Multiple sequence alignment - TraesCS4D01G213000

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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 TraesCS4D01G213000 chr4D 100.000 3026 0 0 1 3026 365852125 365855150 0.000000e+00 5589
1 TraesCS4D01G213000 chr4B 96.990 1827 50 4 1205 3026 450469830 450471656 0.000000e+00 3064
2 TraesCS4D01G213000 chr4B 97.283 552 15 0 20 571 450468652 450469203 0.000000e+00 937
3 TraesCS4D01G213000 chr4B 96.959 296 7 2 620 914 450469529 450469823 2.100000e-136 496
4 TraesCS4D01G213000 chr4A 93.404 1137 46 8 3 1117 99018971 99017842 0.000000e+00 1657
5 TraesCS4D01G213000 chr1D 75.035 1430 296 41 926 2322 314192915 314194316 9.280000e-170 606
6 TraesCS4D01G213000 chr1A 78.113 763 162 5 2262 3021 304988961 304988201 2.110000e-131 479
7 TraesCS4D01G213000 chr7A 73.550 431 101 12 2430 2853 146683468 146683044 5.230000e-33 152
8 TraesCS4D01G213000 chr3B 75.460 326 63 14 2497 2813 9112087 9111770 3.140000e-30 143
9 TraesCS4D01G213000 chr3B 72.525 404 96 14 2432 2827 299753983 299754379 1.910000e-22 117


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 TraesCS4D01G213000 chr4D 365852125 365855150 3025 False 5589 5589 100.000000 1 3026 1 chr4D.!!$F1 3025
1 TraesCS4D01G213000 chr4B 450468652 450471656 3004 False 1499 3064 97.077333 20 3026 3 chr4B.!!$F1 3006
2 TraesCS4D01G213000 chr4A 99017842 99018971 1129 True 1657 1657 93.404000 3 1117 1 chr4A.!!$R1 1114
3 TraesCS4D01G213000 chr1D 314192915 314194316 1401 False 606 606 75.035000 926 2322 1 chr1D.!!$F1 1396
4 TraesCS4D01G213000 chr1A 304988201 304988961 760 True 479 479 78.113000 2262 3021 1 chr1A.!!$R1 759

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
453 474 0.321034 CAGCAGTAGCAGCACTTGGA 60.321 55.0 0.0 0.0 45.49 3.53 F
1481 1787 1.122227 AAACAGCCAGGTGCAATTGT 58.878 45.0 7.4 0.0 44.83 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1792 0.884704 TGTGTTGCTTCGGCTCCTTC 60.885 55.0 0.0 0.0 42.37 3.46 R
2908 3233 0.746659 AGGAACAGCAAACAAGCACC 59.253 50.0 0.0 0.0 36.85 5.01 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
18 19 1.299544 GACGTTGGGGCGGTTTTTG 60.300 57.895 0.00 0.00 35.98 2.44
148 149 1.067916 GTTCACGTACGGGTGGTGT 59.932 57.895 18.57 0.00 38.46 4.16
273 274 0.517316 GTTCGAAGCAAAGCGTGGAT 59.483 50.000 0.00 0.00 0.00 3.41
403 424 3.370527 GGCTACCAACTTCAAGCAGGATA 60.371 47.826 2.82 0.00 36.68 2.59
453 474 0.321034 CAGCAGTAGCAGCACTTGGA 60.321 55.000 0.00 0.00 45.49 3.53
534 555 2.123589 TCAGTGGTTCCTCCTTCAACA 58.876 47.619 0.00 0.00 37.07 3.33
637 938 4.079970 TCCTCTCGCTGAAGAACTTAAGA 58.920 43.478 10.09 0.00 0.00 2.10
638 939 4.156922 TCCTCTCGCTGAAGAACTTAAGAG 59.843 45.833 10.09 0.36 0.00 2.85
639 940 4.420168 CTCTCGCTGAAGAACTTAAGAGG 58.580 47.826 10.09 0.00 0.00 3.69
648 949 9.040939 GCTGAAGAACTTAAGAGGAGATTATTC 57.959 37.037 10.09 5.68 0.00 1.75
671 972 4.273148 TGGAGCAAGAGAAAACTAGTCC 57.727 45.455 0.00 0.00 0.00 3.85
742 1043 4.351054 CAGCTCCACCGGGGCTTT 62.351 66.667 4.17 0.00 38.25 3.51
923 1225 4.656100 TCCTCAAATCCATGACCAAGAA 57.344 40.909 0.00 0.00 0.00 2.52
1119 1421 1.141053 CAGTATACCTGGGGCCAGTTC 59.859 57.143 4.39 0.00 42.15 3.01
1125 1427 3.177884 TGGGGCCAGTTCTGTGCT 61.178 61.111 4.39 0.00 0.00 4.40
1131 1433 1.615392 GGCCAGTTCTGTGCTGAAATT 59.385 47.619 0.00 0.00 36.12 1.82
1134 1436 3.611057 GCCAGTTCTGTGCTGAAATTCTG 60.611 47.826 0.00 0.00 36.12 3.02
1145 1447 3.182372 GCTGAAATTCTGCACCGTTTTTC 59.818 43.478 17.95 0.00 40.47 2.29
1146 1448 4.610945 CTGAAATTCTGCACCGTTTTTCT 58.389 39.130 0.00 0.00 0.00 2.52
1149 1451 1.388547 TTCTGCACCGTTTTTCTGCT 58.611 45.000 0.00 0.00 0.00 4.24
1158 1460 2.225727 CCGTTTTTCTGCTTCCAGTACC 59.774 50.000 0.00 0.00 40.09 3.34
1161 1463 4.935808 CGTTTTTCTGCTTCCAGTACCTAT 59.064 41.667 0.00 0.00 40.09 2.57
1165 1467 5.537300 TTCTGCTTCCAGTACCTATGATC 57.463 43.478 0.00 0.00 40.09 2.92
1167 1469 5.211973 TCTGCTTCCAGTACCTATGATCTT 58.788 41.667 0.00 0.00 40.09 2.40
1171 1473 5.605534 CTTCCAGTACCTATGATCTTGTGG 58.394 45.833 0.00 0.00 0.00 4.17
1172 1474 4.878968 TCCAGTACCTATGATCTTGTGGA 58.121 43.478 8.69 0.00 0.00 4.02
1173 1475 5.277250 TCCAGTACCTATGATCTTGTGGAA 58.723 41.667 8.69 0.00 0.00 3.53
1184 1486 5.957798 TGATCTTGTGGAAAGATTCAATGC 58.042 37.500 2.34 0.00 37.14 3.56
1188 1490 6.449698 TCTTGTGGAAAGATTCAATGCTTTC 58.550 36.000 0.00 0.00 45.68 2.62
1322 1624 4.022935 TGTGAATGGAATGAGAGCAACAAC 60.023 41.667 0.00 0.00 0.00 3.32
1481 1787 1.122227 AAACAGCCAGGTGCAATTGT 58.878 45.000 7.40 0.00 44.83 2.71
1486 1792 0.108520 GCCAGGTGCAATTGTGGATG 60.109 55.000 15.15 6.47 40.77 3.51
1575 1881 1.203001 GGGGACAGTTGGTTTCATGGA 60.203 52.381 0.00 0.00 0.00 3.41
1908 2214 1.292849 ACAGTAGCAGGTGGGGGTATA 59.707 52.381 0.00 0.00 0.00 1.47
1932 2238 0.107165 GGTCTGGTGCTTATGTCCCC 60.107 60.000 0.00 0.00 0.00 4.81
1947 2256 7.654022 TTATGTCCCCACTAAATTCCAAATC 57.346 36.000 0.00 0.00 0.00 2.17
2090 2413 6.029346 AGAAGAATGGGCAACAAATTACTG 57.971 37.500 0.00 0.00 39.74 2.74
2472 2796 6.717084 GCCCTTATGCTTCTCCAGTTATTATT 59.283 38.462 0.00 0.00 0.00 1.40
2513 2837 3.817647 ACTTGGAGACTTTGCACTGATTC 59.182 43.478 0.00 0.00 0.00 2.52
2553 2877 7.559897 TCCATAACTATCAAGGACAAATTTCCC 59.440 37.037 0.00 0.00 36.12 3.97
2560 2884 5.016173 TCAAGGACAAATTTCCCATACCTG 58.984 41.667 8.40 0.00 36.12 4.00
2661 2985 8.350722 CAAATTAGGATGAATGAGGAAGATGTG 58.649 37.037 0.00 0.00 0.00 3.21
2681 3005 2.699846 TGCCCAAAACTGCTTTCAGAAT 59.300 40.909 0.00 0.00 42.95 2.40
2726 3050 4.017958 TCTGGTTATGCCCTTTGGATTGTA 60.018 41.667 0.00 0.00 36.04 2.41
2817 3142 8.937634 ATTGGTTTTCTTTGATGATATCTTGC 57.062 30.769 3.98 0.00 0.00 4.01
2908 3233 6.618287 TCAGTTGTCAGTTAAAATGTCCAG 57.382 37.500 0.00 0.00 0.00 3.86
2937 3262 4.530553 TGTTTGCTGTTCCTCAGGTAGATA 59.469 41.667 0.00 0.00 43.78 1.98
2967 3293 4.397417 GTCATATCATAAATGAGCAGGGGC 59.603 45.833 0.00 0.00 40.64 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.299544 CAAAAACCGCCCCAACGTC 60.300 57.895 0.00 0.00 0.00 4.34
1 2 2.787567 CCAAAAACCGCCCCAACGT 61.788 57.895 0.00 0.00 0.00 3.99
2 3 2.028337 CCAAAAACCGCCCCAACG 59.972 61.111 0.00 0.00 0.00 4.10
3 4 2.423874 CCCAAAAACCGCCCCAAC 59.576 61.111 0.00 0.00 0.00 3.77
4 5 2.844839 CCCCAAAAACCGCCCCAA 60.845 61.111 0.00 0.00 0.00 4.12
5 6 4.944069 CCCCCAAAAACCGCCCCA 62.944 66.667 0.00 0.00 0.00 4.96
34 35 3.215568 CAACGCCACCAAGCACCA 61.216 61.111 0.00 0.00 0.00 4.17
148 149 1.301087 CACGAACGCCACCCTACAA 60.301 57.895 0.00 0.00 0.00 2.41
273 274 0.532573 GTTCTGCCAGATCCGTCTCA 59.467 55.000 0.00 0.00 30.42 3.27
403 424 2.742053 CGGAAATCACCTTTGTCATCGT 59.258 45.455 0.00 0.00 0.00 3.73
453 474 2.303890 TGTGATCATTGTGAGCTGTCCT 59.696 45.455 0.00 0.00 33.24 3.85
637 938 5.605908 TCTCTTGCTCCATGAATAATCTCCT 59.394 40.000 0.00 0.00 0.00 3.69
638 939 5.862845 TCTCTTGCTCCATGAATAATCTCC 58.137 41.667 0.00 0.00 0.00 3.71
639 940 7.798596 TTTCTCTTGCTCCATGAATAATCTC 57.201 36.000 0.00 0.00 0.00 2.75
648 949 4.633565 GGACTAGTTTTCTCTTGCTCCATG 59.366 45.833 0.00 0.00 0.00 3.66
671 972 1.064803 TGCCTGTTAACAGTGCAAACG 59.935 47.619 31.93 19.31 42.68 3.60
742 1043 3.410631 TCTTGAAATTGTAGCGGTCCA 57.589 42.857 0.00 0.00 0.00 4.02
744 1045 5.234543 GGTCTATCTTGAAATTGTAGCGGTC 59.765 44.000 0.00 0.00 0.00 4.79
871 1173 3.419922 CGCATATCGCTTTCAAATGCTTC 59.580 43.478 0.00 0.00 40.56 3.86
923 1225 2.021042 TGAGGGAATTCCATCCTAGGGT 60.021 50.000 30.74 0.00 45.61 4.34
1125 1427 4.358851 CAGAAAAACGGTGCAGAATTTCA 58.641 39.130 0.00 0.00 31.06 2.69
1131 1433 1.333619 GAAGCAGAAAAACGGTGCAGA 59.666 47.619 0.00 0.00 39.80 4.26
1134 1436 0.383949 TGGAAGCAGAAAAACGGTGC 59.616 50.000 0.00 0.00 37.48 5.01
1137 1439 2.225727 GGTACTGGAAGCAGAAAAACGG 59.774 50.000 0.00 0.00 37.60 4.44
1139 1441 5.938125 TCATAGGTACTGGAAGCAGAAAAAC 59.062 40.000 0.00 0.00 41.52 2.43
1145 1447 5.163364 ACAAGATCATAGGTACTGGAAGCAG 60.163 44.000 0.00 0.00 41.52 4.24
1146 1448 4.716784 ACAAGATCATAGGTACTGGAAGCA 59.283 41.667 0.00 0.00 41.52 3.91
1149 1451 5.277250 TCCACAAGATCATAGGTACTGGAA 58.723 41.667 0.00 0.00 41.52 3.53
1158 1460 7.861372 GCATTGAATCTTTCCACAAGATCATAG 59.139 37.037 0.00 0.00 36.07 2.23
1161 1463 5.713389 AGCATTGAATCTTTCCACAAGATCA 59.287 36.000 0.00 0.00 36.07 2.92
1165 1467 6.218019 TGAAAGCATTGAATCTTTCCACAAG 58.782 36.000 18.50 0.00 44.47 3.16
1167 1469 5.787953 TGAAAGCATTGAATCTTTCCACA 57.212 34.783 18.50 6.70 44.47 4.17
1184 1486 9.985318 CAATAGAGAGACTATTTTGCTTGAAAG 57.015 33.333 0.00 0.00 45.99 2.62
1188 1490 7.279536 TCAGCAATAGAGAGACTATTTTGCTTG 59.720 37.037 16.54 13.29 46.39 4.01
1189 1491 7.334090 TCAGCAATAGAGAGACTATTTTGCTT 58.666 34.615 16.54 5.24 46.39 3.91
1191 1493 7.545362 TTCAGCAATAGAGAGACTATTTTGC 57.455 36.000 11.38 11.38 45.99 3.68
1199 1501 9.787532 GATCTGTATATTCAGCAATAGAGAGAC 57.212 37.037 4.54 0.00 38.33 3.36
1322 1624 5.305585 TCAGTGGCCTTAACAGAAACTTAG 58.694 41.667 3.32 0.00 0.00 2.18
1481 1787 1.221840 GCTTCGGCTCCTTCATCCA 59.778 57.895 0.00 0.00 38.08 3.41
1486 1792 0.884704 TGTGTTGCTTCGGCTCCTTC 60.885 55.000 0.00 0.00 42.37 3.46
1575 1881 1.554617 GGGGCCTGTTTGCATTTATGT 59.445 47.619 0.84 0.00 0.00 2.29
1908 2214 3.347216 GACATAAGCACCAGACCACAAT 58.653 45.455 0.00 0.00 0.00 2.71
1932 2238 5.708948 TCTTTGCCGATTTGGAATTTAGTG 58.291 37.500 0.00 0.00 42.00 2.74
1983 2292 4.726825 ACCATGTCATACCCTGGTAAATCT 59.273 41.667 0.00 0.00 40.16 2.40
1984 2293 5.048846 ACCATGTCATACCCTGGTAAATC 57.951 43.478 0.00 0.00 40.16 2.17
2030 2339 4.782019 TGTTGTCATTATCAAAGGCCAC 57.218 40.909 5.01 0.00 0.00 5.01
2042 2362 7.230849 TCATAAGGATTTGCTTGTTGTCATT 57.769 32.000 0.00 0.00 0.00 2.57
2090 2413 3.304726 GCAAAGGAGTTACAAGCAGGAAC 60.305 47.826 0.00 0.00 0.00 3.62
2553 2877 3.181461 GGAGGTCCTCAATGACAGGTATG 60.181 52.174 20.72 0.00 36.97 2.39
2560 2884 1.573108 TCCAGGAGGTCCTCAATGAC 58.427 55.000 20.72 2.64 46.65 3.06
2587 2911 6.477742 GTTTTGTGAAAAACTTTGCTCCATC 58.522 36.000 6.78 0.00 39.05 3.51
2661 2985 2.888834 TTCTGAAAGCAGTTTTGGGC 57.111 45.000 0.00 0.00 42.84 5.36
2681 3005 7.363705 CCAGATATTCAAAATGGCCAAAGTGTA 60.364 37.037 10.96 1.74 0.00 2.90
2817 3142 4.380531 TCTTCCAGACTTGTGCTAAACAG 58.619 43.478 0.00 0.00 40.74 3.16
2908 3233 0.746659 AGGAACAGCAAACAAGCACC 59.253 50.000 0.00 0.00 36.85 5.01
2937 3262 8.481492 TGCTCATTTATGATATGACCCAAATT 57.519 30.769 0.00 0.00 36.02 1.82
2967 3293 4.911390 ACTTTCTCAGGGTATGTGGAAAG 58.089 43.478 16.33 16.33 44.82 2.62
2976 3302 3.901844 ACTGCACTTACTTTCTCAGGGTA 59.098 43.478 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.