Multiple sequence alignment - TraesCS4A01G035100

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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 TraesCS4A01G035100 chr4A 100.000 3599 0 0 1 3599 26650136 26646538 0.000000e+00 6610.0
1 TraesCS4A01G035100 chr4A 99.878 3283 4 0 317 3599 26634521 26631239 0.000000e+00 6041.0
2 TraesCS4A01G035100 chr4A 99.963 2732 1 0 317 3048 26637263 26634532 0.000000e+00 5040.0
3 TraesCS4A01G035100 chr4A 82.802 721 91 13 1670 2381 29380107 29380803 6.600000e-172 614.0
4 TraesCS4A01G035100 chr4A 98.366 306 5 0 1 306 26637637 26637332 4.090000e-149 538.0
5 TraesCS4A01G035100 chr4A 94.915 118 6 0 1 118 85249897 85250014 6.140000e-43 185.0
6 TraesCS4A01G035100 chr4A 86.286 175 13 5 143 306 700327668 700327842 2.850000e-41 180.0
7 TraesCS4A01G035100 chr4A 92.623 122 9 0 1 122 88712455 88712576 3.690000e-40 176.0
8 TraesCS4A01G035100 chr4A 88.276 145 12 1 1 140 501956355 501956499 6.180000e-38 169.0
9 TraesCS4A01G035100 chr4A 86.525 141 19 0 1237 1377 29302933 29303073 4.810000e-34 156.0
10 TraesCS4A01G035100 chr4A 91.071 112 7 2 141 249 700327831 700327942 8.050000e-32 148.0
11 TraesCS4A01G035100 chr4A 85.714 70 4 4 232 295 700327597 700327666 6.450000e-08 69.4
12 TraesCS4A01G035100 chr4A 93.182 44 3 0 258 301 26637844 26637801 8.340000e-07 65.8
13 TraesCS4A01G035100 chr4B 88.288 2109 117 43 611 2642 546578774 546580829 0.000000e+00 2407.0
14 TraesCS4A01G035100 chr4B 93.057 893 38 7 1762 2642 546602190 546603070 0.000000e+00 1284.0
15 TraesCS4A01G035100 chr4B 87.911 943 100 12 1669 2602 546673792 546674729 0.000000e+00 1098.0
16 TraesCS4A01G035100 chr4B 84.623 1008 59 24 611 1560 546600948 546601917 0.000000e+00 915.0
17 TraesCS4A01G035100 chr4B 79.824 1135 165 45 1514 2599 546023763 546024882 0.000000e+00 769.0
18 TraesCS4A01G035100 chr4B 89.333 150 15 1 1 150 634990524 634990672 1.710000e-43 187.0
19 TraesCS4A01G035100 chr4B 88.235 153 18 0 1237 1389 546023506 546023658 2.210000e-42 183.0
20 TraesCS4A01G035100 chr4B 88.281 128 15 0 1237 1364 545179249 545179376 1.730000e-33 154.0
21 TraesCS4A01G035100 chr4B 89.720 107 8 3 2 107 28297255 28297151 2.250000e-27 134.0
22 TraesCS4A01G035100 chr4B 87.671 73 9 0 45 117 102526882 102526810 6.400000e-13 86.1
23 TraesCS4A01G035100 chr4D 93.305 1165 61 10 1490 2642 441058069 441059228 0.000000e+00 1703.0
24 TraesCS4A01G035100 chr4D 85.987 892 59 19 611 1453 441057198 441058072 0.000000e+00 894.0
25 TraesCS4A01G035100 chr4D 81.498 1108 144 25 1509 2602 441064260 441065320 0.000000e+00 854.0
26 TraesCS4A01G035100 chr4D 79.682 1132 160 34 1514 2599 440282832 440283939 0.000000e+00 752.0
27 TraesCS4A01G035100 chr4D 95.522 201 9 0 3399 3599 110021784 110021584 4.480000e-84 322.0
28 TraesCS4A01G035100 chr4D 81.671 371 49 8 1694 2062 440038472 440038825 1.260000e-74 291.0
29 TraesCS4A01G035100 chr4D 86.777 121 16 0 1237 1357 440044922 440045042 6.270000e-28 135.0
30 TraesCS4A01G035100 chrUn 88.136 944 97 9 1669 2602 286309745 286308807 0.000000e+00 1109.0
31 TraesCS4A01G035100 chrUn 88.136 944 97 9 1669 2602 286316028 286315090 0.000000e+00 1109.0
32 TraesCS4A01G035100 chrUn 88.136 944 97 9 1669 2602 295780527 295781465 0.000000e+00 1109.0
33 TraesCS4A01G035100 chrUn 95.522 201 9 0 3399 3599 34436571 34436371 4.480000e-84 322.0
34 TraesCS4A01G035100 chrUn 93.182 44 3 0 258 301 215332719 215332762 8.340000e-07 65.8
35 TraesCS4A01G035100 chrUn 93.182 44 3 0 258 301 396718807 396718764 8.340000e-07 65.8
36 TraesCS4A01G035100 chrUn 92.857 42 2 1 1 41 86832813 86832772 3.880000e-05 60.2
37 TraesCS4A01G035100 chr6B 95.204 563 25 2 2843 3405 77801438 77801998 0.000000e+00 889.0
38 TraesCS4A01G035100 chr6B 90.083 121 12 0 2 122 504606965 504606845 1.340000e-34 158.0
39 TraesCS4A01G035100 chr6B 94.737 95 4 1 2763 2857 77801288 77801381 2.900000e-31 147.0
40 TraesCS4A01G035100 chr6B 85.926 135 18 1 2 136 262047788 262047921 3.750000e-30 143.0
41 TraesCS4A01G035100 chr3D 94.681 564 29 1 2843 3405 508063629 508063066 0.000000e+00 874.0
42 TraesCS4A01G035100 chr3D 95.789 95 3 1 2763 2857 508063767 508063674 6.220000e-33 152.0
43 TraesCS4A01G035100 chr3D 88.043 92 11 0 30 121 427056892 427056801 3.800000e-20 110.0
44 TraesCS4A01G035100 chr7A 94.326 564 31 1 2843 3405 174925709 174925146 0.000000e+00 863.0
45 TraesCS4A01G035100 chr7A 94.737 95 4 1 2763 2857 642992032 642992125 2.900000e-31 147.0
46 TraesCS4A01G035100 chr7A 93.684 95 5 1 2763 2857 174925860 174925767 1.350000e-29 141.0
47 TraesCS4A01G035100 chr5D 94.014 568 32 1 2843 3408 428472083 428471516 0.000000e+00 859.0
48 TraesCS4A01G035100 chr5D 95.522 201 9 0 3399 3599 57118150 57117950 4.480000e-84 322.0
49 TraesCS4A01G035100 chr5D 95.522 201 9 0 3399 3599 205117446 205117246 4.480000e-84 322.0
50 TraesCS4A01G035100 chr5D 88.024 167 10 6 141 301 527892500 527892338 4.740000e-44 189.0
51 TraesCS4A01G035100 chr5D 88.636 132 15 0 10 141 549895817 549895686 1.030000e-35 161.0
52 TraesCS4A01G035100 chr5D 90.265 113 11 0 10 122 41465836 41465948 8.050000e-32 148.0
53 TraesCS4A01G035100 chr1D 93.805 565 32 2 2843 3405 363731018 363731581 0.000000e+00 846.0
54 TraesCS4A01G035100 chr1D 86.175 217 26 4 359 575 374417485 374417273 7.770000e-57 231.0
55 TraesCS4A01G035100 chr1D 85.294 102 15 0 7 108 324488433 324488332 4.910000e-19 106.0
56 TraesCS4A01G035100 chr1D 83.898 118 7 2 1 118 51977266 51977371 6.360000e-18 102.0
57 TraesCS4A01G035100 chr1D 89.552 67 7 0 2768 2834 487978086 487978020 6.400000e-13 86.1
58 TraesCS4A01G035100 chr1D 100.000 29 0 0 143 171 374440838 374440810 2.000000e-03 54.7
59 TraesCS4A01G035100 chr1A 93.783 563 35 0 2843 3405 13017631 13018193 0.000000e+00 846.0
60 TraesCS4A01G035100 chr1A 91.429 140 12 0 1 140 257966440 257966579 3.670000e-45 193.0
61 TraesCS4A01G035100 chr1A 93.137 102 5 2 2760 2860 551911778 551911878 8.050000e-32 148.0
62 TraesCS4A01G035100 chr1A 92.857 98 7 0 1 98 589191007 589190910 3.750000e-30 143.0
63 TraesCS4A01G035100 chr1A 84.298 121 9 3 1 121 592649912 592649802 3.800000e-20 110.0
64 TraesCS4A01G035100 chr1A 81.890 127 17 2 19 140 300394529 300394404 6.360000e-18 102.0
65 TraesCS4A01G035100 chr2B 93.783 563 34 1 2843 3405 762114145 762114706 0.000000e+00 845.0
66 TraesCS4A01G035100 chr2B 95.789 95 3 1 2763 2857 212576089 212575996 6.220000e-33 152.0
67 TraesCS4A01G035100 chr2B 94.898 98 1 3 2763 2857 762113994 762114090 2.240000e-32 150.0
68 TraesCS4A01G035100 chr7D 93.628 565 33 2 2843 3405 150755000 150755563 0.000000e+00 841.0
69 TraesCS4A01G035100 chr7D 95.522 201 9 0 3399 3599 255781818 255782018 4.480000e-84 322.0
70 TraesCS4A01G035100 chr7D 95.522 201 9 0 3399 3599 420369811 420369611 4.480000e-84 322.0
71 TraesCS4A01G035100 chr5B 81.350 563 80 14 3040 3590 697177082 697177631 5.520000e-118 435.0
72 TraesCS4A01G035100 chr5B 90.780 141 11 2 2 141 302838206 302838067 1.710000e-43 187.0
73 TraesCS4A01G035100 chr5B 87.603 121 13 2 2 122 423626076 423626194 4.850000e-29 139.0
74 TraesCS4A01G035100 chr7B 96.020 201 8 0 3399 3599 609008870 609008670 9.630000e-86 327.0
75 TraesCS4A01G035100 chr7B 91.453 117 10 0 2 118 677748611 677748727 1.030000e-35 161.0
76 TraesCS4A01G035100 chr7B 88.636 132 15 0 10 141 692411644 692411513 1.030000e-35 161.0
77 TraesCS4A01G035100 chr7B 94.681 94 4 1 2764 2857 695708771 695708863 1.040000e-30 145.0
78 TraesCS4A01G035100 chr7B 95.652 69 3 0 2766 2834 740001331 740001399 1.060000e-20 111.0
79 TraesCS4A01G035100 chr2A 94.286 140 8 0 1 140 533527622 533527761 7.830000e-52 215.0
80 TraesCS4A01G035100 chr2A 91.589 107 6 2 141 244 8167101 8167207 1.040000e-30 145.0
81 TraesCS4A01G035100 chr2A 95.238 42 2 0 265 306 8167071 8167112 2.320000e-07 67.6
82 TraesCS4A01G035100 chr5A 95.041 121 6 0 1 121 136980907 136980787 1.320000e-44 191.0
83 TraesCS4A01G035100 chr5A 89.041 146 11 1 1 141 447364626 447364771 3.690000e-40 176.0
84 TraesCS4A01G035100 chr2D 87.209 172 14 5 143 306 427587334 427587505 4.740000e-44 189.0
85 TraesCS4A01G035100 chr2D 85.714 70 4 4 232 295 427587263 427587332 6.450000e-08 69.4
86 TraesCS4A01G035100 chr6A 94.737 114 6 0 3 116 109491032 109491145 1.030000e-40 178.0
87 TraesCS4A01G035100 chr6A 86.842 152 16 1 1 148 272976636 272976485 2.220000e-37 167.0
88 TraesCS4A01G035100 chr6D 86.525 141 13 2 1 141 428619433 428619567 2.240000e-32 150.0
89 TraesCS4A01G035100 chr6D 83.871 93 15 0 7 99 24877061 24877153 4.950000e-14 89.8
90 TraesCS4A01G035100 chr6D 86.842 76 8 2 1907 1981 277850653 277850727 2.300000e-12 84.2
91 TraesCS4A01G035100 chr6D 88.732 71 1 1 2315 2385 395396922 395396985 2.980000e-11 80.5
92 TraesCS4A01G035100 chr6D 97.222 36 0 1 87 122 447066515 447066549 3.880000e-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 TraesCS4A01G035100 chr4A 26646538 26650136 3598 True 6610.0 6610 100.00000 1 3599 1 chr4A.!!$R1 3598
1 TraesCS4A01G035100 chr4A 26631239 26637844 6605 True 2921.2 6041 97.84725 1 3599 4 chr4A.!!$R2 3598
2 TraesCS4A01G035100 chr4A 29380107 29380803 696 False 614.0 614 82.80200 1670 2381 1 chr4A.!!$F2 711
3 TraesCS4A01G035100 chr4B 546578774 546580829 2055 False 2407.0 2407 88.28800 611 2642 1 chr4B.!!$F2 2031
4 TraesCS4A01G035100 chr4B 546600948 546603070 2122 False 1099.5 1284 88.84000 611 2642 2 chr4B.!!$F6 2031
5 TraesCS4A01G035100 chr4B 546673792 546674729 937 False 1098.0 1098 87.91100 1669 2602 1 chr4B.!!$F3 933
6 TraesCS4A01G035100 chr4B 546023506 546024882 1376 False 476.0 769 84.02950 1237 2599 2 chr4B.!!$F5 1362
7 TraesCS4A01G035100 chr4D 441057198 441059228 2030 False 1298.5 1703 89.64600 611 2642 2 chr4D.!!$F5 2031
8 TraesCS4A01G035100 chr4D 441064260 441065320 1060 False 854.0 854 81.49800 1509 2602 1 chr4D.!!$F4 1093
9 TraesCS4A01G035100 chr4D 440282832 440283939 1107 False 752.0 752 79.68200 1514 2599 1 chr4D.!!$F3 1085
10 TraesCS4A01G035100 chrUn 286308807 286309745 938 True 1109.0 1109 88.13600 1669 2602 1 chrUn.!!$R3 933
11 TraesCS4A01G035100 chrUn 286315090 286316028 938 True 1109.0 1109 88.13600 1669 2602 1 chrUn.!!$R4 933
12 TraesCS4A01G035100 chrUn 295780527 295781465 938 False 1109.0 1109 88.13600 1669 2602 1 chrUn.!!$F2 933
13 TraesCS4A01G035100 chr6B 77801288 77801998 710 False 518.0 889 94.97050 2763 3405 2 chr6B.!!$F2 642
14 TraesCS4A01G035100 chr3D 508063066 508063767 701 True 513.0 874 95.23500 2763 3405 2 chr3D.!!$R2 642
15 TraesCS4A01G035100 chr7A 174925146 174925860 714 True 502.0 863 94.00500 2763 3405 2 chr7A.!!$R1 642
16 TraesCS4A01G035100 chr5D 428471516 428472083 567 True 859.0 859 94.01400 2843 3408 1 chr5D.!!$R3 565
17 TraesCS4A01G035100 chr1D 363731018 363731581 563 False 846.0 846 93.80500 2843 3405 1 chr1D.!!$F2 562
18 TraesCS4A01G035100 chr1A 13017631 13018193 562 False 846.0 846 93.78300 2843 3405 1 chr1A.!!$F1 562
19 TraesCS4A01G035100 chr2B 762113994 762114706 712 False 497.5 845 94.34050 2763 3405 2 chr2B.!!$F1 642
20 TraesCS4A01G035100 chr7D 150755000 150755563 563 False 841.0 841 93.62800 2843 3405 1 chr7D.!!$F1 562
21 TraesCS4A01G035100 chr5B 697177082 697177631 549 False 435.0 435 81.35000 3040 3590 1 chr5B.!!$F2 550

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
123 331 1.677633 GCTTTTTCGGGCCAGGCTA 60.678 57.895 12.43 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3048 6305 4.63174 TCCACCAGGCCCTCGACA 62.632 66.667 0.0 0.0 33.74 4.35 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
123 331 1.677633 GCTTTTTCGGGCCAGGCTA 60.678 57.895 12.43 0.00 0.0 3.93
301 509 4.003788 CTCACCTTGGGCCGTCGT 62.004 66.667 0.00 0.00 0.0 4.34
3048 6305 0.179081 GGCTTTAGATCGGCGAAGGT 60.179 55.000 15.93 3.71 0.0 3.50
3452 6734 2.093288 GGAGATGTCAAGTCATGCCTGA 60.093 50.000 0.00 0.00 0.0 3.86
3513 6795 0.098200 TACGCACGACAGATCTTCCG 59.902 55.000 10.87 10.87 0.0 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.209273 GCCCGTCATTTTTGCAGTTTT 58.791 42.857 0.00 0.00 0.00 2.43
1 2 1.540146 GGCCCGTCATTTTTGCAGTTT 60.540 47.619 0.00 0.00 0.00 2.66
3 4 1.665442 GGCCCGTCATTTTTGCAGT 59.335 52.632 0.00 0.00 0.00 4.40
4 5 1.079888 GGGCCCGTCATTTTTGCAG 60.080 57.895 5.69 0.00 0.00 4.41
123 331 2.378634 GCTAGTCCTGGCCATGGGT 61.379 63.158 15.13 4.24 0.00 4.51
3048 6305 4.631740 TCCACCAGGCCCTCGACA 62.632 66.667 0.00 0.00 33.74 4.35
3513 6795 0.436531 CGACGCAGCTTGAAGTCTTC 59.563 55.000 5.58 5.58 0.00 2.87


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

AutoCloner maintained by Alex Coulton.