Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008575.1 Kokia drynarioides strain JFW-HI SEQ_123253, 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: 7523
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Found at i:5189 original size:9 final size:10
Alignment explanation
Indices: 5177--5263 Score: 53
Period size: 10 Copynumber: 9.4 Consensus size: 10
5167 AAAATTTATA
5177 TTTTTA-AAT
1 TTTTTATAAT
5186 TTTTTATAAT
1 TTTTTATAAT
* **
5196 TTTCTA-ACG
1 TTTTTATAAT
**
5205 ACTTTATAAT
1 TTTTTATAAT
5215 TTTTT-T-A-
1 TTTTTATAAT
5222 TTTTTATAAT
1 TTTTTATAAT
*
5232 TTTTTCT-AT
1 TTTTTATAAT
* *
5241 TTTTAATAAA
1 TTTTTATAAT
5251 TTTTTAT-AT
1 TTTTTATAAT
5260 TTTT
1 TTTT
5264 ATTAAAATTT
Statistics
Matches: 56, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
7 5 0.09
8 2 0.04
9 24 0.43
10 25 0.45
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:5229 original size:17 final size:17
Alignment explanation
Indices: 5207--5265 Score: 82
Period size: 17 Copynumber: 3.3 Consensus size: 17
5197 TTCTAACGAC
5207 TTTATAATTTTTTTATT
1 TTTATAATTTTTTTATT
5224 TTTATAATTTTTTCTATT
1 TTTATAATTTTTT-TATT
*
5242 TTTAATAAATTTTTATATT
1 TTT-AT-AATTTTTTTATT
5261 TTTAT
1 TTTAT
5266 TAAAATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
17 13 0.34
18 9 0.24
19 9 0.24
20 7 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATAATTTTTTTATT
Found at i:5236 original size:19 final size:18
Alignment explanation
Indices: 5207--5284 Score: 77
Period size: 19 Copynumber: 4.2 Consensus size: 18
5197 TTCTAACGAC
*
5207 TTTAT-AATTTTTTTATT
1 TTTATAAATTTTTATATT
* *
5224 TTTATAATTTTTTCTATT
1 TTTATAAATTTTTATATT
5242 TTTAATAAATTTTTATATT
1 TTT-ATAAATTTTTATATT
* *
5261 TTTATTAAAATTTAATAATT
1 TTTA-TAAATTTTTAT-ATT
5281 TTTA
1 TTTA
5285 GAACTTTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
17 5 0.10
18 14 0.27
19 25 0.49
20 7 0.14
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATAAATTTTTATATT
Found at i:5261 original size:8 final size:9
Alignment explanation
Indices: 5147--5304 Score: 60
Period size: 9 Copynumber: 17.1 Consensus size: 9
5137 TTAGGTACGG
*
5147 TAATTTTCA
1 TAATTTTTA
5156 TAATTTTTTA
1 TAA-TTTTTA
* **
5166 CAAAATTTA
1 TAATTTTTA
5175 T-ATTTTTA
1 TAATTTTTA
5183 -AATTTTTTA
1 TAA-TTTTTA
5192 TAATTTTCTA
1 TAATTTT-TA
*
5202 -ACGA-CTTTA
1 TA--ATTTTTA
5211 TAATTTTT-
1 TAATTTTTA
*
5219 TTATTTTTA
1 TAATTTTTA
5228 TAATTTTT-
1 TAATTTTTA
*
5236 TCTATTTTTAA
1 T-AATTTTT-A
5247 TAAATTTTTA
1 T-AATTTTTA
5257 T-ATTTTTA
1 TAATTTTTA
* *
5265 TTAAAATTTAA
1 -T-AATTTTTA
5276 TAATTTTTA
1 TAATTTTTA
* *
5285 GAACTTTTA
1 TAATTTTTA
*
5294 TTGATTTTTA
1 -TAATTTTTA
5304 T
1 T
5305 TTTTCATCAA
Statistics
Matches: 109, Mismatches: 23, Indels: 34
0.66 0.14 0.20
Matches are distributed among these distances:
8 22 0.20
9 51 0.47
10 23 0.21
11 13 0.12
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.61
Consensus pattern (9 bp):
TAATTTTTA
Found at i:5303 original size:29 final size:29
Alignment explanation
Indices: 5239--5303 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
5229 AATTTTTTCT
* *
5239 ATTTTTAATAAATTTTTATATTTTTATTA
1 ATTTTTAATAAATTTTTAAACTTTTATTA
** *
5268 AAATTTAAT-AATTTTTAGAACTTTTATTG
1 ATTTTTAATAAATTTTTA-AACTTTTATTA
5297 ATTTTTA
1 ATTTTTA
5304 TTTTTCATCA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (29 bp):
ATTTTTAATAAATTTTTAAACTTTTATTA
Done.