Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1664
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: 28801
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3485 original size:17 final size:17
Alignment explanation
Indices: 3463--3502 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3453 GAATTTTATG
*
3463 AAATTATATATCATATT
1 AAATTATATATAATATT
*
3480 AAATTATATTTAATATT
1 AAATTATATATAATATT
3497 -AATTAT
1 AAATTAT
3503 TTAAATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTATATATAATATT
Found at i:3554 original size:88 final size:87
Alignment explanation
Indices: 3425--3608 Score: 241
Period size: 88 Copynumber: 2.1 Consensus size: 87
3415 ATGATTTTAG
* ** *
3425 TAAATT-ATATAAGAACATTTATTATTGAGAATTTTATGAAA-TTATATATCATATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTTA-ATATAATATTAAATTATA
* *
3488 TTTAAT-ATTAATTATTTAAATTGTA
65 TGTAATAATT-A-TATTT-AATTATA
3513 TAAATTCATATAAGAAAATTTATTATCAAG-ATTTTATGAAATTTAATATAATATTAAATTATAT
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTTAATATAATATTAAATTATAT
3577 GTAATAATTATATTTAATTATA
66 GTAATAATTATATTTAATTATA
*
3599 CAAATTCATA
1 TAAATTCATA
3609 AAATATATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
86 15 0.17
87 5 0.06
88 40 0.47
89 26 0.30
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (87 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTTAATATAATATTAAATTATAT
GTAATAATTATATTTAATTATA
Found at i:3862 original size:19 final size:20
Alignment explanation
Indices: 3827--3866 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3817 TTATAAATTC
*
3827 AATAAGAATATTATTATTAA
1 AATAAAAATATTATTATTAA
3847 AATAAAAATA-TATTATTAA
1 AATAAAAATATTATTATTAA
3866 A
1 A
3867 TAATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AATAAAAATATTATTATTAA
Found at i:3873 original size:15 final size:17
Alignment explanation
Indices: 3849--3889 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
3839 ATTATTAAAA
3849 TAAA-AATATA-TT-AT
1 TAAATAATATATTTAAT
3863 TAAATAATATATTTAAT
1 TAAATAATATATTTAAT
*
3880 TAATTAATAT
1 TAAATAATAT
3890 CATAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 6 0.26
16 2 0.09
17 11 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATAATATATTTAAT
Found at i:3925 original size:40 final size:43
Alignment explanation
Indices: 3854--3941 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 43
3844 TAAAATAAAA
* *
3854 ATATATTATTAAATAATATATTTAATTAATTA-ATATCATAATT
1 ATATATAATTAAATAATATATTTAATAAATTATA-ATCATAATT
* *
3897 ATATATAATTATATAATA-A-TTAA-AAATTATAATTATAATT
1 ATATATAATTAAATAATATATTTAATAAATTATAATCATAATT
3937 ATATA
1 ATATA
3942 ATCTAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 18 0.45
41 5 0.12
42 1 0.03
43 16 0.40
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (43 bp):
ATATATAATTAAATAATATATTTAATAAATTATAATCATAATT
Found at i:3932 original size:6 final size:6
Alignment explanation
Indices: 3891--3939 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
3881 AATTAATATC
* *
3891 ATAATT AT-A-T ATAATT AT-ATA ATAATT AAAAATT ATAATT ATAATT
1 ATAATT ATAATT ATAATT ATAATT ATAATT -ATAATT ATAATT ATAATT
3937 ATA
1 ATA
3940 TAATCTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
4 3 0.09
5 6 0.17
6 21 0.60
7 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
ATAATT
Found at i:3980 original size:23 final size:23
Alignment explanation
Indices: 3949--3992 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3939 ATAATCTAAT
3949 ATAATTTAATATTAAATTTTATTA
1 ATAATTTAATATT-AATTTTATTA
*
3973 ATAA-TTAATATTTATTTTAT
1 ATAATTTAATATTAATTTTAT
3993 AAATTTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATAATTTAATATTAATTTTATTA
Found at i:7550 original size:23 final size:23
Alignment explanation
Indices: 7523--7595 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
7513 TTATATTAAT
7523 ATTATATAATCAAAATGATTTTA
1 ATTATATAATCAAAATGATTTTA
* * * ***
7546 ATTATAT-TTC-AATTAAAAAT-
1 ATTATATAATCAAAATGATTTTA
7566 ATTATATAATCAAAATGATTTTA
1 ATTATATAATCAAAATGATTTTA
7589 ATTATAT
1 ATTATAT
7596 TTTAATATAC
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 7 0.20
21 7 0.20
22 7 0.20
23 14 0.40
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (23 bp):
ATTATATAATCAAAATGATTTTA
Found at i:8512 original size:52 final size:52
Alignment explanation
Indices: 8455--8676 Score: 241
Period size: 52 Copynumber: 4.0 Consensus size: 52
8445 GGTGTTAACT
*
8455 CATTTCAAACATTTCAAAGCATTCAAAGTTAATAGTACCAAATTAACAGCAC
1 CATTTCAAACATTTCAAAGCATTCAAAGTTAACAGTACCAAATTAACAGCAC
* ** *
8507 CATTTCAAACATTTATCAGTGAGCAAACATTTCAAAGCATTCAA-AGT-TGAAGTGGTAACAGCA
1 CATTTCAAACA-TT-TC----A--AAGCA-TTCAAAG--TT-AACAGTACCAAAT--TAACAGCA
8570 C
52 C
*
8571 CATTTCAAACATTTCAAAGCATTCAAAGTTAACAGTACCAAATTAACAACAC
1 CATTTCAAACATTTCAAAGCATTCAAAGTTAACAGTACCAAATTAACAGCAC
*
8623 CATTTCAAACATTTCAAAGCATTCAAAATTAACAGTACCAAATTAACAGCAC
1 CATTTCAAACATTTCAAAGCATTCAAAGTTAACAGTACCAAATTAACAGCAC
8675 CA
1 CA
8677 GGACTATGCG
Statistics
Matches: 143, Mismatches: 11, Indels: 32
0.77 0.06 0.17
Matches are distributed among these distances:
52 73 0.51
53 7 0.05
54 5 0.03
55 7 0.05
56 4 0.03
58 2 0.01
60 4 0.03
61 7 0.05
62 5 0.03
63 7 0.05
64 22 0.15
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.26
Consensus pattern (52 bp):
CATTTCAAACATTTCAAAGCATTCAAAGTTAACAGTACCAAATTAACAGCAC
Found at i:8893 original size:21 final size:22
Alignment explanation
Indices: 8847--8901 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
8837 AAGCAGATGG
* *
8847 AGCCACTGCAAATATATTATAT
1 AGCCACTGCAAACATATTACAT
*
8869 AGCCACTGCAAACA-ATTGCAT
1 AGCCACTGCAAACATATTACAT
8890 AGCCACATGCAA
1 AGCCAC-TGCAA
8902 TGGGGGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (22 bp):
AGCCACTGCAAACATATTACAT
Found at i:11053 original size:30 final size:30
Alignment explanation
Indices: 10987--11066 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
10977 AAACTAAGAT
*
10987 ATATAAAATTATTTAAATAATTATGTTGTA
1 ATATAAAATTATATAAATAATTATGTTGTA
* *
11017 ATATAAAATTATATAATTATGTTATGATT-TA
1 ATATAAAATTATATAAATA-ATTATG-TTGTA
11048 A-ATAAAATTACTTATAAAT
1 ATATAAAATTA--TATAAAT
11067 CCGTGTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 26 0.62
31 8 0.19
32 8 0.19
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (30 bp):
ATATAAAATTATATAAATAATTATGTTGTA
Found at i:28073 original size:16 final size:16
Alignment explanation
Indices: 28052--28089 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
28042 GCTTGAACCG
*
28052 AAAAAATTTGAGTTTA
1 AAAAAATTTGAGATTA
28068 AAAAAA--TGAGATTA
1 AAAAAATTTGAGATTA
28082 AAAAAATT
1 AAAAAATT
28090 CAGCTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
14 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (16 bp):
AAAAAATTTGAGATTA
Done.