Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014325.1 Kokia drynarioides strain JFW-HI SEQ_129362, 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: 7288
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Found at i:5652 original size:208 final size:207
Alignment explanation
Indices: 5189--5946 Score: 1056
Period size: 208 Copynumber: 3.7 Consensus size: 207
5179 GATAAAAACA
* * * * * *
5189 AGGCTCGAAACGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCGGGTCGAA
1 AGGCTCGAAACGAGAAAAATCTTCAAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAA
* * *
5254 GCAATAAAAGGTTAGCTTCCTGATGAGATACTAAGAAGTGTACCAAATTAGTCTTCCTGATGAGA
66 GTAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTGATGAGA
* *
5319 TATGGAGAAGCAAATTAAAAAACGATGCAGTCATCTTCC-AGACAAGATACTGAGAAGAAGACCA
131 TACGGAGAAGCGAATT-AAAAACGATGC-GTCATCTTCCGA-ACAAGATACTGAGAAGAAGACCA
5383 AATCAAACCCAAACA-
193 AATCAAACCCAAA-AG
* * *
5398 AGGCTCGAAACGAGCAAAATCTTCAAACCCCAACTTCCTAATGAGACACTAAGAAGCAGGTTGAA
1 AGGCTCGAAACGAGAAAAATCTTCAAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAA
*
5463 GTAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTAATGAGA
66 GTAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTGATGAGA
* *
5528 TACGGAGAAGCGAATTAAAAACGATGCGGTCATCTTCCGAACAAGGTATTGAGAAGAAGACCAAA
131 TACGGAGAAGCGAATTAAAAACGATGC-GTCATCTTCCGAACAAGATACTGAGAAGAAGACCAAA
5593 TCAAACCCAAAAG
195 TCAAACCCAAAAG
** * *
5606 AGGCTCGAAATAAGAAAAATCTTCAAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTTGAA
1 AGGCTCGAAACGAGAAAAATCTTCAAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAA
* *
5671 GAAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCTTGATGAGA
66 GTAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTGATGAGA
* * * *
5736 TACGGAGAAGCGAATTAAAAATGATGCG---------G-ACAAGATACTGAGAAGAATATCGAAT
131 TACGGAGAAGCGAATTAAAAACGATGCGTCATCTTCCGAACAAGATACTGAGAAGAAGACCAAAT
*
5791 CAAACCCAAACG
196 CAAACCCAAAAG
*
5803 AGGCTCGATACGAGAAAAATCTTCAAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAA
1 AGGCTCGAAACGAGAAAAATCTTCAAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAA
* * *
5868 -TCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACAAAATTTGTCTTCCTGATGAG
66 GT-AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTGATGAG
* **
5932 GTATAGAGAAGCGAA
130 ATACGGAGAAGCGAA
5947 CCAAAACAAG
Statistics
Matches: 500, Mismatches: 46, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
197 162 0.32
198 1 0.00
207 2 0.00
208 201 0.40
209 134 0.27
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.21
Consensus pattern (207 bp):
AGGCTCGAAACGAGAAAAATCTTCAAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAA
GTAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTGATGAGA
TACGGAGAAGCGAATTAAAAACGATGCGTCATCTTCCGAACAAGATACTGAGAAGAAGACCAAAT
CAAACCCAAAAG
Found at i:6376 original size:17 final size:17
Alignment explanation
Indices: 6307--6383 Score: 75
Period size: 17 Copynumber: 4.5 Consensus size: 17
6297 CCCAATCAGC
* *
6307 TTAAATTTATTTTAAAA
1 TTAAATTTATTATAAAT
* *
6324 TTAAGTTTATTCTAAAT
1 TTAAATTTATTATAAAT
* *
6341 TTAAATTTGGTT-GAAAT
1 TTAAATTT-ATTATAAAT
*
6358 TTAAATTTATTATATAT
1 TTAAATTTATTATAAAT
6375 TTAAATTTA
1 TTAAATTTA
6384 AAATTTATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
16 2 0.04
17 45 0.92
18 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Found at i:7069 original size:15 final size:14
Alignment explanation
Indices: 7049--7087 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
7039 AAATGAGATT
7049 TATTATTATTTAAAA
1 TATTATTA-TTAAAA
7064 TATTATTA--AAAA
1 TATTATTATTAAAA
7076 TATTATTATTAA
1 TATTATTATTAA
7088 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.55
14 2 0.09
15 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTATTATTAAAA
Done.