Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012497.1 Kokia drynarioides strain JFW-HI SEQ_127501, 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: 2058
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Found at i:823 original size:59 final size:59
Alignment explanation
Indices: 747--1068 Score: 194
Period size: 59 Copynumber: 5.5 Consensus size: 59
737 ATCATATTTG
* *
747 ACCCCAAACCTTTCAAAAATTACCATTTTA-CCATTGAACTTCCAAAAATCCCATTTTTA
1 ACCCCAAACCTTCCAAAAATTACCATTTTATCC-TCGAACTTCCAAAAATCCCATTTTTA
*
806 ACCCCAAACCTTCCAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCTCATTTTT-
1 ACCCCAAACCTTCCAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCATTTTTA
* * * * *
864 ACTCTCAAA-CTT-CAAAAAATCCCATTTT-TGACCTCGAACCTTCTAAAAATTACCA-TTTT-
1 AC-CCCAAACCTTCCAAAAATTACCATTTTAT--CCTCGAA-CTTCCAAAAA-TCCCATTTTTA
* * * * *
923 ACCCTCGAA-CTTCCAAAAA-TCCCATTTT-TGACCCCAAACCTTCCAAAAATTACCA-TTTTA
1 ACCC-CAAACCTTCCAAAAATTACCATTTTAT--CCTCGAA-CTTCCAAAAA-TCCCATTTTTA
* * * *
983 CCCCCGAA-CTTCCAAAAA-T-CTCATTTT-TGACTCTGAACCTTCCAAAAATTACCA-TTTTA
1 ACCCCAAACCTTCCAAAAATTAC-CATTTTAT-CCTC-GAA-CTTCCAAAAA-TCCCATTTTTA
* * *
1042 CCCCCGAA-CTTCCAAAAA-TCCCATTTT
1 ACCCCAAACCTTCCAAAAATTACCATTTT
1069 TGACCCCGAA
Statistics
Matches: 232, Mismatches: 19, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
56 1 0.00
57 14 0.06
58 16 0.07
59 186 0.80
60 15 0.06
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (59 bp):
ACCCCAAACCTTCCAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCATTTTTA
Found at i:864 original size:88 final size:86
Alignment explanation
Indices: 783--1093 Score: 319
Period size: 88 Copynumber: 3.5 Consensus size: 86
773 TTTACCATTG
783 AACTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTATCCTCGAACTTC
1 AACTTCCAAAAATCCCATTTTTAACCCCAAA-CTTCCAAAAATTACCATTTTATCCTCGAACTTC
*
848 CAAAAATCTCATTTTTACTCTCA
65 CAAAAATCTCATTTTTAC-CCCA
* * * * * *
871 AACTTCAAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTC
1 AACTTCCAAAAATCCCATTTTTAACC-CCAAACTTCCAAAAATTACCATTTTATCCTCGAACTTC
*
936 CAAAAATCCCATTTTTGACCCCA
65 CAAAAATCTCATTTTT-ACCCCA
* * * *
959 AACCTTCCAAAAATTACCA-TTTTACCCCCGAACTTCCAAAAA-T-CTCATTTT-TGACTCTGAA
1 AA-CTTCCAAAAA-TCCCATTTTTAACCCCAAACTTCCAAAAATTAC-CATTTTAT-CCTC-GAA
*
1020 CCTTCCAAAAAT-TACCA-TTTTACCCCCG
61 -CTTCCAAAAATCT--CATTTTTA-CCCCA
* *
1048 AACTTCCAAAAATCCCATTTTTGACCCCGAAACATCCAAAAATTAC
1 AACTTCCAAAAATCCCATTTTTAACCCC-AAACTTCCAAAAATTAC
1094 TATCTTACTC
Statistics
Matches: 183, Mismatches: 25, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
86 1 0.01
87 14 0.08
88 108 0.59
89 52 0.28
90 7 0.04
91 1 0.01
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (86 bp):
AACTTCCAAAAATCCCATTTTTAACCCCAAACTTCCAAAAATTACCATTTTATCCTCGAACTTCC
AAAAATCTCATTTTTACCCCA
Found at i:921 original size:147 final size:149
Alignment explanation
Indices: 743--1040 Score: 467
Period size: 147 Copynumber: 2.0 Consensus size: 149
733 TCTAATCATA
*
743 TTTGACCCCAAACCTTTCAAAAATTACCATTTTACCATTGAACTTCCAAAAATCCCATTTTTAAC
1 TTTGACCCCAAACCTTTCAAAAATTACCATTTTACCATCGAACTTCCAAAAATCCCATTTTTAAC
* *
808 CCCAAACCTTCCAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCTCATTTTT-ACTCTCAA
66 CCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACTCTCAA
*
872 ACTT-CAAAAAATCCCATT
131 ACTTCCAAAAAATACCATT
* * * *
890 TTTGACCTCGAACC-TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1 TTTGACCCCAAACCTTTC-AAAAATTACCATTTTACCATCGAACTTCCAAAAATCCCATTTTTAA
*
954 CCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACTCTGA
65 CCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACTCTCA
* *
1019 ACCTTCCAAAAATTACCATT
130 AACTTCCAAAAAATACCATT
1039 TT
1 TT
1041 ACCCCCGAAC
Statistics
Matches: 137, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
146 3 0.02
147 110 0.80
148 10 0.07
149 14 0.10
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (149 bp):
TTTGACCCCAAACCTTTCAAAAATTACCATTTTACCATCGAACTTCCAAAAATCCCATTTTTAAC
CCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACTCTCAA
ACTTCCAAAAAATACCATT
Found at i:1069 original size:59 final size:59
Alignment explanation
Indices: 781--1093 Score: 345
Period size: 59 Copynumber: 5.3 Consensus size: 59
771 ATTTTACCAT
* * * * *
781 TGAA-CTTCCAAAAA-TCCCATTTTTAACCCCAAACCTTCCAAAAATTACCA-TTTT-ATCC
1 TGAACCTTCCAAAAATTACCA-TTTTACCCCCGAA-CTTCCAAAAA-TCCCATTTTTGACCC
* * * *
839 TCGAA-CTTCCAAAAA-T-CTCATTTTTACTCTCAAACTTCAAAAAATCCCATTTTTGA-CC
1 T-GAACCTTCCAAAAATTAC-CA-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC
* *
897 TCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
1 T-GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC
** * *
957 CAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACTC
1 TGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC
1016 TGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC
1 TGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC
* * *
1075 CGAAACATCCAAAAATTAC
1 TGAACCTTCCAAAAATTAC
1094 TATCTTACTC
Statistics
Matches: 225, Mismatches: 22, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
57 4 0.02
58 22 0.10
59 193 0.86
60 5 0.02
61 1 0.00
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (59 bp):
TGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC
Found at i:1149 original size:118 final size:117
Alignment explanation
Indices: 871--1168 Score: 336
Period size: 118 Copynumber: 2.5 Consensus size: 117
861 TTTACTCTCA
* * * *
871 AACTTCAAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTC
1 AACTTCCAAAAATCTCATTTTTGACCTCGAACC-TCTCAAAATTACCATTTTACCCCCGAACTTC
* *
936 CAAAAATCCCATTTTTGACCCCAAACCTTCCAAAAATTACCATTTTACCCCCG
65 CAAAAATCCCATTTTTGACCCCAAACCATCCAAAAATTACCATCTTACCCCCG
989 AACTTCCAAAAATCTCATTTTTGA-CTCTGAACCT-TCCAAAAATTACCATTTTACCCCCGAACT
1 AACTTCCAAAAATCTCATTTTTGACCTC-GAACCTCT-C-AAAATTACCATTTTACCCCCGAACT
* * *
1052 TCCAAAAATCCCATTTTTGACCCCGAAA-CATCCAAAAATTACTATCTTACTCCTG
63 TCCAAAAATCCCATTTTTGACCCC-AAACCATCCAAAAATTACCATCTTACCCCCG
* * * * * **
1107 GA-TGTCTAAAGA-CTCCGTTTTTCGACCTCGAAACTCTCAAAATTACTGTTTTTACCCCCGAA
1 AACT-TCCAAAAATCT-CATTTTT-GACCTCGAACCTCTCAAAATTAC-CATTTTACCCCCGAA
1169 TGTTTTAAAT
Statistics
Matches: 154, Mismatches: 16, Indels: 19
0.81 0.08 0.10
Matches are distributed among these distances:
116 1 0.01
117 7 0.05
118 118 0.77
119 24 0.16
120 4 0.03
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.31
Consensus pattern (117 bp):
AACTTCCAAAAATCTCATTTTTGACCTCGAACCTCTCAAAATTACCATTTTACCCCCGAACTTCC
AAAAATCCCATTTTTGACCCCAAACCATCCAAAAATTACCATCTTACCCCCG
Done.