Multiple sequence alignment - TraesCS4A01G049600

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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 TraesCS4A01G049600 chr4A 100.000 3447 0 0 1 3447 40438054 40434608 0.000000e+00 6366
1 TraesCS4A01G049600 chr4A 98.470 1503 19 2 4 1502 40414519 40413017 0.000000e+00 2645
2 TraesCS4A01G049600 chr4A 99.444 899 5 0 4 902 40493325 40492427 0.000000e+00 1633
3 TraesCS4A01G049600 chr4A 98.265 634 8 1 272 902 40495042 40495675 0.000000e+00 1107
4 TraesCS4A01G049600 chr4A 97.173 566 15 1 1616 2181 40413026 40412462 0.000000e+00 955
5 TraesCS4A01G049600 chr4A 95.626 503 13 2 2951 3445 40286101 40285600 0.000000e+00 798
6 TraesCS4A01G049600 chr4D 93.005 2516 117 16 465 2950 423906177 423908663 0.000000e+00 3616
7 TraesCS4A01G049600 chr4D 86.501 963 107 11 1493 2439 423880697 423881652 0.000000e+00 1037
8 TraesCS4A01G049600 chr4D 83.707 1025 123 22 467 1460 423879686 423880697 0.000000e+00 928
9 TraesCS4A01G049600 chr4D 91.405 477 18 5 2 469 423905641 423906103 1.750000e-177 632
10 TraesCS4A01G049600 chr4D 85.612 417 32 11 2 414 423879190 423879582 2.480000e-111 412
11 TraesCS4A01G049600 chr4B 92.039 1432 97 8 762 2183 520237442 520238866 0.000000e+00 1997
12 TraesCS4A01G049600 chr4B 83.786 2097 238 49 467 2509 520228697 520230745 0.000000e+00 1895
13 TraesCS4A01G049600 chr4B 94.675 676 25 3 2281 2950 520238916 520239586 0.000000e+00 1038
14 TraesCS4A01G049600 chr4B 94.681 470 16 3 2 469 520236557 520237019 0.000000e+00 721
15 TraesCS4A01G049600 chr4B 86.364 418 26 15 2 414 520228198 520228589 8.840000e-116 427
16 TraesCS4A01G049600 chr4B 94.301 193 10 1 533 724 520237251 520237443 9.360000e-76 294
17 TraesCS4A01G049600 chr4B 93.103 87 3 1 465 548 520237099 520237185 1.300000e-24 124
18 TraesCS4A01G049600 chr2A 93.465 505 25 1 2951 3447 103392910 103393414 0.000000e+00 743
19 TraesCS4A01G049600 chr2A 93.069 505 26 2 2951 3447 550520560 550521063 0.000000e+00 730
20 TraesCS4A01G049600 chr7A 92.475 505 27 2 2951 3447 433223689 433224190 0.000000e+00 712
21 TraesCS4A01G049600 chr7A 91.451 503 35 1 2953 3447 600976637 600977139 0.000000e+00 684
22 TraesCS4A01G049600 chr3A 91.124 507 33 4 2951 3447 510422924 510423428 0.000000e+00 676
23 TraesCS4A01G049600 chr3A 89.379 499 49 3 2951 3447 730714221 730714717 2.920000e-175 625
24 TraesCS4A01G049600 chr3A 89.178 499 50 3 2951 3447 731755220 731754724 1.360000e-173 619
25 TraesCS4A01G049600 chr5A 88.600 500 55 2 2950 3447 181748649 181749148 1.060000e-169 606
26 TraesCS4A01G049600 chr5A 88.577 499 55 2 2951 3447 181772000 181772498 3.810000e-169 604
27 TraesCS4A01G049600 chr6D 88.340 506 45 12 2951 3446 452146307 452146808 2.290000e-166 595
28 TraesCS4A01G049600 chr1B 75.636 550 116 16 991 1530 653975544 653975003 1.230000e-64 257
29 TraesCS4A01G049600 chr1B 75.439 456 88 21 991 1435 653938868 653938426 2.100000e-47 200
30 TraesCS4A01G049600 chr1B 75.059 421 103 2 1004 1423 654092636 654093055 9.760000e-46 195
31 TraesCS4A01G049600 chr1A 75.670 448 101 8 991 1435 564345839 564345397 2.080000e-52 217


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 TraesCS4A01G049600 chr4A 40434608 40438054 3446 True 6366.000000 6366 100.000000 1 3447 1 chr4A.!!$R2 3446
1 TraesCS4A01G049600 chr4A 40412462 40414519 2057 True 1800.000000 2645 97.821500 4 2181 2 chr4A.!!$R4 2177
2 TraesCS4A01G049600 chr4A 40492427 40493325 898 True 1633.000000 1633 99.444000 4 902 1 chr4A.!!$R3 898
3 TraesCS4A01G049600 chr4A 40495042 40495675 633 False 1107.000000 1107 98.265000 272 902 1 chr4A.!!$F1 630
4 TraesCS4A01G049600 chr4A 40285600 40286101 501 True 798.000000 798 95.626000 2951 3445 1 chr4A.!!$R1 494
5 TraesCS4A01G049600 chr4D 423905641 423908663 3022 False 2124.000000 3616 92.205000 2 2950 2 chr4D.!!$F2 2948
6 TraesCS4A01G049600 chr4D 423879190 423881652 2462 False 792.333333 1037 85.273333 2 2439 3 chr4D.!!$F1 2437
7 TraesCS4A01G049600 chr4B 520228198 520230745 2547 False 1161.000000 1895 85.075000 2 2509 2 chr4B.!!$F1 2507
8 TraesCS4A01G049600 chr4B 520236557 520239586 3029 False 834.800000 1997 93.759800 2 2950 5 chr4B.!!$F2 2948
9 TraesCS4A01G049600 chr2A 103392910 103393414 504 False 743.000000 743 93.465000 2951 3447 1 chr2A.!!$F1 496
10 TraesCS4A01G049600 chr2A 550520560 550521063 503 False 730.000000 730 93.069000 2951 3447 1 chr2A.!!$F2 496
11 TraesCS4A01G049600 chr7A 433223689 433224190 501 False 712.000000 712 92.475000 2951 3447 1 chr7A.!!$F1 496
12 TraesCS4A01G049600 chr7A 600976637 600977139 502 False 684.000000 684 91.451000 2953 3447 1 chr7A.!!$F2 494
13 TraesCS4A01G049600 chr3A 510422924 510423428 504 False 676.000000 676 91.124000 2951 3447 1 chr3A.!!$F1 496
14 TraesCS4A01G049600 chr6D 452146307 452146808 501 False 595.000000 595 88.340000 2951 3446 1 chr6D.!!$F1 495
15 TraesCS4A01G049600 chr1B 653975003 653975544 541 True 257.000000 257 75.636000 991 1530 1 chr1B.!!$R2 539

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
1197 1413 6.639632 ACTGCAAGAAGCTTCTGAAAATTA 57.36 33.333 29.09 10.79 45.94 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2484 2774 0.251916 CACGGGCCTCCAGTATTTCA 59.748 55.0 0.84 0.0 0.0 2.69 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
1197 1413 6.639632 ACTGCAAGAAGCTTCTGAAAATTA 57.360 33.333 29.09 10.79 45.94 1.40
1375 1627 8.418597 AAGTACAAGAACAACTATACTCCTCA 57.581 34.615 0.00 0.00 0.00 3.86
1544 1799 1.192146 TTCAGCGGCTGAGTACCCTT 61.192 55.000 29.29 0.00 41.75 3.95
1545 1800 1.153549 CAGCGGCTGAGTACCCTTC 60.154 63.158 25.33 0.00 32.44 3.46
1585 1840 3.621715 GTCAAACTTCAGGTGTTCTCGTT 59.378 43.478 0.00 0.00 0.00 3.85
1589 1844 4.073293 ACTTCAGGTGTTCTCGTTTGAT 57.927 40.909 0.00 0.00 0.00 2.57
1596 1851 4.065789 GGTGTTCTCGTTTGATCTTTCCT 58.934 43.478 0.00 0.00 0.00 3.36
1614 1869 4.226427 TCCTCTTGGTTTCTGGATGATG 57.774 45.455 0.00 0.00 34.23 3.07
1881 2136 3.252215 TGCTCGTACAATTCTTGTTTGGG 59.748 43.478 0.00 0.00 42.22 4.12
2065 2320 1.277842 TGAACGGGCAGATAAGCTTCA 59.722 47.619 0.00 0.00 34.17 3.02
2201 2464 3.781079 TTAACCATGTAGTCGGTACCG 57.219 47.619 28.66 28.66 41.35 4.02
2203 2466 2.418368 ACCATGTAGTCGGTACCGTA 57.582 50.000 32.16 16.81 40.74 4.02
2273 2540 2.825532 AGAGGCAGTTCTTCTCTCTGTC 59.174 50.000 0.00 0.00 33.01 3.51
2334 2601 9.883142 TTTTTGTTTTCTTGAACCTATTCATGT 57.117 25.926 0.00 0.00 44.36 3.21
2335 2602 9.528018 TTTTGTTTTCTTGAACCTATTCATGTC 57.472 29.630 0.00 0.00 44.36 3.06
2484 2774 5.327732 TGAGGGAAGATGCTGAATTTCTTT 58.672 37.500 0.00 0.00 30.11 2.52
2500 2790 3.366052 TCTTTGAAATACTGGAGGCCC 57.634 47.619 0.00 0.00 0.00 5.80
2738 3029 8.519526 ACGGTTGAAATATTACAATGTGAACAT 58.480 29.630 0.00 0.00 38.41 2.71
2855 3146 0.853530 ACTCCTCACTTTTGCCCCTT 59.146 50.000 0.00 0.00 0.00 3.95
2862 3153 2.978018 CTTTTGCCCCTTCGCCGTC 61.978 63.158 0.00 0.00 0.00 4.79
2890 3181 2.432444 CCTACGAAAATGCCCTCACAA 58.568 47.619 0.00 0.00 0.00 3.33
2902 3193 1.953686 CCCTCACAACATGTTTCCGTT 59.046 47.619 8.77 0.00 0.00 4.44
2927 3218 2.649312 TCAACCCCCTTTGATCATCACT 59.351 45.455 0.00 0.00 30.29 3.41
2943 3234 4.516321 TCATCACTGACACATTTGTTGGAG 59.484 41.667 0.00 0.00 35.47 3.86
3291 3585 4.646572 CTCAGTTTCTACCTTTCCTTGCT 58.353 43.478 0.00 0.00 0.00 3.91
3304 3598 6.775629 ACCTTTCCTTGCTTTACAACATAAGA 59.224 34.615 0.00 0.00 33.68 2.10
3402 3707 4.473444 GCCATCCCTTTTATCTTCATGGA 58.527 43.478 0.00 0.00 32.51 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1098 1313 2.071778 AAAGACTTGAAAGGCAGCCA 57.928 45.000 15.80 0.00 36.14 4.75
1197 1413 3.243771 CGTTGGTAGAGAAGACCTGTTGT 60.244 47.826 0.00 0.00 37.88 3.32
1375 1627 3.064820 CACGATAAAGCGGCAAATACCTT 59.935 43.478 1.45 0.00 35.12 3.50
1544 1799 4.105388 GGGCCAAATCCCAAACGA 57.895 55.556 4.39 0.00 45.82 3.85
1585 1840 5.072741 CCAGAAACCAAGAGGAAAGATCAA 58.927 41.667 0.00 0.00 38.69 2.57
1589 1844 4.350816 TCATCCAGAAACCAAGAGGAAAGA 59.649 41.667 0.00 0.00 38.69 2.52
1596 1851 3.438216 TGCATCATCCAGAAACCAAGA 57.562 42.857 0.00 0.00 0.00 3.02
1614 1869 1.138464 TGTCTCAGAGAGCCATGATGC 59.862 52.381 0.00 0.00 0.00 3.91
1881 2136 2.996631 AGGCTCATCAACATCAAGACC 58.003 47.619 0.00 0.00 0.00 3.85
2065 2320 8.671028 GTTCACCGGTTCTTATATTGTACAAAT 58.329 33.333 13.23 9.91 0.00 2.32
2201 2464 5.173131 CGACACTCAAAAGCCAAACAAATAC 59.827 40.000 0.00 0.00 0.00 1.89
2203 2466 4.111916 CGACACTCAAAAGCCAAACAAAT 58.888 39.130 0.00 0.00 0.00 2.32
2332 2599 8.647796 CCTCATTAATATTGGTACTACTGGACA 58.352 37.037 0.00 0.00 0.00 4.02
2333 2600 8.648693 ACCTCATTAATATTGGTACTACTGGAC 58.351 37.037 0.00 0.00 0.00 4.02
2334 2601 8.792830 ACCTCATTAATATTGGTACTACTGGA 57.207 34.615 0.00 0.00 0.00 3.86
2484 2774 0.251916 CACGGGCCTCCAGTATTTCA 59.748 55.000 0.84 0.00 0.00 2.69
2500 2790 3.416277 CAAATGATAAACGGAGCACACG 58.584 45.455 0.00 0.00 37.36 4.49
2833 3124 1.478654 GGGGCAAAAGTGAGGAGTTCA 60.479 52.381 0.00 0.00 0.00 3.18
2862 3153 1.135402 GCATTTTCGTAGGGCCACTTG 60.135 52.381 6.18 0.00 0.00 3.16
2874 3165 2.030007 ACATGTTGTGAGGGCATTTTCG 60.030 45.455 0.00 0.00 0.00 3.46
2890 3181 1.600485 GTTGACCGAACGGAAACATGT 59.400 47.619 20.14 0.00 38.96 3.21
2902 3193 0.326927 GATCAAAGGGGGTTGACCGA 59.673 55.000 0.00 0.00 40.22 4.69
2927 3218 3.884895 AGTGTCTCCAACAAATGTGTCA 58.115 40.909 0.00 0.00 40.31 3.58
2943 3234 3.805422 TGACAAAACCACGACATAGTGTC 59.195 43.478 0.00 0.07 43.65 3.67
3304 3598 8.486210 AGATGTAAACCGCCATATGATATGTAT 58.514 33.333 11.20 0.00 0.00 2.29
3402 3707 7.502226 TCACAAGGAGTTAATCATGTTTGAAGT 59.498 33.333 0.00 0.00 34.96 3.01
3415 3720 4.998672 CGGGTTATGTTCACAAGGAGTTAA 59.001 41.667 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.