Multiple sequence alignment - TraesCS6B01G336600

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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 TraesCS6B01G336600 chr6B 100.000 2783 0 0 1 2783 592469051 592466269 0.000000e+00 5140.0
1 TraesCS6B01G336600 chr6B 89.358 1043 59 12 1654 2673 138574079 138573066 0.000000e+00 1264.0
2 TraesCS6B01G336600 chr6B 89.437 284 28 2 2501 2783 392736542 392736260 9.480000e-95 357.0
3 TraesCS6B01G336600 chr6B 88.060 201 23 1 1456 1656 40966777 40966578 1.290000e-58 237.0
4 TraesCS6B01G336600 chr6B 89.103 156 8 2 385 531 479098488 479098333 4.730000e-43 185.0
5 TraesCS6B01G336600 chr6B 93.277 119 8 0 2665 2783 138563078 138562960 2.850000e-40 176.0
6 TraesCS6B01G336600 chr6B 94.048 84 4 1 527 610 479098279 479098197 2.910000e-25 126.0
7 TraesCS6B01G336600 chr5B 96.517 2785 79 9 1 2783 118166259 118163491 0.000000e+00 4590.0
8 TraesCS6B01G336600 chr5B 92.697 849 25 9 611 1455 712862332 712861517 0.000000e+00 1190.0
9 TraesCS6B01G336600 chr5B 96.144 389 12 3 1 389 267664647 267665032 1.410000e-177 632.0
10 TraesCS6B01G336600 chr5B 82.509 566 74 16 864 1426 712857041 712856498 9.020000e-130 473.0
11 TraesCS6B01G336600 chr5B 97.279 147 4 0 385 531 267665069 267665215 1.650000e-62 250.0
12 TraesCS6B01G336600 chr7B 95.057 1133 54 1 1651 2783 525919782 525920912 0.000000e+00 1781.0
13 TraesCS6B01G336600 chr7B 85.311 531 22 21 611 1111 259225 259729 5.350000e-137 497.0
14 TraesCS6B01G336600 chr7B 91.519 283 23 1 2501 2782 371311877 371312159 3.360000e-104 388.0
15 TraesCS6B01G336600 chr7B 90.066 151 15 0 2264 2414 3430514 3430664 2.190000e-46 196.0
16 TraesCS6B01G336600 chr7B 77.576 330 39 23 1648 1957 262617003 262617317 1.710000e-37 167.0
17 TraesCS6B01G336600 chr3B 96.565 1077 13 6 527 1600 194479898 194480953 0.000000e+00 1762.0
18 TraesCS6B01G336600 chr3B 95.200 625 16 2 2159 2783 194480957 194481567 0.000000e+00 976.0
19 TraesCS6B01G336600 chr3B 96.715 487 15 1 46 531 194479359 194479845 0.000000e+00 809.0
20 TraesCS6B01G336600 chr3B 91.045 201 17 1 1456 1656 477806138 477806337 1.270000e-68 270.0
21 TraesCS6B01G336600 chr3B 89.744 156 7 2 385 531 108247555 108247400 1.020000e-44 191.0
22 TraesCS6B01G336600 chr3B 88.079 151 10 7 388 530 343245152 343245002 3.690000e-39 172.0
23 TraesCS6B01G336600 chr1B 94.571 1142 50 4 1651 2783 91967261 91966123 0.000000e+00 1755.0
24 TraesCS6B01G336600 chr1B 89.744 156 7 2 385 531 288240484 288240329 1.020000e-44 191.0
25 TraesCS6B01G336600 chr1B 92.308 78 5 1 2571 2647 346279087 346279164 2.930000e-20 110.0
26 TraesCS6B01G336600 chr1B 94.118 68 4 0 1651 1718 249574963 249575030 1.360000e-18 104.0
27 TraesCS6B01G336600 chr5D 83.257 872 67 29 611 1454 562349635 562348815 0.000000e+00 728.0
28 TraesCS6B01G336600 chr4B 95.652 391 13 3 1 389 175071803 175072191 2.350000e-175 625.0
29 TraesCS6B01G336600 chr4B 96.020 201 7 1 1456 1656 258990400 258990599 2.670000e-85 326.0
30 TraesCS6B01G336600 chr4B 96.599 147 5 0 385 531 175072228 175072374 7.700000e-61 244.0
31 TraesCS6B01G336600 chr4B 90.173 173 17 0 2264 2436 520815008 520815180 2.790000e-55 226.0
32 TraesCS6B01G336600 chr4B 77.134 328 40 19 1651 1958 403384419 403384107 1.030000e-34 158.0
33 TraesCS6B01G336600 chr4B 80.556 72 14 0 1773 1844 225148633 225148704 3.870000e-04 56.5
34 TraesCS6B01G336600 chr6D 95.141 391 15 4 1 389 452340376 452340764 5.090000e-172 614.0
35 TraesCS6B01G336600 chr6D 92.208 154 5 2 385 531 452340801 452340954 7.810000e-51 211.0
36 TraesCS6B01G336600 chr6D 97.297 74 2 0 537 610 452341015 452341088 2.910000e-25 126.0
37 TraesCS6B01G336600 chr5A 94.373 391 19 3 1 390 326922599 326922987 5.130000e-167 597.0
38 TraesCS6B01G336600 chr5A 90.175 285 23 4 2501 2783 361204407 361204688 1.570000e-97 366.0
39 TraesCS6B01G336600 chr5A 93.532 201 10 3 1456 1656 58418855 58419052 2.100000e-76 296.0
40 TraesCS6B01G336600 chr5A 92.537 201 14 1 1456 1656 639426368 639426567 1.260000e-73 287.0
41 TraesCS6B01G336600 chr4A 94.330 388 20 2 2 389 471656716 471656331 6.640000e-166 593.0
42 TraesCS6B01G336600 chr4A 92.941 85 3 2 527 610 213883292 213883374 1.350000e-23 121.0
43 TraesCS6B01G336600 chr4A 86.301 73 10 0 1773 1845 200043419 200043491 2.300000e-11 80.5
44 TraesCS6B01G336600 chr2D 93.165 395 20 6 1 390 157204597 157204205 8.650000e-160 573.0
45 TraesCS6B01G336600 chr2D 86.232 276 33 4 2172 2444 261811938 261812211 7.540000e-76 294.0
46 TraesCS6B01G336600 chr1D 93.333 390 20 4 1 388 296876546 296876931 3.110000e-159 571.0
47 TraesCS6B01G336600 chr2B 89.109 202 20 2 1456 1656 156444328 156444128 1.650000e-62 250.0
48 TraesCS6B01G336600 chr2B 95.181 83 2 1 528 610 703890616 703890536 2.250000e-26 130.0
49 TraesCS6B01G336600 chr6A 82.110 218 20 11 1651 1850 305831642 305831858 4.770000e-38 169.0


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 TraesCS6B01G336600 chr6B 592466269 592469051 2782 True 5140.000000 5140 100.0000 1 2783 1 chr6B.!!$R5 2782
1 TraesCS6B01G336600 chr6B 138573066 138574079 1013 True 1264.000000 1264 89.3580 1654 2673 1 chr6B.!!$R3 1019
2 TraesCS6B01G336600 chr5B 118163491 118166259 2768 True 4590.000000 4590 96.5170 1 2783 1 chr5B.!!$R1 2782
3 TraesCS6B01G336600 chr5B 712861517 712862332 815 True 1190.000000 1190 92.6970 611 1455 1 chr5B.!!$R3 844
4 TraesCS6B01G336600 chr5B 712856498 712857041 543 True 473.000000 473 82.5090 864 1426 1 chr5B.!!$R2 562
5 TraesCS6B01G336600 chr5B 267664647 267665215 568 False 441.000000 632 96.7115 1 531 2 chr5B.!!$F1 530
6 TraesCS6B01G336600 chr7B 525919782 525920912 1130 False 1781.000000 1781 95.0570 1651 2783 1 chr7B.!!$F5 1132
7 TraesCS6B01G336600 chr7B 259225 259729 504 False 497.000000 497 85.3110 611 1111 1 chr7B.!!$F1 500
8 TraesCS6B01G336600 chr3B 194479359 194481567 2208 False 1182.333333 1762 96.1600 46 2783 3 chr3B.!!$F2 2737
9 TraesCS6B01G336600 chr1B 91966123 91967261 1138 True 1755.000000 1755 94.5710 1651 2783 1 chr1B.!!$R1 1132
10 TraesCS6B01G336600 chr5D 562348815 562349635 820 True 728.000000 728 83.2570 611 1454 1 chr5D.!!$R1 843
11 TraesCS6B01G336600 chr4B 175071803 175072374 571 False 434.500000 625 96.1255 1 531 2 chr4B.!!$F4 530
12 TraesCS6B01G336600 chr6D 452340376 452341088 712 False 317.000000 614 94.8820 1 610 3 chr6D.!!$F1 609

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
418 464 0.034574 AAATATGCACTGCGGGGACA 60.035 50.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2178 1.068741 GAACACGAACCTGTCTGGACT 59.931 52.381 2.23 0.0 39.71 3.85 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
57 58 2.989840 CTCAAATCGACGAGTGAGCTTT 59.010 45.455 21.56 7.10 31.80 3.51
334 340 4.511826 GTGAAGTGTACTCCAAAGTCCTTG 59.488 45.833 0.00 0.00 36.92 3.61
418 464 0.034574 AAATATGCACTGCGGGGACA 60.035 50.000 0.00 0.00 0.00 4.02
715 871 2.333014 GCAAGTGACCTCTTCTCTTCG 58.667 52.381 0.00 0.00 36.16 3.79
854 1027 5.513094 GCCCTGGCTCTGTACATTATTATGA 60.513 44.000 0.00 0.00 38.26 2.15
855 1028 6.169094 CCCTGGCTCTGTACATTATTATGAG 58.831 44.000 0.00 0.00 35.65 2.90
856 1029 6.169094 CCTGGCTCTGTACATTATTATGAGG 58.831 44.000 0.00 0.00 35.65 3.86
857 1030 6.114187 TGGCTCTGTACATTATTATGAGGG 57.886 41.667 0.00 0.00 35.65 4.30
858 1031 5.843969 TGGCTCTGTACATTATTATGAGGGA 59.156 40.000 0.00 0.00 35.65 4.20
859 1032 6.014242 TGGCTCTGTACATTATTATGAGGGAG 60.014 42.308 0.00 0.00 35.65 4.30
860 1033 6.402222 GCTCTGTACATTATTATGAGGGAGG 58.598 44.000 0.00 0.00 35.65 4.30
861 1034 6.211584 GCTCTGTACATTATTATGAGGGAGGA 59.788 42.308 0.00 0.00 35.65 3.71
862 1035 7.578571 GCTCTGTACATTATTATGAGGGAGGAG 60.579 44.444 0.00 0.00 35.65 3.69
1477 1669 2.361438 CACCACCGTACTTCTCTATCCC 59.639 54.545 0.00 0.00 0.00 3.85
1620 1812 1.111277 TCCGACATGTGACCATCGAT 58.889 50.000 1.15 0.00 0.00 3.59
1634 1826 0.465705 ATCGATGGCCGTCAGATTGT 59.534 50.000 24.56 5.81 39.75 2.71
1636 1828 1.067060 TCGATGGCCGTCAGATTGTAG 59.933 52.381 24.56 5.86 39.75 2.74
1985 2195 0.387367 CGAGTCCAGACAGGTTCGTG 60.387 60.000 0.00 0.00 39.22 4.35
2154 2364 1.447838 GTCGGCGCAGAGGATCAAA 60.448 57.895 11.47 0.00 37.82 2.69
2513 2749 3.009115 CCGAGAAGGAAGGGGCCA 61.009 66.667 4.39 0.00 45.00 5.36
2521 2757 2.715125 GGAAGGGGCCATTGGGGAT 61.715 63.158 8.79 0.00 40.01 3.85
2722 2959 2.847234 AAGGAGGTGGTGTGGCGA 60.847 61.111 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 7.392953 TGAAGCAGTGTGATTTTATGTTGGATA 59.607 33.333 0.00 0.0 0.00 2.59
93 94 4.517285 CTTGACCCTTGTATGTAGTGCAT 58.483 43.478 0.00 0.0 41.42 3.96
94 95 3.868369 GCTTGACCCTTGTATGTAGTGCA 60.868 47.826 0.00 0.0 0.00 4.57
334 340 4.325119 GGTCTTAAAAGAAGTCCACTCCC 58.675 47.826 0.00 0.0 36.68 4.30
622 732 2.290323 ACTTGCCGATAGCTTTCTTGGT 60.290 45.455 0.00 0.0 44.23 3.67
796 959 9.780186 GCCAATCAGTAATAAGGTATTTACTCT 57.220 33.333 0.00 0.0 0.00 3.24
797 960 9.000486 GGCCAATCAGTAATAAGGTATTTACTC 58.000 37.037 0.00 0.0 0.00 2.59
854 1027 6.744802 ATATCTTCCTACATACTCCTCCCT 57.255 41.667 0.00 0.0 0.00 4.20
855 1028 6.381707 GGAATATCTTCCTACATACTCCTCCC 59.618 46.154 2.65 0.0 46.44 4.30
856 1029 7.412853 GGAATATCTTCCTACATACTCCTCC 57.587 44.000 2.65 0.0 46.44 4.30
1477 1669 3.309682 TCTTTCTTGCTGTTCACTTGTCG 59.690 43.478 0.00 0.0 0.00 4.35
1581 1773 3.391665 GAGCCCAGCCGTGCAGTAT 62.392 63.158 0.00 0.0 0.00 2.12
1620 1812 1.220749 GGCTACAATCTGACGGCCA 59.779 57.895 2.24 0.0 39.38 5.36
1968 2178 1.068741 GAACACGAACCTGTCTGGACT 59.931 52.381 2.23 0.0 39.71 3.85
1975 2185 2.660552 CCGCGAACACGAACCTGT 60.661 61.111 8.23 0.0 34.06 4.00
2513 2749 2.595463 CATGCGCGGATCCCCAAT 60.595 61.111 11.25 0.0 0.00 3.16
2521 2757 2.513666 GTGAATCCCATGCGCGGA 60.514 61.111 8.83 5.0 0.00 5.54


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

AutoCloner maintained by Alex Coulton.