Multiple sequence alignment - TraesCS4D01G326000

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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 TraesCS4D01G326000 chr4D 100.000 2944 0 0 1 2944 485796676 485793733 0.000000e+00 5437.0
1 TraesCS4D01G326000 chr4B 97.255 2951 64 11 1 2944 619990803 619987863 0.000000e+00 4985.0
2 TraesCS4D01G326000 chr4B 89.541 2027 145 28 955 2944 545480439 545478443 0.000000e+00 2507.0
3 TraesCS4D01G326000 chr4B 94.426 1507 50 12 1443 2943 12902495 12901017 0.000000e+00 2287.0
4 TraesCS4D01G326000 chr4B 86.275 816 63 25 519 1318 12903332 12902550 0.000000e+00 841.0
5 TraesCS4D01G326000 chr4B 86.481 503 34 9 23 493 12903816 12903316 3.360000e-144 521.0
6 TraesCS4D01G326000 chr7A 93.610 2817 108 18 164 2944 691411840 691414620 0.000000e+00 4139.0
7 TraesCS4D01G326000 chr7A 85.616 1599 151 39 706 2273 84381197 84379647 0.000000e+00 1605.0
8 TraesCS4D01G326000 chr7A 93.995 383 17 5 426 804 55576329 55576709 2.540000e-160 575.0
9 TraesCS4D01G326000 chr7A 89.754 244 20 4 23 261 55576046 55576289 1.020000e-79 307.0
10 TraesCS4D01G326000 chr7A 84.127 126 10 6 554 669 55573582 55573707 2.400000e-21 113.0
11 TraesCS4D01G326000 chr2B 89.951 2468 147 43 536 2944 725229437 725227012 0.000000e+00 3090.0
12 TraesCS4D01G326000 chr2B 86.856 1164 99 29 1150 2290 728345258 728344126 0.000000e+00 1253.0
13 TraesCS4D01G326000 chr2B 80.660 212 13 10 701 904 728362995 728362804 3.960000e-29 139.0
14 TraesCS4D01G326000 chr7B 87.329 2407 159 77 571 2944 678611130 678613423 0.000000e+00 2621.0
15 TraesCS4D01G326000 chr7B 84.956 565 31 15 1 530 678610492 678611037 9.350000e-145 523.0
16 TraesCS4D01G326000 chr7B 83.549 541 51 20 534 1055 46019102 46019623 3.430000e-129 472.0
17 TraesCS4D01G326000 chr5D 95.508 1536 57 4 1413 2944 445826288 445824761 0.000000e+00 2444.0
18 TraesCS4D01G326000 chr5D 95.216 1505 55 4 1443 2944 445965231 445963741 0.000000e+00 2364.0
19 TraesCS4D01G326000 chr5D 88.906 658 37 17 32 658 445827573 445826921 0.000000e+00 778.0
20 TraesCS4D01G326000 chr5D 84.593 675 40 20 656 1318 445826957 445826335 1.940000e-171 612.0
21 TraesCS4D01G326000 chr7D 95.443 1536 58 4 1413 2944 599164187 599165714 0.000000e+00 2438.0
22 TraesCS4D01G326000 chr7D 94.153 1505 52 7 1443 2944 598893811 598895282 0.000000e+00 2259.0
23 TraesCS4D01G326000 chr7D 85.927 1812 156 54 706 2478 593975157 593976908 0.000000e+00 1842.0
24 TraesCS4D01G326000 chr7D 86.798 1621 125 36 701 2273 82633824 82632245 0.000000e+00 1725.0
25 TraesCS4D01G326000 chr7D 86.873 1356 80 40 1 1318 599162845 599164140 0.000000e+00 1428.0
26 TraesCS4D01G326000 chr7D 89.786 842 34 14 1 804 41035734 41036561 0.000000e+00 1031.0
27 TraesCS4D01G326000 chr7D 83.409 440 41 16 888 1318 598893340 598893756 2.140000e-101 379.0
28 TraesCS4D01G326000 chr2A 86.358 1510 131 38 816 2298 733209328 733207867 0.000000e+00 1578.0
29 TraesCS4D01G326000 chr2A 87.671 73 4 2 1298 1368 713543988 713544057 2.430000e-11 80.5


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 TraesCS4D01G326000 chr4D 485793733 485796676 2943 True 5437.000000 5437 100.000000 1 2944 1 chr4D.!!$R1 2943
1 TraesCS4D01G326000 chr4B 619987863 619990803 2940 True 4985.000000 4985 97.255000 1 2944 1 chr4B.!!$R2 2943
2 TraesCS4D01G326000 chr4B 545478443 545480439 1996 True 2507.000000 2507 89.541000 955 2944 1 chr4B.!!$R1 1989
3 TraesCS4D01G326000 chr4B 12901017 12903816 2799 True 1216.333333 2287 89.060667 23 2943 3 chr4B.!!$R3 2920
4 TraesCS4D01G326000 chr7A 691411840 691414620 2780 False 4139.000000 4139 93.610000 164 2944 1 chr7A.!!$F1 2780
5 TraesCS4D01G326000 chr7A 84379647 84381197 1550 True 1605.000000 1605 85.616000 706 2273 1 chr7A.!!$R1 1567
6 TraesCS4D01G326000 chr7A 55573582 55576709 3127 False 331.666667 575 89.292000 23 804 3 chr7A.!!$F2 781
7 TraesCS4D01G326000 chr2B 725227012 725229437 2425 True 3090.000000 3090 89.951000 536 2944 1 chr2B.!!$R1 2408
8 TraesCS4D01G326000 chr2B 728344126 728345258 1132 True 1253.000000 1253 86.856000 1150 2290 1 chr2B.!!$R2 1140
9 TraesCS4D01G326000 chr7B 678610492 678613423 2931 False 1572.000000 2621 86.142500 1 2944 2 chr7B.!!$F2 2943
10 TraesCS4D01G326000 chr7B 46019102 46019623 521 False 472.000000 472 83.549000 534 1055 1 chr7B.!!$F1 521
11 TraesCS4D01G326000 chr5D 445963741 445965231 1490 True 2364.000000 2364 95.216000 1443 2944 1 chr5D.!!$R1 1501
12 TraesCS4D01G326000 chr5D 445824761 445827573 2812 True 1278.000000 2444 89.669000 32 2944 3 chr5D.!!$R2 2912
13 TraesCS4D01G326000 chr7D 599162845 599165714 2869 False 1933.000000 2438 91.158000 1 2944 2 chr7D.!!$F4 2943
14 TraesCS4D01G326000 chr7D 593975157 593976908 1751 False 1842.000000 1842 85.927000 706 2478 1 chr7D.!!$F2 1772
15 TraesCS4D01G326000 chr7D 82632245 82633824 1579 True 1725.000000 1725 86.798000 701 2273 1 chr7D.!!$R1 1572
16 TraesCS4D01G326000 chr7D 598893340 598895282 1942 False 1319.000000 2259 88.781000 888 2944 2 chr7D.!!$F3 2056
17 TraesCS4D01G326000 chr7D 41035734 41036561 827 False 1031.000000 1031 89.786000 1 804 1 chr7D.!!$F1 803
18 TraesCS4D01G326000 chr2A 733207867 733209328 1461 True 1578.000000 1578 86.358000 816 2298 1 chr2A.!!$R1 1482

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
750 3515 3.426159 CCGATTGAGTGTTTCCCGAATTG 60.426 47.826 0.0 0.0 0.0 2.32 F
1514 4330 0.524862 CAGCCTTGGATGCAGTGAAC 59.475 55.000 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 4746 0.036765 TAGTGCGGTCCATGTCAACC 60.037 55.000 0.00 0.00 0.00 3.77 R
2852 5734 2.874701 AGAACATCAGAACTGTGTGTGC 59.125 45.455 12.93 11.75 33.44 4.57 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
474 3109 8.606040 ATTTCGTTCACAAATTTTGGAATCAT 57.394 26.923 13.42 3.78 34.12 2.45
750 3515 3.426159 CCGATTGAGTGTTTCCCGAATTG 60.426 47.826 0.00 0.00 0.00 2.32
1349 4148 4.388499 CTCCCCCGACCACAACCG 62.388 72.222 0.00 0.00 0.00 4.44
1514 4330 0.524862 CAGCCTTGGATGCAGTGAAC 59.475 55.000 0.00 0.00 0.00 3.18
1526 4342 2.289072 TGCAGTGAACTGGCTAGAGAAC 60.289 50.000 12.20 0.00 43.94 3.01
1530 4346 4.021544 CAGTGAACTGGCTAGAGAACTTCT 60.022 45.833 3.17 0.00 40.20 2.85
1531 4347 4.219725 AGTGAACTGGCTAGAGAACTTCTC 59.780 45.833 3.17 10.43 43.70 2.87
1725 4569 2.898920 AATGCGCTGGGATGACTGGG 62.899 60.000 9.73 0.00 0.00 4.45
1726 4570 4.864334 GCGCTGGGATGACTGGGG 62.864 72.222 0.00 0.00 0.00 4.96
1898 4746 8.499403 TGTATATCAACTATCGAGGATCTCAG 57.501 38.462 0.00 0.00 0.00 3.35
1969 4819 4.607293 TGTGACAGAAGATGTTAGCTGT 57.393 40.909 0.00 0.00 44.17 4.40
2012 4874 2.036387 TGACGTCTCTTTTGACCCTGA 58.964 47.619 17.92 0.00 33.70 3.86
2273 5152 9.732130 AATGGAATAGATTATGCCTTAACTCTC 57.268 33.333 0.00 0.00 34.69 3.20
2318 5197 8.946085 TCTCAACTGTGATAATGAAATTGTACC 58.054 33.333 0.00 0.00 36.99 3.34
2382 5261 1.550524 TGCCTTAACTCTGCTCGTGAT 59.449 47.619 0.00 0.00 0.00 3.06
2786 5665 0.618458 TTGATTGCTTAGCTCCCGGT 59.382 50.000 5.60 0.00 0.00 5.28
2852 5734 7.762382 AGTTGAGTTCTAACTTTGTTGAAAGG 58.238 34.615 0.00 0.00 42.66 3.11
2907 5789 6.823689 TGTTCATTTCTAGAGGCAAATACTCC 59.176 38.462 0.00 0.00 35.58 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
506 3147 0.537188 ACTGCAGCGCCTTACTGTAT 59.463 50.000 15.27 0.00 37.47 2.29
1349 4148 1.739067 ATACCTTTCTTGGACGCAGC 58.261 50.000 0.00 0.00 0.00 5.25
1526 4342 4.272991 GCAGCAATAGTCTGGATTGAGAAG 59.727 45.833 0.31 0.00 36.57 2.85
1530 4346 3.920231 AGCAGCAATAGTCTGGATTGA 57.080 42.857 0.00 0.00 36.57 2.57
1531 4347 6.695429 TCTATAGCAGCAATAGTCTGGATTG 58.305 40.000 0.00 0.00 37.35 2.67
1725 4569 2.481952 GCTGACTGAACATGTGACTTCC 59.518 50.000 0.00 0.00 0.00 3.46
1726 4570 2.481952 GGCTGACTGAACATGTGACTTC 59.518 50.000 0.00 0.00 0.00 3.01
1898 4746 0.036765 TAGTGCGGTCCATGTCAACC 60.037 55.000 0.00 0.00 0.00 3.77
2273 5152 6.522625 TGAGACTTGAGACCTATCTTGAAG 57.477 41.667 0.00 0.00 34.34 3.02
2318 5197 8.687824 AAATAACATATTTCCTGTTTTGCTCG 57.312 30.769 0.00 0.00 37.89 5.03
2382 5261 9.561069 GATTTTTAATATTGGAGCTGAGACCTA 57.439 33.333 0.00 0.00 0.00 3.08
2786 5665 6.976934 AAAAGAATGGTGGAGCTTCTTAAA 57.023 33.333 0.00 0.00 38.05 1.52
2828 5709 6.472486 GCCTTTCAACAAAGTTAGAACTCAAC 59.528 38.462 0.00 0.00 38.57 3.18
2852 5734 2.874701 AGAACATCAGAACTGTGTGTGC 59.125 45.455 12.93 11.75 33.44 4.57
2907 5789 7.603024 GGGATTATAGTTCACTAAGAAATCCGG 59.397 40.741 20.05 0.00 41.37 5.14


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

AutoCloner maintained by Alex Coulton.