Multiple sequence alignment - TraesCS3A01G477700

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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 TraesCS3A01G477700 chr3A 100.000 3659 0 0 1 3659 709373742 709377400 0.000000e+00 6758.0
1 TraesCS3A01G477700 chr3A 79.949 783 91 32 775 1526 14768585 14769332 1.950000e-142 516.0
2 TraesCS3A01G477700 chr3A 100.000 31 0 0 1 31 36657048 36657078 1.420000e-04 58.4
3 TraesCS3A01G477700 chr3B 94.684 3687 145 19 1 3659 764377461 764373798 0.000000e+00 5675.0
4 TraesCS3A01G477700 chr3B 91.189 976 78 6 1444 2412 764055132 764056106 0.000000e+00 1319.0
5 TraesCS3A01G477700 chr3B 92.053 604 47 1 743 1345 764054192 764054795 0.000000e+00 848.0
6 TraesCS3A01G477700 chr3B 92.913 508 31 3 1047 1551 764050192 764050697 0.000000e+00 734.0
7 TraesCS3A01G477700 chr3B 79.455 1027 158 33 443 1440 44782613 44783615 0.000000e+00 678.0
8 TraesCS3A01G477700 chr3B 86.340 571 46 15 2302 2847 764050695 764051258 8.750000e-166 593.0
9 TraesCS3A01G477700 chr3B 86.282 277 34 4 1767 2042 44783616 44783889 7.680000e-77 298.0
10 TraesCS3A01G477700 chr3D 95.111 3150 124 16 1 3131 574424834 574427972 0.000000e+00 4937.0
11 TraesCS3A01G477700 chr3D 81.048 649 111 10 797 1440 26582042 26582683 1.170000e-139 507.0
12 TraesCS3A01G477700 chr3D 85.199 277 34 5 1767 2042 26582684 26582954 1.000000e-70 278.0
13 TraesCS3A01G477700 chr3D 94.400 125 7 0 3351 3475 574428251 574428375 3.730000e-45 193.0
14 TraesCS3A01G477700 chr3D 86.207 58 4 2 1 58 26574660 26574607 3.950000e-05 60.2
15 TraesCS3A01G477700 chr3D 100.000 31 0 0 1 31 26581603 26581633 1.420000e-04 58.4


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 TraesCS3A01G477700 chr3A 709373742 709377400 3658 False 6758.000000 6758 100.00000 1 3659 1 chr3A.!!$F3 3658
1 TraesCS3A01G477700 chr3A 14768585 14769332 747 False 516.000000 516 79.94900 775 1526 1 chr3A.!!$F1 751
2 TraesCS3A01G477700 chr3B 764373798 764377461 3663 True 5675.000000 5675 94.68400 1 3659 1 chr3B.!!$R1 3658
3 TraesCS3A01G477700 chr3B 764050192 764056106 5914 False 873.500000 1319 90.62375 743 2847 4 chr3B.!!$F2 2104
4 TraesCS3A01G477700 chr3B 44782613 44783889 1276 False 488.000000 678 82.86850 443 2042 2 chr3B.!!$F1 1599
5 TraesCS3A01G477700 chr3D 574424834 574428375 3541 False 2565.000000 4937 94.75550 1 3475 2 chr3D.!!$F2 3474
6 TraesCS3A01G477700 chr3D 26581603 26582954 1351 False 281.133333 507 88.74900 1 2042 3 chr3D.!!$F1 2041

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
123 130 0.684805 TTTCCTCGCTCCTCCTCCTC 60.685 60.000 0.0 0.0 0.00 3.71 F
466 479 0.900647 CGTCCTTCACCTCTCCCTGT 60.901 60.000 0.0 0.0 0.00 4.00 F
1183 4466 1.065199 TGATGGAGGATGCACTTGACC 60.065 52.381 0.0 0.0 41.42 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 4671 0.251341 GGAGTTCCATGGCACTGGTT 60.251 55.0 22.45 0.0 37.57 3.67 R
1626 5202 0.606401 AATTGTCAGGTGTGAGGCCG 60.606 55.0 0.00 0.0 31.53 6.13 R
2685 6268 0.388520 CGGTGCGATGTGAGTCAGAA 60.389 55.0 0.00 0.0 0.00 3.02 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
38 45 2.923035 CCTCCTCCACCACACCGT 60.923 66.667 0.00 0.00 0.00 4.83
123 130 0.684805 TTTCCTCGCTCCTCCTCCTC 60.685 60.000 0.00 0.00 0.00 3.71
466 479 0.900647 CGTCCTTCACCTCTCCCTGT 60.901 60.000 0.00 0.00 0.00 4.00
572 592 2.223112 CCCTGTTCGATGAAATGCTTCG 60.223 50.000 0.00 0.00 43.30 3.79
576 596 1.651987 TCGATGAAATGCTTCGGTCC 58.348 50.000 0.00 0.00 42.49 4.46
720 740 4.095782 GTGGTGCCGTACAATGTATTGATT 59.904 41.667 11.29 0.00 40.14 2.57
1183 4466 1.065199 TGATGGAGGATGCACTTGACC 60.065 52.381 0.00 0.00 41.42 4.02
1347 4636 5.557576 ATGCAGCTTCATATTCTCCACTA 57.442 39.130 0.00 0.00 0.00 2.74
1377 4671 5.788533 TGGTTTCTGTAGAAAAGGGGATCTA 59.211 40.000 8.51 0.00 44.58 1.98
1378 4672 6.273730 TGGTTTCTGTAGAAAAGGGGATCTAA 59.726 38.462 8.51 0.00 44.58 2.10
1411 4705 2.764128 TCCACCGGGAGATGGCTC 60.764 66.667 6.32 0.00 46.05 4.70
1471 5042 5.771469 CACTTATCAATGGTTTGTGCAAGA 58.229 37.500 0.00 0.00 34.32 3.02
1496 5072 8.585471 AATAAAAAGATGGATGAAGCTTCTCA 57.415 30.769 26.09 20.30 0.00 3.27
1605 5181 6.698766 GCAATATAAGAAAGGCATTCCAGTTG 59.301 38.462 0.00 0.33 38.94 3.16
1803 5379 0.765510 AAGGAAGGTTGACCGAAGCT 59.234 50.000 0.00 0.00 44.54 3.74
1860 5436 5.642919 AGTCAATCTTGATCTTGTCAGCTTC 59.357 40.000 0.00 0.00 39.73 3.86
1890 5466 3.334691 TGTGTATACAGCCTTGAAGCAC 58.665 45.455 5.62 0.00 34.23 4.40
2100 5676 9.989869 GTTTTAGTAAATAATCTCTGCAAGTCC 57.010 33.333 0.00 0.00 33.76 3.85
2267 5845 1.202582 TCGAGGCTCTCTTGCTAACAC 59.797 52.381 13.50 0.00 0.00 3.32
2275 5853 4.371786 CTCTCTTGCTAACACAGTGACAA 58.628 43.478 7.81 5.37 0.00 3.18
2322 5901 2.503895 AGGTTGGGCAGATTCAAGAG 57.496 50.000 0.00 0.00 0.00 2.85
2388 5971 7.308450 TCCTGATTGCATTAGCTATTCTACT 57.692 36.000 0.00 0.00 42.74 2.57
2487 6070 5.039920 TGAAGCCTGACATTGTAGCATAT 57.960 39.130 8.21 0.00 0.00 1.78
2612 6195 9.823647 CACATATAGAGCTCTTTTCTTAGGAAA 57.176 33.333 23.84 0.00 39.38 3.13
2652 6235 6.385843 CAAGCGAGATACTATACTGCTGAAT 58.614 40.000 0.00 0.00 0.00 2.57
2677 6260 3.818773 CTGATGTTTAGGGTCACCGTTTT 59.181 43.478 0.00 0.00 43.47 2.43
2682 6265 4.276431 TGTTTAGGGTCACCGTTTTCAATC 59.724 41.667 0.00 0.00 43.47 2.67
2685 6268 3.562182 AGGGTCACCGTTTTCAATCTTT 58.438 40.909 0.00 0.00 43.47 2.52
2699 6298 6.471976 TTCAATCTTTTCTGACTCACATCG 57.528 37.500 0.00 0.00 0.00 3.84
2704 6303 0.388520 TTCTGACTCACATCGCACCG 60.389 55.000 0.00 0.00 0.00 4.94
2916 6520 2.212110 CCCTGGGCAGCTGCTTTTT 61.212 57.895 35.82 0.00 41.70 1.94
2937 6541 1.813513 ATACTGTCAGCTGTTGGTGC 58.186 50.000 14.67 0.00 41.10 5.01
2959 6563 4.557496 GCTGTTTCTTCCATGACAGTTTCC 60.557 45.833 10.59 0.00 41.11 3.13
2985 6589 7.012421 CCTTTTGCATAGTATAAGGAGTTGTCC 59.988 40.741 4.06 0.00 44.33 4.02
3010 6614 9.038803 CCGGTTACTCCAAAATAGACTAATTAC 57.961 37.037 0.00 0.00 35.57 1.89
3025 6629 7.743104 AGACTAATTACGTGCTTCATTTCAAG 58.257 34.615 0.00 0.00 0.00 3.02
3033 6637 5.091431 CGTGCTTCATTTCAAGGATTCTTC 58.909 41.667 0.00 0.00 0.00 2.87
3055 6659 6.648879 TCTTTGCTGCCTTTAATTGTAACT 57.351 33.333 0.00 0.00 0.00 2.24
3080 6684 8.158169 TGGAATGAATGAAATAAGGAAGATCG 57.842 34.615 0.00 0.00 0.00 3.69
3125 6729 7.081976 GCAGTTTCCGTTCTTAACATGTAAAT 58.918 34.615 0.00 0.00 0.00 1.40
3177 6872 6.976934 AATTTGGGAAGAAAAGCAAGACTA 57.023 33.333 0.00 0.00 0.00 2.59
3228 6924 6.602410 TGATCAAGAAACATGGGCATTTAA 57.398 33.333 0.00 0.00 0.00 1.52
3245 6945 7.214381 GGCATTTAAACTTTTTAACAGAGGGT 58.786 34.615 0.00 0.00 0.00 4.34
3253 6953 4.919774 TTTTAACAGAGGGTGATGCCTA 57.080 40.909 0.00 0.00 37.43 3.93
3272 6972 4.884164 GCCTAAGGTTTTGAGCATATCAGT 59.116 41.667 0.00 0.00 39.68 3.41
3291 6991 7.578310 ATCAGTGAAATGGATGAATTAGTGG 57.422 36.000 0.00 0.00 0.00 4.00
3306 7006 1.513858 AGTGGTGGTTGGAGTGGTTA 58.486 50.000 0.00 0.00 0.00 2.85
3329 7029 2.290450 TGAATCTGAAGCATGCAGGACA 60.290 45.455 21.98 12.47 44.09 4.02
3343 7043 0.606401 AGGACACATGCCTTGTTCCG 60.606 55.000 0.00 0.00 39.00 4.30
3399 7100 6.499172 CCATGACATAGTATATGTAGCTCCG 58.501 44.000 2.53 0.00 31.52 4.63
3400 7101 6.318900 CCATGACATAGTATATGTAGCTCCGA 59.681 42.308 2.53 0.00 31.52 4.55
3420 7121 4.116238 CGACTCCTCAAAATCTAAGCTCC 58.884 47.826 0.00 0.00 0.00 4.70
3495 7196 9.801873 TTATCTGCCATTTTTATGCTTTAGTTC 57.198 29.630 0.00 0.00 0.00 3.01
3515 7216 7.807977 AGTTCAACTTTAACATCTGTGTGAT 57.192 32.000 0.00 0.00 38.92 3.06
3556 7257 3.286353 TGGACAGAAAACTGAACATGCA 58.714 40.909 0.00 0.00 0.00 3.96
3557 7258 3.890756 TGGACAGAAAACTGAACATGCAT 59.109 39.130 0.00 0.00 0.00 3.96
3558 7259 4.232221 GGACAGAAAACTGAACATGCATG 58.768 43.478 25.09 25.09 0.00 4.06
3559 7260 3.645884 ACAGAAAACTGAACATGCATGC 58.354 40.909 26.53 11.82 0.00 4.06
3574 7275 1.394917 GCATGCTCTGTAACAGGAACG 59.605 52.381 11.37 0.00 31.51 3.95
3617 7318 5.013704 TCTGTACACCATGACCAACCTAATT 59.986 40.000 0.00 0.00 0.00 1.40
3624 7325 6.153340 CACCATGACCAACCTAATTTCTGATT 59.847 38.462 0.00 0.00 0.00 2.57
3630 7331 5.243730 ACCAACCTAATTTCTGATTGTGTGG 59.756 40.000 0.00 0.00 0.00 4.17
3645 7346 3.230976 TGTGTGGTCATCTGTACAGACT 58.769 45.455 27.41 13.83 40.75 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 112 1.076632 GAGGAGGAGGAGCGAGGAA 60.077 63.158 0.00 0.00 0.00 3.36
327 340 1.324005 CGTGGGAGAGGGAGGAGAAC 61.324 65.000 0.00 0.00 0.00 3.01
597 617 1.330521 CGAATCCCAGCCGTGTAAATG 59.669 52.381 0.00 0.00 0.00 2.32
598 618 1.663695 CGAATCCCAGCCGTGTAAAT 58.336 50.000 0.00 0.00 0.00 1.40
720 740 3.342377 TGATTCCTGCACAATCCGTAA 57.658 42.857 10.01 0.00 30.30 3.18
1029 4303 3.921119 TTGCACAGGTTATCAAGCAAG 57.079 42.857 0.00 0.00 37.10 4.01
1183 4466 3.491342 TCTCCCTCATCCTATCGAACAG 58.509 50.000 0.00 0.00 0.00 3.16
1347 4636 5.011023 CCCTTTTCTACAGAAACCAGCAATT 59.989 40.000 3.91 0.00 43.01 2.32
1377 4671 0.251341 GGAGTTCCATGGCACTGGTT 60.251 55.000 22.45 0.00 37.57 3.67
1378 4672 1.380302 GGAGTTCCATGGCACTGGT 59.620 57.895 22.45 0.00 37.57 4.00
1411 4705 1.270550 GTTCCATGCAACACCCTTCTG 59.729 52.381 0.00 0.00 0.00 3.02
1471 5042 8.585471 TGAGAAGCTTCATCCATCTTTTTATT 57.415 30.769 27.57 1.23 0.00 1.40
1496 5072 9.013229 TGCTGTCAATCATCTTATTAAACAACT 57.987 29.630 0.00 0.00 0.00 3.16
1620 5196 1.685765 AGGTGTGAGGCCGCTATCA 60.686 57.895 8.34 0.00 0.00 2.15
1626 5202 0.606401 AATTGTCAGGTGTGAGGCCG 60.606 55.000 0.00 0.00 31.53 6.13
1860 5436 6.542005 TCAAGGCTGTATACACAATAATGGTG 59.458 38.462 0.08 0.00 41.95 4.17
2038 5614 1.999648 TTTGGAAAGCAGCCATCAGT 58.000 45.000 0.00 0.00 34.90 3.41
2100 5676 4.842091 GCGCTGCTCAAATGCCCG 62.842 66.667 0.00 0.00 0.00 6.13
2267 5845 7.539710 CCTTGATCAATGTGTTAATTGTCACTG 59.460 37.037 8.96 6.91 38.46 3.66
2275 5853 7.619302 ACATAACCCCTTGATCAATGTGTTAAT 59.381 33.333 17.69 9.90 0.00 1.40
2322 5901 7.625828 ACACTTACTAATAAGGTCAATTGCC 57.374 36.000 0.00 5.69 41.98 4.52
2388 5971 5.343307 TCTTGCAGAGCTCATGTATTACA 57.657 39.130 17.77 0.00 0.00 2.41
2487 6070 8.976353 ACATTGCACCACCTTATCAAAATATTA 58.024 29.630 0.00 0.00 0.00 0.98
2584 6167 7.069950 TCCTAAGAAAAGAGCTCTATATGTGCA 59.930 37.037 18.59 0.00 37.61 4.57
2612 6195 2.641305 GCTTGCTGGTCATCAGAGAAT 58.359 47.619 0.00 0.00 46.18 2.40
2652 6235 2.498481 CGGTGACCCTAAACATCAGGTA 59.502 50.000 0.00 0.00 31.10 3.08
2677 6260 4.389992 GCGATGTGAGTCAGAAAAGATTGA 59.610 41.667 0.00 0.00 0.00 2.57
2682 6265 2.158449 GGTGCGATGTGAGTCAGAAAAG 59.842 50.000 0.00 0.00 0.00 2.27
2685 6268 0.388520 CGGTGCGATGTGAGTCAGAA 60.389 55.000 0.00 0.00 0.00 3.02
2704 6303 1.835927 AACTGCTCAGGGCACTCCTC 61.836 60.000 0.00 0.00 46.12 3.71
2751 6350 6.255020 GCACCTGAAAGAAGAAATTGCATATG 59.745 38.462 0.00 0.00 34.07 1.78
2796 6395 5.197451 ACCAACAGTTAGGTTGTGATTTGA 58.803 37.500 5.45 0.00 45.16 2.69
2797 6396 5.299279 AGACCAACAGTTAGGTTGTGATTTG 59.701 40.000 8.34 0.00 45.16 2.32
2816 6415 3.646162 ACATGACAGGAAGTACAAGACCA 59.354 43.478 0.00 0.00 0.00 4.02
2855 6455 4.292186 ACTGATACAGCATTGTCAGGTT 57.708 40.909 13.53 0.00 38.76 3.50
2916 6520 3.007940 AGCACCAACAGCTGACAGTATAA 59.992 43.478 23.35 0.00 41.61 0.98
2926 6530 1.678101 GAAGAAACAGCACCAACAGCT 59.322 47.619 0.00 0.00 44.62 4.24
2937 6541 4.022849 GGGAAACTGTCATGGAAGAAACAG 60.023 45.833 8.09 8.09 43.69 3.16
2959 6563 7.012421 GGACAACTCCTTATACTATGCAAAAGG 59.988 40.741 0.00 0.00 38.44 3.11
2985 6589 8.749499 CGTAATTAGTCTATTTTGGAGTAACCG 58.251 37.037 0.00 0.00 42.61 4.44
3010 6614 4.691860 AGAATCCTTGAAATGAAGCACG 57.308 40.909 0.00 0.00 0.00 5.34
3025 6629 3.949842 AAAGGCAGCAAAGAAGAATCC 57.050 42.857 0.00 0.00 0.00 3.01
3033 6637 5.634859 CCAGTTACAATTAAAGGCAGCAAAG 59.365 40.000 0.00 0.00 0.00 2.77
3055 6659 7.992608 TCGATCTTCCTTATTTCATTCATTCCA 59.007 33.333 0.00 0.00 0.00 3.53
3080 6684 2.720891 GCAAACAGTACGCGTTAAGCTC 60.721 50.000 20.78 1.51 45.59 4.09
3199 6894 6.632909 TGCCCATGTTTCTTGATCAAAATAG 58.367 36.000 9.88 0.00 0.00 1.73
3206 6901 7.099120 AGTTTAAATGCCCATGTTTCTTGATC 58.901 34.615 0.00 0.00 0.00 2.92
3207 6902 7.008021 AGTTTAAATGCCCATGTTTCTTGAT 57.992 32.000 0.00 0.00 0.00 2.57
3210 6905 8.518430 AAAAAGTTTAAATGCCCATGTTTCTT 57.482 26.923 0.00 0.00 0.00 2.52
3213 6909 9.178758 TGTTAAAAAGTTTAAATGCCCATGTTT 57.821 25.926 0.00 0.00 0.00 2.83
3228 6924 4.280929 GGCATCACCCTCTGTTAAAAAGTT 59.719 41.667 0.00 0.00 0.00 2.66
3245 6945 3.153369 TGCTCAAAACCTTAGGCATCA 57.847 42.857 0.00 0.00 0.00 3.07
3253 6953 6.899393 TTTCACTGATATGCTCAAAACCTT 57.101 33.333 0.00 0.00 32.14 3.50
3272 6972 5.579047 ACCACCACTAATTCATCCATTTCA 58.421 37.500 0.00 0.00 0.00 2.69
3291 6991 5.010282 AGATTCATTAACCACTCCAACCAC 58.990 41.667 0.00 0.00 0.00 4.16
3306 7006 3.380637 GTCCTGCATGCTTCAGATTCATT 59.619 43.478 20.33 0.00 33.54 2.57
3329 7029 1.039856 AAAAGCGGAACAAGGCATGT 58.960 45.000 0.00 0.00 46.82 3.21
3343 7043 0.318955 ACCGCACAGCATGAAAAAGC 60.319 50.000 0.00 0.00 39.69 3.51
3399 7100 4.116238 CGGAGCTTAGATTTTGAGGAGTC 58.884 47.826 0.00 0.00 0.00 3.36
3400 7101 4.130286 CGGAGCTTAGATTTTGAGGAGT 57.870 45.455 0.00 0.00 0.00 3.85
3420 7121 0.675522 AAACCCTGGTTATGGTCGCG 60.676 55.000 0.00 0.00 37.35 5.87
3515 7216 5.584649 GTCCATTGCAGTTAACATACTAGCA 59.415 40.000 8.61 5.24 33.49 3.49
3556 7257 2.612972 CCACGTTCCTGTTACAGAGCAT 60.613 50.000 14.66 0.00 32.44 3.79
3557 7258 1.270094 CCACGTTCCTGTTACAGAGCA 60.270 52.381 14.66 0.00 32.44 4.26
3558 7259 1.270147 ACCACGTTCCTGTTACAGAGC 60.270 52.381 14.66 2.64 32.44 4.09
3559 7260 2.223971 ACACCACGTTCCTGTTACAGAG 60.224 50.000 14.66 4.29 32.44 3.35
3574 7275 2.029290 AGACCACGATTACAGACACCAC 60.029 50.000 0.00 0.00 0.00 4.16
3604 7305 6.016360 CACACAATCAGAAATTAGGTTGGTCA 60.016 38.462 0.00 0.00 0.00 4.02
3617 7318 4.356405 ACAGATGACCACACAATCAGAA 57.644 40.909 0.00 0.00 0.00 3.02
3624 7325 3.230976 AGTCTGTACAGATGACCACACA 58.769 45.455 27.54 0.00 39.97 3.72
3630 7331 4.792521 AAGTGGAGTCTGTACAGATGAC 57.207 45.455 27.54 19.57 39.97 3.06


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

AutoCloner maintained by Alex Coulton.