Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009324.1 Kokia drynarioides strain JFW-HI SEQ_124031, 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: 21914
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:3254 original size:648 final size:648
Alignment explanation
Indices: 2016--3312 Score: 2387
Period size: 648 Copynumber: 2.0 Consensus size: 648
2006 CCAATGCTAA
2016 ACCTTCTTCCGCTCCACAAAACCCTGAGGCTACACCCCACAATTTCACTGCATTTCCTCACTCCA
1 ACCTTCTTCCGCTCCACAAAACCCTGAGGCTACACCCCACAATTTCACTGCATTTCCTCACTCCA
2081 ACCATTCCCAAAAGAATCTCGGAAATGCGGGGGAGTTCGATTGCGGCTTCGGTTTTGATTCCAGG
66 ACCATTCCCAAAAGAATCTCGGAAATGCGGGGGAGTTCGATTGCGGCTTCGGTTTTGATTCCAGG
*
2146 AGCGGCTTTCATTCCAAGTCCGCCGCTCGGCTAAGGCCGAGGTTGGTCAAGGTGAGGAAGCAGTT
131 AGCGGCTTTCATTCCAAGTCCGCCGCTCGGCTAAGGCCGAGGTTGGTCAAGGTGAGGAAACAGTT
** *
2211 CAATGGGAAGGTGAGAACTGGGGAGTGCAAGGTCGAGTCCGGTTTCAACCCATTTAAGCAGTCTG
196 CAAAAGGAAGGTGAGAACTGGGGAGTGCAAGGTCGAGTCCAGTTTCAACCCATTTAAGCAGTCTG
*
2276 GTCAAGGATCGCGCCCGGTAGGCACTAGTGGTAATCCATCATCGTCCGTGAGTATGAATAGAGTG
261 GTCAAGGATCGCGCCCGGTAGGCACTAGTGGTAATCCATCATCGTCCGAGAGTATGAATAGAGTG
*
2341 AACGATGATAATAGCAATAATAATATTAGTGATAATAATTATTCAAGTTTTGTATTTGGTGCTAA
326 AAAGATGATAATAGCAATAATAATATTAGTGATAATAATTATTCAAGTTTTGTATTTGGTGCTAA
*
2406 TAATGGAAGTGATAGAGAATCTAGTGGAAATGCTGAGGTTGAGAATAGAAATGAGGAGCCTTTGG
391 TAATGGAAGTGATAGAGAATCTAGTGGAAACGCTGAGGTTGAGAATAGAAATGAGGAGCCTTTGG
2471 GCAAGTTTGAGAATGTAGGTTTTGTATTTGGAGCAGATTTGAGCGGTGGCATGGAGAAACTGGGT
456 GCAAGTTTGAGAATGTAGGTTTTGTATTTGGAGCAGATTTGAGCGGTGGCATGGAGAAACTGGGT
* *
2536 TCTGAAAAGTGTGAGCAGTTTGGTTTTGTTTTTGGTGCTAATGGGAGTGATGGACGGGTGAAGCT
521 TCTGAAAAGTGTGAGCAGTTTGGATTTGTTTTTGGTCCTAATGGGAGTGATGGACGGGTGAAGCT
*
2601 GAATCCAGAAAAGGGAGAATCCAGTGATTCTTCCGTGAGTTTGGATGGCTGCAAGGGGAAGAT
586 GAATCCAGAAAAGGGAGAATCCAGTGATTCTTCCATGAGTTTGGATGGCTGCAAGGGGAAGAT
2664 ACCTTCTTCCGCTCCACAAAACCCTGAGGCTACACCCCACAATTTCACTGCATTTCCTCACTCCA
1 ACCTTCTTCCGCTCCACAAAACCCTGAGGCTACACCCCACAATTTCACTGCATTTCCTCACTCCA
*
2729 ACCATTCCCAAAAGAATCTTGGAAATGCGGGGGAGTTCGATTGCGGCTTCGGTTTTGATTCCAGG
66 ACCATTCCCAAAAGAATCTCGGAAATGCGGGGGAGTTCGATTGCGGCTTCGGTTTTGATTCCAGG
2794 AGCGGCTTTCATTCCAAGTCCGCCGCTCGGCTAAGGCCGAGGTTGGTCAAGGTGAGGAAACAGTT
131 AGCGGCTTTCATTCCAAGTCCGCCGCTCGGCTAAGGCCGAGGTTGGTCAAGGTGAGGAAACAGTT
* *
2859 CAAAAGGAAGGTGAGAACTGGGGAGTGCGAGGTTGAGTCCAGTTTCAACCCATTTAAGCAGTCTG
196 CAAAAGGAAGGTGAGAACTGGGGAGTGCAAGGTCGAGTCCAGTTTCAACCCATTTAAGCAGTCTG
* * *
2924 GTCAAGGATCGCGTCTGGTAGGCACTAGTGGTAATCCATCATCGTCTGAGAGTATGAATAGAGTG
261 GTCAAGGATCGCGCCCGGTAGGCACTAGTGGTAATCCATCATCGTCCGAGAGTATGAATAGAGTG
2989 AAAGATGATAATAGCAATAATAATATTAGTGATAATAATTATTCAAGTTTTGTATTTGGTGCTAA
326 AAAGATGATAATAGCAATAATAATATTAGTGATAATAATTATTCAAGTTTTGTATTTGGTGCTAA
*
3054 TAATGGAAGTGATAGAGAATCTAGTGGGAACGCTGAGGTTGAGAATAGAAATGAGGAGCCTTTGG
391 TAATGGAAGTGATAGAGAATCTAGTGGAAACGCTGAGGTTGAGAATAGAAATGAGGAGCCTTTGG
* * * *
3119 GCAAGTTTGAGAATTTAGGTTTTGTATTTGGAGCAGATTTGCGTGGTGGCATGGAGAAAGTGGGT
456 GCAAGTTTGAGAATGTAGGTTTTGTATTTGGAGCAGATTTGAGCGGTGGCATGGAGAAACTGGGT
*
3184 TCTGAAAAGTGTGAGCAGTTTGGATTTGTTTTTGGTCCTAATGGGAGTGATGGACGGGTGAAGTT
521 TCTGAAAAGTGTGAGCAGTTTGGATTTGTTTTTGGTCCTAATGGGAGTGATGGACGGGTGAAGCT
*
3249 GAATCCAGAAAAGGGAGAATCCAGTGATTCTTCCATGAGTTTGGATGGCTGCGAGGGGAAGAT
586 GAATCCAGAAAAGGGAGAATCCAGTGATTCTTCCATGAGTTTGGATGGCTGCAAGGGGAAGAT
3312 A
1 A
3313 AAATTAGAGA
Statistics
Matches: 626, Mismatches: 23, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
648 626 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (648 bp):
ACCTTCTTCCGCTCCACAAAACCCTGAGGCTACACCCCACAATTTCACTGCATTTCCTCACTCCA
ACCATTCCCAAAAGAATCTCGGAAATGCGGGGGAGTTCGATTGCGGCTTCGGTTTTGATTCCAGG
AGCGGCTTTCATTCCAAGTCCGCCGCTCGGCTAAGGCCGAGGTTGGTCAAGGTGAGGAAACAGTT
CAAAAGGAAGGTGAGAACTGGGGAGTGCAAGGTCGAGTCCAGTTTCAACCCATTTAAGCAGTCTG
GTCAAGGATCGCGCCCGGTAGGCACTAGTGGTAATCCATCATCGTCCGAGAGTATGAATAGAGTG
AAAGATGATAATAGCAATAATAATATTAGTGATAATAATTATTCAAGTTTTGTATTTGGTGCTAA
TAATGGAAGTGATAGAGAATCTAGTGGAAACGCTGAGGTTGAGAATAGAAATGAGGAGCCTTTGG
GCAAGTTTGAGAATGTAGGTTTTGTATTTGGAGCAGATTTGAGCGGTGGCATGGAGAAACTGGGT
TCTGAAAAGTGTGAGCAGTTTGGATTTGTTTTTGGTCCTAATGGGAGTGATGGACGGGTGAAGCT
GAATCCAGAAAAGGGAGAATCCAGTGATTCTTCCATGAGTTTGGATGGCTGCAAGGGGAAGAT
Found at i:15740 original size:25 final size:25
Alignment explanation
Indices: 15706--15793 Score: 106
Period size: 25 Copynumber: 3.5 Consensus size: 25
15696 AAATAATTTC
* *
15706 TAAAACTAAATAGAATAATTAATAA
1 TAAAATTAAATACAATAATTAATAA
* *
15731 TAAAATTAAATATAACAATTAATAA
1 TAAAATTAAATACAATAATTAATAA
*
15756 T-AAATTGAATACAATAATTAAATAA
1 TAAAATTAAATACAATAATT-AATAA
*
15781 TAAATTTAAATAC
1 TAAAATTAAATAC
15794 TTTTTAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
24 15 0.28
25 29 0.55
26 9 0.17
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (25 bp):
TAAAATTAAATACAATAATTAATAA
Found at i:15750 original size:13 final size:12
Alignment explanation
Indices: 15706--15792 Score: 54
Period size: 13 Copynumber: 7.0 Consensus size: 12
15696 AAATAATTTC
*
15706 TAAAACTAAATA
1 TAAAATTAAATA
*
15718 GAATAATT-AATAA
1 TAA-AATTAAAT-A
15731 TAAAATTAAATA
1 TAAAATTAAATA
15743 TAACAATT-AATA
1 TAA-AATTAAATA
*
15755 -ATAAATTGAATA
1 TA-AAATTAAATA
*
15767 CAATAATTAAATAA
1 TAA-AATTAAAT-A
*
15781 TAAATTTAAATA
1 TAAAATTAAATA
15793 CTTTTTAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
11 5 0.08
12 24 0.40
13 28 0.47
14 3 0.05
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.32
Consensus pattern (12 bp):
TAAAATTAAATA
Found at i:18191 original size:5 final size:5
Alignment explanation
Indices: 18181--18205 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18171 AGTCTCTTCG
18181 TCTTT TCTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT
18206 ATATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Done.