATGTTGCTAG
54600530 TGATTTATCTACAGATGTTGCTAG
1 TGATTTATCTACAGATGTTGCTAG
54600554 TGA
1 TGA
54600557 ATTGTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (24 bp):
TGATTTATCTACAGATGTTGCTAG
Found at i:54616463 original size:3 final size:3
Alignment explanation
Indices: 54616455--54616505 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
54616445 AGTGACTTCG
* * *
54616455 CAT CAT CAT CAT CAT CAT CAC CAT CAC CAT CAC CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
54616503 CAT
1 CAT
54616506 TCCATATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.27
Consensus pattern (3 bp):
CAT
Found at i:54618986 original size:30 final size:32
Alignment explanation
Indices: 54618943--54619025 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 32
54618933 ATAGTTTTTA
*
54618943 TTTTTATAAATTTTAAAAAATTAAA-T-TAATT
1 TTTTTAT-TATTTTAAAAAATTAAAGTATAATT
**
54618974 TTTTTATTATTTTAAAGGATTAAAGTATAATT
1 TTTTTATTATTTTAAAAAATTAAAGTATAATT
*
54619006 TAAATTTTATTAATTTAAAA
1 T---TTTTATTATTTTAAAA
54619026 TTTTAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
30 14 0.33
31 8 0.19
32 6 0.14
35 14 0.33
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (32 bp):
TTTTTATTATTTTAAAAAATTAAAGTATAATT
Found at i:54619021 original size:15 final size:16
Alignment explanation
Indices: 54619001--54619030 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54618991 GATTAAAGTA
54619001 TAATTT-AAATTTTAT
1 TAATTTAAAATTTTAT
54619016 TAATTTAAAATTTTA
1 TAATTTAAAATTTTA
54619031 AAATTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATTTAAAATTTTAT
Found at i:54622428 original size:14 final size:14
Alignment explanation
Indices: 54622405--54622437 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54622395 TAAATCTTTA
54622405 ATTAAATAAAATTT
1 ATTAAATAAAATTT
*
54622419 ATTAATTAAAATTT
1 ATTAAATAAAATTT
54622433 -TTAAA
1 ATTAAA
54622438 CCCTAAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTAAATAAAATTT
Found at i:54626782 original size:72 final size:72
Alignment explanation
Indices: 54626690--54626825 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
54626680 ACGCATCTCA
* * * *
54626690 TCCGGAAGCGATGTTAAATTGGGCAAA-TCAACGAGAGAAAGAGTTTGCAGATTTATTAGATGTT
1 TCCGAAAGCGATGCTAAATTGGGAAAATTC-ACGAGAGAAAGACTTTGCAGATTTATTAGATGTT
54626754 GAATCCAC
65 GAATCCAC
** *
54626762 TCCGAAAGCGATGCTAAATTGGGAAAATTCTTGAGAGAAAGCCTTTGCAGATTTATTAGATGTT
1 TCCGAAAGCGATGCTAAATTGGGAAAATTCACGAGAGAAAGACTTTGCAGATTTATTAGATGTT
54626826 CCCATTGCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 54 0.96
73 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (72 bp):
TCCGAAAGCGATGCTAAATTGGGAAAATTCACGAGAGAAAGACTTTGCAGATTTATTAGATGTTG
AATCCAC
Found at i:54631910 original size:6 final size:6
Alignment explanation
Indices: 54631876--54631937 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
54631866 TAATAGGGAT
* * * *
54631876 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*
54631923 TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTT
54631938 TGATCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 40 0.85
7 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:54634534 original size:35 final size:35
Alignment explanation
Indices: 54634488--54634559 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
54634478 AAATTTATCA
54634488 TCTGCTACTACCTTGTCTTCTGTGAATCCTGGAAC
1 TCTGCTACTACCTTGTCTTCTGTGAATCCTGGAAC
*
54634523 TCTGCTGCTACCTTGTCTTCTGTGAATCCTGGAAC
1 TCTGCTACTACCTTGTCTTCTGTGAATCCTGGAAC
54634558 TC
1 TC
54634560 CTTTTGGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (35 bp):
TCTGCTACTACCTTGTCTTCTGTGAATCCTGGAAC
Found at i:54640730 original size:16 final size:16
Alignment explanation
Indices: 54640711--54640744 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
54640701 TTAATAATTA
54640711 ATAATAAGAGT-ATAAT
1 ATAA-AAGAGTAATAAT
54640727 ATAAAAGAGTAATAAT
1 ATAAAAGAGTAATAAT
54640743 AT
1 AT
54640745 TTTAAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (16 bp):
ATAAAAGAGTAATAAT
Found at i:54664139 original size:14 final size:14
Alignment explanation
Indices: 54664120--54664158 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
54664110 TTGTTTGACT
*
54664120 GAAAATAGTTTCCG
1 GAAAATAATTTCCG
*
54664134 GAAAATAATTTCTG
1 GAAAATAATTTCCG
54664148 GAAAATGAATT
1 GAAAAT-AATT
54664159 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (14 bp):
GAAAATAATTTCCG
Found at i:54664496 original size:46 final size:46
Alignment explanation
Indices: 54664443--54664530 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
54664433 AAGTGAATTG
* ** * *
54664443 ATGATAACTACAATATTTTCCAAGTGTATAACTAGTATTACATCAC
1 ATGATAACTACAACATCGTCCAAGTGCATAACTAATATTACATCAC
54664489 ATGATAACTACAACATCGTCCAAGTGCATAACTAATATTACA
1 ATGATAACTACAACATCGTCCAAGTGCATAACTAATATTACA
54664531 AATTAGTAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (46 bp):
ATGATAACTACAACATCGTCCAAGTGCATAACTAATATTACATCAC
Found at i:54666173 original size:20 final size:20
Alignment explanation
Indices: 54666128--54666166 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54666118 CGAAAAGAAT
* *
54666128 AAAGAAAGAAAATTAGTTTA
1 AAAGAAAGAAAAATAGCTTA
54666148 AAAGAAAGAAAAATAGCTT
1 AAAGAAAGAAAAATAGCTT
54666167 GACAGAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.21
Consensus pattern (20 bp):
AAAGAAAGAAAAATAGCTTA
Found at i:54669192 original size:72 final size:72
Alignment explanation
Indices: 54669101--54669236 Score: 245
Period size: 72 Copynumber: 1.9 Consensus size: 72
54669091 AAGCATCTCA
*
54669101 TCCGGAAGCGATGTTAAATTGGGCAAATCAACCAGAGAAAGCCTTTGCAGATTTATTAGATGTTG
1 TCCGGAAGCGATGTTAAATTGGGCAAATCAAACAGAGAAAGCCTTTGCAGATTTATTAGATGTTG
54669166 AATCCAC
66 AATCCAC
* *
54669173 TCCGGAAGCGATGTTAAATTGGGCAAATCAAAGAGAGAAAGCTTTTGCAGATTTATTAGATGTT
1 TCCGGAAGCGATGTTAAATTGGGCAAATCAAACAGAGAAAGCCTTTGCAGATTTATTAGATGTT
54669237 CCCATTGCAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (72 bp):
TCCGGAAGCGATGTTAAATTGGGCAAATCAAACAGAGAAAGCCTTTGCAGATTTATTAGATGTTG
AATCCAC
Found at i:54680848 original size:3 final size:3
Alignment explanation
Indices: 54680840--54680877 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
54680830 AAGTGACTTC
* *
54680840 TCA TCA TCA TCA TCA GCA TCA ACA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
54680878 CCAATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (3 bp):
TCA
Found at i:54687654 original size:35 final size:35
Alignment explanation
Indices: 54687603--54687674 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
54687593 AGATTTATCA
*
54687603 TCTGCTGCTACCTTGTCTTCTGTGAATCCTGGAAC
1 TCTGCTGCTACCTTGTCTTCTATGAATCCTGGAAC
*
54687638 TCTGCTGCTACTTTGTCTTCTATGAATCCTGGAAC
1 TCTGCTGCTACCTTGTCTTCTATGAATCCTGGAAC
54687673 TC
1 TC
54687675 CTCCTTGAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.15, C:0.28, G:0.18, T:0.39
Consensus pattern (35 bp):
TCTGCTGCTACCTTGTCTTCTATGAATCCTGGAAC
Found at i:54693819 original size:29 final size:29
Alignment explanation
Indices: 54693787--54693875 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 29
54693777 AGTTTCGAAG
* * * *
54693787 AATTTAAGGTTAAAACGTAATTTTGAGAA
1 AATTTAAGGTCAAAATGTAATTTTAAAAA
* *
54693816 AATTCAAGGATCAAAATGTAAATTTAAAAA
1 AATTTAAGG-TCAAAATGTAATTTTAAAAA
*
54693846 AATTTGAAAGTCAAAATGTAATTTTAAAAA
1 AATTT-AAGGTCAAAATGTAATTTTAAAAA
54693876 TAGTGCGTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 8 0.16
30 38 0.78
31 3 0.06
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (29 bp):
AATTTAAGGTCAAAATGTAATTTTAAAAA
Found at i:54693972 original size:22 final size:22
Alignment explanation
Indices: 54693933--54693974 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
54693923 AAACTACGTC
* *
54693933 TGTATCTAATTTATCTTGTATT
1 TGTATCTAATATACCTTGTATT
*
54693955 TGTATCTAATATGCCTTGTA
1 TGTATCTAATATACCTTGTA
54693975 ATTATGTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (22 bp):
TGTATCTAATATACCTTGTATT
Found at i:54694485 original size:31 final size:31
Alignment explanation
Indices: 54694442--54694511 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
54694432 TTTAAATGTG
54694442 TATAATTGAATCA-AAATTAAAATTTCATTAA
1 TATAATTGAATCACAAA-TAAAATTTCATTAA
* * *
54694473 TATATTTGAATCACAAATAAAATTTTATTTA
1 TATAATTGAATCACAAATAAAATTTCATTAA
54694504 TATAATTG
1 TATAATTG
54694512 CACTGAATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (31 bp):
TATAATTGAATCACAAATAAAATTTCATTAA
Found at i:54697327 original size:2 final size:2
Alignment explanation
Indices: 54697320--54697344 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54697310 ATGAACATAA
54697320 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
54697345 AAAACATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54699966 original size:6 final size:6
Alignment explanation
Indices: 54699956--54699988 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
54699946 AGCGATTTCT
*
54699956 CATCAT CATCAG CATCAG CATCAG CATCAG CAT
1 CATCAG CATCAG CATCAG CATCAG CATCAG CAT
54699989 TCCCTACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.21
Consensus pattern (6 bp):
CATCAG
Found at i:54703450 original size:17 final size:17
Alignment explanation
Indices: 54703402--54703452 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
54703392 AAATTTAATT
*
54703402 ATTTAAT-TGTTATAAAA
1 ATTTAATAT-TTATATAA
* *
54703419 ATTAAATATAT-TATAA
1 ATTTAATATTTATATAA
54703435 ATTTAATATTTATATAA
1 ATTTAATATTTATATAA
54703452 A
1 A
54703453 AATTTTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 13 0.48
17 13 0.48
18 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTTAATATTTATATAA
Found at i:54711257 original size:7 final size:7
Alignment explanation
Indices: 54711245--54711270 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54711235 ATGTAAAATT
54711245 TTATTTA
1 TTATTTA
54711252 TTATTTA
1 TTATTTA
54711259 TTATTTA
1 TTATTTA
54711266 TTATT
1 TTATT
54711271 ATTGATAAAA
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:54719618 original size:17 final size:16
Alignment explanation
Indices: 54719581--54719611 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54719571 TTTAATTTAT
*
54719581 ATAATTATTTTTTAAA
1 ATAATAATTTTTTAAA
54719597 ATAATAATTTTTTAA
1 ATAATAATTTTTTAA
54719612 CATTAATCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAATAATTTTTTAAA
Found at i:54721100 original size:15 final size:17
Alignment explanation
Indices: 54721080--54721117 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
54721070 AATTACAAAT
54721080 ATTTGAA-TAAC-TATA
1 ATTTGAATTAACATATA
54721095 ATTTGAATTAACATTATA
1 ATTTGAATTAACA-TATA
54721113 ATTTG
1 ATTTG
54721118 TTAGGGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 4 0.20
18 9 0.45
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (17 bp):
ATTTGAATTAACATATA
Found at i:54729728 original size:22 final size:22
Alignment explanation
Indices: 54729700--54729743 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
54729690 ATAAATCTAC
*
54729700 CCTTTGTAACAAGGGTTTAACT
1 CCTTTGTAACAAGGGTGTAACT
54729722 CCTTTGTAACAAGGGTGTAACT
1 CCTTTGTAACAAGGGTGTAACT
54729744 AGGAGAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (22 bp):
CCTTTGTAACAAGGGTGTAACT
Found at i:54733016 original size:27 final size:25
Alignment explanation
Indices: 54732962--54733017 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
54732952 CGACTTATCC
*
54732962 TATATTATTTTTAAATTATCTAAAA
1 TATATTATTTTTAAATTATATAAAA
*
54732987 TATATTTATATTTTATAA-TATATAATA
1 TATA-TTAT-TTTTA-AATTATATAAAA
54733014 TATA
1 TATA
54733018 ATACATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 4 0.15
27 16 0.62
28 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATTATTTTTAAATTATATAAAA
Found at i:54736117 original size:24 final size:24
Alignment explanation
Indices: 54736085--54736133 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
54736075 CCAACTTCCA
54736085 ATCAAAAGATGACACATGACGGTT
1 ATCAAAAGATGACACATGACGGTT
54736109 ATCAAAAGATGACACATGACGGTT
1 ATCAAAAGATGACACATGACGGTT
54736133 A
1 A
54736134 AAAGGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (24 bp):
ATCAAAAGATGACACATGACGGTT
Found at i:54739606 original size:30 final size:29
Alignment explanation
Indices: 54739524--54739606 Score: 76
Period size: 31 Copynumber: 2.8 Consensus size: 29
54739514 ATCTCAAAAC
* * * *
54739524 TATACAAGAACTTTGATTTAATGTGCAATTT
1 TATACATGAATTTTAATTTGATGTG--ATTT
* *
54739555 TATCCGTGAATTTTAATTTGATGTGATTT
1 TATACATGAATTTTAATTTGATGTGATTT
*
54739584 TATACATGAATTTTTTATTTGAT
1 TATACATGAA-TTTTAATTTGAT
54739607 CTAATTCTCA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
29 12 0.29
30 11 0.26
31 19 0.45
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.49
Consensus pattern (29 bp):
TATACATGAATTTTAATTTGATGTGATTT
Found at i:54740934 original size:26 final size:26
Alignment explanation
Indices: 54740903--54740953 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
54740893 ATATTTTTCA
54740903 ATTTTCAAAAAATAAAAATAAAAATT
1 ATTTTCAAAAAATAAAAATAAAAATT
* *
54740929 ATTTTCTAAAAATGAAAATAAAAAT
1 ATTTTCAAAAAATAAAAATAAAAAT
54740954 AGAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (26 bp):
ATTTTCAAAAAATAAAAATAAAAATT
Found at i:54745855 original size:14 final size:14
Alignment explanation
Indices: 54745832--54745861 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54745822 CACATTAAAT
*
54745832 ATATTTAATAATAA
1 ATATTAAATAATAA
54745846 ATATTAAATAATAA
1 ATATTAAATAATAA
54745860 AT
1 AT
54745862 TAAAAAAAAG
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATTAAATAATAA
Found at i:54750791 original size:20 final size:20
Alignment explanation
Indices: 54750766--54750827 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
54750756 ATTTTGATAT
54750766 TTTAATAAAATATTAAAAAA
1 TTTAATAAAATATTAAAAAA
* * * *
54750786 TTTAAT-AAATCTTTAGATAT
1 TTTAATAAAAT-ATTAAAAAA
*
54750806 TTTAATAAAATATTAATAAA
1 TTTAATAAAATATTAAAAAA
54750826 TT
1 TT
54750828 AACCTTTCAT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
19 4 0.13
20 23 0.74
21 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTAATAAAATATTAAAAAA
Found at i:54762920 original size:51 final size:51
Alignment explanation
Indices: 54762851--54762950 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
54762841 AAGAAAATTT
* * *
54762851 GAATTTGAATTTTGCTATTTAGAGAAGACTTTGAAAATGAGAAATGCATAG
1 GAATTTGAATTTTCCTATTTACAGAAAACTTTGAAAATGAGAAATGCATAG
*
54762902 GAATTTGATTTTTCCTATTTACAGAAAACTTTGAAAATGAGAAATGCAT
1 GAATTTGAATTTTCCTATTTACAGAAAACTTTGAAAATGAGAAATGCAT
54762951 CTTCATTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (51 bp):
GAATTTGAATTTTCCTATTTACAGAAAACTTTGAAAATGAGAAATGCATAG
Found at i:54763842 original size:16 final size:16
Alignment explanation
Indices: 54763799--54763846 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
54763789 TCAAGTCAAG
* **
54763799 TCACTTCAAGTTCAAA
1 TCACTTCAAATTCTGA
* *
54763815 TCATTTCGAATTCTGA
1 TCACTTCAAATTCTGA
54763831 TCACTTCAAATTCTGA
1 TCACTTCAAATTCTGA
54763847 CCATTTCGGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (16 bp):
TCACTTCAAATTCTGA
Found at i:54771422 original size:19 final size:17
Alignment explanation
Indices: 54771398--54771432 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
54771388 ATTATTTGAA
54771398 TATTGTATAACTTTTATTT
1 TATTGT-TAA-TTTTATTT
54771417 TATTGTTAATTTTATT
1 TATTGTTAATTTTATT
54771433 ACCATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTATTT
Found at i:54779359 original size:55 final size:55
Alignment explanation
Indices: 54779289--54779440 Score: 202
Period size: 55 Copynumber: 2.8 Consensus size: 55
54779279 ATTTTGGGTC
* *
54779289 TGAACTTGACAATTGTTCTCACATTGGAGTTTAAATTTTTTTTCAAGTT-TGTCTT
1 TGAACTTAACAATTGTTCTCACATTGGAGTTTAAATTTTTTTTCAAGTTCT-TCCT
*
54779344 TGAACTTAACAATTGTTCTCACATT-AAGGTTTAAATTTTTTTTCAAGTTCTTCCT
1 TGAACTTAACAATTGTTCTCACATTGGA-GTTTAAATTTTTTTTCAAGTTCTTCCT
* * *
54779399 TGAACTTAGCAATTGCTC-CTACATTGGAGTTTGAATTTTTTT
1 TGAACTTAACAATTGTTCTC-ACATTGGAGTTTAAATTTTTTT
54779441 ATGGTCCAAG
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
54 2 0.02
55 82 0.95
56 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.47
Consensus pattern (55 bp):
TGAACTTAACAATTGTTCTCACATTGGAGTTTAAATTTTTTTTCAAGTTCTTCCT
Found at i:54792022 original size:2 final size:2
Alignment explanation
Indices: 54792015--54792041 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54792005 ACTGACATTG
54792015 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
54792042 TTTAATGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54797626 original size:32 final size:32
Alignment explanation
Indices: 54797580--54797660 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
54797570 TATTGGAATC
*
54797580 TAAACTTGACAATTATTACTGTATTGAAATTT
1 TAAACTTGAGAATTATTACTGTATTGAAATTT
*
54797612 TAAATTTGAGAATTATTACTGTATTGAAATTT
1 TAAACTTGAGAATTATTACTGTATTGAAATTT
54797644 TAAACTTGAGAATTATT
1 TAAACTTGAGAATTATT
54797661 GTCACATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.44
Consensus pattern (32 bp):
TAAACTTGAGAATTATTACTGTATTGAAATTT
Found at i:54798970 original size:16 final size:15
Alignment explanation
Indices: 54798940--54798979 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
54798930 TACGTGAATT
*
54798940 TAAAAATTCATTTAA
1 TAAAAATTAATTTAA
54798955 TAAAATATTAATTTAA
1 TAAAA-ATTAATTTAA
54798971 -AAAAATTAA
1 TAAAAATTAA
54798980 AATCATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 9 0.39
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAAATTAATTTAA
Found at i:54799109 original size:17 final size:19
Alignment explanation
Indices: 54799087--54799127 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
54799077 ATCTATATAT
54799087 TATTATATAA-AA-ATAAA
1 TATTATATAATAACATAAA
*
54799104 TATTATATAATAACATAAT
1 TATTATATAATAACATAAA
54799123 TATTA
1 TATTA
54799128 ATGCCATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 2 0.10
19 9 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TATTATATAATAACATAAA
Found at i:54804651 original size:18 final size:18
Alignment explanation
Indices: 54804628--54804697 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
54804618 AAAATGTAGG
*
54804628 AAATGATGTTAACATTTT
1 AAATGATGTTAACATTTC
*
54804646 AAATGATGTTAACACTTC
1 AAATGATGTTAACATTTC
54804664 AAATGATGTTCAA-ATTTC
1 AAATGATGTT-AACATTTC
54804682 AAATGATGTTAACATT
1 AAATGATGTTAACATT
54804698 GATGGAAACG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
17 2 0.04
18 43 0.91
19 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (18 bp):
AAATGATGTTAACATTTC
Found at i:54805219 original size:72 final size:72
Alignment explanation
Indices: 54805128--54805382 Score: 377
Period size: 72 Copynumber: 3.6 Consensus size: 72
54805118 AATGTTAAAC
* *
54805128 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTAATGTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATATTCTACTTATTTATG
54805193 TGTAATT
66 TGTAATT
* * *
54805200 TAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGAATATTGAATTTATATTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATATTCTACTTATTTATG
* *
54805265 TGCAATC
66 TGTAATT
* * * *
54805272 TAATTTTATCAATAGTTGTTTATGTTTGGTTTTTTGATATTGAATTTATTTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATATTCTACTTATTTATG
*
54805337 TGTATTT
66 TGTAATT
* *
54805344 TAGTTTTATTAATAGTTGTTTATATTTGA-TTTTGGATAT
1 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATAT
54805383 AAAATTTGTT
Statistics
Matches: 163, Mismatches: 20, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
71 9 0.06
72 154 0.94
ACGTcount: A:0.24, C:0.05, G:0.14, T:0.57
Consensus pattern (72 bp):
TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATATTCTACTTATTTATG
TGTAATT
Found at i:54815665 original size:27 final size:27
Alignment explanation
Indices: 54815627--54815687 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
54815617 GTATAAATGG
54815627 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
54815654 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
54815681 GTGGTGC
1 GTGGTGC
54815688 ATTTCTATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.16, C:0.31, G:0.36, T:0.16
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACCA
Found at i:54815858 original size:20 final size:23
Alignment explanation
Indices: 54815821--54815861 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
54815811 TTTTAATAAA
54815821 TATAAGAATTGTAGAAAAAATAT
1 TATAAGAATTGTAGAAAAAATAT
54815844 TATAA-AATT-TA-AAAAAAT
1 TATAAGAATTGTAGAAAAAAT
54815862 TAAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 4 0.22
23 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
TATAAGAATTGTAGAAAAAATAT
Found at i:54815980 original size:57 final size:55
Alignment explanation
Indices: 54815866--54815996 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 55
54815856 AAAAATTAAA
* * *
54815866 TTAAATATTAAATAAAAATAACTCAATATTTTTAAATAAATAATATAAAAAATAT
1 TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
** * *
54815921 TTATTTATCAAAATAATAATAATCTCCAGATTTTTACAAT-AATAATATAAGAGAA-AT
1 TTAAATAT-AAAATAATAATAA-CTCAAGATTTTTA-AATAAATAATATAA-AAAATAT
54815978 TTAAATATAAAA-AATAATA
1 TTAAATATAAAATAATAATA
54815997 CACTTTTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
55 13 0.21
56 15 0.24
57 29 0.46
58 6 0.10
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (55 bp):
TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
Found at i:54816103 original size:27 final size:27
Alignment explanation
Indices: 54816062--54816122 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
54816052 TTTTACAAGA
54816062 GGTGCCTACCAGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
**
54816089 GGTGCCTACTGGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
54816116 GGTGCCT
1 GGTGCCT
54816123 TTGTCAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.39, T:0.21
Consensus pattern (27 bp):
GGTGCCTACCAGGTAGGCGGCACTAGT
Found at i:54816254 original size:26 final size:26
Alignment explanation
Indices: 54816197--54816254 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
54816187 GTAAATTTTT
* * *
54816197 GAAGAAGGAAAGGAAACAAAAGTTTT
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
54816223 GAAGAAGAAAAGGAAACAGAAGGTTA
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
54816249 GCAGAA
1 GAAGAA
54816255 AATTTTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.05, G:0.29, T:0.10
Consensus pattern (26 bp):
GAAGAAGAAAAGGAAACAAAAGGTTA
Found at i:54819056 original size:28 final size:28
Alignment explanation
Indices: 54819003--54819060 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
54818993 CATTTTTCTG
*
54819003 TTGGAATTAATTAAATTTATGATTGAAT
1 TTGGAATTAATTAAATTTATAATTGAAT
**
54819031 TTGGAATTAATTCTATTTA-AATTTGAAT
1 TTGGAATTAATTAAATTTATAA-TTGAAT
54819059 TT
1 TT
54819061 ATTTAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAATTTATAATTGAAT
Found at i:54819101 original size:26 final size:26
Alignment explanation
Indices: 54819052--54819101 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
54819042 TCTATTTAAA
* *
54819052 TTTGAATTTATTTAATAGTTTTTATG
1 TTTGAATTAATTTAATAGTGTTTATG
54819078 TTTGAATTAATTTAATTAG-GTTTA
1 TTTGAATTAATTTAA-TAGTGTTTA
54819102 GCAAATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTAATTTAATAGTGTTTATG
Found at i:54819178 original size:6 final size:6
Alignment explanation
Indices: 54819167--54819225 Score: 84
Period size: 6 Copynumber: 9.8 Consensus size: 6
54819157 ATATTTGCAT
* *
54819167 ACATAA ACATAA ATA-AGA ACATAA ACATAA GCATAA ACATAA ACATAA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATAA ACATAA
54819215 ACATAA ACATA
1 ACATAA ACATA
54819226 TTTAATGGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
5 1 0.02
6 45 0.96
7 1 0.02
ACGTcount: A:0.64, C:0.15, G:0.03, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:54819667 original size:6 final size:6
Alignment explanation
Indices: 54819658--54819682 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54819648 CTGCGACTGC
54819658 GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA G
54819683 CCGGCTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:54821681 original size:17 final size:16
Alignment explanation
Indices: 54821649--54821680 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54821639 TTTTTTTTTA
54821649 AAAATATTTAATATAT
1 AAAATATTTAATATAT
54821665 AAAATATTTAA-ATAT
1 AAAATATTTAATATAT
54821680 A
1 A
54821681 TCAATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTTAATATAT
Found at i:54822680 original size:27 final size:27
Alignment explanation
Indices: 54822650--54822738 Score: 169
Period size: 27 Copynumber: 3.3 Consensus size: 27
54822640 CTGGTAGGTT
54822650 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
54822677 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
*
54822704 GGCACCACTGGTGTCGCCTACCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
54822731 GGCACCAC
1 GGCACCAC
54822739 CCAAAAATAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.22, C:0.40, G:0.26, T:0.11
Consensus pattern (27 bp):
GGCACCACTGGTGCCGCCTACCAGACA
Found at i:54832121 original size:44 final size:44
Alignment explanation
Indices: 54832053--54832158 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
54832043 AGTGCTGAAC
* *
54832053 ACTCATATCCGAAGCATATACTAACATAGGTATTGGTGTCTGAT
1 ACTCGTATCCGAAGCATATACTAACATAGGTATTGGCGTCTGAT
* *
54832097 ACTCGTATCCGAAGCATATACTAACATAGGTATTTGCGTTTGAT
1 ACTCGTATCCGAAGCATATACTAACATAGGTATTGGCGTCTGAT
*
54832141 ACTCGTATCCGAACCATA
1 ACTCGTATCCGAAGCATA
54832159 AAAATCAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (44 bp):
ACTCGTATCCGAAGCATATACTAACATAGGTATTGGCGTCTGAT
Found at i:54841677 original size:30 final size:30
Alignment explanation
Indices: 54841652--54841802 Score: 248
Period size: 30 Copynumber: 5.0 Consensus size: 30
54841642 CAATTTTTTG
54841652 AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* *
54841682 AAAGTTTTGGGGTTAAAATATGATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* *
54841712 AAAGTTCTGGGGTCAAAATATGATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
*
54841742 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
54841772 AAAGTTTTGGGGTCAAAATATAATTTCTGGA
1 AAAGTTTTGGGGTCAAAATATAATTT-TGGA
54841803 CAATTTAGGG
Statistics
Matches: 112, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
30 108 0.96
31 4 0.04
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATATAATTTTGGA
Found at i:54841694 original size:60 final size:58
Alignment explanation
Indices: 54841630--54841802 Score: 224
Period size: 60 Copynumber: 2.9 Consensus size: 58
54841620 AAAAGATTCG
*
54841630 GGGGTAAAATGGCAATTTTTTG-AAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTAAAAT-G-AA-TTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTT
* *
54841690 GGGGTTAAAAT-ATGATTTTGGAAAAGTTCTGGGGTCAAAATATGATTTTGGAAAAGTTTT
1 GGGG-TAAAATGA--ATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTT
54841750 GGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTCTGGA
1 GGGGT-AAAATG-AATTTTGGAAAAGTTTTGGGGTCAAAATATAATTT-TGGA
54841803 CAATTTAGGG
Statistics
Matches: 100, Mismatches: 5, Indels: 15
0.83 0.04 0.12
Matches are distributed among these distances:
58 1 0.01
59 6 0.06
60 82 0.82
61 10 0.10
62 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (58 bp):
GGGGTAAAATGAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTT
Found at i:54843719 original size:6 final size:6
Alignment explanation
Indices: 54843703--54843791 Score: 89
Period size: 6 Copynumber: 15.0 Consensus size: 6
54843693 TTTAATTTTT
**
54843703 TTTATAA TTTAAA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
54843753 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
54843792 ATCAATTTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
4 5 0.07
5 6 0.09
6 48 0.69
7 5 0.07
8 6 0.09
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:54843740 original size:11 final size:11
Alignment explanation
Indices: 54843724--54843774 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
54843714 AATTTAAATT
*
54843724 TAAATTTAAGG
1 TAAATTTAAGA
54843735 TAAATTTAA-A
1 TAAATTTAAGA
* **
54843745 T-AATTAAATT
1 TAAATTTAAGA
54843755 TAAATTTAAGA
1 TAAATTTAAGA
54843766 TAAATTTAA
1 TAAATTTAA
54843775 ATTTAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 24 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (11 bp):
TAAATTTAAGA
Found at i:54843776 original size:37 final size:38
Alignment explanation
Indices: 54843715--54843791 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 38
54843705 TATAATTTAA
*
54843715 ATTTAAATTTAAATTTAAGGTAAATTTAAATAA-TTAA
1 ATTTAAATTTAAATTAAAGGTAAATTTAAATAATTTAA
**
54843752 ATTTAAATTTAAGA-TAAATTTAAATTTAAATAAATTTAA
1 ATTTAAATTTAA-ATTAAAGGTAAATTTAAAT-AATTTAA
54843791 A
1 A
54843792 ATCAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 26 0.76
38 3 0.09
39 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (38 bp):
ATTTAAATTTAAATTAAAGGTAAATTTAAATAATTTAA
Found at i:54843793 original size:17 final size:16
Alignment explanation
Indices: 54843703--54843791 Score: 101
Period size: 17 Copynumber: 5.4 Consensus size: 16
54843693 TTTAATTTTT
54843703 TTTATAATTTAAATTTAAA
1 TTTA-AATTTAAA--TAAA
*
54843722 TTTAAATTTAAGGTAAA
1 TTTAAATTTAA-ATAAA
*
54843739 TTTAAA--TAATTAAA
1 TTTAAATTTAAATAAA
54843753 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
54843770 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
54843786 TTTAAA
1 TTTAAA
54843792 ATCAATTTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
16 14 0.22
17 25 0.40
18 7 0.11
19 4 0.06
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:54856084 original size:33 final size:33
Alignment explanation
Indices: 54856020--54856088 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
54856010 TATATTTGTC
* ***
54856020 TTTGGTATTTGAACTCAGTGAATGGTTTTGGTA
1 TTTGGTATTTGAACTCAGTGAAAGAACTTGGTA
* *
54856053 TTTGGTATTTGAATTCAGTTAAAGAACTTGGTA
1 TTTGGTATTTGAACTCAGTGAAAGAACTTGGTA
54856086 TTT
1 TTT
54856089 CTATGATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTGGTATTTGAACTCAGTGAAAGAACTTGGTA
Found at i:54860208 original size:37 final size:38
Alignment explanation
Indices: 54860158--54860236 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
54860148 GAAACATTAT
54860158 CATCTACTTTTGGTGATT-GGATATCCCAATTTGTGGC
1 CATCTACTTTTGGTGATTGGGATATCCCAATTTGTGGC
*
54860195 CATCTACTTTTGGTGATTGGGATATCCTAATTTGTGGC
1 CATCTACTTTTGGTGATTGGGATATCCCAATTTGTGGC
54860233 CATC
1 CATC
54860237 AAAGGTCTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 18 0.45
38 22 0.55
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (38 bp):
CATCTACTTTTGGTGATTGGGATATCCCAATTTGTGGC
Found at i:54863825 original size:50 final size:49
Alignment explanation
Indices: 54863751--54863847 Score: 176
Period size: 50 Copynumber: 2.0 Consensus size: 49
54863741 CAAAAATTGA
*
54863751 TTGATAGCTTTTTCTCTCAACCTCAGCAAAAATTGATTGATAGTTTTGT
1 TTGATAGCTTTTTCTCTCAACCTCAGCAAAAATTGATTGATAATTTTGT
54863800 TTGATAGTCTTTTTCTCTCAACCTCAGCAAAAATTGATTGATAATTTT
1 TTGATAG-CTTTTTCTCTCAACCTCAGCAAAAATTGATTGATAATTTT
54863848 TTTCTCTCAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 7 0.15
50 39 0.85
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (49 bp):
TTGATAGCTTTTTCTCTCAACCTCAGCAAAAATTGATTGATAATTTTGT
Found at i:54863850 original size:37 final size:37
Alignment explanation
Indices: 54863800--54863873 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
54863790 ATAGTTTTGT
*
54863800 TTGATAGTCTTTTTCTCTCAACCTCAGCAAAAATTGA
1 TTGATAATCTTTTTCTCTCAACCTCAGCAAAAATTGA
*
54863837 TTGATAATTTTTTTCTCTCAACCTCAGCAAAAATTGA
1 TTGATAATCTTTTTCTCTCAACCTCAGCAAAAATTGA
54863874 CTTTCTGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (37 bp):
TTGATAATCTTTTTCTCTCAACCTCAGCAAAAATTGA
Found at i:54868832 original size:16 final size:16
Alignment explanation
Indices: 54868811--54868842 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54868801 TAACTACCAA
54868811 CCACCATAATCAAATT
1 CCACCATAATCAAATT
*
54868827 CCACCATAATTAAATT
1 CCACCATAATCAAATT
54868843 TGTTATTAAC
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:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (16 bp):
CCACCATAATCAAATT
Found at i:54870491 original size:29 final size:29
Alignment explanation
Indices: 54870432--54870490 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
54870422 TATGGTTTAA
* *
54870432 TGTATAATTGTATACATAAATTTTGATTT
1 TGTATAATTGTATACATAAAATTAGATTT
* *
54870461 TGTATATTTTTATACATGAAAATTAGATTT
1 TGTATAATTGTATACAT-AAAATTAGATTT
54870491 GATTTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (29 bp):
TGTATAATTGTATACATAAAATTAGATTT
Found at i:54871874 original size:21 final size:22
Alignment explanation
Indices: 54871836--54871883 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
54871826 TTTTTTAAGG
54871836 TTTTTCTTTTCAGTTTTC-AAC
1 TTTTTCTTTTCAGTTTTCAAAC
*
54871857 TTTTTCTTTTC-CTGTTTCAAAC
1 TTTTTCTTTTCAGT-TTTCAAAC
54871879 TTTTT
1 TTTTT
54871884 TTAATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 15 0.62
22 8 0.33
ACGTcount: A:0.12, C:0.19, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTTCTTTTCAGTTTTCAAAC
Found at i:54872612 original size:6 final size:6
Alignment explanation
Indices: 54872603--54872631 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54872593 TCAGAAAGCT
54872603 AAAGGA AAAGGA AAAGGA AAAGGA AAAGG
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGG
54872632 CATCAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:54872618 original size:18 final size:18
Alignment explanation
Indices: 54872597--54872631 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54872587 AAGAAATCAG
*
54872597 AAAGCTAAAGGAAAAGGA
1 AAAGCAAAAGGAAAAGGA
*
54872615 AAAGGAAAAGGAAAAGG
1 AAAGCAAAAGGAAAAGG
54872632 CATCAAGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.03, G:0.31, T:0.03
Consensus pattern (18 bp):
AAAGCAAAAGGAAAAGGA
Found at i:54876410 original size:16 final size:16
Alignment explanation
Indices: 54876389--54876421 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54876379 ATCAAATTCA
54876389 ATATAGATCTAGAACT
1 ATATAGATCTAGAACT
54876405 ATATAGATCTAGAACT
1 ATATAGATCTAGAACT
54876421 A
1 A
54876422 CAGGTGCCTT
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:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (16 bp):
ATATAGATCTAGAACT
Found at i:54893377 original size:27 final size:26
Alignment explanation
Indices: 54893315--54893399 Score: 84
Period size: 25 Copynumber: 3.2 Consensus size: 26
54893305 ATGTTTGAAA
*
54893315 AAAAGAGTAATCTGAAAAAAACATATT
1 AAAA-AGTAATCTGAAAAAAAAATATT
*
54893342 AATAA-TAATCTGAAAAAAAAATA-T
1 AAAAAGTAATCTGAAAAAAAAATATT
*
54893366 AACAACAGTAATCTGAAAATAAAAAAATT
1 AA-AA-AGTAATCTGAAAA-AAAAATATT
*
54893395 CAAAA
1 AAAAA
54893400 TCATATTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
24 3 0.06
25 18 0.38
26 2 0.04
27 15 0.31
28 8 0.17
29 2 0.04
ACGTcount: A:0.64, C:0.08, G:0.07, T:0.21
Consensus pattern (26 bp):
AAAAAGTAATCTGAAAAAAAAATATT
Found at i:54893384 original size:25 final size:25
Alignment explanation
Indices: 54893320--54893384 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
54893310 TGAAAAAAAG
** *
54893320 AGTAATCTGAAAAAAACATATTAAT
1 AGTAATCTGAAAAAAACATAACAAC
* *
54893345 AATAATCTGAAAAAAAAATATAACAAC
1 AGTAATCTG--AAAAAAACATAACAAC
54893372 AGTAATCTGAAAA
1 AGTAATCTGAAAA
54893385 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 12 0.38
27 20 0.62
ACGTcount: A:0.60, C:0.09, G:0.08, T:0.23
Consensus pattern (25 bp):
AGTAATCTGAAAAAAACATAACAAC
Found at i:54895873 original size:31 final size:31
Alignment explanation
Indices: 54895822--54895889 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
54895812 AGTTTTTATA
* *
54895822 TTTTAATTTAATTAAATTTAGTCTCTATACT
1 TTTTAAATTAATTAAATTTAGTCCCTATACT
* *
54895853 TTTTAAATTAGTTAATTTTAGTCCCTATACT
1 TTTTAAATTAATTAAATTTAGTCCCTATACT
54895884 TTTTAA
1 TTTTAA
54895890 TTTTAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (31 bp):
TTTTAAATTAATTAAATTTAGTCCCTATACT
Found at i:54895904 original size:30 final size:30
Alignment explanation
Indices: 54895822--54895899 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
54895812 AGTTTTTATA
* * *
54895822 TTTTAATTTAATTAAATTTAGTCTCTATACT
1 TTTTAAATT-ATTAATTTTAGTCCCTATACT
54895853 TTTTAAATTAGTTAATTTTAGTCCCTATACT
1 TTTTAAATTA-TTAATTTTAGTCCCTATACT
54895884 TTTT-AATT-TTAATTTT
1 TTTTAAATTATTAATTTT
54895900 TTAGTTTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.19
30 5 0.12
31 30 0.70
ACGTcount: A:0.29, C:0.09, G:0.04, T:0.58
Consensus pattern (30 bp):
TTTTAAATTATTAATTTTAGTCCCTATACT
Found at i:54897611 original size:14 final size:14
Alignment explanation
Indices: 54897592--54897618 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54897582 TAATTAATTT
54897592 AAATTACACAAATA
1 AAATTACACAAATA
54897606 AAATTACACAAAT
1 AAATTACACAAAT
54897619 TATCTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATTACACAAATA
Found at i:54911268 original size:14 final size:16
Alignment explanation
Indices: 54911244--54911276 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
54911234 GATAAAAAAG
54911244 AATATTTTATATA-AA
1 AATATTTTATATATAA
54911259 AATA-TTTATATATAA
1 AATATTTTATATATAA
54911274 AAT
1 AAT
54911277 TTTCTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATTTTATATATAA
Found at i:54911276 original size:15 final size:15
Alignment explanation
Indices: 54911244--54911275 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
54911234 GATAAAAAAG
54911244 AATATTTTATATAAA
1 AATATTTTATATAAA
54911259 AATATTTATATATAAA
1 AATATTT-TATATAAA
54911275 A
1 A
54911276 TTTTCTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATTTTATATAAA
Found at i:54913002 original size:24 final size:24
Alignment explanation
Indices: 54912927--54913002 Score: 56
Period size: 24 Copynumber: 3.3 Consensus size: 24
54912917 ATATAAATAT
* *
54912927 TAAAATAA-TATTAAATAATT-ATA
1 TAAAATAATTAATAAAT-ATTAAAA
54912950 TAAAA-AATTTAATAAATA--AAAA
1 TAAAATAA-TTAATAAATATTAAAA
* *
54912972 T-ATATAATTACTAAATATTAAAA
1 TAAAATAATTAATAAATATTAAAA
54912995 TAAAATAA
1 TAAAATAA
54913003 ATATTTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 13
0.69 0.08 0.22
Matches are distributed among these distances:
21 11 0.27
22 7 0.17
23 11 0.27
24 12 0.29
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAAATAATTAATAAATATTAAAA
Found at i:54913511 original size:13 final size:13
Alignment explanation
Indices: 54913493--54913517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54913483 AGTTTAATTC
54913493 GATTTAAAATTTA
1 GATTTAAAATTTA
54913506 GATTTAAAATTT
1 GATTTAAAATTT
54913518 TACTTAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
GATTTAAAATTTA
Found at i:54919573 original size:96 final size:96
Alignment explanation
Indices: 54919247--54919573 Score: 458
Period size: 96 Copynumber: 3.4 Consensus size: 96
54919237 CGTTTCGGTA
* *
54919247 TCGTTGATTTACTTGTTCTTAATGTTTTTGATGTGTTTTGATTATTTTTTATTCATCATCTGATC
1 TCGTTGATTTACTTGTTCTTTATGTTTTTGA-----TTCGATTATTTTTTATTCATCATCTGATC
* *
54919312 TGAGTTAAATTTCTCAGATCTGTACAAGATCTGGTG
61 TGAGTTAAATTTCCCAGATCTGTACAAGATGTGGTG
* * * *
54919348 TCGTTTATTTACTTGTTCTTTATGATTTTT-ATTTGCTTATTTTTTATTCATCATCTGATCTAAG
1 TCGTTGATTTACTTGTTCTTTATG-TTTTTGATTCGATTATTTTTTATTCATCATCTGATCTGAG
*
54919412 TTAAATTCCCCAGATCTGTACAAGATGTGGTG
65 TTAAATTTCCCAGATCTGTACAAGATGTGGTG
* * * *
54919444 TCATTGATTTACTTGTTCTTTATGTTTTCGATTCGATTGTTTTTGATTCATCATCTGATCTGAGT
1 TCGTTGATTTACTTGTTCTTTATGTTTTTGATTCGATTATTTTTTATTCATCATCTGATCTGAGT
* *
54919509 TACATTTCCCAGATCTGAACAAGATGTGGTG
66 TAAATTTCCCAGATCTGTACAAGATGTGGTG
54919540 TCGTTGATTTACTTGTTCTTTATGTTTTTGATTC
1 TCGTTGATTTACTTGTTCTTTATGTTTTTGATTC
54919574 ATCATCTGAT
Statistics
Matches: 204, Mismatches: 20, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
95 4 0.02
96 172 0.84
101 23 0.11
102 5 0.02
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (96 bp):
TCGTTGATTTACTTGTTCTTTATGTTTTTGATTCGATTATTTTTTATTCATCATCTGATCTGAGT
TAAATTTCCCAGATCTGTACAAGATGTGGTG
Found at i:54929511 original size:38 final size:38
Alignment explanation
Indices: 54929460--54929536 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
54929450 AATCAAGAGT
54929460 TAATTTTTCCATTTGATTTTTTCTTCCTTCTCTAAGTG
1 TAATTTTTCCATTTGATTTTTTCTTCCTTCTCTAAGTG
54929498 TAATTTTTCCATTTGATTTTTTCTTCCTTCTCTAAGTG
1 TAATTTTTCCATTTGATTTTTTCTTCCTTCTCTAAGTG
54929536 T
1 T
54929537 TTTGAGCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.16, C:0.18, G:0.08, T:0.58
Consensus pattern (38 bp):
TAATTTTTCCATTTGATTTTTTCTTCCTTCTCTAAGTG
Found at i:54934418 original size:15 final size:15
Alignment explanation
Indices: 54934388--54934430 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
54934378 AAATTCAACC
*
54934388 CTTAATTTTTC-TTA
1 CTTAATTTTTCAATA
*
54934402 CTTATTTTTTCAATA
1 CTTAATTTTTCAATA
54934417 CTTAATTTTTCAAT
1 CTTAATTTTTCAAT
54934431 TTAAAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (15 bp):
CTTAATTTTTCAATA
Found at i:54938920 original size:30 final size:31
Alignment explanation
Indices: 54938864--54938921 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
54938854 TTTTGCTATT
*
54938864 ATATTGCTATTATTTTGTTGTTATTGTTGGG
1 ATATTGCTATAATTTTGTTGTTATTGTTGGG
54938895 ATATTG-TATAATTCTTGTT-TTATTGTT
1 ATATTGCTATAATT-TTGTTGTTATTGTT
54938922 ATTTTTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.19, C:0.03, G:0.17, T:0.60
Consensus pattern (31 bp):
ATATTGCTATAATTTTGTTGTTATTGTTGGG
Found at i:54939217 original size:13 final size:13
Alignment explanation
Indices: 54939199--54939231 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
54939189 TAATTTATTG
54939199 TTGAAAAGTGTTT
1 TTGAAAAGTGTTT
54939212 TTGAAAAGTGTTT
1 TTGAAAAGTGTTT
*
54939225 GTGAAAA
1 TTGAAAA
54939232 AATAATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.39
Consensus pattern (13 bp):
TTGAAAAGTGTTT
Found at i:54941952 original size:85 final size:85
Alignment explanation
Indices: 54941805--54941971 Score: 298
Period size: 85 Copynumber: 2.0 Consensus size: 85
54941795 CTTATCTTGT
* *
54941805 TTGATGCACTTTGGGTTTTTATATTTACTTTTCTCTATTTAAACAACATGGTTTTTGTGTGTTTT
1 TTGATGCACTTTGGGTTTCTATATTTACTTTTCTCTATTTAAACAACATGGTTTTTGGGTGTTTT
54941870 GCATGGACTTGGTGTTTCCC
66 GCATGGACTTGGTGTTTCCC
*
54941890 TTGATGCACTTTGGGTTTCTATATTTACTTTTCTCTATTTAAACTACATGGTTTTTGGGTGTTTT
1 TTGATGCACTTTGGGTTTCTATATTTACTTTTCTCTATTTAAACAACATGGTTTTTGGGTGTTTT
*
54941955 GCATGGGCTTGGTGTTT
66 GCATGGACTTGGTGTTT
54941972 TGCAATAATT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 78 1.00
ACGTcount: A:0.16, C:0.13, G:0.20, T:0.51
Consensus pattern (85 bp):
TTGATGCACTTTGGGTTTCTATATTTACTTTTCTCTATTTAAACAACATGGTTTTTGGGTGTTTT
GCATGGACTTGGTGTTTCCC
Found at i:54944147 original size:60 final size:60
Alignment explanation
Indices: 54944021--54944150 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 60
54944011 ACTAATAGTC
* * * *
54944021 ACCCAACTATTAGTAAATTTATTTTTGGTCATTTAACTAGGAAAAATTACAAAATGGTCT
1 ACCCAACTATTAGCAAATTTATTTTTGGCCACTAAACTAGGAAAAATTACAAAATGGTCT
* * * *
54944081 -CTCAACTATTAGCAAATTTATTTTTTGGCCACTAAACTATGAAAAGTTACAACATGGT-T
1 ACCCAACTATTAGCAAATTTA-TTTTTGGCCACTAAACTAGGAAAAATTACAAAATGGTCT
54944140 ACCCAACTATT
1 ACCCAACTATT
54944151 CAATTTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 19 0.32
60 40 0.68
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (60 bp):
ACCCAACTATTAGCAAATTTATTTTTGGCCACTAAACTAGGAAAAATTACAAAATGGTCT
Found at i:54944425 original size:189 final size:188
Alignment explanation
Indices: 54944078--54944645 Score: 904
Period size: 190 Copynumber: 3.0 Consensus size: 188
54944068 TACAAAATGG
* * * * * *
54944078 TCTCTCAACTATTAGCAAATTTATTTTTTGGCCACTAAACTATGAAAAGTTACAACATGGTTACC
1 TCTCTCAACTATTAGTAAATTTATTTTTTGGTCACTAAACTATAAAAAGTTACAAAATGATTATC
* *
54944143 CAACTATTCAATTTTTTTCTTTTTTGGTCACCAATTGACTAACATAAAAATGAAAATACTAAAAA
66 CAACTATTCAATTTTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAGTGAAAATACTAAAAA
54944208 ATCCAAGATAGTTGGGTAACTAAAAAAATAGATAAATTAGTTATTATATGTTAGATCAA
131 ATCCAAGATAGTTGGGTAACT-AAAAAATAGATAAATTAGTTATTATATGTTAGATCAA
*
54944267 TCTCTCAACTATTAGTAAGTTTATTTTTTGGTCACTAAACTATAAAAAGTTACAAAATGATTATC
1 TCTCTCAACTATTAGTAAATTTATTTTTTGGTCACTAAACTATAAAAAGTTACAAAATGATTATC
*
54944332 CAACTATTCAATTATTTTTCTTTTTTGGTCATCAGTTGACTAACATAAAAGTGAAAATACTAAAA
66 CAACTATTCAATT-TTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAGTGAAAATACTAAAA
*
54944397 AATCCAAGATAGTTGGGTAACTAAAAAATAGATAAATTAGTCATTATATGTTAGATCAA
130 AATCCAAGATAGTTGGGTAACTAAAAAATAGATAAATTAGTTATTATATGTTAGATCAA
* * *
54944456 TCTCTCAACTATTATAGTAAAATTA-TTTTTGGTCACTTAACTATAAAAAGTTACAAAATAATTA
1 TCTCTCAACTA-T-TAGTAAATTTATTTTTTGGTCACTAAACTATAAAAAGTTACAAAATGATTA
* * *
54944520 TCCAACTATTCAATTCTTTTTCTTTTTTGGTCACCAGTTTAGTAACATAAAAGTGAAAATACTTA
64 TCCAACTATTCAATT-TTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAGTGAAAATACTAA
* * *
54944585 AAAATCCAAGATAATTGGGTAACTAAAAAATAGACAAATTAGTTATTGTATGTTAGATCAA
128 AAAATCCAAGATAGTTGGGTAACTAAAAAATAGATAAATTAGTTATTATATGTTAGATCAA
54944646 AGAGTAAATT
Statistics
Matches: 352, Mismatches: 24, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
189 118 0.34
190 225 0.64
191 9 0.03
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (188 bp):
TCTCTCAACTATTAGTAAATTTATTTTTTGGTCACTAAACTATAAAAAGTTACAAAATGATTATC
CAACTATTCAATTTTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAGTGAAAATACTAAAAA
ATCCAAGATAGTTGGGTAACTAAAAAATAGATAAATTAGTTATTATATGTTAGATCAA
Found at i:54947331 original size:19 final size:19
Alignment explanation
Indices: 54947309--54947353 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
54947299 TTATATTAGG
54947309 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
54947328 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
54947347 ATTTAAT
1 ATTTAAT
54947354 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:54947390 original size:14 final size:15
Alignment explanation
Indices: 54947358--54947390 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
54947348 TTTAATTTAT
54947358 GTTTATCTTTTTGTA
1 GTTTATCTTTTTGTA
54947373 -TTTATCTTTTTG-A
1 GTTTATCTTTTTGTA
54947386 GTTTA
1 GTTTA
54947391 AATTGGATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.06
14 16 0.94
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.67
Consensus pattern (15 bp):
GTTTATCTTTTTGTA
Found at i:54948181 original size:16 final size:15
Alignment explanation
Indices: 54948157--54948186 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54948147 CTTCTTTATT
54948157 TTATATTTCTTTTAA
1 TTATATTTCTTTTAA
54948172 TTATACTTTCTTTTA
1 TTATA-TTTCTTTTA
54948187 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTCTTTTAA
Found at i:54948192 original size:22 final size:21
Alignment explanation
Indices: 54948166--54948212 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
54948156 TTTATATTTC
*
54948166 TTTTAATTATACTTTCTTTTAT
1 TTTTAATTAT-CTTTCTTCTAT
* *
54948188 TTTTAATTCTGTTTCTTCTAT
1 TTTTAATTATCTTTCTTCTAT
54948209 TTTT
1 TTTT
54948213 CCTCAGATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTAATTATCTTTCTTCTAT
Found at i:54949775 original size:21 final size:21
Alignment explanation
Indices: 54949750--54949793 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
54949740 GAATTTCAGC
*
54949750 AGCAATCTATAGATTTCCAAA
1 AGCAAACTATAGATTTCCAAA
* *
54949771 AGCAAACTATGGATTTTCAAA
1 AGCAAACTATAGATTTCCAAA
54949792 AG
1 AG
54949794 AAAATTGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (21 bp):
AGCAAACTATAGATTTCCAAA
Done.