Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 3 of 138
Found at i:335434 original size:17 final size:16
Alignment explanation
Indices: 335407--335447 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
335397 TACTATTAAG
335407 TTTTTTAACCTCAGTA
1 TTTTTTAACCTCAGTA
* *
335423 TCTTTTTCACCTCTGTA
1 T-TTTTTAACCTCAGTA
335440 TTTTTTAA
1 TTTTTTAA
335448 GCTAGCTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.56
Consensus pattern (16 bp):
TTTTTTAACCTCAGTA
Found at i:340017 original size:23 final size:24
Alignment explanation
Indices: 339963--340014 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
339953 GCAAGTCAGT
* * * *
339963 AAAAATTAAATAAAAAAAGAAGTG
1 AAAAAGTAAAAAAAAAAAAAAGAG
339987 AAAAAGTAAAAAAAAAAAAAAGAG
1 AAAAAGTAAAAAAAAAAAAAAGAG
340011 AAAA
1 AAAA
340015 GTATGAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (24 bp):
AAAAAGTAAAAAAAAAAAAAAGAG
Found at i:342953 original size:2 final size:2
Alignment explanation
Indices: 342946--342999 Score: 92
Period size: 2 Copynumber: 27.0 Consensus size: 2
342936 TTGCTTTTCA
342946 CT CT CT CT CT CT CT CT -T GCT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT -CT CT CT CT CT CT CT CT CT CT CT CT
342988 CT CT CT CT CT CT
1 CT CT CT CT CT CT
343000 ATATATATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:343004 original size:2 final size:2
Alignment explanation
Indices: 342999--343023 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
342989 TCTCTCTCTC
342999 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
343024 GCCTAGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:343045 original size:3 final size:3
Alignment explanation
Indices: 343037--343081 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
343027 TAGGTTATTA
343037 CAT CAT CAT CAT CAT CAAT -AT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT C-AT CAT CAT CAT CAT CAT CAT CAT CAT CAT
343082 TGAAGTAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:349009 original size:2 final size:2
Alignment explanation
Indices: 349002--349042 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
348992 TGCGAAGCGC
349002 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
349043 ACTCACTCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:353643 original size:30 final size:29
Alignment explanation
Indices: 353602--353664 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
353592 ATAAAAAAAA
* *
353602 TTTTTTTTTTCAATCGCAGTTACAGTAAT
1 TTTTTTTTTTCAATCACAGCTACAGTAAT
*
353631 TTTTTATTTTTCAATTACAGCTACAGTAAT
1 TTTTT-TTTTTCAATCACAGCTACAGTAAT
353661 TTTT
1 TTTT
353665 ATTACTGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.54
Consensus pattern (29 bp):
TTTTTTTTTTCAATCACAGCTACAGTAAT
Found at i:354848 original size:2 final size:2
Alignment explanation
Indices: 354841--354878 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
354831 AAGCTTGGAC
* *
354841 AG AG AG AG AG AG AG AG AA AG AG AA AG AG AG -G AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
354879 TCGAAGTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:358361 original size:3 final size:3
Alignment explanation
Indices: 358353--358386 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
358343 ATATATATAT
*
358353 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
358387 GAGCTAGTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:358970 original size:26 final size:26
Alignment explanation
Indices: 358937--358987 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
358927 CACATACATT
358937 AATTCTTATATAATTATCATAATCAA
1 AATTCTTATATAATTATCATAATCAA
358963 AATTCTTATATAATTATCATAATCA
1 AATTCTTATATAATTATCATAATCA
358988 TTTTGACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTCTTATATAATTATCATAATCAA
Found at i:359303 original size:61 final size:61
Alignment explanation
Indices: 359238--359353 Score: 137
Period size: 61 Copynumber: 1.9 Consensus size: 61
359228 TTTAATTATT
*
359238 TATAAAAGGATCATTTAAGATA-TTTCTGTAAAAAAA-CGTCTTAAATAATTTTTTTTGTGTA
1 TATAAAAGAATCATTTAAGATATTTTCTGTAAAAAAATC--CTTAAATAATTTTTTTTGTGTA
* * * * * *
359299 TATAAAATAATTATTTAAGGTATTTTTTGTATAAAAATCCTTAAATGATTTTTTT
1 TATAAAAGAATCATTTAAGATATTTTCTGTAAAAAAATCCTTAAATAATTTTTTT
359354 ATTTTTTATA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
61 33 0.72
62 12 0.26
63 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (61 bp):
TATAAAAGAATCATTTAAGATATTTTCTGTAAAAAAATCCTTAAATAATTTTTTTTGTGTA
Found at i:359995 original size:18 final size:17
Alignment explanation
Indices: 359964--359999 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
359954 TTTTTAAATC
359964 AAATTTATTAAATTTTA
1 AAATTTATTAAATTTTA
*
359981 AAATATTATTCAATTTTA
1 AAAT-TTATTAAATTTTA
359999 A
1 A
360000 TCAAAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTATTAAATTTTA
Found at i:362007 original size:2 final size:2
Alignment explanation
Indices: 361995--362032 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
361985 TAGTAGCTTC
*
361995 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
362033 TTGTATTCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:378290 original size:2 final size:2
Alignment explanation
Indices: 378283--378311 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
378273 CTAATTAATT
378283 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
378312 CAGAACTCAG
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:381045 original size:2 final size:2
Alignment explanation
Indices: 381038--381064 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
381028 TAAGATGTTC
381038 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
381065 ATGCATGTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:383569 original size:2 final size:2
Alignment explanation
Indices: 383562--383587 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
383552 TTGTACATTA
383562 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
383588 TTGTGTGTGT
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:388740 original size:21 final size:21
Alignment explanation
Indices: 388714--388756 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
388704 AAATAGAGAA
388714 TGTATCATATTGCAAACAATT
1 TGTATCATATTGCAAACAATT
388735 TGTATCATATTGCAAACAATT
1 TGTATCATATTGCAAACAATT
388756 T
1 T
388757 TATGTACCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (21 bp):
TGTATCATATTGCAAACAATT
Found at i:393808 original size:4 final size:4
Alignment explanation
Indices: 393799--393832 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
393789 GTTCAACCCG
*
393799 TCTT TCTT TCTT TCTT TCTT TCTT TCGT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC
393833 CTATTCATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (4 bp):
TCTT
Found at i:398458 original size:2 final size:2
Alignment explanation
Indices: 398453--398478 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
398443 CAAAAAAAAC
398453 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
398479 TTGTGCATCC
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:407478 original size:18 final size:19
Alignment explanation
Indices: 407444--407481 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
407434 TTAATTTTAA
407444 TTTAATTTTTGTTTTTTGG
1 TTTAATTTTTGTTTTTTGG
407463 TTTAATTTTT-TTTTTTGG
1 TTTAATTTTTGTTTTTTGG
407481 T
1 T
407482 CAAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.11, C:0.00, G:0.13, T:0.76
Consensus pattern (19 bp):
TTTAATTTTTGTTTTTTGG
Found at i:415105 original size:22 final size:22
Alignment explanation
Indices: 415057--415098 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
415047 TTGTTTCTCG
415057 AAAACCTCCAAACACGATCTAT
1 AAAACCTCCAAACACGATCTAT
* *
415079 AAAACCTCCGAACATGATCT
1 AAAACCTCCAAACACGATCT
415099 TTGAAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.31, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAACCTCCAAACACGATCTAT
Found at i:415265 original size:31 final size:34
Alignment explanation
Indices: 415186--415273 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 34
415176 CTCAGCTCAG
* *
415186 TCCAGGTCATTTATTTTTCTAACTTGCGGTTCAG
1 TCCAGGTCATTTATTTTTCTAACCTGCGGTTCAA
* *
415220 TCCCA-ATCACTTATTTTT-T-ACCT-CGGTTCAA
1 T-CCAGGTCATTTATTTTTCTAACCTGCGGTTCAA
415251 TCCAGGTCATTTATTTTTCTAAC
1 TCCAGGTCATTTATTTTTCTAAC
415274 TTGCAATTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
30 3 0.07
31 19 0.43
32 4 0.09
33 3 0.07
34 12 0.27
35 3 0.07
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.44
Consensus pattern (34 bp):
TCCAGGTCATTTATTTTTCTAACCTGCGGTTCAA
Found at i:415269 original size:65 final size:65
Alignment explanation
Indices: 415182--415497 Score: 265
Period size: 65 Copynumber: 4.9 Consensus size: 65
415172 CGACCTCAGC
* *
415182 TCAGTCCAGGTCATTTATTTTTCTAACTTGCGGTTCAGTCCCAATCACTTATTTTTTACCTCGGT
1 TCAGTCCAGGTCATTTATTTTTCTGACTTGCGGTTCAGTCCCAATCACTTATTTTTTACCTCGAT
* * ** *** * ** *
415247 TCAATCCAGGTCATTTATTTTTCTAACTTGCAATTCAGTCCCCGCCACTCATTTTCGACCTCTAT
1 TCAGTCCAGGTCATTTATTTTTCTGACTTGCGGTTCAGTCCCAATCACTTATTTTTTACCTCGAT
* * * * **** * ***
415312 TCAGTCCAAGTCATTAATATTTCTGACTTGCGGTTCACTCTTGGTCACTTAATTTCGGCCTCGAT
1 TCAGTCCAGGTCATTTATTTTTCTGACTTGCGGTTCAGTCCCAATCACTTATTTTTTACCTCGAT
* * * * * **
415377 TCAGTCCAGGTCATTTATTTTTTTGACTTACGGTTCAATCTCGATCACTCGTTTTTTACCTCGAT
1 TCAGTCCAGGTCATTTATTTTTCTGACTTGCGGTTCAGTCCCAATCACTTATTTTTTACCTCGAT
* ** * * * *
415442 TTAGTCCAATTCATTTATTTTTTTGACTTGCAGTTTAGT-CCAGATCATTTATTTTT
1 TCAGTCCAGGTCATTTATTTTTCTGACTTGCGGTTCAGTCCCA-ATCACTTATTTTT
415498 CTAACTTGCG
Statistics
Matches: 197, Mismatches: 53, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
64 1 0.01
65 196 0.99
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (65 bp):
TCAGTCCAGGTCATTTATTTTTCTGACTTGCGGTTCAGTCCCAATCACTTATTTTTTACCTCGAT
Found at i:415426 original size:130 final size:129
Alignment explanation
Indices: 415167--415472 Score: 299
Period size: 130 Copynumber: 2.3 Consensus size: 129
415157 AAACCTAGTT
* * * *
415167 ATTTTCGACCTCAGCTCAGTCCAGGTCATTTATTTTTCTAACTTGCGGTTCAGTCCCAATCACTT
1 ATTTTCGACCTCA-TTCAGTCCAAGTCATTTATTTTTCTGACTTGCGGTTCACTCCCAATCACTT
* ** * * *
415232 ATTTTTTACCTCGGTTCAATCCAGGTCATTTATTTTTCTAACTTGCAATTCAGTCCCCGCCACTC
65 AATTTCGACCTCGATTCAATCCAGGTCATTTATTTTTCTAACTTACAATTCAATCCCCGCCACTC
* * ****
415297 ATTTTCGACCTCTATTCAGTCCAAGTCATTAATATTTCTGACTTGCGGTTCACTCTTGGTCACTT
1 ATTTTCGACCTC-ATTCAGTCCAAGTCATTTATTTTTCTGACTTGCGGTTCACTCCCAATCACTT
* * * * ** * *
415362 AATTTCGGCCTCGATTCAGTCCAGGTCATTTATTTTTTTGACTTACGGTTCAAT-CTCGATCACT
65 AATTTCGACCTCGATTCAATCCAGGTCATTTATTTTTCTAACTTACAATTCAATCCCCG-CCACT
415426 C
129 C
* ** * * *
415427 GTTTTTTACCTCGATTTAGTCCAATTCATTTATTTTTTTGACTTGC
1 ATTTTCGACCTC-ATTCAGTCCAAGTCATTTATTTTTCTGACTTGC
415473 AGTTTAGTCC
Statistics
Matches: 141, Mismatches: 33, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
129 3 0.02
130 137 0.97
131 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (129 bp):
ATTTTCGACCTCATTCAGTCCAAGTCATTTATTTTTCTGACTTGCGGTTCACTCCCAATCACTTA
ATTTCGACCTCGATTCAATCCAGGTCATTTATTTTTCTAACTTACAATTCAATCCCCGCCACTC
Found at i:417330 original size:38 final size:38
Alignment explanation
Indices: 417278--417372 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
417268 TTTTAAAATA
* * *
417278 AAATCTCACTAAACTATTGGGGGATATGCATCAAAGTT
1 AAATCTTACCAAACTATTAGGGGATATGCATCAAAGTT
*
417316 AAATCTTACCAAACTATTAGGGGATGTGCATCAAAGTT
1 AAATCTTACCAAACTATTAGGGGATATGCATCAAAGTT
* *
417354 AAATATTATCAAACTATTA
1 AAATCTTACCAAACTATTA
417373 TTGGAAGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (38 bp):
AAATCTTACCAAACTATTAGGGGATATGCATCAAAGTT
Found at i:419847 original size:19 final size:19
Alignment explanation
Indices: 419809--419848 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
419799 TTCCATTTTA
* **
419809 TAAATAAATCGATTTTTTT
1 TAAATAAATCAATTCATTT
419828 TAAATAAATCAATTCATTT
1 TAAATAAATCAATTCATTT
419847 TA
1 TA
419849 CAAGTTACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (19 bp):
TAAATAAATCAATTCATTT
Found at i:424551 original size:2 final size:2
Alignment explanation
Indices: 424544--424569 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
424534 TTATCCATTA
424544 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
424570 CTTTGAGCGT
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:430308 original size:3 final size:3
Alignment explanation
Indices: 430300--430329 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
430290 AAACTAGTAA
430300 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
430330 CTGTGGACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:438544 original size:2 final size:2
Alignment explanation
Indices: 438537--438564 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
438527 TTCTTGCAGT
438537 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
438565 CGTGTGTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:439401 original size:2 final size:2
Alignment explanation
Indices: 439394--439423 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
439384 TTTTGGTTGC
439394 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
439424 GTAGTCTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:441625 original size:2 final size:2
Alignment explanation
Indices: 441618--441654 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
441608 GAAAAATTGC
441618 AT AT AT AT AT 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
441655 AATCAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:447320 original size:4 final size:4
Alignment explanation
Indices: 447311--447337 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
447301 CAATTTCTTC
447311 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
447338 AAGCAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:456662 original size:29 final size:30
Alignment explanation
Indices: 456630--456696 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
456620 TAATTTTTTT
*
456630 AAATTATATT-AATTTTTTA-AAAATTTTAA
1 AAATTATATTAAATATTTTACAAAA-TTTAA
456659 AAATTATATTAAATATTTTACTAAAATTTAA
1 AAATTATATTAAATATTTTAC-AAAATTTAA
456690 AAATTAT
1 AAATTAT
456697 TCCATAATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.29
30 8 0.24
31 12 0.35
32 4 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
AAATTATATTAAATATTTTACAAAATTTAA
Found at i:461790 original size:2 final size:2
Alignment explanation
Indices: 461783--461810 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
461773 GTTTGAAAAG
461783 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
461811 TCACATCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:463250 original size:2 final size:2
Alignment explanation
Indices: 463243--463267 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
463233 AGCCTGATCA
463243 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
463268 TCGCTTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:469480 original size:2 final size:2
Alignment explanation
Indices: 469469--469499 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
469459 AGTAGTAGAG
469469 TA TA -A 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
469500 GAATGCTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:470294 original size:18 final size:18
Alignment explanation
Indices: 470271--470329 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
470261 CTGCCCTTCT
470271 TTTCTTAAATTCACGCTC
1 TTTCTTAAATTCACGCTC
** * *
470289 TTTCTT-TCTGC-CCCTC
1 TTTCTTAAATTCACGCTC
*
470305 TTTTCTTAAATTCACGTTC
1 -TTTCTTAAATTCACGCTC
470324 TTTCTT
1 TTTCTT
470330 TCTGCCCCTC
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
16 4 0.14
17 8 0.28
18 14 0.48
19 3 0.10
ACGTcount: A:0.14, C:0.29, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTCTTAAATTCACGCTC
Found at i:470307 original size:35 final size:35
Alignment explanation
Indices: 470260--470341 Score: 146
Period size: 35 Copynumber: 2.3 Consensus size: 35
470250 TCTATGGAGA
*
470260 TCTGCCCTTCTTTTCTTAAATTCACGCTCTTTCTT
1 TCTGCCCCTCTTTTCTTAAATTCACGCTCTTTCTT
*
470295 TCTGCCCCTCTTTTCTTAAATTCACGTTCTTTCTT
1 TCTGCCCCTCTTTTCTTAAATTCACGCTCTTTCTT
470330 TCTGCCCCTCTT
1 TCTGCCCCTCTT
470342 CTCCTGATAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.10, C:0.34, G:0.06, T:0.50
Consensus pattern (35 bp):
TCTGCCCCTCTTTTCTTAAATTCACGCTCTTTCTT
Found at i:493338 original size:32 final size:32
Alignment explanation
Indices: 493302--493362 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
493292 CGAAAAGAAG
493302 GCCTCTTTTTGTAACCCAAAAAAAAAAAAGGA
1 GCCTCTTTTTGTAACCCAAAAAAAAAAAAGGA
493334 GCCTCTTTTTGTAACCCAAAAAAAAAAAA
1 GCCTCTTTTTGTAACCCAAAAAAAAAAAA
493363 AGGAAGGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.23
Consensus pattern (32 bp):
GCCTCTTTTTGTAACCCAAAAAAAAAAAAGGA
Found at i:493356 original size:33 final size:34
Alignment explanation
Indices: 493294--493375 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 34
493284 GTGCCTATCG
493294 AAAA-GAAGGCCTCTTTTTGTAACCCAAAAAAAA
1 AAAAGGAAGGCCTCTTTTTGTAACCCAAAAAAAA
493327 AAAAGG-A-GCCTCTTTTTGTAACCCAAAAAAAAA
1 AAAAGGAAGGCCTCTTTTTGTAACCC-AAAAAAAA
493360 AAAAGGAAGGCCTCTT
1 AAAAGGAAGGCCTCTT
493376 ATAGCAGAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
32 17 0.38
33 19 0.42
34 2 0.04
35 7 0.16
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (34 bp):
AAAAGGAAGGCCTCTTTTTGTAACCCAAAAAAAA
Found at i:493894 original size:25 final size:25
Alignment explanation
Indices: 493860--493909 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
493850 TGCATGGCAC
493860 TGTTAGTGTGTTAGTGGTTGAAGCA
1 TGTTAGTGTGTTAGTGGTTGAAGCA
493885 TGTTAGTGTGTTAGTGGTTGAAGCA
1 TGTTAGTGTGTTAGTGGTTGAAGCA
493910 ACTAAGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.36, T:0.40
Consensus pattern (25 bp):
TGTTAGTGTGTTAGTGGTTGAAGCA
Found at i:498188 original size:25 final size:25
Alignment explanation
Indices: 498159--498208 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
498149 CAAGGAGGAG
*
498159 TGTTAGTGTGTTAGTGGTTGAAGCA
1 TGTTAGTGTGTTAATGGTTGAAGCA
498184 TGTTAGTGTGTTAATGGTTGAAGCA
1 TGTTAGTGTGTTAATGGTTGAAGCA
498209 ACTAAGTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.34, T:0.40
Consensus pattern (25 bp):
TGTTAGTGTGTTAATGGTTGAAGCA
Found at i:504881 original size:2 final size:2
Alignment explanation
Indices: 504874--504898 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
504864 CAAAAACACA
504874 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
504899 TACCAGAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:506950 original size:2 final size:2
Alignment explanation
Indices: 506943--506973 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
506933 GACAATCAGT
506943 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
506974 GCACTTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:507391 original size:3 final size:3
Alignment explanation
Indices: 507383--507430 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
507373 TCTTTACTTA
507383 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
507431 GCGTTTTAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:509443 original size:21 final size:21
Alignment explanation
Indices: 509417--509457 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
509407 GGACGAAAGA
509417 GGTGTCCA-TGAGAAAATTTTG
1 GGTGTCCAGT-AGAAAATTTTG
*
509438 GGTGTCTAGTAGAAAATTTT
1 GGTGTCCAGTAGAAAATTTT
509458 CCTTCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (21 bp):
GGTGTCCAGTAGAAAATTTTG
Found at i:513817 original size:115 final size:114
Alignment explanation
Indices: 513612--513822 Score: 291
Period size: 115 Copynumber: 1.8 Consensus size: 114
513602 TGATCCACTT
* *
513612 AGCCCAAAATTTGACCCACTAAAGCATATTTTTGGGCCCACTGCAACAAAAGGGCCTAATTTCGG
1 AGCCCAAAATTTGACCCACTAAAGCAGATTTTTGGGCCCACCGCAACAAAAGGGCCTAATTTCGG
*
513677 CCCAAAGTTGATCCATTAAGACCAATTATGCCAACATTAACCCCAAATTG
66 CCCAAAGTTGATCCACTAAGACCAATT-TGCCAACATTAACCCCAAATTG
* * * **
513727 AGCCCAAAATTTGACCCACTAAAGCAGATTTTT-TGCCCACCGTTAGCTTAA-GGCCTAATTTTC
1 AGCCCAAAATTTGACCCACTAAAGCAGATTTTTGGGCCCACCG-CAACAAAAGGGCCTAA-TTTC
* *
513790 TGCCCAAAGTTGATCCACTAAGCCCAATTTGCC
64 GGCCCAAAGTTGATCCACTAAGACCAATTTGCC
513823 CGAGGTTAGC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
114 18 0.21
115 66 0.79
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (114 bp):
AGCCCAAAATTTGACCCACTAAAGCAGATTTTTGGGCCCACCGCAACAAAAGGGCCTAATTTCGG
CCCAAAGTTGATCCACTAAGACCAATTTGCCAACATTAACCCCAAATTG
Found at i:513843 original size:115 final size:114
Alignment explanation
Indices: 513612--513951 Score: 350
Period size: 114 Copynumber: 3.0 Consensus size: 114
513602 TGATCCACTT
* * * **
513612 AGCCCAAAATTTGACCCACTAAAGCATATTTTTGGGCCCACTG-CAACAAAAGGGCCTAA-TTTC
1 AGCCCAAAATTTGACCCACTAAAGCAGATTTTT-GGCCCACCGTTAACTTAA-GGCCTAATTTTC
* * * *
513675 GGCCCAAAGTTGATCCATTAAGACCAATTATG-CCAACATTAACCCCAAATTG
64 GGCCCAAAGTTGATCCACTAAGCCCAATT-TGCCCAAGATT-AGCCCAAATTG
* * *
513727 AGCCCAAAATTTGACCCACTAAAGCAGATTTTTTGCCCACCGTTAGCTTAAGGCCTAATTTTCTG
1 AGCCCAAAATTTGACCCACTAAAGCAGATTTTTGGCCCACCGTTAACTTAAGGCCTAATTTTCGG
* *
513792 CCCAAAGTTGATCCACTAAGCCCAATTTGCCCGAGGTTAGCCCAAATTTG
66 CCCAAAGTTGATCCACTAAGCCCAATTTGCCCAAGATTAGCCCAAA-TTG
* * * * * * * * *
513842 AGCCCAAAA-ATGA-TCACTGAAGTAGAGTTTTGGGCCCAGCTTTAACTTAAGGTCTTATTTT-G
1 AGCCCAAAATTTGACCCACTAAAGCAGA-TTTTTGGCCCACCGTTAACTTAAGGCCTAATTTTCG
**
513904 GCCCAAAAGTTGATCCACTTTGCCCAATTTGCCCAAGATTAGCCCAAA
65 GCCC-AAAGTTGATCCACTAAGCCCAATTTGCCCAAGATTAGCCCAAA
513952 AATTAACCAA
Statistics
Matches: 189, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
113 14 0.07
114 92 0.49
115 83 0.44
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (114 bp):
AGCCCAAAATTTGACCCACTAAAGCAGATTTTTGGCCCACCGTTAACTTAAGGCCTAATTTTCGG
CCCAAAGTTGATCCACTAAGCCCAATTTGCCCAAGATTAGCCCAAATTG
Found at i:514047 original size:100 final size:100
Alignment explanation
Indices: 513909--514100 Score: 230
Period size: 100 Copynumber: 1.9 Consensus size: 100
513899 TTTTGGCCCA
**
513909 AAAGTTGATCCACTTTGCCCAATTTGCCCAAGATTAGCCCAAAAATTAACCAACT-AA-AGATTC
1 AAAGTTGATCCACTAAGCCCAATTTGCCCAAGA-TAGCCCAAAAATTAACCAACTAAACAGATTC
513972 TTGGGCC-CTCGTTACCTTAAGGCCCAATTCTCTTCCC
65 TTGGGCCTCT-GTTACC-TAAGGCCCAATTCTCTTCCC
* * * *
514009 AAAGTTGATCCACTAAGCCCAATTATGCCCATTG-TAGCCCAAAAGTTCACCCACTAAAACAGAT
1 AAAGTTGATCCACTAAGCCCAATT-TGCCCA-AGATAGCCCAAAAATTAACCAACT-AAACAGAT
* *
514073 TTTTTGGCCTCTGTTACCTAAGGCCCAA
63 TCTTGGGCCTCTGTTACCTAAGGCCCAA
514101 GTTTTGGTCG
Statistics
Matches: 78, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
100 40 0.51
101 6 0.08
102 13 0.17
103 17 0.22
104 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (100 bp):
AAAGTTGATCCACTAAGCCCAATTTGCCCAAGATAGCCCAAAAATTAACCAACTAAACAGATTCT
TGGGCCTCTGTTACCTAAGGCCCAATTCTCTTCCC
Found at i:519864 original size:209 final size:209
Alignment explanation
Indices: 519511--519910 Score: 597
Period size: 209 Copynumber: 1.9 Consensus size: 209
519501 AACTCAAGTT
* * * * *
519511 ATGCTTTCAAGCTTATATGATTCAAATAGTAATCGATCAGCTACTGAGAAAGGTTTTATAAAAGC
1 ATGCTTCCAAGCTCATATGATTCAAATAGTAACCGATCAACTACTGAGAAAGGCTTTATAAAAGC
* * *
519576 TTGAAATGTTGATAAGATTAATTAAATGGGTGGTTAAGCTTAATGAATTCGACTTACATATATTA
66 TTGAAATGTTGATAAGATTAATTAAATAGGTGGTTAAGCTCAATGAATTCGACTTACACATATTA
* * *
519641 TCTAGTTGGTCTTAAAATCACAGGTACT-GACAAACTTTATCGTAGAACTCACTTCGGTATATCT
131 TCTAATTAGTCTTAAAATCACAGGTACTAG-CAAACTTTATCGTAGAACTCACTTCGATATATCT
519705 AAAAAAACTCAGGCC
195 AAAAAAACTCAGGCC
* * * * *
519720 ATGCTTCCAAGCTCATATTATTCATATAGTAACCGATCAACTACTGAGATAGGCTTTATAGAGGC
1 ATGCTTCCAAGCTCATATGATTCAAATAGTAACCGATCAACTACTGAGAAAGGCTTTATAAAAGC
* *
519785 TTGAAATGTTGGTAAGATTAATTAAATATGTGG-TAGAGCTCAATGAATTCGACTTACACATATT
66 TTGAAATGTTGATAAGATTAATTAAATAGGTGGTTA-AGCTCAATGAATTCGACTTACACATATT
*
519849 ATCTAATTAGTCTTAAAATCACAGGTACTAGCAAACTTTGTCGTAGAACTCACTTCGATATA
130 ATCTAATTAGTCTTAAAATCACAGGTACTAGCAAACTTTATCGTAGAACTCACTTCGATATA
519911 CTTGAGAAAA
Statistics
Matches: 170, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
208 2 0.01
209 167 0.98
210 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (209 bp):
ATGCTTCCAAGCTCATATGATTCAAATAGTAACCGATCAACTACTGAGAAAGGCTTTATAAAAGC
TTGAAATGTTGATAAGATTAATTAAATAGGTGGTTAAGCTCAATGAATTCGACTTACACATATTA
TCTAATTAGTCTTAAAATCACAGGTACTAGCAAACTTTATCGTAGAACTCACTTCGATATATCTA
AAAAAACTCAGGCC
Found at i:528660 original size:16 final size:17
Alignment explanation
Indices: 528641--528673 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
528631 ATCAAGGTTA
528641 AACA-TTTAAGCATAAG
1 AACATTTTAAGCATAAG
528657 AACATTTTAAGCATAAG
1 AACATTTTAAGCATAAG
528674 TATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (17 bp):
AACATTTTAAGCATAAG
Found at i:534200 original size:103 final size:103
Alignment explanation
Indices: 534020--534223 Score: 363
Period size: 103 Copynumber: 2.0 Consensus size: 103
534010 AGTCTCGACG
* *
534020 TGCTAATTAAATATGGCATCCTGGTTGTATATTATTTAACAGAAAGATAAATAATGAAATAAAGC
1 TGCTAATTAAATATGGCATCCTGATTATATATTATTTAACAGAAAGATAAATAATGAAATAAAGC
*
534085 AATATTTGGTTATTTTTATTTTAAAAATTTTATTAACA
66 AATATTTAGTTATTTTTATTTTAAAAATTTTATTAACA
534123 TGCTAATTAAATATGGCATCCTGATTATATATTATTTAACAGAAAGATAAATAATGAAATAAAGC
1 TGCTAATTAAATATGGCATCCTGATTATATATTATTTAACAGAAAGATAAATAATGAAATAAAGC
**
534188 AATATTTAGTTATTTTTATTTTAAATTTTTTATTAA
66 AATATTTAGTTATTTTTATTTTAAAAATTTTATTAA
534224 GTTTTTTTAT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.42
Consensus pattern (103 bp):
TGCTAATTAAATATGGCATCCTGATTATATATTATTTAACAGAAAGATAAATAATGAAATAAAGC
AATATTTAGTTATTTTTATTTTAAAAATTTTATTAACA
Found at i:534230 original size:27 final size:28
Alignment explanation
Indices: 534190--534242 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
534180 AATAAAGCAA
*
534190 TATTTAGTTATTTTTATTTTAAATTTTT
1 TATTAAGTTATTTTTATTTTAAATTTTT
534218 TATTAAGTT-TTTTTATTTTAAATTT
1 TATTAAGTTATTTTTATTTTAAATTT
534243 ATATACTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (28 bp):
TATTAAGTTATTTTTATTTTAAATTTTT
Found at i:534897 original size:14 final size:16
Alignment explanation
Indices: 534863--534910 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
534853 ATCTAAATAA
534863 ATTTTTAATATAAATT
1 ATTTTTAATATAAATT
534879 ATTTTTAAGTA-AATATT
1 ATTTTTAA-TATAA-ATT
* *
534896 TTTTTTAATACAAAT
1 ATTTTTAATATAAAT
534911 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTTTTAATATAAATT
Found at i:534974 original size:30 final size:30
Alignment explanation
Indices: 534908--534974 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
534898 TTTTAATACA
*
534908 AATAAAA-A-ATAAAGATGTATTTAAAAAT
1 AATAAAATATATAAAGATGTATTTAAAAAG
* *
534936 AATAAAATATATAAAGATTTATTTAAATAG
1 AATAAAATATATAAAGATGTATTTAAAAAG
*
534966 AATGAAATA
1 AATAAAATA
534975 GCTCATGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 7 0.21
29 1 0.03
30 25 0.76
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (30 bp):
AATAAAATATATAAAGATGTATTTAAAAAG
Found at i:539205 original size:18 final size:17
Alignment explanation
Indices: 539145--539205 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 17
539135 ATATTAACAT
*
539145 AAAAATTCTTTTAAAGAA
1 AAAAATTATTTTAAA-AA
*
539163 AAAAATAATTTT-AAAA
1 AAAAATTATTTTAAAAA
**
539179 AATTA-TATTTTAAATAA
1 AAAAATTATTTTAAA-AA
539196 AAAAATTATT
1 AAAAATTATT
539206 AACATAATCA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
17 7 0.21
18 14 0.42
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAAATTATTTTAAAAA
Found at i:539710 original size:20 final size:21
Alignment explanation
Indices: 539664--539711 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
539654 TAAAATTTTG
*
539664 ATAAATATATAAGAAAAATAT
1 ATAAATAAATAAGAAAAATAT
*
539685 CT-AATAAATAA-AAAAATAT
1 ATAAATAAATAAGAAAAATAT
539704 ATAAATAA
1 ATAAATAA
539712 CATGAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 13 0.57
21 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAAATAAATAAGAAAAATAT
Found at i:540288 original size:17 final size:17
Alignment explanation
Indices: 540262--540389 Score: 70
Period size: 17 Copynumber: 7.4 Consensus size: 17
540252 GTTAAGTCCA
*
540262 TTTT-TTTTCTT-TTCT
1 TTTTATTTTCTTCTTAT
540277 TCTTTATTTTCTTCTTAT
1 T-TTTATTTTCTTCTTAT
* *
540295 TTTTATTTTTTATTTTTAT
1 TTTTA--TTTTCTTCTTAT
* *
540314 TTTTATTTT-TTATTTT
1 TTTTATTTTCTTCTTAT
*
540330 TATTGTATTTTACATTTTTA-
1 T-TT-TATTTT-C-TTCTTAT
*
540350 TTTTATTTTATT-TCTAT
1 TTTTATTTTCTTCT-TAT
*
540367 TTTTATTTTATT-TTAT
1 TTTTATTTTCTTCTTAT
540383 TTTTATT
1 TTTTATT
540390 ATTTTATATA
Statistics
Matches: 93, Mismatches: 8, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
15 2 0.02
16 23 0.25
17 30 0.32
18 16 0.17
19 17 0.18
20 1 0.01
21 4 0.04
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (17 bp):
TTTTATTTTCTTCTTAT
Found at i:540302 original size:6 final size:6
Alignment explanation
Indices: 540291--540389 Score: 109
Period size: 6 Copynumber: 16.8 Consensus size: 6
540281 TATTTTCTTC
*
540291 TTATTT TTATTTT TTATTT TTATTT TTATTTT TTATTT TTA-TT GTATTT
1 TTATTT TTA-TTT TTATTT TTATTT TTA-TTT TTATTT TTATTT TTATTT
* *
540340 TACATTT TTA-TT TTA-TT TTATTT CTATTT TTA-TT TTA-TT TTATTT
1 T-TATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
540385 TTATT
1 TTATT
540390 ATTTTATATA
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
5 24 0.30
6 40 0.49
7 17 0.21
ACGTcount: A:0.18, C:0.02, G:0.01, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:540305 original size:19 final size:19
Alignment explanation
Indices: 540291--540407 Score: 122
Period size: 19 Copynumber: 6.5 Consensus size: 19
540281 TATTTTCTTC
540291 TTATTTTTATTTTTTATTT
1 TTATTTTTATTTTTTATTT
540310 TTATTTTTATTTTTTATTT
1 TTATTTTTATTTTTTATTT
* **
540329 TTA-TTGTATTTTACATTT
1 TTATTTTTATTTTTTATTT
540347 TTA-TTTTA--TTTTATTT
1 TTATTTTTATTTTTTATTT
*
540363 CTATTTTTA--TTTTA-TT
1 TTATTTTTATTTTTTATTT
*
540379 TTATTTTTATTATTTTATAT
1 TTATTTTTATT-TTTTATTT
*
540399 ATATTTTTA
1 TTATTTTTA
540408 GGTATTTATG
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
16 18 0.22
17 10 0.12
18 19 0.23
19 27 0.33
20 9 0.11
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.77
Consensus pattern (19 bp):
TTATTTTTATTTTTTATTT
Found at i:540310 original size:5 final size:5
Alignment explanation
Indices: 540279--540396 Score: 84
Period size: 5 Copynumber: 23.0 Consensus size: 5
540269 TCTTTTCTTC
* * *
540279 TTTAT TTTCT TCTTAT TTT-T ATT-T TTTATT TTTAT TTT-T ATT-T TTTATT
1 TTTAT TTTAT T-TTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTA-T
*
540328 TTTAT TGTAT TTTACATT TTTAT TTTAT TTTAT TTCTATT TTTAT TTTAT
1 TTTAT TTTAT TTT--A-T TTTAT TTTAT TTTAT TT-TA-T TTTAT TTTAT
*
540378 TTTAT TTT-T ATTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT
540397 ATATATTTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
4 15 0.16
5 50 0.54
6 19 0.21
7 4 0.04
8 4 0.04
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:540522 original size:21 final size:21
Alignment explanation
Indices: 540498--540546 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
540488 CAGATTATGT
540498 ATTATCTGTT-ATTTAATTTTA
1 ATTATCTGTTAATTT-ATTTTA
*
540519 ATTATCTGTTAATTTTTTTTA
1 ATTATCTGTTAATTTATTTTA
*
540540 TTTATCT
1 ATTATCT
540547 TATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (21 bp):
ATTATCTGTTAATTTATTTTA
Found at i:540585 original size:34 final size:33
Alignment explanation
Indices: 540530--540595 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
540520 TTATCTGTTA
* * *
540530 ATTTTTTTTATTTATCTTATTTATTTTCTTTTG
1 ATTTTTTTCATTTATCGTATTTATTTTATTTTG
* *
540563 ATTTTTTTACATTTTTCGTATTTTTTTTATTTT
1 ATTTTTTT-CATTTATCGTATTTATTTTATTTT
540596 TTTTTTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 8 0.30
34 19 0.70
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (33 bp):
ATTTTTTTCATTTATCGTATTTATTTTATTTTG
Found at i:540599 original size:9 final size:9
Alignment explanation
Indices: 540534--540599 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
540524 CTGTTAATTT
540534 TTTTTATTTA
1 TTTTT-TTTA
* *
540544 TCTTATTTA
1 TTTTTTTTA
540553 TTTTCTTTTGA
1 TTTT-TTTT-A
*
540564 TTTTTTTACA
1 TTTTTTT-TA
**
540574 TTTTTCGTA
1 TTTTTTTTA
540583 TTTTTTTTA
1 TTTTTTTTA
540592 TTTTTTTT
1 TTTTTTTT
540600 TTATTTACTT
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
9 23 0.53
10 15 0.35
11 5 0.12
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:541462 original size:5 final size:5
Alignment explanation
Indices: 541452--541506 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
541442 TCTTTTCACC
* *
541452 TTTAT TTTATT TTTATT TTTGT TTTACT TTT-T TTTGT TTTAT TTTAT
1 TTTAT TTTA-T TTTA-T TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT
541499 TTT-T TTTA
1 TTTAT TTTA
541507 AATAAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
4 8 0.19
5 21 0.49
6 14 0.33
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:541468 original size:11 final size:10
Alignment explanation
Indices: 541452--541505 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
541442 TCTTTTCACC
541452 TTTATTTTATT
1 TTTATTTT-TT
541463 TTTATTTTTGT
1 TTTATTTTT-T
*
541474 TTTACTTTTT
1 TTTATTTTTT
* *
541484 TTTGTTTTAT
1 TTTATTTTTT
541494 TTTATTTTTT
1 TTTATTTTTT
541504 TT
1 TT
541506 AAATAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
10 19 0.53
11 17 0.47
ACGTcount: A:0.11, C:0.02, G:0.04, T:0.83
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:541491 original size:20 final size:19
Alignment explanation
Indices: 541452--541505 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
541442 TCTTTTCACC
*
541452 TTTATTTTA-TTTTTAT-T
1 TTTATTTTATTTTTTTTGT
*
541469 TTTGTTTTACTTTTTTTTGT
1 TTTATTTTA-TTTTTTTTGT
541489 TTTATTTTATTTTTTTT
1 TTTATTTTATTTTTTTT
541506 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 8 0.26
19 14 0.45
20 9 0.29
ACGTcount: A:0.11, C:0.02, G:0.04, T:0.83
Consensus pattern (19 bp):
TTTATTTTATTTTTTTTGT
Found at i:541582 original size:59 final size:57
Alignment explanation
Indices: 541506--541843 Score: 370
Period size: 59 Copynumber: 5.9 Consensus size: 57
541496 TATTTTTTTT
* * *
541506 AAATAAAAATAAAAAAAATAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAA
1 AAATAAAATTTAAAAAAA-AAT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
* *
541565 AAATAAAATTTAAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAA
1 AAATAAAATTTAAAAAAAA--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
* * *
541624 AAATAAAATCTAAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAA
1 AAATAAAATTTAAAAAAAA--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
* *
541683 AAATCAAAATTTTCAAAAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCCTTAA
1 AAAT-AAAA-TTTAAAAAAAAATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAA
* * *
541742 AAAT-AAATTT----AAAAATTTTAG-GGAAAAGTTGAAAATATCAATTTTTCTTAA
1 AAATAAAATTTAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
* * *
541793 AAAT-AAATTTCCAAAAAATATTTTT-AGGGAAAATTTGAAAGTATCAATTTT
1 AAATAAAATTT-AAAAAAAAATTTTTGA-GGAAAAGTTGAAAGTATCAATTTT
541844 TCCTGCACAA
Statistics
Matches: 245, Mismatches: 21, Indels: 28
0.83 0.07 0.10
Matches are distributed among these distances:
51 36 0.15
52 10 0.04
56 11 0.04
57 25 0.10
58 4 0.02
59 146 0.60
60 5 0.02
61 8 0.03
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.34
Consensus pattern (57 bp):
AAATAAAATTTAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
Found at i:544045 original size:235 final size:236
Alignment explanation
Indices: 543499--544291 Score: 930
Period size: 237 Copynumber: 3.4 Consensus size: 236
543489 AAACTATGAC
* * * * *
543499 AATTCTAAACATAATAAAAATTAAGAACCACCATAATAATATATTATTGTAATGTAAATAATTTT
1 AATTCTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAATGTAAATAA--TT
* * *
543564 AT-TTG-CAACAT-AAATTTT-A--ATTTATTATTTCTTATAAATAT-CTAAGAAAAATAGTTGG
64 ATGTTGACAACATAAAATTTTAATTATTTATTA-TTCTTGTAAATATAC-AAGAAAAATAGCT-A
* * * * * * *
543622 ACATTAAAAAATAAATTGATAACATAAACAAGTAAGAACA-AATGT-AAATTAGTACCAATT-AG
126 AAATTAAAAAACAAATTTATAACGTAAACAAGTAAGAA-ATAATGTAAAATTAATACCATTTGAA
*** * * * * * ** * ***
543684 TGTAAAATGGATAAAAAGGGTTGTAACACGTTAA-AAAGGAGTTATAA
190 AAAAAAAAGGGTTAAAAGTGTTGTAGCACACTAAGAAA-AACCCATAA
* ** * * * *
543731 TAATTGTAAGTATAATGAAAAGTAAAAATAACCGTAAAAA-AAATTATTGTAAAG-ATAATAATT
1 -AATTCTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAATGTA-AATAATT
543794 ATGTTGACAACATAAAATTTTAATTATTTATTATTCTTGTAAATATACAAG-AAAATAGCTAAAA
64 ATGTTGACAACATAAAATTTTAATTATTTATTATTCTTGTAAATATACAAGAAAAATAGCTAAAA
543858 TTAAAAAACAAATTTATAACGTAAACAAGTAAGAAATAATGTAAAATTAATACCATTTGAAAAAA
129 TTAAAAAACAAATTTATAACGTAAACAAGTAAGAAATAATGTAAAATTAATACCATTTGAAAAAA
*
543923 AAAAGGGTTAACAGTGTTGTAGCACACTAAGAAAAACCCATAA
194 AAAAGGGTTAAAAGTGTTGTAGCACACTAAGAAAAACCCATAA
* * *
543966 AATTCTAAACATCATGAAAAGTAAGAACAACTATAAAAATATATTATTGTAATGTAAATAATTAT
1 AATTCTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAATGTAAATAATTAT
* *
544031 GTTGACAGCATAAAATTTTAATTATTTATTATTCTTGTAAATATAAAAGAAAAATAGCTAAAATT
66 GTTGACAACATAAAATTTTAATTATTTATTATTCTTGTAAATATACAAGAAAAATAGCTAAAATT
* * *
544096 AAAAAACAATTTTATTACGTAAACAAGTAAGAAATAATGTAAAATTAATATCATTTGAAAAAAAA
131 AAAAAACAAATTTATAACGTAAACAAGTAAGAAATAATGTAAAATTAATACCATTTGAAAAAAAA
* *
544161 AATAGGTTAATAGTGTTGTAGCACACTAAGAAAAACCCATAA
196 AA-GGGTTAAAAGTGTTGTAGCACACTAAGAAAAACCCATAA
** *
544203 AATTCTAAACACCATGAAAAGTAAAAACAACTATAAAAATATATTATTGTAATGTAAATAATTAT
1 AATTCTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAATGTAAATAATTAT
* *
544268 GATGACAATATAAAATTTTAATTA
66 GTTGACAACATAAAATTTTAATTA
544292 ACTATTGTTA
Statistics
Matches: 485, Mismatches: 59, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
230 4 0.01
231 4 0.01
232 24 0.05
233 75 0.15
234 53 0.11
235 112 0.23
236 92 0.19
237 121 0.25
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (236 bp):
AATTCTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAATGTAAATAATTAT
GTTGACAACATAAAATTTTAATTATTTATTATTCTTGTAAATATACAAGAAAAATAGCTAAAATT
AAAAAACAAATTTATAACGTAAACAAGTAAGAAATAATGTAAAATTAATACCATTTGAAAAAAAA
AAGGGTTAAAAGTGTTGTAGCACACTAAGAAAAACCCATAA
Found at i:552729 original size:15 final size:15
Alignment explanation
Indices: 552709--552750 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
552699 TTCATCCTTA
552709 TATGGCTTGTGACAT
1 TATGGCTTGTGACAT
* *
552724 TATGGCTTTTAACAT
1 TATGGCTTGTGACAT
*
552739 TGTGGCTTGTGA
1 TATGGCTTGTGA
552751 AATTGATATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.43
Consensus pattern (15 bp):
TATGGCTTGTGACAT
Found at i:557294 original size:11 final size:11
Alignment explanation
Indices: 557259--557306 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
557249 TTAATTTAAT
557259 TTTAAAATATA
1 TTTAAAATATA
* *
557270 TTAAAAAAATA
1 TTTAAAATATA
*
557281 TTTAATATATA
1 TTTAAAATATA
* *
557292 TTTAATATATT
1 TTTAAAATATA
557303 TTTA
1 TTTA
557307 GACTTACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTAAAATATA
Found at i:557306 original size:22 final size:22
Alignment explanation
Indices: 557247--557306 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
557237 AAAATTTTTA
* *
557247 ATTTAATTTAATTTTAAAATAT
1 ATTTAATATATTTTTAAAATAT
* * * * *
557269 ATTAAAAAAATATTTAATATAT
1 ATTTAATATATTTTTAAAATAT
557291 ATTTAATATATTTTTA
1 ATTTAATATATTTTTA
557307 GACTTACTTA
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTAATATATTTTTAAAATAT
Found at i:560094 original size:157 final size:157
Alignment explanation
Indices: 559808--560122 Score: 515
Period size: 157 Copynumber: 2.0 Consensus size: 157
559798 AAGTTATAGT
*
559808 ACCAATCTTGCATATACACCTCCTGAGTATCTAAGAAATGGTAACTGCTTTTAACTCTTTTTATT
1 ACCAATCTTGCATATACACCTCCTGAGTATCTAAGAAATGGTAACTGCTTTTAACTCTGTTTATT
* *
559873 ATTTTATTTGTTTCTTTGCTCTCATTAAGAGAAAGAAAACAATATTCTTCCTTTGCATTGTATGT
66 ATTTAATTTCTTTCTTTGCTCTCATTAAGAGAAAGAAAACAATATTCTTCCTTTGCATTGTATGT
*
559938 ATC-TTTAAGTTTGTATATATAAATCTA
131 ATCTTTTAA-TGTGTATATATAAATCTA
* *
559965 ACCAATCTTGCATATACACTTCCTGCGTATCTAAGAAATGGTAACTGCTTTTAACTCTGTTTATT
1 ACCAATCTTGCATATACACCTCCTGAGTATCTAAGAAATGGTAACTGCTTTTAACTCTGTTTATT
* * *
560030 ATTTAATTTCTTTCTTTGCTCTTATTAAGAGGAAGAAAACAATCTTCTTCCTTTGCATTGTATGT
66 ATTTAATTTCTTTCTTTGCTCTCATTAAGAGAAAGAAAACAATATTCTTCCTTTGCATTGTATGT
* *
560095 ATCTTTTAATGTGTGTGTATAAATCTA
131 ATCTTTTAATGTGTATATATAAATCTA
560122 A
1 A
560123 AACTTACTTA
Statistics
Matches: 146, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
157 141 0.97
158 5 0.03
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (157 bp):
ACCAATCTTGCATATACACCTCCTGAGTATCTAAGAAATGGTAACTGCTTTTAACTCTGTTTATT
ATTTAATTTCTTTCTTTGCTCTCATTAAGAGAAAGAAAACAATATTCTTCCTTTGCATTGTATGT
ATCTTTTAATGTGTATATATAAATCTA
Found at i:572438 original size:70 final size:70
Alignment explanation
Indices: 572325--572467 Score: 232
Period size: 70 Copynumber: 2.0 Consensus size: 70
572315 GGTCCAACAC
* * **
572325 TGAAAATTGCGATCAATGATGCATCACCTAACAAAGGGAAATCCAGTGGTTATATTGTGAAGTTC
1 TGAAAATTGCGATCAAAGATACATCACCTAACAAAGCCAAATCCAGTGGTTATATTGTGAAGTTC
572390 TCGTA
66 TCGTA
* *
572395 TGAAAATTGCTATCAAAGATACATCACCTAACGAAGCCAAATCCAGTGGTTATATTGTGAAGTTC
1 TGAAAATTGCGATCAAAGATACATCACCTAACAAAGCCAAATCCAGTGGTTATATTGTGAAGTTC
572460 TCGTA
66 TCGTA
572465 TGA
1 TGA
572468 TCAATAGTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (70 bp):
TGAAAATTGCGATCAAAGATACATCACCTAACAAAGCCAAATCCAGTGGTTATATTGTGAAGTTC
TCGTA
Found at i:573328 original size:20 final size:20
Alignment explanation
Indices: 573299--573344 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
573289 TATTTGAGAT
* *
573299 TATTATAATTAA-ATTTTAA
1 TATTAAAATTAAGAATTTAA
573318 TAATTAAAATTAAGAATTTAA
1 T-ATTAAAATTAAGAATTTAA
573339 TATTAA
1 TATTAA
573345 TTCTTTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 15 0.65
21 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TATTAAAATTAAGAATTTAA
Found at i:573697 original size:3 final size:3
Alignment explanation
Indices: 573691--573726 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
573681 TAATAATAGT
573691 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
573727 GGACTGGCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:576925 original size:3 final size:3
Alignment explanation
Indices: 576917--576946 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
576907 TGAAGCCACT
*
576917 ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
576947 TACAAGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:577404 original size:2 final size:2
Alignment explanation
Indices: 577397--577428 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
577387 AGGCCCATTT
577397 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
577429 ACTTATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:580486 original size:2 final size:2
Alignment explanation
Indices: 580479--580505 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
580469 AATTTATCTG
580479 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 T
580506 GTTTCTATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:585381 original size:37 final size:36
Alignment explanation
Indices: 585314--585384 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
585304 AATTCTGTTA
*
585314 ATAATTATTTATTGAGATTATTTTAAATATATAATTT
1 ATAATTATTTATTGAAATTATTTT-AATATATAATTT
*
585351 ATAATTATTTATTTTAAATTATTATT-ATATATAA
1 ATAATTATTTA-TTGAAATTATT-TTAATATATAA
585385 CATATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
37 19 0.63
38 9 0.30
39 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (36 bp):
ATAATTATTTATTGAAATTATTTTAATATATAATTT
Found at i:590920 original size:2 final size:2
Alignment explanation
Indices: 590907--590945 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
590897 CTACCCTTCA
590907 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
590946 CCACATATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:591198 original size:87 final size:87
Alignment explanation
Indices: 591090--591265 Score: 334
Period size: 87 Copynumber: 2.0 Consensus size: 87
591080 CATGGAATAT
* *
591090 ATATTAGAGTAGTGTCTATCTTCCAAAGTTTCTTTTTTTTTTTTTTTTATTAAACTTAAGTAGTA
1 ATATTAGAGTAGTGTCTATCTTCCAAAGTTTCTTTTTTTTTTATTATTATTAAACTTAAGTAGTA
591155 ATACTCATAAATACATTCCTCA
66 ATACTCATAAATACATTCCTCA
591177 ATATTAGAGTAGTGTCTATCTTCCAAAGTTTCTTTTTTTTTTATTATTATTAAACTTAAGTAGTA
1 ATATTAGAGTAGTGTCTATCTTCCAAAGTTTCTTTTTTTTTTATTATTATTAAACTTAAGTAGTA
591242 ATACTCATAAATACATTCCTCA
66 ATACTCATAAATACATTCCTCA
591264 AT
1 AT
591266 TAACTCCATC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (87 bp):
ATATTAGAGTAGTGTCTATCTTCCAAAGTTTCTTTTTTTTTTATTATTATTAAACTTAAGTAGTA
ATACTCATAAATACATTCCTCA
Found at i:592710 original size:2 final size:2
Alignment explanation
Indices: 592665--592693 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
592655 GTTAATTTTG
592665 AT 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 A
592694 AACAATGAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:592835 original size:145 final size:145
Alignment explanation
Indices: 592665--592950 Score: 563
Period size: 145 Copynumber: 2.0 Consensus size: 145
592655 GTTAATTTTG
592665 ATATATATATATATATATATATATATATAAACAATGAACATATATAGATTGTAAATTACAAGGCT
1 ATATATATATATATATATATATATATATAAACAATGAACATATATAGATTGTAAATTACAAGGCT
592730 AGCTACCATGTCCATACCCTTAACCCTAACTCACGTTGTTCTTTTCTTCAAATCCTACCTTTAAC
66 AGCTACCATGTCCATACCCTTAACCCTAACTCACGTTGTTCTTTTCTTCAAATCCTACCTTTAAC
592795 GAAGATGATATATAT
131 GAAGATGATATATAT
*
592810 ATATATATATATATATATATATATATATAAACAATGAACATATATAGATTGTAAATTATAAGGCT
1 ATATATATATATATATATATATATATATAAACAATGAACATATATAGATTGTAAATTACAAGGCT
592875 AGCTACCATGTCCATACCCTTAACCCTAACTCACGTTGTTCTTTTCTTCAAATCCTACCTTTAAC
66 AGCTACCATGTCCATACCCTTAACCCTAACTCACGTTGTTCTTTTCTTCAAATCCTACCTTTAAC
592940 GAAGATGATAT
131 GAAGATGATAT
592951 TTTATGAGTA
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 140 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (145 bp):
ATATATATATATATATATATATATATATAAACAATGAACATATATAGATTGTAAATTACAAGGCT
AGCTACCATGTCCATACCCTTAACCCTAACTCACGTTGTTCTTTTCTTCAAATCCTACCTTTAAC
GAAGATGATATATAT
Found at i:592855 original size:2 final size:2
Alignment explanation
Indices: 592802--592838 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
592792 AACGAAGATG
592802 AT AT AT AT AT 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
592839 AACAATGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:596506 original size:2 final size:2
Alignment explanation
Indices: 596445--596487 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
596435 ACTTGGTAAG
596445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
596486 AT
1 AT
596488 TGCCCTCCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:602875 original size:2 final size:2
Alignment explanation
Indices: 602868--602900 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
602858 AAGTTTGGCA
602868 AT AT AT 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 A
602901 CATAAAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:605362 original size:13 final size:13
Alignment explanation
Indices: 605344--605368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
605334 GACCATTGTT
605344 TAAAAATAAAAAA
1 TAAAAATAAAAAA
605357 TAAAAATAAAAA
1 TAAAAATAAAAA
605369 TCATGGTAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:606060 original size:8 final size:9
Alignment explanation
Indices: 606043--606067 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
606033 AACAATCAAT
606043 AATAAAAAA
1 AATAAAAAA
606052 AATAAAAAA
1 AATAAAAAA
606061 AATAAAA
1 AATAAAA
606068 TATACAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AATAAAAAA
Found at i:615211 original size:9 final size:9
Alignment explanation
Indices: 615197--615229 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
615187 CAACCATCAT
615197 CACAAGCTG
1 CACAAGCTG
615206 CACAAGC--
1 CACAAGCTG
615213 CACAAGCTG
1 CACAAGCTG
615222 CACAAGCT
1 CACAAGCT
615230 TTTTGGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.32
9 15 0.68
ACGTcount: A:0.36, C:0.36, G:0.18, T:0.09
Consensus pattern (9 bp):
CACAAGCTG
Found at i:615218 original size:16 final size:16
Alignment explanation
Indices: 615197--615228 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
615187 CAACCATCAT
615197 CACAAGCTGCACAAGC
1 CACAAGCTGCACAAGC
615213 CACAAGCTGCACAAGC
1 CACAAGCTGCACAAGC
615229 TTTTTGGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.38, G:0.19, T:0.06
Consensus pattern (16 bp):
CACAAGCTGCACAAGC
Found at i:629621 original size:52 final size:52
Alignment explanation
Indices: 629480--629636 Score: 165
Period size: 52 Copynumber: 3.0 Consensus size: 52
629470 TATAACCATA
* * * * * **
629480 CAAACTTGCCCATTAAGAAT-CCTTCTCCTCTTAGAATTCTTTTCCTATAAGT
1 CAAACTTACCTATTAAGAATCCCTT-TCTTCTTAGAATTCTTCTCTTGCAAGT
* *
629532 CAAACTTGCCTATTAAGAATCCCTTTCTTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATCCCTTTCTTCTTAGAATTCTTCTCTTGCAAGT
** * *
629584 CAAACTTACCTATTAAGAATTTTCTTT-TTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAA-TCCCTTTCTTCTTAGAATTCTTCTCTTGCAAGT
629636 C
1 C
629637 TTTTTGTCCA
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 81 0.90
53 9 0.10
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCCCTTTCTTCTTAGAATTCTTCTCTTGCAAGT
Found at i:629671 original size:21 final size:22
Alignment explanation
Indices: 629653--629699 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
629643 TCCATCAAGC
*
629653 AATATCTGACAAATCTCAAACA
1 AATATCTAACAAATCTCAAACA
* *
629675 AATCTCTAACAAATCCCAAACA
1 AATATCTAACAAATCTCAAACA
629697 AAT
1 AAT
629700 CTCTTATGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.21
Consensus pattern (22 bp):
AATATCTAACAAATCTCAAACA
Found at i:629677 original size:11 final size:11
Alignment explanation
Indices: 629661--629702 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
629651 GCAATATCTG
629661 ACAAATCTCAA
1 ACAAATCTCAA
*
629672 ACAAATCTCTA
1 ACAAATCTCAA
*
629683 ACAAATCCCAA
1 ACAAATCTCAA
629694 ACAAATCTC
1 ACAAATCTC
629703 TTATGGGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:629686 original size:22 final size:22
Alignment explanation
Indices: 629661--629703 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
629651 GCAATATCTG
*
629661 ACAAATCTCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
629683 ACAAATCCCAAACAAATCTCT
1 ACAAATCCCAAACAAATCTCT
629704 TATGGGATTT
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:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:630064 original size:31 final size:31
Alignment explanation
Indices: 630026--630110 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
630016 TTCGAACCTT
*
630026 CAGCTCTGATACTACTTGTTGGGGAACACCA
1 CAGCTCTGATACCACTTGTTGGGGAACACCA
* *
630057 CAGCTCTGATACCACTTGTTGAGGATCACCA
1 CAGCTCTGATACCACTTGTTGGGGAACACCA
* *
630088 TAGCTCTGATACCATTTGTTGGG
1 CAGCTCTGATACCACTTGTTGGG
630111 CTAAAAGCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (31 bp):
CAGCTCTGATACCACTTGTTGGGGAACACCA
Found at i:630663 original size:52 final size:52
Alignment explanation
Indices: 630593--630716 Score: 169
Period size: 52 Copynumber: 2.4 Consensus size: 52
630583 TATAACCATA
* * *
630593 CAAACTTACCCATTAAGAAT-CCTTCTCCTCTTAGAATTCTTTTCTTATAAGT
1 CAAACTTACCTATTAAGAATCCCTT-TCCTCTTAGAATTCTTCTCTTACAAGT
* * * *
630645 CAAACTTGCCTATTAAGAATCCCTTTCTTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTACAAGT
630697 CAAACTTACCTATTAAGAAT
1 CAAACTTACCTATTAAGAAT
630717 TTTCTTTTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 59 0.94
53 4 0.06
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTACAAGT
Found at i:630735 original size:52 final size:52
Alignment explanation
Indices: 630593--630749 Score: 160
Period size: 52 Copynumber: 3.0 Consensus size: 52
630583 TATAACCATA
* * ** * **
630593 CAAACTTACCCATTAAGAATCCTTCTCCTCTT-AGAATTCTTTTCTTATAAGT
1 CAAACTTACCTATTAAGAATCTTTCTTTTCTTGA-AATTCTTCTCTTGCAAGT
* *
630645 CAAACTTGCCTATTAAGAATCCCTTTCTTTT-TAG-AATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAAT--CTTTCTTTTCTTGAAATTCTTCTCTTGCAAGT
*
630697 CAAACTTACCTATTAAGAAT-TTTCTTTTTCTTGAAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAATCTTTC-TTTTCTTGAAATTCTTCTCTTGCAAGT
630749 C
1 C
630750 TTTTTGTCCA
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
49 4 0.05
50 4 0.05
51 2 0.02
52 70 0.80
53 1 0.01
54 6 0.07
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCTTTCTTTTCTTGAAATTCTTCTCTTGCAAGT
Found at i:630784 original size:21 final size:22
Alignment explanation
Indices: 630766--630812 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
630756 TCCATCAAGC
*
630766 AATATTTGACAAATCTCAAACA
1 AATATTTAACAAATCTCAAACA
* *
630788 AATCTTTAACAAATCCCAAACA
1 AATATTTAACAAATCTCAAACA
630810 AAT
1 AAT
630813 CTCTTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.21, G:0.02, T:0.26
Consensus pattern (22 bp):
AATATTTAACAAATCTCAAACA
Found at i:630790 original size:11 final size:11
Alignment explanation
Indices: 630774--630815 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
630764 GCAATATTTG
630774 ACAAATCTCAA
1 ACAAATCTCAA
**
630785 ACAAATCTTTA
1 ACAAATCTCAA
*
630796 ACAAATCCCAA
1 ACAAATCTCAA
630807 ACAAATCTC
1 ACAAATCTC
630816 TTATAAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:635881 original size:2 final size:2
Alignment explanation
Indices: 635874--635903 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
635864 AAATACAACA
635874 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
635904 TAGGTTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:635983 original size:2 final size:2
Alignment explanation
Indices: 635976--636014 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
635966 TTCTCTTGTA
635976 AT AT AT AT AT AT 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 AT A
636015 ATCTACAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:637099 original size:23 final size:23
Alignment explanation
Indices: 637073--637117 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
637063 ATATCAAATT
637073 AAATCCATCAAAATAAA-ATAAAA
1 AAATCCATCAAAA-AAATATAAAA
* *
637096 AAATGCATTAAAAAAATATAAA
1 AAATCCATCAAAAAAATATAAA
637118 CCAAATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.69, C:0.09, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATCCATCAAAAAAATATAAAA
Found at i:643993 original size:2 final size:2
Alignment explanation
Indices: 643986--644016 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
643976 ACAGTAAATA
643986 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
644017 TATGGTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:646540 original size:19 final size:19
Alignment explanation
Indices: 646518--646555 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
646508 ATTGAGATTA
646518 ATTTTTCTCTCAAAGGGTC
1 ATTTTTCTCTCAAAGGGTC
646537 ATTTTTCTCTCAAAGGGTC
1 ATTTTTCTCTCAAAGGGTC
646556 TTCACCTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (19 bp):
ATTTTTCTCTCAAAGGGTC
Found at i:647182 original size:16 final size:18
Alignment explanation
Indices: 647151--647185 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
647141 ATCTAAGCAT
647151 TTTTTCTTTTATTTAAAA
1 TTTTTCTTTTATTTAAAA
647169 TTTTT-TTTTA-TTAAAA
1 TTTTTCTTTTATTTAAAA
647185 T
1 T
647186 GTACCATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTCTTTTATTTAAAA
Found at i:648365 original size:20 final size:21
Alignment explanation
Indices: 648332--648370 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
648322 GCTCAAGCTC
* *
648332 AATGATGCTCAGGT-TAAGAT
1 AATGAGGCTAAGGTCTAAGAT
648352 AATGAGGCTAAGGTCTAAG
1 AATGAGGCTAAGGTCTAAG
648371 TTGGAAGCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.36, C:0.10, G:0.28, T:0.26
Consensus pattern (21 bp):
AATGAGGCTAAGGTCTAAGAT
Found at i:650495 original size:104 final size:105
Alignment explanation
Indices: 650294--650495 Score: 223
Period size: 104 Copynumber: 1.9 Consensus size: 105
650284 AATTATATCT
** *
650294 AATTATTTCACAATTTGGGCCAAATTAAAAATATTTTTTTTTTGAATTTTTAAATTTTCTATAAT
1 AATTATTTCACAATTTGGGCCAAATTAAAAATATTTTTTTTTAAAATTTTTAAATTTTCTACAAT
* * ** * *
650359 TTGGGTCTATTTAGAAATTTTTTTTTATTTTTTATTCATA
66 TTGGGCCTATTTAAAAAAATTTGTTTACTTTTTATTCATA
* * * * *
650399 AATT-TTTCACCATTTTGGTCAATTTAAAAAT-TTTTTTTTTCAAAATTTTTAAATTTT-TCACC
1 AATTATTTCACAATTTGGGCCAAATTAAAAATATTTTTTTTT-AAAATTTTTAAATTTTCT-ACA
650461 ATTTGGGCCTATTTAAAAAAAATTTGTTT-CTTTTT
64 ATTTGGGCCTATTT-AAAAAAATTTGTTTACTTTTT
650496 TTTTTGTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
103 10 0.12
104 56 0.70
105 14 0.17
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (105 bp):
AATTATTTCACAATTTGGGCCAAATTAAAAATATTTTTTTTTAAAATTTTTAAATTTTCTACAAT
TTGGGCCTATTTAAAAAAATTTGTTTACTTTTTATTCATA
Found at i:650785 original size:163 final size:163
Alignment explanation
Indices: 650524--650817 Score: 389
Period size: 163 Copynumber: 1.8 Consensus size: 163
650514 AAATAATATA
* * * ** *
650524 ACAATTATTTTTTACTGAAATTTCATTTAAATTCTTTTACTATTTAGGATAAATTTTAAAAAATT
1 ACAATTATCTTTTACTGAAATTTCATCTAAATTATTCCACTATTTAGGATAAATTTAAAAAAATT
* * * *
650589 TCTCACATAGAGATTTCTTAAGAATTTACTATTTGAAATTTTTAAAAATCTCATCATTGGATAAT
66 TCTCACATAAAAATTTCTTAAGAATTGACTATTTGAAATTTTTAAAAATCTCAACATTGGATAAT
650654 TATCAAATATTTTCAACTAAATTTGAAAAGAAT
131 TATCAAATATTTTCAACTAAATTTGAAAAGAAT
* *
650687 ACAATTA-CTTTTATTGAAATTTCATCTAAATTATTCCA-TAATTTGGGATAAATTTAAAAAAAA
1 ACAATTATCTTTTACTGAAATTTCATCTAAATTATTCCACT-ATTTAGGATAAATTT--AAAAAA
* * *
650750 ATTT-TCACCTAAAAATTTCTT-AGAAATTGACTATTTGAAATTTTTAAGAATCTCAACATTGGG
63 ATTTCTCACATAAAAATTTCTTAAG-AATTGACTATTTGAAATTTTTAAAAATCTCAACATTGGA
650813 TAATT
127 TAATT
650818 TGTACTTAAT
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
161 1 0.01
162 41 0.37
163 61 0.54
164 9 0.08
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (163 bp):
ACAATTATCTTTTACTGAAATTTCATCTAAATTATTCCACTATTTAGGATAAATTTAAAAAAATT
TCTCACATAAAAATTTCTTAAGAATTGACTATTTGAAATTTTTAAAAATCTCAACATTGGATAAT
TATCAAATATTTTCAACTAAATTTGAAAAGAAT
Found at i:651315 original size:19 final size:19
Alignment explanation
Indices: 651293--651330 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
651283 AGATTTTTTT
* *
651293 CAAAAAAAATATTTTTAAA
1 CAAAAAAAAAATCTTTAAA
651312 CAAAAAAAAAATCTTTAAA
1 CAAAAAAAAAATCTTTAAA
651331 GAATTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (19 bp):
CAAAAAAAAAATCTTTAAA
Found at i:651766 original size:42 final size:41
Alignment explanation
Indices: 651728--651869 Score: 180
Period size: 42 Copynumber: 3.4 Consensus size: 41
651718 ATAACTTTGA
*
651728 GAAAAATAAA-TGCTCTTCGAAATAGAGGCACCACAACTTT
1 GAAAAATAAATTGCTCTTCTAAATAGAGGCACCACAACTTT
* *** *
651768 GAAAAACAAAAAAACTCATT-TAAATAGAGGCATCACAACATTT
1 GAAAAA-TAAATTGCTC-TTCTAAATAGAGGCACCACAAC-TTT
*
651811 GAAAAATAAATTGCTCCTCTAAATAGAGGCACCACAACTTT
1 GAAAAATAAATTGCTCTTCTAAATAGAGGCACCACAACTTT
651852 GAAAAATAAATTGCTCTT
1 GAAAAATAAATTGCTCTT
651870 TGACAATCAT
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
40 6 0.07
41 24 0.28
42 44 0.52
43 11 0.13
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (41 bp):
GAAAAATAAATTGCTCTTCTAAATAGAGGCACCACAACTTT
Found at i:652076 original size:23 final size:22
Alignment explanation
Indices: 652050--652095 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
652040 ATATGTAAGA
* *
652050 ATTCATATTTGCAAGATTTCAAG
1 ATTCACATTTGCAA-ATTACAAG
652073 ATTCACATTTGCAAATTACAAG
1 ATTCACATTTGCAAATTACAAG
652095 A
1 A
652096 CTCGCATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
ATTCACATTTGCAAATTACAAG
Found at i:652314 original size:21 final size:21
Alignment explanation
Indices: 652289--652328 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
652279 GGTTTCACAC
652289 TTCAAAGATTCTCATTTGAAA
1 TTCAAAGATTCTCATTTGAAA
*
652310 TTCAAATATTCTCATTTGA
1 TTCAAAGATTCTCATTTGA
652329 GTTTGAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (21 bp):
TTCAAAGATTCTCATTTGAAA
Found at i:652314 original size:79 final size:78
Alignment explanation
Indices: 652180--652407 Score: 303
Period size: 79 Copynumber: 2.9 Consensus size: 78
652170 GTCCAAAGGC
** * * * *
652180 TCACATTTGACAAATTTTGGGGTTTCACACCTCAAAAATTTTTATTTGAAATTCAAATATTCTCA
1 TCACATTCAACAAATTTT--GGTTTCACACTTCAAAGATTCTCATTTGAAATTCAAATATTCTCA
652245 TTTGAGTTCGAAAAT
64 TTTGAGTTCGAAAAT
*
652260 TCACATTCAATAAATTTTAGGTTTCACACTTCAAAGATTCTCATTTGAAATTCAAATATTCTCAT
1 TCACATTCAACAAATTTT-GGTTTCACACTTCAAAGATTCTCATTTGAAATTCAAATATTCTCAT
* *
652325 TTGAGTTTGAAGAT
65 TTGAGTTCGAAAAT
** * *
652339 TCACATTTGACAAATTTTGAGTTTCACACTTCAAAGATTCTCATTTGAAATTCAAATATTTTTAT
1 TCACATTCAACAAATTTTG-GTTTCACACTTCAAAGATTCTCATTTGAAATTCAAATATTCTCAT
652404 TTGA
65 TTGA
652408 AAACTAAAAA
Statistics
Matches: 132, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
78 1 0.01
79 116 0.88
80 15 0.11
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (78 bp):
TCACATTCAACAAATTTTGGTTTCACACTTCAAAGATTCTCATTTGAAATTCAAATATTCTCATT
TGAGTTCGAAAAT
Found at i:652392 original size:21 final size:21
Alignment explanation
Indices: 652368--652409 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
652358 AGTTTCACAC
652368 TTCAAAGATTCTCATTTGAAA
1 TTCAAAGATTCTCATTTGAAA
* * *
652389 TTCAAATATTTTTATTTGAAA
1 TTCAAAGATTCTCATTTGAAA
652410 ACTAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (21 bp):
TTCAAAGATTCTCATTTGAAA
Found at i:653628 original size:11 final size:10
Alignment explanation
Indices: 653603--653700 Score: 71
Period size: 10 Copynumber: 9.8 Consensus size: 10
653593 TTAATTTGAG
653603 TCTTTCTTTTC
1 TCTTT-TTTTC
653614 TCTTTTTTTC
1 TCTTTTTTTC
653624 ATC-TTTTTTC
1 -TCTTTTTTTC
* *
653634 -CATTCTTTC
1 TCTTTTTTTC
653643 AT-TTTTTTTC
1 -TCTTTTTTTC
653653 AT-TTTTTTTC
1 -TCTTTTTTTC
*
653663 -CTTTTTATC
1 TCTTTTTTTC
*
653672 TCTTTTTTTT
1 TCTTTTTTTC
*
653682 TATTTTTTTC
1 TCTTTTTTTC
653692 ATCTTTTTT
1 -TCTTTTTT
653701 CATTTTTAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
8 1 0.01
9 13 0.18
10 43 0.61
11 14 0.20
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (10 bp):
TCTTTTTTTC
Found at i:653630 original size:10 final size:10
Alignment explanation
Indices: 653617--653735 Score: 69
Period size: 10 Copynumber: 12.5 Consensus size: 10
653607 TCTTTTCTCT
653617 TTTTTTCATC
1 TTTTTTCATC
653627 TTTTTTC--C
1 TTTTTTCATC
* *
653635 ATTCTTTCATT
1 -TTTTTTCATC
*
653646 TTTTTTCATT
1 TTTTTTCATC
653656 TTTTTTC--C
1 TTTTTTCATC
653664 TTTTTATC-TC
1 TTTTT-TCATC
*
653674 TTTTTTTTTAT-
1 --TTTTTTCATC
653685 TTTTTTCATC
1 TTTTTTCATC
653695 TTTTTTCA--
1 TTTTTTCATC
*
653703 -TTTTTAAT-
1 TTTTTTCATC
* *
653711 TTTTTTCCTT
1 TTTTTTCATC
653721 TTTTTTCATC
1 TTTTTTCATC
653731 TTTTT
1 TTTTT
653736 CCACCCATTA
Statistics
Matches: 86, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
7 6 0.07
8 6 0.07
9 22 0.26
10 45 0.52
11 1 0.01
12 6 0.07
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTCATC
Found at i:653642 original size:29 final size:28
Alignment explanation
Indices: 653610--653680 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
653600 GAGTCTTTCT
653610 TTTCTCTTTTTTTCATCTTTTTTCCATTC
1 TTTCTCTTTTTTTCATCTTTTTTCC-TTC
* *
653639 TTTCAT-TTTTTTTCATTTTTTTTCCTTT
1 TTTC-TCTTTTTTTCATCTTTTTTCCTTC
653667 TTATCTCTTTTTTT
1 TT-TCTCTTTTTTT
653681 TTATTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 5 0.14
29 31 0.84
30 1 0.03
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTCTCTTTTTTTCATCTTTTTTCCTTC
Found at i:653652 original size:39 final size:37
Alignment explanation
Indices: 653609--653735 Score: 130
Period size: 36 Copynumber: 3.6 Consensus size: 37
653599 TGAGTCTTTC
653609 TTTTCTCTTTTTTTCATCTTTTTTCCATTCTTTCATTTT
1 TTTTCT-TTTTTTTCATCTTTTTT-CATTCTTTCATTTT
653648 TTTTCATTTTTTTTC--C-TTTTT-A-TC--TC-TTTT
1 TTTTC-TTTTTTTTCATCTTTTTTCATTCTTTCATTTT
*
653678 TTTT-TATTTTTTTCATCTTTTTTCATT-TTTAATTTT
1 TTTTCT-TTTTTTTCATCTTTTTTCATTCTTTCATTTT
*
653714 TTTCCTTTTTTTTCATCTTTTT
1 TTTTCTTTTTTTTCATCTTTTT
653736 CCACCCATTA
Statistics
Matches: 75, Mismatches: 2, Indels: 25
0.74 0.02 0.25
Matches are distributed among these distances:
28 1 0.01
29 8 0.11
30 8 0.11
31 3 0.04
32 5 0.07
33 3 0.04
34 2 0.03
35 1 0.01
36 28 0.37
37 2 0.03
39 13 0.17
40 1 0.01
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTTTTCATCTTTTTTCATTCTTTCATTTT
Found at i:653705 original size:19 final size:19
Alignment explanation
Indices: 653617--653735 Score: 79
Period size: 19 Copynumber: 6.3 Consensus size: 19
653607 TCTTTTCTCT
653617 TTTTTTCATCTTTTTTC--C
1 TTTTTTCAT-TTTTTTCATC
* *
653635 ATTCTTTCATTTTTTTTCATT
1 -TTTTTTCA-TTTTTTTCATC
* *
653656 TTTTTTCCTTTTTATCTC-TT
1 TTTTTTCATTTTT-T-TCATC
*
653676 TTTTTTTATTTTTTTCATC
1 TTTTTTCATTTTTTTCATC
*
653695 TTTTTTCA--TTTTTAAT-
1 TTTTTTCATTTTTTTCATC
*
653711 TTTTTTCCTTTTTTTTCATC
1 TTTTTT-CATTTTTTTCATC
653731 TTTTT
1 TTTTT
653736 CCACCCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 19
0.72 0.10 0.17
Matches are distributed among these distances:
16 6 0.08
17 8 0.10
18 2 0.03
19 35 0.44
20 26 0.33
21 2 0.03
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTCATTTTTTTCATC
Done.