Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009083.1 Kokia drynarioides strain JFW-HI SEQ_123783, 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: 18342
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Found at i:958 original size:45 final size:45
Alignment explanation
Indices: 797--1059 Score: 224
Period size: 45 Copynumber: 5.8 Consensus size: 45
787 TTGTCCAAAG
* * * * * * * *
797 GATGCCATTGCGTCTTTCAACTATGCTCTTAGTC-TTATTTACCCT
1 GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATT-TCTATCAT
* * * * *
842 GATGCCATAGCGTCTTTCAGCCACGATCTTACTCACTTCTGAT-AT
1 GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTTCT-ATCAT
* * **
887 GAAGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTCCGTCAT
1 GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTTCTATCAT
* * * * *
932 GATGCCATAGCGTCTTTCAGCCATGGTCTTATTCATTTTTATCTT
1 GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTTCTATCAT
** * * **
977 GATGCCATAGTGTCTTTCAATTATGGTCTTACTCGTCTGAATCAT
1 GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTTCTATCAT
* *
1022 GATGCCATAATGTCTTTCAACTATGGTCTTACTCATTT
1 GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTT
1060 TTCTATCCAA
Statistics
Matches: 175, Mismatches: 40, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
44 1 0.01
45 172 0.98
46 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.40
Consensus pattern (45 bp):
GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTTCTATCAT
Found at i:1022 original size:90 final size:89
Alignment explanation
Indices: 841--1061 Score: 253
Period size: 90 Copynumber: 2.5 Consensus size: 89
831 TTATTTACCC
* * * *
841 TGATGCCATAGCGTCTTTCAGCCACGATCTTACTCACTTCTGATATGAAGCCATAGTGTCTTTCA
1 TGATGCCATAGCGTCTTTCAGCCATGGTCTTACTCA-TTTTTATATGAAGCCATAGTGTCTTTCA
* * * **
906 GCTATGGTCTTATTCATTTCCGTCA
65 ACTATGGTCTTACTCATCTCAATCA
* * *
931 TGATGCCATAGCGTCTTTCAGCCATGGTCTTATTCATTTTTATCTTGATGCCATAGTGTCTTTCA
1 TGATGCCATAGCGTCTTTCAGCCATGGTCTTACTCATTTTTAT-ATGAAGCCATAGTGTCTTTCA
* * *
996 ATTATGGTCTTACTCGTCTGAATCA
65 ACTATGGTCTTACTCATCTCAATCA
** * *
1021 TGATGCCATAATGTCTTTCAACTATGGTCTTACTCATTTTT
1 TGATGCCATAGCGTCTTTCAGCCATGGTCTTACTCATTTTT
1062 CTATCCAATG
Statistics
Matches: 110, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 5 0.05
90 105 0.95
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.41
Consensus pattern (89 bp):
TGATGCCATAGCGTCTTTCAGCCATGGTCTTACTCATTTTTATATGAAGCCATAGTGTCTTTCAA
CTATGGTCTTACTCATCTCAATCA
Found at i:1039 original size:135 final size:134
Alignment explanation
Indices: 797--1059 Score: 314
Period size: 135 Copynumber: 1.9 Consensus size: 134
787 TTGTCCAAAG
* * *
797 GATGCCATTGCGTCTTTCAACTATGCTCTTAGTCTTATTTACCCTGATGCCATAGCGTCTTTCAG
1 GATGCCATAGCGTCTTTCAACCATGCTCTTAGTCTTATTTACCCTGATGCCATAGCGTCTTTCAA
* * * *
862 CCACGATCTTACTCACTTCTGATATGAAGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTCC
66 CCACGATCTTACT-ACGTCTGATATGAAGCCATAATGTCTTTCAACTATGGTCTTACTCATTTCC
927 GTCAT
130 GTCAT
* * * * * *
932 GATGCCATAGCGTCTTTCAGCCATGGTCTTATTCATT-TTTATCTTGATGCCATAGTGTCTTTCA
1 GATGCCATAGCGTCTTTCAACCATGCTCTTAGTC-TTATTTACCCTGATGCCATAGCGTCTTTCA
** * * *
996 ATTATGGTCTTACT-CGTCTGAATCATGATGCCATAATGTCTTTCAACTATGGTCTTACTCATTT
65 ACCACGATCTTACTACGTCTG-AT-ATGAAGCCATAATGTCTTTCAACTATGGTCTTACTCATTT
1060 TTCTATCCAA
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
133 5 0.05
134 2 0.02
135 98 0.92
136 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.40
Consensus pattern (134 bp):
GATGCCATAGCGTCTTTCAACCATGCTCTTAGTCTTATTTACCCTGATGCCATAGCGTCTTTCAA
CCACGATCTTACTACGTCTGATATGAAGCCATAATGTCTTTCAACTATGGTCTTACTCATTTCCG
TCAT
Found at i:4283 original size:26 final size:26
Alignment explanation
Indices: 4247--4438 Score: 179
Period size: 26 Copynumber: 7.4 Consensus size: 26
4237 TATTTGTCAA
* **
4247 TTATTCACCGGCACAAAGCCTATTAT
1 TTATTCACCGGCTCAAAGCCTGCTAT
**
4273 TTATTCACCGGCTTGAAGCCTGCTAT
1 TTATTCACCGGCTCAAAGCCTGCTAT
* * *
4299 CTAATT-ACCGGCTCAAGGCCTGTTAT
1 -TTATTCACCGGCTCAAAGCCTGCTAT
* * *
4325 TTATTCACTGGCTCGACGCCTGCTAT
1 TTATTCACCGGCTCAAAGCCTGCTAT
* * * *
4351 TTAATCACCGGCTCAAGGCTTGATAT
1 TTATTCACCGGCTCAAAGCCTGCTAT
* *
4377 TTATTCACCGGCTCGAAGCCTGCTAC
1 TTATTCACCGGCTCAAAGCCTGCTAT
* * * *
4403 CTAATCATCGGCTCAAGGCCTGCTAT
1 TTATTCACCGGCTCAAAGCCTGCTAT
4429 TTATTCACCG
1 TTATTCACCG
4439 ACTTTCTACT
Statistics
Matches: 128, Mismatches: 36, Indels: 4
0.76 0.21 0.02
Matches are distributed among these distances:
25 4 0.03
26 120 0.94
27 4 0.03
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (26 bp):
TTATTCACCGGCTCAAAGCCTGCTAT
Found at i:4327 original size:52 final size:52
Alignment explanation
Indices: 4251--4438 Score: 259
Period size: 52 Copynumber: 3.6 Consensus size: 52
4241 TGTCAATTAT
* * * *
4251 TCACCGGCACAAAGCCTATTATTTATTCACCGGCTTGAAGCCTGCTATCTAA
1 TCACCGGCTCAAGGCCTGTTATTTATTCACCGGCTCGAAGCCTGCTATCTAA
* * * *
4303 TTACCGGCTCAAGGCCTGTTATTTATTCACTGGCTCGACGCCTGCTATTTAA
1 TCACCGGCTCAAGGCCTGTTATTTATTCACCGGCTCGAAGCCTGCTATCTAA
* * *
4355 TCACCGGCTCAAGGCTTGATATTTATTCACCGGCTCGAAGCCTGCTACCTAA
1 TCACCGGCTCAAGGCCTGTTATTTATTCACCGGCTCGAAGCCTGCTATCTAA
* *
4407 TCATCGGCTCAAGGCCTGCTATTTATTCACCG
1 TCACCGGCTCAAGGCCTGTTATTTATTCACCG
4439 ACTTTCTACT
Statistics
Matches: 118, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.30
Consensus pattern (52 bp):
TCACCGGCTCAAGGCCTGTTATTTATTCACCGGCTCGAAGCCTGCTATCTAA
Found at i:17524 original size:2 final size:2
Alignment explanation
Indices: 17517--17551 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17507 ACATACATAT
17517 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
17552 ACTTATGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.