Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 26 of 325
Found at i:6059140 original size:33 final size:33
Alignment explanation
Indices: 6059098--6059164 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
6059088 TACAAAGGGG
6059098 ATTGATTGTACTGGATTCGAAGAAGAGATCTAA
1 ATTGATTGTACTGGATTCGAAGAAGAGATCTAA
6059131 ATTGATTGTACTGGATTCGAAGAAGAGATCTAA
1 ATTGATTGTACTGGATTCGAAGAAGAGATCTAA
6059164 A
1 A
6059165 GAGAAGAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (33 bp):
ATTGATTGTACTGGATTCGAAGAAGAGATCTAA
Found at i:6060858 original size:11 final size:11
Alignment explanation
Indices: 6060842--6060870 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
6060832 GGAGAAAAGA
6060842 ATTTGTCAGGC
1 ATTTGTCAGGC
6060853 ATTTGTCAGGC
1 ATTTGTCAGGC
6060864 ATTTGTC
1 ATTTGTC
6060871 CTTACGTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.41
Consensus pattern (11 bp):
ATTTGTCAGGC
Found at i:6065907 original size:44 final size:44
Alignment explanation
Indices: 6065856--6066029 Score: 143
Period size: 44 Copynumber: 3.9 Consensus size: 44
6065846 ATAGCGAATT
*
6065856 TTATCTCTCTAAAGTTGCAG-GAGAGCAGATTAAAGCTATAAAAC
1 TTATCTCTCTAAAGTTGCAGTG-GAGCAGATTAAAGCTACAAAAC
* * * * * **
6065900 TTATCTCTCTGAAGTTACAGTGGAGTAGATTGAAGTTACAAGTC
1 TTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAAAC
* * * * * *
6065944 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATC
1 TTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAAAC
* * * * **
6065989 CTATTTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAA
1 TTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAA
6066030 TTATACACCT
Statistics
Matches: 103, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
44 68 0.66
45 35 0.34
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (44 bp):
TTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAAAC
Found at i:6066004 original size:133 final size:132
Alignment explanation
Indices: 6065578--6066026 Score: 420
Period size: 133 Copynumber: 3.3 Consensus size: 132
6065568 TACCGTGGTA
* * * ** * * * *
6065578 AATCTCATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCCATTAACCTTATCTCCCTAAAGTTA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAAACTTATCT-CCTGAAGTTA
* * * * *
6065643 CAGTGGAGCAGGTTGAAGTTACAACAAGTCTGATCTCCTTGAAGTTGCAGTGGAGTAGACTGATG
65 CAGTGGAGCAGATTGAAGTT---ACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAG
6065708 ATAGCG
127 ATAGCG
* * * *
6065714 AATCTTATTGCCTTGAAGTTGTAGTGGAACAGATTAAAGCTACAAATTACAAATATGATCTCCTT
1 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAA--AC---T-T-ATCTCC-T
* * * ** *
6065779 GAAGTTGCAGTGGAGCAGATTGAAGTTA-TA-TCTTATCTCCCTAAAATTATAGTGGAGTA-AAT
58 GAAGTTACAGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACT
* *
6065841 CAGGGATAGCG
123 GA-AGATAGCG
* * * * *
6065852 AATTTTATCTCTCTAAAGTTGCAG-GAGAGCAGATTAAAGCTATAAAACTTATCTCTCTGAAGTT
1 AATCTTATTTCCCTGAAGTTGCAGTG-GAACAGATTAAAGCTATAAAACTTATCTC-CTGAAGTT
* *
6065916 ACAGTGGAGTAGATTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGAT
64 ACAGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAGAT
6065981 AGCG
129 AGCG
* *
6065985 AATCCTATTTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTA
6066027 CAATTATACA
Statistics
Matches: 247, Mismatches: 51, Indels: 33
0.75 0.15 0.10
Matches are distributed among these distances:
131 32 0.13
132 3 0.01
133 66 0.27
134 4 0.02
136 37 0.15
137 4 0.02
138 66 0.27
139 1 0.00
140 1 0.00
141 1 0.00
142 3 0.01
143 29 0.12
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (132 bp):
AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAAACTTATCTCCTGAAGTTAC
AGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAGATAG
CG
Found at i:6067716 original size:18 final size:17
Alignment explanation
Indices: 6067688--6067727 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
6067678 TGAAATTTAG
*
6067688 ATTTCATTACTTTTATT
1 ATTTTATTACTTTTATT
6067705 ACTTTTATTACTTTTATT
1 A-TTTTATTACTTTTATT
6067723 ATTTT
1 ATTTT
6067728 TTCATTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATTACTTTTATT
Found at i:6067728 original size:9 final size:9
Alignment explanation
Indices: 6067693--6067727 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
6067683 TTTAGATTTC
6067693 ATTACTTTT
1 ATTACTTTT
6067702 ATTACTTTT
1 ATTACTTTT
6067711 ATTACTTTT
1 ATTACTTTT
6067720 ATTA-TTTT
1 ATTACTTTT
6067728 TTCATTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.15
9 22 0.85
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTACTTTT
Found at i:6070902 original size:21 final size:21
Alignment explanation
Indices: 6070888--6070926 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6070878 CAAAACTTGT
6070888 ATAA-CTATCATCAAATATTC
1 ATAATCTATCATCAAATATTC
6070908 ATAATCTATCATCAAATAT
1 ATAATCTATCATCAAATAT
6070927 CAAAACTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAATCTATCATCAAATATTC
Found at i:6072366 original size:17 final size:16
Alignment explanation
Indices: 6072339--6072383 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
6072329 TTAAAACATA
6072339 TTAATTTTTTATAATTT
1 TTAA-TTTTTATAATTT
*
6072356 TATAATTTTTAATTATTT
1 T-TAATTTTT-ATAATTT
6072374 TTAATTTTTA
1 TTAATTTTTA
6072384 AAAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 14 0.56
18 10 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTAATTTTTATAATTT
Found at i:6072384 original size:17 final size:17
Alignment explanation
Indices: 6072339--6072384 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
6072329 TTAAAACATA
*
6072339 TTAATTTTTTATAATTT
1 TTAATTTTTAATAATTT
*
6072356 TATAATTTTTAATTATTT
1 T-TAATTTTTAATAATTT
6072374 TTAATTTTTAA
1 TTAATTTTTAA
6072385 AAATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTAATTTTTAATAATTT
Found at i:6072393 original size:9 final size:9
Alignment explanation
Indices: 6072379--6072417 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
6072369 TATTTTTAAT
6072379 TTTTAAAAA
1 TTTTAAAAA
* *
6072388 TATTAAATAT
1 TTTTAAA-AA
6072398 TTTTAAAAA
1 TTTTAAAAA
6072407 TTTTAAAAA
1 TTTTAAAAA
6072416 TT
1 TT
6072418 AATTAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:6072399 original size:19 final size:19
Alignment explanation
Indices: 6072377--6072413 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6072367 ATTATTTTTA
6072377 ATTTTTAAAAATATTAAAT
1 ATTTTTAAAAATATTAAAT
*
6072396 ATTTTTAAAAATTTTAAA
1 ATTTTTAAAAATATTAAA
6072414 AATTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTTAAAAATATTAAAT
Found at i:6081109 original size:20 final size:20
Alignment explanation
Indices: 6081084--6081121 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6081074 GCTGACAAAA
*
6081084 CAGTCACTCAAGTTTCAATT
1 CAGTCACTCAACTTTCAATT
*
6081104 CAGTCACTTAACTTTCAA
1 CAGTCACTCAACTTTCAA
6081122 AAAATAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (20 bp):
CAGTCACTCAACTTTCAATT
Found at i:6083458 original size:152 final size:152
Alignment explanation
Indices: 6083082--6083907 Score: 1115
Period size: 152 Copynumber: 5.5 Consensus size: 152
6083072 TGAACACTAC
* * ** * *
6083082 AAGTTGTTGTAGTATAGTGGTGAGTATTTCCGCCTGTCACGTAGGCGACCCGGGCTCGATCCCCG
1 AAGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCG
** * * *
6083147 GCAATTGCGATCTATCCTCTGATTTATGTTTTCTGACCTTCTAAAGTAATTTATAAGAAAT-A-C
66 GCAACGGCGATCTATCCTCTGATTTATATTTTCTGACCTTCTAAAGTAATTTATAACAAATAATA
* * ** *
6083210 TAATGTCGAAATTATGGTATGG
131 TAATTTCGGAATTATGACATCG
* * *
6083232 GAGCCGTTGTAGTATA---GTGAGTATTTCCCGCCTGTCACGCGGGTGATCCGGGTTCGATCCCC
1 AAGTCGTTGTAGTATAGTGGTGAGTA-TTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCC
* *
6083294 GGCACCGGCGATCTATCCTCTGACTTATATTTTCTGACCTTCTAAAGTAATTTATAACAAATAAT
65 GGCAACGGCGATCTATCCTCTGATTTATATTTTCTGACCTTCTAAAGTAATTTATAACAAATAAT
* *
6083359 ATAATTTTGGAACTATGACATCG
130 ATAATTTCGGAATTATGACATCG
*
6083382 ACGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCG
1 AAGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCG
* *
6083447 GCAACGGCGATCTATCCTCTGATTTATTTTTTCTGACCTTCTAAAGTAATTTATAACAAATAATG
66 GCAACGGCGATCTATCCTCTGATTTATATTTTCTGACCTTCTAAAGTAATTTATAACAAATAATA
*
6083512 TAATTTCGGAA-TACAGACATCG
131 TAATTTCGGAATTA-TGACATCG
* * * * *
6083534 AAGTCGTAGTAGTATAGTGGTGAGTATTCCCGCCTGTCAGGTGGGTGACCCGGCTTCGATCTCCG
1 AAGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCG
* * *
6083599 GCAACGGCGATCTATACTCTGATTTGTATTTTCTGACCTTCTAAAGTAGTTTATAACAAATAATA
66 GCAACGGCGATCTATCCTCTGATTTATATTTTCTGACCTTCTAAAGTAATTTATAACAAATAATA
* *
6083664 TAATCTT-GGAATTAAGACACCG
131 TAAT-TTCGGAATTATGACATCG
** *
6083686 AAGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCTTGTGACCCGGGTTCGATCCGCG
1 AAGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCG
* * * *
6083751 GCAACGGTGATCTATCTTCTGATTTATTTTTTCTGA----C---A-TAATTTATAACAAATAATG
66 GCAACGGCGATCTATCCTCTGATTTATATTTTCTGACCTTCTAAAGTAATTTATAACAAATAATA
6083808 TAATTTCGGAATTATGACATCG
131 TAATTTCGGAATTATGACATCG
*
6083830 AAGTCGTTGTAGTATAGCGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCG
1 AAGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCG
6083895 GCAACGGCGATCT
66 GCAACGGCGATCT
6083908 GATCTAAAGT
Statistics
Matches: 599, Mismatches: 67, Indels: 26
0.87 0.10 0.04
Matches are distributed among these distances:
143 2 0.00
144 107 0.18
145 1 0.00
147 7 0.01
148 89 0.15
149 1 0.00
150 41 0.07
151 2 0.00
152 338 0.56
153 11 0.02
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (152 bp):
AAGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCG
GCAACGGCGATCTATCCTCTGATTTATATTTTCTGACCTTCTAAAGTAATTTATAACAAATAATA
TAATTTCGGAATTATGACATCG
Found at i:6084028 original size:128 final size:128
Alignment explanation
Indices: 6083792--6084028 Score: 314
Period size: 128 Copynumber: 1.9 Consensus size: 128
6083782 TCTGACATAA
* ** * *
6083792 TTTATAACAAATAATGTAATTTCGGAATTATGACATCGAAGTCGTTGTAGTATAGCGGTGAGTAT
1 TTTATAACAAATAATATAATTTCGGAATTACCACATCGAAGTCGTTGTAGTATAGCGGTGAGAAA
* * * *
6083857 TCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGATCTGATCTAAAGTAG
66 TCCCGCCTGTCACGCGGGCGACCAGGGTTCGATCCCAGCCAACGGCGATCTGATCTAAAGTAG
* * * *
6083920 TTTATAACTAATAATATAATTTCGGAATTACCATATCGAAGTCGTTGTAGTATGGTGGTGAGAAA
1 TTTATAACAAATAATATAATTTCGGAATTACCACATCGAAGTCGTTGTAGTATAGCGGTGAGAAA
* * *
6083985 TCCCGCCTGTCACG-GGTGCGGCCAGGGTTCGCTCCCATCCAACG
66 TCCCGCCTGTCACGCGG-GCGACCAGGGTTCGATCCCAGCCAACG
6084029 ACGTTTTGCG
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
127 2 0.02
128 90 0.98
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (128 bp):
TTTATAACAAATAATATAATTTCGGAATTACCACATCGAAGTCGTTGTAGTATAGCGGTGAGAAA
TCCCGCCTGTCACGCGGGCGACCAGGGTTCGATCCCAGCCAACGGCGATCTGATCTAAAGTAG
Found at i:6084365 original size:11 final size:10
Alignment explanation
Indices: 6084349--6084379 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
6084339 TCTAACATTG
6084349 TTTTTTTCTT
1 TTTTTTTCTT
6084359 TTTTTTTCTT
1 TTTTTTTCTT
6084369 TTTTTTT-TT
1 TTTTTTTCTT
6084378 TT
1 TT
6084380 ATAAAACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:6084848 original size:31 final size:31
Alignment explanation
Indices: 6084813--6084873 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
6084803 AATTATACAA
6084813 ATAAAATTTTAATTGT-GATTCAAATGTATAT
1 ATAAAATTTTAATT-TAGATTCAAATGTATAT
*
6084844 ATAAAATTTTAATTTAGATTCAATTGTATA
1 ATAAAATTTTAATTTAGATTCAAATGTATA
6084874 CATTTAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (31 bp):
ATAAAATTTTAATTTAGATTCAAATGTATAT
Found at i:6085918 original size:18 final size:18
Alignment explanation
Indices: 6085895--6085930 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6085885 TGTAACATTT
*
6085895 TATATTATGTTATTTTTA
1 TATATTATGTAATTTTTA
6085913 TATATTATGTAATTTTTA
1 TATATTATGTAATTTTTA
6085931 AGACATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (18 bp):
TATATTATGTAATTTTTA
Found at i:6089449 original size:9 final size:9
Alignment explanation
Indices: 6089434--6089516 Score: 58
Period size: 9 Copynumber: 8.6 Consensus size: 9
6089424 TAATTTTTAT
6089434 TAAAAATTA
1 TAAAAATTA
*
6089443 GAAAAATTTA
1 TAAAAA-TTA
*
6089453 TAAAAATCTT
1 TAAAAAT-TA
6089463 TAAAAATTA
1 TAAAAATTA
*
6089472 TAAAAATTG
1 TAAAAATTA
**
6089481 TAAATTTTTA
1 TAAA-AATTA
6089491 TAAAAATCGTAA
1 TAAAAAT--T-A
*
6089503 AAAAAATTA
1 TAAAAATTA
6089512 TAAAA
1 TAAAA
6089517 TATATAGAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
9 25 0.45
10 23 0.41
11 1 0.02
12 7 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:6089458 original size:19 final size:20
Alignment explanation
Indices: 6089429--6089526 Score: 69
Period size: 19 Copynumber: 4.9 Consensus size: 20
6089419 ATATTTAATT
6089429 TTTATTAAAAAT-TAGAAAAA
1 TTTA-TAAAAATCTAGAAAAA
**
6089449 TTTATAAAAATCTTTAAAAA
1 TTTATAAAAATCTAGAAAAA
**
6089469 -TTATAAAAAT-T-GTAAATT
1 TTTATAAAAATCTAG-AAAAA
*
6089487 TTTATAAAAATCGTAAAAAAA
1 TTTATAAAAATC-TAGAAAAA
* *
6089508 ATTATAAAATATATAGAAA
1 TTTATAAAA-ATCTAGAAA
6089527 TATAGAAATA
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
18 4 0.07
19 27 0.45
20 10 0.17
21 17 0.28
22 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (20 bp):
TTTATAAAAATCTAGAAAAA
Found at i:6089459 original size:10 final size:10
Alignment explanation
Indices: 6089429--6089516 Score: 58
Period size: 10 Copynumber: 8.9 Consensus size: 10
6089419 ATATTTAATT
6089429 TTTATTAAAAA
1 TTTA-TAAAAA
*
6089440 -TTAGAAAAA
1 TTTATAAAAA
6089449 TTTATAAAAA
1 TTTATAAAAA
6089459 TCTT-TAAAAA
1 T-TTATAAAAA
6089469 -TTATAAAAA
1 TTTATAAAAA
* **
6089478 -TTGTAAATT
1 TTTATAAAAA
6089487 TTTATAAAAA
1 TTTATAAAAA
* *
6089497 TCGTAAAAAAA
1 T-TTATAAAAA
*
6089508 ATTATAAAA
1 TTTATAAAA
6089517 TATATAGAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
8 2 0.03
9 17 0.29
10 31 0.53
11 9 0.15
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.36
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:6089837 original size:19 final size:19
Alignment explanation
Indices: 6089822--6089907 Score: 57
Period size: 20 Copynumber: 4.4 Consensus size: 19
6089812 TGATTTTATA
6089822 AAATTTTACAATTTTTA-T
1 AAATTTTACAATTTTTAGT
** *
6089840 ATTTTTTTCTAATTTTTAGT
1 AAATTTTAC-AATTTTTAGT
* *
6089860 AAATTTTAAATATTTTTATT
1 AAATTTTACA-ATTTTTAGT
* * *
6089880 AAAGTTTAATAATTTTTAAT
1 AAA-TTTTACAATTTTTAGT
*
6089900 AATTTTTA
1 AAATTTTA
6089908 TTTTTTATAA
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
18 6 0.12
19 13 0.25
20 27 0.53
21 5 0.10
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
AAATTTTACAATTTTTAGT
Found at i:6089874 original size:20 final size:21
Alignment explanation
Indices: 6089849--6089907 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
6089839 TATTTTTTTC
*
6089849 TAATTTTTAGTAAATTTTAAA
1 TAATTTTTAATAAATTTTAAA
* *
6089870 T-ATTTTTATTAAAGTTT-AA
1 TAATTTTTAATAAATTTTAAA
*
6089889 TAATTTTTAATAATTTTTA
1 TAATTTTTAATAAATTTTA
6089908 TTTTTTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 3 0.10
20 27 0.87
21 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
TAATTTTTAATAAATTTTAAA
Found at i:6089897 original size:10 final size:10
Alignment explanation
Indices: 6089831--6089922 Score: 61
Period size: 10 Copynumber: 9.7 Consensus size: 10
6089821 AAAATTTTAC
6089831 AATTTTT-AT
1 AATTTTTAAT
* **
6089840 ATTTTTTTCT
1 AATTTTTAAT
*
6089850 AATTTTTAGT
1 AATTTTTAAT
*
6089860 AAATTTTAA-
1 AATTTTTAAT
*
6089869 ATATTTTTATT
1 A-ATTTTTAAT
**
6089880 AAAGTTTAAT
1 AATTTTTAAT
6089890 AATTTTTAAT
1 AATTTTTAAT
6089900 AATTTTT-AT
1 AATTTTTAAT
6089909 --TTTTT-AT
1 AATTTTTAAT
6089916 AATTTTT
1 AATTTTT
6089923 TTGTCACATG
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
7 7 0.11
9 14 0.22
10 42 0.66
11 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:6089923 original size:17 final size:16
Alignment explanation
Indices: 6089891--6089922 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6089881 AAGTTTAATA
6089891 ATTTTTAATAATTTTT
1 ATTTTTAATAATTTTT
*
6089907 ATTTTTTATAATTTTT
1 ATTTTTAATAATTTTT
6089923 TTGTCACATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTAATAATTTTT
Found at i:6090169 original size:89 final size:90
Alignment explanation
Indices: 6090059--6090246 Score: 238
Period size: 90 Copynumber: 2.1 Consensus size: 90
6090049 TTGAATGCAA
* * *
6090059 AAAAAAAAAGCAAGGGCTTAATTGCTTGTT-TTGAAAAAATTGAA-GGTC-TTTTTTATACATTT
1 AAAAAAAAAGCAAGGGCTTAATT-ATTGTTCTTGAAAAAATTGAAGGGCCATTTTTT-TACATTC
*
6090121 TGACAGTTCAAGTATCCAATTGAGTGC
64 TGAAAGTTCAAGTATCCAATTGAGTGC
* * * * *
6090148 AAAAAAAAAGTAGGGGCTTAATTATTTTTCTTGAAAAAGTTTAAGGGCCATTTTTTTACATTCTG
1 AAAAAAAAAGCAAGGGCTTAATTATTGTTCTTGAAAAAATTGAAGGGCCATTTTTTTACATTCTG
* *
6090213 AAAGTTCAAGTATCGAATTGAGTGT
66 AAAGTTCAAGTATCCAATTGAGTGC
6090238 AAAAAAAAA
1 AAAAAAAAA
6090247 ACAGAAACTT
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
88 4 0.05
89 33 0.39
90 42 0.49
91 6 0.07
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (90 bp):
AAAAAAAAAGCAAGGGCTTAATTATTGTTCTTGAAAAAATTGAAGGGCCATTTTTTTACATTCTG
AAAGTTCAAGTATCCAATTGAGTGC
Found at i:6090275 original size:90 final size:88
Alignment explanation
Indices: 6090046--6090275 Score: 209
Period size: 90 Copynumber: 2.6 Consensus size: 88
6090036 TGCATTTTAT
* * *
6090046 CAATTGAATGCAAAAAAAAAA-AGCAAGGGCTTAA-TTGCTTGTTTTGAAAAAATTGAAGGTCTT
1 CAATTGAGTGCAAAAAAAAAACAG-AA--ACTTAATTTGCTT-TTTT-AAAAAATTGAAGGCCTT
* *
6090109 TTTTATACATTTTGACAGTTCAAGTATC
61 TTTTATACATTCTGAAAGTTCAAGTATC
** *** * *
6090137 CAATTGAGTGCAAAAAAAAAGTAGGGGCTTAATTAT--TTTTCTTGAAAAAGTTTAAGGGCCATT
1 CAATTGAGTGCAAAAAAAAAACAGAAACTTAATT-TGCTTTT-TT-AAAAAATTGAA-GGCC-TT
6090200 TTTT-TACATTCTGAAAGTTCAAGTATC
61 TTTTATACATTCTGAAAGTTCAAGTATC
* *
6090227 GAATTGAGTGTAAAAAAAAAACAGAAACTTAATTTGCTTTTTTAAAAAA
1 CAATTGAGTGCAAAAAAAAAACAGAAACTTAATTTGCTTTTTTAAAAAA
6090276 AGATTGATGA
Statistics
Matches: 114, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
88 2 0.02
89 26 0.23
90 54 0.47
91 30 0.26
92 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (88 bp):
CAATTGAGTGCAAAAAAAAAACAGAAACTTAATTTGCTTTTTTAAAAAATTGAAGGCCTTTTTTA
TACATTCTGAAAGTTCAAGTATC
Found at i:6093313 original size:32 final size:32
Alignment explanation
Indices: 6093276--6093341 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
6093266 AACCTAAAAC
6093276 ATACATCATCCATATCATATATTCATCAACCT
1 ATACATCATCCATATCATATATTCATCAACCT
* *
6093308 ATACATCATTCATATCATATATTCATTAACCT
1 ATACATCATCCATATCATATATTCATCAACCT
6093340 AT
1 AT
6093342 TTCCTTCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (32 bp):
ATACATCATCCATATCATATATTCATCAACCT
Found at i:6094193 original size:43 final size:43
Alignment explanation
Indices: 6094132--6094220 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
6094122 CAATGCCAAC
* * * *
6094132 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGTC-ATT
1 GTCCCAGACGTGGACTTACACGAAATCAAATA-CGATGCCGATT
6094175 GTCCCAGACAG-GGACTTACACGAAATCAAATACGATGCCGATT
1 GTCCCAGAC-GTGGACTTACACGAAATCAAATACGATGCCGATT
6094218 GTC
1 GTC
6094221 GTAACCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
42 6 0.15
43 33 0.82
44 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
GTCCCAGACGTGGACTTACACGAAATCAAATACGATGCCGATT
Found at i:6095366 original size:23 final size:23
Alignment explanation
Indices: 6095340--6095424 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 23
6095330 ACAAAAAAAG
6095340 AAAATATAATAATAATAATAGTA
1 AAAATATAATAATAATAATAGTA
* * * *
6095363 AAAACACAATAGTAATAATAATGA
1 AAAATATAATAATAATAATAGT-A
* *
6095387 AAAGGTATTATAAT-ATAATAGTA
1 AAA-ATATAATAATAATAATAGTA
* *
6095410 ATAATGATGATAATA
1 AAAAT-ATAATAATA
6095425 GTGGTATTAG
Statistics
Matches: 45, Mismatches: 13, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
22 1 0.02
23 28 0.62
24 11 0.24
25 5 0.11
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.29
Consensus pattern (23 bp):
AAAATATAATAATAATAATAGTA
Found at i:6095412 original size:33 final size:38
Alignment explanation
Indices: 6095370--6095451 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 38
6095360 GTAAAAACAC
6095370 AATAGTAATAATAATGA-AA-A-GGTATTA-TAAT-AT
1 AATAGTAATAATAATGATAATAGGGTATTAGTAATAAT
*
6095403 AATAGTAATAATGATGATAATAGTGGTATTAGTAATAAT
1 AATAGTAATAATAATGATAATAG-GGTATTAGTAATAAT
*
6095442 AATAATAATA
1 AATAGTAATA
6095452 GAAAATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 16 0.39
34 2 0.05
35 1 0.02
37 7 0.17
38 4 0.10
39 11 0.27
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.34
Consensus pattern (38 bp):
AATAGTAATAATAATGATAATAGGGTATTAGTAATAAT
Found at i:6095460 original size:19 final size:18
Alignment explanation
Indices: 6095436--6095477 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
6095426 TGGTATTAGT
*
6095436 AATAATAATAATAATAGAA
1 AATAATAACAATAATA-AA
*
6095455 AATAATAACAATATTAAA
1 AATAATAACAATAATAAA
6095473 AATAA
1 AATAA
6095478 CACTTTCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AATAATAACAATAATAAA
Found at i:6095872 original size:13 final size:13
Alignment explanation
Indices: 6095851--6095965 Score: 101
Period size: 13 Copynumber: 9.8 Consensus size: 13
6095841 GTGGAGTGGT
*
6095851 TGGGATGGTTTAG
1 TGGGGTGGTTTAG
6095864 TGGGGTGG--T--
1 TGGGGTGGTTTAG
6095873 TGGGGTGGTTTAG
1 TGGGGTGGTTTAG
6095886 TGGGGTGG--T--
1 TGGGGTGGTTTAG
*
6095895 TGGAGTGGTTTAG
1 TGGGGTGGTTTAG
*
6095908 TGGAGTGGTTTAG
1 TGGGGTGGTTTAG
6095921 TGGGGTGG--T--
1 TGGGGTGGTTTAG
*
6095930 TGGAGTGGTTTAG
1 TGGGGTGGTTTAG
*
6095943 TGGAGTGGTTTAG
1 TGGGGTGGTTTAG
6095956 TGGGGTGGTT
1 TGGGGTGGTT
6095966 GGAGTGAAGA
Statistics
Matches: 85, Mismatches: 5, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
9 22 0.26
11 6 0.07
13 57 0.67
ACGTcount: A:0.10, C:0.00, G:0.53, T:0.37
Consensus pattern (13 bp):
TGGGGTGGTTTAG
Found at i:6095916 original size:35 final size:35
Alignment explanation
Indices: 6095877--6095971 Score: 190
Period size: 35 Copynumber: 2.7 Consensus size: 35
6095867 GGTGGTTGGG
6095877 GTGGTTTAGTGGGGTGGTTGGAGTGGTTTAGTGGA
1 GTGGTTTAGTGGGGTGGTTGGAGTGGTTTAGTGGA
6095912 GTGGTTTAGTGGGGTGGTTGGAGTGGTTTAGTGGA
1 GTGGTTTAGTGGGGTGGTTGGAGTGGTTTAGTGGA
6095947 GTGGTTTAGTGGGGTGGTTGGAGTG
1 GTGGTTTAGTGGGGTGGTTGGAGTG
6095972 AAGATATTTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.11, C:0.00, G:0.53, T:0.37
Consensus pattern (35 bp):
GTGGTTTAGTGGGGTGGTTGGAGTGGTTTAGTGGA
Found at i:6095968 original size:22 final size:22
Alignment explanation
Indices: 6095840--6095971 Score: 124
Period size: 22 Copynumber: 5.8 Consensus size: 22
6095830 TTTATAGGCA
6095840 AGTGGAGTGGTTGG-GATGGTTT
1 AGTGGAGTGGTTGGAG-TGGTTT
* *
6095862 AGTGGGGTGGTTGGGGTGGTTT
1 AGTGGAGTGGTTGGAGTGGTTT
*
6095884 AGTGGGGTGGTTGGAGTGGTTT
1 AGTGGAGTGGTTGGAGTGGTTT
* **
6095906 AGTGGAGTGGTT-TAGTGGGGT
1 AGTGGAGTGGTTGGAGTGGTTT
*
6095927 GGTTGGAGTGGTTTAGTGGAGTGGTTT
1 AG-TGGAGTGG--T--TGGAGTGGTTT
*
6095954 AGTGGGGTGGTTGGAGTG
1 AGTGGAGTGGTTGGAGTG
6095972 AAGATATTTG
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
21 7 0.08
22 66 0.73
23 1 0.01
24 2 0.02
26 8 0.09
27 7 0.08
ACGTcount: A:0.11, C:0.00, G:0.54, T:0.36
Consensus pattern (22 bp):
AGTGGAGTGGTTGGAGTGGTTT
Found at i:6096092 original size:16 final size:15
Alignment explanation
Indices: 6096051--6096095 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
6096041 CTTTGGAGGT
** *
6096051 TGTTGGGTTTTGGGC
1 TGTTGGGTTTTTAGA
6096066 TGTTGGGTTTTTAGA
1 TGTTGGGTTTTTAGA
6096081 TGTTGGGCTTTTTAG
1 TGTTGGG-TTTTTAG
6096096 CCTGGGCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.07, C:0.04, G:0.38, T:0.51
Consensus pattern (15 bp):
TGTTGGGTTTTTAGA
Found at i:6100307 original size:17 final size:17
Alignment explanation
Indices: 6100285--6100322 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
6100275 TCTTTAGAAT
*
6100285 TTTTTTAAAATTATAAA
1 TTTTTTAAAAATATAAA
6100302 TTTTTTAAAAATATAAA
1 TTTTTTAAAAATATAAA
6100319 TTTT
1 TTTT
6100323 GGATTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTTAAAAATATAAA
Found at i:6100319 original size:24 final size:24
Alignment explanation
Indices: 6100292--6100361 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
6100282 AATTTTTTTA
*
6100292 AAATTATAAATTTTTTAAAAATAT
1 AAATTTTAAATTTTTTAAAAATAT
**
6100316 AAATTTTGGATTTTCTTAAAAA-AT
1 AAATTTTAAATTTT-TTAAAAATAT
*
6100340 --ATTTTAAATTTTTGAAAAATAT
1 AAATTTTAAATTTTTTAAAAATAT
6100362 TTTTTTTGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 6 0.16
22 12 0.32
24 13 0.34
25 7 0.18
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (24 bp):
AAATTTTAAATTTTTTAAAAATAT
Found at i:6100350 original size:22 final size:21
Alignment explanation
Indices: 6100298--6100364 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 21
6100288 TTTAAAATTA
6100298 TAAATTTTTTAAAAATATAAATTT
1 TAAATTTTTTAAAAA-AT--ATTT
**
6100322 TGGATTTTCTTAAAAAATATTT
1 TAAATTTT-TTAAAAAATATTT
*
6100344 TAAA-TTTTTGAAAAATATTT
1 TAAATTTTTTAAAAAATATTT
6100364 T
1 T
6100365 TTTTGTTGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 13 0.35
21 3 0.08
22 6 0.16
24 8 0.22
25 7 0.19
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (21 bp):
TAAATTTTTTAAAAAATATTT
Found at i:6101810 original size:4 final size:4
Alignment explanation
Indices: 6101801--6101828 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6101791 GGATTAATTT
6101801 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
6101829 AAAGAGAGTT
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:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:6102297 original size:11 final size:10
Alignment explanation
Indices: 6102256--6102295 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
6102246 TAGGGTTTGG
6102256 TTAATATGATT
1 TTAATAT-ATT
6102267 TTAATATATT
1 TTAATATATT
6102277 TTAA-ATATAT
1 TTAATATAT-T
6102287 TTAATATAT
1 TTAATATAT
6102296 ATATAGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 4 0.15
10 12 0.44
11 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (10 bp):
TTAATATATT
Found at i:6102909 original size:159 final size:161
Alignment explanation
Indices: 6102602--6102914 Score: 499
Period size: 159 Copynumber: 2.0 Consensus size: 161
6102592 GTTAGTTGGT
* *
6102602 TAAATTTGGCGGTGGTCGGTTAAGTCGGATAAGTCAGGAAAATCGACCAAACTAACTAACAACCA
1 TAAATTTGGCGGT-GTCGGTTAAGTCGGATAAGTCAGGAAAATCGACCAAACCAACTAAAAACCA
* *
6102667 ATTATTCTCCCCTGTTGATGGTGGTTGATGATTGTTCGCATTGTGGTGTCAAGAGCCGATGAGTA
65 ATTACTCTCCCCTGTTAATGGTGGTTGATGATTGTTCGCATTGTGGTGTCAAGAGCCGATGAGTA
6102732 TAGCTTTGGTGATAAAGGAGAAAGTTCCTATA
130 TAGCTTTGGTGATAAAGGAGAAAGTTCCTATA
* * *
6102764 TAAATTTGGCGGT-T-GGTTAAGGT-GGATAAGTCATGAAAATTGACCAATCCAACTAAAAACCA
1 TAAATTTGGCGGTGTCGGTTAA-GTCGGATAAGTCAGGAAAATCGACCAAACCAACTAAAAACCA
6102826 ATTACTCTCCCCTAG-TAATGGTGGTTGATGATTGTTCGCATTGTGGTGTCAAGAGCCGATGAGT
65 ATTACTCTCCCCT-GTTAATGGTGGTTGATGATTGTTCGCATTGTGGTGTCAAGAGCCGATGAGT
*
6102890 ATAGCTTTGGTGATTAAGGAGAAAG
129 ATAGCTTTGGTGATAAAGGAGAAAG
6102915 GTCCAAGGTT
Statistics
Matches: 141, Mismatches: 8, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
159 124 0.88
160 4 0.03
162 13 0.09
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (161 bp):
TAAATTTGGCGGTGTCGGTTAAGTCGGATAAGTCAGGAAAATCGACCAAACCAACTAAAAACCAA
TTACTCTCCCCTGTTAATGGTGGTTGATGATTGTTCGCATTGTGGTGTCAAGAGCCGATGAGTAT
AGCTTTGGTGATAAAGGAGAAAGTTCCTATA
Found at i:6105791 original size:32 final size:33
Alignment explanation
Indices: 6105745--6105810 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
6105735 AATCTTCAGG
6105745 TGGTTTTTTATTTTTTAAATACATTTCCTAAAC
1 TGGTTTTTTATTTTTTAAATACATTTCCTAAAC
6105778 TGGTTTTTT-TTTTTTAAATACATTTCCTAAAC
1 TGGTTTTTTATTTTTTAAATACATTTCCTAAAC
6105810 T
1 T
6105811 ATCTTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 24 0.73
33 9 0.27
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (33 bp):
TGGTTTTTTATTTTTTAAATACATTTCCTAAAC
Found at i:6105818 original size:32 final size:33
Alignment explanation
Indices: 6105748--6105819 Score: 112
Period size: 32 Copynumber: 2.2 Consensus size: 33
6105738 CTTCAGGTGG
*
6105748 TTTTTTATTTTTTAAATACATTTCCTAAACTGG
1 TTTTTTATTTTTTAAATACATTTCCTAAACTGA
6105781 TTTTTT-TTTTTTAAATACATTTCCTAAACT-A
1 TTTTTTATTTTTTAAATACATTTCCTAAACTGA
6105812 TCTTTTTA
1 T-TTTTTA
6105820 AGTCCCTGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 1 0.03
32 29 0.81
33 6 0.17
ACGTcount: A:0.26, C:0.12, G:0.03, T:0.58
Consensus pattern (33 bp):
TTTTTTATTTTTTAAATACATTTCCTAAACTGA
Found at i:6110894 original size:13 final size:13
Alignment explanation
Indices: 6110863--6110895 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6110853 GTCGAATTTT
*
6110863 TTAATTGTTTATA
1 TTAATTTTTTATA
6110876 -TAATTTTTTATA
1 TTAATTTTTTATA
6110888 TTAATTTT
1 TTAATTTT
6110896 CAGATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (13 bp):
TTAATTTTTTATA
Found at i:6110945 original size:21 final size:22
Alignment explanation
Indices: 6110916--6110962 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
6110906 ATTTGACAAA
*
6110916 ATTTTAAAATT-TTTTATAAA-T
1 ATTTAAAAATTATTTT-TAAATT
6110937 ATTTAAAAATTATTTTTAAATT
1 ATTTAAAAATTATTTTTAAATT
6110959 ATTT
1 ATTT
6110963 TCATTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTAAAAATTATTTTTAAATT
Found at i:6110963 original size:11 final size:11
Alignment explanation
Indices: 6110916--6110975 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
6110906 ATTTGACAAA
6110916 ATTTTAAAATT
1 ATTTTAAAATT
6110927 -TTTTATAAA-T
1 ATTTTA-AAATT
*
6110937 ATTTAAAAATT
1 ATTTTAAAATT
*
6110948 ATTTTTAAATT
1 ATTTTAAAATT
*
6110959 ATTTT--CATT
1 ATTTTAAAATT
6110968 ATTTTAAA
1 ATTTTAAA
6110976 TATAAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
9 8 0.21
10 9 0.23
11 22 0.56
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTAAAATT
Found at i:6116149 original size:24 final size:24
Alignment explanation
Indices: 6116122--6116170 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
6116112 ATTTCTAAGT
6116122 ACTTCACAAATGCGTATAAACCGA
1 ACTTCACAAATGCGTATAAACCGA
6116146 ACTTCACAAATGCGTATAAACCGA
1 ACTTCACAAATGCGTATAAACCGA
6116170 A
1 A
6116171 ACTGCACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.20
Consensus pattern (24 bp):
ACTTCACAAATGCGTATAAACCGA
Found at i:6119140 original size:15 final size:15
Alignment explanation
Indices: 6119120--6119150 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6119110 TCCTTTGAGT
6119120 TTTCTTTTCCTTTTC
1 TTTCTTTTCCTTTTC
6119135 TTTCTTTTCCTTTTC
1 TTTCTTTTCCTTTTC
6119150 T
1 T
6119151 ATCCTTGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTTTCCTTTTC
Found at i:6123465 original size:16 final size:16
Alignment explanation
Indices: 6123444--6123476 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6123434 TAAAAGATTA
6123444 AAAGTAA-ATGATATAC
1 AAAGTAATAT-ATATAC
6123460 AAAGTAATATATATAC
1 AAAGTAATATATATAC
6123476 A
1 A
6123477 TGAAAAACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (16 bp):
AAAGTAATATATATAC
Found at i:6125256 original size:131 final size:132
Alignment explanation
Indices: 6125021--6125290 Score: 407
Period size: 131 Copynumber: 2.1 Consensus size: 132
6125011 ACTATTTAGG
* * * *
6125021 GATAAGATCTGTACTTTCCAACTTGTTACCCTATTGCTTAGGGGGTTAAGGGTCGTATCTTCAAC
1 GATAAGATCTGTAATTTCCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTCAAC
* *
6125086 CTGCTCTCTTGTTACCTCAGAGAGATAAGGCCGGTGGCTAAAATCTACTCCATAGCTGATACATG
66 CTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTAAAATCTACTCCATAGCCGATACATG
6125151 GA
131 GA
* * * * *
6125153 GATAAGCTCTGTAATTTTCAGCCTGTTACCCTACTGTTTA-GGGGTTAAGGCTTGTATCTTCAAC
1 GATAAGATCTGTAATTTCCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTCAAC
* * *
6125217 CTGCTCTCTTGCTACCTCAGAGATATAAGGTCGGTGGCTAAAATCTGCTCCATAGCCGATACATG
66 CTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTAAAATCTACTCCATAGCCGATACATG
6125282 GA
131 GA
6125284 GATAAGA
1 GATAAGA
6125291 CTCGCCATTT
Statistics
Matches: 123, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
131 90 0.73
132 33 0.27
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (132 bp):
GATAAGATCTGTAATTTCCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTCAAC
CTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTAAAATCTACTCCATAGCCGATACATG
GA
Found at i:6125453 original size:177 final size:177
Alignment explanation
Indices: 6125128--6125821 Score: 1081
Period size: 177 Copynumber: 3.9 Consensus size: 177
6125118 GGTGGCTAAA
* * *
6125128 ATCTACTCCATAGCTGATACATGGAGATAAGCTCTGTAATTTTCAGCCTGTTACCCTACTGTTTA
1 ATCTACTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTA
* * *
6125193 -GGGGTTAAGGCTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGATATAAGGTCGGTGGCTA
66 GGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTA
*
6125257 AAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTTCG
131 AAATCTGCTCCACAGCCGATACATGGAGATAAGACTCGCCATTTTCG
6125304 ATCTACTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTA-TGGCTT
1 ATCTACTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACT-GCTT
* * *
6125368 AGGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACATCAAAGAGATAAGGCCAGTGGCT
65 AGGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCT
*
6125433 AAAATCTGCTCCACAGCCGATACATGGAGATAAGACTTGCCATTTTCG
130 AAAATCTGCTCCACAGCCGATACATGGAGATAAGACTCGCCATTTTCG
*
6125481 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTA
1 ATCTACTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTA
* *
6125546 GGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGATATAAGGTCGGTGGCTA
66 GGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTA
* * *
6125611 AAATCTGCTCC-CTAGTCGATACATGGAGATAAGACTCGTCA-TTTCTA
131 AAATCTGCTCCAC-AGCCGATACATGGAGATAAGACTCGCCATTTTC-G
** * * *
6125658 ATCTGTTCCATAACCGATACATGAAGATAAGCTCTGTAATTTTCAGCCTGTTACCCTACTGCTTA
1 ATCTACTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTA
* * *
6125723 GCGGGTTAAGGCTCATATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGATGGCTA
66 GGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTA
* * *
6125788 ACATCTGCTCCATAGCCTATACATGGAGATAAGA
131 AAATCTGCTCCACAGCCGATACATGGAGATAAGA
6125822 TCTATAATTT
Statistics
Matches: 478, Mismatches: 34, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
175 1 0.00
176 65 0.14
177 411 0.86
178 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (177 bp):
ATCTACTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTA
GGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTA
AAATCTGCTCCACAGCCGATACATGGAGATAAGACTCGCCATTTTCG
Found at i:6125834 original size:132 final size:132
Alignment explanation
Indices: 6125657--6125953 Score: 468
Period size: 132 Copynumber: 2.2 Consensus size: 132
6125647 CGTCATTTCT
* * * * *
6125657 AATCTGTTCCATAACCGATACATGAAGATAAGCTCTGTAATTTTCAGCCTGTTACCCTACTGCTT
1 AATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGCTT
**
6125722 AGCGGGTTAAGGCTCATATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGATGGCT
66 AAAGGGTTAAGGCTCATATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGATGGCT
6125787 AA
131 AA
* * *
6125789 CATCTGCTCCATAGCCTATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGGTT
1 AATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGCTT
* * *
6125854 AAAGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTCGGTGGCT
66 AAAGGGTTAAGGCTCATATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGATGGCT
6125919 AA
131 AA
*
6125921 AATCTGCTCCATAGTCGATACATGGAGATAAGA
1 AATCTGCTCCATAGCCGATACATGGAGATAAGA
6125954 CTTGTCATTT
Statistics
Matches: 149, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 149 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
AATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGCTT
AAAGGGTTAAGGCTCATATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGATGGCT
AA
Found at i:6125877 original size:309 final size:309
Alignment explanation
Indices: 6125481--6126128 Score: 1064
Period size: 309 Copynumber: 2.1 Consensus size: 309
6125471 GCCATTTTCG
*
6125481 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTA
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGCTTA
** *
6125546 GGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGATATAAGGTCGGTGGCTA
66 AAGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTCGGTGGCTA
* *
6125611 AAATCTGCTCCCTAGTCGATACATGGAGATAAGACTCGTCATTTCTAATCTGTTCCATAACCGAT
131 AAATCTGCTCCATAGTCGATACATGGAGATAAGACTCGTCATTTCTAATCTGCTCCATAACCGAT
* *
6125676 ACATGAAGATAAGCTCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGCGGGTTAAGGCTCATAT
196 ACATGAAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAGCGGGTTAAGGCTCATAT
*
6125741 CTTCAACCTGCTCTCTTGCTACCTC-AGAGAGATAAGGCCGATGGCTAAC
261 CTTCAACCTGCTCTCTTGCTACC-CGAGAGAGATAAGGCCGATGGCTAAA
* *
6125790 ATCTGCTCCATAGCCTATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGGTTA
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGCTTA
6125855 AAGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTCGGTGGCTA
66 AAGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTCGGTGGCTA
* * * **
6125920 AAATCTGCTCCATAGTCGATACATGGAGATAAGACTTGTCATTTCTGATTTGCTCCATAGTCGAT
131 AAATCTGCTCCATAGTCGATACATGGAGATAAGACTCGTCATTTCTAATCTGCTCCATAACCGAT
* * * *
6125985 ACATGGAGATAAGATTTGTAATTTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGTAT
196 ACATGAAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAGCGGGTTAAGGCTCATAT
* *
6126050 CTTCAACCTGCTCTCTTGCTACCCGAGAGAGATAAGGTCGGTGGCTAAA
261 CTTCAACCTGCTCTCTTGCTACCCGAGAGAGATAAGGCCGATGGCTAAA
* *
6126099 ATCTGCTCTATAGTCGATACATGGAGATAA
1 ATCTGCTCCATAGCCGATACATGGAGATAA
6126129 AACTCGCCAT
Statistics
Matches: 313, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
308 1 0.00
309 312 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (309 bp):
ATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGCTTA
AAGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTCGGTGGCTA
AAATCTGCTCCATAGTCGATACATGGAGATAAGACTCGTCATTTCTAATCTGCTCCATAACCGAT
ACATGAAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAGCGGGTTAAGGCTCATAT
CTTCAACCTGCTCTCTTGCTACCCGAGAGAGATAAGGCCGATGGCTAAA
Found at i:6125931 original size:486 final size:486
Alignment explanation
Indices: 6125304--6126222 Score: 1477
Period size: 486 Copynumber: 1.9 Consensus size: 486
6125294 GCCATTTTCG
*
6125304 ATCTACTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTATGGCTTA
1 ATCTACTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTATGGCTTA
**
6125369 GGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACATCAAAGAGATAAGGCCAGTGGCTA
66 AAGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACATCAAAGAGATAAGGCCAGTGGCTA
6125434 AAATCTGCTCCACAGCCGATACATGGAGATAAGACTTGCCATTT-TCGATCTGCTCCATAGCCGA
131 AAATCTGCTCCACAGCCGATACATGGAGATAAGACTTGCCATTTCT-GATCTGCTCCATAGCCGA
*
6125498 TACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTA
195 TACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGTA
* *
6125563 TCTTCAACCTGCTCTCTTGCTACCTC-AGAGATATAAGGTCGGTGGCTAAAATCTGCTCCCTAGT
260 TCTTCAACCTGCTCTCTTGCTACC-CGAGAGAGATAAGGTCGGTGGCTAAAATCTGCTCCATAGT
* * * *
6125627 CGATACATGGAGATAAGACTCGTCATTTCTAATCTGT-TCCATAACCGATACATGAAGATAAGCT
324 CGATACATGGAGATAAAACTCGCCATTTCTAATCT-TCTCCATAACCAATACATGAAGATAAGAT
* * *
6125691 CTGTAATTTTCAGCCTGTTACCCTACTGCTTAGCGGGTTAAGGCTCATATCTTCAACCTGCTCTC
388 CTGTAATTTGCAGCCTGTTACCCTACTACTTAGAGGGTTAAGGCTCATATCTTCAACCTGCTCTC
6125756 TTGCTACCTCAGAGAGATAAGGCCGATGGCTAAC
453 TTGCTACCTCAGAGAGATAAGGCCGATGGCTAAC
* *
6125790 ATCTGCTCCATAGCCTATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGG-TT
1 ATCTACTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTA-TGGCTT
* * * *
6125854 AAAGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTCGGTGGCT
65 AAAGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACATCAAAGAGATAAGGCCAGTGGCT
* * * * *
6125919 AAAATCTGCTCCATAGTCGATACATGGAGATAAGACTTGTCATTTCTGATTTGCTCCATAGTCGA
130 AAAATCTGCTCCACAGCCGATACATGGAGATAAGACTTGCCATTTCTGATCTGCTCCATAGCCGA
*
6125984 TACATGGAGATAAGATTTGTAATTTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGTA
195 TACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGTA
*
6126049 TCTTCAACCTGCTCTCTTGCTACCCGAGAGAGATAAGGTCGGTGGCTAAAATCTGCTCTATAGTC
260 TCTTCAACCTGCTCTCTTGCTACCCGAGAGAGATAAGGTCGGTGGCTAAAATCTGCTCCATAGTC
* * * *
6126114 GATACATGGAGATAAAACTCGCCATTTCTGATCTTCTCTATAGCCAATACATGGAGATAAGATCT
325 GATACATGGAGATAAAACTCGCCATTTCTAATCTTCTCCATAACCAATACATGAAGATAAGATCT
* * *
6126179 GTAATTTGCAGCCTGTTACCTTATTACTTATAGGGTTAAGGCTC
390 GTAATTTGCAGCCTGTTACCCTACTACTTAGAGGGTTAAGGCTC
6126223 GTGACTTCAC
Statistics
Matches: 396, Mismatches: 33, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
485 2 0.01
486 390 0.98
487 4 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (486 bp):
ATCTACTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTATGGCTTA
AAGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACATCAAAGAGATAAGGCCAGTGGCTA
AAATCTGCTCCACAGCCGATACATGGAGATAAGACTTGCCATTTCTGATCTGCTCCATAGCCGAT
ACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGTAT
CTTCAACCTGCTCTCTTGCTACCCGAGAGAGATAAGGTCGGTGGCTAAAATCTGCTCCATAGTCG
ATACATGGAGATAAAACTCGCCATTTCTAATCTTCTCCATAACCAATACATGAAGATAAGATCTG
TAATTTGCAGCCTGTTACCCTACTACTTAGAGGGTTAAGGCTCATATCTTCAACCTGCTCTCTTG
CTACCTCAGAGAGATAAGGCCGATGGCTAAC
Found at i:6125997 original size:177 final size:178
Alignment explanation
Indices: 6125793--6126224 Score: 672
Period size: 177 Copynumber: 2.4 Consensus size: 178
6125783 GGCTAACATC
* * **
6125793 TGCTCCATAGCCTATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGGTTAAAG
1 TGCTCCATAGCCAATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAAAG
6125858 GGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTC-AGAGAGATAAGGTCGGTGGCTAAA
66 GGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACC-CGAGAGAGATAAGGTCGGTGGCTAAA
* * *
6125922 ATCTGCTCCATAGTCGATACATGGAGATAAGACTTGTCATTTCTGAT-T
130 ATCTGCTCCATAGTCGATACATGGAGATAAAACTCGCCATTTCTGATCT
* * * **
6125970 TGCTCCATAGTCGATACATGGAGATAAGATTTGTAATTTTCAGCCTGTTACCCTACTACTTAGGG
1 TGCTCCATAGCCAATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAAAG
6126035 GGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCCGAGAGAGATAAGGTCGGTGGCTAAAA
66 GGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCCGAGAGAGATAAGGTCGGTGGCTAAAA
*
6126100 TCTGCTCTATAGTCGATACATGGAGATAAAACTCGCCATTTCTGATCT
131 TCTGCTCCATAGTCGATACATGGAGATAAAACTCGCCATTTCTGATCT
* * * * *
6126148 T-CTCTATAGCCAATACATGGAGATAAGATCTGTAATTTGCAGCCTGTTACCTTATTACTTATAG
1 TGCTCCATAGCCAATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAAAG
6126212 GGTTAAGGCTCGT
66 GGTTAAGGCTCGT
6126225 GACTTCACCG
Statistics
Matches: 232, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
176 1 0.00
177 229 0.99
178 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (178 bp):
TGCTCCATAGCCAATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAAAG
GGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCCGAGAGAGATAAGGTCGGTGGCTAAAA
TCTGCTCCATAGTCGATACATGGAGATAAAACTCGCCATTTCTGATCT
Found at i:6126429 original size:64 final size:64
Alignment explanation
Indices: 6126303--6126430 Score: 166
Period size: 64 Copynumber: 2.0 Consensus size: 64
6126293 ACTTATGCCG
* * * * * * * **
6126303 AATAATTGGGATGTTATGATCGAAATGAATCAAATGCTCCTAGCTAGATGTGATGTTTATGTCA
1 AATAATTAGGATGCTATGATCAAAATGAAGCAAATGCTCCTAACTAGATGTAATATGAATGTCA
*
6126367 AATAATTAGGATGCTGTGATCAAAATGAAGCAAATGCTCCTAACTAGATGTAATATGAATGTCA
1 AATAATTAGGATGCTATGATCAAAATGAAGCAAATGCTCCTAACTAGATGTAATATGAATGTCA
6126431 TTGGTATGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (64 bp):
AATAATTAGGATGCTATGATCAAAATGAAGCAAATGCTCCTAACTAGATGTAATATGAATGTCA
Found at i:6136112 original size:36 final size:35
Alignment explanation
Indices: 6136071--6136138 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
6136061 AAATAAAAAA
*
6136071 TTTAAATTTCTAAAAAAATAAATATAAGGACTAAAT
1 TTTAAATTTCTAAAAAAA-AAATAGAAGGACTAAAT
* * *
6136107 TTTAAATTTTTCAAAAAAAAATAGAGGGACTA
1 TTTAAATTTCTAAAAAAAAAATAGAAGGACTA
6136139 TAGATATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 12 0.43
36 16 0.57
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (35 bp):
TTTAAATTTCTAAAAAAAAAATAGAAGGACTAAAT
Found at i:6144037 original size:11 final size:11
Alignment explanation
Indices: 6144021--6144073 Score: 88
Period size: 11 Copynumber: 4.8 Consensus size: 11
6144011 AGGTATAGGT
*
6144021 AGGTATGGGAA
1 AGGTATGGGCA
6144032 AGGTATGGGCA
1 AGGTATGGGCA
6144043 AGGTATGGGCA
1 AGGTATGGGCA
6144054 AGGTATGGGCA
1 AGGTATGGGCA
*
6144065 AGGAATGGG
1 AGGTATGGG
6144074 TATATTCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.30, C:0.06, G:0.47, T:0.17
Consensus pattern (11 bp):
AGGTATGGGCA
Found at i:6148116 original size:18 final size:18
Alignment explanation
Indices: 6148093--6148149 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
6148083 CCCAACTACT
*
6148093 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
6148111 GTATACGTGAATAGTTCC
1 GTATACGTGAATAGTACC
6148129 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
6148147 GTA
1 GTA
6148150 AACGGTCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:6148709 original size:11 final size:11
Alignment explanation
Indices: 6148693--6148734 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
6148683 AGGTATAGGT
6148693 AGGTATGGGAA
1 AGGTATGGGAA
*
6148704 AGGTATGGGTA
1 AGGTATGGGAA
*
6148715 AGGTATGGGCA
1 AGGTATGGGAA
*
6148726 AGGAATGGG
1 AGGTATGGG
6148735 TATATTCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:6148721 original size:22 final size:22
Alignment explanation
Indices: 6148682--6148736 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
6148672 TGACCTTTCC
*
6148682 AAGGTATAGGT-AGGTATGGGA
1 AAGGTATGGGTAAGGTATGGGA
*
6148703 AAGGTATGGGTAAGGTATGGGC
1 AAGGTATGGGTAAGGTATGGGA
*
6148725 AAGGAATGGGTA
1 AAGGTATGGGTA
6148737 TATTCTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.33, C:0.02, G:0.44, T:0.22
Consensus pattern (22 bp):
AAGGTATGGGTAAGGTATGGGA
Found at i:6153546 original size:23 final size:24
Alignment explanation
Indices: 6153520--6153564 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
6153510 AGATTGCATG
* *
6153520 TATTAATTTTAGTATT-TTATATT
1 TATTAATTATAATATTATTATATT
*
6153543 TATTTATTATAATATTATTATA
1 TATTAATTATAATATTATTATA
6153565 ATATTTGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TATTAATTATAATATTATTATATT
Found at i:6157101 original size:28 final size:28
Alignment explanation
Indices: 6157055--6157120 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
6157045 TTTTAAGGGG
* *
6157055 TTAGGGTTTTATTTATTTAAATTAGGAT
1 TTAGGGTTTTACTTATTTAAAGTAGGAT
* * *
6157083 TTAGGGTTTTGCTTGTTTAAAGTAGGGT
1 TTAGGGTTTTACTTATTTAAAGTAGGAT
*
6157111 TTAGAGTTTT
1 TTAGGGTTTT
6157121 TTTTGAGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (28 bp):
TTAGGGTTTTACTTATTTAAAGTAGGAT
Found at i:6159045 original size:5 final size:6
Alignment explanation
Indices: 6159030--6159054 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6159020 CAAATTTTAA
6159030 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
6159055 TTATAATTAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:6161242 original size:51 final size:49
Alignment explanation
Indices: 6161134--6161244 Score: 116
Period size: 52 Copynumber: 2.2 Consensus size: 49
6161124 CAAACAGTGG
6161134 TTTTTTTTCCTTCTGCTTTCCCTTCTCTTTCTACTCTCATCTCTTTTTC
1 TTTTTTTTCCTTCTGCTTTCCCTTCTCTTTCTACTCTCATCTCTTTTTC
* * * * * *
6161183 TTTCTTTTTACCTTCCTTC-TTCTCTTCTCTATTCTACTTTCTTTTCTTTCTTT
1 TTT-TTTTT-CCTT-CTGCTTTCCCTTCTCT-TTCTACTCTCATCTCTTT-TTC
6161236 TTTTTTTTC
1 TTTTTTTTC
6161245 ACTCAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
49 3 0.06
50 5 0.10
51 15 0.29
52 23 0.45
53 5 0.10
ACGTcount: A:0.05, C:0.29, G:0.01, T:0.66
Consensus pattern (49 bp):
TTTTTTTTCCTTCTGCTTTCCCTTCTCTTTCTACTCTCATCTCTTTTTC
Found at i:6161243 original size:52 final size:50
Alignment explanation
Indices: 6161134--6161244 Score: 118
Period size: 51 Copynumber: 2.2 Consensus size: 50
6161124 CAAACAGTGG
6161134 TTTTTTTTCCTTCTGCTTTCCCTTCTCTTTCTACTCTCATCTCTTTTTCT
1 TTTTTTTTCCTTCTGCTTTCCCTTCTCTTTCTACTCTCATCTCTTTTTCT
* * * * * *
6161184 TTCTTTTTACCTTCCTTC-TTCTCTTCTCTATTCTACTTTCTTTTCTTTCTT-T
1 TT-TTTTTTCCTT-CTGCTTTCCCTTCTCT-TTCTACTCTCATCTCTTT-TTCT
6161236 TTTTTTTTC
1 TTTTTTTTC
6161245 ACTCAATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
50 2 0.04
51 25 0.50
52 21 0.42
53 2 0.04
ACGTcount: A:0.05, C:0.29, G:0.01, T:0.66
Consensus pattern (50 bp):
TTTTTTTTCCTTCTGCTTTCCCTTCTCTTTCTACTCTCATCTCTTTTTCT
Found at i:6161940 original size:23 final size:24
Alignment explanation
Indices: 6161914--6161960 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6161904 TATTTCAGGG
6161914 ACAAAAAAAG-TCGAATTACAAGT
1 ACAAAAAAAGATCGAATTACAAGT
* *
6161937 ACAAAAAAAGATTGAATTATAAGT
1 ACAAAAAAAGATCGAATTACAAGT
6161961 TGAAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.57, C:0.09, G:0.13, T:0.21
Consensus pattern (24 bp):
ACAAAAAAAGATCGAATTACAAGT
Found at i:6167873 original size:21 final size:22
Alignment explanation
Indices: 6167847--6167898 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
6167837 ATAATCTTTA
6167847 AAAAAATTAATAAATA-AAAAT
1 AAAAAATTAATAAATATAAAAT
** *
6167868 AAAAAATTTCTAAATATTAAAT
1 AAAAAATTAATAAATATAAAAT
6167890 -AAAAATTAA
1 AAAAAATTAA
6167899 CATATTTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAATTAATAAATATAAAAT
Found at i:6169535 original size:27 final size:26
Alignment explanation
Indices: 6169498--6169612 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
6169488 AGCATGGCTG
* *
6169498 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
6169524 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
6169552 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
6169579 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
6169606 CCAGAAC
1 CCAGAAC
6169613 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:6169557 original size:54 final size:54
Alignment explanation
Indices: 6169498--6169612 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
6169488 AGCATGGCTG
*
6169498 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
6169552 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
6169606 CCAGAAC
1 CCAGAAC
6169613 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:6169738 original size:23 final size:24
Alignment explanation
Indices: 6169712--6169757 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6169702 CAAAATTAAC
*
6169712 CCTA-GGGTATAACGGTAATTTTA
1 CCTAGGGGTATAACAGTAATTTTA
6169735 CCTAGGGGTATAACAGTAATTTT
1 CCTAGGGGTATAACAGTAATTTT
6169758 CCATACATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (24 bp):
CCTAGGGGTATAACAGTAATTTTA
Found at i:6171242 original size:26 final size:26
Alignment explanation
Indices: 6171211--6171318 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
6171201 TGAAATGCCC
*
6171211 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
6171237 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * * *
6171263 ATCATGAAATATTTGCCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
6171289 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
6171315 ATCA
1 ATCA
6171319 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:6176495 original size:27 final size:26
Alignment explanation
Indices: 6176458--6176572 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
6176448 AGCATGGCTG
* *
6176458 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
6176484 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
6176512 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
6176539 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
6176566 CCAGAAC
1 CCAGAAC
6176573 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:6176517 original size:54 final size:54
Alignment explanation
Indices: 6176458--6176572 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
6176448 AGCATGGCTG
*
6176458 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
6176512 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
6176566 CCAGAAC
1 CCAGAAC
6176573 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:6178233 original size:26 final size:25
Alignment explanation
Indices: 6178178--6178281 Score: 176
Period size: 25 Copynumber: 4.2 Consensus size: 25
6178168 ATGAAATTCC
6178178 ATCAT-GAACATTTACCTAACCATT
1 ATCATGGAACATTTACCTAACCATT
6178202 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAA-CCATT
6178228 ATCATGGAA-ATTTACCTAACCATT
1 ATCATGGAACATTTACCTAACCATT
6178252 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACC-ATT
6178278 ATCA
1 ATCA
6178282 ATTTGTACAT
Statistics
Matches: 76, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
24 19 0.25
25 36 0.47
26 21 0.28
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.33
Consensus pattern (25 bp):
ATCATGGAACATTTACCTAACCATT
Found at i:6179394 original size:19 final size:19
Alignment explanation
Indices: 6179344--6179396 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 19
6179334 TGTTTTATAT
* *
6179344 TTTATGTTCAATTTAGTCC
1 TTTATGTTCAATTTACTGC
6179363 TTT-TGTT-AATTTACTGC
1 TTTATGTTCAATTTACTGC
*
6179380 TTTATTTTCAATTTACT
1 TTTATGTTCAATTTACT
6179397 TGTTTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 11 0.38
18 7 0.24
19 11 0.38
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (19 bp):
TTTATGTTCAATTTACTGC
Found at i:6179405 original size:20 final size:19
Alignment explanation
Indices: 6179344--6179407 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 19
6179334 TGTTTTATAT
* * *
6179344 TTTATGTTCAATTTAGTCC
1 TTTATTTTCAATTTACTGC
*
6179363 TTT-TGTT-AATTTACTGC
1 TTTATTTTCAATTTACTGC
*
6179380 TTTATTTTCAATTTACTTGT
1 TTTATTTTCAATTTAC-TGC
6179400 TTTATTTT
1 TTTATTTT
6179408 GTTATTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 11 0.29
18 7 0.18
19 10 0.26
20 10 0.26
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTATTTTCAATTTACTGC
Found at i:6179440 original size:18 final size:19
Alignment explanation
Indices: 6179410--6179460 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
6179400 TTTATTTTGT
*
6179410 TATT-TATTAATTATAATA
1 TATTATATTTATTATAATA
*
6179428 T-TTATATTTATTAT-ATT
1 TATTATATTTATTATAATA
*
6179445 TATTGTATTTATTATA
1 TATTATATTTATTATA
6179461 TGTCTTAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTATATTTATTATAATA
Found at i:6179441 original size:9 final size:9
Alignment explanation
Indices: 6179429--6179461 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
6179419 ATTATAATAT
6179429 TTATATTTA
1 TTATATTTA
6179438 TTATATTTA
1 TTATATTTA
*
6179447 TTGTATTTA
1 TTATATTTA
6179456 TTATAT
1 TTATAT
6179462 GTCTTAGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TTATATTTA
Found at i:6179443 original size:15 final size:16
Alignment explanation
Indices: 6179410--6179461 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
6179400 TTTATTTTGT
* *
6179410 TATTTATTAATTATAA
1 TATTTATTATTTATTA
6179426 TATTTA-TATTTATTA
1 TATTTATTATTTATTA
6179441 TATTTATTGTATTTATTA
1 TATTTA-T-TATTTATTA
6179459 TAT
1 TAT
6179462 GTCTTAGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 13 0.42
16 6 0.19
18 12 0.39
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTTATTATTTATTA
Found at i:6179913 original size:12 final size:12
Alignment explanation
Indices: 6179896--6179935 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
6179886 TTTTCGTACC
*
6179896 TTATTATATTTA
1 TTATTATATCTA
6179908 TTATTATATCTA
1 TTATTATATCTA
6179920 TTATT-T-TC-A
1 TTATTATATCTA
6179929 TTATTAT
1 TTATTAT
6179936 CACTTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 6 0.23
10 3 0.12
11 1 0.04
12 16 0.62
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATTATATCTA
Found at i:6180126 original size:23 final size:22
Alignment explanation
Indices: 6180082--6180127 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
6180072 TTTTACTATT
*
6180082 TATGTATAGATTTCAAATACTA
1 TATGTATAGATTTCAAACACTA
* *
6180104 TATGTAGTATATTTCTAACACTA
1 TATGTA-TAGATTTCAAACACTA
6180127 T
1 T
6180128 TACTATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
TATGTATAGATTTCAAACACTA
Found at i:6181497 original size:133 final size:137
Alignment explanation
Indices: 6181313--6181595 Score: 511
Period size: 134 Copynumber: 2.1 Consensus size: 137
6181303 TATTGGGCCT
**
6181313 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
6181378 AG-CCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
6181441 CATATGC
131 CATATGC
6181448 AAGCCCATTTGGGTAACAGT-GTACTGGGCCA-AGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
6181511 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
6181576 CATATGC
131 CATATGC
6181583 AAGCCCATTTGGG
1 AAGCCCATTTGGG
6181596 GAGACTACTC
Statistics
Matches: 143, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
133 34 0.24
134 69 0.48
135 40 0.28
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:6181880 original size:25 final size:27
Alignment explanation
Indices: 6181843--6181895 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
6181833 TCAAACATGC
6181843 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
6181869 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
6181895 A
1 A
6181896 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:6183411 original size:26 final size:26
Alignment explanation
Indices: 6183375--6183483 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
6183365 CATGAAATTC
6183375 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6183401 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
6183427 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
6183453 TTATCATGGAACATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCA
6183478 TTATCA
1 TTATCA
6183484 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
25 9 0.11
26 70 0.89
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:6187424 original size:135 final size:137
Alignment explanation
Indices: 6187181--6187465 Score: 520
Period size: 135 Copynumber: 2.1 Consensus size: 137
6187171 TATTGGGCCT
** *
6187181 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
6187246 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
6187310 CATATGC
131 CATATGC
6187317 AAGCCCATTTGGGTAACAGTGATACTGGGCCA-AGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
6187381 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
6187446 CATATGC
131 CATATGC
6187453 AAGCCCATTTGGG
1 AAGCCCATTTGGG
6187466 GAGACTACTC
Statistics
Matches: 144, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
135 93 0.65
136 51 0.35
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGATACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:6189273 original size:26 final size:26
Alignment explanation
Indices: 6189237--6189345 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
6189227 AATGAAATTC
6189237 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6189263 TTATCATGAAACATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
6189288 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
6189314 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6189340 TTATCA
1 TTATCA
6189346 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 23 0.29
26 55 0.71
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:6189315 original size:51 final size:52
Alignment explanation
Indices: 6189237--6189345 Score: 175
Period size: 51 Copynumber: 2.1 Consensus size: 52
6189227 AATGAAATTC
6189237 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
* * * *
6189288 TTATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
6189340 TTATCA
1 TTATCA
6189346 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
51 44 0.83
52 9 0.17
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (52 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
Found at i:6199098 original size:71 final size:70
Alignment explanation
Indices: 6198972--6199109 Score: 195
Period size: 71 Copynumber: 2.0 Consensus size: 70
6198962 AATTTTTACT
* * * *
6198972 TTTCCAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCTTCAAGACACGTTGAGGTAATTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT-ATTTCAA
6199037 TTTATG
65 TTTATG
** * *
6199043 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTTTTTCAAT
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTCAAT
6199108 TT
66 TT
6199110 CTACTTTCCA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
70 9 0.15
71 50 0.85
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (70 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTCAAT
TTATG
Found at i:6199177 original size:257 final size:258
Alignment explanation
Indices: 6198876--6199427 Score: 1007
Period size: 257 Copynumber: 2.1 Consensus size: 258
6198866 TATGCTTCAA
6198876 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTCAAATTC
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTCAAATTC
* *
6198941 TCTTGTTCAAATCCTGTCTTTAATTTTTACTTTTCCAAAATCAACTCATATTGTGAGAGGTGAGT
66 TCTTGTTCAAATCCTGTCTTTAATTTTTACTTTTCCAAAATCAACTCATATTGCGAGAGGTAAGT
* *
6199006 TGAGCTTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAG
131 TGAGCCTCAAGACACGTTGAGGTAATTTCAATTAATGTTTCAAAAATCAACTCATATTGCGAGAG
6199071 GTGAGTTGAGCCTCGGGGCACGCTGAGGT-TTTTCAATTTCTACTTTCCAATTCCTGTTTTTC
196 GTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTACTTTCCAATTCCTGTTTTTC
* * *
6199133 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGTCTCGGGGCACGTCGAGGTATTTTCAAATTC
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTCAAATTC
6199198 TCTTGTTCAAATCCTGTCTTTAATTTTTACTTTTCCAAAATCAACTCATATTGCGAGAGGTAAGT
66 TCTTGTTCAAATCCTGTCTTTAATTTTTACTTTTCCAAAATCAACTCATATTGCGAGAGGTAAGT
6199263 TGAGCCTCAAGACACGTTGAGGTAATTTCAATTAATGTTTCAAAAATCAACTCATATTGCGAGAG
131 TGAGCCTCAAGACACGTTGAGGTAATTTCAATTAATGTTTCAAAAATCAACTCATATTGCGAGAG
6199328 GTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTACTTTCCAATTCCTGTTTTTC
196 GTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTACTTTCCAATTCCTGTTTTTC
* * *
6199391 AAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
6199428 TTCAATTTAT
Statistics
Matches: 283, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
257 217 0.77
258 66 0.23
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (258 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTCAAATTC
TCTTGTTCAAATCCTGTCTTTAATTTTTACTTTTCCAAAATCAACTCATATTGCGAGAGGTAAGT
TGAGCCTCAAGACACGTTGAGGTAATTTCAATTAATGTTTCAAAAATCAACTCATATTGCGAGAG
GTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTACTTTCCAATTCCTGTTTTTC
Found at i:6199311 original size:71 final size:71
Alignment explanation
Indices: 6199229--6199366 Score: 213
Period size: 71 Copynumber: 1.9 Consensus size: 71
6199219 AATTTTTACT
* *
6199229 TTTCCAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAA
6199294 TTAATG
66 TTAATG
* ** * *
6199300 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAA
6199365 TT
66 TT
6199367 TCTACTTTCC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (71 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAA
TTAATG
Found at i:6199528 original size:54 final size:54
Alignment explanation
Indices: 6199377--6199591 Score: 315
Period size: 54 Copynumber: 4.0 Consensus size: 54
6199367 TCTACTTTCC
* * * *
6199377 AATTCCTGTTTTTCAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTTTC
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
* *
6199431 AATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1 AATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
*
6199486 AATTTCTGTTTTTCAAAAAGCAACTCATATTGCGAGAGGTGAGTTGTA-CCTTTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG-AGCCTTTT
* * *
6199540 AATTTTTGTTTTTCAAAAATCAACCCATATTGCGAGAAGTGAGTTGAGCCTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
6199592 AGGTCATATG
Statistics
Matches: 145, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
53 1 0.01
54 94 0.65
55 50 0.34
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (54 bp):
AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
Found at i:6201524 original size:3 final size:3
Alignment explanation
Indices: 6201518--6201581 Score: 119
Period size: 3 Copynumber: 21.0 Consensus size: 3
6201508 CTTCTTCTTC
6201518 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6201566 TTA TTA TTA TGTA TTA
1 TTA TTA TTA T-TA TTA
6201582 GTTTATGTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:6201813 original size:15 final size:15
Alignment explanation
Indices: 6201780--6201818 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6201770 TTTAATGTCG
*
6201780 TATTATTATGTTTTAA
1 TATTA-TATATTTTAA
*
6201796 TATTATATATTTTCA
1 TATTATATATTTTAA
6201811 TATTATAT
1 TATTATAT
6201819 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAA
Found at i:6204212 original size:17 final size:18
Alignment explanation
Indices: 6204180--6204213 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6204170 TTTTACTTTA
6204180 TATATATATATATGTAAG
1 TATATATATATATGTAAG
*
6204198 TATAT-TATATTTGTAA
1 TATATATATATATGTAA
6204214 TATTGAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
TATATATATATATGTAAG
Found at i:6205096 original size:15 final size:17
Alignment explanation
Indices: 6205069--6205104 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
6205059 ATTTTATTTT
6205069 AATAATAAATTTTAAA-
1 AATAATAAATTTTAAAC
6205085 AATAAT-AATTTTAAAC
1 AATAATAAATTTTAAAC
6205101 AATA
1 AATA
6205105 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATAAATTTTAAAC
Found at i:6206189 original size:26 final size:25
Alignment explanation
Indices: 6206143--6206203 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
6206133 TTAATAATAG
*
6206143 ATTTAATTAAAAATTTTAAAAAT-TT
1 ATTTAATT-TAAATTTTAAAAATATT
6206168 ATTTAATTTAAATTATTAAAAAATATT
1 ATTTAATTTAAATT-TT-AAAAATATT
6206195 -TTT-ATTTAA
1 ATTTAATTTAA
6206204 TAAAATGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 5 0.16
25 16 0.50
26 9 0.28
27 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTAATTTAAATTTTAAAAATATT
Found at i:6206733 original size:17 final size:18
Alignment explanation
Indices: 6206713--6206746 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
6206703 TATTTTTACC
6206713 TTTTTTTT--AAATTGTT
1 TTTTTTTTGAAAATTGTT
6206729 TTTTTTTTGAAAATTGTT
1 TTTTTTTTGAAAATTGTT
6206747 GATAGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (18 bp):
TTTTTTTTGAAAATTGTT
Found at i:6208376 original size:28 final size:28
Alignment explanation
Indices: 6208344--6208403 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
6208334 TATATTAATG
6208344 GGGTATAGGAAAAG-TCTCATAACTTATA
1 GGGTATAGGAAAAGTTCT-ATAACTTATA
* * *
6208372 GGGTATATGAAGAGTTCTATAACTTATG
1 GGGTATAGGAAAAGTTCTATAACTTATA
6208400 GGGT
1 GGGT
6208404 TGATAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.32
Consensus pattern (28 bp):
GGGTATAGGAAAAGTTCTATAACTTATA
Found at i:6214605 original size:26 final size:26
Alignment explanation
Indices: 6214524--6214607 Score: 134
Period size: 26 Copynumber: 3.2 Consensus size: 26
6214514 CATGAAATTC
6214524 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
6214550 TTACCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
6214576 TTATCAT-AGAACATTTACCTAACCTA
1 TTATCATGA-AACATTTACCTAACCCA
6214602 TTATCA
1 TTATCA
6214608 ATTTGTATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
25 1 0.02
26 53 0.98
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:6216866 original size:28 final size:28
Alignment explanation
Indices: 6216834--6216896 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
6216824 TCCTATATTA
6216834 ATGGGGTATAGGAAAAGTCTCATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
* * *
6216862 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
6216890 ATGGGGT
1 ATGGGGT
6216897 TGATAATGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTCTCATAACTT
Found at i:6218826 original size:15 final size:15
Alignment explanation
Indices: 6218806--6218853 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
6218796 ACTATTGTAA
6218806 GGTTTATGTATTATG
1 GGTTTATGTATTATG
* *
6218821 GGTTTAGGGATTAT-
1 GGTTTATGTATTATG
6218835 GGTTTATGGT-TTATG
1 GGTTTAT-GTATTATG
6218850 GGTT
1 GGTT
6218854 AAAGGTTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (15 bp):
GGTTTATGTATTATG
Found at i:6218890 original size:22 final size:22
Alignment explanation
Indices: 6218861--6218919 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
6218851 GTTAAAGGTT
6218861 AGGGTTTAAGTTTTAGGGTATT-
1 AGGGTTTAAGTTTTAGGG-ATTA
* *
6218883 GGGGTTTAAGGTTTAGGGATTA
1 AGGGTTTAAGTTTTAGGGATTA
*
6218905 AGGGTTTATGTTTTA
1 AGGGTTTAAGTTTTA
6218920 TTGTAAGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (22 bp):
AGGGTTTAAGTTTTAGGGATTA
Found at i:6218897 original size:7 final size:7
Alignment explanation
Indices: 6218820--6218912 Score: 62
Period size: 7 Copynumber: 13.0 Consensus size: 7
6218810 TATGTATTAT
6218820 GGGTTTA
1 GGGTTTA
*
6218827 GGGATTA
1 GGGTTTA
*
6218834 TGGTTTA
1 GGGTTTA
*
6218841 TGGTTTA
1 GGGTTTA
*
6218848 TGGGTTAA
1 -GGGTTTA
*
6218856 AGG-TTA
1 GGGTTTA
6218862 GGGTTTA
1 GGGTTTA
* *
6218869 AGTTTTA
1 GGGTTTA
*
6218876 GGGTATTG
1 GGGT-TTA
6218884 GGGTTTA
1 GGGTTTA
*
6218891 AGGTTTA
1 GGGTTTA
*
6218898 GGGATTAA
1 GGG-TTTA
6218906 GGGTTTA
1 GGGTTTA
6218913 TGTTTTATTG
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
6 4 0.06
7 43 0.67
8 17 0.27
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.42
Consensus pattern (7 bp):
GGGTTTA
Found at i:6222071 original size:21 final size:21
Alignment explanation
Indices: 6222007--6222072 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
6221997 AAATTTCAAA
*
6222007 AATTAAACATAATATAATATTTT
1 AATTAAA-ATAAAATAATA-TTT
* *
6222030 AACATAGAAAT-AAATATTATTT
1 AA-TTA-AAATAAAATAATATTT
6222052 AATTAAAATAAAATAATATTT
1 AATTAAAATAAAATAATATTT
6222073 TAAAAGGTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
20 4 0.11
21 12 0.34
22 5 0.14
23 8 0.23
24 4 0.11
25 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTAAAATAAAATAATATTT
Found at i:6222121 original size:43 final size:44
Alignment explanation
Indices: 6222087--6222228 Score: 218
Period size: 43 Copynumber: 3.3 Consensus size: 44
6222077 AGGTTATATT
* *
6222087 TTTAGCGGCGTTTTTAGGAAAAGCGCCGCTAAAA-GTCATGACC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGGTCATGACC
*
6222130 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCT-ACAGGTCATGACC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGGTCATGACC
* *
6222173 TTTAGCGGCGTTTGTGGGAAAAGCGCCG-TTACAGGTCATGACC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGGTCATGACC
6222216 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
6222229 TTTTCTAAAA
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
42 3 0.03
43 91 0.97
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (44 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGGTCATGACC
Found at i:6223737 original size:3 final size:3
Alignment explanation
Indices: 6223729--6223765 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
6223719 TCCTCAGCCC
6223729 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
6223766 TTCTTCAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.35, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:6225113 original size:21 final size:22
Alignment explanation
Indices: 6225057--6225117 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
6225047 GAGGCCGAAA
*
6225057 TTAAATTATAATTTTTATAATAC
1 TTAAATTA-AAATTTTATAATAC
* * * *
6225080 TAAAAATATAATTTTA-AATAG
1 TTAAATTAAAATTTTATAATAC
6225101 TTAAATTAAAATTTTAT
1 TTAAATTAAAATTTTAT
6225118 TATTTTCAGG
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
21 17 0.59
22 6 0.21
23 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAAATTAAAATTTTATAATAC
Found at i:6227452 original size:18 final size:18
Alignment explanation
Indices: 6227417--6227450 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6227407 TTTTGAAATT
6227417 TCTATTTTTTTAATTTTA
1 TCTATTTTTTTAATTTTA
6227435 TCTA-TTTTTTAATTTT
1 TCTATTTTTTTAATTTT
6227451 TAATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TCTATTTTTTTAATTTTA
Found at i:6227460 original size:2 final size:2
Alignment explanation
Indices: 6227455--6227489 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
6227445 AATTTTTAAT
* *
6227455 TA TA TA TG TA TA TA CA 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 TA T
6227490 TCATTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6230383 original size:15 final size:16
Alignment explanation
Indices: 6230360--6230392 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6230350 CGTTTGGTAC
*
6230360 TTCCTCTTGTGG-ATA
1 TTCCCCTTGTGGAATA
6230375 TTCCCCTTGTGGAATA
1 TTCCCCTTGTGGAATA
6230391 TT
1 TT
6230393 TTTAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (16 bp):
TTCCCCTTGTGGAATA
Found at i:6232256 original size:31 final size:28
Alignment explanation
Indices: 6232215--6232310 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 28
6232205 TTAATGTAAC
*
6232215 ATTTGATATTTAAATTTAATATTTTTTTCTA
1 ATTTGGTATTTAAA-TT-AT-TTTTTTTCTA
* *
6232246 ATTTGGTATTTAGA-T-TTTTTTGTCTA
1 ATTTGGTATTTAAATTATTTTTTTTCTA
6232272 ATTTGGTATTTAAAGTTGATTTTTTTTCCTA
1 ATTTGGTATTTAAA-TT-ATTTTTTTT-CTA
*
6232303 CTTTGGTA
1 ATTTGGTA
6232311 CGTAATCTCC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
26 22 0.41
27 1 0.02
28 1 0.02
29 1 0.02
30 7 0.13
31 22 0.41
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.59
Consensus pattern (28 bp):
ATTTGGTATTTAAATTATTTTTTTTCTA
Found at i:6232272 original size:26 final size:25
Alignment explanation
Indices: 6232228--6232284 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 25
6232218 TGATATTTAA
6232228 ATTTAATATTTTTTTCTAATTTGGT
1 ATTTAATATTTTTTTCTAATTTGGT
6232253 ATTTAGAT-TTTTTTGTCTAATTTGGT
1 ATTTA-ATATTTTTT-TCTAATTTGGT
6232279 ATTTAA
1 ATTTAA
6232285 AGTTGATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.40
26 18 0.60
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.61
Consensus pattern (25 bp):
ATTTAATATTTTTTTCTAATTTGGT
Found at i:6236626 original size:15 final size:15
Alignment explanation
Indices: 6236606--6236636 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6236596 GCTGAGAGGT
6236606 AGGCCAATGAATGAA
1 AGGCCAATGAATGAA
6236621 AGGCCAATGAATGAA
1 AGGCCAATGAATGAA
6236636 A
1 A
6236637 CATACTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.26, T:0.13
Consensus pattern (15 bp):
AGGCCAATGAATGAA
Found at i:6237378 original size:33 final size:33
Alignment explanation
Indices: 6237339--6237407 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
6237329 GGTCTGTGTA
6237339 TTATACTTAAATTTCAGATTTAATTTATATATT
1 TTATACTTAAATTTCAGATTTAATTTATATATT
6237372 TTATACTTAAATTTCAGATTTAATTTATATATT
1 TTATACTTAAATTTCAGATTTAATTTATATATT
6237405 TTA
1 TTA
6237408 ATTTTTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (33 bp):
TTATACTTAAATTTCAGATTTAATTTATATATT
Found at i:6239752 original size:27 final size:27
Alignment explanation
Indices: 6239722--6239776 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
6239712 AGTATACATA
*
6239722 CACGATTTATATATAGTAGGAATAAGC
1 CACGATTTATATACAGTAGGAATAAGC
6239749 CACGATTTATATACAGTAGGAATAAGC
1 CACGATTTATATACAGTAGGAATAAGC
6239776 C
1 C
6239777 TAATTGCTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (27 bp):
CACGATTTATATACAGTAGGAATAAGC
Found at i:6253386 original size:26 final size:26
Alignment explanation
Indices: 6253357--6253409 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
6253347 TCAAACATGC
6253357 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
6253383 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
6253409 A
1 A
6253410 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:6253690 original size:8 final size:8
Alignment explanation
Indices: 6253670--6253713 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
6253660 AAAATACCAG
6253670 TTTTCGG-
1 TTTTCGGC
*
6253677 TATTTCGAC
1 T-TTTCGGC
6253686 TTTTCGGC
1 TTTTCGGC
6253694 TTTTCGGC
1 TTTTCGGC
6253702 TTTTCGGC
1 TTTTCGGC
6253710 TTTT
1 TTTT
6253714 GCCGATCTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 1 0.03
8 31 0.94
9 1 0.03
ACGTcount: A:0.05, C:0.20, G:0.20, T:0.55
Consensus pattern (8 bp):
TTTTCGGC
Found at i:6254924 original size:26 final size:26
Alignment explanation
Indices: 6254894--6255001 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
6254884 TGAAATTCCC
6254894 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
6254920 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
6254946 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
*
6254972 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
6254998 ATCA
1 ATCA
6255002 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:6256712 original size:3 final size:3
Alignment explanation
Indices: 6256704--6256747 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
6256694 GTTGATCTGA
6256704 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
6256748 CTTTACTCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.