Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 37 of 240
Found at i:13161571 original size:24 final size:22
Alignment explanation
Indices: 13161526--13161574 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 22
13161516 ATTATTTTAA
13161526 ATTATATTTTATAATATTATAT
1 ATTATATTTTATAATATTATAT
13161548 ATTATAATTTTAATAA-ATTCATAT
1 ATTAT-ATTTT-ATAATATT-ATAT
13161572 ATT
1 ATT
13161575 TTATCAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.21
23 8 0.33
24 11 0.46
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTATATTTTATAATATTATAT
Found at i:13161577 original size:18 final size:17
Alignment explanation
Indices: 13161548--13161589 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
13161538 AATATTATAT
13161548 ATTATA-ATTTTAAT-AA
1 ATTATATATTTT-ATCAA
13161564 ATTCATATATTTTATCAA
1 ATT-ATATATTTTATCAA
13161582 ATTATATA
1 ATTATATA
13161590 ATATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 10 0.43
18 10 0.43
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATATATTTTATCAA
Found at i:13161861 original size:16 final size:16
Alignment explanation
Indices: 13161840--13161907 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
13161830 GATTTGCTAT
13161840 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
* *
13161856 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
13161872 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
13161888 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
13161904 TACA
1 TACA
13161908 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:13163112 original size:114 final size:114
Alignment explanation
Indices: 13162797--13163112 Score: 291
Period size: 114 Copynumber: 2.8 Consensus size: 114
13162787 CTGCAATATG
* * * * **
13162797 CAAGAATTACCGGCG-TTTGGTCATAAACGCCGCAAAAACTGTTAAGAAAAACGCTGTCGTTTTC
1 CAAGAATTAGCGGCGCTTT-ATCAGAAGCGCCGC-AAAACTGTTAAG-AAAACAATGTCGTTTTC
* * * *
13162861 AGTTTAGGTTTTGGGGACTTTAGTGGCGCTTAATGAAAAACGCCGCTATAGT
63 AATTTAGGTTTTAGAGACTTTAGTGGCGATTAATGAAAAACGCCGCTATAGT
* * * *
13162913 CAAGAATTAGCGGCGCTTTATCATAAGCGCCGCAAGACTGTTAAGAAAA-AGTTGCCGTTTTTC-
1 CAAGAATTAGCGGCGCTTTATCAGAAGCGCCGCAAAACTGTTAAGAAAACA-ATGTCG-TTTTCA
** * * ** *
13162976 ATTTATCTTTTCGAGACATTAGTGGCGATTTTTGAAAAATGCCG-TAGTAG-
64 ATTTAGGTTTTAGAGACTTTAGTGGCGATTAATGAAAAACGCCGCTA-TAGT
** * * *
13163026 CAAAGCTTTAGTGGCGCTTTATCAGAAGTGCTGCAAAACTGTTAAGAAAACAATGTCGTTTTCAA
1 C-AAGAATTAGCGGCGCTTTATCAGAAGCGCCGCAAAACTGTTAAGAAAACAATGTCGTTTTCAA
*
13163091 TTTAGGTTTTAAAGACTTTAGT
65 TTTAGGTTTTAGAGACTTTAGT
13163113 AGCGCTTGTC
Statistics
Matches: 162, Mismatches: 31, Indels: 16
0.78 0.15 0.08
Matches are distributed among these distances:
113 8 0.05
114 108 0.67
115 17 0.10
116 26 0.16
117 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (114 bp):
CAAGAATTAGCGGCGCTTTATCAGAAGCGCCGCAAAACTGTTAAGAAAACAATGTCGTTTTCAAT
TTAGGTTTTAGAGACTTTAGTGGCGATTAATGAAAAACGCCGCTATAGT
Found at i:13163823 original size:14 final size:14
Alignment explanation
Indices: 13163806--13163873 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
13163796 TAAGGATTGA
* *
13163806 GGTTAAGGGTTTAG
1 GGTTTAGGGTTAAG
*
13163820 GGTTTAGGGGTCAAG
1 GGTTTA-GGGTTAAG
*
13163835 GGTTAAGGGTTAAG
1 GGTTTAGGGTTAAG
* *
13163849 GG-CTAGGGTTAGG
1 GGTTTAGGGTTAAG
13163862 GGTTTATGGGTT
1 GGTTTA-GGGTT
13163874 TATAGTTAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
13 10 0.24
14 16 0.38
15 16 0.38
ACGTcount: A:0.19, C:0.03, G:0.46, T:0.32
Consensus pattern (14 bp):
GGTTTAGGGTTAAG
Found at i:13163861 original size:6 final size:7
Alignment explanation
Indices: 13163806--13163865 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
13163796 TAAGGATTGA
13163806 GGTTAAG
1 GGTTAAG
*
13163813 GGTTTAG
1 GGTTAAG
*
13163820 GGTTTAGG
1 GG-TTAAG
*
13163828 GGTCAAG
1 GGTTAAG
13163835 GGTTAAG
1 GGTTAAG
13163842 GGTTAAG
1 GGTTAAG
*
13163849 GGCT-AG
1 GGTTAAG
*
13163855 GGTTAGG
1 GGTTAAG
13163862 GGTT
1 GGTT
13163866 TATGGGTTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
6 5 0.12
7 32 0.76
8 5 0.12
ACGTcount: A:0.20, C:0.03, G:0.47, T:0.30
Consensus pattern (7 bp):
GGTTAAG
Found at i:13164070 original size:29 final size:30
Alignment explanation
Indices: 13164034--13164101 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 30
13164024 GGCTTATGGA
*
13164034 TTAT-GGTTTAAGGGTTGGGGTTAAAG-GT
1 TTATGGGTTTAAGGGTTAGGGTTAAAGAGT
* *
13164062 TTATGGGTTT-AGGGTTAGGGTTTATGAGT
1 TTATGGGTTTAAGGGTTAGGGTTAAAGAGT
*
13164091 TTAGGGGTTTA
1 TTATGGGTTTA
13164102 TAGTTAATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (30 bp):
TTATGGGTTTAAGGGTTAGGGTTAAAGAGT
Found at i:13167589 original size:17 final size:17
Alignment explanation
Indices: 13167569--13167618 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
13167559 TTAATATCTA
13167569 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
13167586 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
13167600 -ATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
13167616 TAT
1 TAT
13167619 TTGTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.38
14 2 0.07
16 2 0.07
17 14 0.48
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:13167605 original size:13 final size:13
Alignment explanation
Indices: 13167587--13167614 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13167577 TTCTAAATTT
13167587 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
13167600 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
13167613 AT
1 AT
13167615 TTATTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
ATAAGTTTTCTAA
Found at i:13167645 original size:15 final size:15
Alignment explanation
Indices: 13167610--13167648 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
13167600 ATAAGTTTTC
*
13167610 TAAATTTATTTGTAT
1 TAAATTTATTAGTAT
13167625 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
13167641 TAAATTTA
1 TAAATTTA
13167649 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:13167691 original size:62 final size:61
Alignment explanation
Indices: 13167580--13167728 Score: 174
Period size: 62 Copynumber: 2.4 Consensus size: 61
13167570 ATAAGTTTTC
* *** * *
13167580 TAAATTTATAAGTTTTCTAAATAAGTTTTCTAAATTTATTTGTATTAAAATTTAT-TAGTAT
1 TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGT-GTAT
** *
13167641 TAAATTTACTTCGTTTTCTAAATAAGTGTTCTAAATTTGGGAGAAATAAAATTTATGTGTAT
1 TAAATTTA-TAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGTGTAT
* *
13167703 TAATTTTATAAGTTTTCTACATAAGT
1 TAAATTTATAAGTTTTCTAAATAAGT
13167729 TACATAATAC
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
61 23 0.32
62 49 0.67
63 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.48
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGTGTAT
Found at i:13167867 original size:95 final size:95
Alignment explanation
Indices: 13167765--13167952 Score: 288
Period size: 95 Copynumber: 2.0 Consensus size: 95
13167755 ACAAAACTTA
* * *
13167765 TATAATACATAACTTATATTTAAGCTTGCATAACTTACATAATAA-TTTACATAACTTATATATA
1 TATAATACATAACTTATATATAAGCTTGCATAACTTACAT-ATAAGCTTACATAACTTACATATA
13167829 ATAACATAATAAATTACATAATACTTTATGT
65 ATAACATAATAAATTACATAATACTTTATGT
* * * *
13167860 TATAATACATAACTTGTATATAAGCTTGCATAACTTATATTTAAGCTTGCATAACTTACATATAA
1 TATAATACATAACTTATATATAAGCTTGCATAACTTACATATAAGCTTACATAACTTACATATAA
*
13167925 TAACATAATAAATTACATATTACTTTAT
66 TAACATAATAAATTACATAATACTTTAT
13167953 ATAATAACAT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 3 0.04
95 81 0.96
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (95 bp):
TATAATACATAACTTATATATAAGCTTGCATAACTTACATATAAGCTTACATAACTTACATATAA
TAACATAATAAATTACATAATACTTTATGT
Found at i:13167893 original size:21 final size:21
Alignment explanation
Indices: 13167867--13167924 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
13167857 TGTTATAATA
*
13167867 CATAACTTGTATATAAGCTTG
1 CATAACTTATATATAAGCTTG
*
13167888 CATAACTTATATTTAAGCTTG
1 CATAACTTATATATAAGCTTG
*
13167909 CATAACTTACATATAA
1 CATAACTTATATATAA
13167925 TAACATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
CATAACTTATATATAAGCTTG
Found at i:13167966 original size:8 final size:8
Alignment explanation
Indices: 13167953--13168014 Score: 52
Period size: 8 Copynumber: 7.0 Consensus size: 8
13167943 ATTACTTTAT
13167953 ATAATAAC
1 ATAATAAC
13167961 ATAATAAC
1 ATAATAAC
*
13167969 TTAAATAAC
1 AT-AATAAC
*
13167978 TTAAATAAC
1 AT-AATAAC
13167987 TTATATAATAAC
1 ----ATAATAAC
13167999 ATAATAAC
1 ATAATAAC
13168007 ATAATAAC
1 ATAATAAC
13168015 TAACATACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
8 25 0.53
9 15 0.32
12 6 0.13
13 1 0.02
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (8 bp):
ATAATAAC
Found at i:13168071 original size:9 final size:9
Alignment explanation
Indices: 13168043--13168267 Score: 243
Period size: 9 Copynumber: 24.8 Consensus size: 9
13168033 CATATATAGA
13168043 AACTTACAT
1 AACTTACAT
* *
13168052 AAATTAAAT
1 AACTTACAT
13168061 AACTTACAT
1 AACTTACAT
13168070 AACTTACAT
1 AACTTACAT
* *
13168079 AAATTAAAT
1 AACTTACAT
13168088 AACTTACAT
1 AACTTACAT
13168097 AACTTACAT
1 AACTTACAT
*
13168106 AAACTTGCAT
1 -AACTTACAT
* *
13168116 AAATTAAAT
1 AACTTACAT
13168125 AACTTACAT
1 AACTTACAT
13168134 AACTTACAT
1 AACTTACAT
*
13168143 AACCTACAT
1 AACTTACAT
* *
13168152 AAATTAAAT
1 AACTTACAT
13168161 AACTTACAT
1 AACTTACAT
13168170 AACTTACAT
1 AACTTACAT
* *
13168179 AAATTAAAT
1 AACTTACAT
13168188 AACTTACAT
1 AACTTACAT
13168197 AACTTACAT
1 AACTTACAT
* * *
13168206 AAATTCCGT
1 AACTTACAT
* *
13168215 GGACCTACAT
1 -AACTTACAT
* *
13168225 AAATTAAAT
1 AACTTACAT
13168234 AACTTACAT
1 AACTTACAT
13168243 AACTTACAT
1 AACTTACAT
* *
13168252 AAATTAAAT
1 AACTTACAT
13168261 AACTTAC
1 AACTTAC
13168268 CCGTGAAAAT
Statistics
Matches: 172, Mismatches: 42, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
9 160 0.93
10 12 0.07
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:13168263 original size:73 final size:72
Alignment explanation
Indices: 13168043--13168267 Score: 324
Period size: 73 Copynumber: 3.1 Consensus size: 72
13168033 CATATATAGA
* * * *
13168043 AACTTACATAAATTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAA
1 AACTTACATAACTTACATAAATTACATAACCTACATAAATTAAATAACTTACATAACTTACATAA
**
13168108 ACTTGCAT
66 A-TTAAAT
* * *
13168116 AAATTAAATAACTTACATAACTTACATAACCTACATAAATTAAATAACTTACATAACTTACATAA
1 AACTTACATAACTTACATAAATTACATAACCTACATAAATTAAATAACTTACATAACTTACATAA
13168181 ATTAAAT
66 ATTAAAT
* * *
13168188 AACTTACATAACTTACATAAATTCCGTGGACCTACATAAATTAAATAACTTACATAACTTACATA
1 AACTTACATAACTTACATAAATTACAT-AACCTACATAAATTAAATAACTTACATAACTTACATA
13168253 AATTAAAT
65 AATTAAAT
13168261 AACTTAC
1 AACTTAC
13168268 CCGTGAAAAT
Statistics
Matches: 138, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
72 26 0.19
73 112 0.81
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (72 bp):
AACTTACATAACTTACATAAATTACATAACCTACATAAATTAAATAACTTACATAACTTACATAA
ATTAAAT
Found at i:13173727 original size:21 final size:21
Alignment explanation
Indices: 13173701--13173751 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
13173691 CTACAACTTA
* * *
13173701 AAGCAGATGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAACGAGAG
*
13173722 AAGCAGAGGCTGCAACGAGAG
1 AAGCAGAGGCGGCAACGAGAG
13173743 AAGCAGAGG
1 AAGCAGAGG
13173752 TTCAAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAACGAGAG
Found at i:13174213 original size:21 final size:20
Alignment explanation
Indices: 13174190--13174227 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13174180 CGCTCATATA
13174190 AAAAACACCGCTAAAGAAGG
1 AAAAACACCGCTAAAGAAGG
**
13174210 AAAAATGCCGCTAAAGAA
1 AAAAACACCGCTAAAGAA
13174228 CATGATCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.18, G:0.18, T:0.08
Consensus pattern (20 bp):
AAAAACACCGCTAAAGAAGG
Found at i:13174372 original size:15 final size:15
Alignment explanation
Indices: 13174352--13174381 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13174342 ACGCTACAAA
*
13174352 CGTTAGCGACGTTTT
1 CGTTAGCGACCTTTT
13174367 CGTTAGCGACCTTTT
1 CGTTAGCGACCTTTT
13174382 TTGCGGCGCT
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:0.13, C:0.23, G:0.23, T:0.40
Consensus pattern (15 bp):
CGTTAGCGACCTTTT
Found at i:13174668 original size:43 final size:43
Alignment explanation
Indices: 13174620--13174709 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
13174610 ATACTACCTG
13174620 TATTGGTGCATACTAACTCGTGCTGTTTGGTGTAAGATTTTAA
1 TATTGGTGCATACTAACTCGTGCTGTTTGGTGTAAGATTTTAA
13174663 TATTGGTGCATACTAACTCGTGCTGTTTGGTGTAAGATTTTAA
1 TATTGGTGCATACTAACTCGTGCTGTTTGGTGTAAGATTTTAA
13174706 TATT
1 TATT
13174710 TTAAACCAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.43
Consensus pattern (43 bp):
TATTGGTGCATACTAACTCGTGCTGTTTGGTGTAAGATTTTAA
Found at i:13207410 original size:16 final size:16
Alignment explanation
Indices: 13207389--13207432 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
13207379 TTTCCTATTC
13207389 TTTTTTTTCTTTTTCT
1 TTTTTTTTCTTTTTCT
*
13207405 TTTTTTTTCTGTTTCT
1 TTTTTTTTCTTTTTCT
*
13207421 TTATTGTTTCTT
1 TT-TTTTTTCTT
13207433 AGTAAGGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (16 bp):
TTTTTTTTCTTTTTCT
Found at i:13210211 original size:28 final size:27
Alignment explanation
Indices: 13210172--13210224 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
13210162 GTGTTTTATC
13210172 CTTCTTGCCAAACTCTCAGTTCATATA
1 CTTCTTGCCAAACTCTCAGTTCATATA
13210199 CTTCTCTGCCAAACTCTCAGTTCATA
1 CTTCT-TGCCAAACTCTCAGTTCATA
13210225 CTCATAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.25, C:0.32, G:0.08, T:0.36
Consensus pattern (27 bp):
CTTCTTGCCAAACTCTCAGTTCATATA
Found at i:13211325 original size:22 final size:23
Alignment explanation
Indices: 13211300--13211342 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
13211290 TCAAAATAGA
* *
13211300 ATGATATTTTTAA-ATTTTTTTC
1 ATGATAATATTAATATTTTTTTC
13211322 ATGATAATATTAATATTTTTT
1 ATGATAATATTAATATTTTTT
13211343 AGATGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (23 bp):
ATGATAATATTAATATTTTTTTC
Found at i:13211351 original size:22 final size:22
Alignment explanation
Indices: 13211300--13211351 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
13211290 TCAAAATAGA
* * *
13211300 ATGATATTTTTAAATTTTTTTC
1 ATGATAATATTAAATTTTTTAC
*
13211322 ATGATAATATTAATATTTTTTAG
1 ATGATAATATTAA-ATTTTTTAC
13211345 ATG-TAAT
1 ATGATAAT
13211352 TATGTTAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (22 bp):
ATGATAATATTAAATTTTTTAC
Found at i:13223984 original size:28 final size:28
Alignment explanation
Indices: 13223952--13224008 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
13223942 AGATGGAATG
13223952 TATATTACCTTTACTTCAAAATTCTCTA
1 TATATTACCTTTACTTCAAAATTCTCTA
*
13223980 TATATTACTTTTACTTCAAAATTCTCTA
1 TATATTACCTTTACTTCAAAATTCTCTA
13224008 T
1 T
13224009 CTTCTCTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (28 bp):
TATATTACCTTTACTTCAAAATTCTCTA
Found at i:13233232 original size:20 final size:19
Alignment explanation
Indices: 13233189--13233232 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
13233179 ATTTTTTTAC
**
13233189 ATTTTTTAAAAACTTACCT
1 ATTTTTTAAAAACTTAAAT
*
13233208 TTTTTTTACAAAACTTAAAT
1 ATTTTTTA-AAAACTTAAAT
13233228 ATTTT
1 ATTTT
13233233 AACAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTTTAAAAACTTAAAT
Found at i:13233244 original size:10 final size:10
Alignment explanation
Indices: 13233229--13233261 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
13233219 AACTTAAATA
13233229 TTTTAACAA-T
1 TTTTAA-AACT
13233239 TTTTAAAACT
1 TTTTAAAACT
13233249 TTTTAAAACT
1 TTTTAAAACT
13233259 TTT
1 TTT
13233262 ATATTCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 2 0.09
10 20 0.91
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTTAAAACT
Found at i:13233307 original size:19 final size:19
Alignment explanation
Indices: 13233222--13233309 Score: 54
Period size: 19 Copynumber: 4.5 Consensus size: 19
13233212 TTTACAAAAC
13233222 TTAAATATTTTAAC-AATTT
1 TTAAA-ATTTTAACAAATTT
* *
13233241 TTAAAACTTTTTA-AAACTT
1 TTAAAA-TTTTAACAAATTT
* * *
13233260 TTATATTCTTTAAATAAATTT
1 TTAAAAT-TTT-AACAAATTT
**
13233281 AAAAAATTTTAACAAATTT
1 TTAAAATTTTAACAAATTT
*
13233300 TTATAATTTT
1 TTAAAATTTT
13233310 TTTCATTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 10
0.68 0.19 0.14
Matches are distributed among these distances:
18 2 0.04
19 36 0.72
20 4 0.08
21 8 0.16
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATTTTAACAAATTT
Found at i:13233317 original size:28 final size:29
Alignment explanation
Indices: 13233286--13233340 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
13233276 AATTTAAAAA
* *
13233286 ATTTTAACA-AATTTTTATAATTTTTTTC
1 ATTTTAAAATAATTTTAATAATTTTTTTC
*
13233314 ATTTTAAAATAATTTTAATGATTTTTT
1 ATTTTAAAATAATTTTAATAATTTTTT
13233341 AATCAGTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTAAAATAATTTTAATAATTTTTTTC
Found at i:13237645 original size:24 final size:24
Alignment explanation
Indices: 13237599--13237645 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
13237589 AAAGTCAAAT
* *
13237599 ATATTATGCTAATAAATGCTAAAA
1 ATATTATACTAATAAATACTAAAA
* *
13237623 ATATTATACTCATAAATATTAAA
1 ATATTATACTAATAAATACTAAA
13237646 TCTTCTAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (24 bp):
ATATTATACTAATAAATACTAAAA
Found at i:13242527 original size:25 final size:25
Alignment explanation
Indices: 13242499--13242567 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
13242489 TCCTCCAAGT
*
13242499 TGAATAACGGGAAGCTCATGTGAGC
1 TGAATAACGGGAAGCTCATGCGAGC
* * * *
13242524 TGAATAATGAGAAGTTTATGCGAGC
1 TGAATAACGGGAAGCTCATGCGAGC
* *
13242549 TGAGTATCGGGAAGCTCAT
1 TGAATAACGGGAAGCTCAT
13242568 AAGAGCTTAA
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (25 bp):
TGAATAACGGGAAGCTCATGCGAGC
Found at i:13247233 original size:30 final size:30
Alignment explanation
Indices: 13247174--13247233 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
13247164 CTTCTTCTGG
* ***
13247174 GAAGAAGGCGGCTGCTCCTAAAGCTGCTCC
1 GAAGAAGGCGGCTGCGCCTAAAAAGGCTCC
*
13247204 GAAGAAGGCTGCTGCGCCTAAAAAGGCTCC
1 GAAGAAGGCGGCTGCGCCTAAAAAGGCTCC
13247234 TTCGAAGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.28, G:0.30, T:0.15
Consensus pattern (30 bp):
GAAGAAGGCGGCTGCGCCTAAAAAGGCTCC
Found at i:13251274 original size:20 final size:22
Alignment explanation
Indices: 13251251--13251291 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
13251241 ATAATTTTCA
*
13251251 AAAATAGTTTT-T-AGTTTTTT
1 AAAATAATTTTATGAGTTTTTT
13251271 AAAATAATTTTATGAGTTTTT
1 AAAATAATTTTATGAGTTTTT
13251292 AGAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (22 bp):
AAAATAATTTTATGAGTTTTTT
Found at i:13260972 original size:92 final size:90
Alignment explanation
Indices: 13260866--13261066 Score: 235
Period size: 91 Copynumber: 2.2 Consensus size: 90
13260856 TCAAACTTAA
* *
13260866 AAAAAAAGAGCAATTAAGCCCCTCCTTTTTTTTTACACTCAATTGAGCACCGGAACTTTAAAAAT
1 AAAAAAA-AGCAATTAAGCCCCTACTCTTTTTTT-CACTCAATTGAGCACCGGAACTTTAAAAAT
* *
13260931 GCATAAAAAAGACCCTCAAACTTCTTC
64 ACATAAAAAAGACCCTCAAAATTCTTC
* * * * * ** *
13260958 AAAAAAAATGCAATTAAACTCTTACTCTTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATA
1 AAAAAAAA-GCAATTAAGCCCCTACTCTTTTTTTCACTCAATTGAGCACCGGAACTTTAAAAATA
* *
13261023 CATTAAAAAGACCCTCAAAATTTTTC
65 CATAAAAAAGACCCTCAAAATTCTTC
13261049 --AAAAAAGCAATTAAGCCC
1 AAAAAAAAGCAATTAAGCCC
13261067 ATGCTCTTAT
Statistics
Matches: 92, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
88 10 0.11
89 6 0.07
91 49 0.53
92 27 0.29
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (90 bp):
AAAAAAAAGCAATTAAGCCCCTACTCTTTTTTTCACTCAATTGAGCACCGGAACTTTAAAAATAC
ATAAAAAAGACCCTCAAAATTCTTC
Found at i:13261198 original size:44 final size:44
Alignment explanation
Indices: 13261073--13261205 Score: 126
Period size: 44 Copynumber: 3.0 Consensus size: 44
13261063 GCCCATGCTC
* *
13261073 TTATTAAAAATTAGAATTTTTTTATAAAAAAT-AAAAAAAATAAATT
1 TTATT-AAAATTAGAA-TTTTTTAT-AAAAATCATAAAAAATAAAAT
** * * * * *
13261119 TTAGAAAAATTATTAAATTTTAATAGAAA-CATAAAAATTAAAAT
1 TTATTAAAATTA-GAATTTTTTATAAAAATCATAAAAAATAAAAT
*
13261163 TTATTAAAATTAGAATTTTTTATAAAAATCGTAAAAAATAAAA
1 TTATTAAAATTAGAATTTTTTATAAAAATCATAAAAAATAAAA
13261206 AAATTATAAA
Statistics
Matches: 67, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
43 12 0.18
44 37 0.55
45 13 0.19
46 5 0.07
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (44 bp):
TTATTAAAATTAGAATTTTTTATAAAAATCATAAAAAATAAAAT
Found at i:13261209 original size:37 final size:38
Alignment explanation
Indices: 13261168--13261239 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 38
13261158 AAAATTTATT
**
13261168 AAAATTAGAATTTTTTATAAAAATC-GTAAAAAATAAA
1 AAAATTAGAAAATTTTATAAAAATCAGTAAAAAATAAA
* * *
13261205 AAAATTATAAAATTTTATAAATATCATTAAAAAAT
1 AAAATTAGAAAATTTTATAAAAATCAGTAAAAAAT
13261240 TAACGACCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 21 0.72
38 8 0.28
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (38 bp):
AAAATTAGAAAATTTTATAAAAATCAGTAAAAAATAAA
Found at i:13261434 original size:21 final size:21
Alignment explanation
Indices: 13261410--13261449 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13261400 TTATATTTCT
* * *
13261410 TTACATTTTTTTATAATTTAC
1 TTACAATTTTATAAAATTTAC
13261431 TTACAATTTTATAAAATTT
1 TTACAATTTTATAAAATTT
13261450 TATATTTCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTACAATTTTATAAAATTTAC
Found at i:13261490 original size:21 final size:22
Alignment explanation
Indices: 13261464--13261513 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
13261454 TTTCTATATA
** *
13261464 TTTTATAAATTTTTAC-GATTT
1 TTTTATAAAAATTTACAAATTT
13261485 TTTTATAAAAATTTACAAATTT
1 TTTTATAAAAATTTACAAATTT
13261507 TTTTATA
1 TTTTATA
13261514 TTTCTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTATAAAAATTTACAAATTT
Found at i:13261531 original size:20 final size:20
Alignment explanation
Indices: 13261505--13261558 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
13261495 ATTTACAAAT
*
13261505 TTTTTTATATTTCTTTTATAA
1 TTTTTAATATTT-TTTTATAA
*
13261526 TTTTTAGATATATTTTTATAA
1 TTTTTA-ATATTTTTTTATAA
13261547 TTTTTAATATTT
1 TTTTTAATATTT
13261559 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.17
21 19 0.66
22 5 0.17
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTAATATTTTTTTATAA
Found at i:13261741 original size:91 final size:90
Alignment explanation
Indices: 13261640--13261866 Score: 259
Period size: 91 Copynumber: 2.6 Consensus size: 90
13261630 AATTTTTAAT
* * *
13261640 AAAAGCAGGGGCTTAATTATTTTTTTTGAAAAAAGTTTGAGGGTCTTTTTGATACATTTTGAAAG
1 AAAAG-AGGGGCTTAATTATTTTTTTTGAAAAAAGTTTGAGGGACTTTTTGATACATTTTAAAAA
* * *
13261705 TTCAAGTACCCAATTGAGTGTAAAAA
65 TTCAAGTACCAAAATGAGTGCAAAAA
* * * * * *
13261731 AAAAGTAGGGGTTTAATTGCTTTTTTTTG-AAAAGGTTTGTGGGCCTTTTTGATGCATTTTAAAA
1 AAAAG-AGGGGCTTAATT-ATTTTTTTTGAAAAAAGTTTGAGGGACTTTTTGATACATTTTAAAA
13261795 ATTCAAGTACCAAAATGAGTGCAAAAA
64 ATTCAAGTACCAAAATGAGTGCAAAAA
* *
13261822 AAAA-A--GACTTAATTACTTTTTTTGAAAAAA-TTTGA-GGACTTTTTG
1 AAAAGAGGGGCTTAATTATTTTTTTTGAAAAAAGTTTGAGGGACTTTTTG
13261867 CACTCTTAAT
Statistics
Matches: 115, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
85 9 0.08
86 12 0.10
87 11 0.10
89 1 0.01
91 73 0.63
92 9 0.08
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.37
Consensus pattern (90 bp):
AAAAGAGGGGCTTAATTATTTTTTTTGAAAAAAGTTTGAGGGACTTTTTGATACATTTTAAAAAT
TCAAGTACCAAAATGAGTGCAAAAA
Found at i:13263488 original size:24 final size:24
Alignment explanation
Indices: 13263460--13263507 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
13263450 TTTTTAAAAG
* *
13263460 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
13263484 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
13263508 GTTTGAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:13263522 original size:24 final size:24
Alignment explanation
Indices: 13263460--13263523 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
13263450 TTTTTAAAAG
* * *
13263460 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGAATTTATTAGCATAATAT
*
13263484 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGAATTTATTAGCATAATAT
*
13263508 GTTT-GAATTTGATTAG
1 ATTTAGAATTT-ATTAG
13263524 AATTAGATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 5 0.15
24 29 0.85
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (24 bp):
ATTTAGAATTTATTAGCATAATAT
Found at i:13267905 original size:24 final size:24
Alignment explanation
Indices: 13267878--13267929 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13267868 TTTATAGAAG
* *
13267878 ATTTAGTATTTATGAGTATAATAT
1 ATTTAATATTTATGAGCATAATAT
*
13267902 ATTTAATATTTATTAGCATAATAT
1 ATTTAATATTTATGAGCATAATAT
13267926 ATTT
1 ATTT
13267930 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAATATTTATGAGCATAATAT
Found at i:13269291 original size:19 final size:19
Alignment explanation
Indices: 13269269--13269308 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
13269259 CCTTAATTTA
13269269 TATATATGT-TTTTAACTTT
1 TATATAT-TATTTTAACTTT
13269288 TATATATTATTTTAACTTT
1 TATATATTATTTTAACTTT
13269307 TA
1 TA
13269309 AAATTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
TATATATTATTTTAACTTT
Found at i:13269322 original size:32 final size:31
Alignment explanation
Indices: 13269286--13269351 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
13269276 GTTTTTAACT
*
13269286 TTTATATATTATTTTAACTTT-TAAAATTTATA
1 TTTATATATT-TTATAACTTTATAAAATTT-TA
*
13269318 TTTATATATTTTATAATTTTATAAAATTTTA
1 TTTATATATTTTATAACTTTATAAAATTTTA
13269349 TTT
1 TTT
13269352 TTAAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTATATATTTTATAACTTTATAAAATTTTA
Found at i:13280015 original size:24 final size:23
Alignment explanation
Indices: 13279988--13280037 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
13279978 TAAAATGTTT
13279988 TAAATATTTAAATATAATTTAATA
1 TAAATATTT-AATATAATTTAATA
* *
13280012 TAAAATATTTTATATATTTTAATA
1 T-AAATATTTAATATAATTTAATA
13280036 TA
1 TA
13280038 GAAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 1 0.04
24 14 0.61
25 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAATATTTAATATAATTTAATA
Found at i:13280035 original size:17 final size:17
Alignment explanation
Indices: 13280015--13280060 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
13280005 TTTAATATAA
13280015 AATATTTTATATATTTT
1 AATATTTTATATATTTT
*** *
13280032 AATATAGAAAATATTTT
1 AATATTTTATATATTTT
13280049 AATATTTTATAT
1 AATATTTTATAT
13280061 TTAAATATTA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
AATATTTTATATATTTT
Found at i:13280042 original size:26 final size:24
Alignment explanation
Indices: 13279989--13280057 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
13279979 AAAATGTTTT
* *
13279989 AAATATTTAAATATAATTTAATATA
1 AAATATTT-TATATATTTTAATATA
13280014 AAATATTTTATATATTTTAATATAGA
1 AAATATTTTATATATTTTAATAT--A
13280040 AAATATTTTA-ATATTTTA
1 AAATATTTTATATATTTTA
13280058 TATTTAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 13 0.32
25 16 0.40
26 11 0.28
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
AAATATTTTATATATTTTAATATA
Found at i:13280060 original size:24 final size:24
Alignment explanation
Indices: 13279989--13280060 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 24
13279979 AAAATGTTTT
* *
13279989 AAATATTTAAATATAATTTA-ATATA
1 AAATATTTTAATAT--TTTATATAGA
13280014 AAATATTTTATATATTTTAATATAGA
1 AAATATTTTA-ATATTTT-ATATAGA
13280040 AAATATTTTAATATTTTATAT
1 AAATATTTTAATATTTTATAT
13280061 TTAAATATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 7 0.17
25 17 0.40
26 18 0.43
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (24 bp):
AAATATTTTAATATTTTATATAGA
Found at i:13291539 original size:122 final size:125
Alignment explanation
Indices: 13291387--13291631 Score: 370
Period size: 122 Copynumber: 2.0 Consensus size: 125
13291377 TTTCGTAGAA
** * *
13291387 AGTGAGGATAAAACTTTAATACATGAATAATACCTTCAATTGTTGACCGCTTAAGTTGGCTATTC
1 AGTGAGGATAAAACTCCAATACATGAATAATACCTTCAATTGTTGACAGCTTAAGTTGGATATTC
* *
13291452 AAAAAACAACACTTTGAAGATTTC-T-TACA-GAGTTGATTCTATTGTTAATAGTAGTAG
66 AAAAAACAACACTTTGAAGACTTCTTATACAGGAGTTGATCCTATTGTTAATAGTAGTAG
* *
13291509 AGTGAGGATAAAACTCCAATACATGAATAATATCTTCAATTGTTGACAGTTTAAGTTGGATATTC
1 AGTGAGGATAAAACTCCAATACATGAATAATACCTTCAATTGTTGACAGCTTAAGTTGGATATTC
* * *
13291574 AAAGAACGACACTTTGAAGACTTCTTATAGAGGAGTTGATCCTATTGTTAATAGTAGT
66 AAAAAACAACACTTTGAAGACTTCTTATACAGGAGTTGATCCTATTGTTAATAGTAGT
13291632 CATCAAAGTT
Statistics
Matches: 109, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
122 80 0.73
123 1 0.01
124 3 0.03
125 25 0.23
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (125 bp):
AGTGAGGATAAAACTCCAATACATGAATAATACCTTCAATTGTTGACAGCTTAAGTTGGATATTC
AAAAAACAACACTTTGAAGACTTCTTATACAGGAGTTGATCCTATTGTTAATAGTAGTAG
Found at i:13291739 original size:18 final size:17
Alignment explanation
Indices: 13291716--13291749 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13291706 GACTTGGATT
13291716 GAAAAAATAATTTAAATG
1 GAAAAAATAA-TTAAATG
*
13291734 GAAAAATTAATTAAAT
1 GAAAAAATAATTAAAT
13291750 TTATTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (17 bp):
GAAAAAATAATTAAATG
Found at i:13296126 original size:106 final size:106
Alignment explanation
Indices: 13295934--13296134 Score: 357
Period size: 106 Copynumber: 1.9 Consensus size: 106
13295924 AAAATTTTTC
*
13295934 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTTGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
13295999 TTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTT
66 TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
* *
13296040 TAAATAAGGCAATATTTGGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
13296105 TTCTCGTTCGACTAAACAGCCAAATATCCT
66 TTCTCGTTCGACCAAACAGCCAAATATCCT
13296135 CTTAAAGCTT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 90 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (106 bp):
TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
Found at i:13301840 original size:9 final size:8
Alignment explanation
Indices: 13301820--13301904 Score: 55
Period size: 9 Copynumber: 9.5 Consensus size: 8
13301810 GTAGTGATTC
13301820 AATTCGGTT
1 AATTCGG-T
13301829 AATTCAGGT
1 AATTC-GGT
*
13301838 AATTCGATT
1 AATTCG-GT
13301847 AATTCGGGT
1 AATTC-GGT
13301856 AA-TCTGGTT
1 AATTC-GG-T
*
13301865 AATTCAGTT
1 AATTC-GGT
13301874 AATTCGGGT
1 AATTC-GGT
13301883 AATTCGGTT
1 AATTCGG-T
13301892 AATTCGGTT
1 AATTCGG-T
13301901 AATT
1 AATT
13301905 TTTAACCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
8 7 0.11
9 50 0.79
10 6 0.10
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (8 bp):
AATTCGGT
Found at i:13301843 original size:18 final size:18
Alignment explanation
Indices: 13301820--13301904 Score: 102
Period size: 18 Copynumber: 4.7 Consensus size: 18
13301810 GTAGTGATTC
13301820 AATTCGGTTAATTCAGGT
1 AATTCGGTTAATTCAGGT
* *
13301838 AATTCGATTAATTCGGGT
1 AATTCGGTTAATTCAGGT
*
13301856 AA-TCTGGTTAATTCAGTT
1 AATTC-GGTTAATTCAGGT
*
13301874 AATTCGGGTAATTC-GGTT
1 AATTCGGTTAATTCAGG-T
13301892 AATTCGGTTAATT
1 AATTCGGTTAATT
13301905 TTTAACCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
17 3 0.05
18 51 0.91
19 2 0.04
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (18 bp):
AATTCGGTTAATTCAGGT
Found at i:13301852 original size:27 final size:27
Alignment explanation
Indices: 13301815--13301904 Score: 103
Period size: 27 Copynumber: 3.3 Consensus size: 27
13301805 ATTATGTAGT
* * *
13301815 GATTCAATTCGGTTAATTCAGGTAATTC
1 GATT-AATTCGGGTAATTCGGTTAATTC
13301843 GATTAATTCGGGTAA-TCTGGTTAATTC
1 GATTAATTCGGGTAATTC-GGTTAATTC
13301870 -AGTTAATTCGGGTAATTCGGTTAATTC
1 GA-TTAATTCGGGTAATTCGGTTAATTC
*
13301897 GGTTAATT
1 GATTAATT
13301905 TTTAACCAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.06
27 45 0.83
28 6 0.11
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (27 bp):
GATTAATTCGGGTAATTCGGTTAATTC
Found at i:13302052 original size:9 final size:9
Alignment explanation
Indices: 13302038--13302064 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
13302028 TTTTGAAAGG
13302038 TCGGTTAAT
1 TCGGTTAAT
13302047 TCGGTTAAT
1 TCGGTTAAT
13302056 TCGGTTAAT
1 TCGGTTAAT
13302065 GTTATTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (9 bp):
TCGGTTAAT
Found at i:13302398 original size:30 final size:30
Alignment explanation
Indices: 13302356--13302419 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
13302346 AACTTATTTT
13302356 ATTT-TTAATTTTGTTATTATTTTAAAGAC
1 ATTTGTTAATTTTGTTATTATTTTAAAGAC
* *
13302385 ATTTGTTAGTTTTGTTATTATTTTAGAGAC
1 ATTTGTTAATTTTGTTATTATTTTAAAGAC
13302415 ATTTG
1 ATTTG
13302420 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (30 bp):
ATTTGTTAATTTTGTTATTATTTTAAAGAC
Found at i:13302522 original size:18 final size:18
Alignment explanation
Indices: 13302501--13302540 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
13302491 GGAATATTTA
*
13302501 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
13302519 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
13302537 TTTT
1 TTTT
13302541 TAAAATTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:13307350 original size:6 final size:6
Alignment explanation
Indices: 13307312--13307343 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
13307302 ATTGATAATC
13307312 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
13307344 ACCTATATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTAT
Found at i:13309291 original size:49 final size:48
Alignment explanation
Indices: 13309238--13309466 Score: 228
Period size: 49 Copynumber: 4.7 Consensus size: 48
13309228 ATTATAACTC
* * ** * *
13309238 TGCTCCTAGACGCATGGGGAGAATTTACTAAAAGTAATAATAATGGCCT
1 TGCTCCCAAACGCATGGGGAG-GCTTACGAAAAGTAGTAATAATGGCCT
* *
13309287 TGCTCCCAAATGCATGGAGAGGCTTACGAAAAGTAGTAATAATGGCCCT
1 TGCTCCCAAACGCATGGGGAGGCTTACGAAAAGTAGTAATAATGG-CCT
* * * *
13309336 AG-TCCCAGATGCATTGAGGGAGGCTTACAAAAAGTAGTAATAATGGCCT
1 TGCTCCCAAACGCA-TG-GGGAGGCTTACGAAAAGTAGTAATAATGGCCT
** *
13309385 TGCTCTTAAACGCATGGGGGAGGCTTACGAAAAGTAGTAATAATGGCCC
1 TGCTCCCAAACGCAT-GGGGAGGCTTACGAAAAGTAGTAATAATGGCCT
* * *
13309434 TGCT-CCAAATGCATGGGGGAAGCTTACAAAAAG
1 TGCTCCCAAACGCAT-GGGGAGGCTTACGAAAAG
13309467 CAAAAAAATA
Statistics
Matches: 151, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
48 54 0.36
49 62 0.41
50 35 0.23
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.23
Consensus pattern (48 bp):
TGCTCCCAAACGCATGGGGAGGCTTACGAAAAGTAGTAATAATGGCCT
Found at i:13309327 original size:48 final size:48
Alignment explanation
Indices: 13309262--13309466 Score: 243
Period size: 48 Copynumber: 4.2 Consensus size: 48
13309252 TGGGGAGAAT
* * *
13309262 TTACTAAAAGTAATAATAATGGCCTTGCTCCCAAATGCATGGAGAGGC
1 TTACGAAAAGTAGTAATAATGGCCTTGCTCCCAAATGCATGGGGAGGC
* *
13309310 TTACGAAAAGTAGTAATAATGGCCCTAG-TCCCAGATGCATTGAGGGAGGC
1 TTACGAAAAGTAGTAATAATGG-CCTTGCTCCCAAATGCA-TG-GGGAGGC
* ** *
13309360 TTACAAAAAGTAGTAATAATGGCCTTGCTCTTAAACGCATGGGGGAGGC
1 TTACGAAAAGTAGTAATAATGGCCTTGCTCCCAAATGCAT-GGGGAGGC
* *
13309409 TTACGAAAAGTAGTAATAATGGCCCTGCT-CCAAATGCATGGGGGAAGC
1 TTACGAAAAGTAGTAATAATGGCCTTGCTCCCAAATGCAT-GGGGAGGC
*
13309457 TTACAAAAAG
1 TTACGAAAAG
13309467 CAAAAAAATA
Statistics
Matches: 134, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
48 54 0.40
49 45 0.34
50 35 0.26
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (48 bp):
TTACGAAAAGTAGTAATAATGGCCTTGCTCCCAAATGCATGGGGAGGC
Found at i:13309377 original size:98 final size:97
Alignment explanation
Indices: 13309262--13309466 Score: 288
Period size: 98 Copynumber: 2.1 Consensus size: 97
13309252 TGGGGAGAAT
* *
13309262 TTACTAAAAGTAATAATAATGGCCTTGCTCCCAAATGCAT-GGAGAGGCTTACGAAAAGTAGTAA
1 TTACAAAAAGTAATAATAATGGCCTTGCTCCCAAACGCATGGGAGAGGCTTACGAAAAGTAGTAA
* *
13309326 TAATGGCCCTAG-TCCCAGATGCATTGAGGGAGGC
66 TAATGGCCCT-GCT-CCAAATGCA-TGAGGGAAGC
* ** *
13309360 TTACAAAAAGTAGTAATAATGGCCTTGCTCTTAAACGCATGGGGGAGGCTTACGAAAAGTAGTAA
1 TTACAAAAAGTAATAATAATGGCCTTGCTCCCAAACGCATGGGAGAGGCTTACGAAAAGTAGTAA
*
13309425 TAATGGCCCTGCTCCAAATGCATGGGGGAAGC
66 TAATGGCCCTGCTCCAAATGCATGAGGGAAGC
13309457 TTACAAAAAG
1 TTACAAAAAG
13309467 CAAAAAAATA
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
97 18 0.19
98 44 0.46
99 34 0.35
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (97 bp):
TTACAAAAAGTAATAATAATGGCCTTGCTCCCAAACGCATGGGAGAGGCTTACGAAAAGTAGTAA
TAATGGCCCTGCTCCAAATGCATGAGGGAAGC
Found at i:13316938 original size:20 final size:19
Alignment explanation
Indices: 13316913--13316962 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
13316903 GAATTGTTAG
13316913 AAATCAAAGCAT-TTAACTTC
1 AAATCAAAG-ATATTAAC-TC
*
13316933 AAATCAGAGATATTAACTC
1 AAATCAAAGATATTAACTC
*
13316952 AAATCATAGAT
1 AAATCAAAGAT
13316963 TCATGTCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (19 bp):
AAATCAAAGATATTAACTC
Found at i:13316955 original size:19 final size:20
Alignment explanation
Indices: 13316925--13316962 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
13316915 ATCAAAGCAT
13316925 TTAACTTCAAATCAGAGATA
1 TTAACTTCAAATCAGAGATA
*
13316945 TTAAC-TCAAATCATAGAT
1 TTAACTTCAAATCAGAGAT
13316963 TCATGTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (20 bp):
TTAACTTCAAATCAGAGATA
Found at i:13318488 original size:13 final size:13
Alignment explanation
Indices: 13318470--13318496 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13318460 AGTTCTTCAT
13318470 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
13318483 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
13318496 T
1 T
13318497 TTAGTTTAAA
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:13341130 original size:140 final size:140
Alignment explanation
Indices: 13340876--13341159 Score: 550
Period size: 140 Copynumber: 2.0 Consensus size: 140
13340866 ACCCGTATTC
*
13340876 AACACCAGAATAGGGTACGAGGCATTACCAGAACAAATAAACTGTAAACGTATTGAACCGAGTTA
1 AACACCAGAATAGGGTACGAGGCATTACCAGAACAAATAAACTGTAAACGTATTGAACCAAGTTA
13340941 TAAAATTTCATTAAAAAAATTAAAACTTTCAAATTATTAACATGCTTTTATAATTCTTCACAATA
66 TAAAATTTCATTAAAAAAATTAAAACTTTCAAATTATTAACATGCTTTTATAATTCTTCACAATA
13341006 TATATAATGT
131 TATATAATGT
13341016 AACACCAGAATAGGGTACGAGGCATTACCAGAACAAATAAACTGTAAACGTATTGAACCAAGTTA
1 AACACCAGAATAGGGTACGAGGCATTACCAGAACAAATAAACTGTAAACGTATTGAACCAAGTTA
*
13341081 TAAAATTTCATTAAAAAAATTAAAACTTTCAAATTATTAACATGTTTTTATAATTCTTCACAATA
66 TAAAATTTCATTAAAAAAATTAAAACTTTCAAATTATTAACATGCTTTTATAATTCTTCACAATA
13341146 TATATAATGT
131 TATATAATGT
13341156 AACA
1 AACA
13341160 TTTCCTGTCA
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (140 bp):
AACACCAGAATAGGGTACGAGGCATTACCAGAACAAATAAACTGTAAACGTATTGAACCAAGTTA
TAAAATTTCATTAAAAAAATTAAAACTTTCAAATTATTAACATGCTTTTATAATTCTTCACAATA
TATATAATGT
Found at i:13341402 original size:46 final size:46
Alignment explanation
Indices: 13341349--13341530 Score: 258
Period size: 46 Copynumber: 4.0 Consensus size: 46
13341339 TTGCTATAAT
** * *
13341349 TCAGTATGGTTTTCTTCACAAAAATATCATACCTACTTTTCATAAC
1 TCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAAC
*
13341395 TCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAAC
1 TCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAAC
* * * *
13341441 TCAATATGGTTTTCTTTA-TCGAAATATCATATCTACTTTTCACAAC
1 TCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCACAAC
*
13341487 TCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCACA
1 TCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACA
13341531 CTTTGCCATA
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
45 1 0.01
46 117 0.98
47 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (46 bp):
TCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAAC
Found at i:13341510 original size:92 final size:92
Alignment explanation
Indices: 13341353--13341530 Score: 286
Period size: 92 Copynumber: 1.9 Consensus size: 92
13341343 TATAATTCAG
*
13341353 TATGGTTTTCTTCACAAAAATATCATACCTACTTTTCATAACTCAGTATGGTTTTCTTCACTGAA
1 TATGGTTTTCTTCACAAAAATATCATACCTACTTTTCACAACTCAGTATGGTTTTCTTCACTGAA
*
13341418 ACACCATACCTACTTTTCACAACTCAA
66 ACACCATACCTACGTTTCACAACTCAA
* * *
13341445 TATGGTTTTCTTTATC-GAAATATCATATCTACTTTTCACAACTCAGTATGGTTTTCTTCACTGA
1 TATGGTTTTCTTCA-CAAAAATATCATACCTACTTTTCACAACTCAGTATGGTTTTCTTCACTGA
*
13341509 AATACCATACCTACGTTTCACA
65 AACACCATACCTACGTTTCACA
13341531 CTTTGCCATA
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 78 0.99
93 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.39
Consensus pattern (92 bp):
TATGGTTTTCTTCACAAAAATATCATACCTACTTTTCACAACTCAGTATGGTTTTCTTCACTGAA
ACACCATACCTACGTTTCACAACTCAA
Found at i:13349381 original size:39 final size:39
Alignment explanation
Indices: 13349323--13349403 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
13349313 ATCCACGGAT
* * *
13349323 TAAGTGTCTAAGGTTGAAAGTA-TCGGTTCAAGGACCCAG
1 TAAGTGTATAAGGTGGAAAGTACT-GCTTCAAGGACCCAG
*
13349362 TAAGTGTATAAGGTGGAAAGTACTGCTTCAAGGACCTAG
1 TAAGTGTATAAGGTGGAAAGTACTGCTTCAAGGACCCAG
13349401 TAA
1 TAA
13349404 ATCAATCTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 36 0.97
40 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (39 bp):
TAAGTGTATAAGGTGGAAAGTACTGCTTCAAGGACCCAG
Found at i:13363638 original size:18 final size:17
Alignment explanation
Indices: 13363604--13363638 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
13363594 CTATATAATC
*
13363604 AAATACCATACATATAT
1 AAATACCATAAATATAT
13363621 AAATACCATGAAATATAT
1 AAATACCAT-AAATATAT
13363639 TTTCATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATACCATAAATATAT
Found at i:13364300 original size:42 final size:42
Alignment explanation
Indices: 13364193--13364349 Score: 136
Period size: 43 Copynumber: 3.7 Consensus size: 42
13364183 CTCGTACAAT
* * * * * * *
13364193 GCCAACGTCCTAGACGTGGTCTTACATGTAATCAAACAACAAT
1 GCCAATGTCCCAGACATGGTCTTACACGTAATCATA-AACGAC
* * *
13364236 GCCACTGTCCCAGACAGGGTCTTACACGTAATCATATACGAC
1 GCCAATGTCCCAGACATGGTCTTACACGTAATCATAAACGAC
* * *
13364278 GCCAATGTCCCAGATATGGTCTTACACGAAAATC-TCAAATCGAG
1 GCCAATGTCCCAGACATGGTCTTACACG-TAATCAT-AAA-CGAC
* *
13364322 GCCAACGTCCCAGACGTGGTCTTACACG
1 GCCAATGTCCCAGACATGGTCTTACACG
13364350 ATGTCACATT
Statistics
Matches: 92, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
42 29 0.32
43 35 0.38
44 28 0.30
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (42 bp):
GCCAATGTCCCAGACATGGTCTTACACGTAATCATAAACGAC
Found at i:13366371 original size:15 final size:15
Alignment explanation
Indices: 13366351--13366381 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13366341 CCCCGATAAT
13366351 CATAAGGATGTACGC
1 CATAAGGATGTACGC
13366366 CATAAGGATGTACGC
1 CATAAGGATGTACGC
13366381 C
1 C
13366382 CAAGCGTGTT
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:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (15 bp):
CATAAGGATGTACGC
Found at i:13368706 original size:21 final size:23
Alignment explanation
Indices: 13368683--13368726 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13368673 TTTTTAATTT
**
13368683 AAAT-TTAATTATGAAATATATA
1 AAATGTTAATTAAAAAATATATA
13368705 AAATGTTAATTAAAAAATATAT
1 AAATGTTAATTAAAAAATATAT
13368727 TGAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (23 bp):
AAATGTTAATTAAAAAATATATA
Found at i:13369539 original size:22 final size:22
Alignment explanation
Indices: 13369505--13369546 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
13369495 TGTACAAGTA
* *
13369505 ATATTACTTGAATAGTTATGAG
1 ATATTACTAGAATAATTATGAG
*
13369527 ATATTAGTAGAATAATTATG
1 ATATTACTAGAATAATTATG
13369547 TCTCTTTTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.40
Consensus pattern (22 bp):
ATATTACTAGAATAATTATGAG
Found at i:13373153 original size:30 final size:31
Alignment explanation
Indices: 13373108--13373167 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
13373098 GGAGGTGGGA
13373108 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
* * *
13373139 TGGG-AGGGAGTAAAATTTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAGTTTTAGGGGAAAA
13373168 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:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
Found at i:13373395 original size:9 final size:9
Alignment explanation
Indices: 13373381--13373417 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
13373371 TGTAGTTTGA
13373381 TATTCGAAT
1 TATTCGAAT
13373390 TATTCGAAT
1 TATTCGAAT
*
13373399 TATTCGAGT
1 TATTCGAAT
13373408 TATTCGAAT
1 TATTCGAAT
13373417 T
1 T
13373418 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:13374315 original size:21 final size:21
Alignment explanation
Indices: 13374264--13374316 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
13374254 GTGCTAAACA
** *
13374264 GAAACCCATAAGGGTTGAATG
1 GAAACCCATAACAGCTGAATG
* * *
13374285 GAAGCTCATAACAGCTGATTG
1 GAAACCCATAACAGCTGAATG
13374306 GAAACCCATAA
1 GAAACCCATAA
13374317 GGGTTAAACA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
GAAACCCATAACAGCTGAATG
Found at i:13374486 original size:25 final size:25
Alignment explanation
Indices: 13374428--13374518 Score: 112
Period size: 25 Copynumber: 3.7 Consensus size: 25
13374418 TATATTTATC
* * *
13374428 GTCAATTCATCCTTTGCA-TATACT
1 GTCAATTCATCATTTGCATTTTACA
*
13374452 GTCAATTCATCATTTTCATTTTACA
1 GTCAATTCATCATTTGCATTTTACA
* *
13374477 GTCAATTCATCCTTTGCATTTTACC
1 GTCAATTCATCATTTGCATTTTACA
*
13374502 GTTAATTCATCATTTGC
1 GTCAATTCATCATTTGC
13374519 CAAAAAATAA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
24 16 0.28
25 41 0.72
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.45
Consensus pattern (25 bp):
GTCAATTCATCATTTGCATTTTACA
Found at i:13388037 original size:30 final size:31
Alignment explanation
Indices: 13387996--13388081 Score: 111
Period size: 30 Copynumber: 2.8 Consensus size: 31
13387986 CTCAATATTT
13387996 AATTAATTTTTAAATTTTAAAAA-ATTATAG
1 AATTAATTTTTAAATTTTAAAAATATTATAG
* ** *
13388026 AATTTATTTTTAAAAATTAAAAATATTATAT
1 AATTAATTTTTAAATTTTAAAAATATTATAG
*
13388057 ATAATAATTTTTAAATTTTAAAAAT
1 A-ATTAATTTTTAAATTTTAAAAAT
13388082 TAATTAAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 20 0.43
31 7 0.15
32 19 0.41
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (31 bp):
AATTAATTTTTAAATTTTAAAAATATTATAG
Found at i:13388054 original size:22 final size:22
Alignment explanation
Indices: 13388009--13388054 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13387999 TAATTTTTAA
*
13388009 ATTTTAAAAAATTATAGAATTT
1 ATTTTAAAAAATTATAAAATTT
*
13388031 ATTTTTAAAAATTA-AAAATATT
1 ATTTTAAAAAATTATAAAAT-TT
13388053 AT
1 AT
13388055 ATATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTTAAAAAATTATAAAATTT
Found at i:13392331 original size:37 final size:37
Alignment explanation
Indices: 13392274--13392425 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
13392264 TATGATCACT
*
13392274 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
13392309 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
13392346 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
13392391 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
13392426 GAAGCTATCA
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.54
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:13392409 original size:46 final size:46
Alignment explanation
Indices: 13392342--13392610 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
13392332 TAAGTGTAGC
* **
13392342 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
13392388 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
13392434 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
13392486 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
13392532 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
13392584 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
13392611 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:13392461 original size:52 final size:52
Alignment explanation
Indices: 13392385--13392604 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
13392375 TAGCTAAAGC
* *
13392385 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
13392438 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
13392490 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
13392536 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
13392588 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
13392605 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:13392507 original size:98 final size:98
Alignment explanation
Indices: 13392342--13392610 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
13392332 TAAGTGTAGC
* * *
13392342 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
13392407 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
13392441 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
13392506 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
13392539 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
13392604 GATCAGA
66 GATCAGA
13392611 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:13407110 original size:21 final size:20
Alignment explanation
Indices: 13407080--13407119 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13407070 GTAGAATATG
*
13407080 TGTACCGAAGAATTCTGAACT
1 TGTACAGAAG-ATTCTGAACT
*
13407101 TGTACAGAAGATTTTGAAC
1 TGTACAGAAGATTCTGAAC
13407120 GAAGCTCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (20 bp):
TGTACAGAAGATTCTGAACT
Found at i:13409439 original size:25 final size:25
Alignment explanation
Indices: 13409379--13409483 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 25
13409369 TCTTTGATAT
* * * *
13409379 TGGCTCGCATGAGCTTCCTG-AATA
1 TGGCTCACATGAGCTTCCCGTTACA
**
13409403 TGGCTCTTATGAGCTTCCCGTTACA
1 TGGCTCACATGAGCTTCCCGTTACA
* *
13409428 TGGCTCACATGAGATTCCCATTACA
1 TGGCTCACATGAGCTTCCCGTTACA
* * *
13409453 TGACTCACATAAGCTTCCCGTTATA
1 TGGCTCACATGAGCTTCCCGTTACA
13409478 TGGCTC
1 TGGCTC
13409484 GAGAGAGTGC
Statistics
Matches: 65, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
24 17 0.26
25 48 0.74
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCCGTTACA
Found at i:13417334 original size:27 final size:26
Alignment explanation
Indices: 13417292--13417502 Score: 223
Period size: 27 Copynumber: 7.8 Consensus size: 26
13417282 TACGATTCAT
13417292 GGTAAAATGACTGAAATACCCTCGAAG
1 GGTAAAATGAC-GAAATACCCTCGAAG
13417319 GGTAAAATGATCGAAATACCCTCGAAG
1 GGTAAAATGA-CGAAATACCCTCGAAG
13417346 GGTAAAATGACTGAAATACCCTCGAAG
1 GGTAAAATGAC-GAAATACCCTCGAAG
* *
13417373 GATAAAATGACCGGAATA-CCTCCGAAG
1 GGTAAAATGA-CGAAATACCCT-CGAAG
* *
13417400 GGTAAAATGATCGAAATACCCTTGAAA
1 GGTAAAATGA-CGAAATACCCTCGAAG
*
13417427 GGTAAAATGACCGAAATACCC-CCAGAG
1 GGTAAAATGA-CGAAATACCCTCGA-AG
* *
13417454 GGTAAAAAGATC-AGAATATCCC-CAAAG
1 GGTAAAATGA-CGA-AATA-CCCTCGAAG
13417481 GGTAAAATGACTGAAATACCCT
1 GGTAAAATGAC-GAAATACCCT
13417503 TATAAAGTAA
Statistics
Matches: 158, Mismatches: 15, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.06
27 137 0.87
28 11 0.07
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (26 bp):
GGTAAAATGACGAAATACCCTCGAAG
Found at i:13417355 original size:54 final size:53
Alignment explanation
Indices: 13417292--13417502 Score: 248
Period size: 54 Copynumber: 3.9 Consensus size: 53
13417282 TACGATTCAT
*
13417292 GGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAG
1 GGTAAAATGA-TGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAG
* *
13417346 GGTAAAATGACTGAAATACCCTCGAAGGATAAAATGACCGGAATA-CCTCCGAAG
1 GGTAAAATGA-TGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCT-CGAAG
* * *
13417400 GGTAAAATGATCGAAATACCCTTGAAAGGTAAAATGACCGAAATACCC-CCAGAG
1 GGTAAAATGAT-GAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGA-AG
* * * *
13417454 GGTAAAAAGATCAGAATATCCC-CAAAGGGTAAAATGACTGAAATACCCT
1 GGTAAAATGATGA-AATA-CCCTCGAAGGGTAAAATGACCGAAATACCCT
13417503 TATAAAGTAA
Statistics
Matches: 136, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
53 7 0.05
54 124 0.91
55 5 0.04
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (53 bp):
GGTAAAATGATGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAG
Found at i:13417399 original size:81 final size:80
Alignment explanation
Indices: 13417294--13417502 Score: 260
Period size: 81 Copynumber: 2.6 Consensus size: 80
13417284 CGATTCATGG
* * * *
13417294 TAAAATGACTGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGACTG
1 TAAAATGACCGGAATACCC-CGAAGGGTAAAATGATCGAAATACCCTCGAAAGGTAAAATGACCG
*
13417359 AAATACCCTC-GAAGGA
65 AAATACCCCCAG-AGGA
*
13417375 TAAAATGACCGGAATACCTCCGAAGGGTAAAATGATCGAAATACCCTTGAAAGGTAAAATGACCG
1 TAAAATGACCGGAATACC-CCGAAGGGTAAAATGATCGAAATACCCTCGAAAGGTAAAATGACCG
*
13417440 AAATACCCCCAGAGGG
65 AAATACCCCCAGAGGA
* * * *
13417456 TAAAAAGATCAGAATATCCCCAAAGGGTAAAATGA-CTGAAATACCCT
1 TAAAATGACCGGAATA-CCCCGAAGGGTAAAATGATC-GAAATACCCT
13417503 TATAAAGTAA
Statistics
Matches: 113, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
80 1 0.01
81 108 0.96
82 4 0.04
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (80 bp):
TAAAATGACCGGAATACCCCGAAGGGTAAAATGATCGAAATACCCTCGAAAGGTAAAATGACCGA
AATACCCCCAGAGGA
Found at i:13423700 original size:38 final size:39
Alignment explanation
Indices: 13423648--13423723 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 39
13423638 TATGTTAAAT
* *
13423648 ATAACCCAAGAATCTGCAAC-AAGGCTAGATCTCATTAA
1 ATAACCCAAAAATCTACAACAAAGGCTAGATCTCATTAA
* *
13423686 ATAACCCAAAAATCTATAACAAATGCTAGATCTCATTA
1 ATAACCCAAAAATCTACAACAAAGGCTAGATCTCATTA
13423724 TAACCTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 17 0.52
39 16 0.48
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.24
Consensus pattern (39 bp):
ATAACCCAAAAATCTACAACAAAGGCTAGATCTCATTAA
Found at i:13424622 original size:46 final size:45
Alignment explanation
Indices: 13424534--13424625 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 45
13424524 AGTTGAGCAG
* * * * *
13424534 TTTATCTGCACTGTTGAGTGGTTTATCCACATCGTTTGAGCAACT
1 TTTATCTACACTGTTGAGTGGCTTAACCACACCATTTGAGCAACT
13424579 TTTATCTACACTGTTTGAGTGGCTTAACCACACCATATT-AGCAACT
1 TTTATCTACACTG-TTGAGTGGCTTAACCACACCAT-TTGAGCAACT
13424625 T
1 T
13424626 CAATATGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
45 12 0.30
46 26 0.65
47 2 0.05
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (45 bp):
TTTATCTACACTGTTGAGTGGCTTAACCACACCATTTGAGCAACT
Found at i:13425431 original size:26 final size:27
Alignment explanation
Indices: 13425392--13425442 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
13425382 AAGAAAAAAA
13425392 TTTAAAAATTAAAAATTA-AAAATATTT
1 TTTAAAAATT-AAAATTATAAAATATTT
13425419 TTTAAAAA-TAAAATTATAAAATAT
1 TTTAAAAATTAAAATTATAAAATAT
13425443 ATAAGTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.30
26 8 0.35
27 8 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TTTAAAAATTAAAATTATAAAATATTT
Found at i:13425521 original size:17 final size:16
Alignment explanation
Indices: 13425478--13425532 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
13425468 TTAATATATG
13425478 AAATTTAAAAAAATTAT
1 AAATTTAAAAAAATT-T
*
13425495 AAATATTTAAATAATATTT
1 -AA-ATTTAAA-AAAATTT
13425514 AAATTTAAAAAAATTT
1 AAATTTAAAAAAATTT
13425530 AAA
1 AAA
13425533 AACATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 9 0.27
17 7 0.21
18 4 0.12
19 8 0.24
20 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTTAAAAAAATTT
Found at i:13429981 original size:16 final size:16
Alignment explanation
Indices: 13429960--13429990 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13429950 CACTAGAATT
13429960 GAATAGAGTTGTAATG
1 GAATAGAGTTGTAATG
13429976 GAATAGAGTTGTAAT
1 GAATAGAGTTGTAAT
13429991 TAGTAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (16 bp):
GAATAGAGTTGTAATG
Found at i:13430352 original size:18 final size:18
Alignment explanation
Indices: 13430322--13430361 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
13430312 ATTAATATAT
13430322 ATTAATATTTTATATTAA
1 ATTAATATTTTATATTAA
*
13430340 ATTAATATTTTATCTTAA
1 ATTAATATTTTATATTAA
13430358 ATTA
1 ATTA
13430362 TTTAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTAATATTTTATATTAA
Found at i:13431801 original size:345 final size:343
Alignment explanation
Indices: 13431173--13431855 Score: 1093
Period size: 345 Copynumber: 2.0 Consensus size: 343
13431163 AGTCAGTGCA
* * * *
13431173 AAAGACATTTTTGTAAATATGATGCAGAGTGAATTTAAGATAAGTATGATGGGTGAATTGTCATA
1 AAAGACATTTTTGTAAATATGATGCAGAGCGAATTCAAGATAAATATGATGGGTGAACTGTCATA
*
13431238 CTTTCTTGGGTTTTAGATTAAGGAGATCGGATATGGTACTTTTCTCTTGTAGAAGTATGTGAAGA
66 CTTTCTTGGGTTTTAGATTAAGGAGATCGGATATGGTACTTTTCTCTTGAAGAAGTATGTGAAGA
* * * *
13431303 ACTTAATAAAGAAGTTTGGTACGGAGAGTTGTAAGCCTACCAGGACTCCTTTGTTTATAAGTGAA
131 ACTTAATAAAGAAGTTTAGTACGGAGAATTGTAAGCCTACCAGGACTCCTTTATCTATAAGTGAA
*
13431368 AAAATAAGTGCAGATGCAACGAAAGCCCCACTTTCGATACCACTTATAGAAGCATACTTGAAAGT
196 AAAATAAGCGCAGATGCAACGAAAGCCCCACTTTCGATACCACTTATAGAAGCATACTTGAAAGT
13431433 CTGTTATATCTCGTTACAAGCCTGTTGGGATCTAGTGCCCTTAGTATAGTTTTCCTTCATATGTA
261 CTGTTATATCTCGTTACAAGCCTGTTGGGATCTAGTGCCCTTAGTATAGTTTTCCTTCATATGTA
*
13431498 TTTGTAA-TTTTTCTGCG
326 CTTGTAAGTTTTTCTGCG
*
13431515 AAAGACATTTTTGTAAATATGATGCAGAGCGAATTCAAGATAAATATGATGGGTGAACTGTTATA
1 AAAGACATTTTTGTAAATATGATGCAGAGCGAATTCAAGATAAATATGATGGGTGAACTGTCATA
*
13431580 CTTTCTTGGGTTTTAGATTAAGGAGATGGGATATGGTACTTTTCTCTTGCAGAAGAAGTATGTGA
66 CTTTCTTGGGTTTTAGATTAAGGAGATCGGATATGGTACTTTTCTCTT---GAAGAAGTATGTGA
* * **
13431645 GGAACTTAATAAAGAAGTTTAGTATGGAGAATTGTAAGTTTACCAGGACT-CTCTTATCTATAAG
128 AGAACTTAATAAAGAAGTTTAGTACGGAGAATTGTAAGCCTACCAGGACTCCT-TTATCTATAAG
* * * *
13431709 T-AAGAAAATAAGCGTAGATGCAACGAGAGCCCCACTTTCGATATCACTTATAGAAGTATACTTG
192 TGAA-AAAATAAGCGCAGATGCAACGAAAGCCCCACTTTCGATACCACTTATAGAAGCATACTTG
* *
13431773 GAAGTTTGTTATATCTCGTTACAAGCCTGTTGGGATCTAGTGCCCTTAGTATAGTTTTCCTTCAT
256 AAAGTCTGTTATATCTCGTTACAAGCCTGTTGGGATCTAGTGCCCTTAGTATAGTTTTCCTTCAT
13431838 ATGTACTTGTAAGTTTTT
321 ATGTACTTGTAAGTTTTT
13431856 TGAAAAGATT
Statistics
Matches: 312, Mismatches: 23, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
342 107 0.34
344 4 0.01
345 196 0.63
346 5 0.02
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (343 bp):
AAAGACATTTTTGTAAATATGATGCAGAGCGAATTCAAGATAAATATGATGGGTGAACTGTCATA
CTTTCTTGGGTTTTAGATTAAGGAGATCGGATATGGTACTTTTCTCTTGAAGAAGTATGTGAAGA
ACTTAATAAAGAAGTTTAGTACGGAGAATTGTAAGCCTACCAGGACTCCTTTATCTATAAGTGAA
AAAATAAGCGCAGATGCAACGAAAGCCCCACTTTCGATACCACTTATAGAAGCATACTTGAAAGT
CTGTTATATCTCGTTACAAGCCTGTTGGGATCTAGTGCCCTTAGTATAGTTTTCCTTCATATGTA
CTTGTAAGTTTTTCTGCG
Found at i:13434084 original size:25 final size:24
Alignment explanation
Indices: 13434045--13434092 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
13434035 GTTCAAGTGT
*
13434045 TTTATATGTAGTTTACAATTTTTAA
1 TTTATATATAGTTTA-AATTTTTAA
* *
13434070 TTTATATATATTTTAGATTTTTA
1 TTTATATATAGTTTAAATTTTTA
13434093 TATATTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTATATATAGTTTAAATTTTTAA
Found at i:13434089 original size:17 final size:16
Alignment explanation
Indices: 13434064--13434099 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
13434054 AGTTTACAAT
13434064 TTTTAATTTATATATA
1 TTTTAATTTATATATA
*
13434080 TTTTAGATTTTTATATA
1 TTTTA-ATTTATATATA
13434097 TTT
1 TTT
13434100 GTTTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTTAATTTATATATA
Found at i:13447810 original size:14 final size:13
Alignment explanation
Indices: 13447791--13447820 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
13447781 AGGCTCACAA
13447791 AAAATAATAAAATC
1 AAAATAATAAAA-C
13447805 AAAATAATAAAAC
1 AAAATAATAAAAC
13447818 AAA
1 AAA
13447821 GTCTAAGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATAATAAAAC
Found at i:13447950 original size:21 final size:20
Alignment explanation
Indices: 13447925--13447981 Score: 98
Period size: 21 Copynumber: 2.9 Consensus size: 20
13447915 TAATCTTCAA
13447925 GTATATGCAATCTTAGATAT
1 GTATATGCAATCTTAGATAT
13447945 GATATATGCAATCTTAGATAT
1 G-TATATGCAATCTTAGATAT
13447966 G-ATATGCAATCTTAGA
1 GTATATGCAATCTTAGA
13447982 AGATATGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.42
20 1 0.03
21 20 0.56
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
GTATATGCAATCTTAGATAT
Found at i:13448251 original size:23 final size:23
Alignment explanation
Indices: 13448207--13448251 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
13448197 TCTTATTTTG
* *
13448207 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
13448230 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
13448252 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:13448449 original size:23 final size:23
Alignment explanation
Indices: 13448401--13448450 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
13448391 CCTCTATTTG
** *
13448401 TTATTTTTTTATTATTAAATTAA
1 TTATTTTAATATTATTAAACTAA
13448424 TTATTTTAATATTATTAATACT-A
1 TTATTTTAATATTATTAA-ACTAA
13448447 TTAT
1 TTAT
13448451 GTGGCATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTTTAATATTATTAAACTAA
Found at i:13448754 original size:23 final size:22
Alignment explanation
Indices: 13448724--13448767 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
13448714 ATAATTCACA
13448724 TACATATATATATTTCTTATATG
1 TACATATATATATTT-TTATATG
13448747 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
13448768 TTTATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:13448954 original size:3 final size:3
Alignment explanation
Indices: 13448946--13448985 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
13448936 ATCTTTTCAC
13448946 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13448986 CTTGTTCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13450616 original size:21 final size:21
Alignment explanation
Indices: 13450592--13450632 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
13450582 GAAAAAAAAG
13450592 TGTACAAGCTTAAAA-AGGCTT
1 TGTA-AAGCTTAAAACAGGCTT
*
13450613 TGTATAGCTTAAAACAGGCT
1 TGTAAAGCTTAAAACAGGCT
13450633 CCAAAGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (21 bp):
TGTAAAGCTTAAAACAGGCTT
Found at i:13452478 original size:22 final size:22
Alignment explanation
Indices: 13452438--13452479 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13452428 TTAGTTCTTG
13452438 TTTTTTTTTCTGTTCTTCCTTC
1 TTTTTTTTTCTGTTCTTCCTTC
*
13452460 TTTTATTTTTCT-TTTTTCCT
1 TTTT-TTTTTCTGTTCTTCCT
13452480 GCAATCGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTTTTTTCTGTTCTTCCTTC
Found at i:13462324 original size:25 final size:25
Alignment explanation
Indices: 13462278--13462406 Score: 70
Period size: 25 Copynumber: 5.2 Consensus size: 25
13462268 AAGCTCTTTC
* * * *
13462278 GAGCCATATAACGGGAATCTCATGT
1 GAGCCATGTAACGAGAAGCTCATGA
* *
13462303 GAGCCATGTAACAAGAAGCTCATAA
1 GAGCCATGTAACGAGAAGCTCATGA
*
13462328 GAGCC--GTAATCGAGAAGCTCATGC
1 GAGCCATGTAA-CGAGAAGCTCATGA
* * * **
13462352 GATCCA-ATATCG-GAAAGCTCCGGA
1 GAGCCATGTAACGAG-AAGCTCATGA
* *
13462376 GAGCCAT-TAATCGGGAAGCTCATGT
1 GAGCCATGTAA-CGAGAAGCTCATGA
13462401 GAGCCA
1 GAGCCA
13462407 ATTATCGGGA
Statistics
Matches: 78, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
23 5 0.06
24 31 0.40
25 41 0.53
26 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATGTAACGAGAAGCTCATGA
Found at i:13462413 original size:25 final size:25
Alignment explanation
Indices: 13462317--13462441 Score: 94
Period size: 25 Copynumber: 5.1 Consensus size: 25
13462307 CATGTAACAA
* * * *
13462317 GAAGCTCATAAGAGCC-GTAATCGA
1 GAAGCTCATGAGAGCCAATTATCGG
* *
13462341 GAAGCTCATGCGATCCAA-TATCGG
1 GAAGCTCATGAGAGCCAATTATCGG
* **
13462365 AAAGCTCCGGAGAGCC-ATTAATCGG
1 GAAGCTCATGAGAGCCAATT-ATCGG
*
13462390 GAAGCTCATGTGAGCCAATTATCGG
1 GAAGCTCATGAGAGCCAATTATCGG
* * * *
13462415 GAAGCTCGTGAAAGCTAAATATCGG
1 GAAGCTCATGAGAGCCAATTATCGG
13462440 GA
1 GA
13462442 CACTCATAAG
Statistics
Matches: 77, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
23 1 0.01
24 29 0.38
25 44 0.57
26 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (25 bp):
GAAGCTCATGAGAGCCAATTATCGG
Found at i:13470816 original size:3 final size:3
Alignment explanation
Indices: 13470810--13470841 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
13470800 AAGTTTTTTT
13470810 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
13470842 TGTACAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:13471152 original size:5 final size:5
Alignment explanation
Indices: 13471144--13471176 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
13471134 TATTATTGTA
13471144 AAAAG AAAAG AAAAG AAAAG AAAATG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAA-G AAAAG AAA
13471177 GAATAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 24 0.92
6 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:13476056 original size:15 final size:16
Alignment explanation
Indices: 13476024--13476056 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13476014 GAGTTGCGTT
13476024 AACGGTTAGATGAGCA
1 AACGGTTAGATGAGCA
*
13476040 AACGGTTATAT-AGCA
1 AACGGTTAGATGAGCA
13476055 AA
1 AA
13476057 GCAGGGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.21
Consensus pattern (16 bp):
AACGGTTAGATGAGCA
Found at i:13476474 original size:3 final size:3
Alignment explanation
Indices: 13476466--13476492 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
13476456 TTTCACAGAC
13476466 GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG
13476493 AAGAAGAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:13489365 original size:2 final size:2
Alignment explanation
Indices: 13489358--13489382 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13489348 GAGGGATTTT
13489358 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13489383 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13489783 original size:42 final size:42
Alignment explanation
Indices: 13489681--13489844 Score: 143
Period size: 42 Copynumber: 3.9 Consensus size: 42
13489671 TCTTTAGCGG
* * *
13489681 ATGATCTTTAGCGGCGCTTGGTTAAAAACGCCGCTAAAGATC
1 ATGATTTTTAGCGGCGCTTGGTAAAAAACGCCGCTAAAGAAC
*
13489723 ATG-TTCTTTAGAGGCGCTTGGTAAAAAACGCCGCTAAAGAAC
1 ATGATT-TTTAGCGGCGCTTGGTAAAAAACGCCGCTAAAGAAC
* * ** * ** *
13489765 GTGATTTTTAGCGACGCTTTATTCACTAACGCCACTAAAG-AC
1 ATGATTTTTAGCGGCGC-TTGGTAAAAAACGCCGCTAAAGAAC
* ** *
13489807 ATGATCTTTAGCGGCGCTTTTATAAAAAACGCCACTAA
1 ATGATTTTTAGCGGCGC-TTGGTAAAAAACGCCGCTAA
13489845 TTTTGGGATT
Statistics
Matches: 98, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
41 1 0.01
42 79 0.81
43 18 0.18
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
ATGATTTTTAGCGGCGCTTGGTAAAAAACGCCGCTAAAGAAC
Found at i:13490235 original size:66 final size:66
Alignment explanation
Indices: 13490147--13490281 Score: 216
Period size: 66 Copynumber: 2.0 Consensus size: 66
13490137 TTCTGCTCTG
* * *
13490147 CTCTGCTTCTCTCGATGTCGCATCTGCTTTAAGTCGTAGCTAGAGTTCTTCATATTTCTTTTGAA
1 CTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTCGTAGCTAGAGTTCTTCATATTTCCTTTGAA
13490212 C
66 C
* * *
13490213 CTCTGCTTCCCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
1 CTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTCGTAGCTAGAGTTCTTCATATTTCCTTTGAA
13490278 C
66 C
13490279 CTC
1 CTC
13490282 AACTGTGGTC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.41
Consensus pattern (66 bp):
CTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTCGTAGCTAGAGTTCTTCATATTTCCTTTGAA
C
Found at i:13491397 original size:41 final size:41
Alignment explanation
Indices: 13491294--13491402 Score: 164
Period size: 41 Copynumber: 2.7 Consensus size: 41
13491284 TTTAACATAT
* * *
13491294 TCACCGGCACTTAACCTGCTAAGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
13491335 TCACCGGAACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
13491376 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
13491403 AAGTCCGAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:13492079 original size:115 final size:114
Alignment explanation
Indices: 13491884--13492223 Score: 563
Period size: 115 Copynumber: 3.0 Consensus size: 114
13491874 TCATATATAC
* *
13491884 ATATTCGAACTTCATTAATGCTTATATATAACATTCATACTTAACTAATTTCAATTTATATACTT
1 ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTTATATACTT
13491949 TCAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
66 TCAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
* *
13491998 ATATTCGAACTTCATTTATGCATATATATAACATTCACACATTAACTAATTTCAATTTGTATACT
1 ATATTCGAACTTCATTTATGCATATATATAACATTCATAC-TTAACTAATTTCAATTTATATACT
*
13492063 TTCAATTATAGCTCATCAAATATACAATAGATATGCATATATATTTACAT
65 TTCAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
* * *
13492113 ATATTCAAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTCATATATTT
1 ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTTATATACTT
* * * *
13492178 TTAATTATAGCTCATAAAATATAAAATAAATATACATATATATTTA
66 TCAATTATAGCTCATCAAATATACAATAGATATACATATATATTTA
13492224 TGCTGATTTG
Statistics
Matches: 210, Mismatches: 15, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
114 100 0.48
115 110 0.52
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (114 bp):
ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTTATATACTT
TCAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
Found at i:13493216 original size:13 final size:13
Alignment explanation
Indices: 13493198--13493222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13493188 CAATCAAATG
13493198 CACACAAAATAAA
1 CACACAAAATAAA
13493211 CACACAAAATAA
1 CACACAAAATAA
13493223 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:13497559 original size:25 final size:25
Alignment explanation
Indices: 13497525--13497603 Score: 104
Period size: 25 Copynumber: 3.2 Consensus size: 25
13497515 AGCTCCGAAA
*
13497525 TTATGTAAGTTATGTATTATATAAG
1 TTATGTAAGTTATGTATTATGTAAG
*
13497550 TTATGTAAGTTACGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
* * * *
13497575 CTATGTAAGTTGTATTTTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
13497600 TTAT
1 TTAT
13497604 TTATTATGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.48
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTAAG
Found at i:13497569 original size:41 final size:41
Alignment explanation
Indices: 13497550--13497681 Score: 210
Period size: 41 Copynumber: 3.2 Consensus size: 41
13497540 ATTATATAAG
**
13497550 TTATGTAAGTTACGTATTATGTAAGCTATGTAAGTTGTATT
1 TTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTGTATT
*
13497591 TTATGTAAGTTATTTATTATGTAAGCTACGTAAGTTGTATT
1 TTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTGTATT
* * *
13497632 TTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTATGTA
1 TTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTGTATT
13497673 TTATGTAAG
1 TTATGTAAG
13497682 CTATGTCATA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.48
Consensus pattern (41 bp):
TTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTGTATT
Done.