Multiple sequence alignment - TraesCS4A01G487700

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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 TraesCS4A01G487700 chr4A 100.000 2798 0 0 1 2798 739867839 739870636 0.000000e+00 5168
1 TraesCS4A01G487700 chr4A 87.970 2843 269 28 1 2798 741815383 741812569 0.000000e+00 3288
2 TraesCS4A01G487700 chr4A 89.403 2548 212 29 297 2798 741483721 741481186 0.000000e+00 3157
3 TraesCS4A01G487700 chr4A 91.405 1850 155 4 1 1848 739652294 739654141 0.000000e+00 2532
4 TraesCS4A01G487700 chr4A 91.293 1849 159 2 1 1848 742057573 742059420 0.000000e+00 2521
5 TraesCS4A01G487700 chr4A 91.116 1801 159 1 1 1800 740579293 740581093 0.000000e+00 2438
6 TraesCS4A01G487700 chr4A 89.950 1801 176 3 1 1797 740018867 740017068 0.000000e+00 2318
7 TraesCS4A01G487700 chr4A 89.427 1797 189 1 1 1797 741590646 741592441 0.000000e+00 2265
8 TraesCS4A01G487700 chr4A 85.233 1544 161 40 1293 2798 740453896 740452382 0.000000e+00 1526
9 TraesCS4A01G487700 chr4A 87.723 953 96 9 1860 2798 739654185 739655130 0.000000e+00 1092
10 TraesCS4A01G487700 chr4A 86.081 934 101 15 1882 2798 739736416 739737337 0.000000e+00 977
11 TraesCS4A01G487700 chr4A 86.979 768 94 5 2037 2798 740581393 740582160 0.000000e+00 859
12 TraesCS4A01G487700 chr4A 86.556 781 91 10 2028 2798 740939982 740940758 0.000000e+00 848
13 TraesCS4A01G487700 chr4A 85.824 783 87 16 2037 2798 741592696 741593475 0.000000e+00 809
14 TraesCS4A01G487700 chr4A 86.104 403 32 8 1460 1862 742132398 742132776 2.010000e-111 412
15 TraesCS4A01G487700 chr4A 85.432 405 31 11 1460 1862 739735904 739736282 2.020000e-106 396
16 TraesCS4A01G487700 chr7A 89.286 2828 262 23 1 2798 3207780 3204964 0.000000e+00 3506
17 TraesCS4A01G487700 chr7A 86.486 2849 318 33 1 2798 2117318 2114486 0.000000e+00 3066
18 TraesCS4A01G487700 chr7D 90.843 1780 163 0 1 1780 3786740 3784961 0.000000e+00 2385
19 TraesCS4A01G487700 chr7D 90.241 1783 171 1 1 1780 3632945 3631163 0.000000e+00 2326
20 TraesCS4A01G487700 chr7D 89.899 1782 177 1 2 1780 2357450 2355669 0.000000e+00 2290
21 TraesCS4A01G487700 chr7D 87.887 776 78 11 2037 2798 3630872 3630099 0.000000e+00 898
22 TraesCS4A01G487700 chr7D 87.887 776 78 11 2037 2798 3784670 3783897 0.000000e+00 898
23 TraesCS4A01G487700 chr7D 87.484 767 89 5 2037 2798 2607595 2606831 0.000000e+00 878


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 TraesCS4A01G487700 chr4A 739867839 739870636 2797 False 5168.0 5168 100.0000 1 2798 1 chr4A.!!$F1 2797
1 TraesCS4A01G487700 chr4A 741812569 741815383 2814 True 3288.0 3288 87.9700 1 2798 1 chr4A.!!$R4 2797
2 TraesCS4A01G487700 chr4A 741481186 741483721 2535 True 3157.0 3157 89.4030 297 2798 1 chr4A.!!$R3 2501
3 TraesCS4A01G487700 chr4A 742057573 742059420 1847 False 2521.0 2521 91.2930 1 1848 1 chr4A.!!$F3 1847
4 TraesCS4A01G487700 chr4A 740017068 740018867 1799 True 2318.0 2318 89.9500 1 1797 1 chr4A.!!$R1 1796
5 TraesCS4A01G487700 chr4A 739652294 739655130 2836 False 1812.0 2532 89.5640 1 2798 2 chr4A.!!$F5 2797
6 TraesCS4A01G487700 chr4A 740579293 740582160 2867 False 1648.5 2438 89.0475 1 2798 2 chr4A.!!$F7 2797
7 TraesCS4A01G487700 chr4A 741590646 741593475 2829 False 1537.0 2265 87.6255 1 2798 2 chr4A.!!$F8 2797
8 TraesCS4A01G487700 chr4A 740452382 740453896 1514 True 1526.0 1526 85.2330 1293 2798 1 chr4A.!!$R2 1505
9 TraesCS4A01G487700 chr4A 740939982 740940758 776 False 848.0 848 86.5560 2028 2798 1 chr4A.!!$F2 770
10 TraesCS4A01G487700 chr4A 739735904 739737337 1433 False 686.5 977 85.7565 1460 2798 2 chr4A.!!$F6 1338
11 TraesCS4A01G487700 chr7A 3204964 3207780 2816 True 3506.0 3506 89.2860 1 2798 1 chr7A.!!$R2 2797
12 TraesCS4A01G487700 chr7A 2114486 2117318 2832 True 3066.0 3066 86.4860 1 2798 1 chr7A.!!$R1 2797
13 TraesCS4A01G487700 chr7D 2355669 2357450 1781 True 2290.0 2290 89.8990 2 1780 1 chr7D.!!$R1 1778
14 TraesCS4A01G487700 chr7D 3783897 3786740 2843 True 1641.5 2385 89.3650 1 2798 2 chr7D.!!$R4 2797
15 TraesCS4A01G487700 chr7D 3630099 3632945 2846 True 1612.0 2326 89.0640 1 2798 2 chr7D.!!$R3 2797
16 TraesCS4A01G487700 chr7D 2606831 2607595 764 True 878.0 878 87.4840 2037 2798 1 chr7D.!!$R2 761

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
23 24 0.533951 GGCAGGATTTTTGGCTCTGG 59.466 55.000 0.0 0.0 38.03 3.86 F
253 254 2.284190 GCTACAACAGCCTTCCTCATC 58.716 52.381 0.0 0.0 45.23 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 1158 0.317938 CGTCACCATAGCTAGCCGAC 60.318 60.0 12.13 7.87 0.0 4.79 R
2025 2287 0.036010 CATGACACCTCTCCACCACC 60.036 60.0 0.00 0.00 0.0 4.61 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
23 24 0.533951 GGCAGGATTTTTGGCTCTGG 59.466 55.000 0.00 0.00 38.03 3.86
26 27 2.299867 GCAGGATTTTTGGCTCTGGAAA 59.700 45.455 0.00 0.00 0.00 3.13
28 29 4.752146 CAGGATTTTTGGCTCTGGAAATC 58.248 43.478 0.00 0.00 37.63 2.17
29 30 3.445096 AGGATTTTTGGCTCTGGAAATCG 59.555 43.478 0.00 0.00 38.66 3.34
253 254 2.284190 GCTACAACAGCCTTCCTCATC 58.716 52.381 0.00 0.00 45.23 2.92
313 314 5.383476 CAGAGGGCTCCATAATCTTCAAAT 58.617 41.667 0.00 0.00 0.00 2.32
406 408 6.150976 AGTTGCAGGAATGTATTTCGATGAAA 59.849 34.615 0.00 0.00 35.94 2.69
546 548 7.642071 TTTCGTTGTGGTAGTAGATTACAAC 57.358 36.000 0.00 0.00 44.50 3.32
972 974 3.134458 CAGTCTTCCTCCTCACACAAAC 58.866 50.000 0.00 0.00 0.00 2.93
1087 1089 4.021456 ACGACCATCTGTACAGAAACATGA 60.021 41.667 28.43 5.40 41.36 3.07
1100 1102 5.105877 ACAGAAACATGAATGCTCTGGATTG 60.106 40.000 19.42 4.13 41.62 2.67
1116 1119 7.698130 GCTCTGGATTGTTTAATGTATGAACAC 59.302 37.037 0.00 0.00 38.78 3.32
1150 1153 4.634012 ACTGTAAAACTGGTGGCTCATA 57.366 40.909 0.00 0.00 0.00 2.15
1155 1158 2.898729 AACTGGTGGCTCATAGATCG 57.101 50.000 0.00 0.00 0.00 3.69
1181 1184 2.015736 AGCTATGGTGACGCTTCAAG 57.984 50.000 0.00 0.00 31.90 3.02
1204 1207 4.151883 AGCAAGAGTTGGCTGGATTTTAA 58.848 39.130 0.00 0.00 39.30 1.52
1212 1215 5.656859 AGTTGGCTGGATTTTAAATAGACCC 59.343 40.000 0.00 0.00 0.00 4.46
1225 1228 1.191535 TAGACCCAACCACCATCTCG 58.808 55.000 0.00 0.00 0.00 4.04
1346 1361 4.274459 GGATGGACTGTCAGTAAATGATGC 59.726 45.833 5.21 0.00 40.92 3.91
1503 1530 6.095440 GTGGAATAGCTTGGCTAAGATTTGAA 59.905 38.462 14.82 0.00 44.62 2.69
1506 1533 3.424703 AGCTTGGCTAAGATTTGAAGCA 58.575 40.909 14.82 0.00 36.99 3.91
1530 1557 2.945008 CGCAATGCCTAATCTCTGGAAA 59.055 45.455 0.00 0.00 0.00 3.13
1578 1611 2.031157 CCAAATGGACCAACGACTTGAC 60.031 50.000 0.00 0.00 37.39 3.18
1595 1628 1.209504 TGACCTTTATTCGGAGCCTGG 59.790 52.381 0.00 0.00 0.00 4.45
1938 2163 4.201950 GCTGCATGTTCCAGGTATACTTTG 60.202 45.833 2.25 2.22 0.00 2.77
1945 2170 6.535540 TGTTCCAGGTATACTTTGCTAACAA 58.464 36.000 2.25 0.00 0.00 2.83
1962 2187 5.870978 GCTAACAAAGACAATTTGCCATCAT 59.129 36.000 0.00 0.00 32.93 2.45
2121 2389 3.035305 TCCAGGTGGGAATATGGCA 57.965 52.632 0.00 0.00 44.80 4.92
2226 2494 2.038295 GAGCATTGGATCTACCTCCCTG 59.962 54.545 0.00 0.00 39.86 4.45
2300 2571 2.036256 GTGCCCAAGATGCCACCT 59.964 61.111 0.00 0.00 0.00 4.00
2308 2579 1.614903 CAAGATGCCACCTGCTCAAAA 59.385 47.619 0.00 0.00 42.00 2.44
2327 2610 0.179100 ACGTCATCTGGGATTCGCTG 60.179 55.000 2.19 1.96 0.00 5.18
2331 2614 0.394192 CATCTGGGATTCGCTGGCTA 59.606 55.000 7.58 0.00 0.00 3.93
2345 2628 1.689273 CTGGCTATAGGAACCGAGCTT 59.311 52.381 1.04 0.00 35.23 3.74
2349 2632 2.864489 GCTATAGGAACCGAGCTTCTGC 60.864 54.545 1.04 0.00 40.05 4.26
2360 2643 2.261215 GCTTCTGCTGTTTGGGGAG 58.739 57.895 0.00 0.00 36.03 4.30
2364 2647 3.185203 TGCTGTTTGGGGAGGGCT 61.185 61.111 0.00 0.00 0.00 5.19
2367 2650 4.299796 TGTTTGGGGAGGGCTGGC 62.300 66.667 0.00 0.00 0.00 4.85
2410 2699 3.287867 CAATTCATGGACAGGGCTAGT 57.712 47.619 0.00 0.00 0.00 2.57
2444 2745 2.356553 CCGCGGTTCTCGTTTGGA 60.357 61.111 19.50 0.00 41.72 3.53
2459 2760 0.961019 TTGGATCAGCAAGTGTTGGC 59.039 50.000 0.00 0.00 0.00 4.52
2632 2939 5.421056 AGTTCTATGTGATCGGTGGTCTTAA 59.579 40.000 0.00 0.00 0.00 1.85
2740 3065 4.464008 CTCAACAATATAGCCATGGGTGT 58.536 43.478 26.70 22.10 0.00 4.16
2755 3080 0.321653 GGTGTTCCTCCGCTCATTGT 60.322 55.000 0.00 0.00 0.00 2.71
2760 3085 3.244422 TGTTCCTCCGCTCATTGTAGTTT 60.244 43.478 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.241207 TGAATTCTTCAGGACAACGATTTC 57.759 37.500 7.05 0.00 34.08 2.17
26 27 5.530915 TGTTTGAATTCTTCAGGACAACGAT 59.469 36.000 7.05 0.00 41.38 3.73
28 29 5.168526 TGTTTGAATTCTTCAGGACAACG 57.831 39.130 7.05 0.00 41.38 4.10
29 30 6.564328 ACTTGTTTGAATTCTTCAGGACAAC 58.436 36.000 7.05 6.21 39.94 3.32
406 408 6.071728 GGTTGGATGAATCTTCTGTCAACAAT 60.072 38.462 13.97 0.00 35.14 2.71
498 500 1.139654 TCTTCTGCAGACTTGTGTGCT 59.860 47.619 18.03 0.00 40.54 4.40
546 548 4.229876 GAGAAAGTGCCAAATTCTTTCGG 58.770 43.478 9.62 0.00 46.37 4.30
972 974 1.171308 CAACAGACCAATCCAGCAGG 58.829 55.000 0.00 0.00 0.00 4.85
1087 1089 8.523915 TCATACATTAAACAATCCAGAGCATT 57.476 30.769 0.00 0.00 0.00 3.56
1100 1102 4.095610 GCTGCCGTGTTCATACATTAAAC 58.904 43.478 0.00 0.00 36.50 2.01
1116 1119 1.234821 TTACAGTTTTCAGGCTGCCG 58.765 50.000 13.96 8.60 36.26 5.69
1150 1153 1.169577 CCATAGCTAGCCGACGATCT 58.830 55.000 12.13 0.00 0.00 2.75
1155 1158 0.317938 CGTCACCATAGCTAGCCGAC 60.318 60.000 12.13 7.87 0.00 4.79
1181 1184 1.831580 AATCCAGCCAACTCTTGCTC 58.168 50.000 0.00 0.00 35.12 4.26
1204 1207 2.170607 CGAGATGGTGGTTGGGTCTATT 59.829 50.000 0.00 0.00 0.00 1.73
1212 1215 3.533606 AATCTCTCGAGATGGTGGTTG 57.466 47.619 17.03 1.32 46.75 3.77
1225 1228 4.470334 AAGCTGAGACCTCAAATCTCTC 57.530 45.455 1.08 0.00 42.68 3.20
1453 1480 3.995199 TGAACCTCAGCTTCAAGTACTG 58.005 45.455 0.00 0.00 0.00 2.74
1503 1530 1.134280 AGATTAGGCATTGCGTCTGCT 60.134 47.619 7.19 0.00 43.34 4.24
1506 1533 2.484417 CCAGAGATTAGGCATTGCGTCT 60.484 50.000 7.19 5.74 0.00 4.18
1530 1557 3.196613 GTCGAAAACGAGCCTGAGT 57.803 52.632 0.00 0.00 0.00 3.41
1578 1611 0.819666 GGCCAGGCTCCGAATAAAGG 60.820 60.000 12.43 0.00 0.00 3.11
1595 1628 3.006940 TGTCGATATTGTTTCCACTGGC 58.993 45.455 0.00 0.00 0.00 4.85
1671 1704 0.320946 CAGCTGCACCCCCAAATTTG 60.321 55.000 11.40 11.40 0.00 2.32
1938 2163 5.229423 TGATGGCAAATTGTCTTTGTTAGC 58.771 37.500 0.00 0.00 0.00 3.09
1945 2170 4.020928 TGAAGCATGATGGCAAATTGTCTT 60.021 37.500 0.00 0.00 35.83 3.01
1962 2187 4.196193 CGGGTAATTTATCACCTGAAGCA 58.804 43.478 0.00 0.00 42.85 3.91
2024 2286 0.473694 ATGACACCTCTCCACCACCA 60.474 55.000 0.00 0.00 0.00 4.17
2025 2287 0.036010 CATGACACCTCTCCACCACC 60.036 60.000 0.00 0.00 0.00 4.61
2026 2288 0.036010 CCATGACACCTCTCCACCAC 60.036 60.000 0.00 0.00 0.00 4.16
2121 2389 2.670148 GGTTCAGGGAGGCGATGGT 61.670 63.158 0.00 0.00 0.00 3.55
2171 2439 2.104331 CGACGCAGGCGGTAGATT 59.896 61.111 18.63 0.00 44.69 2.40
2210 2478 0.694444 GGCCAGGGAGGTAGATCCAA 60.694 60.000 0.00 0.00 41.52 3.53
2226 2494 2.108362 CTCGTGGGGATTACGGCC 59.892 66.667 0.00 0.00 41.58 6.13
2253 2524 2.268920 CCCAGTGGACGGGTCATG 59.731 66.667 11.95 0.00 39.05 3.07
2300 2571 1.071542 TCCCAGATGACGTTTTGAGCA 59.928 47.619 0.00 0.00 0.00 4.26
2308 2579 0.179100 CAGCGAATCCCAGATGACGT 60.179 55.000 0.00 0.00 0.00 4.34
2327 2610 1.964933 AGAAGCTCGGTTCCTATAGCC 59.035 52.381 5.33 0.00 35.54 3.93
2345 2628 3.170362 CCCTCCCCAAACAGCAGA 58.830 61.111 0.00 0.00 0.00 4.26
2349 2632 2.036256 CCAGCCCTCCCCAAACAG 59.964 66.667 0.00 0.00 0.00 3.16
2360 2643 1.137872 CTATATCTCATCCGCCAGCCC 59.862 57.143 0.00 0.00 0.00 5.19
2364 2647 2.432146 GGATGCTATATCTCATCCGCCA 59.568 50.000 16.02 0.00 46.23 5.69
2370 2653 8.829746 TGAATTGGTAAGGATGCTATATCTCAT 58.170 33.333 0.00 0.00 0.00 2.90
2408 2697 1.561542 GGGGTGTTCATCTCATCCACT 59.438 52.381 0.00 0.00 37.78 4.00
2410 2699 0.541392 CGGGGTGTTCATCTCATCCA 59.459 55.000 0.00 0.00 37.78 3.41
2444 2745 1.317613 TTTCGCCAACACTTGCTGAT 58.682 45.000 0.00 0.00 0.00 2.90
2459 2760 0.368907 CCACGACATACGCCTTTTCG 59.631 55.000 0.00 0.00 46.94 3.46
2632 2939 2.165845 GTCAATACCTCGTGGCTACTGT 59.834 50.000 2.76 0.00 36.63 3.55
2740 3065 3.695830 AAACTACAATGAGCGGAGGAA 57.304 42.857 0.00 0.00 0.00 3.36
2755 3080 7.538575 GGCATAAAGCTCATTCTTCAAAACTA 58.461 34.615 0.00 0.00 44.79 2.24
2760 3085 3.181497 GCGGCATAAAGCTCATTCTTCAA 60.181 43.478 0.00 0.00 44.79 2.69


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

AutoCloner maintained by Alex Coulton.