Multiple sequence alignment - TraesCS7A01G442100

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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 TraesCS7A01G442100 chr7A 100.000 3079 0 0 1 3079 636125850 636128928 0.000000e+00 5686.0
1 TraesCS7A01G442100 chr7A 89.409 1879 117 36 357 2177 635859649 635861503 0.000000e+00 2292.0
2 TraesCS7A01G442100 chr7A 89.203 1343 89 19 862 2183 636628882 636630189 0.000000e+00 1626.0
3 TraesCS7A01G442100 chr7A 97.661 898 18 3 2185 3079 28167955 28167058 0.000000e+00 1539.0
4 TraesCS7A01G442100 chr7A 96.993 898 23 4 2185 3079 7980706 7979810 0.000000e+00 1506.0
5 TraesCS7A01G442100 chr7A 96.771 898 20 5 2184 3079 731630098 731629208 0.000000e+00 1489.0
6 TraesCS7A01G442100 chr7A 96.322 870 26 4 2185 3049 8118705 8117837 0.000000e+00 1424.0
7 TraesCS7A01G442100 chr7A 89.935 308 26 2 3 309 635859125 635859428 2.880000e-105 392.0
8 TraesCS7A01G442100 chr7A 81.031 543 30 31 323 810 636628254 636628778 6.270000e-97 364.0
9 TraesCS7A01G442100 chr7A 83.566 286 27 15 34 303 636627921 636628202 1.830000e-62 250.0
10 TraesCS7A01G442100 chr7D 90.605 1916 111 23 309 2177 550462228 550464121 0.000000e+00 2477.0
11 TraesCS7A01G442100 chr7D 87.250 1851 105 37 371 2148 550552367 550554159 0.000000e+00 1989.0
12 TraesCS7A01G442100 chr7D 90.333 1231 82 17 959 2177 550800374 550801579 0.000000e+00 1580.0
13 TraesCS7A01G442100 chr7D 89.720 1177 62 16 309 1439 550642494 550643657 0.000000e+00 1448.0
14 TraesCS7A01G442100 chr7D 90.805 261 14 4 23 283 550461983 550462233 1.060000e-89 340.0
15 TraesCS7A01G442100 chr7D 82.952 393 26 20 18 383 550551973 550552351 1.780000e-82 316.0
16 TraesCS7A01G442100 chr7D 79.545 396 35 20 423 810 550799863 550800220 1.100000e-59 241.0
17 TraesCS7A01G442100 chr7D 100.000 40 0 0 809 848 550800239 550800278 1.180000e-09 75.0
18 TraesCS7A01G442100 chr7B 90.828 1341 86 16 862 2177 595007265 595008593 0.000000e+00 1760.0
19 TraesCS7A01G442100 chr7B 89.924 1320 102 10 867 2177 595080395 595081692 0.000000e+00 1672.0
20 TraesCS7A01G442100 chr7B 88.707 1346 87 29 862 2183 595307166 595308470 0.000000e+00 1583.0
21 TraesCS7A01G442100 chr7B 92.056 642 47 2 1533 2173 595172827 595173465 0.000000e+00 900.0
22 TraesCS7A01G442100 chr7B 80.922 1237 91 57 104 1225 595165524 595166730 0.000000e+00 843.0
23 TraesCS7A01G442100 chr7B 88.258 528 31 12 308 810 595006640 595007161 1.220000e-168 603.0
24 TraesCS7A01G442100 chr7B 77.518 854 71 67 31 810 595306042 595306848 4.780000e-108 401.0
25 TraesCS7A01G442100 chr7B 85.393 356 17 15 477 810 595079931 595080273 1.370000e-88 337.0
26 TraesCS7A01G442100 chr7B 88.293 205 12 5 1333 1537 595166770 595166962 5.130000e-58 235.0
27 TraesCS7A01G442100 chr7B 100.000 41 0 0 808 848 595306866 595306906 3.290000e-10 76.8
28 TraesCS7A01G442100 chr3A 97.996 898 14 4 2185 3079 24597563 24596667 0.000000e+00 1555.0
29 TraesCS7A01G442100 chr6A 97.143 910 20 5 2175 3079 573034825 573033917 0.000000e+00 1531.0
30 TraesCS7A01G442100 chr1A 97.213 897 19 4 2185 3079 536940878 536941770 0.000000e+00 1513.0
31 TraesCS7A01G442100 chr5A 96.329 899 22 6 2185 3079 622363016 622362125 0.000000e+00 1467.0
32 TraesCS7A01G442100 chr2A 96.042 859 32 2 2223 3079 94419538 94420396 0.000000e+00 1397.0
33 TraesCS7A01G442100 chr2A 100.000 31 0 0 2184 2214 94419517 94419547 1.190000e-04 58.4
34 TraesCS7A01G442100 chr4D 80.792 1010 131 35 1122 2105 7874005 7873033 0.000000e+00 732.0
35 TraesCS7A01G442100 chr4D 91.111 45 3 1 1055 1098 7874054 7874010 3.320000e-05 60.2
36 TraesCS7A01G442100 chr3D 79.757 1072 120 44 1044 2102 551346276 551345289 0.000000e+00 688.0
37 TraesCS7A01G442100 chr3D 82.147 801 96 27 1305 2093 551430560 551431325 0.000000e+00 643.0
38 TraesCS7A01G442100 chr3D 84.694 98 6 3 1028 1125 551430331 551430419 4.230000e-14 89.8
39 TraesCS7A01G442100 chr3D 80.435 92 3 7 767 845 551346678 551346589 4.290000e-04 56.5
40 TraesCS7A01G442100 chr3D 80.000 95 4 7 764 845 551429979 551430071 4.290000e-04 56.5
41 TraesCS7A01G442100 chr4B 78.623 1104 142 58 1057 2106 14054665 14055728 0.000000e+00 645.0


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 TraesCS7A01G442100 chr7A 636125850 636128928 3078 False 5686.000000 5686 100.000000 1 3079 1 chr7A.!!$F1 3078
1 TraesCS7A01G442100 chr7A 28167058 28167955 897 True 1539.000000 1539 97.661000 2185 3079 1 chr7A.!!$R3 894
2 TraesCS7A01G442100 chr7A 7979810 7980706 896 True 1506.000000 1506 96.993000 2185 3079 1 chr7A.!!$R1 894
3 TraesCS7A01G442100 chr7A 731629208 731630098 890 True 1489.000000 1489 96.771000 2184 3079 1 chr7A.!!$R4 895
4 TraesCS7A01G442100 chr7A 8117837 8118705 868 True 1424.000000 1424 96.322000 2185 3049 1 chr7A.!!$R2 864
5 TraesCS7A01G442100 chr7A 635859125 635861503 2378 False 1342.000000 2292 89.672000 3 2177 2 chr7A.!!$F2 2174
6 TraesCS7A01G442100 chr7A 636627921 636630189 2268 False 746.666667 1626 84.600000 34 2183 3 chr7A.!!$F3 2149
7 TraesCS7A01G442100 chr7D 550642494 550643657 1163 False 1448.000000 1448 89.720000 309 1439 1 chr7D.!!$F1 1130
8 TraesCS7A01G442100 chr7D 550461983 550464121 2138 False 1408.500000 2477 90.705000 23 2177 2 chr7D.!!$F2 2154
9 TraesCS7A01G442100 chr7D 550551973 550554159 2186 False 1152.500000 1989 85.101000 18 2148 2 chr7D.!!$F3 2130
10 TraesCS7A01G442100 chr7D 550799863 550801579 1716 False 632.000000 1580 89.959333 423 2177 3 chr7D.!!$F4 1754
11 TraesCS7A01G442100 chr7B 595006640 595008593 1953 False 1181.500000 1760 89.543000 308 2177 2 chr7B.!!$F2 1869
12 TraesCS7A01G442100 chr7B 595079931 595081692 1761 False 1004.500000 1672 87.658500 477 2177 2 chr7B.!!$F3 1700
13 TraesCS7A01G442100 chr7B 595172827 595173465 638 False 900.000000 900 92.056000 1533 2173 1 chr7B.!!$F1 640
14 TraesCS7A01G442100 chr7B 595306042 595308470 2428 False 686.933333 1583 88.741667 31 2183 3 chr7B.!!$F5 2152
15 TraesCS7A01G442100 chr7B 595165524 595166962 1438 False 539.000000 843 84.607500 104 1537 2 chr7B.!!$F4 1433
16 TraesCS7A01G442100 chr3A 24596667 24597563 896 True 1555.000000 1555 97.996000 2185 3079 1 chr3A.!!$R1 894
17 TraesCS7A01G442100 chr6A 573033917 573034825 908 True 1531.000000 1531 97.143000 2175 3079 1 chr6A.!!$R1 904
18 TraesCS7A01G442100 chr1A 536940878 536941770 892 False 1513.000000 1513 97.213000 2185 3079 1 chr1A.!!$F1 894
19 TraesCS7A01G442100 chr5A 622362125 622363016 891 True 1467.000000 1467 96.329000 2185 3079 1 chr5A.!!$R1 894
20 TraesCS7A01G442100 chr2A 94419517 94420396 879 False 727.700000 1397 98.021000 2184 3079 2 chr2A.!!$F1 895
21 TraesCS7A01G442100 chr4D 7873033 7874054 1021 True 396.100000 732 85.951500 1055 2105 2 chr4D.!!$R1 1050
22 TraesCS7A01G442100 chr3D 551345289 551346678 1389 True 372.250000 688 80.096000 767 2102 2 chr3D.!!$R1 1335
23 TraesCS7A01G442100 chr3D 551429979 551431325 1346 False 263.100000 643 82.280333 764 2093 3 chr3D.!!$F1 1329
24 TraesCS7A01G442100 chr4B 14054665 14055728 1063 False 645.000000 645 78.623000 1057 2106 1 chr4B.!!$F1 1049

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
736 1100 0.375803 AATACAACGCGGCGAATTCC 59.624 50.0 30.94 0.0 0.0 3.01 F
916 1627 1.122019 ACCTCGTCTCTTTGCCACCT 61.122 55.0 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1564 2491 0.531532 GATGATGAGCCTCGTGTGGG 60.532 60.0 0.0 0.0 0.00 4.61 R
2400 3353 1.749334 GCCGAGCCCACTAGCTATGT 61.749 60.0 0.0 0.0 45.15 2.29 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
42 43 3.317711 TGGCACAACTGTGGTTCTATTTG 59.682 43.478 11.63 0.00 45.72 2.32
93 99 2.905959 TAAAAGACGATCGACGCTCA 57.094 45.000 24.34 1.51 46.94 4.26
95 101 2.279582 AAAGACGATCGACGCTCAAT 57.720 45.000 24.34 0.00 46.94 2.57
238 261 5.491070 TGAATGAATGGTCGATCTGTTCTT 58.509 37.500 13.12 6.49 0.00 2.52
251 274 8.879759 GTCGATCTGTTCTTACCAAATCAATTA 58.120 33.333 0.00 0.00 0.00 1.40
252 275 8.879759 TCGATCTGTTCTTACCAAATCAATTAC 58.120 33.333 0.00 0.00 0.00 1.89
287 311 7.616935 TCATTCATTCCCTTCTAATTTTGAGCT 59.383 33.333 0.00 0.00 0.00 4.09
289 313 5.888161 TCATTCCCTTCTAATTTTGAGCTCC 59.112 40.000 12.15 0.00 0.00 4.70
318 374 2.795470 GCCTCTACGCTTATTTTCCTCG 59.205 50.000 0.00 0.00 0.00 4.63
335 400 1.950216 CTCGACCATCTACAGCTAGCA 59.050 52.381 18.83 0.00 0.00 3.49
415 685 0.802222 GCAGATGCAGCGAACGTAGA 60.802 55.000 0.00 0.00 41.59 2.59
456 743 1.819632 CTTCCCCGAATTGCCCTCG 60.820 63.158 0.00 0.00 36.06 4.63
636 975 7.524065 GCCACAACATACTAACTTAAACGATT 58.476 34.615 0.00 0.00 0.00 3.34
736 1100 0.375803 AATACAACGCGGCGAATTCC 59.624 50.000 30.94 0.00 0.00 3.01
743 1107 1.584495 GCGGCGAATTCCTGGTTTT 59.416 52.632 12.98 0.00 0.00 2.43
916 1627 1.122019 ACCTCGTCTCTTTGCCACCT 61.122 55.000 0.00 0.00 0.00 4.00
1170 1985 2.106074 CCTTGTTATGGCGCTGCGA 61.106 57.895 28.07 5.97 0.00 5.10
1173 1988 1.713937 TTGTTATGGCGCTGCGATGG 61.714 55.000 28.07 0.00 0.00 3.51
1273 2124 1.372087 GAGTTCTTGGCGATGGCTGG 61.372 60.000 0.00 0.00 39.81 4.85
1333 2187 4.205587 GCTCAGGAAATGATCACCAAGAT 58.794 43.478 0.00 0.00 37.28 2.40
1525 2452 1.470098 GCTTTTGTCGATGATGCAGGT 59.530 47.619 0.00 0.00 0.00 4.00
1531 2458 2.483877 TGTCGATGATGCAGGTGAAAAC 59.516 45.455 0.00 0.00 0.00 2.43
1547 2474 4.621886 GTGAAAACGATGTGGACTACTCTC 59.378 45.833 0.00 0.00 0.00 3.20
1581 2508 1.888436 GACCCACACGAGGCTCATCA 61.888 60.000 15.95 0.00 0.00 3.07
1826 2762 3.827898 GGCGACGGTCAGGAGGAG 61.828 72.222 9.10 0.00 0.00 3.69
1832 2768 2.680352 GGTCAGGAGGAGGACGCA 60.680 66.667 0.00 0.00 34.87 5.24
1868 2804 2.666098 GGAGAACCAGGCGCCCTTA 61.666 63.158 26.15 0.00 35.97 2.69
1883 2828 1.300233 CTTATGCGCGGAGGAGGAC 60.300 63.158 8.83 0.00 0.00 3.85
2116 3064 2.969443 AGAGTCGGCATTTTGTTTCG 57.031 45.000 0.00 0.00 0.00 3.46
2400 3353 1.734137 GCATAGAGAAGGCCGTCGA 59.266 57.895 13.29 3.31 0.00 4.20
2408 3361 0.666913 GAAGGCCGTCGACATAGCTA 59.333 55.000 17.16 0.00 0.00 3.32
2415 3368 1.033574 GTCGACATAGCTAGTGGGCT 58.966 55.000 11.55 0.00 45.29 5.19
3019 3985 2.421314 CTCATACATGCGGGGCGA 59.579 61.111 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.146342 CAGATAATCATGTCGGTGCCC 58.854 52.381 0.00 0.00 0.00 5.36
238 261 7.774134 TGAGCTAGTACGTAATTGATTTGGTA 58.226 34.615 8.61 0.00 0.00 3.25
251 274 3.961408 AGGGAATGAATGAGCTAGTACGT 59.039 43.478 0.00 0.00 0.00 3.57
252 275 4.592485 AGGGAATGAATGAGCTAGTACG 57.408 45.455 0.00 0.00 0.00 3.67
287 311 1.109920 GCGTAGAGGCAGAGATGGGA 61.110 60.000 0.00 0.00 0.00 4.37
289 313 0.749649 AAGCGTAGAGGCAGAGATGG 59.250 55.000 0.00 0.00 34.64 3.51
318 374 2.478831 GCTTGCTAGCTGTAGATGGTC 58.521 52.381 17.23 0.00 44.27 4.02
347 412 9.750125 TTAATGTGCTGAGATATATATTAGGCG 57.250 33.333 0.00 0.00 0.00 5.52
378 605 2.416202 CTGCATGCAGAATCAACGTACA 59.584 45.455 38.90 2.94 46.30 2.90
415 685 1.069500 GGAAACTGCATGCGTTACGTT 60.069 47.619 22.06 13.34 0.00 3.99
456 743 1.723003 CGTACAAAGCCGTGGTTACTC 59.277 52.381 0.00 0.00 0.00 2.59
636 975 1.421268 CCAAGGCTGGCCATATACTGA 59.579 52.381 5.51 0.00 35.39 3.41
736 1100 7.450323 TCTCCCTAAATTTGGAGTAAAAACCAG 59.550 37.037 19.04 0.00 46.76 4.00
743 1107 6.729100 TCACTCTCTCCCTAAATTTGGAGTAA 59.271 38.462 19.04 10.76 46.76 2.24
765 1130 6.530181 CCTTTTATTTATGGCTTCCGTTTCAC 59.470 38.462 0.00 0.00 0.00 3.18
904 1615 2.629656 CGGGCAAGGTGGCAAAGAG 61.630 63.158 4.09 0.00 45.76 2.85
1039 1822 2.516930 CGGAGGCCATGGCGATTT 60.517 61.111 29.90 15.43 43.06 2.17
1237 2088 0.591659 CTCCGAATACTGATCCGCGA 59.408 55.000 8.23 0.00 0.00 5.87
1273 2124 1.407989 CCTTCTTCACCAGATCAGCCC 60.408 57.143 0.00 0.00 0.00 5.19
1525 2452 4.615223 CGAGAGTAGTCCACATCGTTTTCA 60.615 45.833 0.00 0.00 35.23 2.69
1531 2458 0.316278 CGCGAGAGTAGTCCACATCG 60.316 60.000 0.00 3.29 39.98 3.84
1564 2491 0.531532 GATGATGAGCCTCGTGTGGG 60.532 60.000 0.00 0.00 0.00 4.61
1581 2508 3.148279 GGCCTCCACGGTCGAGAT 61.148 66.667 4.22 0.00 34.25 2.75
1622 2549 1.676529 CGCTCAATCTCCTCGTCCTTA 59.323 52.381 0.00 0.00 0.00 2.69
1804 2731 4.124351 CCTGACCGTCGCCGCTTA 62.124 66.667 0.00 0.00 0.00 3.09
1826 2762 2.807045 CAGCACGACTCTGCGTCC 60.807 66.667 0.00 0.00 43.59 4.79
1832 2768 3.699894 CCCCAGCAGCACGACTCT 61.700 66.667 0.00 0.00 0.00 3.24
2116 3064 6.901265 AGTCGACTCTAGTAAGTTTCAGAAC 58.099 40.000 13.58 0.00 35.97 3.01
2177 3130 2.498885 GTTATTCTGGTAGTGACCCCGT 59.501 50.000 0.00 0.00 46.32 5.28
2178 3131 2.764572 AGTTATTCTGGTAGTGACCCCG 59.235 50.000 0.00 0.00 46.32 5.73
2400 3353 1.749334 GCCGAGCCCACTAGCTATGT 61.749 60.000 0.00 0.00 45.15 2.29
3019 3985 3.614092 CTCTTTAGACATGGCACCACAT 58.386 45.455 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.