Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003639.1 Kokia drynarioides strain JFW-HI SEQ_116537, 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, 709
Length: 1182
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Found at i:799 original size:220 final size:217
Alignment explanation
Indices: 101--1178 Score: 1064
Period size: 220 Copynumber: 4.9 Consensus size: 217
91 ATCCACTTCA
* * * * * * *
101 TCGAGCAAT-TTTCGAACATTCCATTCTCCGGAAA-CTGAATCTTTTGGTTTAAATAGTTTGTCA
1 TCGAGCAATATTCCGAACATTCCATGCTCGGGAAATC-GCATCATTCGGTCTAAATAGTTTGTCA
* * * * ** * *
164 TTTTGTAAACAAC-TTTTGGTCTTTGAATTAAAAACTTATTTATGTGAAAATT-TCACTCTCTTG
65 TTTTGCAAACAACTTTTTAGTCCTTGAATTAAAAACTTATTTATGTGAGAATTATTTCTCTTTTC
* * * * * * *
227 GTTCTTGGACGAACTACCGAACTAGTAAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAA
130 ATTCTTAGACAAACTTCTGAACTAGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAA
* * ** *
292 AGTATTCAAGACCATCCGTTTCT
195 ACTATTCAAGACGATCCAATCCT
* * * * * * * * *
315 ACGAGCAATTTTCCAAACATTCCATGCTCGAGAAATTGAACCTTTTGGTCTAAATAGTTTGTCAT
1 TCGAGCAATATTCCGAACATTCCATGCTCGGGAAATCGCATCATTCGGTCTAAATAGTTTGTCAT
* * * * * * * *
380 TTTGAAAACTAAGTTTTT-GT-CTTCAAACTAAAAACTTATTTACGTGACAATTGTTTCTCCTTT
66 TTTGCAAAC-AACTTTTTAGTCCTT-GAATTAAAAACTTATTTATGTGAGAATTATTTCTCTTTT
** * * *
443 GGTTCTTAGACGAACTTCTGAACTAGTCAAGCTTTTTACGAGTCCTTTTATAACTTTGGTTCCTT
129 CATTCTTAGACAAACTTCTGAACTAGTCAAGC-TTTTACGAGTTCTTTTATAACTTCGGTTCCTT
** * * *
508 GGAGTATTAAAGACGATCCATTCCT
193 AAACTATTCAAGACGATCCAATCCT
* * * *
533 TCAATCAATATTCCGAACATTCCGTGCTCGGGAAATAGCATCATTCGGTCTAAATAGTTTGTCAT
1 TCGAGCAATATTCCGAACATTCCATGCTCGGGAAATCGCATCATTCGGTCTAAATAGTTTGTCAT
598 TTTGCAAACAACTTTTTAGTCCTTGAATTAAAAA-TATATTTATGTGAGAATTATTTCTCTTTTC
66 TTTGCAAACAACTTTTTAGTCCTTGAATTAAAAACT-TATTTATGTGAGAATTATTTCTCTTTTC
* * *
662 ATTCTTAGACAAACTTCTGAACTTGTCAAGCTTTTACTATTTCTTCTGTAATAACTTCGGTTCCT
130 ATTCTTAGACAAACTTCTGAACTAGTCAAGCTTTTACGAGTTCTT-T-T-ATAACTTCGGTTCCT
*
727 TAAACTATTCAAGATGATCCAATCCT
192 TAAACTATTCAAGACGATCCAATCCT
753 TCGAGCAATATTCCGAACATTCCATGCTCGGGAAATCGCATCATTCGGTCTAAATAGTTTGTCAT
1 TCGAGCAATATTCCGAACATTCCATGCTCGGGAAATCGCATCATTCGGTCTAAATAGTTTGTCAT
818 TTTGCAAACAACTTTTTAGTCCTTGAATTAAAAA-TATATTTATGTGAGAATTATTTCTCTTTTC
66 TTTGCAAACAACTTTTTAGTCCTTGAATTAAAAACT-TATTTATGTGAGAATTATTTCTCTTTTC
* * * *
882 ATTCTTAGACAAACTTCTGAACTTGTCAAGCTTTTACTATTTCTTCTGTAATAACTTCAGTTCCT
130 ATTCTTAGACAAACTTCTGAACTAGTCAAGCTTTTACGAGTTCTT-T-T-ATAACTTCGGTTCCT
* * *
947 TAAACTATTCAATATGATCTAATCCT
192 TAAACTATTCAAGACGATCCAATCCT
* * * * *
973 TCGAGCAATATTTCGAATATTCCATGCTCGGGAAATCGCATCATTCGGTCAAAATATTTTGCCAT
1 TCGAGCAATATTCCGAACATTCCATGCTCGGGAAATCGCATCATTCGGTCTAAATAGTTTGTCA-
** * * * * **
1038 TTCTTAAAAAAAAC-TTTTGGTCAC-TGAATTAAATACTTATTTATGTGTA-AATTGTTTCTCCC
65 TT-TTGCAAACAACTTTTTAGTC-CTTGAATTAAAAACTTATTTATGTG-AGAATTATTTCTCTT
** * * * ** * * *
1100 TTGGTTCTTGGACGAACTTTTGAACTAGGAAAACTTTTACTATTTCTGTTT-TAACTTCGGTTCC
127 TTCATTCTTAGACAAACTTCTGAACTAGTCAAGCTTTTACGAGTTCT-TTTATAACTTCGGTTCC
** *
1164 ACAAAGTATTCAAGA
191 TTAAACTATTCAAGA
1179 TGAT
Statistics
Matches: 744, Mismatches: 101, Indels: 34
0.85 0.11 0.04
Matches are distributed among these distances:
214 8 0.01
215 56 0.08
216 28 0.04
217 56 0.08
218 195 0.26
219 4 0.01
220 307 0.41
221 78 0.10
222 12 0.02
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (217 bp):
TCGAGCAATATTCCGAACATTCCATGCTCGGGAAATCGCATCATTCGGTCTAAATAGTTTGTCAT
TTTGCAAACAACTTTTTAGTCCTTGAATTAAAAACTTATTTATGTGAGAATTATTTCTCTTTTCA
TTCTTAGACAAACTTCTGAACTAGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAA
CTATTCAAGACGATCCAATCCT
Found at i:1179 original size:438 final size:430
Alignment explanation
Indices: 151--1182 Score: 1111
Period size: 438 Copynumber: 2.4 Consensus size: 430
141 CTTTTGGTTT
* ** * *
151 AAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAAAATT
1 AAATAGTTTGCCATTTTAAAAAAAACTTTTGGTC-CTGAATT-AAAACTTATTTATGTG-AAATT
** * * * *
216 TCACTCTCTTGGTTCTTGGACGAACTACCGAACTAGTAAAACTTTTACGAGTTCTTTTATAACTT
63 TTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTAGTAAAACTTTTACTATTTCTTTTATAACTT
** ** * *
281 CGGTTCCTTAAAGTATTCAAGACCATCCGTTTCTACGAGCAATTTTCCAAACATTCCATGCTCGA
128 CGGTTCCTTAAAGTATTCAAGATGATCCAATCCTACGAGCAATATTCCAAACATTCCATGCTCGA
* * * *
346 GAAATTGAACCTTTTGGTCTAAATAGTTTGTCATTTTGAAAACTAAGTTTTTGTCTTCAAACTAA
193 GAAATCGAACCATTCGGTCTAAATAGTTTGTCATTTTGAAAACTAACTTTTTGTCTTCAAACTAA
* ** *
411 AAACTTATTTACGTGACAATTGTTTCTCCTTTGGTTCTTAGACGAACTTCTGAACTAGTCAAGCT
258 AAACTTATTTACGTGACAATTATTTCTCCTTTCATTCTTAGACAAACTTCTGAACTAGTCAAGCT
** ** * * *
476 TTTTACGAGTCCTTTTATAACTTTGGTTCCTTGGAGTATTAAAGACGATCCATTCCTTCAATCAA
323 TTTTACGAGTCCTTTTATAACTTCAGTTCCTTAAACTATTAAAGACGATCCAATCCTTCAAGCAA
* *
541 TATTCCGAACATTCCGTGCTCGGGAAATAGCATCATTCGGTCT
388 TATTCCGAACATTCCATGCTCGGGAAATAGCATCATTCGGTCA
* ** * * *
584 AAATAGTTTGTCATTTTGCAAACAACTTTTTAGTCCTTGAATTAAAAATATATTTATGTGAGAAT
1 AAATAGTTTGCCATTTTAAAAAAAAC-TTTTGGTCC-TGAATTAAAACT-TATTTATGTGA-AAT
* ** * * * * *
649 TATTTCTCTTTTCATTCTTAGACAAACTTCTGAACTTGTCAAGCTTTTACTATTTCTTCTGTAAT
62 T-TTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTAGTAAAACTTTTACTATTTCTT-T-T-AT
* * *
714 AACTTCGGTTCCTTAAACTATTCAAGATGATCCAATCCTTCGAGCAATATTCCGAACATTCCATG
123 AACTTCGGTTCCTTAAAGTATTCAAGATGATCCAATCCTACGAGCAATATTCCAAACATTCCATG
* * * *
779 CTCGGGAAATCGCATCATTCGGTCTAAATAGTTTGTCATTTTGCAAAC-AACTTTTTAGTCCTT-
188 CTCGAGAAATCGAACCATTCGGTCTAAATAGTTTGTCATTTTGAAAACTAACTTTTT-GT-CTTC
* * * * * *
842 GAATTAAAAA-TATATTTATGTGAGAATTATTTCTCTTTTCATTCTTAGACAAACTTCTGAACTT
251 AAACTAAAAACT-TATTTACGTGACAATTATTTCTCCTTTCATTCTTAGACAAACTTCTGAACTA
* * * * * * *
906 GTCAAGC-TTTTACTATTTCTTCTGTAATAACTTCAGTTCCTTAAACTATTCAATATGATCTAAT
315 GTCAAGCTTTTTACGAGTCCTT-T-T-ATAACTTCAGTTCCTTAAACTATTAAAGACGATCCAAT
* * * *
970 CCTTCGAGCAATATTTCGAATATTCCATGCTCGGGAAATCGCATCATTCGGTCA
377 CCTTCAAGCAATATTCCGAACATTCCATGCTCGGGAAATAGCATCATTCGGTCA
*
1024 AAATATTTTGCCATTTCTTAAAAAAAACTTTTGGTCACTGAATTAAATACTTATTTATGTGTAAA
1 AAATAGTTTGCCA-TT-TTAAAAAAAACTTTTGGTC-CTGAATTAAA-ACTTATTTATGTG-AAA
* * *
1089 TTGTTTCTCCCTTGGTTCTTGGACGAACTTTTGAACTAGGAAAACTTTTACTATTTCTGTTT-TA
61 TT-TTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTAGTAAAACTTTTACTATTTCT-TTTATA
**
1153 ACTTCGGTTCCACAAAGTATTCAAGATGAT
124 ACTTCGGTTCCTTAAAGTATTCAAGATGAT
Statistics
Matches: 492, Mismatches: 87, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
433 31 0.06
434 27 0.05
435 42 0.09
436 1 0.00
437 20 0.04
438 190 0.39
439 4 0.01
440 87 0.18
441 77 0.16
442 13 0.03
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (430 bp):
AAATAGTTTGCCATTTTAAAAAAAACTTTTGGTCCTGAATTAAAACTTATTTATGTGAAATTTTT
CTCTCTTGGTTCTTGGACGAACTTCTGAACTAGTAAAACTTTTACTATTTCTTTTATAACTTCGG
TTCCTTAAAGTATTCAAGATGATCCAATCCTACGAGCAATATTCCAAACATTCCATGCTCGAGAA
ATCGAACCATTCGGTCTAAATAGTTTGTCATTTTGAAAACTAACTTTTTGTCTTCAAACTAAAAA
CTTATTTACGTGACAATTATTTCTCCTTTCATTCTTAGACAAACTTCTGAACTAGTCAAGCTTTT
TACGAGTCCTTTTATAACTTCAGTTCCTTAAACTATTAAAGACGATCCAATCCTTCAAGCAATAT
TCCGAACATTCCATGCTCGGGAAATAGCATCATTCGGTCA
Done.