Multiple sequence alignment - TraesCS6B01G378400

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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 TraesCS6B01G378400 chr6B 100.000 3114 0 0 1 3114 653195717 653192604 0.000000e+00 5751.0
1 TraesCS6B01G378400 chr6B 95.486 2171 88 6 1 2169 653716540 653714378 0.000000e+00 3458.0
2 TraesCS6B01G378400 chr6B 95.025 2171 85 13 1 2169 653789670 653787521 0.000000e+00 3389.0
3 TraesCS6B01G378400 chr6B 89.661 2186 163 23 4 2169 653857415 653855273 0.000000e+00 2726.0
4 TraesCS6B01G378400 chr6B 89.220 1475 148 9 704 2171 653872848 653871378 0.000000e+00 1832.0
5 TraesCS6B01G378400 chr6B 93.750 48 2 1 590 637 653872953 653872907 1.550000e-08 71.3
6 TraesCS6B01G378400 chr6D 95.724 2175 82 9 1 2171 433260021 433257854 0.000000e+00 3491.0
7 TraesCS6B01G378400 chr6D 91.120 2151 144 20 31 2167 432915301 432913184 0.000000e+00 2870.0
8 TraesCS6B01G378400 chr6D 84.885 2223 256 54 1 2171 433281599 433279405 0.000000e+00 2170.0
9 TraesCS6B01G378400 chr6D 89.891 1464 138 8 715 2171 433155530 433154070 0.000000e+00 1875.0
10 TraesCS6B01G378400 chr6D 80.128 156 20 9 248 396 433590918 433591069 4.250000e-19 106.0
11 TraesCS6B01G378400 chr6D 91.667 48 3 1 590 637 432931832 432931786 7.210000e-07 65.8
12 TraesCS6B01G378400 chr6A 90.367 2180 163 18 4 2169 579125802 579123656 0.000000e+00 2819.0
13 TraesCS6B01G378400 chr6A 89.288 1475 147 9 704 2171 579143336 579141866 0.000000e+00 1838.0
14 TraesCS6B01G378400 chr6A 82.445 319 33 13 2169 2472 52763768 52764078 1.110000e-64 257.0
15 TraesCS6B01G378400 chr4A 93.592 952 26 8 2168 3114 740846368 740845447 0.000000e+00 1387.0
16 TraesCS6B01G378400 chr7D 92.775 955 34 19 2169 3112 62205664 62204734 0.000000e+00 1349.0
17 TraesCS6B01G378400 chr7D 74.654 434 72 26 1 417 500745080 500745492 1.160000e-34 158.0
18 TraesCS6B01G378400 chr7D 79.545 176 31 5 2169 2341 113955985 113956158 1.520000e-23 121.0
19 TraesCS6B01G378400 chr4B 80.656 305 37 11 2169 2472 571915438 571915155 1.880000e-52 217.0
20 TraesCS6B01G378400 chr3D 80.843 261 41 9 2169 2425 315586290 315586545 2.450000e-46 196.0
21 TraesCS6B01G378400 chr2D 80.347 173 33 1 2169 2340 54495667 54495839 2.520000e-26 130.0
22 TraesCS6B01G378400 chr2B 79.618 157 29 3 2169 2323 27985898 27986053 3.280000e-20 110.0
23 TraesCS6B01G378400 chr2B 77.128 188 38 5 2166 2350 749970577 749970762 1.530000e-18 104.0


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 TraesCS6B01G378400 chr6B 653192604 653195717 3113 True 5751.00 5751 100.000 1 3114 1 chr6B.!!$R1 3113
1 TraesCS6B01G378400 chr6B 653714378 653716540 2162 True 3458.00 3458 95.486 1 2169 1 chr6B.!!$R2 2168
2 TraesCS6B01G378400 chr6B 653787521 653789670 2149 True 3389.00 3389 95.025 1 2169 1 chr6B.!!$R3 2168
3 TraesCS6B01G378400 chr6B 653855273 653857415 2142 True 2726.00 2726 89.661 4 2169 1 chr6B.!!$R4 2165
4 TraesCS6B01G378400 chr6B 653871378 653872953 1575 True 951.65 1832 91.485 590 2171 2 chr6B.!!$R5 1581
5 TraesCS6B01G378400 chr6D 433257854 433260021 2167 True 3491.00 3491 95.724 1 2171 1 chr6D.!!$R4 2170
6 TraesCS6B01G378400 chr6D 432913184 432915301 2117 True 2870.00 2870 91.120 31 2167 1 chr6D.!!$R1 2136
7 TraesCS6B01G378400 chr6D 433279405 433281599 2194 True 2170.00 2170 84.885 1 2171 1 chr6D.!!$R5 2170
8 TraesCS6B01G378400 chr6D 433154070 433155530 1460 True 1875.00 1875 89.891 715 2171 1 chr6D.!!$R3 1456
9 TraesCS6B01G378400 chr6A 579123656 579125802 2146 True 2819.00 2819 90.367 4 2169 1 chr6A.!!$R1 2165
10 TraesCS6B01G378400 chr6A 579141866 579143336 1470 True 1838.00 1838 89.288 704 2171 1 chr6A.!!$R2 1467
11 TraesCS6B01G378400 chr4A 740845447 740846368 921 True 1387.00 1387 93.592 2168 3114 1 chr4A.!!$R1 946
12 TraesCS6B01G378400 chr7D 62204734 62205664 930 True 1349.00 1349 92.775 2169 3112 1 chr7D.!!$R1 943

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
77 79 0.482887 AGGGGGAGAAAAGTGTTGGG 59.517 55.0 0.0 0.0 0.0 4.12 F
787 838 0.877071 AAGCACATTCAGCCAAGTCG 59.123 50.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1111 1174 1.065854 GTACTGCACCATCCAGCTCTT 60.066 52.381 0.00 0.0 33.65 2.85 R
2369 2437 1.210234 AGCACCATCCATTCGTGATGA 59.790 47.619 1.97 0.0 41.72 2.92 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
77 79 0.482887 AGGGGGAGAAAAGTGTTGGG 59.517 55.000 0.00 0.00 0.00 4.12
308 313 2.116238 GGCAGGGAAGTATGTCTGGTA 58.884 52.381 0.00 0.00 0.00 3.25
359 365 2.440627 TGAGGCTCATGCAGTCCATATT 59.559 45.455 14.43 0.00 41.91 1.28
360 366 3.647590 TGAGGCTCATGCAGTCCATATTA 59.352 43.478 14.43 0.00 41.91 0.98
361 367 4.287845 TGAGGCTCATGCAGTCCATATTAT 59.712 41.667 14.43 0.00 41.91 1.28
671 710 7.435192 GCTTGTAGAAATTTTATACATGCACCC 59.565 37.037 30.13 14.23 44.05 4.61
675 714 7.436320 AGAAATTTTATACATGCACCCCAAT 57.564 32.000 0.00 0.00 0.00 3.16
687 726 3.055963 TGCACCCCAATGATGAAAATGAC 60.056 43.478 0.00 0.00 0.00 3.06
787 838 0.877071 AAGCACATTCAGCCAAGTCG 59.123 50.000 0.00 0.00 0.00 4.18
835 889 5.512788 CCAAATGCTAAGTACGCTTGATTTG 59.487 40.000 12.20 12.20 37.16 2.32
964 1020 3.004106 AGAAACAAAGCAGAGCACACATC 59.996 43.478 0.00 0.00 0.00 3.06
1111 1174 2.672651 CGATGGTGGCAAGGCACA 60.673 61.111 25.05 13.45 0.00 4.57
1197 1260 0.109532 TGTTCAAGGCCAATGTCGGA 59.890 50.000 5.01 0.00 0.00 4.55
1219 1282 1.068402 TCATCGAGTCGTTTAACGCCA 60.068 47.619 13.06 0.00 42.21 5.69
1306 1370 3.606687 ACAAAGGCTAACAAGGGATACG 58.393 45.455 0.00 0.00 37.60 3.06
1355 1419 4.738740 CGGATTCAGGTACGAGAATGTAAC 59.261 45.833 13.98 2.83 37.89 2.50
1371 1435 2.560981 TGTAACTCTCGATGCACTTCCA 59.439 45.455 0.00 0.00 0.00 3.53
1494 1559 6.780706 TTACTTCTTTTGAGAATGTCGTCC 57.219 37.500 0.00 0.00 0.00 4.79
1618 1683 3.509967 TCTCATTGTCGGAGCAAGAGTTA 59.490 43.478 0.00 0.00 31.68 2.24
1639 1704 2.577563 AGTGGATTGTGATGTCCATGGA 59.422 45.455 11.44 11.44 45.57 3.41
1678 1743 0.109913 GAGGGCTCATGGATGATGCA 59.890 55.000 0.00 0.00 36.02 3.96
1738 1803 4.295201 AGTCCAACTACCCATATACTGCA 58.705 43.478 0.00 0.00 0.00 4.41
2115 2180 3.181461 CCTTCTTACCCCACTGCATAGAG 60.181 52.174 0.00 0.00 0.00 2.43
2207 2274 2.401583 TCCATGACGGATTTCTGGTG 57.598 50.000 0.00 0.00 39.64 4.17
2303 2370 1.452110 TGACGGACGAAGACGGATTA 58.548 50.000 0.00 0.00 44.46 1.75
2403 2471 2.291365 TGGTGCTCATGTATCATGTGC 58.709 47.619 21.74 21.74 38.55 4.57
3007 3084 2.726180 CCGTATCGCTCGCCTTCG 60.726 66.667 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 79 1.465020 CGACACACACAACCAACACAC 60.465 52.381 0.00 0.00 0.00 3.82
308 313 9.554724 CACGTCAAGTGCAATAATTTTAATACT 57.445 29.630 0.00 0.00 44.72 2.12
359 365 8.886719 CACTCATCTTGCATTTTCTGTTCTATA 58.113 33.333 0.00 0.00 0.00 1.31
360 366 7.627939 GCACTCATCTTGCATTTTCTGTTCTAT 60.628 37.037 0.00 0.00 39.93 1.98
361 367 6.348786 GCACTCATCTTGCATTTTCTGTTCTA 60.349 38.462 0.00 0.00 39.93 2.10
483 490 9.685005 GTGTAACACGAACATAATAACTTGATC 57.315 33.333 0.00 0.00 36.32 2.92
656 695 5.896106 TCATCATTGGGGTGCATGTATAAAA 59.104 36.000 0.00 0.00 0.00 1.52
787 838 7.081976 GGTGCACGGATATTATAAATCAAACC 58.918 38.462 11.45 0.00 0.00 3.27
835 889 2.555757 ACGTCTAGTGGGCGGATATTAC 59.444 50.000 5.24 0.00 0.00 1.89
935 989 3.805971 GCTCTGCTTTGTTTCTGCAAATT 59.194 39.130 0.00 0.00 37.66 1.82
964 1020 0.098200 TGCGCTACTACTAGTGTGCG 59.902 55.000 22.92 22.92 46.78 5.34
1056 1119 1.732917 CCGAGCTGCTAGGACTGAG 59.267 63.158 22.50 0.00 0.00 3.35
1059 1122 1.454847 CTCCCGAGCTGCTAGGACT 60.455 63.158 27.54 0.00 0.00 3.85
1111 1174 1.065854 GTACTGCACCATCCAGCTCTT 60.066 52.381 0.00 0.00 33.65 2.85
1197 1260 3.901667 GCGTTAAACGACTCGATGAAT 57.098 42.857 5.20 0.00 46.05 2.57
1355 1419 2.662006 TTCTGGAAGTGCATCGAGAG 57.338 50.000 2.82 0.00 35.89 3.20
1371 1435 2.169330 GTCCTCCAGTCTACGGTTTCT 58.831 52.381 0.00 0.00 0.00 2.52
1639 1704 2.777692 TCCTTCACAACCTTGGTCTTCT 59.222 45.455 0.00 0.00 0.00 2.85
1678 1743 8.137437 CCGCCATTCTTGATAATGAACTTAAAT 58.863 33.333 0.00 0.00 38.84 1.40
1738 1803 3.562973 CACTCTTGCACTTGTCATCTGTT 59.437 43.478 0.00 0.00 0.00 3.16
1971 2036 2.790433 ACCAATACTTTGTGCCATCGT 58.210 42.857 0.00 0.00 0.00 3.73
2227 2294 4.594123 TGTTGATCTGTGACGGTTTCTA 57.406 40.909 0.00 0.00 0.00 2.10
2261 2328 2.579624 TGGGGCTACAGATTTAGGGA 57.420 50.000 0.00 0.00 0.00 4.20
2265 2332 5.512404 CCGTCATAATGGGGCTACAGATTTA 60.512 44.000 0.00 0.00 0.00 1.40
2303 2370 3.119137 TCGATCCATGACAGTTTCGTGAT 60.119 43.478 0.00 0.00 43.20 3.06
2349 2417 8.902806 GTGATGATCCAAATGTTGTATAAGGAA 58.097 33.333 0.00 0.00 0.00 3.36
2369 2437 1.210234 AGCACCATCCATTCGTGATGA 59.790 47.619 1.97 0.00 41.72 2.92
2423 2491 2.679639 GCACAGATTACATCCGACCCAA 60.680 50.000 0.00 0.00 0.00 4.12
2485 2554 6.016860 GCATGCCATTCCTTTTCTTTCTTTTT 60.017 34.615 6.36 0.00 0.00 1.94
2490 2559 3.929094 TGCATGCCATTCCTTTTCTTTC 58.071 40.909 16.68 0.00 0.00 2.62
2651 2728 1.890876 AATGCGTGTGTTTCCTGCTA 58.109 45.000 0.00 0.00 0.00 3.49
3007 3084 2.902343 GCTGGCCGGATTGCTACC 60.902 66.667 18.31 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.