Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1281
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: 186375
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:427 original size:16 final size:15
Alignment explanation
Indices: 407--440 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
397 CTAAAATAAA
*
407 ATTTTAAAATTCAAC
1 ATTTTTAAATTCAAC
*
422 ATTTTTAAATTCAAT
1 ATTTTTAAATTCAAC
437 ATTT
1 ATTT
441 ATAGTAATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTAAATTCAAC
Found at i:1211 original size:2 final size:2
Alignment explanation
Indices: 1204--1234 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1194 TACAAACCCA
1204 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1235 GATATCTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6221 original size:16 final size:16
Alignment explanation
Indices: 6194--6270 Score: 68
Period size: 16 Copynumber: 4.9 Consensus size: 16
6184 GATCGATTCA
6194 AAAC-CGAAATGACCC
1 AAACTCGAAATGACCC
* * *
6209 GAACTCAAAATGATCC
1 AAACTCGAAATGACCC
* *
6225 AAACCCGAAATAACCC
1 AAACTCGAAATGACCC
*
6241 AAAC-CTGAAATGATCC
1 AAACTC-GAAATGACCC
*
6257 GAACTCGAAATGAC
1 AAACTCGAAATGAC
6271 TAGAACAATT
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
15 4 0.09
16 42 0.89
17 1 0.02
ACGTcount: A:0.45, C:0.29, G:0.13, T:0.13
Consensus pattern (16 bp):
AAACTCGAAATGACCC
Found at i:6234 original size:32 final size:32
Alignment explanation
Indices: 6192--6270 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
6182 CCGATCGATT
* *
6192 CAAAACCGAAATGACCCGAA-CTCAAAATGATC
1 CAAACCCGAAATGACCCAAACCT-AAAATGATC
* *
6224 CAAACCCGAAATAACCCAAACCTGAAATGATC
1 CAAACCCGAAATGACCCAAACCTAAAATGATC
* *
6256 CGAACTCGAAATGAC
1 CAAACCCGAAATGAC
6271 TAGAACAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 37 0.95
33 2 0.05
ACGTcount: A:0.46, C:0.29, G:0.13, T:0.13
Consensus pattern (32 bp):
CAAACCCGAAATGACCCAAACCTAAAATGATC
Found at i:7472 original size:28 final size:29
Alignment explanation
Indices: 7406--7476 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 29
7396 TAAAATATTT
* *
7406 AATTATTTGATTAATAATTTTGAAAGGTA
1 AATTATTTAATTAATAATTTTGAAAAGTA
7435 AATTATTTAATTAATAATTTT-AAAAGTA
1 AATTATTTAATTAATAATTTTGAAAAGTA
7463 AATTATTTAATTAA
1 AATTATTTAATTAA
7477 AAAGTAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 20 0.50
29 20 0.50
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (29 bp):
AATTATTTAATTAATAATTTTGAAAAGTA
Found at i:7479 original size:20 final size:20
Alignment explanation
Indices: 7456--7495 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
7446 TAATAATTTT
* *
7456 AAAAGTAAATTATTTAATTA
1 AAAAGTAAACTAATTAATTA
7476 AAAAGTAAACTAATTAATTA
1 AAAAGTAAACTAATTAATTA
7496 TGTTTCAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (20 bp):
AAAAGTAAACTAATTAATTA
Found at i:8941 original size:2 final size:2
Alignment explanation
Indices: 8934--8958 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8924 CTGATGATCT
8934 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 T
8959 TTGATAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9257 original size:13 final size:12
Alignment explanation
Indices: 9232--9282 Score: 63
Period size: 13 Copynumber: 4.3 Consensus size: 12
9222 TTTTTTAAAC
9232 TTTTCAAAAATAA
1 TTTT-AAAAATAA
9245 TTTTAAAAGATAA
1 TTTTAAAA-ATAA
9258 TTTT-AAAAT--
1 TTTTAAAAATAA
9267 TTTTAAAAATAA
1 TTTTAAAAATAA
9279 TTTT
1 TTTT
9283 TTATATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.12
10 5 0.15
11 2 0.06
12 11 0.32
13 12 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (12 bp):
TTTTAAAAATAA
Found at i:9295 original size:21 final size:21
Alignment explanation
Indices: 9243--9282 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
9233 TTTCAAAAAT
9243 AATTTTAAAAGATAATTTTAA
1 AATTTTAAAAGATAATTTTAA
9264 AATTTTTAAAA-ATAATTTT
1 AA-TTTTAAAAGATAATTTT
9283 TTATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AATTTTAAAAGATAATTTTAA
Found at i:11560 original size:109 final size:105
Alignment explanation
Indices: 11375--11628 Score: 261
Period size: 109 Copynumber: 2.4 Consensus size: 105
11365 TTCTATCTAA
* **
11375 ATATAATCTTATTATTTTAAAATTTAAATT--A-ATAAATATTTTGAAATAAAGTTCACATGATA
1 ATATAATTTTATTATTTTAAAATTTAAATTAAATATAAATATTTAAAAATAAAGTTCACATGATA
* * *
11437 TTAATTTACTTTAAAGTTAATAAAAAATTTCTTATTTAAAT
66 TTAATCTACTTTAAAATTAAT-AAAAATTTCATATTTAAAT
* * *
11478 ATATAATTTTATTATTTTAAAATTTAAATCTAAATTTATAAATATTTAAAAATAGAGTTCATATT
1 ATATAATTTTATTATTTTAAAATTTAAAT-TAAA--TATAAATATTTAAAAATAAAGTTCACATG
* *
11543 ATATTAATCTA-TATTAAAATTAATAAAATTTTCATATTTTAAT
63 ATATTAATCTACT-TTAAAATTAATAAAAATTTCATATTTAAAT
* * *
11586 ATGTAAATTTATTAATTT---ATTTAAATTTAAACTAATAAATATT
1 ATATAATTTTATTATTTTAAAATTTAAA-TTAAA-T-ATAAATATT
11629 AGAATCCACA
Statistics
Matches: 127, Mismatches: 15, Indels: 16
0.80 0.09 0.10
Matches are distributed among these distances:
103 28 0.22
104 2 0.02
105 20 0.16
106 2 0.02
108 32 0.25
109 43 0.34
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (105 bp):
ATATAATTTTATTATTTTAAAATTTAAATTAAATATAAATATTTAAAAATAAAGTTCACATGATA
TTAATCTACTTTAAAATTAATAAAAATTTCATATTTAAAT
Found at i:13285 original size:12 final size:11
Alignment explanation
Indices: 13263--13338 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
13253 AGAGAAAGAA
*
13263 GAGAGAGGAGG
1 GAGATAGGAGG
13274 GATGATAGGAGG
1 GA-GATAGGAGG
*
13286 AGAGACAGGA--
1 -GAGATAGGAGG
*
13296 GAGATAGTA--
1 GAGATAGGAGG
13305 GAGATAGGAGG
1 GAGATAGGAGG
13316 GATGATAGGAGG
1 GA-GATAGGAGG
*
13328 AGAGACAGGAG
1 -GAGATAGGAG
13339 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:13314 original size:42 final size:42
Alignment explanation
Indices: 13253--13371 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
13243 TAGCCCTCAA
* *
13253 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
13295 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
13337 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
13372 GAGAGAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:13355 original size:18 final size:18
Alignment explanation
Indices: 13328--13377 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
13318 TGATAGGAGG
*
13328 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
13346 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
13364 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
13378 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:18928 original size:13 final size:13
Alignment explanation
Indices: 18910--18934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18900 AAGTTCCAGC
18910 AGAGAAAAAAAAG
1 AGAGAAAAAAAAG
18923 AGAGAAAAAAAA
1 AGAGAAAAAAAA
18935 CCTTGATACT
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AGAGAAAAAAAAG
Found at i:23103 original size:52 final size:51
Alignment explanation
Indices: 22888--23109 Score: 157
Period size: 51 Copynumber: 4.4 Consensus size: 51
22878 ATAAATTTTC
* * * * * *
22888 TTATAGGGTTTGACCT-T-TCTACTAGGTGCCAACTTATGTGGA-TTTATACT
1 TTATAGGGCTTGACCTCTCTATAC-AAGTGCCAACTAATATGGACTTT-GACT
* * * * * *
22938 CTATAAGGCTTGTCCTTTCTATACAAGTGCTAACTAATTTGGA-TTTAGACT
1 TTATAGGGCTTGACCTCTCTATACAAGTGCCAACTAATATGGACTTT-GACT
* * * * * *
22989 TTATAGGGCTTGACCTCCCTATACATGTGCTAGCTAATGTAGACTTTGA-T
1 TTATAGGGCTTGACCTCTCTATACAAGTGCCAACTAATATGGACTTTGACT
** * * *
23039 TCTATAAAGCTTGATCTCTCTATTATAAGTTCCAACTAATATGGACTTTGACT
1 T-TATAGGGCTTGACCTCTCTA-TACAAGTGCCAACTAATATGGACTTTGACT
23092 TTATAGGGCTTGACCTCT
1 TTATAGGGCTTGACCTCT
23110 TTGTGCCAGC
Statistics
Matches: 133, Mismatches: 33, Indels: 10
0.76 0.19 0.06
Matches are distributed among these distances:
50 14 0.11
51 75 0.56
52 42 0.32
53 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (51 bp):
TTATAGGGCTTGACCTCTCTATACAAGTGCCAACTAATATGGACTTTGACT
Found at i:23140 original size:97 final size:99
Alignment explanation
Indices: 22935--23140 Score: 233
Period size: 103 Copynumber: 2.1 Consensus size: 99
22925 GTGGATTTAT
* * * *
22935 ACTCTATAAGGCTTGTCCTTTCTATACAAGTGCTAACTAATTTGGATTTAGACTTTATAGGGCTT
1 ACTCTATAAAGCTTGTCCTCTCTATACAAGTGCCAACTAATATGGATTTAGACTTTATAGGGCTT
* *
23000 GACCTCCCTATACATGTGCTAGCTAATGTAGACTTTG
66 GACCT-CCTAT--ATGTGCCAGCTAATGTAGACTTCG
* * *
23037 ATTCTATAAAGCTTGAT-CTCTCTATTATAAGTTCCAACTAATATGGACTTT-GACTTTATAGGG
1 ACTCTATAAAGCTTG-TCCTCTCTA-TACAAGTGCCAACTAATATGGA-TTTAGACTTTATAGGG
*
23100 CTTGACCT-CT-T-TGTGCCAGCTAATGTGGACTTCG
63 CTTGACCTCCTATATGTGCCAGCTAATGTAGACTTCG
23134 ACTCTAT
1 ACTCTAT
23141 GTCATAACGT
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
97 26 0.29
100 1 0.01
101 2 0.02
102 19 0.21
103 39 0.43
104 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (99 bp):
ACTCTATAAAGCTTGTCCTCTCTATACAAGTGCCAACTAATATGGATTTAGACTTTATAGGGCTT
GACCTCCTATATGTGCCAGCTAATGTAGACTTCG
Found at i:26414 original size:166 final size:162
Alignment explanation
Indices: 26213--26590 Score: 361
Period size: 166 Copynumber: 2.3 Consensus size: 162
26203 ATTATCTTAT
* * * * * * *
26213 GAAAAAAATGCAAAACTCGTAGAATAAATTGAATTTTGTAAAACTGATTTAATGTAAATTTAAGG
1 GAAAAAAATGAAAAACTCAT-GAAAAAAATGAATTTTGTAAAACTGATTTAATATAAATTAAAGA
*
26278 ACAATATTAGATGAATTTTAAAAATTTTAAACCAAGAAAAA-TTATCGGAAAAACATTTATGAAA
65 ACAATATTAGATAAATTTTAAAAATTTTAAACCAAGAAAAACTT-TC-G-AAAACATTTATGAAA
* * *
26342 TAGAAAAC-TCATTTTTTGAGGAATAAGGGA-ATTTTAA
127 TAGAAAACTTCATATTTCGA--AAT-AGGGAGATTTCAA
* * * * *
26379 GGAAAAAATGAAAAACTCATGAAAACAAATGAATTTT-TCAAAACGGATTTACTATGAATTAAAT
1 GAAAAAAATGAAAAACTCATGAAAA-AAATGAATTTTGT-AAAACTGATTTAATATAAATTAAAG
* * ** * * *
26443 AATAATATTTGATAAATTTTAAAAATTTTAAACTGAGAAAAACCTTTCGAAAACATTTTTGTAGT
64 AACAATATTAGATAAATTTTAAAAATTTTAAACCAAGAAAAA-CTTTCGAAAACATTTATGAAAT
* *
26508 AGTAAACTTCGTATTTCGAAATAGGGAGATTTCAA
128 AGAAAACTTCATATTTCGAAATAGGGAGATTTCAA
* * *
26543 GAAAAAAATGAAAAAATCATGAAATAAAAAGGAATTTTGGAAAA-TGAT
1 GAAAAAAATGAAAAACTCATG-AA-AAAAATGAATTTTGTAAAACTGAT
26591 ACAATGGTAA
Statistics
Matches: 173, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
163 5 0.03
164 31 0.18
165 40 0.23
166 93 0.54
167 2 0.01
168 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (162 bp):
GAAAAAAATGAAAAACTCATGAAAAAAATGAATTTTGTAAAACTGATTTAATATAAATTAAAGAA
CAATATTAGATAAATTTTAAAAATTTTAAACCAAGAAAAACTTTCGAAAACATTTATGAAATAGA
AAACTTCATATTTCGAAATAGGGAGATTTCAA
Found at i:26605 original size:164 final size:164
Alignment explanation
Indices: 26280--26616 Score: 355
Period size: 164 Copynumber: 2.0 Consensus size: 164
26270 ATTTAAGGAC
* *
26280 AATATTAGATGAATTTTAAAAATTTTAAACCAAGAAAAATTATCGGAAAAACATTTATGAAATAG
1 AATATTTGATAAATTTTAAAAATTTTAAACCAAGAAAAATTATCGGAAAAACATTTATGAAATAG
* * * * * * *
26345 AAAACTCATTTTTTGAGGAATAAGGGAATTTTAAGGAAAAAATGAAAAACTCATGAAAACAAATG
66 AAAACTCATATTTCGA-GAATAAGGGAATTTCAAGAAAAAAATGAAAAAATCATGAAAAAAAAGG
* *
26410 AATTTTTCAAAACGGATTTACTATGAATTAAATAAT
130 AATTTTGCAAAACGGA-TTACAATGAATTAAATAAT
** * * *
26446 AATATTTGATAAATTTTAAAAATTTTAAACTGAGAAAAACCTT-TC-G-AAAACATTTTTGTAGT
1 AATATTTGATAAATTTTAAAAATTTTAAACCAAGAAAAA--TTATCGGAAAAACATTTATGAAAT
* *
26508 AGTAAACTTCGTATTTCGA-AAT-AGGGAGATTTCAAGAAAAAAATGAAAAAATCATGAAATAAA
64 AGAAAAC-TCATATTTCGAGAATAAGGGA-ATTTCAAGAAAAAAATGAAAAAATCATGAAA-AAA
* *
26571 AAGGAATTTTGGAAAA-TGA-TACAATGGTAATTAAATAAT
126 AAGGAATTTTGCAAAACGGATTACAAT-G-AATTAAATAAT
*
26610 GATATTT
1 AATATTT
26617 AAAGATTTTT
Statistics
Matches: 143, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
162 5 0.03
163 6 0.04
164 50 0.35
165 34 0.24
166 44 0.31
167 2 0.01
168 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (164 bp):
AATATTTGATAAATTTTAAAAATTTTAAACCAAGAAAAATTATCGGAAAAACATTTATGAAATAG
AAAACTCATATTTCGAGAATAAGGGAATTTCAAGAAAAAAATGAAAAAATCATGAAAAAAAAGGA
ATTTTGCAAAACGGATTACAATGAATTAAATAAT
Found at i:27419 original size:51 final size:51
Alignment explanation
Indices: 27330--27476 Score: 145
Period size: 51 Copynumber: 2.9 Consensus size: 51
27320 ATGTTTACAT
* * * * * *
27330 TCTATAGGGCTTAAACTCCTTATATAGGTGCCAGCTAATGTATACTTCGAC
1 TCTATAAGGCTTAACCTCCTTATACAGGAGCCAACTAATGTAGACTTCGAC
* * * * *
27381 TCTATAAGGCTTGACCTCCTTATACAGGAGCTAACTAATGTAGGCTTTGAT
1 TCTATAAGGCTTAACCTCCTTATACAGGAGCCAACTAATGTAGACTTCGAC
* * * *
27432 TCTATAAGGCTTAACCTCC--CTACAGGTGCCAATTAATGTGGACTT
1 TCTATAAGGCTTAACCTCCTTATACAGGAGCCAACTAATGTAGACTT
27477 TTAACTCTTA
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
49 20 0.26
51 58 0.74
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (51 bp):
TCTATAAGGCTTAACCTCCTTATACAGGAGCCAACTAATGTAGACTTCGAC
Found at i:28130 original size:69 final size:69
Alignment explanation
Indices: 27975--28131 Score: 188
Period size: 69 Copynumber: 2.3 Consensus size: 69
27965 AATATACTCG
* * * * ** *
27975 AGAGAGGCTTTAGAGGTTTTTGAAATATCCTCAAGAGAGACTTTGAAAGTTTTTAATGGAGCATC
1 AGAGAGGCTTTAGAAGTTTATGAAATATCCTCAAGAAAGACTTTGAAAGTATTTAATACAACATC
28040 CTTA
66 CTTA
* ** * * *
28044 AAAGAGGCCATGGAAGTTTATGAAATATCCTCAAGAAAGGCTTTTAAAGTATTTAATACAACATC
1 AGAGAGGCTTTAGAAGTTTATGAAATATCCTCAAGAAAGACTTTGAAAGTATTTAATACAACATC
28109 CTTA
66 CTTA
*
28113 AGAGAGGCTTTAAAAGTTT
1 AGAGAGGCTTTAGAAGTTT
28132 TTGATGAAAT
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (69 bp):
AGAGAGGCTTTAGAAGTTTATGAAATATCCTCAAGAAAGACTTTGAAAGTATTTAATACAACATC
CTTA
Found at i:28196 original size:36 final size:36
Alignment explanation
Indices: 28112--28202 Score: 155
Period size: 36 Copynumber: 2.5 Consensus size: 36
28102 CAACATCCTT
* *
28112 AAGAGAGGCTTTAAAAGTTTTTGATGAAATGTTTTC
1 AAGAGAGGCTTTGAAAGTTTTTGATGAAATGTCTTC
28148 AAGAGAGGCTTTGAAAGTTTTTGATGAAATGTCTTC
1 AAGAGAGGCTTTGAAAGTTTTTGATGAAATGTCTTC
*
28184 AAGAGAGGCTTTGGAAGTT
1 AAGAGAGGCTTTGAAAGTT
28203 ACTTTTTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35
Consensus pattern (36 bp):
AAGAGAGGCTTTGAAAGTTTTTGATGAAATGTCTTC
Found at i:28220 original size:40 final size:36
Alignment explanation
Indices: 28112--28222 Score: 141
Period size: 36 Copynumber: 3.0 Consensus size: 36
28102 CAACATCCTT
* * *
28112 AAGAGAGGCTTTAAAAGTTTTTGATGAAATGTTTTC
1 AAGAGAGGCTTTGAAACTTTTTGATGAAATGTCTTC
*
28148 AAGAGAGGCTTTGAAAGTTTTTGATGAAATGTCTTC
1 AAGAGAGGCTTTGAAACTTTTTGATGAAATGTCTTC
*
28184 AAGAGAGGCTTTGGAAGTTACTTTTTTATGAAATGTCTT
1 AAGAGAGGCTTT-GAA---ACTTTTTGATGAAATGTCTT
28223 TGAGAAAGCC
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
36 46 0.69
37 3 0.04
40 18 0.27
ACGTcount: A:0.31, C:0.07, G:0.23, T:0.39
Consensus pattern (36 bp):
AAGAGAGGCTTTGAAACTTTTTGATGAAATGTCTTC
Found at i:29329 original size:21 final size:21
Alignment explanation
Indices: 29305--29348 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29295 TTTATGATTA
29305 TTAATTTTACTTTTAATTT-TT
1 TTAATTTTA-TTTTAATTTATT
*
29326 TTAATTTTATTTTAGTTTATT
1 TTAATTTTATTTTAATTTATT
29347 TT
1 TT
29349 TAAACTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTAATTTTATTTTAATTTATT
Found at i:29551 original size:21 final size:19
Alignment explanation
Indices: 29518--29565 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
29508 TAATTATAAA
*
29518 AAATAATAA-TAAAAATAATG
1 AAATAA-AATTAAAAA-AATC
29538 AATATAAAATTAAAAAAATC
1 AA-ATAAAATTAAAAAAATC
29558 AAATAAAA
1 AAATAAAA
29566 AAGGATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.24
20 9 0.36
21 10 0.40
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
AAATAAAATTAAAAAAATC
Found at i:31254 original size:17 final size:18
Alignment explanation
Indices: 31225--31258 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
31215 TTAGGGTAAT
31225 ATTTTTAGTAAAATTAAA
1 ATTTTTAGTAAAATTAAA
31243 ATTTTTAG-AAAATTAA
1 ATTTTTAGTAAAATTAA
31259 GGTAATGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTTTAGTAAAATTAAA
Found at i:33237 original size:13 final size:13
Alignment explanation
Indices: 33221--33250 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
33211 ATACATTGTT
33221 CATTGTATCGATA
1 CATTGTATCGATA
33234 CATTGTATCGATA
1 CATTGTATCGATA
33247 CATT
1 CATT
33251 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:33296 original size:20 final size:19
Alignment explanation
Indices: 33273--33339 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 19
33263 AGATGTATTA
33273 ATACATTTTGCATTGTATCG
1 ATACATTTT-CATTGTATCG
*
33293 ATACATTGCTCATTGTATCG
1 ATACATT-TTCATTGTATCG
*
33313 ATACATTTTACAATGTATCG
1 ATACATTTT-CATTGTATCG
33333 ATACATT
1 ATACATT
33340 CAGGCATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (19 bp):
ATACATTTTCATTGTATCG
Found at i:35760 original size:50 final size:49
Alignment explanation
Indices: 35627--35761 Score: 146
Period size: 51 Copynumber: 2.7 Consensus size: 49
35617 TTTCATCTCG
* * * * * *
35627 GGGATACTCCAATCCCGGTTTCATTTTGAAAACATCAATTTTTCTTAATCG
1 GGGATACTCCAAT-CCGATTT-ATTTTCAAAACAACAATTTTCCATAATCA
*
35678 GGGATACTCCAACTCCGATTT-TATTTCTAAAACAACCATTTTCCATAATCA
1 GGGATACTCCAA-TCCGATTTAT-TTTC-AAAACAACAATTTTCCATAATCA
35729 GGGATACTCCAAGTCCGATTTATTTTCAAAACA
1 GGGATACTCCAA-TCCGATTTATTTTCAAAACA
35762 CTGGCTTTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
49 1 0.01
50 9 0.12
51 60 0.83
52 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (49 bp):
GGGATACTCCAATCCGATTTATTTTCAAAACAACAATTTTCCATAATCA
Found at i:35960 original size:79 final size:79
Alignment explanation
Indices: 35781--36107 Score: 398
Period size: 79 Copynumber: 4.2 Consensus size: 79
35771 TACAATTAGA
* * * * *
35781 GATACTCCAACCCCGTTATTTCCAAGGGGACACTCCAACCCC-AGTTTCATTTCTAAAACATCAA
1 GATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGA-TTTTATTTCTAAAACATCAA
35845 TTTTT--T-ATCGGG
65 TTTTTCATAATCGGG
* * * *
35857 GATATTCCAACCCCATTATTTTCGAGGGGATAC-CCTAACCCC-AGCTTTATTTCTAAAATATTA
1 GATACTCCAACCCCATTATTTTCGAGGGGATACTCC-AACCCCGA-TTTTATTTCTAAAACATCA
*
35920 ATTTCTCATAATCGGG
64 ATTTTTCATAATCGGG
*
35936 GATACTCCAATCCCATTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAAT
1 GATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAAT
*
36001 TTTTCATAGTCGGG
66 TTTTCATAATCGGG
** * * * **
36015 GATACTCCAACCCTGTTATTTTCGA-GGGATACTCTAATCCCGATTTTATTTCTAAATCATTGAT
1 GATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAAT
*
36079 TTTTCACAATCGGG
66 TTTTCATAATCGGG
36093 GATACTCCAACCCCA
1 GATACTCCAACCCCA
36108 ATTTTATTTC
Statistics
Matches: 216, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
75 2 0.01
76 56 0.26
78 60 0.28
79 95 0.44
80 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (79 bp):
GATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAAT
TTTTCATAATCGGG
Found at i:41234 original size:20 final size:20
Alignment explanation
Indices: 41197--41270 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
41187 TTCTATAATT
* *
41197 TGTATCAATACAATAAGTTAA
1 TGTATCGATAC-ATAAGTGAA
*
41218 TGTATCGATGCATAAGTGAA
1 TGTATCGATACATAAGTGAA
*
41238 TATATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
*
41258 TGTATTGATACAT
1 TGTATCGATACAT
41271 GCTTGTAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 37 0.80
21 9 0.20
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:44074 original size:78 final size:78
Alignment explanation
Indices: 43781--44070 Score: 295
Period size: 76 Copynumber: 3.7 Consensus size: 78
43771 TCAAAAGCGG
* * * * * * * *
43781 TACTCCAACCCTGTTTTTACTTCTAAAAACACTGAAATTTTCATATCTGGGGATACTCCAACCCT
1 TACTCTAACCCCGTTTTTACTTC-CAAAACAC--AATTTTTCATCTCTAGGGATACTCAAACCCC
* *
43846 ACTATCTTAGAGGGGA
63 ACCATCTTCGAGGGGA
*
43862 TACT-TCAACCCCGTTTTTACTTCCAAAAC-CAA-ATTTCATCTCTAGGGATACTCAAACCCCAC
1 TACTCT-AACCCCGTTTTTACTTCCAAAACACAATTTTTCATCTCTAGGGATACTCAAACCCCAC
43924 CATCTTCGAGGGGA
65 CATCTTCGAGGGGA
* * * * * *
43938 TATTCTAACCCCGTTTTCACTTTCAAAACACCAAATTTTTCATCTTTATGGATATTCAAACCCCA
1 TACTCTAACCCCGTTTTTACTTCCAAAACA-C-AATTTTTCATCTCTAGGGATACTCAAACCCCA
44003 CCATC-TCGAGGGGA
64 CCATCTTCGAGGGGA
* *
44017 TACTCTAA-CTCGTTTTTACTTCCAAAACATCACATTTTTCATCT-TGGGGATACT
1 TACTCTAACCCCGTTTTTACTTCCAAAACA-CA-ATTTTTCATCTCTAGGGATACT
44071 TCAACCTTAG
Statistics
Matches: 177, Mismatches: 25, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
76 61 0.34
77 11 0.06
78 31 0.18
79 19 0.11
80 35 0.20
81 20 0.11
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (78 bp):
TACTCTAACCCCGTTTTTACTTCCAAAACACAATTTTTCATCTCTAGGGATACTCAAACCCCACC
ATCTTCGAGGGGA
Found at i:44695 original size:20 final size:20
Alignment explanation
Indices: 44670--44776 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
44660 TTTACCCAGA
*
44670 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
*
44690 TGTATCGATAAATTGCTCAT
1 TGTATCGATACATTGCTCAT
44710 TGTATCGAT--A-----CAT
1 TGTATCGATACATTGCTCAT
44723 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
* *
44743 TGTATCGATACATTG-TAAAA
1 TGTATCGATACATTGCT-CAT
44763 TGTATCGATACATT
1 TGTATCGATACATT
44777 CAGATATTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
13 12 0.16
15 1 0.01
18 1 0.01
19 1 0.01
20 58 0.78
21 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:44723 original size:13 final size:13
Alignment explanation
Indices: 44707--44759 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
44697 ATAAATTGCT
44707 CATTGTATCGATA
1 CATTGTATCGATA
44720 CATTGTATCGATA
1 CATTGTATCGATA
44733 CATTG---C--T-
1 CATTGTATCGATA
44740 CATTGTATCGATA
1 CATTGTATCGATA
44753 CATTGTA
1 CATTGTA
44760 AAATGTATCG
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 5 0.15
8 1 0.03
10 2 0.06
12 1 0.03
13 25 0.74
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:44729 original size:33 final size:33
Alignment explanation
Indices: 44687--44759 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
44677 ATACATTTTG
44687 CATTGTATCGATAAATTGCTCATTGTATCGATA
1 CATTGTATCGATAAATTGCTCATTGTATCGATA
*
44720 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATAAATTGCTCATTGTATCGATA
44753 CATTGTA
1 CATTGTA
44760 AAATGTATCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (33 bp):
CATTGTATCGATAAATTGCTCATTGTATCGATA
Found at i:44735 original size:53 final size:53
Alignment explanation
Indices: 44670--44776 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 53
44660 TTTACCCAGA
* * *
44670 TGTATCGATACATT-TTGCATTGTATCGATAAATTGCT-CATTGTATCGATACAT
1 TGTATCGATACATTGCT-CATTGTATCGATAAATTG-TAAAATGTATCGATACAT
*
44723 TGTATCGATACATTGCTCATTGTATCGATACATTGTAAAATGTATCGATACAT
1 TGTATCGATACATTGCTCATTGTATCGATAAATTGTAAAATGTATCGATACAT
44776 T
1 T
44777 CAGATATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
52 1 0.02
53 46 0.96
54 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (53 bp):
TGTATCGATACATTGCTCATTGTATCGATAAATTGTAAAATGTATCGATACAT
Found at i:47157 original size:51 final size:52
Alignment explanation
Indices: 47079--47198 Score: 120
Period size: 51 Copynumber: 2.4 Consensus size: 52
47069 TTTTCATCTT
* ** **
47079 GGGGATACTCCAA-TCCCGGTTCCATTTCCAAAACATCAATTTTTCTTAATC
1 GGGGATACTCCAACTCCCGATTCCATTTCCAAAACATCAATTTACCGCAATC
** * * * *
47130 GGGGATACTCCAACT-CCGATTTTATTTCTAAAGCATCGATTTACCGCAATT
1 GGGGATACTCCAACTCCCGATTCCATTTCCAAAACATCAATTTACCGCAATC
47181 GGGGATACTCCAAC-CCCG
1 GGGGATACTCCAACTCCCG
47199 TTATTTCATC
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (52 bp):
GGGGATACTCCAACTCCCGATTCCATTTCCAAAACATCAATTTACCGCAATC
Found at i:47299 original size:107 final size:107
Alignment explanation
Indices: 47176--47408 Score: 279
Period size: 107 Copynumber: 2.2 Consensus size: 107
47166 CGATTTACCG
* * * *
47176 CAATTGGGGATACTCCAACCCCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTTTGAAGGG
1 CAATCGGGGATACTCCAACCCCGTTATGTCATCGAGGATACTCCAACCCCGTTATTTTCGAAGGG
** ***
47241 ATACT-ATAACCCCGGCTTTATATCTAAAATATTGATTTTTCA
66 ATACTCA-AACCCCAACTTTATATCTAAAATACCAATTTTTCA
* * * ** *
47283 TAATCGGGGGTACTCCAACCCCGTTATGTCATCGAGGATACTCCAATCTTGTTATTTTCGAGGGG
1 CAATCGGGGATACTCCAACCCCGTTATGTCATCGAGGATACTCCAACCCCGTTATTTTCGAAGGG
* * * *
47348 ATGCTCAAACCCCAATTTTATTTTTAAAATACCAATTTTTCA
66 ATACTCAAACCCCAACTTTATATCTAAAATACCAATTTTTCA
47390 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
47409 TCCGATTTTA
Statistics
Matches: 104, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
107 103 0.99
108 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (107 bp):
CAATCGGGGATACTCCAACCCCGTTATGTCATCGAGGATACTCCAACCCCGTTATTTTCGAAGGG
ATACTCAAACCCCAACTTTATATCTAAAATACCAATTTTTCA
Found at i:47456 original size:51 final size:51
Alignment explanation
Indices: 47346--47509 Score: 177
Period size: 51 Copynumber: 3.2 Consensus size: 51
47336 ATTTTCGAGG
* * * * * *
47346 GGATGCTCAAACCCCAATTTTATTTTTAAAATACCAATTTTTCACAATCGG
1 GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGA
* *
47397 GGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGA
* ** * * * *
47448 GGATACTCCTACCCCGACCTTA-TTTCTAAAGCATCGATTTTTCACCATCGA
1 GGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTTCACAATCGA
47499 GGATACTCCAA
1 GGATACTCCAA
47510 TCCTATTATT
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
50 4 0.04
51 90 0.96
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGA
Found at i:59939 original size:7 final size:7
Alignment explanation
Indices: 59927--59964 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
59917 CCACTATTAA
59927 AAAAAAC
1 AAAAAAC
59934 AAAAAAC
1 AAAAAAC
59941 AAAAAAC
1 AAAAAAC
59948 AACAAAA-
1 AA-AAAAC
59955 AAAAAAC
1 AAAAAAC
59962 AAA
1 AAA
59965 GAAAAAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 4 0.14
7 21 0.72
8 4 0.14
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:59946 original size:14 final size:13
Alignment explanation
Indices: 59925--59971 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 13
59915 TCCCACTATT
59925 AAAAAAAACAAAA
1 AAAAAAAACAAAA
59938 AACAAAAAACAACAA
1 AA-AAAAAACAA-AA
59953 AAAAAAAACAAAGA
1 AAAAAAAACAAA-A
59967 AAAAA
1 AAAAA
59972 GAGAGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.10
14 24 0.77
15 4 0.13
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:59951 original size:17 final size:15
Alignment explanation
Indices: 59925--59971 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
59915 TCCCACTATT
59925 AAAAAAAACAAAAAA
1 AAAAAAAACAAAAAA
59940 CAAAAAACAACAAAAAA
1 -AAAAAA-AACAAAAAA
* *
59957 AAAACAAAGAAAAAA
1 AAAAAAAACAAAAAA
59972 GAGAGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 8 0.29
16 11 0.39
17 9 0.32
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (15 bp):
AAAAAAAACAAAAAA
Found at i:59955 original size:11 final size:11
Alignment explanation
Indices: 59925--59971 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
59915 TCCCACTATT
*
59925 AAAAA-AAACA
1 AAAAACAAAAA
59935 AAAAAC-AAAA
1 AAAAACAAAAA
*
59945 AACAACAAAAA
1 AAAAACAAAAA
59956 AAAAACAAAGAA
1 AAAAACAAA-AA
59968 AAAA
1 AAAA
59972 GAGAGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 13 0.42
11 12 0.39
12 6 0.19
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:61126 original size:55 final size:55
Alignment explanation
Indices: 61062--61482 Score: 409
Period size: 55 Copynumber: 7.3 Consensus size: 55
61052 TTCACCCTTT
* *
61062 AGTCCTCAAAGAGCAGGACGCCTATCAAAGACCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
61117 AGTCCTCAAAGAGTAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* **
61172 AGTCCTCAAAGAGCAGGATGCTTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTCTC
1 AGTCCTCAAAGAGCAGGA------CGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC-C
* *
61233 AGTCCTCAAAGAGCAGGACGCCTATCAAAGCCCATACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
61288 AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * * * *
61343 AGTCCTTAAAGAGCAAGATGCTTTCGCCTCTT-AAAGCCTATAAAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGC-AG--G---ACGCCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * * *
61404 AGTCCTCAAAGAGTAGGATGCCTTTTTGTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACGCC------TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
*
61465 AGTCCTCAAAGAGTAGGA
1 AGTCCTCAAAGAGCAGGA
61483 TGTCTTTTCC
Statistics
Matches: 305, Mismatches: 38, Indels: 40
0.80 0.10 0.10
Matches are distributed among these distances:
55 163 0.53
56 4 0.01
58 2 0.01
60 6 0.02
61 125 0.41
62 5 0.02
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:61261 original size:116 final size:114
Alignment explanation
Indices: 61086--61482 Score: 439
Period size: 116 Copynumber: 3.4 Consensus size: 114
61076 AGGACGCCTA
* * * *
61086 TCAAAGACCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGATGCCTTTCAAAGCCCA
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTATCAAAGCCCA
*
61151 CACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCTTTCTCCTT
66 TACAAGTTGGTGGCATTTTC-AGTCCTCAAAGAGCAGGATGCTTT-TCCTT
**
61202 TCAAAGCCCACACAAGTTGGTGGCA-CCTCTCAGTCCTCAAAGAGCAGGACGCCTATCAAAGCCC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTC-CAGTCCTCAAAGAGCAGGACGCCTATCAAAGCCC
61266 ATACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG-----CCTT
65 ATACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGATGCTTTTCCTT
* * * * *
61312 TCAAAGCCCACACAAGTTGGTGGTATTTTCCAGTCCTTAAAGAGCAAGATGCTTTCGCCTCTTAA
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC-AG--G---ACGCCTATCAA
* * * * **
61377 AGCCTATAAAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGATGCCTTTTTGTT
60 AGCCCATACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGATG-CTTTTCCTT
* * *
61434 TCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGTAGGA
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
61483 TGTCTTTTCC
Statistics
Matches: 238, Mismatches: 26, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
110 42 0.18
111 4 0.02
113 1 0.00
115 2 0.01
116 141 0.59
117 4 0.02
119 1 0.00
121 2 0.01
122 37 0.16
123 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (114 bp):
TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTATCAAAGCCCA
TACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGATGCTTTTCCTT
Found at i:61356 original size:171 final size:171
Alignment explanation
Indices: 61062--61489 Score: 608
Period size: 171 Copynumber: 2.5 Consensus size: 171
61052 TTCACCCTTT
*
61062 AGTCCTCAAAGAGCAGGACGCCTATCAAAGACCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTATCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
* *
61127 GAGTAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATG
66 GAGTAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGATG
* *
61192 CTTTCTCCT-TTCAAAGCCCACACAAGTTGGTGGCACCTCTC
131 CTTTCGCCTCTT-AAAGCCCACAAAAGTTGGTGGCACCTCTC
*
61233 AGTCCTCAAAGAGCAGGACGCCTATCAAAGCCCATACAAGTTGGTGGCATTTTCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTATCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
* * *
61298 GAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTCCAGTCCTTAAAGAGCAAGATG
66 GAGTAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGATG
* * *
61363 CTTTCGCCTCTTAAAGCCTATAAAAGTTGGTGGCACCTTTC
131 CTTTCGCCTCTTAAAGCCCACAAAAGTTGGTGGCACCTCTC
* * * * *
61404 AGTCCTCAAAGAGTAGGATGCCTTTTTGTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGT
1 AGTCCTCAAAGAGCAGGACGCC------TATCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGT
*
61468 CCTCAAAGAGTAGGATGTCTTT
59 CCTCAAAGAGTAGGATGCCTTT
61490 TCCTTTTTTC
Statistics
Matches: 229, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
171 176 0.77
172 2 0.01
177 47 0.21
178 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (171 bp):
AGTCCTCAAAGAGCAGGACGCCTATCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
GAGTAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGATG
CTTTCGCCTCTTAAAGCCCACAAAAGTTGGTGGCACCTCTC
Found at i:61559 original size:45 final size:41
Alignment explanation
Indices: 61496--61615 Score: 105
Period size: 45 Copynumber: 2.8 Consensus size: 41
61486 CTTTTCCTTT
* *
61496 TTTCCTTTGTCCTTAAAGAGCAAGATACATTTCATTCCCTTC
1 TTTCTTTTGTCCTCAAAGAGCAAGATACATTTCATTCCC-TC
* * * ** *
61538 TTTTCCCTTTTGTCCTCAAAGAGTAGGACACACTTTGTTTTCCTC
1 -TTT--CTTTTGTCCTCAAAGAGCAAGATACA-TTTCATTCCCTC
* *
61583 TTTCTTTTGTCCTCAAAGAGGAAGATGCATTTC
1 TTTCTTTTGTCCTCAAAGAGCAAGATACATTTC
61616 GTTTTCCTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
41 3 0.05
42 22 0.36
43 3 0.05
44 3 0.05
45 23 0.38
46 7 0.11
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (41 bp):
TTTCTTTTGTCCTCAAAGAGCAAGATACATTTCATTCCCTC
Found at i:61620 original size:42 final size:43
Alignment explanation
Indices: 61487--61642 Score: 120
Period size: 42 Copynumber: 3.6 Consensus size: 43
61477 GTAGGATGTC
* * * * * *
61487 TTTTCCTTTTTTCCTTTGTCCTTAAAGAGCAAGATACA-TTTC
1 TTTTCCTTCTTTCTTTTGTCCTCAAAGAGGAAGACACACTTTG
* * * *
61529 ATTCCCTTCTTTTCCCTTTTGTCCTCAAAGAGTAGGACACACTTTG
1 TTTTCCTTC-TTT--CTTTTGTCCTCAAAGAGGAAGACACACTTTG
**
61575 TTTTCC-TCTTTCTTTTGTCCTCAAAGAGGAAGATGCA-TTTCG
1 TTTTCCTTCTTTCTTTTGTCCTCAAAGAGGAAGACACACTTT-G
* * *
61617 TTTTCCTTTTTTCCTTTATCCTCAAA
1 TTTTCCTTCTTTCTTTTGTCCTCAAA
61643 AAATAGGACG
Statistics
Matches: 90, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
41 3 0.03
42 35 0.39
43 19 0.21
44 3 0.03
45 23 0.26
46 7 0.08
ACGTcount: A:0.19, C:0.24, G:0.11, T:0.46
Consensus pattern (43 bp):
TTTTCCTTCTTTCTTTTGTCCTCAAAGAGGAAGACACACTTTG
Found at i:61629 original size:87 final size:86
Alignment explanation
Indices: 61487--61651 Score: 199
Period size: 87 Copynumber: 1.9 Consensus size: 86
61477 GTAGGATGTC
* * *
61487 TTTTCCTTTTTTCCTTTGTCCTTAAAGAGCAAGATACATTTCATTCCCTTCTTTTCCCTTTTGTC
1 TTTTCCTTCTTTCCTTTGTCCTCAAAGAGCAAGATACATTTCATTCCCTTCTTTT-CC-TTTATC
* *
61552 CTCAAAGAGTAGGACACACTTTG
64 CTCAAAAAATAGGACACACTTTG
* * * * *
61575 TTTTCC-TCTTTCTTTTGTCCTCAAAGAGGAAGATGCATTTCGTTTTCCTT-TTTTCCTTTATCC
1 TTTTCCTTCTTTCCTTTGTCCTCAAAGAGCAAGATACATTTC-ATTCCCTTCTTTTCCTTTATCC
61638 TCAAAAAATAGGAC
65 TCAAAAAATAGGAC
61652 GTACTCTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
85 18 0.27
86 2 0.03
87 34 0.52
88 12 0.18
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.44
Consensus pattern (86 bp):
TTTTCCTTCTTTCCTTTGTCCTCAAAGAGCAAGATACATTTCATTCCCTTCTTTTCCTTTATCCT
CAAAAAATAGGACACACTTTG
Found at i:61742 original size:41 final size:40
Alignment explanation
Indices: 61655--61756 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
61645 ATAGGACGTA
** *
61655 CTCTTTTTCACTTTGTCCTCAAGAAGCAGGGCACTTTCCTT
1 CTCTTTTTC-CTTTGTCCTCAAGAAGCAGACCACTTTCATT
* *
61696 TTCTTTTTCCTTTGTCCTCAAGGAGCAAGACCTA-TTTCATT
1 CTCTTTTTCCTTTGTCCTCAAGAAGC-AGACC-ACTTTCATT
*
61737 CTC-TTTTCCTTTATCCTCAA
1 CTCTTTTTCCTTTGTCCTCAA
61757 AAAGTGGGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
40 32 0.62
41 19 0.37
42 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.11, T:0.43
Consensus pattern (40 bp):
CTCTTTTTCCTTTGTCCTCAAGAAGCAGACCACTTTCATT
Found at i:62428 original size:20 final size:19
Alignment explanation
Indices: 62403--62510 Score: 111
Period size: 20 Copynumber: 5.8 Consensus size: 19
62393 TTTACCCAGA
*
62403 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTCT-CAT
62423 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-CTCAT
62443 TGTATCGAT--A---T-AT
1 TGTATCGATACATTCTCAT
62456 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-CTCAT
* *
62476 TGTATCGATACATTTTACAA
1 TGTATCGATACATTCT-CAT
62496 TGTATCGATACATTC
1 TGTATCGATACATTC
62511 AGGCATTTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
13 11 0.15
14 1 0.01
15 1 0.01
18 1 0.01
19 2 0.03
20 58 0.77
21 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTCTCAT
Found at i:62463 original size:33 final size:33
Alignment explanation
Indices: 62421--62485 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
62411 TACATTTTGC
62421 ATTGTATCGATACATTGCTCATTGTATCGATAT
1 ATTGTATCGATACATTGCTCATTGTATCGATAT
62454 ATTGTATCGATACATTGCTCATTGTATCGATA
1 ATTGTATCGATACATTGCTCATTGTATCGATA
62486 CATTTTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (33 bp):
ATTGTATCGATACATTGCTCATTGTATCGATAT
Found at i:62489 original size:13 final size:13
Alignment explanation
Indices: 62440--62470 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
62430 ATACATTGCT
62440 CATTGTATCGATA
1 CATTGTATCGATA
*
62453 TATTGTATCGATA
1 CATTGTATCGATA
62466 CATTG
1 CATTG
62471 CTCATTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:62500 original size:53 final size:53
Alignment explanation
Indices: 62403--62505 Score: 147
Period size: 53 Copynumber: 1.9 Consensus size: 53
62393 TTTACCCAGA
* *
62403 TGTATCGATACATTTTGCATTGTATCGATACATTGCTCATTGTATCGATATAT
1 TGTATCGATACATTCTGCATTGTATCGATACATTGCTCAATGTATCGATATAT
*
62456 TGTATCGATACATTGCT-CATTGTATCGATACATT-TTACAATGTATCGATA
1 TGTATCGATACATT-CTGCATTGTATCGATACATTGCT-CAATGTATCGATA
62506 CATTCAGGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
52 1 0.02
53 43 0.96
54 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.42
Consensus pattern (53 bp):
TGTATCGATACATTCTGCATTGTATCGATACATTGCTCAATGTATCGATATAT
Found at i:64842 original size:51 final size:51
Alignment explanation
Indices: 64787--64930 Score: 171
Period size: 51 Copynumber: 2.8 Consensus size: 51
64777 TCCCAGTTCC
*
64787 ATTTCTAAAACATCAATTTTTCTTAATCGGGGATACTCCAACTCCGATTTT
1 ATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGATTTT
* * ** ** *
64838 ATTTCTAAAGCATCGATTTACCGCAATCGGGGATATTCCAACTCCGATTTT
1 ATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGATTTT
* * * * *
64889 ATTTCAAAAACACCAATTATTCATAATTGGGGATACTACAAC
1 ATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
64931 CCCGTTATTT
Statistics
Matches: 74, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (51 bp):
ATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGATTTT
Found at i:65140 original size:107 final size:106
Alignment explanation
Indices: 64867--65142 Score: 263
Period size: 107 Copynumber: 2.6 Consensus size: 106
64857 ACCGCAATCG
* * * * * *
64867 GGGATATTCCAACTCCGATTTTATT-TCAAAAACACCAATTATTCATAATTGGGGATACTACAAC
1 GGGATACTCTAACCCCGATTTTATTCT-TAAAATACCAATTTTTCATAATTGGGGATACT-CAAC
* * * *
64931 CCCGTTATTTCATCGGGGATACTCCGACCCTGTTATTTCCAAA
64 CCCGTTATGTCATCGAGGATACTCCAACCCTATTATTTCCAAA
** *** *
64974 GGGATACTCTAACCCCGGCTTTATATC-TAAAATATTGATTTTTCATAATTGGGGGTACTCTAAC
1 GGGATACTCTAACCCCGATTTTAT-TCTTAAAATACCAATTTTTCATAATTGGGGATACTC-AAC
* * * *
65038 CCCGTTATGTCATCGAGGATACTCCAA-TCTCATTATTTTCGAG
64 CCCGTTATGTCATCGAGGATACTCCAACCCT-ATTATTTCCAAA
* * *
65081 GGGATACT-TAAATCCCGATTTTATTCTTAAAATACCAATTTTTCACAATCGGGGATACTCAA
1 GGGATACTCT-AACCCCGATTTTATTCTTAAAATACCAATTTTTCATAATTGGGGATACTCAA
65143 ACTTCGATTT
Statistics
Matches: 134, Mismatches: 29, Indels: 13
0.76 0.16 0.07
Matches are distributed among these distances:
106 8 0.06
107 125 0.93
108 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (106 bp):
GGGATACTCTAACCCCGATTTTATTCTTAAAATACCAATTTTTCATAATTGGGGATACTCAACCC
CGTTATGTCATCGAGGATACTCCAACCCTATTATTTCCAAA
Found at i:66343 original size:22 final size:23
Alignment explanation
Indices: 66309--66360 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
66299 CGATAATCCC
*
66309 TTATTTTTATGT-ATTTTGTGCA
1 TTATTTTTATGTAAATTTGTGCA
*
66331 TTTATTTTT-TGTAAATTTGTTCA
1 -TTATTTTTATGTAAATTTGTGCA
66354 TTATTTT
1 TTATTTT
66361 ATTTCATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.19, C:0.04, G:0.10, T:0.67
Consensus pattern (23 bp):
TTATTTTTATGTAAATTTGTGCA
Found at i:68681 original size:167 final size:165
Alignment explanation
Indices: 68479--68875 Score: 473
Period size: 167 Copynumber: 2.4 Consensus size: 165
68469 TTTTCAAATT
* **
68479 ATGGAGTTTTTTACTCCGT-AATTTTTTTCGGGAGGATGTTTCTTGGTTTTTAATTTTTAAAATT
1 ATGGAGTTTTCTACTCTATAAATTTTTTT-GGGAGGAT-TTTCTTGGTTTTTAATTTTTAAAATT
* * **
68543 CATCAAATATCATTATTTATAT-CACATTAAATTAGTTTTCAAAAATTTCTTCATTTTCTTGAGT
64 CATCAAATATCATTATTCAT-TCCACATTAAATTAGTTTTCAAAAAGTAATTCATTTTCTTGAG-
*
68607 TTTTGGATTTTTTCCTTT-AAATTCCTC-TATTT-CCAAAAA
127 TTTTGGATTTTTT-CTTTGAAA-TCCCCAT-TTTCCCAAAAA
*
68646 ATGGAGTTTTCTACTCTATAAATTTTTTTGGGAGGATTTTTCTTAGTTTTTAATTTTTAAAAATT
1 ATGGAGTTTTCTACTCTATAAATTTTTTTGGGAGGA-TTTTCTTGGTTTTTAATTTTT-AAAATT
* * *
68711 CATCAAATATGATTATTCATTCCATATTAAATTTGTTTTCAAAAAGTAATTCATTTTCTTGAGTT
64 CATCAAATATCATTATTCATTCCACATTAAATTAGTTTTCAAAAAGTAATTCATTTTCTTGAGTT
*
68776 TTGGATTTTTTTTTTGAAATCCCCATTTTCCCAAAAA
129 TTGGATTTTTTCTTTGAAATCCCCATTTTCCCAAAAA
* * * * * **
68813 ATCGAGATTTCTATTCTATAAATATTTTTGGG-GAGATTTTCTTTGGTCTAAAATTTTTAAAAT
1 ATGGAGTTTTCTACTCTATAAATTTTTTTGGGAG-GATTTTC-TTGGTTTTTAATTTTTAAAAT
68876 ACATATAATA
Statistics
Matches: 200, Mismatches: 21, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
166 21 0.10
167 109 0.55
168 70 0.35
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (165 bp):
ATGGAGTTTTCTACTCTATAAATTTTTTTGGGAGGATTTTCTTGGTTTTTAATTTTTAAAATTCA
TCAAATATCATTATTCATTCCACATTAAATTAGTTTTCAAAAAGTAATTCATTTTCTTGAGTTTT
GGATTTTTTCTTTGAAATCCCCATTTTCCCAAAAA
Found at i:70116 original size:19 final size:20
Alignment explanation
Indices: 70088--70126 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
70078 ATGAATAATT
70088 AAAATAATAATAAAAAAATA
1 AAAATAATAATAAAAAAATA
*
70108 AAAAT-ATAATAATAAAATA
1 AAAATAATAATAAAAAAATA
70127 GTAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATAATAATAAAAAAATA
Found at i:70131 original size:11 final size:11
Alignment explanation
Indices: 70081--70133 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
70071 ATTTAACATG
70081 AATAATTAAAAT
1 AATAA-TAAAAT
*
70093 AATAATAAAAA
1 AATAATAAAAT
70104 AATAA-AAATAT
1 AATAATAAA-AT
70115 AATAATAAAAT
1 AATAATAAAAT
*
70126 AGTAATAA
1 AATAATAA
70134 TTAAGTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 3 0.08
11 25 0.69
12 8 0.22
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:70131 original size:14 final size:13
Alignment explanation
Indices: 70081--70134 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 13
70071 ATTTAACATG
*
70081 AATAATTAAA-AT
1 AATAATAAAATAT
70093 AATAATAAAA-A-
1 AATAATAAAATAT
70104 AAT-A-AAAATAT
1 AATAATAAAATAT
70115 AATAATAAAATAGT
1 AATAATAAAATA-T
70129 AATAAT
1 AATAAT
70135 TAAGTAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
9 4 0.11
10 2 0.06
11 6 0.17
12 11 0.31
13 6 0.17
14 7 0.19
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
AATAATAAAATAT
Found at i:70833 original size:22 final size:22
Alignment explanation
Indices: 70799--70851 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
70789 TAGCAGCAGC
* * *
70799 TGCTACAACGAAGACATTAACG
1 TGCTGCAATGAAGACATCAACG
70821 TGCTGCAATGAAGACATCAACG
1 TGCTGCAATGAAGACATCAACG
70843 TGCTGCAAT
1 TGCTGCAAT
70852 CAACAAGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (22 bp):
TGCTGCAATGAAGACATCAACG
Found at i:71257 original size:18 final size:18
Alignment explanation
Indices: 71231--71270 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
71221 ATCGCTGCAA
*
71231 GTTTGATTTTCCTTTATT
1 GTTTAATTTTCCTTTATT
71249 GTTTAATTTTCCTTTATT
1 GTTTAATTTTCCTTTATT
71267 GTTT
1 GTTT
71271 TCATTGCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.68
Consensus pattern (18 bp):
GTTTAATTTTCCTTTATT
Found at i:83667 original size:11 final size:11
Alignment explanation
Indices: 83653--83677 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
83643 GAAAAAAATT
83653 AAAAAAAGAAA
1 AAAAAAAGAAA
83664 AAAAAAAGAAA
1 AAAAAAAGAAA
83675 AAA
1 AAA
83678 TCAAATGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:83675 original size:19 final size:19
Alignment explanation
Indices: 83635--83677 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
83625 TATTATGCAT
* **
83635 AAAAAAGAGAAAAAAATTA
1 AAAAAAGAAAAAAAAAAGA
83654 AAAAAAGAAAAAAAAAAGA
1 AAAAAAGAAAAAAAAAAGA
83673 AAAAA
1 AAAAA
83678 TCAAATGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (19 bp):
AAAAAAGAAAAAAAAAAGA
Found at i:84536 original size:44 final size:44
Alignment explanation
Indices: 84473--84620 Score: 149
Period size: 44 Copynumber: 3.4 Consensus size: 44
84463 CAGCCTGATG
* *
84473 TATGGTTAACACCTTAGTCAGATTTTTCTTC-TTCTGATTTGACA
1 TATGGTTACCACCCTAGTCA-ATTTTTCTTCATTCTGATTTGACA
*
84517 TATGGTTACCACCCTAGTCAAATTTTTC-TCATTCTGATTTGATA
1 TATGGTTACCACCCTAGTC-AATTTTTCTTCATTCTGATTTGACA
* * * ** * * *
84561 TCTGGTTACCACCCTGGTCAAATCCTCTTCCTTTCTG-CTTGACT
1 TATGGTTACCACCCTAGTCAATTTTTCTT-CATTCTGATTTGACA
84605 TATGGTTACCACCCTA
1 TATGGTTACCACCCTA
84621 CTTAAACCAT
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
43 7 0.08
44 72 0.84
45 7 0.08
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (44 bp):
TATGGTTACCACCCTAGTCAATTTTTCTTCATTCTGATTTGACA
Found at i:85344 original size:43 final size:43
Alignment explanation
Indices: 84791--85656 Score: 568
Period size: 42 Copynumber: 20.5 Consensus size: 43
84781 AATCTGGCTA
* * *
84791 TCAGCTTTGACCCTAGAGACTTTCTTACCCT-TAGTCTACCTG
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
* * * * * * *
84833 TCGGCTTTGACCTTAGAGACTATCTCA-TCTCAAGTCTGCCTA
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
** * ** *
84875 TTGGCTTTGA-CCTGGAGACTTTCCTA-CCTTTAGTCTGCCTA
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
** ** * *
84916 TCAGCTTTGACCCTTAAGACTGCCTCA-CCTCAAGTCTACCTG
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
** * * * *
84958 TTGGCTTTCACCCTAGAGACTTTCTTACCCTCAAGTTTGCTTG
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
* * * * *
85001 TC-GACTTTGATCTTGGAGACTTTCCTACCTTC-AGTCTGCTTG
1 TCAG-CTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
* * ** * * *
85043 T-AGGCTTTAACCTTGGAGACTACCTCA-TCTCAAGTCTGCATG
1 TCA-GCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
* * ** * * * * *
85085 TCGGCTTTGACCCTAGAGACTACCTCA-CCTTAAATCTGGCTA
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
* * * ** *
85127 TCAGCTTTGACCTTAGAGACTTTCTTACCCT-TAGTCAACCTA
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
* * * * * *
85169 TCGGCTTTGACCTTGGAGACTGTCTCA-TCTCAAGTCTGCCTA
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
** * ** *
85211 TTGGCTTTGA-CCTGGAGACTTTCCTA-CCTTTAGTCTGCCTA
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
** ** * * * *
85252 TCAGCTTTGACCCTTAAGACTGCCTCA-CTTTAAGTCTACCTG
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
** * * *
85294 TTGGCTTTCACCCCGGAGACTTTCTTACCCTCAAGTTTGCCTG
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
85337 TCAGCTTTGACCCTGGAGACTTTCTTACCCTTCAA-TCTGCCTG
1 TCAGCTTTGACCCTGGAGACTTTCTTACCC-TCAAGTCTGCCTG
* * ** *
85380 TCAGCTTTGATCCTGGAGACTTTCTTACCTTTTAGTTTGCCTG
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
** * * *
85423 TCAGCTTTGACCCTGGAGACTGCCTCA-TCTCAAGTCTGCCTA
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
** *
85465 TC-GCTTTGACCCTGGAGACTTTCTTACCCTTTAGTCTGCTTG
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
* * * * ** * ** *
85507 TCGGTTTTGGCCTTGGAGACTGCCTCA-TTTTAAGTCTGCCTG
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
* * * *
85549 TCGGCTTTGACCCTGGAGACTTTCTTA-CCTTAAGTCTACCTA
1 TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
*
85591 TC-GACTTTGACCCTAGAGACTTTCTTACCCTCAAGTCTGCCTG
1 TCAG-CTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
*
85634 TCGGCTTTGACCCTGGAGACTTT
1 TCAGCTTTGACCCTGGAGACTTT
85657 TATACCTTTT
Statistics
Matches: 634, Mismatches: 171, Indels: 37
0.75 0.20 0.04
Matches are distributed among these distances:
41 91 0.14
42 347 0.55
43 191 0.30
44 5 0.01
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (43 bp):
TCAGCTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTG
Found at i:85360 original size:336 final size:338
Alignment explanation
Indices: 84747--85656 Score: 1215
Period size: 336 Copynumber: 2.7 Consensus size: 338
84737 TCAGTATGTC
*
84747 TGTCGGCTTTGACCCTAAAGACTACCTCACCTTAAATCTGGCTATCAGCTTTGACCCTAGAGACT
1 TGTCGGCTTTGACCCTAGAGACTACCTCACCTTAAATCTGGCTATCAGCTTTGACCCTAGAGACT
* *
84812 TTCTTACCCTTAGTCTACCTGTCGGCTTTGACCTTAGAGACTATCTCATCTCAAGTCTGCCTATT
66 TTCTTACCCTTAGTCTACCTGTCGGCTTTGACCTTGGAGACTGTCTCATCTCAAGTCTGCCTATT
84877 GGCTTTGACCTGGAGACTTTCCTACCTTTAGTCTGCCTATCAGCTTTGACCCTTAAGACTGCCTC
131 GGCTTTGACCTGGAGACTTTCCTACCTTTAGTCTGCCTATCAGCTTTGACCCTTAAGACTGCCTC
* *
84942 ACCTCAAGTCTACCTGTTGGCTTTCACCCTAGAGACTTTCTTACCCTCAAGTTTGCTTGTCGACT
196 ACCTCAAGTCTACCTGTTGGCTTTCACCCCAGAGACTTTCTTACCCTCAAGTTTGCCTGTCGACT
* * * *
85007 TTGATCTTGGAGACTTTCCTA-CCTTCAGTCTGCTTGT-AGGCTTT-AACCTTGGAGACTACCTC
261 TTGACCCTGGAGACTTTCCTACCCTTCAATCTGCCTGTCA-GCTTTGAACC-TGGAGACTACCTC
*
85069 ATC-TCAAGTCTGCA
324 ACCTTCAAGTCTGCA
*
85083 TGTCGGCTTTGACCCTAGAGACTACCTCACCTTAAATCTGGCTATCAGCTTTGACCTTAGAGACT
1 TGTCGGCTTTGACCCTAGAGACTACCTCACCTTAAATCTGGCTATCAGCTTTGACCCTAGAGACT
* *
85148 TTCTTACCCTTAGTCAACCTATCGGCTTTGACCTTGGAGACTGTCTCATCTCAAGTCTGCCTATT
66 TTCTTACCCTTAGTCTACCTGTCGGCTTTGACCTTGGAGACTGTCTCATCTCAAGTCTGCCTATT
85213 GGCTTTGACCTGGAGACTTTCCTACCTTTAGTCTGCCTATCAGCTTTGACCCTTAAGACTGCCTC
131 GGCTTTGACCTGGAGACTTTCCTACCTTTAGTCTGCCTATCAGCTTTGACCCTTAAGACTGCCTC
* * *
85278 ACTTTAAGTCTACCTGTTGGCTTTCACCCCGGAGACTTTCTTACCCTCAAGTTTGCCTGTC-AGC
196 ACCTCAAGTCTACCTGTTGGCTTTCACCCCAGAGACTTTCTTACCCTCAAGTTTGCCTGTCGA-C
* * ** *
85342 TTTGACCCTGGAGACTTTCTTACCCTTCAATCTGCCTGTCAGCTTTGATCCTGGAGACTTTCTTA
260 TTTGACCCTGGAGACTTTCCTACCCTTCAATCTGCCTGTCAGCTTTGAACCTGGAGACTACCTCA
** * *
85407 CCTTTTAGTTTGCC
325 CCTTCAAGTCTGCA
* * * * * * * *
85421 TGTCAGCTTTGACCCTGGAGACTGCCTCATCTCAAGTCTGCCTATC-GCTTTGACCCTGGAGACT
1 TGTCGGCTTTGACCCTAGAGACTACCTCACCTTAAATCTGGCTATCAGCTTTGACCCTAGAGACT
* * * * * * * *
85485 TTCTTACCCTTTAGTCTGCTTGTCGGTTTTGGCCTTGGAGACTGCCTCATTTTAAGTCTGCCTGT
66 TTCTTACCC-TTAGTCTACCTGTCGGCTTTGACCTTGGAGACTGTCTCATCTCAAGTCTGCCTAT
* * * * *
85550 CGGCTTTGACCCTGGAGACTTTCTTACCTTAAGTCTACCTATC-GACTTTGACCC-TAGAGACTT
130 TGGCTTTGA-CCTGGAGACTTTCCTACCTTTAGTCTGCCTATCAG-CTTTGACCCTTA-AGACTG
* * * * * **
85613 TCTTACCCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT
192 CCTCA-CCTCAAGTCTACCTGTTGGCTTTCACCCCAGAGACTTT
85657 TATACCTTTT
Statistics
Matches: 507, Mismatches: 57, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
335 1 0.00
336 265 0.52
337 56 0.11
338 106 0.21
339 47 0.09
340 32 0.06
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (338 bp):
TGTCGGCTTTGACCCTAGAGACTACCTCACCTTAAATCTGGCTATCAGCTTTGACCCTAGAGACT
TTCTTACCCTTAGTCTACCTGTCGGCTTTGACCTTGGAGACTGTCTCATCTCAAGTCTGCCTATT
GGCTTTGACCTGGAGACTTTCCTACCTTTAGTCTGCCTATCAGCTTTGACCCTTAAGACTGCCTC
ACCTCAAGTCTACCTGTTGGCTTTCACCCCAGAGACTTTCTTACCCTCAAGTTTGCCTGTCGACT
TTGACCCTGGAGACTTTCCTACCCTTCAATCTGCCTGTCAGCTTTGAACCTGGAGACTACCTCAC
CTTCAAGTCTGCA
Found at i:85716 original size:127 final size:126
Alignment explanation
Indices: 84823--85724 Score: 424
Period size: 127 Copynumber: 7.1 Consensus size: 126
84813 TCTTACCCTT
* * * * * * * * *
84823 AGTCTACCTGTCGGCTTTGACCTTAGAGACTATCTCA-TCTCAAGTCTGCCTATTGGCTTTGA-C
1 AGTCTACCTATCGACTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACC
* * * ** * ** *
84886 CTGGAGACTTTCCTACC-TTTAGTCTGCCTATCAGCTTTGACCCTTAAGACTGCCTCAC-CTCA
66 CTGGAGACTTT-TTACCTTTTAGT-TGCCTGTCGGCTTTGACCCTGGAGAAT-CCTTTCTCTTA
* * * * * * * * *
84948 AGTCTACCTGTTGGCTTTCACCCTAGAGACTTTCTTACCCTCAAGTTTGCTTGTCGACTTTGATC
1 AGTCTACCTATCGACTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACC
* * * * * * * * *
85013 TTGGAGACTTTCCTACC-TTCAGTCTGCTTGTAGGCTTTAACCTTGGAGACTACC--TCATCTCA
66 CTGGAGACTTT-TTACCTTTTAGT-TGCCTGTCGGCTTTGACCCTGGAGAAT-CCTTTC-TCTTA
* * * * * ** * * * * * *
85075 AGTCTGCATGTCGGCTTTGACCCTAGAGACTACCTCA-CCTTAAATCTGGCTATCAGCTTTGACC
1 AGTCTACCTATCGACTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACC
* * * ** * * * * * *
85139 TTAGAGACTTTCTTACC-CTTAGTCAACCTATCGGCTTTGACCTTGGAGACT-GTCTCATCTCA
66 CTGGAGACTTT-TTACCTTTTAGT-TGCCTGTCGGCTTTGACCCTGGAGAATCCTTTC-TCTTA
* * * * ** * *
85201 AGTCTGCCTATTGGCTTTGA-CCTGGAGACTTTCCTA-CCTTTAGTCTGCCTATCAGCTTTGACC
1 AGTCTACCTATCGACTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACC
** *** * * * * * * * * * *
85264 CTTAAGACTGCCT-CACTTTAAGTCTACCTGTTGGCTTTCACCCCGGAGACTTTCTTACCCTCA
66 CTGGAGACTTTTTAC-CTTTTAGT-TGCCTGTCGGCTTTGACCCTGGAGA-ATCCTTTCTCTTA
* * * *
85327 AGTTTGCCTGTC-AGCTTTGACCCTGGAGACTTTCTTACCCTTCAA-TCTGCCTGTCAGCTTTGA
1 AGTCTACCTATCGA-CTTTGACCCTGGAGACTTTCTTACCC-TCAAGTCTGCCTGTCGGCTTTGA
* * *
85390 TCCTGGAGACTTTCTTACCTTTTAGTTTGCCTGTCAGCTTTGACCCTGGAGACTGCC--TCATCT
64 CCCTGGAGACTTT-TTACCTTTTAG-TTGCCTGTCGGCTTTGACCCTGGAGAAT-CCTTTC-TCT
*
85453 CA
125 TA
* ** * * *
85455 AGTCTGCCTATCG-CTTTGACCCTGGAGACTTTCTTACCCTTTAGTCTGCTTGTCGGTTTTGGCC
1 AGTCTACCTATCGACTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACC
* *** * * * *
85519 TTGGAGACTGCCT-CATTTTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTAC-CTTA
66 CTGGAGACTTTTTACCTTTT-AGT-TGCCTGTCGGCTTTGACCCTGGAGA-ATCCTTTCTCTTA
*
85581 AGTCTACCTATCGACTTTGACCCTAGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACC
1 AGTCTACCTATCGACTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACC
* * * *
85646 CTGGAGACTTTTATACCTTTT-GCTTGCCTGTTGGCTTCGACCCGGGAGAATCCTTTCTCTTT
66 CTGGAGACTTTT-TACCTTTTAG-TTGCCTGTCGGCTTTGACCCTGGAGAATCCTTTCTCTTA
* * *
85708 TGTTTACCTGTCGACTT
1 AGTCTACCTATCGACTT
85725 AGTTTTGGGT
Statistics
Matches: 601, Mismatches: 145, Indels: 60
0.75 0.18 0.07
Matches are distributed among these distances:
123 1 0.00
124 2 0.00
125 104 0.17
126 173 0.29
127 239 0.40
128 45 0.07
129 35 0.06
130 2 0.00
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.36
Consensus pattern (126 bp):
AGTCTACCTATCGACTTTGACCCTGGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACC
CTGGAGACTTTTTACCTTTTAGTTGCCTGTCGGCTTTGACCCTGGAGAATCCTTTCTCTTA
Found at i:86440 original size:19 final size:20
Alignment explanation
Indices: 86416--86471 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
86406 GTATCGATAT
**
86416 ATTGTATCGATACATGTTC-
1 ATTGTATCGATACATGGCCA
*
86435 ATTGTATCAATACATGGCCAA
1 ATTGTATCGATACATGGCC-A
86456 ATTGTATCGATACATG
1 ATTGTATCGATACATG
86472 AAACTAGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGCCA
Found at i:86537 original size:13 final size:13
Alignment explanation
Indices: 86516--86546 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
86506 CGATACATGG
*
86516 TACAATGTATCGA
1 TACATTGTATCGA
86529 TACATTGTATCGA
1 TACATTGTATCGA
86542 TACAT
1 TACAT
86547 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:86542 original size:33 final size:32
Alignment explanation
Indices: 86500--86566 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
86490 CTATCACTAT
86500 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
86533 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
86566 T
1 T
86567 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:94578 original size:17 final size:17
Alignment explanation
Indices: 94557--94590 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
94547 AATTTCTATA
94557 AAAAAGGAGAGAAGATAT
1 AAAAAGG-GAGAAGATAT
94575 AAAAAGGGAGAAGATA
1 AAAAAGGGAGAAGATA
94591 ATCGTTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.29, T:0.09
Consensus pattern (17 bp):
AAAAAGGGAGAAGATAT
Found at i:95262 original size:13 final size:13
Alignment explanation
Indices: 95244--95273 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
95234 CGATACATGG
95244 TACAATCTATCGA
1 TACAATCTATCGA
*
95257 TACAATTTATCGA
1 TACAATCTATCGA
95270 TACA
1 TACA
95274 TGAAGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (13 bp):
TACAATCTATCGA
Found at i:96181 original size:3 final size:3
Alignment explanation
Indices: 96165--96227 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
96155 ATTTAACATG
* *
96165 AAT AAT AA- AA- AAT AAT AAT AAAT AAA AAT GA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
96208 AAT AAT AAT -AT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
96228 GTATTAATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
2 9 0.18
3 39 0.76
4 3 0.06
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:96190 original size:17 final size:16
Alignment explanation
Indices: 96172--96225 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
96162 ATGAATAATA
96172 AAAAATAATAATAAAT
1 AAAAATAATAATAAAT
96188 AAAAATGAAATAAT-AAT
1 AAAAAT--AATAATAAAT
*
96205 AATAATAATAATATAAT
1 AAAAATAATAATA-AAT
96222 AAAA
1 AAAA
96226 TAGTATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 14 0.44
18 6 0.19
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAAATAATAATAAAT
Found at i:96920 original size:22 final size:22
Alignment explanation
Indices: 96892--96939 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
96882 GTAGCTACTA
*
96892 CAATGAAGACATTAACGTGCTG
1 CAATGAAGACATCAACGTGCTG
*
96914 CAATGAAGACATCAATGTGCTG
1 CAATGAAGACATCAACGTGCTG
96936 CAAT
1 CAAT
96940 CAACAAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (22 bp):
CAATGAAGACATCAACGTGCTG
Found at i:97075 original size:18 final size:19
Alignment explanation
Indices: 97040--97075 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
97030 CAAAAGAAAT
*
97040 AAAAAAGAAATTGCAACAA
1 AAAAAAGAAATCGCAACAA
97059 AAAAAAGAAATCG-AACA
1 AAAAAAGAAATCGCAACA
97076 GCAGCTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.69, C:0.11, G:0.11, T:0.08
Consensus pattern (19 bp):
AAAAAAGAAATCGCAACAA
Found at i:105109 original size:66 final size:66
Alignment explanation
Indices: 104996--105137 Score: 200
Period size: 66 Copynumber: 2.2 Consensus size: 66
104986 CAGAATGTAC
* * * *
104996 AACCT-AGGGTACCAGCCTCTCCACCTATTATTGTTATCAACCTCGAAA-CGGTACCTCAAGAAT
1 AACCTAAGGGTACCAACCCCTCCACCTATTATTGTTATCAACCCCGAAATC-GTACCTCAAGAAA
105059 CT
65 CT
*
105061 AATCC-AAGGGTACCAACCCCTCCACCTGTTATTGTTATCAACCCCGAAATCGTACCTCAAGAAA
1 AA-CCTAAGGGTACCAACCCCTCCACCTATTATTGTTATCAACCCCGAAATCGTACCTCAAGAAA
105125 CT
65 CT
105127 AACCTAAGGGT
1 AACCTAAGGGT
105138 CAATCTTGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
65 4 0.06
66 63 0.93
67 1 0.01
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (66 bp):
AACCTAAGGGTACCAACCCCTCCACCTATTATTGTTATCAACCCCGAAATCGTACCTCAAGAAAC
T
Found at i:113294 original size:44 final size:44
Alignment explanation
Indices: 113206--113755 Score: 336
Period size: 44 Copynumber: 12.5 Consensus size: 44
113196 CTATTTTACA
* * * *
113206 TATGGTTACCACCTTGGTCAAA-TCTTTTCCTT-TCTATCTGACG
1 TATGGTTACCACCCTGGTCAAATTCTTTTCATTAT-GATTTGACG
* * *
113249 TATGGTTACCACCTTGGCCAAATTGTTTTCATTATGATTTGACG
1 TATGGTTACCACCCTGGTCAAATTCTTTTCATTATGATTTGACG
* * * * *
113293 TATGGTTACCACCCTAGTC-AAGTCTTTTCATTTTTG-TCTAACG
1 TATGGTTACCACCCTGGTCAAATTCTTTTCA-TTATGATTTGACG
* * * * *
113336 TATGGTTACCACCTTGGTCAGATTCTTTTCATTCTAATTTGACA
1 TATGGTTACCACCCTGGTCAAATTCTTTTCATTATGATTTGACG
* * * *
113380 TATGGTTACCACCCTGGTCAAATT-TTCCTCTTTTCTG-TTTGATG
1 TATGGTTACCACCCTGGTCAAATTCTT-TTC-ATTATGATTTGACG
* * * * * * *
113424 TATAGTTACTACCCTAGTCAAACTCTTTTCATTTCAGGA-CTGGCG
1 TATGGTTACCACCCTGGTCAAATTCTTTTCA-TT-ATGATTTGACG
* * *
113469 TATGGTTACCACCCTGGTCAGATTCTTTTCATTATGATTTAACC
1 TATGGTTACCACCCTGGTCAAATTCTTTTCATTATGATTTGACG
* * * * *
113513 TATGGTTACTACCTTGGTCAAATT-TTTCTCTCTTCTG-TTTAACG
1 TATGGTTACCACCCTGGTCAAATTCTTT-TC-ATTATGATTTGACG
* * * * *
113557 TATGGTTACCACCCTAGTCAAACTCTTTTCATT-TCAAGTCTAACG
1 TATGGTTACCACCCTGGTCAAATTCTTTTCATTAT-GA-TTTGACG
* * ** * *
113602 TATGGTTGCCACCCT-ATCTGATTCTCTTCATTCTGATTTGA-G
1 TATGGTTACCACCCTGGTCAAATTCTTTTCATTATGATTTGACG
* ** * * * * *
113644 ATATGGTTACTACCCTGGTCAAA-TCTGCCTCTTTCCT-ATCTAACA
1 -TATGGTTACCACCCTGGTCAAATTCT-TTTCATT-ATGATTTGACG
* * *
113689 TATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATTTGATG
1 TATGGTTACCACCCTGGTCAAATTCTTTTCATTATGATTTGACG
* * *
113733 TATGGTTATCACCTTGGTTAAAT
1 TATGGTTACCACCCTGGTCAAAT
113756 CTGCCTTCTT
Statistics
Matches: 386, Mismatches: 95, Indels: 51
0.73 0.18 0.10
Matches are distributed among these distances:
42 2 0.01
43 86 0.22
44 228 0.59
45 70 0.18
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (44 bp):
TATGGTTACCACCCTGGTCAAATTCTTTTCATTATGATTTGACG
Found at i:113518 original size:133 final size:133
Alignment explanation
Indices: 113206--113721 Score: 542
Period size: 133 Copynumber: 3.9 Consensus size: 133
113196 CTATTTTACA
* * * * * * * *
113206 TATGGTTACCACCTTGGTCA-AATCTTTTCCTTTCT-ATCTGACGTATGGTTACCACCTTGGCCA
1 TATGGTTACCACCCTGGTCAGATTCTTTT-CATTCTGATTTGACATATGGTTACTACCCTGGTCA
* * * * **
113269 AATTGTT-TTC-ATTATGATTTGACGTATGGTTACCACCCTAGTC-AAGTCTTTTCATTT-TTGT
65 AATT-TTCCTCTTTTCTG-TTTGACGTATGGTTACCACCCTAGTCAAACTCTTTTCATTTCAAGT
113330 CTAACG
128 CTAACG
* * *
113336 TATGGTTACCACCTTGGTCAGATTCTTTTCATTCTAATTTGACATATGGTTACCACCCTGGTCAA
1 TATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATTTGACATATGGTTACTACCCTGGTCAA
* * * * * *
113401 ATTTTCCTCTTTTCTGTTTGATGTATAGTTACTACCCTAGTCAAACTCTTTTCATTTCAGGACTG
66 ATTTTCCTCTTTTCTGTTTGACGTATGGTTACCACCCTAGTCAAACTCTTTTCATTTCAAGTCTA
*
113466 GCG
131 ACG
* * * *
113469 TATGGTTACCACCCTGGTCAGATTCTTTTCATTATGATTTAACCTATGGTTACTACCTTGGTCAA
1 TATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATTTGACATATGGTTACTACCCTGGTCAA
* * *
113534 ATTTTTCTCTCTTCTGTTTAACGTATGGTTACCACCCTAGTCAAACTCTTTTCATTTCAAGTCTA
66 ATTTTCCTCTTTTCTGTTTGACGTATGGTTACCACCCTAGTCAAACTCTTTTCATTTCAAGTCTA
113599 ACG
131 ACG
* * * * *
113602 TATGGTTGCCACCCT-ATCTGATTCTCTTCATTCTGATTTGAGATATGGTTACTACCCTGGTCAA
1 TATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATTTGACATATGGTTACTACCCTGGTCAA
* * * * * * * * * *
113666 ATCTGCCTCTTTCCTATCTAACATATGGTTACCACCCTGGTCAGATTCTTTTCATT
66 ATTTTCCTCTTTTCTGTTTGACGTATGGTTACCACCCTAGTCAAACTCTTTTCATT
113722 CTGATTTGAT
Statistics
Matches: 325, Mismatches: 55, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
130 27 0.08
131 60 0.18
132 103 0.32
133 135 0.42
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (133 bp):
TATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATTTGACATATGGTTACTACCCTGGTCAA
ATTTTCCTCTTTTCTGTTTGACGTATGGTTACCACCCTAGTCAAACTCTTTTCATTTCAAGTCTA
ACG
Found at i:113649 original size:88 final size:88
Alignment explanation
Indices: 113556--113783 Score: 223
Period size: 88 Copynumber: 2.6 Consensus size: 88
113546 TCTGTTTAAC
** * *
113556 GTATGGTTACCACCCTAGTCAAACTCT-TTTCATTT-CAAGTCTAACGTATGGTTGCCACCCT-A
1 GTATGGTTACCACCCTAGTCAAA-TCTGCCTC-TTTCCAA-TCTAACATATGGTTACCACCCTGA
*
113618 TCTGATTCTCTTCATTCTGATTTGA-
63 TCAGATTCTCTTCATTCTGATTTGAT
* * * *
113643 GATATGGTTACTACCCTGGTCAAATCTGCCTCTTTCCTATCTAACATATGGTTACCACCCTGGTC
1 G-TATGGTTACCACCCTAGTCAAATCTGCCTCTTTCCAATCTAACATATGGTTACCACCCTGATC
*
113708 AGATTCTTTTCATTCTGATTTGAT
65 AGATTCTCTTCATTCTGATTTGAT
* * * * * * *
113732 GTATGGTTATCACCTTGGTTAAATCTGCCT-TCTTCCTATTTGACATATGGTT
1 GTATGGTTACCACCCTAGTCAAATCTGCCTCT-TTCCAATCTAACATATGGTT
113784 GTCACCCTAA
Statistics
Matches: 119, Mismatches: 16, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
87 28 0.24
88 90 0.76
89 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (88 bp):
GTATGGTTACCACCCTAGTCAAATCTGCCTCTTTCCAATCTAACATATGGTTACCACCCTGATCA
GATTCTCTTCATTCTGATTTGAT
Found at i:113695 original size:220 final size:219
Alignment explanation
Indices: 113205--113757 Score: 577
Period size: 220 Copynumber: 2.5 Consensus size: 219
113195 TCTATTTTAC
* * * *
113205 ATATGGTTACCACCTTGGTCAAATCTTTTCCTTT-CTATCTGACGTATGGTTACCACCTTGGCCA
1 ATATGGTTACTACCCTGGTCAAATCTTTT-CTTTCCTATCTGACGTATGGTTACCACCCTGGTCA
* * * * * *
113269 AATTGTTTTCATTATGATTTGACGTATGGTTACCACCCTAGTCAAGTCTTTTCATTTTTGTCTAA
65 GATTCTTTTCATTATGATTTGACGTATGGTTACTACCTTGGTCAAATCTTTTCATTTTTGTCTAA
* * * * * * *
113334 CGTATGGTTACCACCTTGGTCAGATTCTTTTCATTCTAATTTGACATATGGTTACCACCCTGGTC
130 CGTATGGTTACCACCCTAGTCAAACTCTTTTCATTCTAATCTAACATATGGTTACCACCCTGATC
* *
113399 AAATTTTCCTCTTTTCTGTTTGATG
195 AAATTCTCCTCTATTCTGTTTGATG
* * ** *
113424 -TATAGTTACTACCCTAGTCAAACTCTTTTCATTTCAGGA-CTGGCGTATGGTTACCACCCTGGT
1 ATATGGTTACTACCCTGGTCAAA-TCTTTTC-TTTC-CTATCTGACGTATGGTTACCACCCTGGT
* *
113487 CAGATTCTTTTCATTATGATTTAACCTATGGTTACTACCTTGGTCAAAT-TTTTC-TCTCTTCTG
63 CAGATTCTTTTCATTATGATTTGACGTATGGTTACTACCTTGGTCAAATCTTTTCAT-T-TT-TG
* * *
113550 TTTAACGTATGGTTACCACCCTAGTCAAACTCTTTTCATT-TCAAGTCTAACGTATGGTTGCCAC
125 TCTAACGTATGGTTACCACCCTAGTCAAACTCTTTTCATTCT-AA-TCTAACATATGGTTACCAC
** *
113614 CCT-ATCTGATTCTCTTC-ATTCTGATTTGA-G
188 CCTGATCAAATTCTCCTCTATTCTG-TTTGATG
** * *
113644 ATATGGTTACTACCCTGGTCAAATCTGCCTCTTTCCTATCTAACATATGGTTACCACCCTGGTCA
1 ATATGGTTACTACCCTGGTCAAATCT-TTTCTTTCCTATCTGACGTATGGTTACCACCCTGGTCA
* * *
113709 GATTCTTTTCATTCTGATTTGATGTATGGTTA-TCACCTTGGTTAAATCT
65 GATTCTTTTCATTATGATTTGACGTATGGTTACT-ACCTTGGTCAAATCT
113758 GCCTTCTTCC
Statistics
Matches: 273, Mismatches: 46, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
218 20 0.07
219 17 0.06
220 141 0.52
221 77 0.28
222 18 0.07
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (219 bp):
ATATGGTTACTACCCTGGTCAAATCTTTTCTTTCCTATCTGACGTATGGTTACCACCCTGGTCAG
ATTCTTTTCATTATGATTTGACGTATGGTTACTACCTTGGTCAAATCTTTTCATTTTTGTCTAAC
GTATGGTTACCACCCTAGTCAAACTCTTTTCATTCTAATCTAACATATGGTTACCACCCTGATCA
AATTCTCCTCTATTCTGTTTGATG
Found at i:113790 original size:88 final size:87
Alignment explanation
Indices: 113595--113792 Score: 249
Period size: 88 Copynumber: 2.3 Consensus size: 87
113585 TCATTTCAAG
* *
113595 TCTAACGTATGGTTGCCACCCTATCTGATTCTCTTCATTCTGATTTGAGATATGGTTACTACCCT
1 TCTAACATATGGTTGCCACCCTATCAGATTCTCTTCATTCTGATTTGAGATATGGTTACTACCCT
113660 GGTCAAATCTGCCTCTTTCCTA
66 GGTCAAATCTGCCTCTTTCCTA
* * *
113682 TCTAACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATTTGATG-TATGGTTA-TCAC
1 TCTAACATATGGTTGCCACCCT-ATCAGATTCTCTTCATTCTGATTTGA-GATATGGTTACT-AC
* *
113745 CTTGGTTAAATCTGCCT-TCTTCCTA
63 CCTGGTCAAATCTGCCTCT-TTCCTA
* * *
113770 TTTGACATATGGTTGTCACCCTA
1 TCTAACATATGGTTGCCACCCTA
113793 ATCAAATGAT
Statistics
Matches: 95, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
87 22 0.23
88 72 0.76
89 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.40
Consensus pattern (87 bp):
TCTAACATATGGTTGCCACCCTATCAGATTCTCTTCATTCTGATTTGAGATATGGTTACTACCCT
GGTCAAATCTGCCTCTTTCCTA
Found at i:115357 original size:137 final size:137
Alignment explanation
Indices: 115136--115407 Score: 454
Period size: 137 Copynumber: 2.0 Consensus size: 137
115126 GTATTTTCGA
* *
115136 AAAATAGAGTTTTCTACTTCGTAAATTTTTTCAAGGAGATTTTTCTTGGTTTTTAATTTTTAAAA
1 AAAATAGAGTTTTCTACTCCGTAAATTTTTTCAAGGAGATTTTTCTTGGTTTTTAATTTTCAAAA
* *
115201 TTCATCAAATATTATTATTTATATCACATTAAATCAATTTTCAAAAATTCTTTCATTTTCTTGAG
66 TTCATCAAATATCATTATTTATATCACATTAAATCAATTTTCAAAAATTCCTTCATTTTCTTGAG
115266 TTTTTGG
131 TTTTTGG
* *
115273 AAAATAGAGTTTTCTACTCCGTAAATTTTTTCAGGGAGATTTTTCTTGGTTTTTAATTTTCAAAG
1 AAAATAGAGTTTTCTACTCCGTAAATTTTTTCAAGGAGATTTTTCTTGGTTTTTAATTTTCAAAA
* ** *
115338 TTCATCAAATATCATTATTTATATCATATTAAATCTGTTTTCAAATATTCCTTCATTTTCTTGAG
66 TTCATCAAATATCATTATTTATATCACATTAAATCAATTTTCAAAAATTCCTTCATTTTCTTGAG
115403 TTTTT
131 TTTTT
115408 AGATTTTTTC
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
137 125 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (137 bp):
AAAATAGAGTTTTCTACTCCGTAAATTTTTTCAAGGAGATTTTTCTTGGTTTTTAATTTTCAAAA
TTCATCAAATATCATTATTTATATCACATTAAATCAATTTTCAAAAATTCCTTCATTTTCTTGAG
TTTTTGG
Found at i:115525 original size:304 final size:304
Alignment explanation
Indices: 114992--115574 Score: 883
Period size: 304 Copynumber: 1.9 Consensus size: 304
114982 CTCCTCTATG
*
114992 ATTTTTTCAGGGGGGATTTTTCTTGGTTTTTAAATTTTAAAATTCATCAAATACCATTATTTATA
1 ATTTTTTCAGGGGAGATTTTTCTTGGTTTTTAAATTTTAAAATTCATCAAATACCATTATTTATA
* *
115057 TGACAGTAAATTAGTTTTCAATAATTCCTTCATTTTCTTGAGTTTTTAGATTTTTTCTTTTAAAT
66 TCACAGTAAATTAGTTTTCAATAATTCCTTCATTTTCTTGAGTTTTTAGATTTTTTCCTTTAAAT
* *
115122 TCCTGTATTTTCGAAAAATAGAGTTTTCTACTTCGTAAATTTTTTCAAGGAGATTTTTCTTGGTT
131 T-CTGTATTTTCAAAAAATAGAGTTTTCTACTCCGTAAATTTTTTCAAGGAGATTTTTCTTGGTT
* *
115187 TTTAATTTTTAAAATTCATCAAATATTATTATTTATATCACATTAAATCAATTTTCAAAAA-TTC
195 TTTAAATTTTAAAATTCATCAAATATCATTATTTATATCACATTAAATCAATTTTCAAAAATTTC
115251 TTTCATTTTCTTGAGTTTTTGGAAAATAGAGTTTTCTACTCCGTAA
260 -TTCATTTTCTTGAGTTTTTGGAAAATAGAGTTTTCTACTCCGTAA
* *
115297 ATTTTTTCA-GGGAGATTTTTCTTGGTTTTT-AATTTTCAAAGTTCATCAAATATCATTATTTAT
1 ATTTTTTCAGGGGAGATTTTTCTTGGTTTTTAAATTTT-AAAATTCATCAAATACCATTATTTAT
* *
115360 ATCATATTAAATCT-GTTTTCAA-ATATTCCTTCATTTTCTTGAGTTTTTAGATTTTTTCCTTTA
65 ATCACAGTAAAT-TAGTTTTCAATA-ATTCCTTCATTTTCTTGAGTTTTTAGATTTTTTCCTTTA
* * * *
115423 AATT-TTTTTGTTTCTAAAAAATGGAGTTTTCTACTCCGTAAATTTTTTGGAAGG-GATTTTTCT
128 AATTCTGTAT-TTTC-AAAAAATAGAGTTTTCTACTCCGTAAATTTTTT-CAAGGAGATTTTTCT
* *
115486 TGGTTTTTAAATTTTAAAATTCATCAAATATCATTATTTATATTACATTAAATCAGTTTTCAAAA
190 TGGTTTTTAAATTTTAAAATTCATCAAATATCATTATTTATATCACATTAAATCAATTTTCAAAA
*
115551 CTTTCTTCATTTTCTTGAGTTTTT
255 ATTTCTTCATTTTCTTGAGTTTTT
115575 TCATTTTTTC
Statistics
Matches: 253, Mismatches: 18, Indels: 15
0.88 0.06 0.05
Matches are distributed among these distances:
302 3 0.01
303 11 0.04
304 222 0.88
305 17 0.07
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (304 bp):
ATTTTTTCAGGGGAGATTTTTCTTGGTTTTTAAATTTTAAAATTCATCAAATACCATTATTTATA
TCACAGTAAATTAGTTTTCAATAATTCCTTCATTTTCTTGAGTTTTTAGATTTTTTCCTTTAAAT
TCTGTATTTTCAAAAAATAGAGTTTTCTACTCCGTAAATTTTTTCAAGGAGATTTTTCTTGGTTT
TTAAATTTTAAAATTCATCAAATATCATTATTTATATCACATTAAATCAATTTTCAAAAATTTCT
TCATTTTCTTGAGTTTTTGGAAAATAGAGTTTTCTACTCCGTAA
Found at i:115561 original size:167 final size:166
Alignment explanation
Indices: 115273--115814 Score: 665
Period size: 167 Copynumber: 3.3 Consensus size: 166
115263 GAGTTTTTGG
* * *
115273 AAAATAGAGTTTTCTACTCCGTAAATTTTTT-CAGGGAGATTTTTCTTGGTTTTT-AATTTTCAA
1 AAAATGGAGTTTTCTACTCCGTAAATTTTTTGGAAGG-GATTTTTCTTGGTTTTTAAATTTT-AA
* * *
115336 AGTTCATCAAATATCATTATTTATATCATATTAAATCTGTTTTCAAATATTCCTTCATTTTCTTG
64 AATTCATCAAATATCATTATTTATATCATATTAAATCAGTTTTCAAA-ATTACTTCATTTTCTTG
115401 AGTTTTTAGATTTTTTCCTTTAAATTTTTTTGTTTCT-AA
128 AGTTTTT-GATTTTTTCCTTTAAATTTTTTTGTTTCTCAA
115440 AAAATGGAGTTTTCTACTCCGTAAATTTTTTGGAAGGGATTTTTCTTGGTTTTTAAATTTTAAAA
1 AAAATGGAGTTTTCTACTCCGTAAATTTTTTGGAAGGGATTTTTCTTGGTTTTTAAATTTTAAAA
* * *
115505 TTCATCAAATATCATTATTTATATTACATTAAATCAGTTTTCAAAACTTTCTTCATTTTCTTGAG
66 TTCATCAAATATCATTATTTATATCATATTAAATCAGTTTTCAAAA-TTACTTCATTTTCTTGAG
* *
115570 TTTTTTCATTTTTTCCTTTAAATTTTTTTGTTT-TCGA
130 -TTTTTGATTTTTTCCTTTAAATTTTTTTGTTTCTCAA
* * ** * *
115607 AAAACGGAGTTTTCTATTCCGTAAATTTTTTCAAAGGGATTTTTCTTAGTTTTTAATTTTTAAAA
1 AAAATGGAGTTTTCTACTCCGTAAATTTTTTGGAAGGGATTTTTCTTGGTTTTTAAATTTTAAAA
* * * *
115672 TTCATCAAATATCATTATTCAT-TCCATATTAAATCAGTTTTCAAAAGTAATTCATTTTCATGAG
66 TTCATCAAATATCATTATTTATAT-CATATTAAATCAGTTTTCAAAATTACTTCATTTTCTTGAG
* *
115736 -TTTTGTATTTTTTTCTTTGAAA-TCTTTT-TTTCTCAA
130 TTTTTG-ATTTTTTCCTTT-AAATTTTTTTGTTTCTCAA
* * *
115772 AAAACT-GAGATTTT-TATTCCATAAATATTTTTGG-GGGGATTTT
1 AAAA-TGGAG-TTTTCTACTCCGTAAAT-TTTTTGGAAGGGATTTT
115815 ATTTGGTCTA
Statistics
Matches: 331, Mismatches: 32, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
164 7 0.02
165 45 0.14
166 29 0.09
167 236 0.71
168 14 0.04
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (166 bp):
AAAATGGAGTTTTCTACTCCGTAAATTTTTTGGAAGGGATTTTTCTTGGTTTTTAAATTTTAAAA
TTCATCAAATATCATTATTTATATCATATTAAATCAGTTTTCAAAATTACTTCATTTTCTTGAGT
TTTTGATTTTTTCCTTTAAATTTTTTTGTTTCTCAA
Found at i:116399 original size:22 final size:22
Alignment explanation
Indices: 116371--116422 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
116361 GCTTTTAAGT
*
116371 GAAAGAAGAA-AGAGAAAAGATA
1 GAAAGAA-AAGAGAGAAAAAATA
116393 GAAAGAAAAGAGAGAAAAAATA
1 GAAAGAAAAGAGAGAAAAAATA
116415 G-AAGAAAA
1 GAAAGAAAA
116423 TAAAAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (22 bp):
GAAAGAAAAGAGAGAAAAAATA
Found at i:117563 original size:159 final size:160
Alignment explanation
Indices: 117366--117679 Score: 429
Period size: 161 Copynumber: 2.0 Consensus size: 160
117356 GTGATAAAAT
* **
117366 TAAATTTTAATTTTTTTCTTAATTTTTTATATTCCTATGGGCATCCATAGAGG-TATAAAAGATT
1 TAAATTTTAATTTTTTTCTTAATCTTGCATATTCCTATGGGCATCCATAG-GGATATAAAAGATT
*** * * *
117430 T-T-AAAAATGTTTCATATCCTTTTGGGCTTCCATTAGGGTATAAAATGGTATTTTCGAAAATAA
65 TATAAAAAAACATTCAGATCCTTTCGGGCTTCCATTAGGGTACAAAATGGTATTTTCGAAAATAA
*
117493 ATAAAATTAAATTGAATTAATACTTTATGGA
130 AAAAAATTAAATTGAATTAATACTTTATGGA
* *
117524 TAAATTTTAATTATTTTT-TCTAATCTTGCATATTCCTATGGGCATTCGTAGGGATATAAAAGAT
1 TAAATTTTAATT-TTTTTCT-TAATCTTGCATATTCCTATGGGCATCCATAGGGATATAAAAGAT
* * *
117588 TTATAAAAAAACATTCCGATCCTTTCGGGCTTCTATTAGGGTACAAAATGGTGTTTTCGAAAATA
64 TTATAAAAAAACATTCAGATCCTTTCGGGCTTCCATTAGGGTACAAAATGGTATTTTCGAAAATA
*
117653 AAAAAAATTAAGTTGAATTAATACTTT
129 AAAAAAATTAAATTGAATTAATACTTT
117680 CGAGAAAAAA
Statistics
Matches: 135, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
158 15 0.11
159 43 0.32
160 1 0.01
161 76 0.56
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (160 bp):
TAAATTTTAATTTTTTTCTTAATCTTGCATATTCCTATGGGCATCCATAGGGATATAAAAGATTT
ATAAAAAAACATTCAGATCCTTTCGGGCTTCCATTAGGGTACAAAATGGTATTTTCGAAAATAAA
AAAAATTAAATTGAATTAATACTTTATGGA
Found at i:122256 original size:4 final size:4
Alignment explanation
Indices: 122249--122356 Score: 64
Period size: 4 Copynumber: 28.0 Consensus size: 4
122239 TTTAACATTT
* * *
122249 ATAA ATAA AAAA ATAT A-AA ATAT A-AA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * * * * *
122295 A-AGT GTAT ATAA A-AA ATAT ATAT ATAA A-AT ATAA ATAA ATAA ATTA
1 ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* *
122341 ACAA AGAA ATAA ATAA
1 ATAA ATAA ATAA ATAA
122357 TAATAATAAA
Statistics
Matches: 79, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
3 10 0.13
4 68 0.86
5 1 0.01
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:122353 original size:46 final size:47
Alignment explanation
Indices: 122250--122367 Score: 120
Period size: 46 Copynumber: 2.5 Consensus size: 47
122240 TTAACATTTA
* *
122250 TAAATAAAAAAATATAAAATATAAAATAAATAAATAAATAAATAAAAGTG
1 TAAAT-AAAAAATAT-ATATATAAAAT-AATAAATAAATAAATAAAAGAG
*
122300 TATATAAAAAATATATATATAAAAT-ATAAATAAATAAATTAACAA-AG
1 TAAATAAAAAATATATATATAAAATAATAAATAAATAAA-TAA-AAGAG
*
122347 -AAATAAATAATA-ATA-ATAAAA
1 TAAATAAAAAATATATATATAAAA
122368 CTCAAATGAG
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
44 6 0.10
45 3 0.05
46 23 0.38
47 4 0.07
48 12 0.20
49 9 0.15
50 4 0.07
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (47 bp):
TAAATAAAAAATATATATATAAAATAATAAATAAATAAATAAAAGAG
Found at i:122459 original size:38 final size:38
Alignment explanation
Indices: 122403--122485 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 38
122393 ATATTGCATG
*
122403 CATTTCATGCATTCCATGCATGCATTTTACGTAATTTT
1 CATTTCATGCATTACATGCATGCATTTTACGTAATTTT
* *
122441 CATTTTATGCATTACATGCATGCATTTTATGTAATTTT
1 CATTTCATGCATTACATGCATGCATTTTACGTAATTTT
122479 CATTTCA
1 CATTTCA
122486 AGCAATGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.47
Consensus pattern (38 bp):
CATTTCATGCATTACATGCATGCATTTTACGTAATTTT
Found at i:122541 original size:12 final size:12
Alignment explanation
Indices: 122509--122564 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
122499 TCATGCATTG
122509 CATGCATTACATTT
1 CATGCA-TAC-TTT
122523 CATGCATACTTT
1 CATGCATACTTT
* *
122535 CACGCATACCTT
1 CATGCATACTTT
**
122547 CATGCATGTTTT
1 CATGCATACTTT
122559 CATGCA
1 CATGCA
122565 AATGAAATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
12 27 0.75
13 3 0.08
14 6 0.17
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.38
Consensus pattern (12 bp):
CATGCATACTTT
Found at i:123049 original size:22 final size:23
Alignment explanation
Indices: 123001--123066 Score: 98
Period size: 22 Copynumber: 2.8 Consensus size: 23
122991 GCAAGTAGCG
123001 ACATCGAGCACCAACAGCAGCAACA
1 ACATCGAGCACCAACAGCAG--ACA
*
123026 ACATCAAGCACCAACAGCAG-CA
1 ACATCGAGCACCAACAGCAGACA
123048 ACATCGAGCACCAACAGCA
1 ACATCGAGCACCAACAGCA
123067 ACATCACCGC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
22 20 0.51
25 19 0.49
ACGTcount: A:0.44, C:0.36, G:0.15, T:0.05
Consensus pattern (23 bp):
ACATCGAGCACCAACAGCAGACA
Found at i:135613 original size:9 final size:10
Alignment explanation
Indices: 135588--135644 Score: 57
Period size: 11 Copynumber: 5.7 Consensus size: 10
135578 TATTATGCAT
*
135588 AAAAAAAAGG
1 AAAAAAAATG
135598 AGAAAAAAAGTG
1 A-AAAAAAA-TG
135610 AAAAAAAATG
1 AAAAAAAATG
135620 AAAAAATAAT-
1 AAAAAA-AATG
135630 -AAAAAAA-G
1 AAAAAAAATG
135638 AAAAAAA
1 AAAAAAA
135645 TCGAATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
8 2 0.05
9 11 0.27
10 9 0.22
11 17 0.41
12 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:137359 original size:85 final size:85
Alignment explanation
Indices: 137134--137594 Score: 464
Period size: 85 Copynumber: 5.4 Consensus size: 85
137124 CAATATGAAT
* * * ** **
137134 TTTCTTACCC-TCAGTCTGCCTGTCAGCTTTGATCCTGGAGACTACCTCATTTAAAGTCTACCTG
1 TTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTCACCTAAAGTCTGTCTG
*
137198 TCGACTTTGACCCTAAAGAC
66 TCGACTTTGACCCTAGAGAC
* * * *
137218 TTTCCTACCCCTTCAGTCTGCCTGTCAGCTTTGACTCTGAAGACTACCTCATCTAAAGTCTGTCT
1 TTTCCTA-CCCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTCACCTAAAGTCTGTCT
*
137283 GTCGACTTTGACCCTGGAGAC
65 GTCGACTTTGACCCTAGAGAC
* * *
137304 TTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCACCTAAAGTTTGTATG
1 TTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTCACCTAAAGTCTGTCTG
*
137369 TCGGCTTTGACCCTAGAGAC
66 TCGACTTTGACCCTAGAGAC
* *** * *
137389 TTTGCTACCC-TCAGTCTATTTGTCGGCTTTGACCCTAGAGACTGCCTCACCTAAAGTCTGTCTG
1 TTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTCACCTAAAGTCTGTCTG
*
137453 TC-AGCTTTGACCCTGGAGAC
66 TCGA-CTTTGACCCTAGAGAC
* * * * ** * ** * *
137473 ATTT-TTACCCTTCAATCTGCCTGTCGACTTTGACCCTAGAGACTTTCTTACCCTTTAGTTTGCC
1 -TTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTCA-CCTAAAGTCTGTC
* *
137537 TGTCGGCTTTGACCCTAAAGAC
64 TGTCGACTTTGACCCTAGAGAC
* ** ** *
137559 -TGCCTAATCTAAAGTCTTCCTGTCGGCTTTGACCCT
1 TTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCT
137595 AAAGACTTTC
Statistics
Matches: 317, Mismatches: 52, Indels: 15
0.83 0.14 0.04
Matches are distributed among these distances:
84 77 0.24
85 140 0.44
86 100 0.32
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (85 bp):
TTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTCACCTAAAGTCTGTCTG
TCGACTTTGACCCTAGAGAC
Found at i:137527 original size:212 final size:212
Alignment explanation
Indices: 137276--137684 Score: 577
Period size: 212 Copynumber: 1.9 Consensus size: 212
137266 TCATCTAAAG
* *
137276 TCTGTCTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCT
1 TCTGCCTGTCGACTTTGACCCTAGAGACTTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCT
** * * * * *
137341 GGAGACTGCCTCACCTAAAGT-TTGTATGTCGGCTTTGACCCTAGAGACTTTGCTACCCTCAGTC
66 AAAGACTGCCTAACCTAAAGTCTT-CATGTCGGCTTTGACCCTAAAGACTTTCCTACCCTCAATC
** * * * * *
137405 TATTTGTCGGCTTTGACCCTAGAGACTGCCTCACCTAAAGTCTGTCTGTCAGCTTTGACCCTGGA
130 TACCTATCGGCTTTAACCCTAGAGACTGCCACACCTAAAGTCTGCCTGTCAGCTTTGACCCTAGA
137470 GACATTTTTACCCTTCAA
195 GACATTTTTACCCTTCAA
* * *
137488 TCTGCCTGTCGACTTTGACCCTAGAGACTTTCTTACCCTTTAGTTTGCCTGTCGGCTTTGACCCT
1 TCTGCCTGTCGACTTTGACCCTAGAGACTTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCT
* * *
137553 AAAGACTGCCTAATCTAAAGTCTTCCTGTCGGCTTTGACCCTAAAGACTTTCCTACCCTCAATGT
66 AAAGACTGCCTAACCTAAAGTCTTCATGTCGGCTTTGACCCTAAAGACTTTCCTACCCTCAATCT
* * *
137618 GCCTATCGGCTTTAACCCTAGAGACTGTCACATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
131 ACCTATCGGCTTTAACCCTAGAGACTGCCACACCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
137683 AC
196 AC
137685 TTTCCTACCC
Statistics
Matches: 171, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
212 169 0.99
213 2 0.01
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.33
Consensus pattern (212 bp):
TCTGCCTGTCGACTTTGACCCTAGAGACTTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACCCT
AAAGACTGCCTAACCTAAAGTCTTCATGTCGGCTTTGACCCTAAAGACTTTCCTACCCTCAATCT
ACCTATCGGCTTTAACCCTAGAGACTGCCACACCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
ACATTTTTACCCTTCAA
Found at i:137595 original size:42 final size:42
Alignment explanation
Indices: 137146--137761 Score: 357
Period size: 42 Copynumber: 14.6 Consensus size: 42
137136 TCTTACCCTC
* * * * * **
137146 AGTCTGCCTGTCAGCTTTGATCCTGGAGACTACCTCATTTAA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTAACCTAA
* * * * * **
137188 AGTCTACCTGTCGACTTTGACCCTAAAGACTTTCCTACCCCTTC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCCTA-ACCTAA
* * * * *
137232 AGTCTGCCTGTCAGCTTTGACTCT-GAAGACTACCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTAG-AGACTGCCTAACCTAA
* * * * * **
137274 AGTCTGTCTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCCTAACCTAA
* *
137317 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCACCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTAACCTAA
* ** * *
137359 AGTTTGTATGTCGGCTTTGACCCTAGAGACTTTG-CTACCCT-C
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC--TGCCTAACCTAA
*** *
137401 AGTCTATTTGTCGGCTTTGACCCTAGAGACTGCCTCACCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTAACCTAA
* * * *** * *
137443 AGTCTGTCTGTCAGCTTTGACCCTGGAGACATTTTTACCCTTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCCTAACC-TAA
* * * * **
137487 A-TCTGCCTGTCGACTTTGACCCTAGAGACTTTCTTACCCTTT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCCTAACCTAA
* * *
137529 AGTTTGCCTGTCGGCTTTGACCCTAAAGACTGCCTAATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTAACCTAA
* * * * *
137571 AGTCTTCCTGTCGGCTTTGACCCTAAAGACTTTCCTACCCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCCTAACCTAA
* * * * *
137614 A-TGTGCCTATCGGCTTTAACCCTAGAGACTGTC-ACATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTA-ACCTAA
* * ***
137655 AGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCCT-ACCCCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCCTAACCTAA
* * * * * * * *
137697 AGTCTGCTTATCAGTTTTGACCCTAGAGA-TGTCTCATCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTAACCTAA
* *
137738 AGTTTGCCTGTTGGCTTTGACCCT
1 AGTCTGCCTGTCGGCTTTGACCCT
137762 GAAGACTTTT
Statistics
Matches: 435, Mismatches: 121, Indels: 37
0.73 0.20 0.06
Matches are distributed among these distances:
40 6 0.01
41 32 0.07
42 247 0.57
43 120 0.28
44 30 0.07
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (42 bp):
AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTAACCTAA
Found at i:138299 original size:12 final size:12
Alignment explanation
Indices: 138282--138358 Score: 65
Period size: 12 Copynumber: 6.8 Consensus size: 12
138272 ATTTAACATT
138282 TATAAATAAAAA
1 TATAAATAAAAA
*
138294 TAT-AA-AATAA
1 TATAAATAAAAA
*
138304 -ATAAATAAAAG
1 TATAAATAAAAA
*
138315 TATATATAAAAA
1 TATAAATAAAAA
*
138327 TATATAT-AAAA
1 TATAAATAAAAA
*
138338 TATTAATAAATAA
1 TATAAATAAA-AA
138351 -ATAAATAA
1 TATAAATAA
138359 TAAACTCGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
9 2 0.04
10 6 0.12
11 14 0.27
12 28 0.54
13 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (12 bp):
TATAAATAAAAA
Found at i:138309 original size:21 final size:21
Alignment explanation
Indices: 138283--138360 Score: 88
Period size: 21 Copynumber: 3.6 Consensus size: 21
138273 TTTAACATTT
*
138283 ATAAATAAAAATATAAAATAA
1 ATAAATAAAAATATATAATAA
138304 ATAAATAAAAGTATATATAA-AA
1 ATAAATAAAA--ATATATAATAA
*
138326 ATATATATAAAATAT-TAATAA
1 ATAAATA-AAAATATATAATAA
138347 ATAAATAAATAATA
1 ATAAATAAA-AATA
138361 AACTCGAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.10
21 26 0.53
22 8 0.16
23 10 0.20
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (21 bp):
ATAAATAAAAATATATAATAA
Found at i:138448 original size:38 final size:38
Alignment explanation
Indices: 138397--138469 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
138387 AATATTGCAT
*
138397 GCATTTCATGCATGCATTTTACATAATTTTCATTTTAG
1 GCATTACATGCATGCATTTTACATAATTTTCATTTTAG
*
138435 GCATTACATGCATGCATTTTACGTAATTTTCATTT
1 GCATTACATGCATGCATTTTACATAATTTTCATTT
138470 CATGCAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (38 bp):
GCATTACATGCATGCATTTTACATAATTTTCATTTTAG
Found at i:139019 original size:19 final size:19
Alignment explanation
Indices: 138995--139059 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
138985 AGCAAGCAAG
138995 CAGCAACATCGAGCACCAA
1 CAGCAACATCGAGCACCAA
* * *
139014 CAGCAACAAC-A-CAACAG
1 CAGCAACATCGAGCACCAA
139031 CAGCAACATCGAGCACCAA
1 CAGCAACATCGAGCACCAA
139050 CAGCAACATC
1 CAGCAACATC
139060 ACAGCAGCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 13 0.34
18 2 0.05
19 23 0.61
ACGTcount: A:0.45, C:0.37, G:0.14, T:0.05
Consensus pattern (19 bp):
CAGCAACATCGAGCACCAA
Found at i:139039 original size:36 final size:36
Alignment explanation
Indices: 138993--139073 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
138983 GAAGCAAGCA
138993 AGCAGCAACATCGAGCACCAACAGCAACAACACAAC
1 AGCAGCAACATCGAGCACCAACAGCAACAACACAAC
* *
139029 AGCAGCAACATCGAGCACCAACAGCAACATCACAGC
1 AGCAGCAACATCGAGCACCAACAGCAACAACACAAC
*
139065 AGCAACAAC
1 AGCAGCAAC
139074 GACAGCAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.46, C:0.36, G:0.15, T:0.04
Consensus pattern (36 bp):
AGCAGCAACATCGAGCACCAACAGCAACAACACAAC
Found at i:141234 original size:2 final size:2
Alignment explanation
Indices: 141227--141264 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
141217 TGAAAAACAC
141227 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
141265 CACATCAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:141741 original size:18 final size:19
Alignment explanation
Indices: 141714--141749 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
141704 GTTGGGACCT
141714 TGTATCGATACAT-TGAAA
1 TGTATCGATACATCTGAAA
*
141732 TGTATTGATACATCTGAA
1 TGTATCGATACATCTGAA
141750 CAGAAATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATCTGAAA
Found at i:153646 original size:52 final size:51
Alignment explanation
Indices: 153568--153716 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
153558 CGAAATATGA
153568 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
153620 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
153672 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
153717 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:153723 original size:13 final size:13
Alignment explanation
Indices: 153705--153729 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
153695 CAAAGATCAG
153705 TGTATCGATACAA
1 TGTATCGATACAA
153718 TGTATCGATACA
1 TGTATCGATACA
153730 TTTAAGTGAT
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:153807 original size:33 final size:33
Alignment explanation
Indices: 153770--153836 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
153760 AGTAGCTTAA
153770 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
153803 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
153836 A
1 A
153837 AATCGTTGAC
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:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:153810 original size:13 final size:13
Alignment explanation
Indices: 153792--153816 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
153782 CAAAAAAATA
153792 TGTATCGATACAT
1 TGTATCGATACAT
153805 TGTATCGATACA
1 TGTATCGATACA
153817 ACACTTTATG
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:154702 original size:55 final size:52
Alignment explanation
Indices: 154602--155204 Score: 440
Period size: 43 Copynumber: 12.6 Consensus size: 52
154592 GAAAAGTGAT
* * * * * **
154602 AAAGATGCCAATATGTTGATTCACGGCCA-ATGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCT-ACATTGAACTTAAAGATG-G-A
* *
154656 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
154709 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
154752 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
154795 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
154845 -AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
154888 AAA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
154937 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
154980 AAA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
155029 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
155072 AAA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
155120 AAAGGTGCCAATGTGCTGAGTCAAAGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
155172 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
155205 TATTAGGCTT
Statistics
Matches: 468, Mismatches: 40, Indels: 84
0.79 0.07 0.14
Matches are distributed among these distances:
43 186 0.40
44 10 0.02
46 1 0.00
48 10 0.02
49 151 0.32
51 1 0.00
52 62 0.13
53 6 0.01
54 5 0.01
55 35 0.07
56 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:154756 original size:22 final size:22
Alignment explanation
Indices: 154731--154799 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
154721 ATGCTGATTC
154731 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
154753 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
154774 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
154796 AAGG
1 AAGG
154800 TGCCAATGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:154770 original size:43 final size:43
Alignment explanation
Indices: 154709--155166 Score: 547
Period size: 43 Copynumber: 10.1 Consensus size: 43
154699 TAAAGATGGA
* *
154709 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
154752 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
154795 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
154838 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -AA-A-G--G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
154887 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
154930 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
154979 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
155022 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
155071 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
* *
155120 AAAGGTGCCAATGTGCTGAGTCAAAGCCAGCTACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
155163 AAAG
1 AAAG
155167 ATGGAAAAGG
Statistics
Matches: 363, Mismatches: 28, Indels: 48
0.83 0.06 0.11
Matches are distributed among these distances:
43 198 0.55
44 4 0.01
45 3 0.01
46 1 0.00
47 3 0.01
48 4 0.01
49 150 0.41
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:154777 original size:21 final size:21
Alignment explanation
Indices: 154753--154820 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
154743 ATTGGACTTA
154753 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
* * *
154774 AAGGCCAGCTATAT-TG--GACTTA
1 AAGG--TGCCA-ATGTGCTGA-TTC
154796 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
154817 AAGG
1 AAGG
154821 CCAGCTACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATGTGCTGATTC
Found at i:154804 original size:24 final size:24
Alignment explanation
Indices: 154734--154804 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
154724 CTGATTCAAG
154734 GCCAGCTATATTGGACTTAAAGGT
1 GCCAGCTATATTGGACTTAAAGGT
* * ** *
154758 GCCA-ATGTGCT-GA-TTCAA-G-
1 GCCAGCTATATTGGACTTAAAGGT
154777 GCCAGCTATATTGGACTTAAAGGT
1 GCCAGCTATATTGGACTTAAAGGT
154801 GCCA
1 GCCA
154805 ATGTGCTGAT
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.19
22 6 0.19
23 4 0.12
24 8 0.25
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (24 bp):
GCCAGCTATATTGGACTTAAAGGT
Found at i:154895 original size:92 final size:92
Alignment explanation
Indices: 154708--155165 Score: 757
Period size: 92 Copynumber: 5.0 Consensus size: 92
154698 TTAAAGATGG
* * *
154708 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTG
1 AAAA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
*
154767 CTGATTCAAGGCCAGCTATATTGGACTT
65 CTGATTCAAGGCCAGCGATATTGGACTT
* *
154795 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
154860 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
154887 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
154952 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
154979 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
155044 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
155071 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGC
1 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* * * *
155136 TGAGTCAAAGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
155163 AAA
1 AAA
155166 GATGGAAAAG
Statistics
Matches: 351, Mismatches: 14, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
86 37 0.11
87 3 0.01
90 1 0.00
92 310 0.88
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (92 bp):
AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:155258 original size:33 final size:35
Alignment explanation
Indices: 155215--155284 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
155205 TATTAGGCTT
155215 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
155249 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
155283 AG
1 AG
155285 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:155398 original size:70 final size:70
Alignment explanation
Indices: 155289--156112 Score: 860
Period size: 70 Copynumber: 11.7 Consensus size: 70
155279 AGGAAGGGAG
* * *
155289 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCATGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
155352 AAGAA
66 AAGAA
* *
155357 AAAAGTGCCATGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
155422 ACAGAA
66 A-AGAA
* * ** **
155428 AAAGGTGCCACGGAGTTGTGAGCTTTAAAAAGGGAAAAAGAGTGCCACAAAGTTGTAGGTGCCAT
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGT-GG-GCTTT
* **
155493 -AGAGTT
64 AAAAGAA
*** *** * * * **** **
155499 GTGGGCTTTAAAAGGAAAAGGTGCCACGGAG-TTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCAC
1 AAAGG--TGCCACGG---AGTTG---TGG-GCTT-T--GAAAAGGGAA-----AAAGAGTGCCAC
** *
155563 AAAGTTGTGGGCTTTAAACGAA
49 GGAGTTGTGGGCTTTAAAAGAA
*
155585 AAAGGTGCCACGGAGTTGTGGGCTTT--------AAAAAGAGTGCCACGGAGTCGTGGGCTTTGA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A
155642 AAAGAA
65 AAAGAA
*
155648 GAAGGTGCCACGGAGTTGTGGGCTTT--AAA-GG-AAAAG-GTGCCACGGAGTTGTGGGCTTTGA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT--
155708 AAAAGGAA
64 AAAA-GAA
* * * *
155716 AAAGAATGCCACAGAGTTGTGGGCTTT-AAAAAGAAAAAAG-GTGCCACGGAGTTGTGGGCTTTA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
155779 AAAGAA
65 AAAGAA
* *
155785 AAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
155850 AAGAA
66 AAGAA
* *
155855 AAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
155920 AAGAA
66 AAGAA
*
155925 AAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCC-CGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
155989 AAGAA
66 AAGAA
*
155994 AAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A
156059 AAAGAA
65 AAAGAA
* *
156065 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCAC
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCAC
156113 AAAGTTGTAG
Statistics
Matches: 649, Mismatches: 67, Indels: 77
0.82 0.08 0.10
Matches are distributed among these distances:
62 24 0.04
63 31 0.05
66 21 0.03
67 11 0.02
68 46 0.07
69 108 0.17
70 205 0.32
71 111 0.17
72 30 0.05
73 7 0.01
76 4 0.01
77 2 0.00
78 4 0.01
79 3 0.00
80 2 0.00
81 4 0.01
82 3 0.00
84 4 0.01
85 3 0.00
86 6 0.01
87 20 0.03
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.20
Consensus pattern (70 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
AAGAA
Found at i:155410 original size:37 final size:35
Alignment explanation
Indices: 155269--156112 Score: 859
Period size: 37 Copynumber: 23.9 Consensus size: 35
155259 CACCGACTTG
* *
155269 TGTGGGCTTTAGGAAGGGAGAAAGA-TGCCACGGAGT
1 TGTGGGCTTTA--AAAGGAAAAAGAGTGCCACGGAGT
* *
155305 TGTGGAC-TTAAAAGGGAAAAAGAGTGCCATGGAGT
1 TGTGGGCTTTAAAA-GGAAAAAGAGTGCCACGGAGT
*
155340 TGTGGGCTTTAAAA-GAAAAA-AGTGCCATGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
155373 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
155410 TGTGGGCTTTAAACA-GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGT
* **
155444 TGTGAGCTTTAAAAAGGGAAAAAGAGTGCCACAAAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
** ** *
155481 TGTAGGTGCCATAGAGTTGTGGGCTTTAAAAGGAAAAGGTGCCACGGAGT
1 TGT-GG-GCTTTA-A----AAGG----AAAA---AGA-GTGCCACGGAGT
**
155531 TGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGT
1 TGTGGGCTTT-AAAAGG-AAAAAGAGTGCCACGGAGT
*
155568 TGTGGGCTTT-AAACGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
155601 TGTGGGCTTT------AAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
155630 CGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
155664 TGTGGGCTTT-AAAGG-AAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
155696 TGTGGGCTTTGAAAAAGGAAAAAGAATGCCACAGAGT
1 TGTGGGCTTT--AAAAGGAAAAAGAGTGCCACGGAGT
*
155733 TGTGGGCTTTAAAAAGAAAAA-AGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGA-GTGCCACGGAGT
*
155768 TGTGGGCTTTAAAA-GAAAAAG-GTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
155801 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
*
155838 TGTGGGCTTTAAAA-GAAAAAG-GTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
155871 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
*
155908 TGTGGGCTTTAAAA-GAAAAAG-GTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
155941 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCC-CGGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
*
155977 TGTGGGCTTTAAAA-GAAAAAG-GTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
156010 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
*
156047 TGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
156081 TGTGGGCTTTAAAAAGGGAAAAAGAGTGCCAC
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCAC
156113 AAAGTTGTAG
Statistics
Matches: 701, Mismatches: 44, Indels: 125
0.81 0.05 0.14
Matches are distributed among these distances:
28 6 0.01
29 21 0.03
32 34 0.05
33 133 0.19
34 130 0.19
35 87 0.12
36 90 0.13
37 158 0.23
38 4 0.01
39 4 0.01
41 4 0.01
42 2 0.00
44 2 0.00
46 4 0.01
48 4 0.01
49 5 0.01
50 13 0.02
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (35 bp):
TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
Found at i:155531 original size:33 final size:34
Alignment explanation
Indices: 155484--156120 Score: 730
Period size: 33 Copynumber: 18.5 Consensus size: 34
155474 ACAAAGTTGT
*
155484 AGGTGCCATAGAGTTGTGGGCTTT-AAAAGGAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAA
*
155517 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGG--AAA
* * *
155553 AGAGTGCCACAAAGTTGTGGGCTTT-AAACGAAAA
1 AG-GTGCCACAGAGTTGTGGGCTTTGAAAAGGAAA
* *
155587 AGGTGCCACGGAGTTGTGGGCTTT--AAA--AAG
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAA
* *
155617 A-GTGCCACGGAGTCGTGGGCTTTGAAAA-GAAGA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAA-A
*
155650 AGGTGCCACGGAGTTGTGGGCTTT--AAAGGAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAA
*
155682 AGGTGCCACGGAGTTGTGGGCTTTGAAAAAGGAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTG-AAAAGG-AAA
* * *
155718 AGAATGCCACAGAGTTGTGGGCTTTAAAAAGAAAAA
1 AG-GTGCCACAGAGTTGTGGGCTTTGAAAAG-GAAA
* *
155754 AGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAA
155787 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAA-GG-AAA
*
155823 AGAGTGCCACAGAGTTGTGGGCTTT-AAAAGAAAA
1 AG-GTGCCACAGAGTTGTGGGCTTTGAAAAGGAAA
155857 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAA-GG-AAA
*
155893 AGAGTGCCACAGAGTTGTGGGCTTT-AAAAGAAAA
1 AG-GTGCCACAGAGTTGTGGGCTTTGAAAAGGAAA
155927 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAA-GG-AAA
* *
155963 AGAGTGCC-CGGAGTTGTGGGCTTT-AAAAGAAAA
1 AG-GTGCCACAGAGTTGTGGGCTTTGAAAAGGAAA
155996 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAA-GG-AAA
*
156032 AGAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGA
1 AG-GTGCCACAGAGTTGTGGGCTTTGAAAAGGAA-A
* *
156067 AGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAA-GG-AAA
*
156103 AGAGTGCCACAAAGTTGT
1 AG-GTGCCACAGAGTTGT
156121 AGGTGCCACA
Statistics
Matches: 533, Mismatches: 33, Indels: 72
0.84 0.05 0.11
Matches are distributed among these distances:
29 21 0.04
30 3 0.01
31 3 0.01
32 37 0.07
33 137 0.26
34 92 0.17
35 39 0.07
36 71 0.13
37 130 0.24
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (34 bp):
AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAA
Found at i:155546 original size:87 final size:88
Alignment explanation
Indices: 155406--155570 Score: 287
Period size: 87 Copynumber: 1.9 Consensus size: 88
155396 GAGTGCCACG
*
155406 GAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGAGCTTTAAAAAGGGAAAAAGAGT
1 GAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGAGCTTTAAAAAGGAAAAAAGAGT
155471 GCCACAAAGTTGTAGGTGCCATA
66 GCCACAAAGTTGTAGGTGCCATA
* * *
155494 GAGTTGTGGGCTTTAAA-AGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGT
1 GAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGAGCTTTAAAAAGGAAAAAAGAGT
155558 GCCACAAAGTTGT
66 GCCACAAAGTTGT
155571 GGGCTTTAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
87 56 0.77
88 17 0.23
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.22
Consensus pattern (88 bp):
GAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGAGCTTTAAAAAGGAAAAAAGAGT
GCCACAAAGTTGTAGGTGCCATA
Found at i:155914 original size:140 final size:139
Alignment explanation
Indices: 155494--156213 Score: 939
Period size: 140 Copynumber: 5.4 Consensus size: 139
155484 AGGTGCCATA
* *
155494 GAGTTGTGGGCTTTAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTG
1 GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
* * *
155559 CCACAAAGTTGTGGGCTTTAAACGAAAAAGGTGCCACGGAGTTGTGGGCTTT-------AAAAAG
66 CCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAGGGAAAAAG
155617 AGTGCCACG
131 AGTGCCACG
* *
155626 GAGTCGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT--AAA-GG-AAAAG-GT
1 GAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGT
* * * *
155686 GCCACGGAGTTGTGGGCTTTGAAAAAGGAAAAAGAATGCCACAGAGTTGTGGGCTTTAAAAAGAA
65 GCCACAGAGTTGTGGGCTTT--AAAA-GAAAAAG-GTGCCACAGAGTTGTGGGCTTTAAAAGGGA
155751 AAAAG-GTGCCACG
126 AAAAGAGTGCCACG
*
155764 GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
1 GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
155829 CCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAA
66 CCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTT-AAAAGGGAAAAA
*
155894 GAGTGCCACA
130 GAGTGCCACG
*
155904 GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
1 GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
*
155969 CC-CGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAA
66 CCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTT-AAAAGGGAAAAA
156033 GAGTGCCACG
130 GAGTGCCACG
* *
156043 GAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGT
1 GAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGT
*
156108 GCCACAAAG-T-T--G---T---------AGGTGCCACAGAGTTGTGGGCTTTAAAA--GAAAAA
65 GCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAGGGAAAAA
*
156155 G-GTGCCATG
130 GAGTGCCACG
* *
156164 GAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGACTTTGA
1 GAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
156214 GAAGAGATTG
Statistics
Matches: 540, Mismatches: 27, Indels: 53
0.87 0.04 0.09
Matches are distributed among these distances:
121 55 0.10
122 7 0.01
124 4 0.01
125 24 0.04
128 20 0.04
129 5 0.01
130 4 0.01
131 10 0.02
132 33 0.06
133 31 0.06
134 1 0.00
137 32 0.06
138 42 0.08
139 112 0.21
140 131 0.24
141 8 0.01
142 21 0.04
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (139 bp):
GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
CCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAGGGAAAAAG
AGTGCCACG
Done.