Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004985.1 Kokia drynarioides strain JFW-HI SEQ_118732, 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: 3174
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Found at i:1923 original size:19 final size:21
Alignment explanation
Indices: 1888--1928 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
1878 AAAAATGAGC
1888 ATGTAAATTAAATAC-AAGTT
1 ATGTAAATTAAATACAAAGTT
1908 ATGT-AATT-AATGACAAAGTT
1 ATGTAAATTAAAT-ACAAAGTT
1928 A
1 A
1929 AATAACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.16
19 6 0.32
20 10 0.53
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (21 bp):
ATGTAAATTAAATACAAAGTT
Found at i:1980 original size:14 final size:14
Alignment explanation
Indices: 1951--1995 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
1941 CACGAACAAT
1951 TATACGAATGAATAAA
1 TATACGAA--AATAAA
1967 TATACGAAAATAAA
1 TATACGAAAATAAA
*
1981 TATAAGAAAAATAAA
1 TATACG-AAAATAAA
1996 ATATGAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 11 0.41
15 8 0.30
16 8 0.30
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (14 bp):
TATACGAAAATAAA
Found at i:2221 original size:28 final size:30
Alignment explanation
Indices: 2143--2399 Score: 173
Period size: 29 Copynumber: 8.8 Consensus size: 30
2133 GGAAAGTTTT
* *
2143 AGGGATAAAAAAGTTATTTTTGAGAAGTTCG
1 AGGGA-AAAAATGTAATTTTTGAGAAGTTCG
* * *
2174 AGAGTAAAAATGTGATTTTTG-GAAGTTCG
1 AGGGAAAAAATGTAATTTTTGAGAAGTTCG
*
2203 AGGGAAAAAATATAATTTTTG-GAAGCTT-G
1 AGGGAAAAAATGTAATTTTTGAGAAG-TTCG
*
2232 -GGG-AAAAATGTAATTTTTGAGAAGTTTG
1 AGGGAAAAAATGTAATTTTTGAGAAGTTCG
* *
2260 -GGG-GAAAATGTAATTTTTGAGAAGTTTG
1 AGGGAAAAAATGTAATTTTTGAGAAGTTCG
* ** * *
2288 GGGGTCAAAATGTGATTTTTG-GAAGTT-T
1 AGGGAAAAAATGTAATTTTTGAGAAGTTCG
* *
2316 AGGGATAAAAATGTGATTTTTGA-AAGTTTG
1 AGGGA-AAAAATGTAATTTTTGAGAAGTTCG
* * * *
2346 -GGAGAAAAAAACGTGATTTTTTGA-ATGTTCA
1 AGG-G-AAAAAATGT-AATTTTTGAGAAGTTCG
*
2377 AAGG-AAAAATGTAATTTTT-AGAA
1 AGGGAAAAAATGTAATTTTTGAGAA
2400 ATTTTAGGGG
Statistics
Matches: 186, Mismatches: 27, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
27 18 0.10
28 45 0.24
29 68 0.37
30 38 0.20
31 16 0.09
32 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.34
Consensus pattern (30 bp):
AGGGAAAAAATGTAATTTTTGAGAAGTTCG
Found at i:2265 original size:57 final size:56
Alignment explanation
Indices: 2130--2395 Score: 216
Period size: 59 Copynumber: 4.6 Consensus size: 56
2120 TAAAACGTAA
* * * * *
2130 TTTGGAAAGTTTTAGGGATAAAAAAGTTATTTTTGAGAAGTTCGAGAGTAAAAATGTGATT
1 TTTGG-AAGTTTGAGGGA-AAAAATGTAATTTTTG-GAAGTTTG-G-GGAAAAATGTGATT
* * * *
2191 TTTGGAAGTTCGAGGGAAAAAATATAATTTTTGGAAGCTTGGGGAAAAATGTAATT
1 TTTGGAAGTTTGAGGGAAAAAATGTAATTTTTGGAAGTTTGGGGAAAAATGTGATT
* *
2247 TTTGAGAAGTTTG-GGG-GAAAATGTAATTTTTGAGAAGTTTGGGGGTCAAAATGTGATT
1 TTTG-GAAGTTTGAGGGAAAAAATGTAATTTTTG-GAAGTTT-GGGG-AAAAATGTGATT
* * *
2305 TTTGGAAGTTT-AGGGATAAAAATGTGATTTTTGAAAGTTTGGGAGAAAAAAACGTGATT
1 TTTGGAAGTTTGAGGGA-AAAAATGTAATTTTTGGAAGTTTGGG-G--AAAAATGTGATT
* ** *
2364 TTTTGAATGTTCAAAGG-AAAAATGTAATTTTT
1 TTTGGAA-GTTTGAGGGAAAAAATGTAATTTTT
2396 AGAAATTTTA
Statistics
Matches: 169, Mismatches: 25, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
55 14 0.08
56 25 0.15
57 25 0.15
58 27 0.16
59 57 0.34
60 13 0.08
61 8 0.05
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (56 bp):
TTTGGAAGTTTGAGGGAAAAAATGTAATTTTTGGAAGTTTGGGGAAAAATGTGATT
Found at i:2291 original size:29 final size:28
Alignment explanation
Indices: 2179--2354 Score: 185
Period size: 29 Copynumber: 6.2 Consensus size: 28
2169 GTTCGAGAGT
* * *
2179 AAAAATGTGATTTTTGGAAGTTCGAGGGA
1 AAAAATGTAATTTTTGGAAGTTTG-GGGG
* *
2208 AAAAATATAATTTTTGGAAGCTT-GGGG
1 AAAAATGTAATTTTTGGAAGTTTGGGGG
2235 AAAAATGTAATTTTTGAGAAGTTTGGGGG
1 AAAAATGTAATTTTTG-GAAGTTTGGGGG
2264 -AAAATGTAATTTTTGAGAAGTTTGGGGG
1 AAAAATGTAATTTTTG-GAAGTTTGGGGG
* * **
2292 TCAAAATGTGATTTTTGGAAGTTTAGGGAT
1 -AAAAATGTAATTTTTGGAAGTTT-GGGGG
* * *
2322 AAAAATGTGATTTTTGAAAGTTTGGGAG
1 AAAAATGTAATTTTTGGAAGTTTGGGGG
2350 AAAAA
1 AAAAA
2355 AACGTGATTT
Statistics
Matches: 129, Mismatches: 13, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
27 18 0.14
28 43 0.33
29 51 0.40
30 17 0.13
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (28 bp):
AAAAATGTAATTTTTGGAAGTTTGGGGG
Found at i:2484 original size:30 final size:30
Alignment explanation
Indices: 2402--2484 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
2392 TTTTAGAAAT
* *
2402 TTTAGGGGTTAAATTACAATTTTGGAAAAG
1 TTTAGGGGTTAAAATATAATTTTGGAAAAG
*
2432 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
1 TTTAGGGGTTAAAATATAATTTTGGAAAAG
* *
2462 TTTAGGTGTTAAAATATGATTTT
1 TTTAGGGGTTAAAATATAATTTT
2485 TAGAAAGTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (30 bp):
TTTAGGGGTTAAAATATAATTTTGGAAAAG
Found at i:2492 original size:30 final size:30
Alignment explanation
Indices: 2382--2498 Score: 112
Period size: 30 Copynumber: 3.9 Consensus size: 30
2372 GTTCAAAGGA
* *
2382 AAAATGTAATTTTTAG-AAATTTTAGGGGTT
1 AAAATATAA-TTTTAGAAAAGTTTAGGGGTT
* * *
2412 AAATTACAATTTTGGAAAAGTTTAGGGGTT
1 AAAATATAATTTTAGAAAAGTTTAGGGGTT
* * *
2442 AAAATGTAATTTTGGAAAAGTTTAGGTGTT
1 AAAATATAATTTTAGAAAAGTTTAGGGGTT
* *
2472 AAAATATGATTTTTAG-AAAGTTCAGGG
1 AAAATAT-AATTTTAGAAAAGTTTAGGG
2499 ATCTTCTAGG
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
29 5 0.07
30 60 0.85
31 6 0.08
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (30 bp):
AAAATATAATTTTAGAAAAGTTTAGGGGTT
Done.