Multiple sequence alignment - TraesCS5D01G006200

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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 TraesCS5D01G006200 chr5D 100.000 3787 0 0 1 3787 5276711 5272925 0.000000e+00 6994.0
1 TraesCS5D01G006200 chr5B 95.081 2968 110 19 1 2956 6623138 6626081 0.000000e+00 4639.0
2 TraesCS5D01G006200 chr5B 88.580 1296 129 11 1668 2944 31142509 31143804 0.000000e+00 1555.0
3 TraesCS5D01G006200 chr5B 86.919 1269 159 3 1683 2944 6474723 6475991 0.000000e+00 1417.0
4 TraesCS5D01G006200 chr5B 89.744 663 61 5 2956 3612 6626117 6626778 0.000000e+00 841.0
5 TraesCS5D01G006200 chr5B 83.671 888 125 14 757 1632 6473726 6474605 0.000000e+00 819.0
6 TraesCS5D01G006200 chr5B 90.426 188 9 2 3604 3787 6627094 6627276 4.890000e-59 239.0
7 TraesCS5D01G006200 chr5A 94.763 1623 57 14 1 1614 3504931 3506534 0.000000e+00 2501.0
8 TraesCS5D01G006200 chr5A 96.741 1350 43 1 1608 2956 3515056 3516405 0.000000e+00 2248.0
9 TraesCS5D01G006200 chr5A 90.909 627 51 3 2956 3580 3516441 3517063 0.000000e+00 837.0
10 TraesCS5D01G006200 chr5A 84.467 676 97 3 824 1499 3618325 3617658 0.000000e+00 660.0
11 TraesCS5D01G006200 chr5A 86.228 334 28 12 2629 2944 3615201 3614868 2.800000e-91 346.0
12 TraesCS5D01G006200 chr5A 91.406 128 6 5 2820 2944 700175657 700175532 1.810000e-38 171.0
13 TraesCS5D01G006200 chr4D 89.677 1114 113 2 1655 2767 503998621 503997509 0.000000e+00 1419.0
14 TraesCS5D01G006200 chr4D 84.123 907 121 14 755 1658 503999661 503998775 0.000000e+00 856.0
15 TraesCS5D01G006200 chr4B 89.488 1113 117 0 1655 2767 650408569 650407457 0.000000e+00 1408.0
16 TraesCS5D01G006200 chr4B 89.308 1113 119 0 1655 2767 650488947 650487835 0.000000e+00 1397.0
17 TraesCS5D01G006200 chr4B 89.308 1113 119 0 1655 2767 650528753 650527641 0.000000e+00 1397.0
18 TraesCS5D01G006200 chr4B 85.084 838 110 13 770 1602 650529778 650528951 0.000000e+00 841.0
19 TraesCS5D01G006200 chr4B 84.099 893 117 16 770 1658 650409594 650408723 0.000000e+00 839.0
20 TraesCS5D01G006200 chr4B 84.845 805 108 10 754 1554 650457738 650456944 0.000000e+00 798.0
21 TraesCS5D01G006200 chr4B 91.589 107 7 1 2826 2932 650455438 650455334 3.050000e-31 147.0
22 TraesCS5D01G006200 chr4B 82.609 115 9 4 1544 1658 650489204 650489101 1.450000e-14 91.6
23 TraesCS5D01G006200 chrUn 87.941 1161 130 9 1652 2806 110472949 110474105 0.000000e+00 1360.0
24 TraesCS5D01G006200 chrUn 82.517 755 113 14 910 1653 110472031 110472777 0.000000e+00 645.0
25 TraesCS5D01G006200 chrUn 93.388 121 5 3 2825 2944 110474259 110474377 3.890000e-40 176.0
26 TraesCS5D01G006200 chr7B 87.705 122 13 2 2825 2944 744288424 744288303 1.420000e-29 141.0
27 TraesCS5D01G006200 chr1B 87.387 111 12 2 3678 3787 356913756 356913647 3.970000e-25 126.0
28 TraesCS5D01G006200 chr3D 88.172 93 10 1 3520 3612 417910783 417910692 4.000000e-20 110.0


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 TraesCS5D01G006200 chr5D 5272925 5276711 3786 True 6994.000000 6994 100.000000 1 3787 1 chr5D.!!$R1 3786
1 TraesCS5D01G006200 chr5B 6623138 6627276 4138 False 1906.333333 4639 91.750333 1 3787 3 chr5B.!!$F3 3786
2 TraesCS5D01G006200 chr5B 31142509 31143804 1295 False 1555.000000 1555 88.580000 1668 2944 1 chr5B.!!$F1 1276
3 TraesCS5D01G006200 chr5B 6473726 6475991 2265 False 1118.000000 1417 85.295000 757 2944 2 chr5B.!!$F2 2187
4 TraesCS5D01G006200 chr5A 3504931 3506534 1603 False 2501.000000 2501 94.763000 1 1614 1 chr5A.!!$F1 1613
5 TraesCS5D01G006200 chr5A 3515056 3517063 2007 False 1542.500000 2248 93.825000 1608 3580 2 chr5A.!!$F2 1972
6 TraesCS5D01G006200 chr5A 3614868 3618325 3457 True 503.000000 660 85.347500 824 2944 2 chr5A.!!$R2 2120
7 TraesCS5D01G006200 chr4D 503997509 503999661 2152 True 1137.500000 1419 86.900000 755 2767 2 chr4D.!!$R1 2012
8 TraesCS5D01G006200 chr4B 650407457 650409594 2137 True 1123.500000 1408 86.793500 770 2767 2 chr4B.!!$R1 1997
9 TraesCS5D01G006200 chr4B 650527641 650529778 2137 True 1119.000000 1397 87.196000 770 2767 2 chr4B.!!$R4 1997
10 TraesCS5D01G006200 chr4B 650487835 650489204 1369 True 744.300000 1397 85.958500 1544 2767 2 chr4B.!!$R3 1223
11 TraesCS5D01G006200 chr4B 650455334 650457738 2404 True 472.500000 798 88.217000 754 2932 2 chr4B.!!$R2 2178
12 TraesCS5D01G006200 chrUn 110472031 110474377 2346 False 727.000000 1360 87.948667 910 2944 3 chrUn.!!$F1 2034

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
357 362 1.098869 CGACAGCTCTGCTAGAGGAA 58.901 55.000 12.98 0.0 42.54 3.36 F
1290 1320 1.628340 TCGGCTCATTTCTTCCAAGGA 59.372 47.619 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 1409 2.833794 AGTTTACTTGCTCACTGCGAA 58.166 42.857 0.00 0.0 46.63 4.70 R
2946 4765 3.013921 GAGAAGACGAGGTCATCAGAGT 58.986 50.000 4.15 0.0 33.42 3.24 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
357 362 1.098869 CGACAGCTCTGCTAGAGGAA 58.901 55.000 12.98 0.00 42.54 3.36
431 438 7.881775 AAAATTTCTTAGGCCATAGGTGTAG 57.118 36.000 5.01 0.00 0.00 2.74
544 551 3.056465 CACAGAGTACCTTCTGACCCTTC 60.056 52.174 16.66 0.00 45.95 3.46
680 690 5.772393 AAGGACATACAGGATACAACCAA 57.228 39.130 0.00 0.00 41.41 3.67
688 698 4.312443 ACAGGATACAACCAACACTTACG 58.688 43.478 0.00 0.00 41.41 3.18
803 817 9.353999 GTTATTTTCCCATTCTAACATTGTGAC 57.646 33.333 0.00 0.00 0.00 3.67
857 872 8.311109 GTGAATCACCTTACAAATTAAACCCAT 58.689 33.333 1.10 0.00 0.00 4.00
988 1018 5.126067 AGTTGGCTGCCTACATAACTATTG 58.874 41.667 29.73 0.00 31.96 1.90
1116 1146 2.493278 CCATCATTTGTCCACAAGACCC 59.507 50.000 0.00 0.00 45.68 4.46
1178 1208 5.194432 GCTTTTTAAAAAGGGTTTTGGGGA 58.806 37.500 31.71 2.17 44.24 4.81
1236 1266 9.150348 AGTGTATTTACAATAAATTTGCTTGGC 57.850 29.630 15.54 0.00 38.04 4.52
1290 1320 1.628340 TCGGCTCATTTCTTCCAAGGA 59.372 47.619 0.00 0.00 0.00 3.36
1379 1409 2.158827 TGTATGGTGTAGATGCCGCAAT 60.159 45.455 0.00 0.00 0.00 3.56
1449 1479 4.910956 CGAAGCCTCGTTGATCCA 57.089 55.556 0.00 0.00 40.33 3.41
1640 1715 9.941664 ACGTACATAAGTTGACTATACATGTAC 57.058 33.333 7.96 17.46 41.57 2.90
2198 3734 2.441750 TGGAAAACACCCAAGCTCTAGT 59.558 45.455 0.00 0.00 0.00 2.57
2295 3831 6.538742 GCATATCCTTAGCAAGTACAAGAACA 59.461 38.462 0.00 0.00 0.00 3.18
2543 4079 2.666207 CCGGATCGGTTTGGTCCA 59.334 61.111 0.00 0.00 42.73 4.02
3003 4858 1.408702 GTGTTGTTGTGCCAAGGATGT 59.591 47.619 0.00 0.00 0.00 3.06
3019 4874 4.675190 GGATGTCTATCCGCAATGATTG 57.325 45.455 0.00 0.00 43.27 2.67
3134 4990 5.954296 ATTATATGAAGCACTGCATGGAC 57.046 39.130 3.30 0.00 0.00 4.02
3178 5034 5.997384 ACCGTAAACTAGATGAAGAGGTT 57.003 39.130 0.00 0.00 0.00 3.50
3202 5058 8.543774 GTTCATGGAGACTTATTAGACATTTCG 58.456 37.037 0.00 0.00 0.00 3.46
3207 5063 6.198591 GGAGACTTATTAGACATTTCGAACCG 59.801 42.308 0.00 0.00 0.00 4.44
3260 5116 0.185901 ACACCTTGCAAGTCCACCAT 59.814 50.000 24.35 0.68 0.00 3.55
3261 5117 0.599558 CACCTTGCAAGTCCACCATG 59.400 55.000 24.35 9.35 0.00 3.66
3274 5130 3.370978 GTCCACCATGAGATAAACACACG 59.629 47.826 0.00 0.00 0.00 4.49
3294 5150 5.357032 ACACGGAAAACAATGATTCTATCCC 59.643 40.000 0.00 0.00 0.00 3.85
3350 5208 5.121105 AGTTACGAATATAACAACAGGCCC 58.879 41.667 0.00 0.00 37.49 5.80
3409 5267 9.955102 CCCTACTAGTAAGAAAAATTACAAGGT 57.045 33.333 3.76 0.00 37.98 3.50
3474 5336 1.160137 GTGTGTTCTGGTCCTGATGC 58.840 55.000 0.00 0.00 0.00 3.91
3510 5372 3.933332 GACAAGATTTCGGGTCCTACAAG 59.067 47.826 0.00 0.00 0.00 3.16
3532 5394 8.912787 CAAGTAGTTTGTACTAGATGGTACTG 57.087 38.462 0.00 0.00 41.64 2.74
3586 5448 9.932207 AAGAGTTGATGCAATGATAAATTTTGA 57.068 25.926 0.00 0.00 0.00 2.69
3712 5902 9.740710 AAATAAGAGTTTGGCTAGATTACAACT 57.259 29.630 0.00 0.00 0.00 3.16
3720 5910 8.354426 GTTTGGCTAGATTACAACTTAAACCAA 58.646 33.333 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 74 0.675083 TACACGGACTCAAAAGCGGA 59.325 50.000 0.00 0.00 0.00 5.54
514 521 1.372501 AGGTACTCTGTGGGCCAAAT 58.627 50.000 8.40 0.00 0.00 2.32
664 674 6.071221 TCGTAAGTGTTGGTTGTATCCTGTAT 60.071 38.462 0.00 0.00 39.48 2.29
666 676 4.039488 TCGTAAGTGTTGGTTGTATCCTGT 59.961 41.667 0.00 0.00 39.48 4.00
667 677 4.562082 TCGTAAGTGTTGGTTGTATCCTG 58.438 43.478 0.00 0.00 39.48 3.86
668 678 4.282703 ACTCGTAAGTGTTGGTTGTATCCT 59.717 41.667 0.00 0.00 42.12 3.24
669 679 4.563061 ACTCGTAAGTGTTGGTTGTATCC 58.437 43.478 0.00 0.00 42.12 2.59
680 690 7.251994 GAGATTATCTCACAACTCGTAAGTGT 58.748 38.462 16.53 0.00 43.52 3.55
688 698 5.362430 AGGACAGGAGATTATCTCACAACTC 59.638 44.000 21.89 9.41 45.12 3.01
988 1018 1.935873 CATGTCCATGATGTCGTGTCC 59.064 52.381 0.87 0.00 41.20 4.02
1050 1080 9.595823 GAAATCTTAGTGGCTACAACAGTTATA 57.404 33.333 2.02 0.00 0.00 0.98
1178 1208 8.049117 ACCTTGTGTACAGATCATTGATTGTAT 58.951 33.333 17.12 3.43 0.00 2.29
1290 1320 4.081198 CCAAAGCTAATCTCTGACTCCAGT 60.081 45.833 0.00 0.00 41.16 4.00
1379 1409 2.833794 AGTTTACTTGCTCACTGCGAA 58.166 42.857 0.00 0.00 46.63 4.70
1542 1611 9.778741 GAGGTGTATTGGAGAATATATGAAACA 57.221 33.333 0.00 0.00 0.00 2.83
1639 1714 4.083324 CCATCTTGCGAAAACACATGTAGT 60.083 41.667 0.00 0.00 0.00 2.73
1640 1715 4.406069 CCATCTTGCGAAAACACATGTAG 58.594 43.478 0.00 0.00 0.00 2.74
1641 1716 3.365868 GCCATCTTGCGAAAACACATGTA 60.366 43.478 0.00 0.00 0.00 2.29
2198 3734 4.676799 AGCTCCAGCCCATATACTAGTA 57.323 45.455 4.77 4.77 43.38 1.82
2241 3777 3.071602 TCCTCCATGGCAGCTATTAAGAC 59.928 47.826 6.96 0.00 35.26 3.01
2543 4079 3.268034 ACTTTGTCCTCCTCTCTTCCT 57.732 47.619 0.00 0.00 0.00 3.36
2946 4765 3.013921 GAGAAGACGAGGTCATCAGAGT 58.986 50.000 4.15 0.00 33.42 3.24
2949 4768 3.278574 AGAGAGAAGACGAGGTCATCAG 58.721 50.000 4.15 0.00 33.42 2.90
3003 4858 4.515191 GCTTTACCAATCATTGCGGATAGA 59.485 41.667 0.00 0.00 0.00 1.98
3009 4864 7.339207 CAATTTATGCTTTACCAATCATTGCG 58.661 34.615 0.00 0.00 0.00 4.85
3127 4983 8.438676 AAATGTCTTATAGTTAGTGTCCATGC 57.561 34.615 0.00 0.00 0.00 4.06
3134 4990 8.932791 ACGGTTTGAAATGTCTTATAGTTAGTG 58.067 33.333 0.00 0.00 0.00 2.74
3167 5023 4.751767 AGTCTCCATGAACCTCTTCATC 57.248 45.455 0.00 0.00 44.04 2.92
3178 5034 8.007405 TCGAAATGTCTAATAAGTCTCCATGA 57.993 34.615 0.00 0.00 0.00 3.07
3202 5058 9.365311 CATACATTTATCGACAATTTACGGTTC 57.635 33.333 0.00 0.00 0.00 3.62
3260 5116 6.261158 TCATTGTTTTCCGTGTGTTTATCTCA 59.739 34.615 0.00 0.00 0.00 3.27
3261 5117 6.664515 TCATTGTTTTCCGTGTGTTTATCTC 58.335 36.000 0.00 0.00 0.00 2.75
3274 5130 6.603201 TGAGTGGGATAGAATCATTGTTTTCC 59.397 38.462 0.00 0.00 0.00 3.13
3324 5182 6.482308 GGCCTGTTGTTATATTCGTAACTCAT 59.518 38.462 0.00 0.00 35.94 2.90
3374 5232 5.926580 TCTTACTAGTAGGGTAGAGGCAT 57.073 43.478 11.73 0.00 0.00 4.40
3375 5233 5.722172 TTCTTACTAGTAGGGTAGAGGCA 57.278 43.478 11.73 0.00 0.00 4.75
3404 5262 2.941064 CAGAGGCATGTATCACACCTTG 59.059 50.000 0.00 0.00 26.22 3.61
3405 5263 2.092753 CCAGAGGCATGTATCACACCTT 60.093 50.000 0.00 0.00 26.22 3.50
3510 5372 5.970023 CGCAGTACCATCTAGTACAAACTAC 59.030 44.000 0.00 0.00 44.19 2.73
3628 5814 7.176690 TGAGACATGGATTATCTTATGCGACTA 59.823 37.037 0.00 0.00 0.00 2.59
3632 5818 6.162079 AGTGAGACATGGATTATCTTATGCG 58.838 40.000 0.00 0.00 0.00 4.73
3745 5935 9.060347 CAACTATATATGGTCTGAACTGCATTT 57.940 33.333 1.78 0.00 0.00 2.32
3746 5936 7.173907 GCAACTATATATGGTCTGAACTGCATT 59.826 37.037 13.39 0.00 0.00 3.56
3747 5937 6.652481 GCAACTATATATGGTCTGAACTGCAT 59.348 38.462 13.39 0.00 0.00 3.96
3748 5938 5.991606 GCAACTATATATGGTCTGAACTGCA 59.008 40.000 13.39 0.00 0.00 4.41
3749 5939 5.991606 TGCAACTATATATGGTCTGAACTGC 59.008 40.000 12.05 12.05 0.00 4.40


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

AutoCloner maintained by Alex Coulton.