Multiple sequence alignment - TraesCS4A01G000700

Loading Multiple Alignment...

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 TraesCS4A01G000700 chr4A 100.000 2636 0 0 1 2636 535126 532491 0.000000e+00 4868
1 TraesCS4A01G000700 chr4A 97.597 2580 61 1 1 2580 500426 497848 0.000000e+00 4420
2 TraesCS4A01G000700 chr4A 97.519 2580 64 0 1 2580 238129045 238126466 0.000000e+00 4410
3 TraesCS4A01G000700 chr4A 94.286 560 31 1 207 766 551493634 551493076 0.000000e+00 856
4 TraesCS4A01G000700 chr4A 96.135 207 8 0 1 207 551494425 551494219 3.250000e-89 339
5 TraesCS4A01G000700 chr2A 97.674 2580 60 0 1 2580 5147566 5150145 0.000000e+00 4433
6 TraesCS4A01G000700 chr2A 97.248 763 20 1 1 763 303638000 303637239 0.000000e+00 1291
7 TraesCS4A01G000700 chr2A 91.139 79 5 2 2557 2634 671849023 671848946 3.590000e-19 106
8 TraesCS4A01G000700 chr2A 88.506 87 7 3 2551 2636 681753305 681753389 4.640000e-18 102
9 TraesCS4A01G000700 chr5A 97.171 2580 73 0 1 2580 511206245 511208824 0.000000e+00 4361
10 TraesCS4A01G000700 chr5A 97.905 1814 38 0 767 2580 562122493 562120680 0.000000e+00 3140
11 TraesCS4A01G000700 chr5A 97.795 1814 40 0 767 2580 687970178 687971991 0.000000e+00 3129
12 TraesCS4A01G000700 chr1A 97.016 2580 77 0 1 2580 534687348 534684769 0.000000e+00 4338
13 TraesCS4A01G000700 chr6A 97.685 1814 42 0 767 2580 553572041 553570228 0.000000e+00 3118
14 TraesCS4A01G000700 chr7A 97.299 1814 48 1 767 2580 49821869 49823681 0.000000e+00 3077
15 TraesCS4A01G000700 chr7A 96.711 760 25 0 1 760 49820288 49821047 0.000000e+00 1266
16 TraesCS4A01G000700 chr7A 94.366 71 4 0 2566 2636 711254307 711254237 2.770000e-20 110
17 TraesCS4A01G000700 chr4D 94.487 526 24 1 238 763 295218927 295218407 0.000000e+00 806
18 TraesCS4A01G000700 chr4D 96.800 125 4 0 83 207 295252169 295252045 2.660000e-50 209
19 TraesCS4A01G000700 chr4D 96.522 115 4 0 1 115 295252282 295252168 9.630000e-45 191
20 TraesCS4A01G000700 chr3A 97.101 69 1 1 2566 2634 203955390 203955457 5.960000e-22 115
21 TraesCS4A01G000700 chr5B 97.015 67 2 0 2570 2636 640447625 640447691 2.140000e-21 113
22 TraesCS4A01G000700 chr2B 91.139 79 5 2 2558 2634 372255510 372255432 3.590000e-19 106
23 TraesCS4A01G000700 chr2B 90.909 77 7 0 2558 2634 632641546 632641470 1.290000e-18 104
24 TraesCS4A01G000700 chr2D 96.774 62 2 0 2575 2636 527979477 527979416 1.290000e-18 104
25 TraesCS4A01G000700 chr7B 85.294 102 12 3 2537 2636 461918568 461918668 4.640000e-18 102


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 TraesCS4A01G000700 chr4A 532491 535126 2635 True 4868.0 4868 100.0000 1 2636 1 chr4A.!!$R2 2635
1 TraesCS4A01G000700 chr4A 497848 500426 2578 True 4420.0 4420 97.5970 1 2580 1 chr4A.!!$R1 2579
2 TraesCS4A01G000700 chr4A 238126466 238129045 2579 True 4410.0 4410 97.5190 1 2580 1 chr4A.!!$R3 2579
3 TraesCS4A01G000700 chr4A 551493076 551494425 1349 True 597.5 856 95.2105 1 766 2 chr4A.!!$R4 765
4 TraesCS4A01G000700 chr2A 5147566 5150145 2579 False 4433.0 4433 97.6740 1 2580 1 chr2A.!!$F1 2579
5 TraesCS4A01G000700 chr2A 303637239 303638000 761 True 1291.0 1291 97.2480 1 763 1 chr2A.!!$R1 762
6 TraesCS4A01G000700 chr5A 511206245 511208824 2579 False 4361.0 4361 97.1710 1 2580 1 chr5A.!!$F1 2579
7 TraesCS4A01G000700 chr5A 562120680 562122493 1813 True 3140.0 3140 97.9050 767 2580 1 chr5A.!!$R1 1813
8 TraesCS4A01G000700 chr5A 687970178 687971991 1813 False 3129.0 3129 97.7950 767 2580 1 chr5A.!!$F2 1813
9 TraesCS4A01G000700 chr1A 534684769 534687348 2579 True 4338.0 4338 97.0160 1 2580 1 chr1A.!!$R1 2579
10 TraesCS4A01G000700 chr6A 553570228 553572041 1813 True 3118.0 3118 97.6850 767 2580 1 chr6A.!!$R1 1813
11 TraesCS4A01G000700 chr7A 49820288 49823681 3393 False 2171.5 3077 97.0050 1 2580 2 chr7A.!!$F1 2579
12 TraesCS4A01G000700 chr4D 295218407 295218927 520 True 806.0 806 94.4870 238 763 1 chr4D.!!$R1 525

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
606 1192 0.752658 TGCCACGATCCCATGAGTAG 59.247 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 3987 0.672401 GAGATCCGCCGGTTTTGACA 60.672 55.0 1.63 0.0 0.0 3.58 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
472 1058 4.345854 GAGGTGGGAGAAGAAGAACTCTA 58.654 47.826 0.00 0.00 32.46 2.43
606 1192 0.752658 TGCCACGATCCCATGAGTAG 59.247 55.000 0.00 0.00 0.00 2.57
625 1211 8.846943 TGAGTAGCAAGTTTGATTCTTAATCA 57.153 30.769 0.00 0.00 45.68 2.57
666 1252 4.583073 TGACTGTACTGAAGCTTGTGTCTA 59.417 41.667 2.10 0.00 0.00 2.59
722 1308 6.631016 TGAACTGCACTATAGTAACAAGAGG 58.369 40.000 4.74 0.00 0.00 3.69
800 2201 9.787532 AATTGATTGGTTCAGTTTCGTATATTG 57.212 29.630 0.00 0.00 35.27 1.90
899 2300 3.812053 CCAGCCTTCTATCATGCTTACAC 59.188 47.826 0.00 0.00 30.08 2.90
998 2399 2.781911 GGGAGAAAATCACCCTCGC 58.218 57.895 5.71 0.00 43.04 5.03
1325 2726 8.512138 GTTAACTTGGTACTGCATGAGTTTTAT 58.488 33.333 0.00 0.00 35.96 1.40
1454 2855 7.336975 GTTTATTCGGTTTGAATATTGCATGC 58.663 34.615 11.82 11.82 46.29 4.06
1588 2989 2.106338 TGCATTGGTACCCATCATCGAT 59.894 45.455 10.07 0.00 31.53 3.59
1672 3073 3.267812 ACCATCCACTTCCTCATCAATGT 59.732 43.478 0.00 0.00 0.00 2.71
1729 3130 2.236395 ACAGGTATCTTCCTTGGTTCCG 59.764 50.000 0.00 0.00 35.37 4.30
1796 3197 4.210120 CGAGTATTGTTAGATCTTGCCAGC 59.790 45.833 0.00 0.00 0.00 4.85
2197 3598 7.259290 TGACTATTGAAGTTTTTGTCCTGTC 57.741 36.000 0.00 0.00 39.07 3.51
2394 3795 9.733556 TTTTTGTCTCTGCCAATCTAAATACTA 57.266 29.630 0.00 0.00 0.00 1.82
2580 3981 1.209261 CAAAAAGGCCACAACCCAACT 59.791 47.619 5.01 0.00 0.00 3.16
2581 3982 0.829990 AAAAGGCCACAACCCAACTG 59.170 50.000 5.01 0.00 0.00 3.16
2582 3983 0.325203 AAAGGCCACAACCCAACTGT 60.325 50.000 5.01 0.00 0.00 3.55
2583 3984 0.755327 AAGGCCACAACCCAACTGTC 60.755 55.000 5.01 0.00 0.00 3.51
2584 3985 2.551912 GGCCACAACCCAACTGTCG 61.552 63.158 0.00 0.00 0.00 4.35
2585 3986 2.551912 GCCACAACCCAACTGTCGG 61.552 63.158 0.00 0.00 0.00 4.79
2586 3987 1.153046 CCACAACCCAACTGTCGGT 60.153 57.895 0.00 0.00 0.00 4.69
2587 3988 1.444119 CCACAACCCAACTGTCGGTG 61.444 60.000 0.72 0.00 30.96 4.94
2588 3989 0.746563 CACAACCCAACTGTCGGTGT 60.747 55.000 0.72 0.00 30.96 4.16
2589 3990 0.463116 ACAACCCAACTGTCGGTGTC 60.463 55.000 0.72 0.00 30.96 3.67
2590 3991 0.462937 CAACCCAACTGTCGGTGTCA 60.463 55.000 0.72 0.00 30.96 3.58
2591 3992 0.253610 AACCCAACTGTCGGTGTCAA 59.746 50.000 0.72 0.00 30.96 3.18
2592 3993 0.253610 ACCCAACTGTCGGTGTCAAA 59.746 50.000 0.00 0.00 0.00 2.69
2593 3994 1.340211 ACCCAACTGTCGGTGTCAAAA 60.340 47.619 0.00 0.00 0.00 2.44
2594 3995 1.064952 CCCAACTGTCGGTGTCAAAAC 59.935 52.381 0.00 0.00 0.00 2.43
2595 3996 1.064952 CCAACTGTCGGTGTCAAAACC 59.935 52.381 0.00 0.00 36.82 3.27
2601 4002 2.592287 GGTGTCAAAACCGGCGGA 60.592 61.111 35.78 6.54 0.00 5.54
2602 4003 1.969589 GGTGTCAAAACCGGCGGAT 60.970 57.895 35.78 20.37 0.00 4.18
2603 4004 1.500396 GTGTCAAAACCGGCGGATC 59.500 57.895 35.78 9.52 0.00 3.36
2604 4005 0.953960 GTGTCAAAACCGGCGGATCT 60.954 55.000 35.78 13.84 0.00 2.75
2605 4006 0.672401 TGTCAAAACCGGCGGATCTC 60.672 55.000 35.78 16.90 0.00 2.75
2606 4007 1.447140 TCAAAACCGGCGGATCTCG 60.447 57.895 35.78 16.34 42.76 4.04
2611 4012 3.671411 CCGGCGGATCTCGGGTAG 61.671 72.222 24.41 0.00 42.32 3.18
2612 4013 3.671411 CGGCGGATCTCGGGTAGG 61.671 72.222 0.00 0.00 39.69 3.18
2613 4014 3.303928 GGCGGATCTCGGGTAGGG 61.304 72.222 5.87 0.00 39.69 3.53
2614 4015 3.303928 GCGGATCTCGGGTAGGGG 61.304 72.222 5.87 0.00 39.69 4.79
2615 4016 2.600769 CGGATCTCGGGTAGGGGG 60.601 72.222 0.00 0.00 34.75 5.40
2616 4017 2.613421 GGATCTCGGGTAGGGGGT 59.387 66.667 0.00 0.00 0.00 4.95
2617 4018 1.533513 GGATCTCGGGTAGGGGGTC 60.534 68.421 0.00 0.00 0.00 4.46
2618 4019 1.533513 GATCTCGGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
2619 4020 3.097429 ATCTCGGGTAGGGGGTCCC 62.097 68.421 0.00 0.00 45.90 4.46
2628 4029 2.754254 GGGGGTCCCGAATTGTGC 60.754 66.667 0.48 0.00 36.85 4.57
2629 4030 3.131478 GGGGTCCCGAATTGTGCG 61.131 66.667 0.48 0.00 0.00 5.34
2630 4031 2.359478 GGGTCCCGAATTGTGCGT 60.359 61.111 0.00 0.00 0.00 5.24
2631 4032 2.396157 GGGTCCCGAATTGTGCGTC 61.396 63.158 0.00 0.00 0.00 5.19
2632 4033 1.375523 GGTCCCGAATTGTGCGTCT 60.376 57.895 0.00 0.00 0.00 4.18
2633 4034 0.108520 GGTCCCGAATTGTGCGTCTA 60.109 55.000 0.00 0.00 0.00 2.59
2634 4035 1.673626 GGTCCCGAATTGTGCGTCTAA 60.674 52.381 0.00 0.00 0.00 2.10
2635 4036 1.659098 GTCCCGAATTGTGCGTCTAAG 59.341 52.381 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
472 1058 7.176690 AGCAGCAGTGTTATATTGTTTACCTTT 59.823 33.333 0.00 0.0 0.00 3.11
485 1071 3.688185 CAGATTGTGAGCAGCAGTGTTAT 59.312 43.478 0.00 0.0 0.00 1.89
631 1217 8.770828 GCTTCAGTACAGTCAAAGTGTAATTAA 58.229 33.333 0.00 0.0 35.94 1.40
666 1252 6.900194 AGTTCAGTACCATATGCCTACAATT 58.100 36.000 0.00 0.0 0.00 2.32
722 1308 5.010249 GCAACAAGCATTAAAACAAGCTC 57.990 39.130 0.00 0.0 44.79 4.09
800 2201 4.061596 GCATGATAGAAGGCTAGGTGAAC 58.938 47.826 0.00 0.0 0.00 3.18
899 2300 3.617669 ACTGTCGTGCAAAGAAAAATCG 58.382 40.909 0.00 0.0 0.00 3.34
994 2395 1.290203 GTGATGGTGTACATGGCGAG 58.710 55.000 0.00 0.0 40.72 5.03
998 2399 2.368439 CCAAGGTGATGGTGTACATGG 58.632 52.381 0.00 0.0 40.72 3.66
1325 2726 9.991906 AGTAAATACTCTTTGTGTTAGCAGTAA 57.008 29.630 0.00 0.0 29.71 2.24
1355 2756 4.826733 TGCATACAAAATCTCTGTGTTGGT 59.173 37.500 0.00 0.0 0.00 3.67
1588 2989 1.561717 CCGTTGTTGCATCCGTTCGA 61.562 55.000 0.00 0.0 0.00 3.71
1672 3073 6.925718 GTCGATGATGATCTGGATTGAGTTAA 59.074 38.462 0.00 0.0 0.00 2.01
1729 3130 5.003804 TCACAAAGGCAGGAGAGAATAAAC 58.996 41.667 0.00 0.0 0.00 2.01
1796 3197 7.203255 TCTACTATCACGACCATACATTCAG 57.797 40.000 0.00 0.0 0.00 3.02
2197 3598 7.651304 ACTCTCTCATATTTCTATGCAACTTCG 59.349 37.037 0.00 0.0 35.64 3.79
2584 3985 1.918868 GATCCGCCGGTTTTGACACC 61.919 60.000 1.63 0.0 0.00 4.16
2585 3986 0.953960 AGATCCGCCGGTTTTGACAC 60.954 55.000 1.63 0.0 0.00 3.67
2586 3987 0.672401 GAGATCCGCCGGTTTTGACA 60.672 55.000 1.63 0.0 0.00 3.58
2587 3988 1.693083 CGAGATCCGCCGGTTTTGAC 61.693 60.000 1.63 0.0 0.00 3.18
2588 3989 1.447140 CGAGATCCGCCGGTTTTGA 60.447 57.895 1.63 0.0 0.00 2.69
2589 3990 2.461110 CCGAGATCCGCCGGTTTTG 61.461 63.158 1.63 0.0 40.78 2.44
2590 3991 2.125269 CCGAGATCCGCCGGTTTT 60.125 61.111 1.63 0.0 40.78 2.43
2591 3992 4.157120 CCCGAGATCCGCCGGTTT 62.157 66.667 1.63 0.0 43.93 3.27
2593 3994 4.511246 TACCCGAGATCCGCCGGT 62.511 66.667 1.63 11.6 43.93 5.28
2594 3995 3.671411 CTACCCGAGATCCGCCGG 61.671 72.222 0.00 0.0 44.94 6.13
2595 3996 3.671411 CCTACCCGAGATCCGCCG 61.671 72.222 0.00 0.0 36.84 6.46
2596 3997 3.303928 CCCTACCCGAGATCCGCC 61.304 72.222 0.00 0.0 36.84 6.13
2597 3998 3.303928 CCCCTACCCGAGATCCGC 61.304 72.222 0.00 0.0 36.84 5.54
2598 3999 2.600769 CCCCCTACCCGAGATCCG 60.601 72.222 0.00 0.0 38.18 4.18
2599 4000 1.533513 GACCCCCTACCCGAGATCC 60.534 68.421 0.00 0.0 0.00 3.36
2600 4001 1.533513 GGACCCCCTACCCGAGATC 60.534 68.421 0.00 0.0 0.00 2.75
2601 4002 2.613421 GGACCCCCTACCCGAGAT 59.387 66.667 0.00 0.0 0.00 2.75
2602 4003 3.759101 GGGACCCCCTACCCGAGA 61.759 72.222 0.00 0.0 41.34 4.04
2606 4007 1.695239 AATTCGGGACCCCCTACCC 60.695 63.158 4.46 0.0 42.67 3.69
2607 4008 1.276859 ACAATTCGGGACCCCCTACC 61.277 60.000 4.46 0.0 42.67 3.18
2608 4009 0.107361 CACAATTCGGGACCCCCTAC 60.107 60.000 4.46 0.0 42.67 3.18
2609 4010 1.917336 GCACAATTCGGGACCCCCTA 61.917 60.000 4.46 0.0 42.67 3.53
2610 4011 3.087065 CACAATTCGGGACCCCCT 58.913 61.111 4.46 0.0 42.67 4.79
2611 4012 2.754254 GCACAATTCGGGACCCCC 60.754 66.667 4.46 0.0 41.09 5.40
2612 4013 3.131478 CGCACAATTCGGGACCCC 61.131 66.667 4.46 0.0 0.00 4.95
2613 4014 2.359478 ACGCACAATTCGGGACCC 60.359 61.111 0.00 0.0 0.00 4.46
2614 4015 0.108520 TAGACGCACAATTCGGGACC 60.109 55.000 0.00 0.0 0.00 4.46
2615 4016 1.659098 CTTAGACGCACAATTCGGGAC 59.341 52.381 0.00 0.0 0.00 4.46
2616 4017 2.004583 CTTAGACGCACAATTCGGGA 57.995 50.000 0.00 0.0 0.00 5.14


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

AutoCloner maintained by Alex Coulton.