Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003991.1 Kokia drynarioides strain JFW-HI SEQ_117099, 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, 781
Length: 1302
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Found at i:397 original size:216 final size:213
Alignment explanation
Indices: 1--1302 Score: 1545
Period size: 216 Copynumber: 6.1 Consensus size: 213
* * *
1 AAGATTAAAACTTGTTTACAAAATGAAAAAATATTTAGACCAAATGATGCGATTTCCCCCGCATG
1 AAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATG
* * * * * * * *
66 GAATGGTCGGAGAATTCCTCTACGGAATGGATCGTCATGGACACTTTAAGGAACCGATTTTAAAA
66 GAATGTTC-GAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAATTT-AAA
* * * *
131 AAGAACTTGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAATAGCCAAGAGAGAAACAATTCTCA
129 AAGAACTCGTAAAAG-TTGACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCA
*
196 CATAAATAAGTTTTTAATTCA
193 CGTAAATAAGTTTTTAATTCA
* * **
217 AAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATTATGCGATTTCCCTCGTTTG
1 AAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATG
* *
282 GAATGTTCAGAAAATTACTCGAAGGAATGGATAGTCTTGAACACTTCAAGGAACCGAATTTAAAA
66 GAATGTTC-GAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAATTTAAAA
**
347 GAGAACTCGTAAAAGTGTGACAAGTTCGAAAGTTAATCCAACAACCAAGAGAGAAACAATTCTCA
130 -AGAACTCGTAAAAGT-TGACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCA
412 CGTAAATAAAG-TTTTAATTCA
193 CGTAAAT-AAGTTTTTAATTCA
*
433 AAGATTAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATG
1 AAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATG
* * * * ** * *
498 GAATGGTCAGAGAATTACTCTACGGAATGGATCGTC-ACAGACACTTTAAGGAACCGGATTAAAA
66 GAATGTTC-GAAAATTACTCGAAGGAATGGATCGTCTTGA-ACACTTTAAGGAACCGAATT-TAA
* * * * * *
562 AAAGAACTTGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAACAACCACGAGAAAAATAGTTCTC
128 AAAGAACTCGTAAAAG-TTGACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTC
*
627 ACGTAAGTAAGTTTTTAATTCA
192 ACGTAAATAAGTTTTTAATTCA
** * * * * * **
649 AAGGCCAAAACATGTTTACAAAATGACAAACTTTTTAGACCAAAAGATGCGACTTCCCGAGCATG
1 AAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATG
* * * * * *
714 TAATGTTCGAAAAATTGCTCGAAGGATTGG-TCGTCCTGAATACTTTAAGGAATCGAAGTTGT-A
66 GAATGTTCG-AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAA-TT-TAA
* * *
777 AAAGAAGTCGTAAAAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGACAAACAATTCTC
128 AAAGAACTCGTAAAAGTT-GACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTC
842 ACGTAAATAAGTTTTTAATTCA
192 ACGTAAATAAGTTTTTAATTCA
* *
864 AAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATTATGCGATTTCCCTCGCTTG
1 AAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATG
*
929 GAATGTTCGGAAAATTACTCGAAGTAATGGATCGTCTTGAACACTTTAAGGAACC-AGATTTAAA
66 GAATGTTC-GAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGA-ATTTAAA
* *
993 AAGAACTCGTAAAAGTGTGACAAGTTCGAAAGTTCATCCAACAACCAAGAGAGAAACAATTTTCA
129 AAGAACTCGTAAAAGT-TGACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCA
*
1058 CGTATATAAGTTTTTAATTCA
193 CGTAAATAAGTTTTTAATTCA
* * * * * ** *
1079 ATGGA-C--AA-----TTACAAAATGACAAACTTTTTAGACCAAATGATGCAATTTCTCGAGAAT
1 A-AGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCAT
** * * * *
1136 TTAATGTTCGAAAAATTGCTCGAAGGAATAG-TCGTCTTGAATACTTTAAGGAATCGAAGTTGT-
65 GGAATGTTCG-AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAA-TT-TA
* * * * *
1199 AAAAGAAGTTGTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGACAAACAATTCT
127 AAAAGAACTCGTAAAAGTT-GACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCT
1264 CACGTAAATAAGTTTTTAATTCA
191 CACGTAAATAAGTTTTTAATTCA
1287 AAGATCAAAACTTGTT
1 AAGATCAAAACTTGTT
Statistics
Matches: 924, Mismatches: 132, Indels: 61
0.83 0.12 0.05
Matches are distributed among these distances:
207 27 0.03
208 147 0.16
209 1 0.00
210 2 0.00
213 2 0.00
214 3 0.00
215 270 0.29
216 464 0.50
217 8 0.01
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (213 bp):
AAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATG
GAATGTTCGAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAATTTAAAAA
GAACTCGTAAAAGTTGACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGT
AAATAAGTTTTTAATTCA
Found at i:1206 original size:12 final size:12
Alignment explanation
Indices: 1191--1215 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1181 TTAAGGAATC
1191 GAAGTTGTAAAA
1 GAAGTTGTAAAA
1203 GAAGTTGTAAAA
1 GAAGTTGTAAAA
1215 G
1 G
1216 TTCGACAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (12 bp):
GAAGTTGTAAAA
Done.