Multiple sequence alignment - TraesCS6D01G179500

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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 TraesCS6D01G179500 chr6D 100.000 2310 0 0 1 2310 193574854 193572545 0.000000e+00 4266.0
1 TraesCS6D01G179500 chr6D 91.860 172 12 1 221 390 193574469 193574298 2.970000e-59 239.0
2 TraesCS6D01G179500 chr6D 91.860 172 12 1 386 557 193574634 193574465 2.970000e-59 239.0
3 TraesCS6D01G179500 chr6B 93.116 1932 77 23 395 2310 300936789 300938680 0.000000e+00 2780.0
4 TraesCS6D01G179500 chr6B 92.025 163 11 2 230 391 300936789 300936950 6.420000e-56 228.0
5 TraesCS6D01G179500 chr6A 96.944 1276 25 3 1036 2310 268588080 268586818 0.000000e+00 2128.0
6 TraesCS6D01G179500 chr6A 89.642 811 38 13 1 778 268589256 268588459 0.000000e+00 990.0
7 TraesCS6D01G179500 chr6A 87.781 401 22 8 593 990 268588455 268588079 5.860000e-121 444.0
8 TraesCS6D01G179500 chr6A 94.220 173 8 1 221 391 268588869 268588697 1.760000e-66 263.0
9 TraesCS6D01G179500 chr6A 90.173 173 15 2 386 557 268589036 268588865 8.310000e-55 224.0
10 TraesCS6D01G179500 chr5D 84.391 961 115 17 386 1330 324982103 324983044 0.000000e+00 911.0
11 TraesCS6D01G179500 chr5D 84.478 393 52 7 1 387 502650366 502649977 1.680000e-101 379.0
12 TraesCS6D01G179500 chr5D 83.418 392 50 10 1 387 324981893 324982274 1.310000e-92 350.0
13 TraesCS6D01G179500 chrUn 84.173 973 107 19 386 1337 21283668 21282722 0.000000e+00 900.0
14 TraesCS6D01G179500 chrUn 85.678 391 46 7 1 384 21283888 21283501 9.940000e-109 403.0
15 TraesCS6D01G179500 chr5B 82.970 963 127 21 386 1331 377481230 377482172 0.000000e+00 835.0
16 TraesCS6D01G179500 chr5B 81.612 397 58 9 1 391 377481017 377481404 4.790000e-82 315.0
17 TraesCS6D01G179500 chr3D 84.013 907 102 26 448 1337 537040008 537040888 0.000000e+00 832.0
18 TraesCS6D01G179500 chr3D 86.047 86 11 1 1 86 525954806 525954890 8.790000e-15 91.6
19 TraesCS6D01G179500 chr1A 88.942 633 48 11 718 1337 561332910 561333533 0.000000e+00 761.0
20 TraesCS6D01G179500 chr1B 81.451 965 141 27 387 1330 230951108 230950161 0.000000e+00 756.0
21 TraesCS6D01G179500 chr5A 81.568 944 124 24 386 1312 199142594 199141684 0.000000e+00 734.0
22 TraesCS6D01G179500 chr2B 81.462 944 129 25 386 1311 542249611 542250526 0.000000e+00 732.0
23 TraesCS6D01G179500 chr7B 79.916 951 141 31 400 1330 608367550 608368470 0.000000e+00 652.0
24 TraesCS6D01G179500 chr7B 82.314 605 87 10 718 1311 442357080 442356485 7.360000e-140 507.0
25 TraesCS6D01G179500 chr2A 84.097 698 73 19 386 1059 456500932 456501615 6.960000e-180 640.0
26 TraesCS6D01G179500 chr7D 86.356 579 58 12 762 1329 124606290 124605722 1.520000e-171 612.0
27 TraesCS6D01G179500 chr7D 80.407 393 61 11 760 1148 250080558 250080938 3.760000e-73 285.0
28 TraesCS6D01G179500 chr7D 80.250 400 59 11 760 1148 249949721 249950111 1.350000e-72 283.0
29 TraesCS6D01G179500 chr1D 82.388 670 93 16 679 1335 142333917 142333260 5.570000e-156 560.0
30 TraesCS6D01G179500 chr7A 79.521 459 70 14 718 1162 271160852 271160404 2.880000e-79 305.0
31 TraesCS6D01G179500 chr4D 80.506 395 63 8 1 391 173093992 173093608 8.070000e-75 291.0


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 TraesCS6D01G179500 chr6D 193572545 193574854 2309 True 1581.333333 4266 94.573333 1 2310 3 chr6D.!!$R1 2309
1 TraesCS6D01G179500 chr6B 300936789 300938680 1891 False 1504.000000 2780 92.570500 230 2310 2 chr6B.!!$F1 2080
2 TraesCS6D01G179500 chr6A 268586818 268589256 2438 True 809.800000 2128 91.752000 1 2310 5 chr6A.!!$R1 2309
3 TraesCS6D01G179500 chr5D 324981893 324983044 1151 False 630.500000 911 83.904500 1 1330 2 chr5D.!!$F1 1329
4 TraesCS6D01G179500 chrUn 21282722 21283888 1166 True 651.500000 900 84.925500 1 1337 2 chrUn.!!$R1 1336
5 TraesCS6D01G179500 chr5B 377481017 377482172 1155 False 575.000000 835 82.291000 1 1331 2 chr5B.!!$F1 1330
6 TraesCS6D01G179500 chr3D 537040008 537040888 880 False 832.000000 832 84.013000 448 1337 1 chr3D.!!$F2 889
7 TraesCS6D01G179500 chr1A 561332910 561333533 623 False 761.000000 761 88.942000 718 1337 1 chr1A.!!$F1 619
8 TraesCS6D01G179500 chr1B 230950161 230951108 947 True 756.000000 756 81.451000 387 1330 1 chr1B.!!$R1 943
9 TraesCS6D01G179500 chr5A 199141684 199142594 910 True 734.000000 734 81.568000 386 1312 1 chr5A.!!$R1 926
10 TraesCS6D01G179500 chr2B 542249611 542250526 915 False 732.000000 732 81.462000 386 1311 1 chr2B.!!$F1 925
11 TraesCS6D01G179500 chr7B 608367550 608368470 920 False 652.000000 652 79.916000 400 1330 1 chr7B.!!$F1 930
12 TraesCS6D01G179500 chr7B 442356485 442357080 595 True 507.000000 507 82.314000 718 1311 1 chr7B.!!$R1 593
13 TraesCS6D01G179500 chr2A 456500932 456501615 683 False 640.000000 640 84.097000 386 1059 1 chr2A.!!$F1 673
14 TraesCS6D01G179500 chr7D 124605722 124606290 568 True 612.000000 612 86.356000 762 1329 1 chr7D.!!$R1 567
15 TraesCS6D01G179500 chr1D 142333260 142333917 657 True 560.000000 560 82.388000 679 1335 1 chr1D.!!$R1 656

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
358 363 0.318762 AAAGGAGGTGTCGAGAGTGC 59.681 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 1988 0.03759 TTTACGGGTTCAGGCTGCAT 59.962 50.0 10.34 0.0 0.0 3.96 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
57 58 7.632245 GCTTGGAGCTATTCAAAGAATGGAATT 60.632 37.037 7.20 0.00 38.91 2.17
127 129 5.470098 CGGAGAAAAACTGAGAAGAATTGGA 59.530 40.000 0.00 0.00 0.00 3.53
180 182 5.607939 TGGAGCGAGATTTGGAAGTTATA 57.392 39.130 0.00 0.00 0.00 0.98
234 237 4.052518 ACTGCATGGCACCCTCCC 62.053 66.667 0.00 0.00 33.79 4.30
237 240 3.792736 GCATGGCACCCTCCCGTA 61.793 66.667 0.00 0.00 0.00 4.02
283 287 5.768164 ACACATAAAAGTTACCCAGTTCCTG 59.232 40.000 0.00 0.00 0.00 3.86
289 293 2.152016 GTTACCCAGTTCCTGCTTGTC 58.848 52.381 0.00 0.00 0.00 3.18
306 310 3.703001 TGTCCCTTTGGATCAGAAGAC 57.297 47.619 8.43 2.03 44.28 3.01
310 314 3.394274 TCCCTTTGGATCAGAAGACACAA 59.606 43.478 8.43 0.00 35.03 3.33
312 316 4.217118 CCCTTTGGATCAGAAGACACAAAG 59.783 45.833 0.00 0.00 43.41 2.77
358 363 0.318762 AAAGGAGGTGTCGAGAGTGC 59.681 55.000 0.00 0.00 0.00 4.40
360 365 0.963355 AGGAGGTGTCGAGAGTGCTC 60.963 60.000 0.00 0.00 37.81 4.26
468 475 1.815003 CTGCTTGTCCCTTTGGATCAC 59.185 52.381 0.00 0.00 44.28 3.06
528 535 0.687354 GGAGGTTTGGAGAGTGCTGA 59.313 55.000 0.00 0.00 0.00 4.26
557 585 5.009410 GGATCAGGTCATTAAAAGAGCATGG 59.991 44.000 11.49 3.31 36.03 3.66
684 722 5.243207 ACAACTTGGTACTTATGCTGGTAC 58.757 41.667 0.00 0.00 37.97 3.34
695 733 1.219935 GCTGGTACTTACGGTGGGG 59.780 63.158 0.00 0.00 0.00 4.96
700 738 0.615827 GTACTTACGGTGGGGGAGGT 60.616 60.000 0.00 0.00 0.00 3.85
720 760 5.755849 AGGTGAAAATCGGTCCATAAAGAT 58.244 37.500 0.00 0.00 0.00 2.40
813 1035 7.919151 ACCAAAGGCTACTATAAAAAGAGAGT 58.081 34.615 0.00 0.00 0.00 3.24
896 1134 1.852067 GCTTAGGCGGGTGTTGTGTG 61.852 60.000 0.00 0.00 0.00 3.82
1060 1301 3.881688 CTCAGATAACTTGGAGGCCATTG 59.118 47.826 5.01 0.00 31.53 2.82
1061 1302 3.523157 TCAGATAACTTGGAGGCCATTGA 59.477 43.478 5.01 0.00 31.53 2.57
1062 1303 4.018506 TCAGATAACTTGGAGGCCATTGAA 60.019 41.667 5.01 0.00 31.53 2.69
1063 1304 4.706476 CAGATAACTTGGAGGCCATTGAAA 59.294 41.667 5.01 0.00 31.53 2.69
1064 1305 4.952335 AGATAACTTGGAGGCCATTGAAAG 59.048 41.667 5.01 3.76 31.53 2.62
1065 1306 2.683211 ACTTGGAGGCCATTGAAAGT 57.317 45.000 5.01 4.45 31.53 2.66
1066 1307 2.962859 ACTTGGAGGCCATTGAAAGTT 58.037 42.857 5.01 0.00 31.53 2.66
1490 1750 8.571336 CAAGAAAAGAATGTTCCTGATTGTAGT 58.429 33.333 0.00 0.00 30.66 2.73
1491 1751 8.697507 AGAAAAGAATGTTCCTGATTGTAGTT 57.302 30.769 0.00 0.00 30.66 2.24
1492 1752 8.571336 AGAAAAGAATGTTCCTGATTGTAGTTG 58.429 33.333 0.00 0.00 30.66 3.16
1493 1753 7.823745 AAAGAATGTTCCTGATTGTAGTTGT 57.176 32.000 0.00 0.00 0.00 3.32
1494 1754 8.918202 AAAGAATGTTCCTGATTGTAGTTGTA 57.082 30.769 0.00 0.00 0.00 2.41
1495 1755 8.553459 AAGAATGTTCCTGATTGTAGTTGTAG 57.447 34.615 0.00 0.00 0.00 2.74
1544 1804 1.000896 GCCTTAGGCCTGCTTCCAA 60.001 57.895 17.99 0.00 44.06 3.53
1728 1988 3.385384 CCTCTGGTGCAGCTCCGA 61.385 66.667 18.08 9.81 0.00 4.55
1889 2149 3.311106 CAATGACACGCTTCATTTGCTT 58.689 40.909 8.92 0.00 42.45 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.068024 TCCAAGCAACAAAGTCCAACATC 59.932 43.478 0.00 0.00 0.00 3.06
62 64 2.736144 ACGTAGGCTGATCGAACAAA 57.264 45.000 13.50 0.00 0.00 2.83
63 65 2.751259 ACTACGTAGGCTGATCGAACAA 59.249 45.455 25.63 0.00 0.00 2.83
79 81 0.802494 GGTGTTCCCATTGCACTACG 59.198 55.000 0.00 0.00 33.96 3.51
106 108 7.512992 TCTCTCCAATTCTTCTCAGTTTTTCT 58.487 34.615 0.00 0.00 0.00 2.52
127 129 8.986991 GGATTAATAGTCATATGTCCCATCTCT 58.013 37.037 1.90 0.00 0.00 3.10
217 220 4.052518 GGGAGGGTGCCATGCAGT 62.053 66.667 0.00 0.00 40.08 4.40
289 293 3.423539 TGTGTCTTCTGATCCAAAGGG 57.576 47.619 4.80 0.00 0.00 3.95
306 310 9.356433 TCACATTGAAATAACATATGCTTTGTG 57.644 29.630 1.58 6.17 0.00 3.33
312 316 8.749499 GCTTTCTCACATTGAAATAACATATGC 58.251 33.333 1.58 0.00 33.65 3.14
358 363 3.533606 AATGACTTGATCCAGTCCGAG 57.466 47.619 20.90 0.00 42.39 4.63
360 365 5.874810 TCTTTTAATGACTTGATCCAGTCCG 59.125 40.000 20.90 4.64 42.39 4.79
468 475 9.844790 TTGAAATAACAGATGCTTTGTATCTTG 57.155 29.630 0.00 0.00 32.96 3.02
483 490 8.578308 TTTGCTTTCTCACATTGAAATAACAG 57.422 30.769 0.00 0.00 33.65 3.16
528 535 6.627087 TCTTTTAATGACCTGATCCAGTCT 57.373 37.500 12.06 0.00 0.00 3.24
557 585 3.209410 CTCACCAGCATAATCAACCTCC 58.791 50.000 0.00 0.00 0.00 4.30
684 722 1.196104 TTCACCTCCCCCACCGTAAG 61.196 60.000 0.00 0.00 0.00 2.34
695 733 2.420058 ATGGACCGATTTTCACCTCC 57.580 50.000 0.00 0.00 0.00 4.30
700 738 6.544564 GGGTTATCTTTATGGACCGATTTTCA 59.455 38.462 0.00 0.00 0.00 2.69
720 760 4.721776 AGATCTGGTTAGCATCTTGGGTTA 59.278 41.667 0.00 0.00 0.00 2.85
786 1006 9.315525 CTCTCTTTTTATAGTAGCCTTTGGTAC 57.684 37.037 0.00 0.00 44.08 3.34
896 1134 5.705400 TGAATTTCCCTTTATCATCCCTCC 58.295 41.667 0.00 0.00 0.00 4.30
1061 1302 9.753674 TCCTCTATTATTCATGGTTTCAACTTT 57.246 29.630 0.00 0.00 0.00 2.66
1062 1303 9.178758 GTCCTCTATTATTCATGGTTTCAACTT 57.821 33.333 0.00 0.00 0.00 2.66
1063 1304 7.495934 CGTCCTCTATTATTCATGGTTTCAACT 59.504 37.037 0.00 0.00 0.00 3.16
1064 1305 7.254795 CCGTCCTCTATTATTCATGGTTTCAAC 60.255 40.741 0.00 0.00 0.00 3.18
1065 1306 6.765989 CCGTCCTCTATTATTCATGGTTTCAA 59.234 38.462 0.00 0.00 0.00 2.69
1066 1307 6.126883 ACCGTCCTCTATTATTCATGGTTTCA 60.127 38.462 0.00 0.00 0.00 2.69
1163 1413 5.646692 TTGGCTTCCCTATTATAGTGCTT 57.353 39.130 0.00 0.00 0.00 3.91
1330 1582 3.374058 AGCACTGGTACGCATGTATTTTC 59.626 43.478 0.00 0.00 32.11 2.29
1425 1685 6.370166 CAGGTTCAGGAGTTTTGATAGAAGTC 59.630 42.308 0.00 0.00 0.00 3.01
1490 1750 2.147958 GACATTTGCGGTGACCTACAA 58.852 47.619 0.00 1.04 0.00 2.41
1491 1751 1.346395 AGACATTTGCGGTGACCTACA 59.654 47.619 0.00 0.00 0.00 2.74
1492 1752 2.000447 GAGACATTTGCGGTGACCTAC 59.000 52.381 0.00 0.00 0.00 3.18
1493 1753 1.899814 AGAGACATTTGCGGTGACCTA 59.100 47.619 0.00 0.00 0.00 3.08
1494 1754 0.687354 AGAGACATTTGCGGTGACCT 59.313 50.000 0.00 0.00 0.00 3.85
1495 1755 0.798776 CAGAGACATTTGCGGTGACC 59.201 55.000 0.00 0.00 0.00 4.02
1544 1804 5.563592 TGATCACAATCACATTGGAAGACT 58.436 37.500 0.00 0.00 44.42 3.24
1728 1988 0.037590 TTTACGGGTTCAGGCTGCAT 59.962 50.000 10.34 0.00 0.00 3.96
2258 2518 8.338986 GCTATTCCTAGTGATTTTAGCAGTTTC 58.661 37.037 0.00 0.00 31.59 2.78


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

AutoCloner maintained by Alex Coulton.