Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000038.1 Kokia drynarioides strain JFW-HI SEQ_61130, 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, 717
Length: 1196
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Found at i:887 original size:59 final size:58
Alignment explanation
Indices: 800--1196 Score: 296
Period size: 59 Copynumber: 6.8 Consensus size: 58
790 CGTCAGAACT
* * *
800 TTTCCAAAATTCCATTTTTGACCCCGAATCTTCCAAAAATTA-CATTTTTACTCCCAAAC
1 TTTCCAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCA-TTTTAC-CCCAAAC
** * *
859 TTTCCAAAATTCCATTTTTAACCTCGAATTTTCAAAAAATTA-CATTTTTACCCCTAAAT
1 TTTCCAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCA-TTTTACCCC-AAAC
* * * * ***
918 TTTCAAAAATTCCATTTTTAACCT-TAAACTTTCGAAAATTACCATTTTACCTTTGAAC
1 TTTCCAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTACC-CCAAAC
* * * *
976 -TTCCAAAAATTCAATTTTTGACC-CCAAACTTCCTAAAAATTACCATTTTACCCTCGAAC
1 TTTCC-AAAATTCCATTTTTAACCTCGAAACTTCC-AAAAATTACCATTTTACCC-CAAAC
** *
1035 -TTCCAAAAATTCCATTTTTAACC-C-AAACTTCTTGAAAGTTACCATTTTACCCCTAAAC
1 TTTCC-AAAATTCCATTTTTAACCTCGAAACTTC-CAAAAATTACCATTTTACCCC-AAAC
* * * * * *
1093 -TTCTAAAAATTCCATTTTTGACC-CTAAACTTCCTAAAAATTACCATTATACCTCGAAC
1 TTTC-CAAAATTCCATTTTTAACCTCGAAACTTCC-AAAAATTACCATTTTACCCCAAAC
* * *
1151 -TTCCAAAAAATTACATTTTTGACCT-TAAACTTCTCAAAAATTACCA
1 TTTCC--AAAATTCCATTTTTAACCTCGAAACTTC-CAAAAATTACCA
Statistics
Matches: 282, Mismatches: 40, Indels: 32
0.80 0.11 0.09
Matches are distributed among these distances:
57 4 0.01
58 100 0.35
59 177 0.63
60 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (58 bp):
TTTCCAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTACCCCAAAC
Found at i:1112 original size:117 final size:118
Alignment explanation
Indices: 801--1196 Score: 416
Period size: 117 Copynumber: 3.4 Consensus size: 118
791 GTCAGAACTT
* ** * *
801 TTCC-AAAATTCCATTTTTGACCCCGAATCTTC-CAAAAATTA-CATTTTTACTCCC-AAACTTT
1 TTCCAAAAATTCCATTTTT-AACCTTAAACTTCTCGAAAATTACCA-TTTTAC-CCCTAAAC-TT
* * * * * * * *
862 CC-AAAATTCCATTTTTAACCTCGAATTTTCAAAAAATTA-CATTTTTACCC-CTAAAT
62 CCAAAAATTCCATTTTTGACCCCAAACTTCCTAAAAATTACCA-TTTTACCCTC-GAAC
* ** *
918 TTTCAAAAATTCCATTTTTAACCTTAAACTT-TCGAAAATTACCATTTTACCTTTGAACTTCCAA
1 TTCCAAAAATTCCATTTTTAACCTTAAACTTCTCGAAAATTACCATTTTACCCCTAAACTTCCAA
*
982 AAATTCAATTTTTGACCCCAAACTTCCTAAAAATTACCATTTTACCCTCGAAC
66 AAATTCCATTTTTGACCCCAAACTTCCTAAAAATTACCATTTTACCCTCGAAC
* * * *
1035 TTCCAAAAATTCCATTTTTAACC-CAAACTTCTTGAAAGTTACCATTTTACCCCTAAACTTCTAA
1 TTCCAAAAATTCCATTTTTAACCTTAAACTTCTCGAAAATTACCATTTTACCCCTAAACTTCCAA
* *
1099 AAATTCCATTTTTGACCCTAAACTTCCTAAAAATTACCATTATA-CCTCGAAC
66 AAATTCCATTTTTGACCCCAAACTTCCTAAAAATTACCATTTTACCCTCGAAC
* * *
1151 TTCCAAAAAATTACATTTTTGACCTTAAACTTCTCAAAAATTACCA
1 TTCC-AAAAATTCCATTTTTAACCTTAAACTTCTCGAAAATTACCA
Statistics
Matches: 234, Mismatches: 35, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
116 23 0.10
117 175 0.75
118 36 0.15
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (118 bp):
TTCCAAAAATTCCATTTTTAACCTTAAACTTCTCGAAAATTACCATTTTACCCCTAAACTTCCAA
AAATTCCATTTTTGACCCCAAACTTCCTAAAAATTACCATTTTACCCTCGAAC
Found at i:1190 original size:30 final size:29
Alignment explanation
Indices: 765--1194 Score: 214
Period size: 29 Copynumber: 14.6 Consensus size: 29
755 GGAGGTCCTT
* * * *
765 AAACTGTC-CAAAAATCATATTTTGACGTC
1 AAACT-TCTCAAAAATTACATTTTTACCTC
* * * *
794 AGAACTTTTCCAAAATTCCATTTTTGACCCC
1 A-AACTTCTCAAAAATTACATTTTT-ACCTC
* *
825 GAATCTTC-CAAAAATTACATTTTTACTCCC
1 -AAACTTCTCAAAAATTACATTTTTAC-CTC
* *
855 AAACTT-TCCAAAATTCCATTTTTAACCTC
1 AAACTTCTCAAAAATTACATTTTT-ACCTC
* * *
884 GAA-TTTTCAAAAAATTACATTTTTACCCC
1 AAACTTCTC-AAAAATTACATTTTTACCTC
* * *
913 TAAA-TTTTCAAAAATTCCATTTTTAACCTT
1 -AAACTTCTCAAAAATTACATTTTT-ACCTC
* *
943 AAACTT-TCGAAAATTACCA-TTTTACCTTT
1 AAACTTCTCAAAAATTA-CATTTTTACC-TC
* *
972 GAACTTC-CAAAAATT-CAATTTTTGACCCC
1 AAACTTCTCAAAAATTAC-ATTTTT-ACCTC
1001 AAACTTC-CTAAAAATTACCA-TTTTACCCTC
1 AAACTTCTC-AAAAATTA-CATTTTTA-CCTC
* *
1031 GAACTTC-CAAAAATTCCATTTTTAACC-C
1 AAACTTCTCAAAAATTACATTTTT-ACCTC
** * *
1059 AAACTTCTTGAAAGTTACCA-TTTTACCCC
1 AAACTTCTCAAAAATTA-CATTTTTACCTC
*
1088 TAAACTTCT-AAAAATTCCATTTTTGACC-C
1 -AAACTTCTCAAAAATTACATTTTT-ACCTC
*
1117 TAAACTTC-CTAAAAATTACCA-TTATACCTC
1 -AAACTTCTC-AAAAATTA-CATTTTTACCTC
* *
1147 GAACTTC-CAAAAAATTACATTTTTGACCTT
1 AAACTTCTC-AAAAATTACATTTTT-ACCTC
1177 AAACTTCTCAAAAATTAC
1 AAACTTCTCAAAAATTAC
1195 CA
Statistics
Matches: 315, Mismatches: 49, Indels: 73
0.72 0.11 0.17
Matches are distributed among these distances:
27 1 0.00
28 22 0.07
29 150 0.48
30 129 0.41
31 11 0.03
32 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
AAACTTCTCAAAAATTACATTTTTACCTC
Done.