Multiple sequence alignment - TraesCS4B01G329200

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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 TraesCS4B01G329200 chr4B 100.000 2943 0 0 1 2943 619990804 619987862 0.000000e+00 5435.0
1 TraesCS4B01G329200 chr4B 89.754 2030 135 34 955 2943 545480439 545478442 0.000000e+00 2529.0
2 TraesCS4B01G329200 chr4B 94.562 1508 44 15 1443 2941 12902495 12901017 0.000000e+00 2296.0
3 TraesCS4B01G329200 chr4B 85.276 815 74 26 518 1318 12903332 12902550 0.000000e+00 798.0
4 TraesCS4B01G329200 chr4B 86.667 480 30 8 45 492 12903793 12903316 4.380000e-138 501.0
5 TraesCS4B01G329200 chr4D 97.257 2953 64 11 1 2943 485796677 485793732 0.000000e+00 4988.0
6 TraesCS4B01G329200 chr7A 93.473 2819 107 24 164 2943 691411841 691414621 0.000000e+00 4115.0
7 TraesCS4B01G329200 chr7A 85.370 1620 164 38 705 2296 84381197 84379623 0.000000e+00 1611.0
8 TraesCS4B01G329200 chr7A 92.821 390 21 6 418 803 55576323 55576709 2.560000e-155 558.0
9 TraesCS4B01G329200 chr2B 89.887 2472 142 49 535 2943 725229437 725227011 0.000000e+00 3081.0
10 TraesCS4B01G329200 chr2B 87.138 1174 90 34 1150 2296 728345258 728344119 0.000000e+00 1275.0
11 TraesCS4B01G329200 chr7B 87.026 2428 160 81 554 2943 678611114 678613424 0.000000e+00 2595.0
12 TraesCS4B01G329200 chr7B 84.452 566 32 10 1 529 678610491 678611037 9.410000e-140 507.0
13 TraesCS4B01G329200 chr7B 83.026 542 53 21 533 1055 46019102 46019623 3.460000e-124 455.0
14 TraesCS4B01G329200 chr5D 95.582 1539 50 11 1413 2943 445826288 445824760 0.000000e+00 2449.0
15 TraesCS4B01G329200 chr5D 95.093 1508 51 9 1443 2943 445965231 445963740 0.000000e+00 2353.0
16 TraesCS4B01G329200 chr5D 87.538 658 44 18 33 657 445827573 445826921 0.000000e+00 726.0
17 TraesCS4B01G329200 chr7D 95.517 1539 51 11 1413 2943 599164187 599165715 0.000000e+00 2444.0
18 TraesCS4B01G329200 chr7D 94.098 1508 47 12 1443 2943 598893811 598895283 0.000000e+00 2254.0
19 TraesCS4B01G329200 chr7D 85.832 1814 152 57 705 2475 593975157 593976908 0.000000e+00 1829.0
20 TraesCS4B01G329200 chr7D 86.930 1645 126 39 700 2296 82633824 82632221 0.000000e+00 1764.0
21 TraesCS4B01G329200 chr7D 85.979 1512 125 44 932 2391 41036573 41038049 0.000000e+00 1537.0
22 TraesCS4B01G329200 chr7D 85.914 1356 94 44 1 1318 599162844 599164140 0.000000e+00 1356.0
23 TraesCS4B01G329200 chr7D 89.417 841 39 14 1 803 41035733 41036561 0.000000e+00 1014.0
24 TraesCS4B01G329200 chr4A 87.740 1509 110 39 1180 2660 703478640 703477179 0.000000e+00 1692.0
25 TraesCS4B01G329200 chr2A 86.503 1504 124 39 815 2288 733209328 733207874 0.000000e+00 1580.0
26 TraesCS4B01G329200 chr2A 89.041 73 3 2 1298 1368 713543988 713544057 5.230000e-13 86.1
27 TraesCS4B01G329200 chr1D 82.977 1263 109 43 1087 2300 415488827 415487622 0.000000e+00 1044.0
28 TraesCS4B01G329200 chr2D 85.560 1018 82 39 818 1823 598953460 598952496 0.000000e+00 1005.0


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 TraesCS4B01G329200 chr4B 619987862 619990804 2942 True 5435.000000 5435 100.0000 1 2943 1 chr4B.!!$R2 2942
1 TraesCS4B01G329200 chr4B 545478442 545480439 1997 True 2529.000000 2529 89.7540 955 2943 1 chr4B.!!$R1 1988
2 TraesCS4B01G329200 chr4B 12901017 12903793 2776 True 1198.333333 2296 88.8350 45 2941 3 chr4B.!!$R3 2896
3 TraesCS4B01G329200 chr4D 485793732 485796677 2945 True 4988.000000 4988 97.2570 1 2943 1 chr4D.!!$R1 2942
4 TraesCS4B01G329200 chr7A 691411841 691414621 2780 False 4115.000000 4115 93.4730 164 2943 1 chr7A.!!$F2 2779
5 TraesCS4B01G329200 chr7A 84379623 84381197 1574 True 1611.000000 1611 85.3700 705 2296 1 chr7A.!!$R1 1591
6 TraesCS4B01G329200 chr2B 725227011 725229437 2426 True 3081.000000 3081 89.8870 535 2943 1 chr2B.!!$R1 2408
7 TraesCS4B01G329200 chr2B 728344119 728345258 1139 True 1275.000000 1275 87.1380 1150 2296 1 chr2B.!!$R2 1146
8 TraesCS4B01G329200 chr7B 678610491 678613424 2933 False 1551.000000 2595 85.7390 1 2943 2 chr7B.!!$F2 2942
9 TraesCS4B01G329200 chr7B 46019102 46019623 521 False 455.000000 455 83.0260 533 1055 1 chr7B.!!$F1 522
10 TraesCS4B01G329200 chr5D 445963740 445965231 1491 True 2353.000000 2353 95.0930 1443 2943 1 chr5D.!!$R1 1500
11 TraesCS4B01G329200 chr5D 445824760 445827573 2813 True 1587.500000 2449 91.5600 33 2943 2 chr5D.!!$R2 2910
12 TraesCS4B01G329200 chr7D 598893811 598895283 1472 False 2254.000000 2254 94.0980 1443 2943 1 chr7D.!!$F2 1500
13 TraesCS4B01G329200 chr7D 599162844 599165715 2871 False 1900.000000 2444 90.7155 1 2943 2 chr7D.!!$F4 2942
14 TraesCS4B01G329200 chr7D 593975157 593976908 1751 False 1829.000000 1829 85.8320 705 2475 1 chr7D.!!$F1 1770
15 TraesCS4B01G329200 chr7D 82632221 82633824 1603 True 1764.000000 1764 86.9300 700 2296 1 chr7D.!!$R1 1596
16 TraesCS4B01G329200 chr7D 41035733 41038049 2316 False 1275.500000 1537 87.6980 1 2391 2 chr7D.!!$F3 2390
17 TraesCS4B01G329200 chr4A 703477179 703478640 1461 True 1692.000000 1692 87.7400 1180 2660 1 chr4A.!!$R1 1480
18 TraesCS4B01G329200 chr2A 733207874 733209328 1454 True 1580.000000 1580 86.5030 815 2288 1 chr2A.!!$R1 1473
19 TraesCS4B01G329200 chr1D 415487622 415488827 1205 True 1044.000000 1044 82.9770 1087 2300 1 chr1D.!!$R1 1213
20 TraesCS4B01G329200 chr2D 598952496 598953460 964 True 1005.000000 1005 85.5600 818 1823 1 chr2D.!!$R1 1005

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
888 1089 0.897863 CTTCCATCCAAAACCGGCCA 60.898 55.0 0.0 0.0 0.0 5.36 F
1695 1975 1.160137 CTGGGTAAACTGCACAGCTC 58.840 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 2042 0.184451 CATAGGCAGGCAGGGAATGT 59.816 55.000 0.0 0.0 0.0 2.71 R
2618 3275 5.386924 TCTAGTAGGCAGGAAGATAGGTTC 58.613 45.833 0.0 0.0 0.0 3.62 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
121 122 9.766277 GTTTCATAAATTCAAAAGTTGTTTGCA 57.234 25.926 0.00 0.00 0.00 4.08
212 217 4.894798 TGTTCACGTTTTTCAAAAGTGC 57.105 36.364 9.58 0.26 32.31 4.40
214 219 4.985409 TGTTCACGTTTTTCAAAAGTGCTT 59.015 33.333 9.58 0.00 32.31 3.91
516 588 2.541466 AGGCAGAAGCTACAGTAAGGT 58.459 47.619 0.00 0.00 41.70 3.50
595 731 5.125417 TGTTCTTCAACACAGGAAAGGAAAG 59.875 40.000 0.00 0.00 37.61 2.62
878 1079 1.198094 TCAGGTTCGGCTTCCATCCA 61.198 55.000 0.00 0.00 0.00 3.41
888 1089 0.897863 CTTCCATCCAAAACCGGCCA 60.898 55.000 0.00 0.00 0.00 5.36
1695 1975 1.160137 CTGGGTAAACTGCACAGCTC 58.840 55.000 0.00 0.00 0.00 4.09
1747 2042 4.371786 GACAAGTCACATGTTCAGTCAGA 58.628 43.478 0.00 0.00 0.00 3.27
1844 2141 3.926198 TGGGGATATGTACCTCGGTTTA 58.074 45.455 0.00 0.00 0.00 2.01
1954 2262 4.587891 TGGTGCTATGATGATTGTGACAA 58.412 39.130 0.00 0.00 0.00 3.18
2179 2554 9.866655 TTAATGGAATAGATTATGCCTTGACTT 57.133 29.630 0.00 0.00 34.69 3.01
2397 3053 3.055819 GTGACAGGTCTCAGCTCCAATAA 60.056 47.826 0.65 0.00 0.00 1.40
2533 3189 6.964807 TGAAATCATCAGGTATGGAAATGG 57.035 37.500 0.00 0.00 36.15 3.16
2618 3275 6.312426 CCAGTTCTCTTGCAGTACTATTCAAG 59.688 42.308 18.32 18.32 37.76 3.02
2779 3438 6.245890 ACTATTCCTTGATTGCTTAGCTCT 57.754 37.500 5.60 0.00 0.00 4.09
2900 3563 6.095377 CCAATGTTCATTTCTAGAGGCAAAC 58.905 40.000 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
212 217 6.746104 TTGAACATGTTACGAATTTGCAAG 57.254 33.333 11.95 0.00 0.00 4.01
214 219 8.978564 ATATTTGAACATGTTACGAATTTGCA 57.021 26.923 11.95 0.00 0.00 4.08
770 966 2.809601 GTACGCGTGCCTGAGTGG 60.810 66.667 24.59 0.00 39.35 4.00
1747 2042 0.184451 CATAGGCAGGCAGGGAATGT 59.816 55.000 0.00 0.00 0.00 2.71
1775 2070 7.195474 AGTGGAATAGAAGGATATAGCTGGAT 58.805 38.462 0.00 0.00 0.00 3.41
1844 2141 4.488770 TCAAAGATTGCCCCTTTAAACCT 58.511 39.130 0.00 0.00 33.03 3.50
1981 2289 6.639686 GTCAAAAGAGACGTCACACTTACATA 59.360 38.462 19.50 4.83 0.00 2.29
1982 2290 5.462398 GTCAAAAGAGACGTCACACTTACAT 59.538 40.000 19.50 7.52 0.00 2.29
2179 2554 2.568956 AGCTGAGACCTGTATTGAGCAA 59.431 45.455 0.00 0.00 0.00 3.91
2533 3189 9.720667 ACTAAGTAATTTACAAAAACGGTCAAC 57.279 29.630 9.15 0.00 0.00 3.18
2618 3275 5.386924 TCTAGTAGGCAGGAAGATAGGTTC 58.613 45.833 0.00 0.00 0.00 3.62
2900 3563 5.715070 AGTTCACTAAGAAATCCGAGAGTG 58.285 41.667 0.00 0.00 38.13 3.51


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

AutoCloner maintained by Alex Coulton.