Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 89 of 214
Found at i:25371299 original size:13 final size:13
Alignment explanation
Indices: 25371283--25371322 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
25371273 TTTAAACAAA
25371283 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
25371296 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
25371309 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
25371322 A
1 A
25371323 ACGAAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:25371301 original size:26 final size:26
Alignment explanation
Indices: 25371272--25371322 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
25371262 AACACTCAAA
25371272 TTTT-AAACAAAACTTTTCAAAAGTAC
1 TTTTCAAA-AAAACTTTTCAAAAGTAC
**
25371298 TTTTCAAAAGTACTTTTCAAAAGTA
1 TTTTCAAAAAAACTTTTCAAAAGTA
25371323 ACGAAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (26 bp):
TTTTCAAAAAAACTTTTCAAAAGTAC
Found at i:25374611 original size:18 final size:18
Alignment explanation
Indices: 25374585--25374632 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
25374575 AAAATATGAG
*
25374585 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
*
25374603 AAATTATGTTCACATTTC
1 AAATGATGTTCACATTTC
*
25374621 AAATGATATTCA
1 AAATGATGTTCA
25374633 AATTGATGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:25375179 original size:72 final size:74
Alignment explanation
Indices: 25375057--25375230 Score: 241
Period size: 72 Copynumber: 2.4 Consensus size: 74
25375047 AACAACAATG
* * * *
25375057 CTAAA-CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGAATATTGAATTTTTGTTCTACTT
1 CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTAGAATACTGAATTTATGTTCTACTT
25375121 ATTTATGTA
66 ATTTATGTA
*
25375130 -T-AATCTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTAG-ATACTGAATTTATGTTCTACT
1 CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGT-TTTAGAATACTGAATTTATGTTCTACT
* *
25375192 TATTTTTTTA
65 TATTTATGTA
25375202 CTAAAT-TAGTTTTATCAATAGTTGTTTAT
1 CTAAATCTAGTTTTATCAATAGTTGTTTAT
25375231 ATGTGATTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
71 2 0.02
72 57 0.64
73 27 0.30
74 3 0.03
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (74 bp):
CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTAGAATACTGAATTTATGTTCTACTT
ATTTATGTA
Found at i:25381020 original size:43 final size:43
Alignment explanation
Indices: 25380972--25381155 Score: 212
Period size: 43 Copynumber: 4.3 Consensus size: 43
25380962 GTTTATTTAT
*
25380972 AAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTCCTCAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTCCTCAC
25381015 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTATTCC-CAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCT-TTCCTCAC
* * * **
25381058 AAACGCCGCTAAAGGTTATGTTCTGTCGCGGCGCTTTTTTCAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTCCTCAC
** * * *
25381101 AAACGCCGCT-ATTGT-TTGGTGACATTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGGTCAT-GT-TC-TTTAGCGGCGCTTTCCTCAC
25381145 AAACGCCGCTA
1 AAACGCCGCTA
25381156 TTGTTTGGTG
Statistics
Matches: 122, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 7 0.06
43 83 0.68
44 31 0.25
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTCCTCAC
Found at i:25381145 original size:44 final size:44
Alignment explanation
Indices: 25381085--25381183 Score: 171
Period size: 44 Copynumber: 2.2 Consensus size: 44
25381075 ATGTTCTGTC
*
25381085 GCGGCGCTTTTTTCACAAACGCCGCTATTGTTTGGTGACATTTA
1 GCGGCGCTTTTCTCACAAACGCCGCTATTGTTTGGTGACATTTA
*
25381129 GCGGCGCTTTTCTCACAAACGCCGCTATTGTTTGGTGACCTTTA
1 GCGGCGCTTTTCTCACAAACGCCGCTATTGTTTGGTGACATTTA
*
25381173 GCGGCACTTTT
1 GCGGCGCTTTT
25381184 TCTAAAAACG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.35
Consensus pattern (44 bp):
GCGGCGCTTTTCTCACAAACGCCGCTATTGTTTGGTGACATTTA
Found at i:25381193 original size:44 final size:44
Alignment explanation
Indices: 25381093--25381195 Score: 156
Period size: 44 Copynumber: 2.4 Consensus size: 44
25381083 TCGCGGCGCT
*
25381093 TTTTTC-ACAAACGCCGCTATTGTTTGGTGACATTTAGCGGCGC
1 TTTTTCTACAAACGCCGCTATTGTTTGGTGACATTTAGCGGCAC
*
25381136 -TTTTCTCACAAACGCCGCTATTGTTTGGTGACCTTTAGCGGCAC
1 TTTTTCT-ACAAACGCCGCTATTGTTTGGTGACATTTAGCGGCAC
*
25381180 TTTTTCTAAAAACGCC
1 TTTTTCTACAAACGCC
25381196 AGTAGTTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
42 5 0.09
44 43 0.80
45 6 0.11
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (44 bp):
TTTTTCTACAAACGCCGCTATTGTTTGGTGACATTTAGCGGCAC
Found at i:25381528 original size:21 final size:21
Alignment explanation
Indices: 25381504--25381553 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
25381494 TTCTGCTCTG
25381504 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCCGC
* *
25381525 CTCTGCTTCCCTTGCTGCCGT
1 CTCTGCTTCCCTCGCTGCCGC
25381546 CTCTGCTT
1 CTCTGCTT
25381554 TAATTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.00, C:0.46, G:0.18, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCCGC
Found at i:25384165 original size:38 final size:38
Alignment explanation
Indices: 25384110--25384203 Score: 134
Period size: 38 Copynumber: 2.5 Consensus size: 38
25384100 CTTAAATCCC
* *
25384110 TAACCCCTAACCCCTAAATCCCATTAACCCTTAAAGCA
1 TAACCCCTAACCCCTAAATCCCACTAACCCTTAAAACA
* * * *
25384148 TAACTCTTAACCTCTAAATCCCCCTAACCCTTAAAACA
1 TAACCCCTAACCCCTAAATCCCACTAACCCTTAAAACA
25384186 TAACCCCTAACCCCTAAA
1 TAACCCCTAACCCCTAAA
25384204 CCTTAAATCC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.37, C:0.39, G:0.01, T:0.22
Consensus pattern (38 bp):
TAACCCCTAACCCCTAAATCCCACTAACCCTTAAAACA
Found at i:25384348 original size:29 final size:28
Alignment explanation
Indices: 25384289--25384348 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
25384279 ATCATAAAAT
* *
25384289 ATAGTTAAAATTTATTAAACAATATTTA
1 ATAGTTAAAATTTATTAAACAATAATCA
*
25384317 ATAGTTAAAAATTTATTAAGCAATAATCA
1 ATAGTT-AAAATTTATTAAACAATAATCA
25384346 ATA
1 ATA
25384349 TTATCAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (28 bp):
ATAGTTAAAATTTATTAAACAATAATCA
Found at i:25384863 original size:4 final size:4
Alignment explanation
Indices: 25384854--25384883 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
25384844 TCTCACATAT
25384854 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
25384884 GTATCTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:25385039 original size:17 final size:16
Alignment explanation
Indices: 25384998--25385046 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
25384988 AAACCCTAAG
25384998 CCTCTAACCCCTAAAA
1 CCTCTAACCCCTAAAA
* *
25385014 CCCCTTAACCCCTAAATT
1 CCTC-TAACCCCTAAA-A
*
25385032 CCTCTAACCTCTAAA
1 CCTCTAACCCCTAAA
25385047 GCATAGTCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.11
17 21 0.78
18 3 0.11
ACGTcount: A:0.33, C:0.43, G:0.00, T:0.24
Consensus pattern (16 bp):
CCTCTAACCCCTAAAA
Found at i:25385077 original size:38 final size:37
Alignment explanation
Indices: 25385012--25385107 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 37
25385002 TAACCCCTAA
*
25385012 AACCCCTTAACCCCTAAATTCCTCTAA-CCTCTAAAGCAT
1 AACCCC-TAACCCCTAAA-TCCCCTAACCCT-TAAAGCAT
**
25385051 AGTCCCTAACCCCTAAATCGCCCTAACCCTTAAAGCAT
1 AACCCCTAACCCCTAAATC-CCCTAACCCTTAAAGCAT
*
25385089 AACCCCTAACCCTTAAATC
1 AACCCCTAACCCCTAAATC
25385108 TTAAATCCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 2 0.04
38 40 0.82
39 7 0.14
ACGTcount: A:0.33, C:0.40, G:0.04, T:0.23
Consensus pattern (37 bp):
AACCCCTAACCCCTAAATCCCCTAACCCTTAAAGCAT
Found at i:25385685 original size:41 final size:41
Alignment explanation
Indices: 25385628--25385730 Score: 147
Period size: 41 Copynumber: 2.5 Consensus size: 41
25385618 CGGTGCTTTC
* *
25385628 TCAAAAACG-TCGCTAAAAGCCCGAGCATTAGTGGCG-TTATT
1 TCAAAAACGCT-GCTAAAAGCCCGAGCATTAGCGGCGCTT-CT
*
25385669 TCAAAAACGCTGCTAAAGGCCCGAGCATTAGCGGCGCTTCT
1 TCAAAAACGCTGCTAAAAGCCCGAGCATTAGCGGCGCTTCT
25385710 TCAAAAACGCTGCTAAAAGCC
1 TCAAAAACGCTGCTAAAAGCC
25385731 TCAAAAACTC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
41 53 0.95
42 3 0.05
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (41 bp):
TCAAAAACGCTGCTAAAAGCCCGAGCATTAGCGGCGCTTCT
Found at i:25385837 original size:39 final size:39
Alignment explanation
Indices: 25385779--25385900 Score: 122
Period size: 40 Copynumber: 3.1 Consensus size: 39
25385769 TTTGCGGTGC
* *
25385779 TTTTCAGAAAA-CGCTGCTAATGCTTATTTTTAGCGGCG
1 TTTTCAGAAAAGCGCCGCTAATGCTTATTTTTAGAGGCG
* * *
25385817 TTTTCCA-AAAAGCGCCGCTAATGCTCCATCTTTAGAGGCA
1 TTTT-CAGAAAAGCGCCGCTAATGCT-TATTTTTAGAGGCG
* * * *
25385857 TTTTTAGAAAAGTGCCGCTAATGCTTGATTTTTAGTGGAG
1 TTTTCAGAAAAGCGCCGCTAATGCTT-ATTTTTAGAGGCG
25385897 TTTT
1 TTTT
25385901 TTTATCCAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
38 8 0.12
39 15 0.22
40 44 0.66
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (39 bp):
TTTTCAGAAAAGCGCCGCTAATGCTTATTTTTAGAGGCG
Found at i:25387129 original size:22 final size:22
Alignment explanation
Indices: 25387104--25387149 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
25387094 ACACATGAAC
25387104 TTCAATATAATT-AAACATTCAT
1 TTCAATA-AATTAAAACATTCAT
*
25387126 TTCAATAGATTAAAACATTCAT
1 TTCAATAAATTAAAACATTCAT
25387148 TT
1 TT
25387150 TAACATATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.41
Consensus pattern (22 bp):
TTCAATAAATTAAAACATTCAT
Found at i:25395697 original size:14 final size:14
Alignment explanation
Indices: 25395680--25395706 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25395670 TGAAAATAGC
25395680 TTTTGAAAAATGAT
1 TTTTGAAAAATGAT
25395694 TTTTGAAAAATGA
1 TTTTGAAAAATGA
25395707 CTTACTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (14 bp):
TTTTGAAAAATGAT
Found at i:25396275 original size:16 final size:15
Alignment explanation
Indices: 25396223--25396274 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
25396213 ATGTGAAGAA
25396223 TATTATTTAA-AATT
1 TATTATTTAATAATT
* *
25396237 TATTATTAAAATAATA
1 TATTATT-TAATAATT
*
25396253 AATTATATTAATAATT
1 TATTAT-TTAATAATT
25396269 TATTAT
1 TATTAT
25396275 AATAATTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 7 0.24
15 2 0.07
16 19 0.66
17 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATTTAATAATT
Found at i:25396280 original size:16 final size:16
Alignment explanation
Indices: 25396233--25396280 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
25396223 TATTATTTAA
25396233 AATTTATTATTAA-AAT
1 AATTTATTA-TAATAAT
** *
25396249 AATAAATTATATTAAT
1 AATTTATTATAATAAT
25396265 AATTTATTATAATAAT
1 AATTTATTATAATAAT
25396281 TAAATATGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTATTATAATAAT
Found at i:25396329 original size:31 final size:32
Alignment explanation
Indices: 25396255--25396330 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 32
25396245 AAATAATAAA
*
25396255 TTATATTAATAATTTATTATAATAATTAAATAT
1 TTATATTAATAA-TTATTATAAAAATTAAATAT
*
25396288 GTATATTTAATAA-TATTA-AAAAA-TATAATATT
1 TTATA-TTAATAATTATTATAAAAATTA-AATA-T
25396320 TTATATTAATA
1 TTATATTAATA
25396331 TTTTAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
30 2 0.05
31 14 0.38
32 10 0.27
33 4 0.11
34 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
TTATATTAATAATTATTATAAAAATTAAATAT
Found at i:25396381 original size:21 final size:21
Alignment explanation
Indices: 25396357--25396398 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
25396347 AAATAAAAAT
25396357 AAATTTATTACCAATATAATA
1 AAATTTATTACCAATATAATA
*
25396378 AAATTTATTACCTATATAATA
1 AAATTTATTACCAATATAATA
25396399 CTTTAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTTATTACCAATATAATA
Found at i:25401676 original size:31 final size:31
Alignment explanation
Indices: 25401638--25401701 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
25401628 ATGAACTCAA
25401638 ACTCATCACTTCAAACATCATATAAACTTTT
1 ACTCATCACTTCAAACATCATATAAACTTTT
25401669 ACTCATCACTTCAAACATCATATAAACTTTT
1 ACTCATCACTTCAAACATCATATAAACTTTT
25401700 AC
1 AC
25401702 ATTTGTATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (31 bp):
ACTCATCACTTCAAACATCATATAAACTTTT
Found at i:25402429 original size:22 final size:21
Alignment explanation
Indices: 25402404--25402445 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
25402394 TCATTCTTGT
25402404 TAAACATTTAGAACA-AAAAATC
1 TAAA-ATTTA-AACATAAAAATC
*
25402426 TAAAGTTTAAACATAAAAAT
1 TAAAATTTAAACATAAAAAT
25402446 TTTCACGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.26
Consensus pattern (21 bp):
TAAAATTTAAACATAAAAATC
Found at i:25406260 original size:42 final size:43
Alignment explanation
Indices: 25406188--25406273 Score: 140
Period size: 42 Copynumber: 2.0 Consensus size: 43
25406178 TGATGGAGGA
*
25406188 GACGTTTGAGGGAGAAGTTCAAAGAGTTTGGAGCATGACAAGT
1 GACGTTTGAGGGAGAAGTTCAAAGAATTTGGAGCATGACAAGT
25406231 GACGTTTGA-GGAGGAA-TTCAAAGAATTTGGAGCATGACAAGT
1 GACGTTTGAGGGA-GAAGTTCAAAGAATTTGGAGCATGACAAGT
25406273 G
1 G
25406274 GGGATTTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 29 0.71
43 12 0.29
ACGTcount: A:0.34, C:0.09, G:0.34, T:0.23
Consensus pattern (43 bp):
GACGTTTGAGGGAGAAGTTCAAAGAATTTGGAGCATGACAAGT
Found at i:25412585 original size:18 final size:18
Alignment explanation
Indices: 25412562--25412598 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
25412552 GATATTATAT
25412562 AATCACATAAATTAAGTG
1 AATCACATAAATTAAGTG
25412580 AATCACATAAATTAAGTG
1 AATCACATAAATTAAGTG
25412598 A
1 A
25412599 GGTGGTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (18 bp):
AATCACATAAATTAAGTG
Found at i:25412863 original size:25 final size:25
Alignment explanation
Indices: 25412834--25412884 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
25412824 GAAGTATATG
25412834 AATTTTAGTGTAATAAAACCTATTT
1 AATTTTAGTGTAATAAAACCTATTT
*
25412859 AATTTTAGTGTAATAAAATCTATTT
1 AATTTTAGTGTAATAAAACCTATTT
25412884 A
1 A
25412885 TCCTCTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (25 bp):
AATTTTAGTGTAATAAAACCTATTT
Found at i:25413422 original size:23 final size:26
Alignment explanation
Indices: 25413366--25413427 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
25413356 GTACATACAT
*
25413366 AATTGAGAATTCGGTTCTATAAAAAC
1 AATTGAGAATTTGGTTCTATAAAAAC
*
25413392 AATTGAGATTTTGGTTCT-T-AAAA-
1 AATTGAGAATTTGGTTCTATAAAAAC
25413415 AATTGAGAATTTG
1 AATTGAGAATTTG
25413428 TAAACATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.36
24 4 0.12
25 1 0.03
26 16 0.48
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (26 bp):
AATTGAGAATTTGGTTCTATAAAAAC
Found at i:25413792 original size:18 final size:16
Alignment explanation
Indices: 25413754--25413784 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25413744 TAATCAATTG
*
25413754 TATTATATTTTTGTAT
1 TATTATATTTTTGAAT
25413770 TATTATATTTTTGAA
1 TATTATATTTTTGAA
25413785 AATTATTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TATTATATTTTTGAAT
Found at i:25414088 original size:7 final size:7
Alignment explanation
Indices: 25414069--25414113 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
25414059 AGTGTGCTTA
25414069 ATAAAAT
1 ATAAAAT
25414076 -TAAAAT
1 ATAAAAT
25414082 ATAAAAT
1 ATAAAAT
*
25414089 ATAAAAC
1 ATAAAAT
25414096 ATAAAAT
1 ATAAAAT
25414103 ATAAAA-
1 ATAAAAT
25414109 ATAAA
1 ATAAA
25414114 GTTTTAGCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 11 0.31
7 24 0.69
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (7 bp):
ATAAAAT
Found at i:25417884 original size:48 final size:48
Alignment explanation
Indices: 25417823--25417914 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
25417813 TGTGTATTTT
* * *
25417823 TTGGTGGTAAAGGAGAGGATTGAATAATAGGAGACGCTAGAGTGTTTG
1 TTGGGGGTAAAGGAGAGGACTGAATAATAGGAAACGCTAGAGTGTTTG
* * *
25417871 TTGGGGGTAAAGGAGATGACTGAATAGTAGGAAAGGCTAGAGTG
1 TTGGGGGTAAAGGAGAGGACTGAATAATAGGAAACGCTAGAGTG
25417915 CTAGTGGGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.33, C:0.04, G:0.39, T:0.24
Consensus pattern (48 bp):
TTGGGGGTAAAGGAGAGGACTGAATAATAGGAAACGCTAGAGTGTTTG
Found at i:25422626 original size:16 final size:16
Alignment explanation
Indices: 25422607--25422653 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 16
25422597 AAATTTGAAT
25422607 AATAATAAATTAATCA
1 AATAATAAATTAATCA
25422623 AATAAT-AATT--T-A
1 AATAATAAATTAATCA
*
25422635 AGTAA-AAATTAATCA
1 AATAATAAATTAATCA
25422650 AATA
1 AATA
25422654 TATATTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 9
0.69 0.06 0.25
Matches are distributed among these distances:
12 9 0.36
13 1 0.04
14 1 0.04
15 8 0.32
16 6 0.24
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (16 bp):
AATAATAAATTAATCA
Found at i:25428726 original size:11 final size:11
Alignment explanation
Indices: 25428706--25428766 Score: 58
Period size: 11 Copynumber: 5.6 Consensus size: 11
25428696 AGAAAATTAA
25428706 AAAAAGTATTTT
1 AAAAA-TATTTT
25428718 AAAAATATTTT
1 AAAAATATTTT
*
25428729 AAAAATA---A
1 AAAAATATTTT
25428737 AAAAAGTATTTT
1 AAAAA-TATTTT
25428749 -AAAATACTTTT
1 AAAAATA-TTTT
25428760 AAAAATA
1 AAAAATA
25428767 AAAAATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
10 2 0.05
11 21 0.51
12 11 0.27
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:25428741 original size:31 final size:31
Alignment explanation
Indices: 25428685--25428771 Score: 131
Period size: 31 Copynumber: 2.7 Consensus size: 31
25428675 AATAAACACC
*
25428685 AAAAATTTTTTAGAAAATTAAAAAAAGTATTTT
1 AAAAATATTTTA-AAAA-TAAAAAAAGTATTTT
25428718 AAAAATATTTTAAAAATAAAAAAAGTATTTT
1 AAAAATATTTTAAAAATAAAAAAAGTATTTT
25428749 -AAAATACTTTTAAAAATAAAAAA
1 AAAAATA-TTTTAAAAATAAAAAA
25428772 TATATATTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
30 6 0.12
31 31 0.60
32 4 0.08
33 11 0.21
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (31 bp):
AAAAATATTTTAAAAATAAAAAAAGTATTTT
Found at i:25429468 original size:9 final size:9
Alignment explanation
Indices: 25429449--25429480 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
25429439 TTCTACAGTT
25429449 AATTT-TTC
1 AATTTATTC
25429457 AATTTATTC
1 AATTTATTC
25429466 AATTTATTC
1 AATTTATTC
25429475 AATTTA
1 AATTTA
25429481 GTCCTTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTATTC
Found at i:25432598 original size:9 final size:9
Alignment explanation
Indices: 25432584--25432609 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
25432574 TTAAAACACA
25432584 AACTAAAAT
1 AACTAAAAT
25432593 AACTAAAAT
1 AACTAAAAT
25432602 AACTAAAA
1 AACTAAAA
25432610 ATTAATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AACTAAAAT
Found at i:25432599 original size:21 final size:23
Alignment explanation
Indices: 25432559--25432600 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
25432549 TAATGATGTG
*
25432559 CAAACTATAACATAATTAAAACA
1 CAAACTATAACATAACTAAAACA
25432582 CAAACTA-AA-ATAACTAAAA
1 CAAACTATAACATAACTAAAA
25432601 TAACTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 2 0.11
23 7 0.39
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (23 bp):
CAAACTATAACATAACTAAAACA
Found at i:25440010 original size:19 final size:19
Alignment explanation
Indices: 25439986--25440022 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
25439976 TTTGATGTTG
25439986 TGGTATG-ATAGTTTAAATA
1 TGGTATGTAT-GTTTAAATA
25440005 TGGTATGTATGTTTAAAT
1 TGGTATGTATGTTTAAAT
25440023 CCATGTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (19 bp):
TGGTATGTATGTTTAAATA
Found at i:25442472 original size:3 final size:3
Alignment explanation
Indices: 25442411--25442457 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
25442401 TTGATCAGCA
*
25442411 CAT CAT CAT CAT CAT CAT CAT CAT AAT CAT CAT CAT CAT CAT C-T CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
25442458 TTCATGATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
CAT
Found at i:25452392 original size:39 final size:40
Alignment explanation
Indices: 25452235--25452498 Score: 310
Period size: 40 Copynumber: 6.7 Consensus size: 40
25452225 GCTCCTCGTT
* *
25452235 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
25452275 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
25452315 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
25452355 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
25452394 CAAATGCGTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
25452433 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGT-ATC-TCGCA
25452474 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
25452499 CATCATTCAA
Statistics
Matches: 203, Mismatches: 12, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 73 0.36
40 114 0.56
41 14 0.07
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:25453597 original size:14 final size:14
Alignment explanation
Indices: 25453578--25453604 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25453568 AGGATGAGCA
25453578 TTTTTTTTTCTTTG
1 TTTTTTTTTCTTTG
25453592 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
25453605 CTAGTTTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.04, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTCTTTG
Found at i:25460372 original size:39 final size:40
Alignment explanation
Indices: 25460203--25460464 Score: 301
Period size: 40 Copynumber: 6.7 Consensus size: 40
25460193 GCTCCTCGTT
* *
25460203 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
25460243 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
25460283 CAAATGCCTTCGGGACTTAACCCGG-ATTAGTA-CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
25460321 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
25460360 CAAATGCGTTCGGG-CTTAGCCCGTAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
25460399 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGT-ATC-TCGCA
25460440 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
25460465 CATCATTCAA
Statistics
Matches: 198, Mismatches: 13, Indels: 21
0.85 0.06 0.09
Matches are distributed among these distances:
37 9 0.05
38 29 0.15
39 62 0.31
40 84 0.42
41 14 0.07
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:25460401 original size:78 final size:80
Alignment explanation
Indices: 25460203--25460462 Score: 295
Period size: 77 Copynumber: 3.3 Consensus size: 80
25460193 GCTCCTCGTT
* *
25460203 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGGACTTAGCCC-GTAATTAGT-ATCTCGCACAAATGCCTTCGGGACTTAACCC
*
25460266 GGATTTAGTAACTCGCA
64 GGAATTAGTAACTCGCA
* * *
25460283 CAAATGCCTTCGGGACTTAACCCG-GATTAGTA-CTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGTAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGG
*
25460345 AATTAGTATCTCGCA
66 AATTAGTAACTCGCA
* **
25460360 CAAATGCGTTCGGG-CTTAGCCCGTAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGTAATTAGTATCTCGCACAAATGCCTTCGGGA-CTTAACCCG
* * *
25460423 G-ATATGGTCACTTAGCA
65 GAAT-TAGTAAC-TCGCA
25460440 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
25460463 GACATCATTC
Statistics
Matches: 156, Mismatches: 15, Indels: 18
0.83 0.08 0.10
Matches are distributed among these distances:
76 8 0.05
77 44 0.28
78 40 0.26
79 26 0.17
80 38 0.24
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGTAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCA
Found at i:25461563 original size:13 final size:13
Alignment explanation
Indices: 25461545--25461569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25461535 GGATGAGCAT
25461545 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
25461558 TTTTTTTTCTTT
1 TTTTTTTTCTTT
25461570 CTAGTTTCGG
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:25465118 original size:43 final size:43
Alignment explanation
Indices: 25465057--25465144 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
25465047 TCTAATGCCA
25465057 TTAACCTCTATAGTTTCACAATTCGGGCCTTGAATTGAAAAAT
1 TTAACCTCTATAGTTTCACAATTCGGGCCTTGAATTGAAAAAT
*
25465100 TTAACGTCTATAGTTTCACAATTCGGGCCTTGAATTGAAAAAT
1 TTAACCTCTATAGTTTCACAATTCGGGCCTTGAATTGAAAAAT
25465143 TT
1 TT
25465145 TTCTTCTAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (43 bp):
TTAACCTCTATAGTTTCACAATTCGGGCCTTGAATTGAAAAAT
Found at i:25468474 original size:18 final size:18
Alignment explanation
Indices: 25468447--25468486 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25468437 AAAACAAAAT
* *
25468447 AAAAACTAAAACTGAAAG
1 AAAAAATAAAAATGAAAG
*
25468465 AAAAAATAAAAATGAAAT
1 AAAAAATAAAAATGAAAG
25468483 AAAA
1 AAAA
25468487 TGTACTTGAG
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:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAAAATAAAAATGAAAG
Found at i:25468976 original size:11 final size:11
Alignment explanation
Indices: 25468960--25468984 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25468950 TCTACAAATA
25468960 TTTAATCTATT
1 TTTAATCTATT
25468971 TTTAATCTATT
1 TTTAATCTATT
25468982 TTT
1 TTT
25468985 CCTATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTAATCTATT
Found at i:25468998 original size:9 final size:9
Alignment explanation
Indices: 25468958--25469006 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
25468948 CTTCTACAAA
25468958 TATTTAATC
1 TATTTAATC
25468967 TATTTTTAATC
1 TA--TTTAATC
*
25468978 TATTT-TTCC
1 TATTTAAT-C
25468987 TATTTAATC
1 TATTTAATC
25468996 TATTTAATC
1 TATTTAATC
25469005 TA
1 TA
25469007 CAAATATCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 1 0.03
9 23 0.68
10 1 0.03
11 9 0.26
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTTAATC
Found at i:25484432 original size:100 final size:105
Alignment explanation
Indices: 25484291--25484480 Score: 246
Period size: 100 Copynumber: 1.8 Consensus size: 105
25484281 TCTTGTACTA
* * ** * *
25484291 CCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCAT-A-T-A-GGTGCCCATGCCATG
1 CCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATAACTAATGATGCCAATGCCATG
*
25484352 TCCCAGACATGGTCTTAC-TGGGGACCTCTCATCTTGGTG
66 TCCCAAACATGGTCTTACATGGGGACCTCTCATCTTGGTG
* *
25484391 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTAAATGATGCCAATGCCA
1 CCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATAA-CT-AATGATGCCAATGCCA
25484456 TGTCCCAAACATGGTCTTACATGGG
64 TGTCCCAAACATGGTCTTACATGGG
25484481 ATCTCTTTAC
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
100 37 0.50
101 1 0.01
103 1 0.01
105 1 0.01
106 30 0.41
107 4 0.05
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27
Consensus pattern (105 bp):
CCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATAACTAATGATGCCAATGCCATG
TCCCAAACATGGTCTTACATGGGGACCTCTCATCTTGGTG
Found at i:25484450 original size:56 final size:50
Alignment explanation
Indices: 25484239--25484486 Score: 198
Period size: 50 Copynumber: 4.9 Consensus size: 50
25484229 TGAATATAAC
* * * * *
25484239 ATGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGA--TGT-TTCTTG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* * * * * ** * *
25484286 TACTACCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAG
1 -A-TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* * *
25484338 GTGCCCATGCCATGTCCCAGACATGGTCTTAC-TGGGGACCTCTCATCTTG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATCTTG
*
25484388 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTAAATG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCT---TG
* * *
25484444 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
25484487 TTACCCAAAT
Statistics
Matches: 161, Mismatches: 27, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
48 1 0.01
49 31 0.19
50 78 0.48
51 3 0.02
52 3 0.02
53 4 0.02
56 41 0.25
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (50 bp):
ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
Found at i:25486085 original size:17 final size:17
Alignment explanation
Indices: 25486055--25486109 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
25486045 AGCAACTCAT
25486055 TTATTAATCTAAGATGAG
1 TTATTAA-CTAAGATGAG
*
25486073 TTATTAACTAAGATGAAC
1 TTATTAACTAAGATG-AG
*
25486091 TCAATTAACTAAGATGAG
1 T-TATTAACTAAGATGAG
25486109 T
1 T
25486110 AATTTATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 8 0.25
18 11 0.34
19 13 0.41
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (17 bp):
TTATTAACTAAGATGAG
Found at i:25490405 original size:61 final size:64
Alignment explanation
Indices: 25490335--25490468 Score: 152
Period size: 64 Copynumber: 2.1 Consensus size: 64
25490325 TTAACTTAAG
* * *
25490335 TAAATGAAC-TAAAACAT-ATGCATTAATTATTCC-AGCAACTAG-TTAATTAAAGAAGCAT-AA
1 TAAATGAACTTAAAACATCAT-CAATAAATAATCCTAGCAACTAGATTAATT-AAGAAGCATCAA
25490395 T
64 T
* * *
25490396 TAAATGAACTTAACACATGCATCAATAAATAATCCTAGGAACTAGATTAATTAAGAAGCATCTAT
1 TAAATGAACTTAAAACAT-CATCAATAAATAATCCTAGCAACTAGATTAATTAAGAAGCATCAAT
25490461 TAAATGAA
1 TAAATGAA
25490469 GTTCAATAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
61 9 0.15
62 7 0.11
63 10 0.16
64 19 0.31
65 16 0.26
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.28
Consensus pattern (64 bp):
TAAATGAACTTAAAACATCATCAATAAATAATCCTAGCAACTAGATTAATTAAGAAGCATCAAT
Found at i:25490559 original size:17 final size:17
Alignment explanation
Indices: 25490529--25490583 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
25490519 AGCAACTCAT
25490529 TTATTAATCTAAGATGAG
1 TTATTAA-CTAAGATGAG
*
25490547 TTATTAACTAAGATGAAC
1 TTATTAACTAAGATG-AG
*
25490565 TCAATTAACTAAGATGAG
1 T-TATTAACTAAGATGAG
25490583 T
1 T
25490584 ACTTTATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 8 0.25
18 11 0.34
19 13 0.41
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (17 bp):
TTATTAACTAAGATGAG
Found at i:25512721 original size:76 final size:76
Alignment explanation
Indices: 25512621--25512773 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
25512611 ACAGTAGAAG
25512621 AAAGATTGAATAAAATAACATTTAACCCAGAAATCATGTATACTTCTTTACAAACATGAAATAGA
1 AAAGATTGAATAAAATAACATTTAACCCAGAAATCATGTATACTTCTTTACAAACATGAAATAGA
25512686 AAGTAATCACC
66 AAGTAATCACC
*
25512697 AAAGATTGAATAAAATAACATTTAACCTAGAAATCATGTATACTTCTTTACAAACATGAAATAGA
1 AAAGATTGAATAAAATAACATTTAACCCAGAAATCATGTATACTTCTTTACAAACATGAAATAGA
25512762 AAGTAATCACC
66 AAGTAATCACC
25512773 A
1 A
25512774 GCATTTAGAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (76 bp):
AAAGATTGAATAAAATAACATTTAACCCAGAAATCATGTATACTTCTTTACAAACATGAAATAGA
AAGTAATCACC
Found at i:25531033 original size:25 final size:25
Alignment explanation
Indices: 25530976--25531038 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
25530966 TGGTGAATAT
25530976 TTTGTAAAGCCTTTATGGCAAACTC
1 TTTGTAAAGCCTTTATGGCAAACTC
* * * * *
25531001 TCTATAAAGCTTTTGTGGCGAACTC
1 TTTGTAAAGCCTTTATGGCAAACTC
*
25531026 TTTGTAAAACCTT
1 TTTGTAAAGCCTT
25531039 CTTGGCATAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (25 bp):
TTTGTAAAGCCTTTATGGCAAACTC
Found at i:25536270 original size:21 final size:21
Alignment explanation
Indices: 25536242--25536297 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
25536232 AACAGCGATG
*
25536242 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
25536263 GCGTTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
25536284 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
25536298 AACAATGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:25541885 original size:18 final size:16
Alignment explanation
Indices: 25541862--25541897 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
25541852 ATAGGGTTTT
25541862 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
25541880 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
25541896 TA
1 TA
25541898 TTGGATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:25543720 original size:44 final size:44
Alignment explanation
Indices: 25543672--25543802 Score: 106
Period size: 43 Copynumber: 3.0 Consensus size: 44
25543662 CTTCGATCTG
25543672 CTCCACTACTTCTTAGGGAGATAAGTTCTGTAATTTTCAACCTA
1 CTCCACTACTTCTTAGGGAGATAAGTTCTGTAATTTTCAACCTA
* * * * *** * * *
25543716 CTCCACT-GTTGTTCAGGGAGACAAG-GCTGGGGTCTTCAATCTG
1 CTCCACTACTTCTT-AGGGAGATAAGTTCTGTAATTTTCAACCTA
* * *
25543759 CTCCAATACTGCTCAGGGAGATAAGATT-TGTAATTTTCAACCTA
1 CTCCACTACTTCTTAGGGAGATAAG-TTCTGTAATTTTCAACCTA
25543803 ATTCACTGCT
Statistics
Matches: 60, Mismatches: 23, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
43 31 0.52
44 29 0.48
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (44 bp):
CTCCACTACTTCTTAGGGAGATAAGTTCTGTAATTTTCAACCTA
Found at i:25543751 original size:87 final size:87
Alignment explanation
Indices: 25543660--25543818 Score: 239
Period size: 87 Copynumber: 1.8 Consensus size: 87
25543650 TAGGATTAGA
* * * * *
25543660 GTCTTCGATCTGCTCCACTACTTCTTAGGGAGATAAG-TTCTGTAATTTTCAACCTACTCCACTG
1 GTCTTCAATCTGCTCCAATACTGCTCAGGGAGATAAGATT-TGTAATTTTCAACCTAATCCACTG
*
25543724 TTGTTCAGGGAGACAAGGCTGGG
65 CTGTTCAGGGAGACAAGGCTGGG
*
25543747 GTCTTCAATCTGCTCCAATACTGCTCAGGGAGATAAGATTTGTAATTTTCAACCTAATTCACTGC
1 GTCTTCAATCTGCTCCAATACTGCTCAGGGAGATAAGATTTGTAATTTTCAACCTAATCCACTGC
25543812 TGTTCAG
66 TGTTCAG
25543819 AGAGCTAGGA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
87 62 0.97
88 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (87 bp):
GTCTTCAATCTGCTCCAATACTGCTCAGGGAGATAAGATTTGTAATTTTCAACCTAATCCACTGC
TGTTCAGGGAGACAAGGCTGGG
Found at i:25543872 original size:44 final size:44
Alignment explanation
Indices: 25543840--25544272 Score: 679
Period size: 44 Copynumber: 9.8 Consensus size: 44
25543830 ATGCAATCTC
** * *
25543840 CCACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTACAATCTT
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
** *
25543884 CCACCTATTCCACTGCAAGTAAGGGAACTAGGGCTTACAGTCTT
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
**
25543928 CCACCTATTCCACTATTGGTCAGGGAACTAGGGCTTACAGTCTT
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
*
25543972 CCACCTATTCCAACTGCTGGTCAGGGAACTAGGACTTACAGTCTT
1 CCACCTATTCC-ACTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
*
25544017 CCACCTATTCCGCTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
* *
25544061 TCACCTATTCCACTGCTGGTCAGGGAACTAAGGCTTACAGTCTT
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
*
25544105 CCACCTATTCCAACTGTTGGTCAGGGAACTAGGGCTTACAGTCTT
1 CCACCTATTCC-ACTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
* *
25544150 CCACCTATTCCACTACTGGTCAAGGAACTAGGGCTTACAG-CTT
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
*
25544193 CCACCTATTCCACTGCTGGTCAAGGAACTAGGGCTTACAGTCTT
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
*
25544237 CTACCTATTCCACTGCTGGTCAGGGAACTAGGGCTT
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTT
25544273 GTGATTTCAC
Statistics
Matches: 357, Mismatches: 29, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
43 42 0.12
44 232 0.65
45 83 0.23
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (44 bp):
CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTT
Found at i:25544017 original size:133 final size:132
Alignment explanation
Indices: 25543840--25544268 Score: 673
Period size: 133 Copynumber: 3.2 Consensus size: 132
25543830 ATGCAATCTC
** * **
25543840 CCACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTACAATCTTCCACCTATTCCACTGCAAGTA
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTA
**
25543905 AGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTATTGGTCAGGGAACTAGGGCTTACAGTC
66 AGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTC
25543970 TT
131 TT
*
25543972 CCACCTATTCCAACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCGCTGCTGGT
1 CCACCTATTCC-ACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGT
* * *
25544037 CAGGGAACTAGGGCTTACAGTCTTTCACCTATTCCACTGCTGGTCAGGGAACTAAGGCTTACAGT
65 AAGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGT
25544102 CTT
130 CTT
* * *
25544105 CCACCTATTCCAACTGTTGGTCAGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTACTGGT
1 CCACCTATTCC-ACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGT
*
25544170 CAA-GGAACTAGGGCTTACAG-CTTCCACCTATTCCACTGCTGGTCAAGGAACTAGGGCTTACAG
65 -AAGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAG
25544233 TCTT
129 TCTT
*
25544237 CTACCTATTCCACTGCTGGTCAGGGAACTAGG
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGG
25544269 GCTTGTGATT
Statistics
Matches: 274, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
131 20 0.07
132 65 0.24
133 188 0.69
134 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (132 bp):
CCACCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTA
AGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTC
TT
Found at i:25544037 original size:89 final size:88
Alignment explanation
Indices: 25543840--25544272 Score: 679
Period size: 89 Copynumber: 4.9 Consensus size: 88
25543830 ATGCAATCTC
** * * ** *
25543840 CCACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTACAATCTTCCACCTATTCCACTGCAAGTA
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTGCTGGTC
25543905 AGGGAACTAGGGCTTACAGTCTT
66 AGGGAACTAGGGCTTACAGTCTT
**
25543928 CCACCTATTCCACTATTGGTCAGGGAACTAGGGCTTACAGTCTTCCACCTATTCCAACTGCTGGT
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCCACCTATTCC-ACTGCTGGT
*
25543993 CAGGGAACTAGGACTTACAGTCTT
65 CAGGGAACTAGGGCTTACAGTCTT
* *
25544017 CCACCTATTCCGCTGCTGGTCAGGGAACTAGGGCTTACAGTCTTTCACCTATTCCACTGCTGGTC
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTGCTGGTC
*
25544082 AGGGAACTAAGGCTTACAGTCTT
66 AGGGAACTAGGGCTTACAGTCTT
* *
25544105 CCACCTATTCCAACTGTTGGTCAGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTACTGGT
1 CCACCTATTCC-ACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTGCTGGT
*
25544170 CAAGGAACTAGGGCTTACAG-CTT
65 CAGGGAACTAGGGCTTACAGTCTT
* *
25544193 CCACCTATTCCACTGCTGGTCAAGGAACTAGGGCTTACAGTCTTCTACCTATTCCACTGCTGGTC
1 CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTGCTGGTC
25544258 AGGGAACTAGGGCTT
66 AGGGAACTAGGGCTT
25544273 GTGATTTCAC
Statistics
Matches: 316, Mismatches: 27, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
87 64 0.20
88 105 0.33
89 147 0.47
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (88 bp):
CCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCCACCTATTCCACTGCTGGTC
AGGGAACTAGGGCTTACAGTCTT
Found at i:25546517 original size:60 final size:60
Alignment explanation
Indices: 25546439--25546562 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
25546429 TCTCCTTTTC
*
25546439 TTTTTCCTTTTTTCCTTTTTCTTCTCTCTT-TTTTCATTTTCATTTTGACTTTGACTTTGA
1 TTTTTCCTTTTTTCCTTTTT-TTATCTCTTATTTTCATTTTCATTTTGACTTTGACTTTGA
* * * * * * *
25546499 TTTTT-CTTTTTCTTCTTTTTTTATTTTTTATTTTGATTTTGATTTTGATTTTGATTTTGA
1 TTTTTCCTTTTT-TCCTTTTTTTATCTCTTATTTTCATTTTCATTTTGACTTTGACTTTGA
25546559 TTTT
1 TTTT
25546563 GGTTTTTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 12 0.22
60 42 0.78
ACGTcount: A:0.10, C:0.12, G:0.06, T:0.72
Consensus pattern (60 bp):
TTTTTCCTTTTTTCCTTTTTTTATCTCTTATTTTCATTTTCATTTTGACTTTGACTTTGA
Found at i:25546532 original size:6 final size:6
Alignment explanation
Indices: 25546523--25546568 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
25546513 CTTTTTTTAT
* *
25546523 TTTTTA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGG TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
25546569 TTTTGAATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.13, C:0.00, G:0.15, T:0.72
Consensus pattern (6 bp):
TTTTGA
Found at i:25546538 original size:18 final size:19
Alignment explanation
Indices: 25546516--25546562 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
25546506 TTTTCTTCTT
* *
25546516 TTTTTATTTTTTATTTTGA
1 TTTTGATTTTTGATTTTGA
25546535 TTTTGA-TTTTGATTTTGA
1 TTTTGATTTTTGATTTTGA
25546553 TTTTGATTTT
1 TTTTGATTTT
25546563 GGTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (19 bp):
TTTTGATTTTTGATTTTGA
Found at i:25546572 original size:54 final size:55
Alignment explanation
Indices: 25546467--25546572 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 55
25546457 TTCTTCTCTC
** *
25546467 TTTTTTCATTTTCATTTTGACTTTGACTTTGATTTTTCTTTTTCTTCTTTTTTTA
1 TTTTTTCATTTTCATTTTGACTTTGACTTTGATTTTGATTTTGCTTCTTTTTTTA
* * * *
25546522 TTTTTT-ATTTTGATTTTGATTTTGATTTTGATTTTGATTTTGGTT-TTTTTT
1 TTTTTTCATTTTCATTTTGACTTTGACTTTGATTTTGATTTTGCTTCTTTTTT
25546573 GAATTGGATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 6 0.14
54 32 0.73
55 6 0.14
ACGTcount: A:0.11, C:0.07, G:0.09, T:0.73
Consensus pattern (55 bp):
TTTTTTCATTTTCATTTTGACTTTGACTTTGATTTTGATTTTGCTTCTTTTTTTA
Found at i:25552007 original size:18 final size:16
Alignment explanation
Indices: 25551984--25552019 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
25551974 ATAGGGTTTT
25551984 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
25552002 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
25552018 TA
1 TA
25552020 TTGGATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:25559275 original size:24 final size:23
Alignment explanation
Indices: 25559239--25559283 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
25559229 ATATACATGC
*
25559239 GCATATTTTATATATAATATATAT
1 GCATATTTAATATAT-ATATATAT
25559263 GCATATTTAATATATATATAT
1 GCATATTTAATATATATATAT
25559284 TTATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
GCATATTTAATATATATATATAT
Found at i:25561412 original size:19 final size:20
Alignment explanation
Indices: 25561372--25561415 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
25561362 GTCTCTTTAG
* *
25561372 GCATT-CATTTCATGCATTT
1 GCATTACATTACATGCATAT
25561391 GCATTACATTACAT-CATAT
1 GCATTACATTACATGCATAT
25561410 GCATTA
1 GCATTA
25561416 AACACCGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (20 bp):
GCATTACATTACATGCATAT
Found at i:25564138 original size:40 final size:40
Alignment explanation
Indices: 25563910--25564137 Score: 366
Period size: 40 Copynumber: 5.7 Consensus size: 40
25563900 GCAAACACAT
* * * *
25563910 TTGCCTTCGGGTTTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
25563950 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
25563990 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
25564030 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
25564070 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
25564110 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
25564138 TCCAATGCTC
Statistics
Matches: 173, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 173 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:25569310 original size:45 final size:45
Alignment explanation
Indices: 25569228--25570216 Score: 614
Period size: 45 Copynumber: 22.3 Consensus size: 45
25569218 TGAAAAGCAA
* ** * * * *
25569228 CAGATCCTGTCTTCATATATTGGTAGCAAAGTGGATCGAAGATAG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
* * *
25569273 TAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
** ** * *
25569318 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCAAATATAG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
* *** * * * *
25569363 CAGATCTTGTATTCATGTATTGG-CGTGAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
* * *
25569407 CAGATCTTGTCTTTCCATACTGGTGGCGAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
* ** * *
25569452 CAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCAAATATAG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
*** * * *
25569497 CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
* *
25569541 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
* ** *** * *
25569586 CAAATCTTGTCTTCCTGTACTGGCAACGAAGTAGATCAAATATAG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
*** * * *
25569631 CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
* * * * *
25569675 CAGATCTTGTCTTTCTATACTGGTGGCGAAGTAGAGCGAAGAAAA
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
** * ** * *
25569720 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAATATAG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
* * ** * *
25569765 TAGATCTTGTCTT--CAT-GTATTGAC--A-TA-A--AATAGATAG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA-AGATAG
* *
25569802 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
** * ** *
25569847 TGGATCTTGTCTT--CAT-GTATTGACATGAAGTAGATC-AGAGATAG
1 CAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGA-AGATAG
* ** *
25569891 CAGATCTTGTCTT--CAT-GTATTGACATGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGAAGATAG
* * * *
25569935 CAGATATTGGCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
** * ** *
25569980 TGGATCTTGTCTT--CAT-GTATTGACATGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGAAGATAG
* *
25570024 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
** ** * * ** *
25570069 TGGATCTTGAGTT--TAT-GTTTTGACATGAAGTAGATC-AGAGATAG
1 CAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGA-AGATAG
* * *
25570113 CAGATCTTGTCTTCCCATACTGGTAGTGAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
** * * ** * *
25570158 TGGGTCTTGTCTT--CAT-GTATTGACATGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGAAGATAG
25570202 CAGATCTTGTCTTCC
1 CAGATCTTGTCTTCC
25570217 TGTATTGACA
Statistics
Matches: 721, Mismatches: 187, Indels: 71
0.74 0.19 0.07
Matches are distributed among these distances:
36 2 0.00
37 17 0.02
38 1 0.00
39 5 0.01
40 4 0.01
42 14 0.02
43 16 0.02
44 249 0.35
45 395 0.55
46 10 0.01
47 8 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (45 bp):
CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAG
Found at i:25569413 original size:89 final size:89
Alignment explanation
Indices: 25569228--25570238 Score: 806
Period size: 89 Copynumber: 11.4 Consensus size: 89
25569218 TGAAAAGCAA
* * * * * * * ** *** *
25569228 CAGATCCTGTCTTCATATATTGGTAGCAAAGTGGATCGAAGATAGTAGATCTTGTCTTCCCATAC
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTAT
* * * *
25569293 TGGTGGCGAAGTAGATCGAAGAAAA
66 TGG-CGTGAAGTAGATCGAAGATAG
* * * *
25569318 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCAAATATAGCAGATCTTGTATTCATGTAT
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTAT
*
25569383 TGGCGTGAAGTAGATCGAAGATAA
66 TGGCGTGAAGTAGATCGAAGATAG
* ** * * *
25569407 CAGATCTTGTCTTTCC-ATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTATA
1 CAGATCTTGTC-TTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTA
* * * *
25569471 CTGGCAGCGAAGTAGATCAAATATAG
65 TTGGC-GTGAAGTAGATCGAAGATAG
* * * * *** *
25569497 CAGATCTTGTCTTCATGTATTGGC-GTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATAC
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTAT
* * * *
25569561 TGGTGGCGAAGTAGATCGAAGAAAA
66 TGG-CGTGAAGTAGATCGAAGATAG
* * * * *
25569586 CAAATCTTGTCTTCCTGTACTGGCAACGAAGTAGATCAAATATAGCAGATCTTGTCTTCATGTAT
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTAT
25569651 TGGCGTGAAGTAGATCGAAGATAG
66 TGGCGTGAAGTAGATCGAAGATAG
* * ** * * *
25569675 CAGATCTTGTCTTTCTATACTGGTGGCGAAGTAGAGCGAAGAAAACAGATCTTGTCTTCCTGTAT
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTAT
* * *
25569740 TGGCAGCGAAGTAGATCAAATATAG
66 TGGC-GTGAAGTAGATCGAAGATAG
* * * * * * *** *
25569765 TAGATCTTGTCTTCATGTATTGACA--TAA--A-AT---AGATAGCAGATCTTGTCTTCCCATAC
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTAT
* *
25569822 TGGTGGTGAAGTAGATCGAAGATAA
66 TGG-CGTGAAGTAGATCGAAGATAG
** * * * * *
25569847 TGGATCTTGTCTTCATGTATTGACA-TGAAGTAGATC-AGAGATAGCAGATCTTGTCTTCATGTA
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGA-AGATAACAGATCTTGTCTTCATGTA
* *
25569910 TTGACATGAAGTAGATCGAAGATAG
65 TTGGCGTGAAGTAGATCGAAGATAG
* * ** ** * **
25569935 CAGATATTGGCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTAT
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTAT
* *
25570000 TGACATGAAGTAGATCGAAGATAG
66 TGGCGTGAAGTAGATCGAAGATAG
** ** * ** ** * *
25570024 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGAGTTTATGTTT
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTAT
* *
25570089 TGACATGAAGTAGATC-AGAGATAG
66 TGGCGTGAAGTAGATCGA-AGATAG
** * * ** *
25570113 CAGATCTTGTCTTCCCATACTGGTAGTGAAGTAGATCGAAGATAATGGGTCTTGTCTTCATGTAT
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTAT
* * *
25570178 TGACATGAAGTAGATCAAAGATAG
66 TGGCGTGAAGTAGATCGAAGATAG
* * *
25570202 CAGATCTTGTCTTCCTGTATTGACAGCGAAGAAGATC
1 CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATC
25570239 AAGGCTACAA
Statistics
Matches: 764, Mismatches: 139, Indels: 37
0.81 0.15 0.04
Matches are distributed among these distances:
82 64 0.08
83 2 0.00
85 2 0.00
86 3 0.00
88 35 0.05
89 498 0.65
90 160 0.21
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (89 bp):
CAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTAT
TGGCGTGAAGTAGATCGAAGATAG
Found at i:25569501 original size:134 final size:134
Alignment explanation
Indices: 25569228--25570216 Score: 1176
Period size: 134 Copynumber: 7.4 Consensus size: 134
25569218 TGAAAAGCAA
* * * ** * *
25569228 CAGATCCTGTCTTCATATATTGGTAGCAAAGTGGATCGAAGATAGTAGATCTTGTCTTCCCATAC
1 CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATAC
25569293 TGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCAAA
65 TGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCAAA
25569358 TATAG
130 TATAG
* * *
25569363 CAGATCTTGTATTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCTTGTCTTTCCATACT
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACT
*
25569428 GGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCAAAT
66 GGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCAAAT
25569493 ATAG
131 ATAG
25569497 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACT
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACT
* *
25569562 GGTGGCGAAGTAGATCGAAGAAAACAAATCTTGTCTTCCTGTACTGGCAACGAAGTAGATCAAAT
66 GGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCAAAT
25569627 ATAG
131 ATAG
* *
25569631 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTTCTATACT
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACT
* *
25569696 GGTGGCGAAGTAGAGCGAAGAAAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAT
66 GGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCAAAT
25569761 ATAG
131 ATAG
* * *
25569765 TAGATCTTGTCTTCATGTATTGACAT-AA--A-AT---AGATAGCAGATCTTGTCTTCCCATACT
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACT
* * ** * * * * * *
25569823 GGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACA-TGAAGTAGATCAGAG
66 GGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCAAAT
25569887 ATAG
131 ATAG
* * * *
25569891 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATATTGGCTTCCCATACT
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACT
* * ** * * * * * *
25569956 GGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACA-TGAAGTAGATCGAAG
66 GGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCAAAT
25570020 ATAG
131 ATAG
*** * * *** ** * *
25570024 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGAGTT--TAT-G
1 CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATAC
** * * * ** * *
25570086 TTTTGACATGAAGTAGATC-AGAGATAGCAGATCTTGTCTTCCCATACTGGTAGTGAAGTAGATC
65 TGGTGGC--GAAGTAGATCGA-AGAAAACAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATC
* * *
25570150 GAAGATAA
127 AAATATAG
** * * * *
25570158 TGGGTCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCC
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCC
25570217 TGTATTGACA
Statistics
Matches: 752, Mismatches: 88, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
126 41 0.05
127 69 0.09
129 1 0.00
130 4 0.01
131 4 0.01
132 3 0.00
133 169 0.22
134 441 0.59
135 20 0.03
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (134 bp):
CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACT
GGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCAAAT
ATAG
Found at i:25571434 original size:25 final size:24
Alignment explanation
Indices: 25571403--25571466 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 24
25571393 TATTATTATT
*
25571403 ATATTTTCTATACATATAAATGCGC
1 ATATTTTATATA-ATATAAATGCGC
*
25571428 ATATTTTATATAATATATAT--GC
1 ATATTTTATATAATATAAATGCGC
*
25571450 ATATTTAATATATATAT
1 ATATTTTATATA-ATAT
25571467 TTATATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.37
23 4 0.11
24 7 0.20
25 11 0.31
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (24 bp):
ATATTTTATATAATATAAATGCGC
Found at i:25582756 original size:44 final size:45
Alignment explanation
Indices: 25582702--25582790 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 45
25582692 ATTTTGTTCC
* * *
25582702 ATGAATTTTCCAGCTGAAAACTAAGTTC-ATTTAGCTTATTAATT
1 ATGAAGTTTCCAGCTGAAAACTAAGTTCAATTCAGCTCATTAATT
25582746 ATGAAGTTTCCAGCTGAAAACTAAGTTCAATTCAGCTCATTAATT
1 ATGAAGTTTCCAGCTGAAAACTAAGTTCAATTCAGCTCATTAATT
25582791 TGTAATCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 27 0.66
45 14 0.34
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (45 bp):
ATGAAGTTTCCAGCTGAAAACTAAGTTCAATTCAGCTCATTAATT
Found at i:25583678 original size:32 final size:34
Alignment explanation
Indices: 25583610--25583686 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
25583600 TGGACTTTAT
* * *
25583610 TATATATAATATATATACGTGGTTTTCGGTGTTA
1 TATATATAATATATATACATGGTTCTCAGTGTTA
* *
25583644 TATATATAATATATATGCATGGTTCT-ATTGTATA
1 TATATATAATATATATACATGGTTCTCAGTGT-TA
25583678 TAGTATATA
1 TA-TATATA
25583687 TAATTATGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 3 0.08
34 27 0.75
35 6 0.17
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (34 bp):
TATATATAATATATATACATGGTTCTCAGTGTTA
Found at i:25586439 original size:18 final size:18
Alignment explanation
Indices: 25586416--25586454 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25586406 ACCCAGCTTG
* *
25586416 GAAGATGATTGTTGAAAA
1 GAAGATGATTGCTAAAAA
25586434 GAAGATGATTGCTAAAAA
1 GAAGATGATTGCTAAAAA
25586452 GAA
1 GAA
25586455 TTAAGTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.23
Consensus pattern (18 bp):
GAAGATGATTGCTAAAAA
Found at i:25587584 original size:43 final size:43
Alignment explanation
Indices: 25587483--25587588 Score: 131
Period size: 43 Copynumber: 2.5 Consensus size: 43
25587473 TTACTGAGAG
* * *
25587483 GTGATAACATGTAAGACCATGTCTGGGACATTGGCATCGTTAT
1 GTGATAACATGTAAGACCATGTCTGGAACAGTGGCATCGATAT
* ** * * *
25587526 ATGATTTCATATAAGATCATGTTTGGAACAGTGGCATCGATAT
1 GTGATAACATGTAAGACCATGTCTGGAACAGTGGCATCGATAT
25587569 GTGATAACATGTAAGACCAT
1 GTGATAACATGTAAGACCAT
25587589 ATCTAGGATA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (43 bp):
GTGATAACATGTAAGACCATGTCTGGAACAGTGGCATCGATAT
Found at i:25603004 original size:18 final size:20
Alignment explanation
Indices: 25602983--25603027 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
25602973 TTTTATTGGA
25602983 TTTTGTCTTTTTT-CT-ATT
1 TTTTGTCTTTTTTACTGATT
*
25603001 TTTTGACTTTTTTGACTGATT
1 TTTTGTCTTTTTT-ACTGATT
25603022 TTTTGT
1 TTTTGT
25603028 GCAAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 12 0.55
20 2 0.09
21 8 0.36
ACGTcount: A:0.09, C:0.09, G:0.11, T:0.71
Consensus pattern (20 bp):
TTTTGTCTTTTTTACTGATT
Found at i:25604079 original size:4 final size:4
Alignment explanation
Indices: 25604070--25604094 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25604060 AAACTAAGTA
25604070 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
25604095 TAAAACTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:25608957 original size:18 final size:17
Alignment explanation
Indices: 25608929--25608963 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25608919 ATTATTAAGA
*
25608929 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
25608946 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
25608964 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:25609117 original size:157 final size:157
Alignment explanation
Indices: 25608917--25609233 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
25608907 ATAAGAATAT
25608917 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
25608982 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
*
25609047 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
*
25609074 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTTAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
25609139 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
*
25609204 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
25609231 TAA
1 TAA
25609234 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:25609367 original size:45 final size:44
Alignment explanation
Indices: 25609267--25609376 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
25609257 TTTTCCATTA
25609267 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
25609306 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
25609351 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
25609377 CCTCTATTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:25609376 original size:16 final size:16
Alignment explanation
Indices: 25609355--25609408 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
25609345 TTGATTTGCT
25609355 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
25609371 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
25609387 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
25609403 AATACA
1 ATTACA
25609409 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:25614556 original size:4 final size:4
Alignment explanation
Indices: 25614547--25614596 Score: 91
Period size: 4 Copynumber: 12.5 Consensus size: 4
25614537 GACACTAAGG
*
25614547 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
25614595 AC
1 AC
25614597 CCCAAATTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:25626170 original size:43 final size:41
Alignment explanation
Indices: 25626035--25626223 Score: 252
Period size: 41 Copynumber: 4.5 Consensus size: 41
25626025 CAAACAAAAA
* * **
25626035 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTGTTTGTG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT-TCTAAG
*
25626077 CGCCTCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTAAG
* * **
25626118 CGCCTCTAAAGAGCATGTTCTTTAGCGGCGTTTTTTTTCTATC
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG--TTTTTTCTAAG
*
25626161 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTAAG
*
25626202 CGCCGCTAAAGAACATGGTCTT
1 CGCCGCTAAAGAACATGTTCTT
25626224 CCCTCGCTTC
Statistics
Matches: 132, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
41 63 0.48
42 33 0.25
43 36 0.27
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTAAG
Found at i:25626190 original size:84 final size:83
Alignment explanation
Indices: 25626035--25626223 Score: 288
Period size: 84 Copynumber: 2.3 Consensus size: 83
25626025 CAAACAAAAA
* * * * *
25626035 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTGTTTGTGCGCCTCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTGTTTATCCGCCGCTAAAGAACATGGTCTTT
25626100 AGCGGCGTTTTTTCTAAG
66 AGCGGCGTTTTTTCTAAG
* * *
25626118 CGCCTCTAAAGAGCATGTTCTTTAGCGGCGTTTTTTTTCTATCCGCCGCTAAAGAACATGGTCTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTGTT-TATCCGCCGCTAAAGAACATGGTCTT
25626183 TAGCGGCGTTTTTTCTAAG
65 TAGCGGCGTTTTTTCTAAG
*
25626202 CGCCGCTAAAGAACATGGTCTT
1 CGCCGCTAAAGAACATGTTCTT
25626224 CCCTCGCTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
83 35 0.37
84 60 0.63
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (83 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTGTTTATCCGCCGCTAAAGAACATGGTCTTT
AGCGGCGTTTTTTCTAAG
Found at i:25630503 original size:34 final size:34
Alignment explanation
Indices: 25630464--25630962 Score: 126
Period size: 36 Copynumber: 14.2 Consensus size: 34
25630454 TGTATGCCCC
*
25630464 ATGTAAGTAATTTAAGCTATGTAAGTAATGTATT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
** ** * *
25630498 ATGTAAGTTGTGT-A-CTACATCA-TTATGTGAGTT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGT-A-TT
* * * * *
25630531 GTGT-A-TAATGTAAGTTAAG-AAGGTTATGTATA
1 ATGTAAGTAATGTAAGCTATGTAA-GTAATGTATT
25630563 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
*
25630597 ATGTAAGTTAA-G-AAGGTTATGT-A-TAATGTAAGTT
1 ATGTAAG-TAATGTAA-GCTATGTAAGTAATGT-A-TT
* * * * *
25630631 ACT-TAATTTATGTAAGTTATGTAAGTTATTTAATTT
1 A-TGTAAGTAATGTAAGCTATGTAAGTAATGT-A-TT
* * * * *
25630667 ATGTAAGTTATGTAAGTTATTTAATTTACT-TAATTT
1 ATGTAAGTAATGTAAGCTATGTAA-GTAATGT-A-TT
* * * * *
25630703 ATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGT-A-TT
* * * *
25630739 ATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGT-A-TT
* * * *
25630775 ACT-TAATTTATGTAAGTTATGTAAG-ATATTTAATTT
1 A-TGTAAGTAATGTAAGCTATGTAAGTA-ATGT-A-TT
* * * * *
25630811 ATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGT-A-TT
* * ** *
25630847 ATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGT-A-TT
* * ** *
25630883 ATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGT-A-TT
* * ** * *
25630919 ATGTAAGTTATTTAATTTTTGTAAGTTATGTAATT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGT-ATT
25630954 AATGTAAGT
1 -ATGTAAGT
25630963 TATTTAATTT
Statistics
Matches: 388, Mismatches: 51, Indels: 50
0.79 0.10 0.10
Matches are distributed among these distances:
31 9 0.02
32 19 0.05
33 16 0.04
34 64 0.16
35 16 0.04
36 261 0.67
37 3 0.01
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (34 bp):
ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
Found at i:25630573 original size:9 final size:9
Alignment explanation
Indices: 25630538--25630965 Score: 448
Period size: 9 Copynumber: 48.2 Consensus size: 9
25630528 GTTGTGTATA
25630538 ATGTAAGTT
1 ATGTAAGTT
*
25630547 AAG-AAGGTT
1 ATGTAA-GTT
*
25630556 ATGT-A-TA
1 ATGTAAGTT
*
25630563 ATGTAAGTA
1 ATGTAAGTT
*
25630572 ATGTAAGCT
1 ATGTAAGTT
*
25630581 ATGTAAGTA
1 ATGTAAGTT
25630590 ATGT-A-TT
1 ATGTAAGTT
25630597 ATGTAAGTT
1 ATGTAAGTT
*
25630606 AAG-AAGGTT
1 ATGTAA-GTT
*
25630615 ATGT-A-TA
1 ATGTAAGTT
25630622 ATGTAAGTT
1 ATGTAAGTT
*
25630631 ACT-TAATTT
1 A-TGTAAGTT
25630640 ATGTAAGTT
1 ATGTAAGTT
25630649 ATGTAAGTT
1 ATGTAAGTT
* *
25630658 ATTTAATTT
1 ATGTAAGTT
25630667 ATGTAAGTT
1 ATGTAAGTT
25630676 ATGTAAGTT
1 ATGTAAGTT
* *
25630685 ATTTAATTT
1 ATGTAAGTT
*
25630694 ACT-TAATTT
1 A-TGTAAGTT
25630703 ATGTAAGTT
1 ATGTAAGTT
25630712 ATGTAAGTT
1 ATGTAAGTT
* *
25630721 ATTTAATTT
1 ATGTAAGTT
25630730 ATGTAAGTT
1 ATGTAAGTT
25630739 ATGTAAGTT
1 ATGTAAGTT
25630748 ATGTAAGTT
1 ATGTAAGTT
25630757 ATGTAAGTT
1 ATGTAAGTT
* *
25630766 ATTTAATTT
1 ATGTAAGTT
*
25630775 ACT-TAATTT
1 A-TGTAAGTT
25630784 ATGTAAGTT
1 ATGTAAGTT
*
25630793 ATGTAAGAT
1 ATGTAAGTT
* *
25630802 ATTTAATTT
1 ATGTAAGTT
25630811 ATGTAAGTT
1 ATGTAAGTT
25630820 ATGTAAGTT
1 ATGTAAGTT
* *
25630829 ATTTAATTT
1 ATGTAAGTT
25630838 ATGTAAGTT
1 ATGTAAGTT
25630847 ATGTAAGTT
1 ATGTAAGTT
* *
25630856 ATTTAATTT
1 ATGTAAGTT
25630865 ATGTAAGTT
1 ATGTAAGTT
25630874 ATGTAAGTT
1 ATGTAAGTT
25630883 ATGTAAGTT
1 ATGTAAGTT
* *
25630892 ATTTAATTT
1 ATGTAAGTT
25630901 ATGTAAGTT
1 ATGTAAGTT
25630910 ATGTAAGTT
1 ATGTAAGTT
25630919 ATGTAAGTT
1 ATGTAAGTT
* *
25630928 ATTTAATTT
1 ATGTAAGTT
*
25630937 TTGTAAGTT
1 ATGTAAGTT
25630946 ATGTAA-TT
1 ATGTAAGTT
25630954 AATGTAAGTT
1 -ATGTAAGTT
25630964 AT
1 AT
25630966 TTAATTTGTG
Statistics
Matches: 349, Mismatches: 52, Indels: 36
0.80 0.12 0.08
Matches are distributed among these distances:
7 15 0.04
8 13 0.04
9 316 0.91
10 5 0.01
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.48
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:25638322 original size:115 final size:114
Alignment explanation
Indices: 25638103--25638340 Score: 379
Period size: 115 Copynumber: 2.1 Consensus size: 114
25638093 AAATATTTGT
* *
25638103 GGCGTTTTTAAATACGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAGG
1 GGCGTTTTTAAATACACCACTAAAAGAAAACAACAAAACGGCACCGTCCTTGTTACAGTTAAAGG
* *
25638168 AAATTTGTGGCGTTTCTTCGTAAAACGCCGGTAAAATATCACTTTTAGC
66 AAATTTGCGGCGTTTCTTCGTAAAACGCCGGTAAAATATCACCTTTAGC
* * *
25638217 GGCGTTTTTCAAATGCACCACTAAAGGAAAACAACAAAACGGCACTGTCCTTGTTACAGTTAAAG
1 GGCGTTTTT-AAATACACCACTAAAAGAAAACAACAAAACGGCACCGTCCTTGTTACAGTTAAAG
*
25638282 GAAATTTGCGGCGTTTCTTCAG-AAAACGCCGGTAATATATCACCTTTAGC
65 GAAATTTGCGGCGTTTCTTC-GTAAAACGCCGGTAAAATATCACCTTTAGC
25638332 GGCGTTTTT
1 GGCGTTTTT
25638341 TTATGAAGCG
Statistics
Matches: 114, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
114 9 0.08
115 104 0.91
116 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (114 bp):
GGCGTTTTTAAATACACCACTAAAAGAAAACAACAAAACGGCACCGTCCTTGTTACAGTTAAAGG
AAATTTGCGGCGTTTCTTCGTAAAACGCCGGTAAAATATCACCTTTAGC
Found at i:25638845 original size:21 final size:21
Alignment explanation
Indices: 25638811--25638871 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
25638801 AATCATAAAT
**
25638811 CCTAAACCCCAAACCTAAAAC
1 CCTAAACCGTAAACCTAAAAC
* **
25638832 TCTAAACTTTAAACCGT-AAAC
1 CCTAAACCGTAAACC-TAAAAC
25638853 CCTAAACCGTAAACCTAAA
1 CCTAAACCGTAAACCTAAA
25638872 CCATATTTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.46, C:0.33, G:0.03, T:0.18
Consensus pattern (21 bp):
CCTAAACCGTAAACCTAAAAC
Found at i:25638851 original size:14 final size:14
Alignment explanation
Indices: 25638841--25638873 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
25638831 CTCTAAACTT
25638841 TAAACCGTAAACCC
1 TAAACCGTAAACCC
25638855 TAAACCGTAAA-CC
1 TAAACCGTAAACCC
25638868 TAAACC
1 TAAACC
25638874 ATATTTTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.45, C:0.33, G:0.06, T:0.15
Consensus pattern (14 bp):
TAAACCGTAAACCC
Found at i:25639041 original size:20 final size:21
Alignment explanation
Indices: 25639003--25639052 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
25638993 TCTTCAATTT
25639003 CCAAACT-AAACCCTAAAACC
1 CCAAACTCAAACCCTAAAACC
* *
25639023 CTAAACTCAAA-CCTTAAACC
1 CCAAACTCAAACCCTAAAACC
25639043 CCAAACTCAA
1 CCAAACTCAA
25639053 TCTCTAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.14
Consensus pattern (21 bp):
CCAAACTCAAACCCTAAAACC
Found at i:25641875 original size:37 final size:33
Alignment explanation
Indices: 25641834--25641941 Score: 90
Period size: 37 Copynumber: 3.0 Consensus size: 33
25641824 CAAGATAAAC
25641834 ATTAAATTTAATTTAATATTAAGATAATCACTTTAAT
1 ATTAAATTTAATTTAATATTAAGATAAT-A--TT-AT
** *
25641871 ATTAAATTAATAAAATACTATTAAGATAAGTATTAT
1 ATTAAATT--TAATTTAATATTAAGATAA-TATTAT
*
25641907 ATTAAATTTAATATTAAACTATTAAAATAATATTA
1 ATTAAATTTAAT-TT-AA-TATTAAGATAATATTA
25641942 ATTTTGGAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
34 3 0.05
35 1 0.02
36 16 0.28
37 20 0.34
39 17 0.29
40 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (33 bp):
ATTAAATTTAATTTAATATTAAGATAATATTAT
Found at i:25641894 original size:25 final size:25
Alignment explanation
Indices: 25641840--25641894 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
25641830 AAACATTAAA
*
25641840 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
25641865 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
25641889 TATTAA
1 T-TTAA
25641895 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:25649116 original size:27 final size:27
Alignment explanation
Indices: 25649050--25649259 Score: 175
Period size: 27 Copynumber: 8.0 Consensus size: 27
25649040 TACCCTTGAT
* * *
25649050 GGGTAAAATGACCGAAATATCTC-G-A
1 GGGTAAAATGACCGTAATACCCCTGTA
25649075 TGGGTAAAATGACCGTAATACCCCTGTA
1 -GGGTAAAATGACCGTAATACCCCTGTA
* * * *
25649103 GGGTAAAATAACCGTAATACTCTTATA
1 GGGTAAAATGACCGTAATACCCCTGTA
* * *
25649130 GGGTAAAATGATCGTAAT----TTATCA
1 GGGTAAAATGACCGTAATACCCCTGT-A
*
25649154 -GGTAAAATGACCATAAT-CCCCTTGTA
1 GGGTAAAATGACCGTAATACCCC-TGTA
* * * *
25649180 GGGTAAAATAACCATAATGCCCCTTTA
1 GGGTAAAATGACCGTAATACCCCTGTA
*
25649207 GGGTAAAATGACCGTAATACCTCTGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
* *
25649234 GGGTAAAATGACTGTAATGCCCCTGT
1 GGGTAAAATGACCGTAATACCCCTGT
25649260 TACTGGTGGC
Statistics
Matches: 152, Mismatches: 23, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
23 19 0.12
24 1 0.01
26 21 0.14
27 106 0.70
28 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (27 bp):
GGGTAAAATGACCGTAATACCCCTGTA
Found at i:25649146 original size:54 final size:55
Alignment explanation
Indices: 25649050--25649259 Score: 197
Period size: 54 Copynumber: 4.0 Consensus size: 55
25649040 TACCCTTGAT
* * *
25649050 GGGTAAAATGACCGAAATA-TCTCGAT-GGGTAAAATGACCGTAATACCCCTGTA
1 GGGTAAAATGACCGTAATACTCTCTATAGGGTAAAATGACCGTAATGCCCCTGTA
* * * *
25649103 GGGTAAAATAACCGTAATACTCT-TATAGGGTAAAATGATCGTAAT----TTATCA
1 GGGTAAAATGACCGTAATACTCTCTATAGGGTAAAATGACCGTAATGCCCCTGT-A
* * * * * * *
25649154 -GGTAAAATGACCATAATCCCCT-TGTAGGGTAAAATAACCATAATGCCCCTTTA
1 GGGTAAAATGACCGTAATACTCTCTATAGGGTAAAATGACCGTAATGCCCCTGTA
* *
25649207 GGGTAAAATGACCGTAATAC-CTCTGTAGGGTAAAATGACTGTAATGCCCCTGT
1 GGGTAAAATGACCGTAATACTCTCTATAGGGTAAAATGACCGTAATGCCCCTGT
25649260 TACTGGTGGC
Statistics
Matches: 126, Mismatches: 22, Indels: 17
0.76 0.13 0.10
Matches are distributed among these distances:
50 38 0.30
51 1 0.01
53 22 0.17
54 65 0.52
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (55 bp):
GGGTAAAATGACCGTAATACTCTCTATAGGGTAAAATGACCGTAATGCCCCTGTA
Found at i:25649180 original size:77 final size:77
Alignment explanation
Indices: 25649033--25649224 Score: 219
Period size: 77 Copynumber: 2.5 Consensus size: 77
25649023 CGAATCATGG
* * * * * *
25649033 ACCAAAAT-ACCCTTGATGGGTAAAATGACCGAAATATCTCGATGGGTAAAATGACCGTAATACC
1 ACCATAATGACCCTTTA-GGGTAAAATGACCGTAATTTATC-A--GGTAAAATGACCATAATACC
25649097 CCTGTAGGGTAAAATA
62 CCTGTAGGGTAAAATA
* * *
25649113 ACCGTAAT-ACTCTTATAGGGTAAAATGATCGTAATTTATCAGGTAAAATGACCATAAT-CCCCT
1 ACCATAATGACCCTT-TAGGGTAAAATGACCGTAATTTATCAGGTAAAATGACCATAATACCCC-
25649176 TGTAGGGTAAAATA
64 TGTAGGGTAAAATA
*
25649190 ACCATAATGCCCCTTTAGGGTAAAATGACCGTAAT
1 ACCATAATGACCCTTTAGGGTAAAATGACCGTAAT
25649225 ACCTCTGTAG
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
76 4 0.04
77 56 0.58
78 4 0.04
79 1 0.01
80 30 0.31
81 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (77 bp):
ACCATAATGACCCTTTAGGGTAAAATGACCGTAATTTATCAGGTAAAATGACCATAATACCCCTG
TAGGGTAAAATA
Found at i:25649316 original size:27 final size:27
Alignment explanation
Indices: 25649259--25649319 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
25649249 AATGCCCCTG
*
25649259 TTACTGGTGGCTCTGCCACAATCACTG
1 TTACTGGTGGCTCTGCCACAATCACTA
*
25649286 TTACTGGTGGCT-TGGCCACATAT-ATTA
1 TTACTGGTGGCTCT-GCCACA-ATCACTA
25649313 TTACTGG
1 TTACTGG
25649320 CAGATTTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.03
27 27 0.90
28 2 0.07
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (27 bp):
TTACTGGTGGCTCTGCCACAATCACTA
Found at i:25649406 original size:32 final size:32
Alignment explanation
Indices: 25649366--25649450 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
25649356 GCGATGCTAA
25649366 TAATGGCTTTGTGTCGATCATAGT-ACCGTTAC
1 TAATGGCTTTGTGTCGATCATAGTGA-CGTTAC
* *
25649398 TAATGGCTTGGTG-CTGATCATATTGACGTTAC
1 TAATGGCTTTGTGTC-GATCATAGTGACGTTAC
** *
25649430 CGATGGCTATGTGTCGATCAT
1 TAATGGCTTTGTGTCGATCAT
25649451 TTCACTATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
31 1 0.02
32 41 0.93
33 2 0.05
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (32 bp):
TAATGGCTTTGTGTCGATCATAGTGACGTTAC
Found at i:25649468 original size:32 final size:31
Alignment explanation
Indices: 25649426--25649531 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 31
25649416 CATATTGACG
*
25649426 TTACCGATGGCTATGTGTCGATCATTTCACTA
1 TTACTGATGGCTATGTG-CGATCATTTCACTA
* * *
25649458 TTACTCATGGCTGTGTGCTGATCATATCACTA
1 TTACTGATGGCTATGTGC-GATCATTTCACTA
* * *
25649490 CTACTGATGGCTTTGTGCCGATCATGTT-ACCA
1 TTACTGATGGCTATGTG-CGATCAT-TTCACTA
25649522 TTACTGATGG
1 TTACTGATGG
25649532 TTGTGTACCG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
31 1 0.02
32 58 0.95
33 2 0.03
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACTGATGGCTATGTGCGATCATTTCACTA
Found at i:25649499 original size:64 final size:64
Alignment explanation
Indices: 25649431--25649577 Score: 188
Period size: 64 Copynumber: 2.3 Consensus size: 64
25649421 TGACGTTACC
* * * * *
25649431 GATGGCTATGTGTCGATCAT-TTCACTATTACTCATGGCTGTGTGCTGATCATATCACTACTACT
1 GATGGCTTTGTGCCGATCATGTT-ACCATTACTCATGGCTGTGTACCGATCATATCACTACTACT
* * * *
25649495 GATGGCTTTGTGCCGATCATGTTACCATTACTGATGGTTGTGTACCGGTCATATCACTGCTACT
1 GATGGCTTTGTGCCGATCATGTTACCATTACTCATGGCTGTGTACCGATCATATCACTACTACT
*
25649559 GATGGCTTTGTGCCAATCA
1 GATGGCTTTGTGCCGATCA
25649578 CATTACTGTA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
64 70 0.97
65 2 0.03
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (64 bp):
GATGGCTTTGTGCCGATCATGTTACCATTACTCATGGCTGTGTACCGATCATATCACTACTACT
Found at i:25649559 original size:32 final size:32
Alignment explanation
Indices: 25649444--25649569 Score: 119
Period size: 32 Copynumber: 3.9 Consensus size: 32
25649434 GGCTATGTGT
* * * * *
25649444 CGATCATTTCACTATTACTCATGGCTGTGTGC
1 CGATCATATCACTACTACTGATGGCTTTGTAC
* *
25649476 TGATCATATCACTACTACTGATGGCTTTGTGC
1 CGATCATATCACTACTACTGATGGCTTTGTAC
* * * *
25649508 CGATCATGTTACCATTACTGATGG-TTGTGTAC
1 CGATCATATCACTACTACTGATGGCTT-TGTAC
* *
25649540 CGGTCATATCACTGCTACTGATGGCTTTGT
1 CGATCATATCACTACTACTGATGGCTTTGT
25649570 GCCAATCACA
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
31 2 0.03
32 71 0.95
33 2 0.03
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (32 bp):
CGATCATATCACTACTACTGATGGCTTTGTAC
Found at i:25649613 original size:22 final size:21
Alignment explanation
Indices: 25649588--25649653 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
25649578 CATTACTGTA
25649588 CTTATGGCTTGTAGCCATTCTG
1 CTTATGGCTT-TAGCCATTCTG
* * *
25649610 CTTATAGCTTATAGCTATCCTG
1 CTTATGGCTT-TAGCCATTCTG
* *
25649632 TTTACGGCTCTTAGCCATTCTG
1 CTTATGGCT-TTAGCCATTCTG
25649654 ACTACTGGCA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
CTTATGGCTTTAGCCATTCTG
Found at i:25649676 original size:26 final size:26
Alignment explanation
Indices: 25649647--25649699 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
25649637 GGCTCTTAGC
* *
25649647 CATTCTGACTACTGGCAGCTCTACTG
1 CATTATGACTACTGGCAGCTATACTG
*
25649673 CATTATTACTACTGGCAGCTATACTG
1 CATTATGACTACTGGCAGCTATACTG
25649699 C
1 C
25649700 GATATTGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (26 bp):
CATTATGACTACTGGCAGCTATACTG
Found at i:25653231 original size:14 final size:14
Alignment explanation
Indices: 25653212--25653249 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
25653202 AAAATATCAG
25653212 AAAAAGAAAACGAA
1 AAAAAGAAAACGAA
* *
25653226 AAAAAGGAAACTAA
1 AAAAAGAAAACGAA
25653240 AAAAAGAAAA
1 AAAAAGAAAA
25653250 AGTAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAACGAA
Found at i:25655787 original size:28 final size:28
Alignment explanation
Indices: 25655755--25655812 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
25655745 TGACTCAAAG
25655755 ATTCTATATGTCCTAATCAAAGTGTAGC
1 ATTCTATATGTCCTAATCAAAGTGTAGC
25655783 ATTCTATATGTCCTAATCAAAGTGTAGC
1 ATTCTATATGTCCTAATCAAAGTGTAGC
25655811 AT
1 AT
25655813 AAAGCTAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (28 bp):
ATTCTATATGTCCTAATCAAAGTGTAGC
Found at i:25657946 original size:9 final size:9
Alignment explanation
Indices: 25657924--25657985 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
25657914 TCTAGTATAC
*
25657924 ATAAAAGAT
1 ATAAAAAAT
*
25657933 TTAAAAAAT
1 ATAAAAAAT
*
25657942 ATAAAAAAA
1 ATAAAAAAT
*
25657951 ATAAAATAT
1 ATAAAAAAT
*
25657960 ATAAAAAGT
1 ATAAAAAAT
*
25657969 -TTAAAAAT
1 ATAAAAAAT
25657977 AATAAAAAA
1 -ATAAAAAA
25657986 CAAATATAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
8 6 0.15
9 28 0.70
10 6 0.15
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:25657954 original size:27 final size:27
Alignment explanation
Indices: 25657924--25657983 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
25657914 TCTAGTATAC
*
25657924 ATAAAAGATTTAAAAAATATAAAAAAA
1 ATAAAAGATATAAAAAATATAAAAAAA
* * * *
25657951 ATAAAATATATAAAAAGTTTAAAAATA
1 ATAAAAGATATAAAAAATATAAAAAAA
25657978 ATAAAA
1 ATAAAA
25657984 AACAAATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (27 bp):
ATAAAAGATATAAAAAATATAAAAAAA
Found at i:25660557 original size:98 final size:97
Alignment explanation
Indices: 25660388--25660581 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 97
25660378 ATACAATAAA
* *
25660388 ACTTTTAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
25660453 CTTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CTTTTAGAATCCCAAACTCGGAATA-TTCCTTT
*
25660486 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAA-T
*
25660551 CC-TTTAGAATCTCAAACTCGGAATATTCCTT
65 CCTTTTAGAATCCCAAACTCGGAATATTCCTT
25660582 CATGATTTCT
Statistics
Matches: 91, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
97 6 0.07
98 82 0.90
99 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (97 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CTTTTAGAATCCCAAACTCGGAATATTCCTTT
Found at i:25662561 original size:44 final size:44
Alignment explanation
Indices: 25662498--25663098 Score: 312
Period size: 45 Copynumber: 13.7 Consensus size: 44
25662488 GATCTACCAG
* * * *
25662498 TCTGCTCTACTACAACTTCATGGAGATAGGATTGTCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTCGGCTTTAA
* * ** * *
25662542 TCTGCTCCACTGCAACTTCAGAGAGATAAGATTTTCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGT-CGGCTTTAA
* ** *
25662587 TTTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTGTTTTGC-TTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TTG-TCGGCTTTAA
* * *
25662632 TCTGCTCCACTGCAACTACAGGGAGATAAGACTAGAT--GC---GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-TCGGCTTTAA
* * * *
25662673 TCTACT-CTCTGCAACTTCAGGGAGATAAGATCTG-AGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTCGGCTTTAA
** * *
25662716 TCCACTCCACTGTAACTTCAGGGAGATAGGATTGTCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTCGGCTTTAA
* * ** * *
25662760 TCTGCTCCACTGTAACTTCAGGGAGATAAGATGTGCCTTCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTCGGCTTTAA
* ** *
25662805 TCTGC-CTCACTGCAACTTCA-AGAGGATAAGACTTGCTTTGC-TTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TTG-TCGGCTTTAA
* *
25662850 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGAT--GC---GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-TCGGCTTTAA
* * * * * *
25662891 TCTACT-CTCTGTAACTTCAAGGAGATAAGATCTG-AGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTCGGCTTTAA
** * *
25662934 TCCACTCCACTGTAACTTCAGGGAGATAGGATTGTCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTCGGCTTTAA
* * * ** * *
25662978 TATGCTCCACTGTAACTTCAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTCGGCTTTAA
* * ** *
25663023 CCTGC-CTCACTGCAACTTCA-GGAGGATAAGACTCGCTTTG-TTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TTG-TCGGCTTTAA
*
25663068 TCTGCTTCACTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
25663099 CTAGATGCGA
Statistics
Matches: 433, Mismatches: 88, Indels: 71
0.73 0.15 0.12
Matches are distributed among these distances:
39 2 0.00
40 47 0.11
41 10 0.02
43 20 0.05
44 153 0.35
45 184 0.42
46 16 0.04
47 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTCGGCTTTAA
Found at i:25662889 original size:218 final size:218
Alignment explanation
Indices: 25662511--25663180 Score: 1124
Period size: 218 Copynumber: 3.1 Consensus size: 218
25662501 GCTCTACTAC
* * *
25662511 AACTTCATGGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTT
1 AACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTT
* * *
25662576 TCCATCTTCAGTTTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTTGCTTAGTCTGCTCCA
66 GCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCA
*
25662641 CTGCAACTACAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAGGGAGATAAGATCT
131 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAGGGAGATAAGATCT
25662706 GAGGTTTTAATCCACTCCACTGT
196 GAGGTTTTAATCCACTCCACTGT
*
25662729 AACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATGT
1 AACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTT
* *
25662794 GCCTTCTTCAGTCTGCCTCACTGCAACTTCAAGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCA
66 GCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCA
* *
25662859 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGTAACTTCAAGGAGATAAGATCT
131 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAGGGAGATAAGATCT
25662924 GAGGTTTTAATCCACTCCACTGT
196 GAGGTTTTAATCCACTCCACTGT
*
25662947 AACTTCAGGGAGATAGGATTGTCGGCTTTAATATGCTCCACTGTAACTTCAGGGAGATAAGATTT
1 AACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTT
* * * *
25663012 GCCATCTTCAGCCTGCCTCACTGCAACTTCAGGAGGATAAGACTCGCTTTGTTTAGTCTGCTTCA
66 GCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCA
* *
25663077 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
131 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAGGGAGATAAGATCT
* **
25663142 GAGGTTTTAATCCGCTCCACTAC
196 GAGGTTTTAATCCACTCCACTGT
* *
25663165 AACTTTAAGGAGATAG
1 AACTTCAGGGAGATAG
25663181 AAATCAATTT
Statistics
Matches: 423, Mismatches: 29, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
218 423 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (218 bp):
AACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTT
GCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCA
CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAGGGAGATAAGATCT
GAGGTTTTAATCCACTCCACTGT
Found at i:25702643 original size:11 final size:11
Alignment explanation
Indices: 25702614--25702649 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
25702604 TAGTAGTTTC
*
25702614 TTCAAAAAAAT
1 TTCAAAAAAAA
25702625 TTCGAAAAAAAA
1 TTC-AAAAAAAA
25702637 TTCAAAAAAAA
1 TTCAAAAAAAA
25702648 TT
1 TT
25702650 TGGTTTCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.25
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:25702709 original size:14 final size:15
Alignment explanation
Indices: 25702687--25702725 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
25702677 GATATCAAGT
*
25702687 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTAG
25702702 TGAAAAAAAAATTAG
1 TGAAAAAAAAATTAG
25702717 TGAAAAAAA
1 TGAAAAAAA
25702726 GAAGAAGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.18
Consensus pattern (15 bp):
TGAAAAAAAAATTAG
Found at i:25705689 original size:6 final size:7
Alignment explanation
Indices: 25705653--25705688 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
25705643 CTTGTAAAAG
25705653 GACTTTT
1 GACTTTT
25705660 GACTTTT
1 GACTTTT
25705667 GACTTTT
1 GACTTTT
25705674 GACTTTT
1 GACTTTT
25705681 GA-TTTT
1 GACTTTT
25705687 GA
1 GA
25705689 TCATTTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.56
Consensus pattern (7 bp):
GACTTTT
Found at i:25705695 original size:14 final size:14
Alignment explanation
Indices: 25705653--25705696 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
25705643 CTTGTAAAAG
*
25705653 GACTTTTGACTTTT
1 GACTTTTGACATTT
*
25705667 GACTTTTGACTTTT
1 GACTTTTGACATTT
25705681 GA-TTTTGATCATTT
1 GACTTTTGA-CATTT
25705695 GA
1 GA
25705697 ATGAACTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (14 bp):
GACTTTTGACATTT
Found at i:25706373 original size:13 final size:12
Alignment explanation
Indices: 25706308--25706373 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 12
25706298 AATAAAATCG
25706308 AAAAAAAG-GAA
1 AAAAAAAGTGAA
25706319 AAAAAAAGTGACA
1 AAAAAAAGTGA-A
*
25706332 AAAAAATCGAGTTAA
1 AAAAAA---AGTGAA
**
25706347 AAAAAAAGAAAA
1 AAAAAAAGTGAA
25706359 AAACAAAAGTGAA
1 AAA-AAAAGTGAA
25706372 AA
1 AA
25706374 GTCTTGTGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 8 0.18
12 9 0.20
13 16 0.36
15 7 0.16
16 4 0.09
ACGTcount: A:0.74, C:0.05, G:0.14, T:0.08
Consensus pattern (12 bp):
AAAAAAAGTGAA
Found at i:25711607 original size:7 final size:7
Alignment explanation
Indices: 25711570--25711606 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
25711560 CTTGTAAAAG
25711570 GACTTTT
1 GACTTTT
25711577 GACTTTT
1 GACTTTT
25711584 GACTTTT
1 GACTTTT
25711591 GACTTTT
1 GACTTTT
*
25711598 GATTTTT
1 GACTTTT
25711605 GA
1 GA
25711607 TCATTTGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (7 bp):
GACTTTT
Found at i:25719338 original size:12 final size:12
Alignment explanation
Indices: 25719318--25719366 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
25719308 ATATTACAGT
*
25719318 ATTGTAAAAAAA
1 ATTGAAAAAAAA
*
25719330 ATTGAAAAAAAT
1 ATTGAAAAAAAA
*
25719342 TTTGAAAAAAAA
1 ATTGAAAAAAAA
*
25719354 ATTCAAAAAAAA
1 ATTGAAAAAAAA
25719366 A
1 A
25719367 GTTTGTATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.22
Consensus pattern (12 bp):
ATTGAAAAAAAA
Found at i:25727152 original size:30 final size:30
Alignment explanation
Indices: 25727116--25727212 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25727106 AACTCACTCC
25727116 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
25727146 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
25727176 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
25727206 TAGCTCA
1 TAGCTCA
25727213 TTTTCTCTCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:25727269 original size:6 final size:6
Alignment explanation
Indices: 25727253--25727302 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
25727243 TTTCTTTTTA
*
25727253 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
25727302 T
1 T
25727303 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Done.