Multiple sequence alignment - TraesCS4B01G152200

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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 TraesCS4B01G152200 chr4B 100.000 2393 0 0 1 2393 250505135 250507527 0 4420
1 TraesCS4B01G152200 chr4D 90.984 2418 181 23 1 2392 121927283 121924877 0 3223
2 TraesCS4B01G152200 chr7B 90.705 2410 198 19 1 2393 533065558 533063158 0 3186
3 TraesCS4B01G152200 chr7B 89.842 2412 217 20 1 2393 320686180 320683778 0 3072
4 TraesCS4B01G152200 chr7D 89.780 2407 221 20 1 2393 346536323 346538718 0 3059
5 TraesCS4B01G152200 chr2B 89.581 2409 219 21 4 2393 552060782 552058387 0 3029
6 TraesCS4B01G152200 chr5B 89.174 2420 226 28 1 2393 550946481 550948891 0 2985


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 TraesCS4B01G152200 chr4B 250505135 250507527 2392 False 4420 4420 100.000 1 2393 1 chr4B.!!$F1 2392
1 TraesCS4B01G152200 chr4D 121924877 121927283 2406 True 3223 3223 90.984 1 2392 1 chr4D.!!$R1 2391
2 TraesCS4B01G152200 chr7B 533063158 533065558 2400 True 3186 3186 90.705 1 2393 1 chr7B.!!$R2 2392
3 TraesCS4B01G152200 chr7B 320683778 320686180 2402 True 3072 3072 89.842 1 2393 1 chr7B.!!$R1 2392
4 TraesCS4B01G152200 chr7D 346536323 346538718 2395 False 3059 3059 89.780 1 2393 1 chr7D.!!$F1 2392
5 TraesCS4B01G152200 chr2B 552058387 552060782 2395 True 3029 3029 89.581 4 2393 1 chr2B.!!$R1 2389
6 TraesCS4B01G152200 chr5B 550946481 550948891 2410 False 2985 2985 89.174 1 2393 1 chr5B.!!$F1 2392

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
765 781 1.068055 CGTACTACCAAGCTTCACCGT 60.068 52.381 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 1937 0.677731 CCACATGATGTTGCGGGTCT 60.678 55.0 0.0 0.0 0.0 3.85 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
151 155 6.072452 GCAAAACTGTAACCATAGAGCTTTCT 60.072 38.462 0.00 0.00 0.00 2.52
162 166 3.828875 AGAGCTTTCTACCAGCCATAC 57.171 47.619 0.00 0.00 38.09 2.39
246 252 2.280592 GTGCTGACCCGTTTCGGT 60.281 61.111 7.40 0.00 46.80 4.69
272 279 3.609103 ACGTTCATGTTGCAGACTTTC 57.391 42.857 0.00 0.00 0.00 2.62
280 287 2.224281 TGTTGCAGACTTTCCAGACGAT 60.224 45.455 0.00 0.00 0.00 3.73
291 298 2.803956 TCCAGACGATGAGTAAGGTGT 58.196 47.619 0.00 0.00 0.00 4.16
323 331 3.008266 TGATCTTTCACTCAGTGATGCCA 59.992 43.478 8.74 0.33 42.40 4.92
363 373 4.952335 CACTTTATCTTCCAAGCCTTCCAT 59.048 41.667 0.00 0.00 0.00 3.41
372 382 3.016736 CCAAGCCTTCCATTGTTATCGT 58.983 45.455 0.00 0.00 0.00 3.73
373 383 4.080807 TCCAAGCCTTCCATTGTTATCGTA 60.081 41.667 0.00 0.00 0.00 3.43
382 394 9.273016 CCTTCCATTGTTATCGTATTTAGATGT 57.727 33.333 0.00 0.00 0.00 3.06
438 453 9.917129 TCTTTTGAGACATTCGTAATAAGTGTA 57.083 29.630 0.00 0.00 0.00 2.90
452 467 9.464714 CGTAATAAGTGTATGATTGCTACTCTT 57.535 33.333 0.00 0.00 37.00 2.85
479 494 4.530710 AATCCTTCAAGTACTGTGCGTA 57.469 40.909 0.00 0.00 0.00 4.42
504 519 2.636893 GCACTACAGATCCAGGGATGAT 59.363 50.000 5.35 0.00 34.60 2.45
546 561 1.272490 TGTTTGAGGTCTGGTCGCTAG 59.728 52.381 0.00 0.00 0.00 3.42
549 564 1.174783 TGAGGTCTGGTCGCTAGAAC 58.825 55.000 0.00 1.07 31.98 3.01
553 568 1.204941 GGTCTGGTCGCTAGAACATGT 59.795 52.381 0.00 0.00 44.13 3.21
609 625 5.012561 CCACTAAGCTAAAGCCCTAGATCAT 59.987 44.000 13.05 0.00 43.38 2.45
685 701 1.597937 GCAAGGAACAAGTTCACGCAG 60.598 52.381 14.25 1.70 41.20 5.18
742 758 8.840200 TGAAGGAAGTTACTAGATACCTGAAT 57.160 34.615 0.00 0.00 0.00 2.57
747 763 9.012161 GGAAGTTACTAGATACCTGAATATCGT 57.988 37.037 0.00 0.00 36.78 3.73
765 781 1.068055 CGTACTACCAAGCTTCACCGT 60.068 52.381 0.00 0.00 0.00 4.83
766 782 2.162208 CGTACTACCAAGCTTCACCGTA 59.838 50.000 0.00 0.00 0.00 4.02
767 783 2.738013 ACTACCAAGCTTCACCGTAC 57.262 50.000 0.00 0.00 0.00 3.67
854 871 1.782201 ATGCCAGTCACTGAGCCCAA 61.782 55.000 6.30 0.00 32.44 4.12
899 916 2.167487 CCTGGAGTCTAGGAAAGAGCAC 59.833 54.545 17.42 0.00 37.52 4.40
901 918 2.093106 GGAGTCTAGGAAAGAGCACGA 58.907 52.381 0.00 0.00 33.88 4.35
925 942 2.114670 CACATCACCATGGGACGCC 61.115 63.158 18.09 0.00 35.04 5.68
933 950 1.153289 CATGGGACGCCTTGGAGAG 60.153 63.158 0.00 0.00 0.00 3.20
1071 1088 1.308069 ACCAGCACATTCGATGCCAC 61.308 55.000 5.88 0.00 44.53 5.01
1079 1096 0.806102 ATTCGATGCCACGAGAACCG 60.806 55.000 0.00 0.00 43.04 4.44
1088 1105 0.740868 CACGAGAACCGGATGTGCAT 60.741 55.000 9.46 0.00 43.93 3.96
1150 1167 3.007398 GGAGCTGGAAGAAGAACTCAAGA 59.993 47.826 0.00 0.00 34.07 3.02
1211 1228 5.127682 TCGTGGAGAAGAATGATGATCTGAA 59.872 40.000 0.00 0.00 0.00 3.02
1223 1240 5.599732 TGATGATCTGAAGAAGAAGCTAGC 58.400 41.667 6.62 6.62 38.79 3.42
1225 1242 5.411831 TGATCTGAAGAAGAAGCTAGCAA 57.588 39.130 18.83 0.00 38.79 3.91
1260 1277 2.865598 CGCGCCAGGAGGAGATGAT 61.866 63.158 0.00 0.00 36.74 2.45
1274 1291 4.054671 GGAGATGATGACGATTCCACTTC 58.945 47.826 0.00 0.00 0.00 3.01
1395 1412 5.800296 TCCACCGATCAATTTTTCTAGTCA 58.200 37.500 0.00 0.00 0.00 3.41
1399 1416 5.414765 ACCGATCAATTTTTCTAGTCAACCC 59.585 40.000 0.00 0.00 0.00 4.11
1656 1679 1.973515 TCACTCAGTTGATCCAGCAGT 59.026 47.619 0.00 0.00 0.00 4.40
1713 1742 2.818751 TCAGGGGAACAACAACAACT 57.181 45.000 0.00 0.00 0.00 3.16
1736 1774 4.596585 CCACCACCACCACCACCC 62.597 72.222 0.00 0.00 0.00 4.61
1758 1796 3.335579 GTTGATCACTTAGCCCGTTTCT 58.664 45.455 0.00 0.00 0.00 2.52
1760 1798 3.334691 TGATCACTTAGCCCGTTTCTTG 58.665 45.455 0.00 0.00 0.00 3.02
1766 1804 4.081050 GCCCGTTTCTTGAGGCTT 57.919 55.556 0.00 0.00 42.34 4.35
1797 1835 0.173708 GTTCTCCAGTAGCACCGAGG 59.826 60.000 0.00 0.00 0.00 4.63
1813 1851 1.506493 GAGGCGATAGTTGCAGATGG 58.494 55.000 0.00 0.00 39.35 3.51
1836 1874 0.392998 GCTCCGCAAGATTGGAAGGA 60.393 55.000 0.00 0.00 43.02 3.36
1845 1884 4.161001 GCAAGATTGGAAGGAATTGACCAT 59.839 41.667 0.00 0.00 32.31 3.55
1889 1928 0.459489 AGTGTGTTTTGCCGCACATT 59.541 45.000 7.51 0.00 45.91 2.71
1896 1935 0.388391 TTTGCCGCACATTAGCTTGC 60.388 50.000 0.00 0.00 35.26 4.01
1898 1937 0.392327 TGCCGCACATTAGCTTGCTA 60.392 50.000 6.55 0.00 36.54 3.49
1928 1968 5.394883 GCAACATCATGTGGGAGAATTTCAT 60.395 40.000 0.00 0.00 0.00 2.57
1951 1991 2.104967 CCACTTACCCCATCGACACTA 58.895 52.381 0.00 0.00 0.00 2.74
2057 2097 2.851263 TTGCACCAAGGAAGACGTAT 57.149 45.000 0.00 0.00 0.00 3.06
2060 2100 3.093814 TGCACCAAGGAAGACGTATAGA 58.906 45.455 0.00 0.00 0.00 1.98
2217 2265 3.330126 CCAGGAGTTGGTAGATAGGGA 57.670 52.381 0.00 0.00 42.41 4.20
2237 2291 4.103785 GGGATCTCATGATTGAAGGGAAGA 59.896 45.833 0.00 0.00 32.19 2.87
2245 2299 1.901591 TTGAAGGGAAGAAGCAGCAG 58.098 50.000 0.00 0.00 0.00 4.24
2381 2436 1.271379 ACCACAATGGAGGAAGTTCGG 60.271 52.381 0.84 0.00 40.96 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 6.958255 ACAGTTTTGCATAAAGCCAATTTTC 58.042 32.000 0.00 0.00 44.83 2.29
151 155 3.390967 ACTACATGCATGTATGGCTGGTA 59.609 43.478 33.66 15.05 41.92 3.25
162 166 8.175716 CAGAATAATGCTATCACTACATGCATG 58.824 37.037 25.09 25.09 42.57 4.06
202 207 6.606796 TGGGATATGCTGAAAATGTAACACAT 59.393 34.615 0.00 0.00 41.31 3.21
224 229 1.586154 GAAACGGGTCAGCACATGGG 61.586 60.000 0.00 0.00 0.00 4.00
272 279 2.755655 AGACACCTTACTCATCGTCTGG 59.244 50.000 0.00 0.00 32.70 3.86
280 287 3.504906 CACGACCTAAGACACCTTACTCA 59.495 47.826 0.00 0.00 33.94 3.41
323 331 4.647564 AAGTGAGTCCATCAACTCCAAT 57.352 40.909 1.88 0.00 44.17 3.16
452 467 7.604927 ACGCACAGTACTTGAAGGATTTATAAA 59.395 33.333 0.00 0.00 0.00 1.40
479 494 2.045524 CCCTGGATCTGTAGTGCTGAT 58.954 52.381 0.00 0.22 38.28 2.90
486 501 5.328565 TCAGTATCATCCCTGGATCTGTAG 58.671 45.833 10.63 0.00 31.62 2.74
490 505 3.518705 GCATCAGTATCATCCCTGGATCT 59.481 47.826 0.00 0.00 31.62 2.75
504 519 5.595952 ACAGTATGATCTCTGTGCATCAGTA 59.404 40.000 14.44 6.45 42.30 2.74
523 538 1.000506 GCGACCAGACCTCAAACAGTA 59.999 52.381 0.00 0.00 0.00 2.74
546 561 3.484229 GCGTGTGCTCTGATAACATGTTC 60.484 47.826 15.85 1.96 38.39 3.18
549 564 2.726555 GCGTGTGCTCTGATAACATG 57.273 50.000 0.00 0.00 38.39 3.21
572 587 2.029649 GCTTAGTGGTCGTGTCCTACAA 60.030 50.000 0.00 0.00 0.00 2.41
609 625 6.951198 AGGAGTCAGAAATGAGAAGAGAGTAA 59.049 38.462 0.00 0.00 0.00 2.24
685 701 4.332819 CCAAAAGGTGTATCTTCATCCGAC 59.667 45.833 0.00 0.00 0.00 4.79
742 758 3.065786 CGGTGAAGCTTGGTAGTACGATA 59.934 47.826 2.10 0.00 0.00 2.92
747 763 2.493278 GGTACGGTGAAGCTTGGTAGTA 59.507 50.000 2.10 0.27 0.00 1.82
749 765 1.405121 GGGTACGGTGAAGCTTGGTAG 60.405 57.143 2.10 0.00 0.00 3.18
765 781 1.065998 GGTAAAGTGGCGATGTGGGTA 60.066 52.381 0.00 0.00 0.00 3.69
766 782 0.322187 GGTAAAGTGGCGATGTGGGT 60.322 55.000 0.00 0.00 0.00 4.51
767 783 0.322098 TGGTAAAGTGGCGATGTGGG 60.322 55.000 0.00 0.00 0.00 4.61
854 871 3.960102 TGGTGCATCAAAGGAAAACTCTT 59.040 39.130 0.00 0.00 0.00 2.85
899 916 1.078214 ATGGTGATGTGGGCTGTCG 60.078 57.895 0.00 0.00 0.00 4.35
901 918 1.000521 CCATGGTGATGTGGGCTGT 60.001 57.895 2.57 0.00 0.00 4.40
936 953 4.762289 ATCCTTGAGATCCTTGTGGTAC 57.238 45.455 0.00 0.00 34.23 3.34
967 984 1.271856 TCTCGGCACCCACAAATCTA 58.728 50.000 0.00 0.00 0.00 1.98
1071 1088 1.491670 CTATGCACATCCGGTTCTCG 58.508 55.000 0.00 0.00 38.88 4.04
1088 1105 5.046735 GCCTTCTTCAGATCTATCATGCCTA 60.047 44.000 0.00 0.00 0.00 3.93
1150 1167 2.229062 CCTCATATCCATCGCGTGTAGT 59.771 50.000 5.77 0.00 0.00 2.73
1211 1228 6.002704 CCCATGAATATTGCTAGCTTCTTCT 58.997 40.000 17.23 0.00 0.00 2.85
1257 1274 1.209504 GGGGAAGTGGAATCGTCATCA 59.790 52.381 0.00 0.00 0.00 3.07
1260 1277 1.594833 CGGGGAAGTGGAATCGTCA 59.405 57.895 0.00 0.00 0.00 4.35
1274 1291 2.039418 TGATGATGTAGTTCTCCGGGG 58.961 52.381 0.00 0.00 0.00 5.73
1395 1412 6.729569 GGAATACTACTACTGATATGGGGGTT 59.270 42.308 0.00 0.00 0.00 4.11
1399 1416 5.661759 GGGGGAATACTACTACTGATATGGG 59.338 48.000 0.00 0.00 0.00 4.00
1667 1690 3.548745 TTCTGGACTGGTATCTGCATG 57.451 47.619 0.00 0.00 0.00 4.06
1678 1701 3.433314 CCCCTGATTCTGATTCTGGACTG 60.433 52.174 20.44 8.96 34.97 3.51
1713 1742 1.532728 GTGGTGGTGGTGGGTTGTA 59.467 57.895 0.00 0.00 0.00 2.41
1736 1774 1.722011 AACGGGCTAAGTGATCAACG 58.278 50.000 0.00 0.00 0.00 4.10
1766 1804 1.259142 TGGAGAACACGGGCGGATTA 61.259 55.000 0.00 0.00 0.00 1.75
1797 1835 1.331756 CCAACCATCTGCAACTATCGC 59.668 52.381 0.00 0.00 0.00 4.58
1889 1928 4.027884 TGCGGGTCTAGCAAGCTA 57.972 55.556 1.37 1.37 42.18 3.32
1896 1935 1.935873 CACATGATGTTGCGGGTCTAG 59.064 52.381 0.00 0.00 0.00 2.43
1898 1937 0.677731 CCACATGATGTTGCGGGTCT 60.678 55.000 0.00 0.00 0.00 3.85
1928 1968 1.117150 GTCGATGGGGTAAGTGGCTA 58.883 55.000 0.00 0.00 0.00 3.93
1951 1991 2.881403 GCTGAAACTGGTCCCATGTGAT 60.881 50.000 0.00 0.00 0.00 3.06
2042 2082 4.159879 CACCTTCTATACGTCTTCCTTGGT 59.840 45.833 0.00 0.00 0.00 3.67
2050 2090 6.732896 AAATCATCCACCTTCTATACGTCT 57.267 37.500 0.00 0.00 0.00 4.18
2060 2100 8.107095 TGCTAACTTACTAAAATCATCCACCTT 58.893 33.333 0.00 0.00 0.00 3.50
2215 2263 5.301835 TCTTCCCTTCAATCATGAGATCC 57.698 43.478 0.09 0.00 36.78 3.36
2217 2265 5.131784 GCTTCTTCCCTTCAATCATGAGAT 58.868 41.667 0.09 0.00 36.78 2.75
2237 2291 1.610522 GTGGTTGTCAATCTGCTGCTT 59.389 47.619 0.00 0.00 0.00 3.91
2245 2299 4.137543 ACTTCCTCTTGTGGTTGTCAATC 58.862 43.478 0.00 0.00 0.00 2.67
2358 2413 1.620822 ACTTCCTCCATTGTGGTTGC 58.379 50.000 0.00 0.00 39.03 4.17


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

AutoCloner maintained by Alex Coulton.