Multiple sequence alignment - TraesCS3B01G245900

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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 TraesCS3B01G245900 chr3B 100.000 2321 0 0 1 2321 390306114 390303794 0.000000e+00 4287.0
1 TraesCS3B01G245900 chr3B 92.240 683 40 4 1650 2320 390294987 390294306 0.000000e+00 955.0
2 TraesCS3B01G245900 chr3B 89.168 757 82 0 597 1353 497772209 497771453 0.000000e+00 944.0
3 TraesCS3B01G245900 chr3B 88.580 683 66 4 1650 2321 390315248 390314567 0.000000e+00 819.0
4 TraesCS3B01G245900 chr3B 92.808 292 21 0 1352 1643 390295369 390295078 7.670000e-115 424.0
5 TraesCS3B01G245900 chr3B 93.607 219 8 3 2104 2321 376507173 376507386 2.880000e-84 322.0
6 TraesCS3B01G245900 chr7A 93.897 1360 81 2 1 1358 127846057 127844698 0.000000e+00 2050.0
7 TraesCS3B01G245900 chr7A 93.491 1352 86 2 2 1352 262338778 262337428 0.000000e+00 2008.0
8 TraesCS3B01G245900 chr7A 94.460 704 38 1 650 1353 608968967 608968265 0.000000e+00 1083.0
9 TraesCS3B01G245900 chr7A 95.282 657 30 1 1 656 608978058 608977402 0.000000e+00 1040.0
10 TraesCS3B01G245900 chr7A 88.095 294 31 3 1349 1641 230779243 230779533 1.710000e-91 346.0
11 TraesCS3B01G245900 chr4A 93.875 898 53 2 1 896 36078463 36079360 0.000000e+00 1352.0
12 TraesCS3B01G245900 chr4A 90.129 233 21 2 2090 2321 230296859 230296628 3.750000e-78 302.0
13 TraesCS3B01G245900 chr5B 89.750 761 76 2 594 1353 500440895 500440136 0.000000e+00 972.0
14 TraesCS3B01G245900 chr5B 89.267 764 78 4 589 1352 502921345 502922104 0.000000e+00 953.0
15 TraesCS3B01G245900 chr6B 89.723 759 78 0 594 1352 341434123 341434881 0.000000e+00 970.0
16 TraesCS3B01G245900 chr6B 89.079 760 82 1 594 1353 423614249 423613491 0.000000e+00 942.0
17 TraesCS3B01G245900 chr6B 82.955 176 28 2 1873 2048 449154987 449154814 8.590000e-35 158.0
18 TraesCS3B01G245900 chr4B 89.488 761 79 1 594 1353 215681916 215681156 0.000000e+00 961.0
19 TraesCS3B01G245900 chr4B 89.615 260 21 6 2065 2321 180052477 180052221 2.220000e-85 326.0
20 TraesCS3B01G245900 chr4B 84.659 176 25 2 1873 2048 507055581 507055754 8.520000e-40 174.0
21 TraesCS3B01G245900 chr4B 84.483 174 25 2 1873 2046 507047517 507047688 1.100000e-38 171.0
22 TraesCS3B01G245900 chr4B 92.593 108 6 2 1650 1756 251986439 251986333 1.110000e-33 154.0
23 TraesCS3B01G245900 chr5D 88.966 290 29 2 1352 1641 328968855 328968569 2.840000e-94 355.0
24 TraesCS3B01G245900 chr5D 88.276 290 31 2 1352 1641 338321664 338321378 6.140000e-91 344.0
25 TraesCS3B01G245900 chr2D 88.966 290 29 2 1352 1641 84425987 84425701 2.840000e-94 355.0
26 TraesCS3B01G245900 chr2D 88.621 290 30 2 1352 1641 583251336 583251050 1.320000e-92 350.0
27 TraesCS3B01G245900 chr2D 87.838 296 33 2 1346 1641 173310764 173311056 6.140000e-91 344.0
28 TraesCS3B01G245900 chr2D 82.432 74 7 5 2014 2084 296144104 296144034 2.490000e-05 60.2
29 TraesCS3B01G245900 chr1B 88.176 296 32 2 1346 1641 523908171 523908463 1.320000e-92 350.0
30 TraesCS3B01G245900 chr1B 92.694 219 9 4 2104 2321 393026942 393027154 2.240000e-80 309.0
31 TraesCS3B01G245900 chr7D 87.838 296 33 2 1346 1641 387979763 387980055 6.140000e-91 344.0
32 TraesCS3B01G245900 chr7D 92.544 228 10 7 2098 2321 362977543 362977319 1.030000e-83 320.0
33 TraesCS3B01G245900 chr3A 92.208 231 15 3 2091 2321 262793759 262793532 8.000000e-85 324.0
34 TraesCS3B01G245900 chr3A 90.909 231 20 1 2091 2321 262824925 262824696 2.240000e-80 309.0
35 TraesCS3B01G245900 chr2B 84.659 176 25 2 1873 2048 776924702 776924529 8.520000e-40 174.0
36 TraesCS3B01G245900 chr2B 87.179 117 10 4 1972 2085 149615373 149615487 6.730000e-26 128.0
37 TraesCS3B01G245900 chr7B 84.091 176 26 2 1873 2048 476998711 476998538 3.970000e-38 169.0
38 TraesCS3B01G245900 chr7B 87.179 117 10 4 1972 2085 223896642 223896528 6.730000e-26 128.0


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 TraesCS3B01G245900 chr3B 390303794 390306114 2320 True 4287.0 4287 100.000 1 2321 1 chr3B.!!$R1 2320
1 TraesCS3B01G245900 chr3B 497771453 497772209 756 True 944.0 944 89.168 597 1353 1 chr3B.!!$R3 756
2 TraesCS3B01G245900 chr3B 390314567 390315248 681 True 819.0 819 88.580 1650 2321 1 chr3B.!!$R2 671
3 TraesCS3B01G245900 chr3B 390294306 390295369 1063 True 689.5 955 92.524 1352 2320 2 chr3B.!!$R4 968
4 TraesCS3B01G245900 chr7A 127844698 127846057 1359 True 2050.0 2050 93.897 1 1358 1 chr7A.!!$R1 1357
5 TraesCS3B01G245900 chr7A 262337428 262338778 1350 True 2008.0 2008 93.491 2 1352 1 chr7A.!!$R2 1350
6 TraesCS3B01G245900 chr7A 608968265 608968967 702 True 1083.0 1083 94.460 650 1353 1 chr7A.!!$R3 703
7 TraesCS3B01G245900 chr7A 608977402 608978058 656 True 1040.0 1040 95.282 1 656 1 chr7A.!!$R4 655
8 TraesCS3B01G245900 chr4A 36078463 36079360 897 False 1352.0 1352 93.875 1 896 1 chr4A.!!$F1 895
9 TraesCS3B01G245900 chr5B 500440136 500440895 759 True 972.0 972 89.750 594 1353 1 chr5B.!!$R1 759
10 TraesCS3B01G245900 chr5B 502921345 502922104 759 False 953.0 953 89.267 589 1352 1 chr5B.!!$F1 763
11 TraesCS3B01G245900 chr6B 341434123 341434881 758 False 970.0 970 89.723 594 1352 1 chr6B.!!$F1 758
12 TraesCS3B01G245900 chr6B 423613491 423614249 758 True 942.0 942 89.079 594 1353 1 chr6B.!!$R1 759
13 TraesCS3B01G245900 chr4B 215681156 215681916 760 True 961.0 961 89.488 594 1353 1 chr4B.!!$R2 759

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
640 643 0.810648 ACGCCATGTTTGCACTATGG 59.189 50.0 15.38 15.38 43.31 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 1647 0.326264 GGCCCTGCTTCTTTCTCTCA 59.674 55.0 0.0 0.0 0.0 3.27 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
31 32 2.170166 GGAATGCAAGTGAACCCATGA 58.830 47.619 0.00 0.00 0.00 3.07
61 62 2.852075 TTGCCGAGGGGGTCAACT 60.852 61.111 0.00 0.00 38.44 3.16
106 107 4.567747 GGACACTCCATTATCACCAAGGTT 60.568 45.833 0.00 0.00 36.28 3.50
123 124 4.618920 AGGTTAACGAACTGATTGACCT 57.381 40.909 0.00 0.00 39.34 3.85
171 172 4.938226 GCTGGTAAAAGAGCTATTCACTGT 59.062 41.667 0.00 0.00 32.12 3.55
173 174 6.763610 GCTGGTAAAAGAGCTATTCACTGTAT 59.236 38.462 0.00 0.00 32.12 2.29
306 307 3.093057 GAGTGAGCCTAAAGGAGTCTCA 58.907 50.000 0.00 0.59 37.39 3.27
310 311 3.449018 TGAGCCTAAAGGAGTCTCATCAC 59.551 47.826 0.00 0.00 37.39 3.06
387 389 1.073722 CTGGCAGCTTGAACTCCCA 59.926 57.895 0.00 0.00 0.00 4.37
390 392 1.676967 GCAGCTTGAACTCCCAGGG 60.677 63.158 0.00 0.00 0.00 4.45
401 403 2.124507 CTCCCAGGGAAAGTCCGCAA 62.125 60.000 10.32 0.00 37.43 4.85
441 443 0.834612 ACAACAGTCTTCCAACCCGA 59.165 50.000 0.00 0.00 0.00 5.14
494 496 1.136891 CACGAGATGTCCCATGTGCTA 59.863 52.381 0.00 0.00 0.00 3.49
570 572 4.083057 GCTGTTTGGAGAGAACAATTCCTC 60.083 45.833 0.00 0.00 36.64 3.71
616 619 2.422479 CAGTGCCAAGATCCACAAGATG 59.578 50.000 3.19 0.00 34.42 2.90
640 643 0.810648 ACGCCATGTTTGCACTATGG 59.189 50.000 15.38 15.38 43.31 2.74
778 781 6.470235 CACAAAACACTTGACTGATTTCACTC 59.530 38.462 0.00 0.00 0.00 3.51
781 784 3.181465 ACACTTGACTGATTTCACTCCGT 60.181 43.478 0.00 0.00 0.00 4.69
786 789 2.548057 GACTGATTTCACTCCGTTGCAA 59.452 45.455 0.00 0.00 0.00 4.08
798 801 4.142271 ACTCCGTTGCAAATTCAGAAAACA 60.142 37.500 0.00 0.00 0.00 2.83
804 807 3.130633 GCAAATTCAGAAAACACCCCAC 58.869 45.455 0.00 0.00 0.00 4.61
822 826 2.983592 CCGCAACAACCCCAGGTC 60.984 66.667 0.00 0.00 33.12 3.85
874 878 6.726490 AGATCAATATGGATGCTGCTTTTT 57.274 33.333 0.00 0.00 0.00 1.94
927 931 2.839486 TTGCGAGAGATGAAACTGGT 57.161 45.000 0.00 0.00 0.00 4.00
1191 1195 2.366640 TCATGTTTTGTCCCCGGAAA 57.633 45.000 0.73 0.00 0.00 3.13
1369 1373 0.609131 AAACAATGCTGGGGGTCTCG 60.609 55.000 0.00 0.00 0.00 4.04
1404 1408 1.065126 AGGAGACCAAAGTGGCATAGC 60.065 52.381 0.00 0.00 42.67 2.97
1421 1425 1.602323 GCCGGATTGGTGTGGTTGA 60.602 57.895 5.05 0.00 41.21 3.18
1438 1442 2.203788 AAGTGGACGGCTCAGGGA 60.204 61.111 0.00 0.00 0.00 4.20
1453 1457 1.352352 CAGGGAAACAGGATGACCAGT 59.648 52.381 0.00 0.00 39.69 4.00
1458 1462 2.847327 AACAGGATGACCAGTGACAG 57.153 50.000 0.00 0.00 39.69 3.51
1478 1482 2.343475 CTATGCAAGCGGGTCCCCAT 62.343 60.000 1.00 1.96 35.37 4.00
1479 1483 2.623094 TATGCAAGCGGGTCCCCATG 62.623 60.000 1.00 0.00 35.37 3.66
1510 1514 1.545706 AAGAAGAGGACCAGGGACGC 61.546 60.000 0.00 0.00 0.00 5.19
1525 1529 0.462047 GACGCGGGAACTCATTGGAT 60.462 55.000 12.47 0.00 0.00 3.41
1536 1540 4.524802 ACTCATTGGATAAGGCATTGGA 57.475 40.909 0.00 0.00 0.00 3.53
1539 1543 4.608269 TCATTGGATAAGGCATTGGACAA 58.392 39.130 0.00 0.00 0.00 3.18
1542 1546 3.979911 TGGATAAGGCATTGGACAACAT 58.020 40.909 0.00 0.00 0.00 2.71
1603 1607 4.452733 GGAAGGGGTCGCGTCCAG 62.453 72.222 23.47 0.00 0.00 3.86
1643 1647 2.426023 GTAGCGGATCCGGGCAAT 59.574 61.111 33.98 7.39 40.19 3.56
1645 1649 2.137528 TAGCGGATCCGGGCAATGA 61.138 57.895 33.98 4.15 40.19 2.57
1648 1652 1.301244 CGGATCCGGGCAATGAGAG 60.301 63.158 26.95 0.00 35.56 3.20
1771 1870 3.379445 GGAGGTCCGACGAGGCAA 61.379 66.667 0.00 0.00 40.77 4.52
1934 2033 0.826715 CGGAGCTGGAGAGAAATGGA 59.173 55.000 0.00 0.00 0.00 3.41
1936 2035 1.836802 GGAGCTGGAGAGAAATGGAGT 59.163 52.381 0.00 0.00 0.00 3.85
1937 2036 2.238395 GGAGCTGGAGAGAAATGGAGTT 59.762 50.000 0.00 0.00 0.00 3.01
1938 2037 3.269178 GAGCTGGAGAGAAATGGAGTTG 58.731 50.000 0.00 0.00 0.00 3.16
1963 2062 2.142761 CGGGAGAGGCCATGGATCA 61.143 63.158 18.40 0.00 38.95 2.92
2129 2228 3.083349 CCATCTCGGTGGAGGGCA 61.083 66.667 0.00 0.00 42.02 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.536907 TAGTTGACCCCCTCGGCAA 60.537 57.895 0.00 0.00 33.26 4.52
106 107 6.751157 TGAAACTAGGTCAATCAGTTCGTTA 58.249 36.000 0.00 0.00 31.43 3.18
171 172 6.947158 TGCCATGATAACCTTTGCATCATATA 59.053 34.615 0.00 0.00 37.31 0.86
173 174 5.139001 TGCCATGATAACCTTTGCATCATA 58.861 37.500 0.00 0.00 37.31 2.15
306 307 3.244665 TGTTCCTGCATCTTGACAGTGAT 60.245 43.478 0.00 0.00 31.76 3.06
387 389 0.765510 AGAACTTGCGGACTTTCCCT 59.234 50.000 0.00 0.00 31.13 4.20
390 392 2.287009 CCACAAGAACTTGCGGACTTTC 60.287 50.000 14.18 0.00 43.51 2.62
401 403 1.598130 GCCAGACGCCACAAGAACT 60.598 57.895 0.00 0.00 0.00 3.01
494 496 1.480137 CTCCATCTTCGTCAAGCCTCT 59.520 52.381 0.00 0.00 0.00 3.69
534 536 3.381272 TCCAAACAGCTTTCACCTTCTTG 59.619 43.478 0.00 0.00 0.00 3.02
616 619 1.468520 AGTGCAAACATGGCGTATCAC 59.531 47.619 0.00 0.00 0.00 3.06
640 643 2.660362 CGTGCAACTTCTTTTCTCGCTC 60.660 50.000 0.00 0.00 31.75 5.03
778 781 3.245048 GGTGTTTTCTGAATTTGCAACGG 59.755 43.478 0.00 0.00 0.00 4.44
781 784 3.198635 TGGGGTGTTTTCTGAATTTGCAA 59.801 39.130 0.00 0.00 0.00 4.08
786 789 2.325484 GGGTGGGGTGTTTTCTGAATT 58.675 47.619 0.00 0.00 0.00 2.17
798 801 4.906537 GGTTGTTGCGGGTGGGGT 62.907 66.667 0.00 0.00 0.00 4.95
804 807 4.596585 ACCTGGGGTTGTTGCGGG 62.597 66.667 0.00 0.00 27.29 6.13
827 831 1.351017 TCAAGTTTGTAGCTGGAGGGG 59.649 52.381 0.00 0.00 0.00 4.79
874 878 1.711375 ACCAGTCTCAGACTCCACCTA 59.289 52.381 3.60 0.00 41.37 3.08
927 931 2.746412 TAGCAGCCGCCAAGAAAGCA 62.746 55.000 0.00 0.00 39.83 3.91
957 961 3.624777 CAGGGCAGATCTTACATGGTTT 58.375 45.455 0.00 0.00 0.00 3.27
1191 1195 3.189568 ATGCGCCACATGGTTACAT 57.810 47.368 4.18 0.00 37.70 2.29
1404 1408 0.881118 CTTCAACCACACCAATCCGG 59.119 55.000 0.00 0.00 42.50 5.14
1407 1411 2.293399 GTCCACTTCAACCACACCAATC 59.707 50.000 0.00 0.00 0.00 2.67
1421 1425 1.415672 TTTCCCTGAGCCGTCCACTT 61.416 55.000 0.00 0.00 0.00 3.16
1438 1442 2.811873 GCTGTCACTGGTCATCCTGTTT 60.812 50.000 0.00 0.00 42.61 2.83
1458 1462 2.902343 GGGACCCGCTTGCATAGC 60.902 66.667 0.00 9.89 46.83 2.97
1478 1482 2.224378 CCTCTTCTTGCCTCTGTTCACA 60.224 50.000 0.00 0.00 0.00 3.58
1479 1483 2.037772 TCCTCTTCTTGCCTCTGTTCAC 59.962 50.000 0.00 0.00 0.00 3.18
1510 1514 2.222027 GCCTTATCCAATGAGTTCCCG 58.778 52.381 0.00 0.00 0.00 5.14
1525 1529 3.088532 GGTGATGTTGTCCAATGCCTTA 58.911 45.455 0.00 0.00 0.00 2.69
1536 1540 2.342650 GGCGCCATGGTGATGTTGT 61.343 57.895 29.49 0.00 0.00 3.32
1539 1543 3.286694 AAGGGCGCCATGGTGATGT 62.287 57.895 30.85 8.66 0.00 3.06
1542 1546 4.738998 CCAAGGGCGCCATGGTGA 62.739 66.667 31.88 0.00 0.00 4.02
1561 1565 1.679139 TGAATCCATCATTGGCGGAC 58.321 50.000 0.00 0.00 43.29 4.79
1565 1569 1.677576 TCGCTTGAATCCATCATTGGC 59.322 47.619 0.00 0.00 43.29 4.52
1577 1581 1.677552 GACCCCTTCCTCGCTTGAA 59.322 57.895 0.00 0.00 0.00 2.69
1603 1607 2.131067 CGGCCTCCTTCCTCTCCTC 61.131 68.421 0.00 0.00 0.00 3.71
1627 1631 2.099652 CTCATTGCCCGGATCCGCTA 62.100 60.000 29.12 13.20 38.24 4.26
1643 1647 0.326264 GGCCCTGCTTCTTTCTCTCA 59.674 55.000 0.00 0.00 0.00 3.27
1645 1649 1.298014 CGGCCCTGCTTCTTTCTCT 59.702 57.895 0.00 0.00 0.00 3.10
1648 1652 2.048603 ATGCGGCCCTGCTTCTTTC 61.049 57.895 0.00 0.00 35.36 2.62
1730 1818 4.020617 CTCCTTCCGTGCTGCCCA 62.021 66.667 0.00 0.00 0.00 5.36
1737 1836 2.125912 CTCCGTGCTCCTTCCGTG 60.126 66.667 0.00 0.00 0.00 4.94
1763 1862 2.932234 CGTCCCTCTGTTGCCTCGT 61.932 63.158 0.00 0.00 0.00 4.18
1885 1984 2.105930 CCTGCTACCGCTGCTCTC 59.894 66.667 0.00 0.00 36.97 3.20
1894 1993 3.799755 CAAACGCGCCCTGCTACC 61.800 66.667 5.73 0.00 43.27 3.18
1912 2011 1.267574 ATTTCTCTCCAGCTCCGCCA 61.268 55.000 0.00 0.00 0.00 5.69
1931 2030 2.606519 CCCGTCCTCCCAACTCCA 60.607 66.667 0.00 0.00 0.00 3.86
1934 2033 1.305381 CTCTCCCGTCCTCCCAACT 60.305 63.158 0.00 0.00 0.00 3.16
1936 2035 2.038975 CCTCTCCCGTCCTCCCAA 59.961 66.667 0.00 0.00 0.00 4.12
1937 2036 4.779733 GCCTCTCCCGTCCTCCCA 62.780 72.222 0.00 0.00 0.00 4.37
1963 2062 2.771762 GGGGAGCTCCTCATGCCT 60.772 66.667 31.36 0.00 36.20 4.75


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

AutoCloner maintained by Alex Coulton.