Multiple sequence alignment - TraesCS3A01G492800

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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 TraesCS3A01G492800 chr3A 100.000 1733 0 0 1 1733 719482115 719483847 0.000000e+00 3201
1 TraesCS3A01G492800 chr3A 85.287 1271 100 36 421 1655 719386547 719387766 0.000000e+00 1230
2 TraesCS3A01G492800 chr3A 85.093 483 71 1 947 1429 719461533 719462014 2.190000e-135 492
3 TraesCS3A01G492800 chr3A 89.441 322 25 7 1175 1490 719555481 719555799 4.900000e-107 398
4 TraesCS3A01G492800 chr3A 82.178 505 45 17 421 905 719534630 719535109 2.280000e-105 392
5 TraesCS3A01G492800 chr3A 100.000 190 0 0 2258 2447 719484372 719484561 3.870000e-93 351
6 TraesCS3A01G492800 chr3A 89.151 212 19 2 967 1174 719535138 719535349 6.710000e-66 261
7 TraesCS3A01G492800 chr3A 87.568 185 23 0 2262 2446 719393319 719393503 5.300000e-52 215
8 TraesCS3A01G492800 chr3A 86.400 125 17 0 2310 2434 412035674 412035550 1.180000e-28 137
9 TraesCS3A01G492800 chr3A 85.385 130 16 3 2307 2434 448008149 448008277 5.490000e-27 132
10 TraesCS3A01G492800 chr3A 83.333 126 21 0 71 196 639776047 639775922 1.540000e-22 117
11 TraesCS3A01G492800 chr3D 92.216 1002 51 7 508 1490 589607423 589608416 0.000000e+00 1393
12 TraesCS3A01G492800 chr3D 87.141 1252 78 30 421 1654 589579605 589580791 0.000000e+00 1343
13 TraesCS3A01G492800 chr3D 87.422 644 61 12 647 1283 589582589 589583219 0.000000e+00 723
14 TraesCS3A01G492800 chr3B 88.793 928 55 26 253 1161 788138062 788138959 0.000000e+00 1092
15 TraesCS3A01G492800 chr3B 81.637 1051 96 37 422 1450 788106436 788107411 0.000000e+00 782
16 TraesCS3A01G492800 chr3B 91.275 298 23 1 1175 1472 788153556 788153850 1.050000e-108 403
17 TraesCS3A01G492800 chr3B 92.430 251 19 0 1 251 788137351 788137601 2.310000e-95 359
18 TraesCS3A01G492800 chr3B 85.246 122 18 0 76 197 659705009 659705130 2.550000e-25 126
19 TraesCS3A01G492800 chr4A 86.719 128 17 0 2307 2434 89183260 89183387 2.540000e-30 143
20 TraesCS3A01G492800 chr2B 87.302 126 14 2 2310 2434 311217979 311217855 2.540000e-30 143
21 TraesCS3A01G492800 chr2B 86.364 132 17 1 2304 2434 311308159 311308028 2.540000e-30 143
22 TraesCS3A01G492800 chr2B 84.252 127 20 0 71 197 86326698 86326572 9.190000e-25 124
23 TraesCS3A01G492800 chr2B 82.677 127 22 0 71 197 275404503 275404377 1.990000e-21 113
24 TraesCS3A01G492800 chr5B 86.508 126 15 2 2310 2434 151383664 151383540 1.180000e-28 137
25 TraesCS3A01G492800 chr5B 86.508 126 15 2 2310 2434 155018749 155018625 1.180000e-28 137
26 TraesCS3A01G492800 chr5B 85.965 114 16 0 87 200 276944773 276944660 3.300000e-24 122
27 TraesCS3A01G492800 chr6B 79.679 187 35 2 2260 2446 716227520 716227703 5.490000e-27 132
28 TraesCS3A01G492800 chr7B 84.127 126 20 0 72 197 559995595 559995470 3.300000e-24 122
29 TraesCS3A01G492800 chr1A 83.465 127 21 0 71 197 396958324 396958450 4.270000e-23 119
30 TraesCS3A01G492800 chr1D 82.308 130 23 0 68 197 162348733 162348604 1.990000e-21 113


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 TraesCS3A01G492800 chr3A 719482115 719484561 2446 False 1776.0 3201 100.0000 1 2447 2 chr3A.!!$F6 2446
1 TraesCS3A01G492800 chr3A 719386547 719387766 1219 False 1230.0 1230 85.2870 421 1655 1 chr3A.!!$F2 1234
2 TraesCS3A01G492800 chr3A 719534630 719535349 719 False 326.5 392 85.6645 421 1174 2 chr3A.!!$F7 753
3 TraesCS3A01G492800 chr3D 589607423 589608416 993 False 1393.0 1393 92.2160 508 1490 1 chr3D.!!$F1 982
4 TraesCS3A01G492800 chr3D 589579605 589583219 3614 False 1033.0 1343 87.2815 421 1654 2 chr3D.!!$F2 1233
5 TraesCS3A01G492800 chr3B 788106436 788107411 975 False 782.0 782 81.6370 422 1450 1 chr3B.!!$F2 1028
6 TraesCS3A01G492800 chr3B 788137351 788138959 1608 False 725.5 1092 90.6115 1 1161 2 chr3B.!!$F4 1160


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
942 1496 0.109781 CCAGCACATTAACACACGGC 60.11 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 2935 0.179073 CGCTCTGAACGGGGATGAAT 60.179 55.0 0.0 0.0 0.0 2.57 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
85 86 5.362717 TGTAGCATATATTACCTCCATCCGG 59.637 44.000 0.00 0.00 0.00 5.14
103 104 6.647067 CCATCCGGAAATACTTGTCTTAGATC 59.353 42.308 9.01 0.00 0.00 2.75
204 205 8.840200 TTTAGAACAGAGGGAGTAGATAACAT 57.160 34.615 0.00 0.00 0.00 2.71
251 252 6.373186 AAGTTTGACACAAAGTACTAAGGC 57.627 37.500 0.00 0.00 0.00 4.35
270 730 0.763035 CCCCCTATAAACCAGGACGG 59.237 60.000 0.00 0.00 42.50 4.79
296 757 7.618137 AGACAGTATACCGTTAGTCCAAAAAT 58.382 34.615 0.00 0.00 0.00 1.82
314 775 8.381636 TCCAAAAATTTCATTTACATGTCCCAT 58.618 29.630 0.00 0.00 0.00 4.00
350 811 0.390340 TTTGGCGTTTGCTTGCAACA 60.390 45.000 7.60 0.17 42.25 3.33
381 845 9.794685 CATACTAGCACATATACTGATAACTGG 57.205 37.037 0.00 0.00 0.00 4.00
388 852 8.765219 GCACATATACTGATAACTGGTTAACTG 58.235 37.037 5.42 1.79 0.00 3.16
403 867 9.442047 ACTGGTTAACTGAGAATTATTCTTGAG 57.558 33.333 8.99 10.32 40.87 3.02
465 933 3.547249 AACATGACGTCGTCGCCGT 62.547 57.895 19.81 0.00 42.06 5.68
526 1007 2.069273 GGGTGAGAATGACACGTCAAG 58.931 52.381 3.61 0.00 43.58 3.02
755 1271 1.705997 AACCGACCAGTTCCTTGGCT 61.706 55.000 0.00 0.00 42.18 4.75
826 1346 0.652592 GCTGCACGCTTGTATGTAGG 59.347 55.000 0.00 0.00 35.14 3.18
827 1347 1.739035 GCTGCACGCTTGTATGTAGGA 60.739 52.381 0.00 0.00 35.14 2.94
878 1408 4.080919 ACACATAAGCATAGGCACTTGAGA 60.081 41.667 0.67 0.00 44.61 3.27
879 1409 4.510711 CACATAAGCATAGGCACTTGAGAG 59.489 45.833 0.67 0.00 44.61 3.20
942 1496 0.109781 CCAGCACATTAACACACGGC 60.110 55.000 0.00 0.00 0.00 5.68
982 1536 3.133721 GCCACTAATCTCAGGTGATCACT 59.866 47.826 24.50 8.73 33.32 3.41
1164 1723 2.107750 CTCGTGGCATCGGCAGAT 59.892 61.111 9.05 0.00 43.71 2.90
1479 2041 2.158900 CCATCGGCCAGTCTACTGAATT 60.159 50.000 11.69 0.00 46.59 2.17
1511 2073 6.775708 TGATACTTGGCTACAGTTTTAACCT 58.224 36.000 0.00 0.00 0.00 3.50
1526 2088 9.316730 CAGTTTTAACCTGTACACAGTTTACTA 57.683 33.333 10.86 0.00 42.27 1.82
1622 2184 0.459759 GGTTGGAGTAGTAGTGGCGC 60.460 60.000 0.00 0.00 0.00 6.53
1668 2288 7.220300 GGATAAAGTACTAGTGTTGTGTCATCG 59.780 40.741 5.39 0.00 0.00 3.84
1688 2308 8.234546 GTCATCGAACACAGGTTTATATTTGTT 58.765 33.333 0.00 0.00 37.36 2.83
1700 2320 6.183360 GGTTTATATTTGTTCGTTGAGCGGTA 60.183 38.462 0.00 0.00 41.72 4.02
1716 2336 4.060205 AGCGGTACAGACGTGTTTTATTT 58.940 39.130 0.00 0.00 38.19 1.40
1720 2340 6.013085 CGGTACAGACGTGTTTTATTTCATG 58.987 40.000 0.00 0.00 38.19 3.07
2275 2895 3.651480 CTCCTGCGCGCTTTTTCCG 62.651 63.158 33.29 11.08 0.00 4.30
2305 2925 4.227134 AGCGGCGCTCCATAGTGG 62.227 66.667 31.35 0.00 39.43 4.00
2321 2941 4.331356 GGCAATGCCGCATTCATC 57.669 55.556 15.85 8.06 39.62 2.92
2330 2950 1.439353 CCGCATTCATCCCCGTTCAG 61.439 60.000 0.00 0.00 0.00 3.02
2334 2954 0.179073 ATTCATCCCCGTTCAGAGCG 60.179 55.000 0.00 0.00 0.00 5.03
2341 2961 2.254350 CGTTCAGAGCGGACGTGA 59.746 61.111 0.00 0.00 32.52 4.35
2351 2971 1.303799 GCGGACGTGACCTCTCACTA 61.304 60.000 0.00 0.00 44.27 2.74
2353 2973 0.452585 GGACGTGACCTCTCACTAGC 59.547 60.000 0.00 0.00 44.27 3.42
2355 2975 1.226435 CGTGACCTCTCACTAGCGC 60.226 63.158 0.00 0.00 44.27 5.92
2392 3012 4.838486 CCGCCGAGAGAGTGTCGC 62.838 72.222 0.00 0.00 36.06 5.19
2395 3015 3.062466 CCGAGAGAGTGTCGCCCA 61.062 66.667 0.00 0.00 36.06 5.36
2404 3024 1.142314 GTGTCGCCCATACCGCTTA 59.858 57.895 0.00 0.00 0.00 3.09
2424 3044 1.022735 CTGATGCAGGTGATTGCTCC 58.977 55.000 0.00 0.00 44.38 4.70
2439 3059 0.232303 GCTCCGTGTTCAAACGACAG 59.768 55.000 0.00 0.00 46.49 3.51
2446 3066 1.292992 GTTCAAACGACAGGACGGTT 58.707 50.000 0.00 0.00 44.09 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 9.167311 GGATGGAGGTAATATATGCTACAAAAG 57.833 37.037 0.00 0.00 0.00 2.27
178 179 8.840200 TGTTATCTACTCCCTCTGTTCTAAAT 57.160 34.615 0.00 0.00 0.00 1.40
184 185 8.554490 ACAATATGTTATCTACTCCCTCTGTT 57.446 34.615 0.00 0.00 0.00 3.16
238 239 5.899631 TTATAGGGGGCCTTAGTACTTTG 57.100 43.478 0.84 0.00 34.61 2.77
251 252 0.763035 CCGTCCTGGTTTATAGGGGG 59.237 60.000 0.00 0.00 35.96 5.40
270 730 5.824904 TTGGACTAACGGTATACTGTCTC 57.175 43.478 17.62 11.87 33.61 3.36
314 775 3.756434 GCCAAAGCAGTGACCAATAGTAA 59.244 43.478 0.00 0.00 39.53 2.24
388 852 7.387397 CCATGAGGTAGCTCAAGAATAATTCTC 59.613 40.741 27.06 0.00 39.61 2.87
400 864 1.839994 CTTTCCCCATGAGGTAGCTCA 59.160 52.381 25.72 25.72 37.79 4.26
403 867 3.054361 TCTTTCTTTCCCCATGAGGTAGC 60.054 47.826 0.00 0.00 0.00 3.58
465 933 3.043713 CTTGCACTGCTTCGCCGA 61.044 61.111 1.98 0.00 0.00 5.54
476 944 2.662791 CGCGCATATAATGGACTTGCAC 60.663 50.000 8.75 0.00 32.94 4.57
485 953 1.155889 TTCAGGGCGCGCATATAATG 58.844 50.000 34.42 19.86 0.00 1.90
526 1007 1.516423 GGTGTCTACTCCCGAAGCC 59.484 63.158 0.00 0.00 0.00 4.35
786 1303 0.108585 AGCTGGTTGTGTTGATCGGT 59.891 50.000 0.00 0.00 0.00 4.69
821 1341 2.489329 GGCACAAGTACGTACTCCTACA 59.511 50.000 27.51 0.00 34.99 2.74
822 1342 2.476854 CGGCACAAGTACGTACTCCTAC 60.477 54.545 27.51 17.05 34.99 3.18
823 1343 1.739466 CGGCACAAGTACGTACTCCTA 59.261 52.381 27.51 0.00 34.99 2.94
824 1344 0.524862 CGGCACAAGTACGTACTCCT 59.475 55.000 27.51 11.34 34.99 3.69
825 1345 1.074872 GCGGCACAAGTACGTACTCC 61.075 60.000 27.51 21.71 34.99 3.85
826 1346 1.074872 GGCGGCACAAGTACGTACTC 61.075 60.000 27.51 15.13 34.99 2.59
827 1347 1.080298 GGCGGCACAAGTACGTACT 60.080 57.895 22.45 22.45 38.39 2.73
878 1408 1.228367 CTGTTCTGGTGCTTGGCCT 60.228 57.895 3.32 0.00 0.00 5.19
879 1409 2.924105 GCTGTTCTGGTGCTTGGCC 61.924 63.158 0.00 0.00 0.00 5.36
942 1496 2.918571 CTGTGGTAGCAGTGTGTGG 58.081 57.895 0.00 0.00 0.00 4.17
982 1536 2.011947 CATCTTCGCCTGCTTGATTCA 58.988 47.619 0.00 0.00 0.00 2.57
1383 1945 6.070951 ACTCCATCTCCATTCAGATCAAAA 57.929 37.500 0.00 0.00 30.07 2.44
1479 2041 4.546674 TGTAGCCAAGTATCAGGATCAGA 58.453 43.478 0.00 0.00 0.00 3.27
1526 2088 5.221661 CCCTGGCGAAATAGATTAAGTACCT 60.222 44.000 0.00 0.00 0.00 3.08
1539 2101 4.277476 TGTTCAATATTCCCTGGCGAAAT 58.723 39.130 0.00 0.00 0.00 2.17
1543 2105 2.917933 TCTGTTCAATATTCCCTGGCG 58.082 47.619 0.00 0.00 0.00 5.69
1622 2184 4.444536 TCCATTTCGGTTTATAAGACCCG 58.555 43.478 11.83 11.83 41.75 5.28
1668 2288 8.071368 TCAACGAACAAATATAAACCTGTGTTC 58.929 33.333 0.00 0.00 40.77 3.18
1691 2311 0.386476 AACACGTCTGTACCGCTCAA 59.614 50.000 0.00 0.00 0.00 3.02
1692 2312 0.386476 AAACACGTCTGTACCGCTCA 59.614 50.000 0.00 0.00 0.00 4.26
1700 2320 6.038825 TGGTTCATGAAATAAAACACGTCTGT 59.961 34.615 10.35 0.00 0.00 3.41
2257 2877 2.176792 GGAAAAAGCGCGCAGGAG 59.823 61.111 35.10 0.00 0.00 3.69
2258 2878 3.722295 CGGAAAAAGCGCGCAGGA 61.722 61.111 35.10 0.00 0.00 3.86
2261 2881 2.970324 AGACGGAAAAAGCGCGCA 60.970 55.556 35.10 0.00 0.00 6.09
2291 2911 1.526917 ATTGCCACTATGGAGCGCC 60.527 57.895 2.29 0.00 40.96 6.53
2305 2925 1.300388 GGGATGAATGCGGCATTGC 60.300 57.895 31.03 21.25 33.90 3.56
2315 2935 0.179073 CGCTCTGAACGGGGATGAAT 60.179 55.000 0.00 0.00 0.00 2.57
2330 2950 2.486042 GAGAGGTCACGTCCGCTC 59.514 66.667 10.52 10.52 44.35 5.03
2339 2959 2.407428 CGGCGCTAGTGAGAGGTCA 61.407 63.158 7.64 0.00 0.00 4.02
2341 2961 3.141488 CCGGCGCTAGTGAGAGGT 61.141 66.667 7.64 0.00 0.00 3.85
2351 2971 3.576356 CGATTCAATGCCGGCGCT 61.576 61.111 23.90 9.04 35.36 5.92
2355 2975 4.612536 GCGCCGATTCAATGCCGG 62.613 66.667 0.00 0.00 45.51 6.13
2392 3012 1.202639 TGCATCAGTAAGCGGTATGGG 60.203 52.381 0.00 0.00 0.00 4.00
2395 3015 1.762957 ACCTGCATCAGTAAGCGGTAT 59.237 47.619 0.00 0.00 36.44 2.73
2404 3024 1.681166 GGAGCAATCACCTGCATCAGT 60.681 52.381 0.00 0.00 45.18 3.41
2424 3044 0.228742 CGTCCTGTCGTTTGAACACG 59.771 55.000 0.00 0.00 41.78 4.49



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

AutoCloner maintained by Alex Coulton.