Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000846.1 Hibiscus syriacus cultivar Beakdansim tig00001630_pilon, whole genome shotgun sequence
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: 988667
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:277149 original size:39 final size:39
Alignment explanation
Indices: 277094--277172 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
277084 AGTTATTTTA
*
277094 TCAGGGAGTATAGAAAGCGTAGACTGACTAGAAGACCTC
1 TCAGGGAGTATAGAAAGCGTAGACTGACGAGAAGACCTC
*
277133 TCAGGGAGTATGGAAAGCGTAGACTGACGAGAAGACCTC
1 TCAGGGAGTATAGAAAGCGTAGACTGACGAGAAGACCTC
277172 T
1 T
277173 TAGATCGATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (39 bp):
TCAGGGAGTATAGAAAGCGTAGACTGACGAGAAGACCTC
Found at i:278786 original size:31 final size:30
Alignment explanation
Indices: 278759--278835 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 30
278749 TTGGGGCATG
* *
278759 AGAGCCTACCCAAGATAATTCTCGGGGCCAC
1 AGAGCCTACCCAAGAAAAATCTCGGGG-CAC
* *
278790 AGAGGCTAACCAAAGAAAAATCTCGGGGCAAC
1 AGAGCCT-ACCCAAGAAAAATCTCGGGGC-AC
*
278822 AAAGCCTACCCAAG
1 AGAGCCTACCCAAG
278836 GGTTGCCTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
31 13 0.35
32 24 0.65
ACGTcount: A:0.38, C:0.29, G:0.22, T:0.12
Consensus pattern (30 bp):
AGAGCCTACCCAAGAAAAATCTCGGGGCAC
Found at i:279672 original size:24 final size:24
Alignment explanation
Indices: 279640--279720 Score: 128
Period size: 24 Copynumber: 3.4 Consensus size: 24
279630 ATTTTCCTTT
279640 TTGGGTCAAAGTCAACGGGTCTAG
1 TTGGGTCAAAGTCAACGGGTCTAG
*
279664 TTGGGTCAAATTCAACGGGTCTAG
1 TTGGGTCAAAGTCAACGGGTCTAG
*
279688 TCGGGTCAAAGTCAACGGGTC-AG
1 TTGGGTCAAAGTCAACGGGTCTAG
279711 ATTGGGTCAA
1 -TTGGGTCAA
279721 CGGTTTGGTC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 2 0.04
24 50 0.96
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (24 bp):
TTGGGTCAAAGTCAACGGGTCTAG
Found at i:283866 original size:24 final size:24
Alignment explanation
Indices: 283838--283884 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
283828 TCAACTCTGG
*
283838 TCAAAGTCAATGGGTCGGGTCGGA
1 TCAAAGTCAATGGGTCGGATCGGA
*
283862 TCAAAGTCAATGTGTCGGATCGG
1 TCAAAGTCAATGGGTCGGATCGG
283885 GACAACGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23
Consensus pattern (24 bp):
TCAAAGTCAATGGGTCGGATCGGA
Found at i:288174 original size:89 final size:90
Alignment explanation
Indices: 287974--288337 Score: 484
Period size: 89 Copynumber: 4.0 Consensus size: 90
287964 CCAGAACTGC
* * * *
287974 GTCCGTAAGGTTTACCCTAAGCACACAGCAAATGGGAGCCAACCTAAGGATATGCCTTGGGGCCT
1 GTCCGTAGGGCTTACCCTAAGAACACAACAAA-GGGAGCCAACCTAAGGATATGCCTTGGGGCCT
* * *
288039 ATAGGCCTACCCAAAGGTATACTTAG
65 ATAGGCCTACCTAAGGGTATCCTTAG
** * **
288065 GTTTGTAGGGCTTACCCTAAGAAAACAACAAAGGGAGCCAACCTAAGGATATGTGTTGGGGCCTA
1 GTCCGTAGGGCTTACCCTAAGAACACAACAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTA
288130 T-GGCCTACCTAAGGGTATCCTTAG
66 TAGGCCTACCTAAGGGTATCCTTAG
* * *
288154 GTCCGTAGGGCTTACTCTAAGAACATAACAAAGGGAGCCAACCTAAGGATATGCCTTGGGTCCTA
1 GTCCGTAGGGCTTACCCTAAGAACACAACAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTA
288219 T-GGCCTATCC-AAGGGTATCCTTAG
66 TAGGCCTA-CCTAAGGGTATCCTTAG
* * * *
288243 GTCTGTAGGGCTTACCCTAAGCACACAGCAAAGGGAGCAAAACCTAAGGATATGCCTTGGGGCCT
1 GTCCGTAGGGCTTACCCTAAGAACACAACAAAGGGAGC-CAACCTAAGGATATGCCTTGGGGCCT
*
288308 ATGGGCCTA-CTGAAGGGTATCCTTAG
65 ATAGGCCTACCT-AAGGGTATCCTTAG
288334 GTCC
1 GTCC
288338 ATAAGGATTT
Statistics
Matches: 240, Mismatches: 28, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
89 132 0.55
90 60 0.25
91 48 0.20
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.22
Consensus pattern (90 bp):
GTCCGTAGGGCTTACCCTAAGAACACAACAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTA
TAGGCCTACCTAAGGGTATCCTTAG
Found at i:288307 original size:179 final size:181
Alignment explanation
Indices: 287974--288343 Score: 532
Period size: 179 Copynumber: 2.1 Consensus size: 181
287964 CCAGAACTGC
* * *
287974 GTCCGTAAGGTTTACCCTAAGCACACAGCAAATGGGAGCCAACCTAAGGATATGCCTTGGGGCCT
1 GTCCGTAAGGCTTACCCTAAGAACACAACAAATGGGAGCCAACCTAAGGATATGCCTTGGGGCCT
* *
288039 ATAGGCCTACCCAAAGGTATACTTAGGTTTGTAGGGCTTACCCTAAGAAAACAACAAAGGGAGCC
66 ATAGGCCTACCCAAAGGTATACTTAGGTCTGTAGGGCTTACCCTAAGAAAACAACAAAGGGAGCA
**
288104 AACCTAAGGATATGTGTTGGGGCCTAT-GGCCTACCT-AAGGGTATCCTTAG
131 AACCTAAGGATATGCCTTGGGGCCTATGGGCCTA-CTGAAGGGTATCCTTAG
* * * *
288154 GTCCGTAGGGCTTACTCTAAGAACATAACAAA-GGGAGCCAACCTAAGGATATGCCTTGGGTCCT
1 GTCCGTAAGGCTTACCCTAAGAACACAACAAATGGGAGCCAACCTAAGGATATGCCTTGGGGCCT
* * * * * *
288218 AT-GGCCTATCCAAGGGTATCCTTAGGTCTGTAGGGCTTACCCTAAGCACACAGCAAAGGGAGCA
66 ATAGGCCTACCCAAAGGTATACTTAGGTCTGTAGGGCTTACCCTAAGAAAACAACAAAGGGAGC-
288282 AAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACTGAAGGGTATCCTTAG
130 AAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACTGAAGGGTATCCTTAG
*
288334 GTCCATAAGG
1 GTCCGTAAGG
288344 ATTTACCAGC
Statistics
Matches: 168, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
178 54 0.32
179 60 0.36
180 54 0.32
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (181 bp):
GTCCGTAAGGCTTACCCTAAGAACACAACAAATGGGAGCCAACCTAAGGATATGCCTTGGGGCCT
ATAGGCCTACCCAAAGGTATACTTAGGTCTGTAGGGCTTACCCTAAGAAAACAACAAAGGGAGCA
AACCTAAGGATATGCCTTGGGGCCTATGGGCCTACTGAAGGGTATCCTTAG
Found at i:289818 original size:24 final size:23
Alignment explanation
Indices: 289767--289818 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
289757 CTATTTTTTT
*
289767 CAAAAAAAAAAAAAAAAATAAGG
1 CAAAAAAAAAAAAAAAAATAAGC
*
289790 GAAAAAAATAAAAAATAAAA-AAGC
1 CAAAAAAA-AAAAAA-AAAATAAGC
289814 CAAAA
1 CAAAA
289819 TTTCAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 7 0.29
24 13 0.54
25 4 0.17
ACGTcount: A:0.81, C:0.06, G:0.08, T:0.06
Consensus pattern (23 bp):
CAAAAAAAAAAAAAAAAATAAGC
Found at i:299097 original size:89 final size:89
Alignment explanation
Indices: 298914--299271 Score: 493
Period size: 89 Copynumber: 4.0 Consensus size: 89
298904 GTATCAGTAA
* *
298914 GGCTTACCTTAAGCACACAGCAAAAGGGAGCCAACC-AAAGATTATGCCTTGGGGCCTATAGGCC
1 GGCTTACCCTAAGCACACAGC-AAAGGGAGCCAACCTAAGGA-TATGCCTTGGGGCCTAT-GGCC
* *
298978 TACCCAAAGGTATGCTTAGGTCCGTAG
63 TACCCAAGGGTATCCTTAGGTCCGTAG
* * * *
299005 GGCTTACCCTAAGCACACAGTAAAGGGACCCAACGTAAGGATATGCCTTGGAGCCTATGGCCTAC
1 GGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTATGGCCTAC
*
299070 CCAAGCGTATCCTTAGGTCCGTAG
66 CCAAGGGTATCCTTAGGTCCGTAG
* * * **
299094 GGCTTACTCTAAGCACACAGCAAAGGGAGCCAACCTAAGAATATGCCTTGGGACCTATTACCTAC
1 GGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTATGGCCTAC
*
299159 CCAAGGGTATCCTTAGATCCGTAG
66 CCAAGGGTATCCTTAGGTCCGTAG
* * * *
299183 GGCTTACCCTAAGCACACAGCAAAAGGAGCTAACCTAAGGATATGCCTTGGGGTCGATGAGCCTA
1 GGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTATG-GCCTA
*
299248 CTCAAGGGTATCCTTAGGTCCGTA
65 CCCAAGGGTATCCTTAGGTCCGTA
299272 AGAATTTACT
Statistics
Matches: 234, Mismatches: 31, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
89 157 0.67
90 54 0.23
91 23 0.10
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (89 bp):
GGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTATGGCCTAC
CCAAGGGTATCCTTAGGTCCGTAG
Found at i:302106 original size:11 final size:11
Alignment explanation
Indices: 302090--302128 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
302080 TCGATAAAAC
302090 GTCAACGGTCG
1 GTCAACGGTCG
*
302101 GTCAACGATCAG
1 GTCAACGGTC-G
302113 GTCAACGGT-G
1 GTCAACGGTCG
302123 GTCAAC
1 GTCAAC
302129 AGTCAACGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 7 0.28
11 9 0.36
12 9 0.36
ACGTcount: A:0.26, C:0.26, G:0.31, T:0.18
Consensus pattern (11 bp):
GTCAACGGTCG
Found at i:302948 original size:2 final size:2
Alignment explanation
Indices: 302943--302982 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
302933 GTGTGTGGCA
*
302943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
302983 TAATCGTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:308472 original size:42 final size:41
Alignment explanation
Indices: 308411--308503 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 41
308401 AAATGGTAAG
* * * *
308411 TCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAA
1 TCCTTCGGGCAATCAGTAAGCCTTTTGAGCAAGATG-ATAAA
* * *
308453 TCCTTCGGGTAATCTGTAAGCCTTTTGAGCAAGATGATAAG
1 TCCTTCGGGCAATCAGTAAGCCTTTTGAGCAAGATGATAAA
308494 TCCTTCGGGC
1 TCCTTCGGGC
308504 CATCCATAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 12 0.28
42 31 0.72
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGCAATCAGTAAGCCTTTTGAGCAAGATGATAAA
Found at i:308729 original size:233 final size:233
Alignment explanation
Indices: 308316--309168 Score: 1080
Period size: 233 Copynumber: 3.7 Consensus size: 233
308306 TAAAAAAATG
* * *
308316 AAATGAGAAAGGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * *
308381 ACCTAGCAAACTATTTCCAAAAATGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * *
308446 GCTTAAATCCTTCGGGTAATCTGTAAGCCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCAT
* * * *
308511 AAGACCTTCAGGCATGATGTTTCCACATGACTCTCAAA
196 AAGACCTTCGGGCAGGATGTTTTCACATGACTCTCGAA
* * *
308549 AAATGAGAAAGGTTTCTCATTTAAATCTCAAATTTAAAATTTTTGAAAAGTAAGAAAGGTTACTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * * * *
308614 ACCTAGTCAAGTATTTCTAAAATTGGTAAGTCCTTCAGGCCATAAGTAAGTCTTTCGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * * * * *
308679 GCTTAAATCATTCGGGTCATCAGTAAGCCTTTCGAGTAAGATGGTAAGTCCTTCGAGCTATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCAT
* * *
308744 AAGACCTTCGGGTAGGAT-TTTATCACATGTCTCTTGAA
196 AAGACCTTCGGGCAGGATGTTT-TCACATGACTCTCGAA
* * * * *
308782 AAAGGAGAAAGGTTTCTTATTTAAATCTAAAAATTGAAATTTTTGAACAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * * * *
308847 ACCTAGTAAACTATTTCAAAAATTTATAAGTCCTTTGGGCCATTAGTAAGTTTTTTGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * *
308912 GCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGAAAGATGATAAGTCCTTCGGACCATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCAT
* *
308977 AAGGCCTTCGGGCAGGAGGTTTTCACAT-ATCTCTCGAA
196 AAGACCTTCGGGCAGGATGTTTTCACATGA-CTCTCGAA
* * * * ** *
309015 AAATGAGAAAGTTTTCTCATTTAAAACTGAAATTTATAATTTTTTTAAAGTAAGAAAGATTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * * * *
309080 ACCCAGTAAACTATTTCCCAAATTTATAAGTCATTCGGGCCATCAGTAAGTTTTTCAAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
** * * *
309145 AATTAAACCCTTCAGGTTATCTGT
131 GCTTAAATCCTTCGGGTCATCTGT
309169 TAGTCTCACT
Statistics
Matches: 533, Mismatches: 84, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
232 3 0.01
233 527 0.99
234 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (233 bp):
AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAGGTTTCTT
ACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
GCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCAT
AAGACCTTCGGGCAGGATGTTTTCACATGACTCTCGAA
Found at i:309317 original size:3 final size:3
Alignment explanation
Indices: 309305--309336 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
309295 TTTTTACCAA
309305 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
309337 TTGTTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:310786 original size:17 final size:17
Alignment explanation
Indices: 310764--310796 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
310754 ATCGAAAAAC
310764 ATAAAATATAACTTTTT
1 ATAAAATATAACTTTTT
*
310781 ATAAAATTTAACTTTT
1 ATAAAATATAACTTTT
310797 CTAGTCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAAATATAACTTTTT
Found at i:311323 original size:22 final size:22
Alignment explanation
Indices: 311298--311345 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
311288 TGTCGGGCTA
311298 AGTTTATGAAAGAAAGAGTTTG
1 AGTTTATGAAAGAAAGAGTTTG
311320 AGTTTATGAAAGAAAGAGTTTG
1 AGTTTATGAAAGAAAGAGTTTG
311342 AGTT
1 AGTT
311346 CACTGAACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (22 bp):
AGTTTATGAAAGAAAGAGTTTG
Found at i:315910 original size:2 final size:2
Alignment explanation
Indices: 315899--315945 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
315889 TAAAGGTGAT
315899 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
315940 TA TA TA
1 TA TA TA
315946 CAATAAAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:317755 original size:23 final size:21
Alignment explanation
Indices: 317720--317771 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
317710 ATGTTTCCAC
317720 ATGTCTCTCAAAAAATGAGAA
1 ATGTCTCTCAAAAAATGAGAA
317741 ATGTCTCTCAAAAAATGAGAA
1 ATGTCTCTCAAAAAATGAGAA
*
317762 ATGTTTCTCA
1 ATGTCTCTCA
317772 TTTAATTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (21 bp):
ATGTCTCTCAAAAAATGAGAA
Found at i:318128 original size:42 final size:41
Alignment explanation
Indices: 318076--318177 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
318066 TCTAAAATTT
* *
318076 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATG
* ** * * *
318117 TTTAAATCCTTCAAGTCATCTGTAAGTCTTTCGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATG
*
318159 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
318178 TATAAGACCT
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
41 14 0.30
42 33 0.70
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATG
Found at i:318371 original size:233 final size:233
Alignment explanation
Indices: 317521--318378 Score: 975
Period size: 233 Copynumber: 3.7 Consensus size: 233
317511 GTAAAAAATG
* *
317521 AAATGAGAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAA-AAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
** **
317585 ACCTAGTAAACTATTTCCAAAGA-TGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGA
66 ACCTAGTAAACTATTTCCAAA-ATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGA
* ** *
317649 TGCTTAAATCCTTCAT-GTT-ATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCACGCAGAT
130 TGTTTAAATCCTTC-TGGTTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGC-CAT
* *** * * * *** *** * *
317712 GT-TTCCACATGTC-TCTCAAAAAATGAGAAATGTCTCTCAAA
193 CTATAAGACCT-TCGGCT-AGATGTTTTCACATGTCTCTCGAA
* * * * * *
317753 AAATGAGAAATGTTTCTCATTTAATTCTCAAATTTGAATTTTTTGAAAAGTAATAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
** * * * * * *
317818 ACCTAGTAAACTATTTTTAAAATTTGTAAGTCTTTCGGTCCATTAATAAGTCTTTCGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGAT
* * * * * * *
317883 GTTTAAATCATTC-GGGTCATCAGTAAGCCTTTCGAGCAAGATGGTAATTCCTTCGGGCCATCCA
131 GTTTAAATCCTTCTGGTTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTA
*
317947 TAAGACCTTCAGGC-AGGATGTTTTCACACT-TCTCTTGAA
196 TAAGACCTTC-GGCTA-GATGTTTTCACA-TGTCTCTCGAA
*
317986 AAAGGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
*
318051 ACCTAGTAAACTATTTCTAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGAT
**
318116 GTTTAAATCCTTCAAG-TCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTA
131 GTTTAAATCCTTCTGGTTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTA
318180 TAAGACCTTCGGGCTAGATGTTTTCACATGTCTCTCGAA
196 TAAGACCTTC-GGCTAGATGTTTTCACATGTCTCTCGAA
* * * *
318219 AAATGAGAAAGGTTTCTCATTTAAAACTGAAATTTCAAATTTTTTAAAAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * ** *
318284 ACCCAGTAAACTATTTCCCAAATTTATAAGTCATTTAGGCCATCAGTATGTCTTTCAAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGAT
* *
318349 GATTAAA-CCGTT-TGGTTCATCTGTTAGTCT
131 GTTTAAATCC-TTCTGGTTCATCTGTAAGTCT
318379 CACTTGAGAC
Statistics
Matches: 531, Mismatches: 81, Indels: 27
0.83 0.13 0.04
Matches are distributed among these distances:
232 56 0.11
233 471 0.89
234 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (233 bp):
AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGAT
GTTTAAATCCTTCTGGTTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTA
TAAGACCTTCGGCTAGATGTTTTCACATGTCTCTCGAA
Found at i:318972 original size:26 final size:27
Alignment explanation
Indices: 318933--318984 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
318923 GAGAGGAGAA
* *
318933 AAAAAAAGGTGAAAA-GAAAGAAAAAC
1 AAAAAAAGGAGAAAATAAAAGAAAAAC
318959 AAAAAAAGGAGAAAATAAAAGAAAAA
1 AAAAAAAGGAGAAAATAAAAGAAAAA
318985 TAATATAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (27 bp):
AAAAAAAGGAGAAAATAAAAGAAAAAC
Found at i:319004 original size:31 final size:31
Alignment explanation
Indices: 318969--319028 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
318959 AAAAAAAGGA
* *
318969 GAAAATAAAAG-AAAAATAATATAAGAAAAAG
1 GAAAAGAAAAGTAAAAATAA-AAAAGAAAAAG
*
319000 GAAAAGAAAAGTAGAAATAAAAAAGAAAA
1 GAAAAGAAAAGTAAAAATAAAAAAGAAAA
319029 GAAGCCTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (31 bp):
GAAAAGAAAAGTAAAAATAAAAAAGAAAAAG
Found at i:330484 original size:89 final size:89
Alignment explanation
Indices: 330300--330657 Score: 484
Period size: 89 Copynumber: 4.0 Consensus size: 89
330290 GTATCAGTAA
* *
330300 GGCTTACCTTAAGCACACAGCAAAAGGGAGCCAACC-AAAGATTATGCCTTGGGGCCTATAGGCC
1 GGCTTACCCTAAGCACACAGC-AAAGGGAGCCAACCTAAGGA-TATGCCTTGGGGCCTAT-GGCC
* * *
330364 TACCCAAAGGTATGCTTAGGTTCGTAG
63 TACCCAAGGGTATCCTTAGGTCCGTAG
* * * *
330391 GGCTTACCCTAAGCACACAGTAAAGGGACCCAACGTAAGGATATGCCTTGGAGCCTATGGCCTAC
1 GGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTATGGCCTAC
*
330456 CCAAGCGTATCCTTAGGTCCGTAG
66 CCAAGGGTATCCTTAGGTCCGTAG
* * * * **
330480 GGCTTACTCTAAGCACACAACAAAGGGAGCCAACCTAAGCATATGCCTTGGGACCTATTACCTAC
1 GGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTATGGCCTAC
*
330545 CCAAGGGTATCCTTAGATCCGTAG
66 CCAAGGGTATCCTTAGGTCCGTAG
* * *
330569 GGCTTACCCTAAGCACACAGCAAAAGGAGCTAACCTAAGGATATGCCTTGGGGTCTATGAGCCTA
1 GGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTATG-GCCTA
*
330634 CTCAAGGGTATCCTTAGGTCCGTA
65 CCCAAGGGTATCCTTAGGTCCGTA
330658 AGAATTTACT
Statistics
Matches: 232, Mismatches: 33, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
89 155 0.67
90 54 0.23
91 23 0.10
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (89 bp):
GGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATATGCCTTGGGGCCTATGGCCTAC
CCAAGGGTATCCTTAGGTCCGTAG
Found at i:333492 original size:11 final size:11
Alignment explanation
Indices: 333476--333513 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
333466 TCGATAAAAC
333476 GTCAACGGTCG
1 GTCAACGGTCG
*
333487 GTCAACGATCAG
1 GTCAACGGTC-G
333499 GTCAACGGT-G
1 GTCAACGGTCG
333509 GTCAA
1 GTCAA
333514 TAGTCAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 6 0.25
11 9 0.38
12 9 0.38
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (11 bp):
GTCAACGGTCG
Found at i:334336 original size:2 final size:2
Alignment explanation
Indices: 334329--334355 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
334319 GGGTGTGACA
334329 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
334356 ATCGTGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:339844 original size:42 final size:41
Alignment explanation
Indices: 339783--339875 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 41
339773 AAATGGTAAG
* * * *
339783 TCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAA
1 TCCTTCGGGCAATCAGTAAGCCTTTTGAGCAAGATG-ATAAA
* * *
339825 TCCTTCGGGTAATCTGTAAGCCTTTTGAGCAAGATGATAAG
1 TCCTTCGGGCAATCAGTAAGCCTTTTGAGCAAGATGATAAA
339866 TCCTTCGGGC
1 TCCTTCGGGC
339876 CATCCATAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 12 0.28
42 31 0.72
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGCAATCAGTAAGCCTTTTGAGCAAGATGATAAA
Found at i:340101 original size:233 final size:233
Alignment explanation
Indices: 339688--340540 Score: 1098
Period size: 233 Copynumber: 3.7 Consensus size: 233
339678 AAAAAAAATG
* * *
339688 AAATGAGAAAGGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * *
339753 ACCTAGCAAACTATTTCCAAAAATGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * *
339818 GCTTAAATCCTTCGGGTAATCTGTAAGCCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCAT
* * * *
339883 AAGACCTTCAGGCATGATGTTTCCACATGACTCTCAAA
196 AAGACCTTCGGGCAGGATGTTTTCACATGACTCTCGAA
* * *
339921 AAATGAGAAAGGTTTCTCATTTAAATCTCAAATTTAAAATTTTTGAAAAGTAAGAAAGGTTACTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * * *
339986 ACCTAGTCAAGTATTTCTAAAATTGGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * * * * *
340051 GCTTAAATCATTCGGGTCATCAGTAAGCCTTTCGAGTAAGATGGTAAGTCCTTCGAGCTATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCAT
* * *
340116 AAGACCTTCGGGTAGGAT-TTTATCACATGTCTCTTGAA
196 AAGACCTTCGGGCAGGATGTTT-TCACATGACTCTCGAA
* * * * *
340154 AAAGGAGAAAGGTTTCTTATTTAAATCTAAAAATTGAAATTTTTGAACAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * * * *
340219 ACCTAGTAAACTATTTCAAAAATTTATAAGTCCTTTGGGCCATTAGTAAGTTTTTTGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * *
340284 GCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGAAAGATGATAAGTCCTTCGGACCATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCAT
* *
340349 AAGGCCTTCGGGCAGGAGGTTTTCACAT-ATCTCTCGAA
196 AAGACCTTCGGGCAGGATGTTTTCACATGA-CTCTCGAA
* * * * * *
340387 AAATGAGAAAGTTTTCTCATTTAAAACTGAAATTTATAATTTTTTAAAAGTAAGAAAGATTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * * * *
340452 ACCCAGTAAACTATTTCCCAAATTTATAAGTCATTCGGGCCATCAGTAAGTTTTTCAAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
** * * *
340517 AATTAAACCCTTCAGGTTATCTGT
131 GCTTAAATCCTTCGGGTCATCTGT
340541 TAGTCTCACT
Statistics
Matches: 535, Mismatches: 82, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
232 3 0.01
233 529 0.99
234 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (233 bp):
AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAGGTTTCTT
ACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
GCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCAT
AAGACCTTCGGGCAGGATGTTTTCACATGACTCTCGAA
Found at i:342155 original size:17 final size:17
Alignment explanation
Indices: 342133--342165 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
342123 ATCGAAAAAC
342133 ATAAAATATAACTTTTT
1 ATAAAATATAACTTTTT
*
342150 ATAAAATTTAACTTTT
1 ATAAAATATAACTTTT
342166 CTAGTCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAAATATAACTTTTT
Found at i:342737 original size:22 final size:22
Alignment explanation
Indices: 342712--342761 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
342702 GGTGTCGGGC
342712 TGAGTTTATGAAAGAAAGAGTT
1 TGAGTTTATGAAAGAAAGAGTT
342734 TGAGTTTATGAAAGAAAGAGTT
1 TGAGTTTATGAAAGAAAGAGTT
342756 TGAGTT
1 TGAGTT
342762 CACTGAACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (22 bp):
TGAGTTTATGAAAGAAAGAGTT
Found at i:349167 original size:23 final size:21
Alignment explanation
Indices: 349132--349183 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
349122 ATGTTTCCAC
349132 ATGTCTCTCAAAAAATGAGAA
1 ATGTCTCTCAAAAAATGAGAA
349153 ATGTCTCTCAAAAAATGAGAA
1 ATGTCTCTCAAAAAATGAGAA
*
349174 ATGTTTCTCA
1 ATGTCTCTCA
349184 TTTAATTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (21 bp):
ATGTCTCTCAAAAAATGAGAA
Found at i:349392 original size:233 final size:232
Alignment explanation
Indices: 348933--349767 Score: 1036
Period size: 233 Copynumber: 3.6 Consensus size: 232
348923 TAAAAAAATG
* *
348933 AAATGAGAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAA-AAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
** *
348997 ACCTAGTAAACTATTTCCAAAGA-TGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGA
66 ACCTAGTAAACTATTTCCAAA-ATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * * ** *
349061 TGCTTAAATCCTTCATGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCACGCAGATGT
130 TGTTTAAATCCTTCAAGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGC-CA---
* * * ** * ** * *
349126 TTCCACATG-TCTCTCA-AAAAATG---AGAAATGTCTCTCAAA
191 -TCCATAAGACCT-TCAGGCAGATGTTTTCACATGTCTCTCGAA
* * * * * *
349165 AAATGAGAAATGTTTCTCATTTAATTCTCAAATTTGAATTTTTTGAAAAGTAATAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
** * * * *
349230 ACCTAGTAAACTATTTTTAAAATTTGTAAGTCTTTCGGGCCATTAATAAGTCTTTCGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* ** * * * *
349295 GTTTAAATCATTCGGGTCATCAGTAAGCCTTTCGAGCAAGATGGTAATTCCTTCGGGCCATCCAT
131 GTTTAAATCCTTCAAGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
*
349360 AAGACCTTCAGGCAGGATGTTTTCACATGTCTCTTGAA
196 AAGACCTTCAGGCA-GATGTTTTCACATGTCTCTCGAA
*
349398 AAAGGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
*
349463 ACCTAGTAAACTATTTCTAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
*
349528 GTTTAAATCCTTCAAGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTAT
131 GTTTAAATCCTTCAAGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
*
349593 AAGACCTTCGGGCTAGATGTTTTCACATGTCTCTCGAA
196 AAGACCTTCAGGC-AGATGTTTTCACATGTCTCTCGAA
* * * *
349631 AAATGAGAAAGGTTTCTCATTTAAAACTGAAATTTCAAATTTTTTAAAAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * * * *
349696 ACCCAGTAAACTATTTCCCAAATTTATAAGTCATTCAGGCCATCAGTATGTCTTTCAAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
*
349761 GATTAAA
131 GTTTAAA
349768 CCGTTTGGTT
Statistics
Matches: 522, Mismatches: 72, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
228 9 0.02
229 3 0.01
230 3 0.01
232 46 0.09
233 460 0.88
234 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (232 bp):
AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
GTTTAAATCCTTCAAGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
AAGACCTTCAGGCAGATGTTTTCACATGTCTCTCGAA
Found at i:349540 original size:42 final size:41
Alignment explanation
Indices: 349488--349589 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
349478 TCTAAAATTT
* *
349488 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATG
* ** * *
349529 TTTAAATCCTTCAAGTCATCTGTAAGTCTTTCGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATG
*
349571 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
349590 TATAAGACCT
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
41 14 0.29
42 34 0.71
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATG
Found at i:350385 original size:27 final size:28
Alignment explanation
Indices: 350344--350397 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
350334 GGAGAGGAGA
* *
350344 AAAAAAAAGGTGAAAA-GAAAGAAAAAC
1 AAAAAAAAGGAGAAAATAAAAGAAAAAC
350371 AAAAAAAAGGAGAAAATAAAAGAAAAA
1 AAAAAAAAGGAGAAAATAAAAGAAAAA
350398 TAATATAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.04
Consensus pattern (28 bp):
AAAAAAAAGGAGAAAATAAAAGAAAAAC
Found at i:353606 original size:18 final size:18
Alignment explanation
Indices: 353583--353626 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
353573 TAAGGATACC
353583 AGACGAACGAGATCGATG
1 AGACGAACGAGATCGATG
353601 AGACGAACGAGATCGATG
1 AGACGAACGAGATCGATG
*
353619 AGATGAAC
1 AGACGAAC
353627 ACAATGGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.32, T:0.11
Consensus pattern (18 bp):
AGACGAACGAGATCGATG
Found at i:355936 original size:16 final size:16
Alignment explanation
Indices: 355915--355950 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
355905 TGTTAACGTA
355915 ATATATATACATGTAT
1 ATATATATACATGTAT
*
355931 ATATATATATATGTAT
1 ATATATATACATGTAT
355947 ATAT
1 ATAT
355951 TAATCGTGTA
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:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
ATATATATACATGTAT
Found at i:356213 original size:57 final size:57
Alignment explanation
Indices: 356117--356230 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
356107 CTAAGGATAA
356117 TATTCGTTCATTTTAATATTGTCATAAAATGACTATCTTAACGTATAAGAAAGTTAC
1 TATTCGTTCATTTTAATATTGTCATAAAATGACTATCTTAACGTATAAGAAAGTTAC
* * * * * *
356174 TATTCTTTCCTTTTAATATTTTCATAAAGTGATTGTCTTAACGTATAAGAAAGTTAC
1 TATTCGTTCATTTTAATATTGTCATAAAATGACTATCTTAACGTATAAGAAAGTTAC
356231 GTTCGATAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (57 bp):
TATTCGTTCATTTTAATATTGTCATAAAATGACTATCTTAACGTATAAGAAAGTTAC
Found at i:358629 original size:75 final size:76
Alignment explanation
Indices: 358456--358663 Score: 285
Period size: 75 Copynumber: 2.7 Consensus size: 76
358446 CAAAGCCAAA
* * * **
358456 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCTCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCC-CCCTAAACAG
358521 TTTTGGCCCCGAG
64 TTTTGGCCCCGAG
*
358534 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
358599 TT-GCTCCGAG
66 TTGGCCCCGAG
* * * *
358609 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
358664 CTTGTACAAC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
74 17 0.14
75 40 0.34
76 12 0.10
77 24 0.20
78 25 0.21
ACGTcount: A:0.25, C:0.32, G:0.24, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TTGGCCCCGAG
Found at i:364492 original size:21 final size:21
Alignment explanation
Indices: 364466--364505 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
364456 CCCCCTTTGA
*
364466 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
364487 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
364506 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:366468 original size:9 final size:8
Alignment explanation
Indices: 366446--366496 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
366436 TGTTTCAACA
366446 TTTTGGAT
1 TTTTGGAT
366454 ATTTTGGAT
1 -TTTTGGAT
366463 TGTTT-GAT
1 T-TTTGGAT
366471 TTTGTGGAT
1 TTT-TGGAT
*
366480 TGTTGGA-
1 TTTTGGAT
366487 TTTTGGAT
1 TTTTGGAT
366495 TT
1 TT
366497 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:366480 original size:17 final size:17
Alignment explanation
Indices: 366448--366491 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
366438 TTTCAACATT
366448 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
366465 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
366482 TTGGATTTTG
1 TTGGATTTTG
366492 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:367253 original size:75 final size:76
Alignment explanation
Indices: 367080--367287 Score: 278
Period size: 75 Copynumber: 2.7 Consensus size: 76
367070 CAAAGCCAAA
* * * **
367080 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCTCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCC-CCCTAAACAG
367145 TTTTGGCCCCGAG
64 TTTTGGCCCCGAG
*
367158 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
367223 TT-GCTCCGAG
66 TTGGCCCCGAG
* * *
367233 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGTG-GGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAG-GAGGAACCGATTCCCCC
367288 CTTGTACAAC
Statistics
Matches: 118, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
74 16 0.14
75 41 0.35
76 12 0.10
77 24 0.20
78 25 0.21
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TTGGCCCCGAG
Found at i:371545 original size:17 final size:17
Alignment explanation
Indices: 371511--371552 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
371501 CTCTTCCCTT
* *
371511 TCTTT-GAGAGAAATTC
1 TCTTTCGAGAAAAACTC
371527 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
*
371544 TCGTTCGAG
1 TCTTTCGAG
371553 CAATAAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Found at i:379193 original size:21 final size:22
Alignment explanation
Indices: 379167--379214 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
379157 GAAATTACTT
*
379167 TAGCAGGGTATCGGTA-CACTG
1 TAGCAGGGTATCGATACCACTG
*
379188 TAGCAGGGTATCGATACCCCTG
1 TAGCAGGGTATCGATACCACTG
379210 TAGCA
1 TAGCA
379215 TTCTGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (22 bp):
TAGCAGGGTATCGATACCACTG
Found at i:379258 original size:12 final size:12
Alignment explanation
Indices: 379241--379303 Score: 62
Period size: 12 Copynumber: 5.6 Consensus size: 12
379231 CATTCGGTGT
379241 TGTTCATGGTAC
1 TGTTCATGGTAC
*
379253 TGTTCAT--CAC
1 TGTTCATGGTAC
* *
379263 TGTTCACGGTAA
1 TGTTCATGGTAC
379275 TGTTCAT--TAC
1 TGTTCATGGTAC
*
379285 TATTCATGGTAC
1 TGTTCATGGTAC
379297 TGTTCAT
1 TGTTCAT
379304 ACCGTATAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
10 16 0.41
12 23 0.59
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (12 bp):
TGTTCATGGTAC
Found at i:379273 original size:22 final size:22
Alignment explanation
Indices: 379241--379303 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
379231 CATTCGGTGT
379241 TGTTCATGGTACTGTTCATCAC
1 TGTTCATGGTACTGTTCATCAC
* * *
379263 TGTTCACGGTAATGTTCATTAC
1 TGTTCATGGTACTGTTCATCAC
*
379285 TATTCATGGTACTGTTCAT
1 TGTTCATGGTACTGTTCAT
379304 ACCGTATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (22 bp):
TGTTCATGGTACTGTTCATCAC
Found at i:380355 original size:18 final size:18
Alignment explanation
Indices: 380332--380366 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
380322 TATGTGATAT
*
380332 GTGGTCCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
380350 GTGGTCCTTCGGGACAT
1 GTGGTCCTTCGGGACAT
380367 TTCTACATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.34, T:0.31
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:408582 original size:21 final size:21
Alignment explanation
Indices: 408558--408601 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
408548 CAACTCCGAT
**
408558 AATGATTTTGTAAATGTTATA
1 AATGATTTTAAAAATGTTATA
408579 AATGATTTTAAAAATGTTATA
1 AATGATTTTAAAAATGTTATA
408600 AA
1 AA
408602 GAATAGTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.43
Consensus pattern (21 bp):
AATGATTTTAAAAATGTTATA
Found at i:409019 original size:22 final size:22
Alignment explanation
Indices: 408993--409051 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
408983 TAGCCTCACT
408993 AACAAACTAACTAATTAACAAC
1 AACAAACTAACTAATTAACAAC
* *
409015 AACAACCTAACTAATTATCAAC
1 AACAAACTAACTAATTAACAAC
* *
409037 AGCTTAACTAACTAA
1 AAC-AAACTAACTAA
409052 ATATCTGACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 22 0.71
23 9 0.29
ACGTcount: A:0.53, C:0.24, G:0.02, T:0.22
Consensus pattern (22 bp):
AACAAACTAACTAATTAACAAC
Found at i:414416 original size:31 final size:33
Alignment explanation
Indices: 414354--414419 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
414344 TTTTGTGGAC
*
414354 TTGTTCAATCTTTATGTAAAAAATTAAAAATTA
1 TTGTTCAATCTTTAGGTAAAAAATTAAAAATTA
*
414387 TTGTTCAATCTTTAGGT-ACAAA-TAAAAATTA
1 TTGTTCAATCTTTAGGTAAAAAATTAAAAATTA
414418 TT
1 TT
414420 TAAATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 11 0.35
32 4 0.13
33 16 0.52
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (33 bp):
TTGTTCAATCTTTAGGTAAAAAATTAAAAATTA
Found at i:415396 original size:24 final size:25
Alignment explanation
Indices: 415366--415415 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
415356 TTTCTAATTT
415366 TTTTGAAAAAAATT-AATATTTTTA
1 TTTTGAAAAAAATTAAATATTTTTA
* **
415390 TTTTGAATAATTTTAAATATTTTTA
1 TTTTGAAAAAAATTAAATATTTTTA
415415 T
1 T
415416 ATTTTCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
TTTTGAAAAAAATTAAATATTTTTA
Found at i:416217 original size:16 final size:16
Alignment explanation
Indices: 416196--416226 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
416186 TACACCTATG
416196 AGTGTATCGATACACT
1 AGTGTATCGATACACT
416212 AGTGTATCGATACAC
1 AGTGTATCGATACAC
416227 CCTGCAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (16 bp):
AGTGTATCGATACACT
Found at i:417810 original size:60 final size:60
Alignment explanation
Indices: 417714--417831 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
417704 ATAGTTGGAT
* * * *
417714 GGCCATTTTGTAACCTTTAATAGTTGAGGAACTCAATAAAATAACA-TCCTATAGTCAGAG
1 GGCCATTTTGTAACCTTTAATAGTTCAGAAAATCAATAAAACAACACT-CTATAGTCAGAG
*
417774 GGCCATTTTGTAACTTTTAATAG-TCAGAATAATCAATAAAACAACACTCTATAGTCAG
1 GGCCATTTTGTAACCTTTAATAGTTCAGAA-AATCAATAAAACAACACTCTATAGTCAG
417832 GGTATCATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 4 0.08
60 46 0.90
61 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (60 bp):
GGCCATTTTGTAACCTTTAATAGTTCAGAAAATCAATAAAACAACACTCTATAGTCAGAG
Found at i:418549 original size:23 final size:25
Alignment explanation
Indices: 418496--418550 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
418486 TGGTATCACA
418496 TTAATAAAAAAAATACATTGAAACT
1 TTAATAAAAAAAATACATTGAAACT
* * *
418521 TAAATAAAAATAAT-CATT-AAAGT
1 TTAATAAAAAAAATACATTGAAACT
418544 TTAATAA
1 TTAATAA
418551 TATATCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 10 0.38
24 4 0.15
25 12 0.46
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (25 bp):
TTAATAAAAAAAATACATTGAAACT
Found at i:419684 original size:22 final size:23
Alignment explanation
Indices: 419644--419698 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
419634 TTTGACCAGA
* *
419644 GTTGACTGTTGACCGGTCTTACC
1 GTTGACTGTTGACAGGTCTGACC
*
419667 GTTGACT-TTGACATGTCTGACC
1 GTTGACTGTTGACAGGTCTGACC
419689 GTTGACTGTT
1 GTTGACTGTT
419699 TAATTTAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
GTTGACTGTTGACAGGTCTGACC
Found at i:424266 original size:7 final size:8
Alignment explanation
Indices: 424243--424282 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
424233 ACTTGAAGAA
424243 AAAAAGAAT
1 AAAAA-AAT
424252 GAAAAAAAT
1 -AAAAAAAT
424261 AAAAAAAT
1 AAAAAAAT
*
424269 AAAAAAAG
1 AAAAAAAT
424277 AAAAAA
1 AAAAAA
424283 GAGGAAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 21 0.72
9 3 0.10
10 5 0.17
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (8 bp):
AAAAAAAT
Found at i:424290 original size:16 final size:17
Alignment explanation
Indices: 424270--424311 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
424260 TAAAAAAATA
*
424270 AAAAAAGAAA-AAAGAG
1 AAAAAAGAAAGAAAAAG
*
424286 GAAAAAGAAAGAAAAAG
1 AAAAAAGAAAGAAAAAG
424303 AAAAAAGAA
1 AAAAAAGAA
424312 TAAATAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAGAAAAAG
Found at i:424308 original size:8 final size:8
Alignment explanation
Indices: 424252--424308 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
424242 AAAAAAGAAT
424252 GAAAAAAA
1 GAAAAAAA
*
424260 TAAAAAAA
1 GAAAAAAA
*
424268 TAAAAAAA
1 GAAAAAAA
424276 GAAAAAAGA
1 GAAAAAA-A
424285 GGAAAAAGAA
1 -GAAAAA-AA
*
424295 -AGAAAAA
1 GAAAAAAA
424302 GAAAAAA
1 GAAAAAA
424309 GAATAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 2 0.05
8 30 0.73
9 1 0.02
10 7 0.17
11 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (8 bp):
GAAAAAAA
Found at i:425704 original size:138 final size:138
Alignment explanation
Indices: 425244--425735 Score: 555
Period size: 138 Copynumber: 3.6 Consensus size: 138
425234 TCATCAACTA
* * * * *
425244 CGACCAGATCTCCTCAACAAGTAGGAGCAGCTTCATCCTTAGATAACCAAACTTCCTCATCACGT
1 CGACAAGATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGT
* * * *
425309 AGGAACTGTGTTATCTCCATTTATCCCTAAAGATGGCTAGTCATCTTCATCACGTAGTAATAATG
66 AGGAACCGTGTTATCTCCATTTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAATAATG
*
425374 TCGTCCAC
131 TTGTCCAC
* * * * * * ** * * *
425382 CGAAAAAATATGCTCATCATGTAGGAGGAGCGTCATCCACATATAACCAGACTTCCTCATTAGGT
1 CGACAAGATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGT
* * * * *
425447 AGGAATCGTGTTATCTCTATTTATCCCTAAAGATGACTAGACGTCCTC-T-AC----GAACAATG
66 AGGAACCGTGTTATCTCCATTTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAATAATG
425506 TTGTCCAC
131 TTGTCCAC
* * *
425514 TGACCAGATCTCCTCATCACGTAGGAGTAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGT
1 CGACAAGATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGT
* * *
425579 TGGAACCGTGTTATCTCCATTTATCCCTAATGATGGCTAAACATCCTCATCACGTAGGAATAATG
66 AGGAACCGTGTTATCTCCATTTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAATAATG
425644 TTGTCCAC
131 TTGTCCAC
* * * * * * **
425652 CGACTAGATCTCCTCATCGCGTAGGAGCAGTGCCGTCCTTAGACAATTAGACTTCCTCATCACGT
1 CGACAAGATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGT
* * *
425717 AAGAACCATGTTGTCTCCA
66 AGGAACCGTGTTATCTCCA
425736 AAATTATTTC
Statistics
Matches: 288, Mismatches: 60, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
132 106 0.37
133 1 0.00
134 2 0.01
136 2 0.01
137 1 0.00
138 176 0.61
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (138 bp):
CGACAAGATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGT
AGGAACCGTGTTATCTCCATTTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAATAATG
TTGTCCAC
Found at i:425999 original size:3 final size:3
Alignment explanation
Indices: 425991--426066 Score: 138
Period size: 3 Copynumber: 26.0 Consensus size: 3
425981 CTAACTTTGT
425991 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
426038 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
426067 ATCTTTTTAC
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.06
3 67 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:426768 original size:19 final size:19
Alignment explanation
Indices: 426718--426771 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
426708 AACAAAAAAA
* *
426718 AAAACAATATAGAAAAACC
1 AAAACAAAAAAGAAAAACC
* *
426737 AAAA-AAATTAAGAACAACC
1 AAAACAAA-AAAGAAAAACC
426756 AAAACAAAAAAGAAAA
1 AAAACAAAAAAGAAAA
426772 TAACTGATAG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 2 0.07
19 22 0.81
20 3 0.11
ACGTcount: A:0.74, C:0.13, G:0.06, T:0.07
Consensus pattern (19 bp):
AAAACAAAAAAGAAAAACC
Found at i:427719 original size:2 final size:2
Alignment explanation
Indices: 427712--427756 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
427702 TTATTATGCC
427712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
427754 AT A
1 AT A
427757 CTTAATAGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:427863 original size:2 final size:2
Alignment explanation
Indices: 427856--427902 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
427846 ATAGTTTTTC
427856 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
427898 TA TA T
1 TA TA T
427903 GCACTCGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:432954 original size:3 final size:3
Alignment explanation
Indices: 432946--433040 Score: 147
Period size: 3 Copynumber: 31.7 Consensus size: 3
432936 TTAATATATT
*
432946 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
432994 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA T-A TGGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
433039 TA
1 TA
433041 TGGATAAAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
2 2 0.02
3 81 0.95
4 2 0.02
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:433416 original size:40 final size:40
Alignment explanation
Indices: 433372--433474 Score: 206
Period size: 40 Copynumber: 2.6 Consensus size: 40
433362 AAGTTGAACA
433372 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
1 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
433412 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
1 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
433452 AGTTCTTCTTATTATGAACTTCT
1 AGTTCTTCTTATTATGAACTTCT
433475 CTGGAAAAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.18, C:0.19, G:0.10, T:0.52
Consensus pattern (40 bp):
AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
Found at i:433646 original size:113 final size:113
Alignment explanation
Indices: 433414--433923 Score: 808
Period size: 113 Copynumber: 4.5 Consensus size: 113
433404 TTCAGATGAG
* * *
433414 TTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
433478 GAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAA
433526 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
433591 GAAAGGCTGATCCATCAAATGAT-AGACTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGATGA-ATTCAGGTAAAAGGTTGAACAAA
*
433639 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* ***
433704 GAAAAGTTAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAA
*
433752 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * **
433817 GAAAAGATAATTCATCAAGTGATAGATTTAAGCAAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGAT-GAATTCAGGTAAAAGGTTGAACAAA
433866 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
433924 CGAACTGGAA
Statistics
Matches: 367, Mismatches: 27, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
112 55 0.15
113 234 0.64
114 78 0.21
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAA
Found at i:434754 original size:84 final size:84
Alignment explanation
Indices: 434646--435067 Score: 783
Period size: 84 Copynumber: 5.0 Consensus size: 84
434636 GATCATGCAG
* * *
434646 TTCATCTT-TTAATTCCAACGATTGGTTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCC
1 TTCATCTTCTAAATT-CAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCC
434710 AGAAGATGCTATTGAGCACA
65 AGAAGATGCTATTGAGCACA
*
434730 TTCATCTTCTAAATTCAATGATTGGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
434795 GAAGATGCTATTGAGCACA
66 GAAGATGCTATTGAGCACA
*
434814 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
434879 GAAGATGCTATTGAGCACA
66 GAAGATGCTATTGAGCACA
434898 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
434963 GAAGATGCTATTGAGCACA
66 GAAGATGCTATTGAGCACA
434982 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
435047 GAAGATGCTATTGAGCACA
66 GAAGATGCTATTGAGCACA
435066 TT
1 TT
435068 ATATTTGTTC
Statistics
Matches: 330, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
84 325 0.98
85 5 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (84 bp):
TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATTGAGCACA
Found at i:436241 original size:11 final size:10
Alignment explanation
Indices: 436215--436251 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
436205 TGACCCCCTT
*
436215 TCTTTTTTCT
1 TCTTTTTTCC
436225 TCTTTTTTCC
1 TCTTTTTTCC
436235 TCTTTTTT--
1 TCTTTTTTCC
436243 TCTTTTTTC
1 TCTTTTTTC
436252 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
8 8 0.32
10 17 0.68
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TCTTTTTTCC
Found at i:436245 original size:28 final size:27
Alignment explanation
Indices: 436212--436312 Score: 127
Period size: 28 Copynumber: 3.7 Consensus size: 27
436202 CCTTGACCCC
436212 CTTTCTTTTTTCT-TCTTTTTTCCTCTTT
1 CTTTCTTTTTTCTAT-TTTTTT-CTCTTT
* *
436240 TTTTCTTTTTTCTATTTTTTTTTCTATT
1 CTTTCTTTTTTCTATTTTTTTCTCT-TT
436268 CTTTCTTTTTTCTATTTTCTTTCT-TTT
1 CTTTCTTTTTTCTATTTT-TTTCTCTTT
436295 CTTTCTTTTTTCT-TTTTT
1 CTTTCTTTTTTCTATTTTT
436313 CTTCAAGCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
25 1 0.02
26 4 0.06
27 18 0.27
28 38 0.58
29 5 0.08
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (27 bp):
CTTTCTTTTTTCTATTTTTTTCTCTTT
Found at i:436312 original size:18 final size:18
Alignment explanation
Indices: 436213--436315 Score: 99
Period size: 18 Copynumber: 5.7 Consensus size: 18
436203 CTTGACCCCC
436213 TTTCTTTTTTC-TTCTTT
1 TTTCTTTTTTCTTTCTTT
*
436230 TTTCCTCTTTT-TTTCTTT
1 TTT-CTTTTTTCTTTCTTT
*
436248 TTTCTATTTTTTTTTCTATT
1 TTTCT-TTTTTCTTTCT-TT
*
436268 CTTTCTTTTTTCTATT-TTC
1 -TTTCTTTTTTCT-TTCTTT
436287 TTTC--TTTTCTTTCTTT
1 TTTCTTTTTTCTTTCTTT
436303 TTTCTTTTTTCTT
1 TTTCTTTTTTCTT
436316 CAAGCATAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
15 2 0.03
16 12 0.17
17 5 0.07
18 30 0.42
19 6 0.08
20 9 0.13
21 7 0.10
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTCTTTTTTCTTTCTTT
Found at i:436313 original size:27 final size:27
Alignment explanation
Indices: 436213--436315 Score: 131
Period size: 27 Copynumber: 3.9 Consensus size: 27
436203 CTTGACCCCC
* *
436213 TTTCTTT-TTTCTTCTTTTTTC-CTCT
1 TTTCTTTCTTTTTTCTTTTTTCTTTCT
*
436238 TTT-TTTCTTTTTTCTATTTTTTTTTCT
1 TTTCTTTCTTTTTTCT-TTTTTCTTTCT
* *
436265 ATTCTTTCTTTTTTCTATTTTCTTTCT
1 TTTCTTTCTTTTTTCTTTTTTCTTTCT
436292 TTTCTTTCTTTTTTCTTTTTTCTT
1 TTTCTTTCTTTTTTCTTTTTTCTT
436316 CAAGCATAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
24 3 0.05
25 10 0.15
26 5 0.08
27 36 0.55
28 12 0.18
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTCTTTCTTTTTTCTTTTTTCTTTCT
Found at i:443587 original size:14 final size:15
Alignment explanation
Indices: 443568--443599 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
443558 ATTTTTTTCA
443568 AATTTTAA-TTAATG
1 AATTTTAACTTAATG
443582 AATTTTAACTTAATG
1 AATTTTAACTTAATG
443597 AAT
1 AAT
443600 AAAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (15 bp):
AATTTTAACTTAATG
Found at i:446971 original size:18 final size:19
Alignment explanation
Indices: 446941--446985 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
446931 TGCAAATAAA
446941 ATAAAACAT-ATAAATAT-T
1 ATAAAA-ATAATAAATATAT
*
446959 ATGAAAATAATAAATATAT
1 ATAAAAATAATAAATATAT
446978 ATAAAAAT
1 ATAAAAAT
446986 TTTAAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 13 0.57
19 8 0.35
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAATAATAAATATAT
Found at i:449100 original size:3 final size:3
Alignment explanation
Indices: 449092--449183 Score: 175
Period size: 3 Copynumber: 30.7 Consensus size: 3
449082 TTAATATAGT
449092 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
449140 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
449184 TGGATAAAAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:449481 original size:14 final size:14
Alignment explanation
Indices: 449464--449496 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
449454 ATTTCTATGT
*
449464 AGGGAATTATTTGC
1 AGGGAATTATTTAC
449478 AGGGAATTATTTAC
1 AGGGAATTATTTAC
449492 AGGGA
1 AGGGA
449497 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:449719 original size:3 final size:3
Alignment explanation
Indices: 449711--449735 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
449701 AATCAGAGTT
449711 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
449736 GAGTCTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:453902 original size:10 final size:10
Alignment explanation
Indices: 453883--453949 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 10
453873 AATTTAAATA
453883 ATAAACGAAC
1 ATAAACGAAC
*
453893 ATAAATGAAC
1 ATAAACGAAC
*
453903 ACGAACGAACGAAC
1 A-TAA---ACGAAC
453917 ATAAACGAACAC
1 ATAAACG-A-AC
453929 AATAAACGAAC
1 -ATAAACGAAC
453940 ATAAACGAAC
1 ATAAACGAAC
453950 TACACAAACA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 23 0.50
11 5 0.11
12 3 0.07
13 9 0.20
14 6 0.13
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:453958 original size:23 final size:23
Alignment explanation
Indices: 453885--453958 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
453875 TTTAAATAAT
*
453885 AAACGAACATAAATGAACACGAAC
1 AAACGAACATAAACGAACAC-AAC
* *
453909 GAACGAACATAAACGAACACAAT
1 AAACGAACATAAACGAACACAAC
453932 AAACGAACATAAACGAACTAC-AC
1 AAACGAACATAAACGAAC-ACAAC
453955 AAAC
1 AAAC
453959 ACAAAAAAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
23 24 0.55
24 20 0.45
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (23 bp):
AAACGAACATAAACGAACACAAC
Found at i:454298 original size:6 final size:6
Alignment explanation
Indices: 454287--454315 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
454277 AAGAGCCCTT
454287 TGTTCA TGTTCA TGTTCA TGTTCA TGTTC
1 TGTTCA TGTTCA TGTTCA TGTTCA TGTTC
454316 GTCCATTTAA
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:0.14, C:0.17, G:0.17, T:0.52
Consensus pattern (6 bp):
TGTTCA
Found at i:455071 original size:12 final size:13
Alignment explanation
Indices: 455040--455086 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
455030 GTTATTTTTA
* *
455040 AAATTTTAATATAA
1 AAATATTAATA-AT
*
455054 AAATATTAAT-TT
1 AAATATTAATAAT
455066 AAATATTAATAAT
1 AAATATTAATAAT
455079 AAATATTA
1 AAATATTA
455087 TGTAATTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 10 0.36
13 9 0.32
14 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATATTAATAAT
Found at i:455936 original size:28 final size:31
Alignment explanation
Indices: 455880--455947 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
455870 TATATAAAAT
*
455880 TATTTT-AAATATTTATAAGTTTAA-CT-TA
1 TATTTTAAAATATTTATAAGTATAATCTATA
*
455908 TATTTTAAAATAATTTAT-A-TATAATTTATA
1 TATTTTAAAAT-ATTTATAAGTATAATCTATA
455938 TATTTTAAAA
1 TATTTTAAAA
455948 GATGAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 10 0.29
29 6 0.18
30 18 0.53
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
TATTTTAAAATATTTATAAGTATAATCTATA
Found at i:456767 original size:21 final size:21
Alignment explanation
Indices: 456743--456782 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
456733 TGTATCATAC
456743 ATACATCAGA-CATATATATAT
1 ATACA-CAGATCATATATATAT
*
456764 ATACACATATCATATATAT
1 ATACACAGATCATATATAT
456783 GTACATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (21 bp):
ATACACAGATCATATATATAT
Found at i:456792 original size:21 final size:21
Alignment explanation
Indices: 456753--456792 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
456743 ATACATCAGA
*
456753 CATATATATATATACACATAT
1 CATATATATATACACACATAT
* *
456774 CATATATATGTACATACAT
1 CATATATATATACACACAT
456793 CGTTGATCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (21 bp):
CATATATATATACACACATAT
Found at i:456847 original size:20 final size:20
Alignment explanation
Indices: 456822--456897 Score: 93
Period size: 20 Copynumber: 3.7 Consensus size: 20
456812 CATATATATA
456822 TATATATATACTTAATTACT
1 TATATATATACTTAATTACT
456842 TATATATATATGCTTAATTACT
1 TATATATATA--CTTAATTACT
456864 TATATATATAC-TAATGTA-T
1 TATATATATACTTAAT-TACT
*
456883 ATATATACATACTTA
1 -TATATATATACTTA
456898 CACACACACA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
19 5 0.10
20 23 0.46
21 2 0.04
22 20 0.40
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (20 bp):
TATATATATACTTAATTACT
Found at i:456848 original size:22 final size:22
Alignment explanation
Indices: 456820--456873 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
456810 TACATATATA
456820 TATATATATATACTTAATTACT
1 TATATATATATACTTAATTACT
*
456842 TATATATATATGCTTAATTACT
1 TATATATATATACTTAATTACT
456864 TATATATATA
1 TATATATATA
456874 CTAATGTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
TATATATATATACTTAATTACT
Found at i:456889 original size:22 final size:22
Alignment explanation
Indices: 456816--456897 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
456806 TAATTACATA
456816 TATATATATATATATACTTAAT
1 TATATATATATATATACTTAAT
*
456838 TACT-TATATATATATGCTTAAT
1 TA-TATATATATATATACTTAAT
*
456860 TA-CT-TATATATATAC-TAA-
1 TATATATATATATATACTTAAT
* *
456878 TGTATATATATACATACTTA
1 TATATATATATATATACTTA
456898 CACACACACA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
18 1 0.02
19 4 0.08
20 20 0.40
21 3 0.06
22 21 0.42
23 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (22 bp):
TATATATATATATATACTTAAT
Found at i:456914 original size:2 final size:2
Alignment explanation
Indices: 456909--457039 Score: 64
Period size: 2 Copynumber: 67.5 Consensus size: 2
456899 ACACACACAC
* * **
456909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA ACT GT GC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
** * *
456951 A- AGT AT AT AT GC AT AT AC AT AT ACT -T AT AT AT AT TT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
**
456993 GC AT A- AT -T AT AT A- AGT AT A- AT AT A- AGT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT
457032 AT AT -T AT A
1 AT AT AT AT A
457040 AGTATAACGT
Statistics
Matches: 97, Mismatches: 18, Indels: 28
0.68 0.13 0.20
Matches are distributed among these distances:
1 9 0.09
2 84 0.87
3 4 0.04
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:461557 original size:2 final size:2
Alignment explanation
Indices: 461505--461542 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
461495 TAATTGAAAT
461505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
461543 ACTTCAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:469044 original size:21 final size:21
Alignment explanation
Indices: 468998--469047 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
468988 CATAATTTGC
*
468998 ATATGTGAGGTTGCTTGAATT
1 ATATTTGAGGTTGCTTGAATT
469019 ATATTTGAGGTTGCTTGAATT
1 ATATTTGAGGTTGCTTGAATT
469040 ATATTTGA
1 ATATTTGA
469048 ATCAATGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (21 bp):
ATATTTGAGGTTGCTTGAATT
Found at i:476238 original size:14 final size:14
Alignment explanation
Indices: 476191--476238 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
476181 GTGCTTTCAA
476191 CTTTTCTTGTTT-TT
1 CTTTTCTT-TTTCTT
476205 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
*
476219 CTTTTTTGTTTTCTT
1 CTTTTCT-TTTTCTT
476234 CTTTT
1 CTTTT
476239 GAGTGCTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 3 0.10
14 16 0.52
15 12 0.39
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:477930 original size:90 final size:89
Alignment explanation
Indices: 477819--477985 Score: 298
Period size: 90 Copynumber: 1.9 Consensus size: 89
477809 TAATCTCGAA
* *
477819 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTCAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATATAATTAATTTCAAATAATAAAA-CCCTAATATGAT
477884 TAGGGTAACTTGGATTTAAGAGGAT
65 TAGGGTAACTTGGATTTAAGAGGAT
*
477909 TATTAAATTTCAATTAATTAAATATAGATATAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTTCAATTAATTAAATATAGATATAATTAATTTCAAATAATAAAACCCTAATATGATT
477974 AGGGTAACTTGG
66 AGGGTAACTTGG
477986 CTATAAAAGG
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 25 0.34
90 49 0.66
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.39
Consensus pattern (89 bp):
TATTAAATTTCAATTAATTAAATATAGATATAATTAATTTCAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATTTAAGAGGAT
Found at i:481772 original size:25 final size:26
Alignment explanation
Indices: 481726--481780 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
481716 AAAGAAAGAA
481726 AATAAATGAAAATGAATATAATAAAT
1 AATAAATGAAAATGAATATAATAAAT
* *
481752 AATAAATTACAAT-AATATAATAAAT
1 AATAAATGAAAATGAATATAATAAAT
481777 AATA
1 AATA
481781 TAATACTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (26 bp):
AATAAATGAAAATGAATATAATAAAT
Found at i:481779 original size:12 final size:12
Alignment explanation
Indices: 481735--481785 Score: 68
Period size: 12 Copynumber: 4.1 Consensus size: 12
481725 AAATAAATGA
481735 AAATGAATATAAT
1 AAAT-AATATAAT
481748 AAATAATA-AATT
1 AAATAATATAA-T
481760 ACAATAATATAAT
1 A-AATAATATAAT
481773 AAATAATATAAT
1 AAATAATATAAT
481785 A
1 A
481786 CTATACTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.06
12 18 0.51
13 13 0.37
14 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (12 bp):
AAATAATATAAT
Found at i:481785 original size:20 final size:20
Alignment explanation
Indices: 481735--481790 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
481725 AAATAAATGA
481735 AAATGAATATAATAA-ATAAT
1 AAAT-AATATAATAATATAAT
*
481755 AAAT--TACAATAATATAAT
1 AAATAATATAATAATATAAT
*
481773 AAATAATATAATACTATA
1 AAATAATATAATAATATA
481791 CTATACTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 7 0.23
18 9 0.30
20 14 0.47
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (20 bp):
AAATAATATAATAATATAAT
Found at i:481795 original size:25 final size:26
Alignment explanation
Indices: 481740--481807 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 26
481730 AATGAAAATG
481740 AATATAATAAATAATA-AATTACAAT
1 AATATAATAAATAATATAATTACAAT
*
481765 AATATAATAAATAATATAA-TACTAT
1 AATATAATAAATAATATAATTACAAT
* * *
481790 ACTATACTATATAATATA
1 AATATAATAAATAATATA
481808 TATTTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
AATATAATAAATAATATAATTACAAT
Found at i:481838 original size:37 final size:37
Alignment explanation
Indices: 481797--481995 Score: 170
Period size: 35 Copynumber: 5.6 Consensus size: 37
481787 TATACTATAC
*
481797 TATATAATATATATTTTTAAAATATTTTCAAAAACTA
1 TATATTATATATATTTTTAAAATATTTTCAAAAACTA
* *
481834 TATA-T-TATATATTTTTAAATTTTTTTCAAAAACTA
1 TATATTATATATATTTTTAAAATATTTTCAAAAACTA
*
481869 TATATTAT-T-TA----T---ATGTTTTCAAAAACTA
1 TATATTATATATATTTTTAAAATATTTTCAAAAACTA
* *
481897 TATATTATATATATTTTCAGAATATTTTCAAAAACTA
1 TATATTATATATATTTTTAAAATATTTTCAAAAACTA
* * * *
481934 AATATTATATACATGTTTTCAAAAAAAATTT-AAAAACTA
1 TATATTATATATAT-TTTT--AAAATATTTTCAAAAACTA
* * *
481973 TTTATTATATATGTTTTCAAAAT
1 TATATTATATATATTTTTAAAAT
481996 TTTATATTTT
Statistics
Matches: 129, Mismatches: 19, Indels: 29
0.73 0.11 0.16
Matches are distributed among these distances:
28 22 0.17
29 1 0.01
30 2 0.02
31 1 0.01
35 34 0.26
36 6 0.05
37 32 0.25
38 6 0.05
39 18 0.14
40 7 0.05
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (37 bp):
TATATTATATATATTTTTAAAATATTTTCAAAAACTA
Found at i:481903 original size:28 final size:28
Alignment explanation
Indices: 481839--481910 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
481829 AACTATATAT
* *
481839 TATATATT-TTTAAATTTTTTTCAAAAAC
1 TATATATTATTTATA-TGTTTTCAAAAAC
481867 TATATATTATTTATATGTTTTCAAAAAC
1 TATATATTATTTATATGTTTTCAAAAAC
*
481895 TATATATTATATATAT
1 TATATATTATTTATAT
481911 TTTCAGAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 35 0.88
29 5 0.12
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (28 bp):
TATATATTATTTATATGTTTTCAAAAAC
Found at i:481925 original size:65 final size:63
Alignment explanation
Indices: 481804--481958 Score: 206
Period size: 65 Copynumber: 2.4 Consensus size: 63
481794 TACTATATAA
* *
481804 TATATATT-TTTAAAATATTTTCAAAAACTATATATTATATATTTTTAAATTTTTTTCAAAAAC
1 TATATATTATTT-AAATGTTTTCAAAAACTATATATTATATATTTTTAAATTATTTTCAAAAAC
*
481867 TATATATTATTTATATGTTTTCAAAAACTATATATTATATATATTTTCAGAA-TATTTTCAAAAA
1 TATATATTATTTAAATGTTTTCAAAAACTATATATTATATAT-TTTT-A-AATTATTTTCAAAAA
481931 C
63 C
* * *
481932 TAAATATTATATACATGTTTTCAAAAA
1 TATATATTATTTAAATGTTTTCAAAAA
481959 AAATTTAAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
63 36 0.44
64 7 0.09
65 37 0.45
66 2 0.02
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (63 bp):
TATATATTATTTAAATGTTTTCAAAAACTATATATTATATATTTTTAAATTATTTTCAAAAAC
Found at i:481994 original size:65 final size:64
Alignment explanation
Indices: 481856--481975 Score: 154
Period size: 65 Copynumber: 1.9 Consensus size: 64
481846 TTTTAAATTT
* * * * * *
481856 TTTTCAAAAACTATATATTATTTATATGTTTTCAAAAACTATATATTATATATATTTTCAGAATA
1 TTTTCAAAAACTAAATATTATATACATGTTTTCAAAAAC-AAATATTAAAAATATTTTCAGAATA
481921 TTTTCAAAAACTAAATATTATATACATGTTTTCAAAAA-AAAT-TTAAAAACTATTT
1 TTTTCAAAAACTAAATATTATATACATGTTTTCAAAAACAAATATTAAAAA-TATTT
481976 ATTATATATG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 5 0.10
63 8 0.17
65 35 0.73
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (64 bp):
TTTTCAAAAACTAAATATTATATACATGTTTTCAAAAACAAATATTAAAAATATTTTCAGAATA
Found at i:487985 original size:16 final size:17
Alignment explanation
Indices: 487964--487996 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
487954 AGGTGTCTCA
487964 TTGACT-TTTCAAAACT
1 TTGACTCTTTCAAAACT
*
487980 TTGACTCTTTGAAAACT
1 TTGACTCTTTCAAAACT
487997 CAAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (17 bp):
TTGACTCTTTCAAAACT
Found at i:488577 original size:24 final size:24
Alignment explanation
Indices: 488519--488591 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
488509 TTGCGCATAA
*
488519 AATTTGTAT-CAAAGTGA-CACATAG
1 AATTTGT-TCCAAAG-GACCACGTAG
*
488543 -ATTTGTCCCAAAGGACCACGTAG
1 AATTTGTTCCAAAGGACCACGTAG
* *
488566 AATTTGTTCCAAAAGACCGCGTAG
1 AATTTGTTCCAAAGGACCACGTAG
488590 AA
1 AA
488592 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 2 0.05
23 17 0.41
24 22 0.54
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
AATTTGTTCCAAAGGACCACGTAG
Found at i:496416 original size:24 final size:24
Alignment explanation
Indices: 496382--496495 Score: 95
Period size: 24 Copynumber: 4.8 Consensus size: 24
496372 ACACGGAGAT
496382 ATCAGAAATCA-AAAAAGAATTCAG
1 ATCAGAAATCAGAAAAA-AATTCAG
* * * *
496406 ATCAGATATCATAACAAAATCCAG
1 ATCAGAAATCAGAAAAAAATTCAG
* * *
496430 ATCATAAATCAGAACAAAATTTAG
1 ATCAGAAATCAGAAAAAAATTCAG
* * * *
496454 ATTAGAAATCAGAATAGAATTCAA
1 ATCAGAAATCAGAAAAAAATTCAG
* *
496478 ATCAGAAACCAGATAAAA
1 ATCAGAAATCAGAAAAAA
496496 TATTTATGTG
Statistics
Matches: 70, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
24 66 0.94
25 4 0.06
ACGTcount: A:0.55, C:0.14, G:0.11, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAAAAAAATTCAG
Found at i:496882 original size:27 final size:27
Alignment explanation
Indices: 496837--496924 Score: 122
Period size: 27 Copynumber: 3.3 Consensus size: 27
496827 ATTCTTATCC
***
496837 ATAGATCATCTTGGGAATCATCACTGA
1 ATAGATCATCTTCAAAATCATCACTGA
*
496864 ATAGATCATTTTCAAAATCATCACTGA
1 ATAGATCATCTTCAAAATCATCACTGA
**
496891 ATAGATCATCTTCGGAATCATCACTGA
1 ATAGATCATCTTCAAAATCATCACTGA
496918 ATAGATC
1 ATAGATC
496925 TTAAGGAAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (27 bp):
ATAGATCATCTTCAAAATCATCACTGA
Found at i:498853 original size:24 final size:25
Alignment explanation
Indices: 498815--498862 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
498805 TCAACGGTGG
498815 TCAATGGTAGCCAAT-GGTCAACGA
1 TCAATGGTAGCCAATAGGTCAACGA
* * *
498839 TCAATGGTGGTCAATAGGTTAACG
1 TCAATGGTAGCCAATAGGTCAACG
498863 GGTCAACGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (25 bp):
TCAATGGTAGCCAATAGGTCAACGA
Found at i:501000 original size:12 final size:12
Alignment explanation
Indices: 500973--501065 Score: 55
Period size: 12 Copynumber: 7.8 Consensus size: 12
500963 ACGGAGATAT
* *
500973 CAGAAATCAAAA
1 CAGAATTCATAA
* *
500985 CAGAATTCAGAT
1 CAGAATTCATAA
500997 CAG-ATATCATAA
1 CAGAAT-TCATAA
* *
501009 CAGAATCCATAT
1 CAGAATTCATAA
*
501021 CAGAAATCATAA
1 CAGAATTCATAA
* *
501033 CCGAATTCAGATA
1 CAGAATTCATA-A
* *
501046 -AGAAATCACAA
1 CAGAATTCATAA
501057 CAGAATTCA
1 CAGAATTCA
501066 AATTATAAAT
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
11 3 0.05
12 54 0.90
13 3 0.05
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (12 bp):
CAGAATTCATAA
Found at i:501005 original size:24 final size:24
Alignment explanation
Indices: 500971--501079 Score: 128
Period size: 24 Copynumber: 4.5 Consensus size: 24
500961 ACACGGAGAT
*
500971 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* * *
500995 ATCAGATATCATAACAGAATCCAT
1 ATCAGAAATCATAACAGAATTCAG
*
501019 ATCAGAAATCATAACCGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* * *
501043 ATAAGAAATCACAACAGAATTCAA
1 ATCAGAAATCATAACAGAATTCAG
* *
501067 ATTATAAATCATA
1 ATCAGAAATCATA
501080 TTAAACATAT
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATTCAG
Found at i:501040 original size:48 final size:48
Alignment explanation
Indices: 500969--501062 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
500959 GTACACGGAG
* * *
500969 ATATCAGAAATCAAAACAGAATTCAGATCAGATATCATAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTCAGATAAGAAATCACAACAGAATCC
* *
501017 ATATCAGAAATCATAACCGAATTCAGATAAGAAATCACAACAGAAT
1 ATATCAGAAATCAAAACAGAATTCAGATAAGAAATCACAACAGAAT
501063 TCAAATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAGATAAGAAATCACAACAGAATCC
Found at i:501466 original size:27 final size:27
Alignment explanation
Indices: 501436--501523 Score: 133
Period size: 27 Copynumber: 3.3 Consensus size: 27
501426 ATTCTTATCC
*
501436 ATAGATCTTCTTCGAAATCATCACTGA
1 ATAGATCATCTTCGAAATCATCACTGA
501463 ATAGATCATCTTC-AGAATCATCACTGA
1 ATAGATCATCTTCGA-AATCATCACTGA
* *
501490 ATATATAATCTTCGAAATCATCACTGA
1 ATAGATCATCTTCGAAATCATCACTGA
501517 ATAGATC
1 ATAGATC
501524 TTAAGGAAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.02
27 52 0.96
28 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (27 bp):
ATAGATCATCTTCGAAATCATCACTGA
Found at i:508875 original size:6 final size:6
Alignment explanation
Indices: 508864--508959 Score: 171
Period size: 6 Copynumber: 16.5 Consensus size: 6
508854 GACACGTATT
508864 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
508912 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
508957 ACC
1 ACC
508960 CGAGACGAGA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.17
6 75 0.83
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:509512 original size:6 final size:5
Alignment explanation
Indices: 509453--509508 Score: 85
Period size: 5 Copynumber: 10.6 Consensus size: 5
509443 CCGTCTCGTC
509453 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG
509506 TCG
1 TCG
509509 TGGTAATACG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 33 0.66
6 17 0.34
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:509670 original size:20 final size:19
Alignment explanation
Indices: 509610--509960 Score: 250
Period size: 20 Copynumber: 17.2 Consensus size: 19
509600 ATTTACTCAT
509610 TTTCTGAATCGCGCGTTGCGA
1 TTTCTGAAT--CGCGTTGCGA
*
509631 -TTCTTGGAAGATCGCATTGCGA
1 TTTC-T-G-A-ATCGCGTTGCGA
509653 TTTACTGAATCGCGTTGCGA
1 TTT-CTGAATCGCGTTGCGA
*
509673 TTTTCTTAATCGCGTTGCGA
1 -TTTCTGAATCGCGTTGCGA
509693 -TTCTTGGAAGATCGCGTTGCGA
1 TTTC-T-G-A-ATCGCGTTGCGA
509715 -TTCTTGGAATCGCGTTGCGA
1 TTTC-T-GAATCGCGTTGCGA
509735 -TTCTTGGAATCGCGTTGCGA
1 TTTC-T-GAATCGCGTTGCGA
509755 TTTTCTGAATCGCGTTGCGA
1 -TTTCTGAATCGCGTTGCGA
*
509775 TTTTCTTAATCGCGTTGCGA
1 -TTTCTGAATCGCGTTGCGA
509795 -TTCTTGGAAGATCGCGTTGCGA
1 TTTC-T-G-A-ATCGCGTTGCGA
509817 TTTTCTGAATCGCGTTGCGA
1 -TTTCTGAATCGCGTTGCGA
509837 TTTTCTGAATCGCGTTGCGA
1 -TTTCTGAATCGCGTTGCGA
* *
509857 TTTTATGAATCGCATTGCGA
1 -TTTCTGAATCGCGTTGCGA
509877 TTAT-TGGAAGATCGCGTTGCGA
1 TT-TCT-G-A-ATCGCGTTGCGA
** * *
509899 TCTTCT-TTTCAACGTTGCGCT
1 T-TTCTGAATC-GCGTTGCG-A
* *
509920 TTTCTAAATCGCGTTGCGG
1 TTTCTGAATCGCGTTGCGA
509939 TTT-TGATATCGCGTTGCGA
1 TTTCTGA-ATCGCGTTGCGA
509958 TTT
1 TTT
509961 TGTTGGTCAT
Statistics
Matches: 282, Mismatches: 19, Indels: 60
0.78 0.05 0.17
Matches are distributed among these distances:
18 8 0.03
19 24 0.09
20 164 0.58
21 14 0.05
22 59 0.21
23 7 0.02
24 6 0.02
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (19 bp):
TTTCTGAATCGCGTTGCGA
Found at i:509707 original size:62 final size:61
Alignment explanation
Indices: 509621--509961 Score: 333
Period size: 62 Copynumber: 5.6 Consensus size: 61
509611 TTCTGAATCG
* *
509621 CGCGTTGCGATTCTTGGAAGATCGCATTGCGATTTACTGAATCGCGTTGCGATTTTCTTAAT
1 CGCGTTGCGATT-TTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTTAAT
*
509683 CGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTT-GGAATCGCGTTGCGA--TTCTTGGAAT
1 CGCGTTGCGATT-TTGGAAGATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTTTCTT--AAT
* * ***
509745 CGCGTTGCGATTTTCTG-A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAGAT
1 CGCGTTGCGATTTT-GGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTCTTA-AT
* * *
509807 CGCGTTGCGATTTTCTG-A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTATGAAT
1 CGCGTTGCGATTTT-GGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTTAAT
* * ** * * *
509867 CGCATTGCGATTATTGGAAGATCGCGTTGCGATCTTCT-TTTCAACGTTGCGCTTTTCTAAAT
1 CGCGTTGCGATT-TTGGAAGATCGCGTTGCGATTTTCTGAATC-GCGTTGCGATTTTCTTAAT
* *
509929 CGCGTTGCGGTTTT-G-ATATCGCGTTGCGATTTT
1 CGCGTTGCGATTTTGGAAGATCGCGTTGCGATTTT
509962 GTTGGTCATT
Statistics
Matches: 240, Mismatches: 26, Indels: 29
0.81 0.09 0.10
Matches are distributed among these distances:
59 18 0.08
60 47 0.20
61 14 0.06
62 158 0.66
63 3 0.01
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (61 bp):
CGCGTTGCGATTTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTTAAT
Found at i:509760 original size:82 final size:80
Alignment explanation
Indices: 509621--509959 Score: 393
Period size: 82 Copynumber: 4.2 Consensus size: 80
509611 TTCTGAATCG
* *
509621 CGCGTTGCGATTCTTGGAAGATCGCATTGCGATTTACTGAATCGCGTTGCGATTTTCTTAATCGC
1 CGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTT--TGAATCGCGTTGCGATTTTCTGAATCGC
509686 GTTGCGATTCTTGGAAGAT
64 GTTGCGATT-TT-GAAGAT
509705 CGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGC
1 CGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TT-GAATCGCGTTGCGATTTTCTGAATCGC
**
509768 GTTGCGATTTTCTTA-AT
64 GTTGCGATTTT-GAAGAT
509785 CGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTGAATCGC
1 CGCGTTGCGATTCTTGGAAGATCGCGTTGCGA-TTT-TGAATCGCGTTGCGATTTTCTGAATCGC
*
509850 GTTGCGATTTT-ATGAAT
64 GTTGCGATTTTGAAG-AT
* * ** * * *
509867 CGCATTGCGATTATTGGAAGATCGCGTTGCGATCTTCT-TTTCAACGTTGCGCTTTTCTAAATCG
1 CGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT-TT-TGAATC-GCGTTGCGATTTTCTGAATCG
* *
509931 CGTTGCGGTTTTG-ATAT
63 CGTTGCGATTTTGAAGAT
509948 CGCGTTGCGATT
1 CGCGTTGCGATT
509960 TTGTTGGTCA
Statistics
Matches: 226, Mismatches: 18, Indels: 25
0.84 0.07 0.09
Matches are distributed among these distances:
80 19 0.08
81 21 0.09
82 164 0.73
83 5 0.02
84 17 0.08
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (80 bp):
CGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTGAATCGCGTTGCGATTTTCTGAATCGCGT
TGCGATTTTGAAGAT
Found at i:509799 original size:102 final size:102
Alignment explanation
Indices: 509621--509878 Score: 412
Period size: 102 Copynumber: 2.5 Consensus size: 102
509611 TTCTGAATCG
* *
509621 CGCGTTGCGATTCTTGGAAGATCGCATTGCGATTTACTGAATCGCGTTGCGATTTTCTTAATCGC
1 CGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTTAATCGC
509686 GTTGCGATTCTTGGAAGATCGCGTTGCGATTCTT-GGAAT
64 GTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTCGGAAT
509725 CGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTTAATCGCGT
1 CGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTTAATCGCGT
*
509790 TGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAAT
66 TGCGATTCTTGGAAGATCGCGTTGCGATTTTCGGAAT
* * *
509827 CGCGTTGCGATT-TTCTGAATCGCGTTGCGATTTTATGAATCGCATTGCGATT
1 CGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT
509879 ATTGGAAGAT
Statistics
Matches: 146, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
101 4 0.03
102 124 0.85
103 1 0.01
104 17 0.12
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.37
Consensus pattern (102 bp):
CGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTTAATCGCGT
TGCGATTCTTGGAAGATCGCGTTGCGATTTTCGGAAT
Found at i:513824 original size:20 final size:20
Alignment explanation
Indices: 513785--513825 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
513775 GAATTCCACC
**
513785 ATATGCAACTATATGCTCCT
1 ATATGCAACTATATAATCCT
*
513805 ATATGCATCTATATAATCCT
1 ATATGCAACTATATAATCCT
513825 A
1 A
513826 AATGGGCTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (20 bp):
ATATGCAACTATATAATCCT
Found at i:515228 original size:24 final size:24
Alignment explanation
Indices: 515201--515251 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
515191 TGGTTCTTCC
515201 TCATCGACT-GGCTGGTGAGCATCT
1 TCATCG-CTGGGCTGGTGAGCATCT
* *
515225 TCATTGGTGGGCTGGTGAGCATCT
1 TCATCGCTGGGCTGGTGAGCATCT
515249 TCA
1 TCA
515252 GATGCTTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (24 bp):
TCATCGCTGGGCTGGTGAGCATCT
Found at i:516311 original size:20 final size:18
Alignment explanation
Indices: 516274--516320 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
516264 TGAAGAAGAA
*
516274 GAAGAAATAAAGCAAAGT
1 GAAGAAATAAAACAAAGT
516292 GAAGAAGATAAGAACAAAGT
1 GAAGAA-ATAA-AACAAAGT
*
516312 GAAAAAATA
1 GAAGAAATA
516321 GGGGGTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.24
19 7 0.28
20 12 0.48
ACGTcount: A:0.64, C:0.04, G:0.21, T:0.11
Consensus pattern (18 bp):
GAAGAAATAAAACAAAGT
Found at i:524174 original size:20 final size:21
Alignment explanation
Indices: 524151--524189 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
524141 AACTTTCTAT
524151 TTTG-AAAAGGATCAATCCAC
1 TTTGAAAAAGGATCAATCCAC
*
524171 TTTGAAAAAGGATCGATCC
1 TTTGAAAAAGGATCAATCC
524190 TTTCGATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (21 bp):
TTTGAAAAAGGATCAATCCAC
Found at i:525616 original size:2 final size:2
Alignment explanation
Indices: 525609--525640 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
525599 AAGAAACAGA
525609 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
525641 TAAAACAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:534212 original size:23 final size:23
Alignment explanation
Indices: 534173--534217 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
534163 ATAAATATGC
*
534173 TTATTTCATATGTTATAATATAA
1 TTATTTCATATGATATAATATAA
*
534196 TTATTATCATAT-ATATATTATA
1 TTATT-TCATATGATATAATATA
534218 TCTATGGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATTTCATATGATATAATATAA
Found at i:545108 original size:40 final size:40
Alignment explanation
Indices: 545064--545144 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
545054 TTGTTCCCTT
*
545064 AGTTTCTTATCATTTATTCAACTTTCTCACTAACCAAACA
1 AGTTTCTTAGCATTTATTCAACTTTCTCACTAACCAAACA
* *
545104 AGTTTCTTAGCATTTCTTGAACTTTCTCACTAACCAAACA
1 AGTTTCTTAGCATTTATTCAACTTTCTCACTAACCAAACA
545144 A
1 A
545145 CCAAGTATAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (40 bp):
AGTTTCTTAGCATTTATTCAACTTTCTCACTAACCAAACA
Found at i:545189 original size:17 final size:18
Alignment explanation
Indices: 545162--545203 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
545152 TACATGAAAA
*
545162 TAAACTTAAAAATTAAAC
1 TAAACTAAAAAATTAAAC
545180 -AAACTAAAAAATTAAAC
1 TAAACTAAAAAATTAAAC
545197 TAAACTA
1 TAAACTA
545204 TTAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAACTAAAAAATTAAAC
Done.