Multiple sequence alignment - TraesCS3B01G423000

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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 TraesCS3B01G423000 chr3B 100.000 2885 0 0 1 2885 660314396 660317280 0.000000e+00 5328.0
1 TraesCS3B01G423000 chr3B 97.723 571 2 2 1 561 46471435 46472004 0.000000e+00 972.0
2 TraesCS3B01G423000 chr3B 98.998 499 4 1 547 1044 46485516 46486014 0.000000e+00 893.0
3 TraesCS3B01G423000 chr3B 96.552 58 2 0 272 329 660314388 660314331 2.370000e-16 97.1
4 TraesCS3B01G423000 chr3D 96.875 1696 40 7 1192 2885 499581402 499583086 0.000000e+00 2826.0
5 TraesCS3B01G423000 chr5B 97.816 1099 16 5 1 1095 94287267 94288361 0.000000e+00 1890.0
6 TraesCS3B01G423000 chr5B 90.196 102 10 0 127 228 490421479 490421580 1.800000e-27 134.0
7 TraesCS3B01G423000 chr5B 96.552 58 2 0 272 329 94287259 94287202 2.370000e-16 97.1
8 TraesCS3B01G423000 chr1B 97.597 1082 11 4 1 1068 181219913 181218833 0.000000e+00 1840.0
9 TraesCS3B01G423000 chr1B 91.333 150 7 3 1002 1150 583753918 583753774 1.750000e-47 200.0
10 TraesCS3B01G423000 chr1B 91.667 144 0 8 1002 1144 660817517 660817385 3.790000e-44 189.0
11 TraesCS3B01G423000 chr1B 96.429 56 2 0 274 329 181219923 181219978 3.060000e-15 93.5
12 TraesCS3B01G423000 chr2B 94.964 139 4 2 1002 1140 25672190 25672325 6.260000e-52 215.0
13 TraesCS3B01G423000 chr2B 87.586 145 13 4 996 1138 706804249 706804390 2.300000e-36 163.0
14 TraesCS3B01G423000 chr5A 89.412 170 15 2 950 1118 658503126 658502959 8.100000e-51 211.0
15 TraesCS3B01G423000 chr5A 87.931 58 7 0 272 329 627268857 627268914 5.160000e-08 69.4
16 TraesCS3B01G423000 chrUn 88.344 163 7 7 1002 1160 407251066 407250912 4.910000e-43 185.0
17 TraesCS3B01G423000 chr7A 85.714 161 15 3 885 1045 375510113 375510265 2.300000e-36 163.0
18 TraesCS3B01G423000 chr7A 87.500 112 12 2 127 237 497134634 497134744 8.390000e-26 128.0
19 TraesCS3B01G423000 chr7A 79.897 194 22 7 862 1045 225326985 225326799 3.020000e-25 126.0
20 TraesCS3B01G423000 chr7A 79.290 169 18 10 605 757 247202153 247201986 5.090000e-18 102.0
21 TraesCS3B01G423000 chr3A 84.768 151 15 3 895 1045 344919482 344919624 8.330000e-31 145.0
22 TraesCS3B01G423000 chr3A 84.354 147 14 5 999 1136 12148088 12148234 5.010000e-28 135.0
23 TraesCS3B01G423000 chr3A 89.623 106 8 1 127 229 716105994 716106099 6.490000e-27 132.0
24 TraesCS3B01G423000 chr5D 82.781 151 25 1 73 223 443360779 443360630 1.800000e-27 134.0
25 TraesCS3B01G423000 chr7D 85.156 128 19 0 73 200 77427059 77427186 6.490000e-27 132.0
26 TraesCS3B01G423000 chr7D 87.387 111 12 2 127 237 52355002 52355110 3.020000e-25 126.0
27 TraesCS3B01G423000 chr7D 85.075 67 9 1 286 352 163890825 163890760 1.860000e-07 67.6
28 TraesCS3B01G423000 chr6A 90.909 66 6 0 506 571 65479213 65479278 3.960000e-14 89.8
29 TraesCS3B01G423000 chr2D 97.917 48 1 0 27 74 450914491 450914444 1.840000e-12 84.2
30 TraesCS3B01G423000 chr2A 89.091 55 6 0 275 329 191890131 191890185 5.160000e-08 69.4


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 TraesCS3B01G423000 chr3B 660314396 660317280 2884 False 5328 5328 100.000 1 2885 1 chr3B.!!$F3 2884
1 TraesCS3B01G423000 chr3B 46471435 46472004 569 False 972 972 97.723 1 561 1 chr3B.!!$F1 560
2 TraesCS3B01G423000 chr3D 499581402 499583086 1684 False 2826 2826 96.875 1192 2885 1 chr3D.!!$F1 1693
3 TraesCS3B01G423000 chr5B 94287267 94288361 1094 False 1890 1890 97.816 1 1095 1 chr5B.!!$F1 1094
4 TraesCS3B01G423000 chr1B 181218833 181219913 1080 True 1840 1840 97.597 1 1068 1 chr1B.!!$R1 1067

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
1000 1023 7.497595 AGACATTTAACGTAGGATTAGATGCA 58.502 34.615 0.0 0.0 30.8 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 2631 0.385473 GTTGATGTCCAACGGTTGCG 60.385 55.0 15.31 8.87 44.76 4.85 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
1000 1023 7.497595 AGACATTTAACGTAGGATTAGATGCA 58.502 34.615 0.00 0.00 30.80 3.96
1210 1234 2.829120 TGTACTGGTCGACCATGATTCA 59.171 45.455 36.21 25.03 46.46 2.57
1212 1236 1.902508 ACTGGTCGACCATGATTCAGT 59.097 47.619 36.21 24.96 46.46 3.41
1219 1243 1.209504 GACCATGATTCAGTCGGGGAA 59.790 52.381 0.00 0.00 0.00 3.97
1220 1244 1.210478 ACCATGATTCAGTCGGGGAAG 59.790 52.381 0.00 0.00 0.00 3.46
1242 1266 0.811915 AGTCCGACAAGATCTCCGTG 59.188 55.000 0.00 0.00 0.00 4.94
1247 1271 2.892425 CAAGATCTCCGTGCGGCC 60.892 66.667 5.64 0.00 34.68 6.13
1251 1275 3.781770 GATCTCCGTGCGGCCAGAG 62.782 68.421 2.24 0.10 34.68 3.35
1261 1285 3.202906 GTGCGGCCAGAGTCATATAAAA 58.797 45.455 2.24 0.00 0.00 1.52
1266 1290 4.275689 CGGCCAGAGTCATATAAAATTGCA 59.724 41.667 2.24 0.00 0.00 4.08
1268 1292 5.067674 GGCCAGAGTCATATAAAATTGCACA 59.932 40.000 0.00 0.00 0.00 4.57
1276 1300 2.987413 TAAAATTGCACACAGAGGCG 57.013 45.000 0.00 0.00 0.00 5.52
1288 1313 1.134175 ACAGAGGCGTTTGGTTTTGTG 59.866 47.619 1.79 0.00 0.00 3.33
1291 1316 3.018149 AGAGGCGTTTGGTTTTGTGTTA 58.982 40.909 0.00 0.00 0.00 2.41
1302 1327 5.710984 TGGTTTTGTGTTACAACAAATCGT 58.289 33.333 11.58 0.00 46.44 3.73
1309 1334 5.406175 TGTGTTACAACAAATCGTAGGCTAC 59.594 40.000 14.76 14.76 41.21 3.58
1331 1356 1.467342 ACGACGTCTTGATCGATGTCA 59.533 47.619 14.70 0.00 45.73 3.58
1377 1402 1.155042 GAAGGCGATGATGGCTGATC 58.845 55.000 0.00 0.00 45.07 2.92
1436 1461 4.874966 CAGCAGAAGGAGGTGATAAAGAAG 59.125 45.833 0.00 0.00 36.64 2.85
1680 1705 1.212935 ACCAGGCTAAAGGGTATGCTG 59.787 52.381 0.00 0.00 31.89 4.41
1882 1908 5.744171 TCTCATTAGGTGCTCTGCAAAATA 58.256 37.500 0.00 0.00 41.47 1.40
1951 1977 2.802816 GTTTGTGGACTGCTGTCACTAG 59.197 50.000 23.12 0.00 44.61 2.57
2014 2040 7.148407 GGAGGGATTGTCATTATAAACTATGCG 60.148 40.741 0.00 0.00 0.00 4.73
2045 2071 6.345298 TGTCTCATCGCTTATTCATGGTTAA 58.655 36.000 0.00 0.00 0.00 2.01
2060 2086 5.825679 TCATGGTTAATATGTGTTGTAGGGC 59.174 40.000 0.00 0.00 0.00 5.19
2112 2138 1.587034 GTTCGGTGTACTGCTAATCGC 59.413 52.381 0.00 0.00 39.77 4.58
2126 2152 6.017934 ACTGCTAATCGCTTATATTGGTGTTG 60.018 38.462 0.00 0.00 40.11 3.33
2194 2220 6.127535 ACTCAGCCATGTTTGGAAAGATATTG 60.128 38.462 0.00 0.00 46.92 1.90
2481 2507 2.498167 GCTATGATTCTCAACGGGCAT 58.502 47.619 0.00 0.00 0.00 4.40
2581 2607 9.847224 GAACAGGAATCATACCCTTTAATCTTA 57.153 33.333 0.00 0.00 0.00 2.10
2598 2624 9.674068 TTTAATCTTATAATACATATGCGGCCA 57.326 29.630 2.24 0.00 0.00 5.36
2599 2625 9.845740 TTAATCTTATAATACATATGCGGCCAT 57.154 29.630 2.24 0.00 35.44 4.40
2600 2626 7.734924 ATCTTATAATACATATGCGGCCATG 57.265 36.000 2.24 0.52 32.85 3.66
2601 2627 5.527214 TCTTATAATACATATGCGGCCATGC 59.473 40.000 2.24 0.00 32.85 4.06
2602 2628 0.804364 AATACATATGCGGCCATGCG 59.196 50.000 2.24 0.00 37.81 4.73
2603 2629 1.026182 ATACATATGCGGCCATGCGG 61.026 55.000 2.24 0.00 37.81 5.69
2604 2630 3.740397 CATATGCGGCCATGCGGG 61.740 66.667 2.24 0.00 37.81 6.13
2660 2686 5.503662 TGGCATGTAAGCATTGAACTATG 57.496 39.130 0.00 0.00 35.83 2.23
2682 2708 3.305403 GGTGGAAACTTAGAAGCAAAGGC 60.305 47.826 0.00 0.00 41.61 4.35
2820 2846 0.541863 AACCGTGAGACATCCCCATC 59.458 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
385 406 1.267806 CTGCTCACTGGACGCAAAATT 59.732 47.619 0.00 0.00 32.66 1.82
757 780 2.021355 ACAAGCTGAGCTAGATGCAC 57.979 50.000 7.68 0.00 45.94 4.57
1000 1023 4.225267 AGGTGATATTCTTGGTTTCGTCCT 59.775 41.667 0.00 0.00 0.00 3.85
1176 1200 9.781633 GGTCGACCAGTACATATCTATATCTAT 57.218 37.037 29.75 0.00 35.64 1.98
1177 1201 8.765517 TGGTCGACCAGTACATATCTATATCTA 58.234 37.037 33.23 3.30 42.01 1.98
1178 1202 7.631007 TGGTCGACCAGTACATATCTATATCT 58.369 38.462 33.23 0.00 42.01 1.98
1179 1203 7.860918 TGGTCGACCAGTACATATCTATATC 57.139 40.000 33.23 0.84 42.01 1.63
1210 1234 2.039137 GGACTCCCTTCCCCGACT 59.961 66.667 0.00 0.00 0.00 4.18
1214 1238 1.900545 CTTGTCGGACTCCCTTCCCC 61.901 65.000 9.88 0.00 31.03 4.81
1219 1243 1.686741 GGAGATCTTGTCGGACTCCCT 60.687 57.143 9.88 0.00 40.58 4.20
1220 1244 0.747852 GGAGATCTTGTCGGACTCCC 59.252 60.000 9.88 0.00 40.58 4.30
1242 1266 4.787598 CAATTTTATATGACTCTGGCCGC 58.212 43.478 0.00 0.00 0.00 6.53
1247 1271 7.977904 TCTGTGTGCAATTTTATATGACTCTG 58.022 34.615 0.00 0.00 0.00 3.35
1251 1275 5.973565 GCCTCTGTGTGCAATTTTATATGAC 59.026 40.000 0.00 0.00 0.00 3.06
1261 1285 0.311790 CAAACGCCTCTGTGTGCAAT 59.688 50.000 0.00 0.00 34.84 3.56
1266 1290 1.134175 CAAAACCAAACGCCTCTGTGT 59.866 47.619 0.00 0.00 36.58 3.72
1268 1292 1.134175 CACAAAACCAAACGCCTCTGT 59.866 47.619 0.00 0.00 0.00 3.41
1276 1300 6.950979 CGATTTGTTGTAACACAAAACCAAAC 59.049 34.615 3.28 0.00 46.95 2.93
1288 1313 7.214473 GTAGTAGCCTACGATTTGTTGTAAC 57.786 40.000 0.00 0.00 34.62 2.50
1302 1327 3.251479 TCAAGACGTCGTAGTAGCCTA 57.749 47.619 10.46 0.00 0.00 3.93
1309 1334 3.242316 TGACATCGATCAAGACGTCGTAG 60.242 47.826 10.46 4.23 36.27 3.51
1331 1356 3.539604 CTCCTCGGATGAAATTGAGCTT 58.460 45.455 0.00 0.00 30.48 3.74
1436 1461 5.107798 CCGAAAAGTCTTCTTCTTCGTCTTC 60.108 44.000 13.37 0.00 37.71 2.87
1951 1977 0.591659 GGTTGGCCAGACGAACTTTC 59.408 55.000 5.11 0.00 37.18 2.62
1975 2001 1.060729 TCCCTCCGAAAATCACACCA 58.939 50.000 0.00 0.00 0.00 4.17
1976 2002 2.420058 ATCCCTCCGAAAATCACACC 57.580 50.000 0.00 0.00 0.00 4.16
2014 2040 7.643528 TGAATAAGCGATGAGACAATATCAC 57.356 36.000 0.00 0.00 0.00 3.06
2045 2071 2.092429 CCTGGTGCCCTACAACACATAT 60.092 50.000 0.00 0.00 42.53 1.78
2112 2138 7.864379 GCCTCATTGATTCAACACCAATATAAG 59.136 37.037 0.15 0.00 0.00 1.73
2148 2174 8.958119 TGAGTATCAAAAAGTACACTGAACTT 57.042 30.769 0.00 0.00 45.97 2.66
2166 2192 4.943705 TCTTTCCAAACATGGCTGAGTATC 59.056 41.667 0.00 0.00 0.00 2.24
2481 2507 3.954200 TGAAGCTAATGCAGATCAACCA 58.046 40.909 0.00 0.00 42.74 3.67
2581 2607 2.613595 CGCATGGCCGCATATGTATTAT 59.386 45.455 4.29 0.00 0.00 1.28
2603 2629 3.322706 GATGTCCAACGGTTGCGCC 62.323 63.158 15.31 5.67 0.00 6.53
2604 2630 2.123988 TTGATGTCCAACGGTTGCGC 62.124 55.000 15.31 0.00 0.00 6.09
2605 2631 0.385473 GTTGATGTCCAACGGTTGCG 60.385 55.000 15.31 8.87 44.76 4.85
2606 2632 3.472263 GTTGATGTCCAACGGTTGC 57.528 52.632 15.31 3.60 44.76 4.17
2660 2686 3.305403 GCCTTTGCTTCTAAGTTTCCACC 60.305 47.826 0.00 0.00 33.53 4.61
2820 2846 6.468333 TGGTTTTATGGGATCATGATGTTG 57.532 37.500 14.30 0.00 34.96 3.33


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

AutoCloner maintained by Alex Coulton.