Multiple sequence alignment - TraesCS1A01G163000

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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 TraesCS1A01G163000 chr1A 100.000 2924 0 0 1 2924 292747177 292744254 0.000000e+00 5400
1 TraesCS1A01G163000 chr1D 91.602 2572 115 29 150 2679 225430898 225433410 0.000000e+00 3459
2 TraesCS1A01G163000 chr1D 95.305 213 10 0 2712 2924 225433411 225433623 3.610000e-89 339
3 TraesCS1A01G163000 chr1D 89.677 155 11 2 2 151 225430708 225430862 2.970000e-45 193
4 TraesCS1A01G163000 chr1B 91.650 1964 117 14 958 2904 325297248 325299181 0.000000e+00 2675
5 TraesCS1A01G163000 chr1B 90.395 760 21 16 150 889 325296066 325296793 0.000000e+00 952
6 TraesCS1A01G163000 chr1B 91.738 351 23 1 1285 1635 612222931 612223275 1.580000e-132 483
7 TraesCS1A01G163000 chr1B 94.186 86 5 0 65 150 325295945 325296030 6.580000e-27 132
8 TraesCS1A01G163000 chr5B 91.738 351 23 1 1285 1635 96016973 96016629 1.580000e-132 483
9 TraesCS1A01G163000 chr6B 92.857 322 17 1 1314 1635 713457822 713457507 2.050000e-126 462
10 TraesCS1A01G163000 chr7A 92.260 323 19 1 1313 1635 642102217 642101901 1.240000e-123 453
11 TraesCS1A01G163000 chr3B 91.950 323 20 1 1313 1635 52652193 52651877 5.750000e-122 448
12 TraesCS1A01G163000 chr3B 94.074 135 8 0 1313 1447 815309896 815309762 3.820000e-49 206
13 TraesCS1A01G163000 chr4A 94.815 135 7 0 1313 1447 730989590 730989724 8.210000e-51 211


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 TraesCS1A01G163000 chr1A 292744254 292747177 2923 True 5400.000000 5400 100.000000 1 2924 1 chr1A.!!$R1 2923
1 TraesCS1A01G163000 chr1D 225430708 225433623 2915 False 1330.333333 3459 92.194667 2 2924 3 chr1D.!!$F1 2922
2 TraesCS1A01G163000 chr1B 325295945 325299181 3236 False 1253.000000 2675 92.077000 65 2904 3 chr1B.!!$F2 2839

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
78 83 0.036388 TGGCGCTAAAGAAGACCCAG 60.036 55.0 7.64 0.0 0.0 4.45 F
1175 1637 0.108567 GTCGTCTGGCTCCTTTCCTC 60.109 60.0 0.00 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1268 1730 0.179094 AGCAAAGACGTCGTGTTCCA 60.179 50.0 19.30 0.0 0.00 3.53 R
2514 2997 0.407139 ACTTGATGCAAGAGGCCCTT 59.593 50.0 13.56 0.0 43.42 3.95 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
40 45 2.411748 GGTGTGTGTGTGTGATACGATG 59.588 50.000 0.00 0.00 0.00 3.84
49 54 0.921347 GTGATACGATGACACGGTGC 59.079 55.000 8.30 1.81 37.61 5.01
53 58 0.388006 TACGATGACACGGTGCACAG 60.388 55.000 20.43 18.06 37.61 3.66
78 83 0.036388 TGGCGCTAAAGAAGACCCAG 60.036 55.000 7.64 0.00 0.00 4.45
146 151 7.657761 GGGTATCTCTTGTGTTAACCATCATAG 59.342 40.741 2.48 2.30 0.00 2.23
201 247 4.284746 TCTCAACCAACCAAAACCAAAACT 59.715 37.500 0.00 0.00 0.00 2.66
237 283 4.634443 GGTGGGTATTGAGTATTGACACAC 59.366 45.833 0.00 0.00 42.47 3.82
259 305 1.325640 GTCATGCAGCTGACGTATGTG 59.674 52.381 20.43 4.60 36.50 3.21
311 360 1.136305 GGCTGAATCATGCATGCTTGT 59.864 47.619 27.12 13.56 0.00 3.16
312 361 2.460918 GCTGAATCATGCATGCTTGTC 58.539 47.619 27.12 20.23 0.00 3.18
401 461 6.071560 ACGACTGGTTCAGTACTCAATAATGA 60.072 38.462 0.00 0.00 45.44 2.57
463 523 3.711190 TCATCCACCATACTATGCACTGT 59.289 43.478 0.00 0.00 0.00 3.55
580 650 8.807948 TCTTCCTCCTTAATCAAACCATTTAG 57.192 34.615 0.00 0.00 0.00 1.85
750 826 9.940166 TTGTTCTTTTCCTCGAAACTTATTTAC 57.060 29.630 0.00 0.00 30.83 2.01
884 960 1.178276 CGTCAGTACCTCAGCTCCTT 58.822 55.000 0.00 0.00 0.00 3.36
904 980 0.974010 CTCCCGCCCCGGCTATATAA 60.974 60.000 3.84 0.00 46.86 0.98
905 981 0.974010 TCCCGCCCCGGCTATATAAG 60.974 60.000 3.84 0.00 46.86 1.73
923 1000 1.374252 GCGACTCGACCCACACATT 60.374 57.895 1.63 0.00 0.00 2.71
951 1028 4.431131 CCCCTCCTTGCACGCCAT 62.431 66.667 0.00 0.00 0.00 4.40
952 1029 2.825836 CCCTCCTTGCACGCCATC 60.826 66.667 0.00 0.00 0.00 3.51
953 1030 3.197790 CCTCCTTGCACGCCATCG 61.198 66.667 0.00 0.00 42.43 3.84
954 1031 2.125552 CTCCTTGCACGCCATCGA 60.126 61.111 0.00 0.00 39.41 3.59
955 1032 2.125552 TCCTTGCACGCCATCGAG 60.126 61.111 0.00 0.00 39.41 4.04
956 1033 2.125552 CCTTGCACGCCATCGAGA 60.126 61.111 0.00 0.00 39.41 4.04
988 1450 0.238817 CCTCTCGCGGTCTAGTATGC 59.761 60.000 6.13 0.00 0.00 3.14
1089 1551 1.419374 CAAACTCCTTCGTCTCCGTG 58.581 55.000 0.00 0.00 35.01 4.94
1129 1591 1.002792 CTCTTCTCCCCTCCCTGCT 59.997 63.158 0.00 0.00 0.00 4.24
1168 1630 1.226717 GTCATCGTCGTCTGGCTCC 60.227 63.158 0.00 0.00 0.00 4.70
1169 1631 1.378646 TCATCGTCGTCTGGCTCCT 60.379 57.895 0.00 0.00 0.00 3.69
1170 1632 0.965866 TCATCGTCGTCTGGCTCCTT 60.966 55.000 0.00 0.00 0.00 3.36
1171 1633 0.108615 CATCGTCGTCTGGCTCCTTT 60.109 55.000 0.00 0.00 0.00 3.11
1172 1634 0.173708 ATCGTCGTCTGGCTCCTTTC 59.826 55.000 0.00 0.00 0.00 2.62
1174 1636 1.878656 CGTCGTCTGGCTCCTTTCCT 61.879 60.000 0.00 0.00 0.00 3.36
1175 1637 0.108567 GTCGTCTGGCTCCTTTCCTC 60.109 60.000 0.00 0.00 0.00 3.71
1176 1638 1.219393 CGTCTGGCTCCTTTCCTCC 59.781 63.158 0.00 0.00 0.00 4.30
1178 1640 0.251634 GTCTGGCTCCTTTCCTCCTG 59.748 60.000 0.00 0.00 0.00 3.86
1179 1641 1.077858 CTGGCTCCTTTCCTCCTGC 60.078 63.158 0.00 0.00 0.00 4.85
1180 1642 2.273776 GGCTCCTTTCCTCCTGCC 59.726 66.667 0.00 0.00 0.00 4.85
1264 1726 2.899339 GCGGCATGCTCTTCCCTC 60.899 66.667 18.92 0.00 41.73 4.30
1266 1728 2.203126 GGCATGCTCTTCCCTCCG 60.203 66.667 18.92 0.00 0.00 4.63
1268 1730 1.078143 GCATGCTCTTCCCTCCGTT 60.078 57.895 11.37 0.00 0.00 4.44
1299 1761 1.748122 CTTTGCTGCCGCTCCTGAT 60.748 57.895 0.70 0.00 36.97 2.90
1301 1763 2.467993 TTTGCTGCCGCTCCTGATGA 62.468 55.000 0.70 0.00 36.97 2.92
1359 1821 4.436998 CGGGAAGCGAGAACGGCT 62.437 66.667 0.00 0.00 40.15 5.52
1466 1928 0.178964 CCCAAGGGCAAGAAGGAACA 60.179 55.000 0.00 0.00 0.00 3.18
1469 1931 2.242043 CAAGGGCAAGAAGGAACACAT 58.758 47.619 0.00 0.00 0.00 3.21
1689 2157 1.112113 GGAGGGAGATGCGTAAGTCA 58.888 55.000 0.00 0.00 41.68 3.41
1925 2393 1.655329 CTCCCATCCGCGTCTAGTC 59.345 63.158 4.92 0.00 0.00 2.59
2122 2595 1.102809 CCGCCATTGCATGCCTAGAA 61.103 55.000 16.68 2.46 37.32 2.10
2140 2613 3.709587 AGAAGGAACGATGGAAGGACTA 58.290 45.455 0.00 0.00 0.00 2.59
2149 2622 3.249559 CGATGGAAGGACTACGTAGGTAC 59.750 52.174 25.63 14.93 0.00 3.34
2150 2623 3.719268 TGGAAGGACTACGTAGGTACA 57.281 47.619 25.63 12.14 0.00 2.90
2151 2624 3.614092 TGGAAGGACTACGTAGGTACAG 58.386 50.000 25.63 3.22 0.00 2.74
2152 2625 2.948315 GGAAGGACTACGTAGGTACAGG 59.052 54.545 25.63 0.78 0.00 4.00
2154 2627 1.213926 AGGACTACGTAGGTACAGGGG 59.786 57.143 25.63 0.00 0.00 4.79
2240 2715 3.303135 TCCTGCAGCTTCGGTCGT 61.303 61.111 8.66 0.00 0.00 4.34
2276 2751 5.117355 CGTATGTACGTAGGATCATGGTT 57.883 43.478 8.79 0.00 44.13 3.67
2277 2752 4.915667 CGTATGTACGTAGGATCATGGTTG 59.084 45.833 8.79 0.00 44.13 3.77
2278 2753 5.278120 CGTATGTACGTAGGATCATGGTTGA 60.278 44.000 8.79 0.00 44.13 3.18
2279 2754 4.649088 TGTACGTAGGATCATGGTTGAG 57.351 45.455 0.00 0.00 34.73 3.02
2311 2786 6.534079 AGGAATCAACGCTACATGTAAGTTAC 59.466 38.462 19.64 6.06 0.00 2.50
2383 2858 6.717413 TGCTCAATTTTGCTGTTTCAAATTC 58.283 32.000 1.82 0.00 36.04 2.17
2386 2861 7.164226 TCAATTTTGCTGTTTCAAATTCTCG 57.836 32.000 0.00 0.00 36.04 4.04
2514 2997 5.032327 AGATGTGAGCATGCTTGAGATTA 57.968 39.130 23.61 5.00 35.07 1.75
2533 3016 0.407139 AAGGGCCTCTTGCATCAAGT 59.593 50.000 6.46 0.00 41.66 3.16
2573 3056 9.362539 CACTGATTTAGTATAACTTTGTACCGT 57.637 33.333 0.00 0.00 37.60 4.83
2702 3185 0.947244 GCCAGCCTATTTGGATCGTG 59.053 55.000 0.00 0.00 37.96 4.35
2713 3196 7.492344 GCCTATTTGGATCGTGAAATTCAAATT 59.508 33.333 8.09 0.00 40.42 1.82
2814 3297 3.603965 ACTTGGGTATTTGGTCCACAA 57.396 42.857 0.00 0.00 37.28 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.816925 ACACACCAAGAAAGAAAGCTACTC 59.183 41.667 0.00 0.00 0.00 2.59
3 4 4.576463 CACACACCAAGAAAGAAAGCTACT 59.424 41.667 0.00 0.00 0.00 2.57
15 16 2.708216 ATCACACACACACACCAAGA 57.292 45.000 0.00 0.00 0.00 3.02
40 45 3.566261 CATCCTGTGCACCGTGTC 58.434 61.111 15.69 0.00 0.00 3.67
78 83 1.339644 TACCCATGACTTACGGGCCC 61.340 60.000 13.57 13.57 44.49 5.80
112 117 4.836825 ACACAAGAGATACCCATGACTTG 58.163 43.478 0.00 0.00 39.98 3.16
259 305 3.270877 CTGGAAATAGGGCGCCATATAC 58.729 50.000 31.86 25.92 0.00 1.47
311 360 8.523658 CAGACCATATATACGAAGAAATGGAGA 58.476 37.037 14.60 0.00 37.80 3.71
312 361 8.307483 ACAGACCATATATACGAAGAAATGGAG 58.693 37.037 14.60 8.43 37.80 3.86
346 400 4.288670 TGTACAGAGCGAGTATAACTGC 57.711 45.455 0.00 0.00 32.67 4.40
401 461 0.040425 GCCGTGTTTTCGCTGTGAAT 60.040 50.000 4.26 0.00 36.22 2.57
429 489 7.460910 AGTATGGTGGATGAATACAATATGCA 58.539 34.615 0.00 0.00 30.67 3.96
430 490 7.928307 AGTATGGTGGATGAATACAATATGC 57.072 36.000 0.00 0.00 30.67 3.14
580 650 4.777463 AGTAACCCACATAATGCAGGTAC 58.223 43.478 0.00 0.00 0.00 3.34
655 726 1.779683 GTGCTGCGACCGTTCTTAC 59.220 57.895 0.00 0.00 0.00 2.34
750 826 7.119846 CCTCAACTGGTAGAGTAATTTCCAAAG 59.880 40.741 0.00 0.00 33.09 2.77
904 980 1.816863 AATGTGTGGGTCGAGTCGCT 61.817 55.000 7.92 0.00 0.00 4.93
905 981 1.352156 GAATGTGTGGGTCGAGTCGC 61.352 60.000 7.92 2.87 0.00 5.19
906 982 0.038618 TGAATGTGTGGGTCGAGTCG 60.039 55.000 6.09 6.09 0.00 4.18
938 1015 2.125552 CTCGATGGCGTGCAAGGA 60.126 61.111 0.79 0.00 38.98 3.36
939 1016 2.125552 TCTCGATGGCGTGCAAGG 60.126 61.111 0.79 0.00 38.98 3.61
947 1024 1.005156 GAGGATGGCTCTCGATGGC 60.005 63.158 5.39 5.39 0.00 4.40
948 1025 1.670590 GGAGGATGGCTCTCGATGG 59.329 63.158 0.00 0.00 32.34 3.51
949 1026 1.670590 GGGAGGATGGCTCTCGATG 59.329 63.158 0.00 0.00 32.34 3.84
950 1027 1.535202 GGGGAGGATGGCTCTCGAT 60.535 63.158 0.00 0.00 32.34 3.59
951 1028 2.123251 GGGGAGGATGGCTCTCGA 60.123 66.667 0.00 0.00 32.34 4.04
952 1029 3.237741 GGGGGAGGATGGCTCTCG 61.238 72.222 0.00 0.00 32.34 4.04
988 1450 1.649664 CAGTTCATCTCGGGCAAGAG 58.350 55.000 3.22 3.22 39.52 2.85
1102 1564 0.677098 GGGGAGAAGAGGAAAACGGC 60.677 60.000 0.00 0.00 0.00 5.68
1129 1591 4.467084 GGCGGCGATCCACAGGAA 62.467 66.667 12.98 0.00 34.34 3.36
1163 1625 2.273776 GGCAGGAGGAAAGGAGCC 59.726 66.667 0.00 0.00 34.71 4.70
1168 1630 2.747855 GTGGCGGCAGGAGGAAAG 60.748 66.667 13.91 0.00 0.00 2.62
1169 1631 4.344865 GGTGGCGGCAGGAGGAAA 62.345 66.667 13.91 0.00 0.00 3.13
1264 1726 0.872881 AAGACGTCGTGTTCCAACGG 60.873 55.000 10.46 0.00 43.73 4.44
1266 1728 1.593793 GCAAAGACGTCGTGTTCCAAC 60.594 52.381 19.30 0.00 0.00 3.77
1268 1730 0.179094 AGCAAAGACGTCGTGTTCCA 60.179 50.000 19.30 0.00 0.00 3.53
1450 1912 2.519013 GATGTGTTCCTTCTTGCCCTT 58.481 47.619 0.00 0.00 0.00 3.95
1466 1928 1.388065 CGGCTTCTCCTCCTCGATGT 61.388 60.000 0.00 0.00 0.00 3.06
1469 1931 1.452289 CTCGGCTTCTCCTCCTCGA 60.452 63.158 0.00 0.00 0.00 4.04
1539 2007 3.657448 CTGCCACGCCGTGTCCATA 62.657 63.158 16.99 0.00 0.00 2.74
2024 2497 3.489355 TGTACAGTCTTCCTTCCGTACA 58.511 45.455 0.00 0.00 37.47 2.90
2068 2541 9.534565 TTTGTCTCTTGATGATTATGCTAGTAC 57.465 33.333 0.00 0.00 0.00 2.73
2078 2551 5.357314 CAGGCATCTTTGTCTCTTGATGATT 59.643 40.000 0.00 0.00 34.95 2.57
2122 2595 1.749634 CGTAGTCCTTCCATCGTTCCT 59.250 52.381 0.00 0.00 0.00 3.36
2140 2613 1.217057 TCCTCCCCCTGTACCTACGT 61.217 60.000 0.00 0.00 0.00 3.57
2152 2625 3.958860 CATGGCCGGATCCTCCCC 61.959 72.222 5.05 7.67 31.13 4.81
2154 2627 4.650377 GCCATGGCCGGATCCTCC 62.650 72.222 27.24 11.35 34.56 4.30
2185 2660 1.270518 CCAGTACTGCTTCAGTGTGCT 60.271 52.381 17.86 3.06 45.01 4.40
2236 2711 7.689953 ACATACGGATTTAATCTACAACGAC 57.310 36.000 4.87 0.00 0.00 4.34
2266 2741 3.529533 CTCACTCACTCAACCATGATCC 58.470 50.000 0.00 0.00 34.37 3.36
2270 2745 3.407424 TTCCTCACTCACTCAACCATG 57.593 47.619 0.00 0.00 0.00 3.66
2276 2751 2.610479 GCGTTGATTCCTCACTCACTCA 60.610 50.000 0.00 0.00 0.00 3.41
2277 2752 1.996191 GCGTTGATTCCTCACTCACTC 59.004 52.381 0.00 0.00 0.00 3.51
2278 2753 1.620819 AGCGTTGATTCCTCACTCACT 59.379 47.619 0.00 0.00 0.00 3.41
2279 2754 2.086054 AGCGTTGATTCCTCACTCAC 57.914 50.000 0.00 0.00 0.00 3.51
2311 2786 9.922305 CGCTCTTCATTTATTTAGAGGTTAAAG 57.078 33.333 0.00 0.00 35.72 1.85
2386 2861 2.424733 GCTACGGACAGGGGTCTCC 61.425 68.421 0.00 0.00 43.77 3.71
2481 2964 4.327982 TGCTCACATCTACCTATTCAGC 57.672 45.455 0.00 0.00 0.00 4.26
2514 2997 0.407139 ACTTGATGCAAGAGGCCCTT 59.593 50.000 13.56 0.00 43.42 3.95
2533 3016 8.421249 ACTAAATCAGTGAAATCCAAAATCCA 57.579 30.769 0.00 0.00 35.62 3.41
2592 3075 9.768215 ATTTTAATCCTTTACTCCCTTCAATCA 57.232 29.630 0.00 0.00 0.00 2.57
2598 3081 9.392259 CTTACGATTTTAATCCTTTACTCCCTT 57.608 33.333 0.00 0.00 31.68 3.95
2635 3118 4.021016 GCAATCCTACGATCAGGGATAGTT 60.021 45.833 10.30 0.00 38.73 2.24
2636 3119 3.511934 GCAATCCTACGATCAGGGATAGT 59.488 47.826 10.30 0.00 38.73 2.12
2691 3174 7.385267 TCCAATTTGAATTTCACGATCCAAAT 58.615 30.769 0.00 0.00 36.24 2.32
2702 3185 9.865321 TTCTTCTCATGATCCAATTTGAATTTC 57.135 29.630 0.00 0.00 0.00 2.17
2766 3249 4.580580 AGATTCCCGCATTTTACAATCCTC 59.419 41.667 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.