Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007637.1 Kokia drynarioides strain JFW-HI SEQ_122268, 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: 13326
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:173 original size:6 final size:6
Alignment explanation
Indices: 136--167 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
126 TTTAAAAACA
136 TTTATT TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT
168 ACTTTTGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:832 original size:99 final size:99
Alignment explanation
Indices: 629--1267 Score: 938
Period size: 99 Copynumber: 6.5 Consensus size: 99
619 TCCTTTGCAT
* * * *
629 CTTCGTGGTACTGGATTCACCGTTGCGGCTCAAATCTTTCCCTTCATGTCTCCCGAGGTATAAGG
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTATAAGG
* * *
694 TTCGCCATTGCGACTTAGACCTTTCCCTTTG-TAT
65 TTCGCCTTTGCGACTTAAACCTTTCCCTTTGTTAC
* * * * * * *
728 TTTCGTGGTATTGGATTCGCCGTTGTGGCTTAAATTTTTCCTTTCATGCTTTTGAGGTACAAGGT
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGT
* * * ** *
793 TCGCCATTGCGGCTTAAACCTCTCCCTTCATTAT
66 TCGCCTTTGCGACTTAAACCTTTCCCTTTGTTAC
** * *
827 CTTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTTTCCCTTCATACTACTGAGGTATAAGGT
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGT
892 TCGCCTTTGCGACTTAAACCTTTCCCTTTGTTAC
66 TCGCCTTTGCGACTTAAACCTTTCCCTTTGTTAC
* *
926 CTTCGTGGTACTGAATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGT
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGT
*
991 TCGCCTTTGCGACTTAAACATTTCCCTTTGTTAC
66 TCGCCTTTGCGACTTAAACCTTTCCCTTTGTTAC
* *
1025 CTTCGTGGTACTGGATTAGACGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGT
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGT
* * *
1090 TCGCCTTTGAGACTTAAACTTTTCTCTTTGTTAC
66 TCGCCTTTGCGACTTAAACCTTTCCCTTTGTTAC
1124 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGT
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGT
*
1189 TCGCCTTTGCGACTTAAACCTTTCCCTTTATTAC
66 TCGCCTTTGCGACTTAAACCTTTCCCTTTGTTAC
* * *
1223 CTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATATTTCCCTTC
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTC
1268 GTGGTAATGA
Statistics
Matches: 483, Mismatches: 56, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
98 38 0.08
99 445 0.92
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (99 bp):
CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGT
TCGCCTTTGCGACTTAAACCTTTCCCTTTGTTAC
Found at i:856 original size:50 final size:50
Alignment explanation
Indices: 629--1267 Score: 372
Period size: 50 Copynumber: 12.9 Consensus size: 50
619 TCCTTTGCAT
* * *
629 CTTCGTGGTACTGGATTCACCGTTGCGGCTCAAATCTTTCCCTTCATGT--
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCAT-TAC
* * * * * *
678 CTCCCGAGGTA-TAAGG-TTCGCCATTGCGACTTAGACCTTTCCCTT--TGTAT
1 CT-TCGTGGTACT--GGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCAT-TAC
* * * ** * *
728 TTTCGTGGTATTGGATTCGCCGTTGTGGCTTAAATTTTTCCTTTCA-TGC
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
* * * * * * *
777 TTTTGAGGTACAAGG-TTCGCCATTGCGGCTTAAACCTCTCCCTTCATTAT
1 CTTCGTGGTAC-TGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
** *
827 CTTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTTTCCCTTCA-TA-
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
* * * * **
875 CTACTGAGGTA-TAAGG-TTCGCCTTTGCGACTTAAACCTTTCCCTTTGTTAC
1 CTTC-GTGGTACT--GGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
* * * *
926 CTTCGTGGTACTGAATTCGCCGTTGCAGCTTAAATCTTTCCCTTCA-T-G
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
* * * * **
974 CTTCTGAGGTA-TAAGG-TTCGCCTTTGCGACTTAAACATTTCCCTTTGTTAC
1 CTTC-GTGGTACT--GGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
* * * *
1025 CTTCGTGGTACTGGATTAGACGTTGCGGCTTAAATCTTTCCCTTCA-T-G
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
* * * * * * **
1073 CTTCTGAGGTA-TAAGG-TTCGCCTTTGAGACTTAAACTTTTCTCTTTGTTAC
1 CTTC-GTGGTACT--GGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
* *
1124 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCA-T-G
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
* * * *
1172 CTTCTGAGGTA-TAAGG-TTCGCCTTTGCGACTTAAACCTTTCCCTTTATTAC
1 CTTC-GTGGTACT--GGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
* * **
1223 CTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATATTTCCCTTC
1 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTC
1268 GTGGTAATGA
Statistics
Matches: 434, Mismatches: 116, Indels: 79
0.69 0.18 0.13
Matches are distributed among these distances:
48 24 0.06
49 194 0.45
50 195 0.45
51 21 0.05
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (50 bp):
CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTAC
Found at i:1735 original size:18 final size:18
Alignment explanation
Indices: 1709--1744 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1699 AAAAGTTGCC
*
1709 AATATTTACAAGGAACAA
1 AATAATTACAAGGAACAA
1727 AATAATTACAAGGAACAA
1 AATAATTACAAGGAACAA
1745 TATTAGATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.19
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Found at i:8873 original size:15 final size:16
Alignment explanation
Indices: 8855--8889 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
8845 GTCCAACTCA
8855 AACTTAAATCG-CTTG
1 AACTTAAATCGACTTG
*
8870 AACTTAAATTGACTTG
1 AACTTAAATCGACTTG
8886 AACT
1 AACT
8890 CAAGACAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (16 bp):
AACTTAAATCGACTTG
Done.