Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010921.1 Kokia drynarioides strain JFW-HI SEQ_125889, 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: 4331
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:302 original size:25 final size:25
Alignment explanation
Indices: 281--332 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
271 TAGTTAAATG
*
281 TTGTTTTTAGTTGCCCACTTAAACT
1 TTGTTTTTAGTTGCACACTTAAACT
*
306 TTGTTTTTAGTTTCACACTTAAACT
1 TTGTTTTTAGTTGCACACTTAAACT
331 TT
1 TT
333 TATTAGTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (25 bp):
TTGTTTTTAGTTGCACACTTAAACT
Found at i:2378 original size:22 final size:22
Alignment explanation
Indices: 2353--2400 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
2343 AACAATAAGT
2353 AAAGTATATATTCCAATACCAA
1 AAAGTATATATTCCAATACCAA
2375 AAAGTATATATTCCAATACCAA
1 AAAGTATATATTCCAATACCAA
2397 AAAG
1 AAAG
2401 AAAAAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (22 bp):
AAAGTATATATTCCAATACCAA
Found at i:4114 original size:13 final size:13
Alignment explanation
Indices: 4096--4137 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
4086 TTTTATCCAT
*
4096 AAAGAAAACAGAA
1 AAAGAAAAAAGAA
4109 AAAGAAAAAAGAA
1 AAAGAAAAAAGAA
*
4122 AAAGAAAAAATAA
1 AAAGAAAAAAGAA
4135 AAA
1 AAA
4138 AGATAGACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:4121 original size:20 final size:20
Alignment explanation
Indices: 4096--4140 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
4086 TTTTATCCAT
4096 AAAGAAAACAG-AAAAAGAAA
1 AAAGAAAA-AGAAAAAAGAAA
*
4116 AAAGAAAAAGAAAAAATAAA
1 AAAGAAAAAGAAAAAAGAAA
4136 AAAGA
1 AAAGA
4141 TAGACTTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.02
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAGAAA
Found at i:4123 original size:5 final size:6
Alignment explanation
Indices: 4096--4130 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
4086 TTTTATCCAT
4096 AAAGAA AACAGAA AAAGAAA AAAGAA AAAGAA AAA
1 AAAGAA AA-AGAA AAAG-AA AAAGAA AAAGAA AAA
4131 ATAAAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 15 0.56
7 12 0.44
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:4131 original size:7 final size:7
Alignment explanation
Indices: 4096--4140 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
4086 TTTTATCCAT
4096 AAAGAAA
1 AAAGAAA
*
4103 ACAG-AA
1 AAAGAAA
4109 AAAGAAA
1 AAAGAAA
4116 AAAG-AA
1 AAAGAAA
4122 AAAGAAA
1 AAAGAAA
*
4129 AAATAAA
1 AAAGAAA
4136 AAAGA
1 AAAGA
4141 TAGACTTCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Done.