Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001071.1 Kokia drynarioides strain JFW-HI SEQ_112325, 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: 14168
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Found at i:4298 original size:51 final size:51
Alignment explanation
Indices: 4217--4405 Score: 236
Period size: 51 Copynumber: 3.6 Consensus size: 51
4207 GATATAAATG
*
4217 AAAGAGTCCGATGACTAAGTATCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
4269 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * **
4320 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATACGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
*
4372 AAAGGGGTCCGATGCCTATA-TGTCATCGTGAGTA
1 AAA--GGTCCGATGACTA-AGTGTCATCGTGAGTA
4406 TTAAATGAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
51 79 0.66
52 14 0.12
54 25 0.21
55 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:4357 original size:102 final size:105
Alignment explanation
Indices: 4217--4405 Score: 269
Period size: 102 Copynumber: 1.8 Consensus size: 105
4207 GATATAAATG
* **
4217 AAAGAGTCCGATGACTAAGTATCATCGTGAGTAAATGAA-TCCTTTACGGATTAAA-GGTCCGAT
1 AAAGAGTCCGATGACTAAGTATCATCGTGAGTAAATGAATTCCTATACGGAACAAAGGGTCCGAT
4280 GACTA-AGTGTCATCGTGAGTAAATGAATCCATGACGAATT
66 GACTATA-TGTCATCGTGAGTAAATGAATCCATGACGAATT
* * *
4320 AAAG-GTCCGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATACGGAACAAAGGGGTCCGA
1 AAAGAGTCCGATGACTAAGTATCATCGTGAGTAAATGAATTCCTATACGGAACAAA-GGGTCCGA
*
4384 TGCCTATATGTCATCGTGAGTA
65 TGACTATATGTCATCGTGAGTA
4406 TTAAATGAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
102 31 0.41
103 17 0.23
105 26 0.35
106 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (105 bp):
AAAGAGTCCGATGACTAAGTATCATCGTGAGTAAATGAATTCCTATACGGAACAAAGGGTCCGAT
GACTATATGTCATCGTGAGTAAATGAATCCATGACGAATT
Found at i:13233 original size:32 final size:31
Alignment explanation
Indices: 13195--13322 Score: 83
Period size: 29 Copynumber: 4.2 Consensus size: 31
13185 AAAAATTATA
13195 TTGTTTTTGTTTTATTGTTTTTGGTGTTTTTG
1 TTGTTTTTGTTTTATTGTTTTT-GTGTTTTTG
* *
13227 TTGTTTTAG---TGTTGTTTTTGCTGTTATTT-
1 TTGTTTTTGTTTTATTGTTTTTG-TGTT-TTTG
* * * *
13256 TTGTTATTGTTTTGTTGTTATT-T-TTGTTG
1 TTGTTTTTGTTTTATTGTTTTTGTGTTTTTG
*
13285 TTG-TTTTGATGTTATT-TTTGTTGTTGTTTTTG
1 TTGTTTTTG-TTTTATTGTTT-TTG-TGTTTTTG
13317 TTGTTT
1 TTGTTT
13323 GAATATTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 23
0.68 0.10 0.21
Matches are distributed among these distances:
28 9 0.12
29 32 0.44
30 4 0.05
31 1 0.01
32 25 0.34
33 2 0.03
ACGTcount: A:0.05, C:0.01, G:0.21, T:0.73
Consensus pattern (31 bp):
TTGTTTTTGTTTTATTGTTTTTGTGTTTTTG
Found at i:13251 original size:9 final size:9
Alignment explanation
Indices: 13204--13322 Score: 84
Period size: 9 Copynumber: 13.2 Consensus size: 9
13194 ATTGTTTTTG
*
13204 TTTTATTGT
1 TTTTGTTGT
*
13213 TTTTGGTGT
1 TTTTGTTGT
13222 TTTTGTTGT
1 TTTTGTTGT
13231 TTTAGTGTTGT
1 TTT--TGTTGT
*
13242 TTTTGCTGT
1 TTTTGTTGT
13251 TATTT-TTGT
1 T-TTTGTTGT
*
13260 TATTGTT-T
1 TTTTGTTGT
* *
13268 TGTTGTTAT
1 TTTTGTTGT
13277 TTTTGTTGT
1 TTTTGTTGT
* *
13286 TGTT-TTGA
1 TTTTGTTGT
* *
13294 TGTTATT-T
1 TTTTGTTGT
13302 TTGTTGTTGT
1 TT-TTGTTGT
13312 TTTTGTTGT
1 TTTTGTTGT
13321 TT
1 TT
13323 GAATATTTTT
Statistics
Matches: 88, Mismatches: 14, Indels: 16
0.75 0.12 0.14
Matches are distributed among these distances:
8 17 0.19
9 56 0.64
10 6 0.07
11 9 0.10
ACGTcount: A:0.06, C:0.01, G:0.21, T:0.72
Consensus pattern (9 bp):
TTTTGTTGT
Found at i:13251 original size:12 final size:12
Alignment explanation
Indices: 13224--13321 Score: 112
Period size: 12 Copynumber: 8.4 Consensus size: 12
13214 TTTGGTGTTT
*
13224 TTGTTGTTTTAG
1 TTGTTGTTTTTG
13236 -TGTTGTTTTTG
1 TTGTTGTTTTTG
* *
13247 CTGTTATTTTTG
1 TTGTTGTTTTTG
*
13259 TTATTG-TTTTG
1 TTGTTGTTTTTG
*
13270 TTGTTATTTTTG
1 TTGTTGTTTTTG
13282 TTGTTG-TTTTG
1 TTGTTGTTTTTG
* *
13293 ATGTTATTTTTG
1 TTGTTGTTTTTG
13305 TTGTTGTTTTTG
1 TTGTTGTTTTTG
13317 TTGTT
1 TTGTT
13322 TGAATATTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
11 28 0.39
12 43 0.61
ACGTcount: A:0.06, C:0.01, G:0.21, T:0.71
Consensus pattern (12 bp):
TTGTTGTTTTTG
Found at i:13256 original size:23 final size:23
Alignment explanation
Indices: 13199--13321 Score: 130
Period size: 23 Copynumber: 5.4 Consensus size: 23
13189 ATTATATTGT
*
13199 TTTTGTT-TTATTGTTT-TTGGTG
1 TTTTGTTGTTATT-TTTGTTGTTG
* *
13221 -TTT-TTGTTGTTTTAG-TGTTG
1 TTTTGTTGTTATTTTTGTTGTTG
* *
13241 TTTTTGCTGTTATTTTTGTTATTG
1 -TTTTGTTGTTATTTTTGTTGTTG
13265 TTTTGTTGTTATTTTTGTTGTTG
1 TTTTGTTGTTATTTTTGTTGTTG
*
13288 TTTTGATGTTATTTTTGTTGTTG
1 TTTTGTTGTTATTTTTGTTGTTG
13311 TTTTTGTTGTT
1 -TTTTGTTGTT
13322 TGAATATTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
20 8 0.10
21 7 0.08
22 3 0.04
23 52 0.63
24 13 0.16
ACGTcount: A:0.06, C:0.01, G:0.21, T:0.72
Consensus pattern (23 bp):
TTTTGTTGTTATTTTTGTTGTTG
Found at i:13280 original size:35 final size:36
Alignment explanation
Indices: 13227--13321 Score: 117
Period size: 35 Copynumber: 2.7 Consensus size: 36
13217 GGTGTTTTTG
*
13227 TTGTTTTAG-TGTTGTTTTTGCTGTTATTTT-TGTTA
1 TTGTTTT-GTTGTTGTTTTTGTTGTTATTTTATGTTA
* *
13262 TTGTTTTGTTGTTATTTTTGTTGTTGTTTTGATGTTA
1 TTGTTTTGTTGTTGTTTTTGTTGTTATTTT-ATGTTA
13299 -T-TTTTGTTGTTGTTTTTGTTGTT
1 TTGTTTTGTTGTTGTTTTTGTTGTT
13322 TGAATATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
34 1 0.02
35 46 0.87
36 1 0.02
37 5 0.09
ACGTcount: A:0.06, C:0.01, G:0.21, T:0.72
Consensus pattern (36 bp):
TTGTTTTGTTGTTGTTTTTGTTGTTATTTTATGTTA
Done.