Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001237.1 Kokia drynarioides strain JFW-HI SEQ_112599, 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: 3190
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Found at i:2274 original size:28 final size:28
Alignment explanation
Indices: 2217--2303 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
2207 TTAAGGGTAT
*
2217 AATGGTGATTTTTG-GA-TACTCGAGGCAA
1 AATGGTGATTTTTGAGAGT--TCGGGGCAA
*
2245 AATGGTGATTTTTGAGAGTTCGGGGGAA
1 AATGGTGATTTTTGAGAGTTCGGGGCAA
* * *
2273 AA-AGTAATTTTTGAGAAGTTCGAGGGTAA
1 AATGGTGATTTTTGAG-AGTTCG-GGGCAA
2302 AA
1 AA
2304 ATATAATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 11 0.22
28 29 0.58
29 9 0.18
30 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.31, T:0.31
Consensus pattern (28 bp):
AATGGTGATTTTTGAGAGTTCGGGGCAA
Found at i:2313 original size:29 final size:29
Alignment explanation
Indices: 2254--2590 Score: 216
Period size: 29 Copynumber: 11.6 Consensus size: 29
2244 AAATGGTGAT
* *
2254 TTTTGAG-AGTTCG-GGGGAAAAA-GTAA
1 TTTTGAGAAGTTTGAGGGTAAAAATGTAA
* *
2280 TTTTTGAGAAGTTCGAGGGTAAAAATATAA
1 -TTTTGAGAAGTTTGAGGGTAAAAATGTAA
* *
2310 TTTTTGA-AAATTT-AGGGGTAAAAATGTGA
1 -TTTTGAGAAGTTTGA-GGGTAAAAATGTAA
** * *
2339 TTTT-AGGAAGTACGAGGATAAAAATGTGAT
1 TTTTGA-GAAGTTTGAGGGTAAAAATGT-AA
2369 TTTTG-GAAGTTTG-GAGG-AAAAATGTAAA
1 TTTTGAGAAGTTTGAG-GGTAAAAATGT-AA
* *
2397 TTTTAAGAAGTTT-AGGGGTTAAAATGTAAA
1 TTTTGAGAAGTTTGA-GGGTAAAAATGT-AA
* * * * *
2427 TTTTAAAAAGTTTAAGGGTTAAAATATAA
1 TTTTGAGAAGTTTGAGGGTAAAAATGTAA
* *
2456 TTTTGAGAAGTTTAAGGGTCAAAATGTAAA
1 TTTTGAGAAGTTTGAGGGTAAAAATGT-AA
* * *
2486 ATTTG-GAAGTTTAAGGGTTAAAATGTAA
1 TTTTGAGAAGTTTGAGGGTAAAAATGTAA
* *
2514 TTTTTGAAAAGTTT-AGGTGTCAAAATGTAA
1 -TTTTGAGAAGTTTGAGG-GTAAAAATGTAA
*
2544 TTCTTGAGAAGTTTG-GGGTCAAAATGTAA
1 TT-TTGAGAAGTTTGAGGGTAAAAATGTAA
*
2573 TTTTTGATAAGTTT-AGGG
1 -TTTTGAGAAGTTTGAGGG
2591 ACATTTTAGG
Statistics
Matches: 255, Mismatches: 32, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
27 8 0.03
28 27 0.11
29 133 0.52
30 86 0.34
31 1 0.00
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
TTTTGAGAAGTTTGAGGGTAAAAATGTAA
Found at i:2568 original size:59 final size:58
Alignment explanation
Indices: 2387--2590 Score: 227
Period size: 59 Copynumber: 3.5 Consensus size: 58
2377 GTTTGGAGGA
* * **
2387 AAAATGTAAATTTT-AAGAAGTTTAGGGGTTAAAATGTAAATTTTAAAAAGTTTAAGGGTT
1 AAAATGTAATTTTTGAA-AAGTTTA-GGGTCAAAATGTAAATTTT-GGAAGTTTAAGGGTT
* * *
2447 AAAATATAA-TTTTGAGAAGTTTAAGGGTCAAAATGTAAAATTTGGAAGTTTAAGGGTT
1 AAAATGTAATTTTTGAAAAGTTT-AGGGTCAAAATGTAAATTTTGGAAGTTTAAGGGTT
* *
2505 AAAATGTAATTTTTGAAAAGTTTAGGTGTCAAAATGT-AATTCTTGAGAAGTTT-GGGGTC
1 AAAATGTAATTTTTGAAAAGTTTAGG-GTCAAAATGTAAATT-TTG-GAAGTTTAAGGGTT
*
2564 AAAATGTAATTTTTGATAAGTTTAGGG
1 AAAATGTAATTTTTGAAAAGTTTAGGG
2591 ACATTTTAGG
Statistics
Matches: 126, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
58 28 0.22
59 81 0.64
60 17 0.13
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (58 bp):
AAAATGTAATTTTTGAAAAGTTTAGGGTCAAAATGTAAATTTTGGAAGTTTAAGGGTT
Done.