Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 18 of 28
Found at i:2713851 original size:19 final size:19
Alignment explanation
Indices: 2713820--2713857 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2713810 TAAAATATAT
*
2713820 ATATATATTACATATTTAA
1 ATATATATTACATAATTAA
2713839 ATATA-ATTGACATAATTAA
1 ATATATATT-ACATAATTAA
2713858 TATGACACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (19 bp):
ATATATATTACATAATTAA
Found at i:2713908 original size:17 final size:19
Alignment explanation
Indices: 2713886--2713930 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
2713876 TATATCATAT
2713886 TTATATTTAA-AA-TTTTA
1 TTATATTTAATAATTTTTA
2713903 TTATATTTAATAATTTTTA
1 TTATATTTAATAATTTTTA
2713922 TTATATTTA
1 TTATATTTA
2713931 TATATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 10 0.38
18 2 0.08
19 14 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATTTAATAATTTTTA
Found at i:2713937 original size:19 final size:18
Alignment explanation
Indices: 2713886--2713937 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
2713876 TATATCATAT
*
2713886 TTATATTTAA-AATTTTA
1 TTATATTTAATATTTTTA
2713903 TTATATTTAATAATTTTTA
1 TTATATTTAAT-ATTTTTA
2713922 TTATATTTATATATTT
1 TTATATTTA-ATATTT
2713938 ATAAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 10 0.32
19 19 0.61
20 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATATTTAATATTTTTA
Found at i:2715132 original size:12 final size:13
Alignment explanation
Indices: 2715102--2715133 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2715092 TTGGTCCATT
2715102 TATAT-ATATATA
1 TATATAATATATA
2715114 TATATAATATATA
1 TATATAATATATA
2715127 -ATATAAT
1 TATATAAT
2715134 GAAAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATAATATATA
Found at i:2715629 original size:2 final size:2
Alignment explanation
Indices: 2715622--2715647 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2715612 ACACTAATTG
2715622 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2715648 GTACACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2716917 original size:22 final size:21
Alignment explanation
Indices: 2716892--2716938 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
2716882 ATTCATACTC
2716892 AATTAAGT-TTATAAACTACTTA
1 AATTAAGTATTA-AAA-TACTTA
2716914 AATTAAGTATTAAAATACTTA
1 AATTAAGTATTAAAATACTTA
2716935 AATT
1 AATT
2716939 TGATTCGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.42
22 11 0.46
23 3 0.12
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (21 bp):
AATTAAGTATTAAAATACTTA
Found at i:2716927 original size:21 final size:22
Alignment explanation
Indices: 2716892--2716938 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
2716882 ATTCATACTC
* *
2716892 AATTAAGTTTATAAACTACTTA
1 AATTAAGTATATAAAATACTTA
2716914 AATTAAGTAT-TAAAATACTTA
1 AATTAAGTATATAAAATACTTA
2716935 AATT
1 AATT
2716939 TGATTCGCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTAAGTATATAAAATACTTA
Found at i:2717455 original size:18 final size:17
Alignment explanation
Indices: 2717432--2717472 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 17
2717422 ATTTAAAATT
2717432 TATTAAAAATTATTTTTA
1 TATTAAAAA-TATTTTTA
2717450 TATT--AAATATTTTTA
1 TATTAAAAATATTTTTA
2717465 TAATTAAA
1 T-ATTAAA
2717473 TTTAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
15 9 0.45
16 6 0.30
18 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTAAAAATATTTTTA
Found at i:2717457 original size:16 final size:17
Alignment explanation
Indices: 2717438--2717474 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
2717428 AATTTATTAA
2717438 AAATTATTTTTAT-ATT
1 AAATTATTTTTATAATT
2717454 AAA-TATTTTTATAATT
1 AAATTATTTTTATAATT
2717470 AAATT
1 AAATT
2717475 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 9 0.47
17 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AAATTATTTTTATAATT
Found at i:2723689 original size:17 final size:17
Alignment explanation
Indices: 2723664--2723696 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2723654 GAAGATGAAT
2723664 TTGAATAATTTAAATTA
1 TTGAATAATTTAAATTA
*
2723681 TTGAGTAATTTAAATT
1 TTGAATAATTTAAATT
2723697 TAAAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
TTGAATAATTTAAATTA
Found at i:2723727 original size:19 final size:19
Alignment explanation
Indices: 2723690--2723727 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2723680 ATTGAGTAAT
*
2723690 TTAAATTTAAAATTTTTAA
1 TTAAATTTAAAATTATTAA
2723709 TTAAATTTAATAA-TATTAA
1 TTAAATTTAA-AATTATTAA
2723728 ATGTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATTTAAAATTATTAA
Found at i:2723766 original size:21 final size:23
Alignment explanation
Indices: 2723742--2723783 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2723732 AAATAATTAT
2723742 ATTATA-AAAAATAAT-TAAAAA
1 ATTATATAAAAATAATATAAAAA
*
2723763 ATTATATAAATATAATATAAA
1 ATTATATAAAAATAATATAAA
2723784 TATATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATTATATAAAAATAATATAAAAA
Found at i:2723793 original size:19 final size:18
Alignment explanation
Indices: 2723760--2723815 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
2723750 AAATAATTAA
*
2723760 AAAATTATATAAATATAAT
1 AAAA-TATATTAATATAAT
**
2723779 ATAAATATATTAATATTTT
1 A-AAATATATTAATATAAT
2723798 AAAATATATATAATATAA
1 AAAATATAT-TAATATAA
2723816 ATTATTATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 8 0.27
19 19 0.63
20 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATATTAATATAAT
Found at i:2723888 original size:25 final size:24
Alignment explanation
Indices: 2723860--2723909 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
2723850 CTTTGATCAT
2723860 AAATATAATATA-ATAAAATATATAA
1 AAATATAA-ATACATAAAATAT-TAA
*
2723885 AAATATAAATACATAAATTATTAA
1 AAATATAAATACATAAAATATTAA
2723909 A
1 A
2723910 TTTAATCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATATAAATACATAAAATATTAA
Found at i:2727628 original size:2 final size:2
Alignment explanation
Indices: 2727621--2727648 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2727611 CTCAGCAAAA
2727621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2727649 TATTTTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2727750 original size:2 final size:2
Alignment explanation
Indices: 2727743--2727785 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2727733 CTAGGCAAAC
*
2727743 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2727785 T
1 T
2727786 GTTACATCGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2728526 original size:21 final size:20
Alignment explanation
Indices: 2728474--2728526 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 20
2728464 AAATTTATTT
2728474 TAAAAATATATTTAATATAA
1 TAAAAATATATTTAATATAA
*
2728494 TTAAAA-AT-TTTAATAATAA
1 TAAAAATATATTTAAT-ATAA
2728513 -AAAAATATTATTTA
1 TAAAAATA-TATTTA
2728527 TCAATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 10 0.37
19 7 0.26
20 6 0.22
21 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAAATATATTTAATATAA
Found at i:2730740 original size:20 final size:19
Alignment explanation
Indices: 2730701--2730760 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
2730691 ATTTATCCAC
*
2730701 ATATT-TTATTTGATTTAA
1 ATATTATTATTTAATTTAA
2730719 AT-TTATTATTTTAATTTAAA
1 ATATTATTA-TTTAATTT-AA
* *
2730739 ATATTTTTATTTAATTTTA
1 ATATTATTATTTAATTTAA
2730758 ATA
1 ATA
2730761 ATAAATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 2 0.06
18 5 0.14
19 11 0.31
20 12 0.34
21 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
ATATTATTATTTAATTTAA
Found at i:2730804 original size:15 final size:15
Alignment explanation
Indices: 2730771--2730817 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2730761 ATAAATATAT
2730771 AAATATAAAAATT--A
1 AAAT-TAAAAATTAAA
* *
2730785 AAATTTAACATTAAA
1 AAATTAAAAATTAAA
2730800 AAATTAAAAATTAAA
1 AAATTAAAAATTAAA
2730815 AAA
1 AAA
2730818 AATCATGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 17 0.63
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATTAAAAATTAAA
Found at i:2730953 original size:17 final size:18
Alignment explanation
Indices: 2730931--2730968 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2730921 ATATATTTTT
2730931 AATTAAATTTAATTAA-A
1 AATTAAATTTAATTAATA
* *
2730948 AATTAATTTTTATTAATA
1 AATTAAATTTAATTAATA
2730966 AAT
1 AAT
2730969 AATAATCCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTAAATTTAATTAATA
Found at i:2734840 original size:153 final size:152
Alignment explanation
Indices: 2734563--2734869 Score: 560
Period size: 153 Copynumber: 2.0 Consensus size: 152
2734553 ATATAGTTTT
*
2734563 ATACTAATATGATAGGTGTTACGTAGTTGTATTATGCATATCTCAATGTCTTAAATTTTTTGGCC
1 ATACTAATATGATAGGTGTTACGTAGTAGTATTATGCATATCTCAATGTCTTAAATTTTTTGGCC
*
2734628 TATCTGCTGAGTCCTGTAATAACTACGAAGACTTCATTTGTCTTGGCAAATATGTAAAGCTTTGT
66 TATCTGCTGAGTCCTGTAATAACTACGAAGACTTCATTTGCCTTGGCAAATATGTAAAGCTTTGT
2734693 AGCTCTTCATGTCAATAATATA
131 AGCTCTTCATGTCAATAATATA
*
2734715 ATACTAATATGATAGGTGTTACGTTGTAGTATTATGCATATCTCAATGTCTTAAATTTTTTTGGC
1 ATACTAATATGATAGGTGTTACGTAGTAGTATTATGCATATCTCAATGTCTTAAA-TTTTTTGGC
* *
2734780 CTATCTGCTGAGTCCTGTAATAACTATGAAGCCTTCATTTGCCTTGGCAAATATGTAAAGCTTTG
65 CTATCTGCTGAGTCCTGTAATAACTACGAAGACTTCATTTGCCTTGGCAAATATGTAAAGCTTTG
2734845 TAGCTCTTCATGTCAATAATATA
130 TAGCTCTTCATGTCAATAATATA
2734868 AT
1 AT
2734870 GCGCTTTAGT
Statistics
Matches: 149, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
152 53 0.36
153 96 0.64
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (152 bp):
ATACTAATATGATAGGTGTTACGTAGTAGTATTATGCATATCTCAATGTCTTAAATTTTTTGGCC
TATCTGCTGAGTCCTGTAATAACTACGAAGACTTCATTTGCCTTGGCAAATATGTAAAGCTTTGT
AGCTCTTCATGTCAATAATATA
Found at i:2738020 original size:13 final size:13
Alignment explanation
Indices: 2737996--2738042 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
2737986 TCGAAATTTT
2737996 TTAAATTATTTATA
1 TTAAA-TATTTATA
*
2738010 TTTAATATTTATA
1 TTAAATATTTATA
**
2738023 TTAAATAAATAT-
1 TTAAATATTTATA
2738035 TTAAATAT
1 TTAAATAT
2738043 AATATAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 7 0.25
13 17 0.61
14 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAAATATTTATA
Found at i:2738038 original size:12 final size:13
Alignment explanation
Indices: 2738023--2738069 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
2738013 AATATTTATA
2738023 TTAAATA-AATAT
1 TTAAATATAATAT
2738035 TTAAATATAATA-
1 TTAAATATAATAT
* *
2738047 TAAAATATAATTTT
1 TTAAATATAA-TAT
2738061 TTAAATATA
1 TTAAATATA
2738070 TAAAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 16 0.55
13 5 0.17
14 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAATATAATAT
Found at i:2738047 original size:24 final size:25
Alignment explanation
Indices: 2738007--2738069 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
2737997 TAAATTATTT
* *
2738007 ATATTT-AATATTTATATTAAATA-A
1 ATATTTAAATA-TAATATAAAATATA
2738031 ATATTTAAATATAATATAAAATATA
1 ATATTTAAATATAATATAAAATATA
*
2738056 ATTTTTTAAATATA
1 A-TATTTAAATATA
2738070 TAAAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 16 0.48
25 6 0.18
26 11 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
ATATTTAAATATAATATAAAATATA
Found at i:2738056 original size:26 final size:25
Alignment explanation
Indices: 2738025--2738093 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
2738015 TATTTATATT
2738025 AAATAAATATTTAAATATAATATAAA
1 AAATAAATATTTAAATATAATA-AAA
* * *
2738051 ATATAATTTTTTAAATAT-ATAAAA
1 AAATAAATATTTAAATATAATAAAA
* *
2738075 AAATAAAAAATTAAATATA
1 AAATAAATATTTAAATATA
2738094 TAATCATTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
24 16 0.47
25 3 0.09
26 15 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATAAATATTTAAATATAATAAAA
Found at i:2738740 original size:22 final size:22
Alignment explanation
Indices: 2738714--2738755 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2738704 ATATTTTATT
2738714 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
2738736 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
2738756 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:2738745 original size:29 final size:30
Alignment explanation
Indices: 2738687--2738743 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
2738677 TTGAATTATT
**
2738687 ATTTAATAATAAAAAATATATTTTATTTAA
1 ATTTAATAATAAAAAATATATAATATTTAA
*
2738717 ATTTAATTAT-AAAAATATATAAATATT
1 ATTTAATAATAAAAAATATAT-AATATT
2738744 AATATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
ATTTAATAATAAAAAATATATAATATTTAA
Found at i:2741187 original size:2 final size:2
Alignment explanation
Indices: 2741180--2741224 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2741170 ACTGTCAGTT
*
2741180 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2741222 AG A
1 AG A
2741225 AATTGAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2741892 original size:17 final size:17
Alignment explanation
Indices: 2741872--2741905 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2741862 TTTATTCTCG
2741872 ATAAAATTAATCTGATT
1 ATAAAATTAATCTGATT
* *
2741889 ATAAATTTAATTTGATT
1 ATAAAATTAATCTGATT
2741906 TTTTAATCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (17 bp):
ATAAAATTAATCTGATT
Found at i:2742099 original size:2 final size:2
Alignment explanation
Indices: 2742092--2742122 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2742082 ATTTTGATAC
*
2742092 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2742123 AAATATTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2742515 original size:11 final size:11
Alignment explanation
Indices: 2742501--2742539 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2742491 CTAATTTAAT
*
2742501 TTAATAAAAAA
1 TTAATATAAAA
*
2742512 TTAA-ATTAAA
1 TTAATATAAAA
2742522 TTAATATAAAA
1 TTAATATAAAA
2742533 TTAATAT
1 TTAATAT
2742540 TAATTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TTAATATAAAA
Found at i:2742520 original size:21 final size:22
Alignment explanation
Indices: 2742492--2742545 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
2742482 GATTTAATAC
2742492 TAAT-TTAATTTAATAAAAAAT
1 TAATATTAATTTAATAAAAAAT
* *
2742513 TAA-ATTAAATTAATATAAAAT
1 TAATATTAATTTAATAAAAAAT
2742534 TAATATTAATTT
1 TAATATTAATTT
2742546 TTTATAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATATTAATTTAATAAAAAAT
Found at i:2743093 original size:24 final size:23
Alignment explanation
Indices: 2743052--2743098 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2743042 ATTTTCAATG
2743052 AAATTATAAATAACGATAATAATA
1 AAATTATAAATAACGATAA-AATA
*
2743076 AAATTA-AAATTAATGATAAAATA
1 AAATTATAAA-TAACGATAAAATA
2743099 TATAGTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AAATTATAAATAACGATAAAATA
Found at i:2743238 original size:32 final size:31
Alignment explanation
Indices: 2743187--2743251 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
2743177 AAATTATCTG
*
2743187 TATATTTTTTAATAATATTTAAAAATTTTAA
1 TATATATTTTAATAATATTTAAAAATTTTAA
* *
2743218 TATATATTTTATATATTATTTAAATATTTTAA
1 TATATATTTTA-ATAATATTTAAAAATTTTAA
2743250 TA
1 TA
2743252 AGTAACTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TATATATTTTAATAATATTTAAAAATTTTAA
Found at i:2744993 original size:33 final size:31
Alignment explanation
Indices: 2744919--2745002 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 31
2744909 AAAATTTATT
* *
2744919 TTATTATT-T-ATAATAATATTAAA-ATATTA
1 TTATTATTATAATAATAAT-TTAAATAAAATA
*
2744948 TTATTATTATAATTA-AATTTAAATAAAATA
1 TTATTATTATAATAATAATTTAAATAAAATA
2744978 TTATTATT-TAAATAATAATTTAAAT
1 TTATTATTAT-AATAATAATTTAAAT
2745003 TTATAAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 14 0.30
30 20 0.43
31 12 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TTATTATTATAATAATAATTTAAATAAAATA
Found at i:2745929 original size:2 final size:2
Alignment explanation
Indices: 2745922--2745946 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2745912 TGCTCACCAA
2745922 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2745947 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2746429 original size:19 final size:20
Alignment explanation
Indices: 2746405--2746444 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2746395 TTATTATCTA
2746405 TTTAAC-ATTAAAAATATTT
1 TTTAACAATTAAAAATATTT
* *
2746424 TTTAACAATTTAAATTATTT
1 TTTAACAATTAAAAATATTT
2746444 T
1 T
2746445 AATTTAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAACAATTAAAAATATTT
Found at i:2747726 original size:12 final size:12
Alignment explanation
Indices: 2747709--2747736 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2747699 TTCATCCGAT
2747709 TGAATTTTTTAA
1 TGAATTTTTTAA
2747721 TGAATTTTTTAA
1 TGAATTTTTTAA
2747733 TGAA
1 TGAA
2747737 AGTTAGTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (12 bp):
TGAATTTTTTAA
Found at i:2748050 original size:18 final size:16
Alignment explanation
Indices: 2748019--2748052 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
2748009 AAAAAAAATA
2748019 AAATTAAATTAAATTT
1 AAATTAAATTAAATTT
2748035 AAATATAAACTTAAATTT
1 AAAT-TAAA-TTAAATTT
2748053 TAACACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTAAATTAAATTT
Found at i:2748456 original size:16 final size:17
Alignment explanation
Indices: 2748415--2748456 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2748405 ATTTTTAAAA
*
2748415 TATAATATTTAATAATT
1 TATAATTTTTAATAATT
*
2748432 T-TAAATTTTAAT-ATT
1 TATAATTTTTAATAATT
2748447 TATAATTTTT
1 TATAATTTTT
2748457 CTATTCTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.19
16 16 0.76
17 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATAATTTTTAATAATT
Found at i:2748456 original size:23 final size:24
Alignment explanation
Indices: 2748400--2748456 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
2748390 TTAATTTAAA
*
2748400 TAATTATTTTTAAAATATAATATT
1 TAATAATTTTTAAAATATAATATT
* *
2748424 TAATAA-TTTTAAATTTTAATATT
1 TAATAATTTTTAAAATATAATATT
2748447 T-ATAATTTTT
1 TAATAATTTTT
2748457 CTATTCTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 20 0.69
24 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TAATAATTTTTAAAATATAATATT
Found at i:2749721 original size:2 final size:2
Alignment explanation
Indices: 2749714--2749738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2749704 CTTTATTATC
2749714 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
2749739 GTTTTTATGT
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:2752337 original size:2 final size:2
Alignment explanation
Indices: 2752324--2752354 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
2752314 AAATATTTGT
2752324 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
2752355 CTATTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2753693 original size:5 final size:5
Alignment explanation
Indices: 2753687--2753732 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
2753677 CCGATGACCT
* *
2753687 CACCT CACCT CACCC CACCC CACCC CACCC CACCC CACCC CACCC C
1 CACCC CACCC CACCC CACCC CACCC CACCC CACCC CACCC CACCC C
2753733 TTCACTTCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.20, C:0.76, G:0.00, T:0.04
Consensus pattern (5 bp):
CACCC
Found at i:2754673 original size:16 final size:15
Alignment explanation
Indices: 2754645--2754686 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
2754635 ATATAATTAT
2754645 ATTTAT-TTTTAAAA
1 ATTTATATTTTAAAA
*
2754659 TTTTATATATTTAAAA
1 ATTTATAT-TTTAAAA
2754675 ATTTATATTTTA
1 ATTTATATTTTA
2754687 TATTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 5 0.21
16 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATATTTTAAAA
Found at i:2755017 original size:8 final size:8
Alignment explanation
Indices: 2755004--2755038 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2754994 CAACCATGGG
2755004 TATTTTCA
1 TATTTTCA
2755012 TATTTTCA
1 TATTTTCA
*
2755020 TCTTTTCA
1 TATTTTCA
*
2755028 TCTTTTCA
1 TATTTTCA
2755036 TAT
1 TAT
2755039 CCCATAGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTTTCA
Found at i:2755479 original size:10 final size:10
Alignment explanation
Indices: 2755446--2755490 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
2755436 TTATTAAAAA
2755446 AATATTAATT
1 AATATTAATT
*
2755456 AATA-TCATT
1 AATATTAATT
2755465 AAATATTAATT
1 -AATATTAATT
2755476 AATATTAATT
1 AATATTAATT
2755486 AATAT
1 AATAT
2755491 AATATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 4 0.13
10 23 0.74
11 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (10 bp):
AATATTAATT
Found at i:2755490 original size:20 final size:20
Alignment explanation
Indices: 2755424--2755487 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2755414 TAATTTGTGC
*
2755424 ATTAAAT-TTAATTTAT-TA
1 ATTAAATATTAATTAATATA
** *
2755442 AAAAAATATTAATTAATATC
1 ATTAAATATTAATTAATATA
2755462 ATTAAATATTAATTAATATTA
1 ATTAAATATTAATTAATA-TA
2755483 ATTAA
1 ATTAA
2755488 TATAATATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 5 0.14
19 8 0.22
20 17 0.47
21 6 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAATATTAATTAATATA
Found at i:2757622 original size:17 final size:17
Alignment explanation
Indices: 2757586--2757634 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
2757576 AGTTGTAATC
* **
2757586 AATTTAAAATTAAAAAT
1 AATTTAAATTTAAATTT
2757603 AATTTAAATTTAAATTT
1 AATTTAAATTTAAATTT
*
2757620 AATTT-ATTTTAAATT
1 AATTTAAATTTAAATT
2757635 ATCTATTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTAAATTTAAATTT
Found at i:2758096 original size:16 final size:16
Alignment explanation
Indices: 2758047--2758096 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2758037 ATTGCACTAA
2758047 ATTTAAA-TATAATTT
1 ATTTAAATTATAATTT
*
2758062 -TTTAAATT-TAAATTA
1 ATTTAAATTAT-AATTT
*
2758077 ATTTAAATTATTATTT
1 ATTTAAATTATAATTT
2758093 ATTT
1 ATTT
2758097 TGATATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 7 0.25
15 5 0.18
16 15 0.54
17 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTAAATTATAATTT
Found at i:2758160 original size:21 final size:23
Alignment explanation
Indices: 2758130--2758183 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
2758120 ATAAAAATAA
2758130 TAAA-AAATTTAAAATTTA-T-C
1 TAAATAAATTTAAAATTTATTAC
** *
2758150 TAAATAAATTTTTAATTTATTAT
1 TAAATAAATTTAAAATTTATTAC
2758173 TAAATAAATTT
1 TAAATAAATTT
2758184 TAATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 12 0.43
22 1 0.04
23 11 0.39
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAATAAATTTAAAATTTATTAC
Found at i:2758163 original size:23 final size:23
Alignment explanation
Indices: 2758137--2758184 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2758127 TAATAAAAAA
2758137 TTTAAAAT-TTATCTAAATAAATT
1 TTTAAAATATTAT-TAAATAAATT
**
2758160 TTTAATTTATTATTAAATAAATT
1 TTTAAAATATTATTAAATAAATT
2758183 TT
1 TT
2758185 AATTTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAAAATATTATTAAATAAATT
Found at i:2758187 original size:22 final size:23
Alignment explanation
Indices: 2758145--2758211 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
2758135 AATTTAAAAT
2758145 TTATCTAAATAAATTTTTAATTTA
1 TTAT-TAAATAAATTTTTAATTTA
*
2758169 TTATTAAATAAA-TTTTAATTTT
1 TTATTAAATAAATTTTTAATTTA
*
2758191 TTATTTAAACTTAATTTTTAA
1 TTA-TTAAA-TAAATTTTTAA
2758212 CTTTTAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 12 0.32
23 13 0.34
24 7 0.18
25 6 0.16
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATTAAATAAATTTTTAATTTA
Found at i:2758209 original size:25 final size:23
Alignment explanation
Indices: 2758144--2758221 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 23
2758134 AAATTTAAAA
*
2758144 TTTATCTAAATAAATTTTTAATTT
1 TTTATTTAAAT-AATTTTTAATTT
* *
2758168 ATTA-TTAAATAAATTTTAATTT
1 TTTATTTAAATAATTTTTAATTT
*
2758190 TTTATTTAAACTTAATTTTTAACTT
1 TTTATTTAAA--TAATTTTTAATTT
*
2758215 TTAATTT
1 TTTATTT
2758222 TTATTTAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 14 0.32
23 10 0.23
24 3 0.07
25 17 0.39
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTATTTAAATAATTTTTAATTT
Found at i:2758345 original size:26 final size:26
Alignment explanation
Indices: 2758284--2758347 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
2758274 AATACAAATC
* * *
2758284 AAAATTAAAAGATAAAAATTTTTTTA
1 AAAAATAAAAAATAAAAATTTATTTA
* *
2758310 AGTAAA-AAAAAATATAAATTTATTTA
1 A-AAAATAAAAAATAAAAATTTATTTA
2758336 AAAAATAAAAAA
1 AAAAATAAAAAA
2758348 ATTATCGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
25 3 0.10
26 25 0.83
27 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (26 bp):
AAAAATAAAAAATAAAAATTTATTTA
Found at i:2759980 original size:18 final size:19
Alignment explanation
Indices: 2759951--2759986 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2759941 ATTTTTATTT
2759951 TTAAATAAATTAATTAAAA
1 TTAAATAAATTAATTAAAA
2759970 TTAAA-AAATTAATTAAA
1 TTAAATAAATTAATTAAA
2759987 TAAAATCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAATAAATTAATTAAAA
Found at i:2762621 original size:13 final size:13
Alignment explanation
Indices: 2762605--2762662 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
2762595 ATTTAAAATT
2762605 TAAATTTATTAAA
1 TAAATTTATTAAA
2762618 TAAAATTT-TTAAA
1 T-AAATTTATTAAA
* *
2762631 -AAA-TAATTATA
1 TAAATTTATTAAA
*
2762642 TAAATTAATTAAA
1 TAAATTTATTAAA
2762655 TTAAATTT
1 -TAAATTT
2762663 CAAATCTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 1 0.03
11 7 0.19
12 3 0.08
13 13 0.36
14 12 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATTTATTAAA
Found at i:2762858 original size:16 final size:15
Alignment explanation
Indices: 2762834--2762869 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2762824 CACACCATCC
2762834 TATTAAATATTTATT
1 TATTAAATATTTATT
*
2762849 ATATTTAATATTTATT
1 -TATTAAATATTTATT
2762865 TATTA
1 TATTA
2762870 TCAAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTAAATATTTATT
Found at i:2765775 original size:14 final size:14
Alignment explanation
Indices: 2765756--2765783 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2765746 TATATAAACA
2765756 TGTAAATAAACTTC
1 TGTAAATAAACTTC
2765770 TGTAAATAAACTTC
1 TGTAAATAAACTTC
2765784 CATTATATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TGTAAATAAACTTC
Found at i:2765862 original size:16 final size:16
Alignment explanation
Indices: 2765817--2765863 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
2765807 TATATGTAGA
2765817 TATAAATTTTAAA-AT
1 TATAAATTTTAAATAT
2765832 TATAAATATTT-AATAT
1 TATAAAT-TTTAAATAT
2765848 T-TAATATTTTAAATAT
1 TATAA-ATTTTAAATAT
2765864 CAAATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATAAATTTTAAATAT
Found at i:2765869 original size:23 final size:22
Alignment explanation
Indices: 2765816--2765869 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
2765806 TTATATGTAG
2765816 ATATAAAT-TTTAAAATTATAA
1 ATATAAATATTTAAAATTATAA
* * *
2765837 ATATTTAATATTTAATATTTTAA
1 ATA-TAAATATTTAAAATTATAA
2765860 ATATCAAATA
1 ATAT-AAATA
2765870 AATAAAGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 18 0.69
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATAAATATTTAAAATTATAA
Found at i:2767966 original size:30 final size:31
Alignment explanation
Indices: 2767931--2768014 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 31
2767921 TATGTTAAGC
* *
2767931 TATTAATATT-TTAAAACTT-AATATAAAAAG
1 TATTAA-ATTATTAAAAATTAAATATAAAAAA
*
2767961 TATTAAATTATTAAAAATTAAATTTAAAAAA
1 TATTAAATTATTAAAAATTAAATATAAAAAA
2767992 TATT---TTA-TAAAAATTAAAATATA
1 TATTAAATTATTAAAAATT-AAATATA
2768015 TAATATGGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
27 8 0.17
28 9 0.19
29 3 0.06
30 14 0.30
31 13 0.28
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (31 bp):
TATTAAATTATTAAAAATTAAATATAAAAAA
Found at i:2779561 original size:14 final size:14
Alignment explanation
Indices: 2779544--2779572 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2779534 TTTTTATATT
2779544 TATATTCAGATAAA
1 TATATTCAGATAAA
2779558 TATATTCAGATAAA
1 TATATTCAGATAAA
2779572 T
1 T
2779573 GATTACAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (14 bp):
TATATTCAGATAAA
Found at i:2780016 original size:6 final size:6
Alignment explanation
Indices: 2780007--2780036 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2779997 TGCTGCCCCA
2780007 GCCCTT GCCCTT GCCCTT GCCCTT GCCCTT
1 GCCCTT GCCCTT GCCCTT GCCCTT GCCCTT
2780037 TCACTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
GCCCTT
Found at i:2780021 original size:18 final size:18
Alignment explanation
Indices: 2780000--2780036 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2779990 CTGCTGTTGC
2780000 TGCCCCAGCCCTTGCCCT
1 TGCCCCAGCCCTTGCCCT
**
2780018 TGCCCTTGCCCTTGCCCT
1 TGCCCCAGCCCTTGCCCT
2780036 T
1 T
2780037 TCACTTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.51, G:0.16, T:0.30
Consensus pattern (18 bp):
TGCCCCAGCCCTTGCCCT
Found at i:2782161 original size:16 final size:17
Alignment explanation
Indices: 2782128--2782185 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 17
2782118 AATATAAAAA
*
2782128 ATAAT-TAAAATATGAT
1 ATAATATAAAATATAAT
2782144 ATAATATAAAATAT-AT
1 ATAATATAAAATATAAT
* *
2782160 ATATTTTAAAAT-TAAT
1 ATAATATAAAATATAAT
2782176 ATAATATAAA
1 ATAATATAAA
2782186 TTATTAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 1 0.03
16 27 0.75
17 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
ATAATATAAAATATAAT
Found at i:2782182 original size:32 final size:32
Alignment explanation
Indices: 2782132--2782233 Score: 93
Period size: 32 Copynumber: 3.2 Consensus size: 32
2782122 TAAAAAATAA
*
2782132 TTAAAATATGATATAATATAAAATATATATATT
1 TTAAAAT-TAATATAATATAAAATATATATATT
*
2782165 TTAAAATTAATATAATATAAATTAT-TA-ATT
1 TTAAAATTAATATAATATAAAATATATATATT
* * *
2782195 TAAAAAATTACATA-AATATAGATATAAATATATT
1 T-TAAAATTA-ATATAATATA-AAATATATATATT
*
2782229 ATAAA
1 TTAAA
2782234 TACGATTATG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
30 4 0.07
31 15 0.27
32 22 0.39
33 12 0.21
34 3 0.05
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (32 bp):
TTAAAATTAATATAATATAAAATATATATATT
Found at i:2782669 original size:22 final size:20
Alignment explanation
Indices: 2782643--2782702 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
2782633 TTAATGAAAT
*
2782643 TAAATATTATTTATAAATTAAA
1 TAAATATTATTAAT-AA-TAAA
*
2782665 TAAATTTTATTAATAATAAA
1 TAAATATTATTAATAATAAA
**
2782685 -AAATATTAAAAATAATAA
1 TAAATATTATTAATAATAA
2782703 TTCAAGATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 15 0.45
20 4 0.12
21 2 0.06
22 12 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATATTATTAATAATAAA
Found at i:2782777 original size:3 final size:3
Alignment explanation
Indices: 2782771--2782802 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2782761 ATGTTGTTGC
2782771 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2782803 GTACACTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2783653 original size:36 final size:36
Alignment explanation
Indices: 2783519--2783657 Score: 124
Period size: 36 Copynumber: 3.9 Consensus size: 36
2783509 TGTATGTATA
* * *
2783519 TATAATAAATAATTAAAAA-TTATTAAAATTGTATC
1 TATATTAAATAATTAAAAATTTATTAAAATTATATT
* ** *
2783554 TATATTAAATTA-TAAAATATAAATTAAAATGATATT
1 TATATTAAATAATTAAAA-ATTTATTAAAATTATATT
* *
2783590 TATGTTAAATAATTACAAAATTT-TTAAATTTATATT
1 TATATTAAATAATTA-AAAATTTATTAAAATTATATT
* *
2783626 TAAATTGAATAA-TAAAATATTTATTAAAATTA
1 TATATTAAATAATTAAAA-ATTTATTAAAATTA
2783658 AACTTACTAA
Statistics
Matches: 81, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
34 8 0.10
35 17 0.21
36 49 0.60
37 4 0.05
38 3 0.04
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATTAAATAATTAAAAATTTATTAAAATTATATT
Found at i:2786250 original size:9 final size:9
Alignment explanation
Indices: 2786236--2786269 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
2786226 TTTGAATTTG
2786236 ATTAATAAA
1 ATTAATAAA
2786245 ATTAATATTAA
1 ATTAATA--AA
2786256 ATTAATAAA
1 ATTAATAAA
2786265 ATTAA
1 ATTAA
2786270 CAGTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.61
11 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
ATTAATAAA
Found at i:2786284 original size:21 final size:20
Alignment explanation
Indices: 2786236--2786286 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2786226 TTTGAATTTG
*
2786236 ATTAATAAAATTAATATTAA
1 ATTAATAAAATTAACATTAA
2786256 ATTAATAAAATTAACAGTTTAA
1 ATTAATAAAATTAACA--TTAA
2786278 A-TAATAAAA
1 ATTAATAAAA
2786287 ACTTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 15 0.54
21 8 0.29
22 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTAATAAAATTAACATTAA
Found at i:2787613 original size:49 final size:50
Alignment explanation
Indices: 2787518--2787672 Score: 215
Period size: 49 Copynumber: 3.1 Consensus size: 50
2787508 AGTTGCTTAG
* *
2787518 AGTCAATAATTACGGCCACCTCTT-TCAATTGTCAAAAGTTGGTGAAGAAT
1 AGTCAATAATTACGGTCACCT-TTCTCGATTGTCAAAAGTTGGTGAAGAAT
* * *
2787568 CGTCAATAATTATGGTCACCTTTCTCGA-TGTCAAAAGTTGATGAAGAAT
1 AGTCAATAATTACGGTCACCTTTCTCGATTGTCAAAAGTTGGTGAAGAAT
* * *
2787617 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAATAATTACGGTCACCTTTCTCGATTGTCAAAAGTTGGTGAAGAAT
2787667 AGTCAA
1 AGTCAA
2787673 CAATGGCAAC
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
49 46 0.50
50 46 0.50
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (50 bp):
AGTCAATAATTACGGTCACCTTTCTCGATTGTCAAAAGTTGGTGAAGAAT
Found at i:2787673 original size:50 final size:50
Alignment explanation
Indices: 2787518--2787676 Score: 221
Period size: 50 Copynumber: 3.2 Consensus size: 50
2787508 AGTTGCTTAG
* * * *
2787518 AGTCAATAATTACGGCCACCTCTTTCAATTGTCAAAAGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
* * * * *
2787568 CGTCAATAATTATGGTCACCTTTCTCGA-TGTCAAAAGTTGATGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
*
2787617 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
2787667 AGTCAACAAT
1 AGTCAACAAT
2787677 GGCAACACAT
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
49 44 0.46
50 51 0.54
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
Found at i:2792127 original size:50 final size:50
Alignment explanation
Indices: 2792046--2792203 Score: 201
Period size: 50 Copynumber: 3.2 Consensus size: 50
2792036 AATTGCTTAG
* * ** *
2792046 AGTCAACAATTACGGTAACATCTCTCAATTGTCAAAGGTTGATGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTTGATTGTCAAAAGTTGATGAAGAAT
* *
2792096 CGTCAACAATTACGGTCACCTCTCTTGATTGTCAAAAGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTTGATTGTCAAAAGTTGATGAAGAAT
* * *
2792146 AGTCAACAATTACGATCACCTCT-TTCGATTGTCAAAAATTGATGGAGAAT
1 AGTCAACAATTACGGTCACCTCTCTT-GATTGTCAAAAGTTGATGAAGAAT
*
2792196 AATCAACA
1 AGTCAACA
2792204 GTGACAACAC
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
49 2 0.02
50 92 0.98
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (50 bp):
AGTCAACAATTACGGTCACCTCTCTTGATTGTCAAAAGTTGATGAAGAAT
Found at i:2797199 original size:29 final size:31
Alignment explanation
Indices: 2797167--2797231 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 31
2797157 TAAAAAATAT
*
2797167 TAAAAATTATTTTTA-TAAATAAATT-TAAA
1 TAAAAAATATTTTTATTAAATAAATTATAAA
* *
2797196 TAAAAAATATTTTTATTAATTAAATTATAAT
1 TAAAAAATATTTTTATTAAATAAATTATAAA
2797227 TAAAA
1 TAAAA
2797232 TCATATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 14 0.45
30 9 0.29
31 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TAAAAAATATTTTTATTAAATAAATTATAAA
Found at i:2797232 original size:29 final size:29
Alignment explanation
Indices: 2797148--2797232 Score: 70
Period size: 29 Copynumber: 2.9 Consensus size: 29
2797138 AGTAAACTTA
**
2797148 TTTTATT-ATTAAAAAAT-ATTAAAAATTAT
1 TTTTATTAATTAAATTATAATT-AAAA-TAT
* *
2797177 TTTTA-TAAATAAATT-TAAATAAAAAATAT
1 TTTTATTAATTAAATTAT-AAT-TAAAATAT
2797206 TTTTATTAATTAAATTATAATTAAAAT
1 TTTTATTAATTAAATTATAATTAAAAT
2797233 CATATTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
28 2 0.05
29 23 0.52
30 18 0.41
31 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTTATTAATTAAATTATAATTAAAATAT
Found at i:2798333 original size:19 final size:20
Alignment explanation
Indices: 2798309--2798352 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
2798299 AGTTATATTT
2798309 ATATTTAATTTAA-TTTAAA-
1 ATATTT-ATTTAATTTTAAAC
*
2798328 ATATTTTTTTAATTTTAAAC
1 ATATTTATTTAATTTTAAAC
2798348 ATATT
1 ATATT
2798353 ATCAAGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTTATTTAATTTTAAAC
Found at i:2801253 original size:16 final size:17
Alignment explanation
Indices: 2801234--2801298 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 17
2801224 TTACGATGTA
2801234 AATATATAAATATATA-
1 AATATATAAATATATAT
* *
2801250 AATATTTAAA-AAATTAAT
1 AATATATAAATATA-T-AT
*
2801268 AATATATTAAATTTATAT
1 AATATA-TAAATATATAT
2801286 AA-ATATAAATATA
1 AATATATAAATATA
2801299 AATATTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
15 2 0.05
16 17 0.45
17 4 0.11
18 9 0.24
19 5 0.13
20 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATATAAATATATAT
Found at i:2801609 original size:16 final size:16
Alignment explanation
Indices: 2801578--2801640 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
2801568 TTTAAAATAT
2801578 ATATAAAAATTAATTTAA
1 ATAT-AAAA-TAATTTAA
*
2801596 ATTTAAAATAATTTAA
1 ATATAAAATAATTTAA
* *
2801612 ATATAATATAATTTGA
1 ATATAAAATAATTTAA
* *
2801628 ATGTAAAAAAATT
1 ATATAAAATAATT
2801641 AAAGTTAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
16 31 0.82
17 4 0.11
18 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
ATATAAAATAATTTAA
Found at i:2802367 original size:18 final size:16
Alignment explanation
Indices: 2802346--2802384 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
2802336 ATATAAAAAA
2802346 ATTTAAAAATATAAATTT
1 ATTTAAAAAT-TAAA-TT
*
2802364 ATTTATAAATTAAATT
1 ATTTAAAAATTAAATT
2802380 ATTTA
1 ATTTA
2802385 CCTAACATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 4 0.20
18 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAAAAATTAAATT
Found at i:2803123 original size:2 final size:2
Alignment explanation
Indices: 2803116--2803173 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2803106 TTGTCATACC
2803116 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2803158 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
2803174 TTGTGCTCTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2804640 original size:35 final size:33
Alignment explanation
Indices: 2804588--2804684 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 33
2804578 GTCAAACAGA
2804588 AATTTAAATTTAATTAAAATTTAAAATTT-AAAGTTT
1 AATTTAAA-TTAATTAAAATTT---ATTTAAAAGTTT
*
2804624 AATTTAAACTAATTAAAATTTATTTAAAAAGTTT
1 AATTTAAATTAATTAAAATTTATTT-AAAAGTTT
* *
2804658 AAATTAAATTATTTAAAATTT-TTTAAA
1 AATTTAAATTAATTAAAATTTATTTAAA
2804685 TTAAATATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
32 7 0.13
33 3 0.05
34 25 0.45
35 12 0.22
36 8 0.15
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (33 bp):
AATTTAAATTAATTAAAATTTATTTAAAAGTTT
Found at i:2806173 original size:22 final size:22
Alignment explanation
Indices: 2806146--2806187 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2806136 TTTTATTTTA
2806146 TTAATAAAAAAATATTAAAATT
1 TTAATAAAAAAATATTAAAATT
* * *
2806168 TTAATATAAATATTTTAAAA
1 TTAATAAAAAAATATTAAAA
2806188 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAATAAAAAAATATTAAAATT
Found at i:2814678 original size:19 final size:17
Alignment explanation
Indices: 2814650--2814711 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
2814640 AAACAATCAA
*
2814650 AATAAGAAATAAAATAT
1 AATAAAAAATAAAATAT
*
2814667 GGTATAAAAAATATAAATAT
1 --AATAAAAAATA-AAATAT
2814687 AATAAAAATATAAAATAT
1 AATAAAAA-ATAAAATAT
*
2814705 ATTAAAA
1 AATAAAA
2814712 TTTATATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 19 0.51
19 12 0.32
20 6 0.16
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (17 bp):
AATAAAAAATAAAATAT
Found at i:2814710 original size:27 final size:27
Alignment explanation
Indices: 2814669--2814737 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
2814659 TAAAATATGG
*
2814669 TATAAAAAATA-T-AAATATAATAAAAA
1 TATAAAATATATTAAAAT-TAATAAAAA
* *
2814695 TATAAAATATATTAAAATTTATATAAA
1 TATAAAATATATTAAAATTAATAAAAA
*
2814722 TATAAAATATTTTAAA
1 TATAAAATATATTAAA
2814738 TATATTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 10 0.27
27 23 0.62
28 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TATAAAATATATTAAAATTAATAAAAA
Found at i:2814788 original size:20 final size:19
Alignment explanation
Indices: 2814671--2814789 Score: 81
Period size: 18 Copynumber: 6.5 Consensus size: 19
2814661 AAATATGGTA
*
2814671 TAAAAA-ATATAAATATAA
1 TAAAAATATATAAATATAT
2814689 TAAAAATATA-AAATATAT
1 TAAAAATATATAAATATAT
*
2814707 TAAAATTTATATAAATATA-
1 TAAAA-ATATATAAATATAT
* *
2814726 -AAATAT-TTTAAATATAT
1 TAAAAATATATAAATATAT
* **
2814743 TTATTATATCATAAA-AT-T
1 TAAAAATAT-ATAAATATAT
* *
2814761 CAACAATATATAAATATATT
1 TAAAAATATATAAATATA-T
2814781 TAAAAATAT
1 TAAAAATAT
2814790 TCATGAACTA
Statistics
Matches: 77, Mismatches: 14, Indels: 18
0.71 0.13 0.17
Matches are distributed among these distances:
16 9 0.12
17 6 0.08
18 33 0.43
19 10 0.13
20 19 0.25
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAAATATATAAATATAT
Found at i:2814845 original size:12 final size:11
Alignment explanation
Indices: 2814824--2814884 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
2814814 TTAAAATCTT
2814824 AAATAATTTTA
1 AAATAATTTTA
2814835 AAATCAATTTT-
1 AAAT-AATTTTA
*
2814846 --ATTA-TTTA
1 AAATAATTTTA
*
2814854 AAATAATATTA
1 AAATAATTTTA
2814865 AAA-AATTTTA
1 AAATAATTTTA
*
2814875 AAACAATTTT
1 AAATAATTTT
2814885 TATATTAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
7 3 0.08
8 1 0.03
9 2 0.05
10 12 0.30
11 16 0.40
12 6 0.15
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
AAATAATTTTA
Found at i:2816629 original size:23 final size:25
Alignment explanation
Indices: 2816580--2816631 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
2816570 GTAAGTTTTT
**
2816580 TATATATTTGAAAAATTATATTTTA
1 TATATATTTGAAAAATTATATCATA
*
2816605 TATATATTT-AAATA-TATATCATA
1 TATATATTTGAAAAATTATATCATA
2816628 TATA
1 TATA
2816632 AATATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 4 0.17
25 9 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
TATATATTTGAAAAATTATATCATA
Found at i:2816633 original size:17 final size:16
Alignment explanation
Indices: 2816603--2816636 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2816593 AATTATATTT
*
2816603 TATATATATTTAAATA
1 TATATATATATAAATA
2816619 TATATCATATATAAATA
1 TATAT-ATATATAAATA
2816636 T
1 T
2816637 TTTAAGGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATATATAAATA
Found at i:2818015 original size:2 final size:2
Alignment explanation
Indices: 2818008--2818036 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2817998 TCTGTTACCC
2818008 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
2818037 GAGAATTGTT
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:2818897 original size:14 final size:14
Alignment explanation
Indices: 2818877--2818921 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 14
2818867 TATTTAAAAA
2818877 ATATATTATAATAT
1 ATATATTATAATAT
*
2818891 TTATATT-TAA-AT
1 ATATATTATAATAT
2818903 ATATATTA-AATAT
1 ATATATTATAATAT
2818916 A-ATATT
1 ATATATT
2818922 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 15 0.56
13 6 0.22
14 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATTATAATAT
Found at i:2818909 original size:12 final size:12
Alignment explanation
Indices: 2818866--2818925 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
2818856 ATTTTTTAAA
*
2818866 ATATTTAAAAAAT
1 ATATTT-AAATAT
*
2818879 ATATTATAATATTT
1 ATATT-TAA-ATAT
2818893 ATATTTAAATAT
1 ATATTTAAATAT
2818905 ATA-TTAAATAT
1 ATATTTAAATAT
2818916 AATATTTAAA
1 -ATATTTAAA
2818926 AAAATAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 8 0.20
12 9 0.22
13 15 0.38
14 8 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTTAAATAT
Found at i:2818920 original size:24 final size:26
Alignment explanation
Indices: 2818865--2818927 Score: 85
Period size: 24 Copynumber: 2.5 Consensus size: 26
2818855 TATTTTTTAA
2818865 AATATTTAAAAAATATATTATAATATT
1 AATATTT-AAAAATATATTATAATATT
* *
2818892 TATATTTAAATATATATTA-AATA-T
1 AATATTTAAAAATATATTATAATATT
2818916 AATATTTAAAAA
1 AATATTTAAAAA
2818928 AATAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 11 0.34
25 4 0.12
26 11 0.34
27 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATATTTAAAAATATATTATAATATT
Found at i:2818937 original size:24 final size:25
Alignment explanation
Indices: 2818865--2818937 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 25
2818855 TATTTTTTAA
*
2818865 AATATTTAAAAAATATATTATAATATT
1 AATATTTAAAAAA-ATA-TAAAATATT
* * * *
2818892 TATATTTAAATATATATTAAATA-T
1 AATATTTAAAAAAATATAAAATATT
*
2818916 AATATTTAAAAAAATAAAAAAT
1 AATATTTAAAAAAATATAAAAT
2818938 CGAAATAACA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
24 18 0.50
25 5 0.14
26 3 0.08
27 10 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATTTAAAAAAATATAAAATATT
Found at i:2825412 original size:184 final size:185
Alignment explanation
Indices: 2825102--2825470 Score: 652
Period size: 184 Copynumber: 2.0 Consensus size: 185
2825092 GCCAAAAGGA
* *
2825102 AAGGTCACATATAAGACTTGGTAAACACTTGCTAGTGACTCATTAACAATTGACGGGTCATACAG
1 AAGGTCACATATAAAACTTGGTAAACACTTGCTAGTGACTCAGTAACAATTGACGGGTCATACAG
2825167 CTAGAGTCCATAGAAAACTCAAAACTTAGCGAGAGGCATCCAGTCTTTCTTTCACTCAAAGGCAA
66 CTAGAGTCCATAGAAAACTCAAAACTTAGCGAGAGGCATCCAGTCTTTCTTTCACTCAAAGGCAA
2825232 AGATCTAAAACCATTTTTGGTCAAGATCGGAGCTTGTTAAAATCTTGCCAGTACT
131 AGATCTAAAACCATTTTTGGTCAAGATCGGAGCTTGTTAAAATCTTGCCAGTACT
*
2825287 AAGGTCACATATAAAACTTGGTAAACACTTGCTAGTGACTC-GTAACAATTGACGGTTCATACAG
1 AAGGTCACATATAAAACTTGGTAAACACTTGCTAGTGACTCAGTAACAATTGACGGGTCATACAG
* *
2825351 CTAGAGTCCATAGAAAACTC-AAACTTAGTGAGAGGCATCCAAGTCTTTCTTTCACTCAAAGGTA
66 CTAGAGTCCATAGAAAACTCAAAACTTAGCGAGAGGCATCC-AGTCTTTCTTTCACTCAAAGGCA
* *
2825415 AAGATCTAAAACCATTTTTTGTCAAGATTGGAGCTTGTTAAAATCTTGCCAGTACT
130 AAGATCTAAAACCATTTTTGGTCAAGATCGGAGCTTGTTAAAATCTTGCCAGTACT
2825471 GATAGTACTG
Statistics
Matches: 176, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
183 19 0.11
184 117 0.66
185 40 0.23
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (185 bp):
AAGGTCACATATAAAACTTGGTAAACACTTGCTAGTGACTCAGTAACAATTGACGGGTCATACAG
CTAGAGTCCATAGAAAACTCAAAACTTAGCGAGAGGCATCCAGTCTTTCTTTCACTCAAAGGCAA
AGATCTAAAACCATTTTTGGTCAAGATCGGAGCTTGTTAAAATCTTGCCAGTACT
Found at i:2833419 original size:13 final size:13
Alignment explanation
Indices: 2833401--2833427 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2833391 GTACCTTCTT
2833401 CAATGGCTCATGA
1 CAATGGCTCATGA
2833414 CAATGGCTCATGA
1 CAATGGCTCATGA
2833427 C
1 C
2833428 GGCTGCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (13 bp):
CAATGGCTCATGA
Found at i:2833815 original size:21 final size:21
Alignment explanation
Indices: 2833771--2833817 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2833761 TTTGTCGTTA
* * *
2833771 ATTTTAAAAAATTATAATTTT
1 ATTTAAAAAAATTATAACTCT
*
2833792 ATTTAAAAAAATTGTAACTCT
1 ATTTAAAAAAATTATAACTCT
2833813 ATTTA
1 ATTTA
2833818 TTTCTCTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTAAAAAAATTATAACTCT
Found at i:2834221 original size:19 final size:19
Alignment explanation
Indices: 2834181--2834226 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2834171 GCAAGGTATT
2834181 TTTAAAAATATATATATAA
1 TTTAAAAATATATATATAA
* *
2834200 TTTAATAAATATTTTTAT-A
1 TTTAA-AAATATATATATAA
2834219 TTTAAAAA
1 TTTAAAAA
2834227 ATGCGGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 11 0.46
20 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAAAAATATATATATAA
Found at i:2834228 original size:19 final size:20
Alignment explanation
Indices: 2834184--2834228 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2834174 AGGTATTTTT
2834184 AAAAATATATATATAATTTA
1 AAAAATATATATATAATTTA
* * *
2834204 ATAAATATTTTTAT-ATTTA
1 AAAAATATATATATAATTTA
2834223 AAAAAT
1 AAAAAT
2834229 GCGGTTGAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAATATATATATAATTTA
Found at i:2835056 original size:2 final size:2
Alignment explanation
Indices: 2835043--2835091 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2835033 AAAAGTAAAT
*
2835043 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2835085 TA TA TA T
1 TA TA TA T
2835092 TGATAACCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2836349 original size:19 final size:21
Alignment explanation
Indices: 2836305--2836357 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
2836295 ATTCACTTTA
2836305 ATTTATTAAATATTTAAATTT
1 ATTTATTAAATATTTAAATTT
*
2836326 A-TTATTCAA-ATTT-AATTT
1 ATTTATTAAATATTTAAATTT
2836344 ATTTATGTAAATAT
1 ATTTAT-TAAATAT
2836358 ATTTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 6 0.22
19 8 0.30
20 10 0.37
21 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTATTAAATATTTAAATTT
Found at i:2838599 original size:18 final size:18
Alignment explanation
Indices: 2838576--2838612 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2838566 AGTATTTTTA
2838576 TAAAAAA-TTATTTAATTT
1 TAAAAAATTTA-TTAATTT
2838594 TAAAAAATTTATTAATTT
1 TAAAAAATTTATTAATTT
2838612 T
1 T
2838613 TTTAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAAAAATTTATTAATTT
Found at i:2838613 original size:19 final size:21
Alignment explanation
Indices: 2838569--2838622 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
2838559 TTTGTATAGT
2838569 ATTTTTATAAAAAATTATTTA
1 ATTTTTATAAAAAATTATTTA
*
2838590 A-TTTTA-AAAAATTTA-TTA
1 ATTTTTATAAAAAATTATTTA
*
2838608 ATTTTTTTAAGAAAA
1 ATTTTTATAA-AAAA
2838623 CTAATAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 4 0.15
19 12 0.44
20 7 0.26
21 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTTTTATAAAAAATTATTTA
Found at i:2838741 original size:2 final size:2
Alignment explanation
Indices: 2838734--2838766 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2838724 ACATTATCTC
2838734 TA TA 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 TA TA T
2838767 TGGGCTGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2839352 original size:2 final size:2
Alignment explanation
Indices: 2839307--2839343 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2839297 GGAAAGCATG
*
2839307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2839344 GCTATATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2842026 original size:20 final size:21
Alignment explanation
Indices: 2842001--2842046 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2841991 TACCTTCATC
*
2842001 ATATTTA-AATATATTTTATG
1 ATATTTATAATATATTATATG
*
2842021 ATATTTATCATATATTATATG
1 ATATTTATAATATATTATATG
2842042 A-ATTT
1 ATATTT
2842047 TTTTTAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (21 bp):
ATATTTATAATATATTATATG
Found at i:2842302 original size:27 final size:27
Alignment explanation
Indices: 2842266--2842321 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
2842256 CCAGAATAAT
2842266 ATAATTATTTTATTAATGAATATATTA
1 ATAATTATTTTATTAATGAATATATTA
*
2842293 ATAATTATTTTATTAATTAATATATTA
1 ATAATTATTTTATTAATGAATATATTA
2842320 AT
1 AT
2842322 CTCTTGATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
ATAATTATTTTATTAATGAATATATTA
Found at i:2842306 original size:15 final size:15
Alignment explanation
Indices: 2842266--2842309 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2842256 CCAGAATAAT
2842266 ATAATTATTTTATTA
1 ATAATTATTTTATTA
2842281 ATGAA-TA---TATTA
1 AT-AATTATTTTATTA
2842293 ATAATTATTTTATTA
1 ATAATTATTTTATTA
2842308 AT
1 AT
2842310 TAATATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
11 2 0.08
12 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
ATAATTATTTTATTA
Found at i:2843193 original size:18 final size:19
Alignment explanation
Indices: 2843170--2843215 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
2843160 GTTTAGTTCA
*
2843170 ATTTAAAAATTAAT-TATT
1 ATTTAAAAATTAATAAATT
*
2843188 ATTTAAATATTAATAAATT
1 ATTTAAAAATTAATAAATT
2843207 -TTTAAAAAT
1 ATTTAAAAAT
2843216 ATTTATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTAAAAATTAATAAATT
Found at i:2843253 original size:21 final size:22
Alignment explanation
Indices: 2843228--2843285 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
2843218 TTATATTTTT
2843228 ATAATTAAATTTAAAT-AAATA
1 ATAATTAAATTTAAATAAAATA
*
2843249 ATAATTCAAACTT-AATAAAATA
1 ATAATT-AAATTTAAATAAAATA
*
2843271 A-ATTTAAATTATAAA
1 ATAATTAAATT-TAAA
2843286 AAACTTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 4 0.13
21 13 0.43
22 13 0.43
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAATTAAATTTAAATAAAATA
Found at i:2843624 original size:11 final size:11
Alignment explanation
Indices: 2843590--2843639 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
2843580 TTTAAAATAT
*
2843590 TTATA-TTATT
1 TTATATTTATA
2843600 TTATAATTTA-A
1 TTAT-ATTTATA
*
2843611 TTATTTTTATA
1 TTATATTTATA
2843622 TTATATTTATA
1 TTATATTTATA
*
2843633 TCATATT
1 TTATATT
2843640 ATTATCGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 8 0.24
11 22 0.67
12 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTTATA
Found at i:2843928 original size:17 final size:18
Alignment explanation
Indices: 2843907--2843946 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 18
2843897 ATTCAAATAA
2843907 TAAAAAAT-A-TTATTT-
1 TAAAAAATAATTTATTTC
2843922 TAAAAAATTAATTTATTTC
1 TAAAAAA-TAATTTATTTC
2843941 TAAAAA
1 TAAAAA
2843947 TTATTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 1 0.05
17 1 0.05
18 6 0.29
19 6 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAAAATAATTTATTTC
Found at i:2844526 original size:20 final size:19
Alignment explanation
Indices: 2844486--2844530 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2844476 ATTAAGTTAA
*
2844486 TAAAATATTAAATAATTTT
1 TAAAATATTAAATAATATT
2844505 TAAAATA-TAAATTTAATATT
1 TAAAATATTAAA--TAATATT
2844525 TAAAAT
1 TAAAAT
2844531 TTAGTTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATATTAAATAATATT
Found at i:2844776 original size:30 final size:29
Alignment explanation
Indices: 2844734--2844809 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
2844724 TATAAATTAT
*
2844734 TAAAAT-ATATAAATATTTTAATAAAATAA
1 TAAAATAATATAAATATTTTAAAAAAAT-A
* * * *
2844763 TTATATAATATAAAAAGATTTAAAAAAATA
1 TAAAATAATATAAATA-TTTTAAAAAAATA
2844793 TAAAATAATATAAATAT
1 TAAAATAATATAAATAT
2844810 ATAAATATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
29 4 0.11
30 22 0.61
31 10 0.28
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (29 bp):
TAAAATAATATAAATATTTTAAAAAAATA
Found at i:2844806 original size:20 final size:20
Alignment explanation
Indices: 2844769--2844806 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2844759 ATAATTATAT
*
2844769 AATATAAAAAGATTTAAAAA
1 AATATAAAAAGATATAAAAA
2844789 AATATAAAATA-ATATAAA
1 AATATAAAA-AGATATAAA
2844807 TATATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AATATAAAAAGATATAAAAA
Found at i:2844844 original size:20 final size:22
Alignment explanation
Indices: 2844805--2844857 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
2844795 AAATAATATA
*
2844805 AATATATAAATATTTTATGTAT
1 AATATATAAATATTTAATGTAT
*
2844827 AATATA-AAATA-TTAATGTCT
1 AATATATAAATATTTAATGTAT
2844847 -ATATATGAAAT
1 AATATAT-AAAT
2844858 TACCGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 7 0.26
21 9 0.33
22 6 0.22
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (22 bp):
AATATATAAATATTTAATGTAT
Found at i:2844852 original size:21 final size:21
Alignment explanation
Indices: 2844806--2844857 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
2844796 AATAATATAA
*
2844806 ATATATAAATATTTTATGTAT
1 ATATATAAATATTTAATGTAT
*
2844827 A-ATATAAA-ATATTAATGTCT
1 ATATATAAATAT-TTAATGTAT
2844847 ATATATGAAAT
1 ATATAT-AAAT
2844858 TACCGAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 5 0.20
22 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (21 bp):
ATATATAAATATTTAATGTAT
Found at i:2845148 original size:5 final size:5
Alignment explanation
Indices: 2845134--2845215 Score: 57
Period size: 5 Copynumber: 17.2 Consensus size: 5
2845124 TATACGAGTT
* * * **
2845134 ATTT- ATTTA ATTTA A-TAA ATTTA ATTTA ATTAA ATTAA ATTTA AAATA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
* *
2845182 ATTT- -TTTA ATTTA AATTA A-TAA ATTTTA ATTTA A
1 ATTTA ATTTA ATTTA ATTTA ATTTA A-TTTA ATTTA A
2845216 ATTATTAATT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
3 3 0.05
4 10 0.16
5 45 0.74
6 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (5 bp):
ATTTA
Found at i:2845169 original size:15 final size:14
Alignment explanation
Indices: 2845138--2845215 Score: 67
Period size: 15 Copynumber: 5.8 Consensus size: 14
2845128 CGAGTTATTT
2845138 ATTTAATTTAATAA
1 ATTTAATTTAATAA
2845152 ATTTAATTTAATTAA
1 ATTTAATTTAA-TAA
*
2845167 ATTAAATTT-A-AA
1 ATTTAATTTAATAA
* *
2845179 A--TAATTT-TTTA
1 ATTTAATTTAATAA
*
2845190 ATTTAAATTAATAA
1 ATTTAATTTAATAA
2845204 ATTTTAATTTAA
1 A-TTTAATTTAA
2845216 ATTATTAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
10 5 0.10
11 2 0.04
12 3 0.06
13 5 0.10
14 15 0.30
15 20 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTAATTTAATAA
Done.