Multiple sequence alignment - TraesCS7B01G435500

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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 TraesCS7B01G435500 chr7B 100.000 2171 0 0 1 2171 702234978 702232808 0.000000e+00 4010.0
1 TraesCS7B01G435500 chr7B 85.489 317 35 5 400 710 702179681 702179370 9.670000e-84 320.0
2 TraesCS7B01G435500 chr7B 87.200 250 17 9 1295 1541 702178927 702178690 9.880000e-69 270.0
3 TraesCS7B01G435500 chr7B 81.203 133 19 5 1656 1785 702233367 702233238 3.810000e-18 102.0
4 TraesCS7B01G435500 chr7A 90.978 1585 82 16 1 1541 703562994 703561427 0.000000e+00 2078.0
5 TraesCS7B01G435500 chr7A 83.912 317 40 5 400 710 703547081 703546770 2.110000e-75 292.0
6 TraesCS7B01G435500 chr7A 87.500 240 18 6 1295 1532 703546319 703546090 1.280000e-67 267.0
7 TraesCS7B01G435500 chr7A 89.286 168 16 2 859 1025 703546658 703546492 2.180000e-50 209.0
8 TraesCS7B01G435500 chr7D 93.625 1302 70 5 1 1293 612776218 612774921 0.000000e+00 1932.0
9 TraesCS7B01G435500 chr7D 92.797 236 11 2 1306 1541 612774871 612774642 9.600000e-89 337.0
10 TraesCS7B01G435500 chr7D 84.858 317 33 6 400 710 612709932 612709625 2.710000e-79 305.0
11 TraesCS7B01G435500 chr7D 87.149 249 20 6 1295 1541 612709165 612708927 2.750000e-69 272.0
12 TraesCS7B01G435500 chr7D 91.617 167 12 2 860 1025 612709502 612709337 1.680000e-56 230.0
13 TraesCS7B01G435500 chr3B 98.569 629 8 1 1544 2171 17292095 17292723 0.000000e+00 1110.0
14 TraesCS7B01G435500 chr3B 81.203 133 19 5 1656 1785 17292163 17292292 3.810000e-18 102.0
15 TraesCS7B01G435500 chr1B 98.113 477 8 1 1696 2171 632956294 632955818 0.000000e+00 830.0
16 TraesCS7B01G435500 chr1B 99.003 301 2 1 1548 1847 632956674 632956374 2.450000e-149 538.0
17 TraesCS7B01G435500 chr1B 81.955 133 18 5 1656 1785 632956610 632956481 8.190000e-20 108.0
18 TraesCS7B01G435500 chr1B 90.411 73 3 2 1068 1137 571834624 571834695 2.290000e-15 93.5
19 TraesCS7B01G435500 chr2B 98.494 332 5 0 1840 2171 23154579 23154910 8.630000e-164 586.0
20 TraesCS7B01G435500 chr2B 98.026 304 4 2 1546 1847 23154183 23154486 5.310000e-146 527.0
21 TraesCS7B01G435500 chr2B 81.955 133 18 5 1656 1785 23154250 23154379 8.190000e-20 108.0
22 TraesCS7B01G435500 chr4B 94.569 313 16 1 1859 2171 512736024 512735713 1.170000e-132 483.0
23 TraesCS7B01G435500 chr4B 94.304 158 7 2 1702 1858 512736071 512735915 7.740000e-60 241.0
24 TraesCS7B01G435500 chr4B 86.139 202 13 7 1537 1735 512736184 512735995 1.020000e-48 204.0
25 TraesCS7B01G435500 chr5B 93.930 313 17 2 1859 2171 372203594 372203904 2.520000e-129 472.0
26 TraesCS7B01G435500 chr5B 88.725 204 12 6 1656 1858 372203510 372203703 2.790000e-59 239.0
27 TraesCS7B01G435500 chr5B 87.302 189 12 4 1548 1735 372203446 372203623 2.820000e-49 206.0
28 TraesCS7B01G435500 chr1A 93.930 313 17 2 1860 2171 291968944 291968633 2.520000e-129 472.0
29 TraesCS7B01G435500 chr1A 81.761 318 26 14 1543 1858 291969122 291968835 1.000000e-58 237.0
30 TraesCS7B01G435500 chr1A 84.028 144 13 3 1598 1741 291969042 291968909 1.750000e-26 130.0
31 TraesCS7B01G435500 chr1A 91.781 73 2 3 1068 1137 518935065 518935136 4.930000e-17 99.0
32 TraesCS7B01G435500 chr5A 93.291 313 18 1 1860 2169 683348778 683348466 1.960000e-125 459.0
33 TraesCS7B01G435500 chr5A 92.908 141 6 2 1720 1856 683348808 683348668 3.650000e-48 202.0
34 TraesCS7B01G435500 chr5A 81.132 212 19 10 1538 1741 683348941 683348743 1.340000e-32 150.0
35 TraesCS7B01G435500 chr6A 92.652 313 22 1 1860 2171 593677797 593677485 1.180000e-122 449.0
36 TraesCS7B01G435500 chr6A 94.326 141 6 2 1720 1858 593677827 593677687 4.690000e-52 215.0
37 TraesCS7B01G435500 chr6A 82.870 216 15 7 1537 1741 593677966 593677762 7.970000e-40 174.0
38 TraesCS7B01G435500 chr2A 90.476 315 24 3 1860 2171 80461957 80462268 5.580000e-111 411.0
39 TraesCS7B01G435500 chr2A 81.481 324 26 14 1539 1858 80461775 80462068 3.600000e-58 235.0
40 TraesCS7B01G435500 chr2A 84.722 144 11 4 1598 1741 80461859 80461991 1.350000e-27 134.0
41 TraesCS7B01G435500 chr1D 90.411 73 3 2 1068 1137 422984214 422984285 2.290000e-15 93.5
42 TraesCS7B01G435500 chr1D 81.651 109 14 6 1538 1643 2215233 2215338 3.840000e-13 86.1
43 TraesCS7B01G435500 chr3D 83.000 100 13 4 1546 1643 12545761 12545664 1.070000e-13 87.9


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 TraesCS7B01G435500 chr7B 702232808 702234978 2170 True 2056.0 4010 90.601500 1 2171 2 chr7B.!!$R2 2170
1 TraesCS7B01G435500 chr7B 702178690 702179681 991 True 295.0 320 86.344500 400 1541 2 chr7B.!!$R1 1141
2 TraesCS7B01G435500 chr7A 703561427 703562994 1567 True 2078.0 2078 90.978000 1 1541 1 chr7A.!!$R1 1540
3 TraesCS7B01G435500 chr7A 703546090 703547081 991 True 256.0 292 86.899333 400 1532 3 chr7A.!!$R2 1132
4 TraesCS7B01G435500 chr7D 612774642 612776218 1576 True 1134.5 1932 93.211000 1 1541 2 chr7D.!!$R2 1540
5 TraesCS7B01G435500 chr7D 612708927 612709932 1005 True 269.0 305 87.874667 400 1541 3 chr7D.!!$R1 1141
6 TraesCS7B01G435500 chr3B 17292095 17292723 628 False 606.0 1110 89.886000 1544 2171 2 chr3B.!!$F1 627
7 TraesCS7B01G435500 chr1B 632955818 632956674 856 True 492.0 830 93.023667 1548 2171 3 chr1B.!!$R1 623
8 TraesCS7B01G435500 chr2B 23154183 23154910 727 False 407.0 586 92.825000 1546 2171 3 chr2B.!!$F1 625

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
447 448 0.179032 TGCAGCCGGAGACAGAAAAA 60.179 50.0 5.05 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1862 1.196012 GAGGGGTTCCTTCGAGACAT 58.804 55.0 0.0 0.0 45.05 3.06 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
98 99 1.345415 CCATGGTGCTTTCCAAAAGCT 59.655 47.619 21.20 2.76 43.38 3.74
157 158 5.525012 GCTGTACTGCACTTGATGAATCATA 59.475 40.000 18.75 0.00 36.56 2.15
195 196 2.070028 GTCGTCTGCTTTCTTCCTTCC 58.930 52.381 0.00 0.00 0.00 3.46
256 257 3.809832 CCGTGATATGACCATTGTTCTCC 59.190 47.826 0.00 0.00 0.00 3.71
257 258 4.443457 CCGTGATATGACCATTGTTCTCCT 60.443 45.833 0.00 0.00 0.00 3.69
297 298 2.621998 CCATGCTCATGTGAAATCCTCC 59.378 50.000 8.81 0.00 37.11 4.30
310 311 1.414061 ATCCTCCCATGGCCGAGAAG 61.414 60.000 17.07 4.35 0.00 2.85
324 325 3.506810 CCGAGAAGACTTGTTAGCAGAG 58.493 50.000 0.00 0.00 0.00 3.35
328 329 4.565022 AGAAGACTTGTTAGCAGAGAAGC 58.435 43.478 0.00 0.00 0.00 3.86
334 335 3.751479 TGTTAGCAGAGAAGCTGTTCA 57.249 42.857 0.00 0.00 46.11 3.18
365 366 6.690530 TGATCTGCAAGGGAAAACATAAAAG 58.309 36.000 0.00 0.00 0.00 2.27
366 367 6.267471 TGATCTGCAAGGGAAAACATAAAAGT 59.733 34.615 0.00 0.00 0.00 2.66
416 417 4.275689 TGACAAACTGACAAGCCACAATAG 59.724 41.667 0.00 0.00 0.00 1.73
419 420 4.357918 AACTGACAAGCCACAATAGTCT 57.642 40.909 0.00 0.00 0.00 3.24
447 448 0.179032 TGCAGCCGGAGACAGAAAAA 60.179 50.000 5.05 0.00 0.00 1.94
546 547 6.560253 GACAAGTGTCCACTGATAATTGTT 57.440 37.500 0.00 0.00 46.33 2.83
735 808 1.419387 GCTAGAATCCTCACCATGGCT 59.581 52.381 13.04 0.01 0.00 4.75
748 821 5.431765 TCACCATGGCTAAAGAAGAGAATC 58.568 41.667 13.04 0.00 0.00 2.52
769 842 6.994421 ATCCCCCATTACCAATTAACAATC 57.006 37.500 0.00 0.00 0.00 2.67
814 887 1.279271 AGACCTGGGTGATGTAGTTGC 59.721 52.381 0.00 0.00 0.00 4.17
817 890 3.115390 ACCTGGGTGATGTAGTTGCTAT 58.885 45.455 0.00 0.00 0.00 2.97
823 896 6.186957 TGGGTGATGTAGTTGCTATGAAAAT 58.813 36.000 0.00 0.00 0.00 1.82
857 930 4.007644 GGCAGGGCAAGGGCAAAC 62.008 66.667 0.00 0.00 43.71 2.93
883 956 9.469807 CCAATATTGCTCTGACTTACTAACTAG 57.530 37.037 10.11 0.00 0.00 2.57
970 1054 2.510238 GCTGCTGCTACCTGGTCG 60.510 66.667 0.63 0.00 36.03 4.79
1143 1227 4.526650 GTCTCCCTCTCTCCATCTAAATCC 59.473 50.000 0.00 0.00 0.00 3.01
1249 1356 3.753272 AGTTGCTTGTCATGTATGGTGTC 59.247 43.478 0.00 0.00 0.00 3.67
1284 1395 3.308866 GCTACATAATGGTCGGTTGTGTC 59.691 47.826 0.00 0.00 33.74 3.67
1385 1534 7.038302 AGTCACTGAATAAGAATGTAAGGGTCA 60.038 37.037 0.00 0.00 0.00 4.02
1529 1681 9.554724 GAAAATCTTACATATGCGAAAACAAGA 57.445 29.630 1.58 1.65 0.00 3.02
1541 1693 6.370593 TGCGAAAACAAGAGTGTCAATATTC 58.629 36.000 0.00 0.00 36.80 1.75
1542 1694 6.204688 TGCGAAAACAAGAGTGTCAATATTCT 59.795 34.615 0.00 0.00 36.80 2.40
1543 1695 7.386573 TGCGAAAACAAGAGTGTCAATATTCTA 59.613 33.333 0.00 0.00 36.80 2.10
1544 1696 8.391106 GCGAAAACAAGAGTGTCAATATTCTAT 58.609 33.333 0.00 0.00 36.80 1.98
1712 1864 4.181010 CACCCCTCCCGCCTCATG 62.181 72.222 0.00 0.00 0.00 3.07
1907 2292 2.610859 ACCCCGCACCTCTGGAAT 60.611 61.111 0.00 0.00 0.00 3.01
1990 2375 0.249911 GGATCGATCCCAAACCCTCG 60.250 60.000 30.80 0.00 41.20 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 4.207165 AGCAAAGTTAGAAAGAGTGGCAA 58.793 39.130 0.00 0.00 0.00 4.52
130 131 7.520706 TGATTCATCAAGTGCAGTACAGCAAT 61.521 38.462 15.09 11.25 45.74 3.56
157 158 5.544948 AGACGACTCCCTATATAGTCTCTGT 59.455 44.000 8.92 0.64 40.00 3.41
256 257 5.404466 TGGCAAATAATCCACCTGAAAAG 57.596 39.130 0.00 0.00 0.00 2.27
257 258 5.732633 CATGGCAAATAATCCACCTGAAAA 58.267 37.500 0.00 0.00 34.81 2.29
297 298 0.036010 ACAAGTCTTCTCGGCCATGG 60.036 55.000 7.63 7.63 0.00 3.66
310 311 3.658709 ACAGCTTCTCTGCTAACAAGTC 58.341 45.455 0.00 0.00 46.76 3.01
324 325 5.629097 CAGATCAATTCACTGAACAGCTTC 58.371 41.667 1.46 0.00 34.07 3.86
328 329 5.366829 TTGCAGATCAATTCACTGAACAG 57.633 39.130 0.00 0.00 34.07 3.16
334 335 3.726557 TCCCTTGCAGATCAATTCACT 57.273 42.857 0.00 0.00 33.57 3.41
419 420 2.031012 CCGGCTGCAGTCTCACAA 59.969 61.111 17.70 0.00 0.00 3.33
434 435 2.354510 TGCAAGTGTTTTTCTGTCTCCG 59.645 45.455 0.00 0.00 0.00 4.63
447 448 2.862541 TCAATTGTAGGCTGCAAGTGT 58.137 42.857 33.37 16.36 41.08 3.55
541 542 8.227428 GCTATTGCATATCCTCTCAGGAACAAT 61.227 40.741 13.53 13.53 42.93 2.71
543 544 5.512060 GCTATTGCATATCCTCTCAGGAACA 60.512 44.000 0.00 0.00 42.93 3.18
544 545 4.934602 GCTATTGCATATCCTCTCAGGAAC 59.065 45.833 0.00 0.00 42.93 3.62
545 546 4.019860 GGCTATTGCATATCCTCTCAGGAA 60.020 45.833 0.66 0.00 44.28 3.36
546 547 3.517100 GGCTATTGCATATCCTCTCAGGA 59.483 47.826 0.66 0.00 44.84 3.86
575 582 2.713167 AGGCATTATATGAGTGGTGGCT 59.287 45.455 0.00 0.00 37.61 4.75
735 808 5.734140 TGGTAATGGGGGATTCTCTTCTTTA 59.266 40.000 0.00 0.00 0.00 1.85
748 821 4.346709 GGGATTGTTAATTGGTAATGGGGG 59.653 45.833 0.00 0.00 0.00 5.40
769 842 0.541863 AGCGATTGGTCTGTTAGGGG 59.458 55.000 0.00 0.00 0.00 4.79
814 887 8.873830 CGTCCACTTATATAGGCATTTTCATAG 58.126 37.037 0.00 0.00 0.00 2.23
817 890 5.995282 CCGTCCACTTATATAGGCATTTTCA 59.005 40.000 0.00 0.00 0.00 2.69
853 926 7.383102 AGTAAGTCAGAGCAATATTGGTTTG 57.617 36.000 24.71 24.71 40.74 2.93
857 930 9.469807 CTAGTTAGTAAGTCAGAGCAATATTGG 57.530 37.037 17.02 0.58 0.00 3.16
875 948 9.075678 TCTCTGTTTACTGTTTAGCTAGTTAGT 57.924 33.333 9.74 9.74 0.00 2.24
883 956 5.474825 AGAGCTCTCTGTTTACTGTTTAGC 58.525 41.667 11.45 0.00 38.75 3.09
970 1054 1.018226 ATTCACACTGCTGAGAGCGC 61.018 55.000 0.00 0.00 46.26 5.92
1036 1120 4.033776 ACCCCTGGTCACATGCCG 62.034 66.667 0.00 0.00 0.00 5.69
1046 1130 0.679002 CATCACTGAAGCACCCCTGG 60.679 60.000 0.00 0.00 0.00 4.45
1143 1227 2.351276 CCCCCTCCTCCAAACACG 59.649 66.667 0.00 0.00 0.00 4.49
1249 1356 7.775120 ACCATTATGTAGCTGAAAATTCAAGG 58.225 34.615 0.00 0.00 36.64 3.61
1284 1395 2.849942 TGAACACACTCCCATTCACTG 58.150 47.619 0.00 0.00 0.00 3.66
1529 1681 9.823647 CACAGTCCTTAATAGAATATTGACACT 57.176 33.333 0.00 0.00 0.00 3.55
1541 1693 6.582636 TGCCAGTTATCACAGTCCTTAATAG 58.417 40.000 0.00 0.00 0.00 1.73
1542 1694 6.553953 TGCCAGTTATCACAGTCCTTAATA 57.446 37.500 0.00 0.00 0.00 0.98
1543 1695 5.435686 TGCCAGTTATCACAGTCCTTAAT 57.564 39.130 0.00 0.00 0.00 1.40
1544 1696 4.901197 TGCCAGTTATCACAGTCCTTAA 57.099 40.909 0.00 0.00 0.00 1.85
1545 1697 4.564821 GGTTGCCAGTTATCACAGTCCTTA 60.565 45.833 0.00 0.00 0.00 2.69
1546 1698 3.412386 GTTGCCAGTTATCACAGTCCTT 58.588 45.455 0.00 0.00 0.00 3.36
1710 1862 1.196012 GAGGGGTTCCTTCGAGACAT 58.804 55.000 0.00 0.00 45.05 3.06
1712 1864 1.615165 GGGAGGGGTTCCTTCGAGAC 61.615 65.000 0.00 0.00 45.05 3.36
1983 2368 3.786553 TCCCATATAGTATGCGAGGGTT 58.213 45.455 0.00 0.00 36.24 4.11
1990 2375 8.492673 TCGAAATTTCATCCCATATAGTATGC 57.507 34.615 17.99 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.