Multiple sequence alignment - TraesCS5B01G108000

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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 TraesCS5B01G108000 chr5B 100.000 5129 0 0 1 5129 146920012 146914884 0.000000e+00 9472.0
1 TraesCS5B01G108000 chr5B 92.426 845 43 8 1 834 182508356 182507522 0.000000e+00 1186.0
2 TraesCS5B01G108000 chr5B 89.683 126 11 1 3410 3533 611922703 611922828 5.320000e-35 159.0
3 TraesCS5B01G108000 chr5A 95.664 2122 51 21 2939 5028 169815163 169817275 0.000000e+00 3371.0
4 TraesCS5B01G108000 chr5A 93.466 2158 63 12 817 2942 169810715 169812826 0.000000e+00 3133.0
5 TraesCS5B01G108000 chr5A 92.738 840 42 12 1 832 671201030 671201858 0.000000e+00 1195.0
6 TraesCS5B01G108000 chr5D 94.461 2022 59 17 854 2849 135243799 135241805 0.000000e+00 3064.0
7 TraesCS5B01G108000 chr5D 96.359 1593 39 7 3556 5129 135241322 135239730 0.000000e+00 2603.0
8 TraesCS5B01G108000 chr5D 94.459 379 18 3 2944 3320 135241789 135241412 9.570000e-162 580.0
9 TraesCS5B01G108000 chr5D 97.143 70 1 1 3316 3385 135241384 135241316 3.240000e-22 117.0
10 TraesCS5B01G108000 chr5D 100.000 36 0 0 3611 3646 489897186 489897221 3.310000e-07 67.6
11 TraesCS5B01G108000 chr5D 97.368 38 1 0 3611 3648 366007904 366007867 1.190000e-06 65.8
12 TraesCS5B01G108000 chr6B 93.437 838 40 8 1 832 648263790 648264618 0.000000e+00 1229.0
13 TraesCS5B01G108000 chr6B 92.056 856 47 12 1 842 270810570 270809722 0.000000e+00 1184.0
14 TraesCS5B01G108000 chr6B 88.333 60 3 4 3611 3668 687848092 687848035 9.220000e-08 69.4
15 TraesCS5B01G108000 chr3B 93.270 847 36 11 1 834 670194078 670194916 0.000000e+00 1229.0
16 TraesCS5B01G108000 chr3B 92.623 122 7 1 3403 3522 798492214 798492093 1.900000e-39 174.0
17 TraesCS5B01G108000 chr3B 92.920 113 8 0 3410 3522 790492414 790492526 1.140000e-36 165.0
18 TraesCS5B01G108000 chr3B 91.667 48 2 2 3611 3656 612032912 612032865 1.190000e-06 65.8
19 TraesCS5B01G108000 chr3B 97.143 35 1 0 3611 3645 725843501 725843535 5.550000e-05 60.2
20 TraesCS5B01G108000 chr2B 92.680 847 45 7 3 836 715019439 715020281 0.000000e+00 1205.0
21 TraesCS5B01G108000 chr2B 91.667 48 2 2 3611 3656 726693335 726693288 1.190000e-06 65.8
22 TraesCS5B01G108000 chr7A 92.417 844 46 12 1 835 579596548 579597382 0.000000e+00 1188.0
23 TraesCS5B01G108000 chr7B 92.090 847 44 16 1 835 693327213 693326378 0.000000e+00 1171.0
24 TraesCS5B01G108000 chr7B 91.715 857 49 14 1 852 576350930 576351769 0.000000e+00 1170.0
25 TraesCS5B01G108000 chr7B 92.562 121 6 3 3410 3527 444184129 444184009 2.460000e-38 171.0
26 TraesCS5B01G108000 chr7B 90.756 119 11 0 3404 3522 748124177 748124295 5.320000e-35 159.0
27 TraesCS5B01G108000 chr7B 97.143 35 1 0 3611 3645 529956305 529956339 5.550000e-05 60.2
28 TraesCS5B01G108000 chr2D 92.500 120 7 1 3410 3527 489410187 489410068 2.460000e-38 171.0
29 TraesCS5B01G108000 chr1D 91.803 122 10 0 3401 3522 408872528 408872407 2.460000e-38 171.0
30 TraesCS5B01G108000 chr1D 91.597 119 10 0 3408 3526 28313639 28313521 1.140000e-36 165.0
31 TraesCS5B01G108000 chr6D 91.200 125 10 1 3399 3522 366701094 366701218 8.830000e-38 169.0
32 TraesCS5B01G108000 chr3A 91.057 123 11 0 3404 3526 536776787 536776909 3.180000e-37 167.0
33 TraesCS5B01G108000 chr2A 89.474 133 11 3 3392 3522 389220791 389220922 1.140000e-36 165.0
34 TraesCS5B01G108000 chr4B 90.400 125 11 1 3399 3522 273619976 273619852 4.110000e-36 163.0
35 TraesCS5B01G108000 chr1B 92.035 113 9 0 3410 3522 558228147 558228259 5.320000e-35 159.0


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 TraesCS5B01G108000 chr5B 146914884 146920012 5128 True 9472 9472 100.0000 1 5129 1 chr5B.!!$R1 5128
1 TraesCS5B01G108000 chr5B 182507522 182508356 834 True 1186 1186 92.4260 1 834 1 chr5B.!!$R2 833
2 TraesCS5B01G108000 chr5A 169810715 169817275 6560 False 3252 3371 94.5650 817 5028 2 chr5A.!!$F2 4211
3 TraesCS5B01G108000 chr5A 671201030 671201858 828 False 1195 1195 92.7380 1 832 1 chr5A.!!$F1 831
4 TraesCS5B01G108000 chr5D 135239730 135243799 4069 True 1591 3064 95.6055 854 5129 4 chr5D.!!$R2 4275
5 TraesCS5B01G108000 chr6B 648263790 648264618 828 False 1229 1229 93.4370 1 832 1 chr6B.!!$F1 831
6 TraesCS5B01G108000 chr6B 270809722 270810570 848 True 1184 1184 92.0560 1 842 1 chr6B.!!$R1 841
7 TraesCS5B01G108000 chr3B 670194078 670194916 838 False 1229 1229 93.2700 1 834 1 chr3B.!!$F1 833
8 TraesCS5B01G108000 chr2B 715019439 715020281 842 False 1205 1205 92.6800 3 836 1 chr2B.!!$F1 833
9 TraesCS5B01G108000 chr7A 579596548 579597382 834 False 1188 1188 92.4170 1 835 1 chr7A.!!$F1 834
10 TraesCS5B01G108000 chr7B 693326378 693327213 835 True 1171 1171 92.0900 1 835 1 chr7B.!!$R2 834
11 TraesCS5B01G108000 chr7B 576350930 576351769 839 False 1170 1170 91.7150 1 852 1 chr7B.!!$F2 851

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
949 971 1.074889 GGACCCTCTAAACCCTGCAAA 59.925 52.381 0.00 0.00 0.00 3.68 F
1426 1463 1.422024 TGGAATCCTGGAACGGTTCAA 59.578 47.619 21.36 10.43 0.00 2.69 F
1998 2049 3.242936 GCTGAGGAGTCACTCGATCTAAC 60.243 52.174 9.42 0.00 40.39 2.34 F
2857 2929 3.751175 TGTATACCAGCTGTGCAGTTTTC 59.249 43.478 13.81 0.00 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2049 1.593750 GCCATGCGCAGAGTCCTAG 60.594 63.158 18.32 0.0 37.47 3.02 R
3418 5866 0.937304 CCGGCATGTATTTCCAGACG 59.063 55.000 0.00 0.0 0.00 4.18 R
3512 5960 3.119388 TCAAACCGTTATACCCTCTGTCG 60.119 47.826 0.00 0.0 0.00 4.35 R
4323 6787 1.066454 AGCCAAAACTGTACGCAAACC 59.934 47.619 0.00 0.0 0.00 3.27 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
94 96 4.020617 CTCCGCCCTGTCAAGCCA 62.021 66.667 0.00 0.00 0.00 4.75
299 301 2.359107 ACGACTACCTCCGCGACA 60.359 61.111 8.23 0.00 0.00 4.35
543 554 1.608109 TGACTACACGCGGTTCTACAA 59.392 47.619 12.47 0.00 0.00 2.41
748 768 4.082523 CGACTGGGGGCATCACGT 62.083 66.667 0.00 0.00 0.00 4.49
810 832 2.562953 TTTTTGCCCCTCCTGGAGA 58.437 52.632 25.18 1.62 35.39 3.71
847 869 5.825151 AGATGCCCTTAGATTTAGACTTTGC 59.175 40.000 0.00 0.00 0.00 3.68
949 971 1.074889 GGACCCTCTAAACCCTGCAAA 59.925 52.381 0.00 0.00 0.00 3.68
1426 1463 1.422024 TGGAATCCTGGAACGGTTCAA 59.578 47.619 21.36 10.43 0.00 2.69
1519 1563 6.035220 GGTCGTGATAAATCATGTCGTTGTTA 59.965 38.462 11.04 0.00 42.84 2.41
1606 1651 7.776933 TCATCAGCATAAGTTCATAAGACAC 57.223 36.000 0.00 0.00 0.00 3.67
1607 1652 7.330262 TCATCAGCATAAGTTCATAAGACACA 58.670 34.615 0.00 0.00 0.00 3.72
1688 1733 8.576442 GTTGATCCAAATTCTAAACCTCTGAAA 58.424 33.333 0.00 0.00 0.00 2.69
1701 1746 5.316158 ACCTCTGAAATAATGGAGATGGG 57.684 43.478 0.00 0.00 0.00 4.00
1724 1771 5.348997 GGTCCTCTTAGAAACTCGAAATGTG 59.651 44.000 0.00 0.00 0.00 3.21
1998 2049 3.242936 GCTGAGGAGTCACTCGATCTAAC 60.243 52.174 9.42 0.00 40.39 2.34
2378 2431 4.883585 TGATCTATCAATTCCAACTGTGCC 59.116 41.667 0.00 0.00 33.08 5.01
2575 2635 5.731187 TCCTTCCTGGGATTCTAAAGATTCA 59.269 40.000 0.00 0.00 36.20 2.57
2645 2716 8.016652 TCCTATTGTTGAATCCCTAATCTCCTA 58.983 37.037 0.00 0.00 0.00 2.94
2646 2717 8.660435 CCTATTGTTGAATCCCTAATCTCCTAA 58.340 37.037 0.00 0.00 0.00 2.69
2743 2814 7.473735 TTGGCCACAAATTATACTCAATGAA 57.526 32.000 3.88 0.00 32.66 2.57
2857 2929 3.751175 TGTATACCAGCTGTGCAGTTTTC 59.249 43.478 13.81 0.00 0.00 2.29
2896 2968 5.772393 TTAAGGATTGTTAGAGCTGGGAA 57.228 39.130 0.00 0.00 0.00 3.97
2934 3006 6.367695 AGTTAAGTTTGCTTGTTTGTTTGGTC 59.632 34.615 0.00 0.00 36.22 4.02
3187 5600 4.816385 CCATGCAAACTTAGTATGACCGAT 59.184 41.667 0.00 0.00 31.77 4.18
3206 5619 4.454161 CCGATGGACAACATAAGAAACACA 59.546 41.667 0.00 0.00 40.72 3.72
3397 5845 8.880750 GGTAAAAATGTCCTTACTAACTAGCTG 58.119 37.037 0.00 0.00 0.00 4.24
3418 5866 5.473846 GCTGGCTTTAAATATTACTCCCTCC 59.526 44.000 0.00 0.00 0.00 4.30
3459 5907 5.922544 CGGAGAAATGGATAAAAATGGATGC 59.077 40.000 0.00 0.00 0.00 3.91
3509 5957 6.180472 ACATCCATTTCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
3512 5960 4.335594 CCATTTCTCCGACAAGTATTTCCC 59.664 45.833 0.00 0.00 0.00 3.97
3540 5988 4.828829 AGGGTATAACGGTTTGAAGTGAG 58.171 43.478 0.00 0.00 0.00 3.51
3548 5996 2.096496 CGGTTTGAAGTGAGCCATGATC 59.904 50.000 0.00 0.00 0.00 2.92
3678 6130 3.959535 AAACATTTATGCCCACTGTGG 57.040 42.857 20.01 20.01 37.25 4.17
3942 6403 9.362151 ACTTTCAAGTTTATCCCTGTTCATTTA 57.638 29.630 0.00 0.00 35.21 1.40
4191 6654 4.721776 AGGAAGTCTTCATGGGCATTACTA 59.278 41.667 14.49 0.00 0.00 1.82
4323 6787 3.356529 AGTATCCACCAGGCTTTTCTG 57.643 47.619 0.00 0.00 33.74 3.02
4381 6845 4.040952 GGATGGTAGAATGACACTAGGCAT 59.959 45.833 0.00 0.00 0.00 4.40
4619 7086 4.443394 ACGATTACACAGTTCGTTCACTTC 59.557 41.667 0.00 0.00 42.99 3.01
4627 7094 3.871594 CAGTTCGTTCACTTCTTCTTGGT 59.128 43.478 0.00 0.00 0.00 3.67
4635 7102 2.024414 ACTTCTTCTTGGTGTTGGTGC 58.976 47.619 0.00 0.00 0.00 5.01
4865 7335 3.071457 TGCTCTCATGTTGAAACCTCAGA 59.929 43.478 0.00 0.00 31.69 3.27
5000 7470 1.274728 CCAGTTGCTAGTGTCAGCTCT 59.725 52.381 2.31 0.00 42.30 4.09
5050 7520 3.089284 TCTTCTCGCCTGAGTTGATGTA 58.911 45.455 0.00 0.00 43.09 2.29
5074 7544 4.503817 CCATTGTGGTCGATCTGTATCCAT 60.504 45.833 0.00 0.00 31.35 3.41
5080 7550 3.440522 GGTCGATCTGTATCCATCATCGA 59.559 47.826 0.00 0.00 38.75 3.59
5088 7558 5.305386 TCTGTATCCATCATCGATTCTGGTT 59.695 40.000 18.15 14.03 0.00 3.67
5103 7573 5.923733 TTCTGGTTGAGTATCCTCTCTTC 57.076 43.478 0.00 0.00 38.61 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 87 2.853542 TGGGGCTCTGGCTTGACA 60.854 61.111 0.00 0.00 38.73 3.58
275 277 3.130160 GAGGTAGTCGTCCCGCGT 61.130 66.667 4.92 0.00 42.13 6.01
543 554 0.824759 GTTCTACATGCCGAGGAGGT 59.175 55.000 0.00 0.00 43.70 3.85
949 971 0.546122 TTTCTGTGGCTGTCCAGTGT 59.454 50.000 0.00 0.00 44.48 3.55
1173 1198 1.303643 GGTGAAGGCAGGGGTGAAG 60.304 63.158 0.00 0.00 0.00 3.02
1174 1199 2.840753 GGGTGAAGGCAGGGGTGAA 61.841 63.158 0.00 0.00 0.00 3.18
1175 1200 3.256960 GGGTGAAGGCAGGGGTGA 61.257 66.667 0.00 0.00 0.00 4.02
1176 1201 4.366684 GGGGTGAAGGCAGGGGTG 62.367 72.222 0.00 0.00 0.00 4.61
1177 1202 3.202591 TAGGGGTGAAGGCAGGGGT 62.203 63.158 0.00 0.00 0.00 4.95
1178 1203 2.286121 TAGGGGTGAAGGCAGGGG 60.286 66.667 0.00 0.00 0.00 4.79
1179 1204 2.680370 GGTAGGGGTGAAGGCAGGG 61.680 68.421 0.00 0.00 0.00 4.45
1180 1205 1.923395 TGGTAGGGGTGAAGGCAGG 60.923 63.158 0.00 0.00 0.00 4.85
1181 1206 1.201429 AGTGGTAGGGGTGAAGGCAG 61.201 60.000 0.00 0.00 0.00 4.85
1182 1207 0.117541 TAGTGGTAGGGGTGAAGGCA 59.882 55.000 0.00 0.00 0.00 4.75
1183 1208 0.831307 CTAGTGGTAGGGGTGAAGGC 59.169 60.000 0.00 0.00 0.00 4.35
1184 1209 1.007963 TCCTAGTGGTAGGGGTGAAGG 59.992 57.143 0.00 0.00 45.65 3.46
1221 1258 4.189188 CACGCGACTACCCCGGAG 62.189 72.222 15.93 0.00 0.00 4.63
1426 1463 6.237755 CCGAAGCGTATTAGATTTCGACTTTT 60.238 38.462 6.51 0.00 42.16 2.27
1453 1490 6.039616 GCATAAGAGAATATCATCTCCGACC 58.960 44.000 1.49 0.00 45.70 4.79
1519 1563 1.336755 GCGTTTCTGTGACCCAAACAT 59.663 47.619 7.11 0.00 31.51 2.71
1606 1651 8.286800 TCCAGAAATTCGTTACACTAAAATGTG 58.713 33.333 0.00 0.00 43.07 3.21
1607 1652 8.385898 TCCAGAAATTCGTTACACTAAAATGT 57.614 30.769 0.00 0.00 36.56 2.71
1620 1665 2.890311 TGTGCCATTTCCAGAAATTCGT 59.110 40.909 2.86 0.00 38.84 3.85
1688 1733 5.982391 TCTAAGAGGACCCATCTCCATTAT 58.018 41.667 0.00 0.00 31.94 1.28
1701 1746 5.348997 CCACATTTCGAGTTTCTAAGAGGAC 59.651 44.000 0.00 0.00 0.00 3.85
1724 1771 1.448985 TTCCTACGCTCAAATGCACC 58.551 50.000 0.00 0.00 0.00 5.01
1998 2049 1.593750 GCCATGCGCAGAGTCCTAG 60.594 63.158 18.32 0.00 37.47 3.02
2358 2411 3.270027 CGGCACAGTTGGAATTGATAGA 58.730 45.455 0.00 0.00 0.00 1.98
2366 2419 1.904287 ATAAAGCGGCACAGTTGGAA 58.096 45.000 1.45 0.00 0.00 3.53
2378 2431 7.356641 AGAGTAATGACATGCATATAAAGCG 57.643 36.000 0.00 0.00 35.78 4.68
2441 2494 9.554724 CTTAATTGTGTATGGTGTGTTATTGTC 57.445 33.333 0.00 0.00 0.00 3.18
2719 2790 7.473735 TTCATTGAGTATAATTTGTGGCCAA 57.526 32.000 7.24 0.00 0.00 4.52
2743 2814 3.130734 TCCACCTTCAGGCCTACTAAT 57.869 47.619 3.98 0.00 39.32 1.73
2812 2883 6.810182 ACAAATATTTTCATGCTCTGCAGAAC 59.190 34.615 18.85 14.43 43.65 3.01
2857 2929 5.054477 TCCTTAAAGACACCGTTTCAAGAG 58.946 41.667 0.00 0.00 0.00 2.85
3187 5600 9.522804 GTTTTTATGTGTTTCTTATGTTGTCCA 57.477 29.630 0.00 0.00 0.00 4.02
3397 5845 5.618236 ACGGAGGGAGTAATATTTAAAGCC 58.382 41.667 0.00 0.00 0.00 4.35
3418 5866 0.937304 CCGGCATGTATTTCCAGACG 59.063 55.000 0.00 0.00 0.00 4.18
3512 5960 3.119388 TCAAACCGTTATACCCTCTGTCG 60.119 47.826 0.00 0.00 0.00 4.35
3678 6130 3.474600 ACATAGCTTCTCACATCATGGC 58.525 45.455 0.00 0.00 0.00 4.40
3942 6403 7.691993 ATATCAGGGACTTAACATTACCTGT 57.308 36.000 8.22 0.10 44.39 4.00
3998 6460 2.775911 TCCTCAGTTCAGATTGCTGG 57.224 50.000 0.00 0.00 42.53 4.85
4191 6654 2.432300 CGGCCCCGTCATAGTTCCT 61.432 63.158 0.00 0.00 34.35 3.36
4323 6787 1.066454 AGCCAAAACTGTACGCAAACC 59.934 47.619 0.00 0.00 0.00 3.27
4381 6845 6.129179 ACAAACTTCAGAAAGATGGGAGAAA 58.871 36.000 0.00 0.00 36.30 2.52
4619 7086 1.972872 AGAGCACCAACACCAAGAAG 58.027 50.000 0.00 0.00 0.00 2.85
4627 7094 5.534207 AATCATTTCAAAGAGCACCAACA 57.466 34.783 0.00 0.00 0.00 3.33
4865 7335 2.471815 TCCCCGAGTCCAATGTAGAT 57.528 50.000 0.00 0.00 0.00 1.98
5000 7470 2.297698 TCACCGAGGACTTCAACCTA 57.702 50.000 0.00 0.00 37.93 3.08
5074 7544 5.201713 GGATACTCAACCAGAATCGATGA 57.798 43.478 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.