Multiple sequence alignment - TraesCS7A01G569100

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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 TraesCS7A01G569100 chr7A 100.000 3708 0 0 1 3708 736464728 736468435 0.000000e+00 6848
1 TraesCS7A01G569100 chr7A 81.671 2788 372 71 544 3278 736496363 736499064 0.000000e+00 2189
2 TraesCS7A01G569100 chr7A 87.076 1563 151 21 107 1649 736444353 736445884 0.000000e+00 1720
3 TraesCS7A01G569100 chr7A 82.895 228 31 7 3 226 736495891 736496114 8.120000e-47 198
4 TraesCS7A01G569100 chr7A 94.203 69 4 0 160 228 736452075 736452143 5.060000e-19 106
5 TraesCS7A01G569100 chr7D 97.466 2762 68 2 273 3032 631936397 631933636 0.000000e+00 4711
6 TraesCS7A01G569100 chr7D 82.543 2320 316 51 752 3048 631921795 631919542 0.000000e+00 1958
7 TraesCS7A01G569100 chr7D 96.221 688 25 1 3022 3708 631933614 631932927 0.000000e+00 1125
8 TraesCS7A01G569100 chr7D 81.384 1402 201 35 1905 3291 631958819 631957463 0.000000e+00 1088
9 TraesCS7A01G569100 chr7D 84.273 1100 149 18 767 1857 631968856 631967772 0.000000e+00 1051
10 TraesCS7A01G569100 chr7D 81.760 1091 145 35 774 1857 631959879 631958836 0.000000e+00 863
11 TraesCS7A01G569100 chr7D 82.692 832 128 12 1905 2730 631967755 631966934 0.000000e+00 725
12 TraesCS7A01G569100 chr7D 85.167 627 89 3 1231 1857 631964734 631964112 1.120000e-179 640
13 TraesCS7A01G569100 chr7D 79.202 952 172 15 1905 2851 631962315 631961385 4.040000e-179 638
14 TraesCS7A01G569100 chr7D 82.218 568 81 15 766 1324 631963050 631962494 4.330000e-129 472
15 TraesCS7A01G569100 chr7D 96.029 277 10 1 3 278 631938079 631937803 2.030000e-122 449
16 TraesCS7A01G569100 chr7D 84.706 425 39 16 2884 3291 631966934 631966519 5.770000e-108 401
17 TraesCS7A01G569100 chr7D 82.845 239 29 10 3 236 631922463 631922232 1.750000e-48 204
18 TraesCS7A01G569100 chr7D 85.393 178 25 1 1905 2081 631964095 631963918 2.270000e-42 183
19 TraesCS7A01G569100 chr7B 94.314 3060 153 14 5 3050 743459049 743455997 0.000000e+00 4667
20 TraesCS7A01G569100 chr7B 87.848 1366 149 11 1653 3016 743494061 743492711 0.000000e+00 1587
21 TraesCS7A01G569100 chr7B 85.886 1162 148 12 752 1900 743448264 743447106 0.000000e+00 1223
22 TraesCS7A01G569100 chr7B 78.944 1382 200 50 1915 3278 743433013 743431705 0.000000e+00 856
23 TraesCS7A01G569100 chr7B 86.630 733 82 10 430 1158 743502977 743502257 0.000000e+00 797
24 TraesCS7A01G569100 chr7B 79.826 803 121 26 2174 2962 743489546 743488771 7.000000e-152 547
25 TraesCS7A01G569100 chr7B 87.621 412 39 8 2885 3292 743473283 743473686 5.610000e-128 468
26 TraesCS7A01G569100 chr7B 92.245 245 19 0 3429 3673 743455985 743455741 7.620000e-92 348
27 TraesCS7A01G569100 chr7B 90.148 203 18 2 3092 3292 743489821 743489619 2.840000e-66 263
28 TraesCS7A01G569100 chr7B 83.028 218 30 6 3 216 743448981 743448767 1.360000e-44 191
29 TraesCS7A01G569100 chr7B 86.452 155 18 2 3140 3291 743488652 743488498 2.290000e-37 167
30 TraesCS7A01G569100 chr3B 91.106 416 36 1 3293 3708 169367078 169366664 2.500000e-156 562
31 TraesCS7A01G569100 chr3B 80.726 358 53 12 3293 3641 771742023 771741673 7.900000e-67 265
32 TraesCS7A01G569100 chr1D 82.913 357 49 9 3293 3641 343525589 343525237 1.000000e-80 311
33 TraesCS7A01G569100 chr3D 81.579 228 37 3 3293 3516 613412227 613412453 2.270000e-42 183


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 TraesCS7A01G569100 chr7A 736464728 736468435 3707 False 6848.000000 6848 100.000000 1 3708 1 chr7A.!!$F3 3707
1 TraesCS7A01G569100 chr7A 736444353 736445884 1531 False 1720.000000 1720 87.076000 107 1649 1 chr7A.!!$F1 1542
2 TraesCS7A01G569100 chr7A 736495891 736499064 3173 False 1193.500000 2189 82.283000 3 3278 2 chr7A.!!$F4 3275
3 TraesCS7A01G569100 chr7D 631932927 631938079 5152 True 2095.000000 4711 96.572000 3 3708 3 chr7D.!!$R2 3705
4 TraesCS7A01G569100 chr7D 631919542 631922463 2921 True 1081.000000 1958 82.694000 3 3048 2 chr7D.!!$R1 3045
5 TraesCS7A01G569100 chr7D 631957463 631968856 11393 True 673.444444 1088 82.977222 766 3291 9 chr7D.!!$R3 2525
6 TraesCS7A01G569100 chr7B 743455741 743459049 3308 True 2507.500000 4667 93.279500 5 3673 2 chr7B.!!$R4 3668
7 TraesCS7A01G569100 chr7B 743431705 743433013 1308 True 856.000000 856 78.944000 1915 3278 1 chr7B.!!$R1 1363
8 TraesCS7A01G569100 chr7B 743502257 743502977 720 True 797.000000 797 86.630000 430 1158 1 chr7B.!!$R2 728
9 TraesCS7A01G569100 chr7B 743447106 743448981 1875 True 707.000000 1223 84.457000 3 1900 2 chr7B.!!$R3 1897
10 TraesCS7A01G569100 chr7B 743488498 743494061 5563 True 641.000000 1587 86.068500 1653 3292 4 chr7B.!!$R5 1639

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
706 2159 1.755959 TGCATCACAAAGGCAAACACT 59.244 42.857 0.00 0.00 34.05 3.55 F
2115 3638 1.228228 CACCTGGGGCATGCTACAT 59.772 57.895 18.92 0.18 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2530 4065 0.545071 TGAGACCCTGATCTGCACCA 60.545 55.0 0.00 0.0 0.00 4.17 R
3620 18113 0.038159 GCGGTAGGCATAAGCGAGAT 60.038 55.0 9.72 0.0 43.41 2.75 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
238 241 2.089980 AGAGAAATGCCAGTGATGTGC 58.910 47.619 0.00 0.00 0.00 4.57
376 1794 5.022122 TGTAATTGATCCAAAAGGCCATGA 58.978 37.500 5.01 0.00 0.00 3.07
706 2159 1.755959 TGCATCACAAAGGCAAACACT 59.244 42.857 0.00 0.00 34.05 3.55
798 2289 3.132289 TCGCTTGGATAGGTTCGAGAAAT 59.868 43.478 0.00 0.00 0.00 2.17
1038 2552 9.064706 AGCTCATTAATTTCTTCCATACTCATG 57.935 33.333 0.00 0.00 0.00 3.07
1077 2591 6.467775 CCAATATTACCATCACCCCAGAATCT 60.468 42.308 0.00 0.00 0.00 2.40
1200 2714 5.715439 TCATCAAATTCTATGTGGTCCCT 57.285 39.130 0.00 0.00 0.00 4.20
1427 2941 2.376518 AGATCTTCCAGCCACCTTTCAA 59.623 45.455 0.00 0.00 0.00 2.69
1761 3278 1.229209 ACCGATGTGTGAGGGGAGT 60.229 57.895 0.00 0.00 0.00 3.85
1793 3312 1.834896 TGACATAGCGGCCTCCTTTTA 59.165 47.619 0.00 0.00 0.00 1.52
1832 3351 6.238648 ACGTATGGGTCAAAAGAGAGAAATT 58.761 36.000 0.00 0.00 0.00 1.82
1887 3406 5.075858 AGTAAATGCAACCATGGAATGTG 57.924 39.130 21.47 11.59 44.81 3.21
2115 3638 1.228228 CACCTGGGGCATGCTACAT 59.772 57.895 18.92 0.18 0.00 2.29
2118 3641 1.568597 ACCTGGGGCATGCTACATAAA 59.431 47.619 18.92 0.00 0.00 1.40
2452 3978 2.551912 CGGGAACAACCACCAGCAC 61.552 63.158 0.00 0.00 41.20 4.40
2453 3979 2.200337 GGGAACAACCACCAGCACC 61.200 63.158 0.00 0.00 41.20 5.01
2454 3980 1.454847 GGAACAACCACCAGCACCA 60.455 57.895 0.00 0.00 38.79 4.17
2570 4105 3.003173 TCGGGGCTCAACCTGGAG 61.003 66.667 0.00 0.00 39.10 3.86
2604 4139 1.209019 GATGCTGTCACAGGAGGATGT 59.791 52.381 7.00 0.00 34.87 3.06
2617 4152 2.270850 GATGTTGTGGCCGGGCTA 59.729 61.111 29.87 15.48 0.00 3.93
2714 13166 6.071278 TGACATTTGGCAGAATTGATGATCAA 60.071 34.615 10.65 10.65 41.09 2.57
3238 17731 3.205056 TCCACATCTAATCCAGGGCAAAT 59.795 43.478 0.00 0.00 0.00 2.32
3258 17751 6.572119 GCAAATATTTGTGGTGATGTCCAAGA 60.572 38.462 25.15 0.00 40.24 3.02
3301 17794 4.133820 TGTTTCACACATACTCTGTTGGG 58.866 43.478 0.00 0.00 35.29 4.12
3308 17801 5.299279 CACACATACTCTGTTGGGAAAAAGT 59.701 40.000 0.00 0.00 35.29 2.66
3399 17892 0.905357 GAAGTCTAGGCAGGCCAAGA 59.095 55.000 13.63 3.08 38.92 3.02
3403 17896 0.620556 TCTAGGCAGGCCAAGAAAGG 59.379 55.000 13.63 0.00 38.92 3.11
3443 17936 4.523943 GGGAAATCATGCTATATTGCACCA 59.476 41.667 14.10 4.32 46.33 4.17
3620 18113 0.320374 CACTAGGCGAAGGTCAACCA 59.680 55.000 1.33 0.00 38.89 3.67
3621 18114 1.066143 CACTAGGCGAAGGTCAACCAT 60.066 52.381 1.33 0.00 38.89 3.55
3630 18123 3.738281 CGAAGGTCAACCATCTCGCTTAT 60.738 47.826 1.33 0.00 38.89 1.73
3654 18147 6.127101 TGCCTACCGCTCACATATATAGTAT 58.873 40.000 0.00 0.00 38.78 2.12
3683 18176 8.548880 ACATAGGCTTGGTCTACTAGAAAATA 57.451 34.615 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 156 2.259204 GTGTACCGGTGCACGCTA 59.741 61.111 34.89 7.84 42.52 4.26
254 261 1.647545 GCATGCACGCACATACCTGT 61.648 55.000 14.21 0.00 35.44 4.00
265 272 3.698678 TGCTTTACATGCATGCACG 57.301 47.368 25.37 19.13 35.31 5.34
376 1794 4.471386 TCTCTACCTTCTGCTGCCTAAAAT 59.529 41.667 0.00 0.00 0.00 1.82
706 2159 4.276678 GCCATATGCATGCTTCTCTTGTTA 59.723 41.667 20.33 0.00 40.77 2.41
798 2289 3.709653 ACTTGTGGTGACAGGTAGAAAGA 59.290 43.478 0.00 0.00 40.44 2.52
1038 2552 5.178809 GGTAATATTGGACGCAACCATAGAC 59.821 44.000 0.00 0.00 39.82 2.59
1040 2554 5.060506 TGGTAATATTGGACGCAACCATAG 58.939 41.667 0.00 0.00 39.82 2.23
1200 2714 1.195115 AGGCTTCATCGAGCACCTTA 58.805 50.000 0.00 0.00 44.49 2.69
1372 2886 2.595655 GGCCTTCCAATAGCCGGT 59.404 61.111 1.90 0.00 36.84 5.28
1427 2941 3.265791 GTCTTCTTCATGCCGATGAGTT 58.734 45.455 0.00 0.00 39.81 3.01
1622 3138 4.569761 AGCATGTTGATGATTCATGAGC 57.430 40.909 3.32 0.00 40.64 4.26
1761 3278 3.494223 CCGCTATGTCATGGTGGATGTAA 60.494 47.826 21.03 0.00 43.32 2.41
1832 3351 9.021807 GGCCTACTAGTATGAACATTATCTACA 57.978 37.037 9.15 0.00 0.00 2.74
2530 4065 0.545071 TGAGACCCTGATCTGCACCA 60.545 55.000 0.00 0.00 0.00 4.17
2570 4105 3.124921 CATCGACGCCAACCCACC 61.125 66.667 0.00 0.00 0.00 4.61
2604 4139 2.530672 TTCCTTAGCCCGGCCACAA 61.531 57.895 5.55 0.00 0.00 3.33
2617 4152 2.107726 GTTCCCTGGGTAGTTGTTCCTT 59.892 50.000 13.56 0.00 0.00 3.36
2775 13231 4.967084 ACGGGTTGGCATATATCAACTA 57.033 40.909 13.87 0.00 41.91 2.24
3238 17731 5.491070 CTCTCTTGGACATCACCACAAATA 58.509 41.667 0.00 0.00 39.85 1.40
3326 17819 0.948141 CTAGCGCCTAAGCATGCCTC 60.948 60.000 15.66 0.00 39.83 4.70
3399 17892 4.270008 CCGATTGGGTAGACAATTCCTTT 58.730 43.478 0.00 0.00 40.92 3.11
3547 18040 5.744007 GCCTAGGCGGTAATATAGTTTTGGT 60.744 44.000 20.16 0.00 34.25 3.67
3576 18069 1.366854 GCGGTGCTTAAGTGCCCTAC 61.367 60.000 4.02 0.00 0.00 3.18
3620 18113 0.038159 GCGGTAGGCATAAGCGAGAT 60.038 55.000 9.72 0.00 43.41 2.75
3621 18114 1.362717 GCGGTAGGCATAAGCGAGA 59.637 57.895 9.72 0.00 43.41 4.04
3630 18123 8.286404 ACATACTATATATGTGAGCGGTAGGCA 61.286 40.741 0.00 0.00 39.29 4.75
3654 18147 3.441101 AGTAGACCAAGCCTATGTCACA 58.559 45.455 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.