Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008142.1 Hibiscus syriacus cultivar Beakdansim tig00110704_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 459836
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 2 of 2
Found at i:306116 original size:132 final size:132
Alignment explanation
Indices: 305975--306537 Score: 876
Period size: 132 Copynumber: 4.3 Consensus size: 132
305965 TGGAGATGAG
* * *
305975 AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAGCTAAGAAGAAAGGGAGAGCCGATCATGG
1 AAGAATAAAGAAAAAGAGAGCGACGAGGATGAAAAAACTAAGAAGAAAGGGAGAGCCGGTCATGG
* * *
306040 AAAGATTAAAGAAAAAGAGAGTGAAGATGACGAAAAGTTTAAAAAGAGAGAGAAAGCCGATCATA
66 AAAGATTAAAGAAAAAGAGAGCGAAGATGACGAAAAGTCTAAAAAGAAAGAGAAAGCCGATCATA
306105 GA
131 GA
* * *
306107 AAGGATAAAGAAAAAGAGAGCGACGAGGATGAAAAAACTAAGAAGAATGGGAGAGCCGGTCACGG
1 AAGAATAAAGAAAAAGAGAGCGACGAGGATGAAAAAACTAAGAAGAAAGGGAGAGCCGGTCATGG
* * * * *
306172 TAAGATTAAAGAAAAAAATAGCGAAGATGATGAAAAGTCTAAAACGAAAGAGAAAGCCGATCATA
66 AAAGATTAAAGAAAAAGAGAGCGAAGATGACGAAAAGTCTAAAAAGAAAGAGAAAGCCGATCATA
*
306237 TA
131 GA
* *
306239 AA-AGATAAAGAAAAAGAGATCGACGAGGATGAAAAAACTAAGAAAAAAGGGAGAGCCGGTCATG
1 AAGA-ATAAAGAAAAAGAGAGCGACGAGGATGAAAAAACTAAGAAGAAAGGGAGAGCCGGTCATG
306303 GAAAGATTAAAGAAAAAGAGAGCGAAGATGACGAAAAGTCTAAAAAGAAAGAGAAAGCCGATCAT
65 GAAAGATTAAAGAAAAAGAGAGCGAAGATGACGAAAAGTCTAAAAAGAAAGAGAAAGCCGATCAT
*
306368 AAA
130 AGA
* * * * *
306371 AAGAATAAAGAAATAGAGAGCGACGAGGATGAAAAAGCTAAGAAGAAATGGACAGTCGGTCATGG
1 AAGAATAAAGAAAAAGAGAGCGACGAGGATGAAAAAACTAAGAAGAAAGGGAGAGCCGGTCATGG
306436 AAAGATTAAAGAAAAAGAGAGCGAAGATGACGAAAAGTCTAAAAAGAAAGAGAAAGCCGATCATA
66 AAAGATTAAAGAAAAAGAGAGCGAAGATGACGAAAAGTCTAAAAAGAAAGAGAAAGCCGATCATA
306501 GA
131 GA
* * *
306503 AAGAATAAAGAAAAAGAGAACGACAAAGATGAAAA
1 AAGAATAAAGAAAAAGAGAGCGACGAGGATGAAAA
306538 GAGTAAAGAA
Statistics
Matches: 391, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
132 390 1.00
133 1 0.00
ACGTcount: A:0.54, C:0.09, G:0.27, T:0.11
Consensus pattern (132 bp):
AAGAATAAAGAAAAAGAGAGCGACGAGGATGAAAAAACTAAGAAGAAAGGGAGAGCCGGTCATGG
AAAGATTAAAGAAAAAGAGAGCGAAGATGACGAAAAGTCTAAAAAGAAAGAGAAAGCCGATCATA
GA
Found at i:306519 original size:33 final size:33
Alignment explanation
Indices: 306218--306522 Score: 82
Period size: 33 Copynumber: 9.2 Consensus size: 33
306208 GTCTAAAACG
*
306218 AAAGAGAAAGCCGATCATATAAA-AGATAAAGAA
1 AAAGAGAAAGCCGATCATAGAAAGA-ATAAAGAA
** * ** *
306251 AAAGAGATCGACGAGGAT-GAAAAAACT-AAGAAA
1 AAAGAGAAAGCCGATCATAGAAAGAA-TAAAG-AA
* * * * *
306284 AAAGGGAGAGCCGGTCATGGAAAGATTAAAGAA
1 AAAGAGAAAGCCGATCATAGAAAGAATAAAGAA
** **
306317 AAAGAG--AG-CGAAGATGACGAAAAGTCTAAA-AA
1 AAAGAGAAAGCCGATCAT-A-G-AAAGAATAAAGAA
*
306349 GAAAGAGAAAGCCGATCATAAAAAGAATAAAGAA
1 -AAAGAGAAAGCCGATCATAGAAAGAATAAAGAA
* ** * **
306383 ATAGAGAGCGACGAGGAT-GAAA-AAGCT-AAGAA
1 AAAGAGAAAGCCGATCATAGAAAGAA--TAAAGAA
* * * * *
306415 GAAATG-GACAGTCGGTCATGGAAAGATTAAAGAA
1 -AAA-GAGAAAGCCGATCATAGAAAGAATAAAGAA
** **
306449 AAAGAG--AG-CGAAGATGACGAAAAGTCTAAA-AA
1 AAAGAGAAAGCCGATCAT-A-G-AAAGAATAAAGAA
306481 GAAAGAGAAAGCCGATCATAGAAAGAATAAAGAA
1 -AAAGAGAAAGCCGATCATAGAAAGAATAAAGAA
306515 AAAGAGAA
1 AAAGAGAA
306523 CGACAAAGAT
Statistics
Matches: 191, Mismatches: 52, Indels: 58
0.63 0.17 0.19
Matches are distributed among these distances:
30 8 0.04
31 6 0.03
32 22 0.12
33 115 0.60
34 23 0.12
35 7 0.04
36 10 0.05
ACGTcount: A:0.55, C:0.09, G:0.26, T:0.10
Consensus pattern (33 bp):
AAAGAGAAAGCCGATCATAGAAAGAATAAAGAA
Found at i:306539 original size:33 final size:33
Alignment explanation
Indices: 306502--306587 Score: 109
Period size: 33 Copynumber: 2.5 Consensus size: 33
306492 CCGATCATAG
306502 AAAGAATAAAGAAAAAGAGAACGACAAAGATGA
1 AAAGAATAAAGAAAAAGAGAACGACAAAGATGA
* * * *
306535 AAAGAGTAAAGAAAAAGAGGACGACCATGATGA
1 AAAGAATAAAGAAAAAGAGAACGACAAAGATGA
*
306568 AAAGGATAAAAAGAAAAAGA
1 AAA-GA-ATAAAGAAAAAGA
306588 AAGCCGGACA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 32 0.71
34 2 0.04
35 11 0.24
ACGTcount: A:0.64, C:0.06, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAGAATAAAGAAAAAGAGAACGACAAAGATGA
Found at i:306539 original size:99 final size:99
Alignment explanation
Indices: 306436--306619 Score: 241
Period size: 99 Copynumber: 1.9 Consensus size: 99
306426 TCGGTCATGG
* * ** *
306436 AAAGATTAAAGAAAAAGA-GAGCGAAGATGACGAAAAGTCTAAAAAGAAAGAGAAAGCC-GATCA
1 AAAGAGTAAAGAAAAAGAGGA-CGAACATGACGAAAAGGATAAAAAGAAAAAGAAAGCCGGA-CA
306499 TAG-AAAGAATAAAGAAA-AAGAGAACGACAAAGATGA
64 T-GCAAAGAAT-AAGAAAGAAGAGAACGACAAAGATGA
* *
306535 AAAGAGTAAAGAAAAAGAGGACGACCATGATGAAAAGGATAAAAAGAAAAAGAAAGCCGGACATG
1 AAAGAGTAAAGAAAAAGAGGACGAACATGACGAAAAGGATAAAAAGAAAAAGAAAGCCGGACATG
306600 CAAAGAATAAGAAAGAAGAG
66 CAAAGAATAAGAAAGAAGAG
306620 GGAGCCAGTC
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
98 7 0.09
99 63 0.85
100 4 0.05
ACGTcount: A:0.59, C:0.08, G:0.24, T:0.08
Consensus pattern (99 bp):
AAAGAGTAAAGAAAAAGAGGACGAACATGACGAAAAGGATAAAAAGAAAAAGAAAGCCGGACATG
CAAAGAATAAGAAAGAAGAGAACGACAAAGATGA
Found at i:308916 original size:66 final size:66
Alignment explanation
Indices: 308811--309414 Score: 545
Period size: 66 Copynumber: 9.2 Consensus size: 66
308801 GGATAGTAAC
* * * * * * *
308811 GATGATGAAAAAGCTAAAAAGAAAAAGAGAGTC-AGTTATGAAAAGGGTAAAGAAAACGAGAGTG
1 GATGATGAAAAAGCTAAAAAGAAAGAGAAAGCCGA-TCATGAAAAGGATAAAGAAAAAGAGAGCG
*
308875 AT
65 AA
** * * * *
308877 GATGATGAAAAAATTAAAAAGAAAGGGAAAGCCGATTATGGAAA-GATTAAAGAAAAAAAGAGCG
1 GATGATGAAAAAGCTAAAAAGAAAGAGAAAGCCGATCATGAAAAGGA-TAAAGAAAAAGAGAGCG
308941 AA
65 AA
* * *
308943 GATGACG-AAAAGTCTAAAAAGAGAA-AGAAAGTCGAACATAGAAAA-GATAAAGAAAAAGAGAG
1 GATGATGAAAAAG-CTAAAAAGA-AAGAGAAAGCCGATCAT-GAAAAGGATAAAGAAAAAGAGAG
309005 CGACA
63 CGA-A
* * * * * *
309010 -AAGATGAAAAAGCTAAGAAGAAAGGGAGAGCCGGTCATGGAAA-GATTAAAGAAAAAGAGAGCG
1 GATGATGAAAAAGCTAAAAAGAAAGAGAAAGCCGATCATGAAAAGGA-TAAAGAAAAAGAGAGCG
309073 AA
65 AA
* *
309075 GATGATG-AAAAGTCTAAAAAGAGAGAGAAAGCCGATCATAGAAAA-GATAAAGAAAAAGATAGC
1 GATGATGAAAAAG-CTAAAAAGAAAGAGAAAGCCGATCAT-GAAAAGGATAAAGAAAAAGAGAGC
309138 -AA
64 GAA
* * * * * *
309140 CGAGGATGAAAAAGCTAAGAAGAAAGAGAGATCCGATCATGGAAA-GATTAAAGAAAAAGATAGC
1 -GATGATGAAAAAGCTAAAAAGAAAGAGAAAGCCGATCATGAAAAGGA-TAAAGAAAAAGAGAGC
309204 GAA
64 GAA
* * *
309207 GATGACG-AAAAGACTAAAAAGAGAGAGAAATCCGATCATAGAAAA-GATAAAGAAAAAGAGAGC
1 GATGATGAAAAAG-CTAAAAAGAAAGAGAAAGCCGATCAT-GAAAAGGATAAAGAAAAAGAGAGC
*
309270 GAT
64 GAA
* * * * * * *
309273 GATGATGAAAAAGCTAAGAAGAAAGGGAGATCCGGTCATGGAAA-GATTAACGAAAAAGAGAGCG
1 GATGATGAAAAAGCTAAAAAGAAAGAGAAAGCCGATCATGAAAAGGA-TAAAGAAAAAGAGAGCG
309337 AA
65 AA
* * * *
309339 GATGACG-AAAAGTCTAAAAAGAGAGTGAAAGCCGATCATAAAAAGGATAAAGAAAAAGAGAGCG
1 GATGATGAAAAAG-CTAAAAAGAAAGAGAAAGCCGATCATGAAAAGGATAAAGAAAAAGAGAGCG
*
309403 AC
65 AA
309405 GATGATGAAA
1 GATGATGAAA
309415 GTGAGAGCGA
Statistics
Matches: 442, Mismatches: 73, Indels: 45
0.79 0.13 0.08
Matches are distributed among these distances:
65 43 0.10
66 356 0.81
67 43 0.10
ACGTcount: A:0.54, C:0.08, G:0.26, T:0.12
Consensus pattern (66 bp):
GATGATGAAAAAGCTAAAAAGAAAGAGAAAGCCGATCATGAAAAGGATAAAGAAAAAGAGAGCGA
A
Found at i:308928 original size:132 final size:133
Alignment explanation
Indices: 308787--309414 Score: 788
Period size: 132 Copynumber: 4.8 Consensus size: 133
308777 CGGCGATGAG
* * * * * * *
308787 AAGACTAAAGAAAAGGATAG-TAACGATGATGAAAAAG-CTAAAAAGAAAAAGAGAGTCAG-TTA
1 AAGATTAAAGAAAAAGATAGCGAA-GATGATG-AAAAGTCTAAAAAGAGAAAGAAAGTCCGATCA
* * * * ** * *
308849 T-GAAAAGGGTAAAGAAAACGAGAGTGATGATGATGAAAAAATTAAAAAGAAAGGGAAAGCCGAT
64 TAGAAAA-GATAAAGAAAAAGAGAGCGACGATGATGAAAAAGCTAAGAAGAAAGGGAGAGCCGAT
*
308913 TATGGA
128 CATGGA
* * * *
308919 AAGATTAAAGAAAAAAAGAGCGAAGATGACGAAAAGTCTAAAAAGAGAAAGAAAGT-CGAACATA
1 AAGATTAAAGAAAAAGATAGCGAAGATGATGAAAAGTCTAAAAAGAGAAAGAAAGTCCGATCATA
* * *
308983 GAAAAGATAAAGAAAAAGAGAGCGACAAAGATGAAAAAGCTAAGAAGAAAGGGAGAGCCGGTCAT
66 GAAAAGATAAAGAAAAAGAGAGCGACGATGATGAAAAAGCTAAGAAGAAAGGGAGAGCCGATCAT
309048 GGA
131 GGA
* *
309051 AAGATTAAAGAAAAAGAGAGCGAAGATGATGAAAAGTCTAAAAAGAGAGAGAAAG-CCGATCATA
1 AAGATTAAAGAAAAAGATAGCGAAGATGATGAAAAGTCTAAAAAGAGAAAGAAAGTCCGATCATA
* * * * *
309115 GAAAAGATAAAGAAAAAGATAGCAACGAGGATGAAAAAGCTAAGAAGAAAGAGAGATCCGATCAT
66 GAAAAGATAAAGAAAAAGAGAGCGACGATGATGAAAAAGCTAAGAAGAAAGGGAGAGCCGATCAT
309180 GGA
131 GGA
* * *
309183 AAGATTAAAGAAAAAGATAGCGAAGATGACGAAAAGACTAAAAAGAGAGAGAAA-TCCGATCATA
1 AAGATTAAAGAAAAAGATAGCGAAGATGATGAAAAGTCTAAAAAGAGAAAGAAAGTCCGATCATA
* * *
309247 GAAAAGATAAAGAAAAAGAGAGCGATGATGATGAAAAAGCTAAGAAGAAAGGGAGATCCGGTCAT
66 GAAAAGATAAAGAAAAAGAGAGCGACGATGATGAAAAAGCTAAGAAGAAAGGGAGAGCCGATCAT
309312 GGA
131 GGA
* * * **
309315 AAGATTAACGAAAAAGAGAGCGAAGATGACGAAAAGTCTAAAAAGAGAGTGAAAG-CCGATCATA
1 AAGATTAAAGAAAAAGATAGCGAAGATGATGAAAAGTCTAAAAAGAGAAAGAAAGTCCGATCATA
309379 -AAAAGGATAAAGAAAAAGAGAGCGACGATGATGAAA
66 GAAAA-GATAAAGAAAAAGAGAGCGACGATGATGAAA
309415 GTGAGAGCGA
Statistics
Matches: 440, Mismatches: 48, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
131 10 0.02
132 423 0.96
133 7 0.02
ACGTcount: A:0.54, C:0.08, G:0.26, T:0.12
Consensus pattern (133 bp):
AAGATTAAAGAAAAAGATAGCGAAGATGATGAAAAGTCTAAAAAGAGAAAGAAAGTCCGATCATA
GAAAAGATAAAGAAAAAGAGAGCGACGATGATGAAAAAGCTAAGAAGAAAGGGAGAGCCGATCAT
GGA
Found at i:309199 original size:33 final size:34
Alignment explanation
Indices: 309024--309334 Score: 105
Period size: 33 Copynumber: 9.4 Consensus size: 34
309014 TGAAAAAGCT
* * * *
309024 AAGAAGAAAGGGAGAGCCGGTCATGGAAAGATTA
1 AAGAAGAAAGAGAGATCCGATCATGGAAAGACTA
**** * * *
309058 AAGAA-AAAGAGAGCGAAGATGATGAAAAGTCTA
1 AAGAAGAAAGAGAGATCCGATCATGGAAAGACTA
* * * *
309091 AA-AAGAGAGAGAAAGCCGATCATAGAAAAGA-TA
1 AAGAAGAAAGAGAGATCCGATCAT-GGAAAGACTA
* * ** *
309124 AAGAA-AAAGATAGCA-ACGAGGAT-GAAAAAGCT-
1 AAGAAGAAAGAGAG-ATCCGATCATGGAAAGA-CTA
*
309156 AAGAAGAAAGAGAGATCCGATCATGGAAAGATTA
1 AAGAAGAAAGAGAGATCCGATCATGGAAAGACTA
* **** * * *
309190 AAGAA-AAAGATAGCGAAGATGACGAAAAGACTA
1 AAGAAGAAAGAGAGATCCGATCATGGAAAGACTA
* * *
309223 AA-AAGAGAGAGAAATCCGATCATAGAAAAGA-TA
1 AAGAAGAAAGAGAGATCCGATCAT-GGAAAGACTA
* *
309256 AAGAA-AAAGAGAG---CGATGATGATGAAAAAGCT-
1 AAGAAGAAAGAGAGATCCGATCATG--GAAAGA-CTA
* * *
309288 AAGAAGAAAGGGAGATCCGGTCATGGAAAGATTA
1 AAGAAGAAAGAGAGATCCGATCATGGAAAGACTA
*
309322 ACGAA-AAAGAGAG
1 AAGAAGAAAGAGAG
309335 CGAAGATGAC
Statistics
Matches: 195, Mismatches: 60, Indels: 45
0.65 0.20 0.15
Matches are distributed among these distances:
29 1 0.01
30 6 0.03
31 8 0.04
32 15 0.08
33 117 0.60
34 42 0.22
36 6 0.03
ACGTcount: A:0.53, C:0.08, G:0.27, T:0.11
Consensus pattern (34 bp):
AAGAAGAAAGAGAGATCCGATCATGGAAAGACTA
Found at i:309420 original size:21 final size:21
Alignment explanation
Indices: 309396--309435 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
309386 TAAAGAAAAA
309396 GAGAGCGACGATGATGAAAGT
1 GAGAGCGACGATGATGAAAGT
309417 GAGAGCGACGATGATGAAA
1 GAGAGCGACGATGATGAAA
309436 AGAGTAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.38, T:0.12
Consensus pattern (21 bp):
GAGAGCGACGATGATGAAAGT
Found at i:309439 original size:18 final size:19
Alignment explanation
Indices: 309393--309439 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 19
309383 GGATAAAGAA
309393 AAAGAGAGCGACGATGATG
1 AAAGAGAGCGACGATGATG
309412 AAAGTGAGAGCGACGATGATG
1 AAA--GAGAGCGACGATGATG
309433 AAA-AGAG
1 AAAGAGAG
309440 TAAAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.15
19 3 0.12
21 19 0.73
ACGTcount: A:0.45, C:0.09, G:0.36, T:0.11
Consensus pattern (19 bp):
AAAGAGAGCGACGATGATG
Found at i:309530 original size:33 final size:33
Alignment explanation
Indices: 309488--309550 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
309478 AGAAAAATAA
*
309488 AGCCGGTCATG-CAAAGGAT-AAGAAAGAAGAGGG
1 AGCCAGTCATGCCAAA-GATAAAG-AAGAAGAGGG
309521 AGCCAGTCATGCCAAAGATAAAGAAGAAGA
1 AGCCAGTCATGCCAAAGATAAAGAAGAAGA
309551 AAGTGAGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.46, C:0.14, G:0.30, T:0.10
Consensus pattern (33 bp):
AGCCAGTCATGCCAAAGATAAAGAAGAAGAGGG
Found at i:312229 original size:33 final size:32
Alignment explanation
Indices: 312192--312276 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
312182 ATCATTTCCA
312192 TTAGCATTTGCATGACCGGCACTCTTTTCTTCT
1 TTAGC-TTTGCATGACCGGCACTCTTTTCTTCT
* * * *
312225 TTAGCCTTGGCATGATCGACACTCTTTTTTTCT
1 TTAG-CTTTGCATGACCGGCACTCTTTTCTTCT
*
312258 TTAGTCTTTCCATGACCGG
1 TTAG-CTTTGCATGACCGG
312277 TGCTATCGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
33 41 0.98
34 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.16, T:0.42
Consensus pattern (32 bp):
TTAGCTTTGCATGACCGGCACTCTTTTCTTCT
Found at i:312358 original size:33 final size:33
Alignment explanation
Indices: 312321--312392 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
312311 TCTTTCCTTT
* * * *
312321 TTTAGCCTTTTCATCGCCGACGCTCTCCTTTTC
1 TTTAGCATTTTCATCACCCACACTCTCCTTTTC
*
312354 TTTAGCATTTTCATCACCCACACTCTCTTTTTC
1 TTTAGCATTTTCATCACCCACACTCTCCTTTTC
312387 TTTAGC
1 TTTAGC
312393 TTTCACATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.14, C:0.33, G:0.08, T:0.44
Consensus pattern (33 bp):
TTTAGCATTTTCATCACCCACACTCTCCTTTTC
Found at i:313361 original size:40 final size:43
Alignment explanation
Indices: 313294--313387 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 43
313284 CTCTCTCCAC
* * * * *
313294 AACTGACATTGTTTATCCCAAACCATCTCAATCAGCC-T-T-A
1 AACTGCCATTTTTTAGCCAAAACCATCTCAAGCAGCCTTCTCA
* *
313334 AACTGCCATTTTTTAGCCAAAATCATCTCAAGGAGCCTTCTCA
1 AACTGCCATTTTTTAGCCAAAACCATCTCAAGCAGCCTTCTCA
313377 AACTGCCATTT
1 AACTGCCATTT
313388 GACATTTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 30 0.68
41 1 0.02
42 1 0.02
43 12 0.27
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31
Consensus pattern (43 bp):
AACTGCCATTTTTTAGCCAAAACCATCTCAAGCAGCCTTCTCA
Found at i:322253 original size:20 final size:22
Alignment explanation
Indices: 322213--322259 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
322203 TGAATATTTT
322213 ATAA-TAATAACTATTTGAAAA
1 ATAATTAATAACTATTTGAAAA
322234 A-AATTAAT-ACTATTAT-AAAA
1 ATAATTAATAACTATT-TGAAAA
322254 ATAATT
1 ATAATT
322260 GAACATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAATTAATAACTATTTGAAAA
Found at i:322254 original size:21 final size:21
Alignment explanation
Indices: 322217--322259 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
322207 TATTTTATAA
*
322217 TAATAACTATTTGAAAAAAAT
1 TAATAACTATTTAAAAAAAAT
*
322238 TAAT-ACTATTATAAAAATAAT
1 TAATAACTATT-TAAAAAAAAT
322259 T
1 T
322260 GAACATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
TAATAACTATTTAAAAAAAAT
Found at i:323349 original size:17 final size:17
Alignment explanation
Indices: 323306--323356 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
323296 GTACCAGTAG
323306 AAATATAAATAAAATACTTA
1 AAATATAAA-AAAAT--TTA
* *
323326 AATTATATAAAAATTTA
1 AAATATAAAAAAATTTA
323343 AAATATAAAAAAAT
1 AAATATAAAAAAAT
323357 ATGATTGCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 15 0.56
19 5 0.19
20 7 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATAAAAAAATTTA
Found at i:324855 original size:23 final size:23
Alignment explanation
Indices: 324826--324873 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
324816 AAATAGGTCA
* *
324826 ATATAAGCGCTACCTATTATATT
1 ATATAAGCACTACCTAATATATT
*
324849 ATATAAGCATTACCTAATATATT
1 ATATAAGCACTACCTAATATATT
324872 AT
1 AT
324874 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (23 bp):
ATATAAGCACTACCTAATATATT
Found at i:326906 original size:22 final size:20
Alignment explanation
Indices: 326858--326912 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
326848 TTATTATATT
326858 TATATATTTATAATATAATA
1 TATATATTTATAATATAATA
*
326878 -ATCATATTCTGATTATATAATA
1 TAT-ATATT-T-ATAATATAATA
*
326900 TATATATATATAA
1 TATATATTTATAA
326913 CATATGTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
19 2 0.07
20 8 0.29
21 2 0.07
22 14 0.50
23 2 0.07
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
TATATATTTATAATATAATA
Found at i:327590 original size:25 final size:25
Alignment explanation
Indices: 327562--327615 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
327552 TTGTTTTCGT
327562 CCCT-TAAAAATTTATA-AGTTCACTC
1 CCCTCTAAAAATTTATAGA-TTCAC-C
*
327587 CCCTCTAAAATTTTATAGATTCACC
1 CCCTCTAAAAATTTATAGATTCACC
327612 CCCT
1 CCCT
327616 AATAGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 9 0.35
26 16 0.62
27 1 0.04
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.35
Consensus pattern (25 bp):
CCCTCTAAAAATTTATAGATTCACC
Found at i:332917 original size:15 final size:15
Alignment explanation
Indices: 332893--332922 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
332883 ATCTATTTTT
*
332893 TTACATATTTGGATA
1 TTACAGATTTGGATA
332908 TTACAGATTTGGATA
1 TTACAGATTTGGATA
332923 GTATTCTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (15 bp):
TTACAGATTTGGATA
Found at i:339427 original size:2 final size:2
Alignment explanation
Indices: 339420--339456 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
339410 GCAAAAGTAA
*
339420 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
339457 AAGTTCATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:342254 original size:2 final size:2
Alignment explanation
Indices: 342247--342280 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
342237 CTGACCCAAA
342247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
342281 TTTTTGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:344887 original size:15 final size:15
Alignment explanation
Indices: 344859--344892 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
344849 TTCCGGAAAA
*
344859 TGAATTACTGGAATT
1 TGAATTAATGGAATT
344874 TGAATTAATGGAATT
1 TGAATTAATGGAATT
344889 TGAA
1 TGAA
344893 AGAAAACATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (15 bp):
TGAATTAATGGAATT
Found at i:345090 original size:49 final size:50
Alignment explanation
Indices: 344993--345091 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
344983 TACAAATATT
*
344993 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
345043 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
345092 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:345266 original size:28 final size:26
Alignment explanation
Indices: 345227--345290 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 26
345217 TTTACTAAAA
345227 TATTATTTAAATATATAAATAAAATTAT
1 TATTA-TTAAATATATAAA-AAAATTAT
*
345255 TCATTATTAAATATATAAAAAATTTAT
1 T-ATTATTAAATATATAAAAAAATTAT
345282 TATATATTA
1 TAT-TATTA
345291 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 2 0.06
27 13 0.39
28 14 0.42
29 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTATTAAATATATAAAAAAATTAT
Found at i:345284 original size:30 final size:27
Alignment explanation
Indices: 345226--345329 Score: 79
Period size: 28 Copynumber: 3.6 Consensus size: 27
345216 CTTTACTAAA
345226 ATATTATTTAAATATATAAATAAAATTAT
1 ATATTA-TTAAATATATAAA-AAAATTAT
345255 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATATAAAAAA---ATTAT
*
345285 ATATTATTAAA-ATA-AAAATATAATATCTT
1 ATATTATTAAATATATAAAA-A-AAT-T-AT
345314 ATATTATTATAATATA
1 ATATTATTA-AATATA
345330 ATTGATTATT
Statistics
Matches: 63, Mismatches: 1, Indels: 20
0.75 0.01 0.24
Matches are distributed among these distances:
27 5 0.08
28 19 0.30
29 18 0.29
30 17 0.27
31 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATTATTAAATATATAAAAAAATTAT
Found at i:345360 original size:31 final size:35
Alignment explanation
Indices: 345314--345395 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 35
345304 ATAATATCTT
*
345314 ATATTATTATAATATAAT-TGATTATT-TTA-TATAA
1 ATATTAATA-AATATAATATGA-TATTATTATTATAA
*
345348 A-ATTAA-AAATATAATATTATATTATTATTATAA
1 ATATTAATAAATATAATATGATATTATTATTATAA
345381 ATATTAATAAATATA
1 ATATTAATAAATATA
345396 TTTTAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
31 12 0.29
32 6 0.15
33 10 0.24
34 6 0.15
35 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (35 bp):
ATATTAATAAATATAATATGATATTATTATTATAA
Found at i:345395 original size:49 final size:51
Alignment explanation
Indices: 345292--345395 Score: 124
Period size: 54 Copynumber: 2.0 Consensus size: 51
345282 TATATATTAT
* * **
345292 TAAAATAAAAATATAATATCTTATATTATTATAATATAATTGATTATTTTATA
1 TAAAATAAAAATATAATA-CTTATATTATTAT-ATATAAATGATTAATAAATA
345345 TAAAATTAAAAATATAATA-TTATATTATTAT-TATAAAT-ATTAATAAATA
1 TAAAA-TAAAAATATAATACTTATATTATTATATATAAATGATTAATAAATA
345394 TA
1 TA
345396 TTTTAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
49 10 0.22
50 6 0.13
52 12 0.26
53 5 0.11
54 13 0.28
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (51 bp):
TAAAATAAAAATATAATACTTATATTATTATATATAAATGATTAATAAATA
Found at i:345403 original size:54 final size:52
Alignment explanation
Indices: 345283--345422 Score: 144
Period size: 56 Copynumber: 2.6 Consensus size: 52
345273 AAAATTTATT
*
345283 ATATATTATTAAAA-TAAAAATATAATATCTTATATTATTATAATATAATTGA
1 ATATATTATTAAAATTAAAAATATAATAT-TTATATTATTATAATATAATTAA
* *
345335 TTATTTTATATAAAATTAAAAATATAATATTATATTATTATTATAAATATTAA-TAA
1 ATATATTAT-TAAAATTAAAAATATAATATT-TA-TATTATTAT-AATA-TAATTAA
345391 ATATATT-TTAAAAATTTTAAAAAT-TAATATTT
1 ATATATTATT-AAAA--TTAAAAATATAATATTT
345423 TGATGAAAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
52 7 0.09
53 6 0.08
54 17 0.23
55 15 0.20
56 18 0.24
57 11 0.15
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (52 bp):
ATATATTATTAAAATTAAAAATATAATATTTATATTATTATAATATAATTAA
Found at i:345410 original size:23 final size:24
Alignment explanation
Indices: 345370--345423 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
345360 AATATTATAT
*
345370 TATTATTATAAATATTAATAAA-T-A
1 TATT-TTAAAAATATTAA-AAATTAA
*
345394 TATTTTAAAAATTTTAAAAATTAA
1 TATTTTAAAAATATTAAAAATTAA
345418 TATTTT
1 TATTTT
345424 GATGAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 3 0.12
23 12 0.46
24 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTTTAAAAATATTAAAAATTAA
Found at i:345583 original size:19 final size:19
Alignment explanation
Indices: 345559--345612 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
345549 TATGTTACTA
345559 GGAAAATGAATTACGTTCC
1 GGAAAATGAATTACGTTCC
345578 GGAAAATGAATTACGTTCC
1 GGAAAATGAATTACGTTCC
* *
345597 AGAAAACGAATTACGT
1 GGAAAATGAATTACGT
345613 AAAACAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (19 bp):
GGAAAATGAATTACGTTCC
Found at i:345648 original size:42 final size:42
Alignment explanation
Indices: 345593--345708 Score: 196
Period size: 42 Copynumber: 2.8 Consensus size: 42
345583 ATGAATTACG
*
345593 TTCCAGAAAACGAATTACGTAAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAACATT
*
345635 TTTCGGAAAACGAATTACGTAAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAACATT
* *
345677 TTCCGAAAAACGAATTACATAAAACAAACACG
1 TTCCGGAAAACGAATTACGTAAAACAAACACG
345709 AGATTTCGGG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAACATT
Found at i:348874 original size:42 final size:42
Alignment explanation
Indices: 348827--348909 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
348817 TGGGTTTTGG
* *
348827 AAATTAAAGTTTTTGTTCTTAAAGTTCGTTTTGGAAATTATA
1 AAATTAAAGTTTTTATTCTTAAAGTACGTTTTGGAAATTATA
*
348869 AAATTAAAGTTTTTATTCTTAAAGTACGTTTTGTAAATTAT
1 AAATTAAAGTTTTTATTCTTAAAGTACGTTTTGGAAATTAT
348910 GATGAGATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.48
Consensus pattern (42 bp):
AAATTAAAGTTTTTATTCTTAAAGTACGTTTTGGAAATTATA
Found at i:351301 original size:24 final size:24
Alignment explanation
Indices: 351263--351308 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
351253 TGTTTACATT
* *
351263 ATGTCATTGAGTCAGTGCTTGATG
1 ATGTCATCGAATCAGTGCTTGATG
*
351287 ATGTCATCGAATCAGTTCTTGA
1 ATGTCATCGAATCAGTGCTTGA
351309 AAACAACGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (24 bp):
ATGTCATCGAATCAGTGCTTGATG
Found at i:352673 original size:225 final size:225
Alignment explanation
Indices: 352392--352856 Score: 743
Period size: 225 Copynumber: 2.1 Consensus size: 225
352382 GATACTTATA
* *
352392 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACTGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
352457 TTTGTCAGTTTTTTTA-CATGTTATATTGTTATGGATTAATACATTTTTATAAAGTATCGACACT
66 TTTGTCAGTTTTTTTAGC-TGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACT
*
352521 TTCAATATATATGGTAGCGATTTACCTATTTTGTCATTTATAGACAGGTTTTGTCATTTTTTTAC
130 TTCAATATATACGGTAGCGATTTACCTATTTTGTCATTTATAGACAGGTTTTGTCATTTTTTTAC
* *
352586 ATGTTATATTGTTATGGATCGATACATTTTT
195 ATGTTATATTATTATGGATCAATACATTTTT
* * *
352617 ATAAAGTATCGACACTTTCAATATATCGGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
352682 TTTGTCATTTTTTTTAGCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
66 TTTGTCAGTTTTTTTAGCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTT
* * * ** *
352747 TCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATATACCTGTTTTGTCATTTTTTTACC
131 TCAATATATACGGTAGCGATTTACCTATTTTGTCATTTATAGACAGGTTTTGTCATTTTTTTACA
*
352812 TGTTATATTATTATGGATCAATATATTTTT
196 TGTTATATTATTATGGATCAATACATTTTT
*
352842 ATAAAGTATCTACAC
1 ATAAAGTATCGACAC
352857 AAACCGACAA
Statistics
Matches: 220, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
225 219 1.00
226 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (225 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCAGTTTTTTTAGCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTT
TCAATATATACGGTAGCGATTTACCTATTTTGTCATTTATAGACAGGTTTTGTCATTTTTTTACA
TGTTATATTATTATGGATCAATACATTTTT
Found at i:352754 original size:113 final size:112
Alignment explanation
Indices: 352392--352856 Score: 716
Period size: 113 Copynumber: 4.1 Consensus size: 112
352382 GATACTTATA
* * * * *
352392 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACTGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATAGACCGGT
*
352457 TTTGTCAGTTTTTTTACATGTTATATTGTTATGGATTAATACATTTTT
66 TTTGTCA-TTTTTTTACATGTTATATTGTTATGGATCAATACATTTTT
** * *
352505 ATAAAGTATCGACACTTTCAATATATATGGTAGCGATTTACCTATTTTGTCATTTATAGACAGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATAGACCGGT
*
352570 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCAATACATTTTT
* *
352617 ATAAAGTATCGACACTTTCAATATATCGGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATAGACCGGT
*
352682 TTTGTCATTTTTTTTAGC-TGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTA-CATGTTATATTGTTATGGATCAATACATTTTT
* *
352730 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATATACCTGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATAGACCGGT
* * *
352795 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCAATACATTTTT
*
352842 ATAAAGTATCTACAC
1 ATAAAGTATCGACAC
352857 AAACCGACAA
Statistics
Matches: 326, Mismatches: 23, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
111 1 0.00
112 154 0.47
113 170 0.52
114 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACATGTTATATTGTTATGGATCAATACATTTTT
Found at i:352793 original size:20 final size:20
Alignment explanation
Indices: 352768--352815 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
352758 GGTAGCGATT
352768 TACCTGTTTTGTCATTTATA
1 TACCTGTTTTGTCATTTATA
* *
352788 TACCTGTTTTGTCATTTTTT
1 TACCTGTTTTGTCATTTATA
352808 TACCTGTT
1 TACCTGTT
352816 ATATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.58
Consensus pattern (20 bp):
TACCTGTTTTGTCATTTATA
Found at i:353705 original size:2 final size:2
Alignment explanation
Indices: 353698--353723 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
353688 CATTTACATA
353698 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
353724 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:354201 original size:22 final size:22
Alignment explanation
Indices: 354173--354219 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
354163 GTTCGTCCTC
354173 CGCCTTACGCGACGCATGTACA
1 CGCCTTACGCGACGCATGTACA
354195 CGCCTTACGCGACGCATGTACA
1 CGCCTTACGCGACGCATGTACA
354217 CGC
1 CGC
354220 GCTCGTAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.38, G:0.23, T:0.17
Consensus pattern (22 bp):
CGCCTTACGCGACGCATGTACA
Found at i:367298 original size:45 final size:47
Alignment explanation
Indices: 367247--367336 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 47
367237 CTACTTCTAG
367247 TATAATATT-AACT-TTTATCTACTTCTAGTATATCTCTTACACTAT
1 TATAATATTAAACTATTTATCTACTTCTAGTATATCTCTTACACTAT
*
367292 TATAATATTAAACTCATTTATCTTCTTCTAGTATATCTCTTACAC
1 TATAATATTAAACT-ATTTATCTACTTCTAGTATATCTCTTACAC
367337 CATTGTCATG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
45 9 0.22
46 4 0.10
48 28 0.68
ACGTcount: A:0.31, C:0.19, G:0.02, T:0.48
Consensus pattern (47 bp):
TATAATATTAAACTATTTATCTACTTCTAGTATATCTCTTACACTAT
Found at i:367598 original size:24 final size:24
Alignment explanation
Indices: 367571--367622 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
367561 CGTTCATTTA
* *
367571 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGATTATGTT
* **
367595 CGTTTATGTTCGTTCGATTATGTT
1 CGTTCATGAACGTTCGATTATGTT
367619 CGTT
1 CGTT
367623 TATGTTCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGATTATGTT
Found at i:367609 original size:14 final size:14
Alignment explanation
Indices: 367592--367622 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
367582 GTTCGGTTAT
*
367592 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
367606 GTTCGATTATGTTC
1 GTTCGATTATGTTC
367620 GTT
1 GTT
367623 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:367623 original size:24 final size:24
Alignment explanation
Indices: 367581--367642 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
367571 CGTTCGTGAA
*
367581 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
367605 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
*
367629 CATTC-ATTTATGTT
1 CGTTCGA-TTATGTT
367643 TAACCCAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (24 bp):
CGTTCGATTATGTTCGTTTATGTT
Found at i:368385 original size:10 final size:10
Alignment explanation
Indices: 368370--368444 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
368360 GGGTCTCCAA
368370 CGTTTATGTT
1 CGTTTATGTT
368380 CGTTTATGTT
1 CGTTTATGTT
368390 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
368401 ATGTTCGTGTT
1 -CGTTTATGTT
368412 CGTTTATGTT
1 CGTTTATGTT
368422 CG----TGTT
1 CGTTTATGTT
368428 CGTTTATGTT
1 CGTTTATGTT
368438 CGTTTAT
1 CGTTTAT
368445 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:368401 original size:16 final size:16
Alignment explanation
Indices: 368376--368440 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
368366 CCAACGTTTA
368376 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
368392 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
368408 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
368424 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
368440 T
1 T
368441 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:368531 original size:16 final size:16
Alignment explanation
Indices: 368510--368542 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
368500 AAAAAAATTT
368510 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
368526 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
368542 T
1 T
368543 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:368728 original size:95 final size:95
Alignment explanation
Indices: 368613--368815 Score: 388
Period size: 95 Copynumber: 2.1 Consensus size: 95
368603 AGGCCTACAT
368613 ATAAATATCTTAGTCATTAATTTTATAATTATTTATAAATTATATTAGGTAAAACTTTAGTTTTC
1 ATAAATATC-TAGTCATTAATTTTATAATTATTTATAAATTATATTAGGTAAAACTTTAGTTTTC
368678 TAGAGCCATGCTATTTAGTATTATTTTAATA
65 TAGAGCCATGCTATTTAGTATTATTTTAATA
*
368709 ATAAATATCTAGTCGTTAATTTTATAATTATTTATAAATTATATTAGGTAAAACTTTAGTTTTCT
1 ATAAATATCTAGTCATTAATTTTATAATTATTTATAAATTATATTAGGTAAAACTTTAGTTTTCT
368774 AGAGCCATGCTATTTAGTATTATTTTAATA
66 AGAGCCATGCTATTTAGTATTATTTTAATA
368804 ATAAATATCTAG
1 ATAAATATCTAG
368816 ATAGTTATTA
Statistics
Matches: 106, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
95 97 0.92
96 9 0.08
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (95 bp):
ATAAATATCTAGTCATTAATTTTATAATTATTTATAAATTATATTAGGTAAAACTTTAGTTTTCT
AGAGCCATGCTATTTAGTATTATTTTAATA
Found at i:369656 original size:2 final size:2
Alignment explanation
Indices: 369649--369677 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
369639 TTGGGTGGAG
369649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
369678 CGAGTCGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:376285 original size:48 final size:48
Alignment explanation
Indices: 376232--376327 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
376222 TAAAAGGAAG
* *
376232 TATGATTAGACTTATGAACTATATAATCCAAGTAAAAGGATAACCTAA
1 TATGATTAGACTTAAGAACTATATAATCCAAGTAAAAGAATAACCTAA
*
376280 TATGATTAGACTTAAGAACTATATAATCTAAGTAAAAGAATAACCTAA
1 TATGATTAGACTTAAGAACTATATAATCCAAGTAAAAGAATAACCTAA
376328 CTTACTAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.29
Consensus pattern (48 bp):
TATGATTAGACTTAAGAACTATATAATCCAAGTAAAAGAATAACCTAA
Found at i:380040 original size:14 final size:14
Alignment explanation
Indices: 379988--380033 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
379978 TTATTTAGGG
*
379988 TTTATGATTATAAGA
1 TTTATGATT-TAAAA
*
380003 TTTAT-ATTTAAAG
1 TTTATGATTTAAAA
380016 TTTATGATTTAAAA
1 TTTATGATTTAAAA
380030 TTTA
1 TTTA
380034 GACTTTATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 8 0.30
14 14 0.52
15 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (14 bp):
TTTATGATTTAAAA
Found at i:380040 original size:28 final size:27
Alignment explanation
Indices: 379987--380054 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
379977 TTTATTTAGG
* *
379987 GTTTATGATTATAAGATTTATATTTAAA
1 GTTTATGATT-TAAAATTTAGATTTAAA
*
380015 GTTTATGATTTAAAATTTAGACTTTATA
1 GTTTATGATTTAAAATTTAGA-TTTAAA
* *
380043 GGTTAAGATTTA
1 GTTTATGATTTA
380055 GAGTCCTTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (27 bp):
GTTTATGATTTAAAATTTAGATTTAAA
Found at i:386404 original size:42 final size:42
Alignment explanation
Indices: 386053--386399 Score: 626
Period size: 42 Copynumber: 8.3 Consensus size: 42
386043 TGCGATTTTG
386053 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
386095 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
386137 GACTATCGCAATGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
386179 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
386221 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
386263 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
386305 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
386347 GACTATAGCAACGAATTTGG-A-AAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
386387 GACTATCGCAACG
1 GACTATCGCAACG
386400 CGAATATGGA
Statistics
Matches: 296, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 30 0.10
41 1 0.00
42 265 0.90
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:387703 original size:19 final size:19
Alignment explanation
Indices: 387663--387703 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
387653 AAAATATATT
* *
387663 TATGAACAGTAAGATACGG
1 TATGAACAGTAAGAAACAG
*
387682 TATGAACAGTAATAAACAG
1 TATGAACAGTAAGAAACAG
387701 TAT
1 TAT
387704 TGTAAACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (19 bp):
TATGAACAGTAAGAAACAG
Found at i:387716 original size:22 final size:22
Alignment explanation
Indices: 387686--387733 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
387676 ATACGGTATG
* * *
387686 AACAGTAATAAACAGTATTGTA
1 AACAATAATAAACAGTACTATA
*
387708 AACAATAATGAACAGTACTATA
1 AACAATAATAAACAGTACTATA
387730 AACA
1 AACA
387734 GTAGCCGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.23
Consensus pattern (22 bp):
AACAATAATAAACAGTACTATA
Found at i:388609 original size:32 final size:32
Alignment explanation
Indices: 388559--388634 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
388549 CATGTTCCTT
* *
388559 AGAACATATGT-ATATTGTCCATATGTCCCGAA
1 AGAACATAGGTAATTTTGTCCATATGTCCC-AA
* *
388591 AG-ACATAGGTAATTTTGTCCATATGTTCCAT
1 AGAACATAGGTAATTTTGTCCATATGTCCCAA
388622 AGAACATAGGTAA
1 AGAACATAGGTAA
388635 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 10 0.26
32 28 0.74
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (32 bp):
AGAACATAGGTAATTTTGTCCATATGTCCCAA
Found at i:389666 original size:59 final size:59
Alignment explanation
Indices: 389603--389765 Score: 256
Period size: 59 Copynumber: 2.8 Consensus size: 59
389593 ATGTCACTTT
* *
389603 GTGTGCTAAAATGATAAGGACATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTCA
*
389662 GTGTGCTAATATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTCA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTCA
* ***
389721 GTGTGCT-AAATGATAAGGAAATCATATTGAAAATATAGATTTCCA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCA
389766 GATAGGGCAT
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
58 33 0.34
59 63 0.66
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTCA
Found at i:390036 original size:17 final size:18
Alignment explanation
Indices: 390011--390044 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
390001 ATTATTGTAT
390011 ATTCATTGGA-ATTAAAG
1 ATTCATTGGAGATTAAAG
*
390028 ATTCCTTGGAGATTAAA
1 ATTCATTGGAGATTAAA
390045 TATCAGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTCATTGGAGATTAAAG
Found at i:395566 original size:32 final size:32
Alignment explanation
Indices: 395530--395593 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
395520 GTAATCTTGT
395530 GGTAAGATGAAGCATTATTTTCCTTACAGGTA
1 GGTAAGATGAAGCATTATTTTCCTTACAGGTA
**
395562 GGTAAGATGAAGTGTTATTTTCCTTACAGGTA
1 GGTAAGATGAAGCATTATTTTCCTTACAGGTA
395594 TAAGATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (32 bp):
GGTAAGATGAAGCATTATTTTCCTTACAGGTA
Found at i:398087 original size:17 final size:16
Alignment explanation
Indices: 398060--398099 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
398050 TTTCAGTTCG
*
398060 AAAATATATATTTTCTTT
1 AAAA-ATATATATTC-TT
398078 AAAAATATATATTCTT
1 AAAAATATATATTCTT
398094 AAAAAT
1 AAAAAT
398100 CAAAATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 9 0.43
18 4 0.19
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAAATATATATTCTT
Found at i:398184 original size:20 final size:20
Alignment explanation
Indices: 398156--398195 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
398146 TTAAATCATC
*
398156 TTTTCAAAAAAAT-TGATTT
1 TTTTTAAAAAAATATGATTT
398175 TTTTTAAAAAAATATGATTT
1 TTTTTAAAAAAATATGATTT
398195 T
1 T
398196 AAGAGACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTTAAAAAAATATGATTT
Found at i:398843 original size:17 final size:16
Alignment explanation
Indices: 398811--398851 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
398801 TAGATTAATT
*
398811 TATTTTATATTAATAA
1 TATTTTTTATTAATAA
*
398827 TATGTTTTTATTTATAA
1 TAT-TTTTTATTAATAA
398844 TATTTTTT
1 TATTTTTT
398852 CCAATTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTTTTTATTAATAA
Found at i:402021 original size:18 final size:18
Alignment explanation
Indices: 401983--402021 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
401973 AACAAGCTCA
*
401983 TCATAAACTCTTTTCTCC
1 TCATAAACTCTTCTCTCC
* *
402001 TCATCAACTCTTCTCTGC
1 TCATAAACTCTTCTCTCC
402019 TCA
1 TCA
402022 ACATGAGTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.03, T:0.41
Consensus pattern (18 bp):
TCATAAACTCTTCTCTCC
Found at i:405783 original size:3 final size:3
Alignment explanation
Indices: 405769--405808 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
405759 GAGAATCGAA
* *
405769 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAA AAG -AG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
405809 TCCTTTGATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:409195 original size:7 final size:7
Alignment explanation
Indices: 409185--409212 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
409175 AAGTTTTAAG
409185 GTTTCAT
1 GTTTCAT
409192 GTTTCAT
1 GTTTCAT
409199 GTTTCAT
1 GTTTCAT
409206 GTTTCAT
1 GTTTCAT
409213 TCTCTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (7 bp):
GTTTCAT
Found at i:410359 original size:25 final size:27
Alignment explanation
Indices: 410322--410378 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
410312 TAAAAATATC
*
410322 AAATTTCATAATTTCT-AAAACCTCTA
1 AAATTTCATAATTTCTCAAAACCCCTA
* *
410348 AAATTTTA-AATTTCTCAAAACCCCTT
1 AAATTTCATAATTTCTCAAAACCCCTA
410374 AAATT
1 AAATT
410379 CCCTTAGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATTTCATAATTTCTCAAAACCCCTA
Found at i:410427 original size:20 final size:20
Alignment explanation
Indices: 410402--410439 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
410392 TTTGGTTCAC
* *
410402 GGAATATAAGATTACCAGTG
1 GGAATAAAAAATTACCAGTG
410422 GGAATAAAAAATTACCAG
1 GGAATAAAAAATTACCAG
410440 GAAATAGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (20 bp):
GGAATAAAAAATTACCAGTG
Found at i:412294 original size:19 final size:19
Alignment explanation
Indices: 412270--412310 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
412260 TGAGATCTTA
*
412270 AAATTTA-TAATTTATGATT
1 AAATTTATTAAATTA-GATT
412289 AAATTTATTAAATTAGATT
1 AAATTTATTAAATTAGATT
412308 AAA
1 AAA
412311 ATTAATATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
AAATTTATTAAATTAGATT
Found at i:412409 original size:19 final size:19
Alignment explanation
Indices: 412385--412427 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
412375 ACTATAAAAA
412385 TAATATTTTCGTCAAATAT
1 TAATATTTTCGTCAAATAT
412404 TAATATTTTCGTCAAATAT
1 TAATATTTTCGTCAAATAT
412423 TAATA
1 TAATA
412428 ATAGTTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (19 bp):
TAATATTTTCGTCAAATAT
Found at i:412429 original size:22 final size:21
Alignment explanation
Indices: 412383--412430 Score: 73
Period size: 19 Copynumber: 2.3 Consensus size: 21
412373 TAACTATAAA
412383 AATAATATTTTCGTCAAATAT
1 AATAATATTTTCGTCAAATAT
412404 --TAATATTTTCGTCAAATATT
1 AATAATATTTTCGTCAAATA-T
412424 AATAATA
1 AATAATA
412431 GTTGATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 18 0.75
20 1 0.04
22 5 0.21
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (21 bp):
AATAATATTTTCGTCAAATAT
Found at i:417449 original size:16 final size:16
Alignment explanation
Indices: 417406--417460 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 16
417396 AAAATTTTTA
417406 AAATATATAAAAAATT
1 AAATATATAAAAAATT
*
417422 AAAT-TAT----TATT
1 AAATATATAAAAAATT
417433 AAATATATAAAAAATT
1 AAATATATAAAAAATT
417449 AAA-AT-TAAAAAA
1 AAATATATAAAAAA
417461 ATACAACCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
11 7 0.22
12 3 0.09
14 7 0.22
15 5 0.16
16 10 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATATAAAAAATT
Found at i:417453 original size:28 final size:27
Alignment explanation
Indices: 417393--417455 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
417383 ATGAAATTAT
417393 ATTAAAATT-TTTAAAATATATAAAAA
1 ATTAAAATTATTTAAAATATATAAAAA
*
417419 ATT-AAATTATTATTAAATATATAAAAA
1 ATTAAAATTATT-TAAAATATATAAAAA
417446 ATTAAAATTA
1 ATTAAAATTA
417456 AAAAAATACA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 5 0.15
26 5 0.15
27 17 0.52
28 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATTAAAATTATTTAAAATATATAAAAA
Found at i:417927 original size:2 final size:2
Alignment explanation
Indices: 417920--417966 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
417910 ATTTAACGTG
417920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
417962 TA TA T
1 TA TA T
417967 GGATAAACTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:431294 original size:36 final size:36
Alignment explanation
Indices: 431261--431328 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
431251 TACAAATTGT
*
431261 AAAATATTTATATATTTTTTTTA-AAAATTAAATTC
1 AAAATATTTATATAATTTTTTTACAAAATTAAATTC
*
431296 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTACAAAATTAAA
431329 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 21 0.70
36 9 0.30
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTACAAAATTAAATTC
Found at i:435703 original size:138 final size:138
Alignment explanation
Indices: 435450--436136 Score: 916
Period size: 138 Copynumber: 5.0 Consensus size: 138
435440 TTAAGGTCAA
* *
435450 TTGACCTTTCTGATTGCAAGAGACTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
1 TTGACCTTTCTCATTGCAAGAGTCTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
* * *
435515 ACCCTTTGCTGCAAT-GGATGTGAAAATTTGGTTGAACTATCTT-CTCTCAATCAATTGACATCT
66 AGCCTTTGCTGCAATAGG-TGTGAAAATTTGGTTGAACTACCTTGC-CTCAATCATTTGACATCT
* *
435578 CTTCAACGTC
129 CTTCAAAGCC
* *
435588 TTGACCTTTCTCATTGCAAGAGTCTAAGGAAGATCCCTAATCTATCGGGAGCCGTCAACCTTCAA
1 TTGACCTTTCTCATTGCAAGAGTCTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
* * * *
435653 AGCCTTTGCTGCCATAGGTGTGAAAATTTGATTGAACTACCTTGCGTCAATCAGTTGACATCTCT
66 AGCCTTTGCTGCAATAGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAATCATTTGACATCTCT
435718 TCAAAGCC
131 TCAAAGCC
* *
435726 TTGACCTTTCTCATTGCAAGAGTCTAAGGAAGATCCCTAATCTTTCAGGAGTCATCAACCTTCAA
1 TTGACCTTTCTCATTGCAAGAGTCTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
* * ** *
435791 AGCCTTTGCTGCTATAGGTGTGAAAATTTGATTGAACTACCTTGCCTCAATCATTTGGTATTTCT
66 AGCCTTTGCTGCAATAGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAATCATTTGACATCTCT
*
435856 TGAAAGCC
131 TCAAAGCC
* *
435864 TTGAACTTTCTCATTGCAAGAGTCTAAGGAAGATCTCTAATCTATCAGGAGCCATCAACCTTCAA
1 TTGACCTTTCTCATTGCAAGAGTCTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
* * * ** * *
435929 AGCATTTTCTTCTGTGGGTGTGAAAATCTGGTTGAACTACCTTGCCTCAATCATTTGGA-ATCTC
66 AGCCTTTGCTGCAATAGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAATCATTT-GACATCTC
435993 TT-AAACGCC
130 TTCAAA-GCC
* ** * * * * * **
436002 TTGACCTGTCTTGTTGCAATAATTTAAGGAAGATTCCTAATCTATCCGGAGTTATCAACCTTCAA
1 TTGACCTTTCTCATTGCAAGAGTCTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
* * *
436067 AGCCTTTGCTTCAATGGGTGTGAAAATTTGGTTGAACTACCATGCCTCAATCATTTGACATCTCT
66 AGCCTTTGCTGCAATAGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAATCATTTGACATCTCT
436132 T-AAAG
131 TCAAAG
436137 AGCTAGAATT
Statistics
Matches: 490, Mismatches: 54, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
137 6 0.01
138 480 0.98
139 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (138 bp):
TTGACCTTTCTCATTGCAAGAGTCTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
AGCCTTTGCTGCAATAGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAATCATTTGACATCTCT
TCAAAGCC
Found at i:438784 original size:30 final size:29
Alignment explanation
Indices: 438749--438853 Score: 86
Period size: 30 Copynumber: 3.6 Consensus size: 29
438739 ATTTTTCTTG
438749 TCAATTCAAGTATTCTTCCTTCCCTTCTCC
1 TCAATTCAAGTATT-TTCCTTCCCTTCTCC
* * * * * *
438779 TCAATTGAATTGTTTTCTCTCCCCTCCTCG
1 TCAATTCAAGTATTTTC-CTTCCCTTCTCC
* *
438809 TCGATTCAAGTATTTT-CATCCTCTTCTCC
1 TCAATTCAAGTATTTTCCTTCC-CTTCTCC
* *
438838 TCAGTTGAAGTATTTT
1 TCAATTCAAGTATTTT
438854 TCTTGAGAAC
Statistics
Matches: 56, Mismatches: 17, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
28 3 0.05
29 21 0.38
30 32 0.57
ACGTcount: A:0.17, C:0.30, G:0.09, T:0.45
Consensus pattern (29 bp):
TCAATTCAAGTATTTTCCTTCCCTTCTCC
Found at i:440928 original size:17 final size:18
Alignment explanation
Indices: 440896--440929 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
440886 TAATTAAATA
440896 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
440914 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
440930 ACCTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:442529 original size:30 final size:30
Alignment explanation
Indices: 442475--442696 Score: 175
Period size: 30 Copynumber: 7.4 Consensus size: 30
442465 GCTCTTCTTC
* *
442475 TCAATTGAAGTGTTTTC-ATCCCCTTCTCG
1 TCAATTGAAGTATTTTCTCTCCCCTTCTCG
* * *
442504 TCAGTTGAAGTGTTTTCTCTCCCCTTCTAG
1 TCAATTGAAGTATTTTCTCTCCCCTTCTCG
* **
442534 TCAATTGAAGTATTCTTC-ATCCTTTTCTCG
1 TCAATTGAAGTATT-TTCTCTCCCCTTCTCG
* * * *
442564 TCAACTGAAGTATTTTTTCTCCCCGTCTCA
1 TCAATTGAAGTATTTTCTCTCCCCTTCTCG
* *
442594 TCAATTAAAGTATTTT-TCATCCTCTTCTCG
1 TCAATTGAAGTATTTTCTC-TCCCCTTCTCG
* * *
442624 CCAATTAAAGTATTTT-TCATCCCCTTCTTG
1 TCAATTGAAGTATTTTCTC-TCCCCTTCTCG
* **
442654 TCAATTGAAGGGAACTTC-CTCCCCTTCTCG
1 TCAATTGAA-GTATTTTCTCTCCCCTTCTCG
* *
442684 TAAATTAAAGTAT
1 TCAATTGAAGTAT
442697 CAAGTTTTCT
Statistics
Matches: 153, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
29 22 0.14
30 123 0.80
31 8 0.05
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (30 bp):
TCAATTGAAGTATTTTCTCTCCCCTTCTCG
Found at i:442566 original size:60 final size:58
Alignment explanation
Indices: 442475--442663 Score: 218
Period size: 60 Copynumber: 3.2 Consensus size: 58
442465 GCTCTTCTTC
* * * *
442475 TCAATTGAAGTGTTTTCATCCCCTTCTCGTCAGTTGAAGTGTTTTCTCTCCCCTTCTAG
1 TCAATTGAAGTATTTTCATCCTCTTCTCGTCAATTGAAGTATTTT-TCTCCCCTTCTAG
* * *
442534 TCAATTGAAGTATTCTTCATCCTTTTCTCGTCAACTGAAGTATTTTTTCTCCCCGTCTCA-
1 TCAATTGAAGTATT-TTCATCCTCTTCTCGTCAATTGAAGTA-TTTTTCTCCCCTTCT-AG
* * * *
442594 TCAATTAAAGTATTTTTCATCCTCTTCTCGCCAATTAAAGTATTTTTCATCCCCTTCTTG
1 TCAATTGAAGTA-TTTTCATCCTCTTCTCGTCAATTGAAGTATTTTTC-TCCCCTTCTAG
442654 TCAATTGAAG
1 TCAATTGAAG
442664 GGAACTTCCT
Statistics
Matches: 109, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
59 19 0.17
60 83 0.76
61 7 0.06
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (58 bp):
TCAATTGAAGTATTTTCATCCTCTTCTCGTCAATTGAAGTATTTTTCTCCCCTTCTAG
Found at i:442621 original size:90 final size:91
Alignment explanation
Indices: 442487--442663 Score: 205
Period size: 90 Copynumber: 2.0 Consensus size: 91
442477 AATTGAAGTG
* * * * * * *
442487 TTTTCATCCCCTTCTCGTCAGTTGAAGTGTTTTCTCTCCCCTTCTAGTCAATTGAAGTATTCTTC
1 TTTTCATCCCCGTCTCATCAATTAAAGTATTTTCTCTCCCCTTCTAGCCAATTAAAGTATTCTTC
**
442552 ATCCTTTTCTCGTCAACTGAAGTATT
66 ATCCCCTTCTCGTCAACTGAAGTATT
* * *
442578 TTTTC-TCCCCGTCTCATCAATTAAAGTATTTT-TCATCCTCTTCTCGCCAATTAAAGTATTTTT
1 TTTTCATCCCCGTCTCATCAATTAAAGTATTTTCTC-TCCCCTTCTAGCCAATTAAAGTATTCTT
* *
442641 CATCCCCTTCTTGTCAATTGAAG
65 CATCCCCTTCTCGTCAACTGAAG
442664 GGAACTTCCT
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
89 2 0.03
90 64 0.90
91 5 0.07
ACGTcount: A:0.20, C:0.27, G:0.10, T:0.44
Consensus pattern (91 bp):
TTTTCATCCCCGTCTCATCAATTAAAGTATTTTCTCTCCCCTTCTAGCCAATTAAAGTATTCTTC
ATCCCCTTCTCGTCAACTGAAGTATT
Found at i:454429 original size:34 final size:34
Alignment explanation
Indices: 454386--454509 Score: 194
Period size: 34 Copynumber: 3.6 Consensus size: 34
454376 TTTATTAATT
454386 AACCTGAATTACATAAGATACAAAATGCACTCTA
1 AACCTGAATTACATAAGATACAAAATGCACTCTA
454420 AACCTGAATTACATAAGATACAAAATGCACTCTA
1 AACCTGAATTACATAAGATACAAAATGCACTCTA
* * * *
454454 AACCTGAATTACATAAGATACACATTACTCTCTA
1 AACCTGAATTACATAAGATACAAAATGCACTCTA
* *
454488 ATCCTGAAATACATAAGATACA
1 AACCTGAATTACATAAGATACA
454510 CATTACACTA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 84 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (34 bp):
AACCTGAATTACATAAGATACAAAATGCACTCTA
Done.