Multiple sequence alignment - TraesCS1D01G169900

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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 TraesCS1D01G169900 chr1D 100.000 2930 0 0 1 2930 244391437 244394366 0.000000e+00 5411
1 TraesCS1D01G169900 chr1D 95.732 1898 74 5 828 2720 254481846 254483741 0.000000e+00 3049
2 TraesCS1D01G169900 chr1D 87.799 836 91 6 1 826 91386358 91387192 0.000000e+00 968
3 TraesCS1D01G169900 chr1A 95.578 1990 71 9 828 2809 554473727 554471747 0.000000e+00 3171
4 TraesCS1D01G169900 chr1A 88.200 839 85 9 1 826 130985486 130986323 0.000000e+00 989
5 TraesCS1D01G169900 chr1A 94.118 391 15 3 2541 2930 554471482 554471099 3.250000e-164 588
6 TraesCS1D01G169900 chr1A 90.991 222 12 4 2706 2927 554471464 554471677 2.860000e-75 292
7 TraesCS1D01G169900 chr2D 96.198 1920 64 5 828 2740 643858209 643860126 0.000000e+00 3133
8 TraesCS1D01G169900 chr2D 96.173 1803 59 7 828 2622 628291645 628289845 0.000000e+00 2939
9 TraesCS1D01G169900 chr2D 88.263 835 87 7 1 826 351908160 351907328 0.000000e+00 989
10 TraesCS1D01G169900 chr5D 96.184 1913 63 4 828 2731 483802908 483800997 0.000000e+00 3120
11 TraesCS1D01G169900 chr5D 95.935 1919 68 7 828 2740 6219332 6217418 0.000000e+00 3103
12 TraesCS1D01G169900 chr5D 88.179 829 86 7 4 824 103343169 103342345 0.000000e+00 977
13 TraesCS1D01G169900 chr5D 87.904 835 88 6 1 826 103475046 103474216 0.000000e+00 970
14 TraesCS1D01G169900 chr3B 95.491 1730 62 6 1208 2930 201498791 201500511 0.000000e+00 2748
15 TraesCS1D01G169900 chr3B 95.147 989 41 3 1312 2300 544899265 544900246 0.000000e+00 1554
16 TraesCS1D01G169900 chr3B 96.356 933 32 2 828 1758 201497866 201498798 0.000000e+00 1533
17 TraesCS1D01G169900 chr3B 90.023 852 62 8 828 1675 672880933 672881765 0.000000e+00 1081
18 TraesCS1D01G169900 chr3B 88.961 154 17 0 1107 1260 240800073 240800226 1.070000e-44 191
19 TraesCS1D01G169900 chr3A 93.972 1294 69 3 1645 2930 393238698 393237406 0.000000e+00 1949
20 TraesCS1D01G169900 chr3A 94.171 772 30 6 2165 2930 435414845 435414083 0.000000e+00 1162
21 TraesCS1D01G169900 chr7D 96.865 893 28 0 1313 2205 17212096 17212988 0.000000e+00 1495
22 TraesCS1D01G169900 chr3D 90.767 834 68 4 1 826 68523503 68524335 0.000000e+00 1105
23 TraesCS1D01G169900 chr3D 88.319 839 83 8 1 826 514332956 514332120 0.000000e+00 992
24 TraesCS1D01G169900 chr3D 95.480 177 7 1 2754 2930 589278621 589278796 6.180000e-72 281
25 TraesCS1D01G169900 chr6D 87.872 841 88 8 1 831 34484092 34484928 0.000000e+00 976
26 TraesCS1D01G169900 chr4D 87.952 830 88 6 1 821 326637276 326638102 0.000000e+00 968
27 TraesCS1D01G169900 chr2A 95.588 204 8 1 2715 2918 724271187 724270985 2.820000e-85 326
28 TraesCS1D01G169900 chr5B 95.055 182 9 0 2749 2930 559429707 559429888 1.330000e-73 287
29 TraesCS1D01G169900 chr6B 89.593 221 11 6 2707 2927 664306834 664306626 1.340000e-68 270


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 TraesCS1D01G169900 chr1D 244391437 244394366 2929 False 5411.0 5411 100.0000 1 2930 1 chr1D.!!$F2 2929
1 TraesCS1D01G169900 chr1D 254481846 254483741 1895 False 3049.0 3049 95.7320 828 2720 1 chr1D.!!$F3 1892
2 TraesCS1D01G169900 chr1D 91386358 91387192 834 False 968.0 968 87.7990 1 826 1 chr1D.!!$F1 825
3 TraesCS1D01G169900 chr1A 554471099 554473727 2628 True 1879.5 3171 94.8480 828 2930 2 chr1A.!!$R1 2102
4 TraesCS1D01G169900 chr1A 130985486 130986323 837 False 989.0 989 88.2000 1 826 1 chr1A.!!$F1 825
5 TraesCS1D01G169900 chr2D 643858209 643860126 1917 False 3133.0 3133 96.1980 828 2740 1 chr2D.!!$F1 1912
6 TraesCS1D01G169900 chr2D 628289845 628291645 1800 True 2939.0 2939 96.1730 828 2622 1 chr2D.!!$R2 1794
7 TraesCS1D01G169900 chr2D 351907328 351908160 832 True 989.0 989 88.2630 1 826 1 chr2D.!!$R1 825
8 TraesCS1D01G169900 chr5D 483800997 483802908 1911 True 3120.0 3120 96.1840 828 2731 1 chr5D.!!$R4 1903
9 TraesCS1D01G169900 chr5D 6217418 6219332 1914 True 3103.0 3103 95.9350 828 2740 1 chr5D.!!$R1 1912
10 TraesCS1D01G169900 chr5D 103342345 103343169 824 True 977.0 977 88.1790 4 824 1 chr5D.!!$R2 820
11 TraesCS1D01G169900 chr5D 103474216 103475046 830 True 970.0 970 87.9040 1 826 1 chr5D.!!$R3 825
12 TraesCS1D01G169900 chr3B 201497866 201500511 2645 False 2140.5 2748 95.9235 828 2930 2 chr3B.!!$F4 2102
13 TraesCS1D01G169900 chr3B 544899265 544900246 981 False 1554.0 1554 95.1470 1312 2300 1 chr3B.!!$F2 988
14 TraesCS1D01G169900 chr3B 672880933 672881765 832 False 1081.0 1081 90.0230 828 1675 1 chr3B.!!$F3 847
15 TraesCS1D01G169900 chr3A 393237406 393238698 1292 True 1949.0 1949 93.9720 1645 2930 1 chr3A.!!$R1 1285
16 TraesCS1D01G169900 chr3A 435414083 435414845 762 True 1162.0 1162 94.1710 2165 2930 1 chr3A.!!$R2 765
17 TraesCS1D01G169900 chr7D 17212096 17212988 892 False 1495.0 1495 96.8650 1313 2205 1 chr7D.!!$F1 892
18 TraesCS1D01G169900 chr3D 68523503 68524335 832 False 1105.0 1105 90.7670 1 826 1 chr3D.!!$F1 825
19 TraesCS1D01G169900 chr3D 514332120 514332956 836 True 992.0 992 88.3190 1 826 1 chr3D.!!$R1 825
20 TraesCS1D01G169900 chr6D 34484092 34484928 836 False 976.0 976 87.8720 1 831 1 chr6D.!!$F1 830
21 TraesCS1D01G169900 chr4D 326637276 326638102 826 False 968.0 968 87.9520 1 821 1 chr4D.!!$F1 820

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
703 719 0.030638 CGTTGCCTTGGTTGTCTTGG 59.969 55.0 0.0 0.0 0.0 3.61 F
1159 1180 0.117340 AGTAAGTCCTCAGCCTGGGT 59.883 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2436 0.459585 GAAGTAGGCCATTGTCGCGA 60.460 55.0 3.71 3.71 0.00 5.87 R
2267 2834 1.403814 AGCCACTCGATTAGCTGCTA 58.596 50.0 5.02 5.02 34.53 3.49 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
166 172 2.434428 CTTCAGGAAGACTTGCATGCT 58.566 47.619 20.33 0.00 40.79 3.79
419 432 1.817911 GCTAGGATCCTACCGTGGGC 61.818 65.000 18.00 14.25 34.73 5.36
425 438 4.910585 CCTACCGTGGGCCATCGC 62.911 72.222 10.70 0.00 0.00 4.58
497 510 2.955881 GCCACTACGGAGGTGCCTT 61.956 63.158 0.00 0.00 36.56 4.35
703 719 0.030638 CGTTGCCTTGGTTGTCTTGG 59.969 55.000 0.00 0.00 0.00 3.61
733 749 3.157949 CTCCGGCTTCCCTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
826 842 3.494749 CCCCTACTTTTGTACACCGACAA 60.495 47.826 0.00 0.00 37.54 3.18
886 902 6.013466 ACCATGCCCTCAATTTTCTTTAATGT 60.013 34.615 0.00 0.00 0.00 2.71
1022 1043 7.417811 AGAGTTATAGGGAGGGACTTATGTA 57.582 40.000 0.00 0.00 41.55 2.29
1135 1156 3.999663 GGATACTGATATCTTGGCAGCAC 59.000 47.826 3.98 0.00 37.85 4.40
1159 1180 0.117340 AGTAAGTCCTCAGCCTGGGT 59.883 55.000 0.00 0.00 0.00 4.51
1166 1187 3.551496 CTCAGCCTGGGTTTCCGCA 62.551 63.158 0.00 0.00 35.24 5.69
1276 1840 5.231568 CGTTACAAAGGACGATTCTATCACC 59.768 44.000 0.00 0.00 41.53 4.02
1285 1849 3.075148 CGATTCTATCACCTCGAGCCTA 58.925 50.000 6.99 0.00 33.07 3.93
1289 1853 4.100279 TCTATCACCTCGAGCCTATTGA 57.900 45.455 6.99 4.28 0.00 2.57
1303 1867 3.206150 CCTATTGATGGGGAAGACAACG 58.794 50.000 0.00 0.00 0.00 4.10
1331 1895 7.389232 TGGATCTGTTATGTAGCTTATCCATG 58.611 38.462 0.00 0.00 37.35 3.66
1347 1911 7.172361 GCTTATCCATGAGACCTATTTGAAGAC 59.828 40.741 0.00 0.00 0.00 3.01
1387 1951 7.940137 ACATGTTTACTTCCATTGTAGGTAACA 59.060 33.333 0.00 0.00 41.41 2.41
1607 2173 1.899814 TGAGTGTCTATGTGGTGGACC 59.100 52.381 0.00 0.00 37.51 4.46
1622 2188 4.149598 GGTGGACCTGATTTTACCAAAGT 58.850 43.478 0.00 0.00 32.32 2.66
1813 2379 7.619512 AGAGAATTAGGGGTTCCTATTGTAG 57.380 40.000 0.00 0.00 44.51 2.74
1841 2407 5.036916 TGACTACTTAACTGGGGGATTCAT 58.963 41.667 0.00 0.00 0.00 2.57
1842 2408 6.206787 TGACTACTTAACTGGGGGATTCATA 58.793 40.000 0.00 0.00 0.00 2.15
1869 2436 8.190784 GCAAATACTACTTTGGCTCATTATTGT 58.809 33.333 0.00 0.00 36.76 2.71
1982 2549 3.309682 GCTAAAGCATTGCGTATGTCTGA 59.690 43.478 2.38 0.00 41.59 3.27
2032 2599 7.068470 CAGTAGTAGGTAAGTTAGAAGGGGAAG 59.932 44.444 0.00 0.00 0.00 3.46
2053 2620 5.372547 AGGCGAAATGACTTTAGGTTTTC 57.627 39.130 0.00 0.00 20.56 2.29
2143 2710 4.018415 GGGTATCCATGCCAGGTGTTATAT 60.018 45.833 0.00 0.00 33.83 0.86
2144 2711 4.943705 GGTATCCATGCCAGGTGTTATATG 59.056 45.833 0.00 0.00 32.29 1.78
2205 2772 2.027192 TCTGACCGAAATCTTTGGGGAG 60.027 50.000 8.34 4.38 39.97 4.30
2224 2791 7.418378 TGGGGAGGATTCTGTATTACAATTTT 58.582 34.615 0.00 0.00 0.00 1.82
2267 2834 1.228862 GGGGAAATGCACCTGGTGT 60.229 57.895 26.48 8.05 36.99 4.16
2293 2860 5.053145 CAGCTAATCGAGTGGCTTTAGAAT 58.947 41.667 21.45 0.00 32.30 2.40
2353 2920 5.570262 TCGCGAAGGTAATGAAATTATCG 57.430 39.130 6.20 0.00 44.60 2.92
2364 2931 3.609853 TGAAATTATCGGAGCAGCTTGT 58.390 40.909 0.00 0.00 0.00 3.16
2386 2953 2.254152 ATGGAGTCCTGAACTAGCCA 57.746 50.000 11.33 0.00 38.74 4.75
2388 2955 0.173708 GGAGTCCTGAACTAGCCACG 59.826 60.000 0.41 0.00 38.74 4.94
2439 3006 1.266446 GAGTTCGAGCCGGTAGATACC 59.734 57.143 1.90 0.00 42.98 2.73
2442 3009 1.531423 TCGAGCCGGTAGATACCATC 58.469 55.000 1.90 3.49 46.80 3.51
2449 3016 4.710375 AGCCGGTAGATACCATCGATTAAT 59.290 41.667 1.90 0.00 46.80 1.40
2846 3958 5.800296 TGTCAAATCGGGATTCACTAAGAA 58.200 37.500 0.00 0.00 41.28 2.52
2866 3978 6.916360 AGAAAGAAATAAAGCATTGGGTCA 57.084 33.333 0.00 0.00 0.00 4.02
2887 3999 6.317893 GGTCAAACTCTTCTTTGGTGTTAAGA 59.682 38.462 0.00 0.00 32.78 2.10
2915 4027 3.300857 CTGTGAATAGCCATCGACTACG 58.699 50.000 0.00 0.00 41.26 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.202580 CCGATAAAGTGAGAGGGGCAG 60.203 57.143 0.00 0.00 0.00 4.85
326 338 2.747686 GGCAAGACCCTTGTCGGA 59.252 61.111 8.29 0.00 46.51 4.55
381 394 1.369091 CCGAGGAAATCCACAAGGCG 61.369 60.000 1.67 0.00 38.89 5.52
419 432 0.250234 TGAGAACCAGAAGGCGATGG 59.750 55.000 4.42 4.42 42.60 3.51
425 438 5.117584 CAAGATCAGATGAGAACCAGAAGG 58.882 45.833 0.00 0.00 42.21 3.46
434 447 8.708378 ACCATTAATACACAAGATCAGATGAGA 58.292 33.333 0.00 0.00 0.00 3.27
497 510 1.080354 ATTGGGACCAGGTCTCGGA 59.920 57.895 19.57 8.65 35.49 4.55
503 516 2.062636 ACAACTACATTGGGACCAGGT 58.937 47.619 0.00 0.00 43.20 4.00
703 719 1.746991 CCGGAGAGAAGCCAAAGCC 60.747 63.158 0.00 0.00 41.25 4.35
733 749 3.127533 GCCACACTTAGCAGGGCG 61.128 66.667 0.00 0.00 34.56 6.13
862 878 6.314400 CACATTAAAGAAAATTGAGGGCATGG 59.686 38.462 0.00 0.00 0.00 3.66
946 967 7.201893 GGGTCTACTCGATGTTAATTAGGAGTT 60.202 40.741 7.28 0.00 36.30 3.01
949 970 6.264744 CAGGGTCTACTCGATGTTAATTAGGA 59.735 42.308 0.00 0.00 0.00 2.94
1022 1043 5.394115 CCTGCTTTAGTTTCTGTTTGTGGTT 60.394 40.000 0.00 0.00 0.00 3.67
1135 1156 0.741915 GGCTGAGGACTTACTCGGAG 59.258 60.000 2.83 2.83 44.83 4.63
1159 1180 1.227999 CCTGCTTCTTCGTGCGGAAA 61.228 55.000 0.00 0.00 37.75 3.13
1268 1832 4.100279 TCAATAGGCTCGAGGTGATAGA 57.900 45.455 15.58 0.00 0.00 1.98
1276 1840 1.342074 TCCCCATCAATAGGCTCGAG 58.658 55.000 8.45 8.45 0.00 4.04
1285 1849 3.433306 TTCGTTGTCTTCCCCATCAAT 57.567 42.857 0.00 0.00 0.00 2.57
1289 1853 1.633432 TCCATTCGTTGTCTTCCCCAT 59.367 47.619 0.00 0.00 0.00 4.00
1303 1867 8.097038 TGGATAAGCTACATAACAGATCCATTC 58.903 37.037 0.00 0.00 37.32 2.67
1331 1895 4.865365 CAGAACCGTCTTCAAATAGGTCTC 59.135 45.833 0.00 0.00 33.50 3.36
1347 1911 7.647907 AGTAAACATGTTAGTAACAGAACCG 57.352 36.000 19.87 9.04 45.95 4.44
1387 1951 6.405397 GCACGTAGGGATTTGAAACCAAATAT 60.405 38.462 3.69 0.00 42.47 1.28
1476 2041 8.152023 ACTTATCTCTTTCAACTTGGATACCT 57.848 34.615 0.00 0.00 0.00 3.08
1581 2147 5.425217 TCCACCACATAGACACTCATAACAT 59.575 40.000 0.00 0.00 0.00 2.71
1607 2173 8.479280 CGTTTTCATCAACTTTGGTAAAATCAG 58.521 33.333 0.00 0.00 0.00 2.90
1622 2188 6.127980 TGGTTGTGAGTTTACGTTTTCATCAA 60.128 34.615 0.00 0.00 0.00 2.57
1778 2344 6.252995 ACCCCTAATTCTCTTGCAAATACAA 58.747 36.000 0.00 0.00 0.00 2.41
1813 2379 3.270877 CCCCAGTTAAGTAGTCATGCAC 58.729 50.000 0.00 0.00 0.00 4.57
1841 2407 9.627123 AATAATGAGCCAAAGTAGTATTTGCTA 57.373 29.630 0.00 0.00 38.57 3.49
1842 2408 8.408601 CAATAATGAGCCAAAGTAGTATTTGCT 58.591 33.333 0.00 0.00 38.57 3.91
1869 2436 0.459585 GAAGTAGGCCATTGTCGCGA 60.460 55.000 3.71 3.71 0.00 5.87
1927 2494 7.068103 ACGGAAATGCATACCATGATTTTTCTA 59.932 33.333 18.61 0.00 33.49 2.10
1982 2549 3.143741 ACCAGAGTGGATATGATCTCCCT 59.856 47.826 0.00 0.00 40.96 4.20
2032 2599 5.372547 AGAAAACCTAAAGTCATTTCGCC 57.627 39.130 0.00 0.00 35.66 5.54
2053 2620 6.500775 AAAATCATCGCGCAATAAATCAAG 57.499 33.333 8.75 0.00 0.00 3.02
2143 2710 2.263895 ATACCACCTGAAGCTACCCA 57.736 50.000 0.00 0.00 0.00 4.51
2144 2711 2.504175 TGAATACCACCTGAAGCTACCC 59.496 50.000 0.00 0.00 0.00 3.69
2205 2772 8.190784 CCTCCACAAAATTGTAATACAGAATCC 58.809 37.037 0.00 0.00 39.91 3.01
2224 2791 3.263425 GGATGTCCTAAAGTTCCTCCACA 59.737 47.826 0.00 0.00 0.00 4.17
2267 2834 1.403814 AGCCACTCGATTAGCTGCTA 58.596 50.000 5.02 5.02 34.53 3.49
2293 2860 2.351060 CGTTACGAGCTTGTACACAGGA 60.351 50.000 13.64 0.00 0.00 3.86
2353 2920 2.680339 GACTCCATTTACAAGCTGCTCC 59.320 50.000 1.00 0.00 0.00 4.70
2364 2931 4.081087 GTGGCTAGTTCAGGACTCCATTTA 60.081 45.833 0.00 0.00 39.86 1.40
2386 2953 2.615493 CCTTCCATACTTCACAAGCCGT 60.615 50.000 0.00 0.00 0.00 5.68
2388 2955 1.745653 GCCTTCCATACTTCACAAGCC 59.254 52.381 0.00 0.00 0.00 4.35
2595 3173 9.166173 CATGATCTATTTTTATCCCGCTCAATA 57.834 33.333 0.00 0.00 0.00 1.90
2827 3939 7.996098 TTTCTTTCTTAGTGAATCCCGATTT 57.004 32.000 0.00 0.00 34.24 2.17
2846 3958 7.015584 AGAGTTTGACCCAATGCTTTATTTCTT 59.984 33.333 0.00 0.00 0.00 2.52
2866 3978 6.833933 ACCATCTTAACACCAAAGAAGAGTTT 59.166 34.615 0.00 0.00 36.60 2.66
2887 3999 3.555795 CGATGGCTATTCACAGCTACCAT 60.556 47.826 0.00 0.00 41.50 3.55


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

AutoCloner maintained by Alex Coulton.