Multiple sequence alignment - TraesCS5A01G283100

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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 TraesCS5A01G283100 chr5A 100.000 3264 0 0 1 3264 491521209 491524472 0.000000e+00 6028
1 TraesCS5A01G283100 chr5A 88.734 2441 212 27 282 2706 491368292 491370685 0.000000e+00 2926
2 TraesCS5A01G283100 chr5A 89.025 1713 146 18 904 2615 491319265 491317594 0.000000e+00 2084
3 TraesCS5A01G283100 chr6D 93.808 2794 132 19 1 2794 106891043 106893795 0.000000e+00 4163
4 TraesCS5A01G283100 chr6D 91.351 370 28 2 2896 3264 106893926 106894292 1.350000e-138 503
5 TraesCS5A01G283100 chr6A 91.774 2796 182 21 1 2794 130404811 130407560 0.000000e+00 3845
6 TraesCS5A01G283100 chr6A 90.909 99 6 2 2791 2886 130407607 130407705 2.640000e-26 130
7 TraesCS5A01G283100 chr5D 91.791 2546 170 22 175 2720 388588319 388590825 0.000000e+00 3507
8 TraesCS5A01G283100 chr5D 90.429 2424 189 21 294 2706 388330725 388333116 0.000000e+00 3151
9 TraesCS5A01G283100 chr5D 90.789 1357 101 13 904 2260 388423605 388422273 0.000000e+00 1792
10 TraesCS5A01G283100 chr5D 89.796 294 30 0 2 295 388330271 388330564 8.550000e-101 377
11 TraesCS5A01G283100 chr5D 88.542 192 13 3 1 183 388539166 388539357 1.180000e-54 224
12 TraesCS5A01G283100 chr5B 89.807 1609 138 15 2 1589 466972638 466974241 0.000000e+00 2039
13 TraesCS5A01G283100 chr5B 88.527 1168 107 13 1487 2642 466974234 466975386 0.000000e+00 1389
14 TraesCS5A01G283100 chr5B 87.302 189 21 2 203 388 476018416 476018228 2.550000e-51 213
15 TraesCS5A01G283100 chr1B 86.772 189 22 2 203 388 297293575 297293763 1.190000e-49 207


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 TraesCS5A01G283100 chr5A 491521209 491524472 3263 False 6028.0 6028 100.0000 1 3264 1 chr5A.!!$F2 3263
1 TraesCS5A01G283100 chr5A 491368292 491370685 2393 False 2926.0 2926 88.7340 282 2706 1 chr5A.!!$F1 2424
2 TraesCS5A01G283100 chr5A 491317594 491319265 1671 True 2084.0 2084 89.0250 904 2615 1 chr5A.!!$R1 1711
3 TraesCS5A01G283100 chr6D 106891043 106894292 3249 False 2333.0 4163 92.5795 1 3264 2 chr6D.!!$F1 3263
4 TraesCS5A01G283100 chr6A 130404811 130407705 2894 False 1987.5 3845 91.3415 1 2886 2 chr6A.!!$F1 2885
5 TraesCS5A01G283100 chr5D 388588319 388590825 2506 False 3507.0 3507 91.7910 175 2720 1 chr5D.!!$F2 2545
6 TraesCS5A01G283100 chr5D 388422273 388423605 1332 True 1792.0 1792 90.7890 904 2260 1 chr5D.!!$R1 1356
7 TraesCS5A01G283100 chr5D 388330271 388333116 2845 False 1764.0 3151 90.1125 2 2706 2 chr5D.!!$F3 2704
8 TraesCS5A01G283100 chr5B 466972638 466975386 2748 False 1714.0 2039 89.1670 2 2642 2 chr5B.!!$F1 2640

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
155 165 0.534877 AACGCATGTGACAAGGCTGA 60.535 50.0 14.43 0.0 0.00 4.26 F
1038 1273 0.250727 GAAAGCTGGTGCAGGTGGTA 60.251 55.0 0.00 0.0 41.59 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 1551 0.099436 GATCATGTTGCCGCACTTCC 59.901 55.0 0.0 0.0 0.00 3.46 R
2758 3131 0.468226 TTCTCGGTTGAGTGGCAAGT 59.532 50.0 0.0 0.0 43.09 3.16 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
63 64 7.154656 GCTTGAAAGAAGGATTGTGGTAAAAT 58.845 34.615 0.00 0.00 0.00 1.82
97 107 9.936329 ATTTAAAGGAAAGATTATGGGCTTAGA 57.064 29.630 0.00 0.00 0.00 2.10
98 108 9.936329 TTTAAAGGAAAGATTATGGGCTTAGAT 57.064 29.630 0.00 0.00 0.00 1.98
100 110 8.926092 AAAGGAAAGATTATGGGCTTAGATAC 57.074 34.615 0.00 0.00 0.00 2.24
101 111 6.702329 AGGAAAGATTATGGGCTTAGATACG 58.298 40.000 0.00 0.00 0.00 3.06
102 112 5.875359 GGAAAGATTATGGGCTTAGATACGG 59.125 44.000 0.00 0.00 0.00 4.02
103 113 6.295688 GGAAAGATTATGGGCTTAGATACGGA 60.296 42.308 0.00 0.00 0.00 4.69
104 114 6.875972 AAGATTATGGGCTTAGATACGGAT 57.124 37.500 0.00 0.00 0.00 4.18
105 115 6.227298 AGATTATGGGCTTAGATACGGATG 57.773 41.667 0.00 0.00 0.00 3.51
109 119 1.344763 GGGCTTAGATACGGATGCAGT 59.655 52.381 0.00 0.00 0.00 4.40
155 165 0.534877 AACGCATGTGACAAGGCTGA 60.535 50.000 14.43 0.00 0.00 4.26
173 183 5.536538 AGGCTGATCGTAATGAGAGTATCAA 59.463 40.000 0.00 0.00 42.53 2.57
189 199 8.001881 AGAGTATCAAGTATGTCAACTAGGTG 57.998 38.462 0.00 0.00 37.82 4.00
224 234 8.127150 AGGTAAATGAAGAAAAAGAGGATTGG 57.873 34.615 0.00 0.00 0.00 3.16
228 238 7.468141 AATGAAGAAAAAGAGGATTGGGTAC 57.532 36.000 0.00 0.00 0.00 3.34
449 624 2.038975 TTGTCCCCTCCCTCCTCG 59.961 66.667 0.00 0.00 0.00 4.63
457 632 1.123928 CCTCCCTCCTCGCACTATTT 58.876 55.000 0.00 0.00 0.00 1.40
475 650 7.164803 CACTATTTATTTCCCCTCTCATCTCC 58.835 42.308 0.00 0.00 0.00 3.71
477 652 2.182516 ATTTCCCCTCTCATCTCCGT 57.817 50.000 0.00 0.00 0.00 4.69
516 697 7.378728 CGATTTTTCTCTAAAAACACCTCAACC 59.621 37.037 0.00 0.00 44.95 3.77
540 721 4.995487 GTCCCACGTCTTATTGACTTTCTT 59.005 41.667 0.00 0.00 43.25 2.52
543 724 5.701290 CCCACGTCTTATTGACTTTCTTTCT 59.299 40.000 0.00 0.00 43.25 2.52
544 725 6.872020 CCCACGTCTTATTGACTTTCTTTCTA 59.128 38.462 0.00 0.00 43.25 2.10
545 726 7.549488 CCCACGTCTTATTGACTTTCTTTCTAT 59.451 37.037 0.00 0.00 43.25 1.98
546 727 8.596380 CCACGTCTTATTGACTTTCTTTCTATC 58.404 37.037 0.00 0.00 43.25 2.08
547 728 9.360093 CACGTCTTATTGACTTTCTTTCTATCT 57.640 33.333 0.00 0.00 43.25 1.98
776 1007 6.415573 AGAACCTAAGACAATTAATTCGGCT 58.584 36.000 0.00 0.00 0.00 5.52
793 1024 2.165030 CGGCTCCAAGATTCAAAGCAAT 59.835 45.455 0.00 0.00 34.65 3.56
800 1031 7.201857 GCTCCAAGATTCAAAGCAATATAGGTT 60.202 37.037 0.00 0.00 33.21 3.50
883 1118 8.116026 TCTAGTATGGATATGATAAGGCTGTGA 58.884 37.037 0.00 0.00 0.00 3.58
893 1128 1.915141 AAGGCTGTGACCTCCAAATG 58.085 50.000 0.00 0.00 39.93 2.32
951 1186 7.941919 TGAAGCCTATATATATAGACCGCAAG 58.058 38.462 25.30 11.62 38.30 4.01
1038 1273 0.250727 GAAAGCTGGTGCAGGTGGTA 60.251 55.000 0.00 0.00 41.59 3.25
1062 1297 1.227853 GGACGTTGGACTTGTGGCT 60.228 57.895 0.00 0.00 0.00 4.75
1137 1372 2.422093 GCAAGCCAAGCTAGTTATCCCT 60.422 50.000 0.00 0.00 38.25 4.20
1203 1438 3.052082 GCCAAGCTTCGCTCTGCA 61.052 61.111 8.97 0.00 38.25 4.41
1233 1468 1.966451 GGGCCTCTTTGTGGTGACG 60.966 63.158 0.84 0.00 0.00 4.35
1330 1565 4.927782 AGCGGAAGTGCGGCAACA 62.928 61.111 3.23 0.00 44.52 3.33
1338 1573 0.462581 AGTGCGGCAACATGATCGAT 60.463 50.000 3.23 0.00 0.00 3.59
1374 1609 1.362717 CGAAGGGTACGGCATCGAT 59.637 57.895 0.00 0.00 40.11 3.59
1485 1720 2.355108 GCCACAGAATCTAAGGCACTCA 60.355 50.000 17.00 0.00 44.59 3.41
1489 1724 5.181009 CACAGAATCTAAGGCACTCAATCA 58.819 41.667 0.00 0.00 38.49 2.57
1509 1745 8.865090 TCAATCAACACATTAATTGTTACCCTT 58.135 29.630 12.57 5.35 36.00 3.95
1728 2068 0.104934 CTACTACCCTCCCTGCCCAT 60.105 60.000 0.00 0.00 0.00 4.00
1803 2143 1.203300 TCCTCCTCATGGACAAGGACA 60.203 52.381 0.00 0.00 36.75 4.02
1951 2307 7.538575 ACTTCTACAATGGACAAATATGCAAC 58.461 34.615 0.00 0.00 0.00 4.17
1952 2308 6.117911 TCTACAATGGACAAATATGCAACG 57.882 37.500 0.00 0.00 0.00 4.10
1972 2333 2.226200 CGGTTTGCAGTGATCATGAACA 59.774 45.455 0.00 0.00 0.00 3.18
1990 2351 8.316946 TCATGAACAAGACTCTCATTTCTATGT 58.683 33.333 0.00 0.00 33.34 2.29
2116 2477 2.122413 AGGATCATAGGGCCGCCA 60.122 61.111 12.58 0.00 0.00 5.69
2164 2525 2.436417 GCCATGTTCAAGAAGTGCCTA 58.564 47.619 0.00 0.00 0.00 3.93
2230 2591 0.038526 ATCGCACCGTCGACTTTCTT 60.039 50.000 14.70 0.00 41.62 2.52
2369 2730 4.822026 AGTGTAGTGTGAATAGGAGTTGC 58.178 43.478 0.00 0.00 0.00 4.17
2401 2762 4.456280 TCGTATATGATCACCTCCATGC 57.544 45.455 0.00 0.00 0.00 4.06
2418 2779 5.830912 TCCATGCAATAAAATAAAGAGCCG 58.169 37.500 0.00 0.00 0.00 5.52
2458 2819 3.602390 AACTTGACGAAAATGGTCACG 57.398 42.857 0.00 0.00 43.59 4.35
2521 2883 7.589395 ACATGCAAATACAGTTTTAATCACGA 58.411 30.769 0.00 0.00 0.00 4.35
2556 2918 2.266055 GCTGACTAGGCGCCAAGT 59.734 61.111 31.54 11.17 0.00 3.16
2646 3018 8.993121 CATTACCATCTGTTGTCTAATATGGAC 58.007 37.037 6.18 3.07 37.80 4.02
2689 3062 9.299963 CATTGAAGTGAAACAGTGAATACAAAA 57.700 29.630 0.00 0.00 41.43 2.44
2736 3109 3.262420 AGAGGAAATCAAACCGATGACG 58.738 45.455 0.00 0.00 33.40 4.35
2940 3368 8.469309 AAATATAATAATTGGCTGCAGTCAGT 57.531 30.769 22.01 16.63 42.29 3.41
2941 3369 7.678947 ATATAATAATTGGCTGCAGTCAGTC 57.321 36.000 22.01 0.00 44.94 3.51
2942 3370 2.113860 TAATTGGCTGCAGTCAGTCC 57.886 50.000 22.01 10.75 44.11 3.85
2950 3378 1.448540 GCAGTCAGTCCGGTCCATG 60.449 63.158 0.00 0.00 0.00 3.66
2966 3394 4.215613 GGTCCATGTTTCACAAGTTAGACC 59.784 45.833 0.00 0.00 33.90 3.85
3183 3612 0.904865 TGAGGATCGGCAGTCTGGTT 60.905 55.000 1.14 0.00 38.61 3.67
3201 3630 4.616553 TGGTTGGACACTAGGCTCTTATA 58.383 43.478 0.00 0.00 0.00 0.98
3204 3633 6.267014 TGGTTGGACACTAGGCTCTTATATAC 59.733 42.308 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.721000 AGCCCACAATCCATTCTTTAATTCA 59.279 36.000 0.00 0.00 0.00 2.57
87 88 1.977854 TGCATCCGTATCTAAGCCCAT 59.022 47.619 0.00 0.00 0.00 4.00
94 95 7.441157 CCTTTAAATCAACTGCATCCGTATCTA 59.559 37.037 0.00 0.00 0.00 1.98
97 107 6.119536 TCCTTTAAATCAACTGCATCCGTAT 58.880 36.000 0.00 0.00 0.00 3.06
98 108 5.492895 TCCTTTAAATCAACTGCATCCGTA 58.507 37.500 0.00 0.00 0.00 4.02
99 109 4.331968 TCCTTTAAATCAACTGCATCCGT 58.668 39.130 0.00 0.00 0.00 4.69
100 110 4.963276 TCCTTTAAATCAACTGCATCCG 57.037 40.909 0.00 0.00 0.00 4.18
101 111 6.924111 TCTTTCCTTTAAATCAACTGCATCC 58.076 36.000 0.00 0.00 0.00 3.51
102 112 8.992835 AATCTTTCCTTTAAATCAACTGCATC 57.007 30.769 0.00 0.00 0.00 3.91
103 113 9.783081 AAAATCTTTCCTTTAAATCAACTGCAT 57.217 25.926 0.00 0.00 0.00 3.96
104 114 9.044150 CAAAATCTTTCCTTTAAATCAACTGCA 57.956 29.630 0.00 0.00 0.00 4.41
105 115 9.045223 ACAAAATCTTTCCTTTAAATCAACTGC 57.955 29.630 0.00 0.00 0.00 4.40
132 142 2.819608 AGCCTTGTCACATGCGTTTAAT 59.180 40.909 0.00 0.00 0.00 1.40
155 165 9.067986 TGACATACTTGATACTCTCATTACGAT 57.932 33.333 0.00 0.00 32.72 3.73
316 488 9.587772 GATACCATCTTCGTAATGCATAGTATT 57.412 33.333 0.00 0.00 0.00 1.89
449 624 6.538263 AGATGAGAGGGGAAATAAATAGTGC 58.462 40.000 0.00 0.00 0.00 4.40
457 632 3.330126 ACGGAGATGAGAGGGGAAATA 57.670 47.619 0.00 0.00 0.00 1.40
486 666 8.391075 AGGTGTTTTTAGAGAAAAATCGATGA 57.609 30.769 0.00 0.00 44.29 2.92
492 672 7.147966 ACGGTTGAGGTGTTTTTAGAGAAAAAT 60.148 33.333 0.00 0.00 44.29 1.82
629 860 2.036733 CTCGTGTCCTTTTCAGGTGGTA 59.963 50.000 0.00 0.00 41.69 3.25
630 861 0.834612 TCGTGTCCTTTTCAGGTGGT 59.165 50.000 0.00 0.00 41.69 4.16
635 866 2.548480 GGAAACCTCGTGTCCTTTTCAG 59.452 50.000 0.00 0.00 37.01 3.02
776 1007 7.615365 ACAACCTATATTGCTTTGAATCTTGGA 59.385 33.333 4.53 0.00 32.47 3.53
793 1024 4.202315 CCCATGTCGATCCAACAACCTATA 60.202 45.833 0.00 0.00 0.00 1.31
800 1031 0.035534 CCACCCATGTCGATCCAACA 60.036 55.000 0.00 0.00 0.00 3.33
877 1112 2.012673 CTAGCATTTGGAGGTCACAGC 58.987 52.381 0.00 0.00 0.00 4.40
883 1118 6.267928 ACGTTATCTATCTAGCATTTGGAGGT 59.732 38.462 0.00 0.00 0.00 3.85
893 1128 7.008447 CGCCTATTTCAACGTTATCTATCTAGC 59.992 40.741 0.00 0.00 0.00 3.42
951 1186 3.184581 CCAAGTGCACGTACTCTTTTCTC 59.815 47.826 12.01 0.00 0.00 2.87
1137 1372 2.795973 CGGCTCACGTCCACGATA 59.204 61.111 6.03 0.00 43.02 2.92
1203 1438 2.937689 AGGCCCCATGACTGCAGT 60.938 61.111 21.88 21.88 0.00 4.40
1233 1468 1.518774 CTTTGACATGCCATGGCCC 59.481 57.895 33.44 19.36 37.55 5.80
1316 1551 0.099436 GATCATGTTGCCGCACTTCC 59.901 55.000 0.00 0.00 0.00 3.46
1330 1565 2.205074 GAACTTGACGCCATCGATCAT 58.795 47.619 0.00 0.00 39.41 2.45
1338 1573 0.878523 CGTTCTGGAACTTGACGCCA 60.879 55.000 11.03 0.00 39.08 5.69
1485 1720 8.093927 CCAAGGGTAACAATTAATGTGTTGATT 58.906 33.333 18.35 9.80 42.99 2.57
1489 1724 6.551601 TCACCAAGGGTAACAATTAATGTGTT 59.448 34.615 15.51 15.51 36.52 3.32
1728 2068 3.998672 GTTCACGAGGTCCGGGCA 61.999 66.667 9.07 0.00 42.54 5.36
1866 2206 1.372004 CGCCTACGACGACCAACAA 60.372 57.895 0.00 0.00 43.93 2.83
1951 2307 2.226200 TGTTCATGATCACTGCAAACCG 59.774 45.455 0.00 0.00 0.00 4.44
1952 2308 3.921119 TGTTCATGATCACTGCAAACC 57.079 42.857 0.00 0.00 0.00 3.27
1960 2316 6.981762 AATGAGAGTCTTGTTCATGATCAC 57.018 37.500 5.96 0.00 32.23 3.06
1999 2360 4.381292 GCCTTGAAGATTGCATTGCTAACT 60.381 41.667 10.49 3.56 0.00 2.24
2002 2363 3.090790 TGCCTTGAAGATTGCATTGCTA 58.909 40.909 10.49 2.21 0.00 3.49
2116 2477 0.842030 TCTCATGAACCAGCACCCCT 60.842 55.000 0.00 0.00 0.00 4.79
2205 2566 3.822192 CGACGGTGCGATCTCCCA 61.822 66.667 0.00 0.00 0.00 4.37
2230 2591 4.711399 CCTCAGCATTGATCCTGACATTA 58.289 43.478 0.00 0.00 34.60 1.90
2401 2762 5.739161 GTGCACTCGGCTCTTTATTTTATTG 59.261 40.000 10.32 0.00 45.15 1.90
2458 2819 4.588805 AGCCGCACGTTTTAGTATTAAC 57.411 40.909 0.00 0.00 0.00 2.01
2472 2834 4.573201 TCACCAGTTTAATATAAGCCGCAC 59.427 41.667 0.00 0.00 0.00 5.34
2521 2883 1.134907 AGCGTCGATTTTGTATCCGGT 60.135 47.619 0.00 0.00 0.00 5.28
2758 3131 0.468226 TTCTCGGTTGAGTGGCAAGT 59.532 50.000 0.00 0.00 43.09 3.16
2914 3342 8.917088 ACTGACTGCAGCCAATTATTATATTTT 58.083 29.630 15.27 0.00 46.26 1.82
2935 3363 1.270625 TGAAACATGGACCGGACTGAC 60.271 52.381 9.46 0.00 0.00 3.51
2939 3367 3.315765 TGTGAAACATGGACCGGAC 57.684 52.632 9.46 0.00 45.67 4.79
3151 3580 7.120285 ACTGCCGATCCTCAAATGAATATTATG 59.880 37.037 0.00 0.00 0.00 1.90
3183 3612 9.463902 GATAAGTATATAAGAGCCTAGTGTCCA 57.536 37.037 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.