Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2506
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: 48440
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Found at i:341 original size:17 final size:17
Alignment explanation
Indices: 319--367 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
309 AAAGTCGAAC
319 AATTTAAATTTAAAAAT
1 AATTTAAATTTAAAAAT
*
336 AATTTATAATCT-AAAAT
1 AATTTA-AATTTAAAAAT
353 AATTTAAACTTTAAA
1 AATTTAAA-TTTAAA
368 TAATCGAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 2 0.07
17 19 0.70
18 6 0.22
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTAAATTTAAAAAT
Found at i:3077 original size:23 final size:25
Alignment explanation
Indices: 3043--3105 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
3033 AAAAGTGTGG
* *
3043 ATATGAATATATATTTT-TTTATAT
1 ATATAAATATATATTTTATATATAT
* *
3067 ATTTAAAATATTATATTTTATATTTAT
1 ATAT-AAATA-TATATTTTATATATAT
3094 ATATAAATATAT
1 ATATAAATATAT
3106 GTATACATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 3 0.10
25 7 0.23
26 13 0.42
27 8 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
ATATAAATATATATTTTATATATAT
Found at i:3846 original size:56 final size:56
Alignment explanation
Indices: 3768--3882 Score: 212
Period size: 56 Copynumber: 2.1 Consensus size: 56
3758 AATTAGTATC
*
3768 TAAGCTTGTGCTTTCATTTGTAGTGTCATAGTGTCTCATTTTGTATTGTAAATTTT
1 TAAGCTTGTACTTTCATTTGTAGTGTCATAGTGTCTCATTTTGTATTGTAAATTTT
*
3824 TAAGCTTGTACTTTCATTTGTAGTGTCGTAGTGTCTCATTTTGTATTGTAAATTTT
1 TAAGCTTGTACTTTCATTTGTAGTGTCATAGTGTCTCATTTTGTATTGTAAATTTT
3880 TAA
1 TAA
3883 TAAATACTCA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.51
Consensus pattern (56 bp):
TAAGCTTGTACTTTCATTTGTAGTGTCATAGTGTCTCATTTTGTATTGTAAATTTT
Found at i:14829 original size:2 final size:2
Alignment explanation
Indices: 14822--14848 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14812 TTCACTACAC
14822 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
14849 TCAGAATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15246 original size:2 final size:2
Alignment explanation
Indices: 15239--15267 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15229 AATATAACTC
15239 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
15268 TAAATATTTA
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:15326 original size:25 final size:25
Alignment explanation
Indices: 15281--15356 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
15271 ATATTTAATA
* * *
15281 ATATAATAATTAATGTATTAAATTT
1 ATATAAAAAATAATTTATTAAATTT
*
15306 ATATAAATATAA-AATTT-TTAAATGT
1 ATATAAA-A-AATAATTTATTAAATTT
15331 A-ATAAAAAATAATTTATTAAATTT
1 ATATAAAAAATAATTTATTAAATTT
15355 AT
1 AT
15357 TTTTACCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
22 2 0.05
23 6 0.15
24 13 0.32
25 14 0.34
26 5 0.12
27 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
ATATAAAAAATAATTTATTAAATTT
Found at i:15350 original size:24 final size:27
Alignment explanation
Indices: 15291--15352 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 27
15281 ATATAATAAT
* *
15291 TAATGTATTAAATTTATATAAATATAA
1 TAATTTATTAAATGTATATAAATATAA
15318 -AATTT-TTAAATGTA-ATAAA-A-AA
1 TAATTTATTAAATGTATATAAATATAA
15340 TAATTTATTAAAT
1 TAATTTATTAAAT
15353 TTATTTTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 2 0.06
23 6 0.19
24 11 0.35
25 8 0.26
26 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (27 bp):
TAATTTATTAAATGTATATAAATATAA
Found at i:15785 original size:18 final size:18
Alignment explanation
Indices: 15762--15802 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
15752 TAAACTATTC
15762 ATTTAAA-AAAATATATAA
1 ATTTAAATAAAATATA-AA
*
15780 ATTTAAATAAAATTTAAA
1 ATTTAAATAAAATATAAA
15798 ATTTA
1 ATTTA
15803 TATTTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTAAATAAAATATAAA
Found at i:16131 original size:19 final size:20
Alignment explanation
Indices: 16107--16146 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
16097 ATAATGATTC
16107 AAAAAAGTAAAA-ATAATTT
1 AAAAAAGTAAAATATAATTT
*
16126 AAAAAATTAAAATATAATTT
1 AAAAAAGTAAAATATAATTT
16146 A
1 A
16147 TAATTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
AAAAAAGTAAAATATAATTT
Found at i:17103 original size:14 final size:15
Alignment explanation
Indices: 17078--17107 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17068 TTTAATATGA
17078 TAATTAAATAATTTT
1 TAATTAAATAATTTT
17093 TAATT-AATAATTTT
1 TAATTAAATAATTTT
17107 T
1 T
17108 TTATTAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATTAAATAATTTT
Found at i:17575 original size:16 final size:16
Alignment explanation
Indices: 17549--17593 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
17539 ACTGATTTTT
17549 AATTTAAAAATAATTTA
1 AATTT-AAAATAATTTA
* *
17566 AATTTAAAATTATTTC
1 AATTTAAAATAATTTA
*
17582 AATTCAAAATAA
1 AATTTAAAATAA
17594 ATCATCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTAAAATAATTTA
Found at i:17807 original size:25 final size:25
Alignment explanation
Indices: 17779--17831 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
17769 ATTTGATTTT
* *
17779 AAAATATTTAAAAT-TTAAATGATTC
1 AAAATAATTAAAATATTAAA-AATTC
17804 AAAATAATTAAAATATTAAAAATTC
1 AAAATAATTAAAATATTAAAAATTC
17829 AAA
1 AAA
17832 TTGATCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (25 bp):
AAAATAATTAAAATATTAAAAATTC
Found at i:17817 original size:19 final size:18
Alignment explanation
Indices: 17777--17826 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
17767 TAATTTGATT
*
17777 TTAAAATATTTAAAAT--
1 TTAAAATATTAAAAATAA
*
17793 TT-AAATGATTCAAAATAA
1 TTAAAAT-ATTAAAAATAA
17811 TTAAAATATTAAAAAT
1 TTAAAATATTAAAAAT
17827 TCAAATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 4 0.14
16 10 0.36
18 10 0.36
19 4 0.14
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
TTAAAATATTAAAAATAA
Found at i:18756 original size:18 final size:19
Alignment explanation
Indices: 18733--18770 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
18723 GGATTGAATT
18733 ATTTATTTAA-AATTAAAA
1 ATTTATTTAATAATTAAAA
*
18751 ATTTATTTAATATTTAAAA
1 ATTTATTTAATAATTAAAA
18770 A
1 A
18771 AATTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTATTTAATAATTAAAA
Found at i:20042 original size:26 final size:25
Alignment explanation
Indices: 19977--20061 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 25
19967 ATATTTATAT
* *
19977 TATAATATTATATATATTCTTTATATAA
1 TATAAAATTATATATA-T-TATATA-AA
20005 TA-AAAATTATATA-ATATATATAAA
1 TATAAAATTATATATAT-TATATAAA
*
20029 TATAAAATTAATATATATTATATAAT
1 TATAAAATT-ATATATATTATATAAA
20055 TATAAAA
1 TATAAAA
20062 AATAGAGTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
24 4 0.08
25 12 0.24
26 20 0.40
27 12 0.24
28 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (25 bp):
TATAAAATTATATATATTATATAAA
Found at i:20063 original size:28 final size:25
Alignment explanation
Indices: 19998--20064 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 25
19988 ATATATTCTT
19998 TATAT-AAT-AAAAATTATATAATA
1 TATATAAATAAAAAATTATATAATA
*
20021 TATATAAATATAAAATTA-ATATATA
1 TATATAAATAAAAAATTATATA-ATA
20046 TTATATAATTATAAAAAAT
1 -TATATAA--ATAAAAAAT
20065 AGAGTCAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
23 5 0.14
24 6 0.17
25 10 0.28
26 7 0.19
28 8 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TATATAAATAAAAAATTATATAATA
Found at i:20217 original size:18 final size:20
Alignment explanation
Indices: 20176--20218 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
20166 TATTTTTGTG
*
20176 TAAATCTTTCAAATATTTAA
1 TAAATCTTTCAAATATTAAA
20196 TAAATCTTT-AAAT-TTAAA
1 TAAATCTTTCAAATATTAAA
20214 TAAAT
1 TAAAT
20219 ATCGTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 4 0.18
20 9 0.41
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATCTTTCAAATATTAAA
Found at i:20695 original size:24 final size:26
Alignment explanation
Indices: 20668--20734 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 26
20658 ATAAATATCG
20668 ATATTTAAATTATAAAT-TTAT-TAA
1 ATATTTAAATTATAAATATTATATAA
* *
20692 ATATTATAATTTAAAAATAATTATATAA
1 ATATT-TAAATTATAAAT-ATTATATAA
*
20720 ATTAATTAAATTATA
1 A-TATTTAAATTATA
20735 TTTTAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
24 5 0.15
25 10 0.30
27 4 0.12
28 11 0.33
29 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTTAAATTATAAATATTATATAA
Found at i:20714 original size:17 final size:18
Alignment explanation
Indices: 20675--20716 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
20665 TCGATATTTA
*
20675 AATTATAAATTTATTAAAT
1 AATTAT-AATTTATAAAAT
20694 -ATTATAATTTA-AAAAT
1 AATTATAATTTATAAAAT
20710 AATTATA
1 AATTATA
20717 TAAATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 12 0.57
18 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTATAATTTATAAAAT
Found at i:25521 original size:3 final size:3
Alignment explanation
Indices: 25513--25540 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25503 TCAACAGCCA
25513 CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG C
25541 CGAACAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:26181 original size:6 final size:6
Alignment explanation
Indices: 26161--26233 Score: 57
Period size: 6 Copynumber: 12.8 Consensus size: 6
26151 TTTACACTTG
* *
26161 ATATAA TTATAAA ATATAA ATAT-A ATATAA A-ATAA TTA-AA ATAT-A
1 ATATAA ATAT-AA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
* * *
26206 ATAAAA ATAT-A ATTTAT ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATA
26234 TTAAAATTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
5 21 0.41
6 25 0.49
7 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAA
Found at i:26189 original size:11 final size:11
Alignment explanation
Indices: 26173--26338 Score: 66
Period size: 11 Copynumber: 15.2 Consensus size: 11
26163 ATAATTATAA
26173 AATATAAATAT
1 AATATAAATAT
26184 AATATAAA-AT
1 AATATAAATAT
26194 AAT-TAAAATAT
1 AATAT-AAATAT
*
26205 AATAAAAATAT
1 AATATAAATAT
26216 AAT-T---TAT
1 AATATAAATAT
26223 -ATATAAATAT
1 AATATAAATAT
*
26233 ATTA-AAAT-T
1 AATATAAATAT
* *
26242 TATATAAAATAA
1 AATAT-AAATAT
* *
26254 AATATTATTAT
1 AATATAAATAT
*
26265 ATTA-AATATAT
1 AATATAA-ATAT
26276 AATATTTTAAATAT
1 AATA---TAAATAT
* * *
26290 ATTTTTAATA-
1 AATATAAATAT
*
26300 AATAAAAATATAT
1 AAT-ATAA-ATAT
26313 AATTATAAAATAT
1 AA-TAT-AAATAT
26326 AATATAAATAT
1 AATATAAATAT
26337 AA
1 AA
26339 AAATTATGAA
Statistics
Matches: 112, Mismatches: 22, Indels: 42
0.64 0.12 0.24
Matches are distributed among these distances:
6 2 0.02
7 4 0.04
9 4 0.04
10 18 0.16
11 54 0.48
12 10 0.09
13 9 0.08
14 9 0.08
15 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATAAATAT
Found at i:26215 original size:38 final size:41
Alignment explanation
Indices: 26161--26275 Score: 127
Period size: 38 Copynumber: 2.9 Consensus size: 41
26151 TTTACACTTG
26161 ATATAATTATAAAATATAAATATAATATA-AAATA-ATTAAA
1 ATATAA-TATAAAATATAAATATAATATATAAATATATTAAA
*
26201 ATATAATA-AAAATAT-AAT-TTATATATAAATATATTAAA
1 ATATAATATAAAATATAAATATAATATATAAATATATTAAA
* *
26239 AT-TTATATAAAATA-AAATATTATTATATTAAATATAT
1 ATATAATATAAAATATAAATA-TAATATA-TAAATATAT
26276 AATATTTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
36 6 0.09
37 12 0.19
38 24 0.38
39 2 0.03
40 11 0.17
41 9 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (41 bp):
ATATAATATAAAATATAAATATAATATATAAATATATTAAA
Found at i:26224 original size:20 final size:19
Alignment explanation
Indices: 26201--26352 Score: 54
Period size: 19 Copynumber: 8.1 Consensus size: 19
26191 AATAATTAAA
26201 ATATAATAAAAATATAATTT
1 ATAT-ATAAAAATATAATTT
* *
26221 ATATATAAATATATTAAAATT
1 ATATATAAAAATA-T-AATTT
*
26242 -TATAT-AAAATAAAATATT
1 ATATATAAAAATATAAT-TT
*
26260 ATTATATTAAATATATAA--T
1 A-TATA-TAAAAATATAATTT
* * *
26279 AT-TTTAAATATAT-TTTT
1 ATATATAAAAATATAATTT
* *
26296 AATAAATAAAAATAT-A-TA
1 -ATATATAAAAATATAATTT
*
26314 AT-TAT-AAAATATAATAT
1 ATATATAAAAATATAATTT
*
26331 AAATATAAAAATTATGAATTT
1 ATATATAAAAA-TAT-AATTT
26352 A
1 A
26353 ATTCCTTTTA
Statistics
Matches: 96, Mismatches: 19, Indels: 33
0.65 0.13 0.22
Matches are distributed among these distances:
15 7 0.07
16 12 0.12
17 7 0.07
18 9 0.09
19 27 0.28
20 17 0.18
21 10 0.10
22 7 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (19 bp):
ATATATAAAAATATAATTT
Found at i:26285 original size:16 final size:16
Alignment explanation
Indices: 26221--26291 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
26211 AATATAATTT
26221 ATATATAAATATATTAAA
1 ATATAT-AATATATT-AA
*
26239 ATTTATATAA-A-ATAAA
1 A--TATATAATATATTAA
*
26255 ATAT-TATTATATTAA
1 ATATATAATATATTAA
*
26270 ATATATAATATTTTAA
1 ATATATAATATATTAA
26286 ATATAT
1 ATATAT
26292 TTTTAATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
13 2 0.05
14 4 0.09
15 8 0.19
16 18 0.42
17 2 0.05
18 2 0.05
19 2 0.05
20 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATATAATATATTAA
Found at i:26831 original size:10 final size:10
Alignment explanation
Indices: 26816--26840 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
26806 ATACAAATTT
26816 ATTTATTTAA
1 ATTTATTTAA
26826 ATTTATTTAA
1 ATTTATTTAA
26836 ATTTA
1 ATTTA
26841 AATTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTATTTAA
Found at i:26841 original size:16 final size:14
Alignment explanation
Indices: 26810--26846 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 14
26800 ACTTAAATAC
26810 AAATTTATTTATTT
1 AAATTTATTTATTT
26824 AAATTTATTTAAATTT
1 AAATTTATTT--ATTT
26840 AAATTTA
1 AAATTTA
26847 AAAATTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.48
16 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AAATTTATTTATTT
Found at i:27785 original size:23 final size:22
Alignment explanation
Indices: 27742--27785 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
27732 TATTCGATCA
*
27742 TACAAAATTATTAAATTTAAAT
1 TACAAAATTATTAAATATAAAT
27764 TACAAATATTAATTAAA-ATAAA
1 TACAAA-ATT-ATTAAATATAAA
27786 AATTTTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 7 0.37
24 6 0.32
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
TACAAAATTATTAAATATAAAT
Found at i:31661 original size:21 final size:23
Alignment explanation
Indices: 31630--31673 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
31620 TATTTTTAAA
31630 AATTAAAAAATA-ATAAAATTTT
1 AATTAAAAAATATATAAAATTTT
*
31652 AATT-AAAAATATATAATATTTT
1 AATTAAAAAATATATAAAATTTT
31674 TTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATTAAAAAATATATAAAATTTT
Found at i:31682 original size:21 final size:20
Alignment explanation
Indices: 31635--31682 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
31625 TTAAAAATTA
31635 AAAAATAATAAAATTTTAATT
1 AAAAATAATAAAATTTT-ATT
*
31656 AAAAATATATAATATTTT-TT
1 AAAAATA-ATAAAATTTTATT
31676 AATAAAT
1 AA-AAAT
31683 TTATCTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.17
21 11 0.46
22 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAAATAATAAAATTTTATT
Found at i:32643 original size:14 final size:15
Alignment explanation
Indices: 32605--32646 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
32595 TTTTTAAAAA
*
32605 TTATATT-ATTATAT
1 TTATATTAAATATAT
32619 TTATATTTAAATATAT
1 TTATA-TTAAATATAT
32635 TTATA-TAAATAT
1 TTATATTAAATAT
32647 TAAATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 12 0.48
15 2 0.08
16 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTAAATATAT
Found at i:32673 original size:15 final size:15
Alignment explanation
Indices: 32641--32690 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
32631 ATATTTATAT
*
32641 AAATATTAAATAAT-A
1 AAAT-TTAAAAAATAA
32656 AAATTTAAAAAATAA
1 AAATTTAAAAAATAA
*
32671 AAATTTAAAATAACAA
1 AAATTTAAAA-AATAA
32687 AAAT
1 AAAT
32691 ATATACATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 8 0.26
15 15 0.48
16 8 0.26
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATTTAAAAAATAA
Found at i:32890 original size:29 final size:29
Alignment explanation
Indices: 32857--32918 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
32847 TATAAAAAAG
32857 TAAA-TGAAAATTTTTAATCATTATATTAT
1 TAAATTGAAAATTTTT-ATCATTATATTAT
* * * *
32886 TAAATTTAATATTTTTATCTTTATATTTT
1 TAAATTGAAAATTTTTATCATTATATTAT
32915 TAAA
1 TAAA
32919 GTTATAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (29 bp):
TAAATTGAAAATTTTTATCATTATATTAT
Found at i:32923 original size:14 final size:14
Alignment explanation
Indices: 32877--32924 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
32867 TTTTTAATCA
*
32877 TTATATTATTAAAT
1 TTATATTTTTAAAT
**
32891 TTAATATTTTTATCT
1 TT-ATATTTTTAAAT
*
32906 TTATATTTTTAAAG
1 TTATATTTTTAAAT
32920 TTATA
1 TTATA
32925 ATGAATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (14 bp):
TTATATTTTTAAAT
Found at i:34077 original size:31 final size:31
Alignment explanation
Indices: 34039--34099 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
34029 AATATGTAAT
34039 GTATTATTTATTTTGATTTATTAAATTTTAG
1 GTATTATTTATTTTGATTTATTAAATTTTAG
*
34070 GTATTATTTATTTTGATTTATTAGATTTTA
1 GTATTATTTATTTTGATTTATTAAATTTTA
34100 TGATTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (31 bp):
GTATTATTTATTTTGATTTATTAAATTTTAG
Found at i:34091 original size:17 final size:17
Alignment explanation
Indices: 34040--34092 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
34030 ATATGTAATG
34040 TATTATTTATTTTGATT
1 TATTATTTATTTTGATT
* **
34057 TATTA--AATTTT-AGG
1 TATTATTTATTTTGATT
34071 TATTATTTATTTTGATT
1 TATTATTTATTTTGATT
34088 TATTA
1 TATTA
34093 GATTTTATGA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 6 0.22
15 5 0.19
16 5 0.19
17 11 0.41
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (17 bp):
TATTATTTATTTTGATT
Found at i:35182 original size:21 final size:21
Alignment explanation
Indices: 35143--35183 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35133 TATTATTAAA
* * *
35143 ATATTTTTTATTTATATTTAT
1 ATATTTTATAATTAAATTTAT
35164 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
35184 AATAAAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:35260 original size:21 final size:20
Alignment explanation
Indices: 35235--35290 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
35225 AAAATAATAA
35235 AATTTATAAAAAAATTATTTT
1 AATTTATAAAAAAATTA-TTT
* *
35256 AATTTAT-ATAAATTTATTT
1 AATTTATAAAAAAATTATTT
* *
35275 AATTTTTAAATAAATT
1 AATTTATAAAAAAATT
35291 TAATTAAGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 9 0.32
20 12 0.43
21 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AATTTATAAAAAAATTATTT
Found at i:35291 original size:21 final size:21
Alignment explanation
Indices: 35258--35297 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35248 ATTATTTTAA
* *
35258 TTTATATAAATTTATTTAATT
1 TTTAAATAAATTTAATTAATT
35279 TTTAAATAAATTTAATTAA
1 TTTAAATAAATTTAATTAA
35298 GTCATACGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAAATAAATTTAATTAATT
Found at i:35497 original size:14 final size:15
Alignment explanation
Indices: 35480--35648 Score: 71
Period size: 15 Copynumber: 11.1 Consensus size: 15
35470 TAATAATTTA
35480 AAATATAAT-TAAAT
1 AAATATAATATAAAT
*
35494 AAATATAATATATAT
1 AAATATAATATAAAT
35509 AAAATATAAATTATATAAT
1 -AAATAT-AA-TATA-AAT
35528 ATAATATAATA-AAA-
1 A-AATATAATATAAAT
* * *
35542 ATATATATTTTAAAT
1 AAATATAATATAAAT
** *
35557 TTATATATTATAAATT
1 AAATATAATATAAA-T
* * *
35573 ATTAATAT-ATTTTAGT
1 A--AATATAATATAAAT
* **
35589 AAATATAAAATATTTT
1 AAATATAATATA-AAT
*
35605 AAATATATTAT-AAT
1 AAATATAATATAAAT
* *
35619 AAA-ATAAAATATAT
1 AAATATAATATAAAT
35633 AAATATAATATAAAT
1 AAATATAATATAAAT
35648 A
1 A
35649 TATAAATGAT
Statistics
Matches: 113, Mismatches: 27, Indels: 29
0.67 0.16 0.17
Matches are distributed among these distances:
13 11 0.10
14 27 0.24
15 30 0.27
16 20 0.18
17 7 0.06
18 11 0.10
19 7 0.06
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (15 bp):
AAATATAATATAAAT
Found at i:35581 original size:13 final size:14
Alignment explanation
Indices: 35481--35640 Score: 68
Period size: 14 Copynumber: 11.5 Consensus size: 14
35471 AATAATTTAA
*
35481 AATAT-AATTAAAT
1 AATATAAATTATAT
*
35494 AAATATAATATATATAA
1 -AATATAA-AT-TATAT
35511 AATATAAATTATAT
1 AATATAAATTATAT
35525 AATAT--A--ATAT
1 AATATAAATTATAT
*
35535 AATA-AAAATATAT
1 AATATAAATTATAT
* *
35548 ATTTTAAATTTATAT
1 AATATAAA-TTATAT
*
35563 ATTATAAATTAT-T
1 AATATAAATTATAT
**
35576 AATATATTTTAGTA-
1 AATATAAATTA-TAT
* *
35590 AATATAAAATATTTT
1 AATATAAATTA-TAT
*
35605 AA-ATATATTATAAT
1 AATATAAATTAT-AT
* *
35619 AAAATAAAATATAT
1 AATATAAATTATAT
35633 AAATATAA
1 -AATATAA
35641 TATAAATATA
Statistics
Matches: 110, Mismatches: 21, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
10 8 0.07
11 1 0.01
12 1 0.01
13 16 0.15
14 42 0.38
15 30 0.27
16 9 0.08
17 3 0.03
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (14 bp):
AATATAAATTATAT
Found at i:35603 original size:52 final size:51
Alignment explanation
Indices: 35513--35648 Score: 132
Period size: 52 Copynumber: 2.6 Consensus size: 51
35503 ATATATAAAA
* *
35513 TATAAATTATATAATATAATATAATAAAAATATATATTTTAAATTTATATAT
1 TATAAATTATATAATATAATATAATAAAAATAAATATTTTAAATATAT-TAT
* * * *
35565 TATAAATTAT-TAATATATTTTAGTAAATATAAAATATTTTAAATATATTAT
1 TATAAATTATATAATATAATATAATAAAAAT-AAATATTTTAAATATATTAT
* * * *
35616 AATAAAATA-AAATATATAAATATAATATAAATA
1 TATAAATTATATA-ATAT-AATATAATAAAAATA
35649 TATAAATGAT
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
51 27 0.41
52 30 0.45
53 9 0.14
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (51 bp):
TATAAATTATATAATATAATATAATAAAAATAAATATTTTAAATATATTAT
Found at i:35630 original size:20 final size:20
Alignment explanation
Indices: 35604--35655 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
35594 TAAAATATTT
35604 TAAATATATTATAATAAAATA
1 TAAATATATTA-AATAAAATA
*
35625 -AAATATA-TAAATATAATA
1 TAAATATATTAAATAAAATA
35643 TAAATATA-TAAAT
1 TAAATATATTAAAT
35656 GATTACAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 8 0.28
19 14 0.48
20 7 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAATATATTAAATAAAATA
Found at i:35636 original size:28 final size:29
Alignment explanation
Indices: 35478--35645 Score: 115
Period size: 30 Copynumber: 6.0 Consensus size: 29
35468 CTTAATAATT
* *
35478 TAAAATATAATTAAATAAATATAATATATA
1 TAAAATATAAATATATAAATATAATATA-A
35508 TAAAATATAAAT-TATATAATATAATATAA
1 TAAAATATAAATATATA-AATATAATATAA
* *
35537 TAAAA-ATATATATTTTAAAT-T--TAT-A
1 TAAAATATAAATA-TATAAATATAATATAA
* * * * *
35562 T--ATTATAAAT-TATTAATATATTTTAG
1 TAAAATATAAATATATAAATATAATATAA
* *
35588 T-AAATATAAAATATTTTAAATATATTATAA
1 TAAAATAT-AAATA-TATAAATATAATATAA
35618 TAAAATA-AAATATATAAATATAATATAA
1 TAAAATATAAATATATAAATATAATATAA
35646 ATATATAAAT
Statistics
Matches: 108, Mismatches: 17, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
22 5 0.05
23 2 0.02
24 5 0.05
25 4 0.04
26 4 0.04
27 4 0.04
28 24 0.22
29 17 0.16
30 38 0.35
31 5 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
TAAAATATAAATATATAAATATAATATAA
Found at i:36166 original size:19 final size:18
Alignment explanation
Indices: 36144--36212 Score: 52
Period size: 19 Copynumber: 3.8 Consensus size: 18
36134 TGGTGATTTT
*
36144 AAATAAAAATATGTGTATA
1 AAATAAAAATATAT-TATA
* *
36163 AAATATAAATGTATTATA
1 AAATAAAAATATATTATA
*
36181 AAATAATTAAA-ATATAATA
1 AAATAA--AAATATATTATA
*
36200 TAATAAAAA-ATAT
1 AAATAAAAATATAT
36213 AAATATATCA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 7 0.17
18 9 0.22
19 22 0.54
20 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATAAAAATATATTATA
Found at i:36196 original size:16 final size:17
Alignment explanation
Indices: 36177--36215 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
36167 ATAAATGTAT
*
36177 TATAAAATAAT-TAAAA
1 TATAAAATAATAAAAAA
*
36193 TATAATATAATAAAAAA
1 TATAAAATAATAAAAAA
36210 TATAAA
1 TATAAA
36216 TATATCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TATAAAATAATAAAAAA
Found at i:36258 original size:32 final size:32
Alignment explanation
Indices: 36181--36262 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 32
36171 ATGTATTATA
*
36181 AAATA-ATTAAAATATAATATAATAAAAAATAT
1 AAATATATTAAAAT-TTATATAATAAAAAATAT
* * * *
36213 AAATATATCAAAATTTATATTATATAAAGTAT
1 AAATATATTAAAATTTATATAATAAAAAATAT
* *
36245 TAATGTATTAAAATTTAT
1 AAATATATTAAAATTTAT
36263 TATACATATA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 34 0.83
33 7 0.17
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (32 bp):
AAATATATTAAAATTTATATAATAAAAAATAT
Found at i:36777 original size:23 final size:23
Alignment explanation
Indices: 36729--36772 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
36719 GTTTTTAATA
*
36729 TATTTTTATATCTATATTTATAT
1 TATTTATATATCTATATTTATAT
36752 TATTTATATATC-ATA-TTATAT
1 TATTTATATATCTATATTTATAT
36773 CTTATCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 3 0.15
23 11 0.55
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTATATATCTATATTTATAT
Found at i:36794 original size:39 final size:39
Alignment explanation
Indices: 36737--36812 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 39
36727 TATATTTTTA
36737 TATCTATATTTATATTATTTATATATCATATT-ATATCT
1 TATCTATATTTATATTATTTATATATCATATTCATATCT
*
36775 TATCTCATATTT-TATTTATTTTTATATCATATTCATAT
1 TATCT-ATATTTATA-TTATTTATATATCATATTCATAT
36813 AATATACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 7 0.21
39 23 0.68
40 4 0.12
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (39 bp):
TATCTATATTTATATTATTTATATATCATATTCATATCT
Found at i:40132 original size:19 final size:18
Alignment explanation
Indices: 40110--40169 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
40100 ATTAATTTTT
40110 TAAATAT-TTATTTATAATA
1 TAAATATATT-TTTAT-ATA
40129 TAAATAATATTTTTATATA
1 TAAAT-ATATTTTTATATA
*
40148 TAAATAATATTTTAATA-A
1 TAAAT-ATATTTTTATATA
40166 TAAA
1 TAAA
40170 ATAAATTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
18 5 0.13
19 24 0.63
20 7 0.18
21 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATATATTTTTATATA
Found at i:40137 original size:22 final size:20
Alignment explanation
Indices: 40112--40160 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 20
40102 TAATTTTTTA
40112 AATATTTATTTATAATATAAAT
1 AATATTT-TTTAT-ATATAAAT
40134 AATA-TTTTTATATATAAAT
1 AATATTTTTTATATATAAAT
40153 AATATTTT
1 AATATTTT
40161 AATAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.46
20 8 0.31
21 2 0.08
22 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTTTTATATATAAAT
Found at i:40171 original size:19 final size:20
Alignment explanation
Indices: 40123--40173 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
40113 ATATTTATTT
*
40123 ATAATATAAATAATATTTTT
1 ATAATATAAATAATATTTTA
40143 AT-ATATAAATAATATTTTA
1 ATAATATAAATAATATTTTA
40162 ATAATA-AAATAA
1 ATAATATAAATAA
40174 ATTATCAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 24 0.83
20 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATATAAATAATATTTTA
Found at i:41266 original size:28 final size:26
Alignment explanation
Indices: 41220--41273 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
41210 TTATCATCGC
41220 TTAAATTTGAAAATAATTTAATTTATTT
1 TTAAATTTGAAAATAATTT--TTTATTT
*
41248 TTAAATTTAGATAAT-ATTTTTTATTT
1 TTAAATTT-GAAAATAATTTTTTATTT
41274 CAAGATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.29
28 12 0.50
29 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (26 bp):
TTAAATTTGAAAATAATTTTTTATTT
Found at i:41394 original size:16 final size:18
Alignment explanation
Indices: 41372--41407 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41362 TTTTGTTTTT
*
41372 TATTTTTTTACT-TAAAA
1 TATTTTTTAACTATAAAA
41389 TATTTTTTAACTATAAAA
1 TATTTTTTAACTATAAAA
41407 T
1 T
41408 TATCTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTTTAACTATAAAA
Found at i:43390 original size:23 final size:23
Alignment explanation
Indices: 43343--43390 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
43333 TCATTAAATT
* *
43343 TTTAAATAATAATAATCAATTAA
1 TTTAAATAAAAATAATCAATAAA
* *
43366 TTTAAATAAAAATATTTAATAAA
1 TTTAAATAAAAATAATCAATAAA
43389 TT
1 TT
43391 CATTTCAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTAAATAAAAATAATCAATAAA
Found at i:44230 original size:25 final size:24
Alignment explanation
Indices: 44189--44235 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
44179 AAATGAATTA
*
44189 AAAATTATTACATATTTTATTTTTT
1 AAAATTATTACA-AATTTATTTTTT
44214 AAAATTATTTA-AAATTTATTTT
1 AAAATTA-TTACAAATTTATTTT
44236 AAAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 8 0.40
26 3 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
AAAATTATTACAAATTTATTTTTT
Found at i:44333 original size:29 final size:29
Alignment explanation
Indices: 44291--44352 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
44281 TTTTACTGAT
*
44291 AGTAAATAAGATATTTCTTGTAAAATAAA
1 AGTAAATAAGATATTTATTGTAAAATAAA
*
44320 AGTAAATAAGATATTTATTGTGAAATAAA
1 AGTAAATAAGATATTTATTGTAAAATAAA
44349 AGTA
1 AGTA
44353 TAATTATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.34
Consensus pattern (29 bp):
AGTAAATAAGATATTTATTGTAAAATAAA
Found at i:45808 original size:26 final size:26
Alignment explanation
Indices: 45779--45833 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
45769 ATTTAAATTT
45779 AATTATAAATATTAATAT-AAAAATAA
1 AATT-TAAATATTAATATAAAAAATAA
* * *
45805 AATTTTAATATTATTTTAAAAAATAA
1 AATTTAAATATTAATATAAAAAATAA
45831 AAT
1 AAT
45834 AAATTTTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AATTTAAATATTAATATAAAAAATAA
Done.