Multiple sequence alignment - TraesCS5D01G512500

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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 TraesCS5D01G512500 chr5D 100.000 4590 0 0 1 4590 536759459 536754870 0.000000e+00 8477.0
1 TraesCS5D01G512500 chr5D 75.695 827 152 38 1128 1940 511941291 511942082 7.250000e-98 368.0
2 TraesCS5D01G512500 chr5D 91.111 45 1 1 4509 4550 324940518 324940474 1.780000e-04 58.4
3 TraesCS5D01G512500 chr4A 95.324 3678 113 19 902 4550 634418041 634421688 0.000000e+00 5784.0
4 TraesCS5D01G512500 chr4A 95.160 3678 119 19 902 4550 634450310 634453957 0.000000e+00 5751.0
5 TraesCS5D01G512500 chr4A 95.376 757 30 4 1 753 634414437 634415192 0.000000e+00 1199.0
6 TraesCS5D01G512500 chr4A 95.376 757 30 4 1 753 634446707 634447462 0.000000e+00 1199.0
7 TraesCS5D01G512500 chr4A 95.676 185 8 0 1 185 634414224 634414408 9.650000e-77 298.0
8 TraesCS5D01G512500 chr4A 95.676 185 8 0 1 185 634446494 634446678 9.650000e-77 298.0
9 TraesCS5D01G512500 chr4A 93.284 134 6 3 771 904 634417828 634417958 1.300000e-45 195.0
10 TraesCS5D01G512500 chr4A 92.537 134 7 3 771 904 634450093 634450223 6.060000e-44 189.0
11 TraesCS5D01G512500 chr4A 93.478 46 1 2 4547 4590 634421895 634421940 2.960000e-07 67.6
12 TraesCS5D01G512500 chr4A 93.478 46 1 2 4547 4590 634454164 634454209 2.960000e-07 67.6
13 TraesCS5D01G512500 chr5B 93.947 2478 106 14 2093 4550 677674208 677676661 0.000000e+00 3705.0
14 TraesCS5D01G512500 chr5B 93.339 1171 41 12 898 2047 677673050 677674204 0.000000e+00 1696.0
15 TraesCS5D01G512500 chr5B 90.323 186 9 5 548 732 677672390 677672567 7.680000e-58 235.0
16 TraesCS5D01G512500 chr5B 91.111 45 1 1 4509 4550 375849565 375849609 1.780000e-04 58.4
17 TraesCS5D01G512500 chr5A 76.784 827 157 28 1128 1941 640273840 640274644 9.120000e-117 431.0
18 TraesCS5D01G512500 chr2A 73.658 801 186 17 1130 1919 551721616 551722402 2.090000e-73 287.0
19 TraesCS5D01G512500 chr2A 87.603 242 26 3 2361 2598 20900062 20899821 1.260000e-70 278.0
20 TraesCS5D01G512500 chr2A 88.128 219 22 2 2361 2575 20869886 20869668 1.640000e-64 257.0
21 TraesCS5D01G512500 chr3B 81.006 358 68 0 1126 1483 704134954 704135311 7.520000e-73 285.0
22 TraesCS5D01G512500 chr3B 83.408 223 34 3 2355 2574 752042491 752042269 2.170000e-48 204.0
23 TraesCS5D01G512500 chr3A 81.006 358 68 0 1126 1483 667219122 667219479 7.520000e-73 285.0
24 TraesCS5D01G512500 chr3A 80.447 358 70 0 1126 1483 667262191 667262548 1.630000e-69 274.0
25 TraesCS5D01G512500 chr3A 88.462 52 1 3 4504 4550 167747420 167747471 1.780000e-04 58.4
26 TraesCS5D01G512500 chr1A 87.281 228 22 5 2376 2598 241361003 241360778 2.120000e-63 254.0
27 TraesCS5D01G512500 chr1A 83.471 242 35 4 2361 2598 544945076 544945316 2.150000e-53 220.0
28 TraesCS5D01G512500 chr1A 91.111 45 1 1 4509 4550 159452038 159451994 1.780000e-04 58.4
29 TraesCS5D01G512500 chr7B 73.345 574 144 8 3011 3581 704114029 704114596 2.170000e-48 204.0
30 TraesCS5D01G512500 chr6B 80.992 242 40 5 2361 2598 84759689 84759450 2.180000e-43 187.0
31 TraesCS5D01G512500 chr1D 96.154 52 2 0 4499 4550 409489163 409489214 8.180000e-13 86.1
32 TraesCS5D01G512500 chr7D 77.119 118 19 7 3965 4080 100766080 100765969 1.380000e-05 62.1
33 TraesCS5D01G512500 chr6A 91.111 45 1 1 4509 4550 443816721 443816765 1.780000e-04 58.4


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 TraesCS5D01G512500 chr5D 536754870 536759459 4589 True 8477.000000 8477 100.000000 1 4590 1 chr5D.!!$R2 4589
1 TraesCS5D01G512500 chr5D 511941291 511942082 791 False 368.000000 368 75.695000 1128 1940 1 chr5D.!!$F1 812
2 TraesCS5D01G512500 chr4A 634414224 634421940 7716 False 1508.720000 5784 94.627600 1 4590 5 chr4A.!!$F1 4589
3 TraesCS5D01G512500 chr4A 634446494 634454209 7715 False 1500.920000 5751 94.445400 1 4590 5 chr4A.!!$F2 4589
4 TraesCS5D01G512500 chr5B 677672390 677676661 4271 False 1878.666667 3705 92.536333 548 4550 3 chr5B.!!$F2 4002
5 TraesCS5D01G512500 chr5A 640273840 640274644 804 False 431.000000 431 76.784000 1128 1941 1 chr5A.!!$F1 813
6 TraesCS5D01G512500 chr2A 551721616 551722402 786 False 287.000000 287 73.658000 1130 1919 1 chr2A.!!$F1 789
7 TraesCS5D01G512500 chr7B 704114029 704114596 567 False 204.000000 204 73.345000 3011 3581 1 chr7B.!!$F1 570


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
72 73 0.393537 GAGGGCTGAGGTGACAATGG 60.394 60.000 0.00 0.00 0.00 3.16 F
834 3674 1.897615 CTACTAGGAGGCGGGTCCG 60.898 68.421 4.85 4.85 42.05 4.79 F
1491 4595 0.117140 AGTCCATCAGGTCACAGGGA 59.883 55.000 0.00 0.00 35.89 4.20 F
1855 4980 0.820226 CGAGGATGAAGACCTGCTGA 59.180 55.000 0.00 0.00 37.93 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1010 4111 0.895100 GCTTGACACCTCCATGGCAA 60.895 55.000 6.96 3.35 45.56 4.52 R
2754 5897 0.882927 CCATAACATACGCCCCGTGG 60.883 60.000 0.00 0.00 41.39 4.94 R
2854 5997 1.001378 CCAAGGCGGCATACTAAATGC 60.001 52.381 13.08 1.33 43.85 3.56 R
3791 6950 3.258123 GGCCCATATCAATGCGGTAATTT 59.742 43.478 0.00 0.00 0.00 1.82 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
35 36 8.466617 TCACCAAACCAAAGTAATTAGCTTTA 57.533 30.769 0.00 0.00 34.76 1.85
72 73 0.393537 GAGGGCTGAGGTGACAATGG 60.394 60.000 0.00 0.00 0.00 3.16
88 89 5.936372 TGACAATGGAGATGTCTTGAGAAAG 59.064 40.000 8.01 0.00 45.81 2.62
109 110 7.663493 AGAAAGTCAAGAGAGGTTGGAATTTAG 59.337 37.037 0.00 0.00 0.00 1.85
115 116 7.236847 TCAAGAGAGGTTGGAATTTAGTTAGGA 59.763 37.037 0.00 0.00 0.00 2.94
262 477 6.539826 TGTCACAATAATCTGATACTTGCCAG 59.460 38.462 10.38 0.00 0.00 4.85
279 494 5.316327 TGCCAGTATAGAGATATCTTGCG 57.684 43.478 6.70 0.00 0.00 4.85
311 526 6.490381 GGAATATCTCCCAAATCCACCTAAAC 59.510 42.308 0.00 0.00 38.44 2.01
331 546 9.025041 CCTAAACCAATCCTTGTAATCTCTTTT 57.975 33.333 0.00 0.00 0.00 2.27
430 645 4.363999 TGCGGTTTTCAAAACCTTGTATG 58.636 39.130 26.17 12.88 38.15 2.39
438 653 3.994392 TCAAAACCTTGTATGACGAGAGC 59.006 43.478 0.00 0.00 31.05 4.09
478 693 3.780294 TCCCTTACTGCTTGTATGGTCAT 59.220 43.478 15.57 0.00 41.98 3.06
490 705 6.312426 GCTTGTATGGTCATAGTATCATGCTC 59.688 42.308 0.00 0.00 0.00 4.26
537 752 8.702163 AAGTAAAAGACAACTGAATGGTTTTG 57.298 30.769 0.00 0.00 0.00 2.44
620 836 5.093677 GGCCATTTCCCCCTGATAAATATT 58.906 41.667 0.00 0.00 0.00 1.28
659 876 7.584987 CACCCTTTGTGTGTCTTTTCTATAAG 58.415 38.462 0.00 0.00 40.26 1.73
678 895 9.151471 TCTATAAGAAAAAGTGAAGATTGTCCG 57.849 33.333 0.00 0.00 0.00 4.79
736 953 5.582665 CCGGCTAAATAAGATTCCATCTAGC 59.417 44.000 0.00 0.00 39.08 3.42
740 957 7.663493 GGCTAAATAAGATTCCATCTAGCTTGT 59.337 37.037 0.00 0.00 39.08 3.16
769 3273 4.782019 ATTGAAGAAACTTATTGGCGCA 57.218 36.364 10.83 0.00 0.00 6.09
790 3628 2.413765 GCCCGTCGTTTGCCAAAA 59.586 55.556 0.00 0.00 0.00 2.44
815 3653 3.740115 GCCAGTCGTAACCATGGATATT 58.260 45.455 21.47 4.85 34.60 1.28
825 3665 7.610692 TCGTAACCATGGATATTCTACTAGGAG 59.389 40.741 21.47 0.00 0.00 3.69
834 3674 1.897615 CTACTAGGAGGCGGGTCCG 60.898 68.421 4.85 4.85 42.05 4.79
987 4088 4.757149 GGTTGACAGACAGACTTGCTAATT 59.243 41.667 0.00 0.00 0.00 1.40
988 4089 5.932303 GGTTGACAGACAGACTTGCTAATTA 59.068 40.000 0.00 0.00 0.00 1.40
989 4090 6.128526 GGTTGACAGACAGACTTGCTAATTAC 60.129 42.308 0.00 0.00 0.00 1.89
990 4091 6.096673 TGACAGACAGACTTGCTAATTACA 57.903 37.500 0.00 0.00 0.00 2.41
991 4092 6.159293 TGACAGACAGACTTGCTAATTACAG 58.841 40.000 0.00 0.00 0.00 2.74
1100 4201 3.574780 GCTTACGGCTTGGTCCAC 58.425 61.111 0.00 0.00 38.06 4.02
1491 4595 0.117140 AGTCCATCAGGTCACAGGGA 59.883 55.000 0.00 0.00 35.89 4.20
1521 4625 4.477975 CTCCGGTCCGTCGCTGAC 62.478 72.222 11.06 0.00 0.00 3.51
1855 4980 0.820226 CGAGGATGAAGACCTGCTGA 59.180 55.000 0.00 0.00 37.93 4.26
1874 4999 4.383861 TGTGCTGCTCCGGCTCAG 62.384 66.667 15.67 15.67 34.88 3.35
2051 5188 4.263683 CCCTCCTCTCTTTTCTTGTCCAAT 60.264 45.833 0.00 0.00 0.00 3.16
2057 5194 8.772250 TCCTCTCTTTTCTTGTCCAATATACAT 58.228 33.333 0.00 0.00 0.00 2.29
2197 5336 7.255104 CCAAGTCTGACTTAGCAACAAACAATA 60.255 37.037 21.65 0.00 36.03 1.90
2380 5519 4.843728 TGTCTTGAAACAGACTTTCACCT 58.156 39.130 2.70 0.00 43.32 4.00
2521 5662 2.125766 GAGGCCCGAACAAAGACCCT 62.126 60.000 0.00 0.00 0.00 4.34
2577 5718 2.355837 GAAGCGTCGCCACTGTCA 60.356 61.111 14.86 0.00 0.00 3.58
2582 5723 1.564622 CGTCGCCACTGTCAAGTTG 59.435 57.895 0.00 0.00 32.98 3.16
2592 5733 4.384056 CACTGTCAAGTTGGAGAACAGAT 58.616 43.478 22.44 9.29 32.98 2.90
2691 5834 7.273815 GCTTACTGTAGAATATCGAGTAATGCC 59.726 40.741 0.00 0.00 30.72 4.40
2732 5875 7.849322 TCCTACTGATTAAGCATACATGGTA 57.151 36.000 0.00 0.00 37.57 3.25
2754 5897 6.544931 GGTAACATGGGGTAAGGAGTTTAATC 59.455 42.308 0.00 0.00 0.00 1.75
2773 5916 0.882927 CCACGGGGCGTATGTTATGG 60.883 60.000 0.00 0.00 38.32 2.74
2795 5938 3.446442 AGCAGTTGAAATCATGGGAGT 57.554 42.857 0.00 0.00 0.00 3.85
2854 5997 5.050227 CGTAAGTCTAGGATTGTCGGTAGAG 60.050 48.000 0.00 0.00 0.00 2.43
3058 6201 2.297033 GCTCATGAAAAACCCTGAAGCA 59.703 45.455 0.00 0.00 0.00 3.91
3257 6400 3.139077 GGTTATGACATTCCTAAGGGCG 58.861 50.000 0.00 0.00 0.00 6.13
3266 6409 2.810870 TCCTAAGGGCGCCAAAATAA 57.189 45.000 30.85 6.18 0.00 1.40
3791 6950 8.736244 GCAGGTACAAAACATAGAAAAGGAATA 58.264 33.333 0.00 0.00 0.00 1.75
3804 6963 9.965824 ATAGAAAAGGAATAAATTACCGCATTG 57.034 29.630 0.00 0.00 0.00 2.82
3863 7022 8.726988 TGTTAGACAAATAATAAAGGTGCAGAC 58.273 33.333 0.00 0.00 0.00 3.51
3906 7066 0.966179 ACACAGTATGGACGCAGACA 59.034 50.000 0.00 0.00 43.62 3.41
4096 7263 8.437360 TGATGTAATAGATGAACATGTTGGTC 57.563 34.615 17.58 13.17 34.09 4.02
4262 7429 2.179018 CCGGTTTGCGCAATGGAG 59.821 61.111 25.64 15.08 0.00 3.86
4271 7438 2.034879 CGCAATGGAGTTCGGCACT 61.035 57.895 0.00 0.00 39.07 4.40
4291 7458 3.072038 ACTGACAAACTACCCCCTTGTAC 59.928 47.826 0.00 0.00 33.53 2.90
4454 7621 4.081752 AGTCCACTCTCACATCAAGTCATC 60.082 45.833 0.00 0.00 0.00 2.92
4528 7695 7.546667 TCTCGTACACATAAACCACCTATTTTC 59.453 37.037 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.454859 AATTACTTTGGTTTGGTGAAAAATTCA 57.545 25.926 0.00 0.00 37.33 2.57
58 59 3.197333 AGACATCTCCATTGTCACCTCAG 59.803 47.826 6.59 0.00 44.73 3.35
88 89 7.334671 CCTAACTAAATTCCAACCTCTCTTGAC 59.665 40.741 0.00 0.00 0.00 3.18
109 110 7.342769 TCTTTTTCTTCCAACCTTTCCTAAC 57.657 36.000 0.00 0.00 0.00 2.34
115 116 7.851228 ACTCAATTCTTTTTCTTCCAACCTTT 58.149 30.769 0.00 0.00 0.00 3.11
219 433 0.897621 CACCCTGATTTTGCCCCTTC 59.102 55.000 0.00 0.00 0.00 3.46
279 494 5.532779 GGATTTGGGAGATATTCCTTGACAC 59.467 44.000 0.00 0.00 45.98 3.67
409 624 4.443063 GTCATACAAGGTTTTGAAAACCGC 59.557 41.667 28.26 10.79 44.82 5.68
490 705 2.184385 GATTGTTCATCGCTTGCTGG 57.816 50.000 0.00 0.00 0.00 4.85
499 714 8.892905 GTTGTCTTTTACTTTCGATTGTTCATC 58.107 33.333 0.00 0.00 0.00 2.92
537 752 9.398538 TCACATGTAAAAGGTATAATTACACCC 57.601 33.333 9.36 0.00 40.98 4.61
659 876 5.418310 TCACGGACAATCTTCACTTTTTC 57.582 39.130 0.00 0.00 0.00 2.29
756 3260 1.883021 GCCAGTGCGCCAATAAGTT 59.117 52.632 4.18 0.00 0.00 2.66
790 3628 2.656069 ATGGTTACGACTGGCGGCT 61.656 57.895 8.22 0.00 46.49 5.52
815 3653 1.535685 GGACCCGCCTCCTAGTAGA 59.464 63.158 0.00 0.00 0.00 2.59
825 3665 1.397390 TAGGAGAATTCGGACCCGCC 61.397 60.000 3.13 0.00 39.59 6.13
864 3704 1.379843 GGATGGGACCCGCAAACAT 60.380 57.895 5.91 0.00 0.00 2.71
1008 4109 1.475280 CTTGACACCTCCATGGCAATG 59.525 52.381 6.96 7.13 46.51 2.82
1009 4110 1.843368 CTTGACACCTCCATGGCAAT 58.157 50.000 6.96 0.00 46.51 3.56
1010 4111 0.895100 GCTTGACACCTCCATGGCAA 60.895 55.000 6.96 3.35 45.56 4.52
1099 4200 3.486383 TCTTGGATTTGCTTTTCTCGGT 58.514 40.909 0.00 0.00 0.00 4.69
1100 4201 3.119708 CCTCTTGGATTTGCTTTTCTCGG 60.120 47.826 0.00 0.00 34.57 4.63
1103 4204 2.564504 GGCCTCTTGGATTTGCTTTTCT 59.435 45.455 0.00 0.00 34.57 2.52
1104 4205 2.672195 CGGCCTCTTGGATTTGCTTTTC 60.672 50.000 0.00 0.00 34.57 2.29
1711 4815 2.047274 GCTCAGCCACCGCACTAA 60.047 61.111 0.00 0.00 37.52 2.24
1839 4964 1.277557 ACACTCAGCAGGTCTTCATCC 59.722 52.381 0.00 0.00 0.00 3.51
1855 4980 4.385405 GAGCCGGAGCAGCACACT 62.385 66.667 5.05 0.00 43.56 3.55
1874 4999 3.020237 GCCAACGAGTCCTCCTCCC 62.020 68.421 0.00 0.00 36.82 4.30
2057 5194 7.895429 AGAGGAAAGAACCATGGATGAAATTAA 59.105 33.333 21.47 0.00 0.00 1.40
2059 5196 6.154021 CAGAGGAAAGAACCATGGATGAAATT 59.846 38.462 21.47 0.00 0.00 1.82
2197 5336 7.446319 TGTTCATGATGCTAGCTGCTAAATATT 59.554 33.333 17.23 0.00 43.37 1.28
2277 5416 7.307219 GGACGAACATTATTGATGCTACTAACC 60.307 40.741 0.00 0.00 39.47 2.85
2363 5502 2.158957 AGCGAGGTGAAAGTCTGTTTCA 60.159 45.455 0.00 0.00 36.21 2.69
2521 5662 1.208052 GGGCACTGTCATAGAGCTCAA 59.792 52.381 17.77 0.00 42.36 3.02
2577 5718 6.187727 TGTCCTTTATCTGTTCTCCAACTT 57.812 37.500 0.00 0.00 33.17 2.66
2691 5834 8.171164 TCAGTAGGAACATATCTGTAGACATG 57.829 38.462 0.00 0.00 35.23 3.21
2732 5875 5.015817 TGGATTAAACTCCTTACCCCATGTT 59.984 40.000 0.00 0.00 36.20 2.71
2754 5897 0.882927 CCATAACATACGCCCCGTGG 60.883 60.000 0.00 0.00 41.39 4.94
2773 5916 3.760684 ACTCCCATGATTTCAACTGCTTC 59.239 43.478 0.00 0.00 0.00 3.86
2795 5938 2.100252 GGACTAATCCGACGGTCAATCA 59.900 50.000 14.79 0.00 34.48 2.57
2854 5997 1.001378 CCAAGGCGGCATACTAAATGC 60.001 52.381 13.08 1.33 43.85 3.56
3058 6201 3.281727 TCTATTTGAGCCTTCGCCATT 57.718 42.857 0.00 0.00 34.57 3.16
3218 6361 6.493115 TCATAACCCATGATTTCACAGTTGTT 59.507 34.615 0.00 0.00 38.79 2.83
3257 6400 6.704819 CGAAGGCATTAACATTTATTTTGGC 58.295 36.000 0.00 0.00 0.00 4.52
3791 6950 3.258123 GGCCCATATCAATGCGGTAATTT 59.742 43.478 0.00 0.00 0.00 1.82
3804 6963 8.125978 TGAATCAAATATTTCTGGCCCATATC 57.874 34.615 0.00 0.00 0.00 1.63
3906 7066 2.353406 GGGTGAGTGCGTGTATGTAAGT 60.353 50.000 0.00 0.00 0.00 2.24
3935 7095 0.525242 ATTGTGTTGTGTGCGTGTGC 60.525 50.000 0.00 0.00 43.20 4.57
3936 7096 2.746623 TATTGTGTTGTGTGCGTGTG 57.253 45.000 0.00 0.00 0.00 3.82
3937 7097 2.031245 CCATATTGTGTTGTGTGCGTGT 60.031 45.455 0.00 0.00 0.00 4.49
4071 7238 8.046107 TGACCAACATGTTCATCTATTACATCA 58.954 33.333 8.48 0.00 30.45 3.07
4074 7241 8.806429 ATTGACCAACATGTTCATCTATTACA 57.194 30.769 8.48 0.00 0.00 2.41
4096 7263 7.139392 TCTATCACTAACTAGCGCAACTATTG 58.861 38.462 11.47 0.00 0.00 1.90
4262 7429 1.529865 GGTAGTTTGTCAGTGCCGAAC 59.470 52.381 0.00 0.00 0.00 3.95
4271 7438 3.071892 CAGTACAAGGGGGTAGTTTGTCA 59.928 47.826 0.00 0.00 36.52 3.58
4291 7458 6.408858 ACATAGAACAACGTAATCAAGCAG 57.591 37.500 0.00 0.00 0.00 4.24
4431 7598 3.234353 TGACTTGATGTGAGAGTGGACT 58.766 45.455 0.00 0.00 0.00 3.85
4528 7695 4.170468 AGGTATGGTGGCTATTTTGAGG 57.830 45.455 0.00 0.00 0.00 3.86



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

AutoCloner maintained by Alex Coulton.