Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003915.1 Kokia drynarioides strain JFW-HI SEQ_116983, 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: 26580
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:360 original size:3 final size:3
Alignment explanation
Indices: 352--382 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
342 GGATCTATCC
352 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
383 TTCGAAGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:1378 original size:28 final size:30
Alignment explanation
Indices: 1344--1408 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1334 TTTAAAAAAG
1344 AAAAAC-TT-AACAGTCCAACGACTTAAAT
1 AAAAACTTTGAACAGTCCAACGACTTAAAT
* * *
1372 AAAAACTTTTGAATAGTTCAATGACTTAAAT
1 AAAAAC-TTTGAACAGTCCAACGACTTAAAT
1403 AAAAAC
1 AAAAAC
1409 CTTCGAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 6 0.19
30 2 0.06
31 23 0.74
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (30 bp):
AAAAACTTTGAACAGTCCAACGACTTAAAT
Found at i:1398 original size:31 final size:31
Alignment explanation
Indices: 1363--1423 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1353 ACAGTCCAAC
* *
1363 GACTTAAATAAAAACTTTTGAATAGTTCAAT
1 GACTTAAATAAAAACCTTCGAATAGTTCAAT
1394 GACTTAAATAAAAACCTTCGAATAGTTCAA
1 GACTTAAATAAAAACCTTCGAATAGTTCAA
1424 GATCAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (31 bp):
GACTTAAATAAAAACCTTCGAATAGTTCAAT
Found at i:9037 original size:24 final size:24
Alignment explanation
Indices: 9008--9056 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
8998 TTACAAAATG
9008 ATAACGTCAGTAACTAAAATGTAA
1 ATAACGTCAGTAACTAAAATGTAA
9032 ATAACGTCAGTAACTAAAATGTAA
1 ATAACGTCAGTAACTAAAATGTAA
9056 A
1 A
9057 CTGAGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (24 bp):
ATAACGTCAGTAACTAAAATGTAA
Found at i:11040 original size:11 final size:11
Alignment explanation
Indices: 11020--11052 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
11010 ACTTTCTATA
11020 TAGAAGGAAAG
1 TAGAAGGAAAG
*
11031 TAGAAAGAAAG
1 TAGAAGGAAAG
11042 TAGAAGGAAAG
1 TAGAAGGAAAG
11053 AAAGAGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (11 bp):
TAGAAGGAAAG
Found at i:11528 original size:4 final size:4
Alignment explanation
Indices: 11519--11548 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
11509 TACTCCTCAG
*
11519 GTAT GTAT GTAT GTAT GTAT GTAT ATAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
11549 GTGTGTGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:18919 original size:7 final size:7
Alignment explanation
Indices: 18907--18961 Score: 110
Period size: 7 Copynumber: 7.9 Consensus size: 7
18897 GAGAAGGATC
18907 AGCCATA
1 AGCCATA
18914 AGCCATA
1 AGCCATA
18921 AGCCATA
1 AGCCATA
18928 AGCCATA
1 AGCCATA
18935 AGCCATA
1 AGCCATA
18942 AGCCATA
1 AGCCATA
18949 AGCCATA
1 AGCCATA
18956 AGCCAT
1 AGCCAT
18962 TATCACCATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.42, C:0.29, G:0.15, T:0.15
Consensus pattern (7 bp):
AGCCATA
Found at i:20148 original size:19 final size:18
Alignment explanation
Indices: 20115--20152 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
20105 TGAAAATGTT
*
20115 TGTATAATAATATTAAAA
1 TGTATAAAAATATTAAAA
20133 TGTATAAAATATATTAAAA
1 TGTATAAAA-ATATTAAAA
20152 T
1 T
20153 AAAGTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:24793 original size:23 final size:24
Alignment explanation
Indices: 24764--24811 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
24754 ATTATGTAAA
24764 AAATTTAATAAATA-AAAAATTAT
1 AAATTTAATAAATATAAAAATTAT
* *
24787 AAATTTATTAAATATTAAAATTAT
1 AAATTTAATAAATATAAAAATTAT
24811 A
1 A
24812 TAATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATTTAATAAATATAAAAATTAT
Done.