Multiple sequence alignment - TraesCS1D01G105700

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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 TraesCS1D01G105700 chr1D 100.000 2282 0 0 1 2282 97547889 97545608 0.000000e+00 4215.0
1 TraesCS1D01G105700 chr1A 92.473 2285 125 27 3 2282 92582315 92580073 0.000000e+00 3223.0
2 TraesCS1D01G105700 chr7D 81.168 1301 145 36 3 1297 449542201 449540995 0.000000e+00 953.0
3 TraesCS1D01G105700 chr4D 82.372 919 145 11 159 1069 425253086 425253995 0.000000e+00 784.0
4 TraesCS1D01G105700 chr4D 77.108 415 81 9 878 1284 428710570 428710162 6.340000e-56 228.0
5 TraesCS1D01G105700 chr3D 83.639 709 76 20 597 1293 10825806 10825126 4.140000e-177 630.0
6 TraesCS1D01G105700 chr4B 75.721 1145 255 20 177 1307 166834042 166832907 9.210000e-154 553.0
7 TraesCS1D01G105700 chr1B 76.759 938 197 18 382 1307 220751209 220750281 2.620000e-139 505.0
8 TraesCS1D01G105700 chr1B 88.506 348 32 4 1943 2282 155730353 155730700 4.540000e-112 414.0
9 TraesCS1D01G105700 chr7A 77.297 762 152 18 558 1307 11082043 11082795 1.620000e-116 429.0
10 TraesCS1D01G105700 chr7A 77.165 762 153 18 558 1307 11072447 11073199 7.540000e-115 424.0
11 TraesCS1D01G105700 chr2B 82.164 342 52 8 969 1305 128561495 128561158 3.710000e-73 285.0
12 TraesCS1D01G105700 chr2B 76.860 363 63 17 1663 2009 753007112 753006755 3.870000e-43 185.0
13 TraesCS1D01G105700 chrUn 77.608 393 74 11 918 1302 407447556 407447170 2.280000e-55 226.0
14 TraesCS1D01G105700 chr2D 77.064 436 71 24 1591 2009 617197471 617197048 8.200000e-55 224.0
15 TraesCS1D01G105700 chr2A 74.600 437 79 28 1591 2009 747306201 747306623 1.810000e-36 163.0
16 TraesCS1D01G105700 chr5D 88.000 50 3 3 1750 1796 264027001 264026952 3.170000e-04 56.5
17 TraesCS1D01G105700 chr5A 100.000 30 0 0 1750 1779 350267645 350267616 3.170000e-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 TraesCS1D01G105700 chr1D 97545608 97547889 2281 True 4215 4215 100.000 1 2282 1 chr1D.!!$R1 2281
1 TraesCS1D01G105700 chr1A 92580073 92582315 2242 True 3223 3223 92.473 3 2282 1 chr1A.!!$R1 2279
2 TraesCS1D01G105700 chr7D 449540995 449542201 1206 True 953 953 81.168 3 1297 1 chr7D.!!$R1 1294
3 TraesCS1D01G105700 chr4D 425253086 425253995 909 False 784 784 82.372 159 1069 1 chr4D.!!$F1 910
4 TraesCS1D01G105700 chr3D 10825126 10825806 680 True 630 630 83.639 597 1293 1 chr3D.!!$R1 696
5 TraesCS1D01G105700 chr4B 166832907 166834042 1135 True 553 553 75.721 177 1307 1 chr4B.!!$R1 1130
6 TraesCS1D01G105700 chr1B 220750281 220751209 928 True 505 505 76.759 382 1307 1 chr1B.!!$R1 925
7 TraesCS1D01G105700 chr7A 11082043 11082795 752 False 429 429 77.297 558 1307 1 chr7A.!!$F2 749
8 TraesCS1D01G105700 chr7A 11072447 11073199 752 False 424 424 77.165 558 1307 1 chr7A.!!$F1 749

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
135 136 0.734889 GTCCCAATCTCGCAACATGG 59.265 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 1407 0.032515 TCCCTCTGCGATGGTCCTAA 60.033 55.0 0.0 0.0 0.0 2.69 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
68 69 8.200024 TGTTTCAAATATTTGGGATGAGGAAA 57.800 30.769 24.40 13.60 38.66 3.13
135 136 0.734889 GTCCCAATCTCGCAACATGG 59.265 55.000 0.00 0.00 0.00 3.66
138 139 2.172505 TCCCAATCTCGCAACATGGTAT 59.827 45.455 0.00 0.00 0.00 2.73
139 140 2.291465 CCCAATCTCGCAACATGGTATG 59.709 50.000 0.00 0.00 0.00 2.39
141 142 3.002656 CCAATCTCGCAACATGGTATGTC 59.997 47.826 0.00 0.00 44.07 3.06
142 143 3.827008 ATCTCGCAACATGGTATGTCT 57.173 42.857 0.00 0.00 44.07 3.41
143 144 4.937201 ATCTCGCAACATGGTATGTCTA 57.063 40.909 0.00 0.00 44.07 2.59
144 145 4.729227 TCTCGCAACATGGTATGTCTAA 57.271 40.909 0.00 0.00 44.07 2.10
145 146 5.276461 TCTCGCAACATGGTATGTCTAAT 57.724 39.130 0.00 0.00 44.07 1.73
146 147 5.670485 TCTCGCAACATGGTATGTCTAATT 58.330 37.500 0.00 0.00 44.07 1.40
147 148 6.811954 TCTCGCAACATGGTATGTCTAATTA 58.188 36.000 0.00 0.00 44.07 1.40
148 149 7.441836 TCTCGCAACATGGTATGTCTAATTAT 58.558 34.615 0.00 0.00 44.07 1.28
149 150 7.931407 TCTCGCAACATGGTATGTCTAATTATT 59.069 33.333 0.00 0.00 44.07 1.40
150 151 7.860613 TCGCAACATGGTATGTCTAATTATTG 58.139 34.615 0.00 0.00 44.07 1.90
151 152 7.041440 TCGCAACATGGTATGTCTAATTATTGG 60.041 37.037 0.00 0.00 44.07 3.16
152 153 7.255104 CGCAACATGGTATGTCTAATTATTGGT 60.255 37.037 0.00 0.00 44.07 3.67
153 154 9.062524 GCAACATGGTATGTCTAATTATTGGTA 57.937 33.333 0.00 0.00 44.07 3.25
159 160 9.996554 TGGTATGTCTAATTATTGGTATGACTG 57.003 33.333 0.00 0.00 0.00 3.51
279 280 5.796424 AATTGCTTCATACCAATGGGATC 57.204 39.130 3.55 0.00 38.05 3.36
281 282 2.172505 TGCTTCATACCAATGGGATCGT 59.827 45.455 3.55 0.00 38.05 3.73
318 320 8.994170 GTTAATCTGATTTAGGGTAAGATCTGC 58.006 37.037 8.38 0.00 0.00 4.26
416 431 6.233434 TGCTTGCTAATAGACATATGAAGGG 58.767 40.000 10.38 0.00 0.00 3.95
445 460 2.191400 ACTGCCCTTCTTGCTCATCTA 58.809 47.619 0.00 0.00 0.00 1.98
493 508 6.094048 GCTATTTCTATGTCACAAAGCAAGGA 59.906 38.462 0.00 0.00 0.00 3.36
555 570 3.232213 TCTTGTGAAGTAGATCGTGCC 57.768 47.619 0.00 0.00 0.00 5.01
556 571 2.560981 TCTTGTGAAGTAGATCGTGCCA 59.439 45.455 0.00 0.00 0.00 4.92
662 677 3.576118 GCAATCTGAGCCTGGTATCTCTA 59.424 47.826 0.00 0.00 0.00 2.43
767 782 4.820894 ACTTTATTACCGCAACCTCTCT 57.179 40.909 0.00 0.00 0.00 3.10
812 828 1.677552 GTTCATGTCCTCCGGTGGT 59.322 57.895 21.58 0.01 0.00 4.16
847 863 3.253371 ACGTTGACGCTTCTTTTGATG 57.747 42.857 3.05 0.00 44.43 3.07
942 960 1.893137 AGATAGATTGGTGCGCGGATA 59.107 47.619 8.83 0.00 0.00 2.59
1336 1364 8.709308 AGAATGGTAGTTATGCTCTCAATAGTT 58.291 33.333 0.00 0.00 0.00 2.24
1344 1372 2.302733 TGCTCTCAATAGTTGGTGCTCA 59.697 45.455 0.00 0.00 0.00 4.26
1423 1453 5.594317 AGTAGGGATTGAAATGCGCTTATTT 59.406 36.000 9.73 7.24 33.19 1.40
1425 1455 6.463995 AGGGATTGAAATGCGCTTATTTAA 57.536 33.333 9.73 4.56 30.78 1.52
1472 1502 6.540551 GCCAAGGTTTTAGGAATTGTTTTTCA 59.459 34.615 0.00 0.00 0.00 2.69
1491 1521 7.837202 TTTTCAGTTTTGACGAGTTAGAAGA 57.163 32.000 0.00 0.00 31.71 2.87
1534 1564 8.439993 TTTTTAATAGCCCCAAACAACTTTTC 57.560 30.769 0.00 0.00 0.00 2.29
1607 1637 2.378038 TGGGCAGCCATTACAAAGATC 58.622 47.619 15.19 0.00 0.00 2.75
1615 1645 5.123820 CAGCCATTACAAAGATCGAGGAAAA 59.876 40.000 0.00 0.00 0.00 2.29
1625 1655 2.249844 TCGAGGAAAACCACACTTCC 57.750 50.000 0.00 0.00 41.32 3.46
1633 1663 0.185175 AACCACACTTCCCCCACTTC 59.815 55.000 0.00 0.00 0.00 3.01
1634 1664 0.991355 ACCACACTTCCCCCACTTCA 60.991 55.000 0.00 0.00 0.00 3.02
1664 1694 4.898320 AGGAAACAAAAGGATGATTTGGC 58.102 39.130 4.29 0.00 41.08 4.52
1678 1708 4.880759 TGATTTGGCGTGACAATGAAAAT 58.119 34.783 0.00 0.00 0.00 1.82
1684 1714 5.837437 TGGCGTGACAATGAAAATTTACTT 58.163 33.333 0.00 0.00 0.00 2.24
1818 1850 7.259161 CAATAGACTAGGAAGTGACCAACTAC 58.741 42.308 0.00 0.00 38.56 2.73
1939 1971 9.801873 AGGACGAATTGGAATTATAAAAACATG 57.198 29.630 0.00 0.00 0.00 3.21
1940 1972 9.581099 GGACGAATTGGAATTATAAAAACATGT 57.419 29.630 0.00 0.00 0.00 3.21
1942 1974 9.921637 ACGAATTGGAATTATAAAAACATGTGT 57.078 25.926 0.00 0.00 0.00 3.72
2055 2088 9.314133 TCATATTCAAGATAGCACATAGGTACT 57.686 33.333 0.00 0.00 46.37 2.73
2077 2110 7.209471 ACTCCTAGATGATTAAGACTTAGCG 57.791 40.000 0.00 0.00 0.00 4.26
2116 2149 7.263100 TCACCAAGCTTATATTATGCACAAG 57.737 36.000 0.00 0.00 0.00 3.16
2205 2238 0.242017 ATCGTGCCAGCTTTCTTTGC 59.758 50.000 0.00 0.00 0.00 3.68
2209 2242 1.005748 GCCAGCTTTCTTTGCCACC 60.006 57.895 0.00 0.00 0.00 4.61
2218 2251 0.878523 TCTTTGCCACCGTCACTTCG 60.879 55.000 0.00 0.00 0.00 3.79
2229 2262 1.201704 CGTCACTTCGTCAAGCAATCG 60.202 52.381 0.00 0.00 32.09 3.34
2232 2265 1.792367 CACTTCGTCAAGCAATCGTCA 59.208 47.619 0.00 0.00 32.09 4.35
2235 2268 3.498397 ACTTCGTCAAGCAATCGTCATTT 59.502 39.130 0.00 0.00 32.09 2.32
2243 2276 7.005380 GTCAAGCAATCGTCATTTTTGATTTG 58.995 34.615 0.00 0.00 30.95 2.32
2264 2297 7.872163 TTTGTCACTTGCATGATTGAATAAC 57.128 32.000 6.60 0.00 0.00 1.89
2269 2302 9.571810 GTCACTTGCATGATTGAATAACATAAA 57.428 29.630 6.60 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.227527 CCTTAGATAACAACTGACCCCCTT 59.772 45.833 0.00 0.00 0.00 3.95
1 2 3.780850 CCTTAGATAACAACTGACCCCCT 59.219 47.826 0.00 0.00 0.00 4.79
68 69 6.824958 TGGCTAGAGGGTTTGTCTAATTAT 57.175 37.500 0.00 0.00 0.00 1.28
114 115 2.419990 CCATGTTGCGAGATTGGGACTA 60.420 50.000 0.00 0.00 0.00 2.59
145 146 9.502091 GTTAGGCATAATCAGTCATACCAATAA 57.498 33.333 0.00 0.00 0.00 1.40
146 147 8.880244 AGTTAGGCATAATCAGTCATACCAATA 58.120 33.333 0.00 0.00 0.00 1.90
147 148 7.749666 AGTTAGGCATAATCAGTCATACCAAT 58.250 34.615 0.00 0.00 0.00 3.16
148 149 7.136822 AGTTAGGCATAATCAGTCATACCAA 57.863 36.000 0.00 0.00 0.00 3.67
149 150 6.747414 AGTTAGGCATAATCAGTCATACCA 57.253 37.500 0.00 0.00 0.00 3.25
150 151 7.499232 ACAAAGTTAGGCATAATCAGTCATACC 59.501 37.037 0.00 0.00 0.00 2.73
151 152 8.438676 ACAAAGTTAGGCATAATCAGTCATAC 57.561 34.615 0.00 0.00 0.00 2.39
152 153 9.764363 CTACAAAGTTAGGCATAATCAGTCATA 57.236 33.333 0.00 0.00 0.00 2.15
153 154 7.227512 GCTACAAAGTTAGGCATAATCAGTCAT 59.772 37.037 0.00 0.00 0.00 3.06
154 155 6.538742 GCTACAAAGTTAGGCATAATCAGTCA 59.461 38.462 0.00 0.00 0.00 3.41
155 156 6.763610 AGCTACAAAGTTAGGCATAATCAGTC 59.236 38.462 0.00 0.00 0.00 3.51
156 157 6.653989 AGCTACAAAGTTAGGCATAATCAGT 58.346 36.000 0.00 0.00 0.00 3.41
157 158 7.412853 CAAGCTACAAAGTTAGGCATAATCAG 58.587 38.462 0.00 0.00 0.00 2.90
158 159 6.318648 CCAAGCTACAAAGTTAGGCATAATCA 59.681 38.462 0.00 0.00 0.00 2.57
159 160 6.542370 TCCAAGCTACAAAGTTAGGCATAATC 59.458 38.462 0.00 0.00 0.00 1.75
160 161 6.423182 TCCAAGCTACAAAGTTAGGCATAAT 58.577 36.000 0.00 0.00 0.00 1.28
161 162 5.811190 TCCAAGCTACAAAGTTAGGCATAA 58.189 37.500 0.00 0.00 0.00 1.90
162 163 5.045869 ACTCCAAGCTACAAAGTTAGGCATA 60.046 40.000 0.00 0.00 0.00 3.14
163 164 4.263506 ACTCCAAGCTACAAAGTTAGGCAT 60.264 41.667 0.00 0.00 0.00 4.40
279 280 4.478699 TCAGATTAACTGTGGTTCGTACG 58.521 43.478 9.53 9.53 45.86 3.67
281 282 7.762615 CCTAAATCAGATTAACTGTGGTTCGTA 59.237 37.037 0.00 0.00 45.86 3.43
318 320 3.809832 CCTTAGCCGGACATGATAGTTTG 59.190 47.826 5.05 0.00 0.00 2.93
416 431 1.377856 GAAGGGCAGTTGGGAGAGC 60.378 63.158 0.00 0.00 0.00 4.09
445 460 5.762218 GCATATGCTTTGTATCTTCTGGACT 59.238 40.000 20.64 0.00 38.21 3.85
493 508 6.607198 TCAATTTCCAGTCTTCTCCAAACTTT 59.393 34.615 0.00 0.00 0.00 2.66
535 550 2.560981 TGGCACGATCTACTTCACAAGA 59.439 45.455 0.00 0.00 0.00 3.02
555 570 1.901591 ATTCCAACACTGCCTCACTG 58.098 50.000 0.00 0.00 0.00 3.66
556 571 2.639839 AGTATTCCAACACTGCCTCACT 59.360 45.455 0.00 0.00 0.00 3.41
662 677 2.167662 CCAATTTACGCCTTTCCCACT 58.832 47.619 0.00 0.00 0.00 4.00
817 833 4.330620 AGAAGCGTCAACGTTGAGTTAAAA 59.669 37.500 30.38 5.30 42.02 1.52
820 836 3.088194 AGAAGCGTCAACGTTGAGTTA 57.912 42.857 30.38 7.31 42.02 2.24
847 863 5.763876 ATTATACCCCTAAGCAGGTCATC 57.236 43.478 0.00 0.00 40.79 2.92
942 960 1.670811 CCAAGCTTTCGCCGTCAATAT 59.329 47.619 0.00 0.00 36.60 1.28
992 1015 1.676678 GACTAGCTGCATCCCGTCCA 61.677 60.000 1.02 0.00 0.00 4.02
1073 1100 4.277593 CAAAAACCGCCGCAGCCA 62.278 61.111 0.00 0.00 34.57 4.75
1319 1347 4.878397 AGCACCAACTATTGAGAGCATAAC 59.122 41.667 0.00 0.00 0.00 1.89
1336 1364 2.106338 TCATCACTTTCCTTGAGCACCA 59.894 45.455 0.00 0.00 0.00 4.17
1344 1372 7.581213 TTTATGTTGTGTCATCACTTTCCTT 57.419 32.000 0.00 0.00 44.14 3.36
1371 1399 4.933400 TCTGCGATGGTCCTAAACTTTTAC 59.067 41.667 0.00 0.00 0.00 2.01
1379 1407 0.032515 TCCCTCTGCGATGGTCCTAA 60.033 55.000 0.00 0.00 0.00 2.69
1390 1418 2.119495 TCAATCCCTACTTCCCTCTGC 58.881 52.381 0.00 0.00 0.00 4.26
1436 1466 3.350219 AAACCTTGGCATCATACGTCT 57.650 42.857 0.00 0.00 0.00 4.18
1440 1470 6.715347 ATTCCTAAAACCTTGGCATCATAC 57.285 37.500 0.00 0.00 0.00 2.39
1472 1502 7.714703 AGTTACTCTTCTAACTCGTCAAAACT 58.285 34.615 0.00 0.00 32.45 2.66
1534 1564 9.639601 ACAAAGAAACTCCAAAACTAAAGAAAG 57.360 29.630 0.00 0.00 0.00 2.62
1591 1621 3.797039 TCCTCGATCTTTGTAATGGCTG 58.203 45.455 0.00 0.00 0.00 4.85
1607 1637 1.235724 GGGAAGTGTGGTTTTCCTCG 58.764 55.000 3.56 0.00 42.03 4.63
1615 1645 0.991355 TGAAGTGGGGGAAGTGTGGT 60.991 55.000 0.00 0.00 0.00 4.16
1625 1655 5.128008 TGTTTCCTAAGTTTTTGAAGTGGGG 59.872 40.000 0.00 0.00 0.00 4.96
1633 1663 8.940768 TCATCCTTTTGTTTCCTAAGTTTTTG 57.059 30.769 0.00 0.00 0.00 2.44
1664 1694 7.922505 TTCCAAGTAAATTTTCATTGTCACG 57.077 32.000 0.00 0.00 0.00 4.35
1719 1750 5.560724 TGAGCCAAGTTTGCTATAAGAGTT 58.439 37.500 0.66 0.00 39.69 3.01
1728 1759 1.322442 GTCCTTGAGCCAAGTTTGCT 58.678 50.000 0.14 0.14 39.58 3.91
1768 1799 3.515502 AGCCTTGTCTACACTAAGCATGA 59.484 43.478 0.00 0.00 0.00 3.07
1818 1850 6.692249 TGCATGTTTATGATCGTTATGCTTTG 59.308 34.615 18.51 3.33 39.91 2.77
1866 1898 9.375974 AGTGTTAGTATCCTGCTTATATTACCA 57.624 33.333 0.00 0.00 0.00 3.25
1907 1939 6.699575 ATAATTCCAATTCGTCCTCAAAGG 57.300 37.500 0.00 0.00 36.46 3.11
1913 1945 9.801873 CATGTTTTTATAATTCCAATTCGTCCT 57.198 29.630 0.00 0.00 0.00 3.85
1939 1971 6.119144 ACTTGACTTGTCACATGTTTACAC 57.881 37.500 9.74 0.00 0.00 2.90
1940 1972 5.877564 TGACTTGACTTGTCACATGTTTACA 59.122 36.000 0.00 0.45 39.23 2.41
1941 1973 6.358118 TGACTTGACTTGTCACATGTTTAC 57.642 37.500 0.00 0.00 39.23 2.01
2030 2062 9.579768 GAGTACCTATGTGCTATCTTGAATATG 57.420 37.037 0.00 0.00 37.57 1.78
2031 2063 8.754080 GGAGTACCTATGTGCTATCTTGAATAT 58.246 37.037 0.00 0.00 37.57 1.28
2055 2088 5.334957 CGCGCTAAGTCTTAATCATCTAGGA 60.335 44.000 5.56 0.00 0.00 2.94
2077 2110 1.739466 TGGTGATTCATGCTTTCTCGC 59.261 47.619 0.00 0.00 0.00 5.03
2181 2214 0.169009 GAAAGCTGGCACGATCAACC 59.831 55.000 0.00 0.00 0.00 3.77
2183 2216 1.896220 AAGAAAGCTGGCACGATCAA 58.104 45.000 0.00 0.00 0.00 2.57
2218 2251 6.695292 AATCAAAAATGACGATTGCTTGAC 57.305 33.333 0.00 0.00 31.69 3.18
2229 2262 6.586868 TGCAAGTGACAAATCAAAAATGAC 57.413 33.333 0.00 0.00 36.31 3.06
2232 2265 7.972832 ATCATGCAAGTGACAAATCAAAAAT 57.027 28.000 0.00 0.00 36.31 1.82
2235 2268 6.514063 TCAATCATGCAAGTGACAAATCAAA 58.486 32.000 0.00 0.00 36.31 2.69
2243 2276 9.571810 TTTATGTTATTCAATCATGCAAGTGAC 57.428 29.630 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.