Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000101.1 Kokia drynarioides strain JFW-HI SEQ_110735, 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, 967
Length: 1613
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Found at i:890 original size:29 final size:29
Alignment explanation
Indices: 858--1221 Score: 277
Period size: 29 Copynumber: 12.3 Consensus size: 29
848 TCCCTAAACA
858 TTCCAAAAATTACCATTTTACCCTCGAAC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
887 TTCCAAAAA-T-CCAATTTTTAACCC-CGAATC
1 TTCCAAAAATTACC-A-TTTT-ACCCTCGAA-C
* *
917 TTCCAAAATTTACTATTTTACCCTCGAAC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
* * *
946 TTCTAAAAATTACTATTTTACCC-CTAAAC
1 TTCCAAAAATTACCATTTTACCCTC-GAAC
* *
975 TTCCAAAAA-TCCCATTTTTTGACAC-CGAATC
1 TTCCAAAAATTACCA--TTTT-ACCCTCGAA-C
* *
1006 TTCCAAAAAATTACTATTTTACCCCCGAAC
1 TTCC-AAAAATTACCATTTTACCCTCGAAC
*
1036 TTCCAAAAA-TCCCATTTTAACCC-CGAACC
1 TTCCAAAAATTACCATTTT-ACCCTCGAA-C
* * *
1065 TTCTAAAAATTACCATTTTACCCCCAAAC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
* *
1094 TTCCAAAAA-TCCCATTTTTGA-CCTTGAATC
1 TTCCAAAAATTACCA-TTTT-ACCCTCGAA-C
* *
1124 TTCCAAAAATTACTATTTT-CCTCCCGAA-
1 TTCCAAAAATTACCATTTTACC-CTCGAAC
* *
1152 TTCCCAAAAA-TCCCATTTTTAGCCTCGAATC
1 TT-CCAAAAATTACCA-TTTTACCCTCGAA-C
* *
1183 TTTCAAATATTACCATTTTACCCTCGAAC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
1212 TTCCAAAAAT
1 TTCCAAAAAT
1222 CTTATTTTTG
Statistics
Matches: 267, Mismatches: 37, Indels: 62
0.73 0.10 0.17
Matches are distributed among these distances:
27 2 0.01
28 26 0.10
29 119 0.45
30 83 0.31
31 28 0.10
32 6 0.02
33 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCTCGAAC
Found at i:965 original size:59 final size:59
Alignment explanation
Indices: 853--1221 Score: 253
Period size: 59 Copynumber: 6.2 Consensus size: 59
843 GGAGGTCCCT
* * *
853 AAACATTCCAAAAATTACCATTTT-ACCCTCGAA-CTTCCAAAAA-TCCAATTTTTAACCCCG
1 AAAC-TTCCAAAAATTACCATTTTAACCC-CGAACCTTCTAAAAATTACTA-TTTT-ACCCCG
* * * *
913 AATCTTCCAAAATTTACTATTTT-ACCCTCGAA-CTTCTAAAAATTACTATTTTACCCCT
1 AAACTTCCAAAAATTACCATTTTAACCC-CGAACCTTCTAAAAATTACTATTTTACCCCG
* * * * *
971 AAACTTCCAAAAA-TCCCATTTTTTGACACCGAATCTTCCAAAAAATTACTATTTTACCCCCG
1 AAACTTCCAAAAATTACCA--TTTTAACCCCGAACCTT-CTAAAAATTACTATTTTA-CCCCG
* * *
1033 -AACTTCCAAAAA-TCCCATTTTAACCCCGAACCTTCTAAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTAACCCCGAACCTTCTAAAAATTACTATTTTACCCCG
* * ** * * *
1090 AAACTTCCAAAAA-TCCCATTTTTGACCTTGAATCTTCCAAAAATTACTATTTTCCTCCCG
1 AAACTTCCAAAAATTACCA-TTTTAACCCCGAACCTTCTAAAAATTACTATTTTAC-CCCG
* * * * * *
1150 -AA-TTCCCAAAAA-TCCCATTTTTAGCCTCGAATCTT-TCAAATATTACCATTTTACCCTCG
1 AAACTT-CCAAAAATTACCA-TTTTAACCCCGAACCTTCT-AAAAATTACTATTTTACCC-CG
1209 -AACTTCCAAAAAT
1 AAACTTCCAAAAAT
1222 CTTATTTTTG
Statistics
Matches: 259, Mismatches: 35, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
57 7 0.03
58 53 0.20
59 144 0.56
60 17 0.07
61 34 0.13
62 4 0.02
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTAACCCCGAACCTTCTAAAAATTACTATTTTACCCCG
Found at i:1200 original size:118 final size:117
Alignment explanation
Indices: 902--1232 Score: 402
Period size: 118 Copynumber: 2.8 Consensus size: 117
892 AAAATCCAAT
* * * * * *
902 TTTTAACCCCGAATCTTCCAAAATTTACTATTTTACCCTCGAACTTCTAAAAATTACTATTTTAC
1 TTTTACCCCCGAA-CTTCCAAAA-ATCCCATTTTAACCTCGAACTTCTAAAAATTACCATTTTAC
*
967 CCCTAAACTTCCAAAAATCCCATTTTTTGACACCGAATCTTCCAAAAAATTACTA
64 CCCCAAACTTCCAAAAATCCCA-TTTTTGACACCGAATCTTCCAAAAAATTACTA
*
1022 TTTTACCCCCGAACTTCCAAAAATCCCATTTTAACCCCGAACCTTCTAAAAATTACCATTTTACC
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTAACCTCGAA-CTTCTAAAAATTACCATTTTACC
*
1087 CCCAAACTTCCAAAAATCCCATTTTTGAC-CTTGAATCTTCC-AAAAATTACTA
65 CCCAAACTTCCAAAAATCCCATTTTTGACAC-CGAATCTTCCAAAAAATTACTA
* *
1139 TTTT-CCTCCCGAA-TTCCCAAAAATCCCATTTTTAGCCTCGAATCTT-TCAAATATTACCATTT
1 TTTTACC-CCCGAACTT-CCAAAAATCCCA-TTTTAACCTCGAA-CTTCT-AAAAATTACCATTT
* * **
1201 TACCCTCGAACTTCCAAAAATCTTATTTTTGA
61 TACCCCCAAACTTCCAAAAATCCCATTTTTGA
1233 TTCCAAACAT
Statistics
Matches: 188, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
116 4 0.02
117 35 0.19
118 86 0.46
119 51 0.27
120 12 0.06
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (117 bp):
TTTTACCCCCGAACTTCCAAAAATCCCATTTTAACCTCGAACTTCTAAAAATTACCATTTTACCC
CCAAACTTCCAAAAATCCCATTTTTGACACCGAATCTTCCAAAAAATTACTA
Found at i:1230 original size:59 final size:60
Alignment explanation
Indices: 932--1222 Score: 323
Period size: 59 Copynumber: 4.9 Consensus size: 60
922 AAATTTACTA
* **
932 TTTTACCCTCGAA-C-TTCTAAAAATTACTATTTTACCCCTAAACTTCCAAAAATCCCAT
1 TTTTAGCCTCGAATCTTTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCAT
* * *
990 TTTTTGACAC-CGAATCTTCCAAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCA-
1 TTTTAG-C-CTCGAATCTTTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCAT
* * * * *
1050 TTTTAACCCCGAA-CCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCAT
1 TTTTAGCCTCGAATCTTTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCAT
* *
1109 TTTT-GACCTTGAATC-TTCCAAAAATTACTATTTT-CCTCCCGAA-TTCCCAAAAATCCCAT
1 TTTTAG-CCTCGAATCTTTCTAAAAATTACTATTTTACC-CCCGAACTT-CCAAAAATCCCAT
* * *
1168 TTTTAGCCTCGAATCTTTC-AAATATTACCATTTTACCCTCGAACTTCCAAAAATC
1 TTTTAGCCTCGAATCTTTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATC
1223 TTATTTTTGA
Statistics
Matches: 196, Mismatches: 23, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
58 49 0.25
59 93 0.47
60 15 0.08
61 39 0.20
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (60 bp):
TTTTAGCCTCGAATCTTTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCAT
Done.