Multiple sequence alignment - TraesCS5B01G198100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G198100 chr5B 100.000 2578 0 0 1 2578 357131279 357133856 0.000000e+00 4761.0
1 TraesCS5B01G198100 chr5D 89.951 1821 100 27 20 1787 311352540 311354330 0.000000e+00 2272.0
2 TraesCS5B01G198100 chr5D 89.460 797 60 13 1785 2575 311354513 311355291 0.000000e+00 985.0
3 TraesCS5B01G198100 chr5D 91.489 47 4 0 1930 1976 29158755 29158709 5.950000e-07 65.8
4 TraesCS5B01G198100 chr5A 87.278 1580 106 35 588 2115 404555020 404556556 0.000000e+00 1716.0
5 TraesCS5B01G198100 chr5A 88.056 360 36 5 2211 2568 404557379 404557733 1.100000e-113 420.0
6 TraesCS5B01G198100 chr5A 83.213 417 42 12 20 425 404554264 404554663 8.770000e-95 357.0
7 TraesCS5B01G198100 chr5A 83.102 361 47 8 1518 1875 404556554 404556903 1.490000e-82 316.0
8 TraesCS5B01G198100 chr2A 80.788 203 30 7 1061 1254 735787769 735787567 1.600000e-32 150.0
9 TraesCS5B01G198100 chr2A 96.667 60 2 0 1878 1937 767024252 767024193 1.630000e-17 100.0
10 TraesCS5B01G198100 chr2D 83.916 143 23 0 1112 1254 603648399 603648257 1.240000e-28 137.0
11 TraesCS5B01G198100 chr2B 84.247 146 17 6 1112 1254 734200175 734200033 1.240000e-28 137.0
12 TraesCS5B01G198100 chr1B 91.304 46 4 0 1931 1976 556992478 556992433 2.140000e-06 63.9
13 TraesCS5B01G198100 chr6B 86.207 58 5 3 1815 1871 518390085 518390140 2.770000e-05 60.2
14 TraesCS5B01G198100 chr1D 94.737 38 1 1 1939 1976 413215899 413215863 9.960000e-05 58.4
15 TraesCS5B01G198100 chr7A 87.500 48 4 2 1931 1977 134011823 134011869 1.000000e-03 54.7
16 TraesCS5B01G198100 chr4D 80.000 80 10 6 1901 1977 403149529 403149605 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G198100 chr5B 357131279 357133856 2577 False 4761.00 4761 100.00000 1 2578 1 chr5B.!!$F1 2577
1 TraesCS5B01G198100 chr5D 311352540 311355291 2751 False 1628.50 2272 89.70550 20 2575 2 chr5D.!!$F1 2555
2 TraesCS5B01G198100 chr5A 404554264 404557733 3469 False 702.25 1716 85.41225 20 2568 4 chr5A.!!$F1 2548

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
587 857 0.181114 ATCCAGCGCTTGAGCCATAA 59.819 50.0 16.93 0.0 37.91 1.90 F
895 1188 0.545787 ATACGAGTCCCAACCCACCA 60.546 55.0 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1712 0.178998 ATGCAGGCAGGGAGCTAATG 60.179 55.0 0.00 0.0 44.79 1.90 R
1940 2456 0.881118 GGACGGAGCTGCAATTGAAA 59.119 50.0 10.34 0.0 0.00 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.292159 GCCTCGGGCCGTTGTTTT 61.292 61.111 27.32 0.00 44.06 2.43
67 68 7.375106 GGACACATCCTATCATTTGATGATC 57.625 40.000 6.68 3.40 43.01 2.92
74 75 4.153655 CCTATCATTTGATGATCGGTGCTG 59.846 45.833 6.68 0.00 46.62 4.41
133 134 5.016051 TGAGAAAGATCAGGTCATGCTAC 57.984 43.478 0.00 0.00 0.00 3.58
228 229 0.657840 GCATGTTGTCTCATACGCCC 59.342 55.000 0.00 0.00 0.00 6.13
238 239 0.392706 TCATACGCCCGAGCATCAAT 59.607 50.000 0.00 0.00 39.83 2.57
309 310 1.133637 TCCTCTCTTCTCCCATCTCCG 60.134 57.143 0.00 0.00 0.00 4.63
313 314 0.752009 TCTTCTCCCATCTCCGTCGG 60.752 60.000 4.39 4.39 0.00 4.79
322 323 3.514417 CTCCGTCGGAGCTCATCA 58.486 61.111 27.52 0.00 43.29 3.07
387 398 1.244019 ATGCTCAAGTTCGGCCCAAC 61.244 55.000 4.88 4.88 0.00 3.77
504 771 2.568090 CACCATTGCCGCCTCAAC 59.432 61.111 0.00 0.00 0.00 3.18
505 772 2.676471 ACCATTGCCGCCTCAACC 60.676 61.111 0.00 0.00 0.00 3.77
506 773 2.361610 CCATTGCCGCCTCAACCT 60.362 61.111 0.00 0.00 0.00 3.50
507 774 2.409870 CCATTGCCGCCTCAACCTC 61.410 63.158 0.00 0.00 0.00 3.85
508 775 2.436646 ATTGCCGCCTCAACCTCG 60.437 61.111 0.00 0.00 0.00 4.63
509 776 2.954684 ATTGCCGCCTCAACCTCGA 61.955 57.895 0.00 0.00 0.00 4.04
531 798 1.000955 CAACGACCTAGACTTGGCAGT 59.999 52.381 2.53 0.82 35.17 4.40
539 806 4.264262 ACCTAGACTTGGCAGTAACCTAGA 60.264 45.833 2.53 0.00 36.24 2.43
542 809 2.230750 GACTTGGCAGTAACCTAGACGT 59.769 50.000 0.00 0.00 36.24 4.34
544 811 1.913778 TGGCAGTAACCTAGACGTCA 58.086 50.000 19.50 2.84 0.00 4.35
545 812 2.241160 TGGCAGTAACCTAGACGTCAA 58.759 47.619 19.50 0.00 0.00 3.18
546 813 2.629137 TGGCAGTAACCTAGACGTCAAA 59.371 45.455 19.50 4.26 0.00 2.69
563 833 1.002087 CAAACCGTCTCCAAGGCTACT 59.998 52.381 0.00 0.00 0.00 2.57
573 843 3.826157 CTCCAAGGCTACTAGAGATCCAG 59.174 52.174 0.00 0.00 31.93 3.86
575 845 1.904287 AGGCTACTAGAGATCCAGCG 58.096 55.000 0.00 0.00 32.97 5.18
587 857 0.181114 ATCCAGCGCTTGAGCCATAA 59.819 50.000 16.93 0.00 37.91 1.90
597 867 3.676873 GCTTGAGCCATAAACCAACCATG 60.677 47.826 0.00 0.00 34.31 3.66
615 885 3.386486 CATGCAGTGCACAAAGACAAAT 58.614 40.909 22.44 0.00 43.04 2.32
636 910 2.101783 CCAGGTTAGGATGCATGCAAA 58.898 47.619 26.68 11.77 0.00 3.68
640 914 1.410153 GTTAGGATGCATGCAAAGGGG 59.590 52.381 26.68 0.00 0.00 4.79
814 1099 1.336440 CGGAAATGAACAGTGTTGGCA 59.664 47.619 14.57 6.54 0.00 4.92
823 1108 0.732571 CAGTGTTGGCAAACGTGACT 59.267 50.000 0.00 0.00 39.30 3.41
895 1188 0.545787 ATACGAGTCCCAACCCACCA 60.546 55.000 0.00 0.00 0.00 4.17
896 1189 1.474332 TACGAGTCCCAACCCACCAC 61.474 60.000 0.00 0.00 0.00 4.16
897 1190 2.434774 GAGTCCCAACCCACCACC 59.565 66.667 0.00 0.00 0.00 4.61
960 1253 3.058914 GGTAATCAGCGAGCGCATTTAAT 60.059 43.478 17.68 0.26 44.88 1.40
984 1277 8.595362 ATCGGATATATACATCTGAACCTGAA 57.405 34.615 6.62 0.00 42.24 3.02
986 1279 7.670140 TCGGATATATACATCTGAACCTGAACT 59.330 37.037 0.00 0.00 37.38 3.01
1115 1415 2.451490 AGACGAGGCTGATCAAGAAGA 58.549 47.619 0.00 0.00 0.00 2.87
1181 1481 1.219124 GGCAAGACGGAGAGCATGA 59.781 57.895 0.00 0.00 0.00 3.07
1339 1643 3.871594 CCGTTTCTCCATGTATCCTTGTC 59.128 47.826 0.00 0.00 0.00 3.18
1362 1666 3.474600 CAAGCAAGATCGATCAATCCCT 58.525 45.455 26.47 12.10 0.00 4.20
1401 1712 3.561310 TGCGATGATTCATTAGTTGCTCC 59.439 43.478 0.00 0.00 0.00 4.70
1416 1727 2.537600 CTCCATTAGCTCCCTGCCT 58.462 57.895 0.00 0.00 44.23 4.75
1417 1728 0.108207 CTCCATTAGCTCCCTGCCTG 59.892 60.000 0.00 0.00 44.23 4.85
1418 1729 1.527844 CCATTAGCTCCCTGCCTGC 60.528 63.158 0.00 0.00 44.23 4.85
1419 1730 1.225426 CATTAGCTCCCTGCCTGCA 59.775 57.895 0.00 0.00 44.23 4.41
1451 1762 8.857694 TGATCATCATGTACTGCAAATATGAT 57.142 30.769 12.48 12.48 38.60 2.45
1516 1840 8.955388 TGTTCTCTGAGCTCTGACATATATATC 58.045 37.037 18.39 4.14 0.00 1.63
1529 1853 7.097192 TGACATATATATCTTGTTCGCCTTCC 58.903 38.462 0.00 0.00 0.00 3.46
1542 1866 2.834549 TCGCCTTCCTCTCTGAGATTTT 59.165 45.455 8.00 0.00 0.00 1.82
1547 1871 6.589523 CGCCTTCCTCTCTGAGATTTTATATG 59.410 42.308 8.00 0.00 0.00 1.78
1628 1959 3.128349 CAAGTAAACGTACAGGCTGTGT 58.872 45.455 29.65 17.14 43.86 3.72
1694 2025 6.862608 TGACAATTATTGTTGCAGCAAAGTAG 59.137 34.615 20.20 11.34 45.52 2.57
1695 2026 6.158598 ACAATTATTGTTGCAGCAAAGTAGG 58.841 36.000 20.20 12.00 42.22 3.18
1696 2027 6.015519 ACAATTATTGTTGCAGCAAAGTAGGA 60.016 34.615 20.20 3.52 42.22 2.94
1697 2028 5.627499 TTATTGTTGCAGCAAAGTAGGAG 57.373 39.130 20.20 0.00 31.63 3.69
1698 2029 2.638480 TGTTGCAGCAAAGTAGGAGT 57.362 45.000 10.11 0.00 0.00 3.85
1699 2030 3.762407 TGTTGCAGCAAAGTAGGAGTA 57.238 42.857 10.11 0.00 0.00 2.59
1733 2064 7.690256 AGAACAACAAAACTGAGGGTATATCT 58.310 34.615 0.00 0.00 0.00 1.98
1747 2078 4.819630 GGGTATATCTCGTTTGGATTGCAA 59.180 41.667 0.00 0.00 0.00 4.08
1757 2088 5.471797 TCGTTTGGATTGCAAGATTTCTGTA 59.528 36.000 4.94 0.00 0.00 2.74
1762 2093 7.149569 TGGATTGCAAGATTTCTGTAGAAAG 57.850 36.000 4.94 1.26 45.87 2.62
1857 2373 7.469537 TTTGGTCAAACTTTTTCTAGTCCAA 57.530 32.000 0.00 0.00 30.70 3.53
1904 2420 2.668632 GCAATCCACCGACTCCCA 59.331 61.111 0.00 0.00 0.00 4.37
1937 2453 1.845809 AAAGAAACTGCAGCTCCGCG 61.846 55.000 15.27 0.00 33.35 6.46
1938 2454 2.715532 AAGAAACTGCAGCTCCGCGA 62.716 55.000 15.27 0.00 33.35 5.87
1939 2455 2.046892 AAACTGCAGCTCCGCGAT 60.047 55.556 15.27 0.00 33.35 4.58
1940 2456 1.639298 GAAACTGCAGCTCCGCGATT 61.639 55.000 15.27 0.00 33.35 3.34
1944 2460 1.638388 CTGCAGCTCCGCGATTTTCA 61.638 55.000 8.23 0.00 33.35 2.69
1945 2461 1.233950 TGCAGCTCCGCGATTTTCAA 61.234 50.000 8.23 0.00 33.35 2.69
1946 2462 0.099436 GCAGCTCCGCGATTTTCAAT 59.901 50.000 8.23 0.00 0.00 2.57
1947 2463 1.468054 GCAGCTCCGCGATTTTCAATT 60.468 47.619 8.23 0.00 0.00 2.32
1952 2468 0.641783 CCGCGATTTTCAATTGCAGC 59.358 50.000 8.23 0.00 0.00 5.25
1953 2469 1.621107 CGCGATTTTCAATTGCAGCT 58.379 45.000 0.00 0.00 0.00 4.24
1954 2470 1.580704 CGCGATTTTCAATTGCAGCTC 59.419 47.619 0.00 0.00 0.00 4.09
1955 2471 1.922545 GCGATTTTCAATTGCAGCTCC 59.077 47.619 0.00 0.00 0.00 4.70
1958 2474 2.704725 TTTTCAATTGCAGCTCCGTC 57.295 45.000 0.00 0.00 0.00 4.79
1959 2475 0.881118 TTTCAATTGCAGCTCCGTCC 59.119 50.000 0.00 0.00 0.00 4.79
1960 2476 1.298157 TTCAATTGCAGCTCCGTCCG 61.298 55.000 0.00 0.00 0.00 4.79
1961 2477 3.127533 AATTGCAGCTCCGTCCGC 61.128 61.111 0.00 0.00 0.00 5.54
1962 2478 3.612247 AATTGCAGCTCCGTCCGCT 62.612 57.895 0.00 0.00 38.49 5.52
1963 2479 4.742201 TTGCAGCTCCGTCCGCTC 62.742 66.667 0.00 0.00 35.07 5.03
2001 2517 5.854010 TCCAAGTAGGACATAGTTAGCAG 57.146 43.478 0.00 0.00 43.07 4.24
2072 2589 5.092781 GCAACTATATCCAAACAAACACCG 58.907 41.667 0.00 0.00 0.00 4.94
2073 2590 5.636837 CAACTATATCCAAACAAACACCGG 58.363 41.667 0.00 0.00 0.00 5.28
2092 2609 2.486203 CGGAATTTTGGTCATGGACGAA 59.514 45.455 0.00 0.00 32.65 3.85
2118 3391 0.815615 GGTAGGATGAGCTTTGGCCG 60.816 60.000 0.00 0.00 39.73 6.13
2123 3396 0.819259 GATGAGCTTTGGCCGCCATA 60.819 55.000 14.30 7.77 39.73 2.74
2142 3415 6.404844 CGCCATATAGACATACCCAAGACTAG 60.405 46.154 0.00 0.00 0.00 2.57
2143 3416 6.437793 GCCATATAGACATACCCAAGACTAGT 59.562 42.308 0.00 0.00 0.00 2.57
2144 3417 7.038941 GCCATATAGACATACCCAAGACTAGTT 60.039 40.741 0.00 0.00 0.00 2.24
2145 3418 9.529823 CCATATAGACATACCCAAGACTAGTTA 57.470 37.037 0.00 0.00 0.00 2.24
2149 3422 7.973048 AGACATACCCAAGACTAGTTATCAA 57.027 36.000 0.00 0.00 0.00 2.57
2150 3423 8.375493 AGACATACCCAAGACTAGTTATCAAA 57.625 34.615 0.00 0.00 0.00 2.69
2151 3424 8.993424 AGACATACCCAAGACTAGTTATCAAAT 58.007 33.333 0.00 0.00 0.00 2.32
2152 3425 9.614792 GACATACCCAAGACTAGTTATCAAATT 57.385 33.333 0.00 0.00 0.00 1.82
2185 3459 4.586306 AATACACCCCTTGGACCTTAAG 57.414 45.455 0.00 0.00 34.81 1.85
2192 3466 2.434702 CCCTTGGACCTTAAGCTCGTAT 59.565 50.000 0.00 0.00 0.00 3.06
2401 3678 4.270834 TCCTCTAGTACATATGATCCCGC 58.729 47.826 10.38 0.00 0.00 6.13
2521 3798 2.958355 CACAAAATCCACCAACCTCACT 59.042 45.455 0.00 0.00 0.00 3.41
2567 3844 6.676189 ACATCCTTTCCTTCTCCTAGAGATTT 59.324 38.462 0.00 0.00 38.56 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.241315 ATGAAAACAACGGCCCGAGG 61.241 55.000 11.71 3.24 0.00 4.63
3 4 0.109781 CATGAAAACAACGGCCCGAG 60.110 55.000 11.71 4.15 0.00 4.63
4 5 1.519751 CCATGAAAACAACGGCCCGA 61.520 55.000 11.71 0.00 0.00 5.14
5 6 1.080839 CCATGAAAACAACGGCCCG 60.081 57.895 0.00 0.00 0.00 6.13
6 7 0.319469 CACCATGAAAACAACGGCCC 60.319 55.000 0.00 0.00 0.00 5.80
7 8 0.943835 GCACCATGAAAACAACGGCC 60.944 55.000 0.00 0.00 0.00 6.13
8 9 0.943835 GGCACCATGAAAACAACGGC 60.944 55.000 0.00 0.00 0.00 5.68
9 10 0.387202 TGGCACCATGAAAACAACGG 59.613 50.000 0.00 0.00 0.00 4.44
10 11 1.202348 TGTGGCACCATGAAAACAACG 60.202 47.619 16.26 0.00 0.00 4.10
11 12 2.200899 GTGTGGCACCATGAAAACAAC 58.799 47.619 16.26 0.00 0.00 3.32
12 13 2.593346 GTGTGGCACCATGAAAACAA 57.407 45.000 16.26 0.00 0.00 2.83
40 41 6.100134 TCATCAAATGATAGGATGTGTCCTGA 59.900 38.462 7.23 0.00 43.88 3.86
59 60 2.554142 GATGACAGCACCGATCATCAA 58.446 47.619 8.26 0.00 45.35 2.57
67 68 2.705220 CGCATGATGACAGCACCG 59.295 61.111 0.00 0.00 0.00 4.94
74 75 3.488047 CCTTTTGTGATCCGCATGATGAC 60.488 47.826 0.00 0.00 38.01 3.06
120 121 2.807676 TGACAGAGTAGCATGACCTGA 58.192 47.619 0.00 0.00 0.00 3.86
160 161 2.571212 TCTTCATTTGGCTTGTGTCGT 58.429 42.857 0.00 0.00 0.00 4.34
228 229 8.788813 GTTTTTCATTGTAGTAATTGATGCTCG 58.211 33.333 0.00 0.00 0.00 5.03
309 310 1.040339 AGTCCCTGATGAGCTCCGAC 61.040 60.000 12.15 7.09 0.00 4.79
313 314 1.494960 AAGGAGTCCCTGATGAGCTC 58.505 55.000 6.82 6.82 43.48 4.09
387 398 3.050619 GACGGCTATTGTATCTCCAACG 58.949 50.000 0.00 0.00 0.00 4.10
397 408 3.134804 AGGCTCTTAATGACGGCTATTGT 59.865 43.478 0.00 0.00 31.08 2.71
448 481 4.039124 GGATGGCAAAGAGTTTTTCCTGAA 59.961 41.667 0.00 0.00 31.73 3.02
464 497 0.839277 ATCGTTGGAGATGGATGGCA 59.161 50.000 0.00 0.00 0.00 4.92
506 773 1.199327 CAAGTCTAGGTCGTTGCTCGA 59.801 52.381 0.92 0.92 46.83 4.04
507 774 1.618861 CAAGTCTAGGTCGTTGCTCG 58.381 55.000 0.00 0.00 41.41 5.03
508 775 1.997669 CCAAGTCTAGGTCGTTGCTC 58.002 55.000 0.00 0.00 0.00 4.26
509 776 0.037232 GCCAAGTCTAGGTCGTTGCT 60.037 55.000 0.00 0.00 0.00 3.91
542 809 1.001633 GTAGCCTTGGAGACGGTTTGA 59.998 52.381 0.00 0.00 0.00 2.69
544 811 1.349067 AGTAGCCTTGGAGACGGTTT 58.651 50.000 0.00 0.00 0.00 3.27
545 812 2.100989 CTAGTAGCCTTGGAGACGGTT 58.899 52.381 0.00 0.00 0.00 4.44
546 813 1.284198 TCTAGTAGCCTTGGAGACGGT 59.716 52.381 0.00 0.00 0.00 4.83
563 833 0.387202 GCTCAAGCGCTGGATCTCTA 59.613 55.000 16.51 0.00 0.00 2.43
573 843 0.525761 TTGGTTTATGGCTCAAGCGC 59.474 50.000 0.00 0.00 43.26 5.92
575 845 1.892474 TGGTTGGTTTATGGCTCAAGC 59.108 47.619 0.00 0.00 37.89 4.01
587 857 1.042003 TGTGCACTGCATGGTTGGTT 61.042 50.000 19.41 0.00 41.91 3.67
597 867 2.223782 TGGATTTGTCTTTGTGCACTGC 60.224 45.455 19.41 0.00 0.00 4.40
615 885 0.918258 TGCATGCATCCTAACCTGGA 59.082 50.000 18.46 0.00 40.82 3.86
636 910 7.953493 TCTCAACTTTTACCAAATAATTCCCCT 59.047 33.333 0.00 0.00 0.00 4.79
787 1072 1.280998 ACTGTTCATTTCCGGTAGGGG 59.719 52.381 0.00 0.00 38.33 4.79
814 1099 4.675029 CCGCCGGGAGTCACGTTT 62.675 66.667 14.81 0.00 34.06 3.60
823 1108 2.987596 TTACTCTCCTCCGCCGGGA 61.988 63.158 1.90 0.00 41.08 5.14
854 1139 3.589881 GGATGCGTGCATGGGCTC 61.590 66.667 12.81 0.00 41.91 4.70
896 1189 3.934391 GAAGAGACGGCGGTGGTGG 62.934 68.421 13.24 0.00 0.00 4.61
897 1190 2.432628 GAAGAGACGGCGGTGGTG 60.433 66.667 13.24 0.00 0.00 4.17
960 1253 7.670140 AGTTCAGGTTCAGATGTATATATCCGA 59.330 37.037 5.90 0.00 0.00 4.55
984 1277 1.993956 AGATGGATAGAGAGCGCAGT 58.006 50.000 11.47 0.00 0.00 4.40
986 1279 3.961849 AGATAGATGGATAGAGAGCGCA 58.038 45.455 11.47 0.00 0.00 6.09
1115 1415 1.238896 TCCTCCTGATCCTCCCCCTT 61.239 60.000 0.00 0.00 0.00 3.95
1149 1449 0.034896 CTTGCCCACCTTGTCGTAGT 59.965 55.000 0.00 0.00 0.00 2.73
1181 1481 1.383803 GGCTCCTGATCTCCACCCT 60.384 63.158 0.00 0.00 0.00 4.34
1321 1621 2.499693 TGCGACAAGGATACATGGAGAA 59.500 45.455 0.00 0.00 40.32 2.87
1339 1643 2.349249 GGATTGATCGATCTTGCTTGCG 60.349 50.000 25.02 0.00 0.00 4.85
1362 1666 2.203182 ACGGGGGAGACAAGACCA 59.797 61.111 0.00 0.00 0.00 4.02
1401 1712 0.178998 ATGCAGGCAGGGAGCTAATG 60.179 55.000 0.00 0.00 44.79 1.90
1416 1727 3.020984 ACATGATGATCAACTGCATGCA 58.979 40.909 21.29 21.29 39.82 3.96
1417 1728 3.710326 ACATGATGATCAACTGCATGC 57.290 42.857 21.22 11.82 39.82 4.06
1418 1729 5.748592 CAGTACATGATGATCAACTGCATG 58.251 41.667 20.36 20.36 41.44 4.06
1516 1840 1.273606 TCAGAGAGGAAGGCGAACAAG 59.726 52.381 0.00 0.00 0.00 3.16
1558 1888 7.611467 TGCACCATTTAATACTGTTCATCTTCT 59.389 33.333 0.00 0.00 0.00 2.85
1611 1942 1.868498 GCAACACAGCCTGTACGTTTA 59.132 47.619 0.00 0.00 30.51 2.01
1628 1959 3.648982 CTGCGCCGTGAGTTGCAA 61.649 61.111 4.18 0.00 38.56 4.08
1653 1984 5.596836 ATTGTCAATTTCCGCACCATAAT 57.403 34.783 0.00 0.00 0.00 1.28
1694 2025 5.584253 TGTTGTTCTAGAGCTCATACTCC 57.416 43.478 17.77 0.00 37.39 3.85
1695 2026 7.600752 AGTTTTGTTGTTCTAGAGCTCATACTC 59.399 37.037 17.77 3.99 36.91 2.59
1696 2027 7.386299 CAGTTTTGTTGTTCTAGAGCTCATACT 59.614 37.037 17.77 9.95 0.00 2.12
1697 2028 7.385205 TCAGTTTTGTTGTTCTAGAGCTCATAC 59.615 37.037 17.77 8.39 0.00 2.39
1698 2029 7.441836 TCAGTTTTGTTGTTCTAGAGCTCATA 58.558 34.615 17.77 4.68 0.00 2.15
1699 2030 6.291377 TCAGTTTTGTTGTTCTAGAGCTCAT 58.709 36.000 17.77 3.63 0.00 2.90
1733 2064 4.278170 ACAGAAATCTTGCAATCCAAACGA 59.722 37.500 0.00 0.00 31.94 3.85
1857 2373 2.159572 GCGTTAATGTTCGCCAACTCAT 60.160 45.455 0.00 0.00 45.54 2.90
1904 2420 2.479566 TTCTTTGCTCCGCAGATTCT 57.520 45.000 0.00 0.00 40.61 2.40
1937 2453 3.174375 GACGGAGCTGCAATTGAAAATC 58.826 45.455 10.34 0.00 0.00 2.17
1938 2454 2.094545 GGACGGAGCTGCAATTGAAAAT 60.095 45.455 10.34 0.00 0.00 1.82
1939 2455 1.269448 GGACGGAGCTGCAATTGAAAA 59.731 47.619 10.34 0.00 0.00 2.29
1940 2456 0.881118 GGACGGAGCTGCAATTGAAA 59.119 50.000 10.34 0.00 0.00 2.69
1944 2460 3.127533 GCGGACGGAGCTGCAATT 61.128 61.111 5.91 0.00 39.93 2.32
1945 2461 4.087892 AGCGGACGGAGCTGCAAT 62.088 61.111 5.91 0.00 44.22 3.56
1946 2462 4.742201 GAGCGGACGGAGCTGCAA 62.742 66.667 5.91 0.00 46.13 4.08
1964 2480 4.951963 GGAATCGCTCCGCTCCCG 62.952 72.222 0.00 0.00 33.37 5.14
1982 2498 6.869206 TTTCCTGCTAACTATGTCCTACTT 57.131 37.500 0.00 0.00 0.00 2.24
2060 2577 3.935828 ACCAAAATTCCGGTGTTTGTTTG 59.064 39.130 18.94 13.61 33.05 2.93
2072 2589 4.718940 ATTCGTCCATGACCAAAATTCC 57.281 40.909 0.00 0.00 0.00 3.01
2073 2590 7.420184 AAAAATTCGTCCATGACCAAAATTC 57.580 32.000 0.00 0.00 0.00 2.17
2118 3391 5.746990 AGTCTTGGGTATGTCTATATGGC 57.253 43.478 0.00 0.00 0.00 4.40
2123 3396 9.656323 TTGATAACTAGTCTTGGGTATGTCTAT 57.344 33.333 0.00 0.00 0.00 1.98
2150 3423 9.862149 CAAGGGGTGTATTTTATAGGACTTAAT 57.138 33.333 0.00 0.00 0.00 1.40
2151 3424 8.276477 CCAAGGGGTGTATTTTATAGGACTTAA 58.724 37.037 0.00 0.00 0.00 1.85
2152 3425 7.628505 TCCAAGGGGTGTATTTTATAGGACTTA 59.371 37.037 0.00 0.00 34.93 2.24
2163 3437 4.813133 GCTTAAGGTCCAAGGGGTGTATTT 60.813 45.833 4.29 0.00 34.93 1.40
2203 3477 6.003859 AGACTTCCTACGAGATTTCCTCTA 57.996 41.667 0.00 0.00 39.78 2.43
2213 3487 4.641094 AGGTCATGTTAGACTTCCTACGAG 59.359 45.833 0.00 0.00 38.57 4.18
2216 3490 5.916661 TGAGGTCATGTTAGACTTCCTAC 57.083 43.478 0.00 0.00 42.15 3.18
2394 3671 7.730364 ATATGGATAAATAAATCGCGGGATC 57.270 36.000 16.02 1.11 30.81 3.36
2462 3739 8.279970 TCCTCCATGATAGTTTATTTTGTGTG 57.720 34.615 0.00 0.00 0.00 3.82
2496 3773 3.892588 GAGGTTGGTGGATTTTGTGGTAA 59.107 43.478 0.00 0.00 0.00 2.85
2521 3798 1.138859 CTTGCCATGGTATGTCTCCGA 59.861 52.381 14.67 0.00 0.00 4.55


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.