Multiple sequence alignment - TraesCS1A01G130500

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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 TraesCS1A01G130500 chr1A 100.000 2213 0 0 1 2213 168450321 168452533 0.000000e+00 4087.0
1 TraesCS1A01G130500 chr1A 95.021 723 26 5 1 719 112775789 112776505 0.000000e+00 1127.0
2 TraesCS1A01G130500 chr2D 97.553 899 18 4 717 1613 33933417 33934313 0.000000e+00 1535.0
3 TraesCS1A01G130500 chr2D 97.553 899 19 3 717 1613 272802058 272801161 0.000000e+00 1535.0
4 TraesCS1A01G130500 chr2D 97.442 899 19 3 717 1613 630268829 630269725 0.000000e+00 1530.0
5 TraesCS1A01G130500 chr2D 95.507 601 20 4 1614 2213 319861753 319861159 0.000000e+00 953.0
6 TraesCS1A01G130500 chr3A 97.105 898 23 2 717 1613 672878830 672877935 0.000000e+00 1511.0
7 TraesCS1A01G130500 chr3A 95.568 722 23 4 1 719 393235552 393234837 0.000000e+00 1147.0
8 TraesCS1A01G130500 chr3B 96.885 899 24 3 717 1613 201561173 201560277 0.000000e+00 1502.0
9 TraesCS1A01G130500 chr3B 95.291 722 25 4 1 719 201513371 201512656 0.000000e+00 1136.0
10 TraesCS1A01G130500 chr7B 97.188 889 21 4 717 1603 662738546 662739432 0.000000e+00 1500.0
11 TraesCS1A01G130500 chr7B 93.648 488 24 2 1 486 125509479 125508997 0.000000e+00 723.0
12 TraesCS1A01G130500 chr1B 96.659 898 26 4 717 1612 633729263 633728368 0.000000e+00 1489.0
13 TraesCS1A01G130500 chr5D 96.214 898 32 2 717 1613 432293118 432292222 0.000000e+00 1469.0
14 TraesCS1A01G130500 chr5B 95.991 898 32 3 717 1612 432876325 432877220 0.000000e+00 1456.0
15 TraesCS1A01G130500 chr1D 95.304 724 24 4 1 719 254498243 254497525 0.000000e+00 1140.0
16 TraesCS1A01G130500 chr1D 95.674 601 19 4 1614 2213 345586738 345587332 0.000000e+00 959.0
17 TraesCS1A01G130500 chr3D 94.766 726 26 3 1 719 21904873 21904153 0.000000e+00 1120.0
18 TraesCS1A01G130500 chr3D 96.352 603 18 3 1614 2213 92107546 92108147 0.000000e+00 989.0
19 TraesCS1A01G130500 chr3D 95.826 599 22 3 1614 2211 309511863 309512459 0.000000e+00 965.0
20 TraesCS1A01G130500 chr3D 95.674 601 22 4 1614 2213 137168470 137167873 0.000000e+00 963.0
21 TraesCS1A01G130500 chr3D 95.667 600 19 6 1615 2213 319215349 319215942 0.000000e+00 957.0
22 TraesCS1A01G130500 chr3D 95.507 601 19 4 1614 2213 423673685 423674278 0.000000e+00 953.0
23 TraesCS1A01G130500 chr7D 95.702 698 20 4 26 719 336506862 336507553 0.000000e+00 1114.0
24 TraesCS1A01G130500 chr7D 96.020 603 16 4 1614 2213 515436464 515437061 0.000000e+00 974.0
25 TraesCS1A01G130500 chr6B 94.613 724 29 3 1 719 22426190 22425472 0.000000e+00 1112.0
26 TraesCS1A01G130500 chr6B 95.756 377 11 2 343 719 213357080 213356709 8.740000e-169 603.0
27 TraesCS1A01G130500 chr4D 94.329 723 31 4 1 719 19916741 19916025 0.000000e+00 1099.0
28 TraesCS1A01G130500 chr6D 95.507 601 21 4 1614 2213 390527081 390526486 0.000000e+00 955.0
29 TraesCS1A01G130500 chr6A 97.500 40 0 1 717 755 162649151 162649190 1.420000e-07 67.6


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 TraesCS1A01G130500 chr1A 168450321 168452533 2212 False 4087 4087 100.000 1 2213 1 chr1A.!!$F2 2212
1 TraesCS1A01G130500 chr1A 112775789 112776505 716 False 1127 1127 95.021 1 719 1 chr1A.!!$F1 718
2 TraesCS1A01G130500 chr2D 33933417 33934313 896 False 1535 1535 97.553 717 1613 1 chr2D.!!$F1 896
3 TraesCS1A01G130500 chr2D 272801161 272802058 897 True 1535 1535 97.553 717 1613 1 chr2D.!!$R1 896
4 TraesCS1A01G130500 chr2D 630268829 630269725 896 False 1530 1530 97.442 717 1613 1 chr2D.!!$F2 896
5 TraesCS1A01G130500 chr2D 319861159 319861753 594 True 953 953 95.507 1614 2213 1 chr2D.!!$R2 599
6 TraesCS1A01G130500 chr3A 672877935 672878830 895 True 1511 1511 97.105 717 1613 1 chr3A.!!$R2 896
7 TraesCS1A01G130500 chr3A 393234837 393235552 715 True 1147 1147 95.568 1 719 1 chr3A.!!$R1 718
8 TraesCS1A01G130500 chr3B 201560277 201561173 896 True 1502 1502 96.885 717 1613 1 chr3B.!!$R2 896
9 TraesCS1A01G130500 chr3B 201512656 201513371 715 True 1136 1136 95.291 1 719 1 chr3B.!!$R1 718
10 TraesCS1A01G130500 chr7B 662738546 662739432 886 False 1500 1500 97.188 717 1603 1 chr7B.!!$F1 886
11 TraesCS1A01G130500 chr1B 633728368 633729263 895 True 1489 1489 96.659 717 1612 1 chr1B.!!$R1 895
12 TraesCS1A01G130500 chr5D 432292222 432293118 896 True 1469 1469 96.214 717 1613 1 chr5D.!!$R1 896
13 TraesCS1A01G130500 chr5B 432876325 432877220 895 False 1456 1456 95.991 717 1612 1 chr5B.!!$F1 895
14 TraesCS1A01G130500 chr1D 254497525 254498243 718 True 1140 1140 95.304 1 719 1 chr1D.!!$R1 718
15 TraesCS1A01G130500 chr1D 345586738 345587332 594 False 959 959 95.674 1614 2213 1 chr1D.!!$F1 599
16 TraesCS1A01G130500 chr3D 21904153 21904873 720 True 1120 1120 94.766 1 719 1 chr3D.!!$R1 718
17 TraesCS1A01G130500 chr3D 92107546 92108147 601 False 989 989 96.352 1614 2213 1 chr3D.!!$F1 599
18 TraesCS1A01G130500 chr3D 309511863 309512459 596 False 965 965 95.826 1614 2211 1 chr3D.!!$F2 597
19 TraesCS1A01G130500 chr3D 137167873 137168470 597 True 963 963 95.674 1614 2213 1 chr3D.!!$R2 599
20 TraesCS1A01G130500 chr3D 319215349 319215942 593 False 957 957 95.667 1615 2213 1 chr3D.!!$F3 598
21 TraesCS1A01G130500 chr3D 423673685 423674278 593 False 953 953 95.507 1614 2213 1 chr3D.!!$F4 599
22 TraesCS1A01G130500 chr7D 336506862 336507553 691 False 1114 1114 95.702 26 719 1 chr7D.!!$F1 693
23 TraesCS1A01G130500 chr7D 515436464 515437061 597 False 974 974 96.020 1614 2213 1 chr7D.!!$F2 599
24 TraesCS1A01G130500 chr6B 22425472 22426190 718 True 1112 1112 94.613 1 719 1 chr6B.!!$R1 718
25 TraesCS1A01G130500 chr4D 19916025 19916741 716 True 1099 1099 94.329 1 719 1 chr4D.!!$R1 718
26 TraesCS1A01G130500 chr6D 390526486 390527081 595 True 955 955 95.507 1614 2213 1 chr6D.!!$R1 599

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
392 401 1.027357 GGCGGACGGACACTAAGATA 58.973 55.0 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1852 1.487142 TGAAAGGGTCCACAAGAACGA 59.513 47.619 0.0 0.0 30.31 3.85 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
200 204 6.292596 GCTAACTCTTCGATATTTCTTGCTGG 60.293 42.308 0.00 0.00 0.00 4.85
220 224 3.208922 TGGAAGTATCCCTGATCCCACTA 59.791 47.826 0.00 0.00 45.95 2.74
233 237 5.698104 TGATCCCACTAATAACGAGTAGGA 58.302 41.667 0.00 0.00 38.78 2.94
234 238 6.131264 TGATCCCACTAATAACGAGTAGGAA 58.869 40.000 0.00 0.00 38.08 3.36
255 259 5.126384 GGAACAAATAATTCGATTGGGGTCA 59.874 40.000 1.19 0.00 0.00 4.02
392 401 1.027357 GGCGGACGGACACTAAGATA 58.973 55.000 0.00 0.00 0.00 1.98
401 410 6.016108 GGACGGACACTAAGATAGAATAAGCT 60.016 42.308 0.00 0.00 0.00 3.74
446 455 4.143158 CGCAGCAATATGATGAGAAGCTAC 60.143 45.833 0.00 0.00 35.61 3.58
447 456 4.153835 GCAGCAATATGATGAGAAGCTACC 59.846 45.833 0.00 0.00 35.45 3.18
448 457 4.694509 CAGCAATATGATGAGAAGCTACCC 59.305 45.833 0.00 0.00 35.45 3.69
449 458 4.006319 GCAATATGATGAGAAGCTACCCC 58.994 47.826 0.00 0.00 0.00 4.95
450 459 4.583871 CAATATGATGAGAAGCTACCCCC 58.416 47.826 0.00 0.00 0.00 5.40
487 496 3.228188 AGGATCAAAACCTTCTGCACA 57.772 42.857 0.00 0.00 33.55 4.57
623 632 6.044682 CACCCCTGCAAGAAATAAATGAATC 58.955 40.000 0.00 0.00 34.07 2.52
712 721 4.326826 CAATATACCCAATGCCAGATCGT 58.673 43.478 0.00 0.00 0.00 3.73
821 832 8.581578 GTGAAAGATTACCCTTTGATTTACCAA 58.418 33.333 0.00 0.00 36.58 3.67
1170 1182 4.450348 TCCTTTTACCTATTTCCCTGGGA 58.550 43.478 12.53 12.53 0.00 4.37
1186 1198 6.900194 TCCCTGGGAAATCTCTTATTAACAG 58.100 40.000 14.48 0.00 0.00 3.16
1359 1371 7.809546 TGAGTTATGGTCAACAAACAATACA 57.190 32.000 0.00 0.00 0.00 2.29
1413 1425 5.772393 ACTACCTTATCCCACACAAATCA 57.228 39.130 0.00 0.00 0.00 2.57
1458 1470 9.716507 CTACCCTTATGAAAAATCAATTACACG 57.283 33.333 0.00 0.00 0.00 4.49
1570 1582 6.882656 TGTTGTGGATTGGAGATTTGAAAAA 58.117 32.000 0.00 0.00 0.00 1.94
1837 1852 2.699954 CACGAGCATGGTTTTCTAGGT 58.300 47.619 0.00 0.00 0.00 3.08
1928 1943 6.212840 TGCACATAATCCCCTAAATATGGT 57.787 37.500 0.00 0.00 31.55 3.55
2083 2100 4.021981 CCTTGAAACCATGAAACTTCCTCC 60.022 45.833 0.00 0.00 0.00 4.30
2087 2104 1.271379 ACCATGAAACTTCCTCCGTGG 60.271 52.381 0.00 0.00 37.10 4.94
2108 2125 3.442273 GGTGGTTCGATTTATGAAAGGCA 59.558 43.478 0.00 0.00 0.00 4.75
2109 2126 4.097892 GGTGGTTCGATTTATGAAAGGCAT 59.902 41.667 0.00 0.00 41.08 4.40
2150 2167 9.639601 GGAAAACATTCTCCAATTTTTACTAGG 57.360 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 204 7.387643 GTTATTAGTGGGATCAGGGATACTTC 58.612 42.308 0.00 0.0 0.00 3.01
220 224 9.590451 TCGAATTATTTGTTCCTACTCGTTATT 57.410 29.630 0.00 0.0 0.00 1.40
233 237 6.790232 ATGACCCCAATCGAATTATTTGTT 57.210 33.333 0.00 0.0 0.00 2.83
234 238 6.572519 CAATGACCCCAATCGAATTATTTGT 58.427 36.000 0.00 0.0 0.00 2.83
255 259 3.459598 ACTATGTGGTATGGGTCAGCAAT 59.540 43.478 0.00 0.0 0.00 3.56
392 401 4.833380 TGGGTCTATTAGCGAGCTTATTCT 59.167 41.667 1.86 0.0 0.00 2.40
401 410 3.322828 GGGTACATTGGGTCTATTAGCGA 59.677 47.826 0.00 0.0 0.00 4.93
410 419 2.112815 GCTGCGGGTACATTGGGTC 61.113 63.158 0.00 0.0 0.00 4.46
458 467 4.955811 AGGTTTTGATCCTTTTGTTCCC 57.044 40.909 0.00 0.0 30.18 3.97
552 561 4.020039 TCATGTAACGGGTTTGTATGGTCT 60.020 41.667 0.00 0.0 0.00 3.85
589 598 1.606313 GCAGGGGTGGCTTGCTTTA 60.606 57.895 0.00 0.0 35.05 1.85
643 652 1.202842 GGACGGGAAAACCCTCTTTGA 60.203 52.381 0.00 0.0 34.99 2.69
790 801 6.834168 TCAAAGGGTAATCTTTCACATTCC 57.166 37.500 0.00 0.0 35.04 3.01
821 832 4.081087 TGCTACTAATTCTTCCTCCGCTTT 60.081 41.667 0.00 0.0 0.00 3.51
1012 1024 6.232692 CCATTGTCATTTCCAAACTTCCAAT 58.767 36.000 0.00 0.0 0.00 3.16
1149 1161 4.873724 TCCCAGGGAAATAGGTAAAAGG 57.126 45.455 5.36 0.0 0.00 3.11
1170 1182 8.543774 TGAGAAGAGGCTGTTAATAAGAGATTT 58.456 33.333 0.00 0.0 0.00 2.17
1186 1198 3.879892 AGTGAAACAAGTTGAGAAGAGGC 59.120 43.478 10.54 0.0 41.43 4.70
1359 1371 5.950544 TTGACCTATGTACCTTGTAGCAT 57.049 39.130 0.00 0.0 0.00 3.79
1413 1425 8.488308 AGGGTAGTCAATCGTTATAGGTAAAT 57.512 34.615 0.00 0.0 0.00 1.40
1731 1746 6.314784 GCAATAGTCAACCACAAATGTCTAC 58.685 40.000 0.00 0.0 0.00 2.59
1837 1852 1.487142 TGAAAGGGTCCACAAGAACGA 59.513 47.619 0.00 0.0 30.31 3.85
1928 1943 5.815233 TGGCAATTTTCCAGGTTCATTTA 57.185 34.783 0.00 0.0 0.00 1.40
1945 1960 2.166459 TCACCGTGTTCAAATTTGGCAA 59.834 40.909 17.90 0.0 0.00 4.52
2051 2068 1.917872 TGGTTTCAAGGGGGAAATCG 58.082 50.000 0.00 0.0 40.07 3.34
2083 2100 4.436852 CCTTTCATAAATCGAACCACCACG 60.437 45.833 0.00 0.0 0.00 4.94
2087 2104 4.695217 TGCCTTTCATAAATCGAACCAC 57.305 40.909 0.00 0.0 0.00 4.16
2108 2125 4.699735 TGTTTTCCTTATGTCGTGATGCAT 59.300 37.500 0.00 0.0 0.00 3.96
2109 2126 4.068599 TGTTTTCCTTATGTCGTGATGCA 58.931 39.130 0.00 0.0 0.00 3.96


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

AutoCloner maintained by Alex Coulton.