Multiple sequence alignment - TraesCS5D01G383400

Loading Multiple Alignment...

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 TraesCS5D01G383400 chr5D 100.000 2297 0 0 1 2297 453122381 453120085 0.000000e+00 4242.0
1 TraesCS5D01G383400 chr5D 96.142 1322 50 1 1 1321 350304983 350306304 0.000000e+00 2158.0
2 TraesCS5D01G383400 chr5D 83.447 1323 212 7 3 1321 74471843 74473162 0.000000e+00 1223.0
3 TraesCS5D01G383400 chr5D 80.288 416 59 14 1898 2295 239623502 239623912 2.230000e-75 292.0
4 TraesCS5D01G383400 chr5B 96.637 1130 33 5 204 1332 662648727 662647602 0.000000e+00 1871.0
5 TraesCS5D01G383400 chr5B 91.897 975 62 6 1333 2297 553615876 553614909 0.000000e+00 1347.0
6 TraesCS5D01G383400 chr5B 79.616 417 59 16 1896 2295 263613151 263612744 2.250000e-70 276.0
7 TraesCS5D01G383400 chr7A 85.042 1317 188 8 3 1314 709984457 709985769 0.000000e+00 1332.0
8 TraesCS5D01G383400 chr7A 76.503 183 37 6 330 509 679792003 679792182 6.760000e-16 95.3
9 TraesCS5D01G383400 chr7A 75.956 183 38 6 330 509 23818287 23818466 3.140000e-14 89.8
10 TraesCS5D01G383400 chr3A 84.282 1317 198 8 3 1314 466478130 466476818 0.000000e+00 1277.0
11 TraesCS5D01G383400 chr6A 84.195 1316 200 7 3 1314 521475520 521476831 0.000000e+00 1271.0
12 TraesCS5D01G383400 chr1A 84.091 1320 189 14 3 1314 307482924 307481618 0.000000e+00 1254.0
13 TraesCS5D01G383400 chr1A 79.856 417 55 16 1906 2297 139487781 139488193 6.250000e-71 278.0
14 TraesCS5D01G383400 chr2B 83.268 1273 186 10 33 1303 699117677 699118924 0.000000e+00 1146.0
15 TraesCS5D01G383400 chr1B 94.978 677 31 3 1 676 327316160 327315486 0.000000e+00 1059.0
16 TraesCS5D01G383400 chr1B 87.698 252 24 4 2051 2297 189577830 189578079 1.040000e-73 287.0
17 TraesCS5D01G383400 chr6D 93.638 503 15 8 819 1321 390869229 390869714 0.000000e+00 736.0
18 TraesCS5D01G383400 chr6D 94.352 301 15 2 528 827 390866427 390866726 5.780000e-126 460.0
19 TraesCS5D01G383400 chr6D 85.817 416 51 4 1 409 48665054 48665468 3.500000e-118 435.0
20 TraesCS5D01G383400 chr5A 83.717 565 68 7 1343 1898 571957950 571957401 1.570000e-141 512.0
21 TraesCS5D01G383400 chr5A 80.000 420 56 18 1896 2295 313911539 313911128 3.730000e-73 285.0
22 TraesCS5D01G383400 chr7D 81.840 413 61 12 1893 2292 463791643 463792054 3.660000e-88 335.0
23 TraesCS5D01G383400 chr7D 80.332 422 61 14 1893 2297 353080633 353081049 1.330000e-77 300.0
24 TraesCS5D01G383400 chr7D 76.860 363 58 16 1893 2240 12630908 12630557 5.040000e-42 182.0
25 TraesCS5D01G383400 chr7D 76.584 363 59 15 1893 2240 12641050 12640699 2.350000e-40 176.0
26 TraesCS5D01G383400 chr7D 83.212 137 18 5 1905 2036 229242837 229242701 1.110000e-23 121.0
27 TraesCS5D01G383400 chr7B 79.762 420 64 15 1893 2296 299245153 299245567 3.730000e-73 285.0
28 TraesCS5D01G383400 chr4D 79.215 433 56 17 1893 2297 466838146 466837720 1.050000e-68 270.0
29 TraesCS5D01G383400 chr4D 77.067 375 54 20 1893 2239 340307037 340307407 1.080000e-43 187.0
30 TraesCS5D01G383400 chr2A 78.068 383 40 27 1893 2239 430985845 430985471 3.870000e-48 202.0
31 TraesCS5D01G383400 chr3B 76.247 421 68 24 1893 2292 346606763 346606354 6.470000e-46 195.0
32 TraesCS5D01G383400 chr6B 89.041 146 13 3 1893 2036 514503708 514503852 6.520000e-41 178.0


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 TraesCS5D01G383400 chr5D 453120085 453122381 2296 True 4242 4242 100.000 1 2297 1 chr5D.!!$R1 2296
1 TraesCS5D01G383400 chr5D 350304983 350306304 1321 False 2158 2158 96.142 1 1321 1 chr5D.!!$F3 1320
2 TraesCS5D01G383400 chr5D 74471843 74473162 1319 False 1223 1223 83.447 3 1321 1 chr5D.!!$F1 1318
3 TraesCS5D01G383400 chr5B 662647602 662648727 1125 True 1871 1871 96.637 204 1332 1 chr5B.!!$R3 1128
4 TraesCS5D01G383400 chr5B 553614909 553615876 967 True 1347 1347 91.897 1333 2297 1 chr5B.!!$R2 964
5 TraesCS5D01G383400 chr7A 709984457 709985769 1312 False 1332 1332 85.042 3 1314 1 chr7A.!!$F3 1311
6 TraesCS5D01G383400 chr3A 466476818 466478130 1312 True 1277 1277 84.282 3 1314 1 chr3A.!!$R1 1311
7 TraesCS5D01G383400 chr6A 521475520 521476831 1311 False 1271 1271 84.195 3 1314 1 chr6A.!!$F1 1311
8 TraesCS5D01G383400 chr1A 307481618 307482924 1306 True 1254 1254 84.091 3 1314 1 chr1A.!!$R1 1311
9 TraesCS5D01G383400 chr2B 699117677 699118924 1247 False 1146 1146 83.268 33 1303 1 chr2B.!!$F1 1270
10 TraesCS5D01G383400 chr1B 327315486 327316160 674 True 1059 1059 94.978 1 676 1 chr1B.!!$R1 675
11 TraesCS5D01G383400 chr6D 390866427 390869714 3287 False 598 736 93.995 528 1321 2 chr6D.!!$F2 793
12 TraesCS5D01G383400 chr5A 571957401 571957950 549 True 512 512 83.717 1343 1898 1 chr5A.!!$R2 555

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
192 193 1.133136 AGGGGGCGATGTAGATACACT 60.133 52.381 0.0 0.0 39.3 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 4043 0.034896 CTGTGAACAACTAGGGCCGT 59.965 55.0 2.24 2.24 0.0 5.68 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
24 25 1.152881 GGCTACCAAGGGGCATCTG 60.153 63.158 8.19 0.00 37.90 2.90
31 32 1.379576 AAGGGGCATCTGCAGAAGC 60.380 57.895 30.78 30.78 44.36 3.86
58 59 2.707849 CCAGCAAGGCAGCCATGTC 61.708 63.158 17.89 10.23 34.23 3.06
105 106 2.044650 CACCTCTGGCACATGGGG 60.045 66.667 0.00 0.00 38.20 4.96
192 193 1.133136 AGGGGGCGATGTAGATACACT 60.133 52.381 0.00 0.00 39.30 3.55
318 319 4.380531 TCAAGTCAGAATGTTCAGTGTCC 58.619 43.478 0.00 0.00 37.40 4.02
581 582 5.418310 ACTTATAAATTGTCCGAATGCCG 57.582 39.130 0.00 0.00 38.18 5.69
622 623 5.275263 TCCTGGAAATGGAAGAGGAAAAT 57.725 39.130 0.00 0.00 29.62 1.82
679 681 5.833131 TGGTCTGAAAGGAACAAAGCTAATT 59.167 36.000 0.00 0.00 29.13 1.40
734 736 7.923344 AGTCATATACTCACTACAACTGCATTC 59.077 37.037 0.00 0.00 30.33 2.67
781 783 3.304659 GCGACAGGAGAAAAATTTGCAGA 60.305 43.478 0.00 0.00 0.00 4.26
980 3496 1.489649 AGCTCTTGCCATGCTCTATGT 59.510 47.619 0.00 0.00 40.80 2.29
1261 3777 5.952347 TCCACTTCCTAGGGATCTAAAAC 57.048 43.478 9.46 0.00 0.00 2.43
1321 3837 4.507756 GGAATGCTTTTGTGTTCCTTTCAC 59.492 41.667 0.00 0.00 37.67 3.18
1323 3839 3.843999 TGCTTTTGTGTTCCTTTCACAC 58.156 40.909 0.00 0.00 43.95 3.82
1347 3863 0.400213 AAAATCTCGGTGGCAGTGGA 59.600 50.000 0.00 0.00 0.00 4.02
1372 3889 1.613437 AGCATCGTCAACTTTTTGGGG 59.387 47.619 0.00 0.00 33.06 4.96
1397 3914 2.228480 TTGTGGAGCCCAGGTACCC 61.228 63.158 8.74 0.00 32.34 3.69
1400 3917 2.369001 GGAGCCCAGGTACCCTCT 59.631 66.667 8.74 0.00 0.00 3.69
1420 3937 4.388229 CCATACCGTGTTGGCACA 57.612 55.556 0.00 0.00 45.50 4.57
1425 3942 1.570347 TACCGTGTTGGCACATTCGC 61.570 55.000 0.00 0.00 45.50 4.70
1443 3960 1.014352 GCGCGAGTTTGGATTATGGT 58.986 50.000 12.10 0.00 0.00 3.55
1453 3970 5.123979 AGTTTGGATTATGGTTCGAAGCTTC 59.876 40.000 26.05 16.84 0.00 3.86
1454 3971 4.487714 TGGATTATGGTTCGAAGCTTCT 57.512 40.909 26.05 14.11 0.00 2.85
1455 3972 4.843728 TGGATTATGGTTCGAAGCTTCTT 58.156 39.130 26.05 12.02 0.00 2.52
1498 4018 2.303600 TCGCTTGCCTCCTACCTTTTTA 59.696 45.455 0.00 0.00 0.00 1.52
1518 4038 7.956420 TTTTACACGTGACTTCATTATCACT 57.044 32.000 25.01 0.00 42.56 3.41
1523 4043 4.021456 ACGTGACTTCATTATCACTGTCCA 60.021 41.667 0.00 0.00 42.56 4.02
1527 4047 2.309528 TCATTATCACTGTCCACGGC 57.690 50.000 0.00 0.00 0.00 5.68
1539 4059 1.122632 TCCACGGCCCTAGTTGTTCA 61.123 55.000 0.00 0.00 0.00 3.18
1551 4071 1.421268 AGTTGTTCACAGGCTGGATCA 59.579 47.619 20.34 14.42 0.00 2.92
1556 4076 1.059098 TCACAGGCTGGATCAACACT 58.941 50.000 20.34 0.00 0.00 3.55
1612 4132 2.594592 GGCGGCAGTTTGGTGAGT 60.595 61.111 3.07 0.00 0.00 3.41
1615 4135 1.893808 CGGCAGTTTGGTGAGTGCT 60.894 57.895 4.88 0.00 43.78 4.40
1658 4178 2.158957 TCTCAAGAAGGTGTGCTTTCGT 60.159 45.455 0.00 0.00 36.05 3.85
1963 4492 5.977725 GCAAAGTTTTCCCTCAGTTAAGAAC 59.022 40.000 0.00 0.00 0.00 3.01
1975 4504 6.092259 CCTCAGTTAAGAACCAAGGTTTATCG 59.908 42.308 5.87 0.00 38.60 2.92
1976 4505 6.761312 TCAGTTAAGAACCAAGGTTTATCGA 58.239 36.000 5.87 0.00 38.60 3.59
1991 4520 6.039605 AGGTTTATCGAACTAGTAGGAGCTTC 59.960 42.308 0.00 0.00 38.35 3.86
1992 4521 6.207928 GTTTATCGAACTAGTAGGAGCTTCC 58.792 44.000 0.00 0.00 35.31 3.46
1996 4525 4.710375 TCGAACTAGTAGGAGCTTCCAAAT 59.290 41.667 0.00 0.00 39.61 2.32
2011 4540 8.230472 AGCTTCCAAATTATCCAGATAAACAG 57.770 34.615 4.30 0.00 36.90 3.16
2012 4541 6.920210 GCTTCCAAATTATCCAGATAAACAGC 59.080 38.462 4.30 3.32 36.90 4.40
2016 4545 8.271458 TCCAAATTATCCAGATAAACAGCACTA 58.729 33.333 4.30 0.00 36.90 2.74
2052 4581 7.833285 AAATAAAAACCAGTAGGAGCTTTCA 57.167 32.000 0.00 0.00 38.69 2.69
2057 4586 3.623284 ACCAGTAGGAGCTTTCAAGCCA 61.623 50.000 7.95 0.00 45.38 4.75
2058 4587 5.091646 ACCAGTAGGAGCTTTCAAGCCAA 62.092 47.826 7.95 0.00 45.38 4.52
2069 4598 5.410067 GCTTTCAAGCCAATTGTATTGCTA 58.590 37.500 12.67 3.90 46.20 3.49
2077 4606 7.088589 AGCCAATTGTATTGCTAGTTACAAG 57.911 36.000 4.43 7.72 40.53 3.16
2080 4609 8.190784 GCCAATTGTATTGCTAGTTACAAGATT 58.809 33.333 4.43 7.63 40.53 2.40
2141 4670 8.090214 AGCAGCAAATAAAAAGAGCATTTTCTA 58.910 29.630 0.00 0.00 34.51 2.10
2197 4726 1.486310 CCATAGGCTCACTAGTGGCAA 59.514 52.381 26.96 18.80 36.39 4.52
2232 4761 1.102978 AGGCGAATGGCATGGTAAAC 58.897 50.000 0.00 0.00 46.16 2.01
2244 4773 9.950496 AATGGCATGGTAAACAAATTACAATTA 57.050 25.926 0.00 0.00 44.77 1.40
2246 4775 9.950496 TGGCATGGTAAACAAATTACAATTATT 57.050 25.926 0.00 0.00 44.77 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.009829 CTGGGATGTTACGCTTCTGC 58.990 55.000 0.00 0.00 0.00 4.26
31 32 0.676466 TGCCTTGCTGGGATGTTACG 60.676 55.000 0.00 0.00 36.00 3.18
58 59 9.219603 TCAATCAAGTCTGAAACCTTAGTAATG 57.780 33.333 0.00 0.00 34.49 1.90
105 106 5.941948 AGTTTGTTGGAGCAGTTGTATAC 57.058 39.130 0.00 0.00 0.00 1.47
180 181 3.576861 TGCCAGGCTAGTGTATCTACAT 58.423 45.455 14.15 0.00 38.63 2.29
192 193 4.502950 CCTTTTTGTCAAAATGCCAGGCTA 60.503 41.667 14.15 0.00 31.28 3.93
452 453 0.179084 AGTCGGTGGCATATTGGACG 60.179 55.000 0.00 0.00 0.00 4.79
581 582 2.482142 GGATGTCCTCCATTGTCGAGAC 60.482 54.545 0.00 0.00 44.26 3.36
622 623 6.596888 CACAAGAGGATGCAGATCTTTAGAAA 59.403 38.462 7.83 0.00 30.99 2.52
679 681 5.030147 TGCAGTCCTAATCCTTTCTCCTTA 58.970 41.667 0.00 0.00 0.00 2.69
781 783 1.618343 GTGCCAAACCTGGTTTATGCT 59.382 47.619 30.05 10.23 45.53 3.79
980 3496 2.542020 TCTTGACGCCTCATTCACAA 57.458 45.000 0.00 0.00 0.00 3.33
1214 3730 4.280819 GAGCCATATCTGATAGCTCCTCT 58.719 47.826 20.17 6.19 43.27 3.69
1255 3771 2.218603 ACCAGCGACAAGGTGTTTTAG 58.781 47.619 0.00 0.00 46.29 1.85
1329 3845 0.036010 CTCCACTGCCACCGAGATTT 60.036 55.000 0.00 0.00 0.00 2.17
1330 3846 1.194781 ACTCCACTGCCACCGAGATT 61.195 55.000 0.00 0.00 0.00 2.40
1331 3847 1.610673 ACTCCACTGCCACCGAGAT 60.611 57.895 0.00 0.00 0.00 2.75
1338 3854 0.250234 GATGCTACACTCCACTGCCA 59.750 55.000 0.00 0.00 0.00 4.92
1347 3863 4.024048 CCAAAAAGTTGACGATGCTACACT 60.024 41.667 0.00 0.00 36.83 3.55
1372 3889 1.507141 CTGGGCTCCACAACGACAAC 61.507 60.000 0.00 0.00 0.00 3.32
1397 3914 0.744414 CCAACACGGTATGGCCAGAG 60.744 60.000 13.05 4.69 36.97 3.35
1419 3936 0.096976 AATCCAAACTCGCGCGAATG 59.903 50.000 33.99 28.41 0.00 2.67
1420 3937 1.647346 TAATCCAAACTCGCGCGAAT 58.353 45.000 33.99 23.27 0.00 3.34
1425 3942 2.285602 CGAACCATAATCCAAACTCGCG 60.286 50.000 0.00 0.00 0.00 5.87
1443 3960 0.603569 AGAGGCGAAGAAGCTTCGAA 59.396 50.000 27.60 0.00 46.17 3.71
1453 3970 1.669115 CACCACACCAGAGGCGAAG 60.669 63.158 0.00 0.00 0.00 3.79
1454 3971 2.425592 CACCACACCAGAGGCGAA 59.574 61.111 0.00 0.00 0.00 4.70
1455 3972 4.314440 GCACCACACCAGAGGCGA 62.314 66.667 0.00 0.00 0.00 5.54
1518 4038 1.412453 AACAACTAGGGCCGTGGACA 61.412 55.000 16.40 0.00 0.00 4.02
1523 4043 0.034896 CTGTGAACAACTAGGGCCGT 59.965 55.000 2.24 2.24 0.00 5.68
1527 4047 1.611673 CCAGCCTGTGAACAACTAGGG 60.612 57.143 0.00 0.00 31.41 3.53
1539 4059 0.326264 GGAGTGTTGATCCAGCCTGT 59.674 55.000 0.00 0.00 36.79 4.00
1594 4114 2.594303 CTCACCAAACTGCCGCCA 60.594 61.111 0.00 0.00 0.00 5.69
1612 4132 1.229975 CCAGACATCGTTGCACAGCA 61.230 55.000 0.00 0.00 36.47 4.41
1615 4135 0.179059 ACACCAGACATCGTTGCACA 60.179 50.000 0.00 0.00 0.00 4.57
1658 4178 0.530744 CCAAGATCACCGACGAGGAA 59.469 55.000 8.56 0.00 45.00 3.36
1814 4334 5.404466 AATCTATGGCATCTGCTAGAGTC 57.596 43.478 1.65 0.00 40.91 3.36
1921 4450 2.752030 TGCTGCTATCTACTCACCCTT 58.248 47.619 0.00 0.00 0.00 3.95
1963 4492 6.461110 TCCTACTAGTTCGATAAACCTTGG 57.539 41.667 0.00 0.00 38.76 3.61
1975 4504 7.658167 GGATAATTTGGAAGCTCCTACTAGTTC 59.342 40.741 0.00 0.00 37.46 3.01
1976 4505 7.127339 TGGATAATTTGGAAGCTCCTACTAGTT 59.873 37.037 0.00 0.00 37.46 2.24
1991 4520 7.338800 AGTGCTGTTTATCTGGATAATTTGG 57.661 36.000 4.20 0.00 33.71 3.28
1992 4521 8.072567 GCTAGTGCTGTTTATCTGGATAATTTG 58.927 37.037 4.20 0.46 33.42 2.32
1996 4525 6.049149 GTGCTAGTGCTGTTTATCTGGATAA 58.951 40.000 0.00 0.00 40.48 1.75
2011 4540 6.820470 TTTATTTTGTTTGTGTGCTAGTGC 57.180 33.333 0.00 0.00 40.20 4.40
2012 4541 8.113675 GGTTTTTATTTTGTTTGTGTGCTAGTG 58.886 33.333 0.00 0.00 0.00 2.74
2016 4545 6.652900 ACTGGTTTTTATTTTGTTTGTGTGCT 59.347 30.769 0.00 0.00 0.00 4.40
2052 4581 7.393234 TCTTGTAACTAGCAATACAATTGGCTT 59.607 33.333 10.83 0.00 40.23 4.35
2164 4693 1.229529 CTATGGCCCCGGGGTCTAT 60.230 63.158 42.66 33.72 41.25 1.98
2190 4719 1.621992 TTCGAGAGAGAGTTGCCACT 58.378 50.000 0.00 0.00 43.69 4.00
2197 4726 0.530288 GCCTGCTTTCGAGAGAGAGT 59.470 55.000 7.23 0.00 43.69 3.24


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

AutoCloner maintained by Alex Coulton.