Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013814.1 Kokia drynarioides strain JFW-HI SEQ_128842, 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: 2874
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:200 original size:29 final size:29
Alignment explanation
Indices: 158--504 Score: 164
Period size: 29 Copynumber: 11.9 Consensus size: 29
148 GGAGGGGGGC
* * *
158 AAAATGGTAGTTTTGGAAGGTTCGAAATCA
1 AAAATGGGATTTTTGGAA-GTTCGAGATCA
*
188 AAAATGGGATTTTTGGAAGTTCGAGGGT--
1 AAAATGGGATTTTTGGAAGTTCGA-GATCA
* * *
216 AAAATGGTAATTTTCGAAAGGTTCG-GATCA
1 AAAATGG-GATTTTTGGAA-GTTCGAGATCA
*
246 AAAATGGGATTTTTGGAAGTTCGAGGGT--
1 AAAATGGGATTTTTGGAAGTTCGA-GATCA
* * *
274 AAAATGGTAATTTTTAGAAGGTTCCG-GGTCA
1 AAAATGG-GATTTTTGGAA-GTT-CGAGATCA
* * *
305 AAAATGGGATTTGTGGAAGTTCGGGGGT--
1 AAAATGGGATTTTTGGAAGTTC-GAGATCA
* * * *
333 AAAATGGTAATTTTTGGAAGTT-TAGGGTTA
1 AAAATGG-GATTTTTGGAAGTTCGA-GATCA
* * *
363 AAAATGGGATTTTTGGAAGTTTAGGGGT--
1 AAAATGGGATTTTTGGAAG-TTCGAGATCA
* * * *
391 AAAATGGTAATTTTTAGAAGATTCGGGGTCA
1 AAAATGG-GATTTTTGGAAG-TTCGAGATCA
*
422 AAAATGGGATTTTTGGAAGTTCGAGGGT--
1 AAAATGGGATTTTTGGAAGTTCGA-GATCA
* * * *
450 AAAATGGTAATTTTTGGAAGATTTGGGGTC-
1 AAAATGG-GATTTTTGGAAG-TTCGAGATCA
*
480 AAAATGGGATTTTTGGAAGCTCGAG
1 AAAATGGGATTTTTGGAAGTTCGAG
505 GGTAAAATGG
Statistics
Matches: 252, Mismatches: 38, Indels: 56
0.73 0.11 0.16
Matches are distributed among these distances:
28 49 0.19
29 107 0.42
30 80 0.32
31 16 0.06
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (29 bp):
AAAATGGGATTTTTGGAAGTTCGAGATCA
Found at i:309 original size:117 final size:117
Alignment explanation
Indices: 185--530 Score: 534
Period size: 117 Copynumber: 3.0 Consensus size: 117
175 AGGTTCGAAA
* * * * *
185 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTCGAAAGGTTCGGATCAAAAA
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTAGGGTCAAAAA
250 TGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCCGGG
66 TGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCCGGG
* * *
302 TCAAAAATGGGATTTGTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTAGGGTTAAAAA
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTAGGGTCAAAAA
* * *
367 TGGGATTTTTGGAAGTT-TAGGGGTAAAATGGTAATTTTTAGAAGATTCGGGG
66 TGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTAGAAGGTTCCGGG
*
419 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGATTTGGGGTC-AAA
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAG-TTTAGGGTCAAAA
* *
483 ATGGGATTTTTGGAAGCTCGAGGGTAAAATGGTAATTTTTGGAAGGTT
65 ATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTT
531 TAGGGACCTC
Statistics
Matches: 207, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
116 1 0.00
117 198 0.96
118 8 0.04
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (117 bp):
TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTAGGGTCAAAAA
TGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCCGGG
Found at i:335 original size:59 final size:59
Alignment explanation
Indices: 158--530 Score: 506
Period size: 58 Copynumber: 6.4 Consensus size: 59
148 GGAGGGGGGC
* **
158 AAAATGGT-AGTTTTGGAAGGTT-CGAAATCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCCG-GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
216 AAAATGGTAATTTTCGAAAGGTT-CGGATCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
274 AAAATGGTAATTTTTAGAAGGTTCCGGGTCAAAAATGGGATTTGTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
** * *
333 AAAATGGTAATTTTTGGAA-GTTTAGGGTTAAAAATGGGATTTTTGGAAGTT-TAGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCCGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGT
* * *
391 AAAATGGTAATTTTTAGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* ** *
450 AAAATGGTAATTTTTGGAAGATTTGGGGTC-AAAATGGGATTTTTGGAAGCTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
508 AAAATGGTAATTTTTGGAAGGTT
1 AAAATGGTAATTTTTGGAAGGTT
531 TAGGGACCTC
Statistics
Matches: 283, Mismatches: 27, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
58 159 0.56
59 123 0.43
60 1 0.00
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGGTTCCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:2280 original size:15 final size:15
Alignment explanation
Indices: 2260--2315 Score: 94
Period size: 15 Copynumber: 3.7 Consensus size: 15
2250 TTTTGGGTAG
2260 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
*
2275 TCTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
*
2290 TTTGTTATTGGGCCA
1 TTTGTAATTGGGCCA
2305 TTTGTAATTGG
1 TTTGTAATTGG
2316 ACTTTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.43
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:2340 original size:13 final size:14
Alignment explanation
Indices: 2305--2345 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
2295 TATTGGGCCA
2305 TTTG-TAATTGGAC
1 TTTGTTAATTGGAC
2318 TTTGTT--TTGGAC
1 TTTGTTAATTGGAC
2330 TTT-TTAATTGGAC
1 TTTGTTAATTGGAC
2343 TTT
1 TTT
2346 CTAAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 13 0.52
14 1 0.04
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.56
Consensus pattern (14 bp):
TTTGTTAATTGGAC
Found at i:2369 original size:17 final size:16
Alignment explanation
Indices: 2347--2432 Score: 66
Period size: 17 Copynumber: 5.2 Consensus size: 16
2337 TTGGACTTTC
*
2347 TAAATTTAATTTTATAA
1 TAAATTTAATTTCA-AA
*
2364 TAAATTTAAATGTCAAA
1 TAAATTT-AATTTCAAA
*
2381 TAAATTTAAATTCAAAA
1 TAAATTTAATTTC-AAA
*
2398 TAAACTTAAATTT-AAA
1 TAAA-TTTAATTTCAAA
* * *
2414 TCAATTCAATTTCCAA
1 TAAATTTAATTTCAAA
2430 TAA
1 TAA
2433 GTCCAGACAA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
15 7 0.13
16 14 0.25
17 23 0.42
18 11 0.20
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (16 bp):
TAAATTTAATTTCAAA
Found at i:2385 original size:34 final size:33
Alignment explanation
Indices: 2347--2426 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 33
2337 TTGGACTTTC
* * *
2347 TAAATTTAATTTTATAATAAATTTAAATGTCAAA
1 TAAATTTAATTTCAAAATAAACTTAAAT-TCAAA
* *
2381 TAAATTTAAATTCAAAATAAACTTAAATTTAAA
1 TAAATTTAATTTCAAAATAAACTTAAATTCAAA
* *
2414 TCAATTCAATTTC
1 TAAATTTAATTTC
2427 CAATAAGTCC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 14 0.37
34 24 0.63
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.41
Consensus pattern (33 bp):
TAAATTTAATTTCAAAATAAACTTAAATTCAAA
Done.