Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008113.1 Hibiscus syriacus cultivar Beakdansim tig00110652_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: 992058
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 5
Found at i:164834 original size:64 final size:63
Alignment explanation
Indices: 164701--164861 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
164691 TAATGGAGGT
* * * *
164701 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTCCA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * * * *
164766 ATGCATCGATTCACTCCTTATGCATCGATGCATAAATCCTATTCGATTTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCCATATGCATCGATGCATAAATCCTATTCGA-TGTTTCTATTT-AATGGA
* *
164830 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTCCATATGCATCGATGCA
164862 CCTTAAATAA
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 55 0.68
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTCCATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:170996 original size:23 final size:22
Alignment explanation
Indices: 170970--171033 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
170960 CAGCTCATAT
170970 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* **
170993 AATTGCACCGGAGTGCCGTGTAG
1 AATTGCACC-TAGTGCCACGTAG
*
171016 AATTTCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
171034 TATAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:171173 original size:103 final size:103
Alignment explanation
Indices: 171041--171266 Score: 389
Period size: 103 Copynumber: 2.2 Consensus size: 103
171031 CCATATAATA
* *
171041 ATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTG
1 ATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
*
171106 TCTCACCAGACCACACACATGTTCCAAAGAAGACATAT
66 TCTCACCAGACCACACACATATTCCAAAGAAGACATAT
171144 ATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
* *
171209 TCTCACCAGACCTCACACATATTCCAAAGAATACATAT
66 TCTCACCAGACCACACACATATTCCAAAGAAGACATAT
* *
171247 ATGTCCCGAAGAACCACATA
1 ATGTCCAGAAGGACCACATA
171267 GACCCTCTAC
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 116 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (103 bp):
ATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
TCTCACCAGACCACACACATATTCCAAAGAAGACATAT
Found at i:171825 original size:64 final size:67
Alignment explanation
Indices: 171715--171842 Score: 192
Period size: 64 Copynumber: 2.0 Consensus size: 67
171705 ATTTTCATCT
*
171715 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATACTATTCGATGTTTG
171780 TA
66 TA
* *
171782 TTTAATGG-GG-ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATATTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCGATGCATAAATACTATTCGATGTTT
171843 TCTTTTTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
63 1 0.02
64 31 0.54
65 15 0.26
66 2 0.04
67 8 0.14
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATACTATTCGATGTTTG
TA
Found at i:171860 original size:64 final size:62
Alignment explanation
Indices: 171727--171887 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 62
171717 TAATGGAGGT
* * * *
171727 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATACTATTCGATGTTTCTATTTAAT-GGA
* * *
171792 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATATTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATACTATTCGATG-TTTCTATTT-AATGGA
* *
171856 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
171888 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 56 0.67
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATACTATTCGATGTTTCTATTTAATGGA
Found at i:178308 original size:2 final size:2
Alignment explanation
Indices: 178301--178348 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
178291 AAGTATAGAT
178301 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
178343 TA TA TA
1 TA TA TA
178349 CATGTAAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:183361 original size:15 final size:15
Alignment explanation
Indices: 183343--183373 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
183333 ATAATTAGAA
183343 CATAGAGAATTCAGT
1 CATAGAGAATTCAGT
183358 CATAGAGAATTCAGT
1 CATAGAGAATTCAGT
183373 C
1 C
183374 CACACTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (15 bp):
CATAGAGAATTCAGT
Found at i:216557 original size:12 final size:12
Alignment explanation
Indices: 216540--216584 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
216530 AGCATGTTTA
216540 AAAATAAAACTT
1 AAAATAAAACTT
*
216552 AAAATAAAA-TA
1 AAAATAAAACTT
216563 AAAATGAAAACTT
1 AAAAT-AAAACTT
216576 GAAAATAAA
1 -AAAATAAA
216585 GAAAAGAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 6 0.21
12 13 0.46
13 4 0.14
14 5 0.18
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (12 bp):
AAAATAAAACTT
Found at i:216572 original size:24 final size:24
Alignment explanation
Indices: 216538--216584 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
216528 TTAGCATGTT
216538 TAAAAATAAAACTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAATAAAA
216561 TAAAAATGAAAACTTGAAAATAAA
1 TAAAAAT-AAAACTTGAAAATAAA
216585 GAAAAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (24 bp):
TAAAAATAAAACTTGAAAATAAAA
Found at i:216589 original size:24 final size:23
Alignment explanation
Indices: 216539--216589 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
216529 TAGCATGTTT
*
216539 AAAAATAAAACTTAAAATAAAAT
1 AAAAATAAAACTTAAAATAAAAG
216562 AAAAATGAAAACTTGAAAAT-AAAG
1 AAAAAT-AAAACTT-AAAATAAAAG
216586 AAAA
1 AAAA
216590 GAAGAACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18
Consensus pattern (23 bp):
AAAAATAAAACTTAAAATAAAAG
Found at i:233795 original size:36 final size:35
Alignment explanation
Indices: 233714--233847 Score: 187
Period size: 36 Copynumber: 3.8 Consensus size: 35
233704 AGATGAACAA
*
233714 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
* ** * *
233749 TTGAATCGAAAGTGTCGATGCTTATTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-AC
233785 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
*
233820 TTTGAATCGAAAGTGCCAATGCTTCCTT
1 -TTGAATCGAAAGTGCCGATGCTTCCTT
233848 TAGTTCTTCT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
35 29 0.34
36 56 0.66
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
Found at i:237330 original size:15 final size:16
Alignment explanation
Indices: 237310--237348 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
237300 GTTTACTTCA
*
237310 GAATGATT-AAGCGTT
1 GAATGATTCAAACGTT
*
237325 GAATGATTCAAATGTT
1 GAATGATTCAAACGTT
237341 GAATGATT
1 GAATGATT
237349 TAGAGGCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (16 bp):
GAATGATTCAAACGTT
Found at i:237454 original size:23 final size:22
Alignment explanation
Indices: 237418--237460 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
237408 GATTCAGAAT
*
237418 GTACTTTTTGCTGAATCAATCA
1 GTACTTTTTACTGAATCAATCA
237440 GTACTATTTTACTGAATCAAT
1 GTACT-TTTTACTGAATCAAT
237461 TAGCATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (22 bp):
GTACTTTTTACTGAATCAATCA
Found at i:240156 original size:254 final size:255
Alignment explanation
Indices: 239694--240212 Score: 837
Period size: 254 Copynumber: 2.0 Consensus size: 255
239684 GGTGGCATTT
* * *
239694 CTCCACTTTTAATTATATCCTTGCCTTTTAGCCTAAAATCTTTTATCCATTATTGTTAGATCTGC
1 CTCCACCTGTAATTATATCCTTGCCCTTTAGCCTAAAATCTTTTATCCATTATTGTTAGATCTGC
* * * * *
239759 TTTAGACAATCTATTATATTTTTCTGTCCCCGCATTATTTTCTTTTTTGATTACTTTATCTTATT
66 TTCAGACAATCTATTACATTTTTCCGTACCCACATTATTTTCTTTTTTGATTACTTTATCTTATT
239824 AAAATGGAAAAGCCAACATAGTTGAAGCTCTGAGCAATTAGTTGAATATTTATAAGGAAACTTCA
131 AAAATGGAAAAGCCAACATAGTTGAAGCTCTGAGCAATTAGTTGAATATTTATAAGGAAACTTCA
*
239889 TCATTCTAATTGAGGTCTTTATGATAAGATGAGGTTGGTTTCCTCTGCTTATAATGATCC
196 TCATTCTAATTGAGGTCTTTATGATAAAATGAGGTTGGTTTCCTCTGCTTATAATGATCC
**
239949 CTCCACCTGTAATTATATTGTTGCCCTTTAGCCTAAAATCTTTTATCCATTATTGTTAGATCTGC
1 CTCCACCTGTAATTATATCCTTGCCCTTTAGCCTAAAATCTTTTATCCATTATTGTTAGATCTGC
* *
240014 TTCAGACAATCTATTACATTTTTCCGTACCCATATTCTTTTC-TTTTTGATTACTTTATCTTATT
66 TTCAGACAATCTATTACATTTTTCCGTACCCACATTATTTTCTTTTTTGATTACTTTATCTTATT
* * *
240078 AAAATTTTG-AAA-CCAACTTAGTTGAAGCTCTGAGCAATTAGTTGAATATTTATAAGGAATCTT
131 AAAA--TGGAAAAGCCAACATAGTTGAAGCTCTGAGCAATTAGTTGAATATTTATAAGGAAACTT
* *
240141 CATTATTCTAATTGAGGTCTTTATGATAAAATGAGGTTGGTTTCCTCTGCTTATAATGATCT
194 CATCATTCTAATTGAGGTCTTTATGATAAAATGAGGTTGGTTTCCTCTGCTTATAATGATCC
240203 CTCCACCTGT
1 CTCCACCTGT
240213 TAGCCTAAAT
Statistics
Matches: 244, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
254 144 0.59
255 98 0.40
256 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.43
Consensus pattern (255 bp):
CTCCACCTGTAATTATATCCTTGCCCTTTAGCCTAAAATCTTTTATCCATTATTGTTAGATCTGC
TTCAGACAATCTATTACATTTTTCCGTACCCACATTATTTTCTTTTTTGATTACTTTATCTTATT
AAAATGGAAAAGCCAACATAGTTGAAGCTCTGAGCAATTAGTTGAATATTTATAAGGAAACTTCA
TCATTCTAATTGAGGTCTTTATGATAAAATGAGGTTGGTTTCCTCTGCTTATAATGATCC
Found at i:248243 original size:17 final size:17
Alignment explanation
Indices: 248217--248264 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
248207 TTCGAGTTTA
* *
248217 AGTTCAAGCTTGAATTG
1 AGTTCGAGCTTGAATCG
248234 AGTTCGAGCTTGAATCG
1 AGTTCGAGCTTGAATCG
*
248251 AGCTCGAGTCTTGA
1 AGTTCGAG-CTTGA
248265 GCTTCAATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (17 bp):
AGTTCGAGCTTGAATCG
Found at i:257371 original size:17 final size:18
Alignment explanation
Indices: 257334--257374 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
257324 ATATTATGTA
*
257334 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
257352 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
257369 TTTACT
1 TTTACT
257375 AATATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:262320 original size:12 final size:13
Alignment explanation
Indices: 262284--262333 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
262274 GTCCCGATTA
262284 CCCGATTACCCGG
1 CCCGATTACCCGG
262297 CCCGATTACCCGG
1 CCCGATTACCCGG
*
262310 CCCGA-TACCCGA
1 CCCGATTACCCGG
262322 CCCGA-TACCCGG
1 CCCGATTACCCGG
262334 GTATTCATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 17 0.49
13 18 0.51
ACGTcount: A:0.18, C:0.48, G:0.22, T:0.12
Consensus pattern (13 bp):
CCCGATTACCCGG
Found at i:262325 original size:25 final size:25
Alignment explanation
Indices: 262284--262333 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
262274 GTCCCGATTA
*
262284 CCCGATTACCCGGCCCGATTACCCGG
1 CCCGATTACCCGACCCGA-TACCCGG
262310 CCCGA-TACCCGACCCGATACCCGG
1 CCCGATTACCCGACCCGATACCCGG
262334 GTATTCATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 11 0.48
26 5 0.22
ACGTcount: A:0.18, C:0.48, G:0.22, T:0.12
Consensus pattern (25 bp):
CCCGATTACCCGACCCGATACCCGG
Found at i:264471 original size:29 final size:29
Alignment explanation
Indices: 264439--264500 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
264429 TGTTTATTTG
264439 TTTAATCAATTTCTAATTTGTATCTTGTA
1 TTTAATCAATTTCTAATTTGTATCTTGTA
* *** *
264468 TTTATTTGGTTTCTAATTTGTATGTTGTA
1 TTTAATCAATTTCTAATTTGTATCTTGTA
264497 TTTA
1 TTTA
264501 TTTCAGTCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (29 bp):
TTTAATCAATTTCTAATTTGTATCTTGTA
Found at i:264501 original size:29 final size:29
Alignment explanation
Indices: 264448--264503 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
264438 GTTTAATCAA
264448 TTTCTAATTTGTATCTTGTATTTATTTGG
1 TTTCTAATTTGTATCTTGTATTTATTTGG
*
264477 TTTCTAATTTGTATGTTGTATTTATTT
1 TTTCTAATTTGTATCTTGTATTTATTT
264504 CAGTCTATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.05, G:0.12, T:0.64
Consensus pattern (29 bp):
TTTCTAATTTGTATCTTGTATTTATTTGG
Found at i:266874 original size:25 final size:25
Alignment explanation
Indices: 266836--266886 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
266826 AATCCCCGTA
* *
266836 GTTTTTTAAGCGGGGACGGGTATGG
1 GTTTTTTAAACGGGGACGGGGATGG
266861 GTTTTTTAAACGGGGACGGGGATGG
1 GTTTTTTAAACGGGGACGGGGATGG
266886 G
1 G
266887 GGGACCAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.18, C:0.08, G:0.45, T:0.29
Consensus pattern (25 bp):
GTTTTTTAAACGGGGACGGGGATGG
Found at i:273881 original size:21 final size:20
Alignment explanation
Indices: 273852--273891 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
273842 ATGAAACGGA
273852 TGAATAGTATCGATACTGAT
1 TGAATAGTATCGATACTGAT
273872 TGAAGTAGTATCGATACTGA
1 TGAA-TAGTATCGATACTGA
273892 AGTGGGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TGAATAGTATCGATACTGAT
Found at i:288983 original size:16 final size:16
Alignment explanation
Indices: 288962--288996 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
288952 CAAAGCATCT
288962 GCCACAACATTAGTAC
1 GCCACAACATTAGTAC
288978 GCCACAACATTAGTAC
1 GCCACAACATTAGTAC
288994 GCC
1 GCC
288997 CTTTTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (16 bp):
GCCACAACATTAGTAC
Found at i:310862 original size:17 final size:17
Alignment explanation
Indices: 310840--310878 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
310830 TGAATTAAAT
*
310840 TAATTATATATTATTTA
1 TAATTAGATATTATTTA
310857 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
310874 -AATTA
1 TAATTA
310879 ATTGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:310914 original size:39 final size:36
Alignment explanation
Indices: 310833--310917 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 36
310823 AAGTGTTTGA
* * *
310833 ATTAAATTAATTATATATTATTTATAATTAGATATT
1 ATTAAATTAATTATAAATTATTTATAATTAGAAAAT
* *
310869 ATTTAAATTAATTGTAAATTATTTTTTTAATTAGAAAAAT
1 A-TTAAATTAATTATAAATTA--TTTATAATTAG-AAAAT
310909 ATTAAATTA
1 ATTAAATTA
310918 TAAAATTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
36 1 0.03
37 17 0.43
39 18 0.45
40 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (36 bp):
ATTAAATTAATTATAAATTATTTATAATTAGAAAAT
Found at i:311172 original size:11 final size:10
Alignment explanation
Indices: 311152--311182 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
311142 TAAAACAATT
311152 AAAATGAAAAA
1 AAAAT-AAAAA
311163 AAAATAAAAA
1 AAAATAAAAA
311173 AAAATAAAAA
1 AAAATAAAAA
311183 GTTGGTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:311421 original size:16 final size:17
Alignment explanation
Indices: 311400--311431 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
311390 TTTTATGCCT
311400 GATATT-TATTTTTAGG
1 GATATTATATTTTTAGG
311416 GATATTATATTTTTAG
1 GATATTATATTTTTAG
311432 CCCATGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (17 bp):
GATATTATATTTTTAGG
Found at i:311515 original size:29 final size:28
Alignment explanation
Indices: 311475--311542 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
311465 CCATATTATA
311475 TTTTATTT-TTTTAATTCAG-CCATGTAG
1 TTTTATTTATTTTAATTCAGTCCAT-TAG
* *
311502 TTTTAATTTATTTTAATTTAGTCCATTTG
1 TTTT-ATTTATTTTAATTCAGTCCATTAG
311531 TTTTATTTATTT
1 TTTTATTTATTT
311543 CCATTATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 4 0.11
28 12 0.33
29 16 0.44
30 4 0.11
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (28 bp):
TTTTATTTATTTTAATTCAGTCCATTAG
Found at i:319873 original size:18 final size:18
Alignment explanation
Indices: 319829--319883 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
319819 ATAATCATGC
* *
319829 ATTAAATAAATAA-ATAA
1 ATTAAATTAATAATTTAA
*
319846 ATTATTATTAATAATTTAA
1 ATTA-AATTAATAATTTAA
319865 ATTAAATTAA-AATGTTAA
1 ATTAAATTAATAAT-TTAA
319883 A
1 A
319884 ATGTTATCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 7 0.23
18 17 0.55
19 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATAATTTAA
Found at i:329462 original size:19 final size:18
Alignment explanation
Indices: 329438--329504 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 18
329428 AATTGAAAAT
329438 AGAGAAAGTAAAATAAAGA
1 AGAGAAA-TAAAATAAAGA
* *
329457 AGAGAAA-ATAAGTAAATA
1 AGAGAAATA-AAATAAAGA
*
329475 ACGACAAATAAAATAAAGA
1 A-GAGAAATAAAATAAAGA
* *
329494 AAAAAAATAAA
1 AGAGAAATAAA
329505 CAACATAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
17 1 0.03
18 16 0.42
19 20 0.53
20 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.13, T:0.12
Consensus pattern (18 bp):
AGAGAAATAAAATAAAGA
Found at i:331959 original size:106 final size:106
Alignment explanation
Indices: 331774--332036 Score: 382
Period size: 106 Copynumber: 2.5 Consensus size: 106
331764 GTATTGTTCT
* * * * * *
331774 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTATGGAACTGGAAAATTATTTGCTGATAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGCTGACAG
331839 TAAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGATGTCTC
66 TAAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGATGTCTC
* * * * * *
331880 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGGCAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGCTGACAG
* * *
331945 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
66 TAAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGATGTCTC
*
331986 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTATGAAATTGGGAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAA
332037 CCCCTTCGTC
Statistics
Matches: 138, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
106 138 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGCTGACAG
TAAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGATGTCTC
Found at i:332541 original size:14 final size:14
Alignment explanation
Indices: 332524--332562 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
332514 GTTGCCTATC
332524 TGGAATCTTGATTA
1 TGGAATCTTGATTA
*
332538 TGGAATCTTGATTC
1 TGGAATCTTGATTA
332552 TGGAATCTTGA
1 TGGAATCTTGA
332563 AGTTCCGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (14 bp):
TGGAATCTTGATTA
Found at i:333191 original size:8 final size:7
Alignment explanation
Indices: 333172--333214 Score: 61
Period size: 7 Copynumber: 6.0 Consensus size: 7
333162 ATTTTTCTTC
333172 TCTTTTT
1 TCTTTTT
333179 TCTTTTGT
1 TCTTTT-T
333187 TCTTTTT
1 TCTTTTT
333194 CTCTTTTT
1 -TCTTTTT
333202 TCTTTTT
1 TCTTTTT
333209 T-TTTTT
1 TCTTTTT
333215 CAATTTAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 5 0.15
7 15 0.44
8 14 0.41
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (7 bp):
TCTTTTT
Found at i:333192 original size:15 final size:14
Alignment explanation
Indices: 333172--333214 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
333162 ATTTTTCTTC
333172 TCTTTTTTCTTTTGT
1 TCTTTTTTCTTTT-T
333187 TCTTTTTCTCTTTTT
1 TCTTTTT-TCTTTTT
333202 TCTTTTTT-TTTTT
1 TCTTTTTTCTTTTT
333215 CAATTTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 1 0.04
15 15 0.56
16 6 0.22
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (14 bp):
TCTTTTTTCTTTTT
Found at i:333193 original size:9 final size:8
Alignment explanation
Indices: 333163--333214 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
333153 ACCCACCTTA
333163 TTTTTCTTC
1 TTTTT-TTC
333172 TCTTTTTTC
1 T-TTTTTTC
*
333181 TTTTGTTC
1 TTTTTTTC
*
333189 TTTTTCTC
1 TTTTTTTC
333197 -TTTTTTC
1 TTTTTTTC
333204 TTTTTTT-
1 TTTTTTTC
333211 TTTT
1 TTTT
333215 CAATTTAGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 10 0.27
8 18 0.49
9 5 0.14
10 4 0.11
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:333199 original size:23 final size:21
Alignment explanation
Indices: 333163--333215 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 21
333153 ACCCACCTTA
*
333163 TTTTTCTTCTCTTTTTTCTTT
1 TTTTTTTTCTCTTTTTTCTTT
333184 TGTTCTTTTTCTCTTTTTTCTTT
1 T-TT-TTTTTCTCTTTTTTCTTT
333207 TTTTTTTTC
1 TTTTTTTTC
333216 AATTTAGGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 7 0.24
22 4 0.14
23 18 0.62
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTTTTTCTCTTTTTTCTTT
Found at i:343935 original size:28 final size:28
Alignment explanation
Indices: 343904--344018 Score: 78
Period size: 32 Copynumber: 4.1 Consensus size: 28
343894 AGACTATAAA
*
343904 ATATTAAGAAGTAAAATAATATATATAT
1 ATATTAAGAAATAAAATAATATATATAT
* * *
343932 ATA-TAATAAAT-AAA-AATAGA-A-AC
1 ATATTAAGAAATAAAATAATATATATAT
* *
343955 ATATTAAGAAATAAAATAAAATGTATAT
1 ATATTAAGAAATAAAATAATATATATAT
* * *
343983 ATATATATATATATATATATATATATATATAT
1 ATAT-TA-AGAAATA-AAATA-ATATATATAT
344015 ATAT
1 ATAT
344019 ATATATAATA
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
23 4 0.06
24 8 0.12
25 8 0.12
26 6 0.09
27 7 0.11
28 8 0.12
29 2 0.03
30 5 0.08
31 4 0.06
32 12 0.19
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (28 bp):
ATATTAAGAAATAAAATAATATATATAT
Found at i:343985 original size:2 final size:2
Alignment explanation
Indices: 343978--344030 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
343968 AAATAAAATG
343978 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
344020 TA TA TA -A TA TA
1 TA TA TA TA TA TA
344031 ACACATAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:344128 original size:17 final size:16
Alignment explanation
Indices: 344108--344144 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
344098 AAAAATACTA
344108 ATAATACTATAATATAT
1 ATAATACTATAATA-AT
*
344125 ATAATATTATAATAAT
1 ATAATACTATAATAAT
344141 ATAA
1 ATAA
344145 AAAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATACTATAATAAT
Found at i:348730 original size:59 final size:59
Alignment explanation
Indices: 348637--348768 Score: 185
Period size: 59 Copynumber: 2.3 Consensus size: 59
348627 ATTTAAGGTG
* * * *
348637 ATTATAAGGTAATA-TATTTAAAAAAATTAATTATTAATAATACGTATAGTCTGAAGTA
1 ATTATAAGATAATATTTTTTAAAAAAATTAATTATTAATAATACATATAGTCTAAAGTA
* * *
348695 ATTATAATATAATATTTTTTAAAAAAATTAATTATTAATAATATATATGGTCTAAAGTA
1 ATTATAAGATAATATTTTTTAAAAAAATTAATTATTAATAATACATATAGTCTAAAGTA
*
348754 GTTATAAGATAATAT
1 ATTATAAGATAATAT
348769 ATATCTAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
58 12 0.19
59 52 0.81
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.41
Consensus pattern (59 bp):
ATTATAAGATAATATTTTTTAAAAAAATTAATTATTAATAATACATATAGTCTAAAGTA
Found at i:349118 original size:87 final size:87
Alignment explanation
Indices: 349006--349168 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
348996 TATGTTATAT
* * * *
349006 CATTTAACCGGAAATATTATTAAGTACAATAACATATTAGATAGTGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGATAGCGCTTATATAATGTAATAGAT
349071 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
349093 CATTTAACTGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGATAGCGCTTATATAATGTAATAGAT
349158 AGCGCTTATAT
66 AGCGCTTATAT
349169 TGACCTATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGATAGCGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:349533 original size:198 final size:199
Alignment explanation
Indices: 349193--349880 Score: 800
Period size: 198 Copynumber: 3.5 Consensus size: 199
349183 AGTAAACTGA
* **
349193 TATATTTATACCGGTAACATTACAAATTTACC---T--ATTATAATTATCGGTTTCGATGTTTTT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* * * *
349253 TGGATCGATACAATTT--TAAATGTATCGACACTTTATACGTTCACCTCGTTGGGCATTCATTCT
66 TGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTCT
* * *
349316 GGAAAAAAGTATCGACACAAACTTAA-AGAGTGTCAATACATTAT-TTAGACCTATTTTTTCATA
130 GGACAAAAGTATCGACACAAA-TTAACA-AGTGTCGATACATTATGTTAGACCTATTTTCTCATA
349379 AAACCGG
193 AAACCGG
* * * * * *
349386 TATATTTCTATCGGGTACATTGTAAATTTACCTATCACATTGTAATTATC-GTTTCGAT-ATTTT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* * * *
349449 TGATATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACC-CATTTGGCATTTATTAT
66 TG-GATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTCT
* * * * *
349513 GGACAGAATGTATTGACACAAATTTAACAAGTGTCGATACTTTATGATA-ACATATTTTCTCATA
130 GGACA-AAAGTATCGACACAAA-TTAACAAGTGTCGATACATTATGTTAGACCTATTTTCTCATA
*
349577 AAATCGG
193 AAACCGG
* *
349584 TATATTTATACCGGTTATATTGTAAATTTACATATTACATTATAATTATCGGTTTCGAT-TTTAT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT-T
* * * *
349648 TGGGATCGATACTTTTAATAATTGTATCGACATTTTATGTGTGCACCTCGTTTGGGCATTCATTC
65 TTGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GGCATTCATTC
* *
349713 TGGACAATAAGTATCGACACAAATTACACAAGTGTCGATACGTTATGTT-GACCTGA-TTTCTAA
129 TGGACAA-AAGTATCGACACAAATTA-ACAAGTGTCGATACATTATGTTAGACCT-ATTTTCTCA
**
349776 T-TTACCGG
191 TAAAACCGG
*
349784 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
*
349849 TGGGTCGATACTTTTAGA-AAATGTATCGACAC
66 TGGATCGATACTTTTA-ATAAATGTATCGACAC
349881 ATATTTAGGT
Statistics
Matches: 415, Mismatches: 59, Indels: 35
0.82 0.12 0.07
Matches are distributed among these distances:
193 26 0.06
196 9 0.02
197 33 0.08
198 132 0.32
199 53 0.13
200 99 0.24
201 62 0.15
202 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (199 bp):
TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
TGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTCTG
GACAAAAGTATCGACACAAATTAACAAGTGTCGATACATTATGTTAGACCTATTTTCTCATAAAA
CCGG
Found at i:352988 original size:21 final size:21
Alignment explanation
Indices: 352962--353001 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
352952 CAGAACCCCA
*
352962 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
352983 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
353002 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:361825 original size:201 final size:200
Alignment explanation
Indices: 360900--362069 Score: 1866
Period size: 200 Copynumber: 5.8 Consensus size: 200
360890 CGTGTTATTT
* * * * *
360900 AAAAGTATCGATAAAAATTT-AAAAGTGTTGATACATTATGTTGACCTATTCTCTCATAAAACCG
1 AAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCG
*
360964 GTATATTTATATTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
66 GTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * * * *
361029 TGGGATCGATTCTTTTTAAAAATATATCGACACTTTATGCGTGCAACCCTTTT-GGCATTCATTT
131 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTC-ACCATTTTGGGCATTCATTC
361093 TGGACA
195 TGGACA
* * *
361099 AAAAGTATCGACACAAATCTAAAACA-TGTCGATACGTTATGTTCACCTATTTTCTCATAAAATC
1 AAAAGTATCGACACAAATTTAAAA-AGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACC
*
361163 GGTACATTTATA-TCGGTTACATTG-AGAATTTACCTATTACATTATAATTATCGGTTTCGATGT
65 GGTATATTTATACT-GGTTACATTGTA-AATTTACCTATTACATTATAATTATCGGTTTCGATGT
361226 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCAT
128 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCAT
361291 TCTGGACA
193 TCTGGACA
* *
361299 AAAAGTATCGACACAAATTTAAAAAGTGTCGACACATTATGTTCACCTATTTTCTCATAAAACCA
1 AAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCG
* *
361364 GTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCCATGTTTT
66 GTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
*
361429 TAGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCT
131 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCT
361494 GGACA
196 GGACA
* *
361499 AAAAGTATCGACACAAATTTAAAAAGTGTCGACACATTATGTTCCCCTATTTTCTCATAAAACCG
1 AAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCG
* *
361564 ATATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTT
66 GTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
*
361629 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTTATTCT
131 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCT
361694 GGACA
196 GGACA
**
361699 AAAAGTATCGACACAAATTTAAAAAAGTGTCGATACATTATGTTCACAGATTTTCTCATAAAACC
1 AAAAGTATCGACACAAATTT-AAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACC
*
361764 GGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTT
65 GGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* *
361829 TTGGGATTGATATTTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATT
130 TTGGGATCGATA-CTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATT
*
361894 CCGGACA
194 CTGGACA
* * * * *
361901 AAAAGTATTGACACAAATCTAAAACGTGTCGATACGTTATGTTCACCTATTTTCTCATAAAACCA
1 AAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCG
* * *
361966 GTACATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
66 GTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
*
362031 TGGGATCGATA-TTTTTAAAAAATGTATCGACACTTTATG
131 TGGGATCGATACTTTTT-ATAAATGTATCGACACTTTATG
362070 GGAAACTTTA
Statistics
Matches: 908, Mismatches: 52, Indels: 21
0.93 0.05 0.02
Matches are distributed among these distances:
199 32 0.04
200 573 0.63
201 229 0.25
202 74 0.08
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (200 bp):
AAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCG
GTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCT
GGACA
Found at i:362490 original size:24 final size:24
Alignment explanation
Indices: 362449--362499 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
362439 CGAAATTTAT
362449 ATTGAAACTCAAACTCAAACTCAA
1 ATTGAAACTCAAACTCAAACTCAA
* * * *
362473 ATTGAAATTTAAATTCAAACTCCA
1 ATTGAAACTCAAACTCAAACTCAA
362497 ATT
1 ATT
362500 ACATATGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (24 bp):
ATTGAAACTCAAACTCAAACTCAA
Found at i:366328 original size:400 final size:397
Alignment explanation
Indices: 365324--366477 Score: 1564
Period size: 400 Copynumber: 2.9 Consensus size: 397
365314 ATTTAAAATT
* **
365324 GTATCGACACAAATAT-AAAACGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCGGTA
1 GTATCGACACAAAT-TCAAAA-GTGTCGATACATTATGTTGACCTATTTTCTCATAAAATTGGTA
* * *
365388 AATTTATACCGGTTACATTGTAACTTTACCTATTACATTATAACTATCGGTTTCGATGTTTTTGG
64 TATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
* * **
365453 GATCGATACTTTTTATATATGTATCGACACATTATGTGTTCACCATTTTGACCATTCATTCTGGA
129 GATCGATACTTTTTATAAATGTATCGACACA-TATGTGTTCATCATTTTGGGCATTCATTCTGGA
365518 CAAAAAGTATCGACAC-AAATTCAAAAA-TGTCGACACATTATGTAGACCTATTCTCACATAAAA
193 CAAAAAGTATCGACACAAAATT-AAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAA
* * * * * * *
365581 CCGGTATATTTATATCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTTGATGT
257 CAGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
* * **
365646 TTTTGGGATCGATATTTTTTATATATGTATCG--ACTTTATGCGTTCACCATTTTGGGCATTCAT
322 TTTTGGGATCGATA-TTTTTATAAATGTATCGACACTTTATGAGCACACCATTTTGGGCATTCAT
365709 TATGGACAAAAA
386 TATGGACAAAAA
* * * * * *
365721 GTATCGACACAAATTCAAAAGTGTTGACACATTACGTTGACCTATTCTCACATAAAATTGATATA
1 GTATCGACACAAATTCAAAAGTGTCGATACATTATGTTGACCTATTTTCTCATAAAATTGGTATA
* * * *
365786 TTTAGACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGATATTTTTGGGA
66 TTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGA
* * * * * *
365851 TCAATACCTTTTATAAATGTATTGACACTTTATGCGTTCATCATTTGGGGCATTCATTCTGGACA
131 TCGATACTTTTTATAAATGTATCGACAC-ATATGTGTTCATCATTTTGGGCATTCATTCTGGACA
*
365916 AAAAATATCGACACAAAATTAAAAAGTGTCGACA-ATTTATGTAGACCTATTCTCACATAAAACA
195 AAAAGTATCGACACAAAATTAAAAAGTGTCGACACA-TTATGTAGACCTATTCTCACATAAAACA
* * * *
365980 GGTATATTTATACCGGTTATATTACAAAATTATCTATTATATTATAATTAGGGGCTTCGATGTTT
259 GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * * *
366045 TTGGGATCGACACTTTTTATAAAATCTATCGACACTTTATGAGCACACCCTTTTGGGCATTCCTT
324 TTGGGATCGATA-TTTTTAT-AAATGTATCGACACTTTATGAGCACACCATTTTGGGCATTCATT
* *
366110 CTGGACAAACA
387 ATGGACAAAAA
* *
366121 GTATCGACACAAATTCCATAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAATTGGTAT
1 GTATCGACACAAATT-CAAAAGTGTCGATACATTATGTTGACCTATTTTCTCATAAAATTGGTAT
* * * * * *
366186 AGTTATACCGGTTACATTGTAAATTTACTTATTACATTATATTTATGGGTTTCAATGTTTCTGGG
65 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
* * *
366251 ATCGATATTTTTTATAAATGTATCGACACAAATGTGTTCATCGTTTTGGGCATTCATTCTGGACA
130 ATCGATACTTTTTATAAATGTATCGACACATATGTGTTCATCATTTTGGGCATTCATTCTGGACA
* * * * * * * *
366316 AAAAGTATCGACATAAAATGAGAAAGTATCAATACATTATGTAGACCTATTCTCACATAAATCTG
195 AAAAGTATCGACACAAAATTAAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACAG
366381 GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
260 GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
*
366446 TGGGATCAATATTTTTATAAATGTATCGACAC
325 TGGGATCGATATTTTTATAAATGTATCGACAC
366478 ATATGTTTAC
Statistics
Matches: 655, Mismatches: 92, Indels: 19
0.86 0.12 0.02
Matches are distributed among these distances:
396 168 0.26
397 131 0.20
398 21 0.03
399 7 0.01
400 206 0.31
401 122 0.19
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (397 bp):
GTATCGACACAAATTCAAAAGTGTCGATACATTATGTTGACCTATTTTCTCATAAAATTGGTATA
TTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGA
TCGATACTTTTTATAAATGTATCGACACATATGTGTTCATCATTTTGGGCATTCATTCTGGACAA
AAAGTATCGACACAAAATTAAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACAGG
TATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
GGGATCGATATTTTTATAAATGTATCGACACTTTATGAGCACACCATTTTGGGCATTCATTATGG
ACAAAAA
Found at i:366366 original size:199 final size:198
Alignment explanation
Indices: 365324--366483 Score: 1410
Period size: 199 Copynumber: 5.8 Consensus size: 198
365314 ATTTAAAATT
* ** * * *
365324 GTATCGACACAAATAT-AAAACGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCGGTA
1 GTATCGACACAAAT-TCAAAA-GTGTCGACACATTATGTAGACCTATTCTCACATAAAACTGGTA
* * * *
365388 AATTTATACCGGTTACATTGTAACTTTACCTATTACATTATAACTATCGGTTTCGATGTTTTTGG
64 TATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
* **
365453 GATCGATACTTTTTATATATGTATCGACACATTATGTGTTCACCATTTTGACCATTCATTCTGGA
129 GATCGATACTTTTTATAAATGTATCGACACA-TATGTGTTCACCATTTTGGGCATTCATTCTGGA
365518 CAAAAA
193 CAAAAA
* *
365524 GTATCGACACAAATTCAAAAATGTCGACACATTATGTAGACCTATTCTCACATAAAACCGGTATA
1 GTATCGACACAAATTCAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACTGGTATA
* *
365589 TTTATATCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTTGATGTTTTTGGGA
66 TTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGA
* * ** * *
365654 TCGATATTTTTTATATATGTATCGAC-TTTATGCGTTCACCATTTTGGGCATTCATTATGGACAA
131 TCGATACTTTTTATAAATGTATCGACACATATGTGTTCACCATTTTGGGCATTCATTCTGGACAA
365718 AAA
196 AAA
* * * * *
365721 GTATCGACACAAATTCAAAAGTGTTGACACATTACGTTGACCTATTCTCACATAAAATTGATATA
1 GTATCGACACAAATTCAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACTGGTATA
* * * * *
365786 TTTAGACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGATATTTTTGGGA
66 TTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGA
* * * * * * *
365851 TCAATACCTTTTATAAATGTATTGACACTTTATGCGTTCATCATTTGGGGCATTCATTCTGGACA
131 TCGATACTTTTTATAAATGTATCGACAC-ATATGTGTTCACCATTTTGGGCATTCATTCTGGACA
365916 AAAA
195 AAAA
* * *
365920 ATATCGACACAAAATTAAAAAGTGTCGACA-ATTTATGTAGACCTATTCTCACATAAAACAGGTA
1 GTATCGACAC-AAATTCAAAAGTGTCGACACA-TTATGTAGACCTATTCTCACATAAAACTGGTA
* * * * * ** *
365984 TATTTATACCGGTTATATTACAAAATTATCTATTATATTATAATTAGGGGCTTCGATGTTTTTGG
64 TATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
* * * * ** * *
366049 GATCGACACTTTTTATAAAATCTATCGACACTTTATGAGCACACCCTTTTGGGCATTCCTTCTGG
129 GATCGATACTTTTTAT-AAATGTATCGACAC-ATATGTGTTCACCATTTTGGGCATTCATTCTGG
*
366114 ACAAACA
192 ACAAAAA
* * * * *
366121 GTATCGACACAAATTCCATAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAATTGGTAT
1 GTATCGACACAAATT-CAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACTGGTAT
* * * * * * *
366186 AGTTATACCGGTTACATTGTAAATTTACTTATTACATTATATTTATGGGTTTCAATGTTTCTGGG
65 ATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
* * * *
366251 ATCGATATTTTTTATAAATGTATCGACACAAATGTGTTCATCGTTTTGGGCATTCATTCTGGACA
130 ATCGATACTTTTTATAAATGTATCGACACATATGTGTTCACCATTTTGGGCATTCATTCTGGACA
366316 AAAA
195 AAAA
* * * * * * *
366320 GTATCGACATAAAATGAGAAAGTATCAATACATTATGTAGACCTATTCTCACATAAATCTGGTAT
1 GTATCGACACAAATTCA-AAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACTGGTAT
* * * *
366385 ATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
65 ATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
*
366450 ATCAATA-TTTTTATAAATGTATCGACACATATGT
130 ATCGATACTTTTTATAAATGTATCGACACATATGT
366484 TTACCTATTT
Statistics
Matches: 823, Mismatches: 128, Indels: 20
0.85 0.13 0.02
Matches are distributed among these distances:
197 174 0.21
198 27 0.03
199 317 0.39
200 145 0.18
201 159 0.19
202 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (198 bp):
GTATCGACACAAATTCAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACTGGTATA
TTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGA
TCGATACTTTTTATAAATGTATCGACACATATGTGTTCACCATTTTGGGCATTCATTCTGGACAA
AAA
Found at i:369829 original size:182 final size:182
Alignment explanation
Indices: 369522--370376 Score: 1155
Period size: 182 Copynumber: 4.7 Consensus size: 182
369512 TACGTGTACT
* * * * * * * *
369522 TATTAAAATATCGACACTTTCTATATATCCGGTAGCGCTTTATCGGTTTTGTCATTTCGATACCG
1 TATTAAAATATCGACACTTTCAATATATCTGGTAGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* * *
369587 GTTTTGTCATATTTTTACTTGTTATATCATTATGGATCGATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
*
369652 TTATAGGCGCTACAACTGATTCTCTTTTAAATTCA-ATAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACA-AAGTGTCGATACTTA
* * * *
369704 TATTAAAGTATCGACACTTTCAATATATCTGGTTGCTCTATACCGATTTTGTCTTTTAGAGACCG
1 TATTAAAATATCGACACTTTCAATATATCTGGTAGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* * * *
369769 ATTTTGTCATATTTTTAACTGTTATATCGTTGTGGATCGATTCATTGTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
* * *
369834 TTATAGGCGCTAAAA-TTACTTCTCTTTTAAACTCACAAAGTGTTGATACTTA
131 TTATAGGCGCTAAAACTGA-TTCTCTTTTAAATTCACAAAGTGTCGATACTTA
*
369886 TATTAAAATATCGACACTTTCAATATAT-TCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACC
1 TATTAAAATATCGACACTTTCAATATATCT-GGTAGCTCTATACCGGTTTTGTCCTTTAGAGACC
* *
369950 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGTATCGATACATTGTTATAAAGTATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACAC
*
370015 TTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
130 TTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
370068 TATTAAAGTATCGAGACTTTCAATATAT-TCGGTAGCGT-TTTACCGGTTTTGTCCTTTAGAGA-
1 TATTAAAATATCGACACTTTCAATATATCT-GGTAGC-TCTATACCGGTTTTGTCCTTTAGAGAC
* * * *
370130 CAGTTTTGTCATATTTTTTCCTGTTATATCGTTATGGATTGATACATTTTTATAAAGTATCGACA
64 CGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACA
* *
370195 CTTTATAGGCTCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
129 CTTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * ** * * * * * * * *
370249 TATTAAATTATAGATACTTTCAATATATCCAGTATCGCTTTATCGATTTTGTCTTTTCGTGACCG
1 TATTAAAATATCGACACTTTCAATATATCTGGTAGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* * *
370314 GTTTTGTCATATTTTTTCCTGTTATATTGATGTGGATCGATACATTTTTATAAAGTATCGACA
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACA
370377 TAAACCGACA
Statistics
Matches: 603, Mismatches: 62, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
181 163 0.27
182 437 0.72
183 3 0.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (182 bp):
TATTAAAATATCGACACTTTCAATATATCTGGTAGCTCTATACCGGTTTTGTCCTTTAGAGACCG
GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:371056 original size:51 final size:51
Alignment explanation
Indices: 370980--371081 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
370970 ATAAATTGAA
370980 AATATTAGATAATATAAAATATTTATATATTATTTATAAACTTTGGTTAAT
1 AATATTAGATAATATAAAATATTTATATATTATTTATAAACTTTGGTTAAT
*
371031 AATATTAGATAATATAAAATATTTATATATTATTTATAAATTTTGGTTAAT
1 AATATTAGATAATATAAAATATTTATATATTATTTATAAACTTTGGTTAAT
371082 TCGATTAACT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (51 bp):
AATATTAGATAATATAAAATATTTATATATTATTTATAAACTTTGGTTAAT
Found at i:382401 original size:29 final size:29
Alignment explanation
Indices: 382346--382433 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
382336 AAAATATATA
* * *
382346 ATTAATTTCTTGAATATAAGATATTATTTT
1 ATTAATTT-TTTATTATAAGATGTTATTTT
* **
382376 ATTAATTTTTTATTATTAGATGTTA-TAA
1 ATTAATTTTTTATTATAAGATGTTATTTT
*
382404 AATAATTTTTTAATTATAAGATGTTATTTT
1 ATTAATTTTTT-ATTATAAGATGTTATTTT
382434 GTTGAGTCGA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
28 11 0.24
29 26 0.57
30 9 0.20
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (29 bp):
ATTAATTTTTTATTATAAGATGTTATTTT
Found at i:397992 original size:2 final size:2
Alignment explanation
Indices: 397985--398012 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
397975 TTATTATTAT
397985 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
398013 AAACGGTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:400809 original size:2 final size:2
Alignment explanation
Indices: 400802--400827 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
400792 GGGATAAATC
400802 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
400828 GTTATAGCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:416050 original size:5 final size:5
Alignment explanation
Indices: 416036--416066 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
416026 GCGCCGCCGC
416036 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
416067 GGTCGTGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:416078 original size:6 final size:6
Alignment explanation
Indices: 416067--416093 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
416057 TCTCGTCTCG
416067 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
416094 AATACATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:416211 original size:21 final size:21
Alignment explanation
Indices: 416186--416267 Score: 87
Period size: 21 Copynumber: 3.8 Consensus size: 21
416176 ATTTTGGACT
416186 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
416207 ATCGCAACGAGAACTTTGACT--
1 ATCGCAAC--GAACTTGGAATAA
*
416228 ATCGCAACGAACTTGAAATAA
1 ATCGCAACGAACTTGGAATAA
416249 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
416268 CTATCGCAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
19 8 0.16
21 23 0.47
23 18 0.37
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:416241 original size:42 final size:42
Alignment explanation
Indices: 416179--416276 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
416169 CGTTGCGATT
*
416179 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAGAAC
1 TTGGACTATCGCAACGAACTTGAAATAAATCGCAACGAGAAC
* *
416221 TTTGACTATCGCAACGAACTTGAAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGAAATAAATCGCAACGAGAAC
416263 TTGGACTATCGCAA
1 TTGGACTATCGCAA
416277 TGCGAATATG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGAAATAAATCGCAACGAGAAC
Found at i:416273 original size:21 final size:20
Alignment explanation
Indices: 416179--416282 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 20
416169 CGTTGCGATT
416179 TTGGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
* *
416198 TTGGAATAAATCGCAACGAGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
416221 TTTGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
* *
416240 TTGAAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
416263 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
416283 TATGTCAATC
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
19 14 0.21
21 33 0.50
23 19 0.29
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:416379 original size:19 final size:19
Alignment explanation
Indices: 416357--416400 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
416347 GGAGATCGTG
416357 TTGCGAATTATCGATCGCA
1 TTGCGAATTATCGATCGCA
416376 TTGCGAATTATCGATCGCA
1 TTGCGAATTATCGATCGCA
416395 TTGCGA
1 TTGCGA
416401 TTTAGTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (19 bp):
TTGCGAATTATCGATCGCA
Found at i:417141 original size:181 final size:183
Alignment explanation
Indices: 416785--417168 Score: 573
Period size: 181 Copynumber: 2.1 Consensus size: 183
416775 TTTTTTAATT
* * *
416785 TATATAA-A-ATTAAATA-TTTTTAATTAAAAAAACAGTTTTTAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTGTAATTAATTTAAATAATAAATAA
* *
416847 TTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTCAT
66 TTATAAAATAAAAATTTTATATAA-TATTTT-ATTAATTAATATTGATTTAGATTTAAAAGTCAT
* *
416912 TGAATCTTAAATTATTTATGGAGTTTTAAATAATTTGGGCTGAGCCCATATGTTA
129 TGAATCTTAAATTATTAATGGAGTTTTAAATAATTTGGGCTAAGCCCATATGTTA
416967 TATATAATATATTTAATATTTTTTAATTTAAAAAAACAGTTTGTAATTAATTTAAATAATAAATA
1 TATATAATATATTTAATATTTTTTAA-TTAAAAAAACAGTTTGTAATTAATTTAAATAATAAATA
*
417032 ATTATAAAATAAAAA-TTTATATAA-ATTTT-TTAATTAATATTGATTTAGATTTAAAAGTTATT
65 ATTATAAAATAAAAATTTTATATAATATTTTATTAATTAATATTGATTTAGATTTAAAAGTCATT
* ** * *
417094 GAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGTGTTAAGCCCATATGTTA
130 GAATCTTAAATTATTAATGGAGTTTTAAATAATTTGGGCTAAGCCCATATGTTA
*
417148 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
417169 AATTTCGGTT
Statistics
Matches: 184, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
181 98 0.53
182 7 0.04
183 5 0.03
184 7 0.04
185 16 0.09
186 51 0.28
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTGTAATTAATTTAAATAATAAATAA
TTATAAAATAAAAATTTTATATAATATTTTATTAATTAATATTGATTTAGATTTAAAAGTCATTG
AATCTTAAATTATTAATGGAGTTTTAAATAATTTGGGCTAAGCCCATATGTTA
Found at i:417295 original size:29 final size:30
Alignment explanation
Indices: 417229--417300 Score: 119
Period size: 29 Copynumber: 2.4 Consensus size: 30
417219 CCTTTAATCG
417229 ACCAAACTAATTCGGTGACCGACTGAATTA
1 ACCAAACTAATTCGGTGACCGACTGAATTA
417259 ACCAAACTAATTCGGT-ACCGACTGAATTA
1 ACCAAACTAATTCGGTGACCGACTGAATTA
* *
417288 GCCGAACTAATTC
1 ACCAAACTAATTC
417301 AGTTTGATCG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 24 0.60
30 16 0.40
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (30 bp):
ACCAAACTAATTCGGTGACCGACTGAATTA
Found at i:422106 original size:29 final size:30
Alignment explanation
Indices: 422064--422145 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 30
422054 CCCGAAGGAC
* *
422064 CTATCCAGAGGTCATACAG-ACCCCGGTAA
1 CTATCCAGAGGTCATAAAGAACCCCGGCAA
*
422093 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCATAAAGAACCCCGGCAA
* * **
422123 CTGTCCATAGGTCCCAAAGAACC
1 CTATCCAGAGGTCATAAAGAACC
422146 TAGGTAAACT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 18 0.40
30 27 0.60
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGAACCCCGGCAA
Found at i:422159 original size:31 final size:31
Alignment explanation
Indices: 422121--422215 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
422111 GAACCTCGGC
* *
422121 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
422152 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
422183 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
422214 AA
1 AA
422216 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:426395 original size:31 final size:32
Alignment explanation
Indices: 426307--426401 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 32
426297 GAACCTCGGC
* *
426307 AACTGTCCATAGGTC-CCAAAGAACCTAGGTA
1 AACTGTCCATATGTCTCCAAAGAACATAGGTA
* **
426338 AACTGTTCATATGT-TCCTTAGAACATAGGTA
1 AACTGTCCATATGTCTCCAAAGAACATAGGTA
* *
426369 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTCTCCAAAGAACATAGGTA
426400 AA
1 AA
426402 ACCCTCGACT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
31 47 0.92
32 4 0.08
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (32 bp):
AACTGTCCATATGTCTCCAAAGAACATAGGTA
Found at i:426557 original size:19 final size:19
Alignment explanation
Indices: 426535--426572 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
426525 CATATATCTC
426535 ATATCATAT-CACATGTATT
1 ATAT-ATATACACATGTATT
*
426554 ATATATATATACATGTATT
1 ATATATATACACATGTATT
426573 CATGTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (19 bp):
ATATATATACACATGTATT
Found at i:427317 original size:22 final size:23
Alignment explanation
Indices: 427273--427327 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
427263 ACAACCTACC
*
427273 TTTGAATTC--TAAGCAGCCCCA
1 TTTGAATTCAATAAGCAACCCCA
427294 TTTGAATTCAATAA-CAACCCCA
1 TTTGAATTCAATAAGCAACCCCA
427316 TTTGAATTCAAT
1 TTTGAATTCAAT
427328 TTTAACAGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 9 0.29
22 19 0.61
23 3 0.10
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.33
Consensus pattern (23 bp):
TTTGAATTCAATAAGCAACCCCA
Found at i:428499 original size:144 final size:144
Alignment explanation
Indices: 428188--428468 Score: 393
Period size: 144 Copynumber: 2.0 Consensus size: 144
428178 ATAATGTTTC
* * * *
428188 AACATTTGCAGTCTCTTTTCGTTTTGTCTCGTTCCTTTTCCCTTGATCCTCAGGATTGTCTTCCC
1 AACATTTGCAGTCTCTTTTCGTTTTGCCTCGTTCCTTTTCCCTTGATCCTCAGCACTATCTTCCC
* * * * * *
428253 TGTGCTGTTTCAGAACATTTGCAGTCCCTTTTCCTGTAGCCGCTCGATGTTCGACATTGTCTCTC
66 TGTGCTGTTCCAAAACATTTGCAGCCCCTTTTCCTGTAGCCGCTCGATGTTCAACATTCTCTCCC
*
428318 TTCTGTCGATCCGA
131 ATCTGTCGATCCGA
* * *
428332 AACATTTGCAGTCTCTTTTCGTTTTGCCTCGTTCCTTTTCTCTTGATCCTCAGCACTATCTTTCT
1 AACATTTGCAGTCTCTTTTCGTTTTGCCTCGTTCCTTTTCCCTTGATCCTCAGCACTATCTTCCC
* * *
428397 TTTGCTGTTCCAAAACATTTGCAGCCCCTTTTCCTTTAG-CGCCTCGATTTTCAACATTCTCTCC
66 TGTGCTGTTCCAAAACATTTGCAGCCCCTTTTCCTGTAGCCG-CTCGATGTTCAACATTCTCTCC
428461 CATCTGTC
130 CATCTGTC
428469 TTTCTGAATG
Statistics
Matches: 119, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
143 2 0.02
144 117 0.98
ACGTcount: A:0.14, C:0.30, G:0.14, T:0.42
Consensus pattern (144 bp):
AACATTTGCAGTCTCTTTTCGTTTTGCCTCGTTCCTTTTCCCTTGATCCTCAGCACTATCTTCCC
TGTGCTGTTCCAAAACATTTGCAGCCCCTTTTCCTGTAGCCGCTCGATGTTCAACATTCTCTCCC
ATCTGTCGATCCGA
Found at i:431480 original size:41 final size:41
Alignment explanation
Indices: 431423--431504 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
431413 ACCAACGGTG
*
431423 CTGAACATTGATACACGAATGTACCAAAGCTAAATTGATAA
1 CTGAACATTGATACACGAATGTACCAAAGCTAAACTGATAA
* *
431464 CTGAACATTGATACACGAATGTATCAAAGCTGAACTGATAA
1 CTGAACATTGATACACGAATGTACCAAAGCTAAACTGATAA
431505 GTACTCACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (41 bp):
CTGAACATTGATACACGAATGTACCAAAGCTAAACTGATAA
Found at i:431658 original size:36 final size:36
Alignment explanation
Indices: 431604--431687 Score: 125
Period size: 36 Copynumber: 2.3 Consensus size: 36
431594 ATTTGTATAC
*
431604 GATAATTGTAAAATATCTGATAACTGAAAATCATCT
1 GATAACTGTAAAATATCTGATAACTGAAAATCATCT
431640 GATAACTG-AAAATCATCTGATAACTGAAAATCATCT
1 GATAACTGTAAAAT-ATCTGATAACTGAAAATCATCT
* *
431676 TATAACTATAAA
1 GATAACTGTAAA
431688 TATTTAGAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 5 0.12
36 35 0.81
37 3 0.07
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (36 bp):
GATAACTGTAAAATATCTGATAACTGAAAATCATCT
Found at i:431688 original size:18 final size:18
Alignment explanation
Indices: 431613--431682 Score: 124
Period size: 18 Copynumber: 3.9 Consensus size: 18
431603 CGATAATTGT
431613 AAAAT-ATCTGATAACTG
1 AAAATCATCTGATAACTG
431630 AAAATCATCTGATAACTG
1 AAAATCATCTGATAACTG
431648 AAAATCATCTGATAACTG
1 AAAATCATCTGATAACTG
*
431666 AAAATCATCTTATAACT
1 AAAATCATCTGATAACT
431683 ATAAATATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
17 5 0.10
18 46 0.90
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.30
Consensus pattern (18 bp):
AAAATCATCTGATAACTG
Found at i:432761 original size:15 final size:16
Alignment explanation
Indices: 432728--432761 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
432718 TAATCTAAGC
*
432728 ATAAATATAAAATTCG
1 ATAAAAATAAAATTCG
432744 ATAAAAATAAAA-TCG
1 ATAAAAATAAAATTCG
432759 ATA
1 ATA
432762 CTTGAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
ATAAAAATAAAATTCG
Found at i:434889 original size:12 final size:11
Alignment explanation
Indices: 434872--434910 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
434862 TTTTTGTAAA
434872 AATTATAATTAT
1 AATTATAA-TAT
434884 AATTATAATATT
1 AATTATAATA-T
*
434896 AATTATTATAT
1 AATTATAATAT
434907 AATT
1 AATT
434911 TTATTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 7 0.28
12 18 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AATTATAATAT
Found at i:434915 original size:20 final size:21
Alignment explanation
Indices: 434892--434935 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
434882 ATAATTATAA
434892 TATTAATTA-TTATATAATTT
1 TATTAATTATTTATATAATTT
*
434912 TATTAATTATTTTTATAATTT
1 TATTAATTATTTATATAATTT
434933 TAT
1 TAT
434936 ATTTGTAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTAATTATTTATATAATTT
Found at i:434938 original size:23 final size:22
Alignment explanation
Indices: 434880--434938 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
434870 AAAATTATAA
*
434880 TTATAATTATAATATTAATTATT
1 TTATAATT-TTATATTAATTATT
*
434903 ATATAA-TTT-TATTAATTATTT
1 TTATAATTTTATATTAATTA-TT
434924 TTATAATTTTATATT
1 TTATAATTTTATATT
434939 TGTAGCAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 9 0.30
21 8 0.27
22 4 0.13
23 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATAATTTTATATTAATTATT
Found at i:438790 original size:23 final size:21
Alignment explanation
Indices: 438764--438808 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
438754 ATATTAGTGT
438764 AATAAATCATGTGAATTAATATA
1 AATAAATCATGTG-ATT-ATATA
*
438787 AATAATTCATGTGATTATATA
1 AATAAATCATGTGATTATATA
438808 A
1 A
438809 GTTATATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 12 0.57
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (21 bp):
AATAAATCATGTGATTATATA
Found at i:439231 original size:18 final size:17
Alignment explanation
Indices: 439203--439239 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
439193 GGACATATAT
439203 GATATGTGGTCATTCGG
1 GATATGTGGTCATTCGG
439220 GATATAGTGGTCATTCGG
1 GATAT-GTGGTCATTCGG
439238 GA
1 GA
439240 CAAATTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.22, C:0.11, G:0.35, T:0.32
Consensus pattern (17 bp):
GATATGTGGTCATTCGG
Found at i:440741 original size:54 final size:54
Alignment explanation
Indices: 440541--440747 Score: 243
Period size: 54 Copynumber: 3.8 Consensus size: 54
440531 GTTACACACA
* * *
440541 TAATTCATAATGAGTTTATGAATTACCATATCAACACTATGTATGCAACCCAAA
1 TAATTCATAATGAGTTTATGAATTACCATATCAACACTATGTGTGCAACCTAAG
* * * * * *
440595 TAATTTATAATGAGTTTGTGAATTACCGTATCGATACTATGTGTACAACCTAAG
1 TAATTCATAATGAGTTTATGAATTACCATATCAACACTATGTGTGCAACCTAAG
** *
440649 TAATTCATAATGAGTTTATGAATTACCATATCGTCACTATGTGTGCAACCTATG
1 TAATTCATAATGAGTTTATGAATTACCATATCAACACTATGTGTGCAACCTAAG
* * * * ** *
440703 TAATTCACAATCATTTTGTGAATTACTGTATTAACACTATGTGTG
1 TAATTCATAATGAGTTTATGAATTACCATATCAACACTATGTGTG
440748 AAAAACCACA
Statistics
Matches: 128, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 128 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (54 bp):
TAATTCATAATGAGTTTATGAATTACCATATCAACACTATGTGTGCAACCTAAG
Found at i:440742 original size:108 final size:108
Alignment explanation
Indices: 440541--440746 Score: 286
Period size: 108 Copynumber: 1.9 Consensus size: 108
440531 GTTACACACA
* *
440541 TAATTCATAATGAGTTTATGAATTACCATATCAACACTATGTATGCAACCCAAATAATTTATAAT
1 TAATTCATAATGAGTTTATGAATTACCATATCAACACTATGTATGCAACCCAAATAATTCACAAT
* * *
440606 GAGTTTGTGAATTACCGTATCGATACTATGTGTACAACCTAAG
66 CAGTTTGTGAATTACCGTATCAACACTATGTGTACAACCTAAG
** * * **
440649 TAATTCATAATGAGTTTATGAATTACCATATCGTCACTATGTGTGCAACCTATGTAATTCACAAT
1 TAATTCATAATGAGTTTATGAATTACCATATCAACACTATGTATGCAACCCAAATAATTCACAAT
* * *
440714 CATTTTGTGAATTACTGTATTAACACTATGTGT
66 CAGTTTGTGAATTACCGTATCAACACTATGTGT
440747 GAAAAACCAC
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
108 84 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (108 bp):
TAATTCATAATGAGTTTATGAATTACCATATCAACACTATGTATGCAACCCAAATAATTCACAAT
CAGTTTGTGAATTACCGTATCAACACTATGTGTACAACCTAAG
Found at i:444758 original size:54 final size:54
Alignment explanation
Indices: 444673--444991 Score: 426
Period size: 54 Copynumber: 5.9 Consensus size: 54
444663 TATGTAGTAT
*
444673 TTACCGTATCGACACTATGTGTGCAATCCACGTAATTCATAATGAGTTTGTGAA
1 TTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
*
444727 TTACCGTATC-AGCACTATGTGTGCAACCCACGTAATTCATACTGAGTTTGTGAA
1 TTACCGTATCGA-CACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* * * **
444781 TTACCATATCGGCACTATGTGTCCAACCCAAATAATTCATAATGAGTTTGTGAA
1 TTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* * *
444835 TTACCGTATCGATACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAA
1 TTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* *
444889 TTACCGTATCGATACTATGTGTGCAACCTACGTAATTCATAATGAGTTTGTGAA
1 TTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* * * * * * *
444943 TTACTGTATAGGCACTATATGTGAAAAACCACAG-AATTTATAATGAGTT
1 TTACCGTATCGACACTATGTGTG-CAACCCAC-GTAATTCATAATGAGTT
444992 GTAATATTCA
Statistics
Matches: 237, Mismatches: 24, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.00
54 216 0.91
55 19 0.08
56 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (54 bp):
TTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
Found at i:448558 original size:27 final size:27
Alignment explanation
Indices: 448523--448574 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
448513 TTTTCTTGCG
*
448523 TTTTTAGTTGTACTCTTTTCACTATAT
1 TTTTTAGTTGTACTATTTTCACTATAT
448550 TTTTTAGTTGTACTATTTTCACTAT
1 TTTTTAGTTGTACTATTTTCACTAT
448575 GTTTATGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.13, G:0.08, T:0.60
Consensus pattern (27 bp):
TTTTTAGTTGTACTATTTTCACTATAT
Found at i:448585 original size:27 final size:27
Alignment explanation
Indices: 448528--448585 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
448518 TTGCGTTTTT
* * *
448528 AGTTGTACTCTTTTCACTATATTTTTT
1 AGTTGTACTATTTTCACTATATTTATG
*
448555 AGTTGTACTATTTTCACTATGTTTATG
1 AGTTGTACTATTTTCACTATATTTATG
448582 AGTT
1 AGTT
448586 TTTTAGTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (27 bp):
AGTTGTACTATTTTCACTATATTTATG
Found at i:450012 original size:19 final size:19
Alignment explanation
Indices: 449975--450023 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
449965 TCTTAGGTCT
*
449975 ATTTTCTATTTTAATTATC
1 ATTTTCTATATTAATTATC
449994 ATTTATCTATATTAA-TATC
1 ATTT-TCTATATTAATTATC
*
450013 ATATT-TATATT
1 ATTTTCTATATT
450024 GTTGGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 1 0.04
19 11 0.41
20 9 0.33
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTCTATATTAATTATC
Found at i:450540 original size:20 final size:20
Alignment explanation
Indices: 450515--450552 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
450505 ATGCCCATAA
*
450515 CAGGGTGCATGGATGCACAG
1 CAGGGTGCATCGATGCACAG
450535 CAGGGTGCATCGATGCAC
1 CAGGGTGCATCGATGCAC
450553 TAATTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.37, T:0.16
Consensus pattern (20 bp):
CAGGGTGCATCGATGCACAG
Found at i:450596 original size:19 final size:20
Alignment explanation
Indices: 450572--450625 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
450562 TCGAAATGGA
*
450572 GTGCATGGATGCACT-CATG
1 GTGCATGGATGCACTGCAGG
* *
450591 GTGCATCGACGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
450611 GTGCATGGATGCACT
1 GTGCATGGATGCACT
450626 TTGACACCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:450615 original size:20 final size:19
Alignment explanation
Indices: 450572--450616 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
450562 TCGAAATGGA
* * *
450572 GTGCATGGATGCACTCATG
1 GTGCATCGACGCACTCAGG
450591 GTGCATCGACGCACTGCAGG
1 GTGCATCGACGCACT-CAGG
450611 GTGCAT
1 GTGCAT
450617 GGATGCACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.22
Consensus pattern (19 bp):
GTGCATCGACGCACTCAGG
Found at i:450871 original size:21 final size:21
Alignment explanation
Indices: 450847--450886 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
450837 ATGTTTAATG
450847 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
450868 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
450887 CCAATTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:452399 original size:21 final size:21
Alignment explanation
Indices: 452375--452414 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
452365 AAGACTTTAT
452375 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
452396 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
452415 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:456264 original size:23 final size:23
Alignment explanation
Indices: 456223--456281 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
456213 TTGGCGCATG
456223 AGGTATCGATA-CCCCTTTGAAT
1 AGGTATCGATACCCCCTTTGAAT
*
456245 GGGTATCGATACCCCCTTTGAAT
1 AGGTATCGATACCCCCTTTGAAT
456268 AGGTA-CTGATACCC
1 AGGTATC-GATACCC
456282 TCCCCTAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (23 bp):
AGGTATCGATACCCCCTTTGAAT
Found at i:458303 original size:19 final size:19
Alignment explanation
Indices: 458275--458321 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
458265 ATGTTTGTGG
* *
458275 ATGTTAGAATTTGTTTTGA
1 ATGTTTGAATTTGTTATGA
*
458294 ATGTTTGAATTTGTTATGG
1 ATGTTTGAATTTGTTATGA
458313 ATG-TTGAAT
1 ATGTTTGAAT
458322 GTTTAACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (19 bp):
ATGTTTGAATTTGTTATGA
Found at i:458995 original size:20 final size:20
Alignment explanation
Indices: 458970--459007 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
458960 CAGATTGCCT
*
458970 AGAGGGTACTGATACCCCCA
1 AGAGGGTACCGATACCCCCA
458990 AGAGGGTACCGATACCCC
1 AGAGGGTACCGATACCCC
459008 TATGTAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (20 bp):
AGAGGGTACCGATACCCCCA
Found at i:461048 original size:15 final size:16
Alignment explanation
Indices: 461026--461062 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
461016 TTCTTCTTTT
461026 TCTT-ATTTTTCTT-C
1 TCTTCATTTTTCTTCC
461040 TCTTCA-TTTTCTTCC
1 TCTTCATTTTTCTTCC
461055 TCTTCATT
1 TCTTCATT
461063 CAAAATCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.55
15 8 0.40
16 1 0.05
ACGTcount: A:0.08, C:0.27, G:0.00, T:0.65
Consensus pattern (16 bp):
TCTTCATTTTTCTTCC
Found at i:461049 original size:14 final size:15
Alignment explanation
Indices: 461032--461062 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
461022 TTTTTCTTAT
461032 TTTTCTT-CTCTTCA
1 TTTTCTTCCTCTTCA
461046 TTTTCTTCCTCTTCA
1 TTTTCTTCCTCTTCA
461061 TT
1 TT
461063 CAAAATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTCTTCCTCTTCA
Found at i:462460 original size:20 final size:20
Alignment explanation
Indices: 462435--462472 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
462425 CCGTTGCAGC
*
462435 CAGGGTGCATGGATGCACAG
1 CAGGGTGCATCGATGCACAG
462455 CAGGGTGCATCGATGCAC
1 CAGGGTGCATCGATGCAC
462473 TAATTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.37, T:0.16
Consensus pattern (20 bp):
CAGGGTGCATCGATGCACAG
Found at i:479786 original size:20 final size:19
Alignment explanation
Indices: 479757--479812 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
479747 AAATGACCAA
479757 CAAATTCGCAACGCGAACT
1 CAAATTCGCAACGCGAACT
* * *
479776 CTAATTTCGCAACACAGAAGT
1 C-AAATTCGCAACGC-GAACT
479797 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
479813 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.10
20 22 0.73
21 5 0.17
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.18
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:479820 original size:20 final size:20
Alignment explanation
Indices: 479757--479893 Score: 64
Period size: 20 Copynumber: 6.8 Consensus size: 20
479747 AAATGACCAA
* **
479757 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACACGATTTC
* * **
479777 TAATTTCGCAACACAGAAGT-
1 CAAATTCGCAACAC-GATTTC
*
479797 CAAATTCGCAACGCGATTTC
1 CAAATTCGCAACACGATTTC
** *
479817 CAAATTTACAACACTAAATTT-
1 CAAATTCGCAACAC--GATTTC
*
479838 CAAATTCGCAACTCGATTTC
1 CAAATTCGCAACACGATTTC
** * *
479858 TGAATTCGCAA-ATCAATTTT
1 CAAATTCGCAACA-CGATTTC
*
479878 CGAATTCGCAACACGA
1 CAAATTCGCAACACGA
479894 ATTTTAATTT
Statistics
Matches: 86, Mismatches: 24, Indels: 14
0.69 0.19 0.11
Matches are distributed among these distances:
19 7 0.08
20 59 0.69
21 16 0.19
22 4 0.05
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACACGATTTC
Found at i:479829 original size:40 final size:42
Alignment explanation
Indices: 479757--479857 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 42
479747 AAATGACCAA
** * *
479757 CAAATTCGCAACGCGAACT-CTAATTTCGCAACAC-AGAA-GT
1 CAAATTCGCAACGCGATTTCCAAATTTCACAACACTA-AATGT
*
479797 CAAATTCGCAACGCGATTTCCAAATTT-ACAACACTAAATTT
1 CAAATTCGCAACGCGATTTCCAAATTTCACAACACTAAATGT
*
479838 CAAATTCGCAACTCGATTTC
1 CAAATTCGCAACGCGATTTC
479858 TGAATTCGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
40 25 0.48
41 27 0.52
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.26
Consensus pattern (42 bp):
CAAATTCGCAACGCGATTTCCAAATTTCACAACACTAAATGT
Found at i:480085 original size:14 final size:15
Alignment explanation
Indices: 480066--480103 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
480056 TCTTCATCTC
480066 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
480080 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
480096 TAATTTTT
1 TAATTTTT
480104 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:480693 original size:12 final size:12
Alignment explanation
Indices: 480672--480705 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
480662 ACCACATTTC
*
480672 CAATACCAAACA
1 CAATATCAAACA
480684 CAATATCAAACA
1 CAATATCAAACA
*
480696 CAATCTCAAA
1 CAATATCAAA
480706 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:480956 original size:24 final size:24
Alignment explanation
Indices: 480831--480944 Score: 210
Period size: 24 Copynumber: 4.8 Consensus size: 24
480821 GTATTCGAAA
480831 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
*
480855 TTTGATCTTGGTCAATACCCAAAC
1 TTTGATCTTGGTCAATACCCAGAC
480879 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
*
480903 TTTGATCTTAGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
480927 TTTGATCTTGGTCAATAC
1 TTTGATCTTGGTCAATAC
480945 TCGGATTTTG
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 86 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:484980 original size:21 final size:21
Alignment explanation
Indices: 484956--485014 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
484946 GTGGAAGAGA
484956 CCTCTTGAACGATGACAAGGG
1 CCTCTTGAACGATGACAAGGG
**
484977 CCTCTTGAACGATGGGAAGGG
1 CCTCTTGAACGATGACAAGGG
484998 CCTCTTGAACGATGACA
1 CCTCTTGAACGATGACA
485015 GGTGAATCGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (21 bp):
CCTCTTGAACGATGACAAGGG
Found at i:485377 original size:20 final size:21
Alignment explanation
Indices: 485354--485398 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
485344 CCATTATCAT
485354 CACGTAAACATC-TACCTCAC
1 CACGTAAACATCGTACCTCAC
* *
485374 CACGTAAAGATCGTACCTCAT
1 CACGTAAACATCGTACCTCAC
485395 CACG
1 CACG
485399 CTATGCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.33, C:0.36, G:0.11, T:0.20
Consensus pattern (21 bp):
CACGTAAACATCGTACCTCAC
Found at i:486981 original size:20 final size:20
Alignment explanation
Indices: 486951--487012 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
486941 ACTTAAATTT
486951 GCAACGCGAAAATGAAAATC
1 GCAACGCGAAAATGAAAATC
* *
486971 GCAATGTGAAAATGAAAATC
1 GCAACGCGAAAATGAAAATC
*
486991 GCAACGCGAAACT-AAAATC
1 GCAACGCGAAAATGAAAATC
487010 GCA
1 GCA
487013 TTGCGATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 9 0.24
20 28 0.76
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (20 bp):
GCAACGCGAAAATGAAAATC
Found at i:487043 original size:20 final size:20
Alignment explanation
Indices: 487018--487056 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
487008 TCGCATTGCG
*
487018 ATTTTCGTGTTGCGAATTTT
1 ATTTTCGTATTGCGAATTTT
487038 ATTTTCGTATTGCGAATTT
1 ATTTTCGTATTGCGAATTT
487057 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.54
Consensus pattern (20 bp):
ATTTTCGTATTGCGAATTTT
Found at i:487063 original size:20 final size:20
Alignment explanation
Indices: 487020--487063 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
487010 GCATTGCGAT
* * *
487020 TTTCGTGTTGCGAATTTTAT
1 TTTCGTATTGCGAATTTAAG
487040 TTTCGTATTGCGAATTTAAG
1 TTTCGTATTGCGAATTTAAG
487060 TTTC
1 TTTC
487064 AAAATTCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTATTGCGAATTTAAG
Found at i:487418 original size:22 final size:22
Alignment explanation
Indices: 487391--487441 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
487381 GATGGAGATA
487391 GACGGATTTTACCGGAGATGGG
1 GACGGATTTTACCGGAGATGGG
** * *
487413 GACGGATTTTTTCGTAGATGGT
1 GACGGATTTTACCGGAGATGGG
487435 GACGGAT
1 GACGGAT
487442 GTCGCTGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.37, T:0.29
Consensus pattern (22 bp):
GACGGATTTTACCGGAGATGGG
Found at i:493813 original size:19 final size:18
Alignment explanation
Indices: 493775--493822 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
493765 AAGAGAGAGA
*
493775 AAAAATAAAAAAATTGAG
1 AAAAATAAAAAAATTAAG
493793 -AAAATAAAAAAATGTTAAG
1 AAAAATAAAAAAA--TTAAG
493812 AAAAATAAAAA
1 AAAAATAAAAA
493823 TGAAGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 12 0.46
19 4 0.15
20 10 0.38
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (18 bp):
AAAAATAAAAAAATTAAG
Found at i:495100 original size:33 final size:33
Alignment explanation
Indices: 495052--495128 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
495042 GGTTTAGTAA
* *
495052 CCTGCTGGGTATTCAGGCTTTACCCGACCTTGG
1 CCTGCTGGGTCTTCAGGATTTACCCGACCTTGG
*
495085 CCTGTTGGGTCTTCAGGATTTACCCGACCTTGG
1 CCTGCTGGGTCTTCAGGATTTACCCGACCTTGG
*
495118 CATGCTGGGTC
1 CCTGCTGGGTC
495129 AGTTAGGCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.31
Consensus pattern (33 bp):
CCTGCTGGGTCTTCAGGATTTACCCGACCTTGG
Found at i:495247 original size:21 final size:20
Alignment explanation
Indices: 495222--495280 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
495212 TCAGACGAAA
495222 AATATTAATAAAATAATAAAT
1 AATATTAATAAAATAA-AAAT
* *
495243 AATATTAAATAATATAAATAT
1 AATATT-AATAAAATAAAAAT
495264 AATA-TAA-AAAATAAAAA
1 AATATTAATAAAATAAAAA
495281 ATAAATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 8 0.24
19 2 0.06
20 1 0.03
21 13 0.39
22 9 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATATTAATAAAATAAAAAT
Found at i:495282 original size:21 final size:21
Alignment explanation
Indices: 495222--495284 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 21
495212 TCAGACGAAA
*
495222 AATATTAATAAAATAATAA-AT
1 AATATTAA-AAAATAAAAATAT
* *
495243 AATATTAAATAATATAAATAT
1 AATATTAAAAAATAAAAATAT
495264 AATA-TAAAAAATAAAAA-AT
1 AATATTAAAAAATAAAAATAT
495283 AA
1 AA
495285 ATAAAATCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 18 0.50
21 14 0.39
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AATATTAAAAAATAAAAATAT
Found at i:495327 original size:36 final size:36
Alignment explanation
Indices: 495287--495472 Score: 230
Period size: 36 Copynumber: 5.1 Consensus size: 36
495277 AAAAATAAAT
* **
495287 AAAATCATTTTTAAAACTATATATTATATATGCTCA
1 AAAATTATTTTTAAAACTATATATTATATATTTTCA
* *
495323 AAAATTATTTTTGAAACTATATAATATATGTATTTTCA
1 AAAATTATTTTTAAAACTATAT-AT-TATATATTTTCA
*
495361 AAAATTATTTTTAAAACTATATAATATATATTTTCA
1 AAAATTATTTTTAAAACTATATATTATATATTTTCA
* *
495397 AAAA-TATTTTCAAAATTATATATTATATATATTTTCA
1 AAAATTATTTTTAAAACTATATA-T-TATATATTTTCA
* * *
495434 AAAATTGTTTTTAAAACTATATAATATATATTTTTA
1 AAAATTATTTTTAAAACTATATATTATATATTTTCA
495470 AAA
1 AAA
495473 CTATATAATA
Statistics
Matches: 129, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
35 16 0.12
36 49 0.38
37 19 0.15
38 45 0.35
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (36 bp):
AAAATTATTTTTAAAACTATATATTATATATTTTCA
Found at i:495371 original size:38 final size:38
Alignment explanation
Indices: 495287--495530 Score: 257
Period size: 38 Copynumber: 6.3 Consensus size: 38
495277 AAAAATAAAT
* **
495287 AAAATCATTTTTAAAACTATAT-AT-TATATATGCTCA
1 AAAATTATTTTTAAAACTATATAATATATATATTTTCA
* *
495323 AAAATTATTTTTGAAACTATATAATATATGTATTTTCA
1 AAAATTATTTTTAAAACTATATAATATATATATTTTCA
495361 AAAATTATTTTTAAAACTATAT-A-ATATATATTTTCA
1 AAAATTATTTTTAAAACTATATAATATATATATTTTCA
* * *
495397 AAAA-TATTTTCAAAATTATATATTATATATATTTTCA
1 AAAATTATTTTTAAAACTATATAATATATATATTTTCA
*
495434 AAAATTGTTTTTAAAACTATATAATATATAT-TTTTAAAACTA
1 AAAATTATTTTTAAAACTATATAATATATATATTTT----C-A
* *
495476 TATAATATATATTTTTAAAACTATATATTATATATATTTTTA
1 -A-AA-AT-TATTTTTAAAACTATATAATATATATATTTTCA
495518 AAAATTGATTTTT
1 AAAATT-ATTTTT
495531 TTAAAAACTA
Statistics
Matches: 175, Mismatches: 17, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
35 15 0.09
36 36 0.21
37 24 0.14
38 53 0.30
39 8 0.05
40 2 0.01
41 2 0.01
42 2 0.01
43 1 0.01
44 2 0.01
45 2 0.01
46 24 0.14
47 4 0.02
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (38 bp):
AAAATTATTTTTAAAACTATATAATATATATATTTTCA
Found at i:495445 original size:73 final size:74
Alignment explanation
Indices: 495287--495472 Score: 266
Period size: 73 Copynumber: 2.5 Consensus size: 74
495277 AAAAATAAAT
* * ** **
495287 AAAATCATTTTTAAAACTATATATTATATATGCTCAAAAATTATTTTTGAAACTATATAATATAT
1 AAAATTATTTTTAAAACTATATAATATATATTTTCAAAAATTATTTTCAAAACTATATAATATAT
*
495352 GTATTTTCA
66 ATATTTTCA
* *
495361 AAAATTATTTTTAAAACTATATAATATATATTTTCAAAAA-TATTTTCAAAATTATATATTATAT
1 AAAATTATTTTTAAAACTATATAATATATATTTTCAAAAATTATTTTCAAAACTATATAATATAT
495425 ATATTTTCA
66 ATATTTTCA
* *
495434 AAAATTGTTTTTAAAACTATATAATATATATTTTTAAAA
1 AAAATTATTTTTAAAACTATATAATATATATTTTCAAAA
495473 CTATATAATA
Statistics
Matches: 101, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
73 65 0.64
74 36 0.36
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (74 bp):
AAAATTATTTTTAAAACTATATAATATATATTTTCAAAAATTATTTTCAAAACTATATAATATAT
ATATTTTCA
Found at i:495485 original size:25 final size:23
Alignment explanation
Indices: 495441--495520 Score: 142
Period size: 23 Copynumber: 3.4 Consensus size: 23
495431 TCAAAAATTG
495441 TTTTTAAAACTATATAATATATA
1 TTTTTAAAACTATATAATATATA
495464 TTTTTAAAACTATATAATATATA
1 TTTTTAAAACTATATAATATATA
495487 TTTTTAAAACTATATATTATATATA
1 TTTTTAAAACTATATA--ATATATA
495512 TTTTTAAAA
1 TTTTTAAAA
495521 ATTGATTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 39 0.71
25 16 0.29
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTTAAAACTATATAATATATA
Found at i:496906 original size:230 final size:230
Alignment explanation
Indices: 496497--496978 Score: 646
Period size: 230 Copynumber: 2.1 Consensus size: 230
496487 ATATCCTTTA
* *
496497 TTGTGAAGTTGAAATCCAATATTATATAAGTTGCGTCGTTTCGAGTTCAATATATTTCGTATTGA
1 TTGTGAAGTTGAAATCCAATATTATATAAGTTGCGTCGTTTCGAGTTCAATATATTCCGTAGTGA
* * * *
496562 AGATAAAATCTAGCTCGAAATTTGATCTGAAAAGTTGTTAGTCACAGATGACTCCTTCGTCGTGA
66 AGATAAAATCAAGATCGAAATATGATCTGAAAAGTTGTTAGTCACAGATGACTCATTCGTCGTGA
* * ** * *
496627 AGTTTGATCAATTTTTTTGGTACGATATCCTTCTTCGTGAAGTTGAAATCGTAGATGGCTCATTC
131 AGTTGGATCAATCTTTCAGGTACGATATCCTTCTTCGTGAAGATGAAATCATAGATGGCTCATTC
**
496692 GTTATAAAGTTGAGCTTTGAATTAGACGTCATTCG
196 ACTATAAAGTTGAGCTTTGAATTAGACGTCATTCG
* * * *
496727 TTGTAAAGTTGAAATCCAATCTTGTATAAGTTGTGTCGTTTCGAGTTCAATATATTCCGCT-GTG
1 TTGTGAAGTTGAAATCCAATATTATATAAGTTGCGTCGTTTCGAGTTCAATATATTCCG-TAGTG
* * * *
496791 AAGTTGAAATCAAGATCGAAATATGAAT-TGGAAAGTTGTTTGTCACAGATGACTCATTCGTCGT
65 AAGATAAAATCAAGATCGAAATATG-ATCTGAAAAGTTGTTAGTCACAGATGACTCATTCGTCGT
* * * * *
496855 GAAGTTGGGTCAATCTTTCAGGTATGATATCCTT-TGTCGTGAAGATGAAATCATGGATGGTTCC
129 GAAGTTGGATCAATCTTTCAGGTACGATATCCTTCT-TCGTGAAGATGAAATCATAGATGGCTCA
* *
496919 TTCACTGTGAAGTTGAGCTTTGAATTAGACGTCATTCG
193 TTCACTATAAAGTTGAGCTTTGAATTAGACGTCATTCG
*
496957 TTGTGAAGTTAAAATCCAATAT
1 TTGTGAAGTTGAAATCCAATAT
496979 CGAGTTGTAG
Statistics
Matches: 217, Mismatches: 32, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
229 1 0.00
230 213 0.98
231 3 0.01
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (230 bp):
TTGTGAAGTTGAAATCCAATATTATATAAGTTGCGTCGTTTCGAGTTCAATATATTCCGTAGTGA
AGATAAAATCAAGATCGAAATATGATCTGAAAAGTTGTTAGTCACAGATGACTCATTCGTCGTGA
AGTTGGATCAATCTTTCAGGTACGATATCCTTCTTCGTGAAGATGAAATCATAGATGGCTCATTC
ACTATAAAGTTGAGCTTTGAATTAGACGTCATTCG
Found at i:501647 original size:24 final size:24
Alignment explanation
Indices: 501607--501659 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
501597 AAGTATTATA
* * *
501607 AAAATGAAAAAAGATATTAAAAGT
1 AAAATGAAAAAAAATATAAAAAAT
501631 AAAA-GAAATAAAAATATAAAAAAT
1 AAAATGAAA-AAAAATATAAAAAAT
501655 AAAAT
1 AAAAT
501660 AATAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.19
Consensus pattern (24 bp):
AAAATGAAAAAAAATATAAAAAAT
Found at i:501704 original size:30 final size:30
Alignment explanation
Indices: 501663--501719 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
501653 ATAAAATAAT
501663 AAATAAAAATTTAAAGGATCAAATTGAAAC
1 AAATAAAAATTTAAAGGATCAAATTGAAAC
* * *
501693 AAATCAAAATTTTATGGATCAAATTGA
1 AAATAAAAATTTAAAGGATCAAATTGA
501720 TGCTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (30 bp):
AAATAAAAATTTAAAGGATCAAATTGAAAC
Found at i:502950 original size:26 final size:26
Alignment explanation
Indices: 502887--502951 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
502877 GAAAAATATT
* *
502887 AATAAAATAATAA-ATAAAAATAAAT
1 AATAAAAAAATAATATAAAAATAAAA
*** *
502912 AATTTTAATATAATATAAAAATAAAA
1 AATAAAAAAATAATATAAAAATAAAA
502938 AATAAAAAAATAAT
1 AATAAAAAAATAAT
502952 TTTTAAAACT
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (26 bp):
AATAAAAAAATAATATAAAAATAAAA
Found at i:503047 original size:36 final size:35
Alignment explanation
Indices: 502951--503173 Score: 214
Period size: 36 Copynumber: 6.4 Consensus size: 35
502941 AAAAAAATAA
* * **
502951 TTTTTAAAACTATATATTAAATATGCTCAAAAATT
1 TTTTTAAAACTATATAATATATATTTTCAAAAATT
**
502986 ATTTTCGAAACTATATAATATATATTTTCAAAAATT
1 -TTTTTAAAACTATATAATATATATTTTCAAAAATT
503022 GTTTTTAAAACTATATAATATATATTTTC-AAAA--
1 -TTTTTAAAACTATATAATATATATTTTCAAAAATT
* *
503055 ---CT---A-TATATTATATATATTTTCAAAAATT
1 TTTTTAAAACTATATAATATATATTTTCAAAAATT
*
503083 GTTTTTAAAACTATATAATATATATTTTCAAAAATA
1 -TTTTTAAAACTATATAATATATATTTTCAAAAATT
*
503119 TTTTCAAAACTATATATTATATATATTTTCAAAAACCGTT
1 TTTTTAAAACTATATA--ATATATATTTTCAAAAA---TT
503159 TTTTTAAAACTATAT
1 TTTTTAAAACTATAT
503174 GTTTCAAAAA
Statistics
Matches: 154, Mismatches: 17, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
25 17 0.11
26 5 0.03
29 1 0.01
32 1 0.01
35 20 0.13
36 78 0.51
37 17 0.11
40 15 0.10
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (35 bp):
TTTTTAAAACTATATAATATATATTTTCAAAAATT
Found at i:503054 original size:23 final size:24
Alignment explanation
Indices: 503023--503079 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 24
503013 TCAAAAATTG
*
503023 TTTTTAAAACTATATA-ATATATA
1 TTTTCAAAACTATATATATATATA
503046 TTTTCAAAACTATATATTATATATA
1 TTTTCAAAACTATATA-TATATATA
503071 TTTTCAAAA
1 TTTTCAAAA
503080 ATTGTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 15 0.48
25 16 0.52
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTTCAAAACTATATATATATATA
Found at i:503087 original size:61 final size:59
Alignment explanation
Indices: 502985--503115 Score: 235
Period size: 61 Copynumber: 2.2 Consensus size: 59
502975 GCTCAAAAAT
*
502985 TATTTTCGAAACTATATAATATATATTTTCAAAAATTGTTTTTAAAACTATATAATATA
1 TATTTTCAAAACTATATAATATATATTTTCAAAAATTGTTTTTAAAACTATATAATATA
503044 TATTTTCAAAACTATATATTATATATATTTTCAAAAATTGTTTTTAAAACTATATAATATA
1 TATTTTCAAAACTATATA--ATATATATTTTCAAAAATTGTTTTTAAAACTATATAATATA
503105 TATTTTCAAAA
1 TATTTTCAAAA
503116 ATATTTTCAA
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
59 17 0.25
61 52 0.75
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (59 bp):
TATTTTCAAAACTATATAATATATATTTTCAAAAATTGTTTTTAAAACTATATAATATA
Found at i:503144 original size:37 final size:37
Alignment explanation
Indices: 503043--503153 Score: 181
Period size: 37 Copynumber: 3.0 Consensus size: 37
503033 TATATAATAT
503043 ATATTTTCAAAACTATATATTATATATATTTTCAAAA
1 ATATTTTCAAAACTATATATTATATATATTTTCAAAA
* *
503080 ATTGTTTTTAAAACTATATA--ATATATATTTTCAAAA
1 A-TATTTTCAAAACTATATATTATATATATTTTCAAAA
503116 ATATTTTCAAAACTATATATTATATATATTTTCAAAA
1 ATATTTTCAAAACTATATATTATATATATTTTCAAAA
503153 A
1 A
503154 CCGTTTTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
35 16 0.24
36 17 0.25
37 18 0.27
38 16 0.24
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (37 bp):
ATATTTTCAAAACTATATATTATATATATTTTCAAAA
Done.