Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 121 of 167
Found at i:40480021 original size:10 final size:10
Alignment explanation
Indices: 40480006--40480043 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
40479996 TATGTTTAGT
40480006 TTTAATTAAG
1 TTTAATTAAG
40480016 TTTAATTAA-
1 TTTAATTAAG
40480025 TTTAATTAAG
1 TTTAATTAAG
*
40480035 ATTAATTAA
1 TTTAATTAA
40480044 TTACTAACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (10 bp):
TTTAATTAAG
Found at i:40480030 original size:19 final size:19
Alignment explanation
Indices: 40480006--40480045 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
40479996 TATGTTTAGT
*
40480006 TTTAATTAAGTTTAATTAA
1 TTTAATTAAGATTAATTAA
40480025 TTTAATTAAGATTAATTAA
1 TTTAATTAAGATTAATTAA
40480044 TT
1 TT
40480046 ACTAACCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTAATTAAGATTAATTAA
Found at i:40481264 original size:115 final size:118
Alignment explanation
Indices: 40481109--40481405 Score: 302
Period size: 120 Copynumber: 2.5 Consensus size: 118
40481099 GTATACCAAA
* * * * **
40481109 GATATTTGTGACACAGGTTTAG-CTCGGA-TGAGTAATCTGATGTCAATTTAAAGGTTTAGACT-
1 GATACTTGGGACATAGGTTTAGCCT-GGACT-AGTAACCTGATGTCGTTTTAAAGGTTTAG-CTC
* * ** *
40481171 AAACAAGTAACCTG-A-CAT-TATTTTCAGCTTGGATGAGCAATTGAT-TTATCAAG
63 AAACAAGTAACCTGCAGCATATATTTTCAACTAGGACAAACAATTGATGTT-TCAAG
* *
40481224 GATACTTGGGACATAGGTTTAGCCTGGACTAGTAACCTGATGTCGTTTTAAAGATTTAGCTCGAA
1 GATACTTGGGACATAGGTTTAGCCTGGACTAGTAACCTGATGTCGTTTTAAAGGTTTAGCTCAAA
* * *
40481289 CAAGTAACTTGTCATGTATATATTTTCAACTAGGACAAACAATTGATGTTTCGAG
66 CAAGTAACCTG-CA-GCATATATTTTCAACTAGGACAAACAATTGATGTTTCAAG
* ** * *
40481344 AATACTTGGGACATAGGTTTAGCCTAAACTGGTAACTTGATGTCGTTTTAAAGGTTTAGCTC
1 GATACTTGGGACATAGGTTTAGCCTGGACTAGTAACCTGATGTCGTTTTAAAGGTTTAGCTC
40481406 GGACGAGTAA
Statistics
Matches: 151, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
114 2 0.01
115 59 0.39
116 3 0.02
117 1 0.01
119 2 0.01
120 82 0.54
121 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (118 bp):
GATACTTGGGACATAGGTTTAGCCTGGACTAGTAACCTGATGTCGTTTTAAAGGTTTAGCTCAAA
CAAGTAACCTGCAGCATATATTTTCAACTAGGACAAACAATTGATGTTTCAAG
Found at i:40481363 original size:120 final size:120
Alignment explanation
Indices: 40481208--40481431 Score: 333
Period size: 120 Copynumber: 1.9 Consensus size: 120
40481198 CTTGGATGAG
* **
40481208 CAATTGATTTATCAAGGATACTTGGGACATAGGTTTAGCCTGGACTAGTAACCTGATGTCGTTTT
1 CAATTGATTTATCAAGAATACTTGGGACATAGGTTTAGCCTAAACTAGTAACCTGATGTCGTTTT
*
40481273 AAAGATTTAGCTCGAACAAGTAACTTGTCATGTATATATTTTCAACTAGGACAAA
66 AAAGATTTAGCTCGAACAAGTAACTTGACATGTATATATTTTCAACTAGGACAAA
* * *
40481328 CAATTGATGTT-TCGAGAATACTTGGGACATAGGTTTAGCCTAAACTGGTAACTTGATGTCGTTT
1 CAATTGAT-TTATCAAGAATACTTGGGACATAGGTTTAGCCTAAACTAGTAACCTGATGTCGTTT
* * * *
40481392 TAAAGGTTTAGCTCGGACGAGTAACTTGACATGTGTATAT
65 TAAAGATTTAGCTCGAACAAGTAACTTGACATGTATATAT
40481432 ATATTAAACT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
120 90 0.98
121 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (120 bp):
CAATTGATTTATCAAGAATACTTGGGACATAGGTTTAGCCTAAACTAGTAACCTGATGTCGTTTT
AAAGATTTAGCTCGAACAAGTAACTTGACATGTATATATTTTCAACTAGGACAAA
Found at i:40498156 original size:18 final size:18
Alignment explanation
Indices: 40498133--40498168 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40498123 TCACACTACT
*
40498133 GTGTATCACCATACGGCC
1 GTGTATCACCACACGGCC
*
40498151 GTGTATCGCCACACGGCC
1 GTGTATCACCACACGGCC
40498169 TCCACATGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.36, G:0.25, T:0.19
Consensus pattern (18 bp):
GTGTATCACCACACGGCC
Found at i:40506558 original size:16 final size:16
Alignment explanation
Indices: 40506537--40506604 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
40506527 ATGTAAANGC
40506537 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40506553 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
40506569 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
40506585 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
40506601 TGTA
1 TGTA
40506605 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40506644 original size:45 final size:41
Alignment explanation
Indices: 40506585--40506694 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 41
40506575 GGATTAGAGG
*
40506585 TGTATTGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGG-T
* * ***
40506627 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
40506670 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
40506695 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.39
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
Found at i:40506857 original size:16 final size:16
Alignment explanation
Indices: 40506820--40506861 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40506810 TTAATCATAT
*
40506820 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
40506836 TT-AAATATATTATAA
1 TTAAAATATATTATAA
40506851 TTAAAATATAT
1 TTAAAATATAT
40506862 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:40506868 original size:14 final size:15
Alignment explanation
Indices: 40506829--40506870 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40506819 TTTAAACATA
*
40506829 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40506844 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40506858 A-TATAATTTAATA
1 ATTATAATTAAATA
40506871 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40514977 original size:19 final size:20
Alignment explanation
Indices: 40514955--40514994 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40514945 ATATAATTTT
*
40514955 TTTAAAAAT-AAAATAAAAA
1 TTTAAAAATCAAAAAAAAAA
*
40514974 TTTAAAATTCAAAAAAAAAA
1 TTTAAAAATCAAAAAAAAAA
40514994 T
1 T
40514995 CTCAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
TTTAAAAATCAAAAAAAAAA
Found at i:40517675 original size:21 final size:21
Alignment explanation
Indices: 40517631--40517714 Score: 105
Period size: 21 Copynumber: 4.0 Consensus size: 21
40517621 ACGAGCTGCT
* ** *
40517631 CACACGGGCATGTGTCCCCGC
1 CACACGGGCGTGTGTGGCCTC
* *
40517652 CACATGGGCGTGCGTGGCCTC
1 CACACGGGCGTGTGTGGCCTC
*
40517673 CACACAGGCGTGTGTGGCCTC
1 CACACGGGCGTGTGTGGCCTC
40517694 CACACGGGCGTGTGTGGCCTC
1 CACACGGGCGTGTGTGGCCTC
40517715 TACATGAGCG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.12, C:0.36, G:0.35, T:0.18
Consensus pattern (21 bp):
CACACGGGCGTGTGTGGCCTC
Found at i:40517725 original size:21 final size:21
Alignment explanation
Indices: 40517651--40517727 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
40517641 TGTGTCCCCG
* *
40517651 CCACATGGGCGTGCGTGGCCT
1 CCACATGAGCGTGTGTGGCCT
*
40517672 CCACA-CAGGCGTGTGTGGCCT
1 CCACATGA-GCGTGTGTGGCCT
* *
40517693 CCACACGGGCGTGTGTGGCCT
1 CCACATGAGCGTGTGTGGCCT
*
40517714 CTACATGAGCGTGT
1 CCACATGAGCGTGT
40517728 AGACCCCTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.13, C:0.31, G:0.35, T:0.21
Consensus pattern (21 bp):
CCACATGAGCGTGTGTGGCCT
Found at i:40525883 original size:25 final size:26
Alignment explanation
Indices: 40525849--40525899 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
40525839 TTAGAGAAAT
40525849 GGACTAAGTGATC-TTTAATGCAAAA
1 GGACTAAGTGATCTTTTAATGCAAAA
40525874 GGACTAAGTGATCTTTTAATGCAAAA
1 GGACTAAGTGATCTTTTAATGCAAAA
40525900 CTGAATTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (26 bp):
GGACTAAGTGATCTTTTAATGCAAAA
Found at i:40526589 original size:20 final size:19
Alignment explanation
Indices: 40526560--40526597 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
40526550 AAAGTAGTCT
*
40526560 AATTTATTTTCTTAGAATA
1 AATTTATTTTCTGAGAATA
40526579 AATTCTATTTTCTGAGAAT
1 AATT-TATTTTCTGAGAAT
40526598 TACAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (19 bp):
AATTTATTTTCTGAGAATA
Found at i:40536422 original size:215 final size:215
Alignment explanation
Indices: 40536051--40536483 Score: 785
Period size: 215 Copynumber: 2.0 Consensus size: 215
40536041 AATATTATAT
40536051 TTTTGTCTGCTAATTGAATGCTCATCCTAGTCTGTTTGGGTTTCCCAAGACCTAGTTGTTTAAAC
1 TTTTGTCTGCTAATTGAATGCTCATCCTAGTCTGTTTGGGTTTCCCAAGACCTAGTTGTTTAAAC
* *
40536116 ATTTTGTAAGGCATGACGTTAATACTAGTCCCTAAATCAGCTAGTGCATTATTAACTTCTAAACT
66 ATTTTGTAAGGCATGACGTTAATACTAGTCCCTAAATCAGCTAATGCATTATTAACATCTAAACT
*
40536181 ACCAATTAAGCAAGGAATTGTAAAACTCCCTAGATCTTTGAATTTGTTGGGTACTTTATTCTGTA
131 ACCAATTAAGCAAGGAATTGTAAAACTCCCTAGATCTTTCAATTTGTTGGGTACTTTATTCTGTA
*
40536246 GAATAGCAGAGCAAACTGCG
196 GAATAGCAGAGCAAACCGCG
*
40536266 TTTTGTCTGCTAATTGAATGCTCATCCTAGTCTGTTTGGGTTTCCCAAGACCTAGTTGTTTCAAC
1 TTTTGTCTGCTAATTGAATGCTCATCCTAGTCTGTTTGGGTTTCCCAAGACCTAGTTGTTTAAAC
*
40536331 ATTTTGTAAGGCATGATGTTAATACTAGTCCCTAAATCAGCTAATGCATTATTAACATCTAAACT
66 ATTTTGTAAGGCATGACGTTAATACTAGTCCCTAAATCAGCTAATGCATTATTAACATCTAAACT
* * *
40536396 ACCAATTAAGCAAGGAATTGTAAAACTCCTTGGATCTTTCAATTTGTTGGGTAGTTTATTCTGTA
131 ACCAATTAAGCAAGGAATTGTAAAACTCCCTAGATCTTTCAATTTGTTGGGTACTTTATTCTGTA
40536461 GAATAGCAGAGCAAACCGCG
196 GAATAGCAGAGCAAACCGCG
40536481 TTT
1 TTT
40536484 AGCTTCACAT
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
215 209 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (215 bp):
TTTTGTCTGCTAATTGAATGCTCATCCTAGTCTGTTTGGGTTTCCCAAGACCTAGTTGTTTAAAC
ATTTTGTAAGGCATGACGTTAATACTAGTCCCTAAATCAGCTAATGCATTATTAACATCTAAACT
ACCAATTAAGCAAGGAATTGTAAAACTCCCTAGATCTTTCAATTTGTTGGGTACTTTATTCTGTA
GAATAGCAGAGCAAACCGCG
Found at i:40538282 original size:19 final size:19
Alignment explanation
Indices: 40538245--40538282 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40538235 ACCTACCAGA
*
40538245 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
40538264 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
40538283 TAAATTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:40540851 original size:82 final size:82
Alignment explanation
Indices: 40540714--40540878 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
40540704 ACAATTTTAG
* *
40540714 GGAATCATGACTGCGGACCCAAATCAACTTTTAAAGTGTTTCTTACAAATTTGCGATACATTCAA
1 GGAATCATGACTGCGAACCCAAATCAACGTTTAAAGTGTTTCTTACAAATTTGCGATACATTCAA
*
40540779 ATTTAATAGTGCCACTA
66 ATTTAATAGAGCCACTA
40540796 GGAATCATGACTGCGAACCCAAATCAACGTTTAAAGTGTTTCTTACAAATTTGCGATACATTCAA
1 GGAATCATGACTGCGAACCCAAATCAACGTTTAAAGTGTTTCTTACAAATTTGCGATACATTCAA
*
40540861 ATTTAATAGAGTCACTA
66 ATTTAATAGAGCCACTA
40540878 G
1 G
40540879 TGACACTATT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (82 bp):
GGAATCATGACTGCGAACCCAAATCAACGTTTAAAGTGTTTCTTACAAATTTGCGATACATTCAA
ATTTAATAGAGCCACTA
Found at i:40543797 original size:9 final size:9
Alignment explanation
Indices: 40543783--40543893 Score: 116
Period size: 9 Copynumber: 12.4 Consensus size: 9
40543773 TGTGGTTAAA
40543783 AATTAACCG
1 AATTAACCG
**
40543792 AATTAAATG
1 AATTAACCG
*
40543801 AGTTAACCG
1 AATTAACCG
40543810 AATTAACCG
1 AATTAACCG
40543819 AATTAACCG
1 AATTAACCG
*
40543828 GATTAACCG
1 AATTAACCG
* *
40543837 GATTAATCG
1 AATTAACCG
* **
40543846 GATTAATTG
1 AATTAACCG
*
40543855 AATTAACTG
1 AATTAACCG
40543864 AATTAACCG
1 AATTAACCG
40543873 AATTAACCG
1 AATTAACCG
*
40543882 AA-TACCCG
1 AATTAACCG
40543890 AATT
1 AATT
40543894 GAATCACTAC
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
8 7 0.08
9 81 0.92
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:40543943 original size:20 final size:20
Alignment explanation
Indices: 40543893--40543981 Score: 73
Period size: 17 Copynumber: 4.8 Consensus size: 20
40543883 ATACCCGAAT
40543893 TGAATCACTACATAA-T-TA
1 TGAATCACTACATAAGTCTA
* * * *
40543911 -AAAACATTACATAAGTCTT
1 TGAATCACTACATAAGTCTA
40543930 TGAATCACTACATAA-T-TA
1 TGAATCACTACATAAGTCTA
** *
40543948 AAAAT-ATTACATAAGTCTA
1 TGAATCACTACATAAGTCTA
40543967 TGAATCACTACATAA
1 TGAATCACTACATAA
40543982 TTAAAAACAT
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
17 19 0.37
18 6 0.12
19 7 0.14
20 19 0.37
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (20 bp):
TGAATCACTACATAAGTCTA
Found at i:40544023 original size:72 final size:72
Alignment explanation
Indices: 40543892--40544041 Score: 266
Period size: 72 Copynumber: 2.1 Consensus size: 72
40543882 AATACCCGAA
*
40543892 TTGAATCACTACATAATTAAAAACATTACATAAGTCTTTGAATCACTACATAATTAAAAATATTA
1 TTGAATCACTACATAATTAAAAACATTACA-AAGTCTTTGAATCACTACATAATTAAAAACATTA
40543957 CATAAGTC
65 CATAAGTC
40543965 TATGAATCACTACATAATTAAAAACATTAC-AAGTCTTTGAATCACTACATAATTAAAAACATTA
1 T-TGAATCACTACATAATTAAAAACATTACAAAGTCTTTGAATCACTACATAATTAAAAACATTA
40544029 CATAAGTC
65 CATAAGTC
40544037 TTGAA
1 TTGAA
40544042 ATTAACACAT
Statistics
Matches: 75, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
71 4 0.05
72 42 0.56
73 1 0.01
74 28 0.37
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (72 bp):
TTGAATCACTACATAATTAAAAACATTACAAAGTCTTTGAATCACTACATAATTAAAAACATTAC
ATAAGTC
Found at i:40544055 original size:37 final size:37
Alignment explanation
Indices: 40543892--40544038 Score: 262
Period size: 37 Copynumber: 4.0 Consensus size: 37
40543882 AATACCCGAA
40543892 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
40543929 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
40543966 ATGAATCACTACATAATTAAAAACATTAC--AAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
40544001 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
40544038 T
1 T
40544039 GAAATTAACA
Statistics
Matches: 104, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
35 34 0.33
37 70 0.67
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:40546497 original size:19 final size:20
Alignment explanation
Indices: 40546461--40546519 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 20
40546451 ACAAGAAAAA
40546461 AATTATATAATAACTTAAAATAC
1 AATT-TATAAT-A-TTAAAATAC
40546484 -ATTTATAATATTAAAATAC
1 AATTTATAATATTAAAATAC
40546503 ATATTTATAATATTAAA
1 A-ATTTATAATATTAAA
40546520 CAATTTTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.26
20 1 0.03
21 21 0.62
22 3 0.09
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTATAATATTAAAATAC
Found at i:40546587 original size:12 final size:11
Alignment explanation
Indices: 40546567--40546600 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
40546557 AGAATACTTG
40546567 TTAAATAAAAT
1 TTAAATAAAAT
*
40546578 TTATAATAAAAA
1 TTA-AATAAAAT
40546590 TTAAATAAAAT
1 TTAAATAAAAT
40546601 ATTGGTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TTAAATAAAAT
Found at i:40547157 original size:14 final size:14
Alignment explanation
Indices: 40547138--40547167 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40547128 TTAGTTTTAG
40547138 TAGATTTTTACTTT
1 TAGATTTTTACTTT
*
40547152 TAGATTTTTATTTT
1 TAGATTTTTACTTT
40547166 TA
1 TA
40547168 TTTATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (14 bp):
TAGATTTTTACTTT
Found at i:40554423 original size:16 final size:16
Alignment explanation
Indices: 40554398--40554445 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
40554388 AATTTTATTA
40554398 AATTAT-ATATATTTT
1 AATTATAATATATTTT
40554413 AATTATAATATA-TTT
1 AATTATAATATATTTT
*
40554428 AATAATAAT-TATGTTT
1 AATTATAATATAT-TTT
40554444 AA
1 AA
40554446 ATATGATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 2 0.07
15 17 0.59
16 10 0.34
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AATTATAATATATTTT
Found at i:40554433 original size:18 final size:15
Alignment explanation
Indices: 40554398--40554427 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40554388 AATTTTATTA
40554398 AATTATATATATTTT
1 AATTATATATATTTT
40554413 AATTATAATATATTT
1 AATTAT-ATATATTT
40554428 AATAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTATATATATTTT
Found at i:40554671 original size:45 final size:43
Alignment explanation
Indices: 40554571--40554680 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
40554561 TTTTCCATTA
40554571 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
40554610 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
40554655 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
40554681 CTTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:40554686 original size:16 final size:16
Alignment explanation
Indices: 40554661--40554728 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
40554651 GATTTGCTAT
*
40554661 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
* *
40554677 TACACTTCTAATCCAT
1 TACACCTCTAATCCAA
40554693 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40554709 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40554725 TACA
1 TACA
40554729 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40555527 original size:29 final size:29
Alignment explanation
Indices: 40555495--40555553 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
40555485 AACGTTTTCT
40555495 CTTCACTCCACAGGTTTTAAAAACCTTAC
1 CTTCACTCCACAGGTTTTAAAAACCTTAC
40555524 CTTCACTCCACAGGTTTTAAAAACCTTAC
1 CTTCACTCCACAGGTTTTAAAAACCTTAC
40555553 C
1 C
40555554 CTTTTCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.32, G:0.07, T:0.31
Consensus pattern (29 bp):
CTTCACTCCACAGGTTTTAAAAACCTTAC
Found at i:40557258 original size:95 final size:96
Alignment explanation
Indices: 40557033--40557274 Score: 221
Period size: 94 Copynumber: 2.6 Consensus size: 96
40557023 AATTCTTTTC
* * *
40557033 TAATTTTTTTCTCGGTTTAATAAAATTATTGACTTTTAATTGGTTATATTATGGATTGATAGCAT
1 TAATTTTTTTCTCGGTTTAATAAAAGTATTTAATTTTAATTGGTTATATTATGGATTGATAGCAT
* *
40557098 CAATACACTGACACAATTATGGGTTGACCTT
66 CAATACACTGACACAATTATGGATTAACCTT
* * ** ** *** ** *
40557129 TGATTTTTTTTTCTAATTTTTTCCTAG-AAGTAATTTT-ATTGGTTATATTATGGATTGATAGTA
1 TAATTTTTTTCTC-GGTTTAATAAAAGTATTTAATTTTAATTGGTTATATTATGGATTGATAGCA
*** *
40557192 T-AATACACTGTTGCAATTATGGATTAACTTT
65 TCAATACACTGACACAATTATGGATTAACCTT
*
40557223 TAATTTTTTTCTCGGTTTAATAGAAG----T-ATTTTAATTGGTTATATTATGGATT
1 TAATTTTTTTCTCGGTTTAATAAAAGTATTTAATTTTAATTGGTTATATTATGGATT
40557275 AACTTTTAAC
Statistics
Matches: 114, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
89 5 0.04
90 20 0.18
93 6 0.05
94 35 0.31
95 26 0.23
96 17 0.15
97 5 0.04
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (96 bp):
TAATTTTTTTCTCGGTTTAATAAAAGTATTTAATTTTAATTGGTTATATTATGGATTGATAGCAT
CAATACACTGACACAATTATGGATTAACCTT
Found at i:40557272 original size:58 final size:58
Alignment explanation
Indices: 40557207--40557357 Score: 257
Period size: 58 Copynumber: 2.6 Consensus size: 58
40557197 CACTGTTGCA
*
40557207 ATTATGGATTAACTTTTAATTTTTTTCTCGGTTTAATAGAAGTATTTTAATTGGTTAT
1 ATTATGGATTAACTTTTAATTTTTTTCTCGGTTTAATAGAAGTATTTTAATTGGTTAC
*
40557265 ATTATGGATTAACTTTTAACTTTTTTCTCGGTTTAATAGAAGTATTTTAATTGGTTAC
1 ATTATGGATTAACTTTTAATTTTTTTCTCGGTTTAATAGAAGTATTTTAATTGGTTAC
* * *
40557323 ATTATTGATTGACTTTTAATTTTTTTCTCGATTTA
1 ATTATGGATTAACTTTTAATTTTTTTCTCGGTTTA
40557358 GATAACATGA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 87 1.00
ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54
Consensus pattern (58 bp):
ATTATGGATTAACTTTTAATTTTTTTCTCGGTTTAATAGAAGTATTTTAATTGGTTAC
Found at i:40557681 original size:14 final size:14
Alignment explanation
Indices: 40557662--40557688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40557652 AACCTTTTAT
40557662 ATAATAAAATATTA
1 ATAATAAAATATTA
40557676 ATAATAAAATATT
1 ATAATAAAATATT
40557689 GAACTTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATAAAATATTA
Found at i:40558318 original size:25 final size:26
Alignment explanation
Indices: 40558267--40558318 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
40558257 TTATTATTAT
*
40558267 TTTTATTAAAATATATTTAACAATAA
1 TTTTATTAAAATATATATAACAATAA
*
40558293 TTTTATTAAAATTTA-ATAACAATAA
1 TTTTATTAAAATATATATAACAATAA
40558318 T
1 T
40558319 CATCCACGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTTATTAAAATATATATAACAATAA
Found at i:40564350 original size:22 final size:21
Alignment explanation
Indices: 40564321--40564387 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 21
40564311 TGCATTAATG
40564321 AACAGAGAGCACTGAAGTGCT
1 AACAGAGAGCACTGAAGTGCT
*
40564342 ATACAGAGAGCAC-AAATGTGCT
1 A-ACAGAGAGCACTGAA-GTGCT
*
40564364 AATCAGAGAGCACTGACGTGCT
1 AA-CAGAGAGCACTGAAGTGCT
40564386 AA
1 AA
40564388 ATATCAGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.16
Consensus pattern (21 bp):
AACAGAGAGCACTGAAGTGCT
Found at i:40564400 original size:25 final size:24
Alignment explanation
Indices: 40564365--40564475 Score: 143
Period size: 25 Copynumber: 4.5 Consensus size: 24
40564355 AAATGTGCTA
* *
40564365 ATCAGAGAGCACTGACGTGCTAAAT
1 ATCAGAAAGCACTGGCGTGCT-AAT
40564390 ATCAGAAAGCACTGGCGTGCTAAT
1 ATCAGAAAGCACTGGCGTGCTAAT
40564414 AATCAGAAAGCACTGGCGTGCTAAT
1 -ATCAGAAAGCACTGGCGTGCTAAT
40564439 ATTCA-AAGAGCACTGGCGTGCTAAT
1 A-TCAGAA-AGCACTGGCGTGCTAAT
*
40564464 ATTCAGAGAGCA
1 A-TCAGAAAGCA
40564476 TGCTGAGGTC
Statistics
Matches: 79, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
24 6 0.08
25 72 0.91
26 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (24 bp):
ATCAGAAAGCACTGGCGTGCTAAT
Found at i:40564426 original size:50 final size:50
Alignment explanation
Indices: 40564363--40564475 Score: 167
Period size: 50 Copynumber: 2.3 Consensus size: 50
40564353 ACAAATGTGC
40564363 TAATCAGAGAGCACTGACGTGCTAA-ATATCAGAA-AGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGACGTGCTAATAT-TCA-AAGAGCACTGGCGTGCTAA
* *
40564413 TAATCAGAAAGCACTGGCGTGCTAATATTCAAAGAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGACGTGCTAATATTCAAAGAGCACTGGCGTGCTAA
*
40564463 TATTCAGAGAGCA
1 TAATCAGAGAGCA
40564476 TGCTGAGGTC
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
49 2 0.04
50 53 0.93
51 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (50 bp):
TAATCAGAGAGCACTGACGTGCTAATATTCAAAGAGCACTGGCGTGCTAA
Found at i:40566396 original size:49 final size:49
Alignment explanation
Indices: 40566338--40566435 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
40566328 AATTTCACAG
*
40566338 GTCATACAATTCAGTCCTTGCTCAATTAGACCATCTATTAAGCTAATTT
1 GTCATACAATTCAGTCCTTGCTCAATTAGACCATCTATTAAACTAATTT
40566387 GTCATACAATTCAGTCCTTGCTCAATTAGACCATCTATTAAACTAATTT
1 GTCATACAATTCAGTCCTTGCTCAATTAGACCATCTATTAAACTAATTT
40566436 TTCTCAATTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (49 bp):
GTCATACAATTCAGTCCTTGCTCAATTAGACCATCTATTAAACTAATTT
Found at i:40572051 original size:32 final size:33
Alignment explanation
Indices: 40572005--40572075 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 33
40571995 ACATGAGTCT
* *
40572005 AGTTTCAAGGAAAATTAACAGAACTTAA-TTTG
1 AGTTTCAAGAAAAATTAACAAAACTTAATTTTG
40572037 AGTTTCAAGAAAAATTAACAAAACTTAATTTTG
1 AGTTTCAAGAAAAATTAACAAAACTTAATTTTG
40572070 AGTTTC
1 AGTTTC
40572076 GTAGCTCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 26 0.72
33 10 0.28
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (33 bp):
AGTTTCAAGAAAAATTAACAAAACTTAATTTTG
Found at i:40572906 original size:43 final size:43
Alignment explanation
Indices: 40572859--40572948 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 43
40572849 ACGGGCAAGA
* ** *
40572859 GACACGGTCATGTGTCTCAGCCGTATGAAGGACACGGTCATAG
1 GACACGGGCATGTACCTCAGCCGTATGAAGGACACGATCATAG
* **
40572902 GACACGGGCGTGTACCTTGGCCGTATGAAGGACACGATCATAG
1 GACACGGGCATGTACCTCAGCCGTATGAAGGACACGATCATAG
40572945 GACA
1 GACA
40572949 TGAGCGTGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.19
Consensus pattern (43 bp):
GACACGGGCATGTACCTCAGCCGTATGAAGGACACGATCATAG
Found at i:40572956 original size:43 final size:43
Alignment explanation
Indices: 40572878--40572968 Score: 146
Period size: 43 Copynumber: 2.1 Consensus size: 43
40572868 ATGTGTCTCA
* *
40572878 GCCGTATGAAGGACACGGTCATAGGACACGGGCGTGTACCTTG
1 GCCGTATGAAGGACACGATCATAGGACACGAGCGTGTACCTTG
* *
40572921 GCCGTATGAAGGACACGATCATAGGACATGAGCGTGTGCCTTG
1 GCCGTATGAAGGACACGATCATAGGACACGAGCGTGTACCTTG
40572964 GCCGT
1 GCCGT
40572969 GTAGCTTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.20
Consensus pattern (43 bp):
GCCGTATGAAGGACACGATCATAGGACACGAGCGTGTACCTTG
Found at i:40574027 original size:48 final size:48
Alignment explanation
Indices: 40573963--40574192 Score: 217
Period size: 48 Copynumber: 4.9 Consensus size: 48
40573953 CAGTGCAGGT
*
40573963 GATATGT-ACGCCAGTGTAAGACATGTCTGGGACATGCATCAGTCTCGA
1 GATATGTGA-GCCAGTGTAAGACATGTCTGGGACATGCATCAGACTCGA
* * * *
40574011 GATATGTGTGCTAGTGTAAGACATGTTTGGGACATGCATC-GGC-C-A
1 GATATGTGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGACTCGA
* * * *
40574056 CAT-TGTGAAAGCCAGTGTAAGACATGTCTGGGACATACAT-TGACTTTGA
1 GATATGTG--AGCCAGTGTAAGACATGTCTGGGACATGCATCAGAC-TCGA
* *
40574105 G--ATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCA-ACCTTGA
1 GATATGTGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGA-CTCGA
* * * *
40574151 GATATGTGTGCTAGTGTAATACATGTCTAGGACATGCATCAG
1 GATATGTGAGCCAGTGTAAGACATGTCTGGGACATGCATCAG
40574193 CCACATCGTG
Statistics
Matches: 149, Mismatches: 20, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
44 4 0.03
45 3 0.02
46 66 0.44
47 3 0.02
48 72 0.48
49 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (48 bp):
GATATGTGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGACTCGA
Found at i:40574088 original size:46 final size:45
Alignment explanation
Indices: 40573972--40574239 Score: 186
Period size: 46 Copynumber: 5.7 Consensus size: 45
40573962 TGATATGTAC
* * *
40573972 GCCAGTGTAAGACATGTCTGGGACATGCATCAGTCTCGAGATATGTG-T
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GGC-C-ACAT-TGTGAA
* *
40574020 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCCACATTGTGAAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTGTG-AA
* * *
40574066 GCCAGTGTAAGACATGTCTGGGACATACAT-TG--ACTTTGAGATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATT--G-TGA-A
** * *
40574112 GCCAGTGTAAGACATGTCTGGGACATGCATCAACCTTGAGATATGTG-T
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC---ACAT-TGTGAA
* * * * *
40574160 GCTAGTGTAATACATGTCTAGGACATGCATCAGCCACATCGTGAAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTGTG-AA
* *
40574206 ACTAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
40574240 ACTTGATATG
Statistics
Matches: 176, Mismatches: 27, Indels: 34
0.74 0.11 0.14
Matches are distributed among these distances:
43 4 0.02
44 7 0.04
45 9 0.05
46 70 0.40
47 15 0.09
48 65 0.37
50 2 0.01
51 1 0.01
52 2 0.01
53 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTGTGAA
Found at i:40574282 original size:140 final size:139
Alignment explanation
Indices: 40573972--40574275 Score: 414
Period size: 140 Copynumber: 2.2 Consensus size: 139
40573962 TGATATGTAC
**
40573972 GCCAGTGTAAGACATGTCTGGGACATGCATCAGTCTCGAGATATGTGTGCTAGTGTAAGACATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGATATGTGTGCTAGTGTAAGACATGT
* * * * * *
40574037 TTGGGACATGCATCGGCCACATTGTGAAAGCCAGTGTAAGACATGTCTGGGACATACATTGACTT
66 CTAGGACATGCATCAGCCACATCGTGAAAACCAGTGTAAGACATGTCTGGGACATACATCGACTT
40574102 TGAGATGAGA
131 TGAGAT-AGA
* *
40574112 GCCAGTGTAAGACATGTCTGGGACATGCATCAACCTTGAGATATGTGTGCTAGTGTAATACATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGATATGTGTGCTAGTGTAAGACATGT
* *
40574177 CTAGGACATGCATCAGCCACATCGTGAAAACTAGTGTAAGACCATGTCTGGGACATGGCATCGAC
66 CTAGGACATGCATCAGCCACATCGTGAAAACCAGTGTAAGA-CATGTCTGGGACAT-ACATCGAC
* *
40574242 -TTGATAT-GT
129 TTTGAGATAGA
* * *
40574251 GTCAGTGTAAGACCTGTCCGGGACA
1 GCCAGTGTAAGACATGTCTGGGACA
40574276 CAGCATCGAC
Statistics
Matches: 145, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
139 23 0.16
140 96 0.66
141 20 0.14
142 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (139 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGATATGTGTGCTAGTGTAAGACATGT
CTAGGACATGCATCAGCCACATCGTGAAAACCAGTGTAAGACATGTCTGGGACATACATCGACTT
TGAGATAGA
Found at i:40585135 original size:6 final size:6
Alignment explanation
Indices: 40585126--40585151 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40585116 CCTGACTATG
40585126 ACTGTT ACTGTT ACTGTT ACTGTT AC
1 ACTGTT ACTGTT ACTGTT ACTGTT AC
40585152 CCTACGGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (6 bp):
ACTGTT
Found at i:40586967 original size:46 final size:46
Alignment explanation
Indices: 40586866--40586953 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
40586856 TGTAACCCGC
* * * *
40586866 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
40586912 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
40586954 AACCATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:40601979 original size:12 final size:12
Alignment explanation
Indices: 40601962--40601987 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40601952 GTCATTTTTG
40601962 TTTTTTATTTCT
1 TTTTTTATTTCT
40601974 TTTTTTATTTCT
1 TTTTTTATTTCT
40601986 TT
1 TT
40601988 CCCTTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTATTTCT
Found at i:40608880 original size:11 final size:11
Alignment explanation
Indices: 40608864--40608893 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40608854 GGAAAGAAAT
40608864 ATATAATAAGA
1 ATATAATAAGA
40608875 ATATAATAAGA
1 ATATAATAAGA
*
40608886 ATCTAATA
1 ATATAATA
40608894 GCTTTACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (11 bp):
ATATAATAAGA
Found at i:40612973 original size:23 final size:22
Alignment explanation
Indices: 40612933--40612977 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
40612923 TATTAATTTT
* * *
40612933 TTTTAAAATTAGTTAATATAATA
1 TTTTAAAATAAATAAATA-AATA
40612956 TTTTAAAATAAATAAATAAATA
1 TTTTAAAATAAATAAATAAATA
40612978 AAAACTTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATAAATAAATA
Found at i:40623080 original size:15 final size:16
Alignment explanation
Indices: 40623060--40623089 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40623050 GCTATGATAT
40623060 ATGAAA-TTTTTAAGA
1 ATGAAAGTTTTTAAGA
40623075 ATGAAAGTTTTTAAG
1 ATGAAAGTTTTTAAG
40623090 TTATGGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (16 bp):
ATGAAAGTTTTTAAGA
Found at i:40626116 original size:3 final size:3
Alignment explanation
Indices: 40626108--40626142 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
40626098 ATTTATAATA
40626108 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40626143 ACAGAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40630571 original size:807 final size:807
Alignment explanation
Indices: 40629018--40630636 Score: 2986
Period size: 807 Copynumber: 2.0 Consensus size: 807
40629008 GCCAACCAGT
*
40629018 GTTCTAATCTTTGATTAAATTAGGGAAATACATTAGGGTGTGATGTAGACCTACCGACGAATTTG
1 GTTCTAATCTTCGATTAAATTAGGGAAATACATTAGGGTGTGATGTAGACCTACCGACGAATTTG
* *
40629083 GTCTTCAAATAGAGTGGTCCGCACCAAGCAAGGATATGTGTTCATTTAAGCGAAGCATTACAACA
66 GTCTTCAAACAGAGTGGTCCGCACCAAGCAAGGATATGTGTTCATTTAAGCAAAGCATTACAACA
*
40629148 GATAATGGTTCAACCCAACTCAAAAGGCTTCACACTAGCAGTCCCCTTTGCTGTAGAAGATGTTA
131 GATAATGGTTCAACCCAACTCAAAAGGCTTCACACTAGCAATCCCCTTTGCTGTAGAAGATGTTA
40629213 TAACCGCAAGGAATGTGCTTCGATATTGTTTGGAATGCTTTAACCCCGATAAGTATAGGCGAGGT
196 TAACCGCAAGGAATGTGCTTCGATATTGTTTGGAATGCTTTAACCCCGATAAGTATAGGCGAGGT
*
40629278 GACAACAGATAAGTGGCTGAAGCAGTTGGTGCAGACTTTGAAAAACAAACATGGCCCCATGTGGC
261 GACAACAGATAAGTGGCTGAAGCAGTTGGTGCAAACTTTGAAAAACAAACATGGCCCCATGTGGC
40629343 CAAAAATGATTTGAAACTAATTTCAATAATACGCAATGAGGAACCTAAGAACTTTTTTTACTATT
326 CAAAAATGATTTGAAACTAATTTCAATAATACGCAATGAGGAACCTAAGAACTTTTTTTACTATT
*
40629408 TCTACAGGATTAGACTTTGCCGTTAGATCTCGGTTGTCTCATTGCACAAAGAAAGTGGTACAAAT
391 TCTACAGGATTAGACTTCGCCGTTAGATCTCGGTTGTCTCATTGCACAAAGAAAGTGGTACAAAT
*
40629473 ATTAATTTGATAATTGCTCCTACTGGTACTAGAATTATCGGTGGTGTAGGCACAGCTCGCAATTC
456 ATTAATTTGATAATTGCTCCTACTGATACTAGAATTATCGGTGGTGTAGGCACAGCTCGCAATTC
* *
40629538 TAGAAGCGGCTCGAAGGAAACTACCATTTTATCCTAAGAAATTAAAGATGTTATTGACCTGCGAG
521 TAGAAGCGACTCGAAGGAAACTACCATTTTATCCTAAGAAATTAAAGATGTTATTGACCTACGAG
*
40629603 CTTCTCTGAGGGACATGTGTAAAAAGCACAAAACTAATGTAGAGCCTGTAAAAGTGGTTATTAGC
586 CTTCTCTGAGGGACATGCGTAAAAAGCACAAAACTAATGTAGAGCCTGTAAAAGTGGTTATTAGC
40629668 AACGAATAGGAAGCAGATAGTGGAAAGCTAGAGTATCATCATAAAAGGAGGGCAAATCATGCTGG
651 AACGAATAGGAAGCAGATAGTGGAAAGCTAGAGTATCATCATAAAAGGAGGGCAAATCATGCTGG
* * *
40629733 GCCTTCTACTGTGATAGCAGTTACTCCTACTTCTCCCTCGGTGAGCTCACCATCTATGGCTCGTA
716 GCCTTCTACTATGATAGCAGCTACTCCTACTTCTCCCCCGGTGAGCTCACCATCTATGGCTCGTA
40629798 AGAGCTCTTCGATTGCTACTCGTAGTA
781 AGAGCTCTTCGATTGCTACTCGTAGTA
* *
40629825 GTTCTAATCTTCGATTAAATTGGGGAAATACATTAGGGTGTGATGTAGACCTGCCGACGAATTTG
1 GTTCTAATCTTCGATTAAATTAGGGAAATACATTAGGGTGTGATGTAGACCTACCGACGAATTTG
* *
40629890 GTCTTCAAACAGAGTGGTCCGCACCAAGCAGGGATATGTGTTCATTTAAGCAAAGTATTACAACA
66 GTCTTCAAACAGAGTGGTCCGCACCAAGCAAGGATATGTGTTCATTTAAGCAAAGCATTACAACA
** *
40629955 GATAATGGTTCAACCCAACTCGTAAGGCTTCACACTAGCAATCCCCTTTGTTGTAGAAGATGTTA
131 GATAATGGTTCAACCCAACTCAAAAGGCTTCACACTAGCAATCCCCTTTGCTGTAGAAGATGTTA
*
40630020 TAACCGCAAGGAATGTGCTTCGATATTGTTTGGAATGCTTTAACCCCGATGAGTATAGGCGAGGT
196 TAACCGCAAGGAATGTGCTTCGATATTGTTTGGAATGCTTTAACCCCGATAAGTATAGGCGAGGT
40630085 GACAACAGATAAGTGGCTGAAGCAGTTGGTGCAAACTTTGAAAAACAAACATGGCCCCATGTGGC
261 GACAACAGATAAGTGGCTGAAGCAGTTGGTGCAAACTTTGAAAAACAAACATGGCCCCATGTGGC
* *
40630150 CAAAAATGATTTGAGACTAATTTCAATAATACGCAATGAGGAACCTAAGAACTTTTTTTACTGTT
326 CAAAAATGATTTGAAACTAATTTCAATAATACGCAATGAGGAACCTAAGAACTTTTTTTACTATT
40630215 TCTACAGGATTAGACTTCGCCGTTAGATCTCGGTTGTCTCATTGCACAAAGAAAGTGGTACAAAT
391 TCTACAGGATTAGACTTCGCCGTTAGATCTCGGTTGTCTCATTGCACAAAGAAAGTGGTACAAAT
40630280 ATTAATTTGATAATTGCTCCTACTGATACTAGAATTATCGGTGGTGTAGGCACAGCTCGCAATTC
456 ATTAATTTGATAATTGCTCCTACTGATACTAGAATTATCGGTGGTGTAGGCACAGCTCGCAATTC
40630345 TAGAAGCGACTCGAAGGAAACTACCATTTTATCCTAAGAAATTAAAGATGTTATTGACCTACGAG
521 TAGAAGCGACTCGAAGGAAACTACCATTTTATCCTAAGAAATTAAAGATGTTATTGACCTACGAG
*
40630410 CTTCTCTGAGGGACATGCGTAAGAAGCACAAAACTAATGTAGAGCCTGTAAAAGTGGTTATTAGC
586 CTTCTCTGAGGGACATGCGTAAAAAGCACAAAACTAATGTAGAGCCTGTAAAAGTGGTTATTAGC
* * *
40630475 AGCGAATAGGAGGCAGATAGTGGAAAGCTAGAGTATCATTATAAAAGGAGGGCAAATCATGCTGG
651 AACGAATAGGAAGCAGATAGTGGAAAGCTAGAGTATCATCATAAAAGGAGGGCAAATCATGCTGG
*
40630540 GCCTTCTATTATGATAGCAGCTACTCCTACTTCTCCCCCGGTGAGCTCACCATCTATGGCTCGTA
716 GCCTTCTACTATGATAGCAGCTACTCCTACTTCTCCCCCGGTGAGCTCACCATCTATGGCTCGTA
40630605 AGAGCTCTTCGATTGCTACTCGTAGTA
781 AGAGCTCTTCGATTGCTACTCGTAGTA
40630632 GTTCT
1 GTTCT
40630637 CCTCTTCATA
Statistics
Matches: 784, Mismatches: 28, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
807 784 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (807 bp):
GTTCTAATCTTCGATTAAATTAGGGAAATACATTAGGGTGTGATGTAGACCTACCGACGAATTTG
GTCTTCAAACAGAGTGGTCCGCACCAAGCAAGGATATGTGTTCATTTAAGCAAAGCATTACAACA
GATAATGGTTCAACCCAACTCAAAAGGCTTCACACTAGCAATCCCCTTTGCTGTAGAAGATGTTA
TAACCGCAAGGAATGTGCTTCGATATTGTTTGGAATGCTTTAACCCCGATAAGTATAGGCGAGGT
GACAACAGATAAGTGGCTGAAGCAGTTGGTGCAAACTTTGAAAAACAAACATGGCCCCATGTGGC
CAAAAATGATTTGAAACTAATTTCAATAATACGCAATGAGGAACCTAAGAACTTTTTTTACTATT
TCTACAGGATTAGACTTCGCCGTTAGATCTCGGTTGTCTCATTGCACAAAGAAAGTGGTACAAAT
ATTAATTTGATAATTGCTCCTACTGATACTAGAATTATCGGTGGTGTAGGCACAGCTCGCAATTC
TAGAAGCGACTCGAAGGAAACTACCATTTTATCCTAAGAAATTAAAGATGTTATTGACCTACGAG
CTTCTCTGAGGGACATGCGTAAAAAGCACAAAACTAATGTAGAGCCTGTAAAAGTGGTTATTAGC
AACGAATAGGAAGCAGATAGTGGAAAGCTAGAGTATCATCATAAAAGGAGGGCAAATCATGCTGG
GCCTTCTACTATGATAGCAGCTACTCCTACTTCTCCCCCGGTGAGCTCACCATCTATGGCTCGTA
AGAGCTCTTCGATTGCTACTCGTAGTA
Found at i:40631828 original size:11 final size:12
Alignment explanation
Indices: 40631801--40631825 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40631791 AAAATTGAAC
40631801 TTAAACAAATTT
1 TTAAACAAATTT
40631813 TTAAACAAATTT
1 TTAAACAAATTT
40631825 T
1 T
40631826 AAAAAGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAACAAATTT
Found at i:40632213 original size:157 final size:157
Alignment explanation
Indices: 40631927--40632232 Score: 441
Period size: 157 Copynumber: 1.9 Consensus size: 157
40631917 AAACATTCTA
* * *
40631927 AGTTGTGAATTTTAATTAGCAAACTCAAAGGAACTTAAGCTACGATCTCAAATCAATTAAGCCTT
1 AGTTGTGAATGTTAATCAGCAAAATCAAAGGAACTTAAGCTACGATCTCAAATCAATTAAGCCTT
* * * **
40631992 AAATACCACCCAGGAGGGTAGCCTTGCTAGCTTTGTTGGATCTATGAGCTTAATTATATAAGCAC
66 AAATACCACCCAGGAGGGTAACCTTGCTAGCTGTGTTGAATCTACAAGCTTAATTATATAAGCAC
*
40632057 TTATAATGCCAGCTGAGAGTGTAGGTG
131 TTATAATGCCAGATGAGAGTGTAGGTG
* ** * *
40632084 AGTTGTGAATGTTAATCAGCAAAATCAAAGGAATTTAATTTGCGATCTTAAATCAATTAAGCCTT
1 AGTTGTGAATGTTAATCAGCAAAATCAAAGGAACTTAAGCTACGATCTCAAATCAATTAAGCCTT
* * * *
40632149 AAATACCACCCAGGAGGGTAACCTTGCTAGCTGTGTTGAATCTGCAAGCTTAATTTTGTGAGCAC
66 AAATACCACCCAGGAGGGTAACCTTGCTAGCTGTGTTGAATCTACAAGCTTAATTATATAAGCAC
*
40632214 TTATAATGTCAGATGAGAG
131 TTATAATGCCAGATGAGAG
40632233 CATAGGTCTG
Statistics
Matches: 130, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
157 130 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (157 bp):
AGTTGTGAATGTTAATCAGCAAAATCAAAGGAACTTAAGCTACGATCTCAAATCAATTAAGCCTT
AAATACCACCCAGGAGGGTAACCTTGCTAGCTGTGTTGAATCTACAAGCTTAATTATATAAGCAC
TTATAATGCCAGATGAGAGTGTAGGTG
Found at i:40633841 original size:54 final size:54
Alignment explanation
Indices: 40633754--40633861 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
40633744 GAAAAAGCGT
* * * *
40633754 CTGCACATGTGTTGTCACTTCTGGTGAGCTACTTTATCTGAACTTTGTTAAATC
1 CTGCACATGTGTTGTCACTCCTAGCGAGATACTTTATCTGAACTTTGTTAAATC
40633808 CTGCACATGTGTTGTCACTCCTAGCGAGATACTTTATCTGAACTTTGTTAAATC
1 CTGCACATGTGTTGTCACTCCTAGCGAGATACTTTATCTGAACTTTGTTAAATC
40633862 TTACAAGCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (54 bp):
CTGCACATGTGTTGTCACTCCTAGCGAGATACTTTATCTGAACTTTGTTAAATC
Found at i:40635177 original size:19 final size:20
Alignment explanation
Indices: 40635128--40635169 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
40635118 ATGTTGTGTA
40635128 TCCTAAAAAATGCGAACACC
1 TCCTAAAAAATGCGAACACC
40635148 TCCTAAAAAATGCGAACACC
1 TCCTAAAAAATGCGAACACC
40635168 TC
1 TC
40635170 TAACAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.31, G:0.10, T:0.17
Consensus pattern (20 bp):
TCCTAAAAAATGCGAACACC
Found at i:40643311 original size:17 final size:17
Alignment explanation
Indices: 40643289--40643322 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40643279 ATCCACTAAT
*
40643289 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
40643306 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
40643323 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:40647950 original size:17 final size:17
Alignment explanation
Indices: 40647928--40647961 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40647918 ATCCACTAAT
*
40647928 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
40647945 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
40647962 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:40650326 original size:4 final size:4
Alignment explanation
Indices: 40650317--40650342 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
40650307 TAGATTACAT
40650317 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
40650343 GAAGAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:40657279 original size:16 final size:17
Alignment explanation
Indices: 40657248--40657282 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40657238 ATAATGATAA
*
40657248 TTTATCTAAGTAATTAT
1 TTTATCTAACTAATTAT
40657265 TTTATCTAACT-ATTAT
1 TTTATCTAACTAATTAT
40657281 TT
1 TT
40657283 CTCTCCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTATCTAACTAATTAT
Found at i:40661018 original size:54 final size:52
Alignment explanation
Indices: 40660905--40661025 Score: 181
Period size: 52 Copynumber: 2.3 Consensus size: 52
40660895 TACATGGGAG
*
40660905 CACTTATCACTT-TTCGCCGATGCCATAGCACAACTATGGTCTTATACGAAT
1 CACTTATCACTTGTTTGCCGATGCCATAGCACAACTATGGTCTTATACGAAT
* * *
40660956 CACTTATCACTTGTTTTCCGATGCCATAGCCCAGCTATGGTCTTATACGGATAT
1 CACTTATCACTTGTTTGCCGATGCCATAGCACAACTATGGTCTTATAC-GA-AT
40661010 CACTTATCACTTGTTT
1 CACTTATCACTTGTTT
40661026 CCATGGTCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 12 0.19
52 31 0.49
53 2 0.03
54 18 0.29
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (52 bp):
CACTTATCACTTGTTTGCCGATGCCATAGCACAACTATGGTCTTATACGAAT
Found at i:40663497 original size:25 final size:25
Alignment explanation
Indices: 40663469--40663529 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
40663459 GCAATACAAG
**
40663469 GGGAAGCTCATGTGAGCCGTATAAC
1 GGGAAGCTCATCCGAGCCGTATAAC
* *
40663494 GGGAAGCTTATCCGAGCTGTATAAC
1 GGGAAGCTCATCCGAGCCGTATAAC
*
40663519 GGGAAACTCAT
1 GGGAAGCTCAT
40663530 AAGAGCCATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.21
Consensus pattern (25 bp):
GGGAAGCTCATCCGAGCCGTATAAC
Found at i:40663535 original size:25 final size:25
Alignment explanation
Indices: 40663482--40663536 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
40663472 AAGCTCATGT
* * **
40663482 GAGCCGTATAACGGGAAGCTTATCC
1 GAGCCGTATAACGGGAAACTCATAA
*
40663507 GAGCTGTATAACGGGAAACTCATAA
1 GAGCCGTATAACGGGAAACTCATAA
40663532 GAGCC
1 GAGCC
40663537 ATATTCCAGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (25 bp):
GAGCCGTATAACGGGAAACTCATAA
Found at i:40666409 original size:41 final size:41
Alignment explanation
Indices: 40666350--40666430 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
40666340 GGTAAAAAGT
* *
40666350 GCTTCCAGCTGGTAGCGTTTTTCTGTCAATATGCTAAAAAC
1 GCTTCCAACTGGTAGCGTTTTTCTGTCAATATGCAAAAAAC
40666391 GCTTCCAACTGG-ACGCGTTTTTCTGTCAATATGCAAAAAA
1 GCTTCCAACTGGTA-GCGTTTTTCTGTCAATATGCAAAAAA
40666431 TGCCATGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (41 bp):
GCTTCCAACTGGTAGCGTTTTTCTGTCAATATGCAAAAAAC
Found at i:40677678 original size:55 final size:53
Alignment explanation
Indices: 40677564--40677752 Score: 236
Period size: 55 Copynumber: 3.5 Consensus size: 53
40677554 AACTTACCAT
* * *
40677564 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATCAA
* * *
40677617 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGTCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAA
* * * *
40677672 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAA
*
40677726 TGCCATGCCTTGGCATGGTCTTACATG
1 TGCCATGCCTTGACATGGTCTTACATG
40677753 ATATCCTTAT
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.02
53 34 0.29
54 35 0.30
55 44 0.38
56 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.35
Consensus pattern (53 bp):
TGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAA
Found at i:40677766 original size:109 final size:108
Alignment explanation
Indices: 40677564--40677766 Score: 309
Period size: 109 Copynumber: 1.9 Consensus size: 108
40677554 AACTTACCAT
* *
40677564 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
* *
40677629 GCATGGTCTTACATGGGACCTTTGTCTTATAGTAACTCATCAA
66 GCATGGTCTTACATGAGACCTTTATCTTATAGTAACTCATCAA
* * *
40677672 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTT
*
40677737 GGCATGGTCTTACATGATATCC-TTATCTTA
65 GGCATGGTCTTACATGAGA-CCTTTATCTTA
40677767 CCAAATGCCA
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
108 39 0.46
109 44 0.52
110 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (108 bp):
TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
GCATGGTCTTACATGAGACCTTTATCTTATAGTAACTCATCAA
Found at i:40677794 original size:47 final size:47
Alignment explanation
Indices: 40677739--40677860 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
40677729 CATGCCTTGG
*
40677739 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
*
40677786 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
* *
40677833 CATGGTCTTATATGGTATCCTTCTCTTA
1 CATGGTCTTACATGGTATCCTTATCTTA
40677861 GCGCCAATGC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
Found at i:40687620 original size:24 final size:25
Alignment explanation
Indices: 40687593--40687640 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
40687583 TTAATAAAAC
40687593 AATA-TTATT-TTAAATAAAATATTA
1 AATATTTATTATTAAA-AAAATATTA
40687617 AATATTTATTAATTAAAAAAATAT
1 AATATTTATT-ATTAAAAAAATAT
40687641 CATTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.19
25 5 0.24
26 7 0.33
27 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AATATTTATTATTAAAAAAATATTA
Found at i:40690111 original size:11 final size:11
Alignment explanation
Indices: 40690072--40690151 Score: 52
Period size: 11 Copynumber: 7.7 Consensus size: 11
40690062 TGCATATATG
40690072 ATATAATACATGA
1 ATAT-ATACAT-A
40690085 ATA-ATACGAT-
1 ATATATAC-ATA
40690095 ATATATACATA
1 ATATATACATA
40690106 ATATAT--ATA
1 ATATATACATA
*
40690115 ATA-A-A-AGA
1 ATATATACATA
40690123 ATAATATACATA
1 AT-ATATACATA
40690135 ATATATA-A-A
1 ATATATACATA
40690144 ATATATAC
1 ATATATAC
40690152 GTATATAACA
Statistics
Matches: 56, Mismatches: 2, Indels: 21
0.71 0.03 0.27
Matches are distributed among these distances:
8 5 0.09
9 15 0.27
10 7 0.12
11 20 0.36
12 6 0.11
13 3 0.05
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (11 bp):
ATATATACATA
Found at i:40690326 original size:3 final size:3
Alignment explanation
Indices: 40690318--40690359 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
40690308 ACTAATATAT
* * *
40690318 ATA ATA ATA ATA ATG ATA ATA ATA TTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40690360 CAAGGATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40690744 original size:60 final size:60
Alignment explanation
Indices: 40690633--40690749 Score: 150
Period size: 60 Copynumber: 1.9 Consensus size: 60
40690623 AAGGACCAAA
* * *
40690633 TGCGCAAATTGCCCTTCCGCTAAAAAACACGCGGATCTTGACCTGGAGCGGGTCGGGGAT
1 TGCGCAAATAGCCCCTCCGCTAAAAAACACGCGGATCTAGACCTGGAGCGGGTCGGGGAT
*
40690693 TGCGCAAATAGCCCCTCC-CTTACAAAAACACGCGGATCCTAG-TC-GGAGCGGGTCGGG
1 TGCGCAAATAGCCCCTCCGC-TA-AAAAACACGCGGAT-CTAGACCTGGAGCGGGTCGGG
40690750 TCGACCCGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 1 0.02
60 31 0.62
61 15 0.30
62 3 0.06
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (60 bp):
TGCGCAAATAGCCCCTCCGCTAAAAAACACGCGGATCTAGACCTGGAGCGGGTCGGGGAT
Found at i:40691104 original size:13 final size:13
Alignment explanation
Indices: 40691078--40691127 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
40691068 AAATAAGTAG
*
40691078 AATAGAAAATAAA
1 AATAAAAAATAAA
40691091 AAT-AAAAATAAA
1 AATAAAAAATAAA
40691103 AATAAAATAATAAA
1 AATAAAA-AATAAA
*
40691117 AGTAAATAAAT
1 AATAAA-AAAT
40691128 CACCTCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 11 0.34
13 6 0.19
14 14 0.44
15 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:40691122 original size:6 final size:6
Alignment explanation
Indices: 40691078--40691109 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
40691068 AAATAAGTAG
40691078 AATAGAA AATAAA AATAAA AATAAA AATAAA A
1 AATA-AA AATAAA AATAAA AATAAA AATAAA A
40691110 TAATAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:40692686 original size:87 final size:87
Alignment explanation
Indices: 40692414--40692711 Score: 443
Period size: 88 Copynumber: 3.4 Consensus size: 87
40692404 ATGACCCGAT
* * * * *
40692414 GCTCAACTCACCTCTTGCAATTTGAGTTGATTTTTGAAAAATATAATTTAAAAAAATAGAAATTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATT-GAAAAACAGAAATTG
40692479 AAAATACCTCAGCGTGCCCTGAG
65 AAAATACCTCAGCGTGCCCTGAG
*
40692502 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATGGAAAAAACAGAAATTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTG-AAAAACAGAAATTG
40692567 AAAATACCTCAGCGTGCCCTGAG
65 AAAATACCTCAGCGTGCCCTGAG
* * ** * *
40692590 ACTCAACTCACCTCTCGCAGTATGAGTTGATTTTTGAAAAGCATAACTTGAAAAACGGAAATTGA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAACAGAAATTGA
*
40692655 AAATACCTCAGCGTGTCCTGAG
66 AAATACCTCAGCGTGCCCTGAG
* *
40692677 GCTCAACTCACCTCTTGCAATATGAGTTGGTTTTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
40692712 TTTGAAAACA
Statistics
Matches: 191, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
87 66 0.35
88 125 0.65
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (87 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAACAGAAATTGA
AAATACCTCAGCGTGCCCTGAG
Found at i:40692931 original size:228 final size:230
Alignment explanation
Indices: 40692501--40692939 Score: 597
Period size: 226 Copynumber: 1.9 Consensus size: 230
40692491 CGTGCCCTGA
40692501 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATGGAAAAAACAGAAATT
1 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATGGAAAAAACAGAAATT
* * *
40692566 GAAAATACCTCAGCGTGCCCTGAGACTCAACTCACCTCTCGCAGTATGAGTTGATTTTTGAAAAG
66 GAAAATACCTCAGCGTG-CCTGAGACTCAACTCACCTCTCACAATATGAGTTGATTTCTGAAAAG
* * * *
40692631 CATAACTTGAAAAACGGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCA
130 CAAAACTTGAAAAACAGAAATTGAAAATACCTCAGCATGGCCTGAGGCTCAACTCACCTCTTGCA
*
40692696 ATATGAGTTGGTTTTTTTTGAAAACATGAATTAAAG
195 ATATGAGTTGATTTTTTTTGAAAACATGAATTAAAG
* * * * *
40692732 GGCTCAACTCACCTCTTGCAATATGAGTTGA-TTTTGAAACATA-AAGT-GAAAATATAGAAATT
1 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATGGAAAAAACAGAAATT
*
40692794 GAAAATACCTCAGCGTG-CTGA-AGCTCAACTCACCTTTCACAATATGAGTTGATTTCTGAAAA-
66 GAAAATACCTCAGCGTGCCTGAGA-CTCAACTCACCTCTCACAATATGAGTTGATTTCTGAAAAG
* * *
40692856 CAGAAATTTGAAAAATAGAATTTGAAAATACCTCAGCACATGGGCC-GAGGCTCAACTCACCT-T
130 CA-AAACTTGAAAAACAGAAATTGAAAATACCTCAG--CAT-GGCCTGAGGCTCAACTCACCTCT
*
40692919 TCGCGATATGAGTTGATTTTT
191 T-GCAATATGAGTTGATTTTT
40692940 GAAAACAGAA
Statistics
Matches: 184, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
225 3 0.02
226 67 0.36
227 2 0.01
228 65 0.35
229 6 0.03
230 11 0.06
231 30 0.16
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (230 bp):
GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATGGAAAAAACAGAAATT
GAAAATACCTCAGCGTGCCTGAGACTCAACTCACCTCTCACAATATGAGTTGATTTCTGAAAAGC
AAAACTTGAAAAACAGAAATTGAAAATACCTCAGCATGGCCTGAGGCTCAACTCACCTCTTGCAA
TATGAGTTGATTTTTTTTGAAAACATGAATTAAAG
Found at i:40692934 original size:89 final size:85
Alignment explanation
Indices: 40692732--40692951 Score: 277
Period size: 89 Copynumber: 2.6 Consensus size: 85
40692722 TGAATTAAAG
*
40692732 GGCTCAACTCACCTCTT-GCAATATGAGTTGATTTTG-AAACATAAA-GTGAAAATATAGAAATT
1 GGCTCAACTCACCT-TTCGCAATATGAGTTGATTTTGAAAACAGAAATGTGAAAATATAGAAATT
* *
40692794 GAAAATACCTCAGCGTGCTGA
65 GAAAATACCTCAGCGGGCCGA
* * * *
40692815 AGCTCAACTCACCTTTCACAATATGAGTTGATTTCTGAAAACAGAAATTTGAAAA-ATAGAATTT
1 GGCTCAACTCACCTTTCGCAATATGAGTTGATTT-TGAAAACAGAAATGTGAAAATATAGAAATT
40692879 GAAAATACCTCAGCACATGGGCCGA
65 GAAAATACCTCAG--C--GGGCCGA
*
40692904 GGCTCAACTCACCTTTCGCGATATGAGTTGATTTTTGAAAACAGAAAT
1 GGCTCAACTCACCTTTCGCAATATGAGTTGA-TTTTGAAAACAGAAAT
40692952 AAAACATCAA
Statistics
Matches: 118, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
82 2 0.02
83 29 0.25
84 2 0.02
85 29 0.25
86 6 0.05
87 1 0.01
89 46 0.39
90 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (85 bp):
GGCTCAACTCACCTTTCGCAATATGAGTTGATTTTGAAAACAGAAATGTGAAAATATAGAAATTG
AAAATACCTCAGCGGGCCGA
Found at i:40695411 original size:15 final size:15
Alignment explanation
Indices: 40695391--40695434 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
40695381 ATATTGTAAA
40695391 TATCATATTATGTTT
1 TATCATATTATGTTT
*
40695406 TATCATGTATATGTTT
1 TATCATAT-TATGTTT
40695422 TAAT-ATATTATGT
1 T-ATCATATTATGT
40695435 GTATATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
16 11 0.44
17 2 0.08
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (15 bp):
TATCATATTATGTTT
Found at i:40695514 original size:24 final size:25
Alignment explanation
Indices: 40695459--40695514 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
40695449 GTATGTTATG
* *
40695459 TATATATTATGTATATGCTTTTAAA
1 TATATATTATATATATGATTTTAAA
* *
40695484 TAT-TATTATATATCT-ATTTTCAA
1 TATATATTATATATATGATTTTAAA
40695507 TATATATT
1 TATATATT
40695515 TATGTAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.35
24 14 0.54
25 3 0.12
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (25 bp):
TATATATTATATATATGATTTTAAA
Found at i:40707086 original size:55 final size:55
Alignment explanation
Indices: 40707002--40707176 Score: 305
Period size: 55 Copynumber: 3.2 Consensus size: 55
40706992 TCTGGGGCAC
* *
40707002 CTATTCCCTTTTTATTCATTTTGTATTCCATCAATGTTTGTTGATTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAACAATGTTTGTTGACTGTGATTAAT
*
40707057 CTATTCCCTTTTTATTCATTTTTTATTCCAACAATGTTTGTTGACTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAACAATGTTTGTTGACTGTGATTAAT
* *
40707112 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTATTGACTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAACAATGTTTGTTGACTGTGATTAAT
40707167 CTATTCCCTT
1 CTATTCCCTT
40707177 CAAATTTTGT
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 114 1.00
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.53
Consensus pattern (55 bp):
CTATTCCCTTTTTATTCATTTTGTATTCCAACAATGTTTGTTGACTGTGATTAAT
Found at i:40707827 original size:44 final size:43
Alignment explanation
Indices: 40707693--40707837 Score: 134
Period size: 44 Copynumber: 3.3 Consensus size: 43
40707683 ACCTTAACCA
* *
40707693 CCTAAGCAGTAGGGTAACAGGCTGAAGATATAGATCTTATCAT
1 CCTAAGCAGTAGGGTAACAAGCTGAAGATATAGATCTTATCAC
* * * * * *
40707736 CCTAAGCAGTATGGAAAC-AGATCAAAGGTA-ACGAGCTTTAATC-C
1 CCTAAGCAGTAGGGTAACAAGCT-GAAGATATA-GATC-TT-ATCAC
*
40707780 CCTAAGCAGTAGGGTAACAAGCTGAAGTTTATAGATCTTATCAC
1 CCTAAGCAGTAGGGTAACAAGCTGAAG-ATATAGATCTTATCAC
*
40707824 CCTAAGCAGCAGGG
1 CCTAAGCAGTAGGG
40707838 AAGTAGATCA
Statistics
Matches: 79, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
42 3 0.04
43 27 0.34
44 37 0.47
45 11 0.14
46 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (43 bp):
CCTAAGCAGTAGGGTAACAAGCTGAAGATATAGATCTTATCAC
Found at i:40708280 original size:43 final size:42
Alignment explanation
Indices: 40708222--40708327 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 42
40708212 GGGCTTCAAC
* *
40708222 CCCCTAAGCAATAGGGTAACAAGCCAAATTTTCAAAGCTTAAA
1 CCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAAAGC-TAAA
* *** * *
40708265 CCCCTAAGCAGTAGGGTAACACGTTGAATTTACAGATCTAAA
1 CCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAAAGCTAAA
*
40708307 CCCCTAAGCAGTAGGGAAACA
1 CCCCTAAGCAGTAGGGTAACA
40708328 GATCAATGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 24 0.44
43 30 0.56
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (42 bp):
CCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAAAGCTAAA
Found at i:40710395 original size:15 final size:15
Alignment explanation
Indices: 40710375--40710418 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
40710365 ATATTGTAAA
40710375 TATCATATTATGTTT
1 TATCATATTATGTTT
*
40710390 TATCATGTATATGTTT
1 TATCATAT-TATGTTT
40710406 TAAT-ATATTATGT
1 T-ATCATATTATGT
40710419 GTATATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
16 11 0.44
17 2 0.08
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (15 bp):
TATCATATTATGTTT
Found at i:40710498 original size:24 final size:25
Alignment explanation
Indices: 40710443--40710498 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
40710433 GTATGTTATG
* *
40710443 TATATATTATGTATATGCTTTTAAA
1 TATATATTATATATATGATTTTAAA
* *
40710468 TAT-TATTATATATCT-ATTTTCAA
1 TATATATTATATATATGATTTTAAA
40710491 TATATATT
1 TATATATT
40710499 TATGTAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.35
24 14 0.54
25 3 0.12
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (25 bp):
TATATATTATATATATGATTTTAAA
Found at i:40711886 original size:38 final size:38
Alignment explanation
Indices: 40711835--40711913 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
40711825 AATCAAAGCT
* *
40711835 CCACCCGAGAATGCCTTATTTACGATATATGGTCCTTC
1 CCACCCGAGAATGCCTTATTCACGACATATGGTCCTTC
* * *
40711873 CCACCCGAGAATGCTTTCTTCACGACGTATGGTCCTTC
1 CCACCCGAGAATGCCTTATTCACGACATATGGTCCTTC
40711911 CCA
1 CCA
40711914 ATTTGGTGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (38 bp):
CCACCCGAGAATGCCTTATTCACGACATATGGTCCTTC
Found at i:40724396 original size:26 final size:26
Alignment explanation
Indices: 40724366--40724447 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
40724356 TGAAATTCCC
40724366 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
40724392 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
40724418 ATCATGGAACATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
40724444 ATCA
1 ATCA
40724448 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40730191 original size:26 final size:26
Alignment explanation
Indices: 40730161--40730261 Score: 184
Period size: 26 Copynumber: 3.9 Consensus size: 26
40730151 CCCATAATGG
40730161 AACATTTACCTAACCCATTATCATGA
1 AACATTTACCTAACCCATTATCATGA
40730187 AACATTTACCTAACCCATTATCATGA
1 AACATTTACCTAACCCATTATCATGA
* *
40730213 AACATTTACCTAACACATTATCATGG
1 AACATTTACCTAACCCATTATCATGA
40730239 AACATTTACCTAACCCATTATCA
1 AACATTTACCTAACCCATTATCA
40730262 ATTTGTATCA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.31
Consensus pattern (26 bp):
AACATTTACCTAACCCATTATCATGA
Found at i:40731364 original size:15 final size:16
Alignment explanation
Indices: 40731342--40731380 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
40731332 AAGTTGAATT
*
40731342 TTATTTTTTAAA-AATA
1 TTATTTTTGAAATAA-A
40731358 TTATTTTTGAAATAAA
1 TTATTTTTGAAATAAA
40731374 TTATTTT
1 TTATTTT
40731381 CTCATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTATTTTTGAAATAAA
Found at i:40732582 original size:10 final size:12
Alignment explanation
Indices: 40732556--40732584 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40732546 ATATAGCCAT
40732556 TAAAAAATATAA
1 TAAAAAATATAA
40732568 TAAAAAATATAA
1 TAAAAAATATAA
40732580 -AAAAA
1 TAAAAA
40732585 GGGGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAAAAATATAA
Found at i:40743459 original size:37 final size:37
Alignment explanation
Indices: 40743409--40743487 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
40743399 TTATTACGAA
* *
40743409 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
40743446 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
40743483 GTCTT
1 GTCTT
40743488 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:40743756 original size:47 final size:47
Alignment explanation
Indices: 40743606--40744595 Score: 1829
Period size: 47 Copynumber: 21.1 Consensus size: 47
40743596 CCCTTCGGGA
* * * * * * * *
40743606 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40743653 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40743699 CTTCTCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40743746 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40743793 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40743840 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40743887 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40743934 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40743981 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744028 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744075 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744122 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744169 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744216 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744263 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744310 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744357 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744404 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744451 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744498 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40744545 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40744592 CTTA
1 CTTA
40744596 CTATCATTTC
Statistics
Matches: 925, Mismatches: 17, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
46 39 0.04
47 886 0.96
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40750668 original size:44 final size:44
Alignment explanation
Indices: 40750596--40750707 Score: 138
Period size: 44 Copynumber: 2.5 Consensus size: 44
40750586 ATCCTGTCTT
* * * * *
40750596 CCTGAAGTCTCAGCGAAGCAGA-TCGAAGTCACCAGTCTTATCTC
1 CCTGAAGTCGCAGTGGAGCAGACT-GAAGTCACAAGTCTCATCTC
*
40750640 CCTGAAGT-GCAGTGGAGCAAGACTGAAGTTACAAGTCTCATCTC
1 CCTGAAGTCGCAGTGGAGC-AGACTGAAGTCACAAGTCTCATCTC
40750684 CCTGAAGTCGCAGTGGAGCAGACT
1 CCTGAAGTCGCAGTGGAGCAGACT
40750708 AAATATACAG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
43 7 0.12
44 41 0.69
45 11 0.19
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (44 bp):
CCTGAAGTCGCAGTGGAGCAGACTGAAGTCACAAGTCTCATCTC
Found at i:40751082 original size:43 final size:43
Alignment explanation
Indices: 40750991--40751095 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 43
40750981 GCTTTAACTG
*
40750991 CCTAAGCAGTAGGGTAACAAGCTGAGGATTTACAAATCTTATCA
1 CCTAAGCAGTAGGGTAACAAGCCGA-GATTTACAAATCTTATCA
** *
40751035 -CTAAGCAGTAGGGTAACAAGCCGA-ATTTGTAGATCTTATCA
1 CCTAAGCAGTAGGGTAACAAGCCGAGATTTACAAATCTTATCA
* *
40751076 CCCTAAGTAGTAGGGAAACA
1 -CCTAAGCAGTAGGGTAACA
40751096 GATCAGAGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
41 14 0.26
43 39 0.74
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (43 bp):
CCTAAGCAGTAGGGTAACAAGCCGAGATTTACAAATCTTATCA
Found at i:40751303 original size:262 final size:261
Alignment explanation
Indices: 40750671--40751324 Score: 754
Period size: 262 Copynumber: 2.5 Consensus size: 261
40750661 ACTGAAGTTA
*
40750671 CAAGTCTCATCTCCCTGAAGTCGCAGTGGAGCAGACTAAATATACAGACCTTAAACCCCTAAGCA
1 CAAGTCTCATCTCCCTGAAGTCGCAGT-GAGCAGACTAAATATACAGACCTTAACCCCCTAAGCA
* * *
40750736 GTAGGGTAACAGGTTGAA-TTCAAATGGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATT
65 GTAGGGTAACAGATCGAAGAT--AATGGC-TTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATT
40750800 TGTAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCAGAGAAGATGGGCCTTAACCCCCTAAG
127 TGTAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCAGAGAAGATGGGCCTTAACCCCCTAAG
* *
40750865 CAGTAGGGTAATAGGCTGAAAATCACAGATCTTGCCTCCCTAAAGTTGCAGTGGAGCAGATCAAA
192 CAGTAGGGTAATAGGCTGAAAATCACAGATCTTGCCTCCCTAAAGTTACAGTGGAACAGATCAAA
*
40750930 TACAT
257 TACAG
*** * * * * * * * **
40750935 CGAA-TCTTGCCT-CATCGGA-T-GTAGTGAAGCAGATTCAAACCA-CCA-AGCTTTAACTGCCT
1 C-AAGTCTCATCTCCCT-GAAGTCGCAGTG-AGCAGACT-AAA-TATACAGA-CCTTAACCCCCT
* * *** * *
40750994 AAGCAGTAGGGTAACA-AGCTGAGGATTTACAAATCTT-A-TCACTAAGCAGTAGGGTAACAAGC
60 AAGCAGTAGGGTAACAGATC-GAAGA--TA-ATGGCTTAACCCCCTAAGCAGTAGGGTAACAAGC
40751056 CGAATTTGTAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCAGAGAAGATGGGCCTTAACCC
121 CGAATTTGTAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCAGAGAAGATGGGCCTTAACCC
* * *
40751121 CCTAAGCAGTAGGGTAATAGGCTGAAAATTACAGATCTTGTCTCCCTGAAGTTACAGTGGAACAG
186 CCTAAGCAGTAGGGTAATAGGCTGAAAATCACAGATCTTGCCTCCCTAAAGTTACAGTGGAACAG
* *
40751186 ATCGAATCCAG
251 ATCAAATACAG
* * * *
40751197 CAAGTCTCATCTCCCTGAAGTCGCAGTAGAGCAGACTGAATTTATAGATCTTAACCCCCTAAGCA
1 CAAGTCTCATCTCCCTGAAGTCGCAGT-GAGCAGACTAAATATACAGACCTTAACCCCCTAAGCA
* *
40751262 GTAGGG-AACAGATCGAAGATAATGGGCTTAACCCCCTAAGCAGTATGGTAACAAGCCAAATTT
65 GTAGGGTAACAGATCGAAGATAAT-GGCTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTT
40751325 ACAGACCTTG
Statistics
Matches: 312, Mismatches: 56, Indels: 46
0.75 0.14 0.11
Matches are distributed among these distances:
259 1 0.00
260 5 0.02
261 4 0.01
262 210 0.67
263 62 0.20
264 24 0.08
265 5 0.02
266 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (261 bp):
CAAGTCTCATCTCCCTGAAGTCGCAGTGAGCAGACTAAATATACAGACCTTAACCCCCTAAGCAG
TAGGGTAACAGATCGAAGATAATGGCTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTGTA
GATCTTATCACCCTAAGTAGTAGGGAAACAGATCAGAGAAGATGGGCCTTAACCCCCTAAGCAGT
AGGGTAATAGGCTGAAAATCACAGATCTTGCCTCCCTAAAGTTACAGTGGAACAGATCAAATACA
G
Found at i:40755405 original size:44 final size:44
Alignment explanation
Indices: 40755341--40755428 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
40755331 TGAAAACTCT
*
40755341 CTTTTCCTTTATGTTTTTTTTCCATGAAATAACTTTACATGTTA
1 CTTTCCCTTTATGTTTTTTTTCCATGAAATAACTTTACATGTTA
40755385 CTTTCCCTTTATGTTTTTTTTCCATGAAATAACTTTACATGTTA
1 CTTTCCCTTTATGTTTTTTTTCCATGAAATAACTTTACATGTTA
40755429 TAAATCTGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.23, C:0.17, G:0.07, T:0.53
Consensus pattern (44 bp):
CTTTCCCTTTATGTTTTTTTTCCATGAAATAACTTTACATGTTA
Found at i:40755648 original size:31 final size:31
Alignment explanation
Indices: 40755613--40755690 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
40755603 TTACCAACCT
*
40755613 AGTGACTTAAATAAAATATTTTGAATAGTTC
1 AGTGACTTAAATAAAATATTTTGAATAATTC
* * *
40755644 AGTGACTTAAATGAATTTTTTTGAATAATTC
1 AGTGACTTAAATAAAATATTTTGAATAATTC
* * *
40755675 AATGACTAAAACAAAA
1 AGTGACTTAAATAAAA
40755691 ACTTACCATA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.36
Consensus pattern (31 bp):
AGTGACTTAAATAAAATATTTTGAATAATTC
Found at i:40761648 original size:12 final size:12
Alignment explanation
Indices: 40761631--40761662 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
40761621 TATTTTACCC
40761631 AATTTCTTCAAT
1 AATTTCTTCAAT
40761643 AATTTCTTCAAT
1 AATTTCTTCAAT
40761655 AATTTCTT
1 AATTTCTT
40761663 TTTCTAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTCTTCAAT
Found at i:40764379 original size:44 final size:41
Alignment explanation
Indices: 40764330--40764425 Score: 104
Period size: 42 Copynumber: 2.2 Consensus size: 41
40764320 TATGGGATGT
40764330 TGGCATCGACTTATGATTTACGTATAAGACAATGTCTGGGACA-
1 TGGCATCGA-TT-TGATTT-CGTATAAGACAATGTCTGGGACAG
* ** *
40764373 TCGGCATCGTATTTGATTTCGTGTAAGACCCTGTCTGGGGCAG
1 T-GGCATCG-ATTTGATTTCGTATAAGACAATGTCTGGGACAG
40764416 TGGCATCGAT
1 TGGCATCGAT
40764426 ATTTGATTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
41 2 0.04
42 26 0.57
43 8 0.17
44 9 0.20
45 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (41 bp):
TGGCATCGATTTGATTTCGTATAAGACAATGTCTGGGACAG
Found at i:40764409 original size:42 final size:43
Alignment explanation
Indices: 40764330--40764464 Score: 118
Period size: 43 Copynumber: 3.1 Consensus size: 43
40764320 TATGGGATGT
* *
40764330 TGGCATCGACT-TATGATTTACGTATAAGACAATGTCTGGGACA-
1 TGGCATCGA-TATTTGATTT-CGTGTAAGACAATGTCTGGGACAG
** *
40764373 TCGGCATCG-TATTTGATTTCGTGTAAGACCCTGTCTGGGGCAG
1 T-GGCATCGATATTTGATTTCGTGTAAGACAATGTCTGGGACAG
* * *
40764416 TGGCATCGATATTTGATTACATGTAAGATCACAT-T-TGGGACAT
1 TGGCATCGATATTTGATTTCGTGTAAGA-CA-ATGTCTGGGACAG
40764459 TGGCAT
1 TGGCAT
40764465 TGTACGAGCT
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
42 27 0.36
43 38 0.51
44 9 0.12
45 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (43 bp):
TGGCATCGATATTTGATTTCGTGTAAGACAATGTCTGGGACAG
Found at i:40765099 original size:26 final size:26
Alignment explanation
Indices: 40765069--40765120 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
40765059 TCAAAAATGG
40765069 TATGTTTTGATGCATTCTTGAATGAC
1 TATGTTTTGATGCATTCTTGAATGAC
40765095 TATGTTTTGATGCATTCTTGAATGAC
1 TATGTTTTGATGCATTCTTGAATGAC
40765121 CAAATGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (26 bp):
TATGTTTTGATGCATTCTTGAATGAC
Found at i:40766803 original size:63 final size:63
Alignment explanation
Indices: 40766730--40766888 Score: 169
Period size: 63 Copynumber: 2.5 Consensus size: 63
40766720 TTTAGAGGAG
* * *
40766730 GTGTTGATGCAGAGAATGATTGTGTGTGATATGGTGCTTGTGCAAAATAATCTGGTGCT-AAA
1 GTGTTGATGCAGAGAATGATTGTGTGTGATATGGTACTTGTGCAAAATAAACTGGAGCTGAAA
* * * * * *
40766792 TGTGTTGATGCA-AGGAATGGTTGTGCGTGCTCTGGTACTTGTGTAAAATAAACTGGAGTTGAAA
1 -GTGTTGATGCAGA-GAATGATTGTGTGTGATATGGTACTTGTGCAAAATAAACTGGAGCTGAAA
* * * *
40766856 GTGTTGATGCGGGGAGTGATTGTATGTGATATG
1 GTGTTGATGCAGAGAATGATTGTGTGTGATATG
40766889 ATGTGATACT
Statistics
Matches: 76, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
62 1 0.01
63 72 0.95
64 3 0.04
ACGTcount: A:0.25, C:0.08, G:0.33, T:0.34
Consensus pattern (63 bp):
GTGTTGATGCAGAGAATGATTGTGTGTGATATGGTACTTGTGCAAAATAAACTGGAGCTGAAA
Found at i:40768587 original size:7 final size:7
Alignment explanation
Indices: 40768575--40768620 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
40768565 ATTAAAAAAC
40768575 AATTGAG
1 AATTGAG
40768582 AATTGAG
1 AATTGAG
40768589 AATTGAG
1 AATTGAG
** *
40768596 GGTTGAA
1 AATTGAG
40768603 AATTGAG
1 AATTGAG
*
40768610 GATTGAG
1 AATTGAG
40768617 AATT
1 AATT
40768621 TAAGATTGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (7 bp):
AATTGAG
Found at i:40768594 original size:14 final size:14
Alignment explanation
Indices: 40768575--40768630 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
40768565 ATTAAAAAAC
*
40768575 AATTGAGAATTGAG
1 AATTGAGGATTGAG
* *
40768589 AATTGAGGGTTGAA
1 AATTGAGGATTGAG
40768603 AATTGAGGATTGAG
1 AATTGAGGATTGAG
* *
40768617 AATTTAAGATTGAG
1 AATTGAGGATTGAG
40768631 GAATGAATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (14 bp):
AATTGAGGATTGAG
Found at i:40768606 original size:21 final size:21
Alignment explanation
Indices: 40768577--40768616 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40768567 TAAAAAACAA
*
40768577 TTGAGAATTGAGAATTGAGGG
1 TTGAAAATTGAGAATTGAGGG
*
40768598 TTGAAAATTGAGGATTGAG
1 TTGAAAATTGAGAATTGAG
40768617 AATTTAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (21 bp):
TTGAAAATTGAGAATTGAGGG
Found at i:40773460 original size:15 final size:16
Alignment explanation
Indices: 40773440--40773469 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40773430 CTATTTACTT
40773440 TTCCTC-AAACTTTTA
1 TTCCTCAAAACTTTTA
40773455 TTCCTCAAAACTTTT
1 TTCCTCAAAACTTTT
40773470 TATTTTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (16 bp):
TTCCTCAAAACTTTTA
Found at i:40779310 original size:13 final size:13
Alignment explanation
Indices: 40779292--40779323 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
40779282 ATTTTTTATG
40779292 AAAAAAATAATAT
1 AAAAAAATAATAT
40779305 AAAAAAATAATAT
1 AAAAAAATAATAT
40779318 AAAAAA
1 AAAAAA
40779324 GTTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAAAATAATAT
Found at i:40789992 original size:19 final size:18
Alignment explanation
Indices: 40789934--40790002 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 18
40789924 ATTGAGACTG
40789934 ATACTGAATTGAATTATGGA
1 ATACTGAATTGAATT-T-GA
* *
40789954 ATACTGAATATTACTTTGA
1 ATACTGAAT-TGAATTTGA
40789973 ATACTGAATTGAATTGTGA
1 ATACTGAATTGAATT-TGA
40789992 AGTTACTGAAT
1 A--TACTGAAT
40790003 ATTGTTATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 4 0.10
19 15 0.37
20 10 0.24
21 12 0.29
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (18 bp):
ATACTGAATTGAATTTGA
Found at i:40790517 original size:45 final size:44
Alignment explanation
Indices: 40790453--40790590 Score: 204
Period size: 45 Copynumber: 3.1 Consensus size: 44
40790443 CTGTTACTGC
*
40790453 TACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATATTGT
1 TACTGTTACCGTTACCGATTCG-CACTTTGTGTGTCGAATATTGT
* **
40790498 TACTGTTACCGTTATCGATTCGGCACCCTGTGTGTCGAATATTGT
1 TACTGTTACCGTTACCGATTC-GCACTTTGTGTGTCGAATATTGT
*
40790543 TACTGTTACCGTTACCGATTCTGCACTTTGTGTGTCGGATATTGT
1 TACTGTTACCGTTACCGATTC-GCACTTTGTGTGTCGAATATTGT
40790588 TAC
1 TAC
40790591 CGTACTGTTA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 82 0.99
46 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (44 bp):
TACTGTTACCGTTACCGATTCGCACTTTGTGTGTCGAATATTGT
Found at i:40790677 original size:51 final size:53
Alignment explanation
Indices: 40790593--40790703 Score: 138
Period size: 51 Copynumber: 2.1 Consensus size: 53
40790583 ATTGTTACCG
** *
40790593 TACTGTTACTATTTCGGATTTGTTGTGAAGAGGTACT-T-TGTACCTTACTGT
1 TACTGTTACTATTTCGGATTTGTTGCCAAGAGGTACTCTATGTACCGTACTGT
* * *
40790644 TATTGTTACTGTTTCGGATTTGTT-CCAATGAGGTACTCTATGTACCGTATTGT
1 TACTGTTACTATTTCGGATTTGTTGCCAA-GAGGTACTCTATGTACCGTACTGT
40790697 TACTGTT
1 TACTGTT
40790704 CCGGCTTCAG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 2 0.04
51 30 0.60
52 1 0.02
53 17 0.34
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.46
Consensus pattern (53 bp):
TACTGTTACTATTTCGGATTTGTTGCCAAGAGGTACTCTATGTACCGTACTGT
Found at i:40795795 original size:43 final size:43
Alignment explanation
Indices: 40795734--40796662 Score: 1806
Period size: 43 Copynumber: 21.6 Consensus size: 43
40795724 CCGGCATTAC
* *
40795734 GCCTGCTAGGCATGAAGGCCCGAATACACATCA-CTAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATC-GGCACGAA
*
40795777 GCCTGCTAGGCACAAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40795820 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40795863 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40795906 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40795949 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40795992 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796035 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796078 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796121 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796164 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796207 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796250 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796293 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796336 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796379 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796422 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796465 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796508 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796551 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
40796594 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
*
40796637 GCCTGCTAGGCACGAAGGCCCAAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
40796663 TAATACCAGC
Statistics
Matches: 880, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
43 879 1.00
44 1 0.00
ACGTcount: A:0.30, C:0.32, G:0.25, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
Found at i:40796757 original size:38 final size:38
Alignment explanation
Indices: 40796660--40796762 Score: 120
Period size: 38 Copynumber: 2.7 Consensus size: 38
40796650 GAAGGCCCAA
* *
40796660 ATATAATACCAGCACTAGGCCTGCGGGATTTAACCCGG
1 ATATAATTCCAGCACTAAGCCTGCGGGATTTAACCCGG
* * *
40796698 ATAT-ATTACCAGCACGAAGCCTGTGGGATTTAACTCGG
1 ATATAATT-CCAGCACTAAGCCTGCGGGATTTAACCCGG
*
40796736 ATATAATTCCAGCA-TATAGCCTTCGGG
1 ATATAATTCCAGCACTA-AGCCTGCGGG
40796763 TCTTTAGGCC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
37 3 0.06
38 48 0.89
39 3 0.06
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.25
Consensus pattern (38 bp):
ATATAATTCCAGCACTAAGCCTGCGGGATTTAACCCGG
Found at i:40806427 original size:56 final size:57
Alignment explanation
Indices: 40806327--40806433 Score: 173
Period size: 56 Copynumber: 1.9 Consensus size: 57
40806317 TTTAAAAGGA
* *
40806327 AATTAGACCCAAAATTTATTTGGGCTGGACGGAAAGGGTATGAAATCAGCAAAAAGC
1 AATTAGACCCAAAATTTATTTGGGCTGGACGCAAAGGGCATGAAATCAGCAAAAAGC
40806384 AATTAGACCCAAAA-TTATTTGGGCTGGACAGCAAA-GGCATGAAATCAGCA
1 AATTAGACCCAAAATTTATTTGGGCTGGAC-GCAAAGGGCATGAAATCAGCA
40806434 GGAAAATTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
56 29 0.62
57 18 0.38
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (57 bp):
AATTAGACCCAAAATTTATTTGGGCTGGACGCAAAGGGCATGAAATCAGCAAAAAGC
Found at i:40808787 original size:14 final size:14
Alignment explanation
Indices: 40808768--40808797 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40808758 TATCTTATAC
40808768 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
40808782 ATATGCGTTAATCT
1 ATATGCGTGAATCT
40808796 AT
1 AT
40808798 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:40810946 original size:17 final size:18
Alignment explanation
Indices: 40810914--40810949 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
40810904 AAAATCATAG
40810914 CTTTTTCTCCTTTCTTTCT
1 CTTTTTCT-CTTTCTTTCT
40810933 CTTTTTCT-TTTCTTTCT
1 CTTTTTCTCTTTCTTTCT
40810950 TTCCTTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTTTCTCTTTCTTTCT
Found at i:40810951 original size:25 final size:25
Alignment explanation
Indices: 40810923--40810970 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40810913 GCTTTTTCTC
* * *
40810923 CTTTCTTTCTCTTTTTCTTTTCTTT
1 CTTTCCTTCTCTGTTTCATTTCTTT
40810948 CTTTCCTTCTCTGTTTCATTTCT
1 CTTTCCTTCTCTGTTTCATTTCT
40810971 ACTTTAGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (25 bp):
CTTTCCTTCTCTGTTTCATTTCTTT
Found at i:40810969 original size:21 final size:21
Alignment explanation
Indices: 40810923--40810970 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
40810913 GCTTTTTCTC
*
40810923 CTTTCTTTCTCTTTTTCTTTT
1 CTTTCTTTCTCTTTCTCTTTT
40810944 CTTTCTTTC-C-TTCTCTGTTT
1 CTTTCTTTCTCTTTCTCT-TTT
40810964 CATTTCT
1 C-TTTCT
40810971 ACTTTAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.21
20 5 0.21
21 14 0.58
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (21 bp):
CTTTCTTTCTCTTTCTCTTTT
Found at i:40811008 original size:25 final size:24
Alignment explanation
Indices: 40810980--40811026 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
40810970 TACTTTAGCT
40810980 TTCTTT-TTCTATTTCTATTTATTTA
1 TTCTTTCTT-TATTTCT-TTTATTTA
*
40811005 TTCTTTCTTTATTTGTTTTATT
1 TTCTTTCTTTATTTCTTTTATT
40811027 ATATATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (24 bp):
TTCTTTCTTTATTTCTTTTATTTA
Found at i:40811039 original size:5 final size:5
Alignment explanation
Indices: 40811029--40811187 Score: 318
Period size: 5 Copynumber: 31.8 Consensus size: 5
40811019 GTTTTATTAT
40811029 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
40811079 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
40811129 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
40811179 ATATA ATAT
1 ATATA ATAT
40811188 NNNNNNNNNN
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 154 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:40812606 original size:39 final size:39
Alignment explanation
Indices: 40812513--40812661 Score: 205
Period size: 39 Copynumber: 3.9 Consensus size: 39
40812503 ATTCCACTCC
* * * *
40812513 CCCCATTCTACTTTGTTTTATTATTAATCAAAAAC-ACTT
1 CCCCATACTATTTTGTTTTATTGTTAAT-TAAAACTACTT
* *
40812552 -CCCATGCTATTTTGTTTTATTGTTAATTAAAACTATTT
1 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACTT
40812590 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACTT
1 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACTT
*
40812629 CCTCATACTATTTTGTTTTATT-TTAATTAAAAC
1 CCCCATACTATTTTGTTTTATTGTTAATTAAAAC
40812662 CATACTTTAT
Statistics
Matches: 100, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
37 5 0.05
38 38 0.38
39 57 0.57
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (39 bp):
CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACTT
Found at i:40812611 original size:77 final size:77
Alignment explanation
Indices: 40812513--40812661 Score: 221
Period size: 77 Copynumber: 1.9 Consensus size: 77
40812503 ATTCCACTCC
* *
40812513 CCCCATTCTACTTTGTTTTATTATTAATCAAAAAC-ACTTCC-CATGCTATTTTGTTTTATTGTT
1 CCCCATACTACTTTGTTTTATTATTAAT-AAAAACTACTTCCTCATACTATTTTGTTTTATT-TT
40812576 AATTAAAACTATTT
64 AATTAAAACTATTT
* * *
40812590 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACTTCCTCATACTATTTTGTTTTATTTTAA
1 CCCCATACTACTTTGTTTTATTATTAATAAAAACTACTTCCTCATACTATTTTGTTTTATTTTAA
40812655 TTAAAAC
66 TTAAAAC
40812662 CATACTTTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
76 5 0.08
77 42 0.65
78 18 0.28
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (77 bp):
CCCCATACTACTTTGTTTTATTATTAATAAAAACTACTTCCTCATACTATTTTGTTTTATTTTAA
TTAAAACTATTT
Found at i:40816746 original size:20 final size:20
Alignment explanation
Indices: 40816721--40816761 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40816711 TATATATATT
*
40816721 TGTGATATT-ATTATGAATTA
1 TGTGAT-TTAATTATAAATTA
40816741 TGTGATTTAATTATAAATTA
1 TGTGATTTAATTATAAATTA
40816761 T
1 T
40816762 ATCTTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (20 bp):
TGTGATTTAATTATAAATTA
Found at i:40821755 original size:52 final size:52
Alignment explanation
Indices: 40821677--40821776 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 52
40821667 CTAAGAAAGA
*
40821677 GGGTGTTAGTTACACACATGTTTGCGACGATATGTTGACGAGATCCACACAT
1 GGGTGTTAGTTACACACATGTTTGCGACGATATGCTGACGAGATCCACACAT
*
40821729 GGGTGTTAGTTACACACCTGTTTGCGACGATATGCTGACGAGATCCAC
1 GGGTGTTAGTTACACACATGTTTGCGACGATATGCTGACGAGATCCAC
40821777 GCACGAACTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (52 bp):
GGGTGTTAGTTACACACATGTTTGCGACGATATGCTGACGAGATCCACACAT
Done.