Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000791.1 Kokia drynarioides strain JFW-HI SEQ_111860, 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: 3156
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Found at i:1680 original size:96 final size:96
Alignment explanation
Indices: 1513--1697 Score: 257
Period size: 96 Copynumber: 1.9 Consensus size: 96
1503 GAAAATGATG
* ** *
1513 TTCGATTATCTCGATTTGATGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
*
1578 AGATAAAAAAACGTTGCCTCGATTAAGGGTA
66 AGATAAAAAAACATTGCCTCGATTAAGGGTA
* *
1609 TTCGATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-TC
* *
1673 GAA-ATAAAAGAATATTGCCTCGATT
64 GAAGATAAAAAAACATTGCCTCGATT
1698 TTAAAGTTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
95 1 0.01
96 72 0.92
97 5 0.06
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
AGATAAAAAAACATTGCCTCGATTAAGGGTA
Found at i:2117 original size:29 final size:29
Alignment explanation
Indices: 2064--2551 Score: 382
Period size: 29 Copynumber: 17.2 Consensus size: 29
2054 GTTCAGTGGG
* *
2064 ATTTTTAGAAG-TTCGAGAGTAAAAATGGA
1 ATTTTTGGAAGTTTTGAG-GTAAAAATGGA
*
2093 ATTTTTGGAAGTTTTGAGGTTAAAAATGGG
1 ATTTTTGGAAGTTTTGAGG-TAAAAATGGA
* * *
2123 TTTTTTGGAAG-TTCGAGGGTAAAAATGAA
1 ATTTTTGGAAGTTTTGA-GGTAAAAATGGA
*
2152 ATTTTTGGAAGTTTTGGGGTTAAAAAT-GA
1 ATTTTTGGAAGTTTTGAGG-TAAAAATGGA
*
2181 GATTTTTGGAAG-TTCGAGGGTAAAAAATGGA
1 -ATTTTTGGAAGTTTTGA-GGT-AAAAATGGA
* * *
2212 CTTTTTGGAAGTTTTGGGGTTAAAAATAGA
1 ATTTTTGGAAGTTTTGAGG-TAAAAATGGA
*
2242 ATTTTTGAAAG-TTTGAGGGTAAAAATGGA
1 ATTTTTGGAAGTTTTGA-GGTAAAAATGGA
*
2271 A-TTTT-G--G----G-GTTAAAAATGGA
1 ATTTTTGGAAGTTTTGAGGTAAAAATGGA
*
2291 ATTTTTGGAAG-TTCGAGGTAAAAATGGA
1 ATTTTTGGAAGTTTTGAGGTAAAAATGGA
* *
2319 ATTTTT-G--G----G-GTTAAAAATTGA
1 ATTTTTGGAAGTTTTGAGGTAAAAATGGA
*
2340 ATTTTTGGAAGTTCT-AGGGTAAAAATGGA
1 ATTTTTGGAAGTTTTGA-GGTAAAAATGGA
* * *
2369 ATTTTTGGAAGTTTCGGGGTAAAAAATGGG
1 ATTTTTGGAAGTTTTGAGGT-AAAAATGGA
* *
2399 ATTTTTAGAAGTTCT-AGTGTAAAAATGGA
1 ATTTTTGGAAGTTTTGAG-GTAAAAATGGA
* *
2428 ATTTTTGGAAGTTTTGAAGTCAAAATGGA
1 ATTTTTGGAAGTTTTGAGGTAAAAATGGA
*
2457 ATTTTTGGAAG-TTCGAGGGTAAAAATGGA
1 ATTTTTGGAAGTTTTGA-GGTAAAAATGGA
* * *
2486 ATTTTTGGAAGCTTT-AGGGTCAAAATTGGG
1 ATTTTTGGAAGTTTTGA-GGT-AAAAATGGA
* *
2516 ATTTTTAGAAGTTTTGGGGTAAAAATGGA
1 ATTTTTGGAAGTTTTGAGGTAAAAATGGA
2545 ATTTTTG
1 ATTTTTG
2552 AAAATTTAAG
Statistics
Matches: 369, Mismatches: 53, Indels: 74
0.74 0.11 0.15
Matches are distributed among these distances:
20 12 0.03
21 20 0.05
22 4 0.01
24 2 0.01
25 2 0.01
27 2 0.01
28 25 0.07
29 162 0.44
30 134 0.36
31 6 0.02
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (29 bp):
ATTTTTGGAAGTTTTGAGGTAAAAATGGA
Found at i:2145 original size:59 final size:59
Alignment explanation
Indices: 2060--2551 Score: 526
Period size: 59 Copynumber: 8.7 Consensus size: 59
2050 GGATGTTCAG
* *
2060 TGGGATTTTTAGAAGTTCGAGAGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAA
1 TGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAA
* * *
2119 TGGGTTTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGTTAAAAA
1 TGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAA
* * *
2178 TGAGATTTTTGGAAGTTCGAGGGTAAAAAATGGACTTTTTGGAAGTTTTGGGGTTAAAAA
1 TGGGATTTTTGGAAGTTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAA
* * * *
2238 TAGAATTTTTGAAAGTTTGAGGGTAAAAATGGAA-TTTT----G----G-GGTTAAAAA
1 TGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAA
*
2287 TGGAATTTTTGGAAGTTCGA-GGTAAAAATGGAATTTTT----G----G-GGTTAAAAA
1 TGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAA
* * * * * *
2336 TTGAATTTTTGGAAGTTCTAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAAA
1 TGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAA
* * * * *
2395 TGGGATTTTTAGAAGTTCTAGTGTAAAAATGGAATTTTTGGAAGTTTTGAAG-TCAAAA
1 TGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAA
* * * *
2453 TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGCTTT-AGGGTCAAAAT
1 TGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGA-GGTTAAAAA
* *
2512 TGGGATTTTTAGAAGTTTTG-GGGTAAAAATGGAATTTTTG
1 TGGGATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTG
2552 AAAATTTAAG
Statistics
Matches: 376, Mismatches: 42, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
48 13 0.03
49 59 0.16
50 19 0.05
54 2 0.01
57 1 0.00
58 53 0.14
59 174 0.46
60 55 0.15
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.36
Consensus pattern (59 bp):
TGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAA
Found at i:2285 original size:19 final size:21
Alignment explanation
Indices: 2253--2295 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2243 TTTTTGAAAG
2253 TTTGAGGGT-AAAAATGGAAT
1 TTTGAGGGTAAAAAATGGAAT
*
2273 TTTG-GGGTTAAAAATGGAAT
1 TTTGAGGGTAAAAAATGGAAT
2293 TTT
1 TTT
2296 TGGAAGTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.37
Consensus pattern (21 bp):
TTTGAGGGTAAAAAATGGAAT
Found at i:2293 original size:49 final size:50
Alignment explanation
Indices: 2217--2376 Score: 236
Period size: 49 Copynumber: 3.2 Consensus size: 50
2207 ATGGACTTTT
*
2217 TGGAAGTTTTGGGGTTAAAAATAGAATTTTTGAAAGTTTGAGGGTAAAAA
1 TGGAAGTTTTGGGGTTAAAAATAGAATTTTTGGAAGTTTGAGGGTAAAAA
* *
2267 TGGAA-TTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCGA-GGTAAAAA
1 TGGAAGTTTTGGGGTTAAAAATAGAATTTTTGGAAGTTTGAGGGTAAAAA
* *
2315 TGGAATTTTTGGGGTTAAAAATTGAATTTTTGGAAGTTCT-AGGGTAAAAA
1 TGGAAGTTTTGGGGTTAAAAATAGAATTTTTGGAAGTT-TGAGGGTAAAAA
*
2365 TGGAATTTTTGG
1 TGGAAGTTTTGG
2377 AAGTTTCGGG
Statistics
Matches: 102, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
48 13 0.13
49 64 0.63
50 25 0.25
ACGTcount: A:0.34, C:0.01, G:0.28, T:0.36
Consensus pattern (50 bp):
TGGAAGTTTTGGGGTTAAAAATAGAATTTTTGGAAGTTTGAGGGTAAAAA
Found at i:2538 original size:117 final size:117
Alignment explanation
Indices: 2332--2551 Score: 352
Period size: 117 Copynumber: 1.9 Consensus size: 117
2322 TTTGGGGTTA
* * *
2332 AAAATTGAATTTTTGGAAGTTCTAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAAATG
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTAAAAAATG
*
2397 GGATTTTTAGAAGTTCTAGTGTAAAAATGGAATTTTTGGAAGTTTTGAAGTC
66 GGATTTTTAGAAGTTCTAGGGTAAAAATGGAATTTTTGGAAGTTTTGAAGTC
* *
2449 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGCTTT-AGGGTCAAAATT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAG-TTTCAGGGTAAAAAAT
* *
2513 GGGATTTTTAGAAGTTTTGGGGTAAAAATGGAATTTTTG
65 GGGATTTTTAGAAGTTCTAGGGTAAAAATGGAATTTTTG
2552 AAAATTTAAG
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
117 91 0.97
118 3 0.03
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (117 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTAAAAAATG
GGATTTTTAGAAGTTCTAGGGTAAAAATGGAATTTTTGGAAGTTTTGAAGTC
Done.