Multiple sequence alignment - TraesCS5A01G521200

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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 TraesCS5A01G521200 chr5A 100.000 4089 0 0 1 4089 681900545 681896457 0.000000e+00 7552.0
1 TraesCS5A01G521200 chr5A 99.291 4090 19 3 1 4089 683629981 683634061 0.000000e+00 7384.0
2 TraesCS5A01G521200 chr5A 79.606 1167 152 58 1481 2627 684647752 684648852 0.000000e+00 758.0
3 TraesCS5A01G521200 chr5A 87.029 663 72 9 3429 4077 602793190 602792528 0.000000e+00 736.0
4 TraesCS5A01G521200 chr5A 89.339 469 46 2 993 1461 684646744 684647208 1.640000e-163 586.0
5 TraesCS5A01G521200 chr5A 94.385 374 20 1 2128 2501 12880104 12880476 1.270000e-159 573.0
6 TraesCS5A01G521200 chr5A 93.706 286 17 1 2216 2501 52524242 52524526 1.050000e-115 427.0
7 TraesCS5A01G521200 chr5A 93.793 145 9 0 2357 2501 296677921 296678065 6.880000e-53 219.0
8 TraesCS5A01G521200 chr5A 94.697 132 7 0 2370 2501 591608041 591608172 5.360000e-49 206.0
9 TraesCS5A01G521200 chr5A 94.624 93 5 0 2128 2220 52509817 52509909 1.180000e-30 145.0
10 TraesCS5A01G521200 chr5A 93.333 60 2 2 2980 3037 684649161 684649220 2.020000e-13 87.9
11 TraesCS5A01G521200 chr4D 89.773 3256 178 68 157 3319 500719636 500716443 0.000000e+00 4024.0
12 TraesCS5A01G521200 chr4D 90.213 470 43 1 992 1461 502013340 502013806 9.720000e-171 610.0
13 TraesCS5A01G521200 chr4D 79.072 927 115 51 1720 2623 502014283 502015153 7.670000e-157 564.0
14 TraesCS5A01G521200 chr4D 82.741 197 29 3 1472 1663 502013854 502014050 1.950000e-38 171.0
15 TraesCS5A01G521200 chr4B 90.381 1102 49 27 776 1855 644682008 644680942 0.000000e+00 1395.0
16 TraesCS5A01G521200 chr4B 91.709 989 68 11 1922 2904 644680909 644679929 0.000000e+00 1360.0
17 TraesCS5A01G521200 chr4B 91.048 458 41 0 992 1449 646112703 646113160 1.610000e-173 619.0
18 TraesCS5A01G521200 chr4B 79.235 915 117 45 1713 2604 646113978 646114842 1.650000e-158 569.0
19 TraesCS5A01G521200 chr4B 86.136 440 24 14 2902 3319 644679816 644679392 1.350000e-119 440.0
20 TraesCS5A01G521200 chr4B 87.143 140 18 0 1524 1663 646113676 646113815 4.230000e-35 159.0
21 TraesCS5A01G521200 chr4B 80.282 142 25 3 8 148 64817923 64818062 2.010000e-18 104.0
22 TraesCS5A01G521200 chr2D 80.182 1756 217 82 999 2720 483632975 483631317 0.000000e+00 1194.0
23 TraesCS5A01G521200 chr2D 80.427 843 115 32 999 1822 527491687 527492498 7.570000e-167 597.0
24 TraesCS5A01G521200 chr2A 79.469 1656 227 79 999 2616 627513548 627511968 0.000000e+00 1070.0
25 TraesCS5A01G521200 chr2A 87.311 662 66 10 3429 4077 452786074 452786730 0.000000e+00 741.0
26 TraesCS5A01G521200 chr2A 81.807 841 107 31 999 1822 672368282 672369093 0.000000e+00 664.0
27 TraesCS5A01G521200 chr2A 79.472 682 91 31 1953 2616 672369090 672369740 4.850000e-119 438.0
28 TraesCS5A01G521200 chr7B 88.279 674 65 9 3429 4089 432494878 432494206 0.000000e+00 795.0
29 TraesCS5A01G521200 chr7B 88.084 663 64 11 3429 4077 449033663 449033002 0.000000e+00 773.0
30 TraesCS5A01G521200 chr7B 87.069 116 14 1 32 147 641595030 641595144 3.320000e-26 130.0
31 TraesCS5A01G521200 chr7B 78.231 147 26 5 3 147 468422136 468422278 5.630000e-14 89.8
32 TraesCS5A01G521200 chr5B 88.351 661 58 11 3431 4077 374450362 374449707 0.000000e+00 776.0
33 TraesCS5A01G521200 chr5B 100.000 28 0 0 120 147 163091169 163091196 7.000000e-03 52.8
34 TraesCS5A01G521200 chr1A 88.253 664 59 14 3429 4077 393013903 393013244 0.000000e+00 776.0
35 TraesCS5A01G521200 chr5D 88.182 660 58 11 3429 4077 19508600 19507950 0.000000e+00 769.0
36 TraesCS5A01G521200 chr5D 100.000 28 0 0 120 147 184041173 184041200 7.000000e-03 52.8
37 TraesCS5A01G521200 chr4A 87.259 675 67 12 3429 4089 194759092 194759761 0.000000e+00 752.0
38 TraesCS5A01G521200 chr2B 83.158 855 93 36 999 1834 568469092 568468270 0.000000e+00 734.0
39 TraesCS5A01G521200 chr2B 81.667 840 107 32 999 1822 624768161 624768969 0.000000e+00 654.0
40 TraesCS5A01G521200 chr7D 94.444 198 10 1 2361 2557 134508080 134508277 1.850000e-78 303.0
41 TraesCS5A01G521200 chr3D 85.345 116 16 1 32 147 352929836 352929722 7.180000e-23 119.0
42 TraesCS5A01G521200 chr3D 85.345 116 16 1 32 147 411870131 411870017 7.180000e-23 119.0
43 TraesCS5A01G521200 chr3D 81.333 150 20 7 1 147 442751349 442751493 9.290000e-22 115.0
44 TraesCS5A01G521200 chr6B 83.761 117 17 2 32 147 668715922 668715807 4.320000e-20 110.0


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 TraesCS5A01G521200 chr5A 681896457 681900545 4088 True 7552.000000 7552 100.000000 1 4089 1 chr5A.!!$R2 4088
1 TraesCS5A01G521200 chr5A 683629981 683634061 4080 False 7384.000000 7384 99.291000 1 4089 1 chr5A.!!$F6 4088
2 TraesCS5A01G521200 chr5A 602792528 602793190 662 True 736.000000 736 87.029000 3429 4077 1 chr5A.!!$R1 648
3 TraesCS5A01G521200 chr5A 684646744 684649220 2476 False 477.300000 758 87.426000 993 3037 3 chr5A.!!$F7 2044
4 TraesCS5A01G521200 chr4D 500716443 500719636 3193 True 4024.000000 4024 89.773000 157 3319 1 chr4D.!!$R1 3162
5 TraesCS5A01G521200 chr4D 502013340 502015153 1813 False 448.333333 610 84.008667 992 2623 3 chr4D.!!$F1 1631
6 TraesCS5A01G521200 chr4B 644679392 644682008 2616 True 1065.000000 1395 89.408667 776 3319 3 chr4B.!!$R1 2543
7 TraesCS5A01G521200 chr4B 646112703 646114842 2139 False 449.000000 619 85.808667 992 2604 3 chr4B.!!$F2 1612
8 TraesCS5A01G521200 chr2D 483631317 483632975 1658 True 1194.000000 1194 80.182000 999 2720 1 chr2D.!!$R1 1721
9 TraesCS5A01G521200 chr2D 527491687 527492498 811 False 597.000000 597 80.427000 999 1822 1 chr2D.!!$F1 823
10 TraesCS5A01G521200 chr2A 627511968 627513548 1580 True 1070.000000 1070 79.469000 999 2616 1 chr2A.!!$R1 1617
11 TraesCS5A01G521200 chr2A 452786074 452786730 656 False 741.000000 741 87.311000 3429 4077 1 chr2A.!!$F1 648
12 TraesCS5A01G521200 chr2A 672368282 672369740 1458 False 551.000000 664 80.639500 999 2616 2 chr2A.!!$F2 1617
13 TraesCS5A01G521200 chr7B 432494206 432494878 672 True 795.000000 795 88.279000 3429 4089 1 chr7B.!!$R1 660
14 TraesCS5A01G521200 chr7B 449033002 449033663 661 True 773.000000 773 88.084000 3429 4077 1 chr7B.!!$R2 648
15 TraesCS5A01G521200 chr5B 374449707 374450362 655 True 776.000000 776 88.351000 3431 4077 1 chr5B.!!$R1 646
16 TraesCS5A01G521200 chr1A 393013244 393013903 659 True 776.000000 776 88.253000 3429 4077 1 chr1A.!!$R1 648
17 TraesCS5A01G521200 chr5D 19507950 19508600 650 True 769.000000 769 88.182000 3429 4077 1 chr5D.!!$R1 648
18 TraesCS5A01G521200 chr4A 194759092 194759761 669 False 752.000000 752 87.259000 3429 4089 1 chr4A.!!$F1 660
19 TraesCS5A01G521200 chr2B 568468270 568469092 822 True 734.000000 734 83.158000 999 1834 1 chr2B.!!$R1 835
20 TraesCS5A01G521200 chr2B 624768161 624768969 808 False 654.000000 654 81.667000 999 1822 1 chr2B.!!$F1 823

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
757 764 2.232941 TGTGGTCGTTGGAAGGATAGAC 59.767 50.0 0.0 0.0 0.0 2.59 F
759 766 2.496070 TGGTCGTTGGAAGGATAGACTG 59.504 50.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 3308 6.599638 CCCAGTGTCTTCCTAAGAATTTTAGG 59.400 42.308 15.07 15.07 42.21 2.69 R
3266 4690 5.564651 CGCCAAACAAAGTAGACCATTGATT 60.565 40.000 3.57 0.00 0.00 2.57 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
118 119 7.870509 TGCTATCAATCTGCTTTTAATGTCT 57.129 32.000 0.00 0.0 0.00 3.41
119 120 7.923888 TGCTATCAATCTGCTTTTAATGTCTC 58.076 34.615 0.00 0.0 0.00 3.36
130 131 8.121305 TGCTTTTAATGTCTCAATTGTGGTAT 57.879 30.769 5.13 0.0 0.00 2.73
584 591 5.537188 TGGTGCGCAATTTCTTCTTTTATT 58.463 33.333 14.00 0.0 0.00 1.40
755 762 2.496070 TCTGTGGTCGTTGGAAGGATAG 59.504 50.000 0.00 0.0 0.00 2.08
756 763 2.496070 CTGTGGTCGTTGGAAGGATAGA 59.504 50.000 0.00 0.0 0.00 1.98
757 764 2.232941 TGTGGTCGTTGGAAGGATAGAC 59.767 50.000 0.00 0.0 0.00 2.59
758 765 2.496470 GTGGTCGTTGGAAGGATAGACT 59.504 50.000 0.00 0.0 0.00 3.24
759 766 2.496070 TGGTCGTTGGAAGGATAGACTG 59.504 50.000 0.00 0.0 0.00 3.51
760 767 2.758979 GGTCGTTGGAAGGATAGACTGA 59.241 50.000 0.00 0.0 0.00 3.41
761 768 3.385111 GGTCGTTGGAAGGATAGACTGAT 59.615 47.826 0.00 0.0 0.00 2.90
762 769 4.583489 GGTCGTTGGAAGGATAGACTGATA 59.417 45.833 0.00 0.0 0.00 2.15
2119 3308 5.871524 TGACAGATATCACACTTCTTTCAGC 59.128 40.000 5.32 0.0 0.00 4.26
3266 4690 3.737032 TTGTTGTGACGATACAGGTGA 57.263 42.857 0.00 0.0 0.00 4.02
3800 5235 9.520515 AAAAGAAAAGATCTGTAGGCTTCAATA 57.479 29.630 0.00 0.0 38.79 1.90
3812 5247 2.554032 GGCTTCAATATGTTGCGGCTAT 59.446 45.455 14.68 0.0 35.26 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 7.798596 AATTGCACAAAAATACCACAATTGA 57.201 28.000 13.59 0.00 35.55 2.57
119 120 9.379811 GTTAATTGCACAAAAATACCACAATTG 57.620 29.630 3.24 3.24 37.00 2.32
130 131 8.539770 TCACAGAAAAGTTAATTGCACAAAAA 57.460 26.923 0.00 0.00 0.00 1.94
755 762 3.553511 CGACATGGCAAACTCTATCAGTC 59.446 47.826 0.00 0.00 32.30 3.51
756 763 3.055819 ACGACATGGCAAACTCTATCAGT 60.056 43.478 0.00 0.00 36.64 3.41
757 764 3.525537 ACGACATGGCAAACTCTATCAG 58.474 45.455 0.00 0.00 0.00 2.90
758 765 3.521560 GACGACATGGCAAACTCTATCA 58.478 45.455 0.00 0.00 0.00 2.15
759 766 2.535984 CGACGACATGGCAAACTCTATC 59.464 50.000 0.00 0.00 0.00 2.08
760 767 2.094182 ACGACGACATGGCAAACTCTAT 60.094 45.455 0.00 0.00 0.00 1.98
761 768 1.271379 ACGACGACATGGCAAACTCTA 59.729 47.619 0.00 0.00 0.00 2.43
762 769 0.033504 ACGACGACATGGCAAACTCT 59.966 50.000 0.00 0.00 0.00 3.24
2119 3308 6.599638 CCCAGTGTCTTCCTAAGAATTTTAGG 59.400 42.308 15.07 15.07 42.21 2.69
3266 4690 5.564651 CGCCAAACAAAGTAGACCATTGATT 60.565 40.000 3.57 0.00 0.00 2.57
3800 5235 4.097892 CCTTCCTTTTAATAGCCGCAACAT 59.902 41.667 0.00 0.00 0.00 2.71
3812 5247 7.883311 AGTCGAGAATCAAATCCTTCCTTTTAA 59.117 33.333 0.00 0.00 33.17 1.52


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

AutoCloner maintained by Alex Coulton.