Multiple sequence alignment - TraesCS4A01G233700

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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 TraesCS4A01G233700 chr4A 100.000 2658 0 0 1 2658 542534493 542531836 0.000000e+00 4909
1 TraesCS4A01G233700 chr4A 85.325 1247 146 22 806 2034 551132231 551133458 0.000000e+00 1254
2 TraesCS4A01G233700 chr4A 83.502 891 108 15 908 1767 542556004 542555122 0.000000e+00 795
3 TraesCS4A01G233700 chr4A 87.356 609 43 11 2066 2658 551133542 551134132 0.000000e+00 667
4 TraesCS4A01G233700 chr4A 82.534 521 54 15 134 622 551131512 551132027 8.800000e-115 424
5 TraesCS4A01G233700 chr4D 87.790 2711 191 54 3 2658 54473963 54476588 0.000000e+00 3044
6 TraesCS4A01G233700 chr4D 88.228 1716 146 33 343 2034 54603698 54605381 0.000000e+00 1999
7 TraesCS4A01G233700 chr4D 84.725 982 106 22 806 1763 47336949 47335988 0.000000e+00 942
8 TraesCS4A01G233700 chr4D 93.016 630 31 6 2034 2657 54605430 54606052 0.000000e+00 907
9 TraesCS4A01G233700 chr4D 85.216 832 86 15 908 1712 54446479 54447300 0.000000e+00 821
10 TraesCS4A01G233700 chr4D 84.236 609 60 17 2066 2658 47334689 47334101 6.430000e-156 560
11 TraesCS4A01G233700 chr4D 80.357 672 85 25 131 786 47337701 47337061 1.440000e-127 466
12 TraesCS4A01G233700 chr4D 79.661 236 41 7 1793 2025 54448332 54448563 2.120000e-36 163
13 TraesCS4A01G233700 chr4B 90.796 967 68 3 1708 2658 80594394 80595355 0.000000e+00 1273
14 TraesCS4A01G233700 chr4B 86.894 763 80 13 806 1567 68961913 68961170 0.000000e+00 837
15 TraesCS4A01G233700 chr4B 92.829 516 34 1 1184 1699 80593788 80594300 0.000000e+00 745
16 TraesCS4A01G233700 chr4B 82.005 878 112 23 918 1771 80556912 80557767 0.000000e+00 704
17 TraesCS4A01G233700 chr4B 82.005 878 112 23 918 1771 80585582 80586437 0.000000e+00 704
18 TraesCS4A01G233700 chr4B 86.020 608 52 17 2066 2656 68730183 68729592 2.910000e-174 621
19 TraesCS4A01G233700 chr4B 86.813 364 35 4 304 659 68962424 68962066 6.900000e-106 394
20 TraesCS4A01G233700 chr4B 80.762 551 53 18 8 546 80592494 80593003 5.370000e-102 381
21 TraesCS4A01G233700 chr4B 85.352 355 35 9 806 1153 80593375 80593719 4.210000e-93 351
22 TraesCS4A01G233700 chr4B 92.353 170 10 3 343 509 68730548 68730379 3.420000e-59 239
23 TraesCS4A01G233700 chr4B 84.519 239 18 7 2432 2658 68959248 68959017 4.450000e-53 219
24 TraesCS4A01G233700 chr4B 75.909 440 72 15 2078 2513 80559155 80559564 7.510000e-46 195
25 TraesCS4A01G233700 chr4B 75.909 440 72 15 2078 2513 80587825 80588234 7.510000e-46 195
26 TraesCS4A01G233700 chr6D 93.220 118 8 0 2215 2332 86790549 86790666 9.780000e-40 174


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 TraesCS4A01G233700 chr4A 542531836 542534493 2657 True 4909.000000 4909 100.000000 1 2658 1 chr4A.!!$R1 2657
1 TraesCS4A01G233700 chr4A 542555122 542556004 882 True 795.000000 795 83.502000 908 1767 1 chr4A.!!$R2 859
2 TraesCS4A01G233700 chr4A 551131512 551134132 2620 False 781.666667 1254 85.071667 134 2658 3 chr4A.!!$F1 2524
3 TraesCS4A01G233700 chr4D 54473963 54476588 2625 False 3044.000000 3044 87.790000 3 2658 1 chr4D.!!$F1 2655
4 TraesCS4A01G233700 chr4D 54603698 54606052 2354 False 1453.000000 1999 90.622000 343 2657 2 chr4D.!!$F3 2314
5 TraesCS4A01G233700 chr4D 47334101 47337701 3600 True 656.000000 942 83.106000 131 2658 3 chr4D.!!$R1 2527
6 TraesCS4A01G233700 chr4D 54446479 54448563 2084 False 492.000000 821 82.438500 908 2025 2 chr4D.!!$F2 1117
7 TraesCS4A01G233700 chr4B 80592494 80595355 2861 False 687.500000 1273 87.434750 8 2658 4 chr4B.!!$F3 2650
8 TraesCS4A01G233700 chr4B 68959017 68962424 3407 True 483.333333 837 86.075333 304 2658 3 chr4B.!!$R2 2354
9 TraesCS4A01G233700 chr4B 80556912 80559564 2652 False 449.500000 704 78.957000 918 2513 2 chr4B.!!$F1 1595
10 TraesCS4A01G233700 chr4B 80585582 80588234 2652 False 449.500000 704 78.957000 918 2513 2 chr4B.!!$F2 1595
11 TraesCS4A01G233700 chr4B 68729592 68730548 956 True 430.000000 621 89.186500 343 2656 2 chr4B.!!$R1 2313

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
465 511 0.108585 CCCGTGGTATCCATTCCTGG 59.891 60.0 0.00 0.00 44.64 4.45 F
765 895 0.171007 TTTAGGCGCTTGCAATCTGC 59.829 50.0 7.64 4.26 45.29 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1369 1731 1.107114 ATCGGAACATCAGCGAGTCT 58.893 50.0 0.00 0.0 0.00 3.24 R
2592 4415 0.458370 GCCACAAAATAAGGCTGCCG 60.458 55.0 13.96 0.0 44.92 5.69 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 6.494893 AAAAAGAAAGTCTTTGGTTTTGGC 57.505 33.333 1.60 0.00 45.19 4.52
46 47 8.894731 TGGCGCTGATTGTTTATTTATTTACTA 58.105 29.630 7.64 0.00 0.00 1.82
172 180 7.391833 AGAAACAAGACTTCTATGGATTTGACC 59.608 37.037 0.00 0.00 31.28 4.02
237 256 2.644992 GGTGGCGCCAACTTTCTG 59.355 61.111 37.07 0.00 37.17 3.02
310 343 6.071560 ACAAGTCTATGACCGAACTGATACAA 60.072 38.462 0.00 0.00 32.18 2.41
340 376 2.508751 GGCCGTAGAGTCCCATCCC 61.509 68.421 0.00 0.00 0.00 3.85
341 377 1.760875 GCCGTAGAGTCCCATCCCA 60.761 63.158 0.00 0.00 0.00 4.37
361 397 1.146485 CCCATCAGAGCAGCAGAGG 59.854 63.158 0.00 0.00 0.00 3.69
364 400 0.812014 CATCAGAGCAGCAGAGGCAG 60.812 60.000 0.00 0.00 44.61 4.85
460 506 0.182775 GCCTTCCCGTGGTATCCATT 59.817 55.000 0.00 0.00 35.28 3.16
462 508 1.202770 CCTTCCCGTGGTATCCATTCC 60.203 57.143 0.00 0.00 35.28 3.01
465 511 0.108585 CCCGTGGTATCCATTCCTGG 59.891 60.000 0.00 0.00 44.64 4.45
491 537 3.554934 TCAAGTTCCAGCAACACTTCAT 58.445 40.909 0.00 0.00 37.48 2.57
519 570 2.501723 GAGCATTGAGTACTCCCTTCCA 59.498 50.000 20.11 0.00 0.00 3.53
557 612 0.381801 CCTTCGCTGTTGTTTGCTGT 59.618 50.000 0.00 0.00 0.00 4.40
622 746 1.133482 CCTCCAGTCCTTTTGTTGGGT 60.133 52.381 0.00 0.00 0.00 4.51
624 748 3.031013 CTCCAGTCCTTTTGTTGGGTTT 58.969 45.455 0.00 0.00 0.00 3.27
625 749 3.445987 TCCAGTCCTTTTGTTGGGTTTT 58.554 40.909 0.00 0.00 0.00 2.43
633 757 4.639755 CCTTTTGTTGGGTTTTGCAAGATT 59.360 37.500 0.00 0.00 0.00 2.40
676 801 6.839134 AGGAAACTTTTAGAAATTCCCACAGT 59.161 34.615 0.00 0.00 40.31 3.55
710 837 4.276926 ACAGCTTTCATTCTTGTTGGAGAC 59.723 41.667 0.00 0.00 0.00 3.36
714 841 4.437682 TTCATTCTTGTTGGAGACCAGT 57.562 40.909 0.00 0.00 33.81 4.00
762 892 1.202336 AGCATTTAGGCGCTTGCAATC 60.202 47.619 7.64 0.00 41.71 2.67
764 894 2.456989 CATTTAGGCGCTTGCAATCTG 58.543 47.619 7.64 0.00 41.71 2.90
765 895 0.171007 TTTAGGCGCTTGCAATCTGC 59.829 50.000 7.64 4.26 45.29 4.26
766 896 0.677731 TTAGGCGCTTGCAATCTGCT 60.678 50.000 7.64 0.00 45.31 4.24
768 898 1.804326 GGCGCTTGCAATCTGCTTG 60.804 57.895 7.64 0.00 45.31 4.01
769 899 1.210931 GCGCTTGCAATCTGCTTGA 59.789 52.632 0.00 0.00 45.31 3.02
775 966 2.477845 TGCAATCTGCTTGAGCTGTA 57.522 45.000 4.44 0.00 45.31 2.74
899 1195 4.708726 AAAATTGATGAGTAGTGGCAGC 57.291 40.909 0.00 0.00 0.00 5.25
937 1233 5.121811 TGCAGAGGATAGCAAGATTTTCTC 58.878 41.667 0.00 0.00 37.90 2.87
958 1257 1.975407 GCTGCCAGTGCCAGTCATT 60.975 57.895 2.68 0.00 36.33 2.57
1117 1418 1.611673 GCATGGTAAGCTCAGTGGTGT 60.612 52.381 0.00 0.00 0.00 4.16
1157 1459 9.151471 GTAACTGAATCAGTAGCAATAAGACAA 57.849 33.333 17.04 0.00 44.62 3.18
1345 1707 2.983592 GGGTGGGAGGCGTTTGTG 60.984 66.667 0.00 0.00 0.00 3.33
1369 1731 6.206048 TGGACGCGAATCATATAGTAGAAAGA 59.794 38.462 15.93 0.00 0.00 2.52
1392 1754 1.067060 CTCGCTGATGTTCCGATACCA 59.933 52.381 0.00 0.00 0.00 3.25
1425 1787 2.223805 GCTTCAAGGTTGTGGTCTTTGG 60.224 50.000 0.00 0.00 0.00 3.28
1427 1789 2.374184 TCAAGGTTGTGGTCTTTGGTG 58.626 47.619 0.00 0.00 0.00 4.17
1457 1819 3.884895 TGTGAGAAAGTGGTGTCATGTT 58.115 40.909 0.00 0.00 0.00 2.71
1467 1829 0.164647 GTGTCATGTTCTGCTCGCAC 59.835 55.000 0.00 0.00 0.00 5.34
1628 1996 3.375299 ACGAGCAAGGAAAGATGCAATAC 59.625 43.478 0.00 0.00 44.95 1.89
1635 2003 4.446371 AGGAAAGATGCAATACCTTCTCG 58.554 43.478 0.00 0.00 0.00 4.04
1663 2031 8.215050 TCAGAGGATTTGTCAGGTTAACTTTAA 58.785 33.333 5.42 0.00 0.00 1.52
1669 2037 9.244799 GATTTGTCAGGTTAACTTTAAAACTGG 57.755 33.333 5.42 0.00 33.89 4.00
1670 2038 7.706100 TTGTCAGGTTAACTTTAAAACTGGT 57.294 32.000 5.42 0.00 33.89 4.00
1673 2041 9.240734 TGTCAGGTTAACTTTAAAACTGGTTTA 57.759 29.630 5.42 0.00 33.89 2.01
1742 2211 8.553459 AACTATTTTACAGAAGACAGTCCATG 57.447 34.615 0.00 0.00 0.00 3.66
1797 3207 3.524541 ACGTATTGGAATAACACCCGAC 58.475 45.455 0.00 0.00 0.00 4.79
1843 3254 1.305802 TCACTGGGTGCCCGTCTAT 60.306 57.895 2.44 0.00 39.42 1.98
1845 3256 2.064581 ACTGGGTGCCCGTCTATCC 61.065 63.158 2.44 0.00 39.42 2.59
1849 3260 1.605453 GGTGCCCGTCTATCCCAAA 59.395 57.895 0.00 0.00 0.00 3.28
1856 3267 2.487934 CCGTCTATCCCAAATGCAGAG 58.512 52.381 0.00 0.00 0.00 3.35
1940 3351 3.036084 CACGACCAGTGTCCGTGC 61.036 66.667 17.50 0.00 45.51 5.34
2256 3851 2.224621 CCAATCGTGCCCTGAGGATATT 60.225 50.000 0.00 0.00 33.47 1.28
2287 3882 3.748568 GGACTTCTTTTGCGAGAGACAAT 59.251 43.478 0.00 0.00 0.00 2.71
2429 4024 5.197451 TGACAAGAGGAATAGAGGTCTCTC 58.803 45.833 3.49 0.00 40.93 3.20
2464 4258 4.497300 GCATTTTGTATGTTGCTGATGGT 58.503 39.130 0.00 0.00 32.41 3.55
2465 4259 4.327898 GCATTTTGTATGTTGCTGATGGTG 59.672 41.667 0.00 0.00 32.41 4.17
2466 4260 4.517952 TTTTGTATGTTGCTGATGGTGG 57.482 40.909 0.00 0.00 0.00 4.61
2592 4415 4.092091 CAGACCGTGATTTCTTACTTCAGC 59.908 45.833 0.00 0.00 0.00 4.26
2620 4443 4.627035 GCCTTATTTTGTGGCATGAAGTTC 59.373 41.667 0.00 0.00 45.46 3.01
2640 4467 5.815740 AGTTCAAACTAGTTGTGTTGACGAT 59.184 36.000 9.34 0.00 37.52 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.121611 CGCCAAAACCAAAGACTTTCTTTTT 59.878 36.000 0.00 4.17 43.62 1.94
1 2 4.629634 CGCCAAAACCAAAGACTTTCTTTT 59.370 37.500 0.00 2.75 43.62 2.27
179 187 5.779241 AGGGTGTTGGATTTCATCTTAGA 57.221 39.130 0.00 0.00 0.00 2.10
225 244 1.919918 TGCAAAACAGAAAGTTGGCG 58.080 45.000 0.00 0.00 41.58 5.69
237 256 5.627367 GGTTTGGTCAAAAAGTTTGCAAAAC 59.373 36.000 14.67 6.41 31.33 2.43
282 304 5.250982 TCAGTTCGGTCATAGACTTGTAGA 58.749 41.667 0.00 0.00 32.47 2.59
340 376 0.468648 TCTGCTGCTCTGATGGGATG 59.531 55.000 0.00 0.00 0.00 3.51
341 377 0.759959 CTCTGCTGCTCTGATGGGAT 59.240 55.000 0.00 0.00 0.00 3.85
361 397 2.119801 TTTGCCCTCTCATTCTCTGC 57.880 50.000 0.00 0.00 0.00 4.26
364 400 3.212685 CCTGATTTGCCCTCTCATTCTC 58.787 50.000 0.00 0.00 0.00 2.87
460 506 2.487265 GCTGGAACTTGAAGAACCAGGA 60.487 50.000 27.91 7.30 45.45 3.86
465 511 3.378427 AGTGTTGCTGGAACTTGAAGAAC 59.622 43.478 13.23 1.46 35.37 3.01
491 537 3.575630 GAGTACTCAATGCTCACAACGA 58.424 45.455 18.20 0.00 39.71 3.85
557 612 9.905713 AGGAAAAGAGATACACAAAATGCTATA 57.094 29.630 0.00 0.00 0.00 1.31
661 786 4.287067 AGCTTCTCACTGTGGGAATTTCTA 59.713 41.667 22.38 0.43 36.09 2.10
691 818 4.823989 ACTGGTCTCCAACAAGAATGAAAG 59.176 41.667 0.00 0.00 32.68 2.62
696 823 5.941788 AGTTAACTGGTCTCCAACAAGAAT 58.058 37.500 7.48 0.00 32.68 2.40
710 837 1.468520 CGCACCCATCAAGTTAACTGG 59.531 52.381 9.34 6.22 0.00 4.00
714 841 0.878416 GCACGCACCCATCAAGTTAA 59.122 50.000 0.00 0.00 0.00 2.01
741 871 0.171007 TTGCAAGCGCCTAAATGCTC 59.829 50.000 2.29 0.00 41.46 4.26
845 1134 0.100682 CATGCATGAGGACTGCTTGC 59.899 55.000 22.59 0.00 40.34 4.01
899 1195 3.624861 CCTCTGCAGCACTTTGTATTAGG 59.375 47.826 9.47 1.75 0.00 2.69
958 1257 8.318412 TGTCCTGTAAGCAGAAAAACATAGATA 58.682 33.333 0.00 0.00 45.28 1.98
1117 1418 6.939730 TGATTCAGTTACTTATCAAGGCAACA 59.060 34.615 4.93 0.00 41.41 3.33
1196 1544 4.160439 CACAAAGCTCTCTGGTATGACCTA 59.840 45.833 0.00 0.00 39.58 3.08
1345 1707 6.609533 TCTTTCTACTATATGATTCGCGTCC 58.390 40.000 5.77 0.00 0.00 4.79
1351 1713 8.726988 AGCGAGTCTCTTTCTACTATATGATTC 58.273 37.037 0.00 0.00 0.00 2.52
1369 1731 1.107114 ATCGGAACATCAGCGAGTCT 58.893 50.000 0.00 0.00 0.00 3.24
1392 1754 3.157087 ACCTTGAAGCGACAATTTCCAT 58.843 40.909 0.00 0.00 0.00 3.41
1425 1787 3.248602 CACTTTCTCACAACCACTAGCAC 59.751 47.826 0.00 0.00 0.00 4.40
1427 1789 2.808543 CCACTTTCTCACAACCACTAGC 59.191 50.000 0.00 0.00 0.00 3.42
1467 1829 7.492352 TCTTGATCATTGATATTGCTCTGTG 57.508 36.000 0.00 0.00 0.00 3.66
1567 1935 2.295885 CTTCCACTCTGGCAATCATCC 58.704 52.381 0.00 0.00 37.47 3.51
1628 1996 2.234908 ACAAATCCTCTGACCGAGAAGG 59.765 50.000 0.00 0.00 42.62 3.46
1635 2003 3.425162 AACCTGACAAATCCTCTGACC 57.575 47.619 0.00 0.00 0.00 4.02
1663 2031 8.406730 TGGGATAAAACGTTATAAACCAGTTT 57.593 30.769 0.00 0.86 36.70 2.66
1742 2211 2.354109 TTCAGATGACTCGTGCTCAC 57.646 50.000 0.00 0.00 0.00 3.51
1797 3207 5.488262 TGTATGGGTCTGTATCATCATGG 57.512 43.478 0.00 0.00 0.00 3.66
1843 3254 3.181429 ACTTTCTTCCTCTGCATTTGGGA 60.181 43.478 0.00 0.00 0.00 4.37
1845 3256 4.522022 AGAACTTTCTTCCTCTGCATTTGG 59.478 41.667 0.00 0.00 32.55 3.28
1849 3260 4.630644 TCAGAACTTTCTTCCTCTGCAT 57.369 40.909 0.00 0.00 36.15 3.96
1856 3267 6.318900 TCCAACTTTCTTCAGAACTTTCTTCC 59.681 38.462 0.00 0.00 34.74 3.46
1940 3351 2.100989 AGACAAGACTTACTAGGGCGG 58.899 52.381 0.00 0.00 0.00 6.13
2256 3851 2.586425 CAAAAGAAGTCCAGCCTCCAA 58.414 47.619 0.00 0.00 0.00 3.53
2429 4024 2.224113 ACAAAATGCCAGCACAAAGAGG 60.224 45.455 0.00 0.00 0.00 3.69
2518 4315 5.872070 GGTTTCTTACTCACTCCAGAGAATG 59.128 44.000 0.70 0.00 38.98 2.67
2519 4316 5.782845 AGGTTTCTTACTCACTCCAGAGAAT 59.217 40.000 0.70 0.00 38.98 2.40
2520 4317 5.148502 AGGTTTCTTACTCACTCCAGAGAA 58.851 41.667 0.70 0.00 38.98 2.87
2592 4415 0.458370 GCCACAAAATAAGGCTGCCG 60.458 55.000 13.96 0.00 44.92 5.69
2620 4443 5.403897 ACATCGTCAACACAACTAGTTTG 57.596 39.130 5.07 10.29 41.49 2.93


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

AutoCloner maintained by Alex Coulton.