Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold588
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: 104647
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1577 original size:2 final size:2
Alignment explanation
Indices: 1570--1598 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1560 CATGGCACTC
1570 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
1599 TTGTAGAAAT
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:1891 original size:23 final size:21
Alignment explanation
Indices: 1864--1914 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 21
1854 ACGACATAAA
1864 AAATTATAATTAAAATATAATAT
1 AAATTATAATTAAAA-AT-ATAT
* *
1887 AAATTATTATTATAAATATAT
1 AAATTATAATTAAAAATATAT
1908 AAATTAT
1 AAATTAT
1915 TATATCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 11 0.42
22 2 0.08
23 13 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTATAATTAAAAATATAT
Found at i:1915 original size:21 final size:23
Alignment explanation
Indices: 1864--1917 Score: 76
Period size: 21 Copynumber: 2.4 Consensus size: 23
1854 ACGACATAAA
*
1864 AAATTATAATTAAAATATAATAT
1 AAATTATTATTAAAATATAATAT
*
1887 AAATTATTATTATAA-AT-ATAT
1 AAATTATTATTAAAATATAATAT
1908 AAATTATTAT
1 AAATTATTAT
1918 ATCTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 14 0.48
22 2 0.07
23 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTATTATTAAAATATAATAT
Found at i:2359 original size:2 final size:2
Alignment explanation
Indices: 2344--2381 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2334 ACGTATACAA
2344 AT AT -T AT A- AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2382 ATGTGCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2368 original size:17 final size:17
Alignment explanation
Indices: 2344--2381 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2334 ACGTATACAA
2344 ATAT-TATAATATATAT
1 ATATATATAATATATAT
*
2360 ATATATATATTATATAT
1 ATATATATAATATATAT
2377 ATATA
1 ATATA
2382 ATGTGCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATAATATATAT
Found at i:2944 original size:2 final size:2
Alignment explanation
Indices: 2937--2972 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2927 AGCTAAGAAT
2937 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
2973 GTCTTTGGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3033 original size:6 final size:6
Alignment explanation
Indices: 3022--3048 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3012 ATATTATTTA
3022 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
3049 TGGTTTGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:3427 original size:16 final size:16
Alignment explanation
Indices: 3406--3436 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3396 TTTATTTTAT
*
3406 TTAAATTTAAGTTAAA
1 TTAAATTTAAATTAAA
3422 TTAAATTTAAATTAA
1 TTAAATTTAAATTAA
3437 TTCAAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:3456 original size:8 final size:8
Alignment explanation
Indices: 3443--3467 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3433 TTAATTCAAA
3443 AAATTATT
1 AAATTATT
3451 AAATTATT
1 AAATTATT
3459 AAATTATT
1 AAATTATT
3467 A
1 A
3468 TTAAAATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAATTATT
Found at i:3546 original size:18 final size:17
Alignment explanation
Indices: 3504--3546 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3494 AATATATTAT
3504 TTAAAAAATAATTTAAA
1 TTAAAAAATAATTTAAA
* * *
3521 TTATAAAATATTTTTAA
1 TTAAAAAATAATTTAAA
3538 TTGAAAAAA
1 TT-AAAAAA
3547 ATCAAAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAAAAAATAATTTAAA
Found at i:16203 original size:17 final size:17
Alignment explanation
Indices: 16178--16211 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16168 CGATATTAAA
*
16178 ATATGTATTTTAATTTT
1 ATATGTATTATAATTTT
*
16195 ATATTTATTATAATTTT
1 ATATGTATTATAATTTT
16212 TTTTATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATATGTATTATAATTTT
Found at i:16229 original size:12 final size:11
Alignment explanation
Indices: 16211--16242 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
16201 ATTATAATTT
16211 TTTTTATTAAA
1 TTTTTATTAAA
16222 TTTATTATTAAA
1 TTT-TTATTAAA
16234 TTTTTATTA
1 TTTTTATTA
16243 TTTAACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTATTAAA
Found at i:16252 original size:26 final size:27
Alignment explanation
Indices: 16199--16252 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
16189 AATTTTATAT
* *
16199 TTATTATAATTTTTTTTATTAAATTTA
1 TTATTATAATTTTTATTATTAAACTTA
*
16226 TTATTA-AATTTTTATTATTTAACTTA
1 TTATTATAATTTTTATTATTAAACTTA
16252 T
1 T
16253 AAAATTACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTATAATTTTTATTATTAAACTTA
Found at i:16259 original size:17 final size:17
Alignment explanation
Indices: 16239--16271 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16229 TTAAATTTTT
16239 ATTA-TTTAACTTATAAA
1 ATTACTTTAA-TTATAAA
16256 ATTACTTTAATTATAA
1 ATTACTTTAATTATAA
16272 TAAAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTACTTTAATTATAAA
Found at i:16651 original size:21 final size:22
Alignment explanation
Indices: 16627--16678 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
16617 CATGTACGTG
*
16627 ATATATAA-TAAAAAA-ATATAA
1 ATATATAAGTAAAAAATAAAT-A
16648 ATATATAAGGTAAAAAATAAATA
1 ATATATAA-GTAAAAAATAAATA
16671 ATATATAA
1 ATATATAA
16679 ATATATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 8 0.30
23 16 0.59
24 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (22 bp):
ATATATAAGTAAAAAATAAATA
Found at i:16964 original size:7 final size:6
Alignment explanation
Indices: 16932--17010 Score: 81
Period size: 6 Copynumber: 12.8 Consensus size: 6
16922 AAAATTTTAA
* * *
16932 AATTTT TATTAT AA-TTT AAATTT AATTTTT AATTTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AA-TTTT AA-TTTT AATTTT AATTTT
16981 AA-TTT AATTTAT AAATTTT AATTTT AATTT
1 AATTTT AATTT-T -AATTTT AATTTT AATTT
17011 AAAAAATTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
5 9 0.14
6 35 0.56
7 14 0.22
8 5 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:16971 original size:25 final size:27
Alignment explanation
Indices: 16953--17010 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 27
16943 TAATTTAAAT
16953 TTAATTTTTAATTT-TTAATTTTAATT
1 TTAATTTTTAATTTATTAATTTTAATT
*
16979 TTAA--TTTAATTTATAAATTTTAATT
1 TTAATTTTTAATTTATTAATTTTAATT
17004 TTAATTT
1 TTAATTT
17011 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 8 0.29
25 15 0.54
26 4 0.14
27 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTAATTTTTAATTTATTAATTTTAATT
Found at i:16978 original size:31 final size:31
Alignment explanation
Indices: 16927--17013 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
16917 AATTTAAAAT
* *
16927 TTTAAAATTTTT-ATTATAATTTAAATTTAA
1 TTTATAATTTTTAATTTTAATTTAAATTTAA
* *
16957 TTTTTAATTTTTAATTTTAATTTTAATTTAA
1 TTTATAATTTTTAATTTTAATTTAAATTTAA
*
16988 TTTATAAATTTTAATTTTAATTTAAA
1 TTTATAATTTTTAATTTTAATTTAAA
17014 AAATTAATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 10 0.20
31 39 0.80
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTATAATTTTTAATTTTAATTTAAATTTAA
Found at i:17011 original size:25 final size:24
Alignment explanation
Indices: 16959--17012 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 24
16949 AAATTTAATT
*
16959 TTTAATTTTTAATTTTAATTTTAA
1 TTTAATTTTAAATTTTAATTTTAA
16983 TTTAATTTATAAATTTTAATTTTAA
1 TTTAATTT-TAAATTTTAATTTTAA
17008 TTTAA
1 TTTAA
17013 AAAATTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTAATTTTAAATTTTAATTTTAA
Found at i:17020 original size:19 final size:20
Alignment explanation
Indices: 16979--17021 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
16969 AATTTTAATT
**
16979 TTAA-TTTAATTTATAAATT
1 TTAATTTTAATTTATAAAAA
16998 TTAATTTTAATTTA-AAAAA
1 TTAATTTTAATTTATAAAAA
17017 TTAAT
1 TTAAT
17022 ATATTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATTTTAATTTATAAAAA
Found at i:23237 original size:19 final size:20
Alignment explanation
Indices: 23194--23266 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
23184 ATCAAAATTT
*
23194 ATATAAATATATAATATTTAAA
1 ATATAAAT-TATAATA-TAAAA
*
23216 ATAT-AATTATGATATAAAA
1 ATATAAATTATAATATAAAA
* *
23235 ATAATAAAATATAATATAAAT
1 AT-ATAAATTATAATATAAAA
23256 ATATAAATTAT
1 ATATAAATTAT
23267 TATTAGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.14
20 16 0.37
21 17 0.40
22 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (20 bp):
ATATAAATTATAATATAAAA
Found at i:23257 original size:11 final size:11
Alignment explanation
Indices: 23215--23258 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
23205 TAATATTTAA
*
23215 AATATAATTAT
1 AATATAAATAT
* *
23226 GATATAAAAAT
1 AATATAAATAT
23237 AATA-AAATAT
1 AATATAAATAT
23247 AATATAAATAT
1 AATATAAATAT
23258 A
1 A
23259 TAAATTATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AATATAAATAT
Found at i:23257 original size:27 final size:28
Alignment explanation
Indices: 23151--23263 Score: 83
Period size: 27 Copynumber: 4.1 Consensus size: 28
23141 AATATACATG
* * **
23151 AATATATAATTATATAATTTAAAT-TATT
1 AATATATAA-AATATAATATAAATATAAA
* *
23179 AATATATCAAAAT-TTATATAAATAT-AT
1 AATATAT-AAAATATAATATAAATATAAA
* *
23206 AATATTTAAAATATAAT-TATGATATAAA
1 AATATATAAAATATAATATA-AATATAAA
*
23234 AATA-ATAAAATATAATATAAATATATA
1 AATATATAAAATATAATATAAATATAAA
23261 AAT
1 AAT
23264 TATTATTAGG
Statistics
Matches: 68, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
26 7 0.10
27 42 0.62
28 17 0.25
29 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
AATATATAAAATATAATATAAATATAAA
Found at i:23661 original size:12 final size:12
Alignment explanation
Indices: 23617--23681 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
23607 AAAAATTTTA
*
23617 AAATATTTAAAA
1 AAATATTTAAAT
*
23629 AAAT-TTTAAAAC
1 AAATATTT-AAAT
23641 AAATTTATTTAAAT
1 AAA--TATTTAAAT
23655 AAATATTTAATAT
1 AAATATTTAA-AT
**
23668 TTATATTTAAAT
1 AAATATTTAAAT
23680 AA
1 AA
23682 TATAAATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
11 3 0.07
12 19 0.45
13 10 0.24
14 7 0.17
15 3 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATATTTAAAT
Found at i:27004 original size:89 final size:89
Alignment explanation
Indices: 26903--27080 Score: 311
Period size: 89 Copynumber: 2.0 Consensus size: 89
26893 CTGATCACAG
* * * *
26903 AAAAAGTTCGAAGAAGCTAAGGCTTTGAGAGAGAAAATAGTAATGGCATTAAGTAAATATGCATA
1 AAAAAGTACGAAGAAGCTAAGGCTTTCAGAGAGAAAATAGTAATGGCATTAAGGAAATATGCACA
26968 CCATATGGCTACCAACTTTACCAA
66 CCATATGGCTACCAACTTTACCAA
26992 AAAAAGTACGAAGAAGCTAAGGCTTTCAGAGAGAAAATAGTAATGGCATTAAGGAAATATGCACA
1 AAAAAGTACGAAGAAGCTAAGGCTTTCAGAGAGAAAATAGTAATGGCATTAAGGAAATATGCACA
*
27057 CCATATGGCTACCAAGTTTACCAA
66 CCATATGGCTACCAACTTTACCAA
27081 GCTTAGGATT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (89 bp):
AAAAAGTACGAAGAAGCTAAGGCTTTCAGAGAGAAAATAGTAATGGCATTAAGGAAATATGCACA
CCATATGGCTACCAACTTTACCAA
Found at i:30014 original size:75 final size:78
Alignment explanation
Indices: 29934--30087 Score: 278
Period size: 75 Copynumber: 2.0 Consensus size: 78
29924 GAAATTTGAA
29934 AAAATAAAATGTAGAATCAAGCAATGAATACCGATTTGAAAACATTGT-A-AG-AGAAGAAGAAG
1 AAAATAAAATGTAGAATCAAGCAATGAATACCGATTTGAAAACATTGTAAGAGAAGAAGAAGAAG
29996 AAGCAGTGTAGTT
66 AAGCAGTGTAGTT
*
30009 AAAATAAAATGTATAATCAAGCAATGAATACCGATTTGAAAACATTGTAAGAGAAGAAGAAGAAG
1 AAAATAAAATGTAGAATCAAGCAATGAATACCGATTTGAAAACATTGTAAGAGAAGAAGAAGAAG
30074 AAGCAGTGTAGTT
66 AAGCAGTGTAGTT
30087 A
1 A
30088 GCTAAGTCGG
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
75 47 0.63
76 1 0.01
77 2 0.03
78 25 0.33
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (78 bp):
AAAATAAAATGTAGAATCAAGCAATGAATACCGATTTGAAAACATTGTAAGAGAAGAAGAAGAAG
AAGCAGTGTAGTT
Found at i:35600 original size:3 final size:3
Alignment explanation
Indices: 35585--35619 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
35575 AGGTTTGCAA
* *
35585 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAA GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
35620 CCTGCGCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:36385 original size:21 final size:21
Alignment explanation
Indices: 36360--36414 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
36350 TTTAAAAAAT
36360 TATTTTATATTAATATT-TATA
1 TATTTTATATTAAT-TTATATA
36381 TATTTTTATAATTAATTTATATA
1 TA-TTTTAT-ATTAATTTATATA
* *
36404 AATTTTTTATT
1 TATTTTATATT
36415 TTAAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 5 0.17
22 13 0.45
23 11 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTATATTAATTTATATA
Found at i:36418 original size:23 final size:23
Alignment explanation
Indices: 36356--36418 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
36346 ATATTTTAAA
36356 AAATTATTTTATATTAATATTTAT
1 AAATT-TTTTATATTAATATTTAT
*
36380 ATA-TTTTTATAATTAAT-TTATAT
1 AAATTTTTTAT-ATTAATATT-TAT
*
36403 AAATTTTTTATTTTAA
1 AAATTTTTTATATTAA
36419 ATAATAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 8 0.24
23 16 0.48
24 9 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AAATTTTTTATATTAATATTTAT
Found at i:40164 original size:14 final size:14
Alignment explanation
Indices: 40145--40171 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40135 TTATCTGGTT
40145 ATCTCATCTTGTAA
1 ATCTCATCTTGTAA
40159 ATCTCATCTTGTA
1 ATCTCATCTTGTA
40172 GCCTTAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (14 bp):
ATCTCATCTTGTAA
Found at i:41935 original size:30 final size:29
Alignment explanation
Indices: 41893--41949 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
41883 TATTTAAGTA
41893 AAAAATAAAAAAAAAAATCA-AAATATAAG
1 AAAAATAAAAAAAAAAAT-ATAAATATAAG
*
41922 AAAAATAATAAAAAATAATATAAATATA
1 AAAAATAA-AAAAAAAAATATAAATATA
41950 TAAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (29 bp):
AAAAATAAAAAAAAAAATATAAATATAAG
Found at i:41946 original size:19 final size:19
Alignment explanation
Indices: 41891--41955 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
41881 AATATTTAAG
* *
41891 TAAAAAATAAAAAAAAAAA
1 TAAAAAATAATAAAAATAA
* *
41910 TCAAAATATAAGAAAAATAA
1 T-AAAAAATAATAAAAATAA
*
41930 TAAAAAATAATATAAATATA
1 TAAAAAATAATAAAAATA-A
41950 TAAAAA
1 TAAAAA
41956 TTATATAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 15 0.39
20 23 0.61
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (19 bp):
TAAAAAATAATAAAAATAA
Found at i:41951 original size:32 final size:32
Alignment explanation
Indices: 41881--41952 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
41871 AGAAGACTCG
* *
41881 AATATTTAAGTAAAAAATAAAAAAAAAAATCA
1 AATATATAAGAAAAAAATAAAAAAAAAAATCA
* *
41913 AA-ATATAAGAAAAATAATAAAAAATAATAT-A
1 AATATATAAGAAAAA-AATAAAAAAAAAAATCA
41944 AATATATAA
1 AATATATAA
41953 AAATTATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (32 bp):
AATATATAAGAAAAAAATAAAAAAAAAAATCA
Found at i:46635 original size:14 final size:14
Alignment explanation
Indices: 46618--46645 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46608 GCAATAGATT
46618 TATAATAATAATAA
1 TATAATAATAATAA
46632 TATAATAATAATAA
1 TATAATAATAATAA
46646 CTATTTGGAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TATAATAATAATAA
Found at i:49300 original size:6 final size:6
Alignment explanation
Indices: 49284--49338 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
49274 AAGGAAAATT
* * * * *
49284 TGTAGA TGTATA TGTATA --TATA TATATA TATATA TATATA TATATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
49330 TGTATA TGT
1 TGTATA TGT
49339 TTGAGACCTG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
4 4 0.09
6 41 0.91
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (6 bp):
TGTATA
Found at i:49305 original size:2 final size:2
Alignment explanation
Indices: 49292--49336 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
49282 TTTGTAGATG
* *
49292 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49334 TA T
1 TA T
49337 GTTTGAGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53893 original size:2 final size:2
Alignment explanation
Indices: 53888--53912 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53878 AATTTTTTTA
53888 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 A
53913 AGTGATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55837 original size:2 final size:2
Alignment explanation
Indices: 55818--55860 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
55808 CAACCCTCCA
* *
55818 AT AT AT AA AT AT AA 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 AT AT
55860 A
1 A
55861 CAAAAGAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:57349 original size:2 final size:2
Alignment explanation
Indices: 57333--57364 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
57323 AACGGATGCG
57333 TA TA -A TA TA -A 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
57365 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:57369 original size:2 final size:2
Alignment explanation
Indices: 57364--57390 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57354 ATATATATAT
57364 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
57391 TTGAAACAGA
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:58385 original size:18 final size:20
Alignment explanation
Indices: 58364--58400 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
58354 TTATTAATAT
58364 ATTAAATA-TAA-ATTTTTA
1 ATTAAATATTAATATTTTTA
*
58382 ATTAATTATTAATATTTTT
1 ATTAAATATTAATATTTTT
58401 CATACAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 3 0.19
20 6 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTAAATATTAATATTTTTA
Found at i:59436 original size:2 final size:2
Alignment explanation
Indices: 59424--59455 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
59414 ATTTAATTGA
*
59424 AT AT GT 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
59456 GTTAACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62382 original size:16 final size:15
Alignment explanation
Indices: 62349--62384 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
62339 CAAGATTTTA
62349 TTTTATTTTTTAATT
1 TTTTATTTTTTAATT
*
62364 TTTTATTTATTTGATT
1 TTTTATTT-TTTAATT
62380 TTTTA
1 TTTTA
62385 AACTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTATTTTTTAATT
Found at i:62507 original size:21 final size:21
Alignment explanation
Indices: 62481--62523 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
62471 GTGCACCTAA
62481 TTAAAAATAATTTACTA-TATT
1 TTAAAAATAATTTA-TATTATT
*
62502 TTAAAAATATTTTATATTATT
1 TTAAAAATAATTTATATTATT
62523 T
1 T
62524 GATGTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAAAATAATTTATATTATT
Found at i:62686 original size:4 final size:4
Alignment explanation
Indices: 62660--62708 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
62650 GAAAATAAGC
* * * *
62660 TATA AATA TACA TACA TACA TATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
62708 T
1 T
62709 GAAAAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (4 bp):
TATA
Found at i:62688 original size:6 final size:6
Alignment explanation
Indices: 62660--62708 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
62650 GAAAATAAGC
* * * *
62660 TATAAA TATACA TACATA CATATA TATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
62708 T
1 T
62709 GAAAAATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (6 bp):
TATATA
Found at i:66476 original size:16 final size:18
Alignment explanation
Indices: 66441--66496 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
66431 TAAAAATAAC
66441 TTATATTTTAATTATATT
1 TTATATTTTAATTATATT
*
66459 TTATATTTTAATTATTTT
1 TTATATTTTAATTATATT
* *
66477 ATTATTAATTTAATAATATT
1 -TTA-TATTTTAATTATATT
66497 AAAAATATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 17 0.53
19 3 0.09
20 12 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATATTTTAATTATATT
Found at i:66521 original size:24 final size:23
Alignment explanation
Indices: 66479--66528 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
66469 ATTATTTTAT
*
66479 TATTAATTTAATAATATTAAAAA
1 TATTAATTTAATAAAATTAAAAA
* *
66502 TATTATATTTATTAAAATTATAAA
1 TATTA-ATTTAATAAAATTAAAAA
66526 TAT
1 TAT
66529 AATAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATTTAATAAAATTAAAAA
Found at i:67880 original size:114 final size:114
Alignment explanation
Indices: 67675--67898 Score: 376
Period size: 114 Copynumber: 2.0 Consensus size: 114
67665 GGTTTCAAAA
* *
67675 GAACATAGCTGATGATGATGCCTTTCACCAAAGCTCAACCTCTTCTGGTAGGTAAGGATATGCAT
1 GAACATAGCTGATGATGATGCCTTTCACCAAAGCTCAACCTCTTCTGGTAGGTAAGGATAAGCAC
67740 ATCAAATATTTAAAATCCAATAAGTGTTTTCCTTATACTTTGATCTGTC
66 ATCAAATATTTAAAATCCAATAAGTGTTTTCCTTATACTTTGATCTGTC
* * * *
67789 GAACATAGCTGATGATGATGCCTTTCACCAAAGCTCTACCTCTTTTGGTAGGTAGGGGTAAGCAC
1 GAACATAGCTGATGATGATGCCTTTCACCAAAGCTCAACCTCTTCTGGTAGGTAAGGATAAGCAC
* *
67854 ATCAAATATTTAAAGTCCAATGAGTGTTTTCCTTATACTTTGATC
66 ATCAAATATTTAAAATCCAATAAGTGTTTTCCTTATACTTTGATC
67899 ACATAATAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (114 bp):
GAACATAGCTGATGATGATGCCTTTCACCAAAGCTCAACCTCTTCTGGTAGGTAAGGATAAGCAC
ATCAAATATTTAAAATCCAATAAGTGTTTTCCTTATACTTTGATCTGTC
Found at i:72921 original size:45 final size:45
Alignment explanation
Indices: 72861--72946 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
72851 CTTATTAACC
72861 AAAAAAAAAAACCCTACTTATCTGTGCAACCATTTCATATCCCAA
1 AAAAAAAAAAACCCTACTTATCTGTGCAACCATTTCATATCCCAA
72906 AAAAAAAAAAACCCTACTTATCTGTGCAACCATTTCATATC
1 AAAAAAAAAAACCCTACTTATCTGTGCAACCATTTCATATC
72947 AAGGACTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (45 bp):
AAAAAAAAAAACCCTACTTATCTGTGCAACCATTTCATATCCCAA
Found at i:75922 original size:2 final size:2
Alignment explanation
Indices: 75917--75946 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
75907 ATATACACAC
75917 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
75947 GTATGTGCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76965 original size:3 final size:3
Alignment explanation
Indices: 76957--76988 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
76947 CAAATCAATT
*
76957 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
76989 GCATGCATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:77390 original size:2 final size:2
Alignment explanation
Indices: 77383--77424 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
77373 TGGGAAAAGA
77383 AT AT AT AT AT 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 AT AT
77425 GATCAGATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77900 original size:2 final size:2
Alignment explanation
Indices: 77893--77923 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
77883 CAGCATTGTC
77893 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 T
77924 CTTCTCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78188 original size:2 final size:2
Alignment explanation
Indices: 78139--78173 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
78129 GATATTTGGC
78139 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 T
78174 GCATTTAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:79627 original size:12 final size:12
Alignment explanation
Indices: 79592--79629 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
79582 TATCAATTTT
79592 ATTTTGTAATTCAA
1 ATTTT-TAATT-AA
79606 ATTTTT-ATTAA
1 ATTTTTAATTAA
79617 ATTTTTAATTAA
1 ATTTTTAATTAA
79629 A
1 A
79630 ATAATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.35
12 9 0.39
13 1 0.04
14 5 0.22
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (12 bp):
ATTTTTAATTAA
Found at i:80681 original size:122 final size:122
Alignment explanation
Indices: 80391--80861 Score: 511
Period size: 121 Copynumber: 3.8 Consensus size: 122
80381 CCTGCTCGTG
* * * *
80391 GTATGCTCACAGTTAACCAACTTGTTTGGTGGCAATGACCGGCCTATTT-CAATTATAGATATGT
1 GTATACTCACAGATAACCAACTTGTTTGGTGGCAATGGCTGGCCTATTTCCAA-TATAGATATGT
* *
80455 TTTGAAGTCAAATAACTTGTATTACTAAAC-TATCATCAAGATAATGCAAAGATTTTA
65 TTTGAAGTCAAATAACTTGTATTACTAGACTTTTCATCAAGATAATGCAAAGATTTTA
* * * * * * *
80512 TTATACTCAGAGCTGACCAACTTGTTTGG-GGCCAATGGGTAGCCTATTTCCAATATAGAAATGT
1 GTATACTCACAGATAACCAACTTGTTTGGTGG-CAATGGCTGGCCTATTTCCAATATAGATATGT
* * * *
80576 TTTAAAGTCAAATAACTTGTATCACTAGACTTTTCATCAAGATAATACAAAGATTTCA
65 TTTGAAGTCAAATAACTTGTATTACTAGACTTTTCATCAAGATAATGCAAAGATTTTA
* * ** * *
80634 GTATAGTCACAGATAACCAAATTGTTTAATGGCAATTGCTGGCCTATTTCCATTATATATATATG
1 GTATACTCACAGATAACCAACTTGTTTGGTGGCAATGGCTGGCCTATTTCCA--ATATAGATATG
* * * *
80699 TTTTGAAGTCAAAGAACTTATATTATTTGACTTATATCATCAAAGATAATGCAAAGATTTTA
64 TTTTGAAGTCAAATAACTTGTATTACTAGACTT-T-TCATC-AAGATAATGCAAAGATTTTA
* * *
80761 GTATACTCACA-ATCAACCACCTTGTTTGGTGCCAATGGCTGGCCTATTTTCATCATTATAGGTA
1 GTATACTCACAGAT-AACCAACTTGTTTGGTGGCAATGGCTGGCCTA-TTTC--CAATATA-G-A
*
80825 TATGTTTTGAAGTC-AATAACTTGTATTACCAGACTTT
60 TATGTTTTGAAGTCAAATAACTTGTATTACTAGACTTT
80862 CGATTATAGT
Statistics
Matches: 284, Mismatches: 51, Indels: 23
0.79 0.14 0.06
Matches are distributed among these distances:
120 2 0.01
121 74 0.26
122 65 0.23
123 2 0.01
124 36 0.13
125 1 0.00
126 7 0.02
127 54 0.19
128 9 0.03
129 17 0.06
130 17 0.06
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (122 bp):
GTATACTCACAGATAACCAACTTGTTTGGTGGCAATGGCTGGCCTATTTCCAATATAGATATGTT
TTGAAGTCAAATAACTTGTATTACTAGACTTTTCATCAAGATAATGCAAAGATTTTA
Found at i:84978 original size:25 final size:25
Alignment explanation
Indices: 84924--84972 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
84914 TTGATTTACA
84924 TAAT-TATTTTTAAAATATTAAATT
1 TAATATATTTTTAAAATATTAAATT
*
84948 TAATATATTTTTAATAT-TTAAATT
1 TAATATATTTTTAAAATATTAAATT
84972 T
1 T
84973 TTATATCTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TAATATATTTTTAAAATATTAAATT
Found at i:85667 original size:12 final size:12
Alignment explanation
Indices: 85650--85675 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
85640 CAACTAATTA
85650 TTTTTTTTTCTT
1 TTTTTTTTTCTT
85662 TTTTTTTTTCTT
1 TTTTTTTTTCTT
85674 TT
1 TT
85676 GCTCCGAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:88782 original size:2 final size:2
Alignment explanation
Indices: 88775--88803 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
88765 CTTAAACAAA
88775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
88804 CAAGTTTTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89686 original size:12 final size:13
Alignment explanation
Indices: 89669--89724 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 13
89659 ATATTTTATT
89669 ATTTAAATT-AAA
1 ATTTAAATTAAAA
*
89681 ATTTAAGTTAAATAA
1 ATTTAAATT-AA-AA
*
89696 ATTAAAATT-AAA
1 ATTTAAATTAAAA
89708 ATTT-AATTAAAA
1 ATTTAAATTAAAA
89720 ATTTA
1 ATTTA
89725 TTTTTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
11 4 0.11
12 20 0.57
13 1 0.03
14 1 0.03
15 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
ATTTAAATTAAAA
Found at i:92425 original size:2 final size:2
Alignment explanation
Indices: 92418--92444 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92408 TTTATACATA
92418 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
92445 CACACACACA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95579 original size:3 final size:3
Alignment explanation
Indices: 95571--95596 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
95561 CCAAGAGGAT
95571 CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CT
95597 CCGTCAGATG
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:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
CTG
Found at i:100340 original size:13 final size:14
Alignment explanation
Indices: 100313--100343 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
100303 ATTAAATCAT
100313 TTAAATTTGATTTA
1 TTAAATTTGATTTA
100327 TTAAATTT-ATTTA
1 TTAAATTTGATTTA
100340 TTAA
1 TTAA
100344 TAAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
TTAAATTTGATTTA
Found at i:100369 original size:18 final size:16
Alignment explanation
Indices: 100348--100381 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
100338 TATTAATAAA
100348 AATTTAAATTATATTATT
1 AATTT-AATTA-ATTATT
100366 AATTTAATTAATTATT
1 AATTTAATTAATTATT
100382 GGAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTAATTAATTATT
Found at i:100791 original size:19 final size:18
Alignment explanation
Indices: 100748--100792 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
100738 CCTCAAATGG
100748 AATAAAATTTTAAGTTTA
1 AATAAAATTTTAAGTTTA
100766 AATTAAAATTTTTAA-TATTA
1 AA-TAAAA-TTTTAAGT-TTA
100786 AATAAAA
1 AATAAAA
100793 AACTCTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 11 0.46
20 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
AATAAAATTTTAAGTTTA
Found at i:100793 original size:20 final size:19
Alignment explanation
Indices: 100751--100793 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
100741 CAAATGGAAT
100751 AAAATTTTAAGTTTAAATTA
1 AAAATTTTAAGTTTAAA-TA
*
100771 AAATTTTTAA-TATTAAATA
1 AAAATTTTAAGT-TTAAATA
100790 AAAA
1 AAAA
100794 ACTCTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAAATTTTAAGTTTAAATA
Found at i:102403 original size:21 final size:21
Alignment explanation
Indices: 102379--102418 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
102369 AAAAGAAAAG
102379 AAAAAATAT-TTCTATTTTTCA
1 AAAAAATATCTT-TATTTTTCA
*
102400 AAAATATATCTTTATTTTT
1 AAAAAATATCTTTATTTTT
102419 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAAAATATCTTTATTTTTCA
Found at i:103264 original size:13 final size:12
Alignment explanation
Indices: 103248--103286 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
103238 TACATTGATA
103248 TTAAAAATAAATT
1 TTAAAAA-AAATT
103261 TTAAAAAAAATAT
1 TTAAAAAAAAT-T
*
103274 ATAAAAAAAATT
1 TTAAAAAAAATT
103286 T
1 T
103287 AATTCGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TTAAAAAAAATT
Found at i:103806 original size:18 final size:20
Alignment explanation
Indices: 103772--103813 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
103762 CAACTAATAC
103772 ATTTTATATTATTATTTAAT
1 ATTTTATATTATTATTTAAT
*
103792 ATTTTA-ATT-TTATTTATT
1 ATTTTATATTATTATTTAAT
103810 ATTT
1 ATTT
103814 ACTAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
19 3 0.14
20 6 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTATATTATTATTTAAT
Found at i:103824 original size:25 final size:26
Alignment explanation
Indices: 103750--103824 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 26
103740 TTTTTAAAAA
* ** *
103750 TTATATTTTTATCAACTAATA-CATT
1 TTATATTATTATTTACTAATATAATT
* * *
103775 TTATATTATTATTTAATATTTTAATT
1 TTATATTATTATTTACTAATATAATT
103801 TTAT-TTATTATTTACTAATATAAT
1 TTATATTATTATTTACTAATATAAT
103825 AAATTTTTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
25 32 0.82
26 7 0.18
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATATTATTATTTACTAATATAATT
Found at i:104063 original size:17 final size:18
Alignment explanation
Indices: 104043--104079 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
104033 TTATTAAGGC
104043 ATAAAATAT-ATTTTTTT
1 ATAAAATATAATTTTTTT
104060 ATAAAATATAATTTTTTT
1 ATAAAATATAATTTTTTT
104078 AT
1 AT
104080 TACGAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAAAATATAATTTTTTT
Done.