Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 324 of 444
Found at i:93460730 original size:24 final size:24
Alignment explanation
Indices: 93460703--93460754 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
93460693 CTCATGCTTT
93460703 CTTTACATGTTCATCGTGTTCATG
1 CTTTACATGTTCATCGTGTTCATG
93460727 CTTTACATGTTCATCGTGTTCATG
1 CTTTACATGTTCATCGTGTTCATG
93460751 CTTT
1 CTTT
93460755 CTTTTCATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.48
Consensus pattern (24 bp):
CTTTACATGTTCATCGTGTTCATG
Found at i:93463862 original size:12 final size:13
Alignment explanation
Indices: 93463845--93463869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93463835 AACCCTTTTC
93463845 TTTTTTCCCCAAT
1 TTTTTTCCCCAAT
93463858 TTTTTTCCCCAA
1 TTTTTTCCCCAA
93463870 ATCAGCTCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTTTCCCCAAT
Found at i:93463909 original size:77 final size:78
Alignment explanation
Indices: 93463782--93463958 Score: 256
Period size: 77 Copynumber: 2.3 Consensus size: 78
93463772 ACCCCAAAAA
* *
93463782 TTTTTCCCCAAATCAGTTCCCCC-TCTCTCCAAATCCCTAAGTTTTTTTTCCC-GAACCCTTTTC
1 TTTTTCCCCAAATCAGTTCCCCCTTCTCTCCAAATCCCTAAGTTTTCTTTCCCAG-ACCCCTTTC
93463845 TTTTTTCCCCAATT
65 TTTTTTCCCCAATT
* *
93463859 TTTTTCCCCAAATCAGCTCCCCCTTTTC-CCAAAATCCCTAAG-TTTCTTTCCCAGACCCCTTTC
1 TTTTTCCCCAAATCAGTTCCCCCTTCTCTCC-AAATCCCTAAGTTTTCTTTCCCAGACCCCTTTC
93463922 TTTTTTCCCCAATT
65 TTTTTTCCCCAATT
*
93463936 TTTTT-CCCAAATCAATTCCCCCT
1 TTTTTCCCCAAATCAGTTCCCCCT
93463959 CGAAATCCCT
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
76 16 0.18
77 60 0.66
78 15 0.16
ACGTcount: A:0.18, C:0.38, G:0.03, T:0.41
Consensus pattern (78 bp):
TTTTTCCCCAAATCAGTTCCCCCTTCTCTCCAAATCCCTAAGTTTTCTTTCCCAGACCCCTTTCT
TTTTTCCCCAATT
Found at i:93464625 original size:13 final size:13
Alignment explanation
Indices: 93464609--93464639 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
93464599 ATGGAAGGCT
93464609 GAAATTTTATTAG
1 GAAATTTTATTAG
93464622 GAAATTTTATTAG
1 GAAATTTTATTAG
*
93464635 AAAAT
1 GAAAT
93464640 AATTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (13 bp):
GAAATTTTATTAG
Found at i:93466427 original size:24 final size:22
Alignment explanation
Indices: 93466393--93466438 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
93466383 TAAATTTTAT
*
93466393 ATTTTTTAATTTGTTACTTAAA
1 ATTTTTTAATTTGATACTTAAA
*
93466415 ATTTTTTCAAATTTGATATTTAAA
1 ATTTTTT--AATTTGATACTTAAA
93466439 TTTATCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (22 bp):
ATTTTTTAATTTGATACTTAAA
Found at i:93476444 original size:21 final size:21
Alignment explanation
Indices: 93476362--93476570 Score: 102
Period size: 21 Copynumber: 9.6 Consensus size: 21
93476352 ACAAATTGAG
*
93476362 TTAAAACAACAAAGAATCGA-
1 TTAAAACAGCAAAGAATCGAT
* ** * *
93476382 TTCAAACAATAATGAATTGAT
1 TTAAAACAGCAAAGAATCGAT
*
93476403 TTAAAACAGCAAAAAAATCGAT
1 TTAAAACAGC-AAAGAATCGAT
93476425 TTAAAGA-AGCAAAGAATCGAT
1 TTAAA-ACAGCAAAGAATCGAT
* * *
93476446 TTAAAATAACAATCATGGATCGAT
1 TTAAAACAGCAA--A-GAATCGAT
* *
93476470 TTAAAACAACAATCATGAATTGAT
1 TTAAAACAGCAA--A-GAATCGAT
* * *
93476494 TCAAAGA-AGCAAAAAAATCAAT
1 TTAAA-ACAGC-AAAGAATCGAT
* *
93476516 TTAAAACAACAAACAATCGAT
1 TTAAAACAGCAAAGAATCGAT
* * *
93476537 TCAAAGA-AGAAAAGAATCTAT
1 TTAAA-ACAGCAAAGAATCGAT
*
93476558 TTAAAACAACAAA
1 TTAAAACAGCAAA
93476571 TTCAGTAAAA
Statistics
Matches: 144, Mismatches: 33, Indels: 23
0.72 0.17 0.12
Matches are distributed among these distances:
20 18 0.12
21 58 0.40
22 28 0.19
23 3 0.02
24 34 0.24
25 3 0.02
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.22
Consensus pattern (21 bp):
TTAAAACAGCAAAGAATCGAT
Found at i:93476494 original size:24 final size:24
Alignment explanation
Indices: 93476438--93476494 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
93476428 AAGAAGCAAA
*
93476438 GAATCGATTTAAAATAACAATCAT
1 GAATCGATTTAAAACAACAATCAT
*
93476462 GGATCGATTTAAAACAACAATCAT
1 GAATCGATTTAAAACAACAATCAT
*
93476486 GAATTGATT
1 GAATCGATT
93476495 CAAAGAAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (24 bp):
GAATCGATTTAAAACAACAATCAT
Found at i:93476539 original size:43 final size:43
Alignment explanation
Indices: 93476468--93476571 Score: 138
Period size: 42 Copynumber: 2.4 Consensus size: 43
93476458 TCATGGATCG
* *
93476468 ATTTAAAACAACAATCATGAATTGATTCAAAGAAGCAAAAAAATCA
1 ATTTAAAACAACAA--ATCAATCGATTCAAAGAAG-AAAAAAATCA
* *
93476514 ATTTAAAACAACAAA-CAATCGATTCAAAGAAGAAAAGAATCT
1 ATTTAAAACAACAAATCAATCGATTCAAAGAAGAAAAAAATCA
93476556 ATTTAAAACAACAAAT
1 ATTTAAAACAACAAAT
93476572 TCAGTAAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
42 23 0.43
43 15 0.28
44 1 0.02
46 14 0.26
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.21
Consensus pattern (43 bp):
ATTTAAAACAACAAATCAATCGATTCAAAGAAGAAAAAAATCA
Found at i:93479136 original size:11 final size:11
Alignment explanation
Indices: 93479122--93479157 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
93479112 ATATCCTAAT
*
93479122 AATAATAATAA
1 AATAATAGTAA
93479133 AATAATAGTAA
1 AATAATAGTAA
*
93479144 CATAATAGTAA
1 AATAATAGTAA
93479155 AAT
1 AAT
93479158 GGTAGCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (11 bp):
AATAATAGTAA
Found at i:93479189 original size:22 final size:22
Alignment explanation
Indices: 93479164--93479210 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
93479154 AAATGGTAGC
*
93479164 AAAATAGAAAGAAAACAATAAA
1 AAAATAGAAAGAAAACAACAAA
* **
93479186 AAAATAGCATTAAAACAACAAA
1 AAAATAGAAAGAAAACAACAAA
93479208 AAA
1 AAA
93479211 TAACAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.11
Consensus pattern (22 bp):
AAAATAGAAAGAAAACAACAAA
Found at i:93496435 original size:46 final size:47
Alignment explanation
Indices: 93496382--93496752 Score: 216
Period size: 48 Copynumber: 7.8 Consensus size: 47
93496372 GTGATTGTGT
93496382 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CACATTATGAGA
* * * * *
93496428 GCTAGTGTAAGATCATGTCTGGGACATGACATCAG--TATTGAGACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATT---ATGAGA
* * *
93496476 GATAGTGTAAAACCATGTCTGAGACATGGCATCGG--C--TATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATTATGAGA
* * *
93496519 TGTGTCAGTGTAAGATCATGTCTGGGACATGGCATCGGCACA-GAT-AGA
1 -G-CT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACATTATGAGA
* * * * *
93496567 GGTGTCAATGTAAGACCATGTTTGGGACATAGCATCGGCACAGATATGTGAGA
1 -G-CT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC--AT-TATGAGA
* * * *
93496620 GCCAGTGTAAGACCATGTTTGGGACATGGCGTCGGC-C-TTGATCGCGATA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATT-AT---GAGA
*
93496669 G-TCAGTGTAAGACCATGTTTGGGACATGGCATC-G-AC-TTGATGTATGA
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACATT-ATG-A-GA
* * * *
93496716 GCCAGTATAAGACCATATCTAGGACATGGCATCGGCA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
93496753 TCCTACCCTA
Statistics
Matches: 259, Mismatches: 39, Indels: 51
0.74 0.11 0.15
Matches are distributed among these distances:
43 5 0.02
44 1 0.00
45 6 0.02
46 45 0.17
47 42 0.16
48 87 0.34
49 37 0.14
50 31 0.12
52 2 0.01
53 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (47 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATTATGAGA
Found at i:93496644 original size:50 final size:49
Alignment explanation
Indices: 93496385--93496702 Score: 239
Period size: 48 Copynumber: 6.6 Consensus size: 49
93496375 ATTGTGTGCT
* * *
93496385 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACA-TTA-TGAGAG-C
1 AGTGTAAGACCATGTTTGGGACATGGCATCGG-CACAGATAGAGAGAGTC
* * * * * ** *
93496430 TAGTGTAAGATCATGTCTGGGACATGACATCAGTATTGAGACGAGAGA-T-
1 -AGTGTAAGACCATGTTTGGGACATGGCATCGGCACAGATA-GAGAGAGTC
* * * * *
93496479 AGTGTAAAACCATGTCTGAGACATGGCATCGG--C-TAT-GAGATGTGTC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACAGATAGAGA-GAGTC
* * *
93496525 AGTGTAAGATCATGTCTGGGACATGGCATCGGCACAGATAGAG-GTGTC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACAGATAGAGAGAGTC
* * * *
93496573 AATGTAAGACCATGTTTGGGACATAGCATCGGCACAGATATGTGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACAGATA-GAGAGAGTC
* * * * *
93496623 AGTGTAAGACCATGTTTGGGACATGGCGTCGGC-CTTGATCGCGATAGTC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCAC-AGATAGAGAGAGTC
93496672 AGTGTAAGACCATGTTTGGGACATGGCATCG
1 AGTGTAAGACCATGTTTGGGACATGGCATCG
93496703 ACTTGATGTA
Statistics
Matches: 219, Mismatches: 37, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
43 4 0.02
44 1 0.00
45 2 0.01
46 38 0.17
47 15 0.07
48 75 0.34
49 41 0.19
50 43 0.20
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (49 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGGCACAGATAGAGAGAGTC
Found at i:93496655 original size:98 final size:99
Alignment explanation
Indices: 93496524--93496751 Score: 263
Period size: 98 Copynumber: 2.3 Consensus size: 99
93496514 TGAGATGTGT
* *
93496524 CAGTGTAAGATCATGTCTGGGACATGGCATCGGCAC-AGATAGAGGT-GTCAATGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTAGATAGAGATAGTCAATGTAAGACCATG
93496587 TTTGGGACATAGCATCGGCACAGATATGTGAGAGC
65 TTTGGGACATAGCATCGGCACAGATATGTGAGAGC
* * * * * *
93496622 CAGTGTAAGACCATGTTTGGGACATGGCGTCGGCCTTGATCGCGATAGTCAGTGTAAGACCATGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAGATAGAGATAGTCAATGTAAGACCATGT
* *
93496687 TTGGGACATGGCATC-G-AC--TTGATGT-ATGAGC
66 TTGGGACATAGCATCGGCACAGAT-ATGTGA-GAGC
* * *
93496718 CAGTATAAGACCATATCTAGGACATGGCATCGGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC
93496752 ATCCTACCCT
Statistics
Matches: 111, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
95 2 0.02
96 37 0.33
97 3 0.03
98 38 0.34
99 31 0.28
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (99 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAGATAGAGATAGTCAATGTAAGACCATGT
TTGGGACATAGCATCGGCACAGATATGTGAGAGC
Found at i:93496745 original size:47 final size:49
Alignment explanation
Indices: 93496575--93496749 Score: 171
Period size: 49 Copynumber: 3.6 Consensus size: 49
93496565 GAGGTGTCAA
* * * *
93496575 TGTAAGACCATGTTTGGGACATAGCATCGGCAC-AGATATGTGA-GAGCCAG
1 TGTAAGACCATGTTTGGGACATGGCATC-G-ACTTGAT-CGCGATGAGCCAG
* * *
93496625 TGTAAGACCATGTTTGGGACATGGCGTCGGCCTTGATCGCGAT-AGTCAG
1 TGTAAGACCATGTTTGGGACATGGCATC-GACTTGATCGCGATGAGCCAG
*
93496674 TGTAAGACCATGTTTGGGACATGGCATCGACTTGAT-G-TATGAGCCAG
1 TGTAAGACCATGTTTGGGACATGGCATCGACTTGATCGCGATGAGCCAG
* * * *
93496721 TATAAGACCATATCTAGGACATGGCATCG
1 TGTAAGACCATGTTTGGGACATGGCATCG
93496750 GCATCCTACC
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
46 2 0.02
47 31 0.29
48 7 0.07
49 36 0.34
50 31 0.29
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (49 bp):
TGTAAGACCATGTTTGGGACATGGCATCGACTTGATCGCGATGAGCCAG
Found at i:93500449 original size:43 final size:43
Alignment explanation
Indices: 93500388--93500473 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
93500378 TTGAAGAGTT
93500388 TCCATAACTAGGGTTTTTGGCCAAGCTTCCAAGCTCGATTTTA
1 TCCATAACTAGGGTTTTTGGCCAAGCTTCCAAGCTCGATTTTA
* *
93500431 TCCATAGCTAGGGTTTTTGGCCAAGCTTCCAAGCTTGATTTTA
1 TCCATAACTAGGGTTTTTGGCCAAGCTTCCAAGCTCGATTTTA
93500474 AGTCCGTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (43 bp):
TCCATAACTAGGGTTTTTGGCCAAGCTTCCAAGCTCGATTTTA
Found at i:93503345 original size:27 final size:27
Alignment explanation
Indices: 93503314--93503679 Score: 128
Period size: 27 Copynumber: 13.6 Consensus size: 27
93503304 TAGTTTACCA
*
93503314 AATTACTGAAATACCCTCGATTTGTAG
1 AATTACCGAAATACCCTCGATTTGTAG
** *
93503341 AATTACC-ATTTTACCCTCGATTTATAG
1 AATTACCGA-AATACCCTCGATTTGTAG
** ** *
93503368 AATTACCG-TTTCACCCTCGATTTACAA
1 AATTACCGAAAT-ACCCTCGATTTGTAG
*** * *
93503395 AATTACCGTTTTACCTTCGATTTATAG
1 AATTACCGAAATACCCTCGATTTGTAG
** **
93503422 AATTACC-ATTTTACCCTCGATTTACAG
1 AATTACCGA-AATACCCTCGATTTGTAG
* *** ** *
93503449 AATTACTGTTTTACCCTCGATTTACAA
1 AATTACCGAAATACCCTCGATTTGTAG
**
93503476 AATTACC-ATTTTACCCTCGA-TTGT-G
1 AATTACCGA-AATACCCTCGATTTGTAG
* **
93503501 AAATTACTGAAATACCC-CTG-TAGGATAG
1 -AATTACCGAAATACCCTC-GATTTG-TAG
* * * *
93503529 AATTACCAAAATGCCC-CTAGTTTGTAA
1 AATTACCGAAATACCCTCGA-TTTGTAG
* * *
93503556 AATTACCAAAATACCCTAG-TTTGTAA
1 AATTACCGAAATACCCTCGATTTGTAG
* *
93503582 AATTACTGAAATACCACT-GGTTTGT-G
1 AATTACCGAAATACC-CTCGATTTGTAG
* *
93503608 AAATTACCGAAATACCCTCAATTTGTAA
1 -AATTACCGAAATACCCTCGATTTGTAG
* ** *
93503636 AATTACCAAAATACCC-CTGATTTACAA
1 AATTACCGAAATACCCTC-GATTTGTAG
*
93503663 AATTATCGAAATACCCT
1 AATTACCGAAATACCCT
93503680 TGACTTTCTA
Statistics
Matches: 268, Mismatches: 48, Indels: 45
0.74 0.13 0.12
Matches are distributed among these distances:
25 1 0.00
26 43 0.16
27 218 0.81
28 6 0.02
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (27 bp):
AATTACCGAAATACCCTCGATTTGTAG
Found at i:93503399 original size:54 final size:54
Alignment explanation
Indices: 93503325--93503497 Score: 256
Period size: 54 Copynumber: 3.2 Consensus size: 54
93503315 ATTACTGAAA
** * *
93503325 TACCCTCGATTTGTAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTT
* * *
93503379 CACCCTCGATTTACAAAATTACCGTTTTACCTTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTT
* * *
93503433 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTT
93503487 TACCCTCGATT
1 TACCCTCGATT
93503498 GTGAAATTAC
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (54 bp):
TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTT
Found at i:93503442 original size:81 final size:81
Alignment explanation
Indices: 93503325--93503497 Score: 292
Period size: 81 Copynumber: 2.1 Consensus size: 81
93503315 ATTACTGAAA
* *
93503325 TACCCTCGATTTGTAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATT
*
93503390 TACAAAATTACCGTTT
66 TACAAAATTACCATTT
* * *
93503406 TACCTTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATT
93503471 TACAAAATTACCATTT
66 TACAAAATTACCATTT
93503487 TACCCTCGATT
1 TACCCTCGATT
93503498 GTGAAATTAC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (81 bp):
TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATT
TACAAAATTACCATTT
Found at i:93503612 original size:53 final size:54
Alignment explanation
Indices: 93503529--93503679 Score: 169
Period size: 54 Copynumber: 2.8 Consensus size: 54
93503519 TGTAGGATAG
* * * *
93503529 AATTACCAAAATGCCCCTAGTTTGTAAAATTACCAAAATACCCT-AGTTTGTAA
1 AATTACCAAAATACCACTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAA
** * *
93503582 AATTACTGAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCACTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAA
* * ** * *
93503636 AATTACCAAAATACCCCTGATTTACAAAATTATCGAAATACCCT
1 AATTACCAAAATACCACTGGTTTGTAAAATTACCAAAATACCCT
93503680 TGACTTTCTA
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 37 0.46
54 44 0.54
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (54 bp):
AATTACCAAAATACCACTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAA
Found at i:93503666 original size:54 final size:53
Alignment explanation
Indices: 93503554--93503735 Score: 168
Period size: 54 Copynumber: 3.4 Consensus size: 53
93503544 CCTAGTTTGT
* * ** * **
93503554 AAAATTACCAAAATACCCTAGTTTGTAAAATTACTGAAATACCACTGGTTTGT
1 AAAATTACCGAAATACCCTAATTTGTAAAATTACCAAAATACCACTGATTTAC
* *
93503607 GAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACCGAAATACCCT-AATTTGTAAAATTACCAAAATACCACTGATTTAC
* * * * * *
93503661 AAAATTATCGAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTAC
1 AAAATTACCGAAATACCC-T-AATTTGT-AAAATTACCA-AAATACCACTGATTTAC
*
93503717 AAAATTACTGAAATACCCT
1 AAAATTACCGAAATACCCT
93503736 TGGTTTGTAG
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
53 17 0.16
54 43 0.41
55 8 0.08
56 37 0.35
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (53 bp):
AAAATTACCGAAATACCCTAATTTGTAAAATTACCAAAATACCACTGATTTAC
Found at i:93503729 original size:27 final size:27
Alignment explanation
Indices: 93503554--93503741 Score: 107
Period size: 27 Copynumber: 6.9 Consensus size: 27
93503544 CCTAGTTTGT
** * **
93503554 AAAATTACCAAAATACCCT-AGTTTGT
1 AAAATTACTGAAATACCCTTGGTTTAC
**
93503580 AAAATTACTGAAATACCAC-TGGTTTGT
1 AAAATTACTGAAATACC-CTTGGTTTAC
* * *** **
93503607 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACTGAAATACCCTTGGTTTAC
** * *
93503634 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
*
93503661 AAAATTA-TCGAAATACCCTTGACTTT-C
1 AAAATTACT-GAAATACCCTTG-GTTTAC
*
93503688 TAAAAATTA-TAGAAATACCATTGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
93503717 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
93503742 GTAGATTTAC
Statistics
Matches: 130, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
26 16 0.12
27 87 0.67
28 7 0.05
29 20 0.15
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:93504714 original size:25 final size:24
Alignment explanation
Indices: 93504670--93504739 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
93504660 AGGAAGTGCT
* *
93504670 AAAAGGGCTCTACCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
* *
93504694 GAAAAGGGCTTTGCCCTAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
93504719 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
93504740 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 1 0.03
25 38 0.97
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:93504752 original size:24 final size:23
Alignment explanation
Indices: 93504670--93504766 Score: 77
Period size: 25 Copynumber: 4.0 Consensus size: 23
93504660 AGGAAGTGCT
* * *
93504670 AAAAGGGCTCTACCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAG-TTATC
*
93504694 GAAAAGGGCTTTGCCCTAGTTTATC
1 -AAAAGGGCTTTGCCCCAG-TTATC
*
93504719 AGAAAGGGCTTTGCCCCAGTTATT
1 A-AAAGGGCTTTGCCCCAGTTATC
**
93504743 AAAAGAGGCTAAGCCTCCAGTTAT
1 AAAAG-GGCTTTGCC-CCAGTTAT
93504767 ATGATAAAGC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
23 4 0.07
24 13 0.21
25 44 0.72
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (23 bp):
AAAAGGGCTTTGCCCCAGTTATC
Found at i:93504946 original size:42 final size:42
Alignment explanation
Indices: 93504887--93504978 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
93504877 TAGTCTCCCC
* *
93504887 AAATGGGCTTGCGTACATTCATTAACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
*
93504929 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
93504971 AAATGGGC
1 AAATGGGC
93504979 CTAAGGGCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
Found at i:93505037 original size:31 final size:31
Alignment explanation
Indices: 93505002--93505116 Score: 205
Period size: 31 Copynumber: 3.7 Consensus size: 31
93504992 CGTTTACAGT
*
93505002 AAAGGCTTCGGCCCAGTGATATAATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
93505033 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
93505064 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
93505095 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
93505117 TCAAGACTAA
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
30 5 0.06
31 77 0.94
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:93506053 original size:22 final size:21
Alignment explanation
Indices: 93506005--93506053 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
93505995 AGCTTGTAGC
93506005 ACGGGCACGTCTCAAGGTCAT
1 ACGGGCACGTCTCAAGGTCAT
* * **
93506026 AGGGGCATGTCTCTTGGATCAT
1 ACGGGCACGTCTCAAGG-TCAT
93506048 ACGGGC
1 ACGGGC
93506054 GTGTGACCCC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.22
Consensus pattern (21 bp):
ACGGGCACGTCTCAAGGTCAT
Found at i:93513753 original size:20 final size:20
Alignment explanation
Indices: 93513725--93513776 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
93513715 AAGGCAATGC
*
93513725 ACACGCCCGTGTGCTATGGG
1 ACACACCCGTGTGCTATGGG
93513745 ACACACCCGTGTGCTATGGG
1 ACACACCCGTGTGCTATGGG
*
93513765 ACACACTCGTGT
1 ACACACCCGTGT
93513777 CCTCAGCCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (20 bp):
ACACACCCGTGTGCTATGGG
Found at i:93516636 original size:132 final size:131
Alignment explanation
Indices: 93516255--93516754 Score: 510
Period size: 132 Copynumber: 3.8 Consensus size: 131
93516245 ATTCCAGAGA
* * * *
93516255 GATATTCGATTATTTTG-GACAAACGAGAGATTGCAGCCCAGCACGATAGGGCACTATT-CTCAA
1 GATATTCGATTATTTTGAG-CAAACGAGAAATTGCAACCCAGCACGATAGGGCACTATTCCGCGA
* * * * * *** *
93516318 ATCGCCAAATATCGAACATC--CTTTGTATTGAAAGGTTTTTAATAA-ACATGCGTGAAAACCTA
65 ATTGCCAAATATCGAATATCGTCTTCGT-TTTAAAGATTTTTAA-AAGACATGCGTGAAATTTTG
93516380 AAGG
128 AAGG
* * * * **
93516384 AATATTCGATTGTTTTGAGCAGACGAGGAATTATAACCCAGCACGATAGGGCA-TGATTCC-CGA
1 GATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGATAGGGCACT-ATTCCGCGA
* *** * *** * *
93516447 ATTGTCAAACGCCAAATATTACCTTCGTTTTAAATGATTTTTAGAAGATATGCGTGAAATTTTGA
65 ATTGCCAAATATCGAATATCGTCTTCGTTTTAAA-GATTTTTAAAAGACATGCGTGAAATTTTGA
93516512 AGG
129 AGG
* * *
93516515 GATATTTGATTATTTTAAGCAAACGAGAAATTGCAACCCAGCACGTTAGGGCACTATTCCGCGAA
1 GATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGATAGGGCACTATTCCGCGAA
* **
93516580 TTGCCAAATATCGAATATCGTCTTCGTTTTAAAGAATTTTTAAAAGGCATAAGTGAAATTTTGAA
66 TTGCCAAATATCGAATATCGTCTTCGTTTTAAAG-ATTTTTAAAAGACATGCGTGAAATTTTGAA
93516645 GG
130 GG
* * * *
93516647 GATATTCGATTATTTTGAGCAAATGAGAAATTGCAACCCAACACGTTAGGGCACTATTCTGCGAA
1 GATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGATAGGGCACTATTCCGCGAA
* * *
93516712 ATGCCAAATATCGAGTCTCGTCTTCGTTTTAAAGAATTTTTAA
66 TTGCCAAATATCGAATATCGTCTTCGTTTTAAAG-ATTTTTAA
93516755 TAATTGTGAA
Statistics
Matches: 305, Mismatches: 56, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
128 1 0.00
129 60 0.20
130 9 0.03
131 78 0.26
132 157 0.51
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (131 bp):
GATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGATAGGGCACTATTCCGCGAA
TTGCCAAATATCGAATATCGTCTTCGTTTTAAAGATTTTTAAAAGACATGCGTGAAATTTTGAAG
G
Found at i:93517929 original size:2 final size:2
Alignment explanation
Indices: 93517922--93517946 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
93517912 CCAAAGTGAG
93517922 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
93517947 AAAGTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:93518465 original size:3 final size:3
Alignment explanation
Indices: 93518457--93518529 Score: 101
Period size: 3 Copynumber: 23.7 Consensus size: 3
93518447 AAAAAGTAAC
93518457 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * *
93518506 CAAT AAT AAT GAT GAT GAT AAT AA
1 -AAT AAT AAT AAT AAT AAT AAT AA
93518530 ATAAAGTGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
3 60 0.91
4 6 0.09
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:93527089 original size:13 final size:14
Alignment explanation
Indices: 93527073--93527108 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
93527063 CAATCTCATA
93527073 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
93527086 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
93527099 TCTC-ATTTCA
1 TCTCAATTTCA
93527109 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:93527098 original size:18 final size:19
Alignment explanation
Indices: 93527060--93527100 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
93527050 TGGTTCATGT
93527060 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
93527079 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
93527097 TTTC
1 TTTC
93527101 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:93527290 original size:39 final size:40
Alignment explanation
Indices: 93527247--93527358 Score: 102
Period size: 38 Copynumber: 2.8 Consensus size: 40
93527237 CCGGATAGTT
* *
93527247 CGAAGCAATATTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGAAATATTTGACACCCAGTGTCTCATCGAACCTAGC
* * ** ** * *
93527286 CGAAGTAA-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGAAATATTTGACACCCAGTGTCTCATCGAACCTAGC
*
93527325 CGAAGAAATATAGTGACACCCAGTGTCTCATCGA
1 CGAAGAAATAT-TTGACACCCAGTGTCTCATCGA
93527359 CTCGAGGTCG
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
38 18 0.33
39 18 0.33
40 1 0.02
41 17 0.31
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (40 bp):
CGAAGAAATATTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:93527623 original size:18 final size:19
Alignment explanation
Indices: 93527597--93527635 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
93527587 TTTCAATTCA
93527597 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
93527616 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
93527634 AT
1 AT
93527636 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:93528961 original size:5 final size:5
Alignment explanation
Indices: 93528951--93528995 Score: 54
Period size: 5 Copynumber: 8.4 Consensus size: 5
93528941 TTACTTATTT
*
93528951 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA AT
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA AT
93528996 TTAAATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 24 0.69
6 7 0.20
7 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:93528967 original size:12 final size:12
Alignment explanation
Indices: 93528950--93529004 Score: 60
Period size: 11 Copynumber: 4.5 Consensus size: 12
93528940 TTTACTTATT
93528950 TATATAATATAA
1 TATATAATATAA
93528962 TATATAATATAATA
1 TATATAATAT-A-A
93528976 TACTATAATATAA
1 TA-TATAATATAA
*
93528989 TA-ATAATTTAA
1 TATATAATATAA
93529000 -ATATA
1 TATATA
93529005 TTTTAACACA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 1 0.03
11 11 0.29
12 10 0.26
13 4 0.11
14 4 0.11
15 8 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATAATATAA
Found at i:93528973 original size:17 final size:17
Alignment explanation
Indices: 93528951--93529004 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
93528941 TTACTTATTT
93528951 ATATAATATAATATATA
1 ATATAATATAATATATA
*
93528968 ATATAATAT-A-CTATA
1 ATATAATATAATATATA
*
93528983 ATATAATAATAATTTA-A
1 ATATAAT-ATAATATATA
93529000 ATATA
1 ATATA
93529005 TTTTAACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 11 0.34
16 3 0.09
17 16 0.50
18 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATATAATATATA
Found at i:93528985 original size:27 final size:27
Alignment explanation
Indices: 93528952--93529004 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
93528942 TACTTATTTA
93528952 TATAATATAATATATAATAT-AATATAC
1 TATAATATAATA-ATAATATAAATATAC
*
93528979 TATAATATAATAATAATTTAAATATA
1 TATAATATAATAATAATATAAATATA
93529005 TTTTAACACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TATAATATAATAATAATATAAATATAC
Found at i:93537130 original size:42 final size:42
Alignment explanation
Indices: 93537061--93537145 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
93537051 ATCAGCAACC
*
93537061 AACACCCTCCAAGCCCCTAACCTCAAATATTCTCCAGAATTT
1 AACAACCTCCAAGCCCCTAACCTCAAATATTCTCCAGAATTT
* *
93537103 AACAACCTCTAAGCCCCTAACCTCAAATATTTTCCAGAATTT
1 AACAACCTCCAAGCCCCTAACCTCAAATATTCTCCAGAATTT
93537145 A
1 A
93537146 GTCGTTTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.34, G:0.05, T:0.26
Consensus pattern (42 bp):
AACAACCTCCAAGCCCCTAACCTCAAATATTCTCCAGAATTT
Found at i:93540178 original size:14 final size:13
Alignment explanation
Indices: 93540146--93540206 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 13
93540136 TAATCTATCA
93540146 ATTTATTTTTTTT
1 ATTTATTTTTTTT
**
93540159 GCTTATTTTTCTTT
1 ATTTATTTTT-TTT
93540173 ATTTATTTCTTTTCGTT
1 ATTTA-TT-TTTT--TT
93540190 ATTTATTTGTTTTT
1 ATTTATTT-TTTTT
93540204 ATT
1 ATT
93540207 CCCTTAATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
13 8 0.21
14 11 0.29
15 4 0.11
16 8 0.21
17 7 0.18
ACGTcount: A:0.13, C:0.07, G:0.05, T:0.75
Consensus pattern (13 bp):
ATTTATTTTTTTT
Found at i:93540185 original size:17 final size:17
Alignment explanation
Indices: 93540165--93540202 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
93540155 TTTTGCTTAT
*
93540165 TTTTCTTTATTTATTTC
1 TTTTCGTTATTTATTTC
*
93540182 TTTTCGTTATTTATTTG
1 TTTTCGTTATTTATTTC
93540199 TTTT
1 TTTT
93540203 TATTCCCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTCGTTATTTATTTC
Found at i:93544129 original size:27 final size:26
Alignment explanation
Indices: 93544099--93544152 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
93544089 AACAAATTAG
93544099 TATACAAAACAATTCGAAATGAAATAA
1 TATACAAAACAATTCGAAAT-AAATAA
* * **
93544126 TATATAAAGCAATTTTAAATAAATAA
1 TATACAAAACAATTCGAAATAAATAA
93544152 T
1 T
93544153 TTATGAAGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.30
Consensus pattern (26 bp):
TATACAAAACAATTCGAAATAAATAA
Found at i:93545622 original size:14 final size:15
Alignment explanation
Indices: 93545600--93545633 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
93545590 TTAAGTTTAG
93545600 ATTTATGGGTTTTGA
1 ATTTATGGGTTTTGA
*
93545615 ATTT-TGGGTTTTTA
1 ATTTATGGGTTTTGA
93545629 ATTTA
1 ATTTA
93545634 GGTTTATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (15 bp):
ATTTATGGGTTTTGA
Found at i:93545626 original size:35 final size:35
Alignment explanation
Indices: 93545580--93545655 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
93545570 ATGATTTTTT
93545580 ATTTTGGG-TTTTAAGTTTAGATTTATGGGTTTTGA
1 ATTTTGGGTTTTTAA-TTTAGATTTATGGGTTTTGA
* *
93545615 ATTTTGGGTTTTTAATTTAGGTTTATGTGTTTTGA
1 ATTTTGGGTTTTTAATTTAGATTTATGGGTTTTGA
93545650 ATTTTG
1 ATTTTG
93545656 TAACTGGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 32 0.84
36 6 0.16
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (35 bp):
ATTTTGGGTTTTTAATTTAGATTTATGGGTTTTGA
Found at i:93546257 original size:45 final size:44
Alignment explanation
Indices: 93546207--93546365 Score: 167
Period size: 44 Copynumber: 3.6 Consensus size: 44
93546197 TTTAATCTAT
* * *
93546207 TCCACTACAACTTCAGGGAAATAAGACCTGCTATCTTCAGTCTGC
1 TCCACTACAACTTCAGGGAGATAAGACTTG-TAACTTCAGTCTGC
* *
93546252 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTC-GACCTGC
1 TCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAG-TCTGC
* * * ** * * *
93546296 CCCACTGCAACTTCAGGGGGATAAGGTTTGTAGCTTCAATCTAC
1 TCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAGTCTGC
*
93546340 TCCATTACAACTTCAGGGAGATAAGA
1 TCCACTACAACTTCAGGGAGATAAGA
93546366 TTTACCATGG
Statistics
Matches: 94, Mismatches: 18, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
43 1 0.01
44 66 0.70
45 27 0.29
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (44 bp):
TCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAGTCTGC
Found at i:93546753 original size:44 final size:44
Alignment explanation
Indices: 93546634--93546739 Score: 185
Period size: 44 Copynumber: 2.4 Consensus size: 44
93546624 TTAGGGAAAC
93546634 AAGATCTACAATCTTCAGTCTGCTTCCTTGCTACATCAGGAAGAT
1 AAGA-CTACAATCTTCAGTCTGCTTCCTTGCTACATCAGGAAGAT
* *
93546679 AAGATTACAATCTTCAGTCTGCTTCCTTGCTACATCAGGTAGAT
1 AAGACTACAATCTTCAGTCTGCTTCCTTGCTACATCAGGAAGAT
93546723 AAGACTACAATCTTCAG
1 AAGACTACAATCTTCAG
93546740 CCTGTACCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
44 54 0.93
45 4 0.07
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (44 bp):
AAGACTACAATCTTCAGTCTGCTTCCTTGCTACATCAGGAAGAT
Found at i:93546869 original size:44 final size:43
Alignment explanation
Indices: 93546821--93547217 Score: 320
Period size: 44 Copynumber: 9.1 Consensus size: 43
93546811 AGATTCACCG
*
93546821 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TGTAA
* * * * * *
93546865 TCTTC-AGCCTACTCCACTACTGCTTAAGGAGATAGGATGGT-G
1 TCTTCGA-TCTGCTCCACTACTGCTTAGGGAGATAAGATTGTAA
* ** * * * *
93546907 GCTTAAATCTGCTCCACTACTACTTAGGGAGACAAGATT-CACCG
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTGTA--A
* * *
93546951 TCTTCGATCTGCTCCACTACTACTTAAGGAGATGAGATCTGTAA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TGTAA
* * * * * **
93546995 TCTTC-AGCCTACTCCACTAATGCTTAGGAAGACAAGATTCGCCA
1 TCTTCGA-TCTGCTCCACTACTGCTTAGGGAGATAAGATT-GTAA
*
93547039 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCCGTAA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TGTAA
* * * * *
93547083 TCTTC-AGCCTACTCCACTACTGCTTAGGGAGATAGGATGGT-G
1 TCTTCGA-TCTGCTCCACTACTGCTTAGGGAGATAAGATTGTAA
* ** * * * *
93547125 GCTTAAATCTACTCCACTACTGCTTAGGGAGACAAGGTTCGTCA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATT-GTAA
93547169 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TGTAA
93547213 TCTTC
1 TCTTC
93547218 AGCCTACTCC
Statistics
Matches: 274, Mismatches: 63, Indels: 32
0.74 0.17 0.09
Matches are distributed among these distances:
42 58 0.21
43 11 0.04
44 201 0.73
45 3 0.01
46 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (43 bp):
TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTGTAA
Found at i:93546964 original size:130 final size:131
Alignment explanation
Indices: 93546773--93547020 Score: 392
Period size: 130 Copynumber: 1.9 Consensus size: 131
93546763 GACAAGGCTA
* * *
93546773 GTGGCTTAAATCTGCTTCCTCGCTACCTCAGGGGGACAAGATTCACCGTCTTCGATCTGCTCCAC
1 GTGGCTTAAATCTGCTCCCTCACTACCTCAGGGAGACAAGATTCACCGTCTTCGATCTGCTCCAC
* * *
93546838 TACTGCTTAGGGAGATAAGATCTATAATCTTCAGCCTACTCCACTACTGCTTAAGGAGATAGGAT
66 TACTACTTAAGGAGATAAGATCTATAATCTTCAGCCTACTCCACTAATGCTTAAGGAGATAGGAT
93546903 G
131 G
*
93546904 GTGGCTTAAATCTGCTCCACT-ACTA-CTTAGGGAGACAAGATTCACCGTCTTCGATCTGCTCCA
1 GTGGCTTAAATCTGCTCC-CTCACTACCTCAGGGAGACAAGATTCACCGTCTTCGATCTGCTCCA
* *
93546967 CTACTACTTAAGGAGATGAGATCTGTAATCTTCAGCCTACTCCACTAATGCTTA
65 CTACTACTTAAGGAGATAAGATCTATAATCTTCAGCCTACTCCACTAATGCTTA
93547021 GGAAGACAAG
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
130 85 0.79
131 20 0.19
132 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (131 bp):
GTGGCTTAAATCTGCTCCCTCACTACCTCAGGGAGACAAGATTCACCGTCTTCGATCTGCTCCAC
TACTACTTAAGGAGATAAGATCTATAATCTTCAGCCTACTCCACTAATGCTTAAGGAGATAGGAT
G
Found at i:93547058 original size:218 final size:218
Alignment explanation
Indices: 93546807--93547230 Score: 722
Period size: 218 Copynumber: 1.9 Consensus size: 218
93546797 ACCTCAGGGG
* *
93546807 GACAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAG
1 GACAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCCATAATCTTCAG
*
93546872 CCTACTCCACTACTGCTTAAGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTACTTAGGGA
66 CCTACTCCACTACTGCTTAAGGAGATAGGATGGTGGCTTAAATCTACTCCACTACTACTTAGGGA
* *
93546937 GACAAGATTCACCGTCTTCGATCTGCTCCACTACTACTTAAGGAGATGAGATCTGTAATCTTCAG
131 GACAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTCAG
93547002 CCTACTCCACTAATGCTTAGGAA
196 CCTACTCCACTAATGCTTAGGAA
* *
93547025 GACAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCCGTAATCTTCAG
1 GACAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCCATAATCTTCAG
* *
93547090 CCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTACTCCACTACTGCTTAGGGA
66 CCTACTCCACTACTGCTTAAGGAGATAGGATGGTGGCTTAAATCTACTCCACTACTACTTAGGGA
* ** * *
93547155 GACAAGGTTCGTCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAG
131 GACAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTCAG
93547220 CCTACTCCACT
196 CCTACTCCACT
93547231 GCTGCTCAAG
Statistics
Matches: 192, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
218 192 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (218 bp):
GACAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCCATAATCTTCAG
CCTACTCCACTACTGCTTAAGGAGATAGGATGGTGGCTTAAATCTACTCCACTACTACTTAGGGA
GACAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTCAG
CCTACTCCACTAATGCTTAGGAA
Found at i:93547191 original size:130 final size:130
Alignment explanation
Indices: 93547003--93547236 Score: 414
Period size: 130 Copynumber: 1.8 Consensus size: 130
93546993 AATCTTCAGC
93547003 CTACTCCACTAATGCTTAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
1 CTACTCCACTAATGCTTAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
93547068 AGATAAGATCCGTAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAAT
66 AGATAAGATCCGTAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAAT
* * * *
93547133 CTACTCCACTACTGCTTAGGGAGACAAGGTTCGTCATCTTCGATCTGCTCCACTACTGCTTAGGG
1 CTACTCCACTAATGCTTAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
* *
93547198 AGATAAGATCTGTAATCTTCAGCCTACTCCACTGCTGCT
66 AGATAAGATCCGTAATCTTCAGCCTACTCCACTACTGCT
93547237 CAAGGAAACA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 98 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (130 bp):
CTACTCCACTAATGCTTAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
AGATAAGATCCGTAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAAT
Found at i:93548592 original size:3 final size:3
Alignment explanation
Indices: 93548578--93548612 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
93548568 CCTCTCTTAT
*
93548578 TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
93548613 TTGGTGTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:93553949 original size:27 final size:26
Alignment explanation
Indices: 93553919--93553972 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
93553909 AACAAATTAG
93553919 TATACAAAACAATTTAAAATGAAATAA
1 TATACAAAACAATTTAAAAT-AAATAA
* * *
93553946 TATATAAAGCAATTTTAAATAAATAA
1 TATACAAAACAATTTAAAATAAATAA
93553972 T
1 T
93553973 TCATGAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (26 bp):
TATACAAAACAATTTAAAATAAATAA
Found at i:93554099 original size:10 final size:11
Alignment explanation
Indices: 93554053--93554104 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 11
93554043 ATAATTTATA
93554053 AAAATATTAAAGT
1 AAAATA-TAAA-T
*
93554066 AAAATATAAGT
1 AAAATATAAAT
93554077 AATATATATATAAT
1 AA-A-ATATA-AAT
93554091 AAAATATAAAT
1 AAAATATAAAT
93554102 AAA
1 AAA
93554105 GAAACGGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 9 0.26
12 9 0.26
13 12 0.35
14 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (11 bp):
AAAATATAAAT
Found at i:93555875 original size:156 final size:155
Alignment explanation
Indices: 93555624--93555935 Score: 468
Period size: 157 Copynumber: 2.0 Consensus size: 155
93555614 TTTTTTTTAT
** * *
93555624 AAAAAAGAGAAAGTTTAGATTTTTATTTTAAAAATCTATTTTTTAGTCATATTAAAGGAAAAGTT
1 AAAAAAGAGAAAGTTTAGATTTTTAAATTAAAAATATATTTTTTAGTCATATTAAAGGAAAACTT
* *
93555689 TAAATTCTTAAAATAAAGTTTTGATCTTTTTT-AACTATTTCGATATAAAGTTTTGATTTTTAAG
66 TAAATTCTTAAAATAAAGTTTTGATCTTTTTTCAACTATTTCGAAATAAAATTTTGATTTTTAAG
*
93555753 AAAAATAGTGATTTTTTTAAATAAAA
131 AAAAATAGTAATTTTTTTAAA-AAAA
* *
93555779 AAAAAAGAGAAAGTTTAGATTTTTTAAATTAAAAATATGTTTTTTAGTCATTTTAAA-GAAAATC
1 AAAAAAGAGAAAGTTTAGA-TTTTTAAATTAAAAATATATTTTTTAGTCATATTAAAGGAAAA-C
*
93555843 TTTAAATTTTTGAAAATAAAGTTTTGAT-TTTTTTCAACTATTTCGAAATAAAATTTTGATTTTT
64 TTTAAATTCTT-AAAATAAAGTTTTGATCTTTTTTCAACTATTTCGAAATAAAATTTTGATTTTT
*
93555907 AAGAAAAGTAGTAATTTTTTTAAAAAAA
128 AAGAAAAATAGTAATTTTTTTAAAAAAA
93555935 A
1 A
93555936 TTGATTTTGC
Statistics
Matches: 142, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
155 24 0.17
156 53 0.37
157 65 0.46
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (155 bp):
AAAAAAGAGAAAGTTTAGATTTTTAAATTAAAAATATATTTTTTAGTCATATTAAAGGAAAACTT
TAAATTCTTAAAATAAAGTTTTGATCTTTTTTCAACTATTTCGAAATAAAATTTTGATTTTTAAG
AAAAATAGTAATTTTTTTAAAAAAA
Found at i:93559244 original size:16 final size:17
Alignment explanation
Indices: 93559213--93559244 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
93559203 CTTGATTTTC
93559213 CTAAAATACTAATCAAA
1 CTAAAATACTAATCAAA
93559230 CTAAAATAC-AATCAA
1 CTAAAATACTAATCAA
93559245 CTCAAACAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (17 bp):
CTAAAATACTAATCAAA
Found at i:93560084 original size:16 final size:16
Alignment explanation
Indices: 93560063--93560096 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
93560053 CCCCTCTTGG
*
93560063 TTCTACTAACCCGATT
1 TTCTACTAACCCAATT
93560079 TTCTACTAACCCAATT
1 TTCTACTAACCCAATT
93560095 TT
1 TT
93560097 TGGGATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.41
Consensus pattern (16 bp):
TTCTACTAACCCAATT
Found at i:93561738 original size:16 final size:16
Alignment explanation
Indices: 93561685--93561758 Score: 64
Period size: 16 Copynumber: 4.7 Consensus size: 16
93561675 GAAAAAATAA
93561685 AATTAATAT-AATTATTT
1 AATTAATATAAATTA--T
**
93561702 AATTTTTATAAA-TAT
1 AATTAATATAAATTAT
*
93561717 AA-TAATTTAAATTAT
1 AATTAATATAAATTAT
*
93561732 AATTAATATAAATTAA
1 AATTAATATAAATTAT
*
93561748 AATTAAAATAA
1 AATTAATATAA
93561759 CAATATTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
14 6 0.13
15 8 0.17
16 21 0.46
17 9 0.20
18 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAATATAAATTAT
Found at i:93564788 original size:21 final size:22
Alignment explanation
Indices: 93564753--93564807 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
93564743 ATATACTATA
*
93564753 AAAATAAAATTTTTA-TATTTTC
1 AAAAT-AATTTTTTATTATTTTC
*
93564775 AAAATAATTTTTTATTATTTTT
1 AAAATAATTTTTTATTATTTTC
*
93564797 AAAATTATTTT
1 AAAATAATTTT
93564808 ACTTAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 8 0.28
22 21 0.72
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AAAATAATTTTTTATTATTTTC
Found at i:93576087 original size:24 final size:25
Alignment explanation
Indices: 93576060--93576106 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
93576050 ATACATAACT
93576060 ATATGCACAGTCAGAT-ACAGATAC
1 ATATGCACAGTCAGATAACAGATAC
* * *
93576084 ATATTCAGATTCAGATAACAGAT
1 ATATGCACAGTCAGATAACAGAT
93576107 TCAGTTTCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.26
Consensus pattern (25 bp):
ATATGCACAGTCAGATAACAGATAC
Found at i:93576093 original size:18 final size:19
Alignment explanation
Indices: 93576070--93576110 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
93576060 ATATGCACAG
*
93576070 TCAGATACAGAT-ACATAT
1 TCAGATACAGATAACAGAT
*
93576088 TCAGATTCAGATAACAGAT
1 TCAGATACAGATAACAGAT
93576107 TCAG
1 TCAG
93576111 TTTCAGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (19 bp):
TCAGATACAGATAACAGAT
Found at i:93576110 original size:19 final size:19
Alignment explanation
Indices: 93576070--93576119 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
93576060 ATATGCACAG
* *
93576070 TCAGATACAGAT-ACATAT
1 TCAGATTCAGATAACAGAT
93576088 TCAGATTCAGATAACAGAT
1 TCAGATTCAGATAACAGAT
*
93576107 TCAGTTTCAGATA
1 TCAGATTCAGATA
93576120 TGCAGAATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (19 bp):
TCAGATTCAGATAACAGAT
Found at i:93582819 original size:16 final size:16
Alignment explanation
Indices: 93582798--93582829 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
93582788 AATATATATT
*
93582798 TTGAATTTTGAATTTA
1 TTGAATTATGAATTTA
93582814 TTGAATTATGAATTTA
1 TTGAATTATGAATTTA
93582830 AAAAAAATTA
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:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TTGAATTATGAATTTA
Found at i:93583817 original size:23 final size:22
Alignment explanation
Indices: 93583791--93583856 Score: 54
Period size: 23 Copynumber: 3.2 Consensus size: 22
93583781 ATGTTTTTTT
93583791 AATATTTTATCACACCTTTATAG
1 AATATTTTATCACA-CTTTATAG
**
93583814 AATAACTTATCA-A--TT-T--
1 AATATTTTATCACACTTTATAG
93583830 AATATTTTATCACATCTTTATAG
1 AATATTTTATCACA-CTTTATAG
93583853 AATA
1 AATA
93583857 ACTTATCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
16 10 0.31
17 1 0.03
18 1 0.03
19 2 0.06
20 2 0.06
21 1 0.03
22 1 0.03
23 14 0.44
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.44
Consensus pattern (22 bp):
AATATTTTATCACACTTTATAG
Found at i:93583877 original size:39 final size:39
Alignment explanation
Indices: 93583788--93583866 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
93583778 ATAATGTTTT
93583788 TTTAATATTTTATCACACCTTTATAGAATAACTTATCAA
1 TTTAATATTTTATCACACCTTTATAGAATAACTTATCAA
*
93583827 TTTAATATTTTATCACATCTTTATAGAATAACTTATCAA
1 TTTAATATTTTATCACACCTTTATAGAATAACTTATCAA
93583866 T
1 T
93583867 CCTTAATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.46
Consensus pattern (39 bp):
TTTAATATTTTATCACACCTTTATAGAATAACTTATCAA
Found at i:93591574 original size:49 final size:49
Alignment explanation
Indices: 93591519--93591614 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
93591509 GAAACATCCC
93591519 TTAGTTCATATCTTTGATGTTCAGGAAAAGAAAATATATTTCTTAAAGT
1 TTAGTTCATATCTTTGATGTTCAGGAAAAGAAAATATATTTCTTAAAGT
93591568 TTAGTTCATATCTTTGATGTTCAGGAAAAGAAAATATATTTCTTAAA
1 TTAGTTCATATCTTTGATGTTCAGGAAAAGAAAATATATTTCTTAAA
93591615 ACTTGAGCAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (49 bp):
TTAGTTCATATCTTTGATGTTCAGGAAAAGAAAATATATTTCTTAAAGT
Found at i:93598668 original size:3 final size:3
Alignment explanation
Indices: 93598660--93598709 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
93598650 ACTAATCTCA
93598660 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
93598708 AA
1 AA
93598710 ACCCCTTTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:93606121 original size:26 final size:26
Alignment explanation
Indices: 93606092--93606192 Score: 175
Period size: 26 Copynumber: 3.9 Consensus size: 26
93606082 TGATATAAAT
93606092 TGATAATGGGTTAGGTAAATGTTTTA
1 TGATAATGGGTTAGGTAAATGTTTTA
93606118 TGATAATGGGTTAGGTAAATGTTTTA
1 TGATAATGGGTTAGGTAAATGTTTTA
**
93606144 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTTA
*
93606170 TGATAATGGGTTAGGTAGATGTT
1 TGATAATGGGTTAGGTAAATGTT
93606193 CCATGATGGA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.30, C:0.02, G:0.29, T:0.40
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTTA
Found at i:93606164 original size:13 final size:13
Alignment explanation
Indices: 93606096--93606164 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 13
93606086 ATAAATTGAT
93606096 AATGGGTTAGGTA
1 AATGGGTTAGGTA
** *
93606109 AATGTTTTATG-A
1 AATGGGTTAGGTA
93606121 TAATGGGTTAGGTA
1 -AATGGGTTAGGTA
** *
93606135 AATGTTTTATG-A
1 AATGGGTTAGGTA
93606147 TAATGGGTTAGGTA
1 -AATGGGTTAGGTA
93606161 AATG
1 AATG
93606165 TTCCATGATA
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
12 2 0.05
13 36 0.90
14 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (13 bp):
AATGGGTTAGGTA
Found at i:93607823 original size:26 final size:27
Alignment explanation
Indices: 93607792--93607948 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
93607782 AGGAAGCGTC
*
93607792 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
93607819 -TGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
93607844 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
*
93607872 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
93607899 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* *
93607926 CTGGTGACT-TGTCACAA-TATCTG
1 CTGGTGGCTCTGCCACAATTATCTG
93607949 GCACCTCGCT
Statistics
Matches: 115, Mismatches: 7, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
25 3 0.03
26 41 0.36
27 67 0.58
28 4 0.03
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:93607903 original size:54 final size:54
Alignment explanation
Indices: 93607789--93607948 Score: 247
Period size: 54 Copynumber: 3.0 Consensus size: 54
93607779 TGGAGGAAGC
93607789 GTCCTGGTGGCTATGCCACAATTATCTGAT-TGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
93607842 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* * * *
93607896 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTGACT-TGTCACA-ATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTGGCTCTGCCACATATATCT
93607948 G
1 G
93607949 GCACCTCGCT
Statistics
Matches: 101, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
52 7 0.07
53 42 0.42
54 52 0.51
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:93613208 original size:51 final size:50
Alignment explanation
Indices: 93613153--93613257 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 50
93613143 TGATACAAAT
*
93613153 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAAT-GGTTAGGTAAATGTTCA
93613204 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATGTTCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATGTTCA
93613254 TGAT
1 TGAT
93613258 GGGAATTTCA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 20 0.38
51 33 0.62
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (50 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATGTTCA
Found at i:93613212 original size:25 final size:26
Alignment explanation
Indices: 93613153--93613257 Score: 180
Period size: 25 Copynumber: 4.2 Consensus size: 26
93613143 TGATACAAAT
93613153 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
93613179 TGATAATGGGTTAGGTAAATGTT-TA
1 TGATAATGGGTTAGGTAAATGTTCCA
93613204 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
93613230 TGATAAT-GGTTAGGTAAATGTT-CA
1 TGATAATGGGTTAGGTAAATGTTCCA
93613254 TGAT
1 TGAT
93613258 GGGAATTTCA
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
24 6 0.08
25 39 0.51
26 31 0.41
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:93614868 original size:27 final size:27
Alignment explanation
Indices: 93614837--93614967 Score: 153
Period size: 27 Copynumber: 4.9 Consensus size: 27
93614827 CCTAGTGGCA
*
93614837 TGCCACAATTATCTGATTTGGTGGCTC
1 TGCCACAATTATCTGATCTGGTGGCTC
* *
93614864 TGCCAC-ATATATCTG-TCCTAGTGGCTA
1 TGCCACAAT-TATCTGAT-CTGGTGGCTC
*
93614891 TGCCACAATTATCTAATCTGGTGGCTC
1 TGCCACAATTATCTGATCTGGTGGCTC
*
93614918 TGCCAC-ATATATCTGTTCTGGTGGCTC
1 TGCCACAAT-TATCTGATCTGGTGGCTC
93614945 TGCCACAA-TATCTGTATCTGGTG
1 TGCCACAATTATCTG-ATCTGGTG
93614968 ACTTCGTCAC
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
26 11 0.12
27 73 0.83
28 4 0.05
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (27 bp):
TGCCACAATTATCTGATCTGGTGGCTC
Found at i:93614913 original size:54 final size:54
Alignment explanation
Indices: 93614825--93614967 Score: 209
Period size: 54 Copynumber: 2.7 Consensus size: 54
93614815 TGGAGGAAGC
* *
93614825 GTCCTAGTGGC-ATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCT
1 GTCCTAGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCT
93614878 GTCCTAGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCT
1 GTCCTAGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCT
* * * *
93614932 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 GTCCTAGTGGCTATGCCACAATTATCT-AATCTGGTG
93614968 ACTTCGTCAC
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
53 16 0.20
54 66 0.80
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (54 bp):
GTCCTAGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCT
Found at i:93614978 original size:27 final size:26
Alignment explanation
Indices: 93614837--93614985 Score: 131
Period size: 27 Copynumber: 5.5 Consensus size: 26
93614827 CCTAGTGGCA
*
93614837 TGCCACAATTATCTGATT-TGGTGGCTC
1 TGCCACAA-TATCTG-TTCTGGTGACTC
* * * *
93614864 TGCCACATATATCTGTCCTAGTGGCTA
1 TGCCACA-ATATCTGTTCTGGTGACTC
** *
93614891 TGCCACAATTATCTAATCTGGTGGCTC
1 TGCCACAA-TATCTGTTCTGGTGACTC
*
93614918 TGCCACATATATCTGTTCTGGTGGCTC
1 TGCCACA-ATATCTGTTCTGGTGACTC
93614945 TGCCACAATATCTGTATCTGGTGACT-
1 TGCCACAATATCTGT-TCTGGTGACTC
*
93614971 TCGTCACAATATCTG
1 T-GCCACAATATCTG
93614986 GCAGCTTCGC
Statistics
Matches: 104, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
26 11 0.11
27 91 0.88
28 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (26 bp):
TGCCACAATATCTGTTCTGGTGACTC
Found at i:93616283 original size:49 final size:48
Alignment explanation
Indices: 93616077--93616273 Score: 281
Period size: 48 Copynumber: 4.1 Consensus size: 48
93616067 TTATGTAATC
** *
93616077 CAATGTACCTAATTTATATTACAGAGTTTGTTCCAAGTTTTAATGTTG
1 CAATGTATTTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTG
* *
93616125 TAATGTATTTAATTTATATTATAAAGTTTGTTCCAAGTTTTAATGTTG
1 CAATGTATTTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTG
*
93616173 TC-ATGTATTTAATTTATATTACAAATTTTGTTCCAAGTTTTAATGTTG
1 -CAATGTATTTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTG
**
93616221 CAAT-TAATTTAATTTATGACCACAAAGTTTGTTCCAAGTTTTAATGTTG
1 CAATGT-ATTTAATTTAT-ATTACAAAGTTTGTTCCAAGTTTTAATGTTG
93616270 CAAT
1 CAAT
93616274 TAATCTAATT
Statistics
Matches: 134, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
47 2 0.01
48 100 0.75
49 32 0.24
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (48 bp):
CAATGTATTTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTG
Found at i:93617411 original size:14 final size:14
Alignment explanation
Indices: 93617392--93617420 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
93617382 AAATTACATG
93617392 TTAGAATAGTATCA
1 TTAGAATAGTATCA
93617406 TTAGAATAGTATCA
1 TTAGAATAGTATCA
93617420 T
1 T
93617421 CAAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (14 bp):
TTAGAATAGTATCA
Found at i:93618732 original size:16 final size:16
Alignment explanation
Indices: 93618713--93618785 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 16
93618703 ATAACACGCC
93618713 AAATAAATTACATAAA
1 AAATAAATTACATAAA
93618729 AAATAAATCTA-ATAAA
1 AAATAAAT-TACATAAA
* * *
93618745 CCTAAA-ACA-CACATAAC
1 ---AAATAAATTACATAAA
93618762 AAATAAATTACATAAAA
1 AAATAAATTACAT-AAA
93618779 AAATAAA
1 AAATAAA
93618786 ACATTCTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 15
0.67 0.09 0.23
Matches are distributed among these distances:
14 3 0.07
15 2 0.05
16 18 0.42
17 15 0.35
18 2 0.05
19 3 0.07
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATAAATTACATAAA
Found at i:93619116 original size:12 final size:12
Alignment explanation
Indices: 93619101--93619144 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
93619091 TCTATTTATT
93619101 TTTTTCCTTCTC
1 TTTTTCCTTCTC
93619113 TTTTTCCTTCCCTC
1 TTTTTCCTT--CTC
93619127 TTTTT-CTT-TC
1 TTTTTCCTTCTC
93619137 TTTTTCCT
1 TTTTTCCT
93619145 CTTCCCGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.24
11 2 0.07
12 9 0.31
13 3 0.10
14 8 0.28
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTCCTTCTC
Found at i:93619148 original size:26 final size:25
Alignment explanation
Indices: 93619101--93619177 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 25
93619091 TCTATTTATT
*
93619101 TTTTTCCTTCTCTTTTTCCTTCCCTC
1 TTTTT-CTTCTCTTTTTCCTTCCCGC
93619127 TTTTTCTT-TCTTTTTCCTCTTCCCGC
1 TTTTTCTTCTCTTTTT-C-CTTCCCGC
*
93619153 TCTTTTCTTCTTCTTCTTCTCTTCC
1 T-TTTTCTTC-TCTTTTTC-CTTCC
93619178 TCAAATTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
24 7 0.16
25 4 0.09
26 13 0.30
27 7 0.16
28 7 0.16
29 6 0.14
ACGTcount: A:0.00, C:0.36, G:0.01, T:0.62
Consensus pattern (25 bp):
TTTTTCTTCTCTTTTTCCTTCCCGC
Found at i:93620407 original size:5 final size:6
Alignment explanation
Indices: 93620395--93620420 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
93620385 AGAGGGAAGG
93620395 AAGAAA AAGAAA AAGAAA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AA
93620421 TAAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:93623219 original size:16 final size:16
Alignment explanation
Indices: 93623198--93623252 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
93623188 GTTAATGTCT
93623198 AAATTGAAAATTTTAA
1 AAATTGAAAATTTTAA
*
93623214 AAATTGAATAATGTCT--
1 AAATTGAA-AAT-TTTAA
93623230 AAATTGAAAATTTTAA
1 AAATTGAAAATTTTAA
93623246 AAATTGA
1 AAATTGA
93623253 GTTACCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
16 23 0.70
17 3 0.09
18 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (16 bp):
AAATTGAAAATTTTAA
Found at i:93623227 original size:32 final size:32
Alignment explanation
Indices: 93623190--93623252 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
93623180 ATTTAAACGT
93623190 TAATGTCTAAATTGAAAATTTTAAAAATTGAA
1 TAATGTCTAAATTGAAAATTTTAAAAATTGAA
93623222 TAATGTCTAAATTGAAAATTTTAAAAATTGA
1 TAATGTCTAAATTGAAAATTTTAAAAATTGA
93623253 GTTACCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (32 bp):
TAATGTCTAAATTGAAAATTTTAAAAATTGAA
Found at i:93630342 original size:6 final size:6
Alignment explanation
Indices: 93630331--93630355 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
93630321 TATTTTTCAC
93630331 CTCTTT CTCTTT CTCTTT CTCTTT C
1 CTCTTT CTCTTT CTCTTT CTCTTT C
93630356 AACACACAGA
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
CTCTTT
Found at i:93633654 original size:2 final size:2
Alignment explanation
Indices: 93633647--93633672 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
93633637 CATGTTTTAA
93633647 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
93633673 GAAAATAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93644400 original size:20 final size:20
Alignment explanation
Indices: 93644342--93644393 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
93644332 ACTCTTTTTA
93644342 AATCGATTCATTATTGTTTG
1 AATCGATTCATTATTGTTTG
* **
93644362 AATCTATTTTTTATTGTTTG
1 AATCGATTCATTATTGTTTG
93644382 AATCGATTCATT
1 AATCGATTCATT
93644394 GTGGTTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.54
Consensus pattern (20 bp):
AATCGATTCATTATTGTTTG
Found at i:93647218 original size:10 final size:11
Alignment explanation
Indices: 93647190--93647229 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
93647180 TTGTTTATTG
93647190 TTATTTTT-AT
1 TTATTTTTAAT
*
93647200 GTTGTTTTTAAT
1 -TTATTTTTAAT
93647212 TTATTTTTAAT
1 TTATTTTTAAT
93647223 TTATTTT
1 TTATTTT
93647230 GTTAGTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (11 bp):
TTATTTTTAAT
Found at i:93657173 original size:44 final size:44
Alignment explanation
Indices: 93657119--93657210 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
93657109 TGTTCAGGGA
* * *
93657119 TACTTTGACTTTGAGTCGATGAGGCA-CTATAAGTGTCGTACTGT
1 TACTTCGACTTTAAGTCAATGAGGCACCT-TAAGTGTCGTACTGT
*
93657163 TACTTCGACTTTAAGTCAATGAGGCACCTTATGTGTCGTACTGT
1 TACTTCGACTTTAAGTCAATGAGGCACCTTAAGTGTCGTACTGT
93657207 TACT
1 TACT
93657211 GTTACTTCGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 41 0.95
45 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (44 bp):
TACTTCGACTTTAAGTCAATGAGGCACCTTAAGTGTCGTACTGT
Found at i:93657405 original size:18 final size:18
Alignment explanation
Indices: 93657368--93657467 Score: 53
Period size: 18 Copynumber: 5.6 Consensus size: 18
93657358 TAAATAAAAG
*
93657368 TACTGAATGACTGA-CTGT
1 TACTGAATAACTGATC-GT
*
93657386 TA-TAGAATAATTGATCGT
1 TACT-GAATAACTGATCGT
*
93657404 TACTGAATAACTGATTGCT
1 TACTGAATAACTGATCG-T
* ** * *
93657423 T-TTGAGCAAATGATTGT
1 TACTGAATAACTGATCGT
* * *
93657440 TACTGAATAACTAATTGC
1 TACTGAATAACTGATCGT
93657458 TACTGAATAA
1 TACTGAATAA
93657468 TTGAATGTTA
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
17 3 0.05
18 56 0.89
19 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (18 bp):
TACTGAATAACTGATCGT
Found at i:93657477 original size:36 final size:36
Alignment explanation
Indices: 93657390--93657479 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 36
93657380 GACTGTTATA
* **
93657390 GAATAATTG-ATCGTTACTGAATAACTGATTGCTTTT
1 GAATAATTGAAT-GTTACTGAATAACTAATTGCTACT
** * *
93657426 GAGCAAATGATTGTTACTGAATAACTAATTGCTACT
1 GAATAATTGAATGTTACTGAATAACTAATTGCTACT
93657462 GAATAATTGAATGTTACT
1 GAATAATTGAATGTTACT
93657480 AAATGAAACT
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
36 41 0.98
37 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (36 bp):
GAATAATTGAATGTTACTGAATAACTAATTGCTACT
Found at i:93660158 original size:33 final size:33
Alignment explanation
Indices: 93660088--93660165 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
93660078 GAGCTGGAAG
* * * *
93660088 GAGTGGAGTACTGCGATGGATATAAGCCGGGAG
1 GAGTGGAGTACTGCAATGGATATAAGCCAGAAA
**
93660121 GAGTGGAGTACTGCAATGGATATGTGCCAGAAA
1 GAGTGGAGTACTGCAATGGATATAAGCCAGAAA
*
93660154 GAGTGAAGTACT
1 GAGTGGAGTACT
93660166 ATAGTGGATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.31, C:0.12, G:0.37, T:0.21
Consensus pattern (33 bp):
GAGTGGAGTACTGCAATGGATATAAGCCAGAAA
Found at i:93663296 original size:43 final size:43
Alignment explanation
Indices: 93663231--93663397 Score: 178
Period size: 43 Copynumber: 3.9 Consensus size: 43
93663221 AGCTCATACA
* * *
93663231 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCG
* * * ** *
93663273 ATGCCACTGTCCCA-ATCAGGGTCTTACATGAAATCGTATAACG
1 ATGCCAATGTCCCAGA-CATGGTCTTACATGTAATCACATATCG
* ** *
93663316 ATGCCAATGTCCTAGACATGGTCTTACACATAATCACA-ATACA
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATAT-CG
93663359 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAT
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAT
93663398 CTTGGTAATC
Statistics
Matches: 98, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
42 7 0.07
43 90 0.92
44 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCG
Found at i:93663954 original size:19 final size:18
Alignment explanation
Indices: 93663930--93663976 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
93663920 CACATAATTT
93663930 CAAAATTCACAATTTAGT-C
1 CAAAATTCAC-ATTT-GTAC
* *
93663949 CAAAATTGACATTTTTAC
1 CAAAATTCACATTTGTAC
93663967 CAAAATTCAC
1 CAAAATTCAC
93663977 TTTACAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 14 0.58
19 9 0.38
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (18 bp):
CAAAATTCACATTTGTAC
Found at i:93665865 original size:17 final size:17
Alignment explanation
Indices: 93665831--93665879 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
93665821 AATTAAATCC
* *
93665831 CTTTTTCTTTCCCATTCT
1 CTTTTCCTTT-CCTTTCT
93665849 CTTTTCCTTTCCTTTCT
1 CTTTTCCTTTCCTTTCT
*
93665866 TTTTTCCTTTCCTT
1 CTTTTCCTTTCCTT
93665880 CTCCTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (17 bp):
CTTTTCCTTTCCTTTCT
Found at i:93665876 original size:22 final size:23
Alignment explanation
Indices: 93665851--93665913 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
93665841 CCCATTCTCT
93665851 TTTCCTT-TCCT-TTCTTTTTTCC
1 TTTCCTTCTCCTATT-TTTTTTCC
93665873 TTTCCTTCTCCTATTTTTTTT-C
1 TTTCCTTCTCCTATTTTTTTTCC
*
93665895 TTCTCATTCTCCTCATTTT
1 TT-TCCTTCTCCT-ATTTT
93665914 ACCTATTCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 10 0.28
23 19 0.53
24 7 0.19
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTCCTTCTCCTATTTTTTTTCC
Found at i:93665956 original size:9 final size:9
Alignment explanation
Indices: 93665944--93665970 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
93665934 TTTCTTTCTT
93665944 TTTCCCTTC
1 TTTCCCTTC
93665953 TTTCCCTTC
1 TTTCCCTTC
93665962 TTTCCCTTC
1 TTTCCCTTC
93665971 CCATTCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTCCCTTC
Found at i:93671147 original size:31 final size:31
Alignment explanation
Indices: 93671106--93671171 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
93671096 AAATTAAATA
93671106 AATACATAGATTTGCTTTCGATCTCTGGTCC
1 AATACATAGATTTGCTTTCGATCTCTGGTCC
*
93671137 AATAGATAGATTTGCTTTCGATCTCTGGTCC
1 AATACATAGATTTGCTTTCGATCTCTGGTCC
93671168 AATA
1 AATA
93671172 AAAGTCGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (31 bp):
AATACATAGATTTGCTTTCGATCTCTGGTCC
Found at i:93672712 original size:28 final size:28
Alignment explanation
Indices: 93672645--93672719 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
93672635 TCAAATATGG
** *
93672645 CACTTAGTGTGCAAAATATTGAGAACGG
1 CACTTAGTGTGTGAAATATTGAGAACGA
* *
93672673 CACTTAGTGTGTGAGATATTGAGAATGA
1 CACTTAGTGTGTGAAATATTGAGAACGA
*
93672701 CATTTAGTGTGTGAAATAT
1 CACTTAGTGTGTGAAATAT
93672720 CGAATGGTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.32
Consensus pattern (28 bp):
CACTTAGTGTGTGAAATATTGAGAACGA
Found at i:93673277 original size:13 final size:13
Alignment explanation
Indices: 93673259--93673286 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
93673249 GCTCATGAAT
93673259 TGATTTTGGTTGA
1 TGATTTTGGTTGA
93673272 TGATTTTGGTTGA
1 TGATTTTGGTTGA
93673285 TG
1 TG
93673287 GTTATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.32, T:0.54
Consensus pattern (13 bp):
TGATTTTGGTTGA
Found at i:93679070 original size:28 final size:28
Alignment explanation
Indices: 93679039--93679116 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
93679029 TCAAATATGG
*
93679039 CACTTAGTGTACGAAATATTGAGAACGA
1 CACTTAGTGTGCGAAATATTGAGAACGA
* * *
93679067 CACTTAGTGTGCGAGATATTGAGAATGG
1 CACTTAGTGTGCGAAATATTGAGAACGA
*
93679095 CACTTAGTGTGTGAAATATTGA
1 CACTTAGTGTGCGAAATATTGA
93679117 ATGGTTCAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (28 bp):
CACTTAGTGTGCGAAATATTGAGAACGA
Found at i:93679381 original size:37 final size:37
Alignment explanation
Indices: 93679330--93679403 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
93679320 ATGTTATGTG
93679330 AGATATGAACTATAGTTGCTTTAACTAAATATACATA
1 AGATATGAACTATAGTTGCTTTAACTAAATATACATA
*
93679367 AGATATGAATTATAGTTGCTTTAACTAAATATACATA
1 AGATATGAACTATAGTTGCTTTAACTAAATATACATA
93679404 TGGCAATCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (37 bp):
AGATATGAACTATAGTTGCTTTAACTAAATATACATA
Found at i:93685156 original size:35 final size:35
Alignment explanation
Indices: 93685078--93685158 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
93685068 TGGCATTACG
93685078 GAGTGGCATCATGGCAATAGTCTACTGGCTCTATA
1 GAGTGGCATCATGGCAATAGTCTACTGGCTCTATA
* * * *
93685113 GAGCGGCATCATGGTAATGGTTTACTGGCTCTAT-
1 GAGTGGCATCATGGCAATAGTCTACTGGCTCTATA
93685147 GAAGTGGCATCA
1 G-AGTGGCATCA
93685159 CGGAGATGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 1 0.03
35 39 0.98
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (35 bp):
GAGTGGCATCATGGCAATAGTCTACTGGCTCTATA
Found at i:93685685 original size:28 final size:28
Alignment explanation
Indices: 93685641--93685717 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
93685631 AGAGAAAGAG
93685641 ATGTCCACCAA-AGACTATCTTATGCGGGA
1 ATGTCCACCAAGA-ACTATCTTATG-GGGA
* *
93685670 A-GTCCTCCAAGAACTATCTTATGTGGA
1 ATGTCCACCAAGAACTATCTTATGGGGA
*
93685697 ATGTCCACCAAGGACTATCTT
1 ATGTCCACCAAGAACTATCTT
93685718 GAAGACGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.10
28 36 0.86
29 2 0.05
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (28 bp):
ATGTCCACCAAGAACTATCTTATGGGGA
Found at i:93694472 original size:164 final size:165
Alignment explanation
Indices: 93694158--93694487 Score: 635
Period size: 164 Copynumber: 2.0 Consensus size: 165
93694148 TCAGCATATC
93694158 TTTTCGCTGAAAGCTGCTAGTTGAAACAATACTTTGTCCTTCAAGGGACCCCTCTGTTGGTTAAG
1 TTTTCGCTGAAAGCTGCTAGTTGAAACAATACTTTGTCCTTCAAGGGACCCCTCTGTTGGTTAAG
93694223 CATTCTAGTTTTTCTGTCGTATTGGTGTATCATTTCCTATGGAAATTAAACTGATGAAGCGATCT
66 CATTCTAGTTTTTCTGTCGTATTGGTGTATCATTTCCTATGGAAATTAAACTGATGAAGCGATCT
93694288 CGAATGATCATCTGAAGTGAGACTTGGCTTCTGAA
131 CGAATGATCATCTGAAGTGAGACTTGGCTTCTGAA
*
93694323 TTTTCGCTGAAAGCTGCTAGTTGAAACAATACTTTGTCCTTCAATGGACCCCTCTGTTGGTTAAG
1 TTTTCGCTGAAAGCTGCTAGTTGAAACAATACTTTGTCCTTCAAGGGACCCCTCTGTTGGTTAAG
*
93694388 CATTCTAG-TTTTCTGTCGTATTGGTGTATCATTTCCTATGGGAATTAAACTGATGAAGCGATCT
66 CATTCTAGTTTTTCTGTCGTATTGGTGTATCATTTCCTATGGAAATTAAACTGATGAAGCGATCT
93694452 CGAATGATCATCTGAAGTGAGACTTGGCTTCTGAA
131 CGAATGATCATCTGAAGTGAGACTTGGCTTCTGAA
93694487 T
1 T
93694488 ATTTTACGTC
Statistics
Matches: 163, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
164 91 0.56
165 72 0.44
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (165 bp):
TTTTCGCTGAAAGCTGCTAGTTGAAACAATACTTTGTCCTTCAAGGGACCCCTCTGTTGGTTAAG
CATTCTAGTTTTTCTGTCGTATTGGTGTATCATTTCCTATGGAAATTAAACTGATGAAGCGATCT
CGAATGATCATCTGAAGTGAGACTTGGCTTCTGAA
Found at i:93711337 original size:2 final size:2
Alignment explanation
Indices: 93711332--93711362 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
93711322 ATATAAGTAA
93711332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93711363 GTTACACGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:93712581 original size:41 final size:38
Alignment explanation
Indices: 93712518--93712593 Score: 107
Period size: 41 Copynumber: 1.9 Consensus size: 38
93712508 GTTAATTAAT
* *
93712518 TTTTTTAAAATAAAAATAATTTTTTTATAATTTTATAC
1 TTTTTTAAAAAAAAAATAATTTTTTTAAAATTTTATAC
93712556 TTTTTTAAAAAAATAATATATATTTTTTTAAAATTTTA
1 TTTTTTAAAAAAA-AA-ATA-ATTTTTTTAAAATTTTA
93712594 AAAAATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 12 0.36
39 2 0.06
40 3 0.09
41 16 0.48
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (38 bp):
TTTTTTAAAAAAAAAATAATTTTTTTAAAATTTTATAC
Found at i:93712603 original size:41 final size:38
Alignment explanation
Indices: 93712520--93712607 Score: 95
Period size: 41 Copynumber: 2.2 Consensus size: 38
93712510 TAATTAATTT
* * * ***
93712520 TTTTAAAATAAAAATAATTTTTTTATAATTTTATACTT
1 TTTTAAAAAAAAAATAATTTTTTTAAAATTTTAAAAAA
93712558 TTTTAAAAAAATAATATATATTTTTTTAAAATTTTAAAAAA
1 TTTTAAAAAAA-AA-ATA-ATTTTTTTAAAATTTTAAAAAA
93712599 TTTTAAAAA
1 TTTTAAAAA
93712608 TTAATTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 10 0.24
39 2 0.05
40 3 0.07
41 26 0.63
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (38 bp):
TTTTAAAAAAAAAATAATTTTTTTAAAATTTTAAAAAA
Found at i:93714757 original size:29 final size:29
Alignment explanation
Indices: 93714694--93714759 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
93714684 TTATACTCTT
*
93714694 TTAA-TAA-TTTTTAATTTTTTAAAATAA
1 TTAATTAATTTTTTAAATTTTTAAAATAA
* *
93714721 ATATTTAATTTTTTAAAATTTTTAAAA-AA
1 TTAATTAATTTTTT-AAATTTTTAAAATAA
93714750 TTAATTAATT
1 TTAATTAATT
93714760 GTGACATGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 2 0.06
28 3 0.10
29 15 0.48
30 11 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TTAATTAATTTTTTAAATTTTTAAAATAA
Found at i:93715211 original size:22 final size:24
Alignment explanation
Indices: 93715186--93715230 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
93715176 ATCCCTAAGT
93715186 ATTTGATA-AAAA-AAATTATTTG
1 ATTTGATATAAAAGAAATTATTTG
*
93715208 ATTTTATATAAAAGAAATTATTT
1 ATTTGATATAAAAGAAATTATTT
93715231 TCTTGAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (24 bp):
ATTTGATATAAAAGAAATTATTTG
Found at i:93732202 original size:21 final size:20
Alignment explanation
Indices: 93732174--93732213 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
93732164 AAAAAGATAA
93732174 AATCAAGTT-TATAAGACTTG
1 AATCAAGTTCT-TAAGACTTG
93732194 AATCTAAGTTCTTAAGACTT
1 AATC-AAGTTCTTAAGACTT
93732214 CCTATTAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 13 0.72
22 1 0.06
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (20 bp):
AATCAAGTTCTTAAGACTTG
Found at i:93733422 original size:27 final size:28
Alignment explanation
Indices: 93733376--93733454 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
93733366 TTAAAAATAT
* * **
93733376 AAAAAACTAAAACTAATTAAAATTCCCAA
1 AAAAAACTAAAAAT-TTTAAAAAACCCAA
*
93733405 AAATAA-TAAAAATTTTAAAAAACCCAA
1 AAAAAACTAAAAATTTTAAAAAACCCAA
* *
93733432 AAAAAACTTAAAATTTAAAAAAA
1 AAAAAACTAAAAATTTTAAAAAA
93733455 AACTAATCTG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 16 0.39
28 20 0.49
29 5 0.12
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (28 bp):
AAAAAACTAAAAATTTTAAAAAACCCAA
Found at i:93733651 original size:17 final size:17
Alignment explanation
Indices: 93733631--93733666 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
93733621 TATGCAAGAC
*
93733631 TTCAAAAAATTTAAAAA
1 TTCAAAAAACTTAAAAA
*
93733648 TTCATAAAACTTAAAAA
1 TTCAAAAAACTTAAAAA
93733665 TT
1 TT
93733667 AATTATTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (17 bp):
TTCAAAAAACTTAAAAA
Found at i:93735344 original size:13 final size:13
Alignment explanation
Indices: 93735314--93735352 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
93735304 TTTACTCTTG
* *
93735314 ATTTTACAAAAAG
1 ATTTTACTAAAAT
*
93735327 GTTTTACTAAAAT
1 ATTTTACTAAAAT
93735340 ATTTTACTAAAAT
1 ATTTTACTAAAAT
93735353 TATGATTTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (13 bp):
ATTTTACTAAAAT
Found at i:93737456 original size:90 final size:90
Alignment explanation
Indices: 93737296--93737588 Score: 277
Period size: 90 Copynumber: 3.3 Consensus size: 90
93737286 AATTAATAAT
** * * * **
93737296 CTGCAAC-TCTGGTGGTTCATCCACAAATTATCTGGTAGCTTTTATATGCAAAAATGTTGTGCAT
1 CTGCAACAT-TGGTGGTTCATCCACCCATTTTTTGGCAGCTTTTATATGCAATTATGTTGTGCAT
** *
93737360 TTACAACCATCTGGTAGCGTATTGAC
65 CCACAACCATCTGGCAGCGTATTGAC
* * *
93737386 CTGCAACATTGGTGGTTCATCCACCCATTTTTTGGCAGCTTTTTTTTGCAATTATGTTGTGTATC
1 CTGCAACATTGGTGGTTCATCCACCCATTTTTTGGCAGCTTTTATATGCAATTATGTTGTGCATC
* * *
93737451 CACAACCATCTGGCAACATATTAAC
66 CACAACCATCTGGCAGCGTATTGAC
* * ** * * *
93737476 TTGCAACAATGGTGGTTCATCCACCCACATTTTGGTC-GCTCTCATCTGCAATTATGTTGTGCA-
1 CTGCAACATTGGTGGTTCATCCACCCATTTTTTGG-CAGCTTTTATATGCAATTATGTTGTGCAT
* *
93737539 CTCACAACCATTTGCCAGCGTATTGAC
65 C-CACAACCATCTGGCAGCGTATTGAC
* * * *
93737566 CTGTAACTTTTGTGGTTTATCCA
1 CTGCAACATTGGTGGTTCATCCA
93737589 TAACCCAACG
Statistics
Matches: 164, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
89 1 0.01
90 161 0.98
91 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (90 bp):
CTGCAACATTGGTGGTTCATCCACCCATTTTTTGGCAGCTTTTATATGCAATTATGTTGTGCATC
CACAACCATCTGGCAGCGTATTGAC
Found at i:93738320 original size:21 final size:23
Alignment explanation
Indices: 93738276--93738320 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
93738266 ATGAGTTGTT
* *
93738276 TTTTTTTCTAAAATTAGAATAAA
1 TTTTCTTCTAAAATTAGAACAAA
93738299 TTTTCTTCTAAAA-TA-AACAAA
1 TTTTCTTCTAAAATTAGAACAAA
93738320 T
1 T
93738321 GTTTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 2 0.10
23 12 0.60
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (23 bp):
TTTTCTTCTAAAATTAGAACAAA
Found at i:93738836 original size:15 final size:15
Alignment explanation
Indices: 93738814--93738851 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
93738804 GGATATATTA
*
93738814 TTATATTAATTAATAT
1 TTATATTAA-AAATAT
93738830 TTA-ATTAAAAATAT
1 TTATATTAAAAATAT
93738844 TTATATTA
1 TTATATTA
93738852 TTATCACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 8 0.40
15 9 0.45
16 3 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATATTAAAAATAT
Found at i:93739065 original size:20 final size:20
Alignment explanation
Indices: 93739042--93739091 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
93739032 AAATCCAAAT
93739042 TAAAATACTAAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
* *
93739062 TAAAATCCTGAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
93739082 TAAGAATACT
1 TAA-AATACT
93739092 GATGTGGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (20 bp):
TAAAATACTAAAATTCAGGA
Found at i:93741628 original size:10 final size:10
Alignment explanation
Indices: 93741601--93741666 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 10
93741591 AATTAAAAAG
93741601 ATAAAAATTTT
1 ATAAAAA-TTT
*
93741612 ATTAAAATTT
1 ATAAAAATTT
93741622 ATAAAAATGTT
1 ATAAAAAT-TT
*
93741633 -T-AATATTT
1 ATAAAAATTT
93741641 ATTAAAAGATTT
1 A-TAAAA-ATTT
93741653 AT-AAAA-TT
1 ATAAAAATTT
93741661 ATAAAA
1 ATAAAA
93741667 TCCATAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
8 6 0.13
9 8 0.18
10 15 0.33
11 11 0.24
12 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:93741635 original size:19 final size:19
Alignment explanation
Indices: 93741613--93741666 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
93741603 AAAAATTTTA
93741613 TTAAAATTTATAAAA-ATGT
1 TTAAAATTTATAAAAGAT-T
*
93741632 TTAATATTTATTAAAAGATT
1 TTAAAATTTA-TAAAAGATT
93741652 TATAAAA-TTATAAAA
1 T-TAAAATTTATAAAA
93741667 TCCATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 14 0.47
20 10 0.33
21 6 0.20
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
TTAAAATTTATAAAAGATT
Found at i:93744812 original size:18 final size:18
Alignment explanation
Indices: 93744762--93744812 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
93744752 TAAGAATTAT
**
93744762 TTTTGAGACAAAAAATGC
1 TTTTGAGACAAAAAGCGC
93744780 TTTTGAGACAAAAAGCGC
1 TTTTGAGACAAAAAGCGC
*
93744798 TTTTGAGATAAAAAG
1 TTTTGAGACAAAAAG
93744813 TATTCCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (18 bp):
TTTTGAGACAAAAAGCGC
Done.