Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013295.1 Kokia drynarioides strain JFW-HI SEQ_128317, 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: 3756
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.31
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:3746 original size:818 final size:768
Alignment explanation
Indices: 2171--3756 Score: 2375
Period size: 818 Copynumber: 2.0 Consensus size: 768
2161 AGTGATAGAG
2171 AATATCAGAGTTTTTTAGCCACTTTGAAACAATTACATGTTAATATACCTCTTATTGATGCTCTT
1 AATATCAGAGTTTTTTAGCCACTTTGAAACAATTACATGTTAATATACCTCTTATTGATGCTCTT
*
2236 GTGCAGATTCCTGGTTATGGGAAATTTATGAAGGAGCTCTTATCCAAGAAAAATAAATTGACCAA
66 GTGCAGATTCCTGGTTATGAGAAATTTATGAAGGAGCTCTTATCCAAGAAAAATAAATTGACCAA
2301 CATTGAGACAATTTCACTCAAAGAAGGCTGCAGCACTGTACTGACAAATAAATTACCACCCAAGA
131 CATTGAGACAATTTCACTCAAAGAAGGCTGCAGCACTGTACTGACAAATAAATTACCACCCAAGA
2366 TGAAAGATTCTAATAGTTTTACAATTTCCTGTTCCAGTAAAAATCATTACTTAGGAAAAGCTCTT
196 TGAAAGATTCTAATAGTTTTACAATTTCCTGTTCCAGTAAAAATCATTACTTAGGAAAAGCTCTT
2431 TGTGATCTAGGACCAAGCATCAACCTTATGCTCTTGTCAACATTCCGAAAATTAGGAATTGGTCA
261 TGTGATCTAGGACCAAGCATCAACCTTATGCTCTTGTCAACATTCCGAAAATTAGGAATTGGTCA
2496 CATGAAACCCACTGCATTGACATTGCAGCTGACAGATAAATCTTTGGTGTAACTTGAAGGACAAA
326 CATGAAACCCACTGCATTGACATTGCAGCTGACAGATAAATCTTTGGTGTAACTTGAAGGACAAA
2561 TCAAAGATGTTCTCGTCAAAGTAGATAAGTTTGTGTTCCTAGCAAATTTCATTATTCTTGATTGC
391 TCAAAGATGTTCTCGTCAAAGTAGATAAGTTTGTGTTCCTAGCAAATTTCATTATTCTTGATTGC
2626 AAAGCTGATAAGAAGGTATCCATAATTTTGAGACGCTCATATCTTGCTACGGGTCGCACTCTTAT
456 AAAGCTGATAAGAAGGTATCCATAATTTTGAGACGCTCATATCTTGCTACGGGTCGCACTCTTAT
2691 AGACGTATTCAAGGGCGAGTTAATCAAGCGACACAATGATGAACACGTTACCTTCAGTGTCTTTG
521 AGACGTATTCAAGGGCGAGTTAATCAAGCGACACAATGATGAACACGTTACCTTCAGTGTCTTTG
2756 AAACAATTCCCTGCAAGAGTAAAGAGCATTGTCATCATATTGATGTACTAGACGAATTAATTGTG
586 AAACAATTCCCTGCAAGAGTAAAGAGCATTGTCATCATATTGATGTACTAGACGAATTAATTGTG
2821 GAAGAATTTAATGAGTGAAGTACAATAACTTTAGAGGAACTTGCGGTGACAACTAAAGATAATTT
651 GAAGAATTTAATGAGTGAAGTACAATAACTTTAGAGGAACTTGCGGTGACAACTAAAGATAATTT
2886 CCTACCTGATTGCGACCACGCAGATGGAGTCCTTAGATTTGACCAATAGAACA
716 CCTACCTGATTGCGACCACGCAGATGGAGTCCTTAGATTTGACCAATAGAACA
**************************
2939 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATATCAGAGTTTTT
1 ------------------------AATATCAGAGTTTTTTAGCCACTTTGAA-A-CA-A-----T
* * * * *
3004 TAGCCACT-TTGAAACAATTACATGTTAAT-ATACCTCTTATTGATGCTCTTGTGCAGATTCCTG
34 TA--CA-TGTT--AA-TA-TACCTCTTATTGAT-GCTC-T-T----------GTGCAGATTCCTG
*
3067 GTTATGAGAAATTTATGAAGGAGCTCTTATCCAAGAAAAATAAATTGACCGACATTGAGACAATT
79 GTTATGAGAAATTTATGAAGGAGCTCTTATCCAAGAAAAATAAATTGACCAACATTGAGACAATT
*
3132 TCACTCAAAGAAGGCTGTAGCACTGTACTGACAAATAAATTACCACCCAAGATGAAAGATTCTAA
144 TCACTCAAAGAAGGCTGCAGCACTGTACTGACAAATAAATTACCACCCAAGATGAAAGATTCTAA
3197 TAGTTTTACAATTTCCTGTTCCAGTAAAAATCATTACTTAGGAAAAGCTCTTTGTGATCTAGGAC
209 TAGTTTTACAATTTCCTGTTCCAGTAAAAATCATTACTTAGGAAAAGCTCTTTGTGATCTAGGAC
3262 CAAGCATCAACCTTATGCTCTTGTCAACATTCCGAAAATTAGGAATTGGTCACATGAAACCCACT
274 CAAGCATCAACCTTATGCTCTTGTCAACATTCCGAAAATTAGGAATTGGTCACATGAAACCCACT
3327 GCATTGACATTGCAGCTGACAGATAAATCTTTGGTGTAACTTGAAGGACAAATCAAAGATGTTCT
339 GCATTGACATTGCAGCTGACAGATAAATCTTTGGTGTAACTTGAAGGACAAATCAAAGATGTTCT
3392 CGTCAAAGTAGATAAGTTTGTGTTCCTAGCAAATTTCATTATTCTTGATTGCAAAGCTGATAAGA
404 CGTCAAAGTAGATAAGTTTGTGTTCCTAGCAAATTTCATTATTCTTGATTGCAAAGCTGATAAGA
*
3457 AGGTATCCATAATTTTTAGACGCTCATATCTTGCTACGGGTCGCACTCTTATAGACGTATTCAAG
469 AGGTATCCATAATTTTGAGACGCTCATATCTTGCTACGGGTCGCACTCTTATAGACGTATTCAAG
3522 GGCGAGTTAATCAAGCGACACAATGATGAACACGTTACCTTCAGTGTCTTTGAAACAATTCCCTG
534 GGCGAGTTAATCAAGCGACACAATGATGAACACGTTACCTTCAGTGTCTTTGAAACAATTCCCTG
3587 CAAGAGTAAAGAGCATTGTCATCATATTGATGTACTAGACGAATTAATTGTGGAAGAATTTAATG
599 CAAGAGTAAAGAGCATTGTCATCATATTGATGTACTAGACGAATTAATTGTGGAAGAATTTAATG
3652 AGTGAAGTACAATAACTTTAGAGGAACTTGCGGTGACAACTAAAGATAATTTCCTACCTGATTGC
664 AGTGAAGTACAATAACTTTAGAGGAACTTGCGGTGACAACTAAAGATAATTTCCTACCTGATTGC
3717 GACCACGCAGATGGAGTCCTTAGATTTGACCAATAGAACA
729 GACCACGCAGATGGAGTCCTTAGATTTGACCAATAGAACA
Statistics
Matches: 731, Mismatches: 35, Indels: 30
0.92 0.04 0.04
Matches are distributed among these distances:
792 2 0.00
793 1 0.00
794 2 0.00
795 1 0.00
800 3 0.00
802 4 0.01
803 1 0.00
804 2 0.00
805 3 0.00
806 11 0.02
807 1 0.00
808 1 0.00
818 699 0.96
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.29
Consensus pattern (768 bp):
AATATCAGAGTTTTTTAGCCACTTTGAAACAATTACATGTTAATATACCTCTTATTGATGCTCTT
GTGCAGATTCCTGGTTATGAGAAATTTATGAAGGAGCTCTTATCCAAGAAAAATAAATTGACCAA
CATTGAGACAATTTCACTCAAAGAAGGCTGCAGCACTGTACTGACAAATAAATTACCACCCAAGA
TGAAAGATTCTAATAGTTTTACAATTTCCTGTTCCAGTAAAAATCATTACTTAGGAAAAGCTCTT
TGTGATCTAGGACCAAGCATCAACCTTATGCTCTTGTCAACATTCCGAAAATTAGGAATTGGTCA
CATGAAACCCACTGCATTGACATTGCAGCTGACAGATAAATCTTTGGTGTAACTTGAAGGACAAA
TCAAAGATGTTCTCGTCAAAGTAGATAAGTTTGTGTTCCTAGCAAATTTCATTATTCTTGATTGC
AAAGCTGATAAGAAGGTATCCATAATTTTGAGACGCTCATATCTTGCTACGGGTCGCACTCTTAT
AGACGTATTCAAGGGCGAGTTAATCAAGCGACACAATGATGAACACGTTACCTTCAGTGTCTTTG
AAACAATTCCCTGCAAGAGTAAAGAGCATTGTCATCATATTGATGTACTAGACGAATTAATTGTG
GAAGAATTTAATGAGTGAAGTACAATAACTTTAGAGGAACTTGCGGTGACAACTAAAGATAATTT
CCTACCTGATTGCGACCACGCAGATGGAGTCCTTAGATTTGACCAATAGAACA
Done.