Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012387.1 Kokia drynarioides strain JFW-HI SEQ_127391, 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: 8538
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Found at i:6946 original size:28 final size:28
Alignment explanation
Indices: 6911--6983 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
6901 CGGGGGAAGG
6911 AATGGTAATTTTGGA-TTTTCAGGGGCAA
1 AATGGTAATTTTGGAGTTTTCA-GGGCAA
* *
6939 AATGGTAATTTTGAGAGTTTTGAGGTCAA
1 AATGGTAATTTTG-GAGTTTTCAGGGCAA
*
6968 AATGGAAATTTTGGAG
1 AATGGTAATTTTGGAG
6984 GTTCAAGGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 16 0.40
29 19 0.47
30 5 0.12
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.36
Consensus pattern (28 bp):
AATGGTAATTTTGGAGTTTTCAGGGCAA
Found at i:7129 original size:30 final size:29
Alignment explanation
Indices: 6966--7361 Score: 453
Period size: 29 Copynumber: 13.4 Consensus size: 29
6956 TTTTGAGGTC
* * *
6966 AAAATGGAAATTTTGGAGGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
**
6995 AAAAT-GAGATTTTTGGAAGTTTTAGGGTAAA
1 AAAATGGA-ATTTTTGGAAGTTCGAGGGT--A
* * *
7026 AAAATGGAATTTTTGAAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
7055 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
7084 AAACTGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
7113 AAAATGGAATTTTTTGGAAGTTCGAGGGTA
1 AAAATGGAA-TTTTTGGAAGTTCGAGGGTA
* *
7143 AAAATGAAATTTTTGAAAGTTTCG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* *
7173 AAAATGAAATTTTTGAAAGTTTCG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* *
7203 AAAATGGAATTTTTGGAAGTTTGGGGGT-
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
**
7231 AAAATGGAATTTTTGGAAGTTTCG-GCATCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
*
7261 AAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
7290 AAATTGGAATTTTTGGAAGTTTCG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
*
7320 AAAATGGAATTTTTGGAAGCTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
7349 AAAAAGGAATTTT
1 AAAATGGAATTTT
7362 CGAATAGTTC
Statistics
Matches: 326, Mismatches: 26, Indels: 30
0.85 0.07 0.08
Matches are distributed among these distances:
28 23 0.07
29 146 0.45
30 132 0.40
31 23 0.07
32 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:7156 original size:59 final size:59
Alignment explanation
Indices: 6937--7361 Score: 483
Period size: 59 Copynumber: 7.2 Consensus size: 59
6927 TTTCAGGGGC
* * * * *
6937 AAAATGGTAA-TTTT-GAGAGTTTTGAGGTC-AAAATGGAAATTTTGGAGGTTCAAGGGTA
1 AAAATGG-AATTTTTGGA-AGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
** * * * *
6995 AAAAT-GAGATTTTTGGAAGTTTTAGGGTAAAAAAATGGAATTTTTGAAAGTTTGGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTCGGGGT-CAAAAATGGAATTTTTGGAAGTTCGAGGGTA
*
7055 AAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAACTGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
7113 AAAATGGAATTTTTTGGAAG-TTCGAGGGT-AAAAATGAAATTTTTGAAAGTTTCG-GGGTCA
1 AAAATGGAA-TTTTTGGAAGTTTCG-GGGTCAAAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* * * *
7173 AAAATGAAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGT-
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
** *
7231 AAAATGGAATTTTTGGAAGTTTCGGCATCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
7290 AAATTGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGCTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
*
7349 AAAAAGGAATTTT
1 AAAATGGAATTTT
7362 CGAATAGTTC
Statistics
Matches: 318, Mismatches: 35, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
56 1 0.00
57 2 0.01
58 106 0.33
59 125 0.39
60 82 0.26
61 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:7375 original size:29 final size:29
Alignment explanation
Indices: 6966--7361 Score: 405
Period size: 30 Copynumber: 13.4 Consensus size: 29
6956 TTTTGAGGTC
* *
6966 AAAATGGAAATTTTGG-AGGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-AGGGTA
*
6995 AAAAT-GAGATTTTTGGAAGTTTTAGGGTAAA
1 AAAATGGA-ATTTTTGGAAGTTTCAGGGT--A
* **
7026 AAAATGGAATTTTTGAAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCAGGGTA
7055 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-AGGGTA
*
7084 AAACTGGAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-AGGGTA
7113 AAAATGGAATTTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAA-TTTTTGGAAGTTTC-AGGGTA
* * *
7143 AAAATGAAATTTTTGAAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCAGGGT-A
* * *
7173 AAAATGAAATTTTTGAAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCAGGGT-A
**
7203 AAAATGGAATTTTTGGAAGTTTGGGGGT-
1 AAAATGGAATTTTTGGAAGTTTCAGGGTA
*
7231 AAAATGGAATTTTTGGAAGTTTC-GGCATCA
1 AAAATGGAATTTTTGGAAGTTTCAGG-GT-A
*
7261 AAAATGGAATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-AGGGTA
* *
7290 AAATTGGAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCAGGGT-A
*
7320 AAAATGGAATTTTTGGAAG-CTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-AGGGTA
*
7349 AAAAAGGAATTTT
1 AAAATGGAATTTT
7362 CGAATAGTTC
Statistics
Matches: 325, Mismatches: 25, Indels: 34
0.85 0.07 0.09
Matches are distributed among these distances:
27 2 0.01
28 27 0.08
29 132 0.41
30 137 0.42
31 25 0.08
32 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCAGGGTA
Found at i:8485 original size:12 final size:12
Alignment explanation
Indices: 8470--8516 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
8460 ATTATTAATG
8470 TTATTAATATTA
1 TTATTAATATTA
8482 TTA-TAGATATTA
1 TTATTA-ATATTA
8494 TTATTAATACCATTA
1 TTATTAAT---ATTA
8509 TTATTAAT
1 TTATTAAT
8517 GCTATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.07
12 14 0.47
13 2 0.07
15 12 0.40
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (12 bp):
TTATTAATATTA
Done.