Multiple sequence alignment - TraesCS2A01G578500

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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 TraesCS2A01G578500 chr2A 100.000 2387 0 0 1 2387 771771646 771774032 0.000000e+00 4409
1 TraesCS2A01G578500 chr2A 87.099 1775 148 30 674 2387 773583210 773581456 0.000000e+00 1934
2 TraesCS2A01G578500 chr2A 89.663 1306 112 14 674 1966 773563622 773562327 0.000000e+00 1642
3 TraesCS2A01G578500 chr2A 96.137 673 26 0 1 673 727622773 727622101 0.000000e+00 1099
4 TraesCS2A01G578500 chr2A 83.368 475 50 15 1930 2387 773562321 773561859 1.710000e-111 412
5 TraesCS2A01G578500 chr2D 96.690 1722 48 7 674 2387 645958417 645960137 0.000000e+00 2856
6 TraesCS2A01G578500 chr2B 88.721 1720 148 24 705 2387 789564730 789563020 0.000000e+00 2060
7 TraesCS2A01G578500 chr2B 80.861 209 26 8 2116 2311 152750323 152750116 4.110000e-33 152
8 TraesCS2A01G578500 chr6A 97.028 673 20 0 1 673 13930879 13931551 0.000000e+00 1133
9 TraesCS2A01G578500 chr5A 96.439 674 24 0 1 674 618801594 618802267 0.000000e+00 1112
10 TraesCS2A01G578500 chr5A 96.000 675 27 0 1 675 580151131 580150457 0.000000e+00 1098
11 TraesCS2A01G578500 chr5A 95.858 676 27 1 1 675 580116500 580115825 0.000000e+00 1092
12 TraesCS2A01G578500 chr5A 95.846 674 28 0 1 674 155519603 155518930 0.000000e+00 1090
13 TraesCS2A01G578500 chr5A 95.704 675 28 1 1 675 580140409 580139736 0.000000e+00 1085
14 TraesCS2A01G578500 chr3A 95.988 673 26 1 1 673 10334006 10334677 0.000000e+00 1092
15 TraesCS2A01G578500 chr1A 95.697 674 29 0 1 674 588364039 588363366 0.000000e+00 1085
16 TraesCS2A01G578500 chr1A 81.938 227 35 5 2164 2386 592982032 592982256 1.130000e-43 187
17 TraesCS2A01G578500 chr7B 82.407 216 34 4 2173 2385 132971718 132971932 4.050000e-43 185
18 TraesCS2A01G578500 chr4B 82.386 176 26 4 2173 2347 385620586 385620757 5.320000e-32 148
19 TraesCS2A01G578500 chr5B 84.404 109 16 1 2173 2281 132047880 132047987 3.250000e-19 106


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 TraesCS2A01G578500 chr2A 771771646 771774032 2386 False 4409 4409 100.0000 1 2387 1 chr2A.!!$F1 2386
1 TraesCS2A01G578500 chr2A 773581456 773583210 1754 True 1934 1934 87.0990 674 2387 1 chr2A.!!$R2 1713
2 TraesCS2A01G578500 chr2A 727622101 727622773 672 True 1099 1099 96.1370 1 673 1 chr2A.!!$R1 672
3 TraesCS2A01G578500 chr2A 773561859 773563622 1763 True 1027 1642 86.5155 674 2387 2 chr2A.!!$R3 1713
4 TraesCS2A01G578500 chr2D 645958417 645960137 1720 False 2856 2856 96.6900 674 2387 1 chr2D.!!$F1 1713
5 TraesCS2A01G578500 chr2B 789563020 789564730 1710 True 2060 2060 88.7210 705 2387 1 chr2B.!!$R2 1682
6 TraesCS2A01G578500 chr6A 13930879 13931551 672 False 1133 1133 97.0280 1 673 1 chr6A.!!$F1 672
7 TraesCS2A01G578500 chr5A 618801594 618802267 673 False 1112 1112 96.4390 1 674 1 chr5A.!!$F1 673
8 TraesCS2A01G578500 chr5A 580150457 580151131 674 True 1098 1098 96.0000 1 675 1 chr5A.!!$R4 674
9 TraesCS2A01G578500 chr5A 580115825 580116500 675 True 1092 1092 95.8580 1 675 1 chr5A.!!$R2 674
10 TraesCS2A01G578500 chr5A 155518930 155519603 673 True 1090 1090 95.8460 1 674 1 chr5A.!!$R1 673
11 TraesCS2A01G578500 chr5A 580139736 580140409 673 True 1085 1085 95.7040 1 675 1 chr5A.!!$R3 674
12 TraesCS2A01G578500 chr3A 10334006 10334677 671 False 1092 1092 95.9880 1 673 1 chr3A.!!$F1 672
13 TraesCS2A01G578500 chr1A 588363366 588364039 673 True 1085 1085 95.6970 1 674 1 chr1A.!!$R1 673

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
298 299 2.427232 TGTAAACCGGTGAAGACTCG 57.573 50.0 8.52 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1768 1.546476 GGTGGACTCCTACACAGACAG 59.454 57.143 0.0 0.0 39.31 3.51 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
29 30 9.033481 CATTTGTAGTGCTTTTCAATTTCAAGA 57.967 29.630 0.00 0.00 0.00 3.02
298 299 2.427232 TGTAAACCGGTGAAGACTCG 57.573 50.000 8.52 0.00 0.00 4.18
373 375 8.703604 TGTGATAGTTTGAGAAGTAACATAGC 57.296 34.615 0.00 0.00 29.66 2.97
374 376 8.311109 TGTGATAGTTTGAGAAGTAACATAGCA 58.689 33.333 0.00 0.00 29.66 3.49
615 617 6.984474 CCGGTACTATTGATCACATTAGTGTT 59.016 38.462 16.78 0.00 46.01 3.32
690 692 2.951642 AGTGATTGTTGAACAGTGGTGG 59.048 45.455 0.00 0.00 0.00 4.61
833 843 3.612479 GCCCATTCGGATATGCATTCAAC 60.612 47.826 3.54 0.00 0.00 3.18
880 890 2.851263 ATTTAAGCACCCACGTCTCA 57.149 45.000 0.00 0.00 0.00 3.27
1260 1275 1.600013 CGACAAAAACATGTGTCCGGA 59.400 47.619 0.00 0.00 40.91 5.14
1346 1361 2.949451 CTGTACGAGCAGGAGTTGAT 57.051 50.000 0.00 0.00 33.11 2.57
1442 1457 5.070685 GGTTCCTGGAATGTTGTTAGTTCT 58.929 41.667 13.07 0.00 0.00 3.01
1475 1490 8.773033 ATCCAATAATAAATTGTCCTCTTGCT 57.227 30.769 0.00 0.00 0.00 3.91
1515 1530 5.572211 AGCTTGTCAAAACATACATATGCG 58.428 37.500 1.58 0.00 37.19 4.73
1516 1531 5.353956 AGCTTGTCAAAACATACATATGCGA 59.646 36.000 1.58 0.00 37.19 5.10
1517 1532 5.452302 GCTTGTCAAAACATACATATGCGAC 59.548 40.000 1.58 2.68 37.19 5.19
1518 1533 6.675486 GCTTGTCAAAACATACATATGCGACT 60.675 38.462 1.58 0.00 37.19 4.18
1519 1534 6.735678 TGTCAAAACATACATATGCGACTT 57.264 33.333 1.58 0.00 37.19 3.01
1520 1535 6.541969 TGTCAAAACATACATATGCGACTTG 58.458 36.000 1.58 0.13 37.19 3.16
1745 1768 6.017830 AGTCTATATAAGTGGCCTCCCTAAC 58.982 44.000 3.32 0.00 0.00 2.34
1780 1803 1.080569 CACCGGCCATTTGACTTGC 60.081 57.895 0.00 0.00 0.00 4.01
1873 1897 7.750655 AGGGGATTCCTCATATTTTCTACTTC 58.249 38.462 5.12 0.00 44.06 3.01
1896 1920 5.836821 ACTCGAGTGATAGTGAGCATTTA 57.163 39.130 19.30 0.00 31.64 1.40
2058 2127 6.369065 GCAGCTATCCTAAACAATAAGCGTAT 59.631 38.462 0.00 0.00 0.00 3.06
2100 2169 7.098477 CACAAAGATGGGAAAATTTGAGCATA 58.902 34.615 3.73 0.00 36.41 3.14
2327 2411 2.766828 CTGGACAACTAAGGACCCTAGG 59.233 54.545 0.06 0.06 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
298 299 2.939460 AGAATTTGTGGCCGCAATAC 57.061 45.000 31.20 22.91 0.00 1.89
511 513 2.489329 CACGAACCGGTACTAAAGAGGA 59.511 50.000 8.00 0.00 0.00 3.71
615 617 1.310904 GCCGGTTTGTAACAGAACCA 58.689 50.000 1.90 0.00 44.37 3.67
690 692 6.467723 AATTACAGTTGAGTGTGACGATTC 57.532 37.500 1.79 0.00 31.46 2.52
880 890 4.412528 AGAGTGAGGGGTTCTAAAACAAGT 59.587 41.667 0.00 0.00 37.10 3.16
1068 1083 1.405526 CCCATCGAATCTCCACAACGT 60.406 52.381 0.00 0.00 0.00 3.99
1098 1113 0.532573 CCTCTACTGTCGTGTGCCAT 59.467 55.000 0.00 0.00 0.00 4.40
1465 1480 2.227388 CCACATGACAAAGCAAGAGGAC 59.773 50.000 0.00 0.00 0.00 3.85
1475 1490 2.665165 AGCTCCAAACCACATGACAAA 58.335 42.857 0.00 0.00 0.00 2.83
1515 1530 5.642063 TGTTTTCCCTCATCGTAATCAAGTC 59.358 40.000 0.00 0.00 0.00 3.01
1516 1531 5.556915 TGTTTTCCCTCATCGTAATCAAGT 58.443 37.500 0.00 0.00 0.00 3.16
1517 1532 6.494893 TTGTTTTCCCTCATCGTAATCAAG 57.505 37.500 0.00 0.00 0.00 3.02
1518 1533 6.885952 TTTGTTTTCCCTCATCGTAATCAA 57.114 33.333 0.00 0.00 0.00 2.57
1519 1534 6.432783 ACATTTGTTTTCCCTCATCGTAATCA 59.567 34.615 0.00 0.00 0.00 2.57
1520 1535 6.852664 ACATTTGTTTTCCCTCATCGTAATC 58.147 36.000 0.00 0.00 0.00 1.75
1745 1768 1.546476 GGTGGACTCCTACACAGACAG 59.454 57.143 0.00 0.00 39.31 3.51
1780 1803 6.147000 CCACCACAAAATATTTTTCCCTTTCG 59.853 38.462 10.77 0.53 0.00 3.46
1873 1897 3.706802 ATGCTCACTATCACTCGAGTG 57.293 47.619 34.76 34.76 46.91 3.51
2058 2127 7.265599 TCTTTGTGTCCAGGAAATCCTATTA 57.734 36.000 0.70 0.00 46.65 0.98
2100 2169 4.141846 ACGTTGGAGATGCATCAACTATCT 60.142 41.667 27.81 6.44 38.74 1.98
2327 2411 1.608590 CCTCGATCTCTCCTGAAGCTC 59.391 57.143 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.