Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002723.1 Kokia drynarioides strain JFW-HI SEQ_115019, whole genome shotgun sequence
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: 4719
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:88 original size:9 final size:9
Alignment explanation
Indices: 74--110 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
64 TTTTTTTTCC
74 TCTCCTTCT
1 TCTCCTTCT
83 TCTCCTTCT
1 TCTCCTTCT
*
92 TCTCTTTC-
1 TCTCCTTCT
100 T-TCCTTCT
1 TCTCCTTCT
108 TCT
1 TCT
111 TTCTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 5 0.21
8 2 0.08
9 17 0.71
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (9 bp):
TCTCCTTCT
Found at i:114 original size:4 final size:4
Alignment explanation
Indices: 88--149 Score: 67
Period size: 4 Copynumber: 15.8 Consensus size: 4
78 CTTCTTCTCC
* *
88 TTCT TCTCT TTC- TTCC TTC- TTCT TTCT TTCT TTCT TTCT TTCT CTTTT
1 TTCT T-TCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT
136 TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTC
150 CTTCATTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
3 9 0.18
4 35 0.69
5 7 0.14
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTCT
Found at i:133 original size:25 final size:26
Alignment explanation
Indices: 78--149 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
68 TTTTCCTCTC
*
78 CTTCTTCTCCTTCTTCTCTTTCTTCCTT
1 CTTCTT-TCTTTCTT-TCTTTCTTCCTT
*
106 CTTCTTTCTTTCTTTCTTTCTTTC-T
1 CTTCTTTCTTTCTTTCTTTCTTCCTT
*
131 CTTTTTTCTTTCTTT-TTTC
1 CTTCTTTCTTTCTTTCTTTC
150 CTTCATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
24 4 0.10
25 15 0.37
26 9 0.22
27 7 0.17
28 6 0.15
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (26 bp):
CTTCTTTCTTTCTTTCTTTCTTCCTT
Found at i:146 original size:11 final size:11
Alignment explanation
Indices: 88--160 Score: 65
Period size: 11 Copynumber: 6.3 Consensus size: 11
78 CTTCTTCTCC
*
88 TTCTTCTCTTTC
1 TTCTT-TCTTTT
* *
100 TTCCTTCTTCT
1 TTCTTTCTTTT
111 TTCTTTCTTTCT
1 TTCTTTCTTT-T
123 TTCTTTCTCTTTT
1 TTC-TT-TCTTTT
136 TTCTTTCTTTT
1 TTCTTTCTTTT
* *
147 TTCCTTCATTT
1 TTCTTTCTTTT
158 TTC
1 TTC
161 GTTAGTCCCA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
11 30 0.59
12 10 0.20
13 6 0.12
14 5 0.10
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.71
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:4374 original size:27 final size:27
Alignment explanation
Indices: 4338--4392 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
4328 TACCTAACAC
4338 CCAATGGAGGAACA-CGAAGTGGCGGCA
1 CCAATGGAGGAACATC-AAGTGGCGGCA
*
4365 CCAATGGAGGAATATCAAGTGGCGGCA
1 CCAATGGAGGAACATCAAGTGGCGGCA
4392 C
1 C
4393 TAAGGGGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.22, G:0.35, T:0.11
Consensus pattern (27 bp):
CCAATGGAGGAACATCAAGTGGCGGCA
Found at i:4592 original size:12 final size:12
Alignment explanation
Indices: 4577--4614 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4567 AAATGAAGGG
4577 AAAAAA-AAAGA
1 AAAAAAGAAAGA
4588 AAAAAGAGAAAGA
1 AAAAA-AGAAAGA
*
4601 AAGAAAGAAAGA
1 AAAAAAGAAAGA
4613 AA
1 AA
4615 GAAGAAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 5 0.21
12 10 0.42
13 9 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:4601 original size:4 final size:4
Alignment explanation
Indices: 4583--4617 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
4573 AGGGAAAAAA
*
4583 AAAG AAAA AAGAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AA
4618 GAAGGAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:4615 original size:12 final size:13
Alignment explanation
Indices: 4583--4633 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
4573 AGGGAAAAAA
*
4583 AAAGAAAAAAGAG
1 AAAGAAAGAAGAG
4596 AAAGAAAGAA-AG
1 AAAGAAAGAAGAG
4608 AAAGAAAGAAGAAG
1 AAAGAAAGAAG-AG
* *
4622 GAAGAAGGAAGA
1 AAAGAAAGAAGA
4634 AGGAGAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 12 0.36
13 10 0.30
14 11 0.33
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAG
Found at i:4625 original size:7 final size:7
Alignment explanation
Indices: 4609--4659 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
4599 GAAAGAAAGA
*
4609 AAGAAAG
1 AAGAAGG
4616 AAGAAGG
1 AAGAAGG
4623 AAGAAGG
1 AAGAAGG
4630 AAGAAGG
1 AAGAAGG
4637 -AGAA-G
1 AAGAAGG
*
4642 AAG-GGG
1 AAGAAGG
4648 AAGAAGG
1 AAGAAGG
4655 -AGAAG
1 AAGAAG
4660 AAAAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
5 1 0.03
6 15 0.39
7 22 0.58
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:4626 original size:14 final size:14
Alignment explanation
Indices: 4594--4637 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
4584 AAGAAAAAAG
*
4594 AGAAAGAAAGAAAGAA
1 AGAAAG-AAG-AAGGA
4610 AGAAAGAAGAAGGA
1 AGAAAGAAGAAGGA
*
4624 AGAAGGAAGAAGGA
1 AGAAAGAAGAAGGA
4638 GAAGAAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 17 0.65
15 3 0.12
16 6 0.23
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AGAAAGAAGAAGGA
Found at i:4633 original size:25 final size:24
Alignment explanation
Indices: 4583--4662 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
4573 AGGGAAAAAA
* * *
4583 AAAGAAAAAAGAGAAAGAAAGAAAG
1 AAAGAAAGAAGAGGAAG-AAGGAAG
4608 AAAGAAAGAAGAAGGAAGAAGGAAG
1 AAAGAAAGAAG-AGGAAGAAGGAAG
* *
4633 AAGGAGAAGAAGGGGAAGAAGG-AG
1 AAAGA-AAGAAGAGGAAGAAGGAAG
4657 -AAGAAA
1 AAAGAAA
4663 AAAAAAAGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
22 2 0.04
23 3 0.06
24 2 0.04
25 29 0.62
26 11 0.23
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (24 bp):
AAAGAAAGAAGAGGAAGAAGGAAG
Found at i:4643 original size:9 final size:9
Alignment explanation
Indices: 4614--4661 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
4604 AAAGAAAGAA
4614 AGAAGAA-G
1 AGAAGAAGG
4622 -GAAGAA-G
1 AGAAGAAGG
4629 -GAAGAAGG
1 AGAAGAAGG
4637 AGAAGAAGG
1 AGAAGAAGG
*
4646 GGAAGAAGG
1 AGAAGAAGG
4655 AGAAGAA
1 AGAAGAA
4662 AAAAAAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
7 13 0.36
8 1 0.03
9 22 0.61
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Done.