Multiple sequence alignment - TraesCS3D01G340600

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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 TraesCS3D01G340600 chr3D 100.000 2882 0 0 1 2882 454230055 454232936 0.000000e+00 5323.0
1 TraesCS3D01G340600 chr3D 82.292 288 41 9 6 287 397917049 397916766 1.030000e-59 241.0
2 TraesCS3D01G340600 chr3A 92.141 2901 140 43 1 2881 596361335 596364167 0.000000e+00 4013.0
3 TraesCS3D01G340600 chr3B 90.861 1893 104 29 1 1882 596856035 596857869 0.000000e+00 2473.0
4 TraesCS3D01G340600 chr3B 86.464 857 85 22 1941 2792 596857904 596858734 0.000000e+00 911.0
5 TraesCS3D01G340600 chr3B 94.444 36 2 0 282 317 397560915 397560950 4.010000e-04 56.5
6 TraesCS3D01G340600 chr4B 83.623 806 100 21 2046 2836 567970045 567970833 0.000000e+00 728.0
7 TraesCS3D01G340600 chr4B 80.612 294 47 7 3 289 371980544 371980254 4.830000e-53 219.0
8 TraesCS3D01G340600 chr4B 100.000 30 0 0 602 631 637421078 637421049 4.010000e-04 56.5
9 TraesCS3D01G340600 chr6D 88.211 492 39 10 2346 2819 373342297 373342787 1.160000e-158 569.0
10 TraesCS3D01G340600 chr6D 87.307 323 38 3 2044 2365 373341842 373342162 1.630000e-97 366.0
11 TraesCS3D01G340600 chr2B 83.600 500 48 14 2295 2779 331237626 331238106 3.410000e-119 438.0
12 TraesCS3D01G340600 chr4A 77.061 279 45 10 2 265 338741760 338742034 2.990000e-30 143.0
13 TraesCS3D01G340600 chr5B 93.182 44 2 1 243 286 439266614 439266572 2.400000e-06 63.9
14 TraesCS3D01G340600 chr5B 100.000 34 0 0 247 280 456632904 456632937 2.400000e-06 63.9
15 TraesCS3D01G340600 chr5A 97.297 37 1 0 285 321 342570774 342570810 2.400000e-06 63.9
16 TraesCS3D01G340600 chr6A 89.583 48 5 0 247 294 105009513 105009466 8.620000e-06 62.1
17 TraesCS3D01G340600 chr6A 89.583 48 5 0 247 294 105010207 105010160 8.620000e-06 62.1
18 TraesCS3D01G340600 chr1B 94.444 36 2 0 242 277 367743929 367743964 4.010000e-04 56.5


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 TraesCS3D01G340600 chr3D 454230055 454232936 2881 False 5323.0 5323 100.0000 1 2882 1 chr3D.!!$F1 2881
1 TraesCS3D01G340600 chr3A 596361335 596364167 2832 False 4013.0 4013 92.1410 1 2881 1 chr3A.!!$F1 2880
2 TraesCS3D01G340600 chr3B 596856035 596858734 2699 False 1692.0 2473 88.6625 1 2792 2 chr3B.!!$F2 2791
3 TraesCS3D01G340600 chr4B 567970045 567970833 788 False 728.0 728 83.6230 2046 2836 1 chr4B.!!$F1 790
4 TraesCS3D01G340600 chr6D 373341842 373342787 945 False 467.5 569 87.7590 2044 2819 2 chr6D.!!$F1 775

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
559 565 0.030101 TTTCGCGTTTGCTTTCCTGG 59.970 50.0 5.77 0.0 39.65 4.45 F
967 981 0.181350 ATGCGTCCCCATCTCTTTCC 59.819 55.0 0.00 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 1688 2.015587 GCAGAGAATGGCTTTGGAGAG 58.984 52.381 0.00 0.0 0.00 3.20 R
2859 3065 0.844221 AAGAGCTCCCTGCCCTCTTT 60.844 55.000 10.93 0.0 41.73 2.52 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
119 123 6.468956 CGAGACGGATTTAATGTTGAAAATGG 59.531 38.462 0.00 0.00 0.00 3.16
230 235 9.515226 TGTGGTAAAATAGATAATAATGAGGGC 57.485 33.333 0.00 0.00 0.00 5.19
321 326 8.498358 GGCAAATCTTTTGTCTCCATTTAAAAG 58.502 33.333 0.00 0.00 39.98 2.27
322 327 9.045223 GCAAATCTTTTGTCTCCATTTAAAAGT 57.955 29.630 0.00 0.00 39.73 2.66
334 339 9.726438 TCTCCATTTAAAAGTAGAAGAAGAAGG 57.274 33.333 0.00 0.00 0.00 3.46
385 390 3.255642 TGAGTTAAGCTCCCACAAAATGC 59.744 43.478 0.00 0.00 43.48 3.56
487 492 1.386533 CCACTAGCAGCCAATTCTGG 58.613 55.000 0.00 0.00 46.65 3.86
505 510 0.683412 GGTGGTCGTAACCCAGTCTT 59.317 55.000 0.00 0.00 45.83 3.01
536 542 1.611977 CCCCTTTCTTCCGTTGTTTCC 59.388 52.381 0.00 0.00 0.00 3.13
537 543 2.583143 CCCTTTCTTCCGTTGTTTCCT 58.417 47.619 0.00 0.00 0.00 3.36
538 544 2.956333 CCCTTTCTTCCGTTGTTTCCTT 59.044 45.455 0.00 0.00 0.00 3.36
539 545 3.004419 CCCTTTCTTCCGTTGTTTCCTTC 59.996 47.826 0.00 0.00 0.00 3.46
540 546 3.883489 CCTTTCTTCCGTTGTTTCCTTCT 59.117 43.478 0.00 0.00 0.00 2.85
541 547 4.338400 CCTTTCTTCCGTTGTTTCCTTCTT 59.662 41.667 0.00 0.00 0.00 2.52
542 548 5.163550 CCTTTCTTCCGTTGTTTCCTTCTTT 60.164 40.000 0.00 0.00 0.00 2.52
543 549 5.494632 TTCTTCCGTTGTTTCCTTCTTTC 57.505 39.130 0.00 0.00 0.00 2.62
544 550 3.558418 TCTTCCGTTGTTTCCTTCTTTCG 59.442 43.478 0.00 0.00 0.00 3.46
545 551 1.600485 TCCGTTGTTTCCTTCTTTCGC 59.400 47.619 0.00 0.00 0.00 4.70
546 552 1.658968 CGTTGTTTCCTTCTTTCGCG 58.341 50.000 0.00 0.00 0.00 5.87
547 553 1.004292 CGTTGTTTCCTTCTTTCGCGT 60.004 47.619 5.77 0.00 0.00 6.01
548 554 2.538132 CGTTGTTTCCTTCTTTCGCGTT 60.538 45.455 5.77 0.00 0.00 4.84
549 555 3.431856 GTTGTTTCCTTCTTTCGCGTTT 58.568 40.909 5.77 0.00 0.00 3.60
550 556 3.059634 TGTTTCCTTCTTTCGCGTTTG 57.940 42.857 5.77 0.00 0.00 2.93
551 557 1.779157 GTTTCCTTCTTTCGCGTTTGC 59.221 47.619 5.77 0.00 37.91 3.68
552 558 1.305201 TTCCTTCTTTCGCGTTTGCT 58.695 45.000 5.77 0.00 39.65 3.91
553 559 1.305201 TCCTTCTTTCGCGTTTGCTT 58.695 45.000 5.77 0.00 39.65 3.91
554 560 1.673920 TCCTTCTTTCGCGTTTGCTTT 59.326 42.857 5.77 0.00 39.65 3.51
555 561 2.044135 CCTTCTTTCGCGTTTGCTTTC 58.956 47.619 5.77 0.00 39.65 2.62
556 562 2.044135 CTTCTTTCGCGTTTGCTTTCC 58.956 47.619 5.77 0.00 39.65 3.13
557 563 1.305201 TCTTTCGCGTTTGCTTTCCT 58.695 45.000 5.77 0.00 39.65 3.36
558 564 1.002900 TCTTTCGCGTTTGCTTTCCTG 60.003 47.619 5.77 0.00 39.65 3.86
559 565 0.030101 TTTCGCGTTTGCTTTCCTGG 59.970 50.000 5.77 0.00 39.65 4.45
560 566 1.098712 TTCGCGTTTGCTTTCCTGGT 61.099 50.000 5.77 0.00 39.65 4.00
561 567 1.082104 CGCGTTTGCTTTCCTGGTC 60.082 57.895 0.00 0.00 39.65 4.02
562 568 1.285950 GCGTTTGCTTTCCTGGTCC 59.714 57.895 0.00 0.00 38.39 4.46
563 569 1.452145 GCGTTTGCTTTCCTGGTCCA 61.452 55.000 0.00 0.00 38.39 4.02
627 637 2.096442 CCCTTAAACGTCCGCGGAC 61.096 63.158 41.75 41.75 43.45 4.79
646 656 1.007734 GCGTGAGACGTGACCTTGA 60.008 57.895 0.00 0.00 44.73 3.02
648 658 1.409412 CGTGAGACGTGACCTTGAAG 58.591 55.000 0.00 0.00 36.74 3.02
697 707 7.064728 GTCCTATTGAACAATCACACTCCTTAC 59.935 40.741 3.23 0.00 34.61 2.34
858 872 3.471680 GCGCCTTTCCATCTAGAATTCT 58.528 45.455 13.56 13.56 0.00 2.40
967 981 0.181350 ATGCGTCCCCATCTCTTTCC 59.819 55.000 0.00 0.00 0.00 3.13
975 989 1.407437 CCCATCTCTTTCCCTTCACCG 60.407 57.143 0.00 0.00 0.00 4.94
1053 1068 1.466167 CTGCATCCGAAGTTTGTCCTG 59.534 52.381 0.00 0.00 0.00 3.86
1054 1069 1.202758 TGCATCCGAAGTTTGTCCTGT 60.203 47.619 0.00 0.00 0.00 4.00
1055 1070 1.464997 GCATCCGAAGTTTGTCCTGTC 59.535 52.381 0.00 0.00 0.00 3.51
1056 1071 2.076863 CATCCGAAGTTTGTCCTGTCC 58.923 52.381 0.00 0.00 0.00 4.02
1330 1345 2.399356 GCAAAGCTCCCGCACCTAC 61.399 63.158 0.00 0.00 39.10 3.18
1438 1453 2.048597 TACCGTCGCTGCAACCAG 60.049 61.111 0.00 0.00 42.13 4.00
1670 1688 1.503294 GGAGCTAGCTGAATTACGCC 58.497 55.000 24.99 10.70 0.00 5.68
1690 1708 2.015587 CTCTCCAAAGCCATTCTCTGC 58.984 52.381 0.00 0.00 0.00 4.26
1764 1783 7.807977 TCTGCTGTAACTTCAGATTTTCTTT 57.192 32.000 0.00 0.00 37.61 2.52
1775 1794 8.906867 ACTTCAGATTTTCTTTCTTGTTGATGA 58.093 29.630 0.00 0.00 0.00 2.92
1854 1873 3.820467 CCGGCAATAATATTCTTGGCTCA 59.180 43.478 26.73 0.00 43.53 4.26
1857 1876 5.009010 CGGCAATAATATTCTTGGCTCAAGT 59.991 40.000 26.73 0.85 43.53 3.16
1937 1957 6.861065 AAAAGCTCACTCAAGAACGAATAA 57.139 33.333 0.00 0.00 0.00 1.40
1939 1959 4.883083 AGCTCACTCAAGAACGAATAACA 58.117 39.130 0.00 0.00 0.00 2.41
2125 2157 3.865745 AGCATTACAACTTCTCGATTCGG 59.134 43.478 6.18 0.00 0.00 4.30
2234 2266 3.256631 GGTTGACATCATGGCTTCAAGTT 59.743 43.478 0.00 0.00 0.00 2.66
2302 2335 6.293027 CCTTCTTTTGCAATTTTAAGCTGGTG 60.293 38.462 0.00 0.00 0.00 4.17
2380 2566 6.385649 TTGTGGAGTAGTTTCAACAATTCC 57.614 37.500 0.00 0.00 36.37 3.01
2472 2665 2.288395 GCACAGGAAAATGGACCAACAG 60.288 50.000 0.00 0.00 0.00 3.16
2500 2693 6.928979 TGTTAGAAGGAATTTGTTTGACGA 57.071 33.333 0.00 0.00 0.00 4.20
2511 2704 7.114388 GGAATTTGTTTGACGAGGAAATACAAC 59.886 37.037 0.00 0.00 0.00 3.32
2530 2723 6.559042 ACAACGTACGTGCACTTATATAAC 57.441 37.500 23.57 0.00 0.00 1.89
2557 2750 1.605232 ACCTTAAAAACGTGGAAGGCG 59.395 47.619 14.60 0.00 41.92 5.52
2763 2969 6.144724 GCCTTTCAGATGTATATTCACGTCTC 59.855 42.308 0.00 0.00 41.76 3.36
2774 2980 3.371102 TTCACGTCTCAACTTCCAGAG 57.629 47.619 0.00 0.00 0.00 3.35
2792 2998 1.268079 GAGAACTGCTGGAACCTTTGC 59.732 52.381 0.00 0.00 0.00 3.68
2811 3017 7.885399 ACCTTTGCATAAGAGATAAGAGTGTTT 59.115 33.333 9.37 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 95 4.811908 TCAACATTAAATCCGTCTCGACA 58.188 39.130 0.00 0.00 0.00 4.35
180 184 4.275689 TCAAACAGATGACACAGCGAATTT 59.724 37.500 0.00 0.00 0.00 1.82
182 186 3.402110 TCAAACAGATGACACAGCGAAT 58.598 40.909 0.00 0.00 0.00 3.34
215 220 6.998074 TGATTCAAACGCCCTCATTATTATCT 59.002 34.615 0.00 0.00 0.00 1.98
220 225 7.596494 CAATATGATTCAAACGCCCTCATTAT 58.404 34.615 0.00 0.00 0.00 1.28
229 234 5.722051 GCACAAAGCAATATGATTCAAACGC 60.722 40.000 0.00 0.00 44.79 4.84
230 235 5.778134 GCACAAAGCAATATGATTCAAACG 58.222 37.500 0.00 0.00 44.79 3.60
321 326 5.131784 TCGACTATCCCCTTCTTCTTCTAC 58.868 45.833 0.00 0.00 0.00 2.59
322 327 5.384145 TCGACTATCCCCTTCTTCTTCTA 57.616 43.478 0.00 0.00 0.00 2.10
323 328 4.252570 TCGACTATCCCCTTCTTCTTCT 57.747 45.455 0.00 0.00 0.00 2.85
325 330 4.342665 GTCATCGACTATCCCCTTCTTCTT 59.657 45.833 0.00 0.00 0.00 2.52
326 331 3.892588 GTCATCGACTATCCCCTTCTTCT 59.107 47.826 0.00 0.00 0.00 2.85
327 332 3.637229 TGTCATCGACTATCCCCTTCTTC 59.363 47.826 0.00 0.00 33.15 2.87
333 338 1.620819 AGCATGTCATCGACTATCCCC 59.379 52.381 0.00 0.00 33.15 4.81
334 339 3.759086 TCTAGCATGTCATCGACTATCCC 59.241 47.826 0.00 0.00 33.15 3.85
340 345 5.363979 TGACTATCTAGCATGTCATCGAC 57.636 43.478 0.00 0.00 34.94 4.20
505 510 3.053619 GGAAGAAAGGGGGCAGAAAGATA 60.054 47.826 0.00 0.00 0.00 1.98
536 542 2.044135 GGAAAGCAAACGCGAAAGAAG 58.956 47.619 15.93 0.00 0.00 2.85
537 543 1.673920 AGGAAAGCAAACGCGAAAGAA 59.326 42.857 15.93 0.00 0.00 2.52
538 544 1.002900 CAGGAAAGCAAACGCGAAAGA 60.003 47.619 15.93 0.00 0.00 2.52
539 545 1.398595 CAGGAAAGCAAACGCGAAAG 58.601 50.000 15.93 2.00 0.00 2.62
540 546 0.030101 CCAGGAAAGCAAACGCGAAA 59.970 50.000 15.93 0.00 0.00 3.46
541 547 1.098712 ACCAGGAAAGCAAACGCGAA 61.099 50.000 15.93 0.00 0.00 4.70
542 548 1.503818 GACCAGGAAAGCAAACGCGA 61.504 55.000 15.93 0.00 0.00 5.87
543 549 1.082104 GACCAGGAAAGCAAACGCG 60.082 57.895 3.53 3.53 0.00 6.01
544 550 1.285950 GGACCAGGAAAGCAAACGC 59.714 57.895 0.00 0.00 0.00 4.84
545 551 0.310854 GTGGACCAGGAAAGCAAACG 59.689 55.000 0.00 0.00 0.00 3.60
546 552 1.692411 AGTGGACCAGGAAAGCAAAC 58.308 50.000 0.00 0.00 0.00 2.93
547 553 2.441750 AGTAGTGGACCAGGAAAGCAAA 59.558 45.455 0.00 0.00 0.00 3.68
548 554 2.038557 GAGTAGTGGACCAGGAAAGCAA 59.961 50.000 0.00 0.00 0.00 3.91
549 555 1.623811 GAGTAGTGGACCAGGAAAGCA 59.376 52.381 0.00 0.00 0.00 3.91
550 556 1.623811 TGAGTAGTGGACCAGGAAAGC 59.376 52.381 0.00 0.00 0.00 3.51
551 557 4.223923 AGATTGAGTAGTGGACCAGGAAAG 59.776 45.833 0.00 0.00 0.00 2.62
552 558 4.020218 CAGATTGAGTAGTGGACCAGGAAA 60.020 45.833 0.00 0.00 0.00 3.13
553 559 3.515502 CAGATTGAGTAGTGGACCAGGAA 59.484 47.826 0.00 0.00 0.00 3.36
554 560 3.099905 CAGATTGAGTAGTGGACCAGGA 58.900 50.000 0.00 0.00 0.00 3.86
555 561 2.419297 GCAGATTGAGTAGTGGACCAGG 60.419 54.545 0.00 0.00 0.00 4.45
556 562 2.499289 AGCAGATTGAGTAGTGGACCAG 59.501 50.000 0.00 0.00 0.00 4.00
557 563 2.540383 AGCAGATTGAGTAGTGGACCA 58.460 47.619 0.00 0.00 0.00 4.02
558 564 3.618690 AAGCAGATTGAGTAGTGGACC 57.381 47.619 0.00 0.00 0.00 4.46
559 565 5.967088 TCTAAAGCAGATTGAGTAGTGGAC 58.033 41.667 0.00 0.00 0.00 4.02
560 566 6.214191 CTCTAAAGCAGATTGAGTAGTGGA 57.786 41.667 0.00 0.00 31.13 4.02
630 640 2.667137 CTCTTCAAGGTCACGTCTCAC 58.333 52.381 0.00 0.00 0.00 3.51
633 643 0.039074 CGCTCTTCAAGGTCACGTCT 60.039 55.000 0.00 0.00 0.00 4.18
641 651 0.807667 CCGTCCATCGCTCTTCAAGG 60.808 60.000 0.00 0.00 38.35 3.61
646 656 4.162690 GGGCCGTCCATCGCTCTT 62.163 66.667 0.00 0.00 38.35 2.85
697 707 2.742053 CAACGTACATGAACTTGAGGGG 59.258 50.000 0.00 0.00 0.00 4.79
760 771 2.543777 TGGCTAGCTTTTGACTCGTT 57.456 45.000 15.72 0.00 0.00 3.85
761 772 2.543777 TTGGCTAGCTTTTGACTCGT 57.456 45.000 15.72 0.00 0.00 4.18
762 773 4.425577 AATTTGGCTAGCTTTTGACTCG 57.574 40.909 15.72 0.00 0.00 4.18
764 775 6.294731 CCACTAAATTTGGCTAGCTTTTGACT 60.295 38.462 15.72 0.00 0.00 3.41
765 776 5.863935 CCACTAAATTTGGCTAGCTTTTGAC 59.136 40.000 15.72 0.00 0.00 3.18
766 777 5.538433 ACCACTAAATTTGGCTAGCTTTTGA 59.462 36.000 15.72 0.00 37.69 2.69
858 872 4.008330 GAGACGGGTATCATATTCCTCGA 58.992 47.826 0.00 0.00 0.00 4.04
975 989 5.049129 GCAAATGACATATACTCAGCTTCCC 60.049 44.000 0.00 0.00 0.00 3.97
1053 1068 2.263077 CATCACTGCTGTACGAAGGAC 58.737 52.381 0.00 0.00 0.00 3.85
1054 1069 1.404181 GCATCACTGCTGTACGAAGGA 60.404 52.381 0.00 0.00 45.32 3.36
1055 1070 1.002366 GCATCACTGCTGTACGAAGG 58.998 55.000 0.00 0.00 45.32 3.46
1670 1688 2.015587 GCAGAGAATGGCTTTGGAGAG 58.984 52.381 0.00 0.00 0.00 3.20
1764 1783 6.377996 CCCCAAGTGATAATTCATCAACAAGA 59.622 38.462 0.00 0.00 45.28 3.02
1775 1794 3.531397 TGGTGATCCCCCAAGTGATAATT 59.469 43.478 0.00 0.00 0.00 1.40
2125 2157 3.960102 AGGAGAGAGACCTGATCATTCAC 59.040 47.826 0.00 0.00 36.30 3.18
2234 2266 4.272504 CGCTTCTGGTTGTTCTGAGTTTAA 59.727 41.667 0.00 0.00 0.00 1.52
2302 2335 4.689612 TCCATCTTAGAGCCCATTACAC 57.310 45.455 0.00 0.00 0.00 2.90
2500 2693 2.733026 GTGCACGTACGTTGTATTTCCT 59.267 45.455 20.23 0.00 0.00 3.36
2511 2704 5.058856 CCATCGTTATATAAGTGCACGTACG 59.941 44.000 14.86 15.01 32.65 3.67
2530 2723 3.995705 TCCACGTTTTTAAGGTACCATCG 59.004 43.478 15.94 6.40 0.00 3.84
2709 2915 1.066002 TGAGAAACACAAGCTTGCAGC 59.934 47.619 26.27 11.23 42.84 5.25
2710 2916 3.637998 ATGAGAAACACAAGCTTGCAG 57.362 42.857 26.27 20.37 0.00 4.41
2722 2928 7.820648 TCTGAAAGGCTTCATTTATGAGAAAC 58.179 34.615 0.00 0.00 40.78 2.78
2774 2980 1.032014 TGCAAAGGTTCCAGCAGTTC 58.968 50.000 0.00 0.00 32.48 3.01
2859 3065 0.844221 AAGAGCTCCCTGCCCTCTTT 60.844 55.000 10.93 0.00 41.73 2.52


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

AutoCloner maintained by Alex Coulton.