Multiple sequence alignment - TraesCS1A01G055100

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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 TraesCS1A01G055100 chr1A 100.000 2681 0 0 1 2681 36273082 36270402 0.000000e+00 4951
1 TraesCS1A01G055100 chr1B 92.711 2730 130 33 1 2681 56885072 56882363 0.000000e+00 3875
2 TraesCS1A01G055100 chr1D 93.778 2475 104 29 1 2447 36837647 36835195 0.000000e+00 3672
3 TraesCS1A01G055100 chr1D 97.059 204 6 0 2478 2681 36835127 36834924 7.110000e-91 344


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 TraesCS1A01G055100 chr1A 36270402 36273082 2680 True 4951 4951 100.0000 1 2681 1 chr1A.!!$R1 2680
1 TraesCS1A01G055100 chr1B 56882363 56885072 2709 True 3875 3875 92.7110 1 2681 1 chr1B.!!$R1 2680
2 TraesCS1A01G055100 chr1D 36834924 36837647 2723 True 2008 3672 95.4185 1 2681 2 chr1D.!!$R1 2680

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
340 343 0.729116 GGATGATCAACACTGCACGG 59.271 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2161 0.317603 CGAATTACCTCGGATCGCGT 60.318 55.0 5.77 0.0 35.14 6.01 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
95 96 7.212976 TGCCAATGAATAACAGCAAAAGTAAA 58.787 30.769 0.00 0.00 0.00 2.01
138 139 9.822185 AAATAAAATATGAAAAGCATGACCTCC 57.178 29.630 0.00 0.00 37.87 4.30
340 343 0.729116 GGATGATCAACACTGCACGG 59.271 55.000 0.00 0.00 0.00 4.94
584 587 5.124457 ACATAACAGAACCTGATCACATTGC 59.876 40.000 0.45 0.00 35.18 3.56
693 696 3.361786 ACTAACTTGCACAACCCAAAGT 58.638 40.909 0.00 0.00 0.00 2.66
793 798 3.354948 TGTCTGAAACATAGCCATGCT 57.645 42.857 0.00 0.00 36.32 3.79
907 912 0.751643 ACCACACCTCCAACAGTTGC 60.752 55.000 7.88 0.00 0.00 4.17
1017 1023 2.837337 CGATGCTAACGCCGAATAAG 57.163 50.000 0.00 0.00 34.43 1.73
1239 1245 2.048127 GCGGCGTGGAACTCTTCT 60.048 61.111 9.37 0.00 31.75 2.85
1265 1271 3.346315 CACCTCTGCAACATATGTCCAA 58.654 45.455 9.23 0.00 0.00 3.53
1280 1286 3.415212 TGTCCAAAAGAGGAAGCTCATG 58.585 45.455 0.00 0.00 39.92 3.07
1303 1309 9.229784 CATGATTAAGCTCACAACAAATATGAC 57.770 33.333 0.00 0.00 0.00 3.06
1358 1366 6.016360 CACTGTACAATCAAAATTGACCTGGA 60.016 38.462 0.00 0.00 44.25 3.86
1368 1376 6.930164 TCAAAATTGACCTGGAATTCATGTTG 59.070 34.615 7.93 2.46 31.01 3.33
1374 1382 5.241506 TGACCTGGAATTCATGTTGAGAAAC 59.758 40.000 7.93 0.00 0.00 2.78
1378 1386 6.271488 TGGAATTCATGTTGAGAAACCATC 57.729 37.500 7.93 0.00 33.73 3.51
1380 1388 6.095377 GGAATTCATGTTGAGAAACCATCAC 58.905 40.000 7.93 0.00 0.00 3.06
1382 1390 5.694231 TTCATGTTGAGAAACCATCACAG 57.306 39.130 0.00 0.00 30.04 3.66
1384 1392 5.375773 TCATGTTGAGAAACCATCACAGAA 58.624 37.500 0.00 0.00 30.04 3.02
1388 1398 5.702670 TGTTGAGAAACCATCACAGAATCTC 59.297 40.000 0.00 0.00 34.01 2.75
1391 1401 6.871844 TGAGAAACCATCACAGAATCTCTAG 58.128 40.000 0.00 0.00 34.41 2.43
1413 1423 6.961360 AGGCTAACAAAAATATCCTTAGGC 57.039 37.500 0.00 0.00 39.23 3.93
1417 1427 7.255277 GGCTAACAAAAATATCCTTAGGCTCTG 60.255 40.741 0.00 0.00 37.15 3.35
1418 1428 7.499232 GCTAACAAAAATATCCTTAGGCTCTGA 59.501 37.037 0.00 0.00 0.00 3.27
1419 1429 7.872113 AACAAAAATATCCTTAGGCTCTGAG 57.128 36.000 0.00 0.00 0.00 3.35
1420 1430 6.963322 ACAAAAATATCCTTAGGCTCTGAGT 58.037 36.000 6.53 0.00 0.00 3.41
1421 1431 6.825721 ACAAAAATATCCTTAGGCTCTGAGTG 59.174 38.462 6.53 0.00 0.00 3.51
1422 1432 4.615588 AATATCCTTAGGCTCTGAGTGC 57.384 45.455 6.53 0.00 0.00 4.40
1479 1495 3.006217 GCTTCAAAGATTCCAACCAAGCT 59.994 43.478 0.00 0.00 33.68 3.74
1684 1700 2.342279 CCGGACGAAGCTGAACCA 59.658 61.111 0.00 0.00 0.00 3.67
1931 1949 2.040412 CCACTAAAAGCCCAGGAAGACT 59.960 50.000 0.00 0.00 0.00 3.24
2137 2161 1.523524 GAAATCCGGCGGGTTCCTA 59.476 57.895 26.78 4.76 33.83 2.94
2139 2163 2.582734 AAATCCGGCGGGTTCCTACG 62.583 60.000 26.78 0.00 33.83 3.51
2157 2181 0.040692 CGCGATCCGAGGTAATTCGA 60.041 55.000 0.00 0.00 43.03 3.71
2204 2228 1.852895 GATTTTGTCGATCTCGGTCGG 59.147 52.381 0.00 0.00 41.74 4.79
2222 2246 1.990563 CGGTTTCTCGCTGTAATCGTT 59.009 47.619 0.00 0.00 0.00 3.85
2223 2247 2.222508 CGGTTTCTCGCTGTAATCGTTG 60.223 50.000 0.00 0.00 0.00 4.10
2224 2248 2.474032 GGTTTCTCGCTGTAATCGTTGC 60.474 50.000 0.00 0.00 0.00 4.17
2288 2312 1.617850 CAGATGGGAGAAGGAGATCCG 59.382 57.143 0.00 0.00 42.08 4.18
2291 2315 0.105964 TGGGAGAAGGAGATCCGGAG 60.106 60.000 11.34 0.00 42.08 4.63
2328 2355 3.878519 CGGAGACCTCGACCTCGC 61.879 72.222 0.00 0.00 39.60 5.03
2435 2474 2.751913 CCGAGACCACGTCCTCGAG 61.752 68.421 24.36 5.13 36.28 4.04
2447 2486 4.711178 CGTCCTCGAGCACCATAAGGTC 62.711 59.091 6.99 0.00 42.67 3.85
2459 2525 3.470709 CCATAAGGTCTAGGACGTCGTA 58.529 50.000 16.44 16.44 32.65 3.43
2462 2528 5.450171 CATAAGGTCTAGGACGTCGTATTG 58.550 45.833 17.54 8.10 32.65 1.90
2471 2537 3.255149 AGGACGTCGTATTGTCTGTTCTT 59.745 43.478 9.40 0.00 35.45 2.52
2472 2538 3.364023 GGACGTCGTATTGTCTGTTCTTG 59.636 47.826 9.92 0.00 35.45 3.02
2474 2540 3.734231 ACGTCGTATTGTCTGTTCTTGTG 59.266 43.478 0.00 0.00 0.00 3.33
2475 2541 3.978855 CGTCGTATTGTCTGTTCTTGTGA 59.021 43.478 0.00 0.00 0.00 3.58
2476 2542 4.443063 CGTCGTATTGTCTGTTCTTGTGAA 59.557 41.667 0.00 0.00 0.00 3.18
2477 2543 5.051307 CGTCGTATTGTCTGTTCTTGTGAAA 60.051 40.000 0.00 0.00 33.52 2.69
2478 2544 6.355638 GTCGTATTGTCTGTTCTTGTGAAAG 58.644 40.000 0.00 0.00 33.52 2.62
2479 2545 5.050363 TCGTATTGTCTGTTCTTGTGAAAGC 60.050 40.000 0.00 0.00 33.52 3.51
2480 2546 5.277297 CGTATTGTCTGTTCTTGTGAAAGCA 60.277 40.000 0.00 0.00 33.52 3.91
2485 2561 1.266718 TGTTCTTGTGAAAGCATCCGC 59.733 47.619 0.00 0.00 33.52 5.54
2505 2581 1.739035 CGCTACTGATTTCTGCGGGAA 60.739 52.381 0.00 0.00 42.46 3.97
2512 2588 2.290260 TGATTTCTGCGGGAACTGTGAT 60.290 45.455 0.00 0.00 36.83 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.241403 TGGCAACTTCCTTTATGAGAAGA 57.759 39.130 6.75 0.00 41.69 2.87
151 152 5.605488 TCCTACAAGGTAAAACTGTTCTCCT 59.395 40.000 0.00 0.00 36.53 3.69
340 343 1.219124 TGCCGGAGCAGTGATCTTC 59.781 57.895 5.05 0.00 46.52 2.87
693 696 1.138859 AGTGCACTGTGTAAGCTCACA 59.861 47.619 20.97 7.90 44.54 3.58
793 798 6.187125 GCTTCACTAGATGCTTGAATGAAA 57.813 37.500 0.00 0.00 40.64 2.69
881 886 2.291930 TGTTGGAGGTGTGGTTCCTTTT 60.292 45.455 0.00 0.00 35.20 2.27
917 923 8.768955 GCATCTCGACTAATCTTTAACATTGAT 58.231 33.333 0.00 0.00 0.00 2.57
1017 1023 2.459442 GCAGGTCATCGCTGCAGTC 61.459 63.158 16.64 6.83 42.98 3.51
1226 1232 2.678324 GTGGAGAAGAAGAGTTCCACG 58.322 52.381 6.74 0.00 46.98 4.94
1239 1245 3.264193 ACATATGTTGCAGAGGTGGAGAA 59.736 43.478 1.41 0.00 0.00 2.87
1246 1252 4.701651 TCTTTTGGACATATGTTGCAGAGG 59.298 41.667 10.30 2.19 0.00 3.69
1265 1271 5.753716 AGCTTAATCATGAGCTTCCTCTTT 58.246 37.500 0.09 0.00 45.44 2.52
1280 1286 7.761409 TGGTCATATTTGTTGTGAGCTTAATC 58.239 34.615 0.00 0.00 42.50 1.75
1303 1309 1.209019 AGCTATCCACTGAAGCACTGG 59.791 52.381 0.00 0.00 38.75 4.00
1358 1366 6.491062 TCTGTGATGGTTTCTCAACATGAATT 59.509 34.615 0.00 0.00 34.15 2.17
1368 1376 6.279882 CCTAGAGATTCTGTGATGGTTTCTC 58.720 44.000 0.00 0.00 0.00 2.87
1374 1382 5.069648 TGTTAGCCTAGAGATTCTGTGATGG 59.930 44.000 0.00 0.00 0.00 3.51
1378 1386 7.672983 TTTTTGTTAGCCTAGAGATTCTGTG 57.327 36.000 0.00 0.00 0.00 3.66
1382 1390 9.785982 AGGATATTTTTGTTAGCCTAGAGATTC 57.214 33.333 0.00 0.00 33.78 2.52
1388 1398 7.939588 AGCCTAAGGATATTTTTGTTAGCCTAG 59.060 37.037 0.00 0.00 34.43 3.02
1391 1401 6.773200 AGAGCCTAAGGATATTTTTGTTAGCC 59.227 38.462 0.00 0.00 0.00 3.93
1413 1423 3.577667 CTTGAGAACTCAGCACTCAGAG 58.422 50.000 4.72 0.00 40.82 3.35
1417 1427 2.160822 TGCTTGAGAACTCAGCACTC 57.839 50.000 17.73 0.00 41.13 3.51
1418 1428 2.627515 TTGCTTGAGAACTCAGCACT 57.372 45.000 19.81 0.00 40.59 4.40
1419 1429 3.501445 AGAATTGCTTGAGAACTCAGCAC 59.499 43.478 19.81 13.09 40.59 4.40
1420 1430 3.748083 AGAATTGCTTGAGAACTCAGCA 58.252 40.909 17.73 17.73 41.13 4.41
1421 1431 5.869753 TTAGAATTGCTTGAGAACTCAGC 57.130 39.130 14.46 14.46 41.13 4.26
1422 1432 9.985318 CTTAATTAGAATTGCTTGAGAACTCAG 57.015 33.333 4.72 1.85 41.13 3.35
1479 1495 4.451150 CTCCGGGCACTGCGCTTA 62.451 66.667 9.73 3.31 41.91 3.09
1638 1654 4.778415 CTCCTCACGGTGGTCGCG 62.778 72.222 8.50 0.00 43.89 5.87
1994 2012 4.918037 GACACGTGTCGAGGAATTAGTAT 58.082 43.478 31.03 0.00 35.12 2.12
2137 2161 0.317603 CGAATTACCTCGGATCGCGT 60.318 55.000 5.77 0.00 35.14 6.01
2139 2163 1.406447 GTCGAATTACCTCGGATCGC 58.594 55.000 0.00 0.00 39.35 4.58
2204 2228 2.412089 AGCAACGATTACAGCGAGAAAC 59.588 45.455 0.00 0.00 0.00 2.78
2222 2246 1.536766 CAGGAAATTCACGAAGCAGCA 59.463 47.619 0.00 0.00 0.00 4.41
2223 2247 1.806542 TCAGGAAATTCACGAAGCAGC 59.193 47.619 0.00 0.00 0.00 5.25
2224 2248 3.730061 GCATCAGGAAATTCACGAAGCAG 60.730 47.826 6.33 0.00 0.00 4.24
2312 2339 3.519930 GGCGAGGTCGAGGTCTCC 61.520 72.222 2.94 0.00 43.02 3.71
2447 2486 4.094590 AGAACAGACAATACGACGTCCTAG 59.905 45.833 10.58 0.00 32.33 3.02
2448 2487 4.005650 AGAACAGACAATACGACGTCCTA 58.994 43.478 10.58 3.05 32.33 2.94
2449 2488 2.818432 AGAACAGACAATACGACGTCCT 59.182 45.455 10.58 0.34 32.33 3.85
2451 2490 3.979495 ACAAGAACAGACAATACGACGTC 59.021 43.478 2.43 5.18 0.00 4.34
2452 2491 3.734231 CACAAGAACAGACAATACGACGT 59.266 43.478 5.52 5.52 0.00 4.34
2453 2492 3.978855 TCACAAGAACAGACAATACGACG 59.021 43.478 0.00 0.00 0.00 5.12
2454 2493 5.900339 TTCACAAGAACAGACAATACGAC 57.100 39.130 0.00 0.00 0.00 4.34
2455 2494 5.050363 GCTTTCACAAGAACAGACAATACGA 60.050 40.000 0.00 0.00 32.39 3.43
2459 2525 5.278660 GGATGCTTTCACAAGAACAGACAAT 60.279 40.000 0.00 0.00 32.39 2.71
2462 2528 3.364366 CGGATGCTTTCACAAGAACAGAC 60.364 47.826 0.00 0.00 32.39 3.51
2471 2537 1.079474 TAGCGCGGATGCTTTCACA 60.079 52.632 8.83 0.00 44.46 3.58
2472 2538 1.084370 AGTAGCGCGGATGCTTTCAC 61.084 55.000 8.83 0.00 44.46 3.18
2474 2540 0.806102 TCAGTAGCGCGGATGCTTTC 60.806 55.000 8.83 0.00 44.46 2.62
2475 2541 0.179073 ATCAGTAGCGCGGATGCTTT 60.179 50.000 8.83 0.00 44.46 3.51
2476 2542 0.179073 AATCAGTAGCGCGGATGCTT 60.179 50.000 8.83 0.00 44.46 3.91
2478 2544 0.233332 GAAATCAGTAGCGCGGATGC 59.767 55.000 8.83 0.00 32.44 3.91
2479 2545 1.524355 CAGAAATCAGTAGCGCGGATG 59.476 52.381 8.83 1.56 32.44 3.51
2480 2546 1.858091 CAGAAATCAGTAGCGCGGAT 58.142 50.000 8.83 0.00 33.46 4.18
2505 2581 1.143684 AGCTCACCCACAAATCACAGT 59.856 47.619 0.00 0.00 0.00 3.55
2512 2588 1.064758 ACACTTCAGCTCACCCACAAA 60.065 47.619 0.00 0.00 0.00 2.83
2569 2645 3.306502 CCACCACCTACGTTGTACTCATT 60.307 47.826 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.