Multiple sequence alignment - TraesCS7A01G481900

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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 TraesCS7A01G481900 chr7A 100.000 2606 0 0 1 2606 674116615 674114010 0.000000e+00 4813.0
1 TraesCS7A01G481900 chr7A 97.198 2106 38 2 521 2606 672598934 672596830 0.000000e+00 3542.0
2 TraesCS7A01G481900 chr7A 96.961 2106 43 2 521 2606 113795468 113797572 0.000000e+00 3515.0
3 TraesCS7A01G481900 chr7A 93.805 113 7 0 1964 2076 613712209 613712321 1.240000e-38 171.0
4 TraesCS7A01G481900 chr7A 98.649 74 1 0 2215 2288 113797235 113797308 5.850000e-27 132.0
5 TraesCS7A01G481900 chr7A 98.649 74 1 0 2215 2288 672597167 672597094 5.850000e-27 132.0
6 TraesCS7A01G481900 chr7A 98.630 73 1 0 2094 2166 613713189 613713117 2.100000e-26 130.0
7 TraesCS7A01G481900 chr4A 96.828 2112 40 3 521 2606 17245337 17247447 0.000000e+00 3504.0
8 TraesCS7A01G481900 chr3A 97.260 1788 26 3 521 2288 697520651 697522435 0.000000e+00 3009.0
9 TraesCS7A01G481900 chr3A 97.519 524 11 2 1 522 588525072 588524549 0.000000e+00 894.0
10 TraesCS7A01G481900 chr3A 91.557 533 18 4 1 506 118570660 118571192 0.000000e+00 710.0
11 TraesCS7A01G481900 chr3A 91.149 531 36 6 1 522 708326496 708325968 0.000000e+00 710.0
12 TraesCS7A01G481900 chr3A 98.525 339 4 1 2269 2606 697522362 697522700 4.800000e-167 597.0
13 TraesCS7A01G481900 chr3A 90.732 410 35 3 114 521 691106422 691106830 6.340000e-151 544.0
14 TraesCS7A01G481900 chr3A 90.476 84 6 2 1 84 691106345 691106426 2.740000e-20 110.0
15 TraesCS7A01G481900 chr3A 96.296 54 2 0 469 522 118571183 118571236 3.570000e-14 89.8
16 TraesCS7A01G481900 chr5A 96.868 1788 36 1 521 2288 609823322 609821535 0.000000e+00 2974.0
17 TraesCS7A01G481900 chr5A 91.235 753 47 9 521 1271 688243314 688244049 0.000000e+00 1007.0
18 TraesCS7A01G481900 chr5A 99.704 338 1 0 2269 2606 609821608 609821271 1.020000e-173 619.0
19 TraesCS7A01G481900 chr5A 88.642 405 38 4 1356 1753 688244181 688244584 1.080000e-133 486.0
20 TraesCS7A01G481900 chr5A 89.130 322 33 2 1356 1676 680364945 680365265 1.450000e-107 399.0
21 TraesCS7A01G481900 chr5A 93.805 113 7 0 1700 1812 680365260 680365372 1.240000e-38 171.0
22 TraesCS7A01G481900 chr5A 100.000 73 0 0 2094 2166 605038938 605038866 4.520000e-28 135.0
23 TraesCS7A01G481900 chr4B 89.486 837 65 11 521 1350 649491413 649492233 0.000000e+00 1037.0
24 TraesCS7A01G481900 chr4B 90.351 456 29 2 1356 1811 649492303 649492743 3.740000e-163 584.0
25 TraesCS7A01G481900 chr4D 87.044 795 58 19 556 1344 503669347 503670102 0.000000e+00 856.0
26 TraesCS7A01G481900 chr4D 87.988 641 43 15 721 1359 503639662 503640270 0.000000e+00 726.0
27 TraesCS7A01G481900 chr4D 88.399 431 37 5 1356 1778 503670177 503670602 8.320000e-140 507.0
28 TraesCS7A01G481900 chr4D 93.805 113 7 0 1964 2076 198583169 198583281 1.240000e-38 171.0
29 TraesCS7A01G481900 chr4D 91.071 112 10 0 1700 1811 503642004 503642115 4.490000e-33 152.0
30 TraesCS7A01G481900 chr4D 100.000 73 0 0 2094 2166 198584148 198584076 4.520000e-28 135.0
31 TraesCS7A01G481900 chr1B 93.421 532 20 3 4 520 433629481 433628950 0.000000e+00 774.0
32 TraesCS7A01G481900 chr1B 93.902 492 14 5 521 1005 117290134 117289652 0.000000e+00 728.0
33 TraesCS7A01G481900 chr1B 96.571 350 11 1 2258 2606 117289647 117289298 1.740000e-161 579.0
34 TraesCS7A01G481900 chr3B 90.262 534 33 12 1 520 131579114 131579642 0.000000e+00 680.0
35 TraesCS7A01G481900 chr3B 92.286 350 25 2 2259 2606 742768166 742767817 1.800000e-136 496.0
36 TraesCS7A01G481900 chr5D 95.989 349 12 2 2258 2605 358667904 358667557 1.350000e-157 566.0
37 TraesCS7A01G481900 chr5D 90.984 122 11 0 1818 1939 548027995 548027874 5.770000e-37 165.0
38 TraesCS7A01G481900 chr5D 94.444 90 5 0 1818 1907 358668085 358667996 3.500000e-29 139.0
39 TraesCS7A01G481900 chr2A 93.162 351 15 4 2265 2606 207108769 207109119 8.320000e-140 507.0
40 TraesCS7A01G481900 chr2A 89.655 116 9 2 2175 2288 207108732 207108846 7.520000e-31 145.0
41 TraesCS7A01G481900 chr5B 92.920 113 8 0 1964 2076 386154126 386154238 5.770000e-37 165.0
42 TraesCS7A01G481900 chr5B 90.164 122 12 0 1818 1939 692215141 692215020 2.680000e-35 159.0
43 TraesCS7A01G481900 chr5B 100.000 73 0 0 2094 2166 386155100 386155028 4.520000e-28 135.0
44 TraesCS7A01G481900 chr2D 92.241 116 6 2 2175 2288 107761085 107761199 7.460000e-36 161.0
45 TraesCS7A01G481900 chr2D 89.286 56 6 0 470 525 611123174 611123119 1.290000e-08 71.3
46 TraesCS7A01G481900 chr6A 92.035 113 9 0 1964 2076 36692100 36692212 2.680000e-35 159.0
47 TraesCS7A01G481900 chr1D 90.541 74 6 1 447 520 196450276 196450348 2.130000e-16 97.1


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 TraesCS7A01G481900 chr7A 674114010 674116615 2605 True 4813.0 4813 100.0000 1 2606 1 chr7A.!!$R2 2605
1 TraesCS7A01G481900 chr7A 672596830 672598934 2104 True 1837.0 3542 97.9235 521 2606 2 chr7A.!!$R3 2085
2 TraesCS7A01G481900 chr7A 113795468 113797572 2104 False 1823.5 3515 97.8050 521 2606 2 chr7A.!!$F2 2085
3 TraesCS7A01G481900 chr4A 17245337 17247447 2110 False 3504.0 3504 96.8280 521 2606 1 chr4A.!!$F1 2085
4 TraesCS7A01G481900 chr3A 697520651 697522700 2049 False 1803.0 3009 97.8925 521 2606 2 chr3A.!!$F3 2085
5 TraesCS7A01G481900 chr3A 588524549 588525072 523 True 894.0 894 97.5190 1 522 1 chr3A.!!$R1 521
6 TraesCS7A01G481900 chr3A 708325968 708326496 528 True 710.0 710 91.1490 1 522 1 chr3A.!!$R2 521
7 TraesCS7A01G481900 chr3A 118570660 118571236 576 False 399.9 710 93.9265 1 522 2 chr3A.!!$F1 521
8 TraesCS7A01G481900 chr5A 609821271 609823322 2051 True 1796.5 2974 98.2860 521 2606 2 chr5A.!!$R2 2085
9 TraesCS7A01G481900 chr5A 688243314 688244584 1270 False 746.5 1007 89.9385 521 1753 2 chr5A.!!$F2 1232
10 TraesCS7A01G481900 chr4B 649491413 649492743 1330 False 810.5 1037 89.9185 521 1811 2 chr4B.!!$F1 1290
11 TraesCS7A01G481900 chr4D 503669347 503670602 1255 False 681.5 856 87.7215 556 1778 2 chr4D.!!$F3 1222
12 TraesCS7A01G481900 chr4D 503639662 503642115 2453 False 439.0 726 89.5295 721 1811 2 chr4D.!!$F2 1090
13 TraesCS7A01G481900 chr1B 433628950 433629481 531 True 774.0 774 93.4210 4 520 1 chr1B.!!$R1 516
14 TraesCS7A01G481900 chr1B 117289298 117290134 836 True 653.5 728 95.2365 521 2606 2 chr1B.!!$R2 2085
15 TraesCS7A01G481900 chr3B 131579114 131579642 528 False 680.0 680 90.2620 1 520 1 chr3B.!!$F1 519
16 TraesCS7A01G481900 chr5D 358667557 358668085 528 True 352.5 566 95.2165 1818 2605 2 chr5D.!!$R2 787

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
326 356 2.039951 TCGTACAAGGGGAGGGGG 59.960 66.667 0.00 0.0 0.00 5.40 F
478 516 2.400573 TCTATTTTAGGCCGGCCACTA 58.599 47.619 45.13 28.3 38.92 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 1264 2.431782 AGTTGTTTCAGTGCATGCCTTT 59.568 40.909 16.68 0.0 0.0 3.11 R
2030 3635 3.068590 CACCCAGACAAGCAACAAGAAAT 59.931 43.478 0.00 0.0 0.0 2.17 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
326 356 2.039951 TCGTACAAGGGGAGGGGG 59.960 66.667 0.00 0.0 0.00 5.40
478 516 2.400573 TCTATTTTAGGCCGGCCACTA 58.599 47.619 45.13 28.3 38.92 2.74
601 672 6.320164 ACTTACACAAGTTAGGAAACATGCAA 59.680 34.615 0.00 0.0 42.51 4.08
1184 1264 2.759191 CAGCTGCGCCTGAATTATCTA 58.241 47.619 4.18 0.0 34.77 1.98
1209 1289 3.446799 GCATGCACTGAAACAACTGAAA 58.553 40.909 14.21 0.0 0.00 2.69
1309 1390 2.484594 GGCCAAGCTTTTGTTTTGCCTA 60.485 45.455 0.00 0.0 44.30 3.93
1430 3001 4.221041 TGTGAACGTATTGTAGGTCATGGA 59.779 41.667 0.00 0.0 0.00 3.41
1556 3127 2.766263 TCACACTTTCAGTCACTCTGGT 59.234 45.455 0.00 0.0 43.76 4.00
1604 3181 3.056749 GCGTCTTCTTTCTCTGGGTTCTA 60.057 47.826 0.00 0.0 0.00 2.10
2464 4126 8.624776 GCCAAATAATCTTTGTAGCTAACAGAT 58.375 33.333 0.00 0.0 39.87 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 187 2.900273 CTTCGATTCCTGCCCCGA 59.100 61.111 0.00 0.0 0.00 5.14
326 356 2.522193 CCCTACTCTCTCCCCGCC 60.522 72.222 0.00 0.0 0.00 6.13
327 357 2.522193 CCCCTACTCTCTCCCCGC 60.522 72.222 0.00 0.0 0.00 6.13
802 882 6.164176 GCACACTTGTACTCCTACAATAGTT 58.836 40.000 0.00 0.0 41.17 2.24
1184 1264 2.431782 AGTTGTTTCAGTGCATGCCTTT 59.568 40.909 16.68 0.0 0.00 3.11
1250 1331 6.165700 ACTTGCAGTTTTCCTGAATTTCAT 57.834 33.333 0.00 0.0 44.49 2.57
1309 1390 3.181450 GGCTGCCTTATTCTCATACAGGT 60.181 47.826 12.43 0.0 0.00 4.00
1415 2986 7.290948 ACATGAGAATCTCCATGACCTACAATA 59.709 37.037 21.05 0.0 34.92 1.90
1430 3001 6.156602 ACAGAATCCAGAGAACATGAGAATCT 59.843 38.462 0.00 0.0 34.92 2.40
1556 3127 4.991153 TGCAACAACCATGTAAAGAACA 57.009 36.364 0.00 0.0 43.86 3.18
2030 3635 3.068590 CACCCAGACAAGCAACAAGAAAT 59.931 43.478 0.00 0.0 0.00 2.17
2464 4126 7.510549 TGAAGATATAGTCACATGATCGACA 57.489 36.000 0.00 0.0 34.48 4.35


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

AutoCloner maintained by Alex Coulton.