Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003221.1 Kokia drynarioides strain JFW-HI SEQ_115850, 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: 12675
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:210 original size:6 final size:6
Alignment explanation
Indices: 167--265 Score: 66
Period size: 6 Copynumber: 17.0 Consensus size: 6
157 TTTTATTTAT
* * *
167 TTTAAA TTTTAAA TTTGAAA -ATAAT TTTAAA CTT-AA TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
215 TTTAAA -ATAAA TTTAAA TTTTAAA --CAAA TTTAAT TTTAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
260 TTTAAA
1 TTTAAA
266 GGGAGTATGG
Statistics
Matches: 70, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
4 3 0.04
5 14 0.20
6 38 0.54
7 15 0.21
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:213 original size:11 final size:11
Alignment explanation
Indices: 161--265 Score: 52
Period size: 11 Copynumber: 9.1 Consensus size: 11
151 TTTGGGTTTT
*
161 ATTTATTTTAA
1 ATTTAATTTAA
172 ATTTTAAATTTGAA
1 A-TTT-AATTT-AA
*
186 A-ATAATTTTAA
1 ATTTAA-TTTAA
*
197 ACTTAATTTAA
1 ATTTAATTTAA
208 ATTTAAATTTAA
1 ATTT-AATTTAA
* *
220 AATAAATTTAA
1 ATTTAATTTAA
**
231 ATTTTAA-ACAA
1 A-TTTAATTTAA
242 ATTTAATTTTAA
1 ATTTAA-TTTAA
* *
254 AATAAATTTAA
1 ATTTAATTTAA
265 A
1 A
266 GGGAGTATGG
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
10 5 0.07
11 31 0.44
12 28 0.39
13 4 0.06
14 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:214 original size:17 final size:17
Alignment explanation
Indices: 169--265 Score: 86
Period size: 17 Copynumber: 5.6 Consensus size: 17
159 TTATTTATTT
*
169 TAAATTTTAAATTTGAAAA
1 TAAA-TTTAAACTT-AAAA
* **
188 TAATTTTAAACTTAATT
1 TAAATTTAAACTTAAAA
*
205 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
* *
222 TAAATTTAAATTTTAAA
1 TAAATTTAAACTTAAAA
* **
239 CAAATTTAATTTTAAAA
1 TAAATTTAAACTTAAAA
256 TAAATTTAAA
1 TAAATTTAAA
266 GGGAGTATGG
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
17 53 0.83
18 8 0.12
19 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:222 original size:34 final size:35
Alignment explanation
Indices: 167--265 Score: 121
Period size: 34 Copynumber: 2.8 Consensus size: 35
157 TTTTATTTAT
*
167 TTTAAATTTTAAATTTGAAAATAATTTTAAA-CTTAA
1 TTTAAA-TTTAAATTT-AAAATAAATTTAAATCTTAA
*
203 TTTAAATTTAAATTTAAAATAAATTTAAATTTTAA
1 TTTAAATTTAAATTTAAAATAAATTTAAATCTTAA
** *
238 -ACAAATTTAATTTTAAAATAAATTTAAA
1 TTTAAATTTAAATTTAAAATAAATTTAAA
266 GGGAGTATGG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
34 38 0.67
35 13 0.23
36 6 0.11
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (35 bp):
TTTAAATTTAAATTTAAAATAAATTTAAATCTTAA
Found at i:4009 original size:26 final size:26
Alignment explanation
Indices: 3963--4016 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3953 TTTTCATTAA
* *
3963 ATATTTTAATAACAGAGAATATTTGG
1 ATATTTTAATAACAGAAAATAATTGG
3989 ATATTTTAATAATC-GAAAATAATTGG
1 ATATTTTAATAA-CAGAAAATAATTGG
4015 AT
1 AT
4017 GTGATGCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.39
Consensus pattern (26 bp):
ATATTTTAATAACAGAAAATAATTGG
Found at i:4342 original size:22 final size:23
Alignment explanation
Indices: 4307--4351 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4297 TATGATAGTA
*
4307 AATAATATAAA-TTTATTATTTT
1 AATAATATAAATTTTATAATTTT
* *
4329 AATAATCTATATTTTATAATTTT
1 AATAATATAAATTTTATAATTTT
4352 TAAAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
AATAATATAAATTTTATAATTTT
Found at i:4372 original size:29 final size:30
Alignment explanation
Indices: 4339--4407 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
4329 AATAATCTAT
*
4339 ATTTTATA-ATTTTTAAAAAATTAAATTA-A
1 ATTTTATATATTTTT-AAAAATTAAAATATA
4368 ATTTT-TATATTTTTAAAAATTAAAATATA
1 ATTTTATATATTTTTAAAAATTAAAATATA
4397 ATTTTAT-TATT
1 ATTTTATATATT
4408 ACTAATTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 14 0.39
29 21 0.58
30 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTTTATATATTTTTAAAAATTAAAATATA
Found at i:4389 original size:28 final size:31
Alignment explanation
Indices: 4340--4401 Score: 94
Period size: 28 Copynumber: 2.1 Consensus size: 31
4330 ATAATCTATA
*
4340 TTTTATAATTTTTAAAAAATTAAATTA-AAT
1 TTTTATAATTTTTAAAAAATTAAAATATAAT
4370 TTTTAT-ATTTTT-AAAAATTAAAATATAAT
1 TTTTATAATTTTTAAAAAATTAAAATATAAT
4399 TTT
1 TTT
4402 ATTATTACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 12 0.40
29 12 0.40
30 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTTATAATTTTTAAAAAATTAAAATATAAT
Found at i:4879 original size:19 final size:18
Alignment explanation
Indices: 4847--4894 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
4837 ATATTTTATT
*
4847 AAATAAATTTATAAATTTT
1 AAAT-AATTTATAAATTTA
*
4866 TAATAATTTCATAAATTTA
1 AAATAATTT-ATAAATTTA
4885 AAATAATTTA
1 AAATAATTTA
4895 AAAAACTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAATTTATAAATTTA
Found at i:5047 original size:21 final size:21
Alignment explanation
Indices: 5021--5061 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5011 TCTTACCGTT
5021 GTTTCTAATCTCACCGCTATA
1 GTTTCTAATCTCACCGCTATA
*
5042 GTTTCTAATCTCACTGCTAT
1 GTTTCTAATCTCACCGCTAT
5062 CGCTGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.41
Consensus pattern (21 bp):
GTTTCTAATCTCACCGCTATA
Found at i:7140 original size:13 final size:13
Alignment explanation
Indices: 7111--7152 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
7101 GTTTCCCGAA
7111 AAAGTCAACGAGTC
1 AAAGTCAACG-GTC
7125 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
7138 AAAGTCAATGGTC
1 AAAGTCAACGGTC
7151 AA
1 AA
7153 CGGATCGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:7743 original size:88 final size:88
Alignment explanation
Indices: 7594--7772 Score: 349
Period size: 88 Copynumber: 2.0 Consensus size: 88
7584 AGAAGAACAA
7594 AAGCTGAAAACTTCCTTTCGTCGAAACTCACGAACGACAGCGATTAAAGCGACGTGAAATAAGGG
1 AAGCTGAAAACTTCCTTTCGTCGAAACTCACGAACGACAGCGATTAAAGCGACGTGAAATAAGGG
7659 GTTTTAGTCGCGAGGAAACAAGG
66 GTTTTAGTCGCGAGGAAACAAGG
*
7682 AAGCTGAAAACTTCCTTTCGTCGAAACTCACGAACGACAGCGATTAAAGTGACGTGAAATAAGGG
1 AAGCTGAAAACTTCCTTTCGTCGAAACTCACGAACGACAGCGATTAAAGCGACGTGAAATAAGGG
7747 GTTTTAGTCGCGAGGAAACAAGG
66 GTTTTAGTCGCGAGGAAACAAGG
7770 AAG
1 AAG
7773 ACTTTGATAG
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (88 bp):
AAGCTGAAAACTTCCTTTCGTCGAAACTCACGAACGACAGCGATTAAAGCGACGTGAAATAAGGG
GTTTTAGTCGCGAGGAAACAAGG
Done.