Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013915.1 Kokia drynarioides strain JFW-HI SEQ_128945, 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: 6467
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:3008 original size:27 final size:27
Alignment explanation
Indices: 2962--3016 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2952 TACCTGACAC
*
2962 CCAATGGAGGAACACGAAGTGACGGCA
1 CCAATGGAGGAACACAAAGTGACGGCA
* * *
2989 CCAATGGAGGAATATAAAGTGGCGGCA
1 CCAATGGAGGAACACAAAGTGACGGCA
3016 C
1 C
3017 TAAGGGGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.20, G:0.33, T:0.11
Consensus pattern (27 bp):
CCAATGGAGGAACACAAAGTGACGGCA
Found at i:3197 original size:4 final size:4
Alignment explanation
Indices: 3188--3253 Score: 64
Period size: 4 Copynumber: 16.2 Consensus size: 4
3178 AAATAAACGG
* *
3188 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAAA -AAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA -GAAA GAAA GA-AA GAAA GAAA
*
3238 G-AA GAAT GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
3254 GTAATGTGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
3 5 0.09
4 36 0.68
5 12 0.23
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:3210 original size:17 final size:17
Alignment explanation
Indices: 3188--3221 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3178 AAATAAACGG
3188 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
3205 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
3222 AAGGAGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:3253 original size:29 final size:30
Alignment explanation
Indices: 3188--3254 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
3178 AAATAAACGG
3188 GAAAGAAA-GAAAGGAAAGAAAGAAAGAAA
1 GAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
* * *
3217 GGAA-AAAGGAGAGGAAAGAAAG-AAGAAT
1 GAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
3245 GAAAGAAAGG
1 GAAAGAAAGG
3255 TAATGTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (30 bp):
GAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
Found at i:4126 original size:16 final size:15
Alignment explanation
Indices: 4105--4154 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
4095 ATGATAGGAT
4105 ATTATTTTTATAATTA
1 ATTATTTTT-TAATTA
4121 ATTATTTTTTATATT-
1 ATTATTTTTTA-ATTA
*
4136 A-TATTTTGGTAATTA
1 ATTATTTT-TTAATTA
4151 ATTA
1 ATTA
4155 GCTAAGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 9 0.31
15 6 0.21
16 14 0.48
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (15 bp):
ATTATTTTTTAATTA
Found at i:4405 original size:20 final size:21
Alignment explanation
Indices: 4380--4422 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4370 TACTTACTAC
4380 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
4400 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
4421 TA
1 TA
4423 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:5159 original size:27 final size:27
Alignment explanation
Indices: 5113--5167 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5103 TACCTGACAC
*
5113 CCAATGGAGGAACACGAAGTGACGGCA
1 CCAATGGAGGAACACAAAGTGACGGCA
* * *
5140 CCAATGGAGGAATATAAAGTGGCGGCA
1 CCAATGGAGGAACACAAAGTGACGGCA
5167 C
1 C
5168 TAAGGGGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.20, G:0.33, T:0.11
Consensus pattern (27 bp):
CCAATGGAGGAACACAAAGTGACGGCA
Found at i:5348 original size:4 final size:4
Alignment explanation
Indices: 5339--5404 Score: 64
Period size: 4 Copynumber: 16.2 Consensus size: 4
5329 AAATAAACGG
* *
5339 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAAA -AAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA -GAAA GAAA GA-AA GAAA GAAA
*
5389 G-AA GAAT GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
5405 GTAATGTGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
3 5 0.09
4 36 0.68
5 12 0.23
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:5361 original size:17 final size:17
Alignment explanation
Indices: 5339--5372 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5329 AAATAAACGG
5339 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
5356 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
5373 AAGGAGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:5404 original size:29 final size:30
Alignment explanation
Indices: 5339--5405 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
5329 AAATAAACGG
5339 GAAAGAAA-GAAAGGAAAGAAAGAAAGAAA
1 GAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
* * *
5368 GGAA-AAAGGAGAGGAAAGAAAG-AAGAAT
1 GAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
5396 GAAAGAAAGG
1 GAAAGAAAGG
5406 TAATGTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (30 bp):
GAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
Done.