Multiple sequence alignment - TraesCS4A01G436100

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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 TraesCS4A01G436100 chr4A 100.000 3278 0 0 1 3278 705888443 705891720 0.000000e+00 6054.0
1 TraesCS4A01G436100 chr4A 97.295 2329 63 0 1 2329 707401915 707404243 0.000000e+00 3952.0
2 TraesCS4A01G436100 chr4A 91.381 1427 96 6 908 2322 707177748 707179159 0.000000e+00 1929.0
3 TraesCS4A01G436100 chr4A 91.381 1427 96 6 908 2322 707201273 707202684 0.000000e+00 1929.0
4 TraesCS4A01G436100 chr4A 92.103 1317 86 8 908 2207 707478356 707477041 0.000000e+00 1840.0
5 TraesCS4A01G436100 chr4A 91.167 1234 105 3 908 2137 706094841 706096074 0.000000e+00 1672.0
6 TraesCS4A01G436100 chr4A 94.737 418 14 2 2461 2878 707404244 707404653 0.000000e+00 643.0
7 TraesCS4A01G436100 chr4A 95.250 400 17 2 2880 3278 707405991 707406389 1.660000e-177 632.0
8 TraesCS4A01G436100 chr4A 91.641 323 15 1 1897 2207 705906546 705906868 1.400000e-118 436.0
9 TraesCS4A01G436100 chr4A 85.256 156 8 9 2066 2207 707646043 707645889 2.640000e-31 147.0
10 TraesCS4A01G436100 chr4A 92.045 88 7 0 2235 2322 707477046 707476959 1.230000e-24 124.0
11 TraesCS4A01G436100 chr7D 90.230 1392 106 15 936 2298 24157228 24155838 0.000000e+00 1790.0
12 TraesCS4A01G436100 chr7D 87.604 1436 141 17 908 2310 53793325 53791894 0.000000e+00 1631.0
13 TraesCS4A01G436100 chr7D 80.887 293 32 13 2461 2740 24034005 24034286 3.310000e-50 209.0
14 TraesCS4A01G436100 chrUn 91.734 1234 98 3 908 2137 220054912 220056145 0.000000e+00 1711.0
15 TraesCS4A01G436100 chrUn 100.000 131 0 0 2330 2460 86450494 86450624 3.270000e-60 243.0
16 TraesCS4A01G436100 chrUn 100.000 131 0 0 2330 2460 86456494 86456624 3.270000e-60 243.0
17 TraesCS4A01G436100 chrUn 100.000 131 0 0 2330 2460 222678782 222678652 3.270000e-60 243.0
18 TraesCS4A01G436100 chrUn 100.000 131 0 0 2330 2460 430697321 430697451 3.270000e-60 243.0
19 TraesCS4A01G436100 chr7A 88.293 1435 130 18 908 2310 57219302 57217874 0.000000e+00 1685.0
20 TraesCS4A01G436100 chr7A 79.574 235 21 11 593 806 37408299 37408527 3.410000e-30 143.0
21 TraesCS4A01G436100 chr7A 85.185 81 12 0 770 850 692457566 692457646 2.100000e-12 84.2
22 TraesCS4A01G436100 chr2D 82.038 746 91 14 170 878 611218359 611217620 2.180000e-166 595.0
23 TraesCS4A01G436100 chr2D 78.056 360 47 15 516 853 115595010 115594661 7.170000e-47 198.0
24 TraesCS4A01G436100 chr3A 81.745 745 92 13 168 877 231742764 231742029 1.700000e-162 582.0
25 TraesCS4A01G436100 chr3A 84.211 76 8 4 777 850 80431761 80431834 1.630000e-08 71.3
26 TraesCS4A01G436100 chr3A 82.432 74 9 4 779 850 615925722 615925793 9.820000e-06 62.1
27 TraesCS4A01G436100 chr1B 80.795 755 100 20 159 879 6251482 6250739 1.720000e-152 549.0
28 TraesCS4A01G436100 chr5B 79.310 754 105 21 167 879 437806889 437806146 6.360000e-132 481.0
29 TraesCS4A01G436100 chr1A 78.302 742 104 23 172 879 249024963 249024245 3.020000e-115 425.0
30 TraesCS4A01G436100 chr1A 100.000 131 0 0 2330 2460 238118864 238118994 3.270000e-60 243.0
31 TraesCS4A01G436100 chr1A 100.000 131 0 0 2330 2460 238122785 238122915 3.270000e-60 243.0
32 TraesCS4A01G436100 chr1A 76.471 323 51 17 441 748 408070800 408070488 5.670000e-33 152.0
33 TraesCS4A01G436100 chr1A 74.627 335 60 12 440 751 86652063 86652395 1.230000e-24 124.0
34 TraesCS4A01G436100 chr6A 77.241 725 94 26 170 858 62917544 62916855 3.110000e-95 359.0
35 TraesCS4A01G436100 chr6A 100.000 131 0 0 2330 2460 84444069 84444199 3.270000e-60 243.0
36 TraesCS4A01G436100 chr2A 82.486 354 43 5 168 502 743546913 743546560 3.200000e-75 292.0
37 TraesCS4A01G436100 chr2A 80.899 89 16 1 755 843 12319053 12319140 5.870000e-08 69.4
38 TraesCS4A01G436100 chr4D 100.000 131 0 0 2330 2460 123433646 123433776 3.270000e-60 243.0
39 TraesCS4A01G436100 chr4D 83.594 128 12 6 622 749 52829927 52830045 9.610000e-21 111.0
40 TraesCS4A01G436100 chr1D 100.000 131 0 0 2330 2460 351069529 351069399 3.270000e-60 243.0
41 TraesCS4A01G436100 chr1D 80.449 312 51 6 440 747 91011864 91012169 2.540000e-56 230.0
42 TraesCS4A01G436100 chr6D 81.897 232 37 4 165 395 414472462 414472689 1.200000e-44 191.0
43 TraesCS4A01G436100 chr6D 74.432 352 59 15 548 876 435810889 435810546 4.440000e-24 122.0
44 TraesCS4A01G436100 chr3B 79.365 189 30 3 178 365 170832008 170832188 1.230000e-24 124.0
45 TraesCS4A01G436100 chr3B 84.375 128 11 6 622 749 740038664 740038782 2.070000e-22 117.0
46 TraesCS4A01G436100 chr7B 77.391 115 24 2 755 868 700558844 700558731 2.110000e-07 67.6
47 TraesCS4A01G436100 chr7B 81.707 82 14 1 762 843 747328542 747328462 2.110000e-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 TraesCS4A01G436100 chr4A 705888443 705891720 3277 False 6054.000000 6054 100.000000 1 3278 1 chr4A.!!$F1 3277
1 TraesCS4A01G436100 chr4A 707177748 707179159 1411 False 1929.000000 1929 91.381000 908 2322 1 chr4A.!!$F4 1414
2 TraesCS4A01G436100 chr4A 707201273 707202684 1411 False 1929.000000 1929 91.381000 908 2322 1 chr4A.!!$F5 1414
3 TraesCS4A01G436100 chr4A 707401915 707406389 4474 False 1742.333333 3952 95.760667 1 3278 3 chr4A.!!$F6 3277
4 TraesCS4A01G436100 chr4A 706094841 706096074 1233 False 1672.000000 1672 91.167000 908 2137 1 chr4A.!!$F3 1229
5 TraesCS4A01G436100 chr4A 707476959 707478356 1397 True 982.000000 1840 92.074000 908 2322 2 chr4A.!!$R2 1414
6 TraesCS4A01G436100 chr7D 24155838 24157228 1390 True 1790.000000 1790 90.230000 936 2298 1 chr7D.!!$R1 1362
7 TraesCS4A01G436100 chr7D 53791894 53793325 1431 True 1631.000000 1631 87.604000 908 2310 1 chr7D.!!$R2 1402
8 TraesCS4A01G436100 chrUn 220054912 220056145 1233 False 1711.000000 1711 91.734000 908 2137 1 chrUn.!!$F3 1229
9 TraesCS4A01G436100 chr7A 57217874 57219302 1428 True 1685.000000 1685 88.293000 908 2310 1 chr7A.!!$R1 1402
10 TraesCS4A01G436100 chr2D 611217620 611218359 739 True 595.000000 595 82.038000 170 878 1 chr2D.!!$R2 708
11 TraesCS4A01G436100 chr3A 231742029 231742764 735 True 582.000000 582 81.745000 168 877 1 chr3A.!!$R1 709
12 TraesCS4A01G436100 chr1B 6250739 6251482 743 True 549.000000 549 80.795000 159 879 1 chr1B.!!$R1 720
13 TraesCS4A01G436100 chr5B 437806146 437806889 743 True 481.000000 481 79.310000 167 879 1 chr5B.!!$R1 712
14 TraesCS4A01G436100 chr1A 249024245 249024963 718 True 425.000000 425 78.302000 172 879 1 chr1A.!!$R1 707
15 TraesCS4A01G436100 chr1A 238118864 238122915 4051 False 243.000000 243 100.000000 2330 2460 2 chr1A.!!$F2 130
16 TraesCS4A01G436100 chr6A 62916855 62917544 689 True 359.000000 359 77.241000 170 858 1 chr6A.!!$R1 688

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
385 386 2.111384 CTAAGCCCTCTTGCCAGTAGA 58.889 52.381 0.0 0.0 33.85 2.59 F
1602 1838 0.250793 ACGTTGCGGGGTTGATCATA 59.749 50.000 0.0 0.0 0.00 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1844 0.118346 TGGCTCCCCAGAAGTAAGGA 59.882 55.000 0.00 0.0 35.79 3.36 R
2819 3388 1.821936 CTGAGCCTGTCAGCTAGGG 59.178 63.158 3.19 0.0 46.41 3.53 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
385 386 2.111384 CTAAGCCCTCTTGCCAGTAGA 58.889 52.381 0.00 0.00 33.85 2.59
807 808 7.502226 TGTTGCAGGAAATTAGAGAAGAGAAAA 59.498 33.333 0.00 0.00 0.00 2.29
941 950 3.876914 CTCTATAAATTCCGCTGCCAACA 59.123 43.478 0.00 0.00 0.00 3.33
1372 1390 4.509737 GGGCCCTAGTCGTGTCGC 62.510 72.222 17.04 0.00 0.00 5.19
1391 1409 4.849329 GGAGTACCGTCTGGCGCG 62.849 72.222 0.00 0.00 39.70 6.86
1585 1821 0.640262 CAACGACGACATGATGGACG 59.360 55.000 0.00 11.34 0.00 4.79
1594 1830 2.966732 ATGATGGACGTTGCGGGGT 61.967 57.895 0.00 0.00 0.00 4.95
1602 1838 0.250793 ACGTTGCGGGGTTGATCATA 59.749 50.000 0.00 0.00 0.00 2.15
1608 1844 1.815408 GCGGGGTTGATCATAGTGCAT 60.815 52.381 0.00 0.00 0.00 3.96
1763 2005 0.824182 GACGACCCCTGGATCGATCT 60.824 60.000 23.96 3.75 40.86 2.75
1768 2010 0.827925 CCCCTGGATCGATCTTCCGA 60.828 60.000 23.96 3.86 43.16 4.55
1821 2063 3.680786 CTCGTGACCGTGGCTGGA 61.681 66.667 3.31 0.00 35.01 3.86
1836 2079 1.294659 CTGGAAAGGACACTCTGCGC 61.295 60.000 0.00 0.00 0.00 6.09
2239 2651 6.261603 TCATCACAAACATCCATTATCTGCTC 59.738 38.462 0.00 0.00 0.00 4.26
2322 2734 8.243426 ACGCACACATAAATTAATGTCTCATTT 58.757 29.630 0.37 0.00 38.01 2.32
2485 2897 1.049289 ATGCCCTTCTCCTACCGTCC 61.049 60.000 0.00 0.00 0.00 4.79
2487 2899 0.106318 GCCCTTCTCCTACCGTCCTA 60.106 60.000 0.00 0.00 0.00 2.94
2488 2900 1.689984 CCCTTCTCCTACCGTCCTAC 58.310 60.000 0.00 0.00 0.00 3.18
2499 2911 5.246203 TCCTACCGTCCTACGTATACTACAT 59.754 44.000 0.00 0.00 40.58 2.29
2560 2972 2.224426 TGTTAGTCCTTCACGCCAACAT 60.224 45.455 0.00 0.00 0.00 2.71
2637 3206 4.240096 GTGGGAGCTCAAATTCACAAATG 58.760 43.478 17.19 0.00 0.00 2.32
2674 3243 5.046591 CGGCCAGGGAATTCTATATGAACTA 60.047 44.000 2.24 0.00 37.52 2.24
2675 3244 6.352222 CGGCCAGGGAATTCTATATGAACTAT 60.352 42.308 2.24 0.00 37.52 2.12
2677 3246 7.337942 GGCCAGGGAATTCTATATGAACTATTG 59.662 40.741 5.23 0.00 37.52 1.90
2732 3301 8.877864 AATGTATATTGTTTGTCTTCCCTCAA 57.122 30.769 0.00 0.00 0.00 3.02
2744 3313 4.884164 GTCTTCCCTCAAAATGTATGGGAG 59.116 45.833 0.00 0.00 46.28 4.30
2754 3323 0.185175 TGTATGGGAGCGGCTAGAGA 59.815 55.000 0.60 0.00 0.00 3.10
2791 3360 6.687081 AACAAAATTTCGGTCAGTTGACTA 57.313 33.333 11.67 0.00 44.20 2.59
2797 3366 2.033372 TCGGTCAGTTGACTAACCACA 58.967 47.619 11.67 0.00 44.20 4.17
2819 3388 5.351189 ACAAATTTGTTTCAGTCAACTTGCC 59.649 36.000 18.13 0.00 38.47 4.52
3003 4908 9.651913 TTTTGTAAGAAAGGATGAATTAATGGC 57.348 29.630 0.00 0.00 0.00 4.40
3010 4915 5.587388 AGGATGAATTAATGGCACTGTTG 57.413 39.130 0.00 0.00 0.00 3.33
3167 5090 7.093322 ACTCCAATGAGAAATGAATTAGTGC 57.907 36.000 0.00 0.00 41.42 4.40
3169 5092 5.951148 TCCAATGAGAAATGAATTAGTGCCA 59.049 36.000 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
385 386 1.536922 GGATGTGCTCACGATGACGAT 60.537 52.381 0.00 0.00 42.66 3.73
706 707 7.601508 TCTTCTCTAATTTTCCGTAACAAGACC 59.398 37.037 0.00 0.00 0.00 3.85
807 808 2.387757 AGGACACACTGGTTGCAAAAT 58.612 42.857 0.00 0.00 0.00 1.82
905 906 7.800847 GGAATTTATAGAGCGATTTTCTTCAGC 59.199 37.037 0.00 0.00 0.00 4.26
1362 1380 1.584380 GGTACTCCAGCGACACGACT 61.584 60.000 0.00 0.00 0.00 4.18
1372 1390 2.490217 CGCCAGACGGTACTCCAG 59.510 66.667 0.00 0.00 38.44 3.86
1585 1821 1.670811 CACTATGATCAACCCCGCAAC 59.329 52.381 0.00 0.00 0.00 4.17
1594 1830 6.988580 CAGAAGTAAGGATGCACTATGATCAA 59.011 38.462 0.00 0.00 0.00 2.57
1602 1838 1.561542 CCCCAGAAGTAAGGATGCACT 59.438 52.381 0.00 0.00 0.00 4.40
1608 1844 0.118346 TGGCTCCCCAGAAGTAAGGA 59.882 55.000 0.00 0.00 35.79 3.36
1768 2010 0.179004 AGCGATGAGATCTCCGAGGT 60.179 55.000 20.03 12.74 0.00 3.85
1807 2049 1.966451 CCTTTCCAGCCACGGTCAC 60.966 63.158 0.00 0.00 0.00 3.67
1810 2052 2.430367 GTCCTTTCCAGCCACGGT 59.570 61.111 0.00 0.00 0.00 4.83
1821 2063 1.373497 CTCGCGCAGAGTGTCCTTT 60.373 57.895 17.41 0.00 41.99 3.11
2079 2449 2.686235 CCATACCCAAACACGTCGTTA 58.314 47.619 0.00 0.00 36.59 3.18
2082 2452 0.951525 TGCCATACCCAAACACGTCG 60.952 55.000 0.00 0.00 0.00 5.12
2239 2651 4.259131 ACAACCCCACGGAACCGG 62.259 66.667 17.44 0.00 44.69 5.28
2322 2734 1.073284 GCAGGAACAAGGAGGGTACAA 59.927 52.381 0.00 0.00 0.00 2.41
2674 3243 9.120538 ACACCGAATAATAAGATAAAGCACAAT 57.879 29.630 0.00 0.00 0.00 2.71
2675 3244 8.500753 ACACCGAATAATAAGATAAAGCACAA 57.499 30.769 0.00 0.00 0.00 3.33
2677 3246 8.276325 CAGACACCGAATAATAAGATAAAGCAC 58.724 37.037 0.00 0.00 0.00 4.40
2732 3301 2.037772 CTCTAGCCGCTCCCATACATTT 59.962 50.000 0.00 0.00 0.00 2.32
2744 3313 3.719173 AGTCAACTTATCTCTAGCCGC 57.281 47.619 0.00 0.00 0.00 6.53
2791 3360 6.463360 AGTTGACTGAAACAAATTTGTGGTT 58.537 32.000 23.93 15.38 41.31 3.67
2797 3366 4.875536 GGGCAAGTTGACTGAAACAAATTT 59.124 37.500 9.01 0.00 34.23 1.82
2819 3388 1.821936 CTGAGCCTGTCAGCTAGGG 59.178 63.158 3.19 0.00 46.41 3.53
2838 3407 2.202690 TCCACGTAGCAATCGCCG 60.203 61.111 0.00 0.00 39.83 6.46
2894 4799 8.956426 CCAAAGCCACTTATAATTTCTGTTAGA 58.044 33.333 0.00 0.00 0.00 2.10
2906 4811 6.618196 AGAGGGTAATACCAAAGCCACTTATA 59.382 38.462 12.03 0.00 41.02 0.98
2912 4817 3.714798 CCTAGAGGGTAATACCAAAGCCA 59.285 47.826 12.03 0.00 41.02 4.75
3167 5090 5.185635 TCTTCCTTAAAGTCAATGCCAATGG 59.814 40.000 0.00 0.00 36.31 3.16
3169 5092 6.916360 TTCTTCCTTAAAGTCAATGCCAAT 57.084 33.333 0.00 0.00 36.31 3.16


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

AutoCloner maintained by Alex Coulton.