Multiple sequence alignment - TraesCS7A01G216600

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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 TraesCS7A01G216600 chr7A 100.000 4034 0 0 1 4034 183310046 183306013 0.000000e+00 7450
1 TraesCS7A01G216600 chr7A 95.438 1359 62 0 2676 4034 183654469 183653111 0.000000e+00 2167
2 TraesCS7A01G216600 chr7A 92.449 1470 98 8 1057 2515 183483281 183481814 0.000000e+00 2087
3 TraesCS7A01G216600 chr7A 95.161 1240 60 0 2795 4034 183481789 183480550 0.000000e+00 1958
4 TraesCS7A01G216600 chr7A 88.018 1544 153 14 1072 2608 183655986 183654468 0.000000e+00 1797
5 TraesCS7A01G216600 chr7A 89.321 1311 115 8 1050 2351 182856933 182855639 0.000000e+00 1622
6 TraesCS7A01G216600 chr7A 89.782 597 44 6 426 1010 183656588 183655997 0.000000e+00 749
7 TraesCS7A01G216600 chr7A 87.500 432 29 10 1 431 183657103 183656696 3.650000e-130 475
8 TraesCS7A01G216600 chr7A 84.891 503 35 13 3 467 183484582 183484083 1.700000e-128 470
9 TraesCS7A01G216600 chr7A 95.753 259 11 0 3042 3300 182855638 182855380 6.240000e-113 418
10 TraesCS7A01G216600 chr7A 87.463 335 28 7 733 1057 182857298 182856968 1.370000e-99 374
11 TraesCS7A01G216600 chr7A 92.609 230 12 5 224 450 182857994 182857767 3.890000e-85 326
12 TraesCS7A01G216600 chr7A 90.594 202 15 3 1 202 182858518 182858321 8.600000e-67 265
13 TraesCS7A01G216600 chr7A 83.429 175 20 6 484 651 183483980 183483808 1.940000e-33 154
14 TraesCS7A01G216600 chr7B 94.161 4042 202 18 1 4034 144737733 144733718 0.000000e+00 6126
15 TraesCS7A01G216600 chr7B 92.381 1470 99 8 1057 2515 144813428 144811961 0.000000e+00 2082
16 TraesCS7A01G216600 chr7B 93.245 1362 83 3 2676 4034 145053676 145052321 0.000000e+00 1997
17 TraesCS7A01G216600 chr7B 95.081 1240 61 0 2795 4034 144811936 144810697 0.000000e+00 1953
18 TraesCS7A01G216600 chr7B 88.746 1555 156 10 1068 2608 145055224 145053675 0.000000e+00 1884
19 TraesCS7A01G216600 chr7B 89.571 1141 74 18 1 1128 145056326 145055218 0.000000e+00 1406
20 TraesCS7A01G216600 chr7B 77.197 956 187 25 3046 3987 145028609 145027671 2.760000e-146 529
21 TraesCS7A01G216600 chr7B 84.770 499 36 16 7 467 144814690 144814194 7.900000e-127 464
22 TraesCS7A01G216600 chr7D 98.018 2775 51 3 1 2772 178862974 178860201 0.000000e+00 4817
23 TraesCS7A01G216600 chr7D 92.428 1466 102 5 1059 2515 178940722 178939257 0.000000e+00 2084
24 TraesCS7A01G216600 chr7D 97.210 1183 20 3 2852 4034 178860205 178859036 0.000000e+00 1989
25 TraesCS7A01G216600 chr7D 95.000 1240 62 0 2795 4034 178939232 178937993 0.000000e+00 1947
26 TraesCS7A01G216600 chr7D 88.789 1552 154 13 1072 2608 179123587 179122041 0.000000e+00 1884
27 TraesCS7A01G216600 chr7D 89.358 639 51 7 358 984 179124245 179123612 0.000000e+00 787
28 TraesCS7A01G216600 chr7D 76.761 951 200 19 3046 3987 178990013 178989075 2.780000e-141 512
29 TraesCS7A01G216600 chr7D 84.095 503 39 13 3 467 178942000 178941501 7.950000e-122 448
30 TraesCS7A01G216600 chr7D 91.319 288 19 1 2676 2963 179122042 179121761 4.890000e-104 388
31 TraesCS7A01G216600 chr7D 86.908 359 22 16 1 358 179124637 179124303 2.940000e-101 379


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 TraesCS7A01G216600 chr7A 183306013 183310046 4033 True 7450.000000 7450 100.000000 1 4034 1 chr7A.!!$R1 4033
1 TraesCS7A01G216600 chr7A 183653111 183657103 3992 True 1297.000000 2167 90.184500 1 4034 4 chr7A.!!$R4 4033
2 TraesCS7A01G216600 chr7A 183480550 183484582 4032 True 1167.250000 2087 88.982500 3 4034 4 chr7A.!!$R3 4031
3 TraesCS7A01G216600 chr7A 182855380 182858518 3138 True 601.000000 1622 91.148000 1 3300 5 chr7A.!!$R2 3299
4 TraesCS7A01G216600 chr7B 144733718 144737733 4015 True 6126.000000 6126 94.161000 1 4034 1 chr7B.!!$R1 4033
5 TraesCS7A01G216600 chr7B 145052321 145056326 4005 True 1762.333333 1997 90.520667 1 4034 3 chr7B.!!$R4 4033
6 TraesCS7A01G216600 chr7B 144810697 144814690 3993 True 1499.666667 2082 90.744000 7 4034 3 chr7B.!!$R3 4027
7 TraesCS7A01G216600 chr7B 145027671 145028609 938 True 529.000000 529 77.197000 3046 3987 1 chr7B.!!$R2 941
8 TraesCS7A01G216600 chr7D 178859036 178862974 3938 True 3403.000000 4817 97.614000 1 4034 2 chr7D.!!$R2 4033
9 TraesCS7A01G216600 chr7D 178937993 178942000 4007 True 1493.000000 2084 90.507667 3 4034 3 chr7D.!!$R3 4031
10 TraesCS7A01G216600 chr7D 179121761 179124637 2876 True 859.500000 1884 89.093500 1 2963 4 chr7D.!!$R4 2962
11 TraesCS7A01G216600 chr7D 178989075 178990013 938 True 512.000000 512 76.761000 3046 3987 1 chr7D.!!$R1 941

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
146 151 0.542702 CACCCTTCCCATTTGGCTGT 60.543 55.000 0.0 0.0 0.00 4.40 F
1010 2068 0.467844 AGCAACCACATGGCAGACAA 60.468 50.000 0.0 0.0 39.32 3.18 F
1232 2417 0.683179 GGATTAACACCACCAGGGGC 60.683 60.000 0.0 0.0 44.59 5.80 F
2274 3462 1.734465 CAATCTTCAGTCCGCTCAACC 59.266 52.381 0.0 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1333 2518 0.322975 ACAAGAGATGCAGCGAAGGT 59.677 50.000 0.00 0.00 41.48 3.50 R
2311 3499 0.683973 AGTTCCTCTGCAGTCTGGTG 59.316 55.000 14.67 0.00 0.00 4.17 R
2500 3694 2.028839 CCATTTCTGCAACATGCTGGAA 60.029 45.455 5.56 5.56 45.31 3.53 R
3685 4891 0.955919 GGAGTTCCCGTGGCTTTCTG 60.956 60.000 0.00 0.00 0.00 3.02 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
146 151 0.542702 CACCCTTCCCATTTGGCTGT 60.543 55.000 0.00 0.00 0.00 4.40
206 538 4.483476 ACTTTCTATTCGTGTGTTTGGC 57.517 40.909 0.00 0.00 0.00 4.52
219 551 2.100749 GTGTTTGGCTGTTAGGCTTTGT 59.899 45.455 0.00 0.00 41.96 2.83
327 682 3.138304 TGTCTTATGTGTGTTCTGTGGC 58.862 45.455 0.00 0.00 0.00 5.01
631 1607 3.564053 TCGTCTTTTAACACCAACCCT 57.436 42.857 0.00 0.00 0.00 4.34
1010 2068 0.467844 AGCAACCACATGGCAGACAA 60.468 50.000 0.00 0.00 39.32 3.18
1097 2281 2.548057 TCGTGTCCAGCAGAAATTTGTC 59.452 45.455 0.00 0.00 0.00 3.18
1169 2354 8.436200 GCTATTGTGGAGACATCGTAAATATTC 58.564 37.037 0.00 0.00 46.14 1.75
1232 2417 0.683179 GGATTAACACCACCAGGGGC 60.683 60.000 0.00 0.00 44.59 5.80
1256 2441 3.322541 TCGTGGACACTAAACAAGGATGA 59.677 43.478 0.56 0.00 0.00 2.92
1801 2989 1.895238 CTGCATTTGGCCCTTCCTG 59.105 57.895 0.00 0.00 43.89 3.86
1808 2996 2.286365 TTGGCCCTTCCTGTTTACAG 57.714 50.000 0.00 2.86 43.40 2.74
1857 3045 4.653004 GGAGTAACTACCTTCGTCGTTAC 58.347 47.826 8.84 8.84 45.08 2.50
2268 3456 3.547613 GCAATCATCAATCTTCAGTCCGC 60.548 47.826 0.00 0.00 0.00 5.54
2274 3462 1.734465 CAATCTTCAGTCCGCTCAACC 59.266 52.381 0.00 0.00 0.00 3.77
2311 3499 6.595716 AGAAGATAATACTGCTGAACCACAAC 59.404 38.462 0.00 0.00 0.00 3.32
2500 3694 0.612229 CACAGAGTGCCAGTCTCCAT 59.388 55.000 0.00 0.00 32.93 3.41
2781 3978 2.957474 TCACCTGATGATCCCGACATA 58.043 47.619 0.00 0.00 29.99 2.29
2858 4055 3.457380 AGTCATGGCATAGTGGATGAAGT 59.543 43.478 0.00 0.00 37.82 3.01
2878 4075 1.032014 GCTTTCTGCACCTGTGGAAA 58.968 50.000 0.00 1.31 42.31 3.13
2938 4135 6.326583 TCTGGTTGGAGATAATAACCCTAGTG 59.673 42.308 0.00 0.00 42.44 2.74
3031 4231 5.878116 CCCAATCAAAATGCTGATGACATTT 59.122 36.000 0.00 0.00 46.85 2.32
3384 4584 1.527433 GGAACTGCAGGGAGGCAAAC 61.527 60.000 19.93 0.00 44.40 2.93
3391 4591 1.242076 CAGGGAGGCAAACAAGACTG 58.758 55.000 0.00 0.00 0.00 3.51
3499 4699 4.101448 GGCAGGTGGCGGAGATGT 62.101 66.667 0.00 0.00 46.16 3.06
3797 5003 0.248743 GTGTCGTCTGTGGTCGTCAA 60.249 55.000 0.00 0.00 0.00 3.18
3990 5196 3.439476 CCCTTCTGATTCAAGTTCTGCTG 59.561 47.826 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 140 0.970640 TGCAATGCTCACAGCCAAAT 59.029 45.000 6.82 0.00 41.51 2.32
195 527 0.040425 GCCTAACAGCCAAACACACG 60.040 55.000 0.00 0.00 0.00 4.49
203 535 1.680735 CACAACAAAGCCTAACAGCCA 59.319 47.619 0.00 0.00 0.00 4.75
206 538 5.270853 GTTACACACAACAAAGCCTAACAG 58.729 41.667 0.00 0.00 0.00 3.16
219 551 5.048364 GCATTCAATGGTAGGTTACACACAA 60.048 40.000 0.00 0.00 0.00 3.33
257 611 6.495872 ACACTAACAGATTCTACAGGGTAACA 59.504 38.462 0.00 0.00 39.74 2.41
327 682 7.042523 CCTTTGTTTTTCTTCCAACTGCTATTG 60.043 37.037 0.00 0.00 0.00 1.90
631 1607 3.239449 ACCAACTATCAGAGTCCACACA 58.761 45.455 0.00 0.00 37.44 3.72
1010 2068 3.542676 TGACCACGAACTGCCCGT 61.543 61.111 0.00 0.00 41.36 5.28
1097 2281 2.329267 TGGATACATGGCTAGAGGGTG 58.671 52.381 0.00 0.00 46.17 4.61
1169 2354 2.099427 GCTAGGACTCCAAGAAGTACCG 59.901 54.545 0.00 0.00 29.58 4.02
1232 2417 3.659786 TCCTTGTTTAGTGTCCACGATG 58.340 45.455 0.00 0.00 36.20 3.84
1256 2441 1.133884 CAGGGTCACCAGCATGATGAT 60.134 52.381 13.69 0.00 43.34 2.45
1333 2518 0.322975 ACAAGAGATGCAGCGAAGGT 59.677 50.000 0.00 0.00 41.48 3.50
1801 2989 2.906354 AGCCGGATGATGACTGTAAAC 58.094 47.619 5.05 0.00 0.00 2.01
1808 2996 2.101582 ACAGAAGTAGCCGGATGATGAC 59.898 50.000 5.05 0.00 0.00 3.06
2268 3456 3.181367 GCAGGTGCATCGGTTGAG 58.819 61.111 0.00 0.00 41.59 3.02
2311 3499 0.683973 AGTTCCTCTGCAGTCTGGTG 59.316 55.000 14.67 0.00 0.00 4.17
2427 3621 2.437281 CTGGCTGTTCCCTGATAGATGT 59.563 50.000 0.00 0.00 0.00 3.06
2500 3694 2.028839 CCATTTCTGCAACATGCTGGAA 60.029 45.455 5.56 5.56 45.31 3.53
2843 4040 3.944015 AGAAAGCACTTCATCCACTATGC 59.056 43.478 1.90 0.00 36.40 3.14
2938 4135 2.105006 TCACTGCCAAGAATCTCAGC 57.895 50.000 0.00 0.00 0.00 4.26
3031 4231 4.879197 TCTTCAGATGCTTCTCAGTTCA 57.121 40.909 0.00 0.00 0.00 3.18
3186 4386 3.004354 AACCGGCGATGGTGGGTA 61.004 61.111 9.30 0.00 42.89 3.69
3384 4584 6.492007 AGCACTGATATGAAAACAGTCTTG 57.508 37.500 0.00 0.00 41.93 3.02
3391 4591 6.589830 ACATACGAGCACTGATATGAAAAC 57.410 37.500 0.00 0.00 0.00 2.43
3499 4699 7.307989 GCAAAAATGACTAACTGAGTGCTCTAA 60.308 37.037 0.68 0.00 39.06 2.10
3685 4891 0.955919 GGAGTTCCCGTGGCTTTCTG 60.956 60.000 0.00 0.00 0.00 3.02
3990 5196 4.920340 CCTAGTGTATCATGCATCGAAGAC 59.080 45.833 0.00 2.51 42.51 3.01


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

AutoCloner maintained by Alex Coulton.