Multiple sequence alignment - TraesCS1D01G008500

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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 TraesCS1D01G008500 chr1D 100.000 2263 0 0 741 3003 4307997 4305735 0.000000e+00 4180
1 TraesCS1D01G008500 chr1D 97.849 1395 23 4 741 2131 7180831 7182222 0.000000e+00 2403
2 TraesCS1D01G008500 chr1D 94.159 1421 44 11 741 2124 42896924 42895506 0.000000e+00 2128
3 TraesCS1D01G008500 chr1D 96.585 615 19 2 2138 2750 42894985 42894371 0.000000e+00 1018
4 TraesCS1D01G008500 chr1D 100.000 475 0 0 1 475 4308737 4308263 0.000000e+00 878
5 TraesCS1D01G008500 chr1D 96.674 481 9 4 1 475 7179996 7180475 0.000000e+00 793
6 TraesCS1D01G008500 chr1D 90.667 300 20 5 182 473 42889393 42889692 2.810000e-105 392
7 TraesCS1D01G008500 chr1D 95.781 237 8 1 2768 3002 42894298 42894062 6.070000e-102 381
8 TraesCS1D01G008500 chr1D 90.860 186 17 0 1 186 3859749 3859934 1.790000e-62 250
9 TraesCS1D01G008500 chr4D 97.467 1382 25 4 741 2118 108842563 108843938 0.000000e+00 2350
10 TraesCS1D01G008500 chr4D 92.210 1412 60 23 741 2118 488848894 488850289 0.000000e+00 1953
11 TraesCS1D01G008500 chr4D 96.774 620 18 2 2132 2750 108844442 108845060 0.000000e+00 1033
12 TraesCS1D01G008500 chr4D 94.539 293 10 1 189 475 108842224 108842516 5.910000e-122 448
13 TraesCS1D01G008500 chr4D 93.878 294 12 1 188 475 108850297 108850004 3.550000e-119 438
14 TraesCS1D01G008500 chr4D 95.319 235 11 0 2768 3002 108845138 108845372 1.020000e-99 374
15 TraesCS1D01G008500 chr4D 88.793 232 8 5 2772 3002 488851557 488851771 4.930000e-68 268
16 TraesCS1D01G008500 chr3D 97.327 1384 24 6 741 2118 590153657 590155033 0.000000e+00 2338
17 TraesCS1D01G008500 chr3D 96.270 1394 29 7 741 2124 594954578 594953198 0.000000e+00 2265
18 TraesCS1D01G008500 chr3D 97.569 617 11 2 2138 2750 594952689 594952073 0.000000e+00 1053
19 TraesCS1D01G008500 chr3D 96.774 620 19 1 2132 2750 590155543 590156162 0.000000e+00 1033
20 TraesCS1D01G008500 chr3D 92.953 298 13 3 184 474 594947118 594947414 7.690000e-116 427
21 TraesCS1D01G008500 chr3D 98.723 235 3 0 2768 3002 594952000 594951766 4.630000e-113 418
22 TraesCS1D01G008500 chr3D 92.491 293 15 2 189 474 590160366 590160074 2.150000e-111 412
23 TraesCS1D01G008500 chr3D 92.491 293 15 4 189 474 594954919 594954627 2.150000e-111 412
24 TraesCS1D01G008500 chr3D 93.617 235 15 0 2768 3002 590156238 590156472 4.760000e-93 351
25 TraesCS1D01G008500 chr2D 97.323 1382 28 4 741 2118 380678448 380679824 0.000000e+00 2338
26 TraesCS1D01G008500 chr2D 96.774 620 19 1 2132 2750 380680334 380680953 0.000000e+00 1033
27 TraesCS1D01G008500 chr2D 93.684 285 12 1 188 466 380686270 380685986 3.580000e-114 422
28 TraesCS1D01G008500 chr2D 91.489 235 10 1 2768 3002 380681031 380681255 6.250000e-82 315
29 TraesCS1D01G008500 chr1A 92.892 1421 51 20 741 2124 572001078 571999671 0.000000e+00 2019
30 TraesCS1D01G008500 chr1A 90.110 182 18 0 1 182 6510935 6510754 1.390000e-58 237
31 TraesCS1D01G008500 chr1A 86.047 172 24 0 15 186 5153043 5153214 5.110000e-43 185
32 TraesCS1D01G008500 chr5D 96.906 1196 29 4 929 2118 449488326 449489519 0.000000e+00 1997
33 TraesCS1D01G008500 chr5D 97.915 1055 19 2 741 1795 406899809 406900860 0.000000e+00 1823
34 TraesCS1D01G008500 chr5D 96.935 620 18 1 2132 2750 406910420 406911039 0.000000e+00 1038
35 TraesCS1D01G008500 chr5D 96.613 620 20 1 2132 2750 449490029 449490648 0.000000e+00 1027
36 TraesCS1D01G008500 chr5D 92.177 294 16 2 188 474 406945366 406945073 2.790000e-110 409
37 TraesCS1D01G008500 chr5D 93.927 247 3 2 2768 3002 406911111 406911357 2.200000e-96 363
38 TraesCS1D01G008500 chr5D 94.167 240 6 7 2768 3002 449490721 449490957 2.850000e-95 359
39 TraesCS1D01G008500 chr7D 97.315 894 10 4 750 1643 123498449 123497570 0.000000e+00 1506
40 TraesCS1D01G008500 chr4A 86.944 1371 129 27 741 2099 85531784 85530452 0.000000e+00 1495
41 TraesCS1D01G008500 chr5A 96.417 614 20 2 2138 2750 573009970 573009358 0.000000e+00 1011
42 TraesCS1D01G008500 chr3A 96.091 614 23 1 2138 2750 22759160 22758547 0.000000e+00 1000
43 TraesCS1D01G008500 chr3A 96.575 146 5 0 2857 3002 22756469 22756324 2.990000e-60 243
44 TraesCS1D01G008500 chr3A 94.444 90 5 0 2768 2857 22758474 22758385 4.040000e-29 139
45 TraesCS1D01G008500 chr2A 95.763 236 9 1 2768 3002 38495558 38495323 2.180000e-101 379


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 TraesCS1D01G008500 chr1D 4305735 4308737 3002 True 2529.000000 4180 100.000000 1 3003 2 chr1D.!!$R1 3002
1 TraesCS1D01G008500 chr1D 7179996 7182222 2226 False 1598.000000 2403 97.261500 1 2131 2 chr1D.!!$F3 2130
2 TraesCS1D01G008500 chr1D 42894062 42896924 2862 True 1175.666667 2128 95.508333 741 3002 3 chr1D.!!$R2 2261
3 TraesCS1D01G008500 chr4D 488848894 488851771 2877 False 1110.500000 1953 90.501500 741 3002 2 chr4D.!!$F2 2261
4 TraesCS1D01G008500 chr4D 108842224 108845372 3148 False 1051.250000 2350 96.024750 189 3002 4 chr4D.!!$F1 2813
5 TraesCS1D01G008500 chr3D 590153657 590156472 2815 False 1240.666667 2338 95.906000 741 3002 3 chr3D.!!$F2 2261
6 TraesCS1D01G008500 chr3D 594951766 594954919 3153 True 1037.000000 2265 96.263250 189 3002 4 chr3D.!!$R2 2813
7 TraesCS1D01G008500 chr2D 380678448 380681255 2807 False 1228.666667 2338 95.195333 741 3002 3 chr2D.!!$F1 2261
8 TraesCS1D01G008500 chr1A 571999671 572001078 1407 True 2019.000000 2019 92.892000 741 2124 1 chr1A.!!$R2 1383
9 TraesCS1D01G008500 chr5D 406899809 406900860 1051 False 1823.000000 1823 97.915000 741 1795 1 chr5D.!!$F1 1054
10 TraesCS1D01G008500 chr5D 449488326 449490957 2631 False 1127.666667 1997 95.895333 929 3002 3 chr5D.!!$F3 2073
11 TraesCS1D01G008500 chr5D 406910420 406911357 937 False 700.500000 1038 95.431000 2132 3002 2 chr5D.!!$F2 870
12 TraesCS1D01G008500 chr7D 123497570 123498449 879 True 1506.000000 1506 97.315000 750 1643 1 chr7D.!!$R1 893
13 TraesCS1D01G008500 chr4A 85530452 85531784 1332 True 1495.000000 1495 86.944000 741 2099 1 chr4A.!!$R1 1358
14 TraesCS1D01G008500 chr5A 573009358 573009970 612 True 1011.000000 1011 96.417000 2138 2750 1 chr5A.!!$R1 612
15 TraesCS1D01G008500 chr3A 22756324 22759160 2836 True 460.666667 1000 95.703333 2138 3002 3 chr3A.!!$R1 864

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
34 35 0.169672 CAGAGGCGATTTGGTGCAAG 59.830 55.000 0.0 0.0 0.00 4.01 F
457 465 1.988406 GGACTAACCTGGCCGACCT 60.988 63.158 0.0 0.0 36.63 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1100 1215 0.397564 CCACAAATTTGCCAGCCCTT 59.602 50.0 18.12 0.0 0.0 3.95 R
2203 2865 0.108804 CCACTACGTCGCTCCAACAT 60.109 55.0 0.00 0.0 0.0 2.71 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
34 35 0.169672 CAGAGGCGATTTGGTGCAAG 59.830 55.000 0.00 0.00 0.00 4.01
270 277 6.126409 ACTGACCAAAAACTCCAGTTTATCA 58.874 36.000 5.13 6.65 46.47 2.15
457 465 1.988406 GGACTAACCTGGCCGACCT 60.988 63.158 0.00 0.00 36.63 3.85
1048 1163 4.029520 AGACACTGTGATAGATCCAAGCT 58.970 43.478 15.86 0.00 0.00 3.74
1049 1164 4.469227 AGACACTGTGATAGATCCAAGCTT 59.531 41.667 15.86 0.00 0.00 3.74
1333 1481 3.955650 TGGAACCAAGAGCTAGTGTAC 57.044 47.619 0.00 0.00 0.00 2.90
1594 1742 5.511545 GGTTGAGAAACTGAAGAAGGAGCTA 60.512 44.000 0.00 0.00 0.00 3.32
1800 1948 2.087646 GAAAGAACAGAGGTGCATCCC 58.912 52.381 0.00 0.00 36.75 3.85
2003 2155 3.450096 GGTACCTAGGGTTGGTAAGTGAG 59.550 52.174 14.81 0.00 41.16 3.51
2114 2268 6.567050 CCTATGGTTTCAGATCATTTTGGTG 58.433 40.000 0.00 0.00 0.00 4.17
2118 2272 4.559153 GTTTCAGATCATTTTGGTGGTGG 58.441 43.478 0.00 0.00 0.00 4.61
2121 2275 2.231964 CAGATCATTTTGGTGGTGGTGG 59.768 50.000 0.00 0.00 0.00 4.61
2124 2278 0.249826 CATTTTGGTGGTGGTGGTGC 60.250 55.000 0.00 0.00 0.00 5.01
2126 2280 2.838748 TTTTGGTGGTGGTGGTGCGA 62.839 55.000 0.00 0.00 0.00 5.10
2127 2281 2.632602 TTTGGTGGTGGTGGTGCGAT 62.633 55.000 0.00 0.00 0.00 4.58
2128 2282 3.055719 GGTGGTGGTGGTGCGATG 61.056 66.667 0.00 0.00 0.00 3.84
2129 2283 2.031919 GTGGTGGTGGTGCGATGA 59.968 61.111 0.00 0.00 0.00 2.92
2130 2284 1.377202 GTGGTGGTGGTGCGATGAT 60.377 57.895 0.00 0.00 0.00 2.45
2131 2285 1.078497 TGGTGGTGGTGCGATGATC 60.078 57.895 0.00 0.00 0.00 2.92
2132 2286 1.221840 GGTGGTGGTGCGATGATCT 59.778 57.895 0.00 0.00 0.00 2.75
2133 2287 1.091771 GGTGGTGGTGCGATGATCTG 61.092 60.000 0.00 0.00 0.00 2.90
2134 2288 1.091771 GTGGTGGTGCGATGATCTGG 61.092 60.000 0.00 0.00 0.00 3.86
2135 2289 1.264045 TGGTGGTGCGATGATCTGGA 61.264 55.000 0.00 0.00 0.00 3.86
2136 2290 0.107456 GGTGGTGCGATGATCTGGAT 59.893 55.000 0.00 0.00 0.00 3.41
2203 2865 3.312421 GCATTTGCTTCAGCCGTAGATTA 59.688 43.478 0.00 0.00 41.18 1.75
2660 3346 2.407340 AAAGAGAGGTGGAGTGAGGT 57.593 50.000 0.00 0.00 0.00 3.85
2677 3363 5.601313 AGTGAGGTAGTGGAGAAGTAAAACA 59.399 40.000 0.00 0.00 0.00 2.83
2760 3457 3.548818 GCTGTTAGGTGAAAGTTGTGCAG 60.549 47.826 0.00 0.00 0.00 4.41
2761 3458 2.357637 TGTTAGGTGAAAGTTGTGCAGC 59.642 45.455 0.00 0.00 0.00 5.25
2762 3459 2.340210 TAGGTGAAAGTTGTGCAGCA 57.660 45.000 0.00 0.00 32.81 4.41
2763 3460 1.027357 AGGTGAAAGTTGTGCAGCAG 58.973 50.000 0.00 0.00 32.81 4.24
2764 3461 0.740737 GGTGAAAGTTGTGCAGCAGT 59.259 50.000 0.00 0.00 0.00 4.40
3002 5757 3.876914 TGTTTCAAGACGCAGAATCAAGT 59.123 39.130 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.185797 CCGAGGTTAACTTGCACTTGTAC 59.814 47.826 5.42 0.00 0.00 2.90
209 210 3.070446 AGTTCTGTGGGACGTGAAATGTA 59.930 43.478 0.00 0.00 35.18 2.29
1049 1164 3.011566 TCAGTCACAAGCCCAGAAAAA 57.988 42.857 0.00 0.00 0.00 1.94
1100 1215 0.397564 CCACAAATTTGCCAGCCCTT 59.602 50.000 18.12 0.00 0.00 3.95
1126 1241 1.673477 CTGCCAGTGTCAGTGCCTA 59.327 57.895 1.77 0.00 0.00 3.93
1512 1660 7.275920 ACCAAGGTTCTCTTCATGATACATAC 58.724 38.462 0.00 0.00 32.41 2.39
1800 1948 3.089573 TGATATCAGCTTCACTCTGCG 57.910 47.619 0.00 0.00 0.00 5.18
1808 1956 6.855836 TGGTGTTTTGAATGATATCAGCTTC 58.144 36.000 11.78 11.21 0.00 3.86
2003 2155 9.877178 GGCCAGTTATATATATATGCCTCATAC 57.123 37.037 17.71 7.09 33.64 2.39
2114 2268 1.091771 CAGATCATCGCACCACCACC 61.092 60.000 0.00 0.00 0.00 4.61
2118 2272 1.224075 CATCCAGATCATCGCACCAC 58.776 55.000 0.00 0.00 0.00 4.16
2121 2275 0.585357 GCACATCCAGATCATCGCAC 59.415 55.000 0.00 0.00 0.00 5.34
2124 2278 1.725164 CATCGCACATCCAGATCATCG 59.275 52.381 0.00 0.00 0.00 3.84
2126 2280 3.261137 AGATCATCGCACATCCAGATCAT 59.739 43.478 0.00 0.00 35.52 2.45
2127 2281 2.631545 AGATCATCGCACATCCAGATCA 59.368 45.455 0.00 0.00 35.52 2.92
2128 2282 2.994578 CAGATCATCGCACATCCAGATC 59.005 50.000 0.00 0.00 33.79 2.75
2129 2283 2.289506 CCAGATCATCGCACATCCAGAT 60.290 50.000 0.00 0.00 0.00 2.90
2130 2284 1.069668 CCAGATCATCGCACATCCAGA 59.930 52.381 0.00 0.00 0.00 3.86
2131 2285 1.069668 TCCAGATCATCGCACATCCAG 59.930 52.381 0.00 0.00 0.00 3.86
2132 2286 1.122227 TCCAGATCATCGCACATCCA 58.878 50.000 0.00 0.00 0.00 3.41
2133 2287 2.074576 CATCCAGATCATCGCACATCC 58.925 52.381 0.00 0.00 0.00 3.51
2134 2288 2.735663 GACATCCAGATCATCGCACATC 59.264 50.000 0.00 0.00 0.00 3.06
2135 2289 2.763933 GACATCCAGATCATCGCACAT 58.236 47.619 0.00 0.00 0.00 3.21
2136 2290 1.536709 CGACATCCAGATCATCGCACA 60.537 52.381 0.00 0.00 0.00 4.57
2203 2865 0.108804 CCACTACGTCGCTCCAACAT 60.109 55.000 0.00 0.00 0.00 2.71
2660 3346 5.616270 TGCACATGTTTTACTTCTCCACTA 58.384 37.500 0.00 0.00 0.00 2.74
2677 3363 2.751259 CCTGTCAAATACTGCTGCACAT 59.249 45.455 0.00 0.00 0.00 3.21
2760 3457 6.037500 TGCTCTGAATGTATGTCAAATACTGC 59.962 38.462 0.00 0.00 0.00 4.40
2761 3458 7.064966 TGTGCTCTGAATGTATGTCAAATACTG 59.935 37.037 0.00 0.00 0.00 2.74
2762 3459 7.105588 TGTGCTCTGAATGTATGTCAAATACT 58.894 34.615 0.00 0.00 0.00 2.12
2763 3460 7.307493 TGTGCTCTGAATGTATGTCAAATAC 57.693 36.000 0.00 0.00 0.00 1.89
2764 3461 7.920160 TTGTGCTCTGAATGTATGTCAAATA 57.080 32.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.