Multiple sequence alignment - TraesCS3D01G198600

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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 TraesCS3D01G198600 chr3D 100.000 3185 0 0 1 3185 213995926 213999110 0.000000e+00 5882.0
1 TraesCS3D01G198600 chr3D 77.500 280 33 16 2653 2903 281948697 281948419 1.190000e-29 141.0
2 TraesCS3D01G198600 chr3A 95.879 3179 84 18 1 3162 279437890 279434742 0.000000e+00 5101.0
3 TraesCS3D01G198600 chr3B 97.151 2668 53 5 1 2664 330801910 330799262 0.000000e+00 4484.0
4 TraesCS3D01G198600 chr3B 85.311 531 48 11 2659 3161 330782824 330782296 3.640000e-144 521.0
5 TraesCS3D01G198600 chr3B 76.682 223 28 10 2669 2871 366344186 366344404 5.620000e-18 102.0
6 TraesCS3D01G198600 chr6B 88.191 1194 139 2 996 2188 500894262 500895454 0.000000e+00 1423.0
7 TraesCS3D01G198600 chr6D 88.107 1194 140 2 996 2188 322586944 322585752 0.000000e+00 1417.0
8 TraesCS3D01G198600 chr6D 87.678 1193 145 2 996 2187 322572245 322571054 0.000000e+00 1387.0
9 TraesCS3D01G198600 chr6D 82.939 1184 194 7 1009 2186 136129501 136128320 0.000000e+00 1061.0
10 TraesCS3D01G198600 chr6A 87.782 1195 142 4 996 2188 460006370 460005178 0.000000e+00 1395.0
11 TraesCS3D01G198600 chr6A 87.594 1193 146 2 996 2187 459878385 459877194 0.000000e+00 1382.0
12 TraesCS3D01G198600 chr6A 83.065 1181 195 4 1010 2186 177265014 177266193 0.000000e+00 1068.0
13 TraesCS3D01G198600 chr7A 81.567 217 31 7 2659 2871 533600513 533600302 1.520000e-38 171.0
14 TraesCS3D01G198600 chr7A 79.825 228 26 9 2663 2871 143967000 143967226 7.120000e-32 148.0
15 TraesCS3D01G198600 chr4D 79.926 269 25 14 2661 2905 6076630 6076893 1.520000e-38 171.0
16 TraesCS3D01G198600 chr4D 93.023 43 3 0 2859 2901 242375679 242375721 2.650000e-06 63.9
17 TraesCS3D01G198600 chr1A 82.990 194 25 5 2662 2851 370499489 370499678 5.460000e-38 169.0
18 TraesCS3D01G198600 chr1B 78.755 273 29 15 2660 2903 581659299 581659027 4.250000e-34 156.0
19 TraesCS3D01G198600 chr1B 77.941 272 32 15 2660 2903 415079473 415079202 9.210000e-31 145.0
20 TraesCS3D01G198600 chr1B 76.623 231 29 9 2662 2871 214112490 214112716 1.560000e-18 104.0
21 TraesCS3D01G198600 chr4B 78.388 273 30 16 2660 2903 49711702 49711430 1.980000e-32 150.0
22 TraesCS3D01G198600 chr4B 77.174 276 31 18 2657 2903 565895086 565895358 7.170000e-27 132.0
23 TraesCS3D01G198600 chr7B 77.338 278 32 18 2657 2903 601168853 601169130 5.540000e-28 135.0
24 TraesCS3D01G198600 chr7B 78.512 242 25 11 2650 2871 80387196 80386962 1.990000e-27 134.0
25 TraesCS3D01G198600 chr7B 78.512 242 25 9 2650 2871 80433366 80433132 1.990000e-27 134.0
26 TraesCS3D01G198600 chr5B 76.557 273 34 15 2661 2904 298458974 298458703 4.310000e-24 122.0
27 TraesCS3D01G198600 chrUn 75.285 263 36 14 2664 2897 55606171 55606433 7.270000e-17 99.0
28 TraesCS3D01G198600 chr7D 93.023 43 3 0 2859 2901 427517175 427517217 2.650000e-06 63.9


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 TraesCS3D01G198600 chr3D 213995926 213999110 3184 False 5882 5882 100.000 1 3185 1 chr3D.!!$F1 3184
1 TraesCS3D01G198600 chr3A 279434742 279437890 3148 True 5101 5101 95.879 1 3162 1 chr3A.!!$R1 3161
2 TraesCS3D01G198600 chr3B 330799262 330801910 2648 True 4484 4484 97.151 1 2664 1 chr3B.!!$R2 2663
3 TraesCS3D01G198600 chr3B 330782296 330782824 528 True 521 521 85.311 2659 3161 1 chr3B.!!$R1 502
4 TraesCS3D01G198600 chr6B 500894262 500895454 1192 False 1423 1423 88.191 996 2188 1 chr6B.!!$F1 1192
5 TraesCS3D01G198600 chr6D 322585752 322586944 1192 True 1417 1417 88.107 996 2188 1 chr6D.!!$R3 1192
6 TraesCS3D01G198600 chr6D 322571054 322572245 1191 True 1387 1387 87.678 996 2187 1 chr6D.!!$R2 1191
7 TraesCS3D01G198600 chr6D 136128320 136129501 1181 True 1061 1061 82.939 1009 2186 1 chr6D.!!$R1 1177
8 TraesCS3D01G198600 chr6A 460005178 460006370 1192 True 1395 1395 87.782 996 2188 1 chr6A.!!$R2 1192
9 TraesCS3D01G198600 chr6A 459877194 459878385 1191 True 1382 1382 87.594 996 2187 1 chr6A.!!$R1 1191
10 TraesCS3D01G198600 chr6A 177265014 177266193 1179 False 1068 1068 83.065 1010 2186 1 chr6A.!!$F1 1176

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
282 286 1.306997 TGAGCCCTTCCCACCCTAG 60.307 63.158 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2206 2219 1.381928 CGGCAGCAGCAGGAATGATT 61.382 55.0 2.65 0.0 44.61 2.57 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
190 191 5.475719 TCTGCTGCTATAAAAACTACGTGT 58.524 37.500 0.00 0.00 0.00 4.49
282 286 1.306997 TGAGCCCTTCCCACCCTAG 60.307 63.158 0.00 0.00 0.00 3.02
765 774 6.494893 TCGAGTAGACCAATTGGAATTTTG 57.505 37.500 31.22 14.59 38.94 2.44
768 777 3.317603 AGACCAATTGGAATTTTGGCG 57.682 42.857 31.22 0.28 45.13 5.69
825 834 4.489810 CTTCACTTCGACTGATGTAAGCT 58.510 43.478 0.00 0.00 31.79 3.74
910 919 3.872511 TTAGCATTTTGTGGGCATCTG 57.127 42.857 0.00 0.00 0.00 2.90
1191 1200 2.034066 ATCACCACCAAGGCCACG 59.966 61.111 5.01 0.00 43.14 4.94
1266 1275 0.742505 ATGATGTTGGCCTTGATGCG 59.257 50.000 3.32 0.00 0.00 4.73
2100 2113 0.321653 ACAGGTTCATCAAGACGGCC 60.322 55.000 0.00 0.00 0.00 6.13
2206 2219 3.532232 AGAGGTGGGTATGAAGGAGTCTA 59.468 47.826 0.00 0.00 0.00 2.59
2311 2324 1.228094 TGGACACGCTGAATTGGCA 60.228 52.632 0.00 0.00 0.00 4.92
2337 2350 8.096621 TCTAGTGATTGGTATTTTGGTATGGA 57.903 34.615 0.00 0.00 0.00 3.41
2396 2409 5.911838 GTCTTTTGATGTCTTCTGTGCTTTC 59.088 40.000 0.00 0.00 0.00 2.62
2460 2473 0.818445 TCCTCTATCGGTCGTCCAGC 60.818 60.000 0.00 0.00 0.00 4.85
2549 2562 2.226674 GCTTGGTGCAGTCTTAACCTTC 59.773 50.000 0.00 0.00 42.31 3.46
2581 2594 3.195825 AGTTTGAGCGATAAGGTAGTGCT 59.804 43.478 0.00 0.00 38.89 4.40
2586 2599 3.522553 AGCGATAAGGTAGTGCTGTTTC 58.477 45.455 0.00 0.00 33.99 2.78
2631 2644 2.416547 CTCGATGTTTGCTACCCTGTTG 59.583 50.000 0.00 0.00 0.00 3.33
2644 2657 4.396357 ACCCTGTTGTTCCCAATTCATA 57.604 40.909 0.00 0.00 32.11 2.15
2711 2735 9.686683 ACTTTAGCAAAGATTATCACACCTAAT 57.313 29.630 13.35 0.00 41.02 1.73
2736 2760 6.013206 TGTTAGGCAAGTTTGACCCTTAGATA 60.013 38.462 0.00 0.00 36.67 1.98
2738 2762 5.501156 AGGCAAGTTTGACCCTTAGATAAG 58.499 41.667 0.00 0.00 36.67 1.73
2748 2773 5.929992 TGACCCTTAGATAAGTGTTTGTTCG 59.070 40.000 0.00 0.00 0.00 3.95
2760 2785 1.400494 GTTTGTTCGAGCCACAGTTGT 59.600 47.619 0.00 0.00 0.00 3.32
2763 2788 1.014352 GTTCGAGCCACAGTTGTGTT 58.986 50.000 11.02 0.00 44.21 3.32
2787 2812 4.805192 CCATATGGCATACACACAAAAAGC 59.195 41.667 9.29 0.00 0.00 3.51
2788 2813 5.409211 CATATGGCATACACACAAAAAGCA 58.591 37.500 9.83 0.00 0.00 3.91
2801 2826 6.797995 CACACAAAAAGCATGGCAATATTTTC 59.202 34.615 0.00 0.00 0.00 2.29
2808 2833 4.039609 AGCATGGCAATATTTTCTTAGGCC 59.960 41.667 0.00 0.00 40.29 5.19
2881 2930 4.202141 TGGCAAAATATGTCAATGCTAGGC 60.202 41.667 0.00 0.00 41.69 3.93
2897 2947 1.068121 AGGCCTAGAACCAAACAGCT 58.932 50.000 1.29 0.00 0.00 4.24
2978 3029 1.246649 TTGGCAATCACTCGTGCATT 58.753 45.000 0.00 0.00 42.74 3.56
3002 3053 8.706492 TTAAAATATCAGGCTGAATTTGCTTG 57.294 30.769 22.84 9.23 38.60 4.01
3061 3114 0.602638 CATTAGCGGCCTATTGCGGA 60.603 55.000 0.00 0.00 42.55 5.54
3112 3165 8.396272 TCAAGTTTTGGATTTTTCAAAAACCA 57.604 26.923 9.34 9.34 45.42 3.67
3139 3192 1.133513 TGGAGCTTGGCCTTCAAAAGA 60.134 47.619 3.32 0.00 34.56 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 191 1.290431 TGAAGTGGGTACGGGGGTATA 59.710 52.381 0.00 0.00 0.00 1.47
282 286 1.084370 AGAGACGCGCAGTAATTGGC 61.084 55.000 5.73 0.00 0.00 4.52
470 478 5.848921 AGCAAGACTATTCCCAATATCTCCT 59.151 40.000 0.00 0.00 0.00 3.69
635 644 1.401931 CGGATCTTTTGTGCAGGCAAG 60.402 52.381 0.00 0.00 0.00 4.01
765 774 5.106908 GCTCAATTAAAGAGATGTATCCGCC 60.107 44.000 11.30 0.00 35.09 6.13
768 777 8.589335 TTACGCTCAATTAAAGAGATGTATCC 57.411 34.615 11.30 0.00 35.09 2.59
910 919 8.515414 AGATTTAGAACTCCACAGCAAATTTAC 58.485 33.333 0.00 0.00 0.00 2.01
1191 1200 4.033358 CGCACAATCTTCTCATAGTCAACC 59.967 45.833 0.00 0.00 0.00 3.77
2206 2219 1.381928 CGGCAGCAGCAGGAATGATT 61.382 55.000 2.65 0.00 44.61 2.57
2311 2324 8.723365 TCCATACCAAAATACCAATCACTAGAT 58.277 33.333 0.00 0.00 35.53 1.98
2396 2409 8.587111 GTTTCAGTAGACTCAAAAAGCAAAAAG 58.413 33.333 0.00 0.00 0.00 2.27
2581 2594 2.418368 AACCTGCACTGACAGAAACA 57.582 45.000 10.08 3.21 40.25 2.83
2586 2599 1.102809 TGCCAAACCTGCACTGACAG 61.103 55.000 0.00 0.00 37.42 3.51
2631 2644 5.063817 GCAACAAGCATTATGAATTGGGAAC 59.936 40.000 12.78 0.41 44.79 3.62
2711 2735 3.306472 AAGGGTCAAACTTGCCTAACA 57.694 42.857 0.00 0.00 0.00 2.41
2736 2760 1.670811 CTGTGGCTCGAACAAACACTT 59.329 47.619 0.00 0.00 33.44 3.16
2738 2762 1.014352 ACTGTGGCTCGAACAAACAC 58.986 50.000 0.00 0.00 0.00 3.32
2763 2788 5.394005 GCTTTTTGTGTGTATGCCATATGGA 60.394 40.000 26.47 10.92 37.39 3.41
2787 2812 4.549458 CGGCCTAAGAAAATATTGCCATG 58.451 43.478 0.00 0.00 37.25 3.66
2788 2813 3.005791 GCGGCCTAAGAAAATATTGCCAT 59.994 43.478 0.00 0.00 37.25 4.40
2801 2826 1.369625 CCACAAGTTAGCGGCCTAAG 58.630 55.000 0.00 0.00 34.35 2.18
2808 2833 3.559238 AATGAAAGCCACAAGTTAGCG 57.441 42.857 0.00 0.00 0.00 4.26
2855 2904 5.410355 AGCATTGACATATTTTGCCAAGT 57.590 34.783 0.00 0.00 30.79 3.16
2867 2916 3.181450 GGTTCTAGGCCTAGCATTGACAT 60.181 47.826 31.76 0.00 33.32 3.06
2870 2919 2.477245 TGGTTCTAGGCCTAGCATTGA 58.523 47.619 31.76 14.26 33.32 2.57
2881 2930 4.553330 TTAGGAGCTGTTTGGTTCTAGG 57.447 45.455 0.00 0.00 35.84 3.02
2897 2947 9.751542 GAAACTCGATATTGAAGAGATTTAGGA 57.248 33.333 0.00 0.00 36.03 2.94
2926 2976 9.271828 AGCGACAATAATCACAATACATTATCA 57.728 29.630 0.00 0.00 0.00 2.15
2950 3000 0.244721 GTGATTGCCAAACCTGGAGC 59.755 55.000 0.00 0.00 46.92 4.70
2978 3029 7.123997 TCCAAGCAAATTCAGCCTGATATTTTA 59.876 33.333 0.00 0.00 0.00 1.52
3002 3053 6.803154 ACTTACAAAAAGCTGATAGTGTCC 57.197 37.500 0.00 0.00 0.00 4.02
3061 3114 5.818678 TTCACCTACATAACTTCTGTGGT 57.181 39.130 0.00 0.00 32.11 4.16


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

AutoCloner maintained by Alex Coulton.