Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold782
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: 27412
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:760 original size:19 final size:21
Alignment explanation
Indices: 711--763 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
701 TATTTTTATT
711 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
732 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
752 -AAATTTTAATAT
1 TAAATTTTAATAT
764 TTTAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 11 0.38
22 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:1156 original size:13 final size:13
Alignment explanation
Indices: 1140--1170 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1130 AAATTATATT
1140 TATTTTAAAAATA
1 TATTTTAAAAATA
*
1153 TATTTTAAAATTA
1 TATTTTAAAAATA
1166 TATTT
1 TATTT
1171 CAGTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTTAAAAATA
Found at i:1398 original size:18 final size:18
Alignment explanation
Indices: 1377--1431 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1367 ATATTTTTTT
1377 ATATTATAAATATAATAA
1 ATATTATAAATATAATAA
*
1395 ATATTATAATTAT-ATAA
1 ATATTATAAATATAATAA
*
1412 ATCA-TATCAATAATAATAA
1 AT-ATTATAAAT-ATAATAA
1431 A
1 A
1432 CTTGAAATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 11 0.35
18 15 0.48
19 5 0.16
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATTATAAATATAATAA
Found at i:1908 original size:21 final size:22
Alignment explanation
Indices: 1884--1931 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1874 ATAAGAATTT
*
1884 TTAATATTTTA-ATTTAAGAGA
1 TTAATATTTTATATTTAAGAAA
* *
1905 TTAACATTTTATTTTTAAGAAA
1 TTAATATTTTATATTTAAGAAA
1927 TTAAT
1 TTAAT
1932 TTTATCACAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (22 bp):
TTAATATTTTATATTTAAGAAA
Found at i:2041 original size:19 final size:17
Alignment explanation
Indices: 2017--2082 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 17
2007 AGTTTTTATG
2017 ATTTAAATTATTTTATTTA
1 ATTTAAATTA--TTATTTA
2036 ATTTAAATTATTATTTA
1 ATTTAAATTATTATTTA
* *
2053 ATTAATAATAATATATTTAA
1 ATTTA-AATTAT-TATTT-A
2073 ATTT-AATTAT
1 ATTTAAATTAT
2083 AAAATAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 11 0.28
18 10 0.25
19 15 0.38
20 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAAATTATTATTTA
Found at i:2076 original size:25 final size:26
Alignment explanation
Indices: 2047--2106 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
2037 TTTAAATTAT
*
2047 TATTTAATTA-ATAATAATATATTTAA
1 TATTTAATTATAAAATAAT-TATTTAA
2073 -ATTTAATTATAAAATAATTATTTAA
1 TATTTAATTATAAAATAATTATTTAA
2098 TATTATAAT
1 TATT-TAAT
2107 ATTTATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 16 0.53
26 10 0.33
27 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TATTTAATTATAAAATAATTATTTAA
Found at i:2107 original size:19 final size:18
Alignment explanation
Indices: 2029--2077 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
2019 TTAAATTATT
*
2029 TTATTTAATTTA-AATTA
1 TTATTTAATTTATAATAA
*
2046 TTATTTAATTAATAATAA
1 TTATTTAATTTATAATAA
2064 TATATTTAAATTTA
1 T-TATTT-AATTTA
2078 ATTATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 11 0.42
18 5 0.19
19 5 0.19
20 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTTAATTTATAATAA
Found at i:2112 original size:19 final size:19
Alignment explanation
Indices: 2017--2113 Score: 53
Period size: 19 Copynumber: 5.2 Consensus size: 19
2007 AGTTTTTATG
**
2017 ATTTAA-ATTATTTTATTT
1 ATTTAATATTATAATATTT
2035 AATTTAA-ATTAT--TATTT
1 -ATTTAATATTATAATATTT
* *
2052 AATTAATAATA-ATATATTT
1 ATTTAATATTATA-ATATTT
* *
2071 AAATTTAAT-TATAAAATAATT
1 --ATTTAATAT-TATAATATTT
2092 ATTTAATATTATAATATTT
1 ATTTAATATTATAATATTT
2111 ATT
1 ATT
2114 AAACAGTTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
16 5 0.08
17 8 0.13
19 34 0.55
20 1 0.02
21 13 0.21
22 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAATATTATAATATTT
Found at i:2355 original size:14 final size:13
Alignment explanation
Indices: 2330--2354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2320 TTAAAATTAT
2330 AAAAATTATTTTC
1 AAAAATTATTTTC
2343 AAAAATTATTTT
1 AAAAATTATTTT
2355 TTGCAATCAT
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAAATTATTTTC
Found at i:3340 original size:26 final size:26
Alignment explanation
Indices: 3311--3369 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
3301 TATACATTAG
* * *
3311 ATATAAGTATCGAACAT-ATATATCAA
1 ATATAAATATCAAACATGA-ATATAAA
*
3337 ATATAAATATTAAACATGAATATAAA
1 ATATAAATATCAAACATGAATATAAA
3363 ATATAAA
1 ATATAAA
3370 AGAGGATGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 27 0.96
27 1 0.04
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.31
Consensus pattern (26 bp):
ATATAAATATCAAACATGAATATAAA
Found at i:3944 original size:15 final size:15
Alignment explanation
Indices: 3897--3945 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
3887 TTTAGCATTT
*
3897 AATTTATAATTAAATA
1 AATTT-TAATAAAATA
*
3913 AATTTTAAAATAAATA
1 AATTTTAATA-AAATA
3929 AATTTTAATAAAATA
1 AATTTTAATAAAATA
3944 AA
1 AA
3946 AATTTATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATTTTAATAAAATA
Found at i:3951 original size:16 final size:19
Alignment explanation
Indices: 3907--3945 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3897 AATTTATAAT
3907 TAAATAAA-TTT--TAAAA
1 TAAATAAATTTTAATAAAA
3923 TAAATAAATTTTAATAAAA
1 TAAATAAATTTTAATAAAA
3942 TAAA
1 TAAA
3946 AATTTATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 3 0.15
19 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATAAATTTTAATAAAA
Found at i:4689 original size:17 final size:19
Alignment explanation
Indices: 4667--4707 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
4657 ATTTAAACTC
*
4667 AAAATA-ATTAAAA-TTAA
1 AAAATATATAAAAATTTAA
4684 AAAATATATAAAAATTTAA
1 AAAATATATAAAAATTTAA
4703 AAAAT
1 AAAAT
4708 TCAAATTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 6 0.29
19 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATATATAAAAATTTAA
Found at i:4938 original size:2 final size:2
Alignment explanation
Indices: 4931--4970 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
4921 AAAATCTATC
*
4931 TA TA TA TA TA AA 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
4971 AACAAAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9102 original size:24 final size:25
Alignment explanation
Indices: 9075--9146 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 25
9065 ATAATTCATA
9075 TATTCATATA-AAATTTATAAAATT
1 TATTCATATATAAATTTATAAAATT
* * *
9099 TATTGATATATATATTTTTAAAA-T
1 TATTCATATATAAATTTATAAAATT
* *
9123 TA---ATATATAAATTAATACAATT
1 TATTCATATATAAATTTATAAAATT
9145 TA
1 TA
9147 AATTTAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
21 14 0.36
22 3 0.08
24 12 0.31
25 10 0.26
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (25 bp):
TATTCATATATAAATTTATAAAATT
Found at i:13282 original size:27 final size:27
Alignment explanation
Indices: 13226--13284 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
13216 TTGATAGATA
* *
13226 AATAAATTTCTTTTCTATTTTACTTTT
1 AATAAATTTCTTTTCTATTTTAATTCT
* *
13253 AATAAATTT-TTTTTTTTTTTAATTGCT
1 AATAAATTTCTTTTCTATTTTAATT-CT
13280 AATAA
1 AATAA
13285 GGATTAAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.61
Consensus pattern (27 bp):
AATAAATTTCTTTTCTATTTTAATTCT
Found at i:14600 original size:37 final size:35
Alignment explanation
Indices: 14508--14609 Score: 102
Period size: 37 Copynumber: 2.9 Consensus size: 35
14498 TATCAGTTTA
* * *
14508 TTTTTTA-TTAAAAATAATATTAAA-AATTATTAT
1 TTTTTTATTTAAAAATAATTTTAAATAAATATAAT
*
14541 TTTTTATATTTATAAATAAATTTTAAATAAATATAAT
1 TTTTT-TATTTAAAAAT-AATTTTAAATAAATATAAT
14578 TTTTATTATTTAAATAATAA-TTTAAATTAAAT
1 TTTT-TTATTTAAA-AATAATTTTAAA-TAAAT
14610 CAATTAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
33 5 0.09
34 2 0.04
35 7 0.12
36 14 0.25
37 25 0.44
38 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (35 bp):
TTTTTTATTTAAAAATAATTTTAAATAAATATAAT
Found at i:14606 original size:21 final size:20
Alignment explanation
Indices: 14568--14606 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
14558 AAATTTTAAA
**
14568 TAAATATAATTTTTATTATT
1 TAAATATAATTTAAATTATT
14588 TAAATAATAATTTAAATTA
1 TAAAT-ATAATTTAAATTA
14607 AATCAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAATATAATTTAAATTATT
Found at i:15291 original size:2 final size:2
Alignment explanation
Indices: 15284--15314 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15274 TTCTCTTTAC
15284 AT 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 AT A
15315 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16648 original size:30 final size:30
Alignment explanation
Indices: 16576--16649 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
16566 TAGGCTTTTT
* * *
16576 ATTTTTTAAA-ATATTTATATTTAAAAATT
1 ATTTTTTAAATATATTTAAATATAAAAATA
* *
16605 A-TATTTAATATATATTTAAATATAAATATA
1 ATTTTTTAA-ATATATTTAAATATAAAAATA
16635 ATTTTTTAAATATAT
1 ATTTTTTAAATATAT
16650 AAAAATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
28 6 0.17
29 2 0.06
30 22 0.61
31 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
ATTTTTTAAATATATTTAAATATAAAAATA
Found at i:16658 original size:19 final size:20
Alignment explanation
Indices: 16619--16663 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
16609 TTAATATATA
16619 TTTAAATATAAATATAATTT
1 TTTAAATATAAATATAATTT
16639 TTTAAATATATAA-A-AATTT
1 TTTAAATATA-AATATAATTT
16658 TTTAAA
1 TTTAAA
16664 AAACAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.46
20 11 0.46
21 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAATATAAATATAATTT
Found at i:20166 original size:22 final size:20
Alignment explanation
Indices: 20129--20178 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
20119 ATTTTTTTAA
20129 AAATTTAATTATAAAATATAT
1 AAATTTAATTATAAAATA-AT
20150 AAATATTAATT-TAAAAATAAT
1 AAAT-TTAATTAT-AAAATAAT
*
20171 AATTTTAA
1 AAATTTAA
20179 ATAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.15
21 10 0.38
22 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATTTAATTATAAAATAAT
Found at i:20172 original size:21 final size:21
Alignment explanation
Indices: 20129--20187 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
20119 ATTTTTTTAA
20129 AAATTTAATTATAAAATATAT
1 AAATTTAATTATAAAATATAT
20150 AAATATTAATT-TAAAA-ATAAT
1 AAAT-TTAATTATAAAATAT-AT
* *
20171 AATTTTAAATAATAAAA
1 AAATTT-AATTATAAAA
20188 ATAAATCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 17 0.53
22 11 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTTAATTATAAAATATAT
Found at i:20182 original size:13 final size:14
Alignment explanation
Indices: 20147--20185 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
20137 TTATAAAATA
*
20147 TATAAATATTAATT
1 TATAAATAATAATT
*
20161 TAAAAATAATAATT
1 TATAAATAATAATT
20175 T-TAAATAATAA
1 TATAAATAATAA
20186 AAATAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATAAATAATAATT
Found at i:20567 original size:15 final size:15
Alignment explanation
Indices: 20541--20578 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
20531 ATTATTATTG
*
20541 TAATTATTTTTAATCA
1 TAATTATATTTAAT-A
20557 T-ATTATATTTAATA
1 TAATTATATTTAATA
20571 TAATTATA
1 TAATTATA
20579 AATAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 17 0.85
16 1 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATATTTAATA
Found at i:20592 original size:26 final size:24
Alignment explanation
Indices: 20563--20626 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
20553 ATCATATTAT
20563 ATTTAATATAATTATAAATAAAATAA
1 ATTTAATATAATTAT--ATAAAATAA
* *
20589 ATTTTATGATAATTATTTAAAATAA
1 ATTTAAT-ATAATTATATAAAATAA
20614 ATTTTAATTATAA
1 A-TTTAA-TATAA
20627 AAAATTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 9 0.28
26 14 0.44
27 9 0.28
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTTAATATAATTATATAAAATAA
Found at i:20634 original size:26 final size:25
Alignment explanation
Indices: 20581--20637 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
20571 TAATTATAAA
** *
20581 TAAAATAAATTTTATGATAATTATT
1 TAAAATAAATTTTATGATAAAAAAT
*
20606 TAAAATAAATTTTAATTATAAAAAAT
1 TAAAATAAATTTT-ATGATAAAAAAT
20632 TAAAAT
1 TAAAAT
20638 CGTAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TAAAATAAATTTTATGATAAAAAAT
Found at i:20849 original size:17 final size:16
Alignment explanation
Indices: 20818--20851 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20808 ATAAATCAAT
*
20818 TAAATCAAATTTTAAA
1 TAAATAAAATTTTAAA
*
20834 TAAATAAAATTTTTAA
1 TAAATAAAATTTTAAA
20850 TA
1 TA
20852 TTCAAGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATAAAATTTTAAA
Found at i:21333 original size:2 final size:2
Alignment explanation
Indices: 21326--21350 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21316 TGCCTTGACA
21326 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
21351 ATGAAGGTAA
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:21649 original size:17 final size:17
Alignment explanation
Indices: 21627--21659 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21617 CGTATATTCG
21627 TATTGTG-TATTATTTTA
1 TATTGTGCT-TTATTTTA
21644 TATTGTGCTTTATTTT
1 TATTGTGCTTTATTTT
21660 TCTATATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.18, C:0.03, G:0.12, T:0.67
Consensus pattern (17 bp):
TATTGTGCTTTATTTTA
Found at i:22034 original size:22 final size:22
Alignment explanation
Indices: 21982--22034 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
21972 TTTTTTATGT
*
21982 TTTAT-TTATATTGTGTCTCAA
1 TTTATATTATATTGTGTATCAA
* *
22003 TTTATTTTATATTTTGTAT-AA
1 TTTATATTATATTGTGTATCAA
22024 TTTGATATTAT
1 TTT-ATATTAT
22035 GAATAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.62
Consensus pattern (22 bp):
TTTATATTATATTGTGTATCAA
Found at i:22370 original size:33 final size:30
Alignment explanation
Indices: 22322--22383 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 30
22312 TCATATCTCA
22322 ATTTACTTTTTATTTTATATATTTATTATAATG
1 ATTTACTTTTTATTTTA-A-ATTTATT-TAATG
22355 ATTTA-TTTTTAATTTTAAATTTATTTAAT
1 ATTTACTTTTT-ATTTTAAATTTATTTAAT
22384 TAAGACTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 4 0.14
31 7 0.25
32 6 0.21
33 11 0.39
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (30 bp):
ATTTACTTTTTATTTTAAATTTATTTAATG
Found at i:22762 original size:15 final size:16
Alignment explanation
Indices: 22725--22782 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 16
22715 AATTCACTCA
*
22725 AATTT-AAATTTAATT
1 AATTTAAAAATTAATT
*
22740 AA-TAAAAAATTAA-T
1 AATTTAAAAATTAATT
*
22754 -ATTTTAAAATTAATT
1 AATTTAAAAATTAATT
*
22769 AATTTAAAATTTAA
1 AATTTAAAAATTAA
22783 ATAAATCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.03
14 11 0.33
15 10 0.30
16 11 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAAAAATTAATT
Found at i:22781 original size:22 final size:22
Alignment explanation
Indices: 22756--22823 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
22746 AAATTAATAT
22756 TTTAAAATTAATTAATTTAAAA
1 TTTAAAATTAATTAATTTAAAA
*
22778 TTT-AAATAAATCTAATTTAAAA
1 TTTAAAATTAAT-TAATTTAAAA
* *
22800 TAAATAAAA-TAATTAATTAAAAA
1 T--TTAAAATTAATTAATTTAAAA
22823 T
1 T
22824 AATTTAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.18
22 14 0.37
23 10 0.26
24 4 0.11
25 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATTAATTAATTTAAAA
Found at i:22782 original size:16 final size:15
Alignment explanation
Indices: 22725--22894 Score: 90
Period size: 15 Copynumber: 11.6 Consensus size: 15
22715 AATTCACTCA
22725 AATTTAAATTTAATT
1 AATTTAAATTTAATT
** *
22740 AATAAAAAATTAA-T
1 AATTTAAATTTAATT
* *
22754 ATTTTAAAATTAATT
1 AATTTAAATTTAATT
*
22769 AATTTAAAATTTAAATA
1 AATTT-AAATTT-AATT
* *
22786 AATCT-AATTTAAAAT
1 AATTTAAATTT-AATT
* *
22801 AA-ATAAA-ATAATT
1 AATTTAAATTTAATT
22814 AA-TTAAA---AA-T
1 AATTTAAATTTAATT
*
22824 AATTTAAATTTAAAAT
1 AATTTAAATTT-AATT
22840 AA-TTAAATTTAATT
1 AATTTAAATTTAATT
*
22854 AATTTAAATTTAAAAT
1 AATTTAAATTT-AATT
* *
22870 AATTAAAATTTGAAAT
1 AATTTAAATTT-AATT
22886 AATTTAAAT
1 AATTTAAAT
22895 CTGAATATTA
Statistics
Matches: 122, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
10 3 0.02
11 7 0.06
13 9 0.07
14 18 0.15
15 45 0.37
16 33 0.27
17 7 0.06
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (15 bp):
AATTTAAATTTAATT
Found at i:22899 original size:16 final size:16
Alignment explanation
Indices: 22804--23014 Score: 152
Period size: 16 Copynumber: 13.5 Consensus size: 16
22794 TTAAAATAAA
22804 TAAAATAA-TT-AATT
1 TAAAATAATTTAAATT
*
22818 AAAAATAATTTAAATT
1 TAAAATAATTTAAATT
22834 TAAAATAA-TTAAATT
1 TAAAATAATTTAAATT
*
22849 T-AATTAATTTAAATT
1 TAAAATAATTTAAATT
*
22864 TAAAATAATTAAAATT
1 TAAAATAATTTAAATT
* *
22880 TGAAATAATTTAAATC
1 TAAAATAATTTAAATT
*
22896 T-GAAT-A-TT-AATT
1 TAAAATAATTTAAATT
** * * *
22908 TTGATTAACTCAAATT
1 TAAAATAATTTAAATT
* *
22924 AAAAAATAATTTAAA-A
1 -TAAAATAATTTAAATT
*
22940 TAAAATAATTTAAATA
1 TAAAATAATTTAAATT
* * **
22956 TAAAATTATTCAAAAG
1 TAAAATAATTTAAATT
*
22972 TAAAATAATTTAATTT
1 TAAAATAATTTAAATT
22988 TAAAAATAATTTAAAATTT
1 T-AAAATAATTT-AAA-TT
23007 TAAAATAA
1 TAAAATAA
23015 AATAAAATAA
Statistics
Matches: 154, Mismatches: 30, Indels: 22
0.75 0.15 0.11
Matches are distributed among these distances:
12 4 0.03
13 5 0.03
14 14 0.09
15 35 0.23
16 66 0.43
17 18 0.12
18 9 0.06
19 3 0.02
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAAATAATTTAAATT
Found at i:22905 original size:60 final size:63
Alignment explanation
Indices: 22803--22961 Score: 170
Period size: 60 Copynumber: 2.6 Consensus size: 63
22793 TTTAAAATAA
* * * *
22803 ATAAAATAATT--AATTAAAAATAATTTAAATTTAAAATAATTAAATTTAATTAATTTAAATT
1 ATAAAATAATTAAAATTTAAAATAATTTAAATCTAAAATAATTAAATTTAATTAACTCAAATT
* * * *
22864 -TAAAATAATTAAAATTTGAAATAATTTAAATCT-GAAT-ATTAATTTTGATTAACTCAAATT
1 ATAAAATAATTAAAATTTAAAATAATTTAAATCTAAAATAATTAAATTTAATTAACTCAAATT
* *
22924 AAAAAATAATTTAAAA--TAAAATAATTTAAATATAAAAT
1 ATAAAATAA-TTAAAATTTAAAATAATTTAAATCTAAAAT
22962 TATTCAAAAG
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
60 44 0.54
61 13 0.16
62 24 0.30
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (63 bp):
ATAAAATAATTAAAATTTAAAATAATTTAAATCTAAAATAATTAAATTTAATTAACTCAAATT
Found at i:23007 original size:19 final size:17
Alignment explanation
Indices: 22973--23011 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
22963 ATTCAAAAGT
22973 AAAATAATTTAATTTTA
1 AAAATAATTTAATTTTA
22990 AAAATAATTTAAAATTTTA
1 AAAATAATTT--AATTTTA
23009 AAA
1 AAA
23012 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.50
19 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAATTTAATTTTA
Found at i:23557 original size:16 final size:16
Alignment explanation
Indices: 23536--23587 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
23526 TTTATTGTAT
23536 ATTTTAATTTTATTAA
1 ATTTTAATTTTATTAA
*
23552 ATTTT-A--TTATTTA
1 ATTTTAATTTTATTAA
*
23565 TTTTTAATTTTATTAA
1 ATTTTAATTTTATTAA
*
23581 TTTTTAA
1 ATTTTAA
23588 ATAAAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 10 0.33
14 1 0.03
15 1 0.03
16 18 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTAATTTTATTAA
Found at i:23582 original size:28 final size:31
Alignment explanation
Indices: 23527--23586 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
23517 ATATTTGATT
23527 TTATTGTATATTTTAATTTTATTAAATTTTA
1 TTATTGTATATTTTAATTTTATTAAATTTTA
*
23558 TTATT-TAT-TTTTAATTTTATTAATTTTTA
1 TTATTGTATATTTTAATTTTATTAAATTTTA
23587 AATAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 20 0.71
30 3 0.11
31 5 0.18
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (31 bp):
TTATTGTATATTTTAATTTTATTAAATTTTA
Done.