Multiple sequence alignment - TraesCS2A01G319600

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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 TraesCS2A01G319600 chr2A 100.000 2564 0 0 1 2564 546775310 546772747 0.000000e+00 4735.0
1 TraesCS2A01G319600 chr2A 95.325 1091 46 3 500 1588 568282409 568283496 0.000000e+00 1727.0
2 TraesCS2A01G319600 chr2A 96.695 938 29 2 669 1605 567733378 567734314 0.000000e+00 1559.0
3 TraesCS2A01G319600 chr2A 94.859 389 9 3 1606 1994 27110123 27110500 4.720000e-167 597.0
4 TraesCS2A01G319600 chr2A 88.023 526 35 13 148 670 567732797 567733297 4.720000e-167 597.0
5 TraesCS2A01G319600 chr2A 97.189 249 4 1 2316 2564 27110495 27110740 3.950000e-113 418.0
6 TraesCS2A01G319600 chr2A 95.385 260 9 1 225 481 568282164 568282423 6.600000e-111 411.0
7 TraesCS2A01G319600 chr2D 94.204 1432 71 8 160 1588 421475718 421477140 0.000000e+00 2174.0
8 TraesCS2A01G319600 chr2D 93.899 1426 78 5 164 1588 421790975 421792392 0.000000e+00 2143.0
9 TraesCS2A01G319600 chr2D 95.327 107 5 0 2 108 421790867 421790973 1.220000e-38 171.0
10 TraesCS2A01G319600 chr2D 93.396 106 7 0 2 107 421475614 421475719 9.500000e-35 158.0
11 TraesCS2A01G319600 chr2B 94.242 1424 73 6 166 1584 494259410 494260829 0.000000e+00 2167.0
12 TraesCS2A01G319600 chr2B 95.553 922 39 2 669 1588 493985643 493986564 0.000000e+00 1474.0
13 TraesCS2A01G319600 chr2B 93.496 246 15 1 1602 1847 603915776 603916020 5.210000e-97 364.0
14 TraesCS2A01G319600 chr2B 91.949 236 14 2 436 670 493985329 493985560 2.460000e-85 326.0
15 TraesCS2A01G319600 chr2B 97.647 85 2 0 2 86 494258920 494259004 2.060000e-31 147.0
16 TraesCS2A01G319600 chr3B 98.854 960 11 0 1605 2564 21001736 21000777 0.000000e+00 1712.0
17 TraesCS2A01G319600 chr3B 83.693 417 61 6 1850 2259 460164772 460164356 1.110000e-103 387.0
18 TraesCS2A01G319600 chr4A 91.774 1082 88 1 508 1588 147568087 147567006 0.000000e+00 1504.0
19 TraesCS2A01G319600 chr4A 87.209 172 11 10 2 173 147568447 147568287 4.360000e-43 185.0
20 TraesCS2A01G319600 chr4A 90.179 112 8 1 361 472 147568198 147568090 2.660000e-30 143.0
21 TraesCS2A01G319600 chr4D 91.236 1084 93 2 502 1584 323926641 323927723 0.000000e+00 1474.0
22 TraesCS2A01G319600 chr4D 86.285 1101 123 21 490 1581 394133611 394134692 0.000000e+00 1171.0
23 TraesCS2A01G319600 chr4D 87.281 456 31 10 2 455 323926203 323926633 1.770000e-136 496.0
24 TraesCS2A01G319600 chr4D 77.990 209 25 14 289 478 394133425 394133631 7.500000e-21 111.0
25 TraesCS2A01G319600 chr5D 93.646 724 26 9 1846 2564 501339868 501339160 0.000000e+00 1064.0
26 TraesCS2A01G319600 chr5D 91.617 668 46 9 1846 2512 501497075 501496417 0.000000e+00 915.0
27 TraesCS2A01G319600 chr5D 83.058 726 71 28 1846 2558 508275650 508274964 1.690000e-171 612.0
28 TraesCS2A01G319600 chr5D 91.244 217 18 1 1604 1820 387823926 387823711 6.940000e-76 294.0
29 TraesCS2A01G319600 chr5D 89.954 219 22 0 1602 1820 532658378 532658160 1.500000e-72 283.0
30 TraesCS2A01G319600 chr5A 93.443 671 38 4 1846 2516 626029879 626030543 0.000000e+00 990.0
31 TraesCS2A01G319600 chr5A 82.085 307 42 6 2206 2512 599472501 599472208 1.520000e-62 250.0
32 TraesCS2A01G319600 chr5B 90.430 721 30 12 1846 2564 622967199 622966516 0.000000e+00 913.0
33 TraesCS2A01G319600 chr5B 91.981 424 24 8 2076 2496 628815775 628815359 1.020000e-163 586.0
34 TraesCS2A01G319600 chr5B 91.455 433 26 9 2076 2504 625216684 625216259 3.680000e-163 584.0
35 TraesCS2A01G319600 chr5B 81.302 599 73 15 1846 2428 633161393 633161968 1.400000e-122 449.0
36 TraesCS2A01G319600 chr1B 96.279 215 8 0 1606 1820 170584400 170584186 1.130000e-93 353.0
37 TraesCS2A01G319600 chr1B 90.698 215 20 0 1606 1820 659947957 659947743 1.160000e-73 287.0
38 TraesCS2A01G319600 chr4B 88.760 258 21 4 220 472 404506312 404506566 2.480000e-80 309.0
39 TraesCS2A01G319600 chr4B 91.667 108 8 1 2 108 404506160 404506267 5.720000e-32 148.0
40 TraesCS2A01G319600 chr4B 79.808 208 22 10 289 478 483748920 483749125 1.600000e-27 134.0
41 TraesCS2A01G319600 chr3D 90.411 219 17 3 1602 1819 231171510 231171725 4.180000e-73 285.0
42 TraesCS2A01G319600 chr1D 89.130 230 23 2 1592 1820 359714702 359714474 4.180000e-73 285.0
43 TraesCS2A01G319600 chr1A 90.233 215 21 0 1606 1820 554557868 554557654 5.400000e-72 281.0
44 TraesCS2A01G319600 chr6B 100.000 28 0 0 263 290 138702291 138702264 5.000000e-03 52.8
45 TraesCS2A01G319600 chr3A 96.875 32 0 1 1816 1847 19970580 19970610 5.000000e-03 52.8


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 TraesCS2A01G319600 chr2A 546772747 546775310 2563 True 4735.000000 4735 100.000000 1 2564 1 chr2A.!!$R1 2563
1 TraesCS2A01G319600 chr2A 567732797 567734314 1517 False 1078.000000 1559 92.359000 148 1605 2 chr2A.!!$F2 1457
2 TraesCS2A01G319600 chr2A 568282164 568283496 1332 False 1069.000000 1727 95.355000 225 1588 2 chr2A.!!$F3 1363
3 TraesCS2A01G319600 chr2A 27110123 27110740 617 False 507.500000 597 96.024000 1606 2564 2 chr2A.!!$F1 958
4 TraesCS2A01G319600 chr2D 421475614 421477140 1526 False 1166.000000 2174 93.800000 2 1588 2 chr2D.!!$F1 1586
5 TraesCS2A01G319600 chr2D 421790867 421792392 1525 False 1157.000000 2143 94.613000 2 1588 2 chr2D.!!$F2 1586
6 TraesCS2A01G319600 chr2B 494258920 494260829 1909 False 1157.000000 2167 95.944500 2 1584 2 chr2B.!!$F3 1582
7 TraesCS2A01G319600 chr2B 493985329 493986564 1235 False 900.000000 1474 93.751000 436 1588 2 chr2B.!!$F2 1152
8 TraesCS2A01G319600 chr3B 21000777 21001736 959 True 1712.000000 1712 98.854000 1605 2564 1 chr3B.!!$R1 959
9 TraesCS2A01G319600 chr4A 147567006 147568447 1441 True 610.666667 1504 89.720667 2 1588 3 chr4A.!!$R1 1586
10 TraesCS2A01G319600 chr4D 323926203 323927723 1520 False 985.000000 1474 89.258500 2 1584 2 chr4D.!!$F1 1582
11 TraesCS2A01G319600 chr4D 394133425 394134692 1267 False 641.000000 1171 82.137500 289 1581 2 chr4D.!!$F2 1292
12 TraesCS2A01G319600 chr5D 501339160 501339868 708 True 1064.000000 1064 93.646000 1846 2564 1 chr5D.!!$R2 718
13 TraesCS2A01G319600 chr5D 501496417 501497075 658 True 915.000000 915 91.617000 1846 2512 1 chr5D.!!$R3 666
14 TraesCS2A01G319600 chr5D 508274964 508275650 686 True 612.000000 612 83.058000 1846 2558 1 chr5D.!!$R4 712
15 TraesCS2A01G319600 chr5A 626029879 626030543 664 False 990.000000 990 93.443000 1846 2516 1 chr5A.!!$F1 670
16 TraesCS2A01G319600 chr5B 622966516 622967199 683 True 913.000000 913 90.430000 1846 2564 1 chr5B.!!$R1 718
17 TraesCS2A01G319600 chr5B 633161393 633161968 575 False 449.000000 449 81.302000 1846 2428 1 chr5B.!!$F1 582

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
997 1473 0.978907 GACCAAAGGAGTACCCCGAA 59.021 55.0 0.0 0.0 36.73 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 2284 2.746277 GGCGCGGGTTGAATCAGT 60.746 61.111 8.83 0.0 0.0 3.41 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
100 101 3.687321 CTCCCCACGCTGTCCATGG 62.687 68.421 4.97 4.97 0.00 3.66
210 538 2.498167 AGATTGTGTCAACACCAGCTC 58.502 47.619 10.59 2.97 45.88 4.09
211 539 1.195448 GATTGTGTCAACACCAGCTCG 59.805 52.381 10.59 0.00 45.88 5.03
305 637 9.482627 ACTTTAGAGATTTATTATCTTGAGGCG 57.517 33.333 0.00 0.00 0.00 5.52
342 679 9.787532 TTCTAAAACATTTCTTTGTCAGAACTG 57.212 29.630 0.00 0.00 44.27 3.16
432 783 1.849039 AGGATGGAATAGCAGCCAACT 59.151 47.619 0.00 0.00 37.78 3.16
434 785 2.158696 GGATGGAATAGCAGCCAACTCT 60.159 50.000 0.00 0.00 37.78 3.24
474 825 3.754965 ACCAAATATATGCTCGCCATGT 58.245 40.909 0.00 0.00 35.34 3.21
870 1346 2.658593 GGTCCACGCGGATCATCG 60.659 66.667 12.47 0.00 45.33 3.84
958 1434 1.078567 CAAGTCAGGAGCTCCAGCC 60.079 63.158 33.90 17.33 43.38 4.85
959 1435 1.229464 AAGTCAGGAGCTCCAGCCT 60.229 57.895 33.90 19.58 43.38 4.58
997 1473 0.978907 GACCAAAGGAGTACCCCGAA 59.021 55.000 0.00 0.00 36.73 4.30
998 1474 1.348696 GACCAAAGGAGTACCCCGAAA 59.651 52.381 0.00 0.00 36.73 3.46
1194 1671 3.235200 GGAGGAGTGCTATGACCTGTAT 58.765 50.000 0.00 0.00 32.53 2.29
1268 1745 1.561769 ATCCTGACGGGCAACATCCA 61.562 55.000 0.00 0.00 39.74 3.41
1467 1944 3.431725 CGGCCGGGAAAGAAGCAC 61.432 66.667 20.10 0.00 0.00 4.40
1516 1993 1.547820 ACGAGCTGCTGAAGATCAAGA 59.452 47.619 7.01 0.00 41.66 3.02
1548 2026 4.790962 CGCAGGCAGCAGGTGGAT 62.791 66.667 1.96 0.00 46.13 3.41
1800 2279 2.841988 GCACAAAACCCCCTGCCA 60.842 61.111 0.00 0.00 0.00 4.92
1805 2284 1.055040 CAAAACCCCCTGCCATTTGA 58.945 50.000 0.00 0.00 33.86 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.680237 CGGTGCTGCTCCAACCGA 62.680 66.667 20.63 0.00 45.77 4.69
52 53 2.598394 TGGGCAGCTTTGTGGCTC 60.598 61.111 0.00 0.00 42.56 4.70
148 149 1.610086 TGGATTGCTGCTTTGGGGG 60.610 57.895 0.00 0.00 0.00 5.40
149 150 1.610554 CCTGGATTGCTGCTTTGGGG 61.611 60.000 0.00 0.00 0.00 4.96
150 151 1.610554 CCCTGGATTGCTGCTTTGGG 61.611 60.000 0.00 0.55 0.00 4.12
151 152 1.895238 CCCTGGATTGCTGCTTTGG 59.105 57.895 0.00 0.00 0.00 3.28
161 162 0.981183 TTGACTACGTGCCCTGGATT 59.019 50.000 0.00 0.00 0.00 3.01
210 538 1.024271 CATTTATGGTCCCACTGGCG 58.976 55.000 0.00 0.00 0.00 5.69
211 539 2.435372 TCATTTATGGTCCCACTGGC 57.565 50.000 0.00 0.00 0.00 4.85
260 589 4.554960 AGTTACTAAGCTCCCAGGAAAC 57.445 45.455 0.00 0.00 0.00 2.78
305 637 7.597386 AGAAATGTTTTAGAAAGATGTGAGGC 58.403 34.615 0.00 0.00 0.00 4.70
337 673 3.206150 CATGTAGGCATGTACCCAGTTC 58.794 50.000 0.00 0.00 45.48 3.01
423 774 5.163923 GCATTCAAAATTTAGAGTTGGCTGC 60.164 40.000 0.00 0.00 0.00 5.25
432 783 8.954950 TTGGTTCAAAGCATTCAAAATTTAGA 57.045 26.923 0.00 0.00 36.16 2.10
489 846 3.201290 TGTGCATGGCGAAACAAAAATT 58.799 36.364 0.00 0.00 0.00 1.82
491 848 2.200067 CTGTGCATGGCGAAACAAAAA 58.800 42.857 0.00 0.00 0.00 1.94
492 849 1.135915 ACTGTGCATGGCGAAACAAAA 59.864 42.857 0.00 0.00 0.00 2.44
493 850 0.743688 ACTGTGCATGGCGAAACAAA 59.256 45.000 0.00 0.00 0.00 2.83
496 853 2.697431 TTAACTGTGCATGGCGAAAC 57.303 45.000 0.00 0.00 0.00 2.78
764 1240 2.497138 CTGCAGTTCATCAGGTGTTCA 58.503 47.619 5.25 0.00 0.00 3.18
867 1343 0.748005 CCGGGCTTTCATTGGACGAT 60.748 55.000 0.00 0.00 0.00 3.73
870 1346 1.657751 GCTCCGGGCTTTCATTGGAC 61.658 60.000 0.00 0.00 38.06 4.02
958 1434 0.251916 TCAGTGACCGGGGCATTTAG 59.748 55.000 5.51 0.00 0.00 1.85
959 1435 0.251916 CTCAGTGACCGGGGCATTTA 59.748 55.000 5.51 0.00 0.00 1.40
997 1473 0.183971 TTGTCCCACCGTTCCATGTT 59.816 50.000 0.00 0.00 0.00 2.71
998 1474 0.183971 TTTGTCCCACCGTTCCATGT 59.816 50.000 0.00 0.00 0.00 3.21
1166 1643 0.251209 ATAGCACTCCTCCGCGGATA 60.251 55.000 31.19 19.05 42.12 2.59
1194 1671 2.047844 GTGCTCAGCTTCTCCGCA 60.048 61.111 0.00 0.00 0.00 5.69
1268 1745 3.689872 TCAGGTACAGGAGCCTATTCT 57.310 47.619 0.00 0.00 33.07 2.40
1467 1944 1.078848 CCACGGGAAGCTCCAGAAG 60.079 63.158 8.78 2.62 38.64 2.85
1516 1993 2.434359 GCGCCGCTTACTGGACTT 60.434 61.111 0.00 0.00 0.00 3.01
1764 2243 2.468670 AAAACTGTGCGCGCTGACA 61.469 52.632 33.29 26.57 0.00 3.58
1805 2284 2.746277 GGCGCGGGTTGAATCAGT 60.746 61.111 8.83 0.00 0.00 3.41
2185 2669 5.826208 ACAAATAAACTCCTTTCAACGGACT 59.174 36.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.