Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000985.1 Kokia drynarioides strain JFW-HI SEQ_112178, 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: 47167
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:4397 original size:91 final size:92
Alignment explanation
Indices: 4286--4555 Score: 434
Period size: 91 Copynumber: 2.9 Consensus size: 92
4276 AATCATTCAA
4286 AAAAAACATATTTATCATAAAAATATTAAATCTAATCAATCATATTTAATAAAATTATTTAAATT
1 AAAAAA-ATATTTATCATAAAAATATTAAATCTAATCAATCATATTTAATAAAATTATTTAAATT
4351 AATTTATTGTTTATTCAATCAATCATTT
65 AATTTATTGTTTATTCAATCAATCATTT
* * * * *
4379 -AAAAAATATTTATCATAAAAAAACTAAATTTAATCAATCATATTTAATAAAATTGTCTAAATTA
1 AAAAAAATATTTATCATAAAAATATTAAATCTAATCAATCATATTTAATAAAATTATTTAAATTA
4443 ATTTATTGTTTATTCAATCAATCATTT
66 ATTTATTGTTTATTCAATCAATCATTT
* * * *
4470 AAAAAAATATTTCTCAAAAAAATATTAAATCCAATCAATCATATTTAATAAATTTATTTAAATTA
1 AAAAAAATATTTATCATAAAAATATTAAATCTAATCAATCATATTTAATAAAATTATTTAAATTA
*
4535 ATTTATTTTTTATTCAATCAA
66 ATTTATTGTTTATTCAATCAA
4556 ATATCATAAA
Statistics
Matches: 161, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
91 81 0.50
92 80 0.50
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (92 bp):
AAAAAAATATTTATCATAAAAATATTAAATCTAATCAATCATATTTAATAAAATTATTTAAATTA
ATTTATTGTTTATTCAATCAATCATTT
Found at i:5000 original size:22 final size:22
Alignment explanation
Indices: 4972--5015 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4962 GTGATTAAAA
4972 AGAAATCAAGAATATATCAAAT
1 AGAAATCAAGAATATATCAAAT
4994 AGAAATCAAGAATATATCAAAT
1 AGAAATCAAGAATATATCAAAT
5016 CAAGAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.23
Consensus pattern (22 bp):
AGAAATCAAGAATATATCAAAT
Found at i:11128 original size:15 final size:15
Alignment explanation
Indices: 11108--11142 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11098 TGGTCTTGGG
*
11108 TTTTCAAACAGAGGA
1 TTTTCAAACAGAGAA
*
11123 TTTTCACACAGAGAA
1 TTTTCAAACAGAGAA
11138 TTTTC
1 TTTTC
11143 CATTTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
TTTTCAAACAGAGAA
Found at i:21662 original size:3 final size:3
Alignment explanation
Indices: 21649--21678 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
21639 AAAATGAAAA
*
21649 AGG ATG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
21679 GAATGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.63, T:0.03
Consensus pattern (3 bp):
AGG
Found at i:29272 original size:28 final size:28
Alignment explanation
Indices: 29192--29277 Score: 66
Period size: 28 Copynumber: 3.0 Consensus size: 28
29182 TTAAAGTTAA
*
29192 AAAAATATTTTTTTAAATAATTAAAAATTAT
1 AAAAATA-TTTTTT-AAT-TTTAAAAATTAT
* ** * * *
29223 TAAAAT-TATTTAAAAGTATAAAGATTAT
1 AAAAATAT-TTTTTAATTTTAAAAATTAT
29251 AAAAATATTTTTTAATTTTAAAAATTA
1 AAAAATATTTTTTAATTTTAAAAATTA
29278 ATTAATTGCT
Statistics
Matches: 40, Mismatches: 13, Indels: 7
0.67 0.22 0.12
Matches are distributed among these distances:
28 28 0.70
29 4 0.10
30 3 0.08
31 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AAAAATATTTTTTAATTTTAAAAATTAT
Found at i:29597 original size:4 final size:4
Alignment explanation
Indices: 29590--29621 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
29580 ATTGATTCAA
29590 TTTC TTTC TTTC TTTC TTTC TTTC TTT- TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
29622 GATTTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:40813 original size:246 final size:246
Alignment explanation
Indices: 40379--40872 Score: 952
Period size: 246 Copynumber: 2.0 Consensus size: 246
40369 CATCTGAACA
*
40379 TACAAACAATAACAATGCAGCAATGAAAAAAGAAGTCCAGGAAACTCATGGACCAGAGGAAAGTT
1 TACAAACAATAACAATGCAGCAATGAAAAAAAAAGTCCAGGAAACTCATGGACCAGAGGAAAGTT
40444 CCAGTGCTAATTCAGAAAAAAGCTTAATAATAGAGGTTAAAAGCAAACTTTTTAATATTCCAACA
66 CCAGTGCTAATTCAGAAAAAAGCTTAATAATAGAGGTTAAAAGCAAACTTTTTAATATTCCAACA
40509 ATCTTCAGAATTCAAGGTCTCAGAGAACAAACAAACTAGATTTTTCAGAATATATATTAAGCTTA
131 ATCTTCAGAATTCAAGGTCTCAGAGAACAAACAAACTAGATTTTTCAGAATATATATTAAGCTTA
* *
40574 TTAACAAAATTCTTATGAAATAATGTAGTTTCTTGATCATATATATAAAAG
196 TTAACAAAATTCTTAAGAAATAATATAGTTTCTTGATCATATATATAAAAG
*
40625 TACAAACAATAACAATGCAGCAATGAAAAAAAAAGTCCAGGAAACTCATGGACCGGAGGAAAGTT
1 TACAAACAATAACAATGCAGCAATGAAAAAAAAAGTCCAGGAAACTCATGGACCAGAGGAAAGTT
40690 CCAGTGCTAATTCAGAAAAAAGCTTAATAATAGAGGTTAAAAGCAAACTTTTTAATATTCCAACA
66 CCAGTGCTAATTCAGAAAAAAGCTTAATAATAGAGGTTAAAAGCAAACTTTTTAATATTCCAACA
40755 ATCTTCAGAATTCAAGGTCTCAGAGAACAAACAAACTAGATTTTTCAGAATATATATTAAGCTTA
131 ATCTTCAGAATTCAAGGTCTCAGAGAACAAACAAACTAGATTTTTCAGAATATATATTAAGCTTA
40820 TTAACAAAATTCTTAAGAAATAATATAGTTTCTTGATCATATATATAAAAG
196 TTAACAAAATTCTTAAGAAATAATATAGTTTCTTGATCATATATATAAAAG
40871 TA
1 TA
40873 AAAGAAATAA
Statistics
Matches: 244, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
246 244 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (246 bp):
TACAAACAATAACAATGCAGCAATGAAAAAAAAAGTCCAGGAAACTCATGGACCAGAGGAAAGTT
CCAGTGCTAATTCAGAAAAAAGCTTAATAATAGAGGTTAAAAGCAAACTTTTTAATATTCCAACA
ATCTTCAGAATTCAAGGTCTCAGAGAACAAACAAACTAGATTTTTCAGAATATATATTAAGCTTA
TTAACAAAATTCTTAAGAAATAATATAGTTTCTTGATCATATATATAAAAG
Found at i:43027 original size:39 final size:39
Alignment explanation
Indices: 42980--43055 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
42970 AGAGAAAATG
*
42980 AAAATCACTTTCTTAAATCTAAATGATACCTTGAAAAAC
1 AAAATCACTTTATTAAATCTAAATGATACCTTGAAAAAC
43019 AAAATCACTTTATTAAATCTAAATGATACCTTGAAAA
1 AAAATCACTTTATTAAATCTAAATGATACCTTGAAAA
43056 TTCTTTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (39 bp):
AAAATCACTTTATTAAATCTAAATGATACCTTGAAAAAC
Found at i:46251 original size:5 final size:5
Alignment explanation
Indices: 46241--46274 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
46231 AGAGAAAAGT
46241 GTTTG GTTTG GTTTG GTTTG GTTTG GTTTG GTTT
1 GTTTG GTTTG GTTTG GTTTG GTTTG GTTTG GTTT
46275 TTGAGGCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (5 bp):
GTTTG
Found at i:47122 original size:20 final size:21
Alignment explanation
Indices: 47084--47124 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
47074 AAAATTATGA
*
47084 GATACTAAAAATATTAAAATT
1 GATACTAAAAATATAAAAATT
*
47105 GATA-TAAAATTATAAAAATT
1 GATACTAAAAATATAAAAATT
47125 ATTAAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (21 bp):
GATACTAAAAATATAAAAATT
Found at i:47132 original size:10 final size:9
Alignment explanation
Indices: 47089--47148 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 9
47079 TATGAGATAC
47089 TAAAAA-TA
1 TAAAAATTA
*
47097 TTAAAATTGA
1 TAAAAATT-A
47107 TATAAAATTA
1 TA-AAAATTA
47117 TAAAAATTA
1 TAAAAATTA
47126 TTAAAAACTTA
1 -TAAAAA-TTA
* *
47137 CAAATATTA
1 TAAAAATTA
47146 TAA
1 TAA
47149 TATATATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 5 0.12
9 13 0.31
10 15 0.36
11 9 0.21
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Done.