Multiple sequence alignment - TraesCS2D01G454200

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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 TraesCS2D01G454200 chr2D 100.000 2291 0 0 1 2291 562784603 562786893 0.000000e+00 4231.0
1 TraesCS2D01G454200 chr2D 96.307 677 8 7 919 1595 562735047 562735706 0.000000e+00 1096.0
2 TraesCS2D01G454200 chr2D 96.212 660 16 4 1596 2252 562735753 562736406 0.000000e+00 1072.0
3 TraesCS2D01G454200 chr2D 85.489 951 53 28 1 887 562734121 562735050 0.000000e+00 913.0
4 TraesCS2D01G454200 chr2D 84.899 596 62 17 841 1432 562684872 562685443 5.490000e-161 577.0
5 TraesCS2D01G454200 chr2D 81.806 742 76 36 723 1426 562839378 562840098 3.300000e-158 568.0
6 TraesCS2D01G454200 chr2D 92.042 377 30 0 997 1373 562754098 562754474 4.330000e-147 531.0
7 TraesCS2D01G454200 chr2D 92.701 274 20 0 389 662 562684235 562684508 1.650000e-106 396.0
8 TraesCS2D01G454200 chr2D 86.349 315 31 6 1 315 562753157 562753459 1.310000e-87 333.0
9 TraesCS2D01G454200 chr2D 83.392 283 13 14 24 306 562838804 562839052 4.920000e-57 231.0
10 TraesCS2D01G454200 chr2D 81.053 285 31 17 37 315 562804458 562804725 2.980000e-49 206.0
11 TraesCS2D01G454200 chr2D 89.241 158 9 5 19 175 562683869 562684019 8.350000e-45 191.0
12 TraesCS2D01G454200 chr2D 93.077 130 8 1 620 749 562753689 562753817 3.000000e-44 189.0
13 TraesCS2D01G454200 chr2D 86.719 128 16 1 1459 1585 562588454 562588581 8.530000e-30 141.0
14 TraesCS2D01G454200 chr2D 90.291 103 9 1 668 770 562807539 562807640 1.430000e-27 134.0
15 TraesCS2D01G454200 chr2D 100.000 29 0 0 2263 2291 562736404 562736432 1.000000e-03 54.7
16 TraesCS2D01G454200 chr2D 100.000 28 0 0 191 218 562684021 562684048 4.000000e-03 52.8
17 TraesCS2D01G454200 chr2A 89.220 1141 50 28 485 1597 703290770 703291865 0.000000e+00 1358.0
18 TraesCS2D01G454200 chr2A 94.168 703 30 6 1596 2289 703291910 703292610 0.000000e+00 1061.0
19 TraesCS2D01G454200 chr2A 94.748 476 23 1 857 1332 703282278 703282751 0.000000e+00 739.0
20 TraesCS2D01G454200 chr2A 85.748 421 38 9 841 1260 703207490 703207889 2.100000e-115 425.0
21 TraesCS2D01G454200 chr2A 88.848 269 19 8 550 813 703282018 703282280 1.020000e-83 320.0
22 TraesCS2D01G454200 chr2A 85.404 322 31 11 1 315 703333405 703333717 1.020000e-83 320.0
23 TraesCS2D01G454200 chr2A 88.462 208 15 5 625 832 703337222 703337420 2.270000e-60 243.0
24 TraesCS2D01G454200 chr2A 84.411 263 22 5 57 315 703281655 703281902 8.180000e-60 241.0
25 TraesCS2D01G454200 chr2A 90.110 182 17 1 6 187 703288817 703288997 3.800000e-58 235.0
26 TraesCS2D01G454200 chr2A 80.906 309 28 22 393 688 703122298 703122588 4.960000e-52 215.0
27 TraesCS2D01G454200 chr2A 82.397 267 18 10 389 646 703206589 703206835 2.980000e-49 206.0
28 TraesCS2D01G454200 chr2A 84.507 213 12 6 27 238 703345259 703345451 8.350000e-45 191.0
29 TraesCS2D01G454200 chr2A 86.667 180 13 6 15 185 703121929 703122106 3.000000e-44 189.0
30 TraesCS2D01G454200 chr2A 96.552 58 2 0 454 511 703281964 703282021 1.870000e-16 97.1
31 TraesCS2D01G454200 chr2A 100.000 29 0 0 1404 1432 703208606 703208634 1.000000e-03 54.7
32 TraesCS2D01G454200 chr2B 87.799 877 47 25 502 1353 673092533 673093374 0.000000e+00 972.0
33 TraesCS2D01G454200 chr2B 86.501 563 52 11 824 1373 672646402 672646953 4.210000e-167 597.0
34 TraesCS2D01G454200 chr2B 85.185 540 62 8 841 1373 673050788 673051316 2.590000e-149 538.0
35 TraesCS2D01G454200 chr2B 81.140 737 63 38 655 1340 672776507 672775796 2.610000e-144 521.0
36 TraesCS2D01G454200 chr2B 86.761 423 40 5 887 1301 673003605 673004019 7.460000e-125 457.0
37 TraesCS2D01G454200 chr2B 84.375 384 32 10 464 832 673050353 673050723 3.620000e-93 351.0
38 TraesCS2D01G454200 chr2B 90.833 240 18 4 434 673 672797718 672797483 3.670000e-83 318.0
39 TraesCS2D01G454200 chr2B 86.441 295 24 4 389 674 672645780 672646067 2.210000e-80 309.0
40 TraesCS2D01G454200 chr2B 83.030 330 48 7 1870 2194 672670646 672670972 2.230000e-75 292.0
41 TraesCS2D01G454200 chr2B 88.444 225 21 4 563 786 672666757 672666977 1.350000e-67 267.0
42 TraesCS2D01G454200 chr2B 83.509 285 18 11 31 315 673001808 673002063 2.940000e-59 239.0
43 TraesCS2D01G454200 chr2B 89.730 185 12 2 389 573 673002209 673002386 1.770000e-56 230.0
44 TraesCS2D01G454200 chr2B 90.909 165 12 3 1 165 672798138 672797977 3.830000e-53 219.0
45 TraesCS2D01G454200 chr2B 84.536 194 26 4 2003 2194 672823665 672823474 3.000000e-44 189.0
46 TraesCS2D01G454200 chr2B 89.815 108 9 2 208 315 672797965 672797860 1.100000e-28 137.0
47 TraesCS2D01G454200 chr2B 100.000 29 0 0 1404 1432 673051320 673051348 1.000000e-03 54.7


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 TraesCS2D01G454200 chr2D 562784603 562786893 2290 False 4231.000000 4231 100.000000 1 2291 1 chr2D.!!$F2 2290
1 TraesCS2D01G454200 chr2D 562734121 562736432 2311 False 783.925000 1096 94.502000 1 2291 4 chr2D.!!$F4 2290
2 TraesCS2D01G454200 chr2D 562838804 562840098 1294 False 399.500000 568 82.599000 24 1426 2 chr2D.!!$F7 1402
3 TraesCS2D01G454200 chr2D 562753157 562754474 1317 False 351.000000 531 90.489333 1 1373 3 chr2D.!!$F5 1372
4 TraesCS2D01G454200 chr2D 562683869 562685443 1574 False 304.200000 577 91.710250 19 1432 4 chr2D.!!$F3 1413
5 TraesCS2D01G454200 chr2A 703288817 703292610 3793 False 884.666667 1358 91.166000 6 2289 3 chr2A.!!$F5 2283
6 TraesCS2D01G454200 chr2A 703281655 703282751 1096 False 349.275000 739 91.139750 57 1332 4 chr2A.!!$F4 1275
7 TraesCS2D01G454200 chr2A 703333405 703337420 4015 False 281.500000 320 86.933000 1 832 2 chr2A.!!$F6 831
8 TraesCS2D01G454200 chr2A 703206589 703208634 2045 False 228.566667 425 89.381667 389 1432 3 chr2A.!!$F3 1043
9 TraesCS2D01G454200 chr2A 703121929 703122588 659 False 202.000000 215 83.786500 15 688 2 chr2A.!!$F2 673
10 TraesCS2D01G454200 chr2B 673092533 673093374 841 False 972.000000 972 87.799000 502 1353 1 chr2B.!!$F1 851
11 TraesCS2D01G454200 chr2B 672775796 672776507 711 True 521.000000 521 81.140000 655 1340 1 chr2B.!!$R1 685
12 TraesCS2D01G454200 chr2B 672645780 672646953 1173 False 453.000000 597 86.471000 389 1373 2 chr2B.!!$F2 984
13 TraesCS2D01G454200 chr2B 673050353 673051348 995 False 314.566667 538 89.853333 464 1432 3 chr2B.!!$F5 968
14 TraesCS2D01G454200 chr2B 673001808 673004019 2211 False 308.666667 457 86.666667 31 1301 3 chr2B.!!$F4 1270
15 TraesCS2D01G454200 chr2B 672666757 672670972 4215 False 279.500000 292 85.737000 563 2194 2 chr2B.!!$F3 1631
16 TraesCS2D01G454200 chr2B 672797483 672798138 655 True 224.666667 318 90.519000 1 673 3 chr2B.!!$R3 672

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
363 2146 0.026803 GCGCGAGTCCATTGTTCATC 59.973 55.0 12.1 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 11919 0.552848 AATCTGGAATGGCCGGTCAT 59.447 50.0 17.87 17.87 44.0 3.06 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
32 36 3.825014 AGTGTTACTACTCGAGGAAAGCA 59.175 43.478 18.41 4.73 26.09 3.91
317 2006 1.129998 CATCCTTGAGCTTGAAGTGCG 59.870 52.381 0.00 0.00 35.28 5.34
362 2145 1.695893 CGCGCGAGTCCATTGTTCAT 61.696 55.000 28.94 0.00 0.00 2.57
363 2146 0.026803 GCGCGAGTCCATTGTTCATC 59.973 55.000 12.10 0.00 0.00 2.92
364 2147 1.645034 CGCGAGTCCATTGTTCATCT 58.355 50.000 0.00 0.00 0.00 2.90
365 2148 2.002586 CGCGAGTCCATTGTTCATCTT 58.997 47.619 0.00 0.00 0.00 2.40
366 2149 2.222886 CGCGAGTCCATTGTTCATCTTG 60.223 50.000 0.00 0.00 0.00 3.02
368 2151 3.181516 GCGAGTCCATTGTTCATCTTGTC 60.182 47.826 0.00 0.00 0.00 3.18
370 2153 4.328440 CGAGTCCATTGTTCATCTTGTCTC 59.672 45.833 0.00 0.00 0.00 3.36
372 2155 5.243981 AGTCCATTGTTCATCTTGTCTCTG 58.756 41.667 0.00 0.00 0.00 3.35
380 2163 8.455903 TTGTTCATCTTGTCTCTGAGAAAAAT 57.544 30.769 9.31 4.53 0.00 1.82
382 2165 9.730705 TGTTCATCTTGTCTCTGAGAAAAATAT 57.269 29.630 9.31 4.35 0.00 1.28
385 2168 9.376075 TCATCTTGTCTCTGAGAAAAATATCAC 57.624 33.333 9.31 0.00 0.00 3.06
387 2170 7.378966 TCTTGTCTCTGAGAAAAATATCACGT 58.621 34.615 9.31 0.00 0.00 4.49
432 2273 1.271871 TGGGTATGGCACTTGACTTGG 60.272 52.381 0.00 0.00 0.00 3.61
436 2277 0.038744 ATGGCACTTGACTTGGAGGG 59.961 55.000 0.00 0.00 0.00 4.30
557 2409 2.092646 TGTCTATTATTGGCGTGGGCTT 60.093 45.455 0.00 0.00 39.81 4.35
680 6715 0.317160 TCACACAAGTACAGCCGGAG 59.683 55.000 5.05 0.00 0.00 4.63
681 6716 0.033504 CACACAAGTACAGCCGGAGT 59.966 55.000 5.05 5.20 0.00 3.85
722 6838 7.994425 TTGAGAGTTTTCAAATATGGCTACA 57.006 32.000 0.00 0.00 34.32 2.74
738 6925 2.421424 GCTACATTTCTGGCCTTCACAG 59.579 50.000 3.32 0.00 37.30 3.66
760 6948 6.535150 ACAGAATATCACAACTTACATCACCG 59.465 38.462 0.00 0.00 0.00 4.94
1201 9003 3.858868 GACGCCGTCTGTGCCAAGA 62.859 63.158 10.56 0.00 0.00 3.02
1554 10083 0.881796 CTCGGTCTGTCTGTGCTGTA 59.118 55.000 0.00 0.00 0.00 2.74
1570 10100 5.182950 TGTGCTGTACCGATGAATTGATTTT 59.817 36.000 0.00 0.00 0.00 1.82
1810 10399 5.565455 TCCAGTGACATGCCAATATGATA 57.435 39.130 0.00 0.00 0.00 2.15
1817 10406 6.886459 GTGACATGCCAATATGATATTACCCT 59.114 38.462 0.00 0.00 0.00 4.34
2205 11866 6.494842 ACATGTGTTGTCAAAACATCTACAC 58.505 36.000 17.05 5.91 41.69 2.90
2263 11924 1.134401 ACATGTCCGTGGATCATGACC 60.134 52.381 25.02 2.22 40.64 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 36 0.042274 GCGCGCAATTTGTTTTTGCT 60.042 45.000 29.10 0.00 45.67 3.91
287 337 1.540797 GCTCAAGGATGCTGCTAGAGG 60.541 57.143 0.00 0.00 0.00 3.69
317 2006 1.128412 GCAGATTTTGTTTGCGCGC 59.872 52.632 27.26 27.26 0.00 6.86
329 2086 4.450122 CGCGCGCACTTGCAGATT 62.450 61.111 32.61 0.00 42.21 2.40
355 2112 7.864108 TTTTTCTCAGAGACAAGATGAACAA 57.136 32.000 0.00 0.00 0.00 2.83
362 2145 7.378966 ACGTGATATTTTTCTCAGAGACAAGA 58.621 34.615 0.00 0.00 0.00 3.02
363 2146 7.588143 ACGTGATATTTTTCTCAGAGACAAG 57.412 36.000 0.00 0.00 0.00 3.16
364 2147 8.085909 TGTACGTGATATTTTTCTCAGAGACAA 58.914 33.333 0.00 0.00 0.00 3.18
365 2148 7.599171 TGTACGTGATATTTTTCTCAGAGACA 58.401 34.615 0.00 0.00 0.00 3.41
366 2149 7.253817 GCTGTACGTGATATTTTTCTCAGAGAC 60.254 40.741 0.00 0.00 0.00 3.36
368 2151 6.754209 AGCTGTACGTGATATTTTTCTCAGAG 59.246 38.462 0.00 0.00 0.00 3.35
370 2153 6.531594 TGAGCTGTACGTGATATTTTTCTCAG 59.468 38.462 0.00 0.00 0.00 3.35
372 2155 6.887376 TGAGCTGTACGTGATATTTTTCTC 57.113 37.500 0.00 0.00 0.00 2.87
380 2163 4.112634 GCAATCTTGAGCTGTACGTGATA 58.887 43.478 0.00 0.00 0.00 2.15
382 2165 2.337583 GCAATCTTGAGCTGTACGTGA 58.662 47.619 0.00 0.00 0.00 4.35
383 2166 1.394917 GGCAATCTTGAGCTGTACGTG 59.605 52.381 0.00 0.00 0.00 4.49
385 2168 1.009829 GGGCAATCTTGAGCTGTACG 58.990 55.000 0.00 0.00 0.00 3.67
387 2170 1.210478 GGAGGGCAATCTTGAGCTGTA 59.790 52.381 0.00 0.00 0.00 2.74
436 2277 3.750501 TTAAAAATCTGGAGGTCCCCC 57.249 47.619 0.00 0.00 34.29 5.40
557 2409 3.086143 CAGGTGCCCCACATGGTA 58.914 61.111 0.00 0.00 41.58 3.25
738 6925 5.236478 CCCGGTGATGTAAGTTGTGATATTC 59.764 44.000 0.00 0.00 0.00 1.75
760 6948 1.139455 TCCCGAATAATGAACGTCCCC 59.861 52.381 0.00 0.00 0.00 4.81
847 8608 6.726764 GGAGTGGAGGTCTCAGGTATATATTT 59.273 42.308 0.14 0.00 34.04 1.40
848 8609 6.047359 AGGAGTGGAGGTCTCAGGTATATATT 59.953 42.308 0.14 0.00 34.04 1.28
966 8764 3.462982 TGTGTCAATGTGTGTGTAGGTC 58.537 45.455 0.00 0.00 0.00 3.85
980 8782 5.767665 GCCATGGTATATTGGTATGTGTCAA 59.232 40.000 14.67 0.00 35.34 3.18
981 8783 5.312895 GCCATGGTATATTGGTATGTGTCA 58.687 41.667 14.67 0.00 35.34 3.58
982 8784 4.391830 CGCCATGGTATATTGGTATGTGTC 59.608 45.833 14.67 0.00 35.34 3.67
1201 9003 4.379243 CTGTCTCCGTGCGGCCTT 62.379 66.667 5.64 0.00 34.68 4.35
1554 10083 5.621197 TCGAACAAAATCAATTCATCGGT 57.379 34.783 0.00 0.00 0.00 4.69
1570 10100 1.309950 TGGCCATTTCGTTTCGAACA 58.690 45.000 0.00 0.00 45.64 3.18
1750 10338 9.450807 CCTATAAATCCGAAAAGCATAACAAAG 57.549 33.333 0.00 0.00 0.00 2.77
2066 11726 3.793129 GCCAAGGCATGACAATATCGTTG 60.793 47.826 0.00 0.00 41.49 4.10
2258 11919 0.552848 AATCTGGAATGGCCGGTCAT 59.447 50.000 17.87 17.87 44.00 3.06
2263 11924 3.016736 ACAGTAAAATCTGGAATGGCCG 58.983 45.455 0.00 0.00 40.66 6.13


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

AutoCloner maintained by Alex Coulton.