Multiple sequence alignment - TraesCS2A01G581500

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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 TraesCS2A01G581500 chr2A 100.000 2600 0 0 1 2600 773564428 773561829 0.000000e+00 4802.0
1 TraesCS2A01G581500 chr2A 95.124 2625 79 18 1 2600 773584026 773581426 0.000000e+00 4093.0
2 TraesCS2A01G581500 chr2A 89.663 1306 112 14 807 2102 771772319 771773611 0.000000e+00 1642.0
3 TraesCS2A01G581500 chr2A 83.564 505 54 16 2108 2600 771773575 771774062 1.840000e-121 446.0
4 TraesCS2A01G581500 chr2A 79.699 399 41 14 441 809 771765782 771766170 4.300000e-63 252.0
5 TraesCS2A01G581500 chr2B 87.336 2282 219 23 356 2600 789565238 789562990 0.000000e+00 2549.0
6 TraesCS2A01G581500 chr2B 79.688 1408 219 50 356 1717 789561624 789560238 0.000000e+00 953.0
7 TraesCS2A01G581500 chr2B 79.066 707 140 8 930 1632 697228890 697228188 1.810000e-131 479.0
8 TraesCS2A01G581500 chr2B 78.895 706 144 5 930 1632 697142691 697141988 8.420000e-130 473.0
9 TraesCS2A01G581500 chr2B 78.895 706 144 5 930 1632 697379093 697378390 8.420000e-130 473.0
10 TraesCS2A01G581500 chr2B 92.222 90 7 0 198 287 789565713 789565624 7.550000e-26 128.0
11 TraesCS2A01G581500 chr2D 87.617 1704 148 28 441 2102 645958030 645959712 0.000000e+00 1919.0
12 TraesCS2A01G581500 chr2D 79.364 1415 227 40 356 1717 645961557 645962959 0.000000e+00 935.0
13 TraesCS2A01G581500 chr2D 85.644 202 26 2 1 199 645993018 645993219 2.620000e-50 209.0
14 TraesCS2A01G581500 chr7D 79.503 322 46 9 2288 2600 174985843 174985533 7.290000e-51 211.0
15 TraesCS2A01G581500 chr7D 81.726 197 26 8 2292 2487 338856031 338855844 3.460000e-34 156.0
16 TraesCS2A01G581500 chr4A 83.500 200 25 6 2292 2487 9610311 9610116 2.060000e-41 180.0
17 TraesCS2A01G581500 chr5B 88.971 136 14 1 2354 2488 432703857 432703992 1.600000e-37 167.0
18 TraesCS2A01G581500 chr5D 83.871 155 23 1 2333 2487 130216370 130216218 2.090000e-31 147.0
19 TraesCS2A01G581500 chr3A 79.500 200 37 3 1 197 71064200 71064002 3.490000e-29 139.0
20 TraesCS2A01G581500 chr3A 97.500 40 1 0 2282 2321 669183677 669183716 4.640000e-08 69.4
21 TraesCS2A01G581500 chr4B 81.609 174 25 3 2364 2530 385620584 385620757 1.250000e-28 137.0
22 TraesCS2A01G581500 chr1B 83.495 103 14 3 9 110 303677314 303677414 2.750000e-15 93.5
23 TraesCS2A01G581500 chr1B 83.000 100 17 0 41 140 402978998 402979097 9.910000e-15 91.6
24 TraesCS2A01G581500 chr1B 80.531 113 20 2 42 153 354245226 354245337 4.610000e-13 86.1
25 TraesCS2A01G581500 chr6D 79.208 101 20 1 10 110 133714108 133714207 4.640000e-08 69.4
26 TraesCS2A01G581500 chr7A 97.436 39 1 0 2283 2321 197500131 197500169 1.670000e-07 67.6
27 TraesCS2A01G581500 chr7B 100.000 31 0 0 41 71 638056546 638056576 1.000000e-04 58.4


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 TraesCS2A01G581500 chr2A 773561829 773564428 2599 True 4802 4802 100.000000 1 2600 1 chr2A.!!$R1 2599
1 TraesCS2A01G581500 chr2A 773581426 773584026 2600 True 4093 4093 95.124000 1 2600 1 chr2A.!!$R2 2599
2 TraesCS2A01G581500 chr2A 771772319 771774062 1743 False 1044 1642 86.613500 807 2600 2 chr2A.!!$F2 1793
3 TraesCS2A01G581500 chr2B 789560238 789565713 5475 True 1210 2549 86.415333 198 2600 3 chr2B.!!$R4 2402
4 TraesCS2A01G581500 chr2B 697228188 697228890 702 True 479 479 79.066000 930 1632 1 chr2B.!!$R2 702
5 TraesCS2A01G581500 chr2B 697141988 697142691 703 True 473 473 78.895000 930 1632 1 chr2B.!!$R1 702
6 TraesCS2A01G581500 chr2B 697378390 697379093 703 True 473 473 78.895000 930 1632 1 chr2B.!!$R3 702
7 TraesCS2A01G581500 chr2D 645958030 645962959 4929 False 1427 1919 83.490500 356 2102 2 chr2D.!!$F2 1746

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
162 163 0.830444 TGTCCGTGGACTAGTGCCTT 60.830 55.0 19.17 0.00 44.8 4.35 F
1135 1487 0.306533 TGTCTTCCGCGCAAAGTTTC 59.693 50.0 8.75 6.68 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 1613 0.033208 GATTGGCTCCCACCCATTCA 60.033 55.0 0.00 0.00 34.48 2.57 R
2538 2917 0.749091 GTGTGCATATGCCTGGCTCA 60.749 55.0 24.54 7.77 41.18 4.26 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
73 74 2.503331 TCCATCGTGTTTGCATGAGTT 58.497 42.857 0.00 0.00 43.11 3.01
74 75 2.884012 TCCATCGTGTTTGCATGAGTTT 59.116 40.909 0.00 0.00 43.11 2.66
75 76 3.317711 TCCATCGTGTTTGCATGAGTTTT 59.682 39.130 0.00 0.00 43.11 2.43
92 93 7.455641 TGAGTTTTGTCTGGTTAGTTCAAAA 57.544 32.000 0.00 0.00 36.97 2.44
148 149 1.739466 CAACTCCCACATTCATGTCCG 59.261 52.381 0.00 0.00 39.39 4.79
149 150 0.984230 ACTCCCACATTCATGTCCGT 59.016 50.000 0.00 0.00 39.39 4.69
162 163 0.830444 TGTCCGTGGACTAGTGCCTT 60.830 55.000 19.17 0.00 44.80 4.35
225 226 9.924010 ATAGGGATAGCGTAGAATAGTATTTCT 57.076 33.333 0.00 0.00 39.28 2.52
269 270 3.823304 GAGGTGCATTGAAGGAAGAACTT 59.177 43.478 0.00 0.00 0.00 2.66
290 291 1.821216 ACAAATAAGAGGGCGGTGTG 58.179 50.000 0.00 0.00 0.00 3.82
295 448 1.116536 TAAGAGGGCGGTGTGTGTGA 61.117 55.000 0.00 0.00 0.00 3.58
299 452 2.108157 GGCGGTGTGTGTGAGTGA 59.892 61.111 0.00 0.00 0.00 3.41
300 453 1.956170 GGCGGTGTGTGTGAGTGAG 60.956 63.158 0.00 0.00 0.00 3.51
347 502 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
426 746 1.655597 GTTGCGCGGGTAACTAGTTAC 59.344 52.381 29.86 29.86 43.40 2.50
532 854 4.497507 CCATCAATCTGCAGCAACATACTG 60.498 45.833 9.47 0.00 38.22 2.74
534 856 4.520179 TCAATCTGCAGCAACATACTGAT 58.480 39.130 9.47 0.00 37.32 2.90
537 859 4.743057 TCTGCAGCAACATACTGATAGT 57.257 40.909 9.47 0.00 37.32 2.12
700 1030 8.627208 ATGGCATTTAGATCAATGGTAGTAAG 57.373 34.615 0.00 0.00 35.07 2.34
777 1124 5.830991 TGGGTGTATTTCCATTAGTATTGCC 59.169 40.000 0.00 0.00 0.00 4.52
1020 1371 5.815581 TGTCTATTTAAGCACCCACATCTT 58.184 37.500 0.00 0.00 0.00 2.40
1066 1417 1.797025 GAGTTCACCAAAGTCCCTCG 58.203 55.000 0.00 0.00 32.03 4.63
1071 1422 4.070009 GTTCACCAAAGTCCCTCGTAAAT 58.930 43.478 0.00 0.00 0.00 1.40
1123 1475 6.822170 CCCTTAACCAACTAATAGTGTCTTCC 59.178 42.308 0.00 0.00 0.00 3.46
1135 1487 0.306533 TGTCTTCCGCGCAAAGTTTC 59.693 50.000 8.75 6.68 0.00 2.78
1233 1589 1.866015 TGTGGAGATTCGATGGGACT 58.134 50.000 0.00 0.00 0.00 3.85
1310 1666 4.142045 AGCACATCCAGGAGCTCA 57.858 55.556 17.19 0.00 30.05 4.26
1471 1827 2.637872 TGGTAACTACAAGGCTGAGCTT 59.362 45.455 3.72 0.00 37.61 3.74
1709 2070 7.814107 ACACATAAATAAAACCAGCAATGTCTG 59.186 33.333 0.00 0.00 0.00 3.51
1887 2252 2.669133 CGGCCTCCCTGATTGTCCA 61.669 63.158 0.00 0.00 0.00 4.02
1926 2291 3.005791 CCATTTGACTTGGGAAAGGTGAC 59.994 47.826 0.00 0.00 0.00 3.67
1962 2328 3.942748 GCATCGGTTCCAATAACTACCAA 59.057 43.478 0.00 0.00 0.00 3.67
2199 2567 0.320697 GTCGGCCCTACAACACTCTT 59.679 55.000 0.00 0.00 0.00 2.85
2549 2928 2.599597 GACCCATGAGCCAGGCAT 59.400 61.111 15.80 0.00 0.00 4.40
2578 2957 2.363975 GGTGTGGCCTCGTGGGATA 61.364 63.158 3.32 0.00 37.23 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 4.036734 AGACAAAACTCATGCAAACACGAT 59.963 37.500 0.00 0.00 0.00 3.73
73 74 7.616313 ACCAATTTTTGAACTAACCAGACAAA 58.384 30.769 0.00 0.00 33.53 2.83
74 75 7.176589 ACCAATTTTTGAACTAACCAGACAA 57.823 32.000 0.00 0.00 0.00 3.18
75 76 6.783708 ACCAATTTTTGAACTAACCAGACA 57.216 33.333 0.00 0.00 0.00 3.41
92 93 9.912634 CACTTTCTACATACATTTCAACCAATT 57.087 29.630 0.00 0.00 0.00 2.32
162 163 0.034198 TCGGCATTCTTCACGGACAA 59.966 50.000 0.00 0.00 0.00 3.18
225 226 4.219725 TCAACGCTATCCATATTCATCCGA 59.780 41.667 0.00 0.00 0.00 4.55
269 270 3.244630 ACACACCGCCCTCTTATTTGTTA 60.245 43.478 0.00 0.00 0.00 2.41
290 291 2.099921 ACACTCACTCACTCACTCACAC 59.900 50.000 0.00 0.00 0.00 3.82
295 448 2.103373 ACACACACTCACTCACTCACT 58.897 47.619 0.00 0.00 0.00 3.41
299 452 1.550524 ACACACACACACTCACTCACT 59.449 47.619 0.00 0.00 0.00 3.41
300 453 1.660607 CACACACACACACTCACTCAC 59.339 52.381 0.00 0.00 0.00 3.51
347 502 6.687081 TGACCACTCTAAATCAAACGTTTT 57.313 33.333 11.66 0.00 0.00 2.43
426 746 7.112984 GCAAAAGTTTAGGTTGTTTCTATCACG 59.887 37.037 0.00 0.00 0.00 4.35
497 819 9.219603 GCTGCAGATTGATGGTAATAGTATTAA 57.780 33.333 20.43 0.00 0.00 1.40
675 1005 7.175641 GCTTACTACCATTGATCTAAATGCCAT 59.824 37.037 0.00 0.00 36.42 4.40
690 1020 4.169059 TGGATGCATTGCTTACTACCAT 57.831 40.909 10.49 0.00 0.00 3.55
742 1089 6.597562 TGGAAATACACCCACATAGTAATCC 58.402 40.000 0.00 0.00 32.67 3.01
1020 1371 1.214175 TGAGGGGTTCTGAAACAAGCA 59.786 47.619 7.86 0.00 37.10 3.91
1066 1417 5.098211 GCTTGAGATGGCAAGTCAATTTAC 58.902 41.667 13.43 3.42 45.41 2.01
1071 1422 2.224597 TGAGCTTGAGATGGCAAGTCAA 60.225 45.455 12.67 12.67 45.41 3.18
1123 1475 1.144969 TGGAGTAGAAACTTTGCGCG 58.855 50.000 0.00 0.00 35.56 6.86
1135 1487 2.419297 GCTGGTTGTCCTCATGGAGTAG 60.419 54.545 0.00 0.00 44.16 2.57
1233 1589 1.383523 TGTCGTGTGCCACAATTGAA 58.616 45.000 13.59 0.00 33.40 2.69
1257 1613 0.033208 GATTGGCTCCCACCCATTCA 60.033 55.000 0.00 0.00 34.48 2.57
1310 1666 2.347490 CAACACCGCCCAGCTACT 59.653 61.111 0.00 0.00 0.00 2.57
1471 1827 3.953712 TTCGTCAACTCCTGCTCATAA 57.046 42.857 0.00 0.00 0.00 1.90
1626 1982 3.096092 TGTTTTGACAAGCTCCAAACCT 58.904 40.909 7.97 0.00 34.83 3.50
1869 2234 1.987807 ATGGACAATCAGGGAGGCCG 61.988 60.000 0.00 0.00 0.00 6.13
1887 2252 2.064581 GGCCGGTGGACTCCTACAT 61.065 63.158 1.90 0.00 0.00 2.29
1926 2291 0.518636 CGATGCCACCACAAAGTCTG 59.481 55.000 0.00 0.00 0.00 3.51
1972 2338 5.654209 GGAGGAATCCCCATATTAGCAATTC 59.346 44.000 0.00 0.00 37.41 2.17
1973 2339 5.316992 AGGAGGAATCCCCATATTAGCAATT 59.683 40.000 9.05 0.00 37.41 2.32
1974 2340 4.860278 AGGAGGAATCCCCATATTAGCAAT 59.140 41.667 9.05 0.00 37.41 3.56
2538 2917 0.749091 GTGTGCATATGCCTGGCTCA 60.749 55.000 24.54 7.77 41.18 4.26
2572 2951 1.305802 AGGTGGTGCGACTATCCCA 60.306 57.895 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.