Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2781
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: 21739
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:2054 original size:26 final size:28
Alignment explanation
Indices: 2000--2056 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
1990 CAAACCGGAG
2000 TAAATACTAAAAAAAAAATTAAAATATGA
1 TAAATACT-AAAAAAAAATTAAAATATGA
2029 TAAATACT-AAAAAAAATTAAAA-ATGA
1 TAAATACTAAAAAAAAATTAAAATATGA
2055 TA
1 TA
2057 TACATTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 6 0.21
27 14 0.50
29 8 0.29
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (28 bp):
TAAATACTAAAAAAAAATTAAAATATGA
Found at i:15722 original size:39 final size:39
Alignment explanation
Indices: 15677--15796 Score: 163
Period size: 39 Copynumber: 3.0 Consensus size: 39
15667 ACAAAAACAC
15677 CGCTAAAAACTGAGTAATAGTGGCGTTTTTATCCAAACG
1 CGCTAAAAACTGAGTAATAGTGGCGTTTTTATCCAAACG
*
15716 CGCTAAAAACTGAGTAATAGTGGCGTTTTCATCCAAAACG
1 CGCTAAAAACTGAGTAATAGTGGCGTTTTTATCC-AAACG
* *
15756 CCGCAAAAAACTGAG-ATATAGTGGCG-CTTTATTCCAAACG
1 -CGCTAAAAACTGAGTA-ATAGTGGCGTTTTTA-TCCAAACG
15796 C
1 C
15797 CACAAAAGGT
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
39 34 0.47
40 14 0.19
41 25 0.34
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (39 bp):
CGCTAAAAACTGAGTAATAGTGGCGTTTTTATCCAAACG
Found at i:16397 original size:28 final size:28
Alignment explanation
Indices: 16355--16410 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
16345 TAAAATATAA
16355 GCCTAACCCTAAATCATAACCCATGATC
1 GCCTAACCCTAAATCATAACCCATGATC
16383 GCCTAACCCCT-AATCATAACCCATGATC
1 GCCTAA-CCCTAAATCATAACCCATGATC
16411 TAAACTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.34, C:0.38, G:0.07, T:0.21
Consensus pattern (28 bp):
GCCTAACCCTAAATCATAACCCATGATC
Found at i:17624 original size:19 final size:19
Alignment explanation
Indices: 17600--17636 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17590 CCCCACCCAA
17600 TTTTCCCCAAATCCCTAAC
1 TTTTCCCCAAATCCCTAAC
*
17619 TTTTCCCCTAATCCCTAA
1 TTTTCCCCAAATCCCTAA
17637 ATATTTCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTTCCCCAAATCCCTAAC
Found at i:17651 original size:20 final size:19
Alignment explanation
Indices: 17598--17651 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
17588 TTCCCCACCC
*
17598 AATTTTCCCCAAATCCCTA
1 AATTTTCCCCGAATCCCTA
* *
17617 ACTTTTCCCCTAATCCCTA
1 AATTTTCCCCGAATCCCTA
*
17636 AATATTTCCTCGAATC
1 AAT-TTTCCCCGAATC
17652 AAATGAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.28, C:0.35, G:0.02, T:0.35
Consensus pattern (19 bp):
AATTTTCCCCGAATCCCTA
Found at i:19465 original size:13 final size:13
Alignment explanation
Indices: 19447--19471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19437 GGTTTATAGA
19447 TTTGCTTTTTGCT
1 TTTGCTTTTTGCT
19460 TTTGCTTTTTGC
1 TTTGCTTTTTGC
19472 GTTTATATGT
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:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (13 bp):
TTTGCTTTTTGCT
Found at i:20343 original size:63 final size:63
Alignment explanation
Indices: 20250--20372 Score: 221
Period size: 63 Copynumber: 2.0 Consensus size: 63
20240 TAATATTTCT
*
20250 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAAT-TAATATGTCCCATCTAATATACAA
20314 ATATTTCTATCA-GATTTTTAATAAATTTATTTATTAATTAATATGTCCCATCTAATATA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATTAATATGTCCCATCTAATATA
20373 AATTATTATA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 21 0.36
63 25 0.43
64 12 0.21
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.47
Consensus pattern (63 bp):
ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATTAATATGTCCCATCTAATATACAA
Found at i:20782 original size:9 final size:9
Alignment explanation
Indices: 20770--21073 Score: 166
Period size: 9 Copynumber: 36.1 Consensus size: 9
20760 ATTTAACATA
*
20770 TTACAAAAC
1 TTACATAAC
20779 TTACATAAC
1 TTACATAAC
*
20788 TTATATAAC
1 TTACATAAC
20797 TTACATAA-
1 TTACATAAC
* *
20805 ATATAT-A-
1 TTACATAAC
20812 TT--ATAAC
1 TTACATAAC
20819 TTACATAA-
1 TTACATAAC
20827 -TA-ATAA-
1 TTACATAAC
* *
20833 ATATATAA-
1 TTACATAAC
20841 TTACATAAC
1 TTACATAAC
*
20850 -TAGATAA-
1 TTACATAAC
* *
20857 ATATATAAC
1 TTACATAAC
20866 TTACATAAC
1 TTACATAAC
20875 TTACATAAC
1 TTACATAAC
*
20884 TTATATAAC
1 TTACATAAC
*
20893 TTAGATAA-
1 TTACATAAC
* *
20901 -AATATAAC
1 TTACATAAC
20909 TTACATAAC
1 TTACATAAC
20918 TTACATAAC
1 TTACATAAC
20927 TT--ATAAC
1 TTACATAAC
*
20934 TTAGATAA-
1 TTACATAAC
* *
20942 ATATATAAC
1 TTACATAAC
20951 TTACATAAC
1 TTACATAAC
20960 TTACATAAC
1 TTACATAAC
*
20969 TTA-TTAAC
1 TTACATAAC
*
20977 TTAGATAA-
1 TTACATAAC
* *
20985 ATATATAAC
1 TTACATAAC
20994 TTACATAAC
1 TTACATAAC
**
21003 -TATTTAAC
1 TTACATAAC
* *
21011 TTATAGAAC
1 TTACATAAC
*
21020 TTAGATAA-
1 TTACATAAC
* *
21028 ATATATAAC
1 TTACATAAC
21037 TTACATAA-
1 TTACATAAC
* * *
21045 ATATATATC
1 TTACATAAC
*
21054 ATATCATAAC
1 TTA-CATAAC
21064 TTACATAAC
1 TTACATAAC
21073 T
1 T
21074 CATAATACTT
Statistics
Matches: 231, Mismatches: 44, Indels: 40
0.73 0.14 0.13
Matches are distributed among these distances:
5 2 0.01
6 5 0.02
7 20 0.09
8 62 0.27
9 136 0.59
10 6 0.03
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (9 bp):
TTACATAAC
Found at i:20817 original size:22 final size:23
Alignment explanation
Indices: 20789--20925 Score: 109
Period size: 25 Copynumber: 5.7 Consensus size: 23
20779 TTACATAACT
*
20789 TATATAACTTACATAAATATATA
1 TATATAACTTACATAAATATAAA
20812 T-TATAACTTACAT-AATAATAAA
1 TATATAACTTACATAAAT-ATAAA
*
20834 TATATAA-TTACATAACTAGATAAA
1 TATATAACTTACATAA--ATATAAA
* *
20858 TATATAACTTACATAACTTACATAACT
1 TATATAACTTACATAA---ATATAA-A
* *
20885 TATATAACTTAGATAAAATATAACT
1 TATATAACTTACAT-AAATATAA-A
*
20910 TACATAACTTACATAA
1 TATATAACTTACATAA
20926 CTTATAACTT
Statistics
Matches: 96, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.03
22 23 0.24
23 7 0.07
24 14 0.15
25 28 0.29
26 6 0.06
27 13 0.14
28 2 0.02
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.36
Consensus pattern (23 bp):
TATATAACTTACATAAATATAAA
Found at i:20880 original size:34 final size:36
Alignment explanation
Indices: 20770--21073 Score: 175
Period size: 34 Copynumber: 8.5 Consensus size: 36
20760 ATTTAACATA
* *
20770 TTACAAAACTTACATAACTTATATAACTTACATAAATA
1 TTACATAACTTACATAACTTATATAACTTACAT-AA-C
* *
20808 TATATTATAACTTACATAA-TAATAAATATATAATTACATAAC
1 T-TA-CATAACTTACATAACT--T--ATATA-ACTTACATAAC
* * * *
20850 -TAGATAA-ATATATAACTTACATAACTTACATAAC
1 TTACATAACTTACATAACTTATATAACTTACATAAC
* * *
20884 TTATATAACTTAGATAA--AATATAACTTACATAAC
1 TTACATAACTTACATAACTTATATAACTTACATAAC
* * *
20918 TTACATAACTT--ATAACTTAGATAA-ATATATAAC
1 TTACATAACTTACATAACTTATATAACTTACATAAC
*
20951 TTACATAACTTACATAACTTAT-TAACTTAGATAA-
1 TTACATAACTTACATAACTTATATAACTTACATAAC
* * * * *
20985 ATATATAACTTACATAAC-TATTTAACTTATAGAAC
1 TTACATAACTTACATAACTTATATAACTTACATAAC
* * * * * * *
21020 TTAGATAA-ATATATAACTTACATAA-ATATATATC
1 TTACATAACTTACATAACTTATATAACTTACATAAC
*
21054 ATATCATAACTTACATAACT
1 TTA-CATAACTTACATAACT
21074 CATAATACTT
Statistics
Matches: 207, Mismatches: 39, Indels: 42
0.72 0.14 0.15
Matches are distributed among these distances:
32 4 0.02
33 21 0.10
34 84 0.41
35 39 0.19
36 14 0.07
37 1 0.00
38 7 0.03
39 8 0.04
40 14 0.07
41 1 0.00
43 7 0.03
44 7 0.03
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (36 bp):
TTACATAACTTACATAACTTATATAACTTACATAAC
Found at i:20906 original size:43 final size:44
Alignment explanation
Indices: 20770--21003 Score: 86
Period size: 43 Copynumber: 5.6 Consensus size: 44
20760 ATTTAACATA
* *
20770 TTACAAAACTTACATAACTTATATAACTTACATAAATATAT-A-
1 TTACATAACTTACATAACTTATATAACTTAGATAAATATATAAC
* * * *
20812 TT--ATAACTTACATAA--TA-ATAA-ATATATAATTACATAAC
1 TTACATAACTTACATAACTTATATAACTTAGATAAATATATAAC
* * * * * *
20850 -TAGATAA-ATATATAACTTACATAACTTACATAACTTATATAAC
1 TTACATAACTTACATAACTTATATAACTTAGATAA-ATATATAAC
* * * * * *
20893 TTAGATAA--AATATAACTTACATAACTTACATAACT-TATAAC
1 TTACATAACTTACATAACTTATATAACTTAGATAAATATATAAC
* * * * * *
20934 TTAGATAA-ATATATAACTTACATAACTTACATAACT-TATTAAC
1 TTACATAACTTACATAACTTATATAACTTAGATAAATATA-TAAC
* * * *
20977 TTAGATAA-ATATATAACTTACATAACT
1 TTACATAACTTACATAACTTATATAACT
21004 ATTTAACTTA
Statistics
Matches: 167, Mismatches: 13, Indels: 23
0.82 0.06 0.11
Matches are distributed among these distances:
36 10 0.06
37 6 0.04
38 8 0.05
39 4 0.02
40 14 0.08
41 18 0.11
42 37 0.22
43 63 0.38
44 7 0.04
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (44 bp):
TTACATAACTTACATAACTTATATAACTTAGATAAATATATAAC
Found at i:21021 original size:43 final size:43
Alignment explanation
Indices: 20846--21044 Score: 325
Period size: 43 Copynumber: 4.7 Consensus size: 43
20836 TATAATTACA
20846 TAAC-TAGATAAATATATAACTTACATAACTTACATAACTTAT
1 TAACTTAGATAAATATATAACTTACATAACTTACATAACTTAT
20888 ATAACTTAGATAAA-ATATAACTTACATAACTTACATAACTTA-
1 -TAACTTAGATAAATATATAACTTACATAACTTACATAACTTAT
20930 TAACTTAGATAAATATATAACTTACATAACTTACATAACTTAT
1 TAACTTAGATAAATATATAACTTACATAACTTACATAACTTAT
**
20973 TAACTTAGATAAATATATAACTTACATAAC-TATTTAACTTAT
1 TAACTTAGATAAATATATAACTTACATAACTTACATAACTTAT
*
21015 AGAACTTAGATAAATATATAACTTACATAA
1 -TAACTTAGATAAATATATAACTTACATAA
21045 ATATATATCA
Statistics
Matches: 149, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
41 13 0.09
42 38 0.26
43 90 0.60
44 8 0.05
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (43 bp):
TAACTTAGATAAATATATAACTTACATAACTTACATAACTTAT
Done.