Multiple sequence alignment - TraesCS3D01G334600

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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 TraesCS3D01G334600 chr3D 100.000 2565 0 0 1 2565 446748092 446745528 0.000000e+00 4737.0
1 TraesCS3D01G334600 chr3D 84.655 1766 226 23 802 2537 121210033 121211783 0.000000e+00 1718.0
2 TraesCS3D01G334600 chr3D 93.928 807 43 5 1 801 458201095 458200289 0.000000e+00 1214.0
3 TraesCS3D01G334600 chr3D 92.910 804 51 3 1 801 556579812 556580612 0.000000e+00 1164.0
4 TraesCS3D01G334600 chr3D 85.507 69 9 1 2498 2565 143212936 143213004 1.270000e-08 71.3
5 TraesCS3D01G334600 chr3D 91.837 49 3 1 2488 2536 363254826 363254779 1.650000e-07 67.6
6 TraesCS3D01G334600 chr2B 86.731 1756 208 19 802 2537 599258795 599260545 0.000000e+00 1929.0
7 TraesCS3D01G334600 chr2B 82.664 1817 222 46 802 2563 234361268 234359490 0.000000e+00 1524.0
8 TraesCS3D01G334600 chr5B 88.671 1580 169 9 802 2378 524325810 524327382 0.000000e+00 1917.0
9 TraesCS3D01G334600 chr5B 82.677 127 19 2 2441 2564 466703393 466703267 2.700000e-20 110.0
10 TraesCS3D01G334600 chr1D 88.232 1589 168 12 802 2378 58565732 58564151 0.000000e+00 1881.0
11 TraesCS3D01G334600 chr1D 93.267 802 52 2 1 801 380297333 380298133 0.000000e+00 1181.0
12 TraesCS3D01G334600 chr5D 85.787 1773 212 21 804 2565 476695124 476693381 0.000000e+00 1842.0
13 TraesCS3D01G334600 chr5D 93.159 804 51 3 1 801 499719183 499718381 0.000000e+00 1177.0
14 TraesCS3D01G334600 chr5D 91.837 49 4 0 2498 2546 312055481 312055529 4.580000e-08 69.4
15 TraesCS3D01G334600 chr7D 85.140 1790 224 21 802 2563 585428684 585426909 0.000000e+00 1794.0
16 TraesCS3D01G334600 chr7D 92.928 806 52 4 1 801 329182507 329181702 0.000000e+00 1168.0
17 TraesCS3D01G334600 chr7D 89.091 55 5 1 2488 2542 39131572 39131519 1.650000e-07 67.6
18 TraesCS3D01G334600 chr3B 84.905 1782 231 23 802 2564 713994128 713992366 0.000000e+00 1766.0
19 TraesCS3D01G334600 chr3B 84.671 1670 222 22 802 2462 713974166 713972522 0.000000e+00 1635.0
20 TraesCS3D01G334600 chr3B 97.297 37 1 0 2499 2535 670538881 670538917 2.130000e-06 63.9
21 TraesCS3D01G334600 chr6B 84.701 1791 226 26 800 2553 485126566 485128345 0.000000e+00 1746.0
22 TraesCS3D01G334600 chr7B 84.512 1782 229 26 802 2545 544722627 544724399 0.000000e+00 1718.0
23 TraesCS3D01G334600 chr2D 94.763 802 41 1 1 801 370200172 370199371 0.000000e+00 1247.0
24 TraesCS3D01G334600 chr2D 93.516 802 51 1 1 801 306380091 306380892 0.000000e+00 1192.0
25 TraesCS3D01G334600 chr2D 93.086 810 45 5 1 799 135337258 135336449 0.000000e+00 1175.0
26 TraesCS3D01G334600 chr4D 93.408 804 47 4 1 802 373943682 373944481 0.000000e+00 1186.0
27 TraesCS3D01G334600 chr1B 97.500 40 1 0 2498 2537 105111990 105111951 4.580000e-08 69.4
28 TraesCS3D01G334600 chr4B 90.909 44 3 1 2509 2552 546086257 546086215 9.910000e-05 58.4


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 TraesCS3D01G334600 chr3D 446745528 446748092 2564 True 4737 4737 100.000 1 2565 1 chr3D.!!$R2 2564
1 TraesCS3D01G334600 chr3D 121210033 121211783 1750 False 1718 1718 84.655 802 2537 1 chr3D.!!$F1 1735
2 TraesCS3D01G334600 chr3D 458200289 458201095 806 True 1214 1214 93.928 1 801 1 chr3D.!!$R3 800
3 TraesCS3D01G334600 chr3D 556579812 556580612 800 False 1164 1164 92.910 1 801 1 chr3D.!!$F3 800
4 TraesCS3D01G334600 chr2B 599258795 599260545 1750 False 1929 1929 86.731 802 2537 1 chr2B.!!$F1 1735
5 TraesCS3D01G334600 chr2B 234359490 234361268 1778 True 1524 1524 82.664 802 2563 1 chr2B.!!$R1 1761
6 TraesCS3D01G334600 chr5B 524325810 524327382 1572 False 1917 1917 88.671 802 2378 1 chr5B.!!$F1 1576
7 TraesCS3D01G334600 chr1D 58564151 58565732 1581 True 1881 1881 88.232 802 2378 1 chr1D.!!$R1 1576
8 TraesCS3D01G334600 chr1D 380297333 380298133 800 False 1181 1181 93.267 1 801 1 chr1D.!!$F1 800
9 TraesCS3D01G334600 chr5D 476693381 476695124 1743 True 1842 1842 85.787 804 2565 1 chr5D.!!$R1 1761
10 TraesCS3D01G334600 chr5D 499718381 499719183 802 True 1177 1177 93.159 1 801 1 chr5D.!!$R2 800
11 TraesCS3D01G334600 chr7D 585426909 585428684 1775 True 1794 1794 85.140 802 2563 1 chr7D.!!$R3 1761
12 TraesCS3D01G334600 chr7D 329181702 329182507 805 True 1168 1168 92.928 1 801 1 chr7D.!!$R2 800
13 TraesCS3D01G334600 chr3B 713992366 713994128 1762 True 1766 1766 84.905 802 2564 1 chr3B.!!$R2 1762
14 TraesCS3D01G334600 chr3B 713972522 713974166 1644 True 1635 1635 84.671 802 2462 1 chr3B.!!$R1 1660
15 TraesCS3D01G334600 chr6B 485126566 485128345 1779 False 1746 1746 84.701 800 2553 1 chr6B.!!$F1 1753
16 TraesCS3D01G334600 chr7B 544722627 544724399 1772 False 1718 1718 84.512 802 2545 1 chr7B.!!$F1 1743
17 TraesCS3D01G334600 chr2D 370199371 370200172 801 True 1247 1247 94.763 1 801 1 chr2D.!!$R2 800
18 TraesCS3D01G334600 chr2D 306380091 306380892 801 False 1192 1192 93.516 1 801 1 chr2D.!!$F1 800
19 TraesCS3D01G334600 chr2D 135336449 135337258 809 True 1175 1175 93.086 1 799 1 chr2D.!!$R1 798
20 TraesCS3D01G334600 chr4D 373943682 373944481 799 False 1186 1186 93.408 1 802 1 chr4D.!!$F1 801

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
946 971 1.066143 CCTGTTCGGTAGAATGCCTGT 60.066 52.381 0.0 0.0 39.53 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2499 2645 0.036765 GTCCAACACGCTGACCCATA 60.037 55.0 0.0 0.0 0.0 2.74 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
28 29 1.736126 GACGTGACCGAGACACATCTA 59.264 52.381 0.00 0.00 38.04 1.98
75 76 3.652387 TGGATGCTCATATTGGCTCCTAA 59.348 43.478 12.11 0.00 31.74 2.69
203 205 3.129988 CCTAGTTCAATCTCGTTACCGGT 59.870 47.826 13.98 13.98 33.95 5.28
251 254 4.024218 GCATCATCCTGCAACTAACTCATC 60.024 45.833 0.00 0.00 41.87 2.92
391 395 2.164422 TCGAAGACACCTGTAGAGCATG 59.836 50.000 0.00 0.00 0.00 4.06
477 481 6.291377 GGGAGTTGCATAATCTCATAGTCAA 58.709 40.000 0.00 0.00 0.00 3.18
780 804 9.469807 AATATCAAAAACGACTTTATTGTTGCA 57.530 25.926 0.00 0.00 34.89 4.08
872 897 3.458163 GGCTCGTCATCCGGTGGA 61.458 66.667 0.00 0.00 37.11 4.02
934 959 2.812178 CGCCCGTAACCTGTTCGG 60.812 66.667 11.47 11.47 43.30 4.30
946 971 1.066143 CCTGTTCGGTAGAATGCCTGT 60.066 52.381 0.00 0.00 39.53 4.00
998 1035 2.601067 TTCGAGGGTGGTACGGCA 60.601 61.111 0.00 0.00 0.00 5.69
1150 1196 4.115199 GGACATGGGCGGCTTCCT 62.115 66.667 9.56 0.00 0.00 3.36
1172 1218 0.313043 TCGACCACGAGTTTCTGGAC 59.687 55.000 0.00 0.00 43.81 4.02
1436 1486 2.073816 CACAAGAAGTTTCCGCCGTAT 58.926 47.619 0.00 0.00 0.00 3.06
1448 1498 1.132262 CCGCCGTATCAAATGCAAAGT 59.868 47.619 0.00 0.00 0.00 2.66
1664 1718 4.806775 TCAATATGCTTGCATGCAATTCAC 59.193 37.500 31.96 21.12 46.61 3.18
1673 1727 3.155093 CATGCAATTCACTTGTAGGCC 57.845 47.619 0.00 0.00 37.18 5.19
1752 1806 4.708421 CCCATTGTTGGAGAGTCATCAAAT 59.292 41.667 0.00 0.00 46.92 2.32
1762 1816 5.506649 GGAGAGTCATCAAATACGAGGAGAC 60.507 48.000 0.00 0.00 0.00 3.36
1847 1909 4.373116 GGCGAGAAGGCACGACCA 62.373 66.667 0.00 0.00 45.92 4.02
1872 1934 2.554462 GGAAAGACCAACTCCAAGAAGC 59.446 50.000 0.00 0.00 38.79 3.86
1920 1982 2.358957 CCTTGATCGCAAACATGGAGA 58.641 47.619 0.00 0.00 34.59 3.71
1921 1983 2.096496 CCTTGATCGCAAACATGGAGAC 59.904 50.000 0.00 0.00 34.59 3.36
1971 2033 1.069204 AGAAGCGCTGACAAGACAAGA 59.931 47.619 12.58 0.00 0.00 3.02
2022 2084 2.416680 AAGGAGAAGGCTTGAGATGC 57.583 50.000 3.46 0.00 0.00 3.91
2059 2122 1.767681 GAGGATGCTTGAGATGGAGGT 59.232 52.381 0.00 0.00 0.00 3.85
2067 2130 2.630889 TGAGATGGAGGTGGAGAAGT 57.369 50.000 0.00 0.00 0.00 3.01
2113 2176 0.968405 GCCAATGCAAAGACCAAGGA 59.032 50.000 0.00 0.00 37.47 3.36
2120 2183 3.480470 TGCAAAGACCAAGGAGAAAGAG 58.520 45.455 0.00 0.00 0.00 2.85
2123 2186 4.464947 CAAAGACCAAGGAGAAAGAGGTT 58.535 43.478 0.00 0.00 31.57 3.50
2204 2267 2.939640 GCCAAGGAAGAAGCCGTGATTA 60.940 50.000 0.00 0.00 39.40 1.75
2214 2277 3.742433 AGCCGTGATTAGAGAAGATGG 57.258 47.619 0.00 0.00 0.00 3.51
2255 2319 1.333931 GACGACGAGTGATCTATGGCA 59.666 52.381 0.00 0.00 0.00 4.92
2261 2325 1.339610 GAGTGATCTATGGCAGCGAGT 59.660 52.381 0.00 0.00 0.00 4.18
2331 2402 0.949105 ATGGCGTGGTCGAACTCAAC 60.949 55.000 0.33 0.00 39.71 3.18
2345 2419 2.424793 ACTCAACTCCCACCCCTTTTA 58.575 47.619 0.00 0.00 0.00 1.52
2353 2427 0.532115 CCACCCCTTTTATGTGCTGC 59.468 55.000 0.00 0.00 0.00 5.25
2383 2484 3.453559 GCCGCTGGCTAGTCTTTTA 57.546 52.632 11.61 0.00 46.69 1.52
2394 2513 5.183140 TGGCTAGTCTTTTAAAGTTGGCATC 59.817 40.000 16.33 0.00 0.00 3.91
2408 2528 2.737180 CATCGTATGCCGGCCTCT 59.263 61.111 26.77 11.49 37.11 3.69
2409 2529 1.373497 CATCGTATGCCGGCCTCTC 60.373 63.158 26.77 10.89 37.11 3.20
2439 2580 1.792367 CGACATGAACTTTGAGCGACA 59.208 47.619 0.00 0.00 0.00 4.35
2449 2590 2.742372 GAGCGACAACATGGCCGT 60.742 61.111 0.00 0.00 30.97 5.68
2469 2611 1.072159 GGCATGATCTAAGGCCGCT 59.928 57.895 0.00 0.00 36.58 5.52
2472 2614 1.233019 CATGATCTAAGGCCGCTTGG 58.767 55.000 0.00 0.00 0.00 3.61
2486 2632 2.223845 CCGCTTGGCTTTTCAAATTTGG 59.776 45.455 17.90 3.24 0.00 3.28
2497 2643 2.441410 TCAAATTTGGGCGCAGACATA 58.559 42.857 17.90 0.21 37.00 2.29
2499 2645 3.446873 TCAAATTTGGGCGCAGACATAAT 59.553 39.130 17.90 0.00 37.00 1.28
2507 2653 2.549992 GGCGCAGACATAATATGGGTCA 60.550 50.000 10.83 0.00 37.07 4.02
2544 2691 2.695666 TGCCGACCCAAATCAAAAAGAA 59.304 40.909 0.00 0.00 0.00 2.52
2553 2700 4.219033 CAAATCAAAAAGAAGACGGACGG 58.781 43.478 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.202154 CCGTAGATGTGTCTCGGTCAC 60.202 57.143 0.00 0.00 38.85 3.67
75 76 9.843334 GACCGATAAAGATCTTCGTAGAATATT 57.157 33.333 8.78 0.00 45.90 1.28
251 254 1.933500 GCCTTGCAAGCAATGTGACTG 60.934 52.381 21.43 4.37 35.20 3.51
391 395 7.118101 TCACAACGTAACTGGGTGATTATAAAC 59.882 37.037 0.00 0.00 33.88 2.01
614 624 4.652822 AGATGGTTAAGTTTCCTGACCAC 58.347 43.478 0.00 0.00 39.29 4.16
759 783 7.393551 AGATGCAACAATAAAGTCGTTTTTG 57.606 32.000 0.00 1.35 0.00 2.44
762 786 6.128007 CCCTAGATGCAACAATAAAGTCGTTT 60.128 38.462 0.00 0.00 0.00 3.60
766 790 4.640201 TGCCCTAGATGCAACAATAAAGTC 59.360 41.667 4.64 0.00 35.40 3.01
775 799 4.401925 AGGAAATATGCCCTAGATGCAAC 58.598 43.478 10.38 0.00 42.92 4.17
780 804 4.916424 AGGTGAAGGAAATATGCCCTAGAT 59.084 41.667 0.00 0.00 31.36 1.98
890 915 1.904852 GCATGTCGGCTGGCATATCG 61.905 60.000 13.35 1.56 0.00 2.92
893 918 1.227645 GAGCATGTCGGCTGGCATA 60.228 57.895 13.35 0.00 45.99 3.14
946 971 4.690719 AATCGTCGTTGCCGGCCA 62.691 61.111 26.77 11.12 34.48 5.36
954 979 2.805671 TGTTCTGCATGAAATCGTCGTT 59.194 40.909 0.00 0.00 36.30 3.85
1031 1077 1.648467 GGCTTTGTGTCTCATCGGGC 61.648 60.000 0.00 0.00 0.00 6.13
1079 1125 1.999648 TGCCAGCTTGATCAAAGGTT 58.000 45.000 9.88 0.00 44.21 3.50
1137 1183 2.797278 CGAGTAGGAAGCCGCCCAT 61.797 63.158 0.00 0.00 0.00 4.00
1172 1218 0.651551 CTTCCTCGAGGTCGTAGTCG 59.348 60.000 30.17 7.80 40.80 4.18
1307 1357 2.092968 ACACTCACAAAGGAGCTTGTCA 60.093 45.455 0.00 0.00 37.43 3.58
1390 1440 0.525668 GAACTCGCGATGGACACGAT 60.526 55.000 10.36 0.00 34.94 3.73
1436 1486 0.451957 CGCGCGTACTTTGCATTTGA 60.452 50.000 24.19 0.00 0.00 2.69
1664 1718 2.206576 AAGCTTGGAAGGCCTACAAG 57.793 50.000 31.28 31.28 43.28 3.16
1752 1806 0.524862 GCCTTGAACGTCTCCTCGTA 59.475 55.000 0.00 0.00 43.38 3.43
1814 1876 3.083997 CCCTCCCCAACCTCCTCG 61.084 72.222 0.00 0.00 0.00 4.63
1847 1909 1.057851 TGGAGTTGGTCTTTCCCCGT 61.058 55.000 0.00 0.00 34.77 5.28
1872 1934 3.197790 CGCATCCCGCTTGTCCTG 61.198 66.667 0.00 0.00 39.08 3.86
1920 1982 2.915604 AGTCCTTCTTGGTCATCATGGT 59.084 45.455 0.00 0.00 37.07 3.55
1921 1983 3.054875 TGAGTCCTTCTTGGTCATCATGG 60.055 47.826 0.00 0.00 37.07 3.66
1971 2033 4.877378 TGAAGGCATTCATTTGCTCTTT 57.123 36.364 10.22 0.00 40.54 2.52
2022 2084 1.630244 CTCGTTTGCTTCTCCGCCTG 61.630 60.000 0.00 0.00 0.00 4.85
2059 2122 2.573462 AGCATCTTGGCTTACTTCTCCA 59.427 45.455 0.00 0.00 42.71 3.86
2067 2130 4.145052 TCGATCTCTAGCATCTTGGCTTA 58.855 43.478 0.00 0.00 42.71 3.09
2204 2267 0.324738 TGTCGGCCTCCATCTTCTCT 60.325 55.000 0.00 0.00 0.00 3.10
2214 2277 0.674895 AACTTGAGCATGTCGGCCTC 60.675 55.000 0.00 0.00 0.00 4.70
2255 2319 3.346426 AAAAAGGATGGCACTCGCT 57.654 47.368 0.00 0.00 38.60 4.93
2311 2382 0.250124 TTGAGTTCGACCACGCCATT 60.250 50.000 0.00 0.00 39.58 3.16
2331 2402 1.005924 AGCACATAAAAGGGGTGGGAG 59.994 52.381 0.00 0.00 33.25 4.30
2345 2419 2.967397 GCACACATGGCAGCACAT 59.033 55.556 0.00 0.00 0.00 3.21
2374 2448 7.970384 CATACGATGCCAACTTTAAAAGACTA 58.030 34.615 0.00 0.00 0.00 2.59
2405 2525 2.887568 GTCGGCACCATGCGAGAG 60.888 66.667 0.00 0.00 46.21 3.20
2407 2527 2.512286 ATGTCGGCACCATGCGAG 60.512 61.111 0.00 0.00 46.21 5.03
2408 2528 2.794820 TTCATGTCGGCACCATGCGA 62.795 55.000 0.00 0.00 46.21 5.10
2409 2529 2.397754 TTCATGTCGGCACCATGCG 61.398 57.895 0.00 0.00 46.21 4.73
2449 2590 0.819259 GCGGCCTTAGATCATGCCAA 60.819 55.000 0.00 0.00 44.22 4.52
2469 2611 2.216898 CGCCCAAATTTGAAAAGCCAA 58.783 42.857 19.86 0.00 0.00 4.52
2472 2614 1.195222 CTGCGCCCAAATTTGAAAAGC 59.805 47.619 19.86 17.34 0.00 3.51
2486 2632 2.076863 GACCCATATTATGTCTGCGCC 58.923 52.381 4.18 0.00 0.00 6.53
2497 2643 1.280710 TCCAACACGCTGACCCATATT 59.719 47.619 0.00 0.00 0.00 1.28
2499 2645 0.036765 GTCCAACACGCTGACCCATA 60.037 55.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.