Multiple sequence alignment - TraesCS3D01G073500

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 TraesCS3D01G073500 chr3D 100.000 4970 0 0 1 4970 33357910 33352941 0.000000e+00 9178.0
1 TraesCS3D01G073500 chr3D 90.003 3331 300 19 928 4240 33374805 33371490 0.000000e+00 4276.0
2 TraesCS3D01G073500 chr3D 84.326 3241 448 35 827 4032 33335765 33332550 0.000000e+00 3116.0
3 TraesCS3D01G073500 chr3A 94.276 3267 170 8 777 4032 46009743 46006483 0.000000e+00 4981.0
4 TraesCS3D01G073500 chr3A 89.496 3332 314 21 928 4240 46026361 46023047 0.000000e+00 4181.0
5 TraesCS3D01G073500 chr3A 83.947 760 58 23 37 763 46010599 46009871 0.000000e+00 669.0
6 TraesCS3D01G073500 chr3A 78.049 984 172 23 3071 4032 45940609 45939648 9.270000e-162 580.0
7 TraesCS3D01G073500 chr3A 87.613 444 55 0 1106 1549 45941053 45940610 2.650000e-142 516.0
8 TraesCS3D01G073500 chr3A 93.258 178 11 1 4261 4438 46006048 46005872 1.370000e-65 261.0
9 TraesCS3D01G073500 chr3A 97.368 38 1 0 686 723 46010661 46010624 1.150000e-06 65.8
10 TraesCS3D01G073500 chr3B 89.823 3331 307 19 928 4240 56131767 56128451 0.000000e+00 4244.0
11 TraesCS3D01G073500 chr3B 97.176 2302 60 3 2670 4970 56077957 56075660 0.000000e+00 3886.0
12 TraesCS3D01G073500 chr3B 98.151 1839 34 0 846 2684 56080123 56078285 0.000000e+00 3208.0
13 TraesCS3D01G073500 chr3B 84.173 3216 458 31 827 4016 56071285 56068095 0.000000e+00 3072.0
14 TraesCS3D01G073500 chr3B 96.691 544 18 0 222 765 56080970 56080427 0.000000e+00 905.0
15 TraesCS3D01G073500 chr3B 97.807 228 5 0 1 228 56086263 56086036 1.300000e-105 394.0


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 TraesCS3D01G073500 chr3D 33352941 33357910 4969 True 9178.000000 9178 100.000000 1 4970 1 chr3D.!!$R2 4969
1 TraesCS3D01G073500 chr3D 33371490 33374805 3315 True 4276.000000 4276 90.003000 928 4240 1 chr3D.!!$R3 3312
2 TraesCS3D01G073500 chr3D 33332550 33335765 3215 True 3116.000000 3116 84.326000 827 4032 1 chr3D.!!$R1 3205
3 TraesCS3D01G073500 chr3A 46023047 46026361 3314 True 4181.000000 4181 89.496000 928 4240 1 chr3A.!!$R1 3312
4 TraesCS3D01G073500 chr3A 46005872 46010661 4789 True 1494.200000 4981 92.212250 37 4438 4 chr3A.!!$R3 4401
5 TraesCS3D01G073500 chr3A 45939648 45941053 1405 True 548.000000 580 82.831000 1106 4032 2 chr3A.!!$R2 2926
6 TraesCS3D01G073500 chr3B 56128451 56131767 3316 True 4244.000000 4244 89.823000 928 4240 1 chr3B.!!$R3 3312
7 TraesCS3D01G073500 chr3B 56068095 56071285 3190 True 3072.000000 3072 84.173000 827 4016 1 chr3B.!!$R1 3189
8 TraesCS3D01G073500 chr3B 56075660 56080970 5310 True 2666.333333 3886 97.339333 222 4970 3 chr3B.!!$R4 4748

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
60 87 0.733150 GGGTTCCACGCTTTCTATGC 59.267 55.000 0.0 0.0 0.00 3.14 F
61 88 0.733150 GGTTCCACGCTTTCTATGCC 59.267 55.000 0.0 0.0 0.00 4.40 F
359 409 0.771127 CTGGTCTTCCCACCTTCCAA 59.229 55.000 0.0 0.0 38.72 3.53 F
843 1027 1.269257 GGGTTCTTGAGCTTGTTGTGC 60.269 52.381 0.0 0.0 0.00 4.57 F
2416 2704 2.961526 TCTTCTGCAACCGATACCTC 57.038 50.000 0.0 0.0 0.00 3.85 F
2676 2972 2.032204 CAGAAAGCTTGAGCATATCCGC 60.032 50.000 0.0 0.0 45.16 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1036 1324 2.358737 CCGACCCAGCCTTGTCAC 60.359 66.667 0.00 0.00 0.00 3.67 R
1761 2049 3.487120 AAAAGTGGTAGAAGCTCGGTT 57.513 42.857 0.00 0.00 0.00 4.44 R
1990 2278 7.448161 TGATTGAAAGGACTTCTTCATAAGCAA 59.552 33.333 0.00 0.00 33.94 3.91 R
2676 2972 0.679505 TCCCACTGAGAACCAAGACG 59.320 55.000 0.00 0.00 0.00 4.18 R
3237 3881 1.222661 GAACCTTACGCCCGGGAAT 59.777 57.895 29.31 14.26 0.00 3.01 R
4091 4953 1.636148 TTACACCCCGCTCTTGTACT 58.364 50.000 0.00 0.00 0.00 2.73 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
29 30 9.638239 GTATGACCTTCTTTCATTAAAAATGCA 57.362 29.630 0.00 0.00 35.31 3.96
30 31 8.767478 ATGACCTTCTTTCATTAAAAATGCAG 57.233 30.769 0.00 0.00 28.83 4.41
32 33 8.855110 TGACCTTCTTTCATTAAAAATGCAGTA 58.145 29.630 0.00 0.00 0.00 2.74
33 34 9.129209 GACCTTCTTTCATTAAAAATGCAGTAC 57.871 33.333 0.00 0.00 0.00 2.73
34 35 8.860088 ACCTTCTTTCATTAAAAATGCAGTACT 58.140 29.630 0.00 0.00 0.00 2.73
57 84 1.344065 TCTGGGTTCCACGCTTTCTA 58.656 50.000 0.00 0.00 31.67 2.10
59 86 2.009774 CTGGGTTCCACGCTTTCTATG 58.990 52.381 0.00 0.00 31.67 2.23
60 87 0.733150 GGGTTCCACGCTTTCTATGC 59.267 55.000 0.00 0.00 0.00 3.14
61 88 0.733150 GGTTCCACGCTTTCTATGCC 59.267 55.000 0.00 0.00 0.00 4.40
81 108 4.451774 TGCCTTTGCTTATGAATTGTTTGC 59.548 37.500 0.00 0.00 38.71 3.68
84 111 5.927689 CCTTTGCTTATGAATTGTTTGCTGA 59.072 36.000 0.00 0.00 0.00 4.26
88 115 7.354025 TGCTTATGAATTGTTTGCTGAAATG 57.646 32.000 0.00 0.00 0.00 2.32
89 116 6.930164 TGCTTATGAATTGTTTGCTGAAATGT 59.070 30.769 0.00 0.00 0.00 2.71
94 121 5.754406 TGAATTGTTTGCTGAAATGTCCAAG 59.246 36.000 0.00 0.00 0.00 3.61
107 134 6.319911 TGAAATGTCCAAGTAAACATGTGTGA 59.680 34.615 0.00 0.00 36.28 3.58
108 135 6.707440 AATGTCCAAGTAAACATGTGTGAA 57.293 33.333 0.00 0.00 36.28 3.18
157 185 1.557099 AGTCTCTGGCGTATGGTTCA 58.443 50.000 0.00 0.00 0.00 3.18
171 218 4.630644 ATGGTTCAGAGAAAGAGCTTCA 57.369 40.909 0.00 0.00 36.40 3.02
183 230 6.000219 AGAAAGAGCTTCAAACTTGCAGATA 59.000 36.000 0.00 0.00 36.40 1.98
189 236 5.098211 GCTTCAAACTTGCAGATATGGAAC 58.902 41.667 0.00 0.00 0.00 3.62
194 241 4.574674 ACTTGCAGATATGGAACCTCAA 57.425 40.909 0.00 0.00 0.00 3.02
250 297 3.365265 CCTTGCAAGTGGGACGGC 61.365 66.667 24.35 0.00 0.00 5.68
274 322 5.577945 CGGGATGGAAAATGAAACAAAGATG 59.422 40.000 0.00 0.00 0.00 2.90
359 409 0.771127 CTGGTCTTCCCACCTTCCAA 59.229 55.000 0.00 0.00 38.72 3.53
484 534 4.098654 GTCAAAGCTGCTCCTCTATACTGA 59.901 45.833 1.00 0.00 0.00 3.41
629 687 1.691434 TGGCTTCAACCACAAAATCCC 59.309 47.619 0.00 0.00 33.75 3.85
746 804 4.032104 GCAAACTTCTGTGTTGCTTCTTTG 59.968 41.667 0.53 0.00 0.00 2.77
749 807 4.986622 ACTTCTGTGTTGCTTCTTTGAAC 58.013 39.130 0.00 0.00 0.00 3.18
810 987 6.327177 TCTTGTACGAATTTATGTCTTCGC 57.673 37.500 4.75 0.00 46.11 4.70
811 988 6.097356 TCTTGTACGAATTTATGTCTTCGCT 58.903 36.000 4.75 0.00 46.11 4.93
814 991 2.936498 ACGAATTTATGTCTTCGCTGGG 59.064 45.455 4.75 0.00 46.11 4.45
843 1027 1.269257 GGGTTCTTGAGCTTGTTGTGC 60.269 52.381 0.00 0.00 0.00 4.57
1036 1324 4.154737 TGGATGCTCTCACTTCGAAATTTG 59.845 41.667 0.00 0.00 0.00 2.32
1074 1362 5.755375 TCGGCTTATTGAAGATGAGATTGTC 59.245 40.000 0.00 0.00 34.25 3.18
1626 1914 4.489810 AGACAACGTTAGCTCAGAAGATG 58.510 43.478 0.00 0.00 0.00 2.90
1761 2049 3.834813 AGTGTGATCAGCTAGAGACCAAA 59.165 43.478 0.00 0.00 0.00 3.28
1990 2278 8.757982 AATGAATTACAGTGATGGCTTAGAAT 57.242 30.769 0.00 0.00 0.00 2.40
2050 2338 9.768662 AAATATGTGAATTCAAGAATATTGGCC 57.231 29.630 21.41 0.00 0.00 5.36
2360 2648 5.124457 AGCATGACCACTCAATACATGAAAC 59.876 40.000 0.00 0.00 40.13 2.78
2416 2704 2.961526 TCTTCTGCAACCGATACCTC 57.038 50.000 0.00 0.00 0.00 3.85
2676 2972 2.032204 CAGAAAGCTTGAGCATATCCGC 60.032 50.000 0.00 0.00 45.16 5.54
3629 4276 0.246086 AAACTGAGAGCTCTGCCTCG 59.754 55.000 23.91 6.86 36.95 4.63
3646 4293 4.122776 GCCTCGAGACATGTACATGATTT 58.877 43.478 36.36 22.31 41.20 2.17
3682 4329 0.518636 CCACATTGAAGGTGCTCACG 59.481 55.000 4.19 0.00 34.94 4.35
4002 4670 7.327032 CAGTGAAATAGCTAAGAAAAACTTGCC 59.673 37.037 0.00 0.00 39.38 4.52
4091 4953 1.970640 TGCTCTTCTCACAGGCTTACA 59.029 47.619 0.00 0.00 0.00 2.41
4106 4968 1.549170 CTTACAGTACAAGAGCGGGGT 59.451 52.381 0.00 0.00 0.00 4.95
4118 4980 0.108329 AGCGGGGTGTAATGAAGACG 60.108 55.000 0.00 0.00 0.00 4.18
4204 5073 2.576615 GGCAATGGGAGGTATCTGTTC 58.423 52.381 0.00 0.00 0.00 3.18
4247 5116 7.770801 ATGTTGTTGCTTTTTCTACCTTTTC 57.229 32.000 0.00 0.00 0.00 2.29
4444 5354 4.562143 GGTGTAACTATGGTTGGTTCTCGT 60.562 45.833 4.47 0.00 36.92 4.18
4445 5355 4.387862 GTGTAACTATGGTTGGTTCTCGTG 59.612 45.833 4.47 0.00 36.92 4.35
4533 5443 3.005367 TGCTTAACCTGTTTGCTTAAGCC 59.995 43.478 24.30 9.95 46.29 4.35
4576 5486 0.685785 TGTTTTTGGGCAGGCACTCA 60.686 50.000 0.00 0.00 34.60 3.41
4590 5500 5.535333 CAGGCACTCATCTGAATTTTGTTT 58.465 37.500 0.00 0.00 34.60 2.83
4694 5604 7.422878 ACTTAGACCTCTTCGATTCAAAAAC 57.577 36.000 0.00 0.00 0.00 2.43
4837 5748 9.778741 ATTTTAAAAATTCTTCCAAGAGGTTCC 57.221 29.630 4.44 0.00 36.22 3.62
4851 5762 5.669164 AGAGGTTCCTGTGATAGAAGTTC 57.331 43.478 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.725251 ACTGCATTTTTAATGAAAGAAGGTCA 58.275 30.769 3.70 0.00 0.00 4.02
7 8 9.129209 GTACTGCATTTTTAATGAAAGAAGGTC 57.871 33.333 3.70 0.00 0.00 3.85
19 20 9.914834 AACCCAGATATAGTACTGCATTTTTAA 57.085 29.630 5.39 0.00 33.40 1.52
20 21 9.555727 GAACCCAGATATAGTACTGCATTTTTA 57.444 33.333 5.39 0.00 33.40 1.52
21 22 7.502561 GGAACCCAGATATAGTACTGCATTTTT 59.497 37.037 5.39 0.00 33.40 1.94
22 23 6.998673 GGAACCCAGATATAGTACTGCATTTT 59.001 38.462 5.39 0.00 33.40 1.82
23 24 6.101150 TGGAACCCAGATATAGTACTGCATTT 59.899 38.462 5.39 0.00 33.40 2.32
24 25 5.606749 TGGAACCCAGATATAGTACTGCATT 59.393 40.000 5.39 0.00 33.40 3.56
27 28 4.558898 CGTGGAACCCAGATATAGTACTGC 60.559 50.000 5.39 0.00 32.34 4.40
29 30 3.573110 GCGTGGAACCCAGATATAGTACT 59.427 47.826 0.00 0.00 32.34 2.73
30 31 3.573110 AGCGTGGAACCCAGATATAGTAC 59.427 47.826 0.00 0.00 32.34 2.73
32 33 2.679082 AGCGTGGAACCCAGATATAGT 58.321 47.619 0.00 0.00 32.34 2.12
33 34 3.753294 AAGCGTGGAACCCAGATATAG 57.247 47.619 0.00 0.00 32.34 1.31
34 35 3.709653 AGAAAGCGTGGAACCCAGATATA 59.290 43.478 0.00 0.00 32.34 0.86
36 37 1.906574 AGAAAGCGTGGAACCCAGATA 59.093 47.619 0.00 0.00 32.34 1.98
37 38 0.693049 AGAAAGCGTGGAACCCAGAT 59.307 50.000 0.00 0.00 32.34 2.90
39 40 2.009774 CATAGAAAGCGTGGAACCCAG 58.990 52.381 0.00 0.00 32.34 4.45
40 41 1.948611 GCATAGAAAGCGTGGAACCCA 60.949 52.381 0.00 0.00 0.00 4.51
57 84 5.122711 GCAAACAATTCATAAGCAAAGGCAT 59.877 36.000 0.00 0.00 44.61 4.40
59 86 4.692155 AGCAAACAATTCATAAGCAAAGGC 59.308 37.500 0.00 0.00 41.61 4.35
60 87 5.927689 TCAGCAAACAATTCATAAGCAAAGG 59.072 36.000 0.00 0.00 0.00 3.11
61 88 7.410800 TTCAGCAAACAATTCATAAGCAAAG 57.589 32.000 0.00 0.00 0.00 2.77
81 108 6.638063 CACACATGTTTACTTGGACATTTCAG 59.362 38.462 0.00 0.00 34.42 3.02
84 111 6.707440 TCACACATGTTTACTTGGACATTT 57.293 33.333 0.00 0.00 34.42 2.32
88 115 8.419076 AAAAATTCACACATGTTTACTTGGAC 57.581 30.769 0.00 0.00 0.00 4.02
119 146 4.946157 AGACTTCAACCAGGAGCAAATATG 59.054 41.667 0.00 0.00 0.00 1.78
132 160 2.271800 CATACGCCAGAGACTTCAACC 58.728 52.381 0.00 0.00 0.00 3.77
157 185 4.202441 TGCAAGTTTGAAGCTCTTTCTCT 58.798 39.130 0.00 0.00 36.71 3.10
171 218 4.922206 TGAGGTTCCATATCTGCAAGTTT 58.078 39.130 0.00 0.00 33.76 2.66
183 230 9.933723 CTTTTCTTGATTTTATTGAGGTTCCAT 57.066 29.630 0.00 0.00 0.00 3.41
205 252 9.674068 GAAGACCTTTTCAGTATCTATCCTTTT 57.326 33.333 0.00 0.00 0.00 2.27
250 297 5.132897 TCTTTGTTTCATTTTCCATCCCG 57.867 39.130 0.00 0.00 0.00 5.14
274 322 5.163513 CCTGTCATAGCCACAATCAAAAAC 58.836 41.667 0.00 0.00 0.00 2.43
276 324 3.763360 CCCTGTCATAGCCACAATCAAAA 59.237 43.478 0.00 0.00 0.00 2.44
359 409 4.098960 CACCTCATGGCTGCTTCATTTATT 59.901 41.667 0.00 0.00 36.63 1.40
484 534 5.398012 GGGGATAAAAGAAGCAGTCATACCT 60.398 44.000 0.00 0.00 0.00 3.08
588 646 2.158957 ACGATCAGTTGTGGTCTTGTGT 60.159 45.455 0.00 0.00 30.73 3.72
629 687 3.958147 ATGACGGCGGCACTTCCTG 62.958 63.158 22.09 0.00 0.00 3.86
643 701 1.068748 CAAAGGAGCACAGCACATGAC 60.069 52.381 0.00 0.00 0.00 3.06
746 804 8.329203 ACTCTAGTTGAAAAATCAGGATGTTC 57.671 34.615 0.00 0.00 37.40 3.18
1036 1324 2.358737 CCGACCCAGCCTTGTCAC 60.359 66.667 0.00 0.00 0.00 3.67
1656 1944 4.779696 TGCACAGCCATATATGAACTTGA 58.220 39.130 14.54 0.00 0.00 3.02
1761 2049 3.487120 AAAAGTGGTAGAAGCTCGGTT 57.513 42.857 0.00 0.00 0.00 4.44
1990 2278 7.448161 TGATTGAAAGGACTTCTTCATAAGCAA 59.552 33.333 0.00 0.00 33.94 3.91
2050 2338 8.030692 ACCATCACATTTCTTTACAATGTCATG 58.969 33.333 3.44 3.44 41.91 3.07
2360 2648 4.808364 GCTCAAGGTAATACTCTTCAGCAG 59.192 45.833 10.71 0.00 37.13 4.24
2416 2704 7.441157 TGTTGACTCACCTTTATCTACAAACAG 59.559 37.037 0.00 0.00 0.00 3.16
2676 2972 0.679505 TCCCACTGAGAACCAAGACG 59.320 55.000 0.00 0.00 0.00 4.18
3237 3881 1.222661 GAACCTTACGCCCGGGAAT 59.777 57.895 29.31 14.26 0.00 3.01
3629 4276 9.844790 TCAAATTGAAAATCATGTACATGTCTC 57.155 29.630 30.03 21.80 39.72 3.36
3646 4293 8.180706 TCAATGTGGATTCTCTTCAAATTGAA 57.819 30.769 8.25 8.25 40.25 2.69
3682 4329 5.876612 AGATTGACAACTTCATGAAGCTC 57.123 39.130 30.95 22.68 41.99 4.09
4002 4670 9.383519 TCAGAATAATAAAGCAGTAGAAACAGG 57.616 33.333 0.00 0.00 0.00 4.00
4091 4953 1.636148 TTACACCCCGCTCTTGTACT 58.364 50.000 0.00 0.00 0.00 2.73
4106 4968 4.868171 GCTAACCATCACGTCTTCATTACA 59.132 41.667 0.00 0.00 0.00 2.41
4118 4980 5.810587 TCGAGTATTTTCAGCTAACCATCAC 59.189 40.000 0.00 0.00 0.00 3.06
4204 5073 3.436704 ACATTACACTCCAGCATTTGACG 59.563 43.478 0.00 0.00 0.00 4.35
4247 5116 2.358898 CTGTCAACCACACCAAAAGGAG 59.641 50.000 0.00 0.00 0.00 3.69
4533 5443 4.219288 AGAATTAAAAAGGTGCAGCTCCAG 59.781 41.667 20.46 0.00 0.00 3.86
4576 5486 6.282930 CACAAGTCCCAAACAAAATTCAGAT 58.717 36.000 0.00 0.00 0.00 2.90
4590 5500 5.949354 CCAAAGATAATAACCACAAGTCCCA 59.051 40.000 0.00 0.00 0.00 4.37
4820 5731 3.652869 TCACAGGAACCTCTTGGAAGAAT 59.347 43.478 0.00 0.00 34.03 2.40


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

AutoCloner maintained by Alex Coulton.