Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008967.1 Kokia drynarioides strain JFW-HI SEQ_123663, 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: 1794
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Found at i:412 original size:30 final size:30
Alignment explanation
Indices: 378--695 Score: 264
Period size: 30 Copynumber: 10.8 Consensus size: 30
368 TTTAAGGTCC
*
378 AAAATGGAGATTTTTGGAAGTATGGGGGTA
1 AAAATGGAGATTTTTGGAAGTTTGGGGGTA
* ** *
408 AAAATAGA-ATTTTTGGAAGTTTTAGGATCA
1 AAAATGGAGATTTTTGGAAGTTTGGGGGT-A
* *
438 AAAATGGA-ATTTTTGGAAGTTTTGGGGTCG
1 AAAATGGAGATTTTTGGAAGTTTGGGGGT-A
** *
468 AAAATGG-GATTTTTGGAAGTTCAGGGGTG
1 AAAATGGAGATTTTTGGAAGTTTGGGGGTA
* * *
497 AAAATGGA-ATTTTTGGAAGCTTCGAGGTTA
1 AAAATGGAGATTTTTGGAAG-TTTGGGGGTA
* *
527 AAAATGGA-ATTTTTGGAAGCTCGGGGGTA
1 AAAATGGAGATTTTTGGAAGTTTGGGGGTA
* **
556 AAAAT-GAGATTTTTGGAAGTTTCAGGATTA
1 AAAATGGAGATTTTTGGAAGTTT-GGGGGTA
**
586 AAAATGG-GATTTTTGGAAGTTTAAGGGTA
1 AAAATGGAGATTTTTGGAAGTTTGGGGGTA
* * *
615 AAAATGG-GATTTATAGAAGTTTTGGGGTTA
1 AAAATGGAGATTTTTGGAAG-TTTGGGGGTA
*
645 AAAAT-GAGATTTTTGGAAGTTCGAGGGGT-
1 AAAATGGAGATTTTTGGAAGTTTG-GGGGTA
*
674 -GAATGGA-ATTTTTGGATAGTTT
1 AAAATGGAGATTTTTGGA-AGTTT
696 AGGGACCTCC
Statistics
Matches: 239, Mismatches: 37, Indels: 25
0.79 0.12 0.08
Matches are distributed among these distances:
28 14 0.06
29 90 0.38
30 134 0.56
31 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (30 bp):
AAAATGGAGATTTTTGGAAGTTTGGGGGTA
Found at i:449 original size:89 final size:88
Alignment explanation
Indices: 356--689 Score: 243
Period size: 89 Copynumber: 3.8 Consensus size: 88
346 GGTAAAAGGT
*
356 AATTTT-GAGAGTTTTAAGGTCCAAAATGGAGATTTTTGGAAGTAT-GGGGGTAAAAATAGAATT
1 AATTTTGGA-AGTTTTAAGGTCCAAAATGG-GATTTTTGGAAGT-TCAGGGGTAAAAATAGAATT
**
419 TTTGGAAG-TTTTAGGATCAAAAATGG
63 TTTGGAAGCTTCGAGG-TCAAAAATGG
** * * *
445 AATTTTTGGAAGTTTTGGGGTCGAAAATGGGATTTTTGGAAGTTCAGGGGTGAAAATGGAATTTT
1 AA-TTTTGGAAGTTTTAAGGTCCAAAATGGGATTTTTGGAAGTTCAGGGGTAAAAATAGAATTTT
*
510 TGGAAGCTTCGAGGTTAAAAATGG
65 TGGAAGCTTCGAGGTCAAAAATGG
* **** * * ** * *
534 AATTTTTGGAAGCTCGGGGGT-AAAAATGAGATTTTTGGAAGTTTCAGGATTAAAAATGGGATTT
1 AA-TTTTGGAAGTTTTAAGGTCCAAAATGGGATTTTTGGAAG-TTCAGGGGTAAAAATAGAATTT
**
598 TTGGAAG-TTTAAGGGT-AAAAATGG
64 TTGGAAGCTTCGA-GGTCAAAAATGG
* * ** ** * * *
622 GATTTATAGAAGTTTTGGGGTTAAAAATGAGATTTTTGGAAGTTCGAGGGGT--GAATGGAATTT
1 AATTT-TGGAAGTTTTAAGGTCCAAAATGGGATTTTTGGAAGTTC-AGGGGTAAAAATAGAATTT
685 TTGGA
64 TTGGA
690 TAGTTTAGGG
Statistics
Matches: 207, Mismatches: 29, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
87 17 0.08
88 45 0.22
89 117 0.57
90 26 0.13
91 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (88 bp):
AATTTTGGAAGTTTTAAGGTCCAAAATGGGATTTTTGGAAGTTCAGGGGTAAAAATAGAATTTTT
GGAAGCTTCGAGGTCAAAAATGG
Found at i:465 original size:59 final size:58
Alignment explanation
Indices: 378--695 Score: 268
Period size: 59 Copynumber: 5.4 Consensus size: 58
368 TTTAAGGTCC
* * * *
378 AAAATGGAGATTTTTGGAAGTATGGGGGTAAAAATAGAATTTTTGGAAGTTTTAGGATCA
1 AAAATGGA-ATTTTTGGAAGTTTTGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT-A
* * * *
438 AAAATGGAATTTTTGGAAGTTTTGGGGTCGAAAATGGGATTTTTGGAAG-TTCAGGGGTG
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-AAAAATGGAATTTTTGGAAGTTTTA-GGGTA
* * * * ***
497 AAAATGGAATTTTTGGAAGCTTCGAGGTTAAAAATGGAATTTTTGGAAGCTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTA
* ** * *
556 AAAAT-GAGATTTTTGGAAGTTTCAGGATTAAAAATGGGATTTTTGGAAGTTTAAGGGTA
1 AAAATGGA-ATTTTTGGAAGTTT-TGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTA
* * * **
615 AAAATGGGATTTATAGAAGTTTTGGGGTTAAAAAT-GAGATTTTTGGAAGTTCGAGGGGT-
1 AAAATGGAATTTTTGGAAGTTTTGGGG-TAAAAATGGA-ATTTTTGGAAGTTTTA-GGGTA
*
674 -GAATGGAATTTTTGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
696 AGGGACCTCC
Statistics
Matches: 209, Mismatches: 38, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
58 17 0.08
59 154 0.74
60 38 0.18
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTA
Found at i:695 original size:118 final size:117
Alignment explanation
Indices: 438--695 Score: 306
Period size: 118 Copynumber: 2.2 Consensus size: 117
428 TTTAGGATCA
** * * * *
438 AAAATGGAATTTTTGGAAGTTTTGGGGTCGAAAATGGGATTTTTGGAAGTTCAGGGGTGAAAATG
1 AAAATGGAATTTTTGGAAGTTTCAGGATCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAAATG
* *
503 GAATTTTTGGAAGCTTCGAGGTTAAAAATGGAATTTTTGGAAGCTCGGGGGT
66 GAATTTATAGAAGCTTCGAGGTTAAAAATGGAATTTTTGGAAGCTCGGGGGT
* *
555 AAAAAT-GAGATTTTTGGAAGTTTCAGGATTAAAAATGGGATTTTTGGAAGTTTAAGGGTAAAAA
1 -AAAATGGA-ATTTTTGGAAGTTTCAGGATCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAAA
* * * * *
619 TGGGATTTATAGAAGTTTTGGGGTTAAAAAT-GAGATTTTTGGAAGTTCGAGGGGT
64 TGGAATTTATAGAAGCTTCGAGGTTAAAAATGGA-ATTTTTGGAAGCTCG-GGGGT
*
674 -GAATGGAATTTTTGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
696 AGGGACCTCC
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
117 16 0.13
118 98 0.82
119 5 0.04
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.34
Consensus pattern (117 bp):
AAAATGGAATTTTTGGAAGTTTCAGGATCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAAATG
GAATTTATAGAAGCTTCGAGGTTAAAAATGGAATTTTTGGAAGCTCGGGGGT
Found at i:1691 original size:17 final size:17
Alignment explanation
Indices: 1655--1688 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1645 TAATAAATTT
*
1655 TATTATTATTTTATTAA
1 TATTAATATTTTATTAA
1672 TATTAATATATTTATTA
1 TATTAATAT-TTTATTA
1689 TATCTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTAATATTTTATTAA
Done.