Multiple sequence alignment - TraesCS2D01G475000

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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 TraesCS2D01G475000 chr2D 100.000 2748 0 0 1 2748 577603492 577600745 0.000000e+00 5075
1 TraesCS2D01G475000 chr2D 76.035 459 75 21 1658 2094 582493063 582493508 3.590000e-49 206
2 TraesCS2D01G475000 chr2D 80.913 241 39 6 18 255 477065092 477064856 1.680000e-42 183
3 TraesCS2D01G475000 chr2B 93.630 2653 128 20 111 2748 694990272 694992898 0.000000e+00 3925
4 TraesCS2D01G475000 chr2A 96.832 1231 38 1 837 2067 715813324 715814553 0.000000e+00 2056
5 TraesCS2D01G475000 chr2A 90.349 746 41 10 1 716 715812341 715813085 0.000000e+00 950
6 TraesCS2D01G475000 chr2A 90.544 423 24 9 2339 2748 715814572 715814991 1.860000e-151 545
7 TraesCS2D01G475000 chr2A 95.588 136 5 1 703 838 715813098 715813232 1.660000e-52 217
8 TraesCS2D01G475000 chr3D 78.438 640 107 22 687 1320 297677522 297678136 3.320000e-104 388
9 TraesCS2D01G475000 chr3D 81.132 371 39 20 1419 1783 297678179 297678524 4.510000e-68 268
10 TraesCS2D01G475000 chr3A 78.125 640 108 23 687 1320 394648590 394649203 7.180000e-101 377
11 TraesCS2D01G475000 chr3A 80.323 371 40 22 1419 1783 394649246 394649589 1.630000e-62 250
12 TraesCS2D01G475000 chr3B 77.403 593 106 20 687 1274 392797626 392798195 7.340000e-86 327
13 TraesCS2D01G475000 chr3B 80.645 372 38 22 1419 1783 392809526 392809870 9.760000e-65 257


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 TraesCS2D01G475000 chr2D 577600745 577603492 2747 True 5075.0 5075 100.00000 1 2748 1 chr2D.!!$R2 2747
1 TraesCS2D01G475000 chr2B 694990272 694992898 2626 False 3925.0 3925 93.63000 111 2748 1 chr2B.!!$F1 2637
2 TraesCS2D01G475000 chr2A 715812341 715814991 2650 False 942.0 2056 93.32825 1 2748 4 chr2A.!!$F1 2747
3 TraesCS2D01G475000 chr3D 297677522 297678524 1002 False 328.0 388 79.78500 687 1783 2 chr3D.!!$F1 1096
4 TraesCS2D01G475000 chr3A 394648590 394649589 999 False 313.5 377 79.22400 687 1783 2 chr3A.!!$F1 1096
5 TraesCS2D01G475000 chr3B 392797626 392798195 569 False 327.0 327 77.40300 687 1274 1 chr3B.!!$F1 587

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
74 75 0.237235 GGCAAGCGAACGTCATTTGA 59.763 50.000 0.00 0.00 0.00 2.69 F
1131 1287 1.202651 AGCAATACGTATGTCCCTGCC 60.203 52.381 20.22 7.62 31.09 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1217 1373 0.704076 AAATGCCAGCCCTTGTCCTA 59.296 50.0 0.0 0.0 0.00 2.94 R
2140 2297 0.253044 GGAGCCAACCAGCATCTACA 59.747 55.0 0.0 0.0 34.23 2.74 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
53 54 2.125512 CGTTCGCTGGGAGAAGGG 60.126 66.667 0.00 0.00 31.96 3.95
62 63 2.747855 GGAGAAGGGTGGCAAGCG 60.748 66.667 0.00 0.00 0.00 4.68
66 67 2.966309 GAAGGGTGGCAAGCGAACG 61.966 63.158 0.00 0.00 0.00 3.95
68 69 3.723348 GGGTGGCAAGCGAACGTC 61.723 66.667 0.00 0.00 0.00 4.34
69 70 2.970324 GGTGGCAAGCGAACGTCA 60.970 61.111 0.00 0.00 0.00 4.35
74 75 0.237235 GGCAAGCGAACGTCATTTGA 59.763 50.000 0.00 0.00 0.00 2.69
160 161 4.143543 TGAAGAAACTGACATGGCATTCA 58.856 39.130 15.60 12.85 0.00 2.57
255 278 2.230940 CGCCAGTTATGAGCGTCCG 61.231 63.158 0.00 0.00 39.63 4.79
276 299 3.806521 CGAGAGGATAGGTTTCTGCAATG 59.193 47.826 0.00 0.00 0.00 2.82
289 312 1.723870 GCAATGTTGCGAGCCCTAG 59.276 57.895 1.53 0.00 45.11 3.02
348 378 2.361357 CGGACCTCCTGACCTCGT 60.361 66.667 0.00 0.00 0.00 4.18
354 384 2.203640 TCCTGACCTCGTGGCAGT 60.204 61.111 19.47 0.00 36.45 4.40
358 388 2.338984 GACCTCGTGGCAGTTCGT 59.661 61.111 2.76 0.00 36.63 3.85
420 450 1.467920 CAGGATTCCAGGGTGAAAGC 58.532 55.000 5.29 0.00 0.00 3.51
498 528 2.706341 TACAAGGTGTGCCCCCTCCT 62.706 60.000 0.00 0.00 34.57 3.69
522 552 3.372675 CCGGAAAAATCCCCCTAATCTGT 60.373 47.826 0.00 0.00 0.00 3.41
562 592 3.592856 ATTGGTTGTCGCCCGCGTA 62.593 57.895 4.92 0.00 40.74 4.42
633 663 8.194104 GGATCTGATTATATAGCGAGTGATGTT 58.806 37.037 0.00 0.00 0.00 2.71
641 671 1.899814 AGCGAGTGATGTTTCCCTGTA 59.100 47.619 0.00 0.00 0.00 2.74
649 679 5.181245 AGTGATGTTTCCCTGTAAAATGACG 59.819 40.000 0.00 0.00 0.00 4.35
688 719 8.871125 TGTTAGGCATTCCCTTTTGTTAAATTA 58.129 29.630 0.00 0.00 43.06 1.40
696 727 8.485578 TTCCCTTTTGTTAAATTACATGGTCT 57.514 30.769 0.00 0.00 0.00 3.85
759 818 6.131544 ACTTGCATTGTTCTTACTCGTTTT 57.868 33.333 0.00 0.00 0.00 2.43
838 897 6.767902 CCATGACAGCTGGTTATGTTAACTAT 59.232 38.462 19.93 1.85 40.80 2.12
839 898 7.254898 CCATGACAGCTGGTTATGTTAACTATG 60.255 40.741 19.93 4.28 40.80 2.23
840 899 6.707290 TGACAGCTGGTTATGTTAACTATGT 58.293 36.000 19.93 0.00 0.00 2.29
841 900 6.593770 TGACAGCTGGTTATGTTAACTATGTG 59.406 38.462 19.93 0.00 0.00 3.21
846 998 6.630203 TGGTTATGTTAACTATGTGAGGGT 57.370 37.500 7.22 0.00 0.00 4.34
921 1073 2.480853 TTTGCTTGCTGATGGCTGCG 62.481 55.000 0.00 0.00 41.35 5.18
1080 1236 4.090642 GCGTCTTATGCTGGATTCTATTCG 59.909 45.833 0.00 0.00 0.00 3.34
1092 1248 5.163447 TGGATTCTATTCGTTCACTACCCTG 60.163 44.000 0.00 0.00 0.00 4.45
1095 1251 3.698040 TCTATTCGTTCACTACCCTGGTC 59.302 47.826 0.00 0.00 0.00 4.02
1131 1287 1.202651 AGCAATACGTATGTCCCTGCC 60.203 52.381 20.22 7.62 31.09 4.85
1217 1373 2.912956 TCTCTCCTGCCCAACTTATTGT 59.087 45.455 0.00 0.00 33.60 2.71
1732 1889 1.144503 CTTCTATCCCATGGCCAGCTT 59.855 52.381 13.05 0.00 0.00 3.74
1855 2012 5.324409 TCTTGAATTGTTCTGGCCTGTTAT 58.676 37.500 3.32 0.00 0.00 1.89
1863 2020 2.673258 TCTGGCCTGTTATGACGGATA 58.327 47.619 3.32 0.00 33.82 2.59
1906 2063 3.733077 GCTGAGCTGTTGCAATATCAACC 60.733 47.826 0.59 0.00 44.15 3.77
1977 2134 3.664107 CACCTAGTTGAAGCAAGCACTA 58.336 45.455 0.00 0.00 0.00 2.74
2114 2271 2.290260 CCAGTGACCTTAATCCTGCACA 60.290 50.000 0.00 0.00 0.00 4.57
2116 2273 4.012374 CAGTGACCTTAATCCTGCACATT 58.988 43.478 0.00 0.00 0.00 2.71
2124 2281 5.047802 CCTTAATCCTGCACATTGAGTTGTT 60.048 40.000 0.00 0.00 0.00 2.83
2128 2285 2.287788 CCTGCACATTGAGTTGTTGGTC 60.288 50.000 0.00 0.00 0.00 4.02
2133 2290 2.297033 ACATTGAGTTGTTGGTCCATGC 59.703 45.455 0.00 0.00 0.00 4.06
2161 2318 1.065126 GTAGATGCTGGTTGGCTCCTT 60.065 52.381 0.00 0.00 0.00 3.36
2169 2326 3.680196 GCTGGTTGGCTCCTTAACTAGAG 60.680 52.174 0.00 0.00 37.52 2.43
2180 2337 6.741801 GCTCCTTAACTAGAGGTTTTCAGTGT 60.742 42.308 0.00 0.00 39.17 3.55
2196 2353 0.320508 GTGTCGGTTCAGGAGTTCCC 60.321 60.000 0.00 0.00 36.42 3.97
2266 2423 7.259290 ACGTTGTCAAGAGTCATTTTATTGT 57.741 32.000 0.00 0.00 0.00 2.71
2304 2461 7.820872 CCGGTAGACTTTTAAATACCTTCTCAA 59.179 37.037 11.94 0.00 36.36 3.02
2313 2470 9.474313 TTTTAAATACCTTCTCAATGCTGGTAT 57.526 29.630 0.00 0.00 43.40 2.73
2314 2471 6.949352 AAATACCTTCTCAATGCTGGTATG 57.051 37.500 0.00 0.00 41.48 2.39
2460 2621 5.586243 AGGGTTGATGATTGTTCTATGTTCG 59.414 40.000 0.00 0.00 0.00 3.95
2470 2631 3.192001 TGTTCTATGTTCGGCGAGTAGTT 59.808 43.478 10.46 0.00 0.00 2.24
2472 2633 3.276857 TCTATGTTCGGCGAGTAGTTCT 58.723 45.455 10.46 0.00 0.00 3.01
2473 2634 3.693085 TCTATGTTCGGCGAGTAGTTCTT 59.307 43.478 10.46 0.00 0.00 2.52
2474 2635 2.060326 TGTTCGGCGAGTAGTTCTTG 57.940 50.000 10.46 0.00 0.00 3.02
2475 2636 1.338973 TGTTCGGCGAGTAGTTCTTGT 59.661 47.619 10.46 0.00 0.00 3.16
2500 2665 1.285950 GAGCCTTCGGTTGTTTGCC 59.714 57.895 0.00 0.00 0.00 4.52
2504 2669 0.597377 CCTTCGGTTGTTTGCCTTGC 60.597 55.000 0.00 0.00 0.00 4.01
2514 2679 0.103937 TTTGCCTTGCTTTCCAACGG 59.896 50.000 0.00 0.00 0.00 4.44
2533 2701 7.387673 TCCAACGGAAGCATATATCTGTAAATG 59.612 37.037 0.00 0.00 34.12 2.32
2542 2710 9.060347 AGCATATATCTGTAAATGAAAGTGTGG 57.940 33.333 0.00 0.00 0.00 4.17
2601 2769 7.172361 TGTTATTTTGCCAAACTTTTGCCTATC 59.828 33.333 0.00 0.00 36.86 2.08
2605 2773 2.562738 GCCAAACTTTTGCCTATCAGGT 59.437 45.455 0.00 0.00 37.80 4.00
2615 2783 1.489481 CCTATCAGGTGAGGCAGACA 58.511 55.000 0.00 0.00 0.00 3.41
2670 2838 8.430063 CAATTTACTTAGCACAATGAAAGCAAG 58.570 33.333 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.376037 CACCCTTCTCCCAGCGAAC 60.376 63.158 0.00 0.00 0.00 3.95
53 54 0.040425 AAATGACGTTCGCTTGCCAC 60.040 50.000 0.00 0.00 0.00 5.01
66 67 8.067784 TCTCAACTAAAATTGTCGTCAAATGAC 58.932 33.333 3.43 3.43 41.47 3.06
68 69 8.781067 TTCTCAACTAAAATTGTCGTCAAATG 57.219 30.769 0.00 0.00 37.11 2.32
69 70 8.836413 TCTTCTCAACTAAAATTGTCGTCAAAT 58.164 29.630 0.00 0.00 37.11 2.32
129 130 3.071602 TGTCAGTTTCTTCAGGGAAGGAG 59.928 47.826 6.17 0.00 39.82 3.69
130 131 3.045634 TGTCAGTTTCTTCAGGGAAGGA 58.954 45.455 6.17 0.00 39.82 3.36
160 161 1.349357 GAGGGAGTGGCAGTTTCTTCT 59.651 52.381 0.00 0.00 0.00 2.85
255 278 4.775236 ACATTGCAGAAACCTATCCTCTC 58.225 43.478 0.00 0.00 0.00 3.20
276 299 1.815840 GAAGGCTAGGGCTCGCAAC 60.816 63.158 0.00 0.00 37.50 4.17
380 410 2.591429 CACTGCGGTGTTGCCTGA 60.591 61.111 17.96 0.00 38.54 3.86
498 528 0.705253 TTAGGGGGATTTTTCCGGCA 59.295 50.000 0.00 0.00 0.00 5.69
522 552 2.852495 GATCTCCGCCGTTTCCAGCA 62.852 60.000 0.00 0.00 0.00 4.41
584 614 5.222631 CAGCAAACAATCAGGGAAAAGTAC 58.777 41.667 0.00 0.00 0.00 2.73
633 663 3.773418 TGACCGTCATTTTACAGGGAA 57.227 42.857 0.00 0.00 0.00 3.97
641 671 3.502211 CAGCTAAGGTTGACCGTCATTTT 59.498 43.478 1.09 0.61 42.08 1.82
649 679 2.290071 TGCCTAACAGCTAAGGTTGACC 60.290 50.000 9.89 0.00 35.16 4.02
676 707 7.507616 ACCTGGAGACCATGTAATTTAACAAAA 59.492 33.333 0.00 0.00 30.89 2.44
688 719 4.657814 AAACAATACCTGGAGACCATGT 57.342 40.909 0.00 0.00 36.42 3.21
696 727 2.640826 ACGAGGGAAAACAATACCTGGA 59.359 45.455 0.00 0.00 33.64 3.86
759 818 5.538118 CGTCCACATAGGCTTGACATATTA 58.462 41.667 0.00 0.00 37.29 0.98
838 897 1.629861 TGATTGCTGATGACCCTCACA 59.370 47.619 0.00 0.00 0.00 3.58
839 898 2.286872 CTGATTGCTGATGACCCTCAC 58.713 52.381 0.00 0.00 0.00 3.51
840 899 1.407851 GCTGATTGCTGATGACCCTCA 60.408 52.381 0.00 0.00 38.95 3.86
841 900 1.307097 GCTGATTGCTGATGACCCTC 58.693 55.000 0.00 0.00 38.95 4.30
846 998 2.502142 ACCTTGCTGATTGCTGATGA 57.498 45.000 0.00 0.00 43.37 2.92
1080 1236 1.349067 AGGTGACCAGGGTAGTGAAC 58.651 55.000 3.63 0.00 0.00 3.18
1131 1287 3.127030 GGTCTGTAAAGAAGGGCAATTCG 59.873 47.826 0.00 0.00 34.27 3.34
1217 1373 0.704076 AAATGCCAGCCCTTGTCCTA 59.296 50.000 0.00 0.00 0.00 2.94
1732 1889 3.411446 CTGCAGTTAACCACTTCCATCA 58.589 45.455 5.25 0.00 30.92 3.07
1855 2012 3.953712 TTTTGACTCTGCTATCCGTCA 57.046 42.857 0.00 0.00 34.85 4.35
1863 2020 3.868077 GCATCTACGATTTTGACTCTGCT 59.132 43.478 0.00 0.00 0.00 4.24
1906 2063 7.534085 TCCGCACAGTTTTGACTATTAATAG 57.466 36.000 18.99 18.99 36.46 1.73
1977 2134 2.990740 AGGAGGGATAAGAGATCGCT 57.009 50.000 4.01 4.01 42.84 4.93
2114 2271 2.596346 TGCATGGACCAACAACTCAAT 58.404 42.857 0.00 0.00 0.00 2.57
2116 2273 1.887854 CATGCATGGACCAACAACTCA 59.112 47.619 19.40 0.00 0.00 3.41
2133 2290 3.317149 CCAACCAGCATCTACAATCCATG 59.683 47.826 0.00 0.00 0.00 3.66
2138 2295 2.648059 GAGCCAACCAGCATCTACAAT 58.352 47.619 0.00 0.00 34.23 2.71
2139 2296 1.340017 GGAGCCAACCAGCATCTACAA 60.340 52.381 0.00 0.00 34.23 2.41
2140 2297 0.253044 GGAGCCAACCAGCATCTACA 59.747 55.000 0.00 0.00 34.23 2.74
2141 2298 0.543749 AGGAGCCAACCAGCATCTAC 59.456 55.000 0.00 0.00 34.23 2.59
2142 2299 1.289160 AAGGAGCCAACCAGCATCTA 58.711 50.000 0.00 0.00 34.23 1.98
2161 2318 4.586001 ACCGACACTGAAAACCTCTAGTTA 59.414 41.667 0.00 0.00 37.88 2.24
2169 2326 1.602377 CCTGAACCGACACTGAAAACC 59.398 52.381 0.00 0.00 0.00 3.27
2180 2337 2.280552 CGGGGAACTCCTGAACCGA 61.281 63.158 5.51 0.00 44.90 4.69
2196 2353 0.739112 GCCTGAGCAGAAACTCTCGG 60.739 60.000 0.00 0.00 39.53 4.63
2266 2423 9.941325 TTAAAAGTCTACCGGAAATATTGTGTA 57.059 29.630 9.46 0.00 0.00 2.90
2304 2461 6.440010 AGCTCTACATAGATTCATACCAGCAT 59.560 38.462 0.00 0.00 0.00 3.79
2356 2513 8.946085 CAGTCCTTGTTGATTTTATAACTAGCA 58.054 33.333 0.00 0.00 31.36 3.49
2403 2561 2.955660 CCTTACAAGACAAAGGTTGCCA 59.044 45.455 0.00 0.00 37.96 4.92
2460 2621 3.429135 CCTCCTTACAAGAACTACTCGCC 60.429 52.174 0.00 0.00 0.00 5.54
2488 2653 0.820871 AAAGCAAGGCAAACAACCGA 59.179 45.000 0.00 0.00 0.00 4.69
2494 2659 1.208259 CGTTGGAAAGCAAGGCAAAC 58.792 50.000 0.00 0.00 0.00 2.93
2500 2665 0.667993 TGCTTCCGTTGGAAAGCAAG 59.332 50.000 15.51 0.26 41.54 4.01
2504 2669 5.760253 ACAGATATATGCTTCCGTTGGAAAG 59.240 40.000 0.00 0.00 41.54 2.62
2533 2701 8.751302 TTTTGTTAAGAAGAAACCACACTTTC 57.249 30.769 0.00 0.00 0.00 2.62
2542 2710 7.651704 TGCTATGCCTTTTTGTTAAGAAGAAAC 59.348 33.333 0.00 0.00 0.00 2.78
2605 2773 4.357947 GACGCGGTGTCTGCCTCA 62.358 66.667 12.47 0.00 44.58 3.86
2615 2783 2.660552 CGTTCCTTGTGACGCGGT 60.661 61.111 12.47 0.00 32.11 5.68


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

AutoCloner maintained by Alex Coulton.