Multiple sequence alignment - TraesCS3A01G414800

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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 TraesCS3A01G414800 chr3A 100.000 2636 0 0 1 2636 658289669 658292304 0.000000e+00 4868
1 TraesCS3A01G414800 chr3A 89.180 2098 178 25 2 2072 658304181 658306256 0.000000e+00 2571
2 TraesCS3A01G414800 chr3B 89.516 1612 162 5 2 1611 690431111 690432717 0.000000e+00 2034
3 TraesCS3A01G414800 chr3B 83.859 1964 278 22 8 1958 689006821 689004884 0.000000e+00 1834
4 TraesCS3A01G414800 chr3B 85.673 1738 207 31 1 1724 690443432 690445141 0.000000e+00 1792
5 TraesCS3A01G414800 chr3B 86.156 1618 207 11 6 1615 690460505 690462113 0.000000e+00 1731
6 TraesCS3A01G414800 chr3B 81.836 2092 323 29 6 2072 642214927 642212868 0.000000e+00 1705
7 TraesCS3A01G414800 chr3B 83.553 1672 251 20 1 1663 690447524 690449180 0.000000e+00 1543
8 TraesCS3A01G414800 chr3B 84.802 454 27 14 1641 2072 690432715 690433148 4.060000e-113 418
9 TraesCS3A01G414800 chr3D 83.767 1885 286 14 2 1879 523408494 523410365 0.000000e+00 1768
10 TraesCS3A01G414800 chr3D 82.017 2102 317 38 6 2072 523335198 523337273 0.000000e+00 1731
11 TraesCS3A01G414800 chr3D 82.248 1628 263 21 1 1614 523570201 523571816 0.000000e+00 1382
12 TraesCS3A01G414800 chr3D 86.780 1233 133 20 1 1225 523380072 523381282 0.000000e+00 1347
13 TraesCS3A01G414800 chr3D 95.806 763 28 2 1878 2636 523416204 523416966 0.000000e+00 1229
14 TraesCS3A01G414800 chrUn 84.354 1649 232 20 8 1643 330561712 330563347 0.000000e+00 1592
15 TraesCS3A01G414800 chrUn 79.387 2120 359 58 1 2071 342677899 342679989 0.000000e+00 1423
16 TraesCS3A01G414800 chrUn 80.822 1241 180 42 867 2071 405666953 405668171 0.000000e+00 920
17 TraesCS3A01G414800 chrUn 90.031 321 25 4 1648 1964 353196070 353196387 2.440000e-110 409
18 TraesCS3A01G414800 chrUn 89.815 324 26 4 1648 1967 471390039 471389719 2.440000e-110 409


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 TraesCS3A01G414800 chr3A 658289669 658292304 2635 False 4868.0 4868 100.000 1 2636 1 chr3A.!!$F1 2635
1 TraesCS3A01G414800 chr3A 658304181 658306256 2075 False 2571.0 2571 89.180 2 2072 1 chr3A.!!$F2 2070
2 TraesCS3A01G414800 chr3B 689004884 689006821 1937 True 1834.0 1834 83.859 8 1958 1 chr3B.!!$R2 1950
3 TraesCS3A01G414800 chr3B 690460505 690462113 1608 False 1731.0 1731 86.156 6 1615 1 chr3B.!!$F1 1609
4 TraesCS3A01G414800 chr3B 642212868 642214927 2059 True 1705.0 1705 81.836 6 2072 1 chr3B.!!$R1 2066
5 TraesCS3A01G414800 chr3B 690443432 690449180 5748 False 1667.5 1792 84.613 1 1724 2 chr3B.!!$F3 1723
6 TraesCS3A01G414800 chr3B 690431111 690433148 2037 False 1226.0 2034 87.159 2 2072 2 chr3B.!!$F2 2070
7 TraesCS3A01G414800 chr3D 523408494 523410365 1871 False 1768.0 1768 83.767 2 1879 1 chr3D.!!$F3 1877
8 TraesCS3A01G414800 chr3D 523335198 523337273 2075 False 1731.0 1731 82.017 6 2072 1 chr3D.!!$F1 2066
9 TraesCS3A01G414800 chr3D 523570201 523571816 1615 False 1382.0 1382 82.248 1 1614 1 chr3D.!!$F5 1613
10 TraesCS3A01G414800 chr3D 523380072 523381282 1210 False 1347.0 1347 86.780 1 1225 1 chr3D.!!$F2 1224
11 TraesCS3A01G414800 chr3D 523416204 523416966 762 False 1229.0 1229 95.806 1878 2636 1 chr3D.!!$F4 758
12 TraesCS3A01G414800 chrUn 330561712 330563347 1635 False 1592.0 1592 84.354 8 1643 1 chrUn.!!$F1 1635
13 TraesCS3A01G414800 chrUn 342677899 342679989 2090 False 1423.0 1423 79.387 1 2071 1 chrUn.!!$F2 2070
14 TraesCS3A01G414800 chrUn 405666953 405668171 1218 False 920.0 920 80.822 867 2071 1 chrUn.!!$F4 1204

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
55 56 0.392193 CATGACAGGACTGCAGACCC 60.392 60.000 28.18 22.74 0.00 4.46 F
429 442 1.470098 CTGTACCACATGGCTTTCAGC 59.530 52.381 0.00 0.00 41.46 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1035 1049 1.447838 CACCACGGCTGTTATCGCT 60.448 57.895 0.0 0.0 0.0 4.93 R
2178 6377 0.108138 AGGAAGCTGAATCGAACCGG 60.108 55.000 0.0 0.0 0.0 5.28 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
55 56 0.392193 CATGACAGGACTGCAGACCC 60.392 60.000 28.18 22.74 0.00 4.46
64 65 2.570302 GGACTGCAGACCCTAAACCTTA 59.430 50.000 23.35 0.00 0.00 2.69
308 315 3.564053 TGGATTTACCGGTATTCACCC 57.436 47.619 16.67 12.66 42.43 4.61
408 421 3.334583 TTTAGTGAGCATCCAGGACAC 57.665 47.619 0.00 0.00 0.00 3.67
429 442 1.470098 CTGTACCACATGGCTTTCAGC 59.530 52.381 0.00 0.00 41.46 4.26
524 537 6.116126 GCTTCCTAGACCTATCAAACAATGT 58.884 40.000 0.00 0.00 0.00 2.71
538 551 6.068010 TCAAACAATGTCTTACATGGAGGTT 58.932 36.000 0.00 0.00 37.97 3.50
647 660 6.710744 AGGACATGTCAAGAACGTCTTAAATT 59.289 34.615 26.47 0.00 33.78 1.82
969 983 7.199766 GGAACAACAATGACTTCACATACAAA 58.800 34.615 0.00 0.00 0.00 2.83
1035 1049 8.862325 AGAATGTGGATCATGTTTACAGTTTA 57.138 30.769 0.00 0.00 36.81 2.01
1037 1051 6.494893 TGTGGATCATGTTTACAGTTTAGC 57.505 37.500 0.00 0.00 0.00 3.09
1527 5648 1.172180 TGGGCTTCTTGTTTCGCAGG 61.172 55.000 0.00 0.00 0.00 4.85
1590 5711 2.154462 CAAGCGAAGGTGACCAAGAAT 58.846 47.619 3.63 0.00 39.47 2.40
1685 5816 3.414269 TGGTGTATCGCGTCCTATATCA 58.586 45.455 5.77 0.00 0.00 2.15
1698 5829 5.631096 CGTCCTATATCAAGCATGTGTGTAG 59.369 44.000 0.00 0.00 0.00 2.74
1760 5908 8.460831 AAACGTATTTTCCAGTAATTTGATGC 57.539 30.769 0.00 0.00 0.00 3.91
1790 5938 0.887387 TTGTGGCGCTGAAACCTACC 60.887 55.000 7.64 0.00 0.00 3.18
1864 6027 9.604626 GAATGAGTTCTTTGAAATCAGTTAGTG 57.395 33.333 14.15 0.00 0.00 2.74
2088 6287 8.690203 TCAATTTGAAAGGACTCTGATTGTAA 57.310 30.769 0.00 0.00 0.00 2.41
2126 6325 3.008375 TGGAGCAAAGCACTAGACTCATT 59.992 43.478 0.00 0.00 0.00 2.57
2129 6328 5.394663 GGAGCAAAGCACTAGACTCATTAGA 60.395 44.000 0.00 0.00 0.00 2.10
2130 6329 6.232581 AGCAAAGCACTAGACTCATTAGAT 57.767 37.500 0.00 0.00 0.00 1.98
2144 6343 9.868277 AGACTCATTAGATAAAACTGAAGACTG 57.132 33.333 0.00 0.00 0.00 3.51
2145 6344 9.646427 GACTCATTAGATAAAACTGAAGACTGT 57.354 33.333 0.00 0.00 0.00 3.55
2178 6377 4.211502 GTTGGGCATGGGCATCGC 62.212 66.667 0.00 0.00 43.71 4.58
2197 6396 0.108138 CCGGTTCGATTCAGCTTCCT 60.108 55.000 0.00 0.00 0.00 3.36
2332 6531 8.465201 AGATCATTCAAGTGATTTCCTAAAAGC 58.535 33.333 0.00 0.00 38.88 3.51
2370 6569 3.441500 AAGGGAAGTGGGTCTCATTTC 57.558 47.619 0.00 0.00 40.18 2.17
2386 6585 7.308435 GTCTCATTTCATTAAGTGGACCAAAG 58.692 38.462 0.00 0.00 0.00 2.77
2393 6592 1.247567 AAGTGGACCAAAGCCATTCG 58.752 50.000 0.00 0.00 37.81 3.34
2395 6594 2.331893 TGGACCAAAGCCATTCGCG 61.332 57.895 0.00 0.00 44.76 5.87
2397 6596 1.134694 GACCAAAGCCATTCGCGTC 59.865 57.895 5.77 0.00 44.76 5.19
2402 6601 2.159448 CCAAAGCCATTCGCGTCATTTA 60.159 45.455 5.77 0.00 44.76 1.40
2435 6634 9.516314 AAATGCAAAGAGAAAAAGTAGTAACAC 57.484 29.630 0.00 0.00 0.00 3.32
2503 6706 5.813383 AGGCTCTCTTTTCATCTTGATCAA 58.187 37.500 8.12 8.12 0.00 2.57
2511 6714 9.871238 CTCTTTTCATCTTGATCAATGGAAATT 57.129 29.630 20.55 0.00 31.60 1.82
2521 6724 6.845302 TGATCAATGGAAATTCAAAGACTCG 58.155 36.000 0.00 0.00 0.00 4.18
2525 6728 6.712998 TCAATGGAAATTCAAAGACTCGGTTA 59.287 34.615 0.00 0.00 0.00 2.85
2607 6810 6.686378 GCCTGTCATAGACATAATCCTTCACA 60.686 42.308 0.00 0.00 41.94 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.791545 TGCCCTCCCAAATAGTTATCCTT 59.208 43.478 0.00 0.00 0.00 3.36
202 206 6.264832 CAGAGAAGTTGTTGTTTGCAATGTA 58.735 36.000 0.00 0.00 36.92 2.29
308 315 0.033920 GCAGTTTTGAAAGGCCTGGG 59.966 55.000 5.69 0.00 0.00 4.45
408 421 2.086869 CTGAAAGCCATGTGGTACAGG 58.913 52.381 0.35 0.00 41.80 4.00
429 442 1.038681 TGCCATGCAGCTGGTTATGG 61.039 55.000 17.12 14.10 42.30 2.74
524 537 5.534654 CACTTGGAAAAACCTCCATGTAAGA 59.465 40.000 9.95 0.00 46.67 2.10
538 551 3.976015 AGTCCCAGAAACACTTGGAAAA 58.024 40.909 0.00 0.00 41.21 2.29
944 958 6.312399 TGTATGTGAAGTCATTGTTGTTCC 57.688 37.500 0.00 0.00 0.00 3.62
1002 1016 4.463891 ACATGATCCACATTCTTCCAAACC 59.536 41.667 0.00 0.00 37.07 3.27
1035 1049 1.447838 CACCACGGCTGTTATCGCT 60.448 57.895 0.00 0.00 0.00 4.93
1037 1051 1.813753 CCCACCACGGCTGTTATCG 60.814 63.158 0.00 0.00 0.00 2.92
1169 1189 3.624861 CAGTACCAGATTGCCAATGTCTC 59.375 47.826 0.00 0.00 0.00 3.36
1420 5535 3.056536 TCTTCATCCAGACTCGTTTCAGG 60.057 47.826 0.00 0.00 0.00 3.86
1527 5648 8.756927 TGATAGAATGAATATCTCCATGTCTCC 58.243 37.037 0.00 0.00 32.02 3.71
1620 5741 4.263905 ACACTTCATCATTCAGGCCCTTTA 60.264 41.667 0.00 0.00 0.00 1.85
1651 5772 5.560148 GCGATACACCATTACTTCAACAAG 58.440 41.667 0.00 0.00 35.50 3.16
1685 5816 6.151144 GGAAAGGAAATACTACACACATGCTT 59.849 38.462 0.00 0.00 0.00 3.91
1698 5829 8.080417 GTCCAACTAACAAAGGAAAGGAAATAC 58.920 37.037 0.00 0.00 0.00 1.89
1742 5889 9.859427 CTTGAATAGCATCAAATTACTGGAAAA 57.141 29.630 2.01 0.00 38.75 2.29
1745 5892 8.579850 AACTTGAATAGCATCAAATTACTGGA 57.420 30.769 2.01 0.00 38.75 3.86
1760 5908 3.058293 TCAGCGCCACAAAACTTGAATAG 60.058 43.478 2.29 0.00 0.00 1.73
1790 5938 5.288804 ACCAAACAATCAAATCTGAAACCG 58.711 37.500 0.00 0.00 34.49 4.44
1864 6027 9.578439 AAAGCAAGCTACAGATTCAAATTTATC 57.422 29.630 0.00 0.00 0.00 1.75
1925 6091 3.196463 CACAAAATGGCTGTGCAAGAAA 58.804 40.909 0.00 0.00 37.93 2.52
2088 6287 1.000739 CCACCAATCACAGGGGCAT 59.999 57.895 0.00 0.00 0.00 4.40
2130 6329 9.856488 GATGTGTATAGACAGTCTTCAGTTTTA 57.144 33.333 8.80 0.00 35.82 1.52
2144 6343 5.163447 TGCCCAACTACAGATGTGTATAGAC 60.163 44.000 2.77 0.00 38.51 2.59
2145 6344 4.959839 TGCCCAACTACAGATGTGTATAGA 59.040 41.667 2.77 0.00 38.51 1.98
2178 6377 0.108138 AGGAAGCTGAATCGAACCGG 60.108 55.000 0.00 0.00 0.00 5.28
2334 6533 9.908152 CCACTTCCCTTATGTAAAACTTAAAAG 57.092 33.333 0.00 0.00 0.00 2.27
2370 6569 4.675146 CGAATGGCTTTGGTCCACTTAATG 60.675 45.833 0.00 0.00 36.26 1.90
2386 6585 3.291585 CAGAATAAATGACGCGAATGGC 58.708 45.455 15.93 0.00 38.69 4.40
2393 6592 4.427438 GCATTTGCAGAATAAATGACGC 57.573 40.909 11.37 0.00 44.37 5.19
2428 6627 9.595823 GTTATGTAATGTGTGGATAGTGTTACT 57.404 33.333 0.00 0.00 0.00 2.24
2435 6634 9.161629 TGTTTCAGTTATGTAATGTGTGGATAG 57.838 33.333 0.00 0.00 0.00 2.08
2475 6677 5.105146 TCAAGATGAAAAGAGAGCCTACCTC 60.105 44.000 0.00 0.00 41.07 3.85
2503 6706 5.123979 GCTAACCGAGTCTTTGAATTTCCAT 59.876 40.000 0.00 0.00 0.00 3.41
2511 6714 6.493802 AGGATATATGCTAACCGAGTCTTTGA 59.506 38.462 4.72 0.00 0.00 2.69
2521 6724 4.566004 TGCGACAAGGATATATGCTAACC 58.434 43.478 7.22 0.00 0.00 2.85
2525 6728 4.960938 TCTTTGCGACAAGGATATATGCT 58.039 39.130 0.04 0.04 0.00 3.79
2607 6810 0.036164 TCACCACAACAAGCCGCTAT 59.964 50.000 0.00 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.