Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012806.1 Kokia drynarioides strain JFW-HI SEQ_127819, 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: 11104
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Found at i:1099 original size:86 final size:86
Alignment explanation
Indices: 950--1108 Score: 246
Period size: 86 Copynumber: 1.8 Consensus size: 86
940 TGGCCTTCTG
* * * *
950 CTCAGTATCTCATATGGAAAATGACCGCGTTGCTTGTTTCGATCCGCTTCTCTGTATCCCATCAG
1 CTCAGTATCTCATATGGAAAATGACCGCGTCGCTTGTTTCAATCCACTTCTCTGTATCCCATCAA
1015 GAAGACGAATTTGGTTCATTT
66 GAAGACGAATTTGGTTCATTT
* * * *
1036 CTCAGTATCTCATCTGGAAAATGACCGTGTCGCTTGTTTCAATCTACTTCTCTGTATCTCATCAA
1 CTCAGTATCTCATATGGAAAATGACCGCGTCGCTTGTTTCAATCCACTTCTCTGTATCCCATCAA
1101 GAAGACGA
66 GAAGACGA
1109 CTGCGTCGCT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 65 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (86 bp):
CTCAGTATCTCATATGGAAAATGACCGCGTCGCTTGTTTCAATCCACTTCTCTGTATCCCATCAA
GAAGACGAATTTGGTTCATTT
Found at i:1117 original size:49 final size:49
Alignment explanation
Indices: 1064--1157 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
1054 AAATGACCGT
*
1064 GTCGCTTGTTTCAATCTACTTCTCTGTATCTCATCAAGAAGACGACTGC
1 GTCGCTTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAGACGACTGC
* *
1113 GTCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGA
1 GTCGCTTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAGACGA
1158 ATTTGGTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (49 bp):
GTCGCTTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAGACGACTGC
Found at i:1446 original size:49 final size:49
Alignment explanation
Indices: 1368--1492 Score: 169
Period size: 49 Copynumber: 2.6 Consensus size: 49
1358 ATTTGGTTCA
* ** * * *
1368 CTTCTCAGTATCTCATTTGGAAAATGACCGCATCGCTTATTTCAATCTG
1 CTTCTCTGTATCTCATCAGGAAGACGACCGCATCGCTTATTTCAATCCG
* *
1417 CTTCTCTGTATCTCATCAGGAAGACGACCGCGTCGCTTGTTTCAATCCG
1 CTTCTCTGTATCTCATCAGGAAGACGACCGCATCGCTTATTTCAATCCG
*
1466 CTTCTCTGTGTCTCATCAGGAAGACGA
1 CTTCTCTGTATCTCATCAGGAAGACGA
1493 ATTTGGTTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (49 bp):
CTTCTCTGTATCTCATCAGGAAGACGACCGCATCGCTTATTTCAATCCG
Found at i:1582 original size:335 final size:335
Alignment explanation
Indices: 944--1656 Score: 1151
Period size: 335 Copynumber: 2.1 Consensus size: 335
934 TTAACTTGGC
* * * * *
944 CTTCTGCTCAGTATCTCAT-ATGGAAAATGACCGCGTTGCTTGTTTCGATCCGCTTCTCTGTATC
1 CTTCTTCTCGGTATCTCATCA-GGAAAATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATC
* ** *
1008 CCATCAGGAAGACGAATTTGGTTCATTTCTCAGTATCTCATCTGGAAAATGACCGTGTCGCTTGT
65 CCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAAATGACCGCATCGCTTAT
*
1073 TTCAATCTACTTCTCTGTATCTCATCAAGAAGACGACTGCGTCGCTTGTTTCAATCCGCTTCTCT
130 TTCAATCTACTTCTCTGTATCTCATCAAGAAGACGACCGCGTCGCTTGTTTCAATCCGCTTCTCT
* *
1138 GTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAAGATCTTATCAGGAAGCTAATCTTTATT
195 GTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAAGATCTCATCAGGAAGCTAACCTTTATT
*
1203 TCTTTTACCTGCTTCTCAGTGTCTCATCAAGAAGCTAGGTTTTGAAGATTTCGCTCACTCTGAGC
260 GCTTTTACCTGCTTCTCAGTGTCTCATCAAGAAGCTAGGTTTTGAAGATTTCGCTCACTCTGAGC
1268 CTCGTTTGGGT
325 CTCGTTTGGGT
** *
1279 CTTCTTCTCGGTATCTTGTCAGGAAAATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTGTATCC
1 CTTCTTCTCGGTATCTCATCAGGAAAATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCC
*
1344 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATTTGGAAAATGACCGCATCGCTTATT
66 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAAATGACCGCATCGCTTATT
* *
1409 TCAATCTGCTTCTCTGTATCTCATCAGGAAGACGACCGCGTCGCTTGTTTCAATCCGCTTCTCTG
131 TCAATCTACTTCTCTGTATCTCATCAAGAAGACGACCGCGTCGCTTGTTTCAATCCGCTTCTCTG
* * *
1474 TGTCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGGATGTCATCAGGAAGCTAACCTTTATTG
196 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAAGATCTCATCAGGAAGCTAACCTTTATTG
* * *
1539 CTTTTACCTGCTTCTTAGTGTCTCATCAGGAAGCT-GAGTTTTGAAGATTTCGCTCACTTTGAGC
261 CTTTTACCTGCTTCTCAGTGTCTCATCAAGAAGCTAG-GTTTTGAAGATTTCGCTCACTCTGAGC
1603 CTCGTTTGGGT
325 CTCGTTTGGGT
* *
1614 CTTCTTCTTGGTATCTCATCAGGAAGATGACCGCGTCGTTTGT
1 CTTCTTCTCGGTATCTCATCAGGAAAATGACCGCGTCGTTTGT
1657 GTGTATCGTA
Statistics
Matches: 347, Mismatches: 29, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
334 1 0.00
335 345 0.99
336 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (335 bp):
CTTCTTCTCGGTATCTCATCAGGAAAATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCC
CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAAATGACCGCATCGCTTATT
TCAATCTACTTCTCTGTATCTCATCAAGAAGACGACCGCGTCGCTTGTTTCAATCCGCTTCTCTG
TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAAGATCTCATCAGGAAGCTAACCTTTATTG
CTTTTACCTGCTTCTCAGTGTCTCATCAAGAAGCTAGGTTTTGAAGATTTCGCTCACTCTGAGCC
TCGTTTGGGT
Found at i:2173 original size:29 final size:27
Alignment explanation
Indices: 2133--2194 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
2123 CCAAGAATTC
*
2133 TATTAAAAGAGGATCGAAGGAAACAAT
1 TATTAAAAGAGGATCAAAGGAAACAAT
*
2160 TATTGAAAAGGAGGATTAAAGGAAACAAT
1 TATT-AAAA-GAGGATCAAAGGAAACAAT
*
2189 CATTAA
1 TATTAA
2195 TTGAAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 6 0.20
29 20 0.67
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (27 bp):
TATTAAAAGAGGATCAAAGGAAACAAT
Done.