Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011050.1 Kokia drynarioides strain JFW-HI SEQ_126021, 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: 55233
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:434 original size:6 final size:6
Alignment explanation
Indices: 412--486 Score: 79
Period size: 6 Copynumber: 13.0 Consensus size: 6
402 ATTTAGACTT
*
412 TTTAAT TTTGAAA -TTAAA TTTAAA -TTAAA TTTAAA TTTAAGA -TT-AA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA
*
458 TTTAAA TTTAAA TTTAAA -TCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
487 ATAAATTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
4 1 0.02
5 15 0.25
6 40 0.68
7 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:438 original size:11 final size:12
Alignment explanation
Indices: 412--486 Score: 79
Period size: 11 Copynumber: 6.5 Consensus size: 12
402 ATTTAGACTT
*
412 TTTAATTTTGAAA
1 TTTAAATTT-AAA
425 -TTAAATTTAAA
1 TTTAAATTTAAA
436 -TTAAATTTAAA
1 TTTAAATTTAAA
447 TTTAAGA-TT-AA
1 TTTAA-ATTTAAA
458 TTTAAATTTAAA
1 TTTAAATTTAAA
*
470 TTTAAA-TCAAA
1 TTTAAATTTAAA
481 TTTAAA
1 TTTAAA
487 ATAAATTAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
10 1 0.02
11 33 0.59
12 21 0.38
13 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:447 original size:17 final size:17
Alignment explanation
Indices: 425--493 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
415 AATTTTGAAA
425 TTAAATTTAAATTAAAT
1 TTAAATTTAAATTAAAT
442 TTAAATTTAAGATT-AAT
1 TTAAATTTAA-ATTAAAT
459 TTAAATTTAAATTTAAA-
1 TTAAATTTAAA-TTAAAT
* *
476 TCAAATTTAAAATAAAT
1 TTAAATTTAAATTAAAT
493 T
1 T
494 AAAAAGGACC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
16 5 0.11
17 36 0.78
18 5 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TTAAATTTAAATTAAAT
Found at i:492 original size:11 final size:11
Alignment explanation
Indices: 443--497 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
433 AAATTAAATT
*
443 TAAATTTAAGA
1 TAAATTTAAAA
* *
454 TTAATTTAAATT
1 TAAATTTAAA-A
466 TAAATTT-AAA
1 TAAATTTAAAA
476 TCAAATTTAAAA
1 T-AAATTTAAAA
488 TAAA-TTAAAA
1 TAAATTTAAAA
498 AGGACCCAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
10 7 0.19
11 19 0.53
12 10 0.28
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:1895 original size:23 final size:26
Alignment explanation
Indices: 1838--1897 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 26
1828 TTAAAAAAAT
*
1838 AAATATATCAATTTATTTTTATATTGG
1 AAATATAT-AATTTATTTATATATTGG
1865 ATAA-ATATAA-TTATTTAT-TATT-G
1 A-AATATATAATTTATTTATATATTGG
1888 AAATATATAA
1 AAATATATAA
1898 ACATAAAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
22 2 0.07
23 8 0.27
24 4 0.13
25 7 0.23
26 2 0.07
27 5 0.17
28 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (26 bp):
AAATATATAATTTATTTATATATTGG
Found at i:11504 original size:18 final size:19
Alignment explanation
Indices: 11467--11511 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
11457 AAAAAACTAC
*
11467 AAGATAATAAACTTATTAT
1 AAGATAATAAACTAATTAT
*
11486 AAGATAA-AATCTAATTAT
1 AAGATAATAAACTAATTAT
11504 AAGATAAT
1 AAGATAAT
11512 TATAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (19 bp):
AAGATAATAAACTAATTAT
Found at i:14929 original size:16 final size:16
Alignment explanation
Indices: 14901--14946 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
14891 ACAATTAACC
14901 AATATTATTTTAA-AA
1 AATATTATTTTAATAA
14916 AATATTATTTTTAATAA
1 AATATTA-TTTTAATAA
*
14933 AA-ATTAATTTAATA
1 AATATTATTTTAATA
14947 TTAAAAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 14 0.50
16 10 0.36
17 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTATTTTAATAA
Found at i:14942 original size:17 final size:16
Alignment explanation
Indices: 14901--14938 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
14891 ACAATTAACC
14901 AATATTA-TTTTAAAA
1 AATATTATTTTTAAAA
14916 AATATTATTTTTAATAA
1 AATATTATTTTTAA-AA
14933 AA-ATTA
1 AATATTA
14939 ATTTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 10 0.48
17 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTATTTTTAAAA
Found at i:26485 original size:19 final size:19
Alignment explanation
Indices: 26445--26489 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
26435 TTTTATTAGG
26445 ATTTAATATTTAAGATATT
1 ATTTAATATTTAAGATATT
* *
26464 ATTTATTATTTAA-ATTTGT
1 ATTTAATATTTAAGATAT-T
26483 ATTTAAT
1 ATTTAAT
26490 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAGATATT
Found at i:27334 original size:22 final size:22
Alignment explanation
Indices: 27292--27352 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
27282 TTCGACTTCC
* *
27292 CTATTTTCTATT-TCTTTAATT
1 CTATTTTCTTTTATTTTTAATT
27313 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
* * *
27335 ATGTTTTTTTTTATTTTT
1 CTATTTTCTTTTATTTTT
27353 CCTTAGATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 11 0.32
22 23 0.68
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:30037 original size:8 final size:8
Alignment explanation
Indices: 30024--30073 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
30014 ACCCAATTAT
30024 TTTTTTTA
1 TTTTTTTA
30032 TTTTTTTA
1 TTTTTTTA
*
30040 TTTTTCTA
1 TTTTTTTA
30048 TCTTATTTTA
1 T-TT-TTTTA
*
30058 TTTATTTA
1 TTTTTTTA
30066 TTTATTTT
1 TTT-TTTT
30074 TGTCCAGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 23 0.66
9 7 0.20
10 5 0.14
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTTA
Found at i:30074 original size:18 final size:19
Alignment explanation
Indices: 30034--30074 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
30024 TTTTTTTATT
30034 TTTTTATTTTTCTATCTTA
1 TTTTTATTTTTCTATCTTA
30053 -TTTTATTTATT-TAT-TTA
1 TTTTTATTT-TTCTATCTTA
30070 TTTTT
1 TTTTT
30075 GTCCAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.15
18 15 0.75
19 2 0.10
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTATTTTTCTATCTTA
Found at i:33410 original size:23 final size:23
Alignment explanation
Indices: 33286--33437 Score: 137
Period size: 23 Copynumber: 6.5 Consensus size: 23
33276 ACACTAGCGC
*
33286 GCTCTCTGTTTAGCACGTTT-CGT
1 GCTCTCTGTTTAGCAC-TTTGTGT
* * *
33309 GCCCTCTGATCAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
33332 GCTCTCTGATTAGCAATTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* * *
33355 GCTCTTTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
33378 GCTCTTTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
33401 GCTCTCTGTTGCCCAGCAC-TTATGT
1 GCTCTCTGTT---TAGCACTTTGTGT
33426 GCTCTCTGTTTA
1 GCTCTCTGTTTA
33438 TTCCGTATAT
Statistics
Matches: 107, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
22 4 0.04
23 84 0.79
25 14 0.13
26 5 0.05
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:36382 original size:32 final size:32
Alignment explanation
Indices: 36346--36434 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
36336 AAGCAATCAT
*
36346 AAAGGCATTAATTTCAAGAAAGAAGTTAGGC-A
1 AAAGGCATTAATTTCAAGGAAGAA-TTAGGCAA
* * *
36378 AAAGGCATTAATTTCAGGGGAGATATTATGCAA
1 AAAGGCATTAATTTCAAGGAAGA-ATTAGGCAA
*
36411 AAAGACATTAATTTCAAGGAAGAA
1 AAAGGCATTAATTTCAAGGAAGAA
36435 AGAACGAGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 26 0.54
33 22 0.46
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (32 bp):
AAAGGCATTAATTTCAAGGAAGAATTAGGCAA
Found at i:36713 original size:26 final size:26
Alignment explanation
Indices: 36684--36736 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
36674 TACAAACACA
36684 TACATGTTCTGCAAGAAGACAAGCCT
1 TACATGTTCTGCAAGAAGACAAGCCT
36710 TACATGTTCTGCAAGAAGACAAGCCT
1 TACATGTTCTGCAAGAAGACAAGCCT
36736 T
1 T
36737 TGTCTTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (26 bp):
TACATGTTCTGCAAGAAGACAAGCCT
Done.