Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010536.1 Kokia drynarioides strain JFW-HI SEQ_125454, 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: 3984
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:668 original size:30 final size:28
Alignment explanation
Indices: 621--1007 Score: 292
Period size: 30 Copynumber: 13.2 Consensus size: 28
611 CTAAAAATTA
*
621 CCATTTTACCCCCAAACTTCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* *
649 CCATTTTTGACCCCAAAACTTCCAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAATC
* **
679 CCATTTTAGCCCTGAACTTCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* * *
707 TCAATTTTAACCCCGAAACTTCCAAAAATTA
1 -CCATTTT-ACCCCAAAACTTCCAAAAA-TC
* *
738 CCATTTTACCATC-GAACTTCCAAAAATC
1 CCATTTTACC-CCAAAACTTCCAAAAATC
* *
766 CCATTTTTTACCCCAAAACTTCCAAAATTA
1 CCA--TTTTACCCCAAAACTTCCAAAAATC
* ***
796 TCATTTTACCCTTGAACTTCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* *
824 CCATTTTTGACCCTAAAACTTCCAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
** *
855 CCATTTTACCCCCGAACTTCCAAAAAAC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* *
883 TCATTTTTGACCCCAAAACTTCCAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
* * *
914 CCATTTTACTCTC-GAACTTCTAAAAATC
1 CCATTTTAC-CCCAAAACTTCCAAAAATC
* * * * *
942 TCATTTTTGACCTCGAAACTTCAAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
**
973 CCATTTTACCCCCGAACTTCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
1001 CCATTTT
1 CCATTTT
1008 TACTCACGGA
Statistics
Matches: 283, Mismatches: 56, Indels: 40
0.75 0.15 0.11
Matches are distributed among these distances:
28 58 0.20
29 89 0.31
30 126 0.45
31 10 0.04
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (28 bp):
CCATTTTACCCCAAAACTTCCAAAAATC
Found at i:744 original size:59 final size:58
Alignment explanation
Indices: 613--1008 Score: 535
Period size: 59 Copynumber: 6.7 Consensus size: 58
603 TAAATTGTCT
**
613 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC
1 AAAAATTACCATTTTA-CCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC
* * * *
672 -AAAATTACCATTTTAGCCCTGAACTTCCAAAAATCTCAATTTTAACCCCGAAACTTCC
1 AAAAATTACCATTTTA-CCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC
* *
730 AAAAATTACCATTTTACCATCGAACTTCCAAAAATCCCATTTTTTACCCCAAAACTTCC
1 AAAAATTACCATTTTACCCT-GAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC
* *
789 -AAAATTATCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCC
1 AAAAATTACCATTTTACCC-TGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC
* * *
847 AAAAATTACCATTTTACCCCCGAACTTCCAAAAAACTCATTTTTGACCCCAAAACTTCC
1 AAAAATTACCATTTTA-CCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC
* * * * * *
906 AAAAATTACCATTTTACTCTCGAACTTCTAAAAATCTCATTTTTGACCTCGAAACTTCA
1 AAAAATTACCATTTTACCCT-GAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC
*
965 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT
1 AAAAATTACCATTTTA-CCCTGAACTTCCAAAAATCCCATTTTT
1009 ACTCACGGAT
Statistics
Matches: 298, Mismatches: 32, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
58 108 0.36
59 185 0.62
60 5 0.02
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC
Found at i:756 original size:117 final size:116
Alignment explanation
Indices: 613--1008 Score: 612
Period size: 117 Copynumber: 3.4 Consensus size: 116
603 TAAATTGTCT
*
613 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAATT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAATT
* *
678 ACCATTTTAGCCCTGAACTTCCAAAAATCTCAATTTTAACCCCGAAACTTCC
66 ACCATTTTA-CCCTGAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTCC
** *
730 AAAAATTACCATTTTACCATCGAACTTCCAAAAATCCCATTTTTTACCCCAAAACTTCCAAAATT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAATT
* * **
795 ATCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCC
66 ACCATTTTACCC-TGAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTCC
* *
847 AAAAATTACCATTTTACCCCCGAACTTCCAAAAAACTCATTTTTGACCCCAAAACTTCCAAAAAT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC-AAAAT
* * * *
912 TACCATTTTACTCTCGAACTTCTAAAAATCTCATTTTTGACCTCGAAACTTCA
65 TACCATTTTACCCT-GAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTCC
965 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT
1009 ACTCACGGAT
Statistics
Matches: 251, Mismatches: 25, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
116 3 0.01
117 158 0.63
118 90 0.36
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (116 bp):
AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAATT
ACCATTTTACCCTGAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTCC
Done.