Multiple sequence alignment - TraesCS3B01G133500

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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 TraesCS3B01G133500 chr3B 100.000 2327 0 0 1 2327 116006687 116004361 0.000000e+00 4298
1 TraesCS3B01G133500 chr2A 83.816 2175 321 26 2 2167 95344306 95346458 0.000000e+00 2037
2 TraesCS3B01G133500 chr2A 78.892 2274 410 46 64 2319 206850761 206848540 0.000000e+00 1476
3 TraesCS3B01G133500 chr3D 81.662 2334 372 48 15 2323 537285773 537288075 0.000000e+00 1888
4 TraesCS3B01G133500 chr7D 80.540 2333 404 37 15 2325 51706249 51703945 0.000000e+00 1748
5 TraesCS3B01G133500 chr6A 80.864 2221 372 42 126 2325 228526567 228528755 0.000000e+00 1698
6 TraesCS3B01G133500 chr4B 79.839 2356 397 55 2 2327 31126802 31124495 0.000000e+00 1648
7 TraesCS3B01G133500 chr2D 80.959 2106 359 34 25 2114 516713432 516715511 0.000000e+00 1629
8 TraesCS3B01G133500 chr6B 79.233 2321 437 36 19 2325 448339623 448341912 0.000000e+00 1574
9 TraesCS3B01G133500 chr1B 79.279 2331 423 47 15 2325 337936175 337933885 0.000000e+00 1574
10 TraesCS3B01G133500 chr1B 87.343 877 98 5 1290 2162 178889685 178888818 0.000000e+00 992
11 TraesCS3B01G133500 chr1B 90.676 740 64 4 1 739 178890608 178889873 0.000000e+00 979
12 TraesCS3B01G133500 chr1B 92.105 152 12 0 2174 2325 178888643 178888492 5.040000e-52 215
13 TraesCS3B01G133500 chr2B 82.448 1544 253 17 2 1539 461255072 461256603 0.000000e+00 1334
14 TraesCS3B01G133500 chr5A 81.199 1601 258 27 64 1653 644297054 644295486 0.000000e+00 1249
15 TraesCS3B01G133500 chr6D 82.645 968 150 15 2 955 149474051 149475014 0.000000e+00 841
16 TraesCS3B01G133500 chr6D 77.557 1007 204 16 1104 2104 149501260 149502250 2.580000e-164 588
17 TraesCS3B01G133500 chr5B 85.268 801 107 7 1370 2163 415060557 415061353 0.000000e+00 815
18 TraesCS3B01G133500 chr1D 82.740 365 54 5 1955 2319 200212129 200212484 1.340000e-82 316


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 TraesCS3B01G133500 chr3B 116004361 116006687 2326 True 4298.000000 4298 100.000000 1 2327 1 chr3B.!!$R1 2326
1 TraesCS3B01G133500 chr2A 95344306 95346458 2152 False 2037.000000 2037 83.816000 2 2167 1 chr2A.!!$F1 2165
2 TraesCS3B01G133500 chr2A 206848540 206850761 2221 True 1476.000000 1476 78.892000 64 2319 1 chr2A.!!$R1 2255
3 TraesCS3B01G133500 chr3D 537285773 537288075 2302 False 1888.000000 1888 81.662000 15 2323 1 chr3D.!!$F1 2308
4 TraesCS3B01G133500 chr7D 51703945 51706249 2304 True 1748.000000 1748 80.540000 15 2325 1 chr7D.!!$R1 2310
5 TraesCS3B01G133500 chr6A 228526567 228528755 2188 False 1698.000000 1698 80.864000 126 2325 1 chr6A.!!$F1 2199
6 TraesCS3B01G133500 chr4B 31124495 31126802 2307 True 1648.000000 1648 79.839000 2 2327 1 chr4B.!!$R1 2325
7 TraesCS3B01G133500 chr2D 516713432 516715511 2079 False 1629.000000 1629 80.959000 25 2114 1 chr2D.!!$F1 2089
8 TraesCS3B01G133500 chr6B 448339623 448341912 2289 False 1574.000000 1574 79.233000 19 2325 1 chr6B.!!$F1 2306
9 TraesCS3B01G133500 chr1B 337933885 337936175 2290 True 1574.000000 1574 79.279000 15 2325 1 chr1B.!!$R1 2310
10 TraesCS3B01G133500 chr1B 178888492 178890608 2116 True 728.666667 992 90.041333 1 2325 3 chr1B.!!$R2 2324
11 TraesCS3B01G133500 chr2B 461255072 461256603 1531 False 1334.000000 1334 82.448000 2 1539 1 chr2B.!!$F1 1537
12 TraesCS3B01G133500 chr5A 644295486 644297054 1568 True 1249.000000 1249 81.199000 64 1653 1 chr5A.!!$R1 1589
13 TraesCS3B01G133500 chr6D 149474051 149475014 963 False 841.000000 841 82.645000 2 955 1 chr6D.!!$F1 953
14 TraesCS3B01G133500 chr6D 149501260 149502250 990 False 588.000000 588 77.557000 1104 2104 1 chr6D.!!$F2 1000
15 TraesCS3B01G133500 chr5B 415060557 415061353 796 False 815.000000 815 85.268000 1370 2163 1 chr5B.!!$F1 793

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
186 189 0.250038 ATTCCATCATCGTCGCCCTG 60.250 55.0 0.0 0.0 0.0 4.45 F
1059 1100 0.322546 GGAAGAAGGTGCGGGTTGAT 60.323 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1284 0.392193 AGCATGGTGTAGTCTGCAGC 60.392 55.0 9.47 12.62 37.09 5.25 R
2010 2070 0.620556 ATCTGTTGAACTGGCCCGAT 59.379 50.0 0.00 0.00 0.00 4.18 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
98 99 3.736100 CGCAAATCCCGCAGCACA 61.736 61.111 0.00 0.00 0.00 4.57
114 115 2.418777 CATCTCGCTGCGGATGGA 59.581 61.111 29.40 20.38 36.60 3.41
168 171 1.705997 CCCCTACCCAGCGCCTTAAT 61.706 60.000 2.29 0.00 0.00 1.40
185 188 0.469917 AATTCCATCATCGTCGCCCT 59.530 50.000 0.00 0.00 0.00 5.19
186 189 0.250038 ATTCCATCATCGTCGCCCTG 60.250 55.000 0.00 0.00 0.00 4.45
187 190 1.613317 TTCCATCATCGTCGCCCTGT 61.613 55.000 0.00 0.00 0.00 4.00
262 270 1.627329 TCAGCCATCAGAAGAGCAAGT 59.373 47.619 0.00 0.00 0.00 3.16
423 446 4.969196 CACCGCCGCACTGACTGT 62.969 66.667 0.00 0.00 0.00 3.55
445 469 1.609239 GACCCCATCCACTGCATCA 59.391 57.895 0.00 0.00 0.00 3.07
701 737 1.210478 GTAGGCCATCTTCTTCCTGCA 59.790 52.381 5.01 0.00 32.57 4.41
741 777 3.782244 GCTGCTGACGGCGTCAAG 61.782 66.667 37.97 32.83 42.26 3.02
960 996 2.338620 CACGCCTCCTTCGACACA 59.661 61.111 0.00 0.00 0.00 3.72
963 999 0.892358 ACGCCTCCTTCGACACACTA 60.892 55.000 0.00 0.00 0.00 2.74
981 1017 1.657594 CTACAGCTTCATGTGCGAGTG 59.342 52.381 16.97 10.09 34.56 3.51
1014 1055 0.747644 TGCCCATGCAATACTGGTCG 60.748 55.000 3.47 0.00 46.66 4.79
1017 1058 0.940126 CCATGCAATACTGGTCGCTC 59.060 55.000 0.00 0.00 0.00 5.03
1053 1094 1.675641 CCTTGGGAAGAAGGTGCGG 60.676 63.158 0.00 0.00 38.19 5.69
1059 1100 0.322546 GGAAGAAGGTGCGGGTTGAT 60.323 55.000 0.00 0.00 0.00 2.57
1294 1338 1.449601 CGGGTGGAAGATTGGTCGG 60.450 63.158 0.00 0.00 0.00 4.79
1383 1427 1.754234 GCCCCGCTTCATGGTGATT 60.754 57.895 0.00 0.00 0.00 2.57
1428 1472 2.432628 GACGGCCAACGGAGTGAG 60.433 66.667 2.24 0.00 45.00 3.51
1513 1564 3.749373 GCAACCACGACGACGACG 61.749 66.667 17.60 17.60 42.66 5.12
1655 1714 3.009115 ACCTAGGCGCCACCACAT 61.009 61.111 31.54 9.39 43.14 3.21
1712 1771 4.105733 TGCGAGCAATGCCAAGCG 62.106 61.111 0.00 2.18 35.48 4.68
1943 2002 2.223249 ACTTCGACAACAACATGCACAC 60.223 45.455 0.00 0.00 0.00 3.82
2126 2190 2.162608 CCAACGACAACAAAGACAACCA 59.837 45.455 0.00 0.00 0.00 3.67
2247 2474 1.152247 AGTGCCCACCAGACAGAGA 60.152 57.895 0.00 0.00 0.00 3.10
2259 2486 1.304052 ACAGAGAGCTCGTCAGGCT 60.304 57.895 8.37 0.00 43.26 4.58
2262 2489 4.127040 AGAGCTCGTCAGGCTGCG 62.127 66.667 20.27 20.27 40.40 5.18
2270 2497 2.357881 TCAGGCTGCGAGCAACTG 60.358 61.111 10.34 17.78 44.75 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 3.430862 GTGCTGCGGGATTTGCGA 61.431 61.111 0.00 0.00 34.24 5.10
98 99 2.419198 GTCCATCCGCAGCGAGAT 59.581 61.111 18.75 14.41 0.00 2.75
168 171 1.143838 CAGGGCGACGATGATGGAA 59.856 57.895 0.00 0.00 0.00 3.53
219 227 1.613317 CCGTCCAGCCACAGTCCATA 61.613 60.000 0.00 0.00 0.00 2.74
262 270 4.147449 CGGATCTGAGGCCGCACA 62.147 66.667 4.49 0.00 41.17 4.57
423 446 3.770040 CAGTGGATGGGGTCGCGA 61.770 66.667 3.71 3.71 0.00 5.87
445 469 4.218578 CCTCGGCTGCTCGCAGAT 62.219 66.667 22.09 0.00 46.30 2.90
460 484 2.157738 GCAGTTCTTCTCAATGTGCCT 58.842 47.619 0.00 0.00 0.00 4.75
496 520 3.393360 GCTACTGGCACCTCTGGT 58.607 61.111 0.00 0.00 41.35 4.00
637 673 2.049185 GCGAGTGGCTCTCTCTGGA 61.049 63.158 14.04 0.00 40.75 3.86
680 716 1.475930 GCAGGAAGAAGATGGCCTACC 60.476 57.143 3.32 0.00 0.00 3.18
682 718 1.210478 GTGCAGGAAGAAGATGGCCTA 59.790 52.381 3.32 0.00 0.00 3.93
960 996 1.273606 ACTCGCACATGAAGCTGTAGT 59.726 47.619 0.00 4.46 0.00 2.73
963 999 0.952497 CCACTCGCACATGAAGCTGT 60.952 55.000 0.00 2.51 0.00 4.40
981 1017 2.126031 GGCACCTTCTCGACGACC 60.126 66.667 0.00 0.00 0.00 4.79
1005 1046 1.471119 TTCCTTCGAGCGACCAGTAT 58.529 50.000 0.00 0.00 0.00 2.12
1017 1058 2.235016 AGGATCTCCTCGATTCCTTCG 58.765 52.381 0.00 0.00 44.77 3.79
1053 1094 2.167861 GCTGTCGAGGCGATCAACC 61.168 63.158 0.00 0.00 38.42 3.77
1059 1100 3.749064 GTCCTGCTGTCGAGGCGA 61.749 66.667 5.94 0.00 0.00 5.54
1239 1280 1.738099 GGTGTAGTCTGCAGCGGTG 60.738 63.158 9.47 10.98 0.00 4.94
1240 1281 1.544825 ATGGTGTAGTCTGCAGCGGT 61.545 55.000 9.47 4.25 37.18 5.68
1241 1282 1.086067 CATGGTGTAGTCTGCAGCGG 61.086 60.000 9.47 6.46 37.18 5.52
1243 1284 0.392193 AGCATGGTGTAGTCTGCAGC 60.392 55.000 9.47 12.62 37.09 5.25
1245 1286 0.975887 TGAGCATGGTGTAGTCTGCA 59.024 50.000 0.00 0.00 37.09 4.41
1248 1289 2.169352 GTGGATGAGCATGGTGTAGTCT 59.831 50.000 0.00 0.00 0.00 3.24
1410 1454 2.915659 TCACTCCGTTGGCCGTCT 60.916 61.111 0.00 0.00 33.66 4.18
1729 1788 4.148825 CGGAGAGCGTGGGGAAGG 62.149 72.222 0.00 0.00 0.00 3.46
1768 1827 1.154016 AGATGTCGTTCTGCGTCGG 60.154 57.895 0.00 0.00 42.13 4.79
1965 2024 4.116328 CCGAAGGCGACGAGCTGA 62.116 66.667 0.00 0.00 46.14 4.26
1996 2055 3.089874 CGATGCTTGGGAGGGGGA 61.090 66.667 0.00 0.00 0.00 4.81
2007 2067 1.675641 GTTGAACTGGCCCGATGCT 60.676 57.895 0.00 0.00 40.92 3.79
2010 2070 0.620556 ATCTGTTGAACTGGCCCGAT 59.379 50.000 0.00 0.00 0.00 4.18
2042 2102 2.964310 ATCTCCAGCGTGCAGGCTT 61.964 57.895 30.11 13.73 42.53 4.35
2043 2103 3.397439 ATCTCCAGCGTGCAGGCT 61.397 61.111 27.36 27.36 46.13 4.58
2259 2486 2.597713 CGTCTTGCAGTTGCTCGCA 61.598 57.895 5.62 0.00 42.66 5.10
2301 2528 1.640428 CAAGCTCCTTTACGATGCGA 58.360 50.000 0.00 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.