Multiple sequence alignment - TraesCS2B01G134800

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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 TraesCS2B01G134800 chr2B 100.000 3912 0 0 1 3912 101410466 101414377 0.000000e+00 7225.0
1 TraesCS2B01G134800 chr2B 92.063 126 10 0 613 738 387105735 387105610 1.120000e-40 178.0
2 TraesCS2B01G134800 chr2B 80.292 137 12 6 2840 2961 101413245 101413381 5.380000e-14 89.8
3 TraesCS2B01G134800 chr2B 80.292 137 12 6 2780 2916 101413305 101413426 5.380000e-14 89.8
4 TraesCS2B01G134800 chr2D 96.143 3345 46 17 604 3912 69221135 69217838 0.000000e+00 5385.0
5 TraesCS2B01G134800 chr2D 97.862 608 10 2 1 606 65532390 65532996 0.000000e+00 1048.0
6 TraesCS2B01G134800 chr2D 91.089 101 9 0 1615 1715 290739041 290738941 1.900000e-28 137.0
7 TraesCS2B01G134800 chr2D 90.909 99 9 0 1615 1713 2476681 2476583 2.450000e-27 134.0
8 TraesCS2B01G134800 chr2D 81.884 138 10 6 2779 2916 69218924 69218802 6.920000e-18 102.0
9 TraesCS2B01G134800 chr3B 94.958 119 6 0 613 731 588418291 588418173 1.860000e-43 187.0
10 TraesCS2B01G134800 chr3B 94.286 35 2 0 3459 3493 74282517 74282551 2.000000e-03 54.7
11 TraesCS2B01G134800 chr6A 91.176 136 11 1 601 735 404985888 404986023 2.400000e-42 183.0
12 TraesCS2B01G134800 chr4B 92.248 129 8 2 602 730 664392015 664391889 8.630000e-42 182.0
13 TraesCS2B01G134800 chr4B 87.619 105 12 1 1614 1718 576192125 576192228 1.910000e-23 121.0
14 TraesCS2B01G134800 chr3D 91.603 131 10 1 607 736 525280362 525280492 3.110000e-41 180.0
15 TraesCS2B01G134800 chr3D 91.753 97 8 0 1615 1711 601221851 601221755 6.820000e-28 135.0
16 TraesCS2B01G134800 chr3D 89.796 98 10 0 1615 1712 608238805 608238708 4.100000e-25 126.0
17 TraesCS2B01G134800 chr3D 94.286 35 2 0 3459 3493 47481332 47481366 2.000000e-03 54.7
18 TraesCS2B01G134800 chr6D 88.435 147 12 5 611 753 400083086 400082941 5.200000e-39 172.0
19 TraesCS2B01G134800 chr5B 90.769 130 11 1 601 729 571230020 571230149 5.200000e-39 172.0
20 TraesCS2B01G134800 chr3A 90.769 130 11 1 610 738 1706731 1706602 5.200000e-39 172.0
21 TraesCS2B01G134800 chr3A 89.130 46 5 0 3459 3504 59519080 59519125 1.520000e-04 58.4
22 TraesCS2B01G134800 chrUn 91.919 99 8 0 1615 1713 15903921 15904019 5.270000e-29 139.0
23 TraesCS2B01G134800 chr2A 89.796 98 8 1 1615 1712 315037986 315038081 1.480000e-24 124.0
24 TraesCS2B01G134800 chr1B 85.841 113 12 3 1608 1718 560219698 560219588 2.470000e-22 117.0


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 TraesCS2B01G134800 chr2B 101410466 101414377 3911 False 2468.2 7225 86.861333 1 3912 3 chr2B.!!$F1 3911
1 TraesCS2B01G134800 chr2D 69217838 69221135 3297 True 2743.5 5385 89.013500 604 3912 2 chr2D.!!$R3 3308
2 TraesCS2B01G134800 chr2D 65532390 65532996 606 False 1048.0 1048 97.862000 1 606 1 chr2D.!!$F1 605

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
725 729 2.500098 CAAGTATTTCCGGACAGAGGGA 59.500 50.0 1.83 0.0 0.0 4.20 F
1899 1922 0.176910 TGCAGGACGAGTTTCACACA 59.823 50.0 0.00 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2488 2511 0.320683 TCGTCTGTGGTGCAATCAGG 60.321 55.0 12.07 1.4 0.0 3.86 R
3289 3312 0.037790 ACGCTTCCTGTCTTGCTCTC 60.038 55.0 0.00 0.0 0.0 3.20 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
117 118 7.821359 TGGATTCTCTTGAAATGTTCTCTAGTG 59.179 37.037 0.00 0.00 35.63 2.74
118 119 7.201600 GGATTCTCTTGAAATGTTCTCTAGTGC 60.202 40.741 0.00 0.00 35.63 4.40
280 281 7.031975 GCCTTATACTACGTTTCAAGTACTGT 58.968 38.462 0.00 0.00 31.30 3.55
347 348 5.180868 ACTGCTCTTAACTTTCTCTGCAATG 59.819 40.000 0.00 0.00 0.00 2.82
384 385 3.679389 TGAGGAGGAATCTCTTGTTTGC 58.321 45.455 0.00 0.00 39.86 3.68
411 412 4.083271 GGACCAATTGAGCTAACAACTGTC 60.083 45.833 7.12 0.95 32.50 3.51
725 729 2.500098 CAAGTATTTCCGGACAGAGGGA 59.500 50.000 1.83 0.00 0.00 4.20
864 872 4.517285 ACTCCCACAAACTATACATGCAG 58.483 43.478 0.00 0.00 0.00 4.41
1064 1072 3.853207 TCTATAAGGCGGTTGATAGGGT 58.147 45.455 0.00 0.00 0.00 4.34
1074 1082 2.640184 GTTGATAGGGTACTGGTTGCC 58.360 52.381 0.00 0.00 0.00 4.52
1075 1083 2.238898 GTTGATAGGGTACTGGTTGCCT 59.761 50.000 0.00 0.00 0.00 4.75
1076 1084 2.116238 TGATAGGGTACTGGTTGCCTC 58.884 52.381 0.00 0.00 0.00 4.70
1077 1085 2.292918 TGATAGGGTACTGGTTGCCTCT 60.293 50.000 0.00 0.00 0.00 3.69
1078 1086 3.052414 TGATAGGGTACTGGTTGCCTCTA 60.052 47.826 0.00 0.00 0.00 2.43
1079 1087 1.569653 AGGGTACTGGTTGCCTCTAC 58.430 55.000 0.00 0.00 0.00 2.59
1080 1088 1.078989 AGGGTACTGGTTGCCTCTACT 59.921 52.381 0.00 0.00 0.00 2.57
1081 1089 1.207329 GGGTACTGGTTGCCTCTACTG 59.793 57.143 0.00 0.00 0.00 2.74
1082 1090 1.900486 GGTACTGGTTGCCTCTACTGT 59.100 52.381 0.00 0.00 0.00 3.55
1083 1091 2.353803 GGTACTGGTTGCCTCTACTGTG 60.354 54.545 0.00 0.00 0.00 3.66
1084 1092 1.717032 ACTGGTTGCCTCTACTGTGA 58.283 50.000 0.00 0.00 0.00 3.58
1085 1093 2.047061 ACTGGTTGCCTCTACTGTGAA 58.953 47.619 0.00 0.00 0.00 3.18
1086 1094 2.037772 ACTGGTTGCCTCTACTGTGAAG 59.962 50.000 0.00 0.00 0.00 3.02
1087 1095 2.300152 CTGGTTGCCTCTACTGTGAAGA 59.700 50.000 0.00 0.00 0.00 2.87
1126 1134 9.297586 CAAGATATGATGTCATTCCAAACTTTG 57.702 33.333 0.19 0.00 37.76 2.77
1127 1135 8.812513 AGATATGATGTCATTCCAAACTTTGA 57.187 30.769 2.87 0.00 37.76 2.69
1353 1361 6.653020 TGTTCTGATATATCAACTGCCTGTT 58.347 36.000 16.08 0.00 39.92 3.16
1459 1467 5.163195 GGTGGAAGCCTTCTTTCCATAGATA 60.163 44.000 9.66 0.00 34.44 1.98
1856 1879 0.776810 TCCAAGTGGCCCATCAGAAA 59.223 50.000 0.00 0.00 34.44 2.52
1899 1922 0.176910 TGCAGGACGAGTTTCACACA 59.823 50.000 0.00 0.00 0.00 3.72
2032 2055 3.381272 TGTTGCTCCTTGGTTTCTCTTTG 59.619 43.478 0.00 0.00 0.00 2.77
2077 2100 4.180057 GTTCAAGAATGTTGTGCCAACAA 58.820 39.130 19.94 5.31 44.06 2.83
2117 2140 8.699130 TCATGACTACAAGTATGATCATGTTCT 58.301 33.333 18.72 10.60 41.00 3.01
2295 2318 3.088532 AGACAGCCACTGACAAAAACAA 58.911 40.909 0.78 0.00 35.18 2.83
2340 2363 0.686789 TTGCTAGGTGAAGCTCAGCA 59.313 50.000 0.00 4.56 46.52 4.41
2374 2397 0.394352 GGAATTGGACCATGCGGACT 60.394 55.000 0.00 0.00 35.59 3.85
2488 2511 1.227060 GGGATTGGAAAGCATGCGC 60.227 57.895 13.01 0.00 30.69 6.09
2505 2528 1.878775 GCCTGATTGCACCACAGAC 59.121 57.895 13.32 1.22 34.07 3.51
2741 2764 0.464036 TGCGGGCGATGTTAATCTCT 59.536 50.000 0.00 0.00 0.00 3.10
2849 2872 2.511145 CGCAGGAAGAGCCTCAGC 60.511 66.667 0.00 0.00 46.97 4.26
2850 2873 2.667418 GCAGGAAGAGCCTCAGCA 59.333 61.111 0.00 0.00 46.97 4.41
2851 2874 1.002868 GCAGGAAGAGCCTCAGCAA 60.003 57.895 0.00 0.00 46.97 3.91
2852 2875 1.025647 GCAGGAAGAGCCTCAGCAAG 61.026 60.000 0.00 0.00 46.97 4.01
2853 2876 0.612229 CAGGAAGAGCCTCAGCAAGA 59.388 55.000 0.00 0.00 46.97 3.02
2854 2877 1.002888 CAGGAAGAGCCTCAGCAAGAA 59.997 52.381 0.00 0.00 46.97 2.52
2855 2878 1.278699 AGGAAGAGCCTCAGCAAGAAG 59.721 52.381 0.00 0.00 46.97 2.85
2856 2879 1.003003 GGAAGAGCCTCAGCAAGAAGT 59.997 52.381 0.00 0.00 43.56 3.01
2857 2880 2.075338 GAAGAGCCTCAGCAAGAAGTG 58.925 52.381 0.00 0.00 43.56 3.16
2909 2932 0.839946 ACAACTTCCAGAGCCACAGT 59.160 50.000 0.00 0.00 0.00 3.55
3000 3023 4.746309 GCAGGATGGCCAGGTGCA 62.746 66.667 24.70 0.00 43.89 4.57
3007 3030 4.341783 GGCCAGGTGCAGAGCAGT 62.342 66.667 0.00 0.00 43.89 4.40
3175 3198 1.066286 AGCAGACTAAGGAAGCAGCAG 60.066 52.381 0.00 0.00 0.00 4.24
3289 3312 1.806542 AGAACAATAGCAACAGCGGTG 59.193 47.619 14.13 14.13 0.00 4.94
3376 3399 2.033801 GGCACGCATATTCTTGCAGATT 59.966 45.455 6.20 0.00 42.91 2.40
3377 3400 3.250762 GGCACGCATATTCTTGCAGATTA 59.749 43.478 6.20 0.00 42.91 1.75
3378 3401 4.461405 GCACGCATATTCTTGCAGATTAG 58.539 43.478 0.00 0.00 42.91 1.73
3412 3435 7.952671 TCTGTTTGTAGTCTTGTATCTCAGTT 58.047 34.615 0.00 0.00 0.00 3.16
3415 3438 9.692749 TGTTTGTAGTCTTGTATCTCAGTTAAG 57.307 33.333 0.00 0.00 0.00 1.85
3416 3439 9.694137 GTTTGTAGTCTTGTATCTCAGTTAAGT 57.306 33.333 0.00 0.00 0.00 2.24
3417 3440 9.692749 TTTGTAGTCTTGTATCTCAGTTAAGTG 57.307 33.333 3.73 3.73 0.00 3.16
3512 3551 3.686916 ACCTCTGCTCTTTACCACTTC 57.313 47.619 0.00 0.00 0.00 3.01
3582 3621 0.396139 ATTGAATGCTGGGGTGCGAT 60.396 50.000 0.00 0.00 35.36 4.58
3693 3732 8.944029 AGAGAATGTCACTTTGAATAATCTGTG 58.056 33.333 0.00 0.00 0.00 3.66
3751 3790 6.597280 ACTTGAATGAGGTCTTCTTCTATTGC 59.403 38.462 0.00 0.00 0.00 3.56
3793 3832 8.867112 TTATTTAGCTAGTGATGGTTCTTACG 57.133 34.615 0.00 0.00 0.00 3.18
3796 3835 3.119101 AGCTAGTGATGGTTCTTACGGTG 60.119 47.826 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 8.123639 TGTACTCATAGAAGAACATATAGGGC 57.876 38.462 0.00 0.00 0.00 5.19
184 185 8.797438 TGCAATATGATAAACAACCAACAGTAA 58.203 29.630 0.00 0.00 0.00 2.24
327 328 5.618056 TGCATTGCAGAGAAAGTTAAGAG 57.382 39.130 7.38 0.00 33.32 2.85
347 348 4.154918 CCTCCTCAAATAACAAGTGTCTGC 59.845 45.833 0.00 0.00 0.00 4.26
384 385 3.942829 TGTTAGCTCAATTGGTCCTCTG 58.057 45.455 5.42 0.00 0.00 3.35
446 449 8.102716 CACTAGAGAACGTTTTAAGCGAATAAG 58.897 37.037 8.38 0.87 0.00 1.73
481 484 4.935808 CACACTTGTACCCCATAGAAGAAC 59.064 45.833 0.00 0.00 36.47 3.01
622 625 2.614829 CGGGACAAGTATTTCCGGAT 57.385 50.000 4.15 0.00 37.35 4.18
702 706 3.307480 CCCTCTGTCCGGAAATACTTGTT 60.307 47.826 5.23 0.00 0.00 2.83
787 795 5.006649 TGCAGCAATATAGCTAAACAAGTCG 59.993 40.000 0.00 0.00 44.54 4.18
889 897 9.369904 GTACAAAATAAATGCAGGATGAAACAT 57.630 29.630 0.00 0.00 39.69 2.71
1064 1072 2.884320 TCACAGTAGAGGCAACCAGTA 58.116 47.619 0.00 0.00 37.17 2.74
1074 1082 7.377397 GCTACGTCAATAATCTTCACAGTAGAG 59.623 40.741 0.00 0.00 32.15 2.43
1075 1083 7.148137 TGCTACGTCAATAATCTTCACAGTAGA 60.148 37.037 0.00 0.00 32.15 2.59
1076 1084 6.972901 TGCTACGTCAATAATCTTCACAGTAG 59.027 38.462 0.00 0.00 0.00 2.57
1077 1085 6.859017 TGCTACGTCAATAATCTTCACAGTA 58.141 36.000 0.00 0.00 0.00 2.74
1078 1086 5.720202 TGCTACGTCAATAATCTTCACAGT 58.280 37.500 0.00 0.00 0.00 3.55
1079 1087 6.531594 TCTTGCTACGTCAATAATCTTCACAG 59.468 38.462 0.00 0.00 0.00 3.66
1080 1088 6.394809 TCTTGCTACGTCAATAATCTTCACA 58.605 36.000 0.00 0.00 0.00 3.58
1081 1089 6.887376 TCTTGCTACGTCAATAATCTTCAC 57.113 37.500 0.00 0.00 0.00 3.18
1082 1090 9.196552 CATATCTTGCTACGTCAATAATCTTCA 57.803 33.333 0.00 0.00 0.00 3.02
1083 1091 9.411801 TCATATCTTGCTACGTCAATAATCTTC 57.588 33.333 0.00 0.00 0.00 2.87
1084 1092 9.935241 ATCATATCTTGCTACGTCAATAATCTT 57.065 29.630 0.00 0.00 0.00 2.40
1085 1093 9.363763 CATCATATCTTGCTACGTCAATAATCT 57.636 33.333 0.00 0.00 0.00 2.40
1086 1094 9.144747 ACATCATATCTTGCTACGTCAATAATC 57.855 33.333 0.00 0.00 0.00 1.75
1087 1095 9.144747 GACATCATATCTTGCTACGTCAATAAT 57.855 33.333 0.00 0.00 0.00 1.28
1126 1134 1.405821 CGTAGGGGTCTCACTGATGTC 59.594 57.143 0.00 0.00 0.00 3.06
1127 1135 1.475403 CGTAGGGGTCTCACTGATGT 58.525 55.000 0.00 0.00 0.00 3.06
1610 1618 5.786264 TTTCCGATGAGAGGGAGTAATAC 57.214 43.478 0.00 0.00 33.01 1.89
1856 1879 9.472361 GCATGAAGCAGAATAATGTATTGAAAT 57.528 29.630 0.00 0.00 44.79 2.17
1887 1910 4.201812 ACAGTGTGAAATGTGTGAAACTCG 60.202 41.667 0.00 0.00 38.04 4.18
2032 2055 2.687935 TGCTTGGAAGTTTCACACCTTC 59.312 45.455 0.00 0.00 37.05 3.46
2077 2100 9.436957 CTTGTAGTCATGACCAAAACTATAGTT 57.563 33.333 22.21 12.50 40.50 2.24
2340 2363 1.286248 ATTCCTAACCCGCCTGAACT 58.714 50.000 0.00 0.00 0.00 3.01
2374 2397 4.943705 GGTTTAGGTTCAATGCATCTCAGA 59.056 41.667 0.00 0.00 0.00 3.27
2488 2511 0.320683 TCGTCTGTGGTGCAATCAGG 60.321 55.000 12.07 1.40 0.00 3.86
2505 2528 6.398234 TCTCTTCTAGATCCAAGGATTTCG 57.602 41.667 2.62 0.00 34.60 3.46
2684 2707 8.095792 TCTCATCAAAATTTTGGTGCACAATAT 58.904 29.630 30.90 12.92 46.27 1.28
2764 2787 3.261250 CTCTGGAAGCTGTGGCATT 57.739 52.632 0.00 0.00 41.70 3.56
2786 2809 3.730761 CGGTGGCACTTGCTGCTC 61.731 66.667 18.45 0.00 46.25 4.26
2808 2831 2.110901 CACTTGATGCTGAGGCTCTT 57.889 50.000 16.72 0.00 39.59 2.85
2839 2862 3.931768 CACTTCTTGCTGAGGCTCT 57.068 52.632 16.72 0.00 39.59 4.09
2849 2872 2.620112 CCTGCGGTGGCACTTCTTG 61.620 63.158 18.45 3.99 46.21 3.02
2850 2873 2.281761 CCTGCGGTGGCACTTCTT 60.282 61.111 18.45 0.00 46.21 2.52
2851 2874 2.738213 CTTCCTGCGGTGGCACTTCT 62.738 60.000 18.45 0.00 46.21 2.85
2852 2875 2.281484 TTCCTGCGGTGGCACTTC 60.281 61.111 18.45 9.94 46.21 3.01
2853 2876 2.281761 CTTCCTGCGGTGGCACTT 60.282 61.111 18.45 0.00 46.21 3.16
2854 2877 3.241530 TCTTCCTGCGGTGGCACT 61.242 61.111 18.45 0.00 46.21 4.40
2855 2878 2.743928 CTCTTCCTGCGGTGGCAC 60.744 66.667 9.70 9.70 46.21 5.01
2858 2881 3.710722 AGGCTCTTCCTGCGGTGG 61.711 66.667 0.00 0.00 45.54 4.61
2866 2889 1.449956 CTGCTGCTGAGGCTCTTCC 60.450 63.158 16.72 4.48 39.59 3.46
2867 2890 1.449956 CCTGCTGCTGAGGCTCTTC 60.450 63.158 16.72 7.78 39.59 2.87
2868 2891 2.222727 ACCTGCTGCTGAGGCTCTT 61.223 57.895 16.72 0.00 39.59 2.85
2909 2932 1.220206 GCTGCTGAGGCTCTTGCTA 59.780 57.895 24.86 14.91 39.59 3.49
3000 3023 2.503061 CGCCCATGCTACTGCTCT 59.497 61.111 0.00 0.00 40.48 4.09
3007 3030 1.153249 GTTGCTACCGCCCATGCTA 60.153 57.895 0.00 0.00 34.43 3.49
3175 3198 7.327032 CCATTTACTTGCTTTTCTCTTTACTGC 59.673 37.037 0.00 0.00 0.00 4.40
3289 3312 0.037790 ACGCTTCCTGTCTTGCTCTC 60.038 55.000 0.00 0.00 0.00 3.20
3412 3435 2.615493 GGTGCAGCCTAGCTTTCACTTA 60.615 50.000 4.03 0.00 38.63 2.24
3415 3438 2.175236 GGTGCAGCCTAGCTTTCAC 58.825 57.895 4.03 9.17 36.40 3.18
3416 3439 4.722193 GGTGCAGCCTAGCTTTCA 57.278 55.556 4.03 0.00 36.40 2.69
3512 3551 5.646793 TCTGAAAGATCCAGATTTCTTGCTG 59.353 40.000 6.69 0.00 38.67 4.41
3693 3732 9.959749 TGTTTTTCTCATTCCTGTATAACAAAC 57.040 29.630 0.00 0.00 0.00 2.93
3793 3832 2.127232 ACAACACAGCAAGCCCACC 61.127 57.895 0.00 0.00 0.00 4.61
3796 3835 2.028043 GCACAACACAGCAAGCCC 59.972 61.111 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.