Multiple sequence alignment - TraesCS3B01G019700

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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 TraesCS3B01G019700 chr3B 100.000 2929 0 0 1 2929 8504520 8507448 0.000000e+00 5409.0
1 TraesCS3B01G019700 chr3B 88.940 1736 130 33 683 2365 597427123 597428849 0.000000e+00 2085.0
2 TraesCS3B01G019700 chr3B 79.097 421 61 20 2358 2762 508522545 508522136 6.220000e-67 265.0
3 TraesCS3B01G019700 chr3D 96.622 2931 68 6 1 2929 6990384 6993285 0.000000e+00 4835.0
4 TraesCS3B01G019700 chr3D 94.545 660 29 3 1712 2368 5544737 5545392 0.000000e+00 1013.0
5 TraesCS3B01G019700 chr4D 93.913 1692 87 10 683 2366 459191680 459193363 0.000000e+00 2540.0
6 TraesCS3B01G019700 chr4D 85.333 150 21 1 2613 2762 483599816 483599668 1.410000e-33 154.0
7 TraesCS3B01G019700 chr1B 92.920 1695 83 14 684 2364 127026033 127024362 0.000000e+00 2431.0
8 TraesCS3B01G019700 chr1B 81.805 665 92 22 1 642 668080061 668080719 5.560000e-147 531.0
9 TraesCS3B01G019700 chr1B 81.623 419 57 12 2358 2760 668080711 668081125 2.180000e-86 329.0
10 TraesCS3B01G019700 chr2D 93.005 1687 76 18 683 2362 631749236 631747585 0.000000e+00 2423.0
11 TraesCS3B01G019700 chr2D 91.587 1367 96 10 683 2038 469107597 469106239 0.000000e+00 1869.0
12 TraesCS3B01G019700 chr2D 79.551 401 59 14 2379 2762 155058642 155059036 6.220000e-67 265.0
13 TraesCS3B01G019700 chr2D 87.692 65 6 2 2866 2928 9569009 9569073 1.130000e-09 75.0
14 TraesCS3B01G019700 chr2B 92.318 1549 89 17 841 2368 677292341 677293880 0.000000e+00 2174.0
15 TraesCS3B01G019700 chr2B 94.212 311 17 1 2057 2367 139360993 139360684 9.500000e-130 473.0
16 TraesCS3B01G019700 chr2B 97.436 39 1 0 2890 2928 584482905 584482867 1.880000e-07 67.6
17 TraesCS3B01G019700 chr7B 88.691 1742 128 35 683 2371 551484382 551482657 0.000000e+00 2061.0
18 TraesCS3B01G019700 chr7B 100.000 46 0 0 2883 2928 413592602 413592557 5.200000e-13 86.1
19 TraesCS3B01G019700 chr7A 93.282 1295 61 14 841 2115 48781641 48782929 0.000000e+00 1886.0
20 TraesCS3B01G019700 chr7A 90.895 626 43 10 20 642 688307867 688308481 0.000000e+00 828.0
21 TraesCS3B01G019700 chr7A 81.982 666 91 18 1 642 15683177 15683837 3.320000e-149 538.0
22 TraesCS3B01G019700 chr7A 94.953 317 15 1 2048 2364 48782925 48783240 2.030000e-136 496.0
23 TraesCS3B01G019700 chr7A 80.096 417 65 8 2362 2762 609634090 609633676 7.940000e-76 294.0
24 TraesCS3B01G019700 chr7A 83.881 335 14 14 2360 2689 688308475 688308774 1.720000e-72 283.0
25 TraesCS3B01G019700 chr7A 77.404 416 71 8 2362 2761 15683832 15684240 2.940000e-55 226.0
26 TraesCS3B01G019700 chr7A 85.039 127 19 0 2636 2762 7791481 7791607 2.370000e-26 130.0
27 TraesCS3B01G019700 chr1A 92.033 1343 92 12 702 2038 461966429 461965096 0.000000e+00 1873.0
28 TraesCS3B01G019700 chr1A 92.254 723 44 10 683 1399 35563666 35562950 0.000000e+00 1014.0
29 TraesCS3B01G019700 chr1A 93.488 645 39 2 1 642 556599267 556598623 0.000000e+00 955.0
30 TraesCS3B01G019700 chr1A 83.129 652 84 15 12 642 473039464 473040110 3.270000e-159 571.0
31 TraesCS3B01G019700 chr1A 82.622 656 81 20 12 641 533739451 533740099 1.530000e-152 549.0
32 TraesCS3B01G019700 chr1A 89.552 402 27 5 2362 2748 556598628 556598227 2.030000e-136 496.0
33 TraesCS3B01G019700 chr1A 78.469 418 70 17 2362 2761 70693807 70694222 3.750000e-64 255.0
34 TraesCS3B01G019700 chrUn 92.314 1288 83 7 762 2038 96553413 96554695 0.000000e+00 1816.0
35 TraesCS3B01G019700 chr7D 90.182 988 74 11 1381 2364 422343534 422344502 0.000000e+00 1266.0
36 TraesCS3B01G019700 chr7D 82.239 670 87 20 1 642 558927679 558928344 1.530000e-152 549.0
37 TraesCS3B01G019700 chr5A 83.129 652 84 15 12 642 568705480 568704834 3.270000e-159 571.0
38 TraesCS3B01G019700 chr5A 81.437 668 90 20 1 642 94303801 94303142 1.560000e-142 516.0
39 TraesCS3B01G019700 chr5A 94.231 52 3 0 2877 2928 165243684 165243633 2.420000e-11 80.5
40 TraesCS3B01G019700 chr3A 82.212 669 89 20 1 642 12458863 12458198 1.530000e-152 549.0
41 TraesCS3B01G019700 chr2A 83.443 610 67 18 61 642 516093221 516092618 1.190000e-148 536.0
42 TraesCS3B01G019700 chr2A 94.516 310 15 2 2055 2364 763971125 763970818 7.340000e-131 477.0
43 TraesCS3B01G019700 chr2A 81.979 283 39 8 2470 2751 516092386 516092115 2.270000e-56 230.0
44 TraesCS3B01G019700 chr2A 84.167 120 19 0 2642 2761 118220155 118220274 1.840000e-22 117.0
45 TraesCS3B01G019700 chr5D 81.791 670 86 24 1 642 335860738 335861399 2.000000e-146 529.0
46 TraesCS3B01G019700 chr5D 81.235 421 60 12 2358 2762 335861391 335861808 3.640000e-84 322.0
47 TraesCS3B01G019700 chr5D 78.623 276 31 15 2516 2766 311930936 311930664 1.090000e-34 158.0
48 TraesCS3B01G019700 chr5D 97.917 48 0 1 2881 2928 154533584 154533538 6.730000e-12 82.4
49 TraesCS3B01G019700 chr1D 81.970 660 85 21 12 642 329503726 329504380 2.000000e-146 529.0
50 TraesCS3B01G019700 chr1D 97.959 49 1 0 2880 2928 161408175 161408223 5.200000e-13 86.1
51 TraesCS3B01G019700 chr1D 91.379 58 4 1 2872 2928 452618480 452618537 8.700000e-11 78.7
52 TraesCS3B01G019700 chr4A 78.897 417 70 8 2362 2762 236002543 236002129 1.730000e-67 267.0
53 TraesCS3B01G019700 chr6A 92.857 56 1 3 2875 2928 594435672 594435618 8.700000e-11 78.7


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 TraesCS3B01G019700 chr3B 8504520 8507448 2928 False 5409.0 5409 100.0000 1 2929 1 chr3B.!!$F1 2928
1 TraesCS3B01G019700 chr3B 597427123 597428849 1726 False 2085.0 2085 88.9400 683 2365 1 chr3B.!!$F2 1682
2 TraesCS3B01G019700 chr3D 6990384 6993285 2901 False 4835.0 4835 96.6220 1 2929 1 chr3D.!!$F2 2928
3 TraesCS3B01G019700 chr3D 5544737 5545392 655 False 1013.0 1013 94.5450 1712 2368 1 chr3D.!!$F1 656
4 TraesCS3B01G019700 chr4D 459191680 459193363 1683 False 2540.0 2540 93.9130 683 2366 1 chr4D.!!$F1 1683
5 TraesCS3B01G019700 chr1B 127024362 127026033 1671 True 2431.0 2431 92.9200 684 2364 1 chr1B.!!$R1 1680
6 TraesCS3B01G019700 chr1B 668080061 668081125 1064 False 430.0 531 81.7140 1 2760 2 chr1B.!!$F1 2759
7 TraesCS3B01G019700 chr2D 631747585 631749236 1651 True 2423.0 2423 93.0050 683 2362 1 chr2D.!!$R2 1679
8 TraesCS3B01G019700 chr2D 469106239 469107597 1358 True 1869.0 1869 91.5870 683 2038 1 chr2D.!!$R1 1355
9 TraesCS3B01G019700 chr2B 677292341 677293880 1539 False 2174.0 2174 92.3180 841 2368 1 chr2B.!!$F1 1527
10 TraesCS3B01G019700 chr7B 551482657 551484382 1725 True 2061.0 2061 88.6910 683 2371 1 chr7B.!!$R2 1688
11 TraesCS3B01G019700 chr7A 48781641 48783240 1599 False 1191.0 1886 94.1175 841 2364 2 chr7A.!!$F3 1523
12 TraesCS3B01G019700 chr7A 688307867 688308774 907 False 555.5 828 87.3880 20 2689 2 chr7A.!!$F4 2669
13 TraesCS3B01G019700 chr7A 15683177 15684240 1063 False 382.0 538 79.6930 1 2761 2 chr7A.!!$F2 2760
14 TraesCS3B01G019700 chr1A 461965096 461966429 1333 True 1873.0 1873 92.0330 702 2038 1 chr1A.!!$R2 1336
15 TraesCS3B01G019700 chr1A 35562950 35563666 716 True 1014.0 1014 92.2540 683 1399 1 chr1A.!!$R1 716
16 TraesCS3B01G019700 chr1A 556598227 556599267 1040 True 725.5 955 91.5200 1 2748 2 chr1A.!!$R3 2747
17 TraesCS3B01G019700 chr1A 473039464 473040110 646 False 571.0 571 83.1290 12 642 1 chr1A.!!$F2 630
18 TraesCS3B01G019700 chr1A 533739451 533740099 648 False 549.0 549 82.6220 12 641 1 chr1A.!!$F3 629
19 TraesCS3B01G019700 chrUn 96553413 96554695 1282 False 1816.0 1816 92.3140 762 2038 1 chrUn.!!$F1 1276
20 TraesCS3B01G019700 chr7D 422343534 422344502 968 False 1266.0 1266 90.1820 1381 2364 1 chr7D.!!$F1 983
21 TraesCS3B01G019700 chr7D 558927679 558928344 665 False 549.0 549 82.2390 1 642 1 chr7D.!!$F2 641
22 TraesCS3B01G019700 chr5A 568704834 568705480 646 True 571.0 571 83.1290 12 642 1 chr5A.!!$R3 630
23 TraesCS3B01G019700 chr5A 94303142 94303801 659 True 516.0 516 81.4370 1 642 1 chr5A.!!$R1 641
24 TraesCS3B01G019700 chr3A 12458198 12458863 665 True 549.0 549 82.2120 1 642 1 chr3A.!!$R1 641
25 TraesCS3B01G019700 chr2A 516092115 516093221 1106 True 383.0 536 82.7110 61 2751 2 chr2A.!!$R2 2690
26 TraesCS3B01G019700 chr5D 335860738 335861808 1070 False 425.5 529 81.5130 1 2762 2 chr5D.!!$F1 2761
27 TraesCS3B01G019700 chr1D 329503726 329504380 654 False 529.0 529 81.9700 12 642 1 chr1D.!!$F2 630

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
677 730 0.244721 GTCACCAGCTGGAATTTGCC 59.755 55.000 39.19 13.28 38.94 4.52 F
1520 1673 1.148498 CGGGGCTAAGGGGATGAAC 59.852 63.158 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1736 0.174845 TCTCGCCATTCACCTAACCG 59.825 55.000 0.0 0.0 0.00 4.44 R
2773 3260 1.310373 CTCCCGGGGAACTCCTAGT 59.690 63.158 23.5 0.0 35.95 2.57 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
656 709 0.872388 CTTAGGGTGTGTTCGGTTGC 59.128 55.000 0.00 0.00 0.00 4.17
677 730 0.244721 GTCACCAGCTGGAATTTGCC 59.755 55.000 39.19 13.28 38.94 4.52
931 1067 1.693062 TGCAACATTTTGATGGCTGGT 59.307 42.857 0.00 0.00 34.24 4.00
1026 1170 3.749609 ACAATGTTGAAGTTACCGCTACC 59.250 43.478 0.00 0.00 0.00 3.18
1038 1182 1.153823 CGCTACCAGTGGGAAGTCG 60.154 63.158 15.21 13.47 38.05 4.18
1198 1344 2.005451 ACGAGCAATTCAAGCTAGCTG 58.995 47.619 20.16 12.65 43.58 4.24
1207 1353 3.087370 TCAAGCTAGCTGTCACCTCTA 57.913 47.619 20.16 0.00 0.00 2.43
1444 1596 2.040813 AGACCCACAAACATGATGCTCT 59.959 45.455 0.00 0.00 0.00 4.09
1520 1673 1.148498 CGGGGCTAAGGGGATGAAC 59.852 63.158 0.00 0.00 0.00 3.18
1536 1689 3.810310 TGAACGCAAGGTTTGGAAATT 57.190 38.095 0.00 0.00 37.50 1.82
1571 1736 3.849911 TGACGTTGATGATGAGGAGAAC 58.150 45.455 0.00 0.00 0.00 3.01
1575 1740 3.600388 GTTGATGATGAGGAGAACGGTT 58.400 45.455 0.00 0.00 0.00 4.44
1661 1826 2.603075 AAAAGATGGCCAAGGTGCTA 57.397 45.000 10.96 0.00 0.00 3.49
1675 1840 4.828072 AGGTGCTAAAAGTTCTAGAGGG 57.172 45.455 0.00 0.00 0.00 4.30
1717 1882 7.340743 TCTCAAAGATGGTTTTAAACTTGTGGA 59.659 33.333 7.79 5.05 0.00 4.02
1841 2006 6.108687 CCACTACTATGCTCATCTTGTTGAA 58.891 40.000 0.00 0.00 0.00 2.69
1855 2020 0.031585 GTTGAAAACCCCAAGACGGC 59.968 55.000 0.00 0.00 42.21 5.68
1856 2021 1.448922 TTGAAAACCCCAAGACGGCG 61.449 55.000 4.80 4.80 0.00 6.46
2002 2175 2.324541 AGTGCCATTGGGTTGCTTTAA 58.675 42.857 4.53 0.00 36.17 1.52
2120 2412 9.440773 TGCTACCTTATGATATTATTGCTGAAG 57.559 33.333 0.00 0.00 0.00 3.02
2242 2534 5.450453 TCCATTCTTCCAAACCAAACACTA 58.550 37.500 0.00 0.00 0.00 2.74
2248 2540 4.139859 TCCAAACCAAACACTAGAACGA 57.860 40.909 0.00 0.00 0.00 3.85
2290 2582 1.235724 GCACCTACCAAACACAGGAC 58.764 55.000 0.00 0.00 33.44 3.85
2401 2693 2.382746 GCGAGCACGATCAGTTGCA 61.383 57.895 8.01 0.00 42.66 4.08
2413 2705 3.500448 TCAGTTGCATTGGTTAGGTCA 57.500 42.857 0.00 0.00 0.00 4.02
2632 3113 1.206745 CGTAGGCGGCGAATACACTG 61.207 60.000 12.98 0.00 0.00 3.66
2685 3172 2.474526 CCGCGCAAGTTTCATGACTAAG 60.475 50.000 8.75 0.00 41.68 2.18
2753 3240 6.072064 TGCAAGTTCTAAGACTCCTAGTGTAC 60.072 42.308 0.00 0.00 0.00 2.90
2903 3390 0.550432 AGTACTACTCCCTCCGTCCC 59.450 60.000 0.00 0.00 0.00 4.46
2911 3398 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
677 730 0.609151 TGCCCAGCCATCAAAATGTG 59.391 50.000 0.00 0.0 0.00 3.21
1026 1170 0.109723 TTTTCCCCGACTTCCCACTG 59.890 55.000 0.00 0.0 0.00 3.66
1038 1182 0.614697 CCATGACCCCACTTTTCCCC 60.615 60.000 0.00 0.0 0.00 4.81
1207 1353 8.924511 TTCTTGAGATGGTTTCTAACTTGATT 57.075 30.769 0.00 0.0 33.74 2.57
1435 1587 6.060788 GGGTTATTCAAGAAGAGAGCATCAT 58.939 40.000 0.00 0.0 37.82 2.45
1444 1596 7.505585 AGTGTTCAATTGGGTTATTCAAGAAGA 59.494 33.333 5.42 0.0 0.00 2.87
1520 1673 4.399303 AGGAGATAATTTCCAAACCTTGCG 59.601 41.667 0.00 0.0 37.18 4.85
1536 1689 8.007405 TCATCAACGTCAATAGAAAGGAGATA 57.993 34.615 0.00 0.0 0.00 1.98
1571 1736 0.174845 TCTCGCCATTCACCTAACCG 59.825 55.000 0.00 0.0 0.00 4.44
1575 1740 2.499693 TGTTGATCTCGCCATTCACCTA 59.500 45.455 0.00 0.0 0.00 3.08
1661 1826 4.778427 CCTAGTGGACCCTCTAGAACTTTT 59.222 45.833 20.74 0.0 40.55 2.27
1675 1840 1.555075 TGAGAATGGCACCTAGTGGAC 59.445 52.381 0.00 0.0 37.04 4.02
1717 1882 4.458295 CACCAGATTTCACAAGAGCTTCAT 59.542 41.667 0.00 0.0 0.00 2.57
1808 1973 1.065418 GCATAGTAGTGGGCAAGGTGT 60.065 52.381 0.00 0.0 0.00 4.16
2002 2175 8.853126 CCATACATGTTCACATTCCAAATATCT 58.147 33.333 2.30 0.0 33.61 1.98
2242 2534 3.482147 AACGGGTTGGTTTCGTTCT 57.518 47.368 0.00 0.0 42.40 3.01
2290 2582 2.124860 GGAATGGGTCGGTTCCGG 60.125 66.667 11.37 0.0 35.03 5.14
2330 2622 3.214328 GTTGAGGAACCAACTGTCACAT 58.786 45.455 0.00 0.0 42.20 3.21
2632 3113 1.734707 CGGTCACACTTCCCGTACATC 60.735 57.143 0.00 0.0 37.00 3.06
2685 3172 5.713281 CACAAACTTGCAAAATACGTGTTC 58.287 37.500 0.00 0.0 0.00 3.18
2773 3260 1.310373 CTCCCGGGGAACTCCTAGT 59.690 63.158 23.50 0.0 35.95 2.57
2785 3272 5.699097 TTGAAATTTTACTGAACTCCCGG 57.301 39.130 0.00 0.0 0.00 5.73
2866 3353 5.865085 AGTACTTTTGAACTGGCATCTACA 58.135 37.500 0.00 0.0 0.00 2.74


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

AutoCloner maintained by Alex Coulton.