Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007710.1 Kokia drynarioides strain JFW-HI SEQ_122341, 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: 6131
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Found at i:3103 original size:424 final size:424
Alignment explanation
Indices: 2315--3163 Score: 1407
Period size: 424 Copynumber: 2.0 Consensus size: 424
2305 TTTTCTTGCC
* *
2315 TTATTCAACCTTTAGAGATACAATTTGTATAGTCGCGAATTTCTCACAGTTGAAGAAGTCTATAC
1 TTATTCAACCTTTAGAAATACAATTTGTATAGTCGCGAATCTCTCACAGTTGAAGAAGTCTATAC
*
2380 TTCCTTAGCCTCGTATGACAAGATGAAGCATCTTGTGGCTGGATTCAACTCTTAGGGAGAGGGTC
66 TTCATTAGCCTCGTATGACAAGATGAAGCATCTTGTGGCTGGATTCAACTCTTAGGGAGAGGGTC
* ** *
2445 TCATTGTTCTTGGGAGACAAGAATGAAATATTAGTGATAATCATGGGAGGACACAAGGATGAAAT
131 TCATTATTCTTGGGAGACAAGAATGAAATATTAGTGATAATCATAAGAGGACACAAGAATGAAAT
* **
2510 CCTTGCAATAAATCTAAGGGTAGATCGTGATCTTCAAACAAAGGCAAAATTTGTAATTTCTACAA
196 CCTTGCAATAAATCTAAGGGTAGATCGAGATCTTCAAACAAAGGCAAAACCTGTAATTTCTACAA
* * *
2575 AAAGAAAGGGTACATTAAGTTTGAGTGCTATAAGTTACAGAACAAGATCAAAAGGGAGACTGCGA
261 AAAGAAAGGGCACATTAAGTTTGAGTGCTATAAGTTACAGAACAAGATCAAAAGAGAGACTGCAA
* * *
2640 ATCAAAAGGGAAAACAACCAGAATAATCAGGTGAAGCTGATGTAGTAGAAGACTATAGCGATGGT
326 ATCAAAAAGGAAAACAACCAAAATAATCAGGTGAAGCTGATGTAGTAGAAGACTATAGCAATGGT
* *
2705 GAACTCCTGGTTACTTCTGTTGACAACTATAAAG
391 GAACACCTAGTTACTTCTGTTGACAACTATAAAG
*
2739 TTATTCAACCTTTAGAAATACAATTTGTATAGTCGTGAATCTCTCACAGTTGAAGAAGTCTATAC
1 TTATTCAACCTTTAGAAATACAATTTGTATAGTCGCGAATCTCTCACAGTTGAAGAAGTCTATAC
* * * *
2804 TTCATTAG-CTACGTATGACAAGATGAAGCATCTTGTGGTTGTATTCGACTCTTAGGGGGAGGGT
66 TTCATTAGCCT-CGTATGACAAGATGAAGCATCTTGTGGCTGGATTCAACTCTTAGGGAGAGGGT
2868 CTCATTATTCTTGGGAGACAAGAATGAAATATTAGTGATAATCATAAGAGGACACAAGAATGAAA
130 CTCATTATTCTTGGGAGACAAGAATGAAATATTAGTGATAATCATAAGAGGACACAAGAATGAAA
* * *
2933 TCCTTGCAATAAATCTAAGGGTAGATCGAGATCTTTAAATAGAGGCAAAACCTGTAATTTCTACA
195 TCCTTGCAATAAATCTAAGGGTAGATCGAGATCTTCAAACAAAGGCAAAACCTGTAATTTCTACA
2998 AAAAGAAAGGGCACATTAAGTTTGAGTGCTATAAGTTACAGAACAAGATCAAAAGAGAGAC-GAC
260 AAAAGAAAGGGCACATTAAGTTTGAGTGCTATAAGTTACAGAACAAGATCAAAAGAGAGACTG-C
3062 AAATCAAAAAGGAAAACAACCAAAATAATTC-GGTGAAGCTGATGTAGTAGAAGACTATAGCAAT
324 AAATCAAAAAGGAAAACAACCAAAATAA-TCAGGTGAAGCTGATGTAGTAGAAGACTATAGCAAT
*
3126 GGTGAACACCTAGTTACTTTTGTTGACAACTATAAAG
388 GGTGAACACCTAGTTACTTCTGTTGACAACTATAAAG
3163 T
1 T
3164 AAGCGAGGAG
Statistics
Matches: 395, Mismatches: 27, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
423 3 0.01
424 390 0.99
425 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (424 bp):
TTATTCAACCTTTAGAAATACAATTTGTATAGTCGCGAATCTCTCACAGTTGAAGAAGTCTATAC
TTCATTAGCCTCGTATGACAAGATGAAGCATCTTGTGGCTGGATTCAACTCTTAGGGAGAGGGTC
TCATTATTCTTGGGAGACAAGAATGAAATATTAGTGATAATCATAAGAGGACACAAGAATGAAAT
CCTTGCAATAAATCTAAGGGTAGATCGAGATCTTCAAACAAAGGCAAAACCTGTAATTTCTACAA
AAAGAAAGGGCACATTAAGTTTGAGTGCTATAAGTTACAGAACAAGATCAAAAGAGAGACTGCAA
ATCAAAAAGGAAAACAACCAAAATAATCAGGTGAAGCTGATGTAGTAGAAGACTATAGCAATGGT
GAACACCTAGTTACTTCTGTTGACAACTATAAAG
Done.