Multiple sequence alignment - TraesCS4A01G191800

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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 TraesCS4A01G191800 chr4A 100.000 2885 0 0 1 2885 471939830 471936946 0.000000e+00 5328
1 TraesCS4A01G191800 chr4A 88.869 2228 224 13 672 2880 290325780 290323558 0.000000e+00 2719
2 TraesCS4A01G191800 chr4A 98.063 671 13 0 1 671 471948338 471947668 0.000000e+00 1168
3 TraesCS4A01G191800 chr4A 96.577 672 21 2 1 671 454145364 454144694 0.000000e+00 1112
4 TraesCS4A01G191800 chr3A 90.628 2230 187 8 672 2881 223424513 223426740 0.000000e+00 2940
5 TraesCS4A01G191800 chr3A 89.660 2234 201 10 672 2885 397038712 397036489 0.000000e+00 2819
6 TraesCS4A01G191800 chr3A 87.651 2235 249 15 668 2881 219123173 219125401 0.000000e+00 2573
7 TraesCS4A01G191800 chr3A 84.098 981 128 11 1928 2885 122639017 122638042 0.000000e+00 922
8 TraesCS4A01G191800 chr2A 89.946 2228 198 10 672 2880 340951990 340949770 0.000000e+00 2850
9 TraesCS4A01G191800 chr2A 89.318 2228 213 11 672 2881 294543933 294546153 0.000000e+00 2772
10 TraesCS4A01G191800 chr2A 88.172 2232 226 24 672 2877 500813377 500815596 0.000000e+00 2625
11 TraesCS4A01G191800 chr2A 85.196 716 87 8 2187 2885 182280623 182279910 0.000000e+00 717
12 TraesCS4A01G191800 chr5A 89.264 2161 204 19 672 2812 288883548 288881396 0.000000e+00 2680
13 TraesCS4A01G191800 chr5A 90.118 1609 138 12 1295 2885 240796409 240798014 0.000000e+00 2071
14 TraesCS4A01G191800 chr5A 83.951 243 39 0 2643 2885 212574964 212574722 1.730000e-57 233
15 TraesCS4A01G191800 chr1A 88.298 2239 235 15 668 2884 260132371 260134604 0.000000e+00 2658
16 TraesCS4A01G191800 chr1A 85.357 2240 283 31 671 2885 400930459 400928240 0.000000e+00 2278
17 TraesCS4A01G191800 chr1A 88.627 932 78 23 1 916 18438785 18437866 0.000000e+00 1109
18 TraesCS4A01G191800 chr7D 87.058 2233 251 17 672 2881 288528949 288526732 0.000000e+00 2488
19 TraesCS4A01G191800 chr7D 86.980 2235 258 21 672 2884 292029041 292031264 0.000000e+00 2484
20 TraesCS4A01G191800 chr5D 84.528 2120 295 15 790 2885 85867719 85865609 0.000000e+00 2067
21 TraesCS4A01G191800 chr1D 86.572 1698 202 17 1208 2885 149887305 149885614 0.000000e+00 1849
22 TraesCS4A01G191800 chr2D 84.919 1797 252 15 1090 2880 345162388 345160605 0.000000e+00 1799
23 TraesCS4A01G191800 chr6D 84.459 1377 188 18 1527 2880 242464270 242462897 0.000000e+00 1334
24 TraesCS4A01G191800 chr7A 97.615 671 15 1 1 670 588736978 588737648 0.000000e+00 1149
25 TraesCS4A01G191800 chr2B 97.019 671 20 0 1 671 600514520 600515190 0.000000e+00 1129
26 TraesCS4A01G191800 chr2B 96.736 674 20 2 1 673 600522553 600523225 0.000000e+00 1122
27 TraesCS4A01G191800 chr2B 96.429 672 23 1 1 671 317291022 317291693 0.000000e+00 1107
28 TraesCS4A01G191800 chr1B 96.721 671 22 0 1 671 507240494 507241164 0.000000e+00 1118
29 TraesCS4A01G191800 chr3B 96.577 672 19 2 1 671 486268224 486268892 0.000000e+00 1110
30 TraesCS4A01G191800 chr3D 83.130 409 51 6 2489 2880 350648966 350648559 9.830000e-95 357
31 TraesCS4A01G191800 chr3D 86.709 158 20 1 2729 2885 422633902 422634059 1.060000e-39 174


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 TraesCS4A01G191800 chr4A 471936946 471939830 2884 True 5328 5328 100.000 1 2885 1 chr4A.!!$R3 2884
1 TraesCS4A01G191800 chr4A 290323558 290325780 2222 True 2719 2719 88.869 672 2880 1 chr4A.!!$R1 2208
2 TraesCS4A01G191800 chr4A 471947668 471948338 670 True 1168 1168 98.063 1 671 1 chr4A.!!$R4 670
3 TraesCS4A01G191800 chr4A 454144694 454145364 670 True 1112 1112 96.577 1 671 1 chr4A.!!$R2 670
4 TraesCS4A01G191800 chr3A 223424513 223426740 2227 False 2940 2940 90.628 672 2881 1 chr3A.!!$F2 2209
5 TraesCS4A01G191800 chr3A 397036489 397038712 2223 True 2819 2819 89.660 672 2885 1 chr3A.!!$R2 2213
6 TraesCS4A01G191800 chr3A 219123173 219125401 2228 False 2573 2573 87.651 668 2881 1 chr3A.!!$F1 2213
7 TraesCS4A01G191800 chr3A 122638042 122639017 975 True 922 922 84.098 1928 2885 1 chr3A.!!$R1 957
8 TraesCS4A01G191800 chr2A 340949770 340951990 2220 True 2850 2850 89.946 672 2880 1 chr2A.!!$R2 2208
9 TraesCS4A01G191800 chr2A 294543933 294546153 2220 False 2772 2772 89.318 672 2881 1 chr2A.!!$F1 2209
10 TraesCS4A01G191800 chr2A 500813377 500815596 2219 False 2625 2625 88.172 672 2877 1 chr2A.!!$F2 2205
11 TraesCS4A01G191800 chr2A 182279910 182280623 713 True 717 717 85.196 2187 2885 1 chr2A.!!$R1 698
12 TraesCS4A01G191800 chr5A 288881396 288883548 2152 True 2680 2680 89.264 672 2812 1 chr5A.!!$R2 2140
13 TraesCS4A01G191800 chr5A 240796409 240798014 1605 False 2071 2071 90.118 1295 2885 1 chr5A.!!$F1 1590
14 TraesCS4A01G191800 chr1A 260132371 260134604 2233 False 2658 2658 88.298 668 2884 1 chr1A.!!$F1 2216
15 TraesCS4A01G191800 chr1A 400928240 400930459 2219 True 2278 2278 85.357 671 2885 1 chr1A.!!$R2 2214
16 TraesCS4A01G191800 chr1A 18437866 18438785 919 True 1109 1109 88.627 1 916 1 chr1A.!!$R1 915
17 TraesCS4A01G191800 chr7D 288526732 288528949 2217 True 2488 2488 87.058 672 2881 1 chr7D.!!$R1 2209
18 TraesCS4A01G191800 chr7D 292029041 292031264 2223 False 2484 2484 86.980 672 2884 1 chr7D.!!$F1 2212
19 TraesCS4A01G191800 chr5D 85865609 85867719 2110 True 2067 2067 84.528 790 2885 1 chr5D.!!$R1 2095
20 TraesCS4A01G191800 chr1D 149885614 149887305 1691 True 1849 1849 86.572 1208 2885 1 chr1D.!!$R1 1677
21 TraesCS4A01G191800 chr2D 345160605 345162388 1783 True 1799 1799 84.919 1090 2880 1 chr2D.!!$R1 1790
22 TraesCS4A01G191800 chr6D 242462897 242464270 1373 True 1334 1334 84.459 1527 2880 1 chr6D.!!$R1 1353
23 TraesCS4A01G191800 chr7A 588736978 588737648 670 False 1149 1149 97.615 1 670 1 chr7A.!!$F1 669
24 TraesCS4A01G191800 chr2B 600514520 600515190 670 False 1129 1129 97.019 1 671 1 chr2B.!!$F2 670
25 TraesCS4A01G191800 chr2B 600522553 600523225 672 False 1122 1122 96.736 1 673 1 chr2B.!!$F3 672
26 TraesCS4A01G191800 chr2B 317291022 317291693 671 False 1107 1107 96.429 1 671 1 chr2B.!!$F1 670
27 TraesCS4A01G191800 chr1B 507240494 507241164 670 False 1118 1118 96.721 1 671 1 chr1B.!!$F1 670
28 TraesCS4A01G191800 chr3B 486268224 486268892 668 False 1110 1110 96.577 1 671 1 chr3B.!!$F1 670

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
528 534 1.405526 GCACTTGTATTCGAGCCCTCA 60.406 52.381 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2042 0.784778 CGCGGTTGAGACACTTCTTC 59.215 55.0 0.0 0.0 29.47 2.87 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
22 23 4.826274 TGCTACTTGGAGATGCTACTTT 57.174 40.909 0.00 0.00 0.00 2.66
217 219 5.056894 GTACTTTGGATGAGTACTCACGT 57.943 43.478 27.41 13.28 43.78 4.49
505 511 2.298610 TCCGCTGACTCGTCTATGATT 58.701 47.619 0.00 0.00 0.00 2.57
528 534 1.405526 GCACTTGTATTCGAGCCCTCA 60.406 52.381 0.00 0.00 0.00 3.86
639 646 1.616620 GTACACATTTGCGTGCATGG 58.383 50.000 8.27 0.00 40.73 3.66
854 864 5.047660 CCCTAGATGTCTAGCCTGTATGAAC 60.048 48.000 10.84 0.00 43.47 3.18
882 894 2.243221 AGCCTCTACGGACTAAACCCTA 59.757 50.000 0.00 0.00 33.16 3.53
964 976 5.591067 GGAAATTACATATCCGGACACCAAA 59.409 40.000 6.12 0.00 0.00 3.28
965 977 6.238648 GGAAATTACATATCCGGACACCAAAG 60.239 42.308 6.12 0.00 0.00 2.77
982 994 3.376859 CCAAAGTTGCTATCCACGCATAA 59.623 43.478 0.00 0.00 37.22 1.90
1039 1051 3.804036 CTTTGTATCTTCACGGCCCATA 58.196 45.455 0.00 0.00 0.00 2.74
1114 1127 0.396695 CCTCAGTAGCCCCCGAACTA 60.397 60.000 0.00 0.00 0.00 2.24
1130 1143 4.323868 CCGAACTAGTCTTCAAATGACGAC 59.676 45.833 10.99 10.99 41.81 4.34
1206 1219 0.392461 GGCAGACAATAGTTCGGCCA 60.392 55.000 2.24 0.00 37.98 5.36
1232 1245 4.454504 GCTTCCTTGTTCCGTCTTTATGAA 59.545 41.667 0.00 0.00 0.00 2.57
1344 1361 6.070538 AGCGATGGTGCCTATATAAAGAGATT 60.071 38.462 0.00 0.00 34.65 2.40
1585 1607 2.632377 CCTCAATAGGCAACGATGTGT 58.368 47.619 0.00 0.00 46.39 3.72
1803 1826 3.181483 GCATTGAGGCCCATTCTAAACTG 60.181 47.826 0.00 0.00 0.00 3.16
1817 1841 8.603181 CCATTCTAAACTGTGGAAAAAGTTTTG 58.397 33.333 0.61 5.07 42.51 2.44
1839 1863 3.323286 TTGTCCCCCGCCATCGAA 61.323 61.111 0.00 0.00 38.10 3.71
1938 1962 5.130705 AGAGACATATCCACAGTGGTCTA 57.869 43.478 19.65 12.43 39.03 2.59
1960 1984 4.985538 ACAGAGTGGTTTTACATGGATGT 58.014 39.130 0.00 0.00 44.48 3.06
1977 2001 2.114625 TCGTCCCACTGTCGGACT 59.885 61.111 19.97 0.00 46.48 3.85
1980 2004 1.802337 CGTCCCACTGTCGGACTCAA 61.802 60.000 19.97 0.00 46.48 3.02
2018 2042 0.890683 AATTTTCCAGCGCTCCCTTG 59.109 50.000 7.13 0.00 0.00 3.61
2027 2051 0.603975 GCGCTCCCTTGAAGAAGTGT 60.604 55.000 0.00 0.00 0.00 3.55
2034 2058 3.142174 CCCTTGAAGAAGTGTCTCAACC 58.858 50.000 0.00 0.00 30.70 3.77
2058 2083 0.331616 CCCCGAAGTCCCAAGGATTT 59.668 55.000 0.00 0.00 34.34 2.17
2087 2112 4.223659 CACGGAAATAAAAAGGTTGGTCG 58.776 43.478 0.00 0.00 0.00 4.79
2138 2163 4.390297 GGCTCTCGATAATTGAGGTTATGC 59.610 45.833 1.37 0.00 34.19 3.14
2159 2184 3.313249 GCCCATTGCAATAAAAAGATGCC 59.687 43.478 12.53 0.00 39.31 4.40
2178 2203 1.739750 CTCTAGCCCCTCCATTCCAT 58.260 55.000 0.00 0.00 0.00 3.41
2265 2290 2.983592 CCCAACCGAACTGGCCAC 60.984 66.667 0.00 0.00 43.94 5.01
2451 2481 5.447778 AACAGTCATGGAGGAAGATGATT 57.552 39.130 0.00 0.00 31.40 2.57
2599 2657 5.276461 TGACTCGAATGTGGCTATTACAT 57.724 39.130 0.00 0.00 40.30 2.29
2612 2671 3.901844 GCTATTACATCAGACTACCCCCA 59.098 47.826 0.00 0.00 0.00 4.96
2660 2738 1.256812 AAAGAAATCCCCACTTGCGG 58.743 50.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.489603 AGAAGAGAGTAGATTGAAGTCCTCA 58.510 40.000 0.00 0.00 0.00 3.86
505 511 1.405526 GGGCTCGAATACAAGTGCTCA 60.406 52.381 0.00 0.00 0.00 4.26
586 593 3.056465 GGGACTCACGGGAAGATATCATC 60.056 52.174 5.32 2.04 0.00 2.92
587 594 2.900546 GGGACTCACGGGAAGATATCAT 59.099 50.000 5.32 0.00 0.00 2.45
854 864 3.134574 AGTCCGTAGAGGCTATCAGAG 57.865 52.381 0.00 0.00 40.77 3.35
882 894 5.130477 CCCCTCTGGTGTGTATATAAACTGT 59.870 44.000 4.68 0.00 0.00 3.55
1039 1051 1.734655 ACTGGATGTGGGTCAGACTT 58.265 50.000 0.00 0.00 33.19 3.01
1114 1127 2.061773 CTGCGTCGTCATTTGAAGACT 58.938 47.619 19.52 0.00 46.51 3.24
1130 1143 1.065701 AGACGTAAGCCAGATACTGCG 59.934 52.381 0.00 0.00 45.62 5.18
1171 1184 1.480954 CTGCCCAGTATACGGTGAAGT 59.519 52.381 11.22 0.00 0.00 3.01
1206 1219 0.693049 AGACGGAACAAGGAAGCCAT 59.307 50.000 0.00 0.00 0.00 4.40
1232 1245 0.112606 TCGAGGCGATAGGGAAGGAT 59.887 55.000 0.00 0.00 0.00 3.24
1321 1338 7.323420 TCAATCTCTTTATATAGGCACCATCG 58.677 38.462 0.00 0.00 0.00 3.84
1344 1361 2.041485 TGGATGGCACTTTGAGGATTCA 59.959 45.455 0.00 0.00 0.00 2.57
1585 1607 2.105649 GGTTGGGGAAATTTTCAGCCAA 59.894 45.455 11.09 9.45 32.00 4.52
1620 1642 2.550830 ATGGAACGAAGCACACTCTT 57.449 45.000 0.00 0.00 0.00 2.85
1796 1819 7.812669 AGACACAAAACTTTTTCCACAGTTTAG 59.187 33.333 0.00 0.00 41.42 1.85
1803 1826 5.347635 GGACAAGACACAAAACTTTTTCCAC 59.652 40.000 0.00 0.00 31.35 4.02
1817 1841 3.268103 ATGGCGGGGGACAAGACAC 62.268 63.158 0.00 0.00 30.21 3.67
1839 1863 3.117738 CCCACTTCAAATATGGAGCCTCT 60.118 47.826 0.00 0.00 35.34 3.69
1869 1893 5.163642 CGGATCTAGCTATACGCCATACTTT 60.164 44.000 0.00 0.00 40.39 2.66
1938 1962 4.985538 ACATCCATGTAAAACCACTCTGT 58.014 39.130 0.00 0.00 39.68 3.41
2018 2042 0.784778 CGCGGTTGAGACACTTCTTC 59.215 55.000 0.00 0.00 29.47 2.87
2058 2083 3.254657 CCTTTTTATTTCCGTGCTGTCCA 59.745 43.478 0.00 0.00 0.00 4.02
2087 2112 4.725490 TGGGCTAATAATCTAACCTTGCC 58.275 43.478 0.00 0.00 37.34 4.52
2138 2163 4.773013 AGGCATCTTTTTATTGCAATGGG 58.227 39.130 22.27 7.28 38.12 4.00
2159 2184 1.739750 ATGGAATGGAGGGGCTAGAG 58.260 55.000 0.00 0.00 0.00 2.43
2178 2203 5.521696 TGTAGCACCATAAGGGAGTTACTA 58.478 41.667 6.11 0.00 41.99 1.82
2265 2290 3.159353 TGTACAAATCGATCAGGACCG 57.841 47.619 0.00 0.00 0.00 4.79
2267 2292 3.871594 CCCTTGTACAAATCGATCAGGAC 59.128 47.826 10.03 1.61 0.00 3.85
2359 2385 3.689649 AGCGACACAGGTAATCAAAATCC 59.310 43.478 0.00 0.00 0.00 3.01
2522 2553 7.783090 TCGAACTCTATGTATATATCCGGAC 57.217 40.000 6.12 0.00 0.00 4.79
2586 2644 4.344102 GGGTAGTCTGATGTAATAGCCACA 59.656 45.833 0.00 0.00 34.80 4.17
2599 2657 1.627847 TAGGGATGGGGGTAGTCTGA 58.372 55.000 0.00 0.00 0.00 3.27
2612 2671 3.863086 ACGATGGAGAAAGGATAGGGAT 58.137 45.455 0.00 0.00 0.00 3.85
2660 2738 8.363390 AGTACGGTTTAGTATAAGGGATAAAGC 58.637 37.037 0.00 0.00 34.11 3.51


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

AutoCloner maintained by Alex Coulton.