Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3363
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: 11872
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Found at i:3810 original size:1 final size:1
Alignment explanation
Indices: 3804--3896 Score: 78
Period size: 1 Copynumber: 93.0 Consensus size: 1
3794 TCACCCACAC
* * * * * ****
3804 AAAAAAAAAAAACAAAACAAAAAAAAACAAAAAAAAAACAAAAAAAACACCCCAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
3869 CAAAAAAAAAAAAAACAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
3897 TATAATAATC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3827 original size:15 final size:15
Alignment explanation
Indices: 3806--3896 Score: 103
Period size: 16 Copynumber: 5.7 Consensus size: 15
3796 ACCCACACAA
3806 AAAAAAAAAACAAAAC
1 AAAAAAAAAA-AAAAC
3822 AAAAAAAAACAAAAA-
1 AAAAAAAAA-AAAAAC
3837 AAAAACAAAAAAAACACC
1 AAAAA-AAAAAAAA-A-C
**
3855 CCAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
3870 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
3885 AACAAAAAAAAA
1 AA-AAAAAAAAA
3897 TATAATAATC
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
15 25 0.38
16 28 0.43
17 9 0.14
18 3 0.05
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:3860 original size:35 final size:33
Alignment explanation
Indices: 3804--3896 Score: 118
Period size: 35 Copynumber: 2.8 Consensus size: 33
3794 TCACCCACAC
3804 AAAAAAAAAAAACAAAACAAAAAAAAACAAAAAA
1 AAAAAAAAAAAACAAAACAAAAAAAAA-AAAAAA
*** *
3838 AAAACAAAAAAAACACCCCAAAAAAAAAAAACAA
1 AAAA-AAAAAAAACAAAACAAAAAAAAAAAAAAA
3872 AAAAAAAAAAAAC--AACAAAAAAAAA
1 AAAAAAAAAAAACAAAACAAAAAAAAA
3897 TATAATAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
31 10 0.19
33 9 0.17
34 13 0.25
35 20 0.38
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (33 bp):
AAAAAAAAAAAACAAAACAAAAAAAAAAAAAAA
Found at i:6546 original size:25 final size:25
Alignment explanation
Indices: 6495--6573 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 25
6485 AGGAGTGACA
*
6495 AAAAGGGCTTATG-CCCTAGTTATT
1 AAAAGGGCTTATGCCCCAAGTTATT
6519 -AAAGGGCTTAATGCCCCAAGTTATT
1 AAAAGGGCTT-ATGCCCCAAGTTATT
6544 AAAAAGGGCTTATGCCCCAA-TTATTT
1 -AAAAGGGCTTATGCCCCAAGTTA-TT
6570 AAAA
1 AAAA
6574 AGTGGCATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
23 9 0.18
24 3 0.06
25 17 0.35
26 11 0.22
27 9 0.18
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTATGCCCCAAGTTATT
Found at i:6571 original size:26 final size:25
Alignment explanation
Indices: 6494--6575 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 25
6484 AAGGAGTGAC
* *
6494 AAAAAGGGCTTATGCCCTAGTTATT
1 AAAAAGGGCTTATGCCCCAATTATT
6519 --AAAGGGCTTAATGCCCCAAGTTATT
1 AAAAAGGGCTT-ATGCCCCAA-TTATT
6544 AAAAAGGGCTTATGCCCCAATTATTT
1 AAAAAGGGCTTATGCCCCAATTA-TT
6570 AAAAAG
1 AAAAAG
6576 TGGCATATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
23 9 0.18
24 7 0.14
25 8 0.16
26 17 0.34
27 9 0.18
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (25 bp):
AAAAAGGGCTTATGCCCCAATTATT
Found at i:10104 original size:40 final size:40
Alignment explanation
Indices: 10044--10204 Score: 272
Period size: 40 Copynumber: 4.1 Consensus size: 40
10034 CAATTGAGGA
*
10044 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
10084 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
10124 TTATTTCCGGGTTAAGTCCTGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* *
10164 CTATTT-CGGGTTAAGT-CCGAAGGCATTTGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
10202 TTA
1 TTA
10205 CATCCGGACT
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 22 0.19
39 10 0.09
40 83 0.72
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (40 bp):
TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
Found at i:10228 original size:78 final size:79
Alignment explanation
Indices: 10062--10228 Score: 239
Period size: 78 Copynumber: 2.1 Consensus size: 79
10052 GGGTTAAGTC
*
10062 CCGAAGGCATTCGTGCTGGTTGTTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTA
1 CCGAAGGCATTCGTGCTGGTTGCTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTA
** ** *
10127 TTTCCGGGTTAAGT
66 CATCCGGACTAAAT
*
10141 CCTGAAGGCATTCGTGCTGGTTGCTATTT-CGGGTTAAGT-CCGAAGGCATTTGTGCTGGTTGTT
1 CC-GAAGGCATTCGTGCTGGTTGCTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTT
10204 ACATCCGGACTAAAT
65 ACATCCGGACTAAAT
10219 CCGAGAGGCA
1 CCGA-AGGCA
10229 ATTGGGTTGG
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
77 2 0.03
78 40 0.51
79 12 0.15
80 25 0.32
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (79 bp):
CCGAAGGCATTCGTGCTGGTTGCTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTA
CATCCGGACTAAAT
Done.