Multiple sequence alignment - TraesCS7A01G037800

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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 TraesCS7A01G037800 chr7A 100.000 2303 0 0 1 2303 16878250 16875948 0.000000e+00 4253.0
1 TraesCS7A01G037800 chr7A 97.763 894 18 1 1410 2303 130559382 130560273 0.000000e+00 1539.0
2 TraesCS7A01G037800 chr7A 97.075 889 20 3 1410 2295 699320549 699319664 0.000000e+00 1493.0
3 TraesCS7A01G037800 chr7A 95.761 920 32 2 1389 2303 719950296 719949379 0.000000e+00 1476.0
4 TraesCS7A01G037800 chr7A 96.629 801 27 0 1 801 134595933 134596733 0.000000e+00 1330.0
5 TraesCS7A01G037800 chr7A 96.629 801 27 0 1 801 643609233 643610033 0.000000e+00 1330.0
6 TraesCS7A01G037800 chr7A 96.255 801 30 0 1 801 192624665 192625465 0.000000e+00 1314.0
7 TraesCS7A01G037800 chr7A 95.880 801 32 1 1 801 699322933 699322134 0.000000e+00 1295.0
8 TraesCS7A01G037800 chr2A 95.539 1345 42 7 1 1339 778395561 778396893 0.000000e+00 2135.0
9 TraesCS7A01G037800 chr2A 96.995 965 28 1 1339 2303 677897099 677896136 0.000000e+00 1620.0
10 TraesCS7A01G037800 chr2B 92.587 1349 54 17 1 1342 649657423 649656114 0.000000e+00 1895.0
11 TraesCS7A01G037800 chr2B 89.839 807 56 13 540 1339 42193952 42194739 0.000000e+00 1013.0
12 TraesCS7A01G037800 chr2B 89.362 799 54 12 554 1339 45596552 45597332 0.000000e+00 976.0
13 TraesCS7A01G037800 chr1B 91.789 1364 72 18 1 1342 357902159 357900814 0.000000e+00 1862.0
14 TraesCS7A01G037800 chr1B 88.684 813 61 12 540 1339 38183941 38184735 0.000000e+00 963.0
15 TraesCS7A01G037800 chr4B 89.848 1379 84 27 1 1339 49105655 49107017 0.000000e+00 1720.0
16 TraesCS7A01G037800 chr4B 89.338 816 56 12 540 1342 402786653 402785856 0.000000e+00 996.0
17 TraesCS7A01G037800 chr6A 96.304 920 27 2 1389 2303 79830125 79829208 0.000000e+00 1504.0
18 TraesCS7A01G037800 chr6A 95.978 920 30 2 1389 2303 516295779 516294862 0.000000e+00 1487.0
19 TraesCS7A01G037800 chr1A 95.943 912 30 2 1389 2295 559591876 559592785 0.000000e+00 1472.0
20 TraesCS7A01G037800 chr1A 96.416 837 29 1 1 837 559589434 559590269 0.000000e+00 1378.0
21 TraesCS7A01G037800 chr3A 95.539 919 32 3 1389 2302 22601870 22600956 0.000000e+00 1461.0
22 TraesCS7A01G037800 chr3A 96.050 886 34 1 1410 2295 635314423 635315307 0.000000e+00 1441.0
23 TraesCS7A01G037800 chr3A 92.562 121 9 0 1339 1459 22601986 22601866 8.460000e-40 174.0
24 TraesCS7A01G037800 chr3A 96.154 52 2 0 1339 1390 22602219 22602168 4.080000e-13 86.1
25 TraesCS7A01G037800 chr5A 96.380 801 29 0 1 801 288269117 288268317 0.000000e+00 1319.0
26 TraesCS7A01G037800 chr4A 97.516 765 19 0 1 765 637837240 637836476 0.000000e+00 1308.0
27 TraesCS7A01G037800 chr4A 88.642 810 61 12 540 1336 712878028 712878819 0.000000e+00 957.0
28 TraesCS7A01G037800 chr7B 88.807 813 60 14 540 1339 687041172 687041966 0.000000e+00 968.0


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 TraesCS7A01G037800 chr7A 16875948 16878250 2302 True 4253.0 4253 100.000000 1 2303 1 chr7A.!!$R1 2302
1 TraesCS7A01G037800 chr7A 130559382 130560273 891 False 1539.0 1539 97.763000 1410 2303 1 chr7A.!!$F1 893
2 TraesCS7A01G037800 chr7A 719949379 719950296 917 True 1476.0 1476 95.761000 1389 2303 1 chr7A.!!$R2 914
3 TraesCS7A01G037800 chr7A 699319664 699322933 3269 True 1394.0 1493 96.477500 1 2295 2 chr7A.!!$R3 2294
4 TraesCS7A01G037800 chr7A 134595933 134596733 800 False 1330.0 1330 96.629000 1 801 1 chr7A.!!$F2 800
5 TraesCS7A01G037800 chr7A 643609233 643610033 800 False 1330.0 1330 96.629000 1 801 1 chr7A.!!$F4 800
6 TraesCS7A01G037800 chr7A 192624665 192625465 800 False 1314.0 1314 96.255000 1 801 1 chr7A.!!$F3 800
7 TraesCS7A01G037800 chr2A 778395561 778396893 1332 False 2135.0 2135 95.539000 1 1339 1 chr2A.!!$F1 1338
8 TraesCS7A01G037800 chr2A 677896136 677897099 963 True 1620.0 1620 96.995000 1339 2303 1 chr2A.!!$R1 964
9 TraesCS7A01G037800 chr2B 649656114 649657423 1309 True 1895.0 1895 92.587000 1 1342 1 chr2B.!!$R1 1341
10 TraesCS7A01G037800 chr2B 42193952 42194739 787 False 1013.0 1013 89.839000 540 1339 1 chr2B.!!$F1 799
11 TraesCS7A01G037800 chr2B 45596552 45597332 780 False 976.0 976 89.362000 554 1339 1 chr2B.!!$F2 785
12 TraesCS7A01G037800 chr1B 357900814 357902159 1345 True 1862.0 1862 91.789000 1 1342 1 chr1B.!!$R1 1341
13 TraesCS7A01G037800 chr1B 38183941 38184735 794 False 963.0 963 88.684000 540 1339 1 chr1B.!!$F1 799
14 TraesCS7A01G037800 chr4B 49105655 49107017 1362 False 1720.0 1720 89.848000 1 1339 1 chr4B.!!$F1 1338
15 TraesCS7A01G037800 chr4B 402785856 402786653 797 True 996.0 996 89.338000 540 1342 1 chr4B.!!$R1 802
16 TraesCS7A01G037800 chr6A 79829208 79830125 917 True 1504.0 1504 96.304000 1389 2303 1 chr6A.!!$R1 914
17 TraesCS7A01G037800 chr6A 516294862 516295779 917 True 1487.0 1487 95.978000 1389 2303 1 chr6A.!!$R2 914
18 TraesCS7A01G037800 chr1A 559589434 559592785 3351 False 1425.0 1472 96.179500 1 2295 2 chr1A.!!$F1 2294
19 TraesCS7A01G037800 chr3A 635314423 635315307 884 False 1441.0 1441 96.050000 1410 2295 1 chr3A.!!$F1 885
20 TraesCS7A01G037800 chr3A 22600956 22602219 1263 True 573.7 1461 94.751667 1339 2302 3 chr3A.!!$R1 963
21 TraesCS7A01G037800 chr5A 288268317 288269117 800 True 1319.0 1319 96.380000 1 801 1 chr5A.!!$R1 800
22 TraesCS7A01G037800 chr4A 637836476 637837240 764 True 1308.0 1308 97.516000 1 765 1 chr4A.!!$R1 764
23 TraesCS7A01G037800 chr4A 712878028 712878819 791 False 957.0 957 88.642000 540 1336 1 chr4A.!!$F1 796
24 TraesCS7A01G037800 chr7B 687041172 687041966 794 False 968.0 968 88.807000 540 1339 1 chr7B.!!$F1 799

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
688 869 0.323178 GAGGTAGTGGTGGTCGGAGA 60.323 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1607 2937 3.119291 CCGATTCGTGAGAGATTTGAGG 58.881 50.0 5.2 0.0 43.69 3.86 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
78 79 0.598562 GAGGTGCGTCTGAAGACTCA 59.401 55.000 8.73 4.07 42.66 3.41
147 148 2.105528 GATAACGGCGGCGAAGGA 59.894 61.111 38.93 19.02 0.00 3.36
297 298 2.338809 CCCTCATATTAGGCCAGACCA 58.661 52.381 5.01 0.00 43.14 4.02
415 416 1.728490 GCGGTCATTTCATGGAGGCC 61.728 60.000 0.00 0.00 0.00 5.19
521 531 3.936203 GTCGTGGAGGTGGCACCA 61.936 66.667 36.28 15.49 41.95 4.17
597 778 2.203640 AGGTGGTGGTCGAGCAGA 60.204 61.111 19.24 4.72 30.97 4.26
649 830 0.674895 CAAGTGCTAGAGGTGGTGGC 60.675 60.000 0.00 0.00 0.00 5.01
662 843 3.286751 GTGGCCGAGCAAGCACAA 61.287 61.111 0.00 0.00 0.00 3.33
663 844 2.518112 TGGCCGAGCAAGCACAAA 60.518 55.556 0.00 0.00 0.00 2.83
664 845 1.902918 TGGCCGAGCAAGCACAAAT 60.903 52.632 0.00 0.00 0.00 2.32
665 846 1.444895 GGCCGAGCAAGCACAAATG 60.445 57.895 0.00 0.00 0.00 2.32
679 860 4.207891 CACAAATGCTAGAGGTAGTGGT 57.792 45.455 0.00 0.00 0.00 4.16
680 861 3.935203 CACAAATGCTAGAGGTAGTGGTG 59.065 47.826 0.00 0.00 0.00 4.17
681 862 3.055094 ACAAATGCTAGAGGTAGTGGTGG 60.055 47.826 0.00 0.00 0.00 4.61
682 863 2.552093 ATGCTAGAGGTAGTGGTGGT 57.448 50.000 0.00 0.00 0.00 4.16
683 864 1.848652 TGCTAGAGGTAGTGGTGGTC 58.151 55.000 0.00 0.00 0.00 4.02
684 865 0.739561 GCTAGAGGTAGTGGTGGTCG 59.260 60.000 0.00 0.00 0.00 4.79
685 866 1.390565 CTAGAGGTAGTGGTGGTCGG 58.609 60.000 0.00 0.00 0.00 4.79
686 867 0.994247 TAGAGGTAGTGGTGGTCGGA 59.006 55.000 0.00 0.00 0.00 4.55
687 868 0.323542 AGAGGTAGTGGTGGTCGGAG 60.324 60.000 0.00 0.00 0.00 4.63
688 869 0.323178 GAGGTAGTGGTGGTCGGAGA 60.323 60.000 0.00 0.00 0.00 3.71
689 870 0.323542 AGGTAGTGGTGGTCGGAGAG 60.324 60.000 0.00 0.00 36.95 3.20
690 871 1.321074 GGTAGTGGTGGTCGGAGAGG 61.321 65.000 0.00 0.00 36.95 3.69
691 872 0.323178 GTAGTGGTGGTCGGAGAGGA 60.323 60.000 0.00 0.00 36.95 3.71
692 873 0.406750 TAGTGGTGGTCGGAGAGGAA 59.593 55.000 0.00 0.00 36.95 3.36
693 874 0.900647 AGTGGTGGTCGGAGAGGAAG 60.901 60.000 0.00 0.00 36.95 3.46
694 875 2.283529 TGGTGGTCGGAGAGGAAGC 61.284 63.158 0.00 0.00 36.95 3.86
695 876 2.283529 GGTGGTCGGAGAGGAAGCA 61.284 63.158 0.00 0.00 36.95 3.91
696 877 1.079750 GTGGTCGGAGAGGAAGCAC 60.080 63.158 0.00 0.00 36.95 4.40
697 878 1.533033 TGGTCGGAGAGGAAGCACA 60.533 57.895 0.00 0.00 36.95 4.57
1356 2485 1.072331 ACTCTGGCTCGTTTTGGTCAT 59.928 47.619 0.00 0.00 0.00 3.06
1375 2504 0.114364 TGCAGGAGACCAGACACCTA 59.886 55.000 0.00 0.00 30.29 3.08
1417 2747 0.534412 CCAGTTTGCAACACACCCAA 59.466 50.000 0.00 0.00 0.00 4.12
1601 2931 4.942944 TCACTCTCATCCAGTACCCTAAA 58.057 43.478 0.00 0.00 0.00 1.85
1653 2984 2.882137 GGTTTCACCGTTGGATCTTCAA 59.118 45.455 0.00 0.00 0.00 2.69
1654 2985 3.316868 GGTTTCACCGTTGGATCTTCAAA 59.683 43.478 0.00 0.00 0.00 2.69
1857 3188 2.265367 TGTCCAAGGCTTGTCTCCATA 58.735 47.619 24.57 2.52 0.00 2.74
2127 3463 3.005050 TGTCGTTTCAACTATCGTGGACT 59.995 43.478 0.00 0.00 0.00 3.85
2130 3466 5.229469 GTCGTTTCAACTATCGTGGACTATG 59.771 44.000 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 3.231889 CTCTCGCACTGGCACCACT 62.232 63.158 0.00 0.00 41.24 4.00
297 298 2.907892 TGGTCTCCACCTTCAGAAGAT 58.092 47.619 12.14 0.00 44.17 2.40
415 416 2.355108 CCCACAGTTGATAGTGTCAGGG 60.355 54.545 0.00 0.00 38.29 4.45
494 496 2.943033 CACCTCCACGACTTGTTTTTCT 59.057 45.455 0.00 0.00 0.00 2.52
521 531 1.697432 TCTTCCACCTCGTTCACCATT 59.303 47.619 0.00 0.00 0.00 3.16
597 778 1.070758 CACCACCTCTAGCACTTGTGT 59.929 52.381 2.61 0.00 0.00 3.72
649 830 0.804364 TAGCATTTGTGCTTGCTCGG 59.196 50.000 8.34 0.00 45.83 4.63
662 843 2.766828 GACCACCACTACCTCTAGCATT 59.233 50.000 0.00 0.00 0.00 3.56
663 844 2.389715 GACCACCACTACCTCTAGCAT 58.610 52.381 0.00 0.00 0.00 3.79
664 845 1.848652 GACCACCACTACCTCTAGCA 58.151 55.000 0.00 0.00 0.00 3.49
665 846 0.739561 CGACCACCACTACCTCTAGC 59.260 60.000 0.00 0.00 0.00 3.42
666 847 1.064906 TCCGACCACCACTACCTCTAG 60.065 57.143 0.00 0.00 0.00 2.43
667 848 0.994247 TCCGACCACCACTACCTCTA 59.006 55.000 0.00 0.00 0.00 2.43
668 849 0.323542 CTCCGACCACCACTACCTCT 60.324 60.000 0.00 0.00 0.00 3.69
669 850 0.323178 TCTCCGACCACCACTACCTC 60.323 60.000 0.00 0.00 0.00 3.85
670 851 0.323542 CTCTCCGACCACCACTACCT 60.324 60.000 0.00 0.00 0.00 3.08
671 852 1.321074 CCTCTCCGACCACCACTACC 61.321 65.000 0.00 0.00 0.00 3.18
672 853 0.323178 TCCTCTCCGACCACCACTAC 60.323 60.000 0.00 0.00 0.00 2.73
673 854 0.406750 TTCCTCTCCGACCACCACTA 59.593 55.000 0.00 0.00 0.00 2.74
674 855 0.900647 CTTCCTCTCCGACCACCACT 60.901 60.000 0.00 0.00 0.00 4.00
675 856 1.592223 CTTCCTCTCCGACCACCAC 59.408 63.158 0.00 0.00 0.00 4.16
676 857 2.283529 GCTTCCTCTCCGACCACCA 61.284 63.158 0.00 0.00 0.00 4.17
677 858 2.283529 TGCTTCCTCTCCGACCACC 61.284 63.158 0.00 0.00 0.00 4.61
678 859 1.079750 GTGCTTCCTCTCCGACCAC 60.080 63.158 0.00 0.00 0.00 4.16
679 860 1.118965 TTGTGCTTCCTCTCCGACCA 61.119 55.000 0.00 0.00 0.00 4.02
680 861 0.390472 CTTGTGCTTCCTCTCCGACC 60.390 60.000 0.00 0.00 0.00 4.79
681 862 0.318762 ACTTGTGCTTCCTCTCCGAC 59.681 55.000 0.00 0.00 0.00 4.79
682 863 0.318441 CACTTGTGCTTCCTCTCCGA 59.682 55.000 0.00 0.00 0.00 4.55
683 864 1.294659 GCACTTGTGCTTCCTCTCCG 61.295 60.000 17.36 0.00 0.00 4.63
684 865 0.036022 AGCACTTGTGCTTCCTCTCC 59.964 55.000 20.95 0.00 43.52 3.71
685 866 2.232452 TCTAGCACTTGTGCTTCCTCTC 59.768 50.000 29.37 0.00 43.52 3.20
686 867 2.233431 CTCTAGCACTTGTGCTTCCTCT 59.767 50.000 29.37 10.28 43.52 3.69
687 868 2.615869 CTCTAGCACTTGTGCTTCCTC 58.384 52.381 29.37 0.08 43.52 3.71
688 869 1.277557 CCTCTAGCACTTGTGCTTCCT 59.722 52.381 29.37 11.29 43.52 3.36
689 870 1.002544 ACCTCTAGCACTTGTGCTTCC 59.997 52.381 29.37 1.14 43.52 3.46
690 871 2.072298 CACCTCTAGCACTTGTGCTTC 58.928 52.381 29.37 1.49 43.52 3.86
691 872 1.271054 CCACCTCTAGCACTTGTGCTT 60.271 52.381 29.37 15.68 43.52 3.91
693 874 0.035458 ACCACCTCTAGCACTTGTGC 59.965 55.000 16.98 16.98 0.00 4.57
694 875 1.609061 CCACCACCTCTAGCACTTGTG 60.609 57.143 0.00 0.00 0.00 3.33
695 876 0.687354 CCACCACCTCTAGCACTTGT 59.313 55.000 0.00 0.00 0.00 3.16
696 877 0.687354 ACCACCACCTCTAGCACTTG 59.313 55.000 0.00 0.00 0.00 3.16
697 878 0.687354 CACCACCACCTCTAGCACTT 59.313 55.000 0.00 0.00 0.00 3.16
782 1035 0.900647 CTTCCTCTCCGACCACCACT 60.901 60.000 0.00 0.00 0.00 4.00
1076 1330 2.234908 ACATCCTTCTCCTTCTCCAACG 59.765 50.000 0.00 0.00 0.00 4.10
1308 1568 5.424121 AGGCGACTACATAAAAATCATGC 57.576 39.130 0.00 0.00 40.61 4.06
1356 2485 0.114364 TAGGTGTCTGGTCTCCTGCA 59.886 55.000 0.00 0.00 33.97 4.41
1375 2504 4.335874 GCAAAATGCTCAGACAGATCAGAT 59.664 41.667 0.00 0.00 40.96 2.90
1417 2747 4.660938 GCCAGGGACCTTGGCGTT 62.661 66.667 29.83 0.00 39.06 4.84
1607 2937 3.119291 CCGATTCGTGAGAGATTTGAGG 58.881 50.000 5.20 0.00 43.69 3.86
1857 3188 4.036734 CCACTTCACTAACTTGCACAACAT 59.963 41.667 0.00 0.00 0.00 2.71
2127 3463 7.125053 TGACATAAGTAGTTCATGACCACCATA 59.875 37.037 0.00 0.00 33.31 2.74
2130 3466 5.730550 TGACATAAGTAGTTCATGACCACC 58.269 41.667 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.