Multiple sequence alignment - TraesCS3D01G404700

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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 TraesCS3D01G404700 chr3D 100.000 4282 0 0 1 4282 518968357 518964076 0.000000e+00 7908.0
1 TraesCS3D01G404700 chr3D 97.190 4306 96 4 1 4282 519070182 519065878 0.000000e+00 7258.0
2 TraesCS3D01G404700 chr3D 91.887 2946 164 23 638 3532 547514375 547517296 0.000000e+00 4047.0
3 TraesCS3D01G404700 chr3D 93.787 2688 144 11 861 3532 126245993 126248673 0.000000e+00 4017.0
4 TraesCS3D01G404700 chr3D 92.170 2005 134 8 638 2629 486616395 486618389 0.000000e+00 2811.0
5 TraesCS3D01G404700 chr3D 92.429 1017 61 6 636 1639 574245711 574244698 0.000000e+00 1437.0
6 TraesCS3D01G404700 chr3D 86.667 285 34 3 21 305 519162877 519162597 3.210000e-81 313.0
7 TraesCS3D01G404700 chr3D 88.679 106 12 0 3526 3631 519159300 519159195 3.470000e-26 130.0
8 TraesCS3D01G404700 chr1D 93.002 2915 173 14 638 3532 203258730 203255827 0.000000e+00 4224.0
9 TraesCS3D01G404700 chr1D 91.755 2923 175 27 638 3529 38372907 38370020 0.000000e+00 4002.0
10 TraesCS3D01G404700 chr1D 93.094 2230 127 12 1326 3536 396011799 396009578 0.000000e+00 3240.0
11 TraesCS3D01G404700 chr1D 84.286 210 32 1 3843 4051 11731342 11731133 2.020000e-48 204.0
12 TraesCS3D01G404700 chr1D 97.872 47 1 0 563 609 464757772 464757818 9.870000e-12 82.4
13 TraesCS3D01G404700 chr1D 97.826 46 1 0 564 609 49584491 49584446 3.550000e-11 80.5
14 TraesCS3D01G404700 chr3A 92.099 2911 200 16 638 3532 568451988 568449092 0.000000e+00 4074.0
15 TraesCS3D01G404700 chr3A 84.949 784 64 11 3526 4282 654278817 654278061 0.000000e+00 745.0
16 TraesCS3D01G404700 chr3A 91.018 334 24 3 1 329 654291697 654291365 3.040000e-121 446.0
17 TraesCS3D01G404700 chr3A 84.038 213 33 1 3840 4051 713786037 713786249 2.020000e-48 204.0
18 TraesCS3D01G404700 chr3A 90.323 155 12 1 353 507 654278987 654278836 2.610000e-47 200.0
19 TraesCS3D01G404700 chr3A 83.568 213 34 1 3840 4051 691311053 691310841 9.390000e-47 198.0
20 TraesCS3D01G404700 chr4B 91.861 2912 197 19 638 3532 89045022 89042134 0.000000e+00 4028.0
21 TraesCS3D01G404700 chr2A 91.741 2906 213 7 638 3531 779495159 779492269 0.000000e+00 4012.0
22 TraesCS3D01G404700 chr2D 93.173 2666 161 5 633 3286 9608060 9610716 0.000000e+00 3895.0
23 TraesCS3D01G404700 chr2D 97.872 47 1 0 563 609 589512200 589512246 9.870000e-12 82.4
24 TraesCS3D01G404700 chr3B 90.804 2936 193 33 638 3532 590298309 590295410 0.000000e+00 3855.0
25 TraesCS3D01G404700 chr3B 86.619 1263 106 23 638 1872 767911135 767909908 0.000000e+00 1338.0
26 TraesCS3D01G404700 chr3B 88.471 399 26 2 1350 1728 798271729 798272127 8.390000e-127 464.0
27 TraesCS3D01G404700 chr3B 86.902 397 35 5 1350 1729 147929017 147928621 3.060000e-116 429.0
28 TraesCS3D01G404700 chr3B 85.919 419 27 4 3526 3917 683389554 683389141 6.620000e-113 418.0
29 TraesCS3D01G404700 chr3B 91.912 272 17 3 23 290 683838701 683838431 4.040000e-100 375.0
30 TraesCS3D01G404700 chr3B 81.922 437 29 6 3526 3917 683836888 683836457 1.490000e-84 324.0
31 TraesCS3D01G404700 chr3B 87.324 284 21 7 21 290 683391062 683390780 1.160000e-80 311.0
32 TraesCS3D01G404700 chr3B 97.826 46 1 0 564 609 627322717 627322672 3.550000e-11 80.5
33 TraesCS3D01G404700 chr4D 90.118 2965 172 40 604 3532 479373443 479370564 0.000000e+00 3740.0
34 TraesCS3D01G404700 chr4D 93.694 2236 118 9 1318 3532 491536395 491534162 0.000000e+00 3326.0
35 TraesCS3D01G404700 chr4D 91.606 1239 82 8 638 1856 17233195 17234431 0.000000e+00 1692.0
36 TraesCS3D01G404700 chr5D 92.567 2435 145 10 638 3048 353645567 353647989 0.000000e+00 3461.0
37 TraesCS3D01G404700 chrUn 92.644 2216 140 7 638 2831 42145693 42147907 0.000000e+00 3168.0
38 TraesCS3D01G404700 chrUn 96.000 50 2 0 560 609 22043184 22043233 9.870000e-12 82.4
39 TraesCS3D01G404700 chr7B 92.254 2156 139 10 1397 3539 643345174 643343034 0.000000e+00 3031.0
40 TraesCS3D01G404700 chr1B 88.335 1363 96 14 604 1933 535814779 535813447 0.000000e+00 1578.0
41 TraesCS3D01G404700 chr7D 84.038 213 33 1 3840 4051 548882572 548882360 2.020000e-48 204.0
42 TraesCS3D01G404700 chr7A 83.099 213 35 1 3840 4051 138303800 138304012 4.370000e-45 193.0
43 TraesCS3D01G404700 chr7A 95.918 49 1 1 561 609 463012485 463012438 1.280000e-10 78.7
44 TraesCS3D01G404700 chr4A 83.099 213 35 1 3840 4051 621691695 621691483 4.370000e-45 193.0
45 TraesCS3D01G404700 chr4A 97.778 45 1 0 565 609 632191059 632191015 1.280000e-10 78.7
46 TraesCS3D01G404700 chr6D 97.959 49 1 0 561 609 378742996 378742948 7.630000e-13 86.1
47 TraesCS3D01G404700 chr5B 86.154 65 6 2 383 446 708379440 708379378 2.760000e-07 67.6


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 TraesCS3D01G404700 chr3D 518964076 518968357 4281 True 7908.0 7908 100.0000 1 4282 1 chr3D.!!$R1 4281
1 TraesCS3D01G404700 chr3D 519065878 519070182 4304 True 7258.0 7258 97.1900 1 4282 1 chr3D.!!$R2 4281
2 TraesCS3D01G404700 chr3D 547514375 547517296 2921 False 4047.0 4047 91.8870 638 3532 1 chr3D.!!$F3 2894
3 TraesCS3D01G404700 chr3D 126245993 126248673 2680 False 4017.0 4017 93.7870 861 3532 1 chr3D.!!$F1 2671
4 TraesCS3D01G404700 chr3D 486616395 486618389 1994 False 2811.0 2811 92.1700 638 2629 1 chr3D.!!$F2 1991
5 TraesCS3D01G404700 chr3D 574244698 574245711 1013 True 1437.0 1437 92.4290 636 1639 1 chr3D.!!$R3 1003
6 TraesCS3D01G404700 chr3D 519159195 519162877 3682 True 221.5 313 87.6730 21 3631 2 chr3D.!!$R4 3610
7 TraesCS3D01G404700 chr1D 203255827 203258730 2903 True 4224.0 4224 93.0020 638 3532 1 chr1D.!!$R4 2894
8 TraesCS3D01G404700 chr1D 38370020 38372907 2887 True 4002.0 4002 91.7550 638 3529 1 chr1D.!!$R2 2891
9 TraesCS3D01G404700 chr1D 396009578 396011799 2221 True 3240.0 3240 93.0940 1326 3536 1 chr1D.!!$R5 2210
10 TraesCS3D01G404700 chr3A 568449092 568451988 2896 True 4074.0 4074 92.0990 638 3532 1 chr3A.!!$R1 2894
11 TraesCS3D01G404700 chr3A 654278061 654278987 926 True 472.5 745 87.6360 353 4282 2 chr3A.!!$R4 3929
12 TraesCS3D01G404700 chr4B 89042134 89045022 2888 True 4028.0 4028 91.8610 638 3532 1 chr4B.!!$R1 2894
13 TraesCS3D01G404700 chr2A 779492269 779495159 2890 True 4012.0 4012 91.7410 638 3531 1 chr2A.!!$R1 2893
14 TraesCS3D01G404700 chr2D 9608060 9610716 2656 False 3895.0 3895 93.1730 633 3286 1 chr2D.!!$F1 2653
15 TraesCS3D01G404700 chr3B 590295410 590298309 2899 True 3855.0 3855 90.8040 638 3532 1 chr3B.!!$R2 2894
16 TraesCS3D01G404700 chr3B 767909908 767911135 1227 True 1338.0 1338 86.6190 638 1872 1 chr3B.!!$R4 1234
17 TraesCS3D01G404700 chr3B 683389141 683391062 1921 True 364.5 418 86.6215 21 3917 2 chr3B.!!$R5 3896
18 TraesCS3D01G404700 chr3B 683836457 683838701 2244 True 349.5 375 86.9170 23 3917 2 chr3B.!!$R6 3894
19 TraesCS3D01G404700 chr4D 479370564 479373443 2879 True 3740.0 3740 90.1180 604 3532 1 chr4D.!!$R1 2928
20 TraesCS3D01G404700 chr4D 491534162 491536395 2233 True 3326.0 3326 93.6940 1318 3532 1 chr4D.!!$R2 2214
21 TraesCS3D01G404700 chr4D 17233195 17234431 1236 False 1692.0 1692 91.6060 638 1856 1 chr4D.!!$F1 1218
22 TraesCS3D01G404700 chr5D 353645567 353647989 2422 False 3461.0 3461 92.5670 638 3048 1 chr5D.!!$F1 2410
23 TraesCS3D01G404700 chrUn 42145693 42147907 2214 False 3168.0 3168 92.6440 638 2831 1 chrUn.!!$F2 2193
24 TraesCS3D01G404700 chr7B 643343034 643345174 2140 True 3031.0 3031 92.2540 1397 3539 1 chr7B.!!$R1 2142
25 TraesCS3D01G404700 chr1B 535813447 535814779 1332 True 1578.0 1578 88.3350 604 1933 1 chr1B.!!$R1 1329

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
867 4986 0.736325 CATCCGTTCGAGCTTTCCGT 60.736 55.000 0.00 0.0 0.0 4.69 F
1508 5656 1.475930 GCAAGATCTTAGACAGGCCCC 60.476 57.143 7.86 0.0 0.0 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 6542 0.238289 GCGTGGACATGAACAACTGG 59.762 55.0 0.00 0.00 0.0 4.00 R
3360 8543 0.532417 TGTTTGGTTGCCTGCATTGC 60.532 50.0 0.46 0.46 0.0 3.56 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
317 3915 1.624336 CATGGGCCGATGATCCATTT 58.376 50.000 22.34 0.00 39.07 2.32
335 3933 0.953471 TTTACATCGCACGGCTGCTT 60.953 50.000 0.00 0.00 41.77 3.91
336 3934 1.358725 TTACATCGCACGGCTGCTTC 61.359 55.000 0.00 0.00 41.77 3.86
338 3936 1.519234 CATCGCACGGCTGCTTCTA 60.519 57.895 0.00 0.00 41.77 2.10
356 4456 4.731313 TCTATCATAGCTCCCTCAGTGA 57.269 45.455 0.00 0.00 0.00 3.41
433 4533 2.484062 CCAGCCCATGCACCGATTC 61.484 63.158 0.00 0.00 41.13 2.52
548 4651 5.551305 AACGGGTACAGGTTTAGTAGTTT 57.449 39.130 0.00 0.00 0.00 2.66
567 4670 4.975794 AGTTTAGGAACATAGGCATAGGGT 59.024 41.667 0.00 0.00 38.26 4.34
582 4685 1.042559 AGGGTGTGTTTGGTTGCCTG 61.043 55.000 0.00 0.00 0.00 4.85
726 4842 1.863662 TTCTCTCCTCGTGCGACCAC 61.864 60.000 0.00 0.00 38.62 4.16
810 4927 1.070289 CCGAGTCCACCCCTATTTAGC 59.930 57.143 0.00 0.00 0.00 3.09
867 4986 0.736325 CATCCGTTCGAGCTTTCCGT 60.736 55.000 0.00 0.00 0.00 4.69
902 5021 2.483745 CGACGAGCAGGTAAGCGA 59.516 61.111 0.00 0.00 40.15 4.93
1508 5656 1.475930 GCAAGATCTTAGACAGGCCCC 60.476 57.143 7.86 0.00 0.00 5.80
1626 6413 4.079958 TCCCTCTATGTGTCAGTAGTGCTA 60.080 45.833 0.00 0.00 0.00 3.49
1632 6419 2.963101 TGTGTCAGTAGTGCTAGTTGGT 59.037 45.455 0.00 0.00 0.00 3.67
1713 6542 1.873591 AGGTCGAACAACATGAAGTGC 59.126 47.619 1.87 0.00 0.00 4.40
2084 7158 9.221775 CTAACAACACTTGTGTTTCATTCTTAC 57.778 33.333 15.46 0.00 44.59 2.34
2484 7613 0.459078 CTTCAGCGATGAGGCTCTCA 59.541 55.000 16.72 7.26 44.99 3.27
2491 7620 2.588439 TGAGGCTCTCATGGCAGC 59.412 61.111 16.72 7.98 35.39 5.25
2492 7621 1.993948 TGAGGCTCTCATGGCAGCT 60.994 57.895 16.72 0.00 35.39 4.24
2493 7622 1.227615 GAGGCTCTCATGGCAGCTC 60.228 63.158 7.40 7.99 35.82 4.09
2494 7623 2.203181 GGCTCTCATGGCAGCTCC 60.203 66.667 14.25 0.00 35.82 4.70
2495 7624 2.203181 GCTCTCATGGCAGCTCCC 60.203 66.667 8.99 0.00 32.48 4.30
2621 7758 3.939837 TAGTGCTGCCTGTGAGCGC 62.940 63.158 0.00 0.00 45.50 5.92
2698 7849 5.810587 CGACATACATTTTGTGTAGCTAGGT 59.189 40.000 0.00 0.00 45.94 3.08
2775 7926 0.953727 GTGCTGATGGTGAACTTGCA 59.046 50.000 0.00 0.00 0.00 4.08
2996 8148 2.487762 CAAGTGGTATGCCGTGTTCATT 59.512 45.455 0.00 0.00 37.67 2.57
3261 8443 2.477176 TTGTGGCGTTGGTGTGCTC 61.477 57.895 0.00 0.00 0.00 4.26
3360 8543 2.676121 TTCATGTGCCGCTTGGGG 60.676 61.111 0.00 0.00 35.78 4.96
3404 8587 5.183228 AGTGCACTTGCGTATTACCTAATT 58.817 37.500 15.25 0.00 45.83 1.40
3508 8691 2.430694 AGTGTATGCGATGCAGGAACTA 59.569 45.455 0.00 0.00 43.65 2.24
3697 8880 5.940470 ACAGGGATTCACTTCAATACAGTTC 59.060 40.000 0.00 0.00 0.00 3.01
3710 8911 0.685097 ACAGTTCAGCACCACCGTAT 59.315 50.000 0.00 0.00 0.00 3.06
3785 9011 3.843619 CCCCAAATAACCAAAACCCATCT 59.156 43.478 0.00 0.00 0.00 2.90
3865 9093 8.554835 TGAAAGGACGTATTATCAATTTCACA 57.445 30.769 0.00 0.00 32.66 3.58
3886 9114 3.188460 CACGGTCCCTACAAAGACAAATG 59.812 47.826 0.00 0.00 34.58 2.32
4109 9337 2.764128 CTTCTCCCCTAGCCGGCA 60.764 66.667 31.54 14.00 0.00 5.69
4180 9408 3.431658 CCCCCTCTGGCCAGATTT 58.568 61.111 35.11 0.00 36.76 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
335 3933 4.731313 TCACTGAGGGAGCTATGATAGA 57.269 45.455 3.13 0.00 0.00 1.98
336 3934 5.999205 ATTCACTGAGGGAGCTATGATAG 57.001 43.478 0.00 0.00 0.00 2.08
338 3936 6.021672 TGATATTCACTGAGGGAGCTATGAT 58.978 40.000 0.00 0.00 0.00 2.45
356 4456 2.025037 TCTGTTTGGGCTGGCTGATATT 60.025 45.455 0.00 0.00 0.00 1.28
433 4533 2.874701 CTCTGTGGGTGTTTCTGAACAG 59.125 50.000 0.00 0.00 45.86 3.16
468 4568 1.203364 ACTGAATCCTCCCTGTGGACT 60.203 52.381 0.00 0.00 35.03 3.85
520 4623 3.391506 AAACCTGTACCCGTTACTGAC 57.608 47.619 0.00 0.00 32.61 3.51
548 4651 3.646162 CACACCCTATGCCTATGTTCCTA 59.354 47.826 0.00 0.00 0.00 2.94
567 4670 1.697284 TATGCAGGCAACCAAACACA 58.303 45.000 0.00 0.00 37.17 3.72
902 5021 1.170919 GCCGGCTCATGAAGATGCAT 61.171 55.000 22.15 0.00 0.00 3.96
1508 5656 0.319900 CTGGTTGTCGGACAGGACAG 60.320 60.000 11.14 15.37 46.68 3.51
1713 6542 0.238289 GCGTGGACATGAACAACTGG 59.762 55.000 0.00 0.00 0.00 4.00
2288 7405 0.898326 GGACGGGGTCAAATGGCTTT 60.898 55.000 0.00 0.00 33.68 3.51
2775 7926 0.611340 GAGGGTGTCGTCCTACCACT 60.611 60.000 0.00 0.00 38.74 4.00
2996 8148 0.774491 AAACCCCTGGAGCCTTACCA 60.774 55.000 0.00 0.00 35.96 3.25
3130 8282 2.031012 CAACACTGCTGCCTCCGA 59.969 61.111 0.00 0.00 0.00 4.55
3261 8443 2.394930 TACCCACAATGATCACACCG 57.605 50.000 0.00 0.00 0.00 4.94
3360 8543 0.532417 TGTTTGGTTGCCTGCATTGC 60.532 50.000 0.46 0.46 0.00 3.56
3404 8587 1.489481 CCTGCATCTAGTGTCCCTGA 58.511 55.000 0.00 0.00 0.00 3.86
3473 8656 0.690762 TACACTTCTCAACCCAGCCC 59.309 55.000 0.00 0.00 0.00 5.19
3508 8691 1.478510 TGTTTGGTTGCCGTTGTGAAT 59.521 42.857 0.00 0.00 0.00 2.57
3697 8880 2.540515 CTGAACTATACGGTGGTGCTG 58.459 52.381 0.00 0.00 0.00 4.41
3710 8911 8.856153 TTATGCTTGTATTTGTTCCTGAACTA 57.144 30.769 11.03 1.10 41.67 2.24
3785 9011 9.910267 TCAGTGATAAGTGGTGTAGTACTAATA 57.090 33.333 3.61 0.00 0.00 0.98
3865 9093 3.408634 CATTTGTCTTTGTAGGGACCGT 58.591 45.455 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.