Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003766.1 Kokia drynarioides strain JFW-HI SEQ_116737, 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: 2290
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Found at i:1382 original size:39 final size:39
Alignment explanation
Indices: 1339--1550 Score: 172
Period size: 39 Copynumber: 5.4 Consensus size: 39
1329 CTGCCCTAGA
* *
1339 CTCGGGGTAAGAGATTGAATGACTGCAATTTACCCCAAG
1 CTCGGGGTAAGAGATTGAATGATTGCAATCTACCCCAAG
* * * ** * *
1378 CTCGGGGTAAGAGATTGACTAATAGTGATCTGCCTCAAG
1 CTCGGGGTAAGAGATTGAATGATTGCAATCTACCCCAAG
* * ** * * *
1417 CTTGAGGTAAGAGACCGAATGGTTGCAATCTACCTCAGG
1 CTCGGGGTAAGAGATTGAATGATTGCAATCTACCCCAAG
* ** * * ** *
1456 CTCGGGGTAGGAGATTGGCTAATGGTGATCTACCCCAGG
1 CTCGGGGTAAGAGATTGAATGATTGCAATCTACCCCAAG
* *
1495 CTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCCAAG
1 CTCGGGGTAAGAGATTGAATGATTGCAATCTACCCCAAG
* *
1534 CTCAGTGTAAGAGATTG
1 CTCGGGGTAAGAGATTG
1551 GTGGATGGTG
Statistics
Matches: 127, Mismatches: 46, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
39 127 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (39 bp):
CTCGGGGTAAGAGATTGAATGATTGCAATCTACCCCAAG
Found at i:1551 original size:78 final size:78
Alignment explanation
Indices: 1310--1551 Score: 268
Period size: 78 Copynumber: 3.1 Consensus size: 78
1300 CTCGAGCTAG
* * * * * ** *
1310 GAGATTGGTTGATGATGATCTGCCCTAGACTCGGGGTAAGAGATTGAATGACTGCAATTTACCCC
1 GAGATTGGCTAATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTACCCC
*
1375 AAGCTCGGGGTAA
66 AAGCTCAGGGTAA
* * * * * * ** *
1388 GAGATTGACTAATAGTGATCTGCCTCAAGCTTGAGGTAAGAGACCGAATGGTTGCAATCTACCTC
1 GAGATTGGCTAATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTACCCC
* * *
1453 AGGCTCGGGGTAG
66 AAGCTCAGGGTAA
* *
1466 GAGATTGGCTAATGGTGATCTACCCCAGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
1 GAGATTGGCTAATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTACCCC
*
1531 AAGCTCAGTGTAA
66 AAGCTCAGGGTAA
1544 GAGATTGG
1 GAGATTGG
1552 TGGATGGTGA
Statistics
Matches: 130, Mismatches: 34, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
78 130 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (78 bp):
GAGATTGGCTAATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTACCCC
AAGCTCAGGGTAA
Found at i:1880 original size:49 final size:49
Alignment explanation
Indices: 1827--2280 Score: 233
Period size: 49 Copynumber: 9.2 Consensus size: 49
1817 CGGTTGTAAC
* *
1827 CTTTCCCTCCATATCTTCATGGTACTAGATTCGTCGTTGCGGCTTAAAT
1 CTTTCCCTTCATATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * * * *** * * *
1876 CTTTCCCTTTATGCTTTTGA-GGTACAAGGTTCATTGTTACGACTTAAAC
1 CTTTCCCTTCAT-ATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * *
1925 CTTTCCCTTTTATATCCTTGA-GGTACTGGATTCGCCGTTGCGGCTTAAAT
1 CTTTCCC-TTCATAT-CTTCATGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * * * * *
1975 CTTTCCTTTCAT-GCTTCCGA-GGTACAAGGTTCGGCATTGCGACTTAAAC
1 CTTTCCCTTCATATCTT-C-ATGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * **
2024 CTTTCTCTTCATATCCTCGTGGTACTGGATTTACCGTTGCGGCTTAAAT
1 CTTTCCCTTCATATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * * * * * *
2073 CTCTCCCTTCAT-GCTTC-TGAGGTACAAGGTTCGTCATTACGACTTAAAC
1 CTTTCCCTTCATATCTTCAT--GGTACTAGATTCGCCGTTGCGGCTTAAAT
* * *
2122 CTTTCCC-TCAATATCTTCGTGGTATTGGATTCGCCGTTGCGGCTTAAAT
1 CTTTCCCTTC-ATATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * * * * *
2171 CTTTCCTTTCAT-GCTTCCGA-GGTACAAGGTTTGTCGTTGCGACTTAAAC
1 CTTTCCCTTCATATCTT-C-ATGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * **
2220 CTTTCTCTTCATATCCTCGTGGTACTGGATTTACCGTTGCGGCTTAAAT
1 CTTTCCCTTCATATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAAT
*
2269 CTCTCCCTTCAT
1 CTTTCCCTTCAT
2281 GCTTCTGAGG
Statistics
Matches: 290, Mismatches: 98, Indels: 34
0.69 0.23 0.08
Matches are distributed among these distances:
47 4 0.01
48 8 0.03
49 228 0.79
50 49 0.17
51 1 0.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (49 bp):
CTTTCCCTTCATATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAAT
Found at i:2071 original size:98 final size:98
Alignment explanation
Indices: 1824--2290 Score: 614
Period size: 98 Copynumber: 4.8 Consensus size: 98
1814 TTGCGGTTGT
* * * * *
1824 AACCTTTCCCTCCATATCTTCATGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTT-AT
1 AACCTTTCCCTTCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTT-CCTTTCAT
* * **
1888 GCTTTTGAGGTACAAGGTTCATTGTTACGACTTA
65 GCTTCTGAGGTACAAGGTTCGTCATTACGACTTA
* * *
1922 AACCTTTCCCTTTTATATCCTTGAGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCAT
1 AACCTTTCCC-TTCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCAT
* * *
1987 GCTTCCGAGGTACAAGGTTCGGCATTGCGACTTA
65 GCTTCTGAGGTACAAGGTTCGTCATTACGACTTA
* ** * *
2021 AACCTTTCTCTTCATATCCTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTCTCCCTTCATG
1 AACCTTTCCCTTCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATG
2086 CTTCTGAGGTACAAGGTTCGTCATTACGACTTA
66 CTTCTGAGGTACAAGGTTCGTCATTACGACTTA
* *
2119 AACCTTTCCC-TCAATATCTTCGTGGTATTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCAT
1 AACCTTTCCCTTC-ATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCAT
* * * *
2183 GCTTCCGAGGTACAAGGTTTGTCGTTGCGACTTA
65 GCTTCTGAGGTACAAGGTTCGTCATTACGACTTA
* ** * *
2217 AACCTTTCTCTTCATATCCTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTCTCCCTTCATG
1 AACCTTTCCCTTCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATG
2282 CTTCTGAGG
66 CTTCTGAGG
Statistics
Matches: 320, Mismatches: 45, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
97 2 0.01
98 240 0.75
99 78 0.24
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (98 bp):
AACCTTTCCCTTCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATG
CTTCTGAGGTACAAGGTTCGTCATTACGACTTA
Found at i:2219 original size:196 final size:197
Alignment explanation
Indices: 1824--2290 Score: 722
Period size: 196 Copynumber: 2.4 Consensus size: 197
1814 TTGCGGTTGT
* * * * * *** * *
1824 AACCTTTCCCTCCATATCTTCATGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTTATG
1 AACCTTTCTCTTCATATCCTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTCTCCCTTCATG
* ** **
1889 CTTTTGAGGTACAAGGTTCATTGTTACGACTTAAACCTTTCCCTTTTATATCCTTGAGGTACTGG
66 CTTCTGAGGTACAAGGTTCATCATTACGACTTAAACCTTTCCCTTCAATATCCTTGAGGTACTGG
1954 ATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCCGAGGTACAAGGTTCGGCATTGCGACT
131 ATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCCGAGGTACAAGGTTCGGCATTGCGACT
2019 TA
196 TA
2021 AACCTTTCTCTTCATATCCTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTCTCCCTTCATG
1 AACCTTTCTCTTCATATCCTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTCTCCCTTCATG
* * *
2086 CTTCTGAGGTACAAGGTTCGTCATTACGACTTAAACCTTTCCC-TCAATAT-CTTCGTGGTATTG
66 CTTCTGAGGTACAAGGTTCATCATTACGACTTAAACCTTTCCCTTCAATATCCTT-GAGGTACTG
* * *
2149 GATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCCGAGGTACAAGGTTTGTCGTTGCGAC
130 GATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCCGAGGTACAAGGTTCGGCATTGCGAC
2214 TTA
195 TTA
2217 AACCTTTCTCTTCATATCCTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTCTCCCTTCATG
1 AACCTTTCTCTTCATATCCTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTCTCCCTTCATG
2282 CTTCTGAGG
66 CTTCTGAGG
Statistics
Matches: 248, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
195 3 0.01
196 151 0.61
197 94 0.38
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (197 bp):
AACCTTTCTCTTCATATCCTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTCTCCCTTCATG
CTTCTGAGGTACAAGGTTCATCATTACGACTTAAACCTTTCCCTTCAATATCCTTGAGGTACTGG
ATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCCGAGGTACAAGGTTCGGCATTGCGACT
TA
Done.