Multiple sequence alignment - TraesCS4A01G015300

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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 TraesCS4A01G015300 chr4A 100.000 1895 0 0 1 1895 9554089 9555983 0.000000e+00 3500
1 TraesCS4A01G015300 chr4A 100.000 385 0 0 2174 2558 9556262 9556646 0.000000e+00 712
2 TraesCS4A01G015300 chr4B 93.838 714 33 4 1182 1889 573403417 573402709 0.000000e+00 1064
3 TraesCS4A01G015300 chr4B 90.735 680 25 10 1 656 573404999 573404334 0.000000e+00 872
4 TraesCS4A01G015300 chr4B 86.774 620 47 8 649 1268 573403954 573403370 0.000000e+00 658
5 TraesCS4A01G015300 chr4B 89.351 385 34 4 2181 2558 573402428 573402044 6.400000e-131 477
6 TraesCS4A01G015300 chr4D 91.377 661 26 12 1208 1847 459255735 459255085 0.000000e+00 876
7 TraesCS4A01G015300 chr4D 78.612 533 41 30 244 755 459258244 459257764 4.170000e-73 285
8 TraesCS4A01G015300 chr4D 85.657 251 14 7 8 253 459259277 459259044 7.070000e-61 244
9 TraesCS4A01G015300 chr2D 81.967 122 18 4 2313 2430 600073227 600073106 1.620000e-17 100


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 TraesCS4A01G015300 chr4A 9554089 9556646 2557 False 2106.000000 3500 100.000000 1 2558 2 chr4A.!!$F1 2557
1 TraesCS4A01G015300 chr4B 573402044 573404999 2955 True 767.750000 1064 90.174500 1 2558 4 chr4B.!!$R1 2557
2 TraesCS4A01G015300 chr4D 459255085 459259277 4192 True 468.333333 876 85.215333 8 1847 3 chr4D.!!$R1 1839

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
490 1334 0.181587 CGTGGTGGCATATGGGGTAA 59.818 55.0 4.56 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 4729 0.035056 AGCCTGGTAGATGGTGCAAC 60.035 55.0 0.0 0.0 0.0 4.17 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
95 101 1.594862 CGTGATGGCTTCCTCGAAATC 59.405 52.381 8.54 0.00 0.00 2.17
97 103 3.009723 GTGATGGCTTCCTCGAAATCAA 58.990 45.455 0.00 0.00 0.00 2.57
98 104 3.440173 GTGATGGCTTCCTCGAAATCAAA 59.560 43.478 0.00 0.00 0.00 2.69
99 105 4.078537 TGATGGCTTCCTCGAAATCAAAA 58.921 39.130 0.00 0.00 0.00 2.44
100 106 4.706476 TGATGGCTTCCTCGAAATCAAAAT 59.294 37.500 0.00 0.00 0.00 1.82
101 107 5.185635 TGATGGCTTCCTCGAAATCAAAATT 59.814 36.000 0.00 0.00 0.00 1.82
102 108 4.808558 TGGCTTCCTCGAAATCAAAATTG 58.191 39.130 0.00 0.00 0.00 2.32
199 208 8.677300 GTCTAATGCCAAAGTCAATGATCTTAA 58.323 33.333 0.00 0.00 0.00 1.85
239 248 3.322541 TCAGTTGTAACACCGAGATCCAA 59.677 43.478 0.00 0.00 0.00 3.53
274 1092 2.030540 CGACGGTGAGAAACTTAGGACA 60.031 50.000 0.00 0.00 0.00 4.02
287 1105 4.884247 ACTTAGGACAAGTAGTGTTCTGC 58.116 43.478 0.00 0.00 46.40 4.26
312 1132 1.227674 CCGGCCTTGATAGTGGAGC 60.228 63.158 0.00 0.00 0.00 4.70
328 1148 0.674895 GAGCCGACTTGCTTGGACAT 60.675 55.000 0.00 0.00 42.95 3.06
333 1153 1.462283 CGACTTGCTTGGACATGACAG 59.538 52.381 0.00 0.00 0.00 3.51
342 1162 0.321919 GGACATGACAGCCAAGCTCA 60.322 55.000 0.00 0.00 36.40 4.26
349 1169 2.093288 TGACAGCCAAGCTCAATCTAGG 60.093 50.000 0.00 0.00 36.40 3.02
350 1170 2.169352 GACAGCCAAGCTCAATCTAGGA 59.831 50.000 0.00 0.00 36.40 2.94
351 1171 2.093235 ACAGCCAAGCTCAATCTAGGAC 60.093 50.000 0.00 0.00 36.40 3.85
352 1172 2.170187 CAGCCAAGCTCAATCTAGGACT 59.830 50.000 0.00 0.00 36.40 3.85
353 1173 3.386078 CAGCCAAGCTCAATCTAGGACTA 59.614 47.826 0.00 0.00 36.40 2.59
354 1174 3.640967 AGCCAAGCTCAATCTAGGACTAG 59.359 47.826 0.00 0.00 30.62 2.57
409 1230 6.015688 CACTTGTACTAACTTACCACTCTCCA 60.016 42.308 0.00 0.00 0.00 3.86
419 1240 2.609747 ACCACTCTCCAGCTAAGTTGA 58.390 47.619 0.00 0.00 0.00 3.18
434 1255 2.277591 TTGATGGCCACCTTGCAGC 61.278 57.895 8.16 0.00 0.00 5.25
437 1258 2.833604 GATGGCCACCTTGCAGCTCT 62.834 60.000 8.16 0.00 0.00 4.09
490 1334 0.181587 CGTGGTGGCATATGGGGTAA 59.818 55.000 4.56 0.00 0.00 2.85
566 1410 3.917760 CGCCTCGATCCCACCTCC 61.918 72.222 0.00 0.00 0.00 4.30
569 1413 4.271816 CTCGATCCCACCTCCGCG 62.272 72.222 0.00 0.00 0.00 6.46
692 1932 5.826737 TGTACGTTTATCAAAAACTCCCCAA 59.173 36.000 0.00 0.00 0.00 4.12
703 1943 2.431954 ACTCCCCAATTGCAGAGATG 57.568 50.000 22.62 5.10 0.00 2.90
704 1944 1.030457 CTCCCCAATTGCAGAGATGC 58.970 55.000 14.61 0.00 0.00 3.91
733 1983 7.439356 CAGAGATCGATGTCCAAAAGCTAATTA 59.561 37.037 18.19 0.00 0.00 1.40
790 3717 1.248486 CCAGAGACACTCGAAGTCCA 58.752 55.000 12.56 0.00 36.68 4.02
815 3742 5.518847 CGTGTTCACTCATTGGTATTCGTAT 59.481 40.000 1.53 0.00 0.00 3.06
816 3743 6.693978 CGTGTTCACTCATTGGTATTCGTATA 59.306 38.462 1.53 0.00 0.00 1.47
817 3744 7.305820 CGTGTTCACTCATTGGTATTCGTATAC 60.306 40.741 3.75 3.75 36.66 1.47
818 3745 7.490079 GTGTTCACTCATTGGTATTCGTATACA 59.510 37.037 13.33 0.00 38.71 2.29
819 3746 8.201464 TGTTCACTCATTGGTATTCGTATACAT 58.799 33.333 13.33 0.00 38.71 2.29
820 3747 9.687210 GTTCACTCATTGGTATTCGTATACATA 57.313 33.333 13.33 2.11 38.71 2.29
948 3879 0.827368 AGCCCCTCTTTTCTAGCTCG 59.173 55.000 0.00 0.00 0.00 5.03
961 3892 4.137879 GCTCGAGCTACGGTAGGA 57.862 61.111 29.88 5.10 42.82 2.94
969 3900 0.953003 GCTACGGTAGGAGCTGTAGG 59.047 60.000 16.43 0.00 44.41 3.18
997 3928 2.435234 GCATCCACACGGCCGTAA 60.435 61.111 33.70 17.25 0.00 3.18
999 3930 2.125832 ATCCACACGGCCGTAACG 60.126 61.111 33.70 21.92 37.36 3.18
1000 3931 2.638354 ATCCACACGGCCGTAACGA 61.638 57.895 33.70 24.91 34.93 3.85
1010 3941 0.238817 GCCGTAACGATGCCAAACAA 59.761 50.000 0.00 0.00 0.00 2.83
1032 3963 3.799366 AGTCTACTCGATCGACATGAGT 58.201 45.455 15.15 12.75 44.63 3.41
1096 4027 3.282157 CCATCGCCCATGCCGAAG 61.282 66.667 10.12 6.54 38.31 3.79
1179 4110 4.974438 TCCCCACCGCCACCTTCT 62.974 66.667 0.00 0.00 0.00 2.85
1259 4223 2.203998 CTCCCCACCACCTCCACT 60.204 66.667 0.00 0.00 0.00 4.00
1714 4696 3.644884 TGTTGTTTGGTTGTTCGTGTT 57.355 38.095 0.00 0.00 0.00 3.32
1747 4729 4.665833 TTATCCATACTCAACTCACCCG 57.334 45.455 0.00 0.00 0.00 5.28
1760 4742 0.036765 TCACCCGTTGCACCATCTAC 60.037 55.000 0.00 0.00 0.00 2.59
1763 4745 0.744414 CCCGTTGCACCATCTACCAG 60.744 60.000 0.00 0.00 0.00 4.00
1799 4781 4.966850 ACTCAATCGTGTCTGTTTTACG 57.033 40.909 0.00 0.00 39.04 3.18
1865 4850 3.135712 TGTGGGTGCTTCTCTTTTGAGTA 59.864 43.478 0.00 0.00 46.30 2.59
1866 4851 4.202461 TGTGGGTGCTTCTCTTTTGAGTAT 60.202 41.667 0.00 0.00 46.30 2.12
1867 4852 5.012664 TGTGGGTGCTTCTCTTTTGAGTATA 59.987 40.000 0.00 0.00 46.30 1.47
1870 4855 7.769044 GTGGGTGCTTCTCTTTTGAGTATAATA 59.231 37.037 0.00 0.00 46.30 0.98
2238 5224 2.128507 CCTACCACGGCTCTCCTCC 61.129 68.421 0.00 0.00 0.00 4.30
2255 5241 2.743718 CGCCACTTCCTCACCTGT 59.256 61.111 0.00 0.00 0.00 4.00
2299 5288 4.831674 TGCCAGAGCATATATGTAGCAT 57.168 40.909 14.14 0.00 46.52 3.79
2312 5301 2.265904 TAGCATCCCGGGATCGACG 61.266 63.158 33.87 22.50 39.00 5.12
2317 5306 1.183030 ATCCCGGGATCGACGCAATA 61.183 55.000 31.20 0.35 39.00 1.90
2326 5315 4.355437 GGATCGACGCAATATGGATCTAG 58.645 47.826 0.00 0.00 35.14 2.43
2331 5320 3.866651 ACGCAATATGGATCTAGCCATC 58.133 45.455 2.40 0.00 45.36 3.51
2345 5334 0.392336 GCCATCTCCACTAGCCTCTG 59.608 60.000 0.00 0.00 0.00 3.35
2346 5335 1.047002 CCATCTCCACTAGCCTCTGG 58.953 60.000 0.00 0.00 0.00 3.86
2352 5341 3.660177 TCTCCACTAGCCTCTGGATAGAT 59.340 47.826 14.76 0.00 43.61 1.98
2361 5351 3.328931 GCCTCTGGATAGATTGATCCCAA 59.671 47.826 0.09 0.00 44.32 4.12
2380 5370 4.261197 CCCAAGAACACTAAAGCTTCACAC 60.261 45.833 0.00 0.00 0.00 3.82
2410 5400 1.333619 GCCAAAACGTGTCTGTCATGT 59.666 47.619 0.00 0.00 46.82 3.21
2434 5424 7.315142 GTGGAACAATTGATATCACAACACAT 58.685 34.615 13.59 0.00 44.16 3.21
2451 5443 9.462174 CACAACACATAACAAAACATAATCTGT 57.538 29.630 0.00 0.00 40.84 3.41
2468 5460 1.379044 GTGTGGGAGGCCTTCATGG 60.379 63.158 14.70 0.00 39.35 3.66
2470 5462 1.077429 GTGGGAGGCCTTCATGGTC 60.077 63.158 14.70 0.00 41.82 4.02
2481 5473 1.899437 TTCATGGTCGGTGAGGGAGC 61.899 60.000 0.00 0.00 0.00 4.70
2496 5488 2.104963 AGGGAGCGGTTCCTCAATAATC 59.895 50.000 9.21 0.00 45.98 1.75
2500 5492 2.093658 AGCGGTTCCTCAATAATCGTGT 60.094 45.455 0.00 0.00 33.06 4.49
2535 5527 3.152341 CATGATTCTCCCCCTATTGTGC 58.848 50.000 0.00 0.00 0.00 4.57
2545 5537 2.039084 CCCCTATTGTGCCAGTCCTATC 59.961 54.545 0.00 0.00 0.00 2.08
2547 5539 2.975489 CCTATTGTGCCAGTCCTATCCT 59.025 50.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 101 6.105657 ACGCAGGTTTTCTTTTCAATTTTG 57.894 33.333 0.00 0.00 0.00 2.44
97 103 5.457473 CGTACGCAGGTTTTCTTTTCAATTT 59.543 36.000 0.52 0.00 0.00 1.82
98 104 4.973663 CGTACGCAGGTTTTCTTTTCAATT 59.026 37.500 0.52 0.00 0.00 2.32
99 105 4.035909 ACGTACGCAGGTTTTCTTTTCAAT 59.964 37.500 16.72 0.00 0.00 2.57
100 106 3.374678 ACGTACGCAGGTTTTCTTTTCAA 59.625 39.130 16.72 0.00 0.00 2.69
101 107 2.937799 ACGTACGCAGGTTTTCTTTTCA 59.062 40.909 16.72 0.00 0.00 2.69
102 108 3.285745 CACGTACGCAGGTTTTCTTTTC 58.714 45.455 16.72 0.00 0.00 2.29
199 208 2.957006 CTGAGGCCACGTAGTAGGTAAT 59.043 50.000 5.01 0.00 41.61 1.89
239 248 1.227999 CCGTCGGTTGCAGTGAACAT 61.228 55.000 2.08 0.00 0.00 2.71
274 1092 1.677552 CGGGGGCAGAACACTACTT 59.322 57.895 0.00 0.00 0.00 2.24
312 1132 0.798776 GTCATGTCCAAGCAAGTCGG 59.201 55.000 0.00 0.00 0.00 4.79
328 1148 2.093288 CCTAGATTGAGCTTGGCTGTCA 60.093 50.000 0.00 0.00 39.88 3.58
333 1153 2.998316 AGTCCTAGATTGAGCTTGGC 57.002 50.000 0.00 0.00 31.91 4.52
342 1162 2.050918 GGGCAAGGCTAGTCCTAGATT 58.949 52.381 5.52 0.00 46.94 2.40
349 1169 1.541588 CAAACTTGGGCAAGGCTAGTC 59.458 52.381 0.00 0.00 42.53 2.59
350 1170 1.133482 ACAAACTTGGGCAAGGCTAGT 60.133 47.619 0.00 0.00 42.53 2.57
351 1171 1.270550 CACAAACTTGGGCAAGGCTAG 59.729 52.381 0.00 0.00 42.53 3.42
352 1172 1.133637 TCACAAACTTGGGCAAGGCTA 60.134 47.619 0.00 0.00 42.53 3.93
353 1173 0.396974 TCACAAACTTGGGCAAGGCT 60.397 50.000 0.00 0.00 42.53 4.58
354 1174 0.032540 CTCACAAACTTGGGCAAGGC 59.967 55.000 0.00 0.00 42.53 4.35
404 1225 1.210478 GGCCATCAACTTAGCTGGAGA 59.790 52.381 0.00 0.00 0.00 3.71
409 1230 0.995024 AGGTGGCCATCAACTTAGCT 59.005 50.000 20.62 0.00 41.45 3.32
454 1279 2.609002 CCACGCGCACATATATATGCAT 59.391 45.455 20.46 3.79 42.17 3.96
461 1286 1.885388 GCCACCACGCGCACATATA 60.885 57.895 5.73 0.00 0.00 0.86
462 1287 3.202001 GCCACCACGCGCACATAT 61.202 61.111 5.73 0.00 0.00 1.78
463 1288 2.579684 TATGCCACCACGCGCACATA 62.580 55.000 5.73 2.58 37.93 2.29
490 1334 5.663456 ACCAATATTTTGCGAGAAATGCAT 58.337 33.333 0.00 0.00 42.84 3.96
569 1413 4.832608 CTACGGCCGGGCTGAACC 62.833 72.222 33.58 8.56 38.46 3.62
703 1943 2.808523 TGGACATCGATCTCTGATGC 57.191 50.000 0.00 3.30 45.61 3.91
704 1944 4.025061 GCTTTTGGACATCGATCTCTGATG 60.025 45.833 0.00 7.34 46.79 3.07
747 1997 6.374578 GCTGATCAAGTGGTAAGTTCTTTTC 58.625 40.000 0.00 0.00 0.00 2.29
790 3717 3.678072 CGAATACCAATGAGTGAACACGT 59.322 43.478 0.00 0.00 36.20 4.49
948 3879 1.874872 CTACAGCTCCTACCGTAGCTC 59.125 57.143 0.00 0.00 45.92 4.09
965 3896 3.976701 ATGCACACCGGCTGCCTAC 62.977 63.158 17.92 0.03 33.36 3.18
997 3928 3.740115 AGTAGACTTTGTTTGGCATCGT 58.260 40.909 0.00 0.00 0.00 3.73
999 3930 3.994392 TCGAGTAGACTTTGTTTGGCATC 59.006 43.478 0.00 0.00 0.00 3.91
1000 3931 4.002906 TCGAGTAGACTTTGTTTGGCAT 57.997 40.909 0.00 0.00 0.00 4.40
1010 3941 4.193090 ACTCATGTCGATCGAGTAGACTT 58.807 43.478 20.09 2.15 38.22 3.01
1032 3963 1.310933 GGAGTACAGGAAGCGACGGA 61.311 60.000 0.00 0.00 0.00 4.69
1118 4049 3.152341 GGATACGTAGCTAGGCTTGGTA 58.848 50.000 11.10 3.76 40.44 3.25
1163 4094 3.006728 TAGAAGGTGGCGGTGGGG 61.007 66.667 0.00 0.00 0.00 4.96
1195 4126 3.625897 TGGAGGCGTGGACACTGG 61.626 66.667 0.56 0.00 0.00 4.00
1714 4696 8.475639 GTTGAGTATGGATAAACTGAGGACTAA 58.524 37.037 0.00 0.00 0.00 2.24
1747 4729 0.035056 AGCCTGGTAGATGGTGCAAC 60.035 55.000 0.00 0.00 0.00 4.17
1760 4742 1.550976 AGTTAACTCTCGGAAGCCTGG 59.449 52.381 1.12 0.00 0.00 4.45
1763 4745 3.314541 TTGAGTTAACTCTCGGAAGCC 57.685 47.619 30.47 7.55 43.25 4.35
1799 4781 5.491635 AAAAACACAGAAGCAGAAGAGTC 57.508 39.130 0.00 0.00 0.00 3.36
1844 4829 2.576615 ACTCAAAAGAGAAGCACCCAC 58.423 47.619 0.00 0.00 0.00 4.61
2238 5224 1.374758 GACAGGTGAGGAAGTGGCG 60.375 63.158 0.00 0.00 0.00 5.69
2266 5252 0.678395 CTCTGGCAGATATGACCGCT 59.322 55.000 19.11 0.00 0.00 5.52
2267 5253 0.948141 GCTCTGGCAGATATGACCGC 60.948 60.000 19.11 12.18 38.54 5.68
2288 5277 2.956333 CGATCCCGGGATGCTACATATA 59.044 50.000 40.65 6.64 34.60 0.86
2290 5279 1.182667 CGATCCCGGGATGCTACATA 58.817 55.000 40.65 8.18 34.60 2.29
2291 5280 0.541998 TCGATCCCGGGATGCTACAT 60.542 55.000 40.65 16.54 34.60 2.29
2299 5288 1.183030 ATATTGCGTCGATCCCGGGA 61.183 55.000 29.18 29.18 36.24 5.14
2312 5301 4.080695 TGGAGATGGCTAGATCCATATTGC 60.081 45.833 2.18 1.45 46.29 3.56
2326 5315 0.392336 CAGAGGCTAGTGGAGATGGC 59.608 60.000 0.00 0.00 0.00 4.40
2331 5320 3.517296 TCTATCCAGAGGCTAGTGGAG 57.483 52.381 19.76 10.08 46.09 3.86
2345 5334 5.934781 AGTGTTCTTGGGATCAATCTATCC 58.065 41.667 0.00 0.00 44.14 2.59
2346 5335 8.964476 TTTAGTGTTCTTGGGATCAATCTATC 57.036 34.615 0.00 0.00 31.75 2.08
2352 5341 4.985538 AGCTTTAGTGTTCTTGGGATCAA 58.014 39.130 0.00 0.00 0.00 2.57
2361 5351 5.186198 AGTTGTGTGAAGCTTTAGTGTTCT 58.814 37.500 0.00 0.00 0.00 3.01
2380 5370 3.701241 ACACGTTTTGGCATGTTAGTTG 58.299 40.909 0.00 0.00 0.00 3.16
2410 5400 6.890979 TGTGTTGTGATATCAATTGTTCCA 57.109 33.333 7.07 0.00 0.00 3.53
2434 5424 6.432783 CCTCCCACACAGATTATGTTTTGTTA 59.567 38.462 0.00 0.00 41.41 2.41
2444 5436 1.559682 GAAGGCCTCCCACACAGATTA 59.440 52.381 5.23 0.00 0.00 1.75
2445 5437 0.329596 GAAGGCCTCCCACACAGATT 59.670 55.000 5.23 0.00 0.00 2.40
2451 5443 1.852157 ACCATGAAGGCCTCCCACA 60.852 57.895 5.23 4.94 43.14 4.17
2468 5460 3.644399 GAACCGCTCCCTCACCGAC 62.644 68.421 0.00 0.00 0.00 4.79
2470 5462 4.452733 GGAACCGCTCCCTCACCG 62.453 72.222 0.00 0.00 38.44 4.94
2471 5463 3.003763 AGGAACCGCTCCCTCACC 61.004 66.667 0.00 0.00 46.81 4.02
2481 5473 3.485216 GCAACACGATTATTGAGGAACCG 60.485 47.826 0.00 0.00 0.00 4.44
2490 5482 2.093658 AGGACGGAGCAACACGATTATT 60.094 45.455 0.00 0.00 0.00 1.40
2496 5488 2.022129 GTGAGGACGGAGCAACACG 61.022 63.158 0.00 0.00 0.00 4.49
2500 5492 0.904649 ATCATGTGAGGACGGAGCAA 59.095 50.000 0.00 0.00 0.00 3.91
2535 5527 2.780010 ACCCAAATCAGGATAGGACTGG 59.220 50.000 0.00 0.00 36.62 4.00


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

AutoCloner maintained by Alex Coulton.