Multiple sequence alignment - TraesCS3B01G190700

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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 TraesCS3B01G190700 chr3B 100.000 3166 0 0 1 3166 203611937 203615102 0.000000e+00 5847.0
1 TraesCS3B01G190700 chr3B 78.274 336 70 3 1283 1617 15177920 15177587 2.470000e-51 213.0
2 TraesCS3B01G190700 chr3B 86.747 83 11 0 2503 2585 443688221 443688139 3.360000e-15 93.5
3 TraesCS3B01G190700 chr4D 89.400 2585 189 37 8 2551 375115158 375117698 0.000000e+00 3177.0
4 TraesCS3B01G190700 chr4D 81.023 743 113 17 1283 2018 414328434 414327713 1.650000e-157 566.0
5 TraesCS3B01G190700 chr4D 88.148 135 16 0 1151 1285 414350004 414349870 9.090000e-36 161.0
6 TraesCS3B01G190700 chr4D 86.364 154 14 5 1134 1285 414365609 414365461 9.090000e-36 161.0
7 TraesCS3B01G190700 chr4D 86.000 150 21 0 1136 1285 414371368 414371219 9.090000e-36 161.0
8 TraesCS3B01G190700 chr4D 85.526 152 15 5 1136 1285 414337232 414337086 5.470000e-33 152.0
9 TraesCS3B01G190700 chr3A 87.537 2728 235 47 478 3161 160015926 160018592 0.000000e+00 3057.0
10 TraesCS3B01G190700 chr3A 89.299 1626 127 25 679 2280 159994937 159996539 0.000000e+00 1995.0
11 TraesCS3B01G190700 chr3A 79.534 601 77 13 2593 3161 160003587 160004173 1.380000e-103 387.0
12 TraesCS3B01G190700 chr3A 89.286 308 29 3 342 649 159994634 159994937 1.780000e-102 383.0
13 TraesCS3B01G190700 chr3A 81.548 336 62 0 1283 1618 17485259 17484924 8.650000e-71 278.0
14 TraesCS3B01G190700 chr3A 80.952 336 64 0 1283 1618 17433633 17433968 1.870000e-67 267.0
15 TraesCS3B01G190700 chr3D 89.328 1771 132 24 478 2221 141649958 141651698 0.000000e+00 2170.0
16 TraesCS3B01G190700 chr3D 89.922 774 57 11 2215 2980 141652494 141653254 0.000000e+00 977.0
17 TraesCS3B01G190700 chr3D 87.048 525 40 15 1 500 141451346 141451867 4.580000e-158 568.0
18 TraesCS3B01G190700 chr3D 90.419 334 23 6 482 810 141596788 141597117 6.270000e-117 431.0
19 TraesCS3B01G190700 chr3D 93.782 193 9 3 2971 3161 141653822 141654013 1.440000e-73 287.0
20 TraesCS3B01G190700 chr3D 84.444 90 13 1 2499 2587 343498126 343498037 1.560000e-13 87.9
21 TraesCS3B01G190700 chr4B 80.972 741 117 15 1283 2018 510434778 510434057 1.650000e-157 566.0
22 TraesCS3B01G190700 chr4B 79.079 717 124 16 1283 1995 510562431 510561737 1.330000e-128 470.0
23 TraesCS3B01G190700 chr4B 87.097 155 13 5 1133 1285 510482217 510482068 5.430000e-38 169.0
24 TraesCS3B01G190700 chr4A 80.972 741 111 19 1283 2018 49200043 49200758 7.670000e-156 560.0
25 TraesCS3B01G190700 chr2D 88.043 92 11 0 2496 2587 544207181 544207272 3.340000e-20 110.0
26 TraesCS3B01G190700 chr7A 84.946 93 13 1 2496 2587 204173421 204173329 3.360000e-15 93.5
27 TraesCS3B01G190700 chr6B 84.270 89 12 2 2500 2587 35374111 35374024 5.630000e-13 86.1
28 TraesCS3B01G190700 chr7D 89.231 65 7 0 2522 2586 185911153 185911217 7.280000e-12 82.4
29 TraesCS3B01G190700 chr1B 83.146 89 14 1 2498 2585 111915863 111915951 2.620000e-11 80.5


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 TraesCS3B01G190700 chr3B 203611937 203615102 3165 False 5847.000000 5847 100.000000 1 3166 1 chr3B.!!$F1 3165
1 TraesCS3B01G190700 chr4D 375115158 375117698 2540 False 3177.000000 3177 89.400000 8 2551 1 chr4D.!!$F1 2543
2 TraesCS3B01G190700 chr4D 414327713 414328434 721 True 566.000000 566 81.023000 1283 2018 1 chr4D.!!$R1 735
3 TraesCS3B01G190700 chr3A 160015926 160018592 2666 False 3057.000000 3057 87.537000 478 3161 1 chr3A.!!$F3 2683
4 TraesCS3B01G190700 chr3A 159994634 159996539 1905 False 1189.000000 1995 89.292500 342 2280 2 chr3A.!!$F4 1938
5 TraesCS3B01G190700 chr3A 160003587 160004173 586 False 387.000000 387 79.534000 2593 3161 1 chr3A.!!$F2 568
6 TraesCS3B01G190700 chr3D 141649958 141654013 4055 False 1144.666667 2170 91.010667 478 3161 3 chr3D.!!$F3 2683
7 TraesCS3B01G190700 chr3D 141451346 141451867 521 False 568.000000 568 87.048000 1 500 1 chr3D.!!$F1 499
8 TraesCS3B01G190700 chr4B 510434057 510434778 721 True 566.000000 566 80.972000 1283 2018 1 chr4B.!!$R1 735
9 TraesCS3B01G190700 chr4B 510561737 510562431 694 True 470.000000 470 79.079000 1283 1995 1 chr4B.!!$R3 712
10 TraesCS3B01G190700 chr4A 49200043 49200758 715 False 560.000000 560 80.972000 1283 2018 1 chr4A.!!$F1 735


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
344 371 0.601841 AAGACGTGCGACCCGAAAAT 60.602 50.0 0.0 0.0 0.0 1.82 F
1198 1275 0.032952 GTTCGTCTGCTGTGGGTGTA 59.967 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 1490 0.392863 CACCACATCGGATCTGCCAA 60.393 55.0 0.00 0.00 38.63 4.52 R
3080 4590 0.030638 CCGCCACAAAGTTTGGAGTG 59.969 55.0 19.45 15.03 36.02 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
103 104 6.803154 AAAGTAGCTAAGATTTGTGTGGTC 57.197 37.500 0.00 0.00 0.00 4.02
104 105 5.746990 AGTAGCTAAGATTTGTGTGGTCT 57.253 39.130 0.00 0.00 0.00 3.85
253 278 1.565156 GCTGGCACAACGAACGATCA 61.565 55.000 0.14 0.00 38.70 2.92
304 330 1.535462 CGCATTGAAGAAGAACGGGTT 59.465 47.619 0.00 0.00 0.00 4.11
314 340 1.179814 AGAACGGGTTGAGCGAGACT 61.180 55.000 0.00 0.00 0.00 3.24
330 357 1.597700 GACTGCGTGACGACAAGACG 61.598 60.000 10.10 0.00 39.31 4.18
344 371 0.601841 AAGACGTGCGACCCGAAAAT 60.602 50.000 0.00 0.00 0.00 1.82
361 388 5.278758 CCGAAAATGCACTAAAGGGAAAAGA 60.279 40.000 0.00 0.00 0.00 2.52
380 407 7.169813 GGAAAAGACCAAACAATCAACTGATTC 59.830 37.037 1.87 0.00 42.41 2.52
414 441 2.223112 CGGTGAGATCCGCAAAGAAATG 60.223 50.000 0.00 0.00 43.96 2.32
431 458 4.530553 AGAAATGGGACGGCCTAAAAATTT 59.469 37.500 7.57 6.21 0.00 1.82
434 461 3.436243 TGGGACGGCCTAAAAATTTGAT 58.564 40.909 7.57 0.00 0.00 2.57
455 482 6.995364 TGATCTGAAGCCAAATCAAAATCAA 58.005 32.000 0.00 0.00 0.00 2.57
457 484 8.098286 TGATCTGAAGCCAAATCAAAATCAATT 58.902 29.630 0.00 0.00 0.00 2.32
458 485 9.590451 GATCTGAAGCCAAATCAAAATCAATTA 57.410 29.630 0.00 0.00 0.00 1.40
526 554 3.487202 CGCCGTCGATGTTGTGGG 61.487 66.667 3.52 0.00 38.10 4.61
545 573 2.044555 CCAGGTGCAGTGCAGGATG 61.045 63.158 20.42 16.64 40.08 3.51
569 600 3.552541 CCGTACGATTCGAGGAACATAG 58.447 50.000 18.76 0.00 0.00 2.23
595 626 2.019807 TCCTTTCGTAGACAAGGGGT 57.980 50.000 0.00 0.00 41.63 4.95
627 658 1.523938 GACATCCCAAGGTAGGCGC 60.524 63.158 0.00 0.00 0.00 6.53
641 672 2.489938 AGGCGCCAAGAAAGTCAATA 57.510 45.000 31.54 0.00 0.00 1.90
642 673 3.004752 AGGCGCCAAGAAAGTCAATAT 57.995 42.857 31.54 0.00 0.00 1.28
696 727 5.082059 CGTCAAGCATACACATCTGAAAAC 58.918 41.667 0.00 0.00 0.00 2.43
811 845 8.807948 AAACAACCAGTGATATAATGCTAACT 57.192 30.769 0.00 0.00 0.00 2.24
813 847 8.438676 ACAACCAGTGATATAATGCTAACTTC 57.561 34.615 0.00 0.00 0.00 3.01
1027 1089 2.519771 AGCCATCAGAAGCAAATCCA 57.480 45.000 0.00 0.00 0.00 3.41
1061 1125 4.452455 ACGAACAAACAGATAGGCAAAGAG 59.548 41.667 0.00 0.00 0.00 2.85
1198 1275 0.032952 GTTCGTCTGCTGTGGGTGTA 59.967 55.000 0.00 0.00 0.00 2.90
1446 1525 1.891919 GTGCAAACCAGGCGTCTCA 60.892 57.895 0.00 0.00 0.00 3.27
1628 1711 3.758554 AGGTACACATGCATGAGTTTTCC 59.241 43.478 32.75 27.04 33.68 3.13
1739 1826 0.672401 GGGTGCGGTTCAAGATCGAA 60.672 55.000 0.00 0.00 0.00 3.71
1742 1829 1.019278 TGCGGTTCAAGATCGAAGGC 61.019 55.000 0.00 0.00 0.00 4.35
1775 1862 5.670792 TCAACCTAGTTACCGTGATGAAT 57.329 39.130 0.00 0.00 0.00 2.57
1832 1919 3.990469 TCAAGAGCTCTGATTCAAACGAC 59.010 43.478 19.06 0.00 0.00 4.34
1839 1926 4.248859 CTCTGATTCAAACGACTGGATGT 58.751 43.478 0.00 0.00 0.00 3.06
2040 2129 7.872993 TCTCCGGTGATCAATTTAGAATATGAC 59.127 37.037 0.00 0.00 0.00 3.06
2041 2130 6.934645 TCCGGTGATCAATTTAGAATATGACC 59.065 38.462 0.00 0.00 0.00 4.02
2053 2142 5.097742 AGAATATGACCGGTTCATGAACA 57.902 39.130 33.42 17.50 45.22 3.18
2061 2153 5.163248 TGACCGGTTCATGAACATACCATAT 60.163 40.000 33.42 13.86 42.85 1.78
2062 2154 5.690865 ACCGGTTCATGAACATACCATATT 58.309 37.500 33.42 9.37 42.85 1.28
2115 2207 2.666272 TTGTGCCCTGGTGTTCAATA 57.334 45.000 0.00 0.00 0.00 1.90
2205 2300 9.708222 CTTGTATGTGATTAACTTGTTCTATGC 57.292 33.333 0.00 0.00 0.00 3.14
2267 3164 5.462530 TGACTGATTCTACCGAGTTTCAA 57.537 39.130 0.00 0.00 0.00 2.69
2312 3210 8.646900 ACTTGTGGAAACCAACATTTATAACAT 58.353 29.630 0.00 0.00 34.18 2.71
2332 3230 6.047511 ACATTATAAGGCAAAATGGTTGCA 57.952 33.333 12.66 0.00 46.58 4.08
2481 3380 1.599071 CAACGGAATGTGATCGGATGG 59.401 52.381 0.00 0.00 0.00 3.51
2486 3385 3.242739 CGGAATGTGATCGGATGGTTTTC 60.243 47.826 0.00 0.00 0.00 2.29
2488 3387 4.035675 GGAATGTGATCGGATGGTTTTCTC 59.964 45.833 0.00 0.00 0.00 2.87
2490 3389 3.861840 TGTGATCGGATGGTTTTCTCTC 58.138 45.455 0.00 0.00 0.00 3.20
2515 3414 0.109723 CGAAAAGGAGGACAACCCCA 59.890 55.000 0.00 0.00 36.73 4.96
2553 3454 6.088719 CGGTGCGCACAATTATTTTTATTT 57.911 33.333 38.60 0.00 0.00 1.40
2554 3455 6.529696 CGGTGCGCACAATTATTTTTATTTT 58.470 32.000 38.60 0.00 0.00 1.82
2650 3556 7.076842 TGAGTTCAAGTTCTCACTTTTCTTG 57.923 36.000 0.00 0.00 40.66 3.02
2690 3596 4.771590 ATGTTGTCCACATAAAGCACAG 57.228 40.909 0.00 0.00 45.00 3.66
2704 3611 8.076178 ACATAAAGCACAGTACATCAGAAAAAC 58.924 33.333 0.00 0.00 0.00 2.43
2739 3646 6.616237 ATCCCAAAGAAAGCAAATCATCTT 57.384 33.333 0.00 0.00 33.73 2.40
2824 3738 9.631257 ACACACATATCTCATCCATTAAATCAA 57.369 29.630 0.00 0.00 0.00 2.57
2834 3748 9.941664 CTCATCCATTAAATCAACATAACTGTC 57.058 33.333 0.00 0.00 33.36 3.51
2967 3897 2.102252 GTCCAAGGTGGTCAAATGCAAA 59.898 45.455 0.00 0.00 39.03 3.68
2972 4479 5.337410 CCAAGGTGGTCAAATGCAAATATGA 60.337 40.000 0.00 0.00 31.35 2.15
3133 4645 5.661458 AGTGTACACGGGAGATAAATCAAG 58.339 41.667 19.93 0.00 36.20 3.02
3161 4673 9.344772 ACAAGACCTACAATACAACACAAAATA 57.655 29.630 0.00 0.00 0.00 1.40
3164 4676 9.959721 AGACCTACAATACAACACAAAATATCT 57.040 29.630 0.00 0.00 0.00 1.98
3165 4677 9.988350 GACCTACAATACAACACAAAATATCTG 57.012 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 2.834549 GAGGGAGGAGTGTCAGATTCAA 59.165 50.000 0.00 0.00 0.00 2.69
249 274 2.768834 GGAGAGGCCGTTGTTGATC 58.231 57.895 0.00 0.00 0.00 2.92
304 330 2.255554 GTCACGCAGTCTCGCTCA 59.744 61.111 0.00 0.00 41.61 4.26
314 340 1.942223 CACGTCTTGTCGTCACGCA 60.942 57.895 0.00 0.00 42.27 5.24
330 357 1.442017 GTGCATTTTCGGGTCGCAC 60.442 57.895 0.00 0.00 45.25 5.34
344 371 3.586470 TGGTCTTTTCCCTTTAGTGCA 57.414 42.857 0.00 0.00 0.00 4.57
361 388 5.106157 GGATCGAATCAGTTGATTGTTTGGT 60.106 40.000 11.81 0.00 44.14 3.67
380 407 3.478394 CACCGTGCACGTGGATCG 61.478 66.667 34.81 21.74 46.00 3.69
414 441 3.699538 AGATCAAATTTTTAGGCCGTCCC 59.300 43.478 0.00 0.00 0.00 4.46
431 458 6.593268 TGATTTTGATTTGGCTTCAGATCA 57.407 33.333 0.00 0.00 39.34 2.92
434 461 9.206870 GTTAATTGATTTTGATTTGGCTTCAGA 57.793 29.630 0.00 0.00 0.00 3.27
526 554 3.933048 ATCCTGCACTGCACCTGGC 62.933 63.158 0.00 0.00 45.13 4.85
545 573 0.379669 TTCCTCGAATCGTACGGCTC 59.620 55.000 16.52 11.08 0.00 4.70
569 600 4.425520 CTTGTCTACGAAAGGATGTCTCC 58.574 47.826 0.00 0.00 42.43 3.71
595 626 1.002257 ATGTCCATGTTCGGCTGCA 60.002 52.632 0.50 0.00 0.00 4.41
660 691 7.429920 GTGTATGCTTGACGTTTTCACTTTTAA 59.570 33.333 0.00 0.00 32.26 1.52
661 692 6.908284 GTGTATGCTTGACGTTTTCACTTTTA 59.092 34.615 0.00 0.00 32.26 1.52
663 694 5.163703 TGTGTATGCTTGACGTTTTCACTTT 60.164 36.000 0.00 0.00 32.26 2.66
664 695 4.334203 TGTGTATGCTTGACGTTTTCACTT 59.666 37.500 0.00 0.00 32.26 3.16
665 696 3.874543 TGTGTATGCTTGACGTTTTCACT 59.125 39.130 0.00 0.00 32.26 3.41
768 799 6.587608 GGTTGTTTATTGATCTTTGCTTCAGG 59.412 38.462 0.00 0.00 0.00 3.86
769 800 7.147312 TGGTTGTTTATTGATCTTTGCTTCAG 58.853 34.615 0.00 0.00 0.00 3.02
1027 1089 1.400494 GTTTGTTCGTGTGCTTCAGGT 59.600 47.619 0.00 0.00 34.10 4.00
1061 1125 0.321919 TGAATCTGGGAGCTGTGTGC 60.322 55.000 0.00 0.00 43.29 4.57
1198 1275 4.652131 TTTGTCCGCGGCCATGGT 62.652 61.111 23.51 0.00 0.00 3.55
1348 1425 1.154413 CATCGTTGAACAGCACCGC 60.154 57.895 0.00 0.00 31.87 5.68
1365 1442 4.262089 TGTCCACATGCCGCACCA 62.262 61.111 0.00 0.00 0.00 4.17
1411 1490 0.392863 CACCACATCGGATCTGCCAA 60.393 55.000 0.00 0.00 38.63 4.52
1446 1525 4.295119 GTGGCCGTCACCGTCACT 62.295 66.667 0.00 0.00 40.39 3.41
1524 1603 1.331214 CCATGTCAAAGTGTGGCCTT 58.669 50.000 3.32 0.00 0.00 4.35
1615 1698 7.288810 ACAATCTTTTAGGAAAACTCATGCA 57.711 32.000 0.00 0.00 0.00 3.96
1684 1771 2.397044 TGGGACCCTGCAGAAAAATT 57.603 45.000 17.39 0.00 0.00 1.82
1739 1826 1.628846 AGGTTGAAGTAATCGTGGCCT 59.371 47.619 3.32 0.00 0.00 5.19
1742 1829 5.809051 GGTAACTAGGTTGAAGTAATCGTGG 59.191 44.000 0.00 0.00 0.00 4.94
1832 1919 2.936498 GTTACGGGACATTGACATCCAG 59.064 50.000 0.00 0.00 36.65 3.86
2040 2129 6.633500 AAATATGGTATGTTCATGAACCGG 57.367 37.500 30.66 0.00 40.46 5.28
2041 2130 8.148807 TGTAAATATGGTATGTTCATGAACCG 57.851 34.615 30.66 0.00 40.46 4.44
2088 2180 4.972751 ACACCAGGGCACAAATAAATTT 57.027 36.364 0.00 0.00 0.00 1.82
2312 3210 4.874966 GCATGCAACCATTTTGCCTTATAA 59.125 37.500 14.21 0.00 44.32 0.98
2481 3380 5.774630 TCCTTTTCGAGAGAGAGAGAAAAC 58.225 41.667 0.00 0.00 43.69 2.43
2486 3385 3.377172 GTCCTCCTTTTCGAGAGAGAGAG 59.623 52.174 1.20 3.36 43.69 3.20
2488 3387 3.085533 TGTCCTCCTTTTCGAGAGAGAG 58.914 50.000 1.20 5.57 43.69 3.20
2490 3389 3.580731 GTTGTCCTCCTTTTCGAGAGAG 58.419 50.000 1.20 0.00 43.69 3.20
2681 3587 7.282224 AGTGTTTTTCTGATGTACTGTGCTTTA 59.718 33.333 0.00 0.00 0.00 1.85
2690 3596 7.421530 TTCTAGCAGTGTTTTTCTGATGTAC 57.578 36.000 0.00 0.00 35.20 2.90
2704 3611 5.964958 TTCTTTGGGATTTTCTAGCAGTG 57.035 39.130 0.00 0.00 0.00 3.66
2739 3646 5.733620 AAGAGTTTCTTGTATCCACGGTA 57.266 39.130 0.00 0.00 34.98 4.02
2764 3671 5.860941 AATGGTCATGGACTACTAGTGAG 57.139 43.478 5.39 1.88 32.47 3.51
2824 3738 8.918202 TTGTGATTTTCTAAGGACAGTTATGT 57.082 30.769 0.00 0.00 44.31 2.29
2830 3744 7.361542 CCAGTGATTGTGATTTTCTAAGGACAG 60.362 40.741 0.00 0.00 0.00 3.51
2834 3748 6.824305 ACCAGTGATTGTGATTTTCTAAGG 57.176 37.500 0.00 0.00 0.00 2.69
2967 3897 6.403636 GCTTTTCGTTGGTCATGAAGTCATAT 60.404 38.462 0.00 0.00 34.26 1.78
2972 4479 2.948979 TGCTTTTCGTTGGTCATGAAGT 59.051 40.909 0.00 0.00 31.71 3.01
3080 4590 0.030638 CCGCCACAAAGTTTGGAGTG 59.969 55.000 19.45 15.03 36.02 3.51
3133 4645 7.718272 TTGTGTTGTATTGTAGGTCTTGTAC 57.282 36.000 0.00 0.00 0.00 2.90



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

AutoCloner maintained by Alex Coulton.