Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 186 of 222
Found at i:59484806 original size:42 final size:42
Alignment explanation
Indices: 59484760--59484846 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
59484750 GGCCTGGGAT
*
59484760 ACGGTCATGTGACCCAAGTTAGTGAGTTACACGGGCAGAGAC
1 ACGGTCATGTGACCCAAGTTAGTAAGTTACACGGGCAGAGAC
* * * * *
59484802 ACGGTCGTGTGTCTCAAGTTAGTAAGTTACACGGGCTGGGAC
1 ACGGTCATGTGACCCAAGTTAGTAAGTTACACGGGCAGAGAC
59484844 ACG
1 ACG
59484847 ATCGTATGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (42 bp):
ACGGTCATGTGACCCAAGTTAGTAAGTTACACGGGCAGAGAC
Found at i:59485243 original size:49 final size:49
Alignment explanation
Indices: 59485182--59485275 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
59485172 CCAAGAGGGA
59485182 ATAAATAATGATAAGAGTGTAGACAGTGGAAAACCAAGTTTAGCAATGT
1 ATAAATAATGATAAGAGTGTAGACAGTGGAAAACCAAGTTTAGCAATGT
* * * *
59485231 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGATCAATTTTAGCA
1 ATAAATAATGATAAGAGTGTAGACAGTGGAAAACCAAGTTTAGCA
59485276 TTGCATAGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (49 bp):
ATAAATAATGATAAGAGTGTAGACAGTGGAAAACCAAGTTTAGCAATGT
Found at i:59486256 original size:6 final size:6
Alignment explanation
Indices: 59486245--59486271 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
59486235 AAGACAATTA
59486245 TTAAAT TTAAAT TTAAAT TTAAAT TTA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTA
59486272 TTAAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:59487408 original size:67 final size:67
Alignment explanation
Indices: 59487300--59487429 Score: 188
Period size: 67 Copynumber: 1.9 Consensus size: 67
59487290 AACATACCAG
* * **
59487300 CTATGGGTTCAATCATCTTGAGAGCATAAGTCTCTGCTTATATCAAAGCAAATGAGTTACATATT
1 CTATGGGCTCAATCATCTTGAGAGCATAAGCCTCTAATTATATCAAAGCAAATGAGTTACATATT
59487365 AA
66 AA
* * * *
59487367 CTATGGGCTCGATCATCTTTAGAGCATGAGCCTCTAATTATATCAAAGTAAATGAGTTACATA
1 CTATGGGCTCAATCATCTTGAGAGCATAAGCCTCTAATTATATCAAAGCAAATGAGTTACATA
59487430 CGCATGGTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (67 bp):
CTATGGGCTCAATCATCTTGAGAGCATAAGCCTCTAATTATATCAAAGCAAATGAGTTACATATT
AA
Found at i:59489897 original size:5 final size:5
Alignment explanation
Indices: 59489887--59489924 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
59489877 GAATGATTGT
59489887 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATG
1 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATG
59489925 CTTGTGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (5 bp):
ATGTG
Found at i:59491522 original size:24 final size:25
Alignment explanation
Indices: 59491475--59491539 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 25
59491465 TGAGTATATA
59491475 AACATAAAAAATTAATAATCTAAAT
1 AACATAAAAAATTAATAATCTAAAT
* * *
59491500 AACAT-AATAATTAATTAT-TTAA-
1 AACATAAAAAATTAATAATCTAAAT
*
59491522 AA-TTAAAAAATTAATAAT
1 AACATAAAAAATTAATAAT
59491540 ATTTTTTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.03
22 13 0.39
23 3 0.09
24 11 0.33
25 5 0.15
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.34
Consensus pattern (25 bp):
AACATAAAAAATTAATAATCTAAAT
Found at i:59491581 original size:35 final size:35
Alignment explanation
Indices: 59491522--59491596 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 35
59491512 AATTATTTAA
59491522 AATTAAAAAATTAATAATATTTTTTAACCATTTGT
1 AATTAAAAAATTAATAATATTTTTTAACCATTTGT
* *
59491557 AATTAAATAATTTAATAATATTTTTTTACCATTTGT
1 AATTAAA-AAATTAATAATATTTTTTAACCATTTGT
59491593 AATT
1 AATT
59491597 TAACATCGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 7 0.19
36 30 0.81
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (35 bp):
AATTAAAAAATTAATAATATTTTTTAACCATTTGT
Found at i:59496898 original size:4 final size:4
Alignment explanation
Indices: 59496889--59496916 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
59496879 AAGTTTTATT
59496889 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
59496917 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:59500717 original size:4 final size:4
Alignment explanation
Indices: 59500708--59500735 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
59500698 TATTTTTATT
59500708 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
59500736 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:59523805 original size:21 final size:21
Alignment explanation
Indices: 59523781--59523823 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
59523771 ATATATTCTG
*
59523781 AAATTATAAAAAGACATTAAA
1 AAATTATAAAAAAACATTAAA
*
59523802 AAATTATAAAAAAATATTAAA
1 AAATTATAAAAAAACATTAAA
59523823 A
1 A
59523824 GTTTTCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
AAATTATAAAAAAACATTAAA
Found at i:59533273 original size:5 final size:5
Alignment explanation
Indices: 59533265--59533290 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
59533255 GAGATGGAAT
59533265 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
59533291 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:59533290 original size:26 final size:26
Alignment explanation
Indices: 59533239--59533290 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
59533229 TGAAGTTTTC
* * *
59533239 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
59533265 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
59533291 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:59534131 original size:30 final size:31
Alignment explanation
Indices: 59534092--59534152 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
59534082 GGGTTGGGAG
* *
59534092 GGGAGAGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
59534123 GGGA-AGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
59534153 AAAAAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:59534298 original size:9 final size:9
Alignment explanation
Indices: 59534281--59534311 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
59534271 TCGAGTTGAT
59534281 TCGAATAAC
1 TCGAATAAC
*
59534290 TCGATTAAC
1 TCGAATAAC
59534299 TCGAATAAC
1 TCGAATAAC
59534308 TCGA
1 TCGA
59534312 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:59536048 original size:36 final size:35
Alignment explanation
Indices: 59536000--59536079 Score: 126
Period size: 36 Copynumber: 2.3 Consensus size: 35
59535990 ACAACAGACC
*
59536000 ATCAA-TTACACCATCATAAAAACTTTAATTTGAAT
1 ATCAAGTT-CACCATCATAAAAACCTTAATTTGAAT
59536035 ATCAAAGTTCACCATCATAAAAACCTTAATTTGAAT
1 ATC-AAGTTCACCATCATAAAAACCTTAATTTGAAT
59536071 ATCAAGTTC
1 ATCAAGTTC
59536080 CGTCGGTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 9 0.21
36 31 0.74
37 2 0.05
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (35 bp):
ATCAAGTTCACCATCATAAAAACCTTAATTTGAAT
Found at i:59548054 original size:2 final size:2
Alignment explanation
Indices: 59548047--59548071 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59548037 TATTATGTGT
59548047 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
59548072 GCATGTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59552391 original size:50 final size:50
Alignment explanation
Indices: 59552269--59552517 Score: 282
Period size: 50 Copynumber: 4.8 Consensus size: 50
59552259 GATAATAACA
* * ** * *
59552269 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* * * *
59552320 TGCCCATGCCATGTCCTAGACATGGTCTTATAGGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
59552370 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
59552420 TGCCCATGCCATGTCCCAGGCATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
59552475 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
59552518 TTACCCGAAT
Statistics
Matches: 167, Mismatches: 25, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
50 92 0.55
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:59552460 original size:100 final size:105
Alignment explanation
Indices: 59552268--59552517 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 105
59552258 TGATAATAAC
* ** *
59552268 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGCTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGCTGCCCATGCCATG
* * *
59552333 TCCTAGACATGGTCTTATAGGGGACCTCT-T-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTATGATCTTAAGG
* *
59552370 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGCTGCCCATGCCATGT
*
59552434 CCCAGGCATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCT-ATGATCTTAAGG
*
59552475 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
59552518 TTACCCGAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 47 0.36
101 36 0.27
102 1 0.01
103 3 0.02
104 1 0.01
105 2 0.02
106 41 0.31
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (105 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGCTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTATGATCTTAAGG
Found at i:59552633 original size:13 final size:13
Alignment explanation
Indices: 59552612--59552643 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
59552602 GCTTGGATCA
*
59552612 TCATCAAATAAAT
1 TCATAAAATAAAT
59552625 TCATAAAATAAAT
1 TCATAAAATAAAT
59552638 TCATAA
1 TCATAA
59552644 TTTCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:59552890 original size:30 final size:30
Alignment explanation
Indices: 59552855--59552912 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
59552845 CCTCGACTCT
*
59552855 AACTTTTTCAAAATTACAATTTTT-CCCCTA
1 AACTTTTACAAAATTAC-ATTTTTGCCCCTA
*
59552885 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACATTTTTGCCCC
59552913 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.31, C:0.24, G:0.02, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACATTTTTGCCCCTA
Found at i:59559923 original size:50 final size:50
Alignment explanation
Indices: 59559809--59560057 Score: 309
Period size: 50 Copynumber: 4.8 Consensus size: 50
59559799 GATAATAACA
* * ** *
59559809 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
59559860 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
59559910 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
59559960 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* * *
59560015 ATGCCAATTCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
59560058 TTACCCGAAT
Statistics
Matches: 173, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
50 97 0.56
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:59559995 original size:100 final size:104
Alignment explanation
Indices: 59559808--59560057 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 104
59559798 TGATAATAAC
* ** *
59559808 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGGTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
59559873 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
*
59559910 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
59559974 CCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
59560015 ATGCCAATTCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
59560058 TTACCCGAAT
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
100 51 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (104 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:59560173 original size:13 final size:13
Alignment explanation
Indices: 59560152--59560183 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
59560142 GCTTGGATCA
*
59560152 TCATCAAATAAAT
1 TCATAAAATAAAT
59560165 TCATAAAATAAAT
1 TCATAAAATAAAT
59560178 TCATAA
1 TCATAA
59560184 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:59560446 original size:29 final size:30
Alignment explanation
Indices: 59560395--59560451 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
59560385 CCTCGACTCT
*
59560395 AACTTTTTCAAAATTACGATTTT-CCCCTA
1 AACTTTTACAAAATTACGATTTTACCCCTA
*
59560424 AACTTTTACATAATTAC-ATTTTTACCCC
1 AACTTTTACAAAATTACGA-TTTTACCCC
59560452 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.04
29 19 0.79
30 4 0.17
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.42
Consensus pattern (30 bp):
AACTTTTACAAAATTACGATTTTACCCCTA
Found at i:59572806 original size:13 final size:13
Alignment explanation
Indices: 59572788--59572812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59572778 TAAATTATAT
59572788 GTGTGAAAATTTC
1 GTGTGAAAATTTC
59572801 GTGTGAAAATTT
1 GTGTGAAAATTT
59572813 TTATCGTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:59577839 original size:40 final size:40
Alignment explanation
Indices: 59577764--59577903 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
59577754 AACACACCAG
* * *
59577764 TTTGGCACCCAGTGCCTCATCGGAC-AATTCAAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGG-CTAATCCGAAGTAATAA
* *
59577804 TTTGACACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGCTAATCCGAAGTAATAA
* * * ** *
59577842 -TTGGCACCTAGTGCCTCATTGAATTAATCCGAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCG-GCTAATCCGAAGTAATAA
* *
59577882 ATTGACACCCAGTGTCTCATCG
1 TTTGACACCCAGTGCCTCATCG
59577904 ACTTGAAGCT
Statistics
Matches: 78, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
37 17 0.22
38 12 0.15
39 2 0.03
40 30 0.38
41 17 0.22
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGCTAATCCGAAGTAATAA
Found at i:59578105 original size:24 final size:24
Alignment explanation
Indices: 59578060--59578116 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
59578050 TATATATACC
59578060 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
59578084 AATTC-ATCACATACTAAA-TCAATCA
1 AATTCAATCA-ATA-TAAATTCAAT-A
*
59578109 ATTTCAAT
1 AATTCAAT
59578117 TGAAAAACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 4 0.14
24 13 0.46
25 9 0.32
26 2 0.07
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:59578812 original size:15 final size:15
Alignment explanation
Indices: 59578783--59578842 Score: 75
Period size: 16 Copynumber: 3.9 Consensus size: 15
59578773 TTCTCCTTCA
59578783 TTTCTTTCATTTTTCT
1 TTTCTTTC-TTTTTCT
59578799 TTTCTTTCTTTTTCTT
1 TTTCTTTCTTTTTC-T
* *
59578815 TTTCTTTCTGTTTCG
1 TTTCTTTCTTTTTCT
*
59578830 TTTCTATCTTTTT
1 TTTCTTTCTTTTT
59578843 ATCTTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
15 17 0.44
16 22 0.56
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTCTTTCTTTTTCT
Found at i:59578834 original size:31 final size:32
Alignment explanation
Indices: 59578783--59578842 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
59578773 TTCTCCTTCA
* * *
59578783 TTTCTTTCATTTTTCTTTTCTTTCTTTTTCTT
1 TTTCTTTCATGTTTCGTTTCTATCTTTTTCTT
59578815 TTTCTTTC-TGTTTCGTTTCTATCTTTTT
1 TTTCTTTCATGTTTCGTTTCTATCTTTTT
59578843 ATCTTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (32 bp):
TTTCTTTCATGTTTCGTTTCTATCTTTTTCTT
Found at i:59597074 original size:8 final size:8
Alignment explanation
Indices: 59597061--59597086 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
59597051 TCGGAGCAAT
59597061 AACATGGA
1 AACATGGA
59597069 AACATGGA
1 AACATGGA
59597077 AACATGGA
1 AACATGGA
59597085 AA
1 AA
59597087 ACGTCGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.23, T:0.12
Consensus pattern (8 bp):
AACATGGA
Found at i:59605248 original size:232 final size:233
Alignment explanation
Indices: 59604833--59605290 Score: 801
Period size: 232 Copynumber: 2.0 Consensus size: 233
59604823 CCTGACTCCT
*
59604833 GAGTACTCTCTTCCCTCTAACCCTCTTCCTTGTTTTTTTTGCTACTAATTTCTTGGATGAAGTAG
1 GAGTACTCTCTTCCCTCTAACCCTCTTCCTTGTTTTTTTTGCTACTAATTTCTTGGATAAAGTAG
* * *
59604898 TAGTGACCTCTTTGCCACGAGTTCTCTTTAGAATAGATGAGATGTCTATGTCATGAAGATTTGAG
66 TAGTGAACTCTTTGCCACGAGTTCTCTTTAGAATAGATGAGATGTCCATATCATGAAGATTTGAG
* * *
59604963 TGAGAAGGAAGTCATGTATCACCAATAAGAGAGTTAGCTCAACTGGGAGTAGAAGAGGAAGCTAT
131 TGAGAAGGAAGTCATGTATCACCAATAAAAGAGTTAGCTCAACTGGAAGTAGAAGAGAAAGCTAT
59605028 ATCAAGATTAGTGACGAGATTCTAATTTCAAGACCCCC
196 ATCAAGATTAGTGACGAGATTCTAATTTCAAGACCCCC
* *
59605066 GAGTGCTCTCTTCCCTCTAACCCTCTTCCTTG-TTTTTTTGCTACTAATTTCTTGGTTAAAGTAG
1 GAGTACTCTCTTCCCTCTAACCCTCTTCCTTGTTTTTTTTGCTACTAATTTCTTGGATAAAGTAG
*
59605130 TAGTGAACTCTTTGCCACGAGTTCTCTTTAGAATAGATGAGATGTCCATATCATGAAGGTTTGAG
66 TAGTGAACTCTTTGCCACGAGTTCTCTTTAGAATAGATGAGATGTCCATATCATGAAGATTTGAG
*
59605195 TGAGAAGGAAGTCATGTATCACCAATAAAAGAGTTAGCTCGACTGGAAGTAGAAGAGAAAGCTAT
131 TGAGAAGGAAGTCATGTATCACCAATAAAAGAGTTAGCTCAACTGGAAGTAGAAGAGAAAGCTAT
*
59605260 ATCAAGATTAGTGATGAGATTCTAATTTCAA
196 ATCAAGATTAGTGACGAGATTCTAATTTCAA
59605291 AGAGGAAAGC
Statistics
Matches: 213, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
232 182 0.85
233 31 0.15
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (233 bp):
GAGTACTCTCTTCCCTCTAACCCTCTTCCTTGTTTTTTTTGCTACTAATTTCTTGGATAAAGTAG
TAGTGAACTCTTTGCCACGAGTTCTCTTTAGAATAGATGAGATGTCCATATCATGAAGATTTGAG
TGAGAAGGAAGTCATGTATCACCAATAAAAGAGTTAGCTCAACTGGAAGTAGAAGAGAAAGCTAT
ATCAAGATTAGTGACGAGATTCTAATTTCAAGACCCCC
Found at i:59606854 original size:15 final size:16
Alignment explanation
Indices: 59606834--59606863 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59606824 ATTAAATTAA
59606834 TTAACC-AAATGCAAG
1 TTAACCTAAATGCAAG
59606849 TTAACCTAAATGCAA
1 TTAACCTAAATGCAA
59606864 ATGAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (16 bp):
TTAACCTAAATGCAAG
Found at i:59611213 original size:28 final size:28
Alignment explanation
Indices: 59611169--59611268 Score: 130
Period size: 28 Copynumber: 3.6 Consensus size: 28
59611159 GAACATGGTA
* *
59611169 GAAAATGGAAGCGTTTGTGGCAATCTAT
1 GAAAATGGAAGCCTTTGTGGTAATCTAT
*
59611197 GAAAATAGAAGCCTTTGTGGTAATCTAT
1 GAAAATGGAAGCCTTTGTGGTAATCTAT
* *
59611225 GAAAATGGAAGCCTTTCTGGTAATCTAA
1 GAAAATGGAAGCCTTTGTGGTAATCTAT
*
59611253 GGAAAT-GAAGGCCTTT
1 GAAAATGGAA-GCCTTT
59611269 ATGATAAATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
27 3 0.05
28 61 0.95
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (28 bp):
GAAAATGGAAGCCTTTGTGGTAATCTAT
Found at i:59611283 original size:56 final size:56
Alignment explanation
Indices: 59611169--59611284 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 56
59611159 GAACATGGTA
* * * * * *
59611169 GAAAATGGAAGCGTTTGTGGCAATCTATGAAAATAGAAGCCTTTGTGGTAATCTAT
1 GAAAATGGAAGCCTTTCTGGCAATCTAAGAAAATAGAAGCCTTTATGATAATCGAT
* *
59611225 GAAAATGGAAGCCTTTCTGGTAATCTAAGGAAAT-GAAGGCCTTTATGATAAAT-GAT
1 GAAAATGGAAGCCTTTCTGGCAATCTAAGAAAATAGAA-GCCTTTATGAT-AATCGAT
59611281 GAAA
1 GAAA
59611285 GGAACGCCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
55 3 0.06
56 44 0.88
57 3 0.06
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.28
Consensus pattern (56 bp):
GAAAATGGAAGCCTTTCTGGCAATCTAAGAAAATAGAAGCCTTTATGATAATCGAT
Found at i:59611435 original size:27 final size:27
Alignment explanation
Indices: 59611388--59611451 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
59611378 ATCTTCGATG
* *
59611388 AACTCTGAATGGATAGCATGTATAGCA
1 AACTCTGAAAGGATAGAATGTATAGCA
* *
59611415 AACTCTGAAAGGAT-GAAATGTGTGGCA
1 AACTCTGAAAGGATAG-AATGTATAGCA
*
59611442 AACTTTGAAA
1 AACTCTGAAA
59611452 TAATGGTAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (27 bp):
AACTCTGAAAGGATAGAATGTATAGCA
Found at i:59613926 original size:38 final size:38
Alignment explanation
Indices: 59613883--59613964 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
59613873 AAAGGGGTTT
* *
59613883 ATGCAATTAATTAAACTAAATGATTCTATCCTATATGC
1 ATGCAATTAATTAAAATAAATGATACTATCCTATATGC
*
59613921 ATGCAATTAATTAAAATAAATGATACTATCCTATATGT
1 ATGCAATTAATTAAAATAAATGATACTATCCTATATGC
59613959 ATGCAA
1 ATGCAA
59613965 AATTTCAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (38 bp):
ATGCAATTAATTAAAATAAATGATACTATCCTATATGC
Found at i:59631421 original size:16 final size:17
Alignment explanation
Indices: 59631394--59631425 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
59631384 GCTAGCCCAA
59631394 AATTATAACCCAAACCC
1 AATTATAACCCAAACCC
59631411 AATTA-AACCCAAACC
1 AATTATAACCCAAACC
59631426 TAATCTGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (17 bp):
AATTATAACCCAAACCC
Found at i:59632604 original size:23 final size:24
Alignment explanation
Indices: 59632550--59632607 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
59632540 ATTATTTTAT
* *
59632550 TATGTAGTATTATTTTAAGTTTCC
1 TATGTATTATTATTTTAAGTTTCA
*
59632574 TATATATTATTA-TTTAA-TTTCA
1 TATGTATTATTATTTTAAGTTTCA
59632596 TAATGTATTATT
1 T-ATGTATTATT
59632608 TTATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 5 0.17
23 14 0.48
24 10 0.34
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (24 bp):
TATGTATTATTATTTTAAGTTTCA
Found at i:59636963 original size:18 final size:17
Alignment explanation
Indices: 59636932--59636980 Score: 73
Period size: 18 Copynumber: 2.9 Consensus size: 17
59636922 GATTCAAAAA
*
59636932 AAAAACAAAA-AAAATC
1 AAAATCAAAATAAAATC
59636948 AAAATCAAAATCAAAATC
1 AAAATCAAAAT-AAAATC
59636966 AAAATCAAAATAAAA
1 AAAATCAAAATAAAA
59636981 AAAAGAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 9 0.30
17 4 0.13
18 17 0.57
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAATCAAAATAAAATC
Found at i:59636981 original size:6 final size:6
Alignment explanation
Indices: 59636942--59636980 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
59636932 AAAAACAAAA
59636942 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT- AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
59636981 AAAAGAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.72, C:0.13, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:59636981 original size:12 final size:12
Alignment explanation
Indices: 59636925--59636981 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
59636915 GGGTTCAGAT
59636925 TCAAAA-AAAAA
1 TCAAAATAAAAA
*
59636936 AC-AAA-AAAAA
1 TCAAAATAAAAA
*
59636946 TCAAAATCAAAA
1 TCAAAATAAAAA
*
59636958 TCAAAATCAAAA
1 TCAAAATAAAAA
59636970 TCAAAATAAAAA
1 TCAAAATAAAAA
59636982 AAAGAAAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.22
11 4 0.10
12 27 0.68
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.12
Consensus pattern (12 bp):
TCAAAATAAAAA
Found at i:59637923 original size:7 final size:7
Alignment explanation
Indices: 59637911--59637944 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
59637901 CACTCTGAAA
59637911 AAAAATG
1 AAAAATG
59637918 AAAAATG
1 AAAAATG
59637925 -AAAATG
1 AAAAATG
59637931 AAAAATG
1 AAAAATG
*
59637938 GAAAATG
1 AAAAATG
59637945 GAGAGGCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:59637930 original size:13 final size:14
Alignment explanation
Indices: 59637912--59637944 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
59637902 ACTCTGAAAA
59637912 AAAATGAAAAAT-G
1 AAAATGAAAAATGG
59637925 AAAATGAAAAATGG
1 AAAATGAAAAATGG
59637939 AAAATG
1 AAAATG
59637945 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (14 bp):
AAAATGAAAAATGG
Found at i:59639533 original size:50 final size:50
Alignment explanation
Indices: 59639478--59639877 Score: 339
Period size: 50 Copynumber: 8.0 Consensus size: 50
59639468 CCACAAGCGA
* * *
59639478 TGCAGTGGAATAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGATAT
1 TGCAGTGGAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
** * * * * *
59639528 TGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTAC-TCCCCAGGCAG
1 TGCAGTGGAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCC-GACAT
*
59639578 TGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
** * * * *
59639628 TGCAGTTAAAAAGATTAAAGCTAC-TACAGCGAATCTTAC-TCCCCAAGCGA-
1 TGCAGTGGAAAAGATTAAAGCCACAT-CAGTGAATCTTGCTTCCCCGA-C-AT
* *
59639678 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
* ** * * * * * *
59639728 TGCGGTTAAAAAGATTGAAGCTACAAT-AGCGAATCTTACTTCCCTGGCGA-
1 TGCAGTGGAAAAGATTAAAGCCAC-ATCAGTGAATCTTGCTTCCCCGAC-AT
* * ** *
59639778 TGTAGT-GAAGCAGATTAAAGCCACATTGGTGAATCTTGCTTTCCCGACAT
1 TGCAGTGGAA-AAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
* * * *
59639828 TGCAGT-TAAAAGGATTAAAGTCACAACGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAAAA-GATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
59639878 CACAGTTAAG
Statistics
Matches: 273, Mismatches: 63, Indels: 28
0.75 0.17 0.08
Matches are distributed among these distances:
49 19 0.07
50 238 0.87
51 16 0.06
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (50 bp):
TGCAGTGGAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
Found at i:59639871 original size:100 final size:100
Alignment explanation
Indices: 59639453--59639864 Score: 596
Period size: 100 Copynumber: 4.1 Consensus size: 100
59639443 CCGAAGAATT
* * * *
59639453 ACAGCAAATCTTACTCCACAAGCGATGCAGTGGAATAGATTAAAGCCACATCGGTGAATCTTGCT
1 ACAGCGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
*
59639518 TCCCCGATATTGCAGTTAAAAAGATTAAAGCTACA
66 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* *
59639553 ACAGTGAATCTTACTCCCCAGGC-AGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGC
1 ACAGCGAATCTTACTCCCCAGGCGA-TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGC
*
59639617 TTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACT
65 TTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
*
59639653 ACAGCGAATCTTACTCCCCAAGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
1 ACAGCGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
* *
59639718 TCCCCGACATTGCGGTTAAAAAGATTGAAGCTACA
66 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * * * *
59639753 ATAGCGAATCTTACTTCCCTGGCGATGTAGT-GAAGCAGATTAAAGCCACATTGGTGAATCTTGC
1 ACAGCGAATCTTACTCCCCAGGCGATGCAGTGGAA-CAGATTAAAGCCACATCGGTGAATCTTGC
* *
59639817 TTTCCCGACATTGCAGTTAAAAGGATTAAAG-TCACA
65 TTCCCCGACATTGCAGTTAAAAAGATTAAAGCT-ACA
* *
59639853 ACGGTGAATCTT
1 ACAGCGAATCTT
59639865 GCTTCCCCGA
Statistics
Matches: 281, Mismatches: 27, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
99 5 0.02
100 275 0.98
101 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (100 bp):
ACAGCGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
Found at i:59640242 original size:16 final size:16
Alignment explanation
Indices: 59640215--59640259 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
59640205 GCTAGCCCAA
59640215 AATTATAACCCAAACCC
1 AATTA-AACCCAAACCC
*
59640232 AATTAAACCCAAACCT
1 AATTAAACCCAAACCC
59640248 AATCT-AACCCAA
1 AAT-TAAACCCAA
59640260 TACTAAACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (16 bp):
AATTAAACCCAAACCC
Found at i:59641420 original size:23 final size:24
Alignment explanation
Indices: 59641366--59641423 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
59641356 ATTATTTTAT
* *
59641366 TATGTAGTATTATTTTAAGTTTCC
1 TATGTATTATTATTTTAAGTTTCA
*
59641390 TATATATTATTA-TTTAA-TTTCA
1 TATGTATTATTATTTTAAGTTTCA
59641412 TAATGTATTATT
1 T-ATGTATTATT
59641424 TTATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 5 0.17
23 14 0.48
24 10 0.34
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (24 bp):
TATGTATTATTATTTTAAGTTTCA
Found at i:59650165 original size:25 final size:25
Alignment explanation
Indices: 59650137--59650195 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
59650127 GGCTCTTATA
*
59650137 AGCTTCCCGTTATACAGCTCGA-ATG
1 AGCTTCCCGTTACACAGCTC-ACATG
* **
59650162 AGCTTCCTGTTACATGGCTCACATG
1 AGCTTCCCGTTACACAGCTCACATG
59650187 AGCTTCCCG
1 AGCTTCCCG
59650196 ATTAATGGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (25 bp):
AGCTTCCCGTTACACAGCTCACATG
Found at i:59650203 original size:25 final size:25
Alignment explanation
Indices: 59650011--59650215 Score: 136
Period size: 24 Copynumber: 8.2 Consensus size: 25
59650001 TGGCTTTTCG
*
59650011 GAGCTTCCCGATTAAAGGCTCTTTCAT
1 GAGCTTCCCGATTAATGGCTC--TCAT
* *
59650038 GAGCTTCCCAAATAATTGGCTCTC-T
1 GAGCTTCCCGATTAA-TGGCTCTCAT
*
59650063 AGAGCTTCCCGA-TATTGGCTCTC-T
1 -GAGCTTCCCGATTAATGGCTCTCAT
* * * *
59650087 AGAGCTTCCCGA-CATTGGCTCACTT
1 -GAGCTTCCCGATTAATGGCTCTCAT
* *
59650112 GAACTTCCCGATT-ATGGCTCTTAT
1 GAGCTTCCCGATTAATGGCTCTCAT
* ** **
59650136 AAGCTTCCCG-TTATACAGCTCGAAT
1 GAGCTTCCCGATTA-ATGGCTCTCAT
* *
59650161 GAGCTTCCTG-TTACATGGCTCACAT
1 GAGCTTCCCGATTA-ATGGCTCTCAT
*
59650186 GAGCTTCCCGATTAATGGCTCTCTT
1 GAGCTTCCCGATTAATGGCTCTCAT
59650211 GAGCT
1 GAGCT
59650216 ACCTGTTTAT
Statistics
Matches: 142, Mismatches: 29, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
23 2 0.01
24 55 0.39
25 52 0.37
26 15 0.11
27 13 0.09
28 5 0.04
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGATTAATGGCTCTCAT
Found at i:59654215 original size:3 final size:3
Alignment explanation
Indices: 59654207--59654253 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
59654197 ATTCCCACTC
* * * *
59654207 ATA ATA ATA ATA ATA ATA CTA ATA ATA A-A TTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
59654254 CTTACCTCAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:59654255 original size:12 final size:12
Alignment explanation
Indices: 59654207--59654253 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
59654197 ATTCCCACTC
*
59654207 ATAATAATAATA
1 ATAATATTAATA
*
59654219 ATAATACTAATA
1 ATAATATTAATA
59654231 ATAA-ATTAATA
1 ATAATATTAATA
*
59654242 CTAATATTAATA
1 ATAATATTAATA
59654254 CTTACCTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAATATTAATA
Found at i:59654926 original size:11 final size:11
Alignment explanation
Indices: 59654910--59654935 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59654900 CTTTTTCTTC
59654910 TTTCTCCCCTG
1 TTTCTCCCCTG
59654921 TTTCTCCCCTG
1 TTTCTCCCCTG
59654932 TTTC
1 TTTC
59654936 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:59661281 original size:20 final size:20
Alignment explanation
Indices: 59661253--59661291 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
59661243 TTACATATCA
59661253 CATTTATTCCATC-TATATG
1 CATTTATTCCATCATATATG
59661272 CATTTCATTCCATCATATAT
1 CATTT-ATTCCATCATATAT
59661292 ATATTCCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.28, C:0.23, G:0.03, T:0.46
Consensus pattern (20 bp):
CATTTATTCCATCATATATG
Found at i:59662238 original size:30 final size:30
Alignment explanation
Indices: 59662204--59662262 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
59662194 CTTAATAAGC
59662204 AAATGCCTCTAAAATAATAACAAAATTAAT
1 AAATGCCTCTAAAATAATAACAAAATTAAT
* *
59662234 AAATGTCTTTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
59662263 CAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAT
Found at i:59662843 original size:18 final size:18
Alignment explanation
Indices: 59662820--59662856 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
59662810 TTGGTATACA
59662820 ATTATTCAAACTAATGGT
1 ATTATTCAAACTAATGGT
59662838 ATTATTCAAACTAATGGT
1 ATTATTCAAACTAATGGT
59662856 A
1 A
59662857 ATCTTAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (18 bp):
ATTATTCAAACTAATGGT
Found at i:59668637 original size:63 final size:63
Alignment explanation
Indices: 59668566--59668684 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 63
59668556 AAATACCTGT
* * *
59668566 AGAAGGTGTTGATGCAGGGCACAGTAGTTCATAGTGTGGTGCTTGTGTAAAAATAACAGGTGC
1 AGAAGGTGTTGATGCAAGGCACAGTAGTGCACAGTGTGGTGCTTGTGTAAAAATAACAGGTGC
* ** * *
59668629 AGAAGGTGTTGATGCAAGGTATGGTGGTGCACAGTGTGGTGTTTGTGTAAAAATAA
1 AGAAGGTGTTGATGCAAGGCACAGTAGTGCACAGTGTGGTGCTTGTGTAAAAATAA
59668685 TGAGGTTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.29, C:0.08, G:0.34, T:0.29
Consensus pattern (63 bp):
AGAAGGTGTTGATGCAAGGCACAGTAGTGCACAGTGTGGTGCTTGTGTAAAAATAACAGGTGC
Found at i:59671605 original size:371 final size:371
Alignment explanation
Indices: 59670978--59671663 Score: 1043
Period size: 371 Copynumber: 1.8 Consensus size: 371
59670968 TGAACTAGGG
* * *
59670978 CTACATATCAACTATTAGTAATGATACTGAAATTGTCAGATTTTCTCTAACCAACGGGATTATTC
1 CTACATATCAACTATTAGTAATGATACTAAAATTGTCAGATTCTCTCTAACCAACGGGATTATTA
* * * *
59671043 ATTTGCAAATAAGCTTGGAATCTATTTTGTGATGATCTTGCGTTAGTTGTGCAAGTATGAGGACT
66 ATTTGCAAATAAGCTTGGAATCTATTTTGTGATAATCTTGAGTTAGTTGTGCAAGTATAAGGACC
* * *
59671108 TTCATATTTTTAAATTTCCCAATTTTGTTTCTTTTTCATCAGTTCTACCTTGACCCTCCATTTAT
131 TTCATATTTTCAAATTTCCCAATTTTGTTTCTTTTTCATCAATGCTACCTTGACCCTCCATTTAT
* * *
59671173 ATCTTCGTTACCGCTTTGACACAAACCAACATATTTGGTCATGGTAGAAATTACGACTTTGTAAT
196 ATCTTCGTTACCACTTTAACACAAACCAACATATTTGGTCATGGTAGAAATTACAACTTTGTAAT
* * *
59671238 CCACC-CATAATTTAAAGTTTTCTCCTTGAAA-ACTCCTATAGTGGCCTCCTTTATTGCCTTTAG
261 CCACCTC-GAATTTAAAGTTTTCTCCTT-AAAGACTCATATAGTGGCCTCATTTATTGCCTTTAG
59671301 CTTCGTTTTCTATGCCTTTCAATATGTGATGGAGCATTTGAATCGAGA
324 CTTCGTTTTCTATGCCTTTCAATATGTGATGGAGCATTTGAATCGAGA
* * * * * ***
59671349 CTACATATCAACTATTAGTAATGATACTAAAATTTTTATATTCTCTTTGATTGACGGGATTATTA
1 CTACATATCAACTATTAGTAATGATACTAAAATTGTCAGATTCTCTCTAACCAACGGGATTATTA
59671414 ATTTGCAAATAAGCTTGGAATCTATTTTGTGATAATCTTGAGTTAGTTGTGCAAGTATAAGGACC
66 ATTTGCAAATAAGCTTGGAATCTATTTTGTGATAATCTTGAGTTAGTTGTGCAAGTATAAGGACC
* *
59671479 TTCATATTTTCAAATTTCCTAATTTTGTTTCTTTTTCATCAATGCTACCTTGATCCTCCATTTAT
131 TTCATATTTTCAAATTTCCCAATTTTGTTTCTTTTTCATCAATGCTACCTTGACCCTCCATTTAT
* * ** *
59671544 ATCTTTGTTACTACTTTAACACTCACCAACATATTTGGTCATGGTAGAAATTGCAACTTTGTAAT
196 ATCTTCGTTACCACTTTAACACAAACCAACATATTTGGTCATGGTAGAAATTACAACTTTGTAAT
* *
59671609 CCACCTCGAGTTTAAAGTTTTCTCCTTAAAGGCTCATATAGTGGCCTCATTTATT
261 CCACCTCGAATTTAAAGTTTTCTCCTTAAAGACTCATATAGTGGCCTCATTTATT
59671664 ATAAATTACA
Statistics
Matches: 280, Mismatches: 33, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
370 3 0.01
371 276 0.99
372 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (371 bp):
CTACATATCAACTATTAGTAATGATACTAAAATTGTCAGATTCTCTCTAACCAACGGGATTATTA
ATTTGCAAATAAGCTTGGAATCTATTTTGTGATAATCTTGAGTTAGTTGTGCAAGTATAAGGACC
TTCATATTTTCAAATTTCCCAATTTTGTTTCTTTTTCATCAATGCTACCTTGACCCTCCATTTAT
ATCTTCGTTACCACTTTAACACAAACCAACATATTTGGTCATGGTAGAAATTACAACTTTGTAAT
CCACCTCGAATTTAAAGTTTTCTCCTTAAAGACTCATATAGTGGCCTCATTTATTGCCTTTAGCT
TCGTTTTCTATGCCTTTCAATATGTGATGGAGCATTTGAATCGAGA
Found at i:59677058 original size:14 final size:14
Alignment explanation
Indices: 59677035--59677068 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
59677025 TGTAATATTT
*
59677035 AAATAATAACAATA
1 AAATAGTAACAATA
59677049 AAATAGTAACAATA
1 AAATAGTAACAATA
*
59677063 TAATAG
1 AAATAG
59677069 CGAAATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAGTAACAATA
Found at i:59678060 original size:13 final size:13
Alignment explanation
Indices: 59678039--59678102 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
59678029 TAAATCAAAA
*
59678039 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
*
59678052 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
*
59678065 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
*
59678078 TTTTCAAAAACAC
1 TTTTCAAAAGCAC
59678091 TTTTCAAAAGCA
1 TTTTCAAAAGCA
59678103 ATGAAGAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
12 5 0.12
13 33 0.79
14 4 0.10
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:59685387 original size:38 final size:37
Alignment explanation
Indices: 59685345--59685458 Score: 89
Period size: 38 Copynumber: 3.2 Consensus size: 37
59685335 CTTTGATTAG
59685345 AAAAATTGAGGAATTCCCTAACTCTTAATTTAATTTCT
1 AAAAATTGAGGAATT-CCTAACTCTTAATTTAATTTCT
* * * **
59685383 AAAAAAT-AGG-A-T--TGA-TTTTAATTTTAA-TTAG
1 AAAAATTGAGGAATTCCTAACTCTTAA-TTTAATTTCT
*
59685414 AAAAATCGAGGAATTTCCTAACTCTTAATTTAATTTCT
1 AAAAATTGAGGAA-TTCCTAACTCTTAATTTAATTTCT
59685452 GAAAAAT
1 -AAAAAT
59685459 AGGATTGATT
Statistics
Matches: 55, Mismatches: 11, Indels: 19
0.65 0.13 0.22
Matches are distributed among these distances:
31 12 0.22
32 10 0.18
33 1 0.02
35 2 0.04
36 1 0.02
37 10 0.18
38 13 0.24
39 6 0.11
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.39
Consensus pattern (37 bp):
AAAAATTGAGGAATTCCTAACTCTTAATTTAATTTCT
Found at i:59685451 original size:69 final size:69
Alignment explanation
Indices: 59685340--59685476 Score: 238
Period size: 69 Copynumber: 2.0 Consensus size: 69
59685330 ATTTCCTTTG
* *
59685340 ATTAGAAAAATTGAGGAATTCCCTAACTCTTAATTTAATTTCTAAAAAATAGGATTGATTTTAAT
1 ATTAGAAAAATCGAGGAATTCCCTAACTCTTAATTTAATTTCTAAAAAATAGGATTGATTGTAAT
59685405 TTTA
66 TTTA
* *
59685409 ATTAGAAAAATCGAGGAATTTCCTAACTCTTAATTTAATTTCTGAAAAATAGGATTGATTGTAAT
1 ATTAGAAAAATCGAGGAATTCCCTAACTCTTAATTTAATTTCTAAAAAATAGGATTGATTGTAAT
59685474 TTT
66 TTT
59685477 GATTTGTGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (69 bp):
ATTAGAAAAATCGAGGAATTCCCTAACTCTTAATTTAATTTCTAAAAAATAGGATTGATTGTAAT
TTTA
Found at i:59690550 original size:39 final size:39
Alignment explanation
Indices: 59690474--59690555 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
59690464 GTTTGGACAA
59690474 AAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTTGG
1 AAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTT-G
* * * *
59690514 AAAACGCCGCTAAAAAT-GAGCATTAGCGGTGTTTTTTG
1 AAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTTG
59690552 AAAA
1 AAAA
59690556 GCGCTGCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 5 0.13
39 17 0.45
40 16 0.42
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (39 bp):
AAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTTG
Found at i:59690567 original size:38 final size:39
Alignment explanation
Indices: 59690474--59690555 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 39
59690464 GTTTGGACAA
* *
59690474 AAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTTGG
1 AAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTTGG
* *
59690514 AAAACGCCGCTAAAAATGAGCATTAGCGGTG-TTTTTTG
1 AAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTTTGG
59690552 AAAA
1 AAAA
59690556 GCGCTGCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 10 0.26
39 12 0.32
40 16 0.42
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTTTGG
Found at i:59690665 original size:41 final size:41
Alignment explanation
Indices: 59690603--59690843 Score: 299
Period size: 41 Copynumber: 5.9 Consensus size: 41
59690593 TGAGTTTTTG
* * *
59690603 GGGCATTTAGCGGCGTTTTTGAAAAAGTACCTCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
** ** *
59690644 GGGCCTTTAGCGGTATTTTTGAAAAAG-AGATGCCAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCA-CCGCTAATGCTC
* * *
59690685 AGGCCTTTAGCGGCGTTTTTGAAAAGGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
* * *
59690726 GGGCCTTTAGCGGCGTTTTTGGAAATGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
*
59690767 GGGCCTTTAGCGGCGTTTTTGAAAAGGCACCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
*
59690808 AGGCCTTTAGCGGCG-TTTTGAAAAAG-AGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCA-CCGCTAAT
59690844 AATAATAAAA
Statistics
Matches: 174, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 19 0.11
41 154 0.89
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
Found at i:59691188 original size:21 final size:19
Alignment explanation
Indices: 59691164--59691202 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
59691154 GTTGTAAAGA
59691164 ATAAAAATAGAATAAATTTTT
1 ATAAAAAT--AATAAATTTTT
*
59691185 ATAAGAATAATAAATTTT
1 ATAAAAATAATAAATTTT
59691203 GATAGTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
21 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
ATAAAAATAATAAATTTTT
Found at i:59691965 original size:14 final size:15
Alignment explanation
Indices: 59691938--59691969 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
59691928 AGGTTTATAA
59691938 ATTATGGAATTAGGG
1 ATTATGGAATTAGGG
59691953 ATTATGG-ATTAGGG
1 ATTATGGAATTAGGG
59691967 ATT
1 ATT
59691970 CTGATTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (15 bp):
ATTATGGAATTAGGG
Found at i:59692165 original size:33 final size:32
Alignment explanation
Indices: 59692128--59692190 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
59692118 TAGGGGTTAA
* * *
59692128 GGATTCGGGGTCGGGTTATGGTTTAAAGATTAG
1 GGATTCAGGGTCGAGTTAGGGTTT-AAGATTAG
59692161 GGATTCAGGGTCGAGTTAGGGTTTAAGATT
1 GGATTCAGGGTCGAGTTAGGGTTTAAGATT
59692191 TAGATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 6 0.22
33 21 0.78
ACGTcount: A:0.22, C:0.06, G:0.38, T:0.33
Consensus pattern (32 bp):
GGATTCAGGGTCGAGTTAGGGTTTAAGATTAG
Found at i:59692275 original size:14 final size:14
Alignment explanation
Indices: 59692232--59692282 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
59692222 TAAATAAGGT
59692232 TTAAGGGTTAGTGG
1 TTAAGGGTTAGTGG
* * *
59692246 TTAGGGGTTTGGGG
1 TTAAGGGTTAGTGG
*
59692260 TTAAGAGTTAGTGG
1 TTAAGGGTTAGTGG
*
59692274 TTTAGGGTT
1 TTAAGGGTT
59692283 TAGATATTCG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.43, T:0.39
Consensus pattern (14 bp):
TTAAGGGTTAGTGG
Found at i:59692584 original size:150 final size:150
Alignment explanation
Indices: 59692422--59692692 Score: 463
Period size: 150 Copynumber: 1.8 Consensus size: 150
59692412 AATAAAATAT
* *
59692422 TTTTAGCATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCGGCGTTTTTTGTG
1 TTTTAGCATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCAGCG-TTTTTATG
* * *
59692487 AAAAACGCCGCAAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAAAA-GCCACAAAAAATCATTT
65 AAAAACACCGCAAAAGATAAGCAATAGCGACGTTTTTATAAAAAAAACGCCACAAAAAATCATTT
59692551 TACTTTAAAAAAATAGCGTCC
130 TACTTTAAAAAAATAGCGTCC
*
59692572 TTTTAGCATAGCAAAATAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCAGCGTTTTTATGA
1 TTTTAGCATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCAGCGTTTTTATGA
*
59692637 AAAACACCGCAATAGATAAGCAATAGCGACGTTTTTATAAAAAAAACGCCACAAAA
66 AAAACACCGCAAAAGATAAGCAATAGCGACGTTTTTATAAAAAAAACGCCACAAAA
59692693 TAAAATTTCC
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
149 50 0.44
150 63 0.56
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (150 bp):
TTTTAGCATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCAGCGTTTTTATGA
AAAACACCGCAAAAGATAAGCAATAGCGACGTTTTTATAAAAAAAACGCCACAAAAAATCATTTT
ACTTTAAAAAAATAGCGTCC
Found at i:59693066 original size:16 final size:16
Alignment explanation
Indices: 59693045--59693076 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
59693035 ATAACCCTTT
59693045 GTTTAGGCATCTCAAA
1 GTTTAGGCATCTCAAA
59693061 GTTTAGGCATCTCAAA
1 GTTTAGGCATCTCAAA
59693077 CCCTTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (16 bp):
GTTTAGGCATCTCAAA
Found at i:59694325 original size:44 final size:42
Alignment explanation
Indices: 59694275--59694412 Score: 111
Period size: 43 Copynumber: 3.2 Consensus size: 42
59694265 GTGTCGCTAA
*
59694275 CTTTAGC-TGCGTTTTCAAAAATAAACGCCGTTAAAGACCATGAC
1 CTTTAGCGTGC-TTTTC-AAAAT-AACGCCGCTAAAGACCATGAC
** *
59694319 CTTTAGCGGTGCTTTTCTCACTAACGCCGCTAAAGACCATGAC
1 CTTTAGC-GTGCTTTTCAAAATAACGCCGCTAAAGACCATGAC
* * * * *
59694362 CTTTAACG-GCACTTTTACGACA-AACGCCGCTAAAGATCAGGAC
1 CTTTAGCGTG--CTTTT-CAAAATAACGCCGCTAAAGACCATGAC
59694405 CTTTAGCG
1 CTTTAGCG
59694413 GCGCTTCTAC
Statistics
Matches: 77, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 57 0.74
44 10 0.13
45 5 0.06
46 3 0.04
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (42 bp):
CTTTAGCGTGCTTTTCAAAATAACGCCGCTAAAGACCATGAC
Found at i:59694347 original size:43 final size:43
Alignment explanation
Indices: 59694297--59694431 Score: 173
Period size: 43 Copynumber: 3.1 Consensus size: 43
59694287 TTTCAAAAAT
* *
59694297 AAACGCCGTTAAAGACCATGACCTTTAGCGGTGCTTTT-CTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTAC-CAC
* * * *
59694340 TAACGCCGCTAAAGACCATGACCTTTAACGGCACTTTTACGAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAC
* * *
59694383 AAACGCCGCTAAAGATCAGGACCTTTAGCGGCGCTTCTACCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAC
59694426 AAACGC
1 AAACGC
59694432 TACTATAGGT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 77 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAC
Found at i:59698433 original size:118 final size:123
Alignment explanation
Indices: 59698240--59698461 Score: 289
Period size: 118 Copynumber: 1.8 Consensus size: 123
59698230 AAGAACTTAA
* ** * *
59698240 TTAATATATAAATTAAAAATACTAATTAATTTAAACTTTAAACCCTAACCCGATCTCGAATCTCT
1 TTAATATATAAATTAAAAATACTAATTAATCTAAACCCTAAACCCTAA-CCGATCTCAAATCTAT
59698305 AAATCCTAAATCAC-TAACTCTTAACCTCTAACCCCTAACTACTAACCCCTAAACTTTAT
65 AAATCCTAAATC-CTTAACTCTTAACCTCTAACCCCTAACTACTAACCCCTAAACTTTAT
*
59698364 TTAATATATAGATTAAAAAATACTAATTAATCTAAACCCT-AA-CCTAA-C-A-CT-AAATCTAT
1 TTAATATATAAATT-AAAAATACTAATTAATCTAAACCCTAAACCCTAACCGATCTCAAATCTAT
*
59698423 AAA-CCTTAAATCCTTAACTCTTAATCTCTAACCCCTAAC
65 AAATCC-TAAATCCTTAACTCTTAACCTCTAACCCCTAAC
59698462 CCCTAAATCA
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
117 3 0.03
118 39 0.44
119 2 0.02
120 1 0.01
121 1 0.01
123 5 0.06
124 15 0.17
125 22 0.25
ACGTcount: A:0.42, C:0.25, G:0.01, T:0.32
Consensus pattern (123 bp):
TTAATATATAAATTAAAAATACTAATTAATCTAAACCCTAAACCCTAACCGATCTCAAATCTATA
AATCCTAAATCCTTAACTCTTAACCTCTAACCCCTAACTACTAACCCCTAAACTTTAT
Found at i:59698510 original size:14 final size:15
Alignment explanation
Indices: 59698487--59698519 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
59698477 CTTAAACCAC
59698487 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
59698501 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
59698516 AATC
1 AATC
59698520 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:59698755 original size:30 final size:29
Alignment explanation
Indices: 59698719--59698788 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
59698709 AATTTTAAAA
59698719 TTATTTTAAATAATAGTATTTT-AAT-TTTT
1 TTATTTTAAATAA-A-TATTTTCAATGTTTT
* * *
59698748 TCTATTTTTAACAAATATTTTCTATGTTTT
1 T-TATTTTAAATAAATATTTTCAATGTTTT
59698778 TTATTTTAAAT
1 TTATTTTAAAT
59698789 TATTTCTACG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
28 6 0.18
29 12 0.36
30 15 0.45
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.61
Consensus pattern (29 bp):
TTATTTTAAATAAATATTTTCAATGTTTT
Found at i:59698974 original size:41 final size:40
Alignment explanation
Indices: 59698929--59699028 Score: 173
Period size: 41 Copynumber: 2.5 Consensus size: 40
59698919 GCGCTTTAAC
*
59698929 AAAAACGCTGCTAAAGCTCTGAGCATTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAGC-CTGAGCATTAGCGGCGCTTTTTT
59698970 AAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTTTT
1 AAAAACGCCGCT-AAAGCCTGAGCATTAGCGGCGCTTTTTT
59699011 AAAAACGCCGCTAAAGCC
1 AAAAACGCCGCTAAAGCC
59699029 CCAAAATGTT
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
40 6 0.11
41 46 0.81
42 5 0.09
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGCCTGAGCATTAGCGGCGCTTTTTT
Found at i:59699169 original size:40 final size:39
Alignment explanation
Indices: 59699090--59699199 Score: 141
Period size: 40 Copynumber: 2.8 Consensus size: 39
59699080 TAAAAAAAAT
* * **
59699090 GCCGCTAATGGTC-ATTTTTAGTGGCGCTTTGCTGTAAGC
1 GCCGCTAATGCTCGATTTTTAGCGGCG-TTTTATGTAAGC
*
59699129 GCCGCTAATGCTCGATCTTTAGCGGCGTTTTATGTGAAGC
1 GCCGCTAATGCTCGATTTTTAGCGGCGTTTTATGT-AAGC
*
59699169 GCCGCTAATGCTCGATTTTTAACGGCGTTTT
1 GCCGCTAATGCTCGATTTTTAGCGGCGTTTT
59699200 TTATCCAAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 18 0.29
40 44 0.71
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.35
Consensus pattern (39 bp):
GCCGCTAATGCTCGATTTTTAGCGGCGTTTTATGTAAGC
Found at i:59702525 original size:43 final size:43
Alignment explanation
Indices: 59702464--59702569 Score: 176
Period size: 43 Copynumber: 2.5 Consensus size: 43
59702454 ATGTTTTTAG
*
59702464 CGGCGTTGGTGGGAAAAGCGCCGCTAAAGTTCTTGGTCTTCAA
1 CGGCGTTTGTGGGAAAAGCGCCGCTAAAGTTCTTGGTCTTCAA
* *
59702507 CGGCGTTTGTGGGAAAAGCGCCGCTAAAGTTCTTGGTCTTTAG
1 CGGCGTTTGTGGGAAAAGCGCCGCTAAAGTTCTTGGTCTTCAA
*
59702550 CGGCGTTTATGGGAAAAGCG
1 CGGCGTTTGTGGGAAAAGCG
59702570 TGTATTAATG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (43 bp):
CGGCGTTTGTGGGAAAAGCGCCGCTAAAGTTCTTGGTCTTCAA
Found at i:59705786 original size:19 final size:19
Alignment explanation
Indices: 59705762--59705798 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
59705752 TAATTTCTTG
*
59705762 AAAATGTTTTACTTTTCTA
1 AAAATGATTTACTTTTCTA
59705781 AAAATGATTTACTTTTCT
1 AAAATGATTTACTTTTCT
59705799 GATGTTTGGA
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:0.32, C:0.11, G:0.05, T:0.51
Consensus pattern (19 bp):
AAAATGATTTACTTTTCTA
Found at i:59711459 original size:22 final size:22
Alignment explanation
Indices: 59711431--59711475 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
59711421 GCGAGTAAGG
*
59711431 TTCTATATTTGGTTTTATATGT
1 TTCTATATTCGGTTTTATATGT
59711453 TTCTATATTCGGTTTTATATGT
1 TTCTATATTCGGTTTTATATGT
59711475 T
1 T
59711476 AATGACATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.07, G:0.13, T:0.62
Consensus pattern (22 bp):
TTCTATATTCGGTTTTATATGT
Found at i:59713487 original size:21 final size:23
Alignment explanation
Indices: 59713463--59713507 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
59713453 AGTAAAAAAG
*
59713463 TAAATATAGAT-TAAAAA-ATTT
1 TAAATATAAATATAAAAATATTT
*
59713484 TAAATGTAAATATAAAAATATTT
1 TAAATATAAATATAAAAATATTT
59713507 T
1 T
59713508 TAAGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAATATAAATATAAAAATATTT
Found at i:59713949 original size:33 final size:33
Alignment explanation
Indices: 59713907--59713975 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
59713897 AGCAATTATA
59713907 AAATACAAAAAGTAAATATAAATTAAAAATTTT
1 AAATACAAAAAGTAAATATAAATTAAAAATTTT
59713940 AAATACAAAAAGTAAATATAAATTAAAAATTTT
1 AAATACAAAAAGTAAATATAAATTAAAAATTTT
59713973 AAA
1 AAA
59713976 GAAGTAAATA
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:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (33 bp):
AAATACAAAAAGTAAATATAAATTAAAAATTTT
Found at i:59715260 original size:24 final size:26
Alignment explanation
Indices: 59715233--59715287 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
59715223 AACTAAAAGT
59715233 GTTTATCT-AA-ATTTATATTAATTA
1 GTTTATCTAAAGATTTATATTAATTA
*
59715257 GTTTATTTAAAGGGATTTATATTAATTA
1 GTTTATCTAAA--GATTTATATTAATTA
59715285 GTT
1 GTT
59715288 GACTGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 7 0.27
25 2 0.08
28 17 0.65
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.53
Consensus pattern (26 bp):
GTTTATCTAAAGATTTATATTAATTA
Found at i:59729492 original size:19 final size:19
Alignment explanation
Indices: 59729468--59729504 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
59729458 TGTTGTTTGA
* *
59729468 AATTTGATGTGATAGAAAC
1 AATTTGAGGAGATAGAAAC
59729487 AATTTGAGGAGATAGAAA
1 AATTTGAGGAGATAGAAA
59729505 ACTGGTAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (19 bp):
AATTTGAGGAGATAGAAAC
Found at i:59732226 original size:39 final size:40
Alignment explanation
Indices: 59732183--59732263 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
59732173 TGTACGTTTA
*
59732183 AAAATAACATAAAAT-AAAAAAATTATATACTTTGAAGCT
1 AAAATAACATAAAATAAAAAAAATTATATACTTTGAAACT
* *
59732222 AAAATAACATACAATAAAAAAAATTGTATACTTTGAAACT
1 AAAATAACATAAAATAAAAAAAATTATATACTTTGAAACT
59732262 AA
1 AA
59732264 TAACAATAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 14 0.37
40 24 0.63
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (40 bp):
AAAATAACATAAAATAAAAAAAATTATATACTTTGAAACT
Found at i:59734895 original size:19 final size:19
Alignment explanation
Indices: 59734873--59734909 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
59734863 GATCATTTAA
*
59734873 AAAAAAATAATTCATGATT
1 AAAAAAATAAATCATGATT
*
59734892 AAAAACATAAATCATGAT
1 AAAAAAATAAATCATGAT
59734910 ATAGCTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAAAAATAAATCATGATT
Found at i:59736617 original size:21 final size:19
Alignment explanation
Indices: 59736596--59736633 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
59736586 TTTTGTATTA
59736596 AATAAAATTTATATATTTTT
1 AATAAAATTTAT-TATTTTT
*
59736616 AATTAAATTTATTATTTT
1 AATAAAATTTATTATTTT
59736634 GGGAGCCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATAAAATTTATTATTTTT
Found at i:59740520 original size:42 final size:42
Alignment explanation
Indices: 59740460--59740614 Score: 168
Period size: 42 Copynumber: 3.7 Consensus size: 42
59740450 TCAAAAGCTG
* *
59740460 AACAGAAGCTCATGAGAGCTAAATAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAATAGAAACCCATAAGGGTTA
* * *
59740502 AACAGAAGCTCGTAAGAGCTTAATGGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAATAGAAACCCATAAGGGTTA
* * * * * * *
59740544 AACAAAAGCTTAAAAGAGCTAAA-CGAAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTAAATAG-AAACCCATAAGGGTTA
* *
59740586 AATAGAAGCTCGTAAGAGCTAAATAGAAA
1 AACAGAAGCTCATAAGAGCTAAATAGAAA
59740615 GTAAAACACG
Statistics
Matches: 91, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
41 1 0.01
42 89 0.98
43 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAATAGAAACCCATAAGGGTTA
Found at i:59743809 original size:41 final size:41
Alignment explanation
Indices: 59743752--59743901 Score: 228
Period size: 41 Copynumber: 3.7 Consensus size: 41
59743742 TTTAACATAT
* * *
59743752 TCACCAGCACTTAGCCTGCTAGGCTTATAGCCTGATCCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
59743793 TCACCGGCACTTAGCCTGCTAGGTTTACAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
59743834 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
59743875 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
59743902 AAGTCCGAAT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:59743920 original size:41 final size:41
Alignment explanation
Indices: 59743834--59743960 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 41
59743824 CTGATTCAGA
** * **
59743834 TCACCGGCACTTAGCCTGCTAGGTTTATAA--CCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGACTTA-AAGTCC-GAATTATT
59743875 TCACCGGCACTTAGCCTGCTAGACTTAAAGTCCGAATTATT
1 TCACCGGCACTTAGCCTGCTAGACTTAAAGTCCGAATTATT
* * * * *
59743916 TCACCGACA-TCAAGCCTGCTAGACATAAAGTCTGAAGTATT
1 TCACCGGCACT-TAGCCTGCTAGACTTAAAGTCCGAATTATT
59743957 TCAC
1 TCAC
59743961 TGGTAATAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
40 3 0.04
41 68 0.93
42 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGACTTAAAGTCCGAATTATT
Found at i:59745691 original size:18 final size:19
Alignment explanation
Indices: 59745670--59745724 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
59745660 TTGTTTTTAT
59745670 TATTATAATT-TTATAATA-
1 TATTATAATTATTATAA-AC
*
59745688 TATTATTTATTATTATAAAC
1 TATTA-TAATTATTATAAAC
59745708 T-TTATAATTATTATAAA
1 TATTATAATTATTATAAA
59745725 AACTATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 17 0.53
19 8 0.25
20 7 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTATAATTATTATAAAC
Found at i:59745697 original size:28 final size:28
Alignment explanation
Indices: 59745665--59745721 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
59745655 TATGTTTGTT
*
59745665 TTTATTATTAT-AATTTTATAATATATTA
1 TTTATTATTATAAACTTTATAAT-TATTA
59745693 TTTATTATTATAAACTTTATAATTATTA
1 TTTATTATTATAAACTTTATAATTATTA
59745721 T
1 T
59745722 AAAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTATTATTATAAACTTTATAATTATTA
Found at i:59745733 original size:20 final size:21
Alignment explanation
Indices: 59745694--59745735 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
59745684 AATATATTAT
* *
59745694 TTATTATTATAAACTTTATAA
1 TTATTATTAAAAACTATATAA
59745715 TTATTA-TAAAAACTATATAA
1 TTATTATTAAAAACTATATAA
59745735 T
1 T
59745736 ATATACATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATTATTAAAAACTATATAA
Found at i:59745932 original size:14 final size:15
Alignment explanation
Indices: 59745913--59745941 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59745903 TTACGAAACT
59745913 TTCACACAT-ATAAA
1 TTCACACATAATAAA
59745927 TTCACACATAATAAA
1 TTCACACATAATAAA
59745942 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:59749496 original size:61 final size:61
Alignment explanation
Indices: 59749394--59749548 Score: 177
Period size: 61 Copynumber: 2.5 Consensus size: 61
59749384 GAAATTTTAC
* * * *
59749394 AAATTTTGTAAATTTTGAAGGTTAAATTTATTGAGTTTTTTAGAATTTGA-ACCAAAATGAT
1 AAATTTTGTAAATATTGAAGGTTAAATTTATTGAATATTTTA-AATTTAAGACCAAAATGAT
* * * *
59749455 AAATTTTGTAAATATTGAAGGTTAAATTTGTTGAATATTTTATATTTAAGATCAAATTGAT
1 AAATTTTGTAAATATTGAAGGTTAAATTTATTGAATATTTTAAATTTAAGACCAAAATGAT
* * * *
59749516 AAAATGTGTAAATATTGGAGAGCTAAATTTATT
1 AAATTTTGTAAATATTGAAG-GTTAAATTTATT
59749549 ATTAGAGTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
60 5 0.06
61 64 0.81
62 10 0.13
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.43
Consensus pattern (61 bp):
AAATTTTGTAAATATTGAAGGTTAAATTTATTGAATATTTTAAATTTAAGACCAAAATGAT
Found at i:59752653 original size:25 final size:26
Alignment explanation
Indices: 59752616--59752667 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
59752606 TTTGGATAAT
* *
59752616 AATTTTTACATTTCAAAGT-TTTTAA
1 AATTTTTACATTTAAAAATATTTTAA
59752641 AATTTATTA-ATTTAAAAATATTTTAA
1 AATTT-TTACATTTAAAAATATTTTAA
59752667 A
1 A
59752668 TTAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (26 bp):
AATTTTTACATTTAAAAATATTTTAA
Found at i:59752758 original size:20 final size:20
Alignment explanation
Indices: 59752730--59752767 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
59752720 TTTTTATATC
59752730 ATTTATTTT-TAATATATTAT
1 ATTTATTTTATAAT-TATTAT
*
59752750 ATTTCTTTTATAATTATT
1 ATTTATTTTATAATTATT
59752768 TTTTAACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTATTTTATAATTATTAT
Found at i:59754295 original size:6 final size:6
Alignment explanation
Indices: 59754280--59754354 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
59754270 AGATGATAAA
* * * * *
59754280 GAAGAC GAAGAG GAAGTG GAAGAG CAGAACGAA GAGGAG GAAGAC GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG --GAA-GAG GAAGAG GAAGAG GAAGAG
* *
59754331 GAAGAG GAGGAG GAGGAG GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG
59754355 TTTTCTTTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
6 48 0.87
7 2 0.04
8 3 0.05
9 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.48, T:0.01
Consensus pattern (6 bp):
GAAGAG
Found at i:59754321 original size:21 final size:21
Alignment explanation
Indices: 59754280--59754341 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 21
59754270 AGATGATAAA
59754280 GAAGACGAAGAGGAAGTGGAAGA-
1 GAAGACGAAGAGG-A--GGAAGAC
*
59754303 GCAGAACGAAGAGGAGGAAGAC
1 GAAG-ACGAAGAGGAGGAAGAC
*
59754325 GAAGAGGAAGAGGAGGA
1 GAAGACGAAGAGGAGGA
59754342 GGAGGAGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 18 0.53
22 3 0.09
23 4 0.12
24 9 0.26
ACGTcount: A:0.47, C:0.06, G:0.45, T:0.02
Consensus pattern (21 bp):
GAAGACGAAGAGGAGGAAGAC
Found at i:59754340 original size:9 final size:9
Alignment explanation
Indices: 59754310--59754354 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
59754300 AGAGCAGAAC
59754310 GAAGAGGAG
1 GAAGAGGAG
59754319 GAAGACGAAGAG
1 GAAGA-G--GAG
59754331 GAAGAGGAG
1 GAAGAGGAG
*
59754340 GAGGAGGAG
1 GAAGAGGAG
59754349 GAAGAG
1 GAAGAG
59754355 TTTTCTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 21 0.68
10 1 0.03
11 1 0.03
12 8 0.26
ACGTcount: A:0.44, C:0.02, G:0.53, T:0.00
Consensus pattern (9 bp):
GAAGAGGAG
Found at i:59756229 original size:20 final size:21
Alignment explanation
Indices: 59756200--59756253 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
59756190 ATAAACTTAC
59756200 AAAA-ATTATAAAAATTC-AT
1 AAAATATTATAAAAATTCAAT
*
59756219 AAAATATTATAAACATTCTAAT
1 AAAATATTATAAAAATTC-AAT
59756241 AAAAT-TTATAAAA
1 AAAATATTATAAAA
59756254 TTAAATCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.13
20 12 0.40
21 7 0.23
22 7 0.23
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATATTATAAAAATTCAAT
Found at i:59756253 original size:9 final size:9
Alignment explanation
Indices: 59756172--59756255 Score: 55
Period size: 9 Copynumber: 8.9 Consensus size: 9
59756162 CATAAAACTC
59756172 ATAAAATATT
1 ATAAAAT-TT
*
59756182 -TAAAATGT
1 ATAAAATTT
*
59756190 AT-AAACTT
1 ATAAAATTT
* *
59756198 ACAAAAATT
1 ATAAAATTT
*
59756207 ATAAAAATTC
1 AT-AAAATTT
59756217 ATAAAATATT
1 ATAAAAT-TT
59756227 ATAAACATTCT
1 ATAAA-ATT-T
59756238 AATAAAATTT
1 -ATAAAATTT
59756248 ATAAAATT
1 ATAAAATT
59756256 AAATCAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
8 6 0.10
9 26 0.45
10 15 0.26
11 6 0.10
12 5 0.09
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAAAATTT
Found at i:59756320 original size:18 final size:17
Alignment explanation
Indices: 59756293--59756332 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 17
59756283 ATTTTATAAA
59756293 AAAAACTTATAAATAATAT
1 AAAAACTTATAAAT--TAT
59756312 AAAAA-TTATAAATTAT
1 AAAAACTTATAAATTAT
59756328 AAAAA
1 AAAAA
59756333 AAAGTCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAACTTATAAATTAT
Found at i:59756333 original size:18 final size:19
Alignment explanation
Indices: 59756286--59756334 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
59756276 ATTTAAAATT
59756286 TTATAAAAAAAACTTATAAA
1 TTAT-AAAAAAACTTATAAA
* *
59756306 TAATATAAAAA-TTATAAA
1 TTATAAAAAAACTTATAAA
59756324 TTATAAAAAAA
1 TTATAAAAAAA
59756335 AGTCTAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 16 0.64
19 6 0.24
20 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TTATAAAAAAACTTATAAA
Found at i:59759035 original size:41 final size:40
Alignment explanation
Indices: 59758981--59759124 Score: 209
Period size: 41 Copynumber: 3.5 Consensus size: 40
59758971 GACTTTAAGT
* *
59758981 CTAGTAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
*
59759022 CTAGCAGGTTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
* *
59759063 CTAGCAGGC-ACGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA-C
59759103 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
59759125 ATATGTTAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
39 2 0.02
40 35 0.38
41 56 0.60
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (40 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAC
Found at i:59760010 original size:41 final size:41
Alignment explanation
Indices: 59759885--59760019 Score: 153
Period size: 41 Copynumber: 3.3 Consensus size: 41
59759875 GGGTGCTACA
* * * * *
59759885 TTAGCAGCGTTTATAAGGAAGCGCCGCTAATGTTCTGTGAT
1 TTAGCAGCGTTTTTATGAAAGCGCCGCTAATGTTCTGGGCT
* * * *
59759926 TTAGCGGCGTTTTTCTGTAAGCGCCGCTAATGTTCTGGCCT
1 TTAGCAGCGTTTTTATGAAAGCGCCGCTAATGTTCTGGGCT
** *
59759967 TTAGCAGCGTTTTTATGAAAGCGCCGCTAATAATATGGGCT
1 TTAGCAGCGTTTTTATGAAAGCGCCGCTAATGTTCTGGGCT
*
59760008 TTAGCGGCGTTT
1 TTAGCAGCGTTT
59760020 CTATATAATC
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (41 bp):
TTAGCAGCGTTTTTATGAAAGCGCCGCTAATGTTCTGGGCT
Found at i:59760036 original size:82 final size:82
Alignment explanation
Indices: 59759885--59760036 Score: 187
Period size: 82 Copynumber: 1.9 Consensus size: 82
59759875 GGGTGCTACA
* ** * * * * *
59759885 TTAGCAGCGTTTATAAGGAAGCGCCGCTAATGTTCTGTGATTTAGCGGCGTTTTTCTGTAAGCGC
1 TTAGCAGCGTTTATAAGAAAGCGCCGCTAATAATATGGGATTTAGCGGCGTTTCTATATAAGCGC
59759950 CGCTAATGTTCTGGCCT
66 CGCTAATGTTCTGGCCT
* * * * *
59759967 TTAGCAGCGTTTTTATGAAAGCGCCGCTAATAATATGGGCTTTAGCGGCGTTTCTATATAATCGT
1 TTAGCAGCGTTTATAAGAAAGCGCCGCTAATAATATGGGATTTAGCGGCGTTTCTATATAAGCGC
59760032 CGCTA
66 CGCTA
59760037 TCGTTGTGAG
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
82 57 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (82 bp):
TTAGCAGCGTTTATAAGAAAGCGCCGCTAATAATATGGGATTTAGCGGCGTTTCTATATAAGCGC
CGCTAATGTTCTGGCCT
Found at i:59760547 original size:31 final size:32
Alignment explanation
Indices: 59760491--59760552 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
59760481 AGTTTAAGGG
*
59760491 TTTTATAGTTTAAGGTTTAATGTTTACTATAA
1 TTTTATAGTTTAAGGTTTAAGGTTTACTATAA
* * *
59760523 TTTTA-AGTTTATGGTTTAGGGTTTATTATA
1 TTTTATAGTTTAAGGTTTAAGGTTTACTATA
59760553 TTTGGTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.55
Consensus pattern (32 bp):
TTTTATAGTTTAAGGTTTAAGGTTTACTATAA
Found at i:59763795 original size:18 final size:19
Alignment explanation
Indices: 59763772--59763809 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
59763762 TTTTAATTAA
59763772 AAATCATTC-ATCTATTTT
1 AAATCATTCTATCTATTTT
*
59763790 AAATCATTCTATTTATTTT
1 AAATCATTCTATCTATTTT
59763809 A
1 A
59763810 TTTAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATCATTCTATCTATTTT
Found at i:59764079 original size:21 final size:21
Alignment explanation
Indices: 59764025--59764082 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
59764015 GTATATTAAT
* * *
59764025 GCAGCGAGGGAAACAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCC
*
59764046 GCAGCGAGAGAAGTAGAGGCC
1 GCAGCGAGAGAAGCAGAGGCC
59764067 GCAGCGAGAGAAGCAG
1 GCAGCGAGAGAAGCAG
59764083 CGAGAGAAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.19, G:0.43, T:0.03
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCC
Found at i:59764084 original size:12 final size:12
Alignment explanation
Indices: 59764067--59764094 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
59764057 AGTAGAGGCC
59764067 GCAGCGAGAGAA
1 GCAGCGAGAGAA
59764079 GCAGCGAGAGAA
1 GCAGCGAGAGAA
59764091 GCAG
1 GCAG
59764095 AGGTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:59764637 original size:85 final size:83
Alignment explanation
Indices: 59764529--59764777 Score: 293
Period size: 85 Copynumber: 2.9 Consensus size: 83
59764519 TTTGTGAAAT
* * *** *
59764529 AAGCGCCG-TGAAAGAACACTACTTTCAGCGGCGTTTGTAGATGAAGCGCCGCTAAAGAACATAA
1 AAGCGCCGCT-AAAGAACATTACTTT-AGCGGCGTTTTTTCCT-AAGCGCCGCTAAAGAACATGA
*
59764593 CTTTTATCGGCGTTTTCTACA
63 CTTTTAGCGGCGTTTTCTACA
* *
59764614 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATT
1 AAGCGCCGCTAAAGAACATTAC-TTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGACT
* * *
59764679 TTTAGCGGCGTTTTTTCCC
65 TTTAGCGGCGTTTTCTACA
* * * *
59764698 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCTAAGTGCCACTAAAGAACATGAC
1 AAGCGCCGCTAAAGAACATTA-CTTTAGCGGCG-TTTTTTCCTAAGCGCCGCTAAAGAACATGAC
59764763 TTTTAGCGGCGTTTT
64 TTTTAGCGGCGTTTT
59764778 TTTTGTAAGC
Statistics
Matches: 142, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
84 64 0.45
85 74 0.52
86 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (83 bp):
AAGCGCCGCTAAAGAACATTACTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGACTT
TTAGCGGCGTTTTCTACA
Found at i:59764777 original size:43 final size:42
Alignment explanation
Indices: 59764528--59764797 Score: 285
Period size: 42 Copynumber: 6.4 Consensus size: 42
59764518 GTTTGTGAAA
* * ***
59764528 TAAGCGCCG-TGAAAGAACACT-ACTTTCAGCGGCGTTTGTAGA
1 TAAGCGCCGCT-AAAGAACA-TGACTTTTAGCGGCGTTTTTTCC
* * * *
59764570 TGAAGCGCCGCTAAAGAACATAACTTTTATCGGCGTTTTCTAC
1 T-AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTCC
* * *
59764613 AAAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTCC
*
59764655 TAAGCGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTCC
* *
59764697 CAAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCG-TTTTTTCC
* * **
59764740 TAAGTGCCACTAAAGAACATGACTTTTAGCGGCGTTTTTTTTG
1 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCG-TTTTTTCC
*
59764783 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
59764798 TTAGCGACGT
Statistics
Matches: 194, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 106 0.55
43 85 0.44
44 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTCC
Found at i:59765064 original size:8 final size:8
Alignment explanation
Indices: 59765051--59765109 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
59765041 ATAATTCTAT
59765051 ATATTTTA
1 ATATTTTA
59765059 ATATTTTA
1 ATATTTTA
59765067 ATATTTTA
1 ATATTTTA
*
59765075 TTAGTTTTTAA
1 ATA--TTTT-A
* *
59765086 AAATTATA
1 ATATTTTA
59765094 ATATTTTA
1 ATATTTTA
*
59765102 ATAATTTA
1 ATATTTTA
59765110 TTAGAACTCG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
8 32 0.78
9 3 0.07
10 4 0.10
11 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
ATATTTTA
Found at i:59765787 original size:29 final size:29
Alignment explanation
Indices: 59765719--59765787 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
59765709 TTAATGATAT
*
59765719 TGGCTCAATTAGGTGCAGATTTAGTGTAG
1 TGGCTCAATTGGGTGCAGATTTAGTGTAG
*
59765748 -GAGCTCAATTGGGTGCAGATTTGGTGTAG
1 TG-GCTCAATTGGGTGCAGATTTAGTGTAG
59765777 TGGCTCAATTG
1 TGGCTCAATTG
59765788 ATTTTTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 1 0.03
29 34 0.94
30 1 0.03
ACGTcount: A:0.22, C:0.12, G:0.33, T:0.33
Consensus pattern (29 bp):
TGGCTCAATTGGGTGCAGATTTAGTGTAG
Found at i:59770721 original size:9 final size:9
Alignment explanation
Indices: 59770703--59770760 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
59770693 TTTGGTTAAA
59770703 AATTAACCG
1 AATTAACCG
*
59770712 AATTACCCG
1 AATTAACCG
*
59770721 AATTAATCG
1 AATTAACCG
*
59770730 AATTACCCG
1 AATTAACCG
59770739 AATTAACCG
1 AATTAACCG
*
59770748 AATTAACCA
1 AATTAACCG
59770757 AATT
1 AATT
59770761 GAATCACTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:59770726 original size:18 final size:18
Alignment explanation
Indices: 59770703--59770752 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
59770693 TTTGGTTAAA
59770703 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
59770721 AATTAATCGAATTACCCG
1 AATTAACCGAATTACCCG
59770739 AATTAACCGAATTA
1 AATTAACCGAATTA
59770753 ACCAAATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:59773594 original size:24 final size:24
Alignment explanation
Indices: 59773562--59773609 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
59773552 GTAATATTGG
59773562 GTGCATAGGTGATTAACTTCATTA
1 GTGCATAGGTGATTAACTTCATTA
59773586 GTGCATAGGTGATTAACTTCATTA
1 GTGCATAGGTGATTAACTTCATTA
59773610 CCTGATACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (24 bp):
GTGCATAGGTGATTAACTTCATTA
Found at i:59795197 original size:18 final size:20
Alignment explanation
Indices: 59795154--59795198 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
59795144 TTTAAAAAAT
*
59795154 TATTTTTAGAAAATGATTTAC
1 TATTTTTAGAAAA-GATTTAA
59795175 T-TTTTTAGAAAA-A-TTAA
1 TATTTTTAGAAAAGATTTAA
59795192 TATTTTT
1 TATTTTT
59795199 TTTTGTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
20 11 0.50
21 1 0.05
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (20 bp):
TATTTTTAGAAAAGATTTAA
Found at i:59795356 original size:13 final size:14
Alignment explanation
Indices: 59795328--59795356 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59795318 TTGAGTTTAT
59795328 TTTATATTTATAAA
1 TTTATATTTATAAA
59795342 TTTATATTT-TAAA
1 TTTATATTTATAAA
59795355 TT
1 TT
59795357 ATTTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATATTTATAAA
Done.