Multiple sequence alignment - TraesCS2D01G094900

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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 TraesCS2D01G094900 chr2D 100.000 3018 0 0 1 3018 46908552 46905535 0.000000e+00 5574.0
1 TraesCS2D01G094900 chr2D 97.053 1561 29 7 634 2179 556372350 556373908 0.000000e+00 2612.0
2 TraesCS2D01G094900 chr2D 96.547 753 24 1 2266 3018 6567037 6566287 0.000000e+00 1245.0
3 TraesCS2D01G094900 chr2D 95.618 753 19 1 2266 3018 599598890 599599628 0.000000e+00 1195.0
4 TraesCS2D01G094900 chr2D 95.759 613 17 2 1 604 556371650 556372262 0.000000e+00 979.0
5 TraesCS2D01G094900 chr2D 95.726 585 21 2 1 581 588218320 588217736 0.000000e+00 939.0
6 TraesCS2D01G094900 chr2D 100.000 89 0 0 2179 2267 6567302 6567214 6.690000e-37 165.0
7 TraesCS2D01G094900 chr2D 100.000 89 0 0 2179 2267 599598625 599598713 6.690000e-37 165.0
8 TraesCS2D01G094900 chr2D 100.000 39 0 0 604 642 556372227 556372265 4.170000e-09 73.1
9 TraesCS2D01G094900 chr2D 100.000 36 0 0 569 604 46907949 46907914 1.940000e-07 67.6
10 TraesCS2D01G094900 chr2D 100.000 36 0 0 604 639 46907984 46907949 1.940000e-07 67.6
11 TraesCS2D01G094900 chr1D 95.688 1809 31 8 367 2143 21343322 21345115 0.000000e+00 2865.0
12 TraesCS2D01G094900 chr1D 92.141 1565 48 26 634 2177 33570142 33568632 0.000000e+00 2139.0
13 TraesCS2D01G094900 chr1D 93.415 1382 24 21 635 1959 404205180 404206551 0.000000e+00 1986.0
14 TraesCS2D01G094900 chr1D 97.344 753 20 0 2266 3018 492589783 492589031 0.000000e+00 1280.0
15 TraesCS2D01G094900 chr1D 98.884 627 6 1 2392 3018 21345112 21345737 0.000000e+00 1118.0
16 TraesCS2D01G094900 chr1D 100.000 88 0 0 2179 2266 492590048 492589961 2.410000e-36 163.0
17 TraesCS2D01G094900 chr1D 100.000 36 0 0 604 639 21343524 21343559 1.940000e-07 67.6
18 TraesCS2D01G094900 chr1D 94.444 36 2 0 604 639 404205067 404205102 4.200000e-04 56.5
19 TraesCS2D01G094900 chr3D 94.147 1811 32 18 426 2177 551376004 551374209 0.000000e+00 2689.0
20 TraesCS2D01G094900 chr3D 91.257 1567 62 28 634 2177 584752135 584750621 0.000000e+00 2065.0
21 TraesCS2D01G094900 chr3D 98.276 754 11 2 2266 3018 551374216 551373464 0.000000e+00 1319.0
22 TraesCS2D01G094900 chr3D 98.008 753 15 0 2266 3018 32370413 32371165 0.000000e+00 1308.0
23 TraesCS2D01G094900 chr3D 96.282 753 13 7 2266 3018 580705608 580704871 0.000000e+00 1221.0
24 TraesCS2D01G094900 chr3D 100.000 89 0 0 2179 2267 32370148 32370236 6.690000e-37 165.0
25 TraesCS2D01G094900 chr3D 100.000 39 0 0 604 642 551375861 551375823 4.170000e-09 73.1
26 TraesCS2D01G094900 chr7D 96.778 1583 14 11 634 2179 66522045 66520463 0.000000e+00 2606.0
27 TraesCS2D01G094900 chr7D 97.432 584 12 1 1 581 53328793 53328210 0.000000e+00 992.0
28 TraesCS2D01G094900 chr7D 96.213 581 19 1 1 581 154927846 154928423 0.000000e+00 948.0
29 TraesCS2D01G094900 chr7D 96.661 569 19 0 13 581 27279521 27278953 0.000000e+00 946.0
30 TraesCS2D01G094900 chr7D 95.869 581 21 1 1 581 459892960 459892383 0.000000e+00 937.0
31 TraesCS2D01G094900 chr7D 100.000 88 0 0 2180 2267 154931687 154931774 2.410000e-36 163.0
32 TraesCS2D01G094900 chr7D 100.000 88 0 0 2180 2267 459876872 459876785 2.410000e-36 163.0
33 TraesCS2D01G094900 chr7D 90.476 105 8 2 2299 2402 459876583 459876480 1.460000e-28 137.0
34 TraesCS2D01G094900 chr5D 91.508 1366 35 28 863 2179 520987259 520985926 0.000000e+00 1805.0
35 TraesCS2D01G094900 chr5D 98.274 753 12 1 2266 3018 348509958 348510709 0.000000e+00 1317.0
36 TraesCS2D01G094900 chr5D 90.323 744 40 18 2299 3018 489240191 489240926 0.000000e+00 946.0
37 TraesCS2D01G094900 chr5D 95.890 584 20 2 1 581 494286655 494287237 0.000000e+00 942.0
38 TraesCS2D01G094900 chr5D 95.719 584 22 2 1 581 489236384 489236967 0.000000e+00 937.0
39 TraesCS2D01G094900 chr5D 98.646 517 7 0 2502 3018 435230409 435230925 0.000000e+00 917.0
40 TraesCS2D01G094900 chr5D 86.822 774 43 15 2266 3018 494290798 494291533 0.000000e+00 809.0
41 TraesCS2D01G094900 chr5D 96.604 265 8 1 634 897 520987448 520987184 3.570000e-119 438.0
42 TraesCS2D01G094900 chr5D 100.000 88 0 0 2180 2267 489239925 489240012 2.410000e-36 163.0
43 TraesCS2D01G094900 chr4D 96.813 753 10 1 2266 3018 434989700 434988962 0.000000e+00 1245.0
44 TraesCS2D01G094900 chr4D 94.415 752 27 7 2267 3018 497687261 497686525 0.000000e+00 1142.0
45 TraesCS2D01G094900 chr4D 95.741 587 19 1 1 581 434992174 434991588 0.000000e+00 941.0
46 TraesCS2D01G094900 chr4D 94.173 532 26 2 2487 3018 12305818 12305292 0.000000e+00 806.0
47 TraesCS2D01G094900 chr4D 91.729 532 40 1 2487 3018 51788675 51789202 0.000000e+00 736.0
48 TraesCS2D01G094900 chr4D 100.000 89 0 0 2179 2267 388109830 388109742 6.690000e-37 165.0
49 TraesCS2D01G094900 chr4D 100.000 89 0 0 2179 2267 497687531 497687443 6.690000e-37 165.0
50 TraesCS2D01G094900 chr6A 95.756 754 31 1 2266 3018 53304853 53305606 0.000000e+00 1214.0
51 TraesCS2D01G094900 chr6A 93.359 512 33 1 2508 3018 63180518 63180007 0.000000e+00 756.0
52 TraesCS2D01G094900 chr3A 93.103 783 23 3 2266 3018 71575633 71576414 0.000000e+00 1118.0
53 TraesCS2D01G094900 chr4A 91.079 751 41 16 706 1444 660538209 660538945 0.000000e+00 992.0
54 TraesCS2D01G094900 chr4A 90.110 728 45 17 1392 2108 404426514 404425803 0.000000e+00 920.0
55 TraesCS2D01G094900 chr4A 88.098 731 55 20 1392 2108 642565211 642564499 0.000000e+00 839.0
56 TraesCS2D01G094900 chr4A 84.222 900 83 33 706 1570 731795716 731794841 0.000000e+00 821.0
57 TraesCS2D01G094900 chr4B 89.837 738 45 20 1381 2108 8025019 8024302 0.000000e+00 920.0
58 TraesCS2D01G094900 chr4B 88.732 710 47 15 883 1578 8025613 8024923 0.000000e+00 837.0
59 TraesCS2D01G094900 chr3B 88.947 769 48 23 822 1566 751901457 751900702 0.000000e+00 915.0
60 TraesCS2D01G094900 chr3B 89.115 689 50 17 1427 2108 557702566 557703236 0.000000e+00 833.0
61 TraesCS2D01G094900 chr2B 85.255 902 80 38 706 1578 87173415 87172538 0.000000e+00 880.0
62 TraesCS2D01G094900 chr5A 89.026 729 51 19 1392 2108 596892296 596893007 0.000000e+00 876.0
63 TraesCS2D01G094900 chr5A 87.705 732 69 20 812 1527 1844984 1845710 0.000000e+00 833.0
64 TraesCS2D01G094900 chr1A 93.045 532 33 1 2487 3018 574238604 574238077 0.000000e+00 774.0
65 TraesCS2D01G094900 chr6D 90.731 561 25 4 2460 3018 463820994 463820459 0.000000e+00 723.0
66 TraesCS2D01G094900 chr6D 88.538 506 43 7 2527 3018 284548815 284549319 1.550000e-167 599.0


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 TraesCS2D01G094900 chr2D 46905535 46908552 3017 True 1903.066667 5574 100.000000 1 3018 3 chr2D.!!$R3 3017
1 TraesCS2D01G094900 chr2D 556371650 556373908 2258 False 1221.366667 2612 97.604000 1 2179 3 chr2D.!!$F1 2178
2 TraesCS2D01G094900 chr2D 588217736 588218320 584 True 939.000000 939 95.726000 1 581 1 chr2D.!!$R1 580
3 TraesCS2D01G094900 chr2D 6566287 6567302 1015 True 705.000000 1245 98.273500 2179 3018 2 chr2D.!!$R2 839
4 TraesCS2D01G094900 chr2D 599598625 599599628 1003 False 680.000000 1195 97.809000 2179 3018 2 chr2D.!!$F2 839
5 TraesCS2D01G094900 chr1D 33568632 33570142 1510 True 2139.000000 2139 92.141000 634 2177 1 chr1D.!!$R1 1543
6 TraesCS2D01G094900 chr1D 21343322 21345737 2415 False 1350.200000 2865 98.190667 367 3018 3 chr1D.!!$F1 2651
7 TraesCS2D01G094900 chr1D 404205067 404206551 1484 False 1021.250000 1986 93.929500 604 1959 2 chr1D.!!$F2 1355
8 TraesCS2D01G094900 chr1D 492589031 492590048 1017 True 721.500000 1280 98.672000 2179 3018 2 chr1D.!!$R2 839
9 TraesCS2D01G094900 chr3D 584750621 584752135 1514 True 2065.000000 2065 91.257000 634 2177 1 chr3D.!!$R2 1543
10 TraesCS2D01G094900 chr3D 551373464 551376004 2540 True 1360.366667 2689 97.474333 426 3018 3 chr3D.!!$R3 2592
11 TraesCS2D01G094900 chr3D 580704871 580705608 737 True 1221.000000 1221 96.282000 2266 3018 1 chr3D.!!$R1 752
12 TraesCS2D01G094900 chr3D 32370148 32371165 1017 False 736.500000 1308 99.004000 2179 3018 2 chr3D.!!$F1 839
13 TraesCS2D01G094900 chr7D 66520463 66522045 1582 True 2606.000000 2606 96.778000 634 2179 1 chr7D.!!$R3 1545
14 TraesCS2D01G094900 chr7D 53328210 53328793 583 True 992.000000 992 97.432000 1 581 1 chr7D.!!$R2 580
15 TraesCS2D01G094900 chr7D 27278953 27279521 568 True 946.000000 946 96.661000 13 581 1 chr7D.!!$R1 568
16 TraesCS2D01G094900 chr7D 459892383 459892960 577 True 937.000000 937 95.869000 1 581 1 chr7D.!!$R4 580
17 TraesCS2D01G094900 chr7D 154927846 154931774 3928 False 555.500000 948 98.106500 1 2267 2 chr7D.!!$F1 2266
18 TraesCS2D01G094900 chr5D 348509958 348510709 751 False 1317.000000 1317 98.274000 2266 3018 1 chr5D.!!$F1 752
19 TraesCS2D01G094900 chr5D 520985926 520987448 1522 True 1121.500000 1805 94.056000 634 2179 2 chr5D.!!$R1 1545
20 TraesCS2D01G094900 chr5D 435230409 435230925 516 False 917.000000 917 98.646000 2502 3018 1 chr5D.!!$F2 516
21 TraesCS2D01G094900 chr5D 494286655 494291533 4878 False 875.500000 942 91.356000 1 3018 2 chr5D.!!$F4 3017
22 TraesCS2D01G094900 chr5D 489236384 489240926 4542 False 682.000000 946 95.347333 1 3018 3 chr5D.!!$F3 3017
23 TraesCS2D01G094900 chr4D 434988962 434992174 3212 True 1093.000000 1245 96.277000 1 3018 2 chr4D.!!$R3 3017
24 TraesCS2D01G094900 chr4D 12305292 12305818 526 True 806.000000 806 94.173000 2487 3018 1 chr4D.!!$R1 531
25 TraesCS2D01G094900 chr4D 51788675 51789202 527 False 736.000000 736 91.729000 2487 3018 1 chr4D.!!$F1 531
26 TraesCS2D01G094900 chr4D 497686525 497687531 1006 True 653.500000 1142 97.207500 2179 3018 2 chr4D.!!$R4 839
27 TraesCS2D01G094900 chr6A 53304853 53305606 753 False 1214.000000 1214 95.756000 2266 3018 1 chr6A.!!$F1 752
28 TraesCS2D01G094900 chr6A 63180007 63180518 511 True 756.000000 756 93.359000 2508 3018 1 chr6A.!!$R1 510
29 TraesCS2D01G094900 chr3A 71575633 71576414 781 False 1118.000000 1118 93.103000 2266 3018 1 chr3A.!!$F1 752
30 TraesCS2D01G094900 chr4A 660538209 660538945 736 False 992.000000 992 91.079000 706 1444 1 chr4A.!!$F1 738
31 TraesCS2D01G094900 chr4A 404425803 404426514 711 True 920.000000 920 90.110000 1392 2108 1 chr4A.!!$R1 716
32 TraesCS2D01G094900 chr4A 642564499 642565211 712 True 839.000000 839 88.098000 1392 2108 1 chr4A.!!$R2 716
33 TraesCS2D01G094900 chr4A 731794841 731795716 875 True 821.000000 821 84.222000 706 1570 1 chr4A.!!$R3 864
34 TraesCS2D01G094900 chr4B 8024302 8025613 1311 True 878.500000 920 89.284500 883 2108 2 chr4B.!!$R1 1225
35 TraesCS2D01G094900 chr3B 751900702 751901457 755 True 915.000000 915 88.947000 822 1566 1 chr3B.!!$R1 744
36 TraesCS2D01G094900 chr3B 557702566 557703236 670 False 833.000000 833 89.115000 1427 2108 1 chr3B.!!$F1 681
37 TraesCS2D01G094900 chr2B 87172538 87173415 877 True 880.000000 880 85.255000 706 1578 1 chr2B.!!$R1 872
38 TraesCS2D01G094900 chr5A 596892296 596893007 711 False 876.000000 876 89.026000 1392 2108 1 chr5A.!!$F2 716
39 TraesCS2D01G094900 chr5A 1844984 1845710 726 False 833.000000 833 87.705000 812 1527 1 chr5A.!!$F1 715
40 TraesCS2D01G094900 chr1A 574238077 574238604 527 True 774.000000 774 93.045000 2487 3018 1 chr1A.!!$R1 531
41 TraesCS2D01G094900 chr6D 463820459 463820994 535 True 723.000000 723 90.731000 2460 3018 1 chr6D.!!$R1 558
42 TraesCS2D01G094900 chr6D 284548815 284549319 504 False 599.000000 599 88.538000 2527 3018 1 chr6D.!!$F1 491

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
912 1084 1.004044 CTCCACCATCAAGCAACTCCT 59.996 52.381 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 8798 0.105593 GATCTCATGGAGCCGCTGAA 59.894 55.0 0.0 0.0 0.0 3.02 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
62 72 4.322198 GGATGAGGTCAATGTTGTTGCAAT 60.322 41.667 0.59 0.0 0.00 3.56
128 138 2.795960 TGGTAGTTAGGAGAGGCCCTAT 59.204 50.000 0.00 0.0 38.50 2.57
180 190 3.940209 GTGCAACCTGATTTCATTCCA 57.060 42.857 0.00 0.0 0.00 3.53
217 227 2.655090 TGATGGGTTGCTGTTTGAGA 57.345 45.000 0.00 0.0 0.00 3.27
912 1084 1.004044 CTCCACCATCAAGCAACTCCT 59.996 52.381 0.00 0.0 0.00 3.69
1172 1347 1.841302 AAGGAGCCGCTGGATGTCAA 61.841 55.000 0.00 0.0 0.00 3.18
1504 1981 6.425114 TCTGAAGTTTCTGAAGTAGATGCAAC 59.575 38.462 0.00 0.0 34.80 4.17
1522 2019 5.428253 TGCAACACTAGTTCTGAAGTTCTT 58.572 37.500 2.62 0.0 35.28 2.52
2169 8793 3.760151 TGAACTGGATTTTGATGGAGCTG 59.240 43.478 0.00 0.0 0.00 4.24
2170 8794 3.446442 ACTGGATTTTGATGGAGCTGT 57.554 42.857 0.00 0.0 0.00 4.40
2171 8795 3.771216 ACTGGATTTTGATGGAGCTGTT 58.229 40.909 0.00 0.0 0.00 3.16
2172 8796 3.508793 ACTGGATTTTGATGGAGCTGTTG 59.491 43.478 0.00 0.0 0.00 3.33
2173 8797 3.499338 TGGATTTTGATGGAGCTGTTGT 58.501 40.909 0.00 0.0 0.00 3.32
2174 8798 3.896888 TGGATTTTGATGGAGCTGTTGTT 59.103 39.130 0.00 0.0 0.00 2.83
2175 8799 4.344679 TGGATTTTGATGGAGCTGTTGTTT 59.655 37.500 0.00 0.0 0.00 2.83
2176 8800 4.925646 GGATTTTGATGGAGCTGTTGTTTC 59.074 41.667 0.00 0.0 0.00 2.78
2177 8801 4.998671 TTTTGATGGAGCTGTTGTTTCA 57.001 36.364 0.00 0.0 0.00 2.69
2337 9162 3.428316 CCCGCGCATTGTTTTAATAACCT 60.428 43.478 8.75 0.0 0.00 3.50
2473 9359 1.434188 TTGGCCAGAGGTTCAAGAGA 58.566 50.000 5.11 0.0 0.00 3.10
2962 9900 9.177608 CTCATCAACCTGGATCTTTAAATTGTA 57.822 33.333 0.00 0.0 0.00 2.41
2963 9901 9.527157 TCATCAACCTGGATCTTTAAATTGTAA 57.473 29.630 0.00 0.0 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 72 5.009610 GGTTTTTGCATTGGTGTCTCTTCTA 59.990 40.000 0.00 0.00 0.00 2.10
217 227 4.142790 GGCTCATGTCCATCATCTTCATT 58.857 43.478 0.00 0.00 34.09 2.57
912 1084 2.315176 GGGCTTGAGATAGAGCAGAGA 58.685 52.381 0.00 0.00 40.63 3.10
1363 1544 7.214467 TCAGAACTGGATGTTTTTACCATTC 57.786 36.000 1.93 0.00 39.30 2.67
1504 1981 9.535878 AGAAACTTAAGAACTTCAGAACTAGTG 57.464 33.333 10.09 0.00 0.00 2.74
1522 2019 5.546621 AGTACAGCCAGTTCAGAAACTTA 57.453 39.130 0.00 0.00 43.28 2.24
2169 8793 0.109597 CATGGAGCCGCTGAAACAAC 60.110 55.000 0.00 0.00 0.00 3.32
2170 8794 0.250684 TCATGGAGCCGCTGAAACAA 60.251 50.000 0.00 0.00 0.00 2.83
2171 8795 0.674581 CTCATGGAGCCGCTGAAACA 60.675 55.000 0.00 0.00 0.00 2.83
2172 8796 0.391661 TCTCATGGAGCCGCTGAAAC 60.392 55.000 0.00 0.00 0.00 2.78
2173 8797 0.543277 ATCTCATGGAGCCGCTGAAA 59.457 50.000 0.00 0.00 0.00 2.69
2174 8798 0.105593 GATCTCATGGAGCCGCTGAA 59.894 55.000 0.00 0.00 0.00 3.02
2175 8799 1.744639 GATCTCATGGAGCCGCTGA 59.255 57.895 0.00 0.00 0.00 4.26
2176 8800 1.301558 GGATCTCATGGAGCCGCTG 60.302 63.158 0.00 0.00 40.91 5.18
2177 8801 3.146182 GGATCTCATGGAGCCGCT 58.854 61.111 0.00 0.00 40.91 5.52
2326 9151 3.166679 GTGGTGGCCCAGGTTATTAAAA 58.833 45.455 0.00 0.00 42.94 1.52
2337 9162 4.269523 GCACTGAGTGGTGGCCCA 62.270 66.667 15.24 0.00 38.87 5.36
2962 9900 3.194329 GGAAAAGCTAGCTGAAGGCAATT 59.806 43.478 20.16 2.76 44.79 2.32
2963 9901 2.757314 GGAAAAGCTAGCTGAAGGCAAT 59.243 45.455 20.16 0.00 44.79 3.56


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

AutoCloner maintained by Alex Coulton.