Multiple sequence alignment - TraesCS7B01G397800

Loading Multiple Alignment...

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 TraesCS7B01G397800 chr7B 100.000 3236 0 0 1 3236 663842498 663845733 0.000000e+00 5976.0
1 TraesCS7B01G397800 chr7B 94.335 2330 115 10 1 2323 663751978 663749659 0.000000e+00 3555.0
2 TraesCS7B01G397800 chr7B 93.151 146 10 0 2351 2496 663749592 663749447 7.030000e-52 215.0
3 TraesCS7B01G397800 chr7A 95.679 1967 79 4 360 2323 680681158 680679195 0.000000e+00 3157.0
4 TraesCS7B01G397800 chr7A 84.657 743 92 22 2499 3229 287496272 287497004 0.000000e+00 721.0
5 TraesCS7B01G397800 chr7A 92.388 381 21 6 3 378 680681821 680681444 1.320000e-148 536.0
6 TraesCS7B01G397800 chr7D 93.491 1982 85 20 377 2323 589391688 589389716 0.000000e+00 2905.0
7 TraesCS7B01G397800 chr7D 92.466 146 11 0 2351 2496 589389649 589389504 3.270000e-50 209.0
8 TraesCS7B01G397800 chr2B 80.697 2067 297 65 325 2333 138993768 138991746 0.000000e+00 1513.0
9 TraesCS7B01G397800 chr2B 80.328 1769 264 46 450 2157 12421953 12423698 0.000000e+00 1262.0
10 TraesCS7B01G397800 chr2D 80.020 1987 305 46 325 2247 19586527 19588485 0.000000e+00 1386.0
11 TraesCS7B01G397800 chr2D 81.430 1427 232 15 815 2209 8659797 8661222 0.000000e+00 1136.0
12 TraesCS7B01G397800 chr6B 97.432 740 18 1 2497 3236 19042524 19041786 0.000000e+00 1260.0
13 TraesCS7B01G397800 chr2A 80.687 1455 236 23 815 2228 7727400 7728850 0.000000e+00 1088.0
14 TraesCS7B01G397800 chr2A 81.532 444 63 12 1890 2323 86387306 86386872 6.640000e-92 348.0
15 TraesCS7B01G397800 chrUn 82.471 1198 187 17 1094 2275 3529239 3528049 0.000000e+00 1027.0
16 TraesCS7B01G397800 chr4B 97.593 540 13 0 2497 3036 3714570 3715109 0.000000e+00 926.0
17 TraesCS7B01G397800 chr1D 85.333 750 84 25 2498 3236 270635584 270634850 0.000000e+00 752.0
18 TraesCS7B01G397800 chr1D 94.286 35 2 0 113 147 110661040 110661074 2.000000e-03 54.7
19 TraesCS7B01G397800 chr6D 84.906 742 91 21 2498 3229 441372930 441373660 0.000000e+00 730.0
20 TraesCS7B01G397800 chr6A 84.820 751 86 25 2498 3236 419772840 419773574 0.000000e+00 730.0
21 TraesCS7B01G397800 chr4A 84.771 742 87 25 2500 3227 702725132 702725861 0.000000e+00 721.0
22 TraesCS7B01G397800 chr4A 84.140 744 101 16 2497 3235 534528346 534527615 0.000000e+00 704.0
23 TraesCS7B01G397800 chr3A 84.154 751 91 26 2500 3236 702587594 702588330 0.000000e+00 702.0
24 TraesCS7B01G397800 chr3D 83.495 206 31 2 2046 2249 563992798 563992594 4.260000e-44 189.0
25 TraesCS7B01G397800 chr5B 94.444 36 2 0 113 148 474466674 474466709 4.510000e-04 56.5
26 TraesCS7B01G397800 chr1B 94.286 35 2 0 113 147 168623169 168623203 2.000000e-03 54.7


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 TraesCS7B01G397800 chr7B 663842498 663845733 3235 False 5976.0 5976 100.0000 1 3236 1 chr7B.!!$F1 3235
1 TraesCS7B01G397800 chr7B 663749447 663751978 2531 True 1885.0 3555 93.7430 1 2496 2 chr7B.!!$R1 2495
2 TraesCS7B01G397800 chr7A 680679195 680681821 2626 True 1846.5 3157 94.0335 3 2323 2 chr7A.!!$R1 2320
3 TraesCS7B01G397800 chr7A 287496272 287497004 732 False 721.0 721 84.6570 2499 3229 1 chr7A.!!$F1 730
4 TraesCS7B01G397800 chr7D 589389504 589391688 2184 True 1557.0 2905 92.9785 377 2496 2 chr7D.!!$R1 2119
5 TraesCS7B01G397800 chr2B 138991746 138993768 2022 True 1513.0 1513 80.6970 325 2333 1 chr2B.!!$R1 2008
6 TraesCS7B01G397800 chr2B 12421953 12423698 1745 False 1262.0 1262 80.3280 450 2157 1 chr2B.!!$F1 1707
7 TraesCS7B01G397800 chr2D 19586527 19588485 1958 False 1386.0 1386 80.0200 325 2247 1 chr2D.!!$F2 1922
8 TraesCS7B01G397800 chr2D 8659797 8661222 1425 False 1136.0 1136 81.4300 815 2209 1 chr2D.!!$F1 1394
9 TraesCS7B01G397800 chr6B 19041786 19042524 738 True 1260.0 1260 97.4320 2497 3236 1 chr6B.!!$R1 739
10 TraesCS7B01G397800 chr2A 7727400 7728850 1450 False 1088.0 1088 80.6870 815 2228 1 chr2A.!!$F1 1413
11 TraesCS7B01G397800 chrUn 3528049 3529239 1190 True 1027.0 1027 82.4710 1094 2275 1 chrUn.!!$R1 1181
12 TraesCS7B01G397800 chr4B 3714570 3715109 539 False 926.0 926 97.5930 2497 3036 1 chr4B.!!$F1 539
13 TraesCS7B01G397800 chr1D 270634850 270635584 734 True 752.0 752 85.3330 2498 3236 1 chr1D.!!$R1 738
14 TraesCS7B01G397800 chr6D 441372930 441373660 730 False 730.0 730 84.9060 2498 3229 1 chr6D.!!$F1 731
15 TraesCS7B01G397800 chr6A 419772840 419773574 734 False 730.0 730 84.8200 2498 3236 1 chr6A.!!$F1 738
16 TraesCS7B01G397800 chr4A 702725132 702725861 729 False 721.0 721 84.7710 2500 3227 1 chr4A.!!$F1 727
17 TraesCS7B01G397800 chr4A 534527615 534528346 731 True 704.0 704 84.1400 2497 3235 1 chr4A.!!$R1 738
18 TraesCS7B01G397800 chr3A 702587594 702588330 736 False 702.0 702 84.1540 2500 3236 1 chr3A.!!$F1 736

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
808 1174 0.108615 CCCTCATCGACTGTGTGGTC 60.109 60.0 5.22 0.0 0.0 4.02 F
1564 1994 0.392863 TGGGATGATGCTGGTCGTTG 60.393 55.0 0.00 0.0 0.0 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 2445 1.202336 GCAAGCTAAGCGGATGCAAAT 60.202 47.619 0.0 0.0 46.23 2.32 R
2402 2903 2.178912 TTTAAGAACGAGCAGGTGGG 57.821 50.000 0.0 0.0 0.00 4.61 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
72 75 3.305676 GGACGACCGAAGATGATGATGAT 60.306 47.826 0.00 0.0 0.00 2.45
73 76 3.646946 ACGACCGAAGATGATGATGATG 58.353 45.455 0.00 0.0 0.00 3.07
74 77 2.991866 CGACCGAAGATGATGATGATGG 59.008 50.000 0.00 0.0 0.00 3.51
121 124 7.863375 TGAATTGTACTTGAAATAAAACCACGG 59.137 33.333 0.00 0.0 0.00 4.94
122 125 6.696441 TTGTACTTGAAATAAAACCACGGT 57.304 33.333 0.00 0.0 0.00 4.83
267 270 4.393062 CAGTACTAAAGCATGGAGTTGTGG 59.607 45.833 0.00 0.0 0.00 4.17
281 284 3.679389 AGTTGTGGTTCTCATCATCACC 58.321 45.455 0.00 0.0 0.00 4.02
282 285 3.328931 AGTTGTGGTTCTCATCATCACCT 59.671 43.478 0.00 0.0 0.00 4.00
283 286 3.616956 TGTGGTTCTCATCATCACCTC 57.383 47.619 0.00 0.0 0.00 3.85
295 301 2.026262 TCATCACCTCAGGTAAAAGGGC 60.026 50.000 0.00 0.0 36.95 5.19
488 830 9.535170 TGGAACAATATTAATTTGAACCTACCA 57.465 29.630 13.71 0.0 31.92 3.25
634 982 8.365647 GCCAATATACAGTACAACTACAGGTAT 58.634 37.037 0.00 0.0 33.56 2.73
675 1025 1.594836 GCAACCGTACGTCACCCAA 60.595 57.895 15.21 0.0 0.00 4.12
682 1032 2.354003 CCGTACGTCACCCAACCTTTAT 60.354 50.000 15.21 0.0 0.00 1.40
808 1174 0.108615 CCCTCATCGACTGTGTGGTC 60.109 60.000 5.22 0.0 0.00 4.02
823 1190 2.512515 GTCGCTGTCATGGAGGCC 60.513 66.667 0.00 0.0 0.00 5.19
874 1241 4.158025 GTGAGTCGTTTCATCTCCTTCCTA 59.842 45.833 0.00 0.0 0.00 2.94
898 1268 3.709653 TGAACAAGTACCACTCCTTGAGT 59.290 43.478 6.41 0.0 44.44 3.41
945 1319 2.121948 AGATTGCAGCACCTCCTGATA 58.878 47.619 0.00 0.0 34.77 2.15
1048 1422 1.644509 TGCCATGTACAGAGGACACT 58.355 50.000 18.55 0.0 0.00 3.55
1058 1432 4.320456 AGGACACTGCACGCTGGG 62.320 66.667 0.00 0.0 0.00 4.45
1098 1520 0.738975 TCCAAGATAGTGCCGACTCG 59.261 55.000 0.00 0.0 33.21 4.18
1150 1572 2.031191 TCCAAGCGTTCTCGAACAAAAC 59.969 45.455 10.10 0.0 41.20 2.43
1262 1684 3.790437 CCTGGGTGGATGCGAGCT 61.790 66.667 0.00 0.0 38.35 4.09
1356 1778 6.488006 AGCAAAAGCTCTTGAGATTCTTGTTA 59.512 34.615 3.32 0.0 0.00 2.41
1367 1789 3.997021 AGATTCTTGTTAGAGCACAACGG 59.003 43.478 0.00 0.0 33.04 4.44
1504 1928 6.189859 TCCTCTATTTTGCACTTGAATGGAT 58.810 36.000 0.00 0.0 0.00 3.41
1516 1940 7.998383 TGCACTTGAATGGATATAACCTATTGT 59.002 33.333 0.24 0.0 0.00 2.71
1564 1994 0.392863 TGGGATGATGCTGGTCGTTG 60.393 55.000 0.00 0.0 0.00 4.10
1875 2305 1.662517 ATGTGTTCGCGGATGCATTA 58.337 45.000 6.13 0.0 42.97 1.90
1945 2375 7.292356 AGGGGATGAAAATGGTTAAAAGAAACT 59.708 33.333 0.00 0.0 0.00 2.66
2015 2445 0.813184 GTGGACATAACGGACCTCGA 59.187 55.000 0.00 0.0 42.43 4.04
2082 2536 0.401738 CAAGTGTGACACTGGGGGAT 59.598 55.000 20.19 0.0 44.62 3.85
2233 2693 2.262774 CTTGCCAGGGAGGAAGCGAT 62.263 60.000 0.00 0.0 41.22 4.58
2333 2821 4.216902 CAGATGGATGTGTGTGTTCATGTT 59.783 41.667 0.00 0.0 0.00 2.71
2335 2823 4.998671 TGGATGTGTGTGTTCATGTTTT 57.001 36.364 0.00 0.0 0.00 2.43
2336 2824 5.336150 TGGATGTGTGTGTTCATGTTTTT 57.664 34.783 0.00 0.0 0.00 1.94
2413 2914 0.250124 TACAACAACCCACCTGCTCG 60.250 55.000 0.00 0.0 0.00 5.03
3031 3544 4.100084 CAGCTCGGATGTGGGGCA 62.100 66.667 0.00 0.0 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 75 0.840617 TGGCTGTGTTGTCCTTACCA 59.159 50.000 0.00 0.00 0.00 3.25
73 76 1.812571 CATGGCTGTGTTGTCCTTACC 59.187 52.381 0.00 0.00 0.00 2.85
74 77 2.778299 TCATGGCTGTGTTGTCCTTAC 58.222 47.619 0.00 0.00 0.00 2.34
121 124 5.163332 ACTCCCTCCGATCCAAAATAAGTAC 60.163 44.000 0.00 0.00 0.00 2.73
122 125 4.966805 ACTCCCTCCGATCCAAAATAAGTA 59.033 41.667 0.00 0.00 0.00 2.24
168 171 2.063378 CCAGGTGAGAGGAGGAGGC 61.063 68.421 0.00 0.00 0.00 4.70
255 258 3.678289 TGATGAGAACCACAACTCCATG 58.322 45.455 0.00 0.00 32.84 3.66
267 270 3.902881 ACCTGAGGTGATGATGAGAAC 57.097 47.619 1.77 0.00 32.98 3.01
281 284 2.213499 CTATGCGCCCTTTTACCTGAG 58.787 52.381 4.18 0.00 0.00 3.35
282 285 1.745827 GCTATGCGCCCTTTTACCTGA 60.746 52.381 4.18 0.00 0.00 3.86
283 286 0.663153 GCTATGCGCCCTTTTACCTG 59.337 55.000 4.18 0.00 0.00 4.00
295 301 3.967123 CATTGGCATGATAACGCTATGCG 60.967 47.826 10.49 10.49 46.09 4.73
527 870 2.146342 ACTGTCCGAGCAACATGAAAG 58.854 47.619 0.00 0.00 0.00 2.62
660 1010 1.402107 AAGGTTGGGTGACGTACGGT 61.402 55.000 21.06 5.07 0.00 4.83
665 1015 3.196254 ACGATATAAAGGTTGGGTGACGT 59.804 43.478 0.00 0.00 0.00 4.34
675 1025 6.202954 GCTATTGACTTGCACGATATAAAGGT 59.797 38.462 0.00 0.00 0.00 3.50
682 1032 3.871006 CCAAGCTATTGACTTGCACGATA 59.129 43.478 0.00 0.00 42.57 2.92
808 1174 2.202987 GAGGCCTCCATGACAGCG 60.203 66.667 23.19 0.00 0.00 5.18
823 1190 6.961360 TCACCTGTAACTGTAGATATGGAG 57.039 41.667 0.00 0.00 0.00 3.86
833 1200 4.141482 ACTCACCAATTCACCTGTAACTGT 60.141 41.667 0.00 0.00 0.00 3.55
874 1241 5.163195 ACTCAAGGAGTGGTACTTGTTCATT 60.163 40.000 0.00 0.00 41.76 2.57
898 1268 3.264193 ACCACCTTCTCTATTGTGCATGA 59.736 43.478 0.00 0.00 0.00 3.07
945 1319 0.179187 CGACGACGATGCTGACTCTT 60.179 55.000 0.00 0.00 42.66 2.85
1058 1432 0.887387 TGTTTGGTACCTCAAGGCGC 60.887 55.000 14.36 0.00 39.32 6.53
1150 1572 2.295885 GGCCTTGTCATCATTCTCAGG 58.704 52.381 0.00 0.00 0.00 3.86
1262 1684 3.496331 TCATATGGCCTACGAGACATGA 58.504 45.455 3.32 0.00 0.00 3.07
1303 1725 1.795768 TGTCGGCTGAACATGAAGTC 58.204 50.000 0.00 0.00 0.00 3.01
1367 1789 0.179702 TGCATGATCACCAGGAGAGC 59.820 55.000 0.00 0.00 0.00 4.09
1504 1928 8.467963 TGGTCAAGTATCGACAATAGGTTATA 57.532 34.615 0.00 0.00 34.97 0.98
1516 1940 3.132289 GTCCTTCCATGGTCAAGTATCGA 59.868 47.826 12.58 0.00 0.00 3.59
1564 1994 5.931441 ACTACATCAGAAGCAAACTCAAC 57.069 39.130 0.00 0.00 0.00 3.18
1631 2061 3.555527 TGATGATCTTGCTTCCTCTGG 57.444 47.619 0.00 0.00 0.00 3.86
1875 2305 5.113446 ACTGAGCATGATGATTCCTTCTT 57.887 39.130 0.00 0.00 0.00 2.52
1945 2375 3.193267 GGATGCAAACCATAGCTTGACAA 59.807 43.478 8.18 0.00 33.29 3.18
2015 2445 1.202336 GCAAGCTAAGCGGATGCAAAT 60.202 47.619 0.00 0.00 46.23 2.32
2082 2536 6.768861 GTCTAACACTAGGATCTGCTAGAAGA 59.231 42.308 1.89 1.89 0.00 2.87
2233 2693 4.259356 CAGAATCAGATTTGCAGTCCTCA 58.741 43.478 0.00 0.00 0.00 3.86
2296 2758 7.148474 ACACATCCATCTGTCGTGTTTTATTAC 60.148 37.037 0.00 0.00 37.53 1.89
2307 2769 2.084610 ACACACACATCCATCTGTCG 57.915 50.000 0.00 0.00 0.00 4.35
2349 2837 6.491403 ACAAGTTCAAGGTATGCTTTGAGATT 59.509 34.615 8.29 5.35 40.87 2.40
2389 2890 2.364002 GCAGGTGGGTTGTTGTATTTGT 59.636 45.455 0.00 0.00 0.00 2.83
2392 2893 2.514803 GAGCAGGTGGGTTGTTGTATT 58.485 47.619 0.00 0.00 0.00 1.89
2402 2903 2.178912 TTTAAGAACGAGCAGGTGGG 57.821 50.000 0.00 0.00 0.00 4.61
2452 2953 2.344025 CACCTTACCGAAACCAGCTAC 58.656 52.381 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.