Multiple sequence alignment - TraesCS7A01G534500

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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 TraesCS7A01G534500 chr7A 100.000 3617 0 0 1 3617 712421247 712424863 0.000000e+00 6680
1 TraesCS7A01G534500 chr7A 92.683 123 9 0 3191 3313 594424693 594424571 1.030000e-40 178
2 TraesCS7A01G534500 chr7D 92.955 3492 192 30 1 3476 618872931 618876384 0.000000e+00 5036
3 TraesCS7A01G534500 chr7D 91.870 123 8 1 3191 3313 223504686 223504566 1.730000e-38 171
4 TraesCS7A01G534500 chr7D 90.598 117 8 3 3501 3614 618876447 618876563 6.260000e-33 152
5 TraesCS7A01G534500 chr7D 82.474 97 5 6 3228 3313 618875663 618875758 1.390000e-09 75
6 TraesCS7A01G534500 chr7B 92.642 3017 142 27 624 3617 713288781 713291740 0.000000e+00 4268
7 TraesCS7A01G534500 chr7B 87.047 579 46 13 1 569 713288222 713288781 8.530000e-176 627
8 TraesCS7A01G534500 chr7B 88.693 398 45 0 1201 1598 86005807 86006204 1.510000e-133 486
9 TraesCS7A01G534500 chr7B 88.693 398 45 0 1201 1598 289702397 289702794 1.510000e-133 486
10 TraesCS7A01G534500 chr7B 82.292 96 7 5 3228 3313 713290867 713290962 1.390000e-09 75
11 TraesCS7A01G534500 chr4B 93.017 401 28 0 1201 1601 330524462 330524062 1.450000e-163 586
12 TraesCS7A01G534500 chr4B 89.776 401 41 0 1201 1601 528807636 528807236 6.930000e-142 514
13 TraesCS7A01G534500 chr5B 90.037 271 27 0 1201 1471 534150368 534150098 5.750000e-93 351
14 TraesCS7A01G534500 chr1B 94.309 123 7 0 3191 3313 502323993 502324115 4.770000e-44 189
15 TraesCS7A01G534500 chr1B 88.811 143 13 2 3473 3614 502324291 502324431 4.800000e-39 172
16 TraesCS7A01G534500 chr4A 93.443 122 8 0 3191 3312 535953745 535953866 7.980000e-42 182
17 TraesCS7A01G534500 chr6B 92.683 123 9 0 3191 3313 31284295 31284417 1.030000e-40 178


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 TraesCS7A01G534500 chr7A 712421247 712424863 3616 False 6680.000000 6680 100.000000 1 3617 1 chr7A.!!$F1 3616
1 TraesCS7A01G534500 chr7D 618872931 618876563 3632 False 1754.333333 5036 88.675667 1 3614 3 chr7D.!!$F1 3613
2 TraesCS7A01G534500 chr7B 713288222 713291740 3518 False 1656.666667 4268 87.327000 1 3617 3 chr7B.!!$F3 3616

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
967 995 0.324091 TAGGGTTCCTCTCGTCCACC 60.324 60.000 0.0 0.0 34.61 4.61 F
1674 1702 1.133792 CCCGCTTTGTCCTTATCCCAT 60.134 52.381 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2192 0.526524 GAGATCACGAAGTCGCCCTG 60.527 60.0 0.0 0.0 41.61 4.45 R
3051 3079 0.250234 TGACAGGAGAAGGATTGCCG 59.750 55.0 0.0 0.0 39.96 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
35 36 7.012515 TGGAAACAAACGAGAAGCAAAATAGTA 59.987 33.333 0.00 0.00 37.44 1.82
68 69 6.823689 GCTGAAGTCATTTTCTATAGGTTCCA 59.176 38.462 0.00 0.00 0.00 3.53
99 100 1.044611 TAGCCGCCACATGTATAGCA 58.955 50.000 13.27 0.00 0.00 3.49
365 373 9.823647 TTACCAAAATTTCAGAAGCACAAATTA 57.176 25.926 0.00 0.00 31.06 1.40
539 550 9.657121 TGTTTGAAAAACAATTTCACTTTCAAC 57.343 25.926 7.56 5.99 42.55 3.18
540 551 9.877137 GTTTGAAAAACAATTTCACTTTCAACT 57.123 25.926 7.56 0.00 42.55 3.16
619 630 8.384365 CAACCTTTTAAACATACACCAACAAAC 58.616 33.333 0.00 0.00 0.00 2.93
622 633 9.804758 CCTTTTAAACATACACCAACAAACTTA 57.195 29.630 0.00 0.00 0.00 2.24
653 664 2.805671 TCCACGCACAGTTTCACAATAG 59.194 45.455 0.00 0.00 0.00 1.73
657 668 4.670621 CACGCACAGTTTCACAATAGTTTC 59.329 41.667 0.00 0.00 0.00 2.78
658 669 3.900116 CGCACAGTTTCACAATAGTTTCG 59.100 43.478 0.00 0.00 0.00 3.46
666 679 7.164171 CAGTTTCACAATAGTTTCGTCAAACAG 59.836 37.037 2.97 0.00 43.98 3.16
672 685 8.471457 CACAATAGTTTCGTCAAACAGATTTTG 58.529 33.333 2.97 2.52 43.98 2.44
760 778 3.476295 TCTGATGTGAAGCATTTTCGC 57.524 42.857 0.00 0.00 38.06 4.70
780 798 2.087646 CTGTTCCTTTAGAAGCTGGCC 58.912 52.381 0.00 0.00 34.29 5.36
784 802 1.212935 TCCTTTAGAAGCTGGCCCATC 59.787 52.381 0.00 0.00 0.00 3.51
785 803 1.685148 CTTTAGAAGCTGGCCCATCC 58.315 55.000 0.00 0.00 0.00 3.51
799 817 3.563479 GGCCCATCCTGTTTAGAGGAAAA 60.563 47.826 0.00 0.00 45.53 2.29
800 818 4.086457 GCCCATCCTGTTTAGAGGAAAAA 58.914 43.478 0.00 0.00 45.53 1.94
820 838 4.519906 AAACCTGGGATCATTTCGGTAT 57.480 40.909 0.00 0.00 0.00 2.73
839 859 6.751888 TCGGTATAAAACGTTAAGGCTTCTAC 59.248 38.462 1.30 2.47 0.00 2.59
911 933 4.142026 GCCCATCACTTAAACCCATAAACC 60.142 45.833 0.00 0.00 0.00 3.27
917 939 4.705023 CACTTAAACCCATAAACCCTCCTG 59.295 45.833 0.00 0.00 0.00 3.86
924 946 2.158608 CCATAAACCCTCCTGTCCATCC 60.159 54.545 0.00 0.00 0.00 3.51
962 984 1.324005 GCTGCTAGGGTTCCTCTCGT 61.324 60.000 0.00 0.00 34.61 4.18
967 995 0.324091 TAGGGTTCCTCTCGTCCACC 60.324 60.000 0.00 0.00 34.61 4.61
968 996 2.657066 GGGTTCCTCTCGTCCACCC 61.657 68.421 0.00 0.00 40.52 4.61
1668 1696 2.353573 GCCCCCGCTTTGTCCTTA 59.646 61.111 0.00 0.00 0.00 2.69
1674 1702 1.133792 CCCGCTTTGTCCTTATCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
1698 1726 3.978723 CTCGGTGGAGAGCGTGCTG 62.979 68.421 0.00 0.00 43.27 4.41
1809 1837 1.351076 TGGAGAGCCATGTCAAGACA 58.649 50.000 5.24 5.24 46.44 3.41
1854 1882 4.660938 GGCGCCACTGGGGAAACT 62.661 66.667 24.80 0.00 40.01 2.66
1887 1915 2.292267 GCAGGGAGTGATGGTTATGTG 58.708 52.381 0.00 0.00 0.00 3.21
1945 1973 1.270839 CGATGCGGTATCCCAAGGAAT 60.271 52.381 0.31 0.00 34.34 3.01
1965 1993 3.114616 CTGTCCGTGGCTTGCTCG 61.115 66.667 0.00 0.00 0.00 5.03
2004 2032 2.002018 TTGCCGGGTCTTCAAAGGGT 62.002 55.000 2.18 0.00 0.00 4.34
2048 2076 2.641815 AGAAGAATGCAACAGAGGAGGT 59.358 45.455 0.00 0.00 0.00 3.85
2065 2093 2.904434 GAGGTGGAAGAGGAGGTTGTAA 59.096 50.000 0.00 0.00 0.00 2.41
2164 2192 1.673923 GCCAGAATGAAAAGGCCAAGC 60.674 52.381 5.01 0.00 41.25 4.01
2247 2275 1.707427 AGGAAGTTCAGGCACAAGGAT 59.293 47.619 5.01 0.00 0.00 3.24
2691 2719 2.646930 TCATAGACCATGCTTGCTTGG 58.353 47.619 21.14 21.14 39.02 3.61
2751 2779 4.479786 AGTGCCTAGAGACTTTTGATCC 57.520 45.455 0.00 0.00 0.00 3.36
2813 2841 6.207691 TCAGTATCGATTCAAGTGATGTGA 57.792 37.500 1.71 0.00 0.00 3.58
2927 2955 6.055588 GCCAGAGCTAGAATGGTTACATTTA 58.944 40.000 0.00 0.00 40.82 1.40
2932 2960 8.153550 AGAGCTAGAATGGTTACATTTATCTGG 58.846 37.037 0.00 0.00 46.89 3.86
3020 3048 9.129209 GCCTGTCTTGATATTTTTGTAAACTTC 57.871 33.333 0.00 0.00 0.00 3.01
3027 3055 9.684448 TTGATATTTTTGTAAACTTCGCAATGA 57.316 25.926 0.00 0.00 0.00 2.57
3051 3079 2.034001 CGTCAAACGAGTTCTGGACAAC 60.034 50.000 12.45 0.00 46.05 3.32
3060 3088 0.400213 TTCTGGACAACGGCAATCCT 59.600 50.000 0.00 0.00 33.34 3.24
3085 3113 3.129462 TCCTGTCACAACAAAATTTGCGA 59.871 39.130 5.52 0.00 34.24 5.10
3115 3143 2.806244 TGCTTCTTTCGCACTCCTTAAC 59.194 45.455 0.00 0.00 31.40 2.01
3149 3177 2.436417 TGCTACTTTCACCTTGCATCC 58.564 47.619 0.00 0.00 0.00 3.51
3166 3194 3.821033 GCATCCGGCTATCAGGTATTTTT 59.179 43.478 0.00 0.00 40.25 1.94
3203 3231 6.140303 TCAATCCTAAATTCAATGCTCTGC 57.860 37.500 0.00 0.00 0.00 4.26
3204 3232 5.653330 TCAATCCTAAATTCAATGCTCTGCA 59.347 36.000 0.00 0.00 44.86 4.41
3238 3266 4.023707 GGCCATAATCCTGACTTTTGATCG 60.024 45.833 0.00 0.00 0.00 3.69
3312 3340 3.062774 GTCGCTTATTCCTTGTGCTTCTC 59.937 47.826 0.00 0.00 0.00 2.87
3313 3341 3.002791 CGCTTATTCCTTGTGCTTCTCA 58.997 45.455 0.00 0.00 0.00 3.27
3314 3342 3.624861 CGCTTATTCCTTGTGCTTCTCAT 59.375 43.478 0.00 0.00 0.00 2.90
3315 3343 4.811024 CGCTTATTCCTTGTGCTTCTCATA 59.189 41.667 0.00 0.00 0.00 2.15
3316 3344 5.468072 CGCTTATTCCTTGTGCTTCTCATAT 59.532 40.000 0.00 0.00 0.00 1.78
3317 3345 6.017605 CGCTTATTCCTTGTGCTTCTCATATT 60.018 38.462 0.00 0.00 0.00 1.28
3318 3346 7.467811 CGCTTATTCCTTGTGCTTCTCATATTT 60.468 37.037 0.00 0.00 0.00 1.40
3319 3347 7.646922 GCTTATTCCTTGTGCTTCTCATATTTG 59.353 37.037 0.00 0.00 0.00 2.32
3320 3348 8.579850 TTATTCCTTGTGCTTCTCATATTTGT 57.420 30.769 0.00 0.00 0.00 2.83
3321 3349 5.885230 TCCTTGTGCTTCTCATATTTGTG 57.115 39.130 0.00 0.00 0.00 3.33
3322 3350 4.156556 TCCTTGTGCTTCTCATATTTGTGC 59.843 41.667 0.00 0.00 0.00 4.57
3323 3351 4.157289 CCTTGTGCTTCTCATATTTGTGCT 59.843 41.667 0.00 0.00 0.00 4.40
3324 3352 5.336213 CCTTGTGCTTCTCATATTTGTGCTT 60.336 40.000 0.00 0.00 0.00 3.91
3325 3353 5.300969 TGTGCTTCTCATATTTGTGCTTC 57.699 39.130 0.00 0.00 0.00 3.86
3326 3354 5.005740 TGTGCTTCTCATATTTGTGCTTCT 58.994 37.500 0.00 0.00 0.00 2.85
3400 3446 2.224992 TGGCCAGAGCTAAAATGGTCAA 60.225 45.455 0.00 0.00 45.33 3.18
3419 3465 7.337942 ATGGTCAACATTAGTCTGGAAGAAATC 59.662 37.037 0.00 0.00 40.62 2.17
3497 3578 7.670605 ACTGCATTAAACTAGATGGTACCTA 57.329 36.000 14.36 0.00 0.00 3.08
3542 3629 8.621532 TTCTTAGCTTGTTGAATCATGTACTT 57.378 30.769 0.00 0.00 0.00 2.24
3563 3650 2.842496 TGGAATGACCTGAAGCTCATCT 59.158 45.455 0.00 0.00 39.86 2.90
3606 3693 5.316167 ACATGAGAACTGCTGGTTTTATCA 58.684 37.500 0.00 3.21 38.41 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.418226 CGAGCTATACTATTTTGCTTCTCGTT 59.582 38.462 0.00 0.00 36.13 3.85
35 36 3.550437 AAATGACTTCAGCCGAGCTAT 57.450 42.857 0.00 0.00 36.40 2.97
68 69 4.905429 TGTGGCGGCTACATATTATTGAT 58.095 39.130 15.57 0.00 0.00 2.57
308 316 8.877864 TTCCCAAAGTTTTGTATATCACTGAT 57.122 30.769 4.12 0.00 36.45 2.90
329 337 9.990360 TTCTGAAATTTTGGTAAAACTATTCCC 57.010 29.630 0.00 0.00 32.37 3.97
336 344 7.532682 TGTGCTTCTGAAATTTTGGTAAAAC 57.467 32.000 0.00 0.00 32.37 2.43
514 525 9.877137 AGTTGAAAGTGAAATTGTTTTTCAAAC 57.123 25.926 15.79 4.14 44.49 2.93
527 538 9.173021 TGAGAAAACTATGAGTTGAAAGTGAAA 57.827 29.630 0.00 0.00 38.66 2.69
528 539 8.612619 GTGAGAAAACTATGAGTTGAAAGTGAA 58.387 33.333 0.00 0.00 38.66 3.18
539 550 5.907197 AACGTGTGTGAGAAAACTATGAG 57.093 39.130 0.00 0.00 0.00 2.90
540 551 5.813157 TGAAACGTGTGTGAGAAAACTATGA 59.187 36.000 0.00 0.00 0.00 2.15
657 668 9.536558 TCGTATTATTTCAAAATCTGTTTGACG 57.463 29.630 1.12 1.90 38.05 4.35
744 762 3.568538 GAACAGCGAAAATGCTTCACAT 58.431 40.909 0.00 0.00 44.46 3.21
746 764 2.030805 AGGAACAGCGAAAATGCTTCAC 60.031 45.455 0.00 0.00 44.46 3.18
760 778 2.087646 GGCCAGCTTCTAAAGGAACAG 58.912 52.381 0.00 0.00 0.00 3.16
799 817 2.899303 ACCGAAATGATCCCAGGTTT 57.101 45.000 0.00 0.00 0.00 3.27
800 818 5.640158 TTATACCGAAATGATCCCAGGTT 57.360 39.130 0.00 0.00 33.58 3.50
801 819 5.640158 TTTATACCGAAATGATCCCAGGT 57.360 39.130 0.00 0.00 35.91 4.00
808 826 7.281549 AGCCTTAACGTTTTATACCGAAATGAT 59.718 33.333 5.91 0.00 0.00 2.45
812 830 6.650390 AGAAGCCTTAACGTTTTATACCGAAA 59.350 34.615 5.91 0.00 0.00 3.46
820 838 5.240121 CCCTGTAGAAGCCTTAACGTTTTA 58.760 41.667 5.91 0.00 0.00 1.52
839 859 2.162408 GTCTTCAAGAATTTCGGCCCTG 59.838 50.000 0.00 0.00 0.00 4.45
882 904 1.302383 TTTAAGTGATGGGCCGCGTG 61.302 55.000 4.92 0.00 0.00 5.34
1261 1289 2.338984 GTCCTTGCAGACGGTCGT 59.661 61.111 1.89 0.00 0.00 4.34
1287 1315 2.184579 CGGAAGGAGGGCGAGAAC 59.815 66.667 0.00 0.00 0.00 3.01
1542 1570 2.278596 CGGATGTAGTCGCGGTGG 60.279 66.667 6.13 0.00 0.00 4.61
1656 1684 1.949525 CCATGGGATAAGGACAAAGCG 59.050 52.381 2.85 0.00 0.00 4.68
1887 1915 3.067320 GCTCCCCATAATCAAAGCACTTC 59.933 47.826 0.00 0.00 0.00 3.01
1945 1973 3.286751 GCAAGCCACGGACAGCAA 61.287 61.111 0.00 0.00 0.00 3.91
2004 2032 1.532437 CTTCTGCGCACAAAGATGTCA 59.468 47.619 18.58 0.00 37.82 3.58
2048 2076 2.303022 CTGCTTACAACCTCCTCTTCCA 59.697 50.000 0.00 0.00 0.00 3.53
2079 2107 1.601419 CTGGCTTGGGCATTGTCCAG 61.601 60.000 10.39 6.27 39.05 3.86
2164 2192 0.526524 GAGATCACGAAGTCGCCCTG 60.527 60.000 0.00 0.00 41.61 4.45
2491 2519 1.139498 TTCCTGATGCACCCCCTCAA 61.139 55.000 0.00 0.00 0.00 3.02
2691 2719 4.875536 AGAAACAAGCCAAAATTTCACCAC 59.124 37.500 0.00 0.00 34.22 4.16
2751 2779 5.069251 AGGGGACATACTAGAAGAACAATCG 59.931 44.000 0.00 0.00 0.00 3.34
2813 2841 3.873952 GAGAAGCACAAGGAATAAGCGAT 59.126 43.478 0.00 0.00 0.00 4.58
2872 2900 2.433604 AGCACAGGATACATGGTCTCAG 59.566 50.000 0.00 0.00 41.41 3.35
2927 2955 6.825721 AGCAAAACTATCGATTTCTTCCAGAT 59.174 34.615 1.71 0.00 0.00 2.90
2932 2960 6.743172 GGAACAGCAAAACTATCGATTTCTTC 59.257 38.462 1.71 0.00 0.00 2.87
3020 3048 2.502280 TCGTTTGACGATTCATTGCG 57.498 45.000 0.00 0.00 46.73 4.85
3051 3079 0.250234 TGACAGGAGAAGGATTGCCG 59.750 55.000 0.00 0.00 39.96 5.69
3060 3088 5.108517 GCAAATTTTGTTGTGACAGGAGAA 58.891 37.500 10.65 0.00 37.04 2.87
3085 3113 1.269257 GCGAAAGAAGCAGCCAACTTT 60.269 47.619 8.25 8.25 35.68 2.66
3115 3143 2.738743 AGTAGCATGTTTTGGGATGGG 58.261 47.619 0.00 0.00 0.00 4.00
3149 3177 8.718734 GGTAAGAATAAAAATACCTGATAGCCG 58.281 37.037 0.00 0.00 35.88 5.52
3177 3205 7.009907 GCAGAGCATTGAATTTAGGATTGAAAC 59.990 37.037 0.00 0.00 0.00 2.78
3203 3231 4.834496 AGGATTATGGCCATGTGGTAATTG 59.166 41.667 29.04 0.00 37.57 2.32
3204 3232 4.834496 CAGGATTATGGCCATGTGGTAATT 59.166 41.667 29.04 3.15 37.57 1.40
3273 3301 1.800586 CGACCACATCACTTGAACTGG 59.199 52.381 4.64 4.64 33.31 4.00
3400 3446 6.051717 CCATCGATTTCTTCCAGACTAATGT 58.948 40.000 0.00 0.00 0.00 2.71
3563 3650 4.593956 TGTACAACCCAATGTATCATGCA 58.406 39.130 0.00 0.00 38.03 3.96


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

AutoCloner maintained by Alex Coulton.