Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold474
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: 406844
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 3
Found at i:188366 original size:13 final size:13
Alignment explanation
Indices: 188350--188374 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
188340 CAATTCATCA
188350 TGTATCGATACAT
1 TGTATCGATACAT
188363 TGTATCGATACA
1 TGTATCGATACA
188375 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:188374 original size:33 final size:33
Alignment explanation
Indices: 188330--188392 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
188320 TTTAAAGCAA
188330 TGTATCAATACAAT-T-CATCATGTATCGATACAT
1 TGTATCAATACAATGTGC--CATGTATCGATACAT
*
188363 TGTATCGATACAATGTGCCATGTATCGATA
1 TGTATCAATACAATGTGCCATGTATCGATA
188393 TAAACAGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 25 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCAATACAATGTGCCATGTATCGATACAT
Found at i:190111 original size:20 final size:21
Alignment explanation
Indices: 190086--190130 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
190076 GTTTTGATGT
*
190086 AAAA-TTGATGAAATTTTAA-G
1 AAAATTTGA-GAAATATTAATG
190106 AAAATTTGAGAAATATTAATG
1 AAAATTTGAGAAATATTAATG
190127 AAAA
1 AAAA
190131 ATCATTAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (21 bp):
AAAATTTGAGAAATATTAATG
Found at i:190242 original size:13 final size:13
Alignment explanation
Indices: 190223--190262 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
190213 ATAGTAACCC
*
190223 ATGTATCAATACA
1 ATGTATCGATACA
* *
190236 TTGTATCGATGCA
1 ATGTATCGATACA
190249 ATGTATCGATACA
1 ATGTATCGATACA
190262 A
1 A
190263 AGAACATTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:190293 original size:18 final size:19
Alignment explanation
Indices: 190270--190305 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
190260 CAAAGAACAT
*
190270 TGTATCGATACA-TCTAGG
1 TGTATCAATACATTCTAGG
190288 TGTATCAATACATTCTAG
1 TGTATCAATACATTCTAG
190306 AAAATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (19 bp):
TGTATCAATACATTCTAGG
Found at i:199002 original size:51 final size:51
Alignment explanation
Indices: 198937--199054 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 51
198927 AAAAATAATA
* * *
198937 GGGTTAGAGTATCCCCGATTGTG-GAAAATCAATGCTTTAGAAATAAGGTCG
1 GGGTTAGAGTATCCCCAATTGTGAG-AAATCAATACTTTAGAAATAAAGTCG
* *
198988 GGGTTAGAGTATCCCCAATTGTGAGAAATTAATATTTTAGAAATAAAGTCG
1 GGGTTAGAGTATCCCCAATTGTGAGAAATCAATACTTTAGAAATAAAGTCG
* *
199039 GGTTTGGAGTATCCCC
1 GGGTTAGAGTATCCCC
199055 TCGGAAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 58 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
GGGTTAGAGTATCCCCAATTGTGAGAAATCAATACTTTAGAAATAAAGTCG
Found at i:201630 original size:49 final size:49
Alignment explanation
Indices: 201569--201682 Score: 158
Period size: 49 Copynumber: 2.3 Consensus size: 49
201559 AAAAATGCCT
* *
201569 GAATATATCGATACATTAAAAATTGTATCGATACATCTGGGT-AAACCCA
1 GAATGTATCGATACATGAAAAA-TGTATCGATACATCTGGGTAAAACCCA
* *
201618 GAATGTATCGATATAATGAATAATGTATCGATACATCTGGGTAAAACCCA
1 GAATGTATCGATA-CATGAAAAATGTATCGATACATCTGGGTAAAACCCA
*
201668 GAATGTATTGATACA
1 GAATGTATCGATACA
201683 AATTGTGAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
49 32 0.56
50 25 0.44
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (49 bp):
GAATGTATCGATACATGAAAAATGTATCGATACATCTGGGTAAAACCCA
Found at i:202293 original size:41 final size:42
Alignment explanation
Indices: 202246--202578 Score: 237
Period size: 41 Copynumber: 7.9 Consensus size: 42
202236 AAGGAAATGG
** *
202246 GCGTCCTGCTCTTTGAGGATTAAGGAAAAAAAG-AATGAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAAT
* * * * * *
202287 GGGTCCTACTCCTTGGGGACTAAGGAAAAAAGGAAATAAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAAT
* * * * *
202329 GCATCTTGCCCTTTGAAGACAAAGG-AAAAAGGAAATTAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAAT
** * * * * *
202370 ATGTCTTGCTTTTTAAGGATAAAGG-AAAAAGAAGAAT-AAAGT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGA-AATGAAA-T
* * * *
202412 GCCTCCTACTCTTTGAGAACTAGAAGAGAAAAGAAGGAAATGAAGT
1 GCGTCCTGCTCTTTGAGGAC-A-AAG-GAAAA-AAGGAAATGAAAT
* * *
202458 GCGTCCTGCTCTTTGAGGACAAAAGAAAAAA-GAAA-AAAAG
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAAT
*
202498 GCATCCTGCTCTTTGAGGACAGAAGGGAAAAGAAGGAAATGAAAT
1 GCGTCCTGCTCTTTGAGGACA-AA-GGAAAA-AAGGAAATGAAAT
** * * *
202543 ATGTCATGCTCTTTGAGGACAAAGGAGAGAAGGAAA
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAA
202579 AGGCGTCCTG
Statistics
Matches: 224, Mismatches: 54, Indels: 27
0.73 0.18 0.09
Matches are distributed among these distances:
40 22 0.10
41 75 0.33
42 52 0.23
43 12 0.05
44 11 0.05
45 22 0.10
46 24 0.11
47 6 0.03
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.21
Consensus pattern (42 bp):
GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAAT
Found at i:202529 original size:40 final size:42
Alignment explanation
Indices: 202395--202532 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 42
202385 AGGATAAAGG
* * *
202395 AAAAAGAAGAATAAAGTGCCTCCTACTCTTTGAGAACTAGAAGA
1 AAAAAGAAGAA-AAAGTGCATCCTGCTCTTTGAGGAC-AGAAGA
* * *
202439 GAAAAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGA
1 AAAAAGAA-GAAA--AAGTGCATCCTGCTCTTTGAGGACAGAAGA
*
202484 AAAAAGAA-AAAAAG-GCATCCTGCTCTTTGAGGACAGAAGG
1 AAAAAGAAGAAAAAGTGCATCCTGCTCTTTGAGGACAGAAGA
*
202524 GAAAAGAAG
1 AAAAAGAAG
202533 GAAATGAAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
40 30 0.38
41 3 0.04
43 3 0.04
44 8 0.10
45 15 0.19
46 21 0.26
ACGTcount: A:0.45, C:0.14, G:0.25, T:0.17
Consensus pattern (42 bp):
AAAAAGAAGAAAAAGTGCATCCTGCTCTTTGAGGACAGAAGA
Found at i:202532 original size:85 final size:83
Alignment explanation
Indices: 202249--202600 Score: 268
Period size: 83 Copynumber: 4.2 Consensus size: 83
202239 GAAATGGGCG
** * ** * * * * *
202249 TCCTGCTCTTTGAGGA-TTAAGGAAAAAAAG-AATGAAATGGGTCCTACTCCTTGGGGACTAAGG
1 TCCTGCTCTTTGAGGACAGAAGGAAAAAAGGAAATGAAATATGTCCTGCTCTTTGAGGACAAAAG
*
202312 AAAAAAGGAAATAAAATGCA
66 AAAAAA-GAAA-AAAAGGCA
* * * * * * * *
202332 TCTTGCCCTTTGAAGACA-AAGG-AAAAAGGAAATTAAATATGTCTTGCTTTTTAAGGA-TAAAG
1 TCCTGCTCTTTGAGGACAGAAGGAAAAAAGGAAATGAAATATGTCCTGCTCTTTGAGGACAAAAG
* *
202394 GAAAAAGAAGAATAAAGTGCC
66 AAAAAAGAA-AA-AAAG-GCA
* * * **
202415 TCCTACTCTTTGAGAACTAGAAGAGAAAAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAA
1 TCCTGCTCTTTGAGGAC-AGAAG-GAAAA-AAGGAAATGAAATATGTCCTGCTCTTTGAGGACAA
202480 AAGAAAAAAGAAAAAAAGGCA
63 AAGAAAAAAGAAAAAAAGGCA
*
202501 TCCTGCTCTTTGAGGACAGAAGGGAAAAGAAGGAAATGAAATATGTCATGCTCTTTGAGGACAAA
1 TCCTGCTCTTTGAGGACAGAA-GGAAAA-AAGGAAATGAAATATGTCCTGCTCTTTGAGGACAAA
* * * * *
202566 GGAGAGAAG--GAAAAGGCG
64 AGAAAAAAGAAAAAAAGGCA
*
202584 TCCTGCTTTTTGAGGAC
1 TCCTGCTCTTTGAGGAC
202601 TAAAAAGTGC
Statistics
Matches: 212, Mismatches: 45, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
81 4 0.02
82 19 0.09
83 72 0.34
84 1 0.00
85 51 0.24
86 19 0.09
87 7 0.03
88 27 0.13
89 12 0.06
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.22
Consensus pattern (83 bp):
TCCTGCTCTTTGAGGACAGAAGGAAAAAAGGAAATGAAATATGTCCTGCTCTTTGAGGACAAAAG
AAAAAAGAAAAAAAGGCA
Found at i:202672 original size:61 final size:60
Alignment explanation
Indices: 202575--203170 Score: 612
Period size: 61 Copynumber: 10.0 Consensus size: 60
202565 AGGAGAGAAG
* * **
202575 GAAAAGGCGTCCTGCTTTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA
* * * *
202636 GAAAAAGCGTCTTGCTCTTTGAGGACAAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAA
* * * *
202697 GAGAAA-GCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAATTTGTGTGGGCTTTAAAAA
1 GA-AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA
* *
202758 GAAAAGGCGTCATGCTTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAA
* ** * * *
202818 GGAAAAAGCGTTTTTCTCTTTGAGGACTAAAAAAGTGCCACCAACTTATGTGGGCTTT-AAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA
202880 GGAAAAGGCGTCCTGCTCTTTGAGGACTCAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA
* * * *
202941 GGAAAAGGTGTCCCGCTCTTTGAGGACTAAAGGTGCCACTAGCTTGTGTGGGCTTT-----
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA
* * **
202997 -AAAAGGCATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-----
1 GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAA
* * ** * * * *
203052 G-AAAGGCATCTTGCTCTTTGAGGACTAAAAAATACTACAAACTTGTGTGGGCTTTGAAAG
1 GAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA
* * *
203112 GAGAAGGCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
203171 GGCATTCTAC
Statistics
Matches: 459, Mismatches: 59, Indels: 35
0.83 0.11 0.06
Matches are distributed among these distances:
54 23 0.05
55 70 0.15
56 1 0.00
60 61 0.13
61 247 0.54
62 56 0.12
63 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (60 bp):
GAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA
Found at i:202785 original size:183 final size:180
Alignment explanation
Indices: 202572--203171 Score: 709
Period size: 183 Copynumber: 3.4 Consensus size: 180
202562 CAAAGGAGAG
* * **
202572 AAGGAAAAGGCGTCCTGCTTTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAG
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG
* *
202637 AAAAAGCGTCTTGCTCTTTGAGGACAAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAA
64 AAAAAGCGTCTTACTCTTTGAGGACAAGAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAGAGAA
** *
202702 AGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAATTTGTGTGGGCTTTAA
128 AGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * *
202755 AAAGAAAAGGCGTCATGCTTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAA-G
* * * * *
202820 AAAAAGCGTTTTTCTCTTTGAGGACTAAAAAAGTGCCACCAACTTATGTGGGCTTTAAAAG-GAA
64 AAAAAGCGTCTTACTCTTTGAGGAC-AAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAG-A
* *
202884 AAGGCGTCCTGCTCTTTGAGGACTCAAAGGTGCCACCAACTTGTGTGGGCTTTAA
127 AA-GCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
202939 AAGGAAAAGGTGTCCCGCTCTTTGAGGACTAAAGGTGCCACTAGCTTGTGTGGGCTTTAAAAG--
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
* * * *
203002 ---GCATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTG-AA-AG---GC
66 AAAGCGTCTTACTCTTTGAGGACAAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAAGC
* ** * * * *
203059 ATCTTGCTCTTTGAGGACTAAAAAATACTACAAACTTGTGTGGGCTTTGA
131 ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
203109 AAGGAGAAGGCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAG
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
203172 GCATTCTACT
Statistics
Matches: 365, Mismatches: 46, Indels: 25
0.84 0.11 0.06
Matches are distributed among these distances:
170 100 0.27
175 3 0.01
176 26 0.07
177 16 0.04
182 7 0.02
183 112 0.31
184 101 0.28
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (180 bp):
AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
AAAGCGTCTTACTCTTTGAGGACAAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAAGC
ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA
Found at i:203131 original size:170 final size:171
Alignment explanation
Indices: 202572--203193 Score: 654
Period size: 170 Copynumber: 3.5 Consensus size: 171
202562 CAAAGGAGAG
* * * **
202572 AAGGAAAAGGCGTCCTGCTTTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAG
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAGCTTGTGTGGGCTTT-AAAAG
* * * **
202637 AAAAAGC-GTCTTGCTCTTTGAGGACAAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGA
64 -----GCATTC-TACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTG-AAA-AG-
** *
202701 AAGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAATTTGTGTGGGCTTTAA
120 --GCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
202755 AAAGAAAAGGCGTCATGCTTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAGCTTGTGTGGGCTTTAAAA-G
* * * * *
202820 AAAAAGCGTTTTTCTCTTTGAGGACTAAAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAAA
64 -----GCATTCTACTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTT-----GAAA
* *
202885 AGGCGTCCTGCTCTTTGAGGACTCAAAGGTGCCACCAACTTGTGTGGGCTTTAA
118 AGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * *
202939 AAGGAAAAGGTGTCCCGCTCTTTGAGGACTAAAGGTGCCACTAGCTTGTGTGGGCTTTAAAAGGC
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGC
* *
203004 ATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGGCATCTTGCTC
66 ATTCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGCATCCTGCTC
** * * * *
203068 TTTGAGGACTAAAAAATACTACAAACTTGTGTGGGCTTTGA
131 TTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * *
203109 AAGGAGAAGGCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGGC
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGC
203174 ATTCTACTCTTTGAGGACTA
66 ATTCTACTCTTTGAGGACTA
203194 AAGGGTGAAA
Statistics
Matches: 384, Mismatches: 46, Indels: 31
0.83 0.10 0.07
Matches are distributed among these distances:
170 125 0.33
171 1 0.00
176 22 0.06
177 22 0.06
182 6 0.02
183 105 0.27
184 97 0.25
187 2 0.01
188 3 0.01
189 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (171 bp):
AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGC
ATTCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGCATCCTGCTC
TTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA
Found at i:204274 original size:12 final size:13
Alignment explanation
Indices: 204255--204296 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
204245 CTTAAGCAGG
204255 TTTTTTTTGTT-T
1 TTTTTTTTGTTAT
204267 TGTTTTTTTGTTA-
1 T-TTTTTTTGTTAT
204280 TTTTTTTTGTTAT
1 TTTTTTTTGTTAT
204293 TTTT
1 TTTT
204297 AAAAAAAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.05, C:0.00, G:0.10, T:0.86
Consensus pattern (13 bp):
TTTTTTTTGTTAT
Found at i:204283 original size:11 final size:12
Alignment explanation
Indices: 204255--204296 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
204245 CTTAAGCAGG
*
204255 TTTTTTTTGTTT
1 TTTTTTTTGTTA
204267 TGTTTTTTTGTTA
1 T-TTTTTTTGTTA
204280 TTTTTTTTGTTA
1 TTTTTTTTGTTA
204292 TTTTT
1 TTTTT
204297 AAAAAAAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.05, C:0.00, G:0.10, T:0.86
Consensus pattern (12 bp):
TTTTTTTTGTTA
Found at i:216210 original size:79 final size:79
Alignment explanation
Indices: 215903--216195 Score: 281
Period size: 79 Copynumber: 3.7 Consensus size: 79
215893 TGGGGATAAC
* * *
215903 AACGGGGCTGAAGTATCCTTGATTAT-AGAAAATCAGTGTTTT-GAAAATAAAATCGGGATTGGA
1 AACGGGGTTGAAGTATCCCTGATTGTGA-AAAATCAGTGTTTTAG-AAATAAAATCGGGATTGGA
*
215966 GTATCCCTTCAAAAAT
64 GTATCCCCTCAAAAAT
* * * ** *
215982 AACGGGGTTAAAGTATCTCC-GATTGTGAAAAAT-TGATGCTTTAGAAATAAGGCTAGGG-TTGG
1 AACGGGGTTGAAGTATC-CCTGATTGTGAAAAATCAG-TGTTTTAGAAATAA-AATCGGGATTGG
* *
216044 AGTATCCCCGCCAAAAT
63 AGTATCCCCTCAAAAAT
* ** * * * ** *
216061 AACGGGGTTGGAGTATCCCCAATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGTTTGGAGT
1 AACGGGGTTGAAGTATCCCTGATTGTGAAAAATCAGTGTTTTAGAAATAAAATCGGGATTGGAGT
*
216126 ATCCCCTCGAAAAT
66 ATCCCCTCAAAAAT
* * *
216140 AACGGGGTTGTAGTATCCCTGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGG
1 AACGGGGTTGAAGTATCCCTGATTGTGAAAAATCAGTGTTTTAGAAATAAAATCGG
216196 AGTTGAATTA
Statistics
Matches: 170, Mismatches: 36, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
78 6 0.04
79 157 0.92
80 7 0.04
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (79 bp):
AACGGGGTTGAAGTATCCCTGATTGTGAAAAATCAGTGTTTTAGAAATAAAATCGGGATTGGAGT
ATCCCCTCAAAAAT
Found at i:216216 original size:130 final size:130
Alignment explanation
Indices: 216074--216324 Score: 382
Period size: 130 Copynumber: 1.9 Consensus size: 130
216064 GGGGTTGGAG
* *
216074 TATCCCCAATTGTGAGAAATCAATATTTTAGAAA-TAAAGCCGGGTTTGGAGTATCCCCTC-GAA
1 TATCCCCAATTGTGAAAAATCAATATTTTAGAAATTAAA-CCGGGGTTGGAGTATCCCCTCAG-A
216137 AATAACGGGGTT-GTAGTATCCCTGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGAGTTG
64 AATAACGGGGTTAG-AGTATCCCTGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGAGTTG
216201 AAT
128 AAT
* * * *
216204 TATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATTAAACCGGGGTTGGAGTATCCCCTCAGAAA
1 TATCCCCAATTGTGAAAAATCAATATTTTAGAAATTAAACCGGGGTTGGAGTATCCCCTCAGAAA
* *
216269 TAACGGGGTTAGAGTATCCTTGATTGTGAAAAATTAGTGTTTTGGGAATAAAATCG
66 TAACGGGGTTAGAGTATCCCTGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCG
216325 AGGTTAGAGT
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
130 104 0.95
131 6 0.05
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (130 bp):
TATCCCCAATTGTGAAAAATCAATATTTTAGAAATTAAACCGGGGTTGGAGTATCCCCTCAGAAA
TAACGGGGTTAGAGTATCCCTGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGAGTTGAAT
Found at i:216259 original size:51 final size:51
Alignment explanation
Indices: 216142--216261 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 51
216132 TCGAAAATAA
* * * *
216142 CGGGGTTGTAGTATCCCTGATTGTGAAAAATTAGTGTTTTGGAAATAAAAT
1 CGGGGTTGAAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
* * *
216193 CGGAGTTGAATTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATTAAAC
1 CGGGGTTGAAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
*
216244 CGGGGTTGGAGTATCCCC
1 CGGGGTTGAAGTATCCCC
216262 TCAGAAATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (51 bp):
CGGGGTTGAAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
Found at i:219494 original size:46 final size:44
Alignment explanation
Indices: 219347--219634 Score: 169
Period size: 41 Copynumber: 6.8 Consensus size: 44
219337 GGGGACTACA
* * * *
219347 AAAAAAAGGAAATAAAATGCATCCTACCCTTTGAAGAA-AAA-GG
1 AAAAAAAGGAAATGAAGTGCATCCTGCTCTTTG-AGAACAAAGGG
* ** * * *
219390 --AAAAAGGAAATGAATTGTGTCCTGCTTTTTTAGGACAAA-GG
1 AAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGAGAACAAAGGG
*
219431 --AAAAAGGAGAATAAAGTGCATCCTGCTCTTTGAGAACTAGAAGGG
1 AAAAAAAGGA-AATGAAGTGCATCCTGCTCTTTGAGAAC-A-AAGGG
* *
219476 AAAAAAAGGAAATGAAGTGCGTCTTGCTCTTTGAGAACAAA--G
1 AAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGAGAACAAAGGG
* ** * * *
219518 -AAAAGAGGAAAAACAAG-GCATCTTGCTCTTTAAGGACAAAAGGG
1 AAAAAAAGG-AAATGAAGTGCATCCTGCTCTTTGAGAAC-AAAGGG
* * ** *
219562 AAAAGAAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAA-GG
1 AAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGAGAACAAAGGG
* *
219605 AGAGAAA-G-AA--AAG-GCATCCTGCTCTTTGAG
1 AAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGAG
219635 GACTAAAAAG
Statistics
Matches: 192, Mismatches: 40, Indels: 31
0.73 0.15 0.12
Matches are distributed among these distances:
38 15 0.08
39 2 0.01
40 3 0.02
41 62 0.32
42 32 0.17
43 7 0.04
44 13 0.07
45 25 0.13
46 25 0.13
47 8 0.04
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.20
Consensus pattern (44 bp):
AAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGAGAACAAAGGG
Found at i:219572 original size:86 final size:86
Alignment explanation
Indices: 219284--219642 Score: 300
Period size: 83 Copynumber: 4.3 Consensus size: 86
219274 GAAGGGGGCG
* * ** * *
219284 TCCTGCTCTTTGAGGA-T-TAA-GG--AAAAAGGAGAATGAAATGGGTCCTATTCCTTGGGGACT
1 TCCTGCTCTTTGAGGACTAAAAGGGAAAAAAAGGA-AATGAAATGTGTCCTGCTCTTTGAGGAC-
* *
219344 ACAA-AAAAAAGGAAATAAAATGCA
64 A-AAGAAAAGAGGAAA-AAAAGGCA
* * * * * *
219368 TCCTACCCTTTGAAGA--AAAA-GG--AAAAAGGAAATGAATTGTGTCCTGCTTTTTTAGGACAA
1 TCCTGCTCTTTGAGGACTAAAAGGGAAAAAAAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAA
*
219428 AGGAAAA-AGGAGAATAAAGTGCA
66 A-GAAAAGAGGA-AAAAAAG-GCA
* * * * * *
219451 TCCTGCTCTTTGAGAACTAGAAGGGAAAAAAAGGAAATGAAGTGCGTCTTGCTCTTTGAGAACAA
1 TCCTGCTCTTTGAGGACTAAAAGGGAAAAAAAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAA
219516 AGAAAAGAGGAAAAACAAGGCA
66 AGAAAAGAGGAAAAA-AAGGCA
* * *
219538 TCTTGCTCTTTAAGGAC-AAAAGGGAAAAGAAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAA
1 TCCTGCTCTTTGAGGACTAAAAGGGAAAAAAAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAA
*
219602 AG--GAGA-GAAAGAAAAGGCA
66 AGAAAAGAGGAAA-AAAAGGCA
219621 TCCTGCTCTTTGAGGACTAAAA
1 TCCTGCTCTTTGAGGACTAAAA
219643 AGTGCCACCA
Statistics
Matches: 223, Mismatches: 38, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
81 2 0.01
82 8 0.04
83 66 0.30
84 34 0.15
85 3 0.01
86 45 0.20
87 25 0.11
88 40 0.18
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (86 bp):
TCCTGCTCTTTGAGGACTAAAAGGGAAAAAAAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAA
AGAAAAGAGGAAAAAAAGGCA
Found at i:219709 original size:61 final size:61
Alignment explanation
Indices: 219612--220039 Score: 520
Period size: 61 Copynumber: 7.0 Consensus size: 61
219602 AGGAGAGAAA
* * * * * *
219612 GAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAA-
1 GAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG
* * * * *
219673 GAAAAAGCGTCCTACTCTTTAAAGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAA-
1 GAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG
* * * *
219734 GAGAAAGCATCTTGCTTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
1 GAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
* * * *
219795 GAAAAGGCGTCATGCTCTTTAAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
1 GAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
* * *
219856 GAAAAAGCGTTCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTAAAAAG
1 GAAAAAGCGTCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
* * *
219918 GAAAAAGCGTCCTACTCCTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAG
1 GAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
* ** * * * *
219979 AAAAAAATGTCCTGCTTTTTGAGGACT-GAAGGTGCCACCAGCTTGTATGGGCTTTGAAAG
1 GAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
220039 G
1 G
220040 CGCCCTATTC
Statistics
Matches: 318, Mismatches: 47, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
60 34 0.11
61 227 0.71
62 57 0.18
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (61 bp):
GAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
Found at i:220107 original size:55 final size:54
Alignment explanation
Indices: 219797--220109 Score: 160
Period size: 61 Copynumber: 5.4 Consensus size: 54
219787 TTTAAAAGGA
* * * * *
219797 AAAGGCGTCATGCTCTTTAAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTATGGGCCTT-----G
* * *
219857 AAAAAGCGTTCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGG-CTTAAAAAGG
1 -AAAGGCGTCCTGCTCTTTGAGGACT-GAAAA-TGCCACCAACTTGTATGGGCCTT------G
* * * ** *
219919 AAAAAGCGTCCTACTCCTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAG
1 -AAAGGCGTCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTATGGGCCTT----G
*** * ** * *
219979 AAAAAAATGTCCTGCTTTTTGAGGACTGAAGGTGCCACCAGCTTGTATGGGCTTTG
1 --AAAGGCGTCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTATGGGCCTTG
* ** * *
220035 AAAGGCGCCCTATTCTTTGAGGACTGGAAAATGTCACCAACTTGTGTGGGCCTTG
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTATGGGCCTTG
220090 AAAGGCGTCCTGCTCTTTGA
1 AAAGGCGTCCTGCTCTTTGA
220110 TCTCTCTACC
Statistics
Matches: 211, Mismatches: 36, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
54 18 0.09
55 40 0.19
56 1 0.00
60 31 0.15
61 67 0.32
62 54 0.26
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (54 bp):
AAAGGCGTCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTATGGGCCTTG
Found at i:220256 original size:1 final size:1
Alignment explanation
Indices: 220252--220344 Score: 69
Period size: 1 Copynumber: 93.0 Consensus size: 1
220242 CCCTTTTTCG
* * * * * ** * *
220252 TTTTTTTTTTGTTTTTTTGTTTTTTGTTTTTTTTTTATTTTTTTCTTGGTTTTTTTTGTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** *
220317 TTGTTTTTTTTGCTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
220345 ATACGAAGGA
Statistics
Matches: 69, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:220266 original size:9 final size:9
Alignment explanation
Indices: 220254--220344 Score: 105
Period size: 9 Copynumber: 9.8 Consensus size: 9
220244 CTTTTTCGTT
220254 TTTTTTTTG
1 TTTTTTTTG
220263 -TTTTTTTG
1 TTTTTTTTG
220271 TTTTTTGTT-
1 TTTTTT-TTG
*
220280 TTTTTTTTAT
1 TTTTTTTT-G
220290 TTTTTTCTTGG
1 TTTTTT-TT-G
220301 TTTTTTTTG
1 TTTTTTTTG
220310 TTTTTCTTTG
1 TTTTT-TTTG
220320 TTTTTTTTG
1 TTTTTTTTG
*
220329 CTTTTTTTG
1 TTTTTTTTG
220338 TTTTTTT
1 TTTTTTT
220345 ATACGAAGGA
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
8 10 0.14
9 35 0.49
10 19 0.26
11 8 0.11
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:220266 original size:10 final size:10
Alignment explanation
Indices: 220245--220344 Score: 93
Period size: 10 Copynumber: 10.4 Consensus size: 10
220235 TCTAGACCCC
*
220245 TTTTTCGTTT
1 TTTTTTGTTT
*
220255 TTTTTT-TGT
1 TTTTTTGTTT
220264 TTTTTTGTTT
1 TTTTTTGTTT
220274 TTTGTTT-TTT
1 TTT-TTTGTTT
*
220284 TTTTAT-TTT
1 TTTTTTGTTT
* *
220293 TTTCTTGGTT
1 TTTTTTGTTT
220303 TTTTTTGTTT
1 TTTTTTGTTT
*
220313 TTCTTTG-TT
1 TTTTTTGTTT
*
220322 TTTTTTG-CT
1 TTTTTTGTTT
220331 TTTTTTGTTT
1 TTTTTTGTTT
220341 TTTT
1 TTTT
220345 ATACGAAGGA
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
9 33 0.45
10 37 0.51
11 3 0.04
ACGTcount: A:0.01, C:0.04, G:0.10, T:0.85
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:220273 original size:19 final size:18
Alignment explanation
Indices: 220245--220344 Score: 101
Period size: 19 Copynumber: 5.2 Consensus size: 18
220235 TCTAGACCCC
*
220245 TTTTTCGTTTTTTTTTTGT
1 TTTTTTGTTTTTTTTTT-T
*
220264 TTTTTTGTTTTTTGTTTT
1 TTTTTTGTTTTTTTTTTT
*
220282 TTTTTTATTTTTTTCTTGGTT
1 TTTTTTGTTTTTTT-TT--TT
*
220303 TTTTTTGTTTTTCTTTGTT
1 TTTTTTGTTTTT-TTTTTT
220322 TTTTTTGCTTTTTTTGTTTT
1 TTTTTTG-TTTTTTT-TTTT
220342 TTT
1 TTT
220345 ATACGAAGGA
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 13 0.19
19 28 0.41
20 11 0.16
21 14 0.21
22 2 0.03
ACGTcount: A:0.01, C:0.04, G:0.10, T:0.85
Consensus pattern (18 bp):
TTTTTTGTTTTTTTTTTT
Found at i:222195 original size:15 final size:15
Alignment explanation
Indices: 222175--222205 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
222165 CCCCACATGG
222175 TTACAAAAGTCATTT
1 TTACAAAAGTCATTT
222190 TTACAAAAGTCATTT
1 TTACAAAAGTCATTT
222205 T
1 T
222206 CTCCATATCT
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:0.13, G:0.06, T:0.42
Consensus pattern (15 bp):
TTACAAAAGTCATTT
Found at i:234925 original size:52 final size:52
Alignment explanation
Indices: 234855--234975 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
234845 GAAAATTTAT
*
234855 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
234907 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
234959 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
234976 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:234988 original size:52 final size:51
Alignment explanation
Indices: 234855--234995 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
234845 GAAAATTTAT
234855 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
234907 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
234959 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
234996 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:235002 original size:13 final size:13
Alignment explanation
Indices: 234984--235008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234974 CAAAGATCAG
234984 TGTATCGATACAA
1 TGTATCGATACAA
234997 TGTATCGATACA
1 TGTATCGATACA
235009 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:235090 original size:13 final size:13
Alignment explanation
Indices: 235072--235096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
235062 CAAAAAAATA
235072 TGTATCGATACAT
1 TGTATCGATACAT
235085 TGTATCGATACA
1 TGTATCGATACA
235097 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:235092 original size:33 final size:33
Alignment explanation
Indices: 235050--235116 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
235040 AGTAGCTTAA
235050 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
235083 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
235116 A
1 A
235117 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:235959 original size:92 final size:95
Alignment explanation
Indices: 235836--236035 Score: 298
Period size: 92 Copynumber: 2.1 Consensus size: 95
235826 GGCTAGCGAT
*
235836 ATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT-A-AAA-
1 ATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGACTTAATAAAG
*
235898 GTGCCAATGTGCTGATTCAAGGCCAGCTAC
66 GTGCCAATATGCTGATTCAAGGCCAGCTAC
* *
235928 ATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATA
1 ATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGACTT--A-ATA
*
235993 AAGGTGCCAATATGCTGATTCAAGGCCAGCTAT
63 AAGGTGCCAATATGCTGATTCAAGGCCAGCTAC
*
236026 ATTGGGCTTA
1 ATTGGACTTA
236036 GAAGGGTTGC
Statistics
Matches: 96, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
92 55 0.57
96 1 0.01
97 3 0.03
98 37 0.39
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (95 bp):
ATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGACTTAATAAAG
GTGCCAATATGCTGATTCAAGGCCAGCTAC
Found at i:236023 original size:49 final size:49
Alignment explanation
Indices: 235836--236035 Score: 304
Period size: 49 Copynumber: 4.2 Consensus size: 49
235826 GGCTAGCGAT
*
235836 ATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGAC
1 ATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
235885 ATTGGACTT----A-AAA-GTGCCAATGTGCTGATTCAAGGCCAGCTAC
1 ATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
* *
235928 ATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTAC
1 ATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
* *
235977 ATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTAT
1 ATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
*
236026 ATTGGGCTTA
1 ATTGGACTTA
236036 GAAGGGTTGC
Statistics
Matches: 137, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
43 38 0.28
44 3 0.02
45 1 0.01
47 1 0.01
48 2 0.01
49 92 0.67
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
ATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
Found at i:236079 original size:33 final size:35
Alignment explanation
Indices: 236035--236104 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
236025 TATTGGGCTT
*
236035 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTCGGCTTTAGGA
236069 AGAA-GGTTGCCACCGACTTGTGTCGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTCGGCTTTAGGA
236103 AG
1 AG
236105 GGAGAAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTCGGCTTTAGGA
Found at i:236159 original size:35 final size:35
Alignment explanation
Indices: 236109--236340 Score: 294
Period size: 33 Copynumber: 6.9 Consensus size: 35
236099 AGGAAGGGAG
*
236109 AAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-GGAA
236143 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
236177 AAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAA
236213 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
236247 AAA-AGTGCCACGGAGTTGTGGGCTTT------AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
236275 AAAGAGTGCCACGGAGTTATGGGCTTTGAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGGAA
*
236310 GAAG-GTGCCACGGAGTTGTGGGCTTTGAAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA
236341 AGATGCCACT
Statistics
Matches: 181, Mismatches: 4, Indels: 26
0.86 0.02 0.12
Matches are distributed among these distances:
28 5 0.03
29 22 0.12
33 46 0.25
34 45 0.25
35 26 0.14
36 14 0.08
37 23 0.13
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (35 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
Found at i:236219 original size:70 final size:69
Alignment explanation
Indices: 236109--236340 Score: 320
Period size: 70 Copynumber: 3.4 Consensus size: 69
236099 AGGAAGGGAG
*
236109 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAG-TGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
236173 AGGAA
65 AGGAA
236178 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
*
236243 AGAAA
65 AGGAA
*
236248 AAAGTGCCACGGAGTTGTGGGCTTT-------AAAAAGAGTGCCACGGAGTTATGGGCTTTGAAA
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAA
236306 A-GAA
65 AGGAA
*
236310 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 -AAAGTGCCACGGAGTTGTGGGCTTT-AAAA
236341 AGATGCCACT
Statistics
Matches: 149, Mismatches: 5, Indels: 19
0.86 0.03 0.11
Matches are distributed among these distances:
62 30 0.20
63 28 0.19
68 17 0.11
69 6 0.04
70 68 0.46
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (69 bp):
AAAGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
GGAA
Found at i:236243 original size:29 final size:30
Alignment explanation
Indices: 236211--236364 Score: 186
Period size: 29 Copynumber: 5.0 Consensus size: 30
236201 TTGAAAAGGG
236211 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT--A
*
236243 AGAAAAAAGTGCCACGGAGTTGTGGGCTTT-
1 A-AAAAGAGTGCCACGGAGTTGTGGGCTTTA
*
236273 AAAAAGAGTGCCACGGAGTTATGGGCTTTGA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-A
*
236304 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTG
1 AAA-AAG-A-GTGCCACGGAGTTGTGGGCTTTA
* *
236337 AAAAAGA-TGCCACTGACTTGTGGGCTTT
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT
236365 TGAAGGGTAA
Statistics
Matches: 109, Mismatches: 7, Indels: 15
0.83 0.05 0.11
Matches are distributed among these distances:
29 45 0.41
30 1 0.01
31 4 0.04
32 7 0.06
33 31 0.28
34 21 0.19
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.23
Consensus pattern (30 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTA
Found at i:236287 original size:62 final size:64
Alignment explanation
Indices: 236210--236364 Score: 244
Period size: 63 Copynumber: 2.5 Consensus size: 64
236200 TTTGAAAAGG
236210 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTT
* * *
236273 -AAAAAGAGTGCCACGGAGTTATGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTT
* *
236336 GAAAAAGA-TGCCACTGACTTGTGGGCTTT
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT
236365 TGAAGGGTAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
62 28 0.33
63 49 0.58
64 7 0.08
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (64 bp):
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTT
Found at i:237814 original size:1 final size:1
Alignment explanation
Indices: 237808--237936 Score: 87
Period size: 1 Copynumber: 129.0 Consensus size: 1
237798 CGGACCCCTC
* * * * * * * **
237808 TTTTTTTTTGTTTGTTTTTTTATTGTTTTTTGTTTTTTTTCTTTTGTTTTTTTTTTTTTTTTGGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** ** ** **
237873 TTTTCATTTTTTCGTTTTTTTTTTTTGGTTTTTCATTTTTTTTCGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
237937 GAAGGACGCC
Statistics
Matches: 98, Mismatches: 30, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 98 1.00
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:237836 original size:22 final size:20
Alignment explanation
Indices: 237811--237937 Score: 107
Period size: 21 Copynumber: 6.0 Consensus size: 20
237801 ACCCCTCTTT
237811 TTTTTTGTTTGTTTTTTTATTG
1 TTTTTTGTTT-TTTTTTT-TTG
237833 TTTTTTGTTTTTTTTCTTTTG
1 TTTTTTGTTTTTTTT-TTTTG
*
237854 -TTTTT-TTTTTTTTTTTGG
1 TTTTTTGTTTTTTTTTTTTG
**
237872 TTTTTCATTTTTTCGTTTTTT-
1 TTTTTTGTTTTTT--TTTTTTG
237893 TTTTTTGGTTTTTCATTTTTTTTCG
1 TTTTTT-G-TTTT--TTTTTTTT-G
*
237918 TTTTTTTTTTTTTTTTTTTG
1 TTTTTTGTTTTTTTTTTTTG
237938 AAGGACGCCG
Statistics
Matches: 88, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
18 4 0.05
19 12 0.14
20 12 0.14
21 21 0.24
22 17 0.19
23 14 0.16
25 8 0.09
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.84
Consensus pattern (20 bp):
TTTTTTGTTTTTTTTTTTTG
Found at i:237847 original size:31 final size:31
Alignment explanation
Indices: 237808--237937 Score: 120
Period size: 31 Copynumber: 4.0 Consensus size: 31
237798 CGGACCCCTC
*
237808 TTTTTTTTTGTTTGTTTTTTTATTGTTTTTTG
1 TTTTTTTTCGTTTGTTTTTTT-TTGTTTTTTG
* *
237840 TTTTTTTTCTTTTGTTTTTTTTTTTTTTTTGG
1 TTTTTTTTCGTTTGTTTTTTTTTGTTTTTT-G
**
237872 TTTTTCATTTTTTCGTTT-TTTTTTTTTGGTTTTTCA
1 ---TT--TTTTTTCGTTTGTTTTTTTTT-GTTTTTTG
*
237908 TTTTTTTTCGTTT-TTTTTTTTTTTTTTTTG
1 TTTTTTTTCGTTTGTTTTTTTTTGTTTTTTG
237938 AAGGACGCCG
Statistics
Matches: 81, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
30 5 0.06
31 28 0.35
32 20 0.25
33 2 0.02
35 2 0.02
36 9 0.11
37 15 0.19
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (31 bp):
TTTTTTTTCGTTTGTTTTTTTTTGTTTTTTG
Found at i:241516 original size:1 final size:1
Alignment explanation
Indices: 241510--241538 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
241500 TGATAAAGGC
241510 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
241539 GATGGAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:247660 original size:10 final size:10
Alignment explanation
Indices: 247645--247671 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
247635 ATGTATCAAG
247645 CAAAAACAAA
1 CAAAAACAAA
247655 CAAAAACAAA
1 CAAAAACAAA
247665 CAAAAAC
1 CAAAAAC
247672 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:251874 original size:52 final size:52
Alignment explanation
Indices: 251804--251924 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
251794 GAAAATTTAT
*
251804 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
251856 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
251908 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
251925 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:251937 original size:52 final size:51
Alignment explanation
Indices: 251804--251944 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
251794 GAAAATTTAT
251804 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
251856 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
251908 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
251945 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:251951 original size:13 final size:13
Alignment explanation
Indices: 251933--251957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
251923 CAAAGATCAG
251933 TGTATCGATACAA
1 TGTATCGATACAA
251946 TGTATCGATACA
1 TGTATCGATACA
251958 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:252040 original size:13 final size:13
Alignment explanation
Indices: 252022--252046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
252012 CAAAAAAATA
252022 TGTATCGATACAT
1 TGTATCGATACAT
252035 TGTATCGATACA
1 TGTATCGATACA
252047 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:252042 original size:33 final size:33
Alignment explanation
Indices: 252000--252066 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
251990 AGTAGCTTAA
252000 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
252033 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
252066 A
1 A
252067 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:254873 original size:335 final size:335
Alignment explanation
Indices: 254104--255093 Score: 1892
Period size: 335 Copynumber: 3.0 Consensus size: 335
254094 TCATTTCTCA
254104 TTTTCTTTATTGTTATTTTATGTGAATTATTTTATACAACTTTATTTCACCTATTGTCATACTAA
1 TTTTCTTTATTGTTATTTTATGTGAATTATTTTATACAACTTTATTTCACCTATTGTCATACTAA
* *
254169 TATATTTTTCTTGTGATGATTATTCGCGTTCATATTTCCAAATTTTGTTTACAAAAACTACGAAG
66 TATATTTTTCTTGTGATGATTATTCGCGTTCATATTTTCAAAATTTGTTTACAAAAACTACGAAG
*
254234 GCAATGTTCTGTGTCGGTATCTCTCCAGTGCCTGATATAGAATATCTAATTTTCAAAGCGAAATC
131 GCAATGTTCTGTGTCGGTATCTCTCCAGTGCCTGATACAGAATATCTAATTTTCAAAGCGAAATC
*
254299 TAGAGGTCATTTTATGTCTATATGTTCCCCATCTCTCTATGGTGCATATGAGATTAAAATCTTTA
196 CAGAGGTCATTTTATGTCTATATGTTCCCCATCTCTCTATGGTGCATATGAGATTAAAATCTTTA
*
254364 T-AAAAACCTAGATTTATTTTTTTTATACACAAGATTCATGCATTTAAGGGGATCATATTTTCAT
261 TAAAAAACCTAGATTTATTTTTTTTATACACAAGATTCATGCATTTAAGGGGATCATATTGTCAT
254428 ACTAATATAT
326 ACTAATATAT
254438 TTTTCTTTATTGTTATTTTATGTGAATTATTTTATACAACTTTATTTCACCTATTGTCATACTAA
1 TTTTCTTTATTGTTATTTTATGTGAATTATTTTATACAACTTTATTTCACCTATTGTCATACTAA
254503 TATATTTTTCTTGTGATGATTATTCGCGTTCATATTTTCAAAATTTGTTTACAAAAACTACGAAG
66 TATATTTTTCTTGTGATGATTATTCGCGTTCATATTTTCAAAATTTGTTTACAAAAACTACGAAG
*
254568 GCAATGTTCTGTGTCGGTATCTCTCCAGTGCTTGATACAGAATATCTAATTTTCAAAGCGAAATC
131 GCAATGTTCTGTGTCGGTATCTCTCCAGTGCCTGATACAGAATATCTAATTTTCAAAGCGAAATC
254633 CAGAGGTCATTTTATGTCTATATGTTCCCCATCTCTCTATGGTGCATATGAGATTAAAATCTTTA
196 CAGAGGTCATTTTATGTCTATATGTTCCCCATCTCTCTATGGTGCATATGAGATTAAAATCTTTA
254698 TAAAAAACCTAGATTTATTTTTTTTATACACAAGATTCATGCATTTAAGGGGATCATATTGTCAT
261 TAAAAAACCTAGATTTATTTTTTTTATACACAAGATTCATGCATTTAAGGGGATCATATTGTCAT
254763 ACTAATATAT
326 ACTAATATAT
254773 TTTTCTTTATTGTTATTTTATGTGAATTATTTTATACAACTTTATTTCACCTATTGTCATACTAA
1 TTTTCTTTATTGTTATTTTATGTGAATTATTTTATACAACTTTATTTCACCTATTGTCATACTAA
*
254838 TATATTTTTCTTGTGATGATTATTCACGTTCATATTTTCAAAATTTGTTTACAAAAACTACGAAG
66 TATATTTTTCTTGTGATGATTATTCGCGTTCATATTTTCAAAATTTGTTTACAAAAACTACGAAG
* *
254903 GCAATGTTCTGTGTCAGCATCTCTCCAGTGCCTGATACAGAATATCTAATTTTCAAAGCGAAATC
131 GCAATGTTCTGTGTCGGTATCTCTCCAGTGCCTGATACAGAATATCTAATTTTCAAAGCGAAATC
254968 CAGAGGTCATTTTATGTCTATATGTTCCCCATCTCTCTATGGTGCATATGAGATTAAAATCTTTA
196 CAGAGGTCATTTTATGTCTATATGTTCCCCATCTCTCTATGGTGCATATGAGATTAAAATCTTTA
255033 TAAAAAACCTAGATTTATTTTTTTTATACACAAGATTCATGCATTTAAGGGGATCATATTG
261 TAAAAAACCTAGATTTATTTTTTTTATACACAAGATTCATGCATTTAAGGGGATCATATTG
255094 AAATAATGTC
Statistics
Matches: 645, Mismatches: 10, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
334 256 0.40
335 389 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (335 bp):
TTTTCTTTATTGTTATTTTATGTGAATTATTTTATACAACTTTATTTCACCTATTGTCATACTAA
TATATTTTTCTTGTGATGATTATTCGCGTTCATATTTTCAAAATTTGTTTACAAAAACTACGAAG
GCAATGTTCTGTGTCGGTATCTCTCCAGTGCCTGATACAGAATATCTAATTTTCAAAGCGAAATC
CAGAGGTCATTTTATGTCTATATGTTCCCCATCTCTCTATGGTGCATATGAGATTAAAATCTTTA
TAAAAAACCTAGATTTATTTTTTTTATACACAAGATTCATGCATTTAAGGGGATCATATTGTCAT
ACTAATATAT
Found at i:256448 original size:2 final size:2
Alignment explanation
Indices: 256441--256475 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
256431 TAATTACATC
256441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
256476 TTGAAATCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:257250 original size:16 final size:17
Alignment explanation
Indices: 257220--257257 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
257210 AATATAAAAA
257220 ATAAT-TAAAATATAAT
1 ATAATATAAAATATAAT
257236 ATAATATAAAA-ATAAT
1 ATAATATAAAATATAAT
257252 ATAATA
1 ATAATA
257258 AAATACGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATATAAAATATAAT
Found at i:257272 original size:39 final size:39
Alignment explanation
Indices: 257195--257285 Score: 91
Period size: 39 Copynumber: 2.4 Consensus size: 39
257185 CGATTTAATT
* **
257195 ATATAATATAAATTCAATATAAAAAATAATTAAAATATA
1 ATATAATATAAAATCAATATAAAAAATAACGAAAATATA
*
257234 ATATAATATAAAAAT-AATATAATAAAAT-ACGAATATATA
1 ATATAATAT-AAAATCAATATAA-AAAATAACGAAAATATA
257273 A-AT-ATATTAAAAT
1 ATATAATA-TAAAAT
257286 TTATATGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
37 8 0.18
38 3 0.07
39 25 0.56
40 9 0.20
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (39 bp):
ATATAATATAAAATCAATATAAAAAATAACGAAAATATA
Found at i:257675 original size:24 final size:23
Alignment explanation
Indices: 257648--257700 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
257638 AGATATCCTT
257648 TTATAAAAAGAGTCAAAATT-ATAA
1 TTATAAAAAGA-T-AAAATTAATAA
* *
257672 TTATATAATGATAAAATTAATAA
1 TTATAAAAAGATAAAATTAATAA
257695 TT-TAAA
1 TTATAAA
257701 TATTATATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 9 0.36
23 7 0.28
24 9 0.36
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (23 bp):
TTATAAAAAGATAAAATTAATAA
Found at i:258188 original size:27 final size:27
Alignment explanation
Indices: 258132--258197 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
258122 AGCCTCTATA
*
258132 TTTGACAAATACAAAGGAAACCACCATT
1 TTTGACAAACACAAA-GAAACCACCATT
258160 TTTGACAAACACAAA-ATAACCACCATT
1 TTTGACAAACACAAAGA-AACCACCATT
258187 TTTGACAAACA
1 TTTGACAAACA
258198 TATGGGTGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (27 bp):
TTTGACAAACACAAAGAAACCACCATT
Found at i:262605 original size:20 final size:20
Alignment explanation
Indices: 262580--262625 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
262570 AAGAATTGAA
*
262580 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
262600 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
262620 GAGGGA
1 GAGGGA
262626 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:263302 original size:12 final size:12
Alignment explanation
Indices: 263285--263312 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
263275 TCATGAAATT
263285 AATATTTATAAG
1 AATATTTATAAG
263297 AATATTTATAAG
1 AATATTTATAAG
263309 AATA
1 AATA
263313 ATTGAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (12 bp):
AATATTTATAAG
Found at i:263440 original size:23 final size:24
Alignment explanation
Indices: 263404--263452 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
263394 CAATTTAAGA
*
263404 ATGATTTTTGAAATT-TCTTTTATC
1 ATGATTTTTAAAATTCT-TTTTATC
263428 ATGA-TTTTAAAATTCTTTTTATC
1 ATGATTTTTAAAATTCTTTTTATC
263451 AT
1 AT
263453 ATTGCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (24 bp):
ATGATTTTTAAAATTCTTTTTATC
Found at i:263831 original size:24 final size:24
Alignment explanation
Indices: 263778--263877 Score: 67
Period size: 24 Copynumber: 3.8 Consensus size: 24
263768 AATTAGATTT
* *
263778 AATAATTTTAAATATAAT-TTAATTA
1 AATAA-TTTAAATAAAATATTAA-AA
*
263803 CATAATTTAAATAAAATATTAAAA
1 AATAATTTAAATAAAATATTAAAA
* *
263827 AATAATTAAAATAAATATAACATAAAA
1 AATAATTTAAATAAA-AT-A-TTAAAA
263854 AATAATATAATAAATATAAATATT
1 AATAAT-T--TAAATA-AAATATT
263878 TAAATTATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
24 25 0.42
25 10 0.17
26 1 0.02
27 11 0.19
28 2 0.03
29 1 0.02
30 7 0.12
31 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AATAATTTAAATAAAATATTAAAA
Found at i:263865 original size:26 final size:27
Alignment explanation
Indices: 263822--263872 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
263812 AATAAAATAT
263822 TAAAAAATAATTAAAATAAATATAACA
1 TAAAAAATAATTAAAATAAATATAACA
*
263849 TAAAAAATAA-TATAATAAATATAA
1 TAAAAAATAATTAAAATAAATATAA
263873 ATATTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (27 bp):
TAAAAAATAATTAAAATAAATATAACA
Found at i:263953 original size:19 final size:19
Alignment explanation
Indices: 263914--263949 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
263904 AATATTATTA
*
263914 ATTTATAAAAATTAAATAT
1 ATTTATAAAAATAAAATAT
263933 ATTTAT-AAAATAAAATA
1 ATTTATAAAAATAAAATA
263950 ATATGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTTATAAAAATAAAATAT
Found at i:266805 original size:2 final size:2
Alignment explanation
Indices: 266794--266829 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
266784 AGCAAGACTT
266794 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
266830 CCTTTGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:268117 original size:13 final size:14
Alignment explanation
Indices: 268099--268129 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
268089 GCTTATGTTA
268099 TTTATTTTTT-ATT
1 TTTATTTTTTAATT
268112 TTTATTTTTTAATT
1 TTTATTTTTTAATT
268126 TTTA
1 TTTA
268130 GAATTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTTTAATT
Found at i:269372 original size:2 final size:2
Alignment explanation
Indices: 269359--269416 Score: 53
Period size: 2 Copynumber: 28.5 Consensus size: 2
269349 TTTTAAAATT
* * * * * *
269359 TA TA TT TA TA TA TA AA TA TA TA TA TGA TA AA AA TA TA TT TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
269402 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
269417 TCTCTTAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:270695 original size:18 final size:17
Alignment explanation
Indices: 270674--270727 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
270664 TGTTTAATAT
270674 TTTTTATATTTATATAAA
1 TTTTTATA-TTATATAAA
*
270692 -TTTTA-A-TATATCAA
1 TTTTTATATTATATAAA
*
270706 TAATTTATATTATATAAA
1 T-TTTTATATTATATAAA
270724 TTTT
1 TTTT
270728 AAAATATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
14 7 0.25
16 5 0.18
17 8 0.29
18 8 0.29
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTATATTATATAAA
Found at i:270722 original size:32 final size:33
Alignment explanation
Indices: 270676--270753 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 33
270666 TTTAATATTT
*
270676 TTTATATTTATATAAATTTTAATATATCAATA-A
1 TTTATA-TTATATAAATTTTAAAATATCAATATA
**
270709 TTTATATTATATAAATTTTAAAATATTTATATA
1 TTTATATTATATAAATTTTAAAATATCAATATA
270742 TTTATATTATAT
1 TTTATATTATAT
270754 CTTATCTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 22 0.54
33 19 0.46
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (33 bp):
TTTATATTATATAAATTTTAAAATATCAATATA
Found at i:271057 original size:28 final size:27
Alignment explanation
Indices: 271008--271070 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
270998 AGATCTTATC
* * *
271008 AAAATACAAAAAATAATAAATATAATA
1 AAAATATAAAAAATAACAAATAAAATA
271035 AAAATATAAAAAATAACATAATAAAATA
1 AAAATATAAAAAATAACA-AATAAAATA
*
271063 TAAATATA
1 AAAATATA
271071 TAAATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (27 bp):
AAAATATAAAAAATAACAAATAAAATA
Found at i:271073 original size:15 final size:14
Alignment explanation
Indices: 271018--271079 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
271008 AAAATACAAA
271018 AAATAATAAATATAAT
1 AAATAATAAA-AT-AT
* *
271034 AAAAATATAAAAAAT
1 AAATA-ATAAAATAT
271049 AACATAATAAAATAT
1 AA-ATAATAAAATAT
*
271064 AAATATATAAATTAT
1 AAATA-ATAAAATAT
271079 A
1 A
271080 TTAAAATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 3 0.08
15 23 0.61
16 7 0.18
17 5 0.13
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAATAAAATAT
Found at i:271075 original size:8 final size:8
Alignment explanation
Indices: 271018--271079 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 8
271008 AAAATACAAA
271018 AAATA-AT
1 AAATATAT
271025 AAATATAAT
1 AAATAT-AT
*
271034 AAAAATAT
1 AAATATAT
*
271042 AAA-AAAT
1 AAATATAT
271049 AACATA-AT
1 AA-ATATAT
271057 AAA-ATAT
1 AAATATAT
271064 AAATATAT
1 AAATATAT
271072 AAAT-TAT
1 AAATATAT
271079 A
1 A
271080 TTAAAATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
6 1 0.02
7 20 0.43
8 18 0.38
9 8 0.17
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (8 bp):
AAATATAT
Found at i:271610 original size:39 final size:36
Alignment explanation
Indices: 271534--271616 Score: 87
Period size: 39 Copynumber: 2.2 Consensus size: 36
271524 GATATATGGT
*
271534 AATAATAAAATTATTTTATTTAAAAATTAATTTTTA
1 AATAATAAAATTATTTTATTTAAAAATTAATTATTA
* *
271570 AATAATAAAATTTTATTTTAATTT-TAATTTAAATTATTA
1 AATAATAAAA--TTATTTT-ATTTAAAAATT-AATTATTA
*
271609 AATTATAA
1 AATAATAA
271617 TTTTAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
36 10 0.26
38 11 0.28
39 18 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
AATAATAAAATTATTTTATTTAAAAATTAATTATTA
Found at i:271634 original size:26 final size:26
Alignment explanation
Indices: 271557--271636 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
271547 TTTTATTTAA
*
271557 AAATTA-ATTTTTAAATA-ATAAAATT
1 AAATTATAATTTTAAATATA-AAAATT
** * * *
271582 TTATTTTAATTTT-AATTTAAATTATT
1 AAATTATAATTTTAAATATAAA-AATT
271608 AAATTATAATTTTAAATATAAAAATT
1 AAATTATAATTTTAAATATAAAAATT
271634 AAA
1 AAA
271637 ATTAATTATT
Statistics
Matches: 40, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
25 8 0.20
26 25 0.62
27 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AAATTATAATTTTAAATATAAAAATT
Found at i:272074 original size:42 final size:42
Alignment explanation
Indices: 272013--272095 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
272003 TCAATGGATG
272013 TTAATGGAGAATTAAGGAAGTTCACATGGAGGATTGAGAATA
1 TTAATGGAGAATTAAGGAAGTTCACATGGAGGATTGAGAATA
*
272055 TTAATGGAGAATTATGGAAGTTCACATGGAGGATTGAGAAT
1 TTAATGGAGAATTAAGGAAGTTCACATGGAGGATTGAGAAT
272096 TTCTCGAGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.28
Consensus pattern (42 bp):
TTAATGGAGAATTAAGGAAGTTCACATGGAGGATTGAGAATA
Found at i:272597 original size:10 final size:10
Alignment explanation
Indices: 272582--272607 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
272572 ATTTATTGCT
272582 TTTTTTTTTC
1 TTTTTTTTTC
272592 TTTTTTTTTC
1 TTTTTTTTTC
272602 TTTTTT
1 TTTTTT
272608 ATTTATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:281132 original size:27 final size:27
Alignment explanation
Indices: 281072--281133 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
281062 GTATTTTAAA
* * **
281072 TAAAAAATTTAATATTTATTTTTTATT
1 TAAAAAATTTAAAATTAAAATTTTATT
**
281099 TTTAAAATTTAAAATTAAAATTTTATT
1 TAAAAAATTTAAAATTAAAATTTTATT
281126 TAAAAAAT
1 TAAAAAAT
281134 ATCAAACTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAAAAAATTTAAAATTAAAATTTTATT
Found at i:281300 original size:26 final size:25
Alignment explanation
Indices: 281265--281339 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 25
281255 TGAGAAACAC
*
281265 AAAATATTAAATTATTATTATATAT
1 AAAATATTAAATTATTATTATATAG
* * *
281290 AAATTGATTAAAGTAATTATTATACAG
1 AAAAT-ATTAAA-TTATTATTATATAG
281317 AAAATATTAAATTATTATT-TATA
1 AAAATATTAAATTATTATTATATA
281340 AATACATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
24 3 0.07
25 11 0.27
26 12 0.29
27 15 0.37
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (25 bp):
AAAATATTAAATTATTATTATATAG
Found at i:282751 original size:78 final size:78
Alignment explanation
Indices: 282665--282929 Score: 272
Period size: 79 Copynumber: 3.4 Consensus size: 78
282655 ATCGGTGTTC
282665 TGAAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGTTGGAGTATCCCTGATTATAG
1 TGAAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGTTGGAGTATCCCTGATTATAG
282730 AAAAAT-GACATTT
66 AAAAATAGAC-TTT
* * * * *
282743 TGAAAATAAAATTGGGGTCGAAGTATCCCCTCGAAAATAACGAGGTTAGAGTATCCCTGATTGT-
1 TGAAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAAC-AGGTTGGAGTATCCCTGATTATA
*
282807 GAAAAATCGATGCTTT
65 GAAAAATAGA--CTTT
* *** * * *
282823 AG-AAATAAGGCCGAGGTTGGAGTATCCCCGTC-AAAATAACGGGATTGGAGTATCCCCGATTAT
1 TGAAAATAAAATCGGGGTTGGAGTATCCCC-TCGAAAATAACAGG-TTGGAGTATCCCTGATTAT
*
282886 A-AAAAATAGATGTTT
64 AGAAAAATAGA-CTTT
** *
282901 TGAAAATAAAA-CTTGGTTAGAGTATCCCC
1 TGAAAATAAAATCGGGGTTGGAGTATCCCC
282930 AAGATGAAAA
Statistics
Matches: 153, Mismatches: 26, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
78 66 0.43
79 80 0.52
80 6 0.04
81 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.26
Consensus pattern (78 bp):
TGAAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGTTGGAGTATCCCTGATTATAG
AAAAATAGACTTT
Found at i:285900 original size:62 final size:62
Alignment explanation
Indices: 285800--286488 Score: 820
Period size: 61 Copynumber: 11.3 Consensus size: 62
285790 AATGAAATGG
* * * ** *
285800 GTCCTGCTCCTTGGGGACTAG-AAAGTGCCACCAACTTGTATGGGCTTTGCAAGGAGAAA-GC
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGA-AAAGGC
* * * *
285861 ATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGT
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC
* * ** *
285923 GTCCTGCTCTTTGAAGACTAG-AAGGTGCCACCAACTTGTGTAAGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC
* * ** *
285984 GTCCTGCTCTTTAAGGGCTAGAAAAGCACCACCAACTTGTGTGGGCTTT-AAAAGAAAAATGC
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAGGC
* * * *
286046 GTCCTGCTCCTTGAGGACT-GAAAAGTGCCACCAACTCGTGCGGGCTTTGAAAAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC
* * * * * *
286107 ATCCTACTCTTTGAGGACTA-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGAC
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAGGC
* * * *
286169 GTCCTGCTCTTTGAGGACTA-AGAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGT
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAGGC
*
286231 GTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC
* *
286293 GTCCTGCTCCTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC
* * * *
286354 GTCCTACTCTTTGAGGACT-G-AAGGTGCCA-CAAGCTTGTGTGGGCTTTAAAAGGAAAAGGT
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAA-CTTGTGTGGGCTTTAAAAAGAAAAGGC
* *
286414 GTCATGCTCCTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC
286469 GTCCTGCTCTTTGAGGACTA
1 GTCCTGCTCTTTGAGGACTA
286489 AAGGGTGAAA
Statistics
Matches: 555, Mismatches: 61, Indels: 29
0.86 0.09 0.04
Matches are distributed among these distances:
55 22 0.04
56 1 0.00
59 3 0.01
60 51 0.09
61 237 0.43
62 209 0.38
63 32 0.06
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (62 bp):
GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC
Found at i:285951 original size:123 final size:123
Alignment explanation
Indices: 285794--286488 Score: 880
Period size: 123 Copynumber: 5.7 Consensus size: 123
285784 AAGGAGAATG
* * * *
285794 AAATGGGTCCTGCTCCTTGGGGACT-AGAAAGTGCCACCAACTTGTATGGGCTTTGCAAGGAGAA
1 AAATGCGTCCTGCTCCTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGA-AA
* *
285858 A-GCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
64 AGGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * * ** *
285917 AAATGTGTCCTGCTCTTTGAAGACT-AGAAGGTGCCACCAACTTGTGTAAGCTTTAAAAGGAAAA
1 AAATGCGTCCTGCTCCTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA
* * * ** *
285981 GGCGTCCTGCTCTTTAAGGGCTAGAAAAGCACCACCAACTTGTGTGGGCTTTAAAAGAA
65 GGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * *
286040 AAATGCGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTCGTGCGGGCTTTGAAAAGAAAAG
1 AAATGCGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
* * *
286105 GCATCCTACTCTTTGAGGACTA-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GA
66 GCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * * *
286162 AAAAGACGTCCTGCTCTTTGAGGACT-AAGAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAA
1 AAATG-CGTCCTGCTCCTTGAGGACTGAA-AAGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAA
* *
286226 AAGGTGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGA
63 AAGGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
286287 AAAGGCGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 AAATGCGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
*
286352 GCGTCCTACTCTTTGAGGACT-G-AAGGTGCCA-CAAGCTTGTGTGGGCTTTAAAAGGA
66 GCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAA-CTTGTGTGGGCTTTAAAAGGA
* * *
286408 AAAGGTGTCATGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-----G-AAAG
1 AAATGCGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
286467 GCGTCCTGCTCTTTGAGGACTA
66 GCGTCCTGCTCTTTGAGGACTA
286489 AAGGGTGAAA
Statistics
Matches: 504, Mismatches: 57, Indels: 29
0.85 0.10 0.05
Matches are distributed among these distances:
115 24 0.05
116 1 0.00
120 3 0.01
121 81 0.16
122 35 0.07
123 249 0.49
124 76 0.15
125 35 0.07
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (123 bp):
AAATGCGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
GCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
Found at i:288006 original size:79 final size:80
Alignment explanation
Indices: 287845--288048 Score: 229
Period size: 79 Copynumber: 2.6 Consensus size: 80
287835 ACAATGAGGC
* * * * *
287845 TGGAGTATCTCTGATTATGGAAAATCGGTGTTCTAGAAATAAAAATCGGGGTTGGAGTATCCCCT
1 TGGAGTATCCCCGATTATAGAAAATCGATGTTCTAGAAATAAAAATCGGGATTGGAGTATCCCCT
*
287910 CAAAAATAACAGGGT
66 CAAAAATAACAGAGT
*
287925 TGGAGTATCCCCGATTATAGAAAATCGATGTT-TGGAAA-ATAAAATCGGGATTGGAGTATCCCC
1 TGGAGTATCCCCGATTATAGAAAATCGATGTTCTAGAAATA-AAAATCGGGATTGGAGTATCCCC
287988 GT-AAAAATAATC-GAGT
65 -TCAAAAATAA-CAGAGT
* * * * *
288004 TGGAATATCCCCGATTGTAAAAAAT-TAGTGTTTTAGAAATAAAAA
1 TGGAGTATCCCCGATTATAGAAAATCGA-TGTTCTAGAAATAAAAA
288049 AATGAATGAA
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
78 2 0.02
79 64 0.60
80 39 0.37
81 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (80 bp):
TGGAGTATCCCCGATTATAGAAAATCGATGTTCTAGAAATAAAAATCGGGATTGGAGTATCCCCT
CAAAAATAACAGAGT
Found at i:299123 original size:13 final size:13
Alignment explanation
Indices: 299105--299130 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
299095 CAATTTTTTG
299105 TGTATCGATACAT
1 TGTATCGATACAT
299118 TGTATCGATACAT
1 TGTATCGATACAT
299131 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:299870 original size:21 final size:21
Alignment explanation
Indices: 299829--299872 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
299819 CTCTCTTTTA
* *
299829 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
299850 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
299871 TC
1 TC
299873 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:301515 original size:21 final size:21
Alignment explanation
Indices: 301491--301537 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
301481 TTTGATGCTG
301491 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
301511 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
301532 ATTTTG
1 ATTTTG
301538 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:301676 original size:13 final size:13
Alignment explanation
Indices: 301658--301696 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
301648 ATAATCACCC
*
301658 TGTATCGATACAG
1 TGTATCGATACAA
301671 TGTATCGATACAA
1 TGTATCGATACAA
301684 TGTATCGATACAA
1 TGTATCGATACAA
301697 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:301707 original size:20 final size:20
Alignment explanation
Indices: 301682--301760 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
301672 GTATCGATAC
301682 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
301702 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
301727 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
301747 CATGTATCGATACA
1 AATGTATCGATACA
301761 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:303796 original size:15 final size:15
Alignment explanation
Indices: 303776--303806 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
303766 ATTTCGTTTG
*
303776 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
303791 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
303806 G
1 G
303807 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:305639 original size:21 final size:21
Alignment explanation
Indices: 305610--305654 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
305600 AAGTTTTCAT
*
305610 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
305630 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
305652 TTT
1 TTT
305655 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:307892 original size:13 final size:13
Alignment explanation
Indices: 307874--307899 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
307864 CAATTTTTTG
307874 TGTATCGATACAT
1 TGTATCGATACAT
307887 TGTATCGATACAT
1 TGTATCGATACAT
307900 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:314663 original size:25 final size:26
Alignment explanation
Indices: 314618--314673 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
314608 GTTAGTAAAT
* *
314618 CAAAAAAAATAACAGACAAATTTATA
1 CAAAATAAATAACAGACAAATATATA
314644 CAAAATAAATACACA-A-AAATATATA
1 CAAAATAAATA-ACAGACAAATATATA
314669 -AAAAT
1 CAAAAT
314674 GAGGGACGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 5 0.19
25 8 0.30
26 11 0.41
27 3 0.11
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.20
Consensus pattern (26 bp):
CAAAATAAATAACAGACAAATATATA
Found at i:315247 original size:77 final size:77
Alignment explanation
Indices: 314919--315292 Score: 385
Period size: 79 Copynumber: 4.8 Consensus size: 77
314909 GGGGCTGAAA
* * ** * *
314919 TATCCCCGATTATGGAAAATCGATGTTCTAAAAATAAAATCAGAGTTGGAGTATCCCCTCGAAAA
1 TATCCCCGATTATGAAAAATCGATGTTTTGGAAATAAAATCGGGGTTGGAGTAT-CCC-CGAAAA
**
314984 TAATAGGGTTAGAG
64 TAACGGGGTTAGAG
* * * * *
314998 TATCCCTGATTAT-AGAAAATCGACGTTTTGAAAATAAAATCAGGGTTCGAGTATCCCCTCGAAA
1 TATCCCCGATTATGA-AAAATCGATGTTTTGGAAATAAAATCGGGGTTGGAGTAT-CCC-CGAAA
315062 ATAACGGGGTTAGAG
63 ATAACGGGGTTAGAG
* * * **
315077 TATCCCCGATTGTGAAAAATCGATGCTTTAGAAA-AAAGGCTGGGGTTGGAGTATCTCTGCC-AA
1 TATCCCCGATTATGAAAAATCGATGTTTTGGAAATAAAATC-GGGGTTGGAGTATC-C--CCGAA
*
315140 AATAACGGGGTTGGAG
62 AATAACGGGGTTAGAG
* * *
315156 TATCCCCGACTATGAAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGAAAATA
1 TATCCCCGATTATGAAAAATCGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGAAAATA
* * *
315221 ATGGGATTGGAG
66 ACGGGGTTAGAG
* * * *
315233 TATCCCCGATTATGAAAAATTGATATTTTGGAAATAATACCGGGGTTGGAGTATCCCCGA
1 TATCCCCGATTATGAAAAATCGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGA
315293 GATGAAAAAT
Statistics
Matches: 252, Mismatches: 35, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
76 2 0.01
77 71 0.28
78 6 0.02
79 166 0.66
80 6 0.02
81 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (77 bp):
TATCCCCGATTATGAAAAATCGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGAAAATA
ACGGGGTTAGAG
Found at i:315323 original size:51 final size:51
Alignment explanation
Indices: 315227--315323 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 51
315217 AATAATGGGA
* * ***
315227 TTGGAGTATCCCCGATTATGAAAAATTGATATTTTGGAAATAATACCGGGG
1 TTGGAGTATCCCCGATGATGAAAAATTGAAATTTAACAAATAATACCGGGG
315278 TTGGAGTATCCCCGA-GATGAAAAATCTAGAAATTTAACAAA-AATAC
1 TTGGAGTATCCCCGATGATGAAAAAT-T-GAAATTTAACAAATAATAC
315324 TTTTGAGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
50 9 0.23
51 21 0.54
52 9 0.23
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (51 bp):
TTGGAGTATCCCCGATGATGAAAAATTGAAATTTAACAAATAATACCGGGG
Found at i:318106 original size:348 final size:349
Alignment explanation
Indices: 317464--318143 Score: 1263
Period size: 348 Copynumber: 2.0 Consensus size: 349
317454 ATTTAAATTC
*
317464 CATTCCGACCCAAAAAATGAAACTTAGCATGATTTCTAATGATTCTAGATGCAAAATATGTGTTA
1 CATTCCGACCCAAAAAATGAAACTTAGCATGATTTCTAATGATTCTAGATGCAAAACATGTGTTA
*
317529 AAAACCAAGTTTTGAATGGACAATGCAAGAGCAGAAAAATGACTTGAAATGGTCATAAATGCTTG
66 AAAACCAAGTTTTGAATGGACAATGCAAGAGCAGAAAAATGACTTGAAATGGTCATAAATGCCTG
*
317594 AATGTATCGATACAATGAACAATGTATCGATACAAATTGTGAAAATTTTGAATTTTTGACCGTTG
131 AATGTATCGATACAATGAACAATGTATCGATACAAATTGTGAAAATTTTGAATTTTTGACCGTTA
* *
317659 GGACCTTGTATCGATACATTAAGGGCATGTATCGATACATTTTGGCAAAAGTGTGATTTTTTCAT
196 GGACCTTGTATCGATACATTAAGGGCATGTATCAATACATTTTGACAAAAGTGTGATTTTTTCAT
*
317724 ACTTTTTGTATCCCGAACACGTACCTTTATTAAAGGTGATGGATTCGTATTAGTCGAAAAGCTCA
261 ACTTTTTGTATCCCGAACACGTACCTTCATTAAAGGTGATGGATTCGTATTAGTCGAAAAGCTCA
*
317789 GAAAATCCCGAACATGTATCAATA
326 AAAAATCCCGAACATGTATCAATA
*
317813 CATTCCGACCCCAAAAATGAAACTTAGCATGATTTCTAATG-TTCTAGATGCAAAACATGTGTTA
1 CATTCCGACCCAAAAAATGAAACTTAGCATGATTTCTAATGATTCTAGATGCAAAACATGTGTTA
*
317877 AAAACCAAGTTTTGAATGGACAATGCAAGAGTAGAAAAATGACTTGAAATGGTCATAAATGCCTG
66 AAAACCAAGTTTTGAATGGACAATGCAAGAGCAGAAAAATGACTTGAAATGGTCATAAATGCCTG
317942 AATGTATCGATACAATGAACAATGTATCGATACAAATTGTGAAAATTTTGAATTTTTGACCGTTA
131 AATGTATCGATACAATGAACAATGTATCGATACAAATTGTGAAAATTTTGAATTTTTGACCGTTA
*
318007 GGACCTTGTATCGATACATTAAGGGCATGTATCAATACATTTTGACAAAAGTGTGTTTTTTTCAT
196 GGACCTTGTATCGATACATTAAGGGCATGTATCAATACATTTTGACAAAAGTGTGATTTTTTCAT
318072 ACTTTTTGTATCCCGAACACGTACCTTCATTAAAGGTGATGGATTCGTATTAGTCGAAAAGCTCA
261 ACTTTTTGTATCCCGAACACGTACCTTCATTAAAGGTGATGGATTCGTATTAGTCGAAAAGCTCA
318137 AAAAATC
326 AAAAATC
318144 TAAAAGTCCT
Statistics
Matches: 321, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
348 281 0.88
349 40 0.12
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (349 bp):
CATTCCGACCCAAAAAATGAAACTTAGCATGATTTCTAATGATTCTAGATGCAAAACATGTGTTA
AAAACCAAGTTTTGAATGGACAATGCAAGAGCAGAAAAATGACTTGAAATGGTCATAAATGCCTG
AATGTATCGATACAATGAACAATGTATCGATACAAATTGTGAAAATTTTGAATTTTTGACCGTTA
GGACCTTGTATCGATACATTAAGGGCATGTATCAATACATTTTGACAAAAGTGTGATTTTTTCAT
ACTTTTTGTATCCCGAACACGTACCTTCATTAAAGGTGATGGATTCGTATTAGTCGAAAAGCTCA
AAAAATCCCGAACATGTATCAATA
Found at i:318344 original size:15 final size:14
Alignment explanation
Indices: 318326--318377 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
318316 TATTTTATTT
318326 ATTTAATAATTAAAA
1 ATTT-ATAATTAAAA
* *
318341 ATTTTTATATTAAAT
1 ATTTATA-ATTAAAA
*
318356 ATTTATAATTTTAAA
1 ATTTATAA-TTAAAA
318371 ATTTATA
1 ATTTATA
318378 TTTACATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 3 0.10
15 27 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTATAATTAAAA
Found at i:318348 original size:30 final size:30
Alignment explanation
Indices: 318314--318380 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
318304 AAAATTTATA
**
318314 TTTATTTTATTTATTTAATAA-TTAAAAATT
1 TTTATTTTAAATATTT-ATAATTTAAAAATT
* *
318344 TTTATATTAAATATTTATAATTTTAAAATT
1 TTTATTTTAAATATTTATAATTTAAAAATT
*
318374 TATATTT
1 TTTATTT
318381 ACATATAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTATTTTAAATATTTATAATTTAAAAATT
Found at i:318386 original size:29 final size:30
Alignment explanation
Indices: 318325--318386 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
318315 TTATTTTATT
*
318325 TATTTAATAATTAAAAATTTTTATATTAAA
1 TATTTAATAATTAAAAATTTATATATTAAA
* *
318355 TATTT-ATAATTTTAAAATTTATAT-TTACA
1 TATTTAATAA-TTAAAAATTTATATATTAAA
318384 TAT
1 TAT
318387 AAATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
TATTTAATAATTAAAAATTTATATATTAAA
Found at i:319092 original size:23 final size:21
Alignment explanation
Indices: 319061--319102 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
319051 TATTATTTAA
319061 TTTTTATATTAAAAATATAATT
1 TTTTTATA-TAAAAATATAATT
*
319083 TTTTTAATATATAAATATAA
1 TTTTT-ATATAAAAATATAA
319103 ATTAAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTATATAAAAATATAATT
Found at i:319738 original size:27 final size:27
Alignment explanation
Indices: 319686--319763 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 27
319676 TGACTATAAT
*
319686 TATTCTAT-TTTATTATATCATGTTTAAAA
1 TATTTTATATTTA-TATAT-AT-TTTAAAA
319715 TATTTTATATTTATATATATTTTAAAA
1 TATTTTATATTTATATATATTTTAAAA
* *
319742 TA-CTCATATTATATATATATTT
1 TATTTTATATT-TATATATATTT
319764 ATTATATCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
26 6 0.14
27 20 0.45
28 2 0.05
29 12 0.27
30 4 0.09
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.56
Consensus pattern (27 bp):
TATTTTATATTTATATATATTTTAAAA
Found at i:319773 original size:25 final size:25
Alignment explanation
Indices: 319725--319822 Score: 89
Period size: 23 Copynumber: 4.0 Consensus size: 25
319715 TATTTTATAT
**
319725 TTATATATAT-TTTAAAATACTCATA
1 TTATATATATATTTATTATA-TCATA
319750 TTATATATATATTTATTATATCATA
1 TTATATATATATTTATTATATCATA
* *
319775 TTTTA-AT-TATTTTTTATATCATA
1 TTATATATATATTTATTATATCATA
319798 TT-TATATA-ATCTTATTTAATATCAT
1 TTATATATATAT-TTA-TT-ATATCAT
319823 CAGTTTTTCT
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
22 2 0.03
23 21 0.34
24 4 0.06
25 21 0.34
26 14 0.23
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATATATATATTTATTATATCATA
Found at i:319894 original size:2 final size:2
Alignment explanation
Indices: 319887--319911 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
319877 CATGCACTTA
319887 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 A
319912 CACACACACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:323072 original size:18 final size:19
Alignment explanation
Indices: 323045--323080 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
323035 AGAGTGGAGT
*
323045 AATTTGTTTAAT-TTTAAA
1 AATTTATTTAATATTTAAA
323063 AATTTATTTAATATTTAA
1 AATTTATTTAATATTTAA
323081 GAGAATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
AATTTATTTAATATTTAAA
Found at i:331992 original size:16 final size:16
Alignment explanation
Indices: 331912--331992 Score: 87
Period size: 16 Copynumber: 5.2 Consensus size: 16
331902 AAATAATTTT
331912 AAAT-TTTAAATTTAA
1 AAATATTTAAATTTAA
*
331927 AAAT-TTTAAA-TAAA
1 AAATATTTAAATTTAA
* *
331941 AAATTATTTGAATATAA
1 AAA-TATTTAAATTTAA
* *
331958 AATTATTTGAATTTAA
1 AAATATTTAAATTTAA
331974 AAATATTTAAATTTAA
1 AAATATTTAAATTTAA
331990 AAA
1 AAA
331993 AAATAGATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 6 0.11
15 11 0.20
16 34 0.62
17 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
AAATATTTAAATTTAA
Found at i:332836 original size:151 final size:151
Alignment explanation
Indices: 332679--332960 Score: 422
Period size: 151 Copynumber: 1.9 Consensus size: 151
332669 TTGCTTGTCT
* * * ** *
332679 AATAGATAAACATTTTTAATAAAAGCTTGAAGTATTTTAAAATAAGAAAAGAGCTTTCTTTAT-G
1 AATAGATAAACACTTCTAATAAAAACTAAAAATATTTTAAAATAAGAAAAGAGCTTTCTTTATCG
*
332743 TATTTTTTTCCACATTTTCTTCATAAAAATAGGTGATTTATAAATTTTAAGAGATATTAACAAAA
66 TATTTTTTTCCACATTTTCTTCACAAAAATAGGTGATTTATAAA-TTTAAGAGATATTAACAAAA
332808 CACAACTCACCCTAGCCTGTTC
130 CACAACTCACCCTAGCCTGTTC
* * *
332830 AATAGATAAACACTTCTAATAAAAACTAAAAATATTTTAAAATAAGAGAGGAGCTTTCTTTATCT
1 AATAGATAAACACTTCTAATAAAAACTAAAAATATTTTAAAATAAGAAAAGAGCTTTCTTTATCG
* * * *
332895 TTTTTTTTTCCACATTTTCTTTACAAAAATAGGTGATTTATAAATTTAAGAGATATTGATAAAAC
66 TATTTTTTTCCACATTTTCTTCACAAAAATAGGTGATTTATAAATTTAAGAGATATTAACAAAAC
332960 A
131 A
332961 TGTTTAATCT
Statistics
Matches: 116, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
151 75 0.65
152 41 0.35
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.38
Consensus pattern (151 bp):
AATAGATAAACACTTCTAATAAAAACTAAAAATATTTTAAAATAAGAAAAGAGCTTTCTTTATCG
TATTTTTTTCCACATTTTCTTCACAAAAATAGGTGATTTATAAATTTAAGAGATATTAACAAAAC
ACAACTCACCCTAGCCTGTTC
Found at i:335037 original size:33 final size:33
Alignment explanation
Indices: 334999--335063 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
334989 CATACCTAGA
*
334999 TGTATCGATACATATTGCTAAGTATCGATACAT
1 TGTATCGATACAAATTGCTAAGTATCGATACAT
**
335032 TGTATCGATACAAATTGCTTTGTATCGATACA
1 TGTATCGATACAAATTGCTAAGTATCGATACA
335064 CCATAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAAATTGCTAAGTATCGATACAT
Found at i:341257 original size:32 final size:32
Alignment explanation
Indices: 341208--341270 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
341198 TTTCCAGATC
* *
341208 TATCAATACAAAGAAATTGTATCGATACATTG
1 TATCAATACAAAGAAATTATATCAATACATTG
*
341240 TATCAATACATTA-AAATTATATCAATACATT
1 TATCAATACA-AAGAAATTATATCAATACATT
341271 AAAATTGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (32 bp):
TATCAATACAAAGAAATTATATCAATACATTG
Found at i:341264 original size:19 final size:19
Alignment explanation
Indices: 341240--341289 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
341230 CGATACATTG
341240 TATCAATACATTAAAATTA
1 TATCAATACATTAAAATTA
*
341259 TATCAATACATTAAAATTG
1 TATCAATACATTAAAATTA
*
341278 TATCGATACATT
1 TATCAATACATT
341290 TTGACTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (19 bp):
TATCAATACATTAAAATTA
Found at i:345413 original size:31 final size:31
Alignment explanation
Indices: 345375--345434 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
345365 TTAGGCTTTT
*
345375 GTTTATTGTTAGATTTCTCATTACTATGGTA
1 GTTTATTGTTAGAATTCTCATTACTATGGTA
345406 GTTTATTGTTAGAATTCTCATTACTATGG
1 GTTTATTGTTAGAATTCTCATTACTATGG
345435 CCTTTTATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (31 bp):
GTTTATTGTTAGAATTCTCATTACTATGGTA
Found at i:348182 original size:14 final size:13
Alignment explanation
Indices: 348143--348199 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
348133 CAAATATGCT
*
348143 TGTGCCAGAGTATC
1 TGTGCCA-AGTACC
*
348157 TGTGTCGAAGTACC
1 TGTG-CCAAGTACC
*
348171 TGTGCCATAGTACT
1 TGTGCCA-AGTACC
348185 TGTGCCAAAGTACC
1 TGTGCC-AAGTACC
348199 T
1 T
348200 ATGCTAGATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 2 0.06
14 30 0.86
15 3 0.09
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (13 bp):
TGTGCCAAGTACC
Found at i:348182 original size:28 final size:28
Alignment explanation
Indices: 348122--348517 Score: 141
Period size: 29 Copynumber: 13.9 Consensus size: 28
348112 AAATGCCCAA
*
348122 AGTACTTGTGCCAAA-TATGCTTGTGCCAG
1 AGTACTTGTGCCAAAGTA--CCTGTGCCAG
* * *
348151 AGTA-TCTGTGTCGAAGTACCTGTGCCAT
1 AGTACT-TGTGCCAAAGTACCTGTGCCAG
* *
348179 AGTACTTGTGCCAAAGTACCTATGCTAG
1 AGTACTTGTGCCAAAGTACCTGTGCCAG
**
348207 A-TAACCCTAT-TGCC-AAG-AAATGTGCCA-
1 AGT-A--CT-TGTGCCAAAGTACCTGTGCCAG
* * * * * *
348234 ATGCACTTGTGCCGAAGGTACTTATGTCAA
1 A-GTACTTGTGCC-AAAGTACCTGTGCCAG
* *
348264 AGTATCTATG-CCCAAAGTACCTGTGCCAA
1 AGTA-CT-TGTGCCAAAGTACCTGTGCCAG
* * **
348293 ATGTA-TCTGTGCTAGAGTACCTGTG-TTG
1 A-GTACT-TGTGCCAAAGTACCTGTGCCAG
* *
348321 AAGTACCTGTGCCAAAGGTACCTGTGCCAA
1 -AGTACTTGTGCCAAA-GTACCTGTGCCAG
* * * *
348351 AATACCTGTGCTAAAGGTACCTTTGCCAG
1 AGTACTTGTGCCAAA-GTACCTGTGCCAG
* ** * *
348380 AGTACCTGTGCTTGAA-TACTTGTGCCTAA
1 AGTACTTGTGC-CAAAGTACCTGTGCC-AG
** *
348409 AGTAC-CATGCCAAAGGTACTTGTGCCAG
1 AGTACTTGTGCCAAA-GTACCTGTGCCAG
* * * *
348437 AGTACTCGTGCCAAAGTACTTGTGCTAA
1 AGTACTTGTGCCAAAGTACCTGTGCCAG
* *
348465 AGTACTTATGCCAAATGTGCCTGTGCCAG
1 AGTACTTGTGCCAAA-GTACCTGTGCCAG
* * *
348494 AGTACTAGTGTCGAAGTACCTGTG
1 AGTACTTGTGCCAAAGTACCTGTG
348518 TCGACAATAC
Statistics
Matches: 273, Mismatches: 66, Indels: 57
0.69 0.17 0.14
Matches are distributed among these distances:
25 1 0.00
26 6 0.02
27 4 0.01
28 103 0.38
29 137 0.50
30 19 0.07
31 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (28 bp):
AGTACTTGTGCCAAAGTACCTGTGCCAG
Found at i:348292 original size:14 final size:14
Alignment explanation
Indices: 348261--348535 Score: 164
Period size: 14 Copynumber: 19.1 Consensus size: 14
348251 GTACTTATGT
* *
348261 CAAAGTATCTATGCC
1 CAAAGTACCTGTG-C
348276 CAAAGTACCTGTGC
1 CAAAGTACCTGTGC
*
348290 CAAATGTATCTGTGC
1 CAAA-GTACCTGTGC
* * *
348305 TAGAGTACCTGTGT
1 CAAAGTACCTGTGC
**
348319 TGAAGTACCTGTGC
1 CAAAGTACCTGTGC
348333 CAAAGGTACCTGTGC
1 CAAA-GTACCTGTGC
*
348348 CAAAATACCTGTGC
1 CAAAGTACCTGTGC
* *
348362 TAAAGGTACCTTTGC
1 CAAA-GTACCTGTGC
*
348377 CAGAGTACCTGTGC
1 CAAAGTACCTGTGC
** *
348391 TTGAA-TACTTGTGC
1 -CAAAGTACCTGTGC
*
348405 CTAAAGTACC-ATGC
1 C-AAAGTACCTGTGC
*
348419 CAAAGGTACTTGTGC
1 CAAA-GTACCTGTGC
*
348434 CAGAGTA-CTCGTGC
1 CAAAGTACCT-GTGC
*
348448 CAAAGTACTTGTGC
1 CAAAGTACCTGTGC
* * *
348462 TAAAGTACTTATGC
1 CAAAGTACCTGTGC
*
348476 CAAATGTGCCTGTGC
1 CAAA-GTACCTGTGC
* *
348491 CAGAGTA-CTAGTGT
1 CAAAGTACCT-GTGC
*
348505 CGAAGTACCTGTGTC
1 CAAAGTACCTGTG-C
*
348520 GACAA-TACCTGTGC
1 CA-AAGTACCTGTGC
348534 CA
1 CA
348536 GATGAGAGCT
Statistics
Matches: 197, Mismatches: 48, Indels: 31
0.71 0.17 0.11
Matches are distributed among these distances:
13 6 0.03
14 112 0.57
15 77 0.39
16 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (14 bp):
CAAAGTACCTGTGC
Found at i:348293 original size:29 final size:28
Alignment explanation
Indices: 348227--348517 Score: 144
Period size: 29 Copynumber: 10.1 Consensus size: 28
348217 TGCCAAGAAA
* * * *
348227 TGTGCCAATGCACTTGTGCCGAAGGTACT
1 TGTGCCAAAGTAC-TGTGCCAAAGGTACC
* * *
348256 TATGTCAAAGTATCTATGCCCAAA-GTACC
1 TGTGCCAAAGTA-CTGTG-CCAAAGGTACC
* *
348285 TGTGCCAAATGTATCTGTGCTAGA-GTACC
1 TGTGCCAAA-GTA-CTGTGCCAAAGGTACC
***
348314 TGTGTTGAAGTACCTGTGCCAAAGGTACC
1 TGTGCCAAAGTA-CTGTGCCAAAGGTACC
* *
348343 TGTGCCAAAATACCTGTGCTAAAGGTACC
1 TGTGCCAAAGTA-CTGTGCCAAAGGTACC
* * ** *
348372 TTTGCCAGAGTACCTGTGCTTGAA--TACT
1 TGTGCCAAAGTA-CTGTGC-CAAAGGTACC
** *
348400 TGTGCCTAAAGTACCATGCCAAAGGTACT
1 TGTGCC-AAAGTACTGTGCCAAAGGTACC
* *
348429 TGTGCCAGAGTACTCGTGCCAAA-GTACT
1 TGTGCCAAAGTACT-GTGCCAAAGGTACC
* * * *
348457 TGTGCTAAAGTACTTATGCCAAATGTGCC
1 TGTGCCAAAGTAC-TGTGCCAAAGGTACC
* * *
348486 TGTGCCAGAGTACTAGTGTCGAA-GTACC
1 TGTGCCAAAGTACT-GTGCCAAAGGTACC
348514 TGTG
1 TGTG
348518 TCGACAATAC
Statistics
Matches: 202, Mismatches: 48, Indels: 25
0.73 0.17 0.09
Matches are distributed among these distances:
27 2 0.01
28 61 0.30
29 123 0.61
30 16 0.08
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (28 bp):
TGTGCCAAAGTACTGTGCCAAAGGTACC
Found at i:348326 original size:43 final size:42
Alignment explanation
Indices: 348277--348469 Score: 147
Period size: 43 Copynumber: 4.5 Consensus size: 42
348267 ATCTATGCCC
* * * *
348277 AAAGTACCTGTGCCAAATGTATCTGTGCTAGAGTACCTGTGTT
1 AAAGTACCTGTGCCAAA-GTACCTGTGCTAAAATACCTGTGCT
* *
348320 GAAGTACCTGTGCCAAAGGTACCTGTGCCAAAATACCTGTGCT
1 AAAGTACCTGTGCCAAA-GTACCTGTGCTAAAATACCTGTGCT
* * ** *
348363 AAAGGTACCTTTGCCAGAGTACCTGTGCTTGAATACTTGTGCCT
1 AAA-GTACCTGTGCCAAAGTACCTGTGCTAAAATACCTGTG-CT
* * * * * *
348407 AAAGTACC-ATGCCAAAGGTACTTGTGCCAGAGTA-CTCGTGCC
1 AAAGTACCTGTGCCAAA-GTACCTGTGCTAAAATACCT-GTGCT
* *
348449 AAAGTACTTGTGCTAAAGTAC
1 AAAGTACCTGTGCCAAAGTAC
348470 TTATGCCAAA
Statistics
Matches: 120, Mismatches: 25, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
42 19 0.16
43 84 0.70
44 17 0.14
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (42 bp):
AAAGTACCTGTGCCAAAGTACCTGTGCTAAAATACCTGTGCT
Found at i:348499 original size:57 final size:57
Alignment explanation
Indices: 348329--348517 Score: 170
Period size: 57 Copynumber: 3.3 Consensus size: 57
348319 TGAAGTACCT
* * * * *
348329 GTGCCAAAGGTACCTGTGCC-AAAATACCTGTGCTAAAGGTACCTTTGCCAGAGTACCT-
1 GTGCCAAA-GTACTTGTGCCTAAAGTACC-ATGCCAAAGGTACCTGTGCCAGAGTA-CTA
** * *
348387 GTGCTTGAA-TACTTGTGCCTAAAGTACCATGCCAAAGGTACTTGTGCCAGAGTACTC
1 GTGC-CAAAGTACTTGTGCCTAAAGTACCATGCCAAAGGTACCTGTGCCAGAGTACTA
* * *
348444 GTGCCAAAGTACTTGTG-CTAAAGTACTTATGCCAAATGTGCCTGTGCCAGAGTACTA
1 GTGCCAAAGTACTTGTGCCTAAAGTAC-CATGCCAAAGGTACCTGTGCCAGAGTACTA
* * *
348501 GTGTCGAAGTACCTGTG
1 GTGCCAAAGTACTTGTG
348518 TCGACAATAC
Statistics
Matches: 108, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
56 13 0.12
57 82 0.76
58 11 0.10
59 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (57 bp):
GTGCCAAAGTACTTGTGCCTAAAGTACCATGCCAAAGGTACCTGTGCCAGAGTACTA
Found at i:352648 original size:7 final size:8
Alignment explanation
Indices: 352628--352685 Score: 62
Period size: 8 Copynumber: 6.9 Consensus size: 8
352618 ATAGGATAGA
352628 AAAAAATT
1 AAAAAATT
352636 AAAAAAATT
1 -AAAAAATT
352645 AAAAAATT
1 AAAAAATT
*
352653 AAAAAAGT
1 AAAAAATT
*
352661 ACAAAAATGG
1 A-AAAAAT-T
*
352671 AAAAAAAT
1 AAAAAATT
352679 AAAAAAT
1 AAAAAAT
352686 AAATTTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
8 22 0.54
9 18 0.44
10 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (8 bp):
AAAAAATT
Found at i:352650 original size:17 final size:16
Alignment explanation
Indices: 352628--352685 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 16
352618 ATAGGATAGA
352628 AAAAAATTAAAAAAATT
1 AAAAAATTAAAAAAA-T
*
352645 AAAAAATTAAAAAAGT
1 AAAAAATTAAAAAAAT
*
352661 ACAAAAATGGAAAAAAAT
1 A-AAAAAT-TAAAAAAAT
352679 AAAAAAT
1 AAAAAAT
352686 AAATTTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 2 0.06
17 26 0.72
18 8 0.22
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (16 bp):
AAAAAATTAAAAAAAT
Found at i:357281 original size:56 final size:56
Alignment explanation
Indices: 357112--357281 Score: 157
Period size: 56 Copynumber: 3.1 Consensus size: 56
357102 TGATGCCATA
** * *
357112 GTGGCAGTTAGATTTGGTAGCAACTTAGTGTCACTTGAAGCAGTAATAATGCCTTG
1 GTGGCAGTTAGATTTGGTAGTGACTTGGTGTCACTTGAAGAAGTAATAATGCCTTG
** * * * * * ** *
357168 GTGGCAGCCAGGTCTGG-GGTGACTTGGTGTCAC-TGAGTGATGTGGTGATG-CTGTG
1 GTGGCAGTTAGATTTGGTAGTGACTTGGTGTCACTTGA-AGAAGTAATAATGCCT-TG
**
357223 GTGGCAGTTAGATTTGGTAGTGACTTGGTGTCACTTGAAGAAAAAATAATGCCTTG
1 GTGGCAGTTAGATTTGGTAGTGACTTGGTGTCACTTGAAGAAGTAATAATGCCTTG
357279 GTG
1 GTG
357282 ACGACCAAAT
Statistics
Matches: 83, Mismatches: 26, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
54 5 0.06
55 34 0.41
56 39 0.47
57 5 0.06
ACGTcount: A:0.22, C:0.13, G:0.34, T:0.31
Consensus pattern (56 bp):
GTGGCAGTTAGATTTGGTAGTGACTTGGTGTCACTTGAAGAAGTAATAATGCCTTG
Found at i:357336 original size:111 final size:110
Alignment explanation
Indices: 357086--357337 Score: 308
Period size: 111 Copynumber: 2.3 Consensus size: 110
357076 TAACTCGATA
* *
357086 TCACTTAGTGTTGTGATGATGCCATAGTGGCAGTTAGATTTGGTAGCAACTTAGTGTCACTTGAA
1 TCACTTAGTGATGTG-TGATGCCATGGTGGCAGTTAGATTTGGTAGCAACTTAGTGTCACTTGAA
* ** * ** *
357151 GCAGTAATAATGCCTTGGTGGCAGCCAGGTCTGGGGTGACTTGGTG
65 GAAAAAATAATGCCTTGGTGACAGCCAAATCTGGGGTGACTTAGTG
* ** ** *
357197 TCACTGAGTGATGTGGTGATGCTGTGGTGGCAGTTAGATTTGGTAGTGACTTGGTGTCACTTGAA
1 TCACTTAGTGATGT-GTGATGCCATGGTGGCAGTTAGATTTGGTAGCAACTTAGTGTCACTTGAA
*
357262 GAAAAAATAATGCCTTGGTGAC-GACCAAATCTGTGGTGACTTAGTG
65 GAAAAAATAATGCCTTGGTGACAG-CCAAATCTGGGGTGACTTAGTG
*
357308 TCACTTAGTGGTGTAGTGATGCCATGGTGG
1 TCACTTAGTGATGT-GTGATGCCATGGTGG
357338 TGACCATCGA
Statistics
Matches: 118, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
110 1 0.01
111 116 0.98
112 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (110 bp):
TCACTTAGTGATGTGTGATGCCATGGTGGCAGTTAGATTTGGTAGCAACTTAGTGTCACTTGAAG
AAAAAATAATGCCTTGGTGACAGCCAAATCTGGGGTGACTTAGTG
Found at i:366990 original size:20 final size:20
Alignment explanation
Indices: 366952--366991 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
366942 CATATTTTTT
*
366952 ATTTTGTATCGATTTTATTC
1 ATTTTGTATCGATTATATTC
366972 ATTTT-TATCGTATTATATTC
1 ATTTTGTATCG-ATTATATTC
366992 GTATTGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (20 bp):
ATTTTGTATCGATTATATTC
Found at i:370750 original size:26 final size:26
Alignment explanation
Indices: 370717--370788 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 26
370707 ATAAATAATT
370717 AAAA-ATATAAAA-ATTAAAATAAACA
1 AAAATATATAAAATATTAAAATAAA-A
*
370742 AAAATATATTTATAAATTTTAAAATAAAA
1 AAAATATA--TA-AAATATTAAAATAAAA
370771 ATAAATATATAAAATATT
1 A-AAATATATAAAATATT
370789 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
25 4 0.10
26 3 0.08
27 6 0.15
28 4 0.10
29 5 0.13
30 17 0.44
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAATATATAAAATATTAAAATAAAA
Found at i:370757 original size:30 final size:30
Alignment explanation
Indices: 370722--370780 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
370712 TAATTAAAAA
370722 TATAAAAATTAAAATAAACAA-AAATATATT
1 TATAAAAATTAAAATAAA-AATAAATATATT
**
370752 TATAAATTTTAAAATAAAAATAAATATAT
1 TATAAAAATTAAAATAAAAATAAATATAT
370781 AAAATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (30 bp):
TATAAAAATTAAAATAAAAATAAATATATT
Found at i:379414 original size:20 final size:20
Alignment explanation
Indices: 379322--379415 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 20
379312 AAATTCTCTG
* ** *
379322 ATGTATTGATACAAAGATCA
1 ATGTATCGATACATTGATTA
*
379342 ATGTATCAATACATT-ATTA
1 ATGTATCGATACATTGATTA
*
379361 ATGTATTGATACATTGATTA
1 ATGTATCGATACATTGATTA
* *
379381 ATGTATTGATACATTGAATA
1 ATGTATCGATACATTGATTA
*
379401 ATATATCGATACATT
1 ATGTATCGATACATT
379416 TCCTTGGCAG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.25
20 47 0.75
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTGATTA
Found at i:379560 original size:21 final size:20
Alignment explanation
Indices: 379534--379572 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
379524 GTTGGGACCT
379534 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
379555 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
379573 CAAACATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Done.