Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012201.1 Kokia drynarioides strain JFW-HI SEQ_127202, 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: 1694
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.25
Warning! 179 characters in sequence are not A, C, G, or T
Found at i:1184 original size:208 final size:211
Alignment explanation
Indices: 672--1205 Score: 630
Period size: 215 Copynumber: 2.5 Consensus size: 211
662 NNNNNNNNNN
* * *
672 GTTTTTAATTCAAAGAGTACAAGTTGTTTACAAAATGACAAATTATTTTGACCAAATGATGCGAT
1 GTTTATAATTCAAAGACTACAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGAT
* * * * *
737 TTCCCGAGAAAGGACTGTTCGAAAAATTGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAA
66 TTCCCGAGCATGGAATGTTCGGAAAATTGTTCGAAGGAATGGATAGTCTTGAATACTTTAAAGAA
* * * *
802 CCGAAGTTATAAAAGAACTCGTAAAAATTTGACTAGTTCGAAAGTTCGGCCAAGAACCAAGAGAG
131 CCGAAGTTATAAAAGAACTCGTAAAAATTTAACAAGTT---AAGTTC-ACAAAGAACCAAGAGAG
* * * * *
867 TAACGATTCTTACTTAATAA
192 AAACAATTCTCACTAAAAAA
* * * * * * * *
887 GTTTATATTTCAAACACCAAAAATTGTTTA-AGCAATGAAAAACTATTTAGACCAAATGATGCGA
1 GTTTATAATTCAAAGACTACAAGTTGTTTACA-AAATGACAAACTATTTTGACCAAATGATGCGA
* * * * * *
951 TTTCCCGAGCATGGAATGATCGGAAAGTTGCTCAAAGGAATGGATCGTCTTGAATAC-TTAGAAT
65 TTTCCCGAGCATGGAATGTTCGGAAAATTGTTCGAAGGAATGGATAGTCTTGAATACTTTA-AAG
* * * *
1015 AATCGAAGTTGTAAAAGAACTCGTAAAAGTTTAAGAAGTT-A-TT-ACAAAG-ACCAAGAGAGAA
129 AACCGAAGTTATAAAAGAACTCGTAAAAATTTAACAAGTTAAGTTCACAAAGAACCAAGAGAGAA
1076 ACAATTCTCACGTAAAAAA
194 ACAATTCTCAC-TAAAAAA
*
1095 GTTTCTAATTCAAAGACTACAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGAT
1 GTTTATAATTCAAAGACTACAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGAT
*
1160 TTCCCGAGCATCGAATGTTCGGAAAATTGTTCGAAGGAATGGATAG
66 TTCCCGAGCATGGAATGTTCGGAAAATTGTTCGAAGGAATGGATAG
1206 NNNNNNNNNN
Statistics
Matches: 265, Mismatches: 50, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
207 20 0.08
208 103 0.39
209 1 0.00
210 2 0.01
211 1 0.00
214 4 0.02
215 134 0.51
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (211 bp):
GTTTATAATTCAAAGACTACAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGAT
TTCCCGAGCATGGAATGTTCGGAAAATTGTTCGAAGGAATGGATAGTCTTGAATACTTTAAAGAA
CCGAAGTTATAAAAGAACTCGTAAAAATTTAACAAGTTAAGTTCACAAAGAACCAAGAGAGAAAC
AATTCTCACTAAAAAA
Found at i:1631 original size:216 final size:214
Alignment explanation
Indices: 1256--1693 Score: 576
Period size: 216 Copynumber: 2.0 Consensus size: 214
1246 NNNNNNNNNN
**
1256 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATCGAATGTTCGGAAAATTGTT
1 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATCGAATGTTCAAAAAATTGTT
* *
1321 CGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTG
66 CGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTAGTAAAAGTTTG
** * *
1386 ACAAGTTCGGAAGTTCGACCAATAACCAAGAGAGAAATAACG-CTCATG-TAAATAAGTTTTTAA
131 ACAAGTTCAAAAGTTCGACCAAGAACCAAGAGAG---TAACGACTC-TGATAAATAAGTTTATAA
* *
1449 TTTAAAAACCAAAAGTTGTTTAC
192 TTCAAAAACCAAAAATTGTTTAC
* ** ** *
1472 AAAATGACAAACTATTTAGGCCAAATGATGCGATTTTTCGATTATGGAATGTTCAAAAAATTAG-
1 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATCGAATGTTCAAAAAATT-GT
* * * *
1536 TCGAAGGTATGGATCGTCTTGAATATTTTAAGGAATCAAAGTTATAAAAGAACTAGTAAAAGTTT
65 TCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTAGTAAAAGTTT
* * * *
1601 GACTAGTTCAAAAGTTCGGCCAAGAACCAAGAGAGTAACGATTCTGACTTAATAAGTTTATAATT
130 GACAAGTTCAAAAGTTCGACCAAGAACCAAGAGAGTAACGACTCTGA-TAAATAAGTTTATAATT
*
1666 CAAAGACCAAAAATTGTTTAC
194 CAAAAACCAAAAATTGTTTAC
1687 AAAATGA
1 AAAATGA
1694 A
Statistics
Matches: 193, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
213 7 0.04
214 2 0.01
215 40 0.21
216 143 0.74
217 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (214 bp):
AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATCGAATGTTCAAAAAATTGTT
CGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTAGTAAAAGTTTG
ACAAGTTCAAAAGTTCGACCAAGAACCAAGAGAGTAACGACTCTGATAAATAAGTTTATAATTCA
AAAACCAAAAATTGTTTAC
Done.