Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004396.1 Kokia drynarioides strain JFW-HI SEQ_117773, 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: 8126
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:551 original size:15 final size:15
Alignment explanation
Indices: 531--571 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
521 TAGTATTTGA
531 ATTTTGTAATTAGAC
1 ATTTTGTAATTAGAC
546 ATTTTGTAATTAGAC
1 ATTTTGTAATTAGAC
561 ATTTTGTAATT
1 ATTTTGTAATT
572 GGACTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (15 bp):
ATTTTGTAATTAGAC
Found at i:644 original size:12 final size:12
Alignment explanation
Indices: 629--676 Score: 82
Period size: 11 Copynumber: 4.2 Consensus size: 12
619 ATTGAAACTC
629 AAATTAAATTTA
1 AAATTAAATTTA
641 AAATTAAATTT-
1 AAATTAAATTTA
652 AAATTAAATTTA
1 AAATTAAATTTA
664 AAA-TAAATTTA
1 AAATTAAATTTA
675 AA
1 AA
677 TTTTAAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 21 0.60
12 14 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTAAATTTA
Found at i:655 original size:18 final size:17
Alignment explanation
Indices: 596--711 Score: 101
Period size: 17 Copynumber: 6.7 Consensus size: 17
586 GTAAATATAT
*
596 AATAATTTTAAATTTGAA
1 AATAAATTTAAATTT-AA
* * *
614 AATAAATTGAAACTCAA
1 AATAAATTTAAATTTAA
* *
631 ATTAAATTTAAAATTAA
1 AATAAATTTAAATTTAA
*
648 ATTTAAA-TTAAATTTAA
1 A-ATAAATTTAAATTTAA
665 AATAAATTTAAATTTTAA
1 AATAAATTTAAA-TTTAA
* *
683 AACAAATTT-AATCTTTA
1 AATAAATTTAAAT-TTAA
700 AATAAATTTAAA
1 AATAAATTTAAA
712 ATGAGTTTGG
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
16 5 0.06
17 44 0.55
18 31 0.39
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:664 original size:29 final size:28
Alignment explanation
Indices: 602--711 Score: 91
Period size: 29 Copynumber: 3.8 Consensus size: 28
592 ATATAATAAT
*
602 TTTAAATTTGAAAATAAATTGAAACTCAAA
1 TTTAAATTT-AAAATAAATTTAAA-TCAAA
*
632 -TTAAATTTAAAATTAAATTTAAATTAAA
1 TTTAAATTTAAAA-TAAATTTAAATCAAA
* * *
660 TTTAAA-ATAAATTTAAATTTTAAAACAAA
1 TTTAAATTTAAA-ATAAA-TTTAAATCAAA
*
689 TTT-AATCTTTAAATAAATTTAAA
1 TTTAAAT-TTAAAATAAATTTAAA
712 ATGAGTTTGG
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
28 24 0.37
29 38 0.58
30 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (28 bp):
TTTAAATTTAAAATAAATTTAAATCAAA
Found at i:683 original size:7 final size:6
Alignment explanation
Indices: 602--679 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
592 ATATAATAAT
* * * * *
602 TTTAAA TTTGAAA -ATAAA TTGAAA CTCAAA -TTAAA TTTAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
649 TTTAAA -TTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
680 TAAAACAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
5 16 0.28
6 38 0.67
7 3 0.05
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:875 original size:30 final size:30
Alignment explanation
Indices: 815--876 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 30
805 AAATTTTAAA
815 TTATACATGAATTTTTATTTAATGTGAAATT
1 TTATACATGAATTTTTATTT-ATGTGAAATT
*
846 TTATGCAT-AATTTTTGATTT-TGTGTAAATT
1 TTATACATGAATTTTT-ATTTATGTG-AAATT
876 T
1 T
877 ATAATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 4 0.14
30 13 0.46
31 11 0.39
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.55
Consensus pattern (30 bp):
TTATACATGAATTTTTATTTATGTGAAATT
Found at i:877 original size:29 final size:30
Alignment explanation
Indices: 811--879 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 30
801 GGATAAATTT
811 TAAA-TTATACATGAATTTTTATTTAATGTG
1 TAAATTTATACATGAATTTTTATTT-ATGTG
*
841 -AAATTTTATGCAT-AATTTTTGATTT-TGTG
1 TAAA-TTTATACATGAATTTTT-ATTTATGTG
870 TAAATTTATA
1 TAAATTTATA
880 ATTAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
29 12 0.36
30 10 0.30
31 11 0.33
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (30 bp):
TAAATTTATACATGAATTTTTATTTATGTG
Found at i:1341 original size:29 final size:30
Alignment explanation
Indices: 1287--1353 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
1277 ATCTCAAAAT
*
1287 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTATGATTT-ATGTGCAATTG
* *
1318 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTATGATTTATGTGCAATTG
1347 TATACAT
1 TATACAT
1354 AAAATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 16 0.48
31 17 0.52
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.43
Consensus pattern (30 bp):
TATACATGAACTATGATTTATGTGCAATTG
Found at i:1367 original size:29 final size:29
Alignment explanation
Indices: 1308--1377 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
1298 TATGGTTTAA
* * * *
1308 TGTGCAATTGTATACATGAACTTTGATTT
1 TGTGCAATTTTATACATAAAATTTGAATT
*
1337 TGTGCAATTTTATACATAAAATTTTAATT
1 TGTGCAATTTTATACATAAAATTTGAATT
*
1366 TGATTCAATTTT
1 TG-TGCAATTTT
1378 TATAAATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (29 bp):
TGTGCAATTTTATACATAAAATTTGAATT
Done.