Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 4 of 18
Found at i:475478 original size:28 final size:29
Alignment explanation
Indices: 475438--475492 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
475428 ATTAAAGTTG
475438 ATTAGTTTGATTTTTTTAATT-TTTTTGA
1 ATTAGTTTGATTTTTTTAATTATTTTTGA
* * *
475466 ATTATTTTTATTTTTTTGATTATTTTT
1 ATTAGTTTGATTTTTTTAATTATTTTT
475493 TTTAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (29 bp):
ATTAGTTTGATTTTTTTAATTATTTTTGA
Found at i:475493 original size:19 final size:19
Alignment explanation
Indices: 475443--475493 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
475433 AGTTGATTAG
*
475443 TTTGATT-TTTTTAATTTT
1 TTTGATTATTTTTTATTTT
475461 TTTGAATTA-TTTTTATTTT
1 TTTG-ATTATTTTTTATTTT
475480 TTTGATTATTTTTT
1 TTTGATTATTTTTT
475494 TTAATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.28
19 21 0.72
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (19 bp):
TTTGATTATTTTTTATTTT
Found at i:475511 original size:21 final size:20
Alignment explanation
Indices: 475448--475512 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
475438 ATTAGTTTGA
475448 TTTTTTTAATTTTTTTGAAT
1 TTTTTTTAATTTTTTTGAAT
*
475468 TATTTTT-ATTTTTTTGATTAT
1 TTTTTTTAATTTTTTTGA--AT
*
475489 TTTTTTTAATTTTAATTGAAT
1 TTTTTTTAATTTT-TTTGAAT
475510 TTT
1 TTT
475513 ATTATTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 10 0.26
20 6 0.16
21 13 0.34
22 5 0.13
23 4 0.11
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTTTTAATTTTTTTGAAT
Found at i:475523 original size:9 final size:9
Alignment explanation
Indices: 475466--475524 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
475456 ATTTTTTTGA
475466 ATTATTTTT
1 ATTATTTTT
475475 ATT-TTTTT
1 ATTATTTTT
475483 GATTATTTTT
1 -ATTATTTTT
* *
475493 TTTAATTTTA
1 ATT-ATTTTT
*
475503 ATTGAATTTT
1 ATT-ATTTTT
475513 ATTATTTTT
1 ATTATTTTT
475522 ATT
1 ATT
475525 TTAATTAGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
8 5 0.12
9 16 0.40
10 19 0.47
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (9 bp):
ATTATTTTT
Found at i:475582 original size:23 final size:23
Alignment explanation
Indices: 475524--475595 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
475514 TTATTTTTAT
* *
475524 TTTAATTAGGTTTTTAATTTAAG
1 TTTAAATAGGTTTTTAATTTAAA
*
475547 TTTAGAT-GAGTTTTTAATTTAAA
1 TTTAAATAG-GTTTTTAATTTAAA
* *
475570 TTTAAATAGG-TTTCAGTTTAAA
1 TTTAAATAGGTTTTTAATTTAAA
475592 TTTA
1 TTTA
475596 TATTTTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
22 15 0.37
23 25 0.61
24 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.53
Consensus pattern (23 bp):
TTTAAATAGGTTTTTAATTTAAA
Found at i:475935 original size:31 final size:32
Alignment explanation
Indices: 475897--475963 Score: 111
Period size: 31 Copynumber: 2.1 Consensus size: 32
475887 TCCTCTTTGT
475897 TTGAATCATCTTTTATTCTCATTTTT-TT-TTA
1 TTGAATCATCTTTTATTCTC-TTTTTCTTATTA
475928 TTGAATCATCTTTTATTCTCTTTTTCTTATTA
1 TTGAATCATCTTTTATTCTCTTTTTCTTATTA
475960 TTGA
1 TTGA
475964 TAAAAGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 5 0.15
31 22 0.65
32 7 0.21
ACGTcount: A:0.19, C:0.13, G:0.04, T:0.63
Consensus pattern (32 bp):
TTGAATCATCTTTTATTCTCTTTTTCTTATTA
Found at i:476182 original size:15 final size:15
Alignment explanation
Indices: 476138--476184 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
476128 TTTAGATCTG
* *
476138 TTAATTCTTTTAAAA
1 TTAATTATTTTAAAT
* *
476153 TAAATTAATTTAAAT
1 TTAATTATTTTAAAT
476168 TTAATTATTTTAAAT
1 TTAATTATTTTAAAT
476183 TT
1 TT
476185 TAAATTTCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTATTTTAAAT
Found at i:476234 original size:16 final size:16
Alignment explanation
Indices: 476222--476296 Score: 71
Period size: 16 Copynumber: 4.7 Consensus size: 16
476212 TAATTTAGAA
476222 TTAAATTATTTTAAAT
1 TTAAATTATTTTAAAT
* *
476238 TTAAATTATTTCAAGT
1 TTAAATTATTTTAAAT
** *
476254 CCAAATAATTTTAAAT
1 TTAAATTATTTTAAAT
* *
476270 TTAAGTTA-TTTCAAT
1 TTAAATTATTTTAAAT
476285 TTCAAATTATTT
1 TT-AAATTATTT
476297 AGATTTAACA
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
15 8 0.18
16 34 0.77
17 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.51
Consensus pattern (16 bp):
TTAAATTATTTTAAAT
Found at i:476291 original size:32 final size:32
Alignment explanation
Indices: 476224--476304 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 32
476214 ATTTAGAATT
476224 AAATTATTTTAAATTTAAATTATTTCAAGTCC
1 AAATTATTTTAAATTTAAATTATTTCAAGTCC
* * * *
476256 AAATAATTTTAAATTTAAGTTATTTCAATTTC
1 AAATTATTTTAAATTTAAATTATTTCAAGTCC
*
476288 AAATTA-TTTAGATTTAA
1 AAATTATTTTAAATTTAA
476305 CACTCATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 10 0.23
32 33 0.77
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (32 bp):
AAATTATTTTAAATTTAAATTATTTCAAGTCC
Found at i:477788 original size:20 final size:19
Alignment explanation
Indices: 477751--477789 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
477741 TTAAAATTTT
* *
477751 AAATATTAATATTCAATAA
1 AAATATTAATACTAAATAA
477770 AAATATTTAATACTAAATAA
1 AAATA-TTAATACTAAATAA
477790 TATTTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATTAATACTAAATAA
Found at i:477793 original size:17 final size:17
Alignment explanation
Indices: 477767--477805 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
477757 TAATATTCAA
477767 TAAA-AATATTTAATAC
1 TAAATAATATTTAATAC
* *
477783 TAAATAATATTTTATAT
1 TAAATAATATTTAATAC
477800 TAAATA
1 TAAATA
477806 CTTAAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATAATATTTAATAC
Found at i:478377 original size:17 final size:18
Alignment explanation
Indices: 478326--478383 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 18
478316 TGTTACAATT
*
478326 TATTATTAAAAT-ATTAA
1 TATTATTAAAATAATAAA
* *
478343 TATTATTATATTAA-AAA
1 TATTATTAAAATAATAAA
478360 TATT-TTAAAATAATAAA
1 TATTATTAAAATAATAAA
*
478377 TAATATT
1 TATTATT
478384 CATTATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
16 7 0.22
17 22 0.69
18 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTATTAAAATAATAAA
Found at i:482123 original size:13 final size:13
Alignment explanation
Indices: 482104--482134 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
482094 ACTATTAATC
482104 ATGTATCGATACA
1 ATGTATCGATACA
*
482117 TTGTATCGATACA
1 ATGTATCGATACA
482130 ATGTA
1 ATGTA
482135 CCATGTATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:482219 original size:19 final size:19
Alignment explanation
Indices: 482175--482247 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
482165 CTGCCAGTTT
**
482175 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
482195 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
482214 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
482235 -ATGTATCGATACA
1 CATGTATCGATACA
482248 TCTGGGTGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 29 0.60
21 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:489084 original size:57 final size:57
Alignment explanation
Indices: 488996--490057 Score: 675
Period size: 57 Copynumber: 18.5 Consensus size: 57
488986 ATCATGCCTT
* * * * * *
488996 CAAAATTGTTATCTTC-CAATTGTCAAGGGCTTAAGAATTCGACCATTGCCAAAAGTC
1 CAAAATTATTATC-TCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCTAAGGTC
* * * * *
489053 CAAAATTATTATCTCGCCATTGCTAAAGGCTTAAGAACTCAACCATT-CTCTGAGATC
1 CAAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGC-CTAAGGTC
* * * * * * *
489110 CAAAATTATTATATTGCCATTACCAAAGGCTTAGGAATTCGACCCTTGCCTAAAGTT
1 CAAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCTAAGGTC
* * * * * *
489167 CAAAGATTATTATCTCACCATTGCTAAAAGG-TTAAG-ATTCAACTATT-CTTTAAAGTC
1 CAAA-ATTATTATCTCGCCATTGC-CAAAGGCTTAAGAATTCGACCATTGC-CTAAGGTC
* * ** *
489224 CAAAGTTATTATCTCGCTATTGCCAAAAACTTAAGAATTCGACCATTGCTTAAGGTC
1 CAAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCTAAGGTC
* * * ** * *
489281 CAAAATTATTATCTTGCCATTACCAAAGGCTTAAGAATTTGATAATTG-CTAAAGTTT
1 CAAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCT-AAGGTC
** * * ** ** *
489338 TGAAATTATCATCTCACCATTGCTGAAGGCTCGAGAACTCGACCATT-CTCTAAGGT-
1 CAAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGC-CTAAGGTC
* * * * * *
489394 CAAAAGTTATAATCTCACCATTACCAAAGGCTTAAGAATTTGACCATT-CCTTAAAGTT
1 CAAAA-TTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCC-TAAGGTC
* * * * * * * *
489452 TAATGATTATTATCTCGCCATTACCAATA-GCTTGAGAAGTAGACAATT-CTTTAAGGTC
1 CAA-AATTATTATCTCGCCATTGCCAA-AGGCTTAAGAATTCGACCATTGC-CTAAGGTC
* * * * * * * * * *
489510 CGAAGTTATTATCTCGTCATTGCCAAAGGTTTGAGAATTCTACCACTACATAAAGTC
1 CAAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCTAAGGTC
* * * ** * * *
489567 CAAAGATTGTTATCTCTCCATTGTCAAAGTTTTAAAAATTCTATCATT-CTCTAAGGTC
1 CAAA-ATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGC-CTAAGGTC
* * * * * *
489625 TAAAGTTGTGATCTCGCCATTGCCAAAGGCTTGAGAATTTGACCATTG-CTAAAGGTC
1 CAAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCT-AAGGTC
* * ** **
489682 CAAAAATTATTATCTTGCCATTGCCAAAGGCTTGAGAATTTAACCATTATCTAAGGTC
1 C-AAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCTAAGGTC
* * *
489740 CAAATATTATTATCTCGTCATTGCCAAAGGCTTAAGAATTCGACCATTGCCTACGGTT
1 CAAA-ATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCTAAGGTC
* * * * * * *
489798 TAAAGATTATTATCTCACTATTACCAAGGGCTTAAGAA-TCGGGCTATTGCCTAAGGTC
1 CAAA-ATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTC-GACCATTGCCTAAGGTC
* * * * * *
489856 CAAAGTTATTATCTCGCCATTGTCAAAGGCTTAAGAATTTGACCACTGTCAAAGGTC
1 CAAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCTAAGGTC
* * **
489913 TAAAATCATTATCTCGCCATTGTTAAAGG-TTCAAGAACTT-GACCATT-CTCTAAGGTC
1 CAAAATTATTATCTCGCCATTGCCAAAGGCTT-AAGAA-TTCGACCATTGC-CTAAGGTC
* * * ** * * * * * * *
489970 TAAAGTTATTATTTTACAATTACTAAAGGCTTGAGAATTTGACCATTGACAAAGGTC
1 CAAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCTAAGGTC
* * *
490027 TAAAATTATTATC-CTACCATTGCTAAAGGCT
1 CAAAATTATTATCTC-GCCATTGCCAAAGGCT
490058 CAAGCACTCA
Statistics
Matches: 775, Mismatches: 194, Indels: 72
0.74 0.19 0.07
Matches are distributed among these distances:
55 3 0.00
56 37 0.05
57 473 0.61
58 253 0.33
59 9 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (57 bp):
CAAAATTATTATCTCGCCATTGCCAAAGGCTTAAGAATTCGACCATTGCCTAAGGTC
Found at i:489159 original size:114 final size:114
Alignment explanation
Indices: 489023--489892 Score: 415
Period size: 115 Copynumber: 7.6 Consensus size: 114
489013 AATTGTCAAG
*
489023 GGCTTAAGAATTCGACCATTGCCAAAAGTCCAAAATTATTATCTCGCCATTGCTAAAGGCTTAAG
1 GGCTTAAGAATTCGACCATTGCCTAAAGTCCAAAATTATTATCTCGCCATTGCTAAAGGCTTAAG
* *
489088 AACTCAACCATTCTCTGAGA-TCCAAAATTATTATATTGCCATTACCAAA
66 AACTCAACCATTCT-TGAAAGTCCAAAATTATTATATCGCCATTACCAAA
* * * *
489137 GGCTTAGGAATTCGACCCTTGCCTAAAGTTCAAAGATTATTATCTCACCATTGCTAAAAGG-TTA
1 GGCTTAAGAATTCGACCATTGCCTAAAGTCCAAA-ATTATTATCTCGCCATTGCT-AAAGGCTTA
* * * * * * *
489201 AG-ATTCAACTATTCTTTAAAGTCCAAAGTTATTATCTCGCTATTGCCAAA
64 AGAACTCAACCATTCTTGAAAGTCCAAAATTATTATATCGCCATTACCAAA
** * * * * *
489251 AACTTAAGAATTCGACCATTGCTTAAGGTCCAAAATTATTATCTTGCCATTACCAAAGGCTTAAG
1 GGCTTAAGAATTCGACCATTGCCTAAAGTCCAAAATTATTATCTCGCCATTGCTAAAGGCTTAAG
* ** ** *** * * * * **
489316 AATTTGATAATTGC-T-AAAGTTTTGAAATTATCATCTCACCATTGCTGAA
66 AACTCAACCATT-CTTGAAAG-TCCAAAATTATTATATCGCCATTACCAAA
** * * * * * *
489365 GGCTCGAGAACTCGACCATT-CTCTAAGGT-CAAAAGTTATAATCTCACCATTACCAAAGGCTTA
1 GGCTTAAGAATTCGACCATTGC-CTAAAGTCCAAAA-TTATTATCTCGCCATTGCTAAAGGCTTA
* ** ** * *
489428 AGAATTTGACCATTCCTT-AAAGTTTAATGATTATTATCTCGCCATTACCAATA
64 AGAACTCAACCATT-CTTGAAAGTCCAA-AATTATTATATCGCCATTACCAA-A
* * * * * * * * * * * *
489481 -GCTTGAGAAGTAGACAATT-CTTTAAGGTCCGAAGTTATTATCTCGTCATTGCCAAAGGTTTGA
1 GGCTTAAGAATTCGACCATTGC-CTAAAGTCCAAAATTATTATCTCGCCATTGCTAAAGGCTTAA
* * * * * * * **
489544 GAATTCTACCACTACAT-AAAGTCCAAAGATTGTTATCTCTCCATTGTCAAA
65 GAACTCAACCA-TTCTTGAAAGTCCAAA-ATTATTATATCGCCATTACCAAA
** * * * * * * * * * *
489595 GTTTTAAAAATTCTATCATT-CTCTAAGGTCTAAAGTTGTGATCTCGCCATTGCCAAAGGCTTGA
1 GGCTTAAGAATTCGACCATTGC-CTAAAGTCCAAAATTATTATCTCGCCATTGCTAAAGGCTTAA
* ** * * *
489659 GAATTTGACCATTGC-T-AAAGGTCCAAAAATTATTATCTTGCCATTGCCAAA
65 GAACTCAACCATT-CTTGAAA-GTCC-AAAATTATTATATCGCCATTACCAAA
* ** ** * * *
489710 GGCTTGAGAATTTAACCATTATCTAAGGTCCAAATATTATTATCTCGTCATTGCCAAAGGCTTAA
1 GGCTTAAGAATTCGACCATTGCCTAAAGTCCAAA-ATTATTATCTCGCCATTGCTAAAGGCTTAA
* * * ** ** * * * *
489775 GAATTCGACCATTGCCT-ACGGTTTAAAGATTATTATCTCACTATTACCAAG
65 GAACTCAACCATT-CTTGAAAGTCCAAA-ATTATTATATCGCCATTACCAAA
* * * *
489826 GGCTTAAGAA-TCGGGCTATTGCCTAAGGTCCAAAGTTATTATCTCGCCATTG-TCAAAGGCTTA
1 GGCTTAAGAATTC-GACCATTGCCTAAAGTCCAAAATTATTATCTCGCCATTGCT-AAAGGCTTA
489889 AGAA
64 AGAA
489893 TTTGACCACT
Statistics
Matches: 593, Mismatches: 138, Indels: 49
0.76 0.18 0.06
Matches are distributed among these distances:
112 5 0.01
113 34 0.06
114 189 0.32
115 266 0.45
116 97 0.16
117 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (114 bp):
GGCTTAAGAATTCGACCATTGCCTAAAGTCCAAAATTATTATCTCGCCATTGCTAAAGGCTTAAG
AACTCAACCATTCTTGAAAGTCCAAAATTATTATATCGCCATTACCAAA
Found at i:489998 original size:114 final size:114
Alignment explanation
Indices: 489880--490093 Score: 313
Period size: 114 Copynumber: 1.9 Consensus size: 114
489870 CGCCATTGTC
* * * *
489880 AAAGGCTTAAGAATTTGACCACTGTCAAAGGTCTAAAATCATTAT-CTCGCCATTGTTAAAGGTT
1 AAAGGCTTAAGAATTTGACCACTGACAAAGGTCTAAAATCATTATCCT-ACCATTGCTAAAGGCT
**
489944 CAAGAACTTGACCATTCTCTAAGGTCTAAAGTTATTATTTTACAATTACT
65 CAAGAACTCAACCATTCTCTAAGGTCTAAAGTTATTATTTTACAATTACT
* * *
489994 AAAGGCTTGAGAATTTGACCATTGACAAAGGTCTAAAATTATTATCCTACCATTGCTAAAGGCTC
1 AAAGGCTTAAGAATTTGACCACTGACAAAGGTCTAAAATCATTATCCTACCATTGCTAAAGGCTC
* *
490059 AAGCACTCAACCATTCTTTAAGGTCTAAAGTTATT
66 AAGAACTCAACCATTCTCTAAGGTCTAAAGTTATT
490094 GTCTCTCTAT
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
114 86 0.98
115 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (114 bp):
AAAGGCTTAAGAATTTGACCACTGACAAAGGTCTAAAATCATTATCCTACCATTGCTAAAGGCTC
AAGAACTCAACCATTCTCTAAGGTCTAAAGTTATTATTTTACAATTACT
Found at i:495926 original size:11 final size:11
Alignment explanation
Indices: 495890--495935 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
495880 ACATGATATT
495890 ATATAAAAA-A
1 ATATAAAAATA
495900 ATA-AAAAAT-
1 ATATAAAAATA
495909 ATGATAAAAATA
1 AT-ATAAAAATA
*
495921 ATATAAATATA
1 ATATAAAAATA
495932 ATAT
1 ATAT
495936 GAATATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
9 7 0.23
10 4 0.13
11 18 0.58
12 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:495928 original size:27 final size:28
Alignment explanation
Indices: 495867--495929 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
495857 TAGTATCTTT
* * *
495867 ATATTAATAAAAAACATGATATTATATA
1 ATATAAATAAAAAACATGATATAAAATA
* *
495895 A-AAAAATAAAAAATATGATA-AAAATA
1 ATATAAATAAAAAACATGATATAAAATA
495921 ATATAAATA
1 ATATAAATA
495930 TAATATGAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 5 0.18
27 22 0.79
28 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (28 bp):
ATATAAATAAAAAACATGATATAAAATA
Found at i:495958 original size:17 final size:17
Alignment explanation
Indices: 495920--495957 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 17
495910 TGATAAAAAT
495920 AATATAAATATAATATG
1 AATATAAATATAATATG
495937 AATATAAAT-T-ATATG
1 AATATAAATATAATATG
495952 AATATA
1 AATATA
495958 TGAATATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.52
16 1 0.05
17 9 0.43
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
AATATAAATATAATATG
Found at i:496016 original size:33 final size:33
Alignment explanation
Indices: 495947--496012 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
495937 AATATAAATT
*
495947 ATATGAATATATGAATATCTAAAATTTTATATA
1 ATATGAATATATGAATATATAAAATTTTATATA
*
495980 ATATTAAT-TATGAATATATCAAAA-TTTATATA
1 ATATGAATATATGAATATAT-AAAATTTTATATA
496012 A
1 A
496013 ATATAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (33 bp):
ATATGAATATATGAATATATAAAATTTTATATA
Found at i:496087 original size:14 final size:14
Alignment explanation
Indices: 496041--496088 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
496031 ATAATTTATA
*
496041 AAATAATAAAATAT
1 AAATTATAAAATAT
*
496055 ATAATTACAAATATAT
1 A-AATTATAAA-ATAT
*
496071 AAATTATAAAATTT
1 AAATTATAAAATAT
496085 AAAT
1 AAAT
496089 ATCTCCATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 8 0.29
15 15 0.54
16 5 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATTATAAAATAT
Found at i:496090 original size:22 final size:23
Alignment explanation
Indices: 496041--496083 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
496031 ATAATTTATA
*
496041 AAATA-ATAAAATATATAATTAC
1 AAATATATAAAATATAAAATTAC
*
496063 AAATATATAAATTATAAAATT
1 AAATATATAAAATATAAAATT
496084 TAAATATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATATATAAAATATAAAATTAC
Found at i:496956 original size:21 final size:22
Alignment explanation
Indices: 496930--496970 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
496920 ATTTTTAATT
496930 TTATAATATTTTTAT-TTTAAA
1 TTATAATATTTTTATATTTAAA
*
496951 TTATAATTTTTTTATATTTA
1 TTATAATATTTTTATATTTA
496971 TATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATAATATTTTTATATTTAAA
Found at i:496980 original size:27 final size:28
Alignment explanation
Indices: 496925--496983 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
496915 AAATAATTTT
*
496925 TAATTTTATAATATTTTTATTTTAAATTA
1 TAATTTTATAATATTTATATTTT-AATTA
* *
496954 TAATTTTTTTATATTTATATTTT-ATTA
1 TAATTTTATAATATTTATATTTTAATTA
496981 TAA
1 TAA
496984 AATTCTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
29 20 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TAATTTTATAATATTTATATTTTAATTA
Found at i:502734 original size:52 final size:52
Alignment explanation
Indices: 502588--502716 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
502578 CGAATTATGA
502588 AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
502640 AAATTTACCTGTATGTATCGATACATTTCATAGTGTATCGATATATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
502692 AAATTTGCCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
502717 AAGATCAGTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:502826 original size:19 final size:19
Alignment explanation
Indices: 502802--502866 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
502792 AGCGAAACAT
502802 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
502821 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
502834 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
502853 TGTATCGATACAAA
1 TGTATCGATACAAA
502867 TCGTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:502839 original size:13 final size:13
Alignment explanation
Indices: 502821--502845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
502811 ACAAAACTTA
502821 TGTATCGATACAT
1 TGTATCGATACAT
502834 TGTATCGATACA
1 TGTATCGATACA
502846 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:502839 original size:32 final size:32
Alignment explanation
Indices: 502798--502864 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
502788 TCGTAGCGAA
502798 ACATTGTATCGATACAAAACTTATGTATCGAT
1 ACATTGTATCGATACAAAACTTATGTATCGAT
*
502830 ACATTGTATCGATACAACACTTATGTATCGAT
1 ACATTGTATCGATACAAAACTTATGTATCGAT
502862 ACA
1 ACA
502865 AATCGTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (32 bp):
ACATTGTATCGATACAAAACTTATGTATCGAT
Found at i:504992 original size:17 final size:19
Alignment explanation
Indices: 504957--504994 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
504947 ACTTATAATA
*
504957 AACTTTTTTGAAAGTAAAT
1 AACTTTTTTGAAAGAAAAT
504976 AACTTTTTT-AAA-AAAAT
1 AACTTTTTTGAAAGAAAAT
504993 AA
1 AA
504995 TGCATTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
AACTTTTTTGAAAGAAAAT
Found at i:512053 original size:2 final size:2
Alignment explanation
Indices: 512046--512070 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
512036 CATTACAGCT
512046 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 T
512071 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:512075 original size:2 final size:2
Alignment explanation
Indices: 512070--512102 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
512060 TCTCTCTCTC
512070 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
512103 GTATGTATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:512107 original size:4 final size:4
Alignment explanation
Indices: 512100--512127 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
512090 TATATATATA
512100 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
512128 CCGATTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:513522 original size:2 final size:2
Alignment explanation
Indices: 513515--513552 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
513505 TACAATAATG
513515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
513553 TCTCTGGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:515219 original size:30 final size:30
Alignment explanation
Indices: 515175--515251 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
515165 ATTAATTTGT
* *
515175 ATTCATATTAATTTATACCATATGATGGGC
1 ATTCATGTTAATTTATACCATATAATGGGC
* * * *
515205 ATTCATGTTTATTTATACTATGTAATGGGT
1 ATTCATGTTAATTTATACCATATAATGGGC
515235 ATTCATGTTAATTTATA
1 ATTCATGTTAATTTATA
515252 TTTTGTGATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (30 bp):
ATTCATGTTAATTTATACCATATAATGGGC
Found at i:515854 original size:22 final size:22
Alignment explanation
Indices: 515828--515887 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
515818 TGTGTATAAT
*
515828 GTTATAGTCATATGTATATATTA
1 GTTATAGTCATATGTATATA-CA
*
515851 -TTATAGTGATATGTATATACA
1 GTTATAGTCATATGTATATACA
515872 GTTATAGTCATATGTA
1 GTTATAGTCATATGTA
515888 CATAATTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (22 bp):
GTTATAGTCATATGTATATACA
Found at i:515910 original size:44 final size:44
Alignment explanation
Indices: 515828--515914 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
515818 TGTGTATAAT
* * * *
515828 GTTATAGTCATATGTATATATTATTATAGTGATATGTATATACA
1 GTTATAGTCATATGTACATATTATCACAATGATATGTATATACA
*
515872 GTTATAGTCATATGTACATAATT-TCACAATGATGTGTATATAC
1 GTTATAGTCATATGTACAT-ATTATCACAATGATATGTATATAC
515915 TATGATAGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 34 0.92
45 3 0.08
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.43
Consensus pattern (44 bp):
GTTATAGTCATATGTACATATTATCACAATGATATGTATATACA
Found at i:515978 original size:20 final size:21
Alignment explanation
Indices: 515941--515997 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
515931 TGTGAAAAGG
*
515941 TTGGTTTT-TTAGTGAAATGA
1 TTGGTTTTCTTAATGAAATGA
515961 TTGGTTTTCTTAAT-AAATGA
1 TTGGTTTTCTTAATGAAATGA
* *
515981 TTAGTTCTCTTAATGAA
1 TTGGTTTTCTTAATGAA
515998 GAAGTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (21 bp):
TTGGTTTTCTTAATGAAATGA
Found at i:516177 original size:21 final size:22
Alignment explanation
Indices: 516149--516199 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
516139 TGAAAGGGTT
516149 GATT-TTTTTATATAAAG-A-TA
1 GATTCTTTTTA-ATAAAGAAGTA
*
516169 GATTC-TTTTAATAAAGAAGTT
1 GATTCTTTTTAATAAAGAAGTA
516190 GATTCTTTTT
1 GATTCTTTTT
516200 GTGAAAGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.23
20 10 0.38
21 6 0.23
22 4 0.15
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (22 bp):
GATTCTTTTTAATAAAGAAGTA
Found at i:516279 original size:45 final size:45
Alignment explanation
Indices: 516221--516322 Score: 114
Period size: 45 Copynumber: 2.3 Consensus size: 45
516211 AGTTTTTTTT
* * * *
516221 AAAAAGAGATTGGTTCCTTTAGTAAAAGGGTTAATTTCTTTAATG
1 AAAAAAAGGTTGGTTCCCTTAGTAAAAGGGTTAATTCCTTTAATG
* * * * *
516266 AAAAAAAGGTTGGTTCCCTTGGTGAAGGGGTTGATTCCTTTAGTG
1 AAAAAAAGGTTGGTTCCCTTAGTAAAAGGGTTAATTCCTTTAATG
*
516311 AAAAAAAAGTTG
1 AAAAAAAGGTTG
516323 ATTCTCGGGT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.33
Consensus pattern (45 bp):
AAAAAAAGGTTGGTTCCCTTAGTAAAAGGGTTAATTCCTTTAATG
Found at i:516303 original size:21 final size:21
Alignment explanation
Indices: 516273--516312 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
516263 ATGAAAAAAA
* *
516273 GGTTGGTTCCCTTGGTGAAGG
1 GGTTGATTCCCTTAGTGAAGG
*
516294 GGTTGATTCCTTTAGTGAA
1 GGTTGATTCCCTTAGTGAA
516313 AAAAAAGTTG
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:0.15, C:0.12, G:0.35, T:0.38
Consensus pattern (21 bp):
GGTTGATTCCCTTAGTGAAGG
Found at i:516544 original size:20 final size:20
Alignment explanation
Indices: 516513--516574 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
516503 AAGGTTAATT
516513 TTCTTTT-G-AAAAGATTGG
1 TTCTTTTAGTAAAAGATTGG
*
516531 TTCTTTTAGTAAAAGATTAG
1 TTCTTTTAGTAAAAGATTGG
516551 TTCTTTTAGTGAAAA-AGTTGG
1 TTCTTTTAGT-AAAAGA-TTGG
516572 TTC
1 TTC
516575 CCTTAGTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
18 7 0.18
19 1 0.03
20 20 0.53
21 10 0.26
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (20 bp):
TTCTTTTAGTAAAAGATTGG
Found at i:516574 original size:21 final size:22
Alignment explanation
Indices: 516521--516584 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 22
516511 TTTTCTTTTG
516521 AAAAGATTGGTTCTTTTAGT--
1 AAAAGATTGGTTCTTTTAGTGA
*
516541 AAAAGATTAGTTCTTTTAGTGA
1 AAAAGATTGGTTCTTTTAGTGA
**
516563 AAAAG-TTGGTTCCCTTAGTGA
1 AAAAGATTGGTTCTTTTAGTGA
516584 A
1 A
516585 GAGATTGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 19 0.50
21 14 0.37
22 5 0.13
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (22 bp):
AAAAGATTGGTTCTTTTAGTGA
Found at i:516711 original size:16 final size:16
Alignment explanation
Indices: 516665--516712 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
516655 TTTTGTTGGA
*
516665 TATTCATATTAATGTG
1 TATTCATATTAATTTG
*
516681 TATT-A-A-CAA-TTG
1 TATTCATATTAATTTG
516693 TATTCATATTAATTTG
1 TATTCATATTAATTTG
516709 TATT
1 TATT
516713 ACATGATGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
12 6 0.24
13 3 0.12
14 2 0.08
15 3 0.12
16 11 0.44
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (16 bp):
TATTCATATTAATTTG
Found at i:517243 original size:23 final size:21
Alignment explanation
Indices: 517209--517271 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
517199 AAAAAATGGT
*
517209 AAATAAATCAACCTTTTTACA
1 AAATGAATCAACCTTTTTACA
* *
517230 AAAGTGAATCCAACCCTTTTACT
1 AAA-TGAAT-CAACCTTTTTACA
*
517253 AAATGAATCAATCTTTTTA
1 AAATGAATCAACCTTTTTA
517272 TTAAGGAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 12 0.34
22 9 0.26
23 14 0.40
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (21 bp):
AAATGAATCAACCTTTTTACA
Found at i:517782 original size:29 final size:30
Alignment explanation
Indices: 517747--517826 Score: 117
Period size: 29 Copynumber: 2.7 Consensus size: 30
517737 TCAATTGTAA
**
517747 AATACAAATTAGCATGAATACCCATCA-AT
1 AATACAAATTAATATGAATACCCATCATAT
*
517776 AATACAAATTAATATGAATACCTATCATAT
1 AATACAAATTAATATGAATACCCATCATAT
*
517806 AATATAAATTAATATGAATAC
1 AATACAAATTAATATGAATAC
517827 AAATTATTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 24 0.52
30 22 0.48
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (30 bp):
AATACAAATTAATATGAATACCCATCATAT
Found at i:518013 original size:22 final size:22
Alignment explanation
Indices: 517987--518040 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
517977 AAGAACCAAT
517987 TCCTTCACAAAGAGAAACTAAC
1 TCCTTCACAAAGAGAAACTAAC
*
518009 TCCTTTACAAAGAGAAACTAAC
1 TCCTTCACAAAGAGAAACTAAC
518031 TCC-TCACAAA
1 TCCTTCACAAA
518041 AAGTGACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.44, C:0.28, G:0.07, T:0.20
Consensus pattern (22 bp):
TCCTTCACAAAGAGAAACTAAC
Found at i:518103 original size:16 final size:16
Alignment explanation
Indices: 518082--518112 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
518072 TAAAATTATG
518082 TATATATAATTATAAT
1 TATATATAATTATAAT
518098 TATATATAATTATAA
1 TATATATAATTATAA
518113 CAATATCAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATATAATTATAAT
Found at i:518118 original size:16 final size:16
Alignment explanation
Indices: 518083--518118 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
518073 AAAATTATGT
**
518083 ATATATAATTATAATT
1 ATATATAATTATAACA
518099 ATATATAATTATAACA
1 ATATATAATTATAACA
518115 ATAT
1 ATAT
518119 CAATATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATATAATTATAACA
Found at i:518275 original size:20 final size:20
Alignment explanation
Indices: 518217--518278 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
518207 AGAGCTACTT
*
518217 TCTTCACTAAAAGAATCAAC
1 TCTTCACTAAAAGAACCAAC
* * *
518237 CCTTATACAAAAAGAACCAAC
1 TCTT-CACTAAAAGAACCAAC
*
518258 TCTTCACTAAAGGAACCAAC
1 TCTTCACTAAAAGAACCAAC
518278 T
1 T
518279 TTTTTACAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.45, C:0.27, G:0.06, T:0.21
Consensus pattern (20 bp):
TCTTCACTAAAAGAACCAAC
Found at i:518365 original size:34 final size:33
Alignment explanation
Indices: 518321--518384 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
518311 ATATCACTGT
* *
518321 TATATTATATACATATGACTATAATTGAATATA
1 TATATTATATACATATAACTATAAATGAATATA
*
518354 TATATATATATATATATAACTATAAATGAAT
1 TATAT-TATATACATATAACTATAAATGAAT
518385 CAACCCCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 5 0.19
34 22 0.81
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (33 bp):
TATATTATATACATATAACTATAAATGAATATA
Found at i:518642 original size:22 final size:22
Alignment explanation
Indices: 518513--518643 Score: 84
Period size: 22 Copynumber: 5.9 Consensus size: 22
518503 GCAGAGAATC
* * *
518513 ACTATAATAGTTTTTACACATT
1 ACTATAATAGTATATACATATT
* * * *
518535 ACTACAATATTATATATATATGAG
1 ACTATAATAGTATATACATAT--T
* * *
518559 ACTATAGCTA-TATGTACATATC
1 ACTATA-ATAGTATATACATATT
* *
518581 ACTAAAATAGTATATAAATATT
1 ACTATAATAGTATATACATATT
* *
518603 ATTATAATAGTATTTACATATT
1 ACTATAATAGTATATACATATT
* *
518625 ACTATAACAGAATATACAT
1 ACTATAATAGTATATACAT
518644 TTTTATATCT
Statistics
Matches: 80, Mismatches: 25, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
21 2 0.03
22 62 0.77
24 14 0.17
25 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (22 bp):
ACTATAATAGTATATACATATT
Found at i:519162 original size:30 final size:30
Alignment explanation
Indices: 519081--519193 Score: 93
Period size: 30 Copynumber: 3.8 Consensus size: 30
519071 TAAACCCATC
* * *
519081 AAATATAAATTAATATGAACATCAATTACA
1 AAATATAAATTAATATGAATACCAATCACA
* * *
519111 AAATATAAATTAACATAAATACCTATCACA
1 AAATATAAATTAATATGAATACCAATCACA
* * * *
519141 TAATACAAATTAATATGAATACAAAATTA-A
1 AAATATAAATTAATATGAATAC-CAATCACA
* * *
519171 TAATATACATTAATATGAGTACC
1 AAATATAAATTAATATGAATACC
519194 CAGGAGAAAA
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
30 62 0.95
31 3 0.05
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.30
Consensus pattern (30 bp):
AAATATAAATTAATATGAATACCAATCACA
Found at i:521440 original size:16 final size:16
Alignment explanation
Indices: 521419--521453 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
521409 TTTGGGTCAT
521419 TTTTGGATTCGGATCG
1 TTTTGGATTCGGATCG
* *
521435 TTTTGGGTTCGGATTG
1 TTTTGGATTCGGATCG
521451 TTT
1 TTT
521454 CAGTTTGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.09, G:0.31, T:0.51
Consensus pattern (16 bp):
TTTTGGATTCGGATCG
Found at i:521464 original size:16 final size:16
Alignment explanation
Indices: 521451--521491 Score: 73
Period size: 16 Copynumber: 2.5 Consensus size: 16
521441 GTTCGGATTG
521451 TTTCAGTTTGGGATCA
1 TTTCAGTTTGGGATCA
521467 TTTCAGTTTGGGATCA
1 TTTCAGTTTGGGATCA
521483 TTTCGAGTT
1 TTTC-AGTT
521492 CAGATCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.17, C:0.12, G:0.24, T:0.46
Consensus pattern (16 bp):
TTTCAGTTTGGGATCA
Found at i:522388 original size:16 final size:15
Alignment explanation
Indices: 522346--522406 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 15
522336 TTAAATTTAA
522346 GTTCAGGTCATTTCGG
1 GTTC-GGTCATTTCGG
522362 GTTCGGATCATTTCGG
1 GTTCGG-TCATTTCGG
* * **
522378 ATTTTGGTCATTTTAG
1 -GTTCGGTCATTTCGG
522394 GTTCGGGTCATTT
1 GTTC-GGTCATTT
522407 TTAGGTTCAG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
15 4 0.11
16 28 0.78
17 4 0.11
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.44
Consensus pattern (15 bp):
GTTCGGTCATTTCGG
Found at i:522407 original size:16 final size:17
Alignment explanation
Indices: 522383--522414 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
522373 TTCGGATTTT
522383 GGTCA-TTTTAGGTTCG
1 GGTCATTTTTAGGTTCG
522399 GGTCATTTTTAGGTTC
1 GGTCATTTTTAGGTTC
522415 AGATTGACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.12, G:0.28, T:0.47
Consensus pattern (17 bp):
GGTCATTTTTAGGTTCG
Found at i:531988 original size:52 final size:52
Alignment explanation
Indices: 531910--532038 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
531900 CGAAATATGA
531910 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGAGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGAGC
*
531962 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGAGC
532014 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
532039 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGAGC
Found at i:532049 original size:52 final size:51
Alignment explanation
Indices: 531910--532058 Score: 237
Period size: 52 Copynumber: 2.9 Consensus size: 51
531900 CGAAATATGA
531910 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGAGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGAGC
*
531962 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGAGC
*
532014 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
532059 ATGTATCGAT
Statistics
Matches: 93, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
50 1 0.01
51 2 0.02
52 90 0.97
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGAGC
Found at i:532065 original size:13 final size:13
Alignment explanation
Indices: 532047--532071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
532037 CAAAGATCAG
532047 TGTATCGATACAA
1 TGTATCGATACAA
532060 TGTATCGATACA
1 TGTATCGATACA
532072 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:532151 original size:13 final size:13
Alignment explanation
Indices: 532133--532157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
532123 ACAAAACTTA
532133 TGTATCGATACAT
1 TGTATCGATACAT
532146 TGTATCGATACA
1 TGTATCGATACA
532158 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:532153 original size:32 final size:33
Alignment explanation
Indices: 532112--532177 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
532102 AGTAGCTTAA
532112 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
532144 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
532177 A
1 A
532178 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:536270 original size:17 final size:18
Alignment explanation
Indices: 536232--536271 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
536222 TATGTTTTTT
*
536232 TTTCTTTTTCTTCCTTTC
1 TTTCTTTATCTTCCTTTC
536250 -TTCTTTATCTT-CTTTC
1 TTTCTTTATCTTCCTTTC
536266 TTTCTT
1 TTTCTT
536272 ACCCAACCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTTTATCTTCCTTTC
Found at i:537356 original size:297 final size:288
Alignment explanation
Indices: 537007--537591 Score: 945
Period size: 297 Copynumber: 2.0 Consensus size: 288
536997 AGTGACCCTT
*
537007 TGTCACAAAGGTGGCCTGGGTAAACCCAGGTCACTCATTTTTTTTATTTATTTTAAAAAAACGAG
1 TGTCACAAAGGTGGCCTGGGTAAACCCAGGCCACTCATTTTTTTTATTTATTTTAAAAAAACGAG
*
537072 TGTTTTAAAAATGGTCGGATAAAATTTTGTGTCTACAACTGCCCCTCTTTGGCCGTTGCTGAGTA
66 TGTCTTAAAAATGGTCGGATAAAATTTTGTGTCTACAACTGCCCCTCTTTGGCCGTTGCTGAGTA
* * *
537137 TCAGCAACTGGGCAAAGACAAATGGACACCATTTTATCTGGGGTAGAATTAGACAGGTGTTGTGG
131 TCAACAACAGGGCAAAGACAAATGGACACCATTTTATCTGGGGTAGAATTAGACAGGTGTTGTAG
*
537202 AAGGATATGGCTCCTTGAGGATTGGTGTGGGCATGATCAGTATCCGCGATATGCCCGTGTGCAGA
196 AAGGATATAGCTCCTTGAGGATTGGTGTGGGCATGATCAGTATCCGCGATATGCCCGTGTGCAGA
* *
537267 TTCATGGCCTGCAACATTAGATTTAAAG
261 TTCAAGGCCTGCAACACTAGATTTAAAG
537295 TGTCACAAAGGTGGCCTGGGTTCAAAACCCAGGCCACTCATTTTTTTATTTTTTATTTATTTTAA
1 TGTCACAAAGGTGGCCTGGG-T--AAACCCAGGCCACTCA-----TT-TTTTTTATTTATTTTAA
* **
537360 AAAAACGAGTGTCTTAAAAATGGTCGGATAAAATTTTGTGTCTACAGCTTTCCCTCTTTGGCCGT
57 AAAAACGAGTGTCTTAAAAATGGTCGGATAAAATTTTGTGTCTACAACTGCCCCTCTTTGGCCGT
* *
537425 TGCTGAGTATCAACAACAGGGCAAAGACAAATGGATACTATTTTATCTGGGGTAGAATTAGACAG
122 TGCTGAGTATCAACAACAGGGCAAAGACAAATGGACACCATTTTATCTGGGGTAGAATTAGACAG
* *
537490 GTGTTGTAGAAGGATATAGCTCCTTGAGGATTGGTGTGGGCATGATCAGTATTCGCGATGTGCCC
187 GTGTTGTAGAAGGATATAGCTCCTTGAGGATTGGTGTGGGCATGATCAGTATCCGCGATATGCCC
*
537555 GTGTGCAGATTCAAGGCCTGTAACACTAGATTTAAAG
252 GTGTGCAGATTCAAGGCCTGCAACACTAGATTTAAAG
537592 ATGAGAGGAA
Statistics
Matches: 272, Mismatches: 16, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
288 20 0.07
289 1 0.00
291 15 0.06
296 2 0.01
297 234 0.86
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (288 bp):
TGTCACAAAGGTGGCCTGGGTAAACCCAGGCCACTCATTTTTTTTATTTATTTTAAAAAAACGAG
TGTCTTAAAAATGGTCGGATAAAATTTTGTGTCTACAACTGCCCCTCTTTGGCCGTTGCTGAGTA
TCAACAACAGGGCAAAGACAAATGGACACCATTTTATCTGGGGTAGAATTAGACAGGTGTTGTAG
AAGGATATAGCTCCTTGAGGATTGGTGTGGGCATGATCAGTATCCGCGATATGCCCGTGTGCAGA
TTCAAGGCCTGCAACACTAGATTTAAAG
Found at i:537849 original size:32 final size:32
Alignment explanation
Indices: 537754--537858 Score: 111
Period size: 32 Copynumber: 3.2 Consensus size: 32
537744 AAAGTGGTGA
* * *
537754 TTTGACAAGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAAAGAGTTGCCACCGACTTGTGTGGGC
* * * ** *
537786 TTTAAAAAAAAAGGTGCCACTAACTTATGTGGGC
1 TTT--GAAAAGAGTTGCCACCGACTTGTGTGGGC
537820 TTTGAAAAGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGAGTTGCCACCGACTTGTGTGGGC
537852 TTTGAAA
1 TTTGAAA
537859 GGGTATGCCA
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
32 33 0.59
34 23 0.41
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (32 bp):
TTTGAAAAGAGTTGCCACCGACTTGTGTGGGC
Found at i:537868 original size:32 final size:31
Alignment explanation
Indices: 537754--537934 Score: 97
Period size: 32 Copynumber: 5.8 Consensus size: 31
537744 AAAGTGGTGA
* *
537754 TTTGACAAGGGTTGCCACCGACTTGCGTGGGC
1 TTTGA-AAGAGTTGCCACCGACTTGTGTGGGC
* * * ** *
537786 TTTAAAAAAAAAGGTGCCACTAACTTATGTGGGC
1 TTT---GAAAGAGTTGCCACCGACTTGTGTGGGC
537820 TTTGAAAAGAGTTGCCACCGACTTGTGTGGGC
1 TTTG-AAAGAGTTGCCACCGACTTGTGTGGGC
* ** *
537852 TTTGAAAGGGTATGCCATTGAC-T-TGTGGGT
1 TTTGAAAGAGT-TGCCACCGACTTGTGTGGGC
* * * *
537882 TTTGAAATA-CTGCCACTGAC-T-TGTAGGC
1 TTTGAAAGAGTTGCCACCGACTTGTGTGGGC
*
537910 TTTGAAA-A-TATGCCACTGACTTGTG
1 TTTGAAAGAGT-TGCCACCGACTTGTG
537935 GACTTTGAAA
Statistics
Matches: 116, Mismatches: 25, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
27 1 0.01
28 32 0.28
29 1 0.01
30 15 0.13
31 7 0.06
32 37 0.32
34 22 0.19
35 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (31 bp):
TTTGAAAGAGTTGCCACCGACTTGTGTGGGC
Found at i:537904 original size:28 final size:27
Alignment explanation
Indices: 537795--538310 Score: 393
Period size: 28 Copynumber: 18.0 Consensus size: 27
537785 CTTTAAAAAA
* *
537795 AAAGGTGCCACTAACTTATGTGGGCTTTG
1 AAAGATGCCACTGAC-T-TGTGGGCTTTG
*
537824 AAAAGAGTTGCCACCGACTTGTGTGGGCTTTG
1 -AAAGA--TGCCACTGAC-T-TGTGGGCTTTG
* *
537856 AAAGGGTATGCCATTGACTTGTGGGTTTTG
1 AAA--G-ATGCCACTGACTTGTGGGCTTTG
* *
537886 AAATACTGCCACTGACTTGTAGGCTTTG
1 AAAGA-TGCCACTGACTTGTGGGCTTTG
* *
537914 AAAATATGCCACTGACTTGTGGACTTTG
1 -AAAGATGCCACTGACTTGTGGGCTTTG
* * * *
537942 AAAGGATGCCATTGGCTTGTAGGCTTTA
1 AAA-GATGCCACTGACTTGTGGGCTTTG
* *
537970 AAAGGATACCACTGACTTATGGGCTTTG
1 AAA-GATGCCACTGACTTGTGGGCTTTG
* ** *
537998 AAAAGATGCCACTGGCTTGTAAGCTTTA
1 -AAAGATGCCACTGACTTGTGGGCTTTG
*
538026 AAAGGATGCCACTGACTTGTGGGCTTTA
1 AAA-GATGCCACTGACTTGTGGGCTTTG
* *
538054 AAAGGATGCCAGTGACTTGTGGGCTCTG
1 AAA-GATGCCACTGACTTGTGGGCTTTG
* * *
538082 AAAAGATGCCATTGACTTGTGGGTTTTA
1 -AAAGATGCCACTGACTTGTGGGCTTTG
**
538110 AAAGGATGCCGGTGACTTGTGGGCTTTG
1 AAA-GATGCCACTGACTTGTGGGCTTTG
* * *
538138 AAAAGATGTCACTGACTTGTGAGCTCTG
1 -AAAGATGCCACTGACTTGTGGGCTTTG
*
538166 AAAATATGCCACTGACTTGTGGGCTTTG
1 -AAAGATGCCACTGACTTGTGGGCTTTG
* *
538194 AGATGATGCCACTGACTTATGGGCTTTG
1 A-AAGATGCCACTGACTTGTGGGCTTTG
** *
538222 AAATGAGTTGCCACCAACTTGTGTGGACTTTAA
1 AAA-GA--TGCCACTGACTTGTG-GG-CTTT-G
*
538255 AAAAAGTGCCACTGACTTGTGGGCTTTG
1 AAAGA-TGCCACTGACTTGTGGGCTTTG
* * *
538283 AAAGGGGTGCCACTAACTTATGGGCTTT
1 AAA--GATGCCACTGACTTGTGGGCTTT
538311 AGAAGCGAAT
Statistics
Matches: 393, Mismatches: 71, Indels: 45
0.77 0.14 0.09
Matches are distributed among these distances:
27 12 0.03
28 255 0.65
29 37 0.09
30 31 0.08
31 19 0.05
32 34 0.09
33 4 0.01
34 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (27 bp):
AAAGATGCCACTGACTTGTGGGCTTTG
Found at i:537982 original size:84 final size:84
Alignment explanation
Indices: 537794--538492 Score: 514
Period size: 84 Copynumber: 8.2 Consensus size: 84
537784 GCTTTAAAAA
* *
537794 AAAAGG-TGCCACTAACTTATGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAA
1 AAAAGGATGCCACTGAC-T-TGTGGGCTTTGAAAAGA--TGCCACTGAC-T-TGTGGGCTTTGAA
* *
537858 AGGGTATGCCATTGACTTGTGGGTTTT
60 A-GG-ATGCCACTGACTTGTGGGCTTT
* * * * *
537885 GAAA-TACTGCCACTGACTTGTAGGCTTTGAAAATATGCCACTGACTTGTGGACTTTGAAAGGAT
1 AAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGAT
* * *
537949 GCCATTGGCTTGTAGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * ** *
537969 AAAAGGATACCACTGACTTATGGGCTTTGAAAAGATGCCACTGGCTTGTAAGCTTTAAAAGGATG
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATG
538034 CCACTGACTTGTGGGCTTT
66 CCACTGACTTGTGGGCTTT
* * * * *
538053 AAAAGGATGCCAGTGACTTGTGGGCTCTGAAAAGATGCCATTGACTTGTGGGTTTTAAAAGGATG
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATG
**
538118 CCGGTGACTTGTGGGCTTT
66 CCACTGACTTGTGGGCTTT
* * * * * *
538137 GAAAA-GATGTCACTGACTTGTGAGCTCTGAAAATATGCCACTGACTTGTGGGCTTTGAGATGAT
1 -AAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGAT
*
538201 GCCACTGACTTATGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * ** * *
538221 GAAATGAGTTGCCACCAACTTGTGTGGACTTTAAAAAAAGTGCCACTGACTTGTGGGCTTTGAAA
1 -AAAAG-GATGCCACTGACTTGTG-GG-CTTTGAAAAGA-TGCCACTGACTTGTGGGCTTTGAAA
* * *
538286 GGGGTGCCACTAACTTATGGGCTTT
61 -GGATGCCACTGACTTGTGGGCTTT
* * * * * * * * * * *
538311 AGAAGCGAATGCCACTAAGTTGTGGAC-TTAAAAAGGGTGCCAC-GAAGTTGTGGAC-CTAAAAA
1 AAAAG-G-ATGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACTG-ACTTGTGGGCTTTGAAAG
* * **
538373 GATGCCACCGAGTTGTGGATTTT
62 GATGCCACTGACTTGTGGGCTTT
* * * * * * * * *
538396 AAAAAGG-TGCCACGGAGTTGTGGACTTT-AAAAGGGTGCCACCGAGTTGTGGACTTTAAAAGGG
1 -AAAAGGATGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAGGA
* * **
538459 TGCCACGGAGTTGTGAACTTT
64 TGCCACTGACTTGTGGGCTTT
*
538480 AAAAGGGTGCCAC
1 AAAAGGATGCCAC
538493 GGAGTTGTAG
Statistics
Matches: 500, Mismatches: 90, Indels: 43
0.79 0.14 0.07
Matches are distributed among these distances:
83 45 0.09
84 264 0.53
85 24 0.05
86 35 0.07
87 23 0.05
88 18 0.04
89 29 0.06
90 49 0.10
91 4 0.01
92 9 0.02
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (84 bp):
AAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATG
CCACTGACTTGTGGGCTTT
Found at i:538360 original size:28 final size:28
Alignment explanation
Indices: 538328--538532 Score: 304
Period size: 28 Copynumber: 7.4 Consensus size: 28
538318 AATGCCACTA
* *
538328 AGTTGTGGACTTAAAAAGGGTGCCACGA
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* * * *
538356 AGTTGTGGAC-CTAAAAAGATGCCACCG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* *
538383 AGTTGTGGATTTTAAAAAGGTGCCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
*
538411 AGTTGTGGACTTTAAAAGGGTGCCACCG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
538439 AGTTGTGGACTTTAAAAGGGTGCCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
*
538467 AGTTGTGAACTTTAAAAGGGTGCCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
*
538495 AGTTGTAGACTTTAAAAGGGTGCCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
538523 AGTTGTGGAC
1 AGTTGTGGAC
538533 CAGAGTTGTG
Statistics
Matches: 158, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
27 20 0.13
28 138 0.87
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.24
Consensus pattern (28 bp):
AGTTGTGGACTTTAAAAGGGTGCCACGG
Found at i:538553 original size:41 final size:41
Alignment explanation
Indices: 538494--538573 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
538484 GGGTGCCACG
* **
538494 GAGTTGTAGACTTTAAAAGGGTGCCACGGAGTTGTGGACCA
1 GAGTTGTAGACTTGAAAAGGGTGCCACAAAGTTGTGGACCA
*
538535 GAGTTGTGGACTTGAAAAGGGTGCCACAAAGTTGTGGAC
1 GAGTTGTAGACTTGAAAAGGGTGCCACAAAGTTGTGGAC
538574 TTTAAAAGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.24
Consensus pattern (41 bp):
GAGTTGTAGACTTGAAAAGGGTGCCACAAAGTTGTGGACCA
Found at i:538577 original size:69 final size:69
Alignment explanation
Indices: 538466--538601 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 69
538456 GGGTGCCACG
* ** *
538466 GAGTTGTGAACTTTAAAAGGGTGCCACGGAGTTGTAGACTTTAAAAGGGTGCCACGGAGTTGTGG
1 GAGTTGTGAACTTGAAAAGGGTGCCACAAAGTTGTAGACTTTAAAAGGGTGCCACGAAGTTGTGG
538531 ACCA
66 ACCA
* * *
538535 GAGTTGTGGACTTGAAAAGGGTGCCACAAAGTTGTGGACTTTAAAAGGGTGTCACGAAGTTGTGG
1 GAGTTGTGAACTTGAAAAGGGTGCCACAAAGTTGTAGACTTTAAAAGGGTGCCACGAAGTTGTGG
538600 AC
66 AC
538602 TTTAAAAGGA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.28, C:0.13, G:0.34, T:0.25
Consensus pattern (69 bp):
GAGTTGTGAACTTGAAAAGGGTGCCACAAAGTTGTAGACTTTAAAAGGGTGCCACGAAGTTGTGG
ACCA
Found at i:538604 original size:97 final size:95
Alignment explanation
Indices: 538438--538713 Score: 317
Period size: 97 Copynumber: 3.0 Consensus size: 95
538428 GGGTGCCACC
* * *
538438 GAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGAACTTTAAAAGGGTGCCACGGAGTTGTAG
1 GAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGG
538503 ACTTTAAAAGGGTGCCACGGAGTTGTGGACCA
65 ACTTTAAAAGGGTGCCAC-GAGTTGTGGACCA
* * *
538535 GAGTTGTGGACTTGAAAAGGGTGCCACAAAGTTGTGGACTTTAAAAGGGTGTCACGAAGTTGTGG
1 GAGTTGTGGACTT-AAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGG
*
538600 ACTTTAAAAGGATG-C-C---------A-CA
65 ACTTTAAAAGGGTGCCACGAGTTGTGGACCA
* *
538619 GAGTTATGGACTTAAAAGGGAATGCCACAGAGTTGTGGACTTTAAACGGGTGCCACGGAGTTGTG
1 GAGTTGTGGACTTAAAAGGG--TGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTG
*
538684 GAC-TTAAAAAGGTGCCACTGAGTTGTGGAC
64 GACTTTAAAAGGGTGCCAC-GAGTTGTGGAC
538714 TTAAAACGGG
Statistics
Matches: 149, Mismatches: 14, Indels: 32
0.76 0.07 0.16
Matches are distributed among these distances:
83 7 0.05
84 23 0.15
85 44 0.30
86 1 0.01
95 1 0.01
96 4 0.03
97 69 0.46
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.25
Consensus pattern (95 bp):
GAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGA
CTTTAAAAGGGTGCCACGAGTTGTGGACCA
Found at i:538681 original size:85 final size:82
Alignment explanation
Indices: 538533--538796 Score: 325
Period size: 85 Copynumber: 3.2 Consensus size: 82
538523 AGTTGTGGAC
* *
538533 CAGAGTTGTGGACTTGAAAAGGGTGCCACAAAGTTGTGGACTTTAAAAGGGTGTCACGAAGTTGT
1 CAGAGTTGTGGACTT-AAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGAAGTTGT
*
538598 GGACTTTAAAAGGATGCCA
65 GGACTTAAAAAGG-TGCCA
* * *
538617 CAGAGTTATGGACTTAAAAGGGAATGCCACAGAGTTGTGGACTTTAAACGGGTGCCACGGAGTTG
1 CAGAGTTGTGGACTTAAAAGGG--TGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGAAGTTG
538682 TGGACTTAAAAAGGTGCCA
64 TGGACTTAAAAAGGTGCCA
* * **** *
538701 CTGAGTTGTGGACTTAAAACGGGTGCCACGGAGTTGTGGAC-TTAAAA-AAAACCACTAAGTTGT
1 CAGAGTTGTGGACTTAAAA-GGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGAAGTTGT
538764 GGACTTAAAAAGGTGCCA
65 GGACTTAAAAAGGTGCCA
* * *
538782 CTGAATCGTGGACTT
1 CAGAGTTGTGGACTT
538797 TGAAGAAGTT
Statistics
Matches: 159, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
81 41 0.26
82 5 0.03
83 24 0.15
84 36 0.23
85 53 0.33
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (82 bp):
CAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGAAGTTGTG
GACTTAAAAAGGTGCCA
Found at i:538698 original size:27 final size:27
Alignment explanation
Indices: 538533--538796 Score: 273
Period size: 28 Copynumber: 9.6 Consensus size: 27
538523 AGTTGTGGAC
538533 CAGAGTTGTGGACTTGAAAAGGGTGCCA
1 CAGAGTTGTGGACTT-AAAAGGGTGCCA
* *
538561 CAAAGTTGTGGACTTTAAAAGGGTGTCA
1 CAGAGTTGTGGAC-TTAAAAGGGTGCCA
*
538589 C-GAAGTTGTGGACTTTAAAAGGATGCCA
1 CAG-AGTTGTGGAC-TTAAAAGGGTGCCA
*
538617 CAGAGTTATGGACTTAAAAGGGAATGCCA
1 CAGAGTTGTGGACTTAAAAGGG--TGCCA
*
538646 CAGAGTTGTGGACTTTAAACGGGTGCCA
1 CAGAGTTGTGGAC-TTAAAAGGGTGCCA
* *
538674 CGGAGTTGTGGACTTAAAAAGGTGCCA
1 CAGAGTTGTGGACTTAAAAGGGTGCCA
*
538701 CTGAGTTGTGGACTTAAAACGGGTGCCA
1 CAGAGTTGTGGACTTAAAA-GGGTGCCA
* ****
538729 CGGAGTTGTGGACTTAAAA-AAAACCA
1 CAGAGTTGTGGACTTAAAAGGGTGCCA
*
538755 CTA-AGTTGTGGACTTAAAAAGGTGCCA
1 C-AGAGTTGTGGACTTAAAAGGGTGCCA
* * *
538782 CTGAATCGTGGACTT
1 CAGAGTTGTGGACTT
538797 TGAAGAAGTT
Statistics
Matches: 199, Mismatches: 27, Indels: 21
0.81 0.11 0.09
Matches are distributed among these distances:
26 20 0.10
27 52 0.26
28 99 0.50
29 20 0.10
30 8 0.04
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (27 bp):
CAGAGTTGTGGACTTAAAAGGGTGCCA
Found at i:538721 original size:55 final size:54
Alignment explanation
Indices: 538535--538796 Score: 276
Period size: 55 Copynumber: 4.7 Consensus size: 54
538525 TTGTGGACCA
* * *
538535 GAGTTGTGGACTTGAAAAGGGTGCCACAAAGTTGTGGACTTTAAAAGGGTGTCAC-
1 GAGTTGTGGACTT-AAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAAGGTGCCACT
* * * *
538590 GAAGTTGTGGACTTTAAAAGGATGCCACAGAGTTATGGACTTAAAAGGGAATGCCACA
1 G-AGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGG--TGCCACT
* *
538648 GAGTTGTGGACTTTAAACGGGTGCCACGGAGTTGTGGACTTAAAAAGGTGCCACT
1 GAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGGTGCCACT
* ***
538703 GAGTTGTGGACTTAAAACGGGTGCCACGGAGTTGTGGACTTAAAAA-AAACCACT
1 GAGTTGTGGACTTAAAA-GGGTGCCACAGAGTTGTGGACTTAAAAAGGTGCCACT
* * * * *
538757 AAGTTGTGGACTTAAAAAGGTGCCACTGAATCGTGGACTT
1 GAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTT
538797 TGAAGAAGTT
Statistics
Matches: 182, Mismatches: 19, Indels: 14
0.85 0.09 0.07
Matches are distributed among these distances:
53 19 0.10
54 26 0.14
55 55 0.30
56 32 0.18
57 49 0.27
58 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (54 bp):
GAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGGTGCCACT
Found at i:540203 original size:21 final size:21
Alignment explanation
Indices: 540145--540204 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
540135 CATGTCCTTA
* *
540145 TTTTTTTATTTT-TGTTGTTC
1 TTTTTTTATTTTCTTTTGTAC
540165 TCTTTTTTATTTTGCTTTTGTAC
1 T-TTTTTTATTTT-CTTTTGTAC
540188 TTTTTTTATTTTCTTTT
1 TTTTTTTATTTTCTTTT
540205 CATGATTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.46
22 11 0.31
23 7 0.20
ACGTcount: A:0.07, C:0.08, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTTATTTTCTTTTGTAC
Found at i:540854 original size:19 final size:19
Alignment explanation
Indices: 540830--540912 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
540820 TATCAACGAT
540830 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
540849 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
540863 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
540881 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
540900 TTGTATCGATACA
1 TTGTATCGATACA
540913 ATGTATCGCT
Statistics
Matches: 57, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 2 0.04
19 42 0.74
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:540867 original size:32 final size:32
Alignment explanation
Indices: 540831--540893 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
540821 ATCAACGATT
540831 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
540863 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
540894 TAAGTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:540868 original size:13 final size:13
Alignment explanation
Indices: 540850--540874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
540840 ACATAAGTGT
540850 TGTATCGATACAA
1 TGTATCGATACAA
540863 TGTATCGATACA
1 TGTATCGATACA
540875 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:540983 original size:13 final size:13
Alignment explanation
Indices: 540965--540989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
540955 ATTACTCAAA
540965 TGTATCGATACAT
1 TGTATCGATACAT
540978 TGTATCGATACA
1 TGTATCGATACA
540990 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:541039 original size:32 final size:32
Alignment explanation
Indices: 540998--541073 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
540988 CACTGATCTT
*
540998 TGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATACAGGCAAATTTGCCCAGA
*
541030 TGTATCGATACATACAGGCAAATTTGCCTAGA
1 TGTATCGATACATACAGGCAAATTTGCCCAGA
541062 TGTATCGATACA
1 TGTATCGATACA
541074 CTATGAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (32 bp):
TGTATCGATACATACAGGCAAATTTGCCCAGA
Found at i:550058 original size:17 final size:17
Alignment explanation
Indices: 550036--550077 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
550026 ATTTCATATG
**
550036 TTTTTTTCTTTTTCTTC
1 TTTTTTTCTTCATCTTC
550053 TTTTTTTCTTCATCTTC
1 TTTTTTTCTTCATCTTC
550070 TTTCTTTT
1 TTT-TTTT
550078 TTACTTGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTTCTTCATCTTC
Found at i:550831 original size:17 final size:19
Alignment explanation
Indices: 550809--550846 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
550799 ATTTATTTTT
550809 TATTTTAAAAA-AA-TAAA
1 TATTTTAAAAATAATTAAA
550826 TATTTTAAAAATAATTAAA
1 TATTTTAAAAATAATTAAA
550845 TA
1 TA
550847 AAATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTTTAAAAATAATTAAA
Found at i:552911 original size:18 final size:18
Alignment explanation
Indices: 552873--552916 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
552863 ATTTGTTAAG
* *
552873 CATTAAGTCCAAATTTGA
1 CATTAAGTCCAAATCTCA
*
552891 CATTGAGTCCAAATCTCA
1 CATTAAGTCCAAATCTCA
552909 CATTAAGT
1 CATTAAGT
552917 AATTATGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.32
Consensus pattern (18 bp):
CATTAAGTCCAAATCTCA
Found at i:554836 original size:14 final size:14
Alignment explanation
Indices: 554813--554859 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
554803 AGAAAAAATA
554813 AAAGGAAAAGAAAG
1 AAAGGAAAAGAAAG
*
554827 AAAGGGAAAGAAAG
1 AAAGGAAAAGAAAG
**
554841 AAAATAAAAGAAAAG
1 AAAGGAAAAG-AAAG
554856 AAAG
1 AAAG
554860 AGGGAAGAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (14 bp):
AAAGGAAAAGAAAG
Found at i:554982 original size:20 final size:20
Alignment explanation
Indices: 554957--555005 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
554947 AGTTATTTAT
554957 TTTATGTATATTTTGATACA
1 TTTATGTATATTTTGATACA
554977 TTTATGTATATTTTGATACA
1 TTTATGTATATTTTGATACA
554997 TTTATGTAT
1 TTTATGTAT
555006 TTATATAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (20 bp):
TTTATGTATATTTTGATACA
Found at i:556241 original size:15 final size:15
Alignment explanation
Indices: 556198--556260 Score: 56
Period size: 15 Copynumber: 4.0 Consensus size: 15
556188 TGAGTCACAT
556198 AAATAATTTAAATTA
1 AAATAATTTAAATTA
*
556213 AATTAAATTT-AATTA
1 AAAT-AATTTAAATTA
*
556228 AAATATTTTAAATTTA
1 AAATAATTTAAA-TTA
*
556244 AATTAATATTAATATTA
1 AAATAAT-TTAA-ATTA
556261 TTTAATTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
14 4 0.11
15 13 0.34
16 13 0.34
17 7 0.18
18 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATAATTTAAATTA
Found at i:556668 original size:6 final size:6
Alignment explanation
Indices: 556642--556681 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
556632 TAATTAAAAA
*
556642 AAATTT AAAATTTT AAGTTT AAATTT AAATTT AAATTT AA
1 AAATTT -AAA-TTT AAATTT AAATTT AAATTT AAATTT AA
556682 TTTGATTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 22 0.73
7 5 0.17
8 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:557823 original size:21 final size:22
Alignment explanation
Indices: 557773--557825 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
557763 ACACGATATG
557773 AACAT-AACATAAATAAAAAAT
1 AACATAAACATAAATAAAAAAT
*
557794 AA-TTAAAACAT-AATAAAAAAT
1 AACAT-AAACATAAATAAAAAAT
557815 AACATAAACAT
1 AACATAAACAT
557826 GATACAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.04
21 20 0.74
22 6 0.22
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (22 bp):
AACATAAACATAAATAAAAAAT
Found at i:558480 original size:18 final size:18
Alignment explanation
Indices: 558457--558491 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
558447 AGGTTGTAAA
558457 TTGATTCTTCTTTATTTT
1 TTGATTCTTCTTTATTTT
* *
558475 TTGATTTTTTTTTATTT
1 TTGATTCTTCTTTATTT
558492 AGAAGCTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (18 bp):
TTGATTCTTCTTTATTTT
Found at i:558562 original size:14 final size:14
Alignment explanation
Indices: 558543--558573 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
558533 AAATGGCTAA
*
558543 ATTAATTAAAAATT
1 ATTAATTAAAAAAT
558557 ATTAATTAAAAAAT
1 ATTAATTAAAAAAT
558571 ATT
1 ATT
558574 GAGCAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTAATTAAAAAAT
Found at i:559577 original size:7 final size:7
Alignment explanation
Indices: 559565--559589 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
559555 AGATATATTT
559565 AATTATA
1 AATTATA
559572 AATTATA
1 AATTATA
559579 AATTATA
1 AATTATA
559586 AATT
1 AATT
559590 TATTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTATA
Found at i:560041 original size:15 final size:14
Alignment explanation
Indices: 560019--560062 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
560009 TATTATAATA
560019 TAAATTAAAAAATT
1 TAAATTAAAAAATT
560033 TAAACTTAAAAAATT
1 TAAA-TTAAAAAATT
560048 TGAATATATAAAAAA
1 T-AA-AT-TAAAAAA
560063 AATTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.15
15 11 0.42
16 3 0.12
17 8 0.31
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (14 bp):
TAAATTAAAAAATT
Found at i:560203 original size:2 final size:2
Alignment explanation
Indices: 560191--560226 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
560181 TTAAATTTTG
*
560191 CT CT CT TT CT CT CT 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
560227 GTCTGTCCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:563724 original size:63 final size:63
Alignment explanation
Indices: 563608--563746 Score: 174
Period size: 63 Copynumber: 2.2 Consensus size: 63
563598 GAAAGACGAA
*
563608 AAAAATTAAAAGATAAAAAGTATAAATTTTCTTTCCTTTCATGTCCTCTAATGTATAAGATAG
1 AAAAATTAAAAGATAAAAACTATAAATTTTCTTTCCTTTCATGTCCTCTAATGTATAAGATAG
* * * * *
563671 AAAAATTAAAAGATAGAAAATCTA-AAATTTTCTTTGCTTTCGT-TCCTTTAATGTGTAAGATGG
1 AAAAATTAAAAGATA-AAAA-CTATAAATTTTCTTTCCTTTCATGTCCTCTAATGTATAAGATAG
* *
563734 AAAAGTAAAAAGA
1 AAAAATTAAAAGA
563747 AATTTTTTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 43 0.65
64 21 0.32
65 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (63 bp):
AAAAATTAAAAGATAAAAACTATAAATTTTCTTTCCTTTCATGTCCTCTAATGTATAAGATAG
Found at i:566647 original size:13 final size:13
Alignment explanation
Indices: 566629--566653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
566619 CATTTTATGG
566629 TGTATCGATACAA
1 TGTATCGATACAA
566642 TGTATCGATACA
1 TGTATCGATACA
566654 TACTTTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:566669 original size:32 final size:33
Alignment explanation
Indices: 566606--566673 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
566596 CGTTACAAGC
*
566606 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATCTTATGGTGTATCGATA
566639 CAATGTATCGATACATACTT-T-GTGTATCGATA
1 CAATGTATCGATACAT-CTTATGGTGTATCGATA
566671 CAA
1 CAA
566674 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATCTTATGGTGTATCGATA
Found at i:568750 original size:21 final size:20
Alignment explanation
Indices: 568721--568763 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
568711 GGCTAGTGTG
* *
568721 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGAGACCT
*
568742 GGGAGTGCCGGTCGAGACCT
1 GGGACTGCCGGTCGAGACCT
568762 GG
1 GG
568764 TGGGTGCTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.28, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGAGACCT
Found at i:569223 original size:13 final size:13
Alignment explanation
Indices: 569205--569256 Score: 86
Period size: 13 Copynumber: 4.0 Consensus size: 13
569195 TATAATCCCC
569205 CTGTATCGATACA
1 CTGTATCGATACA
569218 CTGTATCGATACA
1 CTGTATCGATACA
*
569231 CTATATCGATACA
1 CTGTATCGATACA
*
569244 ATGTATCGATACA
1 CTGTATCGATACA
569257 AAAAAAGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:575420 original size:20 final size:20
Alignment explanation
Indices: 575395--575465 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
575385 TACAAGCCAA
575395 TGTATCGATACATTTTATGG
1 TGTATCGATACATTTTATGG
575415 TGTATCGATACATTTTATGG
1 TGTATCGATACATTTTATGG
*
575435 TGTATCGATACATACTT-T-G
1 TGTATCGATACAT-TTTATGG
575454 TGTATCGATACA
1 TGTATCGATACA
575466 AGTTTGGCTA
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
19 13 0.27
20 34 0.69
21 2 0.04
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTTTATGG
Found at i:576404 original size:20 final size:20
Alignment explanation
Indices: 576381--576453 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
576371 ACAATTCAAA
576381 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
576401 GTATCGATACATGAAAATG--AT
1 GTATCGATACATG---TTGCAAT
576422 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
576442 GTATCGATACAT
1 GTATCGATACAT
576454 AAAAAAGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
20 27 0.59
21 15 0.33
23 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:576425 original size:21 final size:21
Alignment explanation
Indices: 576399--576474 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
576389 ACATGTTGCA
576399 ATGTATCGATACATGAAAATG
1 ATGTATCGATACATGAAAATG
*
576420 ATGTATCGATACATG---TTG
1 ATGTATCGATACATGAAAATG
* *
576438 CAATGTATCGATACATAAAAAAG
1 --ATGTATCGATACATGAAAATG
576461 ATGTATCGATACAT
1 ATGTATCGATACAT
576475 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.04
20 14 0.30
21 29 0.63
23 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAATG
Found at i:576432 original size:41 final size:41
Alignment explanation
Indices: 576381--576474 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
576371 ACAATTCAAA
* *
576381 GTATCGATACATGTTGCAATGTATCGATACATGAAAATGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
576422 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
576463 GTATCGATACAT
1 GTATCGATACAT
576475 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:576531 original size:13 final size:13
Alignment explanation
Indices: 576513--576538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
576503 TACAGCAAGT
576513 ATGTATCGATACA
1 ATGTATCGATACA
576526 ATGTATCGATACA
1 ATGTATCGATACA
576539 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:578785 original size:21 final size:21
Alignment explanation
Indices: 578752--578796 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
578742 TTGCAAGTTG
*
578752 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
578774 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
578794 AAA
1 AAA
578797 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:582714 original size:20 final size:21
Alignment explanation
Indices: 582645--582722 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
582635 AATGTCCAAA
*
582645 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
582665 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
582690 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
582710 TTGTATCGATACA
1 ATGTATCGATACA
582723 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 30 0.64
24 3 0.06
25 14 0.30
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:582729 original size:13 final size:13
Alignment explanation
Indices: 582711--582735 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
582701 CATTTTTCTT
582711 TGTATCGATACAA
1 TGTATCGATACAA
582724 TGTATCGATACA
1 TGTATCGATACA
582736 GGGTGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:584606 original size:87 final size:87
Alignment explanation
Indices: 584498--584679 Score: 364
Period size: 87 Copynumber: 2.1 Consensus size: 87
584488 ACAAAAAGGG
584498 GGAGAGAAAATAGGTATGTGCAAATAAATTTTTTGATATGAATTACTTGATTAAGGGGGAGATTT
1 GGAGAGAAAATAGGTATGTGCAAATAAATTTTTTGATATGAATTACTTGATTAAGGGGGAGATTT
584563 GTTAATAAACGGGGGAGATAAA
66 GTTAATAAACGGGGGAGATAAA
584585 GGAGAGAAAATAGGTATGTGCAAATAAATTTTTTGATATGAATTACTTGATTAAGGGGGAGATTT
1 GGAGAGAAAATAGGTATGTGCAAATAAATTTTTTGATATGAATTACTTGATTAAGGGGGAGATTT
584650 GTTAATAAACGGGGGAGATAAA
66 GTTAATAAACGGGGGAGATAAA
584672 GGAGAGAA
1 GGAGAGAA
584680 TGCGTGAATT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 95 1.00
ACGTcount: A:0.40, C:0.03, G:0.29, T:0.29
Consensus pattern (87 bp):
GGAGAGAAAATAGGTATGTGCAAATAAATTTTTTGATATGAATTACTTGATTAAGGGGGAGATTT
GTTAATAAACGGGGGAGATAAA
Found at i:591273 original size:20 final size:20
Alignment explanation
Indices: 591245--591319 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
591235 TCATACCCTG
591245 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
591265 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
591285 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
591305 ATGTATCGATACATT
1 ATGTATCGATACATT
591320 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:591312 original size:40 final size:39
Alignment explanation
Indices: 591245--591322 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
591235 TCATACCCTG
* *
591245 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
591285 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
591323 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:593683 original size:96 final size:96
Alignment explanation
Indices: 593519--593762 Score: 461
Period size: 96 Copynumber: 2.5 Consensus size: 96
593509 TTTTTATTCA
*
593519 TCGGGGATACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGTTTTTAAACTTGCCAAAG
1 TCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGTTTTTAAACTTGCCAAAG
593584 ATCATTCTTATTTTTACTTAAAGTATCATTG
66 ATCATTCTTATTTTTACTTAAAGTATCATTG
* *
593615 TCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCATTTTTAAATTTGCCAAAG
1 TCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGTTTTTAAACTTGCCAAAG
593680 ATCATTCTTATTTTTACTTAAAGTATCATTG
66 ATCATTCTTATTTTTACTTAAAGTATCATTG
593711 TCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGTTTTT
1 TCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGTTTTT
593763 CAATCAAAAA
Statistics
Matches: 144, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 144 1.00
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (96 bp):
TCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGTTTTTAAACTTGCCAAAG
ATCATTCTTATTTTTACTTAAAGTATCATTG
Found at i:603175 original size:15 final size:16
Alignment explanation
Indices: 603155--603184 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
603145 TTTGTCAAAC
603155 CCGCCAGTG-TTGGTA
1 CCGCCAGTGCTTGGTA
603170 CCGCCAGTGCTTGGT
1 CCGCCAGTGCTTGGT
603185 CGTCCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.30, G:0.33, T:0.27
Consensus pattern (16 bp):
CCGCCAGTGCTTGGTA
Found at i:606721 original size:29 final size:29
Alignment explanation
Indices: 606679--608222 Score: 2210
Period size: 28 Copynumber: 53.9 Consensus size: 29
606669 AATGTTCATC
606679 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
606708 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
606737 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
606765 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
606793 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
606822 CTTTTCAAAGCCCACAAGTCAATGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
606850 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
606879 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
606907 CCTTTCAAAGCCCACAAGTCAGTGGCACA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
606936 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
606965 CCTTTCAAAGCCCACAAATCAGTGGAACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
606994 CTTTTCAAAGCCCACAAGTCAATGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607022 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
607050 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
**
607079 TGTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
607108 CTTTTTAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
607137 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607165 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
607194 CCTTTCAAAGCCCATAAATCAGTGGCGCT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
607223 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607252 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607280 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607308 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607336 CCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
607364 CATTGT-GAAGCCCACAATTCAGTGGCACT
1 CCTT-TCAAAGCCCACAAGTCAGTGGCACT
607393 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
607420 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607449 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
607477 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607506 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
607534 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607563 CCTTTCAAAGCCCACATGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
607592 CCTTTCAAAGCCCATAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
607621 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607649 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607677 CCTTTCAAAACCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
607706 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
607735 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
** * *
607764 ATTTTCAACGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
607793 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
607822 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607851 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607879 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607907 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
607935 CCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
607963 CATTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
607992 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
608019 CCTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* * *
608050 CCTTTTAAAGCTCACGCAAGTCAGTGGTAC-
1 CCTTTCAAAGC-C-CACAAGTCAGTGGCACT
*
608080 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
608109 -CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
608136 CCTTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
608164 TCTTTCAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
608194 CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
608223 ACCCTTTTCA
Statistics
Matches: 1380, Mismatches: 111, Indels: 47
0.90 0.07 0.03
Matches are distributed among these distances:
27 2 0.00
28 654 0.47
29 636 0.46
30 62 0.04
31 26 0.02
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:607909 original size:627 final size:626
Alignment explanation
Indices: 606678--608222 Score: 2517
Period size: 627 Copynumber: 2.5 Consensus size: 626
606668 GAATGTTCAT
* *
606678 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
1 CCCTTTCAGAGCCCACAAGTCAGTGGCAC-CCTTTCGAAGCCCACAAATCAGTGGCACTC-TTTC
606743 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
64 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
*
606808 AAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGT
129 AAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGT
606873 GGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACACC
194 GGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
606938 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGAACTCTTTTCAAA
258 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGAACTCTTTTCAAA
*
607003 GCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACAAG
323 GCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAACCCACAAG
** *
607068 TCAGTGGCACTTGTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCACAAATCAGTGG
388 TCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGG
* *
607133 CACTCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTT
453 CACTATTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTT
* * *
607198 TCAAAGCCCATAAATCAGTGGCGCTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGC
518 TCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCCTTTCAAAGC
*
607263 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA
583 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
*
607307 CCCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCAC-CATTGT-
1 CCCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAATCAGTGGCACTC-TT-TC
* * *
607370 GAAGCCCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
64 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
* *
607435 AAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGT
129 AAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGT
607500 GGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCC
194 GGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
* * *
607565 TTTCAAAGCCCACATGTCAGTGGCACTCCTTTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAA
258 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGAACTCTTTTCAAA
* *
607630 GCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAACCCACAAG
323 GCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAACCCACAAG
607695 TCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGG
388 TCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGG
* *
607760 CACTATTTTCAACGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
453 CACTATTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
*
607825 TTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAG
517 TTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCCTTTCAAAG
* *
607889 CCCACAAGTTAGTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCA
582 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
607934 CCCTTTC-GAAGCCCACAAGTCAGTGGCACCATTGCGAAGCCCACAATTCAGTGGCACTCTTTCA
1 CCCTTTCAG-AGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAATCAGTGGCACTCTTTCA
* *
607998 AAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCTC
65 AAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCAC-CCTTTCAAAGC-C
* * *
608063 ACGCAAGTCAGTGGTAC-CTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGT
126 -CACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
* **
608127 CAGTGGCA-TCCTTTCAAAGCCCACGAGTTAGTGGCATTCTTTCAAAGCCCACGCAAGTCAGTGG
190 CAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGG
* *
608191 CACCCTTTTAAAGCCCATGCAAGTCAATGGCA
253 CACCCTTTCAAAGCCCA--CAAGTCAGTGGCA
608223 ACCCTTTTCA
Statistics
Matches: 852, Mismatches: 50, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
626 2 0.00
627 540 0.63
628 111 0.13
629 44 0.05
630 50 0.06
631 66 0.08
632 28 0.03
633 11 0.01
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (626 bp):
CCCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAATCAGTGGCACTCTTTCAA
AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA
GTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG
CACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
CAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGAACTCTTTTCAAAGCC
CACAAGTCAATGGCACCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAACCCACAAGTCA
GTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCAC
TATTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
AAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCCTTTCAAAGCCCA
CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:608776 original size:20 final size:20
Alignment explanation
Indices: 608748--608822 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
608738 TCATACCCTG
608748 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
608768 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
608788 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
608808 ATGTATCGATACATT
1 ATGTATCGATACATT
608823 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:608815 original size:40 final size:39
Alignment explanation
Indices: 608748--608825 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
608738 TCATACCCTG
* *
608748 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
608788 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
608826 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:617129 original size:42 final size:42
Alignment explanation
Indices: 617073--618005 Score: 1038
Period size: 42 Copynumber: 22.2 Consensus size: 42
617063 TAGATGAGGC
* * * * *
617073 AGTCTTCAGGGTCAAAGTCGACAAGCAGACTGAGGGTAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
* * * * *
617115 AATCTCCAGTGTC-AAGACCGACAGGCAGGCTAAAGGAAGGAA
1 AGTCTCCAGGGTCAAAG-CCGACAGGCAGACTAAGGGAAGAAA
* * *
617157 CGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
* * * *
617199 AGTCTTCAAGGTTAAAGTCGACAGGCAGACTAAGGGAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
*
617241 AGTCTCCAGGGTCAAAGCTGACAGGCAGACTAAGGGAA-AGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGA-AA
* * * *
617283 AGTCTCCAAGGTCAAAGTCGACAGGCAGACTAAGGGAAGGAG
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
* * * *
617325 AGTTTCCAGGGTCAAAGCTGACAGGCAGACTAAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
** ** *
617367 AGTCTATAGGGTCAAAGCCGATGGGCAGACTAAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
* *
617409 AGTCTTCAGGGTCAAAGCCGATAGGCAGACTAAGGGTAAG-AA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG-AAGAAA
* * * ** *
617451 AGCCTCCAAGGTCAAATCCGGTAGGCAGACCAAGGGAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
* *
617493 AGTCTCCAAGGTCAAAGTCGACAGGCAGACTAAGGGAA-AGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGA-AA
* * * * *
617535 TGTCTCCAGGGTCAAAACCAACAAGTAGACTAAGGGAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
* *
617577 AGTCTCAAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
* * *
617619 AGTCTCAAGGGTCAAAGCCCACAGGCAGACTAAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
* * * * *
617661 AGTCTCTAAGGTCAAAGCTGACAAGTAGACTAAGGGAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
*
617703 AGTCTCCAGGGTCAAAGCCGATAGGCAGACTAAGGGTAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG-AAGAAA
* *
617746 AGTCTCCAGGGTCAAAGTCC-ACAGG-AAACT-AGAGGAAGGAA
1 AGTCTCCAGGGTCAAAG-CCGACAGGCAGACTAAG-GGAAGAAA
* * * * *
617787 AGTCTCCAAGGTCAAAGCCCACAGGCAAACTAGGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
* * *
617829 AGTCTCCAAGGTCTAAGCCGATAGGCAGACTAAGGGAA-AGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGA-AA
*
617871 AGTCTCCAGGGTCAAAGCCAACAGGCAGACTAAGGGAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
* * ** *
617913 AGTCTCCAGGGTCAAAGTCGATAAACAGACTAAAGGAA-AGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGA-AA
* * *
617955 AGTCTCAAGGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
617997 AGTCTCCAG
1 AGTCTCCAG
618006 ACGTTTAATG
Statistics
Matches: 756, Mismatches: 117, Indels: 36
0.83 0.13 0.04
Matches are distributed among these distances:
40 2 0.00
41 37 0.05
42 679 0.90
43 36 0.05
44 2 0.00
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.13
Consensus pattern (42 bp):
AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAA
Found at i:625361 original size:22 final size:23
Alignment explanation
Indices: 625336--625380 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
625326 ATTCTTAGTA
*
625336 ATTAAGCAAATATTG-ATGAATG
1 ATTAAGAAAATATTGAATGAATG
* *
625358 ATTATGAAAATGTTGAATGAATG
1 ATTAAGAAAATATTGAATGAATG
625381 CCATGAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.33
Consensus pattern (23 bp):
ATTAAGAAAATATTGAATGAATG
Found at i:638327 original size:2 final size:2
Alignment explanation
Indices: 638322--638358 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
638312 TTTTTATTTG
638322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
638359 TTCAATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:641711 original size:16 final size:17
Alignment explanation
Indices: 641685--641716 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
641675 TAATTTGAGT
641685 TATTTTAAATTTAAATC
1 TATTTTAAATTTAAATC
641702 TATTTT-AATTTAAAT
1 TATTTTAAATTTAAAT
641717 AATTTTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTAAATTTAAATC
Done.