Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001625.1 Kokia drynarioides strain JFW-HI SEQ_113261, 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: 5235
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1248 original size:346 final size:345
Alignment explanation
Indices: 616--1306 Score: 1337
Period size: 346 Copynumber: 2.0 Consensus size: 345
606 TTTAAAAAAT
616 AACAAGCATTTCTTTTTATTTGAAATCTCACATTTTTATTTTTTATTTTTAAAAAGAAGAATATT
1 AACAAGCATTTCTTTTTATTTGAAATCTCACATTTTTATTTTTTATTTTTAAAAAGAAGAATATT
*
681 CGATTATTTTGATTCAAAGAAAAACCGCACCTAATAAATAAAGGCACAATTTTTCAAATCACGAA
66 CGATTATTTCGATTCAAAGAAAAACCGCACCTAATAAATAAAGGCACAATTTTTCAAATCACGAA
*
746 ATAATAAACATTGCCTTAATTTTAAAATTATTTATTTTTATCAAAACAAATATATTTTTTAAGGA
131 ATAATAAACATTGCCTCAATTTTAAAATTATTTATTTTTATCAAAACAAATATATTTTTTAAGGA
811 ATGAATTTGAGTGAACATAATATACAATTATAATGATAAAACACAACATGGCATAAATACATAAT
196 ATGAATTTGAGTGAACATAATATACAATTATAATGATAAAACACAACATGGCATAAATACATAAT
876 GACAAGTGTGTACATGATGAAAATAAACAATAATACATACACATTTAATATATGAAACAAATAAA
261 GACAAGTGTGTACATGATGAAAATAAACAATAATACATACACATTTAATATATGAAACAAATAAA
941 AAGATAATAATAAATGAAGA
326 AAGATAATAATAAATGAAGA
*
961 AACAAGCATTTCTTTTTATTTGAAATCTCACGTTTTTATTTTTTATTTTTTAAAAAGAAGAATAT
1 AACAAGCATTTCTTTTTATTTGAAATCTCACATTTTTATTTTTTA-TTTTTAAAAAGAAGAATAT
1026 TCGATTATTTCGATTCAAAGAAAAACCGCACCTAATAAATAAAGGCACAATTTTTCAAATCACGA
65 TCGATTATTTCGATTCAAAGAAAAACCGCACCTAATAAATAAAGGCACAATTTTTCAAATCACGA
*
1091 AGTAATAAACATTGCCTCAATTTTAAAATTATTTATTTTTATCAAAACAAATATATTTTTTAAGG
130 AATAATAAACATTGCCTCAATTTTAAAATTATTTATTTTTATCAAAACAAATATATTTTTTAAGG
1156 AATGAATTTGAGTGAACATAATATACAATTATAATGATAAAACACAACATGGCATAAATACATAA
195 AATGAATTTGAGTGAACATAATATACAATTATAATGATAAAACACAACATGGCATAAATACATAA
1221 TGACAAGTGTGTACATGATGAAAATAAACAATAATACATACACATTTAATATATGAAACAAATAA
260 TGACAAGTGTGTACATGATGAAAATAAACAATAATACATACACATTTAATATATGAAACAAATAA
1286 AAAGATAATAATAAATGAAGA
325 AAAGATAATAATAAATGAAGA
1307 TATATAAACA
Statistics
Matches: 341, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
345 44 0.13
346 297 0.87
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.33
Consensus pattern (345 bp):
AACAAGCATTTCTTTTTATTTGAAATCTCACATTTTTATTTTTTATTTTTAAAAAGAAGAATATT
CGATTATTTCGATTCAAAGAAAAACCGCACCTAATAAATAAAGGCACAATTTTTCAAATCACGAA
ATAATAAACATTGCCTCAATTTTAAAATTATTTATTTTTATCAAAACAAATATATTTTTTAAGGA
ATGAATTTGAGTGAACATAATATACAATTATAATGATAAAACACAACATGGCATAAATACATAAT
GACAAGTGTGTACATGATGAAAATAAACAATAATACATACACATTTAATATATGAAACAAATAAA
AAGATAATAATAAATGAAGA
Found at i:1377 original size:9 final size:9
Alignment explanation
Indices: 1365--1400 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
1355 TGACAAAATT
1365 TTAAAAAAA
1 TTAAAAAAA
* *
1374 TTAAAAGAT
1 TTAAAAAAA
1383 TTAAAAAAA
1 TTAAAAAAA
1392 TTAAAAAAA
1 TTAAAAAAA
1401 CGAATTACGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:3408 original size:35 final size:36
Alignment explanation
Indices: 3362--3431 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 36
3352 TTGTCGAAGT
3362 TTGACAATTTTCAATTTGTGC-TAGCTTAATTGAAC
1 TTGACAATTTTCAATTTGTGCTTAGCTTAATTGAAC
3397 TTGACAATTTTCAATTTGTGCTTAGCTTAATTGAA
1 TTGACAATTTTCAATTTGTGCTTAGCTTAATTGAA
3432 TTTATGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 21 0.62
36 13 0.38
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (36 bp):
TTGACAATTTTCAATTTGTGCTTAGCTTAATTGAAC
Done.