Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001985.1 Kokia drynarioides strain JFW-HI SEQ_113837, 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: 15651
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:38 original size:20 final size:21
Alignment explanation
Indices: 13--55 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3 TACTTACTAC
13 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
33 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
54 TA
1 TA
56 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:439 original size:4 final size:4
Alignment explanation
Indices: 432--470 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
422 TTCTTCCTTC
*
432 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
471 CTTCAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:459 original size:21 final size:20
Alignment explanation
Indices: 430--474 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
420 CCTTCTTCCT
430 TCTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTT-TTTC
*
451 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTCTTTTTTC
471 -CTTC
1 TCTTC
475 AATTTTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTCTTTCTTTTTTC
Found at i:13892 original size:20 final size:19
Alignment explanation
Indices: 13855--13906 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
13845 CCAACATGCC
* *
13855 AAATTAATAAAAAGAAAAGT
1 AAATTAAGAAAACGAAAA-T
*
13875 AAATTAAGAAAACTAAAAT
1 AAATTAAGAAAACGAAAAT
* *
13894 AGATAAAGAAAAC
1 AAATTAAGAAAAC
13907 CCACGAATGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (19 bp):
AAATTAAGAAAACGAAAAT
Found at i:14597 original size:6 final size:6
Alignment explanation
Indices: 14572--14621 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
14562 CCTTTACCAA
14572 TTTTTC -TTTTC -TTTTC -TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
14617 TTTTT
1 TTTTT
14622 TAATTTAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 15 0.35
6 28 0.65
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:15267 original size:16 final size:16
Alignment explanation
Indices: 15236--15274 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
15226 AATATTAAAC
15236 AAATAA-AAAATATTT
1 AAATAATAAAATATTT
*
15251 AAATAATAAAATTTTT
1 AAATAATAAAATATTT
*
15267 AAAAAATA
1 AAATAATA
15275 TTGATAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAATAAAATATTT
Found at i:15333 original size:16 final size:16
Alignment explanation
Indices: 15309--15340 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15299 CTAAATACGA
*
15309 AAGTGGTACAATGGAG
1 AAGTAGTACAATGGAG
15325 AAGTAGTACAATGGAG
1 AAGTAGTACAATGGAG
15341 TGATGTCTAT
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:0.41, C:0.06, G:0.34, T:0.19
Consensus pattern (16 bp):
AAGTAGTACAATGGAG
Found at i:15575 original size:2 final size:2
Alignment explanation
Indices: 15568--15593 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15558 TAATATAAAA
15568 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
15594 TAATCCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.