Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 88 of 175
Found at i:27950801 original size:33 final size:33
Alignment explanation
Indices: 27950755--27951067 Score: 156
Period size: 33 Copynumber: 8.7 Consensus size: 33
27950745 TTAACCGTTA
* *
27950755 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
27950789 TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGAT
1 TCGGGGAATCAGCACTTAGCAA---C---CAC---CAATGAT
27950831 AT-GGTGGAATCAGCACTTAGCAACCACCAATGAT
1 -TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
27950865 TCGGGGAATCAACACTTAGCAACC-CC-----T
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
* *
27950892 TGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGAT
1 TCGGGGAATCAGCACTTAGCAA-CCAC--CA-A--T---GAT
*
27950934 ACGGTGGAATCAGCACTTAGCAACCACCAATGGA-
1 TCGG-GGAATCAGCACTTAGCAACCACCAAT-GAT
* *
27950968 TAGGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGAT
1 TCGGGGAATCAGCACTTAGCAACCACC---A-A--T---GAT
* * * *
27951010 GCGGTGGAATCAACATTTAGCAACCACCAATGAA
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
27951044 TCGGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
27951068 CCTTCATATT
Statistics
Matches: 217, Mismatches: 24, Indels: 77
0.68 0.08 0.24
Matches are distributed among these distances:
27 21 0.10
28 2 0.01
29 1 0.00
31 1 0.00
32 2 0.01
33 77 0.35
34 19 0.09
35 2 0.01
36 2 0.01
37 6 0.03
39 6 0.03
40 4 0.02
41 2 0.01
42 15 0.07
43 57 0.26
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:27950957 original size:43 final size:42
Alignment explanation
Indices: 27950896--27951034 Score: 143
Period size: 43 Copynumber: 3.5 Consensus size: 42
27950886 ACCCCTTGGG
27950896 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCA-ATTTAAAGATACGGT
* *
27950939 GGAATCAGCACTTAGCAA-CCAC--CAA--T--GGATA-GG-
1 GGAATCAGCACTTAGCAACCCCCTTCAATTTAAAGATACGGT
* *
27950972 GGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATGCGGT
1 GGAATCAGCACTTAGCAACCCCCTTCA-ATTTAAAGATACGGT
* *
27951015 GGAATCAACATTTAGCAACC
1 GGAATCAGCACTTAGCAACC
27951035 ACCAATGAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
33 18 0.23
34 5 0.06
35 4 0.05
36 1 0.01
37 2 0.03
39 2 0.03
40 2 0.03
41 3 0.04
42 5 0.06
43 36 0.46
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCAATTTAAAGATACGGT
Found at i:27950974 original size:103 final size:103
Alignment explanation
Indices: 27950791--27950993 Score: 345
Period size: 103 Copynumber: 2.0 Consensus size: 103
27950781 CCAGTGATTC
* *
27950791 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
*
27950856 ACCAATGATTCGGGGAATCAACACTTAGCAACCCCTTG
66 ACCAATGATTAGGGGAATCAACACTTAGCAACCCCTTG
*
27950894 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
*
27950959 ACCAATGGA-TAGGGGAATCAGCACTTAGCAACCCC
66 ACCAAT-GATTAGGGGAATCAACACTTAGCAACCCC
27950994 CTTTATATTT
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 92 0.98
104 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATGATTAGGGGAATCAACACTTAGCAACCCCTTG
Found at i:27950989 original size:76 final size:76
Alignment explanation
Indices: 27950894--27951073 Score: 290
Period size: 76 Copynumber: 2.4 Consensus size: 76
27950884 CAACCCCTTG
*
27950894 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAACACTTAGCAACC
*
27950959 ACCAATGGATA
66 ACCAATGAATA
* * * *
27950970 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATGCGGTGGAATCAACATTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAACACTTAGCAACC
*
27951035 ACCAATGAATC
66 ACCAATGAATA
27951046 GGGGAATCAGCACTTAGCAA-CCCCTTCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCA
27951074 TATTCAATGT
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
75 7 0.07
76 89 0.93
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (76 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAACACTTAGCAACC
ACCAATGAATA
Found at i:27951427 original size:29 final size:30
Alignment explanation
Indices: 27951394--27951454 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
27951384 TAATCCACCA
*
27951394 CCCAACTTTTTG-AAAATTACAATATTGCC
1 CCCAAATTTTTGCAAAATTACAATATTGCC
* * *
27951423 CCCAAATTTTTGCATAATTACACTTTTGCC
1 CCCAAATTTTTGCAAAATTACAATATTGCC
27951453 CC
1 CC
27951455 AAGCTCGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.36
Consensus pattern (30 bp):
CCCAAATTTTTGCAAAATTACAATATTGCC
Found at i:27954689 original size:17 final size:18
Alignment explanation
Indices: 27954669--27954712 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
27954659 TATTAAATTA
*
27954669 TATAAGATATTAT-TTAT
1 TATAAAATATTATCTTAT
27954686 TATAAAATATTATCTTAT
1 TATAAAATATTATCTTAT
27954704 TATAAAATA
1 TATAAAATA
27954713 AAAATCGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TATAAAATATTATCTTAT
Found at i:27955005 original size:7 final size:7
Alignment explanation
Indices: 27954993--27955022 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
27954983 TTATTACATA
27954993 AAAAATG
1 AAAAATG
27955000 AAAAATG
1 AAAAATG
27955007 AAAAATG
1 AAAAATG
27955014 AAAAATG
1 AAAAATG
27955021 AA
1 AA
27955023 TATTTAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:27959554 original size:8 final size:8
Alignment explanation
Indices: 27959541--27959566 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
27959531 GCAAAATTAC
27959541 ATTTTAAA
1 ATTTTAAA
27959549 ATTTTAAA
1 ATTTTAAA
27959557 ATTTTAAA
1 ATTTTAAA
27959565 AT
1 AT
27959567 GGTCATAGGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTTAAA
Found at i:27960691 original size:15 final size:16
Alignment explanation
Indices: 27960658--27960693 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
27960648 GAATAATCAT
*
27960658 TATTTGGAACAATTTG
1 TATTTAGAACAATTTG
27960674 TATTTAGAACAA-TTG
1 TATTTAGAACAATTTG
27960689 TATTT
1 TATTT
27960694 TTTAGAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (16 bp):
TATTTAGAACAATTTG
Found at i:27960851 original size:17 final size:17
Alignment explanation
Indices: 27960826--27960861 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
27960816 AAGTCTAAAT
27960826 AACTATTATTCAAGAAC
1 AACTATTATTCAAGAAC
* *
27960843 AACTTTTATTTAAGAAC
1 AACTATTATTCAAGAAC
27960860 AA
1 AA
27960862 TCATCATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (17 bp):
AACTATTATTCAAGAAC
Found at i:27962933 original size:28 final size:27
Alignment explanation
Indices: 27962876--27962927 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
27962866 TACAAATGAT
*
27962876 CCAAAGAGAATATTCAAAGTAGCATTAA
1 CCAAAGAGAACATTCAAAG-AGCATTAA
*
27962904 CCAAAGATAACATTCAAA-AGCATT
1 CCAAAGAGAACATTCAAAGAGCATT
27962928 GTAACCTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
28 16 0.73
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (27 bp):
CCAAAGAGAACATTCAAAGAGCATTAA
Found at i:27965737 original size:21 final size:21
Alignment explanation
Indices: 27965713--27965752 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27965703 TTAGGATGGA
*
27965713 TGTTTTAGCATGTTTTGAGCT
1 TGTTTAAGCATGTTTTGAGCT
*
27965734 TGTTTAATCATGTTTTGAG
1 TGTTTAAGCATGTTTTGAG
27965753 TAGGTATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.23, T:0.53
Consensus pattern (21 bp):
TGTTTAAGCATGTTTTGAGCT
Found at i:27965762 original size:21 final size:21
Alignment explanation
Indices: 27965721--27965762 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
27965711 GATGTTTTAG
* *
27965721 CATGTTTTGAGCTTGTTTAAT
1 CATGTTTTGAGCTGGTATAAT
27965742 CATGTTTTGAG-TAGGTATAAT
1 CATGTTTTGAGCT-GGTATAAT
27965763 TGATGGTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (21 bp):
CATGTTTTGAGCTGGTATAAT
Found at i:27972772 original size:13 final size:13
Alignment explanation
Indices: 27972754--27972788 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
27972744 CGTGTGACAC
27972754 ACATGGCCACCCT
1 ACATGGCCACCCT
27972767 ACATGGCCACCCT
1 ACATGGCCACCCT
27972780 ACATGGCCA
1 ACATGGCCA
27972789 TGTGTCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.43, G:0.17, T:0.14
Consensus pattern (13 bp):
ACATGGCCACCCT
Found at i:27981202 original size:44 final size:39
Alignment explanation
Indices: 27981105--27981184 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
27981095 TTGATATAAC
27981105 TTATCGAGATCTCTTATTTTCACTATTTTAATATTCAAT
1 TTATCGAGATCTCTTATTTTCACTATTTTAATATTCAAT
27981144 TTATCGAGATCTCTTATTTTCACTATTTTAATATTCAAT
1 TTATCGAGATCTCTTATTTTCACTATTTTAATATTCAAT
27981183 TT
1 TT
27981185 CAGGTATCAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.53
Consensus pattern (39 bp):
TTATCGAGATCTCTTATTTTCACTATTTTAATATTCAAT
Found at i:27990060 original size:27 final size:27
Alignment explanation
Indices: 27990011--27990067 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 27
27990001 AATAAACACT
27990011 AAAAAATAATTTTAAAAATAAAAAATA
1 AAAAAATAATTTTAAAAATAAAAAATA
*
27990038 AAAAAAT-ATTTTAAAATTAAAAAATA
1 AAAAAATAATTTTAAAAATAAAAAATA
27990064 AAAA
1 AAAA
27990068 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (27 bp):
AAAAAATAATTTTAAAAATAAAAAATA
Found at i:27996486 original size:28 final size:27
Alignment explanation
Indices: 27996419--27996486 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
27996409 TTATAGCATG
* *
27996419 TTTATTTTTATTTTAAAAATAGGAATTTT
1 TTTA-TTTT-TTTTAAAAATAGGAAATTA
*
27996448 TTGTATTTTTTTTAAACATAGGAAATTA
1 TT-TATTTTTTTTAAAAATAGGAAATTA
*
27996476 TTTATTATTTT
1 TTTATTTTTTT
27996487 ATTAGTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 8 0.24
28 18 0.53
29 6 0.18
30 2 0.06
ACGTcount: A:0.32, C:0.01, G:0.07, T:0.59
Consensus pattern (27 bp):
TTTATTTTTTTTAAAAATAGGAAATTA
Found at i:28000613 original size:44 final size:41
Alignment explanation
Indices: 28000565--28000663 Score: 92
Period size: 44 Copynumber: 2.3 Consensus size: 41
28000555 AGTATTATAT
28000565 ATTATGATTTTAGTAAATTCATATAAGAATAAGAATT-TTATTAA
1 ATTAT-ATTTTAGTAAATT-ATAT-AGAATAAGAATTATT-TTAA
* ** *
28000609 ATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAA
1 A-T-TATATT-TTAGTAAATTATATAGAATAAGAATTATTTTAA
28000653 ATTATATTTTA
1 ATTATATTTTA
28000664 CAGCTTGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
41 3 0.06
42 6 0.13
43 1 0.02
44 15 0.32
45 10 0.21
46 12 0.26
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (41 bp):
ATTATATTTTAGTAAATTATATAGAATAAGAATTATTTTAA
Found at i:28000652 original size:26 final size:28
Alignment explanation
Indices: 28000598--28000661 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
28000588 TAAGAATAAG
* * *
28000598 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
28000626 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
28000652 AATTATATTT
1 AATTATATTT
28000662 TACAGCTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:28002720 original size:2 final size:2
Alignment explanation
Indices: 28002713--28002741 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28002703 CGGATATGTA
28002713 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
28002742 CTGTACAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:28003039 original size:29 final size:29
Alignment explanation
Indices: 28003001--28003127 Score: 123
Period size: 29 Copynumber: 4.1 Consensus size: 29
28002991 GGACTATATA
28003001 AATCGATAATGATTGAAATACATCAAAAT
1 AATCGATAATGATTGAAATACATCAAAAT
28003030 AATCGATAATGATTGAAATACATCAAAAT
1 AATCGATAATGATTGAAATACATCAAAAT
* * * *
28003059 ACATC-AAAATGAAATTAAAATA-TTAAAATTTATAT
1 A-ATCGATAATG--ATTGAAATACAT-CAA---A-AT
28003094 AAATCGATAATGATTGAAATACATCAAAAT
1 -AATCGATAATGATTGAAATACATCAAAAT
28003124 AATC
1 AATC
28003128 TAAAAATATT
Statistics
Matches: 79, Mismatches: 8, Indels: 22
0.72 0.07 0.20
Matches are distributed among these distances:
29 39 0.49
30 6 0.08
31 11 0.14
34 11 0.14
35 6 0.08
36 6 0.08
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (29 bp):
AATCGATAATGATTGAAATACATCAAAAT
Found at i:28005627 original size:117 final size:117
Alignment explanation
Indices: 28005503--28005845 Score: 643
Period size: 117 Copynumber: 2.9 Consensus size: 117
28005493 AAGTAGATTA
28005503 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
28005568 TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
66 TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
* * *
28005620 TAAATTATATTTTATAACAATTATGTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
28005685 TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
66 TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
*
28005737 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTATCATATATTATGATTTTATTAG
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
28005802 TAAATTCATATAAGAATATTTATTAA-AATTTTATTAAATTATAT
66 TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATAT
28005846 TTTATAACAA
Statistics
Matches: 219, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
116 18 0.08
117 201 0.92
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (117 bp):
TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
Found at i:28005634 original size:15 final size:17
Alignment explanation
Indices: 28005596--28005629 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28005586 TTTATTAACA
28005596 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
28005613 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
28005630 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:28005643 original size:16 final size:15
Alignment explanation
Indices: 28005596--28005643 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
28005586 TTTATTAACA
*
28005596 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
28005613 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
28005628 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
28005644 GTTAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:28005733 original size:17 final size:17
Alignment explanation
Indices: 28005713--28005746 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28005703 TTTATTAACA
28005713 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
28005730 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
28005747 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:28006037 original size:39 final size:41
Alignment explanation
Indices: 28005992--28006097 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
28005982 TTTCCTTATG
*
28005992 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACACCTCTATTCCATTCAACCAAACAAAAGAATTAC
*
28006032 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACACCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
28006077 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
28006098 ACGCATCTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.34
45 5 0.09
46 13 0.23
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.29
Consensus pattern (41 bp):
CTATTACACCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:28006072 original size:44 final size:46
Alignment explanation
Indices: 28006009--28006099 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
28005999 ACCTCTATTC
* *
28006009 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCCATTA
28006053 CATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCCATTA
28006099 C
1 C
28006100 GCATCTATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 19 0.44
45 4 0.09
46 20 0.47
ACGTcount: A:0.40, C:0.31, G:0.03, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCCATTA
Found at i:28006106 original size:16 final size:16
Alignment explanation
Indices: 28006087--28006131 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
28006077 CTATTACACC
28006087 TCTATTCCATTACGCA
1 TCTATTCCATTACGCA
*
28006103 TCTATTCCATTACGCC
1 TCTATTCCATTACGCA
*
28006119 TCTATTCTATTAC
1 TCTATTCCATTAC
28006132 AGCGAACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.22, C:0.31, G:0.04, T:0.42
Consensus pattern (16 bp):
TCTATTCCATTACGCA
Found at i:28029719 original size:20 final size:20
Alignment explanation
Indices: 28029694--28029731 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28029684 CATATGCATC
*
28029694 AACATTTTCATAAAATTATG
1 AACATTTCCATAAAATTATG
*
28029714 AACATTTCCATTAAATTA
1 AACATTTCCATAAAATTA
28029732 CCATTCTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
AACATTTCCATAAAATTATG
Found at i:28031044 original size:21 final size:21
Alignment explanation
Indices: 28031018--28031076 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
28031008 TTAGGGTGGA
*
28031018 TCAGCTCTTACGAGCTTCTAT
1 TCAGCTCTTATGAGCTTCTAT
*
28031039 TCAGCTCTTTTGAGCTTCTAT
1 TCAGCTCTTATGAGCTTCTAT
*
28031060 TTAGCTCTTATGAGCTT
1 TCAGCTCTTATGAGCTT
28031077 TCGTTGGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.44
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTAT
Found at i:28031829 original size:12 final size:13
Alignment explanation
Indices: 28031805--28031833 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28031795 GATTAATATC
28031805 ATTTTGAATTGGT
1 ATTTTGAATTGGT
28031818 ATTTTG-ATTGGT
1 ATTTTGAATTGGT
28031830 ATTT
1 ATTT
28031834 GAGTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (13 bp):
ATTTTGAATTGGT
Found at i:28043407 original size:15 final size:15
Alignment explanation
Indices: 28043387--28043417 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28043377 GTCATGTAAG
28043387 TGAAAGGTCAAAAGT
1 TGAAAGGTCAAAAGT
28043402 TGAAAGGTCAAAAGT
1 TGAAAGGTCAAAAGT
28043417 T
1 T
28043418 ATGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAAAGT
Found at i:28047724 original size:15 final size:15
Alignment explanation
Indices: 28047706--28047734 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28047696 GTTATGTAAG
28047706 TGAAAGGTCAAGAGC
1 TGAAAGGTCAAGAGC
28047721 TGAAAGGTCAAGAG
1 TGAAAGGTCAAGAG
28047735 TTATGTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.10, G:0.34, T:0.14
Consensus pattern (15 bp):
TGAAAGGTCAAGAGC
Found at i:28053795 original size:42 final size:42
Alignment explanation
Indices: 28053701--28053802 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 42
28053691 GTACATATCT
* *
28053701 TTTACTTTCTTTATTAAAGAGATAATTTTTTAAAATTTATAAA
1 TTTACTTTATATATTAAAGAGATAATTTTTT-AAATTTATAAA
28053744 TTTACTTTATATATTAAAGAGATAATTTTTT-AATTTATAAA
1 TTTACTTTATATATTAAAGAGATAATTTTTTAAATTTATAAA
28053785 -TTACTCTTTATATATTAA
1 TTTA--CTTTATATATTAA
28053803 TTATATACAT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
40 3 0.05
41 10 0.18
42 13 0.24
43 29 0.53
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (42 bp):
TTTACTTTATATATTAAAGAGATAATTTTTTAAATTTATAAA
Found at i:28054733 original size:18 final size:15
Alignment explanation
Indices: 28054702--28054750 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
28054692 AATACAATAG
28054702 AAAAAAGATAAGTAA
1 AAAAAAGATAAGTAA
28054717 TAAAAAAGATTATAGT-A
1 -AAAAAAGA-TA-AGTAA
*
28054734 AAAAAACATAAGTAA
1 AAAAAAGATAAGTAA
28054749 AA
1 AA
28054751 GTTTAAGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 3 0.10
15 5 0.17
16 15 0.52
17 3 0.10
18 3 0.10
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.18
Consensus pattern (15 bp):
AAAAAAGATAAGTAA
Found at i:28054735 original size:15 final size:15
Alignment explanation
Indices: 28054697--28054738 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
28054687 TCGACAATAC
28054697 AATAG-AAAAAAGAT
1 AATAGTAAAAAAGAT
*
28054711 AAGTAATAAAAAAGAT
1 AA-TAGTAAAAAAGAT
*
28054727 TATAGTAAAAAA
1 AATAGTAAAAAA
28054739 ACATAAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (15 bp):
AATAGTAAAAAAGAT
Found at i:28059310 original size:14 final size:14
Alignment explanation
Indices: 28059293--28059326 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28059283 TGGAGGACCG
28059293 GAGGTGGATCGGTA
1 GAGGTGGATCGGTA
* *
28059307 GAGGTGGATTGGTG
1 GAGGTGGATCGGTA
28059321 GAGGTG
1 GAGGTG
28059327 AAGGTTGATT
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:0.18, C:0.03, G:0.56, T:0.24
Consensus pattern (14 bp):
GAGGTGGATCGGTA
Found at i:28064568 original size:50 final size:50
Alignment explanation
Indices: 28064486--28064728 Score: 369
Period size: 50 Copynumber: 4.8 Consensus size: 50
28064476 ATTTGGGTAA
*
28064486 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
28064536 AGAGGTACCATGTAAGACCATGTTTGGCACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
28064586 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * *
28064636 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
28064686 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
28064729 TGTTATTATC
Statistics
Matches: 174, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 140 0.80
51 34 0.20
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:28066499 original size:27 final size:27
Alignment explanation
Indices: 28066457--28066524 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
28066447 AACACACTAG
*
28066457 GAAAGGAATGCTTTTGTGGCAATACAT
1 GAAAGGAATGCCTTTGTGGCAATACAT
*
28066484 GAAAGGAATGCCTTTGTGGTAATACAT
1 GAAAGGAATGCCTTTGTGGCAATACAT
*
28066511 GAAAGGAGTGCCTT
1 GAAAGGAATGCCTT
28066525 CATGGCGGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
GAAAGGAATGCCTTTGTGGCAATACAT
Found at i:28069092 original size:27 final size:27
Alignment explanation
Indices: 28069058--28069235 Score: 173
Period size: 27 Copynumber: 6.6 Consensus size: 27
28069048 TAAACTGTAC
28069058 AGCACTAAGTGTGCGATATGACTATGT
1 AGCACTAAGTGTGCGATATGACTATGT
* * *
28069085 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATATGACTATGT
* *
28069111 ATGCACTAAGTGTGCGAAATGA-TCATGC
1 A-GCACTAAGTGTGCGATATGACT-ATGT
* *
28069139 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TATGACTATGT
* * *
28069167 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATATGACTATGT
* * *
28069194 GGCACTAAGTGTGCGAGT-TGATTATAT
1 AGCACTAAGTGTGCGA-TATGACTATGT
*
28069221 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28069236 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.01
27 105 0.81
28 22 0.17
29 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATATGACTATGT
Found at i:28069173 original size:82 final size:81
Alignment explanation
Indices: 28069059--28069209 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 81
28069049 AAACTGTACA
* *
28069059 GCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
28069123 TGCGAAATGATCATGCG
65 TGCGAAATGATCATGCG
* ** *
28069140 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
28069205 TGCGA
65 TGCGA
28069210 GTTGATTATA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAAATGATCATGCG
Found at i:28069226 original size:82 final size:81
Alignment explanation
Indices: 28069055--28069235 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
28069045 GATTAAACTG
* *
28069055 TACAGCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28069120 GTGTGCGAAATGATCA
66 GTGTGCGAAATGATCA
* * * ** *
28069136 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
** *
28069200 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAAATGATCA
* *
28069218 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28069236 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAAATGATCA
Found at i:28076917 original size:27 final size:27
Alignment explanation
Indices: 28076883--28077060 Score: 164
Period size: 27 Copynumber: 6.6 Consensus size: 27
28076873 TAAACTGTAC
28076883 AGCACTAAGTGTGCGATATGACTATGT
1 AGCACTAAGTGTGCGATATGACTATGT
* * *
28076910 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATATGACTATGT
* *
28076936 ATGCACTAAGTGTGCGAAATGA-TCATGC
1 A-GCACTAAGTGTGCGATATGACT-ATGT
* * *
28076964 GGCACTAAGTGTGTGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TATGACTATGT
* * *
28076992 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATATGACTATGT
* * *
28077019 GGCACTAAGTGTGCGAGT-TGATTATAT
1 AGCACTAAGTGTGCGA-TATGACTATGT
*
28077046 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28077061 GGCTCAATAT
Statistics
Matches: 127, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.01
27 104 0.82
28 21 0.17
29 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATATGACTATGT
Found at i:28076997 original size:82 final size:81
Alignment explanation
Indices: 28076884--28077034 Score: 214
Period size: 82 Copynumber: 1.9 Consensus size: 81
28076874 AAACTGTACA
* *
28076884 GCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
28076948 TGCGAAATGATCATGCG
65 TGCGAAATGATCATGCG
* * ** *
28076965 GCACTAAGTGTGTGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
28077030 TGCGA
65 TGCGA
28077035 GTTGATTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 15 0.25
82 46 0.75
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAAATGATCATGCG
Found at i:28077051 original size:82 final size:81
Alignment explanation
Indices: 28076880--28077060 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
28076870 GATTAAACTG
* *
28076880 TACAGCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28076945 GTGTGCGAAATGATCA
66 GTGTGCGAAATGATCA
* * * * ** *
28076961 TGCGGCACTAAGTGTGTGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
** *
28077025 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAAATGATCA
* *
28077043 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28077061 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
81 17 0.21
82 64 0.79
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAAATGATCA
Found at i:28092144 original size:43 final size:42
Alignment explanation
Indices: 28092097--28092191 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
28092087 AGATGTGGTT
* *
28092097 TTACATGTAATCAAATA-ACGATGCCACTATCCCAGACAGGGTC
1 TTACACGTAATCAAATACA-G-TGCCAATATCCCAGACAGGGTC
* * * *
28092140 TTACACGTAATCATATACAGTGCCAATGTCCCAGACATGTTC
1 TTACACGTAATCAAATACAGTGCCAATATCCCAGACAGGGTC
28092182 TTACACGTAA
1 TTACACGTAA
28092192 ATCTCAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 28 0.62
43 16 0.36
44 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (42 bp):
TTACACGTAATCAAATACAGTGCCAATATCCCAGACAGGGTC
Found at i:28094172 original size:27 final size:27
Alignment explanation
Indices: 28094153--28094298 Score: 211
Period size: 27 Copynumber: 5.4 Consensus size: 27
28094143 GGGTATAACA
*
28094153 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28094180 CTCATTTTACCCTATGGAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28094207 GTCATTTTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28094234 GTCATTTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
** * *
28094261 GTCATTTTATTCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
28094288 GTCATTTTACC
1 GTCATTTTACC
28094299 TATTTTGGGG
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 106 1.00
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:28103774 original size:103 final size:103
Alignment explanation
Indices: 28103595--28103798 Score: 329
Period size: 103 Copynumber: 2.0 Consensus size: 103
28103585 TCGTCTCATA
* * * *
28103595 TTTATCCTTGATGCTCAAAAACCCTAGTGTCCCCTCCACAAGGCCTACAGCTTCGGACACTATGG
1 TTTATCCTTGATGCTCAAAAACCCTAGTGTCCCCTCCACAAGGCCCACAGCTTCGCACACCATGA
**
28103660 TTTGCTCTCAGCAACATTGGATGGTAGAATCTTAACGG
66 TTTGCTCTCAGCAACATCAGATGGTAGAATCTTAACGG
28103698 TTTATCCTTGATGCTCAAAAACCCTAGTGTCCCCTCCACAAGGCCCACAGCTTCGCACACCACT-
1 TTTATCCTTGATGCTCAAAAACCCTAGTGTCCCCTCCACAAGGCCCACAGCTTCGCACACCA-TG
*
28103762 ATTTGTTCTCAGCAACATCAGATGGTAGAATCTTAAC
65 ATTTGCTCTCAGCAACATCAGATGGTAGAATCTTAAC
28103799 AGAAATTCCA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 92 0.99
104 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.27
Consensus pattern (103 bp):
TTTATCCTTGATGCTCAAAAACCCTAGTGTCCCCTCCACAAGGCCCACAGCTTCGCACACCATGA
TTTGCTCTCAGCAACATCAGATGGTAGAATCTTAACGG
Found at i:28105320 original size:32 final size:32
Alignment explanation
Indices: 28105279--28105344 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
28105269 AGAAGAAGAT
*
28105279 AAATCTTGGGTTGTTTGAATTATCCTGAAAAA
1 AAATCTTGGGCTGTTTGAATTATCCTGAAAAA
28105311 AAATCTTGGGCTGTTTGAATTATCCTGAAAAA
1 AAATCTTGGGCTGTTTGAATTATCCTGAAAAA
28105343 AA
1 AA
28105345 GAATAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (32 bp):
AAATCTTGGGCTGTTTGAATTATCCTGAAAAA
Found at i:28106727 original size:27 final size:27
Alignment explanation
Indices: 28106697--28106748 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
28106687 AATGACCCTG
*
28106697 GTCTCAACGATAATCTAAATGGTCATA
1 GTCTCAACGATAATCCAAATGGTCATA
* *
28106724 GTCTTAATGATAATCCAAATGGTCA
1 GTCTCAACGATAATCCAAATGGTCA
28106749 GAATGTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (27 bp):
GTCTCAACGATAATCCAAATGGTCATA
Found at i:28106757 original size:27 final size:27
Alignment explanation
Indices: 28106705--28106758 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28106695 TGGTCTCAAC
* * *
28106705 GATAATCTAAATGGTCATAGTCTTAAT
1 GATAATCCAAATGGTCAGAATCTTAAT
*
28106732 GATAATCCAAATGGTCAGAATGTTAAT
1 GATAATCCAAATGGTCAGAATCTTAAT
28106759 TCTCCTATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (27 bp):
GATAATCCAAATGGTCAGAATCTTAAT
Found at i:28112386 original size:27 final size:26
Alignment explanation
Indices: 28112348--28112621 Score: 280
Period size: 27 Copynumber: 10.2 Consensus size: 26
28112338 AGGTCGATAT
* *
28112348 ATGACCGAAATACCCCTATTGGGTAAA
1 ATGACCGAAATACCCCGA-AGGGTAAA
* *
28112375 ATGACCGAAATACCCCTATTGGGTAAA
1 ATGACCGAAATACCCCGA-AGGGTAAA
28112402 ATGACCGAAATACCCCCGAAGGGTAAA
1 ATGACCGAAATA-CCCCGAAGGGTAAA
**
28112429 ATGACCGAAATACCTTTGAAGGGTAAA
1 ATGACCGAAATACC-CCGAAGGGTAAA
**
28112456 ATGACTAAAATACCCTCGAAGGGTAAA
1 ATGACCGAAATACCC-CGAAGGGTAAA
* * *
28112483 ATAACCAAAATACCCTCGAGGGGTAAA
1 ATGACCGAAATACCC-CGAAGGGTAAA
* *
28112510 ATGATC-AAATTACCCTCGAAAGGTAAA
1 ATGACCGAAA-TACCC-CGAAGGGTAAA
**
28112537 ATGACTAAAATACCCTCGAAGGGTAAA
1 ATGACCGAAATACCC-CGAAGGGTAAA
**
28112564 ATGACTAAAATACCCTCGAAGGGTAAA
1 ATGACCGAAATACCC-CGAAGGGTAAA
*
28112591 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCGA-AGGGTAAA
28112618 ATGA
1 ATGA
28112622 TTGATATACC
Statistics
Matches: 220, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
26 7 0.03
27 205 0.93
28 8 0.04
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (26 bp):
ATGACCGAAATACCCCGAAGGGTAAA
Found at i:28112483 original size:81 final size:81
Alignment explanation
Indices: 28112348--28112621 Score: 340
Period size: 81 Copynumber: 3.4 Consensus size: 81
28112338 AGGTCGATAT
* * ** * * *
28112348 ATGACCGAAATACCC-CTATTGGGTAAAATGACCGAAATACCC-CTATTGGGTAAAATGACCGAA
1 ATGACCGAAATACCCTCGA-AGGGTAAAATGACTAAAATACCCTCGA-AGGGTAAAATGACCAAA
*
28112411 ATACCCCCGAAGGGTAAA
64 ATACCCTCGAAGGGTAAA
* * *
28112429 ATGACCGAAATACCTTTGAAGGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATAACCAAAAT
1 ATGACCGAAATACCCTCGAAGGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCAAAAT
*
28112494 ACCCTCGAGGGGTAAA
66 ACCCTCGAAGGGTAAA
* * *
28112510 ATGATC-AAATTACCCTCGAAAGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACTAAAA
1 ATGACCGAAA-TACCCTCGAAGGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCAAAA
28112574 TACCCTCGAAGGGTAAA
65 TACCCTCGAAGGGTAAA
*
28112591 ATGACCGAAATACCC-CCATAGGGTAAAATGA
1 ATGACCGAAATACCCTCGA-AGGGTAAAATGA
28112622 TTGATATACC
Statistics
Matches: 166, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
80 5 0.03
81 155 0.93
82 6 0.04
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (81 bp):
ATGACCGAAATACCCTCGAAGGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCAAAAT
ACCCTCGAAGGGTAAA
Found at i:28112632 original size:54 final size:53
Alignment explanation
Indices: 28112368--28112621 Score: 312
Period size: 54 Copynumber: 4.7 Consensus size: 53
28112358 TACCCCTATT
* * ** *
28112368 GGGTAAAATGACCGAAATACCCCTATTGGGTAAAATGACCGAAATACCCCCGAA
1 GGGTAAAATGACCGAAATACCCCGA-AGGGTAAAATGACTAAAATACCCTCGAA
**
28112422 GGGTAAAATGACCGAAATACCTTTGAAGGGTAAAATGACTAAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACC-CCGAAGGGTAAAATGACTAAAATACCCTCGAA
* * * *
28112476 GGGTAAAATAACCAAAATACCCTCGAGGGGTAAAATGA-TCAAATTACCCTCGAA
1 GGGTAAAATGACCGAAATACCC-CGAAGGGTAAAATGACT-AAAATACCCTCGAA
* **
28112530 AGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACTAAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCC-CGAAGGGTAAAATGACTAAAATACCCTCGAA
*
28112584 GGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGA
1 GGGTAAAATGACCGAAATACCCCGA-AGGGTAAAATGA
28112622 TTGATATACC
Statistics
Matches: 173, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
53 3 0.02
54 168 0.97
55 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (53 bp):
GGGTAAAATGACCGAAATACCCCGAAGGGTAAAATGACTAAAATACCCTCGAA
Found at i:28112999 original size:28 final size:29
Alignment explanation
Indices: 28112959--28113045 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 29
28112949 CATTGTACTG
*
28112959 ATTACTATATTGGGCTAAGGCCGA-A-ACT
1 ATTACTGTATTGGGCTAAGGCC-ACACACT
* *
28112987 ATTACTGTATTGGGCTACGACTCACACACT
1 ATTACTGTATTGGGCTAAGGC-CACACACT
* *
28113017 GTTACTGTAATGGGCTAAGGCC-CACACT
1 ATTACTGTATTGGGCTAAGGCCACACACT
28113045 A
1 A
28113046 CACTGATACT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 25 0.52
29 3 0.06
30 20 0.42
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (29 bp):
ATTACTGTATTGGGCTAAGGCCACACACT
Found at i:28113043 original size:30 final size:30
Alignment explanation
Indices: 28112955--28113043 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
28112945 ACTGCATTGT
* *
28112955 ACTGATTACTATATTGGGCTAAGGCCGA-A-
1 ACTG-TTACTGTATTGGGCTAAGGCCCACAC
* * * *
28112984 ACTATTACTGTATTGGGCTACGACTCACAC
1 ACTGTTACTGTATTGGGCTAAGGCCCACAC
*
28113014 ACTGTTACTGTAATGGGCTAAGGCCCACAC
1 ACTGTTACTGTATTGGGCTAAGGCCCACAC
28113044 TACACTGATA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 18 0.38
29 4 0.09
30 25 0.53
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (30 bp):
ACTGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:28114380 original size:43 final size:43
Alignment explanation
Indices: 28114277--28114501 Score: 335
Period size: 43 Copynumber: 5.3 Consensus size: 43
28114267 TTATAGAAAT
* * *
28114277 AAATGCCACTAAAGGTCATGTTCTTTAGCGGCGC-TTTCACAA
1 AAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCAC
28114319 AAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCAC
1 AAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCAC
* *
28114362 AAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGGTTTTCCTAC
1 AAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCAC
* *
28114405 AAATGCCGCTAAAGGTCATGTTCTTTAACGGCGCTATTCCCAC
1 AAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCAC
* * * *
28114448 AAACGCCGCTAAAGGTCATGTTCTCTCGCGGCGCTTTTTCCAC
1 AAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCAC
*
28114491 AAACGCCGCTA
1 AAATGCCGCTA
28114502 TTGTTTGGTG
Statistics
Matches: 167, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 33 0.20
43 134 0.80
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (43 bp):
AAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCAC
Found at i:28115234 original size:8 final size:8
Alignment explanation
Indices: 28115218--28115248 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
28115208 ATTCGGGCCT
*
28115218 ACAATGCA
1 ACAAGGCA
28115226 ACAAGGCA
1 ACAAGGCA
28115234 ACAAGGCA
1 ACAAGGCA
28115242 ACAAGGC
1 ACAAGGC
28115249 CTTCATGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.48, C:0.26, G:0.23, T:0.03
Consensus pattern (8 bp):
ACAAGGCA
Found at i:28118488 original size:17 final size:16
Alignment explanation
Indices: 28118450--28118505 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
28118440 ACCGTTGAAA
28118450 CCCTAAAT-CCCTAAC
1 CCCTAAATCCCCTAAC
**
28118465 CTTTAAATCCCCATAAC
1 CCCTAAATCCCC-TAAC
28118482 CCCTAAATCCCCCTAAC
1 CCCTAAAT-CCCCTAAC
28118499 CCCTAAA
1 CCCTAAA
28118506 GCATAGCCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.18
16 3 0.09
17 21 0.62
18 4 0.12
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (16 bp):
CCCTAAATCCCCTAAC
Found at i:28118540 original size:21 final size:21
Alignment explanation
Indices: 28118491--28118547 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
28118481 CCCCTAAATC
*
28118491 CCCCTAACCCCTAAAGCATAG
1 CCCCTAACCCCTAAAGCATAA
**
28118512 CCTTTAACCCCTAAAGCATAA
1 CCCCTAACCCCTAAAGCATAA
*
28118533 CCCCTAACCCTTAAA
1 CCCCTAACCCCTAAA
28118548 CCTTAAATCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.40, G:0.05, T:0.19
Consensus pattern (21 bp):
CCCCTAACCCCTAAAGCATAA
Found at i:28119122 original size:41 final size:40
Alignment explanation
Indices: 28119057--28119297 Score: 331
Period size: 41 Copynumber: 5.9 Consensus size: 40
28119047 TTTTTTTATT
28119057 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTT-TCAAAAACGCCGCTAAAGGCCCGAGC
* *
28119098 ATTAGCGGCGCTATTTCAACAACGCCACTAAAGGCCCGAGC
1 ATTAGCGGCGCT-TTTCAAAAACGCCGCTAAAGGCCCGAGC
* **
28119139 ATTAGCGGCGCTTTTTC-AAAACGCCACTAAAGGAACGAGC
1 ATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCCGAGC
*
28119179 ATTAGCGGCGCATTTTCAAAAACACCGCTAAAGGCCCGAGC
1 ATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
28119220 ATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGGCCCGATC
1 ATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCCCGAGC
* *
28119261 ATTAGCGGCGCTTCTTCAAAAACGTCGCTAAAAGCCC
1 ATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCCC
28119298 CTAAAACTCA
Statistics
Matches: 180, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
40 38 0.21
41 139 0.77
42 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (40 bp):
ATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:28119196 original size:81 final size:81
Alignment explanation
Indices: 28119057--28119284 Score: 332
Period size: 81 Copynumber: 2.8 Consensus size: 81
28119047 TTTTTTTATT
* *
28119057 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTATTTCAACAACG
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCT-TTTCAAAAACG
28119122 CCACTAAAGGCCCGAGC
65 CCACTAAAGGCCCGAGC
* ** *
28119139 ATTAGCGGCGCTTTTTC-AAAACGCCACTAAAGGAACGAGCATTAGCGGCGCATTTTCAAAAACA
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC-TTTTCAAAAACG
*
28119203 CCGCTAAAGGCCCGAGC
65 CCACTAAAGGCCCGAGC
* * *
28119220 ATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGGCCCGATCATTAGCGGCGCTTCTTCAAAAACG
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTT-TTCAAAAACG
28119285 TCGCTAAAAG
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
81 74 0.57
82 55 0.43
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (81 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTTTCAAAAACGC
CACTAAAGGCCCGAGC
Found at i:28119279 original size:122 final size:122
Alignment explanation
Indices: 28119057--28119281 Score: 364
Period size: 122 Copynumber: 1.8 Consensus size: 122
28119047 TTTTTTTATT
* *
28119057 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTATTTCAACAACG
1 ATTAGCGGCGCTTTCTCAAAAACACCGCTAAAGGCCCGAGCATTAGCGGCGCTATTTCAAAAACG
*
28119122 CCACTAAAGGCCCGAGCATTAGCGGCGCTTTTTCAAAACGCCACTAAAGGAACGAGC
66 CCACTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAACGCCACTAAAGGAACGAGC
28119179 ATTAGCGGCGCATTT-TCAAAAACACCGCTAAAGGCCCGAGCATTAGCGGCGCT-TCTTCAAAAA
1 ATTAGCGGCGC-TTTCTCAAAAACACCGCTAAAGGCCCGAGCATTAGCGGCGCTAT-TTCAAAAA
* * *
28119242 TGCCGCTAAAGGCCCGATCATTAGCGGCGCTTCTTCAAAA
64 CGCCACTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAA
28119282 ACGTCGCTAA
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
121 1 0.01
122 91 0.96
123 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (122 bp):
ATTAGCGGCGCTTTCTCAAAAACACCGCTAAAGGCCCGAGCATTAGCGGCGCTATTTCAAAAACG
CCACTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAACGCCACTAAAGGAACGAGC
Found at i:28119375 original size:39 final size:39
Alignment explanation
Indices: 28119332--28119407 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
28119322 CGGTCTTAGG
* *
28119332 TTTTTTGCGGCGCTTTTCAAAAAACGTC-GCTAATGCTTA
1 TTTTTAGCGGCACTTTTCAAAAAACG-CAGCTAATGCTTA
* *
28119371 TTTTTAGCGGCATTTTTCAAAAACCGCAGCTAATGCT
1 TTTTTAGCGGCACTTTTCAAAAAACGCAGCTAATGCT
28119408 CCATCTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (39 bp):
TTTTTAGCGGCACTTTTCAAAAAACGCAGCTAATGCTTA
Found at i:28119457 original size:40 final size:39
Alignment explanation
Indices: 28119346--28119457 Score: 100
Period size: 40 Copynumber: 2.8 Consensus size: 39
28119336 TTGCGGCGCT
* * *
28119346 TTTCAAAAAACGTCGCTAATGCTTATTTTTAGCGGCATT
1 TTTCAAAAACCGCCGCTAATGCTTATTTTTAGCGGCATC
* * * **
28119385 TTTCAAAAACCGCAGCTAATGCTCCATCTTTAGCGGTGTC
1 TTTCAAAAACCGCCGCTAATGCT-TATTTTTAGCGGCATC
**
28119425 TTT-AGAAAAGTGCCGCTAATGCTTGATTTTTAG
1 TTTCA-AAAACCGCCGCTAATGCTT-ATTTTTAG
28119458 TGGCGTTTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
39 21 0.37
40 36 0.63
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (39 bp):
TTTCAAAAACCGCCGCTAATGCTTATTTTTAGCGGCATC
Found at i:28120663 original size:69 final size:69
Alignment explanation
Indices: 28120583--28120802 Score: 241
Period size: 69 Copynumber: 3.2 Consensus size: 69
28120573 ATAGTTGACT
* * ** *
28120583 TATGGTTTTACACCTTGTAATCCTTGTGTTTACTATCCCAGTGGACTCTATTGATCGCCATAGCC
1 TATGGTCTTACACCTTGTAATCCTTGTGTTTACTGTCCCAGCAGACTCTATTGATCACCATAGCC
28120648 AAAC
66 AAAC
* * * * * *
28120652 TATAGTCTTACACATTGTAATTCC-TGTGTTTACTGTCCCAACAAACTCTATTGGTCACCATAGT
1 TATGGTCTTACACCTTGTAA-TCCTTGTGTTTACTGTCCCAGCAGACTCTATTGATCACCATAGC
28120716 CAAAC
65 CAAAC
* *
28120721 TATGGTCTTACACCTCT-TAATTCTTGTGCTTT-CTGT-CCTGACAGACTCTATTGATCACCATA
1 TATGGTCTTACACCT-TGTAATCCTTGTG-TTTACTGTCCCAG-CAGACTCTATTGATCACCATA
*
28120783 GCCAAGC
63 GCCAAAC
*
28120790 TATGGTCTCACAC
1 TATGGTCTTACAC
28120803 TCTAAACCTC
Statistics
Matches: 125, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
68 4 0.03
69 114 0.91
70 7 0.06
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (69 bp):
TATGGTCTTACACCTTGTAATCCTTGTGTTTACTGTCCCAGCAGACTCTATTGATCACCATAGCC
AAAC
Found at i:28120704 original size:138 final size:138
Alignment explanation
Indices: 28120500--28120802 Score: 314
Period size: 138 Copynumber: 2.2 Consensus size: 138
28120490 CTTTACCTGA
* * * *
28120500 CGCCATAGCCAAACTATGGTCTTACTCAGTATGAACCCATGTTTATTGTCCTAGCAAACTCTTAT
1 CGCCATAGCCAAACTATGGTCTTACACAGTATGAACCCATGTTTACTGTCCCAACAAACTCTTAT
** ** * **
28120565 TGGTTGCCATAGT-TGACTTATGGTTTTACACCT-TGTAATCCTTGTG-TTTACTATCCCAG-TG
66 TGGTCACCATAGTCAAAC-TATGGTCTTACACCTCT-TAATCCTTGTGCTTT-CTAT-CCAGACA
28120626 GACTCTATTGAT
127 GACTCTATTGAT
* **
28120638 CGCCATAGCCAAACTATAGTCTTACACA-T-TGTAATTCCTGTGTTTACTGTCCCAACAAACTC-
1 CGCCATAGCCAAACTATGGTCTTACACAGTATG-AA--CCCATGTTTACTGTCCCAACAAACTCT
* * *
28120700 TATTGGTCACCATAGTCAAACTATGGTCTTACACCTCTTAATTCTTGTGCTTTCTGTCCTGACAG
63 TATTGGTCACCATAGTCAAACTATGGTCTTACACCTCTTAATCCTTGTGCTTTCTATCCAGACAG
28120765 ACTCTATTGAT
128 ACTCTATTGAT
* * *
28120776 CACCATAGCCAAGCTATGGTCTCACAC
1 CGCCATAGCCAAACTATGGTCTTACAC
28120803 TCTAAACCTC
Statistics
Matches: 137, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
136 2 0.01
137 6 0.04
138 102 0.74
139 27 0.20
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (138 bp):
CGCCATAGCCAAACTATGGTCTTACACAGTATGAACCCATGTTTACTGTCCCAACAAACTCTTAT
TGGTCACCATAGTCAAACTATGGTCTTACACCTCTTAATCCTTGTGCTTTCTATCCAGACAGACT
CTATTGAT
Found at i:28125609 original size:29 final size:29
Alignment explanation
Indices: 28125566--28125815 Score: 249
Period size: 29 Copynumber: 8.6 Consensus size: 29
28125556 ATGGCGATCT
* *
28125566 TCGAATATGATAAGGGATAGCTTCGGCTA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
*
28125595 TCGATTATGAAAAGGGATAGCTTCGACTA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
* * *
28125624 TCGAATATGAAAAGGGATAGATTTGGCTA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
* * * * * *
28125653 TTGATTATGAAAAGGGAT-GGTGACAACCA
1 TCGAATATGAAAAGGGATAGCT-TCGACTA
* *
28125682 TC-AACTATGAAAAGGGAT-GGTGAT-GACCA
1 TCGAA-TATGAAAAGGGATAGCT--TCGACTA
*
28125711 TCGAATATGAAAATGGATAGCTTCGACTA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
* *
28125740 TCAAATATGAAAAGGGATAGCTTCGGCTA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
*
28125769 TCGAATATGAAAAGGAATAGCTTC-AGCTA
1 TCGAATATGAAAAGGGATAGCTTCGA-CTA
*
28125798 TCGATTATGAAAAGGGAT
1 TCGAATATGAAAAGGGAT
28125816 GGTGACGACC
Statistics
Matches: 183, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
28 4 0.02
29 175 0.96
30 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (29 bp):
TCGAATATGAAAAGGGATAGCTTCGACTA
Found at i:28125778 original size:116 final size:116
Alignment explanation
Indices: 28125594--28125844 Score: 335
Period size: 116 Copynumber: 2.2 Consensus size: 116
28125584 AGCTTCGGCT
* * * * *
28125594 ATCGATTATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGATTTGGCTATTGATT
1 ATCGAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGATTCGGCTATCGAAT
* * *
28125659 ATGAAAAGGGAT-GGTGACAACCATCAACTATGAAAAGGGATGGTGATGACC
66 ATGAAAAGGAATAGCT-ACAACCATCAACTATGAAAAGGGATGGTGACGACC
* *
28125710 ATCGAATATGAAAATGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATCGAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGATTCGGCTATCGAAT
* * * * *
28125775 ATGAAAAGGAATAGCTTCAGCTATCGATTATGAAAAGGGATGGTGACGACC
66 ATGAAAAGGAATAGCTACAACCATCAACTATGAAAAGGGATGGTGACGACC
28125826 ATC-AACTATGAAAAGGGAT
1 ATCGAA-TATGAAAAGGGAT
28125845 GGTGACAACC
Statistics
Matches: 117, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
115 2 0.02
116 113 0.97
117 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.24
Consensus pattern (116 bp):
ATCGAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGATTCGGCTATCGAAT
ATGAAAAGGAATAGCTACAACCATCAACTATGAAAAGGGATGGTGACGACC
Found at i:28125829 original size:145 final size:145
Alignment explanation
Indices: 28125566--28125901 Score: 492
Period size: 145 Copynumber: 2.3 Consensus size: 145
28125556 ATGGCGATCT
* * * *
28125566 TCGAATATGATAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATAGCTTCGACTATCGAATA
1 TCGAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGACTATCGAATA
* ** *
28125631 TGAAAAGGGATAGATTTGGCTATTGATTATGAAAAGGGATGGTGACAACCATCAACTATGAAAAG
66 TGAAAAGGAATAGATTCAGCTATCGATTATGAAAAGGGATGGTGACAACCATCAACTATGAAAAG
**
28125696 GGATGGTGATGACCA
131 GGATGGTGACAACCA
* *
28125711 TCGAATATGAAAATGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGGCTATCGAATA
1 TCGAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGACTATCGAATA
* *
28125776 TGAAAAGGAATAGCTTCAGCTATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAG
66 TGAAAAGGAATAGATTCAGCTATCGATTATGAAAAGGGATGGTGACAACCATCAACTATGAAAAG
28125841 GGATGGTGACAACCA
131 GGATGGTGACAACCA
* * * * *
28125856 TCGATTAATGAAAAGGGATGGTTTCAACCATCAAATATGAAAAGGG
1 TCGAAT-ATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGG
28125902 CCGGTTACAA
Statistics
Matches: 170, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
145 136 0.80
146 34 0.20
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (145 bp):
TCGAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGACTATCGAATA
TGAAAAGGAATAGATTCAGCTATCGATTATGAAAAGGGATGGTGACAACCATCAACTATGAAAAG
GGATGGTGACAACCA
Found at i:28125886 original size:59 final size:58
Alignment explanation
Indices: 28125797--28125917 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 58
28125787 AGCTTCAGCT
* * *
28125797 ATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTGACAACC
1 ATCGATTATGAAAAGGGATGGTGACAACCATCAAATATGAAAAGGGACGGTGACAACC
** * *
28125855 ATCGATTAATGAAAAGGGATGGTTTCAACCATCAAATATGAAAAGGGCCGGTTACAACC
1 ATCGATT-ATGAAAAGGGATGGTGACAACCATCAAATATGAAAAGGGACGGTGACAACC
28125914 ATCG
1 ATCG
28125918 TTTAGCACAC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 7 0.13
59 48 0.87
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (58 bp):
ATCGATTATGAAAAGGGATGGTGACAACCATCAAATATGAAAAGGGACGGTGACAACC
Found at i:28125907 original size:29 final size:29
Alignment explanation
Indices: 28125658--28125916 Score: 191
Period size: 29 Copynumber: 8.9 Consensus size: 29
28125648 GGCTATTGAT
* *
28125658 TATGAAAAGGGATGGTGACAACCATCAAC
1 TATGAAAAGGGATGGTTACAACCATCAAA
* ** *
28125687 TATGAAAAGGGATGGTGATGACCATCGAA
1 TATGAAAAGGGATGGTTACAACCATCAAA
* * * *
28125716 TATGAAAATGGATAGCTT-CGACTATCAAA
1 TATGAAAAGGGAT-GGTTACAACCATCAAA
* ** * *
28125745 TATGAAAAGGGATAGCTT-CGGCTATCGAA
1 TATGAAAAGGGAT-GGTTACAACCATCAAA
* * * * * *
28125774 TATGAAAAGGAATAGCTT-CAGCTATCGAT
1 TATGAAAAGGGAT-GGTTACAACCATCAAA
* * *
28125803 TATGAAAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTTACAACCATCAAA
* * *
28125832 TATGAAAAGGGATGGTGACAACCATCGAT
1 TATGAAAAGGGATGGTTACAACCATCAAA
*
28125861 TAATGAAAAGGGATGGTTTCAACCATCAAA
1 T-ATGAAAAGGGATGGTTACAACCATCAAA
**
28125891 TATGAAAAGGGCCGGTTACAACCATC
1 TATGAAAAGGGATGGTTACAACCATC
28125917 GTTTAGCACA
Statistics
Matches: 193, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
28 2 0.01
29 164 0.85
30 27 0.14
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (29 bp):
TATGAAAAGGGATGGTTACAACCATCAAA
Found at i:28139355 original size:24 final size:25
Alignment explanation
Indices: 28139328--28139383 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 25
28139318 CATCAAACTA
*
28139328 AAGTTAGA-AATGTCATTACAACCT
1 AAGTTACAGAATGTCATTACAACCT
28139352 AAG-TACAGAATGTCATTACAACCT
1 AAGTTACAGAATGTCATTACAACCT
28139376 AAG-TACAG
1 AAGTTACAG
28139384 GGACTGAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (25 bp):
AAGTTACAGAATGTCATTACAACCT
Found at i:28144517 original size:13 final size:13
Alignment explanation
Indices: 28144494--28144529 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
28144484 AATGCATGTG
28144494 TAATG-TAATGGT
1 TAATGTTAATGGT
28144506 TAATGTTAATGGT
1 TAATGTTAATGGT
28144519 TAATGTGTAAT
1 TAATGT-TAAT
28144530 CGTGAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 13 0.59
14 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (13 bp):
TAATGTTAATGGT
Found at i:28147792 original size:14 final size:14
Alignment explanation
Indices: 28147753--28147792 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
28147743 AGAAATTTAT
28147753 TTAATTTAA-AAAA
1 TTAATTTAATAAAA
28147766 TTAA-TTAATTAAAA
1 TTAATTTAA-TAAAA
28147780 TTAATTTAATAAA
1 TTAATTTAATAAA
28147793 TAATATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.17
13 4 0.17
14 12 0.50
15 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAATTTAATAAAA
Found at i:28152757 original size:22 final size:22
Alignment explanation
Indices: 28152730--28152773 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28152720 GAAAAACAAG
*
28152730 TCCCTACAAATCAATTCTATGA
1 TCCCTACAAATCAACTCTATGA
*
28152752 TCCCTACAAATCAGCTCTATGA
1 TCCCTACAAATCAACTCTATGA
28152774 ATCAGCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.30
Consensus pattern (22 bp):
TCCCTACAAATCAACTCTATGA
Found at i:28155139 original size:17 final size:17
Alignment explanation
Indices: 28155117--28155170 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
28155107 TTGATACCAT
28155117 GAAAGCAAGCTGTTTCA
1 GAAAGCAAGCTGTTTCA
**
28155134 GAAAGCAA-C-AATT--
1 GAAAGCAAGCTGTTTCA
28155147 -AAAGCAAGCTGTTTCA
1 GAAAGCAAGCTGTTTCA
28155163 GAAAGCAA
1 GAAAGCAA
28155171 TAATTAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
12 7 0.25
13 1 0.04
14 2 0.07
15 2 0.07
16 1 0.04
17 15 0.54
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (17 bp):
GAAAGCAAGCTGTTTCA
Found at i:28155151 original size:29 final size:29
Alignment explanation
Indices: 28155118--28155177 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
28155108 TGATACCATG
28155118 AAAGCAAGCTGTTTCAGAAAGCAACAATT
1 AAAGCAAGCTGTTTCAGAAAGCAACAATT
*
28155147 AAAGCAAGCTGTTTCAGAAAGCAATAATT
1 AAAGCAAGCTGTTTCAGAAAGCAACAATT
28155176 AA
1 AA
28155178 TCAGAAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.22
Consensus pattern (29 bp):
AAAGCAAGCTGTTTCAGAAAGCAACAATT
Found at i:28156350 original size:158 final size:158
Alignment explanation
Indices: 28156062--28156850 Score: 1330
Period size: 158 Copynumber: 5.0 Consensus size: 158
28156052 TATTATTGAG
* *
28156062 TTAAAGAATATATATTGAGAGCATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGACTTTT
1 TTAAAGAATATATATTGAGAACATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
*
28156127 CAATTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCCGCTTTATTTTCAGTGCTTGAAGAGAATT
66 CAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCCGCTTTATTTTCAGTGCTTGAAGAGAATT
28156192 TCTATTGAGAATTCTCACTTTGTGAGAA
131 TCTATTGAGAATTCTCACTTTGTGAGAA
* *
28156220 TTAAAGAATATATATTGAGAACATTTACTTAAACACTTGGTGTGCATTGCTTCTTTGTGGCTTTT
1 TTAAAGAATATATATTGAGAACATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
* * * *
28156285 CAGTTCTCTCGTTTCTTTTTCATTTCGAGTTGCTTCTGCTTTATTTTCTGTGCTTGAAGAGAATT
66 CAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCCGCTTTATTTTCAGTGCTTGAAGAGAATT
28156350 TCTATTGAGAATTCTCACTTTGTGAGAA
131 TCTATTGAGAATTCTCACTTTGTGAGAA
* *
28156378 TTAAAGAATATATATCGA-AAGCATTTACTCAAACACTTGGTGTGCTTTGCTTCCTTGTGGCTTT
1 TTAAAGAATATATATTGAGAA-CATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTT
* *
28156442 TCAGTTCTCTCGTTACTCTTTCATTTCGAGTTGCTTCCGCTTTATTTTCAGTGCTTGAAGAGACT
65 TCAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCCGCTTTATTTTCAGTGCTTGAAGAGAAT
28156507 TTCTATTGAGAATTCTCACTTTGTGAGAA
130 TTCTATTGAGAATTCTCACTTTGTGAGAA
* * * *
28156536 TTAAAGAATATATATTGAGAATATTTACTTAAACACTTGGTGTGGATTGCTTCCTTATGGCTTTT
1 TTAAAGAATATATATTGAGAACATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
* *
28156601 CAGTTCTCTCGTTGCTTTTTCATTTCGAGTTGCTTCCGCTTTATTTTCTGTGCTTGAAGAGAATT
66 CAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCCGCTTTATTTTCAGTGCTTGAAGAGAATT
*
28156666 TCTATTGAGAATTCTCACTTTGCGAGAA
131 TCTATTGAGAATTCTCACTTTGTGAGAA
*
28156694 TTAAAGAATATATATTGAGAGCATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
1 TTAAAGAATATATATTGAGAACATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
* *
28156759 TAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGC-TCCTGCTTTATTTTCAGTGCGTGAAGAGAAT
66 CAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCC-GCTTTATTTTCAGTGCTTGAAGAGAAT
*
28156823 TTCTATTGAGAATTCTCACTTTGCGAGA
130 TTCTATTGAGAATTCTCACTTTGTGAGA
28156851 GCTAGATCGA
Statistics
Matches: 590, Mismatches: 38, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
157 5 0.01
158 583 0.99
159 2 0.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (158 bp):
TTAAAGAATATATATTGAGAACATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
CAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCCGCTTTATTTTCAGTGCTTGAAGAGAATT
TCTATTGAGAATTCTCACTTTGTGAGAA
Found at i:28158755 original size:18 final size:18
Alignment explanation
Indices: 28158718--28158771 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
28158708 ATAAATAGTA
*
28158718 AAATCGAGATAATGACATTG
1 AAAT-GAGA-AATGATATTG
28158738 AAATGAGAAATGATATTG
1 AAATGAGAAATGATATTG
*
28158756 AAATGAAAAATGATAT
1 AAATGAGAAATGATAT
28158772 GGAATGGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 24 0.75
19 4 0.12
20 4 0.12
ACGTcount: A:0.52, C:0.04, G:0.19, T:0.26
Consensus pattern (18 bp):
AAATGAGAAATGATATTG
Found at i:28165442 original size:21 final size:20
Alignment explanation
Indices: 28165411--28165464 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
28165401 ATTGGAGCAG
* * *
28165411 AAATATTGATATCTTAGGAA
1 AAATATCGATACCTTAAGAA
28165431 AATATATCGATACCTTAAGAA
1 AA-ATATCGATACCTTAAGAA
*
28165452 AAGTATCGATACC
1 AAATATCGATACC
28165465 GGATCGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (20 bp):
AAATATCGATACCTTAAGAA
Found at i:28175913 original size:35 final size:36
Alignment explanation
Indices: 28175874--28175976 Score: 111
Period size: 35 Copynumber: 2.9 Consensus size: 36
28175864 TGTGATTTAG
* * *
28175874 AATCAGTACAGTGGCATACTTAACATGCGAATC-AA
1 AATCAGTATAATGGCATGCTTAACATGCGAATCAAA
* * *
28175909 AATCAATATAACGCCATGCTTAACATGCGAA-CAAA
1 AATCAGTATAATGGCATGCTTAACATGCGAATCAAA
* *
28175944 AATAAGTAATAATGGCATGCTTAACATGAGAAT
1 AATCAGT-ATAATGGCATGCTTAACATGCGAAT
28175977 TAGAATATCA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
34 1 0.02
35 32 0.59
36 21 0.39
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (36 bp):
AATCAGTATAATGGCATGCTTAACATGCGAATCAAA
Found at i:28181834 original size:32 final size:30
Alignment explanation
Indices: 28181798--28181867 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 30
28181788 GTTTCACTAT
* *
28181798 AGTTTCAAAATTTATGGTTTTCAGAATCTTAA
1 AGTTTCAAAATTTATAG-TTTCACAATC-TAA
* *
28181830 AGTTTTCACAGTTTATAGTTTCACAATCTAA
1 AG-TTTCAAAATTTATAGTTTCACAATCTAA
28181861 AGTTTCA
1 AGTTTCA
28181868 GTGCGTAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 5 0.15
31 5 0.15
32 11 0.33
33 12 0.36
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (30 bp):
AGTTTCAAAATTTATAGTTTCACAATCTAA
Found at i:28181864 original size:15 final size:15
Alignment explanation
Indices: 28181816--28181867 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
28181806 AATTTATGGT
*
28181816 TTTCAGAATCTTAAAG
1 TTTCACAATC-TAAAG
* * *
28181832 TTTTCACAGTTTATAG
1 -TTTCACAATCTAAAG
28181848 TTTCACAATCTAAAG
1 TTTCACAATCTAAAG
28181863 TTTCA
1 TTTCA
28181868 GTGCGTAAAG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 17 0.61
16 4 0.14
17 7 0.25
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (15 bp):
TTTCACAATCTAAAG
Found at i:28183221 original size:35 final size:35
Alignment explanation
Indices: 28183180--28183275 Score: 138
Period size: 35 Copynumber: 2.7 Consensus size: 35
28183170 AATTTCAGTG
* * *
28183180 GGCATGCTTTACATGCGATTTAGAATCAGTATAGT
1 GGCATGCTTAACATGCGAATTAGAATCAGTATAAT
* *
28183215 GGCATGCTTAACATGCGAATCAGAATTAGTATAAT
1 GGCATGCTTAACATGCGAATTAGAATCAGTATAAT
*
28183250 GACATGCTTAACATGCGAATTAGAAT
1 GGCATGCTTAACATGCGAATTAGAAT
28183276 ACCAACAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (35 bp):
GGCATGCTTAACATGCGAATTAGAATCAGTATAAT
Found at i:28190526 original size:34 final size:35
Alignment explanation
Indices: 28190460--28190526 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28190450 CAAACACCAG
*
28190460 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCTAGTAAATCATTTTACAGAAAAGT
* *
28190495 AAAACATTTTCTAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCTAGTAAATCATTTTACAGAAAA
28190527 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (35 bp):
AAAACATTTTCTAGTAAATCATTTTACAGAAAAGT
Found at i:28190960 original size:24 final size:24
Alignment explanation
Indices: 28190928--28190973 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
28190918 GAGACCCTCG
28190928 AAGCCCCACTTATCCGTGCCTACC
1 AAGCCCCACTTATCCGTGCCTACC
28190952 AAGCCCCACTTATCCGTGCCTA
1 AAGCCCCACTTATCCGTGCCTA
28190974 TTCGAGCGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.43, G:0.13, T:0.22
Consensus pattern (24 bp):
AAGCCCCACTTATCCGTGCCTACC
Found at i:28197300 original size:11 final size:9
Alignment explanation
Indices: 28197284--28197315 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
28197274 CGAAATAAAT
*
28197284 TATATATAG
1 TATATATAA
28197293 TATATATAA
1 TATATATAA
28197302 TATATATAA
1 TATATATAA
28197311 TATAT
1 TATAT
28197316 TTTTTAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
TATATATAA
Found at i:28198748 original size:38 final size:38
Alignment explanation
Indices: 28198706--28198791 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 38
28198696 GACCCATTTT
*
28198706 TAAAATAAA-CATTAAAAAATTATTTTAAAAATAAAAAA
1 TAAAATAAATCATTAAAAAAGTATTTT-AAAATAAAAAA
* * ** *
28198744 TAAAAAAAATTATTTTAAAAGTATTTTAAAATTAAAAA
1 TAAAATAAATCATTAAAAAAGTATTTTAAAATAAAAAA
28198782 TAAAAATAAA
1 T-AAAATAAA
28198792 AAATATATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
38 19 0.49
39 20 0.51
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (38 bp):
TAAAATAAATCATTAAAAAAGTATTTTAAAATAAAAAA
Found at i:28199253 original size:58 final size:59
Alignment explanation
Indices: 28199163--28199287 Score: 216
Period size: 58 Copynumber: 2.1 Consensus size: 59
28199153 AAATAAAAGA
*
28199163 ATTACATGCTAAGGATAATTCAATAAAATCACAAGCAATTCCTATTTCTAATAC-CTCC
1 ATTACTTGCTAAGGATAATTCAATAAAATCACAAGCAATTCCTATTTCTAATACTCTCC
*
28199221 ATTACTTGTTAAGGATAATTCAATAAAATCACAAGCAATTCCTATTTCTAATACTCTCC
1 ATTACTTGCTAAGGATAATTCAATAAAATCACAAGCAATTCCTATTTCTAATACTCTCC
*
28199280 CTTACTTG
1 ATTACTTG
28199288 ATGCATATCT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
58 52 0.83
59 11 0.17
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (59 bp):
ATTACTTGCTAAGGATAATTCAATAAAATCACAAGCAATTCCTATTTCTAATACTCTCC
Found at i:28204560 original size:23 final size:23
Alignment explanation
Indices: 28204534--28204585 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
28204524 TAATGTAAAT
* * *
28204534 TTATTTTCAGCAGTTACAAATCA
1 TTATTTTCAACAATTACAAACCA
*
28204557 TTATTTCCAACAATTACAAACCA
1 TTATTTTCAACAATTACAAACCA
28204580 TT-TTTT
1 TTATTTT
28204586 ACTATTACAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (23 bp):
TTATTTTCAACAATTACAAACCA
Found at i:28208660 original size:23 final size:22
Alignment explanation
Indices: 28208609--28208660 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
28208599 CCTCGTCTTT
*
28208609 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
28208631 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
28208654 TTCTTTT
1 TTCTTTT
28208661 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:28215276 original size:27 final size:27
Alignment explanation
Indices: 28215245--28215422 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28215235 TAAATTGTAC
28215245 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28215272 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28215298 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28215326 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28215354 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28215381 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28215408 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28215423 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28215359 original size:82 final size:81
Alignment explanation
Indices: 28215246--28215401 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28215236 AAATTGTACA
* *
28215246 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28215310 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28215327 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28215392 TGCGAGTTGA
65 TGCGAATTGA
28215402 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28215413 original size:82 final size:81
Alignment explanation
Indices: 28215242--28215422 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28215232 GATTAAATTG
* *
28215242 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28215307 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28215323 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28215387 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28215405 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28215423 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28223872 original size:80 final size:81
Alignment explanation
Indices: 28223735--28223892 Score: 309
Period size: 80 Copynumber: 2.0 Consensus size: 81
28223725 TAATGATCAC
28223735 ATCTCTTAAACATAAACGTAAAACAAAAAAAAGCATGCTTACGATACAAGATTCAAAGGTAATGC
1 ATCTCTTAAACATAAACGTAAAACAAAAAAAAGCATGCTTACGATACAAGATTCAAAGGTAATGC
28223800 AGAGAATATCCTTAAT
66 AGAGAATATCCTTAAT
28223816 ATCTCTTAAACATAAACGTAAAACAAAAAAAA-CATGCTTACGATACAAGATTCAAAGGTAATGC
1 ATCTCTTAAACATAAACGTAAAACAAAAAAAAGCATGCTTACGATACAAGATTCAAAGGTAATGC
28223880 AGAGAATATCCTT
66 AGAGAATATCCTT
28223893 TCTTTTTTTC
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 45 0.58
81 32 0.42
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.23
Consensus pattern (81 bp):
ATCTCTTAAACATAAACGTAAAACAAAAAAAAGCATGCTTACGATACAAGATTCAAAGGTAATGC
AGAGAATATCCTTAAT
Found at i:28232392 original size:31 final size:31
Alignment explanation
Indices: 28232334--28232392 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
28232324 AAAGTATACT
* ****
28232334 AACAGTCACTCAACTTTGATCTCAATAATAA
1 AACAGTCACTCAACTTTCAAAGAAATAATAA
28232365 AACAGTCACTCAACTTTCAAAGAAATAA
1 AACAGTCACTCAACTTTCAAAGAAATAA
28232393 CAAATCAATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (31 bp):
AACAGTCACTCAACTTTCAAAGAAATAATAA
Found at i:28237558 original size:12 final size:11
Alignment explanation
Indices: 28237544--28237596 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
28237534 AACAGGGAAG
28237544 AAAGAAAGAAA
1 AAAGAAAGAAA
*
28237555 GAA-AAAGAAA
1 AAAGAAAGAAA
*
28237565 AAGGAAAGAAA
1 AAAGAAAGAAA
*
28237576 AAGAGAAAAGAAT
1 AA-AG-AAAGAAA
28237589 AAAGAAAG
1 AAAGAAAG
28237597 CCATTGCCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 8 0.24
11 15 0.44
12 3 0.09
13 8 0.24
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:28237571 original size:7 final size:6
Alignment explanation
Indices: 28237552--28237595 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
28237542 AGAAAGAAAG
*
28237552 AAAGAA AAAGAA AAAG-G AAAGAA AAAGAGA AAAGAA TAAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGA-A AAAGAA -AAAGAA A
28237596 GCCATTGCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
6 17 0.52
7 12 0.36
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:28237573 original size:17 final size:17
Alignment explanation
Indices: 28237541--28237585 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
28237531 CGAAACAGGG
*
28237541 AAGAAAGAAAGAAAGAAA
1 AAGAAA-AAGGAAAGAAA
28237559 AAGAAAAAGGAAAGAAA
1 AAGAAAAAGGAAAGAAA
28237576 AAGAGAAAAG
1 AAGA-AAAAG
28237586 AATAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGGAAAGAAA
Found at i:28237573 original size:25 final size:24
Alignment explanation
Indices: 28237541--28237596 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
28237531 CGAAACAGGG
28237541 AAGAAAGAAAGAA-AGAAAAAGAA-A
1 AAGAAAGAAA-AAGAG-AAAAGAATA
28237565 AAGGAAAGAAAAAGAGAAAAGAATA
1 AA-GAAAGAAAAAGAGAAAAGAATA
28237590 AAGAAAG
1 AAGAAAG
28237597 CCATTGCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (24 bp):
AAGAAAGAAAAAGAGAAAAGAATA
Found at i:28239742 original size:11 final size:11
Alignment explanation
Indices: 28239726--28239769 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
28239716 TTCTTTGGAT
28239726 TCAAATATGAC
1 TCAAATATGAC
*
28239737 TCAAATATGAT
1 TCAAATATGAC
* *
28239748 TTAAATATGAA
1 TCAAATATGAC
28239759 TCAAATATGAC
1 TCAAATATGAC
28239770 AAATCAGATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (11 bp):
TCAAATATGAC
Found at i:28239748 original size:22 final size:22
Alignment explanation
Indices: 28239723--28239768 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
28239713 AGCTTCTTTG
*
28239723 GATTCAAATATGACTCAAATAT
1 GATTCAAATATGAATCAAATAT
*
28239745 GATTTAAATATGAATCAAATAT
1 GATTCAAATATGAATCAAATAT
28239767 GA
1 GA
28239769 CAAATCAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (22 bp):
GATTCAAATATGAATCAAATAT
Found at i:28239985 original size:90 final size:90
Alignment explanation
Indices: 28239866--28240184 Score: 449
Period size: 90 Copynumber: 3.5 Consensus size: 90
28239856 ATTTCTTTGG
*
28239866 TTATTGTCTGTCATGTGCATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
1 TTATTGTCTGTCATATGCATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
*
28239931 TGACATAAATGAATTTCTTTGTATT
66 TGACATAAATGGATTTCTTTGTATT
** * *
28239956 TTATTGTCTACCATATGTATGACAAAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
1 TTATTGTCTGTCATATGCATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
*
28240021 AGACATAAATGGATTTCTTTGTATT
66 TGACATAAATGGATTTCTTTGTATT
* ** * *
28240046 TTATTGTCTGTTATATGCATGACAGAAATGAATTTGTTTGTATTAAATTGTTTGGTTATTGAACT
1 TTATTGTCTGTCATATGCATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
*
28240111 TGACAAAAATGGATTTCTTTGTATT
66 TGACATAAATGGATTTCTTTGTATT
** * * * * **
28240136 AAAGTGTATGGCATGTGCATGACAGAAATGAATTTGTTTGTATTAAATT
1 TTATTGTCTGTCATATGCATGACAGAAACAAATTTGTTTGTATTAAATT
28240185 ATTTTTTGTA
Statistics
Matches: 204, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 204 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (90 bp):
TTATTGTCTGTCATATGCATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
TGACATAAATGGATTTCTTTGTATT
Found at i:28240006 original size:44 final size:45
Alignment explanation
Indices: 28239884--28240007 Score: 117
Period size: 46 Copynumber: 2.8 Consensus size: 45
28239874 TGTCATGTGC
* ****
28239884 ATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTA
1 ATGACAAAAACAAATTTGTTTGTATTAAATTGTTACCATATTGTA
* ** * **
28239929 CATGACATAAATGAATTTCTTTGTATTTTATTGTCTACCATA-TGT-
1 -ATGACAAAAACAAATTTGTTTGTATTAAATTGT-TACCATATTGTA
28239974 ATGACAAAAACAAATTTGTTTGTATTAAATTGTT
1 ATGACAAAAACAAATTTGTTTGTATTAAATTGTT
28240008 TGGTTATTGT
Statistics
Matches: 61, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
43 1 0.02
44 27 0.44
46 30 0.49
47 3 0.05
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (45 bp):
ATGACAAAAACAAATTTGTTTGTATTAAATTGTTACCATATTGTA
Found at i:28242210 original size:71 final size:67
Alignment explanation
Indices: 28242104--28242321 Score: 230
Period size: 63 Copynumber: 3.2 Consensus size: 67
28242094 CACTTAAAAC
* * * *
28242104 CGAATGCATATATAATTTAAAACATGAATAGCCGAATGTGTATATACATATATGCTTAACAAATA
1 CGAATGTATATACAATTT-AAACATGAATAGCCGAATG-ATATATAC--ATATGCATAACAAATA
28242169 TTATCA
62 TTATCA
* *
28242175 TCGAATGTATATACAGTTTAAACATGAATAGCCGAATGCT-TATAC--A--CATAACAAATATTA
1 -CGAATGTATATACAATTTAAACATGAATAGCCGAATGATATATACATATGCATAACAAATATTA
28242235 TCA
65 TCA
* * * *
28242238 CCGAATGTATATACACTTTAAACATGAATAGCTGAATGCATATATACATATGCACAACAAGTATT
1 -CGAATGTATATACAATTTAAACATGAATAGCCGAATG-ATATATACATATGCATAACAAATATT
28242303 ATCA
64 ATCA
*
28242307 CTGAATGTAAATACA
1 C-GAATGTATATACA
28242322 TGTTCTTCAA
Statistics
Matches: 127, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
63 51 0.40
64 1 0.01
65 6 0.05
67 1 0.01
68 1 0.01
69 32 0.25
70 1 0.01
71 19 0.15
72 15 0.12
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.30
Consensus pattern (67 bp):
CGAATGTATATACAATTTAAACATGAATAGCCGAATGATATATACATATGCATAACAAATATTAT
CA
Found at i:28242211 original size:31 final size:30
Alignment explanation
Indices: 28242176--28242286 Score: 84
Period size: 31 Copynumber: 3.5 Consensus size: 30
28242166 ATATTATCAT
28242176 CGAATGTATATACAGTTTAAACATGAATAGC
1 CGAATGTATATACA-TTTAAACATGAATAGC
** *
28242207 CGAATGCT-TATACACATAACAAAT-ATTATCA-C
1 CGAATG-TATATACATTTAA-ACATGA--AT-AGC
28242239 CGAATGTATATACACTTTAAACATGAATAGC
1 CGAATGTATATACA-TTTAAACATGAATAGC
*
28242270 TGAATGCATATATACAT
1 CGAATG--TATATACAT
28242287 ATGCACAACA
Statistics
Matches: 62, Mismatches: 7, Indels: 21
0.69 0.08 0.23
Matches are distributed among these distances:
30 5 0.08
31 24 0.39
32 20 0.32
33 13 0.21
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (30 bp):
CGAATGTATATACATTTAAACATGAATAGC
Found at i:28242518 original size:41 final size:41
Alignment explanation
Indices: 28242446--28242552 Score: 126
Period size: 41 Copynumber: 2.6 Consensus size: 41
28242436 ATCGGCTTTT
* * * * *
28242446 AGCCTGCTAGACTTATAGTCC-GAATTGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAG-CCTGAAATATTTCACCGGCATCA
28242487 AGCCTGCTAGACATAAAGCCTGAAATATTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGCCTGAAATATTTCACCGGCATCA
* * *
28242528 AACCTGCTAGACGTAAAGTCTGAAA
1 AGCCTGCTAGACATAAAGCCTGAAA
28242553 CATTCGATCA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 2 0.04
41 55 0.96
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGCCTGAAATATTTCACCGGCATCA
Found at i:28243053 original size:8 final size:8
Alignment explanation
Indices: 28243040--28243073 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
28243030 ATCCGAGCAT
28243040 TATATACA
1 TATATACA
*
28243048 TATATATA
1 TATATACA
*
28243056 CATATACA
1 TATATACA
28243064 TATATACA
1 TATATACA
28243072 TA
1 TA
28243074 CTCATACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
TATATACA
Found at i:28245870 original size:20 final size:20
Alignment explanation
Indices: 28245845--28245884 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28245835 CAAAAATATG
28245845 ATATTTATTTTAATTAATTT
1 ATATTTATTTTAATTAATTT
28245865 ATATTTATTTTAATTAATTT
1 ATATTTATTTTAATTAATTT
28245885 GATTTGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATATTTATTTTAATTAATTT
Found at i:28247865 original size:50 final size:50
Alignment explanation
Indices: 28247634--28247865 Score: 261
Period size: 50 Copynumber: 4.7 Consensus size: 50
28247624 AATAATAACA
* ** * *
28247634 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** * *
28247683 TGCCAATGCCATATCCCAGATATGGTTTTACATGGGAGTTTTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * ** *
28247733 TGCCCATGCTATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
28247783 TGCCAACGCCGTGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
28247833 TGCCAACGCCATGTCCCAGACATGGTCTTACAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAT
28247866 TTGTATTCGA
Statistics
Matches: 154, Mismatches: 27, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
48 1 0.01
49 40 0.26
50 113 0.73
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:28254137 original size:85 final size:85
Alignment explanation
Indices: 28253994--28254161 Score: 261
Period size: 85 Copynumber: 2.0 Consensus size: 85
28253984 CTATTCCGGT
* *
28253994 AACGGAGACGAGTTAGGGGTGTTACACCAACTCACCAAGGAATTGCCCCAACTTACCAAGAAG-T
1 AACGGAGACGAGTTAGGAGTGTTACACCAACTCACCAAGAAATTGCCCCAACTTACCAAGAAGCT
*
28254058 TTCCCCAAGAGAAAAGCTTGC
66 GT-CCCAAGAGAAAAGCTTGC
28254079 AACGGAGAC-AGATTAGGAGTGTTACACCAACTCACCAAGAAATAT-CCCCAACTTACCAAGAAG
1 AACGGAGACGAG-TTAGGAGTGTTACACCAACTCACCAAGAAAT-TGCCCCAACTTACCAAGAAG
28254142 CTGTCCCAAGAGAAAAGCTT
64 CTGTCCCAAGAGAAAAGCTT
28254162 TCATTCAAGA
Statistics
Matches: 77, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
84 2 0.03
85 72 0.94
86 3 0.04
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (85 bp):
AACGGAGACGAGTTAGGAGTGTTACACCAACTCACCAAGAAATTGCCCCAACTTACCAAGAAGCT
GTCCCAAGAGAAAAGCTTGC
Found at i:28255226 original size:50 final size:50
Alignment explanation
Indices: 28255142--28255241 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
28255132 TCAAAAACCT
* *
28255142 CAATACCAACAGTCACATAAGCTGGTTTTCCATTTCAACAACAACAACAA
1 CAATACCAACAGTCACATAAGCTGATTTTCCATTTAAACAACAACAACAA
* * * *
28255192 CAATACCAACTA-TCATATAAGTTGATTTTTCATTTAAACAACAACGACAA
1 CAATACCAAC-AGTCACATAAGCTGATTTTCCATTTAAACAACAACAACAA
28255242 TATTACAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 42 0.98
51 1 0.02
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (50 bp):
CAATACCAACAGTCACATAAGCTGATTTTCCATTTAAACAACAACAACAA
Found at i:28259905 original size:5 final size:5
Alignment explanation
Indices: 28259895--28259919 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28259885 TAGTGATAGA
28259895 GAGAG GAGAG GAGAG GAGAG GAGAG
1 GAGAG GAGAG GAGAG GAGAG GAGAG
28259920 AGATCCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
GAGAG
Found at i:28260405 original size:29 final size:29
Alignment explanation
Indices: 28260340--28260406 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
28260330 TATTTTTTTA
* **
28260340 AATGTATAATTAAATTAAATTAAAAATTT
1 AATGTATATTTAAACCAAATTAAAAATTT
* ** *
28260369 TACATATATTTAAACCAAATTCAAAATTT
1 AATGTATATTTAAACCAAATTAAAAATTT
28260398 AATGTATAT
1 AATGTATAT
28260407 AATTACAAAA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (29 bp):
AATGTATATTTAAACCAAATTAAAAATTT
Found at i:28260731 original size:27 final size:29
Alignment explanation
Indices: 28260699--28260752 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
28260689 AATTTTTTTT
*
28260699 TTCAAAATCTATAAAA-ATT-AAAACAAA
1 TTCAAAATATATAAAATATTCAAAACAAA
28260726 TTCAAAATATATAAAATATTCAAAACA
1 TTCAAAATATATAAAATATTCAAAACA
28260753 TTCTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 15 0.62
28 3 0.12
29 6 0.25
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (29 bp):
TTCAAAATATATAAAATATTCAAAACAAA
Found at i:28260755 original size:27 final size:26
Alignment explanation
Indices: 28260699--28260760 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
28260689 AATTTTTTTT
*
28260699 TTCAAAATCTATAAAAATTAAAACAAA
1 TTCAAAATATATAAAAATTAAAAC-AA
28260726 TTCAAAATATATAAAATATTCAAAAC-A
1 TTCAAAATATATAAAA-ATT-AAAACAA
28260753 TTCTAAAA
1 TTC-AAAA
28260761 AATTCTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 19 0.61
28 7 0.23
29 5 0.16
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (26 bp):
TTCAAAATATATAAAAATTAAAACAA
Found at i:28260765 original size:19 final size:18
Alignment explanation
Indices: 28260723--28260765 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
28260713 AAATTAAAAC
*
28260723 AAATTCAAAATATATAAA
1 AAATTCAAAACATATAAA
* *
28260741 ATATTCAAAACATTCTAAA
1 AAATTCAAAACA-TATAAA
28260760 AAATTC
1 AAATTC
28260766 TATATAGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATTCAAAACATATAAA
Found at i:28261174 original size:170 final size:170
Alignment explanation
Indices: 28260991--28261335 Score: 663
Period size: 170 Copynumber: 2.0 Consensus size: 170
28260981 TTACTCAACC
* *
28260991 TTTTTTTTTCTTGGCATGAACGAGTTATGATAGAATGCGTCTTATTTATCTCGACGAAATGGGTG
1 TTTTTTTTTCTTGGCATGAACAAGTTATGATAGAATGCGTCTTATTTATCTCAACGAAATGGGTG
28261056 AAACGACCATTTCAATTCCCGAAATATTTACGATGTTCAGTATCTTATCCATGGCTTCTCTTGCA
66 AAACGACCATTTCAATTCCCGAAATATTTACGATGTTCAGTATCTTATCCATGGCTTCTCTTGCA
28261121 TTACTAAGCATGAGTGGTTTTGATGCAGAATTGATAGTCT
131 TTACTAAGCATGAGTGGTTTTGATGCAGAATTGATAGTCT
28261161 TTTTTTTTTCTTGGCATGAACAAGTTATGATAGAATGCGTCTTATTTATCTCAACGAAATGGGTG
1 TTTTTTTTTCTTGGCATGAACAAGTTATGATAGAATGCGTCTTATTTATCTCAACGAAATGGGTG
28261226 AAACGACCATTTCAATTCCCGAAATATTTACGATGTTCAGTATCTTATCCATGGCTTCTCTTGCA
66 AAACGACCATTTCAATTCCCGAAATATTTACGATGTTCAGTATCTTATCCATGGCTTCTCTTGCA
*
28261291 TTACTGAGCATGAGTGGTTTTGATGCAGAATTGATAGTCT
131 TTACTAAGCATGAGTGGTTTTGATGCAGAATTGATAGTCT
28261331 TTTTT
1 TTTTT
28261336 GGAATAATTA
Statistics
Matches: 172, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 172 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (170 bp):
TTTTTTTTTCTTGGCATGAACAAGTTATGATAGAATGCGTCTTATTTATCTCAACGAAATGGGTG
AAACGACCATTTCAATTCCCGAAATATTTACGATGTTCAGTATCTTATCCATGGCTTCTCTTGCA
TTACTAAGCATGAGTGGTTTTGATGCAGAATTGATAGTCT
Found at i:28263028 original size:21 final size:21
Alignment explanation
Indices: 28263004--28263047 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28262994 GAAACTTTAG
*
28263004 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
28263025 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
28263046 TA
1 TA
28263048 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Done.