Multiple sequence alignment - TraesCS1D01G164300

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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 TraesCS1D01G164300 chr1D 100.000 3268 0 0 1 3268 235158515 235161782 0.000000e+00 6035
1 TraesCS1D01G164300 chr1B 92.394 2406 69 27 1 2365 340609579 340611911 0.000000e+00 3325
2 TraesCS1D01G164300 chr1A 94.253 1479 45 18 915 2365 312161373 312159907 0.000000e+00 2224
3 TraesCS1D01G164300 chr1A 91.343 901 30 5 1 859 312162265 312161371 0.000000e+00 1188
4 TraesCS1D01G164300 chr6B 88.704 903 92 6 2365 3263 212413273 212412377 0.000000e+00 1094
5 TraesCS1D01G164300 chr7D 89.304 589 59 4 2365 2951 62466815 62467401 0.000000e+00 736
6 TraesCS1D01G164300 chr7D 89.304 589 60 3 2365 2951 62539147 62539734 0.000000e+00 736
7 TraesCS1D01G164300 chr3D 81.326 905 151 16 2366 3262 351133084 351132190 0.000000e+00 719
8 TraesCS1D01G164300 chr5D 85.477 661 89 6 2366 3023 336649920 336649264 0.000000e+00 682
9 TraesCS1D01G164300 chr2D 73.773 591 140 15 2367 2948 50146372 50146956 5.490000e-53 219


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 TraesCS1D01G164300 chr1D 235158515 235161782 3267 False 6035 6035 100.000 1 3268 1 chr1D.!!$F1 3267
1 TraesCS1D01G164300 chr1B 340609579 340611911 2332 False 3325 3325 92.394 1 2365 1 chr1B.!!$F1 2364
2 TraesCS1D01G164300 chr1A 312159907 312162265 2358 True 1706 2224 92.798 1 2365 2 chr1A.!!$R1 2364
3 TraesCS1D01G164300 chr6B 212412377 212413273 896 True 1094 1094 88.704 2365 3263 1 chr6B.!!$R1 898
4 TraesCS1D01G164300 chr7D 62466815 62467401 586 False 736 736 89.304 2365 2951 1 chr7D.!!$F1 586
5 TraesCS1D01G164300 chr7D 62539147 62539734 587 False 736 736 89.304 2365 2951 1 chr7D.!!$F2 586
6 TraesCS1D01G164300 chr3D 351132190 351133084 894 True 719 719 81.326 2366 3262 1 chr3D.!!$R1 896
7 TraesCS1D01G164300 chr5D 336649264 336649920 656 True 682 682 85.477 2366 3023 1 chr5D.!!$R1 657
8 TraesCS1D01G164300 chr2D 50146372 50146956 584 False 219 219 73.773 2367 2948 1 chr2D.!!$F1 581

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
907 955 0.032615 TCTCCCCTCTCTCTTCCTGC 60.033 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2557 2642 1.153168 GCTCGCTCCTGGGCAAATA 60.153 57.895 7.72 0.0 0.0 1.4 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
73 74 5.993055 TCTTTGTTGATGGATGATGAGCTA 58.007 37.500 0.00 0.00 0.00 3.32
200 204 4.025145 CCGGACCATCTTTAAACTAATCGC 60.025 45.833 0.00 0.00 0.00 4.58
223 227 6.085555 CCAGTAGTTTAATGGCGATAGAGA 57.914 41.667 0.00 0.00 37.09 3.10
304 331 4.864334 CACCCTGATCCCCAGCGC 62.864 72.222 0.00 0.00 41.57 5.92
307 334 4.559063 CCTGATCCCCAGCGCCAG 62.559 72.222 2.29 1.58 41.57 4.85
601 649 5.241506 ACTTGTGTTTGTATGTCTGAATGGG 59.758 40.000 0.00 0.00 0.00 4.00
605 653 5.122396 GTGTTTGTATGTCTGAATGGGTCTC 59.878 44.000 0.00 0.00 0.00 3.36
865 913 1.061711 GTTGATCGATGTGCTGTGCTC 59.938 52.381 0.54 0.00 0.00 4.26
867 915 1.207390 GATCGATGTGCTGTGCTCTC 58.793 55.000 0.54 0.00 0.00 3.20
869 917 1.812922 CGATGTGCTGTGCTCTCCC 60.813 63.158 0.00 0.00 0.00 4.30
870 918 1.451028 GATGTGCTGTGCTCTCCCC 60.451 63.158 0.00 0.00 0.00 4.81
871 919 1.908340 GATGTGCTGTGCTCTCCCCT 61.908 60.000 0.00 0.00 0.00 4.79
872 920 1.908340 ATGTGCTGTGCTCTCCCCTC 61.908 60.000 0.00 0.00 0.00 4.30
873 921 2.121385 TGCTGTGCTCTCCCCTCT 59.879 61.111 0.00 0.00 0.00 3.69
874 922 1.986757 TGCTGTGCTCTCCCCTCTC 60.987 63.158 0.00 0.00 0.00 3.20
875 923 1.685421 GCTGTGCTCTCCCCTCTCT 60.685 63.158 0.00 0.00 0.00 3.10
876 924 1.675720 GCTGTGCTCTCCCCTCTCTC 61.676 65.000 0.00 0.00 0.00 3.20
877 925 0.033208 CTGTGCTCTCCCCTCTCTCT 60.033 60.000 0.00 0.00 0.00 3.10
878 926 0.411452 TGTGCTCTCCCCTCTCTCTT 59.589 55.000 0.00 0.00 0.00 2.85
879 927 1.203237 TGTGCTCTCCCCTCTCTCTTT 60.203 52.381 0.00 0.00 0.00 2.52
880 928 1.905894 GTGCTCTCCCCTCTCTCTTTT 59.094 52.381 0.00 0.00 0.00 2.27
881 929 2.304470 GTGCTCTCCCCTCTCTCTTTTT 59.696 50.000 0.00 0.00 0.00 1.94
904 952 3.217321 GGTCTCCCCTCTCTCTTCC 57.783 63.158 0.00 0.00 0.00 3.46
907 955 0.032615 TCTCCCCTCTCTCTTCCTGC 60.033 60.000 0.00 0.00 0.00 4.85
922 970 2.357396 TGCGGCCGCTGCATATAG 60.357 61.111 45.79 7.18 41.16 1.31
1254 1304 5.221441 GGTGCTAACCCTTTTCATGTTTCTT 60.221 40.000 0.00 0.00 41.04 2.52
1324 1374 1.104630 GAGGTACTGGGTCTTCCTCG 58.895 60.000 0.00 0.00 41.55 4.63
1347 1397 4.258543 TCCAAGTCGGAAATCAACCATAC 58.741 43.478 0.00 0.00 42.52 2.39
1350 1400 5.220854 CCAAGTCGGAAATCAACCATACATC 60.221 44.000 0.00 0.00 36.56 3.06
1355 1405 4.512944 CGGAAATCAACCATACATCTGAGG 59.487 45.833 0.00 0.00 0.00 3.86
1356 1406 4.276926 GGAAATCAACCATACATCTGAGGC 59.723 45.833 0.00 0.00 0.00 4.70
1357 1407 4.785346 AATCAACCATACATCTGAGGCT 57.215 40.909 0.00 0.00 0.00 4.58
1358 1408 3.827008 TCAACCATACATCTGAGGCTC 57.173 47.619 7.79 7.79 0.00 4.70
1360 1410 3.133542 TCAACCATACATCTGAGGCTCTG 59.866 47.826 16.72 15.59 0.00 3.35
1361 1411 3.037851 ACCATACATCTGAGGCTCTGA 57.962 47.619 23.74 23.74 0.00 3.27
1363 1413 2.288948 CCATACATCTGAGGCTCTGAGC 60.289 54.545 25.14 21.17 41.46 4.26
1364 1414 2.149973 TACATCTGAGGCTCTGAGCA 57.850 50.000 28.95 10.38 44.75 4.26
1365 1415 0.825410 ACATCTGAGGCTCTGAGCAG 59.175 55.000 28.95 18.50 44.75 4.24
1366 1416 0.825410 CATCTGAGGCTCTGAGCAGT 59.175 55.000 28.95 16.74 44.75 4.40
1367 1417 1.207570 CATCTGAGGCTCTGAGCAGTT 59.792 52.381 28.95 14.99 44.75 3.16
1368 1418 0.607112 TCTGAGGCTCTGAGCAGTTG 59.393 55.000 28.95 16.39 44.75 3.16
1369 1419 0.391395 CTGAGGCTCTGAGCAGTTGG 60.391 60.000 28.95 12.07 44.75 3.77
1370 1420 1.123861 TGAGGCTCTGAGCAGTTGGT 61.124 55.000 28.95 7.65 44.75 3.67
1371 1421 0.036022 GAGGCTCTGAGCAGTTGGTT 59.964 55.000 28.95 6.90 44.75 3.67
1372 1422 1.276421 GAGGCTCTGAGCAGTTGGTTA 59.724 52.381 28.95 0.00 44.75 2.85
1373 1423 1.699634 AGGCTCTGAGCAGTTGGTTAA 59.300 47.619 28.95 0.00 44.75 2.01
1374 1424 2.307098 AGGCTCTGAGCAGTTGGTTAAT 59.693 45.455 28.95 1.08 44.75 1.40
1375 1425 3.084786 GGCTCTGAGCAGTTGGTTAATT 58.915 45.455 28.95 0.00 44.75 1.40
1376 1426 4.019321 AGGCTCTGAGCAGTTGGTTAATTA 60.019 41.667 28.95 0.00 44.75 1.40
1649 1723 3.119101 TCGTGTCTCTCATTTAAGCCCTC 60.119 47.826 0.00 0.00 0.00 4.30
1650 1724 3.368427 CGTGTCTCTCATTTAAGCCCTCA 60.368 47.826 0.00 0.00 0.00 3.86
1651 1725 4.681781 CGTGTCTCTCATTTAAGCCCTCAT 60.682 45.833 0.00 0.00 0.00 2.90
1652 1726 5.189180 GTGTCTCTCATTTAAGCCCTCATT 58.811 41.667 0.00 0.00 0.00 2.57
1806 1880 2.882793 GCGACGCCATTAGTAGGAC 58.117 57.895 9.14 0.00 0.00 3.85
1807 1881 0.101759 GCGACGCCATTAGTAGGACA 59.898 55.000 9.14 0.00 0.00 4.02
1808 1882 1.836383 CGACGCCATTAGTAGGACAC 58.164 55.000 0.00 0.00 0.00 3.67
1830 1912 3.819564 AGCTATTACTGATTGGCACGA 57.180 42.857 0.00 0.00 0.00 4.35
1837 1919 1.002900 ACTGATTGGCACGAAACGTTG 60.003 47.619 0.00 0.00 38.32 4.10
2128 2210 2.118683 CTGTTTGACCGTTGCAATGTG 58.881 47.619 17.19 10.99 0.00 3.21
2161 2243 7.859377 CCATTGCATCACTTGTGTATTTATCTC 59.141 37.037 0.46 0.00 0.00 2.75
2166 2248 6.867519 TCACTTGTGTATTTATCTCTGGGA 57.132 37.500 0.46 0.00 0.00 4.37
2243 2325 4.938575 TTTGTGGGATACTTGGGTGTAT 57.061 40.909 0.00 0.00 36.01 2.29
2244 2326 6.390048 TTTTGTGGGATACTTGGGTGTATA 57.610 37.500 0.00 0.00 33.74 1.47
2337 2419 5.499139 TTAACCCGCATTCAGAATCATTC 57.501 39.130 0.00 0.00 0.00 2.67
2339 2421 3.209410 ACCCGCATTCAGAATCATTCTC 58.791 45.455 0.00 0.00 38.11 2.87
2416 2498 8.137437 CGTATCTTTGCATTGATAAAGGGAAAT 58.863 33.333 9.74 0.00 35.24 2.17
2492 2576 3.005261 TCAAGTGAGCAGACAGAGAAGAC 59.995 47.826 0.00 0.00 0.00 3.01
2501 2585 2.822561 AGACAGAGAAGACGATGCTCAA 59.177 45.455 0.00 0.00 0.00 3.02
2557 2642 1.415672 TTCAGTCCTTTGGCTCCGGT 61.416 55.000 0.00 0.00 0.00 5.28
2647 2732 3.377172 TCGAAGATGACTGAGTTGCGATA 59.623 43.478 0.00 0.00 0.00 2.92
2648 2733 4.105486 CGAAGATGACTGAGTTGCGATAA 58.895 43.478 0.00 0.00 0.00 1.75
2719 2804 3.852307 GCCGGCCGGTATGGTACA 61.852 66.667 42.53 0.00 41.21 2.90
2749 2834 1.349357 GGACAGCCAGAAGAAGAAGGT 59.651 52.381 0.00 0.00 0.00 3.50
2750 2835 2.614229 GGACAGCCAGAAGAAGAAGGTC 60.614 54.545 0.00 0.00 0.00 3.85
2790 2875 2.640989 CCGTCGTTCGACACCAGA 59.359 61.111 21.94 0.00 42.86 3.86
2872 2958 2.044650 GGGCTCCTGCATGCAGAA 60.045 61.111 42.21 27.62 46.30 3.02
2980 3068 0.317160 CACCGACAGAGTAGCACCAA 59.683 55.000 0.00 0.00 0.00 3.67
3033 3121 0.039618 TGGATCCCTCAAACAAGGCC 59.960 55.000 9.90 0.00 34.88 5.19
3035 3123 0.035439 GATCCCTCAAACAAGGCCGA 60.035 55.000 0.00 0.00 34.88 5.54
3054 3142 2.803133 CGAATAGCAGGATGAAGCCGAA 60.803 50.000 0.00 0.00 39.69 4.30
3120 3208 3.922893 GAGAGCGCGACATGCTGC 61.923 66.667 12.10 0.00 44.18 5.25
3125 3213 3.113979 CGCGACATGCTGCAGTCA 61.114 61.111 16.64 14.12 43.27 3.41
3129 3217 1.669115 GACATGCTGCAGTCACCGT 60.669 57.895 16.64 13.70 34.93 4.83
3158 3246 1.255667 ACATACTCAAGGACGGCGGT 61.256 55.000 13.24 0.00 0.00 5.68
3186 3274 1.143838 CGATCCTTGGATGTCCGCA 59.856 57.895 6.92 0.00 39.43 5.69
3196 3284 1.453155 GATGTCCGCAATCCAAGTGT 58.547 50.000 0.00 0.00 0.00 3.55
3225 3313 4.347453 GTCGTGGCCACCGTACGT 62.347 66.667 29.95 0.00 38.80 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 0.528470 GTGTAGTCTTCTCGCTGCCT 59.472 55.000 0.00 0.00 0.00 4.75
200 204 6.085555 TCTCTATCGCCATTAAACTACTGG 57.914 41.667 0.00 0.00 0.00 4.00
332 359 2.028476 CGGGAGATATGTTTATCCGGCA 60.028 50.000 0.00 0.00 35.74 5.69
519 567 0.755698 ACGGCCGATAGATGACACCT 60.756 55.000 35.90 0.00 39.76 4.00
601 649 1.228245 TGGCAGGCACTTTGGAGAC 60.228 57.895 0.00 0.00 34.60 3.36
605 653 3.688159 GGCTGGCAGGCACTTTGG 61.688 66.667 33.28 0.00 40.97 3.28
651 699 1.615107 GCCGGATATCGTACGCTTGC 61.615 60.000 11.24 1.93 37.11 4.01
887 935 1.775385 CAGGAAGAGAGAGGGGAGAC 58.225 60.000 0.00 0.00 0.00 3.36
907 955 0.243907 AGTACTATATGCAGCGGCCG 59.756 55.000 24.05 24.05 40.13 6.13
915 963 3.184581 GCCAACGCAAGAGTACTATATGC 59.815 47.826 14.05 14.05 43.62 3.14
922 970 3.064931 ACTAAAGCCAACGCAAGAGTAC 58.935 45.455 0.00 0.00 43.62 2.73
1209 1258 3.329386 CACTGACCTGACCATGTAGTTG 58.671 50.000 0.00 0.00 0.00 3.16
1254 1304 0.173481 CTCGGCGTCATCTGAAGGAA 59.827 55.000 6.85 0.00 0.00 3.36
1347 1397 0.825410 ACTGCTCAGAGCCTCAGATG 59.175 55.000 20.16 4.04 41.51 2.90
1350 1400 0.391395 CCAACTGCTCAGAGCCTCAG 60.391 60.000 20.16 12.85 41.51 3.35
1355 1405 5.880054 TTAATTAACCAACTGCTCAGAGC 57.120 39.130 16.21 16.21 42.82 4.09
1799 1873 7.268586 CAATCAGTAATAGCTTGTGTCCTACT 58.731 38.462 0.00 0.00 0.00 2.57
1800 1874 6.480320 CCAATCAGTAATAGCTTGTGTCCTAC 59.520 42.308 0.00 0.00 0.00 3.18
1801 1875 6.582636 CCAATCAGTAATAGCTTGTGTCCTA 58.417 40.000 0.00 0.00 0.00 2.94
1802 1876 5.431765 CCAATCAGTAATAGCTTGTGTCCT 58.568 41.667 0.00 0.00 0.00 3.85
1803 1877 4.035675 GCCAATCAGTAATAGCTTGTGTCC 59.964 45.833 0.00 0.00 0.00 4.02
1804 1878 4.635765 TGCCAATCAGTAATAGCTTGTGTC 59.364 41.667 0.00 0.00 0.00 3.67
1805 1879 4.396166 GTGCCAATCAGTAATAGCTTGTGT 59.604 41.667 0.00 0.00 0.00 3.72
1806 1880 4.494690 CGTGCCAATCAGTAATAGCTTGTG 60.495 45.833 0.00 0.00 0.00 3.33
1807 1881 3.623060 CGTGCCAATCAGTAATAGCTTGT 59.377 43.478 0.00 0.00 0.00 3.16
1808 1882 3.871006 TCGTGCCAATCAGTAATAGCTTG 59.129 43.478 0.00 0.00 0.00 4.01
1830 1912 1.997256 TAGGTGCCCCCACAACGTTT 61.997 55.000 0.00 0.00 43.88 3.60
1837 1919 1.619807 ATGTACGTAGGTGCCCCCAC 61.620 60.000 0.00 0.00 41.32 4.61
2052 2134 2.184579 GCCGCGGCTATCTATCCC 59.815 66.667 41.71 9.84 38.26 3.85
2078 2160 2.828520 TGAAGATGAAGCGAAGAGGACT 59.171 45.455 0.00 0.00 0.00 3.85
2161 2243 6.051717 CCATACAAACTAAGATCACTCCCAG 58.948 44.000 0.00 0.00 0.00 4.45
2166 2248 9.988815 GATGATACCATACAAACTAAGATCACT 57.011 33.333 0.00 0.00 32.09 3.41
2337 2419 3.226346 TCGAATCCCTTAACACACGAG 57.774 47.619 0.00 0.00 0.00 4.18
2339 2421 4.735662 TTTTCGAATCCCTTAACACACG 57.264 40.909 0.00 0.00 0.00 4.49
2416 2498 3.194755 ACGTGGCATGACTCTGTATGTTA 59.805 43.478 14.82 0.00 0.00 2.41
2501 2585 1.623811 ACCTGACATTGTAAGCGAGGT 59.376 47.619 0.00 0.00 0.00 3.85
2557 2642 1.153168 GCTCGCTCCTGGGCAAATA 60.153 57.895 7.72 0.00 0.00 1.40
2647 2732 1.665442 GCCTGGACAATTTGGCGTT 59.335 52.632 0.00 0.00 35.79 4.84
2648 2733 2.275380 GGCCTGGACAATTTGGCGT 61.275 57.895 0.00 0.00 45.75 5.68
2705 2790 1.746517 CCTCTGTACCATACCGGCC 59.253 63.158 0.00 0.00 39.03 6.13
2739 2824 1.971357 TGGCTCTTCGACCTTCTTCTT 59.029 47.619 0.00 0.00 0.00 2.52
2740 2825 1.633774 TGGCTCTTCGACCTTCTTCT 58.366 50.000 0.00 0.00 0.00 2.85
2763 2848 1.885850 GAACGACGGCACAACCACT 60.886 57.895 0.00 0.00 39.03 4.00
2980 3068 1.300697 GGCGTCTCGTGTGGAAGTT 60.301 57.895 0.00 0.00 0.00 2.66
3033 3121 1.143305 CGGCTTCATCCTGCTATTCG 58.857 55.000 0.00 0.00 0.00 3.34
3035 3123 3.498774 ATTCGGCTTCATCCTGCTATT 57.501 42.857 0.00 0.00 0.00 1.73
3077 3165 0.308993 GCCAGACGCTATTCATTGGC 59.691 55.000 0.00 0.00 43.54 4.52
3120 3208 0.603065 TGGACATCTGACGGTGACTG 59.397 55.000 0.00 0.00 0.00 3.51
3123 3211 1.266178 ATGTGGACATCTGACGGTGA 58.734 50.000 0.00 0.00 28.78 4.02
3125 3213 2.427453 GAGTATGTGGACATCTGACGGT 59.573 50.000 0.00 0.00 37.76 4.83
3129 3217 4.160439 GTCCTTGAGTATGTGGACATCTGA 59.840 45.833 6.18 0.00 45.87 3.27
3158 3246 3.399181 AAGGATCGCTTGGGCCGA 61.399 61.111 0.00 0.00 34.44 5.54
3196 3284 1.816863 GCCACGACTCTCCTGAACCA 61.817 60.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.