Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012240.1 Kokia drynarioides strain JFW-HI SEQ_127241, 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: 13040
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1521 original size:19 final size:20
Alignment explanation
Indices: 1480--1522 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1470 AAATGATTTT
*
1480 AATTTGAAAATATAAAATAA
1 AATTTGAAAATATAAAAGAA
* *
1500 AATTT-AAAATTTAAAAGGA
1 AATTTGAAAATATAAAAGAA
1519 AATT
1 AATT
1523 AAATTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (20 bp):
AATTTGAAAATATAAAAGAA
Found at i:2284 original size:15 final size:15
Alignment explanation
Indices: 2254--2298 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
2244 AAAAATGAAT
*
2254 TTTTATTTAATTAAA
1 TTTTATTTTATTAAA
2269 TATTTATTTT-TTAAA
1 T-TTTATTTTATTAAA
2284 TTTTATTTTATTAAA
1 TTTTATTTTATTAAA
2299 ACTATTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 8 0.30
15 12 0.44
16 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTATTTTATTAAA
Found at i:2564 original size:31 final size:30
Alignment explanation
Indices: 2526--2657 Score: 94
Period size: 31 Copynumber: 4.4 Consensus size: 30
2516 TTAATATAAT
*
2526 ATTTGGTACCTGAACTTGATACTTTTTCTTA
1 ATTTGGTACCTGAACTT-ATACTTTTTCCTA
* *
2557 ATTTGGTACCT-AAATT-T--TTTTTGACTCA
1 ATTTGGTACCTGAACTTATACTTTTT-CCT-A
* *
2585 ATTTGG-CCCTTAAACTTATCACTTTTTCCTA
1 ATTTGGTACC-TGAACTTAT-ACTTTTTCCTA
* * *
2616 ATTTGGTACCTGAACATGACATTTTTTCCTA
1 ATTTGGTACCTGAAC-TTATACTTTTTCCTA
*
2647 ATTTGTTACCT
1 ATTTGGTACCT
2658 AAGCTTTTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
26 5 0.06
27 3 0.04
28 9 0.11
29 4 0.05
30 5 0.06
31 42 0.53
32 6 0.08
33 5 0.06
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (30 bp):
ATTTGGTACCTGAACTTATACTTTTTCCTA
Found at i:8953 original size:43 final size:43
Alignment explanation
Indices: 8905--9004 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
8895 AACTGCACAA
*
8905 TTAATAACATGTCACAATATTAACAAGAGTTAAGGAATATAAT
1 TTAATAACATGTCACAATATTAACAAGAGTCAAGGAATATAAT
*** * * *
8948 TTAATAACAACCCACGATATTAACACGAGTCAAGTAATATAAT
1 TTAATAACATGTCACAATATTAACAAGAGTCAAGGAATATAAT
8991 TTAATAACATGTCA
1 TTAATAACATGTCA
9005 AAGAATAACA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (43 bp):
TTAATAACATGTCACAATATTAACAAGAGTCAAGGAATATAAT
Found at i:10464 original size:25 final size:25
Alignment explanation
Indices: 10436--10506 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
10426 GGATTAAAAT
10436 AATTAATTTCAACATTTTAGTAACA
1 AATTAATTTCAACATTTTAGTAACA
* *
10461 AATTGA-TT-AACATTTTCAAGGAACA
1 AATTAATTTCAACATTTT--AGTAACA
** *
10486 AATTTTTTTCAACAATTTAGT
1 AATTAATTTCAACATTTTAGT
10507 TAATTTATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
23 8 0.22
24 2 0.06
25 17 0.47
26 2 0.06
27 7 0.19
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (25 bp):
AATTAATTTCAACATTTTAGTAACA
Found at i:11082 original size:31 final size:30
Alignment explanation
Indices: 11035--11141 Score: 80
Period size: 31 Copynumber: 3.6 Consensus size: 30
11025 TTAATATAAC
* *
11035 ATTTGGTACTTGAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTT-CTA
*
11066 ATTTGGTACCTAAACTT-----TTTTGGACTCA
1 ATTTGGTACCTAAACTTGACACTTTT--TCT-A
* * *
11094 ATTTGGTACCTGAATTTGACACTTTCTTCTG
1 ATTTGGTACCTAAACTTGACACTTT-TTCTA
11125 ATTTGGTACCTAAACTT
1 ATTTGGTACCTAAACTT
11142 TTTTTGGACC
Statistics
Matches: 58, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
26 4 0.07
27 2 0.03
28 16 0.28
31 30 0.52
32 2 0.03
33 3 0.05
34 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTA
Found at i:11129 original size:59 final size:60
Alignment explanation
Indices: 11035--11208 Score: 210
Period size: 59 Copynumber: 2.9 Consensus size: 60
11025 TTAATATAAC
* *
11035 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAAC-TTTTTTGGACTCA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGGACCCA
* *
11094 ATTTGGTACCTGAATTTGACACTTTCTT-CTGATTTGGTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACCTGAACTTGACACTTT-TTCCTAATTTGGTACCTAAACTTTTTTTGGACCCA
* * * * *
11154 A-TTGGTACCTAAACTTGGCATTTTTTTTTCTAATTTGGTACCTAAGCCTTTTTTT
1 ATTTGGTACCTGAACTTGACA--CTTTTTCCTAATTTGGTACCTAA-ACTTTTTTT
11209 TTAGATTCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
59 56 0.57
60 17 0.17
61 18 0.18
62 8 0.08
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGGACCCA
Found at i:11292 original size:17 final size:17
Alignment explanation
Indices: 11267--11314 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
11257 CTGGGCCCAA
* *
11267 TAAACTTAAATTTATTT
1 TAAAATTAAATTTATTC
*
11284 TAAAATTAAGTTTATTC
1 TAAAATTAAATTTATTC
* *
11301 TGAATTTAAATTTA
1 TAAAATTAAATTTA
11315 GCTGAAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (17 bp):
TAAAATTAAATTTATTC
Done.