Multiple sequence alignment - TraesCS7B01G273900

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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 TraesCS7B01G273900 chr7B 100.000 2634 0 0 930 3563 503106615 503109248 0.000000e+00 4865
1 TraesCS7B01G273900 chr7B 93.135 1646 108 2 966 2606 502908432 502910077 0.000000e+00 2409
2 TraesCS7B01G273900 chr7B 89.802 1667 152 12 976 2631 654252907 654251248 0.000000e+00 2121
3 TraesCS7B01G273900 chr7B 91.513 813 69 0 2751 3563 731344730 731345542 0.000000e+00 1120
4 TraesCS7B01G273900 chr7B 100.000 284 0 0 1 284 503105686 503105969 3.150000e-145 525
5 TraesCS7B01G273900 chr7D 95.486 1728 76 2 930 2656 477968700 477970426 0.000000e+00 2758
6 TraesCS7B01G273900 chr7D 92.674 1679 116 3 966 2639 477865486 477867162 0.000000e+00 2412
7 TraesCS7B01G273900 chr7D 90.800 1587 134 8 971 2547 585538056 585539640 0.000000e+00 2111
8 TraesCS7B01G273900 chr7D 95.849 265 9 1 19 281 477968368 477968632 9.140000e-116 427
9 TraesCS7B01G273900 chr7D 82.749 342 57 2 3223 3563 340268700 340269040 1.610000e-78 303
10 TraesCS7B01G273900 chr7A 95.038 1733 84 2 930 2661 517895654 517893923 0.000000e+00 2723
11 TraesCS7B01G273900 chr7A 92.138 1679 119 6 966 2639 518505692 518504022 0.000000e+00 2357
12 TraesCS7B01G273900 chr7A 89.448 1668 150 15 977 2622 675574099 675575762 0.000000e+00 2082
13 TraesCS7B01G273900 chr7A 91.515 165 11 3 15 177 517903292 517903129 1.290000e-54 224
14 TraesCS7B01G273900 chr7A 95.935 123 5 0 162 284 517895841 517895719 2.170000e-47 200
15 TraesCS7B01G273900 chr4A 96.251 907 25 3 2657 3563 703333827 703334724 0.000000e+00 1478
16 TraesCS7B01G273900 chr4A 90.187 907 86 3 2659 3563 619942586 619943491 0.000000e+00 1179
17 TraesCS7B01G273900 chr1B 90.909 902 60 12 2663 3563 26861098 26861978 0.000000e+00 1192
18 TraesCS7B01G273900 chr1B 80.405 148 23 6 2662 2807 231934212 231934069 1.350000e-19 108
19 TraesCS7B01G273900 chr3B 87.845 905 96 8 2661 3563 712555813 712554921 0.000000e+00 1050
20 TraesCS7B01G273900 chr3A 75.217 1380 302 37 1182 2541 33137250 33138609 5.050000e-173 617
21 TraesCS7B01G273900 chr5D 74.600 1374 291 47 1206 2544 371862276 371863626 5.200000e-153 551
22 TraesCS7B01G273900 chr2D 75.391 894 199 16 2678 3563 140126985 140126105 2.560000e-111 412
23 TraesCS7B01G273900 chr2B 89.773 264 27 0 3300 3563 765563366 765563629 4.410000e-89 339
24 TraesCS7B01G273900 chr4D 82.749 342 57 2 3223 3563 417904493 417904833 1.610000e-78 303
25 TraesCS7B01G273900 chr1D 86.207 203 28 0 3361 3563 114110495 114110293 1.670000e-53 220


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 TraesCS7B01G273900 chr7B 503105686 503109248 3562 False 2695.0 4865 100.0000 1 3563 2 chr7B.!!$F3 3562
1 TraesCS7B01G273900 chr7B 502908432 502910077 1645 False 2409.0 2409 93.1350 966 2606 1 chr7B.!!$F1 1640
2 TraesCS7B01G273900 chr7B 654251248 654252907 1659 True 2121.0 2121 89.8020 976 2631 1 chr7B.!!$R1 1655
3 TraesCS7B01G273900 chr7B 731344730 731345542 812 False 1120.0 1120 91.5130 2751 3563 1 chr7B.!!$F2 812
4 TraesCS7B01G273900 chr7D 477865486 477867162 1676 False 2412.0 2412 92.6740 966 2639 1 chr7D.!!$F2 1673
5 TraesCS7B01G273900 chr7D 585538056 585539640 1584 False 2111.0 2111 90.8000 971 2547 1 chr7D.!!$F3 1576
6 TraesCS7B01G273900 chr7D 477968368 477970426 2058 False 1592.5 2758 95.6675 19 2656 2 chr7D.!!$F4 2637
7 TraesCS7B01G273900 chr7A 518504022 518505692 1670 True 2357.0 2357 92.1380 966 2639 1 chr7A.!!$R2 1673
8 TraesCS7B01G273900 chr7A 675574099 675575762 1663 False 2082.0 2082 89.4480 977 2622 1 chr7A.!!$F1 1645
9 TraesCS7B01G273900 chr7A 517893923 517895841 1918 True 1461.5 2723 95.4865 162 2661 2 chr7A.!!$R3 2499
10 TraesCS7B01G273900 chr4A 703333827 703334724 897 False 1478.0 1478 96.2510 2657 3563 1 chr4A.!!$F2 906
11 TraesCS7B01G273900 chr4A 619942586 619943491 905 False 1179.0 1179 90.1870 2659 3563 1 chr4A.!!$F1 904
12 TraesCS7B01G273900 chr1B 26861098 26861978 880 False 1192.0 1192 90.9090 2663 3563 1 chr1B.!!$F1 900
13 TraesCS7B01G273900 chr3B 712554921 712555813 892 True 1050.0 1050 87.8450 2661 3563 1 chr3B.!!$R1 902
14 TraesCS7B01G273900 chr3A 33137250 33138609 1359 False 617.0 617 75.2170 1182 2541 1 chr3A.!!$F1 1359
15 TraesCS7B01G273900 chr5D 371862276 371863626 1350 False 551.0 551 74.6000 1206 2544 1 chr5D.!!$F1 1338
16 TraesCS7B01G273900 chr2D 140126105 140126985 880 True 412.0 412 75.3910 2678 3563 1 chr2D.!!$R1 885

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
101 104 0.535102 CCTCCCACAAGAAACGCTGT 60.535 55.0 0.00 0.0 0.00 4.40 F
1021 1024 0.756903 GGCGAACTATAGGGCCTTCA 59.243 55.0 13.45 0.0 42.29 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1893 0.469917 CCAGGTACATGCCCTCGAAT 59.530 55.0 0.96 0.0 0.0 3.34 R
2668 2716 0.786435 AAAGTGGCAGATTCCCCCTT 59.214 50.0 0.00 0.0 0.0 3.95 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
17 18 3.827752 GGTTCTTGCCCCTCCTCT 58.172 61.111 0.00 0.00 0.00 3.69
26 27 0.759060 GCCCCTCCTCTCTTCCTCTC 60.759 65.000 0.00 0.00 0.00 3.20
65 68 5.401531 AACGTCAAGGATGTAGCTAAAGA 57.598 39.130 0.00 0.00 30.95 2.52
81 84 7.936950 AGCTAAAGAAAATTCAGCTTTCAAC 57.063 32.000 0.00 0.00 39.49 3.18
88 91 0.850100 TTCAGCTTTCAACCCTCCCA 59.150 50.000 0.00 0.00 0.00 4.37
101 104 0.535102 CCTCCCACAAGAAACGCTGT 60.535 55.000 0.00 0.00 0.00 4.40
139 142 4.745620 AGAAAGAAGTGAACGACTACAAGC 59.254 41.667 0.00 0.00 33.09 4.01
184 187 2.331893 CCCTCCAATTTGCGACGCA 61.332 57.895 20.50 20.50 36.47 5.24
265 268 4.892934 TCCACATTTAGGTGAGCTTGTTTT 59.107 37.500 0.00 0.00 41.32 2.43
956 959 1.423721 CCTGCGATGATGTCCACACG 61.424 60.000 0.00 0.00 0.00 4.49
1021 1024 0.756903 GGCGAACTATAGGGCCTTCA 59.243 55.000 13.45 0.00 42.29 3.02
1053 1059 1.302033 CTTCTGCGCCTTGTCCTGT 60.302 57.895 4.18 0.00 0.00 4.00
1128 1140 1.688735 CTCATGAAGGAGATACCGGCA 59.311 52.381 0.00 0.00 44.74 5.69
1405 1417 1.073025 AAGATGCGGGCAGTGTTGA 59.927 52.632 0.00 0.00 0.00 3.18
1572 1584 3.982372 CTTTGGCATGCTGCTGCGG 62.982 63.158 18.92 3.55 44.28 5.69
1635 1647 2.597510 GACCCCAACGGCAAGCTT 60.598 61.111 0.00 0.00 33.26 3.74
1701 1713 4.459089 GGCGGCGGAGAGAGCTTT 62.459 66.667 9.78 0.00 34.52 3.51
1722 1734 2.019408 CATCGTCGTGTCGTGGCAA 61.019 57.895 0.00 0.00 0.00 4.52
2143 2175 1.519246 CAGATCTTCGGCTGGCTCA 59.481 57.895 0.00 0.00 0.00 4.26
2178 2210 1.706866 GGGATGATGATCATGGACCCA 59.293 52.381 24.15 13.56 37.98 4.51
2385 2420 0.690762 ACGCCAACTACAGGGACATT 59.309 50.000 0.00 0.00 0.00 2.71
2427 2462 3.513912 TGGTGAACGACATCTCAACCTAT 59.486 43.478 0.00 0.00 0.00 2.57
2484 2519 1.518903 GCAACTTCCAAAGGCTCGCT 61.519 55.000 0.00 0.00 0.00 4.93
2633 2681 5.010820 GCCCAACTAGTAGAATAAGGATCGT 59.989 44.000 3.59 0.00 0.00 3.73
2640 2688 5.715070 AGTAGAATAAGGATCGTGCATAGC 58.285 41.667 0.00 0.00 0.00 2.97
3055 3106 5.945144 TTCAGGATCAGACTCATGATGAA 57.055 39.130 0.00 0.00 40.02 2.57
3156 3207 0.952497 AGACTGCACCATCAGCGTTG 60.952 55.000 0.00 0.00 37.59 4.10
3186 3237 1.779061 ATCCTTGGTCTGGCGGTGTT 61.779 55.000 0.00 0.00 0.00 3.32
3335 3386 0.609957 TCATTCCTTGCCAGCCACAG 60.610 55.000 0.00 0.00 0.00 3.66
3459 3510 2.358619 GGGGCTGCCACCATAACA 59.641 61.111 22.05 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.988063 AAGAGAGGAGGGGCAAGAAC 59.012 55.000 0.00 0.00 0.00 3.01
4 5 0.620121 AGGAAGAGAGGAGGGGCAAG 60.620 60.000 0.00 0.00 0.00 4.01
6 7 1.002274 GAGGAAGAGAGGAGGGGCA 59.998 63.158 0.00 0.00 0.00 5.36
7 8 0.759060 GAGAGGAAGAGAGGAGGGGC 60.759 65.000 0.00 0.00 0.00 5.80
8 9 0.933700 AGAGAGGAAGAGAGGAGGGG 59.066 60.000 0.00 0.00 0.00 4.79
9 10 3.963476 TTAGAGAGGAAGAGAGGAGGG 57.037 52.381 0.00 0.00 0.00 4.30
10 11 4.803452 ACATTAGAGAGGAAGAGAGGAGG 58.197 47.826 0.00 0.00 0.00 4.30
11 12 4.515191 CGACATTAGAGAGGAAGAGAGGAG 59.485 50.000 0.00 0.00 0.00 3.69
12 13 4.164413 TCGACATTAGAGAGGAAGAGAGGA 59.836 45.833 0.00 0.00 0.00 3.71
13 14 4.456535 TCGACATTAGAGAGGAAGAGAGG 58.543 47.826 0.00 0.00 0.00 3.69
14 15 6.443934 TTTCGACATTAGAGAGGAAGAGAG 57.556 41.667 0.00 0.00 0.00 3.20
15 16 6.835819 TTTTCGACATTAGAGAGGAAGAGA 57.164 37.500 0.00 0.00 0.00 3.10
53 56 8.796475 TGAAAGCTGAATTTTCTTTAGCTACAT 58.204 29.630 4.90 0.00 43.37 2.29
65 68 3.324846 GGGAGGGTTGAAAGCTGAATTTT 59.675 43.478 0.00 0.00 0.00 1.82
81 84 1.073199 AGCGTTTCTTGTGGGAGGG 59.927 57.895 0.00 0.00 0.00 4.30
88 91 1.094785 ACTGCAACAGCGTTTCTTGT 58.905 45.000 0.00 0.00 34.37 3.16
101 104 1.719725 TTTCTGGCGCGAAACTGCAA 61.720 50.000 12.10 0.00 34.15 4.08
930 933 1.890979 CATCATCGCAGGGACAGGC 60.891 63.158 0.00 0.00 0.00 4.85
931 934 0.531532 GACATCATCGCAGGGACAGG 60.532 60.000 0.00 0.00 0.00 4.00
938 941 1.423721 CCGTGTGGACATCATCGCAG 61.424 60.000 0.00 0.00 37.49 5.18
956 959 0.732571 CTGTGGTGTGTTGTGTGACC 59.267 55.000 0.00 0.00 0.00 4.02
1010 1013 1.995626 ACCAGCGTGAAGGCCCTAT 60.996 57.895 0.00 0.00 0.00 2.57
1128 1140 2.678934 TTGGCGTAGAGGAGGCGT 60.679 61.111 0.00 0.00 39.97 5.68
1254 1266 4.760047 ACCGCGGACTGGATGTGC 62.760 66.667 35.90 0.00 0.00 4.57
1635 1647 1.747924 CTCATGGAGCTCTTGTCGAGA 59.252 52.381 14.64 2.00 42.62 4.04
1657 1669 4.410400 GGCCCAGAAGTGGTCCGG 62.410 72.222 0.00 0.00 43.23 5.14
1701 1713 2.430075 CACGACACGACGATGCCA 60.430 61.111 0.00 0.00 37.03 4.92
1722 1734 2.925170 ACCGGCAGGAGCTTCACT 60.925 61.111 10.86 0.00 41.02 3.41
1881 1893 0.469917 CCAGGTACATGCCCTCGAAT 59.530 55.000 0.96 0.00 0.00 3.34
1909 1921 1.234615 ATCAACGGCGTCAGGGTTTG 61.235 55.000 15.17 6.09 0.00 2.93
2156 2188 1.005215 GGTCCATGATCATCATCCCCC 59.995 57.143 4.86 0.00 34.28 5.40
2178 2210 2.108976 CTGATGGTGGCGCCGTAT 59.891 61.111 23.90 15.81 41.21 3.06
2385 2420 2.599281 TCGTTCCTGCCGAGGTCA 60.599 61.111 0.00 0.00 40.76 4.02
2427 2462 1.971167 CCAAACCTTGCCGCTGCTA 60.971 57.895 0.70 0.00 38.71 3.49
2484 2519 2.280103 TCCACCTTGCCCTTGGTAATA 58.720 47.619 0.00 0.00 34.79 0.98
2633 2681 4.069304 AGTAACAGAAAAACGGCTATGCA 58.931 39.130 0.00 0.00 0.00 3.96
2668 2716 0.786435 AAAGTGGCAGATTCCCCCTT 59.214 50.000 0.00 0.00 0.00 3.95
2975 3026 2.508891 GCTGCCGAGATCAACGTCG 61.509 63.158 10.44 3.80 35.91 5.12
3055 3106 0.318107 GCAGCAGCATGTCACGTTTT 60.318 50.000 0.00 0.00 41.58 2.43
3141 3192 3.364441 GCCAACGCTGATGGTGCA 61.364 61.111 6.69 0.00 40.23 4.57
3186 3237 1.321474 CCAAAGAAGCTGCCAAGTGA 58.679 50.000 0.00 0.00 0.00 3.41
3335 3386 0.892814 GATCCAGGCTTGCTATGGGC 60.893 60.000 14.14 6.53 42.22 5.36
3459 3510 1.153549 GATGCGCTCGGAGAAAGGT 60.154 57.895 9.73 0.00 34.09 3.50


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

AutoCloner maintained by Alex Coulton.