Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 45 of 82
Found at i:16650069 original size:42 final size:42
Alignment explanation
Indices: 16650010--16650126 Score: 189
Period size: 42 Copynumber: 2.8 Consensus size: 42
16650000 TTAACTCGGT
* *
16650010 TATGTGCAAGTGGGAGTGCGCATAAGTCGTTGCTGACCCGCC
1 TATGTGCGAGTGGGAGTGCGCATAAGCCGTTGCTGACCCGCC
16650052 TATGTGCGAGTGGGAGTGCGCATAAGCCGTTGCTGACCCGCC
1 TATGTGCGAGTGGGAGTGCGCATAAGCCGTTGCTGACCCGCC
* * *
16650094 TATGTGCGAGTAGGAATGCGCATGAGCCGTTGC
1 TATGTGCGAGTGGGAGTGCGCATAAGCCGTTGC
16650127 ATATGAGCTG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (42 bp):
TATGTGCGAGTGGGAGTGCGCATAAGCCGTTGCTGACCCGCC
Found at i:16666351 original size:102 final size:102
Alignment explanation
Indices: 16666117--16666363 Score: 227
Period size: 102 Copynumber: 2.4 Consensus size: 102
16666107 ATAAAAAAAA
* * * ** * *
16666117 TCATATTCAGCCGTTAGCTTTATCGTTTATATTTTGACTATAATTATATTATACTATTGGTTGCA
1 TCATATTCAGCCGATAGCTTTATCGTTTATATTTTGGCTGTAAGAATATTATACTAATGGTTACA
*
16666182 AGCTTTATCGCTCATTCTTTAACCATAGTTCATCACT
66 AGCTTTATCGCTCATTCTTTAACCATAATTCATCACT
* * * *
16666219 T-TTACTTCAGTCC-AAAGCTTTA-C-TACTTATATTTTGGCTGTAAGAATATTGTTCTAAT-GT
1 TCATA-TTCAG-CCGATAGCTTTATCGT--TTATATTTTGGCTGTAAGAATATTATACTAATGGT
* * * *
16666279 TCACAAGTTTTATCGCTCATTCTTTGACCATAATTTATTA-T
62 T-ACAAGCTTTATCGCTCATTCTTTAACCATAATTCATCACT
* * *
16666320 TCATATTCCAGCCGCTAGCTTTATCGTTTATAATTTGGTTGTAA
1 TCATATT-CAGCCGATAGCTTTATCGTTTATATTTTGGCTGTAA
16666364 TGATGTTATG
Statistics
Matches: 114, Mismatches: 21, Indels: 20
0.74 0.14 0.13
Matches are distributed among these distances:
100 1 0.01
101 12 0.11
102 97 0.85
103 3 0.03
104 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.45
Consensus pattern (102 bp):
TCATATTCAGCCGATAGCTTTATCGTTTATATTTTGGCTGTAAGAATATTATACTAATGGTTACA
AGCTTTATCGCTCATTCTTTAACCATAATTCATCACT
Found at i:16667220 original size:21 final size:21
Alignment explanation
Indices: 16667187--16667226 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16667177 TAATCAGAGT
* * *
16667187 AACTCTAATATCATTAATAAC
1 AACTCCAACATCATGAATAAC
16667208 AACTCCAACATCATGAATA
1 AACTCCAACATCATGAATA
16667227 GCCTCAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.28
Consensus pattern (21 bp):
AACTCCAACATCATGAATAAC
Found at i:16669798 original size:21 final size:22
Alignment explanation
Indices: 16669774--16669836 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
16669764 TTTTAATAAT
16669774 ATATATAATAAAAACTTATAC-
1 ATATATAATAAAAACTTATACA
*
16669795 ATATATAATATAAAAATATATACA
1 ATATATAATA-AAAACT-TATACA
*
16669819 ATAAATAAGT-AAAACTTA
1 ATATATAA-TAAAAACTTA
16669837 AAAAAAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 10 0.29
22 7 0.20
23 10 0.29
24 7 0.20
25 1 0.03
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (22 bp):
ATATATAATAAAAACTTATACA
Found at i:16669798 original size:23 final size:23
Alignment explanation
Indices: 16669772--16669836 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
16669762 ATTTTTAATA
16669772 ATATATATAATAAAAACTTATAC
1 ATATATATAATAAAAACTTATAC
16669795 ATATATA-ATATAAAAA-TATATAC
1 ATATATATA-ATAAAAACT-TATAC
*
16669818 A-ATAAATAAGT-AAAACTTA
1 ATATATATAA-TAAAAACTTA
16669837 AAAAAAATCT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (23 bp):
ATATATATAATAAAAACTTATAC
Found at i:16669921 original size:22 final size:21
Alignment explanation
Indices: 16669862--16669921 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 21
16669852 TTCTAATAAC
16669862 AATAACATAATAATAATAAAAT
1 AATAACATAA-AATAATAAAAT
*
16669884 AATTACA-AAATTATAATTACAAA-
1 AATAACATAAA--ATAA-TA-AAAT
16669907 AATAACATAAAATAA
1 AATAACATAAAATAA
16669922 ATCTACCGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
20 1 0.03
21 2 0.06
22 14 0.45
23 8 0.26
24 6 0.19
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAACATAAAATAATAAAAT
Found at i:16671350 original size:35 final size:35
Alignment explanation
Indices: 16671302--16671384 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
16671292 TAATGTACAA
*
16671302 AGAACAA-TCAAAACAAGTGAATCACTAC-TTCACGC
1 AGAACAACT-AAAACAAGTGAAGCACTACGTT-ACGC
* *
16671337 AGAACAACTAAAACAAGTGTAGCGCTACGTTACGC
1 AGAACAACTAAAACAAGTGAAGCACTACGTTACGC
16671372 AGAACAACTAAAA
1 AGAACAACTAAAA
16671385 TTAGTAAAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 40 0.93
36 3 0.07
ACGTcount: A:0.47, C:0.23, G:0.14, T:0.16
Consensus pattern (35 bp):
AGAACAACTAAAACAAGTGAAGCACTACGTTACGC
Found at i:16679323 original size:19 final size:20
Alignment explanation
Indices: 16679294--16679333 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
16679284 TCACTTCTAA
16679294 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
16679314 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
16679333 A
1 A
16679334 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:16683306 original size:2 final size:2
Alignment explanation
Indices: 16683299--16683341 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
16683289 ATCTAGGTTN
16683299 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16683341 T
1 T
16683342 TTGAAAAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16686374 original size:13 final size:13
Alignment explanation
Indices: 16686356--16686380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16686346 AGAGAAATTG
16686356 TGATTTTATAAAA
1 TGATTTTATAAAA
16686369 TGATTTTATAAA
1 TGATTTTATAAA
16686381 TTTTCTAGAA
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):
TGATTTTATAAAA
Found at i:16687639 original size:22 final size:22
Alignment explanation
Indices: 16687596--16687640 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
16687586 ATAATTCCAC
*
16687596 ATGATGATTGTCATAGAAATGA
1 ATGATGATTGTCAAAGAAATGA
*
16687618 ATGATGATTGGT-AAAGAGATGA
1 ATGATGATT-GTCAAAGAAATGA
16687640 A
1 A
16687641 CTAATTAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.42, C:0.02, G:0.27, T:0.29
Consensus pattern (22 bp):
ATGATGATTGTCAAAGAAATGA
Found at i:16688262 original size:59 final size:59
Alignment explanation
Indices: 16688178--16688719 Score: 478
Period size: 59 Copynumber: 9.2 Consensus size: 59
16688168 AGATAATTTA
* * * *
16688178 AAATCGAACTTGTTTTGAAATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTTAATTTTT
1 AAATCGAACCTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTCAATTTTT
* * * *
16688237 AAATCGAATCTGTTTTGACATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTTT
1 AAATCGAACCTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTCAATTTTT
* * * * * * ** *
16688296 TAATCAAACTTGTTTTGCTATAGGTCGAGCCTAGATTGAGTGT-AGAAATTTCAATTTTTT
1 AAATCGAACCTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAAG-AATTTCAA-TTTTT
* * * * *
16688356 AAATCAAACCTATTTTGATATAGGTCCAGCCTAGGTCAAGT-TTAGAAATTCAGTTTTT
1 AAATCGAACCTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTCAATTTTT
* * * * * *
16688414 AAAATCAAACCTATTTTGATATAGGTTGAGCCTAAGTCGAGTTTAGGAATTTCAATTTTT
1 -AAATCGAACCTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTCAATTTTT
* * * * * * ** *
16688474 AAATCGAACCTATTTTGATATAAGTTGAGCTTAAGTCAAATCTAGGAATTTTGATTTTC
1 AAATCGAACCTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTCAATTTTT
* * * * * *
16688533 AATTTGAACTTATTTTGATATAGGTCGAGCCTAAGTCAAGTCTAGGAATTTGAATTTTT
1 AAATCGAACCTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTCAATTTTT
* * * * * *
16688592 AAATCGAACCTATTTCGATATAGGGCGAACCTAGATCAAATCCCAA-AATTTCAATTTTT
1 AAATCGAACCTATTTTGATATAGGTCGAGCCTAGGTCAAGT-CTAAGAATTTCAATTTTT
* * * * * * * * * * *
16688651 AAGTCAAACATATTTTAAGATAGGTCAACCCTAGATTAAGTTTAAGAACTTCAATTGTTT
1 AAATCGAACCTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTCAATT-TTT
16688711 AAATCGAAC
1 AAATCGAAC
16688720 TTGCTTTAAG
Statistics
Matches: 394, Mismatches: 81, Indels: 15
0.80 0.17 0.03
Matches are distributed among these distances:
58 8 0.02
59 321 0.81
60 65 0.16
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (59 bp):
AAATCGAACCTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTCAATTTTT
Found at i:16688591 original size:237 final size:236
Alignment explanation
Indices: 16688174--16688719 Score: 555
Period size: 237 Copynumber: 2.3 Consensus size: 236
16688164 CATTAGATAA
* * * * *
16688174 TTTAAAATCGAACTTGTTTTGAAATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTTAATTTTTAA
1 TTTAAAATCAAACCTATTTTGAAATAGGTCGAGCCTAAGTCAAGTCTAAGAATTTCAATTTTTAA
* * * * * *
16688239 ATCGAATCTGTTTTGACATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTTTTAATCAAA
66 ATCGAACCTATTTTGACATAAGTCGAGCCTAAGTCAAATCTAGGAATTTCAATTTTTCAATCAAA
* * ** *
16688304 CTTGTTTTGCTATAGGTCGAGCCTAGATTGAGTGTAGAAATTTCAATTTTTTAAATCAAACCTAT
131 CTTATTTTGATATAGGTCGAGCCTAGATCAAGTCTAGAAATTTCAA-TTTTTAAATCAAACCTAT
*
16688369 TTTGATATAGGTCCAGCCTAGGTCAAGTTTAGAAATTCAGTT
195 TTCGATATAGGTCCAGCCTAGGTCAAGTTTAGAAATTCAGTT
* * * * *
16688411 TTTAAAATCAAACCTATTTTGATATAGGTTGAGCCTAAGTCGAGTTTAGGAATTTCAATTTTTAA
1 TTTAAAATCAAACCTATTTTGAAATAGGTCGAGCCTAAGTCAAGTCTAAGAATTTCAATTTTTAA
* * * ** **
16688476 ATCGAACCTATTTTGATATAAGTTGAGCTTAAGTCAAATCTAGGAATTTTGA-TTTTCAATTTGA
66 ATCGAACCTATTTTGACATAAGTCGAGCCTAAGTCAAATCTAGGAATTTCAATTTTTCAA-TCAA
* * *
16688540 ACTTATTTTGATATAGGTCGAGCCTA-AGTCAAGTCTAGGAATTTGAATTTTTAAATCGAACCTA
130 ACTTATTTTGATATAGGTCGAGCCTAGA-TCAAGTCTAGAAATTTCAATTTTTAAATCAAACCTA
* * * * * ** *
16688604 TTTCGATATAGGGCGAACCTAGATCAAATCCCA-AAATTTCAATT
194 TTTCGATATAGGTCCAGCCTAGGTCAAGT-TTAGAAA-TTCAGTT
* * * * * * *
16688648 TTT-AAGTCAAACATATTTT-AAGATAGGTCAACCCT-AGATTAAGTTTAAGAACTTCAATTGTT
1 TTTAAAATCAAACCTATTTTGAA-ATAGGTCGAGCCTAAG-TCAAGTCTAAGAATTTCAATT-TT
16688710 TAAATCGAAC
63 TAAATCGAAC
16688720 TTGCTTTAAG
Statistics
Matches: 252, Mismatches: 50, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
235 3 0.01
236 90 0.36
237 159 0.63
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (236 bp):
TTTAAAATCAAACCTATTTTGAAATAGGTCGAGCCTAAGTCAAGTCTAAGAATTTCAATTTTTAA
ATCGAACCTATTTTGACATAAGTCGAGCCTAAGTCAAATCTAGGAATTTCAATTTTTCAATCAAA
CTTATTTTGATATAGGTCGAGCCTAGATCAAGTCTAGAAATTTCAATTTTTAAATCAAACCTATT
TCGATATAGGTCCAGCCTAGGTCAAGTTTAGAAATTCAGTT
Found at i:16688593 original size:178 final size:177
Alignment explanation
Indices: 16688178--16688666 Score: 491
Period size: 178 Copynumber: 2.8 Consensus size: 177
16688168 AGATAATTTA
* * *
16688178 AAATCGAACTTGTTTTGAAATAGGTCGAGCCTAGGTCAAGTCTAAGAATTTTAATTTTTAAATCG
1 AAATCGAACTTATTTTGATATAGGTCGAGCCTAGGTCAAGTCT-AGAATTTCAATTTTTAAATCG
* * * * * * *
16688243 AATCTGTTTTGACATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTTTTAATCAAACTTG
65 AACCTATTTTGATATAGGTCGAGCCTAAGTCAAGTCTAGGAATTTCAATTTTTAAATCAAACCTA
* * ** * * *
16688308 TTTTGCTATAGGTCGAGCCTAGATTGAGTGTAGAAATTTCAATTTTTT
130 TTTTGATATAAGTCGAGCCTAGATCAAATCTAGAAATTTCAATTTTTC
* * * * * * *
16688356 AAATCAAACCTATTTTGATATAGGTCCAGCCTAGGTCAAGTTTAGAAATTCAGTTTTTAAAATCA
1 AAATCGAACTTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAGAATTTCAATTTTT-AAATCG
* * * *
16688421 AACCTATTTTGATATAGGTTGAGCCTAAGTCGAGTTTAGGAATTTCAATTTTTAAATCGAACCTA
65 AACCTATTTTGATATAGGTCGAGCCTAAGTCAAGTCTAGGAATTTCAATTTTTAAATCAAACCTA
* * * **
16688486 TTTTGATATAAGTTGAGCTTA-AGTCAAATCTAGGAATTTTGA-TTTTC
130 TTTTGATATAAGTCGAGCCTAGA-TCAAATCTAGAAATTTCAATTTTTC
* * * *
16688533 AATTTGAACTTATTTTGATATAGGTCGAGCCTAAGTCAAGTCTAGGAATTTGAATTTTTAAATCG
1 AAATCGAACTTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTA-GAATTTCAATTTTTAAATCG
* * * * * * * *
16688598 AACCTATTTCGATATAGGGCGAACCT-AGATCAAATCCCA-AAATTTCAATTTTTAAGTCAAACA
65 AACCTATTTTGATATAGGTCGAGCCTAAG-TCAAGT-CTAGGAATTTCAATTTTTAAATCAAACC
16688661 TATTTT
128 TATTTT
16688667 AAGATAGGTC
Statistics
Matches: 250, Mismatches: 56, Indels: 11
0.79 0.18 0.03
Matches are distributed among these distances:
176 2 0.01
177 111 0.44
178 137 0.55
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (177 bp):
AAATCGAACTTATTTTGATATAGGTCGAGCCTAGGTCAAGTCTAGAATTTCAATTTTTAAATCGA
ACCTATTTTGATATAGGTCGAGCCTAAGTCAAGTCTAGGAATTTCAATTTTTAAATCAAACCTAT
TTTGATATAAGTCGAGCCTAGATCAAATCTAGAAATTTCAATTTTTC
Found at i:16691614 original size:13 final size:13
Alignment explanation
Indices: 16691596--16691620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16691586 ATTTTCAAAA
16691596 ATTTTATAAAATT
1 ATTTTATAAAATT
16691609 ATTTTATAAAAT
1 ATTTTATAAAAT
16691621 CTCATTTTTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:16692797 original size:19 final size:19
Alignment explanation
Indices: 16692773--16692809 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
16692763 CTTCTAAACT
16692773 TCAAATCATACTCCAATAC
1 TCAAATCATACTCCAATAC
16692792 TCAAATCATACTCCAATA
1 TCAAATCATACTCCAATA
16692810 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
TCAAATCATACTCCAATAC
Found at i:16694472 original size:7 final size:7
Alignment explanation
Indices: 16694462--16694487 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16694452 ATGTTAAAAA
16694462 CTAAACC
1 CTAAACC
16694469 CTAAACC
1 CTAAACC
16694476 CTAAACC
1 CTAAACC
16694483 CTAAA
1 CTAAA
16694488 GATGAATGCC
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:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:16695137 original size:3 final size:3
Alignment explanation
Indices: 16695129--16695165 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
16695119 AAATAAGGAA
*
16695129 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16695166 GTTATAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16695329 original size:23 final size:23
Alignment explanation
Indices: 16695290--16695334 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16695280 GAGTAAGATT
16695290 ATAATAATAATGCACA-TAGAGA
1 ATAATAATAATGCACATTAGAGA
* *
16695312 ATAATCAATAGTGGACATTAGAG
1 ATAAT-AATAATGCACATTAGAG
16695335 TTGGTAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (23 bp):
ATAATAATAATGCACATTAGAGA
Found at i:16697143 original size:30 final size:30
Alignment explanation
Indices: 16697107--16697173 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
16697097 TTTAATCAAA
*
16697107 CCCTTATACTTTTATTTTGAACCAAACAAG
1 CCCTTATACTTTTATTTTAAACCAAACAAG
* * * *
16697137 TCCTTATATTTTTATTTTAAATCAAATAAG
1 CCCTTATACTTTTATTTTAAACCAAACAAG
16697167 CCCTTAT
1 CCCTTAT
16697174 GATTAATGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.43
Consensus pattern (30 bp):
CCCTTATACTTTTATTTTAAACCAAACAAG
Found at i:16700596 original size:16 final size:16
Alignment explanation
Indices: 16700575--16700607 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16700565 GAACGCTTAC
16700575 ATTCATATACAGATAT
1 ATTCATATACAGATAT
*
16700591 ATTCATATACATATAT
1 ATTCATATACAGATAT
16700607 A
1 A
16700608 CATTTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTCATATACAGATAT
Found at i:16703454 original size:26 final size:26
Alignment explanation
Indices: 16703425--16703482 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
16703415 TGTCACGATC
16703425 TAAATCAAGGGGCCACGATCGATGCA
1 TAAATCAAGGGGCCACGATCGATGCA
*
16703451 TAAATCAAGGGGCCACGATTGATGCA
1 TAAATCAAGGGGCCACGATCGATGCA
*
16703477 TGAATC
1 TAAATC
16703483 CAACGAGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (26 bp):
TAAATCAAGGGGCCACGATCGATGCA
Found at i:16704509 original size:37 final size:37
Alignment explanation
Indices: 16704468--16704576 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 37
16704458 TCACACACGA
*
16704468 TACTGAAGTAACCGACAGAGGCTCAAATCATGCATAG
1 TACTGAAGTAACCGACAGAGGTTCAAATCATGCATAG
* * * *
16704505 TACTGAAGTAACCTATAGAGGTTCAAATCATGTATGG
1 TACTGAAGTAACCGACAGAGGTTCAAATCATGCATAG
** *
16704542 TACTGAAGTAATTGACGGAGGTTCAAATCATGCAT
1 TACTGAAGTAACCGACAGAGGTTCAAATCATGCAT
16704577 GATGCTAAGG
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (37 bp):
TACTGAAGTAACCGACAGAGGTTCAAATCATGCATAG
Found at i:16706851 original size:2 final size:2
Alignment explanation
Indices: 16706844--16706894 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
16706834 TTCTGTTGAA
* * *
16706844 AT AT AT AT AT AT AT AC AT AT AT AT AT GT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16706886 GT AT AT AT A
1 AT AT AT AT A
16706895 CTATTANNNN
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16706865 original size:16 final size:16
Alignment explanation
Indices: 16706844--16706890 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
16706834 TTCTGTTGAA
*
16706844 ATATATATATATATAC
1 ATATATATATGTATAC
16706860 ATATATATATGTATAC
1 ATATATATATGTATAC
16706876 ATATATATATGTATA
1 ATATATATATGTATA
16706891 TATACTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (16 bp):
ATATATATATGTATAC
Found at i:16707054 original size:2 final size:2
Alignment explanation
Indices: 16707047--16707138 Score: 94
Period size: 2 Copynumber: 45.0 Consensus size: 2
16707037 NNNNNGTTAC
* * * *
16707047 AT AT AT AT AT GT AT AT AT AC AGT AT AT AT AT AT GT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * *
16707090 AGT AT GT AT AT AT GT AT AT AT AC AT AT AT AT AT GT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16707133 AT AT AT
1 AT AT AT
16707139 TTCTAGAGTT
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
2 70 0.97
3 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (2 bp):
AT
Found at i:16707077 original size:23 final size:23
Alignment explanation
Indices: 16707047--16707133 Score: 140
Period size: 23 Copynumber: 3.8 Consensus size: 23
16707037 NNNNNGTTAC
16707047 ATATATATATGTATATATACAGT
1 ATATATATATGTATATATACAGT
16707070 ATATATATATGTATATATACAGT
1 ATATATATATGTATATATACAGT
*
16707093 ATGTATATATGTATATATACA-T
1 ATATATATATGTATATATACAGT
* *
16707115 ATATATATGTATATATATA
1 ATATATATATGTATATATA
16707134 TATATTTCTA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 17 0.28
23 43 0.72
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (23 bp):
ATATATATATGTATATATACAGT
Found at i:16711780 original size:29 final size:29
Alignment explanation
Indices: 16711707--16711781 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
16711697 CATCAGCCGG
* * *
16711707 TGCTCCCAAGAAAGGGAAGCACCGATCAG
1 TGCTCCCAAGAGAGGGAAGCACAGATCAA
*
16711736 TGTTCCCTAAGAGAGGG-AGCACTAGATCAA
1 TGCTCCC-AAGAGAGGGAAGCAC-AGATCAA
*
16711766 TGCTCCCAAGGGAGGG
1 TGCTCCCAAGAGAGGG
16711782 GAGGTTTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 19 0.50
30 19 0.50
ACGTcount: A:0.31, C:0.24, G:0.31, T:0.15
Consensus pattern (29 bp):
TGCTCCCAAGAGAGGGAAGCACAGATCAA
Found at i:16711784 original size:30 final size:29
Alignment explanation
Indices: 16711707--16711784 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 29
16711697 CATCAGCCGG
* * * *
16711707 TGCTCCCAAGAAAGGGAAGCACCGATCAG
1 TGCTCCCAAGAGAGGGGAGCACAGATCAA
*
16711736 TGTTCCCTAAGAGA-GGGAGCACTAGATCAA
1 TGCTCCC-AAGAGAGGGGAGCAC-AGATCAA
*
16711766 TGCTCCCAAGGGAGGGGAG
1 TGCTCCCAAGAGAGGGGAG
16711785 GTTTCTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 18 0.46
30 21 0.54
ACGTcount: A:0.31, C:0.23, G:0.32, T:0.14
Consensus pattern (29 bp):
TGCTCCCAAGAGAGGGGAGCACAGATCAA
Found at i:16713697 original size:13 final size:13
Alignment explanation
Indices: 16713679--16713703 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16713669 GGAAAATGGG
16713679 ATTTTATAAAATA
1 ATTTTATAAAATA
16713692 ATTTTATAAAAT
1 ATTTTATAAAAT
16713704 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:16714608 original size:2 final size:2
Alignment explanation
Indices: 16714601--16714626 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16714591 GATGTTTCAA
16714601 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
16714627 TGTTTTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16719646 original size:58 final size:56
Alignment explanation
Indices: 16719582--16719700 Score: 148
Period size: 58 Copynumber: 2.1 Consensus size: 56
16719572 CATAATCATC
* * * *
16719582 CAAAGTAGTTTACATGTGATTGATTTATTTTATGCAATTTAATAAATGCTATGCAATG
1 CAAAGTAGTATACATATGATAGATTTATTTT-TGCAATTTAATAAATGCCATGC-ATG
** * *
16719640 CAAAGTAGTATGTATATGATAGATTTATTTTTTCGATTTAATAAATGCCATGCATG
1 CAAAGTAGTATACATATGATAGATTTATTTTTGCAATTTAATAAATGCCATGCATG
16719696 CAAAG
1 CAAAG
16719701 ATGAGACCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
56 8 0.15
57 19 0.36
58 26 0.49
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.39
Consensus pattern (56 bp):
CAAAGTAGTATACATATGATAGATTTATTTTTGCAATTTAATAAATGCCATGCATG
Found at i:16726331 original size:62 final size:62
Alignment explanation
Indices: 16726228--16726344 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 62
16726218 TTATAGGGTC
*
16726228 GAAATTATAAAATTTTTTAAAAACACAGGTAAACTATAAAATTTAAAAATGATTGAAAAGAT
1 GAAATTATAAAATTTTTTAAAAACACAGATAAACTATAAAATTTAAAAATGATTGAAAAGAT
* * * * * *
16726290 GAAATTATAAAA-TTTTTAAATATATATATAAATTATGAAAATTTAAAAATTATTG
1 GAAATTATAAAATTTTTTAAAAACACAGATAAACTAT-AAAATTTAAAAATGATTG
16726345 GCCCCGCTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 18 0.38
62 29 0.62
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (62 bp):
GAAATTATAAAATTTTTTAAAAACACAGATAAACTATAAAATTTAAAAATGATTGAAAAGAT
Found at i:16729823 original size:47 final size:47
Alignment explanation
Indices: 16729747--16730026 Score: 312
Period size: 47 Copynumber: 6.0 Consensus size: 47
16729737 ACGTCATGTT
* * ** * * *
16729747 GGGAATGTGTGACACGGCACCGCTCAGAGTTAGTGAGACGCCATGGA
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
* * * * *
16729794 GGAAATCTGTGATATGCCAGAGTTAAGAGTTGGTGACACGCCATGGT
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
* ** * *
16729841 GGGAATGTGTGACACGGTAGCGTTCAGAGTTGGTGAGACGCCATGGA
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
* * * * *
16729888 GGAAATCTGTGACATGCCAGA-TTAAGAGTTGGTGACATGGCATGGA
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
*
16729934 GGGAATCTGTGACACGCCA-ACGTTCAGAGTTGGTGAGACGCCATGGA
1 GGGAATCTGTGACACGCCAGA-GTTCAGAGTTGGTGACACGCCATGGA
* *
16729981 GGGAATCTGTGACACACTAGAGTTCAGAGTTGGTGACACGCCATGG
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGG
16730027 TCATGTTTAG
Statistics
Matches: 189, Mismatches: 41, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
45 1 0.01
46 38 0.20
47 149 0.79
48 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.35, T:0.21
Consensus pattern (47 bp):
GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
Found at i:16729886 original size:94 final size:94
Alignment explanation
Indices: 16729725--16730027 Score: 419
Period size: 94 Copynumber: 3.2 Consensus size: 94
16729715 GGCAAGGTTT
* * * * * * *
16729725 AGAGTTTGTGAAACGTCATGTTGGGAATGTGTGACACGGCACCGCTCAGAGTTAGTGAGACGCCA
1 AGAGTTGGTGACACGCCATGGTGGGAATGTGTGACACGGCAACGTTCAGAGTTGGTGAGACGCCA
*
16729790 TGGAGGAAATCTGTGATATGCCAGAGTTA
66 TGGAGGAAATCTGTGACATGCCAGAGTTA
* *
16729819 AGAGTTGGTGACACGCCATGGTGGGAATGTGTGACACGGTAGCGTTCAGAGTTGGTGAGACGCCA
1 AGAGTTGGTGACACGCCATGGTGGGAATGTGTGACACGGCAACGTTCAGAGTTGGTGAGACGCCA
16729884 TGGAGGAAATCTGTGACATGCCAGA-TTA
66 TGGAGGAAATCTGTGACATGCCAGAGTTA
* * * * *
16729912 AGAGTTGGTGACATGGCATGGAGGGAATCTGTGACACGCCAACGTTCAGAGTTGGTGAGACGCCA
1 AGAGTTGGTGACACGCCATGGTGGGAATGTGTGACACGGCAACGTTCAGAGTTGGTGAGACGCCA
* ** * *
16729977 TGGAGGGAATCTGTGACACACTAGAGTTC
66 TGGAGGAAATCTGTGACATGCCAGAGTTA
16730006 AGAGTTGGTGACACGCCATGGT
1 AGAGTTGGTGACACGCCATGGT
16730028 CATGTTTAGA
Statistics
Matches: 184, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
93 82 0.45
94 102 0.55
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23
Consensus pattern (94 bp):
AGAGTTGGTGACACGCCATGGTGGGAATGTGTGACACGGCAACGTTCAGAGTTGGTGAGACGCCA
TGGAGGAAATCTGTGACATGCCAGAGTTA
Found at i:16730621 original size:31 final size:31
Alignment explanation
Indices: 16730586--16730849 Score: 280
Period size: 31 Copynumber: 8.5 Consensus size: 31
16730576 TTAGTTATTA
* *
16730586 GCGTGTGACAACATATTACTTGATATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
** * *
16730617 GCGTGTCACAGTATTTTACTTTATATGTATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* * *
16730648 TCGTGTCACAAAATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
** * * **
16730679 ATGTTTGACAGTATTTTACTTGATATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* * *
16730710 GCGTGTCATAACGTTTAACTTGATATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* *
16730741 GCGTGTCACAACATTTAACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* * *
16730772 ACGTGTCACAACATTTTACTTGTTATGCATA
1 GCGTGTCACAACATTTTACTTGATATGCATG
*
16730803 GTGTGTCACAACATTTTGA-TTGCA-ATGCATG
1 GCGTGTCACAACATTTT-ACTTG-ATATGCATG
16730834 GCGTGTCACAACATTT
1 GCGTGTCACAACATTT
16730850 ATTCCTTATT
Statistics
Matches: 192, Mismatches: 39, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
31 191 0.99
32 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (31 bp):
GCGTGTCACAACATTTTACTTGATATGCATG
Found at i:16732736 original size:156 final size:155
Alignment explanation
Indices: 16732468--16732978 Score: 626
Period size: 156 Copynumber: 3.3 Consensus size: 155
16732458 ACTTTCCCAC
* * * * * ** * * *
16732468 ATATGTTTATCGAGTAACACAGTAATTTATGTAATTGCAGTTCACTGAAGCGACGATAGGTCCTT
1 ATATGATTATTGAATAACACAGTTATATATGTAATTGCAGTTTGCGGAAGCGACGACAGGTCCTG
* * *
16732533 AAGCACCGATCGATCCAACTCAACCGTAGATAGCTAACGAGCCGGCGGTAAGGATATTAAAGTTG
66 AAGCACCGATCG-TCCAGCTCCACCGCAGATAGCTAACGAGCCGGCGGTAAGGATATTAAAGTTG
** * *
16732598 TAATGGTTAATGTTCAACAATTCCAA
130 TAACAGTTAATGTTCAACAATTTCAT
* *
16732624 ATATGATTATTGAATAACATAGTTATATATGTAATTACAGTTTGCGGAAGCGACGACAGGTCCTG
1 ATATGATTATTGAATAACACAGTTATATATGTAATTGCAGTTTGCGGAAGCGACGACAGGTCCTG
*** * * *
16732689 AAGCACCGATCTGTTTGGCTCCACCGCAGACAGCTAACGAGCCGGCGGTAAGGATAATCAAGTTG
66 AAGCACCGATC-GTCCAGCTCCACCGCAGATAGCTAACGAGCCGGCGGTAAGGATATTAAAGTTG
*
16732754 TAACAGTTAATGTTCAACAATTTTAT
130 TAACAGTTAATGTTCAACAATTTCAT
* * * * *
16732780 ACATGATTATTGAATAACACAGTTAAATATGTAATTGCAGTATGAGGAAGCGACGACAGGTCTTG
1 ATATGATTATTGAATAACACAGTTATATATGTAATTGCAGTTTGCGGAAGCGACGACAGGTCCTG
* * ** *
16732845 AAGCACTGATCGGTCCAGCTCCACCGCAGATTGCTAACGAGCCTCCGGTTAGGATATTAAAGTTG
66 AAGCACCGATC-GTCCAGCTCCACCGCAGATAGCTAACGAGCCGGCGGTAAGGATATTAAAGTTG
* *
16732910 TAACAGTCAATGTTTAACAATTTTCAT
130 TAACAGTTAATGTTCAACAA-TTTCAT
* *
16732937 ATATGATTATTGAATAACACAGTTATATATGTTATTGTAGTT
1 ATATGATTATTGAATAACACAGTTATATATGTAATTGCAGTT
16732979 GACCTAGTCG
Statistics
Matches: 300, Mismatches: 53, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
156 257 0.86
157 43 0.14
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (155 bp):
ATATGATTATTGAATAACACAGTTATATATGTAATTGCAGTTTGCGGAAGCGACGACAGGTCCTG
AAGCACCGATCGTCCAGCTCCACCGCAGATAGCTAACGAGCCGGCGGTAAGGATATTAAAGTTGT
AACAGTTAATGTTCAACAATTTCAT
Found at i:16733362 original size:31 final size:31
Alignment explanation
Indices: 16733325--16733593 Score: 211
Period size: 31 Copynumber: 8.6 Consensus size: 31
16733315 GTTAGCTTTA
*
16733325 GCGTGTCACAACATTTTACTTGTTATTCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * * * *
16733356 GTGTGTCAGAACGTTTGATTTTGATATGCATG
1 GCGTGTCACAACATTTTA-CTTGTTATGCATG
* * * ** *
16733388 GCATGTCAGAACATTTTGCTTGTTACCCTTG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
16733419 GTGTGTCACCA-AGTTTATCTTGTTATGCATG
1 GCGTGTCACAACATTTTA-CTTGTTATGCATG
* * * *
16733450 GCGTGTCACAACATTTTCCTCGTTATCCTTG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
16733481 GCGTGTCACCA-AGTTTATCTTGTTATGCATG
1 GCGTGTCACAACATTTTA-CTTGTTATGCATG
* * * *
16733512 ACGTGTCACGATATTTTACTTGTTTTGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
16733543 GCGTGTGACAACATTTTACTTGGTATGCACT-
1 GCGTGTCACAACATTTTACTTGTTATGCA-TG
* *
16733574 ACGTGTCATAACATTTTACT
1 GCGTGTCACAACATTTTACT
16733594 ATTTATGGTT
Statistics
Matches: 180, Mismatches: 52, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
30 8 0.04
31 139 0.77
32 33 0.18
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (31 bp):
GCGTGTCACAACATTTTACTTGTTATGCATG
Found at i:16733480 original size:62 final size:62
Alignment explanation
Indices: 16733325--16733535 Score: 262
Period size: 62 Copynumber: 3.4 Consensus size: 62
16733315 GTTAGCTTTA
* * * * *
16733325 GCGTGTCACAACATTTTACTTGTTATTCATGGTGTGTCA-GAACGTTTGATTTTGATATGCATG
1 GCGTGTCACAACATTTTACTTGTTATCCTTGGTGTGTCACCAA-GTTT-ATCTTGTTATGCATG
* * * *
16733388 GCATGTCAGAACATTTTGCTTGTTACCCTTGGTGTGTCACCAAGTTTATCTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATCCTTGGTGTGTCACCAAGTTTATCTTGTTATGCATG
* * *
16733450 GCGTGTCACAACATTTTCCTCGTTATCCTTGGCGTGTCACCAAGTTTATCTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATCCTTGGTGTGTCACCAAGTTTATCTTGTTATGCATG
* * *
16733512 ACGTGTCACGATATTTTACTTGTT
1 GCGTGTCACAACATTTTACTTGTT
16733536 TTGCATGGCG
Statistics
Matches: 127, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
62 88 0.69
63 37 0.29
64 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (62 bp):
GCGTGTCACAACATTTTACTTGTTATCCTTGGTGTGTCACCAAGTTTATCTTGTTATGCATG
Found at i:16733545 original size:62 final size:62
Alignment explanation
Indices: 16733326--16733593 Score: 236
Period size: 62 Copynumber: 4.3 Consensus size: 62
16733316 TTAGCTTTAG
* * * * * * *
16733326 CGTGTCACAACATTTTACTTGTTATTCATGGTGTGTCA-GAACGTTTGATTTTGATATGCATGG
1 CGTGTCACAACATTTTACTCGTTATCCATGGCGTGTCACCAA-GTTT-ATCTTGTTATGCATGA
* * * * * * * *
16733389 CATGTCAGAACATTTTGCTTGTTACCCTTGGTGTGTCACCAAGTTTATCTTGTTATGCATGG
1 CGTGTCACAACATTTTACTCGTTATCCATGGCGTGTCACCAAGTTTATCTTGTTATGCATGA
* *
16733451 CGTGTCACAACATTTTCCTCGTTATCCTTGGCGTGTCACCAAGTTTATCTTGTTATGCATGA
1 CGTGTCACAACATTTTACTCGTTATCCATGGCGTGTCACCAAGTTTATCTTGTTATGCATGA
* * * * * * * * *
16733513 CGTGTCACGATATTTTACTTGTTTTGCATGGCGTGTGACAACATTTTA-CTTGGTATGCACT-A
1 CGTGTCACAACATTTTACTCGTTATCCATGGCGTGTCACCA-AGTTTATCTTGTTATGCA-TGA
*
16733575 CGTGTCATAACATTTTACT
1 CGTGTCACAACATTTTACT
16733594 ATTTATGGTT
Statistics
Matches: 172, Mismatches: 30, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
62 128 0.74
63 42 0.24
64 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (62 bp):
CGTGTCACAACATTTTACTCGTTATCCATGGCGTGTCACCAAGTTTATCTTGTTATGCATGA
Found at i:16735120 original size:16 final size:15
Alignment explanation
Indices: 16735089--16735135 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
16735079 GAATTCATTT
*
16735089 TATACACATTTTTTG
1 TATACACATTTATTG
16735104 TATACACAATTTATTG
1 TATACAC-ATTTATTG
*
16735120 TATACA-ATTCATTG
1 TATACACATTTATTG
16735134 TA
1 TA
16735136 AACAGATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.31
15 7 0.24
16 13 0.45
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (15 bp):
TATACACATTTATTG
Found at i:16735128 original size:14 final size:14
Alignment explanation
Indices: 16735075--16735135 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
16735065 TAAATTTTTT
* *
16735075 TATAGAATTCATTT
1 TATACAATTCATTG
**
16735089 TATACACATTTTTTG
1 TATACA-ATTCATTG
*
16735104 TATACACAATTTATTG
1 TAT--ACAATTCATTG
16735120 TATACAATTCATTG
1 TATACAATTCATTG
16735134 TA
1 TA
16735136 AACAGATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 17 0.45
15 8 0.21
16 10 0.26
17 3 0.08
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (14 bp):
TATACAATTCATTG
Found at i:16735866 original size:31 final size:31
Alignment explanation
Indices: 16735798--16735942 Score: 101
Period size: 31 Copynumber: 4.7 Consensus size: 31
16735788 ACACACCAGA
*
16735798 ACTTGTTATGCATGGCGGGTCAGAACAATTT
1 ACTTGTTATGCATGGCGTGTCAGAACAATTT
* *** *
16735829 AATTGTTATGCATGGCGTGTCATTTCATTTT
1 ACTTGTTATGCATGGCGTGTCAGAACAATTT
* * * * * *
16735860 TCTTGTTATGAATGGCGTGTTACAATATTTT
1 ACTTGTTATGCATGGCGTGTCAGAACAATTT
* ** * ** * *
16735891 ATTTAATAAGCACAGCGTGTCACAACATTTT
1 ACTTGTTATGCATGGCGTGTCAGAACAATTT
*
16735922 ACTTGTTATGTATGGCGTGTC
1 ACTTGTTATGCATGGCGTGTC
16735943 TCACATTTAT
Statistics
Matches: 83, Mismatches: 31, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
31 83 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (31 bp):
ACTTGTTATGCATGGCGTGTCAGAACAATTT
Found at i:16739635 original size:55 final size:55
Alignment explanation
Indices: 16739506--16739686 Score: 175
Period size: 55 Copynumber: 3.3 Consensus size: 55
16739496 ACACCAACCT
* * *
16739506 CCGTGACACGCTAAGAACCCAAAAAGTCAGTTAACCCACGACACGCCAGGAACAA
1 CCGTGACACGCTAAAAACCCAAAAAGTCAGTTAACCCACCACACCCCAGGAACAA
* * * * * *
16739561 CCATGACACACTAAAAACCCATAAATTCAGTTAACCCACCACACCCCAGGAATAG
1 CCGTGACACGCTAAAAACCCAAAAAGTCAGTTAACCCACCACACCCCAGGAACAA
* * * * * * ** *
16739616 CCGTGAAACGCTAACAACCCAAATAACT-AGTTAGCCCACAACACACCAATAACAG
1 CCGTGACACGCTAAAAACCCAAA-AAGTCAGTTAACCCACCACACCCCAGGAACAA
*
16739671 TCGTGACACGCTAAAA
1 CCGTGACACGCTAAAA
16739687 TAACTCTTCA
Statistics
Matches: 101, Mismatches: 24, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
55 98 0.97
56 3 0.03
ACGTcount: A:0.41, C:0.33, G:0.13, T:0.13
Consensus pattern (55 bp):
CCGTGACACGCTAAAAACCCAAAAAGTCAGTTAACCCACCACACCCCAGGAACAA
Found at i:16741013 original size:41 final size:39
Alignment explanation
Indices: 16740951--16741053 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 39
16740941 AGAGAGAAAA
*
16740951 AGAGAGAGAGAGGGCTTTTGGGTTACCGTCGACCGATCTAG
1 AGAGAGAAAGAGGGCTTTTGGGTT--CGTCGACCGATCTAG
*
16740992 AGAGAGAAAGAGGG-TTCTTGGGTTGGTCGACCGATCTAG
1 AGAGAGAAAGAGGGCTT-TTGGGTTCGTCGACCGATCTAG
* *
16741031 GGAGCGAAA-A-GGC-TTTGGGTTCG
1 AGAGAGAAAGAGGGCTTTTGGGTTCG
16741054 ACATCGATCG
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
36 8 0.15
37 3 0.05
38 1 0.02
39 21 0.38
40 2 0.04
41 20 0.36
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.22
Consensus pattern (39 bp):
AGAGAGAAAGAGGGCTTTTGGGTTCGTCGACCGATCTAG
Found at i:16741304 original size:71 final size:70
Alignment explanation
Indices: 16741211--16741353 Score: 171
Period size: 71 Copynumber: 2.0 Consensus size: 70
16741201 GTGAAGGAAG
* * * *
16741211 GAAACCCGATTGGCTGGCACAAAGGAAGAAAGAGAGAAAAACTCGATATGCTGGCAC-AAAGGAT
1 GAAACCCGATCGGCGGGCACAAAGGAAGAAAGAGAGAAAAACCCGATAGGCTGGCACAAAAGG--
16741275 AGAAAGA
64 AGAAAGA
* * * * * *
16741282 GAAACTCGATCGGCGGGCACAAAGGGAGAGAGAGAGAGAAACCCGATCGGTTGGCACAAAAGGAG
1 GAAACCCGATCGGCGGGCACAAAGGAAGAAAGAGAGAAAAACCCGATAGGCTGGCACAAAAGGAG
16741347 AAAGA
66 AAAGA
16741352 GA
1 GA
16741354 GAGGGCCGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
70 9 0.15
71 47 0.77
72 5 0.08
ACGTcount: A:0.43, C:0.16, G:0.32, T:0.09
Consensus pattern (70 bp):
GAAACCCGATCGGCGGGCACAAAGGAAGAAAGAGAGAAAAACCCGATAGGCTGGCACAAAAGGAG
AAAGA
Found at i:16741356 original size:37 final size:36
Alignment explanation
Indices: 16741211--16741356 Score: 152
Period size: 37 Copynumber: 4.0 Consensus size: 36
16741201 GTGAAGGAAG
*
16741211 GAAACCCGATTGGCTGGCACAAAGGAAGAAAGAGAGA
1 GAAACCCGATCGGCTGGCACAAAGG-AGAAAGAGAGA
* * ** * *
16741248 AAAACTCGATATGCTGGCACAAA-G-GATAGAAAGA
1 GAAACCCGATCGGCTGGCACAAAGGAGAAAGAGAGA
* * *
16741282 GAAACTCGATCGGCGGGCACAAAGGGAGAGAGAGAGA
1 GAAACCCGATCGGCTGGCACAAA-GGAGAAAGAGAGA
*
16741319 GAAACCCGATCGGTTGGCACAAAAGGAGAAAGAGAGA
1 GAAACCCGATCGGCTGGCAC-AAAGGAGAAAGAGAGA
16741356 G
1 G
16741357 GGCCGGTCAT
Statistics
Matches: 89, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
34 27 0.30
36 2 0.02
37 57 0.64
38 3 0.03
ACGTcount: A:0.42, C:0.16, G:0.33, T:0.09
Consensus pattern (36 bp):
GAAACCCGATCGGCTGGCACAAAGGAGAAAGAGAGA
Found at i:16744445 original size:17 final size:17
Alignment explanation
Indices: 16744425--16744471 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
16744415 AAGAAATTTA
16744425 ATTTATTTTATAATTCC
1 ATTTATTTTATAATTCC
16744442 ATTTATTTTATAATTCC
1 ATTTATTTTATAATTCC
16744459 ATTTATTTTATAA
1 ATTTATTTTATAA
16744472 ATTCATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTATTTTATAATTCC
Found at i:16745723 original size:19 final size:19
Alignment explanation
Indices: 16745699--16745736 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16745689 ACTTCTAAAC
16745699 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
16745718 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
16745737 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:16749897 original size:2 final size:2
Alignment explanation
Indices: 16749890--16749927 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
16749880 CACTCACCAT
16749890 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
16749928 CAAGGATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:16750727 original size:37 final size:37
Alignment explanation
Indices: 16750683--16750758 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
16750673 AATTTTATAA
*
16750683 AAACATGAGGGCCTTGATGTGAGGC-TCTGTACCACAC
1 AAACATGAAGGCCTTGATGTGAGGCGT-TGTACCACAC
*
16750720 AAACATGAAGGTCTTGATGTGAGGCGTTGTACCACAC
1 AAACATGAAGGCCTTGATGTGAGGCGTTGTACCACAC
16750757 AA
1 AA
16750759 CTATGTAGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 35 0.97
38 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.22
Consensus pattern (37 bp):
AAACATGAAGGCCTTGATGTGAGGCGTTGTACCACAC
Found at i:16751129 original size:21 final size:21
Alignment explanation
Indices: 16751101--16751151 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
16751091 ATTCTCAATG
16751101 AAAA-GTATCAATACCTCTCC
1 AAAAGGTATCAATACCTCTCC
* * *
16751121 AGAAGGTATCAATGCCTCTTC
1 AAAAGGTATCAATACCTCTCC
16751142 AAAAGGTATC
1 AAAAGGTATC
16751152 GATATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (21 bp):
AAAAGGTATCAATACCTCTCC
Found at i:16763325 original size:25 final size:25
Alignment explanation
Indices: 16763291--16763340 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
16763281 CTTACAATTT
16763291 GGAATATTCAAATTTTATGAAAATA
1 GGAATATTCAAATTTTATGAAAATA
*
16763316 GGAATATTCAAATTTTATGGAAATA
1 GGAATATTCAAATTTTATGAAAATA
16763341 ATCAAACTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (25 bp):
GGAATATTCAAATTTTATGAAAATA
Found at i:16765541 original size:2 final size:2
Alignment explanation
Indices: 16765534--16765569 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
16765524 TGTAGGTTTA
16765534 TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16765570 AATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:16765559 original size:17 final size:17
Alignment explanation
Indices: 16765537--16765569 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
16765527 AGGTTTATCT
16765537 CTCTCTCTCTCTCTCTC
1 CTCTCTCTCTCTCTCTC
16765554 CTCTCTCTCTCTCTCT
1 CTCTCTCTCTCTCTCT
16765570 AATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (17 bp):
CTCTCTCTCTCTCTCTC
Found at i:16765576 original size:2 final size:2
Alignment explanation
Indices: 16765571--16765612 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
16765561 TCTCTCTCTA
16765571 AT AT AT AT AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
16765613 CTTCCTTAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16766026 original size:9 final size:9
Alignment explanation
Indices: 16766012--16766050 Score: 78
Period size: 9 Copynumber: 4.3 Consensus size: 9
16766002 TTTATAAAAG
16766012 ATTAATAAA
1 ATTAATAAA
16766021 ATTAATAAA
1 ATTAATAAA
16766030 ATTAATAAA
1 ATTAATAAA
16766039 ATTAATAAA
1 ATTAATAAA
16766048 ATT
1 ATT
16766051 TTAAGGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATTAATAAA
Found at i:16769474 original size:8 final size:8
Alignment explanation
Indices: 16769461--16769507 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
16769451 GTACAAAAGC
16769461 TTATTATT
1 TTATTATT
16769469 TTATTATT
1 TTATTATT
16769477 TTATTATT
1 TTATTATT
16769485 TT-TTATT
1 TTATTATT
*
16769492 TAATATAATT
1 T--TATTATT
16769502 TTATTA
1 TTATTA
16769508 CCTTACATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 6 0.18
8 22 0.65
9 1 0.03
10 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTATTATT
Found at i:16784379 original size:42 final size:42
Alignment explanation
Indices: 16784291--16784379 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
16784281 GGACTCGACT
* * ** *
16784291 ATGTGCGAGTAGAAGTGTGCATACGCCAATGATGACCCGGCT
1 ATGTGCGAGTAGAAGTGCGCATAAGCCAATGATGACCCAACC
* * * *
16784333 ATGTGCGAGTAGGAGTGCGCATAAGTCGATGCTGACCCAACC
1 ATGTGCGAGTAGAAGTGCGCATAAGCCAATGATGACCCAACC
16784375 ATGTG
1 ATGTG
16784380 TTAGTGGTGA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.21
Consensus pattern (42 bp):
ATGTGCGAGTAGAAGTGCGCATAAGCCAATGATGACCCAACC
Found at i:16784441 original size:2 final size:2
Alignment explanation
Indices: 16784434--16784477 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
16784424 ATGATGATGG
* *
16784434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16784476 AT
1 AT
16784478 GTGTGTCATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16791171 original size:19 final size:19
Alignment explanation
Indices: 16791147--16791184 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16791137 ACTTCTAAAC
16791147 CTCAAATCATACTCAAATA
1 CTCAAATCATACTCAAATA
*
16791166 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCAAATA
16791185 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCAAATA
Found at i:16794648 original size:19 final size:20
Alignment explanation
Indices: 16794613--16794653 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
16794603 TTTTTGTTTG
*
16794613 AAGAATGAGAGTTAAAATAT
1 AAGAATGAGAGTTAAAAAAT
*
16794633 AAGAATGTGA-TTAAAAAAT
1 AAGAATGAGAGTTAAAAAAT
16794652 AA
1 AA
16794654 ACGTTAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (20 bp):
AAGAATGAGAGTTAAAAAAT
Found at i:16796955 original size:20 final size:20
Alignment explanation
Indices: 16796915--16796955 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16796905 ATATATGCAC
*
16796915 TATATAATAATATATTATTA
1 TATATAATAATAAATTATTA
*
16796935 TATATAATAATAAATTGTTA
1 TATATAATAATAAATTATTA
16796955 T
1 T
16796956 TGACTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TATATAATAATAAATTATTA
Found at i:16800828 original size:29 final size:29
Alignment explanation
Indices: 16800796--16800863 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
16800786 ATATATCTTT
* *
16800796 TTCTCTTGTACCTATTCATGTACAA-CTTC
1 TTCTCTTGTAACTATTCACGTA-AAGCTTC
*
16800825 TTCTCTTGTAACTGTTCACGTAAAGCTTC
1 TTCTCTTGTAACTATTCACGTAAAGCTTC
16800854 TTCTCTTGTA
1 TTCTCTTGTA
16800864 TCTTCTCATG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 2 0.06
29 33 0.94
ACGTcount: A:0.19, C:0.25, G:0.10, T:0.46
Consensus pattern (29 bp):
TTCTCTTGTAACTATTCACGTAAAGCTTC
Found at i:16818726 original size:21 final size:19
Alignment explanation
Indices: 16818700--16818741 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
16818690 CACCCAAAAA
16818700 AAAAAAAGAAAGACATATA-
1 AAAAAAAGAAAGACA-ATAG
*
16818719 AGAAAAAAGGAAGACAATAG
1 A-AAAAAAGAAAGACAATAG
16818739 AAA
1 AAA
16818742 CACCTTCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (19 bp):
AAAAAAAGAAAGACAATAG
Found at i:16830092 original size:39 final size:36
Alignment explanation
Indices: 16830003--16830137 Score: 121
Period size: 36 Copynumber: 3.7 Consensus size: 36
16829993 TCAACTCAGC
*
16830003 TCATGTGCACTCCCACACCACACATAGCTAATATCC
1 TCATGTGCACTCCCACACCACACATAGCTAATATCA
** *
16830039 TCATGTGCACTCCCACACTGCACATGGCATATATCATCA
1 TCATGTGCACTCCCACACCACACATAGC-TA-AT-ATCA
* * * * *
16830078 TCATGTGCTCTCCCACAACGCACAC-TA-TTGACACCA
1 TCATGTGCACTCCCAC-AC-CACACATAGCTAATATCA
*
16830114 TTATGTGCACTCCCACACCACACA
1 TCATGTGCACTCCCACACCACACA
16830138 CGCACAGTTA
Statistics
Matches: 79, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
34 5 0.06
35 2 0.03
36 42 0.53
37 3 0.04
38 3 0.04
39 18 0.23
40 3 0.04
41 3 0.04
ACGTcount: A:0.29, C:0.38, G:0.10, T:0.23
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCACACATAGCTAATATCA
Found at i:16831663 original size:12 final size:12
Alignment explanation
Indices: 16831637--16831674 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
16831627 TCTCATCCTT
16831637 TTTCCTTTCTTTC
1 TTTCCTTT-TTTC
16831650 TTTCCTTTTTTC
1 TTTCCTTTTTTC
16831662 TTT-CTTCTTTTC
1 TTTCCTT-TTTTC
16831674 T
1 T
16831675 CTCTCCTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 3 0.12
12 13 0.54
13 8 0.33
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTCCTTTTTTC
Found at i:16831673 original size:20 final size:20
Alignment explanation
Indices: 16831632--16831671 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16831622 GCTTTTCTCA
16831632 TCCTTTTTCCTTTCTTTCTT
1 TCCTTTTTCCTTTCTTTCTT
*
16831652 TCCTTTTTTCTTTC-TTCTT
1 TCCTTTTTCCTTTCTTTCTT
16831671 T
1 T
16831672 TCTCTCTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TCCTTTTTCCTTTCTTTCTT
Found at i:16834035 original size:3 final size:3
Alignment explanation
Indices: 16834020--16834090 Score: 103
Period size: 3 Copynumber: 24.3 Consensus size: 3
16834010 GAGGAAAAAG
16834020 ATA ATA ATGA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
16834065 ATA AAA AT- ATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16834091 AAGGATCTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 6 0.10
3 53 0.85
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16835682 original size:2 final size:2
Alignment explanation
Indices: 16835675--16835706 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16835665 TTAGACAAAT
16835675 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
16835707 CGTTCTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16841862 original size:173 final size:167
Alignment explanation
Indices: 16841471--16841975 Score: 581
Period size: 173 Copynumber: 2.9 Consensus size: 167
16841461 ACTCATTGTC
*
16841471 ACAATTTAAATC-TTAATTTCTTTTACATGTGAGTAATGAAGATAGCATTATGTTACAATCATTT
1 ACAAATTAAATCTTTAATTTCTTTTACATGTGAGTAATGAAGATAGCATTATGTTACAATCATTT
* * * * * *
16841535 GCCAAATCATAAAGAATGACATATTCAAGATTAGATGATAAGCATCTTCCTTTTTGGGATGAGGA
66 G-----TC--AAAGGATGA-A-A-TCAAAACTAGATAATAAGCATCTTCCTTTTTTGGATGAAGA
*
16841600 TAGCATGTGAGTAAACAATGCACTCATTATCAC-A-ATTTATTCTAAT
121 TAGCATGTGAGT-AACAATGCACTCATTGTCACAATATTTATTCTAAT
* *
16841646 ACAAATTAAATCTTTAATTTCTTTTACATTTGAGTAATGAAGATAGCATTATGTTACAATTATTT
1 ACAAATTAAATCTTTAATTTCTTTTACATGTGAGTAATGAAGATAGCATTATGTTACAATCATTT
16841711 GTCAAAGGATGAAAAACTCAAAACTAGATAATAAGCATCTTCCTTTTTTGGATGAAGATAGCATG
66 GTCAAAGGATG--AAA-TCAAAACTAGATAATAAGCATCTTCCTTTTTTGGATGAAGATAGCATG
* * *
16841776 TGACTAACTAATACACTCATTGTTACAATTTATTTATTCTAAT
128 TGAGTAAC-AATGCACTCATTGTCACAA--TATTTATTCTAAT
* * * * * *
16841819 ACAACTTAAATCTTTAATTTCTTTCACATGCGAGTAATGAAGATAGAATTATTTTAGAATCATTT
1 ACAAATTAAATCTTTAATTTCTTTTACATGTGAGTAATGAAGATAGCATTATGTTACAATCATTT
* *
16841884 GTCAAAGGATG--A-CAAAACTAGATAATAAGCATGCATATTCCTTCTTTGGATGAAGATGGCAT
66 GTCAAAGGATGAAATCAAAACTAGATAATAAGCAT-C---TTCCTTTTTTGGATGAAGATAGCAT
16841946 GTGAGTAACCAATGCACTCATTGTCACAAT
127 GTGAGTAA-CAATGCACTCATTGTCACAAT
16841976 GCAATTGAAT
Statistics
Matches: 290, Mismatches: 27, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
167 20 0.07
168 4 0.01
169 71 0.24
170 2 0.01
171 50 0.17
172 1 0.00
173 80 0.28
175 11 0.04
176 51 0.18
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (167 bp):
ACAAATTAAATCTTTAATTTCTTTTACATGTGAGTAATGAAGATAGCATTATGTTACAATCATTT
GTCAAAGGATGAAATCAAAACTAGATAATAAGCATCTTCCTTTTTTGGATGAAGATAGCATGTGA
GTAACAATGCACTCATTGTCACAATATTTATTCTAAT
Found at i:16849195 original size:3 final size:3
Alignment explanation
Indices: 16849187--16849212 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16849177 AAGTAAGAGA
16849187 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
16849213 AATAAGGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16856704 original size:57 final size:57
Alignment explanation
Indices: 16856641--16856755 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
16856631 ATTTAGTGAA
* * * *
16856641 AATGTCACCTAGTTAGTTTTTTATACCTTCATATTCAAGAACAATGTCCTCTTTTTG
1 AATGTCACCTAGTTAGTCTTTAATACATACATATTCAAGAACAATGTCCTCTTTTTG
*
16856698 AATGTCACCTAGTTAGTCTTTAATACATACATATTCGAGAACAATGTCCTCTTTTTG
1 AATGTCACCTAGTTAGTCTTTAATACATACATATTCAAGAACAATGTCCTCTTTTTG
16856755 A
1 A
16856756 GCATTGTTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (57 bp):
AATGTCACCTAGTTAGTCTTTAATACATACATATTCAAGAACAATGTCCTCTTTTTG
Found at i:16873085 original size:26 final size:26
Alignment explanation
Indices: 16873054--16873106 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
16873044 CTTACAAGTA
16873054 CAAAAGACTCAATCTTTTAGATAACT
1 CAAAAGACTCAATCTTTTAGATAACT
16873080 CAAAAGACTCAATCTTTTAGATAACT
1 CAAAAGACTCAATCTTTTAGATAACT
16873106 C
1 C
16873107 TATCCTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (26 bp):
CAAAAGACTCAATCTTTTAGATAACT
Found at i:16874616 original size:27 final size:27
Alignment explanation
Indices: 16874561--16874790 Score: 219
Period size: 27 Copynumber: 8.4 Consensus size: 27
16874551 GGCGTATAAT
* * *
16874561 AACTAAATTTTTCAACATGACGTGCAAC
1 AACTAAA-TTTTCAACATAATGTGTAAC
*
16874589 AACTAAATCTTCAACATAACT-TGTAAC
1 AACTAAATTTTCAACATAA-TGTGTAAC
* *
16874616 AACTATATTTTTCAACATAATGCGTAAC
1 AACTA-AATTTTCAACATAATGTGTAAC
* *
16874644 AATTAAATTTTCAACATGATGTGTAAC
1 AACTAAATTTTCAACATAATGTGTAAC
* * *
16874671 AACTAAATTTTCAATATGATGTGTAAT
1 AACTAAATTTTCAACATAATGTGTAAC
* * *
16874698 AACTAAATCTTCAACATGATATGTAAC
1 AACTAAATTTTCAACATAATGTGTAAC
* * **
16874725 AATTATATTTTTCAACATAACATGTAAC
1 AACTA-AATTTTCAACATAATGTGTAAC
* * *
16874753 AACTACATTTTCAATATAACGTGTAAC
1 AACTAAATTTTCAACATAATGTGTAAC
*
16874780 AATTAAATTTT
1 AACTAAATTTT
16874791 AAAACATGAC
Statistics
Matches: 168, Mismatches: 30, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
27 118 0.70
28 50 0.30
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (27 bp):
AACTAAATTTTCAACATAATGTGTAAC
Found at i:16874626 original size:55 final size:55
Alignment explanation
Indices: 16874561--16874805 Score: 242
Period size: 55 Copynumber: 4.5 Consensus size: 55
16874551 GGCGTATAAT
*
16874561 AACTAAATTTTTCAACATGACGTGCAACAACTAAATCTTCAACATAACT-TGTAAC
1 AACTAAATTTTTCAACATGACGTGTAACAACTAAATCTTCAACATAA-TATGTAAC
* * * * * * * *
16874616 AACTATATTTTTCAACATAATGCGTAACAATTAAATTTTCAACATGATGTGTAAC
1 AACTAAATTTTTCAACATGACGTGTAACAACTAAATCTTCAACATAATATGTAAC
* * * *
16874671 AACTAAA-TTTTCAATATGATGTGTAATAACTAAATCTTCAACATGATATGTAAC
1 AACTAAATTTTTCAACATGACGTGTAACAACTAAATCTTCAACATAATATGTAAC
* * * * * * * **
16874725 AATTATATTTTTCAACATAACATGTAACAACTACATTTTCAATATAACGTGTAAC
1 AACTAAATTTTTCAACATGACGTGTAACAACTAAATCTTCAACATAATATGTAAC
* **
16874780 AATTAAATTTTAAAACATGACGTGTA
1 AACTAAATTTTTCAACATGACGTGTA
16874806 GTATTATATT
Statistics
Matches: 154, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
54 46 0.30
55 108 0.70
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (55 bp):
AACTAAATTTTTCAACATGACGTGTAACAACTAAATCTTCAACATAATATGTAAC
Found at i:16874658 original size:82 final size:81
Alignment explanation
Indices: 16874564--16874790 Score: 249
Period size: 82 Copynumber: 2.8 Consensus size: 81
16874554 GTATAATAAC
* * *
16874564 TAAATTTTTCAACATGACGTGCAACAACTAAATCTTCAACATAACTTGTAACAACTATATTTTTC
1 TAAA-TTTTCAACATGACGTGTAACAACTAAATTTTCAATATAACTTGTAACAACTA-ATTTTTC
*
16874629 AACATAATGCGTAACAAT
64 AACATAATACGTAACAAT
* * * * *
16874647 TAAATTTTCAACATGATGTGTAACAACTAAATTTTCAATATGA-TGTGTAATAACTAAATCTTCA
1 TAAATTTTCAACATGACGTGTAACAACTAAATTTTCAATATAACT-TGTAACAACTAATTTTTCA
* *
16874711 ACATGATATGTAACAAT
65 ACATAATACGTAACAAT
* * * * * * *
16874728 TATATTTTTCAACATAACATGTAACAACTACATTTTCAATATAACGTGTAACAATTAAATTTT
1 TA-AATTTTCAACATGACGTGTAACAACTAAATTTTCAATATAACTTGTAACAACTAATTTTT
16874791 AAAACATGAC
Statistics
Matches: 120, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.19
82 93 0.77
83 4 0.03
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.36
Consensus pattern (81 bp):
TAAATTTTCAACATGACGTGTAACAACTAAATTTTCAATATAACTTGTAACAACTAATTTTTCAA
CATAATACGTAACAAT
Found at i:16874711 original size:109 final size:109
Alignment explanation
Indices: 16874561--16874803 Score: 308
Period size: 109 Copynumber: 2.2 Consensus size: 109
16874551 GGCGTATAAT
16874561 AACTAAATTTTTCAACATGACGTGCAACAACTAAATCTTCAACATAACT-TGTAACAACTATATT
1 AACTAAA-TTTTCAACATGACGTGCAACAACTAAATCTTCAACATAA-TATGTAACAACTATATT
** * * *
16874625 TTTCAACATAATGCGTAACAATTAAATTTTCAACATGATGTGTAAC
64 TTTCAACATAACACGTAACAACTAAATTTTCAACATAACGTGTAAC
* * * * * *
16874671 AACTAAATTTTCAATATGATGTGTAATAACTAAATCTTCAACATGATATGTAACAATTATATTTT
1 AACTAAATTTTCAACATGACGTGCAACAACTAAATCTTCAACATAATATGTAACAACTATATTTT
* * *
16874736 TCAACATAACATGTAACAACTACATTTTCAATATAACGTGTAAC
66 TCAACATAACACGTAACAACTAAATTTTCAACATAACGTGTAAC
* *
16874780 AATTAAATTTTAAAACATGACGTG
1 AACTAAATTTT-CAACATGACGTG
16874804 TAGTATTATA
Statistics
Matches: 113, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
108 1 0.01
109 96 0.85
110 16 0.14
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (109 bp):
AACTAAATTTTCAACATGACGTGCAACAACTAAATCTTCAACATAATATGTAACAACTATATTTT
TCAACATAACACGTAACAACTAAATTTTCAACATAACGTGTAAC
Found at i:16874812 original size:82 final size:82
Alignment explanation
Indices: 16874567--16874820 Score: 228
Period size: 82 Copynumber: 3.1 Consensus size: 82
16874557 TAATAACTAA
* * * * * * * * *
16874567 ATTTTTCAACATGACGTGCAACAACTAAATCTTCAACATAACTTGTAACAACTATATTTTTCAAC
1 ATTTTTCAACATAACATGTAACAACTAAATTTTCAATATAACGTGTAACAACTA-AATCTTAAAC
16874632 AT-A-ATGCGTAACAATTA-
65 ATGACAT--GTAACAATTAT
* * ** * * * *
16874649 AATTTTCAACATGATGTGTAACAACTAAATTTTCAATATGATGTGTAATAACTAAATCTTCAACA
1 ATTTTTCAACATAACATGTAACAACTAAATTTTCAATATAACGTGTAACAACTAAATCTTAAACA
*
16874714 TGATATGTAACAATTAT
66 TGACATGTAACAATTAT
* * *
16874731 ATTTTTCAACATAACATGTAACAACTACATTTTCAATATAACGTGTAACAATTAAATTTTAAAAC
1 ATTTTTCAACATAACATGTAACAACTAAATTTTCAATATAACGTGTAACAACTAAATCTT-AAAC
* **
16874796 ATGACGTGT-AGTATTAT
65 ATGACATGTAACAATTAT
16874813 ATTTTTCA
1 ATTTTTCA
16874821 TCATGACGCT
Statistics
Matches: 142, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
81 20 0.14
82 110 0.77
83 12 0.08
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (82 bp):
ATTTTTCAACATAACATGTAACAACTAAATTTTCAATATAACGTGTAACAACTAAATCTTAAACA
TGACATGTAACAATTAT
Found at i:16879676 original size:58 final size:58
Alignment explanation
Indices: 16879586--16879699 Score: 228
Period size: 58 Copynumber: 2.0 Consensus size: 58
16879576 CACTCTGGCT
16879586 CATCGCATGAGACATCTGAACAACCTAAGTAATGGTAAAAAGTTTTGAGAATAAAAAA
1 CATCGCATGAGACATCTGAACAACCTAAGTAATGGTAAAAAGTTTTGAGAATAAAAAA
16879644 CATCGCATGAGACATCTGAACAACCTAAGTAATGGTAAAAAGTTTTGAGAATAAAA
1 CATCGCATGAGACATCTGAACAACCTAAGTAATGGTAAAAAGTTTTGAGAATAAAA
16879700 GAATTTATGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.23
Consensus pattern (58 bp):
CATCGCATGAGACATCTGAACAACCTAAGTAATGGTAAAAAGTTTTGAGAATAAAAAA
Found at i:16883050 original size:2 final size:2
Alignment explanation
Indices: 16883043--16883081 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16883033 GTATGCATTA
16883043 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
16883082 GAAAGTCNTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16887529 original size:46 final size:46
Alignment explanation
Indices: 16887462--16887553 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
16887452 ATAAGATTAA
16887462 GGTTTATCACAACGCTTCGGTGAAAACTCTAATCGAATTCTGTACC
1 GGTTTATCACAACGCTTCGGTGAAAACTCTAATCGAATTCTGTACC
16887508 GGTTTATCACAACGCTTCGGTGAAAACTCTAATCGAATTCTGTACC
1 GGTTTATCACAACGCTTCGGTGAAAACTCTAATCGAATTCTGTACC
16887554 AAGAAAAGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (46 bp):
GGTTTATCACAACGCTTCGGTGAAAACTCTAATCGAATTCTGTACC
Found at i:16887811 original size:25 final size:21
Alignment explanation
Indices: 16887752--16887806 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
16887742 TTTCTTTTCT
16887752 TTTTATGTATA-TATACTTATA
1 TTTTATGTA-ACTATACTTATA
16887773 TTTTATGTAACTATACTTATA
1 TTTTATGTAACTATACTTATA
16887794 TTTTATGTAACTA
1 TTTTATGTAACTA
16887807 ACTATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTATGTAACTATACTTATA
Found at i:16891053 original size:24 final size:26
Alignment explanation
Indices: 16891026--16891082 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
16891016 ACATGCCATG
*
16891026 TTGAAA-T-AATTATTACATATCATA
1 TTGAAATTAAATTATTACACATCATA
* *
16891050 TTGAAAATTAAATTGTTATACATCATA
1 TTG-AAATTAAATTATTACACATCATA
16891077 TTGAAA
1 TTGAAA
16891083 ATTTACCGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 3 0.11
25 3 0.11
26 4 0.15
27 17 0.63
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (26 bp):
TTGAAATTAAATTATTACACATCATA
Found at i:16891202 original size:29 final size:31
Alignment explanation
Indices: 16891137--16891207 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 31
16891127 TCTCACCTTA
**
16891137 ATCCTTAATTGTATGGAATCGAAAGTGTTTG
1 ATCCTTAATTGTATACAATCGAAAGTGTTTG
* *
16891168 GTCCTTAATTGT-TACAATTGAAA-TGTTTG
1 ATCCTTAATTGTATACAATCGAAAGTGTTTG
16891197 ATCCTTAATTG
1 ATCCTTAATTG
16891208 ACAAAGTACC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 16 0.46
30 8 0.23
31 11 0.31
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (31 bp):
ATCCTTAATTGTATACAATCGAAAGTGTTTG
Found at i:16904025 original size:22 final size:21
Alignment explanation
Indices: 16903997--16904045 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
16903987 TATTTTTTTT
* *
16903997 ATTTTTAAAAATATAATATTA
1 ATTTTTTAAAATATAATAATA
16904018 ATTTTTT-AAATATAATAATA
1 ATTTTTTAAAATATAATAATA
16904038 ATTTTTTA
1 ATTTTTTA
16904046 TTTTTAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTTTAAAATATAATAATA
Found at i:16911152 original size:24 final size:24
Alignment explanation
Indices: 16911125--16911173 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
16911115 GGAATGCCAT
* *
16911125 CTCCAAGAACCTTCCAGCCTCCAC
1 CTCCAAAAACCATCCAGCCTCCAC
* *
16911149 CTCCAAAAACCATGCTGCCTCCAC
1 CTCCAAAAACCATCCAGCCTCCAC
16911173 C
1 C
16911174 ACCTCCACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.49, G:0.08, T:0.16
Consensus pattern (24 bp):
CTCCAAAAACCATCCAGCCTCCAC
Found at i:16924649 original size:3 final size:3
Alignment explanation
Indices: 16924634--16924672 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
16924624 TGGCCTCAAT
*
16924634 GAA GAA GAG GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
16924673 ATAAGTAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:16924716 original size:2 final size:2
Alignment explanation
Indices: 16924709--16924776 Score: 66
Period size: 2 Copynumber: 33.0 Consensus size: 2
16924699 CTCCTACTGT
* * *
16924709 TG TG TG TG TG TG TG TG TG TG TG CG TG TG ATG -G GG AAG TG NTG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG -TG TG TG -TG TG -TG
*
16924751 TG TG TG TG TG TG TG TG TG TG CG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
16924777 ATGGGAAGTG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
1 1 0.02
2 50 0.89
3 5 0.09
ACGTcount: A:0.04, C:0.03, G:0.50, T:0.41
Consensus pattern (2 bp):
TG
Found at i:16924764 original size:40 final size:38
Alignment explanation
Indices: 16924709--16924788 Score: 142
Period size: 40 Copynumber: 2.1 Consensus size: 38
16924699 CTCCTACTGT
16924709 TGTGTGTGTGTGTGTGTGTGTGCGTGTGATGGGGAAGTG
1 TGTGTGTGTGTGTGTGTGTGTGCGTGTGAT-GGGAAGTG
16924748 NTGTGTGTGTGTGTGTGTGTGTGCGTGTGATGGGAAGTG
1 -TGTGTGTGTGTGTGTGTGTGTGCGTGTGATGGGAAGTG
16924787 TG
1 TG
16924789 GACTGTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 2 0.05
39 8 0.20
40 30 0.75
ACGTcount: A:0.07, C:0.03, G:0.50, T:0.39
Consensus pattern (38 bp):
TGTGTGTGTGTGTGTGTGTGTGCGTGTGATGGGAAGTG
Found at i:16924826 original size:2 final size:2
Alignment explanation
Indices: 16924819--16924850 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
16924809 GATTAAATAG
*
16924819 GA GA GA GA GA GA GA GA GA GA GA GA GC GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
16924851 TTATGATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16934358 original size:18 final size:18
Alignment explanation
Indices: 16934320--16934359 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16934310 ATTAATCATG
*
16934320 TTAATCGTGCTATCGTGT
1 TTAATCGTGCTATCGTAT
* *
16934338 TTAATCGTGTTATCTTAT
1 TTAATCGTGCTATCGTAT
16934356 TTAA
1 TTAA
16934360 ACATGTATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (18 bp):
TTAATCGTGCTATCGTAT
Found at i:16955537 original size:13 final size:13
Alignment explanation
Indices: 16955506--16955543 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
16955496 AAGAGAGAAA
16955506 ATAAA-AAAAATC
1 ATAAACAAAAATC
*
16955518 ATAAAACAAAACTC
1 AT-AAACAAAAATC
16955532 ATAAACAAAAAT
1 ATAAACAAAAAT
16955544 GAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 12 0.55
14 8 0.36
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (13 bp):
ATAAACAAAAATC
Found at i:16955844 original size:24 final size:24
Alignment explanation
Indices: 16955812--16955862 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
16955802 ATCCACGATC
*
16955812 AAACTAAAAAAAAATCAAA-AAGAA
1 AAACCAAAAAAAAA-CAAAGAAGAA
*
16955836 AAACCAAAAATAAACAAAGAAGAA
1 AAACCAAAAAAAAACAAAGAAGAA
16955860 AAA
1 AAA
16955863 AAAAAGAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.78, C:0.10, G:0.06, T:0.06
Consensus pattern (24 bp):
AAACCAAAAAAAAACAAAGAAGAA
Found at i:16957032 original size:19 final size:19
Alignment explanation
Indices: 16956992--16957037 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
16956982 ATTTTATTAT
*
16956992 ATAAAAAAATTAATCAAGA
1 ATAAAAAAATTAATAAAGA
*
16957011 ATAAAAAAA-TATATAAATA
1 ATAAAAAAATTA-ATAAAGA
16957030 ATAAAAAA
1 ATAAAAAA
16957038 TAAAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAAAATTAATAAAGA
Found at i:16957048 original size:17 final size:18
Alignment explanation
Indices: 16957014--16957048 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
16957004 ATCAAGAATA
*
16957014 AAAAAATATATAAATAAT
1 AAAAAATATAAAAATAAT
16957032 AAAAAATA-AAAAATAAT
1 AAAAAATATAAAAATAAT
16957049 TAATTTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAATATAAAAATAAT
Found at i:16958621 original size:18 final size:19
Alignment explanation
Indices: 16958598--16958635 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
16958588 TTTTTCTTGT
16958598 AAAAAT-AAAAAAAAGGAA
1 AAAAATAAAAAAAAAGGAA
16958616 AAAAATAAAAAAAAAGGAA
1 AAAAATAAAAAAAAAGGAA
16958635 A
1 A
16958636 GACAAAGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (19 bp):
AAAAATAAAAAAAAAGGAA
Found at i:16963549 original size:19 final size:20
Alignment explanation
Indices: 16963527--16963581 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 20
16963517 ATCCATCAAC
16963527 ATGAAGATTGAAAAAATG-A
1 ATGAAGATTGAAAAAATGAA
*
16963546 ATGAAGA-AGAAAAAATGAAA
1 ATGAAGATTGAAAAAATG-AA
*
16963566 ATGAAAATTGAAAAAA
1 ATGAAGATTGAAAAAA
16963582 AAGAAAGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 9 0.30
19 7 0.23
20 7 0.23
21 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.16
Consensus pattern (20 bp):
ATGAAGATTGAAAAAATGAA
Found at i:16965516 original size:142 final size:142
Alignment explanation
Indices: 16965260--16965545 Score: 457
Period size: 142 Copynumber: 2.0 Consensus size: 142
16965250 ACATTTCAGA
*
16965260 TAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAATTTTCGAGAAGCCACATTTTCTAAAT
1 TAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAATTTTCGAGAAGCCACATTTCCTAAAT
* * *
16965325 CCTCCGGGTACATTCTTAAGACCTTCGGGCACATTATTCTCTTAAATCCTCCAGACGCATCTTCT
66 CCTCCGGGAACATTCTTAAGACCCTCAGGCACATTATTCTCTTAAATCCTCCAGACGCATCTTCT
16965390 AAAACCTCCGGG
131 AAAACCTCCGGG
* * * *
16965402 TAATTAGTGTCAAGATTTTTTAAAGTTATGTTGCCTCAGTTTTCGAGGAGCCACATTTCCTAAAT
1 TAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAATTTTCGAGAAGCCACATTTCCTAAAT
* **
16965467 CCTCCGGGAACATTCTTAAGACCACT-AGGCACATTATTCTCTTAAATCCTCCGGGTGCATCTTC
66 CCTCCGGGAACATTCTTAAGACC-CTCAGGCACATTATTCTCTTAAATCCTCCAGACGCATCTTC
16965531 TAAAACCTCCGGG
130 TAAAACCTCCGGG
16965544 TA
1 TA
16965546 TATTTTCAAA
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
142 131 0.99
143 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (142 bp):
TAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAATTTTCGAGAAGCCACATTTCCTAAAT
CCTCCGGGAACATTCTTAAGACCCTCAGGCACATTATTCTCTTAAATCCTCCAGACGCATCTTCT
AAAACCTCCGGG
Found at i:16965558 original size:21 final size:21
Alignment explanation
Indices: 16965514--16965657 Score: 137
Period size: 21 Copynumber: 6.8 Consensus size: 21
16965504 TCTCTTAAAT
* *
16965514 CCTCCGGGTGCATCTTCTAAAA
1 CCTCCGGGTACATTTTC-AAAA
*
16965536 CCTCCGGGTATATTTTCAAAA
1 CCTCCGGGTACATTTTCAAAA
* *
16965557 CCTTCGGGTACATTTTTAAAA
1 CCTCCGGGTACATTTTCAAAA
*** *
16965578 CCTCTAAGTATATTTTCAAAA
1 CCTCCGGGTACATTTTCAAAA
*
16965599 CCTCCGGGTACATTCTAT-AAAG
1 CCTCCGGGTACATT-T-TCAAAA
*
16965621 TCTCCGGGTACATTTTCAAAA
1 CCTCCGGGTACATTTTCAAAA
* *
16965642 CCTCCAGGCACATTTT
1 CCTCCGGGTACATTTT
16965658 TCTCTCAAAA
Statistics
Matches: 97, Mismatches: 22, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
20 1 0.01
21 64 0.66
22 31 0.32
23 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (21 bp):
CCTCCGGGTACATTTTCAAAA
Found at i:16965578 original size:42 final size:42
Alignment explanation
Indices: 16965514--16965658 Score: 164
Period size: 43 Copynumber: 3.4 Consensus size: 42
16965504 TCTCTTAAAT
* *
16965514 CCTCCGGGTGCATCTTCTAAAACCTCCGGGTATATTTTCAAAA
1 CCTCCGGGTACAT-TTTTAAAACCTCCGGGTATATTTTCAAAA
* ***
16965557 CCTTCGGGTACATTTTTAAAACCTCTAAGTATATTTTCAAAA
1 CCTCCGGGTACATTTTTAAAACCTCCGGGTATATTTTCAAAA
* ** *
16965599 CCTCCGGGTACATTCTATAAAGTCTCCGGGTACATTTTCAAAA
1 CCTCCGGGTACATT-TTTAAAACCTCCGGGTATATTTTCAAAA
* *
16965642 CCTCCAGGCACATTTTT
1 CCTCCGGGTACATTTTT
16965659 CTCTCAAAAC
Statistics
Matches: 84, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
42 40 0.48
43 44 0.52
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (42 bp):
CCTCCGGGTACATTTTTAAAACCTCCGGGTATATTTTCAAAA
Found at i:16965760 original size:11 final size:10
Alignment explanation
Indices: 16965737--16965848 Score: 93
Period size: 10 Copynumber: 10.8 Consensus size: 10
16965727 CATTTAAATG
*
16965737 AAAAAAAATA
1 AAAAAAAACA
*
16965747 AAACAAAACA
1 AAAAAAAACA
16965757 AAAAAAAGACAA
1 AAAAAAA-AC-A
16965769 AAAAAAAACA
1 AAAAAAAACA
16965779 AAAAAGAAACA
1 AAAAA-AAACA
16965790 AAAAACAAA-A
1 AAAAA-AAACA
16965800 ACAAACAAAA-A
1 A-AAA-AAAACA
* *
16965811 CAACAAAACA
1 AAAAAAAACA
* *
16965821 ACAAAAAACC
1 AAAAAAAACA
*
16965831 AAACAAAACA
1 AAAAAAAACA
16965841 AAAAAAAA
1 AAAAAAAA
16965849 GGAGAAAAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
9 4 0.05
10 45 0.55
11 24 0.29
12 9 0.11
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:16965761 original size:17 final size:17
Alignment explanation
Indices: 16965739--16965845 Score: 107
Period size: 17 Copynumber: 6.4 Consensus size: 17
16965729 TTTAAATGAA
*
16965739 AAAAAATAAAACAAAAC
1 AAAAAACAAAACAAAAC
*
16965756 AAAAAA-AAGACAAAA-
1 AAAAAACAAAACAAAAC
*
16965771 AAAAAACAAAAAAGAAAC
1 AAAAAACAAAACA-AAAC
16965789 AAAAAACAAAA-ACAAAC
1 AAAAAACAAAACA-AAAC
16965806 -AAAAACAACAA-AACAAC
1 AAAAAACAA-AACAA-AAC
*
16965823 AAAAAACCAAACAAAAC
1 AAAAAACAAAACAAAAC
16965840 AAAAAA
1 AAAAAA
16965846 AAAGGAGAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 14
0.80 0.05 0.14
Matches are distributed among these distances:
15 6 0.08
16 21 0.27
17 31 0.40
18 20 0.26
ACGTcount: A:0.82, C:0.15, G:0.02, T:0.01
Consensus pattern (17 bp):
AAAAAACAAAACAAAAC
Found at i:16965797 original size:45 final size:46
Alignment explanation
Indices: 16965746--16965847 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 46
16965736 GAAAAAAAAT
*
16965746 AAAAC-AAAACAAAAAAAAGACAAAAAAAAAACAAAAAA-GAAACAA
1 AAAACAAAAACAAAAAAAA-ACAAAAAAAAAACAAAAAACCAAACAA
* * *
16965791 AAAACAAAAACAAACAAAAACAACAAAACAACAAAAAACCAAACAA
1 AAAACAAAAACAAAAAAAAACAAAAAAAAAACAAAAAACCAAACAA
*
16965837 AACAAAAAAAA
1 AA-AACAAAAA
16965848 AGGAGAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 22 0.45
46 20 0.41
47 7 0.14
ACGTcount: A:0.82, C:0.16, G:0.02, T:0.00
Consensus pattern (46 bp):
AAAACAAAAACAAAAAAAAACAAAAAAAAAACAAAAAACCAAACAA
Found at i:16965857 original size:1 final size:1
Alignment explanation
Indices: 16965737--16965848 Score: 53
Period size: 1 Copynumber: 112.0 Consensus size: 1
16965727 CATTTAAATG
* * * * * * * * * *
16965737 AAAAAAAATAAAACAAAACAAAAAAAAGACAAAAAAAAAACAAAAAAGAAACAAAAAACAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * ** * *
16965802 AAACAAAAACAACAAAACAACAAAAAACCAAACAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16965849 GGAGAAAAAC
Statistics
Matches: 75, Mismatches: 36, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (1 bp):
A
Found at i:16966068 original size:13 final size:13
Alignment explanation
Indices: 16966009--16966069 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
16965999 AGAGAATATC
*
16966009 AAAAAAATCATAA
1 AAAAAAATAATAA
*
16966022 AACAAAAATCATAA
1 AA-AAAAATAATAA
*
16966036 ACAAAAATGAATTAA
1 AAAAAAAT-AA-TAA
16966051 AAAAAAATAATAA
1 AAAAAAATAATAA
*
16966064 TAAAAA
1 AAAAAA
16966070 TAAGAGAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 16 0.39
14 15 0.37
15 10 0.24
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAAATAATAA
Found at i:16966068 original size:14 final size:13
Alignment explanation
Indices: 16966009--16966069 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 13
16965999 AGAGAATATC
*
16966009 AAAAAAATCATAA
1 AAAAAAATAATAA
*
16966022 AACAAAAATCATAA
1 AA-AAAAATAATAA
*
16966036 ACAAAAATGAATTAA
1 AAAAAAAT-AA-TAA
16966051 AAAAAAATAATAA
1 AAAAAAATAATAA
16966064 TAAAAA
1 -AAAAA
16966070 TAAGAGAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 11 0.27
14 20 0.49
15 10 0.24
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAAATAATAA
Found at i:16966327 original size:23 final size:25
Alignment explanation
Indices: 16966296--16966346 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
16966286 ATCCACGATC
16966296 AAACTCAAAAA-AAATCAAA-AAGAA
1 AAACTCAAAAATAAA-CAAAGAAGAA
16966320 AAAC-CAAAAATAAACAAAGAAGAA
1 AAACTCAAAAATAAACAAAGAAGAA
16966344 AAA
1 AAA
16966347 AAAAGAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.76, C:0.12, G:0.06, T:0.06
Consensus pattern (25 bp):
AAACTCAAAAATAAACAAAGAAGAA
Found at i:16971108 original size:26 final size:28
Alignment explanation
Indices: 16971043--16971110 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 28
16971033 TCAAAAAAGC
16971043 ATATTTGATTTAAAAAGTAAAAATACAAA
1 ATATTT-ATTTAAAAAGTAAAAATACAAA
* *
16971072 A-ATTTAATTAAATA-TAATAAA-A-AAA
1 ATATTTATTTAAAAAGTAA-AAATACAAA
16971097 ATATTTATTTAAAA
1 ATATTTATTTAAAA
16971111 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
25 4 0.12
26 14 0.42
27 10 0.30
28 4 0.12
29 1 0.03
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (28 bp):
ATATTTATTTAAAAAGTAAAAATACAAA
Found at i:16972688 original size:2 final size:2
Alignment explanation
Indices: 16972681--16972713 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16972671 ATTGTCGAAT
16972681 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16972714 TCTTCTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16972772 original size:2 final size:2
Alignment explanation
Indices: 16972765--16972797 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16972755 ATTGTCGAAT
16972765 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16972798 TTCTGTCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16985023 original size:13 final size:14
Alignment explanation
Indices: 16984996--16985025 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16984986 TTAAAAAAGT
16984996 AATTTGTTTTAAAA
1 AATTTGTTTTAAAA
*
16985010 AATTTTTTTTAAAA
1 AATTTGTTTTAAAA
16985024 AA
1 AA
16985026 GAGTTTCTAG
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
AATTTGTTTTAAAA
Found at i:16985588 original size:25 final size:23
Alignment explanation
Indices: 16985560--16985610 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
16985550 CATTAGTAAA
*
16985560 TAAAGATAAAAATTTAAAAAAATTT
1 TAAAAATAAAAA-TT-AAAAAATTT
*
16985585 TAAAAATAAACATTAAAAAATTT
1 TAAAAATAAAAATTAAAAAATTT
16985608 TAA
1 TAA
16985611 TGATTAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.50
24 2 0.08
25 10 0.42
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (23 bp):
TAAAAATAAAAATTAAAAAATTT
Found at i:16990295 original size:23 final size:23
Alignment explanation
Indices: 16990242--16990295 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
16990232 ATGAAAGTAA
*
16990242 AAATTATATAACTAATTTAATAT
1 AAATTATTTAACTAATTTAATAT
16990265 AAATTATTTAA-TAATTTAATAAT
1 AAATTATTTAACTAATTTAAT-AT
16990288 AAATTATT
1 AAATTATT
16990296 GATGTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATTATTTAACTAATTTAATAT
Found at i:16990319 original size:134 final size:137
Alignment explanation
Indices: 16990150--16990407 Score: 371
Period size: 134 Copynumber: 1.9 Consensus size: 137
16990140 TTATATCAAT
*
16990150 TAATAAATTATTAATTTTTAATGAAAATAGAAATTAAAAGATTAAAAAATAAAAAATACAAATAG
1 TAATAAATTATTAATGTTTAATGAAAATAGAAATTAAAAGATTAAAAAATAAAAAATACAAATAG
* * *
16990215 AGAAAAAT-ACTCAAA-TAATGAAAGTAAAAATTATATAACTAATTTAAT-ATAAATTATTTAAT
66 AGAAAAATGACTCAAATTAATAAAAGTAAAAATCATACAACTAATTTAATAATAAATTATTTAAT
16990277 AATTTAA
131 AATTTAA
* * * *
16990284 TAATAAATTATTGATGTTTAATGAAAAT-GTAAATTAAAAGATTAAGACATGAAAAATACAAATA
1 TAATAAATTATTAATGTTTAATGAAAATAG-AAATTAAAAGATTAAAAAATAAAAAATACAAATA
* ** *
16990348 GAGAAAAATGATTCAAATTGTTAAAATTAAAAATCATACAACTAATTTAATAATAAATTA
65 GAGAAAAATGACTCAAATTAATAAAAGTAAAAATCATACAACTAATTTAATAATAAATTA
16990408 AAAATATTAA
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
133 1 0.01
134 66 0.61
135 6 0.06
136 27 0.25
137 8 0.07
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (137 bp):
TAATAAATTATTAATGTTTAATGAAAATAGAAATTAAAAGATTAAAAAATAAAAAATACAAATAG
AGAAAAATGACTCAAATTAATAAAAGTAAAAATCATACAACTAATTTAATAATAAATTATTTAAT
AATTTAA
Found at i:16991100 original size:21 final size:21
Alignment explanation
Indices: 16991076--16991118 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
16991066 TTTCTTAACT
16991076 TTTTCATAGCATATATAAACA
1 TTTTCATAGCATATATAAACA
*
16991097 TTTTTATAGCATATATAAACA
1 TTTTCATAGCATATATAAACA
16991118 T
1 T
16991119 CTCTATAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
TTTTCATAGCATATATAAACA
Found at i:16991132 original size:21 final size:21
Alignment explanation
Indices: 16991081--16991126 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
16991071 TAACTTTTTC
* *
16991081 ATAGCATATATAAACATTTTT
1 ATAGCATATATAAACATCTCT
16991102 ATAGCATATATAAACATCTCT
1 ATAGCATATATAAACATCTCT
16991123 ATAG
1 ATAG
16991127 TGTATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (21 bp):
ATAGCATATATAAACATCTCT
Found at i:16991218 original size:35 final size:35
Alignment explanation
Indices: 16991172--16991262 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 35
16991162 CATTAGCTTT
* *
16991172 TGTGCACTCCCTACACGTATAAGGCAATATCATCA
1 TGTGCACTCCCTACACGCACAAGGCAATATCATCA
* ***
16991207 TGTGCACTCCCTACATGCACATTTCAATATCATCA
1 TGTGCACTCCCTACACGCACAAGGCAATATCATCA
* *
16991242 TGTGCACTCCCTGCATGCACA
1 TGTGCACTCCCTACACGCACA
16991263 TTTCAATACC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.27
Consensus pattern (35 bp):
TGTGCACTCCCTACACGCACAAGGCAATATCATCA
Found at i:16991263 original size:35 final size:35
Alignment explanation
Indices: 16991196--16991276 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
16991186 ACGTATAAGG
16991196 CAATATCATCATGTGCACTCCCTACATGCACATTT
1 CAATATCATCATGTGCACTCCCTACATGCACATTT
*
16991231 CAATATCATCATGTGCACTCCCTGCATGCACATTT
1 CAATATCATCATGTGCACTCCCTACATGCACATTT
*
16991266 CAATACCATCA
1 CAATATCATCA
16991277 CACGCACTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.30
Consensus pattern (35 bp):
CAATATCATCATGTGCACTCCCTACATGCACATTT
Found at i:16991284 original size:35 final size:35
Alignment explanation
Indices: 16991210--16991287 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
16991200 ATCATCATGT
* ***
16991210 GCACTCCCTACATGCACATTTCAATATCATCATGT
1 GCACTCCCTACATGCACATTTCAATACCATCACAC
*
16991245 GCACTCCCTGCATGCACATTTCAATACCATCACAC
1 GCACTCCCTACATGCACATTTCAATACCATCACAC
16991280 GCACTCCC
1 GCACTCCC
16991288 GCCCACATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.27, C:0.38, G:0.09, T:0.26
Consensus pattern (35 bp):
GCACTCCCTACATGCACATTTCAATACCATCACAC
Done.