Multiple sequence alignment - TraesCS7B01G205900

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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 TraesCS7B01G205900 chr7B 100.000 4720 0 0 1 4720 376938535 376933816 0.000000e+00 8717.0
1 TraesCS7B01G205900 chr7B 100.000 276 0 0 5041 5316 376933495 376933220 1.320000e-140 510.0
2 TraesCS7B01G205900 chr7B 95.652 46 2 0 835 880 376937656 376937611 2.050000e-09 75.0
3 TraesCS7B01G205900 chr7B 95.652 46 2 0 880 925 376937701 376937656 2.050000e-09 75.0
4 TraesCS7B01G205900 chr7A 95.870 3898 140 7 834 4720 430565842 430561955 0.000000e+00 6287.0
5 TraesCS7B01G205900 chr7A 92.583 809 45 6 1 806 430566640 430565844 0.000000e+00 1147.0
6 TraesCS7B01G205900 chr7A 91.429 280 19 2 5041 5316 430561868 430561590 3.890000e-101 379.0
7 TraesCS7B01G205900 chr7A 92.958 71 5 0 3952 4022 712180956 712181026 2.620000e-18 104.0
8 TraesCS7B01G205900 chr7A 80.741 135 21 5 4545 4677 53293500 53293369 3.390000e-17 100.0
9 TraesCS7B01G205900 chr7A 94.000 50 3 0 876 925 430565845 430565796 5.710000e-10 76.8
10 TraesCS7B01G205900 chr7D 95.300 3872 140 20 831 4677 382527028 382523174 0.000000e+00 6104.0
11 TraesCS7B01G205900 chr7D 95.159 599 28 1 1 599 382532114 382531517 0.000000e+00 944.0
12 TraesCS7B01G205900 chr7D 90.040 251 25 0 5064 5314 382522880 382522630 5.130000e-85 326.0
13 TraesCS7B01G205900 chr7D 91.791 134 10 1 597 729 382527345 382527212 9.090000e-43 185.0
14 TraesCS7B01G205900 chr7D 81.818 132 20 4 4549 4677 80766944 80767074 2.020000e-19 108.0
15 TraesCS7B01G205900 chr7D 80.000 135 24 3 4545 4677 104945732 104945865 4.380000e-16 97.1
16 TraesCS7B01G205900 chr7D 90.141 71 7 0 3952 4022 618489480 618489550 5.670000e-15 93.5
17 TraesCS7B01G205900 chr7D 97.826 46 1 0 880 925 382527024 382526979 4.410000e-11 80.5
18 TraesCS7B01G205900 chr7D 95.349 43 2 0 838 880 382526976 382526934 9.550000e-08 69.4
19 TraesCS7B01G205900 chr1D 92.024 840 64 3 4 843 54021413 54020577 0.000000e+00 1177.0
20 TraesCS7B01G205900 chr1D 80.435 138 18 8 4546 4677 252487517 252487383 4.380000e-16 97.1
21 TraesCS7B01G205900 chr2D 92.811 779 52 3 1 778 517078364 517079139 0.000000e+00 1125.0
22 TraesCS7B01G205900 chr2D 89.474 57 6 0 3555 3611 65690612 65690556 7.390000e-09 73.1
23 TraesCS7B01G205900 chr6A 89.100 844 68 12 1 835 579378060 579378888 0.000000e+00 1027.0
24 TraesCS7B01G205900 chr5A 87.530 834 74 18 3 835 53579595 53580399 0.000000e+00 937.0
25 TraesCS7B01G205900 chr1A 91.473 645 53 2 4 648 53486798 53486156 0.000000e+00 885.0
26 TraesCS7B01G205900 chr1A 89.537 583 50 8 1 580 551172475 551173049 0.000000e+00 728.0
27 TraesCS7B01G205900 chr6D 90.909 583 50 2 256 836 19995364 19995945 0.000000e+00 780.0
28 TraesCS7B01G205900 chr6D 94.355 124 6 1 86 209 19995234 19995356 7.030000e-44 189.0
29 TraesCS7B01G205900 chr4A 93.724 239 15 0 1243 1481 23595868 23596106 5.060000e-95 359.0
30 TraesCS7B01G205900 chr4A 76.221 307 54 12 3498 3802 54107783 54107494 1.540000e-30 145.0
31 TraesCS7B01G205900 chr4A 78.947 171 30 4 4545 4712 16505114 16504947 1.570000e-20 111.0
32 TraesCS7B01G205900 chr4A 83.178 107 17 1 3942 4047 532796834 532796940 4.380000e-16 97.1
33 TraesCS7B01G205900 chr2A 93.724 239 15 0 1243 1481 3515363 3515601 5.060000e-95 359.0
34 TraesCS7B01G205900 chr2A 90.741 54 5 0 3555 3608 68880564 68880617 7.390000e-09 73.1
35 TraesCS7B01G205900 chr3B 91.538 130 10 1 1209 1337 805395905 805396034 1.520000e-40 178.0
36 TraesCS7B01G205900 chr4D 76.221 307 54 12 3498 3802 397094909 397094620 1.540000e-30 145.0
37 TraesCS7B01G205900 chr4D 80.282 142 24 3 3947 4088 397094315 397094178 2.620000e-18 104.0
38 TraesCS7B01G205900 chr4D 86.420 81 11 0 3942 4022 63585457 63585377 7.330000e-14 89.8
39 TraesCS7B01G205900 chrUn 83.200 125 16 5 4545 4666 95294224 95294346 5.630000e-20 110.0
40 TraesCS7B01G205900 chrUn 73.023 215 47 9 3555 3762 270733783 270733573 1.240000e-06 65.8
41 TraesCS7B01G205900 chrUn 73.023 215 47 9 3555 3762 282197155 282197365 1.240000e-06 65.8
42 TraesCS7B01G205900 chr3D 81.481 135 17 7 4548 4676 556988652 556988520 2.620000e-18 104.0
43 TraesCS7B01G205900 chr3A 81.295 139 17 7 4545 4675 602223712 602223849 2.620000e-18 104.0
44 TraesCS7B01G205900 chr4B 83.168 101 16 1 3947 4047 489088139 489088040 2.040000e-14 91.6
45 TraesCS7B01G205900 chr1B 88.732 71 8 0 3952 4022 687276774 687276704 2.640000e-13 87.9
46 TraesCS7B01G205900 chr2B 75.130 193 32 9 3691 3869 105539966 105540156 5.710000e-10 76.8


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 TraesCS7B01G205900 chr7B 376933220 376938535 5315 True 2344.25 8717 97.8260 1 5316 4 chr7B.!!$R1 5315
1 TraesCS7B01G205900 chr7A 430561590 430566640 5050 True 1972.45 6287 93.4705 1 5316 4 chr7A.!!$R2 5315
2 TraesCS7B01G205900 chr7D 382522630 382527345 4715 True 1352.98 6104 94.0612 597 5314 5 chr7D.!!$R2 4717
3 TraesCS7B01G205900 chr7D 382531517 382532114 597 True 944.00 944 95.1590 1 599 1 chr7D.!!$R1 598
4 TraesCS7B01G205900 chr1D 54020577 54021413 836 True 1177.00 1177 92.0240 4 843 1 chr1D.!!$R1 839
5 TraesCS7B01G205900 chr2D 517078364 517079139 775 False 1125.00 1125 92.8110 1 778 1 chr2D.!!$F1 777
6 TraesCS7B01G205900 chr6A 579378060 579378888 828 False 1027.00 1027 89.1000 1 835 1 chr6A.!!$F1 834
7 TraesCS7B01G205900 chr5A 53579595 53580399 804 False 937.00 937 87.5300 3 835 1 chr5A.!!$F1 832
8 TraesCS7B01G205900 chr1A 53486156 53486798 642 True 885.00 885 91.4730 4 648 1 chr1A.!!$R1 644
9 TraesCS7B01G205900 chr1A 551172475 551173049 574 False 728.00 728 89.5370 1 580 1 chr1A.!!$F1 579
10 TraesCS7B01G205900 chr6D 19995234 19995945 711 False 484.50 780 92.6320 86 836 2 chr6D.!!$F1 750

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
756 780 1.008938 AGATCAGGACCCAAGTAGCCT 59.991 52.381 0.00 0.00 0.00 4.58 F
2219 2341 0.107945 ATGAGCAACTTCCTCTCCGC 60.108 55.000 0.00 0.00 0.00 5.54 F
2937 3059 0.178929 ACCTCTCCTGGAACGTCCTT 60.179 55.000 0.00 0.00 37.46 3.36 F
3872 3994 0.105593 ATCGCACCAGGTGAGCATAG 59.894 55.000 24.96 6.53 39.86 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 2519 0.553819 AGAGTATGAGGCGGAGGAGT 59.446 55.0 0.00 0.0 0.00 3.85 R
3360 3482 0.320771 ACAGCTTCTTCACGGCGATT 60.321 50.0 16.62 0.0 0.00 3.34 R
4081 4203 0.613260 CGACCTTGGATCTCACCCAA 59.387 55.0 0.00 0.0 41.04 4.12 R
5045 5215 0.469331 TCCCTACATCTACGGGCTGG 60.469 60.0 0.00 0.0 37.89 4.85 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
82 83 7.841486 TCTTAAAATGAAGCGTAGAATGATCG 58.159 34.615 0.00 0.00 0.00 3.69
236 252 2.832129 GGTGAGTAGATGACCAAGGTGA 59.168 50.000 0.00 0.00 0.00 4.02
247 263 4.021925 AAGGTGAGGAGGCGTGGC 62.022 66.667 0.00 0.00 0.00 5.01
335 351 2.164422 GGCATTTGTTCTACTGGAAGGC 59.836 50.000 0.00 0.00 39.30 4.35
342 358 2.047274 TACTGGAAGGCGCTGCAC 60.047 61.111 7.64 0.00 39.30 4.57
349 365 4.785453 AGGCGCTGCACTTAGGCC 62.785 66.667 7.64 0.00 44.07 5.19
391 407 5.419542 TCTATTTTGTGTCGCTGCTTCTAT 58.580 37.500 0.00 0.00 0.00 1.98
422 438 8.507249 GTTGTCTAATGCATATATTTGGAGGAC 58.493 37.037 0.00 9.35 0.00 3.85
439 456 1.450025 GACTTCGGTCAAATGTCCCC 58.550 55.000 0.00 0.00 43.91 4.81
628 651 8.638873 AGTCCTCACATTATGATACATTACGAA 58.361 33.333 0.00 0.00 36.48 3.85
733 756 5.945191 TGATTCACTGAATGCATAACCAAGA 59.055 36.000 9.08 0.00 31.89 3.02
756 780 1.008938 AGATCAGGACCCAAGTAGCCT 59.991 52.381 0.00 0.00 0.00 4.58
1041 1163 1.449726 CCATGGCCATCATCACCACG 61.450 60.000 17.61 0.44 35.99 4.94
1219 1341 3.341629 CCTCCACCACCATGGCCT 61.342 66.667 13.04 0.00 42.67 5.19
1273 1395 2.659063 CCGCTCCTCACCATCACCA 61.659 63.158 0.00 0.00 0.00 4.17
1686 1808 2.192443 CTCGGCTCCCTCTCCGTA 59.808 66.667 0.47 0.00 45.44 4.02
1692 1814 0.535553 GCTCCCTCTCCGTACTCGAT 60.536 60.000 0.00 0.00 39.71 3.59
1909 2031 1.294659 GCTGCTCGAACACCTTGAGG 61.295 60.000 0.00 0.00 42.17 3.86
2005 2127 3.055719 CGGCAAATGTGTCCGGCT 61.056 61.111 9.99 0.00 39.37 5.52
2219 2341 0.107945 ATGAGCAACTTCCTCTCCGC 60.108 55.000 0.00 0.00 0.00 5.54
2397 2519 1.934220 GACTCTGCACCGATCACCGA 61.934 60.000 0.00 0.00 41.76 4.69
2616 2738 1.452108 GGTCATTTCCCCGAGCCTG 60.452 63.158 0.00 0.00 0.00 4.85
2933 3055 1.155390 TGGACCTCTCCTGGAACGT 59.845 57.895 0.00 0.00 37.48 3.99
2937 3059 0.178929 ACCTCTCCTGGAACGTCCTT 60.179 55.000 0.00 0.00 37.46 3.36
3085 3207 2.112928 ACACCGCTGCAATGTGGA 59.887 55.556 12.16 0.00 39.82 4.02
3132 3254 4.666253 ATGGTGGTGCTGGCGCTT 62.666 61.111 7.64 0.00 36.97 4.68
3174 3296 4.131088 GAGGACGACTCGGTGGCC 62.131 72.222 0.00 0.00 36.29 5.36
3175 3297 4.680537 AGGACGACTCGGTGGCCT 62.681 66.667 3.32 1.42 0.00 5.19
3472 3594 2.659610 GCAACGAGAGGGTGCTCT 59.340 61.111 0.00 0.00 41.38 4.09
3495 3617 2.507944 GTGGAGATGCTCGGCCAT 59.492 61.111 2.24 0.00 30.72 4.40
3669 3791 2.228914 GCGGTACAGAATCGCCGTC 61.229 63.158 0.00 0.00 45.30 4.79
3870 3992 1.450848 CATCGCACCAGGTGAGCAT 60.451 57.895 24.96 12.34 39.86 3.79
3871 3993 0.179076 CATCGCACCAGGTGAGCATA 60.179 55.000 24.96 4.60 39.86 3.14
3872 3994 0.105593 ATCGCACCAGGTGAGCATAG 59.894 55.000 24.96 6.53 39.86 2.23
3873 3995 2.176273 CGCACCAGGTGAGCATAGC 61.176 63.158 24.96 4.64 35.23 2.97
3874 3996 1.078214 GCACCAGGTGAGCATAGCA 60.078 57.895 24.96 0.00 35.23 3.49
3935 4057 1.066656 CGTCGTCGTCGCCATTAACA 61.067 55.000 0.00 0.00 36.96 2.41
3939 4061 1.924524 CGTCGTCGCCATTAACATCTT 59.075 47.619 0.00 0.00 0.00 2.40
3940 4062 2.285026 CGTCGTCGCCATTAACATCTTG 60.285 50.000 0.00 0.00 0.00 3.02
3973 4095 0.664761 AGTACACGTACACACTGCGT 59.335 50.000 9.85 0.00 42.62 5.24
4081 4203 0.251922 AGGGCAGCAACATTGTGGAT 60.252 50.000 0.00 0.00 0.00 3.41
4487 4627 4.112634 CTCAGTATCACCGTGGTATTGTG 58.887 47.826 12.55 7.77 0.00 3.33
4604 4754 7.227156 ACCAAGTCTCAATCAAGTAACAGAAT 58.773 34.615 0.00 0.00 0.00 2.40
5141 5339 2.295909 CCATTGCTTCCGGACAAAGAAA 59.704 45.455 1.83 0.00 0.00 2.52
5202 5400 1.482182 CAGCTACATGCCAGTCCACTA 59.518 52.381 0.00 0.00 44.23 2.74
5282 5480 2.095768 CAGGAAAAATGCACGTCGTCAT 60.096 45.455 0.00 0.00 0.00 3.06
5298 5496 5.515270 CGTCGTCATGTGTCAATGTATAAGT 59.485 40.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 7.653311 GGTTGGCCATTGTGAATCTAATATTTC 59.347 37.037 6.09 0.00 34.09 2.17
236 252 2.270205 CTCAATGCCACGCCTCCT 59.730 61.111 0.00 0.00 0.00 3.69
247 263 1.676746 CCTCCATCAGTGGCTCAATG 58.323 55.000 0.00 0.00 45.63 2.82
335 351 3.188786 GACGGCCTAAGTGCAGCG 61.189 66.667 0.00 0.00 0.00 5.18
342 358 2.657143 AGGACTAAGAGACGGCCTAAG 58.343 52.381 0.00 0.00 0.00 2.18
480 497 5.047377 ACTCACCAACTGTTGTCAAAACAAT 60.047 36.000 18.38 0.00 46.58 2.71
495 514 6.204301 GTCCCTTTTAGTTCTAACTCACCAAC 59.796 42.308 0.00 0.00 40.37 3.77
547 567 8.388484 ACATTTTAAATTGGCTTGCATAACAA 57.612 26.923 13.17 0.00 36.62 2.83
733 756 2.703007 GCTACTTGGGTCCTGATCTCAT 59.297 50.000 0.00 0.00 0.00 2.90
874 996 5.306160 TGGTGCTCTTATGGTTACTATACCC 59.694 44.000 0.00 0.00 37.39 3.69
1041 1163 2.278531 GAGAAGAGAGAGCGCGCC 60.279 66.667 30.33 19.60 0.00 6.53
1681 1803 1.306148 CTGTAGGCATCGAGTACGGA 58.694 55.000 0.00 0.00 40.21 4.69
1888 2010 3.044305 AAGGTGTTCGAGCAGCGC 61.044 61.111 22.85 0.00 41.28 5.92
1909 2031 4.000988 CCATTGTAGCCATTATACCCGAC 58.999 47.826 0.00 0.00 0.00 4.79
1959 2081 3.412879 GAGGTACCGGAGCTGCGTC 62.413 68.421 26.29 12.92 35.50 5.19
1970 2092 2.025727 CGGCGATGTCGAGGTACC 59.974 66.667 2.73 2.73 43.02 3.34
2079 2201 4.825252 GACCACGGCGGCGGTATT 62.825 66.667 35.05 16.27 39.03 1.89
2390 2512 3.148279 GGCGGAGGAGTCGGTGAT 61.148 66.667 0.00 0.00 0.00 3.06
2397 2519 0.553819 AGAGTATGAGGCGGAGGAGT 59.446 55.000 0.00 0.00 0.00 3.85
2478 2600 1.737008 GTTGGACTCGAGCCGAACC 60.737 63.158 14.24 9.94 34.74 3.62
2661 2783 3.573491 GCCCGCCACGTATTGCTC 61.573 66.667 0.00 0.00 0.00 4.26
2688 2810 3.793144 CTCGCCGCCAAGACTTGC 61.793 66.667 9.85 4.80 0.00 4.01
2933 3055 2.742116 GGGATGCTGCCGGTAAGGA 61.742 63.158 1.90 2.65 45.00 3.36
2967 3089 2.211250 AGGTCTCCAGCGTAGTACAA 57.789 50.000 0.38 0.00 0.00 2.41
3085 3207 2.359107 CACTGCCACGGCTGACAT 60.359 61.111 20.34 0.00 41.63 3.06
3219 3341 3.399181 GTCATCCTCCACGGCCCA 61.399 66.667 0.00 0.00 0.00 5.36
3360 3482 0.320771 ACAGCTTCTTCACGGCGATT 60.321 50.000 16.62 0.00 0.00 3.34
3472 3594 2.121538 CGAGCATCTCCACCTCGGA 61.122 63.158 0.00 0.00 43.33 4.55
3495 3617 3.950794 GATGTTGCGGTGGCGGAGA 62.951 63.158 0.00 0.00 44.10 3.71
3870 3992 1.064783 CATGCGCGAGTCTCTGCTA 59.935 57.895 12.10 4.93 0.00 3.49
3871 3993 2.202716 CATGCGCGAGTCTCTGCT 60.203 61.111 12.10 0.07 0.00 4.24
3872 3994 3.922893 GCATGCGCGAGTCTCTGC 61.923 66.667 12.10 4.68 0.00 4.26
3873 3995 1.750572 GAAGCATGCGCGAGTCTCTG 61.751 60.000 12.10 0.00 45.49 3.35
3874 3996 1.518133 GAAGCATGCGCGAGTCTCT 60.518 57.895 12.10 0.00 45.49 3.10
3935 4057 6.483640 GTGTACTCTGAGAAAAACACCAAGAT 59.516 38.462 12.44 0.00 32.94 2.40
3939 4061 4.116961 CGTGTACTCTGAGAAAAACACCA 58.883 43.478 12.44 0.00 35.04 4.17
3940 4062 4.117685 ACGTGTACTCTGAGAAAAACACC 58.882 43.478 12.44 4.86 35.04 4.16
3973 4095 1.579932 GTCGCTCTTCTCGTCCACA 59.420 57.895 0.00 0.00 0.00 4.17
4081 4203 0.613260 CGACCTTGGATCTCACCCAA 59.387 55.000 0.00 0.00 41.04 4.12
4226 4348 4.570663 GTCCCTCATCGACGGCCG 62.571 72.222 26.86 26.86 40.25 6.13
4465 4605 4.112634 CACAATACCACGGTGATACTGAG 58.887 47.826 10.28 0.00 34.52 3.35
4487 4627 3.261981 TCCTTTATCGAGAGGGCAAAC 57.738 47.619 11.13 0.00 33.73 2.93
4651 4803 9.716531 TTGCTATATTCTTGAGATCTTATGTGG 57.283 33.333 0.00 0.00 0.00 4.17
5040 5210 1.048601 ACATCTACGGGCTGGTATGG 58.951 55.000 0.00 0.00 0.00 2.74
5041 5211 2.231478 CCTACATCTACGGGCTGGTATG 59.769 54.545 0.00 0.79 0.00 2.39
5042 5212 2.526432 CCTACATCTACGGGCTGGTAT 58.474 52.381 0.00 0.00 0.00 2.73
5043 5213 1.479942 CCCTACATCTACGGGCTGGTA 60.480 57.143 0.00 0.00 0.00 3.25
5044 5214 0.759436 CCCTACATCTACGGGCTGGT 60.759 60.000 0.00 0.00 0.00 4.00
5045 5215 0.469331 TCCCTACATCTACGGGCTGG 60.469 60.000 0.00 0.00 37.89 4.85
5046 5216 1.633774 ATCCCTACATCTACGGGCTG 58.366 55.000 0.00 0.00 37.89 4.85
5047 5217 3.759815 ATATCCCTACATCTACGGGCT 57.240 47.619 0.00 0.00 37.89 5.19
5168 5366 3.178046 TGTAGCTGGTCCCTAACATTGA 58.822 45.455 0.00 0.00 0.00 2.57
5270 5468 0.528684 TTGACACATGACGACGTGCA 60.529 50.000 4.58 3.74 36.57 4.57
5271 5469 0.790207 ATTGACACATGACGACGTGC 59.210 50.000 4.58 0.00 36.57 5.34
5282 5480 6.020971 ACACTCGACTTATACATTGACACA 57.979 37.500 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.