Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013342.1 Kokia drynarioides strain JFW-HI SEQ_128364, 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: 39361
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:18375 original size:38 final size:38
Alignment explanation
Indices: 18333--18412 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
18323 GTTAATTCAG
* * * *
18333 AATTGTGCCTAGAATTGTCACTGCATGATG-ATGTCCAA
1 AATTGTGCCCAAAATTATCACTGCATGA-GCATGCCCAA
18371 AATTGTGCCCAAAATTATCACTGCATGAGCATGCCCAA
1 AATTGTGCCCAAAATTATCACTGCATGAGCATGCCCAA
18409 AATT
1 AATT
18413 TCATTATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 1 0.03
38 36 0.97
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (38 bp):
AATTGTGCCCAAAATTATCACTGCATGAGCATGCCCAA
Found at i:20541 original size:56 final size:56
Alignment explanation
Indices: 20414--20598 Score: 195
Period size: 56 Copynumber: 3.4 Consensus size: 56
20404 TCTGCTTACA
* *
20414 TCTCGGTTAGAGCATAATGCCATG--TA--T--AGTAGAGCTTTGGAACGCTTATG
1 TCTCGGTTAGAGCATAATGCTATGTATAGCTCAAGTAGAGCTTTGGAATGCTTATG
* * *
20464 TCTCGATTGGAGCATAATGCTATGTATAGCTCAAGTAGAGCTTTGGAATGCTTACG
1 TCTCGGTTAGAGCATAATGCTATGTATAGCTCAAGTAGAGCTTTGGAATGCTTATG
* * ** **
20520 TCTTGGTTAGAG-AGTACTGCTATGTATAGCTCGGGTAGAGCTTTGGGTTGCTTATG
1 TCTCGGTTAGAGCA-TAATGCTATGTATAGCTCAAGTAGAGCTTTGGAATGCTTATG
* *
20576 TCTCGGTTAGAGCGTAAAGCTAT
1 TCTCGGTTAGAGCATAATGCTAT
20599 TTTGGTTCAG
Statistics
Matches: 109, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
50 21 0.19
52 2 0.02
54 1 0.01
55 1 0.01
56 84 0.77
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.34
Consensus pattern (56 bp):
TCTCGGTTAGAGCATAATGCTATGTATAGCTCAAGTAGAGCTTTGGAATGCTTATG
Found at i:29487 original size:39 final size:39
Alignment explanation
Indices: 29401--29623 Score: 205
Period size: 39 Copynumber: 5.7 Consensus size: 39
29391 TGATAACCTG
* * * * * *
29401 GTAGTGTCTACAGTGTCATTACTACTTCAGTATAGCATT
1 GTAGTGTTTACAGTGTCACTGCCAGTTCAGTATAACATT
* * * *
29440 G-CGATGTTTCCAGTGTGACCGCCAGTTCAGTATAACATT
1 GTAG-TGTTTACAGTGTCACTGCCAGTTCAGTATAACATT
* * *
29479 GTAGTGTTTACAGTGTCATTGCCATTTCCGTATAACATT
1 GTAGTGTTTACAGTGTCACTGCCAGTTCAGTATAACATT
* * * *
29518 GTAGTGTTTACAGTGTCACTACCAATTCAGTACAGCATT
1 GTAGTGTTTACAGTGTCACTGCCAGTTCAGTATAACATT
* * * ** *
29557 TTAGTGTTTACATTGTCACTACCAGTTCAGTAATATTATC
1 GTAGTGTTTACAGTGTCACTGCCAGTTCAGT-ATAACATT
*
29597 GTAGTGTTTGCAGTGTCACTGCCAGTT
1 GTAGTGTTTACAGTGTCACTGCCAGTT
29624 ATAAACGTTC
Statistics
Matches: 147, Mismatches: 34, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
38 1 0.01
39 118 0.80
40 28 0.19
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (39 bp):
GTAGTGTTTACAGTGTCACTGCCAGTTCAGTATAACATT
Found at i:32518 original size:34 final size:36
Alignment explanation
Indices: 32480--32554 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
32470 TGACTAATGT
*
32480 TGGGCACAAAA-ATCG-TCGATTATCCAACTAGCGC
1 TGGGCACAAAACATCGTTCGATTATCCAACTAGAGC
* * *
32514 TGGGCGCAAAACATCGTTGGTTTATCCAACTAGAGC
1 TGGGCACAAAACATCGTTCGATTATCCAACTAGAGC
32550 TGGGC
1 TGGGC
32555 TCTCTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 10 0.29
35 4 0.11
36 21 0.60
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (36 bp):
TGGGCACAAAACATCGTTCGATTATCCAACTAGAGC
Found at i:32723 original size:146 final size:145
Alignment explanation
Indices: 32454--32733 Score: 339
Period size: 146 Copynumber: 1.9 Consensus size: 145
32444 TTGAGCGTAA
* **
32454 CTTTCGTCAGTTTATCTGACTAATGTTGGGCACAAAAATCGTCGATTATCCAACTAGCGCTGGGC
1 CTTTCGTCAATTTATCTGACTAATACTGGGCACAAAAATCGTCGATTATCCAACTAGCGCTGGGC
* * * * *
32519 GCAAAACATCGTTGGTTTATCCAACTAGAGCTGGGCTCTCTATTTACATTGCCGGTTTATCCGAC
66 GCAAAACATCGTTGGTATATCCAACTAGAGCTAGGCTCTCTATTGACATCGCCAGTTTATCCGAC
32584 TAGCATTGGGAGCAT
131 TAGCATTGGGAGCAT
* * * * * *
32599 CTTTGGTCAATTTATCTGACTAGTACTGGGCACACATATTCGTCGGTTATCCGAA-TAGCGCTGT
1 CTTTCGTCAATTTATCTGACTAATACTGGGCACA-AAAATCGTCGATTATCC-AACTAGCGCTGG
* * * * * *
32663 GCGCAAAACATTGTTGGTATATCCAACTAGAGCTATGC-CTATTATTGATATCGTCAGTTTATCT
64 GCGCAAAACATCGTTGGTATATCCAACTAGAGCTAGGCTCT-CTATTGACATCGCCAGTTTATCC
32727 GACTAGC
128 GACTAGC
32734 GCTGAGCGTA
Statistics
Matches: 112, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
145 31 0.28
146 79 0.71
147 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (145 bp):
CTTTCGTCAATTTATCTGACTAATACTGGGCACAAAAATCGTCGATTATCCAACTAGCGCTGGGC
GCAAAACATCGTTGGTATATCCAACTAGAGCTAGGCTCTCTATTGACATCGCCAGTTTATCCGAC
TAGCATTGGGAGCAT
Found at i:38158 original size:25 final size:26
Alignment explanation
Indices: 38130--38180 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
38120 TCTCCTGTAA
* *
38130 TTTAGGTTTTAGTTATTTTC-TTTTC
1 TTTAAGTTTTAGTCATTTTCATTTTC
38155 TTTAAGTTTTAGTCATTTTCATTTTC
1 TTTAAGTTTTAGTCATTTTCATTTTC
38181 GTTTTACAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.65
Consensus pattern (26 bp):
TTTAAGTTTTAGTCATTTTCATTTTC
Done.