Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 173 of 322
Found at i:56535873 original size:24 final size:23
Alignment explanation
Indices: 56535829--56535873 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
56535819 TTTTATTAAA
* * *
56535829 ATAATATAAATATTTACATATTT
1 ATAATATAAAAATTCAAATATTT
56535852 ATAATTATAAAAATTCAAATAT
1 ATAA-TATAAAAATTCAAATAT
56535874 GTAATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAATATAAAAATTCAAATATTT
Found at i:56541679 original size:53 final size:53
Alignment explanation
Indices: 56541613--56541744 Score: 192
Period size: 53 Copynumber: 2.5 Consensus size: 53
56541603 GCAAGATTGT
** * *
56541613 AACTGGTGGGTTATGGCATTATATGGGGAAAAGACTATATTGTATAAGACCGC
1 AACTGGTAAGTTATGGCATCATATGGGGAAAAGACTATATTATATAAGACCGC
* * * *
56541666 AATTGGTAAGTTATGGCATCATATGGGGAGAAGACTATATTATGTAAGACCGT
1 AACTGGTAAGTTATGGCATCATATGGGGAAAAGACTATATTATATAAGACCGC
56541719 AACTGGTAAGTTATGGCATCATATGG
1 AACTGGTAAGTTATGGCATCATATGG
56541745 AAAATAATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 70 1.00
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (53 bp):
AACTGGTAAGTTATGGCATCATATGGGGAAAAGACTATATTATATAAGACCGC
Found at i:56541935 original size:31 final size:32
Alignment explanation
Indices: 56541891--56542001 Score: 109
Period size: 32 Copynumber: 3.5 Consensus size: 32
56541881 ACTCTGGACA
* *
56541891 GAAAGGCCTTTGTGGCGAGTAGTGGTTGTAAAG
1 GAAA-GCCTTTGTGGCGAGTACTGGATGTAAAG
* * * *
56541924 GAAAGCC-TTGTGGCTAGTATTGCATGTAAAT
1 GAAAGCCTTTGTGGCGAGTACTGGATGTAAAG
* * *
56541955 GATAGCCTTTGTAGCGAGTACTAGATGTAAAG
1 GAAAGCCTTTGTGGCGAGTACTGGATGTAAAG
56541987 GACAA-CCTTTGTGGC
1 GA-AAGCCTTTGTGGC
56542002 ATAATTCTAG
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
31 25 0.40
32 32 0.52
33 5 0.08
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.29
Consensus pattern (32 bp):
GAAAGCCTTTGTGGCGAGTACTGGATGTAAAG
Found at i:56542104 original size:61 final size:61
Alignment explanation
Indices: 56541964--56542130 Score: 185
Period size: 61 Copynumber: 2.8 Consensus size: 61
56541954 TGATAGCCTT
* * * * * *
56541964 TGTAGCGAGTACTAGATGTAAAGGACAACCTTTGTGGCATAATTCTAGACAGGAAAGCCTT
1 TGTAGCGAGTACTAGATGTAAAGGATAGCCTTTGTGGCAAAACTCTAGACAGGAAAACCTC
* * * * * * *
56542025 TGT-GACTAGTATTGGATGTAAATGATAGCTTTTGTGGCACAACTCTAGATAGGAAAACCTC
1 TGTAG-CGAGTACTAGATGTAAAGGATAGCCTTTGTGGCAAAACTCTAGACAGGAAAACCTC
*
56542086 TGTAGCGAGTACTAGATGTAAGGGAT-GCCTTTGTGGCAAAACTCT
1 TGTAGCGAGTACTAGATGTAAAGGATAGCCTTTGTGGCAAAACTCT
56542131 GGAAAGGTAA
Statistics
Matches: 85, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
60 18 0.21
61 66 0.78
62 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (61 bp):
TGTAGCGAGTACTAGATGTAAAGGATAGCCTTTGTGGCAAAACTCTAGACAGGAAAACCTC
Found at i:56542330 original size:146 final size:146
Alignment explanation
Indices: 56542093--56542374 Score: 354
Period size: 146 Copynumber: 1.9 Consensus size: 146
56542083 CTCTGTAGCG
* * **
56542093 AGTACTAGATGTAAGGGATGCCTTTGTGGCAAAACTCTGGAAAGGTAAGCCCTTATGACAATGTC
1 AGTACTAGATGTAAAGGATGCCTTTATGGCAAAACTCTGGAAAGGTAAGCCCTTATGACAACCTC
* * *
56542158 TGTTTAAGAACGTCTTTATGGTAAATCTCTG-AGAAGAAACATCTTTGTGACGATCTCTGTTAAA
66 TGTTTAAGAACGTCTTTATGGAAAATCTCTGAAG-AGAAACATCTTAGTGACAATCTCTGTTAAA
56542222 AGAAAGTCTTTGTGGCA
130 AGAAAGTCTTTGTGGCA
* * * * * * *
56542239 AGTACTGGATGTAAATGATGCCTTTATGGCAGAACTTTGGAAAGGTAAGTCCTTATGGCAACCTT
1 AGTACTAGATGTAAAGGATGCCTTTATGGCAAAACTCTGGAAAGGTAAGCCCTTATGACAACCTC
* * *
56542304 TGTTTAAGAACG-CTTT-TGTAGAAAATCTTTGAAGGGAAACATCTTAGTGGCAATCTCTGTTAA
66 TGTTTAAGAACGTCTTTATG--GAAAATCTCTGAAGAGAAACATCTTAGTGACAATCTCTGTTAA
*
56542367 AGGAAAGT
129 AAGAAAGT
56542375 TTTTCTGGTA
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
144 2 0.02
145 4 0.03
146 107 0.93
147 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (146 bp):
AGTACTAGATGTAAAGGATGCCTTTATGGCAAAACTCTGGAAAGGTAAGCCCTTATGACAACCTC
TGTTTAAGAACGTCTTTATGGAAAATCTCTGAAGAGAAACATCTTAGTGACAATCTCTGTTAAAA
GAAAGTCTTTGTGGCA
Found at i:56560248 original size:14 final size:14
Alignment explanation
Indices: 56560223--56560256 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
56560213 TTAGAGTTAG
56560223 TAAAAG-AAATAAA
1 TAAAAGAAAATAAA
56560236 TAAAAGAAAATAAA
1 TAAAAGAAAATAAA
56560250 TAAAAGA
1 TAAAAGA
56560257 GTTAGTAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (14 bp):
TAAAAGAAAATAAA
Found at i:56561259 original size:35 final size:34
Alignment explanation
Indices: 56561196--56561267 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 34
56561186 ACTATTGCTG
* *
56561196 GGCACATAACTGTCGGTTAATCCGACTAGCGCTA
1 GGCACATAACTGTCGGTTAATCCAACTAGAGCTA
* * *
56561230 GGCACAATTACTGTTGGTTTATCCAACTAGAGCTA
1 GGCAC-ATAACTGTCGGTTAATCCAACTAGAGCTA
56561265 GGC
1 GGC
56561268 TTATAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 5 0.16
35 27 0.84
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (34 bp):
GGCACATAACTGTCGGTTAATCCAACTAGAGCTA
Found at i:56561635 original size:20 final size:20
Alignment explanation
Indices: 56561610--56561652 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
56561600 CTCGGCATCC
56561610 AGTGAGAATCCCATACTCAA
1 AGTGAGAATCCCATACTCAA
56561630 AGTGAGAATCCCATACTCAA
1 AGTGAGAATCCCATACTCAA
56561650 AGT
1 AGT
56561653 TAGTGACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (20 bp):
AGTGAGAATCCCATACTCAA
Found at i:56564257 original size:15 final size:15
Alignment explanation
Indices: 56564237--56564267 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56564227 GAAGTTACTT
*
56564237 AAAAAATTAAAAATA
1 AAAAAATAAAAAATA
56564252 AAAAAATAAAAAATA
1 AAAAAATAAAAAATA
56564267 A
1 A
56564268 TTTAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAATAAAAAATA
Found at i:56569802 original size:23 final size:23
Alignment explanation
Indices: 56569776--56569823 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
56569766 GCGAATAGGG
* *
56569776 GATGGCGAGTTATGGACGTGGGA
1 GATGGCAAGCTATGGACGTGGGA
*
56569799 GATGGCAAGCTGTGGACGTGGGA
1 GATGGCAAGCTATGGACGTGGGA
56569822 GA
1 GA
56569824 AGGTGAGCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.48, T:0.19
Consensus pattern (23 bp):
GATGGCAAGCTATGGACGTGGGA
Found at i:56569832 original size:23 final size:23
Alignment explanation
Indices: 56569788--56569835 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
56569778 TGGCGAGTTA
*
56569788 TGGACGTGGGAGATGGCAAGCTG
1 TGGACGTGGGAGAAGGCAAGCTG
**
56569811 TGGACGTGGGAGAAGGTGAGCTG
1 TGGACGTGGGAGAAGGCAAGCTG
56569834 TG
1 TG
56569836 AACATCAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.10, G:0.50, T:0.19
Consensus pattern (23 bp):
TGGACGTGGGAGAAGGCAAGCTG
Found at i:56572101 original size:23 final size:23
Alignment explanation
Indices: 56572071--56572116 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
56572061 TCATATCATG
56572071 CGTCAGAAATGCAGGGTTTGGGC
1 CGTCAGAAATGCAGGGTTTGGGC
56572094 CGTCAGAAATGCAGGGTTTGGGC
1 CGTCAGAAATGCAGGGTTTGGGC
56572117 ATAAGGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.22
Consensus pattern (23 bp):
CGTCAGAAATGCAGGGTTTGGGC
Found at i:56590593 original size:16 final size:16
Alignment explanation
Indices: 56590572--56590623 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
56590562 TTTGGTTTGC
56590572 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
56590588 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
* * *
56590604 TGTAATGGAATAGAAG
1 TGTATTGGATTAGAGG
56590620 TGTA
1 TGTA
56590624 ATAACAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:56591232 original size:19 final size:20
Alignment explanation
Indices: 56591194--56591234 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
56591184 TTTTATATTG
56591194 AAAATTTTAGAATATTATAT
1 AAAATTTTAGAATATTATAT
* *
56591214 AAAATTTT-TAATGTTATAT
1 AAAATTTTAGAATATTATAT
56591233 AA
1 AA
56591235 TTTTCTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
AAAATTTTAGAATATTATAT
Found at i:56594764 original size:55 final size:56
Alignment explanation
Indices: 56594661--56594778 Score: 136
Period size: 56 Copynumber: 2.1 Consensus size: 56
56594651 TTTTACATGA
*
56594661 TTTTATTAAATTCATATAAGAATATTTTATATTAAGAATTGTATTAAATTATATAT
1 TTTTATTAAATTCATATAAGAATATATTATATTAAGAATTGTATTAAATTATATAT
* * *
56594717 TTTTATTAAATT-ATATTTAATAATA-ATTATGTTAA-AATATG-ATTAAATTATTTAT
1 TTTTATTAAATTCATA--TAAGAATATATTATATTAAGAAT-TGTATTAAATTATATAT
56594772 TATTTAT
1 T-TTTAT
56594779 ATTAATAATC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
55 20 0.37
56 27 0.50
57 7 0.13
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (56 bp):
TTTTATTAAATTCATATAAGAATATATTATATTAAGAATTGTATTAAATTATATAT
Found at i:56594984 original size:16 final size:16
Alignment explanation
Indices: 56594963--56595013 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
56594953 AATTGATTTG
56594963 CCATTACGCCTCTATT
1 CCATTACGCCTCTATT
**
56594979 CCATTACTTCTCTATT
1 CCATTACGCCTCTATT
56594995 CCATTACGCCTCTATT
1 CCATTACGCCTCTATT
56595011 CCA
1 CCA
56595014 ATACAGCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.20, C:0.37, G:0.04, T:0.39
Consensus pattern (16 bp):
CCATTACGCCTCTATT
Found at i:56599833 original size:17 final size:17
Alignment explanation
Indices: 56599813--56599848 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
56599803 GAGAAAACAC
56599813 ATTTATTTCTGAATATG
1 ATTTATTTCTGAATATG
56599830 ATTTATTTCTGAATATG
1 ATTTATTTCTGAATATG
56599847 AT
1 AT
56599849 CCATTTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (17 bp):
ATTTATTTCTGAATATG
Found at i:56599854 original size:17 final size:17
Alignment explanation
Indices: 56599817--56599856 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
56599807 AAACACATTT
**
56599817 ATTTCTGAATATGATTT
1 ATTTCTGAATATGATCC
56599834 ATTTCTGAATATGATCC
1 ATTTCTGAATATGATCC
56599851 ATTTCT
1 ATTTCT
56599857 CTAACTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (17 bp):
ATTTCTGAATATGATCC
Found at i:56603572 original size:25 final size:25
Alignment explanation
Indices: 56603513--56603574 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
56603503 ACCTTAACGC
**
56603513 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGGCAGT
** *
56603538 AATCTTTGATTATTAGCACGGCAGT
1 GCTCTCTGATTATTAGCACGGCAGT
56603563 GCTCTCTGATTA
1 GCTCTCTGATTA
56603575 GCACATTTGT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGGCAGT
Found at i:56604928 original size:21 final size:21
Alignment explanation
Indices: 56604890--56604929 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56604880 GCCAGATAAT
*
56604890 GTTTGAAAAATGTTAAATCTC
1 GTTTGAAAAATGTAAAATCTC
56604911 GTTTGAATAAATG-AAAATC
1 GTTTGAA-AAATGTAAAATC
56604930 GATGGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (21 bp):
GTTTGAAAAATGTAAAATCTC
Found at i:56618498 original size:29 final size:27
Alignment explanation
Indices: 56618466--56618546 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
56618456 TTAAAGGAAA
*
56618466 ATTTTTTGAGAGTTTAGTGGCCAAATAGT
1 ATTTTTTGA-A-TTAAGTGGCCAAATAGT
*
56618495 ATTTTTTTTAATTAAGTGGCCAAATAGT
1 A-TTTTTTGAATTAAGTGGCCAAATAGT
* *
56618523 ATTTTTTTTAATTAAGTGACCAAA
1 A-TTTTTTGAATTAAGTGGCCAAA
56618547 ACAAAAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
28 39 0.81
29 2 0.04
30 7 0.15
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.44
Consensus pattern (27 bp):
ATTTTTTGAATTAAGTGGCCAAATAGT
Found at i:56618512 original size:28 final size:28
Alignment explanation
Indices: 56618481--56618546 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
56618471 TTGAGAGTTT
56618481 AGTGGCCAAATAGTATTTTTTTTAATTA
1 AGTGGCCAAATAGTATTTTTTTTAATTA
56618509 AGTGGCCAAATAGTATTTTTTTTAATTA
1 AGTGGCCAAATAGTATTTTTTTTAATTA
*
56618537 AGTGACCAAA
1 AGTGGCCAAA
56618547 ACAAAAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (28 bp):
AGTGGCCAAATAGTATTTTTTTTAATTA
Found at i:56623576 original size:23 final size:23
Alignment explanation
Indices: 56623548--56623593 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
56623538 ATTAAACCAT
56623548 TAAATAT-TAAATTAAAAATAATA
1 TAAATATAT-AATTAAAAATAATA
*
56623571 TAAATATATATTTAAAAATAATA
1 TAAATATATAATTAAAAATAATA
56623594 ATATGAGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATATATAATTAAAAATAATA
Found at i:56629344 original size:28 final size:29
Alignment explanation
Indices: 56629312--56629372 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
56629302 ATAAATAAAA
* *
56629312 AAAACATTGTAACGG-ACTTAAATTTATT
1 AAAACATTGTAACGGTACTAAAAATTATT
* *
56629340 AAAACATTTTAATGGTACTAAAAATTATT
1 AAAACATTGTAACGGTACTAAAAATTATT
56629369 AAAA
1 AAAA
56629373 ATTCACATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34
Consensus pattern (29 bp):
AAAACATTGTAACGGTACTAAAAATTATT
Found at i:56630830 original size:15 final size:15
Alignment explanation
Indices: 56630810--56630887 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
56630800 TTTATGAAAA
56630810 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
56630825 ATCAAACA-ATAGAA
1 ATCAAAGATATGGGT
56630839 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
56630855 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
56630869 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
56630885 ATC
1 ATC
56630888 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:56630847 original size:30 final size:30
Alignment explanation
Indices: 56630811--56630887 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
56630801 TTATGAAAAA
56630811 TCAAAGATATGGGTATCAAACAATAGAAAG
1 TCAAAGATATGGGTATCAAACAATAGAAAG
* * *
56630841 TCAAAGATATGGGTATCAAATATTGGAAAG
1 TCAAAGATATGGGTATCAAACAATAGAAAG
56630871 TCAAAGATATGGGTATC
1 TCAAAGATATGGGTATC
56630888 GAGATATTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (30 bp):
TCAAAGATATGGGTATCAAACAATAGAAAG
Found at i:56635509 original size:30 final size:30
Alignment explanation
Indices: 56635468--56635551 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
56635458 CATATTTATG
*
56635468 GAAAATCAAAGATATGGGTATCGAATAATA
1 GAAAGTCAAAGATATGGGTATCGAATAATA
* * *
56635498 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCGAATAATA
56635528 GAAAGTCAAAGATATGGGTATCGA
1 GAAAGTCAAAGATATGGGTATCGA
56635552 GATATTGGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCGAATAATA
Found at i:56638582 original size:14 final size:15
Alignment explanation
Indices: 56638565--56638593 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56638555 GAGTACAATA
56638565 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
56638579 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
56638594 TACTAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:56639646 original size:14 final size:14
Alignment explanation
Indices: 56639627--56639659 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
56639617 CACAGGCAAA
*
56639627 AGTGCGCCTATGTT
1 AGTGCGCCTATGTC
56639641 AGTGCGCCTATGTC
1 AGTGCGCCTATGTC
56639655 AGTGC
1 AGTGC
56639660 ATTTTTACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.24, G:0.30, T:0.30
Consensus pattern (14 bp):
AGTGCGCCTATGTC
Found at i:56648213 original size:13 final size:13
Alignment explanation
Indices: 56648176--56648218 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
56648166 TTTTATTTTA
56648176 ATGTTAATTTCTT
1 ATGTTAATTTCTT
* *
56648189 AT-TTCATATTCTG
1 ATGTTAAT-TTCTT
56648202 ATGTTAATTTCTT
1 ATGTTAATTTCTT
56648215 ATGT
1 ATGT
56648219 CCCATGTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 4 0.17
13 16 0.67
14 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58
Consensus pattern (13 bp):
ATGTTAATTTCTT
Found at i:56657360 original size:29 final size:29
Alignment explanation
Indices: 56657318--56657374 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
56657308 TAAATAAATT
56657318 CTTTTTTGGAACTACATAGATCTATGGAG
1 CTTTTTTGGAACTACATAGATCTATGGAG
56657347 CTTTTTTGGAACTACATAGATCTATGGA
1 CTTTTTTGGAACTACATAGATCTATGGA
56657375 ATCGGTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (29 bp):
CTTTTTTGGAACTACATAGATCTATGGAG
Found at i:56659103 original size:23 final size:23
Alignment explanation
Indices: 56659077--56659122 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
56659067 GGGATATTAG
56659077 ATATTGACTAGTTATATACGAAC
1 ATATTGACTAGTTATATACGAAC
56659100 ATATTGACTAGTTATATACGAAC
1 ATATTGACTAGTTATATACGAAC
56659123 TCAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
ATATTGACTAGTTATATACGAAC
Found at i:56663498 original size:21 final size:21
Alignment explanation
Indices: 56663458--56663514 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
56663448 TTTTGACTTT
56663458 TTTTCTCTT-GTTCGGTTTTTTC
1 TTTTCTCTTGGTT--GTTTTTTC
56663480 TTTTCTCTTGGTTGTTTTTTC
1 TTTTCTCTTGGTTGTTTTTTC
56663501 TTTTCTCTTGGTTG
1 TTTTCTCTTGGTTG
56663515 GAAAAACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 22 0.65
22 9 0.26
23 3 0.09
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (21 bp):
TTTTCTCTTGGTTGTTTTTTC
Found at i:56663802 original size:13 final size:15
Alignment explanation
Indices: 56663784--56663822 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
56663774 GAAGATGGAT
56663784 AAATAAA-AAAA-AG
1 AAATAAATAAAATAG
56663797 AAATAAATAAAATAG
1 AAATAAATAAAATAG
56663812 AATATAAATAA
1 AA-ATAAATAA
56663823 GATAAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 4 0.17
15 4 0.17
16 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (15 bp):
AAATAAATAAAATAG
Found at i:56664509 original size:11 final size:11
Alignment explanation
Indices: 56664493--56664517 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56664483 GCGATTATTG
56664493 TATTTATTGTA
1 TATTTATTGTA
56664504 TATTTATTGTA
1 TATTTATTGTA
56664515 TAT
1 TAT
56664518 AAATATAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TATTTATTGTA
Found at i:56665141 original size:21 final size:21
Alignment explanation
Indices: 56665102--56665141 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
56665092 TTTATTTAAA
*
56665102 AATATAAATGATATAGAATAT
1 AATATAAATGAAATAGAATAT
*
56665123 AATATAAATGAAATGGAAT
1 AATATAAATGAAATAGAAT
56665142 TACTGATAAA
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:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
AATATAAATGAAATAGAATAT
Found at i:56665285 original size:14 final size:14
Alignment explanation
Indices: 56665266--56665294 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56665256 TAGATAAATA
56665266 ATAATCTATATAAC
1 ATAATCTATATAAC
56665280 ATAATCTATATAAC
1 ATAATCTATATAAC
56665294 A
1 A
56665295 AAGTAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATCTATATAAC
Found at i:56667007 original size:19 final size:19
Alignment explanation
Indices: 56666983--56667022 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
56666973 TTATTTTTTT
* *
56666983 ATTAGAATCGAAAAGTTTA
1 ATTAGAATAGAAAAGTATA
56667002 ATTAGAATAGAAAAGTATA
1 ATTAGAATAGAAAAGTATA
56667021 AT
1 AT
56667023 AAAAGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.30
Consensus pattern (19 bp):
ATTAGAATAGAAAAGTATA
Found at i:56668537 original size:16 final size:16
Alignment explanation
Indices: 56668516--56668548 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56668506 TCTTATTCCT
*
56668516 TTGCTACTATAGAATA
1 TTGCTACTATAAAATA
56668532 TTGCTACTATAAAATA
1 TTGCTACTATAAAATA
56668548 T
1 T
56668549 AGAATACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTGCTACTATAAAATA
Found at i:56671862 original size:29 final size:29
Alignment explanation
Indices: 56671811--56671868 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
56671801 GCAACCCATT
* *
56671811 TTTAGTATCATATCGAAATGCTATTCCTA
1 TTTAGTATCATATCAAAACGCTATTCCTA
* *
56671840 TTTATTATCATATTAAAACGCTATTCCTA
1 TTTAGTATCATATCAAAACGCTATTCCTA
56671869 ATAGAAGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTAGTATCATATCAAAACGCTATTCCTA
Found at i:56678427 original size:24 final size:21
Alignment explanation
Indices: 56678393--56678481 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
56678383 ACAAAAAAGA
*
56678393 TTTGTCTAAGTCACTTCGTTTCTT
1 TTTGTCCAAGTCACTTC---TCTT
*
56678417 TTTGTCCAAGTTACTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
**
56678438 TTTGTCCAAGTTGCTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
* *
56678459 TTTGTCTAACTCACTTC-CTT
1 TTTGTCCAAGTCACTTCTCTT
56678479 TTT
1 TTT
56678482 TCTTTGTGAG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 37 0.64
24 15 0.26
ACGTcount: A:0.12, C:0.24, G:0.10, T:0.54
Consensus pattern (21 bp):
TTTGTCCAAGTCACTTCTCTT
Found at i:56678479 original size:20 final size:21
Alignment explanation
Indices: 56678413--56678481 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
56678403 TCACTTCGTT
56678413 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
56678434 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
56678455 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
56678476 -CTTTTT
1 TCTTTTT
56678482 TCTTTGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:56680874 original size:18 final size:18
Alignment explanation
Indices: 56680840--56680915 Score: 95
Period size: 18 Copynumber: 4.4 Consensus size: 18
56680830 AAGGTTTTCT
56680840 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
*
56680855 TATTGATGATAGTGAGGA
1 TATTGATGATAGTGACGA
* *
56680873 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
*
56680891 TATTGATGATAGTGACGC
1 TATTGATGATAGTGACGA
56680909 TATTGAT
1 TATTGAT
56680916 CGTGACCTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
15 11 0.21
16 1 0.02
18 41 0.77
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:56689172 original size:14 final size:14
Alignment explanation
Indices: 56689153--56689180 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56689143 TATATTAGTA
56689153 TTTTCTATTCTATT
1 TTTTCTATTCTATT
56689167 TTTTCTATTCTATT
1 TTTTCTATTCTATT
56689181 AGTATTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:56689188 original size:6 final size:6
Alignment explanation
Indices: 56689177--56689255 Score: 66
Period size: 5 Copynumber: 14.2 Consensus size: 6
56689167 TTTTCTATTC
* *
56689177 TATTAG TATTAGAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG
1 TATTAG TATT--AG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
56689224 -ATTAG TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG T
56689256 TAGTGATCCC
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
4 4 0.06
5 28 0.44
6 26 0.41
8 6 0.09
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (6 bp):
TATTAG
Found at i:56689203 original size:11 final size:11
Alignment explanation
Indices: 56689178--56689259 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
56689168 TTTCTATTCT
56689178 ATTAGTATTAG
1 ATTAGTATTAG
56689189 ---AGTATTAG
1 ATTAGTATTAG
**
56689197 ATTAGTATTCT
1 ATTAGTATTAG
*
56689208 ATT-CTATTAG
1 ATTAGTATTAG
56689218 TATTAG-ATTAG
1 -ATTAGTATTAG
56689229 TATTAGTTAGATTAG
1 -ATTAG-T--ATTAG
56689244 ATTAGTATTAG
1 ATTAGTATTAG
56689255 -TTAGT
1 ATTAGT
56689260 GATCCCGGCT
Statistics
Matches: 56, Mismatches: 6, Indels: 19
0.69 0.07 0.23
Matches are distributed among these distances:
8 8 0.14
10 9 0.16
11 28 0.50
13 1 0.02
14 5 0.09
15 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:56689244 original size:20 final size:21
Alignment explanation
Indices: 56689214--56689259 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
56689204 TTCTATTCTA
56689214 TTAGTATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
56689235 TTAG-ATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
56689255 TTAGT
1 TTAGT
56689260 GATCCCGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (21 bp):
TTAGTATTAGATTAGTATTAG
Found at i:56693449 original size:39 final size:38
Alignment explanation
Indices: 56693405--56693551 Score: 165
Period size: 39 Copynumber: 3.8 Consensus size: 38
56693395 ATAAAGTATG
* *
56693405 GTTTTAATTAATAATAAAACAAAATAATATGAGAAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGTATG-GAAAGTA
56693444 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAA-TA
1 GTTTTAATTAACAATAAAACAAAATAGTAT--GGAAAGTA
* *
56693483 GTTTTAATTAACAATAAAACAAAATAGCATGG-GAGT-
1 GTTTTAATTAACAATAAAACAAAATAGTATGGAAAGTA
* * * *
56693519 GTTTTTGATTAATAATAAAACAAAGTAGCATGG
1 G-TTTTAATTAACAATAAAACAAAATAGTATGG
56693552 GGGGAGTGGA
Statistics
Matches: 97, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
36 2 0.02
37 31 0.32
39 59 0.61
40 4 0.04
41 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (38 bp):
GTTTTAATTAACAATAAAACAAAATAGTATGGAAAGTA
Found at i:56693556 original size:78 final size:78
Alignment explanation
Indices: 56693405--56693553 Score: 196
Period size: 76 Copynumber: 1.9 Consensus size: 78
56693395 ATAAAGTATG
* *
56693405 GTTTTAATTAATAATAAAACAAAATAATATGAGAAAGTAGTTTTAATTAACAATAAAACAAAATA
1 GTTTTAATTAACAATAAAACAAAATAACATGAGAAAGTAGTTTTAATTAACAATAAAACAAAATA
*
56693470 GTATGGGGAAATA
66 GCATGGGGAAATA
* * * * *
56693483 GTTTTAATTAACAATAAAACAAAATAGCATG-G-GAGT-GTTTTTGATTAATAATAAAACAAAGT
1 GTTTTAATTAACAATAAAACAAAATAACATGAGAAAGTAG-TTTTAATTAACAATAAAACAAAAT
56693545 AGCATGGGG
65 AGCATGGGG
56693554 GGAGTGGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
75 1 0.02
76 32 0.52
77 1 0.02
78 28 0.45
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (78 bp):
GTTTTAATTAACAATAAAACAAAATAACATGAGAAAGTAGTTTTAATTAACAATAAAACAAAATA
GCATGGGGAAATA
Found at i:56694178 original size:35 final size:35
Alignment explanation
Indices: 56694137--56694205 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
56694127 TTGTTTTGTA
56694137 TATTTCCTAATATTAT-AT-CGTTTATATATTTTTTT
1 TATTTCC-AATATTATCATAC-TTTATATATTTTTTT
* *
56694172 TATTTCCCATATTATCTTACTTTATATATTTTTT
1 TATTTCCAATATTATCATACTTTATATATTTTTT
56694206 AACTATATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 7 0.23
35 22 0.73
36 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.01, T:0.62
Consensus pattern (35 bp):
TATTTCCAATATTATCATACTTTATATATTTTTTT
Found at i:56695224 original size:21 final size:19
Alignment explanation
Indices: 56695186--56695224 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
56695176 ACTCCCGTTT
*
56695186 TCATTTTTAAAATCGATTC
1 TCATTTTCAAAATCGATTC
56695205 TCATTTTCCAAAACTCGATT
1 TCATTTT-CAAAA-TCGATT
56695225 TGAAAATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
TCATTTTCAAAATCGATTC
Found at i:56697943 original size:14 final size:16
Alignment explanation
Indices: 56697924--56697960 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
56697914 CGATATTCTT
56697924 TTTGCAT-TCAT-ACA
1 TTTGCATCTCATAACA
56697938 TTTGCATCTCATAACA
1 TTTGCATCTCATAACA
56697954 TTT-CATC
1 TTTGCATC
56697961 ACATCATCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.43
Consensus pattern (16 bp):
TTTGCATCTCATAACA
Found at i:56697960 original size:15 final size:15
Alignment explanation
Indices: 56697924--56697973 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
56697914 CGATATTCTT
56697924 TTTGCAT-TCATACA
1 TTTGCATCTCATACA
56697938 TTTGCATCTCATAACA
1 TTTGCATCTCAT-ACA
*
56697954 TTT-CATCACAT-CA
1 TTTGCATCTCATACA
*
56697967 TCTGCAT
1 TTTGCAT
56697974 TCAAGGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 4 0.13
14 10 0.32
15 11 0.35
16 6 0.19
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (15 bp):
TTTGCATCTCATACA
Found at i:56698039 original size:15 final size:15
Alignment explanation
Indices: 56698019--56698047 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56698009 TACTTTCCAA
56698019 AGAGGTAGAAAAGAG
1 AGAGGTAGAAAAGAG
56698034 AGAGGTAGAAAAGA
1 AGAGGTAGAAAAGA
56698048 AAATCTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (15 bp):
AGAGGTAGAAAAGAG
Found at i:56706378 original size:87 final size:87
Alignment explanation
Indices: 56706284--56706640 Score: 714
Period size: 87 Copynumber: 4.1 Consensus size: 87
56706274 TGTTTACAAG
56706284 GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
1 GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
56706349 TTGTCGTCTCTGTATTGTCAGA
66 TTGTCGTCTCTGTATTGTCAGA
56706371 GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
1 GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
56706436 TTGTCGTCTCTGTATTGTCAGA
66 TTGTCGTCTCTGTATTGTCAGA
56706458 GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
1 GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
56706523 TTGTCGTCTCTGTATTGTCAGA
66 TTGTCGTCTCTGTATTGTCAGA
56706545 GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
1 GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
56706610 TTGTCGTCTCTGTATTGTCAGA
66 TTGTCGTCTCTGTATTGTCAGA
56706632 GAACAAATC
1 GAACAAATC
56706641 GAAGTTTGGC
Statistics
Matches: 270, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 270 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (87 bp):
GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
TTGTCGTCTCTGTATTGTCAGA
Found at i:56706425 original size:47 final size:47
Alignment explanation
Indices: 56706372--56706605 Score: 175
Period size: 47 Copynumber: 5.3 Consensus size: 47
56706362 ATTGTCAGAG
56706372 AACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
1 AACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
* * * * *
56706419 AACAAATCTAAG----A--TGATTTGTC-GTCTC-TGTATT--GTCAGA
1 AACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGT-TTACGT-TGA
56706458 GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
1 -AACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
* * * * *
56706506 AACAAATCTAAG----A--TGATTTGTC-GTCTC-TGTATT--GTCAGA
1 AACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGT-TTACGT-TGA
56706545 GAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
1 -AACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
*
56706593 AACAAATCTAAGA
1 AACAAATCAAAGA
56706606 TGATTTGTCG
Statistics
Matches: 140, Mismatches: 21, Indels: 52
0.66 0.10 0.24
Matches are distributed among these distances:
38 4 0.03
39 10 0.07
40 32 0.23
41 16 0.11
43 2 0.01
44 2 0.01
46 16 0.11
47 44 0.31
48 10 0.07
49 4 0.03
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (47 bp):
AACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
Found at i:56706781 original size:210 final size:209
Alignment explanation
Indices: 56706529--56706935 Score: 595
Period size: 210 Copynumber: 1.9 Consensus size: 209
56706519 TGATTTGTCG
*
56706529 TCTCTGTATTGTCAGAGAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAA
1 TCTCTGTATTGTCAGAGAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAA
* *
56706594 ACAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCAT-TTCCA
66 ACAAATCTAAGATGATTTATCGTCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCATCTT-CA
* *
56706658 CTTTGATGCAAG-GCAGACACATAGCAGATCTTACCTTTAGATGTTTACACTGAAGCAGATCCAA
130 CTTTGATG-AAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTACACTGAAGCAGATCCAA
56706722 GATGACAGATCTTATC
194 GATGACAGATCTTATC
* * * *
56706738 TCTCTGTATTCGGT-AGGGAACAAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTTCGATG
1 TCTCTGTATT--GTCAGAGAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATG
* *
56706802 AAGCAAATCTAAGATGATTTATCGTCTCTGTATTGTCAGAGAACGAATCAAAGTTTGGCATCTTC
64 AAACAAATCTAAGATGATTTATCGTCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCATCTTC
* * * * ** *
56706867 ACTTTGATGGAGAGCAGACACATAGCTGATCTCGCCTTCGGATGTTTATGCTGAAGCGGATCCAA
129 ACTTTGATGAAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTACACTGAAGCAGATCCAA
56706932 GATG
194 GATG
56706936 GTTTGGCATC
Statistics
Matches: 176, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
209 12 0.07
210 160 0.91
211 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (209 bp):
TCTCTGTATTGTCAGAGAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAA
ACAAATCTAAGATGATTTATCGTCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCATCTTCAC
TTTGATGAAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTACACTGAAGCAGATCCAAGA
TGACAGATCTTATC
Found at i:56707180 original size:44 final size:45
Alignment explanation
Indices: 56707130--56707234 Score: 140
Period size: 45 Copynumber: 2.4 Consensus size: 45
56707120 AGTTTGCAAT
* * *
56707130 GAGCAGATTGAAGA-AGCAAATTTGGCGTCTCTGTATTAGACGGG
1 GAGCAGATCGAAGATAACAAATTTGGCGTCTCTGTAGTAGACGGG
* *
56707174 GAGCAGATCGAAGATAATAGATTTGGCGTCTCTGTAGTAGACGGG
1 GAGCAGATCGAAGATAACAAATTTGGCGTCTCTGTAGTAGACGGG
* *
56707219 GGGCAGATCAAAGATA
1 GAGCAGATCGAAGATA
56707235 GCAGATATCG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 13 0.25
45 40 0.75
ACGTcount: A:0.31, C:0.13, G:0.32, T:0.23
Consensus pattern (45 bp):
GAGCAGATCGAAGATAACAAATTTGGCGTCTCTGTAGTAGACGGG
Found at i:56707206 original size:45 final size:45
Alignment explanation
Indices: 56707149--56707234 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
56707139 GAAGAAGCAA
* *
56707149 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAATAG
1 ATTTGGCGTCTCTGTAGTAGACGGGGAGCAGATCAAAGATAATAG
*
56707194 ATTTGGCGTCTCTGTAGTAGACGGGGGGCAGATCAAAGATA
1 ATTTGGCGTCTCTGTAGTAGACGGGGAGCAGATCAAAGATA
56707235 GCAGATATCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.26
Consensus pattern (45 bp):
ATTTGGCGTCTCTGTAGTAGACGGGGAGCAGATCAAAGATAATAG
Found at i:56708542 original size:38 final size:39
Alignment explanation
Indices: 56708447--56708556 Score: 150
Period size: 38 Copynumber: 2.8 Consensus size: 39
56708437 TAAAGTATAG
56708447 TTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTAA
1 TTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTAA
* * **
56708486 TTTTAATTAACAATAAAACAAAATAGTATG-GGGAGTGT
1 TTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTAA
* * *
56708524 TTTTTATTAATAATAAAACAAAGTAGCATGAGG
1 TTTTAATTAATAATAAAACAAAATAGTATGAGG
56708557 GGAGTGGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 31 0.50
39 31 0.50
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.32
Consensus pattern (39 bp):
TTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTAA
Found at i:56710709 original size:25 final size:25
Alignment explanation
Indices: 56710675--56710722 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
56710665 TGAGGTTAGA
56710675 TTTTTTTAAAATCAAGACTAAATAG
1 TTTTTTTAAAATCAAGACTAAATAG
56710700 TTTTTTTAAAATCAAGACTAAAT
1 TTTTTTTAAAATCAAGACTAAAT
56710723 TAACCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (25 bp):
TTTTTTTAAAATCAAGACTAAATAG
Found at i:56715390 original size:15 final size:15
Alignment explanation
Indices: 56715370--56715400 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56715360 GATGGGAGGT
56715370 AGCTTAAAATACTAA
1 AGCTTAAAATACTAA
56715385 AGCTTAAAATACTAA
1 AGCTTAAAATACTAA
56715400 A
1 A
56715401 ATGTTGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (15 bp):
AGCTTAAAATACTAA
Found at i:56719397 original size:31 final size:30
Alignment explanation
Indices: 56719362--56719419 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
56719352 TTGTAACCAA
* *
56719362 ACTTAGATACCAACTTGAGATAAAAAAAAAC
1 ACTTAAATACCAAATTGA-ATAAAAAAAAAC
* *
56719393 ACTTAAATACTAAATTGAATATAAAAA
1 ACTTAAATACCAAATTGAATAAAAAAA
56719420 CTGAACACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 8 0.35
31 15 0.65
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (30 bp):
ACTTAAATACCAAATTGAATAAAAAAAAAC
Found at i:56720616 original size:18 final size:18
Alignment explanation
Indices: 56720584--56720619 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56720574 AGATATCATT
**
56720584 ATCTAAAATTTATTAAAA
1 ATCTAAAATAAATTAAAA
56720602 ATCTAAAATAAATTAAAA
1 ATCTAAAATAAATTAAAA
56720620 TATATATAAA
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:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
ATCTAAAATAAATTAAAA
Found at i:56727691 original size:29 final size:29
Alignment explanation
Indices: 56727655--56727758 Score: 74
Period size: 29 Copynumber: 3.7 Consensus size: 29
56727645 TATTTAATTA
56727655 ATATTTTAAAATTTTAAAAATATTTTTTT
1 ATATTTTAAAATTTTAAAAATATTTTTTT
** * **
56727684 ATATTTTATACTTTTTAATAA-ATTTAATT
1 ATATTTTA-AAATTTTAAAAATATTTTTTT
* * *
56727713 A-ATTTT--AATTTTTAAAATAATTTTTA
1 ATATTTTAAAATTTTAAAAATATTTTTTT
* *
56727739 AAATTTTTAAA-TTTAAAAAT
1 ATATTTTAAAATTTTAAAAAT
56727759 CCACATATAT
Statistics
Matches: 56, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
25 7 0.12
26 5 0.09
27 5 0.09
28 13 0.23
29 17 0.30
30 9 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATTTTAAAATTTTAAAAATATTTTTTT
Found at i:56727735 original size:12 final size:12
Alignment explanation
Indices: 56727718--56727742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56727708 TAATTAATTT
56727718 TAATTTTTAAAA
1 TAATTTTTAAAA
56727730 TAATTTTTAAAA
1 TAATTTTTAAAA
56727742 T
1 T
56727743 TTTTAAATTT
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:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATTTTTAAAA
Found at i:56729215 original size:21 final size:19
Alignment explanation
Indices: 56729178--56729216 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
56729168 TCTAAATCTC
*
56729178 TGTTTAACTATGTTTTCTT
1 TGTTTAACTATATTTTCTT
56729197 TGTTGTAACTTATATTTTCT
1 TGTT-TAAC-TATATTTTCT
56729217 CGATAGTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (19 bp):
TGTTTAACTATATTTTCTT
Found at i:56730866 original size:19 final size:19
Alignment explanation
Indices: 56730844--56730881 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
56730834 TTCCTGATTG
56730844 CAGGAATCCAGTATTCAAT
1 CAGGAATCCAGTATTCAAT
*
56730863 CAGGAATGCAGTATTCAAT
1 CAGGAATCCAGTATTCAAT
56730882 ACTGCTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (19 bp):
CAGGAATCCAGTATTCAAT
Found at i:56738741 original size:11 final size:11
Alignment explanation
Indices: 56738706--56738746 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
56738696 CCTTTCACAA
56738706 TTCTCTCTAAAT
1 TTCTCTC-AAAT
56738718 TTCTC-CAAA-
1 TTCTCTCAAAT
56738727 TTCTCTCAAAT
1 TTCTCTCAAAT
*
56738738 TTCTTTCAA
1 TTCTCTCAA
56738747 TTTTTGTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
9 5 0.19
10 7 0.27
11 9 0.35
12 5 0.19
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:56739870 original size:7 final size:7
Alignment explanation
Indices: 56739854--56739900 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
56739844 TAGTCGTTTC
56739854 GTATTTA
1 GTATTTA
*
56739861 GTACTTA
1 GTATTTA
56739868 GTATTTA
1 GTATTTA
56739875 GTATTTA
1 GTATTTA
*
56739882 TTATTTA
1 GTATTTA
56739889 GTATTTA
1 GTATTTA
56739896 GTATT
1 GTATT
56739901 ACGTATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:56742890 original size:16 final size:15
Alignment explanation
Indices: 56742864--56742893 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
56742854 AGTATGTTAA
56742864 ATAATACAATATTAC
1 ATAATACAATATTAC
56742879 ATAATAACAATATTA
1 ATAAT-ACAATATTA
56742894 TTCAAGAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATACAATATTAC
Found at i:56744415 original size:126 final size:126
Alignment explanation
Indices: 56744181--56744489 Score: 453
Period size: 126 Copynumber: 2.5 Consensus size: 126
56744171 AGTCTAAGGC
* * * * *
56744181 TTTTTCAGATACTACTATAGCAATAAATCGTCCACGTGGGAGTTTTTTTCCGTAATTTTGCTGAT
1 TTTTTCAGATACTACTGTAGCAAAAAAGCGTCCACGTGAGAGTTTTTTTCCGTAATTTTGCTGAC
* *
56744246 AGTGCATCCTGCTTGAAGCGTTTTGACACTATTTTTTTCAGAAACATCTTCTCAAAATTAT
66 AGTCCATCCTGCTTGAAGCGTTTTGACACTATTTGTTTCAGAAACATCTTCTCAAAATTAT
* *
56744307 TTTTTCAAATACTACTGTAGCAAAAAAGCGTCCATGTGAGAGTTTTTTTCCGTAATTTTG-TAGA
1 TTTTTCAGATACTACTGTAGCAAAAAAGCGTCCACGTGAGAGTTTTTTTCCGTAATTTTGCT-GA
*
56744371 CAGTCCATCCTTCTTGAAGCGTTTTTGACACTATTTGTTT-AGAAACATCTTCTCAAAATTAT
65 CAGTCCATCCTGCTTGAAGCG-TTTTGACACTATTTGTTTCAGAAACATCTTCTCAAAATTAT
* * *
56744433 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACAT-AGGAGCTTTTTTCCGTAATT
1 TTTTTCAGATACTACTGTAGCAAAAAAGCGTCCACGTGA-GAGTTTTTTTCCGTAATT
56744490 ATTAGTTAAT
Statistics
Matches: 165, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
125 2 0.01
126 146 0.88
127 17 0.10
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (126 bp):
TTTTTCAGATACTACTGTAGCAAAAAAGCGTCCACGTGAGAGTTTTTTTCCGTAATTTTGCTGAC
AGTCCATCCTGCTTGAAGCGTTTTGACACTATTTGTTTCAGAAACATCTTCTCAAAATTAT
Found at i:56744640 original size:16 final size:15
Alignment explanation
Indices: 56744617--56744653 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
56744607 TTAAAACACA
*
56744617 CTAAAACCCTAAACC
1 CTAAAAACCTAAACC
*
56744632 CTAAAAACCTTAACC
1 CTAAAAACCTAAACC
56744647 CTAAAAA
1 CTAAAAA
56744654 ATCAGGACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.16
Consensus pattern (15 bp):
CTAAAAACCTAAACC
Found at i:56744860 original size:28 final size:27
Alignment explanation
Indices: 56744813--56744865 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
56744803 GTTTTCGGGG
*
56744813 AAAATGGCCATTTCCGGTAAATAATAA
1 AAAATGGCCATTTCCAGTAAATAATAA
56744840 AAAATAGGCCCATTT-CAGTAAATAAT
1 AAAAT-GG-CCATTTCCAGTAAATAAT
56744866 GATATAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 12 0.52
29 6 0.26
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (27 bp):
AAAATGGCCATTTCCAGTAAATAATAA
Found at i:56745267 original size:12 final size:12
Alignment explanation
Indices: 56745250--56745274 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56745240 GACGTGTATA
56745250 ATCGGTTAATTG
1 ATCGGTTAATTG
56745262 ATCGGTTAATTG
1 ATCGGTTAATTG
56745274 A
1 A
56745275 CTCGAATTAC
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:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (12 bp):
ATCGGTTAATTG
Found at i:56745289 original size:20 final size:20
Alignment explanation
Indices: 56745266--56745314 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
56745256 TAATTGATCG
*
56745266 GTTAATTGACTCGAATTACC
1 GTTAATTGACTCAAATTACC
*
56745286 GTTAATTGACTCAAATTACT
1 GTTAATTGACTCAAATTACC
*
56745306 ATTAATTGA
1 GTTAATTGA
56745315 ATTAATCGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
GTTAATTGACTCAAATTACC
Found at i:56746810 original size:53 final size:53
Alignment explanation
Indices: 56746746--56746847 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
56746736 TCAATACTGA
56746746 AAAAAAAAATTAAACAATTTTGTTCAAGACC-GAGAACATTGTGTATTACAAAC
1 AAAAAAAAATTAAACAATTTTGTTCAAGACCGGA-AACATTGTGTATTACAAAC
* * * *
56746799 AAAAAATAATTAAACACTTTTGTTCAATACCGGAAACATTGTGTCTTAC
1 AAAAAAAAATTAAACAATTTTGTTCAAGACCGGAAACATTGTGTATTAC
56746848 CAATTGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 42 0.95
54 2 0.05
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (53 bp):
AAAAAAAAATTAAACAATTTTGTTCAAGACCGGAAACATTGTGTATTACAAAC
Found at i:56747997 original size:54 final size:52
Alignment explanation
Indices: 56747938--56748102 Score: 153
Period size: 54 Copynumber: 3.1 Consensus size: 52
56747928 CCCAATTCTA
56747938 AAAAATTCAAAAAAATACATAAATATTTTCTAAAAAATATATAATAATAAATTT
1 AAAAATTCAAAAAAATA-ATAAATATTTTC-AAAAAATATATAATAATAAATTT
*
56747992 AAAAA-TCATATAAAAATAA-AAATGTTGTTCACAACAAATA-ATAATATATAAAATTT
1 AAAAATTCA-A-AAAAATAATAAATATT-TTCA-AA-AAATATATAATA-AT-AAATTT
* *
56748048 AAAAAATAT-ATAAAAATAAATAAATATTTTC-AAAAA-GTATAATAATAAATTT
1 -AAAAAT-TCAAAAAAAT-AATAAATATTTTCAAAAAATATATAATAATAAATTT
56748100 AAA
1 AAA
56748103 TTTTATATTA
Statistics
Matches: 94, Mismatches: 4, Indels: 29
0.74 0.03 0.23
Matches are distributed among these distances:
51 3 0.03
52 6 0.06
53 12 0.13
54 27 0.29
55 16 0.17
56 12 0.13
57 10 0.11
58 7 0.07
59 1 0.01
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (52 bp):
AAAAATTCAAAAAAATAATAAATATTTTCAAAAAATATATAATAATAAATTT
Found at i:56748072 original size:18 final size:18
Alignment explanation
Indices: 56748034--56748074 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
56748024 AACAAATAAT
*
56748034 AATATATAAAATTTAAAA
1 AATATATAAAATATAAAA
56748052 AATATATAAAA-ATAAATA
1 AATATATAAAATATAAA-A
56748070 AATAT
1 AATAT
56748075 TTTCAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATATAAAATATAAAA
Found at i:56748105 original size:29 final size:30
Alignment explanation
Indices: 56748028--56748107 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 30
56748018 GTTCACAACA
* *
56748028 AATAATAATATATAAAATTTAAAAAATATAT
1 AATAATAA-ATTTAAATTTTAAAAAATATAT
* * * *
56748059 AAAAATAAA-TAAATATTTTCAAAAA-GTAT
1 AATAATAAATTTAA-ATTTTAAAAAATATAT
56748088 AATAATAAATTTAAATTTTA
1 AATAATAAATTTAAATTTTA
56748108 TATTAATATT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
29 18 0.47
30 13 0.34
31 7 0.18
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (30 bp):
AATAATAAATTTAAATTTTAAAAAATATAT
Found at i:56749009 original size:19 final size:18
Alignment explanation
Indices: 56748985--56749020 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
56748975 TTAAAAATTT
*
56748985 TAAAAATTATTATTTTTTG
1 TAAAAAATATT-TTTTTTG
56749004 TAAAAAATATTTTTTTT
1 TAAAAAATATTTTTTTT
56749021 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TAAAAAATATTTTTTTTG
Found at i:56749515 original size:6 final size:6
Alignment explanation
Indices: 56749504--56749583 Score: 56
Period size: 6 Copynumber: 13.2 Consensus size: 6
56749494 GCTGGGCAAT
* * * *
56749504 AAAAGA AAAAGA AGAAGCA AAGAAGA AAAAGA AAAAGA AGAA-C AAGAGA
1 AAAAGA AAAAGA AAAAG-A AA-AAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * *
56749553 AGAAGA AGAAGA AAGAGA AAAA-A AATAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA AA-AAGA A
56749584 GAGGAAGAGG
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
5 5 0.09
6 42 0.74
7 7 0.12
8 3 0.05
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:56749562 original size:35 final size:34
Alignment explanation
Indices: 56749504--56749605 Score: 100
Period size: 35 Copynumber: 2.9 Consensus size: 34
56749494 GCTGGGCAAT
56749504 AAAAGAAAA-AGAAGAAGCAAAGAAGAAAAAGAAAA
1 AAAAGAAAAGAGAAGAAG--AAGAAGAAAAAGAAAA
* *
56749539 AGAAGAACAAGAGAAGAAGAAGAAGAAAGAGAAAA
1 AAAAGAA-AAGAGAAGAAGAAGAAGAAAAAGAAAA
*
56749574 AAAATAAGAAGAGGAAGAGGAGAAG-AGAAAAA
1 AAAAGAA-AAGA-GAAGA--AGAAGAAGAAAAA
56749606 TTCTAGAATG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
35 30 0.54
36 7 0.12
37 14 0.25
38 5 0.09
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.01
Consensus pattern (34 bp):
AAAAGAAAAGAGAAGAAGAAGAAGAAAAAGAAAA
Found at i:56749571 original size:26 final size:26
Alignment explanation
Indices: 56749504--56749568 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
56749494 GCTGGGCAAT
56749504 AAAAGAAAAAGAAGAAGCAAAGAAGA
1 AAAAGAAAAAGAAGAAGCAAAGAAGA
56749530 AAAAGAAAAAGAAGAA-CAAGAGAAGA
1 AAAAGAAAAAGAAGAAGCAA-AGAAGA
*
56749556 AGAAGAAGAAAGA
1 AAAAGAA-AAAGA
56749569 GAAAAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
25 3 0.08
26 28 0.78
27 5 0.14
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (26 bp):
AAAAGAAAAAGAAGAAGCAAAGAAGA
Found at i:56749582 original size:18 final size:18
Alignment explanation
Indices: 56749522--56749583 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
56749512 AAGAAGAAGC
*
56749522 AAAGAAGAAAAAGAAAAA
1 AAAGAAGAAAGAGAAAAA
* * *
56749540 GAAGAA-CAAGAGAAGAA
1 AAAGAAGAAAGAGAAAAA
*
56749557 GAAGAAGAAAGAGAAAAA
1 AAAGAAGAAAGAGAAAAA
*
56749575 AAATAAGAA
1 AAAGAAGAA
56749584 GAGGAAGAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (18 bp):
AAAGAAGAAAGAGAAAAA
Found at i:56749585 original size:3 final size:3
Alignment explanation
Indices: 56749506--56749565 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
56749496 TGGGCAATAA
* * * * *
56749506 AAG AAA AAG AAG AAG CA- AAG AAG AAA AAG AAA AAG AAG AAC AAG -AG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
56749552 AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AA
56749566 AGAGAAAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:56749604 original size:27 final size:27
Alignment explanation
Indices: 56749523--56749591 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 27
56749513 AGAAGAAGCA
* * * *
56749523 AAGAAGAAAAAGAAAAAGAAGAACAAGAG
1 AAGAAGAAGAAGAAAGAGAA-AA-AAAAT
56749552 AAGAAGAAGAAGAAAGAGAAAAAAAAT
1 AAGAAGAAGAAGAAAGAGAAAAAAAAT
*
56749579 AAGAAGAGGAAGA
1 AAGAAGAAGAAGA
56749592 GGAGAAGAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 15 0.43
28 2 0.06
29 18 0.51
ACGTcount: A:0.71, C:0.01, G:0.26, T:0.01
Consensus pattern (27 bp):
AAGAAGAAGAAGAAAGAGAAAAAAAAT
Found at i:56757673 original size:40 final size:40
Alignment explanation
Indices: 56757568--56757734 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
56757558 GGATTGATAA
* *
56757568 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
56757608 TCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
56757647 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
56757687 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
56757727 CC-GGCTAA
1 CCGGGCTAA
56757735 ACTCCGAAGG
Statistics
Matches: 114, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
39 42 0.37
40 72 0.63
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:56757733 original size:79 final size:79
Alignment explanation
Indices: 56757568--56757734 Score: 223
Period size: 79 Copynumber: 2.1 Consensus size: 79
56757558 GGATTGATAA
* ** *
56757568 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTTCGGGCTAAGCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGA
56757633 GCGAGTTACTATAT
66 GCGAGTTACTATAT
* *
56757647 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-TTATAACCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGCATTT
*
56757711 GAGCTAG-TAGCTATAT
64 GAGCGAGTTA-CTATAT
56757727 CC-GGCTAA
1 CCGGGCTAA
56757735 ACTCCGAAGG
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
78 3 0.04
79 49 0.63
80 26 0.33
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGA
GCGAGTTACTATAT
Found at i:56783282 original size:29 final size:28
Alignment explanation
Indices: 56783227--56783289 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
56783217 CTGACTCGAA
*
56783227 TATATTATGTTATAAAAATATTTATATTAAT
1 TATA-TATGTTATAAAAATAATTATA-T-AT
*
56783258 TATATATGTTA-AATAATAATTATATAT
1 TATATATGTTATAAAAATAATTATATAT
56783285 TATAT
1 TATAT
56783290 TTATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 7 0.23
28 1 0.03
29 11 0.37
30 7 0.23
31 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
TATATATGTTATAAAAATAATTATATAT
Found at i:56783284 original size:31 final size:31
Alignment explanation
Indices: 56783227--56783295 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 31
56783217 CTGACTCGAA
56783227 TATATTATGTTATAAAAATATTTATATTA-AT
1 TATA-TATGTTATAAAAATATTTATATTATAT
*
56783258 TATATATGTTA-AATAATAATTATATATTATAT
1 TATATATGTTATAAAAAT-ATT-TATATTATAT
56783290 T-TATAT
1 TATATAT
56783296 TAAATCACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
29 5 0.15
30 10 0.29
31 16 0.47
32 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
TATATATGTTATAAAAATATTTATATTATAT
Found at i:56783529 original size:23 final size:23
Alignment explanation
Indices: 56783454--56783529 Score: 54
Period size: 23 Copynumber: 3.4 Consensus size: 23
56783444 TAATAAAATA
* *
56783454 TTTATTATATTTATGATAGTGTT
1 TTTAATATATTTATGATAGTTTT
*
56783477 TTTAATATA---A--ATACTTTT
1 TTTAATATATTTATGATAGTTTT
*
56783495 TAATGTATTATATTTATGATAGTTTT
1 T--T-TAATATATTTATGATAGTTTT
56783521 TTTAATATA
1 TTTAATATA
56783530 AATATTTGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 16
0.64 0.10 0.26
Matches are distributed among these distances:
18 7 0.18
20 2 0.05
21 6 0.15
23 14 0.36
24 2 0.05
26 8 0.21
ACGTcount: A:0.33, C:0.01, G:0.08, T:0.58
Consensus pattern (23 bp):
TTTAATATATTTATGATAGTTTT
Found at i:56783544 original size:44 final size:44
Alignment explanation
Indices: 56783456--56783544 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
56783446 ATAAAATATT
**
56783456 TATTATATTTATGATAGTGTTTTTAATATAAATACTTTTTAATG
1 TATTATATTTATGATAGTGTTTTTAATATAAATACTTTCAAATG
*
56783500 TATTATATTTATGATAGTTTTTTTAATATAAATA-TTTGCAAATG
1 TATTATATTTATGATAGTGTTTTTAATATAAATACTTT-CAAATG
56783544 T
1 T
56783545 GTTACAAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 3 0.07
44 38 0.93
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (44 bp):
TATTATATTTATGATAGTGTTTTTAATATAAATACTTTCAAATG
Found at i:56784067 original size:13 final size:13
Alignment explanation
Indices: 56784049--56784075 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56784039 AGTTTGGCAA
56784049 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
56784062 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
56784075 T
1 T
56784076 TTGATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:56789700 original size:33 final size:33
Alignment explanation
Indices: 56789658--56789724 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
56789648 GAAGTCAGTG
56789658 AATGAAATTATTTTTCCTCACTCTCAATATACT
1 AATGAAATTATTTTTCCTCACTCTCAATATACT
56789691 AATGAAATTATTTTTCCTCACTCTCAATATACT
1 AATGAAATTATTTTTCCTCACTCTCAATATACT
56789724 A
1 A
56789725 TTTCAAATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (33 bp):
AATGAAATTATTTTTCCTCACTCTCAATATACT
Found at i:56794610 original size:60 final size:60
Alignment explanation
Indices: 56794539--56794660 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
56794529 ACATTCAAAA
*
56794539 AATCGAATATGCAAGGTTGACTACTTTCGAAGATTCTACGACATTCACCTACTGCCTTAG
1 AATCGAATATGCAAGGTTGACTACTTTCGAAGATTCTACCACATTCACCTACTGCCTTAG
*
56794599 AATCGAATATGCAAGGTTGACTACTTTTGAAGATTCTACCACATTCACCTACTGCCTTAG
1 AATCGAATATGCAAGGTTGACTACTTTCGAAGATTCTACCACATTCACCTACTGCCTTAG
56794659 AA
1 AA
56794661 GTAAAGAGAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (60 bp):
AATCGAATATGCAAGGTTGACTACTTTCGAAGATTCTACCACATTCACCTACTGCCTTAG
Found at i:56799930 original size:11 final size:11
Alignment explanation
Indices: 56799902--56799936 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
56799892 AATGGTCAAG
56799902 ATCAAAAGGAAA
1 ATCAAAA-GAAA
*
56799914 AACAAAAGAAA
1 ATCAAAAGAAA
56799925 ATCAAAAGAAA
1 ATCAAAAGAAA
56799936 A
1 A
56799937 ACAAGACGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.74, C:0.09, G:0.11, T:0.06
Consensus pattern (11 bp):
ATCAAAAGAAA
Found at i:56805339 original size:22 final size:23
Alignment explanation
Indices: 56805294--56805339 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
56805284 AATATACTTT
*
56805294 TTCTCTAAATTTCTTGTTAGGTA
1 TTCTCTAAATTTCATGTTAGGTA
* *
56805317 TTCTCTCAATTT-ATGTTATGTA
1 TTCTCTAAATTTCATGTTAGGTA
56805339 T
1 T
56805340 GGTTGCATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.54
Consensus pattern (23 bp):
TTCTCTAAATTTCATGTTAGGTA
Found at i:56811732 original size:44 final size:44
Alignment explanation
Indices: 56811664--56811752 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
56811654 TAATGGTTAT
56811664 GTAAAAACAAAACCTGGGTTCATTCCAAAGTGCCACCTATTTAA
1 GTAAAAACAAAACCTGGGTTCATTCCAAAGTGCCACCTATTTAA
* * *
56811708 GTAAGAACAAAATCTGTGTTCATTCCAAAGTGCCACCTATTTAA
1 GTAAAAACAAAACCTGGGTTCATTCCAAAGTGCCACCTATTTAA
56811752 G
1 G
56811753 ATTTGGCCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (44 bp):
GTAAAAACAAAACCTGGGTTCATTCCAAAGTGCCACCTATTTAA
Found at i:56813437 original size:39 final size:39
Alignment explanation
Indices: 56813383--56813458 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
56813373 GAAAAGTCTG
56813383 AATTCATGTGGGTAAACCTAATGGTATATTAACACTCTA
1 AATTCATGTGGGTAAACCTAATGGTATATTAACACTCTA
56813422 AATTCATGTGGGTAAACCTAATGGTATATTAACACTC
1 AATTCATGTGGGTAAACCTAATGGTATATTAACACTC
56813459 AACCACAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (39 bp):
AATTCATGTGGGTAAACCTAATGGTATATTAACACTCTA
Found at i:56821400 original size:22 final size:22
Alignment explanation
Indices: 56821375--56821417 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
56821365 TACTCATCCT
*
56821375 TAACATATATT-AATAGATTTTA
1 TAACATAAATTGAATA-ATTTTA
*
56821397 TAACTTAAATTGAATAATTTT
1 TAACATAAATTGAATAATTTT
56821418 TTTAGAACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (22 bp):
TAACATAAATTGAATAATTTTA
Found at i:56823553 original size:26 final size:25
Alignment explanation
Indices: 56823518--56823581 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
56823508 CCCATTTTTT
*
56823518 CCCAGTAAAATTTTGAT-AGTTTTAC
1 CCCAATAAAATTTTGATGA-TTTTAC
56823543 CCTCAATAAAATTTTGATGATTTTAC
1 CC-CAATAAAATTTTGATGATTTTAC
*
56823569 CCCGATAAAATTT
1 CCCAATAAAATTT
56823582 CAAGAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 12 0.34
26 22 0.63
27 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.39
Consensus pattern (25 bp):
CCCAATAAAATTTTGATGATTTTAC
Found at i:56825420 original size:12 final size:12
Alignment explanation
Indices: 56825394--56825432 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
56825384 TTTAAATCAA
56825394 TTCATTTCCCATT
1 TTCATTT-CCATT
* *
56825407 TTTATTTTCATT
1 TTCATTTCCATT
56825419 TTCATTTCCATT
1 TTCATTTCCATT
56825431 TT
1 TT
56825433 GAGGAAACCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCATTTCCATT
Found at i:56829165 original size:30 final size:30
Alignment explanation
Indices: 56829130--56829187 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
56829120 TAAGCACTTC
*
56829130 CACACGGGT-GATCCATAGGCCCGTGTGTGA
1 CACACGGGTAGA-CCACAGGCCCGTGTGTGA
*
56829160 CACACGGGTAGACCACATGCCCGTGTGT
1 CACACGGGTAGACCACAGGCCCGTGTGT
56829188 CATGACTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (30 bp):
CACACGGGTAGACCACAGGCCCGTGTGTGA
Found at i:56829956 original size:13 final size:13
Alignment explanation
Indices: 56829938--56829962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56829928 GATTTCTATG
56829938 GAATAAGTCAAGT
1 GAATAAGTCAAGT
56829951 GAATAAGTCAAG
1 GAATAAGTCAAG
56829963 GGATATTAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (13 bp):
GAATAAGTCAAGT
Found at i:56843172 original size:20 final size:21
Alignment explanation
Indices: 56843135--56843174 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
56843125 TCATTCTTGG
*
56843135 AAGGTGGATATTGCGATACCC
1 AAGGTGGATATCGCGATACCC
*
56843156 AAGG-GGATATCGTGATACC
1 AAGGTGGATATCGCGATACC
56843175 ATAGAAGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (21 bp):
AAGGTGGATATCGCGATACCC
Found at i:56845661 original size:20 final size:21
Alignment explanation
Indices: 56845633--56845672 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
56845623 TCCTCCTTAG
56845633 AAGGTGGATATCCTGATACCC
1 AAGGTGGATATCCTGATACCC
*
56845654 AAGG-GGATATCGTGATACC
1 AAGGTGGATATCCTGATACC
56845673 ACAGAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (21 bp):
AAGGTGGATATCCTGATACCC
Found at i:56850182 original size:44 final size:42
Alignment explanation
Indices: 56850097--56850258 Score: 141
Period size: 43 Copynumber: 3.8 Consensus size: 42
56850087 ATAGGGTTCT
* * *
56850097 GATATGTGATTTCATGAAAGACCATGTCTAGGAAGTTGGCATC
1 GATATGTAATTTCATGTAAGACCATGTCTGGGAAG-TGGCATC
*
56850140 GATTTGTAATTTACATGTAAGACCATGTCTGGGATA-TCGGCATC
1 GATATGTAATTT-CATGTAAGACCATGTCTGGGA-AGT-GGCATC
* * * * *
56850184 G-TATATAAGTTCGTGTAAGA-CATTTTCTGGGAAAGTGGCATT
1 GATATGTAATTTCATGTAAGACCA-TGTCTGGG-AAGTGGCATC
* * *
56850226 GATATGTGATTACATGTAAGACCATGTTTGGGA
1 GATATGTAATTTCATGTAAGACCATGTCTGGGA
56850259 CGTTGGCGTT
Statistics
Matches: 94, Mismatches: 17, Indels: 17
0.73 0.13 0.13
Matches are distributed among these distances:
41 2 0.02
42 23 0.24
43 40 0.43
44 28 0.30
45 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.33
Consensus pattern (42 bp):
GATATGTAATTTCATGTAAGACCATGTCTGGGAAGTGGCATC
Found at i:56854038 original size:25 final size:25
Alignment explanation
Indices: 56854007--56854103 Score: 104
Period size: 25 Copynumber: 3.9 Consensus size: 25
56853997 AGCTCTTTCG
* *
56854007 AGCTGAATAATGGAAAGCTCATGCA
1 AGCTAAATAATGGGAAGCTCATGCA
* * ** * *
56854032 AGTTGAATAACAGGAAGCTCATACG
1 AGCTAAATAATGGGAAGCTCATGCA
*
56854057 AGCTAAATAATGGGAAGCTCTTGCA
1 AGCTAAATAATGGGAAGCTCATGCA
*
56854082 AGCTAAATAACGGGAAGCTCAT
1 AGCTAAATAATGGGAAGCTCAT
56854104 AAGAGCTGTG
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (25 bp):
AGCTAAATAATGGGAAGCTCATGCA
Found at i:56854075 original size:50 final size:50
Alignment explanation
Indices: 56853996--56854110 Score: 149
Period size: 50 Copynumber: 2.3 Consensus size: 50
56853986 TGTAAATAGT
* * * * *
56853996 AAGCTCTTTCGAGCTGAATAATGGAAAGCTCATGCAAGTTGAATAACAGG
1 AAGCTCATACGAGCTAAATAATGGAAAGCTCATGCAAGCTAAATAACAGG
* * *
56854046 AAGCTCATACGAGCTAAATAATGGGAAGCTCTTGCAAGCTAAATAACGGG
1 AAGCTCATACGAGCTAAATAATGGAAAGCTCATGCAAGCTAAATAACAGG
*
56854096 AAGCTCATAAGAGCT
1 AAGCTCATACGAGCT
56854111 GTGGTGTGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.22
Consensus pattern (50 bp):
AAGCTCATACGAGCTAAATAATGGAAAGCTCATGCAAGCTAAATAACAGG
Found at i:56862921 original size:40 final size:40
Alignment explanation
Indices: 56862866--56862946 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
56862856 TAATTGAATT
56862866 ATTGCACATAAGTGCCCCTATTTGTACTTCGGTACCCCTG
1 ATTGCACATAAGTGCCCCTATTTGTACTTCGGTACCCCTG
* * * **
56862906 ATTGCACATATGTGCCCCTGTTTGTGCTTTTGTACCCCTG
1 ATTGCACATAAGTGCCCCTATTTGTACTTCGGTACCCCTG
56862946 A
1 A
56862947 ACGCACTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (40 bp):
ATTGCACATAAGTGCCCCTATTTGTACTTCGGTACCCCTG
Found at i:56863645 original size:10 final size:10
Alignment explanation
Indices: 56863630--56863689 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
56863620 TAATTCTAGG
56863630 ATTTAT-TTT
1 ATTTATCTTT
56863639 CATTTATCTTT
1 -ATTTATCTTT
56863650 ATTTATCTTT
1 ATTTATCTTT
*
56863660 AGTTATCTTT
1 ATTTATCTTT
*
56863670 AATTAT-TTGT
1 ATTTATCTT-T
56863680 ATTTATCTTT
1 ATTTATCTTT
56863690 TAGAATTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.05
10 37 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.67
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:56864433 original size:17 final size:18
Alignment explanation
Indices: 56864401--56864434 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
56864391 TATTCCTCAT
56864401 TTTAATTTCTGCAATTTA
1 TTTAATTTCTGCAATTTA
56864419 TTTAATTTC-GCAATTT
1 TTTAATTTCTGCAATTT
56864435 CAATTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAATTTCTGCAATTTA
Found at i:56870569 original size:22 final size:22
Alignment explanation
Indices: 56870544--56870587 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56870534 TATTTATTGT
*
56870544 TATTTAAAAAAATTATATATAA
1 TATTTAAAAAAATTAAATATAA
* *
56870566 TATTTATAAATATTAAATATAA
1 TATTTAAAAAAATTAAATATAA
56870588 AATATTAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTTAAAAAAATTAAATATAA
Found at i:56875052 original size:7 final size:7
Alignment explanation
Indices: 56875032--56875113 Score: 58
Period size: 7 Copynumber: 11.7 Consensus size: 7
56875022 CCCATACACA
*
56875032 CTAAACA
1 CTAAACC
*
56875039 CTTAACC
1 CTAAACC
56875046 CTAAACC
1 CTAAACC
* *
56875053 TTAAATC
1 CTAAACC
*
56875060 CTTAACC
1 CTAAACC
* *
56875067 CTTAACA
1 CTAAACC
56875074 CTAAACC
1 CTAAACC
*
56875081 CTTACACC
1 C-TAAACC
* *
56875089 TTAAACT
1 CTAAACC
56875096 CT-AACC
1 CTAAACC
56875102 CTAAACC
1 CTAAACC
56875109 CTAAA
1 CTAAA
56875114 ACATAATCTC
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
6 5 0.09
7 46 0.82
8 5 0.09
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.24
Consensus pattern (7 bp):
CTAAACC
Found at i:56875063 original size:21 final size:21
Alignment explanation
Indices: 56875029--56875113 Score: 84
Period size: 21 Copynumber: 4.0 Consensus size: 21
56875019 TATCCCATAC
*
56875029 ACACTAAACACTTAACCCTAA
1 ACACTAAACCCTTAACCCTAA
* *
56875050 AC-CTTAAATCCTTAACCCTTA
1 ACAC-TAAACCCTTAACCCTAA
*
56875071 ACACTAAACCCTTACACCTTAA
1 ACACTAAACCCTTA-ACCCTAA
* *
56875093 ACTCT-AACCCTAAACCCTAA
1 ACACTAAACCCTTAACCCTAA
56875113 A
1 A
56875114 ACATAATCTC
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
20 8 0.15
21 34 0.65
22 10 0.19
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (21 bp):
ACACTAAACCCTTAACCCTAA
Found at i:56875180 original size:7 final size:7
Alignment explanation
Indices: 56875168--56875214 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
56875158 AATTAACTCC
56875168 TAAACCT
1 TAAACCT
56875175 TAAACCT
1 TAAACCT
*
56875182 TAAACCA
1 TAAACCT
* *
56875189 TATATCT
1 TAAACCT
*
56875196 TAAACCA
1 TAAACCT
56875203 TAAACCT
1 TAAACCT
56875210 TAAAC
1 TAAAC
56875215 TATAATAATA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAACCT
Found at i:56875185 original size:14 final size:14
Alignment explanation
Indices: 56875168--56875219 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
56875158 AATTAACTCC
*
56875168 TAAACCTTAAACCT
1 TAAACCATAAACCT
* *
56875182 TAAACCATATATCT
1 TAAACCATAAACCT
56875196 TAAACCATAAACCT
1 TAAACCATAAACCT
*
56875210 TAAACTATAA
1 TAAACCATAA
56875220 TAATAATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:56875457 original size:41 final size:41
Alignment explanation
Indices: 56875386--56875588 Score: 255
Period size: 41 Copynumber: 5.0 Consensus size: 41
56875376 GTTATATGAC
* * * *
56875386 TTTTAGTGGCGTTTTAGCAAAAGCGTCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
56875427 TTTTAGCGGCGTTTTACCGAAAGTGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
* * *
56875468 TTTTAGAGGCGTTTTATCGAAAGCGCCGCTAATGCGCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
* * *
56875509 TTTTAGCGGTGTTTTACCGAAAGCGCCGCTATTGCTCT-AT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
** * *
56875549 TTTTAGCGGCGTTTTAGCAAAAAACGCCGCTATTGCTCTG
1 TTTTAGCGGCGTTTTA-CCGAAAGCGCCGCTAATGCTCTG
56875589 TATTTTATAA
Statistics
Matches: 141, Mismatches: 19, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
40 16 0.11
41 125 0.89
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
Found at i:56875595 original size:82 final size:82
Alignment explanation
Indices: 56875386--56875588 Score: 282
Period size: 82 Copynumber: 2.5 Consensus size: 82
56875376 GTTATATGAC
* * *
56875386 TTTTAGTGGCGTTTTAGCAAAAGCGTCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAGT
1 TTTTAGAGGCGTTTTAGCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAGC
*
56875451 GCCGCTAATGCTCTGGT
66 GCCGCTAATGCTCTGAT
* * * *
56875468 TTTTAGAGGCGTTTTATCGAAAGCGCCGCTAATGCGCTGGTTTTTAGCGGTGTTTTACCGAAAGC
1 TTTTAGAGGCGTTTTAGCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAGC
*
56875533 GCCGCTATTGCTCT-AT
66 GCCGCTAATGCTCTGAT
* * *
56875549 TTTTAGCGGCGTTTTAGCAAAAAACGCCGCTATTGCTCTG
1 TTTTAGAGGCGTTTTAGC-AAAAGCGCCGCTAATGCTCTG
56875589 TATTTTATAA
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 17 0.16
82 88 0.84
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (82 bp):
TTTTAGAGGCGTTTTAGCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAGC
GCCGCTAATGCTCTGAT
Done.