Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013091.1 Kokia drynarioides strain JFW-HI SEQ_128109, 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: 10564
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.26
Warning! 295 characters in sequence are not A, C, G, or T
Found at i:11 original size:6 final size:6
Alignment explanation
Indices: 1--33 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1 TTTTCT TTTTCT TTTTCT TTTT-T TTTT-T TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
34 ATGGACATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTCT
Found at i:9386 original size:201 final size:201
Alignment explanation
Indices: 9037--9473 Score: 669
Period size: 201 Copynumber: 2.2 Consensus size: 201
9027 CAATTACCCA
* **
9037 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGCGAAATATACCAACTCAGGGATCAATGC
1 AAACAAGTGAGACGGTCATCTTCCTGATGAGATACAAAGAAATATACCAACTCAGGGATCAATGC
*
9102 GAGCAAATCTTCGAACCCCAGATTCCTGATGAGATACGGAGAAGCAGGTCGAAGCAATAAAATGG
66 GAGCAAATCTTCGAACCCCAGATGCCTGATGAGATACGGAGAAGCAGGTCGAAGCAATAAAATGG
* * * *
9167 TTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGC
131 TTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGC
9232 GGATTG
196 GGATTG
* * * *
9238 AAACAAGTGAGACGAG-CATTTTCCTGATGAGGTACAAAGAAGTATACCAACTCAGGGCTCAATG
1 AAACAAGTGAGACG-GTCATCTTCCTGATGAGATACAAAGAAATATACCAACTCAGGGATCAATG
* * * * *
9302 CGAGCAAATCTTCGAACCTCAGCTGCTTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATG
65 CGAGCAAATCTTCGAACCCCAGATGCCTGATGAGATACGGAGAAGCAGGTCGAAGCAATAAAATG
*
9367 GTTAGCTTCCTGTTGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAG
130 GTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAG
9432 CGGATTG
195 CGGATTG
** *
9439 AAACAAGTGAGGTGGACATCTTCCTGATGAGATAC
1 AAACAAGTGAGACGGTCATCTTCCTGATGAGATAC
9474 TGAGAAGCAG
Statistics
Matches: 212, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
200 1 0.00
201 210 0.99
202 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (201 bp):
AAACAAGTGAGACGGTCATCTTCCTGATGAGATACAAAGAAATATACCAACTCAGGGATCAATGC
GAGCAAATCTTCGAACCCCAGATGCCTGATGAGATACGGAGAAGCAGGTCGAAGCAATAAAATGG
TTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGC
GGATTG
Found at i:9569 original size:134 final size:134
Alignment explanation
Indices: 9329--9614 Score: 455
Period size: 134 Copynumber: 2.1 Consensus size: 134
9319 CTCAGCTGCT
* * *
9329 TGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGTTGAGATACTAAGAA
1 TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATAAGATACTAAGAA
* *
9394 GTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAGTGAGGTGGACATC
66 GTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAGCGAGGCGGACATC
9459 TTCC
131 TTCC
* * *
9463 TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGTTTCTTGATAAGATACTGAGAA
1 TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATAAGATACTAAGAA
* * * *
9528 GTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATC
66 GTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAGCGAGGCGGACATC
9593 TTCC
131 TTCC
*
9597 TGATGAGATACTAAGAAG
1 TGATGAGATACTGAGAAG
9615 AAGACTGAAT
Statistics
Matches: 139, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
134 139 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (134 bp):
TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATAAGATACTAAGAA
GTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAGCGAGGCGGACATC
TTCC
Found at i:9976 original size:17 final size:17
Alignment explanation
Indices: 9951--10017 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
9941 CCAACATAAT
9951 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
9968 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAA
** *
9985 TTAAATTTATTGGAAAT
1 TTAAATTTATTTTAAAA
*
10002 TTAAATTTATTATAAA
1 TTAAATTTATTTTAAA
10018 CTTAGAATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:10011 original size:34 final size:34
Alignment explanation
Indices: 9948--10026 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
9938 GGCCCAACAT
** * *
9948 AATTTAAATTTATTTTAAAATTAAGTTTATTTTA
1 AATTTAAATTTATTGGAAAATTAAATTTATTATA
*
9982 AATTTAAATTTATTGGAAATTTAAATTTATTATA
1 AATTTAAATTTATTGGAAAATTAAATTTATTATA
*
10016 AACTTAGAATT
1 AATTTA-AATT
10027 AAATTTATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (34 bp):
AATTTAAATTTATTGGAAAATTAAATTTATTATA
Done.