Multiple sequence alignment - TraesCS2D01G309600

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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 TraesCS2D01G309600 chr2D 100.000 3891 0 0 1 3891 397128146 397132036 0.000000e+00 7186.0
1 TraesCS2D01G309600 chr5D 94.039 3657 148 23 283 3891 16461619 16457985 0.000000e+00 5481.0
2 TraesCS2D01G309600 chr5D 93.410 3384 153 18 557 3885 29769464 29766096 0.000000e+00 4950.0
3 TraesCS2D01G309600 chr5D 91.049 1955 97 29 1974 3887 363992774 363990857 0.000000e+00 2569.0
4 TraesCS2D01G309600 chr5D 90.668 868 42 17 3053 3885 140952538 140951675 0.000000e+00 1118.0
5 TraesCS2D01G309600 chr4A 92.820 3830 192 31 1 3780 24486288 24490084 0.000000e+00 5472.0
6 TraesCS2D01G309600 chr4A 93.796 3095 158 14 1 3090 694214047 694217112 0.000000e+00 4621.0
7 TraesCS2D01G309600 chr4A 89.020 592 51 8 3304 3882 694217272 694217862 0.000000e+00 721.0
8 TraesCS2D01G309600 chr7D 95.638 3278 101 11 1 3255 501761819 501765077 0.000000e+00 5223.0
9 TraesCS2D01G309600 chr4D 95.014 3329 124 12 458 3746 222625566 222622240 0.000000e+00 5190.0
10 TraesCS2D01G309600 chr4D 95.984 3038 90 10 1 3006 261234403 261231366 0.000000e+00 4905.0
11 TraesCS2D01G309600 chr4D 95.511 891 35 3 3002 3891 261223054 261222168 0.000000e+00 1419.0
12 TraesCS2D01G309600 chr4D 89.376 753 54 5 3162 3889 239784800 239784049 0.000000e+00 924.0
13 TraesCS2D01G309600 chr4D 88.571 700 37 12 3227 3885 125802883 125802186 0.000000e+00 809.0
14 TraesCS2D01G309600 chr4D 93.269 104 7 0 3782 3885 125903925 125903822 1.870000e-33 154.0
15 TraesCS2D01G309600 chr3D 94.534 3348 154 11 458 3778 420356489 420359834 0.000000e+00 5142.0
16 TraesCS2D01G309600 chr3D 94.588 1164 58 3 2587 3746 571735992 571734830 0.000000e+00 1796.0
17 TraesCS2D01G309600 chr1D 94.968 3279 116 20 1 3258 463795972 463792722 0.000000e+00 5096.0
18 TraesCS2D01G309600 chr1D 94.798 2249 86 8 1645 3863 417112266 417114513 0.000000e+00 3476.0
19 TraesCS2D01G309600 chr1D 94.189 912 43 5 2869 3779 336729685 336728783 0.000000e+00 1382.0
20 TraesCS2D01G309600 chr1D 93.458 107 5 2 3783 3887 463792198 463792092 1.450000e-34 158.0
21 TraesCS2D01G309600 chr6D 94.544 3244 129 20 557 3779 297173273 297170057 0.000000e+00 4966.0
22 TraesCS2D01G309600 chr6D 93.933 3033 112 26 771 3779 446365950 446362966 0.000000e+00 4516.0
23 TraesCS2D01G309600 chr6D 92.478 811 47 4 3077 3885 46519952 46519154 0.000000e+00 1147.0
24 TraesCS2D01G309600 chr6D 88.889 117 7 4 3775 3887 297170027 297169913 5.240000e-29 139.0
25 TraesCS2D01G309600 chr6D 89.888 89 7 1 3775 3863 446362936 446362850 3.180000e-21 113.0
26 TraesCS2D01G309600 chr6D 97.059 34 1 0 3852 3885 297169968 297169935 1.510000e-04 58.4
27 TraesCS2D01G309600 chr6D 94.737 38 0 2 3852 3887 446362877 446362840 1.510000e-04 58.4
28 TraesCS2D01G309600 chr2B 94.578 3172 129 18 1 3150 738347355 738344205 0.000000e+00 4865.0
29 TraesCS2D01G309600 chr2B 93.316 3157 177 15 458 3585 123797091 123793940 0.000000e+00 4630.0
30 TraesCS2D01G309600 chr7A 91.993 3447 202 23 396 3784 220997394 221000824 0.000000e+00 4769.0
31 TraesCS2D01G309600 chr1B 95.521 2858 109 4 1 2840 600340265 600337409 0.000000e+00 4551.0
32 TraesCS2D01G309600 chrUn 95.392 2843 106 14 1 2840 294409494 294406674 0.000000e+00 4501.0
33 TraesCS2D01G309600 chrUn 90.772 531 35 7 3224 3754 38473552 38474068 0.000000e+00 697.0
34 TraesCS2D01G309600 chrUn 89.302 430 40 4 3327 3754 294406286 294405861 5.720000e-148 534.0
35 TraesCS2D01G309600 chrUn 89.019 428 45 2 3327 3754 34512074 34512499 2.660000e-146 529.0
36 TraesCS2D01G309600 chrUn 89.019 428 45 2 3327 3754 301821898 301821473 2.660000e-146 529.0
37 TraesCS2D01G309600 chrUn 89.019 428 45 2 3327 3754 315136723 315136298 2.660000e-146 529.0
38 TraesCS2D01G309600 chrUn 89.019 428 45 2 3327 3754 322611440 322611865 2.660000e-146 529.0
39 TraesCS2D01G309600 chrUn 89.019 428 45 2 3327 3754 338930162 338930587 2.660000e-146 529.0
40 TraesCS2D01G309600 chrUn 95.439 285 11 2 2869 3151 312613234 312612950 1.650000e-123 453.0
41 TraesCS2D01G309600 chrUn 94.035 285 15 2 2869 3151 38473255 38473539 7.720000e-117 431.0
42 TraesCS2D01G309600 chrUn 94.583 240 11 2 3224 3463 312612937 312612700 1.710000e-98 370.0
43 TraesCS2D01G309600 chrUn 89.630 270 20 5 3327 3593 281295904 281295640 1.730000e-88 337.0
44 TraesCS2D01G309600 chrUn 97.561 82 1 1 3071 3151 34511915 34511996 5.240000e-29 139.0
45 TraesCS2D01G309600 chrUn 98.734 79 0 1 3074 3151 301822054 301821976 5.240000e-29 139.0
46 TraesCS2D01G309600 chrUn 94.366 71 3 1 3223 3293 236932470 236932539 1.480000e-19 108.0
47 TraesCS2D01G309600 chrUn 94.366 71 3 1 3223 3293 281295970 281295901 1.480000e-19 108.0
48 TraesCS2D01G309600 chrUn 78.947 114 9 9 2869 2978 294406675 294406573 3.250000e-06 63.9
49 TraesCS2D01G309600 chr5A 91.752 3213 203 19 396 3549 384027517 384030726 0.000000e+00 4409.0
50 TraesCS2D01G309600 chr6B 91.945 2632 157 35 560 3151 719841328 719843944 0.000000e+00 3635.0
51 TraesCS2D01G309600 chr2A 94.435 1761 84 8 2006 3761 259697662 259699413 0.000000e+00 2697.0
52 TraesCS2D01G309600 chr4B 91.518 672 38 9 3224 3882 200943401 200944066 0.000000e+00 907.0
53 TraesCS2D01G309600 chr3B 91.259 675 43 10 3224 3885 320671699 320671028 0.000000e+00 905.0
54 TraesCS2D01G309600 chr6A 93.431 548 33 3 3223 3768 436399494 436400040 0.000000e+00 809.0
55 TraesCS2D01G309600 chr6A 96.842 285 7 2 2869 3151 136661695 136661979 3.520000e-130 475.0
56 TraesCS2D01G309600 chr1A 93.419 547 34 2 3224 3770 340071843 340072387 0.000000e+00 809.0
57 TraesCS2D01G309600 chr1A 91.362 602 31 5 3224 3806 50632094 50631495 0.000000e+00 804.0
58 TraesCS2D01G309600 chr1A 92.754 552 35 3 3224 3772 539842401 539841852 0.000000e+00 793.0
59 TraesCS2D01G309600 chr1A 95.789 285 10 2 2869 3151 7956517 7956801 3.540000e-125 459.0


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 TraesCS2D01G309600 chr2D 397128146 397132036 3890 False 7186.000000 7186 100.000000 1 3891 1 chr2D.!!$F1 3890
1 TraesCS2D01G309600 chr5D 16457985 16461619 3634 True 5481.000000 5481 94.039000 283 3891 1 chr5D.!!$R1 3608
2 TraesCS2D01G309600 chr5D 29766096 29769464 3368 True 4950.000000 4950 93.410000 557 3885 1 chr5D.!!$R2 3328
3 TraesCS2D01G309600 chr5D 363990857 363992774 1917 True 2569.000000 2569 91.049000 1974 3887 1 chr5D.!!$R4 1913
4 TraesCS2D01G309600 chr5D 140951675 140952538 863 True 1118.000000 1118 90.668000 3053 3885 1 chr5D.!!$R3 832
5 TraesCS2D01G309600 chr4A 24486288 24490084 3796 False 5472.000000 5472 92.820000 1 3780 1 chr4A.!!$F1 3779
6 TraesCS2D01G309600 chr4A 694214047 694217862 3815 False 2671.000000 4621 91.408000 1 3882 2 chr4A.!!$F2 3881
7 TraesCS2D01G309600 chr7D 501761819 501765077 3258 False 5223.000000 5223 95.638000 1 3255 1 chr7D.!!$F1 3254
8 TraesCS2D01G309600 chr4D 222622240 222625566 3326 True 5190.000000 5190 95.014000 458 3746 1 chr4D.!!$R3 3288
9 TraesCS2D01G309600 chr4D 261231366 261234403 3037 True 4905.000000 4905 95.984000 1 3006 1 chr4D.!!$R6 3005
10 TraesCS2D01G309600 chr4D 261222168 261223054 886 True 1419.000000 1419 95.511000 3002 3891 1 chr4D.!!$R5 889
11 TraesCS2D01G309600 chr4D 239784049 239784800 751 True 924.000000 924 89.376000 3162 3889 1 chr4D.!!$R4 727
12 TraesCS2D01G309600 chr4D 125802186 125802883 697 True 809.000000 809 88.571000 3227 3885 1 chr4D.!!$R1 658
13 TraesCS2D01G309600 chr3D 420356489 420359834 3345 False 5142.000000 5142 94.534000 458 3778 1 chr3D.!!$F1 3320
14 TraesCS2D01G309600 chr3D 571734830 571735992 1162 True 1796.000000 1796 94.588000 2587 3746 1 chr3D.!!$R1 1159
15 TraesCS2D01G309600 chr1D 417112266 417114513 2247 False 3476.000000 3476 94.798000 1645 3863 1 chr1D.!!$F1 2218
16 TraesCS2D01G309600 chr1D 463792092 463795972 3880 True 2627.000000 5096 94.213000 1 3887 2 chr1D.!!$R2 3886
17 TraesCS2D01G309600 chr1D 336728783 336729685 902 True 1382.000000 1382 94.189000 2869 3779 1 chr1D.!!$R1 910
18 TraesCS2D01G309600 chr6D 297169913 297173273 3360 True 1721.133333 4966 93.497333 557 3887 3 chr6D.!!$R2 3330
19 TraesCS2D01G309600 chr6D 446362840 446365950 3110 True 1562.466667 4516 92.852667 771 3887 3 chr6D.!!$R3 3116
20 TraesCS2D01G309600 chr6D 46519154 46519952 798 True 1147.000000 1147 92.478000 3077 3885 1 chr6D.!!$R1 808
21 TraesCS2D01G309600 chr2B 738344205 738347355 3150 True 4865.000000 4865 94.578000 1 3150 1 chr2B.!!$R2 3149
22 TraesCS2D01G309600 chr2B 123793940 123797091 3151 True 4630.000000 4630 93.316000 458 3585 1 chr2B.!!$R1 3127
23 TraesCS2D01G309600 chr7A 220997394 221000824 3430 False 4769.000000 4769 91.993000 396 3784 1 chr7A.!!$F1 3388
24 TraesCS2D01G309600 chr1B 600337409 600340265 2856 True 4551.000000 4551 95.521000 1 2840 1 chr1B.!!$R1 2839
25 TraesCS2D01G309600 chrUn 294405861 294409494 3633 True 1699.633333 4501 87.880333 1 3754 3 chrUn.!!$R3 3753
26 TraesCS2D01G309600 chrUn 38473255 38474068 813 False 564.000000 697 92.403500 2869 3754 2 chrUn.!!$F5 885
27 TraesCS2D01G309600 chrUn 312612700 312613234 534 True 411.500000 453 95.011000 2869 3463 2 chrUn.!!$R5 594
28 TraesCS2D01G309600 chrUn 34511915 34512499 584 False 334.000000 529 93.290000 3071 3754 2 chrUn.!!$F4 683
29 TraesCS2D01G309600 chrUn 301821473 301822054 581 True 334.000000 529 93.876500 3074 3754 2 chrUn.!!$R4 680
30 TraesCS2D01G309600 chr5A 384027517 384030726 3209 False 4409.000000 4409 91.752000 396 3549 1 chr5A.!!$F1 3153
31 TraesCS2D01G309600 chr6B 719841328 719843944 2616 False 3635.000000 3635 91.945000 560 3151 1 chr6B.!!$F1 2591
32 TraesCS2D01G309600 chr2A 259697662 259699413 1751 False 2697.000000 2697 94.435000 2006 3761 1 chr2A.!!$F1 1755
33 TraesCS2D01G309600 chr4B 200943401 200944066 665 False 907.000000 907 91.518000 3224 3882 1 chr4B.!!$F1 658
34 TraesCS2D01G309600 chr3B 320671028 320671699 671 True 905.000000 905 91.259000 3224 3885 1 chr3B.!!$R1 661
35 TraesCS2D01G309600 chr6A 436399494 436400040 546 False 809.000000 809 93.431000 3223 3768 1 chr6A.!!$F2 545
36 TraesCS2D01G309600 chr1A 340071843 340072387 544 False 809.000000 809 93.419000 3224 3770 1 chr1A.!!$F2 546
37 TraesCS2D01G309600 chr1A 50631495 50632094 599 True 804.000000 804 91.362000 3224 3806 1 chr1A.!!$R1 582
38 TraesCS2D01G309600 chr1A 539841852 539842401 549 True 793.000000 793 92.754000 3224 3772 1 chr1A.!!$R2 548

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
732 795 1.269448 CCGTTGGTATGCAACTTGCTT 59.731 47.619 14.78 10.86 45.31 3.91 F
1475 1566 1.004044 CTGGAACCTGATGAACCTGCT 59.996 52.381 0.00 0.00 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 2585 0.957395 AGAGCTTGCCATTCACCGTG 60.957 55.000 0.0 0.0 0.0 4.94 R
3289 3690 2.825205 CAAACCAAACCAAGCAAGAGG 58.175 47.619 0.0 0.0 0.0 3.69 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
287 288 8.681486 TGCTTCACATATATAGTTTGCTTCAT 57.319 30.769 0.00 0.00 0.00 2.57
590 635 3.511146 TGATGGTCCAAATGCTTTCCTTC 59.489 43.478 0.00 0.00 0.00 3.46
732 795 1.269448 CCGTTGGTATGCAACTTGCTT 59.731 47.619 14.78 10.86 45.31 3.91
1062 1126 4.743151 GGTGCAATAACGTCGATGATTAGA 59.257 41.667 12.58 0.00 0.00 2.10
1131 1195 7.437713 AGGTAGTGGAGTTATCAATGATGAA 57.562 36.000 5.91 0.00 39.49 2.57
1247 1311 1.708551 CTTGGAGGGTTGGGGTTCTTA 59.291 52.381 0.00 0.00 0.00 2.10
1475 1566 1.004044 CTGGAACCTGATGAACCTGCT 59.996 52.381 0.00 0.00 0.00 4.24
1527 1618 1.439353 GGCGACTACGACGGACCATA 61.439 60.000 0.00 0.00 42.66 2.74
1544 1635 1.667724 CATAAGGAAAGTCTGCTGCGG 59.332 52.381 0.95 0.95 0.00 5.69
1629 1720 2.827051 CGCATGGATGGAAGTGGCG 61.827 63.158 0.00 0.00 36.93 5.69
1634 1725 2.401766 GGATGGAAGTGGCGCTGTG 61.402 63.158 7.64 0.00 0.00 3.66
1717 1808 2.094675 CCCTGTTGCACCTTCTATTGG 58.905 52.381 0.00 0.00 0.00 3.16
2057 2255 1.373570 CAAGAAGCCATCTTCCGGTC 58.626 55.000 0.00 0.00 45.42 4.79
2123 2322 4.762251 AGAACTACATTGGGAAAGTTGCTC 59.238 41.667 0.00 0.00 32.51 4.26
2189 2388 7.992608 TGTTACACCTATGCATGATCACTAATT 59.007 33.333 10.16 0.00 0.00 1.40
2302 2502 6.629128 TGCAGAAAAATTCAAAGAACAGACA 58.371 32.000 0.00 0.00 0.00 3.41
2381 2584 1.607801 CTCCGGTGCCAGATCTGACA 61.608 60.000 24.62 16.55 0.00 3.58
2382 2585 1.448540 CCGGTGCCAGATCTGACAC 60.449 63.158 28.30 28.30 42.18 3.67
2425 2628 1.913419 GGAGATGTGGTCTACCCCAAA 59.087 52.381 0.00 0.00 37.29 3.28
2841 3046 0.178967 TCCATGCTTTGTCCAGCCAA 60.179 50.000 0.00 0.00 39.25 4.52
3289 3690 3.258228 CCTTTGTGTGTTGGTTTGGTTC 58.742 45.455 0.00 0.00 0.00 3.62
3373 3775 4.020396 CCTCCATATGCTAGCTTGAGATGT 60.020 45.833 17.23 0.00 0.00 3.06
3528 3934 0.751643 AACTCCGGCAAAGCAACTGT 60.752 50.000 0.00 0.00 0.00 3.55
3613 4019 3.428532 AGTGATGCAAGAAGAATTGGCT 58.571 40.909 0.00 0.00 0.00 4.75
3642 4048 1.399791 GATGAAGGCGAAAGAAGCTGG 59.600 52.381 0.00 0.00 34.52 4.85
3748 4154 5.755409 TTGGAGCTAAGGTAGTTTGATGA 57.245 39.130 0.00 0.00 0.00 2.92
3780 4248 7.378181 AGTTTGTCTTTGAACATGTGAACTTT 58.622 30.769 0.00 0.00 27.39 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 186 4.505039 GGTTGTGGTACCAGAGACAAGAAT 60.505 45.833 16.93 0.00 38.12 2.40
299 300 5.349738 ACCCTAACCCTATGTATGCTAGA 57.650 43.478 0.00 0.00 0.00 2.43
732 795 6.822442 TGAAACTGACAGTATAACCACAAGA 58.178 36.000 8.91 0.00 0.00 3.02
1062 1126 9.965824 CTACCTTCTTGTACATCATTTGTTTTT 57.034 29.630 0.00 0.00 39.87 1.94
1247 1311 5.195940 AGCACAAGGAAACACATAGCATAT 58.804 37.500 0.00 0.00 0.00 1.78
1475 1566 2.820178 TGCCTTGTGACTCTATCAGGA 58.180 47.619 0.00 0.00 38.28 3.86
1527 1618 0.326264 ATCCGCAGCAGACTTTCCTT 59.674 50.000 0.00 0.00 0.00 3.36
1544 1635 1.028905 CCGAGGTCTCAGAGTCCATC 58.971 60.000 15.27 9.01 0.00 3.51
1629 1720 1.208052 TCCTTCATCTAGGCACACAGC 59.792 52.381 0.00 0.00 44.65 4.40
1634 1725 2.769095 AGTTCCTCCTTCATCTAGGCAC 59.231 50.000 0.00 0.00 35.15 5.01
1717 1808 4.707030 TCATTGATGACAACATTCCTGC 57.293 40.909 0.00 0.00 38.90 4.85
2057 2255 5.344743 TGTATAGCTTGAAGTGAGGAAGG 57.655 43.478 0.00 0.00 0.00 3.46
2189 2388 4.020543 ACAGCAAACAAGGTAGGAACAAA 58.979 39.130 0.00 0.00 0.00 2.83
2302 2502 8.954350 CAAAATACTTCTTCTTGATCTGATGGT 58.046 33.333 0.00 0.00 0.00 3.55
2381 2584 1.228245 AGCTTGCCATTCACCGTGT 60.228 52.632 0.00 0.00 0.00 4.49
2382 2585 0.957395 AGAGCTTGCCATTCACCGTG 60.957 55.000 0.00 0.00 0.00 4.94
2425 2628 3.004752 AGCAGAGACAAACCTTGTGTT 57.995 42.857 0.00 0.00 45.52 3.32
2579 2783 3.762407 ATGTGTGTTGTGTAGTGCCTA 57.238 42.857 0.00 0.00 0.00 3.93
2841 3046 8.519799 TGAGGTTTCTAGACAAAAGTTTGAAT 57.480 30.769 10.66 1.60 40.55 2.57
3289 3690 2.825205 CAAACCAAACCAAGCAAGAGG 58.175 47.619 0.00 0.00 0.00 3.69
3491 3897 4.382147 GGAGTTGTTCCTAGATGACTGGAC 60.382 50.000 0.00 0.00 43.16 4.02
3528 3934 4.350368 TGAACATGAGTAGCCACTTCAA 57.650 40.909 0.00 0.00 34.21 2.69
3613 4019 2.112380 TCGCCTTCATCTTGATTGCA 57.888 45.000 0.00 0.00 0.00 4.08
3654 4060 0.319297 CAGCAGCCAAAGTTCCTTGC 60.319 55.000 0.00 0.00 0.00 4.01
3748 4154 5.957842 TGTTCAAAGACAAACTTCACAGT 57.042 34.783 0.00 0.00 37.93 3.55
3780 4248 3.141398 AGTTCACGACCTACTACGACAA 58.859 45.455 0.00 0.00 0.00 3.18
3833 4331 2.158623 TCACAAGTGCTCCCAGTTTCAT 60.159 45.455 0.00 0.00 32.35 2.57


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

AutoCloner maintained by Alex Coulton.