Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012555.1 Kokia drynarioides strain JFW-HI SEQ_127564, 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: 7042
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Found at i:1724 original size:208 final size:208
Alignment explanation
Indices: 1362--1945 Score: 784
Period size: 208 Copynumber: 2.8 Consensus size: 208
1352 GCGGACGGTG
* * *
1362 ATCAATG-A-CGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAATTAATGAAGCGAAGAT
1 ATCAATGAAGCGGTCATCTTCTTGATGAGATACAGAGAAATAGACCAAATAAATGAAGCGAAGCT
* * *
1425 CAATACGAATGAGACTT----CCCCATCTTCCTGATGAGATACAAAAAAGTGGGTCAAAGAAATA
66 CAATACAAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGGTCAAAGCAATA
* ** * *
1486 AAGTGACCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATAAGATACAT
131 AAGAGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATAAGATACAG
1551 AGAAGTGGATTAA
196 AGAAGTGGATTAA
* ** *
1564 ATCAATGAAGCGGTCATCTTCTTAATGAGATGTAGAGAACTAGACCAAATAAATGAAGCGAAGCT
1 ATCAATGAAGCGGTCATCTTCTTGATGAGATACAGAGAAATAGACCAAATAAATGAAGCGAAGCT
1629 CAATACAAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGGTCAAAGCAATA
66 CAATACAAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGGTCAAAGCAATA
* * * * *
1694 AAGCGGTCATCTTCCTGATAATATACAGAGAAGTGGAGCAAATCCGCCTTCCTGATGAGATACAG
131 AAGAGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATAAGATACAG
*
1759 AGAAGTGGATTTA
196 AGAAGTGGATTAA
* * * * * ** * *
1772 ATCTATGAAGCGGTCATCCTCCTGATAAGATACAGAGAAATAAACTGAATCAATGAAGTGAAGCT
1 ATCAATGAAGCGGTCATCTTCTTGATGAGATACAGAGAAATAGACCAAATAAATGAAGCGAAGCT
** * * * *
1837 CAATACAAATGAGACTTCAAACTGCATCTTCCTGATGAGATACAGAGAAGTGAGCCAAAGCAAAA
66 CAATACAAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGGTCAAAGCAATA
* *
1902 AAGAGGTCATCTTCCTGATGAGATATAGAGAAGTAGACCAAATC
131 AAGAGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATC
1946 AATGAAGCAA
Statistics
Matches: 332, Mismatches: 44, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
202 7 0.02
203 1 0.00
204 65 0.20
208 259 0.78
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (208 bp):
ATCAATGAAGCGGTCATCTTCTTGATGAGATACAGAGAAATAGACCAAATAAATGAAGCGAAGCT
CAATACAAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGGTCAAAGCAATA
AAGAGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATAAGATACAG
AGAAGTGGATTAA
Found at i:1946 original size:123 final size:124
Alignment explanation
Indices: 1783--2066 Score: 302
Period size: 124 Copynumber: 2.3 Consensus size: 124
1773 TCTATGAAGC
* * * * ** ** *
1783 GGTCATCCTCCTGATAAGATACAGAGAAATAAACTGAATCAATGAAGTGAAGCTCAATACAAATG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGATCAATACAAATG
* ** * * * *
1848 AGACTTCAAACTGC-ATCTTCCTGATGAGATACAGAGAAGT-GAGCCAAAGCAAAAAAGA
66 AAACTTCAAACCCCTATCTTCATGATAAGATACAAAAAAGTGGA-CCAAAGCAAAAAAGA
* * * *
1906 GGTCATCTTCCTGATGAGATATAGAGAAGTAGACCAAATCAATGAAGCAAATATCAATGCAAGTG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGATCAATACAAATG
* * * * * *
1971 AAACTTCAAACCCCTATTTTCATGATAAGATACAAAAAAGTGGATCGAAGTAATAAAGC
66 AAACTTCAAACCCCTATCTTCATGATAAGATACAAAAAAGTGGACCAAAGCAAAAAAGA
*
2030 GGTCTTCTTCCTGATGAGATACAGAGAAGTAGACCAA
1 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAA
2067 TAGATGAAGC
Statistics
Matches: 131, Mismatches: 28, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
123 63 0.48
124 66 0.50
125 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (124 bp):
GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGATCAATACAAATG
AAACTTCAAACCCCTATCTTCATGATAAGATACAAAAAAGTGGACCAAAGCAAAAAAGA
Found at i:4772 original size:22 final size:22
Alignment explanation
Indices: 4742--4791 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
4732 TATTACCTCT
*
4742 TTTTTTAAAAAAGAAAC-ATTTA
1 TTTTATAAAAAA-AAACAATTTA
* *
4764 TTTTATAAAACAACACAATTTA
1 TTTTATAAAAAAAAACAATTTA
4786 TTTTAT
1 TTTTAT
4792 TGAAATGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (22 bp):
TTTTATAAAAAAAAACAATTTA
Found at i:4953 original size:23 final size:23
Alignment explanation
Indices: 4926--4982 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
4916 ACATAAAATT
4926 AAATAAAATATATATAAATAGAC
1 AAATAAAATATATATAAATAGAC
* * * *
4949 AAATAATATATATATATATATAT
1 AAATAAAATATATATAAATAGAC
4972 AAGATAAAATA
1 AA-ATAAAATA
4983 ATTAGATAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATAAAATATATATAAATAGAC
Found at i:5068 original size:25 final size:25
Alignment explanation
Indices: 5040--5111 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
5030 AAAAGTATAA
5040 AAAAATGAATT-AATTTAAAAAACAT
1 AAAAA-GAATTAAATTTAAAAAACAT
* * ***
5065 AAAAGGATTTAAATTTTTTAAACAT
1 AAAAAGAATTAAATTTAAAAAACAT
* *
5090 AAAAAGAGTTGAATTTAAAAAA
1 AAAAAGAATTAAATTTAAAAAA
5112 TAAAATATAA
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
24 4 0.11
25 31 0.89
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (25 bp):
AAAAAGAATTAAATTTAAAAAACAT
Found at i:6234 original size:23 final size:23
Alignment explanation
Indices: 6206--6252 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
6196 TTATCTATTG
*
6206 TCTCTGTCTTGGTTCTCTATTTC
1 TCTCTGTCTTGGCTCTCTATTTC
*
6229 TCTCTGTCTTGGCTCTCTGTTTC
1 TCTCTGTCTTGGCTCTCTATTTC
6252 T
1 T
6253 TGTTTTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.02, C:0.28, G:0.15, T:0.55
Consensus pattern (23 bp):
TCTCTGTCTTGGCTCTCTATTTC
Done.