Multiple sequence alignment - TraesCS2B01G378700

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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 TraesCS2B01G378700 chr2B 100.000 2146 0 0 605 2750 541686592 541688737 0.000000e+00 3964
1 TraesCS2B01G378700 chr2B 100.000 347 0 0 1 347 541685988 541686334 2.310000e-180 641
2 TraesCS2B01G378700 chr2B 89.286 308 33 0 1095 1402 178338371 178338678 1.190000e-103 387
3 TraesCS2B01G378700 chr2D 93.699 2095 65 24 605 2653 460648480 460650553 0.000000e+00 3075
4 TraesCS2B01G378700 chr2D 90.230 348 33 1 1 347 460648089 460648436 1.160000e-123 453
5 TraesCS2B01G378700 chr2D 88.673 309 33 2 1095 1402 125324472 125324779 2.590000e-100 375
6 TraesCS2B01G378700 chr2D 81.124 445 52 18 1931 2358 460643414 460643843 7.340000e-86 327
7 TraesCS2B01G378700 chr2A 94.705 1341 52 10 605 1929 603523283 603524620 0.000000e+00 2065
8 TraesCS2B01G378700 chr2A 92.299 844 42 10 1913 2748 603524835 603525663 0.000000e+00 1177
9 TraesCS2B01G378700 chr2A 92.816 348 24 1 1 347 603522892 603523239 1.140000e-138 503
10 TraesCS2B01G378700 chr2A 83.102 432 52 15 1931 2358 603516525 603516939 9.300000e-100 374
11 TraesCS2B01G378700 chr2A 87.702 309 36 2 1095 1402 131682867 131683174 2.600000e-95 359
12 TraesCS2B01G378700 chr3D 89.078 293 32 0 1099 1391 6337870 6338162 5.600000e-97 364
13 TraesCS2B01G378700 chr3B 88.396 293 34 0 1099 1391 7186981 7186689 1.210000e-93 353
14 TraesCS2B01G378700 chr3A 88.396 293 34 0 1099 1391 14044671 14044379 1.210000e-93 353
15 TraesCS2B01G378700 chr1D 86.364 132 18 0 1240 1371 476558359 476558490 7.940000e-31 145


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 TraesCS2B01G378700 chr2B 541685988 541688737 2749 False 2302.500000 3964 100.000000 1 2750 2 chr2B.!!$F2 2749
1 TraesCS2B01G378700 chr2D 460648089 460650553 2464 False 1764.000000 3075 91.964500 1 2653 2 chr2D.!!$F3 2652
2 TraesCS2B01G378700 chr2A 603522892 603525663 2771 False 1248.333333 2065 93.273333 1 2748 3 chr2A.!!$F3 2747

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
677 682 1.147399 AGGAGGATTACCCCGGACTAG 59.853 57.143 0.73 0.0 36.73 2.57 F
1221 1246 0.033504 AGTGCGTGTCCGAGTTCATT 59.966 50.000 0.00 0.0 35.63 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 1722 0.908180 GAACTCCCTTTCCCCTCCGA 60.908 60.0 0.00 0.0 0.0 4.55 R
2687 2976 0.101399 GAGCACCGTGACGATCATCT 59.899 55.0 6.54 0.0 0.0 2.90 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
28 29 6.875972 AGTAGATTACTTGTTGATCCTGGT 57.124 37.500 0.00 0.00 34.86 4.00
216 217 3.008049 GGCCTAGGAACTTCAACTCTTCA 59.992 47.826 14.75 0.00 41.75 3.02
240 241 3.118775 TGATACCATTTCCTGAGGTGACG 60.119 47.826 0.00 0.00 36.87 4.35
288 289 7.704472 GTGAACTGTGTAATGGAATGTTTTTCA 59.296 33.333 0.00 0.00 0.00 2.69
320 322 3.442100 GCACTAGCTGCATGATTTTTCC 58.558 45.455 1.02 0.00 46.29 3.13
324 326 1.829222 AGCTGCATGATTTTTCCCTGG 59.171 47.619 1.02 0.00 0.00 4.45
332 334 5.742838 GCATGATTTTTCCCTGGTTTTCTGT 60.743 40.000 0.00 0.00 0.00 3.41
340 342 5.319043 TCCCTGGTTTTCTGTCTGTTTAT 57.681 39.130 0.00 0.00 0.00 1.40
638 640 3.829948 CTGCACAAATCTCAAAGCGAAT 58.170 40.909 0.00 0.00 0.00 3.34
676 681 1.238615 AGGAGGATTACCCCGGACTA 58.761 55.000 0.73 0.00 36.73 2.59
677 682 1.147399 AGGAGGATTACCCCGGACTAG 59.853 57.143 0.73 0.00 36.73 2.57
697 702 1.847818 GCGTCCAGCGATATACACAA 58.152 50.000 0.00 0.00 44.77 3.33
745 756 2.297033 GGAATGCAGCTGGACTTTTGAA 59.703 45.455 17.12 0.00 0.00 2.69
748 759 2.098614 TGCAGCTGGACTTTTGAACAA 58.901 42.857 17.12 0.00 0.00 2.83
763 774 6.904463 TTTGAACAAGGAAATAAGGTACCC 57.096 37.500 8.74 0.00 0.00 3.69
784 795 4.113354 CCGATGCCTTAGACAAAGTCTAC 58.887 47.826 6.39 0.00 43.65 2.59
830 841 3.696548 GGTAAGCTAAAGCCAGAATTGCT 59.303 43.478 0.00 0.00 43.38 3.91
859 870 4.530857 CGATGCCGTCCTCCCACC 62.531 72.222 0.00 0.00 0.00 4.61
880 891 4.199310 CCCGCATCTCTCCATCTTTAAAA 58.801 43.478 0.00 0.00 0.00 1.52
882 893 4.260948 CCGCATCTCTCCATCTTTAAAAGC 60.261 45.833 0.00 0.00 0.00 3.51
885 896 5.732810 GCATCTCTCCATCTTTAAAAGCAGC 60.733 44.000 0.00 0.00 0.00 5.25
892 903 3.508845 TCTTTAAAAGCAGCTCACCCT 57.491 42.857 0.00 0.00 0.00 4.34
916 930 1.957877 CGATACCTCCTCAACTCCTCC 59.042 57.143 0.00 0.00 0.00 4.30
917 931 2.423660 CGATACCTCCTCAACTCCTCCT 60.424 54.545 0.00 0.00 0.00 3.69
918 932 2.830651 TACCTCCTCAACTCCTCCTC 57.169 55.000 0.00 0.00 0.00 3.71
930 944 2.241176 ACTCCTCCTCTCACTCACCTAG 59.759 54.545 0.00 0.00 0.00 3.02
932 946 3.456644 CTCCTCCTCTCACTCACCTAGTA 59.543 52.174 0.00 0.00 35.76 1.82
947 961 5.426509 TCACCTAGTACCAGTACTACTGCTA 59.573 44.000 12.58 6.35 44.63 3.49
1221 1246 0.033504 AGTGCGTGTCCGAGTTCATT 59.966 50.000 0.00 0.00 35.63 2.57
1664 1689 0.846693 AGGGGGATTGATTTCGAGGG 59.153 55.000 0.00 0.00 0.00 4.30
1823 1848 9.790344 ATAAATGCTGCTACTCTTCTTAATCAT 57.210 29.630 0.00 0.00 0.00 2.45
1934 2194 4.997905 ATGAAATATTCGAGCGATGTGG 57.002 40.909 0.00 0.00 0.00 4.17
1972 2232 4.046286 TGGCACAATCCAGTTTATTCCT 57.954 40.909 0.00 0.00 31.92 3.36
2036 2296 7.271223 CGTAGCAATCAAAACTATTCAAACCTG 59.729 37.037 0.00 0.00 0.00 4.00
2098 2358 0.386838 AGCCTGCAACTGAAACAAGC 59.613 50.000 0.00 0.00 0.00 4.01
2102 2362 2.159198 CCTGCAACTGAAACAAGCAACT 60.159 45.455 0.00 0.00 34.45 3.16
2228 2499 5.523438 TTTGAACCCGAAAAAGCATAAGT 57.477 34.783 0.00 0.00 0.00 2.24
2314 2599 2.982744 GCGCTTTGTCCTGCCCTTC 61.983 63.158 0.00 0.00 0.00 3.46
2342 2627 6.545504 AATGCACAAGATACCATATTCGAC 57.454 37.500 0.00 0.00 0.00 4.20
2372 2658 1.231221 TTTTGCGAGTACGTGGCATT 58.769 45.000 0.00 0.00 41.98 3.56
2464 2750 8.709386 AATGTATGTAAGAGTAGCTTCAAGTG 57.291 34.615 0.00 0.00 38.05 3.16
2465 2751 7.462571 TGTATGTAAGAGTAGCTTCAAGTGA 57.537 36.000 0.00 0.00 38.05 3.41
2466 2752 7.539436 TGTATGTAAGAGTAGCTTCAAGTGAG 58.461 38.462 0.00 0.00 38.05 3.51
2467 2753 6.842437 ATGTAAGAGTAGCTTCAAGTGAGA 57.158 37.500 0.00 0.00 38.05 3.27
2468 2754 6.260870 TGTAAGAGTAGCTTCAAGTGAGAG 57.739 41.667 0.00 0.00 38.05 3.20
2469 2755 5.770663 TGTAAGAGTAGCTTCAAGTGAGAGT 59.229 40.000 0.00 0.00 38.05 3.24
2511 2797 3.514706 TCCATGTATTGCACATTGGCTTT 59.485 39.130 0.00 0.00 46.01 3.51
2516 2802 2.356075 GCACATTGGCTTTGCGCA 60.356 55.556 5.66 5.66 41.67 6.09
2547 2833 6.373216 ACGAATTAGTTAAGGCAATGTAAGCA 59.627 34.615 0.00 0.00 0.00 3.91
2548 2834 6.907212 CGAATTAGTTAAGGCAATGTAAGCAG 59.093 38.462 0.00 0.00 0.00 4.24
2589 2875 1.069765 CCTTCATGGCGACGGCTAT 59.930 57.895 22.70 11.24 41.56 2.97
2670 2959 4.261801 CTCACGAATTAGGTTTGACCCAT 58.738 43.478 0.00 0.00 39.75 4.00
2672 2961 5.806818 TCACGAATTAGGTTTGACCCATTA 58.193 37.500 0.00 0.00 39.75 1.90
2686 2975 8.921670 GTTTGACCCATTATACAAATTGTGTTC 58.078 33.333 9.15 0.00 41.98 3.18
2687 2976 7.767250 TGACCCATTATACAAATTGTGTTCA 57.233 32.000 9.15 0.00 41.98 3.18
2711 3000 2.578163 ATCGTCACGGTGCTCATGGG 62.578 60.000 2.51 0.00 0.00 4.00
2712 3001 3.127533 GTCACGGTGCTCATGGGC 61.128 66.667 11.75 11.75 0.00 5.36
2713 3002 3.635191 TCACGGTGCTCATGGGCA 61.635 61.111 18.52 18.52 40.15 5.36
2714 3003 2.438975 CACGGTGCTCATGGGCAT 60.439 61.111 25.81 4.59 44.34 4.40
2715 3004 2.438975 ACGGTGCTCATGGGCATG 60.439 61.111 25.81 21.32 44.34 4.06
2716 3005 3.214123 CGGTGCTCATGGGCATGG 61.214 66.667 25.81 14.96 44.34 3.66
2717 3006 2.043652 GGTGCTCATGGGCATGGT 60.044 61.111 25.81 0.00 44.34 3.55
2728 3017 1.682451 GGGCATGGTAGCTGGTACGA 61.682 60.000 10.55 7.50 31.59 3.43
2730 3019 0.460311 GCATGGTAGCTGGTACGACT 59.540 55.000 10.55 0.00 31.59 4.18
2735 3024 0.179134 GTAGCTGGTACGACTGGCAG 60.179 60.000 14.16 14.16 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 4.209080 GTGCTTTGGCTTCACATACAAAAC 59.791 41.667 0.00 0.00 39.59 2.43
155 156 1.200519 TTAGTGGAACCGATGAGGGG 58.799 55.000 0.00 0.00 46.96 4.79
205 206 7.890127 AGGAAATGGTATCAATGAAGAGTTGAA 59.110 33.333 0.00 0.00 38.89 2.69
216 217 5.440610 GTCACCTCAGGAAATGGTATCAAT 58.559 41.667 0.00 0.00 32.13 2.57
240 241 3.223589 GGTTGTGCCACCACCCAC 61.224 66.667 6.83 0.00 41.35 4.61
320 322 5.765182 AGTCATAAACAGACAGAAAACCAGG 59.235 40.000 0.00 0.00 38.46 4.45
654 658 1.562942 GTCCGGGGTAATCCTCCTTTT 59.437 52.381 0.00 0.00 35.33 2.27
676 681 0.314302 GTGTATATCGCTGGACGCCT 59.686 55.000 0.00 0.00 43.23 5.52
677 682 0.031585 TGTGTATATCGCTGGACGCC 59.968 55.000 0.00 0.00 43.23 5.68
690 695 3.120338 CGTTCGCTTTGATGGTTGTGTAT 60.120 43.478 0.00 0.00 0.00 2.29
691 696 2.222213 CGTTCGCTTTGATGGTTGTGTA 59.778 45.455 0.00 0.00 0.00 2.90
697 702 2.450609 ACTACGTTCGCTTTGATGGT 57.549 45.000 0.00 0.00 0.00 3.55
763 774 4.113354 GGTAGACTTTGTCTAAGGCATCG 58.887 47.826 8.75 0.00 45.12 3.84
807 818 3.443681 GCAATTCTGGCTTTAGCTTACCA 59.556 43.478 0.00 0.00 41.70 3.25
808 819 3.696548 AGCAATTCTGGCTTTAGCTTACC 59.303 43.478 0.00 0.00 38.81 2.85
830 841 2.584970 GCATCGATGCGGACGGAA 60.585 61.111 32.60 0.00 44.67 4.30
859 870 4.260948 GCTTTTAAAGATGGAGAGATGCGG 60.261 45.833 9.10 0.00 0.00 5.69
882 893 0.249238 GTATCGAGCAGGGTGAGCTG 60.249 60.000 0.00 0.00 43.58 4.24
885 896 0.671251 GAGGTATCGAGCAGGGTGAG 59.329 60.000 0.00 0.00 0.00 3.51
892 903 2.025155 GAGTTGAGGAGGTATCGAGCA 58.975 52.381 0.00 0.00 0.00 4.26
916 930 3.958018 ACTGGTACTAGGTGAGTGAGAG 58.042 50.000 11.30 0.00 39.39 3.20
917 931 4.535294 AGTACTGGTACTAGGTGAGTGAGA 59.465 45.833 11.30 0.00 43.98 3.27
918 932 4.846040 AGTACTGGTACTAGGTGAGTGAG 58.154 47.826 11.30 0.00 43.98 3.51
1092 1117 3.710722 CGGTCCTGCTCCTTGGCT 61.711 66.667 0.00 0.00 0.00 4.75
1161 1186 1.066143 TCCTTGGAGATCTTGGCGTTC 60.066 52.381 0.00 0.00 0.00 3.95
1697 1722 0.908180 GAACTCCCTTTCCCCTCCGA 60.908 60.000 0.00 0.00 0.00 4.55
1972 2232 5.414789 TTGTTAACCGGAGATCTGATTGA 57.585 39.130 9.46 0.00 0.00 2.57
2098 2358 5.639931 GGAGCTTAAGGTCTGACTAAAGTTG 59.360 44.000 28.48 0.00 41.88 3.16
2102 2362 3.194968 CGGGAGCTTAAGGTCTGACTAAA 59.805 47.826 28.48 0.00 41.88 1.85
2314 2599 8.011673 CGAATATGGTATCTTGTGCATTTGTAG 58.988 37.037 0.00 0.00 0.00 2.74
2355 2641 2.081725 TAAATGCCACGTACTCGCAA 57.918 45.000 3.36 0.00 41.18 4.85
2468 2754 2.419739 GCGGAGGGAGGACTCTCAC 61.420 68.421 1.53 0.00 44.80 3.51
2469 2755 2.043852 GCGGAGGGAGGACTCTCA 60.044 66.667 1.53 0.00 44.80 3.27
2511 2797 1.134818 ACTAATTCGTGGATCTGCGCA 60.135 47.619 10.98 10.98 0.00 6.09
2516 2802 5.353394 TGCCTTAACTAATTCGTGGATCT 57.647 39.130 0.00 0.00 0.00 2.75
2547 2833 6.094603 GGTGTGATCTATTTCAGATTGTTGCT 59.905 38.462 0.00 0.00 44.41 3.91
2548 2834 6.094603 AGGTGTGATCTATTTCAGATTGTTGC 59.905 38.462 0.00 0.00 44.41 4.17
2589 2875 1.250328 CAGAAGCCATTCACAAGCCA 58.750 50.000 0.00 0.00 37.94 4.75
2649 2936 3.773418 TGGGTCAAACCTAATTCGTGA 57.227 42.857 0.00 0.00 38.64 4.35
2651 2938 7.340256 TGTATAATGGGTCAAACCTAATTCGT 58.660 34.615 0.00 0.00 38.64 3.85
2661 2950 8.642432 TGAACACAATTTGTATAATGGGTCAAA 58.358 29.630 0.86 0.00 37.51 2.69
2670 2959 9.161629 ACGATCATCTGAACACAATTTGTATAA 57.838 29.630 0.86 0.00 37.51 0.98
2672 2961 7.334171 TGACGATCATCTGAACACAATTTGTAT 59.666 33.333 0.86 0.00 37.51 2.29
2679 2968 2.986479 CGTGACGATCATCTGAACACAA 59.014 45.455 0.00 0.00 0.00 3.33
2686 2975 0.179127 AGCACCGTGACGATCATCTG 60.179 55.000 6.54 0.00 0.00 2.90
2687 2976 0.101399 GAGCACCGTGACGATCATCT 59.899 55.000 6.54 0.00 0.00 2.90
2711 3000 0.460311 AGTCGTACCAGCTACCATGC 59.540 55.000 0.00 0.00 0.00 4.06
2712 3001 1.202417 CCAGTCGTACCAGCTACCATG 60.202 57.143 0.00 0.00 0.00 3.66
2713 3002 1.112113 CCAGTCGTACCAGCTACCAT 58.888 55.000 0.00 0.00 0.00 3.55
2714 3003 1.601419 GCCAGTCGTACCAGCTACCA 61.601 60.000 0.00 0.00 0.00 3.25
2715 3004 1.141234 GCCAGTCGTACCAGCTACC 59.859 63.158 0.00 0.00 0.00 3.18
2716 3005 0.179134 CTGCCAGTCGTACCAGCTAC 60.179 60.000 0.00 0.00 0.00 3.58
2717 3006 0.611062 ACTGCCAGTCGTACCAGCTA 60.611 55.000 0.00 0.00 0.00 3.32
2728 3017 4.065281 GCCGGTCGTACTGCCAGT 62.065 66.667 1.90 1.54 0.00 4.00


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

AutoCloner maintained by Alex Coulton.