Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000200.1 Kokia drynarioides strain JFW-HI SEQ_110889, 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: 18333
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:49 original size:6 final size:6
Alignment explanation
Indices: 40--106 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
30 AATTTTGGAA
40 TTAAAT TTAAAT TTAAA- TTAAAT TTAAATT TTAAGA- TT-AAT TT-AA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAA-AT TTAAAT TTAAAT
* *
85 TTAAA- ATAAAT CTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAA
107 ATAAATTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
4 3 0.06
5 16 0.31
6 27 0.52
7 5 0.10
8 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:60 original size:11 final size:11
Alignment explanation
Indices: 38--113 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
28 TTAATTTTGG
38 AATTAAATTTA
1 AATTAAATTTA
49 AATTTAAA-TTA
1 AA-TTAAATTTA
60 AATTTAAATTTTA
1 AA-TTAAA-TTTA
73 AGATT-AATTT-
1 A-ATTAAATTTA
*
83 AATTAAA-ATA
1 AATTAAATTTA
93 AATCTAAATTTA
1 AAT-TAAATTTA
*
105 AAATAAATT
1 AATTAAATT
114 AAAAAGGGGG
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 4 0.07
10 6 0.11
11 26 0.48
12 11 0.20
13 6 0.11
14 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:60 original size:17 final size:17
Alignment explanation
Indices: 38--113 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
28 TTAATTTTGG
38 AATTAAATTTAAATTTA
1 AATTAAATTTAAATTTA
55 AATTAAATTTAAATTTTA
1 AATTAAATTTAAA-TTTA
73 AGATT-AATTT-AA-TTA
1 A-ATTAAATTTAAATTTA
* *
88 AAATAAATCTAAATTTA
1 AATTAAATTTAAATTTA
*
105 AAATAAATT
1 AATTAAATT
114 AAAAAGGGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 2 0.04
15 8 0.16
16 2 0.04
17 26 0.51
18 10 0.20
19 3 0.06
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
AATTAAATTTAAATTTA
Found at i:285 original size:16 final size:16
Alignment explanation
Indices: 260--308 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
250 AAGTAACCGG
*
260 AATTCGAAATTATTCA
1 AATTCAAAATTATTCA
* *
276 AATTCAAAATAAATCA
1 AATTCAAAATTATTCA
* *
292 AATCCTAAATTATTCA
1 AATTCAAAATTATTCA
308 A
1 A
309 TTTTAAATAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (16 bp):
AATTCAAAATTATTCA
Found at i:1394 original size:19 final size:18
Alignment explanation
Indices: 1378--1442 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
1368 AATTTATATG
1378 TATTTTATAATTTTATAA
1 TATTTTATAATTTTATAA
*
1396 TATTTTAGAATTTCTAT-A
1 TATTTTATAATTT-TATAA
* *
1414 -AGTTTATATATTTTTTAA
1 TATTTTATA-ATTTTATAA
1432 TATTTTTATAA
1 TA-TTTTATAA
1443 AATTTTATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
17 8 0.22
18 18 0.49
19 5 0.14
20 6 0.16
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (18 bp):
TATTTTATAATTTTATAA
Found at i:1400 original size:10 final size:10
Alignment explanation
Indices: 1378--1450 Score: 50
Period size: 10 Copynumber: 7.8 Consensus size: 10
1368 AATTTATATG
1378 TATTTTAT-A
1 TATTTTATAA
1387 -ATTTTATAA
1 TATTTTATAA
*
1396 TATTTTAGAA
1 TATTTTATAA
*
1406 T-TTCTAT-A
1 TATTTTATAA
*
1414 -AGTTTAT-A
1 TATTTTATAA
*
1422 TATTTTTTAA
1 TATTTTATAA
1432 TATTTTTATAA
1 TA-TTTTATAA
*
1443 AATTTTAT
1 TATTTTAT
1451 CTTGTTAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
8 13 0.27
9 10 0.20
10 18 0.37
11 8 0.16
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (10 bp):
TATTTTATAA
Found at i:1864 original size:13 final size:13
Alignment explanation
Indices: 1846--1880 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1836 ATTTGACAAG
1846 GTACACACACTAT
1 GTACACACACTAT
*
1859 GTACACACACTTT
1 GTACACACACTAT
1872 GTACACACA
1 GTACACACA
1881 AGTGCTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.31, G:0.09, T:0.23
Consensus pattern (13 bp):
GTACACACACTAT
Found at i:3695 original size:24 final size:24
Alignment explanation
Indices: 3651--3696 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3641 TGAAAGCTTT
*
3651 TTTTTTTTTTTTACTTGATTATTG
1 TTTTTTTTTTTTACATGATTATTG
3675 TTTTTTTTTTTTA-ATGAATTAT
1 TTTTTTTTTTTTACATG-ATTAT
3697 AAAGGAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (24 bp):
TTTTTTTTTTTTACATGATTATTG
Found at i:13927 original size:16 final size:17
Alignment explanation
Indices: 13895--13928 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13885 TTTTGTTTCA
*
13895 TCTTTCTTCTTCTTCCC
1 TCTTTCTTCTCCTTCCC
13912 TCTTTC-TCTCCTTCCC
1 TCTTTCTTCTCCTTCCC
13928 T
1 T
13929 TATTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (17 bp):
TCTTTCTTCTCCTTCCC
Found at i:17368 original size:59 final size:59
Alignment explanation
Indices: 17312--17679 Score: 383
Period size: 59 Copynumber: 6.2 Consensus size: 59
17302 ATCCGGGGGC
* * * *
17312 AAAATGGTAATTTTTGGCAGTTTCAAGGTGAAAATGGAATTATTGAAAGTTTCGGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTCAAGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCA
* * *
17372 AAAATGGAATTTTTAGAAGTTT-AAGGGGTAAAAATGGAATTTTTGGAAG-TTCAAGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCAA--GGTAAAAATGGAATTTTTGGAAGTTTC-GGGGTCA
* * * *
17432 AAAATGGAATTTTTGGAAGTTTGGAGGGTAAAAATAGAA--TTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTT-CAAGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCA
* *
17490 AAAATGGAATTTTTGGAAG-TTCGAGGATAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCAAGG-TAAAAATGGAATTTTTGGAAGTTTCGGGGTCA
* * * * *
17549 AAAATGGAATTTTTTGAAG-TTCAGGGGTCAAAATGGAATTTTTGGAAGCTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCA-AGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCA
* * * * *
17608 AAAATAGAATTTTTGGAAGCTTCGAGGTTAAAAAT-GAGATTTTTGAAAG-TTCGGGGGCA
1 AAAATGGAATTTTTGGAAGTTTCAAGG-TAAAAATGGA-ATTTTTGGAAGTTTCGGGGTCA
*
17667 AAAATGTAATTTT
1 AAAATGGAATTTT
17680 CGAACAGTTT
Statistics
Matches: 263, Mismatches: 32, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
56 2 0.01
57 12 0.05
58 33 0.13
59 129 0.49
60 86 0.33
62 1 0.00
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.33
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTCAAGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCA
Found at i:17660 original size:29 final size:30
Alignment explanation
Indices: 17312--17658 Score: 361
Period size: 30 Copynumber: 11.7 Consensus size: 30
17302 ATCCGGGGGC
* * *
17312 AAAATGGTAATTTTTGGCAGTTTCAAGG-TG
1 AAAATGG-AATTTTTGGAAGTTTCGAGGTTA
* * * *
17342 AAAATGGAATTATTGAAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* * *
17372 AAAATGGAATTTTTAGAAGTTT-AAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTTA
*
17402 AAAATGGAATTTTTGGAAG-TTCAAGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTTA
* *
17432 AAAATGGAATTTTTGGAAGTTTGGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* *
17462 AAAATAGAA--TTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
*
17490 AAAATGGAATTTTTGGAAG-TTCGAGGATA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
*
17519 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* * *
17549 AAAATGGAATTTTTTGAAG-TTC-AGGGGTC
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTTA
* *
17578 AAAATGGAATTTTTGGAAGCTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* *
17608 AAAATAGAATTTTTGGAAGCTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
*
17638 AAAAT-GAGATTTTTGAAAGTT
1 AAAATGGA-ATTTTTGGAAGTT
17659 CGGGGGCAAA
Statistics
Matches: 266, Mismatches: 40, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
28 25 0.09
29 69 0.26
30 168 0.63
31 4 0.02
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTTA
Done.