Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000106.1 Kokia drynarioides strain JFW-HI SEQ_110743, 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: 39566
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:362 original size:21 final size:21
Alignment explanation
Indices: 338--432 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 21
328 GTTATTGAAT
*
338 CACCGGCATAAAGCCTGAAAA
1 CACCGGCACAAAGCCTGAAAA
*
359 CACCGGCACAAAGCCTGAAAT
1 CACCGGCACAAAGCCTGAAAA
*
380 CACCTGCACAAAGCCT----A
1 CACCGGCACAAAGCCTGAAAA
* *
397 CTA--GTCACAAAGCTTGAAAA
1 C-ACCGGCACAAAGCCTGAAAA
417 CACCGGCACAAAGCCT
1 CACCGGCACAAAGCCT
433 ACTAGGCACA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
16 9 0.16
17 1 0.02
18 1 0.02
19 1 0.02
20 2 0.03
21 44 0.76
ACGTcount: A:0.39, C:0.33, G:0.17, T:0.12
Consensus pattern (21 bp):
CACCGGCACAAAGCCTGAAAA
Found at i:415 original size:37 final size:37
Alignment explanation
Indices: 363--451 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
353 TGAAAACACC
* *
363 GGCACAAAGCCTGAAATCACCTGCACAAAGCCTACTA
1 GGCACAAAGCCTGAAAACACCGGCACAAAGCCTACTA
* *
400 GTCACAAAGCTTGAAAACACCGGCACAAAGCCTACTA
1 GGCACAAAGCCTGAAAACACCGGCACAAAGCCTACTA
437 GGCACAAAGCCTGAA
1 GGCACAAAGCCTGAA
452 TTTGTGTAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.39, C:0.30, G:0.18, T:0.12
Consensus pattern (37 bp):
GGCACAAAGCCTGAAAACACCGGCACAAAGCCTACTA
Found at i:11757 original size:18 final size:18
Alignment explanation
Indices: 11720--11768 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
11710 AACTAATTTA
*
11720 TAAT-TTTAAAAATAATAC
1 TAATATTTAAAAA-AAAAC
11738 TAATATTTAAAAAAAAAC
1 TAATATTTAAAAAAAAAC
*
11756 T-ATAGTTAAAAAA
1 TAATATTTAAAAAA
11769 TTTAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 11 0.39
18 9 0.32
19 8 0.29
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (18 bp):
TAATATTTAAAAAAAAAC
Found at i:12359 original size:21 final size:20
Alignment explanation
Indices: 12321--12359 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
12311 CTATTATAGT
* *
12321 TAAGTCTTTGTTTTTGTGGC
1 TAAGTCTTTATTTATGTGGC
12341 TAAGTGCTTTATTTATGTG
1 TAAGT-CTTTATTTATGTG
12360 TTTGAGATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (20 bp):
TAAGTCTTTATTTATGTGGC
Found at i:13496 original size:30 final size:30
Alignment explanation
Indices: 13421--13496 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
13411 CCATATCTTT
* **
13421 TATTATAAT-TTATATT-ATAGTAGTTATA
1 TATTATAATATTATTTTAATAAAAGTTATA
13449 TATGTATTAATA-T-TTTTAATAAAAGTTATA
1 TAT-TA-TAATATTATTTTAATAAAAGTTATA
13479 TATTATAATATTATTTTA
1 TATTATAATATTATTTTA
13497 TGTATTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
28 8 0.21
29 8 0.21
30 23 0.59
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (30 bp):
TATTATAATATTATTTTAATAAAAGTTATA
Found at i:13544 original size:12 final size:12
Alignment explanation
Indices: 13529--13603 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
13519 CATAAAATAT
13529 TATTATATTATG
1 TATTATATTATG
13541 TATTAGTATT-TG
1 TATTA-TATTATG
*
13553 TATTAGTAATA-G
1 TATTA-TATTATG
13565 T-TATATATTA--
1 TAT-TATATTATG
* *
13575 TATTGTATTATT
1 TATTATATTATG
*
13587 TATTATTTTATG
1 TATTATATTATG
13599 TATTA
1 TATTA
13604 GTAATATACT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
10 7 0.14
11 6 0.12
12 34 0.67
13 4 0.08
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (12 bp):
TATTATATTATG
Found at i:22070 original size:33 final size:33
Alignment explanation
Indices: 22000--22073 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 33
21990 GTCAAAGTTG
* ** * *
22000 TTTATTTTATTAATTTTGTTTTGATTAAATTTA
1 TTTATTTTACTAATTTCATTTTGACTAAAATTA
*
22033 -TTATTTTCCTAATTTCATTTTGACTAAAATTA
1 TTTATTTTACTAATTTCATTTTGACTAAAATTA
22065 TTTATTTTA
1 TTTATTTTA
22074 AGTAAATAGG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.62
Consensus pattern (33 bp):
TTTATTTTACTAATTTCATTTTGACTAAAATTA
Found at i:36526 original size:6 final size:6
Alignment explanation
Indices: 36494--36551 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
36484 TGAATCTAAT
* * *
36494 TTTAAA TTTTAAA -TT-AT TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
36540 TTTAAAA TTTAA
1 TTT-AAA TTTAA
36552 TTAAATGTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
4 1 0.02
5 8 0.19
6 21 0.50
7 12 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:36542 original size:17 final size:17
Alignment explanation
Indices: 36492--36543 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
36482 ATTGAATCTA
36492 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
*
36509 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
36526 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
36543 A
1 A
36544 AAATTTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.19
17 26 0.81
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:36553 original size:12 final size:11
Alignment explanation
Indices: 36511--36557 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
36501 TTTAAATTAT
36511 TTTAAGTTTAAA
1 TTTAA-TTTAAA
*
36523 TTTATTTTAAA
1 TTTAATTTAAA
36534 TTTAAATTTAAAA
1 TTT-AATTT-AAA
36547 TTTAA-TTAAA
1 TTTAATTTAAA
36557 T
1 T
36558 GTCCAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 4 0.13
11 11 0.35
12 10 0.32
13 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
TTTAATTTAAA
Done.