Multiple sequence alignment - TraesCS4D01G052900

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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 TraesCS4D01G052900 chr4D 100.000 2600 0 0 1 2600 29026867 29024268 0.000000e+00 4802.0
1 TraesCS4D01G052900 chr4B 93.771 1493 53 10 736 2189 41556888 41555397 0.000000e+00 2206.0
2 TraesCS4D01G052900 chr4B 84.211 266 26 7 2265 2522 41555300 41555043 7.190000e-61 244.0
3 TraesCS4D01G052900 chr4B 100.000 35 0 0 2566 2600 41554994 41554960 6.010000e-07 65.8
4 TraesCS4D01G052900 chr4A 94.426 1184 35 6 1025 2189 574520716 574521887 0.000000e+00 1792.0
5 TraesCS4D01G052900 chr4A 82.143 448 42 19 2189 2600 574522235 574522680 1.480000e-92 350.0
6 TraesCS4D01G052900 chr4A 88.699 292 17 11 701 985 574520067 574520349 2.480000e-90 342.0
7 TraesCS4D01G052900 chr7D 97.756 713 13 3 1 710 492212589 492211877 0.000000e+00 1225.0
8 TraesCS4D01G052900 chr7D 86.686 338 27 10 1 324 412585120 412584787 2.460000e-95 359.0
9 TraesCS4D01G052900 chr7D 99.219 128 1 0 1 128 492212853 492212726 5.600000e-57 231.0
10 TraesCS4D01G052900 chr7D 87.850 107 13 0 595 701 556322214 556322320 2.720000e-25 126.0
11 TraesCS4D01G052900 chr6D 97.878 707 13 2 1 705 439658479 439659185 0.000000e+00 1221.0
12 TraesCS4D01G052900 chr2D 98.009 703 12 2 1 701 120257860 120257158 0.000000e+00 1219.0
13 TraesCS4D01G052900 chr7B 94.877 527 21 5 1 524 521587601 521587078 0.000000e+00 819.0
14 TraesCS4D01G052900 chr7B 84.203 728 85 22 1 705 426834856 426834136 0.000000e+00 680.0
15 TraesCS4D01G052900 chr7A 83.648 636 73 23 75 700 473808924 473808310 1.040000e-158 569.0
16 TraesCS4D01G052900 chr6A 80.150 267 45 8 451 711 74718129 74717865 2.640000e-45 193.0
17 TraesCS4D01G052900 chr6A 80.150 267 45 8 451 711 74729809 74729545 2.640000e-45 193.0
18 TraesCS4D01G052900 chr6A 80.150 267 45 8 451 711 74741884 74741620 2.640000e-45 193.0


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 TraesCS4D01G052900 chr4D 29024268 29026867 2599 True 4802.0 4802 100.000000 1 2600 1 chr4D.!!$R1 2599
1 TraesCS4D01G052900 chr4B 41554960 41556888 1928 True 838.6 2206 92.660667 736 2600 3 chr4B.!!$R1 1864
2 TraesCS4D01G052900 chr4A 574520067 574522680 2613 False 828.0 1792 88.422667 701 2600 3 chr4A.!!$F1 1899
3 TraesCS4D01G052900 chr7D 492211877 492212853 976 True 728.0 1225 98.487500 1 710 2 chr7D.!!$R2 709
4 TraesCS4D01G052900 chr6D 439658479 439659185 706 False 1221.0 1221 97.878000 1 705 1 chr6D.!!$F1 704
5 TraesCS4D01G052900 chr2D 120257158 120257860 702 True 1219.0 1219 98.009000 1 701 1 chr2D.!!$R1 700
6 TraesCS4D01G052900 chr7B 521587078 521587601 523 True 819.0 819 94.877000 1 524 1 chr7B.!!$R2 523
7 TraesCS4D01G052900 chr7B 426834136 426834856 720 True 680.0 680 84.203000 1 705 1 chr7B.!!$R1 704
8 TraesCS4D01G052900 chr7A 473808310 473808924 614 True 569.0 569 83.648000 75 700 1 chr7A.!!$R1 625

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
703 1012 0.242555 CACCGGCGCATTTACCTTTT 59.757 50.0 10.83 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2825 1.82997 GCTAATGGGGCCTGCTTCC 60.83 63.158 0.84 0.0 0.0 3.46 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
510 811 4.134623 AAAAACGTCGCTCCAGCA 57.865 50.000 0.00 0.00 42.21 4.41
573 881 1.004320 ACGGAAGCGGCATACACAA 60.004 52.632 1.45 0.00 0.00 3.33
701 1010 2.043980 CCACCGGCGCATTTACCTT 61.044 57.895 10.83 0.00 0.00 3.50
702 1011 1.591504 CCACCGGCGCATTTACCTTT 61.592 55.000 10.83 0.00 0.00 3.11
703 1012 0.242555 CACCGGCGCATTTACCTTTT 59.757 50.000 10.83 0.00 0.00 2.27
704 1013 0.963225 ACCGGCGCATTTACCTTTTT 59.037 45.000 10.83 0.00 0.00 1.94
734 1043 8.594881 TGAAACAAGTTTGCTCTTTGTTTTTA 57.405 26.923 13.67 6.14 33.51 1.52
887 1207 1.468520 CCAACTGCCCAAACTACATCG 59.531 52.381 0.00 0.00 0.00 3.84
935 1255 3.641648 CAGCCAAATCGAGATCTCTCTC 58.358 50.000 20.26 0.00 43.86 3.20
936 1256 2.627699 AGCCAAATCGAGATCTCTCTCC 59.372 50.000 20.26 2.93 44.36 3.71
1005 1336 0.967380 CCACCAGAGGAAACATGGCC 60.967 60.000 0.00 0.00 41.75 5.36
1180 1837 0.526524 GCTCGACTCCATGAAGTCCG 60.527 60.000 6.50 2.28 42.23 4.79
1521 2178 0.035915 GGACCAACCTCCAGAAGCTC 60.036 60.000 0.00 0.00 35.41 4.09
1682 2344 2.362397 TGCTAGATTTCGCACCTCTAGG 59.638 50.000 0.00 0.00 39.14 3.02
1683 2345 2.288518 GCTAGATTTCGCACCTCTAGGG 60.289 54.545 0.20 0.00 39.14 3.53
1780 2444 9.214953 GTTATGAGCTTGATTTTTGTAAGATCG 57.785 33.333 0.00 0.00 39.10 3.69
1808 2472 9.000486 ACTATTGATGCATGAGATTTATGTCTG 58.000 33.333 2.46 0.00 0.00 3.51
2057 2739 5.458779 GCCTGTATGTTGAAACAGTTTTGTC 59.541 40.000 0.00 0.00 43.04 3.18
2105 2787 8.409358 AGTCCAAGAATACAACAATTTAGCTT 57.591 30.769 0.00 0.00 0.00 3.74
2125 2807 4.935205 GCTTGTTTTCCTCCTTGTTTTGTT 59.065 37.500 0.00 0.00 0.00 2.83
2133 2815 9.541143 TTTTCCTCCTTGTTTTGTTTATGAATC 57.459 29.630 0.00 0.00 0.00 2.52
2143 2825 7.167302 TGTTTTGTTTATGAATCTGAAGTTGCG 59.833 33.333 0.00 0.00 0.00 4.85
2172 2854 3.361786 GCCCCATTAGCTTTTCCTTGTA 58.638 45.455 0.00 0.00 0.00 2.41
2197 3227 3.064820 TCTGAGAACGTGTTTTTGGCTTC 59.935 43.478 0.00 0.00 0.00 3.86
2198 3228 2.223157 TGAGAACGTGTTTTTGGCTTCG 60.223 45.455 0.00 0.00 0.00 3.79
2200 3230 2.420722 AGAACGTGTTTTTGGCTTCGAA 59.579 40.909 0.00 0.00 0.00 3.71
2203 3233 2.918600 ACGTGTTTTTGGCTTCGAAAAC 59.081 40.909 12.52 12.52 46.95 2.43
2228 3260 8.784043 ACTCTCAAACTATTTTGTGTTGATACC 58.216 33.333 5.56 0.00 42.51 2.73
2229 3261 7.802738 TCTCAAACTATTTTGTGTTGATACCG 58.197 34.615 5.56 0.00 42.51 4.02
2233 3265 5.553123 ACTATTTTGTGTTGATACCGTGGA 58.447 37.500 0.00 0.00 0.00 4.02
2263 3295 3.069872 CAGCTGAGCTCCATCTGAACTAT 59.930 47.826 8.42 0.00 40.49 2.12
2267 3299 5.668471 CTGAGCTCCATCTGAACTATTTCA 58.332 41.667 12.15 0.00 39.55 2.69
2288 3320 6.053632 TCATGTTAGTCTGTTGATGTGGAT 57.946 37.500 0.00 0.00 0.00 3.41
2293 3325 6.212589 TGTTAGTCTGTTGATGTGGATAAGGA 59.787 38.462 0.00 0.00 0.00 3.36
2297 3329 6.825721 AGTCTGTTGATGTGGATAAGGATTTC 59.174 38.462 0.00 0.00 0.00 2.17
2306 3338 6.357367 TGTGGATAAGGATTTCTTAGCTTCC 58.643 40.000 0.00 0.00 42.31 3.46
2322 3354 3.327757 AGCTTCCATGTCCAAGAAGTGTA 59.672 43.478 9.48 0.00 39.36 2.90
2333 3365 8.640063 TGTCCAAGAAGTGTACACTATAGTTA 57.360 34.615 28.13 10.83 41.58 2.24
2383 3415 8.996271 GTCATGATTTCTATCATTCTGTGCATA 58.004 33.333 0.00 0.00 46.88 3.14
2401 3440 9.113838 CTGTGCATAGATCTTATTGGTTTTAGT 57.886 33.333 4.09 0.00 0.00 2.24
2409 3448 9.892130 AGATCTTATTGGTTTTAGTCTAGGTTG 57.108 33.333 0.00 0.00 0.00 3.77
2412 3451 9.933723 TCTTATTGGTTTTAGTCTAGGTTGTAC 57.066 33.333 0.00 0.00 0.00 2.90
2416 3455 7.069877 TGGTTTTAGTCTAGGTTGTACACAT 57.930 36.000 0.00 0.00 0.00 3.21
2417 3456 7.156673 TGGTTTTAGTCTAGGTTGTACACATC 58.843 38.462 0.00 0.00 0.00 3.06
2418 3457 6.309737 GGTTTTAGTCTAGGTTGTACACATCG 59.690 42.308 0.00 0.00 0.00 3.84
2419 3458 6.822667 TTTAGTCTAGGTTGTACACATCGA 57.177 37.500 0.00 0.00 0.00 3.59
2420 3459 7.400599 TTTAGTCTAGGTTGTACACATCGAT 57.599 36.000 0.00 0.00 0.00 3.59
2421 3460 5.916661 AGTCTAGGTTGTACACATCGATT 57.083 39.130 0.00 0.00 0.00 3.34
2423 3462 7.400599 AGTCTAGGTTGTACACATCGATTAA 57.599 36.000 0.00 0.00 0.00 1.40
2424 3463 8.008513 AGTCTAGGTTGTACACATCGATTAAT 57.991 34.615 0.00 0.00 0.00 1.40
2425 3464 8.475639 AGTCTAGGTTGTACACATCGATTAATT 58.524 33.333 0.00 0.00 0.00 1.40
2426 3465 9.095065 GTCTAGGTTGTACACATCGATTAATTT 57.905 33.333 0.00 0.00 0.00 1.82
2437 3476 7.134815 CACATCGATTAATTTAGCCAAAGGAG 58.865 38.462 0.00 0.00 0.00 3.69
2439 3478 7.339466 ACATCGATTAATTTAGCCAAAGGAGTT 59.661 33.333 0.00 0.00 0.00 3.01
2475 3514 2.024176 AATAGACGGTGGACATGCAC 57.976 50.000 0.00 0.00 0.00 4.57
2484 3526 1.812571 GTGGACATGCACCCTAACTTG 59.187 52.381 7.00 0.00 0.00 3.16
2501 3544 5.738619 AACTTGTTTCCAGGAAAAACTGT 57.261 34.783 16.70 9.72 37.48 3.55
2503 3546 4.159693 ACTTGTTTCCAGGAAAAACTGTCC 59.840 41.667 16.70 3.00 37.48 4.02
2511 3554 3.897505 CAGGAAAAACTGTCCCTCCAATT 59.102 43.478 5.22 0.00 35.59 2.32
2512 3555 4.021981 CAGGAAAAACTGTCCCTCCAATTC 60.022 45.833 5.22 0.00 35.59 2.17
2524 3590 4.019174 CCCTCCAATTCATGCTAACAAGT 58.981 43.478 0.00 0.00 0.00 3.16
2543 3609 3.700538 AGTTGACCACATATGCCATGTT 58.299 40.909 1.58 0.00 0.00 2.71
2545 3611 3.084536 TGACCACATATGCCATGTTGT 57.915 42.857 1.58 5.31 31.67 3.32
2547 3613 3.443329 TGACCACATATGCCATGTTGTTC 59.557 43.478 1.58 0.00 29.56 3.18
2548 3614 3.429492 ACCACATATGCCATGTTGTTCA 58.571 40.909 1.58 0.00 0.00 3.18
2550 3616 4.467082 ACCACATATGCCATGTTGTTCAAT 59.533 37.500 1.58 0.00 0.00 2.57
2551 3617 4.806775 CCACATATGCCATGTTGTTCAATG 59.193 41.667 1.58 0.00 0.00 2.82
2552 3618 4.269123 CACATATGCCATGTTGTTCAATGC 59.731 41.667 1.58 0.00 0.00 3.56
2553 3619 4.081586 ACATATGCCATGTTGTTCAATGCA 60.082 37.500 1.58 0.00 39.59 3.96
2554 3620 3.620427 ATGCCATGTTGTTCAATGCAT 57.380 38.095 0.00 0.00 40.21 3.96
2555 3621 2.962125 TGCCATGTTGTTCAATGCATC 58.038 42.857 0.00 0.00 33.73 3.91
2556 3622 2.563620 TGCCATGTTGTTCAATGCATCT 59.436 40.909 0.00 0.00 33.73 2.90
2557 3623 2.927477 GCCATGTTGTTCAATGCATCTG 59.073 45.455 0.00 0.85 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
573 881 9.608617 CATATACGTTTCATTCTCGTATGTAGT 57.391 33.333 16.12 0.00 45.77 2.73
705 1014 7.489574 ACAAAGAGCAAACTTGTTTCAAAAA 57.510 28.000 0.00 0.00 0.00 1.94
706 1015 7.489574 AACAAAGAGCAAACTTGTTTCAAAA 57.510 28.000 0.00 0.00 0.00 2.44
707 1016 7.489574 AAACAAAGAGCAAACTTGTTTCAAA 57.510 28.000 11.07 0.00 32.05 2.69
708 1017 7.489574 AAAACAAAGAGCAAACTTGTTTCAA 57.510 28.000 15.02 0.00 34.06 2.69
709 1018 7.489574 AAAAACAAAGAGCAAACTTGTTTCA 57.510 28.000 15.02 0.00 34.06 2.69
710 1019 8.491950 TGTAAAAACAAAGAGCAAACTTGTTTC 58.508 29.630 15.02 7.51 34.06 2.78
718 1027 7.118535 GGTTTCCTTGTAAAAACAAAGAGCAAA 59.881 33.333 0.00 0.00 37.16 3.68
727 1036 4.962995 TGGGATGGTTTCCTTGTAAAAACA 59.037 37.500 0.00 0.00 44.75 2.83
734 1043 3.922375 TCTTTTGGGATGGTTTCCTTGT 58.078 40.909 0.00 0.00 44.75 3.16
748 1057 2.628178 GTTGGGAGGAGGTTTCTTTTGG 59.372 50.000 0.00 0.00 0.00 3.28
858 1168 0.613292 TGGGCAGTTGGTTGTTGTGT 60.613 50.000 0.00 0.00 0.00 3.72
943 1263 3.706373 CGTGTGGTGGGAGAGGGG 61.706 72.222 0.00 0.00 0.00 4.79
1233 1890 2.464459 GCGGTCCATCTTCTTGGCG 61.464 63.158 0.00 0.00 36.66 5.69
1640 2302 2.293765 CGTAGCAGCGCGGAATAAA 58.706 52.632 13.03 0.00 0.00 1.40
1641 2303 4.006532 CGTAGCAGCGCGGAATAA 57.993 55.556 13.03 0.00 0.00 1.40
1691 2353 7.160049 CACCATGCTGATCTATTCACTTCTAT 58.840 38.462 0.00 0.00 0.00 1.98
1780 2444 8.332996 ACATAAATCTCATGCATCAATAGTCC 57.667 34.615 0.00 0.00 0.00 3.85
1808 2472 9.849166 TTAATGCAGTTTTAAGCCACTAATAAC 57.151 29.630 0.00 0.00 0.00 1.89
2017 2699 4.654091 ACAGGCACATATTTAATGGCAC 57.346 40.909 0.00 0.00 41.15 5.01
2079 2761 8.045176 AGCTAAATTGTTGTATTCTTGGACTC 57.955 34.615 0.00 0.00 0.00 3.36
2105 2787 7.841956 TCATAAACAAAACAAGGAGGAAAACA 58.158 30.769 0.00 0.00 0.00 2.83
2108 2790 8.923270 AGATTCATAAACAAAACAAGGAGGAAA 58.077 29.630 0.00 0.00 0.00 3.13
2125 2807 4.094887 GCTTCCGCAACTTCAGATTCATAA 59.905 41.667 0.00 0.00 35.78 1.90
2143 2825 1.829970 GCTAATGGGGCCTGCTTCC 60.830 63.158 0.84 0.00 0.00 3.46
2172 2854 4.097892 AGCCAAAAACACGTTCTCAGAAAT 59.902 37.500 0.00 0.00 0.00 2.17
2197 3227 8.523464 CAACACAAAATAGTTTGAGAGTTTTCG 58.477 33.333 21.48 8.12 45.99 3.46
2198 3228 9.567848 TCAACACAAAATAGTTTGAGAGTTTTC 57.432 29.630 21.48 0.00 45.99 2.29
2203 3233 7.957484 CGGTATCAACACAAAATAGTTTGAGAG 59.043 37.037 21.48 12.70 45.99 3.20
2228 3260 2.865670 GCTCAGCTGATCCTTATCCACG 60.866 54.545 18.63 1.60 0.00 4.94
2229 3261 2.368221 AGCTCAGCTGATCCTTATCCAC 59.632 50.000 18.63 0.00 37.57 4.02
2233 3265 2.687297 TGGAGCTCAGCTGATCCTTAT 58.313 47.619 28.37 7.24 42.52 1.73
2263 3295 6.295249 TCCACATCAACAGACTAACATGAAA 58.705 36.000 0.00 0.00 0.00 2.69
2267 3299 7.050377 CCTTATCCACATCAACAGACTAACAT 58.950 38.462 0.00 0.00 0.00 2.71
2288 3320 6.069673 TGGACATGGAAGCTAAGAAATCCTTA 60.070 38.462 0.00 0.00 36.34 2.69
2293 3325 5.819991 TCTTGGACATGGAAGCTAAGAAAT 58.180 37.500 0.00 0.00 0.00 2.17
2297 3329 4.394300 CACTTCTTGGACATGGAAGCTAAG 59.606 45.833 8.14 3.66 39.77 2.18
2322 3354 9.288576 GGTTTAAAGGGTGTTTAACTATAGTGT 57.711 33.333 6.06 0.00 0.00 3.55
2333 3365 4.800023 ACTGCTAGGTTTAAAGGGTGTTT 58.200 39.130 0.00 0.00 0.00 2.83
2383 3415 9.892130 CAACCTAGACTAAAACCAATAAGATCT 57.108 33.333 0.00 0.00 0.00 2.75
2393 3432 6.309737 CGATGTGTACAACCTAGACTAAAACC 59.690 42.308 0.00 0.00 0.00 3.27
2407 3446 7.851387 TGGCTAAATTAATCGATGTGTACAA 57.149 32.000 0.00 0.00 0.00 2.41
2409 3448 7.855904 CCTTTGGCTAAATTAATCGATGTGTAC 59.144 37.037 0.00 0.00 0.00 2.90
2412 3451 7.026631 TCCTTTGGCTAAATTAATCGATGTG 57.973 36.000 0.00 0.00 0.00 3.21
2416 3455 8.974060 ATAACTCCTTTGGCTAAATTAATCGA 57.026 30.769 0.00 0.00 0.00 3.59
2424 3463 9.416284 CCCTTATTAATAACTCCTTTGGCTAAA 57.584 33.333 3.71 0.00 0.00 1.85
2425 3464 8.562635 ACCCTTATTAATAACTCCTTTGGCTAA 58.437 33.333 3.71 0.00 0.00 3.09
2426 3465 8.109560 ACCCTTATTAATAACTCCTTTGGCTA 57.890 34.615 3.71 0.00 0.00 3.93
2446 3485 4.081254 GTCCACCGTCTATTAAGAACCCTT 60.081 45.833 0.00 0.00 32.16 3.95
2475 3514 5.362717 AGTTTTTCCTGGAAACAAGTTAGGG 59.637 40.000 21.00 0.00 42.06 3.53
2484 3526 3.296854 AGGGACAGTTTTTCCTGGAAAC 58.703 45.455 21.00 11.87 36.75 2.78
2501 3544 4.263905 ACTTGTTAGCATGAATTGGAGGGA 60.264 41.667 0.00 0.00 0.00 4.20
2503 3546 5.183713 TCAACTTGTTAGCATGAATTGGAGG 59.816 40.000 0.00 0.00 0.00 4.30
2511 3554 3.814625 TGTGGTCAACTTGTTAGCATGA 58.185 40.909 0.00 0.00 0.00 3.07
2512 3555 4.771590 ATGTGGTCAACTTGTTAGCATG 57.228 40.909 0.00 0.00 0.00 4.06
2524 3590 3.429492 ACAACATGGCATATGTGGTCAA 58.571 40.909 15.00 0.00 30.82 3.18
2545 3611 7.391275 TGAATCACTAAGTTCAGATGCATTGAA 59.609 33.333 15.74 15.74 31.24 2.69
2547 3613 7.080353 TGAATCACTAAGTTCAGATGCATTG 57.920 36.000 0.00 1.43 31.24 2.82
2548 3614 7.555195 TGATGAATCACTAAGTTCAGATGCATT 59.445 33.333 0.00 0.00 36.99 3.56
2550 3616 6.408869 TGATGAATCACTAAGTTCAGATGCA 58.591 36.000 0.00 0.00 37.72 3.96
2551 3617 6.760298 TCTGATGAATCACTAAGTTCAGATGC 59.240 38.462 7.63 0.00 37.72 3.91
2552 3618 8.713737 TTCTGATGAATCACTAAGTTCAGATG 57.286 34.615 11.35 0.00 38.24 2.90


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

AutoCloner maintained by Alex Coulton.