Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000009.1 Kokia drynarioides strain JFW-HI SEQ_13751, 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: 4295
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Found at i:846 original size:98 final size:98
Alignment explanation
Indices: 673--1219 Score: 718
Period size: 98 Copynumber: 5.6 Consensus size: 98
663 TTCCATTACG
*
673 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAACATGAAGGG
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGG
* * *
738 AAAGAATTAAGCCGCAACGACTAATCTAGTACC
66 AAAGATTTAAGCCACAACGACGAATCTAGTACC
* * * *
771 ACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCACAAAAACATGAAGGG
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGG
836 AAAGATTTAAGCCACAACGACGAATCTAGTACC
66 AAAGATTTAAGCCACAACGACGAATCTAGTACC
* * * *
869 ACGAAGATATGGAGGAAAAGGTTTAAGTCGCAATGGCGAACCTTGCACCTCAGAAACATGAAGGG
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGG
* * *
934 AAAGATTTAAACCACAATGGCGAATCTAGTACC
66 AAAGATTTAAGCCACAACGACGAATCTAGTACC
* *
967 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAATGGTGAACCTTGTACCTCAGAAACATGAAGGG
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGG
* * ** ** *
1032 AAGGATTGAAGCTGCAACGGTGAATCTGGTACC
66 AAAGATTTAAGCCACAACGACGAATCTAGTACC
* * * * **
1065 ATGAAGATATGGAGGGAAAGATTTAAGTTGCAACGGCGAACCTGGTACCTCAGGAACATGTTGGG
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGG
* * * * *
1130 AAAGATTGAAGTCACAATGGA-AAATCTGGTACC
66 AAAGATTTAAGCCACAA-CGACGAATCTAGTACC
* * * * *
1163 ACGAAGATATGGAGGGAAAGGTTGAAGTTGCAATGGTGAACCTTGTACCTCAGAAAC
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
1220 GTGAGGAAAT
Statistics
Matches: 399, Mismatches: 49, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
98 398 1.00
99 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (98 bp):
ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGG
AAAGATTTAAGCCACAACGACGAATCTAGTACC
Found at i:1211 original size:49 final size:49
Alignment explanation
Indices: 673--1211 Score: 429
Period size: 49 Copynumber: 11.0 Consensus size: 49
663 TTCCATTACG
673 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
* * * * * * * * * * *
722 TCAAAAACATGAAGGGAAAGAATTAAGCCGCAACGACTAATCTAGTACC
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
* *
771 ACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACC
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
* * * * * * * * *
820 ACAAAAACATGAAGGGAAAGATTTAAGCCACAACGACGAATCTAGTACC
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
* * * *
869 ACGAAGATATGGAGGAAAAGGTTTAAGTCGCAATGGCGAACCTTGCACC
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
* * * ** * * * *
918 TCAGAA-ACATGAAGGGAAAGATTTAAACCACAATGGCGAATCTAGTACC
1 AC-GAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
* *
967 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAATGGTGAACCTTGTACC
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
* * * * * * * *
1016 TCAGAA-ACATGAAGGGAAGGATTGAAG-CTGCAACGGTGAATCTGGTACC
1 AC-GAAGATATGGAGGGAAAGATTTAAGTC-GCAACGGCGAACCTTGTACC
* * *
1065 ATGAAGATATGGAGGGAAAGATTTAAGTTGCAACGGCGAACCTGGTACC
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
* * * ** * * * ** * *
1114 TC-AGGAACATGTTGGGAAAGATTGAAGTCACAATGGAAAATCTGGTACC
1 ACGAAG-ATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
* * * * *
1163 ACGAAGATATGGAGGGAAAGGTTGAAGTTGCAATGGTGAACCTTGTACC
1 ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
1212 TCAGAAACGT
Statistics
Matches: 376, Mismatches: 106, Indels: 16
0.76 0.21 0.03
Matches are distributed among these distances:
48 9 0.02
49 359 0.95
50 8 0.02
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.19
Consensus pattern (49 bp):
ACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
Found at i:2527 original size:107 final size:107
Alignment explanation
Indices: 2338--2552 Score: 385
Period size: 107 Copynumber: 2.0 Consensus size: 107
2328 ATATATATAT
*
2338 TACCTATTTATTATTACTGTATTATTTTTATTTATAAACAGATTTTTAAACGTATAAATTAAATA
1 TACCTATTTACTATTACTGTATTATTTTTATTTATAAACAGATTTTTAAACGTATAAATTAAATA
*
2403 AAACAAAAAAAGGGAAATAGTAACACAAAACAATGAAACAGG
66 AAACAAAAAAAGAGAAATAGTAACACAAAACAATGAAACAGG
*
2445 TACCTATTTACTATTACTGTATTATTTTTATTTATAAACAGATTTTTTAACGTATAAATTAAATA
1 TACCTATTTACTATTACTGTATTATTTTTATTTATAAACAGATTTTTAAACGTATAAATTAAATA
* *
2510 AAATAAAAAAAGAGAAATAGTAACACAAAATAATGAAACAGG
66 AAACAAAAAAAGAGAAATAGTAACACAAAACAATGAAACAGG
2552 T
1 T
2553 TTTAAAAGAA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (107 bp):
TACCTATTTACTATTACTGTATTATTTTTATTTATAAACAGATTTTTAAACGTATAAATTAAATA
AAACAAAAAAAGAGAAATAGTAACACAAAACAATGAAACAGG
Done.