Multiple sequence alignment - TraesCS1D01G396100

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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 TraesCS1D01G396100 chr1D 100.000 3084 0 0 1 3084 464438024 464441107 0.000000e+00 5696.0
1 TraesCS1D01G396100 chr1D 81.507 146 16 7 608 749 90554595 90554457 3.250000e-20 110.0
2 TraesCS1D01G396100 chr4A 94.315 1671 65 15 1436 3083 538718138 538716475 0.000000e+00 2532.0
3 TraesCS1D01G396100 chr4A 87.662 851 51 25 626 1441 538720161 538719330 0.000000e+00 941.0
4 TraesCS1D01G396100 chr4A 91.973 598 26 7 1 585 538720702 538720114 0.000000e+00 819.0
5 TraesCS1D01G396100 chr4A 82.635 167 8 12 480 629 557656397 557656235 8.980000e-26 128.0
6 TraesCS1D01G396100 chr1A 93.855 1660 71 12 1436 3083 556840174 556841814 0.000000e+00 2471.0
7 TraesCS1D01G396100 chr1A 87.593 1338 86 38 1 1296 556837678 556838977 0.000000e+00 1478.0
8 TraesCS1D01G396100 chr1B 92.926 1668 55 19 1436 3083 640616837 640615213 0.000000e+00 2368.0
9 TraesCS1D01G396100 chr1B 90.508 1475 65 24 1 1441 640619061 640617628 0.000000e+00 1879.0
10 TraesCS1D01G396100 chr6A 91.870 1476 73 23 1 1441 125150233 125151696 0.000000e+00 2017.0
11 TraesCS1D01G396100 chr6A 94.423 1058 30 10 1682 2718 125153192 125154241 0.000000e+00 1600.0
12 TraesCS1D01G396100 chr6A 77.286 339 26 25 472 805 137638575 137638283 5.330000e-33 152.0
13 TraesCS1D01G396100 chr5A 91.469 1477 79 20 1 1441 412225970 412224505 0.000000e+00 1986.0
14 TraesCS1D01G396100 chr5A 94.023 1305 53 7 1436 2718 412223405 412222104 0.000000e+00 1954.0
15 TraesCS1D01G396100 chr5A 86.396 985 61 31 480 1441 121725503 121724569 0.000000e+00 1009.0
16 TraesCS1D01G396100 chr5A 88.929 840 24 13 1860 2679 121723407 121722617 0.000000e+00 972.0
17 TraesCS1D01G396100 chr5A 95.415 349 16 0 2735 3083 80513682 80513334 9.660000e-155 556.0
18 TraesCS1D01G396100 chr6B 91.547 1467 73 27 1 1441 153236721 153235280 0.000000e+00 1975.0
19 TraesCS1D01G396100 chr6B 94.517 766 34 4 2319 3083 153233451 153232693 0.000000e+00 1175.0
20 TraesCS1D01G396100 chr6B 93.824 680 26 5 1436 2111 153234108 153233441 0.000000e+00 1009.0
21 TraesCS1D01G396100 chr2D 89.214 1502 90 33 1436 2904 571178617 571180079 0.000000e+00 1810.0
22 TraesCS1D01G396100 chr2B 88.919 1498 93 33 1436 2904 683037085 683038538 0.000000e+00 1779.0
23 TraesCS1D01G396100 chr5D 91.942 1241 35 14 1463 2679 118206770 118205571 0.000000e+00 1677.0
24 TraesCS1D01G396100 chr5D 90.000 840 24 9 1860 2679 87544271 87543472 0.000000e+00 1031.0
25 TraesCS1D01G396100 chr5D 87.381 943 45 33 534 1441 87546394 87545491 0.000000e+00 1014.0
26 TraesCS1D01G396100 chr5D 87.729 872 58 23 593 1441 118208476 118207631 0.000000e+00 972.0
27 TraesCS1D01G396100 chr5D 85.596 965 49 40 534 1441 122074005 122073074 0.000000e+00 929.0
28 TraesCS1D01G396100 chr5D 95.702 349 15 0 2735 3083 87543473 87543125 2.080000e-156 562.0
29 TraesCS1D01G396100 chr5D 94.842 349 17 1 2735 3083 122063091 122062744 7.520000e-151 544.0
30 TraesCS1D01G396100 chr5D 92.703 370 15 6 1463 1828 87544631 87544270 9.800000e-145 523.0
31 TraesCS1D01G396100 chr5D 89.560 364 21 5 1 356 87547124 87546770 2.180000e-121 446.0
32 TraesCS1D01G396100 chr5D 89.560 364 20 6 1 356 122074687 122074334 2.180000e-121 446.0
33 TraesCS1D01G396100 chr5D 76.179 424 46 33 408 805 122062882 122062488 4.090000e-39 172.0
34 TraesCS1D01G396100 chr5B 91.385 1242 40 23 1463 2679 117250214 117251413 0.000000e+00 1639.0
35 TraesCS1D01G396100 chr5B 86.548 1011 58 31 472 1441 93477490 93476517 0.000000e+00 1042.0
36 TraesCS1D01G396100 chr5B 95.385 585 15 6 1468 2048 128672529 128673105 0.000000e+00 920.0
37 TraesCS1D01G396100 chr5B 88.206 797 43 23 662 1441 117248590 117249352 0.000000e+00 904.0
38 TraesCS1D01G396100 chr5B 94.269 349 19 1 2735 3083 117251412 117251759 1.630000e-147 532.0
39 TraesCS1D01G396100 chr5B 81.329 316 13 20 472 749 92204935 92204628 6.700000e-52 215.0
40 TraesCS1D01G396100 chr4D 91.104 888 33 13 1436 2300 57874204 57875068 0.000000e+00 1160.0
41 TraesCS1D01G396100 chr4D 93.794 564 28 2 2521 3084 57875362 57875918 0.000000e+00 841.0
42 TraesCS1D01G396100 chr4D 91.837 588 30 10 2 579 57857315 57857894 0.000000e+00 804.0
43 TraesCS1D01G396100 chr2A 89.144 783 51 19 2144 2904 709845217 709845987 0.000000e+00 944.0
44 TraesCS1D01G396100 chr3B 88.889 522 32 15 933 1441 550788588 550789096 1.210000e-173 619.0
45 TraesCS1D01G396100 chr3B 81.818 231 19 11 593 810 550792147 550792367 4.090000e-39 172.0
46 TraesCS1D01G396100 chr3B 79.646 113 13 7 494 604 176343443 176343339 4.270000e-09 73.1
47 TraesCS1D01G396100 chr6D 77.619 420 40 31 408 805 431000923 431001310 4.030000e-49 206.0
48 TraesCS1D01G396100 chr3D 82.397 267 16 16 408 670 579694183 579694422 1.450000e-48 204.0


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 TraesCS1D01G396100 chr1D 464438024 464441107 3083 False 5696.000000 5696 100.000000 1 3084 1 chr1D.!!$F1 3083
1 TraesCS1D01G396100 chr4A 538716475 538720702 4227 True 1430.666667 2532 91.316667 1 3083 3 chr4A.!!$R2 3082
2 TraesCS1D01G396100 chr1A 556837678 556841814 4136 False 1974.500000 2471 90.724000 1 3083 2 chr1A.!!$F1 3082
3 TraesCS1D01G396100 chr1B 640615213 640619061 3848 True 2123.500000 2368 91.717000 1 3083 2 chr1B.!!$R1 3082
4 TraesCS1D01G396100 chr6A 125150233 125154241 4008 False 1808.500000 2017 93.146500 1 2718 2 chr6A.!!$F1 2717
5 TraesCS1D01G396100 chr5A 412222104 412225970 3866 True 1970.000000 1986 92.746000 1 2718 2 chr5A.!!$R3 2717
6 TraesCS1D01G396100 chr5A 121722617 121725503 2886 True 990.500000 1009 87.662500 480 2679 2 chr5A.!!$R2 2199
7 TraesCS1D01G396100 chr6B 153232693 153236721 4028 True 1386.333333 1975 93.296000 1 3083 3 chr6B.!!$R1 3082
8 TraesCS1D01G396100 chr2D 571178617 571180079 1462 False 1810.000000 1810 89.214000 1436 2904 1 chr2D.!!$F1 1468
9 TraesCS1D01G396100 chr2B 683037085 683038538 1453 False 1779.000000 1779 88.919000 1436 2904 1 chr2B.!!$F1 1468
10 TraesCS1D01G396100 chr5D 118205571 118208476 2905 True 1324.500000 1677 89.835500 593 2679 2 chr5D.!!$R2 2086
11 TraesCS1D01G396100 chr5D 87543125 87547124 3999 True 715.200000 1031 91.069200 1 3083 5 chr5D.!!$R1 3082
12 TraesCS1D01G396100 chr5D 122073074 122074687 1613 True 687.500000 929 87.578000 1 1441 2 chr5D.!!$R4 1440
13 TraesCS1D01G396100 chr5D 122062488 122063091 603 True 358.000000 544 85.510500 408 3083 2 chr5D.!!$R3 2675
14 TraesCS1D01G396100 chr5B 93476517 93477490 973 True 1042.000000 1042 86.548000 472 1441 1 chr5B.!!$R2 969
15 TraesCS1D01G396100 chr5B 117248590 117251759 3169 False 1025.000000 1639 91.286667 662 3083 3 chr5B.!!$F2 2421
16 TraesCS1D01G396100 chr5B 128672529 128673105 576 False 920.000000 920 95.385000 1468 2048 1 chr5B.!!$F1 580
17 TraesCS1D01G396100 chr4D 57874204 57875918 1714 False 1000.500000 1160 92.449000 1436 3084 2 chr4D.!!$F2 1648
18 TraesCS1D01G396100 chr4D 57857315 57857894 579 False 804.000000 804 91.837000 2 579 1 chr4D.!!$F1 577
19 TraesCS1D01G396100 chr2A 709845217 709845987 770 False 944.000000 944 89.144000 2144 2904 1 chr2A.!!$F1 760
20 TraesCS1D01G396100 chr3B 550788588 550792367 3779 False 395.500000 619 85.353500 593 1441 2 chr3B.!!$F1 848

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
584 984 0.578683 CTTGACTCTGTGTGCGTGTG 59.421 55.0 0.0 0.0 0.0 3.82 F
585 985 0.809636 TTGACTCTGTGTGCGTGTGG 60.810 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 2224 2.170187 CTGCTGGTGCTTTAGAGAGGAT 59.830 50.000 0.0 0.0 40.48 3.24 R
2343 4829 3.007614 TGACCAGGAGTAAGCAAGTAACC 59.992 47.826 0.0 0.0 0.00 2.85 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
114 126 2.278336 CGCATGCGCCCTTTGATG 60.278 61.111 29.09 1.13 33.11 3.07
187 199 7.083875 TCGGTTATTCTGATTGAAATTGGAC 57.916 36.000 0.00 0.00 38.29 4.02
347 371 4.268884 GGCAGAAAGATTTACTAGAGTGCG 59.731 45.833 0.00 0.00 0.00 5.34
389 504 1.876156 GCTGCTACTTCACAGTGCTTT 59.124 47.619 0.00 0.00 36.26 3.51
579 979 0.815213 TGTGGCTTGACTCTGTGTGC 60.815 55.000 0.00 0.00 0.00 4.57
580 980 1.595109 TGGCTTGACTCTGTGTGCG 60.595 57.895 0.00 0.00 0.00 5.34
581 981 1.595382 GGCTTGACTCTGTGTGCGT 60.595 57.895 0.00 0.00 0.00 5.24
582 982 1.566563 GCTTGACTCTGTGTGCGTG 59.433 57.895 0.00 0.00 0.00 5.34
583 983 1.154205 GCTTGACTCTGTGTGCGTGT 61.154 55.000 0.00 0.00 0.00 4.49
584 984 0.578683 CTTGACTCTGTGTGCGTGTG 59.421 55.000 0.00 0.00 0.00 3.82
585 985 0.809636 TTGACTCTGTGTGCGTGTGG 60.810 55.000 0.00 0.00 0.00 4.17
586 986 2.588877 ACTCTGTGTGCGTGTGGC 60.589 61.111 0.00 0.00 43.96 5.01
587 987 2.280389 CTCTGTGTGCGTGTGGCT 60.280 61.111 0.00 0.00 44.05 4.75
588 988 1.889105 CTCTGTGTGCGTGTGGCTT 60.889 57.895 0.00 0.00 44.05 4.35
589 989 2.109538 CTCTGTGTGCGTGTGGCTTG 62.110 60.000 0.00 0.00 44.05 4.01
590 990 2.124942 TGTGTGCGTGTGGCTTGA 60.125 55.556 0.00 0.00 44.05 3.02
591 991 1.509644 CTGTGTGCGTGTGGCTTGAT 61.510 55.000 0.00 0.00 44.05 2.57
786 1480 8.863049 GCTTTGTTGATTGATTTGGTTGTATAG 58.137 33.333 0.00 0.00 0.00 1.31
790 1484 9.237187 TGTTGATTGATTTGGTTGTATAGCTTA 57.763 29.630 0.00 0.00 0.00 3.09
894 1588 4.665833 TGGTATTGGTAGTTCCTGATCG 57.334 45.455 0.00 0.00 37.07 3.69
1003 1712 2.833943 TCCCAGATCCATATCGACATGG 59.166 50.000 16.93 16.93 45.93 3.66
1077 1788 4.027674 TGCTCCTTGTATTAACTTGGCA 57.972 40.909 0.00 0.00 0.00 4.92
1260 1983 6.093219 CAGAAGATGTGCAGCAAGTAAGTAAT 59.907 38.462 0.00 0.00 0.00 1.89
1320 2044 3.703052 GCCATCTTTCCCAACAGATTGAT 59.297 43.478 0.00 0.00 38.15 2.57
1598 3962 3.640498 TGCCTGATTTCACCATGTTTCAA 59.360 39.130 0.00 0.00 0.00 2.69
1745 4148 8.907222 TCATATTTCTAGCAATGCATGTCTAA 57.093 30.769 8.35 0.00 0.00 2.10
1747 4150 6.630444 ATTTCTAGCAATGCATGTCTAAGG 57.370 37.500 8.35 0.00 0.00 2.69
2078 4525 4.441356 CCAAGGCTGTTGCTGTTAAAAAGA 60.441 41.667 0.00 0.00 39.59 2.52
2343 4829 6.808704 TCAGATTCTGATGAAGTAAGTGTTCG 59.191 38.462 12.38 0.00 35.39 3.95
2596 5419 7.603404 CCAAGGATGATTCTGATGATAGTTCTC 59.397 40.741 0.00 0.00 0.00 2.87
2977 6729 3.292460 CTCACCCCTCTAGAGAAATCGT 58.708 50.000 21.76 6.35 0.00 3.73
3013 6765 9.167311 TCAAGTTCTGGAAATTCTTTATAGCTC 57.833 33.333 0.00 0.00 0.00 4.09
3033 6785 4.395542 GCTCTCTGAGTTTACTTCGGTCTA 59.604 45.833 4.32 0.00 31.39 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 126 5.419542 TGAACATCCATCAAGTACAGTAGC 58.580 41.667 0.00 0.00 0.00 3.58
187 199 0.036010 AATCGACAGAGGGCCAACAG 60.036 55.000 6.18 0.00 0.00 3.16
347 371 5.126061 AGCAACATGAGGAATTACATGGTTC 59.874 40.000 17.74 10.15 45.31 3.62
523 899 0.514255 CACACACACAGAATGGAGCG 59.486 55.000 0.00 0.00 43.62 5.03
524 900 0.877071 CCACACACACAGAATGGAGC 59.123 55.000 0.00 0.00 43.62 4.70
525 901 0.877071 GCCACACACACAGAATGGAG 59.123 55.000 0.00 0.00 43.62 3.86
579 979 0.662619 ACACACAATCAAGCCACACG 59.337 50.000 0.00 0.00 0.00 4.49
580 980 1.405105 ACACACACAATCAAGCCACAC 59.595 47.619 0.00 0.00 0.00 3.82
581 981 1.404748 CACACACACAATCAAGCCACA 59.595 47.619 0.00 0.00 0.00 4.17
582 982 1.405105 ACACACACACAATCAAGCCAC 59.595 47.619 0.00 0.00 0.00 5.01
583 983 1.404748 CACACACACACAATCAAGCCA 59.595 47.619 0.00 0.00 0.00 4.75
584 984 1.405105 ACACACACACACAATCAAGCC 59.595 47.619 0.00 0.00 0.00 4.35
585 985 2.159393 ACACACACACACACAATCAAGC 60.159 45.455 0.00 0.00 0.00 4.01
586 986 3.119884 ACACACACACACACACAATCAAG 60.120 43.478 0.00 0.00 0.00 3.02
587 987 2.816672 ACACACACACACACACAATCAA 59.183 40.909 0.00 0.00 0.00 2.57
588 988 2.161211 CACACACACACACACACAATCA 59.839 45.455 0.00 0.00 0.00 2.57
589 989 2.477694 CCACACACACACACACACAATC 60.478 50.000 0.00 0.00 0.00 2.67
590 990 1.472082 CCACACACACACACACACAAT 59.528 47.619 0.00 0.00 0.00 2.71
591 991 0.877743 CCACACACACACACACACAA 59.122 50.000 0.00 0.00 0.00 3.33
786 1480 5.746245 TGCCGCAACAATATAAAACATAAGC 59.254 36.000 0.00 0.00 0.00 3.09
790 1484 4.101942 CGTGCCGCAACAATATAAAACAT 58.898 39.130 0.00 0.00 0.00 2.71
1003 1712 1.812922 CCTCATCAGACAGCGTGGC 60.813 63.158 0.00 0.00 0.00 5.01
1052 1761 4.702131 CCAAGTTAATACAAGGAGCAAGCT 59.298 41.667 0.00 0.00 0.00 3.74
1053 1762 4.675408 GCCAAGTTAATACAAGGAGCAAGC 60.675 45.833 0.00 0.00 0.00 4.01
1104 1820 1.339151 GGAGCTCCAGTTTCACGGAAT 60.339 52.381 28.43 0.00 35.64 3.01
1107 1823 0.035458 AAGGAGCTCCAGTTTCACGG 59.965 55.000 33.90 0.00 38.89 4.94
1131 1847 8.394971 TGCTCATAAAGTCATATAATGGGTTG 57.605 34.615 0.00 0.00 0.00 3.77
1188 1905 3.365364 GGAAGTCAATCTTGTTTGGAGCG 60.365 47.826 0.00 0.00 36.40 5.03
1286 2010 4.072131 GGAAAGATGGCAGTGTGAAGTAA 58.928 43.478 0.00 0.00 0.00 2.24
1296 2020 2.205022 TCTGTTGGGAAAGATGGCAG 57.795 50.000 0.00 0.00 0.00 4.85
1428 2224 2.170187 CTGCTGGTGCTTTAGAGAGGAT 59.830 50.000 0.00 0.00 40.48 3.24
1598 3962 4.562143 GCTGGCTTCTGAAAACCAATGAAT 60.562 41.667 11.62 0.00 30.35 2.57
1745 4148 6.721318 TGCTTTTGTACTCAATTATCTCCCT 58.279 36.000 0.00 0.00 33.32 4.20
2268 4738 7.961827 CACTAGATTCTTCTTTCTTTGCATCAC 59.038 37.037 0.00 0.00 33.17 3.06
2269 4739 7.120285 CCACTAGATTCTTCTTTCTTTGCATCA 59.880 37.037 0.00 0.00 33.17 3.07
2270 4740 7.120432 ACCACTAGATTCTTCTTTCTTTGCATC 59.880 37.037 0.00 0.00 33.17 3.91
2343 4829 3.007614 TGACCAGGAGTAAGCAAGTAACC 59.992 47.826 0.00 0.00 0.00 2.85
2596 5419 3.459145 CAGGCTCTTCATCACTCTCATG 58.541 50.000 0.00 0.00 0.00 3.07
2977 6729 9.965824 GAATTTCCAGAACTTGAATGAGTAAAA 57.034 29.630 0.00 0.00 0.00 1.52
3013 6765 4.156190 TGCTAGACCGAAGTAAACTCAGAG 59.844 45.833 0.00 0.00 0.00 3.35
3033 6785 4.339247 ACAAACAGAAAGCTAACACATGCT 59.661 37.500 0.00 0.00 41.82 3.79


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

AutoCloner maintained by Alex Coulton.