Multiple sequence alignment - TraesCS4A01G143400

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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 TraesCS4A01G143400 chr4A 100.000 2686 0 0 1 2686 236226264 236228949 0.000000e+00 4961
1 TraesCS4A01G143400 chr4A 90.631 523 44 4 434 952 561094309 561094830 0.000000e+00 689
2 TraesCS4A01G143400 chr7D 95.801 2715 80 16 1 2686 636968414 636965705 0.000000e+00 4351
3 TraesCS4A01G143400 chr6A 93.128 2692 151 17 1 2686 443932324 443929661 0.000000e+00 3916
4 TraesCS4A01G143400 chr3A 94.518 1277 59 5 357 1624 608075713 608076987 0.000000e+00 1960
5 TraesCS4A01G143400 chr3A 93.388 242 15 1 1804 2045 608076983 608077223 9.140000e-95 357
6 TraesCS4A01G143400 chr3A 90.650 246 22 1 1 246 608075476 608075720 2.580000e-85 326
7 TraesCS4A01G143400 chr3A 94.118 102 6 0 2186 2287 608077224 608077325 3.580000e-34 156
8 TraesCS4A01G143400 chr1B 89.944 895 64 11 61 953 206375673 206376543 0.000000e+00 1131
9 TraesCS4A01G143400 chr1B 97.059 68 2 0 1618 1685 206376546 206376613 6.080000e-22 115
10 TraesCS4A01G143400 chr5B 86.520 957 70 10 1 956 166718401 166717503 0.000000e+00 998
11 TraesCS4A01G143400 chr5B 86.373 954 71 10 1 953 166719048 166719943 0.000000e+00 987
12 TraesCS4A01G143400 chr5B 85.893 957 75 16 1 956 161651469 161650572 0.000000e+00 965
13 TraesCS4A01G143400 chr5B 98.529 68 1 0 1618 1685 161650572 161650505 1.310000e-23 121
14 TraesCS4A01G143400 chr5B 98.529 68 1 0 1618 1685 166717503 166717436 1.310000e-23 121
15 TraesCS4A01G143400 chr5B 97.059 68 2 0 1618 1685 166719946 166720013 6.080000e-22 115
16 TraesCS4A01G143400 chr2D 87.372 681 47 14 956 1618 614849940 614850599 0.000000e+00 745
17 TraesCS4A01G143400 chr2D 90.996 522 44 3 434 953 68349984 68350504 0.000000e+00 701
18 TraesCS4A01G143400 chr2D 94.118 68 4 0 1618 1685 68350507 68350574 1.320000e-18 104
19 TraesCS4A01G143400 chr7A 91.358 405 25 5 1220 1619 68882301 68882700 1.820000e-151 545
20 TraesCS4A01G143400 chr7A 89.919 248 21 2 955 1198 68881813 68882060 1.550000e-82 316
21 TraesCS4A01G143400 chr7B 90.819 403 24 6 1225 1619 6236255 6236652 6.590000e-146 527
22 TraesCS4A01G143400 chr7B 89.516 248 22 2 955 1198 6235759 6236006 7.220000e-81 311
23 TraesCS4A01G143400 chr4D 90.604 149 14 0 1 149 285714676 285714528 5.870000e-47 198
24 TraesCS4A01G143400 chr2A 85.955 178 19 6 1964 2138 763967030 763966856 4.570000e-43 185
25 TraesCS4A01G143400 chr2B 88.073 109 11 2 1689 1797 797210153 797210259 7.810000e-26 128
26 TraesCS4A01G143400 chr2B 89.796 98 9 1 1700 1797 797256546 797256642 1.010000e-24 124
27 TraesCS4A01G143400 chr2B 95.455 66 3 0 1618 1683 619205987 619205922 3.660000e-19 106
28 TraesCS4A01G143400 chr6D 97.015 67 2 0 1618 1684 211547822 211547756 2.190000e-21 113


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 TraesCS4A01G143400 chr4A 236226264 236228949 2685 False 4961.00 4961 100.0000 1 2686 1 chr4A.!!$F1 2685
1 TraesCS4A01G143400 chr4A 561094309 561094830 521 False 689.00 689 90.6310 434 952 1 chr4A.!!$F2 518
2 TraesCS4A01G143400 chr7D 636965705 636968414 2709 True 4351.00 4351 95.8010 1 2686 1 chr7D.!!$R1 2685
3 TraesCS4A01G143400 chr6A 443929661 443932324 2663 True 3916.00 3916 93.1280 1 2686 1 chr6A.!!$R1 2685
4 TraesCS4A01G143400 chr3A 608075476 608077325 1849 False 699.75 1960 93.1685 1 2287 4 chr3A.!!$F1 2286
5 TraesCS4A01G143400 chr1B 206375673 206376613 940 False 623.00 1131 93.5015 61 1685 2 chr1B.!!$F1 1624
6 TraesCS4A01G143400 chr5B 166717436 166718401 965 True 559.50 998 92.5245 1 1685 2 chr5B.!!$R2 1684
7 TraesCS4A01G143400 chr5B 166719048 166720013 965 False 551.00 987 91.7160 1 1685 2 chr5B.!!$F1 1684
8 TraesCS4A01G143400 chr5B 161650505 161651469 964 True 543.00 965 92.2110 1 1685 2 chr5B.!!$R1 1684
9 TraesCS4A01G143400 chr2D 614849940 614850599 659 False 745.00 745 87.3720 956 1618 1 chr2D.!!$F1 662
10 TraesCS4A01G143400 chr2D 68349984 68350574 590 False 402.50 701 92.5570 434 1685 2 chr2D.!!$F2 1251
11 TraesCS4A01G143400 chr7A 68881813 68882700 887 False 430.50 545 90.6385 955 1619 2 chr7A.!!$F1 664
12 TraesCS4A01G143400 chr7B 6235759 6236652 893 False 419.00 527 90.1675 955 1619 2 chr7B.!!$F1 664


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
919 976 0.107508 CCGACCTTCACCAGCATCAT 60.108 55.0 0.0 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2421 2740 1.338105 TGGATTGGAGTCTGAAGCACG 60.338 52.381 0.0 0.0 0.0 5.34 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
17 18 2.436109 AACCTCCGGCATGCAACT 59.564 55.556 21.36 0.00 0.00 3.16
164 165 4.293648 CACCCGTGACCAGCGTCA 62.294 66.667 0.00 0.00 46.91 4.35
180 181 1.593196 GTCAGCACAACCAGCTACAA 58.407 50.000 0.00 0.00 41.14 2.41
281 307 1.552799 TCCGGCAAGGAGCATCTCAA 61.553 55.000 0.00 0.00 45.98 3.02
282 308 3.449489 TCCGGCAAGGAGCATCTCAAG 62.449 57.143 0.00 0.00 45.98 3.02
284 310 2.791170 GCAAGGAGCATCTCAAGGG 58.209 57.895 0.00 0.00 44.79 3.95
285 311 1.382692 GCAAGGAGCATCTCAAGGGC 61.383 60.000 0.00 0.00 44.79 5.19
286 312 1.094073 CAAGGAGCATCTCAAGGGCG 61.094 60.000 0.00 0.00 33.73 6.13
287 313 1.557269 AAGGAGCATCTCAAGGGCGT 61.557 55.000 0.00 0.00 33.73 5.68
288 314 1.522580 GGAGCATCTCAAGGGCGTC 60.523 63.158 0.00 0.00 33.73 5.19
289 315 1.522580 GAGCATCTCAAGGGCGTCC 60.523 63.158 0.00 0.00 0.00 4.79
290 316 2.892425 GCATCTCAAGGGCGTCCG 60.892 66.667 0.00 0.00 38.33 4.79
291 317 2.892640 CATCTCAAGGGCGTCCGA 59.107 61.111 0.00 0.00 38.33 4.55
292 318 1.519455 CATCTCAAGGGCGTCCGAC 60.519 63.158 0.00 0.00 38.33 4.79
293 319 3.064987 ATCTCAAGGGCGTCCGACG 62.065 63.158 16.72 16.72 45.88 5.12
294 320 3.744719 CTCAAGGGCGTCCGACGA 61.745 66.667 24.78 1.29 46.05 4.20
295 321 3.685214 CTCAAGGGCGTCCGACGAG 62.685 68.421 24.78 7.82 46.05 4.18
296 322 4.796231 CAAGGGCGTCCGACGAGG 62.796 72.222 24.78 4.46 46.05 4.63
304 330 3.829048 TCCGACGAGGAGCATCTC 58.171 61.111 0.00 0.00 45.98 2.75
305 331 1.077716 TCCGACGAGGAGCATCTCA 60.078 57.895 0.00 0.00 45.98 3.27
802 858 2.272146 GTGTGGGCATCCGGTCAT 59.728 61.111 0.00 0.00 35.24 3.06
887 944 0.391793 TTGTCGTGTGTGGACTGCAA 60.392 50.000 0.00 0.00 35.45 4.08
919 976 0.107508 CCGACCTTCACCAGCATCAT 60.108 55.000 0.00 0.00 0.00 2.45
979 1036 2.637382 TCATGGGTTAAGACACTGCTCA 59.363 45.455 0.00 0.00 0.00 4.26
1155 1220 5.714806 CCCTTTTTCCTAAGCATTGAACCTA 59.285 40.000 0.00 0.00 0.00 3.08
1213 1291 1.888512 CTTGCACAACCATTAGGCAGT 59.111 47.619 0.00 0.00 39.06 4.40
1357 1651 6.292389 ACTTTCTCAACGACAAGATGAAAG 57.708 37.500 0.00 0.00 42.35 2.62
1419 1713 4.306600 TGCATAGCAACATACATACGAGG 58.693 43.478 0.00 0.00 34.76 4.63
1470 1764 6.266103 CACGTATAGGGTGTTTAATCCTCCTA 59.734 42.308 0.00 0.00 32.46 2.94
1609 1906 7.950496 CGCTAGTCGCTTATGTATTTTTATTCC 59.050 37.037 0.00 0.00 36.13 3.01
1712 2009 8.803235 ACATTGATACGAGTAATTGATAGCCTA 58.197 33.333 0.00 0.00 0.00 3.93
1762 2060 4.202461 TGGGCTTGACTACTGAGAAAACAT 60.202 41.667 0.00 0.00 0.00 2.71
1809 2107 7.771361 TCATGAAACAGTTTAGTTAGTCCACAA 59.229 33.333 0.00 0.00 0.00 3.33
1853 2151 5.242393 CCTTGTGAGGTTTCTGAATGAACAT 59.758 40.000 0.00 0.00 38.32 2.71
1937 2235 2.904664 GCTGCCCTTGTTTTTCAGC 58.095 52.632 0.00 0.00 42.46 4.26
2059 2358 6.156519 AGTCTTTTGTGTTTGTTTCAAGGTC 58.843 36.000 0.00 0.00 0.00 3.85
2126 2425 2.418746 GGCTCAGATTTTGACGCCTCTA 60.419 50.000 9.13 0.00 42.23 2.43
2220 2520 5.843673 TTACTTTCAAACTGCAACCATCA 57.156 34.783 0.00 0.00 0.00 3.07
2320 2620 8.547173 ACTCTCTCATGATGAAGTTTCCTAATT 58.453 33.333 0.00 0.00 0.00 1.40
2373 2673 6.596497 GGACTTGTTTTAGGAATGACCGATTA 59.404 38.462 0.00 0.00 44.74 1.75
2455 2774 3.075882 TCCAATCCATCCTTGTTGTCCTT 59.924 43.478 0.00 0.00 0.00 3.36
2487 2806 1.002257 TACAGGTCGTGGGTCGCTA 60.002 57.895 0.00 0.00 39.67 4.26
2505 2824 6.350612 GGTCGCTAGCAGGAGATAAGAATTAT 60.351 42.308 16.45 0.00 45.61 1.28
2507 2826 8.410141 GTCGCTAGCAGGAGATAAGAATTATAT 58.590 37.037 16.45 0.00 42.35 0.86
2511 2830 9.881649 CTAGCAGGAGATAAGAATTATATGCAA 57.118 33.333 0.00 0.00 42.12 4.08
2529 2848 2.551071 GCAACAGGTCACTTAGCTTCCT 60.551 50.000 0.00 0.00 32.16 3.36
2539 2858 4.036734 TCACTTAGCTTCCTTTGCTTTGTG 59.963 41.667 0.00 0.00 41.46 3.33
2567 2887 6.575162 AAAGGTTATCAAAGTTCTCGCAAT 57.425 33.333 0.00 0.00 0.00 3.56
2626 2950 6.432162 AGATTGATTTGTGTATGCTTGTGAGT 59.568 34.615 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.394899 GGAAGGCAGCCTAGTTGCAT 60.395 55.000 16.56 0.00 41.44 3.96
36 37 4.020617 CACGCCAGAGCAAGGGGA 62.021 66.667 12.03 0.00 41.25 4.81
162 163 2.340210 TTTGTAGCTGGTTGTGCTGA 57.660 45.000 0.00 0.00 41.32 4.26
164 165 2.162681 GGATTTGTAGCTGGTTGTGCT 58.837 47.619 0.00 0.00 43.79 4.40
284 310 4.194720 ATGCTCCTCGTCGGACGC 62.195 66.667 24.76 11.42 42.21 5.19
285 311 2.024871 GATGCTCCTCGTCGGACG 59.975 66.667 23.73 23.73 44.19 4.79
286 312 1.357334 GAGATGCTCCTCGTCGGAC 59.643 63.158 0.00 0.00 36.69 4.79
287 313 1.077716 TGAGATGCTCCTCGTCGGA 60.078 57.895 0.00 0.00 40.30 4.55
288 314 1.358402 CTGAGATGCTCCTCGTCGG 59.642 63.158 0.00 0.00 35.99 4.79
289 315 1.358402 CCTGAGATGCTCCTCGTCG 59.642 63.158 0.00 0.00 35.99 5.12
290 316 1.739049 CCCTGAGATGCTCCTCGTC 59.261 63.158 0.00 0.00 35.99 4.20
291 317 1.760086 CCCCTGAGATGCTCCTCGT 60.760 63.158 0.00 0.00 35.99 4.18
292 318 3.136750 CCCCTGAGATGCTCCTCG 58.863 66.667 0.00 0.00 35.99 4.63
293 319 2.828145 GCCCCTGAGATGCTCCTC 59.172 66.667 0.00 0.00 0.00 3.71
294 320 3.160047 CGCCCCTGAGATGCTCCT 61.160 66.667 0.00 0.00 0.00 3.69
295 321 3.157252 TCGCCCCTGAGATGCTCC 61.157 66.667 0.00 0.00 0.00 4.70
296 322 2.420890 CTCGCCCCTGAGATGCTC 59.579 66.667 0.00 0.00 38.28 4.26
297 323 3.160047 CCTCGCCCCTGAGATGCT 61.160 66.667 0.00 0.00 38.28 3.79
298 324 2.735772 TTCCTCGCCCCTGAGATGC 61.736 63.158 0.00 0.00 38.28 3.91
299 325 1.144936 GTTCCTCGCCCCTGAGATG 59.855 63.158 0.00 0.00 38.28 2.90
300 326 0.692419 ATGTTCCTCGCCCCTGAGAT 60.692 55.000 0.00 0.00 38.28 2.75
301 327 1.306141 ATGTTCCTCGCCCCTGAGA 60.306 57.895 0.00 0.00 38.28 3.27
302 328 1.144936 GATGTTCCTCGCCCCTGAG 59.855 63.158 0.00 0.00 35.70 3.35
303 329 1.306141 AGATGTTCCTCGCCCCTGA 60.306 57.895 0.00 0.00 0.00 3.86
304 330 1.144936 GAGATGTTCCTCGCCCCTG 59.855 63.158 0.00 0.00 0.00 4.45
305 331 2.066999 GGAGATGTTCCTCGCCCCT 61.067 63.158 0.00 0.00 43.16 4.79
802 858 0.741326 GCGCTCCACACATCTCTCTA 59.259 55.000 0.00 0.00 0.00 2.43
833 889 1.525077 GGCCACGAGGTCAACAACA 60.525 57.895 0.00 0.00 40.10 3.33
887 944 1.035932 AGGTCGGATTCGGTCATCGT 61.036 55.000 0.00 0.00 40.32 3.73
919 976 4.263068 GGTGAACAGGAGAAGGAAGAATGA 60.263 45.833 0.00 0.00 0.00 2.57
979 1036 0.247736 GATGGCACCTCGAAGTGTCT 59.752 55.000 18.85 5.51 42.94 3.41
1316 1610 7.228706 TGAGAAAGTATATGCATGAGACGAGTA 59.771 37.037 10.16 0.00 0.00 2.59
1357 1651 3.056328 GACGCCCTGCCAAGGTTC 61.056 66.667 0.00 0.00 42.74 3.62
1419 1713 4.680702 GACTAATAACGACCAAGGGAGTC 58.319 47.826 0.00 0.00 0.00 3.36
1470 1764 1.352352 AGTCCAAGCCTGCAAGTACAT 59.648 47.619 0.00 0.00 0.00 2.29
1609 1906 0.599558 CACAAGTGGATGCAACCCAG 59.400 55.000 10.94 3.02 33.75 4.45
1737 2035 5.012664 TGTTTTCTCAGTAGTCAAGCCCATA 59.987 40.000 0.00 0.00 0.00 2.74
1762 2060 3.764237 AGACGAGGCTGGAAACTAAAA 57.236 42.857 2.65 0.00 0.00 1.52
1897 2195 2.772287 AGTTAGCTTGGTTGCAGTCTC 58.228 47.619 0.00 0.00 34.99 3.36
1937 2235 7.870509 TTCCTCTTGAAACAATCTATCCATG 57.129 36.000 0.00 0.00 0.00 3.66
1983 2281 9.337396 TGTTTTAGCTTACTTCTGAAATCTGAA 57.663 29.630 0.00 3.24 33.68 3.02
2059 2358 6.829811 ACTAGCTAGTACTTCCTTACTTCTGG 59.170 42.308 24.97 0.00 34.10 3.86
2220 2520 7.027874 TGGAAAGGACAACCAAATAGTAGAT 57.972 36.000 0.00 0.00 38.94 1.98
2303 2603 7.679783 TGAGACTCAATTAGGAAACTTCATCA 58.320 34.615 1.64 0.00 43.67 3.07
2320 2620 1.942657 GTTGCTGCAGTTTGAGACTCA 59.057 47.619 16.64 0.00 36.10 3.41
2373 2673 6.001460 TCAACAGTTAGAATTTGGACCGATT 58.999 36.000 0.00 0.00 0.00 3.34
2421 2740 1.338105 TGGATTGGAGTCTGAAGCACG 60.338 52.381 0.00 0.00 0.00 5.34
2455 2774 3.341823 GACCTGTACGTGTTCCTCTCTA 58.658 50.000 0.00 0.00 0.00 2.43
2487 2806 8.159447 TGTTGCATATAATTCTTATCTCCTGCT 58.841 33.333 0.00 0.00 0.00 4.24
2505 2824 3.981071 AGCTAAGTGACCTGTTGCATA 57.019 42.857 0.00 0.00 0.00 3.14
2507 2826 2.494059 GAAGCTAAGTGACCTGTTGCA 58.506 47.619 0.00 0.00 0.00 4.08
2511 2830 3.744660 CAAAGGAAGCTAAGTGACCTGT 58.255 45.455 0.00 0.00 0.00 4.00
2539 2858 5.468540 AGAACTTTGATAACCTTTTGCCC 57.531 39.130 0.00 0.00 0.00 5.36



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

AutoCloner maintained by Alex Coulton.