Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001084.1 Kokia drynarioides strain JFW-HI SEQ_112343, 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: 29040
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2848 original size:24 final size:25
Alignment explanation
Indices: 2821--2879 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
2811 ATTTAAACTC
*
2821 TATTTTTTAGGA-TTAATATTATTA
1 TATTTTTTAGGATTTAATATTAATA
* * *
2845 TATTGTTTA-TATTTAATTTTAATA
1 TATTTTTTAGGATTTAATATTAATA
*
2869 TATCTTTTAGG
1 TATTTTTTAGG
2880 CTTTGTAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (25 bp):
TATTTTTTAGGATTTAATATTAATA
Found at i:4121 original size:5 final size:6
Alignment explanation
Indices: 4032--4172 Score: 50
Period size: 6 Copynumber: 21.2 Consensus size: 6
4022 ACTTGAGCAT
* * * *
4032 TTTTTA TTTTTGT TTTATTA TTTGTA TTTTTA ATTTAA TTTTTA TATTTTAA
1 TTTTTA TTTTT-A TTT-TTA TTTTTA TTTTTA TTTTTA TTTTTA T-TTTT-A
** *
4084 TCTTTT- TCTCTTTA TTTAGCCA TTTTTA TTTTTA TTTTCATA TTTTTTG
1 T-TTTTA T-T-TTTA TTT--TTA TTTTTA TTTTTA TTTT--TA -TTTTTA
* * *
4133 TTTTTA ATTTAA TTTTTACA TTTTAA TTTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTT--A TTTTTA -TTTTTA TTTTTA T
4173 AGGTTCTTTT
Statistics
Matches: 100, Mismatches: 21, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
6 56 0.56
7 20 0.20
8 20 0.20
9 4 0.04
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTTTA
Found at i:4136 original size:27 final size:27
Alignment explanation
Indices: 4106--4172 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
4096 TATTTAGCCA
* *
4106 TTTTTATTTTTATTTTCATATTTT-TT
1 TTTTTATTTTTATTTTCACATTTTAAT
* * *
4132 GTTTTTAATTTAATTTTTACATTTTAAT
1 -TTTTTATTTTTATTTTCACATTTTAAT
4160 TTTTTATTTTTAT
1 TTTTTATTTTTAT
4173 AGGTTCTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (27 bp):
TTTTTATTTTTATTTTCACATTTTAAT
Found at i:6182 original size:18 final size:18
Alignment explanation
Indices: 6161--6195 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6151 TTTAAAAATA
6161 AAAAATGAAAAAAAATTG
1 AAAAATGAAAAAAAATTG
**
6179 AAAAATTCAAAAAAATT
1 AAAAATGAAAAAAAATT
6196 AGTACATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAAATGAAAAAAAATTG
Found at i:6226 original size:12 final size:12
Alignment explanation
Indices: 6205--6250 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
6195 TAGTACATTT
*
6205 ATTTTTATTTTC
1 ATTTTCATTTTC
6217 ATTTTCATTTTTC
1 ATTTTCA-TTTTC
6230 A-TTTCATTTT-
1 ATTTTCATTTTC
*
6240 ATTTTTATTTT
1 ATTTTCATTTT
6251 TTATTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 1 0.03
11 12 0.40
12 11 0.37
13 6 0.20
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTCATTTTC
Found at i:6228 original size:18 final size:17
Alignment explanation
Indices: 6202--6260 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
6192 AATTAGTACA
6202 TTTATTTTTATTTTCAT
1 TTTATTTTTATTTTCAT
6219 TTTCATTTTTCA-TTTCAT
1 TTT-ATTTTT-ATTTTCAT
*
6237 TTTATTTTTATTTTTTAT
1 TTTATTTTTA-TTTTCAT
6255 TTTATT
1 TTTATT
6261 ATGCACTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 1 0.03
17 9 0.24
18 26 0.70
19 1 0.03
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTTATTTTCAT
Found at i:6230 original size:13 final size:13
Alignment explanation
Indices: 6212--6257 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
6202 TTTATTTTTA
6212 TTTTCATTTTCAT
1 TTTTCATTTTCAT
6225 TTTTCA-TTTCA-
1 TTTTCATTTTCAT
*
6236 TTTT-ATTTTTAT
1 TTTTCATTTTCAT
*
6248 TTTTTATTTT
1 TTTTCATTTT
6258 ATTATGCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 1 0.03
11 8 0.28
12 9 0.31
13 11 0.38
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCATTTTCAT
Found at i:6276 original size:6 final size:6
Alignment explanation
Indices: 6202--6257 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
6192 AATTAGTACA
* * *
6202 TTTATT TTTATT TTCATT TTCATT TTTCA-T TTCA-T TTTATT TTTATTT
1 TTTATT TTTATT TTTATT TTTATT TTT-ATT TTTATT TTTATT TTTA-TT
6250 TTTATT TT
1 TTTATT TT
6258 ATTATGCACT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
5 5 0.12
6 31 0.72
7 7 0.16
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:6492 original size:20 final size:20
Alignment explanation
Indices: 6467--6507 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6457 AATGTAGATC
6467 TTAAGTGTGGAGAGGTTGGT
1 TTAAGTGTGGAGAGGTTGGT
6487 TTAAGTGTGGAGAGGTTGGT
1 TTAAGTGTGGAGAGGTTGGT
6507 T
1 T
6508 ATGTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.37
Consensus pattern (20 bp):
TTAAGTGTGGAGAGGTTGGT
Found at i:9987 original size:12 final size:12
Alignment explanation
Indices: 9970--10022 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
9960 CAGGTTCAGT
9970 TTCTTCCTTCTC
1 TTCTTCCTTCTC
9982 TTCTTCCTTTCCTTC
1 TTCTTCC-TT-C-TC
* *
9997 TTCTTCTTTTTC
1 TTCTTCCTTCTC
*
10009 TTCATCCTTCTC
1 TTCTTCCTTCTC
10021 TT
1 TT
10023 GATCACCTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 20 0.61
13 2 0.06
14 3 0.09
15 8 0.24
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTTCCTTCTC
Found at i:19279 original size:14 final size:14
Alignment explanation
Indices: 19259--19293 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19249 TTTATTGTTT
19259 AGAAAAAAAAAAGA
1 AGAAAAAAAAAAGA
* *
19273 GGAAAAAAAAGAGA
1 AGAAAAAAAAAAGA
19287 AGAAAAA
1 AGAAAAA
19294 TTGAAAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAAGA
Found at i:19307 original size:17 final size:16
Alignment explanation
Indices: 19286--19318 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19276 AAAAAAAGAG
*
19286 AAGA-AAAATTGAAAA
1 AAGAGAAAATTCAAAA
19301 AAGAGAAAATTCAAAA
1 AAGAGAAAATTCAAAA
19317 AA
1 AA
19319 AAATGTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (16 bp):
AAGAGAAAATTCAAAA
Found at i:20266 original size:13 final size:13
Alignment explanation
Indices: 20250--20277 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20240 AAATTCTATT
20250 TTTAGGATTAATA
1 TTTAGGATTAATA
20263 TTTAGGATTAATA
1 TTTAGGATTAATA
20276 TT
1 TT
20278 ATTATATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TTTAGGATTAATA
Found at i:28488 original size:18 final size:20
Alignment explanation
Indices: 28451--28488 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28441 TAAGCTTCAT
28451 TAAGTTAGAAAATGTAATAAC
1 TAAGTTAGAAAA-GTAATAAC
28472 TAAGTTA-AAAA-TAATAA
1 TAAGTTAGAAAAGTAATAA
28489 AAATGCATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.29
Consensus pattern (20 bp):
TAAGTTAGAAAAGTAATAAC
Done.