Multiple sequence alignment - TraesCS3B01G490200

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 TraesCS3B01G490200 chr3B 100.000 6547 0 0 1 6547 736485013 736491559 0.000000e+00 12091.0
1 TraesCS3B01G490200 chr3B 97.719 2587 41 7 3588 6158 609330051 609327467 0.000000e+00 4434.0
2 TraesCS3B01G490200 chr3B 97.598 1457 30 2 230 1681 609332653 609331197 0.000000e+00 2492.0
3 TraesCS3B01G490200 chr3B 97.842 973 16 4 1180 2148 609334341 609333370 0.000000e+00 1676.0
4 TraesCS3B01G490200 chr3B 98.599 714 10 0 2099 2812 609333377 609332664 0.000000e+00 1264.0
5 TraesCS3B01G490200 chr3B 98.225 676 9 3 2919 3591 609330805 609330130 0.000000e+00 1179.0
6 TraesCS3B01G490200 chr3B 97.283 552 15 0 150 701 609335230 609334679 0.000000e+00 937.0
7 TraesCS3B01G490200 chr3B 92.275 233 17 1 2844 3075 466386203 466385971 4.890000e-86 329.0
8 TraesCS3B01G490200 chr3B 90.291 103 2 7 1 101 430922105 430922009 1.920000e-25 128.0
9 TraesCS3B01G490200 chr2B 98.333 3480 44 10 120 3591 622903839 622907312 0.000000e+00 6093.0
10 TraesCS3B01G490200 chr2B 97.438 2967 37 9 3588 6547 622907401 622910335 0.000000e+00 5022.0
11 TraesCS3B01G490200 chr2B 92.598 2094 94 17 136 2222 690776721 690778760 0.000000e+00 2952.0
12 TraesCS3B01G490200 chr2B 96.970 891 23 3 3588 4476 690780136 690781024 0.000000e+00 1493.0
13 TraesCS3B01G490200 chr2B 96.144 752 19 5 2843 3591 690779303 690780047 0.000000e+00 1219.0
14 TraesCS3B01G490200 chr2B 90.980 765 49 6 5801 6547 690781209 690781971 0.000000e+00 1013.0
15 TraesCS3B01G490200 chr2B 97.232 578 12 3 2268 2843 690778757 690779332 0.000000e+00 976.0
16 TraesCS3B01G490200 chr2B 83.838 99 7 7 2192 2286 37550958 37551051 1.170000e-12 86.1
17 TraesCS3B01G490200 chr5A 97.891 3461 62 8 141 3591 544222295 544225754 0.000000e+00 5976.0
18 TraesCS3B01G490200 chr5A 97.129 2647 59 6 3914 6546 544226352 544228995 0.000000e+00 4451.0
19 TraesCS3B01G490200 chr5A 96.800 2219 56 8 3588 5801 549318700 549316492 0.000000e+00 3690.0
20 TraesCS3B01G490200 chr5A 96.523 2157 59 8 3651 5801 549298017 549295871 0.000000e+00 3554.0
21 TraesCS3B01G490200 chr5A 96.772 1487 25 9 1192 2670 549321084 549319613 0.000000e+00 2459.0
22 TraesCS3B01G490200 chr5A 94.418 1057 42 8 120 1162 549322134 549321081 0.000000e+00 1609.0
23 TraesCS3B01G490200 chr5A 94.282 752 17 7 2843 3591 549319517 549318789 0.000000e+00 1127.0
24 TraesCS3B01G490200 chr5A 89.947 756 43 11 5801 6547 549295833 549295102 0.000000e+00 944.0
25 TraesCS3B01G490200 chr5A 89.550 756 46 11 5801 6547 549316454 549315723 0.000000e+00 928.0
26 TraesCS3B01G490200 chr5A 93.701 127 1 6 1 122 536903495 536903619 4.030000e-42 183.0
27 TraesCS3B01G490200 chr4A 97.804 3461 65 8 141 3591 701702240 701698781 0.000000e+00 5960.0
28 TraesCS3B01G490200 chr4A 97.447 2977 56 7 3588 6546 701698702 701695728 0.000000e+00 5059.0
29 TraesCS3B01G490200 chr4A 99.610 1026 4 0 229 1254 571068302 571067277 0.000000e+00 1873.0
30 TraesCS3B01G490200 chr4A 83.158 95 9 6 2195 2286 428159979 428159889 5.440000e-11 80.5
31 TraesCS3B01G490200 chr6B 99.561 2962 10 2 3588 6547 463398004 463400964 0.000000e+00 5395.0
32 TraesCS3B01G490200 chr6B 99.304 2298 12 2 229 2523 463395289 463397585 0.000000e+00 4152.0
33 TraesCS3B01G490200 chr6B 99.394 330 1 1 3263 3591 463397585 463397914 1.220000e-166 597.0
34 TraesCS3B01G490200 chr6B 92.800 125 2 6 1 123 247046341 247046222 2.430000e-39 174.0
35 TraesCS3B01G490200 chr2D 95.054 2487 64 16 4088 6547 5937025 5934571 0.000000e+00 3856.0
36 TraesCS3B01G490200 chr3D 95.757 2286 70 16 565 2843 434921647 434919382 0.000000e+00 3659.0
37 TraesCS3B01G490200 chr3D 97.454 1964 41 6 3588 5545 434918594 434916634 0.000000e+00 3341.0
38 TraesCS3B01G490200 chr3D 94.779 747 14 6 2844 3588 434919410 434918687 0.000000e+00 1140.0
39 TraesCS3B01G490200 chr3D 89.537 583 35 6 5924 6496 434916639 434916073 0.000000e+00 715.0
40 TraesCS3B01G490200 chr3D 94.595 148 8 0 178 325 434926984 434926837 5.110000e-56 230.0
41 TraesCS3B01G490200 chr4D 94.301 1544 67 12 3588 5129 215155521 215153997 0.000000e+00 2344.0
42 TraesCS3B01G490200 chr4D 88.916 406 33 7 1777 2177 81335144 81335542 2.120000e-134 490.0
43 TraesCS3B01G490200 chr4D 83.439 471 31 18 151 577 215157784 215157317 1.710000e-105 394.0
44 TraesCS3B01G490200 chrUn 98.398 1311 18 3 2284 3591 394865353 394864043 0.000000e+00 2302.0
45 TraesCS3B01G490200 chrUn 92.359 602 34 6 2249 2843 42465400 42465996 0.000000e+00 846.0
46 TraesCS3B01G490200 chrUn 89.171 434 35 7 1749 2177 42464980 42465406 1.250000e-146 531.0
47 TraesCS3B01G490200 chr7D 92.090 177 12 2 3069 3243 535549801 535549977 1.410000e-61 248.0
48 TraesCS3B01G490200 chr7D 83.505 97 6 7 2198 2290 470204878 470204788 1.510000e-11 82.4
49 TraesCS3B01G490200 chr7A 86.957 184 10 13 1 179 111846940 111846766 1.860000e-45 195.0
50 TraesCS3B01G490200 chr7A 93.284 134 0 8 1 127 2015361 2015492 8.670000e-44 189.0
51 TraesCS3B01G490200 chr7A 92.784 97 0 6 1 96 552450840 552450750 4.120000e-27 134.0
52 TraesCS3B01G490200 chr2A 91.379 116 0 7 1 112 587103038 587103147 4.090000e-32 150.0
53 TraesCS3B01G490200 chr1A 89.516 124 6 6 1 120 307053153 307053033 4.090000e-32 150.0
54 TraesCS3B01G490200 chr1A 85.496 131 10 7 1 127 308355549 308355674 1.920000e-25 128.0


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 TraesCS3B01G490200 chr3B 736485013 736491559 6546 False 12091.000000 12091 100.000000 1 6547 1 chr3B.!!$F1 6546
1 TraesCS3B01G490200 chr3B 609327467 609335230 7763 True 1997.000000 4434 97.877667 150 6158 6 chr3B.!!$R3 6008
2 TraesCS3B01G490200 chr2B 622903839 622910335 6496 False 5557.500000 6093 97.885500 120 6547 2 chr2B.!!$F2 6427
3 TraesCS3B01G490200 chr2B 690776721 690781971 5250 False 1530.600000 2952 94.784800 136 6547 5 chr2B.!!$F3 6411
4 TraesCS3B01G490200 chr5A 544222295 544228995 6700 False 5213.500000 5976 97.510000 141 6546 2 chr5A.!!$F2 6405
5 TraesCS3B01G490200 chr5A 549295102 549298017 2915 True 2249.000000 3554 93.235000 3651 6547 2 chr5A.!!$R1 2896
6 TraesCS3B01G490200 chr5A 549315723 549322134 6411 True 1962.600000 3690 94.364400 120 6547 5 chr5A.!!$R2 6427
7 TraesCS3B01G490200 chr4A 701695728 701702240 6512 True 5509.500000 5960 97.625500 141 6546 2 chr4A.!!$R3 6405
8 TraesCS3B01G490200 chr4A 571067277 571068302 1025 True 1873.000000 1873 99.610000 229 1254 1 chr4A.!!$R2 1025
9 TraesCS3B01G490200 chr6B 463395289 463400964 5675 False 3381.333333 5395 99.419667 229 6547 3 chr6B.!!$F1 6318
10 TraesCS3B01G490200 chr2D 5934571 5937025 2454 True 3856.000000 3856 95.054000 4088 6547 1 chr2D.!!$R1 2459
11 TraesCS3B01G490200 chr3D 434916073 434921647 5574 True 2213.750000 3659 94.381750 565 6496 4 chr3D.!!$R2 5931
12 TraesCS3B01G490200 chr4D 215153997 215157784 3787 True 1369.000000 2344 88.870000 151 5129 2 chr4D.!!$R1 4978
13 TraesCS3B01G490200 chrUn 394864043 394865353 1310 True 2302.000000 2302 98.398000 2284 3591 1 chrUn.!!$R1 1307
14 TraesCS3B01G490200 chrUn 42464980 42465996 1016 False 688.500000 846 90.765000 1749 2843 2 chrUn.!!$F1 1094

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
70 71 0.03582 CACGGGCCCTTTTGCTAGTA 60.036 55.0 22.43 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
5661 8328 7.119846 GGTGGAGGATCTAAATATATGTTGTGC 59.88 40.741 0.0 0.0 33.73 4.57 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
26 27 9.758651 ATGTGATCATGACCATTTGAAATTATG 57.241 29.630 0.00 0.00 32.51 1.90
27 28 8.968969 TGTGATCATGACCATTTGAAATTATGA 58.031 29.630 0.00 0.00 0.00 2.15
28 29 9.806203 GTGATCATGACCATTTGAAATTATGAA 57.194 29.630 0.00 0.00 0.00 2.57
62 63 4.265056 AACGAGCACGGGCCCTTT 62.265 61.111 22.43 2.91 44.46 3.11
63 64 3.785122 AACGAGCACGGGCCCTTTT 62.785 57.895 22.43 0.00 44.46 2.27
64 65 3.737172 CGAGCACGGGCCCTTTTG 61.737 66.667 22.43 15.24 42.56 2.44
65 66 4.056125 GAGCACGGGCCCTTTTGC 62.056 66.667 25.23 25.23 42.56 3.68
66 67 4.603535 AGCACGGGCCCTTTTGCT 62.604 61.111 28.14 28.14 42.56 3.91
67 68 2.675075 GCACGGGCCCTTTTGCTA 60.675 61.111 25.28 0.00 32.00 3.49
68 69 2.700773 GCACGGGCCCTTTTGCTAG 61.701 63.158 25.28 9.64 32.00 3.42
69 70 1.303317 CACGGGCCCTTTTGCTAGT 60.303 57.895 22.43 4.23 0.00 2.57
70 71 0.035820 CACGGGCCCTTTTGCTAGTA 60.036 55.000 22.43 0.00 0.00 1.82
71 72 0.916809 ACGGGCCCTTTTGCTAGTAT 59.083 50.000 22.43 0.00 0.00 2.12
72 73 2.121129 ACGGGCCCTTTTGCTAGTATA 58.879 47.619 22.43 0.00 0.00 1.47
73 74 2.709397 ACGGGCCCTTTTGCTAGTATAT 59.291 45.455 22.43 0.00 0.00 0.86
74 75 3.905591 ACGGGCCCTTTTGCTAGTATATA 59.094 43.478 22.43 0.00 0.00 0.86
75 76 4.348754 ACGGGCCCTTTTGCTAGTATATAA 59.651 41.667 22.43 0.00 0.00 0.98
76 77 5.013808 ACGGGCCCTTTTGCTAGTATATAAT 59.986 40.000 22.43 0.00 0.00 1.28
77 78 6.214005 ACGGGCCCTTTTGCTAGTATATAATA 59.786 38.462 22.43 0.00 0.00 0.98
78 79 7.107542 CGGGCCCTTTTGCTAGTATATAATAA 58.892 38.462 22.43 0.00 0.00 1.40
79 80 7.773690 CGGGCCCTTTTGCTAGTATATAATAAT 59.226 37.037 22.43 0.00 0.00 1.28
161 162 0.299895 CTGTCGTACGTCGTCGCTAT 59.700 55.000 16.05 0.00 41.18 2.97
207 208 0.249322 CGATATTCAACCCGCGGTCT 60.249 55.000 26.12 7.51 33.12 3.85
764 818 2.740981 CACCTCAACTGATGCTTCTCAC 59.259 50.000 0.88 0.00 0.00 3.51
776 830 2.846206 TGCTTCTCACCAACAGGGATAT 59.154 45.455 0.00 0.00 41.15 1.63
1531 1760 1.339438 GCTGATGGACTCAAGCTCCAA 60.339 52.381 0.00 0.00 41.27 3.53
1559 1796 6.846325 GCTCCTAGCACGTCTTAATTAATT 57.154 37.500 5.89 5.89 41.89 1.40
1560 1797 7.941795 GCTCCTAGCACGTCTTAATTAATTA 57.058 36.000 3.71 3.71 41.89 1.40
1745 1984 2.231721 GCCTTTTATACAACCCCGCAAA 59.768 45.455 0.00 0.00 0.00 3.68
2683 2988 4.561105 TCGTGCAGTGTACAATGTGATAA 58.439 39.130 22.95 4.63 0.00 1.75
5509 8170 6.469782 ACCTTTTTGTGACATCACTTCATT 57.530 33.333 12.98 0.00 46.55 2.57
5661 8328 1.534163 CGAAGTGCATATGCCAGGATG 59.466 52.381 24.54 6.87 41.18 3.51
5853 8567 8.671921 GCTGCTACGGTAATTAGTATCAGTATA 58.328 37.037 13.16 0.00 38.56 1.47
6116 8864 2.202797 CGGGAGCCGTCACTGATG 60.203 66.667 0.00 0.00 42.73 3.07
6117 8865 2.187946 GGGAGCCGTCACTGATGG 59.812 66.667 12.47 12.47 41.35 3.51
6118 8866 2.187946 GGAGCCGTCACTGATGGG 59.812 66.667 17.54 7.01 39.01 4.00
6289 9069 8.851145 TGCTACTACCTAATAGAAGAAGTCATG 58.149 37.037 0.00 0.00 34.65 3.07
6290 9070 8.852135 GCTACTACCTAATAGAAGAAGTCATGT 58.148 37.037 0.00 0.00 34.65 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.968969 TCATAATTTCAAATGGTCATGATCACA 58.031 29.630 11.75 5.48 0.00 3.58
45 46 3.785122 AAAAGGGCCCGTGCTCGTT 62.785 57.895 18.44 0.00 45.20 3.85
46 47 4.265056 AAAAGGGCCCGTGCTCGT 62.265 61.111 18.44 0.00 45.20 4.18
47 48 3.737172 CAAAAGGGCCCGTGCTCG 61.737 66.667 18.44 0.14 45.20 5.03
48 49 4.056125 GCAAAAGGGCCCGTGCTC 62.056 66.667 30.11 14.00 38.71 4.26
49 50 4.603535 AGCAAAAGGGCCCGTGCT 62.604 61.111 32.86 32.86 42.40 4.40
50 51 2.675075 TAGCAAAAGGGCCCGTGC 60.675 61.111 30.21 30.21 37.26 5.34
51 52 0.035820 TACTAGCAAAAGGGCCCGTG 60.036 55.000 18.44 17.24 0.00 4.94
52 53 0.916809 ATACTAGCAAAAGGGCCCGT 59.083 50.000 18.44 11.44 0.00 5.28
53 54 2.922740 TATACTAGCAAAAGGGCCCG 57.077 50.000 18.44 2.33 0.00 6.13
114 115 9.681062 AACCCTGCGTGCTTTATTATTATATAT 57.319 29.630 0.00 0.00 0.00 0.86
115 116 9.509956 AAACCCTGCGTGCTTTATTATTATATA 57.490 29.630 0.00 0.00 0.00 0.86
116 117 7.996098 AACCCTGCGTGCTTTATTATTATAT 57.004 32.000 0.00 0.00 0.00 0.86
117 118 7.717875 AGAAACCCTGCGTGCTTTATTATTATA 59.282 33.333 0.00 0.00 0.00 0.98
118 119 6.546034 AGAAACCCTGCGTGCTTTATTATTAT 59.454 34.615 0.00 0.00 0.00 1.28
132 133 1.342082 CGTACGACAGAAACCCTGCG 61.342 60.000 10.44 0.00 46.81 5.18
134 135 4.511783 ACGACGTACGACAGAAACCCTG 62.512 54.545 24.41 2.14 45.66 4.45
136 137 0.040067 ACGACGTACGACAGAAACCC 60.040 55.000 24.41 0.00 45.77 4.11
161 162 4.898861 ACCATAGGGACTTTTCTGCAAAAA 59.101 37.500 0.00 0.00 41.75 1.94
222 223 4.695928 AGATCTGGGCTAGAAACGTTTTTC 59.304 41.667 15.89 3.14 41.44 2.29
585 638 0.475632 TCCATGGTGGAGGTCTTGGT 60.476 55.000 12.58 0.00 42.67 3.67
764 818 5.880901 ACCAGCTAAATATATCCCTGTTGG 58.119 41.667 0.00 0.00 0.00 3.77
5661 8328 7.119846 GGTGGAGGATCTAAATATATGTTGTGC 59.880 40.741 0.00 0.00 33.73 4.57
6102 8850 2.187946 CCCCATCAGTGACGGCTC 59.812 66.667 0.00 0.00 0.00 4.70
6103 8851 3.402681 CCCCCATCAGTGACGGCT 61.403 66.667 0.00 0.00 0.00 5.52
6105 8853 4.489771 GGCCCCCATCAGTGACGG 62.490 72.222 0.00 0.00 0.00 4.79
6106 8854 2.032860 CTAGGCCCCCATCAGTGACG 62.033 65.000 0.00 0.00 0.00 4.35
6107 8855 1.700042 CCTAGGCCCCCATCAGTGAC 61.700 65.000 0.00 0.00 0.00 3.67
6108 8856 1.384502 CCTAGGCCCCCATCAGTGA 60.385 63.158 0.00 0.00 0.00 3.41
6109 8857 1.694169 ACCTAGGCCCCCATCAGTG 60.694 63.158 9.30 0.00 0.00 3.66
6110 8858 1.384643 GACCTAGGCCCCCATCAGT 60.385 63.158 9.30 0.00 0.00 3.41
6111 8859 2.150051 GGACCTAGGCCCCCATCAG 61.150 68.421 9.30 0.00 0.00 2.90
6112 8860 2.039831 GGACCTAGGCCCCCATCA 60.040 66.667 9.30 0.00 0.00 3.07
6113 8861 3.242291 CGGACCTAGGCCCCCATC 61.242 72.222 8.79 0.00 0.00 3.51
6114 8862 4.900259 CCGGACCTAGGCCCCCAT 62.900 72.222 8.79 0.00 0.00 4.00
6289 9069 9.539825 TGAAGAAAATAGATGAAGATGCTCTAC 57.460 33.333 0.00 0.00 0.00 2.59
6290 9070 9.539825 GTGAAGAAAATAGATGAAGATGCTCTA 57.460 33.333 0.00 0.00 0.00 2.43
6291 9071 7.224362 CGTGAAGAAAATAGATGAAGATGCTCT 59.776 37.037 0.00 0.00 0.00 4.09
6292 9072 7.010923 ACGTGAAGAAAATAGATGAAGATGCTC 59.989 37.037 0.00 0.00 0.00 4.26
6293 9073 6.820656 ACGTGAAGAAAATAGATGAAGATGCT 59.179 34.615 0.00 0.00 0.00 3.79
6294 9074 6.904011 CACGTGAAGAAAATAGATGAAGATGC 59.096 38.462 10.90 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.