Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004599.1 Kokia drynarioides strain JFW-HI SEQ_118096, 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: 66805
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Warning! 251 characters in sequence are not A, C, G, or T
Found at i:4326 original size:18 final size:18
Alignment explanation
Indices: 4287--4354 Score: 52
Period size: 18 Copynumber: 3.7 Consensus size: 18
4277 ATGTGTTTTT
**
4287 TTTAATTTTAATTATAGT
1 TTTAATTTTAATTATACA
4305 TTTAATTTTACATT-TACA
1 TTTAATTTTA-ATTATACA
4323 TTTACATTTATATATTAT--A
1 TTTA-ATTT-TA-ATTATACA
*
4342 TGTAATTTTAATT
1 TTTAATTTTAATT
4355 TTATACTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 3 0.07
17 2 0.05
18 20 0.48
19 11 0.26
20 5 0.12
21 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAATTTTAATTATACA
Found at i:8255 original size:6 final size:6
Alignment explanation
Indices: 8244--8271 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
8234 TTAGAATATG
8244 TCCACC TCCACC TCCACC TCCACC TCCA
1 TCCACC TCCACC TCCACC TCCACC TCCA
8272 GGAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.64, G:0.00, T:0.18
Consensus pattern (6 bp):
TCCACC
Found at i:14751 original size:17 final size:19
Alignment explanation
Indices: 14716--14759 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
14706 TTTAAAAAAC
14716 ATTTTTAACTCTTCATTTA
1 ATTTTTAACTCTTCATTTA
* *
14735 TTTTTTAA-T-TTCTTTTA
1 ATTTTTAACTCTTCATTTA
14752 ATTTTTAA
1 ATTTTTAA
14760 ACTTGTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 1 0.05
19 7 0.32
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTTAACTCTTCATTTA
Found at i:16347 original size:30 final size:29
Alignment explanation
Indices: 16285--16358 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
16275 GGATTTCAAA
* * * *
16285 ATTTTATGCAATTCTATATATGAATTTTG
1 ATTTTATGTAATTCTATACAAGAATATTG
*
16314 ATTTTATGTAATTTTATACAAGAAATATTG
1 ATTTTATGTAATTCTATACAAG-AATATTG
* *
16344 ATTTGATCTAATTCT
1 ATTTTATGTAATTCT
16359 CATAAAGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (29 bp):
ATTTTATGTAATTCTATACAAGAATATTG
Found at i:17253 original size:24 final size:24
Alignment explanation
Indices: 17222--17274 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
17212 TGCCGGCAGT
*
17222 ATTA-AGATGAATATTAGATTGAC
1 ATTAGAGATGAATATTAGATTAAC
* * *
17245 ATTAGAGATTAATGTTAGATTAAT
1 ATTAGAGATGAATATTAGATTAAC
17269 ATTAGA
1 ATTAGA
17275 TTAGGATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (24 bp):
ATTAGAGATGAATATTAGATTAAC
Found at i:17264 original size:11 final size:11
Alignment explanation
Indices: 17221--17277 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
17211 TTGCCGGCAG
*
17221 TATTAAGATGAA
1 TATT-AGATTAA
*
17233 TATTAGATTGA
1 TATTAGATTAA
*
17244 CATTAGAGATTAA
1 TATT--AGATTAA
*
17257 TGTTAGATTAA
1 TATTAGATTAA
17268 TATTAGATTA
1 TATTAGATTA
17278 GGATTTACTT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
11 24 0.67
12 4 0.11
13 8 0.22
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (11 bp):
TATTAGATTAA
Found at i:24467 original size:19 final size:18
Alignment explanation
Indices: 24435--24471 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
24425 ATCAGCCAGA
24435 CGAAGTTTTAGAGAAAGC
1 CGAAGTTTTAGAGAAAGC
*
24453 CGAAGGTTTTGGAGAAAGC
1 CGAA-GTTTTAGAGAAAGC
24472 AGGAAATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.11, G:0.32, T:0.22
Consensus pattern (18 bp):
CGAAGTTTTAGAGAAAGC
Found at i:39113 original size:23 final size:21
Alignment explanation
Indices: 39075--39128 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
39065 TAAAGTTCAG
39075 TTTATT-TAATGTAT-TTT-AA
1 TTTATTCTAAT-TATATTTAAA
39094 TTTATATACTAATTATATTTAAA
1 TTTAT-T-CTAATTATATTTAAA
39117 TTTATTCTAATT
1 TTTATTCTAATT
39129 TAGATCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.17
20 1 0.03
21 9 0.30
22 8 0.27
23 7 0.23
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTATTCTAATTATATTTAAA
Found at i:39143 original size:32 final size:32
Alignment explanation
Indices: 39077--39145 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
39067 AAGTTCAGTT
* *
39077 TATTTAATGTATTTTAATTTATATACTAATTA
1 TATTTAATGTATTCTAATTTAGATACTAATTA
*
39109 TATTTAAATTTATTCTAATTTAGAT-C-AATATA
1 TATTT-AATGTATTCTAATTTAGATACTAAT-TA
39141 TATTT
1 TATTT
39146 CTATTAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.09
32 13 0.41
33 16 0.50
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (32 bp):
TATTTAATGTATTCTAATTTAGATACTAATTA
Found at i:55628 original size:109 final size:109
Alignment explanation
Indices: 55493--55712 Score: 431
Period size: 109 Copynumber: 2.0 Consensus size: 109
55483 AACATTAACA
*
55493 AACCTCCTACAGTGATTTCTGATTCAGACCTGAAGGCACCGAGGCCCTCCCACAACAAAGAGAAA
1 AACCTCCTACAGTGATTTCTGATTCAGACCTGAAGGCACCAAGGCCCTCCCACAACAAAGAGAAA
55558 TTCCTTGCAAAATGGAGGAAGAATTTCCTCATAGTTTCAAGAAC
66 TTCCTTGCAAAATGGAGGAAGAATTTCCTCATAGTTTCAAGAAC
55602 AACCTCCTACAGTGATTTCTGATTCAGACCTGAAGGCACCAAGGCCCTCCCACAACAAAGAGAAA
1 AACCTCCTACAGTGATTTCTGATTCAGACCTGAAGGCACCAAGGCCCTCCCACAACAAAGAGAAA
55667 TTCCTTGCAAAATGGAGGAAGAATTTCCTCATAGTTTCAAGAAC
66 TTCCTTGCAAAATGGAGGAAGAATTTCCTCATAGTTTCAAGAAC
55711 AA
1 AA
55713 AAGTTTATTC
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (109 bp):
AACCTCCTACAGTGATTTCTGATTCAGACCTGAAGGCACCAAGGCCCTCCCACAACAAAGAGAAA
TTCCTTGCAAAATGGAGGAAGAATTTCCTCATAGTTTCAAGAAC
Found at i:65691 original size:14 final size:15
Alignment explanation
Indices: 65673--65714 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
65663 AAAATAAATA
65673 ATCAAAATAGTATTT
1 ATCAAAATAGTATTT
* *
65688 -TCAAATTATTATTT
1 ATCAAAATAGTATTT
*
65702 ATCAAAATGGTAT
1 ATCAAAATAGTAT
65715 GTTTAGTTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
ATCAAAATAGTATTT
Found at i:65989 original size:27 final size:27
Alignment explanation
Indices: 65914--65995 Score: 121
Period size: 27 Copynumber: 3.0 Consensus size: 27
65904 TACCTTACAC
* * *
65914 CCAATGGAGGAACA-CGAAGTGACGACA
1 CCAATGGAGGAATATC-AAGTGGCGGCA
65941 CCAATGGAGGAATATCAAGTGGCGGCA
1 CCAATGGAGGAATATCAAGTGGCGGCA
65968 CCAATGGAGGAATATCAAGTGGCGGCA
1 CCAATGGAGGAATATCAAGTGGCGGCA
65995 C
1 C
65996 TAAGAGATGT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
27 50 0.98
28 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.32, T:0.12
Consensus pattern (27 bp):
CCAATGGAGGAATATCAAGTGGCGGCA
Found at i:66182 original size:11 final size:11
Alignment explanation
Indices: 66166--66218 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 11
66156 GGGGACCAAC
* *
66166 GAAAAATGAAG
1 GAAAAAAGAAA
66177 GAAAAAAGAAA
1 GAAAAAAGAAA
66188 GAAAAAAGAGAAA
1 G-AAAAA-AGAAA
66201 GAAAGAAAGAAA
1 GAAA-AAAGAAA
66213 GAAAAA
1 GAAAAA
66219 GGATGAAGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
11 12 0.32
12 17 0.46
13 8 0.22
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:66190 original size:4 final size:4
Alignment explanation
Indices: 66177--66216 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
66167 AAAAATGAAG
*
66177 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA
66217 AAGGATGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.09
4 26 0.81
5 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:66631 original size:20 final size:21
Alignment explanation
Indices: 66590--66632 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
66580 TAATTTACTT
66590 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
*
66611 TAATTTAATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
66631 TA
1 TA
66633 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Done.