Multiple sequence alignment - TraesCS7D01G381000

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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 TraesCS7D01G381000 chr7D 100.000 2396 0 0 1 2396 494970835 494968440 0.000000e+00 4425
1 TraesCS7D01G381000 chr7B 90.053 2091 75 52 362 2396 522814994 522812981 0.000000e+00 2586
2 TraesCS7D01G381000 chr7B 87.173 382 22 14 1 358 522815404 522815026 2.220000e-110 409
3 TraesCS7D01G381000 chr7A 89.390 2130 90 53 363 2396 560882459 560880370 0.000000e+00 2556
4 TraesCS7D01G381000 chr7A 92.458 358 18 5 4 359 560882865 560882515 9.890000e-139 503


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 TraesCS7D01G381000 chr7D 494968440 494970835 2395 True 4425.0 4425 100.000 1 2396 1 chr7D.!!$R1 2395
1 TraesCS7D01G381000 chr7B 522812981 522815404 2423 True 1497.5 2586 88.613 1 2396 2 chr7B.!!$R1 2395
2 TraesCS7D01G381000 chr7A 560880370 560882865 2495 True 1529.5 2556 90.924 4 2396 2 chr7A.!!$R1 2392

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
844 979 0.107654 CACCAACCCTAGCTAGCCAC 60.108 60.0 15.74 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2149 0.654683 GATCCTTTGCACGCTAGCTG 59.345 55.0 13.93 11.1 34.99 4.24 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
27 29 9.813446 AGTAATTTACAACGGAGGAAATAGTAG 57.187 33.333 9.15 0.00 0.00 2.57
28 30 9.591792 GTAATTTACAACGGAGGAAATAGTAGT 57.408 33.333 1.62 0.00 0.00 2.73
30 32 9.591792 AATTTACAACGGAGGAAATAGTAGTAC 57.408 33.333 0.69 0.00 0.00 2.73
111 113 2.322081 CCGTGTTTAGTGCCCACCG 61.322 63.158 0.00 0.00 0.00 4.94
120 130 2.759973 TGCCCACCGAGCTCTAGG 60.760 66.667 12.85 9.19 0.00 3.02
204 224 0.737715 GATCCCTCTCGCACACACAC 60.738 60.000 0.00 0.00 0.00 3.82
277 299 0.545548 AGCCTGCCTAGCTATACCCC 60.546 60.000 0.00 0.00 39.29 4.95
301 324 1.825281 GATCAGATGCCCCTCTCCCG 61.825 65.000 0.00 0.00 0.00 5.14
302 325 2.611964 ATCAGATGCCCCTCTCCCGT 62.612 60.000 0.00 0.00 0.00 5.28
303 326 2.444895 AGATGCCCCTCTCCCGTC 60.445 66.667 0.00 0.00 0.00 4.79
304 327 3.551407 GATGCCCCTCTCCCGTCC 61.551 72.222 0.00 0.00 0.00 4.79
312 335 0.178981 CCTCTCCCGTCCCCGTATTA 60.179 60.000 0.00 0.00 0.00 0.98
428 513 3.556004 GGCGAGATAAGATTTCAGAGGGG 60.556 52.174 0.00 0.00 0.00 4.79
486 571 3.816523 AGATCGGCGTAAAACAGGAAAAA 59.183 39.130 6.85 0.00 0.00 1.94
487 572 4.457949 AGATCGGCGTAAAACAGGAAAAAT 59.542 37.500 6.85 0.00 0.00 1.82
491 576 5.914074 TCGGCGTAAAACAGGAAAAATAAAC 59.086 36.000 6.85 0.00 0.00 2.01
574 662 3.689161 GCAGTACTGTGCCACATTTATGA 59.311 43.478 23.44 0.00 37.49 2.15
577 665 2.794103 ACTGTGCCACATTTATGAGCA 58.206 42.857 0.00 7.69 37.92 4.26
578 666 3.156293 ACTGTGCCACATTTATGAGCAA 58.844 40.909 0.00 4.97 40.33 3.91
579 667 3.573538 ACTGTGCCACATTTATGAGCAAA 59.426 39.130 0.00 7.57 40.33 3.68
580 668 4.171005 CTGTGCCACATTTATGAGCAAAG 58.829 43.478 0.00 11.90 40.33 2.77
581 669 3.825585 TGTGCCACATTTATGAGCAAAGA 59.174 39.130 11.67 1.08 40.33 2.52
582 670 4.463539 TGTGCCACATTTATGAGCAAAGAT 59.536 37.500 11.67 0.00 40.33 2.40
583 671 5.047164 TGTGCCACATTTATGAGCAAAGATT 60.047 36.000 11.67 0.00 40.33 2.40
584 672 5.870978 GTGCCACATTTATGAGCAAAGATTT 59.129 36.000 11.67 0.00 40.33 2.17
585 673 6.369615 GTGCCACATTTATGAGCAAAGATTTT 59.630 34.615 11.67 0.00 40.33 1.82
586 674 6.591062 TGCCACATTTATGAGCAAAGATTTTC 59.409 34.615 8.86 0.00 37.54 2.29
587 675 6.237648 GCCACATTTATGAGCAAAGATTTTCG 60.238 38.462 0.00 0.00 33.17 3.46
588 676 7.028962 CCACATTTATGAGCAAAGATTTTCGA 58.971 34.615 0.00 0.00 0.00 3.71
589 677 7.703621 CCACATTTATGAGCAAAGATTTTCGAT 59.296 33.333 0.00 0.00 0.00 3.59
590 678 9.720667 CACATTTATGAGCAAAGATTTTCGATA 57.279 29.630 0.00 0.00 0.00 2.92
594 682 9.950680 TTTATGAGCAAAGATTTTCGATATTCC 57.049 29.630 0.00 0.00 0.00 3.01
595 683 6.377327 TGAGCAAAGATTTTCGATATTCCC 57.623 37.500 0.00 0.00 0.00 3.97
596 684 6.122277 TGAGCAAAGATTTTCGATATTCCCT 58.878 36.000 0.00 0.00 0.00 4.20
597 685 6.038603 TGAGCAAAGATTTTCGATATTCCCTG 59.961 38.462 0.00 0.00 0.00 4.45
598 686 4.978580 GCAAAGATTTTCGATATTCCCTGC 59.021 41.667 0.00 0.00 0.00 4.85
599 687 5.450412 GCAAAGATTTTCGATATTCCCTGCA 60.450 40.000 12.53 0.00 0.00 4.41
600 688 6.563422 CAAAGATTTTCGATATTCCCTGCAA 58.437 36.000 0.00 0.00 0.00 4.08
601 689 6.773976 AAGATTTTCGATATTCCCTGCAAA 57.226 33.333 0.00 0.00 0.00 3.68
602 690 6.773976 AGATTTTCGATATTCCCTGCAAAA 57.226 33.333 0.00 0.00 0.00 2.44
603 691 7.169158 AGATTTTCGATATTCCCTGCAAAAA 57.831 32.000 0.00 0.00 0.00 1.94
844 979 0.107654 CACCAACCCTAGCTAGCCAC 60.108 60.000 15.74 0.00 0.00 5.01
847 982 0.466124 CAACCCTAGCTAGCCACTCC 59.534 60.000 15.74 0.00 0.00 3.85
848 983 0.691413 AACCCTAGCTAGCCACTCCC 60.691 60.000 15.74 0.00 0.00 4.30
849 984 1.839296 CCCTAGCTAGCCACTCCCC 60.839 68.421 15.74 0.00 0.00 4.81
852 987 2.930777 CTAGCTAGCCACTCCCCCGT 62.931 65.000 12.13 0.00 0.00 5.28
853 988 4.162690 GCTAGCCACTCCCCCGTG 62.163 72.222 2.29 0.00 34.71 4.94
859 994 3.391382 CACTCCCCCGTGGTCCTC 61.391 72.222 0.00 0.00 34.77 3.71
860 995 4.716977 ACTCCCCCGTGGTCCTCC 62.717 72.222 0.00 0.00 34.77 4.30
861 996 4.400251 CTCCCCCGTGGTCCTCCT 62.400 72.222 0.00 0.00 34.77 3.69
862 997 3.925914 CTCCCCCGTGGTCCTCCTT 62.926 68.421 0.00 0.00 34.77 3.36
870 1005 3.319198 GGTCCTCCTTGACGGCCA 61.319 66.667 2.24 0.00 36.07 5.36
973 1111 3.134458 AGAGAGCGTTTCTTTCTTGGTG 58.866 45.455 0.00 0.00 32.86 4.17
983 1121 0.251165 TTTCTTGGTGCAGGGTAGGC 60.251 55.000 0.00 0.00 0.00 3.93
993 1135 1.132643 GCAGGGTAGGCGTATAGATCG 59.867 57.143 0.00 0.00 0.00 3.69
1182 1324 3.458163 CCGCTCTTCGTGGGCCTA 61.458 66.667 4.53 0.00 39.71 3.93
1485 1649 6.915843 CGTTGCTTTGTTAATTAGAGTTGGTT 59.084 34.615 0.00 0.00 0.00 3.67
1487 1651 9.738832 GTTGCTTTGTTAATTAGAGTTGGTTTA 57.261 29.630 0.00 0.00 0.00 2.01
1663 1828 8.871742 GATGATGAAAATCGAAGATATTTCCG 57.128 34.615 0.00 0.00 45.12 4.30
1664 1829 8.607441 ATGATGAAAATCGAAGATATTTCCGA 57.393 30.769 0.00 0.00 45.12 4.55
1665 1830 8.607441 TGATGAAAATCGAAGATATTTCCGAT 57.393 30.769 0.00 0.00 45.12 4.18
1666 1831 9.705290 TGATGAAAATCGAAGATATTTCCGATA 57.295 29.630 0.00 0.00 45.12 2.92
1769 1934 6.012858 TGTGGTTGGTAGTATTCTCTTTCCAT 60.013 38.462 0.00 0.00 0.00 3.41
1880 2052 6.764085 TGAAGAACATTAAGTGGTTTCGAAGA 59.236 34.615 0.00 0.00 0.00 2.87
1953 2157 1.795768 TTGAAACTGTCCAGCTAGCG 58.204 50.000 9.55 4.28 0.00 4.26
1976 2201 6.611381 CGTGCAAAGGATCTATTTTCTTTCA 58.389 36.000 0.00 0.00 0.00 2.69
1977 2202 7.083858 CGTGCAAAGGATCTATTTTCTTTCAA 58.916 34.615 0.00 0.00 0.00 2.69
2017 2245 5.588958 AGCTTGCAAAGGATCTATTTTCC 57.411 39.130 0.00 0.00 46.35 3.13
2059 2287 5.955959 TCTACTGTCTGCCTCCTACATTAAA 59.044 40.000 0.00 0.00 0.00 1.52
2076 2304 6.408869 ACATTAAATTTCCCCAATCAAGCAG 58.591 36.000 0.00 0.00 0.00 4.24
2087 2315 2.954318 CAATCAAGCAGGGGATTAGTGG 59.046 50.000 0.00 0.00 32.71 4.00
2309 2554 2.668212 CGCCGCAGTGGAAAGGAA 60.668 61.111 3.39 0.00 42.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 12 6.570692 ACATGTACTACTATTTCCTCCGTTG 58.429 40.000 0.00 0.00 0.00 4.10
22 24 6.218019 AGTGCGACAAAAACATGTACTACTA 58.782 36.000 0.00 0.00 32.57 1.82
27 29 4.212636 ACCTAGTGCGACAAAAACATGTAC 59.787 41.667 0.00 0.00 32.57 2.90
28 30 4.382291 ACCTAGTGCGACAAAAACATGTA 58.618 39.130 0.00 0.00 32.57 2.29
29 31 3.211045 ACCTAGTGCGACAAAAACATGT 58.789 40.909 0.00 0.00 35.90 3.21
30 32 3.896648 ACCTAGTGCGACAAAAACATG 57.103 42.857 0.00 0.00 0.00 3.21
127 137 2.168521 GGTTGGTGATGCTACTGCTAGA 59.831 50.000 0.00 0.00 40.48 2.43
204 224 5.682862 GTGTGTTGCATAGACAGTCTTTTTG 59.317 40.000 8.80 5.99 29.49 2.44
301 324 4.810491 TGAATACGCTTTTAATACGGGGAC 59.190 41.667 0.00 0.00 0.00 4.46
302 325 5.021033 TGAATACGCTTTTAATACGGGGA 57.979 39.130 0.00 0.00 0.00 4.81
303 326 5.738118 TTGAATACGCTTTTAATACGGGG 57.262 39.130 0.00 0.00 0.00 5.73
304 327 6.193228 CGTTTTGAATACGCTTTTAATACGGG 59.807 38.462 0.00 0.00 31.14 5.28
305 328 7.117199 CGTTTTGAATACGCTTTTAATACGG 57.883 36.000 0.00 0.00 31.14 4.02
359 387 8.135529 TCAAGATAATTCTACACGTGACTATGG 58.864 37.037 25.01 1.10 0.00 2.74
428 513 6.238402 GGGCTTATTTAGTTGAGATTCGGTTC 60.238 42.308 0.00 0.00 0.00 3.62
463 548 2.004583 TCCTGTTTTACGCCGATCTG 57.995 50.000 0.00 0.00 0.00 2.90
491 576 7.591057 CCACGTTTATTGTTCAGCCATAATATG 59.409 37.037 0.00 0.00 0.00 1.78
499 584 1.201414 CCCCACGTTTATTGTTCAGCC 59.799 52.381 0.00 0.00 0.00 4.85
500 585 2.156098 TCCCCACGTTTATTGTTCAGC 58.844 47.619 0.00 0.00 0.00 4.26
501 586 6.503589 TTAATCCCCACGTTTATTGTTCAG 57.496 37.500 0.00 0.00 0.00 3.02
574 662 5.221126 GCAGGGAATATCGAAAATCTTTGCT 60.221 40.000 0.00 0.00 0.00 3.91
577 665 6.773976 TTGCAGGGAATATCGAAAATCTTT 57.226 33.333 0.00 0.00 0.00 2.52
578 666 6.773976 TTTGCAGGGAATATCGAAAATCTT 57.226 33.333 0.00 0.00 0.00 2.40
579 667 6.773976 TTTTGCAGGGAATATCGAAAATCT 57.226 33.333 0.00 0.00 0.00 2.40
605 693 7.832187 TCCACCAGGTATATCGAAAATCTTTTT 59.168 33.333 0.00 0.00 35.89 1.94
606 694 7.343357 TCCACCAGGTATATCGAAAATCTTTT 58.657 34.615 0.00 0.00 35.89 2.27
844 979 3.925914 AAGGAGGACCACGGGGGAG 62.926 68.421 9.50 0.00 41.15 4.30
847 982 2.606519 TCAAGGAGGACCACGGGG 60.607 66.667 0.00 0.00 38.94 5.73
848 983 2.663196 GTCAAGGAGGACCACGGG 59.337 66.667 0.00 0.00 38.94 5.28
849 984 2.261671 CGTCAAGGAGGACCACGG 59.738 66.667 0.00 0.00 38.94 4.94
852 987 3.319198 GGCCGTCAAGGAGGACCA 61.319 66.667 0.00 0.00 45.00 4.02
853 988 3.319198 TGGCCGTCAAGGAGGACC 61.319 66.667 0.00 0.00 45.00 4.46
855 990 3.319198 GGTGGCCGTCAAGGAGGA 61.319 66.667 0.00 0.00 45.00 3.71
857 992 1.746615 CATGGTGGCCGTCAAGGAG 60.747 63.158 0.00 0.00 45.00 3.69
858 993 2.350895 CATGGTGGCCGTCAAGGA 59.649 61.111 0.00 0.00 45.00 3.36
859 994 3.443045 GCATGGTGGCCGTCAAGG 61.443 66.667 0.00 0.00 44.97 3.61
860 995 2.672651 TGCATGGTGGCCGTCAAG 60.673 61.111 0.00 0.00 0.00 3.02
861 996 2.672651 CTGCATGGTGGCCGTCAA 60.673 61.111 0.00 0.00 0.00 3.18
973 1111 1.132643 CGATCTATACGCCTACCCTGC 59.867 57.143 0.00 0.00 0.00 4.85
983 1121 5.049612 ACGCCCATATATGTCGATCTATACG 60.050 44.000 23.01 10.15 0.00 3.06
1182 1324 1.684049 CTCCTCGGCCTCCTTGAGT 60.684 63.158 0.00 0.00 0.00 3.41
1444 1590 3.878519 CGAGACGAGGCCGGAGAC 61.879 72.222 5.05 0.00 40.78 3.36
1454 1618 5.921976 TCTAATTAACAAAGCAACGAGACGA 59.078 36.000 0.00 0.00 0.00 4.20
1485 1649 4.406326 TCACATACCTGACCGCCTAATTAA 59.594 41.667 0.00 0.00 0.00 1.40
1487 1651 2.769663 TCACATACCTGACCGCCTAATT 59.230 45.455 0.00 0.00 0.00 1.40
1488 1652 2.394632 TCACATACCTGACCGCCTAAT 58.605 47.619 0.00 0.00 0.00 1.73
1493 1657 2.408050 GATCATCACATACCTGACCGC 58.592 52.381 0.00 0.00 0.00 5.68
1667 1832 9.778741 CTGGTTAATCTATTATAGGCACTGAAA 57.221 33.333 0.00 0.00 41.52 2.69
1668 1833 9.154632 TCTGGTTAATCTATTATAGGCACTGAA 57.845 33.333 0.00 0.00 41.52 3.02
1669 1834 8.721133 TCTGGTTAATCTATTATAGGCACTGA 57.279 34.615 0.00 0.00 41.52 3.41
1670 1835 9.376075 CATCTGGTTAATCTATTATAGGCACTG 57.624 37.037 0.00 0.00 41.52 3.66
1880 2052 6.726490 TTGTGTCTAAACTTGGAGTACTCT 57.274 37.500 21.88 4.14 0.00 3.24
1932 2134 2.744202 CGCTAGCTGGACAGTTTCAAAT 59.256 45.455 13.93 0.00 0.00 2.32
1945 2149 0.654683 GATCCTTTGCACGCTAGCTG 59.345 55.000 13.93 11.10 34.99 4.24
1953 2157 8.992835 ATTGAAAGAAAATAGATCCTTTGCAC 57.007 30.769 0.00 0.00 0.00 4.57
1976 2201 6.418946 CAAGCTAGAGGTCCCTAAAAGAATT 58.581 40.000 0.00 0.00 0.00 2.17
1977 2202 5.630304 GCAAGCTAGAGGTCCCTAAAAGAAT 60.630 44.000 0.00 0.00 0.00 2.40
2059 2287 1.870064 CCCTGCTTGATTGGGGAAAT 58.130 50.000 0.00 0.00 41.25 2.17
2076 2304 0.846693 AGCATCCACCACTAATCCCC 59.153 55.000 0.00 0.00 0.00 4.81
2087 2315 4.585162 ACATAGTACTCCACTAGCATCCAC 59.415 45.833 0.00 0.00 43.01 4.02
2238 2483 1.440708 CTCTGCCACAAGAAGCTCTG 58.559 55.000 0.00 0.00 0.00 3.35
2309 2554 4.505742 GGAAGTTTTGTCTCACTCCATCCT 60.506 45.833 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.