Multiple sequence alignment - TraesCS1D01G402800

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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 TraesCS1D01G402800 chr1D 100.000 3228 0 0 1 3228 467800050 467803277 0.000000e+00 5962.0
1 TraesCS1D01G402800 chr1D 77.395 1190 229 29 1270 2436 47649141 47650313 0.000000e+00 671.0
2 TraesCS1D01G402800 chr1D 75.639 587 104 22 1 555 362255482 362254903 4.130000e-64 255.0
3 TraesCS1D01G402800 chr1D 80.156 257 32 15 305 549 108800508 108800757 1.190000e-39 174.0
4 TraesCS1D01G402800 chr1D 82.456 114 18 2 2548 2660 47650323 47650435 7.370000e-17 99.0
5 TraesCS1D01G402800 chr1A 93.035 2972 117 36 305 3228 560182224 560179295 0.000000e+00 4259.0
6 TraesCS1D01G402800 chr1A 81.905 315 41 12 2 304 560182564 560182254 5.350000e-63 252.0
7 TraesCS1D01G402800 chr1A 75.592 549 106 19 2079 2606 576352985 576352444 2.490000e-61 246.0
8 TraesCS1D01G402800 chr1A 77.922 231 35 13 2904 3133 262339190 262338975 2.610000e-26 130.0
9 TraesCS1D01G402800 chr1A 81.731 104 17 2 2548 2650 47519406 47519508 5.740000e-13 86.1
10 TraesCS1D01G402800 chr1B 92.573 2666 121 31 607 3228 645706780 645709412 0.000000e+00 3755.0
11 TraesCS1D01G402800 chr1B 78.832 137 21 7 310 440 367431394 367431528 5.740000e-13 86.1
12 TraesCS1D01G402800 chr6B 81.015 1222 214 9 1274 2480 123911208 123912426 0.000000e+00 955.0
13 TraesCS1D01G402800 chr6B 77.826 230 37 11 305 527 66736857 66736635 2.610000e-26 130.0
14 TraesCS1D01G402800 chr6A 80.611 1212 210 11 1274 2466 67641981 67643186 0.000000e+00 913.0
15 TraesCS1D01G402800 chr6A 87.607 234 14 5 2999 3228 4867322 4867544 1.150000e-64 257.0
16 TraesCS1D01G402800 chr6D 79.902 1219 223 11 1280 2481 47638373 47637160 0.000000e+00 874.0
17 TraesCS1D01G402800 chr5D 75.101 494 101 19 1953 2441 441238483 441238007 9.070000e-51 211.0
18 TraesCS1D01G402800 chr5D 72.581 496 112 19 1957 2446 441162929 441162452 1.210000e-29 141.0
19 TraesCS1D01G402800 chrUn 78.788 264 46 6 2234 2488 87467476 87467738 5.540000e-38 169.0
20 TraesCS1D01G402800 chr7D 78.439 269 42 14 305 563 208679539 208679277 9.270000e-36 161.0
21 TraesCS1D01G402800 chr2A 77.056 231 37 12 2904 3133 6378088 6378303 5.660000e-23 119.0
22 TraesCS1D01G402800 chr7A 76.724 232 36 13 2904 3133 119835817 119836032 2.630000e-21 113.0
23 TraesCS1D01G402800 chr4D 84.211 95 13 2 436 529 93762602 93762695 1.230000e-14 91.6


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 TraesCS1D01G402800 chr1D 467800050 467803277 3227 False 5962.0 5962 100.0000 1 3228 1 chr1D.!!$F2 3227
1 TraesCS1D01G402800 chr1D 47649141 47650435 1294 False 385.0 671 79.9255 1270 2660 2 chr1D.!!$F3 1390
2 TraesCS1D01G402800 chr1D 362254903 362255482 579 True 255.0 255 75.6390 1 555 1 chr1D.!!$R1 554
3 TraesCS1D01G402800 chr1A 560179295 560182564 3269 True 2255.5 4259 87.4700 2 3228 2 chr1A.!!$R3 3226
4 TraesCS1D01G402800 chr1A 576352444 576352985 541 True 246.0 246 75.5920 2079 2606 1 chr1A.!!$R2 527
5 TraesCS1D01G402800 chr1B 645706780 645709412 2632 False 3755.0 3755 92.5730 607 3228 1 chr1B.!!$F2 2621
6 TraesCS1D01G402800 chr6B 123911208 123912426 1218 False 955.0 955 81.0150 1274 2480 1 chr6B.!!$F1 1206
7 TraesCS1D01G402800 chr6A 67641981 67643186 1205 False 913.0 913 80.6110 1274 2466 1 chr6A.!!$F2 1192
8 TraesCS1D01G402800 chr6D 47637160 47638373 1213 True 874.0 874 79.9020 1280 2481 1 chr6D.!!$R1 1201

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
989 1083 0.817229 GCTGAGGGCACTCCAATAGC 60.817 60.0 14.84 12.09 43.29 2.97 F
1034 1128 0.462759 GAGGAGATTTCCCAGCGGTG 60.463 60.0 7.86 7.86 45.24 4.94 F
2044 2177 0.320334 TTCGCACCATCATGTCACGT 60.320 50.0 0.00 0.00 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2177 2.046023 CCAGAAGCATCACCGGCA 60.046 61.111 0.00 0.0 0.00 5.69 R
2178 2311 2.169978 CTCAAGGTCTGATCCAGCATCA 59.830 50.000 0.00 0.0 39.39 3.07 R
3088 3251 2.795329 ACTTTGTCCAGCAACATAGGG 58.205 47.619 8.43 0.0 36.72 3.53 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
83 93 8.672214 AATTTCAAAACTGTTCATGTTTTTGC 57.328 26.923 0.00 0.00 42.68 3.68
85 95 6.645700 TCAAAACTGTTCATGTTTTTGCTC 57.354 33.333 0.00 0.00 42.68 4.26
94 104 2.861462 TGTTTTTGCTCGGGAGTTTG 57.139 45.000 0.00 0.00 0.00 2.93
97 107 3.193691 TGTTTTTGCTCGGGAGTTTGAAA 59.806 39.130 0.00 0.00 0.00 2.69
99 109 4.457834 TTTTGCTCGGGAGTTTGAAAAA 57.542 36.364 0.00 0.00 0.00 1.94
214 226 9.340695 CATAAAATGTCTGCGTTCTGAATTTTA 57.659 29.630 0.00 0.00 33.89 1.52
240 253 7.897575 TTTGGAATTTCAAAATATGTTCCCG 57.102 32.000 9.56 0.00 33.04 5.14
245 258 8.779303 GGAATTTCAAAATATGTTCCCGTTTTT 58.221 29.630 0.00 0.00 29.55 1.94
262 278 9.819267 TCCCGTTTTTAAATATTTGTGTTTTCT 57.181 25.926 11.05 0.00 0.00 2.52
295 311 7.129109 TCCAGAGTTTCATAAAATGTTCGTC 57.871 36.000 0.00 0.00 0.00 4.20
358 405 9.447157 TTCCAGAGTTTCAAAAATTGTTCATTT 57.553 25.926 0.00 0.00 36.57 2.32
360 407 9.706846 CCAGAGTTTCAAAAATTGTTCATTTTC 57.293 29.630 0.00 0.00 43.20 2.29
391 439 9.958234 AAAAATAAAATCCCGTTTTGGAAAATG 57.042 25.926 0.00 0.00 40.17 2.32
396 444 4.473477 TCCCGTTTTGGAAAATGTTTGT 57.527 36.364 3.92 0.00 42.00 2.83
397 445 4.833390 TCCCGTTTTGGAAAATGTTTGTT 58.167 34.783 3.92 0.00 42.00 2.83
401 449 6.524933 CCCGTTTTGGAAAATGTTTGTTTTTC 59.475 34.615 3.92 0.00 42.00 2.29
442 496 9.691362 AATTAAAAAGTGTCTGCGTTTCATAAT 57.309 25.926 0.00 0.00 0.00 1.28
445 499 5.450376 AAGTGTCTGCGTTTCATAATACG 57.550 39.130 0.00 0.00 40.55 3.06
552 610 5.692204 CGAGCAAAATATTCAGATACGGTCT 59.308 40.000 0.00 0.00 37.80 3.85
555 613 7.697691 AGCAAAATATTCAGATACGGTCTTTG 58.302 34.615 0.00 0.00 34.00 2.77
556 614 6.912591 GCAAAATATTCAGATACGGTCTTTGG 59.087 38.462 0.00 0.00 34.00 3.28
563 621 3.435671 CAGATACGGTCTTTGGTTCAACC 59.564 47.826 0.00 0.00 34.99 3.77
591 660 3.390521 TCGCCTCATTCGCCCACT 61.391 61.111 0.00 0.00 0.00 4.00
593 662 1.592669 CGCCTCATTCGCCCACTAG 60.593 63.158 0.00 0.00 0.00 2.57
702 784 4.840005 GCTACCCCTGCCAGCGAC 62.840 72.222 0.00 0.00 0.00 5.19
703 785 4.162690 CTACCCCTGCCAGCGACC 62.163 72.222 0.00 0.00 0.00 4.79
911 993 9.107177 TCATTCTTCATCTCTTTTCATCTAAGC 57.893 33.333 0.00 0.00 0.00 3.09
922 1016 6.442564 TCTTTTCATCTAAGCACCCTAGGTAA 59.557 38.462 8.29 0.00 32.11 2.85
923 1017 6.824958 TTTCATCTAAGCACCCTAGGTAAT 57.175 37.500 8.29 0.00 32.11 1.89
932 1026 6.189036 AGCACCCTAGGTAATTAGGATTTC 57.811 41.667 8.29 0.00 42.39 2.17
955 1049 4.423625 CCCCCTAATTCAACTCTACCTG 57.576 50.000 0.00 0.00 0.00 4.00
978 1072 1.825474 TGTACTTACTCAGCTGAGGGC 59.175 52.381 39.42 24.18 46.13 5.19
989 1083 0.817229 GCTGAGGGCACTCCAATAGC 60.817 60.000 14.84 12.09 43.29 2.97
999 1093 3.447586 GCACTCCAATAGCCCGATAGATA 59.552 47.826 0.00 0.00 39.76 1.98
1002 1096 6.045318 CACTCCAATAGCCCGATAGATAATG 58.955 44.000 0.00 0.00 39.76 1.90
1003 1097 5.129485 ACTCCAATAGCCCGATAGATAATGG 59.871 44.000 0.00 0.00 39.76 3.16
1004 1098 5.277250 TCCAATAGCCCGATAGATAATGGA 58.723 41.667 0.00 0.00 39.76 3.41
1034 1128 0.462759 GAGGAGATTTCCCAGCGGTG 60.463 60.000 7.86 7.86 45.24 4.94
1044 1138 2.584418 CAGCGGTGAGAGCATCCG 60.584 66.667 9.50 0.00 45.94 4.18
1181 1275 2.154567 ATCAGCCCATTGCATTGACT 57.845 45.000 10.14 4.51 44.83 3.41
1207 1301 2.047655 TTTGTTCGCCGCTCCGAT 60.048 55.556 0.00 0.00 37.06 4.18
1278 1390 1.759299 AGCATTTGCCGGCATCCAT 60.759 52.632 33.25 19.80 43.38 3.41
1343 1473 1.072332 ACCACACTTGTATGCGCCA 59.928 52.632 4.18 0.00 0.00 5.69
1399 1529 1.208293 GACCCTAAGTTCCTCAGCCTG 59.792 57.143 0.00 0.00 0.00 4.85
1446 1576 5.171476 CGTCCTTGGCTTCTACATATATGG 58.829 45.833 16.96 0.39 0.00 2.74
1460 1590 2.326529 ATATGGAGGGTCGGCCTGGA 62.327 60.000 5.77 0.00 34.45 3.86
1492 1622 3.787001 CCCCTGCTCTTCGTCCCC 61.787 72.222 0.00 0.00 0.00 4.81
1819 1952 2.096248 ACAAAAAGTTTCAGGGTGCGA 58.904 42.857 0.00 0.00 0.00 5.10
1822 1955 1.594331 AAAGTTTCAGGGTGCGAGTC 58.406 50.000 0.00 0.00 0.00 3.36
1837 1970 3.118775 TGCGAGTCTATATGTTGCAAGGT 60.119 43.478 0.00 0.00 0.00 3.50
1899 2032 2.024319 GTCTGCTGACGTCACTGGC 61.024 63.158 15.76 17.37 33.15 4.85
2044 2177 0.320334 TTCGCACCATCATGTCACGT 60.320 50.000 0.00 0.00 0.00 4.49
2178 2311 6.072649 TGCATCAGATGTGGGATAATTTGAT 58.927 36.000 12.18 0.00 30.11 2.57
2185 2318 5.777850 TGTGGGATAATTTGATGATGCTG 57.222 39.130 0.00 0.00 0.00 4.41
2297 2434 5.241064 GCTGCATTTTCTATCTGGATGTCAT 59.759 40.000 0.00 0.00 0.00 3.06
2470 2612 8.259049 TGTATATTCCTTTTGTTGAGGTTACG 57.741 34.615 0.00 0.00 35.71 3.18
2472 2614 4.886247 TTCCTTTTGTTGAGGTTACGTG 57.114 40.909 0.00 0.00 35.71 4.49
2816 2973 9.618890 ACTTATGCATGAGATTGTAATACTTGT 57.381 29.630 23.98 0.00 0.00 3.16
3110 3273 3.057315 CCCTATGTTGCTGGACAAAGTTG 60.057 47.826 0.00 0.00 40.82 3.16
3148 3311 7.889589 TCTGAGTGTACATAACATTTGACTG 57.110 36.000 0.00 0.00 41.10 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 9.603921 ACATGAACAGTTTTGAAATTTCTGATT 57.396 25.926 18.64 6.01 0.00 2.57
52 53 9.603921 AACATGAACAGTTTTGAAATTTCTGAT 57.396 25.926 18.64 3.60 0.00 2.90
68 71 2.293122 TCCCGAGCAAAAACATGAACAG 59.707 45.455 0.00 0.00 0.00 3.16
97 107 7.201487 GCACAAAATTACTGAAAACGGACTTTT 60.201 33.333 0.00 0.00 34.56 2.27
99 109 5.746721 GCACAAAATTACTGAAAACGGACTT 59.253 36.000 0.00 0.00 0.00 3.01
101 111 5.038033 TGCACAAAATTACTGAAAACGGAC 58.962 37.500 0.00 0.00 0.00 4.79
103 113 6.523676 AATGCACAAAATTACTGAAAACGG 57.476 33.333 0.00 0.00 0.00 4.44
104 114 9.352163 GTAAAATGCACAAAATTACTGAAAACG 57.648 29.630 0.00 0.00 0.00 3.60
177 189 8.564574 ACGCAGACATTTTATGAAAACTAGAAA 58.435 29.630 0.00 0.00 32.37 2.52
178 190 8.094798 ACGCAGACATTTTATGAAAACTAGAA 57.905 30.769 0.00 0.00 32.37 2.10
250 266 9.883142 TCTGGAACAAAATTAGAAAACACAAAT 57.117 25.926 0.00 0.00 38.70 2.32
360 407 8.831550 TCCAAAACGGGATTTTATTTTTGAAAG 58.168 29.630 6.66 0.00 38.50 2.62
413 467 8.245701 TGAAACGCAGACACTTTTTAATTTTT 57.754 26.923 0.00 0.00 0.00 1.94
429 483 7.775729 AAAAAGAACGTATTATGAAACGCAG 57.224 32.000 0.00 0.00 42.74 5.18
552 610 1.040339 AAGCTGCCGGTTGAACCAAA 61.040 50.000 15.58 0.00 38.47 3.28
611 680 0.179018 AGGCGAGTGGAGCTGTTTTT 60.179 50.000 0.00 0.00 34.52 1.94
612 681 0.886490 CAGGCGAGTGGAGCTGTTTT 60.886 55.000 0.00 0.00 34.52 2.43
700 782 2.939261 TTCCCGGAAGTCAGCGGTC 61.939 63.158 0.73 0.00 0.00 4.79
701 783 2.920912 TTCCCGGAAGTCAGCGGT 60.921 61.111 0.73 0.00 0.00 5.68
702 784 2.434359 GTTCCCGGAAGTCAGCGG 60.434 66.667 0.73 0.00 0.00 5.52
703 785 2.434359 GGTTCCCGGAAGTCAGCG 60.434 66.667 0.73 0.00 0.00 5.18
704 786 2.046217 GGGTTCCCGGAAGTCAGC 60.046 66.667 0.73 0.00 0.00 4.26
705 787 1.192146 TCTGGGTTCCCGGAAGTCAG 61.192 60.000 16.22 17.53 38.44 3.51
706 788 0.546747 ATCTGGGTTCCCGGAAGTCA 60.547 55.000 21.43 1.34 43.82 3.41
707 789 0.178301 GATCTGGGTTCCCGGAAGTC 59.822 60.000 21.43 12.73 43.82 3.01
708 790 1.272554 GGATCTGGGTTCCCGGAAGT 61.273 60.000 21.43 7.89 43.82 3.01
709 791 1.527370 GGATCTGGGTTCCCGGAAG 59.473 63.158 21.43 5.54 43.82 3.46
710 792 2.363975 CGGATCTGGGTTCCCGGAA 61.364 63.158 21.43 0.00 43.82 4.30
711 793 2.762459 CGGATCTGGGTTCCCGGA 60.762 66.667 20.11 20.11 44.61 5.14
712 794 4.547367 GCGGATCTGGGTTCCCGG 62.547 72.222 10.29 10.29 42.02 5.73
713 795 3.447025 GAGCGGATCTGGGTTCCCG 62.447 68.421 3.14 0.00 44.34 5.14
714 796 1.910580 TTGAGCGGATCTGGGTTCCC 61.911 60.000 3.14 0.12 0.00 3.97
715 797 0.035439 TTTGAGCGGATCTGGGTTCC 60.035 55.000 3.14 0.00 0.00 3.62
716 798 1.373570 CTTTGAGCGGATCTGGGTTC 58.626 55.000 3.14 0.00 0.00 3.62
854 936 3.386402 AGAAGAGGAAGGATAAAGGCTCG 59.614 47.826 0.00 0.00 0.00 5.03
908 990 6.410504 GGAAATCCTAATTACCTAGGGTGCTT 60.411 42.308 14.81 3.68 39.26 3.91
909 991 5.073280 GGAAATCCTAATTACCTAGGGTGCT 59.927 44.000 14.81 0.00 39.26 4.40
910 992 5.314529 GGAAATCCTAATTACCTAGGGTGC 58.685 45.833 14.81 0.00 39.26 5.01
911 993 5.222068 GGGGAAATCCTAATTACCTAGGGTG 60.222 48.000 14.81 0.00 39.26 4.61
955 1049 3.452474 CCTCAGCTGAGTAAGTACATGC 58.548 50.000 35.47 0.00 40.48 4.06
978 1072 5.661056 TTATCTATCGGGCTATTGGAGTG 57.339 43.478 0.00 0.00 0.00 3.51
989 1083 3.708631 AGCATCCTCCATTATCTATCGGG 59.291 47.826 0.00 0.00 0.00 5.14
999 1093 0.471617 CCTCGGAAGCATCCTCCATT 59.528 55.000 6.39 0.00 44.17 3.16
1002 1096 0.757188 TCTCCTCGGAAGCATCCTCC 60.757 60.000 6.39 0.00 44.17 4.30
1003 1097 1.337118 ATCTCCTCGGAAGCATCCTC 58.663 55.000 6.39 0.00 44.17 3.71
1004 1098 1.799933 AATCTCCTCGGAAGCATCCT 58.200 50.000 6.39 0.00 44.17 3.24
1034 1128 3.133946 GGGAGACCGGATGCTCTC 58.866 66.667 9.46 10.19 43.64 3.20
1165 1259 2.226962 AAGAGTCAATGCAATGGGCT 57.773 45.000 1.05 0.73 45.15 5.19
1207 1301 0.250727 CTGGACGGAGCCTGGAAAAA 60.251 55.000 0.00 0.00 0.00 1.94
1271 1365 2.528743 CGTCGAGCACCATGGATGC 61.529 63.158 21.47 22.89 43.74 3.91
1278 1390 2.836793 TTGTCGTCGTCGAGCACCA 61.837 57.895 4.68 0.00 46.96 4.17
1424 1554 6.360370 TCCATATATGTAGAAGCCAAGGAC 57.640 41.667 11.73 0.00 0.00 3.85
1446 1576 1.674057 CATATCCAGGCCGACCCTC 59.326 63.158 0.00 0.00 44.09 4.30
1819 1952 3.545703 GCCACCTTGCAACATATAGACT 58.454 45.455 0.00 0.00 0.00 3.24
1822 1955 2.287915 GACGCCACCTTGCAACATATAG 59.712 50.000 0.00 0.00 0.00 1.31
1837 1970 3.923782 ATGCATGCACCAGACGCCA 62.924 57.895 25.37 0.00 0.00 5.69
1899 2032 4.466567 TTATCGTCAACAAGCACAACTG 57.533 40.909 0.00 0.00 0.00 3.16
2044 2177 2.046023 CCAGAAGCATCACCGGCA 60.046 61.111 0.00 0.00 0.00 5.69
2178 2311 2.169978 CTCAAGGTCTGATCCAGCATCA 59.830 50.000 0.00 0.00 39.39 3.07
2185 2318 2.224257 GCTCATCCTCAAGGTCTGATCC 60.224 54.545 0.00 0.00 36.34 3.36
2297 2434 3.493129 CACTTTACGCAGTGTCTTGCTTA 59.507 43.478 0.00 0.00 45.73 3.09
2414 2551 3.961480 AGGCCAAAATAGCAAACCTTC 57.039 42.857 5.01 0.00 0.00 3.46
3088 3251 2.795329 ACTTTGTCCAGCAACATAGGG 58.205 47.619 8.43 0.00 36.72 3.53


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

AutoCloner maintained by Alex Coulton.