Multiple sequence alignment - TraesCS3B01G176200

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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 TraesCS3B01G176200 chr3B 100.000 3056 0 0 1 3056 178926738 178929793 0.000000e+00 5644
1 TraesCS3B01G176200 chr3D 91.850 3092 145 62 3 3056 124864660 124867682 0.000000e+00 4215
2 TraesCS3B01G176200 chr3A 92.877 2822 124 34 1 2785 132580431 132583212 0.000000e+00 4026
3 TraesCS3B01G176200 chr3A 83.333 294 23 11 2782 3056 132583247 132583533 6.540000e-62 248


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 TraesCS3B01G176200 chr3B 178926738 178929793 3055 False 5644 5644 100.000 1 3056 1 chr3B.!!$F1 3055
1 TraesCS3B01G176200 chr3D 124864660 124867682 3022 False 4215 4215 91.850 3 3056 1 chr3D.!!$F1 3053
2 TraesCS3B01G176200 chr3A 132580431 132583533 3102 False 2137 4026 88.105 1 3056 2 chr3A.!!$F1 3055

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
543 561 0.033504 GTGACACGAAAGGCAGGAGA 59.966 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 2246 0.107165 CCCTCTTCCGGGGATTGTTC 60.107 60.0 0.0 0.0 46.5 3.18 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
30 31 8.166726 ACATCACCCTTTTTCTAAGAATTCTCT 58.833 33.333 8.78 2.11 0.00 3.10
31 32 8.672815 CATCACCCTTTTTCTAAGAATTCTCTC 58.327 37.037 8.78 0.00 0.00 3.20
91 102 0.894141 GTAAACATGGTGGGCATGCA 59.106 50.000 21.36 0.00 33.61 3.96
126 137 6.610075 ATGATTTGAGCACAATTAAACCCT 57.390 33.333 0.00 0.00 35.85 4.34
209 221 4.662961 TGGCCGCGTGACAGAGTG 62.663 66.667 4.92 0.00 0.00 3.51
493 505 0.895559 AAAAAGCGGCAGAAGGGAGG 60.896 55.000 1.45 0.00 0.00 4.30
494 506 2.771328 AAAAGCGGCAGAAGGGAGGG 62.771 60.000 1.45 0.00 0.00 4.30
543 561 0.033504 GTGACACGAAAGGCAGGAGA 59.966 55.000 0.00 0.00 0.00 3.71
545 563 0.603569 GACACGAAAGGCAGGAGAGA 59.396 55.000 0.00 0.00 0.00 3.10
658 677 2.515979 TGTTCCGAGCCAGGAGCAA 61.516 57.895 11.26 0.00 46.21 3.91
740 759 3.747852 ACTCCATTCCCCATTCCTTCTA 58.252 45.455 0.00 0.00 0.00 2.10
754 779 1.132500 CTTCTACATCACCCTCCCCC 58.868 60.000 0.00 0.00 0.00 5.40
791 816 0.908198 ATCTCAACAGCACCTCCCTC 59.092 55.000 0.00 0.00 0.00 4.30
803 828 2.123251 TCCCTCATCGCCTCCTCC 60.123 66.667 0.00 0.00 0.00 4.30
848 877 1.378762 CTTTTCGCCTTCCCCTCCA 59.621 57.895 0.00 0.00 0.00 3.86
850 879 2.420466 TTTTCGCCTTCCCCTCCACC 62.420 60.000 0.00 0.00 0.00 4.61
912 942 1.657556 GCCTGCCTTGCGTTTTACA 59.342 52.632 0.00 0.00 0.00 2.41
985 1015 3.244112 CGAGTGGAGTTTTAGGGTGAGTT 60.244 47.826 0.00 0.00 0.00 3.01
1017 1047 1.614711 GATGTGGCCCATGGAGGAA 59.385 57.895 15.22 0.00 41.22 3.36
1062 1092 2.126424 GAGCACGTCGAGGTGACC 60.126 66.667 35.27 23.05 45.23 4.02
1100 1130 4.448976 GGCCAAGGGGAAGGAGGC 62.449 72.222 0.00 0.00 44.48 4.70
1146 1176 1.296715 GGTGAGGGTGTTCTGCGAT 59.703 57.895 0.00 0.00 0.00 4.58
1149 1179 0.904649 TGAGGGTGTTCTGCGATGAT 59.095 50.000 0.00 0.00 0.00 2.45
1170 1200 2.582498 GACGCCACCGATTCCTCG 60.582 66.667 0.00 0.00 44.62 4.63
1710 1740 0.907230 GCTCCTTCCCTCAGTCCACT 60.907 60.000 0.00 0.00 0.00 4.00
1715 1745 1.194781 TTCCCTCAGTCCACTCTGGC 61.195 60.000 0.00 0.00 37.47 4.85
1768 1798 2.197605 TCGTCGTCTTCCAGCACCA 61.198 57.895 0.00 0.00 0.00 4.17
2004 2034 2.357517 CAGCAGGCGGACGAGTTT 60.358 61.111 0.00 0.00 0.00 2.66
2057 2087 2.565645 CCCTCCCCGTCATCTAGCG 61.566 68.421 0.00 0.00 0.00 4.26
2058 2088 1.528542 CCTCCCCGTCATCTAGCGA 60.529 63.158 0.00 0.00 0.00 4.93
2069 2099 4.619760 CGTCATCTAGCGAAACAACTGTAA 59.380 41.667 0.00 0.00 0.00 2.41
2070 2100 5.118050 CGTCATCTAGCGAAACAACTGTAAA 59.882 40.000 0.00 0.00 0.00 2.01
2071 2101 6.346279 CGTCATCTAGCGAAACAACTGTAAAA 60.346 38.462 0.00 0.00 0.00 1.52
2072 2102 6.790825 GTCATCTAGCGAAACAACTGTAAAAC 59.209 38.462 0.00 0.00 0.00 2.43
2122 2152 6.291849 CGGTCAAATTTTGTTTGCATTCGTTA 60.292 34.615 8.89 0.00 0.00 3.18
2123 2153 7.568497 CGGTCAAATTTTGTTTGCATTCGTTAT 60.568 33.333 8.89 0.00 0.00 1.89
2124 2154 8.067189 GGTCAAATTTTGTTTGCATTCGTTATT 58.933 29.630 8.89 0.00 0.00 1.40
2125 2155 9.432077 GTCAAATTTTGTTTGCATTCGTTATTT 57.568 25.926 8.89 0.00 0.00 1.40
2126 2156 9.994432 TCAAATTTTGTTTGCATTCGTTATTTT 57.006 22.222 8.89 0.00 0.00 1.82
2164 2200 9.757227 TTTCTTTTTGTCTTTCTAGAGAGAGAG 57.243 33.333 13.05 7.08 36.18 3.20
2183 2219 8.103305 AGAGAGAGGAGAGAGTATGATGTTATC 58.897 40.741 0.00 0.00 0.00 1.75
2184 2220 6.878923 AGAGAGGAGAGAGTATGATGTTATCG 59.121 42.308 0.00 0.00 0.00 2.92
2424 2465 3.045601 TGAAAAGGCGAAGAGGAGAAG 57.954 47.619 0.00 0.00 0.00 2.85
2425 2466 2.632996 TGAAAAGGCGAAGAGGAGAAGA 59.367 45.455 0.00 0.00 0.00 2.87
2426 2467 3.258228 GAAAAGGCGAAGAGGAGAAGAG 58.742 50.000 0.00 0.00 0.00 2.85
2431 2472 1.001815 GCGAAGAGGAGAAGAGGATCG 60.002 57.143 0.00 0.00 42.67 3.69
2526 2569 1.573829 GGCTGGCAATGAAACGACGA 61.574 55.000 0.00 0.00 0.00 4.20
2561 2604 3.864686 CCGGCGATGTTTGGAGCG 61.865 66.667 9.30 0.00 0.00 5.03
2694 2747 6.878389 CACCCCAACATTAACTGCATTATTTT 59.122 34.615 0.00 0.00 0.00 1.82
2712 2765 1.523154 TTCGGAAATTTGCTGGCGCT 61.523 50.000 7.64 0.00 36.97 5.92
2795 2855 5.006746 GGATTTGCTGGTACGAGATTAGTTG 59.993 44.000 9.33 0.00 0.00 3.16
2796 2856 3.520290 TGCTGGTACGAGATTAGTTGG 57.480 47.619 9.33 0.00 0.00 3.77
2797 2857 2.202566 GCTGGTACGAGATTAGTTGGC 58.797 52.381 9.33 0.00 0.00 4.52
2825 2926 2.093447 CCGAGTCTTGGGCTGTAAGAAT 60.093 50.000 0.00 0.00 36.06 2.40
2923 3025 1.374947 CTGACAAAAGGGAGCGGGA 59.625 57.895 0.00 0.00 0.00 5.14
2936 3038 2.093128 GGAGCGGGAGATTAGGAAAACA 60.093 50.000 0.00 0.00 0.00 2.83
2947 3062 4.584327 TTAGGAAAACAAAAGCTGGCTC 57.416 40.909 0.00 0.00 0.00 4.70
2948 3063 1.338020 AGGAAAACAAAAGCTGGCTCG 59.662 47.619 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.513906 AAGAAGAGAGAATTCTTAGAAAAAGGG 57.486 33.333 9.87 0.00 43.44 3.95
45 46 5.315109 GGGGGTAAATTGGGGAGTATCTTAT 59.685 44.000 0.00 0.00 33.73 1.73
55 56 1.310877 TACCTGGGGGTAAATTGGGG 58.689 55.000 0.00 0.00 45.32 4.96
91 102 1.281867 TCAAATCATTCCTGGCGACCT 59.718 47.619 0.00 0.00 0.00 3.85
209 221 3.645212 GTCAGGGTAGTAAAGGGTATCCC 59.355 52.174 0.00 0.00 45.90 3.85
426 438 5.563842 GCGAATCTGAATCGATTTTTCACT 58.436 37.500 18.52 0.00 42.76 3.41
511 523 1.774217 TGTCACCTTTCCTGCCCCT 60.774 57.895 0.00 0.00 0.00 4.79
543 561 7.233553 CCCCTGTTTTCTTCCTTTTCTATTTCT 59.766 37.037 0.00 0.00 0.00 2.52
545 563 6.270000 CCCCCTGTTTTCTTCCTTTTCTATTT 59.730 38.462 0.00 0.00 0.00 1.40
658 677 2.830285 GCGGCGTCCTGTTGTTTGT 61.830 57.895 9.37 0.00 0.00 2.83
706 725 2.817396 GGAGTTGCTGCTCTCGCC 60.817 66.667 15.05 7.48 35.89 5.54
754 779 2.438795 TTTTTGGGGGCGGAGAGG 59.561 61.111 0.00 0.00 0.00 3.69
791 816 3.237741 GGAGGGGAGGAGGCGATG 61.238 72.222 0.00 0.00 0.00 3.84
904 934 3.689649 CCCTCAAGAATCCCTGTAAAACG 59.310 47.826 0.00 0.00 0.00 3.60
912 942 3.269643 CCTAAAACCCCTCAAGAATCCCT 59.730 47.826 0.00 0.00 0.00 4.20
985 1015 2.556622 GCCACATCGAGGAAAGGAAAAA 59.443 45.455 3.06 0.00 0.00 1.94
1017 1047 2.270352 TCACCGCCATGAAAAACTCT 57.730 45.000 0.00 0.00 0.00 3.24
1088 1118 2.757077 CAAACGCCTCCTTCCCCT 59.243 61.111 0.00 0.00 0.00 4.79
1093 1123 2.597510 GCCACCAAACGCCTCCTT 60.598 61.111 0.00 0.00 0.00 3.36
1100 1130 4.072088 GCTCGACGCCACCAAACG 62.072 66.667 0.00 0.00 0.00 3.60
1146 1176 0.390603 AATCGGTGGCGTCGAAATCA 60.391 50.000 0.00 0.00 40.15 2.57
1149 1179 1.738830 GGAATCGGTGGCGTCGAAA 60.739 57.895 0.00 0.00 40.15 3.46
1170 1200 2.866726 GCCCTCCTCCTCATCGCTC 61.867 68.421 0.00 0.00 0.00 5.03
1326 1356 1.681486 CCTCGGCCTTCCTCTTCCTC 61.681 65.000 0.00 0.00 0.00 3.71
1383 1413 1.606885 CGGCGTACTTACCCCAAGGA 61.607 60.000 0.00 0.00 38.70 3.36
1386 1416 2.265424 GCGGCGTACTTACCCCAA 59.735 61.111 9.37 0.00 0.00 4.12
1443 1473 2.485795 GGCGGTGTCAAAAGTGCCA 61.486 57.895 0.00 0.00 42.03 4.92
1449 1479 1.301401 CTCCTCGGCGGTGTCAAAA 60.301 57.895 7.21 0.00 0.00 2.44
1671 1701 1.305046 GAGGACAGAGGTCGGGGAA 60.305 63.158 0.00 0.00 45.28 3.97
1680 1710 1.671901 GGAAGGAGCGGAGGACAGAG 61.672 65.000 0.00 0.00 0.00 3.35
1683 1713 2.683933 GGGAAGGAGCGGAGGACA 60.684 66.667 0.00 0.00 0.00 4.02
1725 1755 3.966026 CTTGGAGGCGTCGTCGTCC 62.966 68.421 16.44 16.44 43.20 4.79
1735 1765 2.815647 CGACGGCTTCTTGGAGGC 60.816 66.667 0.00 0.00 38.73 4.70
1924 1954 4.606071 GCAGTCGCTGGAGAATGT 57.394 55.556 8.57 0.00 38.35 2.71
1946 1976 2.918802 ACGGGTTGTAGGCCGACA 60.919 61.111 15.44 15.44 0.00 4.35
2004 2034 5.068234 ACAAGTCGGTGATATCTTCGAAA 57.932 39.130 17.73 0.00 33.33 3.46
2010 2040 6.036083 CGATTTGAAACAAGTCGGTGATATCT 59.964 38.462 17.13 0.00 0.00 1.98
2013 2043 5.231702 TCGATTTGAAACAAGTCGGTGATA 58.768 37.500 21.82 6.60 33.46 2.15
2057 2087 5.857517 TCGGTGTTTGTTTTACAGTTGTTTC 59.142 36.000 0.00 0.00 0.00 2.78
2058 2088 5.770417 TCGGTGTTTGTTTTACAGTTGTTT 58.230 33.333 0.00 0.00 0.00 2.83
2069 2099 2.606065 GCGCCTAATTCGGTGTTTGTTT 60.606 45.455 10.89 0.00 36.91 2.83
2070 2100 1.068816 GCGCCTAATTCGGTGTTTGTT 60.069 47.619 10.89 0.00 36.91 2.83
2071 2101 0.519961 GCGCCTAATTCGGTGTTTGT 59.480 50.000 10.89 0.00 36.91 2.83
2072 2102 0.179174 GGCGCCTAATTCGGTGTTTG 60.179 55.000 22.15 0.00 36.91 2.93
2147 2177 6.127026 ACTCTCTCCTCTCTCTCTAGAAAGAC 60.127 46.154 0.00 0.00 0.00 3.01
2164 2200 6.081049 CGAACGATAACATCATACTCTCTCC 58.919 44.000 0.00 0.00 0.00 3.71
2183 2219 2.730672 GCAGCTACACAGGCGAACG 61.731 63.158 0.00 0.00 34.52 3.95
2184 2220 2.391389 GGCAGCTACACAGGCGAAC 61.391 63.158 0.00 0.00 34.52 3.95
2210 2246 0.107165 CCCTCTTCCGGGGATTGTTC 60.107 60.000 0.00 0.00 46.50 3.18
2402 2441 3.703001 TCTCCTCTTCGCCTTTTCATT 57.297 42.857 0.00 0.00 0.00 2.57
2404 2443 2.632996 TCTTCTCCTCTTCGCCTTTTCA 59.367 45.455 0.00 0.00 0.00 2.69
2405 2444 3.258228 CTCTTCTCCTCTTCGCCTTTTC 58.742 50.000 0.00 0.00 0.00 2.29
2424 2465 4.081917 ACTCTTCTGTCTTTTCCGATCCTC 60.082 45.833 0.00 0.00 0.00 3.71
2425 2466 3.835395 ACTCTTCTGTCTTTTCCGATCCT 59.165 43.478 0.00 0.00 0.00 3.24
2426 2467 3.929610 CACTCTTCTGTCTTTTCCGATCC 59.070 47.826 0.00 0.00 0.00 3.36
2431 2472 8.035394 TGATACATACACTCTTCTGTCTTTTCC 58.965 37.037 0.00 0.00 0.00 3.13
2467 2508 0.238289 CGGTCCAACGTACGTACTGT 59.762 55.000 23.12 18.14 0.00 3.55
2468 2509 0.238289 ACGGTCCAACGTACGTACTG 59.762 55.000 23.12 22.07 46.58 2.74
2469 2510 1.803334 TACGGTCCAACGTACGTACT 58.197 50.000 23.12 3.61 46.58 2.73
2503 2546 2.283101 TTTCATTGCCAGCCCGCT 60.283 55.556 0.00 0.00 0.00 5.52
2506 2549 1.212751 GTCGTTTCATTGCCAGCCC 59.787 57.895 0.00 0.00 0.00 5.19
2507 2550 1.154225 CGTCGTTTCATTGCCAGCC 60.154 57.895 0.00 0.00 0.00 4.85
2508 2551 0.179215 CTCGTCGTTTCATTGCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
2509 2552 0.179215 GCTCGTCGTTTCATTGCCAG 60.179 55.000 0.00 0.00 0.00 4.85
2510 2553 1.573829 GGCTCGTCGTTTCATTGCCA 61.574 55.000 0.00 0.00 38.79 4.92
2511 2554 1.134694 GGCTCGTCGTTTCATTGCC 59.865 57.895 0.00 0.00 0.00 4.52
2512 2555 1.134694 GGGCTCGTCGTTTCATTGC 59.865 57.895 0.00 0.00 0.00 3.56
2513 2556 1.419922 CGGGCTCGTCGTTTCATTG 59.580 57.895 0.00 0.00 0.00 2.82
2694 2747 2.566010 GCGCCAGCAAATTTCCGA 59.434 55.556 0.00 0.00 44.35 4.55
2727 2780 2.489938 AGGCAAGGTAAATCTCGCAA 57.510 45.000 0.00 0.00 0.00 4.85
2759 2812 7.148820 CGTACCAGCAAATCCAACTTAATTTTG 60.149 37.037 0.00 0.00 0.00 2.44
2795 2855 0.875059 CCAAGACTCGGAAAGTTGCC 59.125 55.000 0.00 0.00 38.74 4.52
2796 2856 0.875059 CCCAAGACTCGGAAAGTTGC 59.125 55.000 0.00 0.00 38.74 4.17
2797 2857 0.875059 GCCCAAGACTCGGAAAGTTG 59.125 55.000 0.00 0.00 38.74 3.16
2923 3025 4.835056 AGCCAGCTTTTGTTTTCCTAATCT 59.165 37.500 0.00 0.00 0.00 2.40
2936 3038 3.146828 AACCCCCGAGCCAGCTTTT 62.147 57.895 0.00 0.00 0.00 2.27
2947 3062 0.039888 CGCAAGTTTAACAACCCCCG 60.040 55.000 0.00 0.00 32.70 5.73
2948 3063 0.319211 GCGCAAGTTTAACAACCCCC 60.319 55.000 0.30 0.00 41.68 5.40
3033 3148 3.699894 CCCACCAGTCGCTCTGCT 61.700 66.667 2.64 0.00 42.38 4.24


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

AutoCloner maintained by Alex Coulton.