Multiple sequence alignment - TraesCS3B01G300900

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 TraesCS3B01G300900 chr3B 100.000 3143 0 0 1 3143 482786279 482783137 0.000000e+00 5805
1 TraesCS3B01G300900 chr3D 93.253 3068 147 24 101 3143 371871589 371868557 0.000000e+00 4464
2 TraesCS3B01G300900 chr3A 92.577 3085 160 29 49 3095 492738416 492735363 0.000000e+00 4364
3 TraesCS3B01G300900 chr1B 78.987 928 171 17 1112 2030 638783744 638782832 2.070000e-171 612
4 TraesCS3B01G300900 chr1B 78.442 937 172 22 1109 2030 638821853 638820932 4.520000e-163 584
5 TraesCS3B01G300900 chr1A 78.410 931 171 22 1109 2027 555533593 555534505 2.100000e-161 579
6 TraesCS3B01G300900 chr1A 77.908 937 177 22 1109 2030 555523073 555522152 9.850000e-155 556
7 TraesCS3B01G300900 chr1A 77.623 934 173 28 1112 2030 555484955 555484043 4.610000e-148 534
8 TraesCS3B01G300900 chr1D 78.218 909 166 24 1132 2027 463341471 463342360 1.270000e-153 553
9 TraesCS3B01G300900 chr1D 77.801 937 178 22 1109 2030 463326368 463325447 4.580000e-153 551


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 TraesCS3B01G300900 chr3B 482783137 482786279 3142 True 5805 5805 100.000 1 3143 1 chr3B.!!$R1 3142
1 TraesCS3B01G300900 chr3D 371868557 371871589 3032 True 4464 4464 93.253 101 3143 1 chr3D.!!$R1 3042
2 TraesCS3B01G300900 chr3A 492735363 492738416 3053 True 4364 4364 92.577 49 3095 1 chr3A.!!$R1 3046
3 TraesCS3B01G300900 chr1B 638782832 638783744 912 True 612 612 78.987 1112 2030 1 chr1B.!!$R1 918
4 TraesCS3B01G300900 chr1B 638820932 638821853 921 True 584 584 78.442 1109 2030 1 chr1B.!!$R2 921
5 TraesCS3B01G300900 chr1A 555533593 555534505 912 False 579 579 78.410 1109 2027 1 chr1A.!!$F1 918
6 TraesCS3B01G300900 chr1A 555522152 555523073 921 True 556 556 77.908 1109 2030 1 chr1A.!!$R2 921
7 TraesCS3B01G300900 chr1A 555484043 555484955 912 True 534 534 77.623 1112 2030 1 chr1A.!!$R1 918
8 TraesCS3B01G300900 chr1D 463341471 463342360 889 False 553 553 78.218 1132 2027 1 chr1D.!!$F1 895
9 TraesCS3B01G300900 chr1D 463325447 463326368 921 True 551 551 77.801 1109 2030 1 chr1D.!!$R1 921

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
586 617 0.10576 TCCCCACCACACAGCAAAAT 60.106 50.0 0.0 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2522 2590 1.048601 ACTTCTCTTCTGTTGGGCGA 58.951 50.0 0.0 0.0 0.0 5.54 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
87 88 4.454161 CACCGGTGAAAAGTATGATGTGAA 59.546 41.667 31.31 0.00 0.00 3.18
185 196 2.249413 CTGGCACGCCTTCATCCTCT 62.249 60.000 9.92 0.00 36.94 3.69
192 203 1.676916 CGCCTTCATCCTCTTTGAGCA 60.677 52.381 0.00 0.00 0.00 4.26
209 221 0.179018 GCATGATCACCCCTACACCC 60.179 60.000 0.00 0.00 0.00 4.61
210 222 1.511613 CATGATCACCCCTACACCCT 58.488 55.000 0.00 0.00 0.00 4.34
226 238 1.674057 CCTGCTTCTTCGTGACCCT 59.326 57.895 0.00 0.00 0.00 4.34
238 258 0.615850 GTGACCCTCCTCCCTCTTTG 59.384 60.000 0.00 0.00 0.00 2.77
264 284 0.170339 ACGACATCGCGATGAACTGA 59.830 50.000 45.64 9.43 44.43 3.41
267 287 1.449789 GACATCGCGATGAACTGATCG 59.550 52.381 45.64 22.95 46.54 3.69
279 299 1.478631 ACTGATCGTCATGCCTCTGA 58.521 50.000 0.00 0.00 0.00 3.27
292 312 2.948386 CTCTGACGAGGTCCTGTCA 58.052 57.895 17.78 17.78 42.49 3.58
352 372 3.182967 GGCTCTATTCGAATCATAGCGG 58.817 50.000 15.25 4.72 0.00 5.52
358 378 1.418373 TCGAATCATAGCGGCATTCG 58.582 50.000 20.54 20.54 46.66 3.34
401 421 5.712152 AAGCAATCACTTAGTGGAAAAGG 57.288 39.130 12.79 0.00 33.87 3.11
404 424 5.010012 AGCAATCACTTAGTGGAAAAGGTTG 59.990 40.000 12.79 0.00 33.87 3.77
405 425 5.222631 CAATCACTTAGTGGAAAAGGTTGC 58.777 41.667 12.79 0.00 33.87 4.17
406 426 3.219281 TCACTTAGTGGAAAAGGTTGCC 58.781 45.455 12.79 0.00 33.87 4.52
407 427 2.296190 CACTTAGTGGAAAAGGTTGCCC 59.704 50.000 4.14 0.00 0.00 5.36
408 428 1.539827 CTTAGTGGAAAAGGTTGCCCG 59.460 52.381 0.00 0.00 35.12 6.13
409 429 0.891904 TAGTGGAAAAGGTTGCCCGC 60.892 55.000 0.00 0.00 35.12 6.13
430 456 3.735514 GCACTTGTTCGTTTTGGCCTAAA 60.736 43.478 8.37 8.37 0.00 1.85
480 507 0.549169 CCCCCTCCCTTGAACCTGTA 60.549 60.000 0.00 0.00 0.00 2.74
489 516 3.181433 CCCTTGAACCTGTAAACCCTCTT 60.181 47.826 0.00 0.00 0.00 2.85
522 549 2.433145 CGATGCCGTGACTGCAGT 60.433 61.111 21.88 21.88 42.92 4.40
580 611 0.955428 CGACAATCCCCACCACACAG 60.955 60.000 0.00 0.00 0.00 3.66
586 617 0.105760 TCCCCACCACACAGCAAAAT 60.106 50.000 0.00 0.00 0.00 1.82
602 633 6.805271 ACAGCAAAATCGATTGATCTGAAAAG 59.195 34.615 26.60 10.98 32.24 2.27
643 675 9.950496 AGCAAATGTGGAATATATAAGGTAGAG 57.050 33.333 0.00 0.00 0.00 2.43
723 759 5.126396 AGTTTGCATTAACAAGGAGAAGC 57.874 39.130 4.19 0.00 0.00 3.86
818 854 4.278170 TGCCTATTTATTCGGCTTCCATTG 59.722 41.667 0.00 0.00 44.09 2.82
847 883 1.960689 CCCCATCACAAAAAGGTTCGT 59.039 47.619 0.00 0.00 0.00 3.85
848 884 3.150767 CCCCATCACAAAAAGGTTCGTA 58.849 45.455 0.00 0.00 0.00 3.43
849 885 3.570550 CCCCATCACAAAAAGGTTCGTAA 59.429 43.478 0.00 0.00 0.00 3.18
850 886 4.219725 CCCCATCACAAAAAGGTTCGTAAT 59.780 41.667 0.00 0.00 0.00 1.89
865 901 5.163227 GGTTCGTAATTAAATCTCCTCCCCT 60.163 44.000 0.00 0.00 0.00 4.79
956 992 1.685820 CTTTCCCTCCTCACCCCAC 59.314 63.158 0.00 0.00 0.00 4.61
957 993 1.850755 TTTCCCTCCTCACCCCACC 60.851 63.158 0.00 0.00 0.00 4.61
958 994 3.883822 TTCCCTCCTCACCCCACCC 62.884 68.421 0.00 0.00 0.00 4.61
960 996 4.675303 CCTCCTCACCCCACCCCA 62.675 72.222 0.00 0.00 0.00 4.96
1485 1530 0.321564 TCTCCAACCTCAATGCCGTG 60.322 55.000 0.00 0.00 0.00 4.94
2019 2064 1.588239 TCTCCTCCTACCTGTACGGA 58.412 55.000 2.31 0.00 36.31 4.69
2129 2192 3.414700 CGACGTTGGAGGTGCAGC 61.415 66.667 8.11 8.11 0.00 5.25
2244 2308 6.166982 AGTCTAGTTGCACCTATTTCTCAAC 58.833 40.000 0.00 0.00 37.78 3.18
2246 2310 6.426937 GTCTAGTTGCACCTATTTCTCAACAA 59.573 38.462 0.00 0.00 39.39 2.83
2247 2311 5.438761 AGTTGCACCTATTTCTCAACAAC 57.561 39.130 0.00 0.00 39.39 3.32
2248 2312 4.887071 AGTTGCACCTATTTCTCAACAACA 59.113 37.500 0.00 0.00 39.39 3.33
2249 2313 5.359576 AGTTGCACCTATTTCTCAACAACAA 59.640 36.000 0.00 0.00 39.39 2.83
2250 2314 5.181690 TGCACCTATTTCTCAACAACAAC 57.818 39.130 0.00 0.00 0.00 3.32
2295 2359 0.109365 TGCATGCGTGGCACATAAAC 60.109 50.000 19.09 4.25 43.04 2.01
2348 2413 3.664486 GCTAGTTGTGTACATAGCGATCG 59.336 47.826 11.69 11.69 32.13 3.69
2350 2415 3.692576 AGTTGTGTACATAGCGATCGAC 58.307 45.455 21.57 10.46 0.00 4.20
2489 2557 7.402054 TGGTAACATGGACTAACAATCTTCAT 58.598 34.615 0.00 0.00 46.17 2.57
2515 2583 5.568620 ATTTTGGTATCTTCGGAGCCTAT 57.431 39.130 0.00 0.00 0.00 2.57
2516 2584 4.336889 TTTGGTATCTTCGGAGCCTATG 57.663 45.455 0.00 0.00 0.00 2.23
2517 2585 2.248248 TGGTATCTTCGGAGCCTATGG 58.752 52.381 0.00 0.00 0.00 2.74
2540 2611 2.275318 GATCGCCCAACAGAAGAGAAG 58.725 52.381 0.00 0.00 0.00 2.85
2608 2679 3.522362 CGCGTCAACAATTTATCTAGCG 58.478 45.455 0.00 0.00 38.00 4.26
2616 2687 3.063452 ACAATTTATCTAGCGCAACCACG 59.937 43.478 11.47 0.00 0.00 4.94
2621 2692 1.075542 TCTAGCGCAACCACGATTTG 58.924 50.000 11.47 0.00 31.83 2.32
2726 2797 6.485313 TGTTACCTTGACAACCACTAGATTTG 59.515 38.462 0.00 0.00 0.00 2.32
2969 3040 7.319646 TGCATGGTGGTTTTATTCTGTTTATC 58.680 34.615 0.00 0.00 0.00 1.75
2991 3062 7.609097 ATCTACCATATAGTGATGCCCTATG 57.391 40.000 0.00 0.00 0.00 2.23
3028 3099 4.856487 TGCGCACAAAAATAATAGTTCAGC 59.144 37.500 5.66 0.00 0.00 4.26
3060 3131 8.370493 AGTATGAATCATCATTGTTTACTCCG 57.630 34.615 0.00 0.00 43.89 4.63
3115 3186 1.149627 TTGGTTCCCCAACTCCACG 59.850 57.895 0.00 0.00 45.93 4.94
3129 3200 5.449304 CAACTCCACGTTAGAAAAATGGTC 58.551 41.667 1.76 0.00 33.63 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.773856 TTTCACCGGTGGCATGGAGA 61.774 55.000 33.40 9.64 0.00 3.71
57 58 0.893270 CTTTTCACCGGTGGCATGGA 60.893 55.000 33.40 11.27 0.00 3.41
87 88 5.826737 CGATACCTGACCGAACCCTATATAT 59.173 44.000 0.00 0.00 0.00 0.86
99 100 2.025727 GCGACCGATACCTGACCG 59.974 66.667 0.00 0.00 0.00 4.79
167 178 1.841302 AAGAGGATGAAGGCGTGCCA 61.841 55.000 14.29 0.00 38.92 4.92
168 179 0.678048 AAAGAGGATGAAGGCGTGCC 60.678 55.000 1.67 1.67 0.00 5.01
185 196 2.575735 TGTAGGGGTGATCATGCTCAAA 59.424 45.455 0.00 0.00 0.00 2.69
192 203 1.511613 CAGGGTGTAGGGGTGATCAT 58.488 55.000 0.00 0.00 0.00 2.45
209 221 0.390472 GGAGGGTCACGAAGAAGCAG 60.390 60.000 0.00 0.00 0.00 4.24
210 222 0.832135 AGGAGGGTCACGAAGAAGCA 60.832 55.000 0.00 0.00 0.00 3.91
226 238 2.646175 CGTCGGCAAAGAGGGAGGA 61.646 63.158 0.00 0.00 0.00 3.71
279 299 1.371558 GGCTTTGACAGGACCTCGT 59.628 57.895 0.00 0.00 0.00 4.18
352 372 4.800471 CCTTAGGCTTTCAATTTCGAATGC 59.200 41.667 0.00 7.49 42.38 3.56
358 378 6.151144 TGCTTAGACCTTAGGCTTTCAATTTC 59.849 38.462 0.00 0.00 0.00 2.17
401 421 2.051345 CGAACAAGTGCGGGCAAC 60.051 61.111 0.00 0.00 0.00 4.17
404 424 1.065109 AAAACGAACAAGTGCGGGC 59.935 52.632 5.47 0.00 0.00 6.13
405 425 0.593773 CCAAAACGAACAAGTGCGGG 60.594 55.000 5.47 0.00 0.00 6.13
406 426 1.206115 GCCAAAACGAACAAGTGCGG 61.206 55.000 5.47 0.00 0.00 5.69
407 427 1.206115 GGCCAAAACGAACAAGTGCG 61.206 55.000 0.00 0.00 0.00 5.34
408 428 0.102300 AGGCCAAAACGAACAAGTGC 59.898 50.000 5.01 0.00 0.00 4.40
409 429 3.701532 TTAGGCCAAAACGAACAAGTG 57.298 42.857 5.01 0.00 0.00 3.16
430 456 7.361799 GGCAAACCGTTGAAGATAGTTCTAAAT 60.362 37.037 0.00 0.00 36.83 1.40
470 497 3.460340 TGGAAGAGGGTTTACAGGTTCAA 59.540 43.478 0.00 0.00 0.00 2.69
480 507 2.904434 ACATAGACGTGGAAGAGGGTTT 59.096 45.455 0.00 0.00 0.00 3.27
489 516 1.607148 CATCGCCTACATAGACGTGGA 59.393 52.381 0.00 0.00 30.98 4.02
566 597 0.105760 TTTTGCTGTGTGGTGGGGAT 60.106 50.000 0.00 0.00 0.00 3.85
569 600 0.039256 CGATTTTGCTGTGTGGTGGG 60.039 55.000 0.00 0.00 0.00 4.61
580 611 7.044445 GCTACTTTTCAGATCAATCGATTTTGC 60.044 37.037 8.21 0.31 29.66 3.68
586 617 4.744570 ACGCTACTTTTCAGATCAATCGA 58.255 39.130 0.00 0.00 0.00 3.59
602 633 6.185399 CACATTTGCTCTTAACATACGCTAC 58.815 40.000 0.00 0.00 0.00 3.58
643 675 2.893637 TCAACTTGAAGATAGAGCGCC 58.106 47.619 2.29 0.00 0.00 6.53
723 759 9.986833 TTCTCAACACAAATTCGAATATATGTG 57.013 29.630 30.27 30.27 42.78 3.21
818 854 5.510690 CCTTTTTGTGATGGGGGAGTAAAAC 60.511 44.000 0.00 0.00 0.00 2.43
847 883 9.515440 TTTAAGAGAGGGGAGGAGATTTAATTA 57.485 33.333 0.00 0.00 0.00 1.40
848 884 8.407313 TTTAAGAGAGGGGAGGAGATTTAATT 57.593 34.615 0.00 0.00 0.00 1.40
849 885 8.407313 TTTTAAGAGAGGGGAGGAGATTTAAT 57.593 34.615 0.00 0.00 0.00 1.40
850 886 7.824365 TTTTAAGAGAGGGGAGGAGATTTAA 57.176 36.000 0.00 0.00 0.00 1.52
892 928 3.452627 AGCGAGATAAGTGGGAGATTTGT 59.547 43.478 0.00 0.00 0.00 2.83
959 995 3.561120 TTAGCGCTGGGTTGGGGTG 62.561 63.158 22.90 0.00 32.95 4.61
960 996 3.253838 TTAGCGCTGGGTTGGGGT 61.254 61.111 22.90 0.00 34.99 4.95
2019 2064 3.633094 CTGCCGCGTGCTGTACTCT 62.633 63.158 18.14 0.00 42.00 3.24
2129 2192 5.941948 AAGGTTAGATCAAACGGTTTCAG 57.058 39.130 2.51 0.00 0.00 3.02
2170 2233 1.837090 GGCCCATGTTCCGGATACT 59.163 57.895 4.15 0.00 0.00 2.12
2171 2234 1.597027 CGGCCCATGTTCCGGATAC 60.597 63.158 4.15 7.43 41.82 2.24
2172 2235 2.825982 CGGCCCATGTTCCGGATA 59.174 61.111 4.15 0.00 41.82 2.59
2295 2359 2.283298 GTGACACCCATGCATGTCTAG 58.717 52.381 24.58 13.70 44.59 2.43
2348 2413 1.156736 CCACAATCACCAACCTCGTC 58.843 55.000 0.00 0.00 0.00 4.20
2350 2415 1.604604 AACCACAATCACCAACCTCG 58.395 50.000 0.00 0.00 0.00 4.63
2417 2482 2.024176 ACATCCTTCCATTTCGTCCG 57.976 50.000 0.00 0.00 0.00 4.79
2489 2557 6.184789 AGGCTCCGAAGATACCAAAATTTTA 58.815 36.000 2.44 0.00 0.00 1.52
2495 2563 3.071023 CCATAGGCTCCGAAGATACCAAA 59.929 47.826 0.00 0.00 0.00 3.28
2518 2586 1.205655 TCTCTTCTGTTGGGCGATCAG 59.794 52.381 1.55 1.55 0.00 2.90
2519 2587 1.266178 TCTCTTCTGTTGGGCGATCA 58.734 50.000 0.00 0.00 0.00 2.92
2520 2588 2.275318 CTTCTCTTCTGTTGGGCGATC 58.725 52.381 0.00 0.00 0.00 3.69
2521 2589 1.625818 ACTTCTCTTCTGTTGGGCGAT 59.374 47.619 0.00 0.00 0.00 4.58
2522 2590 1.048601 ACTTCTCTTCTGTTGGGCGA 58.951 50.000 0.00 0.00 0.00 5.54
2523 2591 2.743636 TACTTCTCTTCTGTTGGGCG 57.256 50.000 0.00 0.00 0.00 6.13
2524 2592 3.942115 GGAATACTTCTCTTCTGTTGGGC 59.058 47.826 0.00 0.00 0.00 5.36
2525 2593 5.188751 AGAGGAATACTTCTCTTCTGTTGGG 59.811 44.000 0.00 0.00 37.06 4.12
2528 2596 5.483583 AGCAGAGGAATACTTCTCTTCTGTT 59.516 40.000 11.94 5.06 38.19 3.16
2530 2598 5.591099 GAGCAGAGGAATACTTCTCTTCTG 58.409 45.833 7.40 7.40 38.19 3.02
2531 2599 4.338118 CGAGCAGAGGAATACTTCTCTTCT 59.662 45.833 0.00 0.00 38.19 2.85
2532 2600 4.336993 TCGAGCAGAGGAATACTTCTCTTC 59.663 45.833 0.00 0.00 38.19 2.87
2533 2601 4.097286 GTCGAGCAGAGGAATACTTCTCTT 59.903 45.833 0.00 0.00 38.19 2.85
2540 2611 1.407258 AGCAGTCGAGCAGAGGAATAC 59.593 52.381 0.00 0.00 36.85 1.89
2608 2679 7.692291 GCATATACATATACAAATCGTGGTTGC 59.308 37.037 0.00 0.00 0.00 4.17
2616 2687 8.655970 TGACGCAAGCATATACATATACAAATC 58.344 33.333 0.00 0.00 45.62 2.17
2621 2692 7.899841 CACAATGACGCAAGCATATACATATAC 59.100 37.037 0.00 0.00 45.62 1.47
2696 2767 3.880490 GTGGTTGTCAAGGTAACATCACA 59.120 43.478 0.00 0.00 41.41 3.58
2726 2797 9.908152 AACTTACTAATCACCTTTTTGTTATGC 57.092 29.630 0.00 0.00 0.00 3.14
2753 2824 5.944007 AGGCTACATTACAAAACAGGGTTAG 59.056 40.000 0.00 0.00 0.00 2.34
2932 3003 3.758554 ACCACCATGCATCAGTTTTCTAC 59.241 43.478 0.00 0.00 0.00 2.59
2969 3040 6.166984 CCATAGGGCATCACTATATGGTAG 57.833 45.833 0.00 0.00 38.60 3.18
2991 3062 1.732259 GTGCGCACATAGGTATATGCC 59.268 52.381 34.52 0.75 42.26 4.40
3060 3131 9.935241 AATATCATATTATGACCGCCATATCTC 57.065 33.333 8.51 0.00 43.01 2.75
3114 3185 7.532884 CCTTTCTTTACGACCATTTTTCTAACG 59.467 37.037 0.00 0.00 0.00 3.18
3115 3186 7.806487 CCCTTTCTTTACGACCATTTTTCTAAC 59.194 37.037 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.