Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 187 of 345
Found at i:53175143 original size:34 final size:34
Alignment explanation
Indices: 53175078--53175143 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
53175068 CTATTACTAT
*
53175078 TACTGTAATGGGCTAAGGCCTACACTGATACTGA
1 TACTGTAATGGGCTAAGGCCTACACTAATACTGA
*
53175112 TACTGTAATGGGCTATGGCCCTA-ACTAATACT
1 TACTGTAATGGGCTAAGG-CCTACACTAATACT
53175144 AGACTGTCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 25 0.86
35 4 0.14
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (34 bp):
TACTGTAATGGGCTAAGGCCTACACTAATACTGA
Found at i:53182505 original size:40 final size:40
Alignment explanation
Indices: 53182460--53182624 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
53182450 CGGAATATAA
53182460 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
53182500 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
53182540 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTA-A
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
53182579 CCGGATATAATTC-C-AGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAA-TCACTAGCACAAATGCCTTCGGGTCTTAGC
53182617 CCGGATAT
1 CCGGATAT
53182625 CATTCAATTT
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
37 4 0.04
38 24 0.23
39 12 0.11
40 66 0.62
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53183457 original size:17 final size:19
Alignment explanation
Indices: 53183434--53183479 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
53183424 AAGAAGCATG
53183434 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
53183452 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
53183470 AATCATGCTC
1 AATCATGCTC
53183480 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:53190489 original size:40 final size:40
Alignment explanation
Indices: 53190444--53190610 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
53190434 CGGAATATAA
53190444 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
53190484 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
53190524 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
53190564 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
53190603 CCGGATAT
1 CCGGATAT
53190611 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53190594 original size:80 final size:79
Alignment explanation
Indices: 53190444--53190610 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
53190434 CGGAATATAA
* *
53190444 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
53190509 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
53190524 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
53190586 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
53190603 CCGGATAT
1 CCGGATAT
53190611 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:53191451 original size:17 final size:19
Alignment explanation
Indices: 53191428--53191473 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
53191418 AAGAAGCATG
53191428 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
53191446 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
53191464 AATCATGCTC
1 AATCATGCTC
53191474 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:53195386 original size:40 final size:39
Alignment explanation
Indices: 53195342--53195440 Score: 101
Period size: 39 Copynumber: 2.5 Consensus size: 39
53195332 TGATATTCGA
* *
53195342 CTATAATTGGCACTAAGTGTACGGTTTAATATAACTTCAG
1 CTATAA-TGGCACTAAGTGTACGATTTAACATAACTTCAG
* ** *
53195382 CTATAAATGG-ACTAAGTGTGCGATTTGGCATAGCTTCAG
1 CTAT-AATGGCACTAAGTGTACGATTTAACATAACTTCAG
*
53195421 CTATAGAGGGCACTAAGTGT
1 CTATA-ATGGCACTAAGTGT
53195441 GGGATACCGA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
38 1 0.02
39 30 0.61
40 16 0.33
41 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (39 bp):
CTATAATGGCACTAAGTGTACGATTTAACATAACTTCAG
Found at i:53199942 original size:14 final size:14
Alignment explanation
Indices: 53199923--53199950 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53199913 ATAACAAAAC
53199923 ATGAAAATAGGCAT
1 ATGAAAATAGGCAT
53199937 ATGAAAATAGGCAT
1 ATGAAAATAGGCAT
53199951 TATATGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
ATGAAAATAGGCAT
Found at i:53202402 original size:67 final size:63
Alignment explanation
Indices: 53202256--53202402 Score: 154
Period size: 67 Copynumber: 2.3 Consensus size: 63
53202246 CATAATTTTG
* * * * *
53202256 GCTCTCTTGTACACATGGTGAACACTTAGTACCACCCATGTGACCTAGCCAGTTTATCTCGTA
1 GCTCTCTTGTACACATGGTGAACACCTAGAACCACCCATGCGACCTAGCCAGTATATCCCGTA
* * *
53202319 GCTCTCTTGT-CTACATGGTGTCATTCACCTGGAACCACGCATGCGACCTAGCTACA-TATATCC
1 GCTCTCTTGTAC-ACATGGTG--A-ACACCTAGAACCACCCATGCGACCTAGC--CAGTATATCC
53202382 CGTA
60 CGTA
53202386 GCTCTCTTGTACACATG
1 GCTCTCTTGTACACATG
53202403 ATGTGCACTC
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 18 0.26
65 1 0.01
66 22 0.32
67 24 0.35
68 3 0.04
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (63 bp):
GCTCTCTTGTACACATGGTGAACACCTAGAACCACCCATGCGACCTAGCCAGTATATCCCGTA
Found at i:53202944 original size:30 final size:30
Alignment explanation
Indices: 53202910--53202966 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
53202900 TCCTTAACTC
53202910 AAACTTTGGAAAAATTACACTTTTGCCTTT
1 AAACTTTGGAAAAATTACACTTTTGCCTTT
* * * *
53202940 AAACTTTTGCATATTTACACTTTTGCC
1 AAACTTTGGAAAAATTACACTTTTGCC
53202967 CCTAGGCTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCTTT
Found at i:53212080 original size:40 final size:40
Alignment explanation
Indices: 53212026--53212210 Score: 230
Period size: 40 Copynumber: 4.6 Consensus size: 40
53212016 TTTGCACAAG
* * *
53212026 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAGAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
* *
53212066 GCCTTCGGGACTTAGCCCAGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
53212106 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * *
53212146 GCCTTC-GGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAAT
53212187 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
53212211 CATTCAAATA
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.02
40 89 0.73
41 27 0.22
42 3 0.02
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:53213295 original size:40 final size:40
Alignment explanation
Indices: 53213205--53213465 Score: 271
Period size: 40 Copynumber: 6.5 Consensus size: 40
53213195 CTCAAGTAAT
* * * *
53213205 CTTCGGGATTTAG-CCGGATATA-ACTACTTGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
53213243 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAGATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
53213283 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * * *
53213323 CTTCAGGTCTTAGCCCAGATATAATCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
53213363 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
53213403 CTTC-GGATCTTAGTCCAGTTATAGTCACCTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAATGC
53213444 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
53213466 CATTCAAATA
Statistics
Matches: 184, Mismatches: 31, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
38 11 0.06
39 18 0.10
40 126 0.68
41 26 0.14
42 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:53213336 original size:80 final size:79
Alignment explanation
Indices: 53213205--53213465 Score: 303
Period size: 80 Copynumber: 3.3 Consensus size: 79
53213195 CTCAAGTAAT
* * * * * * *
53213205 CTTCGGGATTTAG-CCGGATATAACTACTTGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTC-GGTCTTAGCCCAGATATAGT
*
53213268 CACTAGCACAGATGC
65 CACTAGCACAAATGC
* *
53213283 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCAGGTCTTAGCCCAGATATAA
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTC-GGTCTTAGCCCAGATATAG
*
53213347 TCGCTAGCACAAATGC
64 TCACTAGCACAAATGC
* * * * *
53213363 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACGAATGCCTTCGGATCTTAGTCCAGTTATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGG-TCTTAGCCCAGATATAGT
*
53213428 CACCTAGCACAAAAGC
65 CA-CTAGCACAAATGC
53213444 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
53213466 CATTCAAATA
Statistics
Matches: 156, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
78 12 0.08
79 18 0.12
80 93 0.60
81 33 0.21
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGTCTTAGCCCAGATATAGTC
ACTAGCACAAATGC
Found at i:53216042 original size:40 final size:39
Alignment explanation
Indices: 53215916--53216060 Score: 137
Period size: 40 Copynumber: 3.6 Consensus size: 39
53215906 TGCTGGAAAT
* * * * *
53215916 TATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTCG
* * * *
53215955 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT
1 -TATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTC-G
* *
53215996 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTCG
* * *
53216035 TGATATCCGGGTTAAGTCCCGTAGGC
1 T-ATATCCGGGCTAAGACCCGAAGGC
53216061 CTTGGTGCGG
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
39 1 0.01
40 84 0.99
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTCG
Found at i:53216085 original size:80 final size:81
Alignment explanation
Indices: 53215917--53216105 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
53215907 GCTGGAAATT
* * * *
53215917 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
53215982 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
53215998 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
53216061 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
53216077 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
53216106 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:53223329 original size:40 final size:39
Alignment explanation
Indices: 53223164--53223347 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
53223154 AAATTGAATG
* * *
53223164 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
53223204 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
53223244 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
53223284 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
53223323 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
53223348 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:53223372 original size:80 final size:81
Alignment explanation
Indices: 53223204--53223392 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
53223194 GCTGGAAATT
* * * *
53223204 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
53223269 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
53223285 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
53223348 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
53223364 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
53223393 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:53232373 original size:40 final size:40
Alignment explanation
Indices: 53232313--53232558 Score: 356
Period size: 40 Copynumber: 6.2 Consensus size: 40
53232303 TGAATGATAC
* * *
53232313 CCGGGCTAAG-TCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
53232352 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
53232392 -CGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
53232431 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
53232471 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
53232511 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
53232551 CC-GGCTAA
1 CCGGGCTAA
53232559 ATTCCGAAGA
Statistics
Matches: 189, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
39 53 0.28
40 134 0.71
41 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:53234303 original size:40 final size:40
Alignment explanation
Indices: 53234213--53234473 Score: 271
Period size: 40 Copynumber: 6.5 Consensus size: 40
53234203 CTCAAGTAAT
* * * *
53234213 CTTCGGGATTTAG-CCGGATATA-ACTACTTGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
53234251 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAGATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
53234291 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * * *
53234331 CTTCAGGTCTTAGCCCAGATATAATCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
53234371 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
53234411 CTTC-GGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAGA
1 CTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAATGC
53234452 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
53234474 CATTCAAATA
Statistics
Matches: 185, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
38 11 0.06
39 18 0.10
40 127 0.69
41 26 0.14
42 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:53236785 original size:17 final size:17
Alignment explanation
Indices: 53236757--53236790 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
53236747 GGCCATTTCT
53236757 GGCTATGTGGGCCACACA
1 GGCTATGTGGGCC-CACA
53236775 GGCTA-GTGGGCCCACA
1 GGCTATGTGGGCCCACA
53236791 TGGACTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.21, C:0.29, G:0.35, T:0.15
Consensus pattern (17 bp):
GGCTATGTGGGCCCACA
Found at i:53237113 original size:57 final size:56
Alignment explanation
Indices: 53237025--53237134 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 56
53237015 CTCTTACCAG
*
53237025 GGAATATTTACTGTTTACGCAAGAGAATATTTTATGTTCACTCGTCTTTTCTTTCAA
1 GGAATATTTACTGTTTACGCAAGAGAATATTTCATGTTC-CTCGTCTTTTCTTTCAA
** * *
53237082 GGAATATTTACTGTTTACGGTAGAGAATATTTCATGTTCCTCTTTTTTTCTTT
1 GGAATATTTACTGTTTACGCAAGAGAATATTTCATGTTCCTCGTCTTTTCTTT
53237135 TGCATCCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 12 0.25
57 36 0.75
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.47
Consensus pattern (56 bp):
GGAATATTTACTGTTTACGCAAGAGAATATTTCATGTTCCTCGTCTTTTCTTTCAA
Found at i:53243837 original size:28 final size:27
Alignment explanation
Indices: 53243774--53243843 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
53243764 ATAGTGAGTC
53243774 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
53243801 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
53243829 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53243844 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:53249609 original size:38 final size:38
Alignment explanation
Indices: 53249558--53249634 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
53249548 GAAAATGAGA
53249558 ATAACGAGTTGATACCGACTAGAACAGTTACAGGATGG
1 ATAACGAGTTGATACCGACTAGAACAGTTACAGGATGG
*
53249596 ATAACGAGTTGATACCGACTAGAACGGTTACAGGATGG
1 ATAACGAGTTGATACCGACTAGAACAGTTACAGGATGG
53249634 A
1 A
53249635 GAATTTGCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (38 bp):
ATAACGAGTTGATACCGACTAGAACAGTTACAGGATGG
Found at i:53251467 original size:127 final size:127
Alignment explanation
Indices: 53251241--53251496 Score: 440
Period size: 127 Copynumber: 2.0 Consensus size: 127
53251231 TTCTCGGTCC
*
53251241 TTTTCTGCCATCTTTTAGTCACAGGTACATATTAGTAGCAGTGGACTATGTGTCTAAGTGGGTCG
1 TTTTCCGCCATCTTTTAGTCACAGGTACATATTAGTAGCAGTGGACTATGTGTCTAAGTGGGTCG
* *
53251306 AGCCTGAAACTTATTCGACAAATGATGCTAAGGTTGTAATTAAGTTTTTGCAGAAACATGTG
66 AGCCTGAAACTTATTCGACAAATGATGCTAAGGTTATAATTAAGTTTTTGCAGAAACACGTG
* *
53251368 TTTTCCGCCATCTTTTGGTCACAGGTACATATTAGTAGCAGTGGACTATGTGTTTAAGTGGGTCG
1 TTTTCCGCCATCTTTTAGTCACAGGTACATATTAGTAGCAGTGGACTATGTGTCTAAGTGGGTCG
* * *
53251433 AGCCTGAAGCTTATTTGACAAATGATGCTAAGGTTATAATTAAGTTTTTGTAGAAACACGTG
66 AGCCTGAAACTTATTCGACAAATGATGCTAAGGTTATAATTAAGTTTTTGCAGAAACACGTG
53251495 TT
1 TT
53251497 CACAAGGTTT
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 121 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (127 bp):
TTTTCCGCCATCTTTTAGTCACAGGTACATATTAGTAGCAGTGGACTATGTGTCTAAGTGGGTCG
AGCCTGAAACTTATTCGACAAATGATGCTAAGGTTATAATTAAGTTTTTGCAGAAACACGTG
Found at i:53253811 original size:55 final size:53
Alignment explanation
Indices: 53253668--53253830 Score: 211
Period size: 53 Copynumber: 3.0 Consensus size: 53
53253658 TTTTCCTTTT
* * *
53253668 TGAACTTACCATTGCCATGTCTTGACATGGTCTGACATGGTATCCTTGCCTTA
1 TGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTA
* * *
53253721 TGAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTA
1 TGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC-TTGCCTTA
* * *
53253774 TAGTAACTCATCAATTCCATGTCTTGACATGGCCTTACATGGTATCCTTGCCTTA
1 T-G-AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTA
53253829 TG
1 TG
53253831 TGTAATATCC
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
52 2 0.02
53 45 0.48
54 2 0.02
55 43 0.46
56 2 0.02
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (53 bp):
TGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTA
Found at i:53255176 original size:46 final size:46
Alignment explanation
Indices: 53255123--53255298 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
53255113 TATTTGGGCA
53255123 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
*** * * * *
53255169 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-GCG
* * *
53255216 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
53255262 CCCGAGCTCGTTGAGTTGATTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53255299 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 71 0.66
47 36 0.34
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:53255278 original size:93 final size:93
Alignment explanation
Indices: 53255119--53255290 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
53255109 GGGATATTTG
* *
53255119 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
53255184 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
53255212 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
53255277 TTGATTCCGAGTTC
66 TTGAGTCCGAGTTC
53255291 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:53256673 original size:55 final size:53
Alignment explanation
Indices: 53256602--53256753 Score: 173
Period size: 55 Copynumber: 2.8 Consensus size: 53
53256592 GGGCATTACA
*
53256602 TTAT-GAACTCACCAATGACATGCCTTGGCATGGTCTTACATG-GGACCTTTGCC
1 TTATAGAACTCATCAATG-CATGCCTTGGCATGGTCTTACATGAGGACC-TTGCC
* * ***
53256655 TTATAGTAACTCATCAATGCTATGTCTTGACATGGTCTTACATGATTTCCTTGCC
1 TTATAG-AACTCATCAATGC-ATGCCTTGGCATGGTCTTACATGAGGACCTTGCC
* *
53256710 TTATAGAACTCATCAATGTCATGCCTCGGAATGGTCTTACATGA
1 TTATAGAACTCATCAATG-CATGCCTTGGCATGGTCTTACATGA
53256754 TATCCTTATC
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
53 4 0.05
54 34 0.40
55 44 0.52
56 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (53 bp):
TTATAGAACTCATCAATGCATGCCTTGGCATGGTCTTACATGAGGACCTTGCC
Found at i:53256793 original size:47 final size:47
Alignment explanation
Indices: 53256740--53256860 Score: 215
Period size: 47 Copynumber: 2.6 Consensus size: 47
53256730 ATGCCTCGGA
* *
53256740 ATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAAC
1 ATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAAC
53256787 ATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAAC
1 ATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAAC
*
53256834 ATGGTCTTACATGGTACCCTTGTCTTA
1 ATGGTCTTACATGGTATCCTTGTCTTA
53256861 GTGCCAATGC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (47 bp):
ATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAAC
Found at i:53258371 original size:30 final size:30
Alignment explanation
Indices: 53258316--53258475 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
53258306 ATAGTGAATC
53258316 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
53258345 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
53258375 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
53258404 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
53258432 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
53258462 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53258476 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:53258408 original size:59 final size:57
Alignment explanation
Indices: 53258316--53258475 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
53258306 ATAGTGAATC
*
53258316 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
53258375 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
53258432 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
53258476 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:53261755 original size:28 final size:29
Alignment explanation
Indices: 53261723--53261821 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
53261713 ATAATAAGCC
*
53261723 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
53261751 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
53261779 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
53261808 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53261822 CAATTCATGA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:53269493 original size:28 final size:29
Alignment explanation
Indices: 53269461--53269559 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
53269451 TATAATAAGC
*
53269461 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
53269489 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
53269517 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
53269546 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53269560 CAATTCATGA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:53271422 original size:30 final size:30
Alignment explanation
Indices: 53271386--53271445 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
53271376 TCCCTAACTC
* *
53271386 AAACTTTGGAAAATTACAATTTTGCCCCTA
1 AAACTTTGCAAAATTACAAATTTGCCCCTA
* *
53271416 AAACTTTGCAGAATTACAAATTTGTCCCTA
1 AAACTTTGCAAAATTACAAATTTGCCCCTA
53271446 GGTCGGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (30 bp):
AAACTTTGCAAAATTACAAATTTGCCCCTA
Found at i:53272994 original size:17 final size:18
Alignment explanation
Indices: 53272968--53273001 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53272958 CTTATTTTTA
53272968 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
53272985 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
53273002 ATATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:53273562 original size:17 final size:18
Alignment explanation
Indices: 53273524--53273565 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
53273514 ATTTTCTCCT
*
53273524 AAATT-TTTAATTTTATT
1 AAATTATTTAATTTTATC
*
53273541 TAATTATTTAATTTT-TC
1 AAATTATTTAATTTTATC
53273558 AAATTATT
1 AAATTATT
53273566 GAATCATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
AAATTATTTAATTTTATC
Found at i:53280206 original size:16 final size:17
Alignment explanation
Indices: 53280187--53280225 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
53280177 AATGTAACGC
*
53280187 CCCAAAAATCCCGAAA-
1 CCCAAAAATCCCAAAAT
53280203 CCCAAAAATCCCAAAAT
1 CCCAAAAATCCCAAAAT
53280220 CCCAAA
1 CCCAAA
53280226 CTTTCTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.51, C:0.38, G:0.03, T:0.08
Consensus pattern (17 bp):
CCCAAAAATCCCAAAAT
Found at i:53281467 original size:8 final size:8
Alignment explanation
Indices: 53281454--53281512 Score: 66
Period size: 8 Copynumber: 7.4 Consensus size: 8
53281444 ATGAATCGAC
53281454 AAAAGCCG
1 AAAAGCCG
53281462 AAAAGCC-
1 AAAAGCCG
53281469 AAAATGCCG
1 AAAA-GCCG
53281478 AAAAGCCG
1 AAAAGCCG
**
53281486 AAAAGTTG
1 AAAAGCCG
* *
53281494 AAATGCCA
1 AAAAGCCG
53281502 AAAAGCCG
1 AAAAGCCG
53281510 AAA
1 AAA
53281513 GTTGGGTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
7 4 0.10
8 33 0.80
9 4 0.10
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.07
Consensus pattern (8 bp):
AAAAGCCG
Found at i:53281486 original size:24 final size:24
Alignment explanation
Indices: 53281454--53281512 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
53281444 ATGAATCGAC
*
53281454 AAAAGCCGAAAAGCCAAAATGCCG
1 AAAAGCCGAAAAGCCAAAATGCCA
***
53281478 AAAAGCCGAAAAGTTGAAATGCCA
1 AAAAGCCGAAAAGCCAAAATGCCA
53281502 AAAAGCCGAAA
1 AAAAGCCGAAA
53281513 GTTGGGTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.07
Consensus pattern (24 bp):
AAAAGCCGAAAAGCCAAAATGCCA
Found at i:53281768 original size:29 final size:28
Alignment explanation
Indices: 53281736--53281842 Score: 74
Period size: 29 Copynumber: 3.8 Consensus size: 28
53281726 ATAATATGAT
53281736 TTGGGCCTAATGGGCCATATGAATGAGAA
1 TTGGGCCTAATGGGCCATATGAAT-AGAA
* * * *
53281765 TTGGGCCCTAGTGGACCATAAGAATATAAA
1 TTGGG-CCTAATGGGCCATATGAATA-GAA
* * * *
53281795 CTAGGCCAAATGGGCCATTTGAATA-AGA
1 TTGGGCCTAATGGGCCATATGAATAGA-A
* *
53281823 TTGGGCC-AGTGGGCTATATG
1 TTGGGCCTAATGGGCCATATG
53281843 CATGTATGTA
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
27 11 0.19
28 6 0.10
29 21 0.36
30 21 0.36
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (28 bp):
TTGGGCCTAATGGGCCATATGAATAGAA
Found at i:53284880 original size:42 final size:42
Alignment explanation
Indices: 53284826--53284916 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
53284816 TTATCTTCGG
*
53284826 TAAGTT-AGTGGAAATCAAAGGACCATGGCATGCTAATCCAC
1 TAAGTTAAGTGGAAATCAAAGGACCATGCCATGCTAATCCAC
53284867 TAAGTTAAGTGGAAATCAAAGGACCATGCCATGCTAATCCAC
1 TAAGTTAAGTGGAAATCAAAGGACCATGCCATGCTAATCCAC
53284909 TAAGTTAA
1 TAAGTTAA
53284917 ACTTAATAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 6 0.12
42 42 0.88
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (42 bp):
TAAGTTAAGTGGAAATCAAAGGACCATGCCATGCTAATCCAC
Found at i:53286485 original size:29 final size:29
Alignment explanation
Indices: 53286431--53286489 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
53286421 TATGCGTGGA
*
53286431 ATCTACCAAACAAGAGTCTGGTAGTGACT
1 ATCTACCAAACAAGAGTCTGGCAGTGACT
*
53286460 ATCTACCAAACAAGA-TTTGGGCAGTGACT
1 ATCTACCAAACAAGAGTCT-GGCAGTGACT
53286489 A
1 A
53286490 ACATTTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (29 bp):
ATCTACCAAACAAGAGTCTGGCAGTGACT
Found at i:53290301 original size:10 final size:10
Alignment explanation
Indices: 53290286--53290331 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
53290276 TAAAGTACTC
53290286 AAAAATATAT
1 AAAAATATAT
53290296 AAAAATATAT
1 AAAAATATAT
* * *
53290306 AAATATTTTT
1 AAAAATATAT
53290316 AAAAA-ATAT
1 AAAAATATAT
53290325 AAAAATA
1 AAAAATA
53290332 AAAAATAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
9 7 0.24
10 22 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATATAT
Found at i:53290346 original size:29 final size:30
Alignment explanation
Indices: 53290286--53290346 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
53290276 TAAAGTACTC
* *
53290286 AAAAATATATAAAAATATATAAATATTTTT
1 AAAAATATATAAAAATATAAAAATATTATT
53290316 AAAAA-ATATAAAAATA-AAAAATAATTATT
1 AAAAATATATAAAAATATAAAAAT-ATTATT
53290345 AA
1 AA
53290347 CAAGAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.18
29 18 0.64
30 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAAATATATAAAAATATAAAAATATTATT
Found at i:53290444 original size:19 final size:19
Alignment explanation
Indices: 53290397--53290440 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
53290387 TTTTTTAAAA
53290397 AATA-TAATAATTACATTT
1 AATATTAATAATTACATTT
* *
53290415 CATATTAATAATTATA-TT
1 AATATTAATAATTACATTT
53290433 AATATTAA
1 AATATTAA
53290441 ATAAAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATTAATAATTACATTT
Found at i:53292500 original size:22 final size:22
Alignment explanation
Indices: 53292465--53292511 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
53292455 GAGTATGGCC
*
53292465 ATTTTCTTTAATTTTAG-TTTTT
1 ATTTTATTTAATTTT-GCTTTTT
*
53292487 ATTTTATTTTATTTTGCTTTTT
1 ATTTTATTTAATTTTGCTTTTT
53292509 ATT
1 ATT
53292512 CTTGTTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (22 bp):
ATTTTATTTAATTTTGCTTTTT
Found at i:53303409 original size:49 final size:50
Alignment explanation
Indices: 53303329--53303575 Score: 241
Period size: 49 Copynumber: 5.0 Consensus size: 50
53303319 AGCTATTTTG
* * *
53303329 AGGTCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACTAGATTGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAGTT
* * * *
53303379 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCT-GATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CTAGAT-AGTT
* * * * * *
53303429 CGATCACATGTGTAGTACTAAGTGCAAGCTACTACGTGT-GTCAAATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACT-AGATAGTT
* * ** *
53303479 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAGTT
* * * *
53303529 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAG
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAG
53303576 CTTCAGCTAC
Statistics
Matches: 159, Mismatches: 32, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
49 80 0.50
50 44 0.28
51 35 0.22
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAGTT
Found at i:53303520 original size:101 final size:98
Alignment explanation
Indices: 53303332--53303561 Score: 318
Period size: 100 Copynumber: 2.3 Consensus size: 98
53303322 TATTTTGAGG
* * * *
53303332 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACTAGATTGTTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAAGCTACTACGTGTACTAAATGGTTGGTCACATGTGTAGTACT
*
53303397 AAGTGCAGGCTACTATGCGTACCTGATAACTTCGA
66 AAGTGCAGGCTACTATGCGTACCGGATAA-TT-GA
* *
53303432 TCACATGTGTAGTACTAAGTGCAAGCTACTACGTGT-GTCAAATGGTTAGGTCACGTGTGTAGTA
1 TCACATGTGTAGTACTAAGTGCAAGCTACTACGTGTACT-AAATGGTT-GGTCACATGTGTAGTA
* *
53303496 CTAAGTGCAGGCTACTATGTGTACCGGATAATTGG
64 CTAAGTGCAGGCTACTATGCGTACCGGATAATTGA
* *
53303531 TCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACATGTGTAGTACTAAGTGCAAGCTACTA
53303562 TGCGTACCAG
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
99 31 0.26
100 43 0.37
101 43 0.37
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (98 bp):
TCACATGTGTAGTACTAAGTGCAAGCTACTACGTGTACTAAATGGTTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCGGATAATTGA
Found at i:53306330 original size:16 final size:15
Alignment explanation
Indices: 53306292--53306330 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
53306282 TGGATTCTCG
*
53306292 TATCATGGATTTCTT
1 TATCTTGGATTTCTT
53306307 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
53306322 TATTCTTGG
1 TA-TCTTGG
53306331 CTTCTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:53308420 original size:30 final size:30
Alignment explanation
Indices: 53308373--53308432 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53308363 TTCCCGAGCC
53308373 TAGGGGAAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAAGTGTAATTATGCAAAAGTT
* * *
53308403 TAGGGGCAAAA-TGGTAATTTTGCCAAAGTT
1 TAGGGGAAAAAGT-GTAATTATGCAAAAGTT
53308433 CGTATTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAATTATGCAAAAGTT
Found at i:53308644 original size:19 final size:19
Alignment explanation
Indices: 53308622--53308679 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
53308612 AATTTAAGTA
53308622 ATATAATGTTATTTATATG
1 ATATAATGTTATTTATATG
* *
53308641 ATATGATG--A-TTATTATC
1 ATATAATGTTATTTA-TATG
*
53308658 AT-TAATTTTATTTATATG
1 ATATAATGTTATTTATATG
53308676 ATAT
1 ATAT
53308680 GAAGATTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 10
0.66 0.11 0.23
Matches are distributed among these distances:
16 6 0.21
17 6 0.21
18 6 0.21
19 11 0.38
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (19 bp):
ATATAATGTTATTTATATG
Found at i:53308669 original size:35 final size:35
Alignment explanation
Indices: 53308625--53308691 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
53308615 TTAAGTAATA
*
53308625 TAATGTTATTTATATGATATGATGATTATTATCAT
1 TAATGTTATTTATATGATATGAAGATTATTATCAT
* *
53308660 TAATTTTATTTATATGATATGAAGATTGTTAT
1 TAATGTTATTTATATGATATGAAGATTATTAT
53308692 TATGAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (35 bp):
TAATGTTATTTATATGATATGAAGATTATTATCAT
Found at i:53309085 original size:50 final size:50
Alignment explanation
Indices: 53309010--53309151 Score: 196
Period size: 50 Copynumber: 2.9 Consensus size: 50
53309000 AGCTATTGTG
* **
53309010 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATAATT
**
53309060 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATAATT
* * * *
53309110 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
53309152 GATAGATTCA
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 37 0.45
50 45 0.55
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATAATT
Found at i:53311198 original size:11 final size:10
Alignment explanation
Indices: 53311166--53311202 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
53311156 CATGAGATTT
53311166 TGATAT-ACA
1 TGATATGACA
53311175 TGATATGACA
1 TGATATGACA
53311185 TGATATGCACA
1 TGATATG-ACA
53311196 TGATATG
1 TGATATG
53311203 TTATGAGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.23
10 10 0.38
11 10 0.38
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (10 bp):
TGATATGACA
Found at i:53311198 original size:21 final size:21
Alignment explanation
Indices: 53311172--53311222 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
53311162 ATTTTGATAT
*
53311172 ACATGATATGACATGATATGC
1 ACATGATATGACATGAGATGC
**
53311193 ACATGATATGTTATGAGATGC
1 ACATGATATGACATGAGATGC
*
53311214 GCATGATAT
1 ACATGATAT
53311223 ACTCATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (21 bp):
ACATGATATGACATGAGATGC
Found at i:53311304 original size:25 final size:25
Alignment explanation
Indices: 53311268--53311339 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 25
53311258 GGAGGAAGTG
*
53311268 CAAAAAGGGCTTTGCCCTAGTTTAC
1 CAAAAAGGGCTTTGCCCCAGTTTAC
* * *
53311293 CGAAAAGGGCTTTGCCCCAATTTAT
1 CAAAAAGGGCTTTGCCCCAGTTTAC
53311318 CAAAAAGGGCTTTGCCCCAGTT
1 CAAAAAGGGCTTTGCCCCAGTT
53311340 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (25 bp):
CAAAAAGGGCTTTGCCCCAGTTTAC
Found at i:53311352 original size:24 final size:24
Alignment explanation
Indices: 53311270--53311366 Score: 74
Period size: 25 Copynumber: 4.0 Consensus size: 24
53311260 AGGAAGTGCA
* *
53311270 AAAAG-GGCTTTGCCCTAGTTTACC
1 AAAAGAGGCTTTGCCCCAG-TTATC
*
53311294 GAAAAG-GGCTTTGCCCCAATTTATC
1 -AAAAGAGGCTTTGCCCC-AGTTATC
*
53311319 AAAA-AGGGCTTTGCCCCAGTTATT
1 AAAAGA-GGCTTTGCCCCAGTTATC
**
53311343 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGAGGCTTTGCC-CCAGTTAT
53311367 GATAAAGCAG
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
24 20 0.33
25 39 0.65
26 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGAGGCTTTGCCCCAGTTATC
Found at i:53311625 original size:30 final size:31
Alignment explanation
Indices: 53311558--53311640 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
53311548 CGCTTATAGT
*
53311558 AAAGGCTTCGGCCCAGTGATATGAATTTTGA
1 AAAGGCTTCGGCCCAGTGATATGAATTATGA
* *
53311589 AAAGGCTTCGGTCCAGTGTTATGAATTATG-
1 AAAGGCTTCGGCCCAGTGATATGAATTATGA
**
53311619 AAAGGCTTCAACCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
53311641 TTGATACTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 4 0.09
30 14 0.31
31 27 0.60
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATTATGA
Found at i:53313242 original size:16 final size:16
Alignment explanation
Indices: 53313221--53313252 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53313211 AAATTGATGT
53313221 TAAATTTACTCGTATA
1 TAAATTTACTCGTATA
53313237 TAAATTTACTCGTATA
1 TAAATTTACTCGTATA
53313253 GAGCGAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
TAAATTTACTCGTATA
Found at i:53315439 original size:2 final size:2
Alignment explanation
Indices: 53315432--53315471 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
53315422 TAGGATTCTG
53315432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53315472 GTGCGAGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53317674 original size:18 final size:18
Alignment explanation
Indices: 53317653--53317687 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53317643 TATTTATTTA
* *
53317653 GTAATAGTCAGTTATTCG
1 GTAATAATCAATTATTCG
53317671 GTAATAATCAATTATTC
1 GTAATAATCAATTATTC
53317688 AATAATAATT
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:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (18 bp):
GTAATAATCAATTATTCG
Found at i:53317791 original size:19 final size:19
Alignment explanation
Indices: 53317726--53317796 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 19
53317716 AATAGATCGG
* *
53317726 TTATCCAGTAACAGTC-AA
1 TTATTCAGTAACAATCAAA
* *
53317744 TTATTCAGTAAAAATCAGA
1 TTATTCAGTAACAATCAAA
* *
53317763 -TATACAGTAACAATTAAA
1 TTATTCAGTAACAATCAAA
53317781 TTATTCAGTAACAATC
1 TTATTCAGTAACAATC
53317797 GATCTTTCCA
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
18 27 0.66
19 14 0.34
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.31
Consensus pattern (19 bp):
TTATTCAGTAACAATCAAA
Found at i:53318000 original size:53 final size:53
Alignment explanation
Indices: 53317935--53318051 Score: 155
Period size: 53 Copynumber: 2.2 Consensus size: 53
53317925 GTAATAGTAG
* *
53317935 CAGTACAGTACACAGAGTACCTC-ATCGGAACAAATTTGGAACAATAACAATAA
1 CAGTACAGTACACAGAGTACCTCAAT-GGAACAAATTCGAAACAATAACAATAA
* * *
53317988 CAGTACGGTACACAGAGTACCTCAATGGAACAAATTCGAAACAGTAACAGTAA
1 CAGTACAGTACACAGAGTACCTCAATGGAACAAATTCGAAACAATAACAATAA
*
53318041 CAATAACAGTA
1 CAGT-ACAGTA
53318052 ACAATATCCG
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
53 48 0.87
54 7 0.13
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (53 bp):
CAGTACAGTACACAGAGTACCTCAATGGAACAAATTCGAAACAATAACAATAA
Found at i:53318046 original size:59 final size:58
Alignment explanation
Indices: 53317915--53318051 Score: 151
Period size: 53 Copynumber: 2.4 Consensus size: 58
53317905 CCGGAACAGT
* * * * *
53317915 AACAATAACAGTAATAGTAGCAGTACAGTACACAGAGTACCTCATCGGAACAAATTTG
1 AACAGTAACAGTAACAATAACAGTACAGTACACAGAGTACCTCATCGGAACAAATTCG
* *
53317973 ----G-AACAATAACAATAACAGTACGGTACACAGAGTACCTCAAT-GGAACAAATTCG
1 AACAGTAACAGTAACAATAACAGTACAGTACACAGAGTACCTC-ATCGGAACAAATTCG
53318026 AAACAGTAACAGTAACAATAACAGTA
1 -AACAGTAACAGTAACAATAACAGTA
53318052 ACAATATCCG
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
53 43 0.67
54 2 0.03
58 1 0.02
59 18 0.28
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (58 bp):
AACAGTAACAGTAACAATAACAGTACAGTACACAGAGTACCTCATCGGAACAAATTCG
Found at i:53318047 original size:12 final size:12
Alignment explanation
Indices: 53318027--53318057 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
53318017 ACAAATTCGA
*
53318027 AACAGTAACAGT
1 AACAATAACAGT
53318039 AACAATAACAGT
1 AACAATAACAGT
53318051 AACAATA
1 AACAATA
53318058 TCCGACACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.16
Consensus pattern (12 bp):
AACAATAACAGT
Found at i:53318253 original size:16 final size:16
Alignment explanation
Indices: 53318224--53318257 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
53318214 TAATTCACTT
53318224 TTCAATTTTCAATTAA
1 TTCAATTTTCAATTAA
53318240 TTCATATTTT-AATTAA
1 TTCA-ATTTTCAATTAA
53318256 TT
1 TT
53318258 AACTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (16 bp):
TTCAATTTTCAATTAA
Found at i:53319720 original size:6 final size:6
Alignment explanation
Indices: 53319703--53319863 Score: 145
Period size: 6 Copynumber: 26.8 Consensus size: 6
53319693 AACCAAAATG
* * * *
53319703 AGAATC AAAATC AGAATC AGTAA-A AGAATC AGAATC AGAATC AGTATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
* *
53319751 AGTAA-C AGAATC A-AATC AGAATC AGAATT AGGCGA-C AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
* * *
53319799 AGAATC AGTAA-C AGAACC AGAATC AGAATC AGTATT AGTAA-C AGAATC
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC
53319847 AGAATC AGAATC AGAAT
1 AGAATC AGAATC AGAAT
53319864 GTGAATGCAA
Statistics
Matches: 126, Mismatches: 17, Indels: 24
0.75 0.10 0.14
Matches are distributed among these distances:
5 14 0.11
6 103 0.82
7 8 0.06
8 1 0.01
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:53319737 original size:30 final size:30
Alignment explanation
Indices: 53319703--53319863 Score: 199
Period size: 30 Copynumber: 5.6 Consensus size: 30
53319693 AACCAAAATG
* *
53319703 AGAATCAAAATCAGAATCAGTAAAAGAATC
1 AGAATCAGAATCAGAATCAGTAACAGAATC
* *
53319733 AGAATCAGAATCAGTATTAGTAACAGAATC
1 AGAATCAGAATCAGAATCAGTAACAGAATC
* *
53319763 A-AATCAGAATCAGAATTAG--GC-G-A-C
1 AGAATCAGAATCAGAATCAGTAACAGAATC
*
53319787 AGAATCAGAATCAGAATCAGTAACAGAACC
1 AGAATCAGAATCAGAATCAGTAACAGAATC
* *
53319817 AGAATCAGAATCAGTATTAGTAACAGAATC
1 AGAATCAGAATCAGAATCAGTAACAGAATC
53319847 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
53319864 GTGAATGCAA
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.02
25 18 0.16
26 1 0.01
27 2 0.02
28 1 0.01
29 18 0.16
30 71 0.63
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (30 bp):
AGAATCAGAATCAGAATCAGTAACAGAATC
Found at i:53320018 original size:27 final size:26
Alignment explanation
Indices: 53319981--53320046 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
53319971 AGCATGGCTG
*
53319981 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
53320007 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
53320034 CCAGAATCAGATA
1 CCAGAA-CAGATA
53320047 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:53320051 original size:27 final size:27
Alignment explanation
Indices: 53319981--53320054 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
53319971 AGCATGGCTG
* *
53319981 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
53320007 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
53320034 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
53320055 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:53320061 original size:27 final size:27
Alignment explanation
Indices: 53320005--53320062 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
53319995 GTGACAGAGT
* * *
53320005 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
53320032 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
53320059 CACC
1 CACC
53320063 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:53320267 original size:22 final size:22
Alignment explanation
Indices: 53320219--53320277 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
53320209 GTAAATACGT
*
53320219 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
53320241 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
53320263 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
53320278 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:53320444 original size:27 final size:26
Alignment explanation
Indices: 53320368--53320447 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 26
53320358 ATCGGTCAAT
* *
53320368 AGATATTGTGGCAGAGTCACCAAATAC
1 AGATATTGTGGCAGAGCCACCAGA-AC
53320395 AGATATTGTGGCAGAGCCACCAGAAC
1 AGATATTGTGGCAGAGCCACCAGAAC
*
53320421 AGATATTTGTGGCATAGCCACCAGAAC
1 AGATA-TTGTGGCAGAGCCACCAGAAC
53320448 GCTCCTCCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
26 7 0.14
27 42 0.86
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (26 bp):
AGATATTGTGGCAGAGCCACCAGAAC
Found at i:53320675 original size:27 final size:27
Alignment explanation
Indices: 53320645--53320838 Score: 221
Period size: 27 Copynumber: 7.3 Consensus size: 27
53320635 GGGGCAAAAT
* * *
53320645 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53320672 GGTAATTCTACCCTAC-AGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53320698 -GTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *** *
53320724 GATAATTCTACCCTATGGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53320751 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53320778 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53320805 GGAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53320832 AGTAATT
1 GGTAATT
53320839 TCACAATCAA
Statistics
Matches: 142, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
25 14 0.10
26 19 0.13
27 109 0.77
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:53320832 original size:54 final size:54
Alignment explanation
Indices: 53320645--53320838 Score: 250
Period size: 54 Copynumber: 3.6 Consensus size: 54
53320635 GGGGCAAAAT
* * * * *
53320645 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACA-GGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTC
* * *
53320698 -GTATTTCTACCCTACAAGGGTATTTC-GATAATTCTACCCTATGGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTCAG-TAATTCTACCCTATAGGGGTATTTC
* *
53320751 GGTAATTCTATCCTATAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTC
* *
53320805 GGAAATTCTACCCTACAGGGGTATTTCAGTAATT
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATT
53320839 TCACAATCAA
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
51 1 0.01
52 35 0.29
53 8 0.07
54 76 0.63
55 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTC
Found at i:53320873 original size:27 final size:27
Alignment explanation
Indices: 53320843--53321173 Score: 345
Period size: 27 Copynumber: 12.3 Consensus size: 27
53320833 GTAATTTCAC
* *
53320843 AATCAAGGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAACGATAATTCTGTA
*
53320870 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGATAATTCTGTA
*
53320897 AA-CTGAGGGT-AAACCAGTAATTCTGTA
1 AATC-GAGGGTAAAACGA-TAATTCTGTA
* * **
53320924 AATCAAGGGTAAAACGATAATTTTACA
1 AATCGAGGGTAAAACGATAATTCTGTA
*
53320951 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGATAATTCTGTA
53320978 AATCGA-GGTAAAAC-AGTAATTCTGTA
1 AATCGAGGGTAAAACGA-TAATTCTGTA
*
53321004 AA-CTGAGGGTAAAATGATAATTCTGTA
1 AATC-GAGGGTAAAACGATAATTCTGTA
53321031 AATCGAGGGTAAAAC-AGTAATTCTGTA
1 AATCGAGGGTAAAACGA-TAATTCTGTA
*
53321058 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGATAATTCTGTA
* * * **
53321085 AATCGAGGATAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGATAATTCTGTA
* * *
53321112 AATCGAGGGTAAAACGGTAATTTTATA
1 AATCGAGGGTAAAACGATAATTCTGTA
* * **
53321139 AATCGA-GGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGATAATTCTGTA
53321165 AATCGAGGG
1 AATCGAGGG
53321174 CATTTCAGTA
Statistics
Matches: 262, Mismatches: 28, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.00
26 53 0.20
27 199 0.76
28 9 0.03
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGATAATTCTGTA
Found at i:53321015 original size:161 final size:161
Alignment explanation
Indices: 53320848--53321161 Score: 504
Period size: 161 Copynumber: 2.0 Consensus size: 161
53320838 TTCACAATCA
* *
53320848 AGGGTAAAACGATAATTCTATAAATCGAGGGTAAAAC-GATAATTTTGTAAACTGAGGGTAAACC
1 AGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAG-TAATTCTGTAAACTGAGGGTAAAAC
* *
53320912 AGTAATTCTGTAAATCAAGGGTAAAACGATAATTTTACAAATCGAGGGTAAAACGGTAATTCTGT
65 AGTAATTCTGTAAATCAAGGATAAAACGATAATTTTACAAATCGAGGGTAAAACGGTAATTCTAT
53320977 AAATCGAGGTAAAACAGTAATTCTGTAAACTG
130 AAATCGAGGTAAAACAGTAATTCTGTAAACTG
* * *
53321009 AGGGTAAAATGATAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAACG
1 AGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAACA
* * *
53321074 GTAATTCTGTAAATCGAGGATAAAACGGTAATTTTACAAATCGAGGGTAAAACGGTAATTTTATA
66 GTAATTCTGTAAATCAAGGATAAAACGATAATTTTACAAATCGAGGGTAAAACGGTAATTCTATA
**
53321139 AATCGAGGTAAAATGGTAATTCT
131 AATCGAGGTAAAACAGTAATTCT
53321162 ACAAATCGAG
Statistics
Matches: 140, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
161 139 0.99
162 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.27
Consensus pattern (161 bp):
AGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAACA
GTAATTCTGTAAATCAAGGATAAAACGATAATTTTACAAATCGAGGGTAAAACGGTAATTCTATA
AATCGAGGTAAAACAGTAATTCTGTAAACTG
Found at i:53321191 original size:27 final size:27
Alignment explanation
Indices: 53321099--53321243 Score: 115
Period size: 26 Copynumber: 5.5 Consensus size: 27
53321089 GAGGATAAAA
***
53321099 CGGTAATTTTACAAATCGAGGGTAAAA
1 CGGTAATTTTACAAATCGAGGGTATTT
* **
53321126 CGGTAATTTTATAAATCGA-GGTAAAAT
1 CGGTAATTTTACAAATCGAGGGT-ATTT
* *
53321153 -GGTAATTCTACAAATCGAGGGCATTT
1 CGGTAATTTTACAAATCGAGGGTATTT
* *
53321179 CAGTAATTTTAC-AATCGACGGTATTT
1 CGGTAATTTTACAAATCGAGGGTATTT
*
53321205 CGGTAA-TTTATAAA-CTG-GGGTACTTT
1 CGGTAATTTTACAAATC-GAGGGTA-TTT
53321231 -GGTAATTTTACAA
1 CGGTAATTTTACAA
53321244 CTGGGGGCAT
Statistics
Matches: 96, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
25 14 0.15
26 50 0.52
27 32 0.33
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (27 bp):
CGGTAATTTTACAAATCGAGGGTATTT
Found at i:53321194 original size:26 final size:26
Alignment explanation
Indices: 53321154--53321263 Score: 84
Period size: 26 Copynumber: 4.2 Consensus size: 26
53321144 AGGTAAAATG
* *
53321154 GTAATTCTACAAATCGAGGGCATTTCA
1 GTAATTTTACAACT-GAGGGCATTTCA
* * *
53321181 GTAATTTTACAA-TCGACGGTATTTCG
1 GTAATTTTACAACT-GAGGGCATTTCA
* *
53321207 GTAATTTATA-AACTG-GGGTACTTT-G
1 GTAATTT-TACAACTGAGGGCA-TTTCA
*
53321232 GTAATTTTACAACTGGGGGCATTTCA
1 GTAATTTTACAACTGAGGGCATTTCA
53321258 GTAATT
1 GTAATT
53321264 GGTAAACTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
24 2 0.03
25 20 0.29
26 34 0.49
27 14 0.20
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (26 bp):
GTAATTTTACAACTGAGGGCATTTCA
Found at i:53323220 original size:6 final size:6
Alignment explanation
Indices: 53323209--53323334 Score: 143
Period size: 6 Copynumber: 20.8 Consensus size: 6
53323199 AACCAAAATG
* *
53323209 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATT AG-GTGAC
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAAT--C
* *
53323258 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC AGTATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
53323306 AGTAA-C AGAATC AGAATC AGAATC AGAAT
1 AG-AATC AGAATC AGAATC AGAATC AGAAT
53323335 GTGAATGCAA
Statistics
Matches: 103, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
5 7 0.07
6 88 0.85
7 7 0.07
8 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:53323236 original size:24 final size:24
Alignment explanation
Indices: 53323209--53323334 Score: 175
Period size: 24 Copynumber: 5.2 Consensus size: 24
53323199 AACCAAAATG
53323209 AGAATCAGAATCAGAATCAGTAAC
1 AGAATCAGAATCAGAATCAGTAAC
* *
53323233 AGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCA-GTAAC
53323258 AGAATCAGAATCAGAATCAGTAAC
1 AGAATCAGAATCAGAATCAGTAAC
**
53323282 AGAATCAGAATCAGAATCAGTATT
1 AGAATCAGAATCAGAATCAGTAAC
53323306 AGTAA-CAGAATCAGAATCAG-AATC
1 AG-AATCAGAATCAGAATCAGTAA-C
53323330 AGAAT
1 AGAAT
53323335 GTGAATGCAA
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.03
24 63 0.70
25 24 0.27
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.19
Consensus pattern (24 bp):
AGAATCAGAATCAGAATCAGTAAC
Found at i:53323489 original size:27 final size:26
Alignment explanation
Indices: 53323452--53323517 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
53323442 AGCATGGCTG
*
53323452 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
53323478 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
53323505 CCAGAATCAGATA
1 CCAGAA-CAGATA
53323518 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:53323522 original size:27 final size:27
Alignment explanation
Indices: 53323452--53323525 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
53323442 AGCATGGCTG
* *
53323452 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
53323478 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
53323505 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
53323526 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:53323532 original size:27 final size:27
Alignment explanation
Indices: 53323476--53323533 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
53323466 GTGACAGAGT
* * *
53323476 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
53323503 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
53323530 CACC
1 CACC
53323534 TAATAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:53323915 original size:27 final size:26
Alignment explanation
Indices: 53323836--53323918 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
53323826 TCGATCGGTC
* * *
53323836 AACAGATATTGTGGTAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
53323862 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
53323889 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
53323916 AAC
1 AAC
53323919 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:53324147 original size:27 final size:27
Alignment explanation
Indices: 53324117--53324312 Score: 257
Period size: 27 Copynumber: 7.3 Consensus size: 27
53324107 GGGGCAAAAT
* * *
53324117 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53324144 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53324171 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53324198 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53324225 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53324252 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53324279 GGAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53324306 AGTAATT
1 GGTAATT
53324313 TCACAATCAA
Statistics
Matches: 148, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:53324347 original size:27 final size:27
Alignment explanation
Indices: 53324317--53324648 Score: 373
Period size: 27 Copynumber: 12.3 Consensus size: 27
53324307 GTAATTTCAC
* *
53324317 AATCAAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
53324344 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
53324371 AA-CTGAGGGTAAACCAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
** * *
53324398 AATTAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
53324425 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
53324452 AATCGAGTGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
53324479 AA-CTGAGGGTAAAACGATAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* *
53324506 AAT-GAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
53324532 AATTGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
53324559 AATCGAGGATAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
53324586 AATCGAGGGTGAAACGTTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
53324613 AATCGAGGCTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
53324640 AATCGAGGG
1 AATCGAGGG
53324649 CATTTCAGTA
Statistics
Matches: 255, Mismatches: 45, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
26 26 0.10
27 229 0.90
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTATA
Found at i:53324679 original size:26 final size:27
Alignment explanation
Indices: 53324629--53324690 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
53324619 GGCTAAAATG
* *
53324629 GTAATTCTACAAATCGAGGGCATTTCA
1 GTAATTTTACAAATCGACGGCATTTCA
* *
53324656 GTAATTTTAC-AATCGACGGTATTTCG
1 GTAATTTTACAAATCGACGGCATTTCA
53324682 GTAATTTTA
1 GTAATTTTA
53324691 TAAACTGGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (27 bp):
GTAATTTTACAAATCGACGGCATTTCA
Found at i:53324729 original size:26 final size:25
Alignment explanation
Indices: 53324656--53324741 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 25
53324646 GGGCATTTCA
**
53324656 GTAATTTTACAA-TCGACGGTATTTCG
1 GTAATTTTACAACT-GGGGGTATTT-G
*
53324682 GTAATTTTATAAACTGGGGGTACTTTG
1 GTAATTTTA-CAACTGGGGGTA-TTTG
*
53324709 GTAATTTTACAACTGGGGGTATTTTA
1 GTAATTTTACAACTGGGGGTA-TTTG
53324735 GTAATTT
1 GTAATTT
53324742 GGTAAACTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
26 30 0.59
27 17 0.33
28 4 0.08
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (25 bp):
GTAATTTTACAACTGGGGGTATTTG
Found at i:53327923 original size:41 final size:41
Alignment explanation
Indices: 53327878--53327995 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
53327868 TGAAAGATAA
53327878 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
53327919 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
53327949 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
53327990 ATGTAG
1 ATGTAG
53327996 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:53327934 original size:71 final size:71
Alignment explanation
Indices: 53327846--53328009 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
53327836 GAGATGTATC
53327846 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
53327911 AGGACA
66 AGGACA
53327917 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
53327982 AGGACA
66 AGGACA
53327988 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
53328010 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:53335502 original size:41 final size:41
Alignment explanation
Indices: 53335457--53335574 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
53335447 TGAAAGATAA
53335457 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
53335498 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
53335528 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
53335569 ATGTAG
1 ATGTAG
53335575 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:53335513 original size:71 final size:71
Alignment explanation
Indices: 53335425--53335588 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
53335415 GAGATGTATC
53335425 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
53335490 AGGACA
66 AGGACA
53335496 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
53335561 AGGACA
66 AGGACA
53335567 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
53335589 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:53337367 original size:25 final size:25
Alignment explanation
Indices: 53337339--53337388 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
53337329 CCTTATACCA
* * *
53337339 TAAAAATGACCGTTTTGCCCCTAGG
1 TAAAAATGACCATTATACCCCTAGG
53337364 TAAAAATGACCATTATACCCCTAGG
1 TAAAAATGACCATTATACCCCTAGG
53337389 GTTTATGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (25 bp):
TAAAAATGACCATTATACCCCTAGG
Found at i:53337457 original size:20 final size:20
Alignment explanation
Indices: 53337432--53337490 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
53337422 TAAATATGGT
*
53337432 ATGTATGAGATGCACATGAC
1 ATGTATGATATGCACATGAC
*
53337452 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
53337472 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
53337491 GTAATCATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:53337567 original size:24 final size:24
Alignment explanation
Indices: 53337540--53337682 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
53337530 GAGGAAGTGA
53337540 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
53337564 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
53337588 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
53337611 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * * *
53337635 GAAAGGGCTTTTGACCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
53337659 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
53337683 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
23 23 0.21
24 75 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:53337633 original size:47 final size:47
Alignment explanation
Indices: 53337540--53337682 Score: 198
Period size: 47 Copynumber: 3.0 Consensus size: 47
53337530 GAGGAAGTGA
53337540 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
53337588 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * * *
53337635 GAAAGGGCTTTTGACCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
53337683 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
47 42 0.48
48 34 0.39
49 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:53337656 original size:71 final size:72
Alignment explanation
Indices: 53337540--53337683 Score: 211
Period size: 71 Copynumber: 2.0 Consensus size: 72
53337530 GAGGAAGTGA
* *
53337540 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGACCCAGTTATCAAAAGAGGC-TAGGCCT
53337603 CCAGTTAT
65 CCAGTTAT
** * *
53337611 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGACCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGACCCAGTTATCAAAAGAGGCTAGGCCTC
53337676 CAGTTAT
66 CAGTTAT
53337683 A
1 A
53337684 TGATAAAGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 53 0.82
72 12 0.18
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGACCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:53337912 original size:31 final size:31
Alignment explanation
Indices: 53337874--53337968 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
53337864 CGTTTACAGT
*
53337874 AAAGGCTTCGGTCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
53337905 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
53337936 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
53337967 AA
1 AA
53337969 TATGAAAAGG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:53340106 original size:6 final size:6
Alignment explanation
Indices: 53340095--53340250 Score: 160
Period size: 6 Copynumber: 25.8 Consensus size: 6
53340085 AACCAAAATG
* *
53340095 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC AGTATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
* * *
53340143 AGTAA-C AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC AAAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
* *
53340192 AGTAA-C AGAATC AGAATC AGAATC AGTATT AGTAA-C AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC
53340240 AGAATC AGAAT
1 AGAATC AGAAT
53340251 GTGAATGCAA
Statistics
Matches: 125, Mismatches: 14, Indels: 22
0.78 0.09 0.14
Matches are distributed among these distances:
5 9 0.07
6 107 0.86
7 8 0.06
8 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:53340108 original size:30 final size:29
Alignment explanation
Indices: 53340074--53340250 Score: 174
Period size: 30 Copynumber: 6.3 Consensus size: 29
53340064 AAGAAACATT
* * *
53340074 ATCAGAATTGGAACCAAAATGAGAATCAGA
1 ATCAGAATTGTAA-CAGAATCAGAATCAGA
*
53340104 ATCAGAATCAGTAACAGAATCAGAATCAGA
1 ATCAGAAT-TGTAACAGAATCAGAATCAGA
*
53340134 ATCAGTATTAGTAACAGAATCAGAATCAGA
1 ATCAGAATT-GTAACAGAATCAGAATCAGA
* * *
53340164 ATTAG----GTGACAGAATCAGAATCAAA
1 ATCAGAATTGTAACAGAATCAGAATCAGA
53340189 ATC---A--GTAACAGAATCAGAATCAGA
1 ATCAGAATTGTAACAGAATCAGAATCAGA
*
53340213 ATCAGTATTAGTAACAGAATCAGAATCAGA
1 ATCAGAATT-GTAACAGAATCAGAATCAGA
53340243 ATCAGAAT
1 ATCAGAAT
53340251 GTGAATGCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
24 21 0.17
25 20 0.16
27 1 0.01
30 80 0.64
31 3 0.02
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.20
Consensus pattern (29 bp):
ATCAGAATTGTAACAGAATCAGAATCAGA
Found at i:53340417 original size:27 final size:26
Alignment explanation
Indices: 53340368--53340441 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 26
53340358 AGCATGGCTG
* * *
53340368 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATTGTGGCAGAGCCA
* *
53340394 CCGGATACAGATATTGTGGTAGAGCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCA
*
53340421 CCAGAATCAGATAATGTGGCA
1 CCAGAA-CAGATATTGTGGCA
53340442 AACCCACCGA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 5 0.13
27 33 0.87
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:53340654 original size:22 final size:22
Alignment explanation
Indices: 53340606--53340664 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
53340596 GTAAATACGT
*
53340606 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
53340628 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
53340650 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
53340665 TAATAATGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:53340831 original size:27 final size:26
Alignment explanation
Indices: 53340752--53340834 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 26
53340742 TCGATCGGTC
* *
53340752 AACAGATATTGTGGCAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
53340778 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
53340805 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
53340832 AAC
1 AAC
53340835 GCTTCCTCCG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 8 0.15
27 44 0.85
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:53341076 original size:27 final size:27
Alignment explanation
Indices: 53341033--53341227 Score: 214
Period size: 27 Copynumber: 7.3 Consensus size: 27
53341023 GGGGCAAAAT
* * *
53341033 GGTAATT-TTCCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53341059 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53341086 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53341113 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53341140 GGTAATTCTATCCTATAAAGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
53341167 AGTAATTCTACCCTATAGGGGTATTCC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53341194 GG-AAGTTCTACCCTACAGGGGTATTTC
1 GGTAA-TTCTACCCTACAAGGGTATTTC
*
53341221 AGTAATT
1 GGTAATT
53341228 TCACAATCAA
Statistics
Matches: 141, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
26 9 0.06
27 130 0.92
28 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:53341145 original size:81 final size:81
Alignment explanation
Indices: 53341050--53341227 Score: 241
Period size: 81 Copynumber: 2.2 Consensus size: 81
53341040 TTCCCCACAA
* * * *
53341050 GGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTC-G
1 GGGTATTTCGGTAATTCTACCCTACAAAGGTATTTCAGTAATTCTACCCTACAAGGGTATTCCGG
53341114 ATAATTCTACCCTACAG
66 A-AATTCTACCCTACAG
* * * * *
53341131 GGGTATTTTGGTAATTCTATCCTATAAAGGTATTTCAGTAATTCTACCCTATAGGGGTATTCCGG
1 GGGTATTTCGGTAATTCTACCCTACAAAGGTATTTCAGTAATTCTACCCTACAAGGGTATTCCGG
*
53341196 AAGTTCTACCCTACAG
66 AAATTCTACCCTACAG
*
53341212 GGGTATTTCAGTAATT
1 GGGTATTTCGGTAATT
53341228 TCACAATCAA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 82 0.98
82 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (81 bp):
GGGTATTTCGGTAATTCTACCCTACAAAGGTATTTCAGTAATTCTACCCTACAAGGGTATTCCGG
AAATTCTACCCTACAG
Found at i:53341262 original size:27 final size:27
Alignment explanation
Indices: 53341232--53341564 Score: 393
Period size: 27 Copynumber: 12.3 Consensus size: 27
53341222 GTAATTTCAC
*
53341232 AATCAAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
53341259 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
53341286 AA-CTGAGGGTAAACCAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* * *
53341313 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
53341340 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
53341367 AATCGAGTGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
53341394 AA-CTGAGGGTAAAACGATAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* *
53341421 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
53341448 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* * *
53341475 AATCGAGGATAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
53341502 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
53341529 AATCGAGGCTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
53341556 AATCGAGGG
1 AATCGAGGG
53341565 CATTTCAGTA
Statistics
Matches: 259, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
26 3 0.01
27 253 0.98
28 3 0.01
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTATA
Found at i:53341595 original size:26 final size:27
Alignment explanation
Indices: 53341545--53341606 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
53341535 GGCTAAAATG
* *
53341545 GTAATTCTACAAATCGAGGGCATTTCA
1 GTAATTTTACAAATCGACGGCATTTCA
* *
53341572 GTAATTTTAC-AATCGACGGTATTTCG
1 GTAATTTTACAAATCGACGGCATTTCA
53341598 GTAATTTTA
1 GTAATTTTA
53341607 TAAACTGGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (27 bp):
GTAATTTTACAAATCGACGGCATTTCA
Found at i:53341653 original size:25 final size:26
Alignment explanation
Indices: 53341566--53341655 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
53341556 AATCGAGGGC
**
53341566 ATTTCAGTAATTTTACAA-TCGACGGT
1 ATTTCAGTAATTTTACAACT-GGGGGT
* *
53341592 ATTTCGGTAATTTTATAAACT-GGGGT
1 ATTTCAGTAATTTTA-CAACTGGGGGT
*
53341618 ACTTTGA-TAATTTTACAACTGGGGGT
1 A-TTTCAGTAATTTTACAACTGGGGGT
53341644 ATTT-AGTAATTT
1 ATTTCAGTAATTT
53341656 GGTAAACTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
24 1 0.02
25 13 0.25
26 32 0.62
27 5 0.10
28 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (26 bp):
ATTTCAGTAATTTTACAACTGGGGGT
Found at i:53343624 original size:6 final size:6
Alignment explanation
Indices: 53343613--53343744 Score: 128
Period size: 6 Copynumber: 21.8 Consensus size: 6
53343603 AACCAAAATG
* *
53343613 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC AGTATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
* * *
53343661 AGTAA-C AGAATT AGAATC AGAATT AG-GTGAC AGAATC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
* *
53343710 AGTATT AGTAA-C AGAATC AGAATC AGAATC AGAAT
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAAT
53343745 GTGAATGCAA
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
5 7 0.07
6 89 0.86
7 6 0.06
8 1 0.01
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:53343628 original size:30 final size:29
Alignment explanation
Indices: 53343592--53343744 Score: 161
Period size: 30 Copynumber: 5.3 Consensus size: 29
53343582 AAGAAACATT
* * *
53343592 ATCAGAATTGGAACCAAAATGAGAATCAGA
1 ATCAGAATTGTAA-CAGAATCAGAATCAGA
*
53343622 ATCAGAATCAGTAACAGAATCAGAATCAGA
1 ATCAGAAT-TGTAACAGAATCAGAATCAGA
* *
53343652 ATCAGTATTAGTAACAGAATTAGAATCAGA
1 ATCAGAATT-GTAACAGAATCAGAATCAGA
* *
53343682 ATTAG----GTGACAGAATCAGAATCAGA
1 ATCAGAATTGTAACAGAATCAGAATCAGA
*
53343707 ATCAGTATTAGTAACAGAATCAGAATCAGA
1 ATCAGAATT-GTAACAGAATCAGAATCAGA
53343737 ATCAGAAT
1 ATCAGAAT
53343745 GTGAATGCAA
Statistics
Matches: 103, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
25 22 0.21
30 78 0.76
31 3 0.03
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (29 bp):
ATCAGAATTGTAACAGAATCAGAATCAGA
Found at i:53343899 original size:27 final size:26
Alignment explanation
Indices: 53343862--53343927 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
53343852 AGCATGGCTG
*
53343862 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
53343888 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
53343915 CCAGAATCAGATA
1 CCAGAA-CAGATA
53343928 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:53343932 original size:27 final size:27
Alignment explanation
Indices: 53343862--53343935 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
53343852 AGCATGGCTG
* *
53343862 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
53343888 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
53343915 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
53343936 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:53343942 original size:27 final size:27
Alignment explanation
Indices: 53343886--53343943 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
53343876 GTGACAGAGT
* * *
53343886 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
53343913 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
53343940 CACC
1 CACC
53343944 TAATAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:53344148 original size:22 final size:22
Alignment explanation
Indices: 53344100--53344158 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
53344090 GTAAATACGT
*
53344100 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
53344122 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
53344144 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
53344159 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:53344325 original size:27 final size:26
Alignment explanation
Indices: 53344246--53344327 Score: 110
Period size: 27 Copynumber: 3.1 Consensus size: 26
53344236 TCGATTGGTC
* *
53344246 AACAGATATTGTGGCAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
*
53344272 ATACAGATATTATGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
53344299 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
53344326 AA
1 AA
53344328 GGGCAAAACA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 8 0.16
27 41 0.84
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.20
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:53344394 original size:27 final size:27
Alignment explanation
Indices: 53344364--53344532 Score: 185
Period size: 27 Copynumber: 6.3 Consensus size: 27
53344354 AGGGCAAAAT
* * *
53344364 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53344391 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53344418 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53344445 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * * *
53344472 AGTAATTCTACCCTATAGGGGTGTTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53344499 AGAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53344526 AGTAATT
1 GGTAATT
53344533 TCACAATTAA
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:53344424 original size:54 final size:54
Alignment explanation
Indices: 53344365--53344532 Score: 212
Period size: 54 Copynumber: 3.1 Consensus size: 54
53344355 GGGCAAAATG
* * * * *
53344365 GTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAAGGGTATTTC-
1 GTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCA
* *
53344418 GATAATTCTACCCTACAGGGGTATTTTGGTAATTCTATCCTATAAGGGTATTTCA
1 G-TAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCA
* * * * *
53344473 GTAATTCTACCCTATAGGGGTGTTTTAGAAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCA
53344527 GTAATT
1 GTAATT
53344533 TCACAATTAA
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 97 0.98
55 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (54 bp):
GTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCA
Found at i:53344531 original size:81 final size:81
Alignment explanation
Indices: 53344380--53344532 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 81
53344370 TTTACCCCAC
* * *
53344380 AAGGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTT
1 AAGGGTATCTCAGTAATTCTACCCTACAAGGGTATTTAGATAATTCTACCCTACAGGGGTATTTC
*
53344445 GGTAATTCTATCCTAT
66 AGTAATTCTATCCTAT
* * * *
53344461 AAGGGTATTTCAGTAATTCTACCCTATAGGGGTGTTTTAGA-AATTCTACCCTACAGGGGTATTT
1 AAGGGTATCTCAGTAATTCTACCCTACAAGGGT-ATTTAGATAATTCTACCCTACAGGGGTATTT
53344525 CAGTAATT
65 CAGTAATT
53344533 TCACAATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 58 0.92
82 5 0.08
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (81 bp):
AAGGGTATCTCAGTAATTCTACCCTACAAGGGTATTTAGATAATTCTACCCTACAGGGGTATTTC
AGTAATTCTATCCTAT
Found at i:53344574 original size:27 final size:27
Alignment explanation
Indices: 53344542--53344869 Score: 381
Period size: 27 Copynumber: 12.1 Consensus size: 27
53344532 TTCACAATTA
53344542 AGGGTAAAACGGTAATTCTATAAATCG
1 AGGGTAAAACGGTAATTCTATAAATCG
* * * *
53344569 AGGGTAAAACGATAATTTTGTAAATTG
1 AGGGTAAAACGGTAATTCTATAAATCG
* * * *
53344596 AGGGTAAACCAGTAATTCTGTAAATCA
1 AGGGTAAAACGGTAATTCTATAAATCG
* * *
53344623 AGGGCAAAACGGTAATTTTACAAATCG
1 AGGGTAAAACGGTAATTCTATAAATCG
*
53344650 AGGGTAAAACGGTAATTCTGTAAATCG
1 AGGGTAAAACGGTAATTCTATAAATCG
* * *
53344677 AGTGTAAAACAGTAATTCTGTAAA-CTG
1 AGGGTAAAACGGTAATTCTATAAATC-G
*
53344704 AGGGTAAAACGATAATTCTATAAATCG
1 AGGGTAAAACGGTAATTCTATAAATCG
* *
53344731 AGGGTAAAACAGTAATTCTGTAAA-CTG
1 AGGGTAAAACGGTAATTCTATAAATC-G
*
53344758 AGGGTAAAACGGTAATTCTGTAAATCG
1 AGGGTAAAACGGTAATTCTATAAATCG
* * *
53344785 AGGATAAAACGGTAATTTTACAAATCG
1 AGGGTAAAACGGTAATTCTATAAATCG
* *
53344812 AGGGTGAAACAGTAATTCTATAAATCG
1 AGGGTAAAACGGTAATTCTATAAATCG
* * *
53344839 AGGCTAAAATGGTAATTCTACAAATCG
1 AGGGTAAAACGGTAATTCTATAAATCG
53344866 AGGG
1 AGGG
53344870 CATTTCAGTA
Statistics
Matches: 251, Mismatches: 46, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
26 2 0.01
27 247 0.98
28 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (27 bp):
AGGGTAAAACGGTAATTCTATAAATCG
Done.