Multiple sequence alignment - TraesCS2B01G248500

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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 TraesCS2B01G248500 chr2B 100.000 3052 0 0 1 3052 254788801 254785750 0.000000e+00 5637.0
1 TraesCS2B01G248500 chr2B 93.917 674 35 4 1 669 42484043 42484715 0.000000e+00 1013.0
2 TraesCS2B01G248500 chr2B 97.065 443 11 2 2535 2975 19185896 19185454 0.000000e+00 745.0
3 TraesCS2B01G248500 chr2B 89.286 168 18 0 775 942 702253846 702254013 8.570000e-51 211.0
4 TraesCS2B01G248500 chr7B 92.342 2494 162 13 4 2492 331541242 331538773 0.000000e+00 3520.0
5 TraesCS2B01G248500 chr7B 97.500 520 11 2 2535 3052 701854801 701855320 0.000000e+00 887.0
6 TraesCS2B01G248500 chr7B 89.552 670 50 11 4 657 314866178 314865513 0.000000e+00 832.0
7 TraesCS2B01G248500 chr7B 98.458 389 6 0 2664 3052 702921193 702921581 0.000000e+00 686.0
8 TraesCS2B01G248500 chr7B 90.971 443 32 8 913 1351 53628622 53629060 9.420000e-165 590.0
9 TraesCS2B01G248500 chr7B 91.275 298 13 1 2191 2475 532502280 532501983 7.930000e-106 394.0
10 TraesCS2B01G248500 chr7B 90.397 302 24 3 1896 2192 53630152 53630453 2.850000e-105 392.0
11 TraesCS2B01G248500 chr7B 91.270 126 5 2 1536 1661 53629474 53629593 1.880000e-37 167.0
12 TraesCS2B01G248500 chrUn 97.138 1118 31 1 1427 2543 265946823 265947940 0.000000e+00 1886.0
13 TraesCS2B01G248500 chrUn 96.894 1127 34 1 1427 2552 324063784 324062658 0.000000e+00 1886.0
14 TraesCS2B01G248500 chrUn 95.287 679 29 3 140 816 433015530 433014853 0.000000e+00 1074.0
15 TraesCS2B01G248500 chrUn 94.118 510 30 0 874 1383 265946148 265946657 0.000000e+00 776.0
16 TraesCS2B01G248500 chrUn 93.830 470 29 0 874 1343 433014852 433014383 0.000000e+00 708.0
17 TraesCS2B01G248500 chr7A 91.528 720 51 6 946 1661 100719468 100720181 0.000000e+00 983.0
18 TraesCS2B01G248500 chr7A 91.582 297 13 4 2191 2475 673782103 673782399 1.700000e-107 399.0
19 TraesCS2B01G248500 chr7A 90.690 290 23 1 1896 2181 100720739 100721028 1.720000e-102 383.0
20 TraesCS2B01G248500 chr7A 83.077 195 20 6 1705 1888 100720353 100720545 6.770000e-37 165.0
21 TraesCS2B01G248500 chr7A 89.362 47 5 0 2506 2552 199440623 199440577 3.290000e-05 60.2
22 TraesCS2B01G248500 chr7D 91.903 704 44 6 946 1646 98619953 98620646 0.000000e+00 972.0
23 TraesCS2B01G248500 chr7D 92.282 298 10 1 2191 2475 59967224 59967521 7.880000e-111 411.0
24 TraesCS2B01G248500 chr7D 91.582 297 22 1 1896 2192 98621218 98621511 1.020000e-109 407.0
25 TraesCS2B01G248500 chr7D 91.611 298 12 5 2191 2475 48000997 48001294 1.700000e-107 399.0
26 TraesCS2B01G248500 chr7D 89.231 195 8 5 1705 1888 98620839 98621031 6.580000e-57 231.0
27 TraesCS2B01G248500 chr2A 90.015 661 55 8 4 657 746064708 746065364 0.000000e+00 845.0
28 TraesCS2B01G248500 chr2A 88.350 206 17 6 740 942 133173587 133173788 1.090000e-59 241.0
29 TraesCS2B01G248500 chr2A 89.362 47 5 0 2506 2552 269307130 269307084 3.290000e-05 60.2
30 TraesCS2B01G248500 chr1A 87.967 723 67 15 1 709 566950629 566951345 0.000000e+00 835.0
31 TraesCS2B01G248500 chr1A 88.389 689 58 13 4 674 98351048 98350364 0.000000e+00 809.0
32 TraesCS2B01G248500 chr1B 89.259 661 59 10 4 657 619353039 619352384 0.000000e+00 817.0
33 TraesCS2B01G248500 chr1B 98.458 389 6 0 2664 3052 56050567 56050179 0.000000e+00 686.0
34 TraesCS2B01G248500 chr1B 89.320 206 15 6 740 942 666316309 666316510 5.050000e-63 252.0
35 TraesCS2B01G248500 chr5B 86.863 746 71 17 4 733 58384587 58383853 0.000000e+00 809.0
36 TraesCS2B01G248500 chr5B 98.458 389 6 0 2664 3052 572032537 572032925 0.000000e+00 686.0
37 TraesCS2B01G248500 chr5B 89.119 193 16 4 751 942 58383884 58383696 5.090000e-58 235.0
38 TraesCS2B01G248500 chr6B 97.045 440 11 2 2535 2972 506169791 506170230 0.000000e+00 739.0
39 TraesCS2B01G248500 chr6B 98.201 389 7 0 2664 3052 709226303 709225915 0.000000e+00 680.0
40 TraesCS2B01G248500 chr6B 91.275 298 13 1 2191 2475 64075863 64075566 7.930000e-106 394.0
41 TraesCS2B01G248500 chr6B 80.421 475 52 23 958 1420 17377202 17377647 1.060000e-84 324.0
42 TraesCS2B01G248500 chr4A 95.918 441 15 2 2535 2972 735511682 735512122 0.000000e+00 712.0
43 TraesCS2B01G248500 chr4A 93.617 47 3 0 1374 1420 724134385 724134339 1.520000e-08 71.3
44 TraesCS2B01G248500 chr3B 98.715 389 5 0 2664 3052 35328305 35327917 0.000000e+00 691.0
45 TraesCS2B01G248500 chr1D 92.282 298 10 6 2191 2475 308871690 308871393 7.880000e-111 411.0
46 TraesCS2B01G248500 chr1D 91.611 298 12 5 2191 2475 319795642 319795345 1.700000e-107 399.0
47 TraesCS2B01G248500 chr5A 91.722 302 11 2 2191 2478 81351522 81351823 1.020000e-109 407.0
48 TraesCS2B01G248500 chr5A 80.929 409 31 23 504 903 630075477 630075847 2.320000e-71 279.0
49 TraesCS2B01G248500 chr4D 91.275 298 13 5 2191 2475 17109013 17108716 7.930000e-106 394.0
50 TraesCS2B01G248500 chr4D 85.492 193 22 5 751 942 491803951 491804138 2.400000e-46 196.0
51 TraesCS2B01G248500 chr6D 81.004 458 51 20 985 1434 9346543 9346972 6.310000e-87 331.0
52 TraesCS2B01G248500 chr6A 86.032 315 30 11 964 1269 11252304 11251995 2.930000e-85 326.0
53 TraesCS2B01G248500 chr6A 89.119 193 16 4 751 942 551933178 551932990 5.090000e-58 235.0
54 TraesCS2B01G248500 chr6A 90.541 74 3 4 1365 1434 11251932 11251859 9.010000e-16 95.3
55 TraesCS2B01G248500 chr4B 91.716 169 14 0 774 942 141880373 141880541 5.090000e-58 235.0
56 TraesCS2B01G248500 chr4B 85.938 192 24 1 751 942 137773589 137773777 5.160000e-48 202.0
57 TraesCS2B01G248500 chr3A 89.362 47 5 0 2506 2552 689755561 689755515 3.290000e-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 TraesCS2B01G248500 chr2B 254785750 254788801 3051 True 5637.000000 5637 100.000000 1 3052 1 chr2B.!!$R2 3051
1 TraesCS2B01G248500 chr2B 42484043 42484715 672 False 1013.000000 1013 93.917000 1 669 1 chr2B.!!$F1 668
2 TraesCS2B01G248500 chr7B 331538773 331541242 2469 True 3520.000000 3520 92.342000 4 2492 1 chr7B.!!$R2 2488
3 TraesCS2B01G248500 chr7B 701854801 701855320 519 False 887.000000 887 97.500000 2535 3052 1 chr7B.!!$F1 517
4 TraesCS2B01G248500 chr7B 314865513 314866178 665 True 832.000000 832 89.552000 4 657 1 chr7B.!!$R1 653
5 TraesCS2B01G248500 chr7B 53628622 53630453 1831 False 383.000000 590 90.879333 913 2192 3 chr7B.!!$F3 1279
6 TraesCS2B01G248500 chrUn 324062658 324063784 1126 True 1886.000000 1886 96.894000 1427 2552 1 chrUn.!!$R1 1125
7 TraesCS2B01G248500 chrUn 265946148 265947940 1792 False 1331.000000 1886 95.628000 874 2543 2 chrUn.!!$F1 1669
8 TraesCS2B01G248500 chrUn 433014383 433015530 1147 True 891.000000 1074 94.558500 140 1343 2 chrUn.!!$R2 1203
9 TraesCS2B01G248500 chr7A 100719468 100721028 1560 False 510.333333 983 88.431667 946 2181 3 chr7A.!!$F2 1235
10 TraesCS2B01G248500 chr7D 98619953 98621511 1558 False 536.666667 972 90.905333 946 2192 3 chr7D.!!$F3 1246
11 TraesCS2B01G248500 chr2A 746064708 746065364 656 False 845.000000 845 90.015000 4 657 1 chr2A.!!$F2 653
12 TraesCS2B01G248500 chr1A 566950629 566951345 716 False 835.000000 835 87.967000 1 709 1 chr1A.!!$F1 708
13 TraesCS2B01G248500 chr1A 98350364 98351048 684 True 809.000000 809 88.389000 4 674 1 chr1A.!!$R1 670
14 TraesCS2B01G248500 chr1B 619352384 619353039 655 True 817.000000 817 89.259000 4 657 1 chr1B.!!$R2 653
15 TraesCS2B01G248500 chr5B 58383696 58384587 891 True 522.000000 809 87.991000 4 942 2 chr5B.!!$R1 938

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
908 947 0.539901 ATGGCGGGATAGTCTAGCGT 60.54 55.0 0.0 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2787 3493 1.584724 ACAAGATGAACTCCCCGGAT 58.415 50.0 0.73 0.0 0.0 4.18 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
117 122 7.466746 AAATAAAGAGCAAACTATGAGGCAA 57.533 32.000 0.00 0.00 0.00 4.52
119 124 2.716217 AGAGCAAACTATGAGGCAACC 58.284 47.619 0.00 0.00 37.17 3.77
138 143 3.642141 ACCACAGTTCAAATTTGACCCT 58.358 40.909 20.35 15.48 36.83 4.34
184 189 2.143925 GTCTTTTTCACGAGAGGTGGG 58.856 52.381 0.00 0.00 46.96 4.61
451 460 7.066043 ACAAATTATGCCATTCGAAAATGCATT 59.934 29.630 26.66 5.99 40.85 3.56
520 529 4.326504 AAGCTTTGTTCTCATTGGTTGG 57.673 40.909 0.00 0.00 0.00 3.77
764 803 1.840650 CCCTCATCCTCTCCCGCAT 60.841 63.158 0.00 0.00 0.00 4.73
908 947 0.539901 ATGGCGGGATAGTCTAGCGT 60.540 55.000 0.00 0.00 0.00 5.07
968 1007 2.841988 GCTCGCCTCCTCCTCCAT 60.842 66.667 0.00 0.00 0.00 3.41
1038 1077 3.745803 GGCGTTCTCCGACGGTCT 61.746 66.667 14.79 0.00 42.98 3.85
1042 1081 1.296755 CGTTCTCCGACGGTCTCTCA 61.297 60.000 14.79 0.00 39.27 3.27
1340 1380 2.971660 TTTCCGTGACTTCACTGTGA 57.028 45.000 6.36 6.36 44.34 3.58
1354 1394 7.901029 ACTTCACTGTGATTTCTTGATCTCTA 58.099 34.615 11.86 0.00 0.00 2.43
1410 1450 2.674754 GGGGATTCGGCACAAGGA 59.325 61.111 0.00 0.00 0.00 3.36
1548 1818 1.202394 GCAGATTGTTGTGTGCACCAA 60.202 47.619 15.69 14.90 38.19 3.67
1731 2229 6.942532 AAAGAAGCAGAGAACATGTAACAA 57.057 33.333 0.00 0.00 0.00 2.83
1747 2245 9.921637 ACATGTAACAATTATTTACCAGGTTTG 57.078 29.630 0.00 0.00 0.00 2.93
1905 2601 6.445786 TGGTTACTACCCCAATTGATCTAACT 59.554 38.462 7.12 0.00 44.35 2.24
1908 2604 5.193679 ACTACCCCAATTGATCTAACTTGC 58.806 41.667 7.12 0.00 0.00 4.01
2001 2697 2.096980 GGTTGGAAGTACATAAAGGCGC 59.903 50.000 0.00 0.00 0.00 6.53
2417 3122 9.686683 AATCTCCTAGTTGCATTTATTTACTGT 57.313 29.630 0.00 0.00 0.00 3.55
2501 3206 6.460123 CCAGGTTAATCATTACAGCCAATCAC 60.460 42.308 0.00 0.00 0.00 3.06
2576 3281 6.321435 TCCATAGAACTGAATATCGCGGATAT 59.679 38.462 6.13 5.76 36.89 1.63
2589 3294 3.379057 TCGCGGATATAACTGTTCAGTCA 59.621 43.478 6.13 0.00 0.00 3.41
2623 3328 4.437772 AGTAGCTACTGAAAACCGACTC 57.562 45.455 25.52 0.00 34.72 3.36
2770 3475 6.320164 AGCACTGTAGTAACCTTCTAGATCAG 59.680 42.308 0.00 0.00 0.00 2.90
2841 3547 7.102346 AGATCATGAAGTTTCTAGGACAGTTG 58.898 38.462 0.00 0.00 0.00 3.16
2899 3605 6.797033 GTGTATGAAAGAAACAAGTTGATCCG 59.203 38.462 10.54 0.00 0.00 4.18
3004 3710 4.286032 ACTTAGGAGGCAGTGACATAACAA 59.714 41.667 0.00 0.00 0.00 2.83
3014 3720 6.878923 GGCAGTGACATAACAATATATGCCTA 59.121 38.462 0.00 0.00 44.68 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 122 3.636764 GAGGGTCAAATTTGAACTGTGGT 59.363 43.478 30.02 13.64 44.25 4.16
119 124 5.507985 GGAAGAGGGTCAAATTTGAACTGTG 60.508 44.000 30.02 0.45 44.25 3.66
138 143 1.153568 CGCCGATTCAGCAGGAAGA 60.154 57.895 0.00 0.00 39.30 2.87
184 189 4.991687 TGGTTTGGTGTCAAAAGTTTTGAC 59.008 37.500 37.61 37.61 46.57 3.18
254 259 5.964958 TTTGTTGCAAAATTGGACCAAAA 57.035 30.435 11.82 0.00 37.79 2.44
342 350 9.243105 CTAAGGAGTTTCCATTTCCTTTTGATA 57.757 33.333 9.98 0.00 46.47 2.15
496 505 6.945435 TCCAACCAATGAGAACAAAGCTTATA 59.055 34.615 0.00 0.00 0.00 0.98
631 664 1.000041 TAGGGTTTGGGTGGTTGGGT 61.000 55.000 0.00 0.00 0.00 4.51
1024 1063 0.448593 CTGAGAGACCGTCGGAGAAC 59.551 60.000 20.51 6.36 39.69 3.01
1058 1097 3.316573 CTCAGGGCCCTCACGGTTC 62.317 68.421 25.77 0.00 0.00 3.62
1064 1103 4.980592 TGGTGCTCAGGGCCCTCA 62.981 66.667 25.77 15.54 40.92 3.86
1354 1394 4.275810 GGCCATCCTGCATCAATACATAT 58.724 43.478 0.00 0.00 0.00 1.78
1434 1596 6.972328 CCAATCCAATAAATTAACGGACAGTG 59.028 38.462 0.00 0.00 0.00 3.66
1548 1818 0.106149 ACCGAAACCGAAACAGAGCT 59.894 50.000 0.00 0.00 0.00 4.09
1747 2245 6.278363 AGTGATGCAATGGATAAAGCATTTC 58.722 36.000 0.00 0.00 46.71 2.17
1751 2249 4.823442 CCTAGTGATGCAATGGATAAAGCA 59.177 41.667 0.00 0.00 41.73 3.91
1833 2343 7.147915 GCAGGGAAAACATGATTTATCTTGGTA 60.148 37.037 0.00 0.00 36.57 3.25
1905 2601 4.761227 TGCAAGAGAAACATACAGATGCAA 59.239 37.500 0.00 0.00 38.22 4.08
1908 2604 4.201891 GCCTGCAAGAGAAACATACAGATG 60.202 45.833 0.00 0.00 35.81 2.90
1965 2661 2.025898 CCAACCACGTTTGTTAACCCT 58.974 47.619 2.48 0.00 0.00 4.34
2112 2817 4.003648 AGCCAACCTTCTGAATAGTTTCG 58.996 43.478 3.89 0.55 34.39 3.46
2417 3122 2.106477 TCACGATGGCATAGCAACAA 57.894 45.000 7.56 0.00 0.00 2.83
2501 3206 6.072508 TGCTGAACTTTCTTTATGCAACTAGG 60.073 38.462 0.00 0.00 0.00 3.02
2589 3294 7.185318 TCAGTAGCTACTACTAAGACAGACT 57.815 40.000 25.63 0.00 44.37 3.24
2623 3328 3.066342 AGAGATTTCCATGAAGCAATGCG 59.934 43.478 0.00 0.00 0.00 4.73
2770 3475 6.544564 TCCCCGGATAAAATCACTAAATGAAC 59.455 38.462 0.73 0.00 41.93 3.18
2787 3493 1.584724 ACAAGATGAACTCCCCGGAT 58.415 50.000 0.73 0.00 0.00 4.18
2841 3547 2.149578 CTATCATACAAGCAGGCAGGC 58.850 52.381 0.00 0.00 0.00 4.85
2892 3598 2.235402 GTCACCTAAGGAACCGGATCAA 59.765 50.000 9.46 0.00 0.00 2.57
2899 3605 1.613520 GCCTTGGTCACCTAAGGAACC 60.614 57.143 22.53 5.38 44.98 3.62


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

AutoCloner maintained by Alex Coulton.