Multiple sequence alignment - TraesCS7B01G097500

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 TraesCS7B01G097500 chr7B 100.000 3361 0 0 1 3361 112299117 112295757 0.000000e+00 6207.0
1 TraesCS7B01G097500 chr7B 94.005 1151 44 12 1298 2428 112113987 112112842 0.000000e+00 1720.0
2 TraesCS7B01G097500 chr7B 95.051 586 29 0 1550 2135 727232958 727232373 0.000000e+00 922.0
3 TraesCS7B01G097500 chr7B 85.109 685 57 27 548 1203 112114667 112113999 0.000000e+00 658.0
4 TraesCS7B01G097500 chr7B 92.424 198 14 1 30 226 470949548 470949351 7.100000e-72 281.0
5 TraesCS7B01G097500 chr7B 71.840 1076 214 70 1301 2337 112338819 112337794 3.370000e-55 226.0
6 TraesCS7B01G097500 chr7B 86.528 193 13 2 326 517 112127446 112127266 2.050000e-47 200.0
7 TraesCS7B01G097500 chr7B 89.062 128 12 2 2539 2664 112108749 112108622 1.250000e-34 158.0
8 TraesCS7B01G097500 chr7B 94.253 87 5 0 409 495 112124768 112124682 2.100000e-27 134.0
9 TraesCS7B01G097500 chr4B 96.902 3389 74 11 1 3361 402739671 402736286 0.000000e+00 5648.0
10 TraesCS7B01G097500 chr4B 77.399 469 80 16 2712 3160 500109129 500108667 4.300000e-64 255.0
11 TraesCS7B01G097500 chr4B 71.429 1071 216 70 1306 2337 402763389 402762370 2.050000e-47 200.0
12 TraesCS7B01G097500 chr4B 88.333 60 7 0 1000 1059 62871467 62871526 4.650000e-09 73.1
13 TraesCS7B01G097500 chr7D 90.813 1698 97 26 993 2664 149849946 149848282 0.000000e+00 2217.0
14 TraesCS7B01G097500 chr7D 86.779 416 40 9 368 776 149850532 149850125 1.840000e-122 449.0
15 TraesCS7B01G097500 chr7D 92.893 197 13 1 30 225 72944486 72944290 5.490000e-73 285.0
16 TraesCS7B01G097500 chr7D 78.419 468 80 10 2713 3167 151014493 151014952 5.490000e-73 285.0
17 TraesCS7B01G097500 chr7D 75.451 277 45 13 2726 2984 70750947 70751218 2.740000e-21 113.0
18 TraesCS7B01G097500 chr7D 97.619 42 0 1 873 913 149850035 149849994 1.670000e-08 71.3
19 TraesCS7B01G097500 chr7A 90.861 1324 68 25 1287 2584 150329527 150328231 0.000000e+00 1725.0
20 TraesCS7B01G097500 chr7A 86.836 433 24 12 368 776 150330396 150329973 1.420000e-123 453.0
21 TraesCS7B01G097500 chr7A 86.402 353 26 12 873 1203 150329883 150329531 1.910000e-97 366.0
22 TraesCS7B01G097500 chr7A 75.953 341 63 8 2727 3058 143185361 143185691 1.250000e-34 158.0
23 TraesCS7B01G097500 chr7A 83.544 158 25 1 3203 3360 325717594 325717750 2.700000e-31 147.0
24 TraesCS7B01G097500 chr6A 81.356 472 67 9 2714 3167 608085769 608085301 6.850000e-97 364.0
25 TraesCS7B01G097500 chr1D 80.632 475 82 8 2720 3185 263568059 263567586 3.190000e-95 359.0
26 TraesCS7B01G097500 chr2D 81.023 469 70 8 2714 3165 429043093 429043559 4.120000e-94 355.0
27 TraesCS7B01G097500 chr4D 80.128 468 77 9 2714 3165 460665515 460665048 5.370000e-88 335.0
28 TraesCS7B01G097500 chr4D 79.226 491 79 12 2716 3187 54280955 54280469 1.500000e-83 320.0
29 TraesCS7B01G097500 chr4D 82.486 177 31 0 3184 3360 147911138 147911314 4.490000e-34 156.0
30 TraesCS7B01G097500 chr3D 79.461 482 79 14 2714 3179 568492009 568492486 1.160000e-84 324.0
31 TraesCS7B01G097500 chr3D 79.828 466 72 10 2714 3160 43563968 43564430 1.500000e-83 320.0
32 TraesCS7B01G097500 chr3D 76.338 355 62 8 2714 3048 85594855 85594503 1.600000e-38 171.0
33 TraesCS7B01G097500 chr3B 80.088 457 72 7 2726 3165 775734376 775734830 4.180000e-84 322.0
34 TraesCS7B01G097500 chr3B 82.184 174 29 2 3188 3360 789494775 789494603 7.510000e-32 148.0
35 TraesCS7B01G097500 chr2A 79.281 473 75 13 2714 3167 16843595 16843127 3.260000e-80 309.0
36 TraesCS7B01G097500 chr2A 84.127 63 10 0 1000 1062 53332096 53332034 1.010000e-05 62.1
37 TraesCS7B01G097500 chrUn 92.424 198 14 1 30 226 86973358 86973555 7.100000e-72 281.0
38 TraesCS7B01G097500 chrUn 92.424 198 14 1 30 226 87001479 87001282 7.100000e-72 281.0
39 TraesCS7B01G097500 chr6D 92.424 198 14 1 30 226 221858782 221858979 7.100000e-72 281.0
40 TraesCS7B01G097500 chr6D 92.424 198 14 1 30 226 396922996 396922799 7.100000e-72 281.0
41 TraesCS7B01G097500 chr6D 77.019 161 26 7 3187 3347 164818820 164818969 7.730000e-12 82.4
42 TraesCS7B01G097500 chr5B 92.424 198 14 1 30 226 452127466 452127269 7.100000e-72 281.0
43 TraesCS7B01G097500 chr5B 80.347 173 34 0 3188 3360 241854192 241854020 7.570000e-27 132.0
44 TraesCS7B01G097500 chr4A 92.424 198 14 1 30 226 156840746 156840943 7.100000e-72 281.0
45 TraesCS7B01G097500 chr6B 79.557 406 63 10 2714 3104 662145202 662144802 4.270000e-69 272.0
46 TraesCS7B01G097500 chr6B 78.889 180 34 4 3183 3360 165564838 165565015 5.890000e-23 119.0
47 TraesCS7B01G097500 chr6B 88.333 60 7 0 1000 1059 663786049 663785990 4.650000e-09 73.1
48 TraesCS7B01G097500 chr6B 85.938 64 9 0 1000 1063 45729772 45729835 6.020000e-08 69.4
49 TraesCS7B01G097500 chr1A 86.275 102 9 4 2714 2811 477769060 477769160 4.590000e-19 106.0


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 TraesCS7B01G097500 chr7B 112295757 112299117 3360 True 6207.000000 6207 100.000 1 3361 1 chr7B.!!$R2 3360
1 TraesCS7B01G097500 chr7B 112112842 112114667 1825 True 1189.000000 1720 89.557 548 2428 2 chr7B.!!$R6 1880
2 TraesCS7B01G097500 chr7B 727232373 727232958 585 True 922.000000 922 95.051 1550 2135 1 chr7B.!!$R5 585
3 TraesCS7B01G097500 chr7B 112337794 112338819 1025 True 226.000000 226 71.840 1301 2337 1 chr7B.!!$R3 1036
4 TraesCS7B01G097500 chr4B 402736286 402739671 3385 True 5648.000000 5648 96.902 1 3361 1 chr4B.!!$R1 3360
5 TraesCS7B01G097500 chr7D 149848282 149850532 2250 True 912.433333 2217 91.737 368 2664 3 chr7D.!!$R2 2296
6 TraesCS7B01G097500 chr7A 150328231 150330396 2165 True 848.000000 1725 88.033 368 2584 3 chr7A.!!$R1 2216

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
108 109 1.270826 GCAAGTCCTTCTTTTGCTCCC 59.729 52.381 1.51 0.0 42.84 4.30 F
534 536 1.663702 CACGACTCACCCACGGTTC 60.664 63.158 0.00 0.0 31.02 3.62 F
1181 1271 0.614979 TCCCCTCTGCTCCAGTACAC 60.615 60.000 0.00 0.0 32.61 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1181 1271 0.676466 TTCAATGTAGGCGCTGGTGG 60.676 55.000 7.64 0.0 0.0 4.61 R
2066 2202 2.204705 ACCTCCCTCTCCCCCTCT 60.205 66.667 0.00 0.0 0.0 3.69 R
2943 3138 1.064505 TCTTCGTTCGTCTGTGTTCGT 59.935 47.619 0.00 0.0 0.0 3.85 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
67 68 6.017192 TCGGTATCTTATCATAGGCCTTCTT 58.983 40.000 12.58 0.00 0.00 2.52
77 78 5.188434 TCATAGGCCTTCTTCAAGTCAATG 58.812 41.667 12.58 3.67 0.00 2.82
108 109 1.270826 GCAAGTCCTTCTTTTGCTCCC 59.729 52.381 1.51 0.00 42.84 4.30
188 189 6.258287 CAGGCATGAAACAAACTGATTTTTGA 59.742 34.615 0.00 0.00 38.54 2.69
191 192 7.041916 GGCATGAAACAAACTGATTTTTGATCA 60.042 33.333 0.00 0.00 38.54 2.92
211 212 7.755591 TGATCATGCTTGTCATTCTTCTTAAC 58.244 34.615 0.00 0.00 31.79 2.01
279 280 9.339850 ACTGGAAAAGATGATGAATAGATTGAG 57.660 33.333 0.00 0.00 0.00 3.02
534 536 1.663702 CACGACTCACCCACGGTTC 60.664 63.158 0.00 0.00 31.02 3.62
1181 1271 0.614979 TCCCCTCTGCTCCAGTACAC 60.615 60.000 0.00 0.00 32.61 2.90
1282 1376 4.747810 AGTCTTTTGTGCTTGTTTCTTGG 58.252 39.130 0.00 0.00 0.00 3.61
1445 1545 4.680237 CTCGACTGGCGGTGGCAA 62.680 66.667 2.25 0.00 42.47 4.52
2066 2202 2.603473 AGGAGGCTGCCGTACACA 60.603 61.111 13.96 0.00 0.00 3.72
2404 2564 1.135527 GCTTACACATGGCATGCATGT 59.864 47.619 26.70 24.19 43.29 3.21
2480 2642 1.252904 TGTACTACCTGGTCACCGGC 61.253 60.000 0.63 0.00 0.00 6.13
2764 2944 3.130516 CCAAGTTCGTAGATCACCTAGCA 59.869 47.826 0.00 0.00 35.04 3.49
2824 3019 1.523711 CATTGGCGCGGACATACCT 60.524 57.895 8.83 0.00 36.31 3.08
2860 3055 1.136141 TCGAGAAGTCGTCGTGCTAAC 60.136 52.381 0.00 0.00 46.85 2.34
2873 3068 0.177141 TGCTAACGCCACATAGGACC 59.823 55.000 0.00 0.00 41.22 4.46
2888 3083 0.958382 GGACCAGCGCACCATAACAA 60.958 55.000 11.47 0.00 0.00 2.83
2916 3111 4.868171 CACCGACGATGAAAAGAATCCTAA 59.132 41.667 0.00 0.00 0.00 2.69
2943 3138 2.902608 AGGATCCAACCTGTAGACACA 58.097 47.619 15.82 0.00 39.01 3.72
2945 3140 2.607187 GATCCAACCTGTAGACACACG 58.393 52.381 0.00 0.00 0.00 4.49
2973 3168 0.801067 CGAACGAAGACCGGATCCAC 60.801 60.000 9.46 2.42 43.93 4.02
2974 3169 0.245539 GAACGAAGACCGGATCCACA 59.754 55.000 9.46 0.00 43.93 4.17
3106 3301 2.548920 GGAGGACCTTATTCCATCTGCG 60.549 54.545 0.00 0.00 38.25 5.18
3135 3330 3.193479 TGTCTCAAGCTCGCATCTTAGAA 59.807 43.478 0.00 0.00 0.00 2.10
3154 3349 2.249844 ACAGGACACAAACCCTAACG 57.750 50.000 0.00 0.00 0.00 3.18
3157 3352 3.207778 CAGGACACAAACCCTAACGAAA 58.792 45.455 0.00 0.00 0.00 3.46
3161 3356 4.815846 GGACACAAACCCTAACGAAACTAA 59.184 41.667 0.00 0.00 0.00 2.24
3202 3397 1.718757 GCACGAAGGGGACATGCATC 61.719 60.000 0.00 0.00 36.30 3.91
3203 3398 1.153369 ACGAAGGGGACATGCATCG 60.153 57.895 0.00 0.00 36.45 3.84
3210 3405 2.541120 GGACATGCATCGGCTGAGC 61.541 63.158 0.00 0.00 41.91 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.739462 GGAACGTCATGTGGCATCGA 60.739 55.000 0.00 0.00 0.00 3.59
67 68 7.121611 ACTTGCATATGATGTTCATTGACTTGA 59.878 33.333 6.97 0.00 38.26 3.02
77 78 6.690194 AAGAAGGACTTGCATATGATGTTC 57.310 37.500 6.97 0.28 37.45 3.18
108 109 2.877168 GGCAACTTATGGAGAGATGCAG 59.123 50.000 8.30 0.00 35.90 4.41
188 189 6.183360 CGGTTAAGAAGAATGACAAGCATGAT 60.183 38.462 0.00 0.00 37.28 2.45
191 192 4.396166 CCGGTTAAGAAGAATGACAAGCAT 59.604 41.667 0.00 0.00 39.43 3.79
211 212 3.879295 AGATTATTGTCATTGAGCACCGG 59.121 43.478 0.00 0.00 0.00 5.28
1164 1254 0.904865 TGGTGTACTGGAGCAGAGGG 60.905 60.000 0.00 0.00 35.18 4.30
1181 1271 0.676466 TTCAATGTAGGCGCTGGTGG 60.676 55.000 7.64 0.00 0.00 4.61
2066 2202 2.204705 ACCTCCCTCTCCCCCTCT 60.205 66.667 0.00 0.00 0.00 3.69
2312 2454 4.081697 TGGAGCAGAATCTCGTTGAATGTA 60.082 41.667 0.00 0.00 33.98 2.29
2368 2510 5.805486 TGTGTAAGCAATACTCGATCAGTTC 59.195 40.000 3.63 0.00 36.43 3.01
2480 2642 4.444838 TTCGTCCACCATCCGCGG 62.445 66.667 22.12 22.12 0.00 6.46
2741 2921 3.130693 GCTAGGTGATCTACGAACTTGGT 59.869 47.826 0.00 0.00 0.00 3.67
2745 2925 3.181499 CGTTGCTAGGTGATCTACGAACT 60.181 47.826 0.00 0.00 0.00 3.01
2764 2944 2.480845 GTTCCAGTGCTTGTAGTCGTT 58.519 47.619 0.00 0.00 0.00 3.85
2811 2991 1.296056 ACAACAAGGTATGTCCGCGC 61.296 55.000 0.00 0.00 42.99 6.86
2813 2993 2.968675 ACTACAACAAGGTATGTCCGC 58.031 47.619 0.00 0.00 42.99 5.54
2844 3039 1.671880 GGCGTTAGCACGACGACTTC 61.672 60.000 0.00 0.00 46.84 3.01
2860 3055 2.586079 CGCTGGTCCTATGTGGCG 60.586 66.667 0.00 0.00 36.89 5.69
2873 3068 2.418280 TGTATGTTGTTATGGTGCGCTG 59.582 45.455 9.73 0.00 0.00 5.18
2888 3083 4.182693 TCTTTTCATCGTCGGTGTATGT 57.817 40.909 5.22 0.00 0.00 2.29
2916 3111 1.916181 ACAGGTTGGATCCTTCCGATT 59.084 47.619 14.23 2.78 45.89 3.34
2943 3138 1.064505 TCTTCGTTCGTCTGTGTTCGT 59.935 47.619 0.00 0.00 0.00 3.85
2945 3140 1.785430 GGTCTTCGTTCGTCTGTGTTC 59.215 52.381 0.00 0.00 0.00 3.18
2973 3168 4.665212 CATTTGTCTTCGGTGGATTCATG 58.335 43.478 0.00 0.00 0.00 3.07
2974 3169 3.129287 GCATTTGTCTTCGGTGGATTCAT 59.871 43.478 0.00 0.00 0.00 2.57
3034 3229 1.296392 CATCTTCGGAGGGTGTGCA 59.704 57.895 0.00 0.00 0.00 4.57
3135 3330 1.764134 TCGTTAGGGTTTGTGTCCTGT 59.236 47.619 0.00 0.00 34.75 4.00
3210 3405 3.411351 CGGTTGAACTGTCCCGCG 61.411 66.667 0.00 0.00 33.20 6.46
3218 3413 2.424302 CGTCCCCACGGTTGAACT 59.576 61.111 0.00 0.00 42.73 3.01
3249 3444 3.900892 CGATGCGCGGTCCCTACT 61.901 66.667 8.83 0.00 36.03 2.57
3267 3462 4.189188 CTCCGGGGCGTAGTGTCG 62.189 72.222 0.00 0.00 0.00 4.35
3282 3477 4.148825 ACCGCTGCGTCATCCCTC 62.149 66.667 21.59 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.