Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000132.1 Kokia drynarioides strain JFW-HI SEQ_110779, 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: 63433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1449 original size:16 final size:16
Alignment explanation
Indices: 1428--1459 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1418 CCTGAAATAA
*
1428 TTGCTAAGTCTACAAG
1 TTGCTAAATCTACAAG
1444 TTGCTAAATCTACAAG
1 TTGCTAAATCTACAAG
1460 CAACAAGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (16 bp):
TTGCTAAATCTACAAG
Found at i:4873 original size:20 final size:17
Alignment explanation
Indices: 4828--4860 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4818 TGTAGGTTTA
4828 ATTGTTTTATAATATTT
1 ATTGTTTTATAATATTT
*
4845 ATTGTTTTATATTATT
1 ATTGTTTTATAATATT
4861 ATTATTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
ATTGTTTTATAATATTT
Found at i:13213 original size:41 final size:41
Alignment explanation
Indices: 13156--13239 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
13146 TGCCACATGC
13156 TCTCAAATCTAATTATCACTAATTTACATACTAAGAATATG
1 TCTCAAATCTAATTATCACTAATTTACATACTAAGAATATG
13197 TCTCAAATCTAATTATCACTAATTTACATACTAAGAATATG
1 TCTCAAATCTAATTATCACTAATTTACATACTAAGAATATG
13238 TC
1 TC
13240 ATAATTATCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (41 bp):
TCTCAAATCTAATTATCACTAATTTACATACTAAGAATATG
Found at i:13252 original size:35 final size:38
Alignment explanation
Indices: 13164--13253 Score: 132
Period size: 41 Copynumber: 2.4 Consensus size: 38
13154 GCTCTCAAAT
13164 CTAATTATCACTAATTTACATACTAAGAATATGTCTCAAA
1 CTAATTATCACTAATTTACATACTAAGAATATG-CTC-AA
13204 TCTAATTATCACTAATTTACATACTAAGAATATG-TC-A
1 -CTAATTATCACTAATTTACATACTAAGAATATGCTCAA
13241 -TAATTATCACTAA
1 CTAATTATCACTAA
13254 GTATATAGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
35 13 0.27
37 1 0.02
39 2 0.04
41 33 0.67
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (38 bp):
CTAATTATCACTAATTTACATACTAAGAATATGCTCAA
Found at i:20493 original size:13 final size:13
Alignment explanation
Indices: 20475--20503 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
20465 TTTTTTTTAC
20475 ATTGGGTTAAGAG
1 ATTGGGTTAAGAG
20488 ATTGGGTTAAGAG
1 ATTGGGTTAAGAG
20501 ATT
1 ATT
20504 AGATTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (13 bp):
ATTGGGTTAAGAG
Found at i:27002 original size:15 final size:17
Alignment explanation
Indices: 26982--27013 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
26972 TGGCTGCATG
26982 GTGCTT-TT-TCTTCTT
1 GTGCTTCTTCTCTTCTT
26997 GTGCTTCTTCTCTTCTT
1 GTGCTTCTTCTCTTCTT
27014 TACGGTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.00, C:0.25, G:0.12, T:0.62
Consensus pattern (17 bp):
GTGCTTCTTCTCTTCTT
Found at i:38522 original size:3 final size:3
Alignment explanation
Indices: 38514--38554 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
38504 CCATTTGACT
38514 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
38555 TTAAGGCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:38741 original size:12 final size:11
Alignment explanation
Indices: 38690--38743 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 11
38680 TAAAGTGCTA
38690 AAAATAAATAAT
1 AAAA-AAATAAT
*
38702 AAATAACATAAT
1 AAA-AAAATAAT
*
38714 AATAATAATAAT
1 AA-AAAAATAAT
38726 AAAACAAATAAT
1 AAAA-AAATAAT
38738 AAAAAA
1 AAAAAA
38744 GTAGAGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 4 0.11
12 29 0.83
13 2 0.06
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:40430 original size:13 final size:13
Alignment explanation
Indices: 40412--40436 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40402 ATTGTGTTAA
40412 ATGATTTAATTAC
1 ATGATTTAATTAC
40425 ATGATTTAATTA
1 ATGATTTAATTA
40437 TTTGGATGAT
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:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
ATGATTTAATTAC
Found at i:43876 original size:13 final size:14
Alignment explanation
Indices: 43858--43887 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43848 GTCAACGTAA
43858 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
43871 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
43885 TCA
1 TCA
43888 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:59382 original size:14 final size:15
Alignment explanation
Indices: 59365--59393 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59355 AAACGTAAGA
59365 AGGAGG-AGAAAAAG
1 AGGAGGAAGAAAAAG
59379 AGGAGGAAGAAAAAG
1 AGGAGGAAGAAAAAG
59394 CATCATGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (15 bp):
AGGAGGAAGAAAAAG
Found at i:60965 original size:21 final size:21
Alignment explanation
Indices: 60941--61029 Score: 124
Period size: 21 Copynumber: 4.2 Consensus size: 21
60931 AATTACATGA
60941 TGCCCCTGAATTGCACTACGG
1 TGCCCCTGAATTGCACTACGG
* *
60962 TGCCCTTGAATTGCACTATGG
1 TGCCCCTGAATTGCACTACGG
*
60983 TGCCCCTGACTTGCACTACGG
1 TGCCCCTGAATTGCACTACGG
** *
61004 TGCCCCTGAAAAGCACTGCGG
1 TGCCCCTGAATTGCACTACGG
61025 TGCCC
1 TGCCC
61030 TGATAATTGC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.18, C:0.34, G:0.25, T:0.24
Consensus pattern (21 bp):
TGCCCCTGAATTGCACTACGG
Found at i:63078 original size:16 final size:15
Alignment explanation
Indices: 63049--63082 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
63039 CTATATTTAA
*
63049 ATAAAATTTTATATT
1 ATAAAATTTAATATT
63064 ATAATAATTTAATATT
1 ATAA-AATTTAATATT
63080 ATA
1 ATA
63083 TATTCTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAAAATTTAATATT
Done.