Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010133.1 Kokia drynarioides strain JFW-HI SEQ_124928, 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: 2112
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Found at i:926 original size:201 final size:201
Alignment explanation
Indices: 482--1321 Score: 1346
Period size: 201 Copynumber: 4.2 Consensus size: 201
472 TCAACCTGCC
* *
482 TCTCAATCAAGAAGCTGGGGTTCGAAGATTTTGCTCATTTTGAGCCTCGTTTGGGTCTTCTTCTC
1 TCTC-ATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
** * * * *
547 AGT-TCCTCATCAGGAAGATGATCACATTGCTGTTTGTTTAAATTCGCTCCTCTGTATCTCATCA
65 AGTGT-CTCATCAGGAAGATGA-C-C-GCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCA
* * * *
611 GGAAGACGAATTTGGTTCACTTCTCAATATATCATCAGGAAGCTAA-CTTTTATCGCTTCGACCT
126 GGAAGGCGAATTTGGTTCACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCT
675 GCTTCTCAATG
191 GCTTCTCAATG
* * *
686 TCTCATTAGGAAGCTGGGGTTCGAAGATTTTGTTCACTTTGAGCCTCATTTGGGTCTTCTTCTCA
1 TCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCA
751 GTGTCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAG
66 GTGTCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAG
* *
816 GCGAATTTGGTTAACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTACTTC
131 GCGAATTTGGTTCACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTC
*
881 TCAGTG
196 TCAATG
887 TCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCA
1 TCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCA
*
952 GTGTCTCATCAGGAAGATGACCGCGTTGTTTGTTTCATCTCGCTTCTCTGTATCTCATCAGGAAG
66 GTGTCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAG
* *
1017 GCGAATTTGGTTGACTCCTCAGTATTTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTC
131 GCGAATTTGGTTCACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTC
1082 TCAATG
196 TCAATG
*
1088 TCTCATCAGGAAGCTGAGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCA
1 TCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCA
* *
1153 GTGTCTCATCAGGAAGATGACCGCGTTGTTTTTTTCAACTCGTTTCTCTGTATCTCATCAGGAAG
66 GTGTCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAG
* * *
1218 GCGAATTTGGTTGACTCCTCAGTATCTCATCAGGAAGCTAACC-TTTATTGCTTCTACCTGCTTC
131 GCGAATTTGGTTCACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTC
1282 TCAATG
196 TCAATG
*
1288 TCTCATCAAGG-AGCTGGGGTTCGAAGGTTTTGCT
1 TCTCATC-AGGAAGCTGGGGTTCGAAGATTTTGCT
1322 TGCTTTGTGG
Statistics
Matches: 598, Mismatches: 35, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
200 126 0.21
201 392 0.66
202 1 0.00
203 74 0.12
204 5 0.01
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (201 bp):
TCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCA
GTGTCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAG
GCGAATTTGGTTCACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTC
TCAATG
Found at i:1150 original size:402 final size:404
Alignment explanation
Indices: 229--1321 Score: 1473
Period size: 402 Copynumber: 2.7 Consensus size: 404
219 TGGCTTTCTT
* * ** * * * *
229 CTCAATATCTCATCTGGAAGCTAACCATTTTATTACTTCGACCTGCTTCCCAGTATCTCATCAAG
1 CTCAATATATCATCAGGAAGCTAACC-TTTTATCGCTTCGACCTGCTTCTCAATGTCTCATCAGG
** * * * *
294 ATA-CTGGGGTTCGAAGA-TTTGCTCA-TACCGAGCGTGGGTTTGTTTTGGTCCTCTTCTCAGTA
65 A-AGCTGGGGTTCGAAGATTTTGCTCACT-TTGAGCCT-CGTTTG----GGTCTTCTTCTCAGTG
* * * * * * *
356 TCTCATCAGGAAGATGACTGCATCGTTCGTTTCAATTCGCTTCTCTGTATCGCATCAGGAAGACG
123 TCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCG
** * * * *
421 AATTTGGTCCACTTCTTAGTATCTCATCAAGAAGCTAATCATTTTATTGCTTCAACCTGC--CTC
188 AATTTGGTTAACTCCTCAGTATCTCATCAGGAAGCTAA-CCTTTTATTGCTTCAACCTGCTTCTC
* * *
484 ---TC-AATCAAGAAGCTGGGGTTCGAAGATTTTGCTCATTTTGAGCCTCGTTTGGGTCTTCTTC
252 ATGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
**
545 TCAGTTCCTCATCAGGAAGATGATCACATTGCTGTTTGTTTAAATTCGCTCCTCTGTATCTCATC
317 TCAGTTCCTCATCAGGAAGATGATCACAGCGCTGTTTGTTTAAATTCGCTCCTCTGTATCTCATC
*
610 AGGAAGACGAATTTGGTTCACTT
382 AGGAAGACGAATTTGGTTCACTC
*
633 CTCAATATATCATCAGGAAGCTAA-CTTTTATCGCTTCGACCTGCTTCTCAATGTCTCATTAGGA
1 CTCAATATATCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAATGTCTCATCAGGA
* *
697 AGCTGGGGTTCGAAGATTTTGTTCACTTTGAGCCTCATTTGGGTCTTCTTCTCAGTGTCTCATCA
66 AGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCA
762 GGAAGATGACCGCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGT
131 GGAAGATGACCGCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGT
* * *
827 TAACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTACTTCTCAGTGTCTCA
196 TAACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCAACCTGCTTCTCA-TGTCTCA
892 TCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGT-
260 TCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGT-TC
* * *
956 CTCATCAGGAAGATGA-C-C-GCGTTGTTTGTTT-CATCTCGCTTCTCTGTATCTCATCAGGAAG
324 CTCATCAGGAAGATGATCACAGCGCTGTTTGTTTAAAT-TCGCTCCTCTGTATCTCATCAGGAAG
* *
1017 GCGAATTTGGTTGACTC
388 ACGAATTTGGTTCACTC
* *
1034 CTCAGTATTTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAATGTCTCATCAGGA
1 CTCAATATATCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAATGTCTCATCAGGA
*
1099 AGCTGAGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCA
66 AGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCA
* *
1164 GGAAGATGACCGCGTTGTTTTTTTCAACTCGTTTCTCTGTATCTCATCAGGAAGGCGAATTTGGT
131 GGAAGATGACCGCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGT
* *
1229 TGACTCCTCAGTATCTCATCAGGAAGCTAACC-TTTATTGCTTCTACCTGCTTCTCAATGTCTCA
196 TAACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCAACCTGCTTCTC-ATGTCTCA
*
1293 TCAAGG-AGCTGGGGTTCGAAGGTTTTGCT
260 TC-AGGAAGCTGGGGTTCGAAGATTTTGCT
1322 TGCTTTGTGG
Statistics
Matches: 617, Mismatches: 57, Indels: 33
0.87 0.08 0.05
Matches are distributed among these distances:
397 17 0.03
398 105 0.17
399 3 0.00
400 2 0.00
401 123 0.20
402 250 0.41
403 16 0.03
404 100 0.16
405 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (404 bp):
CTCAATATATCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAATGTCTCATCAGGA
AGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCA
GGAAGATGACCGCGTTGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGT
TAACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCAACCTGCTTCTCATGTCTCAT
CAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTTCCT
CATCAGGAAGATGATCACAGCGCTGTTTGTTTAAATTCGCTCCTCTGTATCTCATCAGGAAGACG
AATTTGGTTCACTC
Done.