Multiple sequence alignment - TraesCS2B01G622600

Loading Multiple Alignment...

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 TraesCS2B01G622600 chr2B 100.000 2884 0 0 1 2884 796755954 796753071 0.000000e+00 5326.0
1 TraesCS2B01G622600 chr2B 94.409 1735 70 8 1165 2884 33473351 33471629 0.000000e+00 2641.0
2 TraesCS2B01G622600 chr2B 98.777 654 7 1 1 654 699014465 699013813 0.000000e+00 1162.0
3 TraesCS2B01G622600 chr2B 98.632 658 5 1 1 654 796771972 796771315 0.000000e+00 1162.0
4 TraesCS2B01G622600 chr2B 98.626 655 8 1 1 655 236247252 236247905 0.000000e+00 1158.0
5 TraesCS2B01G622600 chr2B 98.624 654 8 1 1 654 698991486 698990834 0.000000e+00 1157.0
6 TraesCS2B01G622600 chr2B 92.600 527 29 8 655 1178 193470962 193470443 0.000000e+00 749.0
7 TraesCS2B01G622600 chr5A 94.545 2163 96 8 729 2884 115997429 115995282 0.000000e+00 3321.0
8 TraesCS2B01G622600 chr5A 96.000 50 2 0 655 704 115997523 115997474 6.620000e-12 82.4
9 TraesCS2B01G622600 chr5A 100.000 35 0 0 1449 1483 115996783 115996749 6.670000e-07 65.8
10 TraesCS2B01G622600 chr2D 94.393 2176 85 11 729 2884 13522432 13520274 0.000000e+00 3308.0
11 TraesCS2B01G622600 chr2D 89.789 1939 139 28 980 2884 618324330 618322417 0.000000e+00 2429.0
12 TraesCS2B01G622600 chr2D 100.000 35 0 0 1449 1483 13521787 13521753 6.670000e-07 65.8
13 TraesCS2B01G622600 chr3D 94.188 2185 80 14 729 2884 376078184 376076018 0.000000e+00 3288.0
14 TraesCS2B01G622600 chr3D 100.000 35 0 0 1449 1483 376077538 376077504 6.670000e-07 65.8
15 TraesCS2B01G622600 chr4B 95.050 2101 75 9 801 2884 595724640 595722552 0.000000e+00 3277.0
16 TraesCS2B01G622600 chr4B 94.000 50 3 0 655 704 595724695 595724646 3.080000e-10 76.8
17 TraesCS2B01G622600 chr4B 97.143 35 1 0 1449 1483 595724065 595724031 3.100000e-05 60.2
18 TraesCS2B01G622600 chr3B 95.010 2104 76 9 798 2884 7318875 7320966 0.000000e+00 3277.0
19 TraesCS2B01G622600 chr3B 87.584 596 46 11 986 1577 228014998 228015569 0.000000e+00 665.0
20 TraesCS2B01G622600 chr2A 93.956 1853 85 9 729 2567 613241445 613239606 0.000000e+00 2776.0
21 TraesCS2B01G622600 chr2A 94.631 298 15 1 729 1025 175031652 175031949 7.280000e-126 460.0
22 TraesCS2B01G622600 chr2A 96.000 50 2 0 655 704 613241539 613241490 6.620000e-12 82.4
23 TraesCS2B01G622600 chr5D 96.253 1281 45 1 1607 2884 431176774 431175494 0.000000e+00 2097.0
24 TraesCS2B01G622600 chr5D 92.913 889 43 9 729 1612 431181089 431180216 0.000000e+00 1275.0
25 TraesCS2B01G622600 chr5D 97.143 35 1 0 1449 1483 431180442 431180408 3.100000e-05 60.2
26 TraesCS2B01G622600 chr7B 93.036 1120 50 10 729 1835 33410380 33411484 0.000000e+00 1611.0
27 TraesCS2B01G622600 chr7B 98.777 654 8 0 1 654 679038289 679038942 0.000000e+00 1164.0
28 TraesCS2B01G622600 chr7B 96.000 50 2 0 655 704 33410286 33410335 6.620000e-12 82.4
29 TraesCS2B01G622600 chr7B 100.000 35 0 0 1449 1483 33411014 33411048 6.670000e-07 65.8
30 TraesCS2B01G622600 chr5B 98.779 655 8 0 1 655 67578244 67578898 0.000000e+00 1166.0
31 TraesCS2B01G622600 chr5B 98.624 654 9 0 1 654 67571213 67571866 0.000000e+00 1158.0
32 TraesCS2B01G622600 chr5B 94.918 669 26 4 801 1464 322287388 322286723 0.000000e+00 1040.0
33 TraesCS2B01G622600 chr5B 94.000 50 3 0 655 704 322287443 322287394 3.080000e-10 76.8
34 TraesCS2B01G622600 chr1B 98.779 655 6 2 1 654 295344541 295345194 0.000000e+00 1164.0
35 TraesCS2B01G622600 chr6B 98.624 654 8 1 1 654 157085853 157086505 0.000000e+00 1157.0
36 TraesCS2B01G622600 chr6A 94.070 742 34 6 729 1464 367768648 367767911 0.000000e+00 1118.0
37 TraesCS2B01G622600 chr6A 94.638 690 29 4 729 1413 34077092 34077778 0.000000e+00 1062.0
38 TraesCS2B01G622600 chr6A 96.000 50 2 0 655 704 34076998 34077047 6.620000e-12 82.4
39 TraesCS2B01G622600 chr6A 100.000 32 0 0 1449 1480 34077739 34077770 3.100000e-05 60.2
40 TraesCS2B01G622600 chr6A 97.143 35 1 0 1449 1483 367768001 367767967 3.100000e-05 60.2


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 TraesCS2B01G622600 chr2B 796753071 796755954 2883 True 5326.000000 5326 100.000000 1 2884 1 chr2B.!!$R5 2883
1 TraesCS2B01G622600 chr2B 33471629 33473351 1722 True 2641.000000 2641 94.409000 1165 2884 1 chr2B.!!$R1 1719
2 TraesCS2B01G622600 chr2B 699013813 699014465 652 True 1162.000000 1162 98.777000 1 654 1 chr2B.!!$R4 653
3 TraesCS2B01G622600 chr2B 796771315 796771972 657 True 1162.000000 1162 98.632000 1 654 1 chr2B.!!$R6 653
4 TraesCS2B01G622600 chr2B 236247252 236247905 653 False 1158.000000 1158 98.626000 1 655 1 chr2B.!!$F1 654
5 TraesCS2B01G622600 chr2B 698990834 698991486 652 True 1157.000000 1157 98.624000 1 654 1 chr2B.!!$R3 653
6 TraesCS2B01G622600 chr2B 193470443 193470962 519 True 749.000000 749 92.600000 655 1178 1 chr2B.!!$R2 523
7 TraesCS2B01G622600 chr5A 115995282 115997523 2241 True 1156.400000 3321 96.848333 655 2884 3 chr5A.!!$R1 2229
8 TraesCS2B01G622600 chr2D 618322417 618324330 1913 True 2429.000000 2429 89.789000 980 2884 1 chr2D.!!$R1 1904
9 TraesCS2B01G622600 chr2D 13520274 13522432 2158 True 1686.900000 3308 97.196500 729 2884 2 chr2D.!!$R2 2155
10 TraesCS2B01G622600 chr3D 376076018 376078184 2166 True 1676.900000 3288 97.094000 729 2884 2 chr3D.!!$R1 2155
11 TraesCS2B01G622600 chr4B 595722552 595724695 2143 True 1138.000000 3277 95.397667 655 2884 3 chr4B.!!$R1 2229
12 TraesCS2B01G622600 chr3B 7318875 7320966 2091 False 3277.000000 3277 95.010000 798 2884 1 chr3B.!!$F1 2086
13 TraesCS2B01G622600 chr3B 228014998 228015569 571 False 665.000000 665 87.584000 986 1577 1 chr3B.!!$F2 591
14 TraesCS2B01G622600 chr2A 613239606 613241539 1933 True 1429.200000 2776 94.978000 655 2567 2 chr2A.!!$R1 1912
15 TraesCS2B01G622600 chr5D 431175494 431181089 5595 True 1144.066667 2097 95.436333 729 2884 3 chr5D.!!$R1 2155
16 TraesCS2B01G622600 chr7B 679038289 679038942 653 False 1164.000000 1164 98.777000 1 654 1 chr7B.!!$F1 653
17 TraesCS2B01G622600 chr7B 33410286 33411484 1198 False 586.400000 1611 96.345333 655 1835 3 chr7B.!!$F2 1180
18 TraesCS2B01G622600 chr5B 67578244 67578898 654 False 1166.000000 1166 98.779000 1 655 1 chr5B.!!$F2 654
19 TraesCS2B01G622600 chr5B 67571213 67571866 653 False 1158.000000 1158 98.624000 1 654 1 chr5B.!!$F1 653
20 TraesCS2B01G622600 chr5B 322286723 322287443 720 True 558.400000 1040 94.459000 655 1464 2 chr5B.!!$R1 809
21 TraesCS2B01G622600 chr1B 295344541 295345194 653 False 1164.000000 1164 98.779000 1 654 1 chr1B.!!$F1 653
22 TraesCS2B01G622600 chr6B 157085853 157086505 652 False 1157.000000 1157 98.624000 1 654 1 chr6B.!!$F1 653
23 TraesCS2B01G622600 chr6A 367767911 367768648 737 True 589.100000 1118 95.606500 729 1483 2 chr6A.!!$R1 754
24 TraesCS2B01G622600 chr6A 34076998 34077778 780 False 401.533333 1062 96.879333 655 1480 3 chr6A.!!$F1 825

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
719 745 0.035152 TGATTTGCTCCGTCATGGCT 60.035 50.0 0.0 0.0 37.8 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 5570 2.224992 TGCAATGCCTTTGGTCCTAGAA 60.225 45.455 1.53 0.0 35.75 2.1 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
667 673 3.655615 TCCAACAACAAGGGTAAGTGT 57.344 42.857 0.00 0.00 0.00 3.55
705 731 5.664294 TTGAGTATTTGCTGCCATGATTT 57.336 34.783 0.00 0.00 0.00 2.17
706 732 5.001237 TGAGTATTTGCTGCCATGATTTG 57.999 39.130 0.00 0.00 0.00 2.32
707 733 3.788937 AGTATTTGCTGCCATGATTTGC 58.211 40.909 0.00 0.00 0.00 3.68
709 735 2.373540 TTTGCTGCCATGATTTGCTC 57.626 45.000 0.00 0.00 0.00 4.26
710 736 0.533491 TTGCTGCCATGATTTGCTCC 59.467 50.000 0.00 0.00 0.00 4.70
711 737 1.065273 GCTGCCATGATTTGCTCCG 59.935 57.895 0.00 0.00 0.00 4.63
712 738 1.660560 GCTGCCATGATTTGCTCCGT 61.661 55.000 0.00 0.00 0.00 4.69
713 739 0.379669 CTGCCATGATTTGCTCCGTC 59.620 55.000 0.00 0.00 0.00 4.79
714 740 0.322366 TGCCATGATTTGCTCCGTCA 60.322 50.000 0.00 0.00 0.00 4.35
717 743 2.768833 CATGATTTGCTCCGTCATGG 57.231 50.000 6.67 0.00 43.32 3.66
718 744 1.027357 ATGATTTGCTCCGTCATGGC 58.973 50.000 0.00 0.00 37.80 4.40
719 745 0.035152 TGATTTGCTCCGTCATGGCT 60.035 50.000 0.00 0.00 37.80 4.75
720 746 1.209261 TGATTTGCTCCGTCATGGCTA 59.791 47.619 0.00 0.00 37.80 3.93
721 747 1.599542 GATTTGCTCCGTCATGGCTAC 59.400 52.381 0.00 0.00 37.80 3.58
724 750 0.108186 TGCTCCGTCATGGCTACAAG 60.108 55.000 0.00 0.00 37.80 3.16
725 751 0.811616 GCTCCGTCATGGCTACAAGG 60.812 60.000 0.00 0.00 37.80 3.61
855 881 8.709308 AGTTAGAGATGGATATTTGTTACTGCT 58.291 33.333 0.00 0.00 0.00 4.24
879 905 8.321716 GCTAAATCTACAGTGAAACAATAGACG 58.678 37.037 0.00 0.00 38.05 4.18
1131 1160 8.943002 CCGACTTAACAAATTATAAGGACTTGT 58.057 33.333 9.22 0.00 34.21 3.16
1187 1216 4.462508 TTTGGAAGTTGCACATGTTCAA 57.537 36.364 6.83 6.83 0.00 2.69
1191 1220 4.022416 TGGAAGTTGCACATGTTCAATACC 60.022 41.667 14.00 15.93 0.00 2.73
1197 1226 6.602803 AGTTGCACATGTTCAATACCATGATA 59.397 34.615 14.00 0.00 0.00 2.15
1268 1300 7.117092 GTGATGTTTGAGAAACTCTCTAAGACC 59.883 40.741 5.34 0.00 43.73 3.85
1422 1455 7.094205 ACCCAATACTTGAGAATGAACATGTTC 60.094 37.037 28.10 28.10 39.91 3.18
1442 1475 7.072177 TGTTCGTGTTGATGAGGAAAATATC 57.928 36.000 0.00 0.00 0.00 1.63
1523 1556 4.385310 CCCTGTTCCGATAAAGAAAGGGAT 60.385 45.833 11.94 0.00 40.46 3.85
1725 5246 8.828688 TCAACATGCAATCAAACATGAATTTA 57.171 26.923 9.77 0.00 45.23 1.40
1939 5470 6.235231 TGTAGGTGAGAAAGAACTCTTGTT 57.765 37.500 0.00 0.00 39.42 2.83
2039 5570 4.282703 GGATTGGCTAATTGAGGATGCAAT 59.717 41.667 0.00 0.00 40.04 3.56
2141 5672 1.611673 GCTGCTAGCCTTGAAGGAACA 60.612 52.381 16.93 5.63 37.67 3.18
2318 5849 1.816183 CGGGTTCCTTAGTGGTTGCAA 60.816 52.381 0.00 0.00 37.07 4.08
2420 5951 7.291416 TGGCCATAGTTGGATGTATCTAGTTTA 59.709 37.037 0.00 0.00 46.92 2.01
2450 5981 7.384932 GGGTGTTTTTGATTCTGAAACTAATGG 59.615 37.037 13.02 0.00 35.04 3.16
2564 6107 7.074653 TGATAGGTGTAAAAGAAGTGTTCCT 57.925 36.000 0.00 0.00 0.00 3.36
2585 6128 5.087323 CCTAGAGGCTGAACATAGGGAATA 58.913 45.833 0.00 0.00 31.24 1.75
2717 6263 2.449464 TGCAATGGACATAGCAAAGCT 58.551 42.857 0.00 0.00 43.41 3.74
2728 6274 0.036388 AGCAAAGCTAGCGGCAACTA 60.036 50.000 24.18 0.00 44.79 2.24
2819 6365 3.157932 TGTTACAAACAACTTGGCTGC 57.842 42.857 0.00 0.00 39.56 5.25
2820 6366 2.493675 TGTTACAAACAACTTGGCTGCA 59.506 40.909 0.50 0.00 39.56 4.41
2823 6369 1.755959 ACAAACAACTTGGCTGCATGA 59.244 42.857 0.50 0.00 39.56 3.07
2832 6378 5.664294 ACTTGGCTGCATGATTCAATAAA 57.336 34.783 0.50 0.00 0.00 1.40
2862 6408 4.210331 AGCATCACAAGTCCTTGAACTTT 58.790 39.130 13.69 0.00 42.93 2.66
2865 6411 5.450412 GCATCACAAGTCCTTGAACTTTGAA 60.450 40.000 13.69 0.00 42.93 2.69
2877 6423 6.969473 CCTTGAACTTTGAAGACTTCTTTGAC 59.031 38.462 16.02 4.80 36.11 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
705 731 0.108186 CTTGTAGCCATGACGGAGCA 60.108 55.000 0.00 0.00 36.56 4.26
706 732 0.811616 CCTTGTAGCCATGACGGAGC 60.812 60.000 0.00 0.00 36.56 4.70
707 733 0.179073 CCCTTGTAGCCATGACGGAG 60.179 60.000 0.00 0.00 36.56 4.63
709 735 0.828022 TACCCTTGTAGCCATGACGG 59.172 55.000 0.00 0.00 38.11 4.79
710 736 2.277084 GTTACCCTTGTAGCCATGACG 58.723 52.381 0.00 0.00 0.00 4.35
711 737 3.343941 TGTTACCCTTGTAGCCATGAC 57.656 47.619 0.00 0.00 0.00 3.06
712 738 5.904984 ATATGTTACCCTTGTAGCCATGA 57.095 39.130 0.00 0.00 0.00 3.07
713 739 6.735694 GCAAATATGTTACCCTTGTAGCCATG 60.736 42.308 0.00 0.00 0.00 3.66
714 740 5.301805 GCAAATATGTTACCCTTGTAGCCAT 59.698 40.000 0.00 0.00 0.00 4.40
717 743 6.094881 TGAAGCAAATATGTTACCCTTGTAGC 59.905 38.462 0.00 0.00 0.00 3.58
718 744 7.415206 GGTGAAGCAAATATGTTACCCTTGTAG 60.415 40.741 0.00 0.00 0.00 2.74
719 745 6.376018 GGTGAAGCAAATATGTTACCCTTGTA 59.624 38.462 0.00 0.00 0.00 2.41
720 746 5.185056 GGTGAAGCAAATATGTTACCCTTGT 59.815 40.000 0.00 0.00 0.00 3.16
721 747 5.418840 AGGTGAAGCAAATATGTTACCCTTG 59.581 40.000 0.00 0.00 0.00 3.61
724 750 5.914898 AAGGTGAAGCAAATATGTTACCC 57.085 39.130 0.00 0.00 0.00 3.69
725 751 7.158099 AGAAAGGTGAAGCAAATATGTTACC 57.842 36.000 0.00 0.00 0.00 2.85
793 819 6.120220 TCTTCGATCCATCTCAAGTACACTA 58.880 40.000 0.00 0.00 0.00 2.74
850 876 7.986085 ATTGTTTCACTGTAGATTTAGCAGT 57.014 32.000 0.00 0.00 43.37 4.40
855 881 9.917129 TTCGTCTATTGTTTCACTGTAGATTTA 57.083 29.630 0.00 0.00 0.00 1.40
963 990 8.927721 CAAAAGATCAATTGTGCATGAACATAA 58.072 29.630 7.53 0.00 0.00 1.90
1054 1081 6.237154 AGCATTTGATATCCTTCCTAGCTTC 58.763 40.000 0.00 0.00 0.00 3.86
1131 1160 6.631016 AGTACTGCTCTACGATTGATTCAAA 58.369 36.000 2.68 0.00 0.00 2.69
1215 1244 5.808366 TCTTGGTCAGATGTTACTTCTGT 57.192 39.130 22.02 0.00 41.13 3.41
1268 1300 2.958213 ACAAACAAGTGCACAACCTTG 58.042 42.857 21.04 16.57 0.00 3.61
1523 1556 6.608808 TCTCATGATCAGGAACATAGTCTTCA 59.391 38.462 11.74 0.00 0.00 3.02
1725 5246 3.654414 CACTCTTCTCGGTGCTAAACTT 58.346 45.455 0.00 0.00 0.00 2.66
1762 5283 4.380843 TCCCTTCTTGAACAATAAGCCA 57.619 40.909 7.01 0.00 0.00 4.75
1807 5328 7.660617 ACTCATCTTCCATTGTAGAAGCATATG 59.339 37.037 0.00 0.00 40.48 1.78
1939 5470 6.631971 TTTTGTACTTGAGCAATCATGACA 57.368 33.333 0.00 0.00 0.00 3.58
2007 5538 3.627395 ATTAGCCAATCCTTCACGTGA 57.373 42.857 15.76 15.76 0.00 4.35
2039 5570 2.224992 TGCAATGCCTTTGGTCCTAGAA 60.225 45.455 1.53 0.00 35.75 2.10
2141 5672 5.957132 AGCTTGTATCCCAATCACCATATT 58.043 37.500 0.00 0.00 31.20 1.28
2420 5951 8.193953 AGTTTCAGAATCAAAAACACCCATAT 57.806 30.769 11.30 0.00 35.77 1.78
2450 5981 3.025978 TGCATGAACCAGATCCAATTCC 58.974 45.455 0.00 0.00 0.00 3.01
2564 6107 7.901322 ACATATATTCCCTATGTTCAGCCTCTA 59.099 37.037 0.00 0.00 36.62 2.43
2585 6128 7.936847 TGAAGTTGGACACTAAGTGAAACATAT 59.063 33.333 0.00 0.00 34.34 1.78
2598 6141 5.253330 TGAAACTTCTTGAAGTTGGACACT 58.747 37.500 23.92 11.18 41.76 3.55
2717 6263 5.074804 TCCTAAGATATGTAGTTGCCGCTA 58.925 41.667 0.00 0.00 0.00 4.26
2728 6274 4.471386 AGTGTGCCACTTCCTAAGATATGT 59.529 41.667 0.00 0.00 42.59 2.29
2757 6303 3.691575 TGAGAACTGACTCCTAGACCAG 58.308 50.000 0.00 0.00 36.22 4.00
2832 6378 5.121380 AGGACTTGTGATGCTTAATCCAT 57.879 39.130 0.00 0.00 34.00 3.41


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

AutoCloner maintained by Alex Coulton.