Multiple sequence alignment - TraesCS2A01G464900

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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 TraesCS2A01G464900 chr2A 100.000 5640 0 0 1 5640 710091790 710097429 0.000000e+00 10416
1 TraesCS2A01G464900 chr2A 88.292 4706 518 15 951 5640 710035892 710040580 0.000000e+00 5607
2 TraesCS2A01G464900 chr2A 99.390 2458 13 2 1421 3877 709850411 709852867 0.000000e+00 4455
3 TraesCS2A01G464900 chr2A 94.473 1773 92 4 3872 5640 709858411 709860181 0.000000e+00 2726
4 TraesCS2A01G464900 chr2A 89.993 1439 89 27 1 1389 709848984 709850417 0.000000e+00 1808
5 TraesCS2A01G464900 chr2B 90.955 5716 397 69 1 5640 683041670 683047341 0.000000e+00 7581
6 TraesCS2A01G464900 chr2B 88.365 4753 520 23 910 5640 683067315 683072056 0.000000e+00 5683
7 TraesCS2A01G464900 chr2B 84.223 3334 475 31 1476 4772 683159759 683163078 0.000000e+00 3195
8 TraesCS2A01G464900 chr2B 84.759 2303 324 16 951 3236 683053771 683056063 0.000000e+00 2283
9 TraesCS2A01G464900 chr2B 86.405 1861 231 13 3246 5087 683130214 683132071 0.000000e+00 2015
10 TraesCS2A01G464900 chr2B 84.401 1795 257 14 1459 3236 683128386 683130174 0.000000e+00 1742
11 TraesCS2A01G464900 chr2B 88.355 833 97 0 4808 5640 683132069 683132901 0.000000e+00 1002
12 TraesCS2A01G464900 chr2B 82.128 1175 190 17 4479 5640 794691227 794690060 0.000000e+00 989
13 TraesCS2A01G464900 chr2B 82.128 1175 190 17 4479 5640 794800128 794798961 0.000000e+00 989
14 TraesCS2A01G464900 chr2B 89.310 449 42 5 910 1356 683127776 683128220 4.940000e-155 558
15 TraesCS2A01G464900 chr2D 88.313 4706 517 17 951 5640 571208678 571213366 0.000000e+00 5613
16 TraesCS2A01G464900 chr2D 86.513 4219 490 42 1462 5640 571195366 571199545 0.000000e+00 4566
17 TraesCS2A01G464900 chr2D 84.648 3335 464 30 1476 4772 571443443 571446767 0.000000e+00 3278
18 TraesCS2A01G464900 chr2D 87.437 1385 130 14 1 1356 571193824 571195193 0.000000e+00 1554
19 TraesCS2A01G464900 chr2D 84.436 559 68 11 146 687 645479943 645479387 2.990000e-147 532
20 TraesCS2A01G464900 chr2D 81.353 665 72 27 705 1346 571526372 571527007 1.410000e-135 494
21 TraesCS2A01G464900 chr6B 85.555 1793 215 20 1462 3236 717748721 717746955 0.000000e+00 1836
22 TraesCS2A01G464900 chr6B 84.615 559 67 11 146 687 149349745 149350301 6.430000e-149 538
23 TraesCS2A01G464900 chr6B 83.542 559 73 7 146 687 400794616 400795172 6.520000e-139 505
24 TraesCS2A01G464900 chr6A 85.369 1490 200 11 3254 4729 617078720 617080205 0.000000e+00 1528
25 TraesCS2A01G464900 chr6A 84.973 559 65 11 146 687 69497783 69497227 2.970000e-152 549
26 TraesCS2A01G464900 chr6A 84.615 559 66 12 146 687 402590055 402590610 6.430000e-149 538
27 TraesCS2A01G464900 chr6A 84.755 551 65 9 146 679 39895766 39895218 8.320000e-148 534
28 TraesCS2A01G464900 chr7A 84.615 559 67 11 146 687 476374025 476373469 6.430000e-149 538
29 TraesCS2A01G464900 chrUn 83.921 454 68 4 903 1356 332504373 332504821 4.040000e-116 429
30 TraesCS2A01G464900 chr7B 86.701 391 37 7 312 687 648997957 648997567 2.430000e-113 420
31 TraesCS2A01G464900 chr7B 86.118 389 39 2 312 685 65814932 65814544 6.800000e-109 405
32 TraesCS2A01G464900 chr3B 85.934 391 40 7 312 687 644366988 644367378 2.450000e-108 403


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 TraesCS2A01G464900 chr2A 710091790 710097429 5639 False 10416.00 10416 100.00000 1 5640 1 chr2A.!!$F3 5639
1 TraesCS2A01G464900 chr2A 710035892 710040580 4688 False 5607.00 5607 88.29200 951 5640 1 chr2A.!!$F2 4689
2 TraesCS2A01G464900 chr2A 709848984 709852867 3883 False 3131.50 4455 94.69150 1 3877 2 chr2A.!!$F4 3876
3 TraesCS2A01G464900 chr2A 709858411 709860181 1770 False 2726.00 2726 94.47300 3872 5640 1 chr2A.!!$F1 1768
4 TraesCS2A01G464900 chr2B 683041670 683047341 5671 False 7581.00 7581 90.95500 1 5640 1 chr2B.!!$F1 5639
5 TraesCS2A01G464900 chr2B 683067315 683072056 4741 False 5683.00 5683 88.36500 910 5640 1 chr2B.!!$F3 4730
6 TraesCS2A01G464900 chr2B 683159759 683163078 3319 False 3195.00 3195 84.22300 1476 4772 1 chr2B.!!$F4 3296
7 TraesCS2A01G464900 chr2B 683053771 683056063 2292 False 2283.00 2283 84.75900 951 3236 1 chr2B.!!$F2 2285
8 TraesCS2A01G464900 chr2B 683127776 683132901 5125 False 1329.25 2015 87.11775 910 5640 4 chr2B.!!$F5 4730
9 TraesCS2A01G464900 chr2B 794690060 794691227 1167 True 989.00 989 82.12800 4479 5640 1 chr2B.!!$R1 1161
10 TraesCS2A01G464900 chr2B 794798961 794800128 1167 True 989.00 989 82.12800 4479 5640 1 chr2B.!!$R2 1161
11 TraesCS2A01G464900 chr2D 571208678 571213366 4688 False 5613.00 5613 88.31300 951 5640 1 chr2D.!!$F1 4689
12 TraesCS2A01G464900 chr2D 571443443 571446767 3324 False 3278.00 3278 84.64800 1476 4772 1 chr2D.!!$F2 3296
13 TraesCS2A01G464900 chr2D 571193824 571199545 5721 False 3060.00 4566 86.97500 1 5640 2 chr2D.!!$F4 5639
14 TraesCS2A01G464900 chr2D 645479387 645479943 556 True 532.00 532 84.43600 146 687 1 chr2D.!!$R1 541
15 TraesCS2A01G464900 chr2D 571526372 571527007 635 False 494.00 494 81.35300 705 1346 1 chr2D.!!$F3 641
16 TraesCS2A01G464900 chr6B 717746955 717748721 1766 True 1836.00 1836 85.55500 1462 3236 1 chr6B.!!$R1 1774
17 TraesCS2A01G464900 chr6B 149349745 149350301 556 False 538.00 538 84.61500 146 687 1 chr6B.!!$F1 541
18 TraesCS2A01G464900 chr6B 400794616 400795172 556 False 505.00 505 83.54200 146 687 1 chr6B.!!$F2 541
19 TraesCS2A01G464900 chr6A 617078720 617080205 1485 False 1528.00 1528 85.36900 3254 4729 1 chr6A.!!$F2 1475
20 TraesCS2A01G464900 chr6A 69497227 69497783 556 True 549.00 549 84.97300 146 687 1 chr6A.!!$R2 541
21 TraesCS2A01G464900 chr6A 402590055 402590610 555 False 538.00 538 84.61500 146 687 1 chr6A.!!$F1 541
22 TraesCS2A01G464900 chr6A 39895218 39895766 548 True 534.00 534 84.75500 146 679 1 chr6A.!!$R1 533
23 TraesCS2A01G464900 chr7A 476373469 476374025 556 True 538.00 538 84.61500 146 687 1 chr7A.!!$R1 541

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
287 315 0.109919 TGCGCGTGCTCTATATACCG 60.110 55.000 23.16 0.0 43.34 4.02 F
373 410 0.540365 ATGGGTGCAAGGTTGTGGAG 60.540 55.000 0.00 0.0 0.00 3.86 F
568 617 1.132721 TCCAGGCTGCTATAGGACCAT 60.133 52.381 9.56 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2112 1.261354 CTCGTCTCTCTCTGCATCTCG 59.739 57.143 0.0 0.0 0.00 4.04 R
2119 2300 2.834113 AGTGTTAGCCCCACTACATCT 58.166 47.619 0.0 0.0 41.24 2.90 R
4912 5441 0.178992 CAAACTGCTGGTCCCTTCCA 60.179 55.000 0.0 0.0 36.00 3.53 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
18 19 2.003672 CGCGGGTATGAAAAGTCCG 58.996 57.895 0.00 0.00 43.13 4.79
50 53 9.860650 ATTTTGTACCATATATGTTGCTTCCTA 57.139 29.630 11.73 0.00 0.00 2.94
68 71 3.116512 TCCTAGGCCAGATTACCCATGTA 60.117 47.826 5.01 0.00 0.00 2.29
71 74 1.542547 GGCCAGATTACCCATGTACGG 60.543 57.143 0.00 0.00 0.00 4.02
103 106 2.636647 TGTGCTGTTTGGTCATCTGA 57.363 45.000 0.00 0.00 0.00 3.27
104 107 2.221169 TGTGCTGTTTGGTCATCTGAC 58.779 47.619 1.59 1.59 44.04 3.51
171 197 3.160269 ACTGCCTTCAGAATTTTGGAGG 58.840 45.455 17.43 17.43 45.31 4.30
212 238 1.806623 CGTTTGGGAATCTCTAGGCGG 60.807 57.143 0.00 0.00 0.00 6.13
213 239 1.209747 GTTTGGGAATCTCTAGGCGGT 59.790 52.381 0.00 0.00 0.00 5.68
287 315 0.109919 TGCGCGTGCTCTATATACCG 60.110 55.000 23.16 0.00 43.34 4.02
337 366 3.078891 AGAAACCCTCAAGATCAAGCC 57.921 47.619 0.00 0.00 0.00 4.35
373 410 0.540365 ATGGGTGCAAGGTTGTGGAG 60.540 55.000 0.00 0.00 0.00 3.86
401 450 6.662414 TTCTCATTAATTTGTCGCTAGGTG 57.338 37.500 0.00 0.00 0.00 4.00
446 495 4.276926 GGAGCCATCAACATCAAAGTATCC 59.723 45.833 0.00 0.00 0.00 2.59
520 569 2.504175 TCCCCTACTGCTTGTACCATTC 59.496 50.000 0.00 0.00 0.00 2.67
530 579 5.968254 TGCTTGTACCATTCGTTCAGTATA 58.032 37.500 0.00 0.00 0.00 1.47
568 617 1.132721 TCCAGGCTGCTATAGGACCAT 60.133 52.381 9.56 0.00 0.00 3.55
657 709 2.348666 CCATAAGCTCGTCTTTTCCACG 59.651 50.000 0.00 0.00 38.67 4.94
665 717 1.523758 GTCTTTTCCACGTGGCTGAT 58.476 50.000 30.25 0.00 34.44 2.90
674 726 2.418746 CCACGTGGCTGATAGCTAAGTT 60.419 50.000 24.02 0.00 40.97 2.66
679 731 4.681942 CGTGGCTGATAGCTAAGTTATGTC 59.318 45.833 0.00 0.00 41.99 3.06
680 732 4.991687 GTGGCTGATAGCTAAGTTATGTCC 59.008 45.833 0.00 0.00 41.99 4.02
700 770 7.181569 TGTCCATCAGTCAGTCATACAATAA 57.818 36.000 0.00 0.00 0.00 1.40
701 771 7.619965 TGTCCATCAGTCAGTCATACAATAAA 58.380 34.615 0.00 0.00 0.00 1.40
702 772 8.100164 TGTCCATCAGTCAGTCATACAATAAAA 58.900 33.333 0.00 0.00 0.00 1.52
749 820 5.429762 TGATCAAGGACTTCCATAGTTCCAT 59.570 40.000 0.00 0.00 37.17 3.41
1185 1282 4.087892 GCTGCTGCCGAGGGAAGA 62.088 66.667 3.85 0.00 26.79 2.87
1352 1449 9.260002 TCCATTTTTATTGCTTTCAGTTTCTTC 57.740 29.630 0.00 0.00 0.00 2.87
1934 2112 4.670347 GATTGAGTCTAAGGTGTACGGAC 58.330 47.826 0.00 0.00 0.00 4.79
2119 2300 5.335261 TGGGTCTGTGTATCCACTAACTTA 58.665 41.667 0.00 0.00 42.34 2.24
3857 4098 3.066342 GCTGACATTGATCAGGATGTTGG 59.934 47.826 13.04 10.27 45.35 3.77
4262 4512 2.874086 CTGCATGTTGTCAGAGTGTCAA 59.126 45.455 0.00 0.00 32.26 3.18
4646 4898 8.915057 TGATCTCTCTTTCAAGTGAATCTTTT 57.085 30.769 0.00 0.00 33.63 2.27
4912 5441 9.206690 TCTATCAATCAGTCAACCTAGAGAAAT 57.793 33.333 0.00 0.00 0.00 2.17
5052 5587 0.401395 TCTGGAGTTCTGTGGGGGTT 60.401 55.000 0.00 0.00 0.00 4.11
5054 5589 1.003233 CTGGAGTTCTGTGGGGGTTAC 59.997 57.143 0.00 0.00 0.00 2.50
5087 5622 3.439895 GGATTCACCTCTCTTACGGAC 57.560 52.381 0.00 0.00 35.41 4.79
5178 5716 3.610911 GAAGTTGGATTACTCCCACCAG 58.389 50.000 0.20 0.00 41.29 4.00
5189 5727 2.031120 CTCCCACCAGCACTTGAAAAA 58.969 47.619 0.00 0.00 0.00 1.94
5190 5728 2.031120 TCCCACCAGCACTTGAAAAAG 58.969 47.619 0.00 0.00 0.00 2.27
5209 5747 7.234782 TGAAAAAGTTACTATCAGTCCTCTCCA 59.765 37.037 0.00 0.00 0.00 3.86
5215 5753 5.930837 ACTATCAGTCCTCTCCAAGAAAG 57.069 43.478 0.00 0.00 0.00 2.62
5221 5759 1.023513 CCTCTCCAAGAAAGCCTGCG 61.024 60.000 0.00 0.00 0.00 5.18
5256 5794 0.695347 AGGCCTTCTCCACCTCAAAG 59.305 55.000 0.00 0.00 0.00 2.77
5259 5797 1.948144 GCCTTCTCCACCTCAAAGAGC 60.948 57.143 0.00 0.00 0.00 4.09
5267 5805 3.511934 TCCACCTCAAAGAGCTAAGTCTC 59.488 47.826 0.00 0.00 0.00 3.36
5312 5850 2.691409 TACAGCTGCATTCCTGTACC 57.309 50.000 15.27 0.00 42.02 3.34
5313 5851 0.987294 ACAGCTGCATTCCTGTACCT 59.013 50.000 15.27 0.00 40.30 3.08
5320 5858 2.292918 TGCATTCCTGTACCTCCCTAGT 60.293 50.000 0.00 0.00 0.00 2.57
5366 5904 2.294078 GCTGGCTGTACTGGAGGGT 61.294 63.158 1.65 0.00 0.00 4.34
5492 6030 2.125350 CAGCTGCTTCCTCCGTCC 60.125 66.667 0.00 0.00 0.00 4.79
5580 6118 3.814842 TGCCATCACCAAATTAGCGATAG 59.185 43.478 0.00 0.00 0.00 2.08
5600 6138 2.380084 GGCGTAGTCCAGAATTGACA 57.620 50.000 0.00 0.00 35.15 3.58
5630 6168 2.125147 GGATGCTGCACGGCACTA 60.125 61.111 3.57 0.00 45.36 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.697045 ACAAAATCACCACGGACTTTTCA 59.303 39.130 0.00 0.00 0.00 2.69
37 38 2.477245 TCTGGCCTAGGAAGCAACATA 58.523 47.619 14.75 0.00 0.00 2.29
50 53 1.416401 CGTACATGGGTAATCTGGCCT 59.584 52.381 3.32 0.00 0.00 5.19
68 71 0.321671 CACATCCACTTGGTCTCCGT 59.678 55.000 0.00 0.00 36.34 4.69
71 74 1.271054 ACAGCACATCCACTTGGTCTC 60.271 52.381 0.00 0.00 36.34 3.36
212 238 1.651987 TCGATTCCTTGAATGCGGAC 58.348 50.000 0.00 0.00 31.89 4.79
213 239 2.006888 GTTCGATTCCTTGAATGCGGA 58.993 47.619 0.00 0.00 31.89 5.54
287 315 9.490663 CAACCTTGTATCTATCGACAAAATTTC 57.509 33.333 0.00 0.00 35.24 2.17
337 366 5.504665 GCACCCATCGACAAATTAATGAGAG 60.505 44.000 0.00 0.00 0.00 3.20
373 410 6.124088 AGCGACAAATTAATGAGAATGGTC 57.876 37.500 0.00 0.00 0.00 4.02
446 495 7.144000 GCTAGGCTTAAATTGAATCCTCATTG 58.856 38.462 0.90 0.00 0.00 2.82
485 534 2.649531 AGGGGACAAAACATCACGAA 57.350 45.000 0.00 0.00 0.00 3.85
487 536 2.742053 CAGTAGGGGACAAAACATCACG 59.258 50.000 0.00 0.00 0.00 4.35
520 569 4.381863 GTGGACGCATATGTATACTGAACG 59.618 45.833 4.29 4.65 0.00 3.95
530 579 2.170397 TGGAATCTGTGGACGCATATGT 59.830 45.455 4.29 0.00 0.00 2.29
657 709 4.991687 GGACATAACTTAGCTATCAGCCAC 59.008 45.833 0.00 0.00 43.77 5.01
665 717 6.607600 ACTGACTGATGGACATAACTTAGCTA 59.392 38.462 0.00 0.00 0.00 3.32
674 726 6.790232 TTGTATGACTGACTGATGGACATA 57.210 37.500 0.00 0.00 0.00 2.29
679 731 8.393366 CACTTTTATTGTATGACTGACTGATGG 58.607 37.037 0.00 0.00 0.00 3.51
680 732 7.907045 GCACTTTTATTGTATGACTGACTGATG 59.093 37.037 0.00 0.00 0.00 3.07
700 770 1.598130 GGCTCCACAGTCGCACTTT 60.598 57.895 0.00 0.00 0.00 2.66
701 771 2.031163 GGCTCCACAGTCGCACTT 59.969 61.111 0.00 0.00 0.00 3.16
702 772 2.721971 CTTGGCTCCACAGTCGCACT 62.722 60.000 0.00 0.00 0.00 4.40
769 840 2.679092 CCCCTCATGGCAAGCTCA 59.321 61.111 0.00 0.00 0.00 4.26
1185 1282 4.467769 CCAGAGGCATATTGTCAATCCTT 58.532 43.478 0.07 0.00 0.00 3.36
1352 1449 8.301720 TCTTGGTTACATATTACGCCTACATAG 58.698 37.037 0.00 0.00 0.00 2.23
1934 2112 1.261354 CTCGTCTCTCTCTGCATCTCG 59.739 57.143 0.00 0.00 0.00 4.04
1983 2161 5.164620 TGGCAGAACATTCAGATCACTAA 57.835 39.130 0.00 0.00 0.00 2.24
2119 2300 2.834113 AGTGTTAGCCCCACTACATCT 58.166 47.619 0.00 0.00 41.24 2.90
4912 5441 0.178992 CAAACTGCTGGTCCCTTCCA 60.179 55.000 0.00 0.00 36.00 3.53
5052 5587 3.089284 TGAATCCTGCGAAGTCTCTGTA 58.911 45.455 0.00 0.00 0.00 2.74
5054 5589 2.266554 GTGAATCCTGCGAAGTCTCTG 58.733 52.381 0.00 0.00 0.00 3.35
5178 5716 7.173390 AGGACTGATAGTAACTTTTTCAAGTGC 59.827 37.037 0.00 0.00 42.89 4.40
5189 5727 6.080969 TCTTGGAGAGGACTGATAGTAACT 57.919 41.667 0.00 0.00 0.00 2.24
5190 5728 6.777213 TTCTTGGAGAGGACTGATAGTAAC 57.223 41.667 0.00 0.00 0.00 2.50
5221 5759 0.035915 GCCTTGAGGAGTGAAGGACC 60.036 60.000 0.06 0.00 41.26 4.46
5256 5794 4.130857 GGGCCATAAAAGAGACTTAGCTC 58.869 47.826 4.39 0.00 35.11 4.09
5259 5797 5.440610 ACATGGGCCATAAAAGAGACTTAG 58.559 41.667 20.73 4.33 0.00 2.18
5267 5805 5.047092 AGACTTCAAACATGGGCCATAAAAG 60.047 40.000 20.73 18.35 0.00 2.27
5320 5858 1.457643 CCCGTGATCCCTAGCTCCA 60.458 63.158 0.00 0.00 0.00 3.86
5366 5904 0.110486 GGGAGGTGAGGAACTGCAAA 59.890 55.000 0.00 0.00 41.55 3.68
5492 6030 4.578105 GCCCTGATCTCAAGTTTATCAAGG 59.422 45.833 0.00 0.00 35.29 3.61
5580 6118 1.066430 TGTCAATTCTGGACTACGCCC 60.066 52.381 0.00 0.00 36.26 6.13
5600 6138 2.100128 AGCATCCCAGCTGTAGAGAT 57.900 50.000 13.81 6.47 44.66 2.75


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

AutoCloner maintained by Alex Coulton.