Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3712.1
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: 108462
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.31
Warning! 2217 characters in sequence are not A, C, G, or T
Found at i:4404 original size:28 final size:29
Alignment explanation
Indices: 4348--4403 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
4338 GTTATTTAAA
**
4348 TTTATTAATAAAAATATTAATTTGAAAAT
1 TTTATTAATAAAAATAAGAATTTGAAAAT
4377 TTTATTAATAAAAA-AAGAAGTTTGAAA
1 TTTATTAATAAAAATAAGAA-TTTGAAA
4404 TGGTAATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
TTTATTAATAAAAATAAGAATTTGAAAAT
Found at i:5518 original size:46 final size:46
Alignment explanation
Indices: 5447--5542 Score: 165
Period size: 46 Copynumber: 2.1 Consensus size: 46
5437 TTTCTTGCTC
*
5447 TAACACTATCCCTATATATACATTTCCCGTTTCCGGGAATCCGAGT
1 TAACACTATCCCTATATATACATTTCCCATTTCCGGGAATCCGAGT
* *
5493 TAACACTATCCCTATATTTATATTTCCCATTTCCGGGAATCCGAGT
1 TAACACTATCCCTATATATACATTTCCCATTTCCGGGAATCCGAGT
5539 TAAC
1 TAAC
5543 TTTTTCTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.34
Consensus pattern (46 bp):
TAACACTATCCCTATATATACATTTCCCATTTCCGGGAATCCGAGT
Found at i:8194 original size:4 final size:4
Alignment explanation
Indices: 8187--8215 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
8177 CACCCTTTCT
8187 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
8216 AACTACAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:10348 original size:24 final size:24
Alignment explanation
Indices: 10315--10363 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
10305 GATTGAATTG
10315 TTGTTATCTAAAATTAGGTCTAAT
1 TTGTTATCTAAAATTAGGTCTAAT
*
10339 TTGTTCTCTAAAATTAGGTCTAAT
1 TTGTTATCTAAAATTAGGTCTAAT
10363 T
1 T
10364 CAATTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (24 bp):
TTGTTATCTAAAATTAGGTCTAAT
Found at i:10374 original size:24 final size:24
Alignment explanation
Indices: 10318--10374 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
10308 TGAATTGTTG
**
10318 TTATCTAAAATTAGGTCTAATTTG
1 TTATCTAAAATTAGGTCTAATTAA
*
10342 TTCTCTAAAATTAGGTCTAATTCAA
1 TTATCTAAAATTAGGTCTAATT-AA
10367 TTAT-TAAA
1 TTATCTAAA
10375 TTACTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (24 bp):
TTATCTAAAATTAGGTCTAATTAA
Found at i:10798 original size:21 final size:22
Alignment explanation
Indices: 10757--10813 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
10747 AAACCCAACT
*
10757 AACCTAGCCCAATACCCTAAACC
1 AACCTAGCCCAATA-CCTAAAAC
10780 AACCTAGCCCAAT-CCTAAAAC
1 AACCTAGCCCAATACCTAAAAC
*
10801 TACCTGAGCCCAA
1 AACCT-AGCCCAA
10814 ATTTTAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 11 0.35
22 7 0.23
23 13 0.42
ACGTcount: A:0.39, C:0.40, G:0.07, T:0.14
Consensus pattern (22 bp):
AACCTAGCCCAATACCTAAAAC
Found at i:17657 original size:24 final size:24
Alignment explanation
Indices: 17629--17703 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
17619 GGACACCAGT
17629 GCCAACACCACCACCAGCTCCACC
1 GCCAACACCACCACCAGCTCCACC
* *
17653 GCCAACAGCACCTCC-GACTCCACC
1 GCCAACACCACCACCAG-CTCCACC
* * *
17677 TCCAACTCCACCACCAGCACCACC
1 GCCAACACCACCACCAGCTCCACC
17701 GCC
1 GCC
17704 GCCACCCAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.02
24 39 0.95
25 1 0.02
ACGTcount: A:0.27, C:0.57, G:0.09, T:0.07
Consensus pattern (24 bp):
GCCAACACCACCACCAGCTCCACC
Found at i:19255 original size:160 final size:162
Alignment explanation
Indices: 19046--19348 Score: 423
Period size: 160 Copynumber: 1.9 Consensus size: 162
19036 CATTTAAGTT
* * * * *
19046 ATAAATAAGTGACAATTTCTTCACTATTTTCATTAAAATGATAATTTTAATCCCGCATTGACTAG
1 ATAAATAAATGACAAATTCTTCACTATTTTCATTAAAAAGATAATTTTAATCCCACAATGACTAG
* * *
19111 AGAATATTCTCATAAATCATTTTTTCATAATTTTCATTAAAAAGTT-AATTCGAA-TCTATATTG
66 AGAATACTCTCATAAATCAGTTTTTCATAATTTTCATTAAAAAGTTAAATT-GAATTCCATATTG
19174 ACTAGAAAACACTCTAATATCTCACTTTTTCTA
130 ACTAGAAAACACTCTAATATCTCACTTTTTCTA
* * *
19207 ATAAATAAATGACAAATT-TTCACTATTTTTATTAAAAAGTTTATTTTAATCCCACAATGACTAG
1 ATAAATAAATGACAAATTCTTCACTATTTTCATTAAAAAGATAATTTTAATCCCACAATGACTAG
** * * *
19271 AGAATACTCTCATAGCTTAGTTTTTCATTATTTTCATTAAAAAGTTAAATTTAATTCCATATTGA
66 AGAATACTCTCATAAATCAGTTTTTCATAATTTTCATTAAAAAGTTAAATTGAATTCCATATTGA
*
19336 CTAGAAAAGACTC
131 CTAGAAAACACTC
19349 CTATAACTCA
Statistics
Matches: 123, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
160 82 0.67
161 41 0.33
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (162 bp):
ATAAATAAATGACAAATTCTTCACTATTTTCATTAAAAAGATAATTTTAATCCCACAATGACTAG
AGAATACTCTCATAAATCAGTTTTTCATAATTTTCATTAAAAAGTTAAATTGAATTCCATATTGA
CTAGAAAACACTCTAATATCTCACTTTTTCTA
Found at i:19372 original size:69 final size:69
Alignment explanation
Indices: 19227--19394 Score: 178
Period size: 69 Copynumber: 2.4 Consensus size: 69
19217 GACAAATTTT
* * * * * *
19227 CACTATTTTTATTAAAAAGTTTATTTTAATCCCACAATGACTAGAGAATACTCTCATAGCTTAGT
1 CACTATTTTTATTAAAAAGTTAATTTTAATCCCACAATGACTAGAAAAGACTCTCATAACTCAAT
* *
19292 TTTT
66 TCTG
* * * * * *
19296 CATTATTTTCATTAAAAAGTTAAATTTAATTCCATATTGACTAGAAAAGACTC-CTATAACTCAA
1 CACTATTTTTATTAAAAAGTTAATTTTAATCCCACAATGACTAGAAAAGACTCTC-ATAACTCAA
19360 TTCTG
65 TTCTG
*
19365 CACTATTTTTATTAAACA-TTAATTTTAATC
1 CACTATTTTTATTAAAAAGTTAATTTTAATC
19395 TTTTAAAAAT
Statistics
Matches: 79, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
68 11 0.14
69 68 0.86
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (69 bp):
CACTATTTTTATTAAAAAGTTAATTTTAATCCCACAATGACTAGAAAAGACTCTCATAACTCAAT
TCTG
Found at i:20382 original size:16 final size:16
Alignment explanation
Indices: 20361--20392 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20351 TTTGTAACGC
*
20361 CCCAAAAATTCTGAAA
1 CCCAAAAATCCTGAAA
20377 CCCAAAAATCCTGAAA
1 CCCAAAAATCCTGAAA
20393 TCCTGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (16 bp):
CCCAAAAATCCTGAAA
Found at i:21950 original size:29 final size:28
Alignment explanation
Indices: 21907--21980 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
21897 TATGATTATG
*
21907 AATGTGAATGGGCCTAACGGGACATATA
1 AATGTGATTGGGCCTAACGGGACATATA
* * *
21935 AATGTGATTTGGGCCTAATGGGCCATATG
1 AATGTGA-TTGGGCCTAACGGGACATATA
*
21964 AATATGATTGGGCCTAA
1 AATGTGATTGGGCCTAA
21981 TGGGCCAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.43
29 23 0.57
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (28 bp):
AATGTGATTGGGCCTAACGGGACATATA
Found at i:21981 original size:28 final size:28
Alignment explanation
Indices: 21903--21987 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
21893 TGAGTATGAT
* * *
21903 TATGAATGTGAATGGGCCTAACGGGACA
1 TATGAATGTGATTGGGCCTAATGGGCCA
*
21931 TATAAATGTGATTTGGGCCTAATGGGCCA
1 TATGAATGTGA-TTGGGCCTAATGGGCCA
*
21960 TATGAATATGATTGGGCCTAATGGGCCA
1 TATGAATGTGATTGGGCCTAATGGGCCA
21988 AATACAGGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
28 27 0.54
29 23 0.46
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTAATGGGCCA
Found at i:25586 original size:21 final size:19
Alignment explanation
Indices: 25544--25586 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
25534 TTTGTTTTTC
* *
25544 TTTCTTTTCTTCCTGCCAA
1 TTTCTATTCTTCCTACCAA
25563 TTTCTATTCTTCTCTACACAA
1 TTTCTATTCTTC-CTAC-CAA
25584 TTT
1 TTT
25587 TCTTCGGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 3 0.15
21 6 0.30
ACGTcount: A:0.16, C:0.28, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTCTATTCTTCCTACCAA
Found at i:26219 original size:16 final size:16
Alignment explanation
Indices: 26200--26232 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
26190 CGGTAAAACC
*
26200 CGAAATGCCGAAAAGT
1 CGAAATGCCAAAAAGT
26216 CGAAATGCCAAAAAGT
1 CGAAATGCCAAAAAGT
26232 C
1 C
26233 AAACGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (16 bp):
CGAAATGCCAAAAAGT
Found at i:28517 original size:48 final size:48
Alignment explanation
Indices: 28464--28589 Score: 189
Period size: 48 Copynumber: 2.6 Consensus size: 48
28454 CCGAACTGCT
*
28464 AATATCATGGCCCGAAGCCAAATCAATGAAGCTCATACCCGAAGTACC
1 AATATCATGGCCCGAAGCCAAATCAATGAAGCTCACACCCGAAGTACC
* * ** *
28512 GATATCATGGCCCGAAGCCAAATCAATAAAGCTTGCACCCGAAGTGCC
1 AATATCATGGCCCGAAGCCAAATCAATGAAGCTCACACCCGAAGTACC
*
28560 AATATCATGTCCCGAAGCCAAATCAATGAA
1 AATATCATGGCCCGAAGCCAAATCAATGAA
28590 TTCCTTAATG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.17
Consensus pattern (48 bp):
AATATCATGGCCCGAAGCCAAATCAATGAAGCTCACACCCGAAGTACC
Found at i:28837 original size:59 final size:58
Alignment explanation
Indices: 28753--28869 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 58
28743 TATACGAACT
* ** *
28753 TACCTCAGACGTAGAAACAAAGACACGGGTCAACTAATTTGAGACTTTGTTCTTTCCC
1 TACCTCAGACATAGAAACAAAGACACGGGTCAACTAATCCGAAACTTTGTTCTTTCCC
* * *
28811 TNACCTCGGACATAGAAACGACGACACGGGTCAACTAATCCGAAACTTTGTTCTTTCCC
1 T-ACCTCAGACATAGAAACAAAGACACGGGTCAACTAATCCGAAACTTTGTTCTTTCCC
28870 CGATCTAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 1 0.02
59 50 0.98
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (58 bp):
TACCTCAGACATAGAAACAAAGACACGGGTCAACTAATCCGAAACTTTGTTCTTTCCC
Found at i:35005 original size:16 final size:16
Alignment explanation
Indices: 34980--35018 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
34970 ATGTATCGGC
*
34980 AAAAGCCGAAATGCCA
1 AAAAGTCGAAATGCCA
34996 AAAAGTCGAAATGCCA
1 AAAAGTCGAAATGCCA
35012 AAAAGTC
1 AAAAGTC
35019 AAAAGTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.21, G:0.18, T:0.10
Consensus pattern (16 bp):
AAAAGTCGAAATGCCA
Found at i:35343 original size:28 final size:29
Alignment explanation
Indices: 35233--35347 Score: 146
Period size: 29 Copynumber: 4.0 Consensus size: 29
35223 GTGAGCATGA
* *
35233 ATATGAATGTGA-CTGGGCCTAACGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
35261 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
35290 ATAT-ACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGATTTGGGCCTAATGGGCC
* *
35319 ATATGAATATGA-TTGGGCTTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
35347 A
1 A
35348 AATACCGGTA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
28 28 0.36
29 48 0.62
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:48537 original size:27 final size:27
Alignment explanation
Indices: 48507--48711 Score: 189
Period size: 27 Copynumber: 7.6 Consensus size: 27
48497 ATATCGAGTC
* *
48507 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
48534 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
48561 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
48589 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
48616 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * **
48643 CGCACACTTAGTGCAACATATTCATTT
1 CGCACACTTAGTGCTACATAATCAACT
* *
48670 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
48697 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
48712 GTACAATTTA
Statistics
Matches: 154, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
27 129 0.84
28 25 0.16
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:48672 original size:54 final size:54
Alignment explanation
Indices: 48507--48710 Score: 225
Period size: 54 Copynumber: 3.8 Consensus size: 54
48497 ATATCGAGTC
* * * *
48507 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAGTCAACTCGCACACTTAGTGCCACATAATCAATT
* **
48561 CGCACACTTAGTGC-TACATAGTCAGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAGTCA-ACTCGCACACTTAGTGCCACATAATCAATT
* ** * * *
48616 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATATTCATTT
1 CGCACACTTAGTGCATCATAGTCAACTCGCACACTTAGTGCCACATAATCAATT
*
48670 CGCACACTTAGTGCAACATAGTCGAA-TCGCACACTTAGTGC
1 CGCACACTTAGTGCATCATAGTC-AACTCGCACACTTAGTGC
48711 TGTACAATTT
Statistics
Matches: 127, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
54 78 0.61
55 47 0.37
56 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAGTCAACTCGCACACTTAGTGCCACATAATCAATT
Found at i:52118 original size:48 final size:47
Alignment explanation
Indices: 52047--52218 Score: 166
Period size: 48 Copynumber: 3.6 Consensus size: 47
52037 AAGTTCTCAA
* ** *
52047 ATCATGGCCTGAAGCCAGCTCAATGTATCTCGCACCCAAAGTGCTAAT
1 ATCATGGCCCGAAGCCAAATCAATGAATCTCGCACCCAAAGTGC-AAT
** * *
52095 ATCATGGCCTAAAGCCAAATCAATAAAGT-TCGCACCCGAAGTGCAGAT
1 ATCATGGCCCGAAGCCAAATCAATGAA-TCTCGCACCCAAAGTGCA-AT
* * * * *
52143 ATCATGGCCCGAAGCCAAATTAATGAAGCTCACACTCAATGTGCCAAT
1 ATCATGGCCCGAAGCCAAATCAATGAATCTCGCACCCAAAGTG-CAAT
* *
52191 ATCATAGCCCGAAGCTAAATCAATGAAT
1 ATCATGGCCCGAAGCCAAATCAATGAAT
52219 TCCCTAATGA
Statistics
Matches: 101, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
47 1 0.01
48 97 0.96
49 3 0.03
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.21
Consensus pattern (47 bp):
ATCATGGCCCGAAGCCAAATCAATGAATCTCGCACCCAAAGTGCAAT
Found at i:58010 original size:68 final size:67
Alignment explanation
Indices: 57890--58059 Score: 196
Period size: 68 Copynumber: 2.5 Consensus size: 67
57880 GACAATTTCT
* * *
57890 TCACTATTTTCATTAAAATTTTAATTTTAATCCCACATTGACCAGAGAATACTCCCATAACTCAC
1 TCACTA-TTTCATTAAAA-ATTAATTTTAATCCCACATTAACCAGAGAATACTCCAATAACTCAC
57955 TCCA
64 TCCA
** * * * *
57959 TCACTATTTCATTAAAAGATTAATTTTAATTTCATATTAACTAGAGGATACTCCAATAGCTCACT
1 TCACTATTTCATTAAAA-ATTAATTTTAATCCCACATTAACCAGAGAATACTCCAATAACTCACT
* *
58024 TCT
65 CCA
*
58027 TCACTGTTTTCATTAAAAATTAATTTTAATCCC
1 TCACT-ATTTCATTAAAAATTAATTTTAATCCC
58060 TTAAAAAATA
Statistics
Matches: 85, Mismatches: 15, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
68 68 0.80
69 17 0.20
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (67 bp):
TCACTATTTCATTAAAAATTAATTTTAATCCCACATTAACCAGAGAATACTCCAATAACTCACTC
CA
Found at i:58065 original size:21 final size:21
Alignment explanation
Indices: 58039--58078 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58029 ACTGTTTTCA
*
58039 TTAAAAATTAATTTTAATCCC
1 TTAAAAAATAATTTTAATCCC
58060 TTAAAAAATAATTTTAATC
1 TTAAAAAATAATTTTAATC
58079 TCGCATTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAAAATAATTTTAATCCC
Found at i:59562 original size:48 final size:48
Alignment explanation
Indices: 59486--59577 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
59476 CAACATTACA
* *
59486 ACATTAAAACACTAAAACTTGGATCAAACTTTGTAATATAAATTAAAT
1 ACATTAAAACACTAAAAATTGGAACAAACTTTGTAATATAAATTAAAT
*
59534 ACATTACAACA-TAAAAAATTGGAACAAACTTTGTAATATAAATT
1 ACATTAAAACACT-AAAAATTGGAACAAACTTTGTAATATAAATT
59578 TTTGTTATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 1 0.03
48 39 0.98
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (48 bp):
ACATTAAAACACTAAAAATTGGAACAAACTTTGTAATATAAATTAAAT
Found at i:59587 original size:15 final size:15
Alignment explanation
Indices: 59563--59592 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59553 TGGAACAAAC
59563 TTTGTAATATAAATT
1 TTTGTAATATAAATT
*
59578 TTTGTTATATAAATT
1 TTTGTAATATAAATT
59593 AAATACATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTGTAATATAAATT
Found at i:59590 original size:63 final size:63
Alignment explanation
Indices: 59515--59640 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
59505 TGGATCAAAC
59515 TTTGTAATATAAATTAAATACATTACAACATAAAAAATTGGAACAAACTTTGTAATATAAATT
1 TTTGTAATATAAATTAAATACATTACAACATAAAAAATTGGAACAAACTTTGTAATATAAATT
* * *
59578 TTTGTTATATAAATTAAATACATTACATCATTAAAAATTGGAACAAACTTTGTAATATAAATT
1 TTTGTAATATAAATTAAATACATTACAACATAAAAAATTGGAACAAACTTTGTAATATAAATT
59641 AGGTACATTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.37
Consensus pattern (63 bp):
TTTGTAATATAAATTAAATACATTACAACATAAAAAATTGGAACAAACTTTGTAATATAAATT
Found at i:60576 original size:22 final size:22
Alignment explanation
Indices: 60549--60591 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
60539 GTATTAAAAA
60549 AAGATAAGTTACAGTATTACCT
1 AAGATAAGTTACAGTATTACCT
60571 AAGATAAGTTACAGTATTACC
1 AAGATAAGTTACAGTATTACC
60592 CTAAAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (22 bp):
AAGATAAGTTACAGTATTACCT
Found at i:66465 original size:143 final size:140
Alignment explanation
Indices: 66248--66564 Score: 406
Period size: 143 Copynumber: 2.2 Consensus size: 140
66238 GAATCTTCTT
* * *
66248 CACTGCAACTTCACGAAGATAAGATTTGTGATTTTTAGCTTTAATCTGTTCCACTAAAACGTCAG
1 CACTGCAACTTCAGGAAGATAAGATTTGTCATTTTTAGCTTTAATCTGTTCCACTAAAACGTCAA
* * * *
66313 GGAAATAAGATT-TACTGTCGTCAGTCTGTTCCGCTGCAACTTC-AGGAAGATAAGGCTGGTGGC
66 GGAAATAAGATTCGA-TGTCGTCAGTCTGCTCCACTGCAACTTCAACG-AGATAAGGCTGGTGGC
*
66376 TTCAATATGCTC
129 TTCAATATACTC
* * **
66388 CACTGCAACTTTAGGAAGATAAGATTT-TCCATAATTTATAGCTTTAATTTGTTCCACTGCAACG
1 CACTGCAACTTCAGGAAGATAAGATTTGT-CAT--TTT-TAGCTTTAATCTGTTCCACTAAAACG
*
66452 TCAAGGAAATAAGATTCGATGTCTTCAGTCTGCTCCACTGCAACTTCAACGAGATAAGGCTGGTG
62 TCAAGGAAATAAGATTCGATGTCGTCAGTCTGCTCCACTGCAACTTCAACGAGATAAGGCTGGTG
* *
66517 GCTTCAATCTACTT
127 GCTTCAATATACTC
* *
66531 CACTGCAACTTCAGGAAGATAAGATCTGCCATTT
1 CACTGCAACTTCAGGAAGATAAGATTTGTCATTT
66565 GCAACTTCAA
Statistics
Matches: 152, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
139 1 0.01
140 27 0.18
141 2 0.01
142 3 0.02
143 116 0.76
144 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (140 bp):
CACTGCAACTTCAGGAAGATAAGATTTGTCATTTTTAGCTTTAATCTGTTCCACTAAAACGTCAA
GGAAATAAGATTCGATGTCGTCAGTCTGCTCCACTGCAACTTCAACGAGATAAGGCTGGTGGCTT
CAATATACTC
Found at i:71702 original size:15 final size:15
Alignment explanation
Indices: 71682--71737 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
71672 ATTCTCCTCA
*
71682 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
71697 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
71712 TTGTTTT-TCTCTTTT
1 TTCTTTTCTCTC-TTT
71727 TTCTTTT-TCTC
1 TTCTTTTCTCTC
71738 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 3 0.09
15 32 0.91
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:73802 original size:17 final size:17
Alignment explanation
Indices: 73768--73802 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
73758 TTTTTTTTCT
*
73768 TTTTTTTTAATTCCGAA
1 TTTTTTTTAATACCGAA
*
73785 TTTTTTTTAATACTGAA
1 TTTTTTTTAATACCGAA
73802 T
1 T
73803 ACACAAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTTTTAATACCGAA
Found at i:76126 original size:14 final size:14
Alignment explanation
Indices: 76107--76141 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
76097 ATCAAGTTGA
76107 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
76121 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
76135 AAAAAAA
1 AAAAAAA
76142 GAAGAAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (14 bp):
AAAAAAAATTCGTG
Found at i:83669 original size:22 final size:23
Alignment explanation
Indices: 83621--83669 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
83611 TATTGGTATG
83621 ATTAATGTGTCCTAATAAGTCGT
1 ATTAATGTGTCCTAATAAGTCGT
* *
83644 -TTAATGTGTCTTAATAGGT-GT
1 ATTAATGTGTCCTAATAAGTCGT
83665 ATTAA
1 ATTAA
83670 AGAAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (23 bp):
ATTAATGTGTCCTAATAAGTCGT
Found at i:84820 original size:15 final size:16
Alignment explanation
Indices: 84795--84826 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
84785 TATCTCACAC
84795 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
84811 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
84826 T
1 T
84827 TTCTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:85871 original size:11 final size:11
Alignment explanation
Indices: 85857--85912 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
85847 TTTTTTTAAT
85857 AATTTTTTTTC
1 AATTTTTTTTC
85868 AATTTTTTTTC
1 AATTTTTTTTC
*
85879 ---TTTTTTTG
1 AATTTTTTTTC
*
85887 ATTTTTTTTTC
1 AATTTTTTTTC
85898 AATTTTTTTTAC
1 AATTTTTTTT-C
85910 AAT
1 AAT
85913 ACCTGTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.18
11 27 0.71
12 4 0.11
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (11 bp):
AATTTTTTTTC
Found at i:85883 original size:30 final size:30
Alignment explanation
Indices: 85849--85907 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
85839 ATACAAACTT
85849 TTTTTAAT-AATTTTTTTTCAATTTTTTTTC
1 TTTTT-ATGAATTTTTTTTCAATTTTTTTTC
* *
85879 TTTTTTTGATTTTTTTTTCAATTTTTTTT
1 TTTTTATGAATTTTTTTTCAATTTTTTTT
85908 ACAATACCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (30 bp):
TTTTTATGAATTTTTTTTCAATTTTTTTTC
Found at i:85884 original size:18 final size:18
Alignment explanation
Indices: 85861--85895 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
85851 TTTAATAATT
85861 TTTTTTCAATTTTTTTTC
1 TTTTTTCAATTTTTTTTC
**
85879 TTTTTTTGATTTTTTTT
1 TTTTTTCAATTTTTTTT
85896 TCAATTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTTCAATTTTTTTTC
Found at i:85884 original size:19 final size:19
Alignment explanation
Indices: 85860--85897 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
85850 TTTTAATAAT
85860 TTTTTTTCAATTTTTTTTC
1 TTTTTTTCAATTTTTTTTC
* *
85879 TTTTTTTGATTTTTTTTTC
1 TTTTTTTCAATTTTTTTTC
85898 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTTTTCAATTTTTTTTC
Found at i:98528 original size:150 final size:150
Alignment explanation
Indices: 98257--98556 Score: 600
Period size: 150 Copynumber: 2.0 Consensus size: 150
98247 CGAGACGCAA
98257 AATCCCTTAGCCATTTTTGGAGGACACTATGTGATGTGATCCGGCTCGGTTGATTGAGTCGATTC
1 AATCCCTTAGCCATTTTTGGAGGACACTATGTGATGTGATCCGGCTCGGTTGATTGAGTCGATTC
98322 ACTTGATTGCCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAA
66 ACTTGATTGCCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAA
98387 AGATGCGGAAGCTTTCAAAT
131 AGATGCGGAAGCTTTCAAAT
98407 AATCCCTTAGCCATTTTTGGAGGACACTATGTGATGTGATCCGGCTCGGTTGATTGAGTCGATTC
1 AATCCCTTAGCCATTTTTGGAGGACACTATGTGATGTGATCCGGCTCGGTTGATTGAGTCGATTC
98472 ACTTGATTGCCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAA
66 ACTTGATTGCCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAA
98537 AGATGCGGAAGCTTTCAAAT
131 AGATGCGGAAGCTTTCAAAT
98557 GGTTTTAAAG
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (150 bp):
AATCCCTTAGCCATTTTTGGAGGACACTATGTGATGTGATCCGGCTCGGTTGATTGAGTCGATTC
ACTTGATTGCCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAA
AGATGCGGAAGCTTTCAAAT
Found at i:99008 original size:79 final size:79
Alignment explanation
Indices: 98877--99033 Score: 305
Period size: 79 Copynumber: 2.0 Consensus size: 79
98867 TAGATAAGTT
*
98877 AGATCGAAACTCGTACGTATTTAGAGAGGAGAAAACTCACTCTTTGAACAAAGTTCATTCAAATG
1 AGATCGAAACTCGTACGAATTTAGAGAGGAGAAAACTCACTCTTTGAACAAAGTTCATTCAAATG
98942 ATCAAAAGTCAAAC
66 ATCAAAAGTCAAAC
98956 AGATCGAAACTCGTACGAATTTAGAGAGGAGAAAACTCACTCTTTGAACAAAGTTCATTCAAATG
1 AGATCGAAACTCGTACGAATTTAGAGAGGAGAAAACTCACTCTTTGAACAAAGTTCATTCAAATG
99021 ATCAAAAGTCAAA
66 ATCAAAAGTCAAA
99034 AGTCCTTTAC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (79 bp):
AGATCGAAACTCGTACGAATTTAGAGAGGAGAAAACTCACTCTTTGAACAAAGTTCATTCAAATG
ATCAAAAGTCAAAC
Found at i:100084 original size:30 final size:30
Alignment explanation
Indices: 100050--100146 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
100040 TAAACTAAAA
*
100050 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
100080 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
100110 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
100139 ATGAGCTA
1 -TGAGCTA
100147 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Done.