Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000093.1 Kokia drynarioides strain JFW-HI SEQ_110720, 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: 40055
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:58 original size:6 final size:6
Alignment explanation
Indices: 2--101 Score: 73
Period size: 6 Copynumber: 17.0 Consensus size: 6
1 G
* * * *
2 AATTTA ATTTTA AAGTTTA AGTTTA AAATT- -ATTTCA AATTTA AA-CTA
1 AATTTA AATTTA AA-TTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
** * **
49 AATTTA AATTTA AAAATG AATTTA AATTTA AATTT- AAGGTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
96 AATTTA
1 AATTTA
102 GAAATAAATC
Statistics
Matches: 70, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
4 3 0.04
5 7 0.10
6 51 0.73
7 9 0.13
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:82 original size:41 final size:42
Alignment explanation
Indices: 32--115 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 42
22 GTTTAAAATT
* *
32 ATTTCAAATTTAAACTAAATTTAAATTTAAAAATGAATTTAA
1 ATTTCAAATTTAAACTAAATTTAAATTTAAAAATAAATCTAA
** *
74 ATTT-AAATTTAAGGTAAATTTAAATTTAGAAATAAATCTAA
1 ATTTCAAATTTAAACTAAATTTAAATTTAAAAATAAATCTAA
115 A
1 A
116 ACTAATCTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 33 0.89
42 4 0.11
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (42 bp):
ATTTCAAATTTAAACTAAATTTAAATTTAAAAATAAATCTAA
Found at i:1827 original size:35 final size:35
Alignment explanation
Indices: 1786--1856 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1776 ATTTTAGCTA
1786 CATAGTCTAATTCTCAATTATACTCTATTACTGTT
1 CATAGTCTAATTCTCAATTATACTCTATTACTGTT
1821 CATAGTCTAATTCTCAATTATACTCTATTACTGTT
1 CATAGTCTAATTCTCAATTATACTCTATTACTGTT
1856 C
1 C
1857 CAAATCCGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (35 bp):
CATAGTCTAATTCTCAATTATACTCTATTACTGTT
Found at i:4749 original size:19 final size:19
Alignment explanation
Indices: 4725--4770 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
4715 CATTCAAACA
*
4725 TCAGAAAATATTAAT-TTTT
1 TCAGAAAA-ATAAATATTTT
4744 TCAGAAAAATAAATCATTTT
1 TCAGAAAAATAAAT-ATTTT
4764 TCAGAAA
1 TCAGAAA
4771 TCATTTTCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 8 0.33
20 11 0.46
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.37
Consensus pattern (19 bp):
TCAGAAAAATAAATATTTT
Found at i:4783 original size:13 final size:14
Alignment explanation
Indices: 4754--4793 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4744 TCAGAAAAAT
4754 AAATCATTTTTCAG-
1 AAATCA-TTTTCAGA
*
4768 AAATCATTTTCCGA
1 AAATCATTTTCAGA
4782 AAATCATTTTCA
1 AAATCATTTTCA
4794 ATCAAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (14 bp):
AAATCATTTTCAGA
Found at i:11295 original size:12 final size:12
Alignment explanation
Indices: 11267--11384 Score: 53
Period size: 12 Copynumber: 9.5 Consensus size: 12
11257 TACTGATTTA
* *
11267 GTTGTTATTTTC
1 GTTGTTGTTTTT
11279 G-TGTTGTTTTT
1 GTTGTTGTTTTT
* *
11290 GCTGTT-ATTTT
1 GTTGTTGTTTTT
*
11301 GTTGTTATTTTT
1 GTTGTTGTTTTT
* *
11313 GTTGCTATTTTT
1 GTTGTTGTTTTT
11325 GTTGTT-TTAATGTT
1 GTTGTTGTT--T-TT
*
11339 GTTTGCTGTTATTT
1 G-TTGTTGTT-TTT
* *
11353 TTACTGCTGTTTTT
1 GT--TGTTGTTTTT
*
11367 GTTGTTATTTTT
1 GTTGTTGTTTTT
11379 GTTGTT
1 GTTGTT
11385 TGGATGTTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
11 20 0.24
12 39 0.46
13 2 0.02
14 9 0.11
15 13 0.15
16 2 0.02
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.68
Consensus pattern (12 bp):
GTTGTTGTTTTT
Found at i:11295 original size:23 final size:22
Alignment explanation
Indices: 11269--11332 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
11259 CTGATTTAGT
11269 TGTTATTTTCGTGTTGTTTTTGC
1 TGTTATTTT-GTGTTGTTTTTGC
* *
11292 TGTTATTTTGTTGTTATTTTTGT
1 TGTTATTTTG-TGTTGTTTTTGC
*
11315 TGCTATTTT-TGTTGTTTT
1 TGTTATTTTGTGTTGTTTT
11333 AATGTTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.22
22 1 0.03
23 27 0.75
ACGTcount: A:0.06, C:0.05, G:0.19, T:0.70
Consensus pattern (22 bp):
TGTTATTTTGTGTTGTTTTTGC
Found at i:11353 original size:42 final size:43
Alignment explanation
Indices: 11298--11386 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 43
11288 TTGCTGTTAT
* **
11298 TTTGTTGTTATTTTTGTTGCTATTTTTGTTGTT-TTAATGTTG
1 TTTGCTGTTATTTTTACTGCTATTTTTGTTGTTATTAATGTTG
* **
11340 TTTGCTGTTATTTTTACTGCTGTTTTTGTTGTTATTTTTGTTG
1 TTTGCTGTTATTTTTACTGCTATTTTTGTTGTTATTAATGTTG
11383 TTTG
1 TTTG
11387 GATGTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 29 0.73
43 11 0.28
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.69
Consensus pattern (43 bp):
TTTGCTGTTATTTTTACTGCTATTTTTGTTGTTATTAATGTTG
Found at i:11376 original size:54 final size:52
Alignment explanation
Indices: 11283--11395 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 52
11273 ATTTTCGTGT
*
11283 TGTTTTTGCTGTTATTTTGTTGTTATTTTTGTTGCTATTTTTGTTGTTTTAA
1 TGTTTTTGCTGTTATTTTGTTGCTATTTTTGTTGCTATTTTTGTTGTTTTAA
* * **
11335 TGTTGTTTGCTGTTATTTT-TACTGCTGTTTTTGTTGTTATTTTTGTTGTTTGGA
1 TGTT-TTTGCTGTTATTTTGT--TGCTATTTTTGTTGCTATTTTTGTTGTTTTAA
11389 TGTTTTT
1 TGTTTTT
11396 TTATGTGTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
52 5 0.09
53 17 0.32
54 31 0.58
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.68
Consensus pattern (52 bp):
TGTTTTTGCTGTTATTTTGTTGCTATTTTTGTTGCTATTTTTGTTGTTTTAA
Found at i:11396 original size:42 final size:42
Alignment explanation
Indices: 11298--11398 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
11288 TTGCTGTTAT
* **
11298 TTTGTTGTTATTTTTGTTGCTATTTTTGTTGTTTTAATGTTG
1 TTTGATGTTATTTTTACTGCTATTTTTGTTGTTTTAATGTTG
* * **
11340 TTTGCTGTTATTTTTACTGCTGTTTTTGTTGTTATTTTTGTTG
1 TTTGATGTTATTTTTACTGCTATTTTTGTTGTT-TTAATGTTG
11383 TTTGGATGTT-TTTTTA
1 TTT-GATGTTATTTTTA
11399 TGTGTTTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 29 0.58
43 16 0.32
44 5 0.10
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.68
Consensus pattern (42 bp):
TTTGATGTTATTTTTACTGCTATTTTTGTTGTTTTAATGTTG
Found at i:11593 original size:38 final size:38
Alignment explanation
Indices: 11514--11594 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 38
11504 TATAAAATAA
* * * *
11514 TTTAATGTATTTTAAATTTATTTATTTTTTATGTTTAT
1 TTTAATGTATTTTAAATATATTTATATATTATATTTAT
11552 TTTAATGT-TTTTAAATATATTTGATATATTATATATT-T
1 TTTAATGTATTTTAAATATATTT-ATATATTATAT-TTAT
11590 TTTAA
1 TTTAA
11595 ATTTGTTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 13 0.35
38 22 0.59
39 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (38 bp):
TTTAATGTATTTTAAATATATTTATATATTATATTTAT
Found at i:18607 original size:6 final size:6
Alignment explanation
Indices: 18574--18605 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
18564 AAATTTAAAT
*
18574 TTGATA TTGATA TTGATA TTGATA TTAATA TT
1 TTGATA TTGATA TTGATA TTGATA TTGATA TT
18606 AAATAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (6 bp):
TTGATA
Found at i:20614 original size:45 final size:45
Alignment explanation
Indices: 20558--20646 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
20548 ATGGTTACAT
*
20558 ACCAATGTATATTTGCTGGAGCAGAACTATAGGGGTTAGGCAGGG
1 ACCAATATATATTTGCTGGAGCAGAACTATAGGGGTTAGGCAGGG
* *
20603 ACCAATATATATTTGCTGGGGTAGAACTATAGGGGTTAGGCAGG
1 ACCAATATATATTTGCTGGAGCAGAACTATAGGGGTTAGGCAGG
20647 ACCTTGCACC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (45 bp):
ACCAATATATATTTGCTGGAGCAGAACTATAGGGGTTAGGCAGGG
Found at i:21656 original size:29 final size:27
Alignment explanation
Indices: 21589--21662 Score: 67
Period size: 29 Copynumber: 2.6 Consensus size: 27
21579 CTTCTCAAAA
*
21589 TTAAAATTTAGTCCATATATTTTTATT
1 TTAAAATTTAGTCCATATATTTTGATT
* * *
21616 TTCAGAAGTTTAGTCCCTTTATTTCTAGATT
1 TT-A-AAATTTAGTCCATATATTT-T-GATT
21647 TTAAAATTTAAGTCCA
1 TTAAAATTT-AGTCCA
21663 ATTGTTAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 21 0.58
30 7 0.19
31 5 0.14
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (27 bp):
TTAAAATTTAGTCCATATATTTTGATT
Found at i:35621 original size:29 final size:30
Alignment explanation
Indices: 35569--35652 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 30
35559 ATTTATTAGA
*
35569 ATCACAATTAGAATTTCATGTATATAATT-AC
1 ATCA-AATTA-AATTTCATATATATAATTAAC
*
35600 ATCAAATTAAAGTTCATATATATAATTACAC
1 ATCAAATTAAATTTCATATATATAATTA-AC
* *
35631 ATTAAATCAAATTTCATATATA
1 ATCAAATTAAATTTCATATATA
35653 ATTTTAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 16 0.35
30 5 0.11
31 25 0.54
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (30 bp):
ATCAAATTAAATTTCATATATATAATTAAC
Found at i:37483 original size:25 final size:25
Alignment explanation
Indices: 37462--37508 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
37452 TCCAATTAGG
37462 AAATTAT-TATTTAG-ATTTAATTC
1 AAATTATCTATTTAGAATTTAATTC
*
37485 AAATTATCTTTTTAGAATTTAATT
1 AAATTATCTATTTAGAATTTAATT
37509 TGTATCCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (25 bp):
AAATTATCTATTTAGAATTTAATTC
Done.