Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010510.1 Kokia drynarioides strain JFW-HI SEQ_125422, 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: 8197
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:1516 original size:22 final size:21
Alignment explanation
Indices: 1491--1558 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 21
1481 TTTCCTGGAC
1491 AAAAATAAATA-AACAAATAA-
1 AAAAATAAATAGAA-AAATAAT
1511 ATAAAATAAGATAGAAAAATAAT
1 A-AAAATAA-ATAGAAAAATAAT
*
1534 ---AAT-AATAAAAAAATAAT
1 AAAAATAAATAGAAAAATAAT
1551 AAAAATAA
1 AAAAATAA
1559 TTTGGTTGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
17 12 0.31
18 1 0.03
19 3 0.08
20 4 0.10
21 8 0.21
22 9 0.23
23 2 0.05
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (21 bp):
AAAAATAAATAGAAAAATAAT
Found at i:1547 original size:17 final size:17
Alignment explanation
Indices: 1525--1558 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1515 AATAAGATAG
*
1525 AAAAATAATAATAATAA
1 AAAAATAATAAAAATAA
1542 AAAAATAATAAAAATAA
1 AAAAATAATAAAAATAA
1559 TTTGGTTGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATAATAAAAATAA
Found at i:1548 original size:14 final size:14
Alignment explanation
Indices: 1506--1555 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1496 TAAATAAACA
1506 AATAAATAAAATAA-
1 AATAAA-AAAATAAT
* *
1520 GATAGAAAAATAAT
1 AATAAAAAAATAAT
1534 AATAATAAAAA-AAT
1 AATAA-AAAAATAAT
1548 AATAAAAA
1 AATAAAAA
1556 TAATTTGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 10 0.33
14 15 0.50
15 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (14 bp):
AATAAAAAAATAAT
Found at i:4933 original size:13 final size:13
Alignment explanation
Indices: 4915--4939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4905 CACATCCTCA
4915 AGGAAAAATCTGC
1 AGGAAAAATCTGC
4928 AGGAAAAATCTG
1 AGGAAAAATCTG
4940 TCGAGATCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.24, T:0.16
Consensus pattern (13 bp):
AGGAAAAATCTGC
Found at i:5031 original size:22 final size:22
Alignment explanation
Indices: 4989--5048 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
4979 CGATTTAAGG
* *
4989 AAAAATAGAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
5010 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATAGAATT
*
5032 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
5049 AAGAAGTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.30
22 22 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:5050 original size:16 final size:16
Alignment explanation
Indices: 5009--5050 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4999 GAAACAGAAT
5009 TAAAAATAAAAGAAAA
1 TAAAAATAAAAGAAAA
* *
5025 TATAATTAAAAG-AAA
1 TAAAAATAAAAGAAAA
5040 TAGAAAATAAA
1 TA-AAAATAAA
5051 GAAGTCGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (16 bp):
TAAAAATAAAAGAAAA
Found at i:6460 original size:85 final size:85
Alignment explanation
Indices: 6315--6472 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 85
6305 TCAAACCACA
* * * *
6315 TCTTCTTGATGAGATATAGAGAAGTGGGTCAAAACTATAAAGCGATCATCTTCCTAATGAGATAC
1 TCTTCTTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTAATGAGATAC
6380 AAAGAAGTGGACCAAATCCG
66 AAAGAAGTGGACCAAATCCG
** * * * * * *
6400 TCTTCTTGATGAGATACAAAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCTTGATGAGATAT
1 TCTTCTTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTAATGAGATAC
6465 AAAGAAGT
66 AAAGAAGT
6473 AGATCAGATC
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 61 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (85 bp):
TCTTCTTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTAATGAGATAC
AAAGAAGTGGACCAAATCCG
Found at i:6512 original size:208 final size:208
Alignment explanation
Indices: 6163--6684 Score: 717
Period size: 208 Copynumber: 2.5 Consensus size: 208
6153 ATCTTCTTGT
* *
6163 TGAGATACAGAGAAGTGGACTAAATCCGTCTTCTTGATGAGATACAAAGAAGTGGATTAAAACAA
1 TGAGATACAAAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAAAGAAGTGGATTAAAAC-A
* *
6228 ATGAGGCGGTCATCTTCCTCATGAGATACAGAGAAGTAGACTAAATCAATGAAGCGAAGCTCAAT
65 ATGAGGCGGTCATCTTCTTGATGAGATACAGAGAAGTAGACTAAATCAATGAAGCGAAGCTCAAT
* * * *
6293 ACGAATGAGACTTCAAACCACATCTTCTTGATGAGATATAGAGAAGTGGGTCAAAACT-ATAAAG
130 ACGAATGAGACTTCAAACCACATCTTCCTGATAAGATACAGAGAAGTGGGT-AAAACTAATAAAA
6357 CGATCATCTTCCTAA
194 CGATCATCTTCCTAA
*
6372 TGAGATACAAAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAAAGAAGTGGATTGAAACAA
1 TGAGATACAAAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAAAGAAGTGGATTAAAACAA
* * * * *
6437 TGAGGCGGTCATCTTCTTGATGAGATATAAAGAAGTAGA-TCAGATCAATGAGGTGAAGCTCAAT
66 TGAGGCGGTCATCTTCTTGATGAGATACAGAGAAGTAGACT-AAATCAATGAAGCGAAGCTCAAT
* * * * *
6501 ATGAATGAGACTTCAAACCCCATCTTCCTGATAAGATACAGAGAAGTGGGTTAAAGTAATAAAAT
130 ACGAATGAGACTTCAAACCACATCTTCCTGATAAGATACAGAGAAGTGGGTAAAACTAATAAAAC
* *
6566 GGTCATCTTCCTGA
195 GATCATCTTCCTAA
* * * * * *
6580 CGAGATACAAAGAAGTGAACCAAAAT-TGTCTTCCTGATGAGATACAGAGAAGTGGATCAAAACA
1 TGAGATACAAAGAAGTGGACC-AAATCCGTCTTCTTGATGAGATACAAAGAAGTGGATTAAAACA
* * *
6644 ATGAAGTGGTTATCTTCTTGATGAGATACAGAGAAGTAGAC
65 ATGAGGCGGTCATCTTCTTGATGAGATACAGAGAAGTAGAC
6685 CAAGAAATGA
Statistics
Matches: 276, Mismatches: 33, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
207 5 0.02
208 207 0.75
209 64 0.23
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (208 bp):
TGAGATACAAAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAAAGAAGTGGATTAAAACAA
TGAGGCGGTCATCTTCTTGATGAGATACAGAGAAGTAGACTAAATCAATGAAGCGAAGCTCAATA
CGAATGAGACTTCAAACCACATCTTCCTGATAAGATACAGAGAAGTGGGTAAAACTAATAAAACG
ATCATCTTCCTAA
Found at i:6687 original size:85 final size:85
Alignment explanation
Indices: 6523--6680 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 85
6513 TCAAACCCCA
* * **
6523 TCTTCCTGATAAGATACAGAGAAGTGGGTTAAAGTAATAAAATGGTCATCTTCCTGACGAGATAC
1 TCTTCCTGATAAGATACAGAGAAGTGGATCAAAACAATAAAATGGTCATCTTCCTGACGAGATAC
6588 AAAGAAGTGAACCAAAATTG
66 AAAGAAGTGAACCAAAATTG
* * * * * *
6608 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATGAAGTGGTTATCTTCTTGATGAGATAC
1 TCTTCCTGATAAGATACAGAGAAGTGGATCAAAACAATAAAATGGTCATCTTCCTGACGAGATAC
*
6673 AGAGAAGT
66 AAAGAAGT
6681 AGACCAAGAA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (85 bp):
TCTTCCTGATAAGATACAGAGAAGTGGATCAAAACAATAAAATGGTCATCTTCCTGACGAGATAC
AAAGAAGTGAACCAAAATTG
Done.