Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010949.1 Kokia drynarioides strain JFW-HI SEQ_125917, 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: 8314
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.33
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:352 original size:29 final size:29
Alignment explanation
Indices: 319--930 Score: 124
Period size: 30 Copynumber: 20.8 Consensus size: 29
309 CACGGAGTGG
*
319 CAAAATGGTAGTTTTGGAATGTTCG-GAAT
1 CAAAATGGTAATTTTGGAA-GTTCGAGAAT
* *
348 CAAAAATAGG-ATTTTTGGAAGTTCGAGGAT
1 C-AAAAT-GGTAATTTTGGAAGTTCGAGAAT
* * * *
378 -AAAATGGTAATTTTAGAAGATCCA-AGGT
1 CAAAATGGTAATTTTGGAAGTTCGAGA-AT
* * * **
406 CAAAAATGAG-ATTTTTGGAAGTTTGGGCGT
1 C-AAAATG-GTAATTTTGGAAGTTCGAGAAT
** *
436 -AAAATGGTAATTTTTGGAAAGTTTAAG-GT
1 CAAAATGGTAA-TTTTGG-AAGTTCGAGAAT
* * *
465 CAAAAAT-G-AGATTTTGGGAAGTTTGGGGAT
1 C-AAAATGGTA-ATTTT-GGAAGTTCGAGAAT
* **
495 -AAAATGGTAATTTTTAGAAGGTTCGAGGTT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAAT
* * * **
525 AAAAATGGGATTTTTGGAAGTTC-AGGGGT
1 CAAAATGGTAATTTTGGAAGTTCGA-GAAT
* *
554 -AAAATGGTGATTTTTAGAAGGTTCGAG-AT
1 CAAAATGGT-AATTTTGGAA-GTTCGAGAAT
* * * **
583 CAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAAT
**
613 -AAAATGGTAATTTTTGGAAGGTTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAAT
* * **
642 CAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAAT
* * *
672 -AAAATGGTGATTTTTAGAAGGTTCGAG-GT
1 CAAAATGGT-AATTTTGGAA-GTTCGAGAAT
* * **
701 CAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAAT
* ***
731 -AAAATGGTGATTTTTGGAAGGTTCG-GGGC
1 CAAAATGGT-AATTTTGGAA-GTTCGAGAAT
* * **
760 CAAAAATGGGATTTTTGGAAGTTC-AGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAAT
* * **
789 -AAAATGGTGATTTTTAGAAGGTTC-AGGGT
1 CAAAATGGT-AATTTTGGAA-GTTCGAGAAT
* * * **
818 CAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAAT
* * *
848 -AAAATGGTAATTTTAGAAAGTTCGGGGA-
1 CAAAATGGTAATTTT-GGAAGTTCGAGAAT
* *
876 CAAAAATGGGATTTTTGGAAGTTCGAGGAA-
1 C-AAAATGGTAATTTTGGAAGTTCGA-GAAT
906 -AAAATGGTAATTTTTGGAAAGTTCG
1 CAAAATGGTAA-TTTTGG-AAGTTCG
931 GGGACCTCCA
Statistics
Matches: 464, Mismatches: 64, Indels: 109
0.73 0.10 0.17
Matches are distributed among these distances:
27 10 0.02
28 89 0.19
29 147 0.32
30 165 0.36
31 53 0.11
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (29 bp):
CAAAATGGTAATTTTGGAAGTTCGAGAAT
Found at i:479 original size:30 final size:29
Alignment explanation
Indices: 401--840 Score: 131
Period size: 29 Copynumber: 15.0 Consensus size: 29
391 TAGAAGATCC
401 AAGGTCAAAAATGAGATTTTTGGAAGTTT
1 AAGGTCAAAAATGAGATTTTTGGAAGTTT
* *
430 --GGGCGTAAAATG-GTAATTTTTGGAAAGTTT
1 AAGGTC-AAAAATGAG--ATTTTTGG-AAGTTT
*
460 AAGGTCAAAAATGAGATTTTGGGAAGTTT
1 AAGGTCAAAAATGAGATTTTTGGAAGTTT
** * *
489 --GGGGATAAAATG-GTAATTTTTAGAAGGTTC
1 AAGGTCA-AAAATGAG--ATTTTTGGAA-GTTT
* * * *
519 GAGGTTAAAAATGGGATTTTTGGAAGTTC
1 AAGGTCAAAAATGAGATTTTTGGAAGTTT
* * * *
548 AGGGGT--AAAATGGTGATTTTTAGAAGGTTC
1 A-AGGTCAAAAAT-GAGATTTTTGGAA-GTTT
* * * *
578 GAGATCAAAAATGGGATTTTTGGAAGTTCG
1 AAGGTCAAAAATGAGATTTTTGGAAGTT-T
** *
608 GGGGT--AAAATG-GTAATTTTTGGAAGGTTC
1 AAGGTCAAAAATGAG--ATTTTTGGAA-GTTT
** * *
637 GGGGTCAAAAATGGGATTTTTGGAAGTTCG
1 AAGGTCAAAAATGAGATTTTTGGAAGTT-T
* * * *
667 AGGGT--AAAATGGTGATTTTTAGAAGGTTC
1 AAGGTCAAAAAT-GAGATTTTTGGAA-GTTT
* * *
696 GAGGTCAAAAATGGGATTTTTGGAAGTTCG
1 AAGGTCAAAAATGAGATTTTTGGAAGTT-T
* * *
726 AGGGT--AAAATGGTGATTTTTGGAAGGTTC
1 AAGGTCAAAAAT-GAGATTTTTGGAA-GTTT
** * * *
755 GGGGCCAAAAATGGGATTTTTGGAAGTTC
1 AAGGTCAAAAATGAGATTTTTGGAAGTTT
* * * *
784 AGGGT--AAAATGGTGATTTTTAGAAGGTTC
1 AAGGTCAAAAAT-GAGATTTTTGGAA-GTTT
* *
813 AGGGTCAAAAATGGGATTTTTGGAAGTT
1 AAGGTCAAAAATGAGATTTTTGGAAGTT
841 CGGGGGTAAA
Statistics
Matches: 322, Mismatches: 49, Indels: 80
0.71 0.11 0.18
Matches are distributed among these distances:
27 14 0.04
28 44 0.14
29 111 0.34
30 106 0.33
31 38 0.12
32 9 0.03
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.33
Consensus pattern (29 bp):
AAGGTCAAAAATGAGATTTTTGGAAGTTT
Found at i:486 original size:59 final size:58
Alignment explanation
Indices: 347--930 Score: 760
Period size: 59 Copynumber: 9.9 Consensus size: 58
337 ATGTTCGGAA
* * * * *
347 TCAAAAATAGGATTTTTGGAAGTTCGAGGATAAAATGGTAA-TTTTAGAAGATCCAAGG
1 TCAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
* * * * **
405 TCAAAAATGAGATTTTTGGAAGTTTGGGCGTAAAATGGTAATTTTTGGAAAGTTTAAGG
1 TCAAAAATGGGATTTTTGGAAGTTCGGG-GTAAAATGGTAATTTTTAGAAGGTTCGAGG
* * *
464 TCAAAAATGAGATTTTGGGAAGTTTGGGGATAAAATGGTAATTTTTAGAAGGTTCGAGG
1 TCAAAAATGGGATTTTTGGAAGTTCGGGG-TAAAATGGTAATTTTTAGAAGGTTCGAGG
* * *
523 TTAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTGATTTTTAGAAGGTTCGAGA
1 TCAAAAATGGGATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
* *
582 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGG
1 TCAAAAATGGGATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
*
641 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTGATTTTTAGAAGGTTCGAGG
1 TCAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
* * *
700 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTGATTTTTGGAAGGTTCGGGG
1 TCAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
* * *
759 CCAAAAATGGGATTTTTGGAAGTTCAGGGTAAAATGGTGATTTTTAGAAGGTTC-AGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTTAGAAGGTTCGA-GG
* *
817 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAA-TTTTAGAAAGTTCGGGG
1 TCAAAAATGGGATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
* ** * *
875 ACAAAAATGGGATTTTTGGAAGTTCGAGGAAAAAATGGTAATTTTTGGAAAGTTCG
1 TCAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAATGGTAATTTTTAGAAGGTTCG
931 GGGACCTCCA
Statistics
Matches: 472, Mismatches: 44, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
57 3 0.01
58 139 0.29
59 326 0.69
60 4 0.01
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (58 bp):
TCAAAAATGGGATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
Found at i:1924 original size:3 final size:3
Alignment explanation
Indices: 1916--1960 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
1906 ACCTTTCGAT
*
1916 TTA TTA TTA TTA TTA TTA TTA TCTA ATA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
1961 CATTTAATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2686 original size:16 final size:17
Alignment explanation
Indices: 2658--2689 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2648 AACTTAAATT
2658 AAATTTAAATTTTAAAC
1 AAATTTAAATTTTAAAC
2675 AAATTT-AATTTTAAA
1 AAATTTAAATTTTAAA
2690 ATCAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTAAATTTTAAAC
Found at i:3461 original size:139 final size:139
Alignment explanation
Indices: 3305--3767 Score: 795
Period size: 139 Copynumber: 3.3 Consensus size: 139
3295 GCTTCTCTGT
*
3305 ATCAGGAAGATGAATTTGGTTCACTTCTTAGTA-CCTCATCTGGAAGATTTGCTCGTTTCGAGCC
1 ATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCC-CATCTGGAAGATTTGCTCGTTTCGAGCC
**
3369 TCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTTTTTCAATCCGTTTC
65 TCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTTTTTCAATTTGTTTC
*
3434 TCTATATCTC
130 TCTGTATCTC
3444 ATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCCCATCTGGAAGATTTGCTCGTTTCGAGCCT
1 ATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCCCATCTGGAAGATTTGCTCGTTTCGAGCCT
*
3509 CGTTTGGGTCTTCTTCTTAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTT-AATTTGTTTC
66 CGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACT-TTTTCAATTTGTTTC
3573 TCTGTATCTC
130 TCTGTATCTC
* * *
3583 ATTAGGAAGATTAATTTGGTTCACTTCTCAGTATCCCATCTGGAAGATTTGCTCGTTCCGAGCCT
1 ATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCCCATCTGGAAGATTTGCTCGTTTCGAGCCT
*
3648 CGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATTTGTTTCT
66 CGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTTTTTCAATTTGTTTCT
3713 CTGTATCTC
131 CTGTATCTC
* *
3722 ATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAG
1 ATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCCCATCTGGAAG
3768 CTAACAGTTT
Statistics
Matches: 307, Mismatches: 14, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
138 3 0.01
139 298 0.97
140 6 0.02
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (139 bp):
ATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCCCATCTGGAAGATTTGCTCGTTTCGAGCCT
CGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTTTTTCAATTTGTTTCT
CTGTATCTC
Done.