Multiple sequence alignment - TraesCS4A01G321900

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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 TraesCS4A01G321900 chr4A 100.000 2914 0 0 1 2914 610091656 610088743 0.000000e+00 5382.0
1 TraesCS4A01G321900 chr4A 90.826 1864 144 6 620 2483 610132711 610130875 0.000000e+00 2470.0
2 TraesCS4A01G321900 chr4A 77.809 1415 265 29 956 2338 616017159 616015762 0.000000e+00 828.0
3 TraesCS4A01G321900 chr4A 90.179 560 54 1 1795 2354 610257075 610256517 0.000000e+00 728.0
4 TraesCS4A01G321900 chr4A 90.378 291 18 3 248 537 597727108 597726827 9.860000e-100 374.0
5 TraesCS4A01G321900 chr5D 89.817 1964 160 19 537 2467 557923392 557925348 0.000000e+00 2483.0
6 TraesCS4A01G321900 chr5D 83.415 1435 210 25 953 2370 557891294 557889871 0.000000e+00 1306.0
7 TraesCS4A01G321900 chr5D 88.302 966 104 5 641 1599 557803159 557804122 0.000000e+00 1149.0
8 TraesCS4A01G321900 chr5D 88.448 831 91 5 1591 2421 557821425 557822250 0.000000e+00 998.0
9 TraesCS4A01G321900 chr5D 80.437 869 156 13 965 1825 558722106 558722968 0.000000e+00 651.0
10 TraesCS4A01G321900 chr5D 82.540 441 58 9 1919 2357 557889107 557888684 1.280000e-98 370.0
11 TraesCS4A01G321900 chr5B 91.877 751 60 1 1733 2483 705031497 705032246 0.000000e+00 1048.0
12 TraesCS4A01G321900 chr5B 90.882 669 58 3 1068 1735 705027432 705028098 0.000000e+00 894.0
13 TraesCS4A01G321900 chr5B 77.456 1415 262 32 956 2338 699294635 699293246 0.000000e+00 793.0
14 TraesCS4A01G321900 chr5B 80.000 870 159 13 965 1825 704093143 704092280 1.910000e-176 628.0
15 TraesCS4A01G321900 chr5B 93.596 406 24 2 2510 2914 705033273 705033677 3.210000e-169 604.0
16 TraesCS4A01G321900 chr5B 93.617 47 1 1 2473 2519 705033057 705033101 5.210000e-08 69.4
17 TraesCS4A01G321900 chr3B 95.345 537 21 1 1 537 52750190 52750722 0.000000e+00 850.0
18 TraesCS4A01G321900 chr3B 94.195 534 27 1 4 537 807124272 807123743 0.000000e+00 811.0
19 TraesCS4A01G321900 chr3B 76.923 416 81 5 1936 2350 751058377 751057976 3.780000e-54 222.0
20 TraesCS4A01G321900 chr5A 93.866 538 29 3 1 537 452269886 452270420 0.000000e+00 808.0
21 TraesCS4A01G321900 chr5A 91.248 537 22 9 1 537 701296966 701297477 0.000000e+00 708.0
22 TraesCS4A01G321900 chr5A 92.063 63 5 0 2563 2625 677901365 677901303 4.000000e-14 89.8
23 TraesCS4A01G321900 chr5A 100.000 32 0 0 2587 2618 677907535 677907504 3.140000e-05 60.2
24 TraesCS4A01G321900 chr1B 93.809 533 26 4 4 536 267809633 267809108 0.000000e+00 795.0
25 TraesCS4A01G321900 chr3A 93.321 539 25 5 1 537 714060770 714061299 0.000000e+00 785.0
26 TraesCS4A01G321900 chr6A 93.296 537 24 6 4 537 601247668 601247141 0.000000e+00 782.0
27 TraesCS4A01G321900 chr6A 92.551 537 33 4 4 537 36258492 36257960 0.000000e+00 763.0
28 TraesCS4A01G321900 chr1A 92.764 539 29 3 1 537 4225972 4226502 0.000000e+00 771.0
29 TraesCS4A01G321900 chr1A 90.047 211 10 4 330 537 321885808 321886010 2.230000e-66 263.0
30 TraesCS4A01G321900 chr2A 90.130 537 28 8 1 537 707985682 707986193 0.000000e+00 675.0


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 TraesCS4A01G321900 chr4A 610088743 610091656 2913 True 5382.00 5382 100.0000 1 2914 1 chr4A.!!$R2 2913
1 TraesCS4A01G321900 chr4A 610130875 610132711 1836 True 2470.00 2470 90.8260 620 2483 1 chr4A.!!$R3 1863
2 TraesCS4A01G321900 chr4A 616015762 616017159 1397 True 828.00 828 77.8090 956 2338 1 chr4A.!!$R5 1382
3 TraesCS4A01G321900 chr4A 610256517 610257075 558 True 728.00 728 90.1790 1795 2354 1 chr4A.!!$R4 559
4 TraesCS4A01G321900 chr5D 557923392 557925348 1956 False 2483.00 2483 89.8170 537 2467 1 chr5D.!!$F3 1930
5 TraesCS4A01G321900 chr5D 557803159 557804122 963 False 1149.00 1149 88.3020 641 1599 1 chr5D.!!$F1 958
6 TraesCS4A01G321900 chr5D 557821425 557822250 825 False 998.00 998 88.4480 1591 2421 1 chr5D.!!$F2 830
7 TraesCS4A01G321900 chr5D 557888684 557891294 2610 True 838.00 1306 82.9775 953 2370 2 chr5D.!!$R1 1417
8 TraesCS4A01G321900 chr5D 558722106 558722968 862 False 651.00 651 80.4370 965 1825 1 chr5D.!!$F4 860
9 TraesCS4A01G321900 chr5B 699293246 699294635 1389 True 793.00 793 77.4560 956 2338 1 chr5B.!!$R1 1382
10 TraesCS4A01G321900 chr5B 705027432 705033677 6245 False 653.85 1048 92.4930 1068 2914 4 chr5B.!!$F1 1846
11 TraesCS4A01G321900 chr5B 704092280 704093143 863 True 628.00 628 80.0000 965 1825 1 chr5B.!!$R2 860
12 TraesCS4A01G321900 chr3B 52750190 52750722 532 False 850.00 850 95.3450 1 537 1 chr3B.!!$F1 536
13 TraesCS4A01G321900 chr3B 807123743 807124272 529 True 811.00 811 94.1950 4 537 1 chr3B.!!$R2 533
14 TraesCS4A01G321900 chr5A 452269886 452270420 534 False 808.00 808 93.8660 1 537 1 chr5A.!!$F1 536
15 TraesCS4A01G321900 chr5A 701296966 701297477 511 False 708.00 708 91.2480 1 537 1 chr5A.!!$F2 536
16 TraesCS4A01G321900 chr1B 267809108 267809633 525 True 795.00 795 93.8090 4 536 1 chr1B.!!$R1 532
17 TraesCS4A01G321900 chr3A 714060770 714061299 529 False 785.00 785 93.3210 1 537 1 chr3A.!!$F1 536
18 TraesCS4A01G321900 chr6A 601247141 601247668 527 True 782.00 782 93.2960 4 537 1 chr6A.!!$R2 533
19 TraesCS4A01G321900 chr6A 36257960 36258492 532 True 763.00 763 92.5510 4 537 1 chr6A.!!$R1 533
20 TraesCS4A01G321900 chr1A 4225972 4226502 530 False 771.00 771 92.7640 1 537 1 chr1A.!!$F1 536
21 TraesCS4A01G321900 chr2A 707985682 707986193 511 False 675.00 675 90.1300 1 537 1 chr2A.!!$F1 536

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
728 765 0.894835 TGCATGACCAAGAGCTACGA 59.105 50.0 0.0 0.0 0.0 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 7172 0.174845 ACCTAGCGCTAATTGCACGA 59.825 50.0 19.37 0.0 43.06 4.35 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
49 50 6.092122 CAGTAGATATTGCGTCTTTGTTTGGA 59.908 38.462 0.00 0.00 0.00 3.53
244 245 2.583101 ACTCACTCCTATGGACTCCAGA 59.417 50.000 3.62 0.00 36.75 3.86
451 455 2.543777 TGCGAGCTGTAAGACCTTTT 57.456 45.000 0.00 0.00 34.07 2.27
618 625 4.647291 GCTCGCTGCGTTATATACAAAT 57.353 40.909 22.48 0.00 0.00 2.32
622 653 6.346279 GCTCGCTGCGTTATATACAAATACAA 60.346 38.462 22.48 0.00 0.00 2.41
728 765 0.894835 TGCATGACCAAGAGCTACGA 59.105 50.000 0.00 0.00 0.00 3.43
746 783 1.442769 GAGCAACAGCGGAGATTCAA 58.557 50.000 0.00 0.00 0.00 2.69
776 813 2.961721 CGTCATCGACATGCCGGG 60.962 66.667 2.18 0.00 39.71 5.73
845 882 4.415332 GTTCGCTCTCGCCCGACA 62.415 66.667 0.00 0.00 32.60 4.35
1265 1303 1.005867 TGTTTACCACCGACGAGGC 60.006 57.895 0.00 0.00 46.52 4.70
1338 1376 4.441634 CCTCCGGTCAAAACTATCTACCAG 60.442 50.000 0.00 0.00 0.00 4.00
1378 1428 1.604593 GGTGGCAAGCATGTCTGGT 60.605 57.895 0.00 0.00 33.62 4.00
1627 1689 6.974622 GGATGGCTTGTTCTACATTTTGTATG 59.025 38.462 0.00 0.00 31.66 2.39
1709 1774 1.666872 GCAGCGTGTTACCCTCGTT 60.667 57.895 0.00 0.00 32.79 3.85
1735 5204 7.191918 AGGATATCATACCATGTATCCTGTCA 58.808 38.462 15.85 0.00 43.75 3.58
1793 5262 5.381757 GGACTGGAGTCACATAGATACTCT 58.618 45.833 8.99 0.00 46.47 3.24
1873 5342 1.361668 CCTCGCCCACAAAGATGACG 61.362 60.000 0.00 0.00 0.00 4.35
1912 5381 7.059788 ACAAGATGAGCTAGAGACAGAAGATA 58.940 38.462 0.00 0.00 0.00 1.98
2029 5498 1.116308 TGTTGAAGAGGTCACCACGA 58.884 50.000 0.00 0.00 35.39 4.35
2079 5548 3.007506 TCGATAGACAAAAGCTGGTGGAA 59.992 43.478 0.00 0.00 42.67 3.53
2104 5573 0.392998 GGACATTGGAGACCATGCGT 60.393 55.000 0.00 0.00 31.53 5.24
2197 5666 4.940046 TCTATCTAACGGACGACTGTTCTT 59.060 41.667 15.25 5.03 43.51 2.52
2419 6009 2.029380 GTGGTATGCAAAAGTTGACCCC 60.029 50.000 0.00 0.00 0.00 4.95
2420 6010 2.158385 TGGTATGCAAAAGTTGACCCCT 60.158 45.455 0.00 0.00 0.00 4.79
2514 7134 7.812690 TCTGTTCTAGAGTACACAGTGTTAA 57.187 36.000 12.53 0.00 38.26 2.01
2550 7171 7.921786 TTACTTAAACTAGCTCTACGTGGTA 57.078 36.000 0.00 0.00 0.00 3.25
2551 7172 8.511604 TTACTTAAACTAGCTCTACGTGGTAT 57.488 34.615 0.00 0.00 0.00 2.73
2552 7173 7.025485 ACTTAAACTAGCTCTACGTGGTATC 57.975 40.000 0.00 0.00 0.00 2.24
2557 7178 0.099968 GCTCTACGTGGTATCGTGCA 59.900 55.000 0.00 0.00 43.93 4.57
2603 7224 2.753009 TTTGCATGCTGAGTCCGGCT 62.753 55.000 20.33 0.00 44.89 5.52
2618 7239 2.507058 TCCGGCTAGGACTAGTACTTGA 59.493 50.000 19.35 0.00 45.98 3.02
2638 7259 1.134995 ACCGTAAGCGTAACTAAGGGC 60.135 52.381 0.00 0.00 36.15 5.19
2650 7271 6.483640 GCGTAACTAAGGGCTAACTAGTACTA 59.516 42.308 1.89 1.89 0.00 1.82
2662 7283 6.484977 GCTAACTAGTACTAGTCCGGTTACAT 59.515 42.308 30.81 16.89 44.96 2.29
2689 7310 3.364889 TTCGATTCTATACGCTGGGTG 57.635 47.619 7.71 0.00 0.00 4.61
2697 7318 1.485124 ATACGCTGGGTGAGTCATCA 58.515 50.000 5.60 2.53 0.00 3.07
2728 7349 7.176909 AGTAGGTATAGTTAATCTCCTGGGT 57.823 40.000 0.00 0.00 0.00 4.51
2790 7411 1.798813 GTGGGTCGAGAATTGTGTCAC 59.201 52.381 0.00 0.00 0.00 3.67
2806 7427 3.996480 TGTCACGGACACAATCAACATA 58.004 40.909 3.02 0.00 37.67 2.29
2881 7502 3.438087 AGGTTCAGACATTTCATCAAGCG 59.562 43.478 0.00 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 0.536460 CAACCCCAGCTAACCACGTT 60.536 55.000 0.00 0.00 0.00 3.99
244 245 1.073923 CACCCAGTAACCAAAGGCTCT 59.926 52.381 0.00 0.00 0.00 4.09
466 470 6.404184 GCATGCGGCCCTTTTATTAAAAATTT 60.404 34.615 0.00 0.00 33.44 1.82
562 569 3.726517 CGGGCAAGTTCGCACCTG 61.727 66.667 0.00 0.00 28.57 4.00
728 765 1.160137 GTTGAATCTCCGCTGTTGCT 58.840 50.000 0.00 0.00 36.97 3.91
746 783 2.635229 GATGACGGCATCTGGAGCGT 62.635 60.000 24.36 0.00 45.93 5.07
840 877 2.040544 GGATGGCTGGTTGTGTCGG 61.041 63.158 0.00 0.00 0.00 4.79
845 882 2.048023 CGCATGGATGGCTGGTTGT 61.048 57.895 0.00 0.00 0.00 3.32
1265 1303 3.846430 GGAGGTAAGGGTCGCCGG 61.846 72.222 0.00 0.00 0.00 6.13
1338 1376 3.175324 CGTCGTCATAGAATTCGTCGTTC 59.825 47.826 0.00 0.00 32.59 3.95
1378 1428 2.636412 CGTTCTCGGGGTCAGCAGA 61.636 63.158 0.00 0.00 0.00 4.26
1491 1541 2.221749 CCACTTCGGATTATGCACGATG 59.778 50.000 7.66 7.66 36.43 3.84
1568 1630 3.326747 AGAACGTTGTCAATGTAGCCTC 58.673 45.455 5.00 5.23 0.00 4.70
1570 1632 4.483476 AAAGAACGTTGTCAATGTAGCC 57.517 40.909 5.00 4.28 0.00 3.93
1576 1638 7.022055 TGTCATTGTAAAGAACGTTGTCAAT 57.978 32.000 5.00 5.24 0.00 2.57
1627 1689 3.113260 AGTACCAATAGAGCCATTCGC 57.887 47.619 0.00 0.00 37.98 4.70
1677 1742 1.731700 GCTGCGCATGATCATGGTT 59.268 52.632 31.62 0.00 39.16 3.67
1703 1768 6.531503 ACATGGTATGATATCCTAACGAGG 57.468 41.667 0.00 0.00 45.35 4.63
1709 1774 8.343787 TGACAGGATACATGGTATGATATCCTA 58.656 37.037 16.07 3.50 43.67 2.94
1735 5204 0.976073 AGTTCACCCGATGGACCGAT 60.976 55.000 0.00 0.00 37.56 4.18
1793 5262 4.142315 GGTAAGTGCCACGATACTTGAGTA 60.142 45.833 11.75 0.00 37.66 2.59
1873 5342 5.051374 GCTCATCTTGTAGCTTATTGTCGTC 60.051 44.000 0.00 0.00 35.80 4.20
1912 5381 1.733399 GTTCGCCTTCTTCGTCGCT 60.733 57.895 0.00 0.00 0.00 4.93
2001 5470 1.347707 ACCTCTTCAACAAGCCGATGA 59.652 47.619 0.00 0.00 0.00 2.92
2016 5485 0.247736 GCTCATTCGTGGTGACCTCT 59.752 55.000 2.11 0.00 0.00 3.69
2029 5498 6.213600 TCAACCTTAAAGACTAGGAGCTCATT 59.786 38.462 17.19 5.59 35.45 2.57
2079 5548 2.915869 TGGTCTCCAATGTCCCTTAGT 58.084 47.619 0.00 0.00 0.00 2.24
2104 5573 2.875933 CAGAGTTAAGCCCAACGAACAA 59.124 45.455 0.00 0.00 33.50 2.83
2197 5666 5.981088 TTCCGTAACATTGGACTGTAGTA 57.019 39.130 0.00 0.00 32.95 1.82
2392 5982 5.462068 GTCAACTTTTGCATACCACCTTTTC 59.538 40.000 0.00 0.00 0.00 2.29
2526 7146 6.824305 ACCACGTAGAGCTAGTTTAAGTAA 57.176 37.500 0.00 0.00 0.00 2.24
2529 7149 6.134730 CGATACCACGTAGAGCTAGTTTAAG 58.865 44.000 0.00 0.00 0.00 1.85
2550 7171 1.202533 ACCTAGCGCTAATTGCACGAT 60.203 47.619 19.37 0.00 43.06 3.73
2551 7172 0.174845 ACCTAGCGCTAATTGCACGA 59.825 50.000 19.37 0.00 43.06 4.35
2552 7173 0.301687 CACCTAGCGCTAATTGCACG 59.698 55.000 19.37 4.57 43.06 5.34
2557 7178 6.158023 ACTATTGTACACCTAGCGCTAATT 57.842 37.500 19.37 5.04 0.00 1.40
2565 7186 8.604035 CATGCAAACTAACTATTGTACACCTAG 58.396 37.037 0.00 2.52 0.00 3.02
2566 7187 7.065324 GCATGCAAACTAACTATTGTACACCTA 59.935 37.037 14.21 0.00 0.00 3.08
2567 7188 6.128007 GCATGCAAACTAACTATTGTACACCT 60.128 38.462 14.21 0.00 0.00 4.00
2569 7190 6.742718 CAGCATGCAAACTAACTATTGTACAC 59.257 38.462 21.98 0.00 0.00 2.90
2570 7191 6.652900 TCAGCATGCAAACTAACTATTGTACA 59.347 34.615 21.98 0.00 34.76 2.90
2571 7192 7.072177 TCAGCATGCAAACTAACTATTGTAC 57.928 36.000 21.98 0.00 34.76 2.90
2572 7193 6.878923 ACTCAGCATGCAAACTAACTATTGTA 59.121 34.615 21.98 0.00 34.76 2.41
2573 7194 5.707298 ACTCAGCATGCAAACTAACTATTGT 59.293 36.000 21.98 0.00 34.76 2.71
2603 7224 4.878397 GCTTACGGTCAAGTACTAGTCCTA 59.122 45.833 0.00 0.00 0.00 2.94
2610 7231 3.503748 AGTTACGCTTACGGTCAAGTACT 59.496 43.478 0.00 0.00 46.04 2.73
2618 7239 1.134995 GCCCTTAGTTACGCTTACGGT 60.135 52.381 0.00 0.00 46.04 4.83
2638 7259 9.202273 CTATGTAACCGGACTAGTACTAGTTAG 57.798 40.741 31.14 25.89 45.63 2.34
2650 7271 4.460382 TCGAAACTTCTATGTAACCGGACT 59.540 41.667 9.46 0.00 0.00 3.85
2662 7283 6.436261 CCAGCGTATAGAATCGAAACTTCTA 58.564 40.000 8.91 8.91 39.02 2.10
2689 7310 9.820725 ACTATACCTACTCGTATATGATGACTC 57.179 37.037 0.00 0.00 32.20 3.36
2728 7349 1.339610 CAACATTTTCTCCCGTTGCCA 59.660 47.619 0.00 0.00 33.08 4.92
2762 7383 1.111116 TTCTCGACCCACTCAACCGT 61.111 55.000 0.00 0.00 0.00 4.83
2790 7411 9.051679 TCCTAAATATTATGTTGATTGTGTCCG 57.948 33.333 0.00 0.00 0.00 4.79
2866 7487 4.668576 TCAAGACGCTTGATGAAATGTC 57.331 40.909 15.33 0.00 0.00 3.06
2881 7502 6.425114 TCACACTTGCTAGATTTCTTCAAGAC 59.575 38.462 19.89 0.00 38.04 3.01


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

AutoCloner maintained by Alex Coulton.