Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012944.1 Kokia drynarioides strain JFW-HI SEQ_127962, 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: 1961
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Found at i:63 original size:18 final size:19
Alignment explanation
Indices: 17--63 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
7 GTCATAATCT
* *
17 CATTAATAATAATATCATA
1 CATTAATAATAACATAATA
36 GCATTAAATAATAACATAATA
1 -CATT-AATAATAACATAATA
57 -ATTAATA
1 CATTAATA
64 TTAATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 3 0.12
20 4 0.17
21 13 0.54
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (19 bp):
CATTAATAATAACATAATA
Found at i:1206 original size:59 final size:59
Alignment explanation
Indices: 1114--1623 Score: 697
Period size: 59 Copynumber: 8.7 Consensus size: 59
1104 GTCCCTAAAC
* * *
1114 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAT
* * *
1173 CTTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCAATTTTTAACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAT
* * *
1232 CTTCCAAAAATTACTATTTTACCCCCAAACTTCC-AAAATCCCATTTTTGACATCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAT
* * * *
1290 CTTCCAAAAATTACAATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCGAAC
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAT
* * *
1349 CTTCTAAAAATTACGATTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCTCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAT
** * * *
1408 CTTCC-AAAATTACTATTTTACCCCTAAACTTCCAAAAATCCCATTTTAAACCCCGAAC
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAT
** * * *
1466 CTTCTTAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTTGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAT
* *
1525 CTTCCAAAAATTACTATTTTCCCCCCGAA-TTCCCAAAAATCCCATTTTTAGCC-CTGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTT-CCAAAAATCCCATTTTTAACCTC-GAAT
* *
1584 CTTCC-AAAATTACCATTTTACCCTCGAACTTCCAAAAATC
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATC
1624 TTATTTTTGA
Statistics
Matches: 400, Mismatches: 46, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
58 134 0.34
59 266 0.67
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (59 bp):
CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAT
Found at i:1321 original size:117 final size:118
Alignment explanation
Indices: 1111--1623 Score: 755
Period size: 117 Copynumber: 4.4 Consensus size: 118
1101 GAGGTCCCTA
* *
1111 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAATCTT
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTT
*
1176 CCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCAATTTTTAACCCCG
66 CCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCG
* * * * *
1229 AATCTTCCAAAAATTACTATTTTACCCCCAAACTTCC-AAAATCCCATTTTTGACATCGAATCTT
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTT
* * *
1293 CCAAAAATTACAATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
66 CCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCG
* * *
1346 AACCTTCTAAAAATTACGATTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTT
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTT
* *
1411 CC-AAAATTACTATTTTACCCCTAAACTTCCAAAAATCCCATTTTAAACCCCG
66 CCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCG
** * *
1463 AACCTTCTTAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTTGAATCTT
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTT
* * * *
1528 CCAAAAATTACTATTTTCCCCCCGAA-TTCCCAAAAATCCCATTTTTAGCCCTG
66 CCAAAAATTACTATTTTACCCCCAAACTT-CCAAAAATCCCATTTTTAACCCCG
* *
1581 AATCTTCC-AAAATTACCATTTTACCCTCGAACTTCCAAAAATC
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATC
1624 TTATTTTTGA
Statistics
Matches: 356, Mismatches: 36, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
117 248 0.70
118 108 0.30
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.32
Consensus pattern (118 bp):
AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTT
CCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCG
Found at i:1409 original size:176 final size:174
Alignment explanation
Indices: 1111--1620 Score: 725
Period size: 176 Copynumber: 2.9 Consensus size: 174
1101 GAGGTCCCTA
* *
1111 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAATCTT
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTT
* *
1176 CCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCAATTTTTAACCCCGAATCTTCCAAAA
66 CCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAA-CCCGAATCTTCC-AAA
** *
1241 ATTACTATTTTACCCCCAAACTTCCAAAATCCCATTTTTGACATCG
129 ATTACTATTTTACCCCCAAACTTCCAAAATCCCATTTTAAACACCG
* * * * *
1287 AATCTTCCAAAAATTACAATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCGAACCTT
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTT
* * *
1352 CTAAAAATTACGATTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTTCCAAAA
66 CCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACC-CGAATCTTCCAAAA
* *
1417 TTACTATTTTACCCCTAAACTTCCAAAAATCCCATTTTAAACCCCG
130 TTACTATTTTACCCCCAAACTTCC-AAAATCCCATTTTAAACACCG
** * *
1463 AACCTTCTTAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTTGAATCTT
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTT
* *
1528 CCAAAAATTACTATTTTCCCCCCGAA-TTCCCAAAAATCCCATTTTTAGCCCTGAATCTTCCAAA
66 CCAAAAATTACTATTTTACCCCCGAACTT-CCAAAAATCCCATTTTTAACCC-GAATCTTCCAAA
* * *
1592 ATTACCATTTTACCCTCGAACTTCCAAAA
129 ATTACTATTTTACCCCCAAACTTCCAAAA
1621 ATCTTATTTT
Statistics
Matches: 295, Mismatches: 35, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
175 36 0.12
176 259 0.88
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.32
Consensus pattern (174 bp):
AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAATCTT
CCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCGAATCTTCCAAAAT
TACTATTTTACCCCCAAACTTCCAAAATCCCATTTTAAACACCG
Done.