Multiple sequence alignment - TraesCS4B01G188400

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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 TraesCS4B01G188400 chr4B 100.000 2552 0 0 1 2552 409338245 409340796 0.000000e+00 4713.0
1 TraesCS4B01G188400 chr4B 88.620 949 92 5 1 939 587769874 587770816 0.000000e+00 1140.0
2 TraesCS4B01G188400 chr7B 93.717 939 47 3 1 929 34174323 34173387 0.000000e+00 1397.0
3 TraesCS4B01G188400 chr7B 87.158 950 97 12 1 929 368801239 368802184 0.000000e+00 1055.0
4 TraesCS4B01G188400 chr4D 93.721 860 38 7 930 1786 329311026 329311872 0.000000e+00 1275.0
5 TraesCS4B01G188400 chr4D 92.086 695 35 6 1778 2460 329312048 329312734 0.000000e+00 961.0
6 TraesCS4B01G188400 chr4A 89.915 942 57 16 930 1862 140756064 140755152 0.000000e+00 1179.0
7 TraesCS4B01G188400 chr4A 87.740 938 103 3 1 929 292828434 292827500 0.000000e+00 1085.0
8 TraesCS4B01G188400 chr4A 87.354 941 102 9 1 931 740932728 740931795 0.000000e+00 1062.0
9 TraesCS4B01G188400 chr6B 89.031 939 86 9 3 929 101194373 101193440 0.000000e+00 1147.0
10 TraesCS4B01G188400 chr5A 88.924 939 92 3 1 930 698887112 698888047 0.000000e+00 1147.0
11 TraesCS4B01G188400 chr1B 88.924 939 90 5 3 931 642647046 642647980 0.000000e+00 1146.0
12 TraesCS4B01G188400 chr1B 88.559 944 89 9 1 929 508700021 508699082 0.000000e+00 1127.0
13 TraesCS4B01G188400 chr1B 88.417 941 91 10 1 929 538726424 538725490 0.000000e+00 1118.0
14 TraesCS4B01G188400 chr1B 86.737 950 101 13 1 929 622072510 622071565 0.000000e+00 1033.0
15 TraesCS4B01G188400 chr1B 86.175 962 108 13 1 941 403531543 403530586 0.000000e+00 1016.0
16 TraesCS4B01G188400 chr6A 87.474 950 98 7 1 930 84059045 84059993 0.000000e+00 1075.0
17 TraesCS4B01G188400 chr2B 86.794 939 112 7 1 929 65680529 65681465 0.000000e+00 1037.0
18 TraesCS4B01G188400 chr2B 89.396 745 70 5 1 736 768034782 768035526 0.000000e+00 929.0
19 TraesCS4B01G188400 chr2B 81.330 391 50 19 1004 1375 68201723 68201337 1.920000e-76 296.0
20 TraesCS4B01G188400 chr2B 80.628 382 57 11 1004 1375 68207116 68206742 1.930000e-71 279.0
21 TraesCS4B01G188400 chr3B 89.200 500 45 5 1 491 707626705 707626206 1.300000e-172 616.0
22 TraesCS4B01G188400 chr2A 82.940 381 50 13 1004 1375 45085754 45085380 1.890000e-86 329.0
23 TraesCS4B01G188400 chr2A 82.632 380 44 16 1004 1375 45096199 45095834 1.470000e-82 316.0
24 TraesCS4B01G188400 chr2D 81.551 374 56 9 1004 1375 43300841 43300479 1.920000e-76 296.0
25 TraesCS4B01G188400 chr2D 81.067 375 56 10 1004 1375 43295228 43294866 4.160000e-73 285.0
26 TraesCS4B01G188400 chr1A 84.211 152 20 4 1004 1153 133999366 133999515 7.360000e-31 145.0
27 TraesCS4B01G188400 chr7D 94.595 37 1 1 1887 1923 215221202 215221167 3.550000e-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 TraesCS4B01G188400 chr4B 409338245 409340796 2551 False 4713 4713 100.0000 1 2552 1 chr4B.!!$F1 2551
1 TraesCS4B01G188400 chr4B 587769874 587770816 942 False 1140 1140 88.6200 1 939 1 chr4B.!!$F2 938
2 TraesCS4B01G188400 chr7B 34173387 34174323 936 True 1397 1397 93.7170 1 929 1 chr7B.!!$R1 928
3 TraesCS4B01G188400 chr7B 368801239 368802184 945 False 1055 1055 87.1580 1 929 1 chr7B.!!$F1 928
4 TraesCS4B01G188400 chr4D 329311026 329312734 1708 False 1118 1275 92.9035 930 2460 2 chr4D.!!$F1 1530
5 TraesCS4B01G188400 chr4A 140755152 140756064 912 True 1179 1179 89.9150 930 1862 1 chr4A.!!$R1 932
6 TraesCS4B01G188400 chr4A 292827500 292828434 934 True 1085 1085 87.7400 1 929 1 chr4A.!!$R2 928
7 TraesCS4B01G188400 chr4A 740931795 740932728 933 True 1062 1062 87.3540 1 931 1 chr4A.!!$R3 930
8 TraesCS4B01G188400 chr6B 101193440 101194373 933 True 1147 1147 89.0310 3 929 1 chr6B.!!$R1 926
9 TraesCS4B01G188400 chr5A 698887112 698888047 935 False 1147 1147 88.9240 1 930 1 chr5A.!!$F1 929
10 TraesCS4B01G188400 chr1B 642647046 642647980 934 False 1146 1146 88.9240 3 931 1 chr1B.!!$F1 928
11 TraesCS4B01G188400 chr1B 508699082 508700021 939 True 1127 1127 88.5590 1 929 1 chr1B.!!$R2 928
12 TraesCS4B01G188400 chr1B 538725490 538726424 934 True 1118 1118 88.4170 1 929 1 chr1B.!!$R3 928
13 TraesCS4B01G188400 chr1B 622071565 622072510 945 True 1033 1033 86.7370 1 929 1 chr1B.!!$R4 928
14 TraesCS4B01G188400 chr1B 403530586 403531543 957 True 1016 1016 86.1750 1 941 1 chr1B.!!$R1 940
15 TraesCS4B01G188400 chr6A 84059045 84059993 948 False 1075 1075 87.4740 1 930 1 chr6A.!!$F1 929
16 TraesCS4B01G188400 chr2B 65680529 65681465 936 False 1037 1037 86.7940 1 929 1 chr2B.!!$F1 928
17 TraesCS4B01G188400 chr2B 768034782 768035526 744 False 929 929 89.3960 1 736 1 chr2B.!!$F2 735

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
190 191 1.152963 GTCCTGTTGCACCCACAGT 60.153 57.895 14.34 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 1739 0.03601 ATTCAGCCGTAGCAGCAAGT 60.036 50.0 0.0 0.0 43.56 3.16 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
29 30 2.786777 TGACATCATCAAGCTTGCTGT 58.213 42.857 25.13 21.13 33.02 4.40
190 191 1.152963 GTCCTGTTGCACCCACAGT 60.153 57.895 14.34 0.00 0.00 3.55
258 259 2.754658 CGGACACGGTAGGGAGCT 60.755 66.667 0.00 0.00 36.18 4.09
279 280 1.200519 TCGACATAACCAAGGAGGGG 58.799 55.000 0.00 0.00 43.89 4.79
374 375 1.459592 GGTTGTCGAAGTGGAATGACG 59.540 52.381 0.00 0.00 34.11 4.35
554 601 3.753539 GCGCTGTCGACGACACAC 61.754 66.667 26.04 19.02 37.67 3.82
560 607 1.277739 GTCGACGACACACGAGACA 59.722 57.895 22.66 0.00 44.65 3.41
591 638 2.040544 CGGAAAACAGCGAGCCCAT 61.041 57.895 0.00 0.00 0.00 4.00
817 871 7.690256 AGGTTTTAGGCTGATACCATATTAGG 58.310 38.462 18.50 0.00 0.00 2.69
917 971 4.540359 TTACACAGTTGGGCTACGTTAT 57.460 40.909 0.00 0.00 0.00 1.89
1001 1055 2.685999 GGAGCTGGCAGGGGAAAT 59.314 61.111 17.64 0.00 0.00 2.17
1054 1108 0.739561 CCTCTACGAGGCGCTTAACT 59.260 55.000 7.64 0.00 43.29 2.24
1063 1117 2.322081 GCGCTTAACTCCCGCAACA 61.322 57.895 0.00 0.00 46.32 3.33
1065 1119 1.225376 CGCTTAACTCCCGCAACACA 61.225 55.000 0.00 0.00 0.00 3.72
1153 1207 2.369633 ATGATGCGCCTCCTCACCA 61.370 57.895 4.18 0.00 0.00 4.17
1155 1209 3.005539 ATGCGCCTCCTCACCAGT 61.006 61.111 4.18 0.00 0.00 4.00
1218 1272 2.693762 CGCCTTCGTCTCCACCGTA 61.694 63.158 0.00 0.00 0.00 4.02
1377 1431 1.227853 GGCCACCAAGAACGTCAGT 60.228 57.895 0.00 0.00 0.00 3.41
1439 1493 2.995574 CCCCTCCTCGTCCACGTT 60.996 66.667 0.00 0.00 40.80 3.99
1613 1676 3.361794 TGCTTTGCGTGCTTGAATTAA 57.638 38.095 0.00 0.00 0.00 1.40
1614 1677 3.307674 TGCTTTGCGTGCTTGAATTAAG 58.692 40.909 0.00 0.00 39.49 1.85
1631 1694 9.638239 TTGAATTAAGAGTGTGATTTATTTGGC 57.362 29.630 0.00 0.00 0.00 4.52
1676 1739 4.206958 CTGCTACTGCGGCAATGA 57.793 55.556 3.44 0.00 43.34 2.57
1859 2109 3.181440 TGGAAACTTGCTGAGTCAGGAAT 60.181 43.478 25.07 12.52 40.71 3.01
1862 2112 2.157738 ACTTGCTGAGTCAGGAATTGC 58.842 47.619 25.07 9.93 40.71 3.56
1879 2129 2.750350 CGAGCAACTCAAGGGGGT 59.250 61.111 0.00 0.00 0.00 4.95
1904 2154 2.803956 TCGAACGGACAAGGATTTTGTC 59.196 45.455 10.70 10.70 45.89 3.18
1916 2166 3.057019 GGATTTTGTCCGCTTTTTGTCC 58.943 45.455 0.00 0.00 37.23 4.02
1923 2173 0.882927 CCGCTTTTTGTCCGTCTGGA 60.883 55.000 0.00 0.00 43.88 3.86
1940 2190 4.430765 ATCGCCCGTCCGTGTGTC 62.431 66.667 0.00 0.00 0.00 3.67
1944 2194 4.274700 CCCGTCCGTGTGTCGTGT 62.275 66.667 0.00 0.00 37.94 4.49
1945 2195 3.028019 CCGTCCGTGTGTCGTGTG 61.028 66.667 0.00 0.00 37.94 3.82
1946 2196 2.278336 CGTCCGTGTGTCGTGTGT 60.278 61.111 0.00 0.00 37.94 3.72
1947 2197 2.290789 CGTCCGTGTGTCGTGTGTC 61.291 63.158 0.00 0.00 37.94 3.67
1955 2205 0.308684 GTGTCGTGTGTCCGTGTCTA 59.691 55.000 0.00 0.00 0.00 2.59
2020 2270 1.074319 TTTAGACATGTCCGCGTCGC 61.074 55.000 22.21 7.29 37.23 5.19
2029 2279 4.499023 CCGCGTCGCCATTTCGTG 62.499 66.667 12.44 0.00 35.34 4.35
2030 2280 3.474904 CGCGTCGCCATTTCGTGA 61.475 61.111 12.44 0.00 37.28 4.35
2117 2376 3.570212 ACCCCGACCTTGCTGCTT 61.570 61.111 0.00 0.00 0.00 3.91
2174 2434 2.186125 CCCCGTCCCGTAGCTTTC 59.814 66.667 0.00 0.00 0.00 2.62
2177 2437 2.884207 CGTCCCGTAGCTTTCGCC 60.884 66.667 0.00 0.00 36.60 5.54
2343 2603 1.506718 GACTCGAGGACATGCACGA 59.493 57.895 18.41 0.00 0.00 4.35
2345 2605 1.212751 CTCGAGGACATGCACGACA 59.787 57.895 3.91 0.00 0.00 4.35
2461 2723 4.176851 GGACGGCGAGACGAGGTC 62.177 72.222 16.62 0.00 37.61 3.85
2462 2724 4.517703 GACGGCGAGACGAGGTCG 62.518 72.222 16.62 0.00 46.33 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.742372 CGTTTGCCCAGACCTCCG 60.742 66.667 0.00 0.00 0.00 4.63
157 158 0.032615 AGGACCAAGCGATCCTCTCT 60.033 55.000 0.00 0.00 41.83 3.10
190 191 4.015406 ATCAACCCGGCGCACTGA 62.015 61.111 10.83 3.19 0.00 3.41
258 259 2.969950 CCCCTCCTTGGTTATGTCGATA 59.030 50.000 0.00 0.00 0.00 2.92
297 298 1.452368 TGGCGTGCCAAGGTTCTAA 59.548 52.632 11.96 0.00 44.12 2.10
332 333 1.299562 ATCACGACTCGTCTCACGCT 61.300 55.000 0.00 0.00 42.21 5.07
537 584 3.753539 GTGTGTCGTCGACAGCGC 61.754 66.667 27.60 22.19 43.57 5.92
554 601 2.329690 CCCGATCTCGCTGTCTCG 59.670 66.667 0.00 0.00 38.18 4.04
591 638 0.603707 CTTCTTCAGCACCAAGGCGA 60.604 55.000 0.00 0.00 39.27 5.54
596 643 1.165907 CCGCACTTCTTCAGCACCAA 61.166 55.000 0.00 0.00 0.00 3.67
603 650 2.733218 CGACGCCGCACTTCTTCA 60.733 61.111 0.00 0.00 0.00 3.02
737 784 1.530283 GCCGTGCCCTAAACCCTAT 59.470 57.895 0.00 0.00 0.00 2.57
817 871 1.737793 CAGTTCCCACAAATCCTACGC 59.262 52.381 0.00 0.00 0.00 4.42
889 943 5.461078 CGTAGCCCAACTGTGTAATATGTAC 59.539 44.000 0.00 0.00 0.00 2.90
917 971 6.999950 TGCTGATGGTTAGTGTTAGACTTTA 58.000 36.000 0.00 0.00 35.96 1.85
993 1047 1.931007 GCTGCTCCTCCATTTCCCCT 61.931 60.000 0.00 0.00 0.00 4.79
999 1053 4.845580 CCGCGCTGCTCCTCCATT 62.846 66.667 5.56 0.00 0.00 3.16
1050 1104 1.957186 GCGTGTGTTGCGGGAGTTA 60.957 57.895 0.00 0.00 0.00 2.24
1092 1146 1.186267 GGAACCACCACTCGAGGTCT 61.186 60.000 18.41 0.00 40.77 3.85
1168 1222 1.371558 GGCAGAACCTGAACTCGGT 59.628 57.895 0.00 0.00 35.97 4.69
1208 1262 1.721664 CTCGGCGATTACGGTGGAGA 61.722 60.000 11.27 0.00 40.15 3.71
1368 1422 3.112709 GAGCCCGCACTGACGTTC 61.113 66.667 0.00 0.00 0.00 3.95
1397 1451 2.917713 AGAGGCAGAAGAAGAGGAGA 57.082 50.000 0.00 0.00 0.00 3.71
1507 1561 3.636043 CGACTTGCACACGCGGTT 61.636 61.111 12.47 0.00 42.97 4.44
1613 1676 6.313519 TCTAGGCCAAATAAATCACACTCT 57.686 37.500 5.01 0.00 0.00 3.24
1614 1677 6.767902 TGATCTAGGCCAAATAAATCACACTC 59.232 38.462 5.01 0.00 0.00 3.51
1631 1694 6.119240 ACACACCATAATCCATGATCTAGG 57.881 41.667 0.00 0.00 36.69 3.02
1676 1739 0.036010 ATTCAGCCGTAGCAGCAAGT 60.036 50.000 0.00 0.00 43.56 3.16
1686 1749 8.922676 CAATACGATATACTTTTATTCAGCCGT 58.077 33.333 0.00 0.00 0.00 5.68
1839 2089 4.791974 CAATTCCTGACTCAGCAAGTTTC 58.208 43.478 0.00 0.00 38.74 2.78
1847 2097 1.005340 GCTCGCAATTCCTGACTCAG 58.995 55.000 0.00 0.00 0.00 3.35
1859 2109 1.600636 CCCCTTGAGTTGCTCGCAA 60.601 57.895 0.00 0.00 34.87 4.85
1862 2112 1.672356 CACCCCCTTGAGTTGCTCG 60.672 63.158 0.00 0.00 32.35 5.03
1879 2129 1.254026 ATCCTTGTCCGTTCGAGTCA 58.746 50.000 0.00 0.00 0.00 3.41
1904 2154 0.882927 TCCAGACGGACAAAAAGCGG 60.883 55.000 0.00 0.00 35.91 5.52
1916 2166 4.570663 GGACGGGCGATCCAGACG 62.571 72.222 1.00 0.00 36.15 4.18
1923 2173 4.430765 GACACACGGACGGGCGAT 62.431 66.667 0.00 0.00 0.00 4.58
1940 2190 3.246699 ACAAAAATAGACACGGACACACG 59.753 43.478 0.00 0.00 40.31 4.49
1941 2191 4.806342 ACAAAAATAGACACGGACACAC 57.194 40.909 0.00 0.00 0.00 3.82
1942 2192 5.449314 CCAAACAAAAATAGACACGGACACA 60.449 40.000 0.00 0.00 0.00 3.72
1943 2193 4.973663 CCAAACAAAAATAGACACGGACAC 59.026 41.667 0.00 0.00 0.00 3.67
1944 2194 4.036971 CCCAAACAAAAATAGACACGGACA 59.963 41.667 0.00 0.00 0.00 4.02
1945 2195 4.037089 ACCCAAACAAAAATAGACACGGAC 59.963 41.667 0.00 0.00 0.00 4.79
1946 2196 4.208746 ACCCAAACAAAAATAGACACGGA 58.791 39.130 0.00 0.00 0.00 4.69
1947 2197 4.577834 ACCCAAACAAAAATAGACACGG 57.422 40.909 0.00 0.00 0.00 4.94
1955 2205 1.621317 CCGGCCTACCCAAACAAAAAT 59.379 47.619 0.00 0.00 0.00 1.82
1980 2230 4.424566 CATGCTGCACCCGTTGGC 62.425 66.667 3.57 0.00 33.59 4.52
1994 2244 3.365832 GCGGACATGTCTAAAATGCATG 58.634 45.455 24.50 0.00 43.84 4.06
2020 2270 3.304659 CCTCCAAGTGTTTCACGAAATGG 60.305 47.826 0.00 4.25 39.64 3.16
2029 2279 1.578206 GCTCGCCCTCCAAGTGTTTC 61.578 60.000 0.00 0.00 0.00 2.78
2030 2280 1.600916 GCTCGCCCTCCAAGTGTTT 60.601 57.895 0.00 0.00 0.00 2.83
2218 2478 4.783621 GGAGCTGGCCATCGCACA 62.784 66.667 18.35 0.00 36.38 4.57
2240 2500 1.273606 CGCTAGGTAGCTACATGCCAT 59.726 52.381 24.75 6.26 46.85 4.40
2241 2501 0.673985 CGCTAGGTAGCTACATGCCA 59.326 55.000 24.75 2.76 46.85 4.92
2336 2596 4.760047 GGTCGCCCTGTCGTGCAT 62.760 66.667 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.