Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 19 of 250
Found at i:5301050 original size:22 final size:21
Alignment explanation
Indices: 5301009--5301050 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5300999 TTTAGATAAA
*
5301009 ATTATTAAAAATACAGAAAAT
1 ATTATTAAAAATACAAAAAAT
*
5301030 ATTATTATAAAATATAAAAAA
1 ATTATTA-AAAATACAAAAAA
5301051 AACTGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
ATTATTAAAAATACAAAAAAT
Found at i:5301169 original size:16 final size:17
Alignment explanation
Indices: 5301126--5301181 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
5301116 ATGGTAAAAA
*
5301126 AAATAATAAAGAATTATT
1 AAATATTAAA-AATTATT
5301144 AGAATCATTAAAAATTA-T
1 A-AAT-ATTAAAAATTATT
*
5301162 AAATATTAAAAAATATT
1 AAATATTAAAAATTATT
5301179 AAA
1 AAA
5301182 AATTTAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 10 0.30
17 7 0.21
18 3 0.09
19 8 0.24
20 5 0.15
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
AAATATTAAAAATTATT
Found at i:5301177 original size:10 final size:10
Alignment explanation
Indices: 5301162--5301252 Score: 50
Period size: 10 Copynumber: 9.2 Consensus size: 10
5301152 TAAAAATTAT
5301162 AAATATTAAA
1 AAATATTAAA
5301172 AAATATT-AA
1 AAATATTAAA
5301181 AAAT-TTAGAA
1 AAATATTA-AA
*
5301191 AAATTTTAGAA
1 AAATATTA-AA
*
5301202 AAAT-GTATAA
1 AAATATTA-AA
5301212 AAATA-TAAA
1 AAATATTAAA
*
5301221 TAAT-TCTAAA
1 AAATAT-TAAA
* *
5301231 TAATTATT-TA
1 -AAATATTAAA
5301241 AAATATTAAA
1 AAATATTAAA
5301251 AA
1 AA
5301253 TTAAGATAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
8 2 0.03
9 17 0.27
10 31 0.48
11 13 0.20
12 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (10 bp):
AAATATTAAA
Found at i:5301286 original size:19 final size:19
Alignment explanation
Indices: 5301170--5301290 Score: 56
Period size: 19 Copynumber: 6.3 Consensus size: 19
5301160 ATAAATATTA
*
5301170 AAAAATATTA-AAAATTTAG
1 AAAAATA-TAGAAAATTTAT
* *
5301189 AAAAATTTTAGAAAAATGTAT
1 AAAAA-TATAG-AAAATTTAT
5301210 AAAAATATA-AATAATTCTA-
1 AAAAATATAGAA-AATT-TAT
* ** *
5301229 AATAATTATTTAAAATAT-T
1 AA-AAATATAGAAAATTTAT
*
5301248 AAAAAT-TAAGATAAA-GTAT
1 AAAAATAT-AGA-AAATTTAT
5301267 AAAAATATAGAAAATTTAT
1 AAAAATATAGAAAATTTAT
5301286 AAAAA
1 AAAAA
5301291 GCATATATAG
Statistics
Matches: 76, Mismatches: 13, Indels: 26
0.66 0.11 0.23
Matches are distributed among these distances:
17 1 0.01
18 10 0.13
19 36 0.47
20 15 0.20
21 14 0.18
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAAATATAGAAAATTTAT
Found at i:5301682 original size:18 final size:18
Alignment explanation
Indices: 5301631--5301708 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 18
5301621 ATGTTTAACA
* *
5301631 ATTTTATGATTTTTTTATT
1 ATTTTATAATTTTTCTA-T
*
5301650 ATTTT-TAAATATTTCTAT
1 ATTTTAT-AATTTTTCTAT
*
5301668 CTTTTATAATTTTTCTAT
1 ATTTTATAATTTTTCTAT
*
5301686 ATGTTAT-ATTTTT-TAT
1 ATTTTATAATTTTTCTAT
*
5301702 TTTTTAT
1 ATTTTAT
5301709 TTTAATAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
16 8 0.17
17 6 0.12
18 21 0.44
19 13 0.27
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTTATAATTTTTCTAT
Found at i:5301687 original size:26 final size:27
Alignment explanation
Indices: 5301643--5301701 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
5301633 TTTATGATTT
* *
5301643 TTTTATTATTTTTAAATAT-TTCTATC
1 TTTTATAATTTTTAAATATGTTATATC
** *
5301669 TTTTATAATTTTTCTATATGTTATATT
1 TTTTATAATTTTTAAATATGTTATATC
5301696 TTTTAT
1 TTTTAT
5301702 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTATAATTTTTAAATATGTTATATC
Found at i:5301732 original size:8 final size:8
Alignment explanation
Indices: 5301642--5301740 Score: 58
Period size: 8 Copynumber: 11.8 Consensus size: 8
5301632 TTTTATGATT
5301642 TTTTTATTA
1 TTTTTA-TA
*
5301651 TTTTTAAA
1 TTTTTATA
* *
5301659 TATTTCTA
1 TTTTTATA
5301667 TCTTTTATAA
1 T-TTTTAT-A
*
5301677 TTTTTCTA
1 TTTTTATA
*
5301685 TATGTTATA
1 T-TTTTATA
5301694 TTTTT-TA
1 TTTTTATA
5301701 TTTTT-TA
1 TTTTTATA
*
5301708 TTTTAATAAA
1 TTTT--TATA
5301718 TTTTTTATA
1 -TTTTTATA
5301727 TTTTTATA
1 TTTTTATA
*
5301735 CTTTTA
1 TTTTTA
5301741 ATTAGGGGTG
Statistics
Matches: 70, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
7 13 0.19
8 25 0.36
9 25 0.36
10 3 0.04
11 4 0.06
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (8 bp):
TTTTTATA
Found at i:5302177 original size:23 final size:20
Alignment explanation
Indices: 5302124--5302166 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5302114 TTGTAAAAAA
*
5302124 TTTTAA-TTTTAAAAATTAT
1 TTTTAATTTTTGAAAATTAT
5302143 TTTTAATTTTTGAAAATTAT
1 TTTTAATTTTTGAAAATTAT
5302163 TTTT
1 TTTT
5302167 TGTAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTAATTTTTGAAAATTAT
Found at i:5304133 original size:20 final size:18
Alignment explanation
Indices: 5304077--5304134 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 18
5304067 ATAATAACTT
*
5304077 TAAATTTTCTAATTTTTT
1 TAAATTTTCTAATTTTTA
5304095 TACAATTATTCTTACATTTTTAA
1 TA-AATT-TTC-TA-ATTTTT-A
5304118 TAAATTTTCTATATTTT
1 TAAATTTTCTA-ATTTT
5304135 GCATATTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 10 0.30
21 5 0.15
22 10 0.30
23 2 0.06
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TAAATTTTCTAATTTTTA
Found at i:5308179 original size:26 final size:26
Alignment explanation
Indices: 5308143--5308252 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
5308133 TGATACAAAT
5308143 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5308169 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5308195 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
5308221 TGATAAT-GCGTTAGGTAAATGTTTCA
1 TGATAATAG-GTTAGGTAAATGTTCCA
5308247 TGATAA
1 TGATAA
5308253 GAATTTCATG
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 1 0.01
26 80 0.99
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5311902 original size:34 final size:32
Alignment explanation
Indices: 5311864--5311933 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
5311854 TTGTTAAGTG
*
5311864 ACCAAAAATGAAATTTGCTAATAGTTTGTTGACT
1 ACCAAAAAT--AATTTACTAATAGTTTGTTGACT
*
5311898 ACC-AAGATAATTTACTAATAGTTTGTTGACT
1 ACCAAAAATAATTTACTAATAGTTTGTTGACT
5311929 ACCAA
1 ACCAA
5311934 GATAGTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 25 0.76
32 1 0.03
33 4 0.12
34 3 0.09
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (32 bp):
ACCAAAAATAATTTACTAATAGTTTGTTGACT
Found at i:5311910 original size:31 final size:31
Alignment explanation
Indices: 5311875--5311937 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
5311865 CCAAAAATGA
*
5311875 AATTTGCTAATAGTTTGTTGACTACCAAGAT
1 AATTTACTAATAGTTTGTTGACTACCAAGAT
5311906 AATTTACTAATAGTTTGTTGACTACCAAGAT
1 AATTTACTAATAGTTTGTTGACTACCAAGAT
5311937 A
1 A
5311938 GTAATGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (31 bp):
AATTTACTAATAGTTTGTTGACTACCAAGAT
Found at i:5324148 original size:49 final size:49
Alignment explanation
Indices: 5324092--5324190 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
5324082 TGATATTGGG
5324092 TTTAAAGGCTCGAAGTTTACTTGGTTTAATCTTTGTAATATCTCTGGTC
1 TTTAAAGGCTCGAAGTTTACTTGGTTTAATCTTTGTAATATCTCTGGTC
5324141 TTTAAAGGCTCGAAGTTTACTTGGTTTAATCTTTGTAATATCTCTGGTC
1 TTTAAAGGCTCGAAGTTTACTTGGTTTAATCTTTGTAATATCTCTGGTC
5324190 T
1 T
5324191 CATCCAATAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (49 bp):
TTTAAAGGCTCGAAGTTTACTTGGTTTAATCTTTGTAATATCTCTGGTC
Found at i:5329654 original size:72 final size:72
Alignment explanation
Indices: 5329515--5329657 Score: 180
Period size: 72 Copynumber: 2.0 Consensus size: 72
5329505 AAGTATCATA
** * ** * *
5329515 GATTGATTGCCTCTTTTGTGGCATTTAAAAACGTCACGGAAAATGCTATCCAAAATGTGACACAT
1 GATTGATTGCCTCTTTTGTAACATTTAAAAACATCACAAAAAATGCTATCCAAAACGTCACACAT
5329580 TGTTTGT
66 TGTTTGT
* * *
5329587 GATTGATTGCCTCTTTTTTAACATTTAAAAACATCACAAAAAATTCTATTCAAAACGTCACGA-A
1 GATTGATTGCCTCTTTTGTAACATTTAAAAACATCACAAAAAATGCTATCCAAAACGTCAC-ACA
5329651 TTGTTTG
65 TTGTTTG
5329658 ACTATTTTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 59 0.98
73 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (72 bp):
GATTGATTGCCTCTTTTGTAACATTTAAAAACATCACAAAAAATGCTATCCAAAACGTCACACAT
TGTTTGT
Found at i:5332958 original size:22 final size:23
Alignment explanation
Indices: 5332910--5332958 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
5332900 CAATTTTTGA
*
5332910 TTTA-TTGTTCTATTTTATTTAT
1 TTTATTTGTTCTATTTTAATTAT
* *
5332932 CTTATTTGTT-TATTTTAATTGT
1 TTTATTTGTTCTATTTTAATTAT
5332954 TTTAT
1 TTTAT
5332959 CTAACTTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTATTTGTTCTATTTTAATTAT
Found at i:5334963 original size:24 final size:26
Alignment explanation
Indices: 5334913--5334965 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
5334903 AAAATCTTCG
5334913 CTTTCATTGCTTCTGCTGCCACTTGAT
1 CTTTCATTGCTTCT-CTGCCACTTGAT
*
5334940 CTTTCGTTGCTTCT-T-CCACTTGAT
1 CTTTCATTGCTTCTCTGCCACTTGAT
5334964 CT
1 CT
5334966 CTTGCTAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 11 0.44
25 1 0.04
27 13 0.52
ACGTcount: A:0.09, C:0.30, G:0.13, T:0.47
Consensus pattern (26 bp):
CTTTCATTGCTTCTCTGCCACTTGAT
Found at i:5337107 original size:24 final size:25
Alignment explanation
Indices: 5337069--5337119 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
5337059 CACGGACCAA
5337069 TTTTTAATAGTAAAAATAGATTATT
1 TTTTTAATAGTAAAAATAGATTATT
* *
5337094 TTTTTAATAG-AAAACTAGTTTATT
1 TTTTTAATAGTAAAAATAGATTATT
5337118 TT
1 TT
5337120 ATTCTCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (25 bp):
TTTTTAATAGTAAAAATAGATTATT
Found at i:5342580 original size:18 final size:19
Alignment explanation
Indices: 5342524--5342580 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
5342514 AAACTTACAA
*
5342524 AAAAATACAAAAAATTATTT
1 AAAAATAAAAAAAATTA-TT
*
5342544 AAAAGTAAAAAAGAATTATT
1 AAAAATAAAAAA-AATTATT
*
5342564 AAAAAT-AGAAAAATTAT
1 AAAAATAAAAAAAATTAT
5342581 AACTTTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.19
19 4 0.12
20 17 0.53
21 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAAATAAAAAAAATTATT
Found at i:5342935 original size:39 final size:39
Alignment explanation
Indices: 5342856--5342969 Score: 104
Period size: 41 Copynumber: 2.8 Consensus size: 39
5342846 TATATAAAAG
* **
5342856 TTATAAAAAATATTAAAAACATTATAGAAAATATTTAAATT
1 TTATAAAAAATA-TAAAAA-ATTATAAAAAATATCAAAATT
*
5342897 TTATTAAAAATATAAAAAATTATAAAAAATCA-CAAAATT
1 TTATAAAAAATATAAAAAATTATAAAAAAT-ATCAAAATT
* *
5342936 TATAAAAAAAAATCATAAAGAACTTATAAAAAAT
1 T-T-ATAAAAAAT-ATAAA-AAATTATAAAAAAT
5342970 TGTAAAAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
39 17 0.28
40 8 0.13
41 18 0.30
42 5 0.08
43 13 0.21
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (39 bp):
TTATAAAAAATATAAAAAATTATAAAAAATATCAAAATT
Found at i:5342966 original size:21 final size:19
Alignment explanation
Indices: 5342849--5342986 Score: 75
Period size: 19 Copynumber: 6.8 Consensus size: 19
5342839 GATCAAATAT
*
5342849 ATAAAAGTTATAAAAAAT-
1 ATAAAAATTATAAAAAATC
5342867 ATTAAAAACATTATAGAAAATAT-
1 A-T-AAAA-ATTATA-AAAA-ATC
* ** *
5342890 TTAAATTTTATTAAAAAT-
1 ATAAAAATTATAAAAAATC
5342908 ATAAAAAATTATAAAAAATC
1 AT-AAAAATTATAAAAAATC
* *
5342928 ACAAAATTTATAAAAAAAAATC
1 ATAAAAATTAT---AAAAAATC
*
5342950 ATAAAGAACTTATAAAAAATT
1 ATAAA-AA-TTATAAAAAATC
*
5342971 GTAAAAATTATAAAAA
1 ATAAAAATTATAAAAA
5342987 TATATAGTAA
Statistics
Matches: 93, Mismatches: 15, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.04
19 35 0.38
20 11 0.12
21 19 0.20
22 17 0.18
23 3 0.03
24 4 0.04
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.30
Consensus pattern (19 bp):
ATAAAAATTATAAAAAATC
Found at i:5342982 original size:43 final size:41
Alignment explanation
Indices: 5342902--5342986 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 41
5342892 AAATTTTATT
*
5342902 AAAAATATAAAAAATTATAAAAAATCACAAAATTTATAAAA
1 AAAAATATAAAAAATTATAAAAAATCACAAAAATTATAAAA
* ***
5342943 AAAAATCATAAAGAACTTATAAAAAATTGTAAAAATTATAAAA
1 AAAAAT-ATAAA-AAATTATAAAAAATCACAAAAATTATAAAA
5342986 A
1 A
5342987 TATATAGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 6 0.16
42 5 0.14
43 26 0.70
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (41 bp):
AAAAATATAAAAAATTATAAAAAATCACAAAAATTATAAAA
Found at i:5342992 original size:10 final size:10
Alignment explanation
Indices: 5342843--5343013 Score: 72
Period size: 10 Copynumber: 17.0 Consensus size: 10
5342833 AGAAATGATC
5342843 AAATATATAA
1 AAATATATAA
*
5342853 AAGT-TATAA
1 AAATATATAA
5342862 AAA-ATATTAA
1 AAATATA-TAA
*
5342872 AAACATTATAGA
1 AAATA-TATA-A
*
5342884 AAATAT-TTA
1 AAATATATAA
* *
5342893 AATTTTATTAA
1 AAATATA-TAA
5342904 AAATATA-AA
1 AAATATATAA
5342913 AAAT-TATAA
1 AAATATATAA
*
5342922 AAA-ATCACAA
1 AAATAT-ATAA
* *
5342932 AATTTATAAAA
1 AA-ATATATAA
*
5342943 AAAAATCATAA
1 AAATAT-ATAA
5342954 AGAACT-TATAA
1 A-AA-TATATAA
*
5342965 AAA-ATTGTAA
1 AAATA-TATAA
5342975 AAAT-TATAA
1 AAATATATAA
*
5342984 AAATATATAG
1 AAATATATAA
*
5342994 TAATATATAA
1 AAATATATAA
*
5343004 AAATTTATAA
1 AAATATATAA
5343014 TTTTTTAATA
Statistics
Matches: 119, Mismatches: 23, Indels: 38
0.66 0.13 0.21
Matches are distributed among these distances:
8 2 0.02
9 34 0.29
10 46 0.39
11 25 0.21
12 12 0.10
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (10 bp):
AAATATATAA
Found at i:5343453 original size:9 final size:9
Alignment explanation
Indices: 5343439--5343494 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
5343429 ATAGGATACG
5343439 ATAATTTTT
1 ATAATTTTT
5343448 ATAATTTTTTT
1 ATAA--TTTTT
*
5343459 ATAAATTTT
1 ATAATTTTT
5343468 AT-ATTTCTT
1 ATAATTT-TT
5343477 -TACATTTTT
1 ATA-ATTTTT
5343486 ATAATTTTT
1 ATAATTTTT
5343495 TTAAGACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
8 4 0.10
9 20 0.51
10 6 0.15
11 9 0.23
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5343467 original size:10 final size:10
Alignment explanation
Indices: 5343441--5343586 Score: 56
Period size: 10 Copynumber: 14.9 Consensus size: 10
5343431 AGGATACGAT
5343441 AATTTTTATA
1 AATTTTTATA
*
5343451 ATTTTTTTATA
1 A-ATTTTTATA
5343462 AA-TTTTAT-
1 AATTTTTATA
5343470 -ATTTCTT-TA
1 AATTT-TTATA
*
5343479 CATTTTTAT-
1 AATTTTTATA
*
5343488 AATTTTTTTA
1 AATTTTTATA
*
5343498 AGA-CTTTATA
1 A-ATTTTTATA
*
5343508 AAGTTTTATA
1 AATTTTTATA
* *
5343518 ACTTTTTTCTA
1 A-ATTTTTATA
* *
5343529 TATTTCTATA
1 AATTTTTATA
*
5343539 TA-TTTTATA
1 AATTTTTATA
* *
5343548 TATTTTAATTA
1 AATTTTTA-TA
* *
5343559 AAATTTAAT-
1 AATTTTTATA
*
5343568 AATTCTTATA
1 AATTTTTATA
5343578 AATTTTTAT
1 AATTTTTAT
5343587 TGACTTTTAT
Statistics
Matches: 101, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
7 1 0.01
8 3 0.03
9 32 0.32
10 41 0.41
11 24 0.24
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (10 bp):
AATTTTTATA
Found at i:5345873 original size:35 final size:35
Alignment explanation
Indices: 5345822--5345892 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
5345812 AATATTCCAC
* *
5345822 ATATAAAATTCCGCATCGTCCTATTATTTTTTTTA
1 ATATAAAATTCCGCATCGTCCCATTAATTTTTTTA
*
5345857 ATATGAAATTCCGCATCGTCCCATTAATTTTTTTA
1 ATATAAAATTCCGCATCGTCCCATTAATTTTTTTA
5345892 A
1 A
5345893 CTTTACTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (35 bp):
ATATAAAATTCCGCATCGTCCCATTAATTTTTTTA
Found at i:5348995 original size:13 final size:13
Alignment explanation
Indices: 5348977--5349002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5348967 CATTCAAGCA
5348977 CTCTTTTTATGCT
1 CTCTTTTTATGCT
5348990 CTCTTTTTATGCT
1 CTCTTTTTATGCT
5349003 GCTTTGCCCT
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:0.08, C:0.23, G:0.08, T:0.62
Consensus pattern (13 bp):
CTCTTTTTATGCT
Found at i:5356653 original size:31 final size:31
Alignment explanation
Indices: 5356615--5356681 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
5356605 GAAAACCCTA
* *
5356615 AAGTTCAGGCTTCAATATA-AGAATAATTGTC
1 AAGTTCAGGCTTCAATATAGA-AACAATTGCC
5356646 AAGTTCAGGCTTCAATATAGAAACAATTGCC
1 AAGTTCAGGCTTCAATATAGAAACAATTGCC
5356677 AAGTT
1 AAGTT
5356682 AAAGGACTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (31 bp):
AAGTTCAGGCTTCAATATAGAAACAATTGCC
Found at i:5357485 original size:96 final size:96
Alignment explanation
Indices: 5357321--5357512 Score: 375
Period size: 96 Copynumber: 2.0 Consensus size: 96
5357311 ATGTTTCCCC
*
5357321 CATTCAGGTCCCTGTTTATATCATTTTGTTTTCTTTTTGGCCAATATGAAAAGGATTAATGGAAT
1 CATTCAGGTCCCTGTTTATATCATTTTGTTTTCTTTTTCGCCAATATGAAAAGGATTAATGGAAT
5357386 TTTCTTTCCTCTCAAGTTGGCAAAGATCACT
66 TTTCTTTCCTCTCAAGTTGGCAAAGATCACT
5357417 CATTCAGGTCCCTGTTTATATCATTTTGTTTTCTTTTTCGCCAATATGAAAAGGATTAATGGAAT
1 CATTCAGGTCCCTGTTTATATCATTTTGTTTTCTTTTTCGCCAATATGAAAAGGATTAATGGAAT
5357482 TTTCTTTCCTCTCAAGTTGGCAAAGATCACT
66 TTTCTTTCCTCTCAAGTTGGCAAAGATCACT
5357513 GATGTGGGGG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (96 bp):
CATTCAGGTCCCTGTTTATATCATTTTGTTTTCTTTTTCGCCAATATGAAAAGGATTAATGGAAT
TTTCTTTCCTCTCAAGTTGGCAAAGATCACT
Found at i:5358608 original size:149 final size:151
Alignment explanation
Indices: 5358431--5358732 Score: 554
Period size: 151 Copynumber: 2.0 Consensus size: 151
5358421 TATATTATAA
* * *
5358431 TAGTATAATGATTTTATCCTTCAGTCTTTAT-AA-TTTTTTTTATCAATTTGATTATTATTAATT
1 TAGTATAATGATTTTAGCCTTCAATCTTTATAAATTTTTTTTTATCAATTTAATTATTATTAATT
5358494 TTTTTAATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAA
66 TTTTTAATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAA
5358559 AGACTCGAATTGTTGTTTTCT
131 AGACTCGAATTGTTGTTTTCT
5358580 TAGTATAATGATTTTAGCCTTCAATCTTTATAAATTTTTTTTTATCAATTTAATTATTATTAATT
1 TAGTATAATGATTTTAGCCTTCAATCTTTATAAATTTTTTTTTATCAATTTAATTATTATTAATT
*
5358645 TTTTTAATTAAATTTAATCCTAAATTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAA
66 TTTTTAATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAA
5358710 AGACTCGAATTGTTGTTTTCT
131 AGACTCGAATTGTTGTTTTCT
5358731 TA
1 TA
5358733 CCGAAATTAT
Statistics
Matches: 147, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
149 29 0.20
150 2 0.01
151 116 0.79
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (151 bp):
TAGTATAATGATTTTAGCCTTCAATCTTTATAAATTTTTTTTTATCAATTTAATTATTATTAATT
TTTTTAATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAA
AGACTCGAATTGTTGTTTTCT
Found at i:5358953 original size:62 final size:62
Alignment explanation
Indices: 5358856--5358980 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
5358846 TATAAATTTG
* * *
5358856 AAATTATTTGTTGGTGTGACACATAAAACAAATAGTGTCATGTTAGCATGAAGTATTCGTAA
1 AAATTATTTGTTAGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATTCATAA
5358918 AAATTATTTGTTAGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATTCATAA
1 AAATTATTTGTTAGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATTCATAA
5358980 A
1 A
5358981 CTAACACATG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (62 bp):
AAATTATTTGTTAGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATTCATAA
Found at i:5360453 original size:34 final size:35
Alignment explanation
Indices: 5360380--5360459 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
5360370 CTCGAACCAT
* * * * *
5360380 GAACCCTAAACTCTGAATCTTGAATATTGAACCTA
1 GAACTCTAAACTCTGAATCTCGAACATTAAACCCA
*
5360415 GAACTCTAAACTC-GAATCTCGAACATTAAACCCC
1 GAACTCTAAACTCTGAATCTCGAACATTAAACCCA
*
5360449 GAACTCAAAAC
1 GAACTCTAAAC
5360460 ACTAAACTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 26 0.68
35 12 0.32
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.23
Consensus pattern (35 bp):
GAACTCTAAACTCTGAATCTCGAACATTAAACCCA
Found at i:5360538 original size:20 final size:20
Alignment explanation
Indices: 5360509--5360546 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5360499 TCCCAAATCC
5360509 AAACTCGAACCTTGAACCCT
1 AAACTCGAACCTTGAACCCT
*
5360529 AAACTTGAACCTTGAACC
1 AAACTCGAACCTTGAACC
5360547 TCTGGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.32, G:0.11, T:0.21
Consensus pattern (20 bp):
AAACTCGAACCTTGAACCCT
Found at i:5360909 original size:20 final size:20
Alignment explanation
Indices: 5360886--5360928 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
5360876 AAATCCAAAT
*
5360886 TAAAATATTGAAATTCAGGA
1 TAAAATACTGAAATTCAGGA
*
5360906 TAAAATCCTGAAATTCAGGA
1 TAAAATACTGAAATTCAGGA
5360926 TAA
1 TAA
5360929 GAGTACTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (20 bp):
TAAAATACTGAAATTCAGGA
Found at i:5361552 original size:2 final size:2
Alignment explanation
Indices: 5361545--5361573 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5361535 CCCAAAATTC
5361545 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5361574 GGTATATGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5365021 original size:12 final size:12
Alignment explanation
Indices: 5365004--5365028 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5364994 TTTTAAAATT
5365004 ATGAATAATATA
1 ATGAATAATATA
5365016 ATGAATAATATA
1 ATGAATAATATA
5365028 A
1 A
5365029 AACATAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGAATAATATA
Found at i:5365085 original size:11 final size:11
Alignment explanation
Indices: 5365069--5365114 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
5365059 TATACATAAC
5365069 ATATAATAAAA
1 ATATAATAAAA
*
5365080 AAATAATAAGTAA
1 ATATAATAA--AA
5365093 TATATAATAAAA
1 -ATATAATAAAA
5365105 ATATAATAAA
1 ATATAATAAA
5365115 TGTTATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 18 0.60
12 2 0.07
13 2 0.07
14 8 0.27
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
ATATAATAAAA
Found at i:5365099 original size:25 final size:25
Alignment explanation
Indices: 5365064--5365148 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
5365054 TACGATATAC
*
5365064 ATAACATATAATAAAAAAATAATAA
1 ATAATATATAATAAAAAAATAATAA
* *
5365089 GTAATATATAATAAAAATATAATAA
1 ATAATATATAATAAAAAAATAATAA
**
5365114 ATGTTATATAATAAAATAAA-ATATAA
1 ATAATATATAATAAAA-AAATA-ATAA
5365140 AT-ATATATA
1 ATAATATATA
5365149 GGAAAATAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 42 0.84
26 8 0.16
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAATATATAATAAAAAAATAATAA
Found at i:5377622 original size:14 final size:14
Alignment explanation
Indices: 5377599--5377633 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5377589 ATCCTATAAC
*
5377599 AATCTTTAGGATTT
1 AATCTATAGGATTT
5377613 AATCTATAGGATTT
1 AATCTATAGGATTT
5377627 AATCTAT
1 AATCTAT
5377634 CAATAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (14 bp):
AATCTATAGGATTT
Found at i:5381519 original size:49 final size:47
Alignment explanation
Indices: 5381459--5382248 Score: 1256
Period size: 47 Copynumber: 16.6 Consensus size: 47
5381449 GATAATTGTG
* *
5381459 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
5381506 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
5381553 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
5381602 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
5381649 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5381696 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
5381745 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGACCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
5381792 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
5381841 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
5381890 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5381937 ATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
5381986 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5382035 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
5382082 ATGTGAAAGTGTATATATGTGATCAGGCCTAATAGCCGATATGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5382129 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
5382176 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5382223 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
5382249 TCCCGAAGGG
Statistics
Matches: 698, Mismatches: 37, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
47 422 0.60
49 276 0.40
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:5381527 original size:96 final size:94
Alignment explanation
Indices: 5381459--5382248 Score: 1220
Period size: 96 Copynumber: 8.3 Consensus size: 94
5381449 GATAATTGTG
*
5381459 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* *
5381524 GTGATAAGGCCGAATGGCCAATGTGATGA
66 GTGATAAGGCCTAATGGCCGATGTGATGA
5381553 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
5381618 ATGTGATAAGGCCTAATGGCCGATGTGATGA
64 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
5381649 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATAT
*
5381714 ATGTGATAAGGCCTAATAGCCGATGTGATGA
64 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * *
5381745 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATAT
5381810 ATGTGATAAGGCCTAATGGCCGATGTGATGA
64 ATGTGATAAGGCCTAATGGCCGATGTGATGA
5381841 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
5381906 ATGTGATAAGGCCTAATGGCCGATGTGATGA
64 ATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5381937 ATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
5382002 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
62 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
5382035 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* * *
5382100 GTGATCAGGCCTAATAGCCGATATGATGA
66 GTGATAAGGCCTAATGGCCGATGTGATGA
* *
5382129 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* * * * * * *
5382194 GTGACAGGGCCGAGTGGCCAACGTGATGG
66 GTGATAAGGCCTAATGGCCGATGTGATGA
* *
5382223 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTATATATATGTGATAAG
5382249 TCCCGAAGGG
Statistics
Matches: 654, Mismatches: 34, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
94 193 0.30
96 371 0.57
98 90 0.14
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (94 bp):
ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:5390192 original size:24 final size:24
Alignment explanation
Indices: 5390165--5390216 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5390155 AAAAAAAAAG
* * *
5390165 AAAAGAAAT-CACCATGAATTTAC
1 AAAAAAAATCCACCATAAATCTAC
*
5390188 AAAAAAACTCCACCATAAATCTAC
1 AAAAAAAATCCACCATAAATCTAC
5390212 AAAAA
1 AAAAA
5390217 TCAACATTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.58, C:0.21, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAAAAAATCCACCATAAATCTAC
Found at i:5392821 original size:14 final size:14
Alignment explanation
Indices: 5392802--5392828 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5392792 ACATCTTTAT
5392802 TTTTCTTATTTTTG
1 TTTTCTTATTTTTG
5392816 TTTTCTTATTTTT
1 TTTTCTTATTTTT
5392829 TTCTTTTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTCTTATTTTTG
Found at i:5395314 original size:59 final size:59
Alignment explanation
Indices: 5395174--5395314 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 59
5395164 TTGAGTGTTA
* *
5395174 ACTGGGCCTTAGCCCATATCAATATTAATCAGGGCCATAGCCCCTTACAGTAACAGAGTAT
1 ACTGGGCCTT-GCCCATATCAGTATCAATCAGGGCCATAGCCCCTTACAGT-ACAGAGTAT
* * *
5395235 ACTGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAG-CCCTATACAAGT-C-GAGATAT
1 ACTGGGCCTTGCCCATATCAGTATCAATCAGGGCCATAGCCCCT-TAC-AGTACAGAG-TAT
*
5395294 ATTGGGCCTTGCCCATATCAG
1 ACTGGGCCTTGCCCATATCAG
5395315 CACAGTTGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
58 3 0.04
59 27 0.39
60 28 0.40
61 12 0.17
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.25
Consensus pattern (59 bp):
ACTGGGCCTTGCCCATATCAGTATCAATCAGGGCCATAGCCCCTTACAGTACAGAGTAT
Found at i:5395956 original size:8 final size:8
Alignment explanation
Indices: 5395942--5395971 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5395932 ACAAATGCCA
5395942 GCTTTTCG
1 GCTTTTCG
*
5395950 ACTTTTCG
1 GCTTTTCG
5395958 GCTTTTCG
1 GCTTTTCG
5395966 GCTTTT
1 GCTTTT
5395972 GCTGATCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.23, G:0.20, T:0.53
Consensus pattern (8 bp):
GCTTTTCG
Found at i:5398842 original size:9 final size:9
Alignment explanation
Indices: 5398828--5398852 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5398818 TTTTAGGGGT
5398828 ATTTTAGGA
1 ATTTTAGGA
5398837 ATTTTAGGA
1 ATTTTAGGA
5398846 ATTTTAG
1 ATTTTAG
5398853 CCTCAGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (9 bp):
ATTTTAGGA
Found at i:5403795 original size:23 final size:24
Alignment explanation
Indices: 5403769--5403813 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5403759 ATATCCCCAC
*
5403769 ATGGAGTGTAG-GGTTGGATGGAG
1 ATGGAGTGTAGAGATTGGATGGAG
*
5403792 ATGGTGTGTAGAGATTGGATGG
1 ATGGAGTGTAGAGATTGGATGG
5403814 GTAGGATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.22, C:0.00, G:0.49, T:0.29
Consensus pattern (24 bp):
ATGGAGTGTAGAGATTGGATGGAG
Found at i:5417371 original size:43 final size:43
Alignment explanation
Indices: 5417323--5417473 Score: 196
Period size: 43 Copynumber: 3.5 Consensus size: 43
5417313 TATCCTAGAT
* *
5417323 ATGGTCTTACATGTTATCACATATCGATGCCAATGTCTCAGAC
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
* * * * *
5417366 ATGGTCTTACACGAAATCATATAACGATGCCAATGTCCCAGAA
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
* * *
5417409 ATGATCTTACATGTAATCACA-ATACAATGCCAATGTCCCAAAC
1 ATGGTCTTACATGTAATCACATAT-CGATGCCAATGTCCCAGAC
5417452 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
5417474 CTCAGTCATC
Statistics
Matches: 90, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
42 1 0.01
43 89 0.99
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
Found at i:5419918 original size:48 final size:48
Alignment explanation
Indices: 5419855--5419991 Score: 168
Period size: 48 Copynumber: 2.9 Consensus size: 48
5419845 ATAGTGTCTG
* * *
5419855 GTTAACCGTTTGGGTTAAACCTACATGAATAAA-AGATAATAGTACCTA
1 GTTACCCGTTAGGGTTAAACCTACACGAATAAAGA-ATAATAGTACCTA
* *
5419903 GTTACCCGTTAGGGTTAAACCTACACGAATAATGAATAATAGTGCCTA
1 GTTACCCGTTAGGGTTAAACCTACACGAATAAAGAATAATAGTACCTA
* * * * *
5419951 ATTACCCATTATGGTTAAACCTACACGATTAATGAATAATA
1 GTTACCCGTTAGGGTTAAACCTACACGAATAAAGAATAATA
5419992 ATGTTTGGTT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
48 78 0.99
49 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (48 bp):
GTTACCCGTTAGGGTTAAACCTACACGAATAAAGAATAATAGTACCTA
Found at i:5429951 original size:29 final size:29
Alignment explanation
Indices: 5429911--5429969 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
5429901 TTGTAGAAGA
* *
5429911 GGTGGAGAACTTGTTCGTTAAGAGTTTGT
1 GGTGAAGAACTTGTTCGTTAAGAATTTGT
*
5429940 GGTGAAGAACTTGTTCGTTGAGAATTTGT
1 GGTGAAGAACTTGTTCGTTAAGAATTTGT
5429969 G
1 G
5429970 TCAAGTTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.34, T:0.37
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCGTTAAGAATTTGT
Found at i:5439704 original size:48 final size:48
Alignment explanation
Indices: 5439648--5439797 Score: 183
Period size: 48 Copynumber: 3.1 Consensus size: 48
5439638 CTGAGCTATC
* *
5439648 GACATCGATATGTGATCCCATGAAAGACTATGTCTGGGACATGGCATT
1 GACATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATT
* **
5439696 GACATCGATCTACGATCCCATGTAAGACCATGTCTGGGACATGGCATT
1 GACATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATT
* * * * * * *
5439744 GGCATCAATATGTGATCTCATGTAATACCATATCGGGGATATGGCATT
1 GACATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATT
*
5439792 GGCATC
1 GACATC
5439798 CTACCATGTG
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 87 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (48 bp):
GACATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATT
Found at i:5442116 original size:40 final size:39
Alignment explanation
Indices: 5441975--5442158 Score: 140
Period size: 40 Copynumber: 4.6 Consensus size: 39
5441965 TCAATATCTT
* * *
5441975 GCACACTAAGTGCTAAAGCATAGCAGAAGCTAT-TATAATCTC
1 GCACACTAAGTGCTATA-CATAGCCGAAGCTATCT-GAA--TC
* *
5442017 GCACAC-AAGTGCCT-TTCATAGCCGAAGCTATCTCAACCTC
1 GCACACTAAGTG-CTATACATAGCCGAAGCTATCTGAA--TC
* * * *
5442057 ACACGCTAAGTGCTATATATAGCCGAAGCTATTCTGATTC
1 GCACACTAAGTGCTATACATAGCCGAAGCTA-TCTGAATC
* * * *
5442097 TCACACTAAGTGCTTTATATAGCCGAAGCTATCTTGAAAC
1 GCACACTAAGTGCTATACATAGCCGAAGCTATC-TGAATC
*
5442137 GCACACTAAGTGCTAAACATAG
1 GCACACTAAGTGCTATACATAG
5442159 TTGATTTGTC
Statistics
Matches: 116, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
39 2 0.02
40 77 0.66
41 25 0.22
42 12 0.10
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (39 bp):
GCACACTAAGTGCTATACATAGCCGAAGCTATCTGAATC
Found at i:5442119 original size:81 final size:82
Alignment explanation
Indices: 5441980--5442130 Score: 200
Period size: 81 Copynumber: 1.9 Consensus size: 82
5441970 ATCTTGCACA
5441980 CTAAGTGCTAAAGCATAGCAGAAGCTATTATAATCTCGCACACAAGTGCCTTTCATAGCCGAAGC
1 CTAAGTGCTAAAGCATAGCAGAAGCTATTATAATCTCGCACACAAGTGCCTTTCATAGCCGAAGC
5442045 TATCTCAACCTCACACG
66 TATCTCAACCTCACACG
* * * * * * *
5442062 CTAAGTGCTATA-TATAGCCGAAGCTATTCTGAT-TCTCACACTAAGTG-CTTTATATAGCCGAA
1 CTAAGTGCTAAAGCATAGCAGAAGCTATTATAATCTCGCACAC-AAGTGCCTTT-CATAGCCGAA
5442124 GCTATCT
64 GCTATCT
5442131 TGAAACGCAC
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
80 11 0.18
81 38 0.63
82 11 0.18
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (82 bp):
CTAAGTGCTAAAGCATAGCAGAAGCTATTATAATCTCGCACACAAGTGCCTTTCATAGCCGAAGC
TATCTCAACCTCACACG
Found at i:5447903 original size:24 final size:27
Alignment explanation
Indices: 5447856--5447907 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 27
5447846 AACCGAGGTA
5447856 AGTTCGTATGTTAAATAAGCTTTAATAT
1 AGTTCGTATGTTAAAT-AGCTTTAATAT
5447884 AGTT-GTAT-TTAAAT-GCTTTAATAT
1 AGTTCGTATGTTAAATAGCTTTAATAT
5447908 TGCATGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.42
26 6 0.25
27 4 0.17
28 4 0.17
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (27 bp):
AGTTCGTATGTTAAATAGCTTTAATAT
Found at i:5455775 original size:33 final size:31
Alignment explanation
Indices: 5455714--5455775 Score: 72
Period size: 33 Copynumber: 1.9 Consensus size: 31
5455704 AAGTTGTAAG
*
5455714 AAATAAAATAAAACAACTAAAAACAATAACAA
1 AAATAAAATAAAACAAC-AAAAAAAATAACAA
5455746 AAATAAAAATAAAACTAA-AAAAATAAATAA
1 AAAT-AAAATAAAAC-AACAAAAA-AAATAA
5455776 GATCAGTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
32 9 0.35
33 15 0.58
34 2 0.08
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (31 bp):
AAATAAAATAAAACAACAAAAAAAATAACAA
Found at i:5457184 original size:16 final size:16
Alignment explanation
Indices: 5457159--5457194 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5457149 ATAATATCAT
*
5457159 AATAATAAATAATAAC
1 AATAAAAAATAATAAC
*
5457175 AATAAAAAATAATAAG
1 AATAAAAAATAATAAC
5457191 AATA
1 AATA
5457195 GAACCTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (16 bp):
AATAAAAAATAATAAC
Found at i:5457339 original size:15 final size:15
Alignment explanation
Indices: 5457307--5457370 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
5457297 AGTTAGTAGG
*
5457307 AATAATGAT-AATAA
1 AATAATAATAAATAA
* *
5457321 AATAATACTAAATAT
1 AATAATAATAAATAA
5457336 AATAATAATAAAATTACTA
1 AATAATAAT-AAA-TA--A
5457355 AAT-ATAATAAATAA
1 AATAATAATAAATAA
5457369 AA
1 AA
5457371 GAAAAAGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 10 0.25
15 12 0.30
16 5 0.12
17 5 0.12
18 5 0.12
19 3 0.08
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAATAATAAATAA
Found at i:5457359 original size:24 final size:25
Alignment explanation
Indices: 5457308--5457364 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
5457298 GTTAGTAGGA
*
5457308 ATAATGATAATAAAATAATACTAAAT
1 ATAATAATAATAAAAT-ATACTAAAT
5457334 ATAATAATAATAAAAT-TACTAAAT
1 ATAATAATAATAAAATATACTAAAT
5457358 ATAATAA
1 ATAATAA
5457365 ATAAAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.50
26 15 0.50
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAATAATAATAAAATATACTAAAT
Found at i:5464163 original size:38 final size:39
Alignment explanation
Indices: 5464121--5464196 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 39
5464111 TATGTTACAT
5464121 ATAACCTGAGAATCTACAAC-AAGGCTAGATCTCATTAA
1 ATAACCTGAGAATCTACAACAAAGGCTAGATCTCATTAA
* * **
5464159 ATAACCTGAGGATCTGCAACAAATTCTAGATCTCATTA
1 ATAACCTGAGAATCTACAACAAAGGCTAGATCTCATTA
5464197 TAACATGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 18 0.55
39 15 0.45
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (39 bp):
ATAACCTGAGAATCTACAACAAAGGCTAGATCTCATTAA
Found at i:5466537 original size:14 final size:14
Alignment explanation
Indices: 5466518--5466550 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5466508 TTATTTGATC
*
5466518 TCTAATTATATATG
1 TCTAATTAAATATG
5466532 TCTAATTAAATATG
1 TCTAATTAAATATG
5466546 TCTAA
1 TCTAA
5466551 AGCTTGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (14 bp):
TCTAATTAAATATG
Found at i:5468811 original size:17 final size:19
Alignment explanation
Indices: 5468789--5468831 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
5468779 ATGGAAATAT
5468789 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGC
*
5468806 AATCTTAGATATGATATGC
1 AATCTTACATATGATATGC
5468825 AATCTTA
1 AATCTTA
5468832 GAAGATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 16 0.70
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCTTACATATGATATGC
Found at i:5468821 original size:19 final size:19
Alignment explanation
Indices: 5468797--5468833 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5468787 ATAATCTTCA
5468797 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5468816 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
5468834 AGATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5468859 original size:22 final size:22
Alignment explanation
Indices: 5468797--5468856 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 22
5468787 ATAATCTTCA
5468797 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
5468816 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
5468838 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
5468857 GATTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.43
22 8 0.23
23 12 0.34
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:5475062 original size:44 final size:44
Alignment explanation
Indices: 5475013--5475714 Score: 671
Period size: 44 Copynumber: 15.9 Consensus size: 44
5475003 GATCCAAGAT
* **
5475013 GATTTGGCATCTCTATATTGGCAGAGAGCAGATCGAAGGCAACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
** * *
5475057 GATTTGGTGTCTCTGTATTGGCAGAGAGCAGATCAAAGATGACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * * *
5475101 GATTTGGCATCTCTGTATTTGGCGGAGAGTAGATCGAAGACATAGCT
1 GATTTGGCATCTCTGTA-TTGGCAGAGAGCAGATCGAAG--ATAACA
** * * * ** *
5475148 GATTCAGCTTCCACGTGT-TTACGTTGA-AGCA-AGTCTAAGAT----
1 GATTTGGCAT-CTC-TGTATT-GGCAGAGAGCAGA-TCGAAGATAACA
* *
5475189 GATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
*
5475233 GATTTAGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * *
5475277 GATTTGGCATCTCTGTATTGGCAGAGAGTAGATCAAAGATGACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * * *
5475321 GATTTGGCATCTCTGTATTCGGCGGAGAGTAGATCGAAGACATAGCT
1 GATTTGGCATCTCTGTATT-GGCAGAGAGCAGATCGAAG--ATAACA
* * * ** *
5475368 GATTTGGCTTCCACGTGT-TTACGTTGA-AGCA-AGTCTAAGAT----
1 GATTTGGCAT-CTC-TGTATT-GGCAGAGAGCAGA-TCGAAGATAACA
* *
5475409 GATTTGGCATCTTTGTATTGGCAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * *
5475453 GATTTGGCATCTCTGTATTGGCAGAGAGCATATCAAAGATGACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* *
5475497 GATTTGGCATCTCTGTATTTGGC-GAAGAGCAGATCGAAGACATAGCT
1 GATTTGGCATCTCTGTA-TTGGCAG-AGAGCAGATCGAAG--ATAACA
5475544 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * *
5475588 GATTTGACATTTCTGTATTGGCAGAGAGCAGATCGAAGATAATA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
*
5475632 GATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATAGA-A
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA-ACA
* * * *
5475676 GATTTGGCGTCTCTGTTTTGTCAGAGAGCATATCGAAGA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGA
5475715 GAAGAACAAC
Statistics
Matches: 544, Mismatches: 81, Indels: 66
0.79 0.12 0.10
Matches are distributed among these distances:
39 13 0.02
40 29 0.05
41 18 0.03
44 327 0.60
45 57 0.10
46 21 0.04
47 61 0.11
48 12 0.02
49 6 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
Found at i:5475401 original size:220 final size:219
Alignment explanation
Indices: 5475013--5475714 Score: 927
Period size: 220 Copynumber: 3.2 Consensus size: 219
5475003 GATCCAAGAT
* ** **
5475013 GATTTGGCATCTCTATATTGGCAGAGAGCAGATCGAAGGCAACAGATTTGGTGTCTCTGTATTGG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGG
5475078 CAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTTGGCGGAGAGTAGATCGAAGACA
66 CAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTA-TTGGCGGAGAGTAGATCGAAGACA
**
5475143 TAGCTGATTCAGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATT
130 TAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATT
5475208 GGTAGAGAGCAGATCGAAGATAGCA
195 GGTAGAGAGCAGATCGAAGATAGCA
*
5475233 GATTTAGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGG
*
5475298 CAGAGAGTAGATCAAAGATGACAGATTTGGCATCTCTGTATTCGGCGGAGAGTAGATCGAAGACA
66 CAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATT-GGCGGAGAGTAGATCGAAGACA
*
5475363 TAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTTTGTATT
130 TAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATT
*
5475428 GGCAGAGAGCAGATCGAAGATAGCA
195 GGTAGAGAGCAGATCGAAGATAGCA
* * *
5475453 GATTTGGCATCTCTGTATTGGCAGAGAGCATATCAAAGATGACAGATTTGGCATCTCTGTATTTG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTA-TTG
* * * *
5475518 GC-GAAGAGCAGATCGAAGACAT-AGCTGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAA
65 GCAG-AGAGCAGATC-AA-AGATGA-CAGATTTGGCATCTCTGTATTGGCGGAGAGTAGATCGAA
* * * * * ** *
5475581 G--ATAACAGATTTGACATT--TC-TGTATT-GGCAGAGAGC-AGATCGAAGATAATAGATTTGG
126 GACATAGCTGATTTGGC-TTCCACGTGT-TTACGTTGA-AGCAAG-TCTAAG---AT-GATTTGG
*
5475639 CATCTCTGTATTGGTAGAGAGCAGATCGAAGATAGAA
183 CATCTCTGTATTGGTAGAGAGCAGATCGAAGATAGCA
* * * *
5475676 GATTTGGCGTCTCTGTTTTGTCAGAGAGCATATCGAAGA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGA
5475715 GAAGAACAAC
Statistics
Matches: 433, Mismatches: 35, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
218 8 0.02
219 13 0.03
220 275 0.64
221 16 0.04
222 22 0.05
223 99 0.23
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (219 bp):
GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGG
CAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTGGCGGAGAGTAGATCGAAGACAT
AGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTG
GTAGAGAGCAGATCGAAGATAGCA
Found at i:5475801 original size:179 final size:176
Alignment explanation
Indices: 5475188--5475805 Score: 544
Period size: 176 Copynumber: 3.5 Consensus size: 176
5475178 AAGTCTAAGA
* ** * *
5475188 TGATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATAGCAGATTT-AGCA-TCTCTGTAT
1 TGATTTGGCATCTCCGTATTGACAGAGAGCAGATCCAAGAT---AGATTTGA-CATTC-CTATAT
* * *
5475251 TGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGGCAGAGAGTAGATCAAAGA
61 TGACAGAGAACAGATCGAAGATAACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGA
* * *
5475316 TGACAGATTTGGCATCTCTGTATTCGGCGGAGAGTAGATCGAAGACATAGC
126 TGACAGATTTGGCATCTCTGTATTTGGCGAAGAGCAGATCGAAGACATAGC
* * * * * * * *
5475367 TGATTTGGCTTC-CACGTGTTTAC-GTTGAAGCA-AGTCTAAGAT-GATTTGGCA-TCTTTGTAT
1 TGATTTGGCATCTC-CGTATTGACAG-AG-AGCAGA-TCCAAGATAGATTTGACATTC-CTATAT
* * * *
5475427 TGGCAGAGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGGCAGAGAGCATATCAAAGA
61 TGACAGAGAACAGATCGAAGATAACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGA
5475492 TGACAGATTTGGCATCTCTGTATTTGGCGAAGAGCAGATCGAAGACATAGC
126 TGACAGATTTGGCATCTCTGTATTTGGCGAAGAGCAGATCGAAGACATAGC
* * * * *
5475543 TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGACATTTCTGTATTG
1 TGATTTGGCATCTCCGTATTGACAGAGAGCAGATCCAAGAT---AGATTTGACATTCCTATATTG
* * * * *
5475608 GCAGAGAGCAGATCGAAGATAATAGATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATA
63 ACAGAGAACAGATCGAAGATAACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGAT-
* * * *
5475673 GA-AGATTTGGCGTCTCTGT-TTTGTC-AGAGAGCATATCGAAGAGA-AGAACAAC
127 GACAGATTTGGCATCTCTGTATTTGGCGA-AGAGCAGATCGAAGACATAG-----C
* * * * * *
5475725 AT-ATTTGGCATCTCCGTATTCGACGGGGAGTAGATCCAAGAT-GATTTGGCATTCCTATGTTTA
1 -TGATTTGGCATCTCCGTATT-GACAGAGAGCAGATCCAAGATAGATTTGACATTCCTATATTGA
5475788 CA-AGGAACAGATCGAAGA
64 CAGA-GAACAGATCGAAGA
5475806 CATAGCAGAT
Statistics
Matches: 368, Mismatches: 48, Indels: 46
0.80 0.10 0.10
Matches are distributed among these distances:
175 11 0.03
176 143 0.39
177 5 0.01
178 23 0.06
179 137 0.37
180 14 0.04
182 18 0.05
183 17 0.05
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (176 bp):
TGATTTGGCATCTCCGTATTGACAGAGAGCAGATCCAAGATAGATTTGACATTCCTATATTGACA
GAGAACAGATCGAAGATAACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACA
GATTTGGCATCTCTGTATTTGGCGAAGAGCAGATCGAAGACATAGC
Found at i:5475909 original size:44 final size:44
Alignment explanation
Indices: 5475861--5476268 Score: 139
Period size: 45 Copynumber: 9.1 Consensus size: 44
5475851 GATTTTAACA
* *
5475861 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGTTT
1 TGGCATCCCTGTGTTTACAGGGAACAGA-TTGAAGATAGCAGATT
* * *
5475905 TGGCATCCTTGTGTTTACAGGGAACAGATCGAAGACATAGCAGATC
1 TGGCATCCCTGTGTTTACAGGGAACAGATTGAAG--ATAGCAGATT
* * * * * * **
5475951 TGACATTCTTGTGCTTACAGCGAAGCAGATTGAAAATTTCAGCA--
1 TGGCATCCCTGTGTTTACAGGGAA-CAGATTGAAGATAGCAG-ATT
* * * *
5475995 TGGCATCCCTGTGTTTATAAGGAATA-AGTTGAAGATAGTAGATT
1 TGGCATCCCTGTGTTTACAGGGAACAGA-TTGAAGATAGCAGATT
* * * * * *
5476039 TGGCATCTCCATAT-TTGACAGGGAGCAGATTAAAGACATAGTAGATC
1 TGGCATC-CC-TGTGTTTACAGGGAACAGATTGAAG--ATAGCAGATT
* * * * ** **
5476086 TGACCTTCATGTGTTTACATCGAAGCAGATCCAAGAT-GACAGATT
1 TGGCATCCCTGTGTTTACAGGGAA-CAGATTGAAGATAG-CAGATT
** * * * * * * * *
5476131 TGGCATCTTTGTATTAGACGGGGAGCAAATCGGAGATAACAGATT
1 TGGCATCCCTGTGTT-TACAGGGAACAGATTGAAGATAGCAGATT
* * * *
5476176 TGGCATCTCTGT-TTTAGACGGGGAGCAGATTGAAGA-AGCAAATT
1 TGGCATCCCTGTGTTT--ACAGGGAACAGATTGAAGATAGCAGATT
* * * * * * * *
5476220 TGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATT
1 TGGCATCCCTGTGTT-TACAGGGAACAGATTGAAGATAGCAGATT
5476265 TGGC
1 TGGC
5476269 GTCTCTGTAT
Statistics
Matches: 268, Mismatches: 73, Indels: 45
0.69 0.19 0.12
Matches are distributed among these distances:
42 2 0.01
43 10 0.04
44 91 0.34
45 92 0.34
46 44 0.16
47 29 0.11
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (44 bp):
TGGCATCCCTGTGTTTACAGGGAACAGATTGAAGATAGCAGATT
Found at i:5475929 original size:134 final size:135
Alignment explanation
Indices: 5475767--5476122 Score: 472
Period size: 134 Copynumber: 2.7 Consensus size: 135
5475757 GATCCAAGAT
*
5475767 GATTTGGCATTCCTATGTTTACAAGGAACAGATCGAAGACATAGCAGATCTGACACTTC-TGTGC
1 GATTTGGCATTCCTATGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACACTTCATGTGC
* *
5475831 TTACAGCGAAGCAGATCAAAGATTTTAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGA
66 TTACAGCGAAGCAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAAGGAACAAGTTGAAGA
5475896 TAGCA
131 TAGCA
* * *
5475901 GTTTTGGCA-TCCTTGTGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACA-TTCTTGTG
1 GATTTGGCATTCC-TATGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACACTTCATGTG
* * *
5475964 CTTACAGCGAAGCAGATTGAAA-ATTTCAGCATGGCATCCCTGTGTTTATAAGGAATAAGTTGAA
65 CTTACAGCGAAGCAGA-TCAAAGATTTCAACATGGCATCCCTGTGTTTATAAGGAACAAGTTGAA
*
5476028 GATAGTA
129 GATAGCA
* * ** *
5476035 GATTTGGCATCTCCATAT-TTGACAGGGAGCAGATTAAAGACATAGTAGATCTGAC-CTTCATGT
1 GATTTGGCAT-TCC-TATGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACACTTCATGT
* * *
5476098 GTTTACATCGAAGCAGATCCAAGAT
64 GCTTACAGCGAAGCAGATCAAAGAT
5476123 GACAGATTTG
Statistics
Matches: 193, Mismatches: 22, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
133 6 0.03
134 123 0.64
135 59 0.31
136 5 0.03
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (135 bp):
GATTTGGCATTCCTATGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACACTTCATGTGC
TTACAGCGAAGCAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAAGGAACAAGTTGAAGA
TAGCA
Found at i:5475963 original size:46 final size:46
Alignment explanation
Indices: 5475782--5475980 Score: 135
Period size: 44 Copynumber: 4.4 Consensus size: 46
5475772 GGCATTCCTA
* *
5475782 TGTTTACAAGGAACAGATCGAAGACATAGCAGATCTGACA-CTTCTG
1 TGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACATCCT-TG
* * * *** * *
5475828 TGCTTACAGCGAAGCAGATC-AA-AGATTTTA-A-CATGGCATCCCTG
1 TGTTTACAGGGAA-CAGATCGAAGACATAGCAGATC-TGACATCCTTG
* * * * *
5475872 TGTTTATAGGGAACA-AGTTGAAG--ATAGCAGTTTTGGCATCCTTG
1 TGTTTACAGGGAACAGA-TCGAAGACATAGCAGATCTGACATCCTTG
*
5475916 TGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACATTCTTG
1 TGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACATCCTTG
* *
5475962 TGCTTACAGCGAAGCAGAT
1 TGTTTACAGGGAA-CAGAT
5475981 TGAAAATTTC
Statistics
Matches: 113, Mismatches: 28, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
42 1 0.01
43 7 0.06
44 48 0.42
45 6 0.05
46 40 0.35
47 11 0.10
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (46 bp):
TGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACATCCTTG
Found at i:5476193 original size:45 final size:45
Alignment explanation
Indices: 5476109--5476308 Score: 267
Period size: 45 Copynumber: 4.5 Consensus size: 45
5476099 TTTACATCGA
* * *
5476109 AGCAGATCCAAGATGACAGATTTGGCATCTTTGTATTAGACGGGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* * *
5476154 AGCAAATCGGAGATAACAGATTTGGCATCTCTGTTTTAGACGGGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* * * *
5476199 AGCAGATTGAAGA-AGCAAATTTGGCGTCTCTGTATTAGACGGGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
*
5476243 AGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTAGACGGGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* * *
5476288 AGCATATCAAAGATAGCAGAT
1 AGCAGATCGAAGATAACAGAT
5476309 ATCGCCTTCC
Statistics
Matches: 135, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
44 39 0.29
45 96 0.71
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (45 bp):
AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
Found at i:5476235 original size:89 final size:89
Alignment explanation
Indices: 5476128--5476291 Score: 274
Period size: 89 Copynumber: 1.8 Consensus size: 89
5476118 AAGATGACAG
* * *
5476128 ATTTGGCATCTTTGTATTAGACGGGGAGCAAATCGGAGATAACAGATTTGGCATCTCTGTTTTAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTAG
5476193 ACGGGGAGCAGATTGAAGAAGCAA
66 ACGGGGAGCAGATTGAAGAAGCAA
* * *
5476217 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTAG
5476282 ACGGGGAGCA
66 ACGGGGAGCA
5476292 TATCAAAGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 69 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (89 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTAG
ACGGGGAGCAGATTGAAGAAGCAA
Found at i:5476682 original size:19 final size:19
Alignment explanation
Indices: 5476658--5476724 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 19
5476648 ATAATCTTCA
5476658 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5476677 ATGATATG----C---GAT
1 ATGATATGCAATCTTAGAT
5476689 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5476707 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
5476725 AGATATGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
11 2 0.05
12 8 0.20
15 2 0.05
18 8 0.20
19 20 0.50
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5476698 original size:30 final size:31
Alignment explanation
Indices: 5476658--5476715 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
5476648 ATAATCTTCA
5476658 ATGATATGCAATCTTAGATATGATATGCGAT
1 ATGATATGCAATCTTAGATATGATATGCGAT
5476689 ATGAT-TGCAATCTTAGATATGATATGC
1 ATGATATGCAATCTTAGATATGATATGC
5476716 AATCTTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (31 bp):
ATGATATGCAATCTTAGATATGATATGCGAT
Found at i:5476750 original size:22 final size:22
Alignment explanation
Indices: 5476686--5476747 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 22
5476676 TATGATATGC
5476686 GATATGAT-TGCAATCTT---A
1 GATATGATATGCAATCTTAGAA
5476704 GATATGATATGCAATCTTAGAA
1 GATATGATATGCAATCTTAGAA
* *
5476726 GATATGATTTTGTAATCTTAGA
1 GATATGA-TATGCAATCTTAGA
5476748 GATTTAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.22
19 9 0.24
22 8 0.22
23 12 0.32
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (22 bp):
GATATGATATGCAATCTTAGAA
Found at i:5478397 original size:3 final size:3
Alignment explanation
Indices: 5478389--5478421 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5478379 CAATAATTAC
5478389 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5478422 AACACAACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5478779 original size:17 final size:17
Alignment explanation
Indices: 5478728--5478779 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5478718 TGAATGATGT
*
5478728 TATTTATGTTCTTAATTA
1 TATTTAT-TTATTAATTA
* *
5478746 TA-TTATTTAATACTTA
1 TATTTATTTATTAATTA
*
5478762 TATTTATTTATTATTTA
1 TATTTATTTATTAATTA
5478779 T
1 T
5478780 TTTGGAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 9 0.32
17 17 0.61
18 2 0.07
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (17 bp):
TATTTATTTATTAATTA
Found at i:5481529 original size:3 final size:3
Alignment explanation
Indices: 5481521--5481564 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5481511 CTTTCTTTCT
5481521 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5481565 GCCTTTTCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5482300 original size:3 final size:3
Alignment explanation
Indices: 5482292--5482330 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5482282 GTTATATGGA
5482292 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5482331 GTGGAAAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5493627 original size:29 final size:29
Alignment explanation
Indices: 5493533--5493627 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
5493523 AAAATATTAA
* *
5493533 AATATTGATATAA-AATATTATTAATT-TT
1 AATATT-ATTTAACAATATAATTAATTATT
* *
5493561 AAATATTATTAAAC-ATACTATTTAATTATT
1 -AATATTATTTAACAATA-TAATTAATTATT
5493591 --TA-TATTTAACAATATAATTAATTATT
1 AATATTATTTAACAATATAATTAATTATT
5493617 AATATTATTTA
1 AATATTATTTA
5493628 TTATTTTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
26 18 0.34
27 5 0.09
28 9 0.17
29 19 0.36
30 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (29 bp):
AATATTATTTAACAATATAATTAATTATT
Found at i:5497714 original size:22 final size:24
Alignment explanation
Indices: 5497671--5497716 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
5497661 AATAAATCAT
*
5497671 TTATTTTATTATAATTTTTTTGTA
1 TTATTTTATTATAAGTTTTTTGTA
5497695 TTATTTT-TTA-AAGTTTTTTGTA
1 TTATTTTATTATAAGTTTTTTGTA
5497717 GATTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 3 0.14
24 7 0.33
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (24 bp):
TTATTTTATTATAAGTTTTTTGTA
Found at i:5498652 original size:3 final size:3
Alignment explanation
Indices: 5498644--5498674 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5498634 TACTTTTTTC
*
5498644 TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5498675 TTACTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:5498666 original size:15 final size:15
Alignment explanation
Indices: 5498646--5498675 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5498636 CTTTTTTCTA
5498646 ATAATAATAATAATT
1 ATAATAATAATAATT
5498661 ATAATAATAATAATT
1 ATAATAATAATAATT
5498676 TACTTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATAATAATAATT
Found at i:5500256 original size:145 final size:145
Alignment explanation
Indices: 5500102--5500389 Score: 576
Period size: 145 Copynumber: 2.0 Consensus size: 145
5500092 TATTTTCTTG
5500102 TTGTTTTCTCCCTATTTTGATACCATATTACTATTATATTGCTACTATTTTGTTGTTATTGTTTA
1 TTGTTTTCTCCCTATTTTGATACCATATTACTATTATATTGCTACTATTTTGTTGTTATTGTTTA
5500167 GATATTGTATAAAACTTATTTTATTATTAATTTTGTTATTATTTTAAAGGTATTTCTTAATTTTT
66 GATATTGTATAAAACTTATTTTATTATTAATTTTGTTATTATTTTAAAGGTATTTCTTAATTTTT
5500232 TTATTATTTTAGATA
131 TTATTATTTTAGATA
5500247 TTGTTTTCTCCCTATTTTGATACCATATTACTATTATATTGCTACTATTTTGTTGTTATTGTTTA
1 TTGTTTTCTCCCTATTTTGATACCATATTACTATTATATTGCTACTATTTTGTTGTTATTGTTTA
5500312 GATATTGTATAAAACTTATTTTATTATTAATTTTGTTATTATTTTAAAGGTATTTCTTAATTTTT
66 GATATTGTATAAAACTTATTTTATTATTAATTTTGTTATTATTTTAAAGGTATTTCTTAATTTTT
5500377 TTATTATTTTAGA
131 TTATTATTTTAGA
5500390 GGTATTTACT
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 143 1.00
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (145 bp):
TTGTTTTCTCCCTATTTTGATACCATATTACTATTATATTGCTACTATTTTGTTGTTATTGTTTA
GATATTGTATAAAACTTATTTTATTATTAATTTTGTTATTATTTTAAAGGTATTTCTTAATTTTT
TTATTATTTTAGATA
Found at i:5500372 original size:30 final size:30
Alignment explanation
Indices: 5500338--5500396 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5500328 TATTTTATTA
5500338 TTAATTTTGTTATTATTTTAAAGGTATTTC
1 TTAATTTTGTTATTATTTTAAAGGTATTTC
* *
5500368 TTAATTTTTTTATTATTTTAGAGGTATTT
1 TTAATTTTGTTATTATTTTAAAGGTATTT
5500397 ACTTGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGTATTTC
Found at i:5502454 original size:2 final size:2
Alignment explanation
Indices: 5502447--5502471 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5502437 CTAATATAAA
5502447 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5502472 CTTTGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5502536 original size:54 final size:54
Alignment explanation
Indices: 5502478--5502593 Score: 182
Period size: 56 Copynumber: 2.1 Consensus size: 54
5502468 TATACTTTGA
5502478 AATTTTCACATATTTACATCA-T-GGTCAACTATTAGAAAAAAAAATTACATATAC
1 AATTTTCACATATTTACATCAGTCGGTCAACTATTAG--AAAAAAATTACATATAC
5502532 AATTTTCACATATTTACATCATGGTCGGTCAACTATTAGAAAAAAATTACATATAC
1 AATTTTCACATATTTACATCA--GTCGGTCAACTATTAGAAAAAAATTACATATAC
5502588 AATTTT
1 AATTTT
5502594 ATCCCTTTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
54 21 0.36
56 23 0.40
57 1 0.02
58 13 0.22
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (54 bp):
AATTTTCACATATTTACATCAGTCGGTCAACTATTAGAAAAAAATTACATATAC
Found at i:5507521 original size:93 final size:93
Alignment explanation
Indices: 5507408--5507579 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
5507398 CGCCCATAAG
* *
5507408 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
5507473 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
5507501 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
5507566 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
5507580 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:5507576 original size:46 final size:46
Alignment explanation
Indices: 5507401--5507576 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
5507391 TGTAACCCGC
* * *
5507401 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
5507447 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
5507497 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
5507540 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
5507577 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:5508982 original size:18 final size:18
Alignment explanation
Indices: 5508956--5509032 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
5508946 TTTGGCCCAT
5508956 TGCAGTAACAGTAAACAG
1 TGCAGTAACAGTAAACAG
* *
5508974 TGCAATAACAGTACAGTAATAG
1 TGCAGTAACAGT--A--AACAG
*
5508996 TGCAGTAATAGTAAACAG
1 TGCAGTAACAGTAAACAG
* *
5509014 TGCCGTAACAGTAGACAG
1 TGCAGTAACAGTAAACAG
5509032 T
1 T
5509033 ATGTAAGTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
18 31 0.66
20 2 0.04
22 14 0.30
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.21
Consensus pattern (18 bp):
TGCAGTAACAGTAAACAG
Found at i:5509754 original size:114 final size:114
Alignment explanation
Indices: 5509545--5509769 Score: 351
Period size: 114 Copynumber: 2.0 Consensus size: 114
5509535 CTTTTGCACA
* * * * * *
5509545 TGCCCAGGTTTGAACCCAAGACTTCTCAGACATTTTCCAGAACACTTAACCACTGAGGCAGACAT
1 TGCCCAGGCTTGAACCCAAGACTTCTCAGACACTTCCCAGAACACTTAACCACTAACGCAGACAC
*
5509610 ACAGTTATGTCACTTTCTTGTACAATTAAACATTTATGTGCAGCCTCCG
66 ACAGTTATGTCACTTTCTTGCACAATTAAACATTTATGTGCAGCCTCCG
* * *
5509659 TGCCTAGGCTTGAACCCAAGACTTCTTAGACACTTCCCAGAACACTTAACCACTAACGCAGATAC
1 TGCCCAGGCTTGAACCCAAGACTTCTCAGACACTTCCCAGAACACTTAACCACTAACGCAGACAC
*
5509724 ACAGTTTTGTCACTTTCTTGCACAATTAAACATTTATGTGCAGCCT
66 ACAGTTATGTCACTTTCTTGCACAATTAAACATTTATGTGCAGCCT
5509770 TCTAATTGTT
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (114 bp):
TGCCCAGGCTTGAACCCAAGACTTCTCAGACACTTCCCAGAACACTTAACCACTAACGCAGACAC
ACAGTTATGTCACTTTCTTGCACAATTAAACATTTATGTGCAGCCTCCG
Found at i:5510379 original size:8 final size:8
Alignment explanation
Indices: 5510359--5510411 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
5510349 AAATAAGTAA
5510359 TATATTAAT
1 TATATT-AT
5510368 T-TA-TAT
1 TATATTAT
5510374 TAT-TATAT
1 TATAT-TAT
5510382 TATATTAT
1 TATATTAT
5510390 TATATATAT
1 TATAT-TAT
5510399 TATATTAT
1 TATATTAT
5510407 TATAT
1 TATAT
5510412 ATATATGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
6 3 0.08
7 2 0.05
8 24 0.62
9 10 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATATTAT
Found at i:5510399 original size:17 final size:17
Alignment explanation
Indices: 5510371--5510415 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
5510361 TATTAATTTA
5510371 TATTAT-TATATTATAT
1 TATTATATATATTATAT
5510387 TATTATATATATTATAT
1 TATTATATATATTATAT
5510404 TATTATATATAT
1 TATTATATATAT
5510416 ATGTAAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATATATATTATAT
Found at i:5514388 original size:28 final size:28
Alignment explanation
Indices: 5514356--5514425 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
5514346 TATGGTACTC
*
5514356 AGTGTACGAAATATTGAGAATGACACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
*
5514384 AGTGTGCGAGATATTGAGAATGACACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
*
5514412 AGTGTGCAAAATAT
1 AGTGTGCGAAATAT
5514426 CGAATGATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (28 bp):
AGTGTGCGAAATATTGAGAATGACACTT
Found at i:5520045 original size:31 final size:31
Alignment explanation
Indices: 5520010--5520080 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
5520000 AAATACAAAA
5520010 AAGTCACTAAAATATTCAAAAGTTTTCATTT
1 AAGTCACTAAAATATTCAAAAGTTTTCATTT
* * * ** *
5520041 AAGTCATTGAACTATTTGAAAGTTTTTATTT
1 AAGTCACTAAAATATTCAAAAGTTTTCATTT
5520072 AAGTCACTA
1 AAGTCACTA
5520081 GGCTGTTAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (31 bp):
AAGTCACTAAAATATTCAAAAGTTTTCATTT
Found at i:5528139 original size:12 final size:12
Alignment explanation
Indices: 5528122--5528147 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5528112 GGCACTAATC
5528122 CTGTAAGTATTT
1 CTGTAAGTATTT
5528134 CTGTAAGTATTT
1 CTGTAAGTATTT
5528146 CT
1 CT
5528148 ATATTTGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (12 bp):
CTGTAAGTATTT
Found at i:5535761 original size:17 final size:18
Alignment explanation
Indices: 5535716--5535768 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
5535706 TATAAAATTG
*
5535716 ATAAAAATAATAAAATGTA
1 ATAAAAA-ATTAAAATGTA
5535735 CATAATAAAATTAAAATGT-
1 -ATAA-AAAATTAAAATGTA
5535754 ATAAAAAATTAAAAT
1 ATAAAAAATTAAAAT
5535769 AATTTTTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 11 0.35
18 4 0.13
20 13 0.42
21 3 0.10
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAAAAAATTAAAATGTA
Found at i:5536458 original size:13 final size:13
Alignment explanation
Indices: 5536440--5536468 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5536430 CTTGGTTCAA
5536440 TTAGAAATTTATT
1 TTAGAAATTTATT
5536453 TTAGAAATTTATT
1 TTAGAAATTTATT
5536466 TTA
1 TTA
5536469 TAGTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (13 bp):
TTAGAAATTTATT
Found at i:5539946 original size:30 final size:32
Alignment explanation
Indices: 5539907--5539966 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
5539897 GGGAAGAAGT
*
5539907 AGCAGTTAATA-A-AAAGAAAAGATTTGGAGA
1 AGCACTTAATATATAAAGAAAAGATTTGGAGA
5539937 AGCACTTAATATTATAAAGAAAAGATTTGG
1 AGCACTTAATA-TATAAAGAAAAGATTTGG
5539967 TTAAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.38
32 1 0.04
33 15 0.58
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (32 bp):
AGCACTTAATATATAAAGAAAAGATTTGGAGA
Found at i:5547008 original size:29 final size:29
Alignment explanation
Indices: 5546973--5547046 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
5546963 GTTGTGAGAT
* *
5546973 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
5547002 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
5547031 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
5547047 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:5555383 original size:29 final size:29
Alignment explanation
Indices: 5555348--5555421 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
5555338 GTTGTGAGAT
* *
5555348 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
5555377 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
5555406 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
5555422 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:5557145 original size:18 final size:17
Alignment explanation
Indices: 5557118--5557151 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5557108 AAACGAAAGG
5557118 TATGAGAATGAATTTGA
1 TATGAGAATGAATTTGA
*
5557135 TATGAAGAATGTATTTG
1 TATG-AGAATGAATTTG
5557152 TATCATGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (17 bp):
TATGAGAATGAATTTGA
Found at i:5560112 original size:29 final size:29
Alignment explanation
Indices: 5560067--5560122 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5560057 ACAAAGGCTT
**
5560067 TCATATATAACAAATTCAGTCACAAAGAC
1 TCATATATAACAAATTCAACCACAAAGAC
* *
5560096 TCATATATAATAGATTCAACCACAAAG
1 TCATATATAACAAATTCAACCACAAAG
5560123 GTTCACATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.25
Consensus pattern (29 bp):
TCATATATAACAAATTCAACCACAAAGAC
Found at i:5560357 original size:54 final size:54
Alignment explanation
Indices: 5560286--5560422 Score: 175
Period size: 54 Copynumber: 2.5 Consensus size: 54
5560276 CCAAAGTCCT
* * * *
5560286 AGACTAGGTCTTGCACTATATGGTCTTCGCATTCCTATATAACGCCATAATCTC
1 AGACTAGGTCTTACACTATATGGTCTTCACATCCCCATATAACGCCATAATCTC
* * * * * *
5560340 AGACTAGGTCTTACACTATGTGGTATCCACATCCCCATATGACGCCATAGTCTT
1 AGACTAGGTCTTACACTATATGGTCTTCACATCCCCATATAACGCCATAATCTC
*
5560394 AGACTAGGTCGTACACTATATGGTCTTCA
1 AGACTAGGTCTTACACTATATGGTCTTCA
5560423 TTTGTCATGG
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (54 bp):
AGACTAGGTCTTACACTATATGGTCTTCACATCCCCATATAACGCCATAATCTC
Found at i:5574221 original size:20 final size:20
Alignment explanation
Indices: 5574196--5574240 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
5574186 AACCTGGGGC
5574196 AATATGTTGGAATATTTTCA
1 AATATGTTGGAATATTTTCA
5574216 AATATGTTGGAATATTTTCA
1 AATATGTTGGAATATTTTCA
5574236 AATAT
1 AATAT
5574241 TTATAGTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (20 bp):
AATATGTTGGAATATTTTCA
Found at i:5584271 original size:18 final size:18
Alignment explanation
Indices: 5584248--5584284 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5584238 TTTGCTGAAG
5584248 ACATGTTTTACAACAACA
1 ACATGTTTTACAACAACA
5584266 ACATGTTTTACAACAACA
1 ACATGTTTTACAACAACA
5584284 A
1 A
5584285 GAAACAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (18 bp):
ACATGTTTTACAACAACA
Found at i:5588043 original size:37 final size:35
Alignment explanation
Indices: 5588001--5588076 Score: 120
Period size: 33 Copynumber: 2.2 Consensus size: 35
5587991 CTAATAAAAT
5588001 TTAGATAGTTTTTTGTTTGAATGAATTCAAGTTTAAG
1 TTAGATA--TTTTTGTTTGAATGAATTCAAGTTTAAG
5588038 TTAG--ATTTTTGTTTGAATGAATTCAAGTTTAAG
1 TTAGATATTTTTGTTTGAATGAATTCAAGTTTAAG
5588071 TTAGAT
1 TTAGAT
5588077 TGATCAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
33 32 0.86
35 1 0.03
37 4 0.11
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.49
Consensus pattern (35 bp):
TTAGATATTTTTGTTTGAATGAATTCAAGTTTAAG
Found at i:5588050 original size:33 final size:33
Alignment explanation
Indices: 5588010--5588077 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
5588000 TTTAGATAGT
5588010 TTTTTGTTTGAATGAATTCAAGTTTAAGTTAGA
1 TTTTTGTTTGAATGAATTCAAGTTTAAGTTAGA
5588043 TTTTTGTTTGAATGAATTCAAGTTTAAGTTAGA
1 TTTTTGTTTGAATGAATTCAAGTTTAAGTTAGA
5588076 TT
1 TT
5588078 GATCAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (33 bp):
TTTTTGTTTGAATGAATTCAAGTTTAAGTTAGA
Found at i:5589416 original size:11 final size:11
Alignment explanation
Indices: 5589388--5589430 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
5589378 TTGACCTTTC
5589388 CAAGGTATGGG
1 CAAGGTATGGG
*
5589399 -TAGGTATGGG
1 CAAGGTATGGG
5589409 CAAGGTATGGG
1 CAAGGTATGGG
*
5589420 CAAGGAATGGG
1 CAAGGTATGGG
5589431 TATATTCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.28, C:0.07, G:0.47, T:0.19
Consensus pattern (11 bp):
CAAGGTATGGG
Found at i:5593495 original size:18 final size:18
Alignment explanation
Indices: 5593472--5593546 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
5593462 CTCAACTACT
*
5593472 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
5593490 GTATACGTGAATAGTGCT
1 GTATACGTGAATAGTACC
* **
5593508 GTATACGTAAATAGTGTC
1 GTATACGTGAATAGTACC
*
5593526 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
5593544 GTA
1 GTA
5593547 AACGGTCGTA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:5593529 original size:36 final size:36
Alignment explanation
Indices: 5593470--5593540 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
5593460 ATCTCAACTA
* *
5593470 CTGTATACGTGAACAGTACCGTATACGTGAATAGTG
1 CTGTATACGTAAACAGTACCGTATACATGAATAGTG
* **
5593506 CTGTATACGTAAATAGTGTCGTATACATGAATAGT
1 CTGTATACGTAAACAGTACCGTATACATGAATAGT
5593541 ACCGTAAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (36 bp):
CTGTATACGTAAACAGTACCGTATACATGAATAGTG
Found at i:5594106 original size:11 final size:11
Alignment explanation
Indices: 5594090--5594131 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
5594080 AGGTATGAGT
*
5594090 AGGTATGGGAA
1 AGGTATGGGCA
5594101 AGGTATGGGCA
1 AGGTATGGGCA
5594112 AGGTATGGGCA
1 AGGTATGGGCA
*
5594123 AGGAATGGG
1 AGGTATGGG
5594132 TATATTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.31, C:0.05, G:0.48, T:0.17
Consensus pattern (11 bp):
AGGTATGGGCA
Found at i:5600217 original size:144 final size:144
Alignment explanation
Indices: 5600067--5600338 Score: 447
Period size: 144 Copynumber: 1.9 Consensus size: 144
5600057 GGATAGATGT
*
5600067 AATGTAACCAAATTCGTTAGCCTCCCAATTTCATGCGGAATGGATCCATTGAGTTGGTTGT-CAT
1 AATGTAACCAAATTCGTCAGCCTCCCAATTTCATGCGGAATGGATCCATTGAGTTGGTT-TCCAT
* **
5600131 TAAGAACCAGTGATGCAAGATTGGTTAAGTGGTTGACAGAAGATGGGATTGGACCAACAAGCATA
65 AAAGAACCAACGATGCAAGATTGGTTAAGTGGTTGACAGAAGATGGGATTGGACCAACAAGCATA
5600196 TTAGAAGATAGCTCC
130 TTAGAAGATAGCTCC
* * * *
5600211 AATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGCGGAATGGATCCATTGAGTTGGTTTCCATA
1 AATGTAACCAAATTCGTCAGCCTCCCAATTTCATGCGGAATGGATCCATTGAGTTGGTTTCCATA
*
5600276 AAGAACCAACGATGCAAGATTGGTTAAGTTGTTGACAGAAGATGGGATTGGACCAACAAGCAT
66 AAGAACCAACGATGCAAGATTGGTTAAGTGGTTGACAGAAGATGGGATTGGACCAACAAGCAT
5600339 GTTCCTTGAG
Statistics
Matches: 118, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
143 1 0.01
144 117 0.99
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (144 bp):
AATGTAACCAAATTCGTCAGCCTCCCAATTTCATGCGGAATGGATCCATTGAGTTGGTTTCCATA
AAGAACCAACGATGCAAGATTGGTTAAGTGGTTGACAGAAGATGGGATTGGACCAACAAGCATAT
TAGAAGATAGCTCC
Found at i:5602779 original size:18 final size:18
Alignment explanation
Indices: 5602758--5602792 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5602748 AATTAATAAT
*
5602758 TTTTTATAATTTATTTAA
1 TTTTGATAATTTATTTAA
*
5602776 TTTTGATATTTTATTTA
1 TTTTGATAATTTATTTA
5602793 TATGAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTGATAATTTATTTAA
Found at i:5608055 original size:17 final size:17
Alignment explanation
Indices: 5608029--5608061 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
5608019 TACAAATGCA
5608029 AAAAACCCTAAAAGCCCC
1 AAAAACCCT-AAAGCCCC
5608047 AAAAA-CCTAAAGCCC
1 AAAAACCCTAAAGCCC
5608062 AATGGCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.36, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAACCCTAAAGCCCC
Found at i:5608279 original size:17 final size:16
Alignment explanation
Indices: 5608232--5608288 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
5608222 AGAAGATAGG
**
5608232 AAACAAAAACATCGAA
1 AAACAAAAACAAAGAA
**
5608248 CAAACAAAATGAAAGTAA
1 -AAACAAAAACAAAG-AA
5608266 AAACAAAAACAAAGAA
1 AAACAAAAACAAAGAA
5608282 AAA-AAAA
1 AAACAAAA
5608289 CAATATATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 4 0.12
16 5 0.15
17 22 0.67
18 2 0.06
ACGTcount: A:0.75, C:0.12, G:0.07, T:0.05
Consensus pattern (16 bp):
AAACAAAAACAAAGAA
Found at i:5609753 original size:12 final size:13
Alignment explanation
Indices: 5609736--5609767 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5609726 GAAAATCTTA
5609736 TTATTTTTA-TTT
1 TTATTTTTATTTT
5609748 TTA-TTTTATTTT
1 TTATTTTTATTTT
5609760 TTATTTTT
1 TTATTTTT
5609768 TATTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 9 0.50
13 4 0.22
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTATTTTTATTTT
Found at i:5615923 original size:47 final size:46
Alignment explanation
Indices: 5615868--5615996 Score: 163
Period size: 44 Copynumber: 2.8 Consensus size: 46
5615858 ATGCCATAGG
*
5615868 TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCGCTCGAAG
1 TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTC-CTCGAAA
* * * *
5615915 TATCTATACCATGGCCCAAAGCCAACTCAAGATAAC--CTTCGAAA
1 TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCCTCGAAA
* * *
5615959 TGCCTATACCATGGCCCGAAGCCTACTCAAGGCAACTT
1 TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTT
5615997 GCACCTGAAG
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
44 35 0.51
45 1 0.01
47 33 0.48
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (46 bp):
TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCCTCGAAA
Found at i:5615972 original size:44 final size:46
Alignment explanation
Indices: 5615868--5615989 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
5615858 ATGCCATAGG
* *
5615868 TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCGCTCGAAG
1 TACCTATACCATGGCCCGAAGCCAACTCAAGATAAC-TCGCTCGAAA
* * *
5615915 TATCTATACCATGGCCCAAAGCCAACTCAAGATAAC-C-TTCGAAA
1 TACCTATACCATGGCCCGAAGCCAACTCAAGATAACTCGCTCGAAA
* *
5615959 TGCCTATACCATGGCCCGAAGCCTACTCAAG
1 TACCTATACCATGGCCCGAAGCCAACTCAAG
5615990 GCAACTTGCA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
44 32 0.48
45 1 0.02
47 33 0.50
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (46 bp):
TACCTATACCATGGCCCGAAGCCAACTCAAGATAACTCGCTCGAAA
Found at i:5623677 original size:47 final size:46
Alignment explanation
Indices: 5623559--5623735 Score: 189
Period size: 47 Copynumber: 3.8 Consensus size: 46
5623549 CATACCATAG
*
5623559 GTACCTATACCATGGCCCGAAGCCAACTCAAAGTAACCTATCACT-GAA
1 GTACCTATACCATGGCCCGAAGCCAACTCAAGGTAA-CT-TC-CTCGAA
* *
5623607 GTACCTATACCATGGCCCAAAGCCAACTCAAGGTAACTTCGCTCGGA
1 GTACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTC-CTCGAA
* * * *
5623654 GTATCTATACCATGGCCCGAAGCCAATTCAAGATAACAT-C-CGAA
1 GTACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCCTCGAA
* ** * *
5623698 ATGGCTATACCATGGCCCGAAGCCTACTCAAGGCAACT
1 GTACCTATACCATGGCCCGAAGCCAACTCAAGGTAACT
5623736 CGCACCTGAA
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
44 33 0.30
45 1 0.01
46 4 0.04
47 38 0.35
48 34 0.31
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.19
Consensus pattern (46 bp):
GTACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCCTCGAA
Found at i:5625096 original size:22 final size:24
Alignment explanation
Indices: 5625066--5625113 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
5625056 CACGTTAGAT
5625066 AACATAATATATAAAT-AAAAATA
1 AACATAATATATAAATAAAAAATA
* *
5625089 AACA-AATATTTATATAAAAAATA
1 AACATAATATATAAATAAAAAATA
5625112 AA
1 AA
5625114 ATATAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
AACATAATATATAAATAAAAAATA
Found at i:5626497 original size:4 final size:4
Alignment explanation
Indices: 5626488--5626514 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5626478 ATATTCATTT
5626488 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
5626515 TTTATTTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Done.