Multiple sequence alignment - TraesCS1A01G135400

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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 TraesCS1A01G135400 chr1A 100.000 7111 0 0 1 7111 208704980 208712090 0.000000e+00 13132
1 TraesCS1A01G135400 chr1A 97.432 4439 106 8 2677 7111 14170188 14174622 0.000000e+00 7559
2 TraesCS1A01G135400 chr1A 97.758 1427 30 1 1 1425 14167401 14168827 0.000000e+00 2457
3 TraesCS1A01G135400 chr1A 97.720 1228 26 2 1451 2676 14168823 14170050 0.000000e+00 2111
4 TraesCS1A01G135400 chr1A 81.898 1370 218 23 654 2015 551927634 551928981 0.000000e+00 1129
5 TraesCS1A01G135400 chr1A 78.934 1538 257 47 3694 5188 551930530 551932043 0.000000e+00 983
6 TraesCS1A01G135400 chr1A 83.405 464 70 7 5219 5680 551932034 551932492 2.370000e-114 424
7 TraesCS1A01G135400 chr1A 79.821 446 65 18 1 426 551926974 551927414 1.160000e-77 302
8 TraesCS1A01G135400 chr4A 81.984 1371 215 25 654 2015 78263188 78264535 0.000000e+00 1134
9 TraesCS1A01G135400 chr4A 79.479 1535 259 40 3694 5188 78266097 78267615 0.000000e+00 1038
10 TraesCS1A01G135400 chr4A 81.832 655 103 14 5219 5864 78267606 78268253 2.920000e-148 536
11 TraesCS1A01G135400 chr4A 80.813 443 65 15 1 426 78262529 78262968 5.320000e-86 329
12 TraesCS1A01G135400 chr3B 87.069 580 70 4 1 577 84451804 84452381 0.000000e+00 651
13 TraesCS1A01G135400 chr3B 85.085 590 83 5 1 586 705353071 705353659 1.320000e-166 597
14 TraesCS1A01G135400 chr3B 84.138 580 87 4 1 577 93908512 93907935 2.240000e-154 556
15 TraesCS1A01G135400 chr3A 86.806 576 70 5 1 573 729682938 729683510 7.780000e-179 638
16 TraesCS1A01G135400 chr3A 86.655 577 70 6 1 573 728041362 728040789 3.620000e-177 632
17 TraesCS1A01G135400 chr3A 86.482 577 71 6 1 573 728026330 728025757 1.680000e-175 627
18 TraesCS1A01G135400 chr6A 75.972 566 110 23 3 555 608294390 608293838 1.180000e-67 268
19 TraesCS1A01G135400 chr3D 86.395 147 15 5 1 145 501426478 501426621 9.550000e-34 156


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 TraesCS1A01G135400 chr1A 208704980 208712090 7110 False 13132.000000 13132 100.000000 1 7111 1 chr1A.!!$F1 7110
1 TraesCS1A01G135400 chr1A 14167401 14174622 7221 False 4042.333333 7559 97.636667 1 7111 3 chr1A.!!$F2 7110
2 TraesCS1A01G135400 chr1A 551926974 551932492 5518 False 709.500000 1129 81.014500 1 5680 4 chr1A.!!$F3 5679
3 TraesCS1A01G135400 chr4A 78262529 78268253 5724 False 759.250000 1134 81.027000 1 5864 4 chr4A.!!$F1 5863
4 TraesCS1A01G135400 chr3B 84451804 84452381 577 False 651.000000 651 87.069000 1 577 1 chr3B.!!$F1 576
5 TraesCS1A01G135400 chr3B 705353071 705353659 588 False 597.000000 597 85.085000 1 586 1 chr3B.!!$F2 585
6 TraesCS1A01G135400 chr3B 93907935 93908512 577 True 556.000000 556 84.138000 1 577 1 chr3B.!!$R1 576
7 TraesCS1A01G135400 chr3A 729682938 729683510 572 False 638.000000 638 86.806000 1 573 1 chr3A.!!$F1 572
8 TraesCS1A01G135400 chr3A 728040789 728041362 573 True 632.000000 632 86.655000 1 573 1 chr3A.!!$R2 572
9 TraesCS1A01G135400 chr3A 728025757 728026330 573 True 627.000000 627 86.482000 1 573 1 chr3A.!!$R1 572
10 TraesCS1A01G135400 chr6A 608293838 608294390 552 True 268.000000 268 75.972000 3 555 1 chr6A.!!$R1 552

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
934 996 0.937304 CGTACATGCTTTCCCATCGG 59.063 55.000 0.00 0.0 0.00 4.18 F
1570 1632 0.618458 TATCGGCCACCTTCTTGCTT 59.382 50.000 2.24 0.0 0.00 3.91 F
2021 2083 0.785378 CGGTACAACAATTCGCGTCA 59.215 50.000 5.77 0.0 0.00 4.35 F
2175 2253 1.271871 ACTGGGGCATCGTTCAATTCA 60.272 47.619 0.00 0.0 0.00 2.57 F
3886 5025 0.179056 ACGAACTCCAACCACACCAG 60.179 55.000 0.00 0.0 0.00 4.00 F
3903 5042 0.036388 CAGCCGTTCCACATACCACT 60.036 55.000 0.00 0.0 0.00 4.00 F
4786 5959 0.603707 ACTGACCATTGGACTGCACG 60.604 55.000 10.37 0.0 0.00 5.34 F
4881 6054 1.879575 TGCTAGGAGGTATGCCACTT 58.120 50.000 1.54 0.0 37.19 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2041 1.270147 GCACAAGAGTAGTCCCACGTT 60.270 52.381 0.0 0.0 0.00 3.99 R
2736 2958 4.133820 TGATGCCCGTTAGTAATTCATGG 58.866 43.478 0.0 0.0 0.00 3.66 R
3886 5025 0.321298 ACAGTGGTATGTGGAACGGC 60.321 55.000 0.0 0.0 42.39 5.68 R
3903 5042 2.902705 AGTTAGCAAAGTCGTGGACA 57.097 45.000 0.0 0.0 34.60 4.02 R
5098 6275 0.393267 AATACGCCAAAAGCCGCCTA 60.393 50.000 0.0 0.0 38.78 3.93 R
5101 6278 0.989164 GAAAATACGCCAAAAGCCGC 59.011 50.000 0.0 0.0 38.78 6.53 R
5781 6962 3.385755 GGCCATTTGAATCATAGCCAAGT 59.614 43.478 0.0 0.0 38.79 3.16 R
6449 7630 4.497473 AACACATTCGGTACATTGGTTG 57.503 40.909 0.0 0.0 0.00 3.77 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
274 292 2.092212 AGGAAATTCCACCGCATCATCT 60.092 45.455 15.21 0.0 39.61 2.90
339 357 2.436646 AAGGTCGCATGAAGCCGG 60.437 61.111 0.00 0.0 41.38 6.13
427 445 7.333423 TGTTTATCTGTATTGTCTGTAACCAGC 59.667 37.037 0.00 0.0 38.66 4.85
429 447 6.791867 ATCTGTATTGTCTGTAACCAGCTA 57.208 37.500 0.00 0.0 38.66 3.32
585 621 6.617371 ACCTTCTCCATTACCTCTGTCATTAT 59.383 38.462 0.00 0.0 0.00 1.28
727 789 2.526304 ACCATCAATATCGTCCACCG 57.474 50.000 0.00 0.0 38.13 4.94
877 939 6.763610 AGACCTGCTTTTATCTAAAGATTCCG 59.236 38.462 0.00 0.0 45.00 4.30
934 996 0.937304 CGTACATGCTTTCCCATCGG 59.063 55.000 0.00 0.0 0.00 4.18
972 1034 7.985589 TCATCCCTAAAAGGAGAAAACTAACT 58.014 34.615 0.00 0.0 39.95 2.24
1153 1215 7.981142 AGTTGTTTCTATTGTTTCGTCTTTCA 58.019 30.769 0.00 0.0 0.00 2.69
1251 1313 3.395639 TCTACGTTTTAGCAAGTGGTGG 58.604 45.455 0.00 0.0 0.00 4.61
1420 1482 6.341316 ACGACTATACAGTTCCTACGTTCTA 58.659 40.000 0.00 0.0 34.21 2.10
1425 1487 9.406113 ACTATACAGTTCCTACGTTCTATTCTT 57.594 33.333 0.00 0.0 0.00 2.52
1449 1511 4.020307 GGAATGCCAAAGAAGGGAAATCAA 60.020 41.667 0.00 0.0 30.71 2.57
1570 1632 0.618458 TATCGGCCACCTTCTTGCTT 59.382 50.000 2.24 0.0 0.00 3.91
1613 1675 7.720957 CACATCAATAATTGACTATTGGGGAGA 59.279 37.037 0.82 0.0 43.48 3.71
1746 1808 3.784763 AGACCCATCTTCAAGGATGTCAT 59.215 43.478 2.02 0.0 40.85 3.06
1881 1943 2.825861 TGACAACCTAAACCTCGGAC 57.174 50.000 0.00 0.0 0.00 4.79
1889 1951 5.494390 ACCTAAACCTCGGACTTAACAAT 57.506 39.130 0.00 0.0 0.00 2.71
1979 2041 4.931002 GCTACCACAAGTACCGACAAATTA 59.069 41.667 0.00 0.0 0.00 1.40
2021 2083 0.785378 CGGTACAACAATTCGCGTCA 59.215 50.000 5.77 0.0 0.00 4.35
2077 2153 7.801893 TTATATATATCCACCAAACCTCCGT 57.198 36.000 0.00 0.0 0.00 4.69
2175 2253 1.271871 ACTGGGGCATCGTTCAATTCA 60.272 47.619 0.00 0.0 0.00 2.57
2322 2406 7.327214 TCCTTTTCCAATGCCAAATAACATAC 58.673 34.615 0.00 0.0 0.00 2.39
2490 2574 6.125719 ACAAAAACCTTTGCCCATTAATGTT 58.874 32.000 14.25 0.0 44.96 2.71
2678 2900 4.678509 TTTTCATCGCCACTTACATGTC 57.321 40.909 0.00 0.0 0.00 3.06
2681 2903 3.000041 TCATCGCCACTTACATGTCAAC 59.000 45.455 0.00 0.0 0.00 3.18
2696 2918 7.482654 ACATGTCAACCATTACTTCATATCG 57.517 36.000 0.00 0.0 0.00 2.92
2747 2969 8.579850 TTCTATGCTTTTCACCATGAATTACT 57.420 30.769 0.00 0.0 36.11 2.24
2750 2972 9.722056 CTATGCTTTTCACCATGAATTACTAAC 57.278 33.333 0.00 0.0 36.11 2.34
3211 3435 8.848474 TTCCTTCTTTCCTCACATTACTTAAG 57.152 34.615 0.00 0.0 0.00 1.85
3705 4844 6.920569 ACCCACGATAATTGTTTATCTGAC 57.079 37.500 0.00 0.0 41.00 3.51
3817 4956 6.682113 GCAACGTAATCAATCACCTACTCCTA 60.682 42.308 0.00 0.0 0.00 2.94
3837 4976 4.889409 CCTACTTTACGTCCTACCATACCA 59.111 45.833 0.00 0.0 0.00 3.25
3886 5025 0.179056 ACGAACTCCAACCACACCAG 60.179 55.000 0.00 0.0 0.00 4.00
3903 5042 0.036388 CAGCCGTTCCACATACCACT 60.036 55.000 0.00 0.0 0.00 4.00
4327 5475 9.953825 GTACAAATAACTCATTTCTTCTACACG 57.046 33.333 0.00 0.0 34.49 4.49
4350 5500 5.349270 CGTTCCATTCCTAACGTGTAATTCA 59.651 40.000 0.00 0.0 42.57 2.57
4391 5541 0.951040 CCTCGTCCACAAGCAAGGTC 60.951 60.000 0.00 0.0 0.00 3.85
4420 5570 4.260139 TCAACCGCACTACACAAGATAA 57.740 40.909 0.00 0.0 0.00 1.75
4573 5746 6.238842 GCATGTATATCACCAGCAAATTCTGT 60.239 38.462 0.00 0.0 32.32 3.41
4726 5899 5.505173 ACTTTTGCCCAATTATCTGATCG 57.495 39.130 0.00 0.0 0.00 3.69
4786 5959 0.603707 ACTGACCATTGGACTGCACG 60.604 55.000 10.37 0.0 0.00 5.34
4881 6054 1.879575 TGCTAGGAGGTATGCCACTT 58.120 50.000 1.54 0.0 37.19 3.16
5101 6278 8.217799 TGACAACATTTTCCTATATCCCTTAGG 58.782 37.037 0.00 0.0 38.06 2.69
5104 6281 4.903045 TTTTCCTATATCCCTTAGGCGG 57.097 45.455 0.00 0.0 36.87 6.13
5539 6716 6.500049 ACTCAGCCCAATATAGCTCTCTAAAT 59.500 38.462 0.00 0.0 37.18 1.40
5699 6876 5.193679 AGTGAGTATTTCTAAACCATGCCC 58.806 41.667 0.00 0.0 0.00 5.36
6009 7190 7.468922 AAATCTGCTTGTTTTTACTTTCAGC 57.531 32.000 0.00 0.0 0.00 4.26
6068 7249 2.788786 CGTTGCCAAACTCATTCACAAC 59.211 45.455 0.00 0.0 33.87 3.32
6071 7252 1.930371 GCCAAACTCATTCACAACGCC 60.930 52.381 0.00 0.0 0.00 5.68
6299 7480 8.258007 TCAATTCATAAGTCACTCTTATTCCGT 58.742 33.333 0.00 0.0 44.18 4.69
6449 7630 2.986479 GTTCATTGCAATTTGACGTCCC 59.014 45.455 14.12 0.0 0.00 4.46
6493 7674 5.991328 TTCTTCATCCTTACGATGCAATC 57.009 39.130 0.00 0.0 46.93 2.67
6680 7861 6.518493 TCCCAACAGTTTTACTACTACACAG 58.482 40.000 0.00 0.0 0.00 3.66
6978 8159 8.686334 ACACACATCCACATTCCTAAATTATTC 58.314 33.333 0.00 0.0 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 292 3.578716 AGATTGACCAGAAGGAGAACGAA 59.421 43.478 0.00 0.00 38.69 3.85
427 445 6.949352 ATAGAATTTGCAAGTGGATGGTAG 57.051 37.500 0.00 0.00 0.00 3.18
429 447 6.610075 AAATAGAATTTGCAAGTGGATGGT 57.390 33.333 0.00 0.00 0.00 3.55
553 574 5.367060 AGAGGTAATGGAGAAGGTGGATAAC 59.633 44.000 0.00 0.00 0.00 1.89
585 621 6.094325 GTGGGATGGACGTAAATAATGAACAA 59.906 38.462 0.00 0.00 0.00 2.83
727 789 2.594592 AAGCGTGTTGGGACAGCC 60.595 61.111 0.00 0.00 42.39 4.85
875 937 6.542370 ACCTTGGTTAAATGATGAAGATACGG 59.458 38.462 0.00 0.00 0.00 4.02
934 996 7.922811 CCTTTTAGGGATGAAATAAGATGCAAC 59.077 37.037 0.00 0.00 0.00 4.17
998 1060 3.898123 ACTAGGGCGTGAATATGACATCT 59.102 43.478 0.00 0.00 0.00 2.90
1251 1313 1.576356 GCCCATCAAGACGACTCATC 58.424 55.000 0.00 0.00 0.00 2.92
1425 1487 2.692709 TTCCCTTCTTTGGCATTCCA 57.307 45.000 0.00 0.00 41.55 3.53
1435 1497 7.507277 AGCTTTTAGAACTTGATTTCCCTTCTT 59.493 33.333 0.00 0.00 0.00 2.52
1440 1502 5.047731 AGCAGCTTTTAGAACTTGATTTCCC 60.048 40.000 0.00 0.00 0.00 3.97
1449 1511 4.655963 TGGATTCAGCAGCTTTTAGAACT 58.344 39.130 0.00 0.00 0.00 3.01
1570 1632 3.446310 TGTGTCGTGCTTGTTAGAAGA 57.554 42.857 0.00 0.00 0.00 2.87
1613 1675 7.443575 CAGCTATCCTATCAGTGTTTGCTATTT 59.556 37.037 0.00 0.00 0.00 1.40
1746 1808 2.381911 GGTCGTACCTGGAGGAATACA 58.618 52.381 0.00 0.00 38.94 2.29
1796 1858 4.230657 CGCATGGAATCGGTTAAAAACAA 58.769 39.130 0.00 0.00 0.00 2.83
1889 1951 6.549242 TCTTGGATAAGTATCGTGAGGGATA 58.451 40.000 0.00 0.00 35.38 2.59
1979 2041 1.270147 GCACAAGAGTAGTCCCACGTT 60.270 52.381 0.00 0.00 0.00 3.99
2175 2253 6.828788 TGATGGCCATGTTGCATTATAAATT 58.171 32.000 26.56 0.00 0.00 1.82
2299 2383 6.811170 ACGTATGTTATTTGGCATTGGAAAAG 59.189 34.615 0.00 0.00 0.00 2.27
2665 2750 4.700213 AGTAATGGTTGACATGTAAGTGGC 59.300 41.667 0.00 0.00 40.44 5.01
2672 2757 7.047891 ACGATATGAAGTAATGGTTGACATGT 58.952 34.615 0.00 0.00 40.44 3.21
2736 2958 4.133820 TGATGCCCGTTAGTAATTCATGG 58.866 43.478 0.00 0.00 0.00 3.66
2788 3010 8.659925 TGAAGTATAATAATTTTACCGGCGAA 57.340 30.769 9.30 0.00 0.00 4.70
2789 3011 8.836268 ATGAAGTATAATAATTTTACCGGCGA 57.164 30.769 9.30 0.00 0.00 5.54
2790 3012 8.714179 TGATGAAGTATAATAATTTTACCGGCG 58.286 33.333 0.00 0.00 0.00 6.46
2791 3013 9.821662 GTGATGAAGTATAATAATTTTACCGGC 57.178 33.333 0.00 0.00 0.00 6.13
2831 3053 8.845413 TGAAATTGTATTTTGAGGGGAAAATG 57.155 30.769 0.00 0.00 36.44 2.32
2833 3055 8.100164 GGATGAAATTGTATTTTGAGGGGAAAA 58.900 33.333 0.00 0.00 0.00 2.29
2837 3059 5.662657 AGGGATGAAATTGTATTTTGAGGGG 59.337 40.000 0.00 0.00 0.00 4.79
2952 3175 8.915871 AATCATTGGAAAATGATCGTGTTAAG 57.084 30.769 12.90 0.00 46.12 1.85
2999 3222 8.786826 ATTTGTGTATCGAAAATGACTTAGGA 57.213 30.769 0.00 0.00 0.00 2.94
3217 3441 9.650539 ATGTGTAATGTATGCATGCTTTAAAAA 57.349 25.926 20.33 13.06 35.15 1.94
3545 4489 6.128391 GCAATAAGTCGTCATGTTTGGTTAGA 60.128 38.462 0.00 0.00 0.00 2.10
3625 4757 9.114952 GAAATAAAACCATCTTTTGTGGGAAAA 57.885 29.630 0.00 0.00 41.14 2.29
3662 4795 1.303309 TAGCGCCCGAGAAGTACTAC 58.697 55.000 2.29 0.00 0.00 2.73
3705 4844 2.544694 GGGTGATCGTATCTGCAGACAG 60.545 54.545 20.97 13.33 45.95 3.51
3817 4956 4.527816 TGTTGGTATGGTAGGACGTAAAGT 59.472 41.667 0.00 0.00 0.00 2.66
3837 4976 9.979578 GTCTTCAGAGATAATGATGTAGATGTT 57.020 33.333 0.00 0.00 33.70 2.71
3886 5025 0.321298 ACAGTGGTATGTGGAACGGC 60.321 55.000 0.00 0.00 42.39 5.68
3903 5042 2.902705 AGTTAGCAAAGTCGTGGACA 57.097 45.000 0.00 0.00 34.60 4.02
4150 5298 7.750458 CGAATGCTACAACAAATACAACTTGAT 59.250 33.333 0.00 0.00 0.00 2.57
4327 5475 6.730960 TGAATTACACGTTAGGAATGGAAC 57.269 37.500 0.00 0.00 0.00 3.62
4350 5500 5.006386 GGAAGTCTCACCTGAACAATGAAT 58.994 41.667 0.00 0.00 0.00 2.57
4420 5570 0.110486 GGAGTGTGTGGTTGGGACAT 59.890 55.000 0.00 0.00 39.30 3.06
4786 5959 4.508662 ACTCAGTTTAGGCTGATAAGCAC 58.491 43.478 3.95 0.00 43.61 4.40
5098 6275 0.393267 AATACGCCAAAAGCCGCCTA 60.393 50.000 0.00 0.00 38.78 3.93
5101 6278 0.989164 GAAAATACGCCAAAAGCCGC 59.011 50.000 0.00 0.00 38.78 6.53
5104 6281 5.333035 GGTTCAAAGAAAATACGCCAAAAGC 60.333 40.000 0.00 0.00 38.52 3.51
5198 6375 7.422465 AATACGTAAAGTGTATAGGGAACCA 57.578 36.000 0.00 0.00 40.76 3.67
5270 6447 3.568443 TGTATGGAGCGTACTTCCCATA 58.432 45.455 9.91 10.42 39.80 2.74
5699 6876 5.001874 GGGGTTGAAGTAGTAGGAAAACAG 58.998 45.833 0.00 0.00 0.00 3.16
5781 6962 3.385755 GGCCATTTGAATCATAGCCAAGT 59.614 43.478 0.00 0.00 38.79 3.16
6165 7346 5.872635 AGACATGACTTATTGAATGCAACG 58.127 37.500 0.00 0.00 36.72 4.10
6166 7347 7.062605 CCAAAGACATGACTTATTGAATGCAAC 59.937 37.037 10.82 0.00 36.72 4.17
6341 7522 7.707104 AGTTTCTAAAAGGATTGTTCACACAG 58.293 34.615 0.00 0.00 33.22 3.66
6449 7630 4.497473 AACACATTCGGTACATTGGTTG 57.503 40.909 0.00 0.00 0.00 3.77
6493 7674 6.307077 TCGTCATGTACAGAAGATAAACAACG 59.693 38.462 0.33 0.00 0.00 4.10
6500 7681 7.654116 TGTGTTTTTCGTCATGTACAGAAGATA 59.346 33.333 0.33 0.47 0.00 1.98
6660 7841 9.038803 GTAAAGCTGTGTAGTAGTAAAACTGTT 57.961 33.333 0.00 0.00 0.00 3.16
6933 8114 4.039852 TGTGTGTGCATAAGTCTTCCTACA 59.960 41.667 0.00 0.00 0.00 2.74
6939 8120 3.753272 GGATGTGTGTGTGCATAAGTCTT 59.247 43.478 0.00 0.00 0.00 3.01
6947 8128 1.608109 GAATGTGGATGTGTGTGTGCA 59.392 47.619 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.