Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold572
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: 37503
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 1019 characters in sequence are not A, C, G, or T
Found at i:1036 original size:32 final size:33
Alignment explanation
Indices: 963--1037 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 33
953 TCACCATTTT
* *
963 AATAATCTATATTTTATAATTTTTAAAGGATTAA
1 AATAAT-TTTATTTTATAATTTTTAAAGGACTAA
* *
997 ATTAATTTTATTTT-T-ATTTTTGAGAGGACTAA
1 AATAATTTTATTTTATAATTTTT-AAAGGACTAA
1029 AATAATTTT
1 AATAATTTT
1038 TCTATTACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 6 0.17
32 17 0.49
33 7 0.20
34 5 0.14
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.51
Consensus pattern (33 bp):
AATAATTTTATTTTATAATTTTTAAAGGACTAA
Found at i:1916 original size:3 final size:3
Alignment explanation
Indices: 1903--1932 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1893 TTGTTACTCA
*
1903 ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1933 TAGTCACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:7272 original size:4 final size:4
Alignment explanation
Indices: 7257--7304 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
7247 AAAAAGGAGT
* * *
7257 AATA AGTA AATA AATA AATA AATTA AAAA AATA AATG AATA AATA AAT
1 AATA AATA AATA AATA AATA AA-TA AATA AATA AATA AATA AATA AAT
7305 GCTCGATGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:8026 original size:2 final size:2
Alignment explanation
Indices: 8019--8056 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
8009 TTTTCAAACC
8019 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8057 AACTATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10226 original size:13 final size:13
Alignment explanation
Indices: 10210--10238 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
10200 CTTTAACGAT
10210 TAACGGTTAAAGA
1 TAACGGTTAAAGA
10223 TAACGGTTAAAGA
1 TAACGGTTAAAGA
10236 TAA
1 TAA
10239 GATAGTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (13 bp):
TAACGGTTAAAGA
Found at i:12042 original size:25 final size:25
Alignment explanation
Indices: 12012--12067 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
12002 AATTATAATA
12012 AAATTATACTTTAA-CCTCATGAAAT
1 AAATTA-ACTTTAATCCTCATGAAAT
** *
12037 AAATTAGGTTTAATCCTCGTGAAAT
1 AAATTAACTTTAATCCTCATGAAAT
12062 AAATTA
1 AAATTA
12068 GGTTTAAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (25 bp):
AAATTAACTTTAATCCTCATGAAAT
Found at i:12068 original size:25 final size:24
Alignment explanation
Indices: 12021--12074 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 24
12011 AAAATTATAC
12021 TTTAACCTCATGAAATAAATTAGG
1 TTTAACCTCATGAAATAAATTAGG
*
12045 TTTAATCCTCGTGAAATAAATTAGG
1 TTTAA-CCTCATGAAATAAATTAGG
12070 TTTAA
1 TTTAA
12075 GCTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (24 bp):
TTTAACCTCATGAAATAAATTAGG
Found at i:23966 original size:10 final size:9
Alignment explanation
Indices: 23942--23966 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
23932 GCAATTAATT
23942 AATTTTTAA
1 AATTTTTAA
23951 AATTTTTAA
1 AATTTTTAA
23960 AATTTTT
1 AATTTTT
23967 CTTATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
AATTTTTAA
Found at i:24451 original size:11 final size:11
Alignment explanation
Indices: 24435--24464 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
24425 TGAACCAAAA
24435 TTTTAATAATT
1 TTTTAATAATT
24446 TTTTAATAATT
1 TTTTAATAATT
24457 TATTTAAT
1 T-TTTAAT
24465 CAAATTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTAATAATT
Found at i:27372 original size:14 final size:17
Alignment explanation
Indices: 27339--27378 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 17
27329 TCATTGATAG
27339 ATTATACAAAATAAATT
1 ATTATACAAAATAAATT
27356 ATTATA-AAAAT-AA-T
1 ATTATACAAAATAAATT
27370 ATTATACAA
1 ATTATACAA
27379 TACAAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.32
15 4 0.18
16 5 0.23
17 6 0.27
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTATACAAAATAAATT
Found at i:34387 original size:213 final size:213
Alignment explanation
Indices: 33866--36246 Score: 2706
Period size: 213 Copynumber: 11.3 Consensus size: 213
33856 NNNNNNNNNN
* * *
33866 AATATGAACGACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTGTGTAAATTGAAATCTCTCGA
1 AATATGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA
*
33931 GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGGAGA
66 GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGA
* * * *
33996 GGTTGTATAAACTTGATTTAAGCAGAACGGCTTTGAAGGAATTACCAT-CTCAATTGCCAATCTT
131 GGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTT
34060 ATTGGTCTTAAGGATTTG
196 ATTGGTCTTAAGGATTTG
* * * * * **
34078 AATATGAGCGACTGTGAAAACTTTGTTTGCCTTCCTGACAGCTTGTGTAAATTGAAATCTCTTAA
1 AATATGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA
* * * *
34143 GAGTTTCCATCTTAAAGGTTGCTCAAGATTGGAGATTTTCCCGAAAATCATGGACACCATGAAGA
66 GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGA
* * *
34208 GGTTGTATGAACTTGATTTAAGCGAAACGGCTTTGAAGGAATTACCATCCTCAATTGCCAATCTT
131 GGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTT
34273 ATTGGTCTTAAGGATTTG
196 ATTGGTCTTAAGGATTTG
* * * * *
34291 GATATGATGC-ACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTGTGTAAATTGAAATCTCTTG
1 AATATGA-ACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCG
* * * * *
34355 AGAGATTCTATCTTCATGGCTGCTCGAGATTGGAGATTTTCCCGGAAGTCATGGATACCATG--G
65 AGAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAG
* * ** *
34418 AGGAACTGTAT-ATGCTTGATTTACTCGGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAA
130 AGG--TTGTATGA-ACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAA
34482 TCTTATTGGTCTTAAGGATTTG
192 TCTTATTGGTCTTAAGGATTTG
* * *
34504 ATTATGAACAACTGTCAAAACCTTGTTTGCCTTCCTGACAGCTTTTGTAAATTGAAATCTCTCGA
1 AATATGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA
* * *
34569 GAGATTCTATCTTAAAGGTTGCTCGAGATTGCAGATTTCCCCGGAAATCATGGAAACCATGAAGA
66 GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGA
* *
34634 GGTTGTATCAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGCCAATCTT
131 GGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTT
34699 ATTGGTCTTAAGGATTTG
196 ATTGGTCTTAAGGATTTG
* * * *
34717 GATATGATGC-ACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTGTGTAAATTGAAATCTCTCG
1 AATATGA-ACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCG
**************
34781 AGAGATTCTATCTTAAAGGTTGCTC-------GAGA--TT----G------NNNNNNNNNNNNNN
65 AGAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAG
*****************************************************************
34827 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
130 AGGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCT
***
34892 NNNTGGTCTT-AGGATTTG
195 TATTGGTCTTAAGGATTTG
* *
34910 AAAATGAACAACTGTGAAAACCTTGTTTGCCTTCTTGACAGCTTTTATAAATTGAAATCTCTCGA
1 AATATGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA
* *
34975 GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATTATGGAAACCATGAAGA
66 GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGA
*
35040 GGTTGTATCG-ACTTGATTTAAGCGGAACCGCTTTGAATGAATTACCATCCTCAATTGGCAATCT
131 GGTTGTAT-GAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCT
*
35104 TATTGGTCTTAAGGAATTG
195 TATTGGTCTTAAGGATTTG
* * * * *
35123 AATATGAACAACTGTAAAAACTTTGTTTGCCTTCCTGATAGCTTTTGTAAATTGAAATCTCTCAA
1 AATATGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA
* * *
35188 GAGATTCTATCTTAAAGGTTGCTCAAGATTGGAGATTTTCTCGGAAATCATGGAAACCATGAAGA
66 GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGA
* *
35253 GGTTGTATGAACTTGATTTATGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGCCAATCTT
131 GGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTT
*
35318 ATTGGTCTTAAGTATTTG
196 ATTGGTCTTAAGGATTTG
* * *
35336 AAGATGAACAACTGTGAAAGCCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCCA
1 AATATGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA
*
35401 GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGAAAATCATGGACACCATGAAGA
66 GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGA
*
35466 GGTTGTATCAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTT
131 GGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTT
35531 ATTGGTCTTAAGGATTTG
196 ATTGGTCTTAAGGATTTG
*
35549 AAGATGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA
1 AATATGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA
* *
35614 GAGATTCTATCTTAGAGGTTGCTCGAGATTGGAGATTTTCCCGAAAATCATGGACACCATGAAGA
66 GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGA
* *
35679 GGTTGTATCAACTTGATTTAAGCGGAACCGCTTTGAATGAATTACCATCCTCAATTGGCAATCTT
131 GGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATC-T
*
35744 TATTGGTCTTCAGGATTTG
195 TATTGGTCTTAAGGATTTG
* *
35763 ACAT-TGCAA-AACTGTGAAAATCTTGTTTGCCTTCCTAACAGCTTTTATAAATTGAAATCTCTC
1 A-ATATG-AACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTC
** *
35826 TCGAGATTCTATCTTACAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAA
64 GAGAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAA
35891 GAGGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATC
129 GAGGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATC
35956 TTATTGGTCTTAAGGATTTG
194 TTATTGGTCTTAAGGATTTG
* * * **
35976 AAGATAAAC-ACTGTGAAAACCTTGTTTGGCCTCCCTGACAGCTTTTATAAATT-AAATCTCTTT
1 AATATGAACAACTGTGAAAACCTTGTTT-GCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCG
* * *******************
36039 TGTG--TCNNNNNNNNNNNNNNNNNNNGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAG
65 AGAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAG
36102 AGGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCT
130 AGGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCT
36167 TATTGGTCTTAAGGATTTG
195 TATTGGTCTTAAGGATTTG
* *
36186 AAGATAAAC-ACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCT
1 AATATGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCT
36247 TTTGTGTCTT
Statistics
Matches: 1830, Mismatches: 299, Indels: 82
0.83 0.14 0.04
Matches are distributed among these distances:
192 1 0.00
193 89 0.05
194 7 0.00
200 5 0.00
202 2 0.00
204 1 0.00
206 4 0.00
209 24 0.01
210 159 0.09
211 4 0.00
212 207 0.11
213 1118 0.61
214 202 0.11
215 7 0.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.32
Consensus pattern (213 bp):
AATATGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA
GAGATTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGA
GGTTGTATGAACTTGATTTAAGCGGAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTT
ATTGGTCTTAAGGATTTG
Done.