Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014828.1 Kokia drynarioides strain JFW-HI SEQ_129870, 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: 5126
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Found at i:2819 original size:360 final size:360
Alignment explanation
Indices: 2158--2841 Score: 1235
Period size: 360 Copynumber: 1.9 Consensus size: 360
2148 GAACTGATGA
* *
2158 TGGAATTTGTCCACTCAGTTGGTTCCATGAGAAGTCTAAAAAAGTGAGTTGCAAGAGGCTTCCCA
1 TGGAATTTGTCCACTCAATTGGTTCCATGACAAGTCTAAAAAAGTGAGTTGCAAGAGGCTTCCCA
*
2223 GTGATCTCGGAATTGGTCCTGATAAGTTGGAATTGGAGAGATCCAAAGACTTCAAGGACACAAGA
66 GTGATCTCGGAATTGGTCCTGATAAGTTGGAATTGGAGAGATCCAAAAACTTCAAGGACACAAGA
*
2288 TTCCCCATCGACTCAGGCAATCCTCCACAAAAAGTTGCCCCTCGAATATTCAAGTACTCCAAAGA
131 TTCCCCATCGACTCAGGCAATCCTCCACAAAAAGTTGCCCCTCGAATATCCAAGTACTCCAAAGA
*
2353 TGATAAATTTGTGATTGAGACAGACAATCCTTGAAAGAAACAATTTCTTGATAGATCTAAGTAAT
196 TGATAAATTTGTGATTGAGACAGACAATCCTTGAAAGAAACAATTTCCTGATAGATCTAAGTAAT
2418 TCAAGGCCCGTAGATTATCAACTGAATCAATCAATTCTGTAGAGACGGACATCCACGACAGATCT
261 TCAAGGCCCGTAGATTATCAACTGAATCAATCAATTCTGTAGAGACGGACATCCACGACAGATCT
2483 AAAAAAGTGAGTTGCAAGAGGTTCCCCAATGATCT
326 AAAAAAGTGAGTTGCAAGAGGTTCCCCAATGATCT
** *
2518 TGGAATTTGTCCACTCAATTGGTTCGC-TGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTTCCC
1 TGGAATTTGTCCACTCAATTGGTTC-CATGACAAGTCTAAAAAAGTGAGTTGCAAGAGGCTTCCC
*
2582 AGTGATCTTGGAATTGGTCCTGATAAGTTGGAATTGGAGAGATCCAAAAACTTCAAGGACACAAG
65 AGTGATCTCGGAATTGGTCCTGATAAGTTGGAATTGGAGAGATCCAAAAACTTCAAGGACACAAG
*
2647 ATTCCCCATTGACTCAGGCAATCCTCCACAAAAAGTTGCCCCTCGAATATCCAAGTACTCCAAAG
130 ATTCCCCATCGACTCAGGCAATCCTCCACAAAAAGTTGCCCCTCGAATATCCAAGTACTCCAAAG
* *
2712 ATGATAAATTTGTGATTGAGACAGACAATCCTTGAAAGAAAGAATTTCCTGATAGATCTAAGTAC
195 ATGATAAATTTGTGATTGAGACAGACAATCCTTGAAAGAAACAATTTCCTGATAGATCTAAGTAA
*
2777 TTCAAGGCCCGTAGATTATCAACTGAATCAATCAATTCTGTAGAGACGGACATCCTCGACAGATC
260 TTCAAGGCCCGTAGATTATCAACTGAATCAATCAATTCTGTAGAGACGGACATCCACGACAGATC
2842 CAAATGTTCA
Statistics
Matches: 310, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
360 309 1.00
361 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (360 bp):
TGGAATTTGTCCACTCAATTGGTTCCATGACAAGTCTAAAAAAGTGAGTTGCAAGAGGCTTCCCA
GTGATCTCGGAATTGGTCCTGATAAGTTGGAATTGGAGAGATCCAAAAACTTCAAGGACACAAGA
TTCCCCATCGACTCAGGCAATCCTCCACAAAAAGTTGCCCCTCGAATATCCAAGTACTCCAAAGA
TGATAAATTTGTGATTGAGACAGACAATCCTTGAAAGAAACAATTTCCTGATAGATCTAAGTAAT
TCAAGGCCCGTAGATTATCAACTGAATCAATCAATTCTGTAGAGACGGACATCCACGACAGATCT
AAAAAAGTGAGTTGCAAGAGGTTCCCCAATGATCT
Found at i:5050 original size:13 final size:13
Alignment explanation
Indices: 5032--5057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5022 ATTAAAAAAA
5032 TTAAAAATTATAT
1 TTAAAAATTATAT
5045 TTAAAAATTATAT
1 TTAAAAATTATAT
5058 AAAATATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAAAATTATAT
Done.