Multiple sequence alignment - TraesCS6A01G203100

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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 TraesCS6A01G203100 chr6A 100.000 2336 0 0 1 2336 342553815 342556150 0.000000e+00 4314
1 TraesCS6A01G203100 chr7A 96.009 1378 31 7 1 1354 75026930 75025553 0.000000e+00 2218
2 TraesCS6A01G203100 chr7A 92.472 983 56 13 1363 2336 246161775 246162748 0.000000e+00 1389
3 TraesCS6A01G203100 chr7A 92.418 976 67 5 1363 2336 307440793 307441763 0.000000e+00 1386
4 TraesCS6A01G203100 chr7D 94.412 1378 50 8 1 1354 497005853 497007227 0.000000e+00 2093
5 TraesCS6A01G203100 chr7D 86.950 1341 163 9 3 1338 509254653 509253320 0.000000e+00 1496
6 TraesCS6A01G203100 chr7D 85.766 1370 160 17 9 1350 472803826 472802464 0.000000e+00 1417
7 TraesCS6A01G203100 chr3B 94.340 1378 48 5 1 1354 410610853 410612224 0.000000e+00 2085
8 TraesCS6A01G203100 chr3A 93.614 1378 60 9 1 1354 100036008 100034635 0.000000e+00 2032
9 TraesCS6A01G203100 chr3A 94.274 978 53 3 1361 2336 697972535 697973511 0.000000e+00 1493
10 TraesCS6A01G203100 chr3A 92.966 981 56 10 1361 2336 129193824 129192852 0.000000e+00 1417
11 TraesCS6A01G203100 chr3A 84.191 1341 199 11 1 1336 464916082 464917414 0.000000e+00 1290
12 TraesCS6A01G203100 chr2A 96.915 940 29 0 1 940 54148517 54147578 0.000000e+00 1576
13 TraesCS6A01G203100 chr2A 92.835 977 61 9 1363 2336 365487058 365488028 0.000000e+00 1408
14 TraesCS6A01G203100 chr2D 94.894 940 45 2 1 940 340516633 340517569 0.000000e+00 1467
15 TraesCS6A01G203100 chr2D 89.880 998 79 8 122 1098 62056170 62057166 0.000000e+00 1264
16 TraesCS6A01G203100 chr4A 93.082 983 55 10 1361 2334 517714440 517713462 0.000000e+00 1426
17 TraesCS6A01G203100 chr5A 92.835 977 58 10 1363 2336 401804882 401805849 0.000000e+00 1406
18 TraesCS6A01G203100 chr1A 92.323 977 68 7 1363 2336 266423483 266424455 0.000000e+00 1382
19 TraesCS6A01G203100 chr1A 92.127 978 66 10 1363 2336 49061597 49060627 0.000000e+00 1369
20 TraesCS6A01G203100 chr3D 84.677 1377 178 18 1 1350 339845409 339844039 0.000000e+00 1343
21 TraesCS6A01G203100 chr3D 83.138 1364 201 13 5 1342 177015461 177014101 0.000000e+00 1218
22 TraesCS6A01G203100 chr6B 93.457 917 30 9 461 1353 367351482 367350572 0.000000e+00 1334
23 TraesCS6A01G203100 chr6B 94.217 709 17 2 670 1354 638232545 638231837 0.000000e+00 1061
24 TraesCS6A01G203100 chr5D 95.444 834 37 1 1 834 551855296 551856128 0.000000e+00 1328
25 TraesCS6A01G203100 chr5D 79.148 1362 255 16 5 1339 117351116 117352475 0.000000e+00 915
26 TraesCS6A01G203100 chr5D 91.439 549 23 5 830 1354 551867947 551868495 0.000000e+00 732
27 TraesCS6A01G203100 chr6D 82.612 1363 205 15 5 1339 462399765 462398407 0.000000e+00 1175
28 TraesCS6A01G203100 chr6D 82.025 1363 210 19 5 1339 452072064 452070709 0.000000e+00 1127
29 TraesCS6A01G203100 chr6D 80.320 1377 238 14 5 1354 48683488 48682118 0.000000e+00 1011
30 TraesCS6A01G203100 chr6D 79.808 1357 236 25 14 1339 158872468 158871119 0.000000e+00 953
31 TraesCS6A01G203100 chr6D 79.838 1111 197 11 255 1341 32688767 32687660 0.000000e+00 785
32 TraesCS6A01G203100 chr1D 82.379 1362 210 14 5 1339 176360131 176361489 0.000000e+00 1158
33 TraesCS6A01G203100 chr1D 81.832 1365 211 19 5 1339 356880577 356881934 0.000000e+00 1112
34 TraesCS6A01G203100 chr1B 93.578 763 24 9 614 1351 186795426 186796188 0.000000e+00 1114
35 TraesCS6A01G203100 chrUn 76.490 906 185 10 464 1343 359564625 359565528 3.510000e-128 468
36 TraesCS6A01G203100 chrUn 76.380 906 186 10 464 1343 326372031 326371128 1.640000e-126 462
37 TraesCS6A01G203100 chrUn 71.790 514 127 15 243 747 153414085 153413581 1.880000e-26 130


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 TraesCS6A01G203100 chr6A 342553815 342556150 2335 False 4314 4314 100.000 1 2336 1 chr6A.!!$F1 2335
1 TraesCS6A01G203100 chr7A 75025553 75026930 1377 True 2218 2218 96.009 1 1354 1 chr7A.!!$R1 1353
2 TraesCS6A01G203100 chr7A 246161775 246162748 973 False 1389 1389 92.472 1363 2336 1 chr7A.!!$F1 973
3 TraesCS6A01G203100 chr7A 307440793 307441763 970 False 1386 1386 92.418 1363 2336 1 chr7A.!!$F2 973
4 TraesCS6A01G203100 chr7D 497005853 497007227 1374 False 2093 2093 94.412 1 1354 1 chr7D.!!$F1 1353
5 TraesCS6A01G203100 chr7D 509253320 509254653 1333 True 1496 1496 86.950 3 1338 1 chr7D.!!$R2 1335
6 TraesCS6A01G203100 chr7D 472802464 472803826 1362 True 1417 1417 85.766 9 1350 1 chr7D.!!$R1 1341
7 TraesCS6A01G203100 chr3B 410610853 410612224 1371 False 2085 2085 94.340 1 1354 1 chr3B.!!$F1 1353
8 TraesCS6A01G203100 chr3A 100034635 100036008 1373 True 2032 2032 93.614 1 1354 1 chr3A.!!$R1 1353
9 TraesCS6A01G203100 chr3A 697972535 697973511 976 False 1493 1493 94.274 1361 2336 1 chr3A.!!$F2 975
10 TraesCS6A01G203100 chr3A 129192852 129193824 972 True 1417 1417 92.966 1361 2336 1 chr3A.!!$R2 975
11 TraesCS6A01G203100 chr3A 464916082 464917414 1332 False 1290 1290 84.191 1 1336 1 chr3A.!!$F1 1335
12 TraesCS6A01G203100 chr2A 54147578 54148517 939 True 1576 1576 96.915 1 940 1 chr2A.!!$R1 939
13 TraesCS6A01G203100 chr2A 365487058 365488028 970 False 1408 1408 92.835 1363 2336 1 chr2A.!!$F1 973
14 TraesCS6A01G203100 chr2D 340516633 340517569 936 False 1467 1467 94.894 1 940 1 chr2D.!!$F2 939
15 TraesCS6A01G203100 chr2D 62056170 62057166 996 False 1264 1264 89.880 122 1098 1 chr2D.!!$F1 976
16 TraesCS6A01G203100 chr4A 517713462 517714440 978 True 1426 1426 93.082 1361 2334 1 chr4A.!!$R1 973
17 TraesCS6A01G203100 chr5A 401804882 401805849 967 False 1406 1406 92.835 1363 2336 1 chr5A.!!$F1 973
18 TraesCS6A01G203100 chr1A 266423483 266424455 972 False 1382 1382 92.323 1363 2336 1 chr1A.!!$F1 973
19 TraesCS6A01G203100 chr1A 49060627 49061597 970 True 1369 1369 92.127 1363 2336 1 chr1A.!!$R1 973
20 TraesCS6A01G203100 chr3D 339844039 339845409 1370 True 1343 1343 84.677 1 1350 1 chr3D.!!$R2 1349
21 TraesCS6A01G203100 chr3D 177014101 177015461 1360 True 1218 1218 83.138 5 1342 1 chr3D.!!$R1 1337
22 TraesCS6A01G203100 chr6B 367350572 367351482 910 True 1334 1334 93.457 461 1353 1 chr6B.!!$R1 892
23 TraesCS6A01G203100 chr6B 638231837 638232545 708 True 1061 1061 94.217 670 1354 1 chr6B.!!$R2 684
24 TraesCS6A01G203100 chr5D 551855296 551856128 832 False 1328 1328 95.444 1 834 1 chr5D.!!$F2 833
25 TraesCS6A01G203100 chr5D 117351116 117352475 1359 False 915 915 79.148 5 1339 1 chr5D.!!$F1 1334
26 TraesCS6A01G203100 chr5D 551867947 551868495 548 False 732 732 91.439 830 1354 1 chr5D.!!$F3 524
27 TraesCS6A01G203100 chr6D 462398407 462399765 1358 True 1175 1175 82.612 5 1339 1 chr6D.!!$R5 1334
28 TraesCS6A01G203100 chr6D 452070709 452072064 1355 True 1127 1127 82.025 5 1339 1 chr6D.!!$R4 1334
29 TraesCS6A01G203100 chr6D 48682118 48683488 1370 True 1011 1011 80.320 5 1354 1 chr6D.!!$R2 1349
30 TraesCS6A01G203100 chr6D 158871119 158872468 1349 True 953 953 79.808 14 1339 1 chr6D.!!$R3 1325
31 TraesCS6A01G203100 chr6D 32687660 32688767 1107 True 785 785 79.838 255 1341 1 chr6D.!!$R1 1086
32 TraesCS6A01G203100 chr1D 176360131 176361489 1358 False 1158 1158 82.379 5 1339 1 chr1D.!!$F1 1334
33 TraesCS6A01G203100 chr1D 356880577 356881934 1357 False 1112 1112 81.832 5 1339 1 chr1D.!!$F2 1334
34 TraesCS6A01G203100 chr1B 186795426 186796188 762 False 1114 1114 93.578 614 1351 1 chr1B.!!$F1 737
35 TraesCS6A01G203100 chrUn 359564625 359565528 903 False 468 468 76.490 464 1343 1 chrUn.!!$F1 879
36 TraesCS6A01G203100 chrUn 326371128 326372031 903 True 462 462 76.380 464 1343 1 chrUn.!!$R2 879

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
356 358 1.607225 TACTCCAATGGAATGGGGCT 58.393 50.0 2.61 0.0 45.48 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 1997 0.4546 AACGGAGCTCGCGAGATTTA 59.545 50.0 38.74 0.5 43.89 1.4 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
356 358 1.607225 TACTCCAATGGAATGGGGCT 58.393 50.000 2.61 0.00 45.48 5.19
883 890 2.158143 GGATGGTACTGTCCCCCTAGAT 60.158 54.545 5.96 0.00 0.00 1.98
1491 1534 9.118300 CTCTCAAAATAATCTAAGTGAGGCATT 57.882 33.333 0.00 0.00 34.57 3.56
1524 1567 9.703892 CAATGGTTTCTATAAAACAAATCCACA 57.296 29.630 0.00 0.00 45.14 4.17
1937 1984 7.282916 CAAAACTTGAAAACTTCACAACACAG 58.717 34.615 0.00 0.00 39.87 3.66
1950 1997 7.822822 ACTTCACAACACAGAACTTAAAGTAGT 59.177 33.333 0.00 0.00 0.00 2.73
1959 2007 8.373992 CACAGAACTTAAAGTAGTAAATCTCGC 58.626 37.037 0.00 0.00 0.00 5.03
1987 2035 5.638783 TCCGTTAGCGAAAGAAAACAAAAA 58.361 33.333 0.00 0.00 41.33 1.94
2019 2067 7.676004 TCAAGGTACTGTAATGAACTCATTCA 58.324 34.615 8.19 6.38 44.70 2.57
2274 2329 4.392754 CCAAATAAAAATGGCAGCAGTTCC 59.607 41.667 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
356 358 6.618196 ACTCCAAATAGGGTTAGCTATGGTTA 59.382 38.462 0.00 0.00 38.24 2.85
362 364 9.839185 ATATCTTACTCCAAATAGGGTTAGCTA 57.161 33.333 0.00 0.00 38.24 3.32
1486 1529 5.904362 AGAAACCATTGTTCTCTAATGCC 57.096 39.130 0.00 0.00 34.88 4.40
1694 1737 7.538678 GTGTTTTGCTTGGAGTATCTTGTATTG 59.461 37.037 0.00 0.00 33.73 1.90
1704 1747 6.658816 ACATGATATGTGTTTTGCTTGGAGTA 59.341 34.615 0.00 0.00 43.01 2.59
1705 1748 5.477984 ACATGATATGTGTTTTGCTTGGAGT 59.522 36.000 0.00 0.00 43.01 3.85
1763 1806 4.888239 CCCCTCTTTCGTCTACTTCTATCA 59.112 45.833 0.00 0.00 0.00 2.15
1937 1984 7.513350 GCTCGCGAGATTTACTACTTTAAGTTC 60.513 40.741 38.74 10.60 40.84 3.01
1950 1997 0.454600 AACGGAGCTCGCGAGATTTA 59.545 50.000 38.74 0.50 43.89 1.40
1987 2035 6.182507 TCATTACAGTACCTTGAAGTGGTT 57.817 37.500 0.00 0.00 38.88 3.67
2124 2179 9.021807 AGCTACAGATTACTACAAACTGTTCTA 57.978 33.333 0.00 0.00 41.17 2.10
2274 2329 1.126846 CAGAAACTTTAGCGCTCACGG 59.873 52.381 16.34 5.55 40.57 4.94


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

AutoCloner maintained by Alex Coulton.