Multiple sequence alignment - TraesCS3A01G070800

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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 TraesCS3A01G070800 chr3A 100.000 2371 0 0 1 2371 42883521 42885891 0.000000e+00 4379.0
1 TraesCS3A01G070800 chr3A 95.251 1116 49 4 1 1113 126070615 126069501 0.000000e+00 1764.0
2 TraesCS3A01G070800 chr3A 97.909 526 10 1 1846 2371 21308338 21308862 0.000000e+00 909.0
3 TraesCS3A01G070800 chr7A 96.429 2380 72 8 1 2371 655543840 655546215 0.000000e+00 3912.0
4 TraesCS3A01G070800 chr7A 94.796 1249 61 4 1 1246 630986939 630988186 0.000000e+00 1943.0
5 TraesCS3A01G070800 chr7A 97.540 1138 21 2 1241 2371 630990872 630992009 0.000000e+00 1940.0
6 TraesCS3A01G070800 chr7A 98.292 527 8 1 1846 2371 730329831 730329305 0.000000e+00 922.0
7 TraesCS3A01G070800 chr7A 97.913 527 10 1 1846 2371 730377100 730376574 0.000000e+00 911.0
8 TraesCS3A01G070800 chr7A 97.348 528 12 1 1846 2371 654053204 654053731 0.000000e+00 896.0
9 TraesCS3A01G070800 chr3B 95.964 1115 43 2 1 1113 725022030 725023144 0.000000e+00 1808.0
10 TraesCS3A01G070800 chr2B 95.695 1115 46 2 1 1113 414758289 414757175 0.000000e+00 1792.0
11 TraesCS3A01G070800 chr2B 91.702 952 75 4 1 949 237061437 237060487 0.000000e+00 1317.0
12 TraesCS3A01G070800 chr2B 97.538 528 11 1 1846 2371 692691412 692690885 0.000000e+00 902.0
13 TraesCS3A01G070800 chr4B 95.332 1114 48 4 1 1113 170724955 170726065 0.000000e+00 1766.0
14 TraesCS3A01G070800 chr4B 91.387 952 80 2 1 951 4269328 4268378 0.000000e+00 1303.0
15 TraesCS3A01G070800 chr4B 83.417 597 49 32 1129 1693 1985302 1984724 2.100000e-140 508.0
16 TraesCS3A01G070800 chr6B 94.892 881 33 10 948 1819 442429458 442428581 0.000000e+00 1367.0
17 TraesCS3A01G070800 chr7B 92.163 957 65 7 1 957 227231688 227230742 0.000000e+00 1343.0
18 TraesCS3A01G070800 chr4A 97.533 527 12 1 1846 2371 670766750 670767276 0.000000e+00 900.0
19 TraesCS3A01G070800 chr4A 83.810 315 30 5 1043 1336 603468000 603467686 1.790000e-71 279.0
20 TraesCS3A01G070800 chr2A 96.964 527 15 1 1846 2371 22311130 22310604 0.000000e+00 883.0
21 TraesCS3A01G070800 chr2A 90.574 244 23 0 870 1113 780542440 780542197 8.170000e-85 324.0
22 TraesCS3A01G070800 chr4D 85.309 388 24 8 1127 1506 1326435 1326797 1.040000e-98 370.0
23 TraesCS3A01G070800 chr4D 86.053 337 32 11 1016 1339 1386639 1386305 4.850000e-92 348.0
24 TraesCS3A01G070800 chr4D 92.000 125 7 1 1463 1587 1386270 1386149 3.130000e-39 172.0
25 TraesCS3A01G070800 chr4D 97.500 40 1 0 1548 1587 1326800 1326839 4.230000e-08 69.4
26 TraesCS3A01G070800 chr4D 86.667 60 8 0 1215 1274 1404688 1404629 1.520000e-07 67.6
27 TraesCS3A01G070800 chr5A 97.222 36 0 1 1447 1481 699469995 699469960 2.540000e-05 60.2
28 TraesCS3A01G070800 chr3D 100.000 31 0 0 1791 1821 526279621 526279591 9.150000e-05 58.4


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 TraesCS3A01G070800 chr3A 42883521 42885891 2370 False 4379.0 4379 100.000 1 2371 1 chr3A.!!$F2 2370
1 TraesCS3A01G070800 chr3A 126069501 126070615 1114 True 1764.0 1764 95.251 1 1113 1 chr3A.!!$R1 1112
2 TraesCS3A01G070800 chr3A 21308338 21308862 524 False 909.0 909 97.909 1846 2371 1 chr3A.!!$F1 525
3 TraesCS3A01G070800 chr7A 655543840 655546215 2375 False 3912.0 3912 96.429 1 2371 1 chr7A.!!$F2 2370
4 TraesCS3A01G070800 chr7A 630986939 630992009 5070 False 1941.5 1943 96.168 1 2371 2 chr7A.!!$F3 2370
5 TraesCS3A01G070800 chr7A 730329305 730329831 526 True 922.0 922 98.292 1846 2371 1 chr7A.!!$R1 525
6 TraesCS3A01G070800 chr7A 730376574 730377100 526 True 911.0 911 97.913 1846 2371 1 chr7A.!!$R2 525
7 TraesCS3A01G070800 chr7A 654053204 654053731 527 False 896.0 896 97.348 1846 2371 1 chr7A.!!$F1 525
8 TraesCS3A01G070800 chr3B 725022030 725023144 1114 False 1808.0 1808 95.964 1 1113 1 chr3B.!!$F1 1112
9 TraesCS3A01G070800 chr2B 414757175 414758289 1114 True 1792.0 1792 95.695 1 1113 1 chr2B.!!$R2 1112
10 TraesCS3A01G070800 chr2B 237060487 237061437 950 True 1317.0 1317 91.702 1 949 1 chr2B.!!$R1 948
11 TraesCS3A01G070800 chr2B 692690885 692691412 527 True 902.0 902 97.538 1846 2371 1 chr2B.!!$R3 525
12 TraesCS3A01G070800 chr4B 170724955 170726065 1110 False 1766.0 1766 95.332 1 1113 1 chr4B.!!$F1 1112
13 TraesCS3A01G070800 chr4B 4268378 4269328 950 True 1303.0 1303 91.387 1 951 1 chr4B.!!$R2 950
14 TraesCS3A01G070800 chr4B 1984724 1985302 578 True 508.0 508 83.417 1129 1693 1 chr4B.!!$R1 564
15 TraesCS3A01G070800 chr6B 442428581 442429458 877 True 1367.0 1367 94.892 948 1819 1 chr6B.!!$R1 871
16 TraesCS3A01G070800 chr7B 227230742 227231688 946 True 1343.0 1343 92.163 1 957 1 chr7B.!!$R1 956
17 TraesCS3A01G070800 chr4A 670766750 670767276 526 False 900.0 900 97.533 1846 2371 1 chr4A.!!$F1 525
18 TraesCS3A01G070800 chr2A 22310604 22311130 526 True 883.0 883 96.964 1846 2371 1 chr2A.!!$R1 525

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
556 563 0.039035 CACAATCCCTCCCCCGAAAA 59.961 55.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 4493 1.22184 GCATGTGTGGTCTCCCGAT 59.778 57.895 0.0 0.0 0.0 4.18 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
88 90 0.673644 AACTCATTTCGGGCACTCGG 60.674 55.000 0.00 0.00 0.0 4.63
99 101 1.824852 GGGCACTCGGAAAATGGAAAT 59.175 47.619 0.00 0.00 0.0 2.17
340 344 3.509575 GGTACTGCATTTTGATTGGTCCA 59.490 43.478 0.00 0.00 0.0 4.02
405 409 0.246635 CGGATCCAACGACAGTCCTT 59.753 55.000 13.41 0.00 0.0 3.36
556 563 0.039035 CACAATCCCTCCCCCGAAAA 59.961 55.000 0.00 0.00 0.0 2.29
567 574 2.199652 CCCGAAAACCTTGCTGCCA 61.200 57.895 0.00 0.00 0.0 4.92
715 722 3.253838 CCCAACCCCTTCCCACGA 61.254 66.667 0.00 0.00 0.0 4.35
733 740 3.056107 CACGACTAGGATTTCAAGGGTGA 60.056 47.826 0.00 0.00 0.0 4.02
740 747 1.463444 GATTTCAAGGGTGACGTTCCG 59.537 52.381 0.00 0.00 36.0 4.30
783 790 2.348998 CTGTGCTCCGCCCTCTTT 59.651 61.111 0.00 0.00 0.0 2.52
865 872 2.027314 CCTCATCTCCTCGCTGCG 59.973 66.667 17.25 17.25 0.0 5.18
885 892 1.632164 CCACCTCCTCCCCATCCTA 59.368 63.158 0.00 0.00 0.0 2.94
888 895 0.722676 ACCTCCTCCCCATCCTACAA 59.277 55.000 0.00 0.00 0.0 2.41
1045 1053 0.115152 TCCTTGGTCCTCTCTGCTCA 59.885 55.000 0.00 0.00 0.0 4.26
1121 1129 3.068064 TCGAGCGGGATCAGTGCA 61.068 61.111 0.00 0.00 0.0 4.57
1157 1165 2.736995 CACGTCGTCATGGCCGTT 60.737 61.111 0.00 0.00 0.0 4.44
1274 3974 1.005037 ATCTGTCCGCAAGTTCGCA 60.005 52.632 0.00 0.00 0.0 5.10
1398 4102 4.416516 TGATAGTTGAGGTTCAGTCAGGA 58.583 43.478 0.00 0.00 0.0 3.86
1425 4129 1.705873 AGACGAGGTTCAGGTTCAGT 58.294 50.000 0.00 0.00 0.0 3.41
1458 4175 3.370840 TCTTGGGACCATTCATTCAGG 57.629 47.619 0.00 0.00 0.0 3.86
1628 4362 6.745794 AATTCATTCCTGGGTTTCTTTTCA 57.254 33.333 0.00 0.00 0.0 2.69
1659 4393 4.607293 TGGACTATAACATGCTGCTAGG 57.393 45.455 0.00 0.00 0.0 3.02
2064 4799 6.608405 TGATTGCTAAAAATGACAGGGATGAT 59.392 34.615 0.00 0.00 0.0 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
275 279 6.882610 TGGTCGTAGTTGACTAAAACTAGA 57.117 37.500 0.00 0.00 41.97 2.43
279 283 9.934190 TTTAAATTGGTCGTAGTTGACTAAAAC 57.066 29.630 0.00 0.00 41.70 2.43
340 344 2.337749 GATCCGCGTGAGACGTCCAT 62.338 60.000 13.01 0.00 44.73 3.41
405 409 4.531426 GGTTGGTGTGGTGGGCCA 62.531 66.667 0.00 0.00 43.73 5.36
484 491 1.082690 GGAGGCAGAGAAAGAAAGCG 58.917 55.000 0.00 0.00 0.00 4.68
485 492 2.488204 AGGAGGCAGAGAAAGAAAGC 57.512 50.000 0.00 0.00 0.00 3.51
556 563 2.153401 TAGGTGGTGGCAGCAAGGT 61.153 57.895 22.39 11.15 0.00 3.50
567 574 0.320697 GAACAAGAGGCGTAGGTGGT 59.679 55.000 0.00 0.00 0.00 4.16
622 629 1.531840 GCAGGGGAGCTCGGATCTA 60.532 63.158 7.83 0.00 0.00 1.98
715 722 2.904434 ACGTCACCCTTGAAATCCTAGT 59.096 45.455 0.00 0.00 31.90 2.57
740 747 3.861263 GTCGCGCCGGAATTGGTC 61.861 66.667 5.05 0.00 0.00 4.02
756 763 4.664677 GAGCACAGTCACCGCCGT 62.665 66.667 0.00 0.00 0.00 5.68
783 790 1.220749 GCTAGATTGGTGGGCGTCA 59.779 57.895 0.00 0.00 0.00 4.35
845 852 1.470996 GCAGCGAGGAGATGAGGGAT 61.471 60.000 0.00 0.00 38.85 3.85
865 872 3.493303 GATGGGGAGGAGGTGGCC 61.493 72.222 0.00 0.00 0.00 5.36
880 887 2.202703 GACGCGCCGTTGTAGGAT 60.203 61.111 5.73 0.00 41.37 3.24
1045 1053 2.166907 ATCAGATGGAACGAGGGAGT 57.833 50.000 0.00 0.00 0.00 3.85
1398 4102 2.224066 CCTGAACCTCGTCTTGACAACT 60.224 50.000 1.59 0.00 0.00 3.16
1425 4129 3.079131 CCAAGAAATCGCGATGGGA 57.921 52.632 24.47 0.00 0.00 4.37
1458 4175 4.065789 CCTAACTGAACCTGAACCTGAAC 58.934 47.826 0.00 0.00 0.00 3.18
1628 4362 6.942576 AGCATGTTATAGTCCAAGTTGAAGTT 59.057 34.615 3.87 0.00 0.00 2.66
1659 4393 5.894807 AGTGTTGCAGCATTTATATTCCAC 58.105 37.500 6.50 0.00 0.00 4.02
1758 4493 1.221840 GCATGTGTGGTCTCCCGAT 59.778 57.895 0.00 0.00 0.00 4.18
2064 4799 2.849942 CATCATTCTTGGCGGTGGATA 58.150 47.619 0.00 0.00 0.00 2.59
2323 5060 5.598417 ACTGCAGGTTCAAAAATTTCCTACT 59.402 36.000 19.93 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.