Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 46 of 190
Found at i:12870477 original size:32 final size:32
Alignment explanation
Indices: 12870441--12870506 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
12870431 TCTATTGAAA
*
12870441 TCACATTTCAATTTAGATAATATAAAAAATAT
1 TCACATTTCAATTTAGAGAATATAAAAAATAT
12870473 TCACATTTCAATTTAGAGAATATAAAAAATAT
1 TCACATTTCAATTTAGAGAATATAAAAAATAT
12870505 TC
1 TC
12870507 TTTGCACGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (32 bp):
TCACATTTCAATTTAGAGAATATAAAAAATAT
Found at i:12872605 original size:58 final size:57
Alignment explanation
Indices: 12872473--12872607 Score: 164
Period size: 58 Copynumber: 2.3 Consensus size: 57
12872463 TTTAATTCAT
* ** *
12872473 ATAATAATTATATTAAGAATTTTATTAAATTATATATTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAA-AATATGGTTAAATTATATATTATTTTATGAAATTATATTTA
* * * *
12872531 ATAATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTTATGCAATTATTTTTA
1 ATAATAATTATATTAAAATATGGTTAAATTATATATTA-TTTTATGAAATTATATTTA
12872589 ATAATAATCT-TATTAAAAT
1 ATAATAAT-TATATTAAAAT
12872608 TTAATAACAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 18 0.27
58 47 0.71
59 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATGGTTAAATTATATATTATTTTATGAAATTATATTTA
Found at i:12873280 original size:98 final size:98
Alignment explanation
Indices: 12873111--12873307 Score: 385
Period size: 98 Copynumber: 2.0 Consensus size: 98
12873101 GTGCAATAAA
12873111 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
*
12873176 CCTCTAAAATCCCAAACTTGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
12873209 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
12873274 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
12873307 A
1 A
12873308 TTAATTATTT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:12875623 original size:84 final size:85
Alignment explanation
Indices: 12875518--12875674 Score: 203
Period size: 84 Copynumber: 1.9 Consensus size: 85
12875508 GAAATCTTCA
* * * *
12875518 ATCTGCCTCACTGCAACTTCAG-GAGGATAAGA-CTCACTTATTTAGTCTACTCCACTGCAACTT
1 ATCTGCCTCACTGCAACTTCAGAGA-GATAAGATCTAACGT-TTTAATCCACTCCACTGCAACTT
*
12875581 CAGGGAGATAAGACTAGATGCG
64 CAGAGAGATAAGACTAGATGCG
* * *
12875603 ATCTG-CTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCA
1 ATCTGCCTCACTGCAACTTCAGAGAGATAAGATCTAACGTTTTAATCCACTCCACTGCAACTTCA
12875667 GAGAGATA
66 GAGAGATA
12875675 GGATTGTCAG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
84 51 0.82
85 11 0.18
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (85 bp):
ATCTGCCTCACTGCAACTTCAGAGAGATAAGATCTAACGTTTTAATCCACTCCACTGCAACTTCA
GAGAGATAAGACTAGATGCG
Found at i:12875664 original size:44 final size:43
Alignment explanation
Indices: 12875517--12875891 Score: 238
Period size: 44 Copynumber: 8.7 Consensus size: 43
12875507 TGAAATCTTC
**
12875517 AATCTGC-CTCACTGCAACTTCAG-GAGGATAAGA-CTCACTTATTT
1 AATCTGCTC-CACTGCAACTTCAGAGA-GATAAGATCT-AGGT-TTT
* * * * **
12875561 AGTCTACTCCACTGCAACTTCAGGGAGATAAGA-CTA-GATGC
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTAGGTTTT
* *
12875602 GATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATCT-AGGTTTT
* * * *
12875645 AATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGTCA-GCTTT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TCT-AGGTTTT
* * *
12875689 AATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TTGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTAG--GT-TTT
* * *
12875734 AGTCTGC-CTCACTGCAACTTCAG-GAAGATAAGA-CTTGTTTACTT
1 AATCTGCTC-CACTGCAACTTCAGAG-AGATAAGATCTAGGTT--TT
* * * * * * **
12875778 AGTCTGCTCCATTGTAACTTTAGGGAGATAAGA-CT-GGATGC
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTAGGTTTT
* *
12875819 GATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATCT-AGGTTTT
*
12875862 AATCTGCTCCACTGCAACTTCAGGGAGATA
1 AATCTGCTCCACTGCAACTTCAGAGAGATA
12875892 GGATTATTGG
Statistics
Matches: 259, Mismatches: 50, Indels: 44
0.73 0.14 0.12
Matches are distributed among these distances:
40 41 0.16
41 16 0.06
42 3 0.01
43 23 0.09
44 135 0.52
45 41 0.16
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
AATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTAGGTTTT
Found at i:12875753 original size:217 final size:216
Alignment explanation
Indices: 12875474--12875896 Score: 657
Period size: 217 Copynumber: 2.0 Consensus size: 216
12875464 GCCATCTTCG
** *
12875474 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTGCCTCACTGCAACTTCA
1 ATCTGCTCCACTACAACTTAGAGAGATAAGATCTGAAATCTTCAATCTGCCTCACTGCAACTTCA
* *
12875539 GGAGGATAAGACTCACTTATTTAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
66 GGAAGATAAGACTCACTTACTTAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
12875604 TCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGA
131 TCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGA
12875669 GAGATAGGATTGTCAGCTTTA
196 GAGATAGGATTGTCAGCTTTA
* * ** *
12875690 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
1 ATCTGCTCCACTACAACTT-AGAGAGATAAGATCTGAAATCTTCAATCTGCCTCACTGCAACTTC
*** * * * * *
12875755 AGGAAGATAAGACTTGTTTACTTAGTCTGCTCCATTGTAACTTTAGGGAGATAAGACTGGATGCG
65 AGGAAGATAAGACTCACTTACTTAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
*
12875820 ATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCTGCTCCACTGCAACTTCAG
130 ATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAG
*
12875885 GGAGATAGGATT
195 AGAGATAGGATT
12875897 ATTGGCCACC
Statistics
Matches: 186, Mismatches: 20, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
216 16 0.09
217 170 0.91
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (216 bp):
ATCTGCTCCACTACAACTTAGAGAGATAAGATCTGAAATCTTCAATCTGCCTCACTGCAACTTCA
GGAAGATAAGACTCACTTACTTAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
TCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGA
GAGATAGGATTGTCAGCTTTA
Found at i:12877008 original size:10 final size:10
Alignment explanation
Indices: 12876993--12877017 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12876983 GCCTCTCCCC
12876993 TTTTTTGTTT
1 TTTTTTGTTT
12877003 TTTTTTGTTT
1 TTTTTTGTTT
12877013 TTTTT
1 TTTTT
12877018 AGAAATCAGA
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:12887429 original size:96 final size:98
Alignment explanation
Indices: 12887300--12887494 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
12887290 GTGCAATAAA
12887300 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCC-A-ACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
*
12887363 CCTCTAAAATCCCAAACTTGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
12887396 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
12887461 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
12887494 A
1 A
12887495 TTATTTTTTT
Statistics
Matches: 96, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
96 46 0.48
97 1 0.01
98 49 0.51
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:12889371 original size:16 final size:16
Alignment explanation
Indices: 12889350--12889404 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
12889340 TGAATTACTG
* *
12889350 ATTACAGCTTTAATCC
1 ATTACAGCTCTATTCC
*
12889366 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
12889382 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
12889398 ATTACAG
1 ATTACAG
12889405 TAAACCAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:12891875 original size:19 final size:19
Alignment explanation
Indices: 12891835--12891876 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12891825 ATTTTAAAAC
* *
12891835 AAAATTGAATTTAGTTTTA
1 AAAATTCAATTTAGTTTAA
12891854 AAAATTCAATTTTA-TTTAA
1 AAAATTCAA-TTTAGTTTAA
12891873 AAAA
1 AAAA
12891877 CAATTTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (19 bp):
AAAATTCAATTTAGTTTAA
Found at i:12892885 original size:24 final size:24
Alignment explanation
Indices: 12892835--12892885 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
12892825 ATTCTTATTT
* * *
12892835 TAAAAAATATTTAATATATGTATA
1 TAAAAAATATTTAAAATATGCAAA
12892859 TAAAAAATATTTACAAATAT-CAAA
1 TAAAAAATATTTA-AAATATGCAAA
12892883 TAA
1 TAA
12892886 TAAGGTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAAAAATATTTAAAATATGCAAA
Found at i:12893173 original size:22 final size:23
Alignment explanation
Indices: 12893147--12893208 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
12893137 AGCCCATATT
**
12893147 AAATATATATTTAATAT-CTATA
1 AAATATATATTTAATATAAAATA
*
12893169 AAATATATATTTGAT-TAAAATA
1 AAATATATATTTAATATAAAATA
*
12893191 AAAAATATATTTAATATA
1 AAATATATATTTAATATA
12893209 TAATTCGGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 1 0.03
22 30 0.91
23 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
AAATATATATTTAATATAAAATA
Found at i:12896797 original size:22 final size:24
Alignment explanation
Indices: 12896759--12896807 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
12896749 GTTTATATGT
*
12896759 ATATGTATTTACTAAAA-TA-AAA
1 ATATGTATCTACTAAAAGTATAAA
12896781 ATATGTATCTA-TAAAAAGTATAAA
1 ATATGTATCTACT-AAAAGTATAAA
12896805 ATA
1 ATA
12896808 CAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 2 0.09
24 6 0.26
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
ATATGTATCTACTAAAAGTATAAA
Found at i:12897870 original size:6 final size:6
Alignment explanation
Indices: 12897854--12897891 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
12897844 TGAAACAAGT
12897854 AAATGAA AAATAA AAATAA AAATAA AAA-ATA AAATAA A
1 AAAT-AA AAATAA AAATAA AAATAA AAATA-A AAATAA A
12897892 GAAGATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 1 0.03
6 23 0.79
7 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:12899151 original size:44 final size:44
Alignment explanation
Indices: 12899088--12899290 Score: 214
Period size: 44 Copynumber: 4.6 Consensus size: 44
12899078 NNNNNNGATA
*
12899088 TGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTGACC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACC
* *
12899132 TGCTCTACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACC
* ***** * *
12899176 TGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTT-AAGTC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA-CC
* * * * * *
12899219 TGCTTCACTATTGCTTAGGAAGATAAGAT-TCGCCGTCTTCGATC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCT-ACCATCTTCGACC
12899263 TGCTCCACTACTGCTTAGGGAGATAAGA
1 TGCTCCACTACTGCTTAGGGAGATAAGA
12899291 CTGGTGGTTT
Statistics
Matches: 133, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.01
43 31 0.23
44 100 0.75
45 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (44 bp):
TGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACC
Found at i:12906188 original size:12 final size:12
Alignment explanation
Indices: 12906167--12906191 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12906157 CTGTGTTAGT
12906167 CCTTGTGTTGGG
1 CCTTGTGTTGGG
12906179 CCTTGTGTTGGG
1 CCTTGTGTTGGG
12906191 C
1 C
12906192 TCCTGCCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (12 bp):
CCTTGTGTTGGG
Found at i:12911273 original size:22 final size:24
Alignment explanation
Indices: 12911235--12911283 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
12911225 TGTGTATTGT
*
12911235 ATATGTATTTACTAAAA-TA-AAA
1 ATATGTATGTACTAAAAGTATAAA
12911257 ATATGTATGTA-TAAAAAGTATAAA
1 ATATGTATGTACT-AAAAGTATAAA
12911281 ATA
1 ATA
12911284 CAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 2 0.09
24 6 0.26
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
ATATGTATGTACTAAAAGTATAAA
Found at i:12912378 original size:6 final size:6
Alignment explanation
Indices: 12912362--12912406 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
12912352 TGAAACAAGT
*
12912362 AAATGAA AAATAA AAATAA AAATAA AAATAA AAAAAGA AAATAA A
1 AAAT-AA AAATAA AAATAA AAATAA AAATAA AAATA-A AAATAA A
12912407 GAAGATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 26 0.74
7 9 0.26
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.13
Consensus pattern (6 bp):
AAATAA
Found at i:12912396 original size:13 final size:13
Alignment explanation
Indices: 12912362--12912406 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
12912352 TGAAACAAGT
*
12912362 AAATGAAAAATAA
1 AAATAAAAAATAA
12912375 AAAT-AAAAATAA
1 AAATAAAAAATAA
12912387 AAATAAAAAA-AGA
1 AAATAAAAAATA-A
12912400 AAATAAA
1 AAATAAA
12912407 GAAGATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 13 0.43
13 17 0.57
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.13
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:12916896 original size:40 final size:41
Alignment explanation
Indices: 12916836--12916940 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 41
12916826 GCTTTAGCCA
* * * *
12916836 TTCACCCAAAAAATGATGCTCCTACGTATGTGCTTAAATTG
1 TTCACCCAAAATATGATGCTCCTACGCATGAGCTTAAACTG
* * *
12916877 TTCA-CCAAAATATGGTGCTCTTAGGCATGAGCTTAAACTG
1 TTCACCCAAAATATGATGCTCCTACGCATGAGCTTAAACTG
* *
12916917 ATCATCCAAAATATGATGCTCCTA
1 TTCACCCAAAATATGATGCTCCTA
12916941 AGCACGAGAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 32 0.60
41 21 0.40
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (41 bp):
TTCACCCAAAATATGATGCTCCTACGCATGAGCTTAAACTG
Found at i:12916964 original size:41 final size:41
Alignment explanation
Indices: 12916881--12916968 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
12916871 AAATTGTTCA
* * * * * * *
12916881 CCAAAATATGGTGCTCTTAGGCATGAGCTTAAACTGATCAT
1 CCAAAATATGATGCTCCTAAGCACGAGATTAAACTAAACAT
*
12916922 CCAAAATATGATGCTCCTAAGCACGAGATTAAGCTAAACAT
1 CCAAAATATGATGCTCCTAAGCACGAGATTAAACTAAACAT
12916963 CCAAAA
1 CCAAAA
12916969 ACATTTTGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (41 bp):
CCAAAATATGATGCTCCTAAGCACGAGATTAAACTAAACAT
Found at i:12918652 original size:24 final size:24
Alignment explanation
Indices: 12918625--12918676 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
12918615 AAAAAAGAGG
*
12918625 AAAATTTAAAGAACATAAAAGAAA
1 AAAATTTAAAGAACATAAAACAAA
** *
12918649 AAAA-TTAAATTACTTAAAACAAA
1 AAAATTTAAAGAACATAAAACAAA
12918672 AAAAT
1 AAAAT
12918677 ATAGGAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (24 bp):
AAAATTTAAAGAACATAAAACAAA
Found at i:12918865 original size:31 final size:29
Alignment explanation
Indices: 12918804--12918867 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
12918794 ATAACGTAAA
* *
12918804 TGACTAAAACGTAACATTTCAAACATAAG
1 TGACTAAAACGTAACATGTCAAACAAAAG
12918833 TGACTAAAACGTAACCTAATGT-AAACAAAAG
1 TGACTAAAACGTAA-C--ATGTCAAACAAAAG
12918864 TGAC
1 TGAC
12918868 CATGGGCGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 14 0.47
30 1 0.03
31 12 0.40
32 3 0.10
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.22
Consensus pattern (29 bp):
TGACTAAAACGTAACATGTCAAACAAAAG
Found at i:12924334 original size:37 final size:37
Alignment explanation
Indices: 12924293--12924407 Score: 221
Period size: 37 Copynumber: 3.1 Consensus size: 37
12924283 TCAACTTAAC
*
12924293 TTAATCTATGTCAAGAATGAGCTTGATAGTTCAATGG
1 TTAATCTATGTCAAGAATGAGCTTGCTAGTTCAATGG
12924330 TTAATCTATGTCAAGAATGAGCTTGCTAGTTCAATGG
1 TTAATCTATGTCAAGAATGAGCTTGCTAGTTCAATGG
12924367 TTAATCTATGTCAAGAATGAGCTTGCTAGTTCAATGG
1 TTAATCTATGTCAAGAATGAGCTTGCTAGTTCAATGG
12924404 TTAA
1 TTAA
12924408 GCTTCTGTAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 77 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (37 bp):
TTAATCTATGTCAAGAATGAGCTTGCTAGTTCAATGG
Found at i:12931999 original size:50 final size:50
Alignment explanation
Indices: 12931888--12932134 Score: 219
Period size: 50 Copynumber: 4.8 Consensus size: 50
12931878 ATTTGGGTAA
* * *
12931888 AGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* * *
12931944 AGAGGTGCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
12931994 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * *
12932044 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTAGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * *
12932093 AAACATCCCATGTAAGACCATGTCTGGGACATTGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12932135 TGTTATTATC
Statistics
Matches: 159, Mismatches: 31, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 36 0.23
50 81 0.51
52 1 0.01
53 2 0.01
55 1 0.01
56 37 0.23
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:12939612 original size:35 final size:34
Alignment explanation
Indices: 12939511--12939613 Score: 109
Period size: 35 Copynumber: 3.0 Consensus size: 34
12939501 CCAACAGTAT
* * *
12939511 TTGCGCCCAACGCTAGTCGGATAAACCGACGAATG
1 TTGC-CCCAGCGCTAGTCGGATAAACCGATGAAAG
* * **
12939546 TGTG-CCCAGCACTAGTCAGATAAACTAATGAAAG
1 T-TGCCCCAGCGCTAGTCGGATAAACCGATGAAAG
12939580 TTGCACCCAGCGCTAGTCGGATAAACCGATGAAA
1 TTGC-CCCAGCGCTAGTCGGATAAACCGATGAAA
12939614 TAATTAGTGA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
33 2 0.04
34 24 0.44
35 26 0.48
36 2 0.04
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.18
Consensus pattern (34 bp):
TTGCCCCAGCGCTAGTCGGATAAACCGATGAAAG
Found at i:12939666 original size:75 final size:75
Alignment explanation
Indices: 12939446--12939671 Score: 239
Period size: 75 Copynumber: 3.1 Consensus size: 75
12939436 TTTGCACCAA
* * * **
12939446 CGCTAGTCGGATAAATCGAAAAAATAATTAGTGAGCCCAACTCTAGTTGGATAAACCAACAGTAT
1 CGCTAGTCGGATAAACCGAAGAAATAATTAGTGAGCCCAGCTCTAGTTGGATAAACCAATGGTAT
*
12939511 TTGCGCCCAA
66 TTGCGCCCAG
* * * ** * ** *
12939521 CGCTAGTCGGATAAACCGACG----AA-T-GTGTGCCCAGCACTAGTCAGATAAACTAATGAAAG
1 CGCTAGTCGGATAAACCGAAGAAATAATTAGTGAGCCCAGCTCTAGTTGGATAAACCAATGGTAT
*
12939580 TTGCACCCAG
66 TTGCGCCCAG
* *
12939590 CGCTAGTCGGATAAACCGATGAAATAATTAGTGAGCGCAGCTCTAGTTGGATAAACCAATGGTAT
1 CGCTAGTCGGATAAACCGAAGAAATAATTAGTGAGCCCAGCTCTAGTTGGATAAACCAATGGTAT
12939655 TTGCGCCCAG
66 TTGCGCCCAG
*
12939665 CGGTAGT
1 CGCTAGT
12939672 TGAACGAATC
Statistics
Matches: 117, Mismatches: 28, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
69 52 0.44
70 1 0.01
71 2 0.02
73 2 0.02
74 1 0.01
75 59 0.50
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (75 bp):
CGCTAGTCGGATAAACCGAAGAAATAATTAGTGAGCCCAGCTCTAGTTGGATAAACCAATGGTAT
TTGCGCCCAG
Found at i:12950258 original size:97 final size:97
Alignment explanation
Indices: 12950071--12950334 Score: 465
Period size: 97 Copynumber: 2.7 Consensus size: 97
12950061 CAACTCTTAA
* *
12950071 AACCGAATGTATAATCACTATAAACATGAATAGCCGAATGCATATATACATATATGCTTAACAAA
1 AACCGAATGTATATTTACTATAAACATGAATAGCCGAATGCATATATAC--ATATGCTTAACAAA
12950136 TATTAGCTCCAAATGTATATACACTTTGAACATG
64 TATTAGCTCCAAATGTATATACACTTTGAACATG
* **
12950170 AATCGAATGTATATTTACTATAAACATGAATAGTTGAATGCATATATACATATGCTTAACAAATA
1 AACCGAATGTATATTTACTATAAACATGAATAGCCGAATGCATATATACATATGCTTAACAAATA
12950235 TTAGCTCCAAATGTATATACACTTTGAACATG
66 TTAGCTCCAAATGTATATACACTTTGAACATG
12950267 AACCGAATGTATATTTACTATAAACATGAATAGCCGAATGCATATATACATATGCTTAACAAATA
1 AACCGAATGTATATTTACTATAAACATGAATAGCCGAATGCATATATACATATGCTTAACAAATA
12950332 TTA
66 TTA
12950335 CAACCAATTG
Statistics
Matches: 157, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
97 113 0.72
99 44 0.28
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.31
Consensus pattern (97 bp):
AACCGAATGTATATTTACTATAAACATGAATAGCCGAATGCATATATACATATGCTTAACAAATA
TTAGCTCCAAATGTATATACACTTTGAACATG
Found at i:12950854 original size:41 final size:41
Alignment explanation
Indices: 12950751--12950856 Score: 167
Period size: 41 Copynumber: 2.6 Consensus size: 41
12950741 ACTGGTGCTT
* * * *
12950751 AGCCTGTTAGACGTAAAGTCTAAAATATTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
*
12950792 AGCCAGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
12950833 AGCCTGCTAGACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCTGAA
12950857 TCATCTTACT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
Found at i:12953701 original size:22 final size:22
Alignment explanation
Indices: 12953658--12953721 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 22
12953648 TTCTATACTA
12953658 AAACTATAAAACTTAATATAAT
1 AAACTATAAAACTTAATATAAT
*
12953680 AAACTTTAAAACGTTATGTAATATAAT
1 AAACTATAAAAC----T-TAATATAAT
12953707 AAAACTATAAAACTT
1 -AAACTATAAAACTT
12953722 GACTTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
22 11 0.32
23 1 0.03
24 1 0.03
26 1 0.03
27 9 0.26
28 11 0.32
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (22 bp):
AAACTATAAAACTTAATATAAT
Found at i:12953729 original size:28 final size:28
Alignment explanation
Indices: 12953668--12953738 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
12953658 AAACTATAAA
*
12953668 ACTTAATATAAT-AAACTTTAAAACGTT
1 ACTTAATATAATAAAACTATAAAACGTT
12953695 A-TGTAATATAATAAAACTATAAAAC-TT
1 ACT-TAATATAATAAAACTATAAAACGTT
12953722 GACTTAATATAATAAAA
1 -ACTTAATATAATAAAA
12953739 GTTTACGTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 1 0.03
27 12 0.31
28 25 0.64
29 1 0.03
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (28 bp):
ACTTAATATAATAAAACTATAAAACGTT
Found at i:12955087 original size:42 final size:42
Alignment explanation
Indices: 12955023--12955108 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
12955013 GTCAATAACC
*
12955023 TTAGCCAAACACACTCTTGACTTGCCTCATACATTGCAATTA
1 TTAGCCAAACACACTCTCGACTTGCCTCATACATTGCAATTA
12955065 TTAGCCAAACACACTCTCGACTTGCCTCATACATTGCAATTA
1 TTAGCCAAACACACTCTCGACTTGCCTCATACATTGCAATTA
12955107 TT
1 TT
12955109 TCAGCATGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.31
Consensus pattern (42 bp):
TTAGCCAAACACACTCTCGACTTGCCTCATACATTGCAATTA
Found at i:12961492 original size:15 final size:16
Alignment explanation
Indices: 12961470--12961506 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
12961460 ATGAAGACTT
12961470 ATAT-TATGAAG-AAG
1 ATATCTATGAAGAAAG
12961484 ATATCTATGAAGAAAG
1 ATATCTATGAAGAAAG
12961500 AT-TCTAT
1 ATATCTAT
12961507 AGAGATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 12 0.57
16 5 0.24
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (16 bp):
ATATCTATGAAGAAAG
Found at i:12972627 original size:18 final size:18
Alignment explanation
Indices: 12972604--12972639 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12972594 AGCTCCCAAT
12972604 TCGCATAAAGCCTTGAAC
1 TCGCATAAAGCCTTGAAC
*
12972622 TCGCATAAATCCTTGAAC
1 TCGCATAAAGCCTTGAAC
12972640 ATGGGATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (18 bp):
TCGCATAAAGCCTTGAAC
Found at i:12976710 original size:25 final size:25
Alignment explanation
Indices: 12976676--12976779 Score: 111
Period size: 25 Copynumber: 4.2 Consensus size: 25
12976666 TACCGATTTT
* * * *
12976676 AGCTCTTATGAGCATACTGATACTC
1 AGCTCGTATGAGCTTACTGTTATTC
12976701 AGCTCGTATGAGCTTACTGTTATTC
1 AGCTCGTATGAGCTTACTGTTATTC
* *
12976726 AGCTCGAAGGAGCTTACTGTTATTC
1 AGCTCGTATGAGCTTACTGTTATTC
* **
12976751 AGCTCAG-AGGATTTTACTGTTATTC
1 AGCTC-GTATGAGCTTACTGTTATTC
12976776 AGCT
1 AGCT
12976780 TAGGTGAGCT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
25 69 0.99
26 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACTGTTATTC
Found at i:12976796 original size:25 final size:24
Alignment explanation
Indices: 12976710--12976796 Score: 102
Period size: 25 Copynumber: 3.5 Consensus size: 24
12976700 CAGCTCGTAT
*
12976710 GAGCTTACTGTTATTCAGCTCGAAG
1 GAGCTTACTGTTATTCAGCTC-AGG
12976735 GAGCTTACTGTTATTCAGCTCAGAG
1 GAGCTTACTGTTATTCAGCTCAG-G
** *
12976760 GATTTTACTGTTATTCAGCTTAGG
1 GAGCTTACTGTTATTCAGCTCAGG
*
12976784 TGAGCTTATTGTT
1 -GAGCTTACTGTT
12976797 TATAACTCGT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.04
25 51 0.96
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (24 bp):
GAGCTTACTGTTATTCAGCTCAGG
Found at i:13011584 original size:162 final size:160
Alignment explanation
Indices: 13011287--13011618 Score: 420
Period size: 162 Copynumber: 2.1 Consensus size: 160
13011277 TGTTAAAAAG
* * *
13011287 TGCTAA-AATTATGCTTTTAATGATTAAATTGATATTTAAGCTTTCTGGTCACCTTATTTAAATT
1 TGCTAATATTTATACTTTTAATGATTAAATTGATATTTAAACTTTCTGGTCACCTTATTTAAATT
* *
13011351 TTTAAATAAGCAATAAAGGTGGCCGAATCAAGTACGATTTGAGCCTAACTAACTAGCATGAATAC
66 GTTAAATAAGCAATAAAGGTGGCCGAATCAAGTACGATTTGACCCTAACTAACTAGCATGAATAC
* *
13011416 AAAACTAGTGTGGTTGACAAAATAATTGTA
131 AAAACTAGTATAGTTGACAAAATAATTGTA
*** *
13011446 TGCTAATATTTATACTTTTAATGATTAAATTGATATTTAAACTTGT-TGGTTGGCTTATTTCAAT
1 TGCTAATATTTATACTTTTAATGATTAAATTGATATTTAAACTT-TCTGGTCACCTTATTTAAAT
* * * *
13011510 TGTTAAATAAGCGATTTAAAGGTGGCCGAATTAGGTTA-G-TTTCGACCCTAACTAATTAGCATG
65 TGTTAAATAAGC-A-ATAAAGGTGGCCGAATCAAG-TACGATTT-GACCCTAACTAACTAGCATG
**
13011573 AATACAAAACTAGTATAGTTGACCGAATAATTGTA
126 AATACAAAACTAGTATAGTTGACAAAATAATTGTA
* *
13011608 TGTTGATATTT
1 TGCTAATATTT
13011619 GTGTGATTCA
Statistics
Matches: 148, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
159 6 0.04
160 59 0.40
161 5 0.03
162 76 0.51
163 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (160 bp):
TGCTAATATTTATACTTTTAATGATTAAATTGATATTTAAACTTTCTGGTCACCTTATTTAAATT
GTTAAATAAGCAATAAAGGTGGCCGAATCAAGTACGATTTGACCCTAACTAACTAGCATGAATAC
AAAACTAGTATAGTTGACAAAATAATTGTA
Found at i:13014505 original size:8 final size:9
Alignment explanation
Indices: 13014485--13014509 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
13014475 AAATGACTTC
13014485 AAAAACATA
1 AAAAACATA
13014494 AAAAACATA
1 AAAAACATA
13014503 AAAAACA
1 AAAAACA
13014510 AAGTTCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.12, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAACATA
Found at i:13016302 original size:27 final size:27
Alignment explanation
Indices: 13016203--13016323 Score: 147
Period size: 27 Copynumber: 4.5 Consensus size: 27
13016193 AAAAGGAGTT
*
13016203 TTTGTGGCAATCTATGAAATGGAAGCC
1 TTTGTGGCAATCTGTGAAATGGAAGCC
* * *
13016230 TTTATGGAAAT-TGATGAAATGGAAGGC
1 TTTGTGGCAATCTG-TGAAATGGAAGCC
*
13016257 TTTGTGGCAATCTGTGAAATGGAAGGC
1 TTTGTGGCAATCTGTGAAATGGAAGCC
*
13016284 TTTGTGGCAATCTGCGAAATAGG-AGCC
1 TTTGTGGCAATCTGTGAAAT-GGAAGCC
*
13016311 TTTGTGGCGATCT
1 TTTGTGGCAATCT
13016324 ATGGAAAGGA
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.01
27 77 0.94
28 4 0.05
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.31
Consensus pattern (27 bp):
TTTGTGGCAATCTGTGAAATGGAAGCC
Found at i:13018395 original size:11 final size:11
Alignment explanation
Indices: 13018379--13018413 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
13018369 GGAAGAGAGG
13018379 TTGATTTTTGC
1 TTGATTTTTGC
*
13018390 TTGATTTTAGC
1 TTGATTTTTGC
*
13018401 TTGATTCTTGC
1 TTGATTTTTGC
13018412 TT
1 TT
13018414 AATTGAAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.60
Consensus pattern (11 bp):
TTGATTTTTGC
Found at i:13019817 original size:20 final size:20
Alignment explanation
Indices: 13019792--13019832 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13019782 ATGAAGAACC
13019792 TAGTGTAAGGAAATCTAGTA
1 TAGTGTAAGGAAATCTAGTA
13019812 TAGTGTAAGGAAATCTAGTA
1 TAGTGTAAGGAAATCTAGTA
13019832 T
1 T
13019833 TCTAATATGA
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:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (20 bp):
TAGTGTAAGGAAATCTAGTA
Found at i:13032856 original size:26 final size:26
Alignment explanation
Indices: 13032825--13032889 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
13032815 ATAAGAGCCA
* * *
13032825 TAATCAGGAAGTTTACAAAGAACTTT
1 TAATCAGGAAGCTCACAAAGAACCTT
* *
13032851 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAGCTCACAAAGAACCTT
13032877 TAATCAGG-AGCTC
1 TAATCAGGAAGCTC
13032890 CGGATAGCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 5 0.15
26 29 0.85
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAACCTT
Found at i:13041334 original size:13 final size:12
Alignment explanation
Indices: 13041313--13041368 Score: 58
Period size: 13 Copynumber: 4.4 Consensus size: 12
13041303 ATAATTTTGG
*
13041313 TTTCTATTTTCAT
1 TTTCCATTTT-AT
*
13041326 TTTCAATTTTAT
1 TTTCCATTTTAT
13041338 CTTTCCATTTTATT
1 -TTTCCATTTTA-T
*
13041352 TTTCCATTTCAT
1 TTTCCATTTTAT
13041364 TTTCC
1 TTTCC
13041369 CCTATTAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
12 8 0.21
13 29 0.76
14 1 0.03
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTCCATTTTAT
Found at i:13041680 original size:20 final size:20
Alignment explanation
Indices: 13041655--13041692 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13041645 TAATTCACGG
13041655 TTTAATTTATAAACCAATTC
1 TTTAATTTATAAACCAATTC
13041675 TTTAATTTATAAACCAAT
1 TTTAATTTATAAACCAAT
13041693 CCAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAATTTATAAACCAATTC
Found at i:13045738 original size:48 final size:48
Alignment explanation
Indices: 13045667--13045768 Score: 168
Period size: 48 Copynumber: 2.1 Consensus size: 48
13045657 CAGTGTCGCG
* *
13045667 ACATCAAAGGTAGTTTTGTACTTTCTCCATTATGTTCTCTATGTTGCA
1 ACATCGAAGGTAGTTTCGTACTTTCTCCATTATGTTCTCTATGTTGCA
* *
13045715 ACATCGAAGGTAGTTTCGTACTTTCTTCATTATGTTCTCTATGTTGCG
1 ACATCGAAGGTAGTTTCGTACTTTCTCCATTATGTTCTCTATGTTGCA
13045763 ACATCG
1 ACATCG
13045769 GACTTCCCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.42
Consensus pattern (48 bp):
ACATCGAAGGTAGTTTCGTACTTTCTCCATTATGTTCTCTATGTTGCA
Found at i:13052366 original size:10 final size:10
Alignment explanation
Indices: 13052351--13052399 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
13052341 GAATCTGTCG
13052351 AAAATTAATC
1 AAAATTAATC
13052361 AAAATTAATC
1 AAAATTAATC
*
13052371 AAAATTTAATTAT
1 AAAA-TTAA-T-C
*
13052384 AAAATTAATT
1 AAAATTAATC
13052394 AAAATT
1 AAAATT
13052400 TGACATTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 21 0.60
11 5 0.14
12 5 0.14
13 4 0.11
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATTAATC
Found at i:13052393 original size:12 final size:11
Alignment explanation
Indices: 13052351--13052397 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
13052341 GAATCTGTCG
*
13052351 AAAATTAA-TC
1 AAAATTAATTA
*
13052361 AAAATTAATCA
1 AAAATTAATTA
*
13052372 AAATTTAATTA
1 AAAATTAATTA
13052383 TAAAATTAATTA
1 -AAAATTAATTA
13052395 AAA
1 AAA
13052398 TTTGACATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 8 0.27
11 12 0.40
12 10 0.33
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATTAATTA
Found at i:13054595 original size:8 final size:8
Alignment explanation
Indices: 13054572--13054605 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
13054562 ATTTGACCTG
13054572 TAAAGAAAA
1 TAAAG-AAA
13054581 TTAAAGAAA
1 -TAAAGAAA
13054590 TAAAGAAA
1 TAAAGAAA
13054598 TAAAGAAA
1 TAAAGAAA
13054606 AAGAAAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 3 0.12
10 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (8 bp):
TAAAGAAA
Found at i:13054640 original size:19 final size:18
Alignment explanation
Indices: 13054591--13054642 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
13054581 TTAAAGAAAT
*
13054591 AAAGAAATAAAGAAAAAGA
1 AAAG-AATAAAGAAAAACA
* *
13054610 AAACACTAAAAGAAGAAACA
1 AAAGAAT-AAAGAA-AAACA
13054630 AAAGAATAAAGAA
1 AAAGAATAAAGAA
13054643 TAAATAGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 2 0.08
19 15 0.58
20 9 0.35
ACGTcount: A:0.75, C:0.06, G:0.13, T:0.06
Consensus pattern (18 bp):
AAAGAATAAAGAAAAACA
Found at i:13054981 original size:13 final size:13
Alignment explanation
Indices: 13054963--13054988 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13054953 TTATATAGGC
13054963 TAGTTAATTACAT
1 TAGTTAATTACAT
13054976 TAGTTAATTACAT
1 TAGTTAATTACAT
13054989 AAAAAAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TAGTTAATTACAT
Found at i:13057983 original size:92 final size:92
Alignment explanation
Indices: 13057819--13058010 Score: 260
Period size: 92 Copynumber: 2.1 Consensus size: 92
13057809 TGATAATACT
* * * * ** *
13057819 AGGTATCATAATAAAACACATATTGATAGTTCAGGTACCGTATTGGACATTTTCAAAGTATAGGT
1 AGGTACCATAAGAAAACACATACTGATAGTTCAGATACCACATTGGACATTTTCAAAGTACAGGT
*
13057884 ATCACATTGGATATTTTATGAAAGCAC
66 ATCACATTGAATATTTTATGAAAGCAC
* *
13057911 AGGTACCATAAGAAAACACATACTGATGGTTCAGATACCACATTGGACATTTTCAAAGTACATGT
1 AGGTACCATAAGAAAACACATACTGATAGTTCAGATACCACATTGGACATTTTCAAAGTACAGGT
*
13057976 A-CTACATTGAATATTTTATGAAAGTAC
66 ATC-ACATTGAATATTTTATGAAAGCAC
*
13058003 AAGTACCA
1 AGGTACCA
13058011 AATGCGACAT
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
91 1 0.01
92 86 0.99
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (92 bp):
AGGTACCATAAGAAAACACATACTGATAGTTCAGATACCACATTGGACATTTTCAAAGTACAGGT
ATCACATTGAATATTTTATGAAAGCAC
Found at i:13059887 original size:14 final size:13
Alignment explanation
Indices: 13059868--13059898 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13059858 TTCTCAAAAT
*
13059868 CATTTTTTCAAAG
1 CATTTTTTTAAAG
13059881 CATTTTTTTAAAG
1 CATTTTTTTAAAG
13059894 CATTT
1 CATTT
13059899 CTCAAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (13 bp):
CATTTTTTTAAAG
Found at i:13061655 original size:51 final size:51
Alignment explanation
Indices: 13061579--13061754 Score: 230
Period size: 51 Copynumber: 3.5 Consensus size: 51
13061569 ATTGAACATT
*
13061579 TCTCACATGGTCTTACACCTCATATCATATATGTAAATGCCATGAAGCCTC
1 TCTCACATGGTCTTATACCTCATATCATATATGTAAATGCCATGAAGCCTC
**
13061630 TCTCACATGGTCTTATACCTCATATCATATATGTGGATGCCATGCAA-CCTC
1 TCTCACATGGTCTTATACCTCATATCATATATGTAAATGCCATG-AAGCCTC
* * ** **
13061681 TCTCACATGGTCTTATACCTCATA-CGATATCTGTATATGTTATGGTGCCTC
1 TCTCACATGGTCTTATACCTCATATC-ATATATGTAAATGCCATGAAGCCTC
*
13061732 TCTTACATGGTCTTATACCTCAT
1 TCTCACATGGTCTTATACCTCAT
13061755 TTTCACATAA
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
50 1 0.01
51 108 0.97
52 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (51 bp):
TCTCACATGGTCTTATACCTCATATCATATATGTAAATGCCATGAAGCCTC
Found at i:13064867 original size:20 final size:18
Alignment explanation
Indices: 13064793--13064894 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 18
13064783 AAAAAAATAG
*
13064793 TTTAATAGTTTAATATTAAA
1 TTTAATA-TTAAATATT-AA
*
13064813 TTTAAT-TT-AATACTTAT
1 TTTAATATTAAATA-TTAA
* *
13064830 TTTAATAGTATTATATTAA
1 TTTAATATTA-AATATTAA
13064849 TTTAATATTAAAGTAATT-A
1 TTTAATATTAAA-T-ATTAA
13064868 TCTTAATATTAAAT-TTAA
1 T-TTAATATTAAATATTAA
13064886 TTTAATATT
1 TTTAATATT
13064895 TATCTTGTAG
Statistics
Matches: 68, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
17 21 0.31
18 8 0.12
19 16 0.24
20 23 0.34
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTAATATTAAATATTAA
Found at i:13064867 original size:25 final size:26
Alignment explanation
Indices: 13064831--13064879 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
13064821 AATACTTATT
13064831 TTAATAGTATTATATTAAT-TTAATA
1 TTAATAGTATTATATTAATATTAATA
*
13064856 TTAA-AGTAATTATCTTAATATTAA
1 TTAATAGT-ATTATATTAATATTAA
13064880 ATTTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (26 bp):
TTAATAGTATTATATTAATATTAATA
Found at i:13071024 original size:19 final size:19
Alignment explanation
Indices: 13071000--13071068 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
13070990 AATCTTCAAG
13071000 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
13071019 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
13071038 GATATGCAATCTTAGA-A-
1 GATATGCAATCTTAGATAT
13071055 GATATG--ATCTTAGA
1 GATATGCAATCTTAGA
13071069 GATTTAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
15 8 0.17
17 6 0.12
18 1 0.02
19 33 0.69
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:13071031 original size:36 final size:36
Alignment explanation
Indices: 13070989--13071060 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 36
13070979 TATGGAAACA
13070989 TAATCTT-CA-AGGATATGCAATCTTAGATATGATATG
1 TAATCTTACATAGGATATGCAATCTTAGA-A-GATATG
* *
13071025 TAATCTTAGATATGATATGCAATCTTAGAAGATATG
1 TAATCTTACATAGGATATGCAATCTTAGAAGATATG
13071061 ATCTTAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 13 0.41
37 2 0.06
38 17 0.53
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (36 bp):
TAATCTTACATAGGATATGCAATCTTAGAAGATATG
Found at i:13071521 original size:3 final size:3
Alignment explanation
Indices: 13071513--13071582 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
13071503 ATTAATCTTG
*
13071513 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * *
13071559 TAT TAT TTT TAT TTT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
13071583 ATTCATGGGC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:13071655 original size:21 final size:21
Alignment explanation
Indices: 13071621--13071674 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
13071611 ATATATTGTT
** *
13071621 TTATATATAGTATACGTATGC
1 TTATATATTTTATACATATGC
*
13071642 TTATATATTTTATACATATGT
1 TTATATATTTTATACATATGC
*
13071663 TTTTAT-TTTTAT
1 TTATATATTTTAT
13071675 TTTACTTCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATATTTTATACATATGC
Found at i:13074964 original size:19 final size:19
Alignment explanation
Indices: 13074940--13074979 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
13074930 ATCTTAACAA
13074940 TATTTTATTAATTTACTAT
1 TATTTTATTAATTTACTAT
13074959 TATTTTATTAATTTACTAT
1 TATTTTATTAATTTACTAT
13074978 TA
1 TA
13074980 AAGTGATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTATTAATTTACTAT
Found at i:13074965 original size:11 final size:11
Alignment explanation
Indices: 13074945--13074980 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13074935 AACAATATTT
13074945 TATTAATTTAC
1 TATTAATTTAC
13074956 TATT-ATTT--
1 TATTAATTTAC
13074964 TATTAATTTAC
1 TATTAATTTAC
13074975 TATTAA
1 TATTAA
13074981 AGTGATTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 4 0.18
9 4 0.18
10 4 0.18
11 10 0.45
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTAATTTAC
Found at i:13075426 original size:9 final size:9
Alignment explanation
Indices: 13075412--13075442 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
13075402 GTTAAACGAA
13075412 TCGAGTTAT
1 TCGAGTTAT
*
13075421 TCGAGTTAA
1 TCGAGTTAT
13075430 TCGAGTTAT
1 TCGAGTTAT
13075439 TCGA
1 TCGA
13075443 ATCAACTCGA
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:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:13075516 original size:18 final size:18
Alignment explanation
Indices: 13075495--13075531 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
13075485 TGAGTTTTCG
13075495 AATTCAAATAACTCGAAT
1 AATTCAAATAACTCGAAT
*
13075513 AATTCAAATAATTCGAAT
1 AATTCAAATAACTCGAAT
13075531 A
1 A
13075532 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTCAAATAACTCGAAT
Found at i:13075781 original size:30 final size:31
Alignment explanation
Indices: 13075745--13075804 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
13075735 AAACCTTTTA
*
13075745 TTTTTCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTTCCCCAAAACTTTTACTCCCTTCCCAC
* *
13075775 TTTTTCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTTCCCCAAAACTTTTACTCCCTTCCCA
13075805 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTTCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:13077356 original size:5 final size:5
Alignment explanation
Indices: 13077346--13077381 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
13077336 TTGTTTTCTC
* *
13077346 TCTTT TCTTT TCTTT TCATT TCTTT TCTCT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
13077382 AATTTAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:13077371 original size:20 final size:20
Alignment explanation
Indices: 13077346--13077386 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13077336 TTGTTTTCTC
* *
13077346 TCTTTTCTTTTCTTTTCATT
1 TCTTTTCTCTTCTTTTAATT
13077366 TCTTTTCTCTTCTTTTAATT
1 TCTTTTCTCTTCTTTTAATT
13077386 T
1 T
13077387 AAATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTTTCTCTTCTTTTAATT
Found at i:13079378 original size:25 final size:26
Alignment explanation
Indices: 13079349--13079397 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
13079339 CAACAAAAAT
*
13079349 AAAATATATTC-TAAAAAGAAAAGGG
1 AAAATATAATCTTAAAAAGAAAAGGG
* *
13079374 AAAATCTAATCTTAAAATGAAAAG
1 AAAATATAATCTTAAAAAGAAAAG
13079398 AAAAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.22
Consensus pattern (26 bp):
AAAATATAATCTTAAAAAGAAAAGGG
Found at i:13080648 original size:288 final size:285
Alignment explanation
Indices: 13080132--13080679 Score: 626
Period size: 288 Copynumber: 1.9 Consensus size: 285
13080122 AAGGAACATG
*
13080132 GCAAACCTAAAAGAATAAAAAGCTAAGCATTCATCTCTAAGACCCTTAAGGAATTTAAATTATAT
1 GCAAACCTAAAAGAATAAAAAGCTAAGCAGTCATCTCTAAGACCCTTAAGGAATTTAAATTATAT
* * *
13080197 ATAACCACGCAATGTTTTAATTGAAAAATTAATGATATTAACTATTTGAACTAACTAATAACATT
66 ATAACCACACAATATTTTAATTGAAAAATTAACGATATTAACTATTTGAACTAACTAATAACATT
* * * * * * * * *
13080262 ATGAAAATATAGGGACCAAATTATATTAGAAATTAAAGTGATGCAGTTAAATTTTAAATTTGGGC
131 ATAAAAATATAGAGACCAAATTATATTAGAAATTAAAGTCATGAAATTAAATATAAAATTTAGAC
* *** *
13080327 ATCATAAAGGGACCAAAATTGAAATTTAATCATTTTTGTAAAACTACAAAAAAGAAAAAAAAAAG
196 ATCATAAAGAGACCAAAACAAAAATTTAATCATTTTGGTAAAA-T-CAAAAAAG-AAAAAAAAAG
13080392 AAAAGAAAAGAGATAAGGTAAGACCTAT
258 AAAAGAAAAGAGATAAGGTAAGACCTAT
* * * *
13080420 GCAAACCTAAAAGAAATAGAAAA-CTACG-AGTCAATTTCTAAGACTCTTAAGGTATTTAAA-TA
1 GCAAACCTAAAAG-AATA-AAAAGCTAAGCAGTC-ATCTCTAAGACCCTTAAGGAATTTAAATTA
* * * *
13080482 TATATAA-CATCATAATATTTTAATTGAAAAGTTAACGATATTAACTATTT-AGACTAATTTATA
63 TATATAACCA-CACAATATTTTAATTGAAAAATTAACGATATTAACTATTTGA-ACTAACTAATA
* * * * *
13080545 ATATTATAAAAATATTGAGACTAATTTATGTTA-AAAGTTAAAGTACAT-AAATTAAATATAAAA
126 ACATTATAAAAATATAGAGACCAAATTATATTAGAAA-TTAAAGT-CATGAAATTAAATATAAAA
* * * *
13080608 TTTAGACAT-ATTAGAGATACCAAAACAAAAATTTAATCATTTTGGTAAAATGAAAAAAGAAAAG
189 TTTAGACATCA-TAAAGAGACCAAAACAAAAATTTAATCATTTTGGTAAAATCAAAAAAGAAAAA
13080672 AAAAGAAA
253 AAAAGAAA
13080680 GAGAGCATGG
Statistics
Matches: 217, Mismatches: 35, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
285 12 0.06
286 7 0.03
287 8 0.04
288 152 0.70
289 34 0.16
290 4 0.02
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.29
Consensus pattern (285 bp):
GCAAACCTAAAAGAATAAAAAGCTAAGCAGTCATCTCTAAGACCCTTAAGGAATTTAAATTATAT
ATAACCACACAATATTTTAATTGAAAAATTAACGATATTAACTATTTGAACTAACTAATAACATT
ATAAAAATATAGAGACCAAATTATATTAGAAATTAAAGTCATGAAATTAAATATAAAATTTAGAC
ATCATAAAGAGACCAAAACAAAAATTTAATCATTTTGGTAAAATCAAAAAAGAAAAAAAAAGAAA
AGAAAAGAGATAAGGTAAGACCTAT
Found at i:13082577 original size:62 final size:62
Alignment explanation
Indices: 13082506--13082630 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
13082496 AATATCATAG
* *
13082506 AAAATTTCTTAAATTTAACTATTAATCTAATGTCTTTATGCAAAAACATTAAAACCAAAGAT
1 AAAATTTCTTAAATTAAACTATTAACCTAATGTCTTTATGCAAAAACATTAAAACCAAAGAT
* * *
13082568 AAAATTTCTTAAATTAAACTATTAACCTAATGTCTTTATGCAAAAACTTTAAGAGCAAAGAT
1 AAAATTTCTTAAATTAAACTATTAACCTAATGTCTTTATGCAAAAACATTAAAACCAAAGAT
13082630 A
1 A
13082631 GAACGGCGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.34
Consensus pattern (62 bp):
AAAATTTCTTAAATTAAACTATTAACCTAATGTCTTTATGCAAAAACATTAAAACCAAAGAT
Found at i:13083144 original size:25 final size:26
Alignment explanation
Indices: 13083116--13083174 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 26
13083106 AACTAAATAT
*
13083116 ACTAGT-TTAAATATTTATTTAGGAA
1 ACTAGTGTTAAATAATTATTTAGGAA
*
13083141 ACTAGTTGTGTTAAATAATTATTTAGTAA
1 ACTA---GTGTTAAATAATTATTTAGGAA
13083170 ACTAG
1 ACTAG
13083175 ATGAAGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
25 4 0.14
26 1 0.04
28 2 0.07
29 21 0.75
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (26 bp):
ACTAGTGTTAAATAATTATTTAGGAA
Found at i:13086136 original size:31 final size:31
Alignment explanation
Indices: 13086095--13086156 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
13086085 AGATAATTTT
13086095 AAAGAATTTTATTAAGATTCAATTACTCTTG
1 AAAGAATTTTATTAAGATTCAATTACTCTTG
* *
13086126 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAATTTTATTAAGATTCAATTACTCTTG
13086157 TAATTTGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (31 bp):
AAAGAATTTTATTAAGATTCAATTACTCTTG
Found at i:13086738 original size:12 final size:12
Alignment explanation
Indices: 13086723--13086764 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
13086713 AAGAAGAAGC
13086723 AAAAAGCGCAAA
1 AAAAAGCGCAAA
13086735 AAAAAGCGCAAAA
1 AAAAAGCGC-AAA
*
13086748 AAAAACCGCAAA
1 AAAAAGCGCAAA
13086760 AAAAA
1 AAAAA
13086765 AGTTGCCTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.71, C:0.17, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGCGCAAA
Found at i:13086739 original size:13 final size:13
Alignment explanation
Indices: 13086723--13086766 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
13086713 AAGAAGAAGC
13086723 AAAAAGCGC-AAA
1 AAAAAGCGCAAAA
13086735 AAAAAGCGCAAAA
1 AAAAAGCGCAAAA
*
13086748 AAAAACCGCAAAA
1 AAAAAGCGCAAAA
13086761 AAAAAG
1 AAAAAG
13086767 TTGCCTACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 9 0.31
13 20 0.69
ACGTcount: A:0.70, C:0.16, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAGCGCAAAA
Found at i:13093263 original size:15 final size:15
Alignment explanation
Indices: 13093245--13093279 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
13093235 TACAAATGCC
13093245 ACAATAATAAATACA
1 ACAATAATAAATACA
13093260 ACAATAATAAATACA
1 ACAATAATAAATACA
*
13093275 TCAAT
1 ACAAT
13093280 GGCATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (15 bp):
ACAATAATAAATACA
Found at i:13094276 original size:7 final size:7
Alignment explanation
Indices: 13094264--13094308 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
13094254 CCGGTCATCA
13094264 GGCCACC
1 GGCCACC
13094271 GGCCACC
1 GGCCACC
13094278 GGCCACC
1 GGCCACC
*
13094285 AGCCACC
1 GGCCACC
*
13094292 GACCACC
1 GGCCACC
13094299 GGCCACC
1 GGCCACC
13094306 GGC
1 GGC
13094309 GACGGTGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.18, C:0.56, G:0.27, T:0.00
Consensus pattern (7 bp):
GGCCACC
Found at i:13095746 original size:267 final size:267
Alignment explanation
Indices: 13095391--13095934 Score: 793
Period size: 267 Copynumber: 2.0 Consensus size: 267
13095381 GATTTGTCAT
* *
13095391 TTGCAATGTCGGGGAAACAAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAGGGA
1 TTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTACAACGCCAGGGA
* *
13095456 AGTAAGAGTCACCGTTGTGGTTTCAATCTACTCCACTGTAATGCTAAAGAGATAGAATTCGCTGC
66 AGTAAGAGTCACCGTCGTGGTTTCAATCTACTCCACCGTAATGCTAAAGAGATAGAATTCGCTGC
* * *
13095521 CCACAACTTTAA-TCTGCTCCACTTCAGCTAATCCAAGCCTTAACGCTAGGGAGATAAGATTTGC
131 CCACAACCTTAATTC-GCTCCACTTCAGCTAATCCAAGCCTTAACGCTAAGGAGATAAGATTCGC
*
13095585 CACCGTGGCTTCAATTTGCTCCGCTACAACGCCAGGGAAGTAAGACTCGCCGTCGCGGCTTCAGT
195 CACCGTGGCTTCAATTTGCTCCGCTACAACGCCAGGGAAATAAGACTCGCCGTCGCGGCTTCAGT
13095650 CTTTTAAA
260 CTTTTAAA
* * * * * * *
13095658 TTGCAATGTTGGGGAAACAAGATTCGCTGTCGTAGCTTCAGTCTGTTCCACTACACCGTCAGGGG
1 TTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTACAACGCCAGGGA
* * * *
13095723 AGTAAGATTCACCGTCGTGGTTTCAATCTGCTCGACCGTAATGCTAAAGAGATAGGATTCGCTGC
66 AGTAAGAGTCACCGTCGTGGTTTCAATCTACTCCACCGTAATGCTAAAGAGATAGAATTCGCTGC
*
13095788 CCACAGCCTTAATTCGCTCCACTTCAGCTAATCCAAGCCTTAACGCTAAGGAGATAAGATTCGCC
131 CCACAACCTTAATTCGCTCCACTTCAGCTAATCCAAGCCTTAACGCTAAGGAGATAAGATTCGCC
** * * * * * * *
13095853 GTCGTGGCTTCAATTTGCTCCGCTACAATGCCAGGGAAATAAGATTCGCCATTGTGGCTTTAATC
196 ACCGTGGCTTCAATTTGCTCCGCTACAACGCCAGGGAAATAAGACTCGCCGTCGCGGCTTCAGTC
**
13095918 TTTTCCA
261 TTTTAAA
13095925 TTGCAATGTC
1 TTGCAATGTC
13095935 AAGACGATAA
Statistics
Matches: 244, Mismatches: 32, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
267 242 0.99
268 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (267 bp):
TTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTACAACGCCAGGGA
AGTAAGAGTCACCGTCGTGGTTTCAATCTACTCCACCGTAATGCTAAAGAGATAGAATTCGCTGC
CCACAACCTTAATTCGCTCCACTTCAGCTAATCCAAGCCTTAACGCTAAGGAGATAAGATTCGCC
ACCGTGGCTTCAATTTGCTCCGCTACAACGCCAGGGAAATAAGACTCGCCGTCGCGGCTTCAGTC
TTTTAAA
Found at i:13107004 original size:15 final size:15
Alignment explanation
Indices: 13106986--13107020 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
13106976 TACAAATGCC
13106986 ACAATAATAAATACA
1 ACAATAATAAATACA
*
13107001 ACAATAATATATACA
1 ACAATAATAAATACA
*
13107016 TCAAT
1 ACAAT
13107021 GGCATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (15 bp):
ACAATAATAAATACA
Found at i:13112085 original size:436 final size:435
Alignment explanation
Indices: 13111273--13112545 Score: 2110
Period size: 436 Copynumber: 2.9 Consensus size: 435
13111263 ATTGATTAAG
* * * * * **
13111273 AGCTTATTCAGAGATTTGGGAATTATGGCACTTGATATCTAAATTTAGTAGATGGGTAAGGTATG
1 AGCTTATTAAGAGATTTGAGAATTATGGCACTCGATATCTAGATTCAGTAGATGGGTCGGGTATG
* * *
13111338 GGGTGATACACATATAACCATTTCTTTACAATTTAGTCTATATCTCACCCTTTTTTACCAAATTG
66 GGGTGGTACACATATAACCATTTCTTCACAATTTAGTCTATATCTCACCCTATTTTACCAAATTG
*
13111403 TAAACAATTCAAATTACACTTAGACACAAAAAAATTCGTAATTCAAACATATATACATTACATTA
131 TAAACAATTCAAATTACACTTAGACACAAACAAATTC-TAATTCAAACATATATACATTACATTA
* * *
13111468 CATATAACTACACCATATGAACTTACATGATTAAATGAGTTAAA-AAGTTGAATCGCCAGGACTA
195 CATATAACTACACCATATGAACTTACATGATTAAATGAG-CAAACAAGTTGAATCACCAGAACTA
* *
13111532 ATGGGTAATTTTGTCTTTTCCCTAGTTATCCTCGGTTTAGTTTAATTCTTGATCTATATAATAAT
259 ATGGGTAATTTTGTCTTTTTCCTAGTTATCCTCGGTTCAGTTTAATTCTTGATCTATATAATAAT
*
13111597 TCATTTCAATTTATCAATTCCAAATAACTTATATTC-TCCTATTATATGCATATGTTAAGTCAAT
324 TCATTTCAATTTATCAATTCCAAATAACTTATA-TCATCCTATTATATGCATATGTTAATTCAAT
*
13111661 TTCATCTTTATAATGCCCCCTATTCATTTCAATTTATCAATTCCAAAT
388 TTCATCTTTATAATGCCCCCTATTCATTTCAATTTATCAAATCCAAAT
* *
13111709 AGCTTATTAAGAGATTTGAGAATTGTGGCACTCGATATCCAGATTCAGTAGATGGGTCGGGTATG
1 AGCTTATTAAGAGATTTGAGAATTATGGCACTCGATATCTAGATTCAGTAGATGGGTCGGGTATG
*
13111774 GGGTGGTACACATATAACCATTTCTTCATAATTTAGTCTATATCTCACCCTATTTTACCAAATTG
66 GGGTGGTACACATATAACCATTTCTTCACAATTTAGTCTATATCTCACCCTATTTTACCAAATTG
* *
13111839 TAAATAATTCAAATTACACTTAGACATAAACAAATTCATAATTCAAACATATATACATTACATTA
131 TAAACAATTCAAATTACACTTAGACACAAACAAATTC-TAATTCAAACATATATACATTACATTA
*
13111904 CATATAACTAGACCATATGAACTTACATGATTAAATGAGCAAACAAGTTGAATCACCAGAACTAA
195 CATATAACTACACCATATGAACTTACATGATTAAATGAGCAAACAAGTTGAATCACCAGAACTAA
* *
13111969 TGGGTAATTTTGTCTTTTTCCTAGTTATCCTTGGTTCAGTTTAATTCTTGATCTATGTAATAATT
260 TGGGTAATTTTGTCTTTTTCCTAGTTATCCTCGGTTCAGTTTAATTCTTGATCTATATAATAATT
* *
13112034 CATTTGAATTTATCAATTCCAAATAACTTATATCATCCTATTAGATGCATATGTTAATTCAATTT
325 CATTTCAATTTATCAATTCCAAATAACTTATATCATCCTATTATATGCATATGTTAATTCAATTT
13112099 CATCTTTATAATGCCCCCTATTCATTTCAATTTATCAAATCCAAAT
390 CATCTTTATAATGCCCCCTATTCATTTCAATTTATCAAATCCAAAT
* * *
13112145 AGCTTATTAAGAGGTTTGAGAATTCTGGCACTCGATATCTAGATTCAGTAGACGGGTCGGGTATG
1 AGCTTATTAAGAGATTTGAGAATTATGGCACTCGATATCTAGATTCAGTAGATGGGTCGGGTATG
13112210 GGGTGGTACACATATAACCATTTCTTCACAATTTAGTCTATATCTCACCCTATTTTACCAAATTG
66 GGGTGGTACACATATAACCATTTCTTCACAATTTAGTCTATATCTCACCCTATTTTACCAAATTG
*
13112275 TAAACAACTCAAATTACACTTAGACACAAACAAATTC----TCAAACATATATACATTACATTAC
131 TAAACAATTCAAATTACACTTAGACACAAACAAATTCTAATTCAAACATATATACATTACATTAC
* *
13112336 ATATAACTACACCATATGAACTTACATGATTAAGTGGGCAAACAAGTTGAATCACCAGAACTAAT
196 ATATAACTACACCATATGAACTTACATGATTAAATGAGCAAACAAGTTGAATCACCAGAACTAAT
13112401 GGGTAATTTTGTC-TTTTCCTTAGTTATCCTCGGTTCAGTTTAATTCTTGATCTATATAATAATT
261 GGGTAATTTTGTCTTTTTCC-TAGTTATCCTCGGTTCAGTTTAATTCTTGATCTATATAATAATT
* * * *
13112465 GATTTTAATTTATTAATTCCAAATAACTTATATCATCCTTTTATATGCATATGTTAATTCAATTT
325 CATTTCAATTTATCAATTCCAAATAACTTATATCATCCTATTATATGCATATGTTAATTCAATTT
13112530 CATCTTTATAATGCCC
390 CATCTTTATAATGCCC
13112546 TCTAAAGTTT
Statistics
Matches: 787, Mismatches: 47, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
430 6 0.01
431 217 0.28
435 5 0.01
436 559 0.71
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (435 bp):
AGCTTATTAAGAGATTTGAGAATTATGGCACTCGATATCTAGATTCAGTAGATGGGTCGGGTATG
GGGTGGTACACATATAACCATTTCTTCACAATTTAGTCTATATCTCACCCTATTTTACCAAATTG
TAAACAATTCAAATTACACTTAGACACAAACAAATTCTAATTCAAACATATATACATTACATTAC
ATATAACTACACCATATGAACTTACATGATTAAATGAGCAAACAAGTTGAATCACCAGAACTAAT
GGGTAATTTTGTCTTTTTCCTAGTTATCCTCGGTTCAGTTTAATTCTTGATCTATATAATAATTC
ATTTCAATTTATCAATTCCAAATAACTTATATCATCCTATTATATGCATATGTTAATTCAATTTC
ATCTTTATAATGCCCCCTATTCATTTCAATTTATCAAATCCAAAT
Found at i:13114944 original size:20 final size:20
Alignment explanation
Indices: 13114919--13114961 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
13114909 ACATCATTCA
13114919 CAATAGTAGAATTCATAACC
1 CAATAGTAGAATTCATAACC
13114939 CAATAGTAGAATTCATAACC
1 CAATAGTAGAATTCATAACC
13114959 CAA
1 CAA
13114962 GTAAACGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (20 bp):
CAATAGTAGAATTCATAACC
Found at i:13119932 original size:58 final size:58
Alignment explanation
Indices: 13119796--13119932 Score: 202
Period size: 58 Copynumber: 2.4 Consensus size: 58
13119786 TGGTAAAGGA
* **
13119796 GTAAGACCATGGATGAAAGACGCAATGGCAGCAAGGTAAAAGGTATAAGGTATACAAT
1 GTAAGACCATAGATGAAAGATACAATGGCAGCAAGGTAAAAGGTATAAGGTATACAAT
** * **
13119854 GTAAGACCATAGATGAAAGATACAATGGTGGCAAGGTAAAAGGTCTAAGGTATACGGT
1 GTAAGACCATAGATGAAAGATACAATGGCAGCAAGGTAAAAGGTATAAGGTATACAAT
13119912 GTAAGACCATAGATGAAAGAT
1 GTAAGACCATAGATGAAAGAT
13119933 GCTATAGTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 71 1.00
ACGTcount: A:0.42, C:0.11, G:0.28, T:0.19
Consensus pattern (58 bp):
GTAAGACCATAGATGAAAGATACAATGGCAGCAAGGTAAAAGGTATAAGGTATACAAT
Found at i:13121593 original size:16 final size:16
Alignment explanation
Indices: 13121572--13121609 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
13121562 ATGATTACTG
13121572 ATTTTATTTTTAGAAT
1 ATTTTATTTTTAGAAT
*
13121588 ATTTTA-TTTTAGACT
1 ATTTTATTTTTAGAAT
13121603 ATTTTAT
1 ATTTTAT
13121610 AGCTACCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (16 bp):
ATTTTATTTTTAGAAT
Found at i:13129901 original size:15 final size:15
Alignment explanation
Indices: 13129881--13129914 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
13129871 ATTGATAATG
13129881 TTCTTAGCAAATTCT
1 TTCTTAGCAAATTCT
*
13129896 TTCTTAGCAACTTCT
1 TTCTTAGCAAATTCT
13129911 TTCT
1 TTCT
13129915 CAGTATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.06, T:0.50
Consensus pattern (15 bp):
TTCTTAGCAAATTCT
Found at i:13144097 original size:78 final size:78
Alignment explanation
Indices: 13143967--13144121 Score: 247
Period size: 78 Copynumber: 2.0 Consensus size: 78
13143957 TTGTCGCACT
* * * * *
13143967 GCAATTAGGCTCTGCCCTCGCACGTGCGCCACCGACTCCATGCCACGTGCCTCCAGCTGGTCTCT
1 GCAATCAGGCTCTGCCCTCACACGTGAGCCACCGACTCCACGCCACGCGCCTCCAGCTGGTCTCT
13144032 GCGCCATGCCACC
66 GCGCCATGCCACC
* *
13144045 GCAATCAGGCTCTGCCCTCACATGTGAGCCACCGACTCTACGCCACGCGCCTCCAGCTGGTCTCT
1 GCAATCAGGCTCTGCCCTCACACGTGAGCCACCGACTCCACGCCACGCGCCTCCAGCTGGTCTCT
13144110 GCGCCATGCCAC
66 GCGCCATGCCAC
13144122 GTCACTATAG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.15, C:0.43, G:0.23, T:0.19
Consensus pattern (78 bp):
GCAATCAGGCTCTGCCCTCACACGTGAGCCACCGACTCCACGCCACGCGCCTCCAGCTGGTCTCT
GCGCCATGCCACC
Found at i:13144604 original size:7 final size:8
Alignment explanation
Indices: 13144587--13144621 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
13144577 ATTTTACCCC
13144587 TTTTTATT
1 TTTTTATT
13144595 TTTTTA-T
1 TTTTTATT
13144602 TTTTTATT
1 TTTTTATT
13144610 TTTTTATT
1 TTTTTATT
13144618 TTTT
1 TTTT
13144622 GTTGATGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:13144605 original size:15 final size:15
Alignment explanation
Indices: 13144587--13144621 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
13144577 ATTTTACCCC
13144587 TTTTTATTTTTTTAT
1 TTTTTATTTTTTTAT
13144602 TTTTTATTTTTTTAT
1 TTTTTATTTTTTTAT
13144617 TTTTT
1 TTTTT
13144622 GTTGATGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTATTTTTTTAT
Found at i:13145087 original size:11 final size:14
Alignment explanation
Indices: 13145054--13145092 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
13145044 CTATTCAGAA
13145054 TATTATTATTAATC
1 TATTATTATTAATC
*
13145068 TATTATTATTAATT
1 TATTATTATTAATC
*
13145082 TTTTATTATTA
1 TATTATTATTA
13145093 TCACCATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATTATTAATC
Found at i:13149938 original size:29 final size:29
Alignment explanation
Indices: 13149896--13149956 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
13149886 CTAATCCCAA
*
13149896 AAAAAAAAAGAAAAATCAAGATCAAAAAC
1 AAAAAAAAAGAAAAATCAAAATCAAAAAC
* *
13149925 AAAAAAGAAGAAAAATCAAAATCAAAATC
1 AAAAAAAAAGAAAAATCAAAATCAAAAAC
13149954 AAA
1 AAA
13149957 GTCAAAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.75, C:0.10, G:0.07, T:0.08
Consensus pattern (29 bp):
AAAAAAAAAGAAAAATCAAAATCAAAAAC
Found at i:13149942 original size:23 final size:25
Alignment explanation
Indices: 13149893--13149951 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
13149883 AATCTAATCC
13149893 CAAAAA-AAAAAAGAAAAATCAAGAT
1 CAAAAACAAAAAAGAAAAA-CAAGAT
*
13149918 CAAAAACAAAAAAGAAGAA-AA-AT
1 CAAAAACAAAAAAGAAAAACAAGAT
*
13149941 CAAAATCAAAA
1 CAAAAACAAAA
13149952 TCAAAGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 12 0.39
24 2 0.06
25 6 0.19
26 11 0.35
ACGTcount: A:0.76, C:0.10, G:0.07, T:0.07
Consensus pattern (25 bp):
CAAAAACAAAAAAGAAAAACAAGAT
Found at i:13149945 original size:6 final size:6
Alignment explanation
Indices: 13149936--13149975 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
13149926 AAAAAGAAGA
* * *
13149936 AAAATC AAAATC AAAATC AAAGTC AAAATG AAAATG AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
13149976 AAGAGAGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.68, C:0.10, G:0.07, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:13152302 original size:128 final size:128
Alignment explanation
Indices: 13152065--13152684 Score: 931
Period size: 129 Copynumber: 4.8 Consensus size: 128
13152055 GTGAAATCAT
* * *
13152065 AAGTCCTATATCCTTGGTCAGCGGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAG
1 AAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAA
* ** * * *
13152130 TAGCTGAGCAGATATAA-AGCAGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCAC
66 TAGCAGAGCAGATCGAAGA-CGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
*
13152193 AAGTTCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAA
1 AAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAA
* *
13152258 TAGCAGAGCAGATCGAAGATGGCGAATCTTATCTTCAAGTGTAAGGAAGAAGATTTAAGCCAC
66 TAGCAGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
* *
13152321 AAGTCCTATATCCCTGGTTAGCAGTGGAATAGGTTGGGAAATTACAGATATTGTCTCCCTAAGCA
1 AAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAAGCA
* *
13152386 GTAGC-GAAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGTAGATTTAAGCCAC
65 ATAGCAG-AGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
* * *
13152450 AAGTCCTATACCCCTGGTCAACAGTGGAATAGGTTGGGAAATGACAGATCTTGTCTCCCTAAGCA
1 AAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAAGCA
* * *
13152515 ATAGCGGAGCAGATCGAGGATGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
65 ATAGCAGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
* * *
13152579 AAGTCCTATATCCCTGGTCAGCAGTGGAA-AGGGCTGGGAAATTACAGATATTGTCACCCTAAGC
1 AAGTCCTATATCCCTGGTCAGCAGTGGAATA-GG-TTGGAAATTACAGATCTTGTCTCCCTAAGC
*
13152643 AATAGCAGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGT
64 AATAGCAGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGT
13152685 TTGCAGTAGA
Statistics
Matches: 449, Mismatches: 37, Indels: 11
0.90 0.07 0.02
Matches are distributed among these distances:
128 149 0.33
129 298 0.66
130 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (128 bp):
AAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAA
TAGCAGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
Found at i:13152818 original size:45 final size:44
Alignment explanation
Indices: 13152754--13152872 Score: 129
Period size: 43 Copynumber: 2.7 Consensus size: 44
13152744 AGTAAGCAGG
* * *
13152754 TCTTATCCCCCTGAAGTTGCAGTGGGA-CAGATCGAAGATGGCA-AA
1 TCTTATCTCCCTGAGGTTGCAGTGGGAGCAGA-AGAAGAT-G-ATAA
* *
13152799 TCTTATCTCCTTGAGGTTGCAGT-GGAGCAGAAGAAGCTGATAA
1 TCTTATCTCCCTGAGGTTGCAGTGGGAGCAGAAGAAGATGATAA
*
13152842 TCCTATCTCCCTGAGGTTGCAGT-GGAGCAGA
1 TCTTATCTCCCTGAGGTTGCAGTGGGAGCAGA
13152873 CTGAGAAAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
42 1 0.02
43 32 0.49
44 8 0.12
45 24 0.37
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTGAGGTTGCAGTGGGAGCAGAAGAAGATGATAA
Found at i:13152889 original size:132 final size:132
Alignment explanation
Indices: 13152713--13153000 Score: 366
Period size: 132 Copynumber: 2.2 Consensus size: 132
13152703 CATTAGGTCT
* * * * * **
13152713 TATCTCCCTGAGGTTGCAGCGGAGTAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTG
1 TATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTG
* * * * *
13152778 GGACAGATCGAAGATGGCAAATCTTATC-TCCTTGAGGTTGCAGTGGAGCAGA-AGAAG-CTGAT
66 GGACAGACCGAAGA-AGCAAATATTATCTTCC-CGAGGTTGCAGTGGAACAGATAGAAGTC-GAT
13152840 AATCC
128 AATCC
13152845 TATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTG
1 TATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTG
* * * *
13152910 GGGCAGACCGAAGAAGCAAATATTATCTTCCCGAGGTTGTAGTGGAATAGATTGAAGTCGATAAT
66 GGACAGACCGAAGAAGCAAATATTATCTTCCCGAGGTTGCAGTGGAACAGATAGAAGTCGATAAT
13152975 CC
131 CC
* *
13152977 TATCTCCCTGAAGTTACAGTGGAG
1 TATCTCCCTGAGGTTGCAGTGGAG
13153001 TGGATTAAAA
Statistics
Matches: 135, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
131 27 0.20
132 107 0.79
133 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (132 bp):
TATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTG
GGACAGACCGAAGAAGCAAATATTATCTTCCCGAGGTTGCAGTGGAACAGATAGAAGTCGATAAT
CC
Found at i:13154570 original size:14 final size:14
Alignment explanation
Indices: 13154551--13154589 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
13154541 TATTCAGTAA
13154551 TATTATTATTAATC
1 TATTATTATTAATC
*
13154565 TATTATTATTAATT
1 TATTATTATTAATC
13154579 TATTATTATTA
1 TATTATTATTA
13154590 TCACCATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTATTAATC
Found at i:13154573 original size:17 final size:17
Alignment explanation
Indices: 13154551--13154590 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
13154541 TATTCAGTAA
13154551 TATTATT-ATTAATCTAT
1 TATTATTAATTAAT-TAT
*
13154568 TATTATTAATTTATTAT
1 TATTATTAATTAATTAT
13154585 TATTAT
1 TATTAT
13154591 CACCATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTAATTAATTAT
Found at i:13155079 original size:280 final size:274
Alignment explanation
Indices: 13154576--13155113 Score: 988
Period size: 280 Copynumber: 1.9 Consensus size: 274
13154566 ATTATTATTA
13154576 ATTTATTATTATTATCACCATTATTACTACTGATATTATTATTGATATTGTTATTATATTAAATT
1 ATTTATTATTATTATCACCATTATTACTACTGATATTATTATTGATATTGTTATTATATTAAATT
*
13154641 TAATTGCCATTATTTACGTATATAAATTATTTTATGTTATTATGTAATATTATTTTAGGTTTTTA
66 TAATTGCCATTATTTACGTATATAAATTATTTTATGTTATCATGTAATATTATTTTAGGTTTTTA
13154706 ATATTTTTATACAATACTATTTTATATCTATATACAACTTATATTAAATCATTTTATTAAAACAT
131 ATATTTTTATACAATACTATTTTATATCTATATACAACTTATATTAAATCATTTTATTAAAACAT
13154771 ATACGAGTATATAATACATTATTACATCATTTTATTTATCTATACATATATATAATTTATTTTTT
196 ATACGAGTATATAATACATTATTACATCATTTTATTTATCTATACATATATATAATTTATTTTTT
13154836 AGGACCCTATTTTT
261 AGGACCCTATTTTT
*
13154850 ATTTTTTATTATTATCA-CATTATTACTACTGATATTATTATTGATATTGTTATTATATTAGTTT
1 ATTTATTATTATTATCACCATTATTACTACTGATATTATTATTGATATTGTTATTATATTA----
13154914 GTATATTTAATTGCCATTATTTACGTATATAAATTATTTTATGTTATCATGTAATATTATTTTAG
62 --A-ATTTAATTGCCATTATTTACGTATATAAATTATTTTATGTTATCATGTAATATTATTTTAG
13154979 GTTTTTAATATTTTTATACAATACTATTTTATATCTATATACAACTTATATTAAATCATTTTATT
124 GTTTTTAATATTTTTATACAATACTATTTTATATCTATATACAACTTATATTAAATCATTTTATT
13155044 AAAACATATACGAGTATATAATACATTATTACATCATTTTATTTATCTATACATATATATAATTT
189 AAAACATATACGAGTATATAATACATTATTACATCATTTTATTTATCTATACATATATATAATTT
13155109 ATTTT
254 ATTTT
13155114 GTTTATTTCA
Statistics
Matches: 255, Mismatches: 2, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
273 43 0.17
274 16 0.06
279 1 0.00
280 195 0.76
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (274 bp):
ATTTATTATTATTATCACCATTATTACTACTGATATTATTATTGATATTGTTATTATATTAAATT
TAATTGCCATTATTTACGTATATAAATTATTTTATGTTATCATGTAATATTATTTTAGGTTTTTA
ATATTTTTATACAATACTATTTTATATCTATATACAACTTATATTAAATCATTTTATTAAAACAT
ATACGAGTATATAATACATTATTACATCATTTTATTTATCTATACATATATATAATTTATTTTTT
AGGACCCTATTTTT
Found at i:13160447 original size:13 final size:14
Alignment explanation
Indices: 13160429--13160457 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13160419 TCTTTTATCT
13160429 TTCTTTT-CTTTAA
1 TTCTTTTACTTTAA
13160442 TTCTTTTACTTTAA
1 TTCTTTTACTTTAA
13160456 TT
1 TT
13160458 ATAATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTCTTTTACTTTAA
Found at i:13165542 original size:44 final size:44
Alignment explanation
Indices: 13165437--13165542 Score: 108
Period size: 45 Copynumber: 2.4 Consensus size: 44
13165427 TAATGAATAG
* * **
13165437 AAATAGAGAAATGGAAAACATTTAGAAATGTTACGATTTTCTCTG
1 AAAT-GAGAAATGGAAATCATTTAGAAATGATACGATTTTCTCAA
** *
13165482 AAATGGAGAAAT-GAAATCATTTAGAAATGAATGTGGTTTTCTCAA
1 AAAT-GAGAAATGGAAATCATTTAGAAATG-ATACGATTTTCTCAA
13165527 AAAT-AGAAATGGAAAT
1 AAATGAGAAATGGAAAT
13165543 GAAAATGAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
43 6 0.12
44 21 0.41
45 24 0.47
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (44 bp):
AAATGAGAAATGGAAATCATTTAGAAATGATACGATTTTCTCAA
Found at i:13167984 original size:47 final size:48
Alignment explanation
Indices: 13167821--13168007 Score: 232
Period size: 50 Copynumber: 3.8 Consensus size: 48
13167811 GGCAGTGAGT
* * *
13167821 GTGCCAGTGTAAGACCATGTCTGGGACATCGCATCGGCACAGACCGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA--GATGA
* * *
13167871 GTGCTAGTTTAAGACCACGTCTGGGTCATGGCATCGGCACGAGCAGATGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-AG-AGATGA
* * * *
13167921 GAGTTAGTGTAAGACCATGTCTGGGACATGGCATTGGCTCA-AGATGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAGATGA
*
13167968 GTGCTAGTGTAAGACCATGTCTGGGACATGGAATCGGCAC
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC
13168008 CGATATACGA
Statistics
Matches: 117, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
47 41 0.35
49 1 0.01
50 72 0.62
51 2 0.02
52 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (48 bp):
GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAGATGA
Found at i:13167998 original size:97 final size:99
Alignment explanation
Indices: 13167826--13168007 Score: 269
Period size: 97 Copynumber: 1.8 Consensus size: 99
13167816 TGAGTGTGCC
*
13167826 AGTGTAAGACCATGTCTGGGACATCGCATCGGCACAGACCGAGGAGTGCTAGTTTAAGACCACGT
1 AGTGTAAGACCATGTCTGGGACATCGCATCGGCACAGA-CGAGGAGTGCTAGTGTAAGACCACGT
* *
13167891 CTGGGTCATGGCATCGGCACGAGCAGATGAGAGTT
65 CTGGGACATGGAATCGGCACGAGCAGATGAGAGTT
* * * * *
13167926 AGTGTAAGACCATGTCTGGGACATGGCATTGGCTCA-A-GATGAGTGCTAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATCGCATCGGCACAGACGAGGAGTGCTAGTGTAAGACCACGTC
13167989 TGGGACATGGAATCGGCAC
66 TGGGACATGGAATCGGCAC
13168008 CGATATACGA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
97 40 0.54
99 1 0.01
100 33 0.45
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.21
Consensus pattern (99 bp):
AGTGTAAGACCATGTCTGGGACATCGCATCGGCACAGACGAGGAGTGCTAGTGTAAGACCACGTC
TGGGACATGGAATCGGCACGAGCAGATGAGAGTT
Found at i:13169636 original size:141 final size:141
Alignment explanation
Indices: 13169382--13169640 Score: 518
Period size: 141 Copynumber: 1.8 Consensus size: 141
13169372 TGTGTATGCA
13169382 AAATGGATACAGGAGAGTTTGTGTTTTAGAGTGGGGAATTGGCTTGGAAAATAGCCAACTTCCAA
1 AAATGGATACAGGAGAGTTTGTGTTTTAGAGTGGGGAATTGGCTTGGAAAATAGCCAACTTCCAA
13169447 ACCACACGAGTGTGTGACCCCTGTTTTGACAAAAATTTTCTAAATTTTTCCAATTATAGTATGAT
66 ACCACACGAGTGTGTGACCCCTGTTTTGACAAAAATTTTCTAAATTTTTCCAATTATAGTATGAT
13169512 ACATGTTGATG
131 ACATGTTGATG
13169523 AAATGGATACAGGAGAGTTTGTGTTTTAGAGTGGGGAATTGGCTTGGAAAATAGCCAACTTCCAA
1 AAATGGATACAGGAGAGTTTGTGTTTTAGAGTGGGGAATTGGCTTGGAAAATAGCCAACTTCCAA
13169588 ACCACACGAGTGTGTGACCCCTGTTTTGACAAAAATTTTCTAAATTTTTCCAA
66 ACCACACGAGTGTGTGACCCCTGTTTTGACAAAAATTTTCTAAATTTTTCCAA
13169641 GTGTTTCCAA
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 118 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (141 bp):
AAATGGATACAGGAGAGTTTGTGTTTTAGAGTGGGGAATTGGCTTGGAAAATAGCCAACTTCCAA
ACCACACGAGTGTGTGACCCCTGTTTTGACAAAAATTTTCTAAATTTTTCCAATTATAGTATGAT
ACATGTTGATG
Found at i:13173879 original size:50 final size:50
Alignment explanation
Indices: 13173800--13174081 Score: 306
Period size: 50 Copynumber: 5.7 Consensus size: 50
13173790 TGAGTGTGCC
* *
13173800 AGTGTAAGACCATGTCTGGGACATCGCATCGGCACAGACCGAGGAATGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGAATGCT
* * * *
13173850 AGTGTAAGAGCATGTCTGGGACATGGCATCGACACGGATAGAGGAGA-G-T
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGA-ATGCT
* * * * * *
13173899 CAGTGTAAGACCATGTCTGGGACATGACATCTGCTC-G--AGATGAGTGCC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGAATGCT
* * *
13173947 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGACCGAGGAGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGAATGCT
* ** * *
13173997 AGTGTAAGACCATGTCTGGGACATGGCATCGACATGGGCAGAGGAGA-GCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGA-ATGCT
*
13174047 AGTGTAAGACCATGTCTGGGACATGGAATCGGCAC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC
13174082 CGATATACGA
Statistics
Matches: 194, Mismatches: 30, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
47 37 0.19
48 1 0.01
49 2 0.01
50 153 0.79
51 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.19
Consensus pattern (50 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGAATGCT
Found at i:13174062 original size:147 final size:147
Alignment explanation
Indices: 13173795--13174071 Score: 482
Period size: 147 Copynumber: 1.9 Consensus size: 147
13173785 GGCAGTGAGT
*
13173795 GTGCCAGTGTAAGACCATGTCTGGGACATCGCATCGGCACAGACCGAGGAATGCTAGTGTAAGAG
1 GTGCCAGTGTAAGACCATGTCTGGGACATCGCATCGGCACAGACCGAGGAATGCTAGTGTAAGAC
* *
13173860 CATGTCTGGGACATGGCATCGACACGGATAGAGGAGAGTCAGTGTAAGACCATGTCTGGGACATG
66 CATGTCTGGGACATGGCATCGACACGGACAGAGGAGAGCCAGTGTAAGACCATGTCTGGGACATG
13173925 ACATCTGCTCGAGATGA
131 ACATCTGCTCGAGATGA
* * *
13173942 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGACCGAGGAGTGCTAGTGTAAGAC
1 GTGCCAGTGTAAGACCATGTCTGGGACATCGCATCGGCACAGACCGAGGAATGCTAGTGTAAGAC
* *
13174007 CATGTCTGGGACATGGCATCGACATGGGCAGAGGAGAGCCAGTGTAAGACCATGTCTGGGACATG
66 CATGTCTGGGACATGGCATCGACACGGACAGAGGAGAGCCAGTGTAAGACCATGTCTGGGACATG
13174072 GAATCGGCAC
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
147 122 1.00
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.19
Consensus pattern (147 bp):
GTGCCAGTGTAAGACCATGTCTGGGACATCGCATCGGCACAGACCGAGGAATGCTAGTGTAAGAC
CATGTCTGGGACATGGCATCGACACGGACAGAGGAGAGCCAGTGTAAGACCATGTCTGGGACATG
ACATCTGCTCGAGATGA
Found at i:13176657 original size:25 final size:25
Alignment explanation
Indices: 13176629--13176682 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
13176619 TTTTCTTTTC
* *
13176629 TTTT-TCTTTTCATTTTTAGCTTAGG
1 TTTTCTCTTTTC-TTTTTAGATTAGA
13176654 TTTTCTCTTTTCTTTTTAGATTAGA
1 TTTTCTCTTTTCTTTTTAGATTAGA
13176679 TTTT
1 TTTT
13176683 GTTTTTGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (25 bp):
TTTTCTCTTTTCTTTTTAGATTAGA
Found at i:13180001 original size:2 final size:2
Alignment explanation
Indices: 13179994--13180024 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13179984 ACTTATAATA
13179994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13180025 CTTTTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13183190 original size:29 final size:29
Alignment explanation
Indices: 13183156--13183231 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 29
13183146 TGTGTTGGAA
13183156 AGAAAATTAGAGAAGAAAAAGA-TGTTGGG
1 AGAAAATTAGAGAAGAAAAA-ATTGTTGGG
13183185 AGAAAA-TAGGAGAAGAAAAAATTGTTGGG
1 AGAAAATTA-GAGAAGAAAAAATTGTTGGG
13183214 AG-AAATTGAGAGAAGAAA
1 AGAAAATT-AGAGAAGAAA
13183232 TTTTTTTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
28 6 0.14
29 36 0.84
30 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.30, T:0.16
Consensus pattern (29 bp):
AGAAAATTAGAGAAGAAAAAATTGTTGGG
Found at i:13187729 original size:20 final size:18
Alignment explanation
Indices: 13187684--13187731 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 18
13187674 TTAAAAACAA
13187684 TTTAACTTTGATTGAAAAT
1 TTTAAC-TTGATTGAAAAT
13187703 TTCTAACTTGATTGAAATCAT
1 TT-TAACTTGATTGAAA--AT
13187724 TTTAACTT
1 TTTAACTT
13187732 AATTTAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 12 0.46
20 10 0.38
21 4 0.15
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (18 bp):
TTTAACTTGATTGAAAAT
Found at i:13194698 original size:49 final size:49
Alignment explanation
Indices: 13194626--13194724 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
13194616 ATAGTTTGTG
13194626 TATGCTTCTGAGGGTTTCATTAGTTTCTCTTGACCTTAATTTCTTTTTT
1 TATGCTTCTGAGGGTTTCATTAGTTTCTCTTGACCTTAATTTCTTTTTT
13194675 TATGCTTCTGAGGGTTTCATTAGTTTCTCTTGACCTTAATTTCTTTTTT
1 TATGCTTCTGAGGGTTTCATTAGTTTCTCTTGACCTTAATTTCTTTTTT
13194724 T
1 T
13194725 CTTTTTTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.56
Consensus pattern (49 bp):
TATGCTTCTGAGGGTTTCATTAGTTTCTCTTGACCTTAATTTCTTTTTT
Found at i:13194736 original size:6 final size:7
Alignment explanation
Indices: 13194714--13194745 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
13194704 TTGACCTTAA
13194714 TTTCTTTT
1 TTTC-TTT
13194722 TTTCTTT
1 TTTCTTT
13194729 TTTCTTT
1 TTTCTTT
13194736 TTTCTTT
1 TTTCTTT
13194743 TTT
1 TTT
13194746 GAAAATGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTCTTT
Found at i:13202339 original size:50 final size:50
Alignment explanation
Indices: 13202229--13202475 Score: 210
Period size: 50 Copynumber: 4.8 Consensus size: 50
13202219 ATTTGGGTAA
* * * *
13202229 AGAGATCCCATGAAAGACCATGTCTGGGACATTGCATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* *
13202285 AGAGGTACCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
13202335 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
13202385 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * *
13202434 AAACATCTCATGTAAGACCATGCCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
13202476 TGTTATTATC
Statistics
Matches: 159, Mismatches: 31, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 36 0.23
50 81 0.51
52 1 0.01
53 2 0.01
55 1 0.01
56 37 0.23
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:13206985 original size:20 final size:18
Alignment explanation
Indices: 13206943--13206996 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
13206933 TATAGAACGT
* *
13206943 AATCTTCGAAGATATG-C
1 AATCTTAGAAGATATGTA
13206960 AATCTTAGATAAGATATGTA
1 AATCTTAG--AAGATATGTA
13206980 AATCTTAGAAGATATGT
1 AATCTTAGAAGATATGT
13206997 TTCTATGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 7 0.22
18 9 0.28
19 8 0.25
20 8 0.25
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (18 bp):
AATCTTAGAAGATATGTA
Found at i:13217218 original size:15 final size:17
Alignment explanation
Indices: 13217198--13217234 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
13217188 GTCGACCATT
13217198 ATTATAAT-TATGG-TA
1 ATTATAATATATGGTTA
*
13217213 ATTATAATATTTGGTTA
1 ATTATAATATATGGTTA
13217230 ATTAT
1 ATTAT
13217235 TATGATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 4 0.21
17 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (17 bp):
ATTATAATATATGGTTA
Found at i:13221666 original size:15 final size:16
Alignment explanation
Indices: 13221646--13221683 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
13221636 TAGTCTCCTT
13221646 TAGTTTCAC-ATTCTA
1 TAGTTTCACAATTCTA
13221661 TAGTTTTCACAATTCTA
1 TAG-TTTCACAATTCTA
13221678 TAGTTT
1 TAGTTT
13221684 TCAAAGTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 9 0.43
17 9 0.43
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (16 bp):
TAGTTTCACAATTCTA
Found at i:13221670 original size:16 final size:17
Alignment explanation
Indices: 13221649--13221686 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
13221639 TCTCCTTTAG
13221649 TTTCAC-ATTCTATAGT
1 TTTCACAATTCTATAGT
13221665 TTTCACAATTCTATAGT
1 TTTCACAATTCTATAGT
13221682 TTTCA
1 TTTCA
13221687 AAGTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.50
Consensus pattern (17 bp):
TTTCACAATTCTATAGT
Found at i:13223173 original size:20 final size:20
Alignment explanation
Indices: 13223148--13223186 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13223138 CAAATTAATT
*
13223148 AATTAAATAACATTTTATTA
1 AATTAAATAACATTATATTA
13223168 AATTAAATAACATTATATT
1 AATTAAATAACATTATATT
13223187 TCACTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTAAATAACATTATATTA
Found at i:13227223 original size:43 final size:43
Alignment explanation
Indices: 13227174--13227286 Score: 181
Period size: 43 Copynumber: 2.6 Consensus size: 43
13227164 ATGTTCCAAT
*
13227174 ATCGATTTGAGATTTCGTGTAAGACCATAGTTGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
*
13227217 TTCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
* *
13227260 ATCGATATGAGATTTCCATGTAAGACC
1 ATCGATTTGAGATTT-CGTGTAAGACC
13227287 GTGTCTGGGA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
43 54 0.84
44 10 0.16
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (43 bp):
ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
Found at i:13232570 original size:48 final size:48
Alignment explanation
Indices: 13232497--13232590 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 48
13232487 GATTAAATGA
*
13232497 AAAGAAGTAGTAGAAGTACACGTGCTGAGGCCCAATGTTGTAGCATGG
1 AAAGAAGTAGTAGAAGTACACGTGCTGAGGCCCAATGTCGTAGCATGG
*
13232545 AAAGAAGTAGTAGAAGTACATGTGCTGAGGCCCAATGTCGTAGCAT
1 AAAGAAGTAGTAGAAGTACACGTGCTGAGGCCCAATGTCGTAGCAT
13232591 CGGACCAACG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (48 bp):
AAAGAAGTAGTAGAAGTACACGTGCTGAGGCCCAATGTCGTAGCATGG
Found at i:13251183 original size:21 final size:21
Alignment explanation
Indices: 13251141--13251183 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13251131 GGACCCATGC
*
13251141 GTGTTTGTAATTTACTTGGTA
1 GTGTTTGTAATTTACTTCGTA
*
13251162 GTGTTTGTAATTTAGTTCGTA
1 GTGTTTGTAATTTACTTCGTA
13251183 G
1 G
13251184 CCATGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.26, T:0.51
Consensus pattern (21 bp):
GTGTTTGTAATTTACTTCGTA
Found at i:13251269 original size:142 final size:142
Alignment explanation
Indices: 13251009--13251272 Score: 465
Period size: 142 Copynumber: 1.9 Consensus size: 142
13250999 CACTGCTTCT
13251009 TTTACTTAGTAGTGTTTGTAATTTAGCTCGTAGCCATGATTTTCTTGGATGACTAGTGTTGGAGC
1 TTTACTTAGTAGTGTTTGTAATTTAGCTCGTAGCCATGATTTTCTTGGATGACTAGTGTTGGAGC
*
13251074 TTTTCAAGCATAACTATTTCATAGTTTCTTATTTTGCTAATTGGTTTGAGGGAGGACGGACCCAT
66 TTTTCAAGCATAACTATTTCATAGTTTCTTATTTTGCTAACTGGTTTGAGGGAGGACGGACCCAT
13251139 GCGTGTTTGTAA
131 GCGTGTTTGTAA
* * *
13251151 TTTACTTGGTAGTGTTTGTAATTTAGTTCGTAGCCATGATTTTCTTGGATGACTAGTTTTGGAGC
1 TTTACTTAGTAGTGTTTGTAATTTAGCTCGTAGCCATGATTTTCTTGGATGACTAGTGTTGGAGC
* * *
13251216 TTTTCAAGCATAACTATTTCATGGTTTCTTATTTTGGTAACTGGTTTGTGGGAGGAC
66 TTTTCAAGCATAACTATTTCATAGTTTCTTATTTTGCTAACTGGTTTGAGGGAGGAC
13251273 CCATGCATGT
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 115 1.00
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.43
Consensus pattern (142 bp):
TTTACTTAGTAGTGTTTGTAATTTAGCTCGTAGCCATGATTTTCTTGGATGACTAGTGTTGGAGC
TTTTCAAGCATAACTATTTCATAGTTTCTTATTTTGCTAACTGGTTTGAGGGAGGACGGACCCAT
GCGTGTTTGTAA
Found at i:13251672 original size:22 final size:22
Alignment explanation
Indices: 13251644--13251687 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
13251634 CTGTGTCACC
13251644 TGGTAAAATTGCATATGATCAT
1 TGGTAAAATTGCATATGATCAT
13251666 TGGTAAAATTGCATATGATCAT
1 TGGTAAAATTGCATATGATCAT
13251688 ACCTTGAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
TGGTAAAATTGCATATGATCAT
Found at i:13254519 original size:19 final size:17
Alignment explanation
Indices: 13254481--13254514 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
13254471 TAATAATAAT
13254481 TTTATTTATATATATTA
1 TTTATTTATATATATTA
13254498 TTTATATTAT-TATATTA
1 TTTAT-TTATATATATTA
13254515 AATTTCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATTTATATATATTA
Done.