Multiple sequence alignment - TraesCS5D01G309100

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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 TraesCS5D01G309100 chr5D 100.000 3799 0 0 1 3799 406352971 406349173 0.000000e+00 7016
1 TraesCS5D01G309100 chr5D 99.053 845 8 0 2955 3799 429728590 429727746 0.000000e+00 1517
2 TraesCS5D01G309100 chr5B 96.580 2105 66 5 852 2955 487249581 487247482 0.000000e+00 3483
3 TraesCS5D01G309100 chr5B 91.882 850 45 7 2952 3799 627392221 627393048 0.000000e+00 1166
4 TraesCS5D01G309100 chr5B 91.726 846 44 8 2956 3799 623807098 623807919 0.000000e+00 1151
5 TraesCS5D01G309100 chr5B 88.182 440 40 7 473 902 487250037 487249600 7.280000e-142 514
6 TraesCS5D01G309100 chr5B 87.586 435 45 7 1 430 487250463 487250033 2.640000e-136 496
7 TraesCS5D01G309100 chr5B 79.333 300 43 14 389 680 54390997 54391285 3.870000e-45 193
8 TraesCS5D01G309100 chr5A 93.471 2175 82 16 789 2955 511964861 511962739 0.000000e+00 3175
9 TraesCS5D01G309100 chr5A 85.309 599 55 11 177 769 512025375 512024804 4.230000e-164 588
10 TraesCS5D01G309100 chr5A 87.154 397 37 13 375 764 511965187 511964798 4.510000e-119 438
11 TraesCS5D01G309100 chr5A 80.656 305 46 9 387 680 461805138 461804836 1.370000e-54 224
12 TraesCS5D01G309100 chr5A 90.446 157 14 1 29 185 512037131 512036976 4.970000e-49 206
13 TraesCS5D01G309100 chr5A 86.598 97 7 2 757 853 512024652 512024562 6.710000e-18 102
14 TraesCS5D01G309100 chr2A 85.490 1723 201 28 892 2586 21191505 21193206 0.000000e+00 1751
15 TraesCS5D01G309100 chr2A 85.075 1675 199 25 963 2595 21006723 21005058 0.000000e+00 1661
16 TraesCS5D01G309100 chr2A 84.647 1687 215 20 935 2587 21177283 21178959 0.000000e+00 1640
17 TraesCS5D01G309100 chr2A 85.561 1586 193 17 1035 2596 21148240 21149813 0.000000e+00 1628
18 TraesCS5D01G309100 chr2A 86.813 182 20 2 2545 2725 10550276 10550454 2.310000e-47 200
19 TraesCS5D01G309100 chr2A 79.530 298 45 9 394 679 80230972 80230679 8.320000e-47 198
20 TraesCS5D01G309100 chr2A 84.906 106 10 3 581 680 445022334 445022229 6.710000e-18 102
21 TraesCS5D01G309100 chr2B 85.627 1635 198 15 996 2602 33728328 33729953 0.000000e+00 1683
22 TraesCS5D01G309100 chr2B 84.848 1683 213 20 941 2591 33662961 33664633 0.000000e+00 1657
23 TraesCS5D01G309100 chr2B 83.801 1247 168 20 1383 2602 33579702 33578463 0.000000e+00 1153
24 TraesCS5D01G309100 chr2B 81.467 259 39 6 430 680 356305743 356305486 1.790000e-48 204
25 TraesCS5D01G309100 chr2D 85.218 1671 206 20 963 2602 20381027 20382687 0.000000e+00 1679
26 TraesCS5D01G309100 chr2D 84.250 1727 216 29 892 2586 20189189 20187487 0.000000e+00 1631
27 TraesCS5D01G309100 chr2D 87.267 589 61 8 2050 2635 10314309 10314886 0.000000e+00 660
28 TraesCS5D01G309100 chr2D 85.822 529 66 3 2063 2591 20315438 20314919 1.540000e-153 553
29 TraesCS5D01G309100 chr1D 98.697 844 11 0 2956 3799 491754821 491753978 0.000000e+00 1498
30 TraesCS5D01G309100 chr1D 80.132 302 50 6 389 681 487907553 487907253 2.300000e-52 217
31 TraesCS5D01G309100 chr4D 98.580 845 12 0 2955 3799 19454047 19453203 0.000000e+00 1495
32 TraesCS5D01G309100 chrUn 98.227 846 14 1 2955 3799 358911930 358911085 0.000000e+00 1478
33 TraesCS5D01G309100 chr6B 97.870 845 17 1 2956 3799 289517763 289518607 0.000000e+00 1459
34 TraesCS5D01G309100 chr7A 95.621 845 19 10 2956 3799 58005271 58004444 0.000000e+00 1339
35 TraesCS5D01G309100 chr7A 92.135 89 5 2 2955 3043 624964464 624964378 1.430000e-24 124
36 TraesCS5D01G309100 chr3A 95.212 731 30 5 3072 3799 701587186 701586458 0.000000e+00 1151
37 TraesCS5D01G309100 chr3A 94.382 89 3 2 2956 3043 16211270 16211357 6.620000e-28 135
38 TraesCS5D01G309100 chr7B 80.936 299 42 14 389 680 650119034 650119324 4.940000e-54 222
39 TraesCS5D01G309100 chr7B 78.912 294 53 5 391 675 588494988 588495281 1.390000e-44 191
40 TraesCS5D01G309100 chr6A 94.253 87 4 1 2955 3041 4304524 4304609 8.560000e-27 132
41 TraesCS5D01G309100 chr4A 81.132 159 21 8 141 290 672744079 672743921 6.670000e-23 119
42 TraesCS5D01G309100 chr4A 81.132 159 21 8 141 290 672898223 672898065 6.670000e-23 119
43 TraesCS5D01G309100 chr4A 81.132 159 21 8 141 290 672954409 672954251 6.670000e-23 119
44 TraesCS5D01G309100 chr4A 80.503 159 22 8 141 290 672688564 672688406 3.100000e-21 113
45 TraesCS5D01G309100 chr4A 80.503 159 22 8 141 290 672833826 672833668 3.100000e-21 113
46 TraesCS5D01G309100 chr4A 80.503 159 22 8 141 290 672933403 672933245 3.100000e-21 113


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 TraesCS5D01G309100 chr5D 406349173 406352971 3798 True 7016.000000 7016 100.000000 1 3799 1 chr5D.!!$R1 3798
1 TraesCS5D01G309100 chr5D 429727746 429728590 844 True 1517.000000 1517 99.053000 2955 3799 1 chr5D.!!$R2 844
2 TraesCS5D01G309100 chr5B 487247482 487250463 2981 True 1497.666667 3483 90.782667 1 2955 3 chr5B.!!$R1 2954
3 TraesCS5D01G309100 chr5B 627392221 627393048 827 False 1166.000000 1166 91.882000 2952 3799 1 chr5B.!!$F3 847
4 TraesCS5D01G309100 chr5B 623807098 623807919 821 False 1151.000000 1151 91.726000 2956 3799 1 chr5B.!!$F2 843
5 TraesCS5D01G309100 chr5A 511962739 511965187 2448 True 1806.500000 3175 90.312500 375 2955 2 chr5A.!!$R3 2580
6 TraesCS5D01G309100 chr5A 512024562 512025375 813 True 345.000000 588 85.953500 177 853 2 chr5A.!!$R4 676
7 TraesCS5D01G309100 chr2A 21191505 21193206 1701 False 1751.000000 1751 85.490000 892 2586 1 chr2A.!!$F4 1694
8 TraesCS5D01G309100 chr2A 21005058 21006723 1665 True 1661.000000 1661 85.075000 963 2595 1 chr2A.!!$R1 1632
9 TraesCS5D01G309100 chr2A 21177283 21178959 1676 False 1640.000000 1640 84.647000 935 2587 1 chr2A.!!$F3 1652
10 TraesCS5D01G309100 chr2A 21148240 21149813 1573 False 1628.000000 1628 85.561000 1035 2596 1 chr2A.!!$F2 1561
11 TraesCS5D01G309100 chr2B 33728328 33729953 1625 False 1683.000000 1683 85.627000 996 2602 1 chr2B.!!$F2 1606
12 TraesCS5D01G309100 chr2B 33662961 33664633 1672 False 1657.000000 1657 84.848000 941 2591 1 chr2B.!!$F1 1650
13 TraesCS5D01G309100 chr2B 33578463 33579702 1239 True 1153.000000 1153 83.801000 1383 2602 1 chr2B.!!$R1 1219
14 TraesCS5D01G309100 chr2D 20381027 20382687 1660 False 1679.000000 1679 85.218000 963 2602 1 chr2D.!!$F2 1639
15 TraesCS5D01G309100 chr2D 20187487 20189189 1702 True 1631.000000 1631 84.250000 892 2586 1 chr2D.!!$R1 1694
16 TraesCS5D01G309100 chr2D 10314309 10314886 577 False 660.000000 660 87.267000 2050 2635 1 chr2D.!!$F1 585
17 TraesCS5D01G309100 chr2D 20314919 20315438 519 True 553.000000 553 85.822000 2063 2591 1 chr2D.!!$R2 528
18 TraesCS5D01G309100 chr1D 491753978 491754821 843 True 1498.000000 1498 98.697000 2956 3799 1 chr1D.!!$R2 843
19 TraesCS5D01G309100 chr4D 19453203 19454047 844 True 1495.000000 1495 98.580000 2955 3799 1 chr4D.!!$R1 844
20 TraesCS5D01G309100 chrUn 358911085 358911930 845 True 1478.000000 1478 98.227000 2955 3799 1 chrUn.!!$R1 844
21 TraesCS5D01G309100 chr6B 289517763 289518607 844 False 1459.000000 1459 97.870000 2956 3799 1 chr6B.!!$F1 843
22 TraesCS5D01G309100 chr7A 58004444 58005271 827 True 1339.000000 1339 95.621000 2956 3799 1 chr7A.!!$R1 843
23 TraesCS5D01G309100 chr3A 701586458 701587186 728 True 1151.000000 1151 95.212000 3072 3799 1 chr3A.!!$R1 727

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
33 34 0.463833 GGAGGCGTAAACCATGGAGG 60.464 60.000 21.47 2.65 45.67 4.30 F
494 503 0.605589 CACCTCCGAAAGACTGAGCT 59.394 55.000 0.00 0.00 0.00 4.09 F
1109 1377 1.079127 CCTTGCGTCGTCCTCCAAT 60.079 57.895 0.00 0.00 0.00 3.16 F
1646 1923 1.138036 CGTTCTCGACGCCACCATA 59.862 57.895 0.00 0.00 45.86 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 2108 1.579084 GCCATTTGGTCACCGCGTTA 61.579 55.000 4.92 0.0 37.57 3.18 R
2055 2334 1.497309 ATGGACCGGTTGATGGTGGT 61.497 55.000 9.42 0.0 40.63 4.16 R
2587 2896 4.082679 AGCTTCCTACTTGACACTAGTTCG 60.083 45.833 0.00 0.0 0.00 3.95 R
3395 3710 4.154195 GTCATGTTTCCTGCTGTTTATCGT 59.846 41.667 0.00 0.0 0.00 3.73 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
33 34 0.463833 GGAGGCGTAAACCATGGAGG 60.464 60.000 21.47 2.65 45.67 4.30
67 68 4.713321 ACTATGTGTACCGACCTACCAATT 59.287 41.667 0.00 0.00 0.00 2.32
71 72 2.762327 TGTACCGACCTACCAATTCTCC 59.238 50.000 0.00 0.00 0.00 3.71
181 182 5.733676 AGTTATTGAATTGAATTGGCACCC 58.266 37.500 0.00 0.00 0.00 4.61
293 296 6.761242 GGGATGTGGAGGCAAAAATAAATTAC 59.239 38.462 0.00 0.00 0.00 1.89
305 308 9.708348 GCAAAAATAAATTACGAAGACGAAAAG 57.292 29.630 0.00 0.00 42.66 2.27
359 362 7.443575 CCCTTTCAGTATGGTAGAGATTCAATG 59.556 40.741 0.00 0.00 36.16 2.82
363 366 8.547481 TCAGTATGGTAGAGATTCAATGGTAA 57.453 34.615 0.00 0.00 36.16 2.85
373 376 8.985315 AGAGATTCAATGGTAAAGATAATGCA 57.015 30.769 0.00 0.00 0.00 3.96
432 439 4.301637 TCGTTCACATACACGAGCATAT 57.698 40.909 0.00 0.00 40.43 1.78
440 447 4.022242 ACATACACGAGCATATACTCACCC 60.022 45.833 3.86 0.00 36.42 4.61
459 468 0.796312 CCTATGAACGCACACACACC 59.204 55.000 0.00 0.00 0.00 4.16
465 474 2.358247 CGCACACACACCCCCTAC 60.358 66.667 0.00 0.00 0.00 3.18
468 477 2.064242 GCACACACACCCCCTACCTT 62.064 60.000 0.00 0.00 0.00 3.50
494 503 0.605589 CACCTCCGAAAGACTGAGCT 59.394 55.000 0.00 0.00 0.00 4.09
496 505 0.605589 CCTCCGAAAGACTGAGCTGT 59.394 55.000 0.00 0.00 0.00 4.40
572 581 2.816411 TGTCTCCTCCCACTAAACGAT 58.184 47.619 0.00 0.00 0.00 3.73
616 625 6.435430 AAATACAAGAATAATGCGAGCACA 57.565 33.333 0.00 0.00 0.00 4.57
618 627 4.970662 ACAAGAATAATGCGAGCACAAT 57.029 36.364 0.00 0.00 0.00 2.71
630 639 5.175127 TGCGAGCACAATTGTAAATCTAGA 58.825 37.500 11.53 0.00 0.00 2.43
631 640 5.641636 TGCGAGCACAATTGTAAATCTAGAA 59.358 36.000 11.53 0.00 0.00 2.10
638 647 8.398665 GCACAATTGTAAATCTAGAAACCCTAG 58.601 37.037 11.53 0.00 44.94 3.02
646 655 5.941555 ATCTAGAAACCCTAGTGAACTGG 57.058 43.478 0.00 0.00 44.15 4.00
647 656 4.094476 TCTAGAAACCCTAGTGAACTGGG 58.906 47.826 5.90 5.90 44.15 4.45
695 714 5.008415 CCAATCACATTCATCTCCTACTTGC 59.992 44.000 0.00 0.00 0.00 4.01
791 974 4.278419 GGTGAATTAGAACAAGCACCAAGT 59.722 41.667 0.00 0.00 43.87 3.16
811 994 6.974622 CCAAGTAACTTCCATGCATGTAATTC 59.025 38.462 24.58 9.14 0.00 2.17
815 998 3.378112 ACTTCCATGCATGTAATTCACCG 59.622 43.478 24.58 6.69 0.00 4.94
921 1175 2.956132 TGGGAAGAAACTTCCATGCAA 58.044 42.857 25.26 8.27 40.32 4.08
1109 1377 1.079127 CCTTGCGTCGTCCTCCAAT 60.079 57.895 0.00 0.00 0.00 3.16
1265 1536 2.887568 CCGCTCTGCATCGTGACC 60.888 66.667 0.00 0.00 0.00 4.02
1646 1923 1.138036 CGTTCTCGACGCCACCATA 59.862 57.895 0.00 0.00 45.86 2.74
1670 1947 1.144057 CGCCTACGGGAATCTGCTT 59.856 57.895 0.00 0.00 34.97 3.91
1939 2218 2.579684 GAAGCCCTGTACCTCGGCAG 62.580 65.000 15.09 0.00 45.56 4.85
2055 2334 2.602933 GCGTACATATACTTCGGCGACA 60.603 50.000 10.16 0.00 0.00 4.35
2072 2378 1.674322 CACCACCATCAACCGGTCC 60.674 63.158 8.04 0.00 33.25 4.46
2073 2379 2.150719 ACCACCATCAACCGGTCCA 61.151 57.895 8.04 0.00 33.25 4.02
2074 2380 1.302949 CCACCATCAACCGGTCCAT 59.697 57.895 8.04 0.00 33.25 3.41
2165 2471 2.397597 GAGAAGATCTTCCTCTGGCCT 58.602 52.381 28.01 10.18 40.33 5.19
2794 3105 4.576053 CAGCACGATTTTGATCCTATGGAA 59.424 41.667 0.00 0.00 34.34 3.53
2796 3107 5.652014 AGCACGATTTTGATCCTATGGAAAA 59.348 36.000 0.00 0.00 34.34 2.29
3395 3710 2.799017 AGCAATGCCAACTCAATGAGA 58.201 42.857 18.20 0.00 33.32 3.27
3588 3903 0.528017 CTCCGTGAGTCTAGCAAGCA 59.472 55.000 0.00 0.00 0.00 3.91
3654 3969 2.757868 GAGAAGTTCTGGAGCAGCTCTA 59.242 50.000 21.99 15.47 0.00 2.43
3726 4041 2.681976 GCAGCATAGAAGGTGTCCACAT 60.682 50.000 0.00 0.00 39.13 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.958382 TGGTTTACGCCTCCACATGC 60.958 55.000 0.00 0.00 0.00 4.06
9 10 1.401552 CATGGTTTACGCCTCCACATG 59.598 52.381 0.00 0.00 33.91 3.21
41 42 4.527816 TGGTAGGTCGGTACACATAGTTTT 59.472 41.667 0.00 0.00 0.00 2.43
54 55 3.629142 AAAGGAGAATTGGTAGGTCGG 57.371 47.619 0.00 0.00 0.00 4.79
99 100 9.381033 CATCATACAGACAGAAGATTTTTCTCT 57.619 33.333 0.00 0.00 0.00 3.10
161 162 4.405358 GGAGGGTGCCAATTCAATTCAATA 59.595 41.667 0.00 0.00 0.00 1.90
170 171 1.691434 TGTTTTGGAGGGTGCCAATTC 59.309 47.619 0.00 0.00 46.59 2.17
181 182 8.537049 TTCATATTTTCATGCTTGTTTTGGAG 57.463 30.769 0.00 0.00 0.00 3.86
254 255 4.995058 TCCCACCACCCCTCCACC 62.995 72.222 0.00 0.00 0.00 4.61
255 256 2.614013 ATCCCACCACCCCTCCAC 60.614 66.667 0.00 0.00 0.00 4.02
293 296 3.226347 GCATGGTTTCTTTTCGTCTTCG 58.774 45.455 0.00 0.00 38.55 3.79
432 439 1.479323 GTGCGTTCATAGGGGTGAGTA 59.521 52.381 0.00 0.00 0.00 2.59
440 447 0.796312 GGTGTGTGTGCGTTCATAGG 59.204 55.000 0.00 0.00 0.00 2.57
459 468 2.104963 GAGGTGCTCATAAAGGTAGGGG 59.895 54.545 0.00 0.00 0.00 4.79
465 474 2.691409 TTCGGAGGTGCTCATAAAGG 57.309 50.000 0.00 0.00 31.08 3.11
468 477 2.832129 AGTCTTTCGGAGGTGCTCATAA 59.168 45.455 0.00 0.00 31.08 1.90
514 523 0.108804 CGCCTGTGGTGTCTTCGTAT 60.109 55.000 0.00 0.00 0.00 3.06
522 531 4.626081 GTGAGGCGCCTGTGGTGT 62.626 66.667 38.41 8.09 35.34 4.16
572 581 4.161295 CCAGGCTTCCGGCGATGA 62.161 66.667 9.30 0.00 42.94 2.92
618 627 8.877195 AGTTCACTAGGGTTTCTAGATTTACAA 58.123 33.333 7.00 0.00 46.48 2.41
630 639 2.127651 TCCCCAGTTCACTAGGGTTT 57.872 50.000 9.97 0.00 44.12 3.27
631 640 2.361085 ATCCCCAGTTCACTAGGGTT 57.639 50.000 9.97 0.00 44.12 4.11
638 647 1.628846 ACAGTGGTATCCCCAGTTCAC 59.371 52.381 0.00 0.00 45.06 3.18
646 655 2.699321 GTTAGGAGGACAGTGGTATCCC 59.301 54.545 0.00 0.00 34.82 3.85
647 656 2.699321 GGTTAGGAGGACAGTGGTATCC 59.301 54.545 0.00 0.00 34.60 2.59
695 714 3.321682 TGCATGGAAGTTTCTTCCCAAAG 59.678 43.478 21.09 11.77 37.79 2.77
791 974 5.065859 CGGTGAATTACATGCATGGAAGTTA 59.934 40.000 27.54 20.03 33.38 2.24
811 994 3.914984 TTCTCTTGAAGAGCCGGTG 57.085 52.632 17.14 0.00 42.04 4.94
921 1175 1.587066 TCAGGGGCCGGTTAATTACT 58.413 50.000 1.90 0.00 0.00 2.24
986 1249 0.318360 TACACTGACACGGTGCTTCG 60.318 55.000 8.30 0.00 43.84 3.79
1109 1377 2.927580 GCGGAGGAAGTCGGTGTCA 61.928 63.158 0.00 0.00 0.00 3.58
1568 1845 4.585526 CCGCCGCCGCTCAAGATA 62.586 66.667 0.00 0.00 0.00 1.98
1670 1947 1.675310 CATGGCCTTCTTGTCCGCA 60.675 57.895 3.32 0.00 0.00 5.69
1829 2108 1.579084 GCCATTTGGTCACCGCGTTA 61.579 55.000 4.92 0.00 37.57 3.18
2055 2334 1.497309 ATGGACCGGTTGATGGTGGT 61.497 55.000 9.42 0.00 40.63 4.16
2587 2896 4.082679 AGCTTCCTACTTGACACTAGTTCG 60.083 45.833 0.00 0.00 0.00 3.95
2796 3107 8.869109 TGATTTGAATTCCTTCAGGTTACATTT 58.131 29.630 2.27 0.00 42.19 2.32
3027 3339 8.951787 TGTTACTTGTTAGTGTGTATTGACTT 57.048 30.769 0.00 0.00 35.78 3.01
3395 3710 4.154195 GTCATGTTTCCTGCTGTTTATCGT 59.846 41.667 0.00 0.00 0.00 3.73
3588 3903 9.401058 CTCCTTTTCTAGGTTCAATGTGAATAT 57.599 33.333 0.00 0.00 45.03 1.28
3654 3969 7.770433 TGATCATCGTTTCAATGAGGTATCTTT 59.230 33.333 0.00 0.00 36.63 2.52


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

AutoCloner maintained by Alex Coulton.