Multiple sequence alignment - TraesCS5D01G384200

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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 TraesCS5D01G384200 chr5D 100.000 3234 0 0 1 3234 453819338 453816105 0.000000e+00 5973.0
1 TraesCS5D01G384200 chr5D 83.539 486 76 4 2751 3234 40091747 40092230 4.920000e-123 451.0
2 TraesCS5D01G384200 chr5B 92.449 2119 96 22 295 2356 554517332 554515221 0.000000e+00 2968.0
3 TraesCS5D01G384200 chr5B 96.787 498 16 0 2737 3234 554514833 554514336 0.000000e+00 832.0
4 TraesCS5D01G384200 chr5B 94.960 377 12 3 2452 2821 554515210 554514834 4.650000e-163 584.0
5 TraesCS5D01G384200 chr5B 84.362 486 72 4 2751 3234 33628672 33628189 1.050000e-129 473.0
6 TraesCS5D01G384200 chr5B 94.198 293 10 5 1 291 554518290 554518003 1.070000e-119 440.0
7 TraesCS5D01G384200 chr5A 92.973 1722 84 10 602 2290 572842978 572841261 0.000000e+00 2475.0
8 TraesCS5D01G384200 chr5A 91.291 999 39 14 2261 3234 572841258 572840283 0.000000e+00 1319.0
9 TraesCS5D01G384200 chr5A 94.242 330 18 1 295 623 572843483 572843154 1.340000e-138 503.0
10 TraesCS5D01G384200 chr5A 84.426 488 72 4 2749 3234 28104117 28104602 8.120000e-131 477.0
11 TraesCS5D01G384200 chr5A 91.803 244 14 4 48 291 572844031 572843794 5.170000e-88 335.0
12 TraesCS5D01G384200 chr7D 90.476 63 4 1 512 574 445118615 445118555 7.440000e-12 82.4
13 TraesCS5D01G384200 chr1A 87.692 65 6 2 511 575 429491094 429491032 1.240000e-09 75.0
14 TraesCS5D01G384200 chr7B 92.453 53 1 2 522 574 461473736 461473687 4.480000e-09 73.1
15 TraesCS5D01G384200 chr4B 87.097 62 6 2 513 574 497553617 497553558 5.790000e-08 69.4
16 TraesCS5D01G384200 chr4A 87.097 62 6 2 513 574 59483692 59483633 5.790000e-08 69.4
17 TraesCS5D01G384200 chr7A 90.385 52 2 3 523 574 567378743 567378791 7.490000e-07 65.8


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 TraesCS5D01G384200 chr5D 453816105 453819338 3233 True 5973 5973 100.00000 1 3234 1 chr5D.!!$R1 3233
1 TraesCS5D01G384200 chr5B 554514336 554518290 3954 True 1206 2968 94.59850 1 3234 4 chr5B.!!$R2 3233
2 TraesCS5D01G384200 chr5A 572840283 572844031 3748 True 1158 2475 92.57725 48 3234 4 chr5A.!!$R1 3186

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
581 1270 1.755959 TGCACACAGCCATTCTTTGTT 59.244 42.857 0.0 0.0 44.83 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 3366 0.609662 GCCTCACCACCAATTGCAAT 59.39 50.0 5.99 5.99 0.0 3.56 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
55 56 5.976534 TGTCACTACACACATTTCATTTTGC 59.023 36.000 0.00 0.00 0.00 3.68
84 85 6.069440 TCAGATTAGTGGGATTCAGGATTTGT 60.069 38.462 0.00 0.00 0.00 2.83
225 228 2.429610 GCTGATGATCAGGCAATGGTTT 59.570 45.455 22.69 0.00 44.43 3.27
231 234 4.661222 TGATCAGGCAATGGTTTTCTACA 58.339 39.130 0.00 0.00 0.00 2.74
266 269 9.079833 CATTCTTTCGTTATTCAGATTTTGCAT 57.920 29.630 0.00 0.00 0.00 3.96
267 270 9.643693 ATTCTTTCGTTATTCAGATTTTGCATT 57.356 25.926 0.00 0.00 0.00 3.56
268 271 9.474920 TTCTTTCGTTATTCAGATTTTGCATTT 57.525 25.926 0.00 0.00 0.00 2.32
372 1052 5.102953 TGGGATTGTTAGACAGGATCAAG 57.897 43.478 0.00 0.00 0.00 3.02
399 1079 7.392393 TGAGTTCATGATGCCTTTCCATATATG 59.608 37.037 5.68 5.68 0.00 1.78
408 1088 6.398095 TGCCTTTCCATATATGTCAGTATCG 58.602 40.000 11.73 0.00 0.00 2.92
424 1104 9.945904 TGTCAGTATCGTACTCATAAGATATCT 57.054 33.333 0.00 0.00 35.22 1.98
460 1140 3.881937 AGAAAATCCAGGAGCATTTGC 57.118 42.857 0.00 0.00 42.49 3.68
581 1270 1.755959 TGCACACAGCCATTCTTTGTT 59.244 42.857 0.00 0.00 44.83 2.83
696 1589 8.536175 TGTGTGGTAGTGAATTAGTGATTGATA 58.464 33.333 0.00 0.00 0.00 2.15
725 1618 5.871396 TTGTTACTCCCTCTGATCCATAC 57.129 43.478 0.00 0.00 0.00 2.39
749 1642 6.818644 ACTCATTGTCGCTGATTTAGTACAAT 59.181 34.615 0.00 0.00 41.57 2.71
898 1813 6.932901 AACAAATTGTCTATTGAATGTGCG 57.067 33.333 0.00 0.00 0.00 5.34
917 1832 2.153627 GCGCATTGCAAAACTAACACTG 59.846 45.455 1.71 0.00 45.45 3.66
945 1863 2.276732 TTTGTCTTCCCTCCTTGCAG 57.723 50.000 0.00 0.00 0.00 4.41
962 1880 2.025981 TGCAGGCCAACACTATCTCAAT 60.026 45.455 5.01 0.00 0.00 2.57
971 1889 6.374333 GCCAACACTATCTCAATTCTTACCAA 59.626 38.462 0.00 0.00 0.00 3.67
972 1890 7.094377 GCCAACACTATCTCAATTCTTACCAAA 60.094 37.037 0.00 0.00 0.00 3.28
982 1900 9.733556 TCTCAATTCTTACCAAACATAGCTAAA 57.266 29.630 0.00 0.00 0.00 1.85
997 1916 4.013267 AGCTAAATTGTCAGAGTGCTGT 57.987 40.909 0.00 0.00 42.84 4.40
1028 1947 4.930592 GCTTCAGCTCCTGTCCTC 57.069 61.111 0.00 0.00 38.21 3.71
1038 1957 0.842030 TCCTGTCCTCCATTGCCACT 60.842 55.000 0.00 0.00 0.00 4.00
1220 2140 2.430694 ACTGGGGTTTGAACTTTGAAGC 59.569 45.455 0.00 0.00 0.00 3.86
1253 2173 2.578786 CCTGCATGCCTGAATCACATA 58.421 47.619 16.68 0.00 0.00 2.29
1386 2306 4.367023 TGCTACCGGGTGCGTGTC 62.367 66.667 10.66 0.00 0.00 3.67
1470 2394 7.121759 CAGTAATCTTGATTTCATCAGGTGGTT 59.878 37.037 0.95 0.00 40.94 3.67
1474 2398 3.229293 TGATTTCATCAGGTGGTTTGCA 58.771 40.909 0.00 0.00 33.59 4.08
1650 2574 2.115910 CCTGGCCAAGCTGACCAA 59.884 61.111 7.01 0.00 31.81 3.67
1659 2583 4.681978 GCTGACCAACTCCGCGGT 62.682 66.667 27.15 3.60 38.56 5.68
1686 2610 4.265073 GCCTCATTCAAATCCAGTACACT 58.735 43.478 0.00 0.00 0.00 3.55
1692 2616 5.670792 TTCAAATCCAGTACACTCGGTAT 57.329 39.130 0.00 0.00 33.76 2.73
1800 2724 4.446385 GTCGTGTTAGCATTTGTGTCTGTA 59.554 41.667 0.00 0.00 0.00 2.74
1984 2908 2.937689 ATGCAGCAGTCCTGGGGT 60.938 61.111 0.00 0.00 42.03 4.95
2002 2929 1.148273 TGCGGTGTGGAAGCTTTCT 59.852 52.632 6.25 0.00 0.00 2.52
2005 2932 1.237285 CGGTGTGGAAGCTTTCTGGG 61.237 60.000 6.25 0.00 0.00 4.45
2035 2962 4.570874 GGCCCCTTCTCCATCCGC 62.571 72.222 0.00 0.00 0.00 5.54
2140 3067 2.747686 GTGGCGGTGAGGGAAAGA 59.252 61.111 0.00 0.00 0.00 2.52
2177 3104 2.903547 CGCCACGTGTTTGAAGGGG 61.904 63.158 15.65 1.36 0.00 4.79
2264 3196 0.645868 GTGAGAATGTAAGCCGCGAC 59.354 55.000 8.23 0.00 0.00 5.19
2297 3261 3.700038 GTGTAGCTTAGCCTGGAGTCTTA 59.300 47.826 0.00 0.00 0.00 2.10
2298 3262 3.700038 TGTAGCTTAGCCTGGAGTCTTAC 59.300 47.826 0.00 0.00 0.00 2.34
2300 3264 3.173965 AGCTTAGCCTGGAGTCTTACAA 58.826 45.455 0.00 0.00 0.00 2.41
2301 3265 3.777522 AGCTTAGCCTGGAGTCTTACAAT 59.222 43.478 0.00 0.00 0.00 2.71
2302 3266 4.123506 GCTTAGCCTGGAGTCTTACAATC 58.876 47.826 0.00 0.00 0.00 2.67
2306 3270 3.450457 AGCCTGGAGTCTTACAATCTCTG 59.550 47.826 0.00 0.00 0.00 3.35
2307 3271 3.449018 GCCTGGAGTCTTACAATCTCTGA 59.551 47.826 0.00 0.00 0.00 3.27
2308 3272 4.081420 GCCTGGAGTCTTACAATCTCTGAA 60.081 45.833 0.00 0.00 0.00 3.02
2309 3273 5.659463 CCTGGAGTCTTACAATCTCTGAAG 58.341 45.833 0.00 0.00 0.00 3.02
2310 3274 5.186797 CCTGGAGTCTTACAATCTCTGAAGT 59.813 44.000 0.00 0.00 0.00 3.01
2359 3324 0.597568 TTGGCTGATCAAACAAGCGG 59.402 50.000 7.45 0.00 0.00 5.52
2377 3342 2.896443 CTCGTCCCCTGGAGAAGC 59.104 66.667 0.00 0.00 29.39 3.86
2379 3344 3.068691 CGTCCCCTGGAGAAGCGA 61.069 66.667 0.00 0.00 29.39 4.93
2393 3358 3.265791 AGAAGCGATGTTGTGATCTTCC 58.734 45.455 0.00 0.00 32.62 3.46
2399 3364 4.670221 GCGATGTTGTGATCTTCCTTTCAC 60.670 45.833 0.00 0.00 42.05 3.18
2400 3365 4.142816 CGATGTTGTGATCTTCCTTTCACC 60.143 45.833 0.00 0.00 41.22 4.02
2401 3366 4.163441 TGTTGTGATCTTCCTTTCACCA 57.837 40.909 0.00 0.00 41.22 4.17
2458 3437 7.333921 ACATGATCTAAGCTTTCTTGAGACTTG 59.666 37.037 3.20 7.06 33.85 3.16
2470 3450 3.836365 TGAGACTTGAACCATGTGACA 57.164 42.857 0.00 0.00 0.00 3.58
2478 3458 5.009010 ACTTGAACCATGTGACAAAGATGAC 59.991 40.000 0.00 0.00 31.04 3.06
2480 3460 3.507162 ACCATGTGACAAAGATGACCA 57.493 42.857 0.00 0.00 31.04 4.02
2481 3461 3.831323 ACCATGTGACAAAGATGACCAA 58.169 40.909 0.00 0.00 31.04 3.67
2482 3462 4.214310 ACCATGTGACAAAGATGACCAAA 58.786 39.130 0.00 0.00 31.04 3.28
2483 3463 4.648762 ACCATGTGACAAAGATGACCAAAA 59.351 37.500 0.00 0.00 31.04 2.44
2500 3487 6.481644 TGACCAAAATGCAAACAAAGATAACC 59.518 34.615 0.00 0.00 0.00 2.85
2512 3499 9.528018 CAAACAAAGATAACCAAAACACATAGT 57.472 29.630 0.00 0.00 0.00 2.12
2606 3593 9.130312 GCATAATACAGTACAGTTATGTAGCTC 57.870 37.037 11.53 0.00 42.53 4.09
2741 3728 6.142817 ACAAATTAACGATGCTGAAACAGAC 58.857 36.000 2.81 0.00 32.44 3.51
2744 3731 1.419374 ACGATGCTGAAACAGACGAC 58.581 50.000 15.09 0.00 32.44 4.34
2772 3844 3.256620 GCATATTTGCTCAACGGCC 57.743 52.632 0.35 0.00 45.77 6.13
2919 3991 2.895680 GATCTCAGACTGGCGCCA 59.104 61.111 30.59 30.59 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 6.359804 TCCTGAATCCCACTAATCTGAAATG 58.640 40.000 0.00 0.00 0.00 2.32
84 85 4.955811 TTCTAGAAGAAGAGCACCACAA 57.044 40.909 0.00 0.00 29.50 3.33
184 186 9.029243 CATCAGCTTCTAGTATGTAAACAGAAG 57.971 37.037 5.49 5.49 43.23 2.85
225 228 3.806949 AGAATGTTGGGGCTTGTAGAA 57.193 42.857 0.00 0.00 0.00 2.10
231 234 1.995376 ACGAAAGAATGTTGGGGCTT 58.005 45.000 0.00 0.00 0.00 4.35
284 287 9.784824 CGAGAGCAGATTTTAATAACGAATTAG 57.215 33.333 0.00 0.00 31.68 1.73
291 294 9.774742 AATGAAACGAGAGCAGATTTTAATAAC 57.225 29.630 0.00 0.00 0.00 1.89
372 1052 3.084039 TGGAAAGGCATCATGAACTCAC 58.916 45.455 0.00 0.00 0.00 3.51
447 1127 1.546923 TCAATGTGCAAATGCTCCTGG 59.453 47.619 6.97 0.00 42.66 4.45
515 1204 5.004448 GGTTTCACCCTCCTTTTAGAAGAG 58.996 45.833 0.00 0.00 31.02 2.85
581 1270 2.571202 TGGGACAGATGCACACATTCTA 59.429 45.455 0.00 0.00 36.35 2.10
696 1589 5.319043 TCAGAGGGAGTAACAAAAATGGT 57.681 39.130 0.00 0.00 0.00 3.55
725 1618 6.647212 TTGTACTAAATCAGCGACAATGAG 57.353 37.500 0.00 0.00 31.65 2.90
749 1642 2.367241 TCCGCTCCGATCCATATCAAAA 59.633 45.455 0.00 0.00 31.93 2.44
898 1813 4.209080 GGAACAGTGTTAGTTTTGCAATGC 59.791 41.667 8.88 0.00 32.32 3.56
917 1832 4.471747 AGGAGGGAAGACAAATAGAGGAAC 59.528 45.833 0.00 0.00 0.00 3.62
945 1863 5.297029 GGTAAGAATTGAGATAGTGTTGGCC 59.703 44.000 0.00 0.00 0.00 5.36
962 1880 9.290988 TGACAATTTAGCTATGTTTGGTAAGAA 57.709 29.630 12.64 0.00 0.00 2.52
971 1889 6.093219 CAGCACTCTGACAATTTAGCTATGTT 59.907 38.462 0.00 0.00 42.95 2.71
972 1890 5.583854 CAGCACTCTGACAATTTAGCTATGT 59.416 40.000 0.00 0.00 42.95 2.29
982 1900 3.079578 CCATTCACAGCACTCTGACAAT 58.920 45.455 0.00 0.00 42.95 2.71
984 1902 1.879372 GCCATTCACAGCACTCTGACA 60.879 52.381 0.00 0.00 42.95 3.58
985 1903 0.801251 GCCATTCACAGCACTCTGAC 59.199 55.000 0.00 0.00 42.95 3.51
986 1904 0.689055 AGCCATTCACAGCACTCTGA 59.311 50.000 0.00 0.00 42.95 3.27
1028 1947 5.677091 GCAATAACAACTCTAGTGGCAATGG 60.677 44.000 0.00 0.00 0.00 3.16
1038 1957 6.874134 GGAAGAGTGAAGCAATAACAACTCTA 59.126 38.462 3.75 0.00 33.56 2.43
1204 2124 6.638468 CAGACATTAGCTTCAAAGTTCAAACC 59.362 38.462 0.00 0.00 0.00 3.27
1213 2133 4.397103 CAGGCATCAGACATTAGCTTCAAA 59.603 41.667 0.00 0.00 0.00 2.69
1220 2140 2.031069 GCATGCAGGCATCAGACATTAG 60.031 50.000 20.11 0.00 33.90 1.73
1253 2173 2.040544 GCGCCACCTACAACAGCAT 61.041 57.895 0.00 0.00 0.00 3.79
1429 2353 8.506437 TCAAGATTACTGAATGTCAAATGTCAC 58.494 33.333 0.00 0.00 0.00 3.67
1629 2553 1.115326 GGTCAGCTTGGCCAGGTTTT 61.115 55.000 17.25 0.00 42.98 2.43
1659 2583 1.272592 TGGATTTGAATGAGGCCAGCA 60.273 47.619 5.01 2.36 0.00 4.41
1671 2595 4.679639 GCATACCGAGTGTACTGGATTTGA 60.680 45.833 0.00 0.00 30.62 2.69
1686 2610 4.681074 TCCATCAACTTATGCATACCGA 57.319 40.909 5.74 1.11 0.00 4.69
1718 2642 2.420129 GGCCGTGAAGAGTAACCATGAT 60.420 50.000 0.00 0.00 0.00 2.45
1800 2724 1.068083 CAGTCACAGGTCACGCTGT 59.932 57.895 0.00 0.00 0.00 4.40
1984 2908 1.148273 AGAAAGCTTCCACACCGCA 59.852 52.632 0.00 0.00 0.00 5.69
2020 2947 2.770048 AGGCGGATGGAGAAGGGG 60.770 66.667 0.00 0.00 0.00 4.79
2155 3082 4.893601 TCAAACACGTGGCGCCGA 62.894 61.111 23.90 8.37 0.00 5.54
2323 3288 7.190335 TCAGCCAAGCTACTTATAAGGTTTA 57.810 36.000 16.73 0.00 36.40 2.01
2326 3291 5.366768 TGATCAGCCAAGCTACTTATAAGGT 59.633 40.000 16.73 5.32 36.40 3.50
2328 3293 7.280876 TGTTTGATCAGCCAAGCTACTTATAAG 59.719 37.037 11.05 11.05 36.40 1.73
2329 3294 7.109501 TGTTTGATCAGCCAAGCTACTTATAA 58.890 34.615 0.00 0.00 36.40 0.98
2330 3295 6.649155 TGTTTGATCAGCCAAGCTACTTATA 58.351 36.000 0.00 0.00 36.40 0.98
2331 3296 5.500234 TGTTTGATCAGCCAAGCTACTTAT 58.500 37.500 0.00 0.00 36.40 1.73
2359 3324 2.896443 CTTCTCCAGGGGACGAGC 59.104 66.667 0.00 0.00 0.00 5.03
2377 3342 4.142816 GGTGAAAGGAAGATCACAACATCG 60.143 45.833 8.04 0.00 46.07 3.84
2379 3344 4.728772 TGGTGAAAGGAAGATCACAACAT 58.271 39.130 8.04 0.00 46.07 2.71
2399 3364 1.066716 CCTCACCACCAATTGCAATGG 60.067 52.381 13.82 17.73 43.84 3.16
2400 3365 1.673626 GCCTCACCACCAATTGCAATG 60.674 52.381 13.82 3.77 0.00 2.82
2401 3366 0.609662 GCCTCACCACCAATTGCAAT 59.390 50.000 5.99 5.99 0.00 3.56
2428 3393 6.939622 TCAAGAAAGCTTAGATCATGTCAGA 58.060 36.000 0.00 0.00 31.81 3.27
2458 3437 3.820467 TGGTCATCTTTGTCACATGGTTC 59.180 43.478 0.00 0.00 0.00 3.62
2470 3450 6.822676 TCTTTGTTTGCATTTTGGTCATCTTT 59.177 30.769 0.00 0.00 0.00 2.52
2478 3458 6.857777 TGGTTATCTTTGTTTGCATTTTGG 57.142 33.333 0.00 0.00 0.00 3.28
2480 3460 8.734386 TGTTTTGGTTATCTTTGTTTGCATTTT 58.266 25.926 0.00 0.00 0.00 1.82
2481 3461 8.180920 GTGTTTTGGTTATCTTTGTTTGCATTT 58.819 29.630 0.00 0.00 0.00 2.32
2482 3462 7.335422 TGTGTTTTGGTTATCTTTGTTTGCATT 59.665 29.630 0.00 0.00 0.00 3.56
2483 3463 6.820656 TGTGTTTTGGTTATCTTTGTTTGCAT 59.179 30.769 0.00 0.00 0.00 3.96
2500 3487 6.151985 TGGGCAAGGTATAACTATGTGTTTTG 59.848 38.462 0.00 0.00 39.89 2.44
2606 3593 5.695851 ATTCCTGCTTGAGTTAACACTTG 57.304 39.130 8.61 0.47 31.22 3.16
2772 3844 2.879907 CCTGCCCAGATTGTTGCG 59.120 61.111 0.00 0.00 0.00 4.85
2847 3919 1.303948 CCCCATCATGTGCCTGTCA 59.696 57.895 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.