Multiple sequence alignment - TraesCS7D01G029200

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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 TraesCS7D01G029200 chr7D 100.000 4753 0 0 1 4753 14585729 14590481 0.000000e+00 8778.0
1 TraesCS7D01G029200 chr7D 80.307 1432 228 38 938 2333 59413642 59415055 0.000000e+00 1033.0
2 TraesCS7D01G029200 chr7D 81.448 1008 149 26 2826 3806 59415803 59416799 0.000000e+00 791.0
3 TraesCS7D01G029200 chr7D 88.430 242 19 8 651 884 16644501 16644261 2.800000e-72 283.0
4 TraesCS7D01G029200 chr7D 93.182 132 7 2 755 884 16655498 16655367 4.850000e-45 193.0
5 TraesCS7D01G029200 chr7D 95.918 98 4 0 525 622 16644596 16644499 4.920000e-35 159.0
6 TraesCS7D01G029200 chr7A 95.734 4782 157 16 11 4753 13827486 13832259 0.000000e+00 7657.0
7 TraesCS7D01G029200 chr7A 81.429 1400 217 30 2439 3806 63778405 63779793 0.000000e+00 1105.0
8 TraesCS7D01G029200 chr7A 82.372 919 149 9 883 1789 63777018 63777935 0.000000e+00 787.0
9 TraesCS7D01G029200 chr7A 90.141 142 9 3 1 140 612368071 612367933 3.780000e-41 180.0
10 TraesCS7D01G029200 chr4A 94.964 4269 164 25 528 4753 722300360 722296100 0.000000e+00 6645.0
11 TraesCS7D01G029200 chr4A 94.497 3398 144 21 820 4182 722336183 722332794 0.000000e+00 5199.0
12 TraesCS7D01G029200 chr4A 91.290 597 38 7 336 926 722300948 722300360 0.000000e+00 802.0
13 TraesCS7D01G029200 chr4A 80.108 930 152 28 2867 3779 611269491 611268578 0.000000e+00 662.0
14 TraesCS7D01G029200 chr4A 92.308 338 23 2 359 696 722336515 722336181 1.200000e-130 477.0
15 TraesCS7D01G029200 chr4A 96.207 290 10 1 4465 4753 722295038 722294749 1.550000e-129 473.0
16 TraesCS7D01G029200 chrUn 94.221 2267 74 20 1693 3919 307995664 307993415 0.000000e+00 3408.0
17 TraesCS7D01G029200 chrUn 93.763 930 53 5 764 1691 376985088 376984162 0.000000e+00 1391.0
18 TraesCS7D01G029200 chrUn 94.595 814 37 4 3947 4753 307993420 307992607 0.000000e+00 1253.0
19 TraesCS7D01G029200 chrUn 100.000 410 0 0 2855 3264 477740225 477739816 0.000000e+00 758.0
20 TraesCS7D01G029200 chrUn 94.323 458 20 3 4008 4459 475545259 475544802 0.000000e+00 697.0
21 TraesCS7D01G029200 chrUn 80.868 899 148 22 2872 3759 15425460 15424575 0.000000e+00 686.0
22 TraesCS7D01G029200 chrUn 92.537 335 25 0 336 670 376985726 376985392 9.250000e-132 481.0
23 TraesCS7D01G029200 chrUn 96.207 290 10 1 4465 4753 335449096 335448807 1.550000e-129 473.0
24 TraesCS7D01G029200 chrUn 88.843 242 18 7 651 884 241758769 241758529 6.020000e-74 289.0
25 TraesCS7D01G029200 chrUn 95.918 98 4 0 525 622 241758864 241758767 4.920000e-35 159.0
26 TraesCS7D01G029200 chrUn 91.667 60 4 1 688 746 376985407 376985348 1.100000e-11 82.4
27 TraesCS7D01G029200 chr5D 78.483 1371 240 42 2439 3779 558347246 558345901 0.000000e+00 846.0
28 TraesCS7D01G029200 chr5D 88.406 138 12 2 1 137 432024900 432025034 3.810000e-36 163.0
29 TraesCS7D01G029200 chr3D 80.804 896 159 12 2872 3758 15372166 15371275 0.000000e+00 689.0
30 TraesCS7D01G029200 chr3D 85.348 273 37 3 2439 2708 15348906 15348634 3.620000e-71 279.0
31 TraesCS7D01G029200 chr3D 87.815 238 28 1 2472 2708 15372555 15372318 1.300000e-70 278.0
32 TraesCS7D01G029200 chr3D 81.868 182 23 10 4 180 303562126 303561950 1.380000e-30 145.0
33 TraesCS7D01G029200 chr2D 80.454 926 157 21 2846 3760 2440735 2439823 0.000000e+00 686.0
34 TraesCS7D01G029200 chr2D 88.406 138 12 2 1 137 645666232 645666366 3.810000e-36 163.0
35 TraesCS7D01G029200 chr5B 78.840 931 158 30 2867 3769 704303033 704303952 4.100000e-165 592.0
36 TraesCS7D01G029200 chr5B 87.234 141 14 2 1 140 638783336 638783199 1.770000e-34 158.0
37 TraesCS7D01G029200 chr3B 77.519 516 92 21 2201 2705 22511607 22512109 6.020000e-74 289.0
38 TraesCS7D01G029200 chr3B 85.348 273 37 3 2439 2708 22473345 22473073 3.620000e-71 279.0
39 TraesCS7D01G029200 chr3A 85.348 273 37 3 2439 2708 20933789 20934061 3.620000e-71 279.0
40 TraesCS7D01G029200 chr6A 89.130 138 11 2 1 137 590371026 590370892 8.180000e-38 169.0
41 TraesCS7D01G029200 chr7B 88.489 139 13 3 1 137 12535018 12535155 1.060000e-36 165.0
42 TraesCS7D01G029200 chr1D 88.406 138 12 2 1 137 66380881 66381015 3.810000e-36 163.0


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 TraesCS7D01G029200 chr7D 14585729 14590481 4752 False 8778.000000 8778 100.000000 1 4753 1 chr7D.!!$F1 4752
1 TraesCS7D01G029200 chr7D 59413642 59416799 3157 False 912.000000 1033 80.877500 938 3806 2 chr7D.!!$F2 2868
2 TraesCS7D01G029200 chr7A 13827486 13832259 4773 False 7657.000000 7657 95.734000 11 4753 1 chr7A.!!$F1 4742
3 TraesCS7D01G029200 chr7A 63777018 63779793 2775 False 946.000000 1105 81.900500 883 3806 2 chr7A.!!$F2 2923
4 TraesCS7D01G029200 chr4A 722332794 722336515 3721 True 2838.000000 5199 93.402500 359 4182 2 chr4A.!!$R3 3823
5 TraesCS7D01G029200 chr4A 722294749 722300948 6199 True 2640.000000 6645 94.153667 336 4753 3 chr4A.!!$R2 4417
6 TraesCS7D01G029200 chr4A 611268578 611269491 913 True 662.000000 662 80.108000 2867 3779 1 chr4A.!!$R1 912
7 TraesCS7D01G029200 chrUn 307992607 307995664 3057 True 2330.500000 3408 94.408000 1693 4753 2 chrUn.!!$R6 3060
8 TraesCS7D01G029200 chrUn 15424575 15425460 885 True 686.000000 686 80.868000 2872 3759 1 chrUn.!!$R1 887
9 TraesCS7D01G029200 chrUn 376984162 376985726 1564 True 651.466667 1391 92.655667 336 1691 3 chrUn.!!$R7 1355
10 TraesCS7D01G029200 chr5D 558345901 558347246 1345 True 846.000000 846 78.483000 2439 3779 1 chr5D.!!$R1 1340
11 TraesCS7D01G029200 chr3D 15371275 15372555 1280 True 483.500000 689 84.309500 2472 3758 2 chr3D.!!$R3 1286
12 TraesCS7D01G029200 chr2D 2439823 2440735 912 True 686.000000 686 80.454000 2846 3760 1 chr2D.!!$R1 914
13 TraesCS7D01G029200 chr5B 704303033 704303952 919 False 592.000000 592 78.840000 2867 3769 1 chr5B.!!$F1 902
14 TraesCS7D01G029200 chr3B 22511607 22512109 502 False 289.000000 289 77.519000 2201 2705 1 chr3B.!!$F1 504

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
603 609 0.033504 GAAGTGCCCGAGTCAAGACA 59.966 55.000 2.72 0.00 0.00 3.41 F
873 1288 1.134220 TGAACGGAAAGCAACTGACCT 60.134 47.619 0.00 0.00 0.00 3.85 F
936 1354 1.922135 TTTTCCAGGCGAGCGATTGC 61.922 55.000 3.72 3.72 43.24 3.56 F
2132 2623 1.672363 TGTGCCGATTCTCAATCATGC 59.328 47.619 0.00 0.27 37.78 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 2340 1.000843 TCATCCGCCCTGATATGAACG 59.999 52.381 0.00 0.0 0.00 3.95 R
2132 2623 4.271696 TGTAACCTCATCACTTCACCTG 57.728 45.455 0.00 0.0 0.00 4.00 R
2247 2742 5.124776 CGAAAAATTATTGGTGGCCTGTAGA 59.875 40.000 3.32 0.0 0.00 2.59 R
4130 5198 2.639327 GGGCGCATCTTGCACCTTT 61.639 57.895 10.83 0.0 44.59 3.11 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
36 37 2.534298 CTCCAGTGCTTGTAGTCATCG 58.466 52.381 0.00 0.00 0.00 3.84
64 65 3.366052 GTCCATGGACCTGGTTGTAAT 57.634 47.619 31.37 0.00 39.08 1.89
75 76 7.124448 TGGACCTGGTTGTAATTTTTGTTACTT 59.876 33.333 0.00 0.00 35.94 2.24
93 94 3.668447 ACTTCTGGTGTTCTATGTGCTG 58.332 45.455 0.00 0.00 0.00 4.41
94 95 3.071602 ACTTCTGGTGTTCTATGTGCTGT 59.928 43.478 0.00 0.00 0.00 4.40
102 103 4.452114 GTGTTCTATGTGCTGTCATGACAA 59.548 41.667 27.63 14.62 41.33 3.18
106 107 3.861276 ATGTGCTGTCATGACAAATGG 57.139 42.857 27.63 17.50 41.33 3.16
115 116 6.039047 GCTGTCATGACAAATGGTGAATAGAT 59.961 38.462 27.63 0.00 41.33 1.98
176 177 6.126409 AGGTCACACAGAGAAAAATACCAAA 58.874 36.000 0.00 0.00 0.00 3.28
228 229 5.708736 ATACAATACCATGAGACACCCAA 57.291 39.130 0.00 0.00 0.00 4.12
232 233 5.013704 ACAATACCATGAGACACCCAACTAA 59.986 40.000 0.00 0.00 0.00 2.24
257 258 5.237779 CACTAGTGAAACCAACGGTTACAAT 59.762 40.000 18.45 0.00 46.20 2.71
262 263 6.543100 AGTGAAACCAACGGTTACAATAGAAA 59.457 34.615 0.00 0.00 46.20 2.52
294 295 2.670229 GACTCACCAAGTGCATGCAATG 60.670 50.000 24.58 22.92 42.99 2.82
334 335 7.865706 ATTGAAACCATGTTATCTAGGTGAC 57.134 36.000 0.00 0.00 33.93 3.67
353 354 2.730550 CGGGGTACGTTCTAAACAGT 57.269 50.000 0.00 0.00 37.93 3.55
479 485 5.526506 ACTAGTAAGTCAGTCGTGGTTTT 57.473 39.130 0.00 0.00 0.00 2.43
480 486 5.287226 ACTAGTAAGTCAGTCGTGGTTTTG 58.713 41.667 0.00 0.00 0.00 2.44
561 567 3.004629 TGCTAGAAACAGGCACACAATTG 59.995 43.478 3.24 3.24 0.00 2.32
603 609 0.033504 GAAGTGCCCGAGTCAAGACA 59.966 55.000 2.72 0.00 0.00 3.41
832 1247 6.757897 TGCCTTGATTAGTTCCAAGTAATG 57.242 37.500 4.44 0.00 38.39 1.90
834 1249 7.398829 TGCCTTGATTAGTTCCAAGTAATGTA 58.601 34.615 4.44 0.00 38.39 2.29
873 1288 1.134220 TGAACGGAAAGCAACTGACCT 60.134 47.619 0.00 0.00 0.00 3.85
934 1352 2.941210 TTTTTCCAGGCGAGCGATT 58.059 47.368 0.00 0.00 0.00 3.34
936 1354 1.922135 TTTTCCAGGCGAGCGATTGC 61.922 55.000 3.72 3.72 43.24 3.56
970 1389 2.433868 TAAGTGCACGGACTGAGTTC 57.566 50.000 12.01 0.00 0.00 3.01
1164 1586 2.441164 TTTGCCACTGCCACCGTT 60.441 55.556 0.00 0.00 36.33 4.44
1182 1604 4.759205 GGCCAAGCCCCCGACATT 62.759 66.667 0.00 0.00 44.06 2.71
1738 2166 3.266772 TCAGTTCTATCAAGGCCAACCAT 59.733 43.478 5.01 0.00 39.06 3.55
1750 2178 3.266772 AGGCCAACCATTGATAAGTCTGA 59.733 43.478 5.01 0.00 39.06 3.27
1892 2356 2.743636 ATACGTTCATATCAGGGCGG 57.256 50.000 0.00 0.00 0.00 6.13
2007 2486 7.539034 AAACAAAGAAAAGGTATGCCACTAT 57.461 32.000 1.54 0.00 37.19 2.12
2132 2623 1.672363 TGTGCCGATTCTCAATCATGC 59.328 47.619 0.00 0.27 37.78 4.06
2247 2742 2.427095 GGTGTTTGACTTCCAACAGCTT 59.573 45.455 14.78 0.00 34.53 3.74
2259 2754 0.036875 AACAGCTTCTACAGGCCACC 59.963 55.000 5.01 0.00 0.00 4.61
2536 3441 3.423539 TCTTCACATTCAGGACAAGGG 57.576 47.619 0.00 0.00 0.00 3.95
2780 3757 8.705594 TCCACATTTTATTTTTCTGTTAACCCA 58.294 29.630 2.48 0.00 0.00 4.51
2781 3758 8.769891 CCACATTTTATTTTTCTGTTAACCCAC 58.230 33.333 2.48 0.00 0.00 4.61
3589 4654 1.091771 AATGCAGCCGATCGACCAAG 61.092 55.000 18.66 0.00 0.00 3.61
3791 4856 7.285629 TGTTTACTATGTTTGTGATGTCCCAAA 59.714 33.333 0.00 0.00 0.00 3.28
3822 4887 5.689961 TGATGATATCGTAACCATTGTGTCG 59.310 40.000 0.00 0.00 0.00 4.35
3888 4953 4.948341 TGTTGCTACCTTGACTTCAGTA 57.052 40.909 0.00 0.00 0.00 2.74
3890 4955 4.587262 TGTTGCTACCTTGACTTCAGTAGA 59.413 41.667 8.95 0.00 35.29 2.59
4729 7155 7.523293 TTTTTGCCAGAGAATTATTGACTGA 57.477 32.000 8.70 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.507992 CACTGGAGCGAGCCGAAG 60.508 66.667 0.00 0.00 0.00 3.79
7 8 4.742201 GCACTGGAGCGAGCCGAA 62.742 66.667 0.00 0.00 0.00 4.30
9 10 4.749310 AAGCACTGGAGCGAGCCG 62.749 66.667 0.00 0.00 40.15 5.52
10 11 2.507110 TACAAGCACTGGAGCGAGCC 62.507 60.000 0.00 0.00 40.15 4.70
11 12 1.079819 TACAAGCACTGGAGCGAGC 60.080 57.895 0.00 0.00 40.15 5.03
12 13 0.244994 ACTACAAGCACTGGAGCGAG 59.755 55.000 0.00 0.00 40.05 5.03
13 14 0.243907 GACTACAAGCACTGGAGCGA 59.756 55.000 0.00 0.00 40.05 4.93
64 65 8.402472 CACATAGAACACCAGAAGTAACAAAAA 58.598 33.333 0.00 0.00 0.00 1.94
75 76 2.632512 TGACAGCACATAGAACACCAGA 59.367 45.455 0.00 0.00 0.00 3.86
106 107 8.186178 TGCGAGAGAAACTTTAATCTATTCAC 57.814 34.615 0.00 0.00 0.00 3.18
176 177 2.354821 GCTGAAACTTCGGTGTCAAACT 59.645 45.455 0.47 0.00 41.18 2.66
228 229 4.141869 ACCGTTGGTTTCACTAGTGTTAGT 60.142 41.667 21.99 5.91 34.51 2.24
232 233 2.994186 ACCGTTGGTTTCACTAGTGT 57.006 45.000 21.99 0.00 27.29 3.55
257 258 4.262894 GGTGAGTCACATGGGTTCTTTCTA 60.263 45.833 24.20 0.00 35.86 2.10
262 263 1.434188 TGGTGAGTCACATGGGTTCT 58.566 50.000 24.20 0.00 35.86 3.01
334 335 2.730550 ACTGTTTAGAACGTACCCCG 57.269 50.000 0.00 0.00 44.03 5.73
353 354 3.135712 TGCTAGAAGTTTCCACCTCACAA 59.864 43.478 0.00 0.00 0.00 3.33
479 485 2.830923 CCATTAGAATTTGGCCACCACA 59.169 45.455 3.88 0.00 30.78 4.17
480 486 2.831526 ACCATTAGAATTTGGCCACCAC 59.168 45.455 3.88 0.00 36.41 4.16
561 567 5.712917 TCACTATCCACCAACCAAAATAACC 59.287 40.000 0.00 0.00 0.00 2.85
658 664 4.826274 AAGTTGATCTTGCTGCTACCTA 57.174 40.909 0.00 0.00 34.77 3.08
832 1247 9.448294 CGTTCAGGAGTAGTAACTAATCAATAC 57.552 37.037 0.00 0.00 35.56 1.89
834 1249 7.341256 TCCGTTCAGGAGTAGTAACTAATCAAT 59.659 37.037 0.00 0.00 45.98 2.57
934 1352 4.612712 GCACTTATTTAACAGCAAGTCGCA 60.613 41.667 0.00 0.00 46.13 5.10
936 1354 4.846137 GTGCACTTATTTAACAGCAAGTCG 59.154 41.667 10.32 0.00 33.37 4.18
970 1389 5.304871 TCCTCTTCTCTCAATCCAGATGATG 59.695 44.000 0.00 0.00 32.68 3.07
1738 2166 1.195115 AGCGGCCTCAGACTTATCAA 58.805 50.000 0.00 0.00 0.00 2.57
1750 2178 2.685380 AGTTGGAGCTAGCGGCCT 60.685 61.111 24.05 9.59 43.05 5.19
1876 2340 1.000843 TCATCCGCCCTGATATGAACG 59.999 52.381 0.00 0.00 0.00 3.95
1892 2356 5.825507 GGAATTATCCACAGCTTGTTCATC 58.174 41.667 0.00 0.00 45.79 2.92
2007 2486 9.569122 GGCCCATTCAGAAACTAACTAATTATA 57.431 33.333 0.00 0.00 0.00 0.98
2132 2623 4.271696 TGTAACCTCATCACTTCACCTG 57.728 45.455 0.00 0.00 0.00 4.00
2247 2742 5.124776 CGAAAAATTATTGGTGGCCTGTAGA 59.875 40.000 3.32 0.00 0.00 2.59
2487 3392 7.011857 GTCTTTTAACTGCTATCTCCAATCCAG 59.988 40.741 0.00 0.00 0.00 3.86
3589 4654 4.482386 CATTGCTATAACATCTGCCATGC 58.518 43.478 0.00 0.00 0.00 4.06
3791 4856 9.208022 CAATGGTTACGATATCATCAATACACT 57.792 33.333 3.12 0.00 0.00 3.55
3822 4887 9.668497 AGAATGGACCACTTAAACTTATACTTC 57.332 33.333 0.00 0.00 0.00 3.01
4130 5198 2.639327 GGGCGCATCTTGCACCTTT 61.639 57.895 10.83 0.00 44.59 3.11
4585 7010 3.726557 ATCCAGAAGTCAATCAAGGCA 57.273 42.857 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.