Multiple sequence alignment - TraesCS5A01G072300

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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 TraesCS5A01G072300 chr5A 100.000 4020 0 0 1 4020 83275477 83279496 0.000000e+00 7424
1 TraesCS5A01G072300 chr5D 95.447 4041 134 30 1 4020 89379003 89383014 0.000000e+00 6397
2 TraesCS5A01G072300 chr5B 91.112 4084 214 80 8 4020 94679358 94675353 0.000000e+00 5393
3 TraesCS5A01G072300 chr4B 85.689 566 73 6 2415 2976 74681881 74681320 1.240000e-164 590
4 TraesCS5A01G072300 chr4B 83.008 359 57 4 1928 2284 74682362 74682006 5.010000e-84 322
5 TraesCS5A01G072300 chr4B 77.650 434 70 22 999 1423 74683171 74682756 5.190000e-59 239
6 TraesCS5A01G072300 chr4A 83.752 597 89 5 2384 2976 546211415 546212007 3.510000e-155 558
7 TraesCS5A01G072300 chr4A 83.427 356 55 4 1928 2281 546210960 546211313 1.080000e-85 327
8 TraesCS5A01G072300 chr4A 79.545 440 63 18 993 1423 546210160 546210581 5.080000e-74 289
9 TraesCS5A01G072300 chr4D 83.585 597 90 6 2384 2976 50770653 50770061 1.630000e-153 553
10 TraesCS5A01G072300 chr4D 84.123 359 53 4 1928 2284 50771110 50770754 1.070000e-90 344
11 TraesCS5A01G072300 chr4D 79.630 432 65 15 999 1423 50771914 50771499 5.080000e-74 289


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 TraesCS5A01G072300 chr5A 83275477 83279496 4019 False 7424.000000 7424 100.000000 1 4020 1 chr5A.!!$F1 4019
1 TraesCS5A01G072300 chr5D 89379003 89383014 4011 False 6397.000000 6397 95.447000 1 4020 1 chr5D.!!$F1 4019
2 TraesCS5A01G072300 chr5B 94675353 94679358 4005 True 5393.000000 5393 91.112000 8 4020 1 chr5B.!!$R1 4012
3 TraesCS5A01G072300 chr4B 74681320 74683171 1851 True 383.666667 590 82.115667 999 2976 3 chr4B.!!$R1 1977
4 TraesCS5A01G072300 chr4A 546210160 546212007 1847 False 391.333333 558 82.241333 993 2976 3 chr4A.!!$F1 1983
5 TraesCS5A01G072300 chr4D 50770061 50771914 1853 True 395.333333 553 82.446000 999 2976 3 chr4D.!!$R1 1977

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
414 424 0.037046 CCGGTTACCACGGCTTTACT 60.037 55.0 1.13 0.00 45.34 2.24 F
959 1063 0.467290 TTTGTCTTGGGAAGGCGCTT 60.467 50.0 7.64 0.00 35.37 4.68 F
1426 1554 0.815615 CCCCATTGTAAGAGCTCGCC 60.816 60.0 8.37 0.52 0.00 5.54 F
1442 1570 1.291877 CGCCGTTGTTCCCTTCTCTG 61.292 60.0 0.00 0.00 0.00 3.35 F
1698 2109 1.452110 TGCTGATTGTGATGGGTTCG 58.548 50.0 0.00 0.00 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 2096 0.893270 CCTTGCCGAACCCATCACAA 60.893 55.000 0.0 0.0 0.00 3.33 R
2443 2872 0.179000 CCCCATTCACCTTCCTCTCG 59.821 60.000 0.0 0.0 0.00 4.04 R
2668 3097 0.248949 GCCGGTAGTCCTCGATGAAC 60.249 60.000 1.9 0.0 0.00 3.18 R
2785 3214 1.747145 CTCGATGCTCCATGCCTCT 59.253 57.895 0.0 0.0 42.00 3.69 R
3518 3947 0.105964 CAACAACCACTCTGGACCGA 59.894 55.000 0.0 0.0 40.96 4.69 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
33 35 0.324943 TTTCTCCTCCTCGCAAAGGG 59.675 55.000 2.46 0.00 46.23 3.95
34 36 2.124942 CTCCTCCTCGCAAAGGGC 60.125 66.667 2.46 0.00 46.23 5.19
35 37 2.927856 TCCTCCTCGCAAAGGGCA 60.928 61.111 2.46 0.00 46.23 5.36
36 38 2.034066 CCTCCTCGCAAAGGGCAA 59.966 61.111 2.46 0.00 46.23 4.52
37 39 1.603455 CCTCCTCGCAAAGGGCAAA 60.603 57.895 2.46 0.00 46.23 3.68
85 87 8.038351 TCTTTCCTTGTTTTTCCTTTTAGGTTG 58.962 33.333 0.00 0.00 36.53 3.77
108 110 6.724263 TGTTTCAATTACGCATAGCATAAGG 58.276 36.000 0.00 0.00 0.00 2.69
130 133 3.624326 TTGTTGCTGTTGCTATGTGAC 57.376 42.857 0.00 0.00 40.48 3.67
257 260 0.461870 TGGTCTATGGCGATGCACAC 60.462 55.000 0.00 0.00 0.00 3.82
265 268 1.639298 GGCGATGCACACTGAGAACC 61.639 60.000 0.00 0.00 0.00 3.62
289 292 4.096984 CCAACCACATCTTCTGAATTAGGC 59.903 45.833 0.00 0.00 0.00 3.93
403 413 4.502263 GGCGTAAGACCGGTTACC 57.498 61.111 9.42 0.00 42.36 2.85
414 424 0.037046 CCGGTTACCACGGCTTTACT 60.037 55.000 1.13 0.00 45.34 2.24
421 431 3.067684 ACCACGGCTTTACTTTGCTAT 57.932 42.857 0.00 0.00 0.00 2.97
531 541 9.950680 TTAAACAAAGCAACAACATTTCAAAAA 57.049 22.222 0.00 0.00 0.00 1.94
577 590 4.887071 ACTCTTGCAAACACCATTACAGAA 59.113 37.500 0.00 0.00 0.00 3.02
633 734 8.954350 AGAAAAATCCTGATGTATCACTCAAAG 58.046 33.333 0.00 0.00 32.50 2.77
634 735 7.636150 AAAATCCTGATGTATCACTCAAAGG 57.364 36.000 0.00 0.00 32.50 3.11
664 765 7.514721 ACAGTACAAAGAAAATCCCTGAAGTA 58.485 34.615 0.00 0.00 0.00 2.24
666 767 8.669243 CAGTACAAAGAAAATCCCTGAAGTATC 58.331 37.037 0.00 0.00 0.00 2.24
667 768 8.606830 AGTACAAAGAAAATCCCTGAAGTATCT 58.393 33.333 0.00 0.00 0.00 1.98
670 771 7.826744 ACAAAGAAAATCCCTGAAGTATCTCTC 59.173 37.037 0.00 0.00 0.00 3.20
733 836 1.980052 CGGAGGGTAAGCTCACCAA 59.020 57.895 8.72 0.00 40.65 3.67
843 946 4.106925 CCAGTCTGCTCCCAGCCC 62.107 72.222 0.00 0.00 41.51 5.19
894 997 1.195442 TATTCGCACCCCACTCCACA 61.195 55.000 0.00 0.00 0.00 4.17
897 1000 4.660938 GCACCCCACTCCACACCC 62.661 72.222 0.00 0.00 0.00 4.61
899 1002 4.202030 ACCCCACTCCACACCCCT 62.202 66.667 0.00 0.00 0.00 4.79
959 1063 0.467290 TTTGTCTTGGGAAGGCGCTT 60.467 50.000 7.64 0.00 35.37 4.68
1419 1547 2.041081 CAAGGACACCCCCATTGTAAGA 59.959 50.000 0.00 0.00 34.66 2.10
1426 1554 0.815615 CCCCATTGTAAGAGCTCGCC 60.816 60.000 8.37 0.52 0.00 5.54
1442 1570 1.291877 CGCCGTTGTTCCCTTCTCTG 61.292 60.000 0.00 0.00 0.00 3.35
1478 1632 2.856720 GCTCTAGATTGAGTTCGCTCCG 60.857 54.545 0.00 0.00 43.45 4.63
1565 1958 5.254115 ACTCCTTTTGGCTGGAATTAGTAC 58.746 41.667 0.00 0.00 40.12 2.73
1685 2096 8.340618 ACACTGTATAAAAATGAGTTGCTGAT 57.659 30.769 0.00 0.00 0.00 2.90
1693 2104 4.713824 AATGAGTTGCTGATTGTGATGG 57.286 40.909 0.00 0.00 0.00 3.51
1698 2109 1.452110 TGCTGATTGTGATGGGTTCG 58.548 50.000 0.00 0.00 0.00 3.95
1711 2122 1.595093 GGGTTCGGCAAGGGTTCATG 61.595 60.000 0.00 0.00 0.00 3.07
1761 2173 6.252995 ACATATTGCCACTCTAAAAGGGAAA 58.747 36.000 0.00 0.00 36.33 3.13
1789 2206 6.346096 TGGCTTTCCTTGTATGATACAGTAC 58.654 40.000 5.34 0.00 40.24 2.73
1874 2291 4.243007 GCTACTTGCTGTGAAAAATGGT 57.757 40.909 0.00 0.00 38.95 3.55
2061 2479 2.904747 CTACCGAGTGCGAGACAGCG 62.905 65.000 0.00 0.00 40.82 5.18
2064 2482 4.803426 GAGTGCGAGACAGCGGGG 62.803 72.222 0.00 0.00 40.67 5.73
2217 2635 4.363990 CTCGTCTGGCGCCACACT 62.364 66.667 28.69 0.00 41.07 3.55
2332 2750 3.433615 GGTGGTCTTTTCTCAGTTCATCG 59.566 47.826 0.00 0.00 0.00 3.84
2381 2810 8.797438 GGAGTCTGAAGATTATTGTTCCTTTTT 58.203 33.333 0.00 0.00 0.00 1.94
2410 2839 1.676014 GGTCTGGATCCTTTGACCACG 60.676 57.143 29.92 6.71 45.87 4.94
2668 3097 3.133003 ACTGGGAGACTACCATCAATTCG 59.867 47.826 6.94 0.00 37.38 3.34
2785 3214 0.396435 ACACCAAGACTCGCATGGAA 59.604 50.000 0.00 0.00 37.66 3.53
2809 3238 0.249784 CATGGAGCATCGAGGAGGTG 60.250 60.000 0.00 0.00 34.37 4.00
2888 3317 2.113807 CTGGATCCATCAGTGAGACCA 58.886 52.381 16.63 3.10 0.00 4.02
3096 3525 2.344093 AGGGTAGAAAGAGAAGGGCA 57.656 50.000 0.00 0.00 0.00 5.36
3253 3682 6.406692 TTCAGAGATAATGGTGTAGTAGGC 57.593 41.667 0.00 0.00 0.00 3.93
3458 3887 4.607955 TCATCGTTCCTAATTAGCAGTCG 58.392 43.478 6.99 8.60 0.00 4.18
3475 3904 1.668751 GTCGAGTGTGCTTTGGTTTGA 59.331 47.619 0.00 0.00 0.00 2.69
3476 3905 2.096819 GTCGAGTGTGCTTTGGTTTGAA 59.903 45.455 0.00 0.00 0.00 2.69
3513 3942 6.100714 TCAAACTAACTTTTAGGGGAGACTGT 59.899 38.462 0.00 0.00 0.00 3.55
3516 3945 7.242322 ACTAACTTTTAGGGGAGACTGTAAG 57.758 40.000 0.00 0.00 42.29 2.34
3517 3946 5.500546 AACTTTTAGGGGAGACTGTAAGG 57.499 43.478 0.00 0.00 39.30 2.69
3518 3947 4.500452 ACTTTTAGGGGAGACTGTAAGGT 58.500 43.478 0.00 0.00 39.30 3.50
3519 3948 4.531339 ACTTTTAGGGGAGACTGTAAGGTC 59.469 45.833 0.00 0.00 39.30 3.85
3541 3970 0.836606 TCCAGAGTGGTTGTTGCTCA 59.163 50.000 0.00 0.00 39.03 4.26
3543 3972 2.158623 TCCAGAGTGGTTGTTGCTCATT 60.159 45.455 0.00 0.00 39.03 2.57
3544 3973 3.072330 TCCAGAGTGGTTGTTGCTCATTA 59.928 43.478 0.00 0.00 39.03 1.90
3744 4178 6.719829 CCTTCTTCAACCCCACTTTTACTATT 59.280 38.462 0.00 0.00 0.00 1.73
3812 4246 7.587037 ATTGTTAGTACCATAATGCAGCATT 57.413 32.000 23.96 23.96 37.80 3.56
3825 4259 2.364970 TGCAGCATTAGTGTGGCTTTTT 59.635 40.909 0.00 0.00 35.27 1.94
3843 4277 4.785453 GCCCCCTTCCTGCACTCG 62.785 72.222 0.00 0.00 0.00 4.18
3987 4422 2.744202 AGCTTTGCCTCTTGTGTTATCG 59.256 45.455 0.00 0.00 0.00 2.92
3996 4431 4.455877 CCTCTTGTGTTATCGCTTCCTTTT 59.544 41.667 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 87 6.954944 TCCTTATGCTATGCGTAATTGAAAC 58.045 36.000 4.92 0.00 38.97 2.78
108 110 4.161333 GTCACATAGCAACAGCAACAATC 58.839 43.478 0.00 0.00 0.00 2.67
130 133 8.810427 CAATATTGGATTCACATTTCCTTTTCG 58.190 33.333 7.62 0.00 32.95 3.46
257 260 1.352352 AGATGTGGTTGGGGTTCTCAG 59.648 52.381 0.00 0.00 0.00 3.35
265 268 4.641989 CCTAATTCAGAAGATGTGGTTGGG 59.358 45.833 0.00 0.00 0.00 4.12
402 412 3.006940 TCATAGCAAAGTAAAGCCGTGG 58.993 45.455 0.00 0.00 0.00 4.94
403 413 4.678509 TTCATAGCAAAGTAAAGCCGTG 57.321 40.909 0.00 0.00 0.00 4.94
414 424 5.871465 TCTGCATACGTTTTCATAGCAAA 57.129 34.783 0.00 0.00 0.00 3.68
421 431 6.027131 GCATGTTTATCTGCATACGTTTTCA 58.973 36.000 0.00 0.00 38.28 2.69
474 484 5.049818 GCATGTCATGTAAGCTAGACCATTC 60.050 44.000 14.26 0.00 0.00 2.67
595 608 7.928307 TCAGGATTTTTCTTTAGTGGATCTG 57.072 36.000 0.00 0.00 0.00 2.90
601 614 9.994432 GTGATACATCAGGATTTTTCTTTAGTG 57.006 33.333 0.00 0.00 37.51 2.74
633 734 8.674607 CAGGGATTTTCTTTGTACTGTAATACC 58.325 37.037 0.00 0.00 0.00 2.73
634 735 9.444600 TCAGGGATTTTCTTTGTACTGTAATAC 57.555 33.333 0.00 0.00 0.00 1.89
712 813 1.153549 GTGAGCTTACCCTCCGCTG 60.154 63.158 0.00 0.00 33.47 5.18
733 836 2.039951 TGGCTAGGGTTACCGCCT 59.960 61.111 17.31 3.25 42.07 5.52
865 968 2.034179 GGGGTGCGAATATAAACCAAGC 59.966 50.000 0.00 0.00 34.18 4.01
869 972 2.876550 GAGTGGGGTGCGAATATAAACC 59.123 50.000 0.00 0.00 0.00 3.27
894 997 1.545706 GGCGACAAAGAGAGAGGGGT 61.546 60.000 0.00 0.00 0.00 4.95
959 1063 1.514087 GCGATTACCCGAGACCACA 59.486 57.895 0.00 0.00 0.00 4.17
1419 1547 3.178540 AAGGGAACAACGGCGAGCT 62.179 57.895 16.62 0.00 0.00 4.09
1426 1554 1.884235 AAGCAGAGAAGGGAACAACG 58.116 50.000 0.00 0.00 0.00 4.10
1442 1570 3.999663 TCTAGAGCAAGAAGAAGCAAAGC 59.000 43.478 0.00 0.00 0.00 3.51
1478 1632 2.433868 TTTGTACTCACGAGAGCACC 57.566 50.000 9.97 0.00 46.09 5.01
1685 2096 0.893270 CCTTGCCGAACCCATCACAA 60.893 55.000 0.00 0.00 0.00 3.33
1693 2104 0.893727 ACATGAACCCTTGCCGAACC 60.894 55.000 0.00 0.00 0.00 3.62
1698 2109 2.497273 AGCAAATACATGAACCCTTGCC 59.503 45.455 0.00 0.00 39.94 4.52
1711 2122 7.035004 TCAGATGCCAATTTTGTAGCAAATAC 58.965 34.615 0.00 0.00 38.99 1.89
1761 2173 7.397192 ACTGTATCATACAAGGAAAGCCATTTT 59.603 33.333 0.00 0.00 38.38 1.82
1789 2206 8.519799 AATACACATTATCTGTTAAAGGGGTG 57.480 34.615 0.00 0.00 35.29 4.61
1911 2329 3.386078 TCTCCTGCATAGACCAGATCAAC 59.614 47.826 0.00 0.00 32.03 3.18
2061 2479 2.029964 TTCTTCACGACACGCCCC 59.970 61.111 0.00 0.00 0.00 5.80
2064 2482 2.844146 CGGTTCTTCACGACACGC 59.156 61.111 0.00 0.00 0.00 5.34
2332 2750 6.785463 CGTTTTCGTGCACAGTAGTGTGTC 62.785 50.000 27.23 20.37 45.79 3.67
2381 2810 5.136220 TCAAAGGATCCAGACCCTATAGAGA 59.864 44.000 15.82 0.00 31.36 3.10
2410 2839 2.180017 CCAGCAAACATGCTCGCC 59.820 61.111 0.00 0.00 44.30 5.54
2443 2872 0.179000 CCCCATTCACCTTCCTCTCG 59.821 60.000 0.00 0.00 0.00 4.04
2668 3097 0.248949 GCCGGTAGTCCTCGATGAAC 60.249 60.000 1.90 0.00 0.00 3.18
2785 3214 1.747145 CTCGATGCTCCATGCCTCT 59.253 57.895 0.00 0.00 42.00 3.69
2809 3238 1.918868 GACCGGGAACATTGAACGCC 61.919 60.000 6.32 0.00 0.00 5.68
3096 3525 7.616528 TTTCAAAGATCCAAATCCTCCTTTT 57.383 32.000 0.00 0.00 31.78 2.27
3458 3887 5.831997 ACTATTTCAAACCAAAGCACACTC 58.168 37.500 0.00 0.00 0.00 3.51
3475 3904 9.628500 AAAAGTTAGTTTGACCAGAGACTATTT 57.372 29.630 0.00 0.00 0.00 1.40
3513 3942 0.113776 ACCACTCTGGACCGACCTTA 59.886 55.000 0.00 0.00 40.96 2.69
3516 3945 1.004918 CAACCACTCTGGACCGACC 60.005 63.158 0.00 0.00 40.96 4.79
3517 3946 0.106149 AACAACCACTCTGGACCGAC 59.894 55.000 0.00 0.00 40.96 4.79
3518 3947 0.105964 CAACAACCACTCTGGACCGA 59.894 55.000 0.00 0.00 40.96 4.69
3519 3948 1.507141 GCAACAACCACTCTGGACCG 61.507 60.000 0.00 0.00 40.96 4.79
3744 4178 3.483808 TCACCAACACTTCAGCATGTA 57.516 42.857 0.00 0.00 37.40 2.29
3825 4259 3.650950 GAGTGCAGGAAGGGGGCA 61.651 66.667 0.00 0.00 34.70 5.36
3987 4422 1.270826 GGAGTGGAGCAAAAAGGAAGC 59.729 52.381 0.00 0.00 0.00 3.86
3996 4431 1.407851 GCATCTGATGGAGTGGAGCAA 60.408 52.381 18.60 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.