Multiple sequence alignment - TraesCS7A01G310900

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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 TraesCS7A01G310900 chr7A 100.000 3411 0 0 1 3411 439788045 439784635 0.000000e+00 6300.0
1 TraesCS7A01G310900 chr7A 95.447 571 20 2 1 571 259952990 259952426 0.000000e+00 905.0
2 TraesCS7A01G310900 chr7A 92.810 153 7 3 1506 1657 454048935 454049084 5.730000e-53 219.0
3 TraesCS7A01G310900 chr7B 97.960 2843 44 3 570 3411 645516257 645513428 0.000000e+00 4916.0
4 TraesCS7A01G310900 chr7B 94.158 1763 85 10 1656 3411 149938011 149936260 0.000000e+00 2669.0
5 TraesCS7A01G310900 chr7B 87.644 607 55 8 570 1175 149938998 149938411 0.000000e+00 688.0
6 TraesCS7A01G310900 chr5A 97.679 2844 51 4 570 3411 311020794 311017964 0.000000e+00 4872.0
7 TraesCS7A01G310900 chr5A 95.447 571 20 2 1 571 17181905 17182469 0.000000e+00 905.0
8 TraesCS7A01G310900 chr5B 97.398 2844 48 4 569 3411 394252536 394255354 0.000000e+00 4819.0
9 TraesCS7A01G310900 chr5B 98.801 1418 17 0 1152 2569 394255766 394257183 0.000000e+00 2525.0
10 TraesCS7A01G310900 chr5B 96.429 252 9 0 3160 3411 394257872 394258123 1.890000e-112 416.0
11 TraesCS7A01G310900 chr5B 96.350 137 4 1 1523 1659 431062130 431061995 1.230000e-54 224.0
12 TraesCS7A01G310900 chr2A 97.323 1756 47 0 1656 3411 628362896 628361141 0.000000e+00 2983.0
13 TraesCS7A01G310900 chr2A 95.855 965 38 2 569 1532 628363858 628362895 0.000000e+00 1559.0
14 TraesCS7A01G310900 chr2A 95.447 571 20 2 1 571 392417941 392417377 0.000000e+00 905.0
15 TraesCS7A01G310900 chr6B 96.871 1758 48 6 1656 3411 471179114 471177362 0.000000e+00 2935.0
16 TraesCS7A01G310900 chr6B 94.041 1762 70 13 1656 3411 157567522 157565790 0.000000e+00 2639.0
17 TraesCS7A01G310900 chr6B 87.600 1000 75 24 570 1532 157568508 157567521 0.000000e+00 1114.0
18 TraesCS7A01G310900 chr6B 92.100 481 26 3 709 1189 471180328 471179860 0.000000e+00 667.0
19 TraesCS7A01G310900 chr6B 90.323 248 19 3 3169 3411 44818345 44818592 1.530000e-83 320.0
20 TraesCS7A01G310900 chr6B 80.913 241 26 18 569 803 209243674 209243900 4.530000e-39 172.0
21 TraesCS7A01G310900 chr3A 95.786 1756 56 9 1656 3411 730385584 730387321 0.000000e+00 2817.0
22 TraesCS7A01G310900 chr3A 95.636 825 36 0 708 1532 730384761 730385585 0.000000e+00 1325.0
23 TraesCS7A01G310900 chr2B 94.847 1766 72 11 1656 3411 38060570 38058814 0.000000e+00 2739.0
24 TraesCS7A01G310900 chr2B 95.998 1624 60 3 1656 3278 674296026 674294407 0.000000e+00 2634.0
25 TraesCS7A01G310900 chr2B 93.863 831 44 2 708 1532 674296854 674296025 0.000000e+00 1245.0
26 TraesCS7A01G310900 chr6A 95.889 754 31 0 779 1532 550724658 550723905 0.000000e+00 1221.0
27 TraesCS7A01G310900 chr6A 95.591 567 19 2 5 571 299777152 299777712 0.000000e+00 904.0
28 TraesCS7A01G310900 chr6A 93.836 146 6 1 1531 1673 602454223 602454078 2.060000e-52 217.0
29 TraesCS7A01G310900 chr3D 95.958 569 17 3 1 569 66507645 66508207 0.000000e+00 918.0
30 TraesCS7A01G310900 chr3D 95.622 571 21 2 1 571 335774969 335774403 0.000000e+00 913.0
31 TraesCS7A01G310900 chr3D 95.606 569 18 4 1 569 432530004 432529443 0.000000e+00 905.0
32 TraesCS7A01G310900 chr7D 95.622 571 19 3 1 571 237435792 237436356 0.000000e+00 911.0
33 TraesCS7A01G310900 chr7D 95.113 573 26 2 1 571 533743848 533744420 0.000000e+00 902.0
34 TraesCS7A01G310900 chr1A 89.310 449 38 6 2972 3411 97177455 97177902 3.850000e-154 555.0
35 TraesCS7A01G310900 chr1B 88.864 449 40 6 2972 3411 72022751 72023198 8.320000e-151 544.0
36 TraesCS7A01G310900 chr1B 89.222 167 14 4 1509 1673 471753720 471753556 4.460000e-49 206.0
37 TraesCS7A01G310900 chr2D 86.667 330 23 6 3090 3411 637615281 637614965 2.520000e-91 346.0
38 TraesCS7A01G310900 chr1D 89.286 196 15 3 3222 3411 207276031 207276226 1.220000e-59 241.0
39 TraesCS7A01G310900 chr4B 90.588 170 10 3 1507 1673 464158443 464158277 1.590000e-53 220.0
40 TraesCS7A01G310900 chr4B 82.381 210 23 12 563 764 531105707 531105504 1.630000e-38 171.0
41 TraesCS7A01G310900 chr4B 82.915 199 23 8 570 767 180242121 180241933 5.850000e-38 169.0
42 TraesCS7A01G310900 chr4D 95.349 43 2 0 1109 1151 66002930 66002972 6.110000e-08 69.4


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 TraesCS7A01G310900 chr7A 439784635 439788045 3410 True 6300.000000 6300 100.000000 1 3411 1 chr7A.!!$R2 3410
1 TraesCS7A01G310900 chr7A 259952426 259952990 564 True 905.000000 905 95.447000 1 571 1 chr7A.!!$R1 570
2 TraesCS7A01G310900 chr7B 645513428 645516257 2829 True 4916.000000 4916 97.960000 570 3411 1 chr7B.!!$R1 2841
3 TraesCS7A01G310900 chr7B 149936260 149938998 2738 True 1678.500000 2669 90.901000 570 3411 2 chr7B.!!$R2 2841
4 TraesCS7A01G310900 chr5A 311017964 311020794 2830 True 4872.000000 4872 97.679000 570 3411 1 chr5A.!!$R1 2841
5 TraesCS7A01G310900 chr5A 17181905 17182469 564 False 905.000000 905 95.447000 1 571 1 chr5A.!!$F1 570
6 TraesCS7A01G310900 chr5B 394252536 394258123 5587 False 2586.666667 4819 97.542667 569 3411 3 chr5B.!!$F1 2842
7 TraesCS7A01G310900 chr2A 628361141 628363858 2717 True 2271.000000 2983 96.589000 569 3411 2 chr2A.!!$R2 2842
8 TraesCS7A01G310900 chr2A 392417377 392417941 564 True 905.000000 905 95.447000 1 571 1 chr2A.!!$R1 570
9 TraesCS7A01G310900 chr6B 157565790 157568508 2718 True 1876.500000 2639 90.820500 570 3411 2 chr6B.!!$R1 2841
10 TraesCS7A01G310900 chr6B 471177362 471180328 2966 True 1801.000000 2935 94.485500 709 3411 2 chr6B.!!$R2 2702
11 TraesCS7A01G310900 chr3A 730384761 730387321 2560 False 2071.000000 2817 95.711000 708 3411 2 chr3A.!!$F1 2703
12 TraesCS7A01G310900 chr2B 38058814 38060570 1756 True 2739.000000 2739 94.847000 1656 3411 1 chr2B.!!$R1 1755
13 TraesCS7A01G310900 chr2B 674294407 674296854 2447 True 1939.500000 2634 94.930500 708 3278 2 chr2B.!!$R2 2570
14 TraesCS7A01G310900 chr6A 550723905 550724658 753 True 1221.000000 1221 95.889000 779 1532 1 chr6A.!!$R1 753
15 TraesCS7A01G310900 chr6A 299777152 299777712 560 False 904.000000 904 95.591000 5 571 1 chr6A.!!$F1 566
16 TraesCS7A01G310900 chr3D 66507645 66508207 562 False 918.000000 918 95.958000 1 569 1 chr3D.!!$F1 568
17 TraesCS7A01G310900 chr3D 335774403 335774969 566 True 913.000000 913 95.622000 1 571 1 chr3D.!!$R1 570
18 TraesCS7A01G310900 chr3D 432529443 432530004 561 True 905.000000 905 95.606000 1 569 1 chr3D.!!$R2 568
19 TraesCS7A01G310900 chr7D 237435792 237436356 564 False 911.000000 911 95.622000 1 571 1 chr7D.!!$F1 570
20 TraesCS7A01G310900 chr7D 533743848 533744420 572 False 902.000000 902 95.113000 1 571 1 chr7D.!!$F2 570

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
154 155 0.485543 TGTCCAGTGACCCACTCCTA 59.514 55.000 0.00 0.0 43.43 2.94 F
1063 1098 1.376466 GAGGCCAGGTTCTGCTTCA 59.624 57.895 5.01 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1214 1344 2.196997 CTGTTCGGGGATGGCCTGAA 62.197 60.0 3.32 0.0 0.00 3.02 R
2782 3325 7.630242 TTCTTTAAGCAAGGGATCAACATAG 57.370 36.0 0.00 0.0 32.64 2.23 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
81 82 3.526534 GAGCTCTTTGTCACCTCCATAC 58.473 50.000 6.43 0.00 0.00 2.39
97 98 5.221441 CCTCCATACACGAGAAACATATCCA 60.221 44.000 0.00 0.00 0.00 3.41
145 146 0.946221 CTTGACCGCTGTCCAGTGAC 60.946 60.000 9.35 4.26 41.01 3.67
154 155 0.485543 TGTCCAGTGACCCACTCCTA 59.514 55.000 0.00 0.00 43.43 2.94
421 422 5.298276 TGTGAAAGTCCAATTAAGCGTCTTT 59.702 36.000 0.00 0.00 0.00 2.52
450 453 7.752518 ATCTCTATAGATCTTGATGCCCAAT 57.247 36.000 0.00 0.00 38.04 3.16
451 454 8.851106 ATCTCTATAGATCTTGATGCCCAATA 57.149 34.615 0.00 0.00 38.04 1.90
452 455 8.851106 TCTCTATAGATCTTGATGCCCAATAT 57.149 34.615 0.00 0.00 33.68 1.28
453 456 9.942526 TCTCTATAGATCTTGATGCCCAATATA 57.057 33.333 0.00 0.00 33.68 0.86
598 609 7.190501 ACTACCACTATAAAAGGAAGAGAGGT 58.809 38.462 0.00 0.00 0.00 3.85
927 961 1.994507 CTCAGCTTGGCCTCCTCCT 60.995 63.158 3.32 0.00 0.00 3.69
1051 1086 3.256960 GGGTTGAGGTGGAGGCCA 61.257 66.667 5.01 0.00 0.00 5.36
1063 1098 1.376466 GAGGCCAGGTTCTGCTTCA 59.624 57.895 5.01 0.00 0.00 3.02
1214 1344 2.748058 AAACGCACGCCTCTCCCAAT 62.748 55.000 0.00 0.00 0.00 3.16
1244 1708 2.354188 CGAACAGCGACCACGACA 60.354 61.111 0.00 0.00 44.57 4.35
1654 2188 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
1686 2220 0.960286 GGAGTACCAGCTACCGATCC 59.040 60.000 0.00 0.00 35.97 3.36
1687 2221 1.688772 GAGTACCAGCTACCGATCCA 58.311 55.000 0.00 0.00 0.00 3.41
2782 3325 6.785191 TGATTTCATAGAATTTGACGGAAGC 58.215 36.000 0.00 0.00 0.00 3.86
2890 3438 9.247861 AGTGAACTCCAATTGCTATAATTCTTT 57.752 29.630 0.00 0.00 0.00 2.52
2891 3439 9.860898 GTGAACTCCAATTGCTATAATTCTTTT 57.139 29.630 0.00 0.00 0.00 2.27
3284 3859 2.433446 GCATCCATCTCGCCCCAT 59.567 61.111 0.00 0.00 0.00 4.00
3292 3867 2.511659 CATCTCGCCCCATTTCATCAT 58.488 47.619 0.00 0.00 0.00 2.45
3336 3911 0.395686 CTGCGATCATGGATGACCCT 59.604 55.000 0.00 0.00 40.03 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 6.090483 AGGACTATGGATATGTTTCTCGTG 57.910 41.667 0.00 0.0 0.00 4.35
97 98 9.853177 CATCCTAAAATACCTGAAAAGGACTAT 57.147 33.333 0.00 0.0 34.64 2.12
145 146 5.163332 GGTACCAAAGTAATCTAGGAGTGGG 60.163 48.000 7.15 0.0 0.00 4.61
154 155 3.200165 GCAGGGAGGTACCAAAGTAATCT 59.800 47.826 15.94 0.0 41.20 2.40
451 454 8.580720 CCTCGGTGAAGCTGCTTATATATATAT 58.419 37.037 15.95 10.1 0.00 0.86
452 455 7.560262 ACCTCGGTGAAGCTGCTTATATATATA 59.440 37.037 15.95 0.0 0.00 0.86
453 456 6.381420 ACCTCGGTGAAGCTGCTTATATATAT 59.619 38.462 15.95 0.0 0.00 0.86
454 457 5.715279 ACCTCGGTGAAGCTGCTTATATATA 59.285 40.000 15.95 0.0 0.00 0.86
455 458 4.528596 ACCTCGGTGAAGCTGCTTATATAT 59.471 41.667 15.95 0.0 0.00 0.86
598 609 3.444742 GGATGTGATTGTTTGGATCTGCA 59.555 43.478 0.00 0.0 0.00 4.41
869 903 4.185286 GGATTTAGGGCGGCGGGT 62.185 66.667 9.78 0.0 0.00 5.28
1051 1086 2.699954 CACCGTAATGAAGCAGAACCT 58.300 47.619 0.00 0.0 0.00 3.50
1214 1344 2.196997 CTGTTCGGGGATGGCCTGAA 62.197 60.000 3.32 0.0 0.00 3.02
1654 2188 4.142204 GCTGGTACTCCCTCTGTAAACTAC 60.142 50.000 0.00 0.0 0.00 2.73
1686 2220 4.036616 TGACATGGTGGATAAAATGCGATG 59.963 41.667 0.00 0.0 0.00 3.84
1687 2221 4.206375 TGACATGGTGGATAAAATGCGAT 58.794 39.130 0.00 0.0 0.00 4.58
2782 3325 7.630242 TTCTTTAAGCAAGGGATCAACATAG 57.370 36.000 0.00 0.0 32.64 2.23
3284 3859 2.609002 CGCTTGGTGATCGATGATGAAA 59.391 45.455 0.54 0.0 0.00 2.69
3292 3867 3.239587 TGTAAATCGCTTGGTGATCGA 57.760 42.857 0.00 0.0 31.05 3.59
3336 3911 1.337384 ATAGGGCGGCATGTCTCACA 61.337 55.000 12.47 0.0 0.00 3.58


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

AutoCloner maintained by Alex Coulton.