Multiple sequence alignment - TraesCS3B01G055500

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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 TraesCS3B01G055500 chr3B 100.000 2264 0 0 1 2264 28616925 28619188 0.000000e+00 4181
1 TraesCS3B01G055500 chr3B 96.767 1701 41 4 565 2264 16123873 16122186 0.000000e+00 2824
2 TraesCS3B01G055500 chr2B 96.179 1701 46 8 565 2264 563916576 563914894 0.000000e+00 2763
3 TraesCS3B01G055500 chr2B 95.593 1702 68 6 562 2259 138732356 138734054 0.000000e+00 2721
4 TraesCS3B01G055500 chr2B 97.876 565 12 0 1 565 42192805 42193369 0.000000e+00 977
5 TraesCS3B01G055500 chr2B 97.876 565 12 0 1 565 594089015 594089579 0.000000e+00 977
6 TraesCS3B01G055500 chr2B 97.699 565 13 0 1 565 138731211 138731775 0.000000e+00 972
7 TraesCS3B01G055500 chr2B 90.258 503 40 7 1768 2264 717653789 717654288 0.000000e+00 649
8 TraesCS3B01G055500 chr5B 96.908 1617 34 5 562 2178 464634667 464636267 0.000000e+00 2695
9 TraesCS3B01G055500 chr5B 97.345 565 15 0 1 565 454660338 454660902 0.000000e+00 961
10 TraesCS3B01G055500 chr5B 89.820 501 45 5 1768 2264 530939094 530938596 2.450000e-179 638
11 TraesCS3B01G055500 chr7B 93.805 1711 91 13 562 2264 687041183 687042886 0.000000e+00 2558
12 TraesCS3B01G055500 chr7B 91.652 1725 117 20 562 2264 27327136 27328855 0.000000e+00 2362
13 TraesCS3B01G055500 chr7B 98.053 565 11 0 1 565 713546883 713546319 0.000000e+00 983
14 TraesCS3B01G055500 chr7B 90.040 502 43 6 1768 2264 235456357 235455858 0.000000e+00 643
15 TraesCS3B01G055500 chr7B 89.243 502 47 6 1768 2264 130335697 130336196 2.470000e-174 621
16 TraesCS3B01G055500 chr4A 93.582 1714 89 15 565 2264 712878042 712879748 0.000000e+00 2536
17 TraesCS3B01G055500 chr1B 93.224 1712 87 18 562 2264 38183952 38185643 0.000000e+00 2492
18 TraesCS3B01G055500 chr1B 90.438 502 41 6 1768 2264 550438361 550437862 0.000000e+00 654
19 TraesCS3B01G055500 chr4B 97.100 1414 30 1 565 1978 402786639 402785237 0.000000e+00 2374
20 TraesCS3B01G055500 chr4B 97.522 565 13 1 1 565 402787800 402787237 0.000000e+00 965
21 TraesCS3B01G055500 chr4B 97.345 565 15 0 1 565 576450154 576450718 0.000000e+00 961
22 TraesCS3B01G055500 chr6B 95.573 1423 42 6 565 1978 687513874 687512464 0.000000e+00 2259
23 TraesCS3B01G055500 chr6B 97.699 565 13 0 1 565 650647263 650646699 0.000000e+00 972
24 TraesCS3B01G055500 chr6B 89.662 503 43 7 1768 2264 114143097 114142598 1.140000e-177 632
25 TraesCS3B01G055500 chr6A 97.699 565 13 0 1 565 74992791 74992227 0.000000e+00 972


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 TraesCS3B01G055500 chr3B 28616925 28619188 2263 False 4181.0 4181 100.000 1 2264 1 chr3B.!!$F1 2263
1 TraesCS3B01G055500 chr3B 16122186 16123873 1687 True 2824.0 2824 96.767 565 2264 1 chr3B.!!$R1 1699
2 TraesCS3B01G055500 chr2B 563914894 563916576 1682 True 2763.0 2763 96.179 565 2264 1 chr2B.!!$R1 1699
3 TraesCS3B01G055500 chr2B 138731211 138734054 2843 False 1846.5 2721 96.646 1 2259 2 chr2B.!!$F4 2258
4 TraesCS3B01G055500 chr2B 42192805 42193369 564 False 977.0 977 97.876 1 565 1 chr2B.!!$F1 564
5 TraesCS3B01G055500 chr2B 594089015 594089579 564 False 977.0 977 97.876 1 565 1 chr2B.!!$F2 564
6 TraesCS3B01G055500 chr5B 464634667 464636267 1600 False 2695.0 2695 96.908 562 2178 1 chr5B.!!$F2 1616
7 TraesCS3B01G055500 chr5B 454660338 454660902 564 False 961.0 961 97.345 1 565 1 chr5B.!!$F1 564
8 TraesCS3B01G055500 chr7B 687041183 687042886 1703 False 2558.0 2558 93.805 562 2264 1 chr7B.!!$F3 1702
9 TraesCS3B01G055500 chr7B 27327136 27328855 1719 False 2362.0 2362 91.652 562 2264 1 chr7B.!!$F1 1702
10 TraesCS3B01G055500 chr7B 713546319 713546883 564 True 983.0 983 98.053 1 565 1 chr7B.!!$R2 564
11 TraesCS3B01G055500 chr4A 712878042 712879748 1706 False 2536.0 2536 93.582 565 2264 1 chr4A.!!$F1 1699
12 TraesCS3B01G055500 chr1B 38183952 38185643 1691 False 2492.0 2492 93.224 562 2264 1 chr1B.!!$F1 1702
13 TraesCS3B01G055500 chr4B 402785237 402787800 2563 True 1669.5 2374 97.311 1 1978 2 chr4B.!!$R1 1977
14 TraesCS3B01G055500 chr4B 576450154 576450718 564 False 961.0 961 97.345 1 565 1 chr4B.!!$F1 564
15 TraesCS3B01G055500 chr6B 687512464 687513874 1410 True 2259.0 2259 95.573 565 1978 1 chr6B.!!$R3 1413
16 TraesCS3B01G055500 chr6B 650646699 650647263 564 True 972.0 972 97.699 1 565 1 chr6B.!!$R2 564
17 TraesCS3B01G055500 chr6A 74992227 74992791 564 True 972.0 972 97.699 1 565 1 chr6A.!!$R1 564

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
124 125 0.106335 TCGTGGCCAACTTTTACCGA 59.894 50.0 7.24 6.91 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 3375 0.681733 ATGTGTCTGGTCTTCTGCGT 59.318 50.0 0.0 0.0 0.0 5.24 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
124 125 0.106335 TCGTGGCCAACTTTTACCGA 59.894 50.000 7.24 6.91 0.00 4.69
166 167 2.489329 CAGCAAAGACCTTACCCATGTG 59.511 50.000 0.00 0.00 0.00 3.21
208 209 1.659098 GGTTTCGATGCTCGGTACAAG 59.341 52.381 0.00 0.00 40.88 3.16
355 356 7.202016 TCTGGTAGAATGTTTCAACAATGTC 57.798 36.000 0.00 0.00 43.03 3.06
712 1895 0.243907 TGGTCGAGCTAGCACAAGTC 59.756 55.000 18.83 4.03 0.00 3.01
731 1914 1.038130 CCTAGAGGTGGTGGTCGAGG 61.038 65.000 0.00 0.00 30.41 4.63
742 1925 2.423577 GTGGTCGAGGTAGCACAAATT 58.576 47.619 0.00 0.00 45.11 1.82
1010 2193 4.527816 TCTTTTTGTAGGCATGGCTTCATT 59.472 37.500 28.30 5.01 0.00 2.57
1055 2238 1.296392 CGGACCAAGAGGACATGCA 59.704 57.895 0.00 0.00 38.69 3.96
1104 2287 3.913163 ACAAGGAGAAGGAGAAGGATGTT 59.087 43.478 0.00 0.00 0.00 2.71
1722 2907 4.594123 TGTTATTCGAGACCTTGTGTGA 57.406 40.909 0.00 0.00 0.00 3.58
1872 3076 5.582269 TGAGACTAGCATGCTTTGTTCATAC 59.418 40.000 28.02 12.22 0.00 2.39
1884 3088 5.625311 GCTTTGTTCATACTTAACAGTGTGC 59.375 40.000 0.00 0.00 40.95 4.57
2008 3273 1.474478 CTCACGCAGTAGACCAGACAT 59.526 52.381 0.00 0.00 41.61 3.06
2109 3375 1.428448 CGTCTGGATCGTTTTGCTCA 58.572 50.000 0.00 0.00 0.00 4.26
2127 3393 0.249447 CACGCAGAAGACCAGACACA 60.249 55.000 0.00 0.00 0.00 3.72
2128 3394 0.681733 ACGCAGAAGACCAGACACAT 59.318 50.000 0.00 0.00 0.00 3.21
2129 3395 1.073964 CGCAGAAGACCAGACACATG 58.926 55.000 0.00 0.00 0.00 3.21
2130 3396 0.801251 GCAGAAGACCAGACACATGC 59.199 55.000 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 2.035530 GCTCCTTGCTCTTACATGCT 57.964 50.000 0.00 0.00 38.95 3.79
208 209 0.944386 TCACCGCTGCAAAGAGTTTC 59.056 50.000 0.00 0.00 0.00 2.78
285 286 1.219773 ACCACCATCCTCATGAGCAT 58.780 50.000 17.76 5.02 30.57 3.79
295 296 1.238439 CATATCGCCAACCACCATCC 58.762 55.000 0.00 0.00 0.00 3.51
355 356 3.257933 GCACGAGCACCCTTCAAG 58.742 61.111 0.00 0.00 41.58 3.02
475 476 6.127730 ACCATTCATCAACCTTTTTCGGATAC 60.128 38.462 0.00 0.00 0.00 2.24
712 1895 1.038130 CCTCGACCACCACCTCTAGG 61.038 65.000 0.00 0.00 42.17 3.02
731 1914 4.631813 CACCACCTCTAGAATTTGTGCTAC 59.368 45.833 0.00 0.00 0.00 3.58
742 1925 0.680280 GCTCGACCACCACCTCTAGA 60.680 60.000 0.00 0.00 0.00 2.43
776 1959 2.446994 TCCGACCACCACCACCTT 60.447 61.111 0.00 0.00 0.00 3.50
1010 2193 3.379445 GCCTCGTCCTGGAACCGA 61.379 66.667 8.82 8.82 0.00 4.69
1031 2214 4.680237 CCTCTTGGTCCGCGCACA 62.680 66.667 8.75 0.00 0.00 4.57
1055 2238 1.617947 GGCCTCCATCCACGTCTTCT 61.618 60.000 0.00 0.00 0.00 2.85
1104 2287 3.668147 CCAACATGATGGTGTGGGA 57.332 52.632 13.69 0.00 44.59 4.37
1722 2907 8.633561 TCTCGAATGACATAAGTAGTTCATGAT 58.366 33.333 0.00 0.00 0.00 2.45
1872 3076 2.800544 ACTTGTAGCGCACACTGTTAAG 59.199 45.455 11.47 9.02 36.69 1.85
2008 3273 3.040477 TCCATCAGACACATCAGGCATA 58.960 45.455 0.00 0.00 0.00 3.14
2032 3298 2.359975 GAACCTTGGCGTCTGGGG 60.360 66.667 4.80 0.00 0.00 4.96
2109 3375 0.681733 ATGTGTCTGGTCTTCTGCGT 59.318 50.000 0.00 0.00 0.00 5.24
2115 3381 3.639099 CAGGCATGTGTCTGGTCTT 57.361 52.632 6.72 0.00 43.64 3.01
2127 3393 1.841919 TCCATCAGACACATCAGGCAT 59.158 47.619 0.00 0.00 0.00 4.40
2128 3394 1.065926 GTCCATCAGACACATCAGGCA 60.066 52.381 0.00 0.00 45.55 4.75
2129 3395 1.661341 GTCCATCAGACACATCAGGC 58.339 55.000 0.00 0.00 45.55 4.85
2150 3420 2.359975 GAACCTTGGCGTCTGGGG 60.360 66.667 4.80 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.