Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005144.1 Kokia drynarioides strain JFW-HI SEQ_118982, 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: 35217
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38 TATTTAGACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5380 original size:29 final size:29
Alignment explanation
Indices: 5347--5418 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
5337 CATAATCATT
* *
5347 AATTTAATTCTATTTCATTTATATGCATA
1 AATTTAATTCTATTTCATTTATAAGAATA
* *
5376 AATTTAATTCTATTTTATTTATAAGAATT
1 AATTTAATTCTATTTCATTTATAAGAATA
*
5405 AATTTAATTTTATT
1 AATTTAATTCTATT
5419 ATTCTAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (29 bp):
AATTTAATTCTATTTCATTTATAAGAATA
Found at i:9180 original size:2 final size:2
Alignment explanation
Indices: 9173--9209 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9163 GGTTTTAATC
9173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9210 GTAATTCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11349 original size:4 final size:4
Alignment explanation
Indices: 11340--11370 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
11330 GGTATGAATA
11340 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
11371 AGGCGTGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:12809 original size:23 final size:23
Alignment explanation
Indices: 12759--12801 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
12749 GAGGTAAAAG
*
12759 ATCCTCTCATACTTTTCAATTTA
1 ATCCTCTCAAACTTTTCAATTTA
12782 ATCCTC-CAAACTTTTCAATT
1 ATCCTCTCAAACTTTTCAATT
12802 AGTATCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (23 bp):
ATCCTCTCAAACTTTTCAATTTA
Found at i:17313 original size:90 final size:90
Alignment explanation
Indices: 17187--17569 Score: 236
Period size: 88 Copynumber: 4.3 Consensus size: 90
17177 ACCAGAGGGT
* ** * * *
17187 AAAATGGTAATTTTGGGAAAATTAGGGGTTTAAAAATGGAATTTTTAGATATTC-GGGGGCAACA
1 AAAATGG-AATTTTTGGAAGTTTAGGGGTTTAAAAATGGAATTTTTAGA-AGTCAGAGGGCAAAA
*
17251 TTGGAATTTTTGGAAATTTCGGGATCAA
64 ATGGAATTTTTGGAAATTTCGGGAT-AA
* * *
17279 AAAATGGAATTTTTGGAAGTTTTGGGG-TTAAAAATGGGATTTTTAGAAGTCAGAGGGTAAAAAT
1 AAAATGGAATTTTTGGAAGTTTAGGGGTTTAAAAATGGAATTTTTAGAAGTCAGAGGGCAAAAAT
* * *
17343 GGGATTTTTGGAAGTTTCGGGATGA
66 GGAATTTTTGGAAATTTCGGGATAA
* * * * *** * **
17368 AAAATAGG-ATTTTTGGAAG-TTCGGGG-GT-AAAATGATAATTTTTGGAAGTTTTAAGGTTAAA
1 AAAAT-GGAATTTTTGGAAGTTTAGGGGTTTAAAAATG-GAATTTTTAGAAGTCAGAGGGCAAAA
* * * *
17429 ATGG-GTTTTTTGAAAGTTTTAGGG-TCA
64 ATGGAATTTTTGGAAA--TTTCGGGATAA
* * * * * ** *
17456 AAAATAGCATTTTTGG-AGGTTCGGGG-GTAAAAATGGAATTTTTAGAAGTTTTGAGGTCAAAAA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTTTAAAAATGGAATTTTTAGAAG-TCAGAGGGCAAAAA
* *
17519 T-GAGATTTTT-GAAAGTTCGGGGGT--
65 TGGA-ATTTTTGGAAATTTC-GGGATAA
17543 AAAATGGAATTTTTGGATAGTTTAGGG
1 AAAATGGAATTTTTGGA-AGTTTAGGG
17570 ACCTCCAAGG
Statistics
Matches: 233, Mismatches: 43, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
87 33 0.14
88 68 0.29
89 54 0.23
90 55 0.24
91 16 0.07
92 7 0.03
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (90 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTTTAAAAATGGAATTTTTAGAAGTCAGAGGGCAAAAAT
GGAATTTTTGGAAATTTCGGGATAA
Found at i:17314 original size:30 final size:30
Alignment explanation
Indices: 17187--17565 Score: 226
Period size: 29 Copynumber: 12.7 Consensus size: 30
17177 ACCAGAGGGT
* ** *
17187 AAAATGGTAATTTTGGGAAAATTAGGGGTTTA
1 AAAATGG-AATTTTTGGAAGTTTCGGGG-TTA
* **
17219 AAAATGGAATTTTTAG-A-TATTCGGGGGCA
1 AAAATGGAATTTTTGGAAGT-TTCGGGGTTA
* * * * *
17248 ACATTGGAATTTTTGGAAATTTCGGGATCAA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-TA
*
17279 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTA
* *
17309 AAAATGGGATTTTTAGAAG--TCAGAGGG-TA
1 AAAATGGAATTTTTGGAAGTTTC-G-GGGTTA
* * *
17338 AAAATGGGATTTTTGGAAGTTTCGGGATGA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTA
*
17368 AAAATAGG-ATTTTTGGAAG-TTCGGGGGT-
1 AAAAT-GGAATTTTTGGAAGTTTCGGGGTTA
* ***
17396 AAAATGATAATTTTTGGAAGTTTTAAGGTT-
1 AAAATG-GAATTTTTGGAAGTTTCGGGGTTA
** * ** *
17426 AAAATGGGTTTTTTGAAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTA
* * * *
17456 AAAATAGCATTTTTGG-AGGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTA
* * * *
17485 AAAATGGAATTTTTAGAAGTTTTGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTA
* *
17515 AAAAT-GAGATTTTTGAAAG-TTCGGGGGT-
1 AAAATGGA-ATTTTTGGAAGTTTCGGGGTTA
17543 AAAATGGAATTTTTGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
17566 AGGGACCTCC
Statistics
Matches: 266, Mismatches: 62, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
27 1 0.00
28 19 0.07
29 103 0.39
30 100 0.38
31 36 0.14
32 7 0.03
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTTA
Found at i:17352 original size:59 final size:61
Alignment explanation
Indices: 17278--17556 Score: 233
Period size: 59 Copynumber: 4.7 Consensus size: 61
17268 TTCGGGATCA
* *
17278 AAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAG-TCAGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTAGAAGTTCTGAGGGTC
* * * * * *
17337 AAAAATGGGATTTTTGGAAGTTTCGGGATGAAAAATAGGATTTTTGGAAGTTC-GGGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTAGAAGTTCTGAGGGTC
* *** * *
17396 -AAAATGATAATTTTTGGAAGTTTTAAGGTT-AAAATGGG-TTTTTTGAAAGTT-TTAGGGTC
1 AAAAATG-GAATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTAG-AAGTTCTGAGGGTC
* * * * * *
17455 AAAAATAGCATTTTTGG-AGGTTCGGGGGTAAAAATGGAATTTTTAGAAGTTTTGA-GGTC
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTAGAAGTTCTGAGGGTC
* * *
17514 AAAAAT-GAGATTTTTGAAAG-TTCGGGGGT-AAAATGGAATTTTT
1 AAAAATGGA-ATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTT
17557 GGATAGTTTA
Statistics
Matches: 178, Mismatches: 31, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
57 6 0.03
58 44 0.25
59 111 0.62
60 17 0.10
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (61 bp):
AAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTAGAAGTTCTGAGGGTC
Found at i:17370 original size:29 final size:28
Alignment explanation
Indices: 17256--17565 Score: 171
Period size: 30 Copynumber: 10.5 Consensus size: 28
17246 CAACATTGGA
* *
17256 ATTTTTGGAAATTTCGGGATCAAAAAATGGA
1 ATTTTTGGAAGTTTCGGG-T--AAAAATGGG
*
17287 ATTTTTGGAAGTTTTGGGGTTAAAAATGGG
1 ATTTTTGGAAG-TTTCGGG-TAAAAATGGG
* ***
17317 ATTTTTAGAAGTCAGAGGGTAAAAATGGG
1 ATTTTTGGAAGT-TTCGGGTAAAAATGGG
*
17346 ATTTTTGGAAGTTTCGGGATGAAAAATAGG
1 ATTTTTGGAAGTTTCGGG-T-AAAAATGGG
**
17376 ATTTTTGGAAG-TTCGGGGGT-AAAATGATA
1 ATTTTTGGAAGTTTC--GGGTAAAAATG-GG
** *
17405 ATTTTTGGAAGTTTTAAGGTTAAAATGGG
1 ATTTTTGGAAG-TTTCGGGTAAAAATGGG
* * * * *
17434 TTTTTTGAAAGTTTTAGGGTCAAAAATAGC
1 ATTTTTGGAAG-TTTCGGGT-AAAAATGGG
* *
17464 ATTTTTGG-AGGTTCGGGGGTAAAAATGGA
1 ATTTTTGGAAGTTTC--GGGTAAAAATGGG
* * *
17493 ATTTTTAGAAGTTTTGAGGTCAAAAATGAG
1 ATTTTTGGAAGTTTCG-GGT-AAAAATGGG
* *
17523 ATTTTTGAAAG-TTCGGGGGT-AAAATGGA
1 ATTTTTGGAAGTTTC--GGGTAAAAATGGG
17551 ATTTTTGGATAGTTT
1 ATTTTTGGA-AGTTT
17566 AGGGACCTCC
Statistics
Matches: 216, Mismatches: 43, Indels: 41
0.72 0.14 0.14
Matches are distributed among these distances:
28 25 0.12
29 80 0.37
30 88 0.41
31 16 0.07
32 7 0.03
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.36
Consensus pattern (28 bp):
ATTTTTGGAAGTTTCGGGTAAAAATGGG
Found at i:19276 original size:7 final size:6
Alignment explanation
Indices: 19223--19303 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
19213 AATTGGACAT
19223 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTCAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * * *
19269 TTTAAA -ATAAA CTT-AA TTTAAA -ATAAA TTCAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
19304 CTAATAGGCC
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
4 5 0.08
5 15 0.25
6 35 0.58
7 5 0.08
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:19288 original size:16 final size:17
Alignment explanation
Indices: 19225--19303 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
19215 TTGGACATTT
*
19225 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
19242 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
19259 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
19276 TAAACTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
*
19292 TAAATTCAAATT
1 TAAATTTAAATT
19304 CTAATAGGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
16 14 0.25
17 41 0.75
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:31569 original size:23 final size:23
Alignment explanation
Indices: 31535--31659 Score: 118
Period size: 23 Copynumber: 5.5 Consensus size: 23
31525 AGTGCTGGGG
31535 AAAT-AGTAAGCACACACAGTGC
1 AAATCAGTAAGCACACACAGTGC
31557 -AATCCAGTAAGCACACACAGTGC
1 AAAT-CAGTAAGCACACACAGTGC
* * * *
31580 -AATCAGTAGGCTCACATAGCGC
1 AAATCAGTAAGCACACACAGTGC
*
31602 AAATCAGTAGGCACACA-AGGTGC
1 AAATCAGTAAGCACACACA-GTGC
*
31625 GAAA-CAGTAAGCACACAAAGTGC
1 -AAATCAGTAAGCACACACAGTGC
31648 GAAA-CAGTAAGC
1 -AAATCAGTAAGC
31660 GCGCTAGCGT
Statistics
Matches: 90, Mismatches: 7, Indels: 11
0.83 0.06 0.10
Matches are distributed among these distances:
21 3 0.03
22 16 0.18
23 67 0.74
24 4 0.04
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.13
Consensus pattern (23 bp):
AAATCAGTAAGCACACACAGTGC
Done.