Multiple sequence alignment - TraesCS7A01G396900

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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 TraesCS7A01G396900 chr7A 100.000 3094 0 0 1 3094 575288566 575291659 0 5714
1 TraesCS7A01G396900 chr4D 97.872 3102 58 6 1 3094 123299967 123303068 0 5356
2 TraesCS7A01G396900 chr7B 97.614 3101 67 6 1 3094 644467521 644470621 0 5310
3 TraesCS7A01G396900 chr7D 97.584 3104 65 6 1 3094 203515553 203518656 0 5308
4 TraesCS7A01G396900 chr3A 97.451 3099 73 6 1 3094 633111331 633114428 0 5280
5 TraesCS7A01G396900 chr6B 97.229 3104 76 6 1 3094 306995913 306992810 0 5247
6 TraesCS7A01G396900 chr1B 96.909 3106 82 10 1 3094 638700589 638697486 0 5192


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 TraesCS7A01G396900 chr7A 575288566 575291659 3093 False 5714 5714 100.000 1 3094 1 chr7A.!!$F1 3093
1 TraesCS7A01G396900 chr4D 123299967 123303068 3101 False 5356 5356 97.872 1 3094 1 chr4D.!!$F1 3093
2 TraesCS7A01G396900 chr7B 644467521 644470621 3100 False 5310 5310 97.614 1 3094 1 chr7B.!!$F1 3093
3 TraesCS7A01G396900 chr7D 203515553 203518656 3103 False 5308 5308 97.584 1 3094 1 chr7D.!!$F1 3093
4 TraesCS7A01G396900 chr3A 633111331 633114428 3097 False 5280 5280 97.451 1 3094 1 chr3A.!!$F1 3093
5 TraesCS7A01G396900 chr6B 306992810 306995913 3103 True 5247 5247 97.229 1 3094 1 chr6B.!!$R1 3093
6 TraesCS7A01G396900 chr1B 638697486 638700589 3103 True 5192 5192 96.909 1 3094 1 chr1B.!!$R1 3093

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
524 526 0.033405 CTCGTAGGGGGTGAGAAGGA 60.033 60.0 0.0 0.0 31.31 3.36 F
897 914 0.106894 CCCTAGCCGCCTTCCTTAAG 59.893 60.0 0.0 0.0 0.00 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 1841 0.396695 ACCTCGATCCCGAAGCCTTA 60.397 55.0 0.00 0.0 45.04 2.69 R
2314 2334 0.523519 CGAAGCCTTCAGCCTTTTCC 59.476 55.0 5.14 0.0 45.47 3.13 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
65 66 3.172106 TCTTGGTTGGTGCCGGGA 61.172 61.111 2.18 0.0 0.00 5.14
245 247 8.428063 AGTTCTACCCATAGAAAAGATCATGAG 58.572 37.037 0.09 0.0 46.64 2.90
524 526 0.033405 CTCGTAGGGGGTGAGAAGGA 60.033 60.000 0.00 0.0 31.31 3.36
693 695 4.028852 TCGTCGTATTGATGACCAAGAG 57.971 45.455 0.00 0.0 37.70 2.85
764 766 4.235372 CTCATAGTGGGGAGGGTAAAGAT 58.765 47.826 0.00 0.0 0.00 2.40
774 776 3.467803 GAGGGTAAAGATCATCCAACGG 58.532 50.000 0.00 0.0 0.00 4.44
811 813 1.278637 CTTGTTTCGTCGTGGCACC 59.721 57.895 12.86 0.0 0.00 5.01
860 875 2.218603 GAGACCAGAAAACGCCTTTCA 58.781 47.619 11.81 0.0 45.15 2.69
869 886 0.178947 AACGCCTTTCATTTCCCCCA 60.179 50.000 0.00 0.0 0.00 4.96
897 914 0.106894 CCCTAGCCGCCTTCCTTAAG 59.893 60.000 0.00 0.0 0.00 1.85
1092 1109 1.299939 TCAGGTCAGAGAGAGGCCTA 58.700 55.000 4.42 0.0 0.00 3.93
1182 1200 4.338012 TGACTTACTACTGGGAATCGTGA 58.662 43.478 0.00 0.0 0.00 4.35
1194 1212 3.450578 GGAATCGTGAGTGCCGTATTTA 58.549 45.455 0.00 0.0 0.00 1.40
1265 1283 2.511600 CTTTGGGTAGGCTCCGCG 60.512 66.667 0.00 0.0 0.00 6.46
1327 1345 0.808847 GGTACGGTCATTCGGGAAGC 60.809 60.000 0.00 0.0 0.00 3.86
1329 1347 0.974010 TACGGTCATTCGGGAAGCCT 60.974 55.000 0.00 0.0 0.00 4.58
1406 1424 5.640783 GGTAAAGCACCGTATCCATATAACC 59.359 44.000 0.00 0.0 37.63 2.85
1442 1460 0.740737 CCGCCATCCATTCCAAGTTC 59.259 55.000 0.00 0.0 0.00 3.01
1481 1499 5.211973 AGTATCCCTATCAAAGAGCTGACA 58.788 41.667 0.00 0.0 0.00 3.58
1600 1618 1.296715 GGACCGTCAAGCACATCCT 59.703 57.895 0.00 0.0 30.12 3.24
1637 1655 1.629013 TCTCGTTGTTGCATAGCTCG 58.371 50.000 0.00 0.0 0.00 5.03
1698 1716 1.323271 ACGATCGGGCATGAGTGTCT 61.323 55.000 20.98 0.0 0.00 3.41
1720 1738 9.996554 TGTCTTGAAGAAGAAATTGTATACTCA 57.003 29.630 4.17 0.0 40.00 3.41
1728 1746 9.574516 AGAAGAAATTGTATACTCACTTTGGTT 57.425 29.630 4.17 0.0 0.00 3.67
1778 1797 1.078143 GGCGGGATCTTTCAGCAGT 60.078 57.895 0.00 0.0 0.00 4.40
1822 1841 4.381411 GCGCCTATCAAAAAGATACTCCT 58.619 43.478 0.00 0.0 38.19 3.69
1924 1943 5.187186 ACAGAGACATAGTAAATTGGTCCGT 59.813 40.000 0.00 0.0 0.00 4.69
1957 1976 5.998981 CGATAAGTCCTCTGTCCTACTACAT 59.001 44.000 0.00 0.0 0.00 2.29
1982 2001 2.616842 CTGCGACAACCTTTACCAAGTT 59.383 45.455 0.00 0.0 0.00 2.66
2028 2047 1.344763 GCTGGTCCGCTATATTCACCT 59.655 52.381 0.00 0.0 0.00 4.00
2050 2069 2.041701 AGCCCACAAGCACAAATCTTT 58.958 42.857 0.00 0.0 34.23 2.52
2123 2143 2.337359 AGGTGGTAAGACCCTTGCTA 57.663 50.000 0.00 0.0 37.50 3.49
2244 2264 9.921637 TTTTTCTATTTGGATTTTAGCGAACAT 57.078 25.926 0.00 0.0 0.00 2.71
2314 2334 1.305930 GCTAGTTGTGGGGCTTTCGG 61.306 60.000 0.00 0.0 0.00 4.30
2315 2335 0.676782 CTAGTTGTGGGGCTTTCGGG 60.677 60.000 0.00 0.0 0.00 5.14
2410 2433 7.126421 TGCCTCTTTAGTCTTTCTAATCCTGAT 59.874 37.037 0.00 0.0 38.27 2.90
2467 2490 5.008316 ACGCGTCAGAAAAATAGAACCTTTT 59.992 36.000 5.58 0.0 0.00 2.27
2485 2508 4.951963 CGGCCCGGAAGATCGCTC 62.952 72.222 0.73 0.0 0.00 5.03
2751 2774 3.452474 GTCTATGCACATCGCTCTTTCT 58.548 45.455 0.00 0.0 43.06 2.52
2960 2983 0.108019 AGTCCCCGTTTCAGGTGTTC 59.892 55.000 0.00 0.0 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.285373 AGTAGTCCCATCACTCTCGGT 59.715 52.381 0.00 0.00 0.00 4.69
155 157 2.049435 AAAAAGGGGGAGCAAAGCG 58.951 52.632 0.00 0.00 0.00 4.68
245 247 2.288518 GGTACCATTCTGATCGCCTCTC 60.289 54.545 7.15 0.00 0.00 3.20
339 341 3.447586 CCCACTCTTCTTTGATCCGTCTA 59.552 47.826 0.00 0.00 0.00 2.59
524 526 0.698818 GTTTGGGATGGAGTCAGGGT 59.301 55.000 0.00 0.00 0.00 4.34
618 620 5.049405 CACTACAAGAGGAATTTCGTGCTTT 60.049 40.000 0.00 0.00 30.95 3.51
693 695 5.635417 AGCTTGCTTCTTTTCCATACTTC 57.365 39.130 0.00 0.00 0.00 3.01
764 766 0.672401 GGTCGCTTTCCGTTGGATGA 60.672 55.000 0.00 0.00 38.35 2.92
774 776 2.437413 AGGGAATGAAAGGTCGCTTTC 58.563 47.619 8.17 8.17 42.06 2.62
830 844 0.836400 TTCTGGTCTCCCCTTCGCTT 60.836 55.000 0.00 0.00 0.00 4.68
860 875 4.684623 CCGCTGAATGGGGGAAAT 57.315 55.556 0.00 0.00 44.18 2.17
1054 1071 4.337145 CTGATAACTAGTATCGCCTCCCT 58.663 47.826 0.00 0.00 41.51 4.20
1097 1114 3.374764 CTTTTAAAGGGGGCCAGCTTAT 58.625 45.455 4.39 0.00 0.00 1.73
1134 1152 3.407252 CATATCGCGCATAACAAATCCG 58.593 45.455 8.75 0.00 0.00 4.18
1145 1163 2.021584 GTCATCGGCATATCGCGCA 61.022 57.895 8.75 0.00 43.84 6.09
1265 1283 1.678101 GCAGCTATGGTTGTTGATCCC 59.322 52.381 0.00 0.00 0.00 3.85
1329 1347 1.875422 ATGGGAGTCGTCCTCAGGGA 61.875 60.000 0.00 0.00 43.36 4.20
1333 1351 2.225382 TTGTATGGGAGTCGTCCTCA 57.775 50.000 7.08 0.00 43.36 3.86
1442 1460 5.016459 AGGGATACTATAACCTAGGTCCCTG 59.984 48.000 25.54 15.14 44.76 4.45
1481 1499 0.543749 CTCTTCCGCTCATCCCCTTT 59.456 55.000 0.00 0.00 0.00 3.11
1600 1618 1.925255 AGATCCCCCTCAATCTTTGCA 59.075 47.619 0.00 0.00 0.00 4.08
1609 1627 0.613260 CAACAACGAGATCCCCCTCA 59.387 55.000 0.00 0.00 32.86 3.86
1637 1655 2.360475 GGCACCTTGCTCTGACCC 60.360 66.667 0.00 0.00 44.28 4.46
1720 1738 2.200337 GCCGCCTTCCAACCAAAGT 61.200 57.895 0.00 0.00 0.00 2.66
1778 1797 4.287067 GCCTCTATCTGTATGGGGAATTCA 59.713 45.833 7.93 0.00 0.00 2.57
1822 1841 0.396695 ACCTCGATCCCGAAGCCTTA 60.397 55.000 0.00 0.00 45.04 2.69
1924 1943 1.069090 GGACTTATCGCGATGCCCA 59.931 57.895 31.05 8.69 0.00 5.36
1957 1976 0.941542 GTAAAGGTTGTCGCAGCACA 59.058 50.000 0.00 0.00 0.00 4.57
1982 2001 3.253921 TCTGGTAGTTGACAATCGTTCGA 59.746 43.478 0.00 0.00 0.00 3.71
2028 2047 2.875296 AGATTTGTGCTTGTGGGCTAA 58.125 42.857 0.00 0.00 0.00 3.09
2050 2069 3.259876 ACTTAGGATTATATTCCGCGCCA 59.740 43.478 0.00 0.00 40.94 5.69
2123 2143 3.084786 GCTCTATGCTGTTTGGGAACTT 58.915 45.455 0.00 0.00 38.95 2.66
2217 2237 9.921637 TGTTCGCTAAAATCCAAATAGAAAAAT 57.078 25.926 0.00 0.00 0.00 1.82
2244 2264 6.163476 ACTCAACTAATCTCATGTAAACGCA 58.837 36.000 0.00 0.00 0.00 5.24
2314 2334 0.523519 CGAAGCCTTCAGCCTTTTCC 59.476 55.000 5.14 0.00 45.47 3.13
2410 2433 5.239087 GCAAAATGAATGAAGGAAAAAGGCA 59.761 36.000 0.00 0.00 0.00 4.75
2751 2774 1.424638 GATAGGCAGCCAACCTCCTA 58.575 55.000 15.80 0.00 38.81 2.94


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

AutoCloner maintained by Alex Coulton.