Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 9 of 14
Found at i:1046527 original size:12 final size:12
Alignment explanation
Indices: 1046510--1046549 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
1046500 TTTTATTAAT
1046510 TTAAAAATAAAA
1 TTAAAAATAAAA
1046522 TTAAAAAT-AAA
1 TTAAAAATAAAA
*
1046533 TAAAAAATATAAA
1 TTAAAAATA-AAA
1046546 TTAA
1 TTAA
1046550 TTAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAAAATAAAA
Found at i:1046908 original size:26 final size:24
Alignment explanation
Indices: 1046874--1046941 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 24
1046864 GGTATGAATA
*
1046874 TAAAAATATTATATTTTAAAAATTAT
1 TAAATATATTATATTTTAAAAA--AT
* *
1046900 TAAATATATAAAAAATTTTAAAAAAT
1 TAAATATAT--TATATTTTAAAAAAT
1046926 TAAATATATTCATATT
1 TAAATATATT-ATATT
1046942 AAATAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 4 0.12
26 19 0.56
28 11 0.32
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAATATATTATATTTTAAAAAAT
Found at i:1047624 original size:25 final size:25
Alignment explanation
Indices: 1047587--1047639 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1047577 ACTTCAACTT
* * * *
1047587 TTTACTTTTTTTTAAAATGTTTATA
1 TTTAATTTATTTTAAAATATTTAAA
*
1047612 TTTAATTTATTTTTAAATATTTAAA
1 TTTAATTTATTTTAAAATATTTAAA
1047637 TTT
1 TTT
1047640 TTGTCAAGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTAATTTATTTTAAAATATTTAAA
Found at i:1049814 original size:13 final size:13
Alignment explanation
Indices: 1049769--1049807 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
1049759 CATTTGTTTT
*
1049769 TTTATTAAA-TAA
1 TTTATTAAATTTA
1049781 TTTA-TAAATTTA
1 TTTATTAAATTTA
1049793 TTTATTAAATTTA
1 TTTATTAAATTTA
1049806 TT
1 TT
1049808 ATTTAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 4 0.17
12 10 0.42
13 10 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTATTAAATTTA
Found at i:1050149 original size:29 final size:27
Alignment explanation
Indices: 1050102--1050159 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
1050092 TTTTTTAATT
1050102 TAATTTATTATTTAATAATTA-AAATAA
1 TAATTTATTATTTAATAATTATAAA-AA
1050129 TAATTT-TTATTTAAATTTAATTATAAAAA
1 TAATTTATTATTT-AA--TAATTATAAAAA
1050158 TA
1 TA
1050160 TATAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 6 0.22
27 8 0.30
29 10 0.37
30 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TAATTTATTATTTAATAATTATAAAAA
Found at i:1050165 original size:22 final size:22
Alignment explanation
Indices: 1050140--1050182 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1050130 AATTTTTATT
1050140 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1050162 TAAATATTAATATAAAAATAT
1 TAAATATTAATATAAAAATAT
1050183 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1063821 original size:20 final size:21
Alignment explanation
Indices: 1063796--1063851 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
1063786 CGTGCCGTAA
1063796 CTTATAATTTATTTA-TTTAT
1 CTTATAATTTATTTATTTTAT
1063816 CTTAT-ATTT-TTATATTTTAT
1 CTTATAATTTATT-TATTTTAT
*
1063836 ATTATAATTATATTTA
1 CTTATAATT-TATTTA
1063852 AATATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 2 0.07
19 6 0.20
20 14 0.47
21 3 0.10
22 3 0.10
23 2 0.07
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
CTTATAATTTATTTATTTTAT
Found at i:1063831 original size:19 final size:19
Alignment explanation
Indices: 1063809--1063958 Score: 82
Period size: 19 Copynumber: 7.8 Consensus size: 19
1063799 ATAATTTATT
*
1063809 TATTTATCTTATATTTTTA
1 TATTTATATTATATTTTTA
*
1063828 TATTTTATATTATA--ATTA
1 TA-TTTATATTATATTTTTA
*
1063846 TATTTA-AATATATTTTTTA
1 TATTTATATTATA-TTTTTA
* *
1063865 TATTTAT-TTAAATTTTAA
1 TATTTATATTATATTTTTA
1063883 TATTTTAATAATTTATATTATATTA
1 TA-TTT-AT-A-TTATATT-T-TTA
** *
1063908 -ATTT-TAAAATATATTTA
1 TATTTATATTATATTTTTA
1063925 TATTTATATTATA-TTTTA
1 TATTTATATTATATTTTTA
*
1063943 T-TTTTTATATATATTT
1 TATTTATAT-TATATTT
1063959 AAAAATAATA
Statistics
Matches: 99, Mismatches: 16, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
16 5 0.05
17 13 0.13
18 26 0.26
19 28 0.28
20 13 0.13
21 1 0.01
23 9 0.09
24 2 0.02
25 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTATATTATATTTTTA
Found at i:1063848 original size:18 final size:18
Alignment explanation
Indices: 1063825--1063952 Score: 66
Period size: 17 Copynumber: 7.7 Consensus size: 18
1063815 TCTTATATTT
1063825 TTATATTTTATATTATAA
1 TTATATTTTATATTATAA
1063843 TTATA-TTTA-A--AT-A
1 TTATATTTTATATTATAA
* *
1063856 -TATTTTTTATATT-TAT
1 TTATATTTTATATTATAA
* *
1063872 TTAAATTTTAATATTTTAA
1 TTATATTTT-ATATTATAA
1063891 -TA-A-TTTATATTAT-A
1 TTATATTTTATATTATAA
* * *
1063905 TTA-ATTTTAAAATATAT
1 TTATATTTTATATTATAA
*
1063922 TTATA-TTTATATTATATT
1 TTATATTTTATATTATA-A
*
1063940 TTATTTTTTATAT
1 TTATATTTTATAT
1063953 ATATTTAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
12 3 0.04
13 5 0.06
14 4 0.05
15 10 0.12
16 12 0.14
17 23 0.27
18 18 0.21
19 9 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTTTATATTATAA
Found at i:1063886 original size:63 final size:60
Alignment explanation
Indices: 1063817--1063952 Score: 170
Period size: 63 Copynumber: 2.2 Consensus size: 60
1063807 TTTATTTATC
*
1063817 TTATATTTTTATATTTTATATTATAATT-ATATTTAAATATATTTTTTATATTTAT-TTAAATT
1 TTATATTTTTATATTTTATATTAT-ATTAAT-TTTAAA-ATA-TATTTATATTTATATTAAATT
* * *
1063879 TTAATATTTTAATAATTTATATTATATTAATTTTAAAATATATTTATATTTATATTATATT
1 TT-ATATTTTTATATTTTATATTATATTAATTTTAAAATATATTTATATTTATATTAAATT
1063940 TTAT-TTTTTATAT
1 TTATATTTTTATAT
1063953 ATATTTAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
59 7 0.11
60 14 0.22
61 11 0.17
62 11 0.17
63 22 0.34
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (60 bp):
TTATATTTTTATATTTTATATTATATTAATTTTAAAATATATTTATATTTATATTAAATT
Found at i:1063971 original size:15 final size:16
Alignment explanation
Indices: 1063951--1063991 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
1063941 TATTTTTTAT
1063951 ATATATTTAAAAATA-
1 ATATATTTAAAAATAG
*
1063966 ATATATTT-ATAATAG
1 ATATATTTAAAAATAG
1063981 ATATATTTAAA
1 ATATATTTAAA
1063992 TTTTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 5 0.23
15 16 0.73
16 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
ATATATTTAAAAATAG
Found at i:1063998 original size:85 final size:82
Alignment explanation
Indices: 1063856--1064010 Score: 188
Period size: 85 Copynumber: 1.8 Consensus size: 82
1063846 TATTTAAATA
* ** * * *
1063856 TATTTTTTATATTTATTTAAATTTTAATATTTTAATAATTTATATTATATTAATTTTAAAATATA
1 TATTTTTTATATATATTTAAAAATAAATATTTTAATAATATATATTAAATT-ATTTT-AAATAT-
1063921 TTTATATTTATATTATATTT
63 TTTATATTTATATTATATTT
1063941 TATTTTTTATATATATTTAAAAATAATATATTTATAATAGATATAT-TTAAATT-TTTTAAATAT
1 TATTTTTTATATATATTTAAAAATAA-ATATTT-TAATA-ATATATATTAAATTATTTTAAATAT
1064004 TTTATAT
63 TTTATAT
1064011 ATTTAAAAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
83 7 0.11
84 6 0.10
85 26 0.43
86 6 0.10
87 11 0.18
88 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (82 bp):
TATTTTTTATATATATTTAAAAATAAATATTTTAATAATATATATTAAATTATTTTAAATATTTT
ATATTTATATTATATTT
Found at i:1064015 original size:85 final size:85
Alignment explanation
Indices: 1063856--1064010 Score: 194
Period size: 84 Copynumber: 1.8 Consensus size: 85
1063846 TATTTAAATA
* ** **
1063856 TATTTTTTATATTTATTTAAATTTTAATATTTTAATAATTTATATTATATTAATTTTAAAATATA
1 TATTTTTTATATATATTTAAATAATAATATTTTAATAATAGATATTATATTAATTTTAAAATATA
1063921 TTTATATTTATATTATATTT
66 TTTATATTTATATTATATTT
*
1063941 TATTTTTTATATATATTTAAA-AATAATATATTT-ATAATAGATA-TAT-TTAAATTTTTTAAAT
1 TATTTTTTATATATATTTAAATAATAATAT-TTTAATAATAGATATTATATT-AA-TTTTAAAAT
1064002 AT-TTTATAT
63 ATATTTATAT
1064011 ATTTAAAAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
82 2 0.03
83 12 0.20
84 24 0.39
85 23 0.38
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (85 bp):
TATTTTTTATATATATTTAAATAATAATATTTTAATAATAGATATTATATTAATTTTAAAATATA
TTTATATTTATATTATATTT
Found at i:1064311 original size:20 final size:21
Alignment explanation
Indices: 1064270--1064327 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1064260 ATTGATATAC
* *
1064270 TTTTAAATATATAAATATAAT
1 TTTTAAAAATATAAATAAAAT
1064291 TTTTAAAAATATAAA-AAAAT
1 TTTTAAAAATATAAATAAAAT
*
1064311 TTAATAAAAA-ATAAATA
1 TT-TTAAAAATATAAATA
1064328 TATTAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTTAAAAATATAAATAAAAT
Found at i:1064353 original size:17 final size:17
Alignment explanation
Indices: 1064327--1064383 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
1064317 AAAAATAAAT
*
1064327 ATATTAATATTAAATAC
1 ATATTTATATTAAATAC
*
1064344 ATATTTATATTTAACATTC
1 ATATTTATA-TTAA-ATAC
*
1064363 ATATTTAAATTCAAATA-
1 ATATTTATATT-AAATAC
1064380 ATAT
1 ATAT
1064384 AAAATAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 12 0.36
18 8 0.24
19 13 0.39
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTTATATTAAATAC
Found at i:1067891 original size:24 final size:24
Alignment explanation
Indices: 1067859--1067916 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
1067849 GCAAGCTGCC
1067859 TTCATGCAACTATAGCTCAGTTGG
1 TTCATGCAACTATAGCTCAGTTGG
1067883 TTCATGCAACTATAGCTCAGTTGG
1 TTCATGCAACTATAGCTCAGTTGG
1067907 TTCATGCAAC
1 TTCATGCAAC
1067917 CATCTTAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (24 bp):
TTCATGCAACTATAGCTCAGTTGG
Found at i:1070067 original size:16 final size:16
Alignment explanation
Indices: 1070046--1070081 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1070036 ACCTCGTACT
1070046 TATTATATTGTATAAC
1 TATTATATTGTATAAC
* *
1070062 TATTATATTTTATAAT
1 TATTATATTGTATAAC
1070078 TATT
1 TATT
1070082 TTAATTATCA
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:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TATTATATTGTATAAC
Found at i:1070245 original size:19 final size:19
Alignment explanation
Indices: 1070221--1070267 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1070211 TTCACTATAT
*
1070221 TATTAAAATAT-TATTTTTA
1 TATTAAAATATATA-TTTCA
*
1070240 TATTAATATATATATTTCA
1 TATTAAAATATATATTTCA
1070259 TATTAAAAT
1 TATTAAAAT
1070268 CTAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTAAAATATATATTTCA
Found at i:1072800 original size:16 final size:16
Alignment explanation
Indices: 1072776--1072836 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
1072766 AATTGAATAT
* *
1072776 AAATTAATTTCATAAA
1 AAATAAATTTAATAAA
*
1072792 AAATAAATTTAAT-TA
1 AAATAAATTTAATAAA
1072807 AAA-AAA-TT-ATAAA
1 AAATAAATTTAATAAA
*
1072820 AAATTAATTTAATAAA
1 AAATAAATTTAATAAA
1072836 A
1 A
1072837 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 5 0.14
15 6 0.17
16 17 0.47
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAAATTTAATAAA
Found at i:1078488 original size:46 final size:47
Alignment explanation
Indices: 1078401--1078495 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 47
1078391 GATTTTGTAG
* *
1078401 ATTTAATTTGTTTCTATTGAATTTTAAATATATATTTAATAAT-TAA
1 ATTTAATTTGTTTCTATTGAATTTTAAATATAAATTAAATAATATAA
1078447 ATTTAATTT-TTT-TATT-AATTATTAAATAATAAATATAAATAATATAA
1 ATTTAATTTGTTTCTATTGAATT-TTAAAT-ATAAAT-TAAATAATATAA
1078494 AT
1 AT
1078496 CAATCAAGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
43 4 0.09
44 10 0.23
45 8 0.19
46 16 0.37
47 5 0.12
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (47 bp):
ATTTAATTTGTTTCTATTGAATTTTAAATATAAATTAAATAATATAA
Found at i:1078697 original size:15 final size:15
Alignment explanation
Indices: 1078671--1078716 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
1078661 TAAATTACTT
1078671 ATTTAA-TTTAATAA
1 ATTTAATTTTAATAA
1078685 ATTTAATTTTAATTAA
1 ATTTAATTTTAA-TAA
* *
1078701 ATTAAATTTAAATAA
1 ATTTAATTTTAATAA
1078716 A
1 A
1078717 AATTTGTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 6 0.21
15 9 0.32
16 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTAATTTTAATAA
Found at i:1078802 original size:21 final size:22
Alignment explanation
Indices: 1078764--1078806 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1078754 ACTATTGATT
*
1078764 TTAAAAATTTATATAAATTTAA
1 TTAAAAATATATATAAATTTAA
1078786 TTAAAAATATATA-AAATTTAA
1 TTAAAAATATATATAAATTTAA
1078807 AAACTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAAATATATATAAATTTAA
Found at i:1079003 original size:6 final size:6
Alignment explanation
Indices: 1078986--1079155 Score: 54
Period size: 6 Copynumber: 27.0 Consensus size: 6
1078976 ATGATTTATG
*
1078986 TATTTA TA-TTA TATTTA TA--TA T-TTTA TCATATTA TAATTA TATTTAAAA
1 TATTTA TATTTA TATTTA TATTTA TATTTA T-AT-TTA TATTTA TATTT---A
**
1079035 TATTTA TATTTA TATAAA T-TTTAA TATATTAA TAATTTA TATTATA TAAATTTAAA
1 TATTTA TATTTA TATTTA TATTT-A TAT-TT-A T-ATTTA TATT-TA T--ATTT--A
* * *
1079091 TAATT- TATTTA TATTATTA TATTT- TAATTA T-TTTA TATAT- TA-TTA
1 TATTTA TATTTA TA-T-TTA TATTTA TATTTA TATTTA TATTTA TATTTA
1079136 TATTTA TATAATTA TATTTA
1 TATTTA TAT--TTA TATTTA
1079156 AAATTATAAG
Statistics
Matches: 125, Mismatches: 12, Indels: 54
0.65 0.06 0.28
Matches are distributed among these distances:
4 4 0.03
5 25 0.20
6 47 0.38
7 10 0.08
8 26 0.21
9 11 0.09
10 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (6 bp):
TATTTA
Found at i:1079003 original size:19 final size:18
Alignment explanation
Indices: 1078979--1079018 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1078969 AGATTTAATG
* *
1078979 ATTTATGTATTTATATTAT
1 ATTTATATATTT-TATCAT
1078998 ATTTATATATTTTATCAT
1 ATTTATATATTTTATCAT
1079016 ATT
1 ATT
1079019 ATAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTATATATTTTATCAT
Found at i:1079006 original size:8 final size:8
Alignment explanation
Indices: 1078995--1079152 Score: 65
Period size: 9 Copynumber: 18.4 Consensus size: 8
1078985 GTATTTATAT
1078995 TATATTTA
1 TATATTTA
1079003 TATATTTTA
1 TATA-TTTA
1079012 TCATATTATAA
1 T-ATATT-T-A
1079023 TTATATTTAA
1 -TATATTT-A
*
1079033 AATATTTA
1 TATATTTA
1079041 TAT-TTATA
1 TATATT-TA
*
1079049 TAAATTTTAA
1 TATA-TTT-A
*
1079059 TATATTAA
1 TATATTTA
1079067 TA-ATTTA
1 TATATTTA
*
1079074 TAT-TATA
1 TATATTTA
*
1079081 TAAATTTA
1 TATATTTA
*
1079089 AATAATTTA
1 TAT-ATTTA
*
1079098 TTTATATTA
1 TATAT-TTA
1079107 TTATATTT-
1 -TATATTTA
1079115 TAATTATTT-
1 T-A-TATTTA
1079124 TATATATTA
1 TATAT-TTA
1079133 TTATATTTA
1 -TATATTTA
*
1079142 TATAATTA
1 TATATTTA
1079150 TAT
1 TAT
1079153 TTAAAATTAT
Statistics
Matches: 116, Mismatches: 15, Indels: 38
0.69 0.09 0.22
Matches are distributed among these distances:
7 17 0.15
8 34 0.29
9 36 0.31
10 22 0.19
11 6 0.05
12 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.58
Consensus pattern (8 bp):
TATATTTA
Found at i:1079045 original size:44 final size:43
Alignment explanation
Indices: 1078994--1079163 Score: 125
Period size: 44 Copynumber: 3.8 Consensus size: 43
1078984 TGTATTTATA
1078994 TTATATTTATATATTTTATCATATTATAATTATATTTAAAATAT
1 TTATATTTATATATTTTAT-ATATTATAATTATATTTAAAATAT
1079038 TTATATTTATATAAATTTTAATATATTAATAATTTATATTATATAAAT-T
1 TTATATTTATAT--ATTTT-ATATATT-ATAA-TTATATT-TA-AAATAT
* * * * *
1079087 TAAATAATTTATTTATATTATTATATTTTAATTAT-TTT-ATATATT
1 T-TAT-ATTTATATATTTTA-TATATTATAATTATATTTAAAATA-T
* *
1079132 ATTATATTTATATA-ATTATAT-TTAAAATTATA
1 -TTATATTTATATATTTTATATATTATAATTATA
1079164 AGATGCCTGC
Statistics
Matches: 103, Mismatches: 9, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
41 8 0.08
42 3 0.03
43 7 0.07
44 20 0.19
45 4 0.04
46 13 0.13
47 10 0.10
48 11 0.11
49 14 0.14
50 6 0.06
51 7 0.07
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (43 bp):
TTATATTTATATATTTTATATATTATAATTATATTTAAAATAT
Found at i:1079084 original size:32 final size:33
Alignment explanation
Indices: 1079036--1079146 Score: 110
Period size: 32 Copynumber: 3.5 Consensus size: 33
1079026 TATTTAAAAT
1079036 ATTTATATTTATATAAATTTTAATATATTAATA
1 ATTTATATTTATATAAATTTTAATATATTAATA
*
1079069 ATTTATA-TTATATAAATTTAAATA-ATT--T-
1 ATTTATATTTATATAAATTTTAATATATTAATA
* *
1079097 ATTTATA-TTAT-TATATTTTAATTATTTTATATA
1 ATTTATATTTATATAAATTTTAA-TATATTA-ATA
*
1079130 TTATTATATTTATATAA
1 AT-TTATATTTATATAA
1079147 TTATATTTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
27 8 0.13
28 13 0.21
29 3 0.05
31 3 0.05
32 17 0.27
33 8 0.13
34 5 0.08
35 4 0.06
36 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
ATTTATATTTATATAAATTTTAATATATTAATA
Found at i:1079128 original size:16 final size:15
Alignment explanation
Indices: 1079102--1079154 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
1079092 AATTTATTTA
*
1079102 TATTATTATATTTTAAT
1 TATT-TTATATATT-AT
1079119 TATTTTATATATTAT
1 TATTTTATATATTAT
1079134 TATATTTATATAATTA-
1 TAT-TTTATAT-ATTAT
1079150 TATTT
1 TATTT
1079155 AAAATTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 7 0.21
16 18 0.55
17 8 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTTATATATTAT
Found at i:1079136 original size:26 final size:27
Alignment explanation
Indices: 1079042--1079152 Score: 101
Period size: 26 Copynumber: 4.3 Consensus size: 27
1079032 AAATATTTAT
*
1079042 ATTTATATAAATT-TTAATATATT-AATA
1 ATTTATATATATTATT-ATAT-TTAAATA
*
1079069 ATTTATAT-TA-TA-TAAATTTAAATA
1 ATTTATATATATTATTATATTTAAATA
* * *
1079093 ATTTATTTATATTATTATATTTTAATT
1 ATTTATATATATTATTATATTTAAATA
*
1079120 ATTT-TATATATTATTATATTTATATA
1 ATTTATATATATTATTATATTTAAATA
1079146 A-TTATAT
1 ATTTATAT
1079153 TTAAAATTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
23 2 0.03
24 14 0.21
25 6 0.09
26 25 0.37
27 21 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTATATATATTATTATATTTAAATA
Found at i:1079162 original size:12 final size:14
Alignment explanation
Indices: 1078993--1079163 Score: 105
Period size: 15 Copynumber: 12.4 Consensus size: 14
1078983 ATGTATTTAT
1078993 ATTATATTTATAT-
1 ATTATATTTATATA
* *
1079006 ATTTTATCATATTATA
1 ATTATAT-TTA-TATA
*
1079022 ATTATATTTAAAATA
1 ATTATATTT-ATATA
*
1079037 TTTATATTTATATA
1 ATTATATTTATATA
1079051 A--AT-TTTA-ATA
1 ATTATATTTATATA
*
1079061 TATTAATAATTTATATT
1 -ATT-AT-ATTTATATA
* *
1079078 ATATAAATTTAAATA
1 AT-TATATTTATATA
*
1079093 ATT-TATTTATATT
1 ATTATATTTATATA
1079106 ATTATA-TT-T-TA
1 ATTATATTTATATA
1079117 ATTAT-TTTATATA
1 ATTATATTTATATA
1079130 TTATTATATTTATATA
1 --ATTATATTTATATA
1079146 ATTATATTTA-A-A
1 ATTATATTTATATA
1079158 ATTATA
1 ATTATA
1079164 AGATGCCTGC
Statistics
Matches: 123, Mismatches: 16, Indels: 39
0.69 0.09 0.22
Matches are distributed among these distances:
10 3 0.02
11 13 0.11
12 11 0.09
13 21 0.17
14 21 0.17
15 29 0.24
16 22 0.18
17 3 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTATATTTATATA
Found at i:1079734 original size:20 final size:18
Alignment explanation
Indices: 1079688--1079735 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
1079678 ATTTTATTTA
1079688 AATTTAT-TTATAAAAAT
1 AATTTATATTATAAAAAT
*
1079705 ATATTAATATTAATATAAAAT
1 A-ATTTATATT-ATA-AAAAT
1079726 AATTTATATT
1 AATTTATATT
1079736 TTTATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.04
18 5 0.20
19 2 0.08
20 11 0.44
21 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTTATATTATAAAAAT
Found at i:1079781 original size:15 final size:17
Alignment explanation
Indices: 1079751--1079784 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1079741 TATTTTAATA
1079751 AATTTAATACTAAATTT
1 AATTTAATACTAAATTT
1079768 AATTT-ATA-TAAATTT
1 AATTTAATACTAAATTT
1079783 AA
1 AA
1079785 ATCTCAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 3 0.18
17 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTAATACTAAATTT
Found at i:1080124 original size:3 final size:3
Alignment explanation
Indices: 1080116--1080150 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1080106 AGTTCAAGAG
*
1080116 TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1080151 TTCATGTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1080374 original size:20 final size:19
Alignment explanation
Indices: 1080351--1080388 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1080341 AAGACAGGTC
1080351 TAAATTATATTATAAAATAA
1 TAAATTATATTA-AAAATAA
*
1080371 TAAATTATTTTAAAAATA
1 TAAATTATATTAAAAATA
1080389 TTTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATTATATTAAAAATAA
Found at i:1080874 original size:18 final size:19
Alignment explanation
Indices: 1080835--1080880 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1080825 TAAACTATTG
* *
1080835 TTAT-TTTTACATTTTTTT
1 TTATATTTTACATTTTCTA
1080853 TTATATTTTA-ATTTTCTA
1 TTATATTTTACATTTTCTA
1080871 TTATACTTTT
1 TTATA-TTTT
1080881 TTACACCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATATTTTACATTTTCTA
Found at i:1081060 original size:16 final size:17
Alignment explanation
Indices: 1081039--1081090 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1081029 AAATATTAAT
1081039 AATTTATATTATATA-A
1 AATTTATATTATATATA
*
1081055 AATTTA-ATTTATTTATA
1 AATTTATA-TTATATATA
* *
1081072 TATTTATATTATATTTA
1 AATTTATATTATATATA
1081089 AA
1 AA
1081091 ATTAAATCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 1 0.04
16 12 0.43
17 14 0.50
18 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTATATTATATATA
Found at i:1081080 original size:33 final size:34
Alignment explanation
Indices: 1081014--1081096 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 34
1081004 CAACTAAACA
1081014 TATATATAAATATTAAAATATTAATAATTTATAT
1 TATATATAAATATTAAAATATTAATAATTTATAT
** *
1081048 TATATA-AAAT-TTAATTTATTTATATATTTATAT
1 TATATATAAATATTAAAATATTAATA-ATTTATAT
*
1081081 TATATTTAAA-ATTAAA
1 TATATATAAATATTAAA
1081097 TCATCTAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
32 11 0.27
33 17 0.41
34 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATATATAAATATTAAAATATTAATAATTTATAT
Found at i:1081611 original size:18 final size:18
Alignment explanation
Indices: 1081590--1081703 Score: 56
Period size: 18 Copynumber: 6.1 Consensus size: 18
1081580 ATAATATTTT
1081590 ATATTTAATAAAATTATA
1 ATATTTAATAAAATTATA
*
1081608 ATATATAATAAAATATCATA
1 ATATTTAATAAAAT-T-ATA
1081628 TCATTATTTAA-AAAATTCAT-
1 --A-TATTTAATAAAATT-ATA
* *
1081648 ATTTTATAATTAAATTA-A
1 ATATT-TAATAAAATTATA
* **
1081666 ATATTAAATATTA-TATCA
1 ATATTTAATAAAATTAT-A
**
1081684 ATATTTAATTTAATTATA
1 ATATTTAATAAAATTATA
1081702 AT
1 AT
1081704 TAAAAAATTA
Statistics
Matches: 73, Mismatches: 12, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
16 2 0.03
17 7 0.10
18 36 0.49
19 9 0.12
20 3 0.04
21 4 0.05
22 6 0.08
23 6 0.08
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATTTAATAAAATTATA
Found at i:1082092 original size:14 final size:14
Alignment explanation
Indices: 1082073--1082104 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1082063 TATTAAATAG
*
1082073 ATTTAAATTTTAAA
1 ATTTAAAATTTAAA
1082087 ATTTAAAATTTAAA
1 ATTTAAAATTTAAA
1082101 ATTT
1 ATTT
1082105 TTAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTAAAATTTAAA
Found at i:1082487 original size:22 final size:21
Alignment explanation
Indices: 1082445--1082490 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1082435 TATTTTATTT
* *
1082445 TTAAATAATTATATATATTAA
1 TTAAATAAATATAAATATTAA
*
1082466 TTAAATTAAATATAAATTTTAA
1 TTAAA-TAAATATAAATATTAA
1082488 TTA
1 TTA
1082491 TTTAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATAAATATAAATATTAA
Found at i:1083164 original size:2 final size:2
Alignment explanation
Indices: 1083157--1083193 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1083147 TGCTGCTCTT
1083157 TA TA 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 TA TA T
1083194 GTTTAATTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1089018 original size:19 final size:21
Alignment explanation
Indices: 1088969--1089021 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1088959 TATTTTTATT
1088969 TAAATA-TAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
1088990 TAAATATTAATATAAAA-ATA
1 TAAATATTAATATAAAATATA
*
1089010 -AAATTTTAATAT
1 TAAATATTAATAT
1089022 TTAAATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 11 0.37
20 3 0.10
21 13 0.43
22 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:1089036 original size:27 final size:28
Alignment explanation
Indices: 1088965--1089057 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 28
1088955 ATAATATTTT
*
1088965 TATTTAAAT-ATAATTATAAAATATATAA
1 TATTTAAATAAT-ATAATAAAATATATAA
*
1088993 -ATATTAATATAA-A-AATAAAAT-TTTAA
1 TAT-TTAA-ATAATATAATAAAATATATAA
*
1089019 TATTTAAATAATATAATAAAAAATAATAAA
1 TATTTAAATAATATAATAAAATAT-AT-AA
*
1089049 TTTTTAAAT
1 TATTTAAAT
1089058 TAATTTAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
25 4 0.08
26 9 0.18
27 18 0.35
28 6 0.12
29 3 0.06
30 11 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
TATTTAAATAATATAATAAAATATATAA
Found at i:1089073 original size:19 final size:18
Alignment explanation
Indices: 1089045--1089085 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1089035 TAAAAAATAA
**
1089045 TAAATTTTTAAATTAATT
1 TAAATTTTTAAAAAAATT
1089063 TAAATTTTTTAAAAAAATT
1 TAAA-TTTTTAAAAAAATT
1089082 TAAA
1 TAAA
1089086 ATAAAATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATTTTTAAAAAAATT
Found at i:1089383 original size:22 final size:22
Alignment explanation
Indices: 1089358--1089425 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
1089348 AAATATTTTT
1089358 TATTTAAATATAATTATAAAAA
1 TATTTAAATATAATTATAAAAA
1089380 TATTTAAATATTAA-TATAAAAAA
1 TATTTAAATA-TAATTAT-AAAAA
1089403 TTATTT--AT-TAATTATAAATAA
1 -TATTTAAATATAATTATAAA-AA
1089424 TA
1 TA
1089426 AATATAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
20 8 0.20
21 5 0.12
22 15 0.37
23 8 0.20
24 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTTAAATATAATTATAAAAA
Found at i:1089411 original size:28 final size:27
Alignment explanation
Indices: 1089339--1089428 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 27
1089329 TTAATATTTA
* *
1089339 ATAATTATAAAATATTTTTTATTTAAAT
1 ATAA-TATAAAAAATTATTTATTTAAAT
*
1089367 ATAAT-TATAAAA--A--TATTTAAAT
1 ATAATATAAAAAATTATTTATTTAAAT
*
1089389 ATTAATATAAAAAATTATTTA-TTAATT
1 A-TAATATAAAAAATTATTTATTTAAAT
*
1089416 ATAA-ATAATAAAT
1 ATAATATAAAAAAT
1089429 ATAAATAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
22 10 0.20
23 4 0.08
24 6 0.12
25 8 0.16
26 9 0.18
27 7 0.14
28 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAATATAAAAAATTATTTATTTAAAT
Found at i:1089653 original size:33 final size:30
Alignment explanation
Indices: 1089616--1089687 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
1089606 TAATATTAAA
1089616 TATAATATAAACATAATATAAAAATAATATGAT
1 TATAATATAAACAT-AT-TAAAAATAATAT-AT
** *
1089649 TATAATATAAGTATATTAAAAATTATATAT
1 TATAATATAAACATATTAAAAATAATATAT
1089679 TATATATAT
1 TATA-ATAT
1089688 TTAAAATCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.17
31 15 0.43
32 2 0.06
33 12 0.34
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (30 bp):
TATAATATAAACATATTAAAAATAATATAT
Found at i:1089663 original size:11 final size:11
Alignment explanation
Indices: 1089605--1089663 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
1089595 ATGAGTTTAA
1089605 ATAATATTAAAT
1 ATAATA-TAAAT
*
1089617 ATAATATAAAC
1 ATAATATAAAT
*
1089628 ATAATATAAAA
1 ATAATATAAAT
* *
1089639 ATAATATGATT
1 ATAATATAAAT
*
1089650 ATAATATAAGT
1 ATAATATAAAT
1089661 ATA
1 ATA
1089664 TTAAAAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
11 34 0.85
12 6 0.15
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1089682 original size:25 final size:23
Alignment explanation
Indices: 1089649--1089694 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1089639 ATAATATGAT
1089649 TATAATATAAGTATATTAAAAATTA
1 TATAATAT-A-TATATTAAAAATTA
* *
1089674 TATATTATATATATTTAAAAT
1 TATAATATATATATTAAAAAT
1089695 CTTGACTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 1 0.05
25 7 0.37
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATAATATATATATTAAAAATTA
Found at i:1089980 original size:14 final size:14
Alignment explanation
Indices: 1089950--1090046 Score: 58
Period size: 13 Copynumber: 6.8 Consensus size: 14
1089940 TTTAAAAAAT
*
1089950 TTTAATCATTAATAA
1 TTTAAT-ATTTATAA
1089965 TTTAATATTTATAA
1 TTTAATATTTATAA
* *
1089979 -TTAAAATTTAAAA
1 TTTAATATTTATAA
* **
1089992 TATAGATAATTTAATTTT
1 TTTA-AT-ATTT-A-TAA
1090010 TTTAATATTTAT-A
1 TTTAATATTTATAA
1090023 TTATAATA-TTATAA
1 TT-TAATATTTATAA
1090037 TTT-ATATTTA
1 TTTAATATTTA
1090047 CTTTTTATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
12 3 0.05
13 21 0.33
14 18 0.28
15 8 0.12
16 8 0.12
17 3 0.05
18 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (14 bp):
TTTAATATTTATAA
Found at i:1090604 original size:69 final size:67
Alignment explanation
Indices: 1090486--1090692 Score: 247
Period size: 69 Copynumber: 3.0 Consensus size: 67
1090476 AACCATTGTT
* *
1090486 AAGAATTTGTTAGAAGTTAACCCATTGGATCAGGACGAAAACAGGGAGGGGAGAACCCCCCATCA
1 AAGAATTTGTTAAAAGTTAACCCAATGGATCAGGACGAAAA-AGGGAGGGGAGAACCCCCCATCA
1090551 TTG
65 TTG
* * *
1090554 AACGAATTAGTTAAAAGTTAACCCAATGGATCAGGACGAAAATGGAGAGGGGAGAGGCCCCACCA
1 AA-GAATTTGTTAAAAGTTAACCCAATGGATCAGGACGAAAAAGG-GAGGGGAGA-ACCCC-CCA
*
1090619 TC--GG
62 TCATTG
* * ** *
1090623 AAGAATTTGTGAAAAGTTAACCTAATGGATCAGGACGAACACGGGGAGGTGAGAACCCCCCATCA
1 AAGAATTTGTTAAAAGTTAACCCAATGGATCAGGACGAA-AAAGGGAGGGGAGAACCCCCCATCA
1090688 TTG
65 TTG
1090691 AA
1 AA
1090693 AAGATATATG
Statistics
Matches: 118, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
66 5 0.04
67 4 0.03
68 49 0.42
69 51 0.43
70 4 0.03
71 5 0.04
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (67 bp):
AAGAATTTGTTAAAAGTTAACCCAATGGATCAGGACGAAAAAGGGAGGGGAGAACCCCCCATCAT
TG
Found at i:1091069 original size:17 final size:19
Alignment explanation
Indices: 1091049--1091085 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1091039 AATTTTTAAT
1091049 TAAAT-TTA-ATTATAAAA
1 TAAATATTATATTATAAAA
1091066 TAAATATTATTATTATAAAA
1 TAAATATTA-TATTATAAAA
1091086 AATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
20 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATATTATATTATAAAA
Found at i:1091269 original size:16 final size:16
Alignment explanation
Indices: 1091248--1091280 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1091238 ATATTAAAAT
*
1091248 TATAAAAATTATAATA
1 TATAAAAATAATAATA
1091264 TATAAAAATAATAATA
1 TATAAAAATAATAATA
1091280 T
1 T
1091281 GGGTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TATAAAAATAATAATA
Found at i:1091448 original size:22 final size:21
Alignment explanation
Indices: 1091409--1091456 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
1091399 AGGTTATAAT
*
1091409 TTTAT-TAAAAGTATTTTATA
1 TTTATATAAAAGTATTTTAAA
*
1091429 TTTATATAAAATTATGTTTAAA
1 TTTATATAAAAGTAT-TTTAAA
1091451 TTTATA
1 TTTATA
1091457 ATTTATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.21
21 8 0.33
22 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTATATAAAAGTATTTTAAA
Found at i:1094934 original size:13 final size:13
Alignment explanation
Indices: 1094916--1094940 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1094906 TATGTTCAAT
1094916 TTTTTTTATAAGC
1 TTTTTTTATAAGC
1094929 TTTTTTTATAAG
1 TTTTTTTATAAG
1094941 TCCTTGGAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTTTTTATAAGC
Found at i:1097681 original size:31 final size:31
Alignment explanation
Indices: 1097646--1097706 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1097636 ATTCATCTTG
* *
1097646 TGAATCGATTAAATTTGGTTAATTCGAATCA
1 TGAATCCATTAAATATGGTTAATTCGAATCA
*
1097677 TGAATCCATTAAATATGTTTAATTCGAATC
1 TGAATCCATTAAATATGGTTAATTCGAATC
1097707 TCGGTTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (31 bp):
TGAATCCATTAAATATGGTTAATTCGAATCA
Found at i:1100044 original size:16 final size:16
Alignment explanation
Indices: 1100006--1100050 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1099996 AATAAATTTA
1100006 TAAAT-AAATTAAATT
1 TAAATAAAATTAAATT
* *
1100021 TGATTAAAATTAAATT
1 TAAATAAAATTAAATT
*
1100037 TAAATAAAAATAAA
1 TAAATAAAATTAAA
1100051 AATAATTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 3 0.12
16 21 0.88
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAATAAAATTAAATT
Found at i:1100069 original size:21 final size:21
Alignment explanation
Indices: 1100007--1100070 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1099997 ATAAATTTAT
* *
1100007 AAATAAATTAAATTTGATTAA
1 AAATAATTTAAATTTGAATAA
* ***
1100028 AATTAAATTTAAATAAAAATAA
1 AAAT-AATTTAAATTTGAATAA
1100050 AAATAATTTAAATTTGAATAA
1 AAATAATTTAAATTTGAATAA
1100071 CCTATTATAT
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
AAATAATTTAAATTTGAATAA
Found at i:1102006 original size:2 final size:2
Alignment explanation
Indices: 1101999--1102032 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1101989 CTTCTCCATG
*
1101999 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1102033 AGGGAAGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1105274 original size:2 final size:2
Alignment explanation
Indices: 1105262--1105298 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1105252 TCGTATTTAA
1105262 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1105299 GAAATTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1106380 original size:14 final size:14
Alignment explanation
Indices: 1106361--1106391 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1106351 TAATATAAAA
1106361 ATAATTAAAATATT
1 ATAATTAAAATATT
1106375 ATAATTAAAATATT
1 ATAATTAAAATATT
1106389 ATA
1 ATA
1106392 TGATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATTAAAATATT
Found at i:1106658 original size:35 final size:34
Alignment explanation
Indices: 1106618--1106728 Score: 106
Period size: 35 Copynumber: 3.3 Consensus size: 34
1106608 TTAATTATCA
1106618 TTTATTAAAAATTAATTATTAAATTTAATATATAT
1 TTTATT-AAAATTAATTATTAAATTTAATATATAT
* *
1106653 TTTATT--AATTAATTATTATATTTATTAT-TAT
1 TTTATTAAAATTAATTATTAAATTTAATATATAT
* *
1106684 TAATATTAAAATTATATT-TTAAAATTTAATTTAT-T
1 T-TTATTAAAATTA-ATTATT-AAATTTAATATATAT
1106719 TTTAATTAAA
1 TTT-ATTAAA
1106729 TAATATAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
31 4 0.06
32 24 0.39
34 8 0.13
35 25 0.40
36 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TTTATTAAAATTAATTATTAAATTTAATATATAT
Found at i:1106669 original size:16 final size:15
Alignment explanation
Indices: 1106628--1106692 Score: 55
Period size: 16 Copynumber: 4.3 Consensus size: 15
1106618 TTTATTAAAA
*
1106628 ATTAATTATTA-AAT
1 ATTAATTATTATTAT
*
1106642 -TTAA-TATATATTTT
1 ATTAATTAT-TATTAT
1106656 ATTAATTAATTATTAT
1 ATTAATT-ATTATTAT
*
1106672 ATTTATTATTATTAAT
1 ATTAATTATTATT-AT
1106688 ATTAA
1 ATTAA
1106693 AATTATATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
12 3 0.08
13 6 0.15
14 1 0.03
15 10 0.25
16 18 0.45
17 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAATTATTATTAT
Found at i:1106738 original size:29 final size:28
Alignment explanation
Indices: 1106706--1106769 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1106696 TATATTTTAA
* *
1106706 AATTTAATTTATTT-TTAATTAAATAATAT
1 AATTTAATTAATTTAATAA-TAAATAA-AT
*
1106735 AATTAAATTAATTTAATAATAAATAAAT
1 AATTTAATTAATTTAATAATAAATAAAT
1106763 AATTTAA
1 AATTTAA
1106770 AAAACTCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 8 0.27
29 19 0.63
30 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTTAATTAATTTAATAATAAATAAAT
Found at i:1106751 original size:19 final size:19
Alignment explanation
Indices: 1106721--1106769 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 19
1106711 AATTTATTTT
*
1106721 TAATTAAATAATATAATTAAA
1 TAATTTAATAATA-AA-TAAA
1106742 TTAATTTAATAATAAATAAA
1 -TAATTTAATAATAAATAAA
1106762 TAATTTAA
1 TAATTTAA
1106770 AAAACTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.31
20 4 0.15
21 2 0.08
22 12 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTTAATAATAAATAAA
Found at i:1106755 original size:67 final size:67
Alignment explanation
Indices: 1106620--1106755 Score: 147
Period size: 67 Copynumber: 2.0 Consensus size: 67
1106610 AATTATCATT
* * * *
1106620 TATTAAAAATTAATTATTAAATTTAATATATATTTTATTAATTAATTATTATATTTATTATTATT
1 TATTAAAAATTAATTATTAAATTTAATATATATTTTATTAAATAATTATTATAATTAATATTAAT
1106685 AA
66 AA
*
1106687 TATT-AAAATTATATT-TTAAAATTTAATTTAT-TTTTAATTAAATAATATAATTA-AATTAAT-
1 TATTAAAAATTA-ATTATT-AAATTTAATATATATTTT-ATTAAATAAT-T-ATTATAATTAATA
1106747 TTAATAA
61 TTAATAA
1106754 TA
1 TA
1106756 AATAAATAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
66 13 0.22
67 36 0.61
68 6 0.10
69 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (67 bp):
TATTAAAAATTAATTATTAAATTTAATATATATTTTATTAAATAATTATTATAATTAATATTAAT
AA
Found at i:1106960 original size:18 final size:17
Alignment explanation
Indices: 1106907--1106960 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
1106897 TATTTAAATT
1106907 TAATTA-TAAAAT-ATA
1 TAATTATTAAAATAATA
*
1106922 TAATTATTAAAATAAAAA
1 TAATTATTAAAAT-AATA
*
1106940 TAATTTTTTAAAATAATA
1 TAA-TTATTAAAATAATA
1106958 TAA
1 TAA
1106961 CTTAAGAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
18 11 0.34
19 9 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTATTAAAATAATA
Found at i:1107596 original size:5 final size:5
Alignment explanation
Indices: 1107586--1107617 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1107576 ATTTTAAAAT
1107586 TTATA TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TT
1107618 TTAATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1107867 original size:16 final size:16
Alignment explanation
Indices: 1107846--1107920 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 16
1107836 ATATATATAT
*
1107846 TATATTTAAAGTATTA
1 TATATTTAAAATATTA
* **
1107862 TATATTTTATCTATTA
1 TATATTTAAAATATTA
* *
1107878 -ATAATTTATATTATATA
1 TAT-ATTTAAAATAT-TA
1107895 TATATTTTAAAATATTTA
1 TATA-TTTAAAATA-TTA
1107913 TATATTTA
1 TATATTTA
1107921 TTTTTATTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
15 2 0.04
16 20 0.44
17 7 0.16
18 15 0.33
19 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (16 bp):
TATATTTAAAATATTA
Found at i:1108753 original size:27 final size:27
Alignment explanation
Indices: 1108715--1108766 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1108705 AAAAAAGAGT
1108715 AAAAATAGATTAAAATTAATTTAATAA
1 AAAAATAGATTAAAATTAATTTAATAA
* *
1108742 AAAAATTA-ATTAAATTTGATTTAAT
1 AAAAA-TAGATTAAAATTAATTTAAT
1108767 TGATTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
AAAAATAGATTAAAATTAATTTAATAA
Found at i:1108906 original size:14 final size:14
Alignment explanation
Indices: 1108887--1108914 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1108877 AATTAATATT
1108887 TAAAATATATTTAA
1 TAAAATATATTTAA
1108901 TAAAATATATTTAA
1 TAAAATATATTTAA
1108915 AATTTTAAAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATATATTTAA
Found at i:1109842 original size:25 final size:26
Alignment explanation
Indices: 1109736--1109842 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
1109726 AAATATTTTT
*
1109736 ATATTAATATTTATATAAAAATAATTC
1 ATATTAATATTTATATTAAAA-AATTC
1109763 ATATTAATATTTATATTAAAAAATT-
1 ATATTAATATTTATATTAAAAAATTC
* * *
1109788 TTA-T-ATACGTTAATATT-AATAATTC
1 ATATTAATA--TTTATATTAAAAAATTC
1109813 ATATTAATATTTATATTAAAAAATTC
1 ATATTAATATTTATATTAAAAAATTC
1109839 -TATT
1 ATATT
1109843 TCTATATACA
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
23 3 0.04
24 7 0.10
25 22 0.33
26 12 0.18
27 23 0.34
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.48
Consensus pattern (26 bp):
ATATTAATATTTATATTAAAAAATTC
Found at i:1110088 original size:11 final size:12
Alignment explanation
Indices: 1110056--1110118 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 12
1110046 ACGATTAAAA
1110056 TATAAATAT-AT
1 TATAAATATAAT
*
1110067 TATAAAAATAAT
1 TATAAATATAAT
1110079 TA-AAATATAAT
1 TATAAATATAAT
*
1110090 T-T-AATATAAA
1 TATAAATATAAT
* *
1110100 AAT-AATATAAA
1 TATAAATATAAT
1110111 TATAAATA
1 TATAAATA
1110119 GATAAATATG
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
10 7 0.16
11 28 0.65
12 8 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TATAAATATAAT
Found at i:1110104 original size:16 final size:18
Alignment explanation
Indices: 1110075--1110116 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1110065 ATTATAAAAA
1110075 TAAT-TAAAATATAAT-T
1 TAATATAAAATATAATAT
1110091 TAATATAAAA-ATAATAT
1 TAATATAAAATATAATAT
*
1110108 AAATATAAA
1 TAATATAAA
1110117 TAGATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATATAAAATATAATAT
Found at i:1110105 original size:27 final size:27
Alignment explanation
Indices: 1110049--1110115 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
1110039 ATATGACACG
*
1110049 ATTAAAATATAAATATATTATAAAAATA
1 ATTAAAATAT-AATATAATATAAAAATA
*
1110077 ATTAAAATATAATTTAATATAAAAATA
1 ATTAAAATATAATATAATATAAAAATA
1110104 A-TATAAATATAA
1 ATTA-AAATATAA
1110116 ATAGATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 2 0.06
27 24 0.67
28 10 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
ATTAAAATATAATATAATATAAAAATA
Found at i:1110442 original size:20 final size:22
Alignment explanation
Indices: 1110403--1110459 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
1110393 TATATTTTAA
*
1110403 AATTTATATAATATAAATTATT
1 AATTTATATAATAAAAATTATT
*
1110425 AATTTAT-TAA-AAAAATTA-C
1 AATTTATATAATAAAAATTATT
*
1110444 AATTTAAATACATAAA
1 AATTTATATA-ATAAA
1110460 TTATCGAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 6 0.21
20 9 0.31
21 4 0.14
22 10 0.34
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTTATATAATAAAAATTATT
Found at i:1111167 original size:21 final size:21
Alignment explanation
Indices: 1111142--1111188 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
1111132 TTATAAAATT
**
1111142 AAAATTTTTTTAAATCAATAA
1 AAAATTTAATTAAATCAATAA
1111163 AAAA-TTAATTAAATCAATAA
1 AAAATTTAATTAAATCAATAA
1111183 AAAATT
1 AAAATT
1111189 GAAACATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATTTAATTAAATCAATAA
Found at i:1111174 original size:20 final size:20
Alignment explanation
Indices: 1111151--1111188 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1111141 TAAAATTTTT
1111151 TTAAATCAATAAAAAATTAA
1 TTAAATCAATAAAAAATTAA
1111171 TTAAATCAATAAAAAATT
1 TTAAATCAATAAAAAATT
1111189 GAAACATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAAATCAATAAAAAATTAA
Found at i:1111389 original size:29 final size:28
Alignment explanation
Indices: 1111335--1111390 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1111325 ATTTACGTAT
* *
1111335 TTATATTATATTAATATATTTTTATATA
1 TTATATTATATTAAAATATTTATATATA
1111363 TTATAATTATATTTAAAATA-TTATATAT
1 TTAT-ATTATA-TTAAAATATTTATATAT
1111391 TAATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 13 0.54
30 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTATATTATATTAAAATATTTATATATA
Found at i:1111399 original size:20 final size:20
Alignment explanation
Indices: 1111360--1111415 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1111350 ATATTTTTAT
*
1111360 ATATTATA-ATTATATTTAAA
1 ATATTATATATTA-ATATAAA
1111380 ATATTATATATTAATATAAA
1 ATATTATATATTAATATAAA
* *
1111400 TTTTTATATATTAATA
1 ATATTATATATTAATA
1111416 ATTTATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTATATATTAATATAAA
Found at i:1111547 original size:13 final size:13
Alignment explanation
Indices: 1111529--1111553 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1111519 GATCAAACCT
1111529 AAATTTATTTTAA
1 AAATTTATTTTAA
1111542 AAATTTATTTTA
1 AAATTTATTTTA
1111554 TTATTTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AAATTTATTTTAA
Found at i:1111570 original size:12 final size:12
Alignment explanation
Indices: 1111555--1111625 Score: 60
Period size: 12 Copynumber: 6.0 Consensus size: 12
1111545 TTTATTTTAT
1111555 TATTTATAATAA
1 TATTTATAATAA
* *
1111567 TATTAAAAATATTA
1 TATTTATAATA--A
*
1111581 TTTTTATAATAA
1 TATTTATAATAA
1111593 TATTTAT-ATAA
1 TATTTATAATAA
1111604 T-TTTATAATTAA
1 TATTTATAA-TAA
1111616 -ATTTA-AATAA
1 TATTTATAATAA
1111626 CATATTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
10 8 0.17
11 8 0.17
12 23 0.48
14 9 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATTTATAATAA
Found at i:1111601 original size:23 final size:23
Alignment explanation
Indices: 1111544--1111620 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 23
1111534 TATTTTAAAA
*
1111544 ATTTATTTTATTATTTATAATAAT
1 ATTTATATTATT-TTTATAATAAT
*
1111568 ATTAAAAATATTATTTTTATAATAAT
1 ATT---TATATTATTTTTATAATAAT
*
1111594 ATTTATA-TAATTTTATAATTAA-
1 ATTTATATTATTTTTATAA-TAAT
1111616 ATTTA
1 ATTTA
1111621 AATAACATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 15 0.33
23 6 0.13
24 3 0.07
26 14 0.31
27 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTATATTATTTTTATAATAAT
Found at i:1111610 original size:22 final size:22
Alignment explanation
Indices: 1111582--1111625 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1111572 AAAATATTAT
*
1111582 TTTTATAA-TAATATTTATATAA
1 TTTTATAATTAA-ATTTAAATAA
1111604 TTTTATAATTAAATTTAAATAA
1 TTTTATAATTAAATTTAAATAA
1111626 CATATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTATAATTAAATTTAAATAA
Found at i:1112194 original size:4 final size:4
Alignment explanation
Indices: 1112178--1112208 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1112168 TAAAATTAGT
*
1112178 ATAC ATCC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1112209 TATATGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1113468 original size:12 final size:12
Alignment explanation
Indices: 1113451--1113475 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1113441 TCAGTGGAAG
1113451 TTTTTTTGTTTT
1 TTTTTTTGTTTT
1113463 TTTTTTTGTTTT
1 TTTTTTTGTTTT
1113475 T
1 T
1113476 GAGAGATTAT
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:1124212 original size:3 final size:3
Alignment explanation
Indices: 1124204--1124229 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1124194 CTAGCGCTGG
1124204 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
1124230 TTGCTGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:1124609 original size:24 final size:22
Alignment explanation
Indices: 1124566--1124613 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
1124556 GCATTATTTT
1124566 TTAAATATATAAAAAATAAAAA
1 TTAAATATATAAAAAATAAAAA
*
1124588 TTAAATATTCATAAAAATTAAAAA
1 TTAAATA-T-ATAAAAAATAAAAA
1124612 TT
1 TT
1124614 TTTTATAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.30
23 1 0.04
24 15 0.65
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAAATATATAAAAAATAAAAA
Found at i:1124730 original size:22 final size:22
Alignment explanation
Indices: 1124703--1124763 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
1124693 TAATAAATTA
1124703 AAATATTTTTATATTAATATTT
1 AAATATTTTTATATTAATATTT
*
1124725 ATATATTTTTATAATT-ATATTT
1 AAATATTTTTAT-ATTAATATTT
1124747 AAATAATTTTT-TATTAA
1 AAAT-ATTTTTATATTAA
1124764 AATAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.09
22 22 0.65
23 9 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AAATATTTTTATATTAATATTT
Found at i:1125973 original size:116 final size:108
Alignment explanation
Indices: 1125803--1126077 Score: 333
Period size: 116 Copynumber: 2.5 Consensus size: 108
1125793 TATTATTTTT
* * *
1125803 AATAAAAATAATATTTAATTAACTTTTAAAAAATTTATATTAATAAATTAAAATATTAATTATT-
1 AATAAAAATAATATTTATTTAA-TTTTAAAAAAATTATATTAAAAAATTAAAATATTAATTATTA
*
1125867 T-TTTTAAAATAAAAATAAAAATAAAAAGGCTTTATTATTATTTTTTTAATAA
65 TGTTTT----T----ATAAAAATAAAAAGGATTTATTATTA-TTTTTTAATAA
* * *
1125919 AATTAAAAATAATATTTATTTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTA
1 AA-TAAAAATAATATTTATTTAATTTTAAAAAAATTATATTAAAAAATTAAAATATTAATTATTA
*
1125984 TGTTTTTATAAAAATAAAAAGTATTTATTATTATTTTTTAATAA
65 TGTTTTTATAAAAATAAAAAGGATTTATTATTATTTTTTAATAA
* *
1126028 AATAAAAAT-AT-TTAATTAAATTTTAAAAAAATTATATTAAAAAATTAAAA
1 AATAAAAATAATATTTATTTAATTTTAAAAAAATTATATTAAAAAATTAAAA
1126078 ATAATATTTA
Statistics
Matches: 144, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
106 34 0.24
107 2 0.01
108 7 0.05
109 13 0.09
110 24 0.17
114 1 0.01
116 39 0.27
117 20 0.14
118 4 0.03
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (108 bp):
AATAAAAATAATATTTATTTAATTTTAAAAAAATTATATTAAAAAATTAAAATATTAATTATTAT
GTTTTTATAAAAATAAAAAGGATTTATTATTATTTTTTAATAA
Found at i:1126051 original size:31 final size:32
Alignment explanation
Indices: 1125963--1126045 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 32
1125953 TTACATTAAC
*
1125963 AAATTAAAATA-TTAATTATTATGTTTTTATAA
1 AAATAAAAATATTTAATTATTAT-TTTTTATAA
1125995 AAATAAAAAGTATTT-ATTATTATTTTTTA-ATA
1 AAATAAAAA-TATTTAATTATTATTTTTTATA-A
1126027 AAATAAAAATATTTAATTA
1 AAATAAAAATATTTAATTA
1126046 AATTTTAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
31 6 0.13
32 28 0.61
33 10 0.22
34 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
AAATAAAAATATTTAATTATTATTTTTTATAA
Found at i:1126077 original size:21 final size:22
Alignment explanation
Indices: 1126050--1126108 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
1126040 TAATTAAATT
1126050 TTAAAAAAATTATATTAAAAAA
1 TTAAAAAAATTATATTAAAAAA
**
1126072 TTAAAAATAA-TAT-TTAAGGAA
1 TTAAAAA-AATTATATTAAAAAA
1126093 TTAAAAAAATT-TATTA
1 TTAAAAAAATTATATTA
1126109 TTATTGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 3 0.09
21 17 0.53
22 10 0.31
23 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (22 bp):
TTAAAAAAATTATATTAAAAAA
Found at i:1126564 original size:129 final size:128
Alignment explanation
Indices: 1126373--1126718 Score: 462
Period size: 129 Copynumber: 2.8 Consensus size: 128
1126363 AATAAAAAAA
*
1126373 ATTTTAATTTAAAATTTTTTATTTTAAAAATATAATAATTAATATTTTAATTTGTTAATGTAAAT
1 ATTTTTATTTAAAATTTTTTATTTTAAAAA-ATAATAATTAATATTTTAATTTGTTAATGTAAAT
* *
1126438 TTTTTAAACTTAATTAAATATTTTTTTTTATTTTATT-AAAAATTATAATAA-AAACC-TTTTT
65 TTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAAATAATAATAATAAACCTTTTTT
* *
1126499 ATTTTTATTTTAAAATTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTATTAATGT-
1 ATTTTTA-TTTAAAATTTTT-TATTT-TAAAAA-ATAATAATTAATATTTTAATTTGTTAATGTA
*
1126563 AATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAATAAACCTTTT
62 AATTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAAATAATAATAATAAACCTTTT
1126628 TT
127 TT
* * * *
1126630 ATTTTTATTT-AAATTTGTTGTTTT---AAA-AA-AA-TAATATTTTAATTTGTTAATATAAAAT
1 ATTTTTATTTAAAATTTTTTATTTTAAAAAATAATAATTAATATTTTAATTTGTTAATGTAAATT
* *
1126688 TTTTAAAGTTAATTAAATATTAATTTTTATT
66 TTTTAAACTTAATTAAATATTATTTTTTATT
1126719 AAAAAATAAT
Statistics
Matches: 198, Mismatches: 15, Indels: 19
0.85 0.06 0.08
Matches are distributed among these distances:
120 20 0.10
121 33 0.17
122 2 0.01
123 1 0.01
124 2 0.01
126 6 0.03
127 13 0.07
128 46 0.23
129 55 0.28
130 8 0.04
131 12 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (128 bp):
ATTTTTATTTAAAATTTTTTATTTTAAAAAATAATAATTAATATTTTAATTTGTTAATGTAAATT
TTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAAATAATAATAATAAACCTTTTTT
Found at i:1126672 original size:128 final size:124
Alignment explanation
Indices: 1126373--1126716 Score: 427
Period size: 128 Copynumber: 2.7 Consensus size: 124
1126363 AATAAAAAAA
* * *
1126373 ATTTTAATTTAAAATTTTTTATTTTAAAAATATAATAATTAATATTTTAATTTGTTAATGTAAAT
1 ATTTTTATTTAAAA-TTTTTATTTTAAAAAAATAATAATTAATATTTTAATTTATTAATGT-AAT
* * *
1126438 TTTTTAAACTTAATTAAATATTTTTTTTTATTTTATTAAAAATTATAATAAAAACCTTTTT
64 TTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAATAATAATAAAAACCTTTTT
1126499 ATTTTTATTTTAAAATTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTATTAATGTA
1 ATTTTTA-TTTAAAATTTTTA-TTTTA-AAAAA-ATAATAATTAATATTTTAATTTATTAATGTA
1126564 ATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAATAAACCTTTTT
62 ATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATT-AAAAATAATAATAA-AAACC-TTTT
1126629 T
124 T
* *
1126630 ATTTTTATTT-AAATTTGTTGTTTTAAAAAAATAATATTTTAAT-TTGTTAA--TA-TAA---AA
1 ATTTTTATTTAAAATTT-TTATTTTAAAAAAATAATA-ATTAATATT-TTAATTTATTAATGTAA
*
1126687 -TTTTTAAAGTTAATTAAATATTAATTTTTA
63 TTTTTTAAACTTAATTAAATATT-ATTTTTA
1126717 TTAAAAAATA
Statistics
Matches: 198, Mismatches: 9, Indels: 26
0.85 0.04 0.11
Matches are distributed among these distances:
121 21 0.11
122 9 0.05
125 3 0.02
126 14 0.07
127 20 0.10
128 56 0.28
129 53 0.27
130 10 0.05
131 12 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (124 bp):
ATTTTTATTTAAAATTTTTATTTTAAAAAAATAATAATTAATATTTTAATTTATTAATGTAATTT
TTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAATAATAATAAAAACCTTTTT
Found at i:1127106 original size:2 final size:2
Alignment explanation
Indices: 1127099--1127149 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1127089 AACGAGCATT
1127099 TA TA TA 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
1127141 TA TA TA TA T
1 TA TA TA TA T
1127150 GAGCATGGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1127554 original size:19 final size:19
Alignment explanation
Indices: 1127516--1127554 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1127506 TAAATATTAT
* **
1127516 TATTATTAATTATATTAAA
1 TATTATTAATAATAAAAAA
1127535 TATTATTAATAATAAAAAA
1 TATTATTAATAATAAAAAA
1127554 T
1 T
1127555 TCAAATTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTATTAATAATAAAAAA
Found at i:1128076 original size:27 final size:27
Alignment explanation
Indices: 1128025--1128076 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1128015 ATATTTAAAT
** *
1128025 ATATATTTAAAAAAATATTATATATGA
1 ATATATTTAAAAAAATAAAAAATATGA
*
1128052 ATATTTTTAAAAAAATAAAAAATAT
1 ATATATTTAAAAAAATAAAAAATAT
1128077 AGTATTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
ATATATTTAAAAAAATAAAAAATATGA
Found at i:1129153 original size:37 final size:37
Alignment explanation
Indices: 1129066--1129154 Score: 144
Period size: 39 Copynumber: 2.4 Consensus size: 37
1129056 AGTGTCTAAG
1129066 CGTGATTAAGACACTGTCCAAAAATGAACATAGTCAAAA
1 CGTGATTAAGACACTGTCCAAAAATGAACATAGT--AAA
1129105 CGTGATTAAGACACTGTCCAAAAAATGAACATAGT-AA
1 CGTGATTAAGACACTGTCC-AAAAATGAACATAGTAAA
1129142 CGTGATTAAGACA
1 CGTGATTAAGACA
1129155 TAATGGAGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
37 15 0.31
39 19 0.39
40 15 0.31
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (37 bp):
CGTGATTAAGACACTGTCCAAAAATGAACATAGTAAA
Found at i:1129747 original size:18 final size:19
Alignment explanation
Indices: 1129706--1129748 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1129696 AGTACAAATT
* *
1129706 ATAATATTTTAAATATATA
1 ATAAAATTTTAAATATAAA
1129725 A-AAAATTTTAAA-ATAAA
1 ATAAAATTTTAAATATAAA
1129742 ATAAAAT
1 ATAAAAT
1129749 ATATTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 15 0.71
19 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAAAATTTTAAATATAAA
Found at i:1129791 original size:23 final size:23
Alignment explanation
Indices: 1129748--1129792 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1129738 TAAAATAAAA
*
1129748 TATATTTATATTTAATATGAATC
1 TATATTTATATTAAATATGAATC
*
1129771 TATATTTAT-TCTAAATCTGAAT
1 TATATTTATAT-TAAATATGAAT
1129793 AATATAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (23 bp):
TATATTTATATTAAATATGAATC
Found at i:1131689 original size:36 final size:37
Alignment explanation
Indices: 1131610--1131693 Score: 95
Period size: 36 Copynumber: 2.3 Consensus size: 37
1131600 TTATATTTTA
1131610 AATTATTAAATTTAATATTAATTTTTATATAAATTATT
1 AATTATT-AATTTAATATTAATTTTTATATAAATTATT
*
1131648 AATTATTAATTTTAT-TTAATTTCGTTAT-TAAA-TATCT
1 AATTATTAATTTAATATTAATTT--TTATATAAATTAT-T
1131685 -ATTATTAAT
1 AATTATTAAT
1131694 AAATTAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
36 19 0.45
37 12 0.29
38 11 0.26
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (37 bp):
AATTATTAATTTAATATTAATTTTTATATAAATTATT
Found at i:1131865 original size:13 final size:13
Alignment explanation
Indices: 1131817--1131867 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
1131807 AATTTAATTT
*
1131817 TTTAATAATAAAAA
1 TTTAATAA-AATAA
*
1131831 TTTAATAATATAA
1 TTTAATAAAATAA
1131844 TTTAATAAAATAA
1 TTTAATAAAATAA
1131857 TTTAATAAAAT
1 TTTAATAAAAT
1131868 TAAATATTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 26 0.76
14 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTAATAAAATAA
Found at i:1131872 original size:18 final size:18
Alignment explanation
Indices: 1131821--1131873 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1131811 TAATTTTTTA
*
1131821 ATAATAAAAATTTAATAAT
1 ATAAT-AAAATTAAATAAT
** *
1131840 ATAATTTAATAAAATAAT
1 ATAATAAAATTAAATAAT
*
1131858 TTAATAAAATTAAATA
1 ATAATAAAATTAAATA
1131874 TTCATGATAT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATAAAATTAAATAAT
Found at i:1133814 original size:39 final size:38
Alignment explanation
Indices: 1133771--1133855 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 38
1133761 ATCGTATCCG
*
1133771 GAATAAGATGGTACAGTCTGCTGAAAACT-ATTAGAGCGA
1 GAATAAGA-GATACAGTCTGCTGAAAACTGATT-GAGCGA
* * * *
1133810 GAATATGGAGATGCATTCTGCTGAAAACTGCTTGAGCGA
1 GAATA-AGAGATACAGTCTGCTGAAAACTGATTGAGCGA
1133849 GAATAAG
1 GAATAAG
1133856 GCTTCGAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
38 1 0.03
39 33 0.87
40 4 0.11
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (38 bp):
GAATAAGAGATACAGTCTGCTGAAAACTGATTGAGCGA
Found at i:1138401 original size:17 final size:17
Alignment explanation
Indices: 1138368--1138402 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1138358 AATTTTTATT
* *
1138368 TTTATTTTATATTTAAA
1 TTTATTTTAGATATAAA
1138385 TTTATTTTAGATATAAA
1 TTTATTTTAGATATAAA
1138402 T
1 T
1138403 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTATTTTAGATATAAA
Found at i:1138531 original size:22 final size:22
Alignment explanation
Indices: 1138505--1138547 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1138495 TATCTGAATT
1138505 AAAATATTTTAATTTATTTATA
1 AAAATATTTTAATTTATTTATA
**
1138527 AAAATATTTTTTTTTATTTAT
1 AAAATATTTTAATTTATTTAT
1138548 TTTACCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AAAATATTTTAATTTATTTATA
Found at i:1142947 original size:19 final size:20
Alignment explanation
Indices: 1142910--1142948 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1142900 TAAAAAATGA
*
1142910 TTTTATAATAATATTTATAT
1 TTTTATAATAATATGTATAT
*
1142930 TTTTATAATTA-ATGTATAT
1 TTTTATAATAATATGTATAT
1142949 AAACGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTATAATAATATGTATAT
Found at i:1142949 original size:21 final size:20
Alignment explanation
Indices: 1142910--1142949 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1142900 TAAAAAATGA
*
1142910 TTTTATAATAATATTTATAT
1 TTTTATAATAATATATATAT
*
1142930 TTTTATAATTAATGTATATA
1 TTTTATAA-TAATATATATA
1142950 AACGTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATAATAATATATATAT
Found at i:1143725 original size:22 final size:21
Alignment explanation
Indices: 1143667--1143730 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 21
1143657 TAATTAGACT
* * *
1143667 TTTAATTTAAGTTTAGATAGG
1 TTTAATTTAAATTTAAATTGG
*
1143688 CTTTTAATTTAGATTTAAATTGG
1 --TTTAATTTAAATTTAAATTGG
1143711 TTTAAGTTTAAATTTAAATT
1 TTTAA-TTTAAATTTAAATT
1143731 TATATTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 5 0.14
22 13 0.37
23 17 0.49
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (21 bp):
TTTAATTTAAATTTAAATTGG
Found at i:1145222 original size:24 final size:23
Alignment explanation
Indices: 1145189--1145236 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
1145179 ATTTAATATA
*
1145189 AAATATGATATAATATAAATAAAT
1 AAATACGATATAA-ATAAATAAAT
1145213 AAATACGATATAAATAAATAAAT
1 AAATACGATATAAATAAATAAAT
1145236 A
1 A
1145237 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (23 bp):
AAATACGATATAAATAAATAAAT
Found at i:1146550 original size:12 final size:12
Alignment explanation
Indices: 1146533--1146569 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1146523 AAATTAAGAT
1146533 ATAATATAAAAA
1 ATAATATAAAAA
*
1146545 ATAATAT-AAAT
1 ATAATATAAAAA
1146556 ATAAT-TAAAAA
1 ATAATATAAAAA
1146567 ATA
1 ATA
1146570 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 1 0.05
11 14 0.64
12 7 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:1146606 original size:25 final size:25
Alignment explanation
Indices: 1146526--1146661 Score: 70
Period size: 21 Copynumber: 5.9 Consensus size: 25
1146516 AATAATTAAA
* *
1146526 TTAAGATATAATATAAAAAATAATA-
1 TTAA-ATATAATATATAATATAATAT
1146551 -TAAATATAAT-TA-AA-A-AATA-
1 TTAAATATAATATATAATATAATAT
*
1146570 TTAAA-AT-TTATATAATATAA-A-
1 TTAAATATAATATATAATATAATAT
*
1146591 TTAATATATTAATATATATTATAATATT
1 TTAA-ATA-TAATATATAATATAATA-T
1146619 TTAAATATAAT-TATAATAT-ATA-
1 TTAAATATAATATATAATATAATAT
* *
1146641 -AAAATATAA-ATATAAAATAAT
1 TTAAATATAATATATAATATAAT
1146662 TAAATAAATT
Statistics
Matches: 91, Mismatches: 6, Indels: 31
0.71 0.05 0.24
Matches are distributed among these distances:
18 1 0.01
19 8 0.09
20 7 0.08
21 23 0.25
22 7 0.08
23 8 0.09
24 7 0.08
25 18 0.20
26 5 0.05
27 3 0.03
28 4 0.04
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.40
Consensus pattern (25 bp):
TTAAATATAATATATAATATAATAT
Found at i:1146626 original size:27 final size:27
Alignment explanation
Indices: 1146531--1146653 Score: 78
Period size: 27 Copynumber: 4.5 Consensus size: 27
1146521 TTAAATTAAG
* * *
1146531 ATATAATATAAAAAATAATATAAATATA
1 ATATAAT-TAAATATTAATATATATATA
* * *
1146559 AT-TAA-AAAATATTAAAATTTATATA
1 ATATAATTAAATATTAATATATATATA
1146584 ATATAAATTAATATATTAATATATATTATA
1 ATAT-AATTAA-ATATTAATATATA-TATA
*
1146614 ATAT-TTTAAATA-TAATTATAATATATA
1 ATATAATTAAATATTAA-TAT-ATATATA
1146641 A-A-AATATAAATAT
1 ATATAAT-TAAATAT
1146654 AAAATAATTA
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
25 16 0.22
26 6 0.08
27 22 0.30
28 11 0.15
29 11 0.15
30 8 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATAATTAAATATTAATATATATATA
Found at i:1146654 original size:16 final size:15
Alignment explanation
Indices: 1146620--1146667 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
1146610 TATAATATTT
1146620 TAAATATAATTATAATA
1 TAAA-ATAATTA-AATA
1146637 TATAAA-AATATAAATA
1 TA-AAATAAT-TAAATA
1146653 TAAAATAATTAAATA
1 TAAAATAATTAAATA
1146668 AATTATTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 9 0.32
16 12 0.43
17 5 0.18
18 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAATAATTAAATA
Found at i:1146666 original size:21 final size:21
Alignment explanation
Indices: 1146514--1146667 Score: 68
Period size: 21 Copynumber: 7.7 Consensus size: 21
1146504 TAATTTATAA
1146514 AAAATAATTAAAT-TAAGATAT
1 AAAATAATTAAATATAA-ATAT
*
1146535 AATATAA--AAA-AT-AATAT
1 AAAATAATTAAATATAAATAT
1146552 AAATATAATT-AA-A-AAATATT
1 AAA-ATAATTAAATATAAATA-T
*
1146572 AAAAT-TTATATAATATAAAT-T
1 AAAATAAT-TA-AATATAAATAT
* *
1146593 AATAT-ATT-AATATATAT-T
1 AAAATAATTAAATATAAATAT
* * *
1146611 ATAATATTTTAAATATAATTAT
1 AAAATA-ATTAAATATAAATAT
1146633 AATATATAA--AAATATAAATAT
1 AA-A-ATAATTAAATATAAATAT
1146654 AAAATAATTAAATA
1 AAAATAATTAAATA
1146668 AATTATTGGA
Statistics
Matches: 100, Mismatches: 14, Indels: 38
0.66 0.09 0.25
Matches are distributed among these distances:
17 6 0.06
18 18 0.18
19 18 0.18
20 8 0.08
21 39 0.39
22 3 0.03
23 5 0.05
24 3 0.03
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (21 bp):
AAAATAATTAAATATAAATAT
Found at i:1147701 original size:11 final size:10
Alignment explanation
Indices: 1147685--1147722 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
1147675 ACATAACATA
1147685 AAAAATTAATT
1 AAAAA-TAATT
1147696 AAAAATAATAT
1 AAAAATAAT-T
1147707 AAAAATAA-T
1 AAAAATAATT
1147716 AAAAATA
1 AAAAATA
1147723 TAGTAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.31
10 4 0.15
11 14 0.54
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATAATT
Found at i:1147703 original size:23 final size:20
Alignment explanation
Indices: 1147677--1147722 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 20
1147667 TGAAACAAAC
1147677 ATAACATAAAAAATTAATTAAAA
1 ATAACAT-AAAAA-TAA-TAAAA
*
1147700 ATAATATAAAAATAATAAAA
1 ATAACATAAAAATAATAAAA
1147720 ATA
1 ATA
1147723 TAGTAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 3 0.14
22 5 0.23
23 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
ATAACATAAAAATAATAAAA
Found at i:1147729 original size:14 final size:16
Alignment explanation
Indices: 1147714--1147748 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1147704 TATAAAAATA
1147714 ATAAAAATATAGTAAT
1 ATAAAAATATAGTAAT
1147730 ATAAAAATATA-T-AT
1 ATAAAAATATAGTAAT
1147744 ATAAA
1 ATAAA
1147749 TAAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 1 0.05
16 11 0.58
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
ATAAAAATATAGTAAT
Found at i:1147738 original size:8 final size:8
Alignment explanation
Indices: 1147702--1147740 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1147692 AATTAAAAAT
1147702 AATATAAA
1 AATATAAA
1147710 AATAATAAA
1 AAT-ATAAA
**
1147719 AATATAGT
1 AATATAAA
1147727 AATATAAA
1 AATATAAA
1147735 AATATA
1 AATATA
1147741 TATATAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (8 bp):
AATATAAA
Found at i:1147750 original size:20 final size:19
Alignment explanation
Indices: 1147695--1147750 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 19
1147685 AAAAATTAAT
1147695 TAAAAATAATATA-AAA-A
1 TAAAAATAATATATAAATA
1147712 TAATAAA-AATATAGT-AATA
1 TAA-AAATAATATA-TAAATA
1147731 TAAAAATATATATATAAATA
1 TAAAAATA-ATATATAAATA
1147751 AATTAATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
17 9 0.28
18 8 0.25
19 6 0.19
20 9 0.28
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAATAATATATAAATA
Done.