Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011289.1 Kokia drynarioides strain JFW-HI SEQ_126268, 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, 984
Length: 1640
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.37
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:610 original size:216 final size:216
Alignment explanation
Indices: 5--924 Score: 784
Period size: 216 Copynumber: 4.3 Consensus size: 216
1 GGAT
** * * * * *
5 GAACTTCTAAACTTGACAAACTTTGACGAGTTCTTCTATAACTTCAGCTCTTTAAAGTATTCATG
1 GAACTTCCGAACTTGACAAACTTTTACGAGTTCTTCTAAAATTTCAGTTCCTTAAAGTATTCATG
* * * ** *
70 ACGATCCATTCCTTCTAGAAATTTTTTGAACATTCCATGCTTGGGAAATCACATCATTTTCTCTA
66 ACAATCCATTCCTTCTAGCAATTTTTCGAACATTCCATGCACGGGAAATCACATCATTTTGTCTA
** * * * *
135 AATAGTTTGTCACTTGGTATACAACTTTTGGTCATTGAATTAAAAACTTATTTACTTGAGAATT-
131 AATAGTTTGTCACTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTG
* * * *
199 TATTATCTCTTGGATCATGGAC
196 T-TTCTCTCTTGGTTCTTAGAC
* ** * * * * *
221 -AAGCTTCCGAACTTTACCGACTTTTACTAGTTGTTCTATAACTTT-GGTTCATTAAAGTATTCA
1 GAA-CTTCCGAACTTGACAAACTTTTACGAGTTCTTCTA-AAATTTCAGTTCCTTAAAGTATTCA
* * * * * * * * * *
284 TGACGATCCTTTCCTTCGAGCAA-TTTTCATAACATTCCAAGCACGGGGAACCGCATCATTCTGC
64 TGACAATCCATTCCTTCTAGCAATTTTTC-GAACATTCCATGCACGGGAAATCACATCATTTTGT
* * * *** * * *
348 CTAAACAGTTTTTCACTTTCTAAACAACTTTTGTTCTACAAATTAAACAGTTATTTACGTGAGTG
128 CTAAATAGTTTGTCACTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAG
*
413 TTGTTTCTCTCATT-GTTCTTGGAC
193 TTGTTTCTCTC-TTGGTTCTTAGAC
* *
437 GAACTTCCGAACTTGACGAAA-TTTTACGAGTTCTTCTAAAATTTCAGTTCCTTAAATTATTTAT
1 GAACTTCCGAACTTGAC-AAACTTTTACGAGTTCTTCTAAAATTTCAGTTCCTTAAAGTATTCAT
* * *
501 GACAATCCGTTCCTTCTAGCAATTTTTCGAACAATCCATGCACGGGAAATCGCATCATTTTGTCT
65 GACAATCCATTCCTTCTAGCAATTTTTCGAACATTCCATGCACGGGAAATCACATCATTTTGTCT
* * * ** * *** *
566 AAATTGTTTGTCATTTTCTAAAAAACTTTTTATCTTTGAATTAAAAACCTATTTATACGAGATTT
130 AAATAGTTTGTCACTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTT
** *
631 CCCTT-TCTCTTGCTTCTTAGA-
195 -GTTTCTCTCTTGGTTCTTAGAC
* * * * *
652 TATACTTCC-AAGCTTGACAAACTTGTACGAGTTCTTC-AATAACTTT-GGTTTCTCAAAGTATT
1 GA-ACTTCCGAA-CTTGACAAACTTTTACGAGTTCTTCTAA-AA-TTTCAGTTCCTTAAAGTATT
* ** * ** *
714 CAGGACAATCCATTCCTTAAAGCAATTTGTT-GAACATTCAATGCTTGGGAAATCACATCATTTG
62 CATGACAATCCATTCCTTCTAGCAATTT-TTCGAACATTCCATGCACGGGAAATCACATCATTTT
* * * * ** *
778 GTCTAAATACTTTGTCATTTTCTAAACTACTTTTGGTCTTTGAATGAAAAACTTATCCACGTTAG
126 GTCTAAATAGTTTGTCACTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAG
*
843 AGTTGTTTCTATCTTGGTTCTTAGAC
191 AGTTGTTTCTCTCTTGGTTCTTAGAC
* * * * * * *
869 GAACTTTCGAACTCGGCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCATAAA
1 GAACTTCCGAACTTGACAAACTTTTACGAGTTCTTCTAAAATTTCAGTTCCTTAAA
925 NNNNNNNNNN
Statistics
Matches: 546, Mismatches: 136, Indels: 44
0.75 0.19 0.06
Matches are distributed among these distances:
215 25 0.05
216 496 0.91
217 25 0.05
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (216 bp):
GAACTTCCGAACTTGACAAACTTTTACGAGTTCTTCTAAAATTTCAGTTCCTTAAAGTATTCATG
ACAATCCATTCCTTCTAGCAATTTTTCGAACATTCCATGCACGGGAAATCACATCATTTTGTCTA
AATAGTTTGTCACTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTG
TTTCTCTCTTGGTTCTTAGAC
Found at i:812 original size:432 final size:431
Alignment explanation
Indices: 5--924 Score: 953
Period size: 432 Copynumber: 2.1 Consensus size: 431
1 GGAT
** * * *
5 GAACTTCTAAACTTGACAAACTTTGACGAGTTCTTCTATAACTTCAGCTCTTTAAAGTATTCATG
1 GAACTTCCGAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCTTAAAGTATTCATG
* * * **
70 ACGATCCATTCCTTCTAGAAATTTTTTGAACATTCCATGCTTGGGAAATCACATCATTTTCTCTA
66 ACAATCCATTCCTTCTAGAAATTTTTCGAACAATCCATGCACGGGAAATCACATCATTTTCTCTA
* * * * * *
135 AATAGTTTGTCACTTGGTATACAACTTTTGGTCATTGAATTAAAAACTTATTTACTTGAGAATTT
131 AATAGTTTGTCACTTGCTAAAAAACTTTTGATCATTGAATTAAAAACCTATTTACTCGAGAATTT
* * * ** * * * *
200 ATTATCTCTTGGATCATGGACAAGCTTCCGAACTTTACCGACTTTTACTAGTTGTTCTATAACTT
196 ATTATCTCTTGCATCATAGACAAGCTTCCGAACTTGACAAACTTGTACGAGTTCTTCAATAACTT
* * * * **
265 TGGTTCATTAAAGTATTCATGACGATCCTTTCCTTCGAGCAATTTTCATAACATTCCAAGCACGG
261 TGGTTCATCAAAGTATTCAGGACAATCCATTCCTTAAAGCAATTTT-ATAACATTCCAAGCACGG
* * * * * *
330 GGAACCGCATCATTCTGCCTAAACAGTTTTTCACTTTCTAAACAACTTTTGTTCTACAAATTAAA
325 GAAACCACATCATTCTGCCTAAACACTTTGTCACTTTCTAAACAACTTTTGGTCTACAAATGAAA
* * ** * * *
395 CAGTTATTTACGTGAGTGTTGTTTCTCTCATT-GTTCTTGGAC
390 AACTTATCCACGTGAGAGTTGTTTCTATC-TTGGTTCTTAGAC
* * * *
437 GAACTTCCGAACTTGACGAAA-TTTTACGAGTTCTTCTAAAATTTCAGTTCCTTAAATTATTTAT
1 GAACTTCCGAACTTGAC-AAACTTTTACGAGTTCTTCTATAACTTCAGTTCCTTAAAGTATTCAT
* * * *
501 GACAATCCGTTCCTTCTAGCAATTTTTCGAACAATCCATGCACGGGAAATCGCATCATTTTGTCT
65 GACAATCCATTCCTTCTAGAAATTTTTCGAACAATCCATGCACGGGAAATCACATCATTTTCTCT
* * * * *
566 AAATTGTTTGTCATTTTCTAAAAAACTTTTTATCTTTGAATTAAAAACCTATTTA-TACGAG-AT
130 AAATAGTTTGTCACTTGCTAAAAAACTTTTGATCATTGAATTAAAAACCTATTTACT-CGAGAAT
* * * *
629 TTCCCTT-TCTCTTGCTTCTTAGATATA-CTTCC-AAGCTTGACAAACTTGTACGAGTTCTTCAA
194 TT--ATTATCTCTTGCATCATAGACA-AGCTTCCGAA-CTTGACAAACTTGTACGAGTTCTTCAA
691 TAACTTTGGTTTC-TCAAAGTATTCAGGACAATCCATTCCTTAAAGCAATTTGT-TGAACATT-C
255 TAACTTTGG-TTCATCAAAGTATTCAGGACAATCCATTCCTTAAAGCAATTT-TAT-AACATTCC
** * * * * *
753 AATGCTTGGGAAATCACATCATT-TGGTCTAAATACTTTGTCATTTTCTAAACTACTTTTGGTCT
317 AA-GCACGGGAAACCACATCATTCT-GCCTAAACACTTTGTCACTTTCTAAACAACTTTTGGTCT
*** *
817 TTGAATGAAAAACTTATCCACGTTAGAGTTGTTTCTATCTTGGTTCTTAGAC
380 ACAAATGAAAAACTTATCCACGTGAGAGTTGTTTCTATCTTGGTTCTTAGAC
* * * * *
869 GAACTTTCGAACTCGGCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCATAAA
1 GAACTTCCGAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCTTAAA
925 NNNNNNNNNN
Statistics
Matches: 396, Mismatches: 79, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
431 17 0.04
432 369 0.93
433 10 0.03
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (431 bp):
GAACTTCCGAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCTTAAAGTATTCATG
ACAATCCATTCCTTCTAGAAATTTTTCGAACAATCCATGCACGGGAAATCACATCATTTTCTCTA
AATAGTTTGTCACTTGCTAAAAAACTTTTGATCATTGAATTAAAAACCTATTTACTCGAGAATTT
ATTATCTCTTGCATCATAGACAAGCTTCCGAACTTGACAAACTTGTACGAGTTCTTCAATAACTT
TGGTTCATCAAAGTATTCAGGACAATCCATTCCTTAAAGCAATTTTATAACATTCCAAGCACGGG
AAACCACATCATTCTGCCTAAACACTTTGTCACTTTCTAAACAACTTTTGGTCTACAAATGAAAA
ACTTATCCACGTGAGAGTTGTTTCTATCTTGGTTCTTAGAC
Found at i:1469 original size:215 final size:213
Alignment explanation
Indices: 1085--1639 Score: 535
Period size: 215 Copynumber: 2.6 Consensus size: 213
1075 TTGGTTCATT
* * * * *
1085 AAAGTGTTCATGACGATCCTTTCCTTCGAGCAATTTTCCGAACATTCCAAGCACGGGGAACCGCA
1 AAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCACGGGAAATCGCA
* * * * * *** * **
1150 TCATTCTGCCTAAACAGTTTTTCACTTTCTAAACAACTTTTGTTCTACAAATTAAACAGTTATTT
66 TCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTT-TTCTTTGAATTAAAAACCTATTT
** * * * *
1215 ACGTGAGTGTTGTTTCTCTCACTGTTCTTGGACGAACTTCCGAA-CTTGACGAAGTTTTACGAGT
130 ACACGAGAGTTGTTTCTCT--CTGTTCTTAGACGAACTTCC-AAGCTTGACAAACTTTTACGAGT
*
1279 TCTTCTAA-AAC-TCAATTCCTT
192 TCTTC-AATAACTTCAATTCCTC
* * * *
1300 AAATTATTTATGACGATCCGTTCCTTCTAGCAATTTTCCGAACATTCCATGCACGGGAAATCGCA
1 AAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCACGGGAAATCGCA
* * *
1365 TCATTTTATCTAAATTGTTTGTCATTTTCTAAAAAACTTTTTATCTTTGAATTAAAAACCTATTT
66 TCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTT-TCTTTGAATTAAAAACCTATTT
* *
1430 ATACGAGAGTTGCCTTTCTCT-TGCTTCTTAGATGAACTTCCAAGCTTGACAAACTTTTACGAGT
130 ACACGAGAGTTG--TTTCTCTCTG-TTCTTAGACGAACTTCCAAGCTTGACAAACTTTTACGAGT
*** *
1494 TCTTCAATAACTTTGGTTTCTC
192 TCTTCAATAACTTCAATTCCTC
* * * * * ** *
1516 AAAGTATTCAGGACAATCCATTCCTTAGAGCAATTTGT-TGGACATTCCATGCTTGGGAAATCAC
1 AAAGTATTCATGACGATCCATTCCTTCGAGCAATTT-TCCGAACATTCCATGCACGGGAAATCGC
* * * * *
1580 ATCATTTGGTCTAAATACTTTGTCATTTTCTAAACTACTTTTGGTCTTTGAATGAAAAAC
65 ATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTT-TTCTTTGAATTAAAAAC
1640 T
Statistics
Matches: 276, Mismatches: 55, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
214 7 0.03
215 155 0.56
216 106 0.38
217 8 0.03
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (213 bp):
AAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCACGGGAAATCGCA
TCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTTTCTTTGAATTAAAAACCTATTTA
CACGAGAGTTGTTTCTCTCTGTTCTTAGACGAACTTCCAAGCTTGACAAACTTTTACGAGTTCTT
CAATAACTTCAATTCCTC
Done.