Multiple sequence alignment - TraesCS4A01G373100

Loading Multiple Alignment...

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 TraesCS4A01G373100 chr4A 100.000 2757 0 0 1 2757 648464896 648462140 0.000000e+00 5092.0
1 TraesCS4A01G373100 chr4A 95.725 2222 74 6 1 2206 710919914 710917698 0.000000e+00 3557.0
2 TraesCS4A01G373100 chr4B 95.666 2469 82 8 1 2461 554383097 554380646 0.000000e+00 3943.0
3 TraesCS4A01G373100 chr4B 94.675 2310 85 6 449 2757 226804358 226802086 0.000000e+00 3550.0
4 TraesCS4A01G373100 chr4B 95.658 2211 80 5 1 2200 424254127 424251922 0.000000e+00 3537.0
5 TraesCS4A01G373100 chr3B 96.662 2367 63 5 1 2356 689934372 689932011 0.000000e+00 3919.0
6 TraesCS4A01G373100 chr3B 97.928 724 13 2 2036 2757 797658078 797658801 0.000000e+00 1253.0
7 TraesCS4A01G373100 chr3B 97.790 724 14 2 2036 2757 489091653 489092376 0.000000e+00 1247.0
8 TraesCS4A01G373100 chr3B 95.135 370 5 5 74 432 56532213 56531846 3.080000e-159 571.0
9 TraesCS4A01G373100 chr3B 95.802 262 6 2 1 258 34657024 34657284 4.250000e-113 418.0
10 TraesCS4A01G373100 chr3B 96.739 92 1 2 343 433 688797563 688797653 4.760000e-33 152.0
11 TraesCS4A01G373100 chr7B 96.330 2316 81 3 445 2757 493606647 493604333 0.000000e+00 3803.0
12 TraesCS4A01G373100 chr7B 96.095 1946 70 3 423 2368 680564295 680562356 0.000000e+00 3168.0
13 TraesCS4A01G373100 chr7B 95.895 1949 63 4 423 2368 59507312 59509246 0.000000e+00 3140.0
14 TraesCS4A01G373100 chr7B 98.235 170 3 0 3 172 680564649 680564480 5.770000e-77 298.0
15 TraesCS4A01G373100 chr1B 95.394 2323 87 7 439 2757 666744862 666747168 0.000000e+00 3679.0
16 TraesCS4A01G373100 chr1B 97.652 724 15 2 2036 2757 534144016 534144739 0.000000e+00 1242.0
17 TraesCS4A01G373100 chrUn 94.814 1639 57 4 1 1628 343780595 343782216 0.000000e+00 2531.0
18 TraesCS4A01G373100 chrUn 92.982 171 10 2 143 313 49735176 49735344 5.900000e-62 248.0
19 TraesCS4A01G373100 chr6B 97.790 724 14 2 2036 2757 659285680 659286403 0.000000e+00 1247.0
20 TraesCS4A01G373100 chr2B 97.790 724 14 2 2036 2757 678997821 678998544 0.000000e+00 1247.0
21 TraesCS4A01G373100 chr2B 96.703 91 1 2 343 432 515594220 515594309 1.710000e-32 150.0
22 TraesCS4A01G373100 chr2B 100.000 39 0 0 307 345 300400887 300400849 3.810000e-09 73.1
23 TraesCS4A01G373100 chr5B 95.135 370 5 6 74 432 642584101 642583734 3.080000e-159 571.0
24 TraesCS4A01G373100 chr5B 100.000 39 0 0 307 345 366698260 366698298 3.810000e-09 73.1


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 TraesCS4A01G373100 chr4A 648462140 648464896 2756 True 5092 5092 100.000 1 2757 1 chr4A.!!$R1 2756
1 TraesCS4A01G373100 chr4A 710917698 710919914 2216 True 3557 3557 95.725 1 2206 1 chr4A.!!$R2 2205
2 TraesCS4A01G373100 chr4B 554380646 554383097 2451 True 3943 3943 95.666 1 2461 1 chr4B.!!$R3 2460
3 TraesCS4A01G373100 chr4B 226802086 226804358 2272 True 3550 3550 94.675 449 2757 1 chr4B.!!$R1 2308
4 TraesCS4A01G373100 chr4B 424251922 424254127 2205 True 3537 3537 95.658 1 2200 1 chr4B.!!$R2 2199
5 TraesCS4A01G373100 chr3B 689932011 689934372 2361 True 3919 3919 96.662 1 2356 1 chr3B.!!$R2 2355
6 TraesCS4A01G373100 chr3B 797658078 797658801 723 False 1253 1253 97.928 2036 2757 1 chr3B.!!$F4 721
7 TraesCS4A01G373100 chr3B 489091653 489092376 723 False 1247 1247 97.790 2036 2757 1 chr3B.!!$F2 721
8 TraesCS4A01G373100 chr7B 493604333 493606647 2314 True 3803 3803 96.330 445 2757 1 chr7B.!!$R1 2312
9 TraesCS4A01G373100 chr7B 59507312 59509246 1934 False 3140 3140 95.895 423 2368 1 chr7B.!!$F1 1945
10 TraesCS4A01G373100 chr7B 680562356 680564649 2293 True 1733 3168 97.165 3 2368 2 chr7B.!!$R2 2365
11 TraesCS4A01G373100 chr1B 666744862 666747168 2306 False 3679 3679 95.394 439 2757 1 chr1B.!!$F2 2318
12 TraesCS4A01G373100 chr1B 534144016 534144739 723 False 1242 1242 97.652 2036 2757 1 chr1B.!!$F1 721
13 TraesCS4A01G373100 chrUn 343780595 343782216 1621 False 2531 2531 94.814 1 1628 1 chrUn.!!$F2 1627
14 TraesCS4A01G373100 chr6B 659285680 659286403 723 False 1247 1247 97.790 2036 2757 1 chr6B.!!$F1 721
15 TraesCS4A01G373100 chr2B 678997821 678998544 723 False 1247 1247 97.790 2036 2757 1 chr2B.!!$F2 721

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
822 853 1.081174 AGAGATCTCCCCTTCACCCAA 59.919 52.381 19.3 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 2749 8.189119 AGCTAACCTATGTCATTTTGGAAAAA 57.811 30.769 0.0 0.0 0.0 1.94 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
259 278 8.021396 GGTGATAACATTTGTTAGTGAGGAAAC 58.979 37.037 8.90 0.00 42.94 2.78
526 557 5.888982 AAATTCGGGTACTCCATATGTCT 57.111 39.130 1.24 0.00 34.36 3.41
682 713 3.261643 TGGTCTCTTCTGCTGCTTATCAA 59.738 43.478 0.00 0.00 0.00 2.57
684 715 4.697352 GGTCTCTTCTGCTGCTTATCAAAA 59.303 41.667 0.00 0.00 0.00 2.44
754 785 4.202398 TGGATGCTTCTGAGTTCTTCACTT 60.202 41.667 0.00 0.00 35.01 3.16
759 790 5.237996 TGCTTCTGAGTTCTTCACTTTCATG 59.762 40.000 0.00 0.00 35.01 3.07
779 810 6.647229 TCATGCTTGAGACTTCAGTATCATT 58.353 36.000 5.15 0.00 44.48 2.57
822 853 1.081174 AGAGATCTCCCCTTCACCCAA 59.919 52.381 19.30 0.00 0.00 4.12
937 968 2.164219 CCGCCAAATAATGTGAAGCTGT 59.836 45.455 0.00 0.00 0.00 4.40
988 1019 1.340405 GGGATGTGCAGTTGGTGATCT 60.340 52.381 0.00 0.00 0.00 2.75
1062 1093 1.380302 CCTGCAGCTGGGGTACTTT 59.620 57.895 17.12 0.00 0.00 2.66
1091 1122 2.099062 GTACGACGACGACGCCAT 59.901 61.111 18.98 3.27 43.96 4.40
1254 1285 1.367346 TGGACAGGTAATGGGAGCAA 58.633 50.000 0.00 0.00 0.00 3.91
1604 1635 1.308069 GCCTGACAATGACCACGCAT 61.308 55.000 0.00 0.00 0.00 4.73
1691 1722 1.304713 CCACTGCCTCCATTGCCTT 60.305 57.895 0.00 0.00 0.00 4.35
2461 2855 8.999895 TCCTATAGGTTAGCTCCAAAATAACTT 58.000 33.333 18.51 0.00 36.34 2.66
2466 2860 8.879427 AGGTTAGCTCCAAAATAACTTATGTT 57.121 30.769 0.00 0.00 39.98 2.71
2467 2861 9.969001 AGGTTAGCTCCAAAATAACTTATGTTA 57.031 29.630 3.90 3.90 42.11 2.41
2469 2863 9.717892 GTTAGCTCCAAAATAACTTATGTTAGC 57.282 33.333 7.24 5.12 41.33 3.09
2470 2864 7.938140 AGCTCCAAAATAACTTATGTTAGCA 57.062 32.000 7.24 0.00 41.33 3.49
2471 2865 7.762382 AGCTCCAAAATAACTTATGTTAGCAC 58.238 34.615 7.24 0.00 41.33 4.40
2472 2866 7.393234 AGCTCCAAAATAACTTATGTTAGCACA 59.607 33.333 7.24 0.00 41.33 4.57
2473 2867 8.026607 GCTCCAAAATAACTTATGTTAGCACAA 58.973 33.333 7.24 0.00 41.33 3.33
2474 2868 9.906660 CTCCAAAATAACTTATGTTAGCACAAA 57.093 29.630 7.24 0.00 41.33 2.83
2483 2877 9.630098 AACTTATGTTAGCACAAAATGATCAAG 57.370 29.630 0.00 0.00 36.16 3.02
2484 2878 8.796475 ACTTATGTTAGCACAAAATGATCAAGT 58.204 29.630 0.00 0.00 36.16 3.16
2485 2879 9.630098 CTTATGTTAGCACAAAATGATCAAGTT 57.370 29.630 0.00 0.00 36.16 2.66
2486 2880 9.979578 TTATGTTAGCACAAAATGATCAAGTTT 57.020 25.926 0.00 0.28 36.16 2.66
2488 2882 8.795786 TGTTAGCACAAAATGATCAAGTTTAC 57.204 30.769 0.00 0.00 0.00 2.01
2489 2883 8.409371 TGTTAGCACAAAATGATCAAGTTTACA 58.591 29.630 0.00 1.46 0.00 2.41
2490 2884 9.410556 GTTAGCACAAAATGATCAAGTTTACAT 57.589 29.630 0.00 0.00 0.00 2.29
2736 3130 5.007034 TGAATTGATGGATAACGGTGTTGT 58.993 37.500 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 6.208599 AGTCCAAGTCAAAACAAAAAGTCTGA 59.791 34.615 0.00 0.00 0.00 3.27
147 148 3.345508 ACGGTACCAGGAGGAAATTTC 57.654 47.619 13.54 9.83 38.69 2.17
259 278 2.158623 TGGTGCAGGCCAGGATTAATAG 60.159 50.000 5.01 0.00 33.97 1.73
360 385 5.189928 AGATACAAGTTGAACACACACCAA 58.810 37.500 10.54 0.00 0.00 3.67
503 534 6.989155 AGACATATGGAGTACCCGAATTTA 57.011 37.500 7.80 0.00 37.93 1.40
557 588 6.393720 GCAAATTCATGCTAAAATTCACGT 57.606 33.333 0.00 0.00 43.06 4.49
643 674 9.628500 GAAGAGACCAATTAATACCCTTACAAT 57.372 33.333 0.00 0.00 0.00 2.71
682 713 2.649129 GGCTGCTTCCCGCCATTTT 61.649 57.895 0.00 0.00 45.59 1.82
754 785 6.041423 TGATACTGAAGTCTCAAGCATGAA 57.959 37.500 0.00 0.00 34.49 2.57
759 790 6.760298 TCATGAATGATACTGAAGTCTCAAGC 59.240 38.462 0.00 0.36 35.31 4.01
779 810 7.666623 TCTCGTTTTATATACCTGCATCATGA 58.333 34.615 0.00 0.00 0.00 3.07
822 853 8.743085 AGCAAACAACAGATATCATAATGAGT 57.257 30.769 5.32 0.00 0.00 3.41
988 1019 2.910319 ACAAGTACATGTGGCCCTTCTA 59.090 45.455 9.11 0.00 30.82 2.10
1062 1093 2.740981 GTCGTCGTACCTGAAGAGAAGA 59.259 50.000 0.00 0.00 0.00 2.87
1091 1122 1.276138 ACACCTTCACGATGAGCATGA 59.724 47.619 0.00 0.00 0.00 3.07
1119 1150 3.532138 GCGCATGCGACACATAATT 57.468 47.368 41.98 0.00 42.83 1.40
1121 1152 2.705804 CGTAGCGCATGCGACACATAA 61.706 52.381 41.98 15.67 45.79 1.90
1145 1176 0.039527 CGTACCGGCATCATCATCGA 60.040 55.000 0.00 0.00 0.00 3.59
1254 1285 2.574018 TAGCCAGTGTCGCTGCTGT 61.574 57.895 7.95 0.00 43.71 4.40
1312 1343 3.603158 TCGCTACAGCCAAAATCACTA 57.397 42.857 0.00 0.00 37.91 2.74
1315 1346 2.095263 GCTTTCGCTACAGCCAAAATCA 60.095 45.455 0.00 0.00 37.91 2.57
1571 1602 3.249189 AGGCACCACCACCATCGT 61.249 61.111 0.00 0.00 43.14 3.73
1891 1947 8.755696 CTCTAAGTTAGCATATTAGAGCCAAG 57.244 38.462 4.93 0.00 43.13 3.61
1944 2000 8.630054 TGTGCTAACATAAGTTATTTTGGAGT 57.370 30.769 8.77 0.00 39.36 3.85
2356 2749 8.189119 AGCTAACCTATGTCATTTTGGAAAAA 57.811 30.769 0.00 0.00 0.00 1.94
2462 2856 9.410556 GTAAACTTGATCATTTTGTGCTAACAT 57.589 29.630 11.37 0.00 35.83 2.71
2463 2857 8.409371 TGTAAACTTGATCATTTTGTGCTAACA 58.591 29.630 11.37 5.61 0.00 2.41
2464 2858 8.795786 TGTAAACTTGATCATTTTGTGCTAAC 57.204 30.769 11.37 3.67 0.00 2.34


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

AutoCloner maintained by Alex Coulton.