Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001398.1 Kokia drynarioides strain JFW-HI SEQ_112886, 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: 39052
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Found at i:24655 original size:22 final size:22
Alignment explanation
Indices: 24618--24683 Score: 62
Period size: 26 Copynumber: 2.9 Consensus size: 22
24608 TGATGATGAA
**
24618 AAATTTACCATTATATTG-TGC
1 AAATTTAATATTATATTGATGC
24639 AAATTTAATAATTATATTTGACTTGC
1 AAATTTAAT-ATTATA-TTGA--TGC
*
24665 AAATTTAATATTAAATTGA
1 AAATTTAATATTATATTGA
24684 CCATTATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 7 0.19
22 6 0.16
23 3 0.08
24 4 0.11
25 5 0.14
26 12 0.32
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (22 bp):
AAATTTAATATTATATTGATGC
Found at i:25830 original size:16 final size:16
Alignment explanation
Indices: 25809--25844 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
25799 TCCAATGCAT
*
25809 ACATCTTTTTAACTAA
1 ACATCTTTTTAACCAA
*
25825 ACATCTTTTTCACCAA
1 ACATCTTTTTAACCAA
25841 ACAT
1 ACAT
25845 ATGATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (16 bp):
ACATCTTTTTAACCAA
Found at i:28996 original size:28 final size:28
Alignment explanation
Indices: 28956--29037 Score: 110
Period size: 33 Copynumber: 2.8 Consensus size: 28
28946 CAAAACACCT
*
28956 TATTCTAATTAAAATAAAATAGATGATC
1 TATTCTAATTAAAATAAAATAGATGACC
28984 TATTCTAATTAAAATAAAATAAAATAGATGACC
1 TATTCTAA-T----TAAAATAAAATAGATGACC
29017 TATTCTAATTAAAATAAAATA
1 TATTCTAATTAAAATAAAATA
29038 AAAGAAGTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
28 20 0.42
29 1 0.02
32 1 0.02
33 26 0.54
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (28 bp):
TATTCTAATTAAAATAAAATAGATGACC
Found at i:29007 original size:33 final size:33
Alignment explanation
Indices: 28965--29040 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
28955 TTATTCTAAT
*
28965 TAAAATAAAATAGATGATCTATTCTAATTAAAA
1 TAAAATAAAATAGATGACCTATTCTAATTAAAA
28998 TAAAATAAAATAGATGACCTATTCTAATTAAAA
1 TAAAATAAAATAGATGACCTATTCTAATTAAAA
29031 TAAAATAAAA
1 TAAAATAAAA
29041 GAAGTCTAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (33 bp):
TAAAATAAAATAGATGACCTATTCTAATTAAAA
Found at i:29162 original size:41 final size:41
Alignment explanation
Indices: 29095--29191 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
29085 TGAATTTTAT
*
29095 CTTAACAAGAATTCTAGTCACTCAATTCTAACAATCTCCAC
1 CTTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCAC
* *
29136 TTTAATAAGAATTCTAGTCACCCAATTCTAACAATCTCCAC
1 CTTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCAC
29177 CTTAACAAGAATTCT
1 CTTAACAAGAATTCT
29192 CTACGAACTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (41 bp):
CTTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCAC
Found at i:32168 original size:15 final size:16
Alignment explanation
Indices: 32150--32183 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
32140 ATGGAATTAG
32150 AATAAATTT-TTAATT
1 AATAAATTTATTAATT
32165 AATAAATTTAATTAATT
1 AATAAATTT-ATTAATT
32182 AA
1 AA
32184 AACTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATAAATTTATTAATT
Found at i:32730 original size:29 final size:29
Alignment explanation
Indices: 32669--32739 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
32659 AAATACTAAG
** *
32669 ATAAGTGACTAAAACGTAACATTTCAAAC
1 ATAAGTGACTAAAACGTAACATGACAAAA
* * *
32698 ATAAGTGACTAAAATGTAACCTGAGAAAA
1 ATAAGTGACTAAAACGTAACATGACAAAA
32727 ATAAAAGTGACTA
1 AT--AAGTGACTA
32740 TTTTTGTAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 25 0.74
31 9 0.26
ACGTcount: A:0.51, C:0.13, G:0.14, T:0.23
Consensus pattern (29 bp):
ATAAGTGACTAAAACGTAACATGACAAAA
Found at i:35286 original size:16 final size:16
Alignment explanation
Indices: 35267--35313 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
35257 AAATTTTAAT
35267 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
35283 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
35299 AAATAAAACAATATA
1 AAATAAAA-AATATA
35314 AATATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:38815 original size:51 final size:49
Alignment explanation
Indices: 38731--38832 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 49
38721 CTTTTTAACA
38731 TCTAACAAGGAGTTTACAATGAAAAGGGGAAAAAAGACTAGACCTAGGGCT
1 TCTAACAAGGAGTTTACAATGAAAA-GGGAAAAAA-ACTAGACCTAGGGCT
* * *
38782 TCTAACAAGGAGTTTACAATGAGACGGGAAAAAAACTAGATCTAGGGCT
1 TCTAACAAGGAGTTTACAATGAAAAGGGAAAAAAACTAGACCTAGGGCT
38831 TC
1 TC
38833 AAAAAATGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
49 16 0.33
50 9 0.19
51 23 0.48
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.20
Consensus pattern (49 bp):
TCTAACAAGGAGTTTACAATGAAAAGGGAAAAAAACTAGACCTAGGGCT
Done.