Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397270.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_55.0, 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: 4719911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 90628 characters in sequence are not A, C, G, or T
File 1 of 10
Found at i:1377 original size:170 final size:171
Alignment explanation
Indices: 1100--1452 Score: 380
Period size: 170 Copynumber: 2.1 Consensus size: 171
1090 NNNNNNNNNN
* *
1100 CTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAGGCTATATTCTTTTACATTTTAAGTA
1 CTCGCTTTAAATAGCTTTATAACCTCATAATTGATTTTAGGCTATATTCTTTTACATTTTAAGTA
* ** * ***
1165 AAACAAATTATAATTGAATGTTTGTCTCAATGAACATGAAGAAAA-ATCCATTCATTTATTGA-A
66 AAACAAATTATAATTGAATGTCTACCTCAATGAACATGAAGAAAATAACCATTCA-TTAGCAAGA
* * *
1228 AAAGTTCACTTATAGTCACCCAGGCCTTCGAAAGCCTTATTA
130 AAAGTCCACTTATAGTCACCCAGGCCCTCAAAAGCCTTATTA
* *
1270 CTCGCTTTAAATAGCTTTATTACCTCATAATTGATTTTAAGG-TGA-ATTTTTTTACATTTT-AG
1 CTCGCTTTAAATAGCTTTATAACCTCATAATTGATTTT-AGGCT-ATATTCTTTTACATTTTAAG
* ** *
1332 CTTAAACAAATTATAA-TGAAATGTCTACCTTGA-GAA-ATGTGAAGAAAATAAGCATTCATTAG
64 -TAAAACAAATTATAATTG-AATGTCTACCTCAATGAACA--TGAAGAAAATAACCATTCATTAG
* * ** *
1394 CAAGAAAAGTCCATTTATAGTCATCCATTCCCTCAAAAGCCTTATTG
125 CAAGAAAAGTCCACTTATAGTCACCCAGGCCCTCAAAAGCCTTATTA
1441 CTCGCTTTAAAT
1 CTCGCTTTAAAT
1453 GCTNNNNNNN
Statistics
Matches: 152, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
168 1 0.01
169 7 0.05
170 86 0.57
171 58 0.38
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (171 bp):
CTCGCTTTAAATAGCTTTATAACCTCATAATTGATTTTAGGCTATATTCTTTTACATTTTAAGTA
AAACAAATTATAATTGAATGTCTACCTCAATGAACATGAAGAAAATAACCATTCATTAGCAAGAA
AAGTCCACTTATAGTCACCCAGGCCCTCAAAAGCCTTATTA
Found at i:1668 original size:343 final size:331
Alignment explanation
Indices: 1307--2293 Score: 788
Period size: 340 Copynumber: 2.9 Consensus size: 331
1297 TAATTGATTT
* * * * * * *
1307 TAAGGTGAATTTTTTTACATTTTAGCTT-AAACAAATTATAA-TGAAATGTCTACCTTGAGAAAT
1 TAAGTTGAATTTTTTTACATTTTAGATTAAAACAAACTACAATTG-AATGTCAACCTTGAAAAAC
* * *
1370 GTGAAGAAAATAAGCATTCATTAGCAAGAAAAGTCCATTTAT-AGTCATCCATTCCCTCAAAAGC
65 ATGAAGAAAA-AAGCATTCATCAACAAGAAAAGTCCATTTATGA-TCATCCATTCCCTCAAAAGC
* * ********** * *** *
1434 CTTATTGCTCGCTTTAAATGCTNNNNNNNNNNCATAATTGATTTTAAGTTGAATTTTTTTTATAT
128 CTTATTACTAGCTTTAAATGCTTTTATAATTTCATAATTGATTTTAAATT-AAAAATTTTTACAT
* * * *
1499 TTTTCCTTAAAACAGACTATAATTGAATGTCTGCCTTAGAAAACATATAGAAAATACCATTTATT
192 TTTTCCTTAAAAAAGACTATAATTGAATGTCTGCCTCAG-AAACATATAGAAAAGACCATTCATT
* *
1564 AGGAAGAAAAGTCTATTTATAGTCCCCCATTTATTCAAAAGCTTTATTACTCGCTTTAAATGGTT
256 AGGAAGAAAAGTCTATTTATAGTCCCCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATAGTT
1629 TTATAATCTCA
321 TTATAATCTCA
** *
1640 TAANNNNNNNNNNGTTGAATTTTTTTACATTTTTTATTAAAACAGACTACAATTGAATGTCAACC
1 TAA----------GTTGAATTTTTTTACATTTTAGATTAAAACAAACTACAATTGAATGTCAACC
**
1705 TTGAAAAACATGAAGAAAAAAGCATTCATCAACAAGAAAAGTCCATTTATGATCATCCATTCTTT
56 TTGAAAAACATGAAGAAAAAAGCATTCATCAACAAGAAAAGTCCATTTATGATCATCCATTCCCT
* * *
1770 CGAAAGCTTTATTACTAGCTTTAAATGGTTTTATAATTTCATAATTGATTTTAAATTAAAAATTT
121 CAAAAGCCTTATTACTAGCTTTAAATGCTTTTATAATTTCATAATTGATTTTAAATTAAAAATTT
** * * * * **
1835 TTACATTTTTTGTTAAAAAAGATTATAATTGAATGTCTGTCTCAGAAACGTGTAGAAAAGGTCAT
186 TTACATTTTTCCTTAAAAAAGACTATAATTGAATGTCTGCCTCAGAAACATATAGAAAAGACCAT
* * *
1900 TCATTGGGAAGAAAAGTTTATTTATAGTCCCCCATTCATTCAAAAGCTTTATTACTCGTTTTAAA
251 TCATTAGGAAGAAAAGTCTATTTATAGTCCCCCATTCATTCAAAAGCTTTATTACTCGCTTTAAA
1965 TAGTTTTATAATCTCA
316 TAGTTTTATAATCTCA
* * * * * *
1981 TAA--TCAATTTTAAGTTTNNNNNNNNNNCATTTTTTG-TT-AAACAGACTATAATTGAATGTCT
1 TAAGTTGAATTTT---TTT---------ACA-TTTTAGATTAAAACAAACTACAATTGAATGTCA
* * * * * *
2042 ACCTTGAGAAACGTAAAGAAAAAAGCATTCATCGATAAGAAAATTCCATTTAT-AGTCATCCATT
53 ACCTTGAAAAACATGAAGAAAAAAGCATTCATCAACAAGAAAAGTCCATTTATGA-TCATCCATT
* * ********** * * *
2106 CCTTCAAAAGCCTTATTACTCGCTTTAANNNNNNNNNNAATTTCATAATTGATTTTAAGTTGAAT
117 CCCTCAAAAGCCTTATTACTAGCTTTAAATGCTTTTATAATTTCATAATTGATTTTAAATTAAAA
** * * *
2171 ATTTTTACATTTTTTGTTAAAAAAGATTATAATTGAATGTCTGCCTTAGGAAACATGAGAGAAAA
182 ATTTTTACATTTTTCCTTAAAAAAGACTATAATTGAATGTCTGCCTCA-GAAACAT-ATAGAAAA
* * * * * * * *
2236 -AGCACTCATT-GGTGAGAAAAGTCCATTTATACTCACCCATTCCTTCAAAAGCCTTATT
245 GACCATTCATTAGG-AAGAAAAGTCTATTTATAGTCCCCCATTCATTCAAAAGCTTTATT
2294 NNNNNNNNNN
Statistics
Matches: 529, Mismatches: 95, Indels: 52
0.78 0.14 0.08
Matches are distributed among these distances:
329 7 0.01
332 3 0.01
333 3 0.01
339 1 0.00
340 173 0.33
341 148 0.28
342 54 0.10
343 102 0.19
344 36 0.07
345 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (331 bp):
TAAGTTGAATTTTTTTACATTTTAGATTAAAACAAACTACAATTGAATGTCAACCTTGAAAAACA
TGAAGAAAAAAGCATTCATCAACAAGAAAAGTCCATTTATGATCATCCATTCCCTCAAAAGCCTT
ATTACTAGCTTTAAATGCTTTTATAATTTCATAATTGATTTTAAATTAAAAATTTTTACATTTTT
CCTTAAAAAAGACTATAATTGAATGTCTGCCTCAGAAACATATAGAAAAGACCATTCATTAGGAA
GAAAAGTCTATTTATAGTCCCCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATAGTTTTATA
ATCTCA
Found at i:1778 original size:171 final size:162
Alignment explanation
Indices: 1653--2133 Score: 217
Period size: 170 Copynumber: 2.9 Consensus size: 162
1643 NNNNNNNNNN
*
1653 GTTGAA-TTTTTTTACATTTTTTATTAAAACAGACTACAATTGAATGTCAACCTT-GAAAAACAT
1 GTTGAATTTTTTTTACATTTTTCATTAAAACAGACTACAATTGAATGTCAACCTTAG-AAAACAT
* * *
1716 GA-AGAAAAAAGCATTCATCAACAAGAAAAGTCCATTTAT-GATCATCCATTCT-TTCGAAAGCT
65 -ATAGAAAAAACCATTCATCAACAAGAAAAGTCCATTTATAG-TCACCCATT-TATTCAAAAGCT
*
1778 TTATTACTAGCTTTAAATGGTTTTATAATTTCATAA
127 TTATTACTAGCTTTAAATGGTTTTATAATCTCATAA
* * ** * * * *** *
1814 TTGATTTTAAATTAAAAATTTTTACATTTTTTGTTAAAAAAGATTATAATTGAATGTCTGTCTCA
1 --G---TTGAATT----TTTTTTACATTTTTCATTAAAACAGACTACAATTGAATGTCAACCTTA
* * *** **** ** * *
1879 G-AAACGTGTAGAAAAGGTCATTCATTGGGAAGAAAAGTTTATTTATAGTCCCCCATTCATTCAA
57 GAAAACATATAGAAAAAACCATTCATCAACAAGAAAAGTCCATTTATAGTCACCCATTTATTCAA
* * *
1943 AAGCTTTATTACTCGTTTTAAATAGTTTTATAATCTCATAA
122 AAGCTTTATTACTAGCTTTAAATGGTTTTATAATCTCATAA
* ** ** * *
1984 --TCAATTTTAAGTTTNNNNNNNNNNCATTTTTTGTT-AAACAGACTATAATTGAATGTCTACCT
1 GTTGAATTTT---TTT--------TACATTTTTCATTAAAACAGACTACAATTGAATGTCAACCT
* * * * * * * **
2046 T-GAGAAACGTAAAGAAAAAAGCATTCATCGATAAGAAAATTCCATTTATAGTCATCCATTCCTT
55 TAGA-AAACATATAGAAAAAACCATTCATCAACAAGAAAAGTCCATTTATAGTCACCCATTTATT
* *
2110 CAAAAGCCTTATTACTCGCTTTAA
119 CAAAAGCTTTATTACTAGCTTTAA
2134 NNNNNNNNNN
Statistics
Matches: 239, Mismatches: 54, Indels: 43
0.71 0.16 0.13
Matches are distributed among these distances:
159 1 0.00
162 3 0.01
163 6 0.03
166 4 0.02
167 1 0.00
168 1 0.00
169 23 0.10
170 160 0.67
171 39 0.16
172 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.37
Consensus pattern (162 bp):
GTTGAATTTTTTTTACATTTTTCATTAAAACAGACTACAATTGAATGTCAACCTTAGAAAACATA
TAGAAAAAACCATTCATCAACAAGAAAAGTCCATTTATAGTCACCCATTTATTCAAAAGCTTTAT
TACTAGCTTTAAATGGTTTTATAATCTCATAA
Found at i:1974 original size:170 final size:169
Alignment explanation
Indices: 715--2504 Score: 936
Period size: 171 Copynumber: 10.5 Consensus size: 169
705 CATTCACAAT
* ** ** *
715 AAAAGTCCCTTTATAGTCACCCATTTC-TTCAAAAGCCCTATTACTAACATTAAATGGTTTTATA
1 AAAAGTCCATTTATAGTCACCCA-TTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATA
* * ** * * * *********
779 ATCTGAAAATTGATTTTAAGTGGACTTTTTTGTACATTTTTAGTTAAAACATA-TNNNNNNNNNN
65 ATCTCATAATTGATTTTAAGTTAAATTTTTT-TACATTTTTTGTTAAAACAGACT-ATAATTGAA
* * * * * * *
843 TGTTTACCTTAAGAAACATGA-AGGAAAGGCATTCACTGGCAAG
128 TGTCTGCC-TCAGAAACAT-ATAGAAAAAGCATTCATTGGGAAG
* * * * * * ** **
886 AAAAGTCCATTTTTAGTCACCCATTCCTTCAAATGCCTTACTACACATTTTAAATCATTTTATAA
1 AAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAA
********** * * * *
951 TCTCATAATTGATTTNNNNNNNNNNTTTTTTACATTCTTTATTAAAACA-ATTTATAATTCAATG
66 TCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGTTAAAACAGA-CTATAATTGAATG
* * * *
1015 TCTGTCTTGAGAAACA-AAAGAAAAAAGCCATTCATTGGCAAG
130 TCTG-CCTCAGAAACATATAG-AAAAAG-CATTCATTGGGAAG
* * * ********** *
1057 AAAAATCCGTTTATAGTCACCCATTCCTTCAAANNNNNNNNNNCTCGCTTTAAATAGTTTTATAA
1 AAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAA
* * * * ** * *
1122 TCTCATAATTGATTTTAGGCTATATTCTTTTACATTTTAAG-TAAAACAAATTATAATTGAATGT
66 TCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGT
* * * * *
1186 TTGTCTCA-ATGAACATGA-AGAAAAATCCATTCATT--TATTG
131 CTGCCTCAGA--AACAT-ATAGAAAAA-GCATTCATTGGGA-AG
* * ** * * * * * *
1226 AAAAAGTTCACTTATAGTCACCCAGGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGCTTTATT
1 -AAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATA
* * * * * *
1291 ACCTCATAATTGATTTTAAGGTGAATTTTTTTACA-TTTTAGCTT-AAACAAATTATAA-TGAAA
65 ATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTG-TTAAAACAGACTATAATTG-AA
* * ** * *
1353 TGTCTACCTTGAGAAATGTGA-AGAAAATAAGCATTCATTAGCAAG
128 TGTCTGCC-TCAGAAACAT-ATAG-AAA-AAGCATTCATTGGGAAG
* ** * * * *******
1398 AAAAGTCCATTTATAGTCATCCATTCCCTCAAAAGCCTTATTGCTCGCTTTAAATGCTNNNNNNN
1 AAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAA
*** * * **
1463 NNNCATAATTGATTTTAAGTTGAATTTTTTTTATATTTTTCCTTAAAACAGACTATAATTGAATG
66 TCTCATAATTGATTTTAAGTT-AAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATG
* * * *
1528 TCTGCCTTAGAAAACATATAGAAAATACCATTTATTAGGAAG
130 TCTGCCTCAG-AAACATATAGAAAA-AGCATTCATTGGGAAG
* * *
1570 AAAAGTCTATTTATAGTCCCCCATTTATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAA
1 AAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAA
********** * * *
1635 TCTCATAANNNNNNNNNNGTTGAATTTTTTTACATTTTTTATTAAAACAGACTACAATTGAATGT
66 TCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGT
** * * ****
1700 CAACCTTGAAAAACATGA-AGAAAAAAGCATTCATCAACAAG
131 CTGCC-TCAGAAACAT-ATAG-AAAAAGCATTCATTGGGAAG
* * * *
1741 AAAAGTCCATTTAT-GATCATCCATTCTTTCGAAAGCTTTATTACTAGCTTTAAATGGTTTTATA
1 AAAAGTCCATTTATAG-TCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATA
* * ** * *
1805 ATTTCATAATTGATTTTAAATTAAAAATTTTTACATTTTTTGTTAAAAAAGATTATAATTGAATG
65 ATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATG
* * * *
1870 TCTGTCTCAGAAACGTGTAGAAAAGGTCATTCATTGGGAAG
130 TCTGCCTCAGAAACATATAGAAAAAG-CATTCATTGGGAAG
** * * *
1911 AAAAGTTTATTTATAGTCCCCCATTCATTCAAAAGCTTTATTACTCGTTTTAAATAGTTTTATAA
1 AAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAA
** ***********
1976 TCTCATAATCAATTTTAAGTTTNNNNNNNNNNCATTTTTTGTT-AAACAGACTATAATTGAATGT
66 TCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGT
* * * * * **
2040 CTACCTTGAGAAACGTAAAGAAAAAAGCATTCATCGATAAG
131 CTGCC-TCAGAAACATATAG-AAAAAGCATTCATTGGGAAG
* * * * **********
2081 AAAATTCCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCGCTTTAANNNNNNNNNNAA
1 AAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAA
* * * * *
2146 TTTCATAATTGATTTTAAGTTGAATATTTTTACATTTTTTGTTAAAAAAGATTATAATTGAATGT
66 TCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGT
* * *
2211 CTGCCTTAGGAAACATGAGAGAAAAAGCACTCATTGGTG-AG
131 CTGCCTCA-GAAACAT-ATAGAAAAAGCATTCATTGG-GAAG
* * * ********** *
2252 AAAAGTCCATTTATACTCACCCATTCCTTCAAAAGCCTTATTNNNNNNNNNNAATGGTTTTACAA
1 AAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAA
* * * ** * *
2317 TCTCATAATTGATTTCAAGTTGAATTTTTTTTATATTTTTCCTTAAAATAGATTATAATTGAATG
66 TCTCATAATTGATTTTAAGTT-AAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATG
*
2382 -CTTGCCTCAGAAAACATATAGAAAAGGCTATTCATTGGGAAG
130 TC-TGCCTCAG-AAACATATAGAAAAAGC-ATTCATTGGGAAG
* * **
2424 AAAAGTCTATTTATAGTCATCCATTCATTCAAAAGCTTTATTACTCATTTTAAATGGTTTTATAA
1 AAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAA
2489 TCTCATAATTGATTTT
66 TCTCATAATTGATTTT
2505 NNNNNNNNNN
Statistics
Matches: 1204, Mismatches: 366, Indels: 97
0.72 0.22 0.06
Matches are distributed among these distances:
168 3 0.00
169 40 0.03
170 377 0.31
171 525 0.44
172 226 0.19
173 31 0.03
174 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.36
Consensus pattern (169 bp):
AAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAA
TCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGT
CTGCCTCAGAAACATATAGAAAAAGCATTCATTGGGAAG
Found at i:5364 original size:171 final size:170
Alignment explanation
Indices: 4529--5532 Score: 677
Period size: 171 Copynumber: 5.9 Consensus size: 170
4519 NNNNNNNNNN
* * * * **
4529 TCAATTATAAGATTATAAAACTATTTAAAGCGAGCAATAAGGCTTTTGAAAGAACAGGTGACTAT
1 TCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCTTTTGAAAGAATGGGTGACTAT
* * * * * *
4594 AAATGGACTTTTCTTGCTAATGAATGTCTTTTTCTTCTCTTTTCT-AGAGATAAACATTCAATTA
66 AAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCTCCTTTCTCA-AGGTAGACATTCAATTA
* * * ****
4658 GAATCTGTTTTAACT-AAAATGTAAAAAAATTTAACTTNNNN
130 TAGTCTGTTTTAACTAAAAATGT-AAAAAATTCAACTTAAAA
****** * * * * *
4699 NNNNNNATGAGATTATAAAACCTTTTAAA-ATGACTAATAAGGCTTTCGAAAGAATGGGAGACTA
1 TCAATTATGAGATTATAAAACCATTTAAAGCT-AGTAATAAGGCTTTTGAAAGAATGGGTGACTA
* *** * * * *
4763 TAAGTAGACTTTTCTTTAAAATGAATTG-CTTTTTCTACATGC-TTCCCAAGGCAGACATTCAAT
65 TAAATAGACTTTTCTTGCCAATGAA-TGCCTTTTTCTTC-TCCTTTCTCAAGGTAGACATTCAAT
*
4826 TATAGTCTGTTTTAA-TAATAAATGTAAACAAATTCAACTTGAAA
128 TATAGTCTGTTTTAACTAA-AAATGTAAA-AAATTCAACTTAAAA
* ********** * *
4870 TCAATTATGAGATTATAAAACAATTNNNNNNNNNNAATAAGGCTTTTGACAGAATGAGTGACTAT
1 TCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCTTTTGAAAGAATGGGTGACTAT
* ** * * *
4935 AAATGGACTTTTCTT-CTCAATGAATGCCTTTTGATTCACGTTTCTCAAGGTAGGCATTCAATTA
66 AAATAGACTTTTCTTGC-CAATGAATGCCTTTTTCTTCTCCTTTCTCAAGGTAGACATTCAATTA
********** *
4999 TAGNNNNNNNNNNCCAAAAATGTAAAAAATTCAACTTAAAA
130 TAGTCTGTTTTAACTAAAAATGTAAAAAATTCAACTTAAAA
* * * ** *
5040 TGAATTTTGAGATTAT-AAACCATATAAAG-TGAGTAATAAGGCTTTTGATGGAATGGGTAACTA
1 TCAATTATGAGATTATAAAACCATTTAAAGCT-AGTAATAAGGCTTTTGAAAGAATGGGTGACTA
* * * *
5103 TAAATAGACTTTTATTGTCAATGAATGCCTTTTTCTT-TACGTTTCTTAAGGTAGACATTCAATT
65 TAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCT-CCTTTCTCAAGGTAGACATTCAATT
************* *
5167 ATAGTCTNNNNNNNNNNNNNATGTAAAAACATTCAACCTAAAA
129 ATAGTCTGTTTTAACTAAAAATGTAAAAA-ATTCAACTTAAAA
* * * *
5210 TCAATTATGACATTATAAAACCATTTAAAGCTAGTAACAAGGCTTCTGAAAGGATGGGTGACTAT
1 TCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCTTTTGAAAGAATGGGTGACTAT
* * *
5275 AAATAGACTTTTCTTGCCAATGAATGCCTTTTTGTTCTCCTTTCTCAAGATAAACATTCAATTAT
66 AAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCTCCTTTCTCAAGGTAGACATTCAATTAT
* * *
5340 AATCTGTTTTAAGTAAAAATGTAAAAATATTTAACTTAAAA
131 AGTCTGTTTTAACTAAAAATGTAAAAA-ATTCAACTTAAAA
** * * * ****
5381 TCAATTATGAGATTATAAATTC-TGTTAAAGCGAGTAATAACGCTTTTGAAGGAATAAAAGACTA
1 TCAATTATGAGATTATAAAACCAT-TTAAAGCTAGTAATAAGGCTTTTGAAAGAATGGGTGACTA
* * * * **
5445 TAAATGGACTTTTCTT-CCAAATGAATAG-CTTTTTCTACAT-GTTTCTCGAGACAGACATTCAA
65 TAAATAGACTTTTCTTGCC-AATGAAT-GCCTTTTTCTTC-TCCTTTCTCAAGGTAGACATTCAA
* * *
5507 TTATATTCTATTTTAACAAAAAATGT
127 TTATAGTCTGTTTTAACTAAAAATGT
5533 TTAAGCACAA
Statistics
Matches: 636, Mismatches: 175, Indels: 45
0.74 0.20 0.05
Matches are distributed among these distances:
169 106 0.17
170 165 0.26
171 359 0.56
172 6 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Consensus pattern (170 bp):
TCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCTTTTGAAAGAATGGGTGACTAT
AAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCTCCTTTCTCAAGGTAGACATTCAATTAT
AGTCTGTTTTAACTAAAAATGTAAAAAATTCAACTTAAAA
Found at i:14891 original size:25 final size:22
Alignment explanation
Indices: 14831--14892 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
14821 ATATGTTGTC
14831 TTAA-TTAAGACAAGAGTTATT
1 TTAATTTAAGACAAGAGTTATT
14852 TTAATTTAA-ACAAGAGTATATGT
1 TTAATTTAAGACAAGAGT-TAT-T
*
14875 GTTGATTTAAGACAAGAG
1 -TTAATTTAAGACAAGAG
14893 ATGTCTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 12 0.34
22 7 0.20
23 1 0.03
24 8 0.23
25 7 0.20
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (22 bp):
TTAATTTAAGACAAGAGTTATT
Found at i:22877 original size:25 final size:26
Alignment explanation
Indices: 22847--22928 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 26
22837 GTGGTCGTAA
*
22847 CCACGTA-AATCAACGCATGGCCTTG
1 CCACGTATAATCAACCCATGGCCTTG
*
22872 CCACGTATAA-CAACCCGTGGCCTTG
1 CCACGTATAATCAACCCATGGCCTTG
* * *
22897 CCAGGTATAATCACAAACCATGGCCTAG
1 CCACGTATAAT--CAACCCATGGCCTTG
22925 CCAC
1 CCAC
22929 ATCTAATAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
25 29 0.63
26 2 0.04
28 15 0.33
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (26 bp):
CCACGTATAATCAACCCATGGCCTTG
Found at i:24866 original size:22 final size:22
Alignment explanation
Indices: 24840--24882 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24830 CTTTTTCTAT
*
24840 TTTTGTTTTTGTTA-TTTCTTAG
1 TTTTGTTTCT-TTAGTTTCTTAG
24862 TTTTGTTTCTTTAGTTTCTTA
1 TTTTGTTTCTTTAGTTTCTTA
24883 TTACACCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.09, C:0.07, G:0.12, T:0.72
Consensus pattern (22 bp):
TTTTGTTTCTTTAGTTTCTTAG
Found at i:29171 original size:77 final size:76
Alignment explanation
Indices: 29045--29207 Score: 254
Period size: 77 Copynumber: 2.1 Consensus size: 76
29035 AATACCATTT
* *
29045 ATTTTAATTTTGGGTGATCCATAAAAATAGAAAATTGTTTCCTACTTTAAAAGCAATTCCTAAAA
1 ATTTTAATTTTGAGTGATCCATAAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAAA
*
29110 TTAAGGATAGA
66 TTAAGAATAGA
* * *
29121 ATTTTAATTTTGAGTGATTCATAAAAAATAGGAAATTGTTTCCTACTTTAAAAGAAATTCTTAAA
1 ATTTTAATTTTGAGTGATCCAT-AAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
*
29186 ATTAAGAATAGT
65 ATTAAGAATAGA
29198 ATTTTAATTT
1 ATTTTAATTT
29208 GAGAAATTCA
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
76 20 0.25
77 59 0.75
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (76 bp):
ATTTTAATTTTGAGTGATCCATAAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAAA
TTAAGAATAGA
Found at i:40446 original size:72 final size:72
Alignment explanation
Indices: 40329--40475 Score: 267
Period size: 72 Copynumber: 2.0 Consensus size: 72
40319 AGAAACAAGA
* *
40329 GATTGAGTCTTGCCAAAGGCTAAGGCAAGAGTGAGTGGAAATTTAGGTGAAAGTATGAGACATTT
1 GATTGAGTCCTGCCAAAGGCTAAGGCAAGAGTAAGTGGAAATTTAGGTGAAAGTATGAGACATTT
40394 GTAAAGG
66 GTAAAGG
*
40401 GATTGGGTCCTGCCAAAGGCTAAGGCAAGAGTAAGTGGAAATTTAGGTGAAAGTATGAGACATTT
1 GATTGAGTCCTGCCAAAGGCTAAGGCAAGAGTAAGTGGAAATTTAGGTGAAAGTATGAGACATTT
40466 GTAAAGG
66 GTAAAGG
40473 GAT
1 GAT
40476 GCCAATACCA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (72 bp):
GATTGAGTCCTGCCAAAGGCTAAGGCAAGAGTAAGTGGAAATTTAGGTGAAAGTATGAGACATTT
GTAAAGG
Found at i:52975 original size:21 final size:21
Alignment explanation
Indices: 52950--52989 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52940 CTTCTGTTGA
*
52950 AAATGTATCGATACATTTATG
1 AAATGCATCGATACATTTATG
* *
52971 AAATGCATTGATACTTTTA
1 AAATGCATCGATACATTTA
52990 CGGCAATAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
AAATGCATCGATACATTTATG
Found at i:53052 original size:80 final size:81
Alignment explanation
Indices: 52951--53129 Score: 243
Period size: 80 Copynumber: 2.2 Consensus size: 81
52941 TTCTGTTGAA
* * * *
52951 AATGTATCGATACATTTATGAAATGCATTGATACTTTTACGGCAATAAGCATTCTGTCTGAATTC
1 AATGTATCGATACATTTATGAAATGCATCGATACTTCTACGGCAATAAGCATTCTATCTCAATTC
*
53016 TATCAATACAATTAAG
66 TATCAACACAATTAAG
* ** *
53032 AATG-ATTGATACATTTATGAAATGTGTCGATACTTCTACGGCAATAAGTATTCTATCTCAATTC
1 AATGTATCGATACATTTATGAAATGCATCGATACTTCTACGGCAATAAGCATTCTATCTCAATTC
**
53096 TATTGACACAATTAAG
66 TATCAACACAATTAAG
*
53112 AATGTATCGATATATTTA
1 AATGTATCGATACATTTA
53130 AGTTTGACTT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 69 0.82
81 15 0.18
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (81 bp):
AATGTATCGATACATTTATGAAATGCATCGATACTTCTACGGCAATAAGCATTCTATCTCAATTC
TATCAACACAATTAAG
Found at i:58319 original size:54 final size:54
Alignment explanation
Indices: 58260--58364 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
58250 TTTTAGTATA
* *
58260 AAATATTACGTATGTAATAAAATAATAATAAAGTAATAATATCTTATTGAGGTC
1 AAATATTACGTATGCAATAAAATAATAATAAACTAATAATATCTTATTGAGGTC
** *
58314 AAATATTTTGTATGCAATAAAATAATAATAAACTAATAATATTTTATTGAG
1 AAATATTACGTATGCAATAAAATAATAATAAACTAATAATATCTTATTGAG
58365 ATCGAAGTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (54 bp):
AAATATTACGTATGCAATAAAATAATAATAAACTAATAATATCTTATTGAGGTC
Found at i:58472 original size:19 final size:19
Alignment explanation
Indices: 58448--58486 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
58438 GCTAGAGGAA
58448 AATTTTAAAATAAAATAAT
1 AATTTTAAAATAAAATAAT
* *
58467 AATTTTTAGATAAAATAAT
1 AATTTTAAAATAAAATAAT
58486 A
1 A
58487 TTAAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTTTAAAATAAAATAAT
Found at i:67668 original size:15 final size:15
Alignment explanation
Indices: 67648--67677 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
67638 AACAATATCT
67648 AATATTAATTAATTA
1 AATATTAATTAATTA
*
67663 AATATTTATTAATTA
1 AATATTAATTAATTA
67678 TTTATAAATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTAATTAATTA
Found at i:67687 original size:21 final size:21
Alignment explanation
Indices: 67647--67704 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
67637 TAACAATATC
*
67647 TAATATTAATTA-ATTAAATATT
1 TAATATT-ATTATA-TAAATAAT
*
67669 TATTAATTATT-TATAAATAAT
1 TAAT-ATTATTATATAAATAAT
67690 TAATATTATTATATA
1 TAATATTATTATATA
67705 TCAGGTGGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 6 0.20
21 14 0.47
22 7 0.23
23 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATATTATTATATAAATAAT
Found at i:68617 original size:17 final size:16
Alignment explanation
Indices: 68579--68609 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
68569 TTTGGAAACC
68579 GAAAATTAATTTTTAA
1 GAAAATTAATTTTTAA
68595 GAAAATTAATTTTTA
1 GAAAATTAATTTTTA
68610 TGGAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
GAAAATTAATTTTTAA
Found at i:69373 original size:24 final size:24
Alignment explanation
Indices: 69343--69392 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
69333 ATTTAAAATA
*
69343 TTAAAAACTATTAACAT-TTAATTTT
1 TTAAAAA-AATTAA-ATATTAATTTT
69368 TTAAAAAAATTAAATATTAATTTT
1 TTAAAAAAATTAAATATTAATTTT
69392 T
1 T
69393 AAATTATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 14 0.61
25 7 0.30
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAAAAAATTAAATATTAATTTT
Found at i:73772 original size:12 final size:13
Alignment explanation
Indices: 73757--73792 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
73747 AGAGATTTTT
73757 GAGGCAGCAAGA-
1 GAGGCAGCAAGAG
73769 GAGGCAGCAA-AG
1 GAGGCAGCAAGAG
73781 GAGGCAGCAAGA
1 GAGGCAGCAAGA
73793 AACTATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (13 bp):
GAGGCAGCAAGAG
Found at i:75464 original size:35 final size:35
Alignment explanation
Indices: 75416--75608 Score: 235
Period size: 35 Copynumber: 5.5 Consensus size: 35
75406 NNNAAGTTGT
* *
75416 GCCTAATTCATTAAATTGTTTAATTAAGTCATTGG
1 GCCTAATTGATTAAATTGTTTAATTAAGTTATTGG
* * * **** *
75451 GCCTACTTAATTAACTTAAACAATTACGTTATTGG
1 GCCTAATTGATTAAATTGTTTAATTAAGTTATTGG
* *
75486 GTCTAATTGATTAAATTTGTTTAATCAAGTTATTGG
1 GCCTAATTGATTAAA-TTGTTTAATTAAGTTATTGG
*
75522 GCCTAAATGATTAAATTGTTTAATTAAGTTATT-G
1 GCCTAATTGATTAAATTGTTTAATTAAGTTATTGG
*
75556 GACTCAATTGATTAAATTGTTTAATTAAGTTATTGG
1 GCCT-AATTGATTAAATTGTTTAATTAAGTTATTGG
75592 GCCTAATTGATTAAATT
1 GCCTAATTGATTAAATT
75609 AACACTTCCG
Statistics
Matches: 130, Mismatches: 25, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
34 4 0.03
35 95 0.73
36 31 0.24
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (35 bp):
GCCTAATTGATTAAATTGTTTAATTAAGTTATTGG
Found at i:97451 original size:21 final size:21
Alignment explanation
Indices: 97413--97455 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
97403 CCTCCTTACC
*
97413 CCTTTTTCTCCTTCCTTTCTT
1 CCTTTATCTCCTTCCTTTCTT
97434 CCTTTATCTTCCTT-CTTTCTT
1 CCTTTATC-TCCTTCCTTTCTT
97455 C
1 C
97456 TCCTTTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.60
Consensus pattern (21 bp):
CCTTTATCTCCTTCCTTTCTT
Found at i:104058 original size:31 final size:31
Alignment explanation
Indices: 103954--104064 Score: 118
Period size: 31 Copynumber: 3.5 Consensus size: 31
103944 TGCCGTAGGA
* * *
103954 ACTAAATTGAATAAAAGTGTATGA-TAAAAGG
1 ACTAAATTGAACAAAAATGTA-GAGTATAAGG
* *
103985 ACTAAATTGAATAAAAATGTAGAGTATGAGG
1 ACTAAATTGAACAAAAATGTAGAGTATAAGG
* *
104016 ACTAAATTGAACAAAATTG-AGATGTTTAAGG
1 ACTAAATTGAACAAAAATGTAGA-GTATAAGG
104047 ACTAAATTGAACCAAAAA
1 ACTAAATTGAA-CAAAAA
104065 AATATTTTGC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.07
31 59 0.86
32 5 0.07
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.25
Consensus pattern (31 bp):
ACTAAATTGAACAAAAATGTAGAGTATAAGG
Found at i:106549 original size:40 final size:41
Alignment explanation
Indices: 106480--106559 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
106470 TTGGCTGTTT
* *
106480 TTCACTTTAGTGGGGTTTTCTAACTTTGCCAAGATTGGTGG
1 TTCACCTTAGTGGAGTTTTCTAACTTTGCCAAGATTGGTGG
*
106521 TTCACCTTAGTGGAG-TTTCTAA-TCTTGCCACGATTGGTG
1 TTCACCTTAGTGGAGTTTTCTAACT-TTGCCAAGATTGGTG
106560 TCTTTTACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 1 0.03
40 21 0.60
41 13 0.37
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.40
Consensus pattern (41 bp):
TTCACCTTAGTGGAGTTTTCTAACTTTGCCAAGATTGGTGG
Found at i:106893 original size:21 final size:21
Alignment explanation
Indices: 106855--106911 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
106845 AGCTCTCTAC
** *
106855 CTCAAGGTTGACTCTATGTTA
1 CTCAAGGTCAACTATATGTTA
* * *
106876 GTTAAGGTCAACTATATGTTC
1 CTCAAGGTCAACTATATGTTA
106897 CTCAAGGTCAACTAT
1 CTCAAGGTCAACTAT
106912 GGCTTTGTGT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (21 bp):
CTCAAGGTCAACTATATGTTA
Found at i:111577 original size:20 final size:20
Alignment explanation
Indices: 111521--111569 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
111511 TTTCCAGAAC
111521 CAAATGTATAGATACATGGG
1 CAAATGTATAGATACATGGG
111541 CAAATGTATAGATACATGGG
1 CAAATGTATAGATACATGGG
*
111561 CTAATGTAT
1 CAAATGTAT
111570 TGACACATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (20 bp):
CAAATGTATAGATACATGGG
Found at i:118075 original size:31 final size:30
Alignment explanation
Indices: 118004--118110 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
117994 AATCAACTAT
118004 TGTAAGGTTATACCTCTTTTACAAAAGGTAG
1 TGTAAGGTTATACCT-TTTTACAAAAGGTAG
** **
118035 -AAAATGGTTATACCTTTATTGTAAAAGGTAG
1 TGTAA-GGTTATACCTTT-TTACAAAAGGTAG
** *
118066 TGTAAGGTTATACCTTCATAAAAAAGGTAG
1 TGTAAGGTTATACCTTTTTACAAAAGGTAG
* * *
118096 AGAAAAGTTATACCT
1 TGTAAGGTTATACCT
118111 CCTCTATAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
30 26 0.43
31 32 0.53
32 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (30 bp):
TGTAAGGTTATACCTTTTTACAAAAGGTAG
Found at i:118121 original size:61 final size:62
Alignment explanation
Indices: 118004--118138 Score: 143
Period size: 61 Copynumber: 2.2 Consensus size: 62
117994 AATCAACTAT
** * * * * * *
118004 TGTAAGGTTATACCTCTTTTACAAAAGGTAGAAAATGGTTATACCTTTATTGTAAAAGGTAG
1 TGTAAGGTTATACCTCTCATAAAAAAGGTAGAAAATAGTTATACCTCTACTATAAAAGGTAA
118066 TGTAAGGTTATACCT-TCATAAAAAAGGTAGAGAAA-AGTTATACCTCCT-CTATAAAAGGTAA
1 TGTAAGGTTATACCTCTCATAAAAAAGGTAGA-AAATAGTTATACCT-CTACTATAAAAGGTAA
118127 TGTACA-GTTATA
1 TGTA-AGGTTATA
118139 GCTCCACTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
61 42 0.68
62 20 0.32
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (62 bp):
TGTAAGGTTATACCTCTCATAAAAAAGGTAGAAAATAGTTATACCTCTACTATAAAAGGTAA
Found at i:118125 original size:31 final size:31
Alignment explanation
Indices: 118056--118217 Score: 97
Period size: 31 Copynumber: 5.3 Consensus size: 31
118046 ACCTTTATTG
* *
118056 TAAAAGGTAGTGTAAGGTTATACCT--TCATA
1 TAAAAGGTAGAGTAAAGTTATACCTCCTC-TA
* *
118086 AAAAAGGTAGAGAAAAGTTATACCTCCTCTA
1 TAAAAGGTAGAGTAAAGTTATACCTCCTCTA
* * * *
118117 TAAAAGGTA-ATGTACAGTTATAGCTCCACTG
1 TAAAAGGTAGA-GTAAAGTTATACCTCCTCTA
* * * *
118148 TCAAAGGTAGTGCAAGGTTATA---CCTCTA
1 TAAAAGGTAGAGTAAAGTTATACCTCCTCTA
*
118176 TAGAAAGGTAAAG-AAAGCTTATACCTCCT-TAA
1 TA-AAAGGTAGAGTAAAG-TTATACCTCCTCT-A
*
118208 GAAAAGGTAG
1 TAAAAGGTAG
118218 CGTGTTAAAG
Statistics
Matches: 99, Mismatches: 23, Indels: 19
0.70 0.16 0.13
Matches are distributed among these distances:
28 8 0.08
29 13 0.13
30 22 0.22
31 49 0.49
32 7 0.07
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (31 bp):
TAAAAGGTAGAGTAAAGTTATACCTCCTCTA
Found at i:123101 original size:20 final size:20
Alignment explanation
Indices: 123076--123142 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
123066 GTATTTCATA
*
123076 GCAAAGAATGATGCTTACAT
1 GCAAAGAATGATGCTAACAT
* ** *
123096 GCAAAGAATGATACCCATAT
1 GCAAAGAATGATGCTAACAT
123116 GACAAAGAATGATGCTAACAT
1 G-CAAAGAATGATGCTAACAT
*
123137 TCAAAG
1 GCAAAG
123143 TGCAGTAGCC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 22 0.59
21 15 0.41
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (20 bp):
GCAAAGAATGATGCTAACAT
Found at i:135617 original size:12 final size:12
Alignment explanation
Indices: 135596--135628 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
135586 AGTTCTATAA
*
135596 ATGCAACATGAC
1 ATGCATCATGAC
135608 ATGCATCATGAC
1 ATGCATCATGAC
135620 ATGCATCAT
1 ATGCATCAT
135629 CAAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (12 bp):
ATGCATCATGAC
Found at i:151821 original size:35 final size:34
Alignment explanation
Indices: 151782--151875 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 34
151772 TTGGGTTTTG
*
151782 GTTGATCCTAGGAAAAACCATTGTTG-AAGATTGTA
1 GTTGAGCCT-GGAAAAACCATTGTTGAAAG-TTGTA
* * *
151817 GTTGAGCCTTTGAAAAACAATTGTTGAAAGTTGTG
1 GTTGAGCC-TGGAAAAACCATTGTTGAAAGTTGTA
*
151852 GTTGAGCCTGTGAAAAGCCATTGT
1 GTTGAGCCTG-GAAAAACCATTGT
151876 AAAAGCTTGN
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
34 1 0.02
35 44 0.90
36 4 0.08
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.32
Consensus pattern (34 bp):
GTTGAGCCTGGAAAAACCATTGTTGAAAGTTGTA
Found at i:167532 original size:68 final size:68
Alignment explanation
Indices: 167422--167655 Score: 254
Period size: 68 Copynumber: 3.4 Consensus size: 68
167412 ATGTTTGGTT
* *
167422 TGATGAATGCCATAAGATTAG-GTATATGATGTAAATTTCATATACCATATGAGATAATTAAGTA
1 TGATGAATACCATAAGATT-GTGTATATGATGTAAATTCCATATACCATATGAGATAATTAAGTA
167486 TGCA
65 TGCA
** * * ** *
167490 TGATGTCTACTATAAGATTGTGTATATGATGTAAATTCCATATAACATAAAATATAATTAAGTAT
1 TGATGAATACCATAAGATTGTGTATATGATGTAAATTCCATATACCATATGAGATAATTAAGTAT
167555 GCA
66 GCA
* * * * * * * * *
167558 TGATGAATGCCATGAGATTATGTATATGATGTATATTCCATATACTACATGAGATGATTAAGGAA
1 TGATGAATACCATAAGATTGTGTATATGATGTAAATTCCATATACCATATGAGATAATTAAGTAT
167623 GCA
66 GCA
* * **
167626 TGATGAATCCCATGAGATAATGTATATGAT
1 TGATGAATACCATAAGATTGTGTATATGAT
167656 ATATTTTTCA
Statistics
Matches: 138, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
67 1 0.01
68 137 0.99
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (68 bp):
TGATGAATACCATAAGATTGTGTATATGATGTAAATTCCATATACCATATGAGATAATTAAGTAT
GCA
Found at i:171499 original size:43 final size:43
Alignment explanation
Indices: 171450--171540 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
171440 TTAGGTGCAC
* * *
171450 AAAGAACCAATATCTGGAA-AAGAAAGAATTAATTCTCAATCAA
1 AAAGAACCAATATCT-AAAGAAGAAAGAATCAATTCTCAAACAA
* * *
171493 GAAGAACTAATATCTAAAGAAGCAAGAATCAATTCTCAAACAA
1 AAAGAACCAATATCTAAAGAAGAAAGAATCAATTCTCAAACAA
171536 AAAGA
1 AAAGA
171541 GCAGACTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 2 0.05
43 38 0.95
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.19
Consensus pattern (43 bp):
AAAGAACCAATATCTAAAGAAGAAAGAATCAATTCTCAAACAA
Found at i:174483 original size:28 final size:28
Alignment explanation
Indices: 174451--174520 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
174441 CTGTTTGCTT
* *
174451 TTTACTATTTATTTAAACAAAACAAATC
1 TTTACTAGTTACTTAAACAAAACAAATC
** *
174479 TTTACTAGTTACTTCTAGAAAACAAATC
1 TTTACTAGTTACTTAAACAAAACAAATC
* *
174507 TTAACCAGTTACTT
1 TTTACTAGTTACTT
174521 TTTTAAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.39
Consensus pattern (28 bp):
TTTACTAGTTACTTAAACAAAACAAATC
Found at i:175694 original size:25 final size:25
Alignment explanation
Indices: 175658--175723 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
175648 CGAAAAGTGG
* *
175658 ATGGATAGTTTTGCCATCAGAATCT
1 ATGGATAATTTTACCATCAGAATCT
* *
175683 ATGGATAATTTTACCTTCAGAATGT
1 ATGGATAATTTTACCATCAGAATCT
** *
175708 AAAGATAATTCTACCA
1 ATGGATAATTTTACCA
175724 CGAAAAGTGG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (25 bp):
ATGGATAATTTTACCATCAGAATCT
Found at i:190060 original size:27 final size:27
Alignment explanation
Indices: 190022--190074 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
190012 TTTGTCACGT
*
190022 AAAATGAAATAAAA-TATTTATTATATG
1 AAAATAAAATAAAATTA-TTATTATATG
190049 AAAATAAAATAAAATTATTATTATAT
1 AAAATAAAATAAAATTATTATTATAT
190075 AATTTAGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
AAAATAAAATAAAATTATTATTATATG
Found at i:190287 original size:13 final size:13
Alignment explanation
Indices: 190269--190295 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
190259 AATTTATTAC
190269 TAAATTATTAATA
1 TAAATTATTAATA
190282 TAAATTATTAATA
1 TAAATTATTAATA
190295 T
1 T
190296 TTTAACTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTATTAATA
Found at i:190364 original size:21 final size:20
Alignment explanation
Indices: 190325--190364 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
190315 ATTGAATAAT
*
190325 TAATTTTTAAATTAGTTATA
1 TAATTTTTAAATTAATTATA
*
190345 TAATTTTTAATTTTAATTAT
1 TAATTTTTAA-ATTAATTAT
190365 TTGAATCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TAATTTTTAAATTAATTATA
Found at i:190463 original size:23 final size:23
Alignment explanation
Indices: 190433--190488 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
190423 ATTAAACATC
190433 AATAATTTATTATTAAATT-ATTA
1 AATAATTT-TTATTAAATTAATTA
*
190456 AATAATTTCTATTAAATTAATTA
1 AATAATTTTTATTAAATTAATTA
*
190479 TATAATTTTT
1 AATAATTTTT
190489 TATTTTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
AATAATTTTTATTAAATTAATTA
Found at i:190496 original size:26 final size:24
Alignment explanation
Indices: 190438--190496 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 24
190428 ACATCAATAA
190438 TTTATTATTAAATTATTAAATAATT
1 TTTATT-TTAAATTATTAAATAATT
* *
190463 TCTA--TTAAATTAATTATATAATTT
1 TTTATTTTAAATT-ATTAAATAA-TT
190487 TTTATTTTAA
1 TTTATTTTAA
190497 TAATTTGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
22 7 0.26
23 8 0.30
24 5 0.19
25 3 0.11
26 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTATTTTAAATTATTAAATAATT
Found at i:190544 original size:135 final size:136
Alignment explanation
Indices: 190302--190572 Score: 404
Period size: 135 Copynumber: 2.0 Consensus size: 136
190292 ATATTTTAAC
* * * *
190302 TTATTATTAAATTATTGAATAATTAATTTTTAAATTAGTTATATAATTTTTAATTTTAATTATTT
1 TTATTATTAAATTATTAAATAATT-ATTATTAAATTAATTATATAATTTTTAATTTTAATAATTT
*
190367 GAATCATTTTTCTCTATTATTATTTTTCATATCTTAATCTTTTAATTTCTATTTTCATTAAACAT
65 GAATCATTTTTCTCTATTAGTATTTTTCATATCTTAATCTTTTAATTTCTATTTTCATTAAACAT
190432 CAATAAT
130 CAATAAT
*
190439 TTATTATTAAATTATTAAATAATT-TCTATTAAATTAATTATATAATTTTTTATTTTAATAATTT
1 TTATTATTAAATTATTAAATAATTAT-TATTAAATTAATTATATAATTTTTAATTTTAATAATTT
* * * *
190503 GAAT-ATTTTTCTCTATCT-GTATTTTTCATTTTTTAATCTTTTAATTTTTATTTTTATTAAACA
65 GAATCATTTTTCTCTAT-TAGTATTTTTCATATCTTAATCTTTTAATTTCTATTTTCATTAAACA
190566 TCAATAA
129 TCAATAA
190573 GGGAGAAAAA
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
135 60 0.49
136 39 0.32
137 23 0.19
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (136 bp):
TTATTATTAAATTATTAAATAATTATTATTAAATTAATTATATAATTTTTAATTTTAATAATTTG
AATCATTTTTCTCTATTAGTATTTTTCATATCTTAATCTTTTAATTTCTATTTTCATTAAACATC
AATAAT
Found at i:207632 original size:43 final size:42
Alignment explanation
Indices: 207531--207642 Score: 152
Period size: 42 Copynumber: 2.6 Consensus size: 42
207521 GCTATTATGA
* * *
207531 TTAAATTTAAACAAATTAAATTTAAATATAATTAATCTTTAT
1 TTAAATTTAAACAAATTAAATTTAAATATAATGAATCATAAT
* * * *
207573 TTAAATTTAAACAAATTAAATTTATATATAGTGGATAGATAAT
1 TTAAATTTAAACAAATTAAATTTAAATATAATGAAT-CATAAT
207616 TTAAATTTAAACAAATTAAATTTAAAT
1 TTAAATTTAAACAAATTAAATTTAAAT
207643 TTATATTCTA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
42 32 0.52
43 29 0.48
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (42 bp):
TTAAATTTAAACAAATTAAATTTAAATATAATGAATCATAAT
Found at i:219348 original size:20 final size:20
Alignment explanation
Indices: 219311--219348 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
219301 GAAGAAACAA
*
219311 AGAGAAAAAGAACAAAAATC
1 AGAGAAAAAGAAAAAAAATC
219331 AGAGAAAAAGAAAAAAAA
1 AGAGAAAAAGAAAAAAAA
219349 GGGAAAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.03
Consensus pattern (20 bp):
AGAGAAAAAGAAAAAAAATC
Found at i:234395 original size:17 final size:18
Alignment explanation
Indices: 234347--234394 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
234337 TTTTCTAGGA
234347 AATTGATGAAAAATGCTC
1 AATTGATGAAAAATGCTC
234365 AATTGATGAAAAATGCTC
1 AATTGATGAAAAATGCTC
*
234383 ATTTGATGAAAA
1 AATTGATGAAAA
234395 TCAGTGCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (18 bp):
AATTGATGAAAAATGCTC
Found at i:238023 original size:16 final size:17
Alignment explanation
Indices: 238004--238036 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
237994 GAAGATATTA
238004 AGAG-AAGAAAAAAAAG
1 AGAGAAAGAAAAAAAAG
*
238020 AGAGAAAGAAAGAAAAG
1 AGAGAAAGAAAAAAAAG
238037 GCTTGAGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
AGAGAAAGAAAAAAAAG
Found at i:244750 original size:25 final size:25
Alignment explanation
Indices: 244715--244774 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
244705 AATTTGTGAT
* * *
244715 ATATACATGGCAAGGCCATAGGTTG
1 ATATACGTGGCAAGGCCATAAGCTG
* *
244740 ATATATGTGGCCAGGCCATAAGCTG
1 ATATACGTGGCAAGGCCATAAGCTG
244765 ATATACGTGG
1 ATATACGTGG
244775 TTGTGACCAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (25 bp):
ATATACGTGGCAAGGCCATAAGCTG
Found at i:248356 original size:68 final size:67
Alignment explanation
Indices: 248256--248471 Score: 220
Period size: 68 Copynumber: 3.2 Consensus size: 67
248246 CATCTTATAA
* * * * * *
248256 GGTATATGGAAAATGCCTCATATACATAATCTCATAGTATTCATCATGCTTTCTCAATCATCCCA
1 GGTATATGGAATATACATCATATACATAATCTCATAGTATT-ATCATGCATACTTAATCATCCCA
248321 TAT
65 TAT
* * *
248324 AGTATATGGAATATACATCATATACATTATCTCA-AGGCATTTATCATGCATACTTAATCA-CCT
1 GGTATATGGAATATACATCATATACATAATCTCATA-GTA-TTATCATGCATACTTAATCATCC-
248387 CATAT
63 CATAT
* * * * * * * *
248392 GGTATATGGAATTTACATTATAAACACAATCTTATAGTGTATATCTTGCATACTTAATCATCTCA
1 GGTATATGGAATATACATCATATACATAATCTCATAGTAT-TATCATGCATACTTAATCATCCCA
248457 TAT
65 TAT
248460 GGTATATGGAAT
1 GGTATATGGAAT
248472 TTATATCGCA
Statistics
Matches: 122, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
67 4 0.03
68 114 0.93
69 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (67 bp):
GGTATATGGAATATACATCATATACATAATCTCATAGTATTATCATGCATACTTAATCATCCCAT
AT
Found at i:251312 original size:16 final size:16
Alignment explanation
Indices: 251291--251328 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
251281 CCTTTTGGTC
*
251291 TTGTAATGTCATTACA
1 TTGTAATATCATTACA
251307 TTGTAATATCATTACA
1 TTGTAATATCATTACA
*
251323 TCGTAA
1 TTGTAA
251329 AAGTACCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (16 bp):
TTGTAATATCATTACA
Found at i:253749 original size:9 final size:8
Alignment explanation
Indices: 253735--253813 Score: 67
Period size: 7 Copynumber: 10.1 Consensus size: 8
253725 AGATTCGGCT
253735 AGGAAGCAA
1 AGGAAG-AA
253744 AGGAAGAAA
1 AGGAAG-AA
253753 AGGAA-AA
1 AGGAAGAA
*
253760 AGAAAGAA
1 AGGAAGAA
253768 AGG-AGAA
1 AGGAAGAA
*
253775 AGGAGGAA
1 AGGAAGAA
253783 AGGAAGAA
1 AGGAAGAA
* * *
253791 CGGGAGAG
1 AGGAAGAA
253799 AGG-AGAA
1 AGGAAGAA
253806 A-GAAGAA
1 AGGAAGAA
253813 A
1 A
253814 AGTGAAAGTG
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
6 1 0.02
7 22 0.39
8 21 0.37
9 13 0.23
ACGTcount: A:0.59, C:0.03, G:0.38, T:0.00
Consensus pattern (8 bp):
AGGAAGAA
Found at i:262996 original size:37 final size:37
Alignment explanation
Indices: 262955--263027 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
262945 ATGATATTTA
**
262955 CAAATCACTGTTTTTTAAT-GATCAAGCACAACCTTTG
1 CAAATCACTGCCTTTT-ATGGATCAAGCACAACCTTTG
* *
262992 CAAATCATTGCCTTTTATGGATCAAGCATAACCTTT
1 CAAATCACTGCCTTTTATGGATCAAGCACAACCTTT
263028 CTACCTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.06
37 29 0.94
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.36
Consensus pattern (37 bp):
CAAATCACTGCCTTTTATGGATCAAGCACAACCTTTG
Found at i:263166 original size:61 final size:62
Alignment explanation
Indices: 263057--263172 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 62
263047 ATAAACTTTC
* * * * * * *
263057 TACCTTTTCCAATGGATGTATAACCATTCATTCCCCTTTTTAAGAGAGGTATAACTATATAG
1 TACCTTTTCAAATGGAGGTATAACCACTCACTCACCTTTTCAAAAGAGGTATAACTATATAG
263119 TACCTTTT-AAATGGAGGTATAACCACTCACT-ACCTTTTCCAAAAGAGGTATAAC
1 TACCTTTTCAAATGGAGGTATAACCACTCACTCACCTTTT-CAAAAGAGGTATAAC
263173 CTTTCTACCC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
60 6 0.13
61 32 0.70
62 8 0.17
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34
Consensus pattern (62 bp):
TACCTTTTCAAATGGAGGTATAACCACTCACTCACCTTTTCAAAAGAGGTATAACTATATAG
Found at i:266015 original size:30 final size:30
Alignment explanation
Indices: 265979--266046 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
265969 CCAGAGAGCT
*
265979 CAGCGCTTCAGCTCTGGCGAAGTAACACCG
1 CAGCGCTGCAGCTCTGGCGAAGTAACACCG
* *
266009 CAGCGCTGCAGCTCTGGTGAAGTAACGCCG
1 CAGCGCTGCAGCTCTGGCGAAGTAACACCG
266039 CAGCGCTG
1 CAGCGCTG
266047 GACGACTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.21, C:0.32, G:0.31, T:0.16
Consensus pattern (30 bp):
CAGCGCTGCAGCTCTGGCGAAGTAACACCG
Found at i:273590 original size:14 final size:14
Alignment explanation
Indices: 273571--273599 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
273561 GAACTTCTGC
273571 ATCCTAAGTTTAAG
1 ATCCTAAGTTTAAG
273585 ATCCTAAGTTTAAG
1 ATCCTAAGTTTAAG
273599 A
1 A
273600 GACTTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (14 bp):
ATCCTAAGTTTAAG
Found at i:278544 original size:14 final size:13
Alignment explanation
Indices: 278516--278575 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
278506 TCCTCTAGCT
278516 TTTCTTCTTTTTTC
1 TTTC-TCTTTTTTC
278530 TTTCTCTTTTCTTC
1 TTTCTCTTTT-TTC
*
278544 TATCTCCTTTTTTCC
1 TTTCT-CTTTTTT-C
278559 TTTCT-TTTTTTAC
1 TTTCTCTTTTTT-C
278572 TTTC
1 TTTC
278576 AAAACTGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 17 0.43
14 13 0.32
15 10 0.25
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTCTTTTTTC
Found at i:278553 original size:21 final size:21
Alignment explanation
Indices: 278514--278553 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
278504 CTTCCTCTAG
* * *
278514 CTTTTCTTCTTTTTTCTTTCT
1 CTTTTCTTCTATCTCCTTTCT
278535 CTTTTCTTCTATCTCCTTT
1 CTTTTCTTCTATCTCCTTT
278554 TTTCCTTTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.70
Consensus pattern (21 bp):
CTTTTCTTCTATCTCCTTTCT
Found at i:281108 original size:69 final size:69
Alignment explanation
Indices: 281035--281191 Score: 179
Period size: 69 Copynumber: 2.3 Consensus size: 69
281025 TTGGTGAACA
* * *
281035 TACCATATTTTCCCTTTATAAAAGCCCGGTGTGAGGGTAACAATAAAAGAGGGTCAAGATTAATG
1 TACCATCTTTTCCCTTTATAAAAGCCCGGTGTGAGGGTAACAATAAAACAGAGTCAAGATTAATG
281100 AATG
66 AATG
* * ** * * ** * **
281104 TACCATCTCTTCCCCTTATAAAAGGTCGGTGTGGGGGTAAGAATACCACAGAGTTAAGATTGGTG
1 TACCATCTTTTCCCTTTATAAAAGCCCGGTGTGAGGGTAACAATAAAACAGAGTCAAGATTAATG
281169 AATG
66 AATG
*
281173 TGCCATCTTTTCCCTTTAT
1 TACCATCTTTTCCCTTTAT
281192 GAATCCTAGT
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (69 bp):
TACCATCTTTTCCCTTTATAAAAGCCCGGTGTGAGGGTAACAATAAAACAGAGTCAAGATTAATG
AATG
Found at i:285837 original size:72 final size:73
Alignment explanation
Indices: 285731--285914 Score: 210
Period size: 72 Copynumber: 2.5 Consensus size: 73
285721 GATAGAGAAT
* * * * *
285731 ACTTAGTCGACCAAG-AGACAATGTTAGTCAACTAAGAGCTTAGTACCAAAAACTGGGTTCAGAG
1 ACTTAATCGACTAAGAAG-CAATGTTAGTCGACTAAGAGCTTACTACCAAAAACTAGGTTCAGAG
*
285795 ATAAAAATG
65 ATAAAAACG
* ** *** *
285804 ACTTAATTGACTAAGAAG-TTTGTTAGTCGACTAAGAGCTTACTGTTAAAAACTAGGTTTAGAGA
1 ACTTAATCGACTAAGAAGCAATGTTAGTCGACTAAGAGCTTACTACCAAAAACTAGGTTCAGAGA
*
285868 TAAAGACG
66 TAAAAACG
*
285876 ACTTAATCGACTAAGTAGCAATGTTAGTCGACTAAGAGC
1 ACTTAATCGACTAAGAAGCAATGTTAGTCGACTAAGAGC
285915 ATTTTGTCTG
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
72 59 0.65
73 30 0.33
74 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (73 bp):
ACTTAATCGACTAAGAAGCAATGTTAGTCGACTAAGAGCTTACTACCAAAAACTAGGTTCAGAGA
TAAAAACG
Found at i:297950 original size:73 final size:73
Alignment explanation
Indices: 297822--297985 Score: 188
Period size: 73 Copynumber: 2.2 Consensus size: 73
297812 CAAGAGACAG
* ** *
297822 TGTTAGTCGACTAAGAGCTTACTGCCAAAAACTGGATTCAGTGACAGAAATGACTTAATCAACTA
1 TGTTAGTCGACTAAGAGCTTACTACCAAAAACTGGATTCAAAGACAGAAACGACTTAATCAACTA
297887 AGAAGTTT
66 AGAAGTTT
* * *
297895 TGTTCGTCGACTAAGAGCTTACTACCAAAAACTAGG-TTCAAAGATA-AAGACGACTTAATCGAC
1 TGTTAGTCGACTAAGAGCTTACTACCAAAAACT-GGATTCAAAGACAGAA-ACGACTTAATCAAC
* ***
297958 TAAGTAGCAA
64 TAAGAAGTTT
*
297968 TGTTAGTCAACTAAGAGC
1 TGTTAGTCGACTAAGAGC
297986 ATTCTATTTG
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
72 2 0.03
73 72 0.95
74 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.26
Consensus pattern (73 bp):
TGTTAGTCGACTAAGAGCTTACTACCAAAAACTGGATTCAAAGACAGAAACGACTTAATCAACTA
AGAAGTTT
Found at i:311569 original size:11 final size:11
Alignment explanation
Indices: 311555--311591 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
311545 AATATATTAA
311555 TATTTTAATAT
1 TATTTTAATAT
311566 TATTTT-AT-T
1 TATTTTAATAT
311575 TA-TTTAATAT
1 TATTTTAATAT
311585 TATTTTA
1 TATTTTA
311592 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 3 0.13
9 5 0.22
10 5 0.22
11 10 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTTAATAT
Found at i:312460 original size:20 final size:20
Alignment explanation
Indices: 312431--312468 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
312421 TTAAAAATAA
* *
312431 TTTTATTTAAAATTAATTTC
1 TTTTAATTAAAAATAATTTC
312451 TTTTAATTAAAAATAATT
1 TTTTAATTAAAAATAATT
312469 AAAATTATAA
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:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAATTAAAAATAATTTC
Found at i:336667 original size:7 final size:7
Alignment explanation
Indices: 336657--336704 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
336647 TGAAAGCACA
336657 AAGAAAG
1 AAGAAAG
336664 AAGAAAG
1 AAGAAAG
*
336671 GAGAAAG
1 AAGAAAG
336678 AAGGAAAG
1 AA-GAAAG
336686 -AGAAA-
1 AAGAAAG
336691 AGAGAAAG
1 A-AGAAAG
336699 AAGAAA
1 AAGAAA
336705 AAGGCTTGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
6 4 0.11
7 25 0.71
8 6 0.17
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:336695 original size:21 final size:22
Alignment explanation
Indices: 336659--336701 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
336649 AAAGCACAAA
*
336659 GAAAGAAGAAAGGAGAAAGAAG
1 GAAAGAAGAAAAGAGAAAGAAG
336681 GAAAG-AGAAAAGAGAAAGAAG
1 GAAAGAAGAAAAGAGAAAGAAG
336702 AAAAAGGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (22 bp):
GAAAGAAGAAAAGAGAAAGAAG
Found at i:337609 original size:13 final size:13
Alignment explanation
Indices: 337593--337617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
337583 AGGTTATTTA
337593 TATATATATAAAC
1 TATATATATAAAC
337606 TATATATATAAA
1 TATATATATAAA
337618 GGGTTTTAGA
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:338074 original size:23 final size:26
Alignment explanation
Indices: 338013--338074 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 26
338003 CACGTGGAAA
*
338013 GGCCAC-AGGATGATATATGTGGCTT
1 GGCCACAAGTATGATATATGTGGCTT
*
338038 GGCCAGAAGT-TGATATATGTGG-TT
1 GGCCACAAGTATGATATATGTGGCTT
*
338062 -GCGACAA-TATGAT
1 GGCCACAAGTATGAT
338075 TTCTTCGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 1 0.03
23 9 0.29
24 2 0.06
25 17 0.55
26 2 0.06
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (26 bp):
GGCCACAAGTATGATATATGTGGCTT
Found at i:346709 original size:16 final size:17
Alignment explanation
Indices: 346688--346727 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
346678 CTTTTTCCTC
346688 CTTTCTTCCTTT-TTTT
1 CTTTCTTCCTTTATTTT
346704 CTTTC-TCCTTTATTTT
1 CTTTCTTCCTTTATTTT
346720 CTTT-TTCC
1 CTTTCTTCC
346728 CTTTCTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.70
Consensus pattern (17 bp):
CTTTCTTCCTTTATTTT
Found at i:347888 original size:17 final size:17
Alignment explanation
Indices: 347868--347935 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
347858 TTAATATTTT
*
347868 AATATTATTTTATTAAA
1 AATAATATTTTATTAAA
**
347885 AATAATATTTTAATATTTTA
1 AATAATA-TTT--TATTAAA
* *
347905 ATTATTATTTTATTAAA
1 AATAATATTTTATTAAA
347922 AATAATATTTTATT
1 AATAATATTTTATT
347936 CTAAAATTCT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
17 23 0.59
18 3 0.08
19 3 0.08
20 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATAATATTTTATTAAA
Found at i:347892 original size:20 final size:20
Alignment explanation
Indices: 347867--347930 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
347857 ATTAATATTT
347867 TAATATTATTTTATTAAAAA
1 TAATATTATTTTATTAAAAA
* **
347887 TAATATT-TTAATATT-TTAA
1 TAATATTATT-TTATTAAAAA
347906 T--TATTATTTTATTAAAAA
1 TAATATTATTTTATTAAAAA
347924 TAATATT
1 TAATATT
347931 TTATTCTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 5 0.15
20 15 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATATTATTTTATTAAAAA
Found at i:347919 original size:37 final size:36
Alignment explanation
Indices: 347858--347933 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 36
347848 AATTAAAATA
347858 TTAATATTTTAATATTATTTTATTAAAAATAATATT
1 TTAATATTTTAATATTATTTTATTAAAAATAATATT
347894 TTAATATTTTAATTATTATTTTATTAAAAATAATATT
1 TTAATATTTTAA-TATTATTTTATTAAAAATAATATT
347931 TTA
1 TTA
347934 TTCTAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
36 12 0.31
37 27 0.69
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (36 bp):
TTAATATTTTAATATTATTTTATTAAAAATAATATT
Found at i:348746 original size:18 final size:18
Alignment explanation
Indices: 348723--348760 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
348713 TTGTTAATTA
348723 TTTAG-TTAATTAATTAAT
1 TTTAGTTTAATTAA-TAAT
348741 TTTAGTTTAATTAATAAT
1 TTTAGTTTAATTAATAAT
348759 TT
1 TT
348761 GAAATTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTAGTTTAATTAATAAT
Found at i:348962 original size:22 final size:21
Alignment explanation
Indices: 348937--349004 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 21
348927 GATATTAGTT
348937 TTTCTTGTCTGAGAATCGATTC
1 TTTCTT-TCTGAGAATCGATTC
348959 TTTCCTTTCT-AGATATC-AGTTC
1 TTT-CTTTCTGAGA-ATCGA-TTC
348981 TTTCTTCTCTGAGAATCGATTC
1 TTTCTT-TCTGAGAATCGATTC
349003 TT
1 TT
349005 GCCTTTCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
21 7 0.17
22 26 0.65
23 7 0.17
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.49
Consensus pattern (21 bp):
TTTCTTTCTGAGAATCGATTC
Found at i:348994 original size:44 final size:43
Alignment explanation
Indices: 348925--349026 Score: 150
Period size: 44 Copynumber: 2.3 Consensus size: 43
348915 ATTCATTCTT
* * *
348925 GAGATATTAGTTTTTCTTGTCTGAGAATCGATTCTTTCCTTTC
1 GAGATATCAGTTTTTCTTCTCTGAGAATCGATTCTTGCCTTTC
*
348968 TAGATATCAGTTCTTTCTTCTCTGAGAATCGATTCTTGCCTTTC
1 GAGATATCAGTT-TTTCTTCTCTGAGAATCGATTCTTGCCTTTC
*
349012 GATATATCAGTTTTT
1 GAGATATCAGTTTTT
349027 ATTGCTTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 13 0.25
44 39 0.75
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (43 bp):
GAGATATCAGTTTTTCTTCTCTGAGAATCGATTCTTGCCTTTC
Found at i:351863 original size:240 final size:240
Alignment explanation
Indices: 351440--351889 Score: 837
Period size: 240 Copynumber: 1.9 Consensus size: 240
351430 CAATGTAAGC
*
351440 ATATGAGAAATAATAAATTCAAGCACAAGAAGCATCAAACATAGCATTTTCAACACTTTACCAGC
1 ATATGAGAAATAATAAATTCAAGCACAAGAAGCATCAAACATAGCATTTTCAACACTTTACCAAC
* **
351505 GTATGGACAAAAATGCCTTGAGGTCATTCAAACATTCATTTGTAACAAGAACATGTCATAATAGC
66 ATATGGACAAAAATGCCTCAAGGTCATTCAAACATTCATTTGTAACAAGAACATGTCATAATAGC
351570 ATTTTCAATGTTAGAGACACTTGTTCAATTTTTGAAACATTGTAACCTTAAGCATTGCAACAAGT
131 ATTTTCAATGTTAGAGACACTTGTTCAATTTTTGAAACATTGTAACCTTAAGCATTGCAACAAGT
*
351635 TTTTTCCATTTGAAAAATGTTATTAGCATCAACTTATGATGCTAT
196 CTTTTCCATTTGAAAAATGTTATTAGCATCAACTTATGATGCTAT
*
351680 ATATGAGAAATAATAAATTCAAGCACAAGAAGCATCAAACATAGCATTTTCAACATTTTACCAAC
1 ATATGAGAAATAATAAATTCAAGCACAAGAAGCATCAAACATAGCATTTTCAACACTTTACCAAC
351745 ATATGGACAAAAATGCCTCAAGGTCATTCAAACATTCATTTGTAACAAGAACATGTCATAATAGC
66 ATATGGACAAAAATGCCTCAAGGTCATTCAAACATTCATTTGTAACAAGAACATGTCATAATAGC
*
351810 ATTTTCAATGTTAGGGACACTTGTTCAATTTTTGAAACATTGTAACCTTAAGCATTGCAACAAGT
131 ATTTTCAATGTTAGAGACACTTGTTCAATTTTTGAAACATTGTAACCTTAAGCATTGCAACAAGT
351875 CTTTTCCATTTGAAA
196 CTTTTCCATTTGAAA
351890 CGAGATTTGT
Statistics
Matches: 203, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
240 203 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (240 bp):
ATATGAGAAATAATAAATTCAAGCACAAGAAGCATCAAACATAGCATTTTCAACACTTTACCAAC
ATATGGACAAAAATGCCTCAAGGTCATTCAAACATTCATTTGTAACAAGAACATGTCATAATAGC
ATTTTCAATGTTAGAGACACTTGTTCAATTTTTGAAACATTGTAACCTTAAGCATTGCAACAAGT
CTTTTCCATTTGAAAAATGTTATTAGCATCAACTTATGATGCTAT
Found at i:354913 original size:25 final size:26
Alignment explanation
Indices: 354885--354942 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
354875 AATATCACTG
354885 ATGGCCTAGCCAC-ATATAACAACCT
1 ATGGCCTAGCCACGATATAACAACCT
* * *
354910 ATGGCCTTGCCACGTATATCACAGCCT
1 ATGGCCTAGCCACG-ATATAACAACCT
354937 ATGGCC
1 ATGGCC
354943 CCAGCCATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 12 0.43
27 16 0.57
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (26 bp):
ATGGCCTAGCCACGATATAACAACCT
Found at i:360606 original size:24 final size:23
Alignment explanation
Indices: 360567--360611 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
360557 GCTAGGAAGC
360567 AAAGGAAGAAAGAAAGAAAGGAG
1 AAAGGAAGAAAGAAAGAAAGGAG
360590 AAAGGAAGCAAAGAAAGAAAGG
1 AAAGGAAG-AAAGAAAGAAAGG
360612 TTCGGACTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.64, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
AAAGGAAGAAAGAAAGAAAGGAG
Found at i:364642 original size:20 final size:20
Alignment explanation
Indices: 364610--364651 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
364600 AATTTATAAA
364610 AAAATAATATAAAATT-AACT
1 AAAATAATAT-AAATTAAACT
364630 AAAATAACT-TAAATTAAACT
1 AAAATAA-TATAAATTAAACT
364650 AA
1 AA
364652 TCAACATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.25
20 14 0.70
21 1 0.05
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATAATATAAATTAAACT
Found at i:367751 original size:6 final size:6
Alignment explanation
Indices: 367743--367796 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
367733 TTTTTAATTG
* * * *
367743 ATTTTG ATTTTA ATTTTC ATCTTT ATTTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT A-TTTTT ATTTTT ATTTTT ATTTTT
367792 ATTTT
1 ATTTT
367797 ACATTTTACT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
6 37 0.88
7 5 0.12
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:367777 original size:19 final size:18
Alignment explanation
Indices: 367749--367796 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
367739 ATTGATTTTG
*
367749 ATTTTAATTTTCATCTTT
1 ATTTTTATTTTCATCTTT
* *
367767 ATTTTTTATTTTTATTTTT
1 A-TTTTTATTTTCATCTTT
367786 ATTTTTATTTT
1 ATTTTTATTTT
367797 ACATTTTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTATTTTCATCTTT
Found at i:367778 original size:25 final size:25
Alignment explanation
Indices: 367744--367796 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
367734 TTTTAATTGA
367744 TTTTGATTTTAATTTTCATCTTTAT
1 TTTTGATTTTAATTTTCATCTTTAT
* * * *
367769 TTTTTATTTTTATTTTTATTTTTAT
1 TTTTGATTTTAATTTTCATCTTTAT
367794 TTT
1 TTT
367797 ACATTTTACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTTGATTTTAATTTTCATCTTTAT
Found at i:368423 original size:25 final size:25
Alignment explanation
Indices: 368376--368423 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
368366 AAACCACAAC
**
368376 GAAAATAAAAAAATGTCGTAGAACA
1 GAAAATAAAAAAATGTCAAAGAACA
368401 GAAAATAAAAAATATG-CAAAGAA
1 GAAAATAAAAAA-ATGTCAAAGAA
368424 GATGTAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.15
Consensus pattern (25 bp):
GAAAATAAAAAAATGTCAAAGAACA
Found at i:375401 original size:20 final size:21
Alignment explanation
Indices: 375365--375406 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
375355 TTGTGCACAA
*
375365 AGAAAGAAAAGAAAGGATGAG
1 AGAAAGAAAAGAAAGGAAGAG
*
375386 AGAAGGAAAA-AAAGGAAGAG
1 AGAAAGAAAAGAAAGGAAGAG
375406 A
1 A
375407 CAAGAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (21 bp):
AGAAAGAAAAGAAAGGAAGAG
Found at i:380861 original size:12 final size:13
Alignment explanation
Indices: 380836--380867 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
380826 CTATGTGAAC
380836 ATTTTGATAATGA
1 ATTTTGATAATGA
380849 ATTTTGA-AATGA
1 ATTTTGATAATGA
380861 ATTTTGA
1 ATTTTGA
380868 GGGCTTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (13 bp):
ATTTTGATAATGA
Found at i:387721 original size:21 final size:22
Alignment explanation
Indices: 387695--387746 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
387685 GTGCATTGTC
*
387695 TAAAACCTCTGGGTACA-TTCT
1 TAAAACCTCTAGGTACATTTCT
* * *
387716 TAAAACTTCTAGGTGCATTTTT
1 TAAAACCTCTAGGTACATTTCT
387738 TAAAACCTC
1 TAAAACCTC
387747 CGAGTATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (22 bp):
TAAAACCTCTAGGTACATTTCT
Found at i:387860 original size:22 final size:22
Alignment explanation
Indices: 387834--387910 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
387824 ACATTTTCTC
*
387834 TTAAAACCTCCAAGTGTATTTT
1 TTAAAACCTCCAAGTGCATTTT
* * *
387856 TTAAAATCTCCAAGTACA-TTC
1 TTAAAACCTCCAAGTGCATTTT
* * *
387877 TTAAAATCTCTAGGTGCATTTT
1 TTAAAACCTCCAAGTGCATTTT
387899 TTAAAACCTCCA
1 TTAAAACCTCCA
387911 GGTACATCTT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
21 17 0.39
22 27 0.61
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.38
Consensus pattern (22 bp):
TTAAAACCTCCAAGTGCATTTT
Found at i:387882 original size:21 final size:22
Alignment explanation
Indices: 387832--387931 Score: 80
Period size: 22 Copynumber: 4.6 Consensus size: 22
387822 CAACATTTTC
**
387832 TCTTAAAACCTCCAAGTGTATT
1 TCTTAAAACCTCCAAGTACATT
* *
387854 TTTTAAAATCTCCAAGTACA-T
1 TCTTAAAACCTCCAAGTACATT
* * * *
387875 TCTTAAAATCTCTAGGTGCATT
1 TCTTAAAACCTCCAAGTACATT
* *
387897 TTTTAAAACCTCCAGGTACA--
1 TCTTAAAACCTCCAAGTACATT
387917 TCTTCAAAACCTCCA
1 TCTT-AAAACCTCCA
387932 GATATATTCT
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
20 3 0.05
21 27 0.43
22 33 0.52
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (22 bp):
TCTTAAAACCTCCAAGTACATT
Found at i:387882 original size:43 final size:42
Alignment explanation
Indices: 387832--387931 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 42
387822 CAACATTTTC
* *
387832 TCTTAAAACCTCCAAGTGTATTTTTTAAAATCTCCAAGTACA
1 TCTTAAAACCTCCAAGTGCATTTTTTAAAACCTCCAAGTACA
* * * *
387874 TTCTTAAAATCTCTAGGTGCATTTTTTAAAACCTCCAGGTACA
1 -TCTTAAAACCTCCAAGTGCATTTTTTAAAACCTCCAAGTACA
387917 TCTTCAAAACCTCCA
1 TCTT-AAAACCTCCA
387932 GATATATTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 4 0.08
43 44 0.92
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (42 bp):
TCTTAAAACCTCCAAGTGCATTTTTTAAAACCTCCAAGTACA
Found at i:387892 original size:162 final size:162
Alignment explanation
Indices: 387611--387909 Score: 424
Period size: 162 Copynumber: 1.8 Consensus size: 162
387601 ATTCTAGGTA
* * *
387611 ATTAGTTTCAAGATTTTTAAAGTTATGTGGCCTCATTTTTTAAGAGCAACCTTTTTTTTAAAATA
1 ATTAGTTTCAAGATTTTTAAAGTTATGTAGCCTCATTTTTTAAGAGCAACATTTTTCTT--AATA
***
387676 AACCTCCAAGTGCATTGTCTAAAACCTCTGGGTACATTCTTAAAACTTCTAGGTGCATTTTTTAA
64 AACCTCCAAGTGCATTGTCTAAAACCTCCAAGTACATTCTTAAAACTTCTAGGTGCATTTTTTAA
387741 AACCTCCGAGTATATTCTCCAAAACCTTCGGATG
129 AACCTCCGAGTATATTCTCCAAAACCTTCGGATG
* *
387775 ATTAGTTTGAAGATTTTTTAAAGTTATGTAGCCTCATTTTTTAGGAGCAACATTTTCTCTT-A-A
1 ATTAGTTTCAAGA-TTTTTAAAGTTATGTAGCCTCATTTTTTAAGAGCAACATTTT-TCTTAATA
* * * *
387838 AACCTCCAAGTGTATTTTTTAAAATCTCCAAGTACATTCTTAAAA-TCTCTAGGTGCATTTTTTA
64 AACCTCCAAGTGCATTGTCTAAAACCTCCAAGTACATTCTTAAAACT-TCTAGGTGCATTTTTTA
387902 AAACCTCC
128 AAACCTCC
387910 AGGTACATCT
Statistics
Matches: 120, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
161 1 0.01
162 64 0.53
163 1 0.01
164 12 0.10
165 39 0.32
166 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (162 bp):
ATTAGTTTCAAGATTTTTAAAGTTATGTAGCCTCATTTTTTAAGAGCAACATTTTTCTTAATAAA
CCTCCAAGTGCATTGTCTAAAACCTCCAAGTACATTCTTAAAACTTCTAGGTGCATTTTTTAAAA
CCTCCGAGTATATTCTCCAAAACCTTCGGATG
Found at i:387913 original size:22 final size:21
Alignment explanation
Indices: 387834--387932 Score: 83
Period size: 21 Copynumber: 4.6 Consensus size: 21
387824 ACATTTTCTC
*
387834 TTAAAACCTCCAAGTGTA-TTTT
1 TTAAAACCTCC-AG-GTACATTT
* * *
387856 TTAAAATCTCCAAGTACATTC
1 TTAAAACCTCCAGGTACATTT
* * *
387877 TTAAAATCTCTAGGTGCATTTT
1 TTAAAACCTCCAGGTACA-TTT
*
387899 TTAAAACCTCCAGGTACATCT
1 TTAAAACCTCCAGGTACATTT
*
387920 TCAAAACCTCCAG
1 TTAAAACCTCCAG
387933 ATATATTCTC
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
20 3 0.05
21 32 0.52
22 27 0.44
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (21 bp):
TTAAAACCTCCAGGTACATTT
Found at i:387932 original size:21 final size:22
Alignment explanation
Indices: 387901--387957 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
387891 TGCATTTTTT
*
387901 AAAACCTCCAGGTACA-TCTTC
1 AAAACCTCCAGGTACATTCTCC
* *
387922 AAAACCTCCAGATATATTCTCC
1 AAAACCTCCAGGTACATTCTCC
*
387944 AAAAACTCCAGGTA
1 AAAACCTCCAGGTA
387958 ATTAGTTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.39, C:0.30, G:0.09, T:0.23
Consensus pattern (22 bp):
AAAACCTCCAGGTACATTCTCC
Found at i:388066 original size:119 final size:120
Alignment explanation
Indices: 387943--388171 Score: 352
Period size: 120 Copynumber: 1.9 Consensus size: 120
387933 ATATATTCTC
* * * *
387943 CAAAAACTCCAGGTAATTAGTTTCAAGA-TTTTTTAAAGTTACGTAGCCTTATTTTTTAGGAGTA
1 CAAAAACTCCAAGTAATTAGTTTCAAGACTTTTTTAAAGTTACGTAGCCTCATTTTTGAGGAGCA
* * *
388007 ACCTTTTCTTTTAAAAACCTTTGGGTACACATTCTAAAACCTTCGAGTACATCTT
66 ACCTTTTCTTTTAAAAACCTTTAGATACACATTCCAAAACCTTCGAGTACATCTT
* *
388062 CAAAACCTCCAAGTAATTAGTTTCAAGACTTTTTTAAAGTTATGTAGCCTCATTTTTGAGGAGCA
1 CAAAAACTCCAAGTAATTAGTTTCAAGACTTTTTTAAAGTTACGTAGCCTCATTTTTGAGGAGCA
**
388127 ACCTTTTCTTTTAAAAACCTTTAGATACATTTTCCAAAACCTTCG
66 ACCTTTTCTTTTAAAAACCTTTAGATACACATTCCAAAACCTTCG
388172 GGTAATCAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
119 26 0.27
120 72 0.73
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (120 bp):
CAAAAACTCCAAGTAATTAGTTTCAAGACTTTTTTAAAGTTACGTAGCCTCATTTTTGAGGAGCA
ACCTTTTCTTTTAAAAACCTTTAGATACACATTCCAAAACCTTCGAGTACATCTT
Found at i:388068 original size:21 final size:22
Alignment explanation
Indices: 388020--388069 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
388010 TTTTCTTTTA
* *
388020 AAAACCTTTGGGTACACATTCT
1 AAAACCTTCGAGTACACATTCT
388042 AAAACCTTCGAGTACATC-TTC-
1 AAAACCTTCGAGTACA-CATTCT
388063 AAAACCT
1 AAAACCT
388070 CCAAGTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.28
22 17 0.68
23 1 0.04
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (22 bp):
AAAACCTTCGAGTACACATTCT
Found at i:388255 original size:99 final size:97
Alignment explanation
Indices: 388041--388266 Score: 251
Period size: 99 Copynumber: 2.3 Consensus size: 97
388031 GTACACATTC
* * * * ** **
388041 TAAAACCTTCGAGTACATCTTCAAAACCTCCAAGTAATTAGTTTCAAGACTTTTTTAAAGTTATG
1 TAAAACCTTCGAGTACATTTTCAAAACCTCCAAGTAATCAATTTCAAGAATTTTCAAAAGTTACA
*
388106 TAGCCTCATTTTTGAGGAGCAACCTTTTCTTT
66 TAGCCTCATTTTTGAGGAGCAACCTTTTCTTA
* * **
388138 TAAAAACCTT-TAGATACATTTTCCAAAACCTTCGGGTAATCAATTTCAAGAATTCTTCAAAAGT
1 T-AAAACCTTCGAG-TACATTTT-CAAAACCTCCAAGTAATCAATTTCAAGAATT-TTCAAAAGT
*
388202 TACATAGTCTCATCTTTT-AGGAGCAACCTTTTCTTA
62 TACATAGCCTCAT-TTTTGAGGAGCAACCTTTTCTTA
*
388238 TAAAACCTTCGAGTACATTCT-AAAACCTC
1 TAAAACCTTCGAGTACATTTTCAAAACCTC
388267 TAGATACATC
Statistics
Matches: 106, Mismatches: 17, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
97 10 0.09
98 15 0.14
99 40 0.38
100 37 0.35
101 4 0.04
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (97 bp):
TAAAACCTTCGAGTACATTTTCAAAACCTCCAAGTAATCAATTTCAAGAATTTTCAAAAGTTACA
TAGCCTCATTTTTGAGGAGCAACCTTTTCTTA
Found at i:388274 original size:20 final size:20
Alignment explanation
Indices: 388238--388275 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
388228 CCTTTTCTTA
*
388238 TAAAACCTTCGAGTACATTC
1 TAAAACCTTAGAGTACATTC
388258 TAAAACCTCTAGA-TACAT
1 TAAAACCT-TAGAGTACAT
388276 CTTCAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (20 bp):
TAAAACCTTAGAGTACATTC
Found at i:388288 original size:21 final size:22
Alignment explanation
Indices: 388259--388308 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
388249 AGTACATTCT
*
388259 AAAACCTCTAGATACATCTT-C
1 AAAATCTCTAGATACATCTTCC
* * *
388280 AAAATCTCTAGGTAGATTTTCC
1 AAAATCTCTAGATACATCTTCC
388302 AAAATCT
1 AAAATCT
388309 TTGAGTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (22 bp):
AAAATCTCTAGATACATCTTCC
Found at i:388531 original size:51 final size:51
Alignment explanation
Indices: 388420--388569 Score: 189
Period size: 51 Copynumber: 2.9 Consensus size: 51
388410 AAGTTGTTTA
*
388420 AGCCTCGAATGAGGAGTTGTTTATTTTTCC-AATTGA-TTTCAAAGTGGTAG
1 AGCCTCGGATGAGGAGTTGTTTATTTTTCCAAATTGATTTTC-AAGTGGTAG
*
388470 AGCCTCGGATGAGGAGTTGTTTATTTTTCCAAATTGATTTTCAAGTGGTGG
1 AGCCTCGGATGAGGAGTTGTTTATTTTTCCAAATTGATTTTCAAGTGGTAG
* * * *
388521 AGCCTTGGATGAGGAGTTATTTGTCCTTTTCAAAATT-ACTTTTCAAGTG
1 AGCCTCGGATGAGGAGTTGTTTAT--TTTTCCAAATTGA-TTTTCAAGTG
388570 TGTAAAACTT
Statistics
Matches: 89, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
50 29 0.33
51 35 0.39
52 5 0.06
53 20 0.22
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (51 bp):
AGCCTCGGATGAGGAGTTGTTTATTTTTCCAAATTGATTTTCAAGTGGTAG
Found at i:388742 original size:18 final size:17
Alignment explanation
Indices: 388721--388768 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
388711 TTTGATTTTA
*
388721 ATTTTAATTTTCACCTTT
1 ATTTTTATTTT-ACCTTT
388739 ATTTTTATTTGTACCTTT
1 ATTTTTATTT-TACCTTT
388757 -TTTTTATTTTAC
1 ATTTTTATTTTAC
388769 ATTATACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 3 0.11
17 9 0.32
18 15 0.54
19 1 0.04
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTTTTATTTTACCTTT
Found at i:389955 original size:19 final size:20
Alignment explanation
Indices: 389931--389972 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
389921 AGGATCTTCG
389931 TGGTGGTA-ATGGTTTT-GTT
1 TGGTGGTAGAT-GTTTTGGTT
389950 TGGTGGTAGATGTTTTGGTT
1 TGGTGGTAGATGTTTTGGTT
389970 TGG
1 TGG
389973 AGAGAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (20 bp):
TGGTGGTAGATGTTTTGGTT
Found at i:396095 original size:25 final size:25
Alignment explanation
Indices: 396057--396115 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
396047 GGTTTGTGAT
* * * *
396057 TATACATGGGAAGGCCACGGGTTGT
1 TATACGTGGCAAGGCCACGAGTTGA
*
396082 TATAGGTGGCAAGGCCACGAGTTGA
1 TATACGTGGCAAGGCCACGAGTTGA
396107 TATACGTGG
1 TATACGTGG
396116 TTACAACCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.36, T:0.24
Consensus pattern (25 bp):
TATACGTGGCAAGGCCACGAGTTGA
Found at i:412820 original size:44 final size:43
Alignment explanation
Indices: 412726--412825 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 43
412716 TTCATTCTTG
* * * * *
412726 AGATATTAGTTCTTCTTGTTTGAGAATTAATTCTTGCCACTCT
1 AGATATCAGTTCTTCTTGTCTGAGAATCAATTCTAGCCACTCA
* *
412769 AGATATCAGTTCATTCTTGTCTGAGAATCGATTCTAGCCTCTCCA
1 AGATATCAGTTC-TTCTTGTCTGAGAATCAATTCTAGCCACT-CA
412814 AG-TATCAGTTCT
1 AGATATCAGTTCT
412826 CCTTACTTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
43 12 0.25
44 33 0.69
45 3 0.06
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (43 bp):
AGATATCAGTTCTTCTTGTCTGAGAATCAATTCTAGCCACTCA
Found at i:416199 original size:20 final size:20
Alignment explanation
Indices: 416174--416249 Score: 143
Period size: 20 Copynumber: 3.8 Consensus size: 20
416164 TTCTTAGCAA
416174 GAATGTATCAATACATCAGT
1 GAATGTATCAATACATCAGT
416194 GAATGTATCAATACATCAGT
1 GAATGTATCAATACATCAGT
416214 GAATGTATCAATACATCAGT
1 GAATGTATCAATACATCAGT
*
416234 GAATGTACCAATACAT
1 GAATGTATCAATACAT
416250 TTGCTCCAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (20 bp):
GAATGTATCAATACATCAGT
Found at i:416611 original size:37 final size:38
Alignment explanation
Indices: 416544--416620 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 38
416534 AAATATCCTC
*
416544 AAACATAATAGCATTCAAAGTCATTTTCTATAGACCAT
1 AAACATAATAGCATTCAAAGTCATTTTCTATAAACCAT
416582 AAACATAAT-GACATTC-AAGTCATTTTCTATAAACCAT
1 AAACATAATAG-CATTCAAAGTCATTTTCTATAAACCAT
416619 AA
1 AA
416621 GATAATCGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
37 23 0.62
38 14 0.38
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.31
Consensus pattern (38 bp):
AAACATAATAGCATTCAAAGTCATTTTCTATAAACCAT
Found at i:421294 original size:33 final size:32
Alignment explanation
Indices: 421257--421318 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
421247 CTAATTTCGA
421257 TAAC-AATAATATTAATATTTTAATATTTTTTAT
1 TAACAAATAATATT-ATATTTTAA-ATTTTTTAT
* *
421290 TAACAAATATTATTTTATTTTAAATTTTT
1 TAACAAATAATATTATATTTTAAATTTTT
421319 CTACTCGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 6 0.23
33 12 0.46
34 8 0.31
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (32 bp):
TAACAAATAATATTATATTTTAAATTTTTTAT
Found at i:421433 original size:572 final size:572
Alignment explanation
Indices: 420339--421466 Score: 1821
Period size: 572 Copynumber: 2.0 Consensus size: 572
420329 CTTGATAAGG
420339 AAATTCCCCTATTAAACTTCAAATTTTGAAATTACAAATGAGTCCTAAAACTTTTTCTTATTTAT
1 AAATTCCCCTATTAAACTTCAAATTTTGAAATTACAAATGAGTCCTAAAACTTTTTCTTATTTAT
* *
420404 CATGTGACCTTCCAAACTTTCATGCTTTATAATTTAGTCTTTTAAACACTTCTTAAATTCCAATT
66 CATGTGACCCTCCAAACTTTCATGCTTTATAATTTAGTCTTTCAAACACTTCTTAAATTCCAATT
* * * *
420469 TCCTCCTATTTTTTCCTTTACATGTGTACAAATATAATATAAGGTTTTCACTTTATTAAGGCGTC
131 TCCTCCTATTTTTTCCTTTACATGTGTACAAATATAATATAAGGTTTGCACTTCATCAAGGCATC
*
420534 ACCATAATATTTAAATATATACTTACCCACGCTAGCTTTATTTAATAAAGACACGCGGGCCCTAC
196 ACCATAATATTTAAATATATACTTACCCACGCTAGCTTTATTTAATAAAGACACGCAGGCCCTAC
* * * * *
420599 CTATGTTGTTTTTTTCGAAATCCTTTCTTACTTCATCTCCCCTGATTCGATTAGTCATATAATCC
261 CAATGTCGTTTTTTTCAAAATCCTTTCTTACTTCATCTCCCCTAATTCAATTAGTCATATAATCC
* * *
420664 TCCTTTATGACTAATTTCGATAACAATAATATTAATATTTTAATATTATTTTATTAATAAGTATT
326 TCCTTTATAACTAATTTCGATAACAATAATATTAATATTTTAATATTATTTTATTAACAAATATT
*
420729 ATTTTATTTTAAATTTTTCTACTCGTCTCCTCGAGACCCAAAATGTCTCATTTTGTCTCAGTTCA
391 ATTTTATTTTAAATTTTTCTACTCGTCTCCTCGAGACCCAAAATGTCTCACTTTGTCTCAGTTCA
*** *
420794 CCTCCGATTCACCTTTTAACTTGTTAATTCATCCTCGATAAAAGTATTATTATTAAATTTATATT
456 CCTCCGATTCACCTTTTAACTAACTAATTCATCCTCAATAAAAGTATTATTATTAAATTTATATT
*
420859 TTCTCACATATGAAATATTTTATTCTGAATTATTCCATTCTCCTTGGTTAGA
521 TTCTCACATACGAAATATTTTATTCTGAATTATTCCATTCTCCTTGGTTAGA
* * ******
420911 AAATTCTCCTATTAAACTTCAAATTTTGAAATTACAAATGAGTCCTCAAACTTTTTCTTNNNNNN
1 AAATTCCCCTATTAAACTTCAAATTTTGAAATTACAAATGAGTCCTAAAACTTTTTCTTATTTAT
**** * *
420976 NNNNTGACCCTCTAAACTTTCATGCTTTATAATTTAGTCTTTCAAACACTTCTTAAATTCTAATT
66 CATGTGACCCTCCAAACTTTCATGCTTTATAATTTAGTCTTTCAAACACTTCTTAAATTCCAATT
* * *
421041 TTCTCCTATTTTTTCCTTTATATGTGTACAAATATTATATAAGGTTTGCA-TCTCATCAAGGCAT
131 TCCTCCTATTTTTTCCTTTACATGTGTACAAATATAATATAAGGTTTGCACT-TCATCAAGGCAT
* *
421105 CACCATAATATTTAAATATATACTTACCCACGTTAGCTTTATTTAATAAGGACACGCAGGCCCTA
195 CACCATAATATTTAAATATATACTTACCCACGCTAGCTTTATTTAATAAAGACACGCAGGCCCTA
421170 CCAATGTCGTTTTTTTTCAAAATCCTTTCTTACTTCATCTCCTCC-AATTCAATTAGTCATATAA
260 CCAATGTCG-TTTTTTTCAAAATCCTTTCTTACTTCATCTCC-CCTAATTCAATTAGTCATATAA
421234 TCCTCCTTTATAACTAATTTCGATAACAATAATATTAATATTTTAATATT-TTTTATTAACAAAT
323 TCCTCCTTTATAACTAATTTCGATAACAATAATATTAATATTTTAATATTATTTTATTAACAAAT
421298 ATTATTTTATTTTAAATTTTTCTACTCGTCTCCTCGAGACCCAAAATGTCTCACTTTGTCTCAGT
388 ATTATTTTATTTTAAATTTTTCTACTCGTCTCCTCGAGACCCAAAATGTCTCACTTTGTCTCAGT
* *
421363 TCACCTCTGATTCACCTTTTAACTAACTAATTCATCCTCAATAAAAGTATTATTATTAAATTTTT
453 TCACCTCCGATTCACCTTTTAACTAACTAATTCATCCTCAATAAAAGTATTATTATTAAATTTAT
*
421428 ATTTTCTCGCATACGAAATATTTTATTCTGAATTATTCC
518 ATTTTCTCACATACGAAATATTTTATTCTGAATTATTCC
421467 TTTCACCCTC
Statistics
Matches: 510, Mismatches: 43, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
571 1 0.00
572 410 0.80
573 97 0.19
574 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.43
Consensus pattern (572 bp):
AAATTCCCCTATTAAACTTCAAATTTTGAAATTACAAATGAGTCCTAAAACTTTTTCTTATTTAT
CATGTGACCCTCCAAACTTTCATGCTTTATAATTTAGTCTTTCAAACACTTCTTAAATTCCAATT
TCCTCCTATTTTTTCCTTTACATGTGTACAAATATAATATAAGGTTTGCACTTCATCAAGGCATC
ACCATAATATTTAAATATATACTTACCCACGCTAGCTTTATTTAATAAAGACACGCAGGCCCTAC
CAATGTCGTTTTTTTCAAAATCCTTTCTTACTTCATCTCCCCTAATTCAATTAGTCATATAATCC
TCCTTTATAACTAATTTCGATAACAATAATATTAATATTTTAATATTATTTTATTAACAAATATT
ATTTTATTTTAAATTTTTCTACTCGTCTCCTCGAGACCCAAAATGTCTCACTTTGTCTCAGTTCA
CCTCCGATTCACCTTTTAACTAACTAATTCATCCTCAATAAAAGTATTATTATTAAATTTATATT
TTCTCACATACGAAATATTTTATTCTGAATTATTCCATTCTCCTTGGTTAGA
Found at i:422001 original size:22 final size:22
Alignment explanation
Indices: 421976--422018 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
421966 AGTAACTACA
421976 ATTTATCATGTACACTAAAGTG
1 ATTTATCATGTACACTAAAGTG
*
421998 ATTTATCATGTACCCTAAAGT
1 ATTTATCATGTACACTAAAGT
422019 CTTTTTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (22 bp):
ATTTATCATGTACACTAAAGTG
Found at i:422880 original size:18 final size:18
Alignment explanation
Indices: 422854--422888 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
422844 TTAATATAAT
*
422854 TTTTTAATTTTTTATTTA
1 TTTTCAATTTTTTATTTA
422872 TTTTCAATTTTTTATTT
1 TTTTCAATTTTTTATTT
422889 TCTTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCAATTTTTTATTTA
Found at i:427285 original size:22 final size:22
Alignment explanation
Indices: 427238--427316 Score: 108
Period size: 21 Copynumber: 3.7 Consensus size: 22
427228 ATTAATGATC
427238 TTTGAACTTATTTAAATGA-TT
1 TTTGAACTTATTTAAATGAGTT
* *
427259 TTTGAAGTTATTTGAATGAGTT
1 TTTGAACTTATTTAAATGAGTT
*
427281 TTTGAACTTGTTTAAAT-AGTT
1 TTTGAACTTATTTAAATGAGTT
*
427302 TTTAAACTTATTTAA
1 TTTGAACTTATTTAA
427317 TTAAATTTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 34 0.68
22 16 0.32
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.52
Consensus pattern (22 bp):
TTTGAACTTATTTAAATGAGTT
Found at i:427380 original size:21 final size:21
Alignment explanation
Indices: 427356--427403 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
427346 TATGGAGAGG
427356 TTTAAAATTGCTTGAATGAGT
1 TTTAAAATTGCTTGAATGAGT
* *
427377 TTTAGAATTGCTTGAATGATT
1 TTTAAAATTGCTTGAATGAGT
427398 TTTAAA
1 TTTAAA
427404 CTTGTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (21 bp):
TTTAAAATTGCTTGAATGAGT
Found at i:427613 original size:20 final size:20
Alignment explanation
Indices: 427567--427646 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
427557 GGTTCTACCC
* * *
427567 AAAATGTATGGATACATTTCC
1 AAAATGTATAGATGCATTT-T
427588 AAAATGTATCA-ATGCATTTT
1 AAAATGTAT-AGATGCATTTT
427608 AAAATGTATAGATGCATTTT
1 AAAATGTATAGATGCATTTT
*
427628 AAAATGTATAGATACATTT
1 AAAATGTATAGATGCATTT
427647 GGTCCAGAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 36 0.68
21 16 0.30
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (20 bp):
AAAATGTATAGATGCATTTT
Found at i:430703 original size:57 final size:57
Alignment explanation
Indices: 430615--430728 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
430605 CTTAGAAAAG
*
430615 TTAGATTTTAGGTTTTGGTTAATCTAGTGAAAAACCATTGTTGAAAGGTTGTGGCTA
1 TTAGATTTTAAGTTTTGGTTAATCTAGTGAAAAACCATTGTTGAAAGGTTGTGGCTA
*
430672 TTAGATTTTAAGTTTTGGTTAATCTCGTGAAAAACCATTGTTGAAAGGTTGTGGCTA
1 TTAGATTTTAAGTTTTGGTTAATCTAGTGAAAAACCATTGTTGAAAGGTTGTGGCTA
430729 AGCCTATGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (57 bp):
TTAGATTTTAAGTTTTGGTTAATCTAGTGAAAAACCATTGTTGAAAGGTTGTGGCTA
Found at i:432088 original size:13 final size:13
Alignment explanation
Indices: 432070--432094 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
432060 TATATATAAA
432070 TTGCACAAATTGT
1 TTGCACAAATTGT
432083 TTGCACAAATTG
1 TTGCACAAATTG
432095 CTTTTTGCTT
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):
TTGCACAAATTGT
Found at i:435776 original size:4 final size:4
Alignment explanation
Indices: 435767--435815 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
435757 TAGTTTTGAG
*
435767 GAAA GAAA GAAA AAAA GAAA GAAA G-AA -AAA GAAA -AAA G-AA GAGAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA
435812 GAAA
1 GAAA
435816 TAAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 10 0.26
4 24 0.63
5 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:435788 original size:16 final size:17
Alignment explanation
Indices: 435767--435811 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
435757 TAGTTTTGAG
435767 GAAAGAAAGAAAAA-AA
1 GAAAGAAAGAAAAAGAA
435783 GAAAGAAAGAAAAAGAA
1 GAAAGAAAGAAAAAGAA
*
435800 AAAAGAAGAGAA
1 GAAAGAA-AGAA
435812 GAAATAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 14 0.54
17 8 0.31
18 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAAAGAA
Found at i:435800 original size:22 final size:21
Alignment explanation
Indices: 435772--435815 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
435762 TTGAGGAAAG
435772 AAAGAAAAAAAGAA-AGAAAGAA
1 AAAG-AAAAAAGAAGAG-AAGAA
435794 AAAGAAAAAAGAAGAGAAGAA
1 AAAGAAAAAAGAAGAGAAGAA
435815 A
1 A
435816 TAAAACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAAGAAGAGAAGAA
Found at i:436814 original size:21 final size:21
Alignment explanation
Indices: 436780--436827 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
436770 AAATTGCTTC
*
436780 AATGATCTTGGAACTTGTTTG
1 AATGATCTTGGAACTTGGTTG
*
436801 AGTGATCCTT-GAACTTGGTTG
1 AATGAT-CTTGGAACTTGGTTG
436822 AATGAT
1 AATGAT
436828 TTTTAAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (21 bp):
AATGATCTTGGAACTTGGTTG
Found at i:436969 original size:21 final size:21
Alignment explanation
Indices: 436943--436983 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
436933 AAATTACTTG
436943 AATGATCTTTGAACTTGTTTA
1 AATGATCTTTGAACTTGTTTA
* *
436964 AATGATTTTTGAAGTTGTTT
1 AATGATCTTTGAACTTGTTT
436984 GATTAAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.17, T:0.51
Consensus pattern (21 bp):
AATGATCTTTGAACTTGTTTA
Found at i:437013 original size:21 final size:22
Alignment explanation
Indices: 436969--437026 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
436959 GTTTAAATGA
* * *
436969 TTTTTGAAGTTGTTTGATTAAG
1 TTTTTTAAATTGTTTGAATAAG
436991 TTTTTTAAATTGTTTGAAT-AG
1 TTTTTTAAATTGTTTGAATAAG
437012 -TTTTTAAACTTGTTT
1 TTTTTTAAA-TTGTTT
437027 ANNNNNNNNN
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.25
21 8 0.25
22 16 0.50
ACGTcount: A:0.24, C:0.02, G:0.16, T:0.59
Consensus pattern (22 bp):
TTTTTTAAATTGTTTGAATAAG
Found at i:437097 original size:21 final size:21
Alignment explanation
Indices: 437073--437113 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
437063 AGAGGTCTAA
*
437073 AATTGCTTGAATGAGTTTTGG
1 AATTGCTCGAATGAGTTTTGG
*
437094 AATTGCTCGAATGATTTTTG
1 AATTGCTCGAATGAGTTTTG
437114 AACTTGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (21 bp):
AATTGCTCGAATGAGTTTTGG
Found at i:437132 original size:21 final size:21
Alignment explanation
Indices: 437108--437158 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
437098 GCTCGAATGA
*
437108 TTTTTGAACTTGTTTAAATAG
1 TTTTTAAACTTGTTTAAATAG
437129 TTTTTAAACTTGTTTAAATTA-
1 TTTTTAAACTTGTTTAAA-TAG
437150 TTTTTAAAC
1 TTTTTAAAC
437159 CTCCTTTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (21 bp):
TTTTTAAACTTGTTTAAATAG
Found at i:437771 original size:32 final size:31
Alignment explanation
Indices: 437704--437771 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 31
437694 ATTCAAAATT
* * * *
437704 GTATTGAAAGGTTGTGCTTAATCCTTGAAAG
1 GTATTGAAAGGTTATGCTTAAGCCTTAAAAA
*
437735 GTATTGTAAAGGTTATGCTTGAGCCTTAAAAA
1 GTATTG-AAAGGTTATGCTTAAGCCTTAAAAA
437767 GTATT
1 GTATT
437772 TTTCATAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 6 0.19
32 25 0.81
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.37
Consensus pattern (31 bp):
GTATTGAAAGGTTATGCTTAAGCCTTAAAAA
Found at i:446031 original size:21 final size:21
Alignment explanation
Indices: 446000--446074 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
445990 GGATATGTTT
446000 ATGCAATTCATGACAAAGACTG
1 ATGC-ATTCATGACAAAGACTG
*
446022 ATACATTCATGACAAAGACTG
1 ATGCATTCATGACAAAGACTG
* * *
446043 ATGCATTCATAATAAAGACCG
1 ATGCATTCATGACAAAGACTG
446064 ATGCATT-ATGA
1 ATGCATTCATGA
446075 TAAGGATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 41 0.87
22 3 0.06
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.25
Consensus pattern (21 bp):
ATGCATTCATGACAAAGACTG
Found at i:446285 original size:12 final size:12
Alignment explanation
Indices: 446254--446278 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
446244 CCACAATGGG
446254 AAAAAAGTAAGT
1 AAAAAAGTAAGT
446266 AAAAAAGTAAGT
1 AAAAAAGTAAGT
446278 A
1 A
446279 GTAAAGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AAAAAAGTAAGT
Done.