Multiple sequence alignment - TraesCS2D01G384000

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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 TraesCS2D01G384000 chr2D 100.000 3235 0 0 1 3235 488455207 488451973 0.000000e+00 5975
1 TraesCS2D01G384000 chr2D 94.432 3125 104 24 123 3235 488554431 488551365 0.000000e+00 4743
2 TraesCS2D01G384000 chr2D 93.828 2414 81 23 123 2534 489370570 489368223 0.000000e+00 3570
3 TraesCS2D01G384000 chr2D 87.515 1626 150 25 936 2556 82143733 82145310 0.000000e+00 1829
4 TraesCS2D01G384000 chr2D 84.182 1492 161 38 1232 2684 450992708 450994163 0.000000e+00 1378
5 TraesCS2D01G384000 chr2D 91.865 713 22 6 2528 3235 489367851 489367170 0.000000e+00 963
6 TraesCS2D01G384000 chr2D 93.904 607 32 2 123 725 82142910 82143515 0.000000e+00 911
7 TraesCS2D01G384000 chr2D 87.433 557 51 6 123 660 450991035 450991591 9.860000e-175 623
8 TraesCS2D01G384000 chr2D 80.855 491 52 25 731 1210 450992179 450992638 6.640000e-92 348
9 TraesCS2D01G384000 chr2D 84.838 277 34 7 936 1210 450984494 450984764 4.110000e-69 272
10 TraesCS2D01G384000 chr2D 99.275 138 0 1 1 137 488554593 488554456 6.930000e-62 248
11 TraesCS2D01G384000 chr2D 98.551 138 1 1 1 137 489370732 489370595 3.220000e-60 243
12 TraesCS2D01G384000 chr2D 97.826 138 2 1 1 137 82142748 82142885 1.500000e-58 237
13 TraesCS2D01G384000 chr2D 94.203 138 7 1 1 137 450990873 450991010 3.270000e-50 209
14 TraesCS2D01G384000 chr2D 94.615 130 7 0 2405 2534 489368218 489368089 5.470000e-48 202
15 TraesCS2D01G384000 chr2B 94.863 2453 94 5 123 2574 572706070 572703649 0.000000e+00 3803
16 TraesCS2D01G384000 chr2B 85.773 1961 216 31 936 2891 133980235 133982137 0.000000e+00 2017
17 TraesCS2D01G384000 chr2B 83.333 1494 170 44 1232 2684 531131561 531133016 0.000000e+00 1306
18 TraesCS2D01G384000 chr2B 92.160 676 38 11 2570 3234 572692785 572692114 0.000000e+00 941
19 TraesCS2D01G384000 chr2B 87.253 557 52 6 123 660 531129858 531130414 4.590000e-173 617
20 TraesCS2D01G384000 chr2B 90.351 456 25 5 123 577 133979480 133979917 6.020000e-162 580
21 TraesCS2D01G384000 chr2B 79.800 500 70 18 731 1210 531131003 531131491 5.170000e-88 335
22 TraesCS2D01G384000 chr2B 98.551 138 1 1 1 137 572706232 572706095 3.220000e-60 243
23 TraesCS2D01G384000 chr2B 95.652 138 5 1 1 137 133979318 133979455 1.510000e-53 220
24 TraesCS2D01G384000 chr2B 94.928 138 6 1 1 137 531129696 531129833 7.030000e-52 215
25 TraesCS2D01G384000 chr2B 94.737 76 3 1 616 690 133979914 133979989 2.040000e-22 117
26 TraesCS2D01G384000 chr2A 85.212 1366 146 34 1232 2575 598621591 598620260 0.000000e+00 1352
27 TraesCS2D01G384000 chr2A 87.321 560 52 8 123 663 598623225 598622666 9.860000e-175 623
28 TraesCS2D01G384000 chr2A 80.730 493 55 26 731 1213 598622120 598621658 6.640000e-92 348
29 TraesCS2D01G384000 chr2A 95.652 138 5 1 1 137 598623387 598623250 1.510000e-53 220
30 TraesCS2D01G384000 chr3D 75.635 394 78 16 136 520 390658705 390659089 2.560000e-41 180


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 TraesCS2D01G384000 chr2D 488451973 488455207 3234 True 5975.000000 5975 100.000000 1 3235 1 chr2D.!!$R1 3234
1 TraesCS2D01G384000 chr2D 488551365 488554593 3228 True 2495.500000 4743 96.853500 1 3235 2 chr2D.!!$R2 3234
2 TraesCS2D01G384000 chr2D 489367170 489370732 3562 True 1244.500000 3570 94.714750 1 3235 4 chr2D.!!$R3 3234
3 TraesCS2D01G384000 chr2D 82142748 82145310 2562 False 992.333333 1829 93.081667 1 2556 3 chr2D.!!$F2 2555
4 TraesCS2D01G384000 chr2D 450990873 450994163 3290 False 639.500000 1378 86.668250 1 2684 4 chr2D.!!$F3 2683
5 TraesCS2D01G384000 chr2B 572703649 572706232 2583 True 2023.000000 3803 96.707000 1 2574 2 chr2B.!!$R2 2573
6 TraesCS2D01G384000 chr2B 572692114 572692785 671 True 941.000000 941 92.160000 2570 3234 1 chr2B.!!$R1 664
7 TraesCS2D01G384000 chr2B 133979318 133982137 2819 False 733.500000 2017 91.628250 1 2891 4 chr2B.!!$F1 2890
8 TraesCS2D01G384000 chr2B 531129696 531133016 3320 False 618.250000 1306 86.328500 1 2684 4 chr2B.!!$F2 2683
9 TraesCS2D01G384000 chr2A 598620260 598623387 3127 True 635.750000 1352 87.228750 1 2575 4 chr2A.!!$R1 2574

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
543 600 0.173481 GCGAGGTGCTGTGATACTCA 59.827 55.0 0.0 0.0 41.73 3.41 F
1326 2147 0.519519 CACCGCCGATACTGCAAAAA 59.480 50.0 0.0 0.0 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 2533 0.442699 GGACCGAATGCGAAGTGAAC 59.557 55.000 0.00 0.00 40.82 3.18 R
2698 3966 1.402259 ACCGAGAATGCTCAGTCTACG 59.598 52.381 0.51 6.14 41.36 3.51 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
359 400 3.060000 ACGCCGATGGACTCGTCA 61.060 61.111 0.00 0.00 46.18 4.35
543 600 0.173481 GCGAGGTGCTGTGATACTCA 59.827 55.000 0.00 0.00 41.73 3.41
729 1423 6.147164 TGTTGCTACTGATTTGTGTACTTAGC 59.853 38.462 0.00 0.00 32.94 3.09
873 1639 0.976641 TCTCACTTGCCGATTCCAGT 59.023 50.000 0.00 0.00 0.00 4.00
888 1654 4.320608 TTCCAGTTTGTGCTTCATTTCC 57.679 40.909 0.00 0.00 0.00 3.13
901 1667 5.045872 GCTTCATTTCCACTATTTCATGGC 58.954 41.667 0.00 0.00 35.81 4.40
923 1689 3.923017 GGATCAACAAACTTGGTCCAG 57.077 47.619 7.38 0.00 46.40 3.86
924 1690 3.486383 GGATCAACAAACTTGGTCCAGA 58.514 45.455 7.38 0.00 46.40 3.86
925 1691 3.253432 GGATCAACAAACTTGGTCCAGAC 59.747 47.826 7.38 0.00 46.40 3.51
926 1692 5.817700 GGATCAACAAACTTGGTCCAGACC 61.818 50.000 10.02 10.02 46.40 3.85
934 1700 2.114411 GGTCCAGACCCCGCAAAA 59.886 61.111 5.46 0.00 45.68 2.44
935 1701 1.529713 GGTCCAGACCCCGCAAAAA 60.530 57.895 5.46 0.00 45.68 1.94
1010 1780 9.978044 CTATGTCAAGATTGATATGAAGTCTGA 57.022 33.333 13.24 0.00 39.05 3.27
1089 1859 1.002134 CACACCGGGCATCCTTCTT 60.002 57.895 6.32 0.00 0.00 2.52
1141 1911 2.579201 CTCCCTCAACGTGCGGAT 59.421 61.111 0.00 0.00 0.00 4.18
1196 1966 6.877611 TGAGGAGGTGAGAAAACAAATTAC 57.122 37.500 0.00 0.00 0.00 1.89
1219 2010 6.494842 ACGAATCATTGCCAAATATGTGTAC 58.505 36.000 0.00 0.00 0.00 2.90
1326 2147 0.519519 CACCGCCGATACTGCAAAAA 59.480 50.000 0.00 0.00 0.00 1.94
1410 2231 2.609916 CGAGCGAGTGTTCTCAGAGATA 59.390 50.000 0.00 0.00 40.44 1.98
1573 2400 7.258022 TGTGATAAACAATTGGATACGATGG 57.742 36.000 10.83 0.00 40.96 3.51
1642 2469 2.787473 TGATCTTTTCGGCATCCAGT 57.213 45.000 0.00 0.00 0.00 4.00
1766 2603 9.985730 ATCACAAACATTAGAACAAATGTCAAT 57.014 25.926 2.94 0.00 46.72 2.57
1938 2776 2.294979 TCATAGCGACATACGGACACT 58.705 47.619 0.00 0.00 42.83 3.55
2044 2882 5.013599 GGGAGGAATTATCTCTTGGCATAGT 59.986 44.000 7.83 0.00 0.00 2.12
2134 2972 9.026121 TCATAAGAAGTTTCAGAGCTACTTAGT 57.974 33.333 0.00 0.00 32.58 2.24
2271 3110 8.035394 ACATAATGTAACTTGGTAGAGTGTCTG 58.965 37.037 0.00 0.00 0.00 3.51
2285 3124 1.067142 GTGTCTGGCGAGTTACCATCA 60.067 52.381 0.00 0.00 36.36 3.07
2297 3136 6.021596 CGAGTTACCATCATTAGTGTTTTGC 58.978 40.000 0.00 0.00 0.00 3.68
2334 3173 4.809815 GCATTAGCTCTGAGTTTCCATC 57.190 45.455 6.53 0.00 37.91 3.51
2621 3879 4.776795 TGTCGACTAACTACAGATGCAA 57.223 40.909 17.92 0.00 0.00 4.08
2911 4185 9.300681 ACACATATGGCTAGCAATTACATAAAT 57.699 29.630 18.24 4.63 0.00 1.40
2937 4211 9.282569 TGCTATTTTGCTTATTTGGAAATTTGT 57.717 25.926 0.00 0.00 0.00 2.83
3141 4416 9.158233 CTTGATCCATTCAGCAATACAAATTTT 57.842 29.630 0.00 0.00 35.27 1.82
3142 4417 9.504708 TTGATCCATTCAGCAATACAAATTTTT 57.495 25.926 0.00 0.00 35.27 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 167 4.276739 CGCAGAAGATGAGCGCGC 62.277 66.667 26.66 26.66 45.14 6.86
382 423 1.437772 CGTACTCTGGCGATCCGAGT 61.438 60.000 11.38 11.38 43.46 4.18
543 600 4.336713 ACGAAAAAGAGAGCAAAGAAAGCT 59.663 37.500 0.00 0.00 46.82 3.74
729 1423 8.241367 ACTATGCTTTTTACCAGTTAATTTCCG 58.759 33.333 0.00 0.00 0.00 4.30
768 1462 0.249238 TTTGTTTTCATGGCGCGCTT 60.249 45.000 32.29 16.45 0.00 4.68
873 1639 7.048629 TGAAATAGTGGAAATGAAGCACAAA 57.951 32.000 0.00 0.00 0.00 2.83
888 1654 4.641541 TGTTGATCCAGCCATGAAATAGTG 59.358 41.667 0.00 0.00 0.00 2.74
901 1667 3.221771 TGGACCAAGTTTGTTGATCCAG 58.778 45.455 0.00 0.00 31.25 3.86
1010 1780 4.012374 GGCATCATACCCATCGATTTCAT 58.988 43.478 0.00 0.00 0.00 2.57
1089 1859 9.625747 TGGAGCTTATACAATGATTTGTTCATA 57.374 29.630 0.00 0.00 44.51 2.15
1196 1966 6.634035 CAGTACACATATTTGGCAATGATTCG 59.366 38.462 0.00 0.00 0.00 3.34
1410 2231 4.612264 ATTGACAAGCCTTTTCATTGCT 57.388 36.364 0.00 0.00 36.79 3.91
1573 2400 1.977009 GGGGTAGTTGCTTGTGCCC 60.977 63.158 0.00 0.00 38.71 5.36
1642 2469 1.841556 AAGCACAACCTCCCCTCGA 60.842 57.895 0.00 0.00 0.00 4.04
1706 2533 0.442699 GGACCGAATGCGAAGTGAAC 59.557 55.000 0.00 0.00 40.82 3.18
1707 2534 1.011968 CGGACCGAATGCGAAGTGAA 61.012 55.000 8.64 0.00 46.80 3.18
1798 2635 7.149569 TGAAAATTTTGTGATGGCAAACAAA 57.850 28.000 21.18 21.18 42.82 2.83
1799 2636 6.183360 CCTGAAAATTTTGTGATGGCAAACAA 60.183 34.615 8.47 13.30 37.98 2.83
1901 2739 0.606096 TGAACTCGATGGCGGAAAGA 59.394 50.000 0.00 0.00 38.28 2.52
1938 2776 2.248280 TTGTACAAAGCGAGGAAGCA 57.752 45.000 5.64 0.00 40.15 3.91
2044 2882 7.816995 GCTGGTCATTATTTTGTTTCAATGGTA 59.183 33.333 0.00 0.00 0.00 3.25
2271 3110 3.793559 ACACTAATGATGGTAACTCGCC 58.206 45.455 0.00 0.00 37.61 5.54
2285 3124 7.843490 ACGTGTATATCAGCAAAACACTAAT 57.157 32.000 0.00 0.00 38.59 1.73
2407 3247 8.579006 TCAACAAAGAAATAGATCAGCACAAAT 58.421 29.630 0.00 0.00 0.00 2.32
2425 3265 7.816945 AACAAAAGTGTTCTGATCAACAAAG 57.183 32.000 1.79 0.00 45.00 2.77
2526 3510 3.610040 ACAAATGCACCGAGACATAGA 57.390 42.857 0.00 0.00 0.00 1.98
2621 3879 5.771165 TGATGGCATCATTTACTATGTGCAT 59.229 36.000 25.63 0.00 33.59 3.96
2692 3960 3.921021 AGAATGCTCAGTCTACGAAAACG 59.079 43.478 0.00 0.00 33.56 3.60
2698 3966 1.402259 ACCGAGAATGCTCAGTCTACG 59.598 52.381 0.51 6.14 41.36 3.51
2778 4046 7.630242 TTGAAATTTGGTCATATGAGGACTC 57.370 36.000 5.42 0.00 35.61 3.36
2911 4185 9.282569 ACAAATTTCCAAATAAGCAAAATAGCA 57.717 25.926 0.00 0.00 36.85 3.49
2937 4211 9.366216 CGCCAAGTATATTCTTATGTAATAGCA 57.634 33.333 0.00 0.00 0.00 3.49
2968 4242 4.489810 TCACGTTTGTGTTGCAGAATTTT 58.510 34.783 0.00 0.00 46.49 1.82
3045 4319 9.685828 TGTAGAATTTAGTTTTGTATTGTTGCC 57.314 29.630 0.00 0.00 0.00 4.52
3141 4416 8.756927 TGGATGGATCAAGTTTTTATATTGCAA 58.243 29.630 0.00 0.00 0.00 4.08
3142 4417 8.303780 TGGATGGATCAAGTTTTTATATTGCA 57.696 30.769 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.