Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012224.1 Kokia drynarioides strain JFW-HI SEQ_127225, 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: 25442
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:752 original size:45 final size:45
Alignment explanation
Indices: 670--788 Score: 157
Period size: 45 Copynumber: 2.6 Consensus size: 45
660 TCAAAGGGGA
* * * * *
670 ACCATATTTTTCTTTTGATTTAGACCACTTTGATTTGTGACTTTT
1 ACCATAATTTTCTTTTAATTTGGACCACTGTGATTTGTAACTTTT
** *
715 ACCATAATTTTCTTTTAATTTGGGTCACTGTGGTTTGTAACTTTT
1 ACCATAATTTTCTTTTAATTTGGACCACTGTGATTTGTAACTTTT
*
760 ACTATAATTTTCTTTTAATTTGGACCACT
1 ACCATAATTTTCTTTTAATTTGGACCACT
789 TTTTTTTGGA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (45 bp):
ACCATAATTTTCTTTTAATTTGGACCACTGTGATTTGTAACTTTT
Found at i:2738 original size:183 final size:182
Alignment explanation
Indices: 2428--2796 Score: 569
Period size: 183 Copynumber: 2.0 Consensus size: 182
2418 AATTGGAGTG
* * *
2428 GTCCCCTCAAGTCATTGCAATTCTCATCTCCATATTTGCAGGAACTACCTGATTCAATTGGCAAT
1 GTCCCCTCAAGTCATTGCAAGTCCCATCTCCATATTTACAGGAACTACCTGATTCAATTGGCAAT
* * * * * *
2493 CTTAGATCTATGGAGATATTGGATCTTCGCTTCAGTAATTTGAAAGGGCCAATTATAGCATCTCT
66 CTTAGATCTATGGAGATACTGAATCTTCGCGTCAATAATTTAAAAGGGCCAATTACAGCATCTC-
*
2558 CGTAAACCTCACACAACTTGAATATCTACATCTTTCCTATAACAACTTTGGTA
130 CGAAAACCTCACACAACTTGAATATCTACATCTTTCCTATAACAACTTTGGTA
2611 GTCCCCTCAAGTCATTGCAAGTCCCATCTCCATATTTACAGGAACTACCTGATTCAATTGGCAAT
1 GTCCCCTCAAGTCATTGCAAGTCCCATCTCCATATTTACAGGAACTACCTGATTCAATTGGCAAT
* * *
2676 CTTAGATCTCTGGAGATACTGAATCTTTGCCGT-AATAATTTAAAAGGGCCAATTCCAGCATCTC
66 CTTAGATCTATGGAGATACTGAATCTTCG-CGTCAATAATTTAAAAGGGCCAATTACAGCATCTC
* * *
2740 CGAAAACCTCACACAACTTGAATATCTATATCTTTCCTATAATAACTTTGGTT
130 CGAAAACCTCACACAACTTGAATATCTACATCTTTCCTATAACAACTTTGGTA
2793 GTCC
1 GTCC
2797 TATTCTATGT
Statistics
Matches: 169, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
182 53 0.31
183 114 0.67
184 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (182 bp):
GTCCCCTCAAGTCATTGCAAGTCCCATCTCCATATTTACAGGAACTACCTGATTCAATTGGCAAT
CTTAGATCTATGGAGATACTGAATCTTCGCGTCAATAATTTAAAAGGGCCAATTACAGCATCTCC
GAAAACCTCACACAACTTGAATATCTACATCTTTCCTATAACAACTTTGGTA
Found at i:10533 original size:14 final size:15
Alignment explanation
Indices: 10501--10535 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
10491 TACTAAAAAT
*
10501 AAATAAAATTAATCA
1 AAATAAAATTAAGCA
10516 AAATAAAATT-AGCA
1 AAATAAAATTAAGCA
10530 AAATAA
1 AAATAA
10536 CAACTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (15 bp):
AAATAAAATTAAGCA
Found at i:14817 original size:219 final size:219
Alignment explanation
Indices: 14438--14881 Score: 870
Period size: 219 Copynumber: 2.0 Consensus size: 219
14428 ACCTCACACA
14438 ACTTGAATATCTAGATCTTTCCCATAATAACTTTGGTGGTCCTATTCCATGTTCAGTTTTCAACC
1 ACTTGAATATCTAGATCTTTCCCATAATAACTTTGGTGGTCCTATTCCATGTTCAGTTTTCAACC
14503 TCACTCAAGTTCAGTTTCTAGATCTTTCGGAAAACAAGTTGGCGGGTTCCCTTCCATCAAAAGTG
66 TCACTCAAGTTCAGTTTCTAGATCTTTCGGAAAACAAGTTGGCGGGTTCCCTTCCATCAAAAGTG
14568 AGTGGGCTTTCACAACTTAGTATTCTACGCCTTGATCACAACTTTCTCACTGGCAGGGTACCATC
131 AGTGGGCTTTCACAACTTAGTATTCTACGCCTTGATCACAACTTTCTCACTGGCAGGGTACCATC
14633 CTGGTTGTTCTCTCTTCCATCTTT
196 CTGGTTGTTCTCTCTTCCATCTTT
*
14657 ACTTGAATATCTAGATCTTTCGCATAATAACTTTGGTGGTCCTATTCCATGTTCAGTTTTCAACC
1 ACTTGAATATCTAGATCTTTCCCATAATAACTTTGGTGGTCCTATTCCATGTTCAGTTTTCAACC
14722 TCACTCAAGTTCAGTTTCTAGATCTTTCGGAAAACAAGTTGGCGGGTTCCCTTCCATCAAAAGTG
66 TCACTCAAGTTCAGTTTCTAGATCTTTCGGAAAACAAGTTGGCGGGTTCCCTTCCATCAAAAGTG
14787 AGTGGGCTTTCACAACTTAGTATTCTACGCCTTGATCACAACTTTCTCACTGGCAGGGTACCATC
131 AGTGGGCTTTCACAACTTAGTATTCTACGCCTTGATCACAACTTTCTCACTGGCAGGGTACCATC
14852 CTGGTTGTTCTCTCTTCCATCTTT
196 CTGGTTGTTCTCTCTTCCATCTTT
*
14876 AGTTGA
1 ACTTGA
14882 GTTAATGCTT
Statistics
Matches: 223, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
219 223 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (219 bp):
ACTTGAATATCTAGATCTTTCCCATAATAACTTTGGTGGTCCTATTCCATGTTCAGTTTTCAACC
TCACTCAAGTTCAGTTTCTAGATCTTTCGGAAAACAAGTTGGCGGGTTCCCTTCCATCAAAAGTG
AGTGGGCTTTCACAACTTAGTATTCTACGCCTTGATCACAACTTTCTCACTGGCAGGGTACCATC
CTGGTTGTTCTCTCTTCCATCTTT
Done.