Multiple sequence alignment - TraesCS7A01G391700

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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 TraesCS7A01G391700 chr7A 100.000 2996 0 0 1 2996 567586365 567589360 0 5533
1 TraesCS7A01G391700 chr7D 96.234 2018 49 6 983 2996 501099771 501101765 0 3280
2 TraesCS7A01G391700 chr7D 85.992 1185 77 42 1 1137 501098323 501099466 0 1186
3 TraesCS7A01G391700 chr7B 91.731 2322 119 41 1 2283 530382463 530384750 0 3157
4 TraesCS7A01G391700 chr7B 92.857 728 32 15 2282 2995 530384885 530385606 0 1038


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 TraesCS7A01G391700 chr7A 567586365 567589360 2995 False 5533.0 5533 100.000 1 2996 1 chr7A.!!$F1 2995
1 TraesCS7A01G391700 chr7D 501098323 501101765 3442 False 2233.0 3280 91.113 1 2996 2 chr7D.!!$F1 2995
2 TraesCS7A01G391700 chr7B 530382463 530385606 3143 False 2097.5 3157 92.294 1 2995 2 chr7B.!!$F1 2994

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
159 163 0.251033 AGGGCGTTACCTTTCCAACC 60.251 55.0 0.0 0.0 37.69 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2548 0.038744 ACCAAGAGATGCCACCAAGG 59.961 55.0 0.0 0.0 41.84 3.61 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
25 28 2.664916 CAACATTCTTTTCCACCGCAG 58.335 47.619 0.00 0.00 0.00 5.18
31 34 1.856265 CTTTTCCACCGCAGCTCACC 61.856 60.000 0.00 0.00 0.00 4.02
41 44 1.002868 CAGCTCACCCCCACTGAAG 60.003 63.158 0.00 0.00 31.67 3.02
46 49 1.379044 CACCCCCACTGAAGCCATC 60.379 63.158 0.00 0.00 0.00 3.51
80 83 2.620115 CCACAACAAGAACAGATGCAGT 59.380 45.455 0.00 0.00 0.00 4.40
125 128 0.868406 GACCAAGAACTGACGGCAAG 59.132 55.000 0.00 0.00 0.00 4.01
159 163 0.251033 AGGGCGTTACCTTTCCAACC 60.251 55.000 0.00 0.00 37.69 3.77
195 202 2.105466 CGGAAGCCAGAAGAGCAGC 61.105 63.158 0.00 0.00 0.00 5.25
196 203 1.002868 GGAAGCCAGAAGAGCAGCA 60.003 57.895 0.00 0.00 0.00 4.41
197 204 1.025647 GGAAGCCAGAAGAGCAGCAG 61.026 60.000 0.00 0.00 0.00 4.24
242 249 2.805099 CAGAGAAGAACTTGTGGACTGC 59.195 50.000 0.00 0.00 0.00 4.40
303 331 2.158957 TCCAGCCAGCCTCGTTTTATAG 60.159 50.000 0.00 0.00 0.00 1.31
304 332 1.599542 CAGCCAGCCTCGTTTTATAGC 59.400 52.381 0.00 0.00 0.00 2.97
306 334 1.805120 GCCAGCCTCGTTTTATAGCGA 60.805 52.381 0.00 0.00 35.70 4.93
356 384 0.318445 GCCAATCAATCAGCGCATCC 60.318 55.000 11.47 0.00 0.00 3.51
357 385 1.026584 CCAATCAATCAGCGCATCCA 58.973 50.000 11.47 0.00 0.00 3.41
395 423 3.155167 CCGCTACAGGTCCCCTCC 61.155 72.222 0.00 0.00 0.00 4.30
454 486 3.308866 CGGCGGGAATAATAAATCCGATC 59.691 47.826 0.00 0.00 42.94 3.69
494 526 1.153568 TGCTCCTCGGAATCTTGCG 60.154 57.895 0.00 0.00 43.70 4.85
497 529 2.897350 CCTCGGAATCTTGCGGGC 60.897 66.667 4.02 0.00 41.46 6.13
532 564 2.412937 CCGGGCGATTGGATTTGC 59.587 61.111 0.00 0.00 0.00 3.68
714 772 5.220700 CCAACAGCGTCTTTGTTTAGTACAA 60.221 40.000 0.00 0.00 44.81 2.41
715 773 5.399604 ACAGCGTCTTTGTTTAGTACAAC 57.600 39.130 0.00 0.00 46.09 3.32
736 794 3.936453 ACACACGTGTTCTCTGCTAAAAA 59.064 39.130 20.79 0.00 41.83 1.94
746 805 4.307432 TCTCTGCTAAAAAGACGACCAAG 58.693 43.478 0.00 0.00 0.00 3.61
782 841 8.059153 CGTATTGTCAACGTAAAAACGTATTC 57.941 34.615 3.77 0.00 46.41 1.75
785 844 5.976586 TGTCAACGTAAAAACGTATTCTGG 58.023 37.500 3.77 0.00 46.41 3.86
786 845 5.752472 TGTCAACGTAAAAACGTATTCTGGA 59.248 36.000 3.77 0.00 46.41 3.86
836 895 4.436998 GGTGACGGCGTGAGGGAG 62.437 72.222 21.19 0.00 0.00 4.30
837 896 4.436998 GTGACGGCGTGAGGGAGG 62.437 72.222 21.19 0.00 0.00 4.30
947 1014 4.109675 GACCACCCCACCCCATCG 62.110 72.222 0.00 0.00 0.00 3.84
961 1028 4.015406 ATCGCACCCGCACCTCAA 62.015 61.111 0.00 0.00 38.40 3.02
963 1030 2.819984 ATCGCACCCGCACCTCAATT 62.820 55.000 0.00 0.00 38.40 2.32
973 1042 1.082206 ACCTCAATTCCCCTCCCGA 59.918 57.895 0.00 0.00 0.00 5.14
974 1043 1.272554 ACCTCAATTCCCCTCCCGAC 61.273 60.000 0.00 0.00 0.00 4.79
1047 1578 4.570663 GGCATCGACGAGGACGGG 62.571 72.222 14.58 0.00 44.46 5.28
1138 1669 1.685765 CACTCCGACATCTCCCCCA 60.686 63.158 0.00 0.00 0.00 4.96
1218 1749 2.567049 GACCACGACCTCGACCTG 59.433 66.667 0.78 0.00 43.02 4.00
1641 2184 4.776322 CCGGTGCCGCTGGATGAA 62.776 66.667 4.91 0.00 46.81 2.57
1917 2460 2.976490 GCTGCCCACTGATGACCCT 61.976 63.158 0.00 0.00 0.00 4.34
2005 2548 0.737219 GCAGATGTGAGCATGGGTTC 59.263 55.000 0.00 0.00 35.07 3.62
2101 2644 1.750780 GCTTGGAGGTTGCTAGGGC 60.751 63.158 0.00 0.00 39.26 5.19
2105 2648 1.152881 GGAGGTTGCTAGGGCCATG 60.153 63.158 6.18 0.00 37.74 3.66
2239 2783 7.823745 ATAACACAGAAAACCAATTCACTCT 57.176 32.000 0.00 0.00 0.00 3.24
2345 3025 3.258372 AGTTACCGGCATCGTGATATCAT 59.742 43.478 9.02 0.00 33.95 2.45
2356 3036 6.798476 GCATCGTGATATCATAAACACCATTG 59.202 38.462 9.02 0.00 0.00 2.82
2410 3090 7.961326 ATCTGGTATGCTTTAATCAAACCTT 57.039 32.000 0.00 0.00 0.00 3.50
2431 3111 5.406780 CCTTAGTGTTGCTCTTCTGTACTTG 59.593 44.000 0.00 0.00 0.00 3.16
2484 3164 1.067283 TGAGCTTCTCTGCTGCACTAC 60.067 52.381 0.00 0.00 44.17 2.73
2558 3238 1.614413 GAGAAACCTCACTCGGTGACT 59.386 52.381 3.02 0.00 37.67 3.41
2562 3242 1.178276 ACCTCACTCGGTGACTGATC 58.822 55.000 0.00 0.00 37.67 2.92
2687 3367 3.999769 GCATATATGTCATGCTGCTTCG 58.000 45.455 14.14 0.00 44.35 3.79
2761 3441 4.689612 TGTGGCAGAACTTTCTTCTACT 57.310 40.909 6.67 0.00 34.18 2.57
2806 3488 6.997476 TGCATGATTTACTGCCATCATAGTTA 59.003 34.615 0.00 0.00 37.93 2.24
2928 3613 8.968969 AGTTACTTTTCTGTACTGGGAGTATAG 58.031 37.037 0.00 0.00 40.11 1.31
2929 3614 8.747471 GTTACTTTTCTGTACTGGGAGTATAGT 58.253 37.037 7.22 0.00 39.83 2.12
2930 3615 9.979897 TTACTTTTCTGTACTGGGAGTATAGTA 57.020 33.333 7.22 0.00 39.83 1.82
2931 3616 8.522542 ACTTTTCTGTACTGGGAGTATAGTAG 57.477 38.462 7.22 6.51 39.83 2.57
2932 3617 8.114743 ACTTTTCTGTACTGGGAGTATAGTAGT 58.885 37.037 7.22 6.95 39.83 2.73
2933 3618 9.624373 CTTTTCTGTACTGGGAGTATAGTAGTA 57.376 37.037 7.22 0.00 39.83 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.884704 GTGAGCTGCGGTGGAAAAGA 60.885 55.000 0.00 0.00 0.00 2.52
25 28 2.360475 GCTTCAGTGGGGGTGAGC 60.360 66.667 0.00 0.00 0.00 4.26
31 34 0.256752 TGATGATGGCTTCAGTGGGG 59.743 55.000 9.09 0.00 37.89 4.96
37 40 3.353370 TGTGTGATGATGATGGCTTCA 57.647 42.857 5.47 5.47 39.12 3.02
41 44 2.292569 GTGGATGTGTGATGATGATGGC 59.707 50.000 0.00 0.00 0.00 4.40
46 49 4.456566 TCTTGTTGTGGATGTGTGATGATG 59.543 41.667 0.00 0.00 0.00 3.07
80 83 4.380843 TTCTTGCCTGGTATGGAGAAAA 57.619 40.909 0.00 0.00 0.00 2.29
125 128 1.267121 GCCCTTTTCTCCCTTTTCCC 58.733 55.000 0.00 0.00 0.00 3.97
159 163 1.787057 CGGATCCCGGAGAGACTTCG 61.787 65.000 0.73 0.00 44.15 3.79
179 186 0.036577 TCTGCTGCTCTTCTGGCTTC 60.037 55.000 0.00 0.00 0.00 3.86
195 202 3.978723 CTGGCTCTGGTCGCGTCTG 62.979 68.421 5.77 4.41 0.00 3.51
196 203 3.753434 CTGGCTCTGGTCGCGTCT 61.753 66.667 5.77 0.00 0.00 4.18
197 204 3.749064 TCTGGCTCTGGTCGCGTC 61.749 66.667 5.77 0.00 0.00 5.19
280 308 2.056906 AAAACGAGGCTGGCTGGACT 62.057 55.000 19.55 3.79 0.00 3.85
281 309 0.321298 TAAAACGAGGCTGGCTGGAC 60.321 55.000 19.55 0.00 0.00 4.02
282 310 0.618458 ATAAAACGAGGCTGGCTGGA 59.382 50.000 19.55 0.00 0.00 3.86
283 311 2.213499 CTATAAAACGAGGCTGGCTGG 58.787 52.381 9.06 10.51 0.00 4.85
284 312 1.599542 GCTATAAAACGAGGCTGGCTG 59.400 52.381 9.06 3.76 0.00 4.85
285 313 1.806623 CGCTATAAAACGAGGCTGGCT 60.807 52.381 2.24 2.24 0.00 4.75
286 314 0.582005 CGCTATAAAACGAGGCTGGC 59.418 55.000 0.00 0.00 0.00 4.85
289 317 1.402968 TCGTCGCTATAAAACGAGGCT 59.597 47.619 0.00 0.00 42.24 4.58
304 332 4.225340 CTCCGCGTCTCCTCGTCG 62.225 72.222 4.92 0.00 0.00 5.12
356 384 1.338105 TGACAGCGAGAGGTTTGGATG 60.338 52.381 0.00 0.00 41.81 3.51
357 385 0.976641 TGACAGCGAGAGGTTTGGAT 59.023 50.000 0.00 0.00 41.81 3.41
515 547 2.412937 GCAAATCCAATCGCCCGG 59.587 61.111 0.00 0.00 0.00 5.73
516 548 2.024588 CGCAAATCCAATCGCCCG 59.975 61.111 0.00 0.00 0.00 6.13
517 549 2.412937 CCGCAAATCCAATCGCCC 59.587 61.111 0.00 0.00 0.00 6.13
518 550 2.412937 CCCGCAAATCCAATCGCC 59.587 61.111 0.00 0.00 0.00 5.54
519 551 2.063541 CTCCCCGCAAATCCAATCGC 62.064 60.000 0.00 0.00 0.00 4.58
520 552 0.748005 ACTCCCCGCAAATCCAATCG 60.748 55.000 0.00 0.00 0.00 3.34
521 553 1.474330 AACTCCCCGCAAATCCAATC 58.526 50.000 0.00 0.00 0.00 2.67
522 554 1.824852 GAAACTCCCCGCAAATCCAAT 59.175 47.619 0.00 0.00 0.00 3.16
523 555 1.253100 GAAACTCCCCGCAAATCCAA 58.747 50.000 0.00 0.00 0.00 3.53
524 556 0.958382 CGAAACTCCCCGCAAATCCA 60.958 55.000 0.00 0.00 0.00 3.41
525 557 1.800681 CGAAACTCCCCGCAAATCC 59.199 57.895 0.00 0.00 0.00 3.01
595 628 4.189580 ACCCGCCATTCCCATCGG 62.190 66.667 0.00 0.00 41.41 4.18
596 629 2.901840 CACCCGCCATTCCCATCG 60.902 66.667 0.00 0.00 0.00 3.84
597 630 2.519302 CCACCCGCCATTCCCATC 60.519 66.667 0.00 0.00 0.00 3.51
598 631 2.572333 CTTCCACCCGCCATTCCCAT 62.572 60.000 0.00 0.00 0.00 4.00
602 635 2.106683 CGTCTTCCACCCGCCATTC 61.107 63.158 0.00 0.00 0.00 2.67
640 698 2.897350 GAAATGCGAGGCTCCGGG 60.897 66.667 9.32 0.00 0.00 5.73
679 737 3.726517 CTGTTGGTTCGGCTGGCG 61.727 66.667 18.26 18.26 0.00 5.69
686 744 0.655733 ACAAAGACGCTGTTGGTTCG 59.344 50.000 0.00 0.00 0.00 3.95
715 773 4.270084 TCTTTTTAGCAGAGAACACGTGTG 59.730 41.667 24.16 10.51 0.00 3.82
736 794 1.853963 AGCCATACTCTTGGTCGTCT 58.146 50.000 0.00 0.00 39.11 4.18
746 805 4.440103 CGTTGACAATACGTAGCCATACTC 59.560 45.833 0.08 0.00 34.47 2.59
782 841 2.510238 CGCTTTCGCCCTCTCCAG 60.510 66.667 0.00 0.00 0.00 3.86
808 867 0.105408 GCCGTCACCCCATAATACGT 59.895 55.000 0.00 0.00 31.87 3.57
837 896 4.112341 CACTCCGTCCGTCCGTCC 62.112 72.222 0.00 0.00 0.00 4.79
838 897 4.112341 CCACTCCGTCCGTCCGTC 62.112 72.222 0.00 0.00 0.00 4.79
883 950 2.104859 CGCGTCTCCGTCTCTGGTA 61.105 63.158 0.00 0.00 36.15 3.25
947 1014 2.700773 GGAATTGAGGTGCGGGTGC 61.701 63.158 0.00 0.00 43.20 5.01
948 1015 2.046285 GGGAATTGAGGTGCGGGTG 61.046 63.158 0.00 0.00 0.00 4.61
953 1020 1.076705 GGGAGGGGAATTGAGGTGC 60.077 63.158 0.00 0.00 0.00 5.01
954 1021 1.224592 CGGGAGGGGAATTGAGGTG 59.775 63.158 0.00 0.00 0.00 4.00
955 1022 1.082206 TCGGGAGGGGAATTGAGGT 59.918 57.895 0.00 0.00 0.00 3.85
958 1025 1.999002 GGGTCGGGAGGGGAATTGA 60.999 63.158 0.00 0.00 0.00 2.57
959 1026 2.595655 GGGTCGGGAGGGGAATTG 59.404 66.667 0.00 0.00 0.00 2.32
961 1028 4.837421 GGGGGTCGGGAGGGGAAT 62.837 72.222 0.00 0.00 0.00 3.01
1388 1922 3.827898 CAGGGACGGAGGCGTCTC 61.828 72.222 8.99 8.99 39.49 3.36
1641 2184 1.581954 CAGCACCTCGAACTCGTCT 59.418 57.895 0.00 0.00 40.80 4.18
1761 2304 2.359107 CACACAGCGCATCCCTGT 60.359 61.111 11.47 0.63 43.92 4.00
1917 2460 2.104928 CGCCGCTGCTCATAGTCA 59.895 61.111 0.00 0.00 34.43 3.41
1959 2502 2.263741 GCCCAACTGTGCTGTGGAG 61.264 63.158 0.00 0.00 0.00 3.86
2005 2548 0.038744 ACCAAGAGATGCCACCAAGG 59.961 55.000 0.00 0.00 41.84 3.61
2059 2602 3.898123 TCCTAACTGAGCAAGTCAAGAGT 59.102 43.478 0.00 0.00 38.56 3.24
2101 2644 6.048509 ACACTTAAAAACCAAAGAAGCATGG 58.951 36.000 0.00 0.00 42.60 3.66
2105 2648 5.575019 TCGACACTTAAAAACCAAAGAAGC 58.425 37.500 0.00 0.00 0.00 3.86
2239 2783 7.064134 ACAATACGAATAAAACAAGCATCGAGA 59.936 33.333 0.00 0.00 34.62 4.04
2301 2981 7.636150 ACTGATGCAATAAGAAAAGCAGTAT 57.364 32.000 0.00 0.00 40.71 2.12
2345 3025 8.836413 CAAAAGAGTCTTCTACAATGGTGTTTA 58.164 33.333 5.70 0.00 39.30 2.01
2410 3090 4.587262 TCCAAGTACAGAAGAGCAACACTA 59.413 41.667 0.00 0.00 0.00 2.74
2431 3111 5.807011 GCATCACCACAAAGAAATTACATCC 59.193 40.000 0.00 0.00 0.00 3.51
2484 3164 8.995220 TGTGCTAATTAAAACCTACAGTACTTG 58.005 33.333 0.00 0.00 0.00 3.16
2558 3238 5.446860 ACCTCGAAGTATCCTAACTGATCA 58.553 41.667 0.00 0.00 0.00 2.92
2562 3242 4.641094 AGTGACCTCGAAGTATCCTAACTG 59.359 45.833 0.00 0.00 0.00 3.16
2687 3367 9.356433 GTGACTAAGAAACTTCTCTGTATTACC 57.644 37.037 0.00 0.00 36.28 2.85
2761 3441 1.351017 AGTAAGCAAAGCAGTAGGCCA 59.649 47.619 5.01 0.00 46.50 5.36
2894 3579 6.421202 CAGTACAGAAAAGTAACTCACAGGTC 59.579 42.308 0.00 0.00 0.00 3.85
2933 3618 9.717942 GAAGCTCACCTTACAGAAATGATATAT 57.282 33.333 0.00 0.00 32.78 0.86
2934 3619 8.928448 AGAAGCTCACCTTACAGAAATGATATA 58.072 33.333 0.00 0.00 32.78 0.86
2935 3620 7.800092 AGAAGCTCACCTTACAGAAATGATAT 58.200 34.615 0.00 0.00 32.78 1.63


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

AutoCloner maintained by Alex Coulton.