Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012743.1 Kokia drynarioides strain JFW-HI SEQ_127754, 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: 4156
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Found at i:379 original size:216 final size:216
Alignment explanation
Indices: 2--4156 Score: 4090
Period size: 216 Copynumber: 19.3 Consensus size: 216
1 A
* *
2 TTGAATTAAATACTTATTTATGTGTA-AATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAAC
1 TTGAATTAAAAACTTATTTACGTG-AGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAAC
* ** * * * *
66 TAGGAAAACTTTTACTA-TTAC-TGTAGTAACTTCGGTTCCTCAAAGTATTCAAGATGATCCATT
65 TTGTCAAACTTTTACGAGTT-CTTTTA-TAACTTTGGTTCCTTAAAGTATTCAAGATGATCCA-T
* * * * *
129 TCTTT-GAGCAATTTTGCGAACATTCCATGCTCGAGAAATTGCATCACTTGGTTTAAATAGTTTG
127 TCTTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
*
193 TCATTTTGTAAACAACTTTTTGTCT
192 TCATTTTGTAAACAACTTTTGGTCT
* * * *
218 TTAAATTAAAAACTTATTTATGTGAGAATCGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * * * * *
283 TTTCAAGCTTTCAAGAATTCTTTTTTAACTTTGGTTCCTTAAAGTATTCAAGATGATCGATTATT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCTT
* * * * *
348 TCAAGCAATATTCCAAACATTCCATGCTCGAGAAATTGTATCATTTGGTCTAAATATTTTGTCAT
131 TCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
413 TTTGTAAACAACTTTTGGTCT
196 TTTGTAAACAACTTTTGGTCT
* * * * * **
434 TTGAATTAAAAACCTATTTACGAGAGAATTGTTTCTCTCCTAGTTCTTGGATGAACTTAGGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * *
499 TGTCAAACTTTTACTAGTTCTTTTATAACTTAGGTTCCTTAAAGCATTC-TG-TGCGATCCATTC
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGAT--GATCCATTC
* * * * * * * * * *
562 CTTCTA-CAAATTTTTCGAACATTCAATGTTCAAAAAATCGCATCATTTGATCTAAATACTTTGT
129 TTTCGAGC-AATTTTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGT
*
626 CATTTTGTAAACAACTTTCGGTCT
193 CATTTTGTAAACAACTTTTGGTCT
* * * * * *
650 TTGAATAAAAAACTTATTGACGTGGGATTTGTTTCTCTCTTGGTTCTTGGACGAACCTCCGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * *
715 TGTCAAACTTTTACAAGTTCAATTTAAAACTTCT-GTTCCTTGAAGTATT-ATAAATGATCCACT
66 TGTCAAACTTTTACGAGTTC-TTTTATAACTT-TGGTTCCTTAAAGTATTCA-AGATGATCCA-T
* ** * * * *
778 TCATT-GAGCAATTTT-TGAACATTCCATTCTCCGA-AAATCGAATCTTTTGGTTTAAATAGTTT
127 TCTTTCGAGCAATTTTCCAAACATTCCATGCT-CGAGAAATCGCATCATTTGGTCTAAATAGTTT
* * * *
840 GACGTTCTGTAAACAACTTTTGCTCT
191 GTCATTTTGTAAACAACTTTTGGTCT
* * *
866 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTTTCTCTTAGTTCTTAGACGAACTTCTGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * * *
931 TTTCAAGCTTTTATGAGTTCTTTTATAACTTTCGTTCCTTAAAGTATTCAAGACGATCCATTTTT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCTT
* * * *
996 TCGAGC-ATTATTCCAAACATTCCATG-TCGGGAAATCGCATCATTCGGCCTAAATATTTTGTCA
131 TCGAGCAATT-TTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
1059 TTTTGTAAACAACTTTTGGTCT
195 TTTTGTAAACAACTTTTGGTCT
* * * * * * * * *
1081 TTAAATTAAAAACTTAATGACGTGGGAATTGTCTCTCCCTTAGTTATTGGATGAACTT-TCGAAC
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCT-GAAC
* * * * *
1145 TAGTCTAACTTTTATGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCTATG-TGATCCATTC
65 TTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC-AAGATGATCCATT-
* * ** * * * * **
1209 CTTCTAGAG-ATTTTTTTAGAACATTGCATGTTCGAAAAATTGCATCATTTTATCTAAATAGTTT
128 CTT-TCGAGCAATTTTCCA-AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTT
* *
1273 GTCATTTTGTCAACAACTATTGGTCT
191 GTCATTTTGTAAACAACTTTTGGTCT
* * * * * * * *
1299 TTGAATTAAAATCATATTTATGTGAG-ATTATTTCTCTCTTGATTCTTAGACAAACTTCTAAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * * * *
1363 TGTCAAGCTTTTACTATTTCTTTTATAACTTTAGTTCTTTAAGGTATTCAAGATGATCCATTCCT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCTT
* * * * * ** *
1428 TCAAGCAATATTCCGAATATTCCATGCTTGAGAAATCGCATCATTCAGTCAAAATTA-TTTGTCA
131 TCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAA-TAGTTTGTCA
*
1492 TTTTGTAAACAACTTTTGGTCA
195 TTTTGTAAACAACTTTTGGTCT
* * *
1514 TTGAATTAAATACTTATTTATGTGTA-AATTGTTTCTCTCTTGGTTTTTGGACGAACTT-TCGAA
1 TTGAATTAAAAACTTATTTACGTG-AGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCT-GAA
** * * * *
1577 CTTGGAAAACTTTTACTATTTCTATTATAACTTTGG-TCCATTAAAGTATTCAAGATGATCTATT
64 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCC-TTAAAGTATTCAAGATGATCCA-T
* * * **
1641 TCTTT-GAGCAATTTTGCGAACATTCCATGCTCAAGAAATTACATCATTTGGTCTAAATAGTTTG
127 TCTTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
* ** *
1705 GCATTTTACAAACATCTTTTGGTCT
192 TCATTTTGTAAACAACTTTTGGTCT
* * * * **
1730 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTAGTCAAACTTCTTTACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * *
1795 TTTCAAGCTTTTACGA-TTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCTT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCTT
* * * *
1859 TCGAGCTATGTTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTTGTCAT
131 TCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
**
1924 TTTGTAAACAACTTTTATTCT
196 TTTGTAAACAACTTTTGGTCT
* * * * *
1945 TTGAATTAAAAACTTATTTACATGATAATTGTTTCTCTCTTAGTTCTTGCATGAACTTCTGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * *
2010 TGTCAAACTTTTATC-AGTTCTTTTATAACTTAGGTTCCTTAAAGCATTCTATG-GGATCAATTC
66 TGTCAAACTTTTA-CGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC-AAGATGATCCATTC
* * *** * * * * *
2073 CTTCTA-CAAATTTTTGGAACATTCAATGTTCG-GAAAATCGCATCATTTGATTTAAATACTTTG
129 TTTCGAGC-AATTTTCCAAACATTCCATGCTCGAG-AAATCGCATCATTTGGTCTAAATAGTTTG
* * *
2136 TCATTATGTAAACAACATTCGGTCT
192 TCATTTTGTAAACAACTTTTGGTCT
* * * * * *
2161 TTGAATTAAAAACTTATTGACGTGGGATTTGTTTCTCTCTTGGTTCTTGGATGAACCTCCGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * * * *
2226 TGTCAAACTTTTACAAGTTCTTTAAAAACTTCT-GTTCCCTGAAGTATT-ATAAAAGATCCACTT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTT-TGGTTCCTTAAAGTATTCA-AGATGATCCA-TT
* * * * * *
2289 C-ATCGAGCAATTTTCGAAA-ATTCCATTCTCCGA-AAATCGAATCTTTTGGTTTAAATAGTTTG
128 CTTTCGAGCAATTTTCCAAACATTCCATGCT-CGAGAAATCGCATCATTTGGTCTAAATAGTTTG
*
2351 TCATTTTATAAACAACTTTTGGTCT
192 TCATTTTGTAAACAACTTTTGGTCT
* * * *
2376 TTGAATT-AAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCCTAGACAAACTTCTGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * *
2440 TTTCAAGCTTTTACGAGTTCTTTTATAACTTTCGTTCCTTAAAGTATTCAAGACGATCCATTTTT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCTT
* * * *
2505 TCGAGC-ATTATTCCAAACATTCCATG-TCGGGAAATCGCATCATTCGGCCTAAATATTTTGTCA
131 TCGAGCAATT-TTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
2568 TTTTGTAAACAACTTTTGGTCT
195 TTTTGTAAACAACTTTTGGTCT
* * * * * * * * *
2590 TTAAATTAAAAACTTAATGACGTGGGAATTGTCTCTCCCTTAGTTATTGGATGAACTT-TCGAAC
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCT-GAAC
** * * * *
2654 CAGTCTAACTTTTATGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCTATG-TGATCCATTC
65 TTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC-AAGATGATCCATT-
* * ** * * * * * **
2718 CTTCTAGAG-ATTTTTTTAGAACGTTGCATGTTCGAAAAATTGCATCATTTTATCTAAATAGTTT
128 CTT-TCGAGCAATTTTCCA-AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTT
* *
2782 GTCATTTTGTCAACAACTATTGGTCT
191 GTCATTTTGTAAACAACTTTTGGTCT
* * * * * * * *
2808 TTGAATTAAAATCATATTTATGTGAG-ATTATTTCTCTCTTGATTCTTAGACAAACTTCTAAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * * * *
2872 TGTCAAGCTTTTACTATTTCTTTTATAACTTTAGTTCTTTAAGGTATTCAAGATGATCCATTCCT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCTT
* * * * * ** *
2937 TCAAGCAATATTCCGAATATTCCATGCTTGAGAAATCGCATCATTCAGTCAAAATTA-TTTGTCA
131 TCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAA-TAGTTTGTCA
*
3001 TTTTGTAAACAACTTTTGGTCA
195 TTTTGTAAACAACTTTTGGTCT
* * *
3023 TTGAATTAAATACTTATTTATGTGTA-AATTGTTTCTCTCTTGGTTTTTGGACGAACTT-TCGAA
1 TTGAATTAAAAACTTATTTACGTG-AGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCT-GAA
** * * * *
3086 CTTGGAAAACTTTTACTATTTCTATTATAACTTTGG-TCCATTAAAGTATTCAAGATGATCTATT
64 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCC-TTAAAGTATTCAAGATGATCCA-T
* * **
3150 TCTTT-GAGCAATTTTGCGAACATTCCATGCTCGAGAAATTACATCATTTGGTCTAAATAGTTTG
127 TCTTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
* ** *
3214 GCATTTTACAAACATCTTTTGGTCT
192 TCATTTTGTAAACAACTTTTGGTCT
* * * * ***
3239 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGATTCTTAGTCAAACTTCTTTTCT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * *
3304 TTTCAAGCTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCTT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCTT
* * * *
3369 TCGAGCTATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTTGTCAT
131 TCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
**
3434 TTTGTAAACAACTTTTATTCT
196 TTTGTAAACAACTTTTGGTCT
* * * *
3455 TTGAATTAAAAACTTATTTACATGATAATTGTTTCTCTCTTAGTTCTTGGATGAACTTCTGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * *
3520 TGTCAAACTTTTATC-AGTTCTTTTATAACTTAGGTTCCTTAAAGCATTCTATG-GGATCAATTC
66 TGTCAAACTTTTA-CGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC-AAGATGATCCATT-
* *** * * * *
3583 CTTT-TA-CAAATTTTTGGAACATTCAATGTTCG-GAAAATCGCATCATTTGATCTAAATACTTT
128 CTTTCGAGC-AATTTTCCAAACATTCCATGCTCGAG-AAATCGCATCATTTGGTCTAAATAGTTT
* * *
3645 GTCATTATGTAAACAACATTCGGTCT
191 GTCATTTTGTAAACAACTTTTGGTCT
* * * * * *
3671 TTGAATTAAAAACTTATTGACGTGGGATTTGTTTCTCTCTTGGTTCTTGGATGAACCTCCGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * * *
3736 TGTCAAACTTTTACAAGTTCTTTTAAAACTTCT-GTTCCCTGAAGTATT-ATAAAAGATCCACTT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTT-TGGTTCCTTAAAGTATTCA-AGATGATCCA-TT
* * * * * *
3799 C-ATCGAGCAATTTTCGAAA-ATTCCATTCTCCGA-AAATCGAATCTTTTGGTTTAAATAGTTTG
128 CTTTCGAGCAATTTTCCAAACATTCCATGCT-CGAGAAATCGCATCATTTGGTCTAAATAGTTTG
*
3861 TCATTTTATAAACAACTTTTGGTCT
192 TCATTTTGTAAACAACTTTTGGTCT
* * * * *
3886 TTGAATT-AAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCCTAGACAAACTTTTGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
* * * * *
3950 TTTCAAGCTTTTACGAGTTCTTTTATAACTTTCGTTCCTTAAAGTATTCAAGACGATCCATTTTT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCTT
* * *
4015 TCGAGC-ATTATTCCTAACATTCCATG-TCGGGAAATCGCATCATTCGGTCTAAATA-TTCTGTC
131 TCGAGCAATT-TTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTT-TGTC
4077 ATTTTGTAAACAACTTTTGGTCT
194 ATTTTGTAAACAACTTTTGGTCT
* * * * *
4100 TTGAATTAAAAACTTAATGACGTGGGAATTGTTTCTCTCTTAGTTCTTGGATGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACT
Statistics
Matches: 3188, Mismatches: 646, Indels: 211
0.79 0.16 0.05
Matches are distributed among these distances:
213 18 0.01
214 340 0.11
215 816 0.26
216 1619 0.51
217 250 0.08
218 144 0.05
219 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (216 bp):
TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACT
TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCTT
TCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
TTTGTAAACAACTTTTGGTCT
Done.