Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009378.1 Kokia drynarioides strain JFW-HI SEQ_124085, 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: 62581
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6276 original size:2 final size:2
Alignment explanation
Indices: 6271--6309 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6261 ATATATATAT
6271 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6310 ACAGTTTGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10010 original size:31 final size:32
Alignment explanation
Indices: 9970--10030 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
9960 TCTATGTAAG
* * *
9970 AACGTTTTTGCTAAAAAGA-CGCTCACGTGAA
1 AACGCTTTTGCCAAAAAGAGCGCACACGTGAA
*
10001 AACGCTTTTGCCCAAAAGAGCGCACACGTG
1 AACGCTTTTGCCAAAAAGAGCGCACACGTG
10031 GACGTGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (32 bp):
AACGCTTTTGCCAAAAAGAGCGCACACGTGAA
Found at i:10394 original size:24 final size:25
Alignment explanation
Indices: 10344--10407 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 25
10334 ATGGTAAGAG
*
10344 TTAATTTTAATTTTTTTTATATTAT
1 TTAATTTTAATTTTTTTTATATAAT
10369 TTAATTTT-ATTTTATTTT-TATAAT
1 TTAATTTTAATTTT-TTTTATATAAT
10393 TTAATTATATAATTT
1 TTAATT-T-TAATTT
10408 AATTAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 16 0.47
25 13 0.38
26 1 0.03
27 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTAATTTTAATTTTTTTTATATAAT
Found at i:14144 original size:30 final size:31
Alignment explanation
Indices: 14080--14156 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
14070 ACAACAAGAG
* * * *
14080 GACTATTTTGTCACTTTTCGATAACTTTAGT
1 GACTGTTTTGTCACATTTCCATAACTTGAGT
*
14111 GACTGTTTTGTCACATTTCCA-AAGTTGAGT
1 GACTGTTTTGTCACATTTCCATAACTTGAGT
*
14141 GACTGTTTTGTTACAT
1 GACTGTTTTGTCACAT
14157 GTAACTGGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 22 0.55
31 18 0.45
ACGTcount: A:0.22, C:0.16, G:0.17, T:0.45
Consensus pattern (31 bp):
GACTGTTTTGTCACATTTCCATAACTTGAGT
Found at i:14301 original size:30 final size:31
Alignment explanation
Indices: 14249--14308 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
14239 AAAAGAACTT
*
14249 TTTTGTCACATTTTCAAAAGTTGAGGGACTA
1 TTTTGTCACATTTTCAAAAGTTGAAGGACTA
*
14280 TTTTGTCATATTTTC-AAAGTTGAAGGACT
1 TTTTGTCACATTTTCAAAAGTTGAAGGACT
14309 GAAATGTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (31 bp):
TTTTGTCACATTTTCAAAAGTTGAAGGACTA
Found at i:25385 original size:19 final size:19
Alignment explanation
Indices: 25361--25400 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
25351 GCTTTTGGGT
25361 TTAAATTTAATTTTGAGGA
1 TTAAATTTAATTTTGAGGA
25380 TTAAATTTAATTTTGAGGA
1 TTAAATTTAATTTTGAGGA
25399 TT
1 TT
25401 GAGGGGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (19 bp):
TTAAATTTAATTTTGAGGA
Found at i:31359 original size:54 final size:54
Alignment explanation
Indices: 31291--31399 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
31281 TAAACTCAAA
31291 ATTGGATCTGCAAAGAGCATAAGGACAATACAAAGACGACATGAAAGAAAATAC
1 ATTGGATCTGCAAAGAGCATAAGGACAATACAAAGACGACATGAAAGAAAATAC
* *
31345 ATTGGATCTGCAAAGAGCATAAGGATAATACAAAGACGACGTGAAAGAAAATAC
1 ATTGGATCTGCAAAGAGCATAAGGACAATACAAAGACGACATGAAAGAAAATAC
31399 A
1 A
31400 AAAGAAAGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.16
Consensus pattern (54 bp):
ATTGGATCTGCAAAGAGCATAAGGACAATACAAAGACGACATGAAAGAAAATAC
Found at i:39671 original size:6 final size:6
Alignment explanation
Indices: 39660--39687 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39650 TTGCGTGAAC
39660 AAAACA AAAACA AAAACA AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAA
39688 TGGTTGTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:48750 original size:31 final size:31
Alignment explanation
Indices: 48681--48750 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
48671 TTTTTTTATT
* *
48681 ATTAAATTTGATTCTCTATCTTTTAAAAAGA
1 ATTAAATTTGATTATCAATCTTTTAAAAAGA
* *
48712 ATCAAATTTGATTATCAA-CTTTTTAAAAGGA
1 ATTAAATTTGATTATCAATC-TTTTAAAAAGA
*
48743 GTTAAATT
1 ATTAAATT
48751 GTTGTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (31 bp):
ATTAAATTTGATTATCAATCTTTTAAAAAGA
Found at i:48862 original size:17 final size:17
Alignment explanation
Indices: 48836--48887 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
48826 TCCATGCTAG
*
48836 TTTTTGAATTTTTTATT
1 TTTTTAAATTTTTTATT
*
48853 TTTTTAAATTTTTTATAA
1 TTTTTAAATTTTTTAT-T
* *
48871 TTATTAAATTATTTATT
1 TTTTTAAATTTTTTATT
48888 GATGTGACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTTAAATTTTTTATT
Found at i:48877 original size:18 final size:17
Alignment explanation
Indices: 48842--48886 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
48832 CTAGTTTTTG
* *
48842 AATTTTTTATTTTTTTA
1 AATTTTTTATATTATTA
48859 AATTTTTTATAATTATTA
1 AATTTTTTAT-ATTATTA
*
48877 AATTATTTAT
1 AATTTTTTAT
48887 TGATGTGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTTTTATATTATTA
Found at i:50335 original size:23 final size:22
Alignment explanation
Indices: 50294--50340 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
50284 TACTTAACAA
50294 TAAGCACACACAGTACAATCCAG
1 TAAGCACACACAGTACAAT-CAG
*
50317 TAAGCACACACAGTGCAATCAG
1 TAAGCACACACAGTACAATCAG
50339 TA
1 TA
50341 GGTGCACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.15
Consensus pattern (22 bp):
TAAGCACACACAGTACAATCAG
Found at i:50385 original size:23 final size:23
Alignment explanation
Indices: 50359--50412 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
50349 TAACGCAAAT
50359 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
50382 CAGTAAGCACATGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
50405 TAGTAAGC
1 CAGTAAGC
50413 GCGCTAGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:55309 original size:22 final size:22
Alignment explanation
Indices: 55252--55331 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
55242 GCTGGGGAAA
* *
55252 CAGTAAGCACACACAGTTCAAT
1 CAGTAAGCACACATAGTGCAAT
55274 CCAGTAAGCACACATAGTGCAAT
1 -CAGTAAGCACACATAGTGCAAT
* * *
55297 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACATAGTGC-AAT
55320 CAGTAAGCACAC
1 CAGTAAGCACAC
55332 GAAGTGTGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.39, C:0.28, G:0.19, T:0.15
Consensus pattern (22 bp):
CAGTAAGCACACATAGTGCAAT
Found at i:55373 original size:23 final size:23
Alignment explanation
Indices: 55323--55367 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
55313 CGCAAATCAG
55323 TAAGCACACGAAGTGTGAAACAA
1 TAAGCACACGAAGTGTGAAACAA
55346 TAAGCACACGAAGTGTGAAACA
1 TAAGCACACGAAGTGTGAAACA
55368 GAAAGCGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (23 bp):
TAAGCACACGAAGTGTGAAACAA
Done.