Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009560.1 Kokia drynarioides strain JFW-HI SEQ_124272, 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: 14051
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Found at i:315 original size:24 final size:23
Alignment explanation
Indices: 288--332 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
278 GTACTTGGAC
288 ATTTAAAATAAATTTTAAATTTAA
1 ATTTAAAATAAA-TTTAAATTTAA
*
312 ATTTATAATAAATTTAAATTT
1 ATTTAAAATAAATTTAAATTT
333 CAACCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAAAATAAATTTAAATTTAA
Found at i:323 original size:17 final size:17
Alignment explanation
Indices: 303--385 Score: 80
Period size: 17 Copynumber: 4.9 Consensus size: 17
293 AAATAAATTT
303 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
*
320 TAAATTTAAATTTCA-AC
1 TAAATTTAAATTT-ATAA
* *
337 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTATAA
* *
354 TAAACTT-AATTTGAAAA
1 TAAATTTAAATTT-ATAA
*
371 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
386 TGGGCCCAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
16 6 0.11
17 42 0.79
18 5 0.09
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:376 original size:34 final size:34
Alignment explanation
Indices: 303--384 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
293 AAATAAATTT
* * * *
303 TAAATTTAAATTTATAATAAATTTAAATTTCAAC
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
*
337 CAAATTTAAATTTAGAATAAACTT-AATTTGAAAA
1 TAAATTTAAATTTAGAATAAACTTAAATTT-AAAA
*
371 TAAATTTAAGTTTA
1 TAAATTTAAATTTA
385 TTGGGCCCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 5 0.12
34 35 0.88
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (34 bp):
TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
Found at i:1107 original size:206 final size:206
Alignment explanation
Indices: 753--1316 Score: 824
Period size: 206 Copynumber: 2.7 Consensus size: 206
743 TGTTTTAATC
* * * * * *
753 CACTTCTCTGCGTTTCATCAGGAAGCTATCCGTTTTATTACTTCGACCTGCTCCTCAGTATCTTA
1 CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
818 TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTATTCTTCTCAG
66 TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTATTCTTCTCAG
* * *
883 TATTTCATCGGGAAGATGACTGCTTCATTTGTTTCAATCCGCTTCTCAGTATTTCATCAAGAAGT
131 TATTTCATCAGGAAGATGACTGCGTCATTTGTTTCAATCCGCTTCTCAGTATTTCATCAAGAAGA
948 CGAATTTGGTT
196 CGAATTTGGTT
* * *
959 CACTTCTCAGTGTCTCATCTGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCA
1 CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
* * *
1024 TCAGGAAGCTGTAGTTCGAAGATTTGCTCACATCGAGCGTGGGTCTGATTTGGTCTTCTTCTCAG
66 TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTATTCTTCTCAG
* * *
1089 TATTTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATCCGCTTCTCTGTATTTCATCAGGAAGA
131 TATTTCATCAGGAAGATGACTGCGTCATTTGTTTCAATCCGCTTCTCAGTATTTCATCAAGAAGA
1154 CGAATTTGGTT
196 CGAATTTGGTT
* * * *
1165 GACTTCTCAATATCTCATCAGGAAGCTAACCG-TTTATTGCTTCGACCTGCTTCTCAGTATCTCA
1 CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
* * * * * *
1229 TCAGAAAGCTGGGGTTCGAAGATTTGTTCACATCGAACGTGGGTTTGACTTGGTTTTCTTCTTAA
66 TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTATTCTTC-T--
* *
1294 AAGTATCTCATCAGGAAGATGAC
128 CAGTATTTCATCAGGAAGATGAC
1317 CGCATCGTTT
Statistics
Matches: 320, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
205 82 0.26
206 217 0.68
208 21 0.07
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (206 bp):
CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTATTCTTCTCAG
TATTTCATCAGGAAGATGACTGCGTCATTTGTTTCAATCCGCTTCTCAGTATTTCATCAAGAAGA
CGAATTTGGTT
Found at i:1837 original size:27 final size:28
Alignment explanation
Indices: 1807--1867 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
1797 TCAAGAATTC
1807 TATTAAAAAG-AGGATCAAAGGAAACAA
1 TATTAAAAAGAAGGATCAAAGGAAACAA
1834 TATTAAAAAGAAGGATCAAAGGAAACAA
1 TATTAAAAAGAAGGATCAAAGGAAACAA
1862 TCATTA
1 T-ATTA
1868 GTTGGAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 10 0.31
28 18 0.56
29 4 0.12
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.18
Consensus pattern (28 bp):
TATTAAAAAGAAGGATCAAAGGAAACAA
Found at i:9348 original size:10 final size:10
Alignment explanation
Indices: 9333--9363 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
9323 TTAGGATTAT
9333 TATGCAAAAA
1 TATGCAAAAA
9343 TATGCAAAAA
1 TATGCAAAAA
9353 TATGCAAAAA
1 TATGCAAAAA
9363 T
1 T
9364 GTGATGTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.23
Consensus pattern (10 bp):
TATGCAAAAA
Found at i:13285 original size:30 final size:30
Alignment explanation
Indices: 13225--13666 Score: 404
Period size: 30 Copynumber: 14.9 Consensus size: 30
13215 TTTAGAAGTC
* *
13225 AAAAATTGGATTTTTGGAAGTTCG-GGGTA
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTA
**
13254 AAAAATGGGATTTTTAAAAGTTTGAGGGTA
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTA
** *
13284 AAAAATGAAATTTTTGGAAGTTTTG-GGGTT
1 AAAAATGGGATTTTTGGAAG-TTTGAGGGTA
* * *
13314 AAAAATAGGATTTTTGGAAGTTCGGGGGT-
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTA
* * * *
13343 AAAAATGGAATTTTTGGATGTTTTAGGGTC
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTA
* *
13373 AAAAATAGGATTTTTGGAAGTTTGTGGGT-
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTA
* * *
13402 AAAAATGGAATTTTTGAAAGTTTTAGGGTTA
1 AAAAATGGGATTTTTGGAAGTTTGAGGG-TA
*
13433 AAAAATGGGATTTTTGGAAGTTTTG-GGGTC
1 AAAAATGGGATTTTTGGAAG-TTTGAGGGTA
*** *
13463 AAAAATGGGATTTTAAAAAGTTCGAGGGTA
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTA
* *
13493 AAAAATGGAATTTTTGAAAGTTTCGA-GGTA
1 AAAAATGGGATTTTTGGAAGTTT-GAGGGTA
* * *
13523 AAAAATGGGATTTTTGGAAG-TTCAAGGTT
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTA
* * *
13552 AAAAATGGAATTTTTGGAAGTTCGGGGGT-
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTA
* *
13581 AAAAATGGAATTTTTGGAAGTTTCGA-GGTC
1 AAAAATGGGATTTTTGGAAGTTT-GAGGGTA
* *
13611 AAAAATGGGATTATTGGAAGTTCG-GGGT-
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTA
* *
13639 AAAAGTGGAATTTTTGGATAGTTT-AGGG
1 AAAAATGGGATTTTTGGA-AGTTTGAGGG
13667 ACATCCGGAG
Statistics
Matches: 337, Mismatches: 60, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
28 16 0.05
29 132 0.39
30 159 0.47
31 27 0.08
32 3 0.01
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.34
Consensus pattern (30 bp):
AAAAATGGGATTTTTGGAAGTTTGAGGGTA
Found at i:13288 original size:59 final size:58
Alignment explanation
Indices: 13225--13662 Score: 393
Period size: 59 Copynumber: 7.4 Consensus size: 58
13215 TTTAGAAGTC
**
13225 AAAAATTGGATTTTTGGAAG-TTCGGGGTAAAAAATGGGATTTTTAAAAGTTTGAGGGT
1 AAAAA-TGGATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTGGAAGTTTGAGGGT
* * * * * *
13283 AAAAAATGAAATTTTTGGAAGTTTTGGGGTTAAAAATAGGATTTTTGGAAGTTCGGGGGT
1 -AAAAATG-GATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTGGAAGTTTGAGGGT
* ** * * *
13343 AAAAATGGAATTTTTGGATGTTTTAGGGTCAAAAATAGGATTTTTGGAAGTTTGTGGGT
1 AAAAATGG-ATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTGGAAGTTTGAGGGT
* * *
13402 AAAAATGGAATTTTTGAAAGTTTTAGGGTTAAAAAATGGGATTTTTGGAAGTTTTG-GGGT
1 AAAAATGG-ATTTTTGGAAG-TTTCGGGGTAAAAAATGGGATTTTTGGAAG-TTTGAGGGT
*** * *
13462 CAAAAATGGGATTTTAAAAAG-TTCGAGGGTAAAAAATGGAATTTTTGAAAGTTTCGA-GGT
1 -AAAAAT-GGATTTTTGGAAGTTTCG-GGGTAAAAAATGGGATTTTTGGAAGTTT-GAGGGT
** * * * *
13522 AAAAAATGGGATTTTTGGAAG-TTCAAGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGT
1 -AAAAAT-GGATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTGGAAGTTTGAGGGT
* * * *
13581 AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTATTGGAAGTTCG-GGGT
1 AAAAATGG-ATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTGGAAGTTTGAGGGT
*
13639 AAAAGTGGAATTTTTGGATAGTTT
1 AAAAATGG-ATTTTTGGA-AGTTT
13663 AGGGACATCC
Statistics
Matches: 323, Mismatches: 42, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
57 2 0.01
58 41 0.13
59 153 0.47
60 106 0.33
61 19 0.06
62 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (58 bp):
AAAAATGGATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTGGAAGTTTGAGGGT
Done.