Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001153.1 Kokia drynarioides strain JFW-HI SEQ_112464, 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: 51166
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:606 original size:4 final size:4
Alignment explanation
Indices: 599--626 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
589 GCATGCATGC
599 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
627 GATATTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:12554 original size:3 final size:3
Alignment explanation
Indices: 12546--12577 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12536 TGGATCTTGT
12546 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
12578 TTGTGTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:13586 original size:19 final size:19
Alignment explanation
Indices: 13562--13600 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13552 AAAATTAAGC
*
13562 ATCGAAACTAAATTAAAAT
1 ATCGAAACCAAATTAAAAT
*
13581 ATCGAAGCCAAATTAAAAT
1 ATCGAAACCAAATTAAAAT
13600 A
1 A
13601 ATTTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.13, G:0.08, T:0.23
Consensus pattern (19 bp):
ATCGAAACCAAATTAAAAT
Found at i:17916 original size:4 final size:5
Alignment explanation
Indices: 17891--17928 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
17881 GTTAAACCCT
17891 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
17929 GCTTCAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:17916 original size:9 final size:9
Alignment explanation
Indices: 17892--17928 Score: 65
Period size: 9 Copynumber: 4.0 Consensus size: 9
17882 TTAAACCCTT
17892 TTTATTTTA
1 TTTATTTTA
17901 TTTTATTTTA
1 -TTTATTTTA
17911 TTTATTTTA
1 TTTATTTTA
17920 TTTATTTTA
1 TTTATTTTA
17929 GCTTCAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:17916 original size:14 final size:14
Alignment explanation
Indices: 17892--17928 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
17882 TTAAACCCTT
17892 TTTATTTTATTTTA
1 TTTATTTTATTTTA
17906 TTT-TATTTATTTTA
1 TTTAT-TTTATTTTA
17920 TTTATTTTA
1 TTTATTTTA
17929 GCTTCAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 19 0.90
15 1 0.05
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:20369 original size:2 final size:2
Alignment explanation
Indices: 20362--20388 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20352 TCTTTAAAGA
20362 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20389 AAAGAAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21783 original size:2 final size:2
Alignment explanation
Indices: 21776--21802 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21766 CTTTGCTCAT
21776 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 T
21803 GTATGTTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24303 original size:27 final size:27
Alignment explanation
Indices: 24273--24337 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
24263 CCAATTCAAT
* *
24273 TAATTAAAAATATT-TTTATTTAAAAAG
1 TAATTAAAAATATTCTTT-TATAAAAAA
24300 TAA-TAAAAATTATTCTTTTATAAAAAA
1 TAATTAAAAA-TATTCTTTTATAAAAAA
*
24327 TAATTTAAAAT
1 TAATTAAAAAT
24338 CAAAATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 6 0.19
27 18 0.56
28 8 0.25
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
TAATTAAAAATATTCTTTTATAAAAAA
Found at i:26212 original size:11 final size:11
Alignment explanation
Indices: 26196--26228 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
26186 AAATGCTACA
26196 TGCAGTTGGTG
1 TGCAGTTGGTG
26207 TGCAGTTGGTG
1 TGCAGTTGGTG
*
26218 TGCAGATGGTG
1 TGCAGTTGGTG
26229 GGACTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.12, C:0.09, G:0.45, T:0.33
Consensus pattern (11 bp):
TGCAGTTGGTG
Found at i:30164 original size:17 final size:17
Alignment explanation
Indices: 30142--30180 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
30132 CTCCACCTTG
* * *
30142 ACAAGAATTCTCTAGGA
1 ACAAGAACTCTCAACGA
30159 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
30176 ACAAG
1 ACAAG
30181 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:36324 original size:3 final size:3
Alignment explanation
Indices: 36316--36342 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
36306 TGAAATAATG
36316 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
36343 GGTAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:37245 original size:3 final size:3
Alignment explanation
Indices: 37232--37270 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
37222 GAATTGCTTT
*
37232 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
37271 TAAACTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:48495 original size:63 final size:62
Alignment explanation
Indices: 48420--48544 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 62
48410 GTGGTAACTC
48420 CAAATACTATAATAAAAT-ACACATTAATAATTTACGTACCACATTAAATAATTTATAAAAATA
1 CAAATACTATAAT-AAATCACACATTAATAATTTACGTACCACATT-AATAATTTATAAAAATA
* * * * * *
48483 CAAATA-TAATAATAAATCACATATTTATAATTTATGTACCATATTAATATTTTATGAAAATA
1 CAAATACT-ATAATAAATCACACATTAATAATTTACGTACCACATTAATAATTTATAAAAATA
48545 TATGTACCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
62 20 0.37
63 34 0.63
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.36
Consensus pattern (62 bp):
CAAATACTATAATAAATCACACATTAATAATTTACGTACCACATTAATAATTTATAAAAATA
Done.