Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 75 of 438
Found at i:20127358 original size:13 final size:14
Alignment explanation
Indices: 20127340--20127370 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
20127330 TTCTGAAGAC
20127340 ATACTATATA-TAT
1 ATACTATATATTAT
20127353 ATACTATATATTAT
1 ATACTATATATTAT
20127367 ATAC
1 ATAC
20127371 AACAATGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (14 bp):
ATACTATATATTAT
Found at i:20132174 original size:16 final size:16
Alignment explanation
Indices: 20132150--20132201 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
20132140 TGGTTCACTA
* *
20132150 TAATGGAATAGGGTTG
1 TAATGGAATAGAGCTG
*
20132166 TAATTGAATAGAGCTG
1 TAATGGAATAGAGCTG
*
20132182 TAATGGAATAGATCTG
1 TAATGGAATAGAGCTG
20132198 TAAT
1 TAAT
20132202 TAGTAATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.33
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:20134621 original size:21 final size:21
Alignment explanation
Indices: 20134596--20134637 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20134586 AAACCATCCA
20134596 AAAATACAATACTACTTAATC
1 AAAATACAATACTACTTAATC
*
20134617 AAAATGCAATACTACTTAATC
1 AAAATACAATACTACTTAATC
20134638 GATACTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATACAATACTACTTAATC
Found at i:20136890 original size:20 final size:20
Alignment explanation
Indices: 20136865--20136904 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20136855 TCGTTCTTTA
20136865 ATTGATATATAATAAAATAG
1 ATTGATATATAATAAAATAG
* *
20136885 ATTGATTTATAGTAAAATAG
1 ATTGATATATAATAAAATAG
20136905 CCAAGACTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (20 bp):
ATTGATATATAATAAAATAG
Found at i:20137981 original size:11 final size:9
Alignment explanation
Indices: 20137965--20137991 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
20137955 GACAGAGCAC
20137965 GAGAGAGAA
1 GAGAGAGAA
20137974 GAGAGAGAA
1 GAGAGAGAA
20137983 GAGAGAGAA
1 GAGAGAGAA
20137992 TACGGGGAAA
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:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
GAGAGAGAA
Found at i:20141058 original size:23 final size:21
Alignment explanation
Indices: 20141028--20141071 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
20141018 AAATTAAATC
20141028 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC--AATCATATCT
*
20141051 TCTAAGATTGCAATCATATCT
1 TCTAAGATTACAATCATATCT
20141072 AAGATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
23 10 0.50
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (21 bp):
TCTAAGATTACAATCATATCT
Found at i:20141085 original size:17 final size:18
Alignment explanation
Indices: 20141051--20141103 Score: 81
Period size: 17 Copynumber: 2.9 Consensus size: 18
20141041 AATCATATCT
20141051 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
20141069 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
20141086 TCTAAGATTGCATATCAT
1 TCTAAGATTGCA-ATCAT
20141104 TGAAGATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:20141955 original size:204 final size:205
Alignment explanation
Indices: 20141482--20142259 Score: 1270
Period size: 205 Copynumber: 3.8 Consensus size: 205
20141472 CTGCTTCTTC
* *
20141482 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAATGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
* * *
20141547 AAGCCAAATCAGCTACGTCTACGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
* **
20141612 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGTTATGTGTCTGCCCTCCGTCAAAGTGGAGAT
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGTTATGTATCTGTTCTCCGTCAAAGTGGAGAT
*
20141677 GCCAGACTTC
196 GCCAGACTTT
* *
20141687 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTCCAACATAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
*
20141752 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
* * * *
20141817 CTACTTCAGTATAAACTTCCGAA-GTTAGATCTGTTATGTATATGTTCTCCGTCAAAGTGGAGAT
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGTTATGTATCTGTTCTCCGTCAAAGTGGAGAT
* *
20141881 GGCAAACTTT
196 GCCAGACTTT
* *
20141891 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
*
20141956 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATTTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
* * * *
20142021 CTGCTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTATCTGTTCTCCATCGAAGTGGAGAT
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGTTATGTATCTGTTCTCCGTCAAAGTGGAGAT
20142086 GCCAGACTTT
196 GCCAGACTTT
*
20142096 GATTTGTTCTCTGACAATACAGAGATGTCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
*
20142161 AAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
* * * *
20142226 CTGCTTCAGTATAAACATTTGAAGGCTAGATCTG
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTG
20142260 CTATACTTTA
Statistics
Matches: 532, Mismatches: 40, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
204 187 0.35
205 345 0.65
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (205 bp):
GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
CTACTTCAGTATAAACATCTGAAGGTTGGATCTGTTATGTATCTGTTCTCCGTCAAAGTGGAGAT
GCCAGACTTT
Found at i:20142172 original size:409 final size:409
Alignment explanation
Indices: 20141482--20142241 Score: 1324
Period size: 409 Copynumber: 1.9 Consensus size: 409
20141472 CTGCTTCTTC
*
20141482 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAATGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAATGTAAACACGTGA
*
20141547 AAGCCAAATCAGCTACGTCTACGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTACGTCTACGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
* * *
20141612 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGTTATGTGTCTGCCCTCCGTCAAAGTGGAGAT
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTATCTGCCCTCCATCAAAGTGGAGAT
20141677 GCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTCCAACAT
196 GCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTCCAACAT
* *
20141742 AAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAAC
261 AAGCACGTGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAAC
20141807 CATCTTGGATCTACTTCAGTATAAACTTCCGAAGTTAGATCTGTTATGTATATGTTCTCCGTCAA
326 CATCTTGGATCTACTTCAGTATAAACTTCCGAAGTTAGATCTGTTATGTATATGTTCTCCGTCAA
20141872 AGTGGAGATGGCAAACTTT
391 AGTGGAGATGGCAAACTTT
*
20141891 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTC-ATCGTAAACACGTG
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAAT-GTAAACACGTG
* * *
20141955 AAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATTTTGGA
65 AAAGCCAAATCAGCTACGTCTACGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGA
* ** *
20142020 TCTGCTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTATCTGTTCTCCATCGAAGTGGAGA
130 TCTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTATCTGCCCTCCATCAAAGTGGAGA
* * * *
20142085 TGCCAGACTTTGATTTGTTCTCTGACAATACAGAGATGTCAAATCATCTTAGATTTGCTTCAACG
195 TGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTCCAACA
20142150 TAAGCACGTGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAA
260 TAAGCACGTGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAA
*
20142215 CCATCTTGGATCTGCTTCAGTATAAAC
325 CCATCTTGGATCTACTTCAGTATAAAC
20142242 ATTTGAAGGC
Statistics
Matches: 330, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
408 2 0.01
409 328 0.99
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (409 bp):
GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAATGTAAACACGTGA
AAGCCAAATCAGCTACGTCTACGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTATCTGCCCTCCATCAAAGTGGAGAT
GCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTCCAACAT
AAGCACGTGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAAC
CATCTTGGATCTACTTCAGTATAAACTTCCGAAGTTAGATCTGTTATGTATATGTTCTCCGTCAA
AGTGGAGATGGCAAACTTT
Found at i:20142367 original size:84 final size:84
Alignment explanation
Indices: 20142266--20142802 Score: 852
Period size: 84 Copynumber: 6.4 Consensus size: 84
20142256 TCTGCTATAC
* * * *
20142266 TTTAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCGCA-TCTTCGATCTGCTCTATTACTGTTT
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG-AGTCTTCGATCTGCTCCACTACTGCTT
**
20142330 AGGGAGATAAGATCTGCAGT
65 AGGGAGATAAGATCTGCAAA
* *
20142350 TTTGACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGATCTGCTCCACTACTGCTTA
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
20142415 GGGAGATAAGATCTGCAAA
66 GGGAGATAAGATCTGCAAA
20142434 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTTGTCGATCTGCTCCACTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTC--T-TCGATCTGCTCCACTACTGC
*
20142499 TTAGGGAGATAATATCTGC---
63 TTAGGGAGATAAGATCTGCAAA
* *
20142518 --GAACCTATTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
*
20142581 GGGAGATAAGATCTGTAAA
66 GGGAGATAAGATCTGCAAA
**
20142600 TTTAACCTGTTACCCTACCACTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
*
20142665 GGGAGATAAGATCCGCAAA
66 GGGAGATAAGATCTGCAAA
20142684 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
20142749 GGGAGATAAGATCTGCAAA
66 GGGAGATAAGATCTGCAAA
*
20142768 TTTAACCTGTTACCTTACTGCTTAGGGGATTAAGG
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGG
20142803 TGCTAAATTT
Statistics
Matches: 419, Mismatches: 25, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
79 37 0.09
80 1 0.00
82 37 0.09
83 1 0.00
84 305 0.73
87 38 0.09
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (84 bp):
TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCTGCAAA
Found at i:20142716 original size:250 final size:248
Alignment explanation
Indices: 20142269--20142802 Score: 838
Period size: 250 Copynumber: 2.1 Consensus size: 248
20142259 GCTATACTTT
* * * *
20142269 AACCTGTTACCCTACTGCTTAGGGGGTTAAGGCGCATCTTCGATCTGCTCTATTACTGTTTAGGG
1 AACCTGTTACCCTACTGCTTAGGGGATTAAGGCGCATCTTCGATCTGCTCCACTACTGCTTAGGG
** * **
20142334 AGATAAGATCTGCAGTTTTGACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGATCT
66 AGATAAGATCTGCAAATTTAACCTGTTACCCTACCACTTAGGGGATTAAGGCGAGTCGTCGATCT
*
20142399 GCTCCACTACTGCTTAGGGAGATAAGATCTGCAAATTTAACCTGTTACCCTACTGCTTAGGGGAT
131 GCTCCACTACTGCTTAGGGAGATAAGATCCGCAAATTTAACCTGTTACCCTACTGCTTAGGGGAT
*
20142464 TAAGGCGAGTCGTTGTCGATCTGCTCCACTACTGCTTAGGGAGATAATATCTGC-G
196 TAAGGCGAGTC--T-TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAG
*
20142519 AACCTATTACCCTACTGCTTAGGGGATTAAGGCG-AGTCTTCGATCTGCTCCACTACTGCTTAGG
1 AACCTGTTACCCTACTGCTTAGGGGATTAAGGCGCA-TCTTCGATCTGCTCCACTACTGCTTAGG
* *
20142583 GAGATAAGATCTGTAAATTTAACCTGTTACCCTACCACTTAGGGGATTAAGGCGAGTCTTCGATC
65 GAGATAAGATCTGCAAATTTAACCTGTTACCCTACCACTTAGGGGATTAAGGCGAGTCGTCGATC
20142648 TGCTCCACTACTGCTTAGGGAGATAAGATCCGCAAATTTAACCTGTTACCCTACTGCTTAGGGGA
130 TGCTCCACTACTGCTTAGGGAGATAAGATCCGCAAATTTAACCTGTTACCCTACTGCTTAGGGGA
*
20142713 TTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAATTT
195 TTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGC--A--G
*
20142771 AACCTGTTACCTTACTGCTTAGGGGATTAAGG
1 AACCTGTTACCCTACTGCTTAGGGGATTAAGG
20142803 TGCTAAATTT
Statistics
Matches: 261, Mismatches: 17, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
247 38 0.15
248 1 0.00
249 1 0.00
250 191 0.73
252 30 0.11
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (248 bp):
AACCTGTTACCCTACTGCTTAGGGGATTAAGGCGCATCTTCGATCTGCTCCACTACTGCTTAGGG
AGATAAGATCTGCAAATTTAACCTGTTACCCTACCACTTAGGGGATTAAGGCGAGTCGTCGATCT
GCTCCACTACTGCTTAGGGAGATAAGATCCGCAAATTTAACCTGTTACCCTACTGCTTAGGGGAT
TAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAG
Found at i:20143770 original size:8 final size:8
Alignment explanation
Indices: 20143752--20143829 Score: 65
Period size: 8 Copynumber: 9.8 Consensus size: 8
20143742 GGCCTCTCCA
20143752 TTTTTTC-
1 TTTTTTCT
20143759 TTTTTTCT
1 TTTTTTCT
20143767 TTTTTTCT
1 TTTTTTCT
20143775 CTTTTTTCT
1 -TTTTTTCT
*
20143784 TTTTATATATT
1 TTTT-T-T-CT
20143795 TTTTTTCT
1 TTTTTTCT
*
20143803 CTTTTTC-
1 TTTTTTCT
20143810 --TTTTCT
1 TTTTTTCT
*
20143816 TTTTTCCT
1 TTTTTTCT
20143824 TTTTTT
1 TTTTTT
20143830 TTGAAATAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
5 5 0.09
7 7 0.12
8 29 0.50
9 10 0.17
10 2 0.03
11 5 0.09
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTCT
Found at i:20143807 original size:11 final size:10
Alignment explanation
Indices: 20143752--20143820 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 10
20143742 GGCCTCTCCA
*
20143752 TTTTTTCTTTT
1 TTTTTT-TTTC
20143763 TTCTTTTTTTC
1 TT-TTTTTTTC
*
20143774 -TCTTTTTTC
1 TTTTTTTTTC
* * *
20143783 TTTTTATATA
1 TTTTTTTTTC
20143793 TTTTTTTTCTC
1 TTTTTTTT-TC
20143804 TTTTTCTTTTC
1 TTTTT-TTTTC
20143815 TTTTTT
1 TTTTTT
20143821 CCTTTTTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
9 7 0.16
10 13 0.29
11 18 0.40
12 7 0.16
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:20143831 original size:13 final size:12
Alignment explanation
Indices: 20143752--20143831 Score: 60
Period size: 12 Copynumber: 6.4 Consensus size: 12
20143742 GGCCTCTCCA
20143752 TTTTTTCTTTT-
1 TTTTTTCTTTTC
20143763 TTCTTTT-TTTCTC
1 TT-TTTTCTTT-TC
20143776 TTTTTTCTTTT-
1 TTTTTTCTTTTC
*
20143787 TATATATTTTTTTTC
1 T-T-T-TTTCTTTTC
20143802 TCTTTTTCTTTTC
1 T-TTTTTCTTTTC
20143815 TTTTTTCCTTTT-
1 TTTTTT-CTTTTC
20143827 TTTTT
1 TTTTT
20143832 GAAATAGAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
11 6 0.11
12 21 0.37
13 20 0.35
14 8 0.14
15 2 0.04
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:20147849 original size:17 final size:17
Alignment explanation
Indices: 20147824--20147867 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
20147814 CACTATCCTG
*
20147824 CACGGAGGCGAAAACCT
1 CACGAAGGCGAAAACCT
20147841 CACGAAGGCGAAAACCT
1 CACGAAGGCGAAAACCT
*
20147858 CATGAAGGCG
1 CACGAAGGCG
20147868 TAATTTCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.36, C:0.27, G:0.30, T:0.07
Consensus pattern (17 bp):
CACGAAGGCGAAAACCT
Found at i:20149231 original size:64 final size:64
Alignment explanation
Indices: 20149158--20149282 Score: 223
Period size: 64 Copynumber: 2.0 Consensus size: 64
20149148 AATAGCTCAA
*
20149158 CCCGCCCAGCCCAACACTCCACAGTTGCAGCCTTGCTGCTCAGTTAACAATAAATTGAGGCTTT
1 CCCGCCCAGCCCAACACTCCACAGTTGCAGCATTGCTGCTCAGTTAACAATAAATTGAGGCTTT
* *
20149222 CCCGCCCAGCCCAACACTCCACAGTTGCAGCATTGCTGCTGAGTTAATAATAAATTGAGGC
1 CCCGCCCAGCCCAACACTCCACAGTTGCAGCATTGCTGCTCAGTTAACAATAAATTGAGGC
20149283 AAAGCCTCCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.22
Consensus pattern (64 bp):
CCCGCCCAGCCCAACACTCCACAGTTGCAGCATTGCTGCTCAGTTAACAATAAATTGAGGCTTT
Found at i:20150968 original size:26 final size:26
Alignment explanation
Indices: 20150937--20150990 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
20150927 TGAAATGCCC
20150937 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
20150963 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
20150989 AT
1 AT
20150991 TGTAACACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:20151860 original size:37 final size:37
Alignment explanation
Indices: 20151805--20151913 Score: 200
Period size: 37 Copynumber: 2.9 Consensus size: 37
20151795 AGCTCAGACG
*
20151805 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
20151842 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
20151879 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
20151914 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:20152196 original size:47 final size:47
Alignment explanation
Indices: 20152117--20152498 Score: 586
Period size: 47 Copynumber: 8.1 Consensus size: 47
20152107 TATATATACT
* * * **
20152117 TCACA-TGAGCCATTCGGCTTTACCACATATATGCATATTCGTATTCA
1 TCACATTG-GCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
20152164 CCACATTGGCCATTCGGCCTTATCACAGATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
20152211 TCACATTGGCCATTCGGCCTTATCACATGTATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
20152258 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
20152305 TCACATTGGTCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
20152352 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
20152399 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
20152446 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
20152493 TCACAT
1 TCACAT
20152499 AAAATCCTAA
Statistics
Matches: 307, Mismatches: 27, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
47 305 0.99
48 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:20154978 original size:26 final size:26
Alignment explanation
Indices: 20154949--20155007 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
20154939 GGCTGTCACA
* *
20154949 ATTATCATGGAATATTTACCTAATCC
1 ATTATCATGGAACATTTACCTAACCC
20154975 ATTATCATGGAACATTTACCTAACCC
1 ATTATCATGGAACATTTACCTAACCC
20155001 ATTATCA
1 ATTATCA
20155008 ATTTGTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (26 bp):
ATTATCATGGAACATTTACCTAACCC
Found at i:20157530 original size:28 final size:28
Alignment explanation
Indices: 20157490--20157547 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
20157480 GCTAAAACAA
*
20157490 GTTAGGAGTATTTGCATGTAGTTTAAAG
1 GTTAGGAGTATTTGCATGTAGTTGAAAG
*
20157518 GTTAGGAGTATTTGTATGTAGTTGAAAG
1 GTTAGGAGTATTTGCATGTAGTTGAAAG
20157546 GT
1 GT
20157548 GGAGAAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.02, G:0.31, T:0.40
Consensus pattern (28 bp):
GTTAGGAGTATTTGCATGTAGTTGAAAG
Found at i:20160967 original size:20 final size:21
Alignment explanation
Indices: 20160923--20160975 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
20160913 ATTTTCGTAA
*
20160923 AATAATTTTTGAAAAATAATT
1 AATATTTTTTGAAAAATAATT
*
20160944 --TATTTTTTTAAAAA-AATT
1 AATATTTTTTGAAAAATAATT
20160962 AATATTTTTTGAAA
1 AATATTTTTTGAAA
20160976 GAATTTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.15
19 12 0.44
20 11 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
AATATTTTTTGAAAAATAATT
Found at i:20161025 original size:31 final size:31
Alignment explanation
Indices: 20160945--20161026 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 31
20160935 AAAATAATTT
* * *
20160945 ATTTTTTTAAAAAAATTAATATTTTTTGAAAG
1 ATTTTTTTAAAAATATT-TTATTATTTGAAAG
* * *
20160977 AATTTTGTAAAATATATTTTATTATTTGACAG
1 ATTTTTTTAAAA-ATATTTTATTATTTGAAAG
20161009 ATTTTTTTAAAAATATTT
1 ATTTTTTTAAAAATATTT
20161027 AATAAAAACC
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 6 0.15
32 31 0.76
33 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.52
Consensus pattern (31 bp):
ATTTTTTTAAAAATATTTTATTATTTGAAAG
Found at i:20161358 original size:27 final size:27
Alignment explanation
Indices: 20161320--20161386 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
20161310 TAAGCATAAT
20161320 TTGAAATATTCATATTTTTATACTAGG
1 TTGAAATATTCATATTTTTATACTAGG
20161347 TTGAAATATTCATATTTTTATACTAGG
1 TTGAAATATTCATATTTTTATACTAGG
*
20161374 TTCAAATATTCAT
1 TTGAAATATTCAT
20161387 GTAATTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (27 bp):
TTGAAATATTCATATTTTTATACTAGG
Found at i:20172483 original size:43 final size:43
Alignment explanation
Indices: 20172394--20172509 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 43
20172384 TGTGATTACA
* * *
20172394 TGTAAAACCATGT-TTGAGACATTGGCATTGTATTGTGATTATG
1 TGTAAGACCATGTCTTG-GACATTGGCATCGTATTGCGATTATG
20172437 TGTAAGACCATGTCTTGGACATTGGCATCGTTATT-CGATT-TCG
1 TGTAAGACCATGTCTTGGACATTGGCATCG-TATTGCGATTAT-G
* * * * *
20172480 TGTAAGGCCTTGTCTGGGACAGTGGTATCG
1 TGTAAGACCATGTCTTGGACATTGGCATCG
20172510 ATAAGTGATA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
42 1 0.02
43 54 0.87
44 7 0.11
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (43 bp):
TGTAAGACCATGTCTTGGACATTGGCATCGTATTGCGATTATG
Found at i:20173531 original size:30 final size:30
Alignment explanation
Indices: 20173485--20173549 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
20173475 GTGGCTTGAC
* *
20173485 CGTGTGTGACACATGGCCTTGGTACATAGT
1 CGTGTGCGACACATGGCCTTGGTACACAGT
* * *
20173515 CGTGTGCGACATATGGCCTTTGTACACGGT
1 CGTGTGCGACACATGGCCTTGGTACACAGT
20173545 CGTGT
1 CGTGT
20173550 ATCCCCTGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.31
Consensus pattern (30 bp):
CGTGTGCGACACATGGCCTTGGTACACAGT
Found at i:20177311 original size:5 final size:5
Alignment explanation
Indices: 20177301--20177344 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
20177291 TCAAGAATAC
20177301 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACAT
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACAT
20177345 TCATTATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.59, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
ACATA
Found at i:20179671 original size:27 final size:27
Alignment explanation
Indices: 20179641--20179697 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
20179631 AATAAATTCT
20179641 TTCTCACCTTATATTCAGTTATAATAC
1 TTCTCACCTTATATTCAGTTATAATAC
20179668 TTCTCACCTTATATTCAGTTATAATAC
1 TTCTCACCTTATATTCAGTTATAATAC
20179695 TTC
1 TTC
20179698 AGTTTCCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.46
Consensus pattern (27 bp):
TTCTCACCTTATATTCAGTTATAATAC
Found at i:20181410 original size:17 final size:16
Alignment explanation
Indices: 20181347--20181406 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 16
20181337 CCTAATTGGT
*
20181347 TTATTGATTTATTTCA
1 TTATTTATTTATTTCA
* *
20181363 TTTGTTTATTT-TTTCT
1 -TTATTTATTTATTTCA
* *
20181379 TTATTTGTTTCCTTTCA
1 TTATTTATTT-ATTTCA
20181396 TTATTTATTTA
1 TTATTTATTTA
20181407 CTTTTGTTCC
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 21 0.64
ACGTcount: A:0.17, C:0.08, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTATTTATTTCA
Found at i:20187963 original size:29 final size:29
Alignment explanation
Indices: 20187931--20188014 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
20187921 TAAGTGAGCT
20187931 TTTTTGGATATCTCTGTTATAAGGAAACC
1 TTTTTGGATATCTCTGTTATAAGGAAACC
* * **
20187960 TTTTTGGCA-ATCTCTATTCTAAGGAAGTC
1 TTTTTGG-ATATCTCTGTTATAAGGAAACC
* *
20187989 TTTGTGG-TGATCTTTGTTATAAGGAA
1 TTTTTGGAT-ATCTCTGTTATAAGGAA
20188015 GTCTTTGTGG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 43 0.98
30 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (29 bp):
TTTTTGGATATCTCTGTTATAAGGAAACC
Found at i:20188015 original size:29 final size:29
Alignment explanation
Indices: 20187940--20188229 Score: 141
Period size: 29 Copynumber: 10.1 Consensus size: 29
20187930 TTTTTTGGAT
* ** * *
20187940 ATCTCTGTTATAAGGAAACCTTTTTGGCA
1 ATCTTTGTTATAAGGAAGTCTTTGTGGCG
* * * *
20187969 ATCTCTATTCTAAGGAAGTCTTTGTGGTG
1 ATCTTTGTTATAAGGAAGTCTTTGTGGCG
20187998 ATCTTTGTTATAAGGAAGTCTTTGTGGCG
1 ATCTTTGTTATAAGGAAGTCTTTGTGGCG
* * * *
20188027 ATCTTTGTTAAAAGGATGCCTTTGTGGGCT
1 ATCTTTGTTATAAGGAAGTCTTTGT-GGCG
* * * *
20188057 ATCTATG--A-ATGGACG-CTTTTGTGGCT
1 ATCTTTGTTATAAGGAAGTC-TTTGTGGCG
*
20188083 ATC--TG--A-AAAGAAGCCTCCTTTGTGGCG
1 ATCTTTGTTATAAGGAAG--T-CTTTGTGGCG
* * * ** * *
20188110 ATATATGTTATAATGAAACCTTTGTAGCT
1 ATCTTTGTTATAAGGAAGTCTTTGTGGCG
*
20188139 ATCTTTGTTATAAGGAAGCCTTTGTGGCG
1 ATCTTTGTTATAAGGAAGTCTTTGTGGCG
*** * * *
20188168 ATCTCCATTA-AATGAAAGCCTTTGTGGCT
1 ATCTTTGTTATAA-GGAAGTCTTTGTGGCG
* * *
20188197 ATCTCTGTTATAAGGAAGCCTTTGTGGCT
1 ATCTTTGTTATAAGGAAGTCTTTGTGGCG
20188226 ATCT
1 ATCT
20188230 ATTGATGAAT
Statistics
Matches: 206, Mismatches: 42, Indels: 26
0.75 0.15 0.09
Matches are distributed among these distances:
24 7 0.03
26 8 0.04
27 20 0.10
28 4 0.02
29 150 0.73
30 11 0.05
31 1 0.00
32 5 0.02
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (29 bp):
ATCTTTGTTATAAGGAAGTCTTTGTGGCG
Found at i:20188168 original size:58 final size:58
Alignment explanation
Indices: 20188099--20188224 Score: 182
Period size: 58 Copynumber: 2.2 Consensus size: 58
20188089 AAAGAAGCCT
** *
20188099 CCTTTGTGGCGATATATGTTATAATGAAA-CCTTTGTAGCTATCTTTGTTATAAGGAAG
1 CCTTTGTGGCGATATACATTA-AATGAAAGCCTTTGTAGCTATCTCTGTTATAAGGAAG
* * *
20188157 CCTTTGTGGCGATCTCCATTAAATGAAAGCCTTTGTGGCTATCTCTGTTATAAGGAAG
1 CCTTTGTGGCGATATACATTAAATGAAAGCCTTTGTAGCTATCTCTGTTATAAGGAAG
20188215 CCTTTGTGGC
1 CCTTTGTGGC
20188225 TATCTATTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 7 0.11
58 54 0.89
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (58 bp):
CCTTTGTGGCGATATACATTAAATGAAAGCCTTTGTAGCTATCTCTGTTATAAGGAAG
Found at i:20194452 original size:18 final size:18
Alignment explanation
Indices: 20194431--20194468 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20194421 ATTTTTTGAA
* *
20194431 AAAAATTAATATTAAAAT
1 AAAAAGTAATAGTAAAAT
20194449 AAAAAGTAATAGTAAAAT
1 AAAAAGTAATAGTAAAAT
20194467 AA
1 AA
20194469 TCAAAACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAAGTAATAGTAAAAT
Found at i:20195449 original size:17 final size:17
Alignment explanation
Indices: 20195427--20195459 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20195417 GAACAAATAT
*
20195427 TTAAAATTTATAAAAAA
1 TTAAAAGTTATAAAAAA
20195444 TTAAAAGTTATAAAAA
1 TTAAAAGTTATAAAAA
20195460 GTAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAAAAGTTATAAAAAA
Found at i:20196462 original size:2 final size:2
Alignment explanation
Indices: 20196449--20196479 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20196439 CAACAGAAGA
*
20196449 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
20196480 AGCTGGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:20199108 original size:15 final size:14
Alignment explanation
Indices: 20199080--20199106 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20199070 TGATATATCT
20199080 TTTTTTAATATTTA
1 TTTTTTAATATTTA
20199094 TTTTTTAATATTT
1 TTTTTTAATATTT
20199107 TACTGTACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:20203482 original size:18 final size:18
Alignment explanation
Indices: 20203459--20203495 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20203449 ATGTCGGGAA
20203459 TGCTGGGCACCCTATTTG
1 TGCTGGGCACCCTATTTG
20203477 TGCTGGGCACCCTATTTG
1 TGCTGGGCACCCTATTTG
20203495 T
1 T
20203496 AGATTACACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.27, G:0.27, T:0.35
Consensus pattern (18 bp):
TGCTGGGCACCCTATTTG
Found at i:20204653 original size:21 final size:21
Alignment explanation
Indices: 20204628--20204669 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20204618 TTTTTATCAT
20204628 TTTTGAGC-TTTAGTATCGATA
1 TTTTG-GCATTTAGTATCGATA
*
20204649 TTTTGGCATTTGGTATCGATA
1 TTTTGGCATTTAGTATCGATA
20204670 CTTGACCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (21 bp):
TTTTGGCATTTAGTATCGATA
Found at i:20206817 original size:24 final size:24
Alignment explanation
Indices: 20206774--20206856 Score: 138
Period size: 24 Copynumber: 3.6 Consensus size: 24
20206764 AATCTCAAAT
20206774 GCACTATGTGTGCGA--T--TATG
1 GCACTATGTGTGCGATTTACTATG
20206794 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
20206818 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
20206842 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
20206857 ACATAATAAG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
20 15 0.25
22 1 0.02
24 43 0.73
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:20206870 original size:48 final size:44
Alignment explanation
Indices: 20206774--20206878 Score: 122
Period size: 48 Copynumber: 2.3 Consensus size: 44
20206764 AATCTCAAAT
** * *
20206774 GCACTATGTGTGCGATTATGGCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTATGGCACTATGTGTGCGACATAATATA
20206818 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATA-A
1 GCACTATGTGTGCGA--T--TATGGCACTATGTGTGCG-ACATAATATA
20206866 GCACTATGTGTGC
1 GCACTATGTGTGC
20206879 AACATTCGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
44 15 0.29
46 1 0.02
48 31 0.60
49 5 0.10
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (44 bp):
GCACTATGTGTGCGATTATGGCACTATGTGTGCGACATAATATA
Found at i:20217349 original size:24 final size:24
Alignment explanation
Indices: 20217317--20217379 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
20217307 AATCTCAAAT
* *
20217317 GCACTATGTGTGTGATTTATTATG
1 GCACTATGTGTGCGATTTACTATG
20217341 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
20217365 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
20217380 ACATAATAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:20223364 original size:54 final size:54
Alignment explanation
Indices: 20223282--20223386 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
20223272 CATGTGTCAC
* * *
20223282 GACCGTGTAACTCTTTGCCTTGAGTCACAC-AGGCGTGTGTCAGGTTGTGTGCCA
1 GACCGTGTAACTCTTTGACTTGAGTCACACGA-CCGTGTGACAGGTTGTGTGCCA
20223336 GACCGTGTAACTCTCTT-ACTTG-GATCACACGACCGTGTGACAGGTTGTGTG
1 GACCGTGTAACTCT-TTGACTTGAG-TCACACGACCGTGTGACAGGTTGTGTG
20223387 AGGCATTGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
53 1 0.02
54 41 0.91
55 3 0.07
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.30
Consensus pattern (54 bp):
GACCGTGTAACTCTTTGACTTGAGTCACACGACCGTGTGACAGGTTGTGTGCCA
Found at i:20226469 original size:46 final size:46
Alignment explanation
Indices: 20226419--20226594 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
20226409 TGGTTGAGCA
20226419 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
20226465 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* * * * *
20226510 CATCCAAACTCGTTAAGTCGAGTCCGAGTTCACTCATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
20226558 ACCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20226595 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 59 0.57
47 26 0.25
48 4 0.04
50 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:20226575 original size:93 final size:93
Alignment explanation
Indices: 20226416--20226587 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
20226406 GGATGGTTGA
* * * * *
20226416 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTAAGTCGAGTCCGAGTTCACTCATGGATGCAAATGACCGAACTCGTTGAGT
20226481 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
20226509 GCATCCAAACTCGTTAAGTCGAGTCCGAGTTCACTCATGGATGCGAATGACCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTAAGTCGAGTCCGAGTTCACTCATGGATGCAAATGACCGAACTCGTTGAGT
20226574 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
20226588 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GCATCCAAACTCGTTAAGTCGAGTCCGAGTTCACTCATGGATGCAAATGACCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:20234058 original size:36 final size:36
Alignment explanation
Indices: 20233988--20234058 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
20233978 GGAGCACATC
* *
20233988 AGTCAGAATAGATCCAAAAGGCTACTGAATTGAATT
1 AGTCAGAATAGATCCAAAAGGATACTGAACTGAATT
*
20234024 AGTCAGAATAGATCCAAAAGGATACTGAGCTGAAT
1 AGTCAGAATAGATCCAAAAGGATACTGAACTGAAT
20234059 AGAGTTTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (36 bp):
AGTCAGAATAGATCCAAAAGGATACTGAACTGAATT
Found at i:20254314 original size:40 final size:40
Alignment explanation
Indices: 20254259--20254515 Score: 324
Period size: 40 Copynumber: 6.5 Consensus size: 40
20254249 CGGATGATAA
* * *
20254259 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
20254299 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
20254338 CTGAGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
20254378 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
20254418 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTCCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
20254458 CCGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
20254498 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
20254516 TACTTGGCTT
Statistics
Matches: 194, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
38 1 0.01
39 46 0.24
40 147 0.76
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:20254504 original size:119 final size:119
Alignment explanation
Indices: 20254259--20254515 Score: 331
Period size: 119 Copynumber: 2.2 Consensus size: 119
20254249 CGGATGATAA
* * *
20254259 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGTTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGG
* * * * *
20254324 TGCAGTTACTATATCTGAGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
66 TGCAGTTACTATATCCGAGCTAAGTCCCAAAGGCATTCGAGCAAGTTACTATAT
* *
20254378 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTG
1 CCGGGTTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTG
* * * *
20254442 GTGCGAGTTCCTATATCCGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATAT
65 GTGC-AGTTACTATATCCGAGCTAAGTCCCAAAGGCATTCGAGCAAGTTA-CTATAT
*
20254498 CC-GGTTAAATCCCGAAGG
1 CCGGGTTAAGTCCCGAAGG
20254516 TACTTGGCTT
Statistics
Matches: 120, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
118 1 0.01
119 78 0.65
120 41 0.34
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (119 bp):
CCGGGTTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGG
TGCAGTTACTATATCCGAGCTAAGTCCCAAAGGCATTCGAGCAAGTTACTATAT
Found at i:20257808 original size:28 final size:28
Alignment explanation
Indices: 20257762--20257830 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
20257752 TTTAAAACCC
*
20257762 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
20257789 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
20257817 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
20257831 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:20259466 original size:20 final size:20
Alignment explanation
Indices: 20259443--20259480 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20259433 CACATCCAAA
*
20259443 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
20259463 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
20259481 GCGAATAAAC
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:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:20261274 original size:26 final size:26
Alignment explanation
Indices: 20261245--20261354 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
20261235 TGATACAAAT
20261245 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
20261271 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
20261297 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
20261323 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
20261349 TGATAA
1 TGATAA
20261355 GAAATTCATG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:20271400 original size:40 final size:40
Alignment explanation
Indices: 20271338--20271578 Score: 290
Period size: 40 Copynumber: 6.1 Consensus size: 40
20271328 CGGAGTTTAG
** * *
20271338 CGGATATAGCCACTAGCTCAAATGCCTTCGGGACTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
20271378 CGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
20271418 CGG-TATAATAACTCGTACAAATGCCTTCGGGACTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* * *
20271457 CGGATATAATAGCTCGCACAAACGCCTTCGGGACTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
20271497 CGGATATAGTAGCTCGCACGAATGCCTTCGGGACTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* ** * *
20271537 CGAAT-TAGCCACTAGCTCAAATG-CTCTCGGGACTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCT-TCGGGACTTAGCC
20271576 CGG
1 CGG
20271579 TTATCATCGA
Statistics
Matches: 177, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
38 2 0.01
39 63 0.36
40 112 0.63
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
Found at i:20271454 original size:79 final size:79
Alignment explanation
Indices: 20271356--20271579 Score: 290
Period size: 79 Copynumber: 2.8 Consensus size: 79
20271346 GCCACTAGCT
* *
20271356 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
*
20271421 TATAATAACTCGTA
66 TATAATAACTCGCA
* * * *
20271435 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCACAAACGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
* *
20271500 ATATAGTAGCTCGCA
66 -TATAATAACTCGCA
* * ** *
20271515 CGAATGCCTTCGGGACTTAGCCCGAAT-TAGCCACTAGCTCAAATG-CTCTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCT-TCGGGACTTAGCCCG
20271578 GT
65 GT
20271580 TATCATCGAA
Statistics
Matches: 126, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
78 3 0.02
79 87 0.69
80 36 0.29
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
TATAATAACTCGCA
Found at i:20271558 original size:119 final size:119
Alignment explanation
Indices: 20271356--20271578 Score: 308
Period size: 119 Copynumber: 1.9 Consensus size: 119
20271346 GCCACTAGCT
* * * *
20271356 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
* *
20271421 TATAATAACTCGTACAAATGC-CTTCGGGACTTAGCCCGGATATAATAGCTCGCA
66 TATAACAACTAGTACAAATGCTC-TCGGGACTTAGCCCGGATATAATAGCTCGCA
* *
20271475 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACGAATGCCTTCGGGACTTAGCCCGA
1 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
* *
20271540 -ATTAGCCACTAGCT-CAAATGCTCTCGGGACTTAGCCCGG
66 TA-TAACAACTAG-TACAAATGCTCTCGGGACTTAGCCCGG
20271579 TTATCATCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
118 1 0.01
119 88 0.97
120 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (119 bp):
CAAACGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
TATAACAACTAGTACAAATGCTCTCGGGACTTAGCCCGGATATAATAGCTCGCA
Found at i:20278829 original size:40 final size:40
Alignment explanation
Indices: 20278776--20278960 Score: 300
Period size: 40 Copynumber: 4.6 Consensus size: 40
20278766 ACTACTTGCT
*
20278776 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
20278816 CAAATGCCTTCGGGACTTATCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
20278856 AAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
20278896 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
20278936 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
20278961 TTATCATCCG
Statistics
Matches: 135, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
39 1 0.01
40 134 0.99
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:20280886 original size:17 final size:17
Alignment explanation
Indices: 20280864--20280896 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20280854 ATATTATGGG
20280864 TATAAATGTTTT-TAATA
1 TATAAAT-TTTTATAATA
20280881 TATAAATTTTTATAAT
1 TATAAATTTTTATAAT
20280897 TTTATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TATAAATTTTTATAATA
Found at i:20281031 original size:44 final size:44
Alignment explanation
Indices: 20280965--20281055 Score: 119
Period size: 44 Copynumber: 2.1 Consensus size: 44
20280955 AATTCTATTT
* * *
20280965 TTAGTTTACCACTTAAACTCTGATTAGTATAGGTTATATTAATA
1 TTAGTTTACCACATAAAATCTGATTAGTACAGGTTATATTAATA
* * * *
20281009 TTAGTTTCCCACATAAAATCTGATTAGTGCCGGTTATTTTAATA
1 TTAGTTTACCACATAAAATCTGATTAGTACAGGTTATATTAATA
20281053 TTA
1 TTA
20281056 TTTGGCCTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (44 bp):
TTAGTTTACCACATAAAATCTGATTAGTACAGGTTATATTAATA
Found at i:20282457 original size:12 final size:12
Alignment explanation
Indices: 20282440--20282465 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20282430 TCAGACGATA
20282440 TTAAGGTATCTC
1 TTAAGGTATCTC
20282452 TTAAGGTATCTC
1 TTAAGGTATCTC
20282464 TT
1 TT
20282466 GAGGCTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (12 bp):
TTAAGGTATCTC
Found at i:20282986 original size:44 final size:43
Alignment explanation
Indices: 20282918--20283007 Score: 126
Period size: 44 Copynumber: 2.1 Consensus size: 43
20282908 AACTCAATTT
* *
20282918 TTAGTTTACCACTTAAAATCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTACCACTTAAAATCTGATTA-TATAGATTATTTTAATA
* * *
20282962 TTAGTTTCCCACTTAAACTTTGATTATATAGATTATTTTAATA
1 TTAGTTTACCACTTAAAATCTGATTATATAGATTATTTTAATA
20283005 TTA
1 TTA
20283008 CTTGACCTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 18 0.44
44 23 0.56
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (43 bp):
TTAGTTTACCACTTAAAATCTGATTATATAGATTATTTTAATA
Found at i:20283597 original size:19 final size:18
Alignment explanation
Indices: 20283575--20283619 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
20283565 TTAAGCACTA
20283575 TTTTTAAAATTATTGAAT-T
1 TTTTTAAAATT-TT-AATAT
*
20283594 TTTTAAAAATTTTAATAT
1 TTTTTAAAATTTTAATAT
20283612 TTTTTAAA
1 TTTTTAAA
20283620 TCTTTATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 10 0.43
19 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTTAAAATTTTAATAT
Found at i:20283614 original size:17 final size:19
Alignment explanation
Indices: 20283573--20283614 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
20283563 AATTAAGCAC
*
20283573 TATTTTTAAAATTATTGAA
1 TATTTTAAAAATTATTGAA
*
20283592 TTTTTTAAAAATT-TT-AA
1 TATTTTAAAAATTATTGAA
20283609 TATTTT
1 TATTTT
20283615 TTAAATCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
19 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTTTAAAAATTATTGAA
Found at i:20283620 original size:17 final size:17
Alignment explanation
Indices: 20283573--20283625 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
20283563 AATTAAGCAC
20283573 TATTTTTAAAATTATTGAA
1 TATTTTTAAAATT-TT-AA
20283592 T-TTTTTAAAAATTTTAA
1 TATTTTT-AAAATTTTAA
*
20283609 TATTTTTTAAATCTTTA
1 TATTTTTAAAAT-TTTA
20283626 TGAAGTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 7 0.23
18 16 0.53
19 7 0.23
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTTTAAAATTTTAA
Found at i:20284475 original size:22 final size:21
Alignment explanation
Indices: 20284447--20284519 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 21
20284437 TTTTTAAATT
20284447 TTTATAAAATTTTAAATTAAAA
1 TTTATAAAATTTTAAA-TAAAA
* *
20284469 TTTATAAAAATATTAAATAAAG
1 TTTAT-AAAATTTTAAATAAAA
* *
20284491 TTCAAAAAATTTTAAA-AAAA
1 TTTATAAAATTTTAAATAAAA
20284511 -TTA-AAAATT
1 TTTATAAAATT
20284520 AATAAAAATC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 6 0.14
19 2 0.05
20 3 0.07
21 10 0.23
22 12 0.28
23 10 0.23
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (21 bp):
TTTATAAAATTTTAAATAAAA
Found at i:20284574 original size:14 final size:14
Alignment explanation
Indices: 20284555--20284596 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
20284545 TCAAAATGAA
20284555 TCTAGA-CATAGTTG
1 TCTAGATCATA-TTG
20284569 TCTAGATTCATATTG
1 TCTAGA-TCATATTG
20284584 TCTAGATTCATAT
1 TCTAGA-TCATAT
20284597 CAAAACAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.23
15 16 0.62
16 4 0.15
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
TCTAGATCATATTG
Found at i:20284586 original size:15 final size:15
Alignment explanation
Indices: 20284561--20284596 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
20284551 TGAATCTAGA
20284561 CATAGTTGTCTAGATT
1 CATA-TTGTCTAGATT
20284577 CATATTGTCTAGATT
1 CATATTGTCTAGATT
20284592 CATAT
1 CATAT
20284597 CAAAACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (15 bp):
CATATTGTCTAGATT
Found at i:20285192 original size:15 final size:17
Alignment explanation
Indices: 20285159--20285199 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
20285149 ATTAATAATG
*
20285159 TTTTAAAAATTTATATT
1 TTTTAAAAATATATATT
20285176 TTTTAAAAA-ATAT-TT
1 TTTTAAAAATATATATT
20285191 TTTTAAAAA
1 TTTTAAAAA
20285200 GTTAACCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.48
16 3 0.13
17 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTAAAAATATATATT
Found at i:20289622 original size:28 final size:28
Alignment explanation
Indices: 20289581--20289634 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
20289571 ATGCTGTTGA
*
20289581 ATACTCAATGTCTCGCACACTAAGTGTC
1 ATACTCAATATCTCGCACACTAAGTGTC
* *
20289609 ATACTCGATATCTCTCACACTAAGTG
1 ATACTCAATATCTCGCACACTAAGTG
20289635 CCGTACATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (28 bp):
ATACTCAATATCTCGCACACTAAGTGTC
Found at i:20289749 original size:40 final size:42
Alignment explanation
Indices: 20289624--20289759 Score: 129
Period size: 40 Copynumber: 3.3 Consensus size: 42
20289614 CGATATCTCT
* * * * **
20289624 CACACTAAGTGCC--GTACATAGTCGAAGCTATCTAAAATCG
1 CACACTAAGTGCCATTTATATAGCCGAAGCTATGTCGAATCG
*
20289664 CACACTAAGTGCCATTTATATAGCTGAAGCTATGTCGAATCG
1 CACACTAAGTGCCATTTATATAGCCGAAGCTATGTCGAATCG
* * *
20289706 CACACTAAGTGCCA-TT-TATAGCCGAAGGTATG-CTGTATTG
1 CACACTAAGTGCCATTTATATAGCCGAAGCTATGTC-GAATCG
*
20289746 CACATTAAGTGCCA
1 CACACTAAGTGCCA
20289760 AAAATAGCCG
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 44 0.54
41 2 0.02
42 34 0.42
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
CACACTAAGTGCCATTTATATAGCCGAAGCTATGTCGAATCG
Found at i:20293640 original size:25 final size:25
Alignment explanation
Indices: 20293586--20293677 Score: 64
Period size: 25 Copynumber: 3.7 Consensus size: 25
20293576 GTTTTGGTCG
* * *
20293586 AGCTCGTATA-AGCTTACCGATTTATC
1 AGCTCGTA-AGAGCTTA-CTATTTTTT
20293612 AGCTCGTAAGAGCTTACTATTTTTT
1 AGCTCGTAAGAGCTTACTATTTTTT
* ** * *
20293637 AGCTCATTGGAGTTTACCA--TTTT
1 AGCTCGTAAGAGCTTACTATTTTTT
*
20293660 AGCTCGTATGAGCTTACT
1 AGCTCGTAAGAGCTTACT
20293678 GTTCAGCTTG
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
23 17 0.33
25 21 0.40
26 14 0.27
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (25 bp):
AGCTCGTAAGAGCTTACTATTTTTT
Found at i:20293694 original size:22 final size:22
Alignment explanation
Indices: 20293669--20293727 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
20293659 TAGCTCGTAT
**
20293669 GAGCTTACTGTTCAGCTTGATA
1 GAGCTTACTGTTCAGCTCAATA
* *
20293691 GAGCTTACCGTTTTAGCTCAATA
1 GAGCTTACTG-TTCAGCTCAATA
20293714 GAGCTTACTGTTCA
1 GAGCTTACTGTTCA
20293728 TCAGCTCAGG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 12 0.40
23 18 0.60
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (22 bp):
GAGCTTACTGTTCAGCTCAATA
Found at i:20293714 original size:23 final size:23
Alignment explanation
Indices: 20293633--20293721 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 23
20293623 GCTTACTATT
* * * *
20293633 TTTTAGCTCATTGGAGTTTACCA
1 TTTTAGCTCAATAGAGCTTACCG
* *
20293656 TTTTAGCTC-GTATGAGCTTACTG
1 TTTTAGCTCAATA-GAGCTTACCG
* **
20293679 -TTCAGCTTGATAGAGCTTACCG
1 TTTTAGCTCAATAGAGCTTACCG
20293701 TTTTAGCTCAATAGAGCTTAC
1 TTTTAGCTCAATAGAGCTTAC
20293722 TGTTCATCAG
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
22 16 0.31
23 35 0.69
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (23 bp):
TTTTAGCTCAATAGAGCTTACCG
Found at i:20296394 original size:20 final size:20
Alignment explanation
Indices: 20296365--20296462 Score: 119
Period size: 20 Copynumber: 4.9 Consensus size: 20
20296355 GGAGCATCGT
* * *
20296365 AGTGCTATCAGGGGCACTGA
1 AGTGCAATCAGAGGCACCGA
20296385 AGTGCAATCAGAGGCACCGA
1 AGTGCAATCAGAGGCACCGA
20296405 AGTGCAATCAGAGGCACCGA
1 AGTGCAATCAGAGGCACCGA
* *
20296425 AGTACAAACAGAGGCA-C-A
1 AGTGCAATCAGAGGCACCGA
20296443 ATTGTGCAATCAGAGGCACC
1 A--GTGCAATCAGAGGCACC
20296463 AAAATGCAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
18 2 0.03
19 1 0.01
20 64 0.94
21 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.29, T:0.13
Consensus pattern (20 bp):
AGTGCAATCAGAGGCACCGA
Found at i:20302125 original size:40 final size:40
Alignment explanation
Indices: 20302044--20302218 Score: 264
Period size: 40 Copynumber: 4.4 Consensus size: 40
20302034 AAACCAAGTA
* * ** *
20302044 CCTTCGGGATTTAGCC-AGATATAGCT-ACTCGTTCAACTG
1 CCTTCGGGACTTAGCCTGGATATAG-TAACTCGCACAAATG
20302083 CCTTCGGGACTTAGCCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCTGGATATAGTAACTCGCACAAATG
*
20302123 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCTGGATATAGTAACTCGCACAAATG
*
20302163 CCTTTGGGACTTAGCCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCTGGATATAGTAACTCGCACAAATG
20302203 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
20302219 CGGTTGTCAT
Statistics
Matches: 125, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 16 0.13
40 109 0.87
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCTGGATATAGTAACTCGCACAAATG
Found at i:20303452 original size:24 final size:24
Alignment explanation
Indices: 20303422--20303467 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
20303412 CACCCCCCAA
20303422 TTTTTATTATT-TTATTACTAACCC
1 TTTTTATT-TTATTATTACTAACCC
*
20303446 TTTTTATTTTATTATTTCTAAC
1 TTTTTATTTTATTATTACTAAC
20303468 ATAAAGCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTTATTTTATTATTACTAACCC
Found at i:20306399 original size:39 final size:39
Alignment explanation
Indices: 20306355--20306627 Score: 501
Period size: 39 Copynumber: 7.0 Consensus size: 39
20306345 ATTATATTAT
* *
20306355 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
20306394 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
20306433 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
20306472 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
20306511 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
20306550 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
20306589 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
20306628 AGTGTCTTGC
Statistics
Matches: 226, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 226 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:20312037 original size:2 final size:2
Alignment explanation
Indices: 20312030--20312054 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20312020 TGCATCACTT
20312030 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
20312055 TAATTTAATT
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:20312265 original size:39 final size:39
Alignment explanation
Indices: 20312222--20312497 Score: 471
Period size: 39 Copynumber: 7.1 Consensus size: 39
20312212 ATTATATTAT
* * *
20312222 CAGCACAAAGCCTGCGGGACTTTAACCCAGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
20312261 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
20312300 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
20312339 CAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
20312378 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
20312417 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
20312456 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
20312495 CAG
1 CAG
20312498 TGTCTTGCAT
Statistics
Matches: 224, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 224 1.00
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:20314375 original size:27 final size:28
Alignment explanation
Indices: 20314319--20314388 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
20314309 AAATTTGTAC
20314319 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
20314347 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
20314374 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
20314389 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:20317485 original size:6 final size:6
Alignment explanation
Indices: 20317474--20317514 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
20317464 TACATTGTGT
*
20317474 CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA TAGTAA CAGTA
1 CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
20317515 GCGGTACACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (6 bp):
CAGTAA
Found at i:20317585 original size:14 final size:16
Alignment explanation
Indices: 20317556--20317587 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
20317546 CCAAAACAGT
20317556 AATAGTAGTCGACACA
1 AATAGTAGTCGACACA
20317572 AATAGT-GT-GACACA
1 AATAGTAGTCGACACA
20317586 AA
1 AA
20317588 GTCAGAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (16 bp):
AATAGTAGTCGACACA
Found at i:20318144 original size:19 final size:19
Alignment explanation
Indices: 20318120--20318156 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20318110 TCGATTTTTC
*
20318120 CTTTTTCTTTCTTTCCTTT
1 CTTTTTCCTTCTTTCCTTT
20318139 CTTTTTCCTTCTTTCCTT
1 CTTTTTCCTTCTTTCCTT
20318157 CCCTTGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTTCCTTCTTTCCTTT
Found at i:20319274 original size:9 final size:9
Alignment explanation
Indices: 20319260--20319454 Score: 109
Period size: 9 Copynumber: 22.1 Consensus size: 9
20319250 TATGTATTAC
*
20319260 GTAAGTTAA
1 GTAAGTTAT
*
20319269 GTAAGTTTT
1 GTAAGTTAT
20319278 GTAAGTTAT
1 GTAAGTTAT
20319287 GTAAGTTAT
1 GTAAGTTAT
* *
20319296 GATATGATAT
1 G-TAAGTTAT
* *
20319306 -AAATTTAT
1 GTAAGTTAT
*
20319314 GTAAGGTAT
1 GTAAGTTAT
*
20319323 GTAAATTAT
1 GTAAGTTAT
*
20319332 GTAAATTAT
1 GTAAGTTAT
* * *
20319341 GTTA-TGAA
1 GTAAGTTAT
* *
20319349 ATATATTTAT
1 GTA-AGTTAT
*
20319359 GT-A-TTAC
1 GTAAGTTAT
20319366 GTAAGTTAT
1 GTAAGTTAT
20319375 GTAAGTTAT
1 GTAAGTTAT
*
20319384 GTAAGTTAC
1 GTAAGTTAT
20319393 GTAAGTTAT
1 GTAAGTTAT
*
20319402 -TATA-TGAT
1 GTA-AGTTAT
* *
20319410 ATATATTTAT
1 GTA-AGTTAT
*
20319420 AT-A-TTAT
1 GTAAGTTAT
20319427 GTAAGTTAT
1 GTAAGTTAT
*
20319436 ATAAGTTAT
1 GTAAGTTAT
20319445 GTAAGTTAT
1 GTAAGTTAT
20319454 G
1 G
20319455 ATATCATGTA
Statistics
Matches: 144, Mismatches: 31, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
7 10 0.07
8 16 0.11
9 104 0.72
10 14 0.10
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:20319326 original size:45 final size:43
Alignment explanation
Indices: 20319277--20319384 Score: 135
Period size: 45 Copynumber: 2.5 Consensus size: 43
20319267 AAGTAAGTTT
*
20319277 TGTAAGTTATGTAAGTTATGATATGATATAAATTTATGTAAGGTA
1 TGTAAGTTATGTAAGTTATGATATGAAATAAATTTATGT-A-GTA
* * * * *
20319322 TGTAAATTATGTAAATTATGTTATGAAATATATTTATGTATTA
1 TGTAAGTTATGTAAGTTATGATATGAAATAAATTTATGTAGTA
*
20319365 CGTAAGTTATGTAAGTTATG
1 TGTAAGTTATGTAAGTTATG
20319385 TAAGTTACGT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 19 0.35
44 1 0.02
45 34 0.63
ACGTcount: A:0.37, C:0.01, G:0.18, T:0.44
Consensus pattern (43 bp):
TGTAAGTTATGTAAGTTATGATATGAAATAAATTTATGTAGTA
Found at i:20319375 original size:61 final size:61
Alignment explanation
Indices: 20319310--20319454 Score: 202
Period size: 61 Copynumber: 2.4 Consensus size: 61
20319300 TGATATAAAT
* * *
20319310 TTATGTAAGGTATGTAAATTATGTAAATTATGT-TATGAAATATATTTATGTATTACGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAATTAT-TATATGAAATATATTTATATATTACGTAAG
* * * *
20319371 TTATGTAAGTTATGTAAGTTACGTAAGTTATTATATGATATATATTTATATATTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAATTATTATATGAAATATATTTATATATTACGTAAG
*
20319432 TTATATAAGTTATGTAAGTTATG
1 TTATGTAAGTTATGTAAGTTATG
20319455 ATATCATGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 1 0.01
61 73 0.99
ACGTcount: A:0.37, C:0.01, G:0.16, T:0.46
Consensus pattern (61 bp):
TTATGTAAGTTATGTAAGTTATGTAAATTATTATATGAAATATATTTATATATTACGTAAG
Found at i:20319656 original size:15 final size:15
Alignment explanation
Indices: 20319638--20319692 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
20319628 AAAAATTTAT
20319638 TTTAATTAAATAATA
1 TTTAATTAAATAATA
20319653 TTT-A-TAAA-AATTA
1 TTTAATTAAATAA-TA
20319666 TTTTAATTAAATAATA
1 -TTTAATTAAATAATA
*
20319682 TTTAAATAAAT
1 TTTAATTAAAT
20319693 TAATCCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.18
14 4 0.12
15 14 0.41
16 6 0.18
17 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAATTAAATAATA
Found at i:20319666 original size:29 final size:28
Alignment explanation
Indices: 20319628--20319694 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 28
20319618 AATCACCTAG
*
20319628 AAAAATTTATTTTAATTAAATAATATTT
1 AAAAAATTATTTTAATTAAATAATATTT
20319656 ATAAAAATTATTTTAATTAAATAATATTT
1 A-AAAAATTATTTTAATTAAATAATATTT
20319685 AAATAAATTA
1 AAA-AAATTA
20319695 ATCCAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 3 0.08
29 33 0.92
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AAAAAATTATTTTAATTAAATAATATTT
Found at i:20319683 original size:16 final size:16
Alignment explanation
Indices: 20319635--20319684 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
20319625 TAGAAAAATT
20319635 TATTTTAATTAAATAA
1 TATTTTAATTAAATAA
20319651 TA-TTT-A-TAAA-AA
1 TATTTTAATTAAATAA
20319663 TTATTTTAATTAAATAA
1 -TATTTTAATTAAATAA
20319680 TATTT
1 TATTT
20319685 AAATAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 2 0.07
13 6 0.21
14 4 0.14
15 4 0.14
16 11 0.38
17 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTTTAATTAAATAA
Found at i:20319711 original size:39 final size:39
Alignment explanation
Indices: 20319660--20319750 Score: 157
Period size: 39 Copynumber: 2.4 Consensus size: 39
20319650 ATATTTATAA
*
20319660 AAATTATTTTAATTAAATAATATTTAAATAAATTAATCC
1 AAATTATATTAATTAAATAATATTTAAATAAATTAATCC
*
20319699 AAATTATATTAATTAATTAATATTTAAATAAATTAATCC
1 AAATTATATTAATTAAATAATATTTAAATAAATTAATCC
20319738 AAATTATA-TAATT
1 AAATTATATTAATT
20319751 TAAAAAATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 5 0.10
39 45 0.90
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (39 bp):
AAATTATATTAATTAAATAATATTTAAATAAATTAATCC
Found at i:20319714 original size:19 final size:19
Alignment explanation
Indices: 20319690--20319750 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
20319680 TATTTAAATA
20319690 AATTAATCCAAATTATATT
1 AATTAATCCAAATTATATT
* * *
20319709 AATTAAT-TAATATTTAAATA
1 AATTAATCCAA-A-TTATATT
20319729 AATTAATCCAAATTATA-T
1 AATTAATCCAAATTATATT
20319747 AATT
1 AATT
20319751 TAAAAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 6 0.18
19 12 0.36
20 13 0.39
21 2 0.06
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTAATCCAAATTATATT
Found at i:20319735 original size:20 final size:20
Alignment explanation
Indices: 20319670--20319735 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
20319660 AAATTATTTT
*
20319670 AATTAAATAATATTTAAATA
1 AATTAATTAATATTTAAATA
* * *
20319690 AATTAATCCAA-A-TTATATT
1 AATTAAT-TAATATTTAAATA
20319709 AATTAATTAATATTTAAATA
1 AATTAATTAATATTTAAATA
20319729 AATTAAT
1 AATTAAT
20319736 CCAAATTATA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.06
19 13 0.36
20 19 0.53
21 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTAATTAATATTTAAATA
Found at i:20319753 original size:19 final size:19
Alignment explanation
Indices: 20319687--20319753 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
20319677 TAATATTTAA
20319687 ATAAATTAATCCAAATTAT
1 ATAAATTAATCCAAATTAT
* * *
20319706 ATTAATTAAT-TAATATTTAA
1 ATAAATTAATCCAA-A-TTAT
20319726 ATAAATTAATCCAAATTAT
1 ATAAATTAATCCAAATTAT
*
20319745 ATAATTTAA
1 ATAAATTAA
20319754 AAAATTACGT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
18 2 0.05
19 21 0.55
20 13 0.34
21 2 0.05
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAATTAATCCAAATTAT
Found at i:20322374 original size:115 final size:114
Alignment explanation
Indices: 20322202--20322514 Score: 285
Period size: 115 Copynumber: 2.7 Consensus size: 114
20322192 AACGTGGACG
* ** * * ** * * * *
20322202 TTTTGCACTCTTAATACAACTTAGCGGCATTTTT-CCGAAAACGCCTGTAATGCACAACCTTTTG
1 TTTTGCACTCTTAATGCAGTTTTGCGGCGTTTTTGTTGAAAACACCAGTAAAGAACAACCTTTTG
* * * * * *
20322266 CGGCTTTTTTTGGGGAAATGCCACTAAAAACAAGGAT-AACAACCGACAACA
66 CGGC-GTTTATGAGGAAACGACACTAAAAACAAGCATGAA-AA-CGACAACA
* * ** * *
20322317 TTTTGTACTCTTAATGCA-TTTTGTGGCGTTTTTGTTGTGAACACCGGTAAAGAACAACATTTTG
1 TTTTGCACTCTTAATGCAGTTTTGCGGCGTTTTTGTTGAAAACACCAGTAAAGAACAACCTTTTG
* *
20322381 CGGCGTTTATGAGGAAACGACACTATAAACAAGCATGGAAAACGACGACA
66 CGGCGTTTATGAGGAAACGACACTAAAAACAAGCAT-GAAAACGACAACA
*
20322431 TTTTGCACTCTTAATGCAGTTTTGCGGCGTTTTTGTTGAAAACGCCAGTAAAGAACAA-CTTATT
1 TTTTGCACTCTTAATGCAGTTTTGCGGCGTTTTTGTTGAAAACACCAGTAAAGAACAACCTT-TT
* *
20322495 GCGACGTGCT-TGAGGAAACG
65 GCGGCGT-TTATGAGGAAACG
20322515 CCGCTAAAGA
Statistics
Matches: 160, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
114 62 0.39
115 95 0.59
116 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (114 bp):
TTTTGCACTCTTAATGCAGTTTTGCGGCGTTTTTGTTGAAAACACCAGTAAAGAACAACCTTTTG
CGGCGTTTATGAGGAAACGACACTAAAAACAAGCATGAAAACGACAACA
Found at i:20322657 original size:7 final size:7
Alignment explanation
Indices: 20322645--20322695 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
20322635 CACTGGTAAT
20322645 CCTAAAC
1 CCTAAAC
20322652 CCTAAAC
1 CCTAAAC
*
20322659 ACT-AAC
1 CCTAAAC
*
20322665 CCTTAAC
1 CCTAAAC
*
20322672 CCTTAAC
1 CCTAAAC
*
20322679 CTTTAAAC
1 C-CTAAAC
20322687 CCTAAAC
1 CCTAAAC
20322694 CC
1 CC
20322696 CAAATCCCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 5 0.14
7 27 0.73
8 5 0.14
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (7 bp):
CCTAAAC
Found at i:20322878 original size:6 final size:7
Alignment explanation
Indices: 20322857--20322961 Score: 56
Period size: 7 Copynumber: 15.0 Consensus size: 7
20322847 ACTAATTACT
20322857 CTAAACC
1 CTAAACC
20322864 CTAAACC
1 CTAAACC
*
20322871 CTAACCC
1 CTAAACC
* *
20322878 TCTATACT
1 -CTAAACC
20322886 CTAAACC
1 CTAAACC
* *
20322893 TTAAA-T
1 CTAAACC
* *
20322899 CAAAATC
1 CTAAACC
*
20322906 ATAAACC
1 CTAAACC
*
20322913 ATAAACCTC
1 CTAAA-C-C
20322922 CT-AACC
1 CTAAACC
20322928 CTAAACC
1 CTAAACC
20322935 CTAAACC
1 CTAAACC
20322942 CATAAA--
1 C-TAAACC
*
20322948 TTAAACC
1 CTAAACC
20322955 CTAAACC
1 CTAAACC
20322962 ATAATCATCA
Statistics
Matches: 73, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
5 4 0.05
6 6 0.08
7 50 0.68
8 11 0.15
9 2 0.03
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:20323026 original size:28 final size:28
Alignment explanation
Indices: 20322995--20323055 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
20322985 CCAAAAACTC
*
20322995 TAAACCATATACCCT-AAGCATTAAACCT
1 TAAACCATATACCCTAAACCA-TAAACCT
*
20323023 TAAATCATATACCCTAAACCATAAACCT
1 TAAACCATATACCCTAAACCATAAACCT
20323051 TAAAC
1 TAAAC
20323056 TATAATGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.25
Consensus pattern (28 bp):
TAAACCATATACCCTAAACCATAAACCT
Found at i:20323045 original size:14 final size:14
Alignment explanation
Indices: 20322858--20323060 Score: 76
Period size: 14 Copynumber: 14.2 Consensus size: 14
20322848 CTAATTACTC
*
20322858 TAAACCCTAAACCC
1 TAAACCCTAAACCA
* *
20322872 TAACCCTCTATACTC-
1 TAAACC-CTAAAC-CA
* *
20322887 TAAACCTTAAATCA
1 TAAACCCTAAACCA
* *
20322901 -AAATCATAAACCA
1 TAAACCCTAAACCA
*
20322914 TAAACCTCCT-AACCC
1 TAAA-C-CCTAAACCA
20322929 TAAACCCTAAACCCA
1 TAAACCCTAAA-CCA
* *
20322944 TAAA--TTAAACCC
1 TAAACCCTAAACCA
* *
20322956 TAAACCATAATCATCA
1 TAAACCCTAA--ACCA
*
20322972 CTAAACCCATAATCCA
1 -TAAACCC-TAAACCA
* *
20322988 AAAACTCTAAACCA
1 TAAACCCTAAACCA
* *
20323002 TATACCCT-AAGCA
1 TAAACCCTAAACCA
* *
20323015 TTAAACCTTAAATCA
1 -TAAACCCTAAACCA
*
20323030 TATACCCTAAACCA
1 TAAACCCTAAACCA
* *
20323044 TAAACCTTAAACTA
1 TAAACCCTAAACCA
20323058 TAA
1 TAA
20323061 TGATAATTAA
Statistics
Matches: 136, Mismatches: 37, Indels: 32
0.66 0.18 0.16
Matches are distributed among these distances:
12 6 0.04
13 22 0.16
14 59 0.43
15 33 0.24
16 7 0.05
17 6 0.04
18 3 0.02
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:20323527 original size:40 final size:40
Alignment explanation
Indices: 20323445--20323561 Score: 119
Period size: 40 Copynumber: 2.9 Consensus size: 40
20323435 TTAATTTTTT
* * **
20323445 GCGGTGTTTTTTCAAAAAA-CGCAGCTAATGGGTTGACCTATA
1 GCGGTG-TTTTT-AAAAAAGCGCAGCTAAT-GCTCGATATATA
*
20323487 GCGGTGTTTTTAAAAAAGCGCAGTTAATGCTCGATATATA
1 GCGGTGTTTTTAAAAAAGCGCAGCTAATGCTCGATATATA
** * *
20323527 GCGGTGTTTTTCTACAAGCGCCGCTAATGCTCGAT
1 GCGGTGTTTTTAAAAAAGCGCAGCTAATGCTCGAT
20323562 CTGTAGCAAC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 44 0.69
41 14 0.22
42 6 0.09
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (40 bp):
GCGGTGTTTTTAAAAAAGCGCAGCTAATGCTCGATATATA
Found at i:20323684 original size:196 final size:196
Alignment explanation
Indices: 20323350--20323763 Score: 537
Period size: 196 Copynumber: 2.1 Consensus size: 196
20323340 TTCAAAAACT
****
20323350 GCCGCTAATGCTCGATCTATAGCGGGGTTTTCCAAAAAGCGCCGCTAATGCAACTAAAGCTCAAC
1 GCCGCTAATGCTCGATCTATAGCAACATTTTCCAAAAAGCGCCGCTAATGCAACTAAAGCTCAAC
* * ** *
20323415 ATAAAACGATTGTGTTGTGCTTAATTTTTTGCGGTGTTTTTTCAAAAAACGCAGCTAATGGGTTG
66 ATAAAACGATGGCGTTGTGCTTAATTTTTTGCGGCATTTTTTCAAAAAACGCAGCTAATGGGTCG
** * * * *
20323480 ACCTATAGCGGTGTTTTTAAAAAAGCGCAGTTAATGCTCGAT-ATATAGCGGTGTTTTTCTACAA
131 ACCTATAGCGGCATTTTTAAAAAAGCGCAGCTAATGCTCAATCA-ATAGCGGTGATTTTATACAA
20323544 GC
195 GC
* **
20323546 GCCGCTAATGCTCGATCTGTAGCAACATTTTCCAAAAAGCGCCGCTAATGCCCCTAAAGCTCAAC
1 GCCGCTAATGCTCGATCTATAGCAACATTTTCCAAAAAGCGCCGCTAATGCAACTAAAGCTCAAC
* * * *
20323611 ATAAAATGATGGCGTTGTGCTTAATTTTTTTGCGGCATTTTTTGAAAAAGCGCTGCTAAT-GGTC
66 ATAAAACGATGGCGTTGTGCTTAA-TTTTTTGCGGCATTTTTTCAAAAAACGCAGCTAATGGGTC
* * *
20323675 GGCCTATAGCGGCATTTTTTAAAAAGCGCAGCTAATGCTCAATCAATAGCGGTGATTTTATAGAA
130 GACCTATAGCGGCATTTTTAAAAAAGCGCAGCTAATGCTCAATCAATAGCGGTGATTTTATACAA
20323740 GC
195 GC
* *
20323742 GCCACTAATTG-TCAATCTATAG
1 GCCGCTAA-TGCTCGATCTATAG
20323764 TGGCGTTTTT
Statistics
Matches: 187, Mismatches: 28, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
196 154 0.82
197 33 0.18
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (196 bp):
GCCGCTAATGCTCGATCTATAGCAACATTTTCCAAAAAGCGCCGCTAATGCAACTAAAGCTCAAC
ATAAAACGATGGCGTTGTGCTTAATTTTTTGCGGCATTTTTTCAAAAAACGCAGCTAATGGGTCG
ACCTATAGCGGCATTTTTAAAAAAGCGCAGCTAATGCTCAATCAATAGCGGTGATTTTATACAAG
C
Found at i:20323733 original size:41 final size:41
Alignment explanation
Indices: 20323642--20323726 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 41
20323632 TAATTTTTTT
* * ** *
20323642 GCGGCATTTTTTGAAAAAGCGCTGCTAATGGTCGGCCTATA
1 GCGGCATTTTTTGAAAAAGCGCAGCTAATGCTCAACCAATA
*
20323683 GCGGCATTTTTT-AAAAAGCGCAGCTAATGCTCAATCAATA
1 GCGGCATTTTTTGAAAAAGCGCAGCTAATGCTCAACCAATA
20323723 GCGG
1 GCGG
20323727 TGATTTTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 26 0.68
41 12 0.32
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (41 bp):
GCGGCATTTTTTGAAAAAGCGCAGCTAATGCTCAACCAATA
Found at i:20323791 original size:40 final size:39
Alignment explanation
Indices: 20323678--20323815 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 39
20323668 AATGGTCGGC
* * *
20323678 CTATAGCGGCATTTTTTAAAAAGCGCAGCTAA-TGCTCAAT
1 CTATAGCGGCGTTTTTT-AGAAGCGCCGCTAATTG-TCAAT
* * * *
20323718 CAATAGCGGTGATTTTATAGAAGCGCCACTAATTGTCAAT
1 CTATAGCGGCG-TTTTTTAGAAGCGCCGCTAATTGTCAAT
* * *
20323758 CTATAGTGGCGTTTTTTAGGAAGCGCCGCTAATTCTCGAT
1 CTATAGCGGCGTTTTTTA-GAAGCGCCGCTAATTGTCAAT
* *
20323798 CTTTAGTGGCGTTTTTTA
1 CTATAGCGGCGTTTTTTA
20323816 TTCAAACGCC
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 6 0.08
40 67 0.84
41 7 0.09
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (39 bp):
CTATAGCGGCGTTTTTTAGAAGCGCCGCTAATTGTCAAT
Found at i:20333248 original size:20 final size:19
Alignment explanation
Indices: 20333223--20333316 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 19
20333213 TATGTAACAA
20333223 AGGCACCGAAGTGCAGATAG
1 AGGCACCGAAGTGCA-ATAG
* *
20333243 AGGCA-CGATTGTGCAATCAA
1 AGGCACCGA-AGTGCAAT-AG
* *
20333263 AGGCACCAAAGTGCAAACAG
1 AGGCACCGAAGTGC-AATAG
* * *
20333283 AGACACCAAAGTGTAATAG
1 AGGCACCGAAGTGCAATAG
*
20333302 AGGCATCGAAGTGCA
1 AGGCACCGAAGTGCA
20333317 GACCCATACA
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
19 20 0.35
20 33 0.58
21 4 0.07
ACGTcount: A:0.39, C:0.20, G:0.28, T:0.13
Consensus pattern (19 bp):
AGGCACCGAAGTGCAATAG
Found at i:20334103 original size:7 final size:7
Alignment explanation
Indices: 20334091--20334115 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20334081 AATACAACCC
20334091 AAAATAA
1 AAAATAA
20334098 AAAATAA
1 AAAATAA
20334105 AAAATAA
1 AAAATAA
20334112 AAAA
1 AAAA
20334116 ATGAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:20335312 original size:19 final size:19
Alignment explanation
Indices: 20335288--20335325 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20335278 TTGAGATTGC
*
20335288 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
20335307 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
20335326 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:20337085 original size:26 final size:26
Alignment explanation
Indices: 20337055--20337113 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
20337045 TTTACCACAA
*
20337055 GTAAAAT-TGTCAAAGTTTTA-TAAGG
1 GTAAAATCT-TCAAAATTTTACTAAGG
20337080 GATAAAATCTTCAAAATTTTACTAAGG
1 G-TAAAATCTTCAAAATTTTACTAAGG
20337107 GTAAAAT
1 GTAAAAT
20337114 AGGCATGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.03
26 22 0.73
27 7 0.23
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (26 bp):
GTAAAATCTTCAAAATTTTACTAAGG
Found at i:20340498 original size:28 final size:27
Alignment explanation
Indices: 20340447--20340519 Score: 103
Period size: 28 Copynumber: 2.7 Consensus size: 27
20340437 TTTAAAACCC
*
20340447 TAGGGGT-ATATCGGTAATTATGCTCTT
1 TAGGGGTAATTTC-GTAATTATGCTCTT
*
20340474 TAGGGGTAATTTCAGTAATTTTGCTCTT
1 TAGGGGTAATTTC-GTAATTATGCTCTT
20340502 TAGGGGTAATTTCGTAAT
1 TAGGGGTAATTTCGTAAT
20340520 CTACGCTACT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 12 0.29
28 30 0.71
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (27 bp):
TAGGGGTAATTTCGTAATTATGCTCTT
Found at i:20341166 original size:27 final size:27
Alignment explanation
Indices: 20341136--20341197 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
20341126 GGGCAAAATG
20341136 GTAATTTTACCCTACAAGGGTATTTCA
1 GTAATTTTACCCTACAAGGGTATTTCA
* *
20341163 GTAATTTTACCCTACAGGGGTATTTTA
1 GTAATTTTACCCTACAAGGGTATTTCA
20341190 GTAATTTT
1 GTAATTTT
20341198 TCAAACCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (27 bp):
GTAATTTTACCCTACAAGGGTATTTCA
Found at i:20341210 original size:27 final size:27
Alignment explanation
Indices: 20341180--20341249 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
20341170 TACCCTACAG
* *
20341180 GGGTATTTTAGTAATTTT-TCAAACCAT
1 GGGTATTTTAGTAATTTTAT-AAACAAA
*
20341207 GGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTAGTAATTTTATAAACAAA
20341234 GGGTATTTTAGTAATT
1 GGGTATTTTAGTAATT
20341250 GGTAAACTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTATAAACAAA
Found at i:20347611 original size:40 final size:40
Alignment explanation
Indices: 20347486--20347692 Score: 204
Period size: 40 Copynumber: 5.2 Consensus size: 40
20347476 CAATTGAATG
* * ** * **
20347486 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
* * **
20347526 ATATCCGGGTTAAGA-CCGAAGGCCATT-GTGCTAG-TGACC
1 ATATCCGGGCTAAGACCCGAAGG-CATTCGTGCAAGTTG-TT
*
20347565 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
* * * *
20347605 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
* * *
20347645 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
20347685 ATATCCGG
1 ATATCCGG
20347693 TCGTATTCCG
Statistics
Matches: 138, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
39 29 0.21
40 107 0.78
41 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
Found at i:20360049 original size:16 final size:17
Alignment explanation
Indices: 20360028--20360060 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20360018 GACCTTAAGT
*
20360028 TTTGATTCC-ATAGCTA
1 TTTGATACCTATAGCTA
20360044 TTTGATACCTATAGCTA
1 TTTGATACCTATAGCTA
20360061 CTAGAACCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (17 bp):
TTTGATACCTATAGCTA
Found at i:20364742 original size:32 final size:32
Alignment explanation
Indices: 20364683--20364743 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
20364673 TCTTTAAATA
* * *
20364683 AAAAACATAAAATTTTAAAAATTATATTTTTC
1 AAAAACAAAAAATTTGAAAAATAATATTTTTC
20364715 AAAAACAAAAAATTATGAAAAA-AATATTT
1 AAAAACAAAAAATT-TGAAAAATAATATTT
20364744 AAAATTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 19 0.76
33 6 0.24
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (32 bp):
AAAAACAAAAAATTTGAAAAATAATATTTTTC
Found at i:20368530 original size:26 final size:27
Alignment explanation
Indices: 20368501--20368556 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
20368491 TTTCCATAGG
*
20368501 ACCAATTTTTGTA-AA-CATTTCATACA
1 ACCAA-TTTTGTATAACCAATTCATACA
*
20368527 ACC-ATTTTGTATAACCAATTCATATA
1 ACCAATTTTGTATAACCAATTCATACA
20368553 ACCA
1 ACCA
20368557 TTAGTCATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 7 0.28
25 3 0.12
26 15 0.60
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (27 bp):
ACCAATTTTGTATAACCAATTCATACA
Found at i:20368542 original size:13 final size:13
Alignment explanation
Indices: 20368516--20368558 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
20368506 TTTTTGTAAA
*
20368516 CATTTCATACAAC
1 CATTTCATATAAC
**
20368529 CATTTTGTATAAC
1 CATTTCATATAAC
*
20368542 CAATTCATATAAC
1 CATTTCATATAAC
20368555 CATT
1 CATT
20368559 AGTCATCTGG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (13 bp):
CATTTCATATAAC
Found at i:20368557 original size:26 final size:24
Alignment explanation
Indices: 20368507--20368558 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
20368497 TAGGACCAAT
*
20368507 TTTTGTAAACATTTCATACAACCA
1 TTTTGTAAACAATTCATACAACCA
*
20368531 TTTTGTATAACCAATTCATATAACCA
1 TTTTGTA-AA-CAATTCATACAACCA
20368557 TT
1 TT
20368559 AGTCATCTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 2 0.08
26 15 0.62
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (24 bp):
TTTTGTAAACAATTCATACAACCA
Found at i:20373318 original size:14 final size:14
Alignment explanation
Indices: 20373299--20373370 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
20373289 TATATAACCA
20373299 TTTCATATATCTAT
1 TTTCATATATCTAT
* *
20373313 TTTCATATAACCGA-
1 TTTCATAT-ATCTAT
* *
20373327 -TTCATAAAT-GA-
1 TTTCATATATCTAT
20373338 TTTCATATATCTAT
1 TTTCATATATCTAT
20373352 TTTCATATAT-TCAT
1 TTTCATATATCT-AT
20373366 TTTCA
1 TTTCA
20373371 CCCAATGAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
11 2 0.04
12 9 0.19
13 8 0.17
14 25 0.53
15 3 0.06
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (14 bp):
TTTCATATATCTAT
Found at i:20373347 original size:27 final size:28
Alignment explanation
Indices: 20373283--20373347 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
20373273 CCAATGTTCC
* *
20373283 ATTTCATATATAACCATTTCATATATCT
1 ATTTCATATATAACCATTTCATAAATCG
20373311 ATTT--TCATATAACCGA-TTCATAAAT-G
1 ATTTCAT-ATATAACC-ATTTCATAAATCG
20373337 ATTTCATATAT
1 ATTTCATATAT
20373348 CTATTTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
26 5 0.16
27 20 0.65
28 6 0.19
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.45
Consensus pattern (28 bp):
ATTTCATATATAACCATTTCATAAATCG
Found at i:20381395 original size:45 final size:45
Alignment explanation
Indices: 20381339--20381429 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
20381329 GAACTATGTG
*
20381339 ATCTGAACTCATTAAGTTGTGGTCTAAGTTCATGATATATGTGAC
1 ATCTGAACTCATTAAGTTATGGTCTAAGTTCATGATATATGTGAC
* * * *
20381384 ATCTGAACTCATTGAGTTATGGTCTGAGTTTATGATGTATGTGAC
1 ATCTGAACTCATTAAGTTATGGTCTAAGTTCATGATATATGTGAC
20381429 A
1 A
20381430 CATGTTTTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (45 bp):
ATCTGAACTCATTAAGTTATGGTCTAAGTTCATGATATATGTGAC
Found at i:20388884 original size:44 final size:44
Alignment explanation
Indices: 20388660--20388884 Score: 186
Period size: 46 Copynumber: 5.0 Consensus size: 44
20388650 TATGTGAGCC
* * **
20388660 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAAATGCT
1 AGTGTAAGACATGTCTGGGACATGCATTGG-CACA-GA-GATGTGCT
* * * *
20388707 AGTGTAAGACATATTTGGGACATGCATTGGCATTGAGACGA-GAGCT
1 AGTGTAAGACATGTCTGGGACATGCATTGGCA--CAGA-GATGTGCT
* * * ** * *
20388753 TGTGTGAGACATGTTTGGGACATGCATCAGC-CTCGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATTGGCAC-AGAGATGT--GCT
20388799 AGTGTAAGACATGTCTGGGACATGCATTGGCTAC-GAGATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATTGGC-ACAGAGATGTGCT
* *
20388843 ACTGTAAGACATGTCTGGGACATGCATTGGCACAGATATGTG
1 AGTGTAAGACATGTCTGGGACATGCATTGGCACAGAGATGTG
20388885 AGAGCCAGTG
Statistics
Matches: 144, Mismatches: 25, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
43 4 0.03
44 42 0.29
46 66 0.46
47 30 0.21
48 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATTGGCACAGAGATGTGCT
Found at i:20388891 original size:92 final size:91
Alignment explanation
Indices: 20388662--20388911 Score: 258
Period size: 92 Copynumber: 2.7 Consensus size: 91
20388652 TGTGAGCCAG
* * * *
20388662 TGTAAGACATGTCTGGGACATGCATCGGCCACATTATG-AAATGCTAGTGTAAGACATATTTGGG
1 TGTAAGACATGTCTGGGACATGCATCGGCCAGA-TATGTGAA-GCCAGTGTAAGACATATCTGGG
**
20388726 ACATGCATTGGCATTGAGACGAGAGCTTG
64 ACATGCATTGGCA-TGAGACGAGAGCTAC
* * * * * *
20388755 TGTGAGACATGTTTGGGACATGCATCAGCCTCGAGATGT-AAGCCAGTGTAAGACATGTCTGGGA
1 TGTAAGACATGTCTGGGACATGCATCGGCC-AGATATGTGAAGCCAGTGTAAGACATATCTGGGA
*
20388819 CATGCATTGGC-T-ACGA-GATGTGCTAC
65 CATGCATTGGCATGA-GACGA-GAGCTAC
*
20388845 TGTAAGACATGTCTGGGACATGCATTGGCACAGATATGTGAGAGCCAGTGTAAGACCATATCTGG
1 TGTAAGACATGTCTGGGACATGCATCGGC-CAGATATGTGA-AGCCAGTGTAAGA-CATATCTGG
20388910 GA
63 GA
20388912 TATGGCATCG
Statistics
Matches: 130, Mismatches: 19, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
89 3 0.02
90 38 0.29
91 2 0.02
92 44 0.34
93 42 0.32
94 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (91 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCAGATATGTGAAGCCAGTGTAAGACATATCTGGGAC
ATGCATTGGCATGAGACGAGAGCTAC
Found at i:20388911 original size:139 final size:138
Alignment explanation
Indices: 20388651--20388920 Score: 312
Period size: 139 Copynumber: 1.9 Consensus size: 138
20388641 CACTGTTGTT
* * *
20388651 ATGTGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAAATGCTAGTGTAAGA
1 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATG--ATGCTACTGTAAGA
* ** ** * * *
20388716 CATATTTGGGACATGCATTGGCATTGAGACGAGAGCTTGTGTGAGACATGTTTGGGACAT-GCAT
64 CATATCTGGGACATGCATTGGCACAGAGACGAGAGCCAGTGTAAGACATATCTGGGACATGGCAT
20388780 CAGCCTCGAG
129 CAGCCTCGAG
* *
20388790 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATTGGCTACGA-GATG-TGCTACTGTAAGAC
1 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGATGCTACTGTAAGAC
* * * *
20388853 ATGTCTGGGACATGCATTGGCACAGATATGTGAGAGCCAGTGTAAGACCATATCTGGGATATGGC
65 ATATCTGGGACATGCATTGGCACAGAGA--CGAGAGCCAGTGTAAGA-CATATCTGGGACATGGC
20388918 ATC
127 ATC
20388921 GACATCGATA
Statistics
Matches: 109, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
136 36 0.33
138 13 0.12
139 54 0.50
140 6 0.06
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (138 bp):
ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGATGCTACTGTAAGACA
TATCTGGGACATGCATTGGCACAGAGACGAGAGCCAGTGTAAGACATATCTGGGACATGGCATCA
GCCTCGAG
Found at i:20388976 original size:26 final size:26
Alignment explanation
Indices: 20388935--20388987 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
20388925 TCGATATGTG
*
20388935 TAAGATTTCTCAATTATCCTCTAGTA
1 TAAGATTTCCCAATTATCCTCTAGTA
* *
20388961 TAAGATTTCCCGATTATCCTCTGGTA
1 TAAGATTTCCCAATTATCCTCTAGTA
20388987 T
1 T
20388988 TCCAAGTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (26 bp):
TAAGATTTCCCAATTATCCTCTAGTA
Found at i:20396202 original size:39 final size:39
Alignment explanation
Indices: 20396001--20396185 Score: 259
Period size: 39 Copynumber: 4.8 Consensus size: 39
20395991 TGAGGTCTGC
*
20396001 AGGC-TTTATGCTGGTATTATATCCGGGATAAGTCCCGA
1 AGGCATTTATGCTGGTATTATATCCGGGCTAAGTCCCGA
* * * *
20396039 AGGCATTTGTGCTGGTGTTATATTCGGGCTAAGTCCTGA
1 AGGCATTTATGCTGGTATTATATCCGGGCTAAGTCCCGA
* *
20396078 AGGCATTTGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
1 AGGCATTTATGCTGGTATTATATCCGGGCTAAGTCCCGA
*
20396117 AGGCATTTATGCTAGTATTATATCCGGGCTAAAGTCCCGCA
1 AGGCATTTATGCTGGTATTATATCCGGGCT-AAGTCCCG-A
20396158 A-GC-TTTATGCTGGTATTATATCCGGGCT
1 AGGCATTTATGCTGGTATTATATCCGGGCT
20396186 TAAAGTCCGC
Statistics
Matches: 133, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
38 4 0.03
39 117 0.88
40 10 0.08
41 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (39 bp):
AGGCATTTATGCTGGTATTATATCCGGGCTAAGTCCCGA
Done.