Multiple sequence alignment - TraesCS2D01G318900

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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 TraesCS2D01G318900 chr2D 100.000 3312 0 0 1 3312 409285627 409282316 0.000000e+00 6117.0
1 TraesCS2D01G318900 chr2B 94.920 3110 121 19 1 3096 484489648 484492734 0.000000e+00 4833.0
2 TraesCS2D01G318900 chr2B 90.135 223 15 4 3091 3312 484492773 484492989 1.950000e-72 283.0
3 TraesCS2D01G318900 chr2B 87.500 152 15 4 524 674 117888376 117888228 4.390000e-39 172.0
4 TraesCS2D01G318900 chr2A 95.855 2099 73 4 999 3094 577213657 577211570 0.000000e+00 3382.0
5 TraesCS2D01G318900 chr2A 93.494 538 33 2 404 940 577214189 577213653 0.000000e+00 798.0
6 TraesCS2D01G318900 chr2A 91.358 405 27 5 1 401 577215077 577214677 6.250000e-152 547.0
7 TraesCS2D01G318900 chr2A 94.619 223 11 1 3091 3312 577211529 577211307 8.800000e-91 344.0
8 TraesCS2D01G318900 chr2A 86.441 59 5 3 2450 2505 757995686 757995628 9.920000e-06 62.1
9 TraesCS2D01G318900 chr5B 91.870 123 10 0 525 647 541090770 541090648 4.390000e-39 172.0
10 TraesCS2D01G318900 chr6B 90.076 131 13 0 524 654 172715766 172715896 1.580000e-38 171.0
11 TraesCS2D01G318900 chr4B 90.551 127 12 0 528 654 608977225 608977351 5.680000e-38 169.0
12 TraesCS2D01G318900 chr7B 87.143 140 17 1 525 663 460995739 460995600 1.230000e-34 158.0
13 TraesCS2D01G318900 chr7B 87.143 140 16 2 524 661 689906055 689905916 1.230000e-34 158.0
14 TraesCS2D01G318900 chr1B 88.372 129 15 0 525 653 15649018 15649146 4.430000e-34 156.0
15 TraesCS2D01G318900 chr1B 85.714 133 15 3 2375 2505 49864499 49864629 1.600000e-28 137.0
16 TraesCS2D01G318900 chr3A 97.368 38 0 1 2450 2486 691505942 691505905 2.760000e-06 63.9
17 TraesCS2D01G318900 chr1D 88.679 53 4 2 2454 2504 270036791 270036843 2.760000e-06 63.9
18 TraesCS2D01G318900 chr7D 100.000 33 0 0 2454 2486 563516535 563516503 9.920000e-06 62.1
19 TraesCS2D01G318900 chr6D 87.273 55 4 2 2456 2508 84476211 84476158 3.570000e-05 60.2
20 TraesCS2D01G318900 chr1A 88.000 50 5 1 2456 2504 375466733 375466782 1.280000e-04 58.4


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 TraesCS2D01G318900 chr2D 409282316 409285627 3311 True 6117.00 6117 100.0000 1 3312 1 chr2D.!!$R1 3311
1 TraesCS2D01G318900 chr2B 484489648 484492989 3341 False 2558.00 4833 92.5275 1 3312 2 chr2B.!!$F1 3311
2 TraesCS2D01G318900 chr2A 577211307 577215077 3770 True 1267.75 3382 93.8315 1 3312 4 chr2A.!!$R2 3311

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
923 1415 1.595093 GCCACTGAACCAAATCGGGG 61.595 60.0 0.0 0.0 40.22 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2864 3364 0.615331 TGAGGGAATTTGCTCGAGCT 59.385 50.0 35.27 17.76 42.66 4.09 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
34 35 9.026074 GTTATGAGACTTGCTGAGTATCTTTAC 57.974 37.037 13.79 9.34 44.94 2.01
64 65 5.010012 CCCTTGCAACAATAACTTGAAGAGT 59.990 40.000 0.00 0.00 41.47 3.24
65 66 6.206634 CCCTTGCAACAATAACTTGAAGAGTA 59.793 38.462 0.00 0.00 37.72 2.59
116 120 5.695363 CAGATGCTATGTTGACTTCGATGAT 59.305 40.000 5.16 0.00 0.00 2.45
119 123 5.178061 TGCTATGTTGACTTCGATGATGTT 58.822 37.500 5.16 0.00 0.00 2.71
123 127 4.631131 TGTTGACTTCGATGATGTTGACT 58.369 39.130 5.16 0.00 0.00 3.41
243 248 2.515926 TGACTCATGCTATCTTCCGC 57.484 50.000 0.00 0.00 0.00 5.54
270 275 4.331717 GGTAATGTAATGTTGGACCGACTG 59.668 45.833 13.25 0.00 0.00 3.51
316 322 6.880529 AGGATTTTCACAATTTTATTGCCCTG 59.119 34.615 0.00 0.00 0.00 4.45
424 915 6.832520 TGTTATGAAGCCATGTGTTACAAT 57.167 33.333 0.00 0.00 34.31 2.71
431 922 4.009675 AGCCATGTGTTACAATGGTACTG 58.990 43.478 19.67 0.00 32.79 2.74
435 926 6.094881 GCCATGTGTTACAATGGTACTGTATT 59.905 38.462 19.67 0.00 32.79 1.89
451 942 9.836076 GGTACTGTATTTGTTTCTATTCCAAAC 57.164 33.333 0.00 0.00 34.79 2.93
571 1062 3.569701 ACACGGAGCAAAATGAGTGAATT 59.430 39.130 0.19 0.00 34.16 2.17
790 1282 8.922058 ATGAGCAAGATAACAAGCAAAATTAG 57.078 30.769 0.00 0.00 0.00 1.73
923 1415 1.595093 GCCACTGAACCAAATCGGGG 61.595 60.000 0.00 0.00 40.22 5.73
949 1441 9.909644 GAGTGAAATATCGCCTAAGATAAGTAA 57.090 33.333 0.00 0.00 36.77 2.24
977 1469 9.744468 ATTTTAAAACGGATTAATGGCATAGTC 57.256 29.630 0.00 0.00 0.00 2.59
978 1470 7.867305 TTAAAACGGATTAATGGCATAGTCA 57.133 32.000 0.00 0.00 0.00 3.41
981 1473 4.632153 ACGGATTAATGGCATAGTCAGAC 58.368 43.478 0.00 0.00 0.00 3.51
1038 1530 0.892755 CGTACTACTTCAGCCCACCA 59.107 55.000 0.00 0.00 0.00 4.17
1241 1733 2.750237 GCCGGCCGTCCATTCTTT 60.750 61.111 26.12 0.00 0.00 2.52
1265 1757 3.142162 CCCGCAAGCATGGCATCA 61.142 61.111 0.00 0.00 30.95 3.07
1529 2021 2.697761 CCGGACGTCGACATCCACT 61.698 63.158 28.35 0.00 42.43 4.00
1669 2161 1.216977 CGGGCACGAGGTATTCACA 59.783 57.895 0.00 0.00 44.60 3.58
1686 2178 2.758979 TCACACTCGGGAATAACTCCTC 59.241 50.000 0.00 0.00 44.68 3.71
1834 2329 1.226603 GCGCTACAGGACGTTCGAT 60.227 57.895 0.00 0.00 0.00 3.59
1870 2365 1.067776 CCTCGTTTCGCCTACAACTCT 60.068 52.381 0.00 0.00 0.00 3.24
1897 2392 1.530771 GCATCTGGCAGATCTGGGT 59.469 57.895 26.62 3.35 43.97 4.51
1943 2438 0.736672 GACCTCGAAGACGGCCTTTC 60.737 60.000 0.00 1.08 40.21 2.62
2115 2610 2.611971 GGTTGTACTGGTGCGATGAGAA 60.612 50.000 0.00 0.00 0.00 2.87
2166 2661 4.218635 CCTGGAAGATATCGATTTCGAGGA 59.781 45.833 24.27 0.00 45.26 3.71
2421 2917 1.825474 CTCGCTACTTCTCTTTCCCCA 59.175 52.381 0.00 0.00 0.00 4.96
2488 2984 4.955335 TGAGAGTAATGGAAAGGGGTAGA 58.045 43.478 0.00 0.00 0.00 2.59
2736 3235 6.772233 TGATTTTTGTTCATCCAGTCAAGAGA 59.228 34.615 0.00 0.00 0.00 3.10
2864 3364 4.216257 CGAGATTTTGCTCTTCCCTTTCAA 59.784 41.667 0.00 0.00 32.71 2.69
3148 3692 6.795590 TCCACCCATCTGGAAAATTAAAGTA 58.204 36.000 0.00 0.00 37.39 2.24
3192 3736 8.455903 ACCAGATGAGATTGTACCAAATTATG 57.544 34.615 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.324846 ACTCAGCAAGTCTCATAACCACA 59.675 43.478 0.00 0.00 30.02 4.17
10 11 8.191446 GTGTAAAGATACTCAGCAAGTCTCATA 58.809 37.037 7.20 0.00 39.55 2.15
34 35 3.569701 AGTTATTGTTGCAAGGGTGAGTG 59.430 43.478 0.00 0.00 0.00 3.51
65 66 9.270640 GAATCTGCATCTCAATTGTAGAAGTAT 57.729 33.333 5.13 0.00 38.92 2.12
80 81 4.041815 ACATAGCATCTGGAATCTGCATCT 59.958 41.667 0.00 0.00 38.37 2.90
116 120 7.201794 CGGAATCCACTATTCTACTAGTCAACA 60.202 40.741 0.00 0.00 43.14 3.33
119 123 5.768662 CCGGAATCCACTATTCTACTAGTCA 59.231 44.000 0.00 0.00 43.14 3.41
123 127 4.758674 CGTCCGGAATCCACTATTCTACTA 59.241 45.833 5.23 0.00 43.14 1.82
173 178 7.615757 CCTAAGAGGATGGAAAATAAAACAGGT 59.384 37.037 0.00 0.00 37.67 4.00
175 180 7.122650 TGCCTAAGAGGATGGAAAATAAAACAG 59.877 37.037 0.00 0.00 37.67 3.16
184 189 3.266772 ACATGTGCCTAAGAGGATGGAAA 59.733 43.478 0.00 0.00 37.67 3.13
243 248 4.094294 CGGTCCAACATTACATTACCACAG 59.906 45.833 0.00 0.00 0.00 3.66
326 332 5.007039 CACCACTACAGATGATGCAACATAC 59.993 44.000 9.71 4.15 0.00 2.39
424 915 9.575868 TTTGGAATAGAAACAAATACAGTACCA 57.424 29.630 0.00 0.00 0.00 3.25
435 926 6.037098 CGGTTTGTGTTTGGAATAGAAACAA 58.963 36.000 10.60 0.00 43.18 2.83
451 942 6.987992 TCTAAATATAGGCCTTACGGTTTGTG 59.012 38.462 12.58 4.40 0.00 3.33
531 1022 7.223971 GCTCCGTGTGTAGTTCATATTTGAATA 59.776 37.037 1.79 0.00 43.49 1.75
545 1036 3.067106 ACTCATTTTGCTCCGTGTGTAG 58.933 45.455 0.00 0.00 0.00 2.74
546 1037 2.805671 CACTCATTTTGCTCCGTGTGTA 59.194 45.455 0.00 0.00 0.00 2.90
550 1041 3.837213 ATTCACTCATTTTGCTCCGTG 57.163 42.857 0.00 0.00 0.00 4.94
586 1077 6.482641 AGGCTACATACGGATGTATATAGACG 59.517 42.308 20.64 8.55 46.42 4.18
630 1121 7.272144 ACCCTCCATTTCTAAATACAAGTCT 57.728 36.000 0.00 0.00 0.00 3.24
923 1415 9.909644 TTACTTATCTTAGGCGATATTTCACTC 57.090 33.333 0.00 0.00 0.00 3.51
970 1462 2.496718 GCTACGCGTCTGACTATGC 58.503 57.895 18.63 4.86 0.00 3.14
1033 1525 1.230635 CCGTCTGCTTGAGTTGGTGG 61.231 60.000 0.00 0.00 0.00 4.61
1038 1530 0.249911 GGTGTCCGTCTGCTTGAGTT 60.250 55.000 0.00 0.00 0.00 3.01
1225 1717 0.958382 TGAAAAGAATGGACGGCCGG 60.958 55.000 31.76 11.88 36.79 6.13
1241 1733 1.753848 CATGCTTGCGGGGGATGAA 60.754 57.895 0.07 0.00 35.08 2.57
1330 1822 1.001764 TGCCTCGTCCTCGAAGGTA 60.002 57.895 2.20 0.00 45.61 3.08
1386 1878 4.260194 TCACGTTCGTGATGCCTG 57.740 55.556 21.38 0.00 39.83 4.85
1529 2021 2.507452 CGATGGAGGCCTCATGCA 59.493 61.111 33.29 22.33 43.89 3.96
1834 2329 2.283821 GGAGGGCATGGCACCAAA 60.284 61.111 22.06 0.00 28.43 3.28
1870 2365 2.203112 GCCAGATGCTCGATGCCA 60.203 61.111 4.73 0.00 42.00 4.92
1969 2464 2.663520 CGCGGCAACCACAGTGTA 60.664 61.111 0.00 0.00 0.00 2.90
2010 2505 3.427098 GGCACCAAAGCCGAAATAACTAC 60.427 47.826 0.00 0.00 46.12 2.73
2115 2610 3.499918 CACTTTTTCAACATCTCCGCTCT 59.500 43.478 0.00 0.00 0.00 4.09
2166 2661 3.864921 GCAGTAGTTTGAGTCGTCCCATT 60.865 47.826 0.00 0.00 0.00 3.16
2421 2917 2.638363 GGTAACTGGAAGAACAGGAGGT 59.362 50.000 0.00 0.00 42.75 3.85
2488 2984 9.857957 TTTAATTTTTATTTTATTCGAGCCGGT 57.142 25.926 1.90 0.00 0.00 5.28
2641 3140 5.416952 CACTTCTCTTTTATGGAGGTTGCAT 59.583 40.000 0.00 0.00 31.80 3.96
2696 3195 9.759259 GAACAAAAATCAGAAACCTTTTCAAAG 57.241 29.630 1.72 0.00 35.79 2.77
2697 3196 9.277783 TGAACAAAAATCAGAAACCTTTTCAAA 57.722 25.926 1.72 0.00 0.00 2.69
2712 3211 7.206981 TCTCTTGACTGGATGAACAAAAATC 57.793 36.000 0.00 0.00 0.00 2.17
2794 3294 7.439655 GGCGAGTCAATTGAGAGTTAGAAATAT 59.560 37.037 8.80 0.00 0.00 1.28
2864 3364 0.615331 TGAGGGAATTTGCTCGAGCT 59.385 50.000 35.27 17.76 42.66 4.09
3148 3692 2.817844 GGTCACTCCAATTTTAACGCCT 59.182 45.455 0.00 0.00 35.97 5.52
3192 3736 2.636519 GAAACTGTCGCGTTTTCTTCC 58.363 47.619 5.77 0.00 37.24 3.46
3265 3810 4.806342 ATAATGCGACCGTAATTTGTCC 57.194 40.909 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.