Multiple sequence alignment - TraesCS3D01G137700

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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 TraesCS3D01G137700 chr3D 100.000 3002 0 0 1 3002 96392414 96389413 0.000000e+00 5544.0
1 TraesCS3D01G137700 chr3D 91.658 995 38 10 1115 2096 96366053 96365091 0.000000e+00 1336.0
2 TraesCS3D01G137700 chr3D 97.619 42 1 0 1222 1263 332634773 332634732 4.150000e-09 73.1
3 TraesCS3D01G137700 chr3B 94.796 980 45 4 1 980 147544431 147543458 0.000000e+00 1522.0
4 TraesCS3D01G137700 chr3B 94.220 692 29 3 1350 2030 147543104 147542413 0.000000e+00 1046.0
5 TraesCS3D01G137700 chr3B 88.470 451 38 3 2087 2525 741495948 741496396 1.580000e-147 532.0
6 TraesCS3D01G137700 chr3B 93.438 320 16 1 980 1299 147543416 147543102 1.260000e-128 470.0
7 TraesCS3D01G137700 chr5B 96.053 912 31 4 2094 3002 617666665 617667574 0.000000e+00 1480.0
8 TraesCS3D01G137700 chr5B 87.755 441 40 3 2097 2525 520103551 520103989 1.240000e-138 503.0
9 TraesCS3D01G137700 chr2B 95.912 905 31 5 2100 3002 686045233 686044333 0.000000e+00 1461.0
10 TraesCS3D01G137700 chr1B 95.652 897 38 1 2107 3002 72016758 72017654 0.000000e+00 1439.0
11 TraesCS3D01G137700 chr6B 93.608 923 44 6 2088 3002 9361300 9362215 0.000000e+00 1363.0
12 TraesCS3D01G137700 chr6B 90.068 443 31 2 2095 2525 652381553 652381994 2.020000e-156 562.0
13 TraesCS3D01G137700 chr3A 94.163 908 31 14 2096 3002 682274581 682273695 0.000000e+00 1363.0
14 TraesCS3D01G137700 chr3A 91.239 993 69 5 1 980 114423628 114422641 0.000000e+00 1336.0
15 TraesCS3D01G137700 chr3A 85.047 642 51 23 1453 2079 114422241 114421630 1.980000e-171 612.0
16 TraesCS3D01G137700 chr3A 91.716 169 14 0 981 1149 114422598 114422430 5.000000e-58 235.0
17 TraesCS3D01G137700 chr4A 93.282 908 37 14 2098 3002 613745690 613746576 0.000000e+00 1317.0
18 TraesCS3D01G137700 chr1A 92.763 912 34 14 2095 3002 545856659 545857542 0.000000e+00 1290.0
19 TraesCS3D01G137700 chr6D 88.030 919 72 18 2110 3002 110724922 110725828 0.000000e+00 1053.0
20 TraesCS3D01G137700 chr5D 89.415 803 58 9 2220 3002 462039755 462038960 0.000000e+00 987.0
21 TraesCS3D01G137700 chr5A 87.760 866 69 19 2169 3002 672453780 672452920 0.000000e+00 977.0
22 TraesCS3D01G137700 chr5A 86.415 714 59 13 2097 2778 7572306 7573013 0.000000e+00 747.0
23 TraesCS3D01G137700 chr2A 92.308 39 3 0 1225 1263 23951649 23951687 4.180000e-04 56.5


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 TraesCS3D01G137700 chr3D 96389413 96392414 3001 True 5544.000000 5544 100.000000 1 3002 1 chr3D.!!$R2 3001
1 TraesCS3D01G137700 chr3D 96365091 96366053 962 True 1336.000000 1336 91.658000 1115 2096 1 chr3D.!!$R1 981
2 TraesCS3D01G137700 chr3B 147542413 147544431 2018 True 1012.666667 1522 94.151333 1 2030 3 chr3B.!!$R1 2029
3 TraesCS3D01G137700 chr5B 617666665 617667574 909 False 1480.000000 1480 96.053000 2094 3002 1 chr5B.!!$F2 908
4 TraesCS3D01G137700 chr2B 686044333 686045233 900 True 1461.000000 1461 95.912000 2100 3002 1 chr2B.!!$R1 902
5 TraesCS3D01G137700 chr1B 72016758 72017654 896 False 1439.000000 1439 95.652000 2107 3002 1 chr1B.!!$F1 895
6 TraesCS3D01G137700 chr6B 9361300 9362215 915 False 1363.000000 1363 93.608000 2088 3002 1 chr6B.!!$F1 914
7 TraesCS3D01G137700 chr3A 682273695 682274581 886 True 1363.000000 1363 94.163000 2096 3002 1 chr3A.!!$R1 906
8 TraesCS3D01G137700 chr3A 114421630 114423628 1998 True 727.666667 1336 89.334000 1 2079 3 chr3A.!!$R2 2078
9 TraesCS3D01G137700 chr4A 613745690 613746576 886 False 1317.000000 1317 93.282000 2098 3002 1 chr4A.!!$F1 904
10 TraesCS3D01G137700 chr1A 545856659 545857542 883 False 1290.000000 1290 92.763000 2095 3002 1 chr1A.!!$F1 907
11 TraesCS3D01G137700 chr6D 110724922 110725828 906 False 1053.000000 1053 88.030000 2110 3002 1 chr6D.!!$F1 892
12 TraesCS3D01G137700 chr5D 462038960 462039755 795 True 987.000000 987 89.415000 2220 3002 1 chr5D.!!$R1 782
13 TraesCS3D01G137700 chr5A 672452920 672453780 860 True 977.000000 977 87.760000 2169 3002 1 chr5A.!!$R1 833
14 TraesCS3D01G137700 chr5A 7572306 7573013 707 False 747.000000 747 86.415000 2097 2778 1 chr5A.!!$F1 681

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
293 294 0.178967 TCAGCACCAATTTCTGCCCA 60.179 50.000 1.22 0.0 33.57 5.36 F
668 669 1.000396 GTGGCTGGAAATGGAGGCT 60.000 57.895 0.00 0.0 35.81 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1260 0.176680 ATAACCAGCGAGGCAGTGAG 59.823 55.0 0.0 0.0 43.14 3.51 R
2624 2792 0.875059 GAGTGGAACGGGAAAGCAAG 59.125 55.0 0.0 0.0 45.86 4.01 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
59 60 2.134287 ACCATCCGCGATACTGCCT 61.134 57.895 8.23 0.00 0.00 4.75
107 108 1.373590 AAATGGTGTATGCGTCCGGC 61.374 55.000 0.00 0.00 43.96 6.13
209 210 0.943673 CAGTCCAAACACGCACATCA 59.056 50.000 0.00 0.00 0.00 3.07
227 228 5.181811 CACATCACTTACTTGAGGCATTTCA 59.818 40.000 0.00 0.00 30.18 2.69
269 270 1.410932 CCCAAGTCCCCACACTTCAAA 60.411 52.381 0.00 0.00 34.17 2.69
293 294 0.178967 TCAGCACCAATTTCTGCCCA 60.179 50.000 1.22 0.00 33.57 5.36
316 317 5.091261 AGAACACTGTCCATTCCATCTAC 57.909 43.478 0.00 0.00 0.00 2.59
395 396 3.429080 CTCCGAGCAGAGCTGGAGC 62.429 68.421 17.92 0.00 42.28 4.70
461 462 2.358737 AAAGCCTCCGCCAAGTCG 60.359 61.111 0.00 0.00 34.57 4.18
503 504 1.734477 CTGCAGGTTCACGTCGGAG 60.734 63.158 5.57 0.00 0.00 4.63
668 669 1.000396 GTGGCTGGAAATGGAGGCT 60.000 57.895 0.00 0.00 35.81 4.58
671 672 2.421399 GCTGGAAATGGAGGCTGCC 61.421 63.158 11.65 11.65 0.00 4.85
743 756 1.008538 GCGTGGTTTGGTCTTGCAG 60.009 57.895 0.00 0.00 0.00 4.41
806 819 2.747446 CCCCTCACATTCCGTAAAACTG 59.253 50.000 0.00 0.00 0.00 3.16
830 843 6.484977 TGACAAAATGACACATGTTAGCTACA 59.515 34.615 0.00 0.00 41.97 2.74
887 901 5.471116 ACCATTTTCTAACGAGGGTGTTTAC 59.529 40.000 0.00 0.00 33.32 2.01
894 908 6.454795 TCTAACGAGGGTGTTTACGTAAAAT 58.545 36.000 21.67 6.52 38.00 1.82
906 920 7.858879 GTGTTTACGTAAAATTTCATGGACTGT 59.141 33.333 21.67 0.00 0.00 3.55
907 921 8.071368 TGTTTACGTAAAATTTCATGGACTGTC 58.929 33.333 21.67 0.00 0.00 3.51
908 922 5.277601 ACGTAAAATTTCATGGACTGTCG 57.722 39.130 1.07 0.00 0.00 4.35
909 923 4.153475 ACGTAAAATTTCATGGACTGTCGG 59.847 41.667 1.07 0.00 0.00 4.79
910 924 4.153475 CGTAAAATTTCATGGACTGTCGGT 59.847 41.667 1.07 0.00 0.00 4.69
1009 1065 3.044873 AGAGAGGAGAAATGGGAGGAG 57.955 52.381 0.00 0.00 0.00 3.69
1037 1093 1.329906 GCAGCATCACCAAATCTCTCG 59.670 52.381 0.00 0.00 0.00 4.04
1040 1096 1.063174 GCATCACCAAATCTCTCGCAC 59.937 52.381 0.00 0.00 0.00 5.34
1125 1181 9.530633 ACATTGTAGTTATCTCCTTTTCGATAC 57.469 33.333 0.00 0.00 0.00 2.24
1167 1260 2.618709 AGTGTGTTTAAGCTCCTTGTGC 59.381 45.455 0.00 0.00 0.00 4.57
1171 1264 2.878406 TGTTTAAGCTCCTTGTGCTCAC 59.122 45.455 0.00 0.00 40.22 3.51
1234 1333 5.558818 ACATACTATACTACTCCCTCCGTG 58.441 45.833 0.00 0.00 0.00 4.94
1237 1336 0.822532 ATACTACTCCCTCCGTGCCG 60.823 60.000 0.00 0.00 0.00 5.69
1252 1351 1.396996 GTGCCGAATTACTTGTCGCAT 59.603 47.619 0.00 0.00 35.93 4.73
1326 1425 4.720649 TCCTCTCTTGGTTTCAGTATCG 57.279 45.455 0.00 0.00 0.00 2.92
1367 1466 3.057946 GGCAGTTCACTGGAAATCACTTC 60.058 47.826 9.01 0.00 43.94 3.01
1498 1607 1.825090 TTTGGTAGCACCTGCAGATG 58.175 50.000 17.39 10.34 45.16 2.90
1790 1903 5.687285 CACAGATGTAGTTTGTTTCCTTTGC 59.313 40.000 0.00 0.00 0.00 3.68
1829 1953 1.153529 TCGTTGTGACAAGGCGTGT 60.154 52.632 12.73 5.57 45.74 4.49
1878 2002 1.047801 AAGACGGGCAGCCAAATTTT 58.952 45.000 15.19 0.00 0.00 1.82
1977 2101 2.360483 GGAGCTGATTGATCGTCTGAGA 59.640 50.000 0.00 0.00 30.59 3.27
2158 2293 7.229506 TCTCACATCTAAGTATGATGTCATCGT 59.770 37.037 12.18 12.18 37.76 3.73
2454 2614 2.163815 TGTCACTACTCGAAGCTAAGGC 59.836 50.000 0.00 0.00 39.06 4.35
2567 2730 1.811645 TTGCCCACTTTTTAGCGGCC 61.812 55.000 0.00 0.00 38.92 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 3.888323 TCTTGAAGTGCATTGCTGGTTTA 59.112 39.130 10.49 0.00 0.00 2.01
107 108 2.669569 CACTGCTGTGGGGTTCGG 60.670 66.667 15.43 0.00 40.33 4.30
209 210 6.265196 TGTTTGATGAAATGCCTCAAGTAAGT 59.735 34.615 0.00 0.00 31.11 2.24
227 228 2.887152 GAGTGCAAGAAGGGTGTTTGAT 59.113 45.455 0.00 0.00 0.00 2.57
269 270 3.382546 GGCAGAAATTGGTGCTGATGTAT 59.617 43.478 11.07 0.00 39.76 2.29
293 294 4.647564 AGATGGAATGGACAGTGTTCTT 57.352 40.909 2.55 0.00 0.00 2.52
478 479 0.445436 CGTGAACCTGCAGATTCAGC 59.555 55.000 24.26 16.60 35.55 4.26
743 756 4.068599 GCCTAATCCAGAAAGCTATCCAC 58.931 47.826 0.00 0.00 0.00 4.02
791 804 6.915843 GTCATTTTGTCAGTTTTACGGAATGT 59.084 34.615 0.00 0.00 0.00 2.71
806 819 6.898041 TGTAGCTAACATGTGTCATTTTGTC 58.102 36.000 0.00 0.00 31.43 3.18
830 843 1.561643 TCGATGGAGCAGAAAGGACT 58.438 50.000 0.00 0.00 0.00 3.85
861 874 3.326880 ACACCCTCGTTAGAAAATGGTCT 59.673 43.478 0.00 0.00 0.00 3.85
862 875 3.671716 ACACCCTCGTTAGAAAATGGTC 58.328 45.455 0.00 0.00 0.00 4.02
863 876 3.782656 ACACCCTCGTTAGAAAATGGT 57.217 42.857 0.00 0.00 0.00 3.55
887 901 4.153475 ACCGACAGTCCATGAAATTTTACG 59.847 41.667 0.00 0.00 0.00 3.18
894 908 4.753516 ATGATACCGACAGTCCATGAAA 57.246 40.909 0.00 0.00 0.00 2.69
906 920 3.893200 ACGGAGATGGTAAATGATACCGA 59.107 43.478 0.00 0.00 40.39 4.69
907 921 3.987868 CACGGAGATGGTAAATGATACCG 59.012 47.826 0.00 0.00 40.39 4.02
908 922 4.750098 CACACGGAGATGGTAAATGATACC 59.250 45.833 0.00 0.00 38.07 2.73
909 923 4.750098 CCACACGGAGATGGTAAATGATAC 59.250 45.833 0.00 0.00 33.74 2.24
910 924 4.742440 GCCACACGGAGATGGTAAATGATA 60.742 45.833 0.00 0.00 39.02 2.15
1009 1065 1.456296 TGGTGATGCTGCATGAGAAC 58.544 50.000 21.53 12.04 0.00 3.01
1037 1093 1.499502 GCTTTTCGCAGAGGAGTGC 59.500 57.895 0.00 0.00 38.43 4.40
1040 1096 2.744768 GCCGCTTTTCGCAGAGGAG 61.745 63.158 3.58 0.00 38.43 3.69
1063 1119 0.464373 TGGAGAGCAAATGATCCGGC 60.464 55.000 0.00 0.00 34.39 6.13
1125 1181 6.757947 ACACTGACCTTGATGAAAATGTTTTG 59.242 34.615 0.00 0.00 0.00 2.44
1167 1260 0.176680 ATAACCAGCGAGGCAGTGAG 59.823 55.000 0.00 0.00 43.14 3.51
1171 1264 2.604046 AAGTATAACCAGCGAGGCAG 57.396 50.000 0.00 0.00 43.14 4.85
1234 1333 3.936902 TTATGCGACAAGTAATTCGGC 57.063 42.857 0.00 0.00 35.73 5.54
1237 1336 8.230486 CCTATCCATTTATGCGACAAGTAATTC 58.770 37.037 0.00 0.00 0.00 2.17
1252 1351 6.826741 GCCTGTTTTGTACTCCTATCCATTTA 59.173 38.462 0.00 0.00 0.00 1.40
1326 1425 1.734465 CCACTCGGTCAGATTGAAAGC 59.266 52.381 0.00 0.00 31.90 3.51
1406 1505 5.409826 GAGGTTTTCTCATCAGTGGTTACTG 59.590 44.000 1.12 1.12 46.47 2.74
1446 1548 0.463116 ACTTCACCAAAAGACCGCGT 60.463 50.000 4.92 0.00 0.00 6.01
1498 1607 2.510238 AGCGCGATGGAGAGCAAC 60.510 61.111 12.10 0.00 39.42 4.17
1829 1953 1.311859 CTCTGAAAGCACAAGCCACA 58.688 50.000 0.00 0.00 43.56 4.17
1977 2101 1.557099 TATCAGACGACCAAGCACCT 58.443 50.000 0.00 0.00 0.00 4.00
2043 2176 4.159120 GCAAGAAAAGTCGATTGTAAGCC 58.841 43.478 0.00 0.00 0.00 4.35
2176 2311 8.698854 TGACAAATCAAAATCGAACAAATAAGC 58.301 29.630 0.00 0.00 0.00 3.09
2234 2369 2.180769 CATCGAGGCGGACGTGAA 59.819 61.111 0.00 0.00 0.00 3.18
2506 2667 6.979238 ACAAATCGATGGTAGAGCTACTTTAC 59.021 38.462 0.00 0.00 36.36 2.01
2567 2730 2.618241 AGAAGCTAGCGATCAGAGACAG 59.382 50.000 20.87 0.00 0.00 3.51
2624 2792 0.875059 GAGTGGAACGGGAAAGCAAG 59.125 55.000 0.00 0.00 45.86 4.01


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

AutoCloner maintained by Alex Coulton.