Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000715.1 Kokia drynarioides strain JFW-HI SEQ_111728, 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, 974
Length: 1624
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Found at i:819 original size:216 final size:214
Alignment explanation
Indices: 300--1620 Score: 1654
Period size: 216 Copynumber: 6.1 Consensus size: 214
290 CGGATGTTAC
* * * * * *
300 AAGTATTCAAGACGATCTATTCTTTTGAACAATTTTTCGAACATTCCATGCTTGTGAAATCTCAT
1 AAGTATTCAACAAGATCTATTCCTTCGAA-AATTTTTCGAACATTCCATGCTTGGGAAATCGCAT
365 CATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
65 CATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
*
430 CGTGAGAATTGTTTCTCTC---GTTCTTTGACGAAC-TCCGAACTTGTCAAACTTTTACTAGTTC
130 CGTGAGAATTGTTTCTCTCTTTGTTC-TTGACGAACTTCCAAACTTGTCAAACTTTTACTAGTTC
491 TTTTATAACATCGGATCCTTA
194 TTTTATAACATCGGATCCTTA
* * * * * *
512 AAGTATTCAAGACGATCTATTCTTTCGTACAATTTTTTGAACATTCCACGCTTGGGAAATCGCAT
1 AAGTATTCAACAAGATCTATTCCTTCG-AAAATTTTTCGAACATTCCATGCTTGGGAAATCGCAT
* * *
577 CATTTGGTCGAAATTGTTTATCATTTTGCAAACAAGTTTTGGTCGTTGTAA-TAAAAACTTATTT
65 CATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTG-AATTAAAAACTTATTT
* *
641 ACGTGAGAATTGTTTCTCTCTTTGTTCTTGAACGAACTTTCAAACTTGTCAAACTTTTACGAGTT
129 ACGTGAGAATTGTTTCTCTCTTTGTTCTTG-ACGAACTTCCAAACTTGTCAAACTTTTACTAGTT
* * * ** * *
706 ATTTTTTAACTTTTGTTCCCTA
193 CTTTTATAACATCGGATCCTTA
* * * * * * **
728 AAGTATTCAACAAGATCCATTCCTTAGAGAAAGTATCCGAACATTCCATGCTCGGGAAATCAAAT
1 AAGTATTCAACAAGATCTATTCCTTCGA-AAATTTTTCGAACATTCCATGCTTGGGAAATCGCAT
* * *
793 CATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTA
65 CATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* * *
858 CGTGAGAATTGTTTCTCTCTTTGTTGTTTGACGAACTTCCGAACTTATCAAACTTTTACTAGTTC
130 CGTGAGAATTGTTTCTCTCTTTGTT-CTTGACGAACTTCCAAACTTGTCAAACTTTTACTAGTTC
*
923 TTTTATAACATCAGATCCTTA
194 TTTTATAACATCGGATCCTTA
* * * * *
944 AAGTATTCAAGAAGATCTATT-ATTCCGTACAATTTTTTGAAAATTCCATGCTTGGGAAATCGCA
1 AAGTATTCAACAAGATCTATTCCTT-CG-AAAATTTTTCGAACATTCCATGCTTGGGAAATCGCA
* *
1008 TCATTTGGT-TGAAATTGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGTATTAAAAACTTATT
64 TCATTTGGTCT-AAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT
* * * * * *
1072 TACGTGAGAATTCTTTCTCTCCTTGTTTTCTGGACAAACTTTCAAACTTGTCAAACTTTTACGAG
128 TACGTGAGAATTGTTTCTCT-CTT-TGTTCTTGACGAACTTCCAAACTTGTCAAACTTTTACTAG
* * *
1137 TTATTTTTTAACATTGGAT-CTGTA
191 TTCTTTTATAACATCGGATCCT-TA
* * * **
1161 AAGTATTCAACAAGATCCATTCCTTAGAGCAAATTTTT-GAACATTCCATGCTCGGGAAATCAAA
1 AAGTATTCAACAAGATCTATTCCTTCGA--AAATTTTTCGAACATTCCATGCTTGGGAAATCGCA
* * * *
1225 TCATTTGCTCTAAATAGTTTGTCATTTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTATTT
64 TCATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTT
* *
1290 ACGTGACATTTTTGTTTCTCTCTTTGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTACTAG
129 ACGTGAGA--ATTGTTTCTCTCTTTGTTCTT-GACGAACTTCCAAACTTGTCAAACTTTTACTAG
* *
1355 TTCTTCTATAACATCGGATACTTA
191 TTCTTTTATAACATCGGATCCTTA
* * *
1379 AAGTATTCAACACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCTTGTGAAATCGCAT
1 AAGTATTCAACAAGATCTATTCCTTCGAA-AATTTTTCGAACATTCCATGCTTGGGAAATCGCAT
* **
1444 CGTTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAATTTTATTTA
65 CATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* * * *
1509 CGTGAGAATTTTTTCTCTCTTCGTTCTTTGATGAAC-TCCGAACTTGTCAAACTTTTACTAGTTC
130 CGTGAGAATTGTTTCTCTCTTTGTTC-TTGACGAACTTCCAAACTTGTCAAACTTTTACTAGTTC
1573 TTTTATAACATCGGATCCTTA
194 TTTTATAACATCGGATCCTTA
* * *
1594 AAGTATTCAAGACGATCTATTCTTTCG
1 AAGTATTCAACAAGATCTATTCCTTCG
1621 TACA
Statistics
Matches: 949, Mismatches: 133, Indels: 51
0.84 0.12 0.05
Matches are distributed among these distances:
212 135 0.14
213 3 0.00
214 3 0.00
215 88 0.09
216 362 0.38
217 173 0.18
218 174 0.18
219 11 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (214 bp):
AAGTATTCAACAAGATCTATTCCTTCGAAAATTTTTCGAACATTCCATGCTTGGGAAATCGCATC
ATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTAC
GTGAGAATTGTTTCTCTCTTTGTTCTTGACGAACTTCCAAACTTGTCAAACTTTTACTAGTTCTT
TTATAACATCGGATCCTTA
Found at i:1555 original size:433 final size:429
Alignment explanation
Indices: 330--1603 Score: 1891
Period size: 433 Copynumber: 3.0 Consensus size: 429
320 TCTTTTGAAC
* * ** * *
330 AATTTTTCGAACATTCCATGCTTGTGAAATCTCATCATTTGGTCTAAATAGTTTATCATTTTGCA
1 AATTTTT-GAACATTCCATGCTCGGGAAATCAAATCATTTGGTCTAAATAGTTTGTCATTTTGTA
*
395 AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC---GTTCTTTG
65 AACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTTG
457 ACGAAC-TCCGAACTTGTCAAACTTTTACTAGTTCTTTTATAACATCGGATCCTTAAAGTATTCA
130 ACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTATAACATCGGATCCTTAAAGTATTCA
*
521 AGACGATCTATTCTTTCGTACAATTTTTTGAACATTCCACGCTTGGGAAATCGCATCATTTGGTC
195 AGACGATCTATTCTTTCGTACAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTC
* *
586 GAAATTGTTTATCATTTTGCAAACAAGTTTTGGTCGTTGTAA-TAAAAACTTATTTACGTGAGAA
260 TAAATTGTTTATCATTTTGCAAACAAGTTTTGGTCTTTG-AATTAAAAACTTATTTACGTGAGAA
*
650 TTGTTTCTCTCTTTGTTC-TTGAACGAACTTTCAAACTTGTCAAACTTTTACGAGTTATTTTTTA
324 TTCTTTCTCTC-TTGTTCTTTG-ACGAACTTTCAAACTTGTCAAACTTTTACGAGTTATTTTTTA
* * * *
714 ACTTTTGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGAGA
387 ACATTGGAT-CTTAAAGTATTCAACAAGATCCATTCCTTAGAGA
* **
758 AAGTATCCGAACATTCCATGCTCGGGAAATCAAATCATTTGGTCTAAATAGTTTGTCATTTTGTA
1 AA-TTTTTGAACATTCCATGCTCGGGAAATCAAATCATTTGGTCTAAATAGTTTGTCATTTTGTA
*
823 AACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTGTTTG
65 AACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTTG
* *
888 ACGAACTTCCGAACTTATCAAACTTTTACTAGTTCTTTTATAACATCAGATCCTTAAAGTATTCA
130 ACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTATAACATCGGATCCTTAAAGTATTCA
* * * *
953 AGAAGATCTATTATTCCGTACAATTTTTTGAAAATTCCATGCTTGGGAAATCGCATCATTTGGT-
195 AGACGATCTATTCTTTCGTACAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTC
*
1017 TGAAATTGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGTATTAAAAACTTATTTACGTGAGAA
260 T-AAATTGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAA
*
1082 TTCTTTCTCTCCTTGTT-TTCTGGACAAACTTTCAAACTTGTCAAACTTTTACGAGTTATTTTTT
324 TTCTTTCTCT-CTTGTTCTT-T-GACGAACTTTCAAACTTGTCAAACTTTTACGAGTTATTTTTT
1146 AACATTGGATCTGTAAAGTATTCAACAAGATCCATTCCTTAGAGCA
386 AACATTGGATCT-TAAAGTATTCAACAAGATCCATTCCTTAGAG-A
*
1192 AATTTTTGAACATTCCATGCTCGGGAAATCAAATCATTTGCTCTAAATAGTTTGTCATTTTGTAA
1 AATTTTTGAACATTCCATGCTCGGGAAATCAAATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
* * *
1257 ACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGACATTTTTGTTTCTCTCTTTGTTCTTG
66 ACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGA--ATTGTTTCTCTCTTTGTTCTTT
* * *
1322 GACGAACTTCCAAACTTGTCAAACTTTTACTAGTTCTTCTATAACATCGGATACTTAAAGTATTC
129 GACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTATAACATCGGATCCTTAAAGTATTC
* * * * *
1387 AACACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCTTGTGAAATCGCATCGTTTGGT
194 AAGACGATCTATTCTTTCGTACAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGT
* **
1452 CTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAATTTTATTTACGTGAGAA
259 CTAAATTGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAA
* * * * * * *
1517 TTTTTTCTCTCTTCGTTCTTTGATGAAC-TCCGAACTTGTCAAACTTTTACTAGTTCTTTTATAA
324 TTCTTTCTCTCTT-GTTCTTTGACGAACTTTCAAACTTGTCAAACTTTTACGAGTTATTTTTTAA
*
1581 CATCGGATCCTTAAAGTATTCAA
388 CATTGGAT-CTTAAAGTATTCAA
1604 GACGATCTAT
Statistics
Matches: 765, Mismatches: 62, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
428 106 0.14
429 2 0.00
431 14 0.02
432 190 0.25
433 229 0.30
434 14 0.02
435 207 0.27
436 3 0.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (429 bp):
AATTTTTGAACATTCCATGCTCGGGAAATCAAATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
ACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTTGA
CGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTATAACATCGGATCCTTAAAGTATTCAA
GACGATCTATTCTTTCGTACAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCT
AAATTGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
CTTTCTCTCTTGTTCTTTGACGAACTTTCAAACTTGTCAAACTTTTACGAGTTATTTTTTAACAT
TGGATCTTAAAGTATTCAACAAGATCCATTCCTTAGAGA
Done.