Multiple sequence alignment - TraesCS2D01G454100

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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 TraesCS2D01G454100 chr2D 100.000 2291 0 0 1 2291 562753102 562755392 0.000000e+00 4231.0
1 TraesCS2D01G454100 chr2D 86.329 907 61 24 728 1585 562684738 562685630 0.000000e+00 929.0
2 TraesCS2D01G454100 chr2D 90.468 598 46 9 879 1467 562807791 562808386 0.000000e+00 778.0
3 TraesCS2D01G454100 chr2D 86.404 684 54 16 721 1374 562845084 562845758 0.000000e+00 712.0
4 TraesCS2D01G454100 chr2D 89.564 527 44 6 853 1368 562839519 562840045 0.000000e+00 658.0
5 TraesCS2D01G454100 chr2D 89.764 508 44 6 1790 2291 562687301 562687806 0.000000e+00 643.0
6 TraesCS2D01G454100 chr2D 91.031 446 36 2 929 1373 562735043 562735485 1.170000e-167 599.0
7 TraesCS2D01G454100 chr2D 92.042 377 30 0 997 1373 562785599 562785975 4.330000e-147 531.0
8 TraesCS2D01G454100 chr2D 81.783 516 81 9 789 1296 562850609 562851119 9.790000e-114 420.0
9 TraesCS2D01G454100 chr2D 85.792 366 35 8 7 358 562784555 562784917 2.780000e-99 372.0
10 TraesCS2D01G454100 chr2D 85.237 359 21 17 91 433 562804458 562804800 7.840000e-90 340.0
11 TraesCS2D01G454100 chr2D 93.627 204 10 3 1589 1792 562685754 562685954 3.700000e-78 302.0
12 TraesCS2D01G454100 chr2D 85.377 212 11 6 593 785 562734778 562734988 3.860000e-48 202.0
13 TraesCS2D01G454100 chr2D 82.008 239 31 6 1593 1823 562588642 562588876 2.320000e-45 193.0
14 TraesCS2D01G454100 chr2D 93.077 130 8 1 588 716 562785222 562785351 3.000000e-44 189.0
15 TraesCS2D01G454100 chr2D 87.500 136 17 0 7 142 562844378 562844513 8.470000e-35 158.0
16 TraesCS2D01G454100 chr2D 97.500 80 2 0 637 716 562807540 562807619 1.100000e-28 137.0
17 TraesCS2D01G454100 chr2D 87.879 66 2 1 721 780 562807657 562807722 3.160000e-09 73.1
18 TraesCS2D01G454100 chr2D 95.349 43 0 2 352 393 562844643 562844684 1.470000e-07 67.6
19 TraesCS2D01G454100 chr2B 85.343 1617 131 45 481 2012 673050382 673051977 0.000000e+00 1576.0
20 TraesCS2D01G454100 chr2B 85.250 800 65 31 728 1489 672646293 672647077 0.000000e+00 774.0
21 TraesCS2D01G454100 chr2B 85.556 720 65 21 798 1489 672797150 672796442 0.000000e+00 717.0
22 TraesCS2D01G454100 chr2B 86.929 482 31 13 825 1296 672776308 672775849 1.570000e-141 512.0
23 TraesCS2D01G454100 chr2B 81.520 671 81 28 789 1426 673003481 673004141 1.570000e-141 512.0
24 TraesCS2D01G454100 chr2B 82.420 529 54 17 789 1296 673170460 673170970 2.100000e-115 425.0
25 TraesCS2D01G454100 chr2B 92.933 283 17 2 2012 2291 673053359 673053641 2.120000e-110 409.0
26 TraesCS2D01G454100 chr2B 80.332 422 68 10 879 1290 673628550 673628966 2.860000e-79 305.0
27 TraesCS2D01G454100 chr2B 81.356 413 41 9 1 392 672645261 672645658 1.030000e-78 303.0
28 TraesCS2D01G454100 chr2B 79.747 474 44 20 1 454 672798193 672797752 1.720000e-76 296.0
29 TraesCS2D01G454100 chr2B 85.603 257 30 5 2030 2283 672670659 672670911 1.750000e-66 263.0
30 TraesCS2D01G454100 chr2B 86.486 222 23 5 1 215 673049813 673050034 1.060000e-58 237.0
31 TraesCS2D01G454100 chr2B 84.746 236 23 4 6 228 672626500 672626735 8.240000e-55 224.0
32 TraesCS2D01G454100 chr2B 85.345 232 12 4 588 798 672666812 672667042 1.070000e-53 220.0
33 TraesCS2D01G454100 chr2B 79.514 288 29 12 90 371 673001813 673002076 6.500000e-41 178.0
34 TraesCS2D01G454100 chr2B 87.097 155 18 1 2136 2290 672637081 672637233 8.410000e-40 174.0
35 TraesCS2D01G454100 chr2B 83.784 185 9 5 621 784 673092656 673092840 3.050000e-34 156.0
36 TraesCS2D01G454100 chr2B 85.496 131 16 3 1361 1490 672825432 672825304 1.430000e-27 134.0
37 TraesCS2D01G454100 chr2A 92.500 720 39 8 1585 2291 703208836 703209553 0.000000e+00 1016.0
38 TraesCS2D01G454100 chr2A 90.254 472 29 7 913 1373 703291153 703291618 3.260000e-168 601.0
39 TraesCS2D01G454100 chr2A 86.679 548 44 10 728 1260 703207356 703207889 4.240000e-162 580.0
40 TraesCS2D01G454100 chr2A 94.720 322 15 1 1969 2290 703284397 703284716 1.220000e-137 499.0
41 TraesCS2D01G454100 chr2A 87.678 422 32 9 40 441 703333389 703333810 7.410000e-130 473.0
42 TraesCS2D01G454100 chr2A 81.250 528 71 17 789 1296 703353582 703354101 3.550000e-108 401.0
43 TraesCS2D01G454100 chr2A 84.921 378 40 11 1341 1703 703283095 703283470 1.290000e-97 366.0
44 TraesCS2D01G454100 chr2A 92.188 256 15 4 1717 1968 703283746 703284000 7.780000e-95 357.0
45 TraesCS2D01G454100 chr2A 82.660 421 53 13 879 1295 703448113 703448517 2.800000e-94 355.0
46 TraesCS2D01G454100 chr2A 85.970 335 23 12 591 910 703337220 703337545 1.010000e-88 337.0
47 TraesCS2D01G454100 chr2A 86.061 330 14 11 1256 1585 703208508 703208805 2.190000e-85 326.0
48 TraesCS2D01G454100 chr2A 90.196 204 12 3 588 785 703290897 703291098 2.260000e-65 259.0
49 TraesCS2D01G454100 chr2A 91.329 173 11 2 588 758 703282088 703282258 1.370000e-57 233.0
50 TraesCS2D01G454100 chr2A 95.385 130 6 0 458 587 703333916 703334045 8.290000e-50 207.0
51 TraesCS2D01G454100 chr2A 80.672 238 19 12 6 232 703121885 703122106 2.360000e-35 159.0
52 TraesCS2D01G454100 chr2A 95.455 44 2 0 493 536 703349877 703349920 1.140000e-08 71.3


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 TraesCS2D01G454100 chr2D 562753102 562755392 2290 False 4231.000000 4231 100.000000 1 2291 1 chr2D.!!$F2 2290
1 TraesCS2D01G454100 chr2D 562839519 562840045 526 False 658.000000 658 89.564000 853 1368 1 chr2D.!!$F3 515
2 TraesCS2D01G454100 chr2D 562684738 562687806 3068 False 624.666667 929 89.906667 728 2291 3 chr2D.!!$F5 1563
3 TraesCS2D01G454100 chr2D 562850609 562851119 510 False 420.000000 420 81.783000 789 1296 1 chr2D.!!$F4 507
4 TraesCS2D01G454100 chr2D 562734778 562735485 707 False 400.500000 599 88.204000 593 1373 2 chr2D.!!$F6 780
5 TraesCS2D01G454100 chr2D 562784555 562785975 1420 False 364.000000 531 90.303667 7 1373 3 chr2D.!!$F7 1366
6 TraesCS2D01G454100 chr2D 562804458 562808386 3928 False 332.025000 778 90.271000 91 1467 4 chr2D.!!$F8 1376
7 TraesCS2D01G454100 chr2D 562844378 562845758 1380 False 312.533333 712 89.751000 7 1374 3 chr2D.!!$F9 1367
8 TraesCS2D01G454100 chr2B 673049813 673053641 3828 False 740.666667 1576 88.254000 1 2291 3 chr2B.!!$F9 2290
9 TraesCS2D01G454100 chr2B 672645261 672647077 1816 False 538.500000 774 83.303000 1 1489 2 chr2B.!!$F6 1488
10 TraesCS2D01G454100 chr2B 672796442 672798193 1751 True 506.500000 717 82.651500 1 1489 2 chr2B.!!$R3 1488
11 TraesCS2D01G454100 chr2B 673170460 673170970 510 False 425.000000 425 82.420000 789 1296 1 chr2B.!!$F4 507
12 TraesCS2D01G454100 chr2B 673001813 673004141 2328 False 345.000000 512 80.517000 90 1426 2 chr2B.!!$F8 1336
13 TraesCS2D01G454100 chr2B 672666812 672670911 4099 False 241.500000 263 85.474000 588 2283 2 chr2B.!!$F7 1695
14 TraesCS2D01G454100 chr2A 703207356 703209553 2197 False 640.666667 1016 88.413333 728 2291 3 chr2A.!!$F3 1563
15 TraesCS2D01G454100 chr2A 703290897 703291618 721 False 430.000000 601 90.225000 588 1373 2 chr2A.!!$F5 785
16 TraesCS2D01G454100 chr2A 703282088 703284716 2628 False 363.750000 499 90.789500 588 2290 4 chr2A.!!$F4 1702
17 TraesCS2D01G454100 chr2A 703333389 703337545 4156 False 339.000000 473 89.677667 40 910 3 chr2A.!!$F6 870
18 TraesCS2D01G454100 chr2A 703349877 703354101 4224 False 236.150000 401 88.352500 493 1296 2 chr2A.!!$F7 803

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
450 629 0.254462 TCACAAGTTGCTGGTGTGGA 59.746 50.0 1.81 0.0 42.35 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 14438 2.363038 GGTACCCAAAACCAAACAGGAC 59.637 50.0 0.0 0.0 41.22 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
23 24 1.204941 CGGAGGAAGATGTCGACCTTT 59.795 52.381 14.12 4.51 32.53 3.11
37 38 1.296056 ACCTTTTCCCGATGTTCGCG 61.296 55.000 0.00 0.00 38.82 5.87
71 74 2.354188 TCCGACGCGTCAGTGTTG 60.354 61.111 35.71 19.60 41.83 3.33
99 108 4.996122 TCGAGGAAGCCGTAAAAACAAATA 59.004 37.500 0.00 0.00 0.00 1.40
185 203 3.050275 GGACTGCGAGGTGCCAAC 61.050 66.667 0.00 0.00 45.60 3.77
247 292 2.203001 TGCCACGCCATGATACGG 60.203 61.111 0.00 0.00 0.00 4.02
289 334 0.321298 GCTAAACGAACCTGGCTGGA 60.321 55.000 18.12 0.00 39.71 3.86
331 380 6.779117 ACAGCTCAATGATCTCGTATTTTTG 58.221 36.000 0.00 0.00 0.00 2.44
361 410 5.006386 AGTATCCTTGAGCCTGAAGTTTTG 58.994 41.667 0.00 0.00 0.00 2.44
444 623 0.309922 CACTGCTCACAAGTTGCTGG 59.690 55.000 1.81 0.00 0.00 4.85
450 629 0.254462 TCACAAGTTGCTGGTGTGGA 59.746 50.000 1.81 0.00 42.35 4.02
452 656 1.095228 ACAAGTTGCTGGTGTGGACG 61.095 55.000 1.81 0.00 0.00 4.79
540 3342 4.290155 GCATTGGTGTCTATTATTTGCCG 58.710 43.478 0.00 0.00 0.00 5.69
719 10368 5.769662 AGCCTTCACAAAATATCACAAGACA 59.230 36.000 0.00 0.00 0.00 3.41
780 10477 0.319297 CCGTCGTTTTCCTCTCGGTT 60.319 55.000 0.00 0.00 34.38 4.44
785 10482 1.605712 CGTTTTCCTCTCGGTTGAGCT 60.606 52.381 0.00 0.00 42.26 4.09
856 12348 1.738099 CCTTTGCCGTCTCCGTCTG 60.738 63.158 0.00 0.00 0.00 3.51
940 12481 3.977244 CGCACCACCAACCAAGCC 61.977 66.667 0.00 0.00 0.00 4.35
961 12509 0.326264 ACCACCAAGCTAAGCTCTGG 59.674 55.000 0.00 0.00 38.25 3.86
1003 12581 1.965643 ACCTACACACACGTACCATGT 59.034 47.619 0.00 0.00 0.00 3.21
1007 12585 1.731613 ACACACGTACCATGTCGCG 60.732 57.895 0.00 0.00 0.00 5.87
1298 13511 2.434185 CGCAAGCTAACCGGCTGA 60.434 61.111 0.00 0.00 42.24 4.26
1349 13938 7.989741 ACAAGATCCGAATTCAGAAGAATACAT 59.010 33.333 6.22 0.00 43.52 2.29
1386 13975 0.658368 ATCATCGTCGTCTCCGTCTG 59.342 55.000 0.00 0.00 35.01 3.51
1437 14036 2.433446 CACCAGAGGCAGCTTGGT 59.567 61.111 0.95 0.95 0.00 3.67
1525 14161 2.252535 ATTAGGCTGCCCAAATGGTT 57.747 45.000 16.57 0.00 36.04 3.67
1628 14420 0.673644 TGCGCCCTCTCTTGTTTAGC 60.674 55.000 4.18 0.00 0.00 3.09
1646 14438 5.596836 TTAGCTTGCCTTTAATGATTGGG 57.403 39.130 0.00 0.00 0.00 4.12
1963 16381 9.774742 GTTTGTTCACTCATTTTGGTCTATATC 57.225 33.333 0.00 0.00 0.00 1.63
2090 19213 4.022329 CCCACATGGTGAACCTTAAGTTTC 60.022 45.833 5.84 5.84 39.40 2.78
2246 19371 1.136305 TGTCATTCCTAGGCTACACGC 59.864 52.381 2.96 0.00 38.13 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.545526 TCGGACGTAATCATCGGAGTAC 59.454 50.000 0.00 0.00 40.31 2.73
71 74 2.503920 TTACGGCTTCCTCGATTAGC 57.496 50.000 5.31 5.31 0.00 3.09
99 108 1.795768 TTTCTCGAGATTTGCGTGCT 58.204 45.000 17.44 0.00 0.00 4.40
185 203 0.110599 CGGATCGACTCGAGATTCCG 60.111 60.000 21.68 21.39 45.00 4.30
233 260 0.804544 ACGTTCCGTATCATGGCGTG 60.805 55.000 0.00 0.00 38.73 5.34
247 292 3.186047 CGGGGATCGTGCACGTTC 61.186 66.667 35.74 33.86 40.80 3.95
289 334 8.128322 TGAGCTGTTTAAGTAGAGAGAGATTT 57.872 34.615 0.00 0.00 0.00 2.17
361 410 1.153958 GCGGCCATTTGCAGTCTTC 60.154 57.895 2.24 0.00 43.89 2.87
444 623 0.946221 CCTTCAGCTGTCGTCCACAC 60.946 60.000 14.67 0.00 0.00 3.82
450 629 1.271102 GTCTTCTCCTTCAGCTGTCGT 59.729 52.381 14.67 0.00 0.00 4.34
452 656 1.899142 AGGTCTTCTCCTTCAGCTGTC 59.101 52.381 14.67 0.00 33.52 3.51
540 3342 1.557269 ATGAGACAGGTGCCCCAGAC 61.557 60.000 0.00 0.00 0.00 3.51
719 10368 3.494398 CGACCAGGTCCCGAATAATGAAT 60.494 47.826 14.46 0.00 0.00 2.57
856 12348 3.254060 CTCAGGTATATATGGTGCGTGC 58.746 50.000 0.00 0.00 0.00 5.34
940 12481 0.326264 AGAGCTTAGCTTGGTGGTGG 59.674 55.000 8.58 0.00 39.88 4.61
1223 12807 1.153107 TCCGTCTCCGCCGAGAATA 60.153 57.895 6.33 0.00 46.74 1.75
1264 13477 2.663196 GACGGACACCTTCCTGGG 59.337 66.667 0.00 0.00 43.25 4.45
1298 13511 3.482436 TCCATACAAAACTTTCAGCGGT 58.518 40.909 0.00 0.00 0.00 5.68
1349 13938 7.720442 ACGATGATTCTTCAGAATACAGATGA 58.280 34.615 1.90 0.00 44.14 2.92
1525 14161 3.133362 ACCGAGAACAAGTACACTTTCCA 59.867 43.478 0.00 0.00 33.11 3.53
1628 14420 4.026052 AGGACCCAATCATTAAAGGCAAG 58.974 43.478 0.00 0.00 0.00 4.01
1646 14438 2.363038 GGTACCCAAAACCAAACAGGAC 59.637 50.000 0.00 0.00 41.22 3.85
1912 16330 7.796660 ACAAATTAAAGCGTGCGTACATATATG 59.203 33.333 11.29 11.29 0.00 1.78
1919 16337 4.438471 ACAAACAAATTAAAGCGTGCGTAC 59.562 37.500 0.00 0.00 0.00 3.67
1922 16340 4.027295 TGAACAAACAAATTAAAGCGTGCG 60.027 37.500 0.00 0.00 0.00 5.34
2246 19371 5.153513 ACAAATCATCGTGAAAATGTTCGG 58.846 37.500 0.00 0.00 36.46 4.30


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

AutoCloner maintained by Alex Coulton.