Multiple sequence alignment - TraesCS5D01G091600

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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 TraesCS5D01G091600 chr5D 100.000 2507 0 0 1 2507 98750514 98748008 0.000000e+00 4630.0
1 TraesCS5D01G091600 chr5D 93.502 831 20 3 1 797 281538171 281539001 0.000000e+00 1205.0
2 TraesCS5D01G091600 chr5D 93.261 831 20 4 1 797 534068763 534069591 0.000000e+00 1192.0
3 TraesCS5D01G091600 chr5D 95.441 680 21 1 127 796 90257020 90257699 0.000000e+00 1075.0
4 TraesCS5D01G091600 chr5D 78.345 822 121 26 1 797 440707860 440708649 1.740000e-131 479.0
5 TraesCS5D01G091600 chr5D 77.818 834 108 41 1 793 538210826 538211623 6.360000e-121 444.0
6 TraesCS5D01G091600 chr5D 86.234 385 31 9 1664 2048 123562035 123562397 5.020000e-107 398.0
7 TraesCS5D01G091600 chr5D 86.007 293 21 7 1756 2048 104697259 104696987 1.890000e-76 296.0
8 TraesCS5D01G091600 chr5D 98.113 53 1 0 2455 2507 123978764 123978816 2.660000e-15 93.5
9 TraesCS5D01G091600 chr1A 97.141 1714 35 4 796 2507 294140842 294139141 0.000000e+00 2881.0
10 TraesCS5D01G091600 chr1A 87.270 652 62 8 1147 1783 168742296 168741651 0.000000e+00 725.0
11 TraesCS5D01G091600 chr1A 94.505 91 5 0 2314 2404 168741639 168741549 9.350000e-30 141.0
12 TraesCS5D01G091600 chr3A 95.771 1277 37 2 796 2055 356524040 356525316 0.000000e+00 2043.0
13 TraesCS5D01G091600 chr3A 98.031 457 9 0 2051 2507 356534809 356535265 0.000000e+00 795.0
14 TraesCS5D01G091600 chr6B 97.155 1160 30 2 1350 2507 512881506 512882664 0.000000e+00 1956.0
15 TraesCS5D01G091600 chr6B 88.403 1259 109 14 1171 2404 109138551 109137305 0.000000e+00 1482.0
16 TraesCS5D01G091600 chr6B 74.946 459 64 35 865 1288 117993862 117994304 2.000000e-36 163.0
17 TraesCS5D01G091600 chr5B 97.814 1098 24 0 1410 2507 489106882 489105785 0.000000e+00 1895.0
18 TraesCS5D01G091600 chr5B 81.658 965 130 22 801 1745 170565398 170566335 0.000000e+00 758.0
19 TraesCS5D01G091600 chr5B 87.821 312 36 2 1435 1745 392491679 392491989 5.100000e-97 364.0
20 TraesCS5D01G091600 chr3D 97.959 882 16 2 1594 2473 199201144 199202025 0.000000e+00 1528.0
21 TraesCS5D01G091600 chr3D 97.938 97 2 0 2411 2507 199202007 199202103 4.290000e-38 169.0
22 TraesCS5D01G091600 chr4D 93.486 829 21 5 1 796 349581055 349581883 0.000000e+00 1201.0
23 TraesCS5D01G091600 chr4D 93.486 829 19 4 1 795 67309303 67308476 0.000000e+00 1199.0
24 TraesCS5D01G091600 chr4D 85.219 981 95 24 1070 2048 264318574 264317642 0.000000e+00 963.0
25 TraesCS5D01G091600 chr4D 78.832 822 117 37 1 797 328178598 328179387 3.720000e-138 501.0
26 TraesCS5D01G091600 chr4D 89.877 326 19 7 505 819 357246929 357247251 8.350000e-110 407.0
27 TraesCS5D01G091600 chr2D 93.020 831 24 3 1 797 497969037 497968207 0.000000e+00 1182.0
28 TraesCS5D01G091600 chr2D 92.874 828 30 5 1 800 106998574 106999400 0.000000e+00 1175.0
29 TraesCS5D01G091600 chr2D 92.788 832 21 8 1 795 182737285 182736456 0.000000e+00 1168.0
30 TraesCS5D01G091600 chr2D 94.404 679 28 1 127 795 110262560 110263238 0.000000e+00 1035.0
31 TraesCS5D01G091600 chr2D 84.958 718 80 20 1510 2215 193400413 193399712 0.000000e+00 702.0
32 TraesCS5D01G091600 chr2D 98.113 53 1 0 2455 2507 412931305 412931357 2.660000e-15 93.5
33 TraesCS5D01G091600 chr7D 93.292 805 21 2 24 795 65778071 65777267 0.000000e+00 1157.0
34 TraesCS5D01G091600 chr7D 91.832 808 35 12 1 795 616137978 616137189 0.000000e+00 1098.0
35 TraesCS5D01G091600 chr7D 89.056 731 45 10 65 795 500980855 500980160 0.000000e+00 874.0
36 TraesCS5D01G091600 chr7D 79.487 819 106 31 1 795 183335503 183336283 2.210000e-145 525.0
37 TraesCS5D01G091600 chr7D 93.355 301 10 1 506 796 626741741 626741441 1.060000e-118 436.0
38 TraesCS5D01G091600 chr6D 93.572 669 17 3 127 795 452927048 452927690 0.000000e+00 974.0
39 TraesCS5D01G091600 chr6D 81.116 466 55 21 1 445 23533011 23532558 2.390000e-90 342.0
40 TraesCS5D01G091600 chr3B 84.302 981 103 28 1070 2048 608369220 608370151 0.000000e+00 911.0
41 TraesCS5D01G091600 chr3B 86.927 589 34 13 1858 2404 414808785 414809372 2.740000e-174 621.0
42 TraesCS5D01G091600 chr3B 80.851 611 89 13 807 1401 284566344 284565746 2.940000e-124 455.0
43 TraesCS5D01G091600 chr3B 85.581 215 20 4 807 1015 608368446 608368655 5.430000e-52 215.0
44 TraesCS5D01G091600 chr5A 84.109 988 100 22 1070 2048 219530944 219531883 0.000000e+00 902.0
45 TraesCS5D01G091600 chr5A 79.879 661 82 26 895 1526 259087787 259088425 1.060000e-118 436.0
46 TraesCS5D01G091600 chr5A 77.578 834 108 43 1 796 459318893 459318101 4.950000e-117 431.0
47 TraesCS5D01G091600 chr5A 80.275 436 65 14 865 1298 503384158 503383742 2.420000e-80 309.0
48 TraesCS5D01G091600 chr5A 82.432 222 25 6 807 1022 104470688 104470475 5.510000e-42 182.0
49 TraesCS5D01G091600 chr5A 79.227 207 23 6 815 1015 219530649 219530841 2.620000e-25 126.0
50 TraesCS5D01G091600 chr1D 94.228 589 10 2 1 565 110761280 110760692 0.000000e+00 878.0
51 TraesCS5D01G091600 chr1D 77.191 833 116 40 1 795 222406605 222405809 3.860000e-113 418.0
52 TraesCS5D01G091600 chr1D 90.033 301 20 5 505 795 420778310 420778610 5.060000e-102 381.0
53 TraesCS5D01G091600 chr7B 82.114 984 109 26 1070 2048 283360941 283360020 0.000000e+00 780.0
54 TraesCS5D01G091600 chr7B 81.855 981 105 28 1070 2048 386250183 386251092 0.000000e+00 758.0
55 TraesCS5D01G091600 chr7B 82.511 223 31 6 1070 1292 246267912 246267698 3.290000e-44 189.0
56 TraesCS5D01G091600 chr7B 87.200 125 13 3 1070 1191 299408569 299408445 3.360000e-29 139.0
57 TraesCS5D01G091600 chr7B 88.889 45 5 0 1147 1191 272711828 272711784 3.480000e-04 56.5
58 TraesCS5D01G091600 chr4A 86.987 707 64 16 1344 2048 324014314 324014994 0.000000e+00 771.0
59 TraesCS5D01G091600 chr4A 76.655 831 121 41 1 795 638644301 638645094 2.340000e-105 392.0
60 TraesCS5D01G091600 chr4A 84.878 205 16 4 807 1005 324013806 324014001 2.540000e-45 193.0
61 TraesCS5D01G091600 chr4B 86.421 707 60 18 1344 2048 305326529 305325857 0.000000e+00 741.0
62 TraesCS5D01G091600 chr4B 84.932 219 22 4 807 1019 305327984 305327771 7.030000e-51 211.0
63 TraesCS5D01G091600 chr2B 87.746 661 42 7 1759 2404 341008426 341009062 0.000000e+00 736.0
64 TraesCS5D01G091600 chr2B 88.750 80 4 1 817 896 576065579 576065505 2.660000e-15 93.5
65 TraesCS5D01G091600 chr1B 85.263 665 66 18 1144 1783 223896142 223896799 0.000000e+00 656.0
66 TraesCS5D01G091600 chr1B 87.895 190 22 1 1338 1526 358962655 358962466 3.250000e-54 222.0
67 TraesCS5D01G091600 chr7A 77.262 818 125 42 1 798 159515639 159514863 8.290000e-115 424.0
68 TraesCS5D01G091600 chr2A 89.349 169 15 2 1990 2157 207594368 207594202 2.530000e-50 209.0
69 TraesCS5D01G091600 chr2A 83.568 213 21 3 807 1013 355387355 355387559 1.180000e-43 187.0


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 TraesCS5D01G091600 chr5D 98748008 98750514 2506 True 4630.0 4630 100.0000 1 2507 1 chr5D.!!$R1 2506
1 TraesCS5D01G091600 chr5D 281538171 281539001 830 False 1205.0 1205 93.5020 1 797 1 chr5D.!!$F4 796
2 TraesCS5D01G091600 chr5D 534068763 534069591 828 False 1192.0 1192 93.2610 1 797 1 chr5D.!!$F6 796
3 TraesCS5D01G091600 chr5D 90257020 90257699 679 False 1075.0 1075 95.4410 127 796 1 chr5D.!!$F1 669
4 TraesCS5D01G091600 chr5D 440707860 440708649 789 False 479.0 479 78.3450 1 797 1 chr5D.!!$F5 796
5 TraesCS5D01G091600 chr5D 538210826 538211623 797 False 444.0 444 77.8180 1 793 1 chr5D.!!$F7 792
6 TraesCS5D01G091600 chr1A 294139141 294140842 1701 True 2881.0 2881 97.1410 796 2507 1 chr1A.!!$R1 1711
7 TraesCS5D01G091600 chr1A 168741549 168742296 747 True 433.0 725 90.8875 1147 2404 2 chr1A.!!$R2 1257
8 TraesCS5D01G091600 chr3A 356524040 356525316 1276 False 2043.0 2043 95.7710 796 2055 1 chr3A.!!$F1 1259
9 TraesCS5D01G091600 chr6B 512881506 512882664 1158 False 1956.0 1956 97.1550 1350 2507 1 chr6B.!!$F2 1157
10 TraesCS5D01G091600 chr6B 109137305 109138551 1246 True 1482.0 1482 88.4030 1171 2404 1 chr6B.!!$R1 1233
11 TraesCS5D01G091600 chr5B 489105785 489106882 1097 True 1895.0 1895 97.8140 1410 2507 1 chr5B.!!$R1 1097
12 TraesCS5D01G091600 chr5B 170565398 170566335 937 False 758.0 758 81.6580 801 1745 1 chr5B.!!$F1 944
13 TraesCS5D01G091600 chr3D 199201144 199202103 959 False 848.5 1528 97.9485 1594 2507 2 chr3D.!!$F1 913
14 TraesCS5D01G091600 chr4D 349581055 349581883 828 False 1201.0 1201 93.4860 1 796 1 chr4D.!!$F2 795
15 TraesCS5D01G091600 chr4D 67308476 67309303 827 True 1199.0 1199 93.4860 1 795 1 chr4D.!!$R1 794
16 TraesCS5D01G091600 chr4D 264317642 264318574 932 True 963.0 963 85.2190 1070 2048 1 chr4D.!!$R2 978
17 TraesCS5D01G091600 chr4D 328178598 328179387 789 False 501.0 501 78.8320 1 797 1 chr4D.!!$F1 796
18 TraesCS5D01G091600 chr2D 497968207 497969037 830 True 1182.0 1182 93.0200 1 797 1 chr2D.!!$R3 796
19 TraesCS5D01G091600 chr2D 106998574 106999400 826 False 1175.0 1175 92.8740 1 800 1 chr2D.!!$F1 799
20 TraesCS5D01G091600 chr2D 182736456 182737285 829 True 1168.0 1168 92.7880 1 795 1 chr2D.!!$R1 794
21 TraesCS5D01G091600 chr2D 110262560 110263238 678 False 1035.0 1035 94.4040 127 795 1 chr2D.!!$F2 668
22 TraesCS5D01G091600 chr2D 193399712 193400413 701 True 702.0 702 84.9580 1510 2215 1 chr2D.!!$R2 705
23 TraesCS5D01G091600 chr7D 65777267 65778071 804 True 1157.0 1157 93.2920 24 795 1 chr7D.!!$R1 771
24 TraesCS5D01G091600 chr7D 616137189 616137978 789 True 1098.0 1098 91.8320 1 795 1 chr7D.!!$R3 794
25 TraesCS5D01G091600 chr7D 500980160 500980855 695 True 874.0 874 89.0560 65 795 1 chr7D.!!$R2 730
26 TraesCS5D01G091600 chr7D 183335503 183336283 780 False 525.0 525 79.4870 1 795 1 chr7D.!!$F1 794
27 TraesCS5D01G091600 chr6D 452927048 452927690 642 False 974.0 974 93.5720 127 795 1 chr6D.!!$F1 668
28 TraesCS5D01G091600 chr3B 414808785 414809372 587 False 621.0 621 86.9270 1858 2404 1 chr3B.!!$F1 546
29 TraesCS5D01G091600 chr3B 608368446 608370151 1705 False 563.0 911 84.9415 807 2048 2 chr3B.!!$F2 1241
30 TraesCS5D01G091600 chr3B 284565746 284566344 598 True 455.0 455 80.8510 807 1401 1 chr3B.!!$R1 594
31 TraesCS5D01G091600 chr5A 219530649 219531883 1234 False 514.0 902 81.6680 815 2048 2 chr5A.!!$F2 1233
32 TraesCS5D01G091600 chr5A 259087787 259088425 638 False 436.0 436 79.8790 895 1526 1 chr5A.!!$F1 631
33 TraesCS5D01G091600 chr5A 459318101 459318893 792 True 431.0 431 77.5780 1 796 1 chr5A.!!$R2 795
34 TraesCS5D01G091600 chr1D 110760692 110761280 588 True 878.0 878 94.2280 1 565 1 chr1D.!!$R1 564
35 TraesCS5D01G091600 chr1D 222405809 222406605 796 True 418.0 418 77.1910 1 795 1 chr1D.!!$R2 794
36 TraesCS5D01G091600 chr7B 283360020 283360941 921 True 780.0 780 82.1140 1070 2048 1 chr7B.!!$R3 978
37 TraesCS5D01G091600 chr7B 386250183 386251092 909 False 758.0 758 81.8550 1070 2048 1 chr7B.!!$F1 978
38 TraesCS5D01G091600 chr4A 324013806 324014994 1188 False 482.0 771 85.9325 807 2048 2 chr4A.!!$F2 1241
39 TraesCS5D01G091600 chr4A 638644301 638645094 793 False 392.0 392 76.6550 1 795 1 chr4A.!!$F1 794
40 TraesCS5D01G091600 chr4B 305325857 305327984 2127 True 476.0 741 85.6765 807 2048 2 chr4B.!!$R1 1241
41 TraesCS5D01G091600 chr2B 341008426 341009062 636 False 736.0 736 87.7460 1759 2404 1 chr2B.!!$F1 645
42 TraesCS5D01G091600 chr1B 223896142 223896799 657 False 656.0 656 85.2630 1144 1783 1 chr1B.!!$F1 639
43 TraesCS5D01G091600 chr7A 159514863 159515639 776 True 424.0 424 77.2620 1 798 1 chr7A.!!$R1 797

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
647 829 0.032912 TGCCACGGTGGATAGAGGTA 60.033 55.0 30.65 0.0 40.96 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 3276 1.61785 TGGACAATGCCAGCGAAAAAT 59.382 42.857 0.0 0.0 33.1 1.82 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
143 180 8.531982 GCCTACTTCATACCATGTCAATCTATA 58.468 37.037 0.00 0.00 0.00 1.31
436 519 0.689080 GAGAGGGGGAGTGCAGATGA 60.689 60.000 0.00 0.00 0.00 2.92
447 530 3.536917 CAGATGACCGCCGCCCTA 61.537 66.667 0.00 0.00 0.00 3.53
488 578 2.540910 AGGGTGGGGGAGGAGAGA 60.541 66.667 0.00 0.00 0.00 3.10
647 829 0.032912 TGCCACGGTGGATAGAGGTA 60.033 55.000 30.65 0.00 40.96 3.08
934 1134 2.037367 CCCTCCTCTCCCACGTCA 59.963 66.667 0.00 0.00 0.00 4.35
1304 2575 3.056328 GCGTTTGGCCACTCCTCC 61.056 66.667 3.88 0.00 34.80 4.30
1584 3237 7.834821 AACAATGAAAATGCAAAATTTACGC 57.165 28.000 0.00 5.73 0.00 4.42
1615 3276 0.250553 GATTGTCGGTGGGGTGTGAA 60.251 55.000 0.00 0.00 0.00 3.18
1621 3282 1.957877 TCGGTGGGGTGTGAATTTTTC 59.042 47.619 0.00 0.00 0.00 2.29
1661 3327 5.241506 TGCAGTTTTTGGATTTCTACTGAGG 59.758 40.000 0.00 0.00 36.07 3.86
1801 3471 6.373774 AGCAATGTTGTTTTTGTTTGGAATGA 59.626 30.769 0.00 0.00 0.00 2.57
1913 3584 8.911662 GCACAAAAATAGGTAACATAGTTGTTG 58.088 33.333 1.76 0.00 45.56 3.33
2472 4263 3.697799 CCAAATGGGGCCTCTCTTT 57.302 52.632 3.07 0.28 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 206 8.331931 AGAATGTGGTTTGGATAGATAGGTTA 57.668 34.615 0.00 0.00 0.00 2.85
327 410 2.128535 AGGTACTCTCCTCCGATCTCA 58.871 52.381 0.00 0.00 31.32 3.27
436 519 1.029947 CAGAAAAATAGGGCGGCGGT 61.030 55.000 9.78 0.00 0.00 5.68
447 530 4.020307 CCCCATTGGCAGTTACAGAAAAAT 60.020 41.667 0.00 0.00 0.00 1.82
699 890 2.423577 CTAACCCTTTTGTGTAGCGCT 58.576 47.619 17.26 17.26 0.00 5.92
1005 1572 1.524002 CTGATGGCATCCCTGACGT 59.476 57.895 23.92 0.00 30.50 4.34
1304 2575 1.621301 CGACGGACTTGAGCTTGCTG 61.621 60.000 0.00 0.00 0.00 4.41
1564 3216 7.548780 ACCATAGCGTAAATTTTGCATTTTCAT 59.451 29.630 14.99 0.00 0.00 2.57
1584 3237 4.991056 CCACCGACAATCATTAGACCATAG 59.009 45.833 0.00 0.00 0.00 2.23
1615 3276 1.617850 TGGACAATGCCAGCGAAAAAT 59.382 42.857 0.00 0.00 33.10 1.82
1661 3327 8.460831 AAAACAAATCTCAAAACACTGTACAC 57.539 30.769 0.00 0.00 0.00 2.90
1724 3393 3.845781 ATAGTGATGCCTCCGTCAATT 57.154 42.857 0.00 0.00 38.64 2.32
1801 3471 9.965902 ATAACAGAATAGAAATTGAGAACTGGT 57.034 29.630 0.00 0.00 0.00 4.00
1906 3577 3.058016 CCAAATCGAGCATGACAACAACT 60.058 43.478 0.00 0.00 0.00 3.16
1913 3584 3.559238 ACAAACCAAATCGAGCATGAC 57.441 42.857 0.00 0.00 0.00 3.06
2104 3779 7.933577 TGATTTCATAATCTAGTCCACCATGTC 59.066 37.037 0.00 0.00 40.68 3.06


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

AutoCloner maintained by Alex Coulton.