Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 180 of 211
Found at i:53500148 original size:521 final size:521
Alignment explanation
Indices: 53499319--53500366 Score: 2087
Period size: 521 Copynumber: 2.0 Consensus size: 521
53499309 GAGGTTACTT
*
53499319 AAACATATAATATTACTACCTCGTTGAATCTAAACATGCATGCACGAAACATTAACACTTAACCC
1 AAACATATAAGATTACTACCTCGTTGAATCTAAACATGCATGCACGAAACATTAACACTTAACCC
53499384 AGAACCAGGAAGTTTCCTTCCTTGCACACCAGTCTGACACTTAATCAAAAACATGTAAACAACCT
66 AGAACCAGGAAGTTTCCTTCCTTGCACACCAGTCTGACACTTAATCAAAAACATGTAAACAACCT
53499449 TAAAAATTAACGTAGGGTTCATTAGTAATTACCAGAGAATTATAGGAAACGTATAAGTTGTCTGA
131 TAAAAATTAACGTAGGGTTCATTAGTAATTACCAGAGAATTATAGGAAACGTATAAGTTGTCTGA
53499514 CTACAATGAACCCAACTTCAGACAAGTTTTCTGGACTTTGTTTCTTCAGAAAATGCAAAGAAGAT
196 CTACAATGAACCCAACTTCAGACAAGTTTTCTGGACTTTGTTTCTTCAGAAAATGCAAAGAAGAT
53499579 CAAGGAGGAAGATGAACACAAGGAAAACGTAAAAATTTTCAATCAAGGCACTACTATCCTTACAT
261 CAAGGAGGAAGATGAACACAAGGAAAACGTAAAAATTTTCAATCAAGGCACTACTATCCTTACAT
53499644 CCCTAAGCACGGGGACAAATTTTAGTGGAAAAATCAAATAATTCTACTAACACTTTTGATTCTCA
326 CCCTAAGCACGGGGACAAATTTTAGTGGAAAAATCAAATAATTCTACTAACACTTTTGATTCTCA
53499709 TGATTAAGTACACTTATCAAGAACATCTACAGAGCTTAGTTCCATTCTAACTAAGTCTCAATTTA
391 TGATTAAGTACACTTATCAAGAACATCTACAGAGCTTAGTTCCATTCTAACTAAGTCTCAATTTA
53499774 ACTAACTAATTTTCCTTATTTAATAATAAACAAATCTATTCAACAATAAACCAAGTAAGATCGCC
456 ACTAACTAATTTTCCTTATTTAATAATAAACAAATCTATTCAACAATAAACCAAGTAAGATCGCC
53499839 A
521 A
53499840 AAACATATAAGATTACTACCTCGTTGAATCTAAACATGCATGCACGAAACATTAACACTTAACCC
1 AAACATATAAGATTACTACCTCGTTGAATCTAAACATGCATGCACGAAACATTAACACTTAACCC
53499905 AGAACCAGGAAGTTTCCTTCCTTGCACACCAGTCTGACACTTAATCAAAAACATGTAAACAACCT
66 AGAACCAGGAAGTTTCCTTCCTTGCACACCAGTCTGACACTTAATCAAAAACATGTAAACAACCT
53499970 TAAAAATTAACGTAGGGTTCATTAGTAATTACCAGAGAATTATAGGAAACGTATAAGTTGTCTGA
131 TAAAAATTAACGTAGGGTTCATTAGTAATTACCAGAGAATTATAGGAAACGTATAAGTTGTCTGA
53500035 CTACAATGAACCCAACTTCAGACAAGTTTTCTGGACTTTGTTTCTTCAGAAAATGCAAAGAAGAT
196 CTACAATGAACCCAACTTCAGACAAGTTTTCTGGACTTTGTTTCTTCAGAAAATGCAAAGAAGAT
53500100 CAAGGAGGAAGATGAACACAAGGAAAACGTAAAAATTTTCAATCAAGGCACTACTATCCTTACAT
261 CAAGGAGGAAGATGAACACAAGGAAAACGTAAAAATTTTCAATCAAGGCACTACTATCCTTACAT
53500165 CCCTAAGCACGGGGACAAATTTTAGTGGAAAAATCAAATAATTCTACTAACACTTTTGATTCTCA
326 CCCTAAGCACGGGGACAAATTTTAGTGGAAAAATCAAATAATTCTACTAACACTTTTGATTCTCA
53500230 TGATTAAGTACACTTATCAAGAACATCTACAGAGCTTAGTTCCATTCTAACTAAGTCTCAATTTA
391 TGATTAAGTACACTTATCAAGAACATCTACAGAGCTTAGTTCCATTCTAACTAAGTCTCAATTTA
53500295 ACTAACTAATTTTCCTTATTTAATAATAAACAAATCTATTCAACAATAAACCAAGTAAGATCGCC
456 ACTAACTAATTTTCCTTATTTAATAATAAACAAATCTATTCAACAATAAACCAAGTAAGATCGCC
53500360 A
521 A
53500361 AAACAT
1 AAACAT
53500367 CTGATTGGCG
Statistics
Matches: 526, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
521 526 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.28
Consensus pattern (521 bp):
AAACATATAAGATTACTACCTCGTTGAATCTAAACATGCATGCACGAAACATTAACACTTAACCC
AGAACCAGGAAGTTTCCTTCCTTGCACACCAGTCTGACACTTAATCAAAAACATGTAAACAACCT
TAAAAATTAACGTAGGGTTCATTAGTAATTACCAGAGAATTATAGGAAACGTATAAGTTGTCTGA
CTACAATGAACCCAACTTCAGACAAGTTTTCTGGACTTTGTTTCTTCAGAAAATGCAAAGAAGAT
CAAGGAGGAAGATGAACACAAGGAAAACGTAAAAATTTTCAATCAAGGCACTACTATCCTTACAT
CCCTAAGCACGGGGACAAATTTTAGTGGAAAAATCAAATAATTCTACTAACACTTTTGATTCTCA
TGATTAAGTACACTTATCAAGAACATCTACAGAGCTTAGTTCCATTCTAACTAAGTCTCAATTTA
ACTAACTAATTTTCCTTATTTAATAATAAACAAATCTATTCAACAATAAACCAAGTAAGATCGCC
A
Found at i:53501280 original size:17 final size:17
Alignment explanation
Indices: 53501260--53501295 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
53501250 TAATTTAAAT
*
53501260 AATTAATTAATTTTCTC
1 AATTAAATAATTTTCTC
53501277 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
53501294 AA
1 AA
53501296 CTGAATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:53509233 original size:24 final size:22
Alignment explanation
Indices: 53509186--53509234 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 22
53509176 AAAATATTAG
53509186 TAGGTAATAGAGTAATATATAAA
1 TAGGTAATAGAG-AATATATAAA
53509209 TAGGTAAATAGA-AATATTATCAAA
1 TAGGT-AATAGAGAATA-TAT-AAA
53509233 TA
1 TA
53509235 TAATAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
24 11 0.48
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (22 bp):
TAGGTAATAGAGAATATATAAA
Found at i:53509257 original size:24 final size:23
Alignment explanation
Indices: 53509230--53509285 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
53509220 AAATATTATC
*
53509230 AAATATAATAGTAATAACAAGAAT
1 AAATATAATA-TAAAAACAAGAAT
* *
53509254 AAATAGTAATATAAAAATAATAAT
1 AAATA-TAATATAAAAACAAGAAT
53509278 AAAT-TAAT
1 AAATATAAT
53509286 TAATAGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 4 0.14
24 19 0.68
25 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (23 bp):
AAATATAATATAAAAACAAGAAT
Found at i:53511116 original size:89 final size:87
Alignment explanation
Indices: 53510943--53511230 Score: 317
Period size: 89 Copynumber: 3.2 Consensus size: 87
53510933 CTTTAATCTG
* ** * * * *
53510943 CTCCGCTGCAACGCCAGGGACACAAGGTTGGTGTTTTTGATCTGTTTCGCTGTCAGTACAGGAAG
1 CTCCGCTGCAAC-CCAAGGAGGCAAGGCTGGTATCTTCGATCTGTTTCGCTGTCAGTACAGGAAG
* * *
53511008 GCAAAATCTGTTATATTCAGTCTA
65 GCAAGATCTCTT-TCTTCAGTCTA
* * * *
53511032 CTCTGCTGGCAACCCATGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTATCAGTACAGGAAG
1 CTCCGCT-GCAACCCAAGGAGGCAAGGCTGGTATCTTCGATCTGTTTCGCTGTCAGTACAGGAAG
53511097 GCAAGATCTACTTTCTTCAGTCTGA
65 GCAAGATCT-CTTTCTTCAGTCT-A
* * *
53511122 -TCCACTGCAAGCCCAAGGAGGCAAGGCTGGTGTCTTCGATCTGTTTCGCTGTCAGTATAGGAAG
1 CTCCGCTGCAA-CCCAAGGAGGCAAGGCTGGTATCTTCGATCTGTTTCGCTGTCAGTACAGGAAG
* *
53511186 GCAAGATCTGCTTTCTTTAGTCTG
65 GCAAGATCT-CTTTCTTCAGTCTA
*
53511210 CTCCGCTGCAAACCCAGGGAG
1 CTCCGCTGC-AACCCAAGGAG
53511231 ATAAGACTTG
Statistics
Matches: 168, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
88 4 0.02
89 154 0.92
90 10 0.06
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (87 bp):
CTCCGCTGCAACCCAAGGAGGCAAGGCTGGTATCTTCGATCTGTTTCGCTGTCAGTACAGGAAGG
CAAGATCTCTTTCTTCAGTCTA
Found at i:53511309 original size:44 final size:41
Alignment explanation
Indices: 53511224--53511318 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 41
53511214 GCTGCAAACC
*
53511224 CAGGGAGATAAGACTTGATGTGATCTGCTCTACTGCAACTT
1 CAGGGAGATAAGACTTGATGTGATCCGCTCTACTGCAACTT
* * *
53511265 CAGGGAGATAAGATCTATTATTTGATTCCGCTCTACTGCCACTT
1 CAGGGAGATAAGA-CT-TGATGTGA-TCCGCTCTACTGCAACTT
53511309 CAGGGAGATA
1 CAGGGAGATA
53511319 GGATTACTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
41 13 0.28
42 2 0.04
43 6 0.13
44 26 0.55
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (41 bp):
CAGGGAGATAAGACTTGATGTGATCCGCTCTACTGCAACTT
Found at i:53511530 original size:44 final size:44
Alignment explanation
Indices: 53511343--53512203 Score: 325
Period size: 44 Copynumber: 19.8 Consensus size: 44
53511333 AATTCACCAT
* * * * *
53511343 CTTCAGTCTGCCCCACTGCAACTTCAGGGGGATAAGACTTGCT-T
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTACTGA
* * * * * *
53511387 CCTCAGTCAGCTTCGCTGCAACCTCAGGGAGAT-A-A-TACCTGA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTA-CTGA
* * * * * *
53511429 -TGT-GATCTGCTCTATTGCAACTTCAGAGAGACAAGATCTA-TTA
1 CT-TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TACTGA
* * ** * *
53511472 TTTGAATCCACTCCACTGCCACTTCAGGGAGATAGGATTACTGA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTGA
*
53511516 CTTCAATCTGCTCCACTGCAAAC-TCAGGGAGATAAGATTCAC-CA
1 CTTCAATCTGCTCCACTGC-AACTTCAGGGAGATAAGATT-ACTGA
* * * * * **
53511560 TCTTCAGTCTGCCCCACTGCAACTTTAGGGGGATAAGACTTGCTTT
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTACTGA
* * *** * *
53511606 C-TCAGTCTACTCTGTTGCAACCTCAGGGAGATAAGACT--TGA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTGA
* * * * * *
53511647 -TGT-GATCTGCACTACTGCAAATTCAGAGAGATAAGATCTA-T-T
1 CT-TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TACTGA
* * * * *
53511689 TTTGAATCTGCTCCACTGCCACTTCAGGGAGATAGGATTACTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTGA
* * * * *
53511733 CTTCAATATGCTCCCCTACAAAC-TCAGAGAGATAAGATTCAC-CA
1 CTTCAATCTGCTCCACTGC-AACTTCAGGGAGATAAGATT-ACTGA
* * *
53511777 TCTTCAATCTGCTCCACTACAGCTT-AGGGAGATAAGA--CCTGA
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTGA
* * * * * * * *
53511819 -TGCGATTTACTCTACTGCAACTTTAGAGAGATAAGATCTATTG-
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TACTGA
* * * * *
53511862 TTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTA-TCGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACT-GA
* *
53511906 CTTCAATCTGCTCCACTGCAACCTCAGCGAGATAAGATT--TGCCA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTG--A
* * * * * *
53511950 TCTTCGATCTGCTCCACTACTACTT-AGGGAGATAAAATTTGCT-T
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTACTGA
** ** * * * *
53511994 CTTCGGTCTGCTCTGCTGTAACCTCAGGGGGATAAGA--CCTGA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTGA
* * * * * *
53512036 -TACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTG-
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TACTGA
* * * * * *
53512079 TTTTAATC-CCTCCACTACAACTTCAGGGAGATAGGATTACTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTGA
* * *
53512122 CTTTAATCTGCTCCACTACAAAC-TCAGGGAGATAAGATTCAC-CA
1 CTTCAATCTGCTCCACTGC-AACTTCAGGGAGATAAGATT-ACTGA
* * * *
53512166 TCTTCAGTCTACCCCACTGCAACTTCAGGGGGATAAGA
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
53512204 CTAGCGATTT
Statistics
Matches: 597, Mismatches: 166, Indels: 107
0.69 0.19 0.12
Matches are distributed among these distances:
40 17 0.03
41 88 0.15
42 15 0.03
43 90 0.15
44 271 0.45
45 113 0.19
46 2 0.00
47 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTGA
Found at i:53511836 original size:172 final size:173
Alignment explanation
Indices: 53511630--53511984 Score: 509
Period size: 173 Copynumber: 2.1 Consensus size: 173
53511620 TTGCAACCTC
* * *
53511630 AGGGAGATAAGACTTGATGTGATCTGCACTACTGCAAATTCAGAGAGATAAGATCTATT-TTTGA
1 AGGGAGATAAGACCTGATGCGATCTACACTACTGCAAATTCAGAGAGATAAGATCTATTGTTTGA
* *
53511694 ATCTGCTCCACTGCCACTTCAGGGAGATAGGATTA-CTGGCTTCAATATGCTCCCCTACAAACTC
66 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATC-GGCTTCAATATGCTCCACTACAAACTC
53511758 AGAGAGATAAGATTCACCATCTTCAATCTGCTCCACTAC-AGCTT
130 AGAGAGATAAGATTCACCATCTTCAATCTGCTCCACTACTA-CTT
* * * * *
53511802 AGGGAGATAAGACCTGATGCGATTTACTCTACTGCAACTTTAGAGAGATAAGATCTATTGTTTTA
1 AGGGAGATAAGACCTGATGCGATCTACACTACTGCAAATTCAGAGAGATAAGATCTATTGTTTGA
* * * *
53511867 ATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCA
66 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTCAATATGCTCCACTACAAACTCA
* ** *
53511932 GCGAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTACTT
131 GAGAGATAAGATTCACCATCTTCAATCTGCTCCACTACTACTT
53511975 AGGGAGATAA
1 AGGGAGATAA
53511985 AATTTGCTTC
Statistics
Matches: 162, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
172 52 0.32
173 108 0.67
174 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (173 bp):
AGGGAGATAAGACCTGATGCGATCTACACTACTGCAAATTCAGAGAGATAAGATCTATTGTTTGA
ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTCAATATGCTCCACTACAAACTCA
GAGAGATAAGATTCACCATCTTCAATCTGCTCCACTACTACTT
Found at i:53511916 original size:217 final size:217
Alignment explanation
Indices: 53511482--53512160 Score: 671
Period size: 217 Copynumber: 3.1 Consensus size: 217
53511472 TTTGAATCCA
* * *
53511482 CTCCACTGCCACTTCAGGGAGATAGGATTACTGACTTCAATCTGCTCCACTGCAAACTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTACTGACTTCAATCTGCTCCACTACAAACTCAGGGAG
* * * * * *
53511547 ATAAGATTCACCATCTTCAGTCTGCCCCACTGCAACTTTAGGGGGATAAGACTTGCTTTCTCAGT
66 ATAAGATTCACCATCTTCAGTCTGCTCCACTACAAC-TTAGGGGGATAAGACCTG-ATAC-GA-T
** * * * * * * * * *
53511612 CTACTCTGTTGCAACCTCAGGGAGATAAGA-C--TTGATGTGATCTGCACTACTGCAAATTCAGA
127 CTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCTGCTCCACTGCAACTTCAGG
* ** *
53511674 GAGATAAGATCTAT--TTTTGAATCTG
192 GAGATAGGAT-TATCGGCTTCAATCTG
* * * * * *
53511699 CTCCACTGCCACTTCAGGGAGATAGGATTACTGGCTTCAATATGCTCCCCTACAAACTCAGAGAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTACTGACTTCAATCTGCTCCACTACAAACTCAGGGAG
* * * * *
53511764 ATAAGATTCACCATCTTCAATCTGCTCCACTACAGCTTAGGGAGATAAGACCTGATGCGATTTAC
66 ATAAGATTCACCATCTTCAGTCTGCTCCACTACAACTTAGGGGGATAAGACCTGATACGATCTAC
* *
53511829 TCTACTGCAACTTTAGAGAGATAAGATCTATTGTTTTAATCTGCTCCACTGTAACTTCAGGGAGA
131 TCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCTGCTCCACTGCAACTTCAGGGAGA
53511894 TAGGATTATCGGCTTCAATCTG
196 TAGGATTATCGGCTTCAATCTG
* * * * *
53511916 CTCCACTGCAACCTCAGCGAGATAAGATT--TGCCATCTTCGATCTGCTCCACTAC-TACTTAGG
1 CTCCACTGCAACTTCAGGGAGATAAGATTACTG--A-CTTCAATCTGCTCCACTACAAACTCAGG
* ** * * ** ** *
53511978 GAGATAAAATT-TGCTTCTTCGGTCTGCTCTGCTGTAACCTCAGGGGGATAAGACCTGATACGAT
63 GAGATAAGATTCACCATCTTCAGTCTGCTCCACTACAA-CTTAGGGGGATAAGACCTGATACGAT
* *
53512042 CTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTAATC-CCTCCACTACAACTTCAGG
127 CTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCTGCTCCACTGCAACTTCAGG
*
53512106 GAGATAGGATTA-CTGGCTTTAATCTG
192 GAGATAGGATTATC-GGCTTCAATCTG
*
53512132 CTCCACTACAAAC-TCAGGGAGATAAGATT
1 CTCCACTGC-AACTTCAGGGAGATAAGATT
53512161 CACCATCTTC
Statistics
Matches: 386, Mismatches: 65, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
213 25 0.06
214 2 0.01
215 8 0.02
216 126 0.33
217 209 0.54
218 16 0.04
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (217 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTACTGACTTCAATCTGCTCCACTACAAACTCAGGGAG
ATAAGATTCACCATCTTCAGTCTGCTCCACTACAACTTAGGGGGATAAGACCTGATACGATCTAC
TCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCTGCTCCACTGCAACTTCAGGGAGA
TAGGATTATCGGCTTCAATCTG
Found at i:53512102 original size:43 final size:44
Alignment explanation
Indices: 53512053--53512160 Score: 132
Period size: 43 Copynumber: 2.5 Consensus size: 44
53512043 TACTCTACTG
* * *
53512053 CAACTTCAGAGAGATAAGATCTA-TTGTTTTAATC-CCTCCACTA
1 CAACTTCAGGGAGATAAGAT-TACTGGCTTTAATCTCCTCCACTA
* *
53512096 CAACTTCAGGGAGATAGGATTACTGGCTTTAATCTGCTCCACTA
1 CAACTTCAGGGAGATAAGATTACTGGCTTTAATCTCCTCCACTA
53512140 CAAAC-TCAGGGAGATAAGATT
1 C-AACTTCAGGGAGATAAGATT
53512161 CACCATCTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.04
43 27 0.48
44 24 0.43
45 3 0.05
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGATTACTGGCTTTAATCTCCTCCACTA
Found at i:53513455 original size:14 final size:14
Alignment explanation
Indices: 53513416--53513448 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
53513406 CTATTTTTAC
53513416 TTTTTCCATTTTCCA
1 TTTTT-CATTTTCCA
53513431 TTTTTCATTTT-CA
1 TTTTTCATTTTCCA
53513444 TTTTT
1 TTTTT
53513449 TAGTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTCATTTTCCA
Found at i:53514372 original size:16 final size:16
Alignment explanation
Indices: 53514351--53514387 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
53514341 TTAACCTCTC
**
53514351 TTTTTTCTTTTTCTTT
1 TTTTTTCTTCCTCTTT
53514367 TTTTTTCTTCCTCTTT
1 TTTTTTCTTCCTCTTT
53514383 TTTTT
1 TTTTT
53514388 CATTTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTTCCTCTTT
Found at i:53518825 original size:17 final size:18
Alignment explanation
Indices: 53518803--53518836 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53518793 ACAATGAAGT
53518803 TATATAT-GTATAAAATA
1 TATATATAGTATAAAATA
*
53518820 TATATATAGTTTAAAAT
1 TATATATAGTATAAAAT
53518837 TAAATAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TATATATAGTATAAAATA
Found at i:53518968 original size:24 final size:23
Alignment explanation
Indices: 53518941--53518993 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
53518931 AAATATTATC
*
53518941 AAATATAATAGTAATAACAATAAT
1 AAATATAATA-TAAAAACAATAAT
* *
53518965 AAATTGTAATATAAAAATAATAAT
1 AAA-TATAATATAAAAACAATAAT
53518989 AAATA
1 AAATA
53518994 AATTAATAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.04
24 17 0.71
25 6 0.25
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AAATATAATATAAAAACAATAAT
Found at i:53526613 original size:89 final size:89
Alignment explanation
Indices: 53526462--53526641 Score: 342
Period size: 89 Copynumber: 2.0 Consensus size: 89
53526452 GCTTCTTTGC
*
53526462 AAATGATCGAATACTTCAGAGGAAATCAGGTTCTCTATTCTCTCCATTTTTGTTGAATTTCTTTT
1 AAATGATCGAATACTTCAGAGGAAATCAGGTTCTCTATTCTCTCCATTTTTGTTAAATTTCTTTT
53526527 TATAAATTTCAATATAATGATTAT
66 TATAAATTTCAATATAATGATTAT
*
53526551 AAATGATCGAATATTTCAGAGGAAATCAGGTTCTCTATTCTCTCCATTTTTGTTAAATTTCTTTT
1 AAATGATCGAATACTTCAGAGGAAATCAGGTTCTCTATTCTCTCCATTTTTGTTAAATTTCTTTT
53526616 TATAAATTTCAATATAATGATTAT
66 TATAAATTTCAATATAATGATTAT
53526640 AA
1 AA
53526642 TATATGTATT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.44
Consensus pattern (89 bp):
AAATGATCGAATACTTCAGAGGAAATCAGGTTCTCTATTCTCTCCATTTTTGTTAAATTTCTTTT
TATAAATTTCAATATAATGATTAT
Found at i:53540843 original size:16 final size:17
Alignment explanation
Indices: 53540814--53540847 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
53540804 TTACATCGAC
*
53540814 AAAATAAATTAATTTAA
1 AAAATAAATAAATTTAA
53540831 AAAATAAA-AAATTTAA
1 AAAATAAATAAATTTAA
53540847 A
1 A
53540848 TTTAACGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAATAAATTTAA
Found at i:53548355 original size:20 final size:19
Alignment explanation
Indices: 53548328--53548365 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
53548318 TTAGAAAAAA
53548328 TTTAATTTCTTTA-AATTTT
1 TTTAATTT-TTTAGAATTTT
53548347 TTTATATTTTTTAGAATTT
1 TTTA-ATTTTTTAGAATTT
53548366 GTTATGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTAATTTTTTAGAATTTT
Found at i:53548421 original size:19 final size:20
Alignment explanation
Indices: 53548399--53548464 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
53548389 AAAATTTGGA
*
53548399 AATTTTTTTAAA-TATTTTG
1 AATTTTTTAAAATTATTTTG
* *
53548418 AA-TTTTAAAAATTGTTTTG
1 AATTTTTTAAAATTATTTTG
* *
53548437 AATTTTTGAAAATTATATTG
1 AATTTTTTAAAATTATTTTG
53548457 AATTTTTT
1 AATTTTTT
53548465 TTTGTAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 7 0.18
19 10 0.26
20 21 0.55
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
AATTTTTTAAAATTATTTTG
Found at i:53549006 original size:31 final size:29
Alignment explanation
Indices: 53548970--53549036 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
53548960 ATATGCCCTC
*
53548970 AGTCCCTGTACTTTTCACTATTTTGAAATT-T
1 AGTCCCTGTACTTTT-A-T-TTTTAAAATTAT
* *
53549001 AGTCCCTTTGCTTTTATTTTTAAAATTAT
1 AGTCCCTGTACTTTTATTTTTAAAATTAT
53549030 AGTCCCT
1 AGTCCCT
53549037 TTGATTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.28
29 9 0.28
30 1 0.03
31 13 0.41
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.49
Consensus pattern (29 bp):
AGTCCCTGTACTTTTATTTTTAAAATTAT
Found at i:53552359 original size:25 final size:26
Alignment explanation
Indices: 53552329--53552390 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
53552319 ATGTATATTG
*
53552329 ATATATATATTTCTTTTAT-TCACATAC
1 ATATATAT-TTTCTTATATGT-ACATAC
*
53552356 ATATA-ATTTTCTTATATGTACATAT
1 ATATATATTTTCTTATATGTACATAC
53552381 ATATAT-TTTT
1 ATATATATTTT
53552391 ATATTTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 23 0.74
26 3 0.10
27 5 0.16
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.55
Consensus pattern (26 bp):
ATATATATTTTCTTATATGTACATAC
Found at i:53558536 original size:87 final size:88
Alignment explanation
Indices: 53558140--53558643 Score: 708
Period size: 88 Copynumber: 5.8 Consensus size: 88
53558130 TTTTCTTGGA
*
53558140 GTTGTAGCGGAGCAAATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
* * *
53558205 TAACGAGTATTCTTTTCCCTAGT
66 CAACGAGTCTTCTTTTCCCTAGC
* * *
53558228 GTTGTAGCGGAGCAGATTAAAGTTGAAGGCAGCGAATCTTATCTCCCTAGCATTAAGATCGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
*
53558293 GAACGAGTCTTCTTTTCCCTAGC
66 CAACGAGTCTTCTTTTCCCTAGC
* * * *
53558316 GTTGTAGCGGAGCAGATTAAAGCTGAAGACAGCGAATCTTATCTCCCTCGCATTAAGATCGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
* *
53558381 TAACGAGTCTTCTTTTCCCT-GAT
66 CAACGAGTCTTCTTTTCCCTAG-C
* * * * ** *
53558404 GTTTTAACGGAGTAGATTAAAACTGAAGGCAATGAATCTTATCTCCTTAGCGTTAAGACCGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
*
53558469 CAACGAGTCTTC-TTTCCCTGGC
66 CAACGAGTCTTCTTTTCCCTAGC
* * * *
53558491 GTTGTAGTGGAGCAGATTAAAGCTGAAGGCAGTGAATCTTATCTCCCTGGCGTTAAGACTGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
*
53558556 CAGCGAGTCTT-TTTTCCCTAGC
66 CAACGAGTCTTCTTTTCCCTAGC
* * *
53558578 GTTGTAGCGGAGCAGATTAAAGCTGAAAGTAGCGAATCTTATCTCCCTAGCGTTAAGACAGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
53558643 C
66 C
53558644 GTGGAATAAG
Statistics
Matches: 371, Mismatches: 42, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
87 143 0.39
88 228 0.61
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
CAACGAGTCTTCTTTTCCCTAGC
Found at i:53558777 original size:50 final size:50
Alignment explanation
Indices: 53558714--53559284 Score: 408
Period size: 50 Copynumber: 11.4 Consensus size: 50
53558704 TTTAGTGTTA
* * * *
53558714 TAGTGGAATAGATTAAAACTACAACGGTGAATCTTACTTCCCTGGCGGTG
1 TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
* * **
53558764 TAGTGGAACAGATTGAAGCTACAACAGTGAATCTTACTTCCCTAACATTG
1 TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
* * * * * * * *
53558814 CAAT-TAATTAGATTAAAGCTACAACGGCGAATCTTCCTTCCCTGGCGGTG
1 TAGTGGAA-CAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
* * * **
53558864 TAGTAGAGCAGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGA-GGTG
1 TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCT-GACGGTG
* * * * ** **
53558914 CAGTGGAACAGCTTGAAGCTACAACGATGAATCTTGCTTCCCCAACATTG
1 TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
* * ** * * ** *
53558964 CAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTG
1 TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
* * * ** **
53559014 CAGTGGAACAAATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACATTG
1 TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
* ** * * * ** *
53559064 TAATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTCTCTGGTGGTA
1 TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
* * * * * **
53559114 CAGTGGAATAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTG
1 TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
** * * ***
53559164 TAGTTAAAAAGGTTGAAGCTACAACAACGAATCTTACTTCCCTGACGGTG
1 TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
* **** * * *
53559214 TAATGGAACAGATTGAAGCTACAATAACGAATCTTACTTTCCTGAAGTTG
1 TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
* *
53559264 CAGTGGAGCAGATTGAAGCTA
1 TAGTGGAACAGATTGAAGCTA
53559285 TAAATTACCG
Statistics
Matches: 393, Mismatches: 124, Indels: 8
0.75 0.24 0.02
Matches are distributed among these distances:
49 3 0.01
50 388 0.99
51 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (50 bp):
TAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACGGTG
Found at i:53558933 original size:100 final size:99
Alignment explanation
Indices: 53558715--53559237 Score: 494
Period size: 100 Copynumber: 5.2 Consensus size: 99
53558705 TTAGTGTTAT
* * * * * * ** * *
53558715 AGTGGAATAGATTAAAACTACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGA
1 AGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGTAGT-AAAAAGATTGA
* * * * **
53558780 AGCTACAACAGTGAATCTTACTTCCCT-AACATTGC
65 AGCCACAACGGCGAATCTTACTTCCCTGGA-GGTGC
* * * * * * * * ** **
53558815 AAT-TAATTAGATTAAAGCTACAACGGCGAATCTTCCTTCCCTGGCGGTGTAGTAGAGCAGATTG
1 AGTGGAA-CAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGTAGTA-AAAAGATTG
*
53558879 AAGCCACAACGGCAAATCTTACTTCCCTGGAGGTGC
64 AAGCCACAACGGCGAATCTTACTTCCCTGGAGGTGC
* * * * *
53558915 AGTGGAACAGCTTGAAGCTACAACGATGAATCTTGCTTCCCCAACATTGCAATTAAAAAGATTGA
1 AGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTG-TAGTAAAAAGATTGA
* *
53558980 AGCCACAACGACGAATCTTACTTCCCTGGCGGTGC
65 AGCCACAACGGCGAATCTTACTTCCCTGGAGGTGC
* * *
53559015 AGTGGAACAAATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGTAATTAAAAAGATTGA
1 AGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGT-AGTAAAAAGATTGA
* * * *
53559080 AGCCACAACGGTGAATCTTACTTCTCTGGTGGTAC
65 AGCCACAACGGCGAATCTTACTTCCCTGGAGGTGC
* * *
53559115 AGTGGAATAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGTAGTTAAAAAGGTTGA
1 AGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGTAG-TAAAAAGATTGA
* ** *
53559180 AGCTACAACAACGAATCTTACTTCCCT-GACGGTGT
65 AGCCACAACGGCGAATCTTACTTCCCTGGA-GGTGC
*
53559215 AATGGAACAGATTGAAGCTACAA
1 AGTGGAACAGATTGAAGCTACAA
53559238 TAACGAATCT
Statistics
Matches: 356, Mismatches: 59, Indels: 16
0.83 0.14 0.04
Matches are distributed among these distances:
99 4 0.01
100 346 0.97
101 6 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (99 bp):
AGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGTAGTAAAAAGATTGAA
GCCACAACGGCGAATCTTACTTCCCTGGAGGTGC
Found at i:53558995 original size:150 final size:150
Alignment explanation
Indices: 53558734--53559055 Score: 457
Period size: 150 Copynumber: 2.1 Consensus size: 150
53558724 GATTAAAACT
* *
53558734 ACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACAACAGTGAATCTT
1 ACAACGGTGAATCTTACTTCCCTGGAGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTT
* ** * * *
53558799 ACTTCCCTAACATTGCAATTAATTAGATTAAAGCTACAACGGCGAATCTTCCTTCCCTGGCGGTG
66 ACTTCCCCAACATTGCAATTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCCCTGGCGGTG
* * *
53558864 TAGTAGAGCAGATTGAAGCC
131 CAGTAGAACAAATTGAAGCC
** *
53558884 ACAACGGCAAATCTTACTTCCCTGGAGGTGCAGTGGAACAGCTTGAAGCTACAAC-GATGAATCT
1 ACAACGGTGAATCTTACTTCCCTGGAGGTGCAGTGGAACAGATTGAAGCTACAACAG-TGAATCT
* *
53558948 TGCTTCCCCAACATTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGT
65 TACTTCCCCAACATTGCAATTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCCCTGGCGGT
* *
53559013 GCAGTGGAACAAATTGAAGCT
130 GCAGTAGAACAAATTGAAGCC
*
53559034 ACAACGGTGAATCTTGCTTCCC
1 ACAACGGTGAATCTTACTTCCC
53559056 CAACATTGTA
Statistics
Matches: 150, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
149 1 0.01
150 149 0.99
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (150 bp):
ACAACGGTGAATCTTACTTCCCTGGAGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTT
ACTTCCCCAACATTGCAATTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCCCTGGCGGTG
CAGTAGAACAAATTGAAGCC
Found at i:53559079 original size:200 final size:200
Alignment explanation
Indices: 53558873--53559237 Score: 561
Period size: 200 Copynumber: 1.8 Consensus size: 200
53558863 GTAGTAGAGC
* *
53558873 AGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGAGGTGCAGTGGAACAGCTTGAAGCTACAA
1 AGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGAGGTACAGTGGAACAGATTGAAGCTACAA
*
53558938 C-GATGAATCTTGCTTCCCCAACATTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACT
66 CAG-TGAATCTTGCTTCCCCAACATTGCAATTAAAAAGATTGAAGCCACAACAACGAATCTTACT
* *
53559002 TCCCTGGCGGTGCAGTGGAACAAATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGTAA
130 TCCCTGACGGTGCAATGGAACAAATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGTAA
53559067 TTAAAA
195 TTAAAA
** * * *
53559073 AGATTGAAGCCACAACGGTGAATCTTACTTCTCTGGTGGTACAGTGGAATAGATTGAAGCTACAA
1 AGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGAGGTACAGTGGAACAGATTGAAGCTACAA
* * * * *
53559138 CAGTGAATCTTGCTTCCCCGACATTGTAGTTAAAAAGGTTGAAGCTACAACAACGAATCTTACTT
66 CAGTGAATCTTGCTTCCCCAACATTGCAATTAAAAAGATTGAAGCCACAACAACGAATCTTACTT
* *
53559203 CCCTGACGGTGTAATGGAACAGATTGAAGCTACAA
131 CCCTGACGGTGCAATGGAACAAATTGAAGCTACAA
53559238 TAACGAATCT
Statistics
Matches: 147, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
200 146 0.99
201 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.25
Consensus pattern (200 bp):
AGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGAGGTACAGTGGAACAGATTGAAGCTACAA
CAGTGAATCTTGCTTCCCCAACATTGCAATTAAAAAGATTGAAGCCACAACAACGAATCTTACTT
CCCTGACGGTGCAATGGAACAAATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGTAAT
TAAAA
Found at i:53559246 original size:100 final size:100
Alignment explanation
Indices: 53558873--53559248 Score: 502
Period size: 100 Copynumber: 3.8 Consensus size: 100
53558863 GTAGTAGAGC
* * *
53558873 AGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGA-GGTGCAGTGGAACAGCTTGAAGCTACA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCT-GACGGTGCAGTGGAACAGATTGAAGCTACA
* *
53558937 ACGATGAATCTTGCTTCCCCAACATTGCAATTAAAA
65 ACAATGAATCTTGCTTCCCCAACATTGTAATTAAAA
* *
53558973 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGCAGTGGAACAAATTGAAGCTACAA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGACGGTGCAGTGGAACAGATTGAAGCTACAA
**
53559038 CGGTGAATCTTGCTTCCCCAACATTGTAATTAAAA
66 CAATGAATCTTGCTTCCCCAACATTGTAATTAAAA
** * ** * *
53559073 AGATTGAAGCCACAACGGTGAATCTTACTTCTCTGGTGGTACAGTGGAATAGATTGAAGCTACAA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGACGGTGCAGTGGAACAGATTGAAGCTACAA
* * *
53559138 CAGTGAATCTTGCTTCCCCGACATTGTAGTTAAAA
66 CAATGAATCTTGCTTCCCCAACATTGTAATTAAAA
* * * * *
53559173 AGGTTGAAGCTACAACAACGAATCTTACTTCCCTGACGGTGTAATGGAACAGATTGAAGCTACAA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGACGGTGCAGTGGAACAGATTGAAGCTACAA
* *
53559238 TAACGAATCTT
66 CAATGAATCTT
53559249 ACTTTCCTGA
Statistics
Matches: 243, Mismatches: 32, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
99 1 0.00
100 242 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (100 bp):
AGATTGAAGCCACAACGACGAATCTTACTTCCCTGACGGTGCAGTGGAACAGATTGAAGCTACAA
CAATGAATCTTGCTTCCCCAACATTGTAATTAAAA
Found at i:53559438 original size:45 final size:45
Alignment explanation
Indices: 53559298--53559554 Score: 206
Period size: 45 Copynumber: 5.8 Consensus size: 45
53559288 ATTACCGATT
* * * * *
53559298 TTATCTCTCTGAAGTTGCAGTAGAGCAGA-T---CATATCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATC
* * * ** * *
53559339 TTATCTCTCTGAAGTTGTAGTAGAGCAGGTTGAA-ATCA-CTAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AGCAAATC
* * * * * *
53559383 TTATCCCCCTGAAATTGCAGTGGGGCA-AGTTGAAGATAGCGAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTGAAGATAGCAAATC
* *
53559428 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTA-CTAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATC
* * *
53559472 CTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATC
* * *
53559517 TTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAGGATA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA
53559555 CAAGTCATAT
Statistics
Matches: 176, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
41 27 0.15
42 1 0.01
44 73 0.41
45 74 0.42
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (45 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATC
Found at i:53559454 original size:89 final size:90
Alignment explanation
Indices: 53559333--53559549 Score: 262
Period size: 89 Copynumber: 2.4 Consensus size: 90
53559323 CAGATCATAT
* * * *
53559333 CAAACCTTATCTCTCTGAAGTTGTAGTAGAGCAGGTTGAAATC-ACTAA-CCTTATCCCCCTGAA
1 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAGCTACTAATCC-TATCCCCCTGAA
* * *
53559396 ATTGCAGTGGGGCA-AGTTGAAGATAG
65 ATTACAGTGGAGCAGA-CTGAAGATAG
* ** * * * *
53559422 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AAGCTACTAATCCTATCTCCCTGAAG
1 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAGCTACTAATCCTATCCCCCTGAAA
53559486 TTACAGTGGAGCAGACTGAAGATAG
66 TTACAGTGGAGCAGACTGAAGATAG
53559511 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGA
1 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGA
53559550 GGATACAAGT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
88 3 0.03
89 99 0.94
90 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (90 bp):
CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAGCTACTAATCCTATCCCCCTGAAA
TTACAGTGGAGCAGACTGAAGATAG
Found at i:53559486 original size:44 final size:45
Alignment explanation
Indices: 53559298--53559554 Score: 217
Period size: 44 Copynumber: 5.8 Consensus size: 45
53559288 ATTACCGATT
* * * *
53559298 TTATCTCTCTGAAGTTGCAGTAGAGCAGA-T---CATATCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACC
* * * ** *
53559339 TTATCTCTCTGAAGTTGTAGTAGAGCAGGTTGAA-ATCA-CTAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AGCAAACC
* * * * * **
53559383 TTATCCCCCTGAAATTGCAGTGGGGCA-AGTTGAAGATAGCGAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTGAAGATAGCAAACC
* *
53559428 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTA-CTAATCC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGC-AAACC
*
53559473 -TATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACC
* * *
53559517 TTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAGGATA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA
53559555 CAAGTCATAT
Statistics
Matches: 176, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
41 27 0.15
42 1 0.01
44 74 0.42
45 73 0.41
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (45 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACC
Found at i:53560767 original size:46 final size:46
Alignment explanation
Indices: 53560672--53560823 Score: 211
Period size: 46 Copynumber: 3.4 Consensus size: 46
53560662 TACGTATGAT
* * * *
53560672 CACTTATCAC-TTGTCTC-TGATTAGATAAGTGTAACT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
53560715 CACTTATCATTTTGTCACTTGATCAGATAAGTGTAGCTAAATCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
53560761 CACTTATCACTTTGTCACTTGATCAGATAAGGGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
53560807 CACTTATCACTTTGTCA
1 CACTTATCACTTTGTCA
53560824 TTTGTCACTG
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
43 9 0.09
44 6 0.06
45 17 0.18
46 64 0.67
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:53564456 original size:23 final size:24
Alignment explanation
Indices: 53564422--53564475 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
53564412 TATATATATT
53564422 TATTTCTTTTAT-T-CACATACATA
1 TATTT-TTTTATATGCACATACATA
* *
53564445 TATTTTTCTTATATGTACATATATA
1 TATTTTT-TTATATGCACATACATA
53564470 TATTTT
1 TATTTT
53564476 ATATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 2 0.08
23 9 0.35
24 1 0.04
25 14 0.54
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTTTTTATATGCACATACATA
Found at i:53564477 original size:21 final size:21
Alignment explanation
Indices: 53564439--53564479 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53564429 TTTATTCACA
*
53564439 TACATATATTTTTCTTATATG
1 TACATATATTATTCTTATATG
53564460 TACATATATATATT-TTATAT
1 TACATATAT-TATTCTTATAT
53564480 TTTTTTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TACATATATTATTCTTATATG
Found at i:53570840 original size:16 final size:15
Alignment explanation
Indices: 53570798--53570844 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
53570788 AGCTCAATTC
53570798 CAAA-ATATTTTTT-
1 CAAACATATTTTTTA
*
53570811 C-AGCATATTTTTTA
1 CAAACATATTTTTTA
53570825 CAAACATATGTTTTTA
1 CAAACATAT-TTTTTA
53570841 CAAA
1 CAAA
53570845 TGATTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 1 0.04
13 10 0.36
14 1 0.04
15 6 0.21
16 10 0.36
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (15 bp):
CAAACATATTTTTTA
Found at i:53582347 original size:4 final size:4
Alignment explanation
Indices: 53582338--53582362 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
53582328 AGATTCTCTT
53582338 TTTG TTTG TTTG TTTG TTTG TTTG T
1 TTTG TTTG TTTG TTTG TTTG TTTG T
53582363 ATGGTTGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TTTG
Found at i:53584297 original size:12 final size:12
Alignment explanation
Indices: 53584282--53584306 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53584272 GATTTTTTCA
53584282 CATAATTTTTGT
1 CATAATTTTTGT
53584294 CATAATTTTTGT
1 CATAATTTTTGT
53584306 C
1 C
53584307 GATATTGGAA
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:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (12 bp):
CATAATTTTTGT
Found at i:53586599 original size:25 final size:25
Alignment explanation
Indices: 53586562--53586613 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
53586552 CATCACAATT
**
53586562 TTTTTTAATAAATTTTATT-TTTTA
1 TTTTTTAATAAATAATATTATTTTA
*
53586586 TTTTTTATTAAAATAATATTATTTTA
1 TTTTTTAAT-AAATAATATTATTTTA
53586612 TT
1 TT
53586614 AGTGGTGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
25 8 0.35
26 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTTTAATAAATAATATTATTTTA
Found at i:53586608 original size:28 final size:26
Alignment explanation
Indices: 53586559--53586610 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
53586549 CGGCATCACA
* *
53586559 ATTTTTTTTAATAAATTTTATTTTTT
1 ATTTTTTTTAAAAAATATTATTTTTT
53586585 ATTTTTTATTAAAATAATATTATTTT
1 ATTTTTT-TTAAAA-AATATTATTTT
53586611 ATTAGTGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 5 0.23
28 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
ATTTTTTTTAAAAAATATTATTTTTT
Found at i:53586861 original size:18 final size:17
Alignment explanation
Indices: 53586838--53586900 Score: 83
Period size: 18 Copynumber: 3.5 Consensus size: 17
53586828 AATAACAGAA
53586838 GAGAAGGAAAG-AGAAAGG
1 GAGAA-GAAAGAAGAAA-G
53586856 GAGAAGAAAGAAAGAAAG
1 GAGAAGAAAG-AAGAAAG
53586874 GAGAAGAAAGAAAGAAAG
1 GAGAAGAAAG-AAGAAAG
53586892 GAGAAGAAA
1 GAGAAGAAA
53586901 AATGATAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.12
18 33 0.77
19 5 0.12
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (17 bp):
GAGAAGAAAGAAGAAAG
Found at i:53586863 original size:11 final size:10
Alignment explanation
Indices: 53586834--53586900 Score: 70
Period size: 8 Copynumber: 6.8 Consensus size: 10
53586824 AAAAAATAAC
53586834 AGAAGAGAAGG
1 AGAAGA-AAGG
*
53586845 AAAGAGAAAGGG
1 AGA-AGAAA-GG
53586857 AGAAGAAA-G
1 AGAAGAAAGG
53586866 A-AAGAAAGG
1 AGAAGAAAGG
53586875 AGAAGAAA-G
1 AGAAGAAAGG
53586884 A-AAGAAAGG
1 AGAAGAAAGG
53586893 AGAAGAAA
1 AGAAGAAA
53586901 AATGATAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
8 12 0.25
9 8 0.17
10 12 0.25
11 9 0.19
12 7 0.15
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (10 bp):
AGAAGAAAGG
Found at i:53587061 original size:25 final size:26
Alignment explanation
Indices: 53587015--53587063 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
53587005 GTTTTTAATT
*
53587015 TATTTTAAAGTTATTTTGTTAGTTAC
1 TATTATAAAGTTATTTTGTTAGTTAC
53587041 TATTATAAA-TTA-TTTGTTTAGTT
1 TATTATAAAGTTATTTTG-TTAGTT
53587064 TAATGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 9 0.43
26 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (26 bp):
TATTATAAAGTTATTTTGTTAGTTAC
Found at i:53591031 original size:33 final size:33
Alignment explanation
Indices: 53590988--53591066 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
53590978 GAGCTCGAAT
* * * *
53590988 GAGTGAAGTACTGCGGTGGATATGGGTCAG-GAG
1 GAGTGGAGTACTGAGGTGGATACGAG-CAGAGAG
* *
53591021 GAGTGGAGTACTAAGGTGGATACGAGCTGAGAG
1 GAGTGGAGTACTGAGGTGGATACGAGCAGAGAG
53591054 GAGTGGAGTACTG
1 GAGTGGAGTACTG
53591067 TGATGGTAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.27, C:0.09, G:0.44, T:0.20
Consensus pattern (33 bp):
GAGTGGAGTACTGAGGTGGATACGAGCAGAGAG
Found at i:53593129 original size:107 final size:108
Alignment explanation
Indices: 53592985--53593777 Score: 872
Period size: 107 Copynumber: 7.3 Consensus size: 108
53592975 CATTATAACG
* * * *
53592985 AATCACAATACACATTAAACT-GA-ACAAATAATTTATAACCTAATCATAAATTACTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
53593048 AACTTTAAAATAATTTAAAAAAACAAAAAAAT-ATTCATAAAA
66 AACTTTAAAATAATTTAAAAAAACAAAAAAATAATTCATAAAA
* * *
53593090 AATCACAATAAATACTAAACTAAACACAAGCAATTTATAATCTAATCATAAATTACTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* ** * * *
53593155 AAATTTAAAATAATTTAAAAAACACAAAAATTTTCATTTATAACA
66 AACTTTAAAATAATTTAAAAAA-ACAAAAA-AATAATTCATAAAA
* * * * * * *
53593200 AGTCACAATAAACAATAAACTAAATACAAAAAAATTATAATCTAATCATAAATTGCTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* *
53593265 AACTTTAAAATAATTTTAAAAAACAAAAAAAAATACATTCGTAAAA
66 AACTTTAAAATAA-TTTAAAAAA-ACAAAAAAATA-ATTCATAAAA
* * *
53593311 GATCACAATAAACACTAAACTAAATACAAACAATTTATAACCTAATCATAAATTACTAACAAAAC
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* * *
53593376 AACATTCAAATAA-TTAAAAAAACAAAAAAAAATACATTAATAAAA
66 AACTTTAAAATAATTTAAAAAAAC--AAAAAAATA-ATTCATAAAA
* *
53593421 AATCACAATAAACATTAAACTAAAGACACAAACAATTTATAACCTAACCATAAATTACTAACAAA
1 AATCACAATAAACACTAAACT-AA-ACACAAACAATTTATAACCTAATCATAAATTACTAACAAA
* * *
53593486 ATGACTATAAAATAATTTAAAAAATATAAAAAAATTACATTCATAAAA
64 ATAACTTTAAAATAATTTAAAAAA-ACAAAAAAA-TA-ATTCATAAAA
* * *
53593534 AATCAC-A-GAGCACTAAACTAAACACAAACAA-TT-TAACCTAACCATAAATTACTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* * *
53593595 AACTATAAAATAATTAAAAAAAAACAAAAAAATTACATTAATAAAA
66 AACTTTAAAATAATT-TAAAAAAACAAAAAAA-TA-ATTCATAAAA
* * * * * *
53593641 ATTTAC-A-AAACGCTAAACTAAACACAAAAAATTTAGAATCTAATCATAAATTACTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* * * *
53593704 AACTTTAAAATAATTTTAAAATATAAAAAAATTTACATTCATAACA
66 AACTTTAAAATAATTTAAAAAAACAAAAAAA--TA-ATTCATAAAA
* *
53593750 AATCAC-A-AATCACTAAACTAAATACAAA
1 AATCACAATAAACACTAAACTAAACACAAA
53593778 AAAAAAAACT
Statistics
Matches: 590, Mismatches: 80, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
105 18 0.03
106 1 0.00
107 146 0.25
108 30 0.05
109 93 0.16
110 117 0.20
111 102 0.17
112 56 0.09
113 26 0.04
114 1 0.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (108 bp):
AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
AACTTTAAAATAATTTAAAAAAACAAAAAAATAATTCATAAAA
Found at i:53593406 original size:328 final size:326
Alignment explanation
Indices: 53592967--53593771 Score: 925
Period size: 328 Copynumber: 2.5 Consensus size: 326
53592957 AATCATAAAT
* * * * * *
53592967 AAAATTTACATT-ATAACGAATCACAATACACATTAAACT-GAACAAATAATTTATAACCTAATC
1 AAAAATTACATTAATAA-AAATCACAATAAACACTAAACTAAAACAAAAAATTTATAACCTAATC
*
53593030 ATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAAC-AAAAAAAT-ATTCATAAAAAAT
65 ATAAATTACTAACAAAATAACTTTAAAATAA-TTAAAAAAACAAAAAAAATAATTAATAAAAAAT
* * * *
53593093 CACAATAAATACTAAACT-AA-ACACAAGCAATTTATAATCTAATCATAAATTACTAACAAAATA
129 CACAATAAACACTAAACTAAAGACACAAACAATTTATAACCTAACCATAAATTACTAACAAAATA
* * * * * * *
53593156 AATTTAAAATAATTTAAAAAACA-CAAAAATTTTCATTTATAACAAGTCACAATAAACAATAAAC
194 AATATAAAATAATTTAAAAAACATAAAAAAATTACATTCATAAAAAATCAC-A-AAACAATAAAC
* * * * *
53593220 TAAATACAAAAAAATTATAATCTAATCATAAATTGCTAACAAAATAACTTTAAAATAATTTTAAA
257 TAAACAC-AAAAAATT-TAACCTAACCATAAATTACTAACAAAATAACTATAAAATAA--TTAAA
*
53593285 AAACAA-AA
318 AAAAAACAA
** *
53593293 AAAAA-TACATTCGTAAAAGATCACAATAAACACTAAACTAAATACAAACAATTTATAACCTAAT
1 AAAAATTACATTAATAAAA-ATCACAATAAACACTAAACTAAA-ACAAAAAATTTATAACCTAAT
* * *
53593357 CATAAATTACTAACAAAACAACATTCAAATAATTAAAAAAACAAAAAAAAATACATTAATAAAAA
64 CATAAATTACTAACAAAATAACTTTAAAATAATTAAAAAAAC-AAAAAAAATA-ATTAATAAAAA
*
53593422 ATCACAATAAACATTAAACTAAAGACACAAACAATTTATAACCTAACCATAAATTACTAACAAAA
127 ATCACAATAAACACTAAACTAAAGACACAAACAATTTATAACCTAACCATAAATTACTAACAAAA
* * * * * *
53593487 TGACTATAAAATAATTTAAAAAATATAAAAAAATTACATTCATAAAAAATCACAGAGCACTAAAC
192 TAAATATAAAATAATTTAAAAAACATAAAAAAATTACATTCATAAAAAATCACAAAACAATAAAC
*
53593552 TAAACACAAACAATTTAACCTAACCATAAATTACTAACAAAATAACTATAAAATAATTAAAAAAA
257 TAAACACAAAAAATTTAACCTAACCATAAATTACTAACAAAATAACTATAAAATAATTAAAAAAA
53593617 AACAA
322 AACAA
* * * *
53593622 AAAAATTACATTAATAAAAATTTAC-A-AAACGCTAAACTAAACACAAAAAATTTAGAATCTAAT
1 AAAAATTACATTAATAAAAA-TCACAATAAACACTAAACTAAA-ACAAAAAATTTATAACCTAAT
* * * * * *
53593685 CATAAATTACTAACAAAATAACTTTAAAATAATTTTAAAATATAAAAAAATTTACATTCATAACA
64 CATAAATTACTAACAAAATAACTTTAAAATAA-TTAAAAAAACAAAAAAA-ATA-ATTAATAAAA
*
53593750 AATCAC-A-AATCACTAAACTAAA
126 AATCACAATAAACACTAAACTAAA
53593772 TACAAAAAAA
Statistics
Matches: 408, Mismatches: 55, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
325 7 0.02
326 25 0.06
327 24 0.06
328 128 0.31
329 41 0.10
330 51 0.12
331 35 0.09
332 16 0.04
333 60 0.15
334 21 0.05
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (326 bp):
AAAAATTACATTAATAAAAATCACAATAAACACTAAACTAAAACAAAAAATTTATAACCTAATCA
TAAATTACTAACAAAATAACTTTAAAATAATTAAAAAAACAAAAAAAATAATTAATAAAAAATCA
CAATAAACACTAAACTAAAGACACAAACAATTTATAACCTAACCATAAATTACTAACAAAATAAA
TATAAAATAATTTAAAAAACATAAAAAAATTACATTCATAAAAAATCACAAAACAATAAACTAAA
CACAAAAAATTTAACCTAACCATAAATTACTAACAAAATAACTATAAAATAATTAAAAAAAAACA
A
Found at i:53593429 original size:221 final size:217
Alignment explanation
Indices: 53592985--53593777 Score: 969
Period size: 221 Copynumber: 3.6 Consensus size: 217
53592975 CATTATAACG
* * *
53592985 AATCACAATACACATTAAACT-GAACAAATAATTTATAACCTAATCATAAATTACTAACAAAATA
1 AATCACAATAAACATTAAACTAAAACAAAAAATTTATAACCTAATCATAAATTACTAACAAAATA
* *
53593049 ACTTTAAAATAATTTAAAAAA-ACAAAAAAAT--ATTCATAAAAAATCACAATAAATACTAAACT
66 ACTTTAAAATAATTTAAAAAATAAAAAAAAATACATTCATAAAAAATCAC-A-AAACACTAAACT
* * *
53593111 AAACACAAGCAATTTATAATCTAATCATAAATTACTAACAAAATAA-ATTTAAAATAATTTAAAA
129 AAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAATAACA-TTAAAATAATTAAAAA
* ** * * *
53593175 AACACAAAAATTTTCATTTATAACA
193 AACAAAAAAAAATACATTAATAAAA
* * * * *
53593200 AGTCACAATAAACAATAAACTAAATACAAAAAAATTATAATCTAATCATAAATTGCTAACAAAAT
1 AATCACAATAAACATTAAACTAAA-ACAAAAAATTTATAACCTAATCATAAATTACTAACAAAAT
* * *
53593265 AACTTTAAAATAATTTTAAAAAACAAAAAAAAATACATTCGTAAAAGATCACAATAAACACTAAA
65 AACTTTAAAATAA-TTTAAAAAATAAAAAAAAATACATTCATAAAAAATCAC-A-AAACACTAAA
* * *
53593330 CTAAATACAAACAATTTATAACCTAATCATAAATTACTAACAAAACAACATTCAAATAATTAAAA
127 CTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAATAACATTAAAATAATTAAAA
53593395 AAACAAAAAAAAATACATTAATAAAA
192 AAACAAAAAAAAATACATTAATAAAA
*
53593421 AATCACAATAAACATTAAACTAAAGACACAAACAATTTATAACCTAACCATAAATTACTAACAAA
1 AATCACAATAAACATTAAACTAAA-ACA-AAA-AATTTATAACCTAATCATAAATTACTAACAAA
* * * * *
53593486 ATGACTATAAAATAATTTAAAAAATATAAAAAAATTACATTCATAAAAAATCACAGAGCACTAAA
63 ATAACTTTAAAATAATTTAAAAAATA-AAAAAAAATACATTCATAAAAAATCACAAAACACTAAA
*
53593551 CTAAACACAAACAA-TT-TAACCTAACCATAAATTACTAACAAAATAAC-TATAAAATAATTAAA
127 CTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAATAACAT-TAAAATAATTAAA
53593613 AAAA-AACAAAAAAATTACATTAATAAAA
191 AAAACAA-AAAAAAA-TACATTAATAAAA
* * ** * *
53593641 ATTTAC-A-AAACGCTAAACTAAACACAAAAAATTTAGAATCTAATCATAAATTACTAACAAAAT
1 AATCACAATAAACATTAAACTAAA-ACAAAAAATTTATAACCTAATCATAAATTACTAACAAAAT
* ** * *
53593704 AACTTTAAAATAATTTTAAAATATAAAAAAATTTACATTCATAACAAATCACAAATCACTAAACT
65 AACTTTAAAATAA-TTTAAAAAATAAAAAAAAATACATTCATAAAAAATCACAAAACACTAAACT
*
53593769 AAATACAAA
129 AAACACAAA
53593778 AAAAAAAACT
Statistics
Matches: 505, Mismatches: 59, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
215 18 0.04
216 87 0.17
217 62 0.12
218 28 0.06
219 62 0.12
220 19 0.04
221 149 0.30
222 15 0.03
223 65 0.13
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (217 bp):
AATCACAATAAACATTAAACTAAAACAAAAAATTTATAACCTAATCATAAATTACTAACAAAATA
ACTTTAAAATAATTTAAAAAATAAAAAAAAATACATTCATAAAAAATCACAAAACACTAAACTAA
ACACAAACAATTTATAACCTAATCATAAATTACTAACAAAATAACATTAAAATAATTAAAAAAAC
AAAAAAAAATACATTAATAAAA
Found at i:53593948 original size:4 final size:4
Alignment explanation
Indices: 53593941--53593965 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
53593931 CATACATACA
53593941 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
53593966 CTCATTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:53593974 original size:95 final size:97
Alignment explanation
Indices: 53593803--53593997 Score: 331
Period size: 95 Copynumber: 2.0 Consensus size: 97
53593793 CTTTAAATTA
53593803 AAAAAAAAACATTAATTACTAAAATGATATATACATACATACATTCTTTCTTTCTTTCTTTATTT
1 AAAAAAAAACATTAATTACTAAAATG--A-ATACATACATACATTCTTTCTTTCTTTCTTTATTT
*
53593868 CTTCTCCTTCCTCTCTTTTCTTTCCCT-TTTTTTT
63 CTTCTCATTCCTCTCTTTTCTTTCCCTCTTTTTTT
*
53593902 AAAAAAAAACATTAATTACTAAAATG-ATACATACATACATTCTTTCTTTCTTTCTTTCTTTCTT
1 AAAAAAAAACATTAATTACTAAAATGAATACATACATACATTCTTTCTTTCTTTCTTTATTTCTT
53593966 CTCATTCCTCTCTTTTCTTTCCCTCTTTTTTT
66 CTCATTCCTCTCTTTTCTTTCCCTCTTTTTTT
53593998 TTTTTCACTA
Statistics
Matches: 93, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
95 60 0.65
96 7 0.08
99 26 0.28
ACGTcount: A:0.27, C:0.22, G:0.01, T:0.50
Consensus pattern (97 bp):
AAAAAAAAACATTAATTACTAAAATGAATACATACATACATTCTTTCTTTCTTTCTTTATTTCTT
CTCATTCCTCTCTTTTCTTTCCCTCTTTTTTT
Found at i:53597417 original size:16 final size:17
Alignment explanation
Indices: 53597381--53597419 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
53597371 TATGTTATAT
* *
53597381 AAGTGTCATAGGTATTA
1 AAGTGTCATAGGAAATA
53597398 AAGTGTCAT-GGAAATA
1 AAGTGTCATAGGAAATA
53597414 AAGTGT
1 AAGTGT
53597420 AGATACCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (17 bp):
AAGTGTCATAGGAAATA
Found at i:53601528 original size:17 final size:17
Alignment explanation
Indices: 53601508--53601566 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
53601498 TTAATAGATA
53601508 ATTGAAGTGAATATGAT
1 ATTGAAGTGAATATGAT
*
53601525 ATTG-AGTTGATTAATAGAT
1 ATTGAAG-TGAAT-AT-GAT
*
53601544 AATTGAAGTGAATGTGAT
1 -ATTGAAGTGAATATGAT
53601562 ATTGA
1 ATTGA
53601567 GTTATGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 4 0.12
20 8 0.24
21 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (17 bp):
ATTGAAGTGAATATGAT
Found at i:53601536 original size:37 final size:37
Alignment explanation
Indices: 53601495--53601569 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
53601485 AATTAATGAA
53601495 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
*
53601532 TGATTAATAGATAATTGAAGTGAATGTGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
53601569 T
1 T
53601570 ATGAAATGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (37 bp):
TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
Found at i:53601548 original size:20 final size:19
Alignment explanation
Indices: 53601495--53601554 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
53601485 AATTAATGAA
53601495 TGATTAATAGATAATTGAAG
1 TGATTAATAGATAATTG-AG
*
53601515 TGAAT-AT-GAT-ATTGAG
1 TGATTAATAGATAATTGAG
53601531 TTGATTAATAGATAATTGAAG
1 -TGATTAATAGATAATTG-AG
53601552 TGA
1 TGA
53601555 ATGTGATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 2 0.06
17 8 0.24
18 5 0.15
19 5 0.15
20 11 0.33
21 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TGATTAATAGATAATTGAG
Found at i:53601583 original size:20 final size:21
Alignment explanation
Indices: 53601560--53601598 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53601550 AGTGAATGTG
*
53601560 ATATTGAG-TTATGAAATGCA
1 ATATTAAGATTATGAAATGCA
53601580 ATATTAAGATTATGAAATG
1 ATATTAAGATTATGAAATG
53601599 TGATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (21 bp):
ATATTAAGATTATGAAATGCA
Found at i:53601760 original size:35 final size:35
Alignment explanation
Indices: 53601721--53601907 Score: 121
Period size: 35 Copynumber: 5.1 Consensus size: 35
53601711 GGTATACTCG
*
53601721 ACTAGCACTAGGTGCAAATATCGTTGGTTTATCCA
1 ACTAGCACTGGGTGCAAATATCGTTGGTTTATCCA
* * *
53601756 ACTAG-AGCTGGGCT-CACTTTTTATATCGTCGGTTTATCCG
1 ACTAGCA-CTGGG-TGCA-----AATATCGTTGGTTTATCCA
* *
53601796 ACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCA
1 ACTAGCACTGGGTGCAAATATCGTTGGTTTATCCA
* *
53601831 ACTAG-AGCTGGGCT-CACTATTTATATTGTCGGTTTATCCA
1 ACTAGCA-CTGGG-TGCA--A---ATATCGTTGGTTTATCCA
* * *
53601871 ACTAGCGCTGGGCGCAAATATCATTGGTTTATCCA
1 ACTAGCACTGGGTGCAAATATCGTTGGTTTATCCA
53601906 AC
1 AC
53601908 CAGAGTTGGG
Statistics
Matches: 116, Mismatches: 18, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
34 1 0.01
35 56 0.48
36 1 0.01
37 1 0.01
38 1 0.01
40 56 0.48
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (35 bp):
ACTAGCACTGGGTGCAAATATCGTTGGTTTATCCA
Found at i:53601767 original size:75 final size:75
Alignment explanation
Indices: 53601629--53601958 Score: 381
Period size: 75 Copynumber: 4.4 Consensus size: 75
53601619 TGAGTAATTG
* *
53601629 ATATTGTCGGT-TCATCCGACTAGCGCTGGGCGC-AATCATCGTT-GTTCATCCAACTAGAGCTG
1 ATATCGTCGGTAT-ATCCGACTAGCGCTGGGCGCAAAT-ATCGTTGGTTTATCCAACTAGAGCTG
53601691 GGCTCACAATTAT
64 GGCTCAC-ATTAT
* * * *
53601704 A-ATCGTTGGTATA-CTCGACTAGCACTAGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTGG
1 ATATCGTCGGTATATC-CGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGG
* *
53601767 GCTCACTTTTT
65 GCTCACATTAT
*
53601778 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
1 ATATCGTCGGTATATCCGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
53601843 CTCACTATT-T
66 CTCAC-ATTAT
* * * * * *
53601853 ATATTGTCGGTTTATCCAACTAGCGCTGGGCGCAAATATCATTGGTTTATCCAACCAGAGTTGGG
1 ATATCGTCGGTATATCCGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
*
53601918 CTCAC-TGAT
66 CTCACATTAT
*
53601927 -TATTCGTTGGTATATCTC-ACTAGCGCTGGGCG
1 ATA-TCGTCGGTATATC-CGACTAGCGCTGGGCG
53601959 TAACTTCCGT
Statistics
Matches: 222, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
73 4 0.02
74 57 0.26
75 158 0.71
76 3 0.01
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (75 bp):
ATATCGTCGGTATATCCGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
CTCACATTAT
Found at i:53601793 original size:40 final size:39
Alignment explanation
Indices: 53601738--53601883 Score: 174
Period size: 40 Copynumber: 3.8 Consensus size: 39
53601728 CTAGGTGCAA
*
53601738 ATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTTTTT
1 ATATCGTCGGTTTATCCAACTAGAGCTGGGCTCAC-TTTT
* * * *
53601778 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCA----A
1 ATATCGTCGGTTTATCCAACTAGAGCTGGGCTCACTTTT
*
53601813 ATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTATTT
1 ATATCGTCGGTTTATCCAACTAGAGCTGGGCTCACT-TTT
* *
53601853 ATATTGTCGGTTTATCCAACTAGCGCTGGGC
1 ATATCGTCGGTTTATCCAACTAGAGCTGGGC
53601884 GCAAATATCA
Statistics
Matches: 88, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
35 30 0.34
40 58 0.66
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (39 bp):
ATATCGTCGGTTTATCCAACTAGAGCTGGGCTCACTTTT
Found at i:53601918 original size:35 final size:35
Alignment explanation
Indices: 53601734--53601918 Score: 147
Period size: 40 Copynumber: 5.0 Consensus size: 35
53601724 AGCACTAGGT
*
53601734 GCAAATATCGTTGGTTTATCCAACTAGAGCTGGGC
1 GCAAATATCATTGGTTTATCCAACTAGAGCTGGGC
* * * * * *
53601769 TCACTTTTTATATCGTCGGTTTATCCGACTAGCGCTGGGC
1 GCA-----AATATCATTGGTTTATCCAACTAGAGCTGGGC
*
53601809 GCAAATATCGTTGGTTTATCCAACTAGAGCTGGGC
1 GCAAATATCATTGGTTTATCCAACTAGAGCTGGGC
* * *
53601844 TCACTATTTAT-ATTGTCGGTTTATCCAACTAGCGCTGGGC
1 GCA--A-ATATCA-T-T-GGTTTATCCAACTAGAGCTGGGC
* *
53601884 GCAAATATCATTGGTTTATCCAACCAGAGTTGGGC
1 GCAAATATCATTGGTTTATCCAACTAGAGCTGGGC
53601919 TCACTGATTA
Statistics
Matches: 119, Mismatches: 19, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
35 52 0.44
36 1 0.01
37 5 0.04
38 6 0.05
39 1 0.01
40 54 0.45
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (35 bp):
GCAAATATCATTGGTTTATCCAACTAGAGCTGGGC
Found at i:53602609 original size:23 final size:24
Alignment explanation
Indices: 53602561--53602610 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
53602551 TATTTGATAT
**
53602561 TATTAGAATAAGGAGTTTCACTCC
1 TATTAGAATAAGGAGTTTCAAGCC
*
53602585 TATTAGAATAAGG-TTTTCAAGCC
1 TATTAGAATAAGGAGTTTCAAGCC
53602608 TAT
1 TAT
53602611 AAATAGGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (24 bp):
TATTAGAATAAGGAGTTTCAAGCC
Found at i:53608112 original size:69 final size:69
Alignment explanation
Indices: 53608000--53608138 Score: 244
Period size: 69 Copynumber: 2.0 Consensus size: 69
53607990 AGCCACACTA
53608000 CCGTGTGAACCCTGTAGTAAAAATTTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
1 CCGTGTGAACCCTGTAGTAAAAATTTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
53608065 GTCC
66 GTCC
* *
53608069 CCGTGTGAACCTTGTAGTCAAAAA-TTTTGCAAATTCTTGTTTAACTTTTCAAATGATTTCTATT
1 CCGTGTGAACCCTGTAGT-AAAAATTTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATT
53608133 AGTCC
65 AGTCC
53608138 C
1 C
53608139 AAAGTGTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 62 0.93
70 5 0.07
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (69 bp):
CCGTGTGAACCCTGTAGTAAAAATTTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
GTCC
Found at i:53609161 original size:75 final size:75
Alignment explanation
Indices: 53609031--53609208 Score: 175
Period size: 75 Copynumber: 2.4 Consensus size: 75
53609021 AAAGTCATCG
*
53609031 TTGGTTCATCCAACTAGAGCT-AGGCTCACAATTATAACCGTCGGTATACCTGACTAGAACTGAG
1 TTGGTTTATCCAACTAGAGCTGA-GCTCACAATTATAACCGTCGGTATACCTGACTAGAACTGAG
53609095 -TGCAAATACCA
65 CT-CAAATACCA
* ** * ** *
53609106 TTGGTTTATCCAACTAGAGCTGAGCTCACTATT-TATATTGTCGGTTTATCC-GACTAGCGCTGG
1 TTGGTTTATCCAACTAGAGCTGAGCTCACAATTATA-ACCGTCGGTATA-CCTGACTAGAACTGA
* *
53609169 GCTCAAATATCG
64 GCTCAAATACCA
* * *
53609181 CTGGTTTATCCAACCAGAGCTGGGCTCA
1 TTGGTTTATCCAACTAGAGCTGAGCTCA
53609209 TTGATTATTA
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
74 2 0.02
75 80 0.93
76 4 0.05
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (75 bp):
TTGGTTTATCCAACTAGAGCTGAGCTCACAATTATAACCGTCGGTATACCTGACTAGAACTGAGC
TCAAATACCA
Found at i:53609263 original size:74 final size:75
Alignment explanation
Indices: 53609109--53609263 Score: 181
Period size: 74 Copynumber: 2.1 Consensus size: 75
53609099 AATACCATTG
* * * *
53609109 GTTTATCCAACTAGAGCTGAGCTCACTATTTATATTGTCGGTTTATCCGACTAGCGCTGGGCTCA
1 GTTTATCCAACCAGAGCTGAGCTCACTATTTATATAGTCGGTATATCCGACTAGCGCTGGGCACA
*
53609174 AATATCGCTG
66 AATATCGCTA
* * * *
53609184 GTTTATCCAACCAGAGCTGGGCTCATTGA-TTAT-TAGTCGGTATATCTGACTAGCGTTGGGCAC
1 GTTTATCCAACCAGAGCTGAGCTCACT-ATTTATATAGTCGGTATATCCGACTAGCGCTGGGCAC
*
53609247 AACT-TCCGCTA
65 AAATAT-CGCTA
53609258 GTTTAT
1 GTTTAT
53609264 TTGACTAGTG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
73 1 0.01
74 38 0.56
75 28 0.41
76 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (75 bp):
GTTTATCCAACCAGAGCTGAGCTCACTATTTATATAGTCGGTATATCCGACTAGCGCTGGGCACA
AATATCGCTA
Found at i:53612248 original size:35 final size:35
Alignment explanation
Indices: 53612202--53612271 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
53612192 TGAACCACTG
53612202 ATCCAACCGACTAACCTGAATAACTTTAACCCCAA
1 ATCCAACCGACTAACCTGAATAACTTTAACCCCAA
*
53612237 ATCCAACCGACTAACCTGAATAATTTTAACCCCAA
1 ATCCAACCGACTAACCTGAATAACTTTAACCCCAA
53612272 TTTTGGGGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.40, C:0.33, G:0.06, T:0.21
Consensus pattern (35 bp):
ATCCAACCGACTAACCTGAATAACTTTAACCCCAA
Found at i:53614945 original size:17 final size:17
Alignment explanation
Indices: 53614893--53614945 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
53614883 TATGGAAACA
* *
53614893 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
*
53614910 CAATCTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
53614929 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
53614946 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:53614945 original size:22 final size:23
Alignment explanation
Indices: 53614917--53614961 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53614907 ATGCAATCTT
53614917 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
53614939 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
53614962 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:53614971 original size:22 final size:23
Alignment explanation
Indices: 53614927--53614971 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53614917 AGATATGATA
*
53614927 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
53614950 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
53614972 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:53615155 original size:19 final size:21
Alignment explanation
Indices: 53615131--53615169 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
53615121 TGTTTTCTTT
*
53615131 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
53615150 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
53615170 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:53615397 original size:15 final size:15
Alignment explanation
Indices: 53615373--53615410 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
53615363 GTTTTTAGCC
53615373 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
53615387 TGTTATTATTATTTT
1 TATTATTATTAATTT
53615402 TATTATTAT
1 TATTATTAT
53615411 ATTATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:53615404 original size:12 final size:12
Alignment explanation
Indices: 53615375--53615425 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
53615365 TTTTAGCCTA
53615375 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
53615387 TGTTATTATTAT
1 TTTTATTATTAT
53615399 TTTTATTATTAT
1 TTTTATTATTAT
53615411 ATTATATATTATTAT
1 -TT-T-TATTATTAT
53615426 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 3 0.09
12 18 0.55
13 2 0.06
14 1 0.03
15 9 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:53615420 original size:15 final size:13
Alignment explanation
Indices: 53615389--53615426 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
53615379 ATTAATTTTG
53615389 TTATTATTAT-TT
1 TTATTATTATATT
53615401 TTATTATTATATT
1 TTATTATTATATT
53615414 ATATATTATTATA
1 -T-TATTATTATA
53615427 CCTACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATTATATT
Found at i:53620696 original size:17 final size:17
Alignment explanation
Indices: 53620667--53620716 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
53620657 CAAAATAAAA
*
53620667 ATAAAAA-ATAAAAATG
1 ATAAAAAGAAAAAAATG
*
53620683 ATAAAAAGAAAAAAAAAG
1 ATAAAAAG-AAAAAAATG
53620701 A-AAAAAGAAAGAAAAT
1 ATAAAAAGAAA-AAAAT
53620717 AGAGAGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 10 0.36
17 10 0.36
18 8 0.29
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (17 bp):
ATAAAAAGAAAAAAATG
Found at i:53620698 original size:10 final size:10
Alignment explanation
Indices: 53620685--53620715 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
53620675 TAAAAATGAT
53620685 AAAAAGAAAA
1 AAAAAGAAAA
53620695 AAAAAGAAAA
1 AAAAAGAAAA
53620705 AAGAAAGAAAA
1 AA-AAAGAAAA
53620716 TAGAGAGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.60
11 8 0.40
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:53622045 original size:44 final size:43
Alignment explanation
Indices: 53621997--53622135 Score: 102
Period size: 44 Copynumber: 3.2 Consensus size: 43
53621987 AGTCACCAGC
*
53621997 CTTGCCTCCCTCGGTTGCAGTGGAGTAGGCTAAAAATAGCAGAT
1 CTTGCCTCCCT-GGTTGCAGTGGAGTAGGATAAAAATAGCAGAT
* *** * * * * * *
53622041 CTTGCCTTCCTGCACCGACAGTGAAGTA-GATCGAAGACACCAGCT
1 CTTGCCTCCCTG-GTTG-CAGTGGAGTAGGAT-AAAAATAGCAGAT
* *
53622086 -TTGCCTCCCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCT-GGTTGCAGTGGAGTAGGATAAAAATAGCAGAT
53622129 CTTGCCT
1 CTTGCCT
53622136 TCTTGCACTG
Statistics
Matches: 66, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
43 17 0.26
44 31 0.47
45 18 0.27
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.24
Consensus pattern (43 bp):
CTTGCCTCCCTGGTTGCAGTGGAGTAGGATAAAAATAGCAGAT
Found at i:53622090 original size:88 final size:88
Alignment explanation
Indices: 53621939--53622250 Score: 471
Period size: 88 Copynumber: 3.5 Consensus size: 88
53621929 AACAGATCGG
* *
53621939 TAAAAATAGCAGATCTTGCCTTACTGCACCGACAGCGAAGCAGATCGAAGTCACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
53622004 CCCTCGGTTGCAGTGGAGTAGGC
66 CCCTGGGTTGCAGTGGAGCAGGT
* * *
53622027 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGTGAAGTAGATCGAAGACACCAGCTTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
53622092 CCCTGGGTTGCAGTGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * * *
53622115 TAAAAATAGCAGATCTTGCCTTCTTGCACTGACAGCGAAGTAGATCAAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
53622180 CCCTGGGTTGCAGCGGCGCACGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* *
53622203 TAAAAATAGCAGATCTTGCCTTCCTACACCGATAGCGAAGCAGATCGA
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
53622251 TGACCTCAGT
Statistics
Matches: 202, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 202 1.00
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGTGGAGCAGGT
Found at i:53622326 original size:44 final size:44
Alignment explanation
Indices: 53622260--53622724 Score: 563
Period size: 44 Copynumber: 10.7 Consensus size: 44
53622250 ATGACCTCAG
* ** * *
53622260 TCCTATCTCCCTGGTCAATAGTGGAATAGTTTGAAGATTGAGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
53622304 TCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATTGTGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
*
53622348 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
53622392 TCCTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGATTGAGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
53622436 TTCTATCTCCCTAGG-CAGCAGTGGAATAGATT--A-A---AGAA
1 TCCTATCTCCCT-GGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
53622474 TCCTATCTCCCTGGACAGCAGTGGAAGAGGTTAAAGATTGTGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
53622518 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
53622562 TCCCATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGAGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* * * *
53622606 TTCTATCTCCCTAGG-TAGCAGTGGAATAGATTAAAGATTGTAG-G
1 TCCTATCTCCCT-GGACAGCAGTGGAATAGGTTAAAGATTG-AGAA
* * * * *
53622650 TCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATCGTGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
53622694 CCCTATCTCCCT-GAGCAGCAGTGGAGTAGGT
1 TCCTATCTCCCTGGA-CAGCAGTGGAATAGGT
53622725 GGAAAATAGC
Statistics
Matches: 368, Mismatches: 40, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
37 2 0.01
38 30 0.08
40 1 0.00
41 2 0.01
42 1 0.00
43 4 0.01
44 323 0.88
45 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
Found at i:53622499 original size:170 final size:170
Alignment explanation
Indices: 53622300--53622724 Score: 645
Period size: 170 Copynumber: 2.5 Consensus size: 170
53622290 TTGAAGATTG
53622300 AGAATCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACA
1 AGAATCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACA
* * *
53622365 GCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGAT
66 GCAGTGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTAGACAGCAGTGGAATAGGTTAAAGAT
53622430 TGAGAATTCTATCTCCCTAGGCAGCAGTGGAATAGATTAA
131 TGAGAATTCTATCTCCCTAGGCAGCAGTGGAATAGATTAA
* * *
53622470 AGAATCCTATCTCCCTGGACAGCAGTGGAAGAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCA
1 AGAATCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACA
* * *
53622535 GCAGTGGAATAGGTTGAAGATTGAGAATCCCATCTCCCTGGACAGCAGTGGAATAGGTTGAAGAT
66 GCAGTGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTAGACAGCAGTGGAATAGGTTAAAGAT
*
53622600 TGAGAATTCTATCTCCCTAGGTAGCAGTGGAATAGATTAA
131 TGAGAATTCTATCTCCCTAGGCAGCAGTGGAATAGATTAA
* * * *
53622640 AGATTGTAGGTCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATCGTGAACCCTATCTCCC
1 AGA----A--TCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCC
*
53622705 T-GAGCAGCAGTGGAGTAGGT
60 TGGA-CAGCAGTGGAATAGGT
53622725 GGAAAATAGC
Statistics
Matches: 230, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
170 163 0.71
174 1 0.00
175 1 0.00
176 65 0.28
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (170 bp):
AGAATCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACA
GCAGTGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTAGACAGCAGTGGAATAGGTTAAAGAT
TGAGAATTCTATCTCCCTAGGCAGCAGTGGAATAGATTAA
Found at i:53622629 original size:214 final size:214
Alignment explanation
Indices: 53622260--53622678 Score: 619
Period size: 214 Copynumber: 2.0 Consensus size: 214
53622250 ATGACCTCAG
* * * * * *
53622260 TCCTATCTCCCTGGTCAATAGTGGAATAGTTTGAAGATTGAGAATCCTATCTCCCTGGACAGTAG
1 TCCTATCTCCCTGGACAACAGTGGAAGAGGTTAAAGATTGAGAATCCTATCTCCCTGGACAGCAG
* * *
53622325 TGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTG
66 TGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAG
* *
53622390 AATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGATTG-AGAATTCTATCTCCCTAGG-CA
131 AATCCTATCTCCCTAGTCAGCAGTGGAATAGATTAAAGATTGTAG-ATCCTATCTCCCT-GGTCA
53622453 GCAGTGGAATAGATTAAAGAA
194 GCAGTGGAATAGATTAAAGAA
* * *
53622474 TCCTATCTCCCTGGACAGCAGTGGAAGAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAG
1 TCCTATCTCCCTGGACAACAGTGGAAGAGGTTAAAGATTGAGAATCCTATCTCCCTGGACAGCAG
* *
53622539 TGGAATAGGTTGAAGATTGAGAATCCCATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGAG
66 TGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAG
* *
53622604 AATTCTATCTCCCTAGGT-AGCAGTGGAATAGATTAAAGATTGTAGGTCCTATCTCCCTGGTCAG
131 AATCCTATCTCCCTA-GTCAGCAGTGGAATAGATTAAAGATTGTAGATCCTATCTCCCTGGTCAG
*
53622668 TAGTGGAATAG
195 CAGTGGAATAG
53622679 GTTGAAGATC
Statistics
Matches: 183, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
213 2 0.01
214 177 0.97
215 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (214 bp):
TCCTATCTCCCTGGACAACAGTGGAAGAGGTTAAAGATTGAGAATCCTATCTCCCTGGACAGCAG
TGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAG
AATCCTATCTCCCTAGTCAGCAGTGGAATAGATTAAAGATTGTAGATCCTATCTCCCTGGTCAGC
AGTGGAATAGATTAAAGAA
Found at i:53623607 original size:17 final size:17
Alignment explanation
Indices: 53623555--53623607 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
53623545 TATGGAAACA
* *
53623555 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
*
53623572 CAATCTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
53623591 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
53623608 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:53623607 original size:22 final size:23
Alignment explanation
Indices: 53623579--53623623 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53623569 ATGCAATCTT
53623579 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
53623601 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
53623624 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:53623633 original size:22 final size:23
Alignment explanation
Indices: 53623589--53623633 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53623579 AGATATGATA
*
53623589 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
53623612 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
53623634 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:53635466 original size:21 final size:21
Alignment explanation
Indices: 53635440--53635481 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
53635430 CAAACAATTA
53635440 CAAAAAGTAACAATACCTTTT
1 CAAAAAGTAACAATACCTTTT
* *
53635461 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTAACAATACCTTTT
53635482 ACCAGGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (21 bp):
CAAAAAGTAACAATACCTTTT
Found at i:53639796 original size:20 final size:21
Alignment explanation
Indices: 53639758--53639796 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53639748 ATACTGCTTC
* *
53639758 TTTTGAATCGATTGTTTATAT
1 TTTTAAATCGATTGATTATAT
53639779 TTTTAAATCGATT-ATTAT
1 TTTTAAATCGATTGATTAT
53639797 GTTGGAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.56
Consensus pattern (21 bp):
TTTTAAATCGATTGATTATAT
Found at i:53639825 original size:55 final size:55
Alignment explanation
Indices: 53639741--53639853 Score: 163
Period size: 55 Copynumber: 2.1 Consensus size: 55
53639731 TCTTCTTAAT
* * *
53639741 TGTTGGAATACTGCTTCTTTTGAATCGATTGTTTATATTTTTAAATCGATTATTA
1 TGTTGGAATACTACTTCTTTTGAATCGATTATTTATATGTTTAAATCGATTATTA
* * * *
53639796 TGTTGGAATATTACTTCTTTTGAATCGATTATTTATATGTTTACATTGATTGTTA
1 TGTTGGAATACTACTTCTTTTGAATCGATTATTTATATGTTTAAATCGATTATTA
53639851 TGT
1 TGT
53639854 AGCGCATCTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (55 bp):
TGTTGGAATACTACTTCTTTTGAATCGATTATTTATATGTTTAAATCGATTATTA
Found at i:53655526 original size:26 final size:27
Alignment explanation
Indices: 53655494--53655603 Score: 91
Period size: 26 Copynumber: 4.0 Consensus size: 27
53655484 TTATATATTT
53655494 TTATTAAATTATATTTAATAATAATTA
1 TTATTAAATTATATTTAATAATAATTA
* * *
53655521 TT-TTAAATTATTTTTTATAGT-ATTA
1 TTATTAAATTATATTTAATAATAATTA
* * * * *
53655546 TATATTATGATTTTAGTAAATTCATATATT-
1 T-TATTA-AATTATATTTAA-TAATA-ATTA
53655576 TTATTAAATTATATTTAATAATAATTA
1 TTATTAAATTATATTTAATAATAATTA
53655603 T
1 T
53655604 GTTAAAATAT
Statistics
Matches: 60, Mismatches: 16, Indels: 14
0.67 0.18 0.16
Matches are distributed among these distances:
25 5 0.08
26 20 0.33
27 10 0.17
28 14 0.23
29 7 0.12
30 1 0.02
31 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (27 bp):
TTATTAAATTATATTTAATAATAATTA
Found at i:53655550 original size:61 final size:61
Alignment explanation
Indices: 53655378--53655572 Score: 174
Period size: 64 Copynumber: 3.2 Consensus size: 61
53655368 AAGTAGATTA
53655378 TAAATTATATTTAAGAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAG
1 TAAATTATATTTAAGAATAATTATTTTAAATTAT-TTTTATAGTATTATATA-TAT-ATTTTAG
* ** * *
53655442 TAAATTCATA--TAAGAATATTTAATACTAAGA--A-TTTTATCA--AAT-TATATAT-TTTTAT
1 TAAATT-ATATTTAAGAATAATT-ATTTTAA-ATTATTTTTAT-AGTATTATATATATATTTTAG
*
53655498 TAAATTATATTTAATAATAATTATTTTAAATTATTTTTTATAGTATTATATATTATGATTTTAG
1 TAAATTATATTTAAGAATAATTATTTTAAATTA-TTTTTATAGTATTATATA-TAT-ATTTTAG
53655562 TAAATTCATAT
1 TAAATT-ATAT
53655573 ATTTTATTAA
Statistics
Matches: 103, Mismatches: 11, Indels: 33
0.70 0.07 0.22
Matches are distributed among these distances:
55 4 0.04
56 16 0.16
57 10 0.10
58 4 0.04
59 10 0.10
60 4 0.04
61 10 0.10
62 4 0.04
63 11 0.11
64 22 0.21
65 8 0.08
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (61 bp):
TAAATTATATTTAAGAATAATTATTTTAAATTATTTTTATAGTATTATATATATATTTTAG
Found at i:53655578 original size:18 final size:17
Alignment explanation
Indices: 53655555--53655589 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53655545 ATATATTATG
53655555 ATTTTAGTAAATTCATAT
1 ATTTTAGTAAATT-ATAT
*
53655573 ATTTTATTAAATTATAT
1 ATTTTAGTAAATTATAT
53655590 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTAGTAAATTATAT
Found at i:53655780 original size:39 final size:41
Alignment explanation
Indices: 53655735--53655840 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
53655725 TTTCCTTATG
* * *
53655735 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAT
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
53655775 C-ATTACGCCTCTATTTCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTC----T-ATTCCATTCAACCAAACAAAAGAATTAC
53655820 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
53655841 ACGCATCTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 9 0.16
40 1 0.02
41 8 0.14
42 1 0.02
43 1 0.02
44 23 0.41
45 3 0.05
46 10 0.18
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:53655815 original size:44 final size:46
Alignment explanation
Indices: 53655748--53655840 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
53655738 TTACACCTCT
* * *
53655748 ATTCCATTCAACCAAACACAAGAA-TATC-ATTACGCCTCTATTTC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
53655792 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
53655838 ATT
1 ATT
53655841 ACGCATCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.52
45 3 0.07
46 18 0.41
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:53655843 original size:16 final size:16
Alignment explanation
Indices: 53655822--53655874 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
53655812 AGAATTACCT
53655822 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
53655838 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
** *
53655854 ATTATACCTCTATTCT
1 ATTACGCCTCTATTCC
53655870 ATTAC
1 ATTAC
53655875 AGCGAACCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:53657003 original size:11 final size:11
Alignment explanation
Indices: 53656982--53657028 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
53656972 GTGTAGTTTG
53656982 TTTATTGTTATT
1 TTTA-TGTTATT
53656994 TTTATGTTATT
1 TTTATGTTATT
53657005 TTTAAT-TTATT
1 TTT-ATGTTATT
* *
53657016 TTAAAGTTATT
1 TTTATGTTATT
53657027 TT
1 TT
53657029 GTTAGCAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 1 0.03
11 24 0.77
12 6 0.19
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.70
Consensus pattern (11 bp):
TTTATGTTATT
Found at i:53661379 original size:18 final size:19
Alignment explanation
Indices: 53661351--53661388 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
53661341 ATAGTTTATA
*
53661351 TATATATACATTTACATTT
1 TATATATACATATACATTT
53661370 TATA-ATACATATACATTT
1 TATATATACATATACATTT
53661388 T
1 T
53661389 TCCATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATACATATACATTT
Found at i:53661383 original size:24 final size:25
Alignment explanation
Indices: 53661345--53661406 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
53661335 TTATATATAG
*
53661345 TTTAT-ATATATATACA-TTTACAT
1 TTTATAATACATATACATTTTACAT
*
53661368 TTTATAATACATATACATTTTTCCAT
1 TTTATAATACATATACA-TTTTACAT
*
53661394 TTTATAATTCATA
1 TTTATAATACATA
53661407 CATATTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.15
24 10 0.30
26 18 0.55
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTATAATACATATACATTTTACAT
Found at i:53661413 original size:26 final size:26
Alignment explanation
Indices: 53661365--53661414 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
53661355 TATACATTTA
*
53661365 CATTTTATAATACATATACATTTTTC
1 CATTTTATAATACATACACATTTTTC
* *
53661391 CATTTTATAATTCATACATATTTT
1 CATTTTATAATACATACACATTTT
53661415 CACATACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (26 bp):
CATTTTATAATACATACACATTTTTC
Found at i:53663240 original size:8 final size:8
Alignment explanation
Indices: 53663218--53663269 Score: 51
Period size: 7 Copynumber: 7.1 Consensus size: 8
53663208 CCTTAGCCTC
53663218 TCCATTTT
1 TCCATTTT
*
53663226 TAC-TTTT
1 TCCATTTT
53663233 TCCA-TTT
1 TCCATTTT
53663240 TCCATTTT
1 TCCATTTT
53663248 T-C-TTTT
1 TCCATTTT
53663254 T-CATTTT
1 TCCATTTT
*
53663261 TTCATTTT
1 TCCATTTT
53663269 T
1 T
53663270 TTCACATCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 6 0.16
7 19 0.50
8 13 0.34
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (8 bp):
TCCATTTT
Found at i:53663807 original size:1 final size:1
Alignment explanation
Indices: 53663803--53663855 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
53663793 TCTTTTTTCC
* * * * * *
53663803 TTTTTTATTTTTTTTATTTTTTTTGTTTTTTTATATTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53663856 GCATTGAATC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.89
Consensus pattern (1 bp):
T
Found at i:53663815 original size:9 final size:9
Alignment explanation
Indices: 53663803--53663854 Score: 70
Period size: 9 Copynumber: 5.7 Consensus size: 9
53663793 TCTTTTTTCC
53663803 TTTTTTATT
1 TTTTTTATT
53663812 TTTTTTATT
1 TTTTTTATT
*
53663821 TTTTTTGTT
1 TTTTTTATT
53663830 TTTTTATATT
1 TTTTT-TATT
53663840 TTTTTGT-TT
1 TTTTT-TATT
53663849 TTTTTT
1 TTTTTT
53663855 TGCATTGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
8 1 0.03
9 29 0.74
10 9 0.23
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:53663824 original size:18 final size:17
Alignment explanation
Indices: 53663803--53663854 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 17
53663793 TCTTTTTTCC
*
53663803 TTTTTTATTTTTTTTAT
1 TTTTTTTTTTTTTTTAT
53663820 TTTTTTTGTTTTTTTATAT
1 TTTTTTT-TTTTTTT-TAT
53663839 TTTTTTGTTTTTTTTT
1 TTTTTT-TTTTTTTTT
53663855 TGCATTGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 6 0.19
18 8 0.26
19 16 0.52
20 1 0.03
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTTTTTTTAT
Found at i:53668047 original size:18 final size:19
Alignment explanation
Indices: 53668024--53668061 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
53668014 ATAAAATGGA
*
53668024 AAAATGTATATGTAT-TAT
1 AAAATGTAAATGTATATAT
53668042 AAAATGTAAATGTATATAT
1 AAAATGTAAATGTATATAT
53668061 A
1 A
53668062 TATAAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (19 bp):
AAAATGTAAATGTATATAT
Found at i:53668060 original size:26 final size:26
Alignment explanation
Indices: 53667998--53668047 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
53667988 TATGTATGTG
*
53667998 AAAATATGTATGAATTATAAAATGGA
1 AAAATATATATGAATTATAAAATGGA
* *
53668024 AAAATGTATATGTATTATAAAATG
1 AAAATATATATGAATTATAAAATG
53668048 TAAATGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (26 bp):
AAAATATATATGAATTATAAAATGGA
Found at i:53668209 original size:3 final size:3
Alignment explanation
Indices: 53668201--53668231 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
53668191 ATGTATAAGT
53668201 ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
53668232 TAACAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:53670164 original size:48 final size:48
Alignment explanation
Indices: 53670087--53670206 Score: 136
Period size: 48 Copynumber: 2.5 Consensus size: 48
53670077 AATGTACTCT
* * * * *
53670087 AATGTATCTAATTTATATTGCAAAGTTTGTTCCGCA-TTTTAATATTGC
1 AATGAATCTAATTTAAATTACAAACTTTGTT-CGAAGTTTTAATATTGC
* * *
53670135 AATTAATCTAATTTAAATTACAAACTTTGTTCTAAGTTTTAATGTTGC
1 AATGAATCTAATTTAAATTACAAACTTTGTTCGAAGTTTTAATATTGC
53670183 AATGAATCTCAA-TTAAATTACAAA
1 AATGAATCT-AATTTAAATTACAAA
53670207 GTTATTCTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
47 2 0.03
48 57 0.93
49 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (48 bp):
AATGAATCTAATTTAAATTACAAACTTTGTTCGAAGTTTTAATATTGC
Found at i:53670235 original size:47 final size:48
Alignment explanation
Indices: 53670123--53670247 Score: 137
Period size: 47 Copynumber: 2.6 Consensus size: 48
53670113 TTGTTCCGCA
* * * *
53670123 TTTTAATATTGCAATTAATCT-AATTTAAATTACAAACTTTGTTCTAAG
1 TTTTAATGTTGCAATGAATCTCAA-TTAAATTACAAACGTTATTCTAAG
**
53670171 TTTTAATGTTGCAATGAATCTCAATTAAATTACAAA-GTTATTCTGTG
1 TTTTAATGTTGCAATGAATCTCAATTAAATTACAAACGTTATTCTAAG
** * *
53670218 TTTTAATGTTGTGATGAAACCCAATTAAAT
1 TTTTAATGTTGCAATGAATCTCAATTAAAT
53670248 AAATACAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
47 33 0.50
48 31 0.47
49 2 0.03
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (48 bp):
TTTTAATGTTGCAATGAATCTCAATTAAATTACAAACGTTATTCTAAG
Found at i:53672501 original size:21 final size:22
Alignment explanation
Indices: 53672471--53672534 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 22
53672461 ATTATCAAGA
* * *
53672471 TACATTAATATTATACATACAG
1 TACAATAATAATATAAATACAG
** *
53672493 TA-AATAATACGATAAATATAG
1 TACAATAATAATATAAATACAG
*
53672514 TACAATAATAATATAAGTACA
1 TACAATAATAATATAAATACA
53672535 ATAAAAAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.31
Consensus pattern (22 bp):
TACAATAATAATATAAATACAG
Found at i:53672532 original size:17 final size:16
Alignment explanation
Indices: 53672507--53672538 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
53672497 TAATACGATA
53672507 AATATAGTACAATAAT
1 AATATAGTACAATAAT
53672523 AATATAAGTACAATAA
1 AATAT-AGTACAATAA
53672539 AAAATTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (16 bp):
AATATAGTACAATAAT
Found at i:53673139 original size:104 final size:102
Alignment explanation
Indices: 53673017--53673251 Score: 312
Period size: 102 Copynumber: 2.3 Consensus size: 102
53673007 ATAAAAAATC
*
53673017 ACACTAAACTAAACACAAACAATTTA-ACACCTAATCATAAATTATTAA-AAAATAACTTTAAAA
1 ACACTAAACTAAACACAAACAATTTATA-ACCTAATCATAAATTACTAACAAAATAACTTTAAAA
** * ***
53673080 TAATTTTTTTTAAAATTTACATTCATAAAAAATCACAATAA
65 TAA--TTTTAAAAAAATTA-AAAAATAAAAAATCACAATAA
* *
53673121 ACACTAAGCTAAACACAAACAATATATAACCTAATCATAAATTACTAACAAAATAACTTTAAAAT
1 ACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTAAAAT
* **
53673186 GATTTTAAAAAAATTAAAAAATTTAAAATCACAATAA
66 AATTTTAAAAAAATTAAAAAATAAAAAATCACAATAA
53673223 ACACTAAACTAAACACAAACAATTTATAA
1 ACACTAAACTAAACACAAACAATTTATAA
53673252 TAATTATTAA
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
102 43 0.37
103 11 0.10
104 43 0.37
105 18 0.16
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (102 bp):
ACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTAAAAT
AATTTTAAAAAAATTAAAAAATAAAAAATCACAATAA
Found at i:53673325 original size:27 final size:28
Alignment explanation
Indices: 53673295--53673355 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
53673285 AAAACAACAT
*
53673295 AAAAAATAAATAATCCCTTC-TA-TTTAA
1 AAAAAAT-AATAATCCCTTCAAATTTTAA
*
53673322 AAAAAATATTAATCCCTTCAAATTTTAA
1 AAAAAATAATAATCCCTTCAAATTTTAA
53673350 AAAAAA
1 AAAAAA
53673356 ATTACAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 11 0.37
27 8 0.27
28 11 0.37
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAAAATAATAATCCCTTCAAATTTTAA
Found at i:53673334 original size:26 final size:28
Alignment explanation
Indices: 53673295--53673359 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
53673285 AAAACAACAT
* *
53673295 AAAAAATAAATAATCCCTTC-TA-TTTAA
1 AAAAAAT-ATTAATCCCTTCAAATTTTAA
53673322 AAAAAATATTAATCCCTTCAAATTTTAA
1 AAAAAATATTAATCCCTTCAAATTTTAA
53673350 AAAAAA-ATTA
1 AAAAAATATTA
53673360 CAAATATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 11 0.32
27 12 0.35
28 11 0.32
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAAAATATTAATCCCTTCAAATTTTAA
Found at i:53673359 original size:27 final size:25
Alignment explanation
Indices: 53673294--53673359 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 25
53673284 AAAAACAACA
*
53673294 TAAAAAATAAA-TAATCCCTTCTATT
1 TAAAAAA-AAATTAATCCCTTCAATT
53673319 TAAAAAAAATATTAATCCCTTCAAATTT
1 TAAAAAAAA-ATTAATCCCTTC-AA-TT
53673347 TAAAAAAAAATTA
1 TAAAAAAAAATTA
53673360 CAAATATACA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
24 2 0.06
25 8 0.22
26 10 0.28
27 5 0.14
28 11 0.31
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (25 bp):
TAAAAAAAAATTAATCCCTTCAATT
Found at i:53673385 original size:4 final size:4
Alignment explanation
Indices: 53673378--53673429 Score: 58
Period size: 4 Copynumber: 13.5 Consensus size: 4
53673368 CATACCTTCC
53673378 CTTT CTTT -TTT CTTT -TTT -TTT CTTT CTTT CTTCT CATTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT-T C-TTT CTTT CTTT
53673425 -TTT CT
1 CTTT CT
53673430 CCTTCTATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 12 0.28
4 25 0.58
5 4 0.09
6 2 0.05
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (4 bp):
CTTT
Found at i:53673391 original size:7 final size:8
Alignment explanation
Indices: 53673378--53673429 Score: 58
Period size: 7 Copynumber: 6.8 Consensus size: 8
53673368 CATACCTTCC
53673378 CTTTCTTT
1 CTTTCTTT
53673386 -TTTCTTT
1 CTTTCTTT
53673393 -TTT-TTT
1 CTTTCTTT
53673399 CTTTCTTT
1 CTTTCTTT
53673407 CTTCTCATTT
1 CTT-TC-TTT
53673417 CTTTCTTT
1 CTTTCTTT
53673425 -TTTCT
1 CTTTCT
53673430 CCTTCTATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.08
7 18 0.45
8 9 0.22
9 4 0.10
10 6 0.15
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (8 bp):
CTTTCTTT
Found at i:53673409 original size:18 final size:18
Alignment explanation
Indices: 53673396--53673430 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53673386 TTTCTTTTTT
53673396 TTTCTTTCTTTCTTCTCA
1 TTTCTTTCTTTCTTCTCA
*
53673414 TTTCTTTCTTTTTTCTC
1 TTTCTTTCTTTCTTCTC
53673431 CTTCTATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTTCTTTCTTCTCA
Found at i:53681835 original size:14 final size:15
Alignment explanation
Indices: 53681816--53681846 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
53681806 ATTCTATGCA
53681816 TTTTCTTTA-AATTT
1 TTTTCTTTATAATTT
53681830 TTTTCTTTATAATTT
1 TTTTCTTTATAATTT
53681845 TT
1 TT
53681847 ATATATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCTTTATAATTT
Found at i:53682584 original size:28 final size:29
Alignment explanation
Indices: 53682547--53682631 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
53682537 TCTTACAACT
53682547 TATAAAATTTTATAATTTTTTTATATTTA
1 TATAAAATTTTATAATTTTTTTATATTTA
* * * *
53682576 TGT-ATATTTTATACTTTTTTTACTATTTT
1 TATAAAATTTTATAATTTTTTTA-TATTTA
*
53682605 TATAAAATTTTACAATTTTTTGTATAT
1 TATAAAATTTTATAATTTTTT-TATAT
53682632 ATTTTTTATG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
28 17 0.38
29 9 0.20
30 17 0.38
31 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (29 bp):
TATAAAATTTTATAATTTTTTTATATTTA
Found at i:53682646 original size:22 final size:23
Alignment explanation
Indices: 53682621--53682663 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
53682611 ATTTTACAAT
*
53682621 TTTTTGTATAT-ATTTTTTATGA
1 TTTTTATATATGATTTTTTATGA
*
53682643 TTTTTATATTTGATTTTTTAT
1 TTTTTATATATGATTTTTTAT
53682664 TAAAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (23 bp):
TTTTTATATATGATTTTTTATGA
Found at i:53682876 original size:21 final size:21
Alignment explanation
Indices: 53682828--53682878 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
53682818 AAAAAAGGTA
*
53682828 GGAGC-TTAATTGCTTTTTTT
1 GGAGCATTAAGTGCTTTTTTT
*
53682848 GAAAAGCATTAAGTGCTTTTTTT
1 G--GAGCATTAAGTGCTTTTTTT
53682871 GGAGCATT
1 GGAGCATT
53682879 TTGAGAGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 6 0.24
22 3 0.12
23 15 0.60
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.45
Consensus pattern (21 bp):
GGAGCATTAAGTGCTTTTTTT
Found at i:53689399 original size:15 final size:16
Alignment explanation
Indices: 53689381--53689419 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
53689371 GAAAACTGAA
53689381 AGAAAG-AAGAAAAAT
1 AGAAAGAAAGAAAAAT
*
53689396 AGAAAGAAAGAAAAAG
1 AGAAAGAAAGAAAAAT
53689412 A-AAAGAAA
1 AGAAAGAAA
53689420 CCAAGGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AGAAAGAAAGAAAAAT
Found at i:53689418 original size:19 final size:19
Alignment explanation
Indices: 53689367--53689419 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
53689357 ATAAACACAG
53689367 AAAAGAAAACTGAAAGAAAGA
1 AAAAGAAAA--GAAAGAAAGA
*
53689388 AGAAA-AATAGAAAGAAAGA
1 A-AAAGAAAAGAAAGAAAGA
53689407 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
53689420 CCAAGGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 3 0.11
19 18 0.64
21 4 0.14
22 3 0.11
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (19 bp):
AAAAGAAAAGAAAGAAAGA
Found at i:53696688 original size:17 final size:17
Alignment explanation
Indices: 53696668--53696743 Score: 50
Period size: 17 Copynumber: 4.4 Consensus size: 17
53696658 AGTAATAAAG
53696668 TGTGAAATAATATAATA
1 TGTGAAATAATATAATA
* *
53696685 TGTG-AATAAGGAAAATA
1 TGTGAAATAA-TATAATA
* *
53696702 TGGTAAAAGTTTAATA-AA-G
1 T-GTGAAA---TAATATAATA
53696721 TGTGAAATAATATAATA
1 TGTGAAATAATATAATA
53696738 TGTGAA
1 TGTGAA
53696744 TAAGGAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
15 5 0.11
16 7 0.16
17 16 0.36
18 7 0.16
19 3 0.07
20 2 0.05
21 1 0.02
22 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (17 bp):
TGTGAAATAATATAATA
Found at i:53696717 original size:53 final size:53
Alignment explanation
Indices: 53696660--53696769 Score: 220
Period size: 53 Copynumber: 2.1 Consensus size: 53
53696650 GGTAAATTAG
53696660 TAATAAAGTGTGAAATAATATAATATGTGAATAAGGAAAATATGGTAAAAGTT
1 TAATAAAGTGTGAAATAATATAATATGTGAATAAGGAAAATATGGTAAAAGTT
53696713 TAATAAAGTGTGAAATAATATAATATGTGAATAAGGAAAATATGGTAAAAGTT
1 TAATAAAGTGTGAAATAATATAATATGTGAATAAGGAAAATATGGTAAAAGTT
53696766 TAAT
1 TAAT
53696770 GAGTGTGTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (53 bp):
TAATAAAGTGTGAAATAATATAATATGTGAATAAGGAAAATATGGTAAAAGTT
Found at i:53698637 original size:16 final size:18
Alignment explanation
Indices: 53698616--53698651 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
53698606 TTTTAATTTT
53698616 TTAAAAAAC-A-ATAAAA
1 TTAAAAAACTATATAAAA
53698632 TTAAAAAACTATATAAAA
1 TTAAAAAACTATATAAAA
53698650 TT
1 TT
53698652 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
TTAAAAAACTATATAAAA
Found at i:53698902 original size:13 final size:13
Alignment explanation
Indices: 53698884--53698917 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
53698874 TTTTGTTGAG
*
53698884 AAGTGCTTTTAAA
1 AAGTGCTTTGAAA
53698897 AAGTGCTTTGAAA
1 AAGTGCTTTGAAA
53698910 AAGTGCTT
1 AAGTGCTT
53698918 CACAAGTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (13 bp):
AAGTGCTTTGAAA
Found at i:53715148 original size:51 final size:50
Alignment explanation
Indices: 53715083--53715184 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 50
53715073 ACTTTACTTG
* * * * *
53715083 AAAAAGAAGGGACCAAAGTGAAAACCTGCAAAGGGCGCTTTGATTCCTAAA
1 AAAAAGAAGAGACCAAAGTGAAAACCCGCAAAAGGAGCTTTGAGT-CTAAA
*
53715134 AAAAAGGAGAGACCAAAGTGAAAACCCGCAAAAGGAGCTTTGAGTCTAAA
1 AAAAAGAAGAGACCAAAGTGAAAACCCGCAAAAGGAGCTTTGAGTCTAAA
53715184 A
1 A
53715185 TAATAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
50 6 0.13
51 39 0.87
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.14
Consensus pattern (50 bp):
AAAAAGAAGAGACCAAAGTGAAAACCCGCAAAAGGAGCTTTGAGTCTAAA
Found at i:53716654 original size:44 final size:45
Alignment explanation
Indices: 53716606--53716702 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 45
53716596 ATTGAGTTTT
* *
53716606 TAGTGGAGCAGACTG-AG-TAAGCAGGTCTTATCCCCCTAAAGTTA
1 TAGTGGAGCAAACTGAAGAT-AGCAGATCTTATCCCCCTAAAGTTA
* * * *
53716650 TAGTGGGGCAAACTGAAGATGGCAGATCTTATCTCCCTAAAGTTG
1 TAGTGGAGCAAACTGAAGATAGCAGATCTTATCCCCCTAAAGTTA
*
53716695 CAGTGGAG
1 TAGTGGAG
53716703 TAGATTAAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
44 13 0.30
45 29 0.67
46 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (45 bp):
TAGTGGAGCAAACTGAAGATAGCAGATCTTATCCCCCTAAAGTTA
Done.