Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005796.1 Kokia drynarioides strain JFW-HI SEQ_120069, 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, 867
Length: 1445
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Found at i:1027 original size:29 final size:29
Alignment explanation
Indices: 984--1277 Score: 133
Period size: 29 Copynumber: 10.0 Consensus size: 29
974 TTATACTTTA
*
984 ACCCCCGAACTTTCTAAAAATTACATTTTT
1 ACCCTCGAA-TTTCTAAAAATTACATTTTT
* *
1014 ACCCTTGAATTTCTTTGAAAATTACATTTTT
1 ACCCTCGAATTTC--TAAAAATTACATTTTT
* * *
1045 ACCCTCGAACATTCTAAAATTTCCA-TTTT
1 ACCCTCGAA-TTTCTAAAAATTACATTTTT
* * *
1074 ACTCCT-AAACTTTC-CAAAATTACAATTTT
1 AC-CCTCGAA-TTTCTAAAAATTACATTTTT
* * *
1103 ACACTCGAATTT-TCCAAAATTCCATTTTT
1 ACCCTCGAATTTCT-AAAAATTACATTTTT
** *
1132 AATCTCG-ATTTCACGAAAAATTACCA-TTTT
1 ACCCTCGAATTT--CTAAAAATTA-CATTTTT
* * *
1162 ACCCCCGAACTTTC-CAAAATTCCATTTTT
1 ACCCTCGAA-TTTCTAAAAATTACATTTTT
*
1191 A-CCTCGAATTTC-ACCCAAAATTCCATTTTTT
1 ACCCTCGAATTTCTA---AAAATTACA-TTTTT
* * * **
1222 A-TCTTGATTTTTCTAAAAATTACCGTTTT
1 ACCCTCGA-ATTTCTAAAAATTACATTTTT
* *
1251 ACCCTCGAATGTCT-AAAATTCCATTTT
1 ACCCTCGAATTTCTAAAAATTACATTTT
1278 AATCCCCAAA
Statistics
Matches: 200, Mismatches: 42, Indels: 46
0.69 0.15 0.16
Matches are distributed among these distances:
27 4 0.02
28 34 0.17
29 62 0.31
30 53 0.26
31 36 0.18
32 10 0.05
33 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.40
Consensus pattern (29 bp):
ACCCTCGAATTTCTAAAAATTACATTTTT
Found at i:1176 original size:59 final size:59
Alignment explanation
Indices: 1089--1219 Score: 176
Period size: 59 Copynumber: 2.2 Consensus size: 59
1079 TAAACTTTCC
* * * * *
1089 AAAATTACAATTTTACACTCGAATTTTCCAAAATTCCATTTTTAATCTCG-ATTTCACGA
1 AAAATTACCATTTTACACCCGAACTTTCCAAAATTCCATTTTT-ACCTCGAATTTCACCA
* *
1148 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTACCTCGAATTTCACCC
1 AAAATTACCATTTTACACCCGAACTTTCCAAAATTCCATTTTTACCTCGAATTTCACCA
1207 AAAATT-CCATTTT
1 AAAATTACCATTTT
1220 TTATCTTGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
58 12 0.19
59 52 0.81
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (59 bp):
AAAATTACCATTTTACACCCGAACTTTCCAAAATTCCATTTTTACCTCGAATTTCACCA
Found at i:1290 original size:89 final size:89
Alignment explanation
Indices: 1060--1308 Score: 231
Period size: 89 Copynumber: 2.8 Consensus size: 89
1050 CGAACATTCT
* * ** * * * *
1060 AAAATTTCCATTTTACTCCTAAACTTTCCAAAATTACAATTTT-ACACTCGAATTTT--CCAAAA
1 AAAATTACCATTTTACCCCCGAACTGTCCAAAATT-CCATTTTAAC-CCCAAATTTTCACCAAAA
1122 TTCCATTTTTAATCTCGATTTCACGA
64 TTCCATTTTTAATCTCGATTTCACGA
* * * *
1148 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTACCTCGAA-TTTCACCCAAAAT
1 AAAATTACCATTTTACCCCCGAACTGTCCAAAATTCCATTTTAACCCCAAATTTTCA-CCAAAAT
* * ** *
1212 TCCATTTTTTATCTTGATTTTTCTA
65 TCCATTTTTAATCTCGATTTCACGA
* * *
1237 AAAATTACCGTTTTACCCTCGAA-TGTCTAAAATTCCATTTTAATCCCCAAATTTTCA-CAAAAT
1 AAAATTACCATTTTACCCCCGAACTGTCCAAAATTCCATTTTAA-CCCCAAATTTTCACCAAAA-
1300 TTCCATTTT
64 TTCCATTTT
1309 ACCCTCGAGA
Statistics
Matches: 137, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
86 3 0.02
87 12 0.09
88 55 0.40
89 62 0.45
90 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (89 bp):
AAAATTACCATTTTACCCCCGAACTGTCCAAAATTCCATTTTAACCCCAAATTTTCACCAAAATT
CCATTTTTAATCTCGATTTCACGA
Done.