Multiple sequence alignment - TraesCS2D01G088100

Loading Multiple Alignment...

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 TraesCS2D01G088100 chr2D 100.000 2591 0 0 1 2591 38185612 38183022 0.000000e+00 4785
1 TraesCS2D01G088100 chr2D 80.117 342 51 8 4 339 38259405 38259075 3.330000e-59 239
2 TraesCS2D01G088100 chr2D 90.667 150 13 1 2443 2591 38129082 38128933 5.660000e-47 198
3 TraesCS2D01G088100 chr2B 90.460 2631 137 53 4 2580 66719445 66716875 0.000000e+00 3363
4 TraesCS2D01G088100 chr2B 91.837 147 11 1 2443 2588 66664625 66664479 1.220000e-48 204
5 TraesCS2D01G088100 chr2B 84.173 139 18 3 4 141 67210342 67210207 5.820000e-27 132
6 TraesCS2D01G088100 chr2A 94.746 1142 51 3 546 1680 43180966 43179827 0.000000e+00 1768
7 TraesCS2D01G088100 chr2A 92.337 783 42 5 1819 2591 43178813 43178039 0.000000e+00 1098
8 TraesCS2D01G088100 chr2A 94.118 544 22 7 4 541 43181679 43181140 0.000000e+00 819
9 TraesCS2D01G088100 chr2A 87.525 505 34 12 1575 2057 43163001 43162504 8.100000e-155 556
10 TraesCS2D01G088100 chr2A 98.765 81 1 0 1712 1792 43179830 43179750 7.470000e-31 145


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 TraesCS2D01G088100 chr2D 38183022 38185612 2590 True 4785.0 4785 100.0000 1 2591 1 chr2D.!!$R2 2590
1 TraesCS2D01G088100 chr2B 66716875 66719445 2570 True 3363.0 3363 90.4600 4 2580 1 chr2B.!!$R2 2576
2 TraesCS2D01G088100 chr2A 43178039 43181679 3640 True 957.5 1768 94.9915 4 2591 4 chr2A.!!$R2 2587

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
973 1158 2.680312 TCCACTACATCAAGCAGCTC 57.32 50.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2566 3697 1.000385 TCATTTTGCCTTGCCAGTTCG 60.0 47.619 0.0 0.0 0.0 3.95 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
131 132 8.393366 CACAATGGAAGACAAATGTATGTAGAG 58.607 37.037 0.00 0.00 33.49 2.43
132 133 7.554118 ACAATGGAAGACAAATGTATGTAGAGG 59.446 37.037 0.00 0.00 33.17 3.69
290 293 4.752101 CGAGACAGAAGGACAACAAATTCT 59.248 41.667 0.00 0.00 32.31 2.40
334 337 4.927422 TGCCTACACACTTTTGCTTTTAC 58.073 39.130 0.00 0.00 0.00 2.01
440 448 2.684943 TGGGGACAACACAGACTTCTA 58.315 47.619 0.00 0.00 37.44 2.10
475 483 3.269178 CTGCCCATCTGAACTTCTCTTC 58.731 50.000 0.00 0.00 0.00 2.87
481 489 5.942236 CCCATCTGAACTTCTCTTCATTCAA 59.058 40.000 0.00 0.00 31.00 2.69
484 492 6.551385 TCTGAACTTCTCTTCATTCAAAGC 57.449 37.500 0.00 0.00 31.00 3.51
506 514 3.606687 GGAACAAGTCCAACATATCCGT 58.393 45.455 0.00 0.00 46.97 4.69
586 763 4.751600 ACAGCTAAAGCAAAGGCATTTTTC 59.248 37.500 4.54 0.00 45.16 2.29
604 781 6.843069 TTTTTCTTTTTAGCACATTGGAGC 57.157 33.333 0.00 0.00 0.00 4.70
923 1108 5.352284 AGCATATATATAACACGCAGAGCC 58.648 41.667 0.00 0.00 0.00 4.70
973 1158 2.680312 TCCACTACATCAAGCAGCTC 57.320 50.000 0.00 0.00 0.00 4.09
1601 1803 5.971763 ACTCCTTGATTAAGTGTGCTAGAG 58.028 41.667 0.00 0.00 31.80 2.43
1607 1809 2.921634 TAAGTGTGCTAGAGCTGTCG 57.078 50.000 2.72 0.00 42.66 4.35
1685 1888 1.541233 CCACTTGAGAGCTCCGTTTGT 60.541 52.381 10.93 0.47 0.00 2.83
1693 1896 2.007608 GAGCTCCGTTTGTGATTACCC 58.992 52.381 0.87 0.00 0.00 3.69
1706 1909 5.258051 TGTGATTACCCCTTGATTTGTACC 58.742 41.667 0.00 0.00 0.00 3.34
1708 1911 2.406596 TACCCCTTGATTTGTACCGC 57.593 50.000 0.00 0.00 0.00 5.68
1713 1916 2.614057 CCCTTGATTTGTACCGCATCTC 59.386 50.000 0.00 0.00 0.00 2.75
1772 1975 6.743627 CACATTTGATGCAATAAATTTGGCAC 59.256 34.615 13.79 9.79 39.34 5.01
1792 1999 4.641989 GCACAGGATGGTTGTTCAATAGAT 59.358 41.667 0.00 0.00 43.62 1.98
1793 2000 5.449588 GCACAGGATGGTTGTTCAATAGATG 60.450 44.000 0.00 0.00 43.62 2.90
1795 2002 6.544931 CACAGGATGGTTGTTCAATAGATGAT 59.455 38.462 0.00 0.00 43.62 2.45
1796 2003 6.544931 ACAGGATGGTTGTTCAATAGATGATG 59.455 38.462 0.00 0.00 43.62 3.07
1797 2004 6.016527 CAGGATGGTTGTTCAATAGATGATGG 60.017 42.308 0.00 0.00 38.03 3.51
1798 2005 5.829924 GGATGGTTGTTCAATAGATGATGGT 59.170 40.000 0.00 0.00 38.03 3.55
1799 2006 6.322201 GGATGGTTGTTCAATAGATGATGGTT 59.678 38.462 0.00 0.00 38.03 3.67
1800 2007 6.513806 TGGTTGTTCAATAGATGATGGTTG 57.486 37.500 0.00 0.00 38.03 3.77
1802 2009 5.418840 GGTTGTTCAATAGATGATGGTTGGT 59.581 40.000 0.00 0.00 38.03 3.67
1805 2012 6.244654 TGTTCAATAGATGATGGTTGGTCAA 58.755 36.000 0.00 0.00 38.03 3.18
1806 2013 6.891361 TGTTCAATAGATGATGGTTGGTCAAT 59.109 34.615 0.00 0.00 38.03 2.57
1807 2014 7.067372 TGTTCAATAGATGATGGTTGGTCAATC 59.933 37.037 0.00 0.00 38.03 2.67
1808 2015 6.903516 TCAATAGATGATGGTTGGTCAATCT 58.096 36.000 0.00 0.00 31.50 2.40
1811 2018 9.293404 CAATAGATGATGGTTGGTCAATCTATT 57.707 33.333 9.01 9.01 37.18 1.73
1812 2019 9.872684 AATAGATGATGGTTGGTCAATCTATTT 57.127 29.630 9.01 0.00 35.63 1.40
1955 3077 6.857964 ACGATCAAAGAAGCACAATAAAAGTG 59.142 34.615 0.00 0.00 39.92 3.16
1971 3093 9.766277 CAATAAAAGTGAAGATTCAACTCTAGC 57.234 33.333 0.00 0.00 39.21 3.42
2012 3134 5.786401 ACTTATGACGAAATCAAGTGAGC 57.214 39.130 0.00 0.00 41.93 4.26
2013 3135 5.482908 ACTTATGACGAAATCAAGTGAGCT 58.517 37.500 0.00 0.00 41.93 4.09
2014 3136 5.934625 ACTTATGACGAAATCAAGTGAGCTT 59.065 36.000 0.00 0.00 41.93 3.74
2040 3167 6.476380 GTCTCTCTTATGTTCTGCTCATGAAG 59.524 42.308 0.00 0.00 0.00 3.02
2092 3219 1.064463 AGCATAATGTCCAGGGTGGTG 60.064 52.381 0.00 0.00 39.03 4.17
2109 3236 4.462483 GGTGGTGATGTAACAATCATGGTT 59.538 41.667 0.00 0.00 38.76 3.67
2217 3344 5.471116 TGTAGACGTCTGTTACAGAAGCTAA 59.529 40.000 28.12 9.76 42.46 3.09
2266 3393 0.609131 AGTGGTGTAAGTGCCATGGC 60.609 55.000 30.54 30.54 37.09 4.40
2276 3403 2.276740 GCCATGGCTGTAGGGCTT 59.723 61.111 29.98 0.00 43.81 4.35
2277 3404 1.531748 GCCATGGCTGTAGGGCTTA 59.468 57.895 29.98 0.00 43.81 3.09
2278 3405 0.536006 GCCATGGCTGTAGGGCTTAG 60.536 60.000 29.98 0.00 43.81 2.18
2279 3406 0.536006 CCATGGCTGTAGGGCTTAGC 60.536 60.000 0.00 0.00 41.48 3.09
2280 3407 0.181114 CATGGCTGTAGGGCTTAGCA 59.819 55.000 6.53 0.00 39.15 3.49
2281 3408 0.918983 ATGGCTGTAGGGCTTAGCAA 59.081 50.000 6.53 0.00 39.15 3.91
2282 3409 0.253044 TGGCTGTAGGGCTTAGCAAG 59.747 55.000 6.53 0.00 39.15 4.01
2352 3481 7.201376 CGGATTCAATTCATAAAGTGCAAACAG 60.201 37.037 0.00 0.00 30.66 3.16
2367 3496 7.305474 AGTGCAAACAGTTTAAAAGATATCCG 58.695 34.615 0.00 0.00 0.00 4.18
2401 3530 9.892130 TTAGAGAATTTTCCTGGTCTAAAGATC 57.108 33.333 0.00 0.00 0.00 2.75
2493 3624 7.817418 TTTAACATGGTTGCTAGAGTTCTTT 57.183 32.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.969260 TTATCTCTTGCAGATCAATAATGTGT 57.031 30.769 0.00 0.00 41.39 3.72
148 149 5.623956 TCTTTGACCAGTAAGGACTTTCA 57.376 39.130 0.00 0.00 41.22 2.69
252 254 8.973378 CCTTCTGTCTCGAGAATCAATATTTAC 58.027 37.037 18.55 0.83 31.51 2.01
253 255 8.914011 TCCTTCTGTCTCGAGAATCAATATTTA 58.086 33.333 18.55 0.00 31.51 1.40
290 293 6.036953 GGCATCAATCAACAACAAAAACAAGA 59.963 34.615 0.00 0.00 0.00 3.02
334 337 6.100404 TGGATTGACCAGGATTTTTGAAAG 57.900 37.500 0.00 0.00 44.64 2.62
449 457 3.840666 AGAAGTTCAGATGGGCAGTTCTA 59.159 43.478 5.50 0.00 0.00 2.10
475 483 2.933769 GGACTTGTTCCGCTTTGAATG 58.066 47.619 0.00 0.00 33.46 2.67
499 507 1.686587 TCTGATTGTCGCCACGGATAT 59.313 47.619 0.00 0.00 0.00 1.63
506 514 4.009002 TGATGAATTTCTGATTGTCGCCA 58.991 39.130 0.00 0.00 0.00 5.69
586 763 2.253603 GCGCTCCAATGTGCTAAAAAG 58.746 47.619 0.00 0.00 40.01 2.27
754 939 3.028130 GGAGTGGTTTCCAGTTTTCCAA 58.972 45.455 0.00 0.00 37.30 3.53
875 1060 1.265635 GGTGCGTGCAATTGTGAGTTA 59.734 47.619 7.40 0.00 0.00 2.24
879 1064 1.794151 CTGGGTGCGTGCAATTGTGA 61.794 55.000 7.40 0.00 0.00 3.58
884 1069 2.360350 CTCCTGGGTGCGTGCAAT 60.360 61.111 0.00 0.00 0.00 3.56
923 1108 2.496070 TGGTTTACTGAGTCCTGATCGG 59.504 50.000 0.00 0.00 0.00 4.18
989 1174 0.027194 CTTCATCATTGGCGTGCGAG 59.973 55.000 0.00 0.00 0.00 5.03
992 1177 1.672363 TCATCTTCATCATTGGCGTGC 59.328 47.619 0.00 0.00 0.00 5.34
994 1179 1.935873 CGTCATCTTCATCATTGGCGT 59.064 47.619 0.00 0.00 32.88 5.68
996 1181 1.672363 TGCGTCATCTTCATCATTGGC 59.328 47.619 0.00 0.00 0.00 4.52
998 1183 2.604462 TCGTGCGTCATCTTCATCATTG 59.396 45.455 0.00 0.00 0.00 2.82
999 1184 2.604914 GTCGTGCGTCATCTTCATCATT 59.395 45.455 0.00 0.00 0.00 2.57
1591 1793 0.456995 GACCGACAGCTCTAGCACAC 60.457 60.000 4.54 0.00 45.16 3.82
1607 1809 1.165270 CAAGAATGAACGGTGGGACC 58.835 55.000 0.00 0.00 34.05 4.46
1685 1888 4.519213 CGGTACAAATCAAGGGGTAATCA 58.481 43.478 0.00 0.00 0.00 2.57
1693 1896 2.614057 GGAGATGCGGTACAAATCAAGG 59.386 50.000 0.00 0.00 0.00 3.61
1706 1909 3.624410 TCACAAATGAATCAGGAGATGCG 59.376 43.478 0.00 0.00 31.86 4.73
1708 1911 6.754702 AAGTCACAAATGAATCAGGAGATG 57.245 37.500 0.00 0.00 36.31 2.90
1713 1916 5.846203 ACCAAAAGTCACAAATGAATCAGG 58.154 37.500 0.00 0.00 36.31 3.86
1772 1975 6.016527 CCATCATCTATTGAACAACCATCCTG 60.017 42.308 0.00 0.00 38.03 3.86
1805 2012 9.784531 CACTGGGATACATAAAGTCAAATAGAT 57.215 33.333 0.00 0.00 39.74 1.98
1806 2013 8.988060 TCACTGGGATACATAAAGTCAAATAGA 58.012 33.333 0.00 0.00 39.74 1.98
1807 2014 9.784531 ATCACTGGGATACATAAAGTCAAATAG 57.215 33.333 0.00 0.00 33.37 1.73
1811 2018 7.861629 AGAATCACTGGGATACATAAAGTCAA 58.138 34.615 0.00 0.00 34.28 3.18
1812 2019 7.437713 AGAATCACTGGGATACATAAAGTCA 57.562 36.000 0.00 0.00 34.28 3.41
1815 2022 8.834465 CAGAAAGAATCACTGGGATACATAAAG 58.166 37.037 0.00 0.00 34.28 1.85
1816 2023 8.548025 TCAGAAAGAATCACTGGGATACATAAA 58.452 33.333 0.00 0.00 34.28 1.40
1817 2024 7.987458 GTCAGAAAGAATCACTGGGATACATAA 59.013 37.037 0.00 0.00 34.28 1.90
1818 2025 7.345653 AGTCAGAAAGAATCACTGGGATACATA 59.654 37.037 0.00 0.00 34.28 2.29
1821 2028 5.983540 AGTCAGAAAGAATCACTGGGATAC 58.016 41.667 0.00 0.00 34.28 2.24
1955 3077 9.825109 ATTAACCTTAGCTAGAGTTGAATCTTC 57.175 33.333 16.61 0.00 0.00 2.87
2012 3134 5.718146 TGAGCAGAACATAAGAGAGACAAG 58.282 41.667 0.00 0.00 0.00 3.16
2013 3135 5.728637 TGAGCAGAACATAAGAGAGACAA 57.271 39.130 0.00 0.00 0.00 3.18
2014 3136 5.420104 TCATGAGCAGAACATAAGAGAGACA 59.580 40.000 0.00 0.00 0.00 3.41
2015 3137 5.900425 TCATGAGCAGAACATAAGAGAGAC 58.100 41.667 0.00 0.00 0.00 3.36
2016 3138 6.406737 CCTTCATGAGCAGAACATAAGAGAGA 60.407 42.308 0.00 0.00 0.00 3.10
2040 3167 5.200483 TGGACATAATGTTCAGGGAAATCC 58.800 41.667 0.00 0.00 29.19 3.01
2092 3219 7.995289 TGACCATTAACCATGATTGTTACATC 58.005 34.615 0.00 0.00 34.31 3.06
2123 3250 6.780522 TCCTTTCTGTGTTTAAAAATAGGGCT 59.219 34.615 2.62 0.00 0.00 5.19
2134 3261 6.472887 CCTACCTCAATCCTTTCTGTGTTTA 58.527 40.000 0.00 0.00 0.00 2.01
2192 3319 3.913163 GCTTCTGTAACAGACGTCTACAC 59.087 47.826 19.57 15.87 40.46 2.90
2266 3393 3.198872 GCTAACTTGCTAAGCCCTACAG 58.801 50.000 0.00 0.00 0.00 2.74
2278 3405 4.037208 ACATATTGGAGCATGCTAACTTGC 59.963 41.667 22.74 6.74 45.00 4.01
2279 3406 5.762825 ACATATTGGAGCATGCTAACTTG 57.237 39.130 22.74 15.43 0.00 3.16
2280 3407 5.887598 TGAACATATTGGAGCATGCTAACTT 59.112 36.000 22.74 9.00 0.00 2.66
2281 3408 5.439721 TGAACATATTGGAGCATGCTAACT 58.560 37.500 22.74 9.00 0.00 2.24
2282 3409 5.756195 TGAACATATTGGAGCATGCTAAC 57.244 39.130 22.74 17.25 0.00 2.34
2325 3454 5.895636 TGCACTTTATGAATTGAATCCGT 57.104 34.783 0.00 0.00 0.00 4.69
2493 3624 2.852449 AGGGAATGCCAAGGTTCATAGA 59.148 45.455 0.00 0.00 35.15 1.98
2566 3697 1.000385 TCATTTTGCCTTGCCAGTTCG 60.000 47.619 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.