Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 125 of 189
Found at i:35677832 original size:22 final size:21
Alignment explanation
Indices: 35677807--35677855 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
35677797 TAGCAAATCG
*
35677807 ATTGATTGAAATAAAGAAATAA
1 ATTGAATGAAA-AAAGAAATAA
* *
35677829 ATTGAATGCAAAAATAAATAA
1 ATTGAATGAAAAAAGAAATAA
*
35677850 ACTGAA
1 ATTGAA
35677856 ATATATTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.24
Consensus pattern (21 bp):
ATTGAATGAAAAAAGAAATAA
Found at i:35680014 original size:41 final size:41
Alignment explanation
Indices: 35679968--35680054 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
35679958 CACATCTCAC
* *
35679968 GTGAGATGCATCGTATAGCTACGTTCCAACCCACAACTTGT
1 GTGAGATGCATCGTATAGCTACGTTACAACCCACAACTCGT
*
35680009 GTGAGATGCATCGTATAGCTACGTTACAACCCACAGCTCGT
1 GTGAGATGCATCGTATAGCTACGTTACAACCCACAACTCGT
35680050 GTGAG
1 GTGAG
35680055 CATACTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.25
Consensus pattern (41 bp):
GTGAGATGCATCGTATAGCTACGTTACAACCCACAACTCGT
Found at i:35682489 original size:57 final size:57
Alignment explanation
Indices: 35682376--35682489 Score: 149
Period size: 56 Copynumber: 2.0 Consensus size: 57
35682366 AAATGGTGAA
* * * * *
35682376 AATGGAGAAATTGAAAGCATTTGGAAATGATTATGGTTTTCTCCAAATGATAATGAC
1 AATGGAGAAATTGAAAGCATTTGAAAATGAATATCGTTTTCTCCAAAAGAAAATGAC
* *
35682433 AATGGAGAAATT-AAATCATTTGAAAATGAATGTCGTTTTCTCCAAAAAGAAAATGAC
1 AATGGAGAAATTGAAAGCATTTGAAAATGAATATCGTTTTCTCC-AAAAGAAAATGAC
35682490 CTGGAAATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
56 26 0.53
57 23 0.47
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (57 bp):
AATGGAGAAATTGAAAGCATTTGAAAATGAATATCGTTTTCTCCAAAAGAAAATGAC
Found at i:35685321 original size:32 final size:34
Alignment explanation
Indices: 35685258--35685321 Score: 78
Period size: 32 Copynumber: 1.9 Consensus size: 34
35685248 TTGTAAAGAC
*
35685258 ATAACTTTTGTATGTAAAGTTGTCTTATAAAAAT
1 ATAACTTTTGTATGTAAAGTTATCTTATAAAAAT
* * *
35685292 ATAAC-TTT-TATGTAAGGTTATTTTTTAAAA
1 ATAACTTTTGTATGTAAAGTTATCTTATAAAA
35685322 TAACACAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 18 0.69
33 3 0.12
34 5 0.19
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.47
Consensus pattern (34 bp):
ATAACTTTTGTATGTAAAGTTATCTTATAAAAAT
Found at i:35691051 original size:25 final size:25
Alignment explanation
Indices: 35691023--35691070 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35691013 CAAATGTTTC
*
35691023 ATTTGAAAATTTTAAAACTTTTCTT
1 ATTTGAAAATTATAAAACTTTTCTT
* *
35691048 ATTTGATAATTATAATACTTTTC
1 ATTTGAAAATTATAAAACTTTTC
35691071 AGAAATCGAA
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:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (25 bp):
ATTTGAAAATTATAAAACTTTTCTT
Found at i:35694201 original size:14 final size:14
Alignment explanation
Indices: 35694182--35694218 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
35694172 AATATTTTCT
35694182 TATA-AAATA-ATA
1 TATATAAATATATA
35694194 TATATAAATATATA
1 TATATAAATATATA
35694208 TATATGAAATA
1 TATAT-AAATA
35694219 GAATGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 5 0.23
14 8 0.36
15 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TATATAAATATATA
Found at i:35694271 original size:24 final size:24
Alignment explanation
Indices: 35694207--35694277 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 24
35694197 ATAAATATAT
*
35694207 ATATAT-GAAATAGAATGAAAATA
1 ATATATGGAAATAAAATGAAAATA
*
35694230 GTATATGGAAAATCAAAATGAAAAGTA
1 ATATATGG-AAAT-AAAATGAAAA-TA
35694257 ATA-ATGGAAATAAAAT-AAAAT
1 ATATATGGAAATAAAATGAAAAT
35694278 TTTAAAGGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.02
23 9 0.22
24 6 0.15
25 8 0.20
26 13 0.32
27 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.14, T:0.24
Consensus pattern (24 bp):
ATATATGGAAATAAAATGAAAATA
Found at i:35695068 original size:19 final size:21
Alignment explanation
Indices: 35695046--35695094 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 21
35695036 ATTATATAAA
35695046 TGTTTATATTTTA-ATTT-AT
1 TGTTTATATTTTAGATTTGAT
* *
35695065 TGTTAATA-GTTAGATTTGAT
1 TGTTTATATTTTAGATTTGAT
35695085 T-TTTATATTT
1 TGTTTATATTT
35695095 AATATTTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 4 0.17
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (21 bp):
TGTTTATATTTTAGATTTGAT
Found at i:35699791 original size:27 final size:27
Alignment explanation
Indices: 35699624--35699801 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
35699614 TAAATTGTAC
*
35699624 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
35699651 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
35699677 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
35699705 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
35699733 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
35699760 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
35699787 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35699802 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:35699792 original size:82 final size:81
Alignment explanation
Indices: 35699621--35699801 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
35699611 GATTAAATTG
* * * *
35699621 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
35699686 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
35699702 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
35699766 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
35699784 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35699802 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:35707798 original size:27 final size:27
Alignment explanation
Indices: 35707631--35707808 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
35707621 TAAATTGTAC
*
35707631 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
35707658 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
35707684 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
35707712 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
35707740 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
35707767 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
35707794 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35707809 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:35707799 original size:82 final size:81
Alignment explanation
Indices: 35707628--35707808 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
35707618 GATTAAATTG
* * * *
35707628 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
35707693 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
35707709 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
35707773 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
35707791 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35707809 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:35715264 original size:26 final size:26
Alignment explanation
Indices: 35715233--35715296 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
35715223 TGACCTGCAA
*
35715233 CTCGTGTGAGCAGGCCCATTTCACAG
1 CTCGTGTGAGCAGACCCATTTCACAG
* *
35715259 CTCGTGTGAGCATACCTATTTCACAG
1 CTCGTGTGAGCAGACCCATTTCACAG
*
35715285 CTCGTATGAGCA
1 CTCGTGTGAGCA
35715297 ACTATGTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (26 bp):
CTCGTGTGAGCAGACCCATTTCACAG
Found at i:35726121 original size:20 final size:20
Alignment explanation
Indices: 35726096--35726134 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35726086 TACTTTCTTC
35726096 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
35726116 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
35726135 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:35727928 original size:51 final size:50
Alignment explanation
Indices: 35727870--35728094 Score: 231
Period size: 51 Copynumber: 4.4 Consensus size: 50
35727860 TTTGGGGGTT
* * * * * *
35727870 TTCACATAGTACCACCCATGTTACTATTATCATTCGATACACGTAGTAGCC
1 TTCACATAGTACTACACACGTGACCATTAT-TTTCGATACACGTAGTAGCC
* * * *
35727921 TTCACATAGTACTACACACGTTATCA--AGTTTTACGGTTCACGTAGTAGCC
1 TTCACATAGTACTACACACGTGACCATTA-TTTT-CGATACACGTAGTAGCC
* * *
35727971 TTCACATAGTACTACACACGTGACCA-GAGCTTTTCGGTACACATAGTAGCC
1 TTCACATAGTACTACACACGTGACCATTA--TTTTCGATACACGTAGTAGCC
* * *
35728022 TTCACTTAGTACTACACATGTGACCATTATTTATCGATATACGTAGTAGCC
1 TTCACATAGTACTACACACGTGACCATTATTT-TCGATACACGTAGTAGCC
35728073 TTCACATAGTACTACACACGTG
1 TTCACATAGTACTACACACGTG
35728095 TTCATCAATA
Statistics
Matches: 147, Mismatches: 21, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
49 3 0.02
50 43 0.29
51 96 0.65
52 5 0.03
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (50 bp):
TTCACATAGTACTACACACGTGACCATTATTTTCGATACACGTAGTAGCC
Found at i:35728091 original size:102 final size:101
Alignment explanation
Indices: 35727902--35728094 Score: 273
Period size: 101 Copynumber: 1.9 Consensus size: 101
35727892 ACTATTATCA
* * *
35727902 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTTATCAAGTTTTACGGTTCACGTAGT
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGATTCACGTAGT
35727967 AGCCTTCACATAGTACTACACACGTGACCAGAGCTT
66 AGCCTTCACATAGTACTACACACGTGACCAGAGCTT
* * * * *
35728003 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGA-CCATTATTTATCGATAT-ACGT
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTA-CGAT-TCACGT
35728066 AGTAGCCTTCACATAGTACTACACACGTG
63 AGTAGCCTTCACATAGTACTACACACGTG
35728095 TTCATCAATA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
100 3 0.04
101 41 0.51
102 36 0.44
103 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (101 bp):
TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGATTCACGTAGT
AGCCTTCACATAGTACTACACACGTGACCAGAGCTT
Found at i:35730605 original size:30 final size:31
Alignment explanation
Indices: 35730566--35730625 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
35730556 AGAGGTGGGA
*
35730566 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
35730597 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
35730626 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:35730915 original size:9 final size:9
Alignment explanation
Indices: 35730898--35730928 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
35730888 TTAGGTTGAT
35730898 TCGAATAAC
1 TCGAATAAC
*
35730907 TCGATTAAC
1 TCGAATAAC
35730916 TCGAATAAC
1 TCGAATAAC
35730925 TCGA
1 TCGA
35730929 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:35734259 original size:29 final size:27
Alignment explanation
Indices: 35734213--35734342 Score: 66
Period size: 28 Copynumber: 4.6 Consensus size: 27
35734203 TTCTATAAGA
* *
35734213 AAGCCTTTGTGTCGATCTTTGTTAAAAGG
1 AAGCCTTTGTG-CAATCTCTG-TAAAAGG
* *
35734242 AAGCCTTTGTAGCAATCTCTGTCAAATG
1 AAGCCTTTGT-GCAATCTCTGTAAAAGG
* * ** *
35734270 ATGCCTTTGTGGCAATATCCATCAAAGG
1 AAGCCTTTGT-GCAATCTCTGTAAAAGG
* *
35734298 ACGCCTTTGTGGCAAGACTC--TAAAAGG
1 AAGCCTTTGT-GCAA-TCTCTGTAAAAGG
* *
35734325 AAAGCCTTTTTGCTATCT
1 -AAGCCTTTGTGCAATCT
35734343 TTGGAAAGGA
Statistics
Matches: 80, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
26 2 0.03
27 9 0.11
28 49 0.61
29 19 0.24
30 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (27 bp):
AAGCCTTTGTGCAATCTCTGTAAAAGG
Found at i:35734284 original size:28 final size:28
Alignment explanation
Indices: 35734237--35734312 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
35734227 ATCTTTGTTA
* * * **
35734237 AAAGGAAGCCTTTGTAGCAATCTCTGTC
1 AAAGGACGCCTTTGTGGCAATATCCATC
* *
35734265 AAATGATGCCTTTGTGGCAATATCCATC
1 AAAGGACGCCTTTGTGGCAATATCCATC
35734293 AAAGGACGCCTTTGTGGCAA
1 AAAGGACGCCTTTGTGGCAA
35734313 GACTCTAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (28 bp):
AAAGGACGCCTTTGTGGCAATATCCATC
Found at i:35736225 original size:23 final size:24
Alignment explanation
Indices: 35736199--35736244 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
35736189 GGGTGGAAAT
35736199 AAGGAGGGTTTAAG-GGTAAAAAA
1 AAGGAGGGTTTAAGAGGTAAAAAA
** *
35736222 AAGGATTGTTTAAGAGGTCAAAA
1 AAGGAGGGTTTAAGAGGTAAAAA
35736245 TGCTCAGGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (24 bp):
AAGGAGGGTTTAAGAGGTAAAAAA
Found at i:35741286 original size:10 final size:10
Alignment explanation
Indices: 35741271--35741295 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35741261 TCAATTATTA
35741271 ATAAATTTTC
1 ATAAATTTTC
35741281 ATAAATTTTC
1 ATAAATTTTC
35741291 ATAAA
1 ATAAA
35741296 AGTTAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (10 bp):
ATAAATTTTC
Found at i:35741678 original size:12 final size:12
Alignment explanation
Indices: 35741661--35741687 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
35741651 AAATTGAATC
35741661 TAGATAAATGTA
1 TAGATAAATGTA
35741673 TAGATAAATGTA
1 TAGATAAATGTA
35741685 TAG
1 TAG
35741688 GAGTGAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (12 bp):
TAGATAAATGTA
Found at i:35745332 original size:19 final size:20
Alignment explanation
Indices: 35745287--35745332 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
35745277 CTGAAAACTC
35745287 ATATTTAATAATAAGTTTTA
1 ATATTTAATAATAAGTTTTA
* *
35745307 ACA-TTAATAAT-ATTTTTA
1 ATATTTAATAATAAGTTTTA
35745325 ATATTTAA
1 ATATTTAA
35745333 AAAATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 8 0.36
19 12 0.55
20 2 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATTTAATAATAAGTTTTA
Found at i:35746364 original size:23 final size:23
Alignment explanation
Indices: 35746338--35746386 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
35746328 ATTCAGATAC
35746338 AATAAAATACCATCT-TTTCTAAA
1 AATAAAAT-CCATCTATTTCTAAA
* *
35746361 AATAAAATTCATCTATTTTTAAA
1 AATAAAATCCATCTATTTCTAAA
35746384 AAT
1 AAT
35746387 TCTTTTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAAAATCCATCTATTTCTAAA
Found at i:35747164 original size:16 final size:16
Alignment explanation
Indices: 35747124--35747164 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
35747114 TATTCTTTAG
35747124 AATTTTTA-ATTTTTT
1 AATTTTTATATTTTTT
* *
35747139 AATATATATATTTTTT
1 AATTTTTATATTTTTT
35747155 AATTTTTATA
1 AATTTTTATA
35747165 AATATTTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATTTTTATATTTTTT
Found at i:35747198 original size:19 final size:18
Alignment explanation
Indices: 35747151--35747198 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
35747141 TATATATATT
35747151 TTTTAATTTTTATAAATA
1 TTTTAATTTTTATAAATA
35747169 TTTTGAA-TTTTA-AAATTTA
1 TTTT-AATTTTTATAAA--TA
35747188 TTTTAATTTTT
1 TTTTAATTTTT
35747199 TTATTTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.12
18 11 0.42
19 12 0.46
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTAATTTTTATAAATA
Found at i:35747204 original size:18 final size:18
Alignment explanation
Indices: 35747124--35747204 Score: 55
Period size: 16 Copynumber: 4.7 Consensus size: 18
35747114 TATTCTTTAG
35747124 AATTTTTA-A-TT-TTTT
1 AATTTTTATATTTATTTT
* *
35747139 AATATATATA-TT-TTTT
1 AATTTTTATATTTATTTT
**
35747155 AATTTTTATAAATATTTT
1 AATTTTTATATTTATTTT
* *
35747173 GAATTTTAAAATTTATTTT
1 -AATTTTTATATTTATTTT
*
35747192 AATTTTTTTATTT
1 AATTTTTATATTT
35747205 GTTGTTGAGA
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
15 6 0.12
16 15 0.30
17 1 0.02
18 14 0.28
19 14 0.28
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (18 bp):
AATTTTTATATTTATTTT
Found at i:35748041 original size:16 final size:15
Alignment explanation
Indices: 35748020--35748050 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
35748010 ATATCAAGGT
35748020 TAATTAAGTAAATTAA
1 TAATTAAGT-AATTAA
35748036 TAATTAAGTAATTAA
1 TAATTAAGTAATTAA
35748051 AATAAGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
TAATTAAGTAATTAA
Found at i:35748936 original size:30 final size:31
Alignment explanation
Indices: 35748902--35748964 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
35748892 TTGATTATGG
*
35748902 AAGGGGATGGTGACGACCATC-AACAATGAA
1 AAGGGGATAGTGACGACCATCAAACAATGAA
*
35748932 AA-GGGATAGTGACGATCATCAAACAATGAA
1 AAGGGGATAGTGACGACCATCAAACAATGAA
35748962 AAG
1 AAG
35748965 AGATGGCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.44, C:0.14, G:0.27, T:0.14
Consensus pattern (31 bp):
AAGGGGATAGTGACGACCATCAAACAATGAA
Found at i:35748991 original size:30 final size:30
Alignment explanation
Indices: 35748957--35749030 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
35748947 TCATCAAACA
* *
35748957 ATGAAAAGAGATGGCTTCAACTATCGATTT
1 ATGAAAAGAGATGGCTTCAACTATCAAATT
* * *
35748987 ATGAAAAGGGATAGCTTCGACTATCAAATT
1 ATGAAAAGAGATGGCTTCAACTATCAAATT
* *
35749017 ATAAAAAGCGATGG
1 ATGAAAAGAGATGG
35749031 TGACGACCCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (30 bp):
ATGAAAAGAGATGGCTTCAACTATCAAATT
Found at i:35756672 original size:30 final size:28
Alignment explanation
Indices: 35756599--35756673 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 28
35756589 GGCTATCGAT
35756599 TATGAAAACGGATGGTGATGACCATCAAC
1 TATGAAAA-GGATGGTGATGACCATCAAC
* *
35756628 AAAGAAAAGGGATGGTGACT-ACCATCAAAC
1 TATGAAAA-GGATGGTGA-TGACCATC-AAC
35756658 TATGAAAAGAGATGGT
1 TATGAAAAG-GATGGT
35756674 TTCGGCTATC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
29 22 0.58
30 16 0.42
ACGTcount: A:0.43, C:0.13, G:0.25, T:0.19
Consensus pattern (28 bp):
TATGAAAAGGATGGTGATGACCATCAAC
Found at i:35756685 original size:30 final size:30
Alignment explanation
Indices: 35756651--35756755 Score: 75
Period size: 30 Copynumber: 3.5 Consensus size: 30
35756641 GGTGACTACC
* *
35756651 ATCAAACTATGAAAAGAGATGGTTTCGGCT
1 ATCAAACTATGAAAAGAGATAGCTTCGGCT
** * *
35756681 ATCAATTTATTAAAAGGGATAGCTTCGGCT
1 ATCAAACTATGAAAAGAGATAGCTTCGGCT
* * * * * **
35756711 ATCGAATTTTGAAAAGGGATAGATTCATCT
1 ATCAAACTATGAAAAGAGATAGCTTCGGCT
* *
35756741 GTCGAACTATGAAAA
1 ATCAAACTATGAAAA
35756756 AGGGATTATG
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (30 bp):
ATCAAACTATGAAAAGAGATAGCTTCGGCT
Found at i:35770062 original size:49 final size:48
Alignment explanation
Indices: 35769979--35770071 Score: 159
Period size: 49 Copynumber: 1.9 Consensus size: 48
35769969 TGCTATGCAA
*
35769979 TGCTAAACTTGGTCTTCACTGTCTACACTATTATCACTATTTATACAT
1 TGCTAAACTTAGTCTTCACTGTCTACACTATTATCACTATTTATACAT
*
35770027 TGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATTTAT
1 TGCTAAACTTAGTCTT-CACTGTCTACACTATTATCACTATTTAT
35770072 CCCTTCTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
48 15 0.36
49 27 0.64
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.42
Consensus pattern (48 bp):
TGCTAAACTTAGTCTTCACTGTCTACACTATTATCACTATTTATACAT
Found at i:35771871 original size:25 final size:27
Alignment explanation
Indices: 35771833--35771884 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
35771823 CTCAATTCAC
*
35771833 ATATATACATAATCAATATATTTCATA
1 ATATATACATAATCAATACATTTCATA
*
35771860 ATATATA-A-AATCAATCCATTTCATA
1 ATATATACATAATCAATACATTTCATA
35771885 TCAATTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
26 1 0.04
27 7 0.30
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.38
Consensus pattern (27 bp):
ATATATACATAATCAATACATTTCATA
Found at i:35775226 original size:20 final size:17
Alignment explanation
Indices: 35775165--35775230 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 17
35775155 CTTCCATATC
35775165 AAAAAAGAAAAAGAAAT
1 AAAAAAGAAAAAGAAAT
*
35775182 -AAAAAGGAAAAGAAAAT
1 AAAAAAGAAAAAG-AAAT
35775199 AAAGAAAGTAAAAAGAACAT
1 AAA-AAAG-AAAAAGAA-AT
35775219 AGAAAAAGAAAA
1 A-AAAAAGAAAA
35775231 TAAAGAAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
16 11 0.27
17 4 0.10
18 2 0.05
19 10 0.24
20 12 0.29
21 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAAAAGAAAAAGAAAT
Found at i:35775777 original size:61 final size:61
Alignment explanation
Indices: 35775710--35775836 Score: 184
Period size: 61 Copynumber: 2.1 Consensus size: 61
35775700 TTAAAAAAAC
* * *
35775710 TAATTAATTGC-TAGAGTGGCAATCCACATGTATGGCACAGTTCAACAAAGTTAATAAAAGT
1 TAATTAATTGCTTA-AGTGACAATCCACATATATGGCACACTTCAACAAAGTTAATAAAAGT
* * *
35775771 TAATTAATTGCTTACGTGACAATCCACGTATATGGCACACTTCAACATAGTTAATAAAAGT
1 TAATTAATTGCTTAAGTGACAATCCACATATATGGCACACTTCAACAAAGTTAATAAAAGT
35775832 TAATT
1 TAATT
35775837 TTTTCCATCT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 57 0.97
62 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (61 bp):
TAATTAATTGCTTAAGTGACAATCCACATATATGGCACACTTCAACAAAGTTAATAAAAGT
Found at i:35778445 original size:57 final size:57
Alignment explanation
Indices: 35778377--35778523 Score: 183
Period size: 57 Copynumber: 2.6 Consensus size: 57
35778367 TTAACTAGCT
* * * *
35778377 GGTGACCAAAAAAGAAAAACCATAAATAAGTGGCTATTTTATAACTTTTCATAGTTG
1 GGTGACAAAAAAAGAAAAACCATAAATAAGTGACCATTTTAAAACTTTTCATAGTTG
*
35778434 GGTGACAAAAAAA-AAACAGACCAT-AATGAGTGACCATTTTAAAACTTTTCATAGTTG
1 GGTGACAAAAAAAGAAA-A-ACCATAAATAAGTGACCATTTTAAAACTTTTCATAGTTG
* * *
35778491 AGTGACAAAAAAAG-AAAACCATAATTGAGTGAC
1 GGTGACAAAAAAAGAAAAACCATAAATAAGTGAC
35778524 TGCTAAAATA
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
55 5 0.06
56 13 0.16
57 56 0.71
58 5 0.06
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (57 bp):
GGTGACAAAAAAAGAAAAACCATAAATAAGTGACCATTTTAAAACTTTTCATAGTTG
Found at i:35778912 original size:17 final size:19
Alignment explanation
Indices: 35778879--35778913 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
35778869 GTTGTTTGGA
35778879 TATTATATAACTTTTGTTT
1 TATTATATAACTTTTGTTT
35778898 TATTAT-TAA-TTTTGTT
1 TATTATATAACTTTTGTT
35778914 ACTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (19 bp):
TATTATATAACTTTTGTTT
Found at i:35783938 original size:22 final size:24
Alignment explanation
Indices: 35783912--35783955 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
35783902 GAAAAATATT
35783912 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
35783934 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
35783956 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:35784066 original size:9 final size:9
Alignment explanation
Indices: 35784052--35784079 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
35784042 TTTTGTTACA
35784052 ACAATTAAT
1 ACAATTAAT
35784061 ACAATTAAT
1 ACAATTAAT
35784070 ACAATTAAT
1 ACAATTAAT
35784079 A
1 A
35784080 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:35784101 original size:68 final size:68
Alignment explanation
Indices: 35784022--35784222 Score: 289
Period size: 59 Copynumber: 3.1 Consensus size: 68
35784012 TCAAGTTTGT
*
35784022 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
35784087 AAA
66 AAA
35784090 TTTACTAATCAAATGTTAGATTTTATT------A-T-A-ACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
35784146 AAA
66 AAA
* *
35784149 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAACTAAAAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
35784212 AAT
66 AAA
35784215 TTTACTAA
1 TTTACTAA
35784223 CAATTAATTT
Statistics
Matches: 120, Mismatches: 4, Indels: 20
0.83 0.03 0.14
Matches are distributed among these distances:
59 56 0.47
60 1 0.01
61 1 0.01
62 1 0.01
65 1 0.01
66 26 0.22
67 2 0.02
68 32 0.27
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:35784232 original size:16 final size:16
Alignment explanation
Indices: 35784211--35784252 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
35784201 AAAAATTTGA
*
35784211 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
35784227 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
35784243 TAGTTTTAAT
1 TAATTTTAAT
35784253 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:35784236 original size:22 final size:23
Alignment explanation
Indices: 35784226--35784287 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
35784216 TTACTAACAA
* * *
35784226 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
35784248 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
35784271 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
35784288 CAGGCCGTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:35789864 original size:22 final size:22
Alignment explanation
Indices: 35789836--35789957 Score: 70
Period size: 22 Copynumber: 5.3 Consensus size: 22
35789826 TTCCACATCC
35789836 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * * *
35789858 ATCACATATGTACACTTTC-ACATT
1 ATCACAT-TG-GC-CATTCGGCCTT
35789882 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
35789905 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
35789929 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
35789952 ATCACA
1 ATCACA
35789958 CATACACATG
Statistics
Matches: 72, Mismatches: 16, Indels: 24
0.64 0.14 0.21
Matches are distributed among these distances:
22 26 0.36
23 13 0.18
24 13 0.18
25 20 0.28
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:35789872 original size:47 final size:47
Alignment explanation
Indices: 35789808--35790500 Score: 921
Period size: 47 Copynumber: 14.6 Consensus size: 47
35789798 CCCTTCGGGA
* * *
35789808 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
35789855 CTTATCACATATGTACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
35789902 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * * *
35789949 CTTATCACACATACACA-TGTTCAAATTCATCACATTGGCCATTTGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
35789996 CTTATCACACATACACA-TGTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
35790043 CTTATCACACATACACA-TGTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
35790090 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
35790137 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
35790184 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
35790231 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
35790280 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
35790329 CTTATCACATATATATACACTTTCACATTCATCACATTGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
35790378 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
35790427 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
35790474 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
35790501 TATTCAAATA
Statistics
Matches: 617, Mismatches: 25, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
46 1 0.00
47 424 0.69
48 1 0.00
49 191 0.31
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:35791896 original size:85 final size:85
Alignment explanation
Indices: 35791775--35791945 Score: 333
Period size: 85 Copynumber: 2.0 Consensus size: 85
35791765 TGCCCGTGCC
35791775 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
1 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
35791840 ACATCTTATCCACCCATGCT
66 ACATCTTATCCACCCATGCT
35791860 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
1 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
*
35791925 ACATCTTGTCCACCCATGCT
66 ACATCTTATCCACCCATGCT
35791945 C
1 C
35791946 ATGGCCGGCC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.39
Consensus pattern (85 bp):
CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
ACATCTTATCCACCCATGCT
Found at i:35796053 original size:19 final size:19
Alignment explanation
Indices: 35796015--35796053 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35796005 ACTCAAAATA
*
35796015 AAAGAAAATTGAGAAGAAG
1 AAAGAAAATTGAGAAAAAG
35796034 AAAGAAAAATTGA-AAAAAG
1 AAAG-AAAATTGAGAAAAAG
35796053 A
1 A
35796054 GAGTGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (19 bp):
AAAGAAAATTGAGAAAAAG
Found at i:35800317 original size:24 final size:24
Alignment explanation
Indices: 35800283--35800344 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
35800273 CCTTTTTGAG
*
35800283 CCATTTCGTACCGAAAATCCCATA
1 CCATTTCGTACCAAAAATCCCATA
* *
35800307 CCATTTTGTACCAAAAATCCGATA
1 CCATTTCGTACCAAAAATCCCATA
*
35800331 CCATTTCATACCAA
1 CCATTTCGTACCAA
35800345 TACCCAATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.35, C:0.31, G:0.06, T:0.27
Consensus pattern (24 bp):
CCATTTCGTACCAAAAATCCCATA
Found at i:35802146 original size:26 final size:26
Alignment explanation
Indices: 35802110--35802171 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
35802100 ACATATTTTC
35802110 TCAAAATTTTACCAAGGGCAAAATCA
1 TCAAAATTTTACCAAGGGCAAAATCA
* * *
35802136 TCAAAATTTTACTATGGGTAAAATCA
1 TCAAAATTTTACCAAGGGCAAAATCA
35802162 TCAAAATTTT
1 TCAAAATTTT
35802172 GTTGGGGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACCAAGGGCAAAATCA
Found at i:35802180 original size:26 final size:26
Alignment explanation
Indices: 35802110--35802185 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
35802100 ACATATTTTC
* * *
35802110 TCAAAATTTTACCAAGGGCAAAATCA
1 TCAAAATTTTACTAGGGGTAAAATCA
*
35802136 TCAAAATTTTACTATGGGTAAAATCA
1 TCAAAATTTTACTAGGGGTAAAATCA
** *
35802162 TCAAAATTTTGTTGGGGGTAAAAT
1 TCAAAATTTTACTAGGGGTAAAAT
35802186 AGGGATGAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGTAAAATCA
Found at i:35808186 original size:15 final size:16
Alignment explanation
Indices: 35808166--35808195 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35808156 TGGTGCCTTG
35808166 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
35808181 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
35808196 AGCATATTAG
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:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:35811072 original size:15 final size:15
Alignment explanation
Indices: 35811048--35811077 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35811038 TACGGTGTAT
*
35811048 TGGTGCTTGATAACA
1 TGGTGATTGATAACA
35811063 TGGTGATTGATAACA
1 TGGTGATTGATAACA
35811078 CAGTGTCTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (15 bp):
TGGTGATTGATAACA
Found at i:35830974 original size:34 final size:34
Alignment explanation
Indices: 35830936--35831003 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
35830926 TTTCTTATCC
35830936 ATCGTCATCATCTTCCTCTGGCTCCAACAAAACT
1 ATCGTCATCATCTTCCTCTGGCTCCAACAAAACT
35830970 ATCGTCATCATCTTCCTCTGGCTCCAACAAAACT
1 ATCGTCATCATCTTCCTCTGGCTCCAACAAAACT
35831004 TTCTTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.35, G:0.09, T:0.29
Consensus pattern (34 bp):
ATCGTCATCATCTTCCTCTGGCTCCAACAAAACT
Found at i:35831069 original size:15 final size:15
Alignment explanation
Indices: 35831049--35831081 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
35831039 GGTAAGGTTT
35831049 TTCTGAAGGGATTTC
1 TTCTGAAGGGATTTC
35831064 TTCTGAAGGGATTTC
1 TTCTGAAGGGATTTC
35831079 TTC
1 TTC
35831082 ATGGCCGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.42
Consensus pattern (15 bp):
TTCTGAAGGGATTTC
Found at i:35836554 original size:21 final size:20
Alignment explanation
Indices: 35836516--35836578 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
35836506 ATTCAATTTC
35836516 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATAATATCATT
35836533 TCAATACCACAATAAT-TCATT
1 TCAAT-CCA-AATAATATCATT
*
35836554 T-AATTCAAATAATATCATT
1 TCAATCCAAATAATATCATT
35836573 TGCAAT
1 T-CAAT
35836579 TTCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATAATATCATT
Found at i:35836619 original size:15 final size:17
Alignment explanation
Indices: 35836589--35836620 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
35836579 TTCCATTTAA
35836589 TTCATATACAGTTCAAT
1 TTCATATACAGTTCAAT
35836606 TTCAT-TAC-GTTCAAT
1 TTCATATACAGTTCAAT
35836621 ACTAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (17 bp):
TTCATATACAGTTCAAT
Found at i:35837704 original size:13 final size:13
Alignment explanation
Indices: 35837686--35837718 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
35837676 CCAAACGTCA
35837686 AAATTTTCGAACG
1 AAATTTTCGAACG
35837699 AAATTTTCGAACG
1 AAATTTTCGAACG
35837712 AAATTTT
1 AAATTTT
35837719 GTGAAATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (13 bp):
AAATTTTCGAACG
Found at i:35856033 original size:25 final size:25
Alignment explanation
Indices: 35856005--35856083 Score: 131
Period size: 25 Copynumber: 3.2 Consensus size: 25
35855995 TCATTAGGGT
35856005 TACTGATTTATAGCTCATGAGAGCA
1 TACTGATTTATAGCTCATGAGAGCA
*
35856030 TACTGATTTATAGCACATGAGAGCA
1 TACTGATTTATAGCTCATGAGAGCA
* *
35856055 TACCGATTTATAGCTCGTGAGAGCA
1 TACTGATTTATAGCTCATGAGAGCA
35856080 TACT
1 TACT
35856084 AATCTTTAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (25 bp):
TACTGATTTATAGCTCATGAGAGCA
Found at i:35860108 original size:50 final size:53
Alignment explanation
Indices: 35860006--35860194 Score: 158
Period size: 50 Copynumber: 3.6 Consensus size: 53
35859996 ATGAGATCCA
**
35860006 ATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AGG-TATGAGAGGTCCC
35860062 ATGTAAGACCATGTCTGGGACATGG-AGTTGGCACCA-A-G-ATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCA-TTGGCACCATAGGTATGAGAGGTCCC
** * * * * * * **
35860112 CCGTAAGACCCTGCCTGGGACATGGTATGGGCA-C-T-GATATGAAAACTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGGTATGAGAGGTCCC
* * *
35860162 ATGTAAGACCATATCTAGGATATGGCATTGGCA
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA
35860195 GTACAGGAGA
Statistics
Matches: 108, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
49 1 0.01
50 71 0.66
51 1 0.01
52 1 0.01
53 1 0.01
55 1 0.01
56 32 0.30
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (53 bp):
ATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGGTATGAGAGGTCCC
Found at i:35860472 original size:20 final size:20
Alignment explanation
Indices: 35860447--35860495 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
35860437 TGAGTTATTT
*
35860447 AAGTAAGCAAGTGAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
35860467 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
35860487 AAG-AAGCAA
1 AAGTAAGCAA
35860496 AGACCACGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.55, C:0.06, G:0.27, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:35869614 original size:29 final size:28
Alignment explanation
Indices: 35869542--35869607 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
35869532 TGCGACTTGG
*
35869542 CACACGGCCCACACATATTCGTGTGTCA
1 CACACGGCCCACACATAGTCGTGTGTCA
* * *
35869570 CACATGGCCCATCACATGGTCGTGTGTTA
1 CACACGGCCCA-CACATAGTCGTGTGTCA
35869599 CACACGGCC
1 CACACGGCC
35869608 TACCACACGG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (28 bp):
CACACGGCCCACACATAGTCGTGTGTCA
Found at i:35871541 original size:21 final size:23
Alignment explanation
Indices: 35871515--35871556 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
35871505 GGTAGGAATG
35871515 TTTTTGAAAAA-CT-TGCATTGA
1 TTTTTGAAAAAGCTCTGCATTGA
35871536 TTTTTGAAAAAGCTCTGCATT
1 TTTTTGAAAAAGCTCTGCATT
35871557 AACATCCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (23 bp):
TTTTTGAAAAAGCTCTGCATTGA
Found at i:35872059 original size:47 final size:47
Alignment explanation
Indices: 35872001--35872095 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
35871991 AATTAGTATT
35872001 TGATAACATTATGCATGAAGCTTGGTTTTTATTAAAACCTGACAAAA
1 TGATAACATTATGCATGAAGCTTGGTTTTTATTAAAACCTGACAAAA
*
35872048 TGATAAGATTATGCATGAAGCTTGGTTTTTATTAAAACCTGACAAAA
1 TGATAACATTATGCATGAAGCTTGGTTTTTATTAAAACCTGACAAAA
35872095 T
1 T
35872096 CACTCTTTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (47 bp):
TGATAACATTATGCATGAAGCTTGGTTTTTATTAAAACCTGACAAAA
Found at i:35881543 original size:20 final size:21
Alignment explanation
Indices: 35881481--35881548 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 21
35881471 TGTCACTCAG
*
35881481 TCACACTGGCGTGTGCCTCCTT
1 TCACACAGGCGTGTGCCT-CTT
** *
35881503 TTGCACAGGCGTGTGCTTC-T
1 TCACACAGGCGTGTGCCTCTT
*
35881523 TCACACAGGCGTGTTCCTCTT
1 TCACACAGGCGTGTGCCTCTT
35881544 TCACA
1 TCACA
35881549 TGGGTGTGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 16 0.43
21 7 0.19
22 14 0.38
ACGTcount: A:0.13, C:0.32, G:0.22, T:0.32
Consensus pattern (21 bp):
TCACACAGGCGTGTGCCTCTT
Found at i:35894030 original size:70 final size:70
Alignment explanation
Indices: 35893912--35894047 Score: 254
Period size: 70 Copynumber: 1.9 Consensus size: 70
35893902 TAAGCCATGA
35893912 AAATAGCTTGAGTATTCGACCACTTGAGGTATTGCATGTAAGTCCATTTTAAACTCATTTCTTGT
1 AAATAGCTTGAGTATTCGACCACTTGAGGTATTGCATGTAAGTCCATTTTAAACTCATTTCTTGT
35893977 AATTT
66 AATTT
* *
35893982 AAATGGCTTGAGTATTTGACCACTTGAGGTATTGCATGTAAGTCCATTTTAAACTCATTTCTTGT
1 AAATAGCTTGAGTATTCGACCACTTGAGGTATTGCATGTAAGTCCATTTTAAACTCATTTCTTGT
35894047 A
66 A
35894048 TTTTTTTATG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (70 bp):
AAATAGCTTGAGTATTCGACCACTTGAGGTATTGCATGTAAGTCCATTTTAAACTCATTTCTTGT
AATTT
Found at i:35898517 original size:21 final size:20
Alignment explanation
Indices: 35898491--35898537 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
35898481 CATGAGGGAA
35898491 ATGTATCGA-TACATCCCTTAG
1 ATGTATC-ACTACAT-CCTTAG
*
35898512 ATGTATCACTACATCTTTAG
1 ATGTATCACTACATCCTTAG
35898532 ATGTAT
1 ATGTAT
35898538 TGGTACAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCACTACATCCTTAG
Found at i:35899252 original size:13 final size:13
Alignment explanation
Indices: 35899234--35899258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35899224 TATTTTATTT
35899234 TAGAAAATTTTTG
1 TAGAAAATTTTTG
35899247 TAGAAAATTTTT
1 TAGAAAATTTTT
35899259 AAAATACCAT
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TAGAAAATTTTTG
Found at i:35899418 original size:18 final size:17
Alignment explanation
Indices: 35899395--35899428 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
35899385 CCCAAATATA
*
35899395 GAAATATATATATATAAG
1 GAAATAAATATA-ATAAG
35899413 GAAATAAATATAATAA
1 GAAATAAATATAATAA
35899429 AAGTCTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (17 bp):
GAAATAAATATAATAAG
Found at i:35900836 original size:21 final size:19
Alignment explanation
Indices: 35900810--35900860 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
35900800 CTTTAAACTT
35900810 ATTATTATTATAATTTTAAA
1 ATTATTATTATAATTTT-AA
*
35900830 ATGTATTATACTATTATTTTAA
1 AT-TATTAT--TATAATTTTAA
35900852 ATTATTATT
1 ATTATTATT
35900861 GACATGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 12 0.44
22 4 0.15
23 8 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTATTATTATAATTTTAA
Found at i:35900860 original size:24 final size:22
Alignment explanation
Indices: 35900801--35900860 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
35900791 CGACATTACC
35900801 TTTAAACTTATTATTATTATAAT
1 TTTAAA-TTATTATTATTATAAT
* *
35900824 TTTAAAATGTATTA-TACTATTAT
1 TTT-AAAT-TATTATTATTATAAT
35900847 TTTAAATTATTATT
1 TTTAAATTATTATT
35900861 GACATGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 5 0.16
22 5 0.16
23 14 0.44
24 8 0.25
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTAAATTATTATTATTATAAT
Found at i:35900891 original size:21 final size:21
Alignment explanation
Indices: 35900867--35900910 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
35900857 TATTGACATG
*
35900867 TTTTAAATTTATCATACATTT
1 TTTTAAATCTATCATACATTT
* * *
35900888 TTTTATATCTATTATATATTT
1 TTTTAAATCTATCATACATTT
35900909 TT
1 TT
35900911 ATCTTCAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTAAATCTATCATACATTT
Found at i:35903193 original size:24 final size:24
Alignment explanation
Indices: 35903164--35903239 Score: 98
Period size: 30 Copynumber: 2.9 Consensus size: 24
35903154 ATTTTGATAG
35903164 AATCTAAATTTAAAGATTAAAATA
1 AATCTAAATTTAAAGATTAAAATA
35903188 AATCTAATTACTAATTTAAAGATTAAAATA
1 AATC----TA--AATTTAAAGATTAAAATA
35903218 AATCTAAATTTAAAGATTAAAA
1 AATCTAAATTTAAAGATTAAAA
35903240 AATATAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
24 20 0.43
26 2 0.04
28 2 0.04
30 22 0.48
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (24 bp):
AATCTAAATTTAAAGATTAAAATA
Found at i:35903310 original size:29 final size:29
Alignment explanation
Indices: 35903278--35903337 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
35903268 AAAATTTTAA
*
35903278 AAATAAAACA-AATTTAAAA-ATTAAATAAT
1 AAATAAAA-AGAATATAAAATATTAAA-AAT
35903307 AAATAAAAAGAATATAAAATATTAAAAAT
1 AAATAAAAAGAATATAAAATATTAAAAAT
35903336 AA
1 AA
35903338 TCTATTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 1 0.04
29 21 0.75
30 6 0.21
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (29 bp):
AAATAAAAAGAATATAAAATATTAAAAAT
Found at i:35904270 original size:18 final size:19
Alignment explanation
Indices: 35904228--35904271 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
35904218 AATTTTAAAC
35904228 TATTTTAGGAAAATTTTTA
1 TATTTTAGGAAAATTTTTA
*
35904247 TATTTTA-GAAAGTTTATTA
1 TATTTTAGGAAAATTT-TTA
35904266 T-TTTTA
1 TATTTTA
35904272 AAATTTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
TATTTTAGGAAAATTTTTA
Found at i:35904825 original size:19 final size:20
Alignment explanation
Indices: 35904772--35904824 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
35904762 CAAAGATTAC
*
35904772 AAAATAATTCAAAATAATTT-T
1 AAAA-AATTCAAAAT-GTTTAT
35904793 AAAAAATTCAAAATGTTTAT
1 AAAAAATTCAAAATGTTTAT
*
35904813 AAAAATTTCAAA
1 AAAAAATTCAAA
35904825 TTTTTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAAATTCAAAATGTTTAT
Found at i:35904830 original size:19 final size:19
Alignment explanation
Indices: 35904777--35904832 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
35904767 ATTACAAAAT
35904777 AATTCAAAATAATTTTA-AAA
1 AATTCAAAAT--TTTTATAAA
*
35904797 AATTCAAAATGTTTATAAA
1 AATTCAAAATTTTTATAAA
35904816 AATTTC-AAATTTTTATA
1 AA-TTCAAAATTTTTATA
35904833 TTTTTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 4 0.12
19 15 0.47
20 13 0.41
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTCAAAATTTTTATAAA
Found at i:35909388 original size:25 final size:27
Alignment explanation
Indices: 35909359--35909424 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 27
35909349 AAGTTATTAG
*
35909359 AAATATTTAAAATTTTGTAAAA-T-AA
1 AAATATTAAAAATTTTGTAAAATTAAA
* * *
35909384 AAATA-TCATAATCTTTTTAAAATTAAA
1 AAATATTAAAAAT-TTTGTAAAATTAAA
35909411 AAATATTAAAAATT
1 AAATATTAAAAATT
35909425 AATTAATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 5 0.16
25 13 0.41
26 1 0.03
27 8 0.25
28 5 0.16
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (27 bp):
AAATATTAAAAATTTTGTAAAATTAAA
Found at i:35914730 original size:9 final size:10
Alignment explanation
Indices: 35914710--35914738 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
35914700 ATTGCGTGTT
35914710 TGAATAGAAA
1 TGAATAGAAA
35914720 TGAAT-GAAA
1 TGAATAGAAA
35914729 TGAATAGAAA
1 TGAATAGAAA
35914739 AGAGAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:35915030 original size:26 final size:26
Alignment explanation
Indices: 35914996--35915085 Score: 144
Period size: 26 Copynumber: 3.5 Consensus size: 26
35914986 TGAATGAATT
35914996 TTGTCAAAATTTTAGCAGGGGCAAAA
1 TTGTCAAAATTTTAGCAGGGGCAAAA
35915022 TTGTCAAAATTTTAGCAGGGGCAAAA
1 TTGTCAAAATTTTAGCAGGGGCAAAA
* * *
35915048 TTGTCAAAATTTTATCGGGGGTAAAA
1 TTGTCAAAATTTTAGCAGGGGCAAAA
*
35915074 TTGTTAAAATTT
1 TTGTCAAAATTT
35915086 ACTGGTAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 60 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (26 bp):
TTGTCAAAATTTTAGCAGGGGCAAAA
Found at i:35919310 original size:18 final size:18
Alignment explanation
Indices: 35919284--35919318 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35919274 TTATGCATGC
*
35919284 TCACATATCATTTTCATT
1 TCACATATCACTTTCATT
*
35919302 TCACTTATCACTTTCAT
1 TCACATATCACTTTCAT
35919319 ATAATTCACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACATATCACTTTCATT
Found at i:35933031 original size:20 final size:20
Alignment explanation
Indices: 35933006--35933044 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35932996 TCAAAAGTAT
*
35933006 AAAAATTTAGAAAT-TATAAA
1 AAAAATATA-AAATATATAAA
35933026 AAAAATATAAAATATATAA
1 AAAAATATAAAATATATAA
35933045 TAAATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAAATATAAAATATATAAA
Found at i:35933200 original size:14 final size:14
Alignment explanation
Indices: 35933181--35933221 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
35933171 CATATAGAAA
35933181 TTATTATAAAAAAT
1 TTATTATAAAAAAT
*
35933195 TTATTA-ATAAAAT
1 TTATTATAAAAAAT
*
35933208 TTA-TATACAAAAT
1 TTATTATAAAAAAT
35933221 T
1 T
35933222 ACAATCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 2 0.08
13 16 0.67
14 6 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATTATAAAAAAT
Found at i:35934620 original size:10 final size:10
Alignment explanation
Indices: 35934571--35934618 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
35934561 TAAACTCCCA
35934571 AAAGATAAAT
1 AAAGATAAAT
** *
35934581 AAATTTAATT
1 AAAGATAAAT
*
35934591 CAAGATAAAT
1 AAAGATAAAT
35934601 AAAGATAAAT
1 AAAGATAAAT
35934611 AAA-ATAAA
1 AAAGATAAA
35934619 ATCCTAAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:35936619 original size:21 final size:21
Alignment explanation
Indices: 35936602--35936652 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
35936592 TATTAATATC
35936602 CAAATAAAATAAAGTAATAAA
1 CAAATAAAATAAAGTAATAAA
* *
35936623 TAAATAAAATAAAATAA-AATA
1 CAAATAAAATAAAGTAATAA-A
*
35936644 AAAATAAAA
1 CAAATAAAA
35936653 ATTAGGTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
CAAATAAAATAAAGTAATAAA
Found at i:35936632 original size:26 final size:25
Alignment explanation
Indices: 35936603--35936651 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
35936593 ATTAATATCC
*
35936603 AAATAAAATAAAGTAATAAATAAATA
1 AAATAAAATAAAATAA-AAATAAATA
35936629 AAATAAAATAAAATAAAAATAAA
1 AAATAAAATAAAATAAAAATAAA
35936652 AATTAGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (25 bp):
AAATAAAATAAAATAAAAATAAATA
Found at i:35936654 original size:6 final size:5
Alignment explanation
Indices: 35936603--35936652 Score: 57
Period size: 5 Copynumber: 9.6 Consensus size: 5
35936593 ATTAATATCC
*
35936603 AAATA AAATA AAGTA ATAA-A TAAATA AAATA AAATA AAATAA AAATA
1 AAATA AAATA AAATA A-AATA -AAATA AAATA AAATA AAAT-A AAATA
35936650 AAA
1 AAA
35936653 ATTAGGTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 31 0.79
6 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:35940125 original size:15 final size:14
Alignment explanation
Indices: 35940104--35940139 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
35940094 ATAATCCTTA
*
35940104 ATAATTATCTTAAT
1 ATAATTATCCTAAT
35940118 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
35940133 ATAATTA
1 ATAATTA
35940140 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:35942333 original size:6 final size:6
Alignment explanation
Indices: 35942324--35942352 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
35942314 AAATAAAATT
35942324 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
35942353 TTCTAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:35942404 original size:9 final size:9
Alignment explanation
Indices: 35942392--35942459 Score: 109
Period size: 9 Copynumber: 7.6 Consensus size: 9
35942382 TCAATTCAGT
35942392 TAATTCGGG
1 TAATTCGGG
35942401 TAATTCGGG
1 TAATTCGGG
*
35942410 TAATTCGGT
1 TAATTCGGG
*
35942419 TAATTCGGT
1 TAATTCGGG
35942428 TAATTCGGG
1 TAATTCGGG
35942437 TAATTCGGG
1 TAATTCGGG
*
35942446 TAATTCGGT
1 TAATTCGGG
35942455 TAATT
1 TAATT
35942460 TTTAACCAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (9 bp):
TAATTCGGG
Found at i:35954020 original size:13 final size:13
Alignment explanation
Indices: 35954002--35954034 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
35953992 AATATTGTAT
*
35954002 ATAATTTTTATTA
1 ATAATTTTTAATA
35954015 ATAATTTTTAATA
1 ATAATTTTTAATA
35954028 ATAATTT
1 ATAATTT
35954035 ATATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATAATTTTTAATA
Found at i:35954057 original size:26 final size:25
Alignment explanation
Indices: 35954000--35954057 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
35953990 GTAATATTGT
* * * *
35954000 ATATAATTTTTATTAATAATTTTTA
1 ATATAATTTATATTAAAAAATTTGA
35954025 ATAATAATTTATATATAAAAAATTTGA
1 AT-ATAATTTATAT-TAAAAAATTTGA
35954052 ATATAA
1 ATATAA
35954058 AAATTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 2 0.07
26 14 0.52
27 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
ATATAATTTATATTAAAAAATTTGA
Found at i:35954340 original size:20 final size:20
Alignment explanation
Indices: 35954309--35954347 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
35954299 TATTAATTAC
35954309 TTTATATATTTTTAAAAAATA
1 TTTATATA-TTTTAAAAAATA
35954330 TTTAT-TATTTTAAAAAAT
1 TTTATATATTTTAAAAAAT
35954348 TGAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 2 0.11
21 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTATATATTTTAAAAAATA
Found at i:35955829 original size:20 final size:20
Alignment explanation
Indices: 35955804--35955845 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
35955794 ATAACATTCT
35955804 TAATATAATTTTTATTAAAA
1 TAATATAATTTTTATTAAAA
35955824 TAATATAATTTTTATTAAAA
1 TAATATAATTTTTATTAAAA
35955844 TA
1 TA
35955846 TGAATTAATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATATAATTTTTATTAAAA
Found at i:35958103 original size:16 final size:16
Alignment explanation
Indices: 35958082--35958114 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35958072 CAAAACAATG
35958082 AATATTTGAGATGATA
1 AATATTTGAGATGATA
*
35958098 AATATTTTAGATGATA
1 AATATTTGAGATGATA
35958114 A
1 A
35958115 GCTAGACCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (16 bp):
AATATTTGAGATGATA
Found at i:35958830 original size:20 final size:20
Alignment explanation
Indices: 35958805--35958865 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
35958795 GCAGCAGATG
35958805 GGGAAATAAGAAGGAAAAAA
1 GGGAAATAAGAAGGAAAAAA
* *
35958825 GGGAAATAA-TATG----AA
1 GGGAAATAAGAAGGAAAAAA
35958840 GGGAAATAAGAAGGAAAAAA
1 GGGAAATAAGAAGGAAAAAA
35958860 GGGAAA
1 GGGAAA
35958866 CGCAGAGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 11 0.34
16 2 0.06
19 2 0.06
20 17 0.53
ACGTcount: A:0.61, C:0.00, G:0.31, T:0.08
Consensus pattern (20 bp):
GGGAAATAAGAAGGAAAAAA
Found at i:35977377 original size:20 final size:20
Alignment explanation
Indices: 35977348--35977464 Score: 89
Period size: 20 Copynumber: 5.9 Consensus size: 20
35977338 TACGGGACTA
35977348 CACTTCGGTGCCTCTGTTTG
1 CACTTCGGTGCCTCTGTTTG
* *
35977368 CACTTTGGTGCCTCTG-TTA
1 CACTTCGGTGCCTCTGTTTG
* * *
35977387 CACTTCGGTG-TTCCTATTCG
1 CACTTCGGTGCCT-CTGTTTG
* *
35977407 CACTTCGATGCCTCTGATTG
1 CACTTCGGTGCCTCTGTTTG
* * *
35977427 CACAATT--GTGTCTCTGTCTA
1 CAC--TTCGGTGCCTCTGTTTG
35977447 CACTTCGGTGCCTCTGTT
1 CACTTCGGTGCCTCTGTT
35977465 ACACATCTAC
Statistics
Matches: 71, Mismatches: 19, Indels: 14
0.68 0.18 0.13
Matches are distributed among these distances:
18 3 0.04
19 13 0.18
20 52 0.73
21 1 0.01
22 2 0.03
ACGTcount: A:0.11, C:0.29, G:0.21, T:0.39
Consensus pattern (20 bp):
CACTTCGGTGCCTCTGTTTG
Found at i:35989597 original size:26 final size:27
Alignment explanation
Indices: 35989529--35989599 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
35989519 AATTTTCTTG
* *
35989529 AAATTTTATCGAGGGT-AAAATAGTTA
1 AAATTTTATCAAGGGTAAAAATAGTCA
*
35989555 AAATTTTATCAAAGGTAAAAAT-GTCA
1 AAATTTTATCAAGGGTAAAAATAGTCA
* *
35989581 AAATTTTATTAGGGGTAAA
1 AAATTTTATCAAGGGTAAA
35989600 TTTGGGGTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 33 0.87
27 5 0.13
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (27 bp):
AAATTTTATCAAGGGTAAAAATAGTCA
Found at i:35993940 original size:95 final size:95
Alignment explanation
Indices: 35993837--35994016 Score: 247
Period size: 95 Copynumber: 1.9 Consensus size: 95
35993827 AACATAACCT
*
35993837 CATGTTTAACGTCTT-ATCGGACTACCCCGTGTTTATTATCCCGGTGGACTCTC-TATGTTGCCA
1 CATGTTTAACGTCTTGAT-GGACTACCCCGTGTTTATTATCCCAGTGGACTC-CATATGTTGCCA
*
35993900 TAGTCAAGCTATGGTCTTACACAATATAACTC
64 TAGTCAAGCTATCGTCTTACACAATATAACTC
* * * * * *
35993932 CATGTTTAATGTCTTGGTGGATTACCCTGTGTTTATTATCCTAGTGGACTCCATATGTTGTCATA
1 CATGTTTAACGTCTTGATGGACTACCCCGTGTTTATTATCCCAGTGGACTCCATATGTTGCCATA
*
35993997 GTCGAGCTATCGTCTTACAC
66 GTCAAGCTATCGTCTTACAC
35994017 GTCATACCCA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
94 1 0.01
95 72 0.97
96 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (95 bp):
CATGTTTAACGTCTTGATGGACTACCCCGTGTTTATTATCCCAGTGGACTCCATATGTTGCCATA
GTCAAGCTATCGTCTTACACAATATAACTC
Found at i:35997273 original size:16 final size:16
Alignment explanation
Indices: 35997252--35997299 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
35997242 TGGATTGTTT
35997252 TTAAGTATATTATATG
1 TTAAGTATATTATATG
35997268 TTAAGTTATATT-TAT-
1 TTAAG-TATATTATATG
35997283 TTAA-TA-A-TATATG
1 TTAAGTATATTATATG
35997296 TTAA
1 TTAA
35997300 AATAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
11 1 0.03
12 4 0.14
13 6 0.21
15 4 0.14
16 8 0.28
17 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (16 bp):
TTAAGTATATTATATG
Found at i:36002359 original size:17 final size:16
Alignment explanation
Indices: 36002339--36002376 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
36002329 ATTTAATCAA
36002339 TTAATTAAATTAATTTC
1 TTAATTAAA-TAATTTC
*
36002356 TTAATTAAATAATTTT
1 TTAATTAAATAATTTC
36002372 TTAAT
1 TTAAT
36002377 CTAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATTAAATAATTTC
Found at i:36004283 original size:18 final size:18
Alignment explanation
Indices: 36004261--36004294 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
36004251 TTTCTCACTT
36004261 TTTTTTAAT-TTTTATTA
1 TTTTTTAATATTTTATTA
36004278 TTTTTTAATATTTTATT
1 TTTTTTAATATTTTATT
36004295 TTATTCTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTAATATTTTATTA
Found at i:36004414 original size:23 final size:22
Alignment explanation
Indices: 36004359--36004415 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
36004349 ATTCTCATTT
*
36004359 AGTTAAAAATATATTTTTTGAA
1 AGTTAAAAATATATTATTTGAA
* *
36004381 ATTGTACAAATATATTATTTGATA
1 AGT-TAAAAATATATTATTTGA-A
36004405 AGTTAAAAATA
1 AGTTAAAAATA
36004416 AACAAGTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 2 0.07
23 23 0.82
24 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (22 bp):
AGTTAAAAATATATTATTTGAA
Found at i:36006501 original size:20 final size:20
Alignment explanation
Indices: 36006476--36006516 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
36006466 CTCATCGAGT
36006476 CAGAGTCAAAGCCACCCAAA
1 CAGAGTCAAAGCCACCCAAA
36006496 CAGAGTCAAAGCCACCCAAA
1 CAGAGTCAAAGCCACCCAAA
36006516 C
1 C
36006517 CCCCCAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.37, G:0.15, T:0.05
Consensus pattern (20 bp):
CAGAGTCAAAGCCACCCAAA
Found at i:36007176 original size:47 final size:47
Alignment explanation
Indices: 36007107--36007201 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
36007097 AAAGAATATA
*
36007107 CAATTTAATCATGGTCATATTTTAAAAAATATAACTT-TCTGCCTTCT
1 CAATTTAATCATGGCCATATTTTAAAAAATATAACTTCT-TGCCTTCT
*
36007154 CAATTTAATCATGGCCATATTTTAAAAAATATATCTTCTTGCCTTCT
1 CAATTTAATCATGGCCATATTTTAAAAAATATAACTTCTTGCCTTCT
36007201 C
1 C
36007202 GTGAATTACA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 44 0.98
48 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (47 bp):
CAATTTAATCATGGCCATATTTTAAAAAATATAACTTCTTGCCTTCT
Found at i:36011352 original size:13 final size:14
Alignment explanation
Indices: 36011334--36011362 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
36011324 GTAGGATACT
36011334 AACTAAAAT-ATGA
1 AACTAAAATCATGA
36011347 AACTAAAATCATGA
1 AACTAAAATCATGA
36011361 AA
1 AA
36011363 GGTAGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (14 bp):
AACTAAAATCATGA
Found at i:36012412 original size:68 final size:68
Alignment explanation
Indices: 36012334--36012469 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
36012324 CTAACTTTTC
36012334 CCATGTTGGAATTTTTAGAATAGTATAAATTATGGAAGTTGCCATCATATAGAAATTTAAGTTTT
1 CCATGTTGGAATTTTTAGAATAGTATAAATTATGGAAGTTGCCATCATATAGAAATTTAAGTTTT
36012399 TGG
66 TGG
36012402 CCATGTTGGAATTTTTAGAATAGTATAAATTATGGAAGTTGCCATCATATAGAAATTTAAGTTTT
1 CCATGTTGGAATTTTTAGAATAGTATAAATTATGGAAGTTGCCATCATATAGAAATTTAAGTTTT
36012467 TGG
66 TGG
36012470 TGTTGTTTTG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (68 bp):
CCATGTTGGAATTTTTAGAATAGTATAAATTATGGAAGTTGCCATCATATAGAAATTTAAGTTTT
TGG
Found at i:36021767 original size:26 final size:26
Alignment explanation
Indices: 36021736--36021912 Score: 192
Period size: 26 Copynumber: 6.8 Consensus size: 26
36021726 TTTAAGTTTT
36021736 TGCCACAAAGGCTTTCTTTCATATTA
1 TGCCACAAAGGCTTTCTTTCATATTA
*
36021762 TGCCACAAAGCCTTTCTTTCATATTA
1 TGCCACAAAGGCTTTCTTTCATATTA
**
36021788 TGCCACAAAGATTTTCTTTCATATTA
1 TGCCACAAAGGCTTTCTTTCATATTA
* * * *
36021814 CGCTACAAAGGCCTCCTTTCATATTA
1 TGCCACAAAGGCTTTCTTTCATATTA
** * * *
36021840 CACCAGAAAGACTTTTTTTTCATATTA
1 TGCCACAAAGGC-TTTCTTTCATATTA
* * *
36021867 CGTCATAAAGGCTTTCTTTCATATTA
1 TGCCACAAAGGCTTTCTTTCATATTA
* *
36021893 TGCCATAAAGGCTTTTTTTC
1 TGCCACAAAGGCTTTCTTTC
36021913 CTAACGTGTT
Statistics
Matches: 126, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 107 0.85
27 19 0.15
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.40
Consensus pattern (26 bp):
TGCCACAAAGGCTTTCTTTCATATTA
Found at i:36021877 original size:53 final size:53
Alignment explanation
Indices: 36021736--36021911 Score: 180
Period size: 53 Copynumber: 3.4 Consensus size: 53
36021726 TTTAAGTTTT
* * * * *
36021736 TGCCACAAAGGC-TTTCTTTCATATTATGCCACAAA-GCCTTTCTTTCATATTA
1 TGCCACAAAGACTTTTTTTTCATATTACGCTACAAAGGCC-TCCTTTCATATTA
*
36021788 TGCCACAAAGA-TTTTCTTTCATATTACGCTACAAAGGCCTCCTTTCATATTA
1 TGCCACAAAGACTTTTTTTTCATATTACGCTACAAAGGCCTCCTTTCATATTA
** * * * *
36021840 CACCAGAAAGACTTTTTTTTCATATTACG-TCATAAAGGCTTTCTTTCATATTA
1 TGCCACAAAGACTTTTTTTTCATATTACGCT-ACAAAGGCCTCCTTTCATATTA
* *
36021893 TGCCATAAAGGCTTTTTTT
1 TGCCACAAAGACTTTTTTT
36021912 CCTAACGTGT
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
52 52 0.50
53 53 0.50
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (53 bp):
TGCCACAAAGACTTTTTTTTCATATTACGCTACAAAGGCCTCCTTTCATATTA
Found at i:36024555 original size:33 final size:35
Alignment explanation
Indices: 36024517--36024586 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 35
36024507 ATATTTCTAT
36024517 AATTTTTGA-AAATTTA-ATACTTTGTATTATA-AA
1 AATTTTT-ATAAATTTATATACTTTGTATTATATAA
* *
36024550 AA-TTTTATATATTTATATATTTTGTATTATATAA
1 AATTTTTATAAATTTATATACTTTGTATTATATAA
36024584 AAT
1 AAT
36024587 ATATCATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
31 1 0.03
32 10 0.32
33 16 0.52
34 4 0.13
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (35 bp):
AATTTTTATAAATTTATATACTTTGTATTATATAA
Found at i:36027129 original size:17 final size:16
Alignment explanation
Indices: 36027086--36027138 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
36027076 AAAACATTTA
*
36027086 GAAAATTGTCATTTTTGG
1 GAAAATT-TTATTTTT-G
* *
36027104 GAAACTTTTCTTCTTTG
1 GAAAATTTTATT-TTTG
36027121 GAAAATTTTATTTTTG
1 GAAAATTTTATTTTTG
36027137 GA
1 GA
36027139 CTTTTTAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 6 0.21
17 14 0.48
18 9 0.31
ACGTcount: A:0.26, C:0.08, G:0.17, T:0.49
Consensus pattern (16 bp):
GAAAATTTTATTTTTG
Found at i:36060109 original size:88 final size:88
Alignment explanation
Indices: 36059960--36060131 Score: 317
Period size: 88 Copynumber: 2.0 Consensus size: 88
36059950 TCAAAGGCTA
36059960 TTTTGCAAGCCAAATAATCAGCCAAACAAGCTGATTGGGTCAGCATGTGGGACGGTTTTGGGTTG
1 TTTTGCAAGCCAAATAATCAGCCAAACAAGCTGATTGGGTCAGCATGTGGGACGGTTTTGGGTTG
* *
36060025 CCCAGTTCTCGGTTGGATCGATT
66 CCCAGTGCTCGATTGGATCGATT
*
36060048 TTTTGCAATCCAAATAATCAGCCAAACAAGCTGATTGGGTCAGCATGTGGGACGGTTTTGGGTTG
1 TTTTGCAAGCCAAATAATCAGCCAAACAAGCTGATTGGGTCAGCATGTGGGACGGTTTTGGGTTG
36060113 CCCAGTGCTCGATTGGATC
66 CCCAGTGCTCGATTGGATC
36060132 AGTTTTCTCG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (88 bp):
TTTTGCAAGCCAAATAATCAGCCAAACAAGCTGATTGGGTCAGCATGTGGGACGGTTTTGGGTTG
CCCAGTGCTCGATTGGATCGATT
Found at i:36062397 original size:3 final size:3
Alignment explanation
Indices: 36062389--36062471 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
36062379 CTCTGTGAGA
*
36062389 TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
36062437 TTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
36062472 GGGATCCTCA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:36082409 original size:25 final size:25
Alignment explanation
Indices: 36082382--36082562 Score: 119
Period size: 25 Copynumber: 7.6 Consensus size: 25
36082372 CTAGACAAAG
* *
36082382 ATACACCACAAAGGCATCATATGGG
1 ATACGCCACAAAGGCATCATATGGA
* * **
36082407 ATATGCCATAAAGGC-T-A-ACAGA
1 ATACGCCACAAAGGCATCATATGGA
* *
36082429 ATATGCCACAAAAGCATCATATGGA
1 ATACGCCACAAAGGCATCATATGGA
* * *
36082454 ATACGCCATAAAGGC-T-A-ACGAA
1 ATACGCCACAAAGGCATCATATGGA
* * *
36082476 ATATGCCACAAAGGCATCTTATAGA
1 ATACGCCACAAAGGCATCATATGGA
* * *
36082501 ATACACCATAAAGGC-T-A-ATAGA
1 ATACGCCACAAAGGCATCATATGGA
* *
36082523 ATATGCCAAAAAGGCATCATATGGA
1 ATACGCCACAAAGGCATCATATGGA
*
36082548 ATACACCACAAAGGC
1 ATACGCCACAAAGGC
36082563 TAACAGAATA
Statistics
Matches: 115, Mismatches: 32, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
22 48 0.42
23 5 0.04
24 5 0.04
25 57 0.50
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (25 bp):
ATACGCCACAAAGGCATCATATGGA
Found at i:36082434 original size:22 final size:22
Alignment explanation
Indices: 36082411--36082593 Score: 98
Period size: 22 Copynumber: 7.9 Consensus size: 22
36082401 TATGGGATAT
* *
36082411 GCCATAAAGGCTAACAGAATAT
1 GCCACAAAGGCTAACAGAATAC
* **
36082433 GCCACAAAAGCATCATATGGAATAC
1 GCCACAAAGGC-T-A-ACAGAATAC
* *
36082458 GCCATAAAGGCTAAC-GAAATAT
1 GCCACAAAGGCTAACAG-AATAC
* *
36082480 GCCACAAAGGCATCTTATAGAATAC
1 GCCACAAAGG---CTAACAGAATAC
* * * *
36082505 ACCATAAAGGCTAATAGAATAT
1 GCCACAAAGGCTAACAGAATAC
* **
36082527 GCCAAAAAGGCATCATATGGAATAC
1 GCCACAAAGGC-T-A-ACAGAATAC
*
36082552 ACCACAAAGGCTAACAGAATAC
1 GCCACAAAGGCTAACAGAATAC
*
36082574 GCAACAAAGGCTAAACAGAA
1 GCCACAAAGGCT-AACAGAA
36082594 AACCATCCAG
Statistics
Matches: 122, Mismatches: 27, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
21 1 0.01
22 59 0.48
23 11 0.09
24 4 0.03
25 46 0.38
26 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.16
Consensus pattern (22 bp):
GCCACAAAGGCTAACAGAATAC
Found at i:36082524 original size:94 final size:94
Alignment explanation
Indices: 36082356--36082584 Score: 291
Period size: 94 Copynumber: 2.4 Consensus size: 94
36082346 AGATTTGTCA
* * * * * **
36082356 GAATACACCACAAGGGCTAGACAAAGATACACCACAAAGGCATCATATGGGATATGCCATAAAGG
1 GAATACACCACAAAGGCTA-ACAGA-ATACGCCACAAAGGCATCATATAGAATACACCATAAAGG
36082421 CTAACAGAATATGCCACAAAA-GCATCATATG
64 CTAACAGAATATGCCA-AAAAGGCATCATATG
* * * *
36082452 GAATACGCCATAAAGGCTAAC-GAAATATGCCACAAAGGCATCTTATAGAATACACCATAAAGGC
1 GAATACACCACAAAGGCTAACAG-AATACGCCACAAAGGCATCATATAGAATACACCATAAAGGC
*
36082516 TAATAGAATATGCCAAAAAGGCATCATATG
65 TAACAGAATATGCCAAAAAGGCATCATATG
*
36082546 GAATACACCACAAAGGCTAACAGAATACGCAACAAAGGC
1 GAATACACCACAAAGGCTAACAGAATACGCCACAAAGGC
36082585 TAAACAGAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
93 4 0.04
94 90 0.79
95 4 0.04
96 16 0.14
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (94 bp):
GAATACACCACAAAGGCTAACAGAATACGCCACAAAGGCATCATATAGAATACACCATAAAGGCT
AACAGAATATGCCAAAAAGGCATCATATG
Found at i:36082583 original size:47 final size:47
Alignment explanation
Indices: 36082387--36082584 Score: 272
Period size: 47 Copynumber: 4.2 Consensus size: 47
36082377 CAAAGATACA
* **
36082387 CCACAAAGGCATCATATGGGATATGCCATAAAGGCTAACAGAATATG
1 CCACAAAGGCATCATATGGAATACACCATAAAGGCTAACAGAATATG
* *
36082434 CCACAAAAGCATCATATGGAATACGCCATAAAGGCTAAC-GAAATATG
1 CCACAAAGGCATCATATGGAATACACCATAAAGGCTAACAG-AATATG
* * *
36082481 CCACAAAGGCATCTTATAGAATACACCATAAAGGCTAATAGAATATG
1 CCACAAAGGCATCATATGGAATACACCATAAAGGCTAACAGAATATG
* * *
36082528 CCAAAAAGGCATCATATGGAATACACCACAAAGGCTAACAGAATACG
1 CCACAAAGGCATCATATGGAATACACCATAAAGGCTAACAGAATATG
*
36082575 CAACAAAGGC
1 CCACAAAGGC
36082585 TAAACAGAAA
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
46 1 0.01
47 131 0.98
48 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (47 bp):
CCACAAAGGCATCATATGGAATACACCATAAAGGCTAACAGAATATG
Found at i:36085006 original size:27 final size:27
Alignment explanation
Indices: 36084968--36085021 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
36084958 TAATTGAGTA
36084968 TAAATCATATTGGGTTCAAGTTTAAGG
1 TAAATCATATTGGGTTCAAGTTTAAGG
36084995 TAAATCATATTGGGTTCAAGTTTAAGG
1 TAAATCATATTGGGTTCAAGTTTAAGG
36085022 CTTAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (27 bp):
TAAATCATATTGGGTTCAAGTTTAAGG
Found at i:36087656 original size:29 final size:29
Alignment explanation
Indices: 36087599--36087660 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
36087589 GGATGGGAGG
*
36087599 GAAGTAAAAGTTTTGGGAAAAAGTGAAAA
1 GAAGTAAAAGTTTAGGGAAAAAGTGAAAA
36087628 GAAGTAAAAGTATTAGGGAAAAAGT-AAAA
1 GAAGTAAAAGT-TTAGGGAAAAAGTGAAAA
36087657 -AAGT
1 GAAGT
36087661 TTAGAGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 4 0.13
29 15 0.48
30 12 0.39
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (29 bp):
GAAGTAAAAGTTTAGGGAAAAAGTGAAAA
Found at i:36088462 original size:21 final size:21
Alignment explanation
Indices: 36088437--36088505 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
36088427 TCAAATTATG
36088437 TATTGTAGTTAATATTCATAA
1 TATTGTAGTTAATATTCATAA
* *
36088458 TATTGTAGCTCAA-ATT-AT-G
1 TATTGTAG-TTAATATTCATAA
36088477 TATTGTAGTTAATATTCATAA
1 TATTGTAGTTAATATTCATAA
36088498 TATTGTAG
1 TATTGTAG
36088506 CTCAAATTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 3 0.08
19 11 0.28
20 4 0.10
21 19 0.47
22 3 0.08
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (21 bp):
TATTGTAGTTAATATTCATAA
Done.