Multiple sequence alignment - TraesCS2A01G303000

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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 TraesCS2A01G303000 chr2A 100.000 3462 0 0 1 3462 520056902 520053441 0.000000e+00 6394
1 TraesCS2A01G303000 chr2A 91.801 2110 140 14 1094 3174 309469119 309471224 0.000000e+00 2907
2 TraesCS2A01G303000 chr1A 97.291 3470 54 11 1 3462 537043932 537040495 0.000000e+00 5851
3 TraesCS2A01G303000 chr1A 88.372 1118 89 18 709 1811 221812302 221811211 0.000000e+00 1306
4 TraesCS2A01G303000 chr3A 97.762 2636 43 3 828 3462 679891840 679889220 0.000000e+00 4527
5 TraesCS2A01G303000 chr3A 96.655 837 21 6 1 831 679905957 679905122 0.000000e+00 1384
6 TraesCS2A01G303000 chr3A 95.406 283 13 0 3180 3462 238341197 238340915 5.270000e-123 451
7 TraesCS2A01G303000 chr3A 95.053 283 14 0 3180 3462 24804255 24803973 2.450000e-121 446
8 TraesCS2A01G303000 chr4A 93.821 2201 86 29 1 2184 535950795 535948628 0.000000e+00 3265
9 TraesCS2A01G303000 chr4A 94.686 1355 47 6 1380 2710 311931881 311933234 0.000000e+00 2080
10 TraesCS2A01G303000 chr4A 91.992 1049 57 13 2146 3174 535948628 535947587 0.000000e+00 1447
11 TraesCS2A01G303000 chr2D 94.274 2113 91 9 1089 3174 341958782 341960891 0.000000e+00 3205
12 TraesCS2A01G303000 chr2D 95.053 283 14 0 3180 3462 353278750 353279032 2.450000e-121 446
13 TraesCS2A01G303000 chr6B 95.029 1046 45 5 1 1040 4738769 4739813 0.000000e+00 1637
14 TraesCS2A01G303000 chr6B 94.943 1048 44 7 1 1040 4735766 4736812 0.000000e+00 1633
15 TraesCS2A01G303000 chr6B 94.275 1048 51 9 1 1040 4741771 4742817 0.000000e+00 1594
16 TraesCS2A01G303000 chr6B 95.053 283 13 1 3180 3462 378826394 378826113 8.820000e-121 444
17 TraesCS2A01G303000 chr1B 94.444 1026 47 9 1 1019 295052436 295051414 0.000000e+00 1570
18 TraesCS2A01G303000 chr7B 90.804 1120 85 10 709 1813 289287107 289288223 0.000000e+00 1482
19 TraesCS2A01G303000 chr7B 95.053 283 14 0 3180 3462 209849054 209849336 2.450000e-121 446
20 TraesCS2A01G303000 chr5D 90.351 1140 67 13 1814 2915 364369942 364368808 0.000000e+00 1456
21 TraesCS2A01G303000 chr5B 90.009 1131 72 16 1814 2912 429930649 429929528 0.000000e+00 1424
22 TraesCS2A01G303000 chr7A 89.581 1123 94 13 709 1816 401657022 401655908 0.000000e+00 1404
23 TraesCS2A01G303000 chr7A 90.870 690 51 7 777 1461 339108819 339109501 0.000000e+00 915
24 TraesCS2A01G303000 chr5A 88.964 1042 67 26 1814 2814 139787705 139786671 0.000000e+00 1243
25 TraesCS2A01G303000 chr5A 85.362 1134 123 18 2076 3174 207740255 207741380 0.000000e+00 1134
26 TraesCS2A01G303000 chr5A 86.667 1065 91 22 2150 3174 384463490 384462437 0.000000e+00 1133
27 TraesCS2A01G303000 chr7D 86.596 1134 109 18 2076 3174 289881161 289880036 0.000000e+00 1212
28 TraesCS2A01G303000 chr6D 87.230 1065 81 22 2150 3174 248009003 248007954 0.000000e+00 1162
29 TraesCS2A01G303000 chr4B 92.437 714 41 8 1 705 341928071 341927362 0.000000e+00 1007
30 TraesCS2A01G303000 chr2B 94.216 657 30 6 1 650 275148973 275148318 0.000000e+00 996
31 TraesCS2A01G303000 chr3B 90.306 588 49 6 1232 1816 80771387 80770805 0.000000e+00 763
32 TraesCS2A01G303000 chr3B 95.406 283 13 0 3180 3462 628862702 628862984 5.270000e-123 451
33 TraesCS2A01G303000 chr3B 94.718 284 13 2 3180 3462 126564657 126564939 1.140000e-119 440


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 TraesCS2A01G303000 chr2A 520053441 520056902 3461 True 6394.000000 6394 100.0000 1 3462 1 chr2A.!!$R1 3461
1 TraesCS2A01G303000 chr2A 309469119 309471224 2105 False 2907.000000 2907 91.8010 1094 3174 1 chr2A.!!$F1 2080
2 TraesCS2A01G303000 chr1A 537040495 537043932 3437 True 5851.000000 5851 97.2910 1 3462 1 chr1A.!!$R2 3461
3 TraesCS2A01G303000 chr1A 221811211 221812302 1091 True 1306.000000 1306 88.3720 709 1811 1 chr1A.!!$R1 1102
4 TraesCS2A01G303000 chr3A 679889220 679891840 2620 True 4527.000000 4527 97.7620 828 3462 1 chr3A.!!$R3 2634
5 TraesCS2A01G303000 chr3A 679905122 679905957 835 True 1384.000000 1384 96.6550 1 831 1 chr3A.!!$R4 830
6 TraesCS2A01G303000 chr4A 535947587 535950795 3208 True 2356.000000 3265 92.9065 1 3174 2 chr4A.!!$R1 3173
7 TraesCS2A01G303000 chr4A 311931881 311933234 1353 False 2080.000000 2080 94.6860 1380 2710 1 chr4A.!!$F1 1330
8 TraesCS2A01G303000 chr2D 341958782 341960891 2109 False 3205.000000 3205 94.2740 1089 3174 1 chr2D.!!$F1 2085
9 TraesCS2A01G303000 chr6B 4735766 4742817 7051 False 1621.333333 1637 94.7490 1 1040 3 chr6B.!!$F1 1039
10 TraesCS2A01G303000 chr1B 295051414 295052436 1022 True 1570.000000 1570 94.4440 1 1019 1 chr1B.!!$R1 1018
11 TraesCS2A01G303000 chr7B 289287107 289288223 1116 False 1482.000000 1482 90.8040 709 1813 1 chr7B.!!$F2 1104
12 TraesCS2A01G303000 chr5D 364368808 364369942 1134 True 1456.000000 1456 90.3510 1814 2915 1 chr5D.!!$R1 1101
13 TraesCS2A01G303000 chr5B 429929528 429930649 1121 True 1424.000000 1424 90.0090 1814 2912 1 chr5B.!!$R1 1098
14 TraesCS2A01G303000 chr7A 401655908 401657022 1114 True 1404.000000 1404 89.5810 709 1816 1 chr7A.!!$R1 1107
15 TraesCS2A01G303000 chr7A 339108819 339109501 682 False 915.000000 915 90.8700 777 1461 1 chr7A.!!$F1 684
16 TraesCS2A01G303000 chr5A 139786671 139787705 1034 True 1243.000000 1243 88.9640 1814 2814 1 chr5A.!!$R1 1000
17 TraesCS2A01G303000 chr5A 207740255 207741380 1125 False 1134.000000 1134 85.3620 2076 3174 1 chr5A.!!$F1 1098
18 TraesCS2A01G303000 chr5A 384462437 384463490 1053 True 1133.000000 1133 86.6670 2150 3174 1 chr5A.!!$R2 1024
19 TraesCS2A01G303000 chr7D 289880036 289881161 1125 True 1212.000000 1212 86.5960 2076 3174 1 chr7D.!!$R1 1098
20 TraesCS2A01G303000 chr6D 248007954 248009003 1049 True 1162.000000 1162 87.2300 2150 3174 1 chr6D.!!$R1 1024
21 TraesCS2A01G303000 chr4B 341927362 341928071 709 True 1007.000000 1007 92.4370 1 705 1 chr4B.!!$R1 704
22 TraesCS2A01G303000 chr2B 275148318 275148973 655 True 996.000000 996 94.2160 1 650 1 chr2B.!!$R1 649
23 TraesCS2A01G303000 chr3B 80770805 80771387 582 True 763.000000 763 90.3060 1232 1816 1 chr3B.!!$R1 584

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
506 517 2.361610 GGACGACCCCGACCACTA 60.362 66.667 0.0 0.0 46.95 2.74 F
720 3738 2.369860 TGAGCTTTCAGTCCATGTGTCT 59.630 45.455 0.0 0.0 0.00 3.41 F
986 4010 2.893489 AGGTTCCAGATTGCCAAAAGTC 59.107 45.455 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 7427 2.617276 CCATCCCGCTGCTCATCAATAT 60.617 50.000 0.0 0.0 0.00 1.28 R
1880 7545 4.177026 AGTAACGAGATGCAAGCTTAGTG 58.823 43.478 0.0 0.0 22.26 2.74 R
2461 8229 6.441924 TGACAGGGTCTAAGAGAGATCAATTT 59.558 38.462 0.0 0.0 36.98 1.82 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
265 266 9.790389 ACGTTATGTTGTTTTCATACTTTCAAA 57.210 25.926 0.00 0.00 0.00 2.69
506 517 2.361610 GGACGACCCCGACCACTA 60.362 66.667 0.00 0.00 46.95 2.74
720 3738 2.369860 TGAGCTTTCAGTCCATGTGTCT 59.630 45.455 0.00 0.00 0.00 3.41
805 3829 6.428465 TGCTCCGTTAAATCACTTGTTTCATA 59.572 34.615 0.00 0.00 0.00 2.15
863 3887 4.649674 AGTAGCTTGCACTAGCCTATACAA 59.350 41.667 6.77 0.00 42.20 2.41
986 4010 2.893489 AGGTTCCAGATTGCCAAAAGTC 59.107 45.455 0.00 0.00 0.00 3.01
1189 6421 3.593442 ACATGGGAAAAGGTCAGTTCA 57.407 42.857 0.00 0.00 0.00 3.18
1240 6476 7.531857 TTATTTGGAGTGGTTAGCAATTCAA 57.468 32.000 1.22 1.22 0.00 2.69
1880 7545 8.757164 AGTATTTGCAAATTTGTAACCTAAGC 57.243 30.769 28.45 8.49 32.53 3.09
1996 7662 6.652481 AGTGTATTCTCTCATCTTGGTTGTTG 59.348 38.462 0.00 0.00 0.00 3.33
2461 8229 8.567948 GTGAAAAATGGAGTGAAAGAGTATTGA 58.432 33.333 0.00 0.00 0.00 2.57
2591 8365 3.150767 TGTTATGCCCAGTACAAACCAC 58.849 45.455 0.00 0.00 0.00 4.16
3112 8894 4.516698 CACCACACTCAGCTTTGTTCTATT 59.483 41.667 0.00 0.00 0.00 1.73
3300 9084 5.235516 TCGGAACCATTCAAAACTACTCTC 58.764 41.667 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
440 451 2.689983 GTTGATTCATCACCCATCCACC 59.310 50.000 0.00 0.00 36.36 4.61
720 3738 2.594303 CCGGCCACAACAGCAAGA 60.594 61.111 2.24 0.00 0.00 3.02
863 3887 0.322975 ACAACGGCTTGAGATGCTCT 59.677 50.000 4.13 0.00 0.00 4.09
986 4010 3.056250 CCCATCCATCTCACTATCTTCGG 60.056 52.174 0.00 0.00 0.00 4.30
1240 6476 9.220767 GAACTGATGTGTCCTTTTTCTAGTTAT 57.779 33.333 0.00 0.00 0.00 1.89
1423 6912 8.103935 ACACTCATCGAGGTAGATATCATTCTA 58.896 37.037 5.32 0.00 33.35 2.10
1762 7427 2.617276 CCATCCCGCTGCTCATCAATAT 60.617 50.000 0.00 0.00 0.00 1.28
1862 7527 6.308041 GCTTAGTGCTTAGGTTACAAATTTGC 59.692 38.462 18.12 1.99 38.95 3.68
1880 7545 4.177026 AGTAACGAGATGCAAGCTTAGTG 58.823 43.478 0.00 0.00 22.26 2.74
2461 8229 6.441924 TGACAGGGTCTAAGAGAGATCAATTT 59.558 38.462 0.00 0.00 36.98 1.82
2591 8365 8.147058 TGCTATTAGAAGCCTCTTCAGATTTAG 58.853 37.037 8.98 4.44 42.05 1.85
2836 8616 7.979115 TTTCCAAACTGATCGTTGTTTTTAG 57.021 32.000 8.07 3.01 35.61 1.85
3112 8894 1.301716 GAGCAAGGCGAGGACAACA 60.302 57.895 0.00 0.00 0.00 3.33
3417 9201 7.602644 AGTCATGTTGAACGCTTTCTCTATTTA 59.397 33.333 4.43 0.00 32.36 1.40
3420 9204 5.482908 AGTCATGTTGAACGCTTTCTCTAT 58.517 37.500 4.43 0.00 32.36 1.98
3429 9213 3.813529 AAGCTTAGTCATGTTGAACGC 57.186 42.857 0.00 0.00 0.00 4.84


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

AutoCloner maintained by Alex Coulton.