Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000501.1 Kokia drynarioides strain JFW-HI SEQ_111378, 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, 954
Length: 1591
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Found at i:639 original size:86 final size:85
Alignment explanation
Indices: 470--1108 Score: 593
Period size: 86 Copynumber: 7.4 Consensus size: 85
460 CCTGCACATG
* * ** * *
470 CAAGGTGCCGATGC-TCTCCGACGGTCCCGCATAACCATCGGCCTAAGTTACCGATAGTGTCCGA
1 CAAGGT-CCGATACTTC-CCGATGGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGA
*
534 TGCTCTCGCACATCGAAGGCAC
64 TGCTCTCGCACATCCAAGGCAC
* * * * *
556 CATAGTGT-CGATACTTCTCGATGGTCCCGTACCACCATCGGCCTTAGTTGTCGATGGTGCCCGA
1 CA-AG-GTCCGATACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGA
* ** *
620 TGCTCCCATACACCCAAGGCAC
64 TGCTCTCGCACATCCAAGGCAC
* * * *
642 CAAGGTACCGATGCTTCTCGATGGTCCCGCACCACCATCGACCTAAG-TGACCGAAGGTGTCCGA
1 CAAGGT-CCGATACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTG-CCGATGGTGTCCGA
* *
706 TGCTCTTGCACATCCAAGGCAG
64 TGCTCTCGCACATCCAAGGCAC
** * * * * *
728 CAAGGTCCCGACGGC-TCCCGATTGTCCTGCACCACCATCGACCTAAGTTACCGAAGGTGTCCGA
1 CAAGGT-CCGA-TACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGA
* *
792 TGTTTTCGCACATCCAAGGCAC
64 TGCTCTCGCACATCCAAGGCAC
* * * *
814 CAAGGTACCGATACTTCCCGATGGTCCCGCACCACCATCAGCCTTAGTTACCAATGGTGTCCGAT
1 CAAGGT-CCGATACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGAT
* * *
879 GCTCCCGCACATCGAAGGTAC
65 GCTCTCGCACATCCAAGGCAC
* * * * * *
900 CAAGGTACCGATACTTCCCGATGGTCCTGCATCATCAACGGCCTTAGCTGCCAATACGATGGTGT
1 CAAGGT-CCGATACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTG-C----CGATGGTGT
*
965 CCGATTCTCTCGCACATCCAAGGCAC
60 CCGATGCTCTCGCACATCCAAGGCAC
* *** * * * *
991 CAAGGTGTCGATGGATCCCGATTGTCTCGCACCACCATCGACCTAAGCTGCCGATGGTGTCCGAT
1 CAAGGT-CCGATACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGAT
* *
1056 GCTCCCGCACATCGAAGGCAC
65 GCTCTCGCACATCCAAGGCAC
*
1077 CATGGTGCCGATACTTCCCGATGGTCCCGCAC
1 CAAGGT-CCGATACTTCCCGATGGTCCCGCAC
1109 ATCCAAGGTA
Statistics
Matches: 450, Mismatches: 89, Indels: 28
0.79 0.16 0.05
Matches are distributed among these distances:
84 2 0.00
85 5 0.01
86 365 0.81
87 8 0.02
88 2 0.00
90 1 0.00
91 67 0.15
ACGTcount: A:0.22, C:0.34, G:0.23, T:0.21
Consensus pattern (85 bp):
CAAGGTCCGATACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGATG
CTCTCGCACATCCAAGGCAC
Found at i:764 original size:172 final size:171
Alignment explanation
Indices: 470--1108 Score: 653
Period size: 172 Copynumber: 3.7 Consensus size: 171
460 CCTGCACATG
* * ** * *
470 CAAGGTGCCGATGC-TCTCCGACGGTCCCGCATAACCATCGGCCTAAGTTACCGATA-GTGTCCG
1 CAAGGTACCGATGCTTC-CCGATGGTCCCGCACCACCATCGACCTAAGTGACCGA-AGGTGTCCG
* * * *
533 ATGCTCTCGCACATCGAAGGCACCATAGTGT-CGATACTTCTCGATGGTCCCGTACCACCATCGG
64 ATGCTCCCGCACATCGAAGGCACCA-AG-GTCCGATACTTCCCGATGGTCCTGCACCACCATCGG
* * ** *
597 CCTTAGTTGTCGATGGTGCCCGATGCTCCCATACACCCAAGGCAC
127 CCTTAGTTGTCGATGGTGTCCGATGCTCTCGCACATCCAAGGCAC
*
642 CAAGGTACCGATGCTTCTCGATGGTCCCGCACCACCATCGACCTAAGTGACCGAAGGTGTCCGAT
1 CAAGGTACCGATGCTTCCCGATGGTCCCGCACCACCATCGACCTAAGTGACCGAAGGTGTCCGAT
** * * ** * *
707 GCTCTTGCACATCCAAGGCAGCAAGGTCCCGACGGC-TCCCGATTGTCCTGCACCACCATCGACC
66 GCTCCCGCACATCGAAGGCACCAAGGT-CCGA-TACTTCCCGATGGTCCTGCACCACCATCGGCC
* ** * * *
771 TAAGTTACCGAAGGTGTCCGATGTTTTCGCACATCCAAGGCAC
129 TTAGTTGTCGATGGTGTCCGATGCTCTCGCACATCCAAGGCAC
* * *
814 CAAGGTACCGATACTTCCCGATGGTCCCGCACCACCATC-AGCCTTAGTTACC-AATGGTGTCCG
1 CAAGGTACCGATGCTTCCCGATGGTCCCGCACCACCATCGA-CCTAAGTGACCGAA-GGTGTCCG
* * * *
877 ATGCTCCCGCACATCGAAGGTACCAAGGTACCGATACTTCCCGATGGTCCTGCATCATCAACGGC
64 ATGCTCCCGCACATCGAAGGCACCAAGGT-CCGATACTTCCCGATGGTCCTGCACCACCATCGGC
* *
942 CTTAGCTGCCAATACGATGGTGTCCGATTCTCTCGCACATCCAAGGCAC
128 CTTAGTTG----T-CGATGGTGTCCGATGCTCTCGCACATCCAAGGCAC
** ** * * *
991 CAAGGTGTCGATGGATCCCGATTGTCTCGCACCACCATCGACCTAAGCTG-CCGATGGTGTCCGA
1 CAAGGTACCGATGCTTCCCGATGGTCCCGCACCACCATCGACCTAAG-TGACCGAAGGTGTCCGA
* *
1055 TGCTCCCGCACATCGAAGGCACCATGGTGCCGATACTTCCCGATGGTCCCGCAC
65 TGCTCCCGCACATCGAAGGCACCAAGGT-CCGATACTTCCCGATGGTCCTGCAC
1109 ATCCAAGGTA
Statistics
Matches: 383, Mismatches: 68, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
170 2 0.01
171 7 0.02
172 240 0.63
173 3 0.01
177 128 0.33
178 3 0.01
ACGTcount: A:0.22, C:0.34, G:0.23, T:0.21
Consensus pattern (171 bp):
CAAGGTACCGATGCTTCCCGATGGTCCCGCACCACCATCGACCTAAGTGACCGAAGGTGTCCGAT
GCTCCCGCACATCGAAGGCACCAAGGTCCGATACTTCCCGATGGTCCTGCACCACCATCGGCCTT
AGTTGTCGATGGTGTCCGATGCTCTCGCACATCCAAGGCAC
Found at i:824 original size:43 final size:43
Alignment explanation
Indices: 691--824 Score: 107
Period size: 43 Copynumber: 3.1 Consensus size: 43
681 GACCTAAGTG
*
691 ACCGAAGGTGTCCGATGCTCTT-GCACATCCAAGGCAGCAAGGT
1 ACCGAAGGTGTCCGATG-TCTTCGCACATCCAAGGCACCAAGGT
* * * * ** *
734 CCCGACGGCT-CCCGATTGTCCT-GCACCA-CCATCG-ACCTAAGTT
1 ACCGAAGG-TGTCCGA-TGTCTTCGCA-CATCCAAGGCACC-AAGGT
*
777 ACCGAAGGTGTCCGATGTTTTCGCACATCCAAGGCACCAAGGT
1 ACCGAAGGTGTCCGATGTCTTCGCACATCCAAGGCACCAAGGT
820 ACCGA
1 ACCGA
825 TACTTCCCGA
Statistics
Matches: 67, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
42 9 0.13
43 50 0.75
44 8 0.12
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (43 bp):
ACCGAAGGTGTCCGATGTCTTCGCACATCCAAGGCACCAAGGT
Found at i:845 original size:43 final size:43
Alignment explanation
Indices: 798--1141 Score: 157
Period size: 43 Copynumber: 7.9 Consensus size: 43
788 CCGATGTTTT
*
798 CGCACATCCAAGGCACCAAGGTACCGATACTTCCCGATGGTCC
1 CGCACATCCAAGGCACCAAGGTGCCGATACTTCCCGATGGTCC
** * * * ** *
841 CGCACCA-CCATCA-GC-CTTAGTTACCAATGGTGT-CCGATGCTCC
1 CGCA-CATCCA--AGGCACCAAGGTGCCGATACT-TCCCGATGGTCC
* * *
884 CGCACATCGAAGGTACCAAGGTACCGATACTTCCCGATGGTCC
1 CGCACATCCAAGGCACCAAGGTGCCGATACTTCCCGATGGTCC
* ** * * * ** *
927 TGCATCAT-CAACGGC-CTTAGCTGCCAATACGATGGTGTCCGATTCTCT
1 CGCA-CATCCAA-GGCACCAAGGTGCCGATAC--T--T-CCCGATGGTCC
* *** * *
975 CGCACATCCAAGGCACCAAGGTGTCGATGGATCCCGATTGTCT
1 CGCACATCCAAGGCACCAAGGTGCCGATACTTCCCGATGGTCC
** * ** *
1018 CGCACCA-CCATCG-ACCTAAGCTGCCGATGGTGT-CCGATGCTCC
1 CGCA-CATCCAAGGCACC-AAGGTGCCGATACT-TCCCGATGGTCC
* *
1061 CGCACATCGAAGGCACCATGGTGCCGATACTTCCCGATGGTCC
1 CGCACATCCAAGGCACCAAGGTGCCGATACTTCCCGATGGTCC
* * *
1104 CGCACATCCAAGGTACCATGGTTCCGATACTTCCCGAT
1 CGCACATCCAAGGCACCAAGGTGCCGATACTTCCCGAT
1142 AGTTTCGAAC
Statistics
Matches: 220, Mismatches: 58, Indels: 46
0.68 0.18 0.14
Matches are distributed among these distances:
41 1 0.00
42 10 0.05
43 162 0.74
44 17 0.08
45 2 0.01
47 7 0.03
48 21 0.10
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.21
Consensus pattern (43 bp):
CGCACATCCAAGGCACCAAGGTGCCGATACTTCCCGATGGTCC
Found at i:1195 original size:129 final size:129
Alignment explanation
Indices: 975--1229 Score: 309
Period size: 129 Copynumber: 2.0 Consensus size: 129
965 CCGATTCTCT
** * *
975 CGCACATCCAAGGCACCAAGGTGTCGATGGATCCCGATTGTCTCGCACCACCATCGACCTAAGCT
1 CGCACATCCAAGGCACCAAGGTGTCGATACATCCCGATAGTCTCGAACCACCATCGACCTAAGCT
* * * * *
1040 GCCGATGGTGTCCGATGCTCCCGCACATC-GAAGGCACCATGGTGCCGAT-ACTTCCCGATGGTC
66 ACCGATGGTGTCCAATGCTCCCGCACATCTG-AGGCACCAAGATACCGATGA-TTCCCGATGGTC
1103 C
129 C
* * * * * * *
1104 CGCACATCCAAGGTACCATGGT-TCCGATACTTCCCGATAGTTTCGAACCACCATCGGCCTCAGT
1 CGCACATCCAAGGCACCAAGGTGT-CGATACATCCCGATAGTCTCGAACCACCATCGACCTAAGC
*
1168 TACCGGTGGTGTCCAATGCTCCCGCACATCTGAGGCACCAAGATACCGATGATTCCCGATGG
65 TACCGATGGTGTCCAATGCTCCCGCACATCTGAGGCACCAAGATACCGATGATTCCCGATGG
1230 CTTAGGCCGA
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
128 1 0.01
129 103 0.97
130 2 0.02
ACGTcount: A:0.22, C:0.34, G:0.24, T:0.21
Consensus pattern (129 bp):
CGCACATCCAAGGCACCAAGGTGTCGATACATCCCGATAGTCTCGAACCACCATCGACCTAAGCT
ACCGATGGTGTCCAATGCTCCCGCACATCTGAGGCACCAAGATACCGATGATTCCCGATGGTCC
Found at i:1334 original size:19 final size:18
Alignment explanation
Indices: 1312--1347 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1302 AAAAACTTTT
1312 TAAAATTCAAAATATTTAA
1 TAAAATTCAAAAT-TTTAA
*
1331 TAAAATTCCAAATTTTA
1 TAAAATTCAAAATTTTA
1348 TATTTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTCAAAATTTTAA
Done.