Multiple sequence alignment - TraesCS2B01G363200

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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 TraesCS2B01G363200 chr2B 100.000 6262 0 0 1 6262 517595231 517601492 0.000000e+00 11564.0
1 TraesCS2B01G363200 chr2D 97.656 4692 50 14 1616 6262 439564114 439568790 0.000000e+00 8000.0
2 TraesCS2B01G363200 chr2D 94.676 1634 47 18 1 1619 439562269 439563877 0.000000e+00 2499.0
3 TraesCS2B01G363200 chr2D 90.667 75 4 2 5722 5795 376701251 376701179 5.170000e-16 97.1
4 TraesCS2B01G363200 chr2D 93.846 65 1 3 5721 5784 8495912 8495974 1.860000e-15 95.3
5 TraesCS2B01G363200 chr2D 91.429 70 2 2 5721 5789 327614836 327614902 6.680000e-15 93.5
6 TraesCS2B01G363200 chr2A 94.269 5217 162 63 525 5647 549294798 549289625 0.000000e+00 7851.0
7 TraesCS2B01G363200 chr2A 94.059 505 9 6 5777 6262 549289433 549288931 0.000000e+00 747.0
8 TraesCS2B01G363200 chr2A 91.776 535 32 4 1 526 549295589 549295058 0.000000e+00 734.0
9 TraesCS2B01G363200 chr2A 91.503 153 12 1 4847 4998 79316158 79316006 6.360000e-50 209.0
10 TraesCS2B01G363200 chr2A 90.667 75 4 2 5721 5794 754039077 754039005 5.170000e-16 97.1
11 TraesCS2B01G363200 chr2A 97.436 39 1 0 5686 5724 549289558 549289520 4.050000e-07 67.6
12 TraesCS2B01G363200 chr3B 89.866 523 43 3 1 513 40870223 40869701 0.000000e+00 664.0
13 TraesCS2B01G363200 chr3B 94.030 67 2 2 5723 5787 445886096 445886030 3.990000e-17 100.0
14 TraesCS2B01G363200 chr4B 93.151 146 9 1 4854 4998 146469362 146469217 4.920000e-51 213.0
15 TraesCS2B01G363200 chr5B 92.105 152 9 2 4848 4998 665744619 665744470 1.770000e-50 211.0
16 TraesCS2B01G363200 chr4D 90.683 161 12 3 4845 5002 74079508 74079348 1.770000e-50 211.0
17 TraesCS2B01G363200 chr5D 90.184 163 9 5 4841 4998 233044603 233044443 8.230000e-49 206.0
18 TraesCS2B01G363200 chr7B 90.000 160 13 3 4842 4998 505937474 505937315 2.960000e-48 204.0
19 TraesCS2B01G363200 chr3D 89.937 159 13 3 4842 4998 76231151 76230994 1.060000e-47 202.0
20 TraesCS2B01G363200 chr3D 85.484 124 14 4 3205 3328 613071481 613071362 6.590000e-25 126.0
21 TraesCS2B01G363200 chr6A 94.118 68 1 3 5721 5785 611567687 611567754 3.990000e-17 100.0
22 TraesCS2B01G363200 chr6D 93.750 64 2 2 5722 5784 469492349 469492411 1.860000e-15 95.3
23 TraesCS2B01G363200 chr7D 91.304 69 4 2 5721 5788 447760444 447760511 6.680000e-15 93.5


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 TraesCS2B01G363200 chr2B 517595231 517601492 6261 False 11564.0 11564 100.000 1 6262 1 chr2B.!!$F1 6261
1 TraesCS2B01G363200 chr2D 439562269 439568790 6521 False 5249.5 8000 96.166 1 6262 2 chr2D.!!$F3 6261
2 TraesCS2B01G363200 chr2A 549288931 549295589 6658 True 2349.9 7851 94.385 1 6262 4 chr2A.!!$R3 6261
3 TraesCS2B01G363200 chr3B 40869701 40870223 522 True 664.0 664 89.866 1 513 1 chr3B.!!$R1 512


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
523 789 0.392706 CCCCAAAACTGTTCAAGGGC 59.607 55.000 15.52 0.0 34.93 5.19 F
697 971 0.470268 AGTAGGCGAGGGAGGATTCC 60.470 60.000 0.00 0.0 43.23 3.01 F
774 1048 1.461911 GGGCTCGACTAACCCGCTAT 61.462 60.000 0.00 0.0 32.92 2.97 F
1296 1572 1.666553 CGACAAGTGGCGCAACCTA 60.667 57.895 12.38 0.0 40.91 3.08 F
2892 3448 0.401395 AAGAGGAGGTGGGGTGTTGA 60.401 55.000 0.00 0.0 0.00 3.18 F
3736 4317 3.574826 ACTGGAGAGACACCTCAACTAAC 59.425 47.826 0.00 0.0 41.87 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 2213 0.250945 TTAATTGGCGGTGCACAGGA 60.251 50.000 20.43 0.0 0.00 3.86 R
1836 2362 1.742768 CGAGCTGGAGACCCATACC 59.257 63.158 0.00 0.0 42.59 2.73 R
2412 2964 9.592196 AAATTATGTATCTTACCATCTGGCAAT 57.408 29.630 0.00 0.0 39.32 3.56 R
3010 3574 0.613260 TCTCGCCAGGCAGTTACAAT 59.387 50.000 13.30 0.0 0.00 2.71 R
4253 4835 1.137697 CCCTCCCACCATAAGTACCC 58.862 60.000 0.00 0.0 0.00 3.69 R
5649 6253 1.734465 GAATCTCAAACAGCCTGGTCG 59.266 52.381 0.00 0.0 0.00 4.79 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
187 195 6.128902 ACTGTTCGTCAATAGTTCGATTCAAC 60.129 38.462 0.00 0.00 30.08 3.18
188 196 5.164129 TGTTCGTCAATAGTTCGATTCAACG 60.164 40.000 0.00 0.00 33.72 4.10
297 308 1.956802 CCAACAAAAGACCGGAGCC 59.043 57.895 9.46 0.00 0.00 4.70
315 326 4.247380 GCCCCTGCGGAGGATGAG 62.247 72.222 26.49 11.02 42.93 2.90
338 349 1.753078 CTGATGCCATGCCAGCTGT 60.753 57.895 13.81 0.00 0.00 4.40
369 380 3.703052 GCCATTGGAGTTCAATCCTGATT 59.297 43.478 6.95 0.00 43.70 2.57
487 498 6.370442 TCGTAATTATCAGTCAAAACCACCTG 59.630 38.462 0.00 0.00 0.00 4.00
513 524 2.593436 CACGTCGGCCCCAAAACT 60.593 61.111 0.00 0.00 0.00 2.66
523 789 0.392706 CCCCAAAACTGTTCAAGGGC 59.607 55.000 15.52 0.00 34.93 5.19
541 812 2.361789 GGCTTGCCGGTTTTGTAGATA 58.638 47.619 1.90 0.00 0.00 1.98
544 815 4.351192 GCTTGCCGGTTTTGTAGATATTG 58.649 43.478 1.90 0.00 0.00 1.90
576 848 0.611714 GGGGTTATGTGTCCGTGAGT 59.388 55.000 0.00 0.00 0.00 3.41
580 852 2.093658 GGTTATGTGTCCGTGAGTCCAT 60.094 50.000 0.00 0.00 0.00 3.41
693 967 1.447099 ATAGAGTAGGCGAGGGAGGA 58.553 55.000 0.00 0.00 0.00 3.71
695 969 0.558712 AGAGTAGGCGAGGGAGGATT 59.441 55.000 0.00 0.00 0.00 3.01
696 970 0.963225 GAGTAGGCGAGGGAGGATTC 59.037 60.000 0.00 0.00 0.00 2.52
697 971 0.470268 AGTAGGCGAGGGAGGATTCC 60.470 60.000 0.00 0.00 43.23 3.01
751 1025 4.702131 ACTTGGATGTGCTACCTGAAATTC 59.298 41.667 0.00 0.00 0.00 2.17
766 1040 3.007506 TGAAATTCACTGGGCTCGACTAA 59.992 43.478 0.00 0.00 0.00 2.24
774 1048 1.461911 GGGCTCGACTAACCCGCTAT 61.462 60.000 0.00 0.00 32.92 2.97
920 1194 1.997874 GAGCCTCCACTCCCACCAT 60.998 63.158 0.00 0.00 0.00 3.55
929 1205 2.284625 TCCCACCATCGCTCACCT 60.285 61.111 0.00 0.00 0.00 4.00
930 1206 2.187946 CCCACCATCGCTCACCTC 59.812 66.667 0.00 0.00 0.00 3.85
950 1226 4.374702 GCCTCACGCACGCAACAG 62.375 66.667 0.00 0.00 37.47 3.16
971 1247 2.765807 CTCGCTCCCAGACCCCAT 60.766 66.667 0.00 0.00 0.00 4.00
1296 1572 1.666553 CGACAAGTGGCGCAACCTA 60.667 57.895 12.38 0.00 40.91 3.08
2892 3448 0.401395 AAGAGGAGGTGGGGTGTTGA 60.401 55.000 0.00 0.00 0.00 3.18
2959 3523 8.242325 AGAGAGGTAATAAATAGGAGGATGGAA 58.758 37.037 0.00 0.00 0.00 3.53
3736 4317 3.574826 ACTGGAGAGACACCTCAACTAAC 59.425 47.826 0.00 0.00 41.87 2.34
3893 4475 9.391006 TGGATTAGTATTTGTTCTGGTTATGTC 57.609 33.333 0.00 0.00 0.00 3.06
3994 4576 5.695816 TGCAATTTTTAGAATGTGGAAGCAC 59.304 36.000 0.00 0.00 0.00 4.40
4253 4835 6.035368 CCTCATACAGGTGGAGATAATCAG 57.965 45.833 0.00 0.00 37.53 2.90
4764 5348 7.062138 CCTGTGTTTGTATGCACATTGTTATTC 59.938 37.037 0.00 0.00 43.52 1.75
5171 5757 1.227853 GCGTGGTTGGACACTCCTT 60.228 57.895 0.00 0.00 39.19 3.36
5264 5850 2.463876 CGCTCGCTTGTAGATTGATCA 58.536 47.619 0.00 0.00 0.00 2.92
5351 5938 0.178961 GCCAAGGTGGAGAGGGTTTT 60.179 55.000 0.00 0.00 40.96 2.43
5352 5939 1.620822 CCAAGGTGGAGAGGGTTTTG 58.379 55.000 0.00 0.00 40.96 2.44
5353 5940 0.961753 CAAGGTGGAGAGGGTTTTGC 59.038 55.000 0.00 0.00 0.00 3.68
5366 5966 0.250424 GTTTTGCTTGCCCATTGCCT 60.250 50.000 0.00 0.00 40.16 4.75
5367 5967 0.250381 TTTTGCTTGCCCATTGCCTG 60.250 50.000 0.00 0.00 40.16 4.85
5538 6140 4.798585 TCCTGTATTCGGGAGCCA 57.201 55.556 0.00 0.00 43.49 4.75
5539 6141 3.240670 TCCTGTATTCGGGAGCCAT 57.759 52.632 0.00 0.00 43.49 4.40
5639 6243 0.100325 TTTGCTCGGTGCTGTTGTTG 59.900 50.000 3.53 0.00 43.37 3.33
5649 6253 1.656441 CTGTTGTTGCAGGAGCCAC 59.344 57.895 0.00 0.00 41.13 5.01
5738 6370 8.408743 ACTGACACGTAAAGAAATATAAGAGC 57.591 34.615 0.00 0.00 0.00 4.09
5814 6480 5.364157 TGGCAAAACTAACACATAGGGTTTT 59.636 36.000 0.00 0.00 39.60 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 0.736053 GTTTGACGGGAAGCACAACA 59.264 50.000 0.00 0.00 0.00 3.33
81 83 3.502621 AAGCCTCAGCAGCAGCCAA 62.503 57.895 0.00 0.00 43.56 4.52
187 195 3.257393 AGCTGAAAATAGTCAGAGCACG 58.743 45.455 6.39 0.00 46.76 5.34
188 196 5.290643 CACTAGCTGAAAATAGTCAGAGCAC 59.709 44.000 6.39 0.00 46.76 4.40
315 326 3.589881 GGCATGGCATCAGCGACC 61.590 66.667 15.47 0.00 43.41 4.79
338 349 1.067295 ACTCCAATGGCTGTGAGGAA 58.933 50.000 0.00 0.00 30.64 3.36
369 380 7.064609 CAGATCAATTTAGGCAGTCTTCGTTAA 59.935 37.037 0.00 0.00 0.00 2.01
487 498 1.495951 GGCCGACGTGTCACATTTC 59.504 57.895 3.42 0.00 0.00 2.17
513 524 2.597217 CCGGCAAGCCCTTGAACA 60.597 61.111 11.96 0.00 42.93 3.18
523 789 4.202010 CCCAATATCTACAAAACCGGCAAG 60.202 45.833 0.00 0.00 0.00 4.01
541 812 1.509548 CCCCCTGAAGTGACCCCAAT 61.510 60.000 0.00 0.00 0.00 3.16
544 815 0.843343 TAACCCCCTGAAGTGACCCC 60.843 60.000 0.00 0.00 0.00 4.95
576 848 8.778059 AGTTCATAGTTCACCCTAAAATATGGA 58.222 33.333 4.20 0.00 36.09 3.41
675 949 1.447099 ATCCTCCCTCGCCTACTCTA 58.553 55.000 0.00 0.00 0.00 2.43
703 977 1.133809 CCTCCTCAAGGTCCCACCAA 61.134 60.000 0.00 0.00 41.95 3.67
704 978 1.538876 CCTCCTCAAGGTCCCACCA 60.539 63.158 0.00 0.00 41.95 4.17
705 979 0.621862 ATCCTCCTCAAGGTCCCACC 60.622 60.000 0.00 0.00 46.32 4.61
706 980 1.210722 GAATCCTCCTCAAGGTCCCAC 59.789 57.143 0.00 0.00 46.32 4.61
707 981 1.584724 GAATCCTCCTCAAGGTCCCA 58.415 55.000 0.00 0.00 46.32 4.37
708 982 0.466124 CGAATCCTCCTCAAGGTCCC 59.534 60.000 0.00 0.00 46.32 4.46
751 1025 1.218316 GGGTTAGTCGAGCCCAGTG 59.782 63.158 0.00 0.00 41.93 3.66
766 1040 2.146724 TATGGCCAGCATAGCGGGT 61.147 57.895 13.05 0.00 45.32 5.28
774 1048 2.374525 ATGACCCGTATGGCCAGCA 61.375 57.895 13.05 0.00 37.83 4.41
920 1194 3.134792 GAGGCGAGAGGTGAGCGA 61.135 66.667 0.00 0.00 0.00 4.93
950 1226 2.419739 GGGTCTGGGAGCGAGACTC 61.420 68.421 0.00 0.00 45.45 3.36
1296 1572 2.548920 CGCCTTCTTGAACTCCTTGAGT 60.549 50.000 0.00 0.00 45.64 3.41
1652 2168 7.116075 ACCTAAATTTACACTGATGCATACCA 58.884 34.615 0.00 0.00 0.00 3.25
1658 2174 5.064198 TGCGTACCTAAATTTACACTGATGC 59.936 40.000 0.00 0.00 0.00 3.91
1696 2213 0.250945 TTAATTGGCGGTGCACAGGA 60.251 50.000 20.43 0.00 0.00 3.86
1836 2362 1.742768 CGAGCTGGAGACCCATACC 59.257 63.158 0.00 0.00 42.59 2.73
2412 2964 9.592196 AAATTATGTATCTTACCATCTGGCAAT 57.408 29.630 0.00 0.00 39.32 3.56
2892 3448 5.128663 GCTCCTCTCTCTCTATCCACTTTTT 59.871 44.000 0.00 0.00 0.00 1.94
3010 3574 0.613260 TCTCGCCAGGCAGTTACAAT 59.387 50.000 13.30 0.00 0.00 2.71
3261 3825 2.265367 CCCTTTTAAACAGCCCCCAAT 58.735 47.619 0.00 0.00 0.00 3.16
3736 4317 4.500127 TCATTGTGTATGAACCAGTACCG 58.500 43.478 0.00 0.00 40.29 4.02
3893 4475 6.830838 AGGTTTCTTAAAGGAGCAGGATATTG 59.169 38.462 0.00 0.00 0.00 1.90
3994 4576 7.542477 CCAGCGAGTAATAATACTATCAACTGG 59.458 40.741 8.58 8.58 42.47 4.00
3996 4578 7.039644 AGCCAGCGAGTAATAATACTATCAACT 60.040 37.037 0.00 0.00 42.47 3.16
4006 4588 2.874701 CAGCAAGCCAGCGAGTAATAAT 59.125 45.455 0.00 0.00 40.15 1.28
4253 4835 1.137697 CCCTCCCACCATAAGTACCC 58.862 60.000 0.00 0.00 0.00 3.69
4669 5252 4.497291 AGCATCAAAATGAATGCCCATT 57.503 36.364 3.85 0.00 40.63 3.16
4764 5348 9.791820 TTGCTTCATACATATTGAGACAATTTG 57.208 29.630 11.26 11.26 0.00 2.32
5171 5757 4.664064 ACTCTGTAGCCACTATACTCCCTA 59.336 45.833 0.00 0.00 0.00 3.53
5264 5850 3.119388 CCTTTGTCGGACAAATGATGCAT 60.119 43.478 30.18 0.00 45.79 3.96
5366 5966 2.045280 CCCATTCGGCCAAAACACA 58.955 52.632 2.24 0.00 0.00 3.72
5367 5967 4.985845 CCCATTCGGCCAAAACAC 57.014 55.556 2.24 0.00 0.00 3.32
5427 6029 4.605183 TGGTGGACATTAATTTAGGGGTG 58.395 43.478 0.00 0.00 0.00 4.61
5570 6172 9.908152 GTTTGTTTCCATGGCTATATATTTACC 57.092 33.333 6.96 0.00 0.00 2.85
5639 6243 4.767255 CCTGGTCGTGGCTCCTGC 62.767 72.222 0.00 0.00 38.76 4.85
5649 6253 1.734465 GAATCTCAAACAGCCTGGTCG 59.266 52.381 0.00 0.00 0.00 4.79
5738 6370 9.953697 ATAAGAGCTACTTTAGTGATCTAAACG 57.046 33.333 4.15 0.00 40.05 3.60



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

AutoCloner maintained by Alex Coulton.