Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005975.1 Kokia drynarioides strain JFW-HI SEQ_120393, 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: 8348
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.33
Warning! 171 characters in sequence are not A, C, G, or T
Found at i:562 original size:30 final size:29
Alignment explanation
Indices: 528--992 Score: 225
Period size: 29 Copynumber: 16.0 Consensus size: 29
518 TTCGGGGGAA
* *
528 AAAAATGAAATTCTTGGAAATTTTAGGGT
1 AAAAATGAGATTTTTGGAAATTTTAGGGT
** * * *
557 CAAAAATGACCTTTTTGG-AAGTTCAAGGT
1 -AAAAATGAGATTTTTGGAAATTTTAGGGT
* * **
586 AAAAATGGGATTCTTGGAAATTTCGGGGT
1 AAAAATGAGATTTTTGGAAATTTTAGGGT
* *
615 AAAAAATGGGATTTTT-GAAAGTTTGAGGGT
1 -AAAAATGAGATTTTTGGAAA-TTTTAGGGT
* *
645 AAAAATGGGATTTTTGGAAGTTTTAGGGT
1 AAAAATGAGATTTTTGGAAATTTTAGGGT
* * ***
674 CAAAAATAAGATTTTTGGAAGTTCGGGGGT
1 -AAAAATGAGATTTTTGGAAATTTTAGGGT
* *
704 AAAAATGAAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGAGATTTTTGGAAATTTTAGGG-T
* * *
734 AAAAATGAGTTTTTTGG-AAGTTTGGGGT
1 AAAAATGAGATTTTTGGAAATTTTAGGGT
* * *
762 -AAAATG-GAATTTTTAGAATTTTTGGGGT
1 AAAAATGAG-ATTTTTGGAAATTTTAGGGT
* * * *
790 CAAAAATGGGATTTTTTGAAGTTTTGGGGT
1 -AAAAATGAGATTTTTGGAAATTTTAGGGT
** ** *
820 CAAAAATG-GGGTTTTCAAAAGTTTGAGGGT
1 -AAAAATGAGATTTTTGGAAA-TTTTAGGGT
* * ***
850 -TAAATG-GAATTTTTGGAAGTTACGGGGT
1 AAAAATGAG-ATTTTTGGAAATTTTAGGGT
* * **
878 CAAAAATGTGATTTTTGG-AAGTTCGGGGT
1 -AAAAATGAGATTTTTGGAAATTTTAGGGT
* * *
907 AAAAATG-GAATTTTTTGAAGTTTTGGGGT
1 AAAAATGAG-ATTTTTGGAAATTTTAGGGT
* * **
936 AAAAA-AAGGATTTTTGGAAGTTCGAGGGT
1 AAAAATGA-GATTTTTGGAAATTTTAGGGT
* *
965 AAAAATG-GAATTTTTGGATAGTTTAGGG
1 AAAAATGAG-ATTTTTGGAAATTTTAGGG
993 ACCTCCAGGG
Statistics
Matches: 339, Mismatches: 74, Indels: 45
0.74 0.16 0.10
Matches are distributed among these distances:
26 1 0.00
27 13 0.04
28 50 0.15
29 142 0.42
30 131 0.39
31 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAAATGAGATTTTTGGAAATTTTAGGGT
Found at i:941 original size:58 final size:57
Alignment explanation
Indices: 583--988 Score: 322
Period size: 58 Copynumber: 6.9 Consensus size: 57
573 GGAAGTTCAA
* * *
583 GGTAAAAATGGGATTCTTGGAAATTTCGGGGTAAAAAATGGGA-TTTTTGAAAG-TTTGAG
1 GGTAAAAATGGGATTTTTGG-AAGTTCGGGGT-AAAAATGGAATTTTTTG-AAGTTTTG-G
** * * **
642 GGTAAAAATGGGATTTTTGGAAGTTTTAGGGTCAAAAAT-AAGATTTTTGGAAGTTCGGG
1 GGTAAAAATGGGATTTTTGGAAG-TTCGGGGT-AAAAATGGA-ATTTTTTGAAGTTTTGG
** * * *
701 GGTAAAAATGAAATTTTTGGAAGTTTTAGGGTTAAAAAT-GAGTTTTTTGGAAG-TTTGG
1 GGTAAAAATGGGATTTTTGGAAG--TTCGGGGTAAAAATGGAATTTTTT-GAAGTTTTGG
* * * * *
759 GGT-AAAATGGAATTTTTAGAATTTTTGGGGTCAAAAATGGGATTTTTTGAAGTTTTGG
1 GGTAAAAATGGGATTTTTGGAA-GTTCGGGGT-AAAAATGGAATTTTTTGAAGTTTTGG
* *** * * * **
817 GGTCAAAAATGGGGTTTTCAAAAGTTTGAGGGT-TAAATGGAATTTTTGGAAGTTACGG
1 GGT-AAAAATGGGATTTTTGGAAGTTCG-GGGTAAAAATGGAATTTTTTGAAGTTTTGG
*
875 GGTCAAAAATGTGATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTTTGAAGTTTTGG
1 GGT-AAAAATGGGATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTTTGAAGTTTTGG
** *
933 GGTAAAAAAAGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGATAGTTT
1 GGTAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAAATGGAATTTTTTGA-AGTTT
989 AGGGACCTCC
Statistics
Matches: 280, Mismatches: 51, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
56 6 0.02
57 51 0.18
58 115 0.41
59 77 0.28
60 31 0.11
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (57 bp):
GGTAAAAATGGGATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTTTGAAGTTTTGG
Found at i:992 original size:29 final size:28
Alignment explanation
Indices: 528--992 Score: 307
Period size: 30 Copynumber: 16.0 Consensus size: 28
518 TTCGGGGGAA
* * *
528 AAAAATGAAATTCTTGGAAATTTTAGGGT
1 AAAAATGGAATTTTTGG-AAGTTTAGGGT
* * *
557 CAAAAAT-GACCTTTTTGGAAGTTCAAGGT
1 -AAAAATGGA-ATTTTTGGAAGTTTAGGGT
* * * *
586 AAAAATGGGATTCTTGGAAATTTCGGGGT
1 AAAAATGGAATTTTTGGAAGTTT-AGGGT
* *
615 AAAAAATGGGATTTTTGAAAGTTTGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTT-AGGGT
*
645 AAAAATGGGATTTTTGGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAG-TTTAGGGT
* **
674 CAAAAAT-AAGATTTTTGGAAGTTCGGGGGT
1 -AAAAATGGA-ATTTTTGGAAGTT-TAGGGT
*
704 AAAAATGAAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGAAG-TTTAGGG-T
* *
734 AAAAAT-GAGTTTTTTGGAAGTTTGGGGT
1 AAAAATGGA-ATTTTTGGAAGTTTAGGGT
* * *
762 -AAAATGGAATTTTTAGAATTTTTGGGGT
1 AAAAATGGAATTTTTGGAA-GTTTAGGGT
* * *
790 CAAAAATGGGATTTTTTGAAGTTTTGGGGT
1 -AAAAATGGAATTTTTGGAAG-TTTAGGGT
** ***
820 CAAAAATGGGGTTTTCAAAAGTTTGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTT-AGGGT
*
850 -TAAATGGAATTTTTGGAAG-TTACGGGGT
1 AAAAATGGAATTTTTGGAAGTTTA--GGGT
**
878 CAAAAATGTG-ATTTTTGGAAGTTCGGGGT
1 -AAAAATG-GAATTTTTGGAAGTTTAGGGT
* *
907 AAAAATGGAATTTTTTGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAG-TTTAGGGT
* *
936 AAAAAAAGG-ATTTTTGGAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGGAAGTT-TAGGGT
965 AAAAATGGAATTTTTGGATAGTTTAGGG
1 AAAAATGGAATTTTTGGA-AGTTTAGGG
993 ACCTCCAGGG
Statistics
Matches: 349, Mismatches: 56, Indels: 61
0.75 0.12 0.13
Matches are distributed among these distances:
26 1 0.00
27 16 0.05
28 70 0.20
29 107 0.31
30 153 0.44
31 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTTAGGGT
Found at i:2795 original size:17 final size:17
Alignment explanation
Indices: 2770--2844 Score: 59
Period size: 17 Copynumber: 4.4 Consensus size: 17
2760 TAACTGGACC
*
2770 TTTTCAATT-AATTTAAA
1 TTTTAAATTAAATTT-AA
2787 TTTTAAATTCAAATTTAA
1 TTTTAAATT-AAATTTAA
*
2805 -TTTAAATTTAAACTTAA
1 TTTTAAA-TTAAATTTAA
*
2822 -TTTAAACTTAAA-CTAA
1 TTTTAAA-TTAAATTTAA
2838 TTTTAAA
1 TTTTAAA
2845 CCCAAAATGA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
16 3 0.06
17 38 0.76
18 4 0.08
19 5 0.10
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTAAATTAAATTTAA
Found at i:2812 original size:6 final size:6
Alignment explanation
Indices: 2779--2833 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
2769 CTTTTCAATT
* *
2779 AATTTA AATTTTA AATTCA AATTT- AATTTA AATTTA AACTT- AATTTA
1 AATTTA AA-TTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
2826 AACTTA AA
1 AATTTA AA
2834 CTAATTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
5 9 0.22
6 26 0.63
7 6 0.15
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:2845 original size:17 final size:17
Alignment explanation
Indices: 2788--2845 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
2778 TAATTTAAAT
*
2788 TTTAAA-TTCAAATTTAA
1 TTTAAACTT-AAACTTAA
*
2805 TTTAAATTTAAACTTAA
1 TTTAAACTTAAACTTAA
2822 TTTAAACTTAAAC-TAA
1 TTTAAACTTAAACTTAA
2838 TTTTAAAC
1 -TTTAAAC
2846 CCAAAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.08
17 32 0.86
18 2 0.05
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAACTTAAACTTAA
Found at i:3749 original size:201 final size:206
Alignment explanation
Indices: 3230--3749 Score: 602
Period size: 207 Copynumber: 2.5 Consensus size: 206
3220 TTGACTTGGC
* * * * * * ** *
3230 CTTCTTCTCAGTATGTCATCAGGAAGATGACCGTACCACTTGTTTCAATTCACTTCTCTGTATCT
1 CTTCTTCTTAATATCTCATCAGGAAGATAACCGCACCGCTTGTTTCAAACCGCTTCTCTGTATCT
* * * *
3295 TATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGGAGCTAACCACTTTTATTGCT
66 AATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTTATTGCT
* * * * * *
3360 TCGACCTGCTTCTCTGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCACATCGAGCGTGG
131 TCGACATACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTGA
* *
3425 GTTTGATTTGGT
196 GTTTGATAT-GA
* * ** *
3437 CTTCTTCTTAATATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATTCGCTTCTCTGTAACT
1 CTTCTTCTTAATATCTCATCAGGAAGATAACCGCACCGCTTGTTTCAAACCGCTTCTCTGTATCT
* * * * *
3502 AATTAGGAAGACGAATTAGGTTTACTTCTTAGTATCTCATCAGGAAGCTAACC-GTTTTATTGCT
66 AATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTTATTGCT
*
3566 TCGACATACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCGAGTCCTG
131 TCGACATACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAG-CCTG
*
3631 AG-TTGGTAT-A
195 AGTTTGATATGA
* * * * * *
3641 CTTC-TC-T-GTATCTCATTAGGAAGATAATCGCCCCGTTTGTTTCAAACCGCTTCTCTATATCT
1 CTTCTTCTTAATATCTCATCAGGAAGATAACCGCACCGCTTGTTTCAAACCGCTTCTCTGTATCT
* * *
3703 CATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAG
66 AATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAG
3750 ATGACCGCAT
Statistics
Matches: 267, Mismatches: 45, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
201 84 0.31
202 1 0.00
203 2 0.01
204 4 0.01
206 70 0.26
207 106 0.40
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (206 bp):
CTTCTTCTTAATATCTCATCAGGAAGATAACCGCACCGCTTGTTTCAAACCGCTTCTCTGTATCT
AATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTTATTGCT
TCGACATACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTGA
GTTTGATATGA
Done.