Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013794.1 Kokia drynarioides strain JFW-HI SEQ_128822, 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: 4133
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Found at i:377 original size:215 final size:216
Alignment explanation
Indices: 1--4114 Score: 5011
Period size: 216 Copynumber: 19.1 Consensus size: 216
* * * * * * * * *
1 TGTCAAACTTTTACTAGTTCTTCTATAACATCGGATACTTAAAGTATTCAACACGATCTATTCTT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* * * * * * *
66 TCGAACAATTTTTCAAACACTCCATGCTTGTGAAATCGCATCATTTGGTCTAAATAGTTTATCAT
66 TAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
131 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
131 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
* * *
196 TCTTTGACAAAC-TCCGAACT
196 TCTTGGACGAACTTTCGAACT
* * * * * * * *
216 TGTCAAACTTTTACTAGTTCTTTTATAACATCGGATCCTTAAAGTATTCAAGACGATCTATTCTT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* * * * * *
281 TCGTA-CAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCGAAATTGTTTATCA
66 TAG-AGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
* * *
345 TTTTGCAAACAAGTTTTGGTCTTTGTATTAAAAAATTATTTACGTGAGAATTGTTTCTCTCATTG
130 TTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
* * *
410 TTTTTTGGTCGAACTTTCAAACT
195 -TTCTTGGACGAACTTTCGAACT
* * * * * *
433 TGTCAAAATTTTACGAGCTATTTTTTAACTTTGGATCCGTAAAGTATTCAACAAGATCCATTTCT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* * * **
498 TAGAGAAAATTTTCGAGCATTCCATGCTCGGGAAATCAAATCATTTGGTCTAAATAGTTTGTCAT
66 TAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
* * *
563 TTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTTGT
131 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
* * *
628 TCTTTGACGAACTTCCGTACT
196 TCTTGGACGAACTTTCGAACT
* * * * * * * *
649 TGTCAAACTTTTACTAGTTCTTTTATAACATCGGATCCTTAAAGTATTCAAGACGATCTATTCTT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* * * * * *
714 TCGATCAATTTTTTGAACATTCCATGCTTGTGAAATCGCATCA-TTGGTCTAAATAGTTTATCAT
66 TAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
778 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
131 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
* *
843 TCTTTGACGAAC-TCCGAACT
196 TCTTGGACGAACTTTCGAACT
* ** * * * * * *
863 TGTCAAACTTTTACTAGTTCTTTTAAAACATCGGATCCTTAAAGTATTCAAGACGATCTATTCTT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* * * * * *
928 TCGTA-CAATTTTTTGAACATTCCATGCTTGAGAAATCGCATCATTTGGT-TGAAATTGTTTATC
66 TAG-AGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT-AAATAGTTTGTC
* *
991 ATTTTGCAAACAAATTTTGGTCTTTGTATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTT
129 ATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTT
* *
1056 GTTCTTTGACGAAC-TCCGAACT
194 GTTCTTGGACGAACTTTCGAACT
* * * * * * * * * * * *
1078 AGTCAAACTTTTTCTAGTTCTTCTATAACATCGGATACTTAAAGTATTCAAGATGATCTATTCTT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* * * * *
1143 TCGAACAATTTTTCGAACATTCCATGCTTGTGAAATCGCATCATTTGGTCTAAATAGTTTATCAT
66 TAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
* *
1208 TTTGCAAACAAGTTTTAGTCTTTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTTGT
131 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
*
1273 TCTTGGACGAACTTTTGAA-T
196 TCTTGGACGAACTTTCGAACT
* * * * *
1293 TG-CAAAACTTTTACGAGTTCTTTTTTAACTTCGGTTCCCTAAAGTTTTCAACAATATCCATTCC
1 TGTC-AAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCC
* * * * *
1357 TTAGAGCTATTTTCCGAACACTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTATGCCA
65 TTAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
* * * * * *
1422 TTTTGTAAACAAGTTTTGTTCGTTGAGTTAACAATTTATTCT-CGTGAGAATTGTTTCTCTCTTT
130 TTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT-TACGTGAGAATTGTTTCTCTCTTT
* *
1486 GTTCTTGGACGTACTTCCGAACT
194 GTTCTTGGACGAACTTTCGAACT
* * * * * * * *
1509 TGGT-AAATTTTTACGAGTTATTTTTTATCTTTGGTTCCCTACAGTATTCAATAAGATCCAATCC
1 T-GTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCC
* * *
1573 TTAAAGCAATTTTCCTAACATTCCATGCGT-GGGAAATCGCATCATTTGGTCTAAATAGTTTGTC
65 TTAGAGCAATTTTTCGAACATTCCATGC-TCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTC
* * *
1637 ATTTTTCAAACAAGTATTGGTCTTTGAATTAAAAATTTATTTACGTGAGAATTGTTTCTCTCTTT
129 ATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTT
*
1702 GTTCTTGGACGAACTTTCAAACT
194 GTTCTTGGACGAACTTTCGAACT
* * * *
1725 TGTCAAACTTTTACAAGTTATTTTTTAACTTTGGTTCCCTACAGTATTCAACAAGATCCATTCCT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* * * * * **
1790 TAGAGAAAATTTTGGATCATTCCATGGTCGGGAAATCAAATCATTTGGTCTAAATAGTTTGTCAT
66 TAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
*** * *
1855 TTCATAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTTGT
131 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
1920 TCTTGGACGAACTTTCGAACT
196 TCTTGGACGAACTTTCGAACT
* * * * * * * *
1941 TGTCAAACTTTTACTAGGTCTTTTATAACTTTGGATCCATAAGGTATTCAAGACGATCCATTCCT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* *** *
2006 TCGAGCAATTTTTCGAACATTCCATGCTCTACAAATCGCATCATTTGGTCTAAATAGTTTGTCTT
66 TAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
* *
2071 TTTGCAAACAAGTTTTGGCCTTTGAATTAAATACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
131 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
* *
2136 TCTTGGACGAACTTCCGAATT
196 TCTTGGACGAACTTTCGAACT
* * * * * * * * * *
2157 TGTCAAACTTTTACTAGTTCTTCTATAACATCGGATACTTAAAGTATTCAAGACGATCTATTCTT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* * * * *
2222 TAGAACAATTTTTCGAACATTCCATGCTTGTGAAATCTCATCATTTGGTCTAAATAGTTTATCAT
66 TAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
* * * *
2287 TTTGCAAATAAGTTTTGGTCTTAGAATTCAAAACTTATTTACGTGACAATTGTTTCTCTCTTTGT
131 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
* *
2352 TCTTGCACGAACTTTCAAACT
196 TCTTGGACGAACTTTCGAACT
* * * *
2373 TGTCAAACTTTTACGAGTTATTTTTTAACTTTGGTTCCCTGAAGTATTCAACAAGATCCATTCCT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
** * * ** *
2438 TAGAG-AAAATTTCGAAACATTCCACGGTCGGGAAATCAAATCATTTGGTCTAAATAGTTTTTCA
66 TAGAGCAATTTTTCG-AACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
* * *
2502 TTTAGTAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
130 TTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
*
2567 TTCTTGGACGAACTTCCGAACT
195 TTCTTGGACGAACTTTCGAACT
* * * * * * * * * * *
2589 TGTCAAACTTTTTCTAGTTCTTCTATAACGTCGGATACTTAAAGTATTCAAGACGATCTATTCTT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* * * * * *
2654 TCGAACCATTTTTCGAACATTCCATGCTTGTGAAATCGCATCATTTGGTCTAAATAGTTTATCAT
66 TAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
2719 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
131 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
*
2784 TCTTGGACGAACTTTCAAACT
196 TCTTGGACGAACTTTCGAACT
* * *
2805 TGTCAAACTCTTA-TGAGTTATTTTTTAACTTTGGTTCCCTAAAGTATTCAACAAGATCCATTCC
1 TGTCAAACTTTTACT-AGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCC
* ** * * *
2869 TTAGAGAAAGTTTTT-GAACATTCCATGCTCGGGAAATCAAATTATTTGGTCT-AATTGTTTGTG
65 TTAGAGCAA-TTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTC
* * * * * *
2932 ATTTTGTAAACAAGTTTTGTTCTTTGAGTTTAAAACTTATTCACGTGAGAATTGTTTTTCTCTTT
129 ATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTT
* *
2997 GTTCTTGGACGGAC-TGCTGAACT
194 GTTCTTGGACGAACTTTC-GAACT
* * * * *
3020 TGGT-AAACTTTTACGAGTTATTTTTTAACTTCGGTTACCTACAGTATTCAACAAGATCCAATCC
1 T-GTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCC
* * * * * *
3084 GTAAAGCAATTTTCCTAACATTCCATGCGCGGGAAATCACATCATTTGGTCTAAATAGTTTGTCA
65 TTAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
*
3149 TTTT-CAAACAAGTTTAGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
130 TTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
* * *
3213 TTCTTGGATGAACTGTCAAACT
195 TTCTTGGACGAACTTTCGAACT
* * * *
3235 TGTCAAACTTTTACGAGTTATTTTTTAAGTTTGGTTCCCTAAAGTATTCAACAAGATCCATTCCT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
* * ** ** *
3300 TAGAGCAAATTTCCGAACATTCCATGCTCGGGAAATCAAAGAATTTTGTCTAAATAGTTTGTCAT
66 TAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
* *
3365 TTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
131 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
3430 TCTTGGACGAACTTTCGAA-T
196 TCTTGGACGAACTTTCGAACT
* * * * * *
3450 TG-CAAAATTTTTACGAGTTATTTTTTAACTACGGTTCCCTAAAGTTTTCAACAAGATACATTCC
1 TGTC-AAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCC
* * * *
3514 TTAGAGCTATTTTTCGAACACTCCATGCTCGGGAAATCGCATCTTTTGGTCGAAATAGTTTGTCA
65 TTAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
** * * *
3579 TTTTGTTAACAAGTTTTGTTCTTTGAGTTAAAAACTTATTCACGTGAGAATTGTTTCTCTCTTTG
130 TTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
*
3644 TTCTTGGACGAACTTTTGAACT
195 TTCTTGGACGAACTTTCGAACT
* * * *
3666 TGGT-AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTAAACAAGATCCAGTCC
1 T-GTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCC
* * * * *
3730 TTAAAGCAATTTTCCTAACATTCCATGCGCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTAA
65 TTAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
* * *
3795 TTTTGCAAACAAGTATTGGTCTTTGCATTGAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
130 TTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
*
3860 TTCTTGGACGAACTTTCAAACT
195 TTCTTGGACGAACTTTCGAACT
* * *
3882 TGTCAAACTTTTACGAGTTATTTTTTAACTTTGGTTCCCTAAAGTATTCAACAAGATCCATTCCT
1 TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
*** * ** *
3947 TAGAG-AAAACTTCTGAACATTCCATGGTCGGGAAATCAAATCATTTGGTCT-AATAGTTTGTGA
66 TAGAGCAATTTTTC-GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
** * * * *
4010 TTTTTTAAACAAGTTTTGTTCTTTGAGTT-TAAACTTATTCACGTGAGAATTGTTTCTCTCTTTG
130 TTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
*
4074 TTCTTGGACGAACTTTCAAACT
195 TTCTTGGACGAACTTTCGAACT
4096 TGTCAAACTTTTACTAGTT
1 TGTCAAACTTTTACTAGTT
4115 CTTCTATAAC
Statistics
Matches: 3396, Mismatches: 466, Indels: 75
0.86 0.12 0.02
Matches are distributed among these distances:
214 196 0.06
215 1343 0.40
216 1675 0.49
217 182 0.05
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (216 bp):
TGTCAAACTTTTACTAGTTATTTTTTAACTTCGGATCCCTAAAGTATTCAACAAGATCCATTCCT
TAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
TCTTGGACGAACTTTCGAACT
Done.