Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012316.1 Kokia drynarioides strain JFW-HI SEQ_127318, 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: 2460
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Found at i:398 original size:15 final size:15
Alignment explanation
Indices: 386--456 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
376 TTTTGGGTAG
386 TTTGTAATTGGGTCA
1 TTTGTAATTGGGTCA
* *
401 TTTGTATTTGGGCCA
1 TTTGTAATTGGGTCA
* *
416 TCTGTAACTGGG-CTA
1 TTTGTAATTGGGTC-A
* * *
431 TTTGTTATTAGGCCA
1 TTTGTAATTGGGTCA
446 TTTGTAATTGG
1 TTTGTAATTGG
457 ACTTTGTTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
14 1 0.02
15 41 0.95
16 1 0.02
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.45
Consensus pattern (15 bp):
TTTGTAATTGGGTCA
Found at i:422 original size:30 final size:30
Alignment explanation
Indices: 388--456 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
378 TTGGGTAGTT
*
388 TGTAATTGGG-TCATTTG-TATTTGGGCCATC
1 TGTAATTGGGCT-ATTTGTTA-TTAGGCCATC
* *
418 TGTAACTGGGCTATTTGTTATTAGGCCATT
1 TGTAATTGGGCTATTTGTTATTAGGCCATC
448 TGTAATTGG
1 TGTAATTGG
457 ACTTTGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 30 0.91
31 3 0.09
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.43
Consensus pattern (30 bp):
TGTAATTGGGCTATTTGTTATTAGGCCATC
Found at i:572 original size:16 final size:17
Alignment explanation
Indices: 488--573 Score: 106
Period size: 17 Copynumber: 5.2 Consensus size: 17
478 TTGGACTTTC
*
488 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
505 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
522 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
539 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
* *
555 TAAA-TTCAATTTCCAA
1 TAAATTTAAATTTCAAA
571 TAA
1 TAA
574 GTCCAGACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
15 7 0.11
16 12 0.19
17 38 0.60
18 6 0.10
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:1235 original size:139 final size:139
Alignment explanation
Indices: 1075--1683 Score: 936
Period size: 139 Copynumber: 4.4 Consensus size: 139
1065 TCAATTCGCT
* * * *
1075 TATCTCATCAGGAAGATGAATTTGGTTCACTTCTCAGTACCTCATCTAGAAGATCTGCTCGTTTC
1 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTTAGTACCTCATCTGGAAGATTTGCTCGTTTC
*
1140 GAGCCTCTTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCC
66 GAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCC
*
1205 GCTTCTTTG
131 GCTTCTCTG
* * *
1214 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTA-TTCCATTTGGAAGATTTGCTCGTTT
1 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTTAGTACCT-CATCTGGAAGATTTGCTCGTTT
*
1278 CGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAAGAAGATGATCCCATCACTGTTTCAATC
65 CGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATC
*
1343 TGCTTCTCTG
130 CGCTTCTCTG
* *
1353 TATTTCATCAGGAAGACGAATTTTGGTTCACTTCTTAGTATCC-CATCTGGAGGATTTGCTCGTT
1 TATCTCATCAGGAAGACGAA-TTTGGTTCACTTCTTAGTA-CCTCATCTGGAAGATTTGCTCGTT
* *
1417 TCGAGCCTCGTTTGGGTTTTCTTCTCAATGTCTCATCAGGAAGATGATCCCATCACTGTTTCAAT
64 TCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAAT
*
1482 CCGTTTCTCTG
129 CCGCTTCTCTG
*
1493 TATCTCATCAAGAAGACGAATTTGGTTCACTTCTTAGTATCC-CATCTGGAAGATTTGCTCGTTT
1 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTTAGTA-CCTCATCTGGAAGATTTGCTCGTTT
* *
1557 CGAGCCTTGTTTGGGTTTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATC
65 CGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATC
* *
1622 TGTTTCTCTG
130 CGCTTCTCTG
** * *
1632 TATCTCATCAGGAAGATAAATTTGGTTCACTTCTTAGTATCTCATCAGGAAG
1 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTTAGTACCTCATCTGGAAG
1684 CTAACCGTTT
Statistics
Matches: 435, Mismatches: 30, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
138 2 0.00
139 307 0.71
140 126 0.29
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (139 bp):
TATCTCATCAGGAAGACGAATTTGGTTCACTTCTTAGTACCTCATCTGGAAGATTTGCTCGTTTC
GAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCC
GCTTCTCTG
Found at i:1601 original size:279 final size:277
Alignment explanation
Indices: 1075--1677 Score: 974
Period size: 279 Copynumber: 2.2 Consensus size: 277
1065 TCAATTCGCT
*
1075 TATCTCATCAGGAAGATGAATTTGGTTCACTTCTCAGTA-CCTCATCTAGAAGATCTGCTCGTTT
1 TATCTCATCAGGAAGA-GAATTTGGTTCACTTCTTAGTATCC-CATCTAGAAGATCTGCTCGTTT
* *
1139 CGAGCCTCTTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATC
64 CGAGCCTCGTTTGGGTCTTCTTCTCAATGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATC
* * * *
1204 CGCTTCTTTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATTCCATTTGGAAGATT
129 CGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCCCATCTGGAAGATT
1269 TGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAAGAAGATGATCCCATCACT
194 TGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAAGAAGATGATCCCATCACT
1334 GTTTCAATCTGCTTCTCTG
259 GTTTCAATCTGCTTCTCTG
* * * *
1353 TATTTCATCAGGAAGACGAATTTTGGTTCACTTCTTAGTATCCCATCTGGAGGATTTGCTCGTTT
1 TATCTCATCAGGAAGA-GAA-TTTGGTTCACTTCTTAGTATCCCATCTAGAAGATCTGCTCGTTT
*
1418 CGAGCCTCGTTTGGGTTTTCTTCTCAATGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATC
64 CGAGCCTCGTTTGGGTCTTCTTCTCAATGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATC
* *
1483 CGTTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTCTTAGTATCCCATCTGGAAGATT
129 CGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCCCATCTGGAAGATT
* * *
1548 TGCTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACT
194 TGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAAGAAGATGATCCCATCACT
*
1613 GTTTCAATCTGTTTCTCTG
259 GTTTCAATCTGCTTCTCTG
* *
1632 TATCTCATCAGGAAGATAAATTTGGTTCACTTCTTAGTATCTCATC
1 TATCTCATCAGGAAGA-GAATTTGGTTCACTTCTTAGTATCCCATC
1678 AGGAAGCTAA
Statistics
Matches: 300, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
278 43 0.14
279 255 0.85
280 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (277 bp):
TATCTCATCAGGAAGAGAATTTGGTTCACTTCTTAGTATCCCATCTAGAAGATCTGCTCGTTTCG
AGCCTCGTTTGGGTCTTCTTCTCAATGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCCG
CTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCCCATCTGGAAGATTTG
CTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAAGAAGATGATCCCATCACTGT
TTCAATCTGCTTCTCTG
Done.