Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002000.1 Kokia drynarioides strain JFW-HI SEQ_113859, 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: 15941
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:779 original size:55 final size:55
Alignment explanation
Indices: 640--794 Score: 175
Period size: 55 Copynumber: 2.8 Consensus size: 55
630 GTTATGCTAA
** * * ** * *
640 AATATTGCTCCTTTTGGATCGATTGTTTTTATGTTTAAATAAATTGTCATGTTGG
1 AATATTGCTTATTTTGAATCGATTGTTTATATGTTTAAATCGATTATCACGTTGG
* * **
695 AATTTTGCTTATTTTGAATTGATAATTTATATGTTTAAATCGATTATCACGTTGG
1 AATATTGCTTATTTTGAATCGATTGTTTATATGTTTAAATCGATTATCACGTTGG
* * *
750 AATATTGCTTTTTTTGAATCAATTGTTTATCTGTTTAAATCGATT
1 AATATTGCTTATTTTGAATCGATTGTTTATATGTTTAAATCGATT
795 GTTACTGCTT
Statistics
Matches: 81, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 81 1.00
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.50
Consensus pattern (55 bp):
AATATTGCTTATTTTGAATCGATTGTTTATATGTTTAAATCGATTATCACGTTGG
Found at i:6670 original size:22 final size:21
Alignment explanation
Indices: 6642--6683 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
6632 TAATTCAAAC
*
6642 TCAAACATGCAACTTTAAGCTA
1 TCAAACATGCAA-TTCAAGCTA
6664 TCAAACATGCAATTCAAGCT
1 TCAAACATGCAATTCAAGCT
6684 CAATTGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (21 bp):
TCAAACATGCAATTCAAGCTA
Found at i:11166 original size:3 final size:3
Alignment explanation
Indices: 11158--11203 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
11148 TTTTCAAAGT
11158 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11204 GATACTTTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11325 original size:19 final size:19
Alignment explanation
Indices: 11303--11340 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11293 TTATATATTC
*
11303 TTTAGACTTTTTTAAAAAT
1 TTTAGAATTTTTTAAAAAT
*
11322 TTTATAATTTTTTAAAAAT
1 TTTAGAATTTTTTAAAAAT
11341 ATAAAATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTAGAATTTTTTAAAAAT
Found at i:11348 original size:18 final size:19
Alignment explanation
Indices: 11310--11349 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
11300 TTCTTTAGAC
* *
11310 TTTTTTAAAAATTTTATAA
1 TTTTTTAAAAATTATAAAA
11329 TTTTTTAAAAA-TATAAAA
1 TTTTTTAAAAATTATAAAA
11347 TTT
1 TTT
11350 GGATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTTTAAAAATTATAAAA
Found at i:11716 original size:16 final size:18
Alignment explanation
Indices: 11695--11727 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11685 TTAATTAAAA
11695 TTTAAA-TA-AAAATAAT
1 TTTAAATTAGAAAATAAT
11711 TTTAAATTAGAAAATAA
1 TTTAAATTAGAAAATAA
11728 ATCCAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TTTAAATTAGAAAATAAT
Found at i:15147 original size:10 final size:10
Alignment explanation
Indices: 15134--15159 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
15124 TTTTACGAAT
15134 TTTATATTTA
1 TTTATATTTA
15144 TTTATATTTA
1 TTTATATTTA
15154 TTTATA
1 TTTATA
15160 ATTCTCTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATATTTA
Found at i:15248 original size:28 final size:28
Alignment explanation
Indices: 15217--15286 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 28
15207 TTTTATAATT
15217 TTTTTCTAATTTTAAT-AAATATTAAAT-A
1 TTTTT-TAATTTTAATCAAA-ATTAAATCA
* *
15245 TTTTTTATATTTTTATCAAAATTTAATCA
1 TTTTTTA-ATTTTAATCAAAATTAAATCA
15274 TTTTTATAATTTT
1 TTTTT-TAATTTT
15287 TATTTCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 2 0.06
28 18 0.50
29 14 0.39
30 2 0.06
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTTAATTTTAATCAAAATTAAATCA
Found at i:15270 original size:29 final size:30
Alignment explanation
Indices: 15217--15289 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
15207 TTTTATAATT
* *
15217 TTTTTCTAATTTTAAT--AAATATTAAAT-A
1 TTTTTATAATTTTTATCAAAATATT-AATCA
15245 TTTTT-TATATTTTTATCAAAAT-TTAATCA
1 TTTTTATA-ATTTTTATCAAAATATTAATCA
15274 TTTTTATAATTTTTAT
1 TTTTTATAATTTTTAT
15290 TTCTTTTATC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
27 2 0.05
28 15 0.38
29 16 0.41
30 6 0.15
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTTATAATTTTTATCAAAATATTAATCA
Found at i:15910 original size:2 final size:2
Alignment explanation
Indices: 15903--15933 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15893 TTTCAATCCC
15903 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15934 TTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.