Multiple sequence alignment - TraesCS6A01G021400

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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 TraesCS6A01G021400 chr6A 100.000 3149 0 0 1 3149 10512146 10508998 0.000000e+00 5816
1 TraesCS6A01G021400 chr6A 90.915 1530 104 17 642 2161 10544828 10543324 0.000000e+00 2023
2 TraesCS6A01G021400 chr6A 99.219 640 4 1 1 640 10545718 10545080 0.000000e+00 1153
3 TraesCS6A01G021400 chr6A 90.326 889 63 8 642 1520 10593271 10592396 0.000000e+00 1144
4 TraesCS6A01G021400 chr6A 79.766 1196 215 24 977 2154 8212560 8211374 0.000000e+00 843
5 TraesCS6A01G021400 chr6A 94.019 418 22 3 1 416 10594559 10594143 5.730000e-177 630
6 TraesCS6A01G021400 chr6A 97.183 284 8 0 1878 2161 10586190 10585907 6.110000e-132 481
7 TraesCS6A01G021400 chr6A 89.218 371 37 3 1513 1882 10591708 10591340 7.960000e-126 460
8 TraesCS6A01G021400 chr6A 77.761 661 135 11 1508 2162 8393089 8392435 2.280000e-106 396
9 TraesCS6A01G021400 chr6A 93.860 228 11 2 419 643 10593743 10593516 1.080000e-89 340
10 TraesCS6A01G021400 chr6D 95.863 2103 77 2 685 2778 9548525 9546424 0.000000e+00 3393
11 TraesCS6A01G021400 chr6D 80.067 1199 209 26 977 2154 7999087 7997898 0.000000e+00 863
12 TraesCS6A01G021400 chr6D 78.356 1192 230 24 981 2155 8552814 8551634 0.000000e+00 747
13 TraesCS6A01G021400 chr6D 78.133 1189 227 27 988 2157 8967572 8968746 0.000000e+00 725
14 TraesCS6A01G021400 chr6D 78.403 1102 205 26 1068 2155 7678873 7679955 0.000000e+00 686
15 TraesCS6A01G021400 chr6D 77.296 1176 246 18 987 2155 33895040 33896201 0.000000e+00 673
16 TraesCS6A01G021400 chr6D 95.465 419 16 3 1 417 9549853 9549436 0.000000e+00 665
17 TraesCS6A01G021400 chr6D 77.014 1105 208 34 1086 2166 8987326 8988408 2.700000e-165 592
18 TraesCS6A01G021400 chr6D 95.816 239 10 0 2775 3013 9545945 9545707 1.370000e-103 387
19 TraesCS6A01G021400 chr6D 91.954 261 19 2 265 524 444471233 444470974 6.420000e-97 364
20 TraesCS6A01G021400 chr6B 94.666 2156 92 4 642 2787 17501070 17498928 0.000000e+00 3323
21 TraesCS6A01G021400 chr6B 93.421 608 30 6 9 609 17501947 17501343 0.000000e+00 893
22 TraesCS6A01G021400 chr6B 77.908 1109 209 31 1068 2154 14323600 14324694 0.000000e+00 658
23 TraesCS6A01G021400 chr6B 76.667 1200 231 29 973 2155 16267363 16268530 1.240000e-173 619
24 TraesCS6A01G021400 chr6B 94.667 375 19 1 2775 3149 17498268 17497895 5.850000e-162 580
25 TraesCS6A01G021400 chr6B 80.100 598 112 5 1559 2154 14629157 14628565 3.730000e-119 438
26 TraesCS6A01G021400 chr2B 77.490 1195 239 25 981 2157 709426188 709425006 0.000000e+00 689
27 TraesCS6A01G021400 chr2D 91.941 273 21 1 256 527 535240023 535240295 6.370000e-102 381
28 TraesCS6A01G021400 chr2A 91.985 262 20 1 265 525 578489077 578488816 1.780000e-97 366
29 TraesCS6A01G021400 chrUn 90.943 265 22 2 265 528 29715035 29714772 3.860000e-94 355
30 TraesCS6A01G021400 chr5A 89.855 276 25 2 252 526 281122084 281122357 5.000000e-93 351


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 TraesCS6A01G021400 chr6A 10508998 10512146 3148 True 5816.000000 5816 100.000000 1 3149 1 chr6A.!!$R3 3148
1 TraesCS6A01G021400 chr6A 10543324 10545718 2394 True 1588.000000 2023 95.067000 1 2161 2 chr6A.!!$R5 2160
2 TraesCS6A01G021400 chr6A 8211374 8212560 1186 True 843.000000 843 79.766000 977 2154 1 chr6A.!!$R1 1177
3 TraesCS6A01G021400 chr6A 10591340 10594559 3219 True 643.500000 1144 91.855750 1 1882 4 chr6A.!!$R6 1881
4 TraesCS6A01G021400 chr6A 8392435 8393089 654 True 396.000000 396 77.761000 1508 2162 1 chr6A.!!$R2 654
5 TraesCS6A01G021400 chr6D 9545707 9549853 4146 True 1481.666667 3393 95.714667 1 3013 3 chr6D.!!$R4 3012
6 TraesCS6A01G021400 chr6D 7997898 7999087 1189 True 863.000000 863 80.067000 977 2154 1 chr6D.!!$R1 1177
7 TraesCS6A01G021400 chr6D 8551634 8552814 1180 True 747.000000 747 78.356000 981 2155 1 chr6D.!!$R2 1174
8 TraesCS6A01G021400 chr6D 8967572 8968746 1174 False 725.000000 725 78.133000 988 2157 1 chr6D.!!$F2 1169
9 TraesCS6A01G021400 chr6D 7678873 7679955 1082 False 686.000000 686 78.403000 1068 2155 1 chr6D.!!$F1 1087
10 TraesCS6A01G021400 chr6D 33895040 33896201 1161 False 673.000000 673 77.296000 987 2155 1 chr6D.!!$F4 1168
11 TraesCS6A01G021400 chr6D 8987326 8988408 1082 False 592.000000 592 77.014000 1086 2166 1 chr6D.!!$F3 1080
12 TraesCS6A01G021400 chr6B 17497895 17501947 4052 True 1598.666667 3323 94.251333 9 3149 3 chr6B.!!$R2 3140
13 TraesCS6A01G021400 chr6B 14323600 14324694 1094 False 658.000000 658 77.908000 1068 2154 1 chr6B.!!$F1 1086
14 TraesCS6A01G021400 chr6B 16267363 16268530 1167 False 619.000000 619 76.667000 973 2155 1 chr6B.!!$F2 1182
15 TraesCS6A01G021400 chr6B 14628565 14629157 592 True 438.000000 438 80.100000 1559 2154 1 chr6B.!!$R1 595
16 TraesCS6A01G021400 chr2B 709425006 709426188 1182 True 689.000000 689 77.490000 981 2157 1 chr2B.!!$R1 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
965 1643 0.179 ATTCGCACCCTGTCTCCATC 59.821 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2794 4883 1.199789 TCATCAGCGGTTGACATTTGC 59.8 47.619 0.0 0.0 38.99 3.68 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
882 1560 1.840737 CCGGTCTCTTCTCCTCTTCA 58.159 55.000 0.00 0.0 0.00 3.02
956 1634 2.308722 ACCATCCCATTCGCACCCT 61.309 57.895 0.00 0.0 0.00 4.34
957 1635 1.825191 CCATCCCATTCGCACCCTG 60.825 63.158 0.00 0.0 0.00 4.45
958 1636 1.077501 CATCCCATTCGCACCCTGT 60.078 57.895 0.00 0.0 0.00 4.00
965 1643 0.179000 ATTCGCACCCTGTCTCCATC 59.821 55.000 0.00 0.0 0.00 3.51
1455 2154 1.410648 CGGTACTACCTGCCCCTCTTA 60.411 57.143 3.68 0.0 35.66 2.10
1539 2945 0.893727 GGACGGTCAAGCCCAATGTT 60.894 55.000 10.76 0.0 0.00 2.71
1600 3010 0.460987 CAAGCTGTCCCTCGCTAAGG 60.461 60.000 0.00 0.0 45.77 2.69
2369 3779 5.276773 CGCTTACAATCTCTGAAATGAGAGC 60.277 44.000 0.00 0.0 44.98 4.09
2477 3887 4.141733 ACCCATGAACCAGAAAACAAAAGG 60.142 41.667 0.00 0.0 0.00 3.11
2640 4050 6.775594 AATAAGTTTCTATTGGGTGCCTTC 57.224 37.500 0.00 0.0 0.00 3.46
2718 4128 4.425520 AGCTGATTTTACTACGCTGAGAC 58.574 43.478 0.00 0.0 0.00 3.36
2794 4883 8.602328 TGATGAAACACTTTTGCATAAAAACTG 58.398 29.630 0.00 0.0 35.50 3.16
2806 4895 5.236047 TGCATAAAAACTGCAAATGTCAACC 59.764 36.000 0.00 0.0 46.06 3.77
2932 5021 4.142469 GCAATTATAGTTTCCGTGCCTTGT 60.142 41.667 0.00 0.0 0.00 3.16
3015 5104 3.409026 AGTTCTGTGGTAAGAGCAAGG 57.591 47.619 0.00 0.0 30.38 3.61
3022 5111 3.118038 TGTGGTAAGAGCAAGGAGTGTTT 60.118 43.478 0.00 0.0 0.00 2.83
3023 5112 3.498777 GTGGTAAGAGCAAGGAGTGTTTC 59.501 47.826 0.00 0.0 0.00 2.78
3024 5113 3.135712 TGGTAAGAGCAAGGAGTGTTTCA 59.864 43.478 0.00 0.0 0.00 2.69
3025 5114 3.748568 GGTAAGAGCAAGGAGTGTTTCAG 59.251 47.826 0.00 0.0 0.00 3.02
3026 5115 3.845781 AAGAGCAAGGAGTGTTTCAGA 57.154 42.857 0.00 0.0 0.00 3.27
3027 5116 4.363991 AAGAGCAAGGAGTGTTTCAGAT 57.636 40.909 0.00 0.0 0.00 2.90
3028 5117 3.672808 AGAGCAAGGAGTGTTTCAGATG 58.327 45.455 0.00 0.0 0.00 2.90
3029 5118 3.072184 AGAGCAAGGAGTGTTTCAGATGT 59.928 43.478 0.00 0.0 0.00 3.06
3044 5133 3.134623 TCAGATGTGGGTATTGTAGCTGG 59.865 47.826 0.00 0.0 0.00 4.85
3050 5139 4.704540 TGTGGGTATTGTAGCTGGATTTTG 59.295 41.667 0.00 0.0 0.00 2.44
3067 5156 5.220567 GGATTTTGTTTTGCGATTGTTGTGT 60.221 36.000 0.00 0.0 0.00 3.72
3081 5170 4.530710 TGTTGTGTACTCTGTATCCACC 57.469 45.455 0.00 0.0 0.00 4.61
3093 5182 2.439880 TGTATCCACCTTTGGTCACACA 59.560 45.455 0.00 0.0 44.35 3.72
3116 5205 9.194271 CACATGTGATATGAGAACTGAGATAAG 57.806 37.037 21.64 0.0 0.00 1.73
3121 5210 7.384660 GTGATATGAGAACTGAGATAAGCCTTG 59.615 40.741 0.00 0.0 0.00 3.61
3122 5211 4.478206 TGAGAACTGAGATAAGCCTTGG 57.522 45.455 0.00 0.0 0.00 3.61
3129 5218 5.463154 ACTGAGATAAGCCTTGGAGACTAT 58.537 41.667 0.00 0.0 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
779 1457 3.149196 TGTGAGTGGAGAGGAAAAATGC 58.851 45.455 0.00 0.00 0.00 3.56
862 1540 0.458260 GAAGAGGAGAAGAGACCGGC 59.542 60.000 0.00 0.00 0.00 6.13
882 1560 1.371558 GTGAAGGCACGGAGGAAGT 59.628 57.895 0.00 0.00 34.94 3.01
927 1605 2.668632 GGATGGTGCTTCGGTGGA 59.331 61.111 0.00 0.00 0.00 4.02
957 1635 3.323403 AGAGATTGATTCCCGATGGAGAC 59.677 47.826 0.00 0.00 43.07 3.36
958 1636 3.576118 GAGAGATTGATTCCCGATGGAGA 59.424 47.826 0.00 0.00 43.07 3.71
965 1643 0.601311 GGCGGAGAGATTGATTCCCG 60.601 60.000 0.00 0.00 39.88 5.14
1384 2083 2.128507 GGACGAAGGAGAGCGGGAT 61.129 63.158 0.00 0.00 0.00 3.85
1455 2154 1.380650 GAGGTTCTCCGAGGAGCCT 60.381 63.158 15.32 15.32 46.93 4.58
1600 3010 4.828925 GCTGCTCAGGACTCCGCC 62.829 72.222 0.00 0.00 0.00 6.13
1805 3215 3.519973 CTCAGCACACACGGAGCCA 62.520 63.158 0.00 0.00 0.00 4.75
2477 3887 2.289195 TGGAAACGGATGTGGTACAGTC 60.289 50.000 0.00 0.00 41.80 3.51
2640 4050 6.777782 AGAAGCATAAGGGGAAAGATATCAG 58.222 40.000 5.32 0.00 0.00 2.90
2709 4119 2.869801 TGTTCGAAAATTGTCTCAGCGT 59.130 40.909 0.00 0.00 0.00 5.07
2718 4128 7.651704 AGGTTACCTTTTCATGTTCGAAAATTG 59.348 33.333 0.00 0.00 42.39 2.32
2794 4883 1.199789 TCATCAGCGGTTGACATTTGC 59.800 47.619 0.00 0.00 38.99 3.68
2806 4895 4.201940 TGTTAATCTTGCCAATCATCAGCG 60.202 41.667 0.00 0.00 0.00 5.18
3015 5104 5.003804 ACAATACCCACATCTGAAACACTC 58.996 41.667 0.00 0.00 0.00 3.51
3022 5111 3.134623 CCAGCTACAATACCCACATCTGA 59.865 47.826 0.00 0.00 0.00 3.27
3023 5112 3.134623 TCCAGCTACAATACCCACATCTG 59.865 47.826 0.00 0.00 0.00 2.90
3024 5113 3.384168 TCCAGCTACAATACCCACATCT 58.616 45.455 0.00 0.00 0.00 2.90
3025 5114 3.838244 TCCAGCTACAATACCCACATC 57.162 47.619 0.00 0.00 0.00 3.06
3026 5115 4.796110 AATCCAGCTACAATACCCACAT 57.204 40.909 0.00 0.00 0.00 3.21
3027 5116 4.584638 AAATCCAGCTACAATACCCACA 57.415 40.909 0.00 0.00 0.00 4.17
3028 5117 4.705023 ACAAAATCCAGCTACAATACCCAC 59.295 41.667 0.00 0.00 0.00 4.61
3029 5118 4.929479 ACAAAATCCAGCTACAATACCCA 58.071 39.130 0.00 0.00 0.00 4.51
3044 5133 5.794720 ACACAACAATCGCAAAACAAAATC 58.205 33.333 0.00 0.00 0.00 2.17
3050 5139 4.670621 CAGAGTACACAACAATCGCAAAAC 59.329 41.667 0.00 0.00 0.00 2.43
3093 5182 7.235193 AGGCTTATCTCAGTTCTCATATCACAT 59.765 37.037 0.00 0.00 0.00 3.21
3116 5205 1.804372 CGTCAGCATAGTCTCCAAGGC 60.804 57.143 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.