Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005441.1 Kokia drynarioides strain JFW-HI SEQ_119472, 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: 26341
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:2592 original size:19 final size:19
Alignment explanation
Indices: 2555--2594 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2545 TGTAAATAGA
*
2555 ATTGATATATACTTCAATT
1 ATTGATATATACGTCAATT
2574 ATTGATATATA-GTCGAATT
1 ATTGATATATACGTC-AATT
2593 AT
1 AT
2595 GTTGCGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (19 bp):
ATTGATATATACGTCAATT
Found at i:2735 original size:17 final size:17
Alignment explanation
Indices: 2715--2757 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2705 CTGAATGTGT
* *
2715 GAGCTCACCACAGCTGC
1 GAGCTCACCACAACTGA
* *
2732 GAGCTCATCACAATTGA
1 GAGCTCACCACAACTGA
2749 GAGCTCACC
1 GAGCTCACC
2758 TAAGTTAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.35, G:0.21, T:0.16
Consensus pattern (17 bp):
GAGCTCACCACAACTGA
Found at i:4012 original size:120 final size:120
Alignment explanation
Indices: 3799--4038 Score: 471
Period size: 120 Copynumber: 2.0 Consensus size: 120
3789 TAAAGATTAA
3799 TTCTCATAATCTTTGAAAGTTTTTGATTTAATCAATTTCATCCGTCAATGAGTTGAATTTTTATT
1 TTCTCATAATCTTTGAAAGTTTTTGATTTAATCAATTTCATCCGTCAATGAGTTGAATTTTTATT
3864 GAATGGCTTTTGGCTTTTAGGTGGGAATTAAAGAAGTTAGGTGAATTTCAACATT
66 GAATGGCTTTTGGCTTTTAGGTGGGAATTAAAGAAGTTAGGTGAATTTCAACATT
3919 TTCTCATAATCTTTGAAAGTTTTTGATTTAATCAATTTCATCCGTCAATGAGTTGAATTTTTATT
1 TTCTCATAATCTTTGAAAGTTTTTGATTTAATCAATTTCATCCGTCAATGAGTTGAATTTTTATT
*
3984 GAATGGCTTTTGGCTTTTAGGTGGGAATTAAAGAAGTTAGGTGAATTTCGACATT
66 GAATGGCTTTTGGCTTTTAGGTGGGAATTAAAGAAGTTAGGTGAATTTCAACATT
4039 CTTTACCTCA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (120 bp):
TTCTCATAATCTTTGAAAGTTTTTGATTTAATCAATTTCATCCGTCAATGAGTTGAATTTTTATT
GAATGGCTTTTGGCTTTTAGGTGGGAATTAAAGAAGTTAGGTGAATTTCAACATT
Found at i:15480 original size:16 final size:16
Alignment explanation
Indices: 15461--15513 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
15451 GAGATAATAC
15461 AAACTTAATATGATCT
1 AAACTTAATATGATCT
* *
15477 AAACTT-TTATAATAC-
1 AAACTTAATATGAT-CT
15492 AAACTTAATATGATCT
1 AAACTTAATATGATCT
15508 AAACTT
1 AAACTT
15514 TTATAATGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (16 bp):
AAACTTAATATGATCT
Found at i:15491 original size:31 final size:31
Alignment explanation
Indices: 15454--15520 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
15444 TAAACTTGAG
15454 ATAATACAAACTTAATATGATCTAAACTTTT
1 ATAATACAAACTTAATATGATCTAAACTTTT
15485 ATAATACAAACTTAATATGATCTAAACTTTT
1 ATAATACAAACTTAATATGATCTAAACTTTT
15516 ATAAT
1 ATAAT
15521 GGGACTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39
Consensus pattern (31 bp):
ATAATACAAACTTAATATGATCTAAACTTTT
Found at i:20045 original size:23 final size:23
Alignment explanation
Indices: 20015--20061 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
20005 ATAATTCAAG
20015 CCATGTGATCTAATCTCCTACTT
1 CCATGTGATCTAATCTCCTACTT
20038 CCATGTGATCTAATCTCCTACTT
1 CCATGTGATCTAATCTCCTACTT
20061 C
1 C
20062 TAATATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.32, G:0.09, T:0.38
Consensus pattern (23 bp):
CCATGTGATCTAATCTCCTACTT
Found at i:23407 original size:33 final size:35
Alignment explanation
Indices: 23329--23420 Score: 107
Period size: 37 Copynumber: 2.6 Consensus size: 35
23319 ATAATAAATT
* *
23329 ATATTTAAATAATTTACTATAATGATATTTGTAAACA
1 ATATTTAAATAATTTAATATAATGATATATG--AACA
* *
23366 ATATTTAAATAATCTAATATAATTATATATG-A-A
1 ATATTTAAATAATTTAATATAATGATATATGAACA
*
23399 ATATTTAAATAATTTCATATAA
1 ATATTTAAATAATTTAATATAA
23421 AGAAAAATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 21 0.43
34 1 0.02
37 27 0.55
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (35 bp):
ATATTTAAATAATTTAATATAATGATATATGAACA
Found at i:23913 original size:41 final size:40
Alignment explanation
Indices: 23868--23947 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
23858 CATTTAGCAG
* *
23868 CGTTTGGAAAGAAAACGCCGCAAAAGGTAAAGCAATAACAA
1 CGTTTGGAAA-AAAACACCGCAAAAGGTAAAGAAATAACAA
** * *
23909 CGTTTTTACACAAACACCGCAAAAGGTAAAGAAATAACA
1 CGTTTGGAAAAAAACACCGCAAAAGGTAAAGAAATAACA
23948 GCATTTTTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 26 0.79
41 7 0.21
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (40 bp):
CGTTTGGAAAAAAACACCGCAAAAGGTAAAGAAATAACAA
Found at i:23955 original size:40 final size:40
Alignment explanation
Indices: 23880--23955 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
23870 TTTGGAAAGA
* * *
23880 AAACGCCGCAAAAGGTAAAGCAATAACAACGTTTTTACAC
1 AAACACCGCAAAAGGTAAAGAAATAACAACATTTTTACAC
*
23920 AAACACCGCAAAAGGTAAAGAAATAACAGCATTTTT
1 AAACACCGCAAAAGGTAAAGAAATAACAACATTTTT
23956 GAGAAAGCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.18
Consensus pattern (40 bp):
AAACACCGCAAAAGGTAAAGAAATAACAACATTTTTACAC
Found at i:24775 original size:20 final size:20
Alignment explanation
Indices: 24737--24789 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
24727 TAAATCCCTA
24737 ATTTCATTCTCCA---CTCC
1 ATTTCATTCTCCACTCCTCC
*
24754 ATTTCATTTTCCACTCCTCC
1 ATTTCATTCTCCACTCCTCC
24774 ATTTCATTCTCCACTC
1 ATTTCATTCTCCACTC
24790 AAATCTACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 12 0.39
20 19 0.61
ACGTcount: A:0.17, C:0.40, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTCATTCTCCACTCCTCC
Done.