Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 46 of 85
Found at i:15350675 original size:25 final size:27
Alignment explanation
Indices: 15350636--15350715 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 27
15350626 TATTATTATT
*
15350636 ATATTTATATTTATATTTACTTATTTAA
1 ATATTAATA-TTATATTTACTTATTTAA
* * *
15350664 ATTTTAA-A-TATATTTGTCTTA-TTAT
1 ATATTAATATTATATTT-ACTTATTTAA
15350689 ATATTAATATTATTATTTACTTATTTA
1 ATATTAATATTA-TATTTACTTATTTA
15350716 TATCTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
25 16 0.39
26 5 0.12
27 7 0.17
28 13 0.32
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (27 bp):
ATATTAATATTATATTTACTTATTTAA
Found at i:15356685 original size:32 final size:32
Alignment explanation
Indices: 15356649--15356717 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
15356639 ATATTTCATT
15356649 AATTTATTAAACAATTACTTGGTTTTAACAAC
1 AATTTATTAAACAATTACTTGGTTTTAACAAC
*
15356681 AATTTATTAAACAATTACTTGGTTTTAACAAT
1 AATTTATTAAACAATTACTTGGTTTTAACAAC
15356713 AATTT
1 AATTT
15356718 TAAGTAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (32 bp):
AATTTATTAAACAATTACTTGGTTTTAACAAC
Found at i:15356712 original size:17 final size:17
Alignment explanation
Indices: 15356658--15356712 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
15356648 TAATTTATTA
15356658 AACAATTACTTGGTTTT
1 AACAATTACTTGGTTTT
* * *
15356675 AACAA-CAATT--TATTA
1 AACAATTACTTGGT-TTT
15356690 AACAATTACTTGGTTTT
1 AACAATTACTTGGTTTT
15356707 AACAAT
1 AACAAT
15356713 AATTTTAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 1 0.04
15 7 0.25
16 6 0.21
17 13 0.46
18 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (17 bp):
AACAATTACTTGGTTTT
Found at i:15363116 original size:96 final size:96
Alignment explanation
Indices: 15363006--15363189 Score: 289
Period size: 96 Copynumber: 1.9 Consensus size: 96
15362996 CTCTAGTTAA
* * *
15363006 ATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACTAATAACATTGCACAAAAG
1 ATATTTAATTGGACACTGGAAACCCTTATGATCTTTTGAACT-CACCAATAACAGTGCACAAAAG
*
15363071 GTGATATCTCAATTGTA-TTCTCCCTATTTGG
65 GTGATATCTCAATCGTATTTCTCCCTATTTGG
* * *
15363102 ATATTTAATTGGACACTGGAAGCTCTTATGATCTTTTGAACTCACCAGTAACAGTGCACAAAAGG
1 ATATTTAATTGGACACTGGAAACCCTTATGATCTTTTGAACTCACCAATAACAGTGCACAAAAGG
15363167 TGATATCTCAATCGTATTTCTCC
66 TGATATCTCAATCGTATTTCTCC
15363190 TTTCATTTGG
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 35 0.44
96 45 0.56
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (96 bp):
ATATTTAATTGGACACTGGAAACCCTTATGATCTTTTGAACTCACCAATAACAGTGCACAAAAGG
TGATATCTCAATCGTATTTCTCCCTATTTGG
Found at i:15364494 original size:17 final size:17
Alignment explanation
Indices: 15364457--15364504 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
15364447 GAATTTAGAA
*
15364457 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
15364473 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
15364490 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
15364505 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:15365501 original size:46 final size:46
Alignment explanation
Indices: 15365434--15365625 Score: 312
Period size: 46 Copynumber: 4.2 Consensus size: 46
15365424 NNNNNNNCAT
*
15365434 ACTGAGTTGTGAAAAGTAGGTATGATGTTTCGGTAAAGAAAACCAC
1 ACTGAGTTGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCAC
15365480 ACTGAGTTGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCAC
1 ACTGAGTTGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCAC
* *
15365526 ATTGAGTTGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCAT
1 ACTGAGTTGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCAC
* ** * *
15365572 ACTGAGTTGTGAAAAGTAGGTATGGTATTTCCATGAAGAAAACCAT
1 ACTGAGTTGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCAC
15365618 ACTGAGTT
1 ACTGAGTT
15365626 ATAGCAATGT
Statistics
Matches: 138, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 138 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (46 bp):
ACTGAGTTGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCAC
Found at i:15371027 original size:75 final size:75
Alignment explanation
Indices: 15370944--15371100 Score: 278
Period size: 75 Copynumber: 2.1 Consensus size: 75
15370934 ACTCTAGTGC
* *
15370944 TTCAAAAGATTTGTTTTATGTTTTGATTTATCTTAGCTTGAGAAATAATGTTATGTGATTTTAAA
1 TTCAAAAGATTTGTTGTATGTTTTGATTTATCTTAGCTTGAGAAATAAAGTTATGTGATTTTAAA
15371009 ATGTACATCT
66 ATGTACATCT
15371019 TTCAAAAGATTTGTTGTATGTTTTGATTTATCTTAGCTTGAGAAATAAAGTTATGTGATTTTAAA
1 TTCAAAAGATTTGTTGTATGTTTTGATTTATCTTAGCTTGAGAAATAAAGTTATGTGATTTTAAA
*
15371084 ATGTGCATCT
66 ATGTACATCT
15371094 TTGCAAA
1 TT-CAAA
15371101 TGTGAAAATT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 74 0.95
76 4 0.05
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (75 bp):
TTCAAAAGATTTGTTGTATGTTTTGATTTATCTTAGCTTGAGAAATAAAGTTATGTGATTTTAAA
ATGTACATCT
Found at i:15372800 original size:49 final size:49
Alignment explanation
Indices: 15372711--15372817 Score: 115
Period size: 49 Copynumber: 2.2 Consensus size: 49
15372701 TATGGTCATA
* * * *
15372711 GGTTTAAGTATAACTAGAACTCCCAGTTGACGGTGATTATGCGGTCACG
1 GGTTTAAGTATAACTAGAACCCCCAGTTAACGATGATTATGCAGTCACG
* ** * *
15372760 GGTTTAAGTATAACTGGGCCCCCCAGTTAATGATGGTTATGCAGTCACG
1 GGTTTAAGTATAACTAGAACCCCCAGTTAACGATGATTATGCAGTCACG
* *
15372809 AGTTCAAGT
1 GGTTTAAGT
15372818 TTCATAACAC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
GGTTTAAGTATAACTAGAACCCCCAGTTAACGATGATTATGCAGTCACG
Found at i:15385908 original size:50 final size:50
Alignment explanation
Indices: 15385851--15386027 Score: 257
Period size: 50 Copynumber: 3.5 Consensus size: 50
15385841 CCGGTTCACA
15385851 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTAGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTAGTACACG
* * ** * * * *
15385901 TAGTAGCCTGCATATAGTACTACACATGTGATCGAAGC-TATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGCGA-CCTATCAT-TCTAGTACACG
15385952 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTAGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTAGTACACG
15386002 TAGTAGCCTGCACATAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
15386028 CGAGACCATC
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
50 67 0.62
51 41 0.38
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTAGTACACG
Found at i:15386070 original size:101 final size:100
Alignment explanation
Indices: 15385844--15386032 Score: 324
Period size: 101 Copynumber: 1.9 Consensus size: 100
15385834 AATGATACCG
15385844 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTAGTACACGTAGTAGCC
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTAGTACACGTAGTAGCC
* * *
15385909 TGCATATAGTACTACACATGTGATCGAAGCTATCT
66 TGCACATAGTACTACACACGAGATCGAAGCTATCT
* *
15385944 GGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTAGTACACGTAGTAGC
1 -GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTAGTACACGTAGTAGC
15386009 CTGCACATAGTACTACACACGAGA
65 CTGCACATAGTACTACACACGAGA
15386033 CCATCAATTT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 83 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (100 bp):
GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTAGTACACGTAGTAGCC
TGCACATAGTACTACACACGAGATCGAAGCTATCT
Found at i:15390431 original size:23 final size:23
Alignment explanation
Indices: 15390400--15390475 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 23
15390390 GACGAACTGA
*
15390400 CATGTGAACCCTTACCTATTATG
1 CATGCGAACCCTTACCTATTATG
* *
15390423 TATGCGAACCC-T--C-ATAAT-
1 CATGCGAACCCTTACCTATTATG
* *
15390441 CATGCGAACCCTTACTTGTTATG
1 CATGCGAACCCTTACCTATTATG
15390464 CATGCGAACCCT
1 CATGCGAACCCT
15390476 CATAAGTTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
18 10 0.24
19 5 0.12
20 1 0.02
22 4 0.10
23 21 0.51
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.30
Consensus pattern (23 bp):
CATGCGAACCCTTACCTATTATG
Found at i:15390463 original size:41 final size:41
Alignment explanation
Indices: 15390400--15390480 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
15390390 GACGAACTGA
* *
15390400 CATGTGAACCCTTACCTATTATGTATGCGAACCCTCATAAT
1 CATGCGAACCCTTACCTATTATGCATGCGAACCCTCATAAT
* *
15390441 CATGCGAACCCTTACTTGTTATGCATGCGAACCCTCATAA
1 CATGCGAACCCTTACCTATTATGCATGCGAACCCTCATAA
15390481 GTTGTGAGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (41 bp):
CATGCGAACCCTTACCTATTATGCATGCGAACCCTCATAAT
Found at i:15390958 original size:27 final size:26
Alignment explanation
Indices: 15390928--15390984 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
15390918 GTGGATGTCT
*
15390928 TTTGGCGAACTATGTTTGCAAATATG
1 TTTGGCGAACTATGTTCGCAAATATG
*
15390954 ATTTGGCGAACTTTGTTCGCAAATATG
1 -TTTGGCGAACTATGTTCGCAAATATG
15390981 TTTG
1 TTTG
15390985 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (26 bp):
TTTGGCGAACTATGTTCGCAAATATG
Found at i:15392684 original size:23 final size:22
Alignment explanation
Indices: 15392640--15392683 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
15392630 TAATTGTAGA
15392640 CTTATTATTCTATTTTAATTTT
1 CTTATTATTCTATTTTAATTTT
15392662 CTTAGTTATT-TATTTTAATTTT
1 CTTA-TTATTCTATTTTAATTTT
15392684 TTTACCAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (22 bp):
CTTATTATTCTATTTTAATTTT
Found at i:15393080 original size:16 final size:15
Alignment explanation
Indices: 15393052--15393094 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
15393042 AAAAAGTGAA
*
15393052 AAAAATACAAAAATAG
1 AAAAATA-AAAAAAAG
*
15393068 AAAAATAAGAAAAAAT
1 AAAAATAA-AAAAAAG
15393084 AAAAATAAAAA
1 AAAAATAAAAA
15393095 TATTTTGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAAAAAG
Found at i:15395631 original size:73 final size:73
Alignment explanation
Indices: 15395539--15395684 Score: 265
Period size: 73 Copynumber: 2.0 Consensus size: 73
15395529 TGAGGAAGGG
* *
15395539 GGAATGATGCGAGTCTCAAGGCCCAATTTCAGACCTATGTATGTGATTTGCTCACACTACCTCAA
1 GGAATGATGCGAGTCTCAAGGCCCAATTTCAGACCTATGGATGTGATGTGCTCACACTACCTCAA
15395604 GGCTCAAC
66 GGCTCAAC
*
15395612 GGAATGATGTGAGTCTCAAGGCCCAATTTCAGACCTATGGATGTGATGTGCTCACACTACCTCAA
1 GGAATGATGCGAGTCTCAAGGCCCAATTTCAGACCTATGGATGTGATGTGCTCACACTACCTCAA
15395677 GGCTCAAC
66 GGCTCAAC
15395685 AACAATGTCA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (73 bp):
GGAATGATGCGAGTCTCAAGGCCCAATTTCAGACCTATGGATGTGATGTGCTCACACTACCTCAA
GGCTCAAC
Found at i:15400413 original size:50 final size:50
Alignment explanation
Indices: 15400272--15400415 Score: 182
Period size: 50 Copynumber: 2.9 Consensus size: 50
15400262 TCCTGTACTA
* * * * *
15400272 CCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCCCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACGTGAGACTTCTCATATCGGTG
* * *
15400322 CCCATGCCATGTCCCAGACATGGTCTTACAG-GGGACTTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTAC-GTGAGACTTCTCATATCGGTG
* *
15400372 CCAATGCCACGTCCCAGACATGGTCTTACGTGAGACCTCTCATA
1 CCAATGCCATGTCCCAGACATGGTCTTACGTGAGACTTCTCATA
15400416 ACCTCAATAA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.01
50 78 0.99
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACGTGAGACTTCTCATATCGGTG
Found at i:15407667 original size:15 final size:15
Alignment explanation
Indices: 15407643--15407690 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
15407633 TTATATACTA
15407643 AAACTTTAGATTGTG
1 AAACTTTAGATTGTG
* * *
15407658 AAACTATAGACTATG
1 AAACTTTAGATTGTG
*
15407673 AAACTTTAGATAGTG
1 AAACTTTAGATTGTG
15407688 AAA
1 AAA
15407691 ATTGTGACTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (15 bp):
AAACTTTAGATTGTG
Found at i:15409316 original size:21 final size:21
Alignment explanation
Indices: 15409292--15409332 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
15409282 ATTTTGTAAT
*
15409292 TTAATGAAAAATTAAAACAAA
1 TTAAAGAAAAATTAAAACAAA
*
15409313 TTAAAGAAAGATTAAAACAA
1 TTAAAGAAAAATTAAAACAA
15409333 TTTTTATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (21 bp):
TTAAAGAAAAATTAAAACAAA
Found at i:15415557 original size:21 final size:20
Alignment explanation
Indices: 15415533--15415571 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
15415523 ATTTGGTAGC
* *
15415533 TTGTCTACATTATCTGGTGGG
1 TTGTCCACAATAT-TGGTGGG
15415554 TTGTCCACAATATTGGTG
1 TTGTCCACAATATTGGTG
15415572 TGTTAATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (20 bp):
TTGTCCACAATATTGGTGGG
Found at i:15422564 original size:39 final size:39
Alignment explanation
Indices: 15422479--15422581 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
15422469 ATTAAAATCC
*
15422479 TTATTATAATTATTGTAATTATAA--TTTAGGATCAAATA
1 TTATTATAATTA-TGTAATTATAATTTTTAGGATCAAACA
* **
15422517 TTATTATAATTACTGTAATTGTAATTTTTTTG-TCAAACA
1 TTATTATAATTA-TGTAATTATAATTTTTAGGATCAAACA
15422556 TTATTATAATTATGGTAATTATAATT
1 TTATTATAATTAT-GTAATTATAATT
15422582 ATTATATTCG
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 23 0.41
39 29 0.52
40 4 0.07
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (39 bp):
TTATTATAATTATGTAATTATAATTTTTAGGATCAAACA
Found at i:15430111 original size:16 final size:16
Alignment explanation
Indices: 15430092--15430122 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15430082 TTTGATCATA
15430092 TTTTTATTTAAATAAG
1 TTTTTATTTAAATAAG
*
15430108 TTTTTATTTTAATAA
1 TTTTTATTTAAATAA
15430123 ATTAATAGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTTATTTAAATAAG
Found at i:15439160 original size:16 final size:16
Alignment explanation
Indices: 15439141--15439171 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15439131 TTTGATCATA
15439141 TTTTTATTTAAATAAG
1 TTTTTATTTAAATAAG
*
15439157 TTTTTATTTTAATAA
1 TTTTTATTTAAATAA
15439172 ATTAATAGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTTATTTAAATAAG
Found at i:15443311 original size:13 final size:13
Alignment explanation
Indices: 15443268--15443316 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
15443258 TAAAAGAAAG
15443268 TGAAGAAACA-AAA
1 TGAAGAAA-ATAAA
15443281 -GAAGAAAA-AAA
1 TGAAGAAAATAAA
15443292 TGAAGAAAATAAA
1 TGAAGAAAATAAA
15443305 TTG-AGAAAATAA
1 -TGAAGAAAATAA
15443317 GTGTGTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.12
12 15 0.45
13 12 0.36
14 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.16, T:0.12
Consensus pattern (13 bp):
TGAAGAAAATAAA
Found at i:15462086 original size:47 final size:47
Alignment explanation
Indices: 15462017--15462110 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
15462007 AAGAAATATA
* **
15462017 AAAGAGAACCAGATGCATATGTTGTTTGGCCAGTCAATCCATTTTTT
1 AAAGAGAACCAGATGCAGATGTTGTTTAACCAGTCAATCCATTTTTT
*
15462064 AAAGAGAATCAGATGCAGATGTTGTTTAACCAGTCAATCCATTTTTT
1 AAAGAGAACCAGATGCAGATGTTGTTTAACCAGTCAATCCATTTTTT
15462111 GAATCTCAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (47 bp):
AAAGAGAACCAGATGCAGATGTTGTTTAACCAGTCAATCCATTTTTT
Found at i:15463682 original size:49 final size:49
Alignment explanation
Indices: 15463628--15463876 Score: 336
Period size: 49 Copynumber: 5.0 Consensus size: 49
15463618 AACAAAAAAC
* *
15463628 AAACAATCAATGAAGCATAAATGAAACAACTCTATTTATGAATGCAACA
1 AAACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAACA
*
15463677 AAACAATCAATGAAGCATAATTAAAACACCACTTTATTTATGAATGCAACA
1 AAACAATCAATGAAGCATAAATAAAACA--ACTTTATTTATGAATGCAACA
* * * *
15463728 TAACAATGAATGAAGCATAAATAAAACAACTCTATTAATGAATGCAACA
1 AAACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAACA
* * *
15463777 AAACAATCAATGAAGCATAAATAAAGCAACTTTATTTATGAACGCAAAAAAA
1 AAACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGC---AACA
* *
15463829 ACAACAATCAATGAAGTATAAATAAAACAACTTTATTTTTGAATGCAA
1 A-AACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAA
15463877 GTATGCTTTA
Statistics
Matches: 175, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
49 84 0.48
50 2 0.01
51 45 0.26
52 4 0.02
53 40 0.23
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (49 bp):
AAACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAACA
Found at i:15466812 original size:21 final size:21
Alignment explanation
Indices: 15466786--15466837 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
15466776 CTCTTTTATT
15466786 TTTTTCTTTTCCCTCATGCTC
1 TTTTTCTTTTCCCTCATGCTC
15466807 TTTTTCTTTTCCCTCATGCTC
1 TTTTTCTTTTCCCTCATGCTC
15466828 TTTTTCTTTT
1 TTTTTCTTTT
15466838 TCTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.04, C:0.29, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTTTCTTTTCCCTCATGCTC
Found at i:15470154 original size:49 final size:49
Alignment explanation
Indices: 15470049--15470387 Score: 386
Period size: 49 Copynumber: 7.0 Consensus size: 49
15470039 AACAAAAAAC
* * *
15470049 AAACAAAT-AATGAAGCATAATTAAAACACCACTTTATTTTTGAATGCAATA
1 AAAC-AATCAATGAAGCATAAATAAAACA--ACTTTATTTATGAATGCAACA
* * * * * *
15470100 GAACAATCAATGAAGCATAAATGAAGCAACTCTATTTATGGATGCAATA
1 AAACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAACA
* *
15470149 AAACAATCAATGAATCATAATTAAAACACCACTTTATTTATGAATGCAACA
1 AAACAATCAATGAAGCATAAATAAAACA--ACTTTATTTATGAATGCAACA
* * * *
15470200 GAACAATGAATGAAGCATAAATAAAACAACTCTATTTATGAATGCAATA
1 AAACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAACA
* * * *
15470249 AAACAATCAATGAAGCAT---T---GCAATTTTATTTATGAATGTAGCA
1 AAACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAACA
*
15470292 AAACAATCAATGAAGCATAAATAAAGCAACTTTATTTATGAATGCAACA
1 AAACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAACA
* *
15470341 AAACAATCAATAAATCATAAATAAAACAACTTTATTTATGAATGCAA
1 AAACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAA
15470388 GTATGCTTTA
Statistics
Matches: 244, Mismatches: 35, Indels: 20
0.82 0.12 0.07
Matches are distributed among these distances:
43 36 0.15
46 2 0.01
49 141 0.58
50 3 0.01
51 62 0.25
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (49 bp):
AAACAATCAATGAAGCATAAATAAAACAACTTTATTTATGAATGCAACA
Found at i:15470178 original size:100 final size:98
Alignment explanation
Indices: 15470049--15470387 Score: 431
Period size: 100 Copynumber: 3.5 Consensus size: 98
15470039 AACAAAAAAC
* *
15470049 AAACAAAT-AATGAAGCATAATTAAAACACCACTTTATTTTTGAATGCAATAGAACAATCAATGA
1 AAAC-AATCAATGAAGCATAATTAAAACA--ACTTTATTTATGAATGCAACAGAACAATCAATGA
* *
15470113 AGCATAAATGAAGCAACTCTATTTATGGATGCAATA
63 AGCATAAATAAAGCAACTCTATTTATGAATGCAATA
* *
15470149 AAACAATCAATGAATCATAATTAAAACACCACTTTATTTATGAATGCAACAGAACAATGAATGAA
1 AAACAATCAATGAAGCATAATTAAAACA--ACTTTATTTATGAATGCAACAGAACAATCAATGAA
*
15470214 GCATAAATAAAACAACTCTATTTATGAATGCAATA
64 GCATAAATAAAGCAACTCTATTTATGAATGCAATA
* * * * *
15470249 AAACAATCAATGAAGC---ATT---GCAATTTTATTTATGAATGTAGCAAAACAATCAATGAAGC
1 AAACAATCAATGAAGCATAATTAAAACAACTTTATTTATGAATGCAACAGAACAATCAATGAAGC
* *
15470308 ATAAATAAAGCAACTTTATTTATGAATGCAACA
66 ATAAATAAAGCAACTCTATTTATGAATGCAATA
* * *
15470341 AAACAATCAATAAATCATAAATAAAACAACTTTATTTATGAATGCAA
1 AAACAATCAATGAAGCATAATTAAAACAACTTTATTTATGAATGCAA
15470388 GTATGCTTTA
Statistics
Matches: 208, Mismatches: 24, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
92 76 0.37
94 2 0.01
95 2 0.01
97 3 0.01
98 18 0.09
99 3 0.01
100 104 0.50
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (98 bp):
AAACAATCAATGAAGCATAATTAAAACAACTTTATTTATGAATGCAACAGAACAATCAATGAAGC
ATAAATAAAGCAACTCTATTTATGAATGCAATA
Found at i:15470297 original size:92 final size:92
Alignment explanation
Indices: 15470181--15470351 Score: 279
Period size: 92 Copynumber: 1.9 Consensus size: 92
15470171 AAAACACCAC
* *
15470181 TTTATTTATGAATGCAACAGAACAATGAATGAAGCATAAATAAAACAACTCTATTTATGAATGCA
1 TTTATTTATGAATGCAACAAAACAATCAATGAAGCATAAATAAAACAACTCTATTTATGAATGCA
*
15470246 ATAAAACAATCAATGAAGCATTGCAAT
66 ACAAAACAATCAATGAAGCATTGCAAT
* * * *
15470273 TTTATTTATGAATGTAGCAAAACAATCAATGAAGCATAAATAAAGCAACTTTATTTATGAATGCA
1 TTTATTTATGAATGCAACAAAACAATCAATGAAGCATAAATAAAACAACTCTATTTATGAATGCA
15470338 ACAAAACAATCAAT
66 ACAAAACAATCAAT
15470352 AAATCATAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 72 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (92 bp):
TTTATTTATGAATGCAACAAAACAATCAATGAAGCATAAATAAAACAACTCTATTTATGAATGCA
ACAAAACAATCAATGAAGCATTGCAAT
Found at i:15471060 original size:26 final size:23
Alignment explanation
Indices: 15471029--15471088 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
15471019 TCATGATTGC
* *
15471029 TTAATTTTGTTGGTGTTAGAATTAT
1 TTAATTTTGTTAG-CTTAG-ATTAT
15471054 TTAAATTTTG-TAGCTTAGATTAT
1 TT-AATTTTGTTAGCTTAGATTAT
15471077 TTAATTTTGTTA
1 TTAATTTTGTTA
15471089 AAGATGTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 7 0.23
23 9 0.29
24 4 0.13
25 4 0.13
26 7 0.23
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.57
Consensus pattern (23 bp):
TTAATTTTGTTAGCTTAGATTAT
Found at i:15471574 original size:14 final size:15
Alignment explanation
Indices: 15471544--15471576 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
15471534 TCTTTAGAAA
*
15471544 TCTTCTGAAATATTT
1 TCTTCAGAAATATTT
15471559 TCTTCAGAAA-ATTT
1 TCTTCAGAAATATTT
15471573 TCTT
1 TCTT
15471577 TACAACTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (15 bp):
TCTTCAGAAATATTT
Found at i:15479436 original size:50 final size:50
Alignment explanation
Indices: 15479373--15479552 Score: 182
Period size: 50 Copynumber: 3.5 Consensus size: 50
15479363 CAATTTCATA
* * * *
15479373 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGGGACTTCTCATCTCGGTGCCAATGCCATG
* * * *
15479423 TCCCAGACATGGTCTTAC-GGTGGACCTCTCATCTCGGTGCCAACGTCATG
1 TCCCAGACATGGTCTTACATG-GGACTTCTCATCTCGGTGCCAATGCCATG
* * **
15479473 TCCCAGACATGGTCTTACACGGGACCTCTCTTAATCTCAATAATGCCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGA-CT-TC-TCATCTC---GGTGCCAATGCCATG
15479529 TCCCAGACATGGTCTTACATGGGA
1 TCCCAGACATGGTCTTACATGGGA
15479553 TCTCATTCCC
Statistics
Matches: 106, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
49 1 0.01
50 61 0.58
51 2 0.02
52 2 0.02
53 6 0.06
56 34 0.32
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACTTCTCATCTCGGTGCCAATGCCATG
Found at i:15481355 original size:20 final size:20
Alignment explanation
Indices: 15481332--15481381 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
15481322 GGGCACCAAT
15481332 GTGCAAACAAGGGAATTGAA
1 GTGCAAACAAGGGAATTGAA
* * *
15481352 GTGCAAGCAAGGGCATTGAT
1 GTGCAAACAAGGGAATTGAA
15481372 GTGCAAACAA
1 GTGCAAACAA
15481382 TATAAGCGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.30, T:0.16
Consensus pattern (20 bp):
GTGCAAACAAGGGAATTGAA
Found at i:15489321 original size:60 final size:60
Alignment explanation
Indices: 15489257--15489371 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
15489247 CACTATTCGG
* * * *
15489257 CCCATTATTCTGTCCACTAACCGGCCCAAGAAATTGGCCTGCATTTGGCCCAAAATACTA
1 CCCATTATTCTGTCCACTAACAGGCCCAAGAAACTGACCTACATTTGGCCCAAAATACTA
* * *
15489317 CCCATTATTCTGTCTACTAACATGCCCAAGAGACTGACCTACATTTGGCCCAAAA
1 CCCATTATTCTGTCCACTAACAGGCCCAAGAAACTGACCTACATTTGGCCCAAAA
15489372 CACAACCTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (60 bp):
CCCATTATTCTGTCCACTAACAGGCCCAAGAAACTGACCTACATTTGGCCCAAAATACTA
Found at i:15495440 original size:19 final size:20
Alignment explanation
Indices: 15495416--15495468 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
15495406 CAGCGATTAA
15495416 AAATTATTTTTTAT-AAAAT
1 AAATTATTTTTTATGAAAAT
* *
15495435 AAATTATATTATTATGAGAAT
1 AAATTAT-TTTTTATGAAAAT
*
15495456 -ATTTATTTTTTAT
1 AAATTATTTTTTAT
15495469 TTTATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 13 0.46
20 11 0.39
21 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
AAATTATTTTTTATGAAAAT
Found at i:15498145 original size:13 final size:13
Alignment explanation
Indices: 15498127--15498152 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15498117 TTTCGAATCA
15498127 TGATAATTTAATT
1 TGATAATTTAATT
15498140 TGATAATTTAATT
1 TGATAATTTAATT
15498153 CCGTTCGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TGATAATTTAATT
Found at i:15500740 original size:59 final size:56
Alignment explanation
Indices: 15500669--15500779 Score: 150
Period size: 59 Copynumber: 1.9 Consensus size: 56
15500659 ATCACTTTAA
* * **
15500669 TATTAAATTAATATAATATTTATCTTGATAAATAATAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATCTACA-AAATAA-AGATTAAATTTAAT-TTAAATCT
*
15500728 TATTAAAATAATAGAATATTTATCTACAAAATAAATATTAAATTTAATTTAA
1 TATTAAAATAATAGAATATTTATCTACAAAATAAAGATTAAATTTAATTTAA
15500780 TATTAAGATA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
56 4 0.09
57 13 0.28
58 6 0.13
59 24 0.51
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (56 bp):
TATTAAAATAATAGAATATTTATCTACAAAATAAAGATTAAATTTAATTTAAATCT
Found at i:15500824 original size:25 final size:25
Alignment explanation
Indices: 15500770--15500824 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
15500760 AAATATTAAA
*
15500770 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGACAATCAC
*
15500795 TTTAATATTAA-ATTAATACAAT-AC
1 TTTAAT-TTAATATTAAGACAATCAC
15500819 TATTAA
1 T-TTAA
15500825 GATAAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGACAATCAC
Found at i:15500858 original size:37 final size:39
Alignment explanation
Indices: 15500761--15500867 Score: 104
Period size: 37 Copynumber: 2.9 Consensus size: 39
15500751 CTACAAAATA
*
15500761 AATATTAAATTTAAT-TT-AA-TATTAAGATAATCACTTT
1 AATATTAAATTTAATATTAAACTATTAAGATAATCAC-AT
*
15500798 AATATTAAA-TTAATA-CAATACTATTAAGATAAGT-A-AT
1 AATATTAAATTTAATATTAA-ACTATTAAGATAA-TCACAT
*
15500835 AA-ATTAAATTTAATATTAAACTATTAAAATAAT
1 AATATTAAATTTAATATTAAACTATTAAGATAAT
15500868 ATTATTTTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
36 12 0.20
37 31 0.53
38 3 0.05
39 12 0.20
40 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (39 bp):
AATATTAAATTTAATATTAAACTATTAAGATAATCACAT
Found at i:15508305 original size:50 final size:50
Alignment explanation
Indices: 15508188--15508370 Score: 228
Period size: 50 Copynumber: 3.7 Consensus size: 50
15508178 TCACATATCG
* * *
15508188 GTGCCGATGCCATGTCCCAGATATGGTCTTACACTAACACTCATCT-CAA
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACTCCTCTACCA
* * *
15508237 GT--CGATGCCACGTCCCAGACATGGTCTTACACTAACTCTCCTCTACCC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACTCCTCTACCA
* * * * * *
15508285 GTGCCGATGCCATGTCCCAGATATGGTCTTACACTAGCACTTCTCGATCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACTCCTCTACCA
*
15508335 GTGCTGATGCCATGTCCCAGACATGGTCTTACACTA
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTA
15508371 GCACACTCAC
Statistics
Matches: 115, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
47 38 0.33
48 3 0.03
49 2 0.02
50 72 0.63
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.27
Consensus pattern (50 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACTCCTCTACCA
Found at i:15508310 original size:97 final size:99
Alignment explanation
Indices: 15508188--15508370 Score: 284
Period size: 97 Copynumber: 1.9 Consensus size: 99
15508178 TCACATATCG
15508188 GTGCCGATGCCATGTCCCAGATATGGTCTTACACTAACACTCATCTC-A-AGT-C-GATGCCACG
1 GTGCCGATGCCATGTCCCAGATATGGTCTTACACTAACACT--TCTCGACAGTGCTGATGCCACG
15508249 TCCCAGACATGGTCTTACACTAACTCTCCTCTACCC
64 TCCCAGACATGGTCTTACACTAACTCTCCTCTACCC
* * *
15508285 GTGCCGATGCCATGTCCCAGATATGGTCTTACACTAGCACTTCTCGATCTGTGCTGATGCCATGT
1 GTGCCGATGCCATGTCCCAGATATGGTCTTACACTAACACTTCTCGA-CAGTGCTGATGCCACGT
15508350 CCCAGACATGGTCTTACACTA
65 CCCAGACATGGTCTTACACTA
15508371 GCACACTCAC
Statistics
Matches: 78, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
95 4 0.05
96 1 0.01
97 40 0.51
98 2 0.03
99 1 0.01
100 30 0.38
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.27
Consensus pattern (99 bp):
GTGCCGATGCCATGTCCCAGATATGGTCTTACACTAACACTTCTCGACAGTGCTGATGCCACGTC
CCAGACATGGTCTTACACTAACTCTCCTCTACCC
Found at i:15508831 original size:42 final size:42
Alignment explanation
Indices: 15508783--15508875 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
15508773 TTGGTATTGT
* * *
15508783 ACACTTAGTGCCCTTTATTCGACATCGCCATTTTTGTTTCAC
1 ACACTTAGTGCCCGTTATTCAACATCGCCATTTTAGTTTCAC
* * **
15508825 ACACTTAGTGCCCGTTATTCAACGTCGTCATTTTAGTTTCGT
1 ACACTTAGTGCCCGTTATTCAACATCGCCATTTTAGTTTCAC
15508867 ACACTTAGT
1 ACACTTAGT
15508876 TCCATTCGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (42 bp):
ACACTTAGTGCCCGTTATTCAACATCGCCATTTTAGTTTCAC
Found at i:15511700 original size:20 final size:18
Alignment explanation
Indices: 15511653--15511701 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
15511643 CAAGATAAAC
15511653 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
15511670 ATT-AATATAATCACTTTAAT
1 ATTAAAT-TAAT-A-TTTAAT
15511690 ATTAAATTAATA
1 ATTAAATTAATA
15511702 AAACACTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.11
17 6 0.22
19 2 0.07
20 13 0.48
21 3 0.11
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:15512077 original size:197 final size:197
Alignment explanation
Indices: 15511720--15512077 Score: 497
Period size: 197 Copynumber: 1.8 Consensus size: 197
15511710 CTAAGATAAG
* *
15511720 TATTAAATTAAATTTAATATTAAACTATTAGAATAATATTATTTTTGGAATAATTAATATGAAAT
1 TATTAAATTAAATTTAATATTAAACTATTAAAATAATATTATTTTTGGAATAATTAATATAAAAT
*
15511785 CAAATTCTCCTGTAGAATTCCAGTAGGAGTGTAACTCTTCCAATGCTCAACCACCAATGACCAAC
66 CAAATTCTCCTGTAGAATTCCAATAGGAGTGTAACTCTTCCAATGCTCAACCACCAATGACCAAC
* * * *
15511850 TGCCACCGGCCACCGAGACGCCACTGTCGCAATCGCCAGCACCGTCGTGTCCGATGGTGCAGGTG
131 CGCCACCGGCCACCAAAACACCACTGTCGCAATCGCCAGCACCGTCGTGTCCGATGGTGCAGGTG
15511915 TT
196 TT
*
15511917 TATTAAA-TATAATTTAATATTAAACTATTAAAATAATATTATTTTTGGAATAATTAATCTAAAA
1 TATTAAATTA-AATTTAATATTAAACTATTAAAATAATATTATTTTTGGAATAATTAATATAAAA
* * * * * *
15511981 TCAAATTCT-CTGGTAGAGTTCGAATAGGAGTGTAACTTTTTCACTGCTCAACCACCTAA-GATC
65 TCAAATTCTCCT-GTAGAATTCCAATAGGAGTGTAACTCTTCCAATGCTCAACCACC-AATGACC
* * * * *
15512044 AACCGCCGCTGGCCATCAAAACATCATTGTCGCA
128 AACCGCCACCGGCCACCAAAACACCACTGTCGCA
15512078 GTTGTCATCA
Statistics
Matches: 139, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
196 4 0.03
197 133 0.96
198 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (197 bp):
TATTAAATTAAATTTAATATTAAACTATTAAAATAATATTATTTTTGGAATAATTAATATAAAAT
CAAATTCTCCTGTAGAATTCCAATAGGAGTGTAACTCTTCCAATGCTCAACCACCAATGACCAAC
CGCCACCGGCCACCAAAACACCACTGTCGCAATCGCCAGCACCGTCGTGTCCGATGGTGCAGGTG
TT
Found at i:15514043 original size:50 final size:51
Alignment explanation
Indices: 15513982--15514122 Score: 196
Period size: 51 Copynumber: 2.8 Consensus size: 51
15513972 TATCATTCGA
* * *
15513982 TACACGTAGTAGCCT-TCACATAGTACTACACACGTGATCAAA-CTTTTCGG
1 TACACGTAGTAGCCTGT-ACATAGTACTACACACGTGACCAAAGCCTTCCGG
*
15514032 TTCACGTAGTAGCCTGTACATAGTACTACACACGTGACCAAAGCCTTCCGG
1 TACACGTAGTAGCCTGTACATAGTACTACACACGTGACCAAAGCCTTCCGG
* * *
15514083 TACACATAGTAGCGTGTACATAGTACTACACATGTGACCA
1 TACACGTAGTAGCCTGTACATAGTACTACACACGTGACCA
15514123 TTATCTATCG
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
50 38 0.47
51 43 0.53
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (51 bp):
TACACGTAGTAGCCTGTACATAGTACTACACACGTGACCAAAGCCTTCCGG
Found at i:15514138 original size:51 final size:50
Alignment explanation
Indices: 15513978--15514149 Score: 161
Period size: 51 Copynumber: 3.4 Consensus size: 50
15513968 TTATTATCAT
* * *
15513978 TCGATACACGTAGTAGCCT-TCACATAGTACTACACACGTGATCA-AACTTT
1 TCGATACACGTAGTAGCCTGT-ACATAGTACTACACACGTGACCATATC-TA
* * * *
15514028 TCGGTTCACGTAGTAGCCTGTACATAGTACTACACACGTGACCAAAGCCT-
1 TCGATACACGTAGTAGCCTGTACATAGTACTACACACGTGACCATA-TCTA
* * * *
15514078 TCCGGTACACATAGTAGCGTGTACATAGTACTACACATGTGACCATTATCTA
1 T-CGATACACGTAGTAGCCTGTACATAGTACTACACACGTGACCA-TATCTA
* *
15514130 TCGATACACGTTGTAACCTG
1 TCGATACACGTAGTAGCCTG
15514150 CANNNNNNNN
Statistics
Matches: 101, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
50 40 0.40
51 58 0.57
52 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (50 bp):
TCGATACACGTAGTAGCCTGTACATAGTACTACACACGTGACCATATCTA
Found at i:15517767 original size:20 final size:20
Alignment explanation
Indices: 15517742--15517817 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
15517732 TTCATGTGGT
15517742 TCAGCTCACTT-GAGCTCAAG
1 TCAGCTCA-TTCGAGCTCAAG
15517762 TCAGCTCATTCGAGCTCAAG
1 TCAGCTCATTCGAGCTCAAG
* *
15517782 TCAGCTCATTCGAGCTTAAT
1 TCAGCTCATTCGAGCTCAAG
15517802 TCAGCTCATT-GAGCTC
1 TCAGCTCATTCGAGCTC
15517818 GTTATTAGCT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.13
20 45 0.87
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (20 bp):
TCAGCTCATTCGAGCTCAAG
Found at i:15517797 original size:10 final size:10
Alignment explanation
Indices: 15517764--15517817 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
15517754 AGCTCAAGTC
15517764 AGCTCATTCG
1 AGCTCATTCG
*
15517774 AGCTCAAGTC-
1 AGCTC-ATTCG
15517784 AGCTCATTCG
1 AGCTCATTCG
*
15517794 AGCTTAATTC-
1 AGC-TCATTCG
15517804 AGCTCATT-G
1 AGCTCATTCG
15517813 AGCTC
1 AGCTC
15517818 GTTATTAGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
9 12 0.33
10 16 0.44
11 8 0.22
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (10 bp):
AGCTCATTCG
Found at i:15526189 original size:23 final size:22
Alignment explanation
Indices: 15526154--15526198 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
15526144 TATTTTAACC
15526154 TAATTTAAAAATATGAATATTT
1 TAATTTAAAAATATGAATATTT
* *
15526176 TAATTATATAAATATGAGTATTT
1 TAATT-TAAAAATATGAATATTT
15526199 GTTTAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (22 bp):
TAATTTAAAAATATGAATATTT
Found at i:15526643 original size:16 final size:19
Alignment explanation
Indices: 15526607--15526647 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 19
15526597 ATCTAAACAT
15526607 TAAAAAATATTATATTATC
1 TAAAAAATATTATATTATC
15526626 TAAAAAAT-TTAT-TT-TC
1 TAAAAAATATTATATTATC
15526642 TAAAAA
1 TAAAAA
15526648 TTACTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 4 0.18
19 8 0.36
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAAATATTATATTATC
Found at i:15528580 original size:21 final size:21
Alignment explanation
Indices: 15528554--15528598 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
15528544 AGAATATTAT
*
15528554 AAAAAATA-TTAAAATTTGTAA
1 AAAAAATATTTAAAA-TGGTAA
15528575 AAAAAATATTTAAAATGGTAA
1 AAAAAATATTTAAAATGGTAA
15528596 AAA
1 AAA
15528599 TTATACATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAAAATATTTAAAATGGTAA
Found at i:15528803 original size:9 final size:9
Alignment explanation
Indices: 15528759--15528827 Score: 79
Period size: 10 Copynumber: 7.4 Consensus size: 9
15528749 TTGACATAAT
15528759 ATTATAAAA
1 ATTATAAAA
*
15528768 ATTATTAAGA
1 ATTA-TAAAA
15528778 A-TAGTAAAA
1 ATTA-TAAAA
15528787 ATTAT-AAA
1 ATTATAAAA
15528795 ATTATTAAAA
1 ATTA-TAAAA
15528805 ATTATAATAA
1 ATTATAA-AA
15528815 ATTATAAAA
1 ATTATAAAA
15528824 ATTA
1 ATTA
15528828 ATAATTATTG
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
8 7 0.13
9 22 0.42
10 23 0.44
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (9 bp):
ATTATAAAA
Found at i:15528808 original size:37 final size:36
Alignment explanation
Indices: 15528754--15528843 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 36
15528744 CATCATTGAC
*
15528754 ATAATATTA-TAAAAATTAT-TAAGAATAGTAAAAATT
1 ATAAAATTATTAAAAATTATATAA-AATA-TAAAAATT
*
15528790 ATAAAATTATTAAAAATTATAATAAATTATAAAAATT
1 ATAAAATTATTAAAAATTAT-ATAAAATATAAAAATT
*
15528827 A-ATAATTATTGAAAAAT
1 ATAAAATTATT-AAAAAT
15528844 AACATACAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
36 16 0.34
37 25 0.53
38 3 0.06
39 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (36 bp):
ATAAAATTATTAAAAATTATATAAAATATAAAAATT
Found at i:15528841 original size:17 final size:17
Alignment explanation
Indices: 15528782--15528843 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 17
15528772 TTAAGAATAG
*
15528782 TAAAAATTATAAAATTAT
1 TAAAAATTA-ATAATTAT
15528800 TAAAAATTATAATAAATTA-
1 TAAAAA-T-TAAT-AATTAT
15528819 TAAAAATTAATAATTAT
1 TAAAAATTAATAATTAT
15528836 TGAAAAAT
1 T-AAAAAT
15528844 AACATACAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
16 5 0.13
17 5 0.13
18 13 0.34
19 8 0.21
20 7 0.18
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAAAATTAATAATTAT
Found at i:15535280 original size:30 final size:30
Alignment explanation
Indices: 15535246--15535317 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
15535236 GTAGAACTCT
*
15535246 TTGTGGCTGTTCTCTATTATATGTGAGCCC
1 TTGTGGCTGTTCTCTATTACATGTGAGCCC
** * *
15535276 TTGTGGCTG-AATCTGTTACATGTGAGCCT
1 TTGTGGCTGTTCTCTATTACATGTGAGCCC
15535305 TTGTGGCTGTTCT
1 TTGTGGCTGTTCT
15535318 ATTATGGGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.12, C:0.18, G:0.26, T:0.43
Consensus pattern (30 bp):
TTGTGGCTGTTCTCTATTACATGTGAGCCC
Found at i:15539065 original size:15 final size:15
Alignment explanation
Indices: 15539045--15539074 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15539035 GTCAAACATT
15539045 ATTATAATCATTATA
1 ATTATAATCATTATA
*
15539060 ATTATAATTATTATA
1 ATTATAATCATTATA
15539075 TTCGGTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAATCATTATA
Found at i:15545844 original size:34 final size:35
Alignment explanation
Indices: 15545783--15545850 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
15545773 NNNNNNNATG
* *
15545783 TTATTTTTTTAATTTTAATTCATAAAATATTTAAT
1 TTATTTTTTAAATTTTAACTCATAAAATATTTAAT
15545818 TTATTTTTTAAATTTTAAACT-A-AAAATATTTAA
1 TTATTTTTTAAATTTT-AACTCATAAAATATTTAA
15545851 AATTCAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 11 0.37
35 16 0.53
36 3 0.10
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (35 bp):
TTATTTTTTAAATTTTAACTCATAAAATATTTAAT
Found at i:15547828 original size:2 final size:2
Alignment explanation
Indices: 15547821--15547852 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15547811 TATTATATGC
15547821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15547853 CTATGAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15547877 original size:17 final size:17
Alignment explanation
Indices: 15547855--15547891 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
15547845 ATATATATCT
15547855 ATGAATTTAAGGGAATA
1 ATGAATTTAAGGGAATA
15547872 ATGAATTTAAGGGAATA
1 ATGAATTTAAGGGAATA
15547889 ATG
1 ATG
15547892 CATGATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (17 bp):
ATGAATTTAAGGGAATA
Found at i:15547901 original size:21 final size:19
Alignment explanation
Indices: 15547859--15547899 Score: 59
Period size: 17 Copynumber: 2.2 Consensus size: 19
15547849 ATATCTATGA
15547859 ATTTAAGGGAATAATGA--
1 ATTTAAGGGAATAATGATG
15547876 ATTTAAGGGAATAATGCATG
1 ATTTAAGGGAATAATG-ATG
15547896 ATTT
1 ATTT
15547900 TATTTTGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 16 0.76
18 1 0.05
20 4 0.19
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.34
Consensus pattern (19 bp):
ATTTAAGGGAATAATGATG
Found at i:15551026 original size:20 final size:20
Alignment explanation
Indices: 15550983--15551027 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
15550973 TTATGCTAAG
* *
15550983 TAAATGAAATGGAAAGTAAG
1 TAAATGAAATGGAAAGAAAA
* *
15551003 TAAATGGAATGGTAAGAAAA
1 TAAATGAAATGGAAAGAAAA
15551023 TAAAT
1 TAAAT
15551028 AGAGTGGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (20 bp):
TAAATGAAATGGAAAGAAAA
Found at i:15556955 original size:17 final size:17
Alignment explanation
Indices: 15556933--15556967 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
15556923 GGATGGTTGT
15556933 GGACGATTCTGCTAATG
1 GGACGATTCTGCTAATG
15556950 GGACGATTCTGCTAATG
1 GGACGATTCTGCTAATG
15556967 G
1 G
15556968 TGCTCTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (17 bp):
GGACGATTCTGCTAATG
Found at i:15564294 original size:18 final size:17
Alignment explanation
Indices: 15564261--15564299 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
15564251 TTTTATAAAT
15564261 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
15564279 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
15564296 TGTG
1 TGTG
15564300 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:15564560 original size:23 final size:23
Alignment explanation
Indices: 15564525--15564623 Score: 119
Period size: 23 Copynumber: 4.3 Consensus size: 23
15564515 AGTGTTATTG
* * *
15564525 ATCAATGGTAGCTTCGGGTACA-
1 ATCAGTGGTAGCTACGGCTACAT
15564547 ATTCAGTGGTAGCTACGGCTACAT
1 A-TCAGTGGTAGCTACGGCTACAT
* *
15564571 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
15564594 TTCAATGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
15564617 ATCAGTG
1 ATCAGTG
15564624 TGGCACTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 1 0.02
23 62 0.97
24 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:15564583 original size:46 final size:46
Alignment explanation
Indices: 15564525--15564623 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 46
15564515 AGTGTTATTG
* * * *
15564525 ATCAATGGTAGCTTCGGGTACAATTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAATTCAATGGTAGCTACGGCTACAT
*
15564571 ATCAGTGGTAGCTTCAGCTACATTTCAATGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAATTCAATGGTAGCTACGGCTACAT
15564617 ATCAGTG
1 ATCAGTG
15564624 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCAGCTACAATTCAATGGTAGCTACGGCTACAT
Found at i:15564873 original size:23 final size:25
Alignment explanation
Indices: 15564827--15564874 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
15564817 GAAATTGCTA
* *
15564827 AGAAATGTTTGATTGGTTATATGAG
1 AGAAATGTTTAATTGGTTAAATGAG
15564852 AGAAATG-TTAATT-GTTAAATGAG
1 AGAAATGTTTAATTGGTTAAATGAG
15564875 TATTTATAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (25 bp):
AGAAATGTTTAATTGGTTAAATGAG
Found at i:15571484 original size:20 final size:21
Alignment explanation
Indices: 15571447--15571485 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
15571437 TTGAACGGAA
*
15571447 TGTTGTTAAAATATATTAAAT
1 TGTTGTTAAAATAGATTAAAT
*
15571468 TGTT-TTAATATAGATTAA
1 TGTTGTTAAAATAGATTAA
15571486 GAAAGAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (21 bp):
TGTTGTTAAAATAGATTAAAT
Found at i:15571639 original size:18 final size:17
Alignment explanation
Indices: 15571606--15571644 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
15571596 TTTTATAAAT
15571606 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
15571624 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
15571641 TGTG
1 TGTG
15571645 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:15571884 original size:23 final size:23
Alignment explanation
Indices: 15571855--15572074 Score: 171
Period size: 23 Copynumber: 9.4 Consensus size: 23
15571845 GTGTTATTGA
*
15571855 TCAGTGGTAGCTTCGGGTACAAT
1 TCAGTGGTAGCTTCGGCTACAAT
*
15571878 TCAGTGGTAGCTACGGCTAC-AT
1 TCAGTGGTAGCTTCGGCTACAAT
* *
15571900 ATCAGTGGTAGCTTCGGCTGCATT
1 -TCAGTGGTAGCTTCGGCTACAAT
* * * * *
15571924 TTAGTGGTAGCTACTGCTGCATT
1 TCAGTGGTAGCTTCGGCTACAAT
*
15571947 TCAGTGGTAGCTACGGCTAC-AT
1 TCAGTGGTAGCTTCGGCTACAAT
* *
15571969 ATCAGTGGTAGCTTCGTTTTGTGTTA-GA-
1 -TCAGTGGTAGCTTC-----G-GCTACAAT
*
15571997 TCAGTGGTAGCTTCGGGTACAAT
1 TCAGTGGTAGCTTCGGCTACAAT
*
15572020 TCAGTGGTAGCTACGGCTAC-AT
1 TCAGTGGTAGCTTCGGCTACAAT
* *
15572042 ATCAGTGGTAGCTTCGGCTGCATT
1 -TCAGTGGTAGCTTCGGCTACAAT
*
15572066 TTAGTGGTA
1 TCAGTGGTA
15572075 TAGTTATGTG
Statistics
Matches: 161, Mismatches: 22, Indels: 28
0.76 0.10 0.13
Matches are distributed among these distances:
21 3 0.02
22 7 0.04
23 130 0.81
24 2 0.01
27 14 0.09
28 1 0.01
29 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACAAT
Found at i:15571906 original size:46 final size:46
Alignment explanation
Indices: 15571854--15572074 Score: 230
Period size: 46 Copynumber: 4.7 Consensus size: 46
15571844 TGTGTTATTG
*
15571854 ATCAGTGGTAGCTTCGGGTACAATTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACAT
* * * * *
15571900 ATCAGTGGTAGCTTCGGCTGCATTTTAGTGGTAGCTACTGCTGCAT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACAT
* * * ** *
15571946 TTCAGTGGTAGCTACGGCTAC-ATATCAGTGGTAGCTTCGTTTTG-TGTTAG
1 ATCAGTGGTAGCTTCGGCTACAAT-TCAGTGGTAGCTACG----GCT-ACAT
*
15571996 ATCAGTGGTAGCTTCGGGTACAATTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACAT
* * *
15572042 ATCAGTGGTAGCTTCGGCTGCATTTTAGTGGTA
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTA
15572075 TAGTTATGTG
Statistics
Matches: 140, Mismatches: 27, Indels: 16
0.77 0.15 0.09
Matches are distributed among these distances:
45 1 0.01
46 101 0.72
47 1 0.01
49 1 0.01
50 34 0.24
51 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACAT
Found at i:15572028 original size:96 final size:96
Alignment explanation
Indices: 15571900--15572074 Score: 251
Period size: 96 Copynumber: 1.8 Consensus size: 96
15571890 ACGGCTACAT
* * * * * *
15571900 ATCAGTGGTAGCTTCGGCTGCATTTTAGTGGTAGCTACTGCTGCATTTCAGTGGTAGCTACGGCT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTACGGCT
15571965 ACATATCAGTGGTAGCTTCGTTTTGTGTTAG
66 ACATATCAGTGGTAGCTTCGTTTTGTGTTAG
* *
15571996 ATCAGTGGTAGCTTCGGGTACAATTCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTACGGCT
* * *
15572061 GCATTTTAGTGGTA
66 ACATATCAGTGGTA
15572075 TAGTTATGTG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 68 1.00
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (96 bp):
ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTACGGCT
ACATATCAGTGGTAGCTTCGTTTTGTGTTAG
Found at i:15602134 original size:25 final size:27
Alignment explanation
Indices: 15602072--15602135 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 27
15602062 AGCGAGCCAC
* *
15602072 ATCGAGAAGCTCACAAAGAGCCAATTA
1 ATCGGGAAGCTCACAAAGAACCAATTA
*
15602099 A-CGGGAAGCTCACAAA-AACCCA-TA
1 ATCGGGAAGCTCACAAAGAACCAATTA
15602123 ATCGGGAAGCTCA
1 ATCGGGAAGCTCA
15602136 TAAGAGCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 3 0.09
25 15 0.45
26 14 0.42
27 1 0.03
ACGTcount: A:0.42, C:0.25, G:0.20, T:0.12
Consensus pattern (27 bp):
ATCGGGAAGCTCACAAAGAACCAATTA
Found at i:15603531 original size:49 final size:48
Alignment explanation
Indices: 15603471--15603711 Score: 180
Period size: 49 Copynumber: 4.8 Consensus size: 48
15603461 GACAATAACA
* *
15603471 TGCCAAAGCCATGTCCCATACATGGTCTTACATGGGATGTT-TCTTATAC-
1 TGCCAATGCCATGTCCCA-ACATGGTCTTACATGGGA-GTTCTCATAT-CG
* *
15603520 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCA-ACATGGTCTTACATGGGAGTTCTCATATC-G
* ** ** *
15603570 TGCCCATGCCATGTCCCAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAACATGGTCTTACATGGGAGTTCTCATATC-G
* ** * **
15603619 TGTCAACACCATGTCCCAGACACGGTCTTACATGGGACCTCTCATAATCTCAATG
1 TGCCAATGCCATGTCCCA-ACATGGTCTTACATGGGAGTTCTCAT-A--TC---G
*
15603674 ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCA-ACATGGTCTTACATGGGA
15603712 TCTCTTTACC
Statistics
Matches: 155, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
48 4 0.03
49 77 0.50
50 39 0.25
53 2 0.01
55 1 0.01
56 32 0.21
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAACATGGTCTTACATGGGAGTTCTCATATCG
Found at i:15609282 original size:26 final size:26
Alignment explanation
Indices: 15609246--15609300 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
15609236 CTAACCAAAA
*
15609246 GAAGTCATTGGTTTTTGGGGTTGTCT
1 GAAGTCATTGGTTTTTAGGGTTGTCT
*
15609272 GAAGTCCTTGGTTTTTAGGGTTGTCT
1 GAAGTCATTGGTTTTTAGGGTTGTCT
15609298 GAA
1 GAA
15609301 TTTTTTGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.09, G:0.33, T:0.44
Consensus pattern (26 bp):
GAAGTCATTGGTTTTTAGGGTTGTCT
Found at i:15610087 original size:15 final size:15
Alignment explanation
Indices: 15610063--15610092 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15610053 CAATACAGAC
*
15610063 TTCAGTCCAATACCA
1 TTCAGCCCAATACCA
15610078 TTCAGCCCAATACCA
1 TTCAGCCCAATACCA
15610093 CTAGCCCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.37, G:0.07, T:0.23
Consensus pattern (15 bp):
TTCAGCCCAATACCA
Found at i:15610965 original size:15 final size:15
Alignment explanation
Indices: 15610942--15610993 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
15610932 TGTTTTTATT
* *
15610942 TATTTTTATTATTAA
1 TATTATTATTATTAC
*
15610957 TATTATTATTACTAC
1 TATTATTATTATTAC
15610972 T-TTCATTATTATTAC
1 TATT-ATTATTATTAC
15610987 TATTATT
1 TATTATT
15610994 GCTATTATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:15611176 original size:9 final size:9
Alignment explanation
Indices: 15611159--15611195 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
15611149 TGAGTTTTCG
15611159 AATTCGAAT
1 AATTCGAAT
*
15611168 AACTCGAAT
1 AATTCGAAT
15611177 AATTCGAAT
1 AATTCGAAT
15611186 AATTCGAAT
1 AATTCGAAT
15611195 A
1 A
15611196 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:15611464 original size:30 final size:29
Alignment explanation
Indices: 15611408--15611464 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
15611398 AACCTTTTAT
* *
15611408 TTTTTCCCAAAATTTTTACTCCCTTCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCAC
* *
15611437 TTTTCCCCTAAAACTTTTATTCTCTTCC
1 TTTTCCCC-AAAACTTTTACTCCCTTCC
15611465 CATNNNNNNN
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCAC
Found at i:15611959 original size:5 final size:5
Alignment explanation
Indices: 15611949--15611974 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
15611939 CTCGAAAATT
15611949 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
15611975 CGAATGCTCA
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:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:15615991 original size:24 final size:24
Alignment explanation
Indices: 15615959--15616006 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
15615949 GAAGGTATGT
15615959 GTGCCTTTGTAGTAGCCATGCTCA
1 GTGCCTTTGTAGTAGCCATGCTCA
15615983 GTGCCTTTGTAGTAGCCATGCTCA
1 GTGCCTTTGTAGTAGCCATGCTCA
15616007 CCTTCACCTT
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:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (24 bp):
GTGCCTTTGTAGTAGCCATGCTCA
Found at i:15616784 original size:28 final size:28
Alignment explanation
Indices: 15616741--15616797 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
15616731 TCTTTCTCTG
* *
15616741 GTTAGCACTTATTGATCTGTTAGTATTT
1 GTTAGCACTTAATGATCTGTTACTATTT
15616769 GTTAGCACTTAATGATCTGTTACTATTT
1 GTTAGCACTTAATGATCTGTTACTATTT
15616797 G
1 G
15616798 ATGCTAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (28 bp):
GTTAGCACTTAATGATCTGTTACTATTT
Found at i:15617725 original size:35 final size:36
Alignment explanation
Indices: 15617648--15617728 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
15617638 TACTAACTCA
* *
15617648 TATATATAATCAAATTTCTGTTAATGTATATTTTTT
1 TATAAATAATCAAATTTCTATTAATGTATATTTTTT
15617684 TATAAATAATCAAATTTCTATTAATGTATA-TTTTT
1 TATAAATAATCAAATTTCTATTAATGTATATTTTTT
15617719 TATAAATAAT
1 TATAAATAAT
15617729 ATGTTAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 15 0.35
36 28 0.65
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.52
Consensus pattern (36 bp):
TATAAATAATCAAATTTCTATTAATGTATATTTTTT
Found at i:15619718 original size:35 final size:36
Alignment explanation
Indices: 15619674--15619742 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
15619664 ATTTGTTAGA
15619674 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
15619710 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAA
15619743 ATGATTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
Found at i:15622313 original size:22 final size:23
Alignment explanation
Indices: 15622288--15622331 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
15622278 TTGAAAACAA
15622288 ATTTGACTA-AAAATTAAAATTT
1 ATTTGACTATAAAATTAAAATTT
* *
15622310 ATTTTATTATAAAATTAAAATT
1 ATTTGACTATAAAATTAAAATT
15622332 AAAATCATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTTGACTATAAAATTAAAATTT
Found at i:15624101 original size:32 final size:32
Alignment explanation
Indices: 15624065--15624130 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
15624055 GATATGAAAC
15624065 ATGATTGACAAGTTTTTTTTTTTTTGAAAGGG
1 ATGATTGACAAGTTTTTTTTTTTTTGAAAGGG
15624097 ATGATTGACAAGTTTTTTTTTTTTTGAAAGGG
1 ATGATTGACAAGTTTTTTTTTTTTTGAAAGGG
15624129 AT
1 AT
15624131 TATTTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (32 bp):
ATGATTGACAAGTTTTTTTTTTTTTGAAAGGG
Found at i:15625951 original size:18 final size:18
Alignment explanation
Indices: 15625930--15625995 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
15625920 TATAAAATGA
15625930 AATAATTATTTCAAATAT
1 AATAATTATTTCAAATAT
**
15625948 AATAATTATTT-TTATAT
1 AATAATTATTTCAAATAT
** *
15625965 GTTAAATATTTCAAATAT
1 AATAATTATTTCAAATAT
* *
15625983 AATTATTTTTTCA
1 AATAATTATTTCA
15625996 TCTACATTAT
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
17 12 0.34
18 23 0.66
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (18 bp):
AATAATTATTTCAAATAT
Found at i:15626720 original size:4 final size:4
Alignment explanation
Indices: 15626711--15626737 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
15626701 CTCATATAAT
15626711 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
15626738 TAATAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:15629905 original size:27 final size:26
Alignment explanation
Indices: 15629857--15629907 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
15629847 TAGAATTAAT
*
15629857 TTGTTATTCATCATTTGCTTTGTATA
1 TTGTTAATCATCATTTGCTTTGTATA
15629883 TTGTTAATCAATCATATTG-TTTGTA
1 TTGTTAATC-ATCAT-TTGCTTTGTA
15629908 AGAATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.55
Consensus pattern (26 bp):
TTGTTAATCATCATTTGCTTTGTATA
Found at i:15643154 original size:44 final size:44
Alignment explanation
Indices: 15643043--15643527 Score: 252
Period size: 44 Copynumber: 10.8 Consensus size: 44
15643033 TGAAGCCAGA
* * *
15643043 AATCTTATCTCCCTGAGATTACAG-CGAGCAGACTGAAGCT--AG
1 AATCTTATCTCCCTGAGATTACAGTAGAGCAGA-TTAAGATAAAG
* * **
15643085 TAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAGATAAAG
1 -AATCTTATCTCCCTGAGATTACAGTAGAGCAGATTAAGATAAAG
* * *
15643130 GATCTTATCTCTCTGA-AGTTACAGT--AG-AG--T-AGAT--CG
1 AATCTTATCTCCCTGAGA-TTACAGTAGAGCAGATTAAGATAAAG
* * * *
15643166 CATCTTATCTCCTTGAGATTACAGCAGAGCAGATTAA-AGT-TAG
1 AATCTTATCTCCCTGAGATTACAGTAGAGCAGATTAAGA-TAAAG
* * *
15643209 TAATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG
1 -AATCTTATCTCCCTGAGATTACAGTAGAGCAGATTAAGATAAAG
* * * * *
15643254 GATCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAG
1 AATCTTATCTCCCTGAGA-TTACAGTAGAGCAGAT----TAAGA-T-AA---AG
* *
15643307 AAATCTTATCTCCCTGAGATTACAGTGGAGCAAATTAAGATAAAG
1 -AATCTTATCTCCCTGAGATTACAGTAGAGCAGATTAAGATAAAG
* * *
15643352 AATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCACCAGATTGAAGCCAG
1 AATCTTATCTCCCTGAGA-TTACAGTAGAGCAGAT--TA--AGA-T-AA---AG
** *
15643405 AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT--AG
1 -AATCTTATCTCCCTGAGATTACAGTAGAGCAGATT-AAGATAAAG
* * *
15643449 TAATCCTATCTCCCTGAGATTACAGTGGAGCAAATTAAGATAAAG
1 -AATCTTATCTCCCTGAGATTACAGTAGAGCAGATTAAGATAAAG
* *
15643494 AATCTTATCTCTCTGA-AGTTACAGTAGAGTAGAT
1 AATCTTATCTCCCTGAGA-TTACAGTAGAGCAGAT
15643528 CGCATCAGGT
Statistics
Matches: 340, Mismatches: 58, Indels: 87
0.70 0.12 0.18
Matches are distributed among these distances:
36 20 0.06
37 1 0.00
38 6 0.02
39 3 0.01
41 3 0.01
42 4 0.01
43 38 0.11
44 172 0.51
45 9 0.03
46 1 0.00
48 8 0.02
49 3 0.01
50 9 0.03
51 2 0.01
53 5 0.01
54 53 0.16
55 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTAGAGCAGATTAAGATAAAG
Found at i:15643188 original size:36 final size:36
Alignment explanation
Indices: 15643131--15643199 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
15643121 AAGATAAAGG
* *
15643131 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGC
1 ATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGC
15643167 ATCTTATCTC-CTTG-AGATTACAGCAGAGCAGAT
1 ATCTTATCTCTC-TGAAG-TTACAGCAGAGCAGAT
15643200 TAAAGTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 3 0.10
36 26 0.90
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (36 bp):
ATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGC
Found at i:15643219 original size:124 final size:123
Alignment explanation
Indices: 15643044--15643293 Score: 419
Period size: 124 Copynumber: 2.0 Consensus size: 123
15643034 GAAGCCAGAA
*
15643044 ATCTTATCTCCCTGAGATTACAGCGAGCAGACTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 ATCTTATCTCCCTGAGATTACAGCGAGCAGACTAAAGCTAGTAATCCTATCTCCCTGAGATTACA
* * *
15643109 GTGGAGTGGATTAAGATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGC
66 GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGC
* * * *
15643167 ATCTTATCTCCTTGAGATTACAGCAGAGCAGATTAAAGTTAGTAATCTTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGC-GAGCAGACTAAAGCTAGTAATCCTATCTCCCTGAGATTAC
15643232 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGC
65 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGC
15643291 ATC
1 ATC
15643294 AGATTGAAGC
Statistics
Matches: 118, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
123 23 0.19
124 95 0.81
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (123 bp):
ATCTTATCTCCCTGAGATTACAGCGAGCAGACTAAAGCTAGTAATCCTATCTCCCTGAGATTACA
GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGC
Found at i:15643364 original size:98 final size:98
Alignment explanation
Indices: 15643210--15643436 Score: 391
Period size: 98 Copynumber: 2.3 Consensus size: 98
15643200 TAAAGTTAGT
** *
15643210 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAAATTAAAATAAAGAATCTTATCTCTCTAAAGTTA
*
15643275 CAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
66 CAGTAGAGTAGATCGCACCAGATTGAAGCCAGA
* *
15643308 AATCTTATCTCCCTGAGATTACAGTGGAGCAAATTAAGATAAAGAATCTTATCTCTCTGAAGTTA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAAATTAAAATAAAGAATCTTATCTCTCTAAAGTTA
15643373 CAGTAGAGTAGATCGCACCAGATTGAAGCCAGA
66 CAGTAGAGTAGATCGCACCAGATTGAAGCCAGA
*
15643406 AATCTTATCTCCCTGAGATTACAGCGGAGCA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCA
15643437 GATTGAAGCT
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 122 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (98 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAAATTAAAATAAAGAATCTTATCTCTCTAAAGTTA
CAGTAGAGTAGATCGCACCAGATTGAAGCCAGA
Found at i:15643459 original size:98 final size:97
Alignment explanation
Indices: 15643210--15643474 Score: 381
Period size: 98 Copynumber: 2.7 Consensus size: 97
15643200 TAAAGTTAGT
* * * *
15643210 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAGAT-AAGAATCTTATCTCTCTGAAGTTA
*
15643275 CAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
65 CAGTAGAGTAGATCGCACCAGATTGAAGCCAGA
*
15643308 AATCTTATCTCCCTGAGATTACAGTGGAGCAAATTAAGATAAAGAATCTTATCTCTCTGAAGTTA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAGAT-AAGAATCTTATCTCTCTGAAGTTA
15643373 CAGTAGAGTAGATCGCACCAGATTGAAGCCAGA
65 CAGTAGAGTAGATCGCACCAGATTGAAGCCAGA
* * * *
15643406 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATCCTATCTCCCTG-AGAT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAGATAAG-AATCTTATCTCTCTGAAG-T
15643469 TACAGT
63 TACAGT
15643475 GGAGCAAATT
Statistics
Matches: 153, Mismatches: 11, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
97 4 0.03
98 145 0.95
99 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (97 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAGATAAGAATCTTATCTCTCTGAAGTTAC
AGTAGAGTAGATCGCACCAGATTGAAGCCAGA
Found at i:15648030 original size:17 final size:16
Alignment explanation
Indices: 15648002--15648048 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
15647992 TCAAAAAACA
15648002 TTTTTTC-TTTTTTCT
1 TTTTTTCATTTTTTCT
15648017 TTTTTTCATATTTTTCT
1 TTTTTTCAT-TTTTTCT
* *
15648034 ATTTTTCACTTTTTC
1 TTTTTTCATTTTTTC
15648049 GATCACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.25
16 7 0.25
17 14 0.50
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTCATTTTTTCT
Found at i:15649314 original size:16 final size:17
Alignment explanation
Indices: 15649281--15649314 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15649271 AGATTCGTCC
15649281 TCAAAACTTGTATTTGA
1 TCAAAACTTGTATTTGA
*
15649298 TCAAATCTTGT-TTTGA
1 TCAAAACTTGTATTTGA
15649314 T
1 T
15649315 TTGCTTGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TCAAAACTTGTATTTGA
Found at i:15655395 original size:50 final size:50
Alignment explanation
Indices: 15655327--15655566 Score: 246
Period size: 50 Copynumber: 4.7 Consensus size: 50
15655317 TTTTTTGTAC
* * * **
15655327 TGCCAATGCCATATCCCAGATATGGTGTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* ** * * *
15655377 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * * *
15655427 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * *
15655477 TGCCAATGCCATGTCCCAGACATGGTCTTATATGAGACATCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--TC---GG
* *
15655533 TGCCAATGCCATGTCTCAGGCATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
15655567 GGATCTTATT
Statistics
Matches: 157, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
50 124 0.79
53 2 0.01
56 31 0.20
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:15655520 original size:100 final size:102
Alignment explanation
Indices: 15655327--15655569 Score: 274
Period size: 100 Copynumber: 2.4 Consensus size: 102
15655317 TTTTTTGTAC
* * * * ** * *
15655327 TGCCAATGCCATATCCCAGATATGGTGTTACATGAGAGTTCTCATATCGGTGCCCATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAATGCCATGTC
* * * *
15655392 CCAGACATGGTCTTACGGGGGACCTCTC-ATCT-TGG
66 CCAGACATGGTCTTACAGGAGACATCTCAATCTATGA
* *
15655427 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAATGCCATGTC
* *
15655492 CCAGACATGGTCTTATATGAGACATCTCATAATCTCAATGA
66 CCAGACATGGTCTTACAGGAGACATCTC--AATCT--ATGA
* *
15655533 TGCCAATGCCATGTCTCAGGCATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
15655570 TCTTATTCCC
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
100 78 0.66
103 4 0.03
106 36 0.31
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (102 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAATGCCATGTC
CCAGACATGGTCTTACAGGAGACATCTCAATCTATGA
Found at i:15662539 original size:50 final size:50
Alignment explanation
Indices: 15662466--15662706 Score: 266
Period size: 50 Copynumber: 4.7 Consensus size: 50
15662456 TTCTGTACTA
* * * **
15662466 CCAATGCTATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * *** *
15662516 CCCATGCCATATCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * *
15662566 CCAAAGCCATGTCCCAGACATGGTGTTACATGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * * *
15662616 CCAACGCCATGTCCTAGACATGGTCTTACATGGGACATCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTG
15662672 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
15662707 TCTTATTCCC
Statistics
Matches: 161, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
50 123 0.76
53 2 0.01
56 36 0.22
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
Found at i:15665074 original size:19 final size:20
Alignment explanation
Indices: 15665033--15665071 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
15665023 CATAGTTCAA
15665033 TCCATCATTTCATGTTCCAT
1 TCCATCATTTCATGTTCCAT
15665053 TCCA-CATTTCAT-TTCCAT
1 TCCATCATTTCATGTTCCAT
15665071 T
1 T
15665072 TCCCAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 8 0.42
20 4 0.21
ACGTcount: A:0.21, C:0.31, G:0.03, T:0.46
Consensus pattern (20 bp):
TCCATCATTTCATGTTCCAT
Found at i:15667019 original size:20 final size:20
Alignment explanation
Indices: 15666994--15667052 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
15666984 ATGCATAATG
*
15666994 GAGGCACCGAAGTGCAGACA
1 GAGGCACCGAAGTGCAAACA
* *
15667014 GAGGCACCAAAGTGCAAATA
1 GAGGCACCGAAGTGCAAACA
*
15667034 GAGGCACCGAAGTGAAAAC
1 GAGGCACCGAAGTGCAAAC
15667053 CTGTACAAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.22, G:0.31, T:0.07
Consensus pattern (20 bp):
GAGGCACCGAAGTGCAAACA
Found at i:15670757 original size:16 final size:17
Alignment explanation
Indices: 15670726--15670763 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
15670716 ACAAAATCTG
15670726 AATTTATTTCCCAATTT
1 AATTTATTTCCCAATTT
15670743 AATTTATTT-CCAATTT
1 AATTTATTTCCCAATTT
15670759 -ATTTA
1 AATTTA
15670764 ATTGTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 7 0.33
17 9 0.43
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTATTTCCCAATTT
Found at i:15672157 original size:16 final size:16
Alignment explanation
Indices: 15672127--15672163 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
15672117 CAAAATCAAA
15672127 ATTTATTTCCCAATTT
1 ATTTATTTCCCAATTT
15672143 CATTTATTT-CCAATTT
1 -ATTTATTTCCCAATTT
15672159 ATTTA
1 ATTTA
15672164 ACTGTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTATTTCCCAATTT
Found at i:15682522 original size:18 final size:19
Alignment explanation
Indices: 15682487--15682528 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
15682477 CTCATTTTCT
*
15682487 TTTCTTTCTTCAATCTCAA
1 TTTCTTTCTTCAACCTCAA
15682506 TTTCTTT-TTCAACCTCAA
1 TTTCTTTCTTCAACCTCAA
15682524 TTTCT
1 TTTCT
15682529 CTCATACACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTCTTTCTTCAACCTCAA
Found at i:15685271 original size:23 final size:23
Alignment explanation
Indices: 15685245--15685313 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
15685235 CACAAAATAC
15685245 GCCACAAAAGCTTTATAGAACAT
1 GCCACAAAAGCTTTATAGAACAT
* *
15685268 GCCACAAAGGCTTTATTGAGTACA-
1 GCCACAAAAGCTTTA-T-AGAACAT
* *
15685292 -CCACAAAACCTTTAAAGAACAT
1 GCCACAAAAGCTTTATAGAACAT
15685314 TAAATGTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
21 5 0.14
23 26 0.70
24 1 0.03
25 5 0.14
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.22
Consensus pattern (23 bp):
GCCACAAAAGCTTTATAGAACAT
Found at i:15685635 original size:119 final size:119
Alignment explanation
Indices: 15685424--15685905 Score: 730
Period size: 119 Copynumber: 4.1 Consensus size: 119
15685414 CATCTTACTG
* * * *
15685424 GAGGCAACACCATGAATATTTTCATTGTCATATGATGTCATAGGTCTCTACCACATGGTTTTACA
1 GAGGCAACACCATGAATATTTTCATTATCATATGATGCCATGGGTCTCTACCACATGGTCTTACA
* ** *
15685489 CATATCTGTATGTTGTGATCTGCCAGTCCGGTTAGCAATGTACCTACCCTATCA
66 CATATCTGCATGTCATGATCTGCCAGTCCGGTTAGCAATGTACCTACCCTACCA
* * * *
15685543 GAGGCAACACCATGAACATTTTCATTGTCATATGATGTCATGGGTCTCTACCACGTGGTCTTACA
1 GAGGCAACACCATGAATATTTTCATTATCATATGATGCCATGGGTCTCTACCACATGGTCTTACA
* * * * *
15685608 CATATCTGCATGTTATGACCTGACAGTCCTGTTAGCAATGTACCTACCTTACCA
66 CATATCTGCATGTCATGATCTGCCAGTCCGGTTAGCAATGTACCTACCCTACCA
*
15685662 GAGGCAACACCATGAATATTTTCATTATCATATGATGCCATCGGTCTCTACCACATGGTCTTACA
1 GAGGCAACACCATGAATATTTTCATTATCATATGATGCCATGGGTCTCTACCACATGGTCTTACA
* * * *
15685727 AATATCTGCATGTCGTGATTTGCCAGTCCGGTTAGCAATGTACCTACCCTACCG
66 CATATCTGCATGTCATGATCTGCCAGTCCGGTTAGCAATGTACCTACCCTACCA
*
15685781 GAGGCAACACCATGAATATTTTCATTATCATATGATCCCATGGGTCTCTACCACATGGTCTTACA
1 GAGGCAACACCATGAATATTTTCATTATCATATGATGCCATGGGTCTCTACCACATGGTCTTACA
* * *
15685846 CATATCTACATGTCATGATCTGCCAGTCCGGTTAGCAATGTACCTGCCCTACCG
66 CATATCTGCATGTCATGATCTGCCAGTCCGGTTAGCAATGTACCTACCCTACCA
15685900 GAGGCA
1 GAGGCA
15685906 TCACAAATGG
Statistics
Matches: 331, Mismatches: 32, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
119 331 1.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (119 bp):
GAGGCAACACCATGAATATTTTCATTATCATATGATGCCATGGGTCTCTACCACATGGTCTTACA
CATATCTGCATGTCATGATCTGCCAGTCCGGTTAGCAATGTACCTACCCTACCA
Found at i:15686698 original size:25 final size:29
Alignment explanation
Indices: 15686660--15686713 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 29
15686650 TATAAAAGAG
15686660 AATCTGATGCAGATG-CT-T-GACCAATC
1 AATCTGATGCAGATGACTCTCGACCAATC
*
15686686 AATCT-ATTCAGATGACTCTCGACCAATC
1 AATCTGATGCAGATGACTCTCGACCAATC
15686714 GCATTACAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
26 7 0.29
27 1 0.04
28 8 0.33
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (29 bp):
AATCTGATGCAGATGACTCTCGACCAATC
Found at i:15687464 original size:21 final size:21
Alignment explanation
Indices: 15687427--15687466 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15687417 TTCAATTATT
15687427 TAATTAAAATCAATTAAATAA
1 TAATTAAAATCAATTAAATAA
*
15687448 TAATTCAAAA-CATTTAAAT
1 TAATT-AAAATCAATTAAAT
15687467 TAATTTCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATTAAAATCAATTAAATAA
Found at i:15690313 original size:50 final size:50
Alignment explanation
Indices: 15690249--15690381 Score: 151
Period size: 50 Copynumber: 2.7 Consensus size: 50
15690239 CAATGCTTTA
* * ** * *
15690249 TCCCAGATATGGTCTTACATGGAAGTTCTCATATTGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACAGGGAACCTCTCATATTGGTGCCAACGCCATG
* * *
15690299 TCCCAGACATGGTCTTACGGGGGACCTCTCATTTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACAGGGAACCTCTCATATTGGTGCCAACGCCATG
* *
15690349 TCCCGGACATGGTCTTAC-GTGGGACCTCTCATA
1 TCCCAGACATGGTCTTACAG-GGAACCTCTCATA
15690382 ACCTCAATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 1 0.01
50 70 0.99
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.29
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACAGGGAACCTCTCATATTGGTGCCAACGCCATG
Found at i:15690414 original size:56 final size:50
Alignment explanation
Indices: 15690286--15690428 Score: 151
Period size: 50 Copynumber: 2.7 Consensus size: 50
15690276 CTCATATTGG
* * * **
15690286 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATTTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATTATAA
* *
15690336 TGCCAACGCCATGTCCCGGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT----T--ATAA
* *
15690392 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGA
15690429 TCTCATCCCC
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 41 0.54
54 1 0.01
56 34 0.45
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATTATAA
Found at i:15693622 original size:52 final size:51
Alignment explanation
Indices: 15693493--15693624 Score: 185
Period size: 50 Copynumber: 2.6 Consensus size: 51
15693483 ATGTGTTCTG
* * * *
15693493 CATTTAATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTCTGCAT
* *
15693544 CA-TAAATTATGACATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAG-TTAAGTCTGCAT
*
15693595 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTATGTAACTC
15693625 ATTTATTCAT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 31 0.44
51 15 0.21
52 24 0.34
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTCTGCAT
Found at i:15695938 original size:18 final size:19
Alignment explanation
Indices: 15695901--15695954 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
15695891 AAAGCATGTC
15695901 AAAAAGAAAAAGA-AATTG
1 AAAAAGAAAAAGAGAATTG
15695919 AAAAAGAAAAAGAGAA-TG
1 AAAAAGAAAAAGAGAATTG
15695937 AAAGAGAGCAAAAAGAGA
1 AAA-A-AG-AAAAAGAGA
15695955 TTGTGAGCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 18 0.56
19 3 0.09
20 2 0.06
21 9 0.28
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.06
Consensus pattern (19 bp):
AAAAAGAAAAAGAGAATTG
Found at i:15695967 original size:17 final size:16
Alignment explanation
Indices: 15695942--15695988 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
15695932 GAATGAAAGA
*
15695942 GAGCAAAAAGAGATTGT
1 GAGCAAAAA-AGAATGT
*
15695959 GAGCGAAAAAGAATGT
1 GAGCAAAAAAGAATGT
15695975 GAGCAAGAAAAGAA
1 GAGCAA-AAAAGAA
15695989 AGCTGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.53, C:0.06, G:0.30, T:0.11
Consensus pattern (16 bp):
GAGCAAAAAAGAATGT
Found at i:15695977 original size:16 final size:16
Alignment explanation
Indices: 15695942--15695980 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
15695932 GAATGAAAGA
15695942 GAGCAAAAAGAGATTGT
1 GAGCAAAAAGA-ATTGT
15695959 GAGCGAAAAAGAA-TGT
1 GAGC-AAAAAGAATTGT
15695975 GAGCAA
1 GAGCAA
15695981 GAAAAGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 7 0.33
17 5 0.24
18 7 0.33
ACGTcount: A:0.49, C:0.08, G:0.31, T:0.13
Consensus pattern (16 bp):
GAGCAAAAAGAATTGT
Found at i:15700948 original size:23 final size:21
Alignment explanation
Indices: 15700922--15700975 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
15700912 TATATAAACT
*
15700922 TAATATTGTATTTATTAATTTTA
1 TAATATT-TATTT-TAAATTTTA
15700945 TAATTTATTTATTTTAAATTTTA
1 TAA--TATTTATTTTAAATTTTA
15700968 TAATATTT
1 TAATATTT
15700976 TTAAATGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 5 0.18
23 14 0.50
24 5 0.18
25 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TAATATTTATTTTAAATTTTA
Found at i:15700968 original size:16 final size:16
Alignment explanation
Indices: 15700931--15700965 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
15700921 TTAATATTGT
15700931 ATTTATTAATTTTATA
1 ATTTATTAATTTTATA
*
15700947 ATTTATTTATTTTA-A
1 ATTTATTAATTTTATA
15700962 ATTT
1 ATTT
15700966 TATAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTATTAATTTTATA
Found at i:15701584 original size:27 final size:27
Alignment explanation
Indices: 15701554--15701614 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
15701544 ATTTTTTTTG
*
15701554 AAAAAATGTAAATA-TTCATAAAATTCT
1 AAAAAAT-TAAAAATTTCATAAAATTCT
*
15701581 AAAAAATTAAAAATTTCCTAAAATTCT
1 AAAAAATTAAAAATTTCATAAAATTCT
15701608 AAAAAAT
1 AAAAAAT
15701615 ATATCTAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAAAATTAAAAATTTCATAAAATTCT
Found at i:15702867 original size:40 final size:40
Alignment explanation
Indices: 15702810--15702919 Score: 139
Period size: 40 Copynumber: 2.8 Consensus size: 40
15702800 GAATGATGGC
* * * * * *
15702810 ACATACATGTCCTTGTTTGTACTTTGGTACCTCTATTTGT
1 ACATACGTGTCCCTGTTTGTACTTCGGTACATCTAATTGA
15702850 ACATACGTGTCCCTGTTTGTACTTCGGTACATCTAATTGA
1 ACATACGTGTCCCTGTTTGTACTTCGGTACATCTAATTGA
* * *
15702890 ACATACGTGCCCCTATTTGTACTACGGTAC
1 ACATACGTGTCCCTGTTTGTACTTCGGTAC
15702920 CCCTTGTAAC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (40 bp):
ACATACGTGTCCCTGTTTGTACTTCGGTACATCTAATTGA
Found at i:15704982 original size:42 final size:41
Alignment explanation
Indices: 15704852--15704986 Score: 130
Period size: 41 Copynumber: 3.2 Consensus size: 41
15704842 TCCCGAACGT
*
15704852 GGTCTTACATGTAATCACATATCGATGCC-ACTGTCCCAGACAA
1 GGTCTTACACGTAA-CACA-ATCGATGCCAAC-GTCCCAGACAA
* ** * * *
15704895 TGTCTTACACAAAACA-AATACGATGCCAATGTCCCAGATAT
1 GGTCTTACACGTAACACAAT-CGATGCCAACGTCCCAGACAA
* *
15704936 GGTCTTACACGTAACACAAGTCGATGCCAACGTCCTAGACGA
1 GGTCTTACACGTAACACAA-TCGATGCCAACGTCCCAGACAA
15704978 GGTCTTACA
1 GGTCTTACA
15704987 TGATAACATA
Statistics
Matches: 73, Mismatches: 15, Indels: 9
0.75 0.15 0.09
Matches are distributed among these distances:
40 2 0.03
41 30 0.41
42 30 0.41
43 11 0.15
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (41 bp):
GGTCTTACACGTAACACAATCGATGCCAACGTCCCAGACAA
Found at i:15709659 original size:19 final size:19
Alignment explanation
Indices: 15709635--15709673 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
15709625 AATAAATTAC
15709635 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTGAGT
*
15709654 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTGAGT
15709673 T
1 T
15709674 GCTGGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (19 bp):
TCATCTTAGTTAATTGAGT
Done.