Multiple sequence alignment - TraesCS7A01G135200

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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 TraesCS7A01G135200 chr7A 100.000 4265 0 0 1 4265 88128155 88123891 0 7877
1 TraesCS7A01G135200 chr7A 97.434 4287 85 9 1 4263 88014898 88010613 0 7284
2 TraesCS7A01G135200 chr7A 96.954 4268 103 6 1 4263 88178906 88174661 0 7136
3 TraesCS7A01G135200 chr7A 92.342 4309 261 26 1 4263 88442409 88438124 0 6065
4 TraesCS7A01G135200 chr7A 91.798 2658 175 12 1 2636 88324207 88321571 0 3661
5 TraesCS7A01G135200 chr7A 93.223 1446 82 12 2646 4079 88320596 88319155 0 2113
6 TraesCS7A01G135200 chr7D 93.271 4310 225 26 1 4263 87212978 87208687 0 6292
7 TraesCS7A01G135200 chr7D 93.968 4078 215 16 1 4054 86769031 86764961 0 6139
8 TraesCS7A01G135200 chr7D 93.760 3750 200 19 538 4263 86924514 86920775 0 5598
9 TraesCS7A01G135200 chr7D 89.799 3823 311 33 476 4263 86800998 86797220 0 4826
10 TraesCS7A01G135200 chr7D 94.396 2516 126 8 1 2511 86927802 86925297 0 3851
11 TraesCS7A01G135200 chr7D 87.193 2241 244 23 232 2446 86298581 86296358 0 2508
12 TraesCS7A01G135200 chr7B 90.232 4013 296 38 309 4263 35313792 35309818 0 5151
13 TraesCS7A01G135200 chr7B 90.294 3400 237 33 1 3357 35513792 35510443 0 4364


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 TraesCS7A01G135200 chr7A 88123891 88128155 4264 True 7877.0 7877 100.0000 1 4265 1 chr7A.!!$R2 4264
1 TraesCS7A01G135200 chr7A 88010613 88014898 4285 True 7284.0 7284 97.4340 1 4263 1 chr7A.!!$R1 4262
2 TraesCS7A01G135200 chr7A 88174661 88178906 4245 True 7136.0 7136 96.9540 1 4263 1 chr7A.!!$R3 4262
3 TraesCS7A01G135200 chr7A 88438124 88442409 4285 True 6065.0 6065 92.3420 1 4263 1 chr7A.!!$R4 4262
4 TraesCS7A01G135200 chr7A 88319155 88324207 5052 True 2887.0 3661 92.5105 1 4079 2 chr7A.!!$R5 4078
5 TraesCS7A01G135200 chr7D 87208687 87212978 4291 True 6292.0 6292 93.2710 1 4263 1 chr7D.!!$R4 4262
6 TraesCS7A01G135200 chr7D 86764961 86769031 4070 True 6139.0 6139 93.9680 1 4054 1 chr7D.!!$R2 4053
7 TraesCS7A01G135200 chr7D 86797220 86800998 3778 True 4826.0 4826 89.7990 476 4263 1 chr7D.!!$R3 3787
8 TraesCS7A01G135200 chr7D 86920775 86927802 7027 True 4724.5 5598 94.0780 1 4263 2 chr7D.!!$R5 4262
9 TraesCS7A01G135200 chr7D 86296358 86298581 2223 True 2508.0 2508 87.1930 232 2446 1 chr7D.!!$R1 2214
10 TraesCS7A01G135200 chr7B 35309818 35313792 3974 True 5151.0 5151 90.2320 309 4263 1 chr7B.!!$R1 3954
11 TraesCS7A01G135200 chr7B 35510443 35513792 3349 True 4364.0 4364 90.2940 1 3357 1 chr7B.!!$R2 3356

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
108 110 3.479489 TCGCTGAAACATGGCATATGAT 58.521 40.909 6.97 0.00 0.00 2.45 F
1133 3971 2.242196 CAATAGTCAACCAGGGGTGGAT 59.758 50.000 3.05 0.00 38.02 3.41 F
2077 4944 0.109781 GTTGCCGCACATCAACGAAT 60.110 50.000 0.00 0.00 34.12 3.34 F
2765 6638 0.616395 TGGAAGTCTATGGCCGTGGA 60.616 55.000 6.97 6.97 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 4490 1.140161 CCCATTGATGTGCGGCAAG 59.86 57.895 3.23 0.0 0.00 4.01 R
2862 6735 0.389817 CGCTTTGTCCCTGACGATGA 60.39 55.000 0.00 0.0 34.95 2.92 R
2938 6811 0.610232 GGCTTGCCAGGTGACAGAAT 60.61 55.000 6.79 0.0 0.00 2.40 R
3713 7597 3.790089 AGGGTCTCTTGGACGAAAAAT 57.21 42.857 0.00 0.0 45.35 1.82 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
88 89 6.237648 CGAAGCAAAAGCCATTTATGAACATC 60.238 38.462 0.00 0.00 0.00 3.06
108 110 3.479489 TCGCTGAAACATGGCATATGAT 58.521 40.909 6.97 0.00 0.00 2.45
255 306 7.581814 TGAGAGAGAGAGAGATGGAAGATAAA 58.418 38.462 0.00 0.00 0.00 1.40
753 833 3.492102 TCAATACTCAATAGGCCTGCC 57.508 47.619 17.99 0.00 0.00 4.85
946 1032 7.834881 TCAATCTACTTTAGTATGGACCGAT 57.165 36.000 0.00 0.00 0.00 4.18
1133 3971 2.242196 CAATAGTCAACCAGGGGTGGAT 59.758 50.000 3.05 0.00 38.02 3.41
1201 4039 4.023536 ACACCAACAAAATCATGTACGACC 60.024 41.667 0.00 0.00 32.02 4.79
1242 4080 3.990469 AGAAGCACAACTACATCGTGAAG 59.010 43.478 0.00 0.00 32.23 3.02
1361 4199 3.971971 GGGACCCATGTTACTAGTGGTAT 59.028 47.826 5.33 0.00 0.00 2.73
1523 4368 4.508861 GGCAACAATCATGGACAATAATGC 59.491 41.667 0.00 0.00 0.00 3.56
1645 4490 7.339466 ACAATATTTCCATAGACCAACCAGTTC 59.661 37.037 0.00 0.00 0.00 3.01
2077 4944 0.109781 GTTGCCGCACATCAACGAAT 60.110 50.000 0.00 0.00 34.12 3.34
2086 4953 3.670055 GCACATCAACGAATGTTTTGGAG 59.330 43.478 0.00 0.00 37.78 3.86
2765 6638 0.616395 TGGAAGTCTATGGCCGTGGA 60.616 55.000 6.97 6.97 0.00 4.02
2796 6669 2.540515 ACATATCCAAGCACTTCGTCG 58.459 47.619 0.00 0.00 0.00 5.12
2938 6811 6.957920 TGAGCTATTGGCAGCAAATAATAA 57.042 33.333 3.71 0.00 44.35 1.40
2949 6822 6.183360 GGCAGCAAATAATAATTCTGTCACCT 60.183 38.462 0.00 0.00 27.49 4.00
3099 6972 0.325933 TCAGCCAATGTGGAGTGAGG 59.674 55.000 0.00 0.00 40.96 3.86
3146 7019 3.116959 TGTTATGGACGGGGTAGGAAAT 58.883 45.455 0.00 0.00 0.00 2.17
3438 7316 4.273318 AGTGTTTGCCATCTCCCTTATTC 58.727 43.478 0.00 0.00 0.00 1.75
3502 7384 5.985530 CGTACATGATGTCTCAATATGTGGT 59.014 40.000 0.00 0.00 34.37 4.16
3650 7532 7.884816 TTACTTGAAAATCAGACCTTCTACG 57.115 36.000 0.00 0.00 0.00 3.51
3713 7597 0.554305 ATGCATGATGGCTCTTCCCA 59.446 50.000 0.00 0.00 39.65 4.37
3736 7620 1.183549 TTCGTCCAAGAGACCCTAGC 58.816 55.000 0.00 0.00 43.08 3.42
3773 7658 2.180862 TTGCTACGTTGCGGCAACA 61.181 52.632 36.28 22.04 43.70 3.33
3869 7772 3.454371 AGTTCGCAGTTTGTCACTAGT 57.546 42.857 0.00 0.00 32.76 2.57
3905 7808 9.362151 AGAGAAACCAATCAGTTATAAAAACCA 57.638 29.630 0.00 0.00 0.00 3.67
3918 7821 7.559897 AGTTATAAAAACCATACCCTCACCATG 59.440 37.037 0.00 0.00 0.00 3.66
4243 8150 1.349688 TGTAGATTGGACCGTTGGCTT 59.650 47.619 0.00 0.00 0.00 4.35
4253 8160 4.222145 TGGACCGTTGGCTTATATCTATCC 59.778 45.833 0.00 0.00 0.00 2.59
4264 8171 8.198109 TGGCTTATATCTATCCTATTTTCTCGC 58.802 37.037 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 3.909776 ATCATATGCCATGTTTCAGCG 57.090 42.857 0.00 0.00 0.00 5.18
336 390 7.510001 AGATTCAATACATGGGCCAATCAATTA 59.490 33.333 11.89 0.00 0.00 1.40
753 833 6.017605 ACTCAAGATTGCTAGAAACAACACAG 60.018 38.462 0.00 0.00 0.00 3.66
1201 4039 5.570262 TTCTTGTTCTTGTCATCGTTACG 57.430 39.130 0.00 0.00 0.00 3.18
1242 4080 2.019984 GGGAACAATGCATGGAGAGAC 58.980 52.381 8.45 0.00 0.00 3.36
1361 4199 2.035632 AGGTGAAAATGTTTTGCGGGA 58.964 42.857 0.00 0.00 0.00 5.14
1523 4368 4.158394 CCATAGGACAACCAAAGGACAATG 59.842 45.833 0.00 0.00 38.94 2.82
1645 4490 1.140161 CCCATTGATGTGCGGCAAG 59.860 57.895 3.23 0.00 0.00 4.01
1873 4722 4.929819 AAGTTTTCATTAACAAGGCCGT 57.070 36.364 0.00 0.00 0.00 5.68
2077 4944 3.130340 GTGTTCCTCTTTGCTCCAAAACA 59.870 43.478 0.00 0.00 32.75 2.83
2086 4953 4.318831 CGACTAACTTGTGTTCCTCTTTGC 60.319 45.833 0.00 0.00 37.59 3.68
2718 6591 7.253422 CCATAAAGAAATGACCTGTGAACATC 58.747 38.462 0.00 0.00 0.00 3.06
2765 6638 5.183904 GTGCTTGGATATGTTTTTCCAGTCT 59.816 40.000 0.00 0.00 42.73 3.24
2796 6669 1.198759 TGGACAGGGGTCTTAGTGGC 61.199 60.000 0.00 0.00 43.77 5.01
2862 6735 0.389817 CGCTTTGTCCCTGACGATGA 60.390 55.000 0.00 0.00 34.95 2.92
2938 6811 0.610232 GGCTTGCCAGGTGACAGAAT 60.610 55.000 6.79 0.00 0.00 2.40
2949 6822 1.039856 GTGAAAGAAAGGGCTTGCCA 58.960 50.000 14.04 0.00 0.00 4.92
3099 6972 2.681848 CAACAGAACCCATCATCTGCTC 59.318 50.000 2.86 0.00 45.50 4.26
3466 7344 5.610398 ACATCATGTACGCTTTCATATGGA 58.390 37.500 2.13 0.00 0.00 3.41
3502 7384 6.318648 GGCAAATTATGATACAACAGTCAGGA 59.681 38.462 0.00 0.00 0.00 3.86
3650 7532 8.819974 GTTAGTATAGTAGGATCTGACTATCGC 58.180 40.741 17.83 13.74 39.19 4.58
3713 7597 3.790089 AGGGTCTCTTGGACGAAAAAT 57.210 42.857 0.00 0.00 45.35 1.82
3736 7620 7.218014 CGTAGCAACACCACACAATATTAATTG 59.782 37.037 0.00 0.00 46.66 2.32
3869 7772 5.436175 TGATTGGTTTCTCTGTTTGACTCA 58.564 37.500 0.00 0.00 0.00 3.41
3905 7808 6.782494 GGGATTTAAAATCATGGTGAGGGTAT 59.218 38.462 0.00 0.00 0.00 2.73
3918 7821 6.834168 TGGAGAGTGTTGGGATTTAAAATC 57.166 37.500 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.