Multiple sequence alignment - TraesCS7A01G390600

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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 TraesCS7A01G390600 chr7A 100.000 3113 0 0 1 3113 566787490 566790602 0.000000e+00 5749
1 TraesCS7A01G390600 chr7A 88.281 1425 147 14 735 2144 603331689 603330270 0.000000e+00 1688
2 TraesCS7A01G390600 chr7A 78.545 536 43 39 2491 2993 566909830 566910326 1.410000e-73 287
3 TraesCS7A01G390600 chr7A 82.517 286 24 14 2187 2462 566988828 566989097 8.680000e-56 228
4 TraesCS7A01G390600 chr7A 81.496 254 19 12 2499 2737 566989086 566989326 1.910000e-42 183
5 TraesCS7A01G390600 chr7A 100.000 96 0 0 3010 3105 566989673 566989768 8.870000e-41 178
6 TraesCS7A01G390600 chr7A 96.970 99 0 1 3010 3105 566910398 566910496 2.480000e-36 163
7 TraesCS7A01G390600 chr7A 89.831 118 9 2 2237 2352 566909654 566909770 6.960000e-32 148
8 TraesCS7A01G390600 chr7B 91.193 2725 143 36 398 3074 73173848 73176523 0.000000e+00 3613
9 TraesCS7A01G390600 chr7B 93.735 2123 117 8 302 2416 528871190 528873304 0.000000e+00 3169
10 TraesCS7A01G390600 chr7B 87.850 1465 153 10 701 2144 557491665 557490205 0.000000e+00 1696
11 TraesCS7A01G390600 chr7B 87.026 1449 168 11 705 2140 557257487 557256046 0.000000e+00 1616
12 TraesCS7A01G390600 chr7B 85.915 1427 184 14 675 2094 557460718 557459302 0.000000e+00 1506
13 TraesCS7A01G390600 chr7B 85.000 560 34 21 2474 3010 528873308 528873840 9.890000e-145 523
14 TraesCS7A01G390600 chr7B 87.560 418 24 6 2 399 73173278 73173687 2.830000e-125 459
15 TraesCS7A01G390600 chr7B 88.235 221 17 6 7 220 528870940 528871158 3.980000e-64 255
16 TraesCS7A01G390600 chr7B 75.000 712 50 53 2493 3103 664399451 664398767 8.750000e-51 211
17 TraesCS7A01G390600 chr7D 93.428 2176 119 8 302 2471 500773301 500775458 0.000000e+00 3205
18 TraesCS7A01G390600 chr7D 93.451 1649 99 5 398 2043 113581187 113582829 0.000000e+00 2438
19 TraesCS7A01G390600 chr7D 88.746 1404 138 17 756 2144 523057027 523055629 0.000000e+00 1700
20 TraesCS7A01G390600 chr7D 87.509 1401 163 10 701 2094 523128208 523126813 0.000000e+00 1607
21 TraesCS7A01G390600 chr7D 90.459 566 27 8 2472 3010 500775617 500776182 0.000000e+00 721
22 TraesCS7A01G390600 chr7D 85.948 427 23 10 2 399 113580513 113580931 3.710000e-114 422
23 TraesCS7A01G390600 chr7D 92.784 291 12 2 2809 3096 113582861 113583145 2.230000e-111 412
24 TraesCS7A01G390600 chr7D 88.841 233 17 6 7 232 500773047 500773277 8.500000e-71 278
25 TraesCS7A01G390600 chr7D 93.458 107 4 1 3010 3113 500776216 500776322 4.160000e-34 156
26 TraesCS7A01G390600 chr3D 88.477 972 71 14 485 1434 603682150 603683102 0.000000e+00 1136
27 TraesCS7A01G390600 chr3D 86.344 227 22 4 2187 2405 598726927 598726702 4.010000e-59 239
28 TraesCS7A01G390600 chr3D 80.233 258 19 14 2499 2737 598726670 598726426 6.910000e-37 165
29 TraesCS7A01G390600 chrUn 84.645 521 31 20 2491 2988 86611602 86612096 1.010000e-129 473
30 TraesCS7A01G390600 chrUn 93.333 90 3 1 3010 3096 86612154 86612243 2.520000e-26 130
31 TraesCS7A01G390600 chrUn 89.216 102 6 2 2187 2288 86611297 86611393 4.220000e-24 122
32 TraesCS7A01G390600 chr3A 77.823 487 53 35 2539 2994 732405069 732404607 1.850000e-62 250
33 TraesCS7A01G390600 chr3B 86.784 227 21 4 2187 2405 806016605 806016380 8.620000e-61 244
34 TraesCS7A01G390600 chr3B 77.640 483 44 40 2539 2994 810195314 810194869 5.190000e-58 235
35 TraesCS7A01G390600 chr3B 88.119 202 17 5 2187 2384 805979808 805979610 1.870000e-57 233
36 TraesCS7A01G390600 chr3B 87.222 180 18 3 2248 2422 805812637 805812458 1.890000e-47 200
37 TraesCS7A01G390600 chr3B 80.952 252 21 12 2499 2736 805977934 805977696 1.150000e-39 174
38 TraesCS7A01G390600 chr3B 80.237 253 23 12 2499 2737 805812446 805812207 6.910000e-37 165
39 TraesCS7A01G390600 chr3B 82.069 145 6 2 2313 2457 810195482 810195358 4.250000e-19 106
40 TraesCS7A01G390600 chr5A 92.000 100 5 1 3017 3113 605245730 605245631 1.510000e-28 137
41 TraesCS7A01G390600 chr5B 90.909 99 6 1 3018 3113 595010251 595010153 2.520000e-26 130


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 TraesCS7A01G390600 chr7A 566787490 566790602 3112 False 5749.000000 5749 100.000000 1 3113 1 chr7A.!!$F1 3112
1 TraesCS7A01G390600 chr7A 603330270 603331689 1419 True 1688.000000 1688 88.281000 735 2144 1 chr7A.!!$R1 1409
2 TraesCS7A01G390600 chr7B 73173278 73176523 3245 False 2036.000000 3613 89.376500 2 3074 2 chr7B.!!$F1 3072
3 TraesCS7A01G390600 chr7B 557490205 557491665 1460 True 1696.000000 1696 87.850000 701 2144 1 chr7B.!!$R3 1443
4 TraesCS7A01G390600 chr7B 557256046 557257487 1441 True 1616.000000 1616 87.026000 705 2140 1 chr7B.!!$R1 1435
5 TraesCS7A01G390600 chr7B 557459302 557460718 1416 True 1506.000000 1506 85.915000 675 2094 1 chr7B.!!$R2 1419
6 TraesCS7A01G390600 chr7B 528870940 528873840 2900 False 1315.666667 3169 88.990000 7 3010 3 chr7B.!!$F2 3003
7 TraesCS7A01G390600 chr7B 664398767 664399451 684 True 211.000000 211 75.000000 2493 3103 1 chr7B.!!$R4 610
8 TraesCS7A01G390600 chr7D 523055629 523057027 1398 True 1700.000000 1700 88.746000 756 2144 1 chr7D.!!$R1 1388
9 TraesCS7A01G390600 chr7D 523126813 523128208 1395 True 1607.000000 1607 87.509000 701 2094 1 chr7D.!!$R2 1393
10 TraesCS7A01G390600 chr7D 113580513 113583145 2632 False 1090.666667 2438 90.727667 2 3096 3 chr7D.!!$F1 3094
11 TraesCS7A01G390600 chr7D 500773047 500776322 3275 False 1090.000000 3205 91.546500 7 3113 4 chr7D.!!$F2 3106
12 TraesCS7A01G390600 chr3D 603682150 603683102 952 False 1136.000000 1136 88.477000 485 1434 1 chr3D.!!$F1 949
13 TraesCS7A01G390600 chr3D 598726426 598726927 501 True 202.000000 239 83.288500 2187 2737 2 chr3D.!!$R1 550
14 TraesCS7A01G390600 chrUn 86611297 86612243 946 False 241.666667 473 89.064667 2187 3096 3 chrUn.!!$F1 909
15 TraesCS7A01G390600 chr3B 805977696 805979808 2112 True 203.500000 233 84.535500 2187 2736 2 chr3B.!!$R3 549


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
386 423 0.250901 TGGAAGAGCAAAGAGTGGGC 60.251 55.0 0.00 0.00 0.0 5.36 F
1007 1328 0.250234 CTTCTGGAGTCCATGCGGAA 59.750 55.0 13.56 11.56 45.2 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 1901 0.170561 GCTCACATACACGACGGACT 59.829 55.0 0.00 0.0 0.00 3.85 R
2857 5239 0.600255 CAAGTCGAAGTCGGGCTTGT 60.600 55.0 20.38 0.0 42.08 3.16 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
77 84 6.548321 TCCACCTGGAAATAAAGAAGCTAAA 58.452 36.000 0.00 0.00 42.18 1.85
156 173 9.581099 CTTCTTTACCATTTGTTTTGTTACTGT 57.419 29.630 0.00 0.00 0.00 3.55
196 214 5.246203 AGGTTAGTGCTCTCAACTTATGTCA 59.754 40.000 0.00 0.00 0.00 3.58
202 220 4.040339 TGCTCTCAACTTATGTCACTGGAA 59.960 41.667 0.00 0.00 0.00 3.53
228 246 8.177119 TGCATTTGAATCTGGTTAGTTTTAGT 57.823 30.769 0.00 0.00 0.00 2.24
274 299 7.312154 TGCAACAGATCACATTATTAAACACC 58.688 34.615 0.00 0.00 0.00 4.16
345 382 1.454847 GGTTGTCACCAAGGCCACA 60.455 57.895 5.01 0.00 43.61 4.17
372 409 5.050837 GCTAAGTGCAAAACATGTTTGGAAG 60.051 40.000 26.65 16.44 42.31 3.46
373 410 4.734398 AGTGCAAAACATGTTTGGAAGA 57.266 36.364 26.65 8.77 31.74 2.87
374 411 4.685924 AGTGCAAAACATGTTTGGAAGAG 58.314 39.130 26.65 12.84 31.74 2.85
386 423 0.250901 TGGAAGAGCAAAGAGTGGGC 60.251 55.000 0.00 0.00 0.00 5.36
418 712 5.762179 TTAGATGTCACCTGGATCTGTTT 57.238 39.130 0.00 0.00 0.00 2.83
466 760 9.559958 AAGATGACAAAATAATTTCGATCACAC 57.440 29.630 0.00 0.00 0.00 3.82
543 837 3.389741 GTGTCTACCACACGGTACG 57.610 57.895 0.00 0.00 46.71 3.67
621 927 3.873952 CAGCTAACTGGAAAGATGCTACC 59.126 47.826 0.00 0.00 40.48 3.18
622 928 3.777522 AGCTAACTGGAAAGATGCTACCT 59.222 43.478 0.00 0.00 0.00 3.08
623 929 4.962995 AGCTAACTGGAAAGATGCTACCTA 59.037 41.667 0.00 0.00 0.00 3.08
624 930 5.051153 GCTAACTGGAAAGATGCTACCTAC 58.949 45.833 0.00 0.00 0.00 3.18
648 954 3.942115 GGAGGTCACTTCTAATTTGGAGC 59.058 47.826 0.00 0.00 0.00 4.70
657 963 7.277981 TCACTTCTAATTTGGAGCGTTCTTATC 59.722 37.037 0.00 0.00 0.00 1.75
733 1043 1.619332 TGAGCTGCCATCAAATTTGCA 59.381 42.857 13.54 7.00 0.00 4.08
904 1218 2.027625 CACAACCTCCGCCGTCTTC 61.028 63.158 0.00 0.00 0.00 2.87
1007 1328 0.250234 CTTCTGGAGTCCATGCGGAA 59.750 55.000 13.56 11.56 45.20 4.30
1101 1450 2.108976 ATGCCGTTCGCCATCGAT 59.891 55.556 0.00 0.00 45.04 3.59
1116 1465 2.496817 GATGTCGCCGAGGAGCTT 59.503 61.111 0.00 0.00 0.00 3.74
1191 1544 0.613260 TGTCTATGCCCAAGCTCGTT 59.387 50.000 0.00 0.00 40.80 3.85
1308 1663 0.882042 ACTGCACTGAACAAGGCGAG 60.882 55.000 0.00 0.00 0.00 5.03
1544 1901 3.311110 GGACAGCCACGAGGACCA 61.311 66.667 1.86 0.00 36.89 4.02
1557 1914 2.187073 GGACCAGTCCGTCGTGTAT 58.813 57.895 0.05 0.00 40.36 2.29
1635 1992 2.541466 GGCCTGGTAGCTACTGGATAT 58.459 52.381 28.19 0.00 0.00 1.63
1922 2282 4.083862 GAGGACGGGGCTGGACAC 62.084 72.222 0.00 0.00 0.00 3.67
2359 2836 6.289064 AGTCACTTGGTTCTACTTTGTAAGG 58.711 40.000 0.00 0.00 0.00 2.69
2446 4544 7.351223 GCATGAGCATCTTTCTATTCAAGTAC 58.649 38.462 0.00 0.00 41.58 2.73
2523 4779 1.172812 ACTGCGGTTTTGAAGAGCCC 61.173 55.000 0.00 0.00 0.00 5.19
2669 4960 2.427320 CCATGGCATCGATCCGGT 59.573 61.111 0.00 0.00 0.00 5.28
2826 5181 0.040336 CCCGTCCATGACTCGTATCG 60.040 60.000 0.00 0.00 0.00 2.92
2832 5187 1.269102 CCATGACTCGTATCGGTCCAC 60.269 57.143 0.00 0.00 0.00 4.02
2907 5292 4.380655 GGTCCTGGTGTACGAGCATATATC 60.381 50.000 0.00 0.00 0.00 1.63
3058 5532 4.816984 TCGGCCTCGTCCTCCTCC 62.817 72.222 0.00 0.00 37.69 4.30
3060 5534 3.151022 GGCCTCGTCCTCCTCCTG 61.151 72.222 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.053145 GGACTACTCCATGTTCATTAGCTG 58.947 45.833 0.00 0.00 36.42 4.24
77 84 5.123027 GCTTGTTCTTAGAGCTGCTAATTGT 59.877 40.000 0.15 0.00 38.36 2.71
184 201 4.650734 TGCATTCCAGTGACATAAGTTGA 58.349 39.130 0.00 0.00 0.00 3.18
196 214 4.091549 ACCAGATTCAAATGCATTCCAGT 58.908 39.130 13.38 0.00 0.00 4.00
202 220 8.806146 ACTAAAACTAACCAGATTCAAATGCAT 58.194 29.630 0.00 0.00 0.00 3.96
228 246 5.825151 TGCAATCCATCACGGTATGAAATAA 59.175 36.000 1.18 0.00 41.93 1.40
345 382 6.015519 TCCAAACATGTTTTGCACTTAGCTAT 60.016 34.615 21.10 0.00 45.94 2.97
372 409 2.970974 GCGTGCCCACTCTTTGCTC 61.971 63.158 0.00 0.00 0.00 4.26
373 410 2.980233 GCGTGCCCACTCTTTGCT 60.980 61.111 0.00 0.00 0.00 3.91
374 411 1.305219 TATGCGTGCCCACTCTTTGC 61.305 55.000 0.00 0.00 0.00 3.68
386 423 5.277490 CCAGGTGACATCTAATTTATGCGTG 60.277 44.000 0.00 0.00 0.00 5.34
418 712 8.521170 TCTTCTCCTTTATCATCGTTCTTCTA 57.479 34.615 0.00 0.00 0.00 2.10
466 760 4.450080 TGTACTGTACTGTGACTCTGTACG 59.550 45.833 17.98 13.19 46.96 3.67
543 837 4.575885 TGGTCCTACTTGCACTATTTGAC 58.424 43.478 0.00 0.00 0.00 3.18
621 927 6.070767 TCCAAATTAGAAGTGACCTCCAGTAG 60.071 42.308 0.00 0.00 0.00 2.57
622 928 5.783360 TCCAAATTAGAAGTGACCTCCAGTA 59.217 40.000 0.00 0.00 0.00 2.74
623 929 4.597507 TCCAAATTAGAAGTGACCTCCAGT 59.402 41.667 0.00 0.00 0.00 4.00
624 930 5.165961 TCCAAATTAGAAGTGACCTCCAG 57.834 43.478 0.00 0.00 0.00 3.86
648 954 3.374058 AGAAACCATTGGCGATAAGAACG 59.626 43.478 1.54 0.00 0.00 3.95
657 963 0.811281 GGAGGAAGAAACCATTGGCG 59.189 55.000 1.54 0.00 0.00 5.69
783 1097 4.410400 GGCCAGGGGAACACGAGG 62.410 72.222 0.00 0.00 0.00 4.63
1101 1450 4.069232 CCAAGCTCCTCGGCGACA 62.069 66.667 4.99 0.00 37.29 4.35
1434 1789 1.211969 GCCTACAGCGAAGACGTCA 59.788 57.895 19.50 0.00 41.98 4.35
1544 1901 0.170561 GCTCACATACACGACGGACT 59.829 55.000 0.00 0.00 0.00 3.85
2257 2638 2.362077 ACTGCCTTGAAATGGTGTCAAC 59.638 45.455 0.00 0.00 32.80 3.18
2359 2836 8.297426 GCTGGTACTAATAAGCATAATTTTCCC 58.703 37.037 0.00 0.00 35.69 3.97
2446 4544 4.929808 AGAACATAAGCACTTAACCAGTCG 59.070 41.667 0.00 0.00 30.92 4.18
2523 4779 3.197766 TCAGTAACAGTTGCATAGGGGAG 59.802 47.826 4.03 0.00 0.00 4.30
2669 4960 3.319198 GTTGTCCTCGCCCCTCCA 61.319 66.667 0.00 0.00 0.00 3.86
2826 5181 4.368543 GTCGGACACGGGTGGACC 62.369 72.222 0.00 5.65 41.39 4.46
2857 5239 0.600255 CAAGTCGAAGTCGGGCTTGT 60.600 55.000 20.38 0.00 42.08 3.16
2907 5292 1.760192 CCTGGCCCTCTCTTCAATTG 58.240 55.000 0.00 0.00 0.00 2.32
3058 5532 2.099141 TTGGGATTCAGAACGAGCAG 57.901 50.000 0.00 0.00 0.00 4.24
3060 5534 1.672881 CCATTGGGATTCAGAACGAGC 59.327 52.381 0.00 0.00 35.59 5.03



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

AutoCloner maintained by Alex Coulton.