Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold750
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: 38430
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:4561 original size:46 final size:46
Alignment explanation
Indices: 4508--4680 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
4498 ATATTGAGCA
*
4508 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
4554 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
4601 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
4647 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
4681 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 62 0.58
47 29 0.27
48 3 0.03
50 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:4664 original size:93 final size:93
Alignment explanation
Indices: 4505--4675 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
4495 AGGATATTGA
* *
4505 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
4570 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
4598 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
4663 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
4676 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:10497 original size:20 final size:20
Alignment explanation
Indices: 10472--10535 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
10462 TCAAATACAT
10472 TACATATATATATTATCATA
1 TACATATATATATTATCATA
*
10492 TACATAAATATCA-TATCA-A
1 TACATATATAT-ATTATCATA
*
10511 AACAT-TATATACTTATACATA
1 TACATATATATA-TTAT-CATA
10532 TACA
1 TACA
10536 AATGCCGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
17 1 0.03
18 4 0.11
19 8 0.23
20 17 0.49
21 5 0.14
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (20 bp):
TACATATATATATTATCATA
Found at i:11208 original size:13 final size:15
Alignment explanation
Indices: 11181--11211 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11171 TAAAAAATTC
11181 CAATCCAAAACATAT
1 CAATCCAAAACATAT
*
11196 CAATCCAAAATATAT
1 CAATCCAAAACATAT
11211 C
1 C
11212 TTTCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (15 bp):
CAATCCAAAACATAT
Found at i:17548 original size:33 final size:34
Alignment explanation
Indices: 17506--17577 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
17496 GACAGCCTAG
* *
17506 TATCAGTGT-GGCCTTAGCCTATTATAGTAACAA
1 TATCAGTGTGGGCCTTAGCCCATTACAGTAACAA
*
17539 TATCAGTGTGGGCTTTAGCCCATTACAGTAACAA
1 TATCAGTGTGGGCCTTAGCCCATTACAGTAACAA
17573 TATCA
1 TATCA
17578 TAAATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 9 0.26
34 26 0.74
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (34 bp):
TATCAGTGTGGGCCTTAGCCCATTACAGTAACAA
Found at i:20990 original size:27 final size:27
Alignment explanation
Indices: 20857--20991 Score: 110
Period size: 27 Copynumber: 5.0 Consensus size: 27
20847 CAATTTGATG
* *
20857 AAATGACTATTTTGCCCTTATGAGGTA
1 AAATGACTATTTTGCCCCTATGTGGTA
*
20884 AAATGACTGTTTTGCCCCTATGTGGTA
1 AAATGACTATTTTGCCCCTATGTGGTA
** * * * * *
20911 AAAAAATTGTTTTGCCCTTAGGTAGTA
1 AAATGACTATTTTGCCCCTATGTGGTA
* ** **
20938 AAATAACTGA-AATGCCCCTACATGGTA
1 AAATGACT-ATTTTGCCCCTATGTGGTA
*
20965 AATTGACTATTTTGCCCCTATGTGGTA
1 AAATGACTATTTTGCCCCTATGTGGTA
20992 TATGTTTAGA
Statistics
Matches: 82, Mismatches: 24, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
26 1 0.01
27 81 0.99
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (27 bp):
AAATGACTATTTTGCCCCTATGTGGTA
Found at i:27376 original size:29 final size:28
Alignment explanation
Indices: 27334--27388 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
27324 TCTCTTTACT
27334 AGTAACTTACTAGTAGTGGTTTCAACAC
1 AGTAACTTACTAGTAGTGGTTTCAACAC
27362 AGTAACTTTACTAGTAGTGGTTTCAAC
1 AGTAAC-TTACTAGTAGTGGTTTCAAC
27389 CATAATACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (28 bp):
AGTAACTTACTAGTAGTGGTTTCAACAC
Found at i:33958 original size:40 final size:38
Alignment explanation
Indices: 33899--34079 Score: 163
Period size: 39 Copynumber: 4.6 Consensus size: 38
33889 TAACTCATTC
* *
33899 AATGCCTTC-GGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTGT--AACTCGCACA
*
33938 AATGCCTTCGGGACTTAACCCGGAATTGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTGTAACTCGCACA
* *
33977 AAGGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATT-GTAACTCGCACA
** * *
34017 AA-GCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAT-T-GTAAC-TCGCACA
*
34057 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
34080 CAGCATTCAA
Statistics
Matches: 125, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
38 5 0.04
39 62 0.50
40 51 0.41
41 7 0.06
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (38 bp):
AATGCCTTCGGGACTTAACCCGGATTGTAACTCGCACA
Done.