Multiple sequence alignment - TraesCS3D01G019600

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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 TraesCS3D01G019600 chr3D 100.000 2288 0 0 1 2288 6530972 6528685 0.000000e+00 4226
1 TraesCS3D01G019600 chr3D 86.984 1744 175 29 1 1720 5431483 5429768 0.000000e+00 1916
2 TraesCS3D01G019600 chr3D 86.678 1749 178 28 1 1724 121530699 121532417 0.000000e+00 1888
3 TraesCS3D01G019600 chr7D 91.519 1745 115 16 1 1726 533932795 533934525 0.000000e+00 2372
4 TraesCS3D01G019600 chr7D 91.304 575 41 5 1157 1728 121215538 121214970 0.000000e+00 776
5 TraesCS3D01G019600 chr2B 89.902 1733 138 14 4 1723 54775218 54776926 0.000000e+00 2196
6 TraesCS3D01G019600 chr2B 90.251 995 73 8 736 1726 783932631 783931657 0.000000e+00 1279
7 TraesCS3D01G019600 chr2B 88.202 534 40 6 1198 1728 612692317 612691804 1.160000e-172 616
8 TraesCS3D01G019600 chr7A 88.218 1740 176 23 1 1725 221704930 221706655 0.000000e+00 2050
9 TraesCS3D01G019600 chr1D 87.228 1746 164 32 1 1725 209755854 209757561 0.000000e+00 1934
10 TraesCS3D01G019600 chr2D 87.115 1754 167 37 1 1725 644388798 644390521 0.000000e+00 1932
11 TraesCS3D01G019600 chr3B 86.865 1751 184 22 1 1728 97752893 97751166 0.000000e+00 1917
12 TraesCS3D01G019600 chr3B 90.669 568 40 7 1726 2288 6751623 6752182 0.000000e+00 743
13 TraesCS3D01G019600 chr6B 86.564 1749 185 29 1 1726 618934432 618936153 0.000000e+00 1882
14 TraesCS3D01G019600 chr6B 86.049 1749 186 28 1 1728 643872269 643870558 0.000000e+00 1825
15 TraesCS3D01G019600 chr5B 86.465 1751 172 34 1 1728 693957780 693956072 0.000000e+00 1860
16 TraesCS3D01G019600 chr5B 86.400 1750 172 36 1 1726 369339858 369338151 0.000000e+00 1853
17 TraesCS3D01G019600 chr5A 88.103 891 88 14 846 1728 404056790 404055910 0.000000e+00 1042
18 TraesCS3D01G019600 chr5A 90.417 720 65 2 1010 1726 392131784 392132502 0.000000e+00 944
19 TraesCS3D01G019600 chr5A 89.342 441 38 4 1294 1727 511895724 511896162 1.550000e-151 545
20 TraesCS3D01G019600 chr3A 90.796 565 40 9 1726 2288 13736603 13737157 0.000000e+00 745


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 TraesCS3D01G019600 chr3D 6528685 6530972 2287 True 4226 4226 100.000 1 2288 1 chr3D.!!$R2 2287
1 TraesCS3D01G019600 chr3D 5429768 5431483 1715 True 1916 1916 86.984 1 1720 1 chr3D.!!$R1 1719
2 TraesCS3D01G019600 chr3D 121530699 121532417 1718 False 1888 1888 86.678 1 1724 1 chr3D.!!$F1 1723
3 TraesCS3D01G019600 chr7D 533932795 533934525 1730 False 2372 2372 91.519 1 1726 1 chr7D.!!$F1 1725
4 TraesCS3D01G019600 chr7D 121214970 121215538 568 True 776 776 91.304 1157 1728 1 chr7D.!!$R1 571
5 TraesCS3D01G019600 chr2B 54775218 54776926 1708 False 2196 2196 89.902 4 1723 1 chr2B.!!$F1 1719
6 TraesCS3D01G019600 chr2B 783931657 783932631 974 True 1279 1279 90.251 736 1726 1 chr2B.!!$R2 990
7 TraesCS3D01G019600 chr2B 612691804 612692317 513 True 616 616 88.202 1198 1728 1 chr2B.!!$R1 530
8 TraesCS3D01G019600 chr7A 221704930 221706655 1725 False 2050 2050 88.218 1 1725 1 chr7A.!!$F1 1724
9 TraesCS3D01G019600 chr1D 209755854 209757561 1707 False 1934 1934 87.228 1 1725 1 chr1D.!!$F1 1724
10 TraesCS3D01G019600 chr2D 644388798 644390521 1723 False 1932 1932 87.115 1 1725 1 chr2D.!!$F1 1724
11 TraesCS3D01G019600 chr3B 97751166 97752893 1727 True 1917 1917 86.865 1 1728 1 chr3B.!!$R1 1727
12 TraesCS3D01G019600 chr3B 6751623 6752182 559 False 743 743 90.669 1726 2288 1 chr3B.!!$F1 562
13 TraesCS3D01G019600 chr6B 618934432 618936153 1721 False 1882 1882 86.564 1 1726 1 chr6B.!!$F1 1725
14 TraesCS3D01G019600 chr6B 643870558 643872269 1711 True 1825 1825 86.049 1 1728 1 chr6B.!!$R1 1727
15 TraesCS3D01G019600 chr5B 693956072 693957780 1708 True 1860 1860 86.465 1 1728 1 chr5B.!!$R2 1727
16 TraesCS3D01G019600 chr5B 369338151 369339858 1707 True 1853 1853 86.400 1 1726 1 chr5B.!!$R1 1725
17 TraesCS3D01G019600 chr5A 404055910 404056790 880 True 1042 1042 88.103 846 1728 1 chr5A.!!$R1 882
18 TraesCS3D01G019600 chr5A 392131784 392132502 718 False 944 944 90.417 1010 1726 1 chr5A.!!$F1 716
19 TraesCS3D01G019600 chr3A 13736603 13737157 554 False 745 745 90.796 1726 2288 1 chr3A.!!$F1 562

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
181 195 0.104725 CTCCTCCTTAGGCTCCCCAT 60.105 60.0 0.0 0.0 43.31 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2293 0.03582 GCACAAACGGGGGATAGTCA 60.036 55.0 0.0 0.0 0.0 3.41 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
181 195 0.104725 CTCCTCCTTAGGCTCCCCAT 60.105 60.000 0.00 0.00 43.31 4.00
225 239 1.250328 CCGTGTCCCAGTACACTACA 58.750 55.000 5.68 0.00 46.13 2.74
228 243 2.555325 CGTGTCCCAGTACACTACAGAA 59.445 50.000 5.68 0.00 46.13 3.02
240 255 5.056894 ACACTACAGAAGTCGGTCATTAC 57.943 43.478 0.00 0.00 35.76 1.89
249 264 1.227263 CGGTCATTACGAGCCCAGG 60.227 63.158 0.00 0.00 39.03 4.45
294 309 0.167470 CCTCTGTTTAGCGTCGTCGA 59.833 55.000 6.17 0.00 39.71 4.20
317 332 4.613143 GCCTGATTCATGGCCCAT 57.387 55.556 0.00 0.00 43.11 4.00
404 419 3.200593 GCCCTCATGAGCACTGCG 61.201 66.667 17.76 2.31 0.00 5.18
456 472 0.868406 GAAGTTCAAGCACACCTCCG 59.132 55.000 0.00 0.00 0.00 4.63
649 669 3.244112 GCAGGGTGAGTAAATATAGGCGT 60.244 47.826 0.00 0.00 0.00 5.68
721 743 5.164620 TCAATAAGCCATGAACTCTGTGA 57.835 39.130 0.00 0.00 0.00 3.58
804 834 1.134848 GTTGACAACAAGGGCAAGCAA 60.135 47.619 13.52 0.00 36.64 3.91
820 850 0.887933 GCAACCGGTTCATCCAATGT 59.112 50.000 19.24 0.00 35.57 2.71
1074 1121 1.891919 GAACAACACCGGCTGCTCA 60.892 57.895 0.00 0.00 0.00 4.26
1159 1206 2.006888 CCGCCGTTCAACATATCAAGT 58.993 47.619 0.00 0.00 0.00 3.16
1183 1230 2.611971 GGCTACATGGTGACGTTCAAGA 60.612 50.000 0.00 0.00 0.00 3.02
1203 1250 2.650116 CCTCACTCCCGACACCCTG 61.650 68.421 0.00 0.00 0.00 4.45
1254 1310 1.525077 GGTGGTCAACAAGTGCGGA 60.525 57.895 0.00 0.00 0.00 5.54
1325 1395 6.207025 TCCTTCCTAAGTATTATCGAGTCTGC 59.793 42.308 0.00 0.00 0.00 4.26
1372 1477 7.959733 TGTTTGAACTATCGTTATGATGTGTC 58.040 34.615 0.00 0.00 37.99 3.67
1382 1487 7.481275 TCGTTATGATGTGTCGTACTATGTA 57.519 36.000 0.00 0.00 0.00 2.29
1394 1499 9.596677 GTGTCGTACTATGTAATCTGAACTATC 57.403 37.037 0.00 0.00 0.00 2.08
1422 1532 7.219484 AGTAGTTGATGCTTTGTTTATGCTT 57.781 32.000 0.00 0.00 0.00 3.91
1558 1668 2.162681 GGCTTTGTCCACTAACATGCT 58.837 47.619 0.00 0.00 32.84 3.79
1559 1669 2.558359 GGCTTTGTCCACTAACATGCTT 59.442 45.455 0.00 0.00 32.84 3.91
1574 1684 2.975732 TGCTTGCAATCAAACACCAA 57.024 40.000 0.00 0.00 0.00 3.67
1580 1690 2.954989 TGCAATCAAACACCAAGCAGTA 59.045 40.909 0.00 0.00 0.00 2.74
1701 1828 2.286831 GCTATGCAATGCAGCTACTGTG 60.287 50.000 14.98 0.00 43.65 3.66
1794 1922 2.325082 CGTGCCCCTTCGGTTCTTG 61.325 63.158 0.00 0.00 0.00 3.02
1816 1948 5.424068 TGACTCCTGAATGGGGGATATAAT 58.576 41.667 0.00 0.00 41.89 1.28
1943 2075 1.412710 CCCTTTGTCTAGCGCCTATCA 59.587 52.381 2.29 0.00 0.00 2.15
1970 2102 0.838987 AAGGCGACTAGGGTTTCCCA 60.839 55.000 7.60 0.00 44.27 4.37
2084 2216 9.057089 CCATTTTTAGTTAGAGTGTTGAGTTCT 57.943 33.333 0.00 0.00 0.00 3.01
2091 2223 8.644374 AGTTAGAGTGTTGAGTTCTCTTAGAT 57.356 34.615 0.00 0.00 39.03 1.98
2113 2245 4.142780 GTCCTATTTGAGGGCGGC 57.857 61.111 0.00 0.00 46.70 6.53
2152 2284 4.147321 CCTGAATGGGATAATGTCCTTGG 58.853 47.826 0.00 0.00 46.91 3.61
2154 2286 3.205056 TGAATGGGATAATGTCCTTGGCT 59.795 43.478 0.00 0.00 46.91 4.75
2155 2287 3.515602 ATGGGATAATGTCCTTGGCTC 57.484 47.619 0.00 0.00 46.91 4.70
2156 2288 1.494721 TGGGATAATGTCCTTGGCTCC 59.505 52.381 0.00 0.00 46.91 4.70
2157 2289 1.777272 GGGATAATGTCCTTGGCTCCT 59.223 52.381 0.00 0.00 46.91 3.69
2158 2290 2.175715 GGGATAATGTCCTTGGCTCCTT 59.824 50.000 0.00 0.00 46.91 3.36
2159 2291 3.217626 GGATAATGTCCTTGGCTCCTTG 58.782 50.000 0.00 0.00 44.16 3.61
2160 2292 2.128771 TAATGTCCTTGGCTCCTTGC 57.871 50.000 0.00 0.00 41.94 4.01
2161 2293 0.407139 AATGTCCTTGGCTCCTTGCT 59.593 50.000 0.00 0.00 42.39 3.91
2191 2323 0.716926 CGTTTGTGCGTTGCGTCTAC 60.717 55.000 0.00 0.00 0.00 2.59
2197 2329 1.011968 TGCGTTGCGTCTACCATCAC 61.012 55.000 0.00 0.00 0.00 3.06
2215 2348 3.322466 CGGAGGGCCTGTGAAGGT 61.322 66.667 12.95 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 214 0.036765 GTACTGGGACACGGCAATCA 60.037 55.000 0.00 0.00 0.00 2.57
210 224 3.119919 CGACTTCTGTAGTGTACTGGGAC 60.120 52.174 0.00 0.00 37.17 4.46
225 239 1.134560 GGCTCGTAATGACCGACTTCT 59.865 52.381 0.00 0.00 0.00 2.85
228 243 0.968901 TGGGCTCGTAATGACCGACT 60.969 55.000 0.00 0.00 0.00 4.18
240 255 0.895530 TACAAGAACTCCTGGGCTCG 59.104 55.000 0.00 0.00 0.00 5.03
249 264 4.338379 AGTGGTCCAAGTACAAGAACTC 57.662 45.455 0.00 0.00 0.00 3.01
294 309 0.749454 GCCATGAATCAGGCCGTCTT 60.749 55.000 11.11 0.00 45.18 3.01
317 332 0.530288 TGGCAGTCGACATCATTCGA 59.470 50.000 19.50 0.00 45.62 3.71
456 472 2.479560 GCACCAAGTTTGAGAACACCAC 60.480 50.000 0.00 0.00 38.26 4.16
557 574 1.301558 CTCCATCGCCATGAGCTCC 60.302 63.158 12.15 0.00 40.39 4.70
649 669 2.313041 TCACTCTTCCTCCTCTCCATCA 59.687 50.000 0.00 0.00 0.00 3.07
721 743 0.111061 TGCAAAGGAGTCAGGCACAT 59.889 50.000 0.00 0.00 0.00 3.21
778 808 1.890041 CCTTGTTGTCAACGGCCGA 60.890 57.895 35.90 6.51 0.00 5.54
804 834 0.392461 CGGACATTGGATGAACCGGT 60.392 55.000 0.00 0.00 43.58 5.28
820 850 4.680237 CGGCAGCACAACCTCGGA 62.680 66.667 0.00 0.00 0.00 4.55
913 948 1.525718 TAGTGGTCGTAGTTGCGGCA 61.526 55.000 0.00 0.00 38.35 5.69
1074 1121 0.257039 GCTTCACCATCACCCTCCAT 59.743 55.000 0.00 0.00 0.00 3.41
1149 1196 4.141711 ACCATGTAGCCGAACTTGATATGT 60.142 41.667 0.00 0.00 0.00 2.29
1159 1206 0.319083 AACGTCACCATGTAGCCGAA 59.681 50.000 0.00 0.00 0.00 4.30
1183 1230 1.686110 GGGTGTCGGGAGTGAGGAT 60.686 63.158 0.00 0.00 0.00 3.24
1254 1310 2.235546 GAAGGCTTCGTCGTGCTTT 58.764 52.632 12.12 9.18 0.00 3.51
1313 1369 7.042051 GCATAAACCATAAAGCAGACTCGATAA 60.042 37.037 0.00 0.00 0.00 1.75
1325 1395 8.761575 AACAGTTCAATGCATAAACCATAAAG 57.238 30.769 16.99 7.10 0.00 1.85
1394 1499 7.698130 GCATAAACAAAGCATCAACTACTTAGG 59.302 37.037 0.00 0.00 0.00 2.69
1422 1532 3.011818 CCACACATCATAAGCAGAGCAA 58.988 45.455 0.00 0.00 0.00 3.91
1453 1563 0.036164 TTACCAGCACACTTCGGCAT 59.964 50.000 0.00 0.00 0.00 4.40
1540 1650 3.004629 TGCAAGCATGTTAGTGGACAAAG 59.995 43.478 0.00 0.00 32.47 2.77
1558 1668 2.168106 ACTGCTTGGTGTTTGATTGCAA 59.832 40.909 0.00 0.00 0.00 4.08
1559 1669 1.755959 ACTGCTTGGTGTTTGATTGCA 59.244 42.857 0.00 0.00 0.00 4.08
1701 1828 0.589708 GTGTTTGGTTGCCGTAGTCC 59.410 55.000 0.00 0.00 0.00 3.85
1794 1922 5.251700 ACATTATATCCCCCATTCAGGAGTC 59.748 44.000 0.00 0.00 41.22 3.36
1816 1948 9.656040 TTCTACCTTGCTAATAATAACGAAACA 57.344 29.630 0.00 0.00 0.00 2.83
1846 1978 6.205270 ACATGCATCGACATTCTAATATTGCA 59.795 34.615 0.00 4.60 41.25 4.08
1943 2075 0.389948 CCTAGTCGCCTTGTTCGCTT 60.390 55.000 0.00 0.00 0.00 4.68
1970 2102 1.899437 ATGACGTCAACGGGAGCCAT 61.899 55.000 24.13 0.00 44.95 4.40
1973 2105 0.802607 GAGATGACGTCAACGGGAGC 60.803 60.000 24.13 0.00 44.95 4.70
2043 2175 0.620556 AATGGAGCGGGATCACACTT 59.379 50.000 0.00 0.00 0.00 3.16
2139 2271 2.620585 GCAAGGAGCCAAGGACATTATC 59.379 50.000 0.00 0.00 37.23 1.75
2152 2284 0.107643 GGGGATAGTCAGCAAGGAGC 59.892 60.000 0.00 0.00 46.19 4.70
2154 2286 1.048724 CGGGGGATAGTCAGCAAGGA 61.049 60.000 0.00 0.00 0.00 3.36
2155 2287 1.338136 ACGGGGGATAGTCAGCAAGG 61.338 60.000 0.00 0.00 0.00 3.61
2156 2288 0.541863 AACGGGGGATAGTCAGCAAG 59.458 55.000 0.00 0.00 0.00 4.01
2157 2289 0.988832 AAACGGGGGATAGTCAGCAA 59.011 50.000 0.00 0.00 0.00 3.91
2158 2290 0.251916 CAAACGGGGGATAGTCAGCA 59.748 55.000 0.00 0.00 0.00 4.41
2159 2291 0.252197 ACAAACGGGGGATAGTCAGC 59.748 55.000 0.00 0.00 0.00 4.26
2160 2292 2.012051 GCACAAACGGGGGATAGTCAG 61.012 57.143 0.00 0.00 0.00 3.51
2161 2293 0.035820 GCACAAACGGGGGATAGTCA 60.036 55.000 0.00 0.00 0.00 3.41
2191 2323 4.181010 CAGGCCCTCCGGTGATGG 62.181 72.222 4.76 0.00 37.47 3.51
2197 2329 4.101448 CCTTCACAGGCCCTCCGG 62.101 72.222 0.00 0.00 37.47 5.14
2203 2335 0.603975 GAGACACACCTTCACAGGCC 60.604 60.000 0.00 0.00 45.56 5.19
2215 2348 4.346127 CCTGGGATATTCATCAGAGACACA 59.654 45.833 0.00 0.00 32.32 3.72


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

AutoCloner maintained by Alex Coulton.