Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003385.1 Kokia drynarioides strain JFW-HI SEQ_116119, 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: 31367
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 55 characters in sequence are not A, C, G, or T
Found at i:1100 original size:18 final size:19
Alignment explanation
Indices: 1077--1119 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1067 TTAGTCATTT
1077 TTTTATTATTT-ATTTTTA
1 TTTTATTATTTCATTTTTA
1095 TTTTATTATTTGCATTTTTA
1 TTTTATTATTT-CATTTTTA
*
1115 ATTTA
1 TTTTA
1120 ATTTTTCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
20 11 0.50
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTATTATTTCATTTTTA
Found at i:6613 original size:17 final size:17
Alignment explanation
Indices: 6591--6628 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
6581 AATTAGTATA
6591 TTTATTTTCAATTTTAT
1 TTTATTTTCAATTTTAT
*
6608 TTTATTTTTAATTTTAT
1 TTTATTTTCAATTTTAT
6625 TTTA
1 TTTA
6629 ATTATGCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTCAATTTTAT
Found at i:7573 original size:8 final size:8
Alignment explanation
Indices: 7556--7584 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
7546 TATTGTTTAG
7556 AAAAAA-A
1 AAAAAAGA
7563 AAAAAAGA
1 AAAAAAGA
7571 AAAAAAGA
1 AAAAAAGA
7579 AAAAAA
1 AAAAAA
7585 AAGTCGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:7573 original size:14 final size:15
Alignment explanation
Indices: 7554--7583 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
7544 GTTATTGTTT
7554 AGAAAAAAA-AAAAA
1 AGAAAAAAAGAAAAA
7568 AGAAAAAAAGAAAAA
1 AGAAAAAAAGAAAAA
7583 A
1 A
7584 AAAGTCGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAGAAAAA
Found at i:7594 original size:18 final size:18
Alignment explanation
Indices: 7554--7600 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
7544 GTTATTGTTT
7554 AGAAAA-AAAAAAAAAGA
1 AGAAAAGAAAAAAAAAGA
* *
7571 AAAAAAGAAAAAAAAAGT
1 AGAAAAGAAAAAAAAAGA
*
7589 CGAAAAGAAAAA
1 AGAAAAGAAAAA
7601 TTGAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (18 bp):
AGAAAAGAAAAAAAAAGA
Found at i:8849 original size:20 final size:20
Alignment explanation
Indices: 8824--8862 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
8814 CCCTAGTCGT
8824 CAGAGATTATTAAAGGAAAA
1 CAGAGATTATTAAAGGAAAA
8844 CAGAGATTATTAAAGGAAA
1 CAGAGATTATTAAAGGAAA
8863 CAACTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.21
Consensus pattern (20 bp):
CAGAGATTATTAAAGGAAAA
Found at i:23003 original size:74 final size:74
Alignment explanation
Indices: 22908--23066 Score: 185
Period size: 74 Copynumber: 2.1 Consensus size: 74
22898 ACAGGTAATT
* * ** ** *
22908 AGGCACTATTGTTCATGATTAGTTTGAACGAGCAATTGATACTTGTTGTGTAAGTTTAACCCGAA
1 AGGCACTATTATTCATGATTAGCTCAAACGAGCAATTGATACTTAATGTGTAAGTTTAACCCAAA
22973 CAAGTAACC
66 CAAGTAACC
* * * *
22982 AGGCACTATTATTCACT-ATTAGCTCAAATGAGTAATTGATATTTAATGTGTAGGTTTAACCCAA
1 AGGCACTATTATTCA-TGATTAGCTCAAACGAGCAATTGATACTTAATGTGTAAGTTTAACCCAA
**
23046 ACGGGTAACC
65 ACAAGTAACC
23056 AGGCACTATTA
1 AGGCACTATTA
23067 ATTTCACTTG
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
74 70 0.99
75 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (74 bp):
AGGCACTATTATTCATGATTAGCTCAAACGAGCAATTGATACTTAATGTGTAAGTTTAACCCAAA
CAAGTAACC
Found at i:26208 original size:14 final size:13
Alignment explanation
Indices: 26182--26206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26172 ATTAATATTC
26182 GATCAATTTTTTA
1 GATCAATTTTTTA
26195 GATCAATTTTTT
1 GATCAATTTTTT
26207 TAAAATTATA
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:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (13 bp):
GATCAATTTTTTA
Found at i:26233 original size:20 final size:21
Alignment explanation
Indices: 26193--26236 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
26183 ATCAATTTTT
*
26193 TAGATCAATTTTTTTAAAATTA
1 TAGATCAATTTTTCT-AAATTA
26215 TAGATCAATTTTTCT-AATTA
1 TAGATCAATTTTTCTAAATTA
26235 TA
1 TA
26237 TTTGAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
TAGATCAATTTTTCTAAATTA
Found at i:30331 original size:6 final size:7
Alignment explanation
Indices: 30288--30313 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
30278 AATTTTATAT
30288 AAAAATA
1 AAAAATA
30295 AAAAATA
1 AAAAATA
30302 AAAAATA
1 AAAAATA
30309 AAAAA
1 AAAAA
30314 CAGTTTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:31211 original size:4 final size:4
Alignment explanation
Indices: 31198--31236 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
31188 AAAATTGAAG
*
31198 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAA
31237 GAAGAAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:31228 original size:21 final size:20
Alignment explanation
Indices: 31198--31238 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
31188 AAAATTGAAG
31198 GAAAAAAGAAAGAAAAAAGA
1 GAAAAAAGAAAGAAAAAAGA
*
31218 GAAAGAAAGAAAGAAAGAAGA
1 GAAA-AAAGAAAGAAAAAAGA
31239 AGAAGGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
GAAAAAAGAAAGAAAAAAGA
Found at i:31241 original size:18 final size:18
Alignment explanation
Indices: 31202--31287 Score: 63
Period size: 18 Copynumber: 4.9 Consensus size: 18
31192 TTGAAGGAAA
*
31202 AAAGAAAGAAAAAAG-AG
1 AAAGAAAGAAAGAAGAAG
31219 AAAGAAAGAAAGAAAGAAG
1 AAAGAAAGAAAG-AAGAAG
* *
31238 -AAG-AAGGAAGAAGGAG
1 AAAGAAAGAAAGAAGAAG
* * *
31254 -AAGAAGGGGAAGAAGGAG
1 AAAGAA-AGAAAGAAGAAG
*
31272 AAAGAAAAAAAGAAGA
1 AAAGAAAGAAAGAAGA
31288 TAATGTGTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
16 8 0.14
17 18 0.32
18 23 0.41
19 7 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAGAAGAAG
Found at i:31248 original size:25 final size:24
Alignment explanation
Indices: 31194--31287 Score: 83
Period size: 25 Copynumber: 4.1 Consensus size: 24
31184 AACGAAAATT
*
31194 GAAGGAAAAAAGAAAGAA-AA-AA
1 GAAGGAAGAAAGAAAGAAGAAGAA
*
31216 G-AGAAAGAAAGAAAGAAAGAAGAA
1 GAAGGAAGAAAGAAAG-AAGAAGAA
* **
31240 GAAGGAAGAAGGAGAAGAAGGGGAA
1 GAAGGAAGAAAGA-AAGAAGAAGAA
31265 GAAGG-AGAAAGAAA-AA-AAGAA
1 GAAGGAAGAAAGAAAGAAGAAGAA
31286 GA
1 GA
31288 TAATGTGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
21 17 0.29
22 5 0.09
23 4 0.07
24 9 0.16
25 20 0.34
26 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
GAAGGAAGAAAGAAAGAAGAAGAA
Found at i:31258 original size:9 final size:9
Alignment explanation
Indices: 31233--31273 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
31223 AAAGAAAGAA
*
31233 AGAAGAAGA
1 AGAAGAAGG
31242 AGGAAGAAGG
1 A-GAAGAAGG
31252 AGAAGAAGG
1 AGAAGAAGG
*
31261 GGAAGAAGG
1 AGAAGAAGG
31270 AGAA
1 AGAA
31274 AGAAAAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Done.