Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013553.1 Kokia drynarioides strain JFW-HI SEQ_128579, 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: 28509
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Found at i:4296 original size:771 final size:765
Alignment explanation
Indices: 2817--4333 Score: 2163
Period size: 771 Copynumber: 2.0 Consensus size: 765
2807 GAGCATCTAG
* * * * *
2817 TAAAAACTCGTGACTGACGAAATTCCTATCCATTTTGATGTAGATAAATAAGTAACAAAAAAATT
1 TAAAAACTCGTGACTAAAGAAATTCCTATCCATTTAGACGTAGACAAATAAGTAACAAAAAAATT
* * *
2882 TATAAAATTAACAAAATATAACATATAAGTTATCGAACTTTAAAATAATATATTAAATATGCAAT
66 TATAAAATTAACAAAATAGAACATATAAGTTATCGAAATTTAAAATAATATATGAAATATGCAAT
* *
2947 CAATTTACAAGTTTTTAGAACTGAGCTGGGTAAGAAAAAATAACAAATAGTTCATACGTCATATT
131 CAACTTACAAGTTTTTAAAACTGAGCTGGGTAAGAAAAAATAACAAATAGTTCATACGTCATATT
** * * * *
3012 GAAATTCACTTAATCTCGGATTAAATGGAAAATTGATAATGTCGTTCATAAAAAATTTTAGTTCA
196 GAAATTCACTTAATCTCAAATTAAATGGAAAATTAATAATGTCATTCATAAAAAATATTAGCTCA
* * *
3077 TCAATAGCAACTCCGACTTCTATCTTTCCAGCATCTAAATCAGGTAAATATTTTACCCACCTATT
261 TCAATAGCAACTCCGACTTCTATCTTACCAACATCTAAATCAGGTAAAAATTTTACCCACCTATT
**
3142 GAAATTAATAACGAATAAAGACTTTGTCGCATTTTTTGTGTAAATGCTTTAATTCCTTGCCCATT
326 GAAATTAATAACGAATAAAGACTTTGTCGCA-TTTTTGTGTAAATGCTTTAATTCCAAGCCCATT
* * * * *
3207 TACAAACAATATCCTGGAAGATCTTATTGAAATCACCTTTGATGTAATTGAAACACTCATGCTGA
390 T---AACAATATCATGAAAGATCATATTGAAATCACCTTTAATGTAATTGAAACACTCATGCTAA
* *
3272 TTTTGGTTTTAACAACTACCTTTCCACTCCCTCACCTTGTCTTCAAAGTAAGAAAGAACGTTCTT
452 TTTTGGTTTTAACAACTACCTTTCCACTCCCTCACCTTGTCTTCAAAGTAAGAAAAAACGTTCGT
* *
3337 AGATGGTTCTAACGCAAGCAACCATTTATCTTAATAGTATACAAGATTATGGCAGAACAATATCT
517 AGAAGGTTCTAACGCAAGCAACCATTTATCTTAATAGTATACAAGATTATGGCAAAACAATATCT
* * * *
3402 GATCATCATGATTTTTAGCTACATATTTGTACACTGTTAGAGCTTCCTCTTTTTCTTTGAAAGGT
582 GATCATCATGATTTTCAGCTACATATTTGTACACTGTTAGAGCTTCCTCATTTTCTTTAAAAGGC
*
3467 AGGAAAGTGGGTTTAATTTCTATGCTTGAAATTTTTAATATTCTATCATACGCATGTGTACCCCA
647 AAGAAAGTGGGTTTAATTTCTATGCTTGAAATTTTTAATATTCTATCATACGCATGTGTACCCCA
* *
3532 TTTGTTGATGTAACACTTTGGTACCACCATAACTATAAGCATCCAGACATGTTT
712 TTTGTTGATATAACACTTCGGTACCACCATAACTATAAGCATCCAGACATGTTT
*
3586 TAAAAACTCGTGACTAAAGAAATTCCTATCCATTTAGACGTAGGCAAATAAGTAACAAAAAAATT
1 TAAAAACTCGTGACTAAAGAAATTCCTATCCATTTAGACGTAGACAAATAAGTAACAAAAAAATT
* * *
3651 TATGAAATTAATAAAATAGAATATATAAGTTATCGAAATTTAAAATAAATATATGAAATATGCAA
66 TATAAAATTAACAAAATAGAACATATAAGTTATCGAAATTTAAAAT-AATATATGAAATATGCAA
* *
3716 TCAACTTACAAGTTTTTAAAACTGAGTTGGGTAAGAAAAGATAACAGACAT-G-TCATACGTCAT
130 TCAACTTACAAGTTTTTAAAACTGAGCTGGGTAAGAAAAAATAACA-A-ATAGTTCATACGTCAT
* *
3779 ATTGAAATTCA-TATATTCTCAAATACTAGAATCGAATGGCAAATTAATAATGTCATTCATAAAA
193 ATTGAAATTCACT-TAATCTCAAAT--T---A---AATGGAAAATTAATAATGTCATTCATAAAA
* *
3843 AATATTAGCTCTTCAATAGCAACTCCGACTTTTATCTTACCAACATCTAAATCAGGTAAAAATTT
249 AATATTAGCTCATCAATAGCAACTCCGACTTCTATCTTACCAACATCTAAATCAGGTAAAAATTT
* * * * * * *
3908 TACCCGCCTATTGGAATTAGTAACGTATAAAGATTTTGTCGCA-TTTTGTGTAAATGTTTTGATT
314 TACCCACCTATTGAAATTAATAACGAATAAAGACTTTGTCGCATTTTTGTGTAAATGCTTTAATT
* * *
3972 CCAAGCCCA-TT-ACAATATCATGAAAGATCATATTGAAATCA-TTTCTAATGTATTTGAACCAC
379 CCAAGCCCATTTAACAATATCATGAAAGATCATATTGAAATCACCTT-TAATGTAATTGAAACAC
* *
4034 TCTTGCTAATTTT-GTTTTAAACAACTACCTTTCCACTCCC-CTACCTTGTCTTCAACGTAAGAA
443 TCATGCTAATTTTGGTTTT-AACAACTACCTTTCCACTCCCTC-ACCTTGTCTTCAAAGTAAGAA
* *
4097 AAAACGTTCGTAGAAGGTTCTAACGCAAG-AAGCCATTTATCTTGATGGTATACAAGATTATGGC
506 AAAACGTTCGTAGAAGGTTCTAACGCAAGCAA-CCATTTATCTTAATAGTATACAAGATTATGGC
* * * *
4161 AAAACAATATTTTATCATCATGATTTTCAGTTACATATTTGTACACTTTTAGAGCTTCCTCATTT
570 AAAACAATATCTGATCATCATGATTTTCAGCTACATATTTGTACACTGTTAGAGCTTCCTCATTT
* *
4226 TCTTTAAAAGGCAAGAAAGTGGGTTTGATTTCTTTGCTTGAAATTTTTAATATTCTATCATACGC
635 TCTTTAAAAGGCAAGAAAGTGGGTTTAATTTCTATGCTTGAAATTTTTAATATTCTATCATACGC
* *
4291 ATGTGTATCCCATTTGTTGATATAACACTTCGGTTCCACCATA
700 ATGTGTACCCCATTTGTTGATATAACACTTCGGTACCACCATA
4334 GCTGTAAGGC
Statistics
Matches: 663, Mismatches: 69, Indels: 30
0.87 0.09 0.04
Matches are distributed among these distances:
769 101 0.15
770 99 0.15
771 308 0.46
772 3 0.00
775 3 0.00
776 26 0.04
778 123 0.19
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (765 bp):
TAAAAACTCGTGACTAAAGAAATTCCTATCCATTTAGACGTAGACAAATAAGTAACAAAAAAATT
TATAAAATTAACAAAATAGAACATATAAGTTATCGAAATTTAAAATAATATATGAAATATGCAAT
CAACTTACAAGTTTTTAAAACTGAGCTGGGTAAGAAAAAATAACAAATAGTTCATACGTCATATT
GAAATTCACTTAATCTCAAATTAAATGGAAAATTAATAATGTCATTCATAAAAAATATTAGCTCA
TCAATAGCAACTCCGACTTCTATCTTACCAACATCTAAATCAGGTAAAAATTTTACCCACCTATT
GAAATTAATAACGAATAAAGACTTTGTCGCATTTTTGTGTAAATGCTTTAATTCCAAGCCCATTT
AACAATATCATGAAAGATCATATTGAAATCACCTTTAATGTAATTGAAACACTCATGCTAATTTT
GGTTTTAACAACTACCTTTCCACTCCCTCACCTTGTCTTCAAAGTAAGAAAAAACGTTCGTAGAA
GGTTCTAACGCAAGCAACCATTTATCTTAATAGTATACAAGATTATGGCAAAACAATATCTGATC
ATCATGATTTTCAGCTACATATTTGTACACTGTTAGAGCTTCCTCATTTTCTTTAAAAGGCAAGA
AAGTGGGTTTAATTTCTATGCTTGAAATTTTTAATATTCTATCATACGCATGTGTACCCCATTTG
TTGATATAACACTTCGGTACCACCATAACTATAAGCATCCAGACATGTTT
Found at i:10670 original size:11 final size:11
Alignment explanation
Indices: 10654--10685 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
10644 GAGATGTGGT
10654 CACATTTGCAC
1 CACATTTGCAC
10665 CACATTTGCAC
1 CACATTTGCAC
10676 CACATTTGCA
1 CACATTTGCA
10686 AACCCCACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.34, G:0.09, T:0.28
Consensus pattern (11 bp):
CACATTTGCAC
Found at i:16338 original size:25 final size:25
Alignment explanation
Indices: 16310--16361 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
16300 GCAATCAACT
*
16310 TACAAGTTTTTAGAATTGAACTGGG
1 TACAAGTTTTTAAAATTGAACTGGG
16335 TACAAGTTTTTAAAATTGAACTGGG
1 TACAAGTTTTTAAAATTGAACTGGG
16360 TA
1 TA
16362 AGAAAAGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (25 bp):
TACAAGTTTTTAAAATTGAACTGGG
Found at i:25795 original size:19 final size:19
Alignment explanation
Indices: 25773--25818 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
25763 AAATTTACTT
* *
25773 ATATTTGTATTCAATTAGG
1 ATATTTGTATTCAACTAAG
25792 ATATTTGTATTCAACTAAG
1 ATATTTGTATTCAACTAAG
25811 ATATTTGT
1 ATATTTGT
25819 TTAAAGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (19 bp):
ATATTTGTATTCAACTAAG
Done.