Multiple sequence alignment - TraesCS7A01G500500

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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 TraesCS7A01G500500 chr7A 100.000 2810 0 0 1 2810 690438204 690441013 0.000000e+00 5190.0
1 TraesCS7A01G500500 chr7A 90.667 900 77 4 1122 2018 690517887 690518782 0.000000e+00 1190.0
2 TraesCS7A01G500500 chr7A 90.694 677 49 6 401 1077 690517135 690517797 0.000000e+00 889.0
3 TraesCS7A01G500500 chr7A 89.720 642 50 4 2169 2810 690564706 690564081 0.000000e+00 806.0
4 TraesCS7A01G500500 chr7A 84.000 750 108 7 1127 1866 690425994 690426741 0.000000e+00 710.0
5 TraesCS7A01G500500 chr7A 83.261 693 86 18 388 1077 690195938 690195273 6.650000e-171 610.0
6 TraesCS7A01G500500 chr7A 82.845 682 114 3 1135 1816 690400412 690401090 2.390000e-170 608.0
7 TraesCS7A01G500500 chr7A 88.235 170 19 1 216 384 690196064 690195895 4.750000e-48 202.0
8 TraesCS7A01G500500 chr7A 82.979 188 30 2 214 399 690425078 690425265 4.810000e-38 169.0
9 TraesCS7A01G500500 chr7A 100.000 51 0 0 386 436 690438542 690438592 8.290000e-16 95.3
10 TraesCS7A01G500500 chr7A 100.000 51 0 0 339 389 690438589 690438639 8.290000e-16 95.3
11 TraesCS7A01G500500 chr7D 96.540 1734 57 1 1077 2810 597569664 597567934 0.000000e+00 2867.0
12 TraesCS7A01G500500 chr7D 90.805 957 73 4 1077 2031 597545852 597544909 0.000000e+00 1266.0
13 TraesCS7A01G500500 chr7D 90.919 936 69 4 1079 2012 597620379 597621300 0.000000e+00 1243.0
14 TraesCS7A01G500500 chr7D 98.415 694 10 1 385 1077 597570410 597569717 0.000000e+00 1219.0
15 TraesCS7A01G500500 chr7D 92.185 691 45 5 385 1074 597619639 597620321 0.000000e+00 968.0
16 TraesCS7A01G500500 chr7D 91.728 677 48 4 401 1077 597546573 597545905 0.000000e+00 933.0
17 TraesCS7A01G500500 chr7D 96.345 383 12 2 9 389 597570740 597570358 1.840000e-176 628.0
18 TraesCS7A01G500500 chr7D 92.638 163 9 2 228 389 597619531 597619691 6.050000e-57 231.0
19 TraesCS7A01G500500 chr7D 79.897 194 28 9 214 399 597580623 597580433 6.320000e-27 132.0
20 TraesCS7A01G500500 chr7D 92.000 50 4 0 166 215 597623227 597623178 1.400000e-08 71.3
21 TraesCS7A01G500500 chr7B 90.090 999 81 7 1077 2070 676534371 676533386 0.000000e+00 1280.0
22 TraesCS7A01G500500 chr7B 89.710 1001 82 8 1077 2069 676861767 676860780 0.000000e+00 1258.0
23 TraesCS7A01G500500 chr7B 90.879 910 72 5 1077 1986 676993892 676994790 0.000000e+00 1210.0
24 TraesCS7A01G500500 chr7B 80.196 1530 243 44 385 1866 676452153 676453670 0.000000e+00 1092.0
25 TraesCS7A01G500500 chr7B 92.219 694 43 6 389 1077 676535111 676534424 0.000000e+00 972.0
26 TraesCS7A01G500500 chr7B 92.541 429 24 4 649 1077 676993419 676993839 2.390000e-170 608.0
27 TraesCS7A01G500500 chr7B 82.590 695 104 12 387 1077 676217142 676216461 5.180000e-167 597.0
28 TraesCS7A01G500500 chr7B 82.184 696 105 13 387 1077 676211189 676210508 5.220000e-162 580.0
29 TraesCS7A01G500500 chr7B 92.787 305 20 2 72 374 676987946 676988250 9.240000e-120 440.0
30 TraesCS7A01G500500 chr7B 88.839 224 21 2 434 653 676988247 676988470 3.570000e-69 272.0
31 TraesCS7A01G500500 chr7B 91.573 178 11 2 1894 2069 676863527 676863352 2.800000e-60 243.0
32 TraesCS7A01G500500 chr7B 89.535 172 17 1 214 384 676211316 676211145 1.700000e-52 217.0
33 TraesCS7A01G500500 chr7B 89.535 172 17 1 214 384 676217269 676217098 1.700000e-52 217.0
34 TraesCS7A01G500500 chr7B 97.368 38 0 1 385 421 676988213 676988250 2.340000e-06 63.9
35 TraesCS7A01G500500 chr7B 100.000 32 0 0 406 437 676862277 676862246 3.020000e-05 60.2
36 TraesCS7A01G500500 chr6D 79.263 434 64 14 2130 2554 199634656 199634240 2.130000e-71 279.0
37 TraesCS7A01G500500 chr6D 75.652 345 66 13 2245 2579 109278954 109278618 3.750000e-34 156.0
38 TraesCS7A01G500500 chr6D 87.755 49 4 2 2338 2385 171375572 171375525 3.910000e-04 56.5
39 TraesCS7A01G500500 chr6A 77.825 469 73 19 2130 2587 252828665 252828217 7.720000e-66 261.0
40 TraesCS7A01G500500 chr3D 77.556 401 65 14 2156 2542 541389870 541390259 4.710000e-53 219.0
41 TraesCS7A01G500500 chr6B 77.838 370 57 14 2130 2491 321275611 321275259 3.670000e-49 206.0
42 TraesCS7A01G500500 chr6B 76.489 319 59 11 2245 2553 198451597 198451285 2.900000e-35 159.0
43 TraesCS7A01G500500 chr2A 100.000 28 0 0 6 33 744544639 744544612 5.000000e-03 52.8


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 TraesCS7A01G500500 chr7A 690438204 690441013 2809 False 1793.533333 5190 100.0000 1 2810 3 chr7A.!!$F3 2809
1 TraesCS7A01G500500 chr7A 690517135 690518782 1647 False 1039.500000 1190 90.6805 401 2018 2 chr7A.!!$F4 1617
2 TraesCS7A01G500500 chr7A 690564081 690564706 625 True 806.000000 806 89.7200 2169 2810 1 chr7A.!!$R1 641
3 TraesCS7A01G500500 chr7A 690400412 690401090 678 False 608.000000 608 82.8450 1135 1816 1 chr7A.!!$F1 681
4 TraesCS7A01G500500 chr7A 690425078 690426741 1663 False 439.500000 710 83.4895 214 1866 2 chr7A.!!$F2 1652
5 TraesCS7A01G500500 chr7A 690195273 690196064 791 True 406.000000 610 85.7480 216 1077 2 chr7A.!!$R2 861
6 TraesCS7A01G500500 chr7D 597567934 597570740 2806 True 1571.333333 2867 97.1000 9 2810 3 chr7D.!!$R4 2801
7 TraesCS7A01G500500 chr7D 597544909 597546573 1664 True 1099.500000 1266 91.2665 401 2031 2 chr7D.!!$R3 1630
8 TraesCS7A01G500500 chr7D 597619531 597621300 1769 False 814.000000 1243 91.9140 228 2012 3 chr7D.!!$F1 1784
9 TraesCS7A01G500500 chr7B 676533386 676535111 1725 True 1126.000000 1280 91.1545 389 2070 2 chr7B.!!$R3 1681
10 TraesCS7A01G500500 chr7B 676452153 676453670 1517 False 1092.000000 1092 80.1960 385 1866 1 chr7B.!!$F1 1481
11 TraesCS7A01G500500 chr7B 676993419 676994790 1371 False 909.000000 1210 91.7100 649 1986 2 chr7B.!!$F3 1337
12 TraesCS7A01G500500 chr7B 676860780 676863527 2747 True 520.400000 1258 93.7610 406 2069 3 chr7B.!!$R4 1663
13 TraesCS7A01G500500 chr7B 676216461 676217269 808 True 407.000000 597 86.0625 214 1077 2 chr7B.!!$R2 863
14 TraesCS7A01G500500 chr7B 676210508 676211316 808 True 398.500000 580 85.8595 214 1077 2 chr7B.!!$R1 863
15 TraesCS7A01G500500 chr7B 676987946 676988470 524 False 258.633333 440 92.9980 72 653 3 chr7B.!!$F2 581

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
38 39 0.417035 TGGGCCTTTGGATCCCAATT 59.583 50.0 9.9 0.0 46.35 2.32 F
352 356 0.515564 ACACTTTGACCGCATAACGC 59.484 50.0 0.0 0.0 41.76 4.84 F
353 357 0.796312 CACTTTGACCGCATAACGCT 59.204 50.0 0.0 0.0 41.76 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 2387 1.288127 GTCCGTGGACGTGTAGCTT 59.712 57.895 2.78 0.0 37.74 3.74 R
1800 2780 1.488393 ACTGGATTCTCCTAGCAAGCC 59.512 52.381 0.00 0.0 37.46 4.35 R
2071 3061 5.859205 ACTCCTTTGATGCTTGAAACTTT 57.141 34.783 0.00 0.0 0.00 2.66 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
21 22 4.219264 AGAGAAAGAAGAAGGCAGATGG 57.781 45.455 0.00 0.00 0.00 3.51
38 39 0.417035 TGGGCCTTTGGATCCCAATT 59.583 50.000 9.90 0.00 46.35 2.32
340 344 8.484641 ACAGTCATCTTGATATACACACTTTG 57.515 34.615 0.00 0.00 0.00 2.77
341 345 8.314021 ACAGTCATCTTGATATACACACTTTGA 58.686 33.333 0.00 0.00 0.00 2.69
342 346 8.598924 CAGTCATCTTGATATACACACTTTGAC 58.401 37.037 0.00 0.00 0.00 3.18
343 347 7.766278 AGTCATCTTGATATACACACTTTGACC 59.234 37.037 0.00 0.00 31.36 4.02
344 348 6.756542 TCATCTTGATATACACACTTTGACCG 59.243 38.462 0.00 0.00 0.00 4.79
346 350 4.195225 TGATATACACACTTTGACCGCA 57.805 40.909 0.00 0.00 0.00 5.69
348 352 5.908341 TGATATACACACTTTGACCGCATA 58.092 37.500 0.00 0.00 0.00 3.14
350 354 4.939509 ATACACACTTTGACCGCATAAC 57.060 40.909 0.00 0.00 0.00 1.89
351 355 1.529438 ACACACTTTGACCGCATAACG 59.471 47.619 0.00 0.00 43.15 3.18
352 356 0.515564 ACACTTTGACCGCATAACGC 59.484 50.000 0.00 0.00 41.76 4.84
353 357 0.796312 CACTTTGACCGCATAACGCT 59.204 50.000 0.00 0.00 41.76 5.07
354 358 1.076332 ACTTTGACCGCATAACGCTC 58.924 50.000 0.00 0.00 41.76 5.03
355 359 1.337823 ACTTTGACCGCATAACGCTCT 60.338 47.619 0.00 0.00 41.76 4.09
358 362 2.882927 TGACCGCATAACGCTCTAAT 57.117 45.000 0.00 0.00 41.76 1.73
359 363 3.994204 TGACCGCATAACGCTCTAATA 57.006 42.857 0.00 0.00 41.76 0.98
365 369 7.062956 TGACCGCATAACGCTCTAATATAAATG 59.937 37.037 0.00 0.00 41.76 2.32
366 370 6.312918 ACCGCATAACGCTCTAATATAAATGG 59.687 38.462 0.00 0.00 41.76 3.16
367 371 6.238103 CCGCATAACGCTCTAATATAAATGGG 60.238 42.308 0.00 0.00 41.76 4.00
368 372 6.238103 CGCATAACGCTCTAATATAAATGGGG 60.238 42.308 0.00 0.00 39.08 4.96
369 373 6.821665 GCATAACGCTCTAATATAAATGGGGA 59.178 38.462 0.00 0.00 37.77 4.81
371 375 8.830580 CATAACGCTCTAATATAAATGGGGATG 58.169 37.037 0.00 0.00 0.00 3.51
372 376 6.620877 ACGCTCTAATATAAATGGGGATGA 57.379 37.500 0.00 0.00 0.00 2.92
373 377 7.016153 ACGCTCTAATATAAATGGGGATGAA 57.984 36.000 0.00 0.00 0.00 2.57
374 378 7.106239 ACGCTCTAATATAAATGGGGATGAAG 58.894 38.462 0.00 0.00 0.00 3.02
375 379 6.540189 CGCTCTAATATAAATGGGGATGAAGG 59.460 42.308 0.00 0.00 0.00 3.46
376 380 6.830838 GCTCTAATATAAATGGGGATGAAGGG 59.169 42.308 0.00 0.00 0.00 3.95
377 381 7.311929 GCTCTAATATAAATGGGGATGAAGGGA 60.312 40.741 0.00 0.00 0.00 4.20
379 383 8.390921 TCTAATATAAATGGGGATGAAGGGAAC 58.609 37.037 0.00 0.00 0.00 3.62
490 1353 7.597288 TCTATTTGTAACCAGATAGCTAGCA 57.403 36.000 18.83 3.19 36.30 3.49
519 1386 1.075601 TCCCCTGTTCAGCCAGATTT 58.924 50.000 0.00 0.00 34.23 2.17
532 1399 3.788142 AGCCAGATTTCTAAGATGGGGAA 59.212 43.478 0.00 0.00 0.00 3.97
992 1893 1.993369 GCTATTGCGCTCAACCCCAC 61.993 60.000 9.73 0.00 34.60 4.61
1152 2116 7.703328 TGTGTTCTTGGTCAACTTATTCTTTC 58.297 34.615 0.00 0.00 0.00 2.62
1515 2489 4.464008 TGAAACAAGAGATCACCAAGCTT 58.536 39.130 0.00 0.00 0.00 3.74
1538 2512 4.003788 ACAGAACCCCGGCGTGAG 62.004 66.667 6.01 0.00 0.00 3.51
1800 2780 1.811266 CGACATCCCGTTGCTCCAG 60.811 63.158 0.00 0.00 0.00 3.86
1974 2959 4.441792 GAAAAGTGCAACAGTGGGAAAAT 58.558 39.130 0.00 0.00 41.43 1.82
2292 3282 7.834881 ATGATTATAAACTAGTCCCGAGTCA 57.165 36.000 0.00 0.00 0.00 3.41
2374 3364 0.110295 TCACAAGTCATGGTGGTGGG 59.890 55.000 0.00 0.00 35.74 4.61
2381 3371 0.844221 TCATGGTGGTGGGGATGTCA 60.844 55.000 0.00 0.00 0.00 3.58
2442 3432 3.391296 ACAGACCCAACTTGACACATAGT 59.609 43.478 0.00 0.00 0.00 2.12
2555 3545 1.579429 GGGTTGCCAAACGCTACTG 59.421 57.895 0.00 0.00 43.86 2.74
2557 3547 1.515521 GGTTGCCAAACGCTACTGCT 61.516 55.000 0.00 0.00 42.16 4.24
2563 3553 2.418628 GCCAAACGCTACTGCTTTATCA 59.581 45.455 0.00 0.00 36.97 2.15
2580 3570 9.474313 TGCTTTATCAGATGGTTATAAAGGTTT 57.526 29.630 13.16 0.00 40.84 3.27
2618 3608 2.043992 ACAACCACAGTGTAGCTACCA 58.956 47.619 21.01 6.67 0.00 3.25
2732 3722 1.153229 GTATCCACCTCAACCCCGC 60.153 63.158 0.00 0.00 0.00 6.13
2762 3752 3.071479 CAACTACGGCCATGTTACACTT 58.929 45.455 2.24 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.277715 CCCATCTGCCTTCTTCTTTCTC 58.722 50.000 0.00 0.00 0.00 2.87
2 3 2.620108 GCCCATCTGCCTTCTTCTTTCT 60.620 50.000 0.00 0.00 0.00 2.52
4 5 1.844687 GCCCATCTGCCTTCTTCTTT 58.155 50.000 0.00 0.00 0.00 2.52
38 39 0.892755 AATTCGCACTCCACCGTCTA 59.107 50.000 0.00 0.00 0.00 2.59
148 151 6.823689 TGAAAGATAAGACTGGGTTTCTATGC 59.176 38.462 0.00 0.00 0.00 3.14
344 348 6.821665 TCCCCATTTATATTAGAGCGTTATGC 59.178 38.462 0.00 0.00 46.98 3.14
346 350 8.768397 TCATCCCCATTTATATTAGAGCGTTAT 58.232 33.333 0.00 0.00 0.00 1.89
348 352 7.016153 TCATCCCCATTTATATTAGAGCGTT 57.984 36.000 0.00 0.00 0.00 4.84
350 354 6.540189 CCTTCATCCCCATTTATATTAGAGCG 59.460 42.308 0.00 0.00 0.00 5.03
351 355 6.830838 CCCTTCATCCCCATTTATATTAGAGC 59.169 42.308 0.00 0.00 0.00 4.09
352 356 8.162848 TCCCTTCATCCCCATTTATATTAGAG 57.837 38.462 0.00 0.00 0.00 2.43
353 357 8.390921 GTTCCCTTCATCCCCATTTATATTAGA 58.609 37.037 0.00 0.00 0.00 2.10
354 358 7.615757 GGTTCCCTTCATCCCCATTTATATTAG 59.384 40.741 0.00 0.00 0.00 1.73
355 359 7.475299 GGTTCCCTTCATCCCCATTTATATTA 58.525 38.462 0.00 0.00 0.00 0.98
358 362 4.107311 GGGTTCCCTTCATCCCCATTTATA 59.893 45.833 0.00 0.00 35.32 0.98
359 363 3.116746 GGGTTCCCTTCATCCCCATTTAT 60.117 47.826 0.00 0.00 35.32 1.40
365 369 0.186143 GATGGGTTCCCTTCATCCCC 59.814 60.000 15.90 0.00 39.20 4.81
366 370 1.226311 AGATGGGTTCCCTTCATCCC 58.774 55.000 20.78 0.00 38.33 3.85
367 371 2.242196 TCAAGATGGGTTCCCTTCATCC 59.758 50.000 20.78 0.81 38.33 3.51
368 372 3.282885 GTCAAGATGGGTTCCCTTCATC 58.717 50.000 20.78 11.10 37.97 2.92
369 373 2.024941 GGTCAAGATGGGTTCCCTTCAT 60.025 50.000 20.78 10.13 34.06 2.57
371 375 1.679032 CGGTCAAGATGGGTTCCCTTC 60.679 57.143 13.76 13.76 0.00 3.46
372 376 0.328258 CGGTCAAGATGGGTTCCCTT 59.672 55.000 9.43 2.60 0.00 3.95
373 377 1.991230 CGGTCAAGATGGGTTCCCT 59.009 57.895 9.43 0.00 0.00 4.20
374 378 1.749258 GCGGTCAAGATGGGTTCCC 60.749 63.158 0.12 0.12 0.00 3.97
375 379 0.394352 ATGCGGTCAAGATGGGTTCC 60.394 55.000 0.00 0.00 0.00 3.62
376 380 2.325583 TATGCGGTCAAGATGGGTTC 57.674 50.000 0.00 0.00 0.00 3.62
377 381 2.365582 GTTATGCGGTCAAGATGGGTT 58.634 47.619 0.00 0.00 0.00 4.11
379 383 0.937304 CGTTATGCGGTCAAGATGGG 59.063 55.000 0.00 0.00 36.85 4.00
380 384 0.304705 GCGTTATGCGGTCAAGATGG 59.695 55.000 0.00 0.00 41.69 3.51
381 385 3.806257 GCGTTATGCGGTCAAGATG 57.194 52.632 0.00 0.00 41.69 2.90
490 1353 1.196012 GAACAGGGGAAGAGACGGAT 58.804 55.000 0.00 0.00 0.00 4.18
519 1386 3.388024 CGACTGGAATTCCCCATCTTAGA 59.612 47.826 21.90 0.00 35.33 2.10
532 1399 1.078848 GAGCTGTGGCGACTGGAAT 60.079 57.895 7.79 0.00 44.37 3.01
992 1893 5.227908 AGTTGTACCTTGACATGAAGTACG 58.772 41.667 0.00 0.00 0.00 3.67
1242 2213 2.927477 GTGCGTATGATCGAAGAACCAA 59.073 45.455 0.00 0.00 43.58 3.67
1413 2387 1.288127 GTCCGTGGACGTGTAGCTT 59.712 57.895 2.78 0.00 37.74 3.74
1515 2489 1.675219 GCCGGGGTTCTGTGACTTA 59.325 57.895 2.18 0.00 0.00 2.24
1538 2512 4.152045 CGTAGTAGTCACCGTAGATGATCC 59.848 50.000 0.00 0.00 0.00 3.36
1551 2525 1.913778 TGAAGGCACCGTAGTAGTCA 58.086 50.000 0.00 0.00 0.00 3.41
1653 2627 3.610619 CTGGTCGCACAGATGGCCA 62.611 63.158 8.56 8.56 40.97 5.36
1800 2780 1.488393 ACTGGATTCTCCTAGCAAGCC 59.512 52.381 0.00 0.00 37.46 4.35
2071 3061 5.859205 ACTCCTTTGATGCTTGAAACTTT 57.141 34.783 0.00 0.00 0.00 2.66
2360 3350 0.846427 ACATCCCCACCACCATGACT 60.846 55.000 0.00 0.00 0.00 3.41
2374 3364 6.449635 TGCCACATTATTAGTTTGACATCC 57.550 37.500 0.00 0.00 0.00 3.51
2381 3371 7.613801 TCCTAACACATGCCACATTATTAGTTT 59.386 33.333 0.00 0.00 0.00 2.66
2555 3545 9.952188 GAAACCTTTATAACCATCTGATAAAGC 57.048 33.333 7.71 0.00 39.91 3.51
2580 3570 4.547532 GTTGTTCGAGCTGAGTAAGAAGA 58.452 43.478 0.00 0.00 0.00 2.87
2618 3608 6.268847 GGATCTTCTATGTTGGATGGTACTCT 59.731 42.308 0.00 0.00 0.00 3.24
2732 3722 0.741221 GGCCGTAGTTGCTCCTTCTG 60.741 60.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.