Multiple sequence alignment - TraesCS1A01G376700

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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 TraesCS1A01G376700 chr1A 100.000 1649 0 0 1 1649 550648769 550650417 0.000000e+00 3046
1 TraesCS1A01G376700 chr1A 92.479 1303 91 4 1 1303 550663377 550664672 0.000000e+00 1857
2 TraesCS1A01G376700 chr1A 94.482 743 35 2 1 739 550677170 550677910 0.000000e+00 1140
3 TraesCS1A01G376700 chr1A 94.482 743 36 2 1 739 550686951 550687692 0.000000e+00 1140
4 TraesCS1A01G376700 chr1A 84.065 866 99 26 693 1527 550788104 550788961 0.000000e+00 798
5 TraesCS1A01G376700 chr1A 86.835 714 64 13 2 689 550781477 550782186 0.000000e+00 771
6 TraesCS1A01G376700 chr1A 88.530 558 55 4 693 1243 550820828 550821383 0.000000e+00 667
7 TraesCS1A01G376700 chr1A 80.988 810 104 33 753 1526 550783732 550784527 4.120000e-167 597
8 TraesCS1A01G376700 chr1A 83.053 714 66 17 2 687 550808031 550808717 4.120000e-167 597
9 TraesCS1A01G376700 chr1A 86.789 545 44 7 1109 1649 550689036 550689556 1.150000e-162 582
10 TraesCS1A01G376700 chr1A 86.606 545 45 7 1109 1649 550679402 550679922 5.370000e-161 577
11 TraesCS1A01G376700 chr1A 92.632 380 19 7 1260 1630 550664656 550665035 2.530000e-149 538
12 TraesCS1A01G376700 chr1A 79.049 883 111 34 696 1528 550720577 550721435 2.530000e-149 538
13 TraesCS1A01G376700 chr1A 81.268 694 75 26 2 681 550787287 550787939 5.530000e-141 510
14 TraesCS1A01G376700 chr1A 83.301 509 69 11 956 1463 550700595 550701088 2.630000e-124 455
15 TraesCS1A01G376700 chr1A 100.000 242 0 0 2002 2243 550650770 550651011 4.390000e-122 448
16 TraesCS1A01G376700 chr1A 81.977 516 70 15 956 1465 550829812 550830310 1.240000e-112 416
17 TraesCS1A01G376700 chr1A 93.827 243 14 1 2002 2243 550665305 550665547 4.550000e-97 364
18 TraesCS1A01G376700 chr1A 92.562 242 13 2 2002 2243 550679966 550680202 2.130000e-90 342
19 TraesCS1A01G376700 chr1A 92.149 242 14 2 2002 2243 550689598 550689834 9.920000e-89 337
20 TraesCS1A01G376700 chr1A 92.571 175 11 2 1477 1649 550830966 550831140 1.330000e-62 250
21 TraesCS1A01G376700 chr1A 89.922 129 13 0 2009 2137 550831575 550831703 1.380000e-37 167
22 TraesCS1A01G376700 chr1A 86.765 136 18 0 2002 2137 550705549 550705684 3.860000e-33 152
23 TraesCS1A01G376700 chr1D 84.633 859 91 24 720 1564 458233701 458234532 0.000000e+00 817
24 TraesCS1A01G376700 chr1D 86.031 766 70 9 2 736 458232692 458233451 0.000000e+00 787
25 TraesCS1A01G376700 chr1D 83.568 852 92 32 720 1551 458164324 458165147 0.000000e+00 754
26 TraesCS1A01G376700 chr1D 86.325 702 68 10 2 681 458265427 458266122 0.000000e+00 739
27 TraesCS1A01G376700 chr1D 80.743 888 102 35 693 1551 458266304 458267151 1.460000e-176 628
28 TraesCS1A01G376700 chr1D 86.124 418 34 6 276 673 458163911 458164324 1.590000e-116 429
29 TraesCS1A01G376700 chr1D 84.615 377 52 5 280 652 458223739 458224113 9.780000e-99 370
30 TraesCS1A01G376700 chr1D 85.345 348 46 3 276 619 458271638 458271984 2.740000e-94 355
31 TraesCS1A01G376700 chr1D 91.667 240 18 1 2 241 458163353 458163590 4.620000e-87 331
32 TraesCS1A01G376700 chr1D 92.571 175 11 2 1477 1649 458170898 458171072 1.330000e-62 250
33 TraesCS1A01G376700 chr1D 91.429 175 13 2 1477 1649 458281558 458281732 2.880000e-59 239
34 TraesCS1A01G376700 chr1D 89.130 184 17 3 1284 1465 458280720 458280902 2.240000e-55 226
35 TraesCS1A01G376700 chr1D 87.978 183 20 2 1284 1465 458169979 458170160 4.850000e-52 215
36 TraesCS1A01G376700 chr1D 90.441 136 13 0 2002 2137 458281780 458281915 1.770000e-41 180
37 TraesCS1A01G376700 chr1D 89.062 128 13 1 2002 2128 458170723 458170850 8.290000e-35 158
38 TraesCS1A01G376700 chr1D 90.598 117 7 2 2013 2128 458281397 458281510 3.860000e-33 152
39 TraesCS1A01G376700 chr1D 95.238 63 2 1 239 300 458163847 458163909 5.100000e-17 99
40 TraesCS1A01G376700 chr1B 84.056 715 84 20 852 1539 628804427 628805138 0.000000e+00 662
41 TraesCS1A01G376700 chr1B 83.119 699 91 18 956 1649 629035481 629036157 1.470000e-171 612
42 TraesCS1A01G376700 chr1B 80.626 511 71 15 956 1465 628980181 628980664 9.780000e-99 370
43 TraesCS1A01G376700 chr1B 84.722 288 38 4 281 563 629052496 629052782 1.310000e-72 283
44 TraesCS1A01G376700 chr1B 91.860 172 13 1 14 184 628833833 628834004 2.880000e-59 239
45 TraesCS1A01G376700 chr1B 91.429 175 12 2 1477 1649 628905247 628905420 1.040000e-58 237
46 TraesCS1A01G376700 chr1B 91.429 175 12 2 1477 1649 628981234 628981407 1.040000e-58 237
47 TraesCS1A01G376700 chr1B 91.150 113 7 2 2012 2123 628818866 628818976 1.390000e-32 150


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 TraesCS1A01G376700 chr1A 550648769 550651011 2242 False 1747.000000 3046 100.000000 1 2243 2 chr1A.!!$F6 2242
1 TraesCS1A01G376700 chr1A 550663377 550665547 2170 False 919.666667 1857 92.979333 1 2243 3 chr1A.!!$F7 2242
2 TraesCS1A01G376700 chr1A 550677170 550680202 3032 False 686.333333 1140 91.216667 1 2243 3 chr1A.!!$F8 2242
3 TraesCS1A01G376700 chr1A 550686951 550689834 2883 False 686.333333 1140 91.140000 1 2243 3 chr1A.!!$F9 2242
4 TraesCS1A01G376700 chr1A 550781477 550788961 7484 False 669.000000 798 83.289000 2 1527 4 chr1A.!!$F10 1525
5 TraesCS1A01G376700 chr1A 550820828 550821383 555 False 667.000000 667 88.530000 693 1243 1 chr1A.!!$F5 550
6 TraesCS1A01G376700 chr1A 550808031 550808717 686 False 597.000000 597 83.053000 2 687 1 chr1A.!!$F4 685
7 TraesCS1A01G376700 chr1A 550720577 550721435 858 False 538.000000 538 79.049000 696 1528 1 chr1A.!!$F3 832
8 TraesCS1A01G376700 chr1A 550829812 550831703 1891 False 277.666667 416 88.156667 956 2137 3 chr1A.!!$F11 1181
9 TraesCS1A01G376700 chr1D 458232692 458234532 1840 False 802.000000 817 85.332000 2 1564 2 chr1D.!!$F5 1562
10 TraesCS1A01G376700 chr1D 458265427 458267151 1724 False 683.500000 739 83.534000 2 1551 2 chr1D.!!$F6 1549
11 TraesCS1A01G376700 chr1D 458163353 458165147 1794 False 403.250000 754 89.149250 2 1551 4 chr1D.!!$F3 1549
12 TraesCS1A01G376700 chr1D 458169979 458171072 1093 False 207.666667 250 89.870333 1284 2128 3 chr1D.!!$F4 844
13 TraesCS1A01G376700 chr1B 628804427 628805138 711 False 662.000000 662 84.056000 852 1539 1 chr1B.!!$F1 687
14 TraesCS1A01G376700 chr1B 629035481 629036157 676 False 612.000000 612 83.119000 956 1649 1 chr1B.!!$F5 693
15 TraesCS1A01G376700 chr1B 628980181 628981407 1226 False 303.500000 370 86.027500 956 1649 2 chr1B.!!$F7 693

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
370 666 0.892755 TTGAAGGCGACACCGTATCT 59.107 50.0 0.0 0.0 46.52 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 11479 0.179184 GACTCGTCGTGCCTCTCTTC 60.179 60.0 0.0 0.0 0.0 2.87 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
65 66 7.935755 ACATTGTTTATGTCAGGATAGGATCAG 59.064 37.037 0.00 0.00 44.15 2.90
179 181 1.878953 CTTCTTGTTAGGTGTGGCGT 58.121 50.000 0.00 0.00 0.00 5.68
180 182 2.218603 CTTCTTGTTAGGTGTGGCGTT 58.781 47.619 0.00 0.00 0.00 4.84
181 183 2.335316 TCTTGTTAGGTGTGGCGTTT 57.665 45.000 0.00 0.00 0.00 3.60
274 544 9.866655 AACCTGCTTATATATGAGGATTTTTCA 57.133 29.630 6.64 0.00 0.00 2.69
340 636 2.616376 GTGTTGTGGCATGTGTAACTGA 59.384 45.455 0.00 0.00 38.04 3.41
357 653 2.480419 ACTGAAATCGCGAACTTGAAGG 59.520 45.455 15.24 1.47 0.00 3.46
370 666 0.892755 TTGAAGGCGACACCGTATCT 59.107 50.000 0.00 0.00 46.52 1.98
406 706 5.931724 TGAACAATAGATATATGTGGCACGG 59.068 40.000 13.77 0.00 0.00 4.94
459 759 7.222000 AGTCATCGTCTTTCTTCTTCTACTT 57.778 36.000 0.00 0.00 0.00 2.24
496 798 9.880157 CTTTTATGATGAAGATTTGTCCCAAAT 57.120 29.630 2.02 2.02 0.00 2.32
540 6606 7.148641 GGATATGAGTCATCACTAAACACGAT 58.851 38.462 9.42 0.00 38.57 3.73
555 6621 2.907431 CGATCACGTGGTTCCAACA 58.093 52.632 17.00 0.00 34.56 3.33
697 6958 6.867816 AGCGAAATTTCTTTTATGATGCAACA 59.132 30.769 15.92 0.00 0.00 3.33
775 7305 1.559682 GTGGATTCCCCTAGTCAGCAA 59.440 52.381 0.00 0.00 35.38 3.91
790 7320 2.562912 CAATGAGTGCACGTGGGC 59.437 61.111 18.88 3.97 0.00 5.36
850 7380 4.779475 CCCATTCGGCGAGCTTAT 57.221 55.556 10.46 0.00 0.00 1.73
854 7390 3.074412 CCCATTCGGCGAGCTTATAAAT 58.926 45.455 10.46 0.00 0.00 1.40
860 7396 2.222027 GGCGAGCTTATAAATGGCTGT 58.778 47.619 2.67 0.00 36.37 4.40
940 7518 8.109634 ACCCTATAAATCAAGAAAGAAGAGCAA 58.890 33.333 0.00 0.00 0.00 3.91
1140 8986 3.003173 TTCTGGAGGGTGAGGCGG 61.003 66.667 0.00 0.00 0.00 6.13
1243 9094 2.351244 CCAGCTCACCGCCTGTAGA 61.351 63.158 0.00 0.00 40.39 2.59
1252 9110 1.613317 CCGCCTGTAGATGACACCCA 61.613 60.000 0.00 0.00 33.31 4.51
1292 9185 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1293 9186 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1295 9188 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1298 9191 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1299 9192 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1302 9195 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1340 9235 0.103390 GCCCGAGGCTAGAGAGTTTC 59.897 60.000 7.58 0.00 46.69 2.78
1350 9245 1.871080 AGAGAGTTTCAAGCGTGGTG 58.129 50.000 0.00 0.00 0.00 4.17
1366 9261 1.419762 TGGTGACCTTGTACTGCACAT 59.580 47.619 2.11 0.00 36.90 3.21
1454 9366 5.818336 TCTGAAACTACCAACGAAATGACAA 59.182 36.000 0.00 0.00 0.00 3.18
1465 9378 8.397906 ACCAACGAAATGACAATGTATCTATTG 58.602 33.333 0.00 0.00 42.38 1.90
1504 10533 1.135960 TGCCACGATGGAATGGGATA 58.864 50.000 8.04 0.00 40.96 2.59
1511 10540 5.412594 CCACGATGGAATGGGATATAAACTG 59.587 44.000 0.00 0.00 40.96 3.16
1611 10641 7.577426 GCATATTGGGAGTGAACTGAATTTTCA 60.577 37.037 0.00 0.00 35.57 2.69
2060 11369 3.258123 TCCACGTGATCAGAATGTTCAGA 59.742 43.478 19.30 0.00 44.68 3.27
2100 11409 9.878599 CCATTTGGTAGATAATTGATCGTTTAC 57.121 33.333 0.00 0.00 39.80 2.01
2123 11432 4.083003 CGCTGAGATCCATCCTTACTAGAC 60.083 50.000 0.00 0.00 0.00 2.59
2130 11439 3.958147 TCCATCCTTACTAGACGCATCAA 59.042 43.478 0.00 0.00 0.00 2.57
2205 11514 3.615811 TCCAGGTCCCCAGCTCCT 61.616 66.667 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.551071 CCAAACAGTCTCAGAGAACCCC 60.551 54.545 0.20 0.0 0.00 4.95
202 205 2.815647 GAAGGCCGCCGACTCAAG 60.816 66.667 3.05 0.0 0.00 3.02
357 653 2.334838 AGTTTCAAGATACGGTGTCGC 58.665 47.619 0.00 0.0 40.63 5.19
406 706 1.226018 GCTTTACACGCACGATGGC 60.226 57.895 0.00 0.0 0.00 4.40
496 798 7.389607 TCATATCCGATCACGAAGATGTAGTTA 59.610 37.037 0.00 0.0 42.66 2.24
540 6606 1.346395 AGCTATGTTGGAACCACGTGA 59.654 47.619 19.30 0.0 0.00 4.35
697 6958 6.923199 ATCACATTTGGAACATCTTTTCCT 57.077 33.333 3.66 0.0 44.89 3.36
843 7373 5.126067 TCCTCAACAGCCATTTATAAGCTC 58.874 41.667 0.00 0.0 33.70 4.09
844 7374 5.116084 TCCTCAACAGCCATTTATAAGCT 57.884 39.130 0.00 0.0 37.32 3.74
845 7375 4.261363 GCTCCTCAACAGCCATTTATAAGC 60.261 45.833 0.00 0.0 0.00 3.09
846 7376 5.429957 GCTCCTCAACAGCCATTTATAAG 57.570 43.478 0.00 0.0 0.00 1.73
860 7396 0.899717 GCACAAATGGGGCTCCTCAA 60.900 55.000 3.07 0.0 0.00 3.02
940 7518 5.118664 CACGATTGATTAAACACGACTCTGT 59.881 40.000 3.32 0.0 0.00 3.41
1120 8966 1.761174 GCCTCACCCTCCAGAACAA 59.239 57.895 0.00 0.0 0.00 2.83
1173 9024 3.452627 AGCTCTTGAGGTCGTATCCAAAT 59.547 43.478 0.00 0.0 0.00 2.32
1176 9027 2.145397 AGCTCTTGAGGTCGTATCCA 57.855 50.000 0.00 0.0 0.00 3.41
1252 9110 0.325272 GAAGAAGAAGAAGCCCCCGT 59.675 55.000 0.00 0.0 0.00 5.28
1292 9185 1.153549 CCGGGCGGAGAAGAAGAAG 60.154 63.158 0.00 0.0 37.50 2.85
1293 9186 2.978824 CCGGGCGGAGAAGAAGAA 59.021 61.111 0.00 0.0 37.50 2.52
1295 9188 4.840005 GGCCGGGCGGAGAAGAAG 62.840 72.222 14.21 0.0 37.50 2.85
1323 9218 2.737039 GCTTGAAACTCTCTAGCCTCGG 60.737 54.545 0.00 0.0 44.36 4.63
1340 9235 0.865769 GTACAAGGTCACCACGCTTG 59.134 55.000 0.00 0.0 37.08 4.01
1350 9245 4.994852 TCAAACTATGTGCAGTACAAGGTC 59.005 41.667 0.00 0.0 43.77 3.85
1454 9366 5.300286 GGCTTCCAAACTGCAATAGATACAT 59.700 40.000 0.00 0.0 0.00 2.29
1465 9378 1.235724 AGTAACGGCTTCCAAACTGC 58.764 50.000 0.00 0.0 0.00 4.40
1511 10540 5.604815 GCATGTGCGACATAAACATAAAC 57.395 39.130 0.00 0.0 36.53 2.01
1611 10641 4.773674 TCATGCCTCCTGAAAATTGACATT 59.226 37.500 0.00 0.0 0.00 2.71
2060 11369 0.481128 AAATGGGTGTTTCGAGGGGT 59.519 50.000 0.00 0.0 0.00 4.95
2100 11409 4.075682 TCTAGTAAGGATGGATCTCAGCG 58.924 47.826 0.00 0.0 31.40 5.18
2130 11439 1.741770 GGAGTTTCCGAGCGCATGT 60.742 57.895 11.47 0.0 0.00 3.21
2170 11479 0.179184 GACTCGTCGTGCCTCTCTTC 60.179 60.000 0.00 0.0 0.00 2.87
2217 11526 1.654220 CTTTGTCTTGGGTGGTGCG 59.346 57.895 0.00 0.0 0.00 5.34


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

AutoCloner maintained by Alex Coulton.