Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006109.1 Kokia drynarioides strain JFW-HI SEQ_120618, 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: 1788
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Found at i:859 original size:216 final size:215
Alignment explanation
Indices: 479--1788 Score: 1250
Period size: 216 Copynumber: 6.1 Consensus size: 215
469 TCCTTTTGTA
* * * * * * * *
479 AAAAACTTATTTACGTGAGAATTATTTCCCTCTTGGATCTAGGCCAAACTTTCGAGCTT-T-ATA
1 AAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCA-A
* * * * *
542 CACTTTTTCGAATTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATAC-ATTTCTTCAA
65 -ACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAATGAT-CGATTCCTTCAG
* * * **
606 ACAATTTTTCGAACATTTCATTCTCAAGAAATCGCATCATTTGGTCCAAATAGCCAGTCATTTTG
128 ACAATTTTCCGAACATTCCATTCTC-GGAAATCGCATCATTTGGTCCAAATAGTTAGTCATTTTG
*
671 TAAACAACTTTGGGTCTTTGAATT
192 TAAACAACTTTCGGTCTTTGAATT
** * *
695 AAAATTTTATTTATATGAGAATTGTTTCTCTCTTAGTTCTTGGCCGAACTTCCGAACTTGTCAAA
1 AAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAA
760 CTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAATGATCGATTCCTTCATGA-
66 CTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAATGATCGATTCCTTCA-GAC
* *
824 AATTTTCCAAACATTCCATTCTCTGGAAATCGCATCATTTGGTCCAAATAGTTAGTCGTTTTGTA
130 AATTTTCCGAACATTCCATTCTC-GGAAATCGCATCATTTGGTCCAAATAGTTAGTCATTTTGTA
* * *
889 AAAAACTTTTGGTCTTTGAGTT
194 AACAACTTTCGGTCTTTGAATT
* * * * * *
911 AAAAACTTATTTACGTAAGAATTATTTCTCTTTTGGTTCTAGGCTGAACTTCCGAACTTGTCAAA
1 AAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAA
* * *
976 CTTTTTGGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACA-G-TCCATTTCTTC-GA
66 CTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA-A-ATGATCGATTCCTTCAG-
* *** * *
1038 ACAATTTTTCGAACATTTTGTTCTCGGAAAATCACATCATTTGATCCAAATA---A-TC----TG
128 ACAATTTTCCGAACATTCCATTCTCGG-AAATCGCATCATTTGGTCCAAATAGTTAGTCATTTTG
* *
1095 T-CACAACTTAT-GGTCTTTGGATT
192 TAAACAACTT-TCGGTCTTTGAATT
* * * * *
1118 AAAAATTTATTTTTGTGAGAATTGTTTCTCTCTTGTTTCTTGACCGAACTTCCTAACTTGTCAAA
1 AAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAA
* * * *
1183 CTTTTTCAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCATGACT-ATCGATTCCTTC-GAG
66 CTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCA-AAATGATCGATTCCTTCAGA-
* * * * * *
1246 CAAGTATCTGAACATTCCATGCTCGGTAAATCTCATCATTTGGTCCAAATAGTTTGTCATTTTGT
129 CAATTTTCCGAACATTCCATTCTCGG-AAATCGCATCATTTGGTCCAAATAGTTAGTCATTTTGT
** *
1311 AAACAACTTTTTGTCTTAGAATT
193 AAACAACTTTCGGTCTTTGAATT
* * * * * * *
1334 AAAAACTTATTTACGTGAGAATAGTTTTTCCCTTGGTTCTTGAG--TAAGCTTTCGAAATTGTCA
1 AAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTG-GCCGAA-CTTCCGAACTTGTCA
* * * ** *
1397 AACTTTTACAAGTTATTTTATAA-TTTCGGTTCCTTAAAGTA-TCAAAGACAATCCATTCCTTC-
64 AACTTTTTCGAGTTCTTTTATAACTTT-GGTTCCTTAAAGTATTCAAA-ATGATCGATTCCTTCA
* ** * * * *
1459 GAGCAATTTTCCAAACATTCCATGGTCGAGAAATCGCATCATTTGGTTCGAATATTTTA-TCTTT
127 GA-CAATTTTCCGAACATTCCATTCTCG-GAAATCGCATCATTTGGTCCAAATA-GTTAGTCATT
*
1523 TTGTAAACAACTTTCGGTTTTTGAATT
189 TTGTAAACAACTTTCGGTCTTTGAATT
* * * **
1550 AAAAACTTAATTATGTGATAATTGTTTCTCTCTTCGTTCTTCTCCGAACTTCCGAACTTGTCAAA
1 AAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAA
* * ** * * **
1615 TTTTTTTGAGTTCTTTTATAACTTCAGTTCCTTAAATTATTCAAAATGATAGATT-CTTTTGAGC
66 CTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAATGATCGATTCCTTCAGA-C
* * ** ** * * **
1679 AATTTTCCTAACATTTCAGCCTCAGGAAATCATACCATTTGGTCCAAATAGTTTGTCCCTTTGTA
130 AATTTTCCGAACATTCCATTCTC-GGAAATCGCATCATTTGGTCCAAATAGTTAGTCATTTTGTA
*
1744 AAAAACTTTCGGTCTTTGAATT
194 AACAACTTTCGGTCTTTGAATT
*
1766 AAAAACTTATTTATGTAAGAATT
1 AAAAACTTATTTATGTGAGAATT
Statistics
Matches: 892, Mismatches: 164, Indels: 76
0.79 0.14 0.07
Matches are distributed among these distances:
206 1 0.00
207 161 0.18
208 4 0.00
211 2 0.00
212 2 0.00
213 1 0.00
214 2 0.00
215 20 0.02
216 679 0.76
217 18 0.02
218 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (215 bp):
AAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAA
CTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAATGATCGATTCCTTCAGACA
ATTTTCCGAACATTCCATTCTCGGAAATCGCATCATTTGGTCCAAATAGTTAGTCATTTTGTAAA
CAACTTTCGGTCTTTGAATT
Found at i:1346 original size:639 final size:623
Alignment explanation
Indices: 9--1751 Score: 1824
Period size: 639 Copynumber: 2.8 Consensus size: 623
1 CATTCTCG
* * *
9 AGAAATTGCATCATTTGGTCCAAATAGTTAGTTC-CTTTGTAAAAAACTTTTGGTCTTTGAATTA
1 AGAAATCGCATCATTTGGTCCAAATAGTTAG-TCATTTTGTAAACAACTTTTGGTCTTTGAATTA
* * * * *
73 AAAACTTATTTACGTGAGAATTATTTCTCTTTTAGTTCTAGGCCAAACTTTCAAACTTTTCAAAC
65 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGCCAAACTTTCGAACTTGTCAAAC
* * * *
138 ATTTTCGAGTCCTTTTATAACTTTGGTTCCTTTAAGTATTCAATACGATCCATTTCC-TC-GAAC
130 TTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAACGATCCA-TTCCTTCAG-A-
* * * * * *
201 AATTTTTCAAATATTTCGTTCTCGAGAAATCGCATCATTTGATCCAAAGAATCT-GTCATTTTGT
192 AATTTTCCAAACATTCCATTCTCGAGAAATCGCATCATTTGGTCCAAATAAT-TAGTCATTTTGT
* *
265 AAACAACTTTTGGTCTTTG-GATTAAAAATTTATTTATATGAGAATTGTTT-TCTCTTGGTTCTT
256 AAACAACTTTTGGTCTTTGAG-TTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTT
* *
328 GGCCGAACTTCTGAACTTGTCAAATTTCTCGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTC
320 GGCCGAACTTCCGAACTTGTCAAATTTTTCGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTC
* * *
393 AAGACGATCGATTCTTTCAATCAATTTTCGGACATTCCTTTCTCAGGAAATCACATCATTTGGTC
385 AAGACGATCCATTCTTTCAATCAATTTTCGAACATTCCTTTCTCAGGAAATCACATCATTTGATC
* *
458 CAAATAGTTAGTCCTTTTGTAAAAAACTTATTTACGTGAGAATTATTTCCCTCTTGGATCTAGGC
450 CAAATAGTTAGTCCTTTGGTAAAAAACTTATTTACGTGAGAATTATTTCCCTCTTGGATCTAGAC
* * *
523 CAAACTTTCGAGCTTTATACACTTTTTCGAATTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
515 CAAACTTCCGAACTTTATACACTTTTTCGAATTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA
* * * * *
588 GACGATACATTTCTTCAAACAATTTTTCGAACATTTCATTCTCA
580 GACGATACATTCCTTCAAACAATATCTCGAACATTCCATGCTCA
** *
632 AGAAATCGCATCATTTGGTCCAAATAGCCAGTCATTTTGTAAACAACTTTGGGTCTTTGAATTAA
1 AGAAATCGCATCATTTGGTCCAAATAGTTAGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
** ** * *
697 AATTTTATTTATATGAGAATTGTTTCTCTCTTAGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
66 AAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGCCAAACTTTCGAACTTGTCAAACT
* *
762 TTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAATGATCGATTCCTTCATGAAAT
131 TTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAACGATCCATTCCTTCA-GAAAT
* *
827 TTTCCAAACATTCCATTCTCTG-GAAATCGCATCATTTGGTCCAAATAGTTAGTCGTTTTGTAAA
195 TTTCCAAACATTCCATTCTC-GAGAAATCGCATCATTTGGTCCAAATAATTAGTCATTTTGTAAA
* * * * * * *
891 AAACTTTTGGTCTTTGAGTTAAAAACTTATTTACGTAAGAATTATTTCTCTTTTGGTTCTAGGCT
259 CAACTTTTGGTCTTTGAGTTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCC
* **
956 GAACTTCCGAACTTGTCAAACTTTTTGGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAG
324 GAACTTCCGAACTTGTCAAA-TTTTTCGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTCAAG
*
1021 AC-AGTCCATT-TCTTCGAA-CAATTTTTCGAACATT-TTGTTCTC-GGAAAATCACATCATTTG
388 ACGA-TCCATTCT-TTC-AATCAA-TTTTCGAACATTCCT-TTCTCAGG-AAATCACATCATTTG
* * ** *
1081 ATCCAAATAATCTGTCACAACTTATGGT-CTTTGGATTAAAAATTTATTTTTGTGAGAATTGTTT
447 ATCCAAAT-A---G-------TTA--GTCCTTTGG-TAAAAAACTTATTTACGTGAGAATTATTT
* ** * * *
1145 CTCTCTTGTTTCTTGACCGAACTTCCTAACTTGTCA-A-ACTTTTTC-AAGTTCTTTTATAACTT
498 CCCTCTTGGATCTAGACCAAACTTCCGAACTT-T-ATACACTTTTTCGAA-TTCTTTTATAACTT
* * * *
1207 CGGTTCCTTAAAGTATTCATGACTAT-CGATTCCTTCGAGCAAGTATCT-GAACATTCCATGCTC
560 CGGTTCCTTAAAGTATTCAAGACGATAC-ATTCCTTCAAACAA-TATCTCGAACATTCCATGCTC
1270 -
623 A
* * * * *
1270 GGTAAATCTCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTAGAATTA
1 AG-AAATCGCATCATTTGGTCCAAATAGTTAGTCATTTTGTAAACAACTTTTGGTCTTTGAATTA
* * * * * * *
1335 AAAACTTATTTACGTGAGAATAGTTTTTCCCTTGGTTCTTGAG-TAAGCTTTCGAAATTGTCAAA
65 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTG-GCCAAACTTTCGAACTTGTCAAA
* * * *
1399 CTTTTACAAGTTATTTTATAA-TTTCGGTTCCTTAAAGTA-TCAAAGACAATCCATTCCTTCGAG
129 CTTTTTCGAGTTCTTTTATAACTTT-GGTTCCTTAAAGTATTCAAA-ACGATCCATTCCTTC-AG
* ** * * * *
1462 CAATTTTCCAAACATTCCATGGTCGAGAAATCGCATCATTTGGTTCGAATATTTTA-TCTTTTTG
191 AAATTTTCCAAACATTCCATTCTCGAGAAATCGCATCATTTGGTCCAAATA-ATTAGTCATTTTG
* * * * * *
1526 TAAACAACTTTCGGTTTTTGAATTAAAAACTTAATTATGTGATAATTGTTTCTCTCTTCGTTCTT
255 TAAACAACTTTTGGTCTTTGAGTTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTT
** * *
1591 CTCCGAACTTCCGAACTTGTCAAATTTTTTTGAGTTCTTTTATAACTTCAGTTCCTTAAATTATT
320 GGCCGAACTTCCGAACTTGTCAAA-TTTTTCGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATT
* * ** ** * * * *** * * *
1656 CAAAATGATAGATTCTTTTGAGCAATTTTCCTAACATTTCAGCCTCAGGAAATCATACCATTTGG
384 CAAGACGATCCATTCTTTCAATCAATTTT-CGAACATTCCTTTCTCAGGAAATCACATCATTTGA
*
1721 TCCAAATAGTTTGTCCCTTT-GTAAAAAACTT
448 TCCAAATAGTTAGT-CCTTTGGTAAAAAACTT
1752 TCGGTCTTTG
Statistics
Matches: 926, Mismatches: 145, Indels: 95
0.79 0.12 0.08
Matches are distributed among these distances:
622 7 0.01
623 251 0.27
624 38 0.04
625 57 0.06
626 50 0.05
627 2 0.00
628 6 0.01
630 1 0.00
635 1 0.00
637 3 0.00
638 24 0.03
639 471 0.51
640 14 0.02
641 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (623 bp):
AGAAATCGCATCATTTGGTCCAAATAGTTAGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
AAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGCCAAACTTTCGAACTTGTCAAACT
TTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAAACGATCCATTCCTTCAGAAATT
TTCCAAACATTCCATTCTCGAGAAATCGCATCATTTGGTCCAAATAATTAGTCATTTTGTAAACA
ACTTTTGGTCTTTGAGTTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGA
ACTTCCGAACTTGTCAAATTTTTCGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTCAAGACG
ATCCATTCTTTCAATCAATTTTCGAACATTCCTTTCTCAGGAAATCACATCATTTGATCCAAATA
GTTAGTCCTTTGGTAAAAAACTTATTTACGTGAGAATTATTTCCCTCTTGGATCTAGACCAAACT
TCCGAACTTTATACACTTTTTCGAATTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAT
ACATTCCTTCAAACAATATCTCGAACATTCCATGCTCA
Done.