Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 90 of 204
Found at i:28043290 original size:54 final size:54
Alignment explanation
Indices: 28043232--28043519 Score: 246
Period size: 54 Copynumber: 5.4 Consensus size: 54
28043222 TATAACAATT
*
28043232 ATTTTACCCTTCGGGGGTATTTCAGTCATTTTACCCTATGAGGGTAGTTT-GGTC
1 ATTTTACCCTTCGGGGGTATTTCAGTCATTTTACCCTATGAGGGTA-TTTCGATC
* ** * *
28043286 ATTTT-GCCTTATAGGGGTAATTCAGTCATTTTAACCTATG-GGAGTATTTCGATC
1 ATTTTACCCTT-CGGGGGTATTTCAGTCATTTTACCCTATGAGG-GTATTTCGATC
* * * * * * *
28043340 ATTCTACCCTACGGAGGTATTT-TGATCATTTTACCCT-TCAAGGGTTTTTCAATC
1 ATTTTACCCTTCGGGGGTATTTCAG-TCATTTTACCCTAT-GAGGGTATTTCGATC
* ** * * * * * *
28043394 CTTTTAGTCTTC-GGGGTATTTCGGTCATTTTAACCTTTGAAGGTATTTTGATT
1 ATTTTACCCTTCGGGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTCGATC
* * * *
28043447 ATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCCTTTGAGGGTATTTCGATT
1 ATTTTACCCTTCGGGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTCGATC
*
28043501 ATTTTACCCTTCGAGGGTA
1 ATTTTACCCTTCGGGGGTA
28043520 ATTCGATATT
Statistics
Matches: 182, Mismatches: 42, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
53 47 0.26
54 130 0.71
55 5 0.03
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (54 bp):
ATTTTACCCTTCGGGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTCGATC
Found at i:28043438 original size:80 final size:81
Alignment explanation
Indices: 28043217--28043511 Score: 233
Period size: 81 Copynumber: 3.7 Consensus size: 81
28043207 TTCATCTCCT
** * * * * * *
28043217 AAGGGTATAACAATTATTTTACCCTTCGGGGGTATTTC-AGTCATTTTACCCTATGAGGGTAGTT
1 AAGGGTATTTCAATCATTTTACCCTTCGAGGGTATTTCGA-TCATTTTAACCTTTGAAGGTATTT
* *
28043281 TGGTCATTTT-GCCTT-
65 TGATCATTTTACCCTTC
* * * * * ** *
28043296 ATAGGGGTAATTCAGTCATTTTAACCTAT-G-GGAGTATTTCGATCATTCTACCCTACGGAGGTA
1 A-A-GGGTATTTCAATCATTTTACCCT-TCGAGG-GTATTTCGATCATTTTAACCTTTGAAGGTA
28043359 TTTTGATCATTTTACCCTTC
62 TTTTGATCATTTTACCCTTC
* * ** *
28043379 AAGGGTTTTTCAATCCTTTTAGTCTTCG-GGGTATTTCGGTCATTTTAACCTTTGAAGGTATTTT
1 AAGGGTATTTCAATCATTTTACCCTTCGAGGGTATTTCGATCATTTTAACCTTTGAAGGTATTTT
* *
28043443 GATTATTTTACCCTTT
66 GATCATTTTACCCTTC
* * * * *
28043459 GAGGGTATTTCAGTCATTTTACCCTTTGAGGGTATTTCGATTATTTTACCCTT
1 AAGGGTATTTCAATCATTTTACCCTTCGAGGGTATTTCGATCATTTTAACCTT
28043512 CGAGGGTAAT
Statistics
Matches: 170, Mismatches: 37, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
79 1 0.01
80 67 0.39
81 94 0.55
82 7 0.04
83 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (81 bp):
AAGGGTATTTCAATCATTTTACCCTTCGAGGGTATTTCGATCATTTTAACCTTTGAAGGTATTTT
GATCATTTTACCCTTC
Found at i:28043530 original size:35 final size:35
Alignment explanation
Indices: 28043491--28043559 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
28043481 CCTTTGAGGG
28043491 TATTTCGATTATTTTACCCTTCGAGGGTAATTCGA
1 TATTTCGATTATTTTACCCTTCGAGGGTAATTCGA
* * *
28043526 TATTTCGGTTATTTTACCCTTCGGGGGTATTTCG
1 TATTTCGATTATTTTACCCTTCGAGGGTAATTCG
28043560 GTCATTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.45
Consensus pattern (35 bp):
TATTTCGATTATTTTACCCTTCGAGGGTAATTCGA
Found at i:28043543 original size:62 final size:62
Alignment explanation
Indices: 28043464--28043587 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
28043454 CCTTTGAGGG
* *
28043464 TATTTCAGTCATTTTACCCTTTGAGGGTATTTCGATTATTTTACCCTTCGAGGGTAATTCGA
1 TATTTCAGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTAATTCGA
* * * * * * *
28043526 TATTTCGGTTATTTTACCCTTCGGGGGTATTTCGGTCATTTTACCTTTTGAGGGTATTTCGA
1 TATTTCAGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTAATTCGA
28043588 GAGCTCTTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (62 bp):
TATTTCAGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTAATTCGA
Found at i:28064718 original size:4 final size:4
Alignment explanation
Indices: 28064709--28064769 Score: 113
Period size: 4 Copynumber: 15.2 Consensus size: 4
28064699 ATTAAATCAA
28064709 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
28064757 TATG TATA TATG T
1 TATG TATG TATG T
28064770 CTATTGTATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:28065774 original size:42 final size:42
Alignment explanation
Indices: 28065726--28065902 Score: 234
Period size: 42 Copynumber: 4.2 Consensus size: 42
28065716 GGTTTAGCGC
28065726 CTAGCAGGCTT-ATAGCCAGTGAAACAATATCAGACTTTACTT
1 CTAGCAGGCTTAAT-GCCAGTGAAACAATATCAGACTTTACTT
* *
28065768 CTAGCAGGCTTAATGCCAGTGAAATAATTTCAGACTTTACTT
1 CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACTT
* * * *
28065810 CTAGCAGGTTTAATGTCGGTGAAACAATATCAGACTTTACGT
1 CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACTT
* * *
28065852 CTAGCAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATA-TGT
1 CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACT-T
28065893 CTAGCAGGCT
1 CTAGCAGGCT
28065903 AAGTGTCGGT
Statistics
Matches: 120, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
41 22 0.18
42 96 0.80
43 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACTT
Found at i:28072326 original size:4 final size:4
Alignment explanation
Indices: 28072317--28072382 Score: 123
Period size: 4 Copynumber: 16.5 Consensus size: 4
28072307 ATCAAAATCA
*
28072317 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT TTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28072365 GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GT
28072383 CTATTGTATT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
GTAT
Found at i:28073443 original size:84 final size:83
Alignment explanation
Indices: 28073313--28073471 Score: 246
Period size: 84 Copynumber: 1.9 Consensus size: 83
28073303 CTTATTTCTA
* * * *
28073313 GTGAAACAATATTAGGCTTTACGTCTAGCAGGGTTAATGCCGGTGAAATAATTTCAGACTTTACA
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA-AATTTCAGACTATACA
28073378 TCTAGCAGGCTTAATGCTG
65 TCTAGCAGGCTTAATGCTG
* **
28073397 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATATGT
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAAATTTCAGACTATACAT
28073462 CTAGCAGGCT
66 CTAGCAGGCT
28073472 AAGTGCCGGT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
83 23 0.34
84 45 0.66
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (83 bp):
GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAAATTTCAGACTATACAT
CTAGCAGGCTTAATGCTG
Found at i:28073465 original size:41 final size:41
Alignment explanation
Indices: 28073329--28073482 Score: 211
Period size: 42 Copynumber: 3.7 Consensus size: 41
28073319 CAATATTAGG
* *
28073329 CTTTACGTCTAGCAGGGTTAATGCCGGTGAAATAATTTCAGA
1 CTTTACGTCTAGCAGGCTTAATGCCGGTGAAA-CATTTCAGA
* * *
28073371 CTTTACATCTAGCAGGCTTAATGCTGGTGAAACAATATCAGA
1 CTTTACGTCTAGCAGGCTTAATGCCGGTGAAAC-ATTTCAGA
28073413 CTTTACGTCTAGCAGGCTTAATGCCGGTGAAACATTTCAGA
1 CTTTACGTCTAGCAGGCTTAATGCCGGTGAAACATTTCAGA
* *
28073454 CTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CTTTACGTCTAGCAGGCTTAA-TGCCGGTG
28073483 CACTGAATCA
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
40 3 0.03
41 30 0.30
42 67 0.67
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (41 bp):
CTTTACGTCTAGCAGGCTTAATGCCGGTGAAACATTTCAGA
Found at i:28086245 original size:50 final size:49
Alignment explanation
Indices: 28086127--28086296 Score: 171
Period size: 50 Copynumber: 3.4 Consensus size: 49
28086117 TGCCAAAGAT
* * * * *
28086127 ATGTCCCAGACATAGTCTTACATGGGATGTT-TCTTGTACTGCCAATTCC
1 ATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATAGTGCCAATGCC
* * * *
28086176 ATATCCCAGATATTGTCTTACATGGGAGTTCTCATATAGGTGCCCATGCC
1 ATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATA-GTGCCAATGCC
** ** * *
28086226 ATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAGTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGAGTTCTCATAT-AGTGCCAATGCC
28086276 ATGTCCCAGACATGGTCTTAC
1 ATGTCCCAGACATGGTCTTAC
28086297 TTGAAACCTC
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
48 3 0.03
49 29 0.29
50 67 0.67
51 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (49 bp):
ATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGTGCCAATGCC
Found at i:28086306 original size:50 final size:54
Alignment explanation
Indices: 28086223--28086351 Score: 158
Period size: 50 Copynumber: 2.4 Consensus size: 54
28086213 AGGTGCCCAT
**
28086223 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTC-ATCTC-A-G-TGCCAAC
1 GCCATGTCCCAGACATGGTCTTACGGGAAACCTCTCAATCTCAATGATGCCAAC
** *
28086273 GCCATGTCCCAGACATGGTCTTACTTGAAACCTCTCATAATCTCAATGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACGGGAAACCTCTC--AATCTCAATGATGCCAAC
*
28086329 GCCATGTGCCAGACATGGTCTTA
1 GCCATGTCCCAGACATGGTCTTA
28086352 TATGAGATCT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
50 32 0.48
53 5 0.07
54 1 0.01
55 1 0.01
56 28 0.42
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (54 bp):
GCCATGTCCCAGACATGGTCTTACGGGAAACCTCTCAATCTCAATGATGCCAAC
Found at i:28104674 original size:25 final size:25
Alignment explanation
Indices: 28104612--28104723 Score: 86
Period size: 25 Copynumber: 4.5 Consensus size: 25
28104602 ACACACCACG
**
28104612 GCTCGTATGAGCTTACCGATTTGTA
1 GCTCGTATGAGCTTACCGATTTACA
* *
28104637 ACTCGTGA-AAGCTTACCGATTCT-CA
1 GCTCGT-ATGAGCTTACCGATT-TACA
*
28104662 GCTCGTATGAGCTTACTGATTTACA
1 GCTCGTATGAGCTTACCGATTTACA
* * * * *
28104687 ACTCGTGA-GAGCATACTGATTCATA
1 GCTCGT-ATGAGCTTACCGATTTACA
28104712 GCTCGTATGAGC
1 GCTCGTATGAGC
28104724 ATACATGTAC
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
24 3 0.04
25 64 0.91
26 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (25 bp):
GCTCGTATGAGCTTACCGATTTACA
Found at i:28104690 original size:50 final size:50
Alignment explanation
Indices: 28104612--28104723 Score: 154
Period size: 50 Copynumber: 2.2 Consensus size: 50
28104602 ACACACCACG
** *
28104612 GCTCGTATGAGCTTACCGATTTGTAACTCGTGAAAGCTTACCGATTC-TCA
1 GCTCGTATGAGCTTACCGATTTACAACTCGTGAAAGCATACCGATTCAT-A
* * *
28104662 GCTCGTATGAGCTTACTGATTTACAACTCGTGAGAGCATACTGATTCATA
1 GCTCGTATGAGCTTACCGATTTACAACTCGTGAAAGCATACCGATTCATA
28104712 GCTCGTATGAGC
1 GCTCGTATGAGC
28104724 ATACATGTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 54 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (50 bp):
GCTCGTATGAGCTTACCGATTTACAACTCGTGAAAGCATACCGATTCATA
Found at i:28104724 original size:25 final size:25
Alignment explanation
Indices: 28104654--28104727 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
28104644 AAAGCTTACC
* *
28104654 GATTCTCAGCTCGTATGAGCTTACT
1 GATTCACAGCTCGTATGAGCATACT
* *
28104679 GATTTACAACTCGTGA-GAGCATACT
1 GATTCACAGCTCGT-ATGAGCATACT
*
28104704 GATTCATAGCTCGTATGAGCATAC
1 GATTCACAGCTCGTATGAGCATAC
28104728 ATGTACAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.03
25 38 0.95
26 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (25 bp):
GATTCACAGCTCGTATGAGCATACT
Found at i:28106320 original size:51 final size:51
Alignment explanation
Indices: 28106255--28106424 Score: 186
Period size: 51 Copynumber: 3.4 Consensus size: 51
28106245 ACACAGACTG
* * * *
28106255 TGTGTAGGCCACTATGTG-AAAGTAAAAGTGATGGTCACGTGTGTAGTACTA
1 TGTGCAGGCTACTATGTGTAACG-AATAGTGATGGTCACGTGTGTAGTACTA
* * *
28106306 TGTGCAGGCTACTATGTGTACCGGATAGCT--TCGATCACGTGTGTAGTACTA
1 TGTGCAGGCTACTATGTGTAACGAATAG-TGAT-GGTCACGTGTGTAGTACTA
* * *
28106357 TGTGCAGGCTACTACGTGTATCGAATAGTGATGGTCA-ATGTGTAGTACTA
1 TGTGCAGGCTACTATGTGTAACGAATAGTGATGGTCACGTGTGTAGTACTA
*
28106407 TGTGTAGGCTACTATGTG
1 TGTGCAGGCTACTATGTG
28106425 AACCAGTATC
Statistics
Matches: 100, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
50 30 0.30
51 66 0.66
52 4 0.04
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.32
Consensus pattern (51 bp):
TGTGCAGGCTACTATGTGTAACGAATAGTGATGGTCACGTGTGTAGTACTA
Found at i:28106420 original size:50 final size:51
Alignment explanation
Indices: 28106281--28106420 Score: 187
Period size: 51 Copynumber: 2.8 Consensus size: 51
28106271 TGAAAGTAAA
* *
28106281 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAT
1 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT
* *
28106332 AGCT--TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAT
1 AG-TGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT
* *
28106383 AGTGATGGTCA-ATGTGTAGTACTATGTGTAGGCTACTA
1 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTA
28106421 TGTGAACCAG
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
50 27 0.35
51 49 0.63
52 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (51 bp):
AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT
Found at i:28106667 original size:38 final size:37
Alignment explanation
Indices: 28106625--28106697 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
28106615 ATGTGTGGTA
* *
28106625 TTGAATTGAATATTGACTTGAAAATGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TTGAAAATGAAAAAGTGAATT
*
28106663 TTGAATTGAATAGTGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTGAAAATGAAAAAGTGAA
28106698 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 17 0.53
38 15 0.47
ACGTcount: A:0.44, C:0.01, G:0.23, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTGAAAATGAAAAAGTGAATT
Found at i:28110110 original size:50 final size:50
Alignment explanation
Indices: 28109986--28110218 Score: 270
Period size: 50 Copynumber: 4.7 Consensus size: 50
28109976 GAATATAACA
* * * * ** * * * *
28109986 TGCCAAAGCTATGTCCCAGATATAGTCTTACATGGGATGTTTCTTGT-AC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * ** * *
28110035 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
28110085 TGCCCATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * *
28110135 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
28110185 TGCCAATGTCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
28110219 AGATCTCATT
Statistics
Matches: 159, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 38 0.24
50 121 0.76
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:28127776 original size:25 final size:25
Alignment explanation
Indices: 28127713--28127779 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
28127703 GGATACACCA
28127713 CAGCTCGTATGAGCTTACCGATTTG
1 CAGCTCGTATGAGCTTACCGATTTG
** * *
28127738 TGGCTCATGA-GAGCTTACTGATTCT-
1 CAGCTCGT-ATGAGCTTACCGATT-TG
28127763 CAGCTCGTATGAGCTTA
1 CAGCTCGTATGAGCTTA
28127780 TCAATTTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
24 1 0.03
25 29 0.91
26 2 0.06
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACCGATTTG
Found at i:28127794 original size:50 final size:51
Alignment explanation
Indices: 28127713--28127826 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 51
28127703 GGATACACCA
* * * * *
28127713 CAGCTCGTATGAGCTTACCGATTTGTGGCTCATGAGAGCTTACTGATTC-T
1 CAGCTCGTATGAGCTTACCAATTTATAGCTCATAAGAGCATACTGATTCAT
*
28127763 CAGCTCGTATGAGCTTATCAATTTATAGCTCATAAGAGCATACTGATTCAT
1 CAGCTCGTATGAGCTTACCAATTTATAGCTCATAAGAGCATACTGATTCAT
*
28127814 -AGCTTGTATGAGC
1 CAGCTCGTATGAGC
28127827 ATACATGTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 55 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (51 bp):
CAGCTCGTATGAGCTTACCAATTTATAGCTCATAAGAGCATACTGATTCAT
Found at i:28142796 original size:3 final size:3
Alignment explanation
Indices: 28142788--28142830 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
28142778 ACCTCCAGTC
28142788 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28142831 CAACAACAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28142835 original size:3 final size:3
Alignment explanation
Indices: 28142829--28142862 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
28142819 TAATAATAAT
* *
28142829 AAC AAC AAC AAC AAC AAC AAT AAT AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
28142863 GATGGAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.06
Consensus pattern (3 bp):
AAC
Found at i:28142871 original size:18 final size:15
Alignment explanation
Indices: 28142788--28142862 Score: 60
Period size: 15 Copynumber: 5.0 Consensus size: 15
28142778 ACCTCCAGTC
* * *
28142788 ATAATAATAATAATA
1 ATAATAACAACAACA
* * *
28142803 ATAATAATAATAATA
1 ATAATAACAACAACA
* *
28142818 ATAATAATAATAACA
1 ATAATAACAACAACA
* *
28142833 ACAACAACAACAACA
1 ATAATAACAACAACA
28142848 ATAATAACAACAACA
1 ATAATAACAACAACA
28142863 GATGGAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAATAACAACAACA
Found at i:28143938 original size:18 final size:18
Alignment explanation
Indices: 28143915--28143950 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28143905 AAACAAACCA
28143915 TTTGGTCATGGTGAACAT
1 TTTGGTCATGGTGAACAT
28143933 TTTGGTCATGGTGAACAT
1 TTTGGTCATGGTGAACAT
28143951 GTTGAGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (18 bp):
TTTGGTCATGGTGAACAT
Found at i:28148039 original size:20 final size:20
Alignment explanation
Indices: 28148006--28148059 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
28147996 ATACCAACTA
* **
28148006 AAAAATATAAATACTTTTGC
1 AAAAATATAGATACTCATGC
* *
28148026 AAAAATATCGATACTCATGT
1 AAAAATATAGATACTCATGC
*
28148046 AAAAATATTGATAC
1 AAAAATATAGATAC
28148060 CACGAGGCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAAATATAGATACTCATGC
Found at i:28153741 original size:50 final size:50
Alignment explanation
Indices: 28153680--28153821 Score: 230
Period size: 50 Copynumber: 2.8 Consensus size: 50
28153670 GATAATAACA
* *
28153680 TGCCAAAGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
28153730 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
28153780 TGCCAACGCCATGTCCCAAACATGGTCTTACACGGGAACTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
28153822 TTACCCAAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 86 1.00
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.23
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:28158269 original size:24 final size:24
Alignment explanation
Indices: 28158237--28158290 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
28158227 TTTTTCTTCA
*
28158237 GTTTCTCGATCTAAATCAACCTCG
1 GTTTCTCGAACTAAATCAACCTCG
28158261 GTTTCTCGAACTAAATCAACCTCG
1 GTTTCTCGAACTAAATCAACCTCG
28158285 GTTTCT
1 GTTTCT
28158291 TCAGTTAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (24 bp):
GTTTCTCGAACTAAATCAACCTCG
Found at i:28163001 original size:19 final size:19
Alignment explanation
Indices: 28162973--28163010 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28162963 CAACAATCAC
28162973 AAAAACATAAAAATTACAA
1 AAAAACATAAAAATTACAA
*
28162992 AAAAATATAAAAATTACAA
1 AAAAACATAAAAATTACAA
28163011 GAAGCAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAACATAAAAATTACAA
Found at i:28165686 original size:27 final size:26
Alignment explanation
Indices: 28165669--28165738 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
28165659 ATATTAAGTC
28165669 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
28165696 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
28165724 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
28165739 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:28165732 original size:28 final size:28
Alignment explanation
Indices: 28165669--28165766 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
28165659 ATATTAAGTC
*
28165669 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
28165696 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
28165724 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
28165753 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28165767 CGAGATCAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28166184 original size:2 final size:2
Alignment explanation
Indices: 28166177--28166206 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28166167 CATACTTATG
*
28166177 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28166207 CTTCGGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28166192 original size:14 final size:14
Alignment explanation
Indices: 28166173--28166203 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28166163 TGGGCATACT
28166173 TATGTATATATATA
1 TATGTATATATATA
28166187 TATGTATATATATA
1 TATGTATATATATA
28166201 TAT
1 TAT
28166204 ATACTTCGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:28173607 original size:27 final size:26
Alignment explanation
Indices: 28173590--28173659 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
28173580 ATATTAAGTC
28173590 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
28173617 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
28173645 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
28173660 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:28173653 original size:28 final size:28
Alignment explanation
Indices: 28173590--28173687 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
28173580 ATATTAAGTC
*
28173590 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
28173617 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
28173645 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
28173674 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28173688 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28174151 original size:12 final size:12
Alignment explanation
Indices: 28174134--28174160 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28174124 TGGGCATACT
28174134 TATGTATATATA
1 TATGTATATATA
28174146 TATGTATATATA
1 TATGTATATATA
28174158 TAT
1 TAT
28174161 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:28185751 original size:14 final size:15
Alignment explanation
Indices: 28185729--28185757 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28185719 TTTTAATGTG
28185729 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
28185744 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
28185758 AGTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:28186960 original size:43 final size:42
Alignment explanation
Indices: 28186898--28187022 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 42
28186888 GATTTCTGAG
28186898 ATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCATCGACT
1 ATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-T
** *
28186942 -TGTGTTTACGTGTAAGACCTTGTCTGGGACAG-TAGCATCGAT
1 ATGTG-TTACGTGTAAGACCACGTCTGGGAC-GTTGGCATCGAT
* *
28186984 ACGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCAT
28187023 TGTAAGAGTT
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
42 2 0.03
43 62 0.91
44 4 0.06
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (42 bp):
ATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
Found at i:28187891 original size:23 final size:23
Alignment explanation
Indices: 28187864--28187936 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
28187854 ATGAGTTGAA
*
28187864 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTGCATATATGCTGT
* * *
28187887 CCAATTTTGATGCTTACATGCTG-
1 CCAA-TTTGTTGCATATATGCTGT
28187910 CCTAATTTGTTGCATATATGCTGT
1 CC-AATTTGTTGCATATATGCTGT
28187934 CCA
1 CCA
28187937 GTTTTGGTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
23 22 0.55
24 18 0.45
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (23 bp):
CCAATTTGTTGCATATATGCTGT
Found at i:28188007 original size:23 final size:23
Alignment explanation
Indices: 28187967--28188010 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28187957 CTCAAACTGT
28187967 TGTATATATGCTACCCAAATTGA
1 TGTATATATGCTACCCAAATTGA
* **
28187990 TGTATTTATGCTGTCCAAATT
1 TGTATATATGCTACCCAAATT
28188011 TTGGTGTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (23 bp):
TGTATATATGCTACCCAAATTGA
Found at i:28188028 original size:25 final size:24
Alignment explanation
Indices: 28187997--28188058 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 24
28187987 TGATGTATTT
*
28187997 ATGCTGTCCAAATTTTGGTGTGA-AA
1 ATGCTGT-CAAATTTTGGTAT-ATAA
*
28188022 ATGCTGTCTAA-TTTGGTATATAA
1 ATGCTGTCAAATTTTGGTATATAA
28188045 ATGCTGTTCAAATT
1 ATGCTG-TCAAATT
28188059 GATGTATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.03
23 15 0.48
24 7 0.23
25 8 0.26
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (24 bp):
ATGCTGTCAAATTTTGGTATATAA
Found at i:28188066 original size:23 final size:23
Alignment explanation
Indices: 28187982--28188068 Score: 61
Period size: 23 Copynumber: 3.7 Consensus size: 23
28187972 ATATGCTACC
** *
28187982 CAAATTGATGTATTTATGCTGTC
1 CAAATTGATGTATAAATGCTGTT
*
28188005 CAAATTTTGGTGTGA-AAATGCTG-T
1 CAAA--TTGATGT-ATAAATGCTGTT
* * *
28188029 CTAATTTGGTATATAAATGCTGTT
1 C-AAATTGATGTATAAATGCTGTT
28188053 CAAATTGATGTATAAA
1 CAAATTGATGTATAAA
28188069 AGCTATCCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
22 1 0.02
23 30 0.61
24 3 0.06
25 14 0.29
26 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (23 bp):
CAAATTGATGTATAAATGCTGTT
Found at i:28189669 original size:75 final size:75
Alignment explanation
Indices: 28189546--28189696 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
28189536 TCCTTGTTGG
* *
28189546 AGGAGCATGCTTTCTAAAACCCATGTGGAAGTGTGAGGAAGGAAAATGCAAGAGGTCTTCCGATA
1 AGGAGCATGCTTTATAAAACCCATGTGGAAGTGTGAGGAAGGAAAATGCAAGAGGTCTTCCAATA
28189611 TAATCAAGTA
66 TAATCAAGTA
28189621 AGGAGCATGCTTTATAAAACCCATGTGGAAGTGTGAGGAAGGAAAATGCAAGAGGTCTTCCAATA
1 AGGAGCATGCTTTATAAAACCCATGTGGAAGTGTGAGGAAGGAAAATGCAAGAGGTCTTCCAATA
28189686 TAATCAAGTA
66 TAATCAAGTA
28189696 A
1 A
28189697 TTCATGTTGC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.23
Consensus pattern (75 bp):
AGGAGCATGCTTTATAAAACCCATGTGGAAGTGTGAGGAAGGAAAATGCAAGAGGTCTTCCAATA
TAATCAAGTA
Found at i:28193481 original size:17 final size:16
Alignment explanation
Indices: 28193451--28193499 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
28193441 GGTTTTTGGA
28193451 TTTTAGGG-TTTAGAG
1 TTTTAGGGTTTTAGAG
*
28193466 TTTTAGGGTTTTTAGAAT
1 TTTTAGGG-TTTTAG-AG
28193484 TTTTAGGGTTTTAGAG
1 TTTTAGGGTTTTAGAG
28193500 AAAAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 8 0.28
16 1 0.03
17 11 0.38
18 9 0.31
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (16 bp):
TTTTAGGGTTTTAGAG
Found at i:28198894 original size:50 final size:50
Alignment explanation
Indices: 28198767--28199007 Score: 240
Period size: 50 Copynumber: 4.9 Consensus size: 50
28198757 GATAATAACA
* * *
28198767 TGCCAAAGCCATGTCCC-GACATGGTCTTACATGGGA--TGTT-TC-CTGTAC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTC-G--G
* * * ** * *
28198815 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTTATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * ** * *
28198865 TGCCCATGCCATGTCCTGGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
** * *
28198915 TGCCAACGTTATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
28198965 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
28199008 TACCCAACAT
Statistics
Matches: 157, Mismatches: 31, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
48 15 0.10
49 18 0.11
50 119 0.76
51 3 0.02
52 2 0.01
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
Found at i:28206127 original size:12 final size:12
Alignment explanation
Indices: 28206112--28206136 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28206102 ACGCCATGAA
28206112 CCCAGGTTATCC
1 CCCAGGTTATCC
28206124 CCCAGGTTATCC
1 CCCAGGTTATCC
28206136 C
1 C
28206137 ATAAAGTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.44, G:0.16, T:0.24
Consensus pattern (12 bp):
CCCAGGTTATCC
Found at i:28209262 original size:41 final size:41
Alignment explanation
Indices: 28209206--28209336 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
28209196 TGATTCGGTA
* * *
28209206 CACCGGCTTTTAGCCTGCTAGACTTATAGTCCG-A-AATGTAT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAAT-T-T
*
28209247 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATAATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAATTT
* * * * *
28209288 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAATTT
*
28209329 CACTGGCA
1 CACCGGCA
28209337 ATAAATCAGA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
41 74 0.94
42 2 0.03
43 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAATTT
Found at i:28210991 original size:25 final size:25
Alignment explanation
Indices: 28210946--28210994 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28210936 TATTTGTTTA
*
28210946 ATTATAATATTATAATATAATATAT
1 ATTATAACATTATAATATAATATAT
28210971 ATTATAACATTTATAAT-TAATATA
1 ATTATAACA-TTATAATATAATATA
28210995 AAAACTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATAACATTATAATATAATATAT
Found at i:28213517 original size:19 final size:19
Alignment explanation
Indices: 28213479--28213518 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28213469 GTGCATATTG
*
28213479 GCGTACAAAATGCATTCTA
1 GCGTACAAAATGCATACTA
* *
28213498 GCGTACAAAGTGCGTACTA
1 GCGTACAAAATGCATACTA
28213517 GC
1 GC
28213519 ATGTAAAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.23
Consensus pattern (19 bp):
GCGTACAAAATGCATACTA
Found at i:28225989 original size:23 final size:21
Alignment explanation
Indices: 28225947--28225987 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
28225937 AAAGAAAGAA
28225947 AAGAAAATAAATAAATAAATC
1 AAGAAAATAAATAAATAAATC
28225968 AAGAGAAATAAA-ATAATAAA
1 AAGA-AAATAAATA-AATAAA
28225988 ATAAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (21 bp):
AAGAAAATAAATAAATAAATC
Found at i:28229584 original size:99 final size:99
Alignment explanation
Indices: 28229410--28229605 Score: 304
Period size: 99 Copynumber: 2.0 Consensus size: 99
28229400 TCTCAAGCAG
28229410 GTAATCAATACAAATTGGAATGAAATGAGCTGACTTAGTCAGTCAGTCAACAATAACCCAGATCG
1 GTAATCAATACAAATTGGAATGAAATGAGCTGACTTAGTCAGTCAGTCAACAATAACCCAGATCG
** * *
28229475 AGTCTTTCTTTCTCAGTGTCATTGGAAGTCCCTA
66 AGTCCATCTTTATCAGTGCCATTGGAAGTCCCTA
* * * *
28229509 GTAATCAGTACAAATTGGAATGAAATGAGTTGACTTAGTTAGT-AGGTCAATAATAACCCAGATC
1 GTAATCAATACAAATTGGAATGAAATGAGCTGACTTAGTCAGTCA-GTCAACAATAACCCAGATC
28229573 GAGTCCATCTTTATCAGTGCCATTGGAAGTCCC
65 GAGTCCATCTTTATCAGTGCCATTGGAAGTCCC
28229606 ATTACAACAT
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 1 0.01
99 87 0.99
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (99 bp):
GTAATCAATACAAATTGGAATGAAATGAGCTGACTTAGTCAGTCAGTCAACAATAACCCAGATCG
AGTCCATCTTTATCAGTGCCATTGGAAGTCCCTA
Found at i:28235192 original size:37 final size:37
Alignment explanation
Indices: 28235133--28235237 Score: 104
Period size: 37 Copynumber: 2.8 Consensus size: 37
28235123 AATTAAACAT
** * * *
28235133 CATTCATTATAACAGTAAGATTTGTTC-AGTTAAGCTC
1 CATTCATTATAATGGTATGATTTGGTCGA-TTAAGATC
* * *
28235170 CATTCAATATAATGGTATGATTTGGTCGATTGAGATT
1 CATTCATTATAATGGTATGATTTGGTCGATTAAGATC
*
28235207 CATTCATTATAATGATATGATTTGGCTCGAT
1 CATTCATTATAATGGTATGATTTGG-TCGAT
28235238 AAAGCGTACT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
37 50 0.89
38 6 0.11
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (37 bp):
CATTCATTATAATGGTATGATTTGGTCGATTAAGATC
Found at i:28256563 original size:120 final size:120
Alignment explanation
Indices: 28256331--28256589 Score: 296
Period size: 120 Copynumber: 2.2 Consensus size: 120
28256321 TTGAATGATG
* * *
28256331 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
**
28256396 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CTAAA
66 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TAGCTAAA
* * **
28256451 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCGAGGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
28256514 TTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGTAGCTATA
64 TTGTACGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGCTAAA
* *
28256571 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28256590 TACGTGATTT
Statistics
Matches: 119, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
119 18 0.15
120 91 0.76
121 10 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTAAA
Found at i:28256570 original size:40 final size:40
Alignment explanation
Indices: 28256331--28256556 Score: 298
Period size: 40 Copynumber: 5.7 Consensus size: 40
28256321 TTGAATGATG
* * * *
28256331 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* *
28256371 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28256411 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28256451 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28256491 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28256532 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28256557 AACGAGTAGC
Statistics
Matches: 171, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.01
40 160 0.94
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28265784 original size:16 final size:16
Alignment explanation
Indices: 28265763--28265793 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28265753 GGACTTTGAT
28265763 ACAAACTTGTAATGCC
1 ACAAACTTGTAATGCC
28265779 ACAAACTTGTAATGC
1 ACAAACTTGTAATGC
28265794 TTAACTATTA
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:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (16 bp):
ACAAACTTGTAATGCC
Found at i:28267279 original size:133 final size:132
Alignment explanation
Indices: 28267027--28267292 Score: 523
Period size: 133 Copynumber: 2.0 Consensus size: 132
28267017 TGTAAATGCA
28267027 ATGGTTTAATATGATGTCAATTCATGAATAAGTCTACCTAGGTTACATAAGGCTTTTCGATTTGT
1 ATGGTTTAATATGATGTCAATTCATGAATAAGTCTACCTAGGTTACATAAGGCTTTTCGATTTGT
28267092 AACATTCTGAGGCTTAAGACAAGTATGGAGTTCAAGAACAATAAGCATCAAAACAGTTTCAAGCA
66 AACATTCTGAGGCTTAAGACAAGTATGGAGTTCAAGAACAATAAGCATCAAAACAGTTTCAAGCA
28267157 CG
131 CG
28267159 ATGGTTTAATATGATTGTCAATTCATGAATAAGTCTACCTAGGTTACATAAGGCTTTTCGATTTG
1 ATGGTTTAATATGA-TGTCAATTCATGAATAAGTCTACCTAGGTTACATAAGGCTTTTCGATTTG
28267224 TAACATTCTGAGGCTTAAGACAAGTATGGAGTTCAAGAACAATAAGCATCAAAACAGTTTCAAGC
65 TAACATTCTGAGGCTTAAGACAAGTATGGAGTTCAAGAACAATAAGCATCAAAACAGTTTCAAGC
28267289 ACG
130 ACG
28267292 A
1 A
28267293 AAATAGTTTG
Statistics
Matches: 133, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
132 14 0.11
133 119 0.89
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (132 bp):
ATGGTTTAATATGATGTCAATTCATGAATAAGTCTACCTAGGTTACATAAGGCTTTTCGATTTGT
AACATTCTGAGGCTTAAGACAAGTATGGAGTTCAAGAACAATAAGCATCAAAACAGTTTCAAGCA
CG
Found at i:28270149 original size:22 final size:22
Alignment explanation
Indices: 28270108--28270149 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28270098 AATAGTTAAA
*
28270108 AGGGTTTTGATATTTTAAATGG
1 AGGGTTTTGATATTTAAAATGG
* *
28270130 AGGGTTTTTATGTTTAAAAT
1 AGGGTTTTGATATTTAAAAT
28270150 TAGTTAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (22 bp):
AGGGTTTTGATATTTAAAATGG
Found at i:28285941 original size:50 final size:50
Alignment explanation
Indices: 28285830--28286027 Score: 164
Period size: 50 Copynumber: 3.8 Consensus size: 50
28285820 ATTTGGGTAA
* * * *
28285830 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGAATTGGCA-C--CGAG---ATG
*
28285886 AGAGGTCCCATGTAAGACCATGTCTGAGAAATGGAATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGAATTGGCACCGAGATG
** * * * *
28285936 AGAGGTCCCCCGTAAGACCATGTCTCAGACAT-AACATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGA-ATTGGCACCGAGATG
*** * * * *
28285986 AGAACCCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGAATTGGCA
28286028 GTACAAGAAA
Statistics
Matches: 116, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
49 1 0.01
50 73 0.63
53 3 0.03
55 1 0.01
56 38 0.33
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGAGACATGGAATTGGCACCGAGATG
Found at i:28298145 original size:24 final size:20
Alignment explanation
Indices: 28298114--28298162 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 20
28298104 TGAGGGGTGT
*
28298114 GGGGAAGTGTGAGAGTGAATTTA
1 GGGGAAGTG-GA-AG-GAAATTA
28298137 GGGGTAAGTGGAAGGAAATTA
1 GGGG-AAGTGGAAGGAAATTA
28298158 GGGGA
1 GGGGA
28298163 TTATGGGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
22 2 0.08
23 6 0.25
24 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.47, T:0.20
Consensus pattern (20 bp):
GGGGAAGTGGAAGGAAATTA
Found at i:28309600 original size:101 final size:102
Alignment explanation
Indices: 28309485--28309669 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 102
28309475 AAAGTGATGG
* * * * *
28309485 TCACATGTGTAGTACTATGTGCATGCTACTACGTGTGCCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACATGTATAGTACTATGTGCAGGATACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
*
28309548 ACTATGTGTAGGCTACTATGCGTACCGGATAACTTCAA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAACTTCAA
* * *
28309586 TCACGTGTATAGTACTATGTGCAGGATACTACGTGTATCAGATAGTGATTGTCACATGTGTAGTA
1 TCACATGTATAGTACTATGTGCAGGATACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
28309651 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
28309670 TGAATCGGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
101 36 0.49
102 33 0.45
103 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (102 bp):
TCACATGTATAGTACTATGTGCAGGATACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAACTTCAA
Found at i:28309650 original size:51 final size:50
Alignment explanation
Indices: 28309479--28309667 Score: 191
Period size: 51 Copynumber: 3.7 Consensus size: 50
28309469 AAAGTGAAAG
* *
28309479 TGATGGTCACATGTGTAGTACTATGTGCATGCTACTACGTGTGCCAGA-A
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA
* * * * *
28309528 TGATAGGTCGCATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATA
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA
*** ** * * * *
28309579 ACTTCAATCACGTGTATAGTACTATGTGCAGGATACTACGTGTATCAGATA
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA
*
28309630 GTGATTGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 -TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
28309668 TGTGAATCGG
Statistics
Matches: 107, Mismatches: 30, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
49 4 0.04
50 37 0.35
51 65 0.61
52 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (50 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA
Found at i:28312706 original size:12 final size:11
Alignment explanation
Indices: 28312679--28312707 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28312669 TTAGCTTTAG
28312679 TTTCTCTAAGT
1 TTTCTCTAAGT
28312690 TTTCTCTAAGT
1 TTTCTCTAAGT
28312701 TTT-TCTA
1 TTTCTCTA
28312708 CAACTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (11 bp):
TTTCTCTAAGT
Found at i:28323296 original size:23 final size:23
Alignment explanation
Indices: 28323261--28323315 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
28323251 CTTGTTTTAT
* *
28323261 TGTTGTTTCGCAACTGTTTATTG
1 TGTTATTTCGCAACTGTTTATTA
* * *
28323284 TGTTATTTTGCAATTTTTTATTA
1 TGTTATTTCGCAACTGTTTATTA
*
28323307 TGTTGTTTC
1 TGTTATTTC
28323316 ACTGTAGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.15, C:0.09, G:0.16, T:0.60
Consensus pattern (23 bp):
TGTTATTTCGCAACTGTTTATTA
Found at i:28324961 original size:26 final size:26
Alignment explanation
Indices: 28324920--28324995 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
28324910 ACATATTTTC
* *
28324920 TCAAAATTTTACTAGGGTTAAAATCG
1 TCAAAATTTTACTAGGGGTAAAATCA
* * *
28324946 TTAAAATCTTATTAGGGGTAAAATCA
1 TCAAAATTTTACTAGGGGTAAAATCA
28324972 TCAAAATTTTACTAGGGGTAAAAT
1 TCAAAATTTTACTAGGGGTAAAAT
28324996 AGAGATGAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGTAAAATCA
Found at i:28326445 original size:22 final size:22
Alignment explanation
Indices: 28326420--28326464 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28326410 TAATGCTTAG
28326420 TAAGTTCATAAATCATAAACAA
1 TAAGTTCATAAATCATAAACAA
28326442 TAAGTTCATAAATCATAAACAA
1 TAAGTTCATAAATCATAAACAA
28326464 T
1 T
28326465 GCTTACCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (22 bp):
TAAGTTCATAAATCATAAACAA
Found at i:28329584 original size:24 final size:25
Alignment explanation
Indices: 28329547--28329613 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
28329537 TACCGATATT
* * *
28329547 CAGCTCATATGAGCTTACCG-TTTA
1 CAGCTCGTATGAGCATACCGATTCA
*
28329571 CAGCTCGTAAGAGCATACCGATTCA
1 CAGCTCGTATGAGCATACCGATTCA
*
28329596 GAGCTCGTATGAGCATAC
1 CAGCTCGTATGAGCATAC
28329614 ATGTACAGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 17 0.47
25 19 0.53
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (25 bp):
CAGCTCGTATGAGCATACCGATTCA
Found at i:28334986 original size:6 final size:6
Alignment explanation
Indices: 28334977--28335001 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28334967 AATAATAAAG
28334977 TTATAT TTATAT TTATAT TTATAT T
1 TTATAT TTATAT TTATAT TTATAT T
28335002 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:28337228 original size:30 final size:30
Alignment explanation
Indices: 28337178--28337237 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
28337168 GCGAGAAGAA
28337178 GCCATGGTTGCCAAAGAGCAAG-TGCATGGC
1 GCCATGGTTGCCAAAGAGCAAGCT-CATGGC
*
28337208 GCCATGGTTGCTGAAA-AGCAAGCTCATGGC
1 GCCATGGTTGC-CAAAGAGCAAGCTCATGGC
28337238 AAGGCTCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.27, C:0.23, G:0.32, T:0.18
Consensus pattern (30 bp):
GCCATGGTTGCCAAAGAGCAAGCTCATGGC
Found at i:28337654 original size:18 final size:18
Alignment explanation
Indices: 28337613--28337654 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
28337603 GAATTTTGGA
*
28337613 ATTTTTATAAATATTTTG
1 ATTTTTATAAATATATTG
*
28337631 AATTTTA-AAATTATATTG
1 ATTTTTATAAA-TATATTG
28337649 ATTTTT
1 ATTTTT
28337655 TTTTTTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTTTTATAAATATATTG
Found at i:28343171 original size:20 final size:20
Alignment explanation
Indices: 28343130--28343183 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
28343120 AATTAGATTT
* **
28343130 ATTTAAAATAAAAATATTAA
1 ATTTAAATTAAAAATAGAAA
28343150 ATTTAAATTAAAAATAGAAA
1 ATTTAAATTAAAAATAGAAA
28343170 ATTATAATATTAAA
1 ATT-TAA-ATTAAA
28343184 TATTTCAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 20 0.69
21 3 0.10
22 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTTAAATTAAAAATAGAAA
Found at i:28343352 original size:19 final size:19
Alignment explanation
Indices: 28343305--28343352 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
28343295 TATTATATTG
*
28343305 ATTTAAAATATATAAAATC
1 ATTTAAAATATATAAAATA
* *
28343324 ATATATAATATA-AAAATAA
1 ATTTAAAATATATAAAAT-A
28343343 ATTTAAAATA
1 ATTTAAAATA
28343353 ATTTTTTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTTAAAATATATAAAATA
Found at i:28343664 original size:22 final size:19
Alignment explanation
Indices: 28343639--28343692 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 19
28343629 TTTCTTCTAG
28343639 ATTTTATATATATAGTTTCTGA
1 ATTTTATATATATA-TTT-T-A
* *
28343661 ATTTTATATATTTATTTTC
1 ATTTTATATATATATTTTA
28343680 ATTTTATATATAT
1 ATTTTATATATAT
28343693 TTTAATATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 12 0.41
20 1 0.03
21 3 0.10
22 13 0.45
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (19 bp):
ATTTTATATATATATTTTA
Found at i:28343693 original size:17 final size:18
Alignment explanation
Indices: 28343661--28343695 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28343651 TAGTTTCTGA
28343661 ATTTTATATATTTATTTTC
1 ATTTTATATA-TTATTTTC
28343680 ATTTTATATA-TATTTT
1 ATTTTATATATTATTTT
28343696 AATATTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTATATATTATTTTC
Found at i:28344716 original size:5 final size:6
Alignment explanation
Indices: 28344694--28344724 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28344684 CCCCCACCGT
*
28344694 TCCCCT TCCCCC TCCCCC TCCCCC TCCCCC T
1 TCCCCC TCCCCC TCCCCC TCCCCC TCCCCC T
28344725 ACCGTCGGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.77, G:0.00, T:0.23
Consensus pattern (6 bp):
TCCCCC
Found at i:28345279 original size:6 final size:6
Alignment explanation
Indices: 28345268--28345297 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
28345258 TCGACCAAAA
28345268 AAATTT AAATTT AAATTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT
28345298 TCTTATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:28345574 original size:19 final size:19
Alignment explanation
Indices: 28345547--28345628 Score: 74
Period size: 19 Copynumber: 4.0 Consensus size: 19
28345537 TCCTCTCATC
*
28345547 GCTGGTTCTTTGTTCCTCT
1 GCTGCTTCTTTGTTCCTCT
*
28345566 GCTGCTTCTTTGATCCTCT
1 GCTGCTTCTTTGTTCCTCT
28345585 GCTAGTGCTGGTTCTTTGTTCCTCT
1 GC---TGC---TTCTTTGTTCCTCT
* *
28345610 GCTGGTGCTTTGTTCCTCT
1 GCTGCTTCTTTGTTCCTCT
28345629 TCTCCACCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
19 32 0.62
22 5 0.10
25 15 0.29
ACGTcount: A:0.02, C:0.27, G:0.22, T:0.49
Consensus pattern (19 bp):
GCTGCTTCTTTGTTCCTCT
Found at i:28345599 original size:25 final size:25
Alignment explanation
Indices: 28345565--28345618 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
28345555 TTTGTTCCTC
28345565 TGCTGCTTCTTTGATCCTCTGCTAG
1 TGCTGCTTCTTTGATCCTCTGCTAG
* * *
28345590 TGCTGGTTCTTTGTTCCTCTGCTGG
1 TGCTGCTTCTTTGATCCTCTGCTAG
28345615 TGCT
1 TGCT
28345619 TTGTTCCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.04, C:0.26, G:0.24, T:0.46
Consensus pattern (25 bp):
TGCTGCTTCTTTGATCCTCTGCTAG
Found at i:28348544 original size:18 final size:18
Alignment explanation
Indices: 28348521--28348568 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
28348511 AAAATATGAG
* *
28348521 AAATGATGTTCACTTTTT
1 AAATGATGTTCACATTTC
28348539 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
28348557 AAATGATGTTCA
1 AAATGATGTTCA
28348569 AATTGATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:28350808 original size:20 final size:20
Alignment explanation
Indices: 28350758--28350808 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
28350748 AATCCAAATA
28350758 TATG-TAATATTTTAATTTGT
1 TATGTTAATATTTT-ATTTGT
* *
28350778 TAGGTTTATATTTT-TTATGT
1 TATGTTAATATTTTATT-TGT
28350798 TATGTTAATAT
1 TATGTTAATAT
28350809 CTAATATGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 8 0.32
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (20 bp):
TATGTTAATATTTTATTTGT
Found at i:28351661 original size:22 final size:24
Alignment explanation
Indices: 28351635--28351678 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
28351625 GAAAAATATT
28351635 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
28351657 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
28351679 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:28351792 original size:9 final size:9
Alignment explanation
Indices: 28351778--28351805 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28351768 TTTTGTTACA
28351778 ACAATTAAT
1 ACAATTAAT
28351787 ACAATTAAT
1 ACAATTAAT
28351796 ACAATTAAT
1 ACAATTAAT
28351805 A
1 A
28351806 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:28351826 original size:68 final size:66
Alignment explanation
Indices: 28351748--28351889 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
28351738 TCAAGTTTGT
*
28351748 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
28351813 AAA
64 AAA
28351816 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
28351881 T
66 A
28351882 TTTACTAA
1 TTTACTAA
28351890 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:28351899 original size:16 final size:16
Alignment explanation
Indices: 28351878--28351919 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
28351868 AATAATTTGA
*
28351878 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
28351894 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
28351910 TAGTTTTAAT
1 TAATTTTAAT
28351920 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:28351903 original size:22 final size:23
Alignment explanation
Indices: 28351893--28351954 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
28351883 TTACTAACAA
* * *
28351893 TTAATTTTA-ATAACAATTAGTT
1 TTAATTTTATATAAAAAATAATT
*
28351915 TTAATTTTATTTAAAAAATAATT
1 TTAATTTTATATAAAAAATAATT
*
28351938 TTAATTTTA-ATTAAAAA
1 TTAATTTTATATAAAAAA
28351955 CGGGCCGAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAATTTTATATAAAAAATAATT
Found at i:28351908 original size:59 final size:66
Alignment explanation
Indices: 28351748--28351911 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 66
28351738 TCAAGTTTGT
*
28351748 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
28351813 AAA
64 AAA
28351816 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
28351879 AAT
64 AAA
*
28351882 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
28351912 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:28356513 original size:92 final size:91
Alignment explanation
Indices: 28356356--28356564 Score: 271
Period size: 92 Copynumber: 2.3 Consensus size: 91
28356346 TTGATTTTAG
* *
28356356 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATTAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
28356421 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
28356448 TAAATTCATATAAGAAAATTTATT-TTCAAGAATTTTATGAAATT-TAATATTAATTATTAAATT
1 TAAATTCATATAAGAAAATTTATTATT-AAGAATTTTATGAAATTAT-ATA-TAACTATTAAATT
28356511 ATATGTAATAATTATTATTTTAAATTATA
63 ATATGTAATAATTATTATTTTAAATTATA
* * * *
28356540 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
28356565 GTTATAATTA
Statistics
Matches: 103, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
90 3 0.03
91 27 0.26
92 70 0.68
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:28356527 original size:24 final size:25
Alignment explanation
Indices: 28356492--28356539 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
28356482 TTATGAAATT
28356492 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
28356516 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
28356540 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:28356603 original size:17 final size:17
Alignment explanation
Indices: 28356581--28356614 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28356571 ATTATTTTAA
28356581 ATTTT-ATTAAATCATAT
1 ATTTTAATTAAAT-ATAT
28356598 ATTTTAATTAAATATAT
1 ATTTTAATTAAATATAT
28356615 TTAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:28356788 original size:120 final size:120
Alignment explanation
Indices: 28356580--28356876 Score: 485
Period size: 120 Copynumber: 2.5 Consensus size: 120
28356570 AATTATTTTA
* *
28356580 AATTTTATTAAATCATATATTTTAATTA-AATATATTTAATATTAATTAT-TTCAAATTTTCATT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTTTCATT
*
28356643 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
28356699 AATTTTATTAAATTATATATTTTAATTATAATATATTTAGTAATAATTATGTT-AATTTAT-ATT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTT-TCA-T
*
28356762 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAT
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
28356819 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
28356877 AAGATTAAAT
Statistics
Matches: 166, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
119 33 0.20
120 126 0.76
121 4 0.02
122 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTTTCATTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:28356853 original size:18 final size:18
Alignment explanation
Indices: 28356807--28356854 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
28356797 TATAAGAATA
*
28356807 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
28356823 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
28356840 TTAATTATAATATAT
1 TTAATTATAATATAT
28356855 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:28356854 original size:16 final size:16
Alignment explanation
Indices: 28356807--28356874 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
28356797 TATAAGAATA
28356807 TTAATTATTAATA-ATT
1 TTAATTA-TAATATATT
*
28356823 TT-ATTAAATTATATATT
1 TTAATT--ATAATATATT
28356840 TTAATTATAATATA-T
1 TTAATTATAATATATT
*
28356855 TTAATAATAAT-TATGT
1 TTAATTATAATATAT-T
28356871 TTAA
1 TTAA
28356875 ATAAGATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.05
15 14 0.33
16 18 0.42
17 6 0.14
18 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (16 bp):
TTAATTATAATATATT
Found at i:28356859 original size:15 final size:15
Alignment explanation
Indices: 28356824--28356865 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28356814 TTAATAATTT
*
28356824 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28356838 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28356852 TATTTAATAATAAT
1 TATTTAATTATAAT
28356866 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28356936 original size:76 final size:76
Alignment explanation
Indices: 28356856--28357092 Score: 166
Period size: 76 Copynumber: 3.1 Consensus size: 76
28356846 ATAATATATT
28356856 TAATAATAATTATGTTTAAATAAGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAAT
1 TAATAATAATTATGTTTAAATAAGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAAT
28356921 TTAAATAACAA
66 TTAAATAACAA
*** * * * ** * * *
28356932 TAATAAT--TTA--CCAAAACAA-ATTTCTGCTAATTATTAAGAATT-TTATTCAATTAT-ATAT
1 TAATAATAATTATGTTTAAATAAGA--T-T--AAATTATTTATTATTGATATT-AATAATCTTAT
** * **
28356990 TTTAATTAAAATATA-GT
60 TAAAATTTAAATA-ACAA
* * * *
28357007 TAATAATAATTATGTTTAAATATGATTAAAATATTTATTATTGATAATACTAATCTTATTAAAAT
1 TAATAATAATTATGTTTAAATAAGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAAT
28357072 TTAAATAACAA
66 TTAAATAACAA
*
28357083 TAACAATAAT
1 TAATAATAAT
28357093 CATTTACCAA
Statistics
Matches: 109, Mismatches: 37, Indels: 30
0.62 0.21 0.17
Matches are distributed among these distances:
71 1 0.01
72 5 0.05
73 1 0.01
74 4 0.04
75 39 0.36
76 49 0.45
77 4 0.04
78 1 0.01
79 4 0.04
80 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (76 bp):
TAATAATAATTATGTTTAAATAAGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAAT
TTAAATAACAA
Found at i:28356963 original size:151 final size:154
Alignment explanation
Indices: 28356808--28357118 Score: 493
Period size: 151 Copynumber: 2.0 Consensus size: 154
28356798 ATAAGAATAT
* * *
28356808 TAATTATTAATAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATAGTTAATAATAATTATGTTT
* *
28356873 AAATAAGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAAT-AAT-
66 AAATAAGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAAATA
*
28356936 A-ATTTACCAAAACAAATTTCTGC
131 ACATTTACCAAAACAAATTTATGC
*
28356959 TAATTATTAAGAATTTTATTCAATTATATATTTTAATTAAAATATAGTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATAGTTAATAATAATTATGTTT
* *
28357024 AAATATGATTAAAATATTTATTATTGATAATACTAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATAAGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAAT-A-AA
28357089 TAATCATTTACCAAAACAAATTTATGC
129 TAA-CATTTACCAAAACAAATTTATGC
28357116 TAA
1 TAA
28357119 GGGTATTCTA
Statistics
Matches: 145, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
151 117 0.81
154 3 0.02
155 1 0.01
157 24 0.17
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (154 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATAGTTAATAATAATTATGTTT
AAATAAGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAAATA
ACATTTACCAAAACAAATTTATGC
Found at i:28362933 original size:41 final size:41
Alignment explanation
Indices: 28362876--28362955 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
28362866 TGATCGAATG
* * *
28362876 TAATTCAGACTTATTGTCTAGCAGGCTTGATGCCGGTGATA
1 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGATA
28362917 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGA
1 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGA
28362956 AATTATTTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (41 bp):
TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGATA
Found at i:28362977 original size:41 final size:41
Alignment explanation
Indices: 28362876--28362980 Score: 113
Period size: 41 Copynumber: 2.6 Consensus size: 41
28362866 TGATCGAATG
* * * * *
28362876 TAATTCAGACTTATTGTCTAGCAGGCTTGATGCCGGTGATA
1 TAATTCAGACTCATAGTCTAGCAGGCTTAATGCCAGTGAAA
*
28362917 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGAAA
1 TAATTCAGACTCATAGTCTAGCAGGCTTAATGCCAGTGAAA
* * *
28362958 TTATTTAGA-TTATAAGTCTAGCA
1 TAATTCAGACTCAT-AGTCTAGCA
28362981 AGCTAAAAGC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 3 0.05
41 52 0.95
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (41 bp):
TAATTCAGACTCATAGTCTAGCAGGCTTAATGCCAGTGAAA
Found at i:28363128 original size:21 final size:21
Alignment explanation
Indices: 28363087--28363128 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28363077 TATGTAAATA
*
28363087 ATATATATTTGAAGATCAAGT
1 ATATATATTTGAAAATCAAGT
28363108 ATATATATTTGATAAAT-AAGT
1 ATATATATTTGA-AAATCAAGT
28363129 TTGATGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.40
Consensus pattern (21 bp):
ATATATATTTGAAAATCAAGT
Found at i:28368045 original size:16 final size:16
Alignment explanation
Indices: 28368007--28368058 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
28367997 TTATATAAGT
* *
28368007 AAATAAATAATTAAAT
1 AAATAAATAATAAAAC
*
28368023 AATTAAATAATAAAAC
1 AAATAAATAATAAAAC
*
28368039 AAATAAAATAA-AAACC
1 AAAT-AAATAATAAAAC
28368055 AAAT
1 AAAT
28368059 TACCTTGTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 24 0.80
17 6 0.20
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAATAATAAAAC
Found at i:28374741 original size:19 final size:18
Alignment explanation
Indices: 28374702--28374740 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28374692 TATCTTTTAC
*
28374702 AAATTAAATACACTATTA
1 AAATTAAATACAATATTA
28374720 AAATTGAAATA-AATATTA
1 AAATT-AAATACAATATTA
28374738 AAA
1 AAA
28374741 AATATCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATTAAATACAATATTA
Found at i:28376010 original size:50 final size:52
Alignment explanation
Indices: 28375942--28376064 Score: 169
Period size: 50 Copynumber: 2.4 Consensus size: 52
28375932 GCATTTAATA
* *
28375942 AAGTCATGCATTATGTAACTCTCATGTTAGTT-AAGATTATATC-ATAAATT
1 AAGTCATGCATTATGTAACTCCCATGTTAGTTAAAGATTACATCTATAAATT
* * * *
28375992 ATGTCATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCATCTTTAAATT
1 AAGTCATGCATTATGTAACTCCCATGTTAGTTAAAGATTACATCTATAAATT
*
28376044 AAGTCATGCATTAAGTAACTC
1 AAGTCATGCATTATGTAACTC
28376065 ATTTGTTCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 30 0.48
51 8 0.13
52 25 0.40
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (52 bp):
AAGTCATGCATTATGTAACTCCCATGTTAGTTAAAGATTACATCTATAAATT
Found at i:28378811 original size:30 final size:30
Alignment explanation
Indices: 28378776--28378833 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28378766 ATTTTTTTAA
* *
28378776 TTATTGTTCAACATTAATATAATTTTAAAG
1 TTATTGTACAACATAAATATAATTTTAAAG
* *
28378806 TTATTGTACAATATAAATATGATTTTAA
1 TTATTGTACAACATAAATATAATTTTAA
28378834 TATTTTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (30 bp):
TTATTGTACAACATAAATATAATTTTAAAG
Found at i:28381850 original size:41 final size:40
Alignment explanation
Indices: 28381777--28381856 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 40
28381767 AAGATATTCC
***
28381777 ATCTATTTAAAGTGATTTGACAAATCGTACAAGTCTAAAT
1 ATCTATTTAAAGTGATTTGACAAATAACACAAGTCTAAAT
* * *
28381817 ATCTATTTTAAATTGATTTGATAAATAACACAAGTTTAAA
1 ATCTA-TTTAAAGTGATTTGACAAATAACACAAGTCTAAA
28381857 AATTAAAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (40 bp):
ATCTATTTAAAGTGATTTGACAAATAACACAAGTCTAAAT
Found at i:28383529 original size:40 final size:40
Alignment explanation
Indices: 28383485--28383571 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
28383475 CATAATTCTT
* *
28383485 TATCAAATATGCACAATAATAAAAAA-ATATAATATAAGTA
1 TATCAAATATGAAAAATAATAAAAAATA-ATAATATAAGTA
* *
28383525 TATCATATATGAAAAATAATTAAAAATAATAATATAAGTA
1 TATCAAATATGAAAAATAATAAAAAATAATAATATAAGTA
28383565 TATCAAA
1 TATCAAA
28383572 CTCGATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 40 0.98
41 1 0.02
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.30
Consensus pattern (40 bp):
TATCAAATATGAAAAATAATAAAAAATAATAATATAAGTA
Found at i:28387593 original size:17 final size:17
Alignment explanation
Indices: 28387553--28387593 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
28387543 CTTAAATGGA
*
28387553 TTAATTTTTACCAACAT
1 TTAATTTTTAACAACAT
*
28387570 TTGAATTTTTAACAAGAT
1 TT-AATTTTTAACAACAT
28387588 TTAATT
1 TTAATT
28387594 AGAGAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (17 bp):
TTAATTTTTAACAACAT
Found at i:28388503 original size:28 final size:28
Alignment explanation
Indices: 28388454--28388521 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 28
28388444 AATAAAGCCC
* * * *
28388454 TTTTTTTCACAATTACGGAAATAGGCTAA
1 TTTTTTT-AAAATGACGAAAATAGGCCAA
* *
28388483 TTTTTTTAAAATGACGAAAATGGGCCGA
1 TTTTTTTAAAATGACGAAAATAGGCCAA
*
28388511 TTTTGTTAAAA
1 TTTTTTTAAAA
28388522 CACGTTCAGC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (28 bp):
TTTTTTTAAAATGACGAAAATAGGCCAA
Found at i:28398548 original size:33 final size:35
Alignment explanation
Indices: 28398494--28398559 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 35
28398484 AAAGGAAATT
28398494 TAAAATTATCAATATATAAACAATAAATTATATGCA
1 TAAAATTATCAATATATAAACAATAAA-TATATGCA
*
28398530 TAAAATT-TCAA-A-ATAAACAATATATATATG
1 TAAAATTATCAATATATAAACAATAAATATATG
28398560 AATTTGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 6 0.21
33 11 0.38
34 1 0.03
35 4 0.14
36 7 0.24
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (35 bp):
TAAAATTATCAATATATAAACAATAAATATATGCA
Found at i:28399052 original size:25 final size:25
Alignment explanation
Indices: 28399019--28399066 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28399009 AAAAATATAT
28399019 AAAATAATACATGATAAATTTAAGA
1 AAAATAATACATGATAAATTTAAGA
**
28399044 AAAATAATATGTGATAAATTTAA
1 AAAATAATACATGATAAATTTAA
28399067 AATATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.31
Consensus pattern (25 bp):
AAAATAATACATGATAAATTTAAGA
Found at i:28399068 original size:21 final size:21
Alignment explanation
Indices: 28399018--28399094 Score: 75
Period size: 25 Copynumber: 3.5 Consensus size: 21
28399008 AAAAAATATA
*
28399018 TAAAATAATACATGATAAATT
1 TAAAATAATATATGATAAATT
*
28399039 TAAGAAAAATAATATGTGATAAATT
1 T----AAAATAATATATGATAAATT
* *
28399064 TAAAATATTA-ATGATGAATT
1 TAAAATAATATATGATAAATT
28399084 TAAAATAATAT
1 TAAAATAATAT
28399095 TAAGCTTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
20 17 0.38
21 9 0.20
25 19 0.42
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.35
Consensus pattern (21 bp):
TAAAATAATATATGATAAATT
Found at i:28400822 original size:44 final size:43
Alignment explanation
Indices: 28400774--28400879 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 43
28400764 TCCGCCCCAT
* * *
28400774 TGCAACTTCAAGG-AGATAGGATTGGTGACTTCAATCTGCTTCAC
1 TGCAACTTC-AGGAAGATAGG-CTGATGACTTCAATCTGCTCCAC
* *
28400818 TGCAACTTTAGGAAGATAAGGCTGATGGCTTCAATCTGCTCCAC
1 TGCAACTTCAGGAAGAT-AGGCTGATGACTTCAATCTGCTCCAC
*
28400862 TACAACTTCAGGAAGATA
1 TGCAACTTCAGGAAGATA
28400880 AGATCCGCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
43 4 0.08
44 46 0.87
45 3 0.06
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
TGCAACTTCAGGAAGATAGGCTGATGACTTCAATCTGCTCCAC
Found at i:28400965 original size:51 final size:51
Alignment explanation
Indices: 28400897--28401349 Score: 647
Period size: 51 Copynumber: 8.9 Consensus size: 51
28400887 CCATAATTTG
* * * * *
28400897 CAGCTTTAATCTATTCCACTGTAACACCAGAGAAATAAGATTCGCTACCTT
1 CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTT
* * *
28400948 TAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAGATTCGCTACCTT
1 CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTT
* *
28400999 CAACTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGCCTT
1 CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTT
28401050 CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTT
1 CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTT
* * * *
28401101 CAGCTTTAGTCTGTTCCACTGCAATGCCAGGGAAAAAAGATTCGCTGTCTT
1 CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTT
* * * *
28401152 CAGCTTTAATCTGTTCCACTGCAATGCTA-GGAAAAAAAATTCGCTGCCTT
1 CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTT
* * * * *
28401202 CAGCTTCAATCTGTTCCACTGCAATGCCAGGTAAATAAGATTTGTTGCCTT
1 CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTT
*
28401253 CAGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGATTCGCTGCCTT
1 CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTT
* * * *
28401304 CAGCTTTAATCTGTTCCACTGTAACACCAGAGAAATAATATTCGCT
1 CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCT
28401350 ATAATGACTT
Statistics
Matches: 366, Mismatches: 35, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
50 46 0.13
51 320 0.87
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (51 bp):
CAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTT
Found at i:28401265 original size:203 final size:204
Alignment explanation
Indices: 28400897--28401350 Score: 658
Period size: 203 Copynumber: 2.2 Consensus size: 204
28400887 CCATAATTTG
* * * *
28400897 CAGCTTTAATCTATTCCACTGTAACACCAGAGAAATAAGATTCGCTACCTTTAGCTTTAATCTGT
1 CAGCTTTAATCTGTTCCACTGCAACACCAGAGAAAAAAGATTCGCTACCTTCAGCTTTAATCTGT
* * *
28400962 TCCACTGCAACACCAGGGAAATAAGATTCGCTACCTTCAACTTTAATCTGTTCCACTACAACGCC
66 TCCACTGCAACACCAGGGAAAAAAAATTCGCTACCTTCAACTTCAATCTGTTCCACTACAACGCC
28401027 AGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATT
131 AGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATT
28401092 CGCTGCCTT
196 CGCTGCCTT
* ** * **
28401101 CAGCTTTAGTCTGTTCCACTGCAATGCCAGGGAAAAAAGATTCGCTGTCTTCAGCTTTAATCTGT
1 CAGCTTTAATCTGTTCCACTGCAACACCAGAGAAAAAAGATTCGCTACCTTCAGCTTTAATCTGT
** * * * * *
28401166 TCCACTGCAATGCTA-GGAAAAAAAATTCGCTGCCTTCAGCTTCAATCTGTTCCACTGCAATGCC
66 TCCACTGCAACACCAGGGAAAAAAAATTCGCTACCTTCAACTTCAATCTGTTCCACTACAACGCC
* * * *
28401230 AGGTAAATAAGATTTGTTGCCTTCAGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGATT
131 AGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATT
28401295 CGCTGCCTT
196 CGCTGCCTT
* * *
28401304 CAGCTTTAATCTGTTCCACTGTAACACCAGAGAAATAATATTCGCTA
1 CAGCTTTAATCTGTTCCACTGCAACACCAGAGAAAAAAGATTCGCTA
28401351 TAATGACTTT
Statistics
Matches: 218, Mismatches: 32, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
203 151 0.69
204 67 0.31
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (204 bp):
CAGCTTTAATCTGTTCCACTGCAACACCAGAGAAAAAAGATTCGCTACCTTCAGCTTTAATCTGT
TCCACTGCAACACCAGGGAAAAAAAATTCGCTACCTTCAACTTCAATCTGTTCCACTACAACGCC
AGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATT
CGCTGCCTT
Found at i:28408612 original size:12 final size:13
Alignment explanation
Indices: 28408595--28408623 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28408585 TTCGAAAAAC
28408595 GAAAATGGAAAT-
1 GAAAATGGAAATA
28408607 GAAAATGGAAATA
1 GAAAATGGAAATA
28408620 GAAA
1 GAAA
28408624 CTTGCAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (13 bp):
GAAAATGGAAATA
Found at i:28408833 original size:25 final size:25
Alignment explanation
Indices: 28408764--28408840 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 25
28408754 ATGAATTTTC
* *
28408764 TCAAAATTTTACCAGGGTTAAAATCG
1 TCAAAATTTTACAAGGG-TAAAATTG
*
28408790 TCAAAAATTTACAATGGGTAAAATTG
1 TCAAAATTTTACAA-GGGTAAAATTG
*
28408816 TCAAAATTTTACTAGGGTAAAATTG
1 TCAAAATTTTACAAGGGTAAAATTG
28408841 GGGTGAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 11 0.24
26 31 0.69
27 3 0.07
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (25 bp):
TCAAAATTTTACAAGGGTAAAATTG
Found at i:28410747 original size:461 final size:461
Alignment explanation
Indices: 28409885--28410806 Score: 1772
Period size: 461 Copynumber: 2.0 Consensus size: 461
28409875 AGTGGATGAA
*
28409885 CCAATTTTCACAAAATAAATGTAAAAAAATATTTCTAATAGACTTTTTAGTTCCAAGCCTTATAA
1 CCAATTTTCACAAAATAAATGTAAAAAAATATTTCTAATAGACTTTTTAGTTCCAAACCTTATAA
28409950 GTCTTCTCAAATCCTCATATCTACAATCATTTTGTATAACAGGTGCATGGGAAACATCATCAATT
66 GTCTTCTCAAATCCTCATATCTACAATCATTTTGTATAACAGGTGCATGGGAAACATCATCAATT
28410015 TTTAAAGGAAAATATGCTGAAAACGTCAGTATTTTTATCTCAAGTATATTATTATAATTAAACAC
131 TTTAAAGGAAAATATGCTGAAAACGTCAGTATTTTTATCTCAAGTATATTATTATAATTAAACAC
28410080 ATCACTATTTATAGCAAGAAATATATGTGCAACACTAACTTCAACATAGTTAATGAACATGGAAC
196 ATCACTATTTATAGCAAGAAATATATGTGCAACACTAACTTCAACATAGTTAATGAACATGGAAC
28410145 TGGAATTCATTTTCCTTTTCTTAAGAACAGAAGACATGATTTTTAGACACCTCCACATTTTCATA
261 TGGAATTCATTTTCCTTTTCTTAAGAACAGAAGACATGATTTTTAGACACCTCCACATTTTCATA
*
28410210 CATTTTAAGTTAAAAAAATAATGTTCAAAACATAATGTGTCTTATCATTATCATCTAAGGAATCT
326 CATTTTAAGTTAAAAAAATAATGTTCAAAACATAACGTGTCTTATCATTATCATCTAAGGAATCT
*
28410275 AACACACACAAATACTATGCAAATAATTTTCAAGTATACTCGCATTAACAATTGCACATTTTGGT
391 AACACACACAAATACTATGCAAATAATTTTCAAGTATACTCGAATTAACAATTGCACATTTTGGT
28410340 GAGTAT
456 GAGTAT
28410346 CCAATTTTCACAAAATAAATGTAAAAAAATATTTCTAATAGACTTTTTAGTTCCAAACCTTATAA
1 CCAATTTTCACAAAATAAATGTAAAAAAATATTTCTAATAGACTTTTTAGTTCCAAACCTTATAA
28410411 GTCTTCTCAAATCCTCATATCTACAATCATTTTGTATAACAGGTGCATGGGAAACATCATCAATT
66 GTCTTCTCAAATCCTCATATCTACAATCATTTTGTATAACAGGTGCATGGGAAACATCATCAATT
*
28410476 TTTAAAGGAAAATATGCTGAAAACGTCAGTATTTTTATCTCAAGTATATTATTATAATTAAACAT
131 TTTAAAGGAAAATATGCTGAAAACGTCAGTATTTTTATCTCAAGTATATTATTATAATTAAACAC
*
28410541 ATCACTATTTATAGCAAGAAATATATGTGCAACACTAACTTCAACATAGTTAATGAACATGGAAT
196 ATCACTATTTATAGCAAGAAATATATGTGCAACACTAACTTCAACATAGTTAATGAACATGGAAC
*
28410606 TGGAATTCATTTTCCTTTTCTTAAGAACAGAAGACATGATTTTTAGACACCTTCACATTTTCATA
261 TGGAATTCATTTTCCTTTTCTTAAGAACAGAAGACATGATTTTTAGACACCTCCACATTTTCATA
* *
28410671 CATTTTAAGTTATAAAAATAATGTTCAAAGCATAACGTGTCTTATCATTATCATCTAAGGAATCT
326 CATTTTAAGTTAAAAAAATAATGTTCAAAACATAACGTGTCTTATCATTATCATCTAAGGAATCT
28410736 AACACACACAAATACTATGCAAATAATTTTCAAGTATACTCGAATTAACAATTGCACATTTTGGT
391 AACACACACAAATACTATGCAAATAATTTTCAAGTATACTCGAATTAACAATTGCACATTTTGGT
28410801 GAGTAT
456 GAGTAT
28410807 TTTAATGCCC
Statistics
Matches: 453, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
461 453 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (461 bp):
CCAATTTTCACAAAATAAATGTAAAAAAATATTTCTAATAGACTTTTTAGTTCCAAACCTTATAA
GTCTTCTCAAATCCTCATATCTACAATCATTTTGTATAACAGGTGCATGGGAAACATCATCAATT
TTTAAAGGAAAATATGCTGAAAACGTCAGTATTTTTATCTCAAGTATATTATTATAATTAAACAC
ATCACTATTTATAGCAAGAAATATATGTGCAACACTAACTTCAACATAGTTAATGAACATGGAAC
TGGAATTCATTTTCCTTTTCTTAAGAACAGAAGACATGATTTTTAGACACCTCCACATTTTCATA
CATTTTAAGTTAAAAAAATAATGTTCAAAACATAACGTGTCTTATCATTATCATCTAAGGAATCT
AACACACACAAATACTATGCAAATAATTTTCAAGTATACTCGAATTAACAATTGCACATTTTGGT
GAGTAT
Found at i:28411640 original size:5 final size:5
Alignment explanation
Indices: 28411630--28411654 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28411620 TTTGTTTTAT
28411630 TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA
28411655 AAATGACCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:28411989 original size:364 final size:364
Alignment explanation
Indices: 28411289--28412018 Score: 1435
Period size: 365 Copynumber: 2.0 Consensus size: 364
28411279 AATTGACTGG
28411289 AAAAATGACCACACAATTATATCATCTTCTTCGACTAAATTGACATTTGGCTTAACAGGTTATCA
1 AAAAATGACCACACAATTATATCATCTTCTTCGACTAAATTGACATTTGGCTTAACAGGTTATCA
28411354 TTCCTCCATTATTGATTTCTGTACAGAGTTATATAGTAGCTCAATTTGTCATCACAATTGGGTAC
66 TTCCTCCATTATTGATTTCTGTACAGAGTTATATAGTAGCTCAATTTGTCATCACAATTGGGTAC
28411419 TAGGATAGTGAGCACAGAATTGATGAATAAAACACGAGGTAAATTCCTAAGAAAGAGAGGTGGTG
131 TAGGATAGTGAGCACAGAATTGATGAATAAAACACGAGGTAAATTCCTAAGAAAGAGAGGTGGTG
*
28411484 TATATGACACACTTGCTTTGTGTCTTTCTCCTTGCTTTGAAACCCTTGCTTTGTGTCTTTCTCCT
196 TATATGACACACTTGCTTTGTGTCTTTCTCCTTACTTTGAAACCCTTGCTTTGTGTCTTTCTCCT
28411549 TCTTTCCTTTTTCTTTTTTTTTTGCCCTTTCTGTTTCGTTGACTTTGTTCTTTTTCTATTTCTTT
261 TCTTTCCTTTTTCTTTTTTTTTTGCCCTTTCTGTTTCGTTGACTTTGTTCTTTTTCTATTTCTTT
28411614 TATTTCTTTGTTTTATTATAATATAATATAATATAATAT
326 TATTTCTTTGTTTTATTATAATATAATATAATATAATAT
28411653 AAAAATGACCACACAATTATATCATCTTCTTCGACTAAATTGACATTTGGCTTAACAGGATTATC
1 AAAAATGACCACACAATTATATCATCTTCTTCGACTAAATTGACATTTGGCTTAACAGG-TTATC
28411718 ATTCCTCCATTATTGATTTCTGTACAGAGTTATATAGTAGCTCAATTTGTCATCACAATTGGGTA
65 ATTCCTCCATTATTGATTTCTGTACAGAGTTATATAGTAGCTCAATTTGTCATCACAATTGGGTA
28411783 CTAGGATAGTGAGCACAGAATTGATGAATAAAACACGAGGTAAATTCCTAAGAAAGAGAGGTGGT
130 CTAGGATAGTGAGCACAGAATTGATGAATAAAACACGAGGTAAATTCCTAAGAAAGAGAGGTGGT
28411848 GTATATGACACACTTGCTTTGTGTCTTTCTCCTTACTTTGAAACCCTTGCTTTGTGTCTTTCTCC
195 GTATATGACACACTTGCTTTGTGTCTTTCTCCTTACTTTGAAACCCTTGCTTTGTGTCTTTCTCC
28411913 TTCTTTCCTTTTTC-TTTTTTTTTGCCCTTTCTGTTTCGTTGACTTTGTTCTTTTTCTATTTCTT
260 TTCTTTCCTTTTTCTTTTTTTTTTGCCCTTTCTGTTTCGTTGACTTTGTTCTTTTTCTATTTCTT
28411977 TTATTTCTTTGTTTTATTATAATATAATATAATATAATAT
325 TTATTTCTTTGTTTTATTATAATATAATATAATATAATAT
28412017 AA
1 AA
28412019 TATAATATAA
Statistics
Matches: 364, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
364 151 0.41
365 213 0.59
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (364 bp):
AAAAATGACCACACAATTATATCATCTTCTTCGACTAAATTGACATTTGGCTTAACAGGTTATCA
TTCCTCCATTATTGATTTCTGTACAGAGTTATATAGTAGCTCAATTTGTCATCACAATTGGGTAC
TAGGATAGTGAGCACAGAATTGATGAATAAAACACGAGGTAAATTCCTAAGAAAGAGAGGTGGTG
TATATGACACACTTGCTTTGTGTCTTTCTCCTTACTTTGAAACCCTTGCTTTGTGTCTTTCTCCT
TCTTTCCTTTTTCTTTTTTTTTTGCCCTTTCTGTTTCGTTGACTTTGTTCTTTTTCTATTTCTTT
TATTTCTTTGTTTTATTATAATATAATATAATATAATAT
Found at i:28412004 original size:5 final size:5
Alignment explanation
Indices: 28411994--28412056 Score: 126
Period size: 5 Copynumber: 12.6 Consensus size: 5
28411984 TTTGTTTTAT
28411994 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
28412044 TATAA TATAA TAT
1 TATAA TATAA TAT
28412057 TAATTAAACA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 58 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:28418960 original size:5 final size:5
Alignment explanation
Indices: 28418950--28418998 Score: 80
Period size: 5 Copynumber: 9.4 Consensus size: 5
28418940 TTCTTTGTTT
28418950 TAATA TAATA TAATATA TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA T-A-ATA TAATA TAATA TAATA TAATA TAATA TAATA TA
28418999 TTACTTAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 36 0.86
6 2 0.05
7 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:28426269 original size:49 final size:48
Alignment explanation
Indices: 28426198--28426291 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 48
28426188 GGTTAGCGTA
28426198 AAAACAACGATGGAAGTAAGATTAAATACTA-TAACTATACTGTAGTAT
1 AAAACAACGATGGAAGTAAGATTAAATAC-AGTAACTATACTGTAGTAT
* * * *
28426246 AAAACTAACGATGGGAGTGAGATTAGATACAGTAGCTATACTGTAG
1 AAAAC-AACGATGGAAGTAAGATTAAATACAGTAACTATACTGTAG
28426292 CATGAGACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 6 0.15
49 34 0.85
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.26
Consensus pattern (48 bp):
AAAACAACGATGGAAGTAAGATTAAATACAGTAACTATACTGTAGTAT
Found at i:28426902 original size:17 final size:17
Alignment explanation
Indices: 28426865--28426913 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
28426855 ATTTTATATT
28426865 TTTATAATATCAAAAAATA
1 TTTATAATAT--AAAAATA
*
28426884 TTTATAATATAAAATTA
1 TTTATAATATAAAAATA
* *
28426901 TTTTTAAAATAAA
1 TTTATAATATAAA
28426914 TCAATGTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 17 0.63
19 10 0.37
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTATAATATAAAAATA
Found at i:28426906 original size:19 final size:19
Alignment explanation
Indices: 28426860--28426911 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
28426850 TAATAATTTT
28426860 ATATTTTTATAATATCAAA
1 ATATTTTTATAATATCAAA
* *
28426879 AAATATTTATAATAT-AAA
1 ATATTTTTATAATATCAAA
*
28426897 ATTATTTTTAAAATA
1 A-TATTTTTATAATA
28426912 AATCAATGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATTTTTATAATATCAAA
Done.