Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013402.1 Kokia drynarioides strain JFW-HI SEQ_128427, 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: 1743
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:234 original size:20 final size:20
Alignment explanation
Indices: 209--250 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
199 GGTGTCACTG
209 TTTCATTCAATCCTTTTCCA
1 TTTCATTCAATCCTTTTCCA
229 TTTCATTCAATCCTTTTCCA
1 TTTCATTCAATCCTTTTCCA
249 TT
1 TT
251 AAAGAAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.29, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTCATTCAATCCTTTTCCA
Found at i:476 original size:20 final size:20
Alignment explanation
Indices: 451--492 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
441 GCTTTCACTG
* *
451 TTTTATTTAATCCTTTTCCA
1 TTTTATTAAATCATTTTCCA
471 TTTTATTAAATCATTTTCCA
1 TTTTATTAAATCATTTTCCA
491 TT
1 TT
493 GAAGAAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATTAAATCATTTTCCA
Found at i:1042 original size:221 final size:221
Alignment explanation
Indices: 479--1743 Score: 1917
Period size: 221 Copynumber: 5.7 Consensus size: 221
469 CATTTTATTA
* * * *
479 AATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAAGGATATTATCCCTTTCCAATAGC
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGT
* * *
544 TTTATGCCACACCAACAATTTCATCCTAAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGG
66 TTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
* * *
609 ATGAAAATGTTGACATTAAGAATGAAAATACTGATGTGGCATAAAAAC-AATAGAAAAGGGACAC
131 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGT-AAAACTAATGGAAAAGGGACAC
*
673 AAATGACGAGGTGTCACTGTTTCATTC
195 AAATGACGTGGTGTCACTGTTTCATTC
* * *
700 AATCCTTTTCCATTGAAGAA-AAAAAGGATTGTATAAAACAGGGATATTACCCCATTCCAATAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGT
** * *
764 TTTATGCCACATCAACAATTTCATATTGAATTTCAGGATTTTGATTTTAATTTGATTTTTTTAGG
66 TTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
* * ** *
829 ATGAAAATGTTAAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAAGAAACACC
131 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACA
*
894 AATGACGTGGTGCCACTGTTTCATTC
196 AATGACGTGGTGTCACTGTTTCATTC
* * * * *
920 AATCATTTTCCACTGAAGAAGAGAAAGGATTCTATGAAACAGGGATATTATCCCTTTTCAATAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGT
* *
985 TTTATGCCACATCAACAATTTCATCCTGAATTTCAGAATGTTAATTTTAATTTGATTTTTTCAGG
66 TTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
* * * * * *
1050 ATGAAAATGATGAAATTAAGAAAGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGTGACATA
131 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACA
* *
1115 GATGACGTCGTGTCACTGTTTCATTC
196 AATGACGTGGTGTCACTGTTTCATTC
*
1141 AATCCTTTTCCATTGAAGAAGAGGAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGT
* *
1206 TTTATGCCAC-TCCAACAATTTCATCCTGTATTTCAGGATTTTAATTTTTATTTGATTTTTTCAG
66 TTTATGCCACAT-CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAG
* * *
1270 GATGAAAATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTACTGTAAAAGGGACAC
130 GATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACAC
*
1335 AAATGATGTGGTGTCACTGTTTCATTC
195 AAATGACGTGGTGTCACTGTTTCATTC
* * * *
1362 AATCCTTTTCCATTGAAGAAGAGAAAGGATTCTATGAAACTGGGATATTATCCCTTTCCATTAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGT
** * * * *
1427 TTTATGCCACATCAACAATTTCATTTTCAATTTCAAGATTTTAATTTTAATTTTAATTTTTCAGG
66 TTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
*
1492 ATGAAAATGTTGAAATTAAGATTGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACA
131 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACA
*
1557 ATTGACGTGGTGTCACTGTTTCATTC
196 AATGACGTGGTGTCACTGTTTCATTC
*
1583 AATCCTTTTCCATTGAAGAGGAGAAAGGATTGTATAAAACTA-GGATATTATCCCTTTCCAATAG
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAAC-AGGGATATTATCCCTTTCCAATAG
*
1647 TTTTATGCCACATCAACAATTTCATCCTGTATTTCAGGATTTTAATTTTAATTTGATTTTTTCAG
65 TTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAG
* *
1712 GATGAAAATGTTAAAATTAAGAATCAAAATAC
130 GATGAAAATGTTGAAATTAAGAATGAAAATAC
Statistics
Matches: 935, Mismatches: 104, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
219 5 0.01
220 190 0.20
221 739 0.79
222 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (221 bp):
AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGT
TTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACA
AATGACGTGGTGTCACTGTTTCATTC
Done.