Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011518.1 Kokia drynarioides strain JFW-HI SEQ_126504, 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: 22286
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:12269 original size:29 final size:29
Alignment explanation
Indices: 12233--12437 Score: 150
Period size: 29 Copynumber: 6.9 Consensus size: 29
12223 GTGTCAAAAC
12233 GTAATTTTTGGAAGTTTGAGGGTAAAATG
1 GTAATTTTTGGAAGTTTGAGGGTAAAATG
* ** *
12262 GTAATTTTTAGAAAAAATT-AGGATCAAAGAT-
1 GTAATTTTT-G-GAAGTTTGAGGGT-AAA-ATG
* *
12293 GTAATCTTTGGAAGTTTGGGGGTAAAATG
1 GTAATTTTTGGAAGTTTGAGGGTAAAATG
** *
12322 GTAATTTTTGGAAAAATCGA-GGTAAAAAATG
1 GTAATTTTTGG-AAGTTTGAGGGT--AAAATG
**
12353 G-AATTTTTGGAAGTTCAAGGGTAAAATG
1 GTAATTTTTGGAAGTTTGAGGGTAAAATG
* ***
12381 GTAAATTTTGGAAAAATGAGGGTAAAAATG
1 GTAATTTTTGGAAGTTTGAGGGT-AAAATG
*
12411 G-AATTTTGTGGAAGTTTGGGGGTAAAA
1 GTAATTTT-TGGAAGTTTGAGGGTAAAA
12438 ATATAACTTT
Statistics
Matches: 134, Mismatches: 29, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
28 9 0.07
29 58 0.43
30 43 0.32
31 22 0.16
32 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.28, T:0.32
Consensus pattern (29 bp):
GTAATTTTTGGAAGTTTGAGGGTAAAATG
Found at i:12360 original size:30 final size:29
Alignment explanation
Indices: 12316--12481 Score: 110
Period size: 29 Copynumber: 5.7 Consensus size: 29
12306 GTTTGGGGGT
12316 AAAATGGTAATTTTTGGAAAAATCGAGGTAA
1 AAAATGG-AATTTTTGGAAAAATCGAGGT-A
** *
12347 AAAATGGAATTTTTGG-AAGTTCAAGGGT-
1 AAAATGGAATTTTTGGAAAAATCGA-GGTA
*
12375 AAAATGGTAAATTTTGGAAAAAT-GAGGGTA
1 AAAATGG-AATTTTTGGAAAAATCGA-GGTA
*** * *
12405 AAAATGGAATTTTGTGGAAGTTTGGGGGTA
1 AAAATGGAATTTT-TGGAAAAATCGAGGTA
** *
12435 AAAATATAA-CTTTGGAAAAATCG-GTGTCA
1 AAAATGGAATTTTTGGAAAAATCGAG-GT-A
12464 AAAATGGAA-TTTTGGAAA
1 AAAATGGAATTTTTGGAAA
12482 GTTCAGAGGT
Statistics
Matches: 105, Mismatches: 22, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
27 1 0.01
28 16 0.15
29 41 0.39
30 39 0.37
31 8 0.08
ACGTcount: A:0.42, C:0.03, G:0.26, T:0.30
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAAATCGAGGTA
Found at i:12375 original size:59 final size:58
Alignment explanation
Indices: 12171--12480 Score: 273
Period size: 59 Copynumber: 5.3 Consensus size: 58
12161 GTTCGAGATT
* * *
12171 AAAAATGGAATTTTTAGACA-TCT-AGGGGTAAAATGGTAATTTTAT--AAAAACG-GTGTC
1 AAAAATGGAATTTTTGGA-AGTTTGA-GGGTAAAATGGTAATTTT-TGGAAAAATGAG-GTC
* * * *
12228 -AAAACGTAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAAAAATTAGGATC
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTT-GGAAAAATGAGG-TC
* * * * *
12287 AAAGATGTAATCTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTA
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAAAAT-GAGGTC
** *
12346 AAAAATGGAATTTTTGGAAGTTCAAGGGTAAAATGGTAAATTTTGGAAAAATGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAAAATGA-GGTC
* * *
12404 AAAAATGGAATTTTGTGGAAGTTTGGGGGTAAAAAT-ATAA-CTTTGGAAAAATCG-GTGTC
1 AAAAATGGAATTTT-TGGAAGTTTGAGGGT-AAAATGGTAATTTTTGGAAAAAT-GAG-GTC
12463 AAAAATGGAA-TTTTGGAA
1 AAAAATGGAATTTTTGGAA
12481 AGTTCAGAGG
Statistics
Matches: 213, Mismatches: 25, Indels: 30
0.79 0.09 0.11
Matches are distributed among these distances:
55 2 0.01
56 34 0.16
57 7 0.03
58 38 0.18
59 85 0.40
60 47 0.22
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAAAATGAGGTC
Found at i:12509 original size:59 final size:55
Alignment explanation
Indices: 12299--12505 Score: 168
Period size: 59 Copynumber: 3.5 Consensus size: 55
12289 AGATGTAATC
** * *
12299 TTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAAATGGAATT
1 TTTGGAAGTTCAGAGGTAAAAT-ATAA-TTTTGGAAAAATCGAGGT-AAAAATGGAA-T
*
12358 TTTGGAAGTTCA-AGGGTAAAATGGTAAATTTTGGAAAAAT-GAGGGTAAAAATGGAATT
1 TTTGGAAGTTCAGA-GGTAAAAT-AT-AATTTTGGAAAAATCGA-GGTAAAAATGGAA-T
** * *
12416 TTGTGGAAGTTTGGGGGTAAAAATATAACTTTGGAAAAATCG-GTGTCAAAAATGGAAT
1 TT-TGGAAGTTCAGAGGT-AAAATATAATTTTGGAAAAATCGAG-GT-AAAAATGGAAT
*
12474 TTTGGAAAGTTCAGAGGTCAAAATATGATTTT
1 TTTGG-AAGTTCAGAGGT-AAAATATAATTTT
12506 TGGATAATTT
Statistics
Matches: 124, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
57 4 0.03
58 54 0.44
59 59 0.48
60 7 0.06
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.31
Consensus pattern (55 bp):
TTTGGAAGTTCAGAGGTAAAATATAATTTTGGAAAAATCGAGGTAAAAATGGAAT
Found at i:13581 original size:12 final size:12
Alignment explanation
Indices: 13564--13631 Score: 52
Period size: 12 Copynumber: 5.9 Consensus size: 12
13554 TTGCTACCAT
*
13564 TTATTATTAATG
1 TTATTATTAATA
*
13576 TTATTATTACTA
1 TTATTATTAATA
13588 TTATTATT-ATA
1 TTATTATTAATA
* *
13599 --ATAAATAATA
1 TTATTATTAATA
* *
13609 TTATAATTAGTA
1 TTATTATTAATA
*
13621 TTAATATTAAT
1 TTATTATTAAT
13632 GACATTCATT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
9 4 0.09
10 3 0.07
11 2 0.05
12 34 0.79
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:14333 original size:6 final size:6
Alignment explanation
Indices: 14324--14375 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
14314 TATTTGGACT
* * *
14324 TTTAAA TTTAAA TTCAAA -TTACA TTTAAA CTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
14370 CTTAAA
1 TTTAAA
14376 AGAAAATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 7 0.19
6 30 0.81
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:14366 original size:17 final size:17
Alignment explanation
Indices: 14324--14374 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
14314 TATTTGGACT
14324 TTTAAATTTAAA-TTCAA
1 TTTAAATTTAAACTT-AA
* *
14341 ATTACATTTAAACTTAA
1 TTTAAATTTAAACTTAA
14358 TTTAAATTTAAACTTAA
1 TTTAAATTTAAACTTAA
14375 AAGAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAACTTAA
Found at i:15516 original size:20 final size:19
Alignment explanation
Indices: 15483--15530 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
15473 ATCTCATTAA
15483 AAAAAATCC-CCTCTGAAT
1 AAAAAATCCTCCTCTGAAT
*
15501 ACAAAAATCCTTCTCTGAAT
1 A-AAAAATCCTCCTCTGAAT
15521 AAAAAATCCT
1 AAAAAATCCT
15531 ATCAATCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 17 0.63
20 9 0.33
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAAAATCCTCCTCTGAAT
Done.