Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 168 of 226
Found at i:53586678 original size:217 final size:217
Alignment explanation
Indices: 53586002--53586648 Score: 1132
Period size: 217 Copynumber: 3.0 Consensus size: 217
53585992 TCGGTGGCCA
* *
53586002 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTTGGGTCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
*
53586067 TGCAGAGAGCAGATCGCATTTAGTCTTATCTCCCGGAAGTTGCAGTGGAACAGACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATTTAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
53586132 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
131 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
53586197 GCAGTGGAGTAGATTAAAGCCG
196 GCAGTGGAGTAGATTAAAGCCG
* *
53586219 ATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTTTGAAGT
1 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
* * *
53586284 TGCAGAGAGCAGATCGCATATAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
66 TGCAGAGAGCAGATCGCATTTAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
** * * *
53586349 AGTCTTATCCTCCTGAAGTTATAGTGAGGCAGACTAAAGATGGCAAATCTTAACTCCCTGAGGTT
131 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
53586414 GCAGTGGAGTAGATTAAAGCCG
196 GCAGTGGAGTAGATTAAAGCCG
*
53586436 ATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
* *
53586501 TACAGAGAGCAGATCGCATTTAGTCTTATCTCCCGGATGTTGCAGTGGAGCAGACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATTTAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
53586566 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
131 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* *
53586631 GTAGTGGAGTGGATTAAA
196 GCAGTGGAGTAGATTAAA
53586649 ACCTTGGATC
Statistics
Matches: 402, Mismatches: 28, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 402 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (217 bp):
ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
TGCAGAGAGCAGATCGCATTTAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
GCAGTGGAGTAGATTAAAGCCG
Found at i:53586733 original size:390 final size:390
Alignment explanation
Indices: 53586221--53586964 Score: 1272
Period size: 390 Copynumber: 1.9 Consensus size: 390
53586211 TAAAGCCGAT
*
53586221 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTTTGAAGTTG
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
*
53586286 CAGAGAGCAGATCGCATATAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAG
66 CAGAGAGCAGATCGCATATAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAACAAG
* *
53586351 TCTTATCCTCCTGAAGTTATAGTGAGGCAGACTAAAGATGGCAAATCTTAACTCCCTGAGGTTGC
131 TCTTATCCTCCTAAAGTTACAGTGAGGCAGACTAAAGATGGCAAATCTTAACTCCCTGAGGTTGC
* *
53586416 AGTGGAGTAGATTAAAGCCGATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCTT
196 AGTGGAGTAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACATT
* * *
53586481 GGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATTTAGTCTTATCTCCCGGATGTTGCAG
261 AGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCGGAAGTTGCAG
53586546 TGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
326 TGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
* ** *
53586611 AATCTTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
* * *
53586676 CAGAGAGCAGATCGCATCTAGTCTTATCTCGCTGAAGTTGCAGTGGAGCAAACTAAGTAAATAAG
66 CAGAGAGCAGATCGCATATAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAACAAG
* * *
53586741 TCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAGGTTGC
131 TCTTATCCTCCTAAAGTTACAGTGAGGCAGACTAAAGATGGCAAATCTTAACTCCCTGAGGTTGC
*
53586806 AGTGGAGTAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATATT
196 AGTGGAGTAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACATT
* * *
53586871 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGTAG
261 AGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCGGAAGTTGCAG
*
53586936 TGGAGCAGACTAAGTGAGCAAGTCTTATC
326 TGGAGCAGACTAAGTAAGCAAGTCTTATC
53586965 TTTCTGAAAT
Statistics
Matches: 330, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
390 330 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (390 bp):
AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
CAGAGAGCAGATCGCATATAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAACAAG
TCTTATCCTCCTAAAGTTACAGTGAGGCAGACTAAAGATGGCAAATCTTAACTCCCTGAGGTTGC
AGTGGAGTAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACATT
AGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCGGAAGTTGCAG
TGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
Found at i:53586745 original size:217 final size:218
Alignment explanation
Indices: 53586002--53586904 Score: 998
Period size: 217 Copynumber: 4.2 Consensus size: 218
53585992 TCGGTGGCCA
* * * *
53586002 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTTGGGTCTTATCTCTCTGAAGT
1 ATAATCCTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCTTAGATCTTATCTCTCTGAAGT
* * * * *
53586067 TGCAGAGAGCAGATCG-CATTTAGTCTTATCTCCCGGAAGTTGCAGTGGAACAGACTAAGTAAGC
66 TGCAGAGAGCAGATAGTAAATAAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAGACTAAGTAAGC
53586131 AAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGT
131 AAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGT
*
53586196 TGCAGTGGAGTAGATTAAAGCCG
196 TGCAGTGGAGTAGATTAAAACCG
* * * * * *
53586219 ATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTTTGAAGT
1 ATAATCCTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCTTAGATCTTATCTCTCTGAAGT
* * * * *
53586284 TGCAGAGAGCAGATCGCATAT-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAC
66 TGCAGAGAGCAGATAGTAAATAAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAGACTAAGTAAGC
** * * *
53586348 AAGTCTTATCCTCCTGAAGTTATAGTGAGGCAGACTAAAGATGGCAAATCTTAACTCCCTGAGGT
131 AAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGT
*
53586413 TGCAGTGGAGTAGATTAAAGCCG
196 TGCAGTGGAGTAGATTAAAACCG
* * *
53586436 ATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCTTAGATCTTATCTCTCTGAAGT
* * * * * *
53586501 TACAGAGAGCAGATCG-CATTTAGTCTTATCTCCCGGATGTTGCAGTGGAGCAGACTAAGTAAGC
66 TGCAGAGAGCAGATAGTAAATAAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAGACTAAGTAAGC
53586565 AAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGT
131 AAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGT
* *
53586630 TGTAGTGGAGTGGATTAAAACC-
196 TGCAGTGGAGTAGATTAAAACCG
* * * *** * *
53586652 TTGGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATC-TAG-TCTTATCTCGCTGAAG
1 AT-AATCCTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCTTAGATCTTATCTCTCTGAAG
* * **
53586713 TTGCAGTGGAGCAAACTAAGTAAATAAGTCTTATC-CTCCTAAAGTTGCAGT-GAGGCAGACTGA
65 TTGCAG-AGAGCAGA-T-AGTAAATAAGTCTTATCTC-CCGGAAGTTGCAGTGGA-GCAGACT-A
* * * * * * *
53586776 AG-ATGGCAAATCTTAT-CTCCCTGAGGTTGCAGTG-GAGTAGA-TTAA-A-GCCGATAATCCTA
124 AGTA-AGCAAGTCTTATCCT-CCTGAAGTTGCAGTGAG-GCAGACTGAAGATGGC-A-AATCTTA
** *
53586835 TCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA--T
184 TCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCG
*
53586868 ATTAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGAT
1 A-TA-ATCCTATCTCTCTGAAGTTGCAGTAGAGCAGAT
53586905 CGCATCTAGT
Statistics
Matches: 602, Mismatches: 65, Indels: 37
0.86 0.09 0.05
Matches are distributed among these distances:
213 20 0.03
214 8 0.01
215 6 0.01
216 14 0.02
217 522 0.87
218 32 0.05
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (218 bp):
ATAATCCTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCTTAGATCTTATCTCTCTGAAGT
TGCAGAGAGCAGATAGTAAATAAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAGACTAAGTAAGC
AAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGT
TGCAGTGGAGTAGATTAAAACCG
Found at i:53586851 original size:173 final size:173
Alignment explanation
Indices: 53586438--53586821 Score: 633
Period size: 173 Copynumber: 2.2 Consensus size: 173
53586428 TAAAGCCGAT
* * * *
53586438 AATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
* * * *
53586503 CAGAGAGCAGATCGCATTTAGTCTTATCTCCCGGATGTTGCAGTGGAGCAGACTAAGTAAGCAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAAACTAAGTAAACAAG
*
53586568 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
131 TCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCA
*
53586611 AATCTTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
* * *
53586676 CAGAGAGCAGATCGCATCTAGTCTTATCTCGCTGAAGTTGCAGTGGAGCAAACTAAGTAAATAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAAACTAAGTAAACAAG
53586741 TCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCA
131 TCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCA
* *
53586784 AATCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
53586822 GCCGATAATC
Statistics
Matches: 195, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
173 195 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (173 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
CAGAGAGCAGATCGCATCTAGTCTTATCTCCCGGAAGTTGCAGTGGAGCAAACTAAGTAAACAAG
TCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCA
Found at i:53586946 original size:173 final size:173
Alignment explanation
Indices: 53586438--53586901 Score: 518
Period size: 173 Copynumber: 2.7 Consensus size: 173
53586428 TAAAGCCGAT
* * ** * * * * *
53586438 AATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCATGAATCCTATCTCCCTGAAGTTG
*** * * * * * * * **
53586503 CAGAGAGCAGATCGCATTTAGTCTTATCTCCCGGATGTTGCAGTGGAGCAGACTAAGTAAGCAAG
66 CAGAGAGCAGATAAAATCTAGTCTTATCTCGCTGAAGTTGCAGTAGAGCAAACTAAGCAAATAAG
53586568 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
131 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
* * * * * *
53586611 AATCTTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCATGAATCCTATCTCCCTGAAGTTG
*** * *
53586676 CAGAGAGCAGATCGCATCTAGTCTTATCTCGCTGAAGTTGCAGTGGAGCAAACTAAGTAAATAAG
66 CAGAGAGCAGATAAAATCTAGTCTTATCTCGCTGAAGTTGCAGTAGAGCAAACTAAGCAAATAAG
*
53586741 TCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCA
131 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
* *
53586784 AATCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTAAAGCCGAT-AATCCTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACC-ATGAATCCTATCTCCCTGAAGTT
* * * *
53586848 GCAGTGGAGCGGATTAAAATATTAGATCTTATCTCTCTGAAGTTGCAG-AGAGCA
65 GCAG-AGAGCAGA-TAAAAT-CTAG-TCTTATCTCGCTGAAGTTGCAGTAGAGCA
53586902 GATCGCATCT
Statistics
Matches: 257, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
173 218 0.85
174 7 0.03
175 3 0.01
176 8 0.03
177 21 0.08
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (173 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCATGAATCCTATCTCCCTGAAGTTG
CAGAGAGCAGATAAAATCTAGTCTTATCTCGCTGAAGTTGCAGTAGAGCAAACTAAGCAAATAAG
TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
Found at i:53589030 original size:30 final size:30
Alignment explanation
Indices: 53588986--53589043 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
53588976 CTTCTTTTCT
* *
53588986 TTATTTATTTTGTTTGC-TTTCTTCATTCG
1 TTATTTATTGTGTTTGCATTTATTCATTCG
53589015 TTATTTAATTGTGTTTGCATTTATTCATT
1 TTATTT-ATTGTGTTTGCATTTATTCATT
53589044 TAATATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.24
30 10 0.40
31 9 0.36
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.64
Consensus pattern (30 bp):
TTATTTATTGTGTTTGCATTTATTCATTCG
Found at i:53597173 original size:30 final size:30
Alignment explanation
Indices: 53597137--53597220 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 30
53597127 TTCCTGGGAT
53597137 AGGATGTTTGAAAATTATCTTGGGTTTCCC
1 AGGATGTTTGAAAATTATCTTGGGTTTCCC
* * *
53597167 AGGATGTTTGAAAATTATCTCGAGATTCCC
1 AGGATGTTTGAAAATTATCTTGGGTTTCCC
* * *
53597197 AAG-T-TTTGAAAATTTTCATGGGTT
1 AGGATGTTTGAAAATTATCTTGGGTT
53597221 AAGGTTAGGG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 15 0.33
29 1 0.02
30 29 0.64
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.39
Consensus pattern (30 bp):
AGGATGTTTGAAAATTATCTTGGGTTTCCC
Found at i:53597580 original size:21 final size:21
Alignment explanation
Indices: 53597553--53597607 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
53597543 ATAGCGGTGA
*
53597553 CAGTGAGATTAGTTACTGTAG
1 CAGTGAGATTAGATACTGTAG
* *
53597574 CGGTGAGATTGGATACTGTAG
1 CAGTGAGATTAGATACTGTAG
53597595 CAGTGAGATTAGA
1 CAGTGAGATTAGA
53597608 AAGAATGGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.33, T:0.29
Consensus pattern (21 bp):
CAGTGAGATTAGATACTGTAG
Found at i:53598784 original size:13 final size:14
Alignment explanation
Indices: 53598766--53598802 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
53598756 ACGATGGCAT
53598766 AAATAATATAAAC-
1 AAATAATATAAACG
53598779 AAATAA-ATAAACG
1 AAATAATATAAACG
53598792 AAACTAATATA
1 AAA-TAATATA
53598803 CATGAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (14 bp):
AAATAATATAAACG
Found at i:53601103 original size:44 final size:44
Alignment explanation
Indices: 53601039--53601457 Score: 403
Period size: 44 Copynumber: 9.5 Consensus size: 44
53601029 ACCAGTATGG
* * * * *
53601039 GAAGACAAGATCTACTATCTTTGATCAAATTCATGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
53601083 GAAGACAAGATCTG-TCATCTTCGATCTACTTCACGCCAATACGT
1 GAAGACAAGATCTGCT-ATCTTCGATCTACTTCACGCCAATACAT
* * * *
53601127 AAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * * ***
53601171 GAAGACAAGATCTGCTTTCTTCGATCTATTTCGCCACCAGT-GGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
* * * * *
53601215 GAAGACAAGATTTGTTACCTTTGATCTACTTCATGCCGAAT-CAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC-AATACAT
* * ***
53601259 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCGCCAATATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
*
53601304 GAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * ** *
53601348 GAAGACAAGCTCTGCTATTTTTAATCCACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * ***
53601392 GAAGACAAGATCTGCTTTCTTCGATTTACTTCGCCACCAATATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
53601437 GAAGACAAGATCTGCTATCTT
1 GAAGACAAGATCTGCTATCTT
53601458 TAACCTGCTC
Statistics
Matches: 297, Mismatches: 71, Indels: 13
0.78 0.19 0.03
Matches are distributed among these distances:
43 3 0.01
44 229 0.77
45 65 0.22
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
Found at i:53601379 original size:133 final size:132
Alignment explanation
Indices: 53601034--53601457 Score: 476
Period size: 133 Copynumber: 3.2 Consensus size: 132
53601024 TCACTACCAG
* * * *
53601034 TATGGGAAGACAAGATCTACTATCTTTGATCAAATTCATGCCAATACATGAAGACAAGATCTGTC
1 TATGGGAAGACAAGATCTGCTATCTTCGATCTAATTCACGCCAATACATGAAGACAAGATCTGT-
* * * ** * **
53601099 ATCTTCGATCTACTTCACGCCAATACGTAAAGACAAGATCTGCTACCTTTGATCTACTTC-ATGC
65 ATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCGC
53601163 CAA
130 CAA
*** * * * * * *** *
53601166 TACATGAAGACAAGATCTGCTTTCTTCGATCTATTTCGCCACCAGT-GGGGAAGACAAGATTTGT
1 TATGGGAAGACAAGATCTGCTATCTTCGATCTAATTC-ACGCCAATACATGAAGACAAGATCTG-
* *
53601230 TACCTTTGATCTACTTCATGCCGAAT-CATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
64 TATCTTTGATCTACTTCACGCC-AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
53601294 GCCAA
128 GCCAA
* * *
53601299 TATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGCTCTGCT
1 TATGGGAAGACAAGATCTGCTATCTTCGATCTAATTCACGCCAATACATGAAGACAAGATCTG-T
* * * * *
53601364 ATTTTTAATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATTTACTTCGCCAC
65 ATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCGC
53601429 CAA
130 CAA
53601432 TATGGGAAGACAAGATCTGCTATCTT
1 TATGGGAAGACAAGATCTGCTATCTT
53601458 TAACCTGCTC
Statistics
Matches: 237, Mismatches: 49, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
132 98 0.41
133 139 0.59
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (132 bp):
TATGGGAAGACAAGATCTGCTATCTTCGATCTAATTCACGCCAATACATGAAGACAAGATCTGTA
TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCGCC
AA
Found at i:53601536 original size:221 final size:220
Alignment explanation
Indices: 53601073--53601545 Score: 549
Period size: 221 Copynumber: 2.1 Consensus size: 220
53601063 TCAAATTCAT
* * *
53601073 GCCAATACATGAAGACAAGATCTGTCATCTTCGATCTACTTCACGCCAATACGTAAAGACAAGAT
1 GCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACATAAAGACAAGAT
* * * *
53601138 CTGCTACCTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTATTTC
66 CTGCTACCTTTAATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC
* * * * * * *
53601203 GCCACCAGTGGGGAAGACAAGATTTGTTACCTTTGATCTACTTCATGCCGAATCATGAAGACAAG
131 GCCACCAATGGGGAAGACAAGATCTGCTACCTTTAACCTACTTCATGCC-AACCAGGAAGACAAG
* * * *
53601268 ATCTGCTTTCTTCGATCTACTTCGCC
195 AGCTGCTGTCTTCAATCTACTTCACC
** * *
53601294 GCCAATATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGCT
1 GCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACATAAAGACAAGAT
** *
53601359 CTGCTATTTTTAATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATTTACTTC
66 CTGCTACCTTTAATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC
* * * * *
53601424 GCCACCAATATGGGAAGACAAGATCTGCTATCTTTAACCTGCTCTGC-TGCC-ACCGAGGGAGGC
131 GCCACCAAT-GGGGAAGACAAGATCTGCTACCTTTAACCTACT-T-CATGCCAACC-AGGAAGAC
* *
53601487 AAG-GCTAG-TGTCTTCAATCTGCTTCACT
192 AAGAGCT-GCTGTCTTCAATCTACTTCACC
* * *
53601515 GTCAGTACAGGAAGGCAAGATCTGTTATCTT
1 GCCAATACAGGAAGACAAGATCTGTTATCTT
53601546 TAACCTACTC
Statistics
Matches: 210, Mismatches: 37, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
221 169 0.80
222 35 0.17
223 5 0.02
224 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (220 bp):
GCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACATAAAGACAAGAT
CTGCTACCTTTAATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC
GCCACCAATGGGGAAGACAAGATCTGCTACCTTTAACCTACTTCATGCCAACCAGGAAGACAAGA
GCTGCTGTCTTCAATCTACTTCACC
Found at i:53601558 original size:88 final size:88
Alignment explanation
Indices: 53601436--53602248 Score: 934
Period size: 88 Copynumber: 9.2 Consensus size: 88
53601426 CACCAATATG
* * * *
53601436 GGAAGACAAGATCTGCTATCTTTAACCTGCTCTGCTGCCACCGAGGGAGGCAAGGCTAGTGTCTT
1 GGAAGACAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTT
* *
53601501 CAATCTGCTTCACTGTCAGTACA
66 CGATCTGCTTCGCTGTCAGTACA
* * * * * * *
53601524 GGAAGGCAAGATCTGTTATCTTTAACCTACTCTGCTGCCACCGAGGGAGGCAAGGCTAGTGTCTT
1 GGAAGACAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTT
* *
53601589 CAATCTGCTTCACTGTCAGTACA
66 CGATCTGCTTCGCTGTCAGTACA
* * * * *
53601612 GGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTACCACCGAGGGAGGCAAGGCTAGTGTCTT
1 GGAAGACAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTT
* * * * * *
53601677 CGATCTACTCCACT-ACTGCT-TA
66 CGATCTGCTTCGCTGTCAG-TACA
* * * * *
53601699 GGGAGATAAGATCTGCAAT-TTTCAACCTGCTCTGCTGCAACCCAGGGAGGCAAGACTGGTGTCT
1 GGAAGACAAGATCTGCTATCTTT-AACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCT
* * * *
53601763 TTGATCTGCTTCACTGCCGGTACA
65 TCGATCTGCTTCGCTGTCAGTACA
* * *
53601787 GGAAGACAAGATCTGCTATTTTTAACCTGCTCCGTTGCAACCCAGGGAGGCAAGGCTAGTGTCTT
1 GGAAGACAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTT
* *
53601852 CGATCTGCTTCGCTGTTATTACA
66 CGATCTGCTTCGCTGTCAGTACA
* *
53601875 GGAAGGCAAGATCTGCTAT-TTTCAACCTGCTCCGTTGCAACCCAGGGAGGCAAGGCTGGTGTCT
1 GGAAGACAAGATCTGCTATCTTT-AACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCT
* *
53601939 TTGATCTGCTTCGCTG-CCGATACA
65 TCGATCTGCTTCGCTGTCAG-TACA
* * ** * * * *
53601963 GGAAAACAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAAGGAGGCAAGACTGGTGTCTT
1 GGAAGACAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTT
*
53602028 CGATCTGCTTCGCTGTCATTACA
66 CGATCTGCTTCGCTGTCAGTACA
* * * *
53602051 GGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGCAACCCAGGGAGGCAAGACTGGTGTCTT
1 GGAAGACAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTT
* * *
53602116 TGATCTGCTTCGCTGTCGGTGCA
66 CGATCTGCTTCGCTGTCAGTACA
* * * * *
53602139 GGAAGACAAGATCTGCTATTTTTAACCTGCTGCACTGCAACCCAGGGAGGAAAGACTGGTGTCTT
1 GGAAGACAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTT
* * *
53602204 TGATCTGCTTCGCTGCCGGTACA
66 CGATCTGCTTCGCTGTCAGTACA
*
53602227 GGAAGGCAAGATCTGCTATCTT
1 GGAAGACAAGATCTGCTATCTT
53602249 CAATGATCTG
Statistics
Matches: 633, Mismatches: 83, Indels: 18
0.86 0.11 0.02
Matches are distributed among these distances:
86 3 0.00
87 69 0.11
88 555 0.88
89 6 0.01
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (88 bp):
GGAAGACAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTT
CGATCTGCTTCGCTGTCAGTACA
Found at i:53601663 original size:44 final size:43
Alignment explanation
Indices: 53601442--53601665 Score: 141
Period size: 44 Copynumber: 5.1 Consensus size: 43
53601432 TATGGGAAGA
*
53601442 CAAGATCTGCTATCTTTAACCTGCTCTGCTGCCACCGAGGGAGG
1 CAAGATCTG-TATCTTTAACCTGCTCCGCTGCCACCGAGGGAGG
* * * * * * * * *
53601486 CAAG-GCTAGTGTCTTCAATCTGCTTCACTGTCAGTAC-AGGAAGG
1 CAAGATCT-GTATCTTTAACCTGCTCCGCTGCCA--CCGAGGGAGG
* *
53601530 CAAGATCTGTTATCTTTAACCTACTCTGCTGCCACCGAGGGAGG
1 CAAGATCTG-TATCTTTAACCTGCTCCGCTGCCACCGAGGGAGG
* * * * * * * * *
53601574 CAAG-GCTAGTGTCTTCAATCTGCTTCACTGTCAGTAC-AGGAAGG
1 CAAGATCT-GTATCTTTAACCTGCTCCGCTGCCA--CCGAGGGAGG
*
53601618 CAAGATCTGCTATCTTTAACCTGCTCCGCTACCACCGAGGGAGG
1 CAAGATCTG-TATCTTTAACCTGCTCCGCTGCCACCGAGGGAGG
53601662 CAAG
1 CAAG
53601666 GCTAGTGTCT
Statistics
Matches: 126, Mismatches: 42, Indels: 24
0.66 0.22 0.12
Matches are distributed among these distances:
43 39 0.31
44 48 0.38
45 39 0.31
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (43 bp):
CAAGATCTGTATCTTTAACCTGCTCCGCTGCCACCGAGGGAGG
Found at i:53601926 original size:44 final size:44
Alignment explanation
Indices: 53601706--53602252 Score: 209
Period size: 44 Copynumber: 12.4 Consensus size: 44
53601696 TTAGGGAGAT
* *
53601706 AAGATCTGCAATTTTCAACCTGC-TCTGCTGCAACCCAGGGAGGC
1 AAGATCTGCTATTTTCAATCTGCTTC-GCTGCAACCCAGGGAGGC
* * * * **** * *
53601750 AAGA-CTGGTGTCTTT-GATCTGCTTCACTGCCGGTACAGGAAGAC
1 AAGATCTGCTAT-TTTCAATCTGCTTCGCTG-CAACCCAGGGAGGC
* * * *
53601794 AAGATCTGCTATTTTTAACCTGCTCCGTTGCAACCCAGGGAGGC
1 AAGATCTGCTATTTTCAATCTGCTTCGCTGCAACCCAGGGAGGC
* * * * * *** *
53601838 AAG-GCTAG-TGTCTTCGATCTGCTTCGCTGTTATTACAGGAAGGC
1 AAGATCT-GCTATTTTCAATCTGCTTCGCTG-CAACCCAGGGAGGC
* * *
53601882 AAGATCTGCTATTTTCAACCTGCTCCGTTGCAACCCAGGGAGGC
1 AAGATCTGCTATTTTCAATCTGCTTCGCTGCAACCCAGGGAGGC
* * * * * ** * **
53601926 AAG-GCTGGTGTCTTT-GATCTGCTTCGCTGCCGATACAGGAAAAC
1 AAGATCTGCTAT-TTTCAATCTGCTTCGCTG-CAACCCAGGGAGGC
* * * * * *
53601970 AAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAAGGAGGC
1 AAGATCTGCTATTTTCAATCTGCTTCGCTGCAACCCAGGGAGGC
* * * * *** *
53602014 AAGA-CTGGTGTCTTCGATCTGCTTCGCTGTCATTACAGGAAGGC
1 AAGATCTGCTATTTTCAATCTGCTTCGCTG-CAACCCAGGGAGGC
* *
53602058 AAGATCTGCTATTTTTAACCTGCTTCGCTGCAACCCAGGGAGGC
1 AAGATCTGCTATTTTCAATCTGCTTCGCTGCAACCCAGGGAGGC
* * * **** * *
53602102 AAGA-CTGGTGTCTTT-GATCTGCTTCGCTGTCGGTGCAGGAAGAC
1 AAGATCTGCTAT-TTTCAATCTGCTTCGCTG-CAACCCAGGGAGGC
* * * * *
53602146 AAGATCTGCTATTTTTAACCTGCTGCACTGCAACCCAGGGAGGA
1 AAGATCTGCTATTTTCAATCTGCTTCGCTGCAACCCAGGGAGGC
* * * **** *
53602190 AAGA-CTGGTGTCTTT-GATCTGCTTCGCTGCCGGTACAGGAAGGC
1 AAGATCTGCTAT-TTTCAATCTGCTTCGCTG-CAACCCAGGGAGGC
*
53602234 AAGATCTGCTATCTTCAAT
1 AAGATCTGCTATTTTCAAT
53602253 GATCTGTTCT
Statistics
Matches: 340, Mismatches: 140, Indels: 45
0.65 0.27 0.09
Matches are distributed among these distances:
43 94 0.28
44 159 0.47
45 87 0.26
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (44 bp):
AAGATCTGCTATTTTCAATCTGCTTCGCTGCAACCCAGGGAGGC
Found at i:53602035 original size:43 final size:43
Alignment explanation
Indices: 53601732--53602219 Score: 170
Period size: 43 Copynumber: 11.1 Consensus size: 43
53601722 AACCTGCTCT
* *
53601732 GCTGCAACCCAGGGAGGCAAGACTGGTGTCTTTGATCTGCTTC
1 GCTGCAACCTAAGGAGGCAAGACTGGTGTCTTTGATCTGCTTC
* * * * * * * * *
53601775 ACTGC--CGGTACAGGAAGACAAGATCTGCTATTTTTAACCTGCTCC
1 GCTGCAAC-CTA-AGG-AGGCAAGA-CTGGTGTCTTTGATCTGCTTC
* * * * * *
53601820 GTTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTC
1 GCTGCAACCTAAGGAGGCAAGACTGGTGTCTTTGATCTGCTTC
** * * * * * *
53601863 GCTGTTA-TTACAGGAAGGCAAGATCTGCTAT-TTTCAACCTGCTCC
1 GCTGCAACCTA-AGG-AGGCAAGA-CTGGTGTCTTT-GATCTGCTTC
* * * *
53601908 GTTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTC
1 GCTGCAACCTAAGGAGGCAAGACTGGTGTCTTTGATCTGCTTC
* ** * * * *
53601951 GCTGC--CGATACAGGAAAACAAGATCTGCTATC-TTCAGTCTGCTCC
1 GCTGCAAC-CTA-AGG-AGGCAAGA-CTGGTGTCTTTGA-TCTGCTTC
* *
53601996 ACTGCAACCTAAGGAGGCAAGACTGGTGTCTTCGATCTGCTTC
1 GCTGCAACCTAAGGAGGCAAGACTGGTGTCTTTGATCTGCTTC
* * * * * *
53602039 GCTGTC-A-TTACAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTC
1 GCTG-CAACCTA-AGG-AGGCAAGA-CTGGTGTCTTTGATCTGCTTC
* *
53602084 GCTGCAACCCAGGGAGGCAAGACTGGTGTCTTTGATCTGCTTC
1 GCTGCAACCTAAGGAGGCAAGACTGGTGTCTTTGATCTGCTTC
** * * * * * * * *
53602127 GCTGTC--GGTGCAGGAAGACAAGATCTGCTATTTTTAACCTGCTGC
1 GCTG-CAACCT-AAGG-AGGCAAGA-CTGGTGTCTTTGATCTGCTTC
* * * *
53602172 ACTGCAACCCAGGGAGGAAAGACTGGTGTCTTTGATCTGCTTC
1 GCTGCAACCTAAGGAGGCAAGACTGGTGTCTTTGATCTGCTTC
53602215 GCTGC
1 GCTGC
53602220 CGGTACAGGA
Statistics
Matches: 298, Mismatches: 115, Indels: 64
0.62 0.24 0.13
Matches are distributed among these distances:
41 2 0.01
42 5 0.02
43 104 0.35
44 81 0.27
45 99 0.33
46 5 0.02
47 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.27
Consensus pattern (43 bp):
GCTGCAACCTAAGGAGGCAAGACTGGTGTCTTTGATCTGCTTC
Found at i:53602092 original size:264 final size:263
Alignment explanation
Indices: 53601436--53602251 Score: 1051
Period size: 264 Copynumber: 3.1 Consensus size: 263
53601426 CACCAATATG
* * * * *
53601436 GGAAGACAAGATCTGCTATCTTTAACCTGCTCTGCTGCCACCGAGGGAGGCAAGGCTAGTGTCTT
1 GGAAGACAAGATCTGCTATCTTCAACCTGCTCTGCTGCAACCCAGGGAGGCAAGACTGGTGTCTT
* * * * *
53601501 CAATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGTTATCTTTAACCTAC-TCTGCTGCCAC
66 CGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTC-GCTGCAAC
* * *
53601565 CGAGGGAGGCAAGGCTAGTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTA
130 CCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * * * * * * *
53601630 TCTTTAACCTGCTCCGCTACCACCGAGGGAGGCAAGGCTAGTGTCTTCGATCTACTCCACTACTG
195 T-TTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCG
* *
53601695 CT-TA
259 ATACA
* * * *
53601699 GGGAGATAAGATCTGCAATTTTCAACCTGCTCTGCTGCAACCCAGGGAGGCAAGACTGGTGTCTT
1 GGAAGACAAGATCTGCTATCTTCAACCTGCTCTGCTGCAACCCAGGGAGGCAAGACTGGTGTCTT
* * * * * *
53601764 TGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTATTTTTAACCTGCTCCGTTGCAACC
66 CGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGCAACC
* *
53601829 CAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTTATTACAGGAAGGCAAGATCTGCTAT
131 CAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTAT
*
53601894 TTTCAACCTGCTCCGTTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCGA
196 TTT-AACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCGA
53601959 TACA
260 TACA
* ** ** * *
53601963 GGAAAACAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAAGGAGGCAAGACTGGTGTCTT
1 GGAAGACAAGATCTGCTATCTTCAACCTGCTCTGCTGCAACCCAGGGAGGCAAGACTGGTGTCTT
* *
53602028 CGATCTGCTTCGCTGTCATTACAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGCAACC
66 CGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGCAACC
* * * * * *
53602093 CAGGGAGGCAAGACTGGTGTCTTTGATCTGCTTCGCTGTCGGTGCAGGAAGACAAGATCTGCTAT
131 CAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA-
* * * * *
53602158 TTTTAACCTGCTGCACTGCAACCCAGGGAGGAAAGACTGGTGTCTTTGATCTGCTTCGCTGCCGG
195 TTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCGA
53602223 TACA
260 TACA
*
53602227 GGAAGGCAAGATCTGCTATCTTCAA
1 GGAAGACAAGATCTGCTATCTTCAA
53602252 TGATCTGTTC
Statistics
Matches: 475, Mismatches: 74, Indels: 7
0.85 0.13 0.01
Matches are distributed among these distances:
262 3 0.01
263 218 0.46
264 250 0.53
265 4 0.01
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (263 bp):
GGAAGACAAGATCTGCTATCTTCAACCTGCTCTGCTGCAACCCAGGGAGGCAAGACTGGTGTCTT
CGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGCAACC
CAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTAT
TTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCGAT
ACA
Found at i:53603542 original size:14 final size:15
Alignment explanation
Indices: 53603519--53603551 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
53603509 ATCGACGCTT
53603519 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
53603533 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
53603548 TTCC
1 TTCC
53603552 CTGCTTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:53627678 original size:44 final size:45
Alignment explanation
Indices: 53627613--53627892 Score: 259
Period size: 44 Copynumber: 6.4 Consensus size: 45
53627603 TAAAAAACAG
* * * *
53627613 CAGATCTTGTCTTCATGTATTGGT-GTGAAGTAGATCGAAGATAA
1 CAGATCCTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAA
* * * * *
53627657 CAGATCATGTTTTCCTATATTGGTAGCCAAGTGGATCGAAGAT-G
1 CAGATCCTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAA
* * * *
53627701 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA-AA
1 CAGATCCTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAA
* * * * * *
53627745 GTAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAA
1 -CAGATCCTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAA
* * *
53627790 CAGATCCTGTCTTCCTATATTGGTAGCCAAGTGGATCGAAGAT-G
1 CAGATCCTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAA
* * *
53627834 CAGATCCTGTCTTCCTATATTGGTA-AGAAGTGGATCGAAGA-AG
1 CAGATCCTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAA
* *
53627877 CAGATCTTGCCTTCCT
1 CAGATCCTGTCTTCCT
53627893 GCACCGACAG
Statistics
Matches: 194, Mismatches: 36, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
43 29 0.15
44 115 0.59
45 50 0.26
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (45 bp):
CAGATCCTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAA
Found at i:53627783 original size:88 final size:87
Alignment explanation
Indices: 53627640--53627891 Score: 245
Period size: 89 Copynumber: 2.9 Consensus size: 87
53627630 TATTGGTGTG
* * * * *
53627640 AAGTAGATCGAAGATAACAGATCATGTTTTCCTATATTGG-TAGCCAAGTGGATCGAAGATGCAG
1 AAGTAGATCGAAGA-AGCAGATCCTGTCTTCATATATTGGCAAG--AAGTGGATCGAAGATGCAG
* *
53627704 ATCTTGTCTTCCCATACTGGTGGCG
63 ATCTTGTCTTCCCATACTGGTAGCC
* * * ** * *
53627729 AAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGA
1 AAGTAGATCGAAG-AAGCAGATCCTGTCTTCATATATTGGCAAGAAGTGGATCGAAGAT-GCAGA
* * *
53627794 TCCTGTCTTCCTATATTGGTAGCC
64 TCTTGTCTTCCCATACTGGTAGCC
* * * * *
53627818 AAGTGGATCGAAGATGCAGATCCTGTCTTCCTATATTGGTAAGAAGTGGATCGAAGAAGCAGATC
1 AAGTAGATCGAAGAAGCAGATCCTGTCTTCATATATTGGCAAGAAGTGGATCGAAGATGCAGATC
*
53627883 TTGCCTTCC
66 TTGTCTTCC
53627892 TGCACCGACA
Statistics
Matches: 131, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
87 13 0.10
88 49 0.37
89 67 0.51
90 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (87 bp):
AAGTAGATCGAAGAAGCAGATCCTGTCTTCATATATTGGCAAGAAGTGGATCGAAGATGCAGATC
TTGTCTTCCCATACTGGTAGCC
Found at i:53627932 original size:44 final size:44
Alignment explanation
Indices: 53627883--53628020 Score: 107
Period size: 44 Copynumber: 3.1 Consensus size: 44
53627873 GAAGCAGATC
53627883 TTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCT
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCT
* **** * * * * * * * *
53627927 TTGCCTCCCTGGGTTG-CAACGGAGCAGGTTAAAAATAGCAGAT
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCT
* * * *
53627970 CTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACTAGCC
1 -TTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCT
53628015 TTGCCT
1 TTGCCT
53628021 CCCTAGGTTG
Statistics
Matches: 62, Mismatches: 30, Indels: 4
0.65 0.31 0.04
Matches are distributed among these distances:
43 19 0.31
44 28 0.45
45 15 0.24
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (44 bp):
TTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCT
Found at i:53628024 original size:88 final size:88
Alignment explanation
Indices: 53627875--53628096 Score: 354
Period size: 88 Copynumber: 2.5 Consensus size: 88
53627865 GGATCGAAGA
* * *
53627875 AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCTTTGCCTCCCTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGG
*
53627940 TTGCAACGGAGCAGGTTAAAAAT
66 TTGCAACGGAACAGGTTAAAAAT
* *
53627963 AGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTAGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGG
* *
53628028 TTGCAGCGGAACAGTTTAAAAAT
66 TTGCAACGGAACAGGTTAAAAAT
* *
53628051 AGCAGATCTTGCCTTCCTGCACCGACAACAAAGCAGATCGAAGACA
1 AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACA
53628097 TCAGTCTTAT
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 123 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (88 bp):
AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGG
TTGCAACGGAACAGGTTAAAAAT
Found at i:53628505 original size:44 final size:44
Alignment explanation
Indices: 53628409--53628566 Score: 135
Period size: 44 Copynumber: 3.7 Consensus size: 44
53628399 AAGATGACGA
* *
53628409 ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCAATT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATG
* * * *
53628453 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAATCCACA-G
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-ATG
** * * * * * * *
53628497 ATCTTATCTTTCTGAAGTTGCTGTAGAGTAGA-TCACGTC--GG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATG
*
53628538 CTCTTATCTCCCTGAAGTTGCAGTGGAGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC
53628567 GAACTCAAGA
Statistics
Matches: 89, Mismatches: 23, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
41 24 0.27
43 3 0.03
44 61 0.69
45 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATG
Found at i:53634967 original size:22 final size:22
Alignment explanation
Indices: 53634942--53634985 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
53634932 TACCTTCATA
53634942 CTTTAAAGCTTCAAACCAAACT
1 CTTTAAAGCTTCAAACCAAACT
* * *
53634964 CTTTAAATCTTGATACCAAACT
1 CTTTAAAGCTTCAAACCAAACT
53634986 TAAATTTTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (22 bp):
CTTTAAAGCTTCAAACCAAACT
Found at i:53638703 original size:11 final size:11
Alignment explanation
Indices: 53638687--53638711 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53638677 AGTCACGAAT
53638687 CGTTTCTAAAG
1 CGTTTCTAAAG
53638698 CGTTTCTAAAG
1 CGTTTCTAAAG
53638709 CGT
1 CGT
53638712 CAAAGGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (11 bp):
CGTTTCTAAAG
Found at i:53645063 original size:50 final size:50
Alignment explanation
Indices: 53644999--53645147 Score: 172
Period size: 50 Copynumber: 3.0 Consensus size: 50
53644989 TGTCATATCT
* ** * *
53644999 CAGATATGGTCTTACATGAGATTTCTCATATAGGTGCCCATGCCATGTCC
1 CAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCC
* ** * * *
53645049 TAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACGCCATGTCC
1 CAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCC
* * *
53645099 CAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 CAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTC
53645148 TCATCTCGGT
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
CAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCC
Found at i:53645154 original size:24 final size:24
Alignment explanation
Indices: 53645122--53645171 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
53645112 ACATGGGACC
53645122 TCTCATCTCGGTGCCAACGCCATG
1 TCTCATCTCGGTGCCAACGCCATG
53645146 TCTCATCTCGGTGCCAACGCCATG
1 TCTCATCTCGGTGCCAACGCCATG
53645170 TC
1 TC
53645172 CCAGACATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.38, G:0.20, T:0.26
Consensus pattern (24 bp):
TCTCATCTCGGTGCCAACGCCATG
Found at i:53653549 original size:25 final size:25
Alignment explanation
Indices: 53653521--53653693 Score: 172
Period size: 25 Copynumber: 7.4 Consensus size: 25
53653511 GGAGTTTAGC
*
53653521 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATTA
* *
53653546 GTGCTATCTGATTATTAGCACGTTA
1 GTGCTCTCTGATTATTAGCACATTA
* * *
53653571 TTGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACATTA
* *
53653596 GTGCTCTCTTATTACTAGCAC----
1 GTGCTCTCTGATTATTAGCACATTA
53653617 --GCTCTCTGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACATTA
*
53653640 GTGCTCTCTG--T-TTAGCACATTT
1 GTGCTCTCTGATTATTAGCACATTA
*
53653662 GTGCTCTCTG--TA-TAGCACTTTA
1 GTGCTCTCTGATTATTAGCACATTA
53653684 GTGCTCTCTG
1 GTGCTCTCTG
53653694 TTTAATAGTG
Statistics
Matches: 127, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
19 17 0.13
22 39 0.31
23 1 0.01
25 70 0.55
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATTA
Found at i:53653622 original size:19 final size:19
Alignment explanation
Indices: 53653598--53653635 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53653588 GCACGTCAGT
*
53653598 GCTCTCTTATTACTAGCAC
1 GCTCTCTGATTACTAGCAC
*
53653617 GCTCTCTGATTATTAGCAC
1 GCTCTCTGATTACTAGCAC
53653636 ATTAGTGCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (19 bp):
GCTCTCTGATTACTAGCAC
Found at i:53653657 original size:22 final size:22
Alignment explanation
Indices: 53653629--53653697 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
53653619 TCTCTGATTA
53653629 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
*
53653651 TTAGCACATTTGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
53653673 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
53653695 TTA
1 TTA
53653698 ATAGTGCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:53655496 original size:50 final size:50
Alignment explanation
Indices: 53655362--53655708 Score: 353
Period size: 50 Copynumber: 6.9 Consensus size: 50
53655352 ATTTGGGTAA
*
53655362 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATT
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA---AGATG
* * *
53655415 ATGAGAAGTCCCATG-AAGACCATGTCTAGGACATGGCGTTGGCATCGAGATG
1 A-GAG-A-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAGATG
* ** *
53655467 AGAGATCCCATGTAAGACCATGTCTAGGACATGGTGTTGGCACCAAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAGATG
* * *
53655517 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAGATG
* ** * * * *
53655567 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAGATG
* * *
53655617 AGA-ACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGA--
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-T-CAAGATG
* * * *
53655667 A-ACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCAT
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
53655709 GTTATATTTA
Statistics
Matches: 254, Mismatches: 32, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
48 1 0.00
49 39 0.15
50 162 0.64
51 3 0.01
52 8 0.03
53 1 0.00
54 3 0.01
55 30 0.12
56 7 0.03
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAGATG
Found at i:53665081 original size:38 final size:39
Alignment explanation
Indices: 53665029--53665120 Score: 116
Period size: 38 Copynumber: 2.4 Consensus size: 39
53665019 AGTTTAAGTC
* * * *
53665029 TTTAACTATATCATAATTTGAACAT-TATTAATATGAG-T
1 TTTAATTATGTCATAATCTGAACATCT-TTAATAAGAGTT
*
53665067 TTTAATTATGTCATAATCTGAACATCTTTAATAAGGGTT
1 TTTAATTATGTCATAATCTGAACATCTTTAATAAGAGTT
53665106 TTTAATTATGTCATA
1 TTTAATTATGTCATA
53665121 GTTTAGGACA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
38 30 0.64
39 17 0.36
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (39 bp):
TTTAATTATGTCATAATCTGAACATCTTTAATAAGAGTT
Found at i:53671863 original size:33 final size:33
Alignment explanation
Indices: 53671826--53671901 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
53671816 TTAAAACTTG
*
53671826 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
53671859 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
53671892 AATTATACAT
1 AATTATACAT
53671902 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:53675136 original size:92 final size:91
Alignment explanation
Indices: 53674979--53675187 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
53674969 TTGATTTTAG
* * *
53674979 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
53675044 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
53675071 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
53675135 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
53675163 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
53675188 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:53675150 original size:24 final size:25
Alignment explanation
Indices: 53675115--53675162 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
53675105 TTATGAAATT
53675115 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
53675139 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
53675163 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:53675316 original size:66 final size:63
Alignment explanation
Indices: 53675241--53675451 Score: 192
Period size: 66 Copynumber: 3.4 Consensus size: 63
53675231 AAATATATTT
53675241 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
53675306 G
63 G
* * * * **
53675307 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
*
53675361 AATAATAATTATGTT-AATTTATAATTTAGAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-T-ATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
53675425 AG
62 AG
*
53675427 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
53675452 AAATTATATA
Statistics
Matches: 113, Mismatches: 15, Indels: 35
0.69 0.09 0.21
Matches are distributed among these distances:
53 5 0.04
54 12 0.11
55 6 0.05
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 4 0.04
65 10 0.09
66 31 0.27
67 5 0.04
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:53675341 original size:120 final size:120
Alignment explanation
Indices: 53675203--53675495 Score: 509
Period size: 120 Copynumber: 2.4 Consensus size: 120
53675193 AATTATTTTA
* * * *
53675203 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATAAT
*
53675266 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTAGAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
53675323 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAATTT
53675388 AGAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 AGAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
53675443 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
53675496 TAAATATGAT
Statistics
Matches: 166, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
119 5 0.03
120 159 0.96
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAATTT
AGAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:53675363 original size:15 final size:15
Alignment explanation
Indices: 53675328--53675385 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
53675318 TTAAGAATTT
*
53675328 TATTAAATTAT-ATA
1 TATTTAATTATAATA
53675342 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
53675356 TATTTAATAATAAT-
1 TATTTAATTATAATA
53675370 TATGTTAATTTATAAT
1 TAT-TTAA-TTATAAT
53675386 TTAGAGTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 8 0.22
14 8 0.22
15 15 0.41
16 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:53675478 original size:16 final size:16
Alignment explanation
Indices: 53675457--53675498 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
53675447 TTATTAAATT
*
53675457 ATATATTTTAATTATA
1 ATATATTTTAATAATA
53675473 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
53675488 AT-TATGTTTAA
1 ATATAT-TTTAA
53675499 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:53675483 original size:15 final size:15
Alignment explanation
Indices: 53675448--53675489 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53675438 TTAAGAATTT
*
53675448 TATTAAATTAT-ATA
1 TATTTAATTATAATA
53675462 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
53675476 TATTTAATAATAAT
1 TATTTAATTATAAT
53675490 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:53675514 original size:75 final size:75
Alignment explanation
Indices: 53675433--53675671 Score: 189
Period size: 75 Copynumber: 3.1 Consensus size: 75
53675423 TAAGAATATT
53675433 AATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTA
53675498 AATATGATTA
66 AATATGATTA
* ** * * * ** ** * * *
53675508 AATTATTTATTATTGATATT-AATAATCTTATTAAAATT-TAA-ATA-ACAATAACAATAATAAT
1 AATTATTAAGAATT-TTATTAAATTAT-ATATTTTAATTATAATATATTTAATAATAATTAT-GT
* ** *
53675569 TTACCAAAACAAATTTCTGCT
63 TTA--AATA-TGA--T-T--A
*
53675590 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTA
53675655 AATATGATTA
66 AATATGATTA
53675665 AATTATT
1 AATTATT
53675672 TATTATTGAT
Statistics
Matches: 114, Mismatches: 35, Indels: 30
0.64 0.20 0.17
Matches are distributed among these distances:
73 10 0.09
74 7 0.06
75 26 0.23
76 15 0.13
77 2 0.02
78 1 0.01
79 1 0.01
80 2 0.02
81 15 0.13
82 18 0.16
83 7 0.06
84 10 0.09
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (75 bp):
AATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTA
AATATGATTA
Found at i:53675604 original size:157 final size:157
Alignment explanation
Indices: 53675432--53675748 Score: 598
Period size: 157 Copynumber: 2.0 Consensus size: 157
53675422 ATAAGAATAT
*
53675432 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
53675497 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
53675562 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
53675589 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
53675654 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
53675719 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
53675746 TAA
1 TAA
53675749 GGGTATTCTA
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:53675629 original size:18 final size:17
Alignment explanation
Indices: 53675601--53675635 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53675591 ATTATTAAGA
*
53675601 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
53675618 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
53675636 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:53675892 original size:16 final size:16
Alignment explanation
Indices: 53675871--53675906 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
53675861 GATTTGCTAT
*
53675871 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
53675887 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
53675903 TACA
1 TACA
53675907 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:53689901 original size:17 final size:18
Alignment explanation
Indices: 53689875--53689908 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53689865 TATTCTTTAA
*
53689875 AATTTTAAAA-TAAAATC
1 AATTTAAAAATTAAAATC
53689892 AATTTAAAAATTAAAAT
1 AATTTAAAAATTAAAAT
53689909 TAAAATGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTTAAAAATTAAAATC
Found at i:53694355 original size:25 final size:25
Alignment explanation
Indices: 53694327--53694375 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
53694317 AAATCTTTGT
*
53694327 ACAAAAAGTTTAAAGGATAATACAA
1 ACAAAAAGTTCAAAGGATAATACAA
53694352 ACAAAAAGTTCAAAGGATAATACA
1 ACAAAAAGTTCAAAGGATAATACA
53694376 TTTACAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.18
Consensus pattern (25 bp):
ACAAAAAGTTCAAAGGATAATACAA
Found at i:53694422 original size:16 final size:16
Alignment explanation
Indices: 53694401--53694431 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53694391 CAATCAATTC
*
53694401 TTAGATATCATTTTTG
1 TTAGATATAATTTTTG
53694417 TTAGATATAATTTTT
1 TTAGATATAATTTTT
53694432 TCTCGGTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (16 bp):
TTAGATATAATTTTTG
Found at i:53707494 original size:30 final size:30
Alignment explanation
Indices: 53707460--53707518 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
53707450 AATTGCCGGA
53707460 AAATTTGAATCCAATTTCAAATGATTCGAG
1 AAATTTGAATCCAATTTCAAATGATTCGAG
*
53707490 AAATTTGAATCCAATTTCAAATTATTCGA
1 AAATTTGAATCCAATTTCAAATGATTCGA
53707519 AAAGCAAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (30 bp):
AAATTTGAATCCAATTTCAAATGATTCGAG
Found at i:53708148 original size:19 final size:19
Alignment explanation
Indices: 53708124--53708160 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53708114 GAAAGAAGAA
* *
53708124 AAGGAAAACATGGAAAAAG
1 AAGGAAAAAAGGGAAAAAG
53708143 AAGGAAAAAAGGGAAAAA
1 AAGGAAAAAAGGGAAAAA
53708161 ATGGAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.27, T:0.03
Consensus pattern (19 bp):
AAGGAAAAAAGGGAAAAAG
Found at i:53709612 original size:9 final size:9
Alignment explanation
Indices: 53709595--53709631 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
53709585 TGAGTTTTCG
53709595 AATTCGAAT
1 AATTCGAAT
*
53709604 AACTCGAAT
1 AATTCGAAT
*
53709613 AATTCAAAT
1 AATTCGAAT
53709622 AATTCGAAT
1 AATTCGAAT
53709631 A
1 A
53709632 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53712488 original size:27 final size:27
Alignment explanation
Indices: 53712452--53712593 Score: 169
Period size: 27 Copynumber: 5.3 Consensus size: 27
53712442 AGAGGTCAAT
*
53712452 AAATGACCGAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCATAGGGTA
* * *
53712479 AAATGACCGAGTTAACCCCACAGGGTA
1 AAATGACCGAATTACCCCCATAGGGTA
*
53712506 AAATGACCGAGTTACCCCCATAGGGTA
1 AAATGACCGAATTACCCCCATAGGGTA
* **
53712533 AAATGATCC-AAATACCCTTATAGGGTA
1 AAATGA-CCGAATTACCCCCATAGGGTA
* * *
53712560 AAATGGCCGAAATACCCCCATTGGGTA
1 AAATGACCGAATTACCCCCATAGGGTA
53712587 AAATGAC
1 AAATGAC
53712594 TGTTATGGCC
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
26 2 0.02
27 96 0.96
28 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (27 bp):
AAATGACCGAATTACCCCCATAGGGTA
Found at i:53712967 original size:28 final size:27
Alignment explanation
Indices: 53712926--53712996 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
53712916 ATTGCACTGT
*
53712926 ATTGATACTATATTGGGCTAAGGCCCAC
1 ATTG-TACTGTATTGGGCTAAGGCCCAC
* *
53712954 ATTGTTACTGTATTAGGCTAGGGCCCAC
1 ATTG-TACTGTATTGGGCTAAGGCCCAC
*
53712982 ACTGTACTGTTATTG
1 ATTGTACTG-TATTG
53712997 AATAGGGCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 5 0.14
28 31 0.86
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (27 bp):
ATTGTACTGTATTGGGCTAAGGCCCAC
Found at i:53714881 original size:6 final size:6
Alignment explanation
Indices: 53714870--53714898 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
53714860 TAGAAAATTC
53714870 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
53714899 GTAGATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:53729221 original size:24 final size:24
Alignment explanation
Indices: 53729193--53729239 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
53729183 ACTTTAGCAG
53729193 ATAAACGCCGCTAAAGATCATGAA
1 ATAAACGCCGCTAAAGATCATGAA
53729217 ATAAACGCCGCTAAAGATCATGA
1 ATAAACGCCGCTAAAGATCATGA
53729240 CCTTTAGCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (24 bp):
ATAAACGCCGCTAAAGATCATGAA
Found at i:53729267 original size:43 final size:43
Alignment explanation
Indices: 53729219--53729491 Score: 266
Period size: 43 Copynumber: 6.3 Consensus size: 43
53729209 ATCATGAAAT
* *
53729219 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAC
* *
53729262 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAT
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAC
* * *
53729305 AAACGTCGCTAAAGACCATGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAC
*
53729348 AAACGCCGCTAAAGACCA-GTACCTTTAGCGGCGCTTCTACCAC
1 AAACGCCGCTAAAGACCATG-ACCTTTAGCGGCGCTTTTACCAC
* ** * * * **
53729391 AAACTTTTACCGCTAAAGGTCATAACTTTTAGCGGCGCTTATATTAC
1 AAAC----GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAC
* * * * **
53729438 AAACGCCGCTATAA-A-AATGACTTTTAGCGAC-ATTTTTTCAC
1 AAACGCCGCTA-AAGACCATGACCTTTAGCGGCGCTTTTACCAC
53729479 AAACGCCGCTAAA
1 AAACGCCGCTAAA
53729492 AACATAACTT
Statistics
Matches: 195, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
40 2 0.01
41 17 0.09
42 14 0.07
43 126 0.65
44 2 0.01
47 34 0.17
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAC
Found at i:53729462 original size:42 final size:41
Alignment explanation
Indices: 53729411--53729504 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
53729401 CGCTAAAGGT
* *
53729411 CATAACTTTTAGCGGCGCTTATATT-ACAAACGCCGCTATAAAA
1 CATAACTTTTAGCGAC-ATT-TATTCACAAACGCCGCTA-AAAA
* *
53729454 -ATGACTTTTAGCGACATTTTTTCACAAACGCCGCTAAAAA
1 CATAACTTTTAGCGACATTTATTCACAAACGCCGCTAAAAA
53729494 CATAACTTTTA
1 CATAACTTTTA
53729505 AAAAAATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
40 7 0.16
41 24 0.55
42 13 0.30
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (41 bp):
CATAACTTTTAGCGACATTTATTCACAAACGCCGCTAAAAA
Found at i:53731053 original size:5 final size:5
Alignment explanation
Indices: 53731043--53731074 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
53731033 CTTTCTTGCC
53731043 AATAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA
53731075 AACAAGAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:53731383 original size:5 final size:5
Alignment explanation
Indices: 53731341--53731365 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53731331 TCGATTCTTG
53731341 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
53731366 GGTAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:53734018 original size:22 final size:21
Alignment explanation
Indices: 53733975--53734020 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
53733965 TCTTGGATGT
*
53733975 GGGAAATTAGGGATTTTAGGG
1 GGGAAATTAGGGATTTCAGGG
* *
53733996 GGGAAAGTTGGGGATTTCGGGG
1 GGGAAA-TTAGGGATTTCAGGG
53734018 GGG
1 GGG
53734021 GGGGGGAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.22, C:0.02, G:0.52, T:0.24
Consensus pattern (21 bp):
GGGAAATTAGGGATTTCAGGG
Found at i:53734395 original size:148 final size:150
Alignment explanation
Indices: 53734186--53734557 Score: 570
Period size: 149 Copynumber: 2.5 Consensus size: 150
53734176 ATATTTTGTG
* * * * *
53734186 GCGTTTTTTATAAAAATGCCGCTAAAAAATTATTTTATTTGGAATAAAACGACACTATTTTGCTA
1 GCGTTTTTCATAAAAACGCAGC-AAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTA
53734251 TGCTAAAAGGGCGCTA-TTTTTTAAAGTAAAATTA-TTTTTTGTGGCATTTTTTTATAAAAACAC
65 TGCTAAAAGGGCGCTATTTTTTTAAAGTAAAATTATTTTTTTGTGGCATTTTTTTATAAAAACAC
*
53734314 CGCTATTACTTACTTTTTGCA
130 CGCTATTACTTACCTTTTGCA
*
53734335 GCGTTTGTCATAAAAACGCAGCAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTAT
1 GCGTTTTTCATAAAAACGCAGCAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTAT
* * *
53734400 -ATAAAATGGCGCTATTTTTTTAAAGTAAAATTATTTTTTTGTGGCATTTTTTTATAAAAACGCC
66 GCTAAAAGGGCGCTATTTTTTTAAAGTAAAATTATTTTTTTGTGGCATTTTTTTATAAAAACACC
* **
53734464 GCTATTGCTTACCTTTTGTG
131 GCTATTACTTACCTTTTGCA
*
53734484 GCGTTTTTCATAAAAAAACGCTGCAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCT
1 GCGTTTTTCAT--AAAAACGCAGCAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCT
53734549 ATGCTAAAA
64 ATGCTAAAA
53734558 ATCTTTTATT
Statistics
Matches: 202, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
147 12 0.06
148 59 0.29
149 73 0.36
151 53 0.26
152 5 0.02
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (150 bp):
GCGTTTTTCATAAAAACGCAGCAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTAT
GCTAAAAGGGCGCTATTTTTTTAAAGTAAAATTATTTTTTTGTGGCATTTTTTTATAAAAACACC
GCTATTACTTACCTTTTGCA
Found at i:53735608 original size:21 final size:21
Alignment explanation
Indices: 53735584--53735637 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
53735574 TGAATCCATA
* * *
53735584 AACCCTAAATCCCTAACTCTT
1 AACCCTAAACCCCTAACCCCT
53735605 AACCTCT-AACCCCTAACCCCT
1 AACC-CTAAACCCCTAACCCCT
53735626 AACCCCTAAACC
1 AA-CCCTAAACC
53735638 TTAAATTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCCTAAACCCCTAACCCCT
Found at i:53735621 original size:14 final size:14
Alignment explanation
Indices: 53735594--53735634 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
53735584 AACCCTAAAT
* *
53735594 CCCTAACTCTTAAC
1 CCCTAACCCCTAAC
*
53735608 CTCTAACCCCTAAC
1 CCCTAACCCCTAAC
53735622 CCCTAACCCCTAA
1 CCCTAACCCCTAA
53735635 ACCTTAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.49, G:0.00, T:0.22
Consensus pattern (14 bp):
CCCTAACCCCTAAC
Found at i:53735680 original size:14 final size:15
Alignment explanation
Indices: 53735661--53735693 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
53735651 CTTAAATCAG
53735661 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
53735675 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
53735690 AATC
1 AATC
53735694 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:53736158 original size:41 final size:41
Alignment explanation
Indices: 53736099--53736377 Score: 323
Period size: 41 Copynumber: 6.9 Consensus size: 41
53736089 AAATGTTTTT
*
53736099 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
** *
53736140 GCGGCGCTTCTTGGAAAACGCCGCTAAAGCCCCAAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* *
53736181 GCGGCGCTTCTTAAAAAATGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
****
53736222 GCGGCGCTT-TTCCAAAAACGCCGCTAAA-AATAGAGCATTA
1 GCGGCGCTTCTT-CAAAAACGCCGCTAAAGCCCCGAGCATTA
* ****
53736262 GCGCCGCTT-TTCCAAAAACGCCGCTAAA-AATAGAGCATTA
1 GCGGCGCTTCTT-CAAAAACGCCGCTAAAGCCCCGAGCATTA
* *
53736302 GCGCCGCTTCTTCAAAAACGCCGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* * **
53736343 GCGACGCTTCTTCAAAAATGCCGAGAAAGCCCCGA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGA
53736378 AAACTCAAAA
Statistics
Matches: 212, Mismatches: 23, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
40 74 0.35
41 138 0.65
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:53758433 original size:28 final size:29
Alignment explanation
Indices: 53758379--53758433 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
53758369 ACAGAATTGG
*
53758379 GAAAAGTTCTCTCCTTTTAATGTGAAAAT
1 GAAAAGTTCTCTCCTTTTAATGAGAAAAT
*
53758408 GAAAA-TTCTCTCTTCTTTAAT-AGAAA
1 GAAAAGTTCTCTCCT-TTTAATGAGAAA
53758434 CCAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (29 bp):
GAAAAGTTCTCTCCTTTTAATGAGAAAAT
Found at i:53765556 original size:49 final size:51
Alignment explanation
Indices: 53765480--53765576 Score: 146
Period size: 49 Copynumber: 1.9 Consensus size: 51
53765470 ACATGTGAAA
*
53765480 ATGTGATTATGTGATTTCTGTGTAAGACCATAGCTAGG-CTATGGCATCGGT
1 ATGTGATTATGTGATTACTGTGTAAGACCATAG-TAGGACTATGGCATCGGT
*
53765531 ATGTGA-TATGTGATTAC-GTGTAAGACCATAGTTGGACTATGGCATC
1 ATGTGATTATGTGATTACTGTGTAAGACCATAGTAGGACTATGGCATC
53765577 AAGAAAACGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 3 0.07
49 24 0.56
50 10 0.23
51 6 0.14
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (51 bp):
ATGTGATTATGTGATTACTGTGTAAGACCATAGTAGGACTATGGCATCGGT
Found at i:53769720 original size:11 final size:12
Alignment explanation
Indices: 53769699--53769727 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
53769689 AACTTATTTC
53769699 GAGAGATTTTAG
1 GAGAGATTTTAG
53769711 GAGA-ATTTTAG
1 GAGAGATTTTAG
53769722 GAGAGA
1 GAGAGA
53769728 AATGGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (12 bp):
GAGAGATTTTAG
Found at i:53776779 original size:16 final size:16
Alignment explanation
Indices: 53776758--53776795 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
53776748 GATGCGATAT
53776758 TGTGATATGAAACATG
1 TGTGATATGAAACATG
53776774 TGTGATATGAAACATG
1 TGTGATATGAAACATG
53776790 TGTGAT
1 TGTGAT
53776796 GAATATTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (16 bp):
TGTGATATGAAACATG
Found at i:53780229 original size:17 final size:18
Alignment explanation
Indices: 53780191--53780232 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
53780181 GCCCAATAAT
*
53780191 CCCATACGCCCGTGTGGG
1 CCCACACGCCCGTGTGGG
*
53780209 CCCACACGCTCGTGT-GG
1 CCCACACGCCCGTGTGGG
53780226 CCCACAC
1 CCCACAC
53780233 CACCCAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.14, C:0.45, G:0.26, T:0.14
Consensus pattern (18 bp):
CCCACACGCCCGTGTGGG
Found at i:53789089 original size:21 final size:21
Alignment explanation
Indices: 53789058--53789110 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
53789048 CTATTGTTGT
*
53789058 GAAGAAAGTTGATGCTGCAGAA
1 GAAG-AAGTTGATGCTGAAGAA
*
53789080 GAAGAAGTTGTTGCTGAAGAA
1 GAAGAAGTTGATGCTGAAGAA
*
53789101 GAAGGAGTTG
1 GAAGAAGTTG
53789111 CTAAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.38, C:0.06, G:0.36, T:0.21
Consensus pattern (21 bp):
GAAGAAGTTGATGCTGAAGAA
Found at i:53789110 original size:18 final size:18
Alignment explanation
Indices: 53789077--53789112 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53789067 TGATGCTGCA
**
53789077 GAAGAAGAAGTTGTTGCT
1 GAAGAAGAAGGAGTTGCT
53789095 GAAGAAGAAGGAGTTGCT
1 GAAGAAGAAGGAGTTGCT
53789113 AAAAATAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.22
Consensus pattern (18 bp):
GAAGAAGAAGGAGTTGCT
Found at i:53810910 original size:189 final size:189
Alignment explanation
Indices: 53810590--53810957 Score: 569
Period size: 189 Copynumber: 1.9 Consensus size: 189
53810580 GAAATCCATC
* * * *
53810590 GAAAAGAATAGAAATTGGGAGATGGTCGACTTGCCAGAAGACAGAATTACAATTGGTTTGAAATG
1 GAAAAGAATAGAAATTGGGACATGGTCGACTTGCCAGAAGAAAAAAATACAATTGGTTTGAAATG
*
53810655 GGTGTTTAAGACAAAATTTGGTGCAGATGGAAGCATCCAAAAGCACAAAGCTCGTCTTGTGGCGA
66 GGTGTTCAAGACAAAATTTGGTGCAGATGGAAGCATCCAAAAGCACAAAGCTCGTCTTGTGGCGA
* *
53810720 AAGGTTATGCATAGCAATATGGTGTTGATTTCGAAGAAACCTTCTCTCCTGTTTCTATT
131 AAGGTTATGCATAACAATATGGTGTTGATTTCAAAGAAACCTTCTCTCCTGTTTCTATT
* * ** * *
53810779 GAAAAGAATGGAACTTGGGACATGGTCGACTTATC-GAAAGAAAAAAATGCAATTGGTTTGAAGT
1 GAAAAGAATAGAAATTGGGACATGGTCGACTTGCCAG-AAGAAAAAAATACAATTGGTTTGAAAT
* *
53810843 GGGTGTTCAAGA-AAAACTTTGGTGTAGATGGAAGCATCCAAAAGCACAAAGCTTGTCTTGTGGC
65 GGGTGTTCAAGACAAAA-TTTGGTGCAGATGGAAGCATCCAAAAGCACAAAGCTCGTCTTGTGGC
53810907 GAAAGGTTATGCATAACAATATGGTGTTGATTTCAAAGAAACCTTCTCTCC
129 GAAAGGTTATGCATAACAATATGGTGTTGATTTCAAAGAAACCTTCTCTCC
53810958 GGTAGCTCAA
Statistics
Matches: 162, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
188 5 0.03
189 157 0.97
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (189 bp):
GAAAAGAATAGAAATTGGGACATGGTCGACTTGCCAGAAGAAAAAAATACAATTGGTTTGAAATG
GGTGTTCAAGACAAAATTTGGTGCAGATGGAAGCATCCAAAAGCACAAAGCTCGTCTTGTGGCGA
AAGGTTATGCATAACAATATGGTGTTGATTTCAAAGAAACCTTCTCTCCTGTTTCTATT
Found at i:53812821 original size:50 final size:50
Alignment explanation
Indices: 53812746--53812846 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
53812736 CAAGTTTACG
53812746 TGGCATTACACATGATATTATGTTTGTTGCATTAGATTTTAGAAATAGCC
1 TGGCATTACACATGATATTATGTTTGTTGCATTAGATTTTAGAAATAGCC
53812796 TGGCATTACACATGATATTATGTTTGTTGCATTAGATTTTAGAAATAGCC
1 TGGCATTACACATGATATTATGTTTGTTGCATTAGATTTTAGAAATAGCC
53812846 T
1 T
53812847 AAGTTGAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.41
Consensus pattern (50 bp):
TGGCATTACACATGATATTATGTTTGTTGCATTAGATTTTAGAAATAGCC
Found at i:53813996 original size:61 final size:61
Alignment explanation
Indices: 53813869--53813989 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 61
53813859 TTTATTAATT
* **
53813869 TTTTTAGAATCAGAACTAAATTGACAAATTTTGTAAATTTTGAGGACTAAATTTATTGAAC
1 TTTTTAGAATCAGAACTAAAATGACAAATTTTGTAAACATTGAGGACTAAATTTATTGAAC
* *
53813930 TTTTTAGAATTCA-AACTAAAATGACAAGTTTTGTAAACATTGAGTG-CTAAATTTGTTGAA
1 TTTTTAGAA-TCAGAACTAAAATGACAAATTTTGTAAACATTGAG-GACTAAATTTATTGAA
53813990 TATTTTATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
61 49 0.92
62 4 0.08
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (61 bp):
TTTTTAGAATCAGAACTAAAATGACAAATTTTGTAAACATTGAGGACTAAATTTATTGAAC
Found at i:53824113 original size:17 final size:17
Alignment explanation
Indices: 53824091--53824125 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
53824081 GAACAGAGAA
53824091 TTTCGAAACAATCAACT
1 TTTCGAAACAATCAACT
53824108 TTTCGAAACAATCAACT
1 TTTCGAAACAATCAACT
53824125 T
1 T
53824126 AATACATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (17 bp):
TTTCGAAACAATCAACT
Found at i:53828684 original size:10 final size:9
Alignment explanation
Indices: 53828669--53828750 Score: 58
Period size: 10 Copynumber: 8.3 Consensus size: 9
53828659 TACTATTTTT
53828669 ATTTTTATGA
1 ATTTTTAT-A
53828679 ATTTTTAATA
1 ATTTTT-ATA
53828689 A-TTTTATAA
1 ATTTTTAT-A
*
53828698 ATTCTTATA
1 ATTTTTATA
53828707 ATTCTTTATATA
1 A-T-TTT-TATA
*
53828719 TATTTTTAAA
1 -ATTTTTATA
53828729 TATTTTTATA
1 -ATTTTTATA
*
53828739 TTTTTTATA
1 ATTTTTATA
53828748 ATT
1 ATT
53828751 ATTTGAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
8 2 0.03
9 18 0.31
10 26 0.44
11 7 0.12
12 5 0.08
13 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:53828695 original size:19 final size:18
Alignment explanation
Indices: 53828671--53828709 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
53828661 CTATTTTTAT
* *
53828671 TTTTATGAATTTTTAATAA
1 TTTTATAAATTCTT-ATAA
53828690 TTTTATAAATTCTTATAA
1 TTTTATAAATTCTTATAA
53828708 TT
1 TT
53828710 CTTTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTATAAATTCTTATAA
Found at i:53828744 original size:20 final size:21
Alignment explanation
Indices: 53828668--53828754 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 21
53828658 TTACTATTTT
53828668 TATTTTTATGA-ATTTT-T-AA
1 TATTTTTAT-ATATTTTATAAA
* * *
53828687 TAATTTTATAAATTCTTATAAT
1 TATTTTTATATATT-TTATAAA
* *
53828709 TCTTTATATATATTTT-TAAA
1 TATTTTTATATATTTTATAAA
* *
53828729 TATTTTTATATTTTTTATAAT
1 TATTTTTATATATTTTATAAA
53828750 TATTT
1 TATTT
53828755 GAAAAATCAT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
18 1 0.02
19 11 0.21
20 18 0.35
21 11 0.21
22 11 0.21
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (21 bp):
TATTTTTATATATTTTATAAA
Found at i:53829051 original size:16 final size:16
Alignment explanation
Indices: 53829027--53829057 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53829017 ATTATTGATG
53829027 AATTAAAATAAGTATA
1 AATTAAAATAAGTATA
*
53829043 AATTGAAATAAGTAT
1 AATTAAAATAAGTAT
53829058 GAGTTTATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (16 bp):
AATTAAAATAAGTATA
Found at i:53829936 original size:25 final size:23
Alignment explanation
Indices: 53829908--53829968 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
53829898 AATCCATTGC
53829908 TAATAATTTGAAATAAATAATGAGT
1 TAATAATTTGAAATAAA-AATG-GT
53829933 TAATAATTATTG--ATAAAAATGGT
1 TAATAA-T-TTGAAATAAAAATGGT
*
53829956 TAATAGTTTGAAA
1 TAATAATTTGAAA
53829969 GTGTTGGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
21 3 0.10
22 1 0.03
23 8 0.26
24 4 0.13
25 11 0.35
26 1 0.03
27 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (23 bp):
TAATAATTTGAAATAAAAATGGT
Found at i:53852977 original size:25 final size:25
Alignment explanation
Indices: 53852914--53852961 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
53852904 GCTTTCTCTC
*
53852914 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCCCATGT
*
53852939 GAGCCATGTAACGGGAAGCCCAT
1 GAGCCATATAACGGGAAGCCCAT
53852962 TAGAGCTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCCCATGT
Found at i:53853791 original size:18 final size:18
Alignment explanation
Indices: 53853768--53853803 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53853758 ATTAATTTCA
53853768 TAAAAGTTGTTTATCTAT
1 TAAAAGTTGTTTATCTAT
53853786 TAAAAGTTGTTTATCTAT
1 TAAAAGTTGTTTATCTAT
53853804 CAACAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
TAAAAGTTGTTTATCTAT
Found at i:53865756 original size:10 final size:11
Alignment explanation
Indices: 53865726--53865750 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53865716 GAATACCTAA
53865726 AAAAAATAATG
1 AAAAAATAATG
53865737 AAAAAATAATG
1 AAAAAATAATG
53865748 AAA
1 AAA
53865751 TATAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAAATAATG
Found at i:53881451 original size:5 final size:5
Alignment explanation
Indices: 53881429--53881472 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
53881419 AGCAAAACCC
* *
53881429 AAAGA AAAGGC AAGGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1 AAAGA AAA-GA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
53881473 AGCTTTGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 31 0.91
6 3 0.09
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:53895001 original size:12 final size:12
Alignment explanation
Indices: 53894984--53895008 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53894974 GGTGTTCATT
53894984 CGGTTAACCGAC
1 CGGTTAACCGAC
53894996 CGGTTAACCGAC
1 CGGTTAACCGAC
53895008 C
1 C
53895009 CGAAATAACA
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:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:53895182 original size:9 final size:9
Alignment explanation
Indices: 53895171--53895273 Score: 118
Period size: 9 Copynumber: 11.4 Consensus size: 9
53895161 TTTGGTTAAA
*
53895171 AATTAACCA
1 AATTAACCG
53895180 AATTAACCG
1 AATTAACCG
53895189 AATTAACCG
1 AATTAACCG
*
53895198 AATTACCCG
1 AATTAACCG
*
53895207 AATTAATCG
1 AATTAACCG
53895216 AATT-ACTCG
1 AATTAAC-CG
*
53895225 AATTACCCG
1 AATTAACCG
*
53895234 AATTAACCT
1 AATTAACCG
*
53895243 AATTACCCG
1 AATTAACCG
*
53895252 AATTAACCA
1 AATTAACCG
*
53895261 AATTAACCA
1 AATTAACCG
53895270 AATT
1 AATT
53895274 GAATCACTAC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
8 1 0.01
9 78 0.98
10 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:53895419 original size:18 final size:18
Alignment explanation
Indices: 53895379--53895422 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
53895369 TAATTTTATG
**
53895379 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
53895397 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
53895415 CTTGGGTT
1 ATTGGGTT
53895423 TAGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:53897325 original size:21 final size:22
Alignment explanation
Indices: 53897301--53897341 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53897291 CTTGAAAAGA
*
53897301 TAATCACA-AAAAATAAAAAAT
1 TAATCAAATAAAAATAAAAAAT
*
53897322 TAATTAAATAAAAATAAAAA
1 TAATCAAATAAAAATAAAAA
53897342 TAAAAAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (22 bp):
TAATCAAATAAAAATAAAAAAT
Found at i:53899427 original size:12 final size:12
Alignment explanation
Indices: 53899410--53899434 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53899400 TTTGAGTCAT
53899410 TTTAATTATTGG
1 TTTAATTATTGG
53899422 TTTAATTATTGG
1 TTTAATTATTGG
53899434 T
1 T
53899435 CTTCATATGT
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:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TTTAATTATTGG
Found at i:53911323 original size:6 final size:6
Alignment explanation
Indices: 53911302--53911340 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
53911292 ATTTTAAAAA
53911302 TTTTA- TTTTAAG TTTTAG TTTTAG TTTTAG TTTTA- TTTT
1 TTTTAG TTTT-AG TTTTAG TTTTAG TTTTAG TTTTAG TTTT
53911341 TCATTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 8 0.25
6 20 0.62
7 4 0.12
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (6 bp):
TTTTAG
Found at i:53911341 original size:18 final size:18
Alignment explanation
Indices: 53911302--53911349 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
53911292 ATTTTAAAAA
*
53911302 TTTTATTTTAAGTTTTAG
1 TTTTATTTTTAGTTTTAG
* *
53911320 TTTTAGTTTTAGTTTTAT
1 TTTTATTTTTAGTTTTAG
53911338 TTTTCATTTTTA
1 TTTT-ATTTTTA
53911350 TCTTTATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.19, C:0.02, G:0.08, T:0.71
Consensus pattern (18 bp):
TTTTATTTTTAGTTTTAG
Found at i:53911348 original size:7 final size:6
Alignment explanation
Indices: 53911302--53911389 Score: 52
Period size: 6 Copynumber: 14.3 Consensus size: 6
53911292 ATTTTAAAAA
* * * * *
53911302 TTTTAT TTTAAG TTTTAG TTTTAG TTTTAG TTTTAT TTTTCAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT-AT TTTTAT
* * * * *
53911351 CTTTAT CTTTGTCT TTGTA- TTTAAT TTTTAT TTTAAT TT
1 TTTTAT -TTT-TAT TTTTAT TTTTAT TTTTAT TTTTAT TT
53911390 AATTTGTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
5 3 0.05
6 50 0.77
7 10 0.15
8 2 0.03
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (6 bp):
TTTTAT
Found at i:53911790 original size:19 final size:19
Alignment explanation
Indices: 53911766--53911804 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
53911756 AAATTTTCCC
**
53911766 CAAAACACTTTTCTTGTCA
1 CAAAACACTAGTCTTGTCA
*
53911785 CAAAACCCTAGTCTTGTCA
1 CAAAACACTAGTCTTGTCA
53911804 C
1 C
53911805 TGTAAGCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (19 bp):
CAAAACACTAGTCTTGTCA
Found at i:53912513 original size:59 final size:59
Alignment explanation
Indices: 53912421--53912539 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
53912411 CTTCAACAAG
53912421 TGTGTAATGTTGTGACAAATCTAGGATCTCAATGGATTATAAGAAAGCTTGGTAGTCAT
1 TGTGTAATGTTGTGACAAATCTAGGATCTCAATGGATTATAAGAAAGCTTGGTAGTCAT
53912480 TGTGTAATGTTGTGACAAATCTAGGATCTCAATGGATTATAAGAAAGCTTGGTAGTCAT
1 TGTGTAATGTTGTGACAAATCTAGGATCTCAATGGATTATAAGAAAGCTTGGTAGTCAT
53912539 T
1 T
53912540 CTCGCCGAAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (59 bp):
TGTGTAATGTTGTGACAAATCTAGGATCTCAATGGATTATAAGAAAGCTTGGTAGTCAT
Found at i:53915705 original size:36 final size:36
Alignment explanation
Indices: 53915665--53915735 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
53915655 GGAGCGCATC
*
53915665 AGTCAGAATAAATCCAAAAGGCTACTGAACTGAATT
1 AGTCAAAATAAATCCAAAAGGCTACTGAACTGAATT
* * **
53915701 AGTCAAAATAGATCCAAAAGGTTGTTGAACTGAAT
1 AGTCAAAATAAATCCAAAAGGCTACTGAACTGAAT
53915736 AGAGTTCACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (36 bp):
AGTCAAAATAAATCCAAAAGGCTACTGAACTGAATT
Found at i:53916678 original size:37 final size:35
Alignment explanation
Indices: 53916621--53916691 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
53916611 TAACTTTAAT
*
53916621 ATTAAATTAATAAAATACTATTAAGATAAGTACTAA
1 ATTAAATTAATAAAATACTATTAAAATAA-TACTAA
*
53916657 ATTAAATTTAATATTAA-ACTATTAAAATAATACTA
1 ATTAAA-TTAATA-AAATACTATTAAAATAATACTA
53916692 TTTTTTGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 11 0.35
37 18 0.58
38 2 0.06
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.37
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAAATAATACTAA
Found at i:53925289 original size:22 final size:22
Alignment explanation
Indices: 53925261--53925303 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
53925251 ACAATTCCTG
53925261 AATATATCATAATAATCAACAT
1 AATATATCATAATAATCAACAT
** *
53925283 AATATATTTTAATAATTAACA
1 AATATATCATAATAATCAACA
53925304 AATCATTCTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATATCATAATAATCAACAT
Found at i:53928088 original size:17 final size:19
Alignment explanation
Indices: 53928068--53928102 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
53928058 TTACTTCTAA
53928068 TTCACTT-AT-TATTCTTC
1 TTCACTTAATCTATTCTTC
53928085 TTCACTTAATCTATTCTT
1 TTCACTTAATCTATTCTT
53928103 AAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (19 bp):
TTCACTTAATCTATTCTTC
Found at i:53931758 original size:20 final size:20
Alignment explanation
Indices: 53931735--53931893 Score: 81
Period size: 20 Copynumber: 7.8 Consensus size: 20
53931725 ATATGGCATA
53931735 TTAGAAATTTTGGTAAATTC
1 TTAGAAATTTTGGTAAATTC
*
53931755 TTAGATACTAATTTTGGTAAAGTC
1 TTAG--A--AATTTTGGTAAATTC
* *
53931779 TTAGGAATTTTTGTGT-AACT-
1 TTA-GAAATTTTG-GTAAATTC
*** * *
53931799 TTAGAAATTTCAATAATTTA
1 TTAGAAATTTTGGTAAATTC
* *
53931819 TTAGAAATTTTGGTAACTAC
1 TTAGAAATTTTGGTAAATTC
* * * *
53931839 TTAGAAGTTTTTGTAAGTCC
1 TTAGAAATTTTGGTAAATTC
* *
53931859 TTAAAAATTTTGG-AATTTCC
1 TTAGAAATTTTGGTAAATT-C
*
53931879 TTATAAATTTTGGTA
1 TTAGAAATTTTGGTA
53931894 TGTACCAAAA
Statistics
Matches: 104, Mismatches: 25, Indels: 19
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.01
19 11 0.11
20 60 0.58
21 10 0.10
22 3 0.03
23 1 0.01
24 17 0.16
25 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (20 bp):
TTAGAAATTTTGGTAAATTC
Found at i:53935557 original size:23 final size:23
Alignment explanation
Indices: 53935506--53935551 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
53935496 GGTTTTCACT
*
53935506 GCATTAGAAGATTAATTGTTTAA
1 GCATTAGAAGATTAATGGTTTAA
53935529 GCATTAGAAGATTAATGGTTTAA
1 GCATTAGAAGATTAATGGTTTAA
53935552 TGATTAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (23 bp):
GCATTAGAAGATTAATGGTTTAA
Found at i:53937702 original size:19 final size:20
Alignment explanation
Indices: 53937677--53937736 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
53937667 AATCTTTTTA
53937677 ATTTAATGTTATTTATAATG
1 ATTTAATGTTATTTATAATG
*
53937697 -TTTAATCTTAATTT-TAATTG
1 ATTTAATGTT-ATTTATAA-TG
*
53937717 ATTTAATGCTATATTATAAT
1 ATTTAATGTTAT-TTATAAT
53937737 AATTAAGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 11 0.34
20 8 0.25
21 10 0.31
22 3 0.09
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (20 bp):
ATTTAATGTTATTTATAATG
Found at i:53942141 original size:13 final size:13
Alignment explanation
Indices: 53942120--53942152 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
53942110 TTTTATTATT
*
53942120 ATTTGACCTATGA
1 ATTTAACCTATGA
53942133 ATTTAACCTATGA
1 ATTTAACCTATGA
53942146 ATTTAAC
1 ATTTAAC
53942153 TTATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (13 bp):
ATTTAACCTATGA
Found at i:53946625 original size:45 final size:45
Alignment explanation
Indices: 53946544--53946719 Score: 230
Period size: 45 Copynumber: 4.0 Consensus size: 45
53946534 AACCGTTACA
* * *
53946544 CGGTGG-ATCAACACATAGC-ACCACCCTTATAATCAATTATATT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATATT
** *
53946587 CGGTGGAATCAGCACATAGCAACCACCTTTATTTTCAATGATTTT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATATT
* * * * **
53946632 CGGTGGAGTCAGCACATATCAACCACATTTATAATCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATATT
53946677 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATA
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATA
53946720 CTCAGTACAC
Statistics
Matches: 112, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 6 0.05
44 12 0.11
45 94 0.84
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATATT
Found at i:53963992 original size:18 final size:18
Alignment explanation
Indices: 53963971--53964007 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53963961 CAACACTTTG
53963971 TCATCAATCAACTACATA
1 TCATCAATCAACTACATA
53963989 TCATCAATCAACTACATA
1 TCATCAATCAACTACATA
53964007 T
1 T
53964008 TAGTCTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (18 bp):
TCATCAATCAACTACATA
Found at i:53973071 original size:14 final size:15
Alignment explanation
Indices: 53973034--53973145 Score: 76
Period size: 14 Copynumber: 7.7 Consensus size: 15
53973024 CATAATTAGT
*
53973034 TAATATATATTTATCA
1 TAATATA-ATTTACCA
53973050 TAAT-TAATTTA-CA
1 TAATATAATTTACCA
*
53973063 TGATATAATTTACCA
1 TAATATAATTTACCA
*
53973078 TAAT-TAGTTTA-CA
1 TAATATAATTTACCA
*
53973091 TAATATAAATTCACCA
1 TAATAT-AATTTACCA
* *
53973107 TAAT-TAGTTTA-AA
1 TAATATAATTTACCA
* *
53973120 TGATATAAATTCACCA
1 TAATAT-AATTTACCA
53973136 TAAT-TAATTT
1 TAATATAATTT
53973146 TCATATTTAT
Statistics
Matches: 74, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
13 15 0.20
14 28 0.38
15 17 0.23
16 14 0.19
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.43
Consensus pattern (15 bp):
TAATATAATTTACCA
Found at i:53973073 original size:28 final size:29
Alignment explanation
Indices: 53973048--53973145 Score: 144
Period size: 29 Copynumber: 3.4 Consensus size: 29
53973038 ATATATTTAT
*
53973048 CATAATTAATTTACATGATAT-AATTTAC
1 CATAATTAATTTACATGATATAAATTCAC
* *
53973076 CATAATTAGTTTACATAATATAAATTCAC
1 CATAATTAATTTACATGATATAAATTCAC
* *
53973105 CATAATTAGTTTAAATGATATAAATTCAC
1 CATAATTAATTTACATGATATAAATTCAC
53973134 CATAATTAATTT
1 CATAATTAATTT
53973146 TCATATTTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 19 0.30
29 44 0.70
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (29 bp):
CATAATTAATTTACATGATATAAATTCAC
Found at i:53973109 original size:57 final size:58
Alignment explanation
Indices: 53973034--53973150 Score: 155
Period size: 57 Copynumber: 2.0 Consensus size: 58
53973024 CATAATTAGT
* * * * * *
53973034 TAATATATATTTATCATAATTAATTTACATGATAT-AATTTACCATAATTAGTTTACA
1 TAATATAAATTCACCATAATTAATTTAAATGATATAAATTCACCATAATTAATTTACA
* *
53973091 TAATATAAATTCACCATAATTAGTTTAAATGATATAAATTCACCATAATTAATTTTCA
1 TAATATAAATTCACCATAATTAATTTAAATGATATAAATTCACCATAATTAATTTACA
53973149 TA
1 TA
53973151 TTTATGTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 30 0.59
58 21 0.41
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (58 bp):
TAATATAAATTCACCATAATTAATTTAAATGATATAAATTCACCATAATTAATTTACA
Found at i:53973111 original size:29 final size:29
Alignment explanation
Indices: 53973034--53973150 Score: 137
Period size: 29 Copynumber: 4.1 Consensus size: 29
53973024 CATAATTAGT
* * *
53973034 TAATATATATTTATCATAATTAATTTACA
1 TAATATAAATTCACCATAATTAATTTACA
* * *
53973063 TGATAT-AATTTACCATAATTAGTTTACA
1 TAATATAAATTCACCATAATTAATTTACA
* *
53973091 TAATATAAATTCACCATAATTAGTTTAAA
1 TAATATAAATTCACCATAATTAATTTACA
* *
53973120 TGATATAAATTCACCATAATTAATTTTCA
1 TAATATAAATTCACCATAATTAATTTACA
53973149 TA
1 TA
53973151 TTTATGTTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
28 24 0.32
29 51 0.68
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (29 bp):
TAATATAAATTCACCATAATTAATTTACA
Found at i:53985730 original size:18 final size:18
Alignment explanation
Indices: 53985699--53985733 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53985689 GGGAGTAACT
* *
53985699 TCGAGCATATCTTGGTGA
1 TCGAGAATAACTTGGTGA
53985717 TCGAGAATAACTTGGTG
1 TCGAGAATAACTTGGTG
53985734 GAGAGCGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (18 bp):
TCGAGAATAACTTGGTGA
Found at i:53986494 original size:33 final size:34
Alignment explanation
Indices: 53986457--53986536 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 34
53986447 TTAGTTGAAA
*
53986457 GTGTCTTCAACAGAGTACTC-TAATACTTCATTG
1 GTGTCTTCAACACAGTACTCTTAATACTTCATTG
* *
53986490 GTGTCTTCAACACAGTACTCTTATTACTTCGTTG
1 GTGTCTTCAACACAGTACTCTTAATACTTCATTG
53986524 GTGTCTTCAACAC
1 GTGTCTTCAACAC
53986537 TTTCAATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
33 19 0.44
34 24 0.56
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (34 bp):
GTGTCTTCAACACAGTACTCTTAATACTTCATTG
Found at i:53988751 original size:26 final size:28
Alignment explanation
Indices: 53988708--53988761 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
53988698 ATAATTCGGG
*
53988708 AAATATATATAATCTTAA-ATTATAATAA
1 AAATATATAAAATCTTAATATTA-AATAA
53988736 AAATAT-TAAAAT-TTAATATTAAATAA
1 AAATATATAAAATCTTAATATTAAATAA
53988762 TTAATATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 9 0.38
27 9 0.38
28 6 0.25
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
AAATATATAAAATCTTAATATTAAATAA
Found at i:53991307 original size:12 final size:12
Alignment explanation
Indices: 53991290--53991318 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
53991280 CCACATTTAT
53991290 TGAAGAAATGTC
1 TGAAGAAATGTC
53991302 TGAAGAAATGTC
1 TGAAGAAATGTC
53991314 TGAAG
1 TGAAG
53991319 GATAAGCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.28, T:0.24
Consensus pattern (12 bp):
TGAAGAAATGTC
Found at i:54003092 original size:49 final size:50
Alignment explanation
Indices: 54002991--54003119 Score: 170
Period size: 49 Copynumber: 2.6 Consensus size: 50
54002981 CGACCCACAA
* * * * * *
54002991 CTCGTATGAGCATGCTGATTTACAGCTTGTGTGAGCATACCGATATATAG
1 CTCGTGTGAGCATACTGATTTACAGCTCGTGAGAGCATACCAATATACAG
*
54003041 CTCGTGTGAGCATACTGATTT-CAGCTCGTGAGAGCATACCAATTTACAG
1 CTCGTGTGAGCATACTGATTTACAGCTCGTGAGAGCATACCAATATACAG
* *
54003090 CTCGTGTGAGCATACCGATTTACAACTCGT
1 CTCGTGTGAGCATACTGATTTACAGCTCGT
54003120 CTAAGCATAC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 43 0.62
50 26 0.38
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (50 bp):
CTCGTGTGAGCATACTGATTTACAGCTCGTGAGAGCATACCAATATACAG
Found at i:54003110 original size:25 final size:25
Alignment explanation
Indices: 54002991--54003129 Score: 163
Period size: 25 Copynumber: 5.6 Consensus size: 25
54002981 CGACCCACAA
* * *
54002991 CTCGTATGAGCATGCTGATTTACAG
1 CTCGTGTGAGCATACCGATTTACAG
* * *
54003016 CTTGTGTGAGCATACCGATATATAG
1 CTCGTGTGAGCATACCGATTTACAG
*
54003041 CTCGTGTGAGCATACTGATTT-CAG
1 CTCGTGTGAGCATACCGATTTACAG
* *
54003065 CTCGTGAGAGCATACCAATTTACAG
1 CTCGTGTGAGCATACCGATTTACAG
*
54003090 CTCGTGTGAGCATACCGATTTACAA
1 CTCGTGTGAGCATACCGATTTACAG
* *
54003115 CTCGTCTAAGCATAC
1 CTCGTGTGAGCATAC
54003130 ATGTACAAGA
Statistics
Matches: 95, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
24 20 0.21
25 75 0.79
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (25 bp):
CTCGTGTGAGCATACCGATTTACAG
Found at i:54004263 original size:20 final size:20
Alignment explanation
Indices: 54004230--54004268 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
54004220 ATCGTATGGT
54004230 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATGGTATC
54004250 TTGG-TTGTGATTATGGTAT
1 TTGGCTTGTG-TTATGGTAT
54004269 TTTGAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.05, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTATC
Found at i:54004783 original size:42 final size:42
Alignment explanation
Indices: 54004708--54004820 Score: 145
Period size: 42 Copynumber: 2.7 Consensus size: 42
54004698 GAAAATTGGT
* * * * * *
54004708 GGTAGACGGCCTGGCGCACGAGCATGTGAGGCTATTTCGAAG
1 GGTACACGGCCTAGCACACGGGCGTGTGGGGCTATTTCGAAG
**
54004750 GGTACACGGCCTAGCACACGGGCGTGTGGGGCTATTTTTAAG
1 GGTACACGGCCTAGCACACGGGCGTGTGGGGCTATTTCGAAG
*
54004792 GGTACACGGCCTAGCACACGGTCGTGTGG
1 GGTACACGGCCTAGCACACGGGCGTGTGG
54004821 CTTGACCGTG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.19, C:0.23, G:0.37, T:0.20
Consensus pattern (42 bp):
GGTACACGGCCTAGCACACGGGCGTGTGGGGCTATTTCGAAG
Found at i:54006914 original size:21 final size:21
Alignment explanation
Indices: 54006874--54006914 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54006864 TCCCTTTAGT
**
54006874 GGTATCACGATATCCTCCTTG
1 GGTATCACGATATCAACCTTG
54006895 GGTATCACGATATCAACCTT
1 GGTATCACGATATCAACCTT
54006915 TCAAAGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (21 bp):
GGTATCACGATATCAACCTTG
Found at i:54020587 original size:18 final size:18
Alignment explanation
Indices: 54020564--54020607 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
54020554 TTTGGTTTGG
54020564 TTATTTTACTTAGTGGTT
1 TTATTTTACTTAGTGGTT
* *
54020582 TTATTTAACTTAGTGTTT
1 TTATTTTACTTAGTGGTT
54020600 TTACTTTT
1 TTA-TTTT
54020608 TATAGTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (18 bp):
TTATTTTACTTAGTGGTT
Found at i:54024646 original size:36 final size:36
Alignment explanation
Indices: 54024599--54024673 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
54024589 GTAATGTATG
54024599 TGATAGTAACTAGCACAATGAATTATATGAAATGCA
1 TGATAGTAACTAGCACAATGAATTATATGAAATGCA
54024635 TGATAGTAACTAGCACAATGAATTATATGAAATGCA
1 TGATAGTAACTAGCACAATGAATTATATGAAATGCA
54024671 TGA
1 TGA
54024674 ATAAAGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (36 bp):
TGATAGTAACTAGCACAATGAATTATATGAAATGCA
Found at i:54028194 original size:20 final size:19
Alignment explanation
Indices: 54028171--54028234 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 19
54028161 TTTTTTGAAT
*
54028171 TTTTATTAACATTTTATATA
1 TTTTATTAA-ATTTTAAATA
*
54028191 TTTT-TTTAATTTTAAATA
1 TTTTATTAAATTTTAAATA
* *
54028209 TTTTA-TAATTTTTAATTA
1 TTTTATTAAATTTTAAATA
54028227 -TTTATTAA
1 TTTTATTAA
54028235 TGTGACATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 4 0.11
18 26 0.70
19 3 0.08
20 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTATTAAATTTTAAATA
Done.