Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014417.1 Kokia drynarioides strain JFW-HI SEQ_129455, 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: 24510
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:562 original size:30 final size:30
Alignment explanation
Indices: 519--977 Score: 290
Period size: 30 Copynumber: 15.5 Consensus size: 30
509 GTTTTACCCC
519 CGAA-CTTCC-AAAATCCCATTTTTGACCT
1 CGAACCTTCCAAAAATCCCATTTTTGACCT
* * *
547 CGAACCTTCCCAAAATTACCATTTTT-ACCC
1 CGAACCTT-CCAAAAATCCCATTTTTGACCT
* * *
577 CCAAACTTCCAAAAATCCCAATTTTGACCT
1 CGAACCTTCCAAAAATCCCATTTTTGACCT
* *
607 CGAACCTTCCAAAAATTACCATTTTT-ACCC
1 CGAACCTTCCAAAAA-TCCCATTTTTGACCT
* * * * *
637 CCAAACTTCTAAAAATCTCATTTTTGACCA
1 CGAACCTTCCAAAAATCCCATTTTTGACCT
* *
667 CGAACCTTCCCAAAAATACCATTTTT-ACCCC
1 CGAACCTT-CCAAAAATCCCATTTTTGA-CCT
*
698 CGAA-CTTCCAAAAATCCCATTTTTGACTT
1 CGAACCTTCCAAAAATCCCATTTTTGACCT
* *
727 CGAACCTTCCCAAAATTACCA-TTTT-ACCCT
1 CGAACCTT-CCAAAAATCCCATTTTTGA-CCT
* * * * *
757 C-AAACTTCAAAAAATCTCATTTTGGACCC
1 CGAACCTTCCAAAAATCCCATTTTTGACCT
* * * * * ***
786 CAAACCTTCCCAATATTACCATTATACCCCT
1 CGAACCTT-CCAAAAATCCCATTTTTGACCT
*
817 C-AA-CTTCCAAAAATCTCATTTTTGACCT
1 CGAACCTTCCAAAAATCCCATTTTTGACCT
* *
845 CGAACCTTCCAAAAATTACCA--TTT-AACT
1 CGAACCTTCCAAAAA-TCCCATTTTTGACCT
* * *
873 CCCAAACTTCCAAAAATCCCA-TTTTGACCC
1 -CGAACCTTCCAAAAATCCCATTTTTGACCT
* * *
903 CGAACCTTCCCAAAATTACCA-TTTT-ACCCC
1 CGAACCTT-CCAAAAATCCCATTTTTGA-CCT
* *
933 CAAACC-TCCTAAAATCCCATTTTTGACCT
1 CGAACCTTCCAAAAATCCCATTTTTGACCT
*
962 CGAGA-CATCCAAAAAT
1 CGA-ACCTTCCAAAAAT
978 TACTATTTTA
Statistics
Matches: 326, Mismatches: 77, Indels: 54
0.71 0.17 0.12
Matches are distributed among these distances:
28 43 0.13
29 99 0.30
30 118 0.36
31 66 0.20
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (30 bp):
CGAACCTTCCAAAAATCCCATTTTTGACCT
Found at i:615 original size:60 final size:59
Alignment explanation
Indices: 500--1045 Score: 645
Period size: 59 Copynumber: 9.2 Consensus size: 59
490 TAAACTGCCA
* * *
500 AAAATTATCGTTTTACCCCCGAACTTCC-AAAATCCCATTTTTGACCTCGAACCTTCCC
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCC
* *
558 AAAATTACCATTTTTACCCCCAAACTTCCAAAAATCCCAATTTTGACCTCGAACCTTCCA
1 AAAATTACCA-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCC
* * *
618 AAAATTACCATTTTTACCCCCAAACTTCTAAAAATCTCATTTTTGACCACGAACCTTCCC
1 AAAATTACCA-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCC
* * *
678 AAAAATACCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTTCGAACCTTCCC
1 AAAATTACCA-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCC
* * * * * *
738 AAAATTACCATTTTACCCTCAAACTTCAAAAAATCTCATTTTGGACCCCAAACCTTCCC
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCC
* * * *
797 AATATTACCATTATACCCCTC-AACTTCCAAAAATCTCATTTTTGACCTCGAACCTTCCA
1 AAAATTACCATTTTACCCC-CAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCC
* * *
856 AAAATTACCATTTAACTCCCAAACTTCCAAAAATCCCA-TTTTGACCCCGAACCTTCCC
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCC
* * * *
914 AAAATTACCATTTTACCCCCAAACCTCCTAAAATCCCATTTTTGACCTCGAGA-CATCCA
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGA-ACCTTCCC
* * ** * ** * * *
973 AAAATTACTATTTTACTCCCGGA-TGTCCAAAGACTCCGTTTTTTGACCTTGAAAC-TCTC
1 AAAATTACCATTTTACCCCCAAACT-TCCAAA-AATCCCATTTTTGACCTCGAACCTTCCC
1032 AAAATTACCATTTT
1 AAAATTACCATTTT
1046 TACTCCCGAA
Statistics
Matches: 419, Mismatches: 60, Indels: 17
0.84 0.12 0.03
Matches are distributed among these distances:
58 61 0.15
59 193 0.46
60 165 0.39
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCC
Found at i:2186 original size:29 final size:30
Alignment explanation
Indices: 2134--2190 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
2124 GAATTGGATC
2134 AAATCAAAATTTCATACATACAATTATATA
1 AAATCAAAATTTCATACATACAATTATATA
*
2164 AAATCAAAA-TTCA-AGTATACAATTATA
1 AAATCAAAATTTCATA-CATACAATTATA
2191 AATTAAACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 15 0.60
30 9 0.36
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATACATACAATTATATA
Found at i:15684 original size:20 final size:20
Alignment explanation
Indices: 15655--15696 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
15645 CTAGATTATA
15655 TATTTGAATTTTTATATATT
1 TATTTGAATTTTTATATATT
* *
15675 TATTTTAATTTTTATATTTT
1 TATTTGAATTTTTATATATT
15695 TA
1 TA
15697 ATGTGTATAT
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:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TATTTGAATTTTTATATATT
Found at i:23114 original size:2 final size:2
Alignment explanation
Indices: 23107--23135 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23097 AACCATTTAG
23107 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23136 TTGGACATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24022 original size:23 final size:22
Alignment explanation
Indices: 23996--24040 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
23986 ATGCGTTTCT
23996 ATTTTGAT-TATTAATTTATTTTA
1 ATTTT-ATGTATTAA-TTATTTTA
*
24019 ATTTTATGTTTTAATTATTTTA
1 ATTTTATGTATTAATTATTTTA
24041 TTGTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
ATTTTATGTATTAATTATTTTA
Done.