Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011233.1 Kokia drynarioides strain JFW-HI SEQ_126211, 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: 2867
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.38
Warning! 146 characters in sequence are not A, C, G, or T
Found at i:1682 original size:243 final size:243
Alignment explanation
Indices: 1228--1865 Score: 754
Period size: 245 Copynumber: 2.6 Consensus size: 243
1218 ATCATAATTG
* * * * * * * *
1228 ACCTTTATATATCCTCTCCTCTCACTCAGATAAACTTAATTTTTCTGCCATTCAAACTTATATCT
1 ACCTGTATATATTCTCTCTTCTCACTTAGAT-AACTTAATTCTTCTCCCATTCAAATTTATTTCT
* * * * * *
1293 TCTCTTAT-TTAATTTCATCATCTTTTACAATTAGTTAGTTCATGCTAAGATGATGAAAGGAAAA
65 TCTCTTCTCTT-ATTTCTTCATCTTTTTCTATTTGTTAGTTCATGTTAAGATGATGAAAGGAAAA
* ***
1357 CGAAAAGTGAGTAATGAGGTTACTGGTTAACCTTCAGATAAACCTTTATATATATATAGACATAA
129 GGAAAAGTGAGTAATGAGGTTACTGCCAAACCTTCAGATAAACCTTTATATATATATAGACATAA
*
1422 TCTTAGC-ATTATATATATTTATATTTGC-CATTACTCAATGTCAAAATGA
194 TCTTAGCAATTATATATATTTATATTTGCTC-TTACTCAATGTCAAAATAA
1471 ACCTGTATATATTCTCTCTTAC-CACTTAGATGAACTTAATTCTTCTCCCATTCAAATTTATTTC
1 ACCTGTATATATTCTCTCTT-CTCACTTAGAT-AACTTAATTCTTCTCCCATTCAAATTTATTTC
* * * *
1535 TTCCCTTCTCTTATTTCTTCATCTTTTTCTCTTTGTTAGTTTATGTTAAGATGATTAAAGGAAAA
64 TTCTCTTCTCTTATTTCTTCATCTTTTTCTATTTGTTAGTTCATGTTAAGATGATGAAAGGAAAA
* * * * * * * *
1600 GGAGAAGTGGGTAATGATGTTGCTGCCAAACTTTTAGATAAACCTTTATATATATATATA-TTGG
129 GGAAAAGTGAGTAATGAGGTTACTGCCAAACCTTCAGATAAACCTTTATATATATATAGACAT--
*
1664 CAATCTTA-CAATTATATATATTTATATTTGCTCTTACTCAATGTTAAAATAA
192 -AATCTTAGCAATTATATATATTTATATTTGCTCTTACTCAATGTCAAAATAA
*
1716 ACCTGTATATATTCTCTGTTCTCA-TTCAGATAAGCTTAATTCTTCTCCCATTCAAACTTT-TTT
1 ACCTGTATATATTCTCTCTTCTCACTT-AGATAA-CTTAATTCTTCTCCCATTCAAA-TTTATTT
* * * * *
1779 CTTCTCTTCTCTCATTTCTTCATCTTTTTCTTTTTGTTAGTTGATGTTAATATGATGAAAGAAAA
63 CTTCTCTTCTCTTATTTCTTCATCTTTTTCTATTTGTTAGTTCATGTTAAGATGATGAAAGGAAA
*
1844 AGAAAAAGTGAGTGAA-GAGGTT
128 AGGAAAAGTGAGT-AATGAGGTT
1866 GCTACAAAGC
Statistics
Matches: 338, Mismatches: 45, Indels: 22
0.83 0.11 0.05
Matches are distributed among these distances:
242 1 0.00
243 154 0.46
244 9 0.03
245 168 0.50
246 6 0.02
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (243 bp):
ACCTGTATATATTCTCTCTTCTCACTTAGATAACTTAATTCTTCTCCCATTCAAATTTATTTCTT
CTCTTCTCTTATTTCTTCATCTTTTTCTATTTGTTAGTTCATGTTAAGATGATGAAAGGAAAAGG
AAAAGTGAGTAATGAGGTTACTGCCAAACCTTCAGATAAACCTTTATATATATATAGACATAATC
TTAGCAATTATATATATTTATATTTGCTCTTACTCAATGTCAAAATAA
Found at i:2643 original size:256 final size:247
Alignment explanation
Indices: 2077--2740 Score: 780
Period size: 256 Copynumber: 2.7 Consensus size: 247
2067 ATCATAATTG
* * * * * *
2077 ACCTTTATATATCCTCTCCTCTCACTCAGATGAACTTAATTTTTCTGCCATTCAAACTTA----T
1 ACCTATATATATTCTCTCATCTCACTCAGATAAACTTAATTCTTCTCCCATTCAAACTTATTTCT
* ** * * * *
2138 TTCTTCTCTTATCTCATTTCTTCATCTTTTTCAATTAGTTAGTTGATGTTAAGATGATGAAAAGA
66 TTCTTCTCTTCTCTCATTTCTTCATCTTTTTCTCTTTGTTAGTTGATGTTAAAATGATTAAAGGA
* * *
2203 AAACGAAAAGTGTGTAAAGAGGTTCCTAGCTAACCTTTAGATAAACCTTTATATATATATTGACA
131 AAACGAAAAGTGAGTAAAGAGGTTCCTAGCAAACCTTCAGATAAACCTTTATATATATATTGACA
* * * * *
2268 TCATCTTAGCATTATATATATTTATATTTGCCATTACTTAATGTCAAAATGA
196 ACATCTTAGCATTATACATATTTATATTTGCCATTACTGAATGCCAAAACGA
* *
2320 ACCTGTATATATTCTCTCTTCTCACTCAGATAAACTTAATTCTTCTCCCATTCAAACTTATTTCT
1 ACCTATATATATTCTCTCATCTCACTCAGATAAACTTAATTCTTCTCCCATTCAAACTTATTTCT
* *
2385 TCTCTTCTCTTCTCTCATTTCTTCAACTTTTTCTCTTTGTTAGTTTATGTTAAAATGATTAAAGG
66 T-TCTTCTCTTCTCTCATTTCTTCATCTTTTTCTCTTTGTTAGTTGATGTTAAAATGATTAAAGG
* * *
2450 AAAACGAAAAGTGAGTAATGAGGTTGCT-GCCAAACCTTCAGTTAAACCTTTATATATATGTATA
130 AAAACGAAAAGTGAGTAAAGAGGTTCCTAG-CAAACCTTCAGATAAACC-TT-TATATA--TATA
*
2514 TAGACTGACAACATCTTAG-ATTTATACATATTGTCAT-TTT-CCTTTACTGAATGCCAAAACGA
190 T----TGACAACATCTTAGCA-TTATACATATT-T-ATATTTGCCATTACTGAATGCCAAAACGA
* *
2576 ACCTATATATATTCTCTCATCTCACTCAGATAAACATAATTCTTCTCCCATTAAAACTTATTTC-
1 ACCTATATATATTCTCTCATCTCACTCAGATAAACTTAATTCTTCTCCCATTCAAACTTATTTCT
**
2640 TTC-T-T-TTCTCTCATTTCTTCATCCCTTTCTCTTTGTTAGTTGATGTTAAAATGATTAAAGGA
66 TTCTTCTCTTCTCTCATTTCTTCATCTTTTTCTCTTTGTTAGTTGATGTTAAAATGATTAAAGGA
* *
2702 AAA-GAAAAAGTGAGTAAAGAGGCTACTA-CAAAGCCTTCA
131 AAACG-AAAAGTGAGTAAAGAGGTTCCTAGCAAA-CCTTCA
2741 ATTGTCTCCA
Statistics
Matches: 363, Mismatches: 38, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
243 54 0.15
247 3 0.01
248 94 0.26
249 2 0.01
250 11 0.03
251 81 0.22
252 6 0.02
253 1 0.00
254 2 0.01
255 2 0.01
256 101 0.28
257 4 0.01
258 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (247 bp):
ACCTATATATATTCTCTCATCTCACTCAGATAAACTTAATTCTTCTCCCATTCAAACTTATTTCT
TTCTTCTCTTCTCTCATTTCTTCATCTTTTTCTCTTTGTTAGTTGATGTTAAAATGATTAAAGGA
AAACGAAAAGTGAGTAAAGAGGTTCCTAGCAAACCTTCAGATAAACCTTTATATATATATTGACA
ACATCTTAGCATTATACATATTTATATTTGCCATTACTGAATGCCAAAACGA
Done.