Multiple sequence alignment - TraesCS2D01G024200

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 TraesCS2D01G024200 chr2D 100.000 3738 0 0 1 3738 10801402 10797665 0.000000e+00 6903
1 TraesCS2D01G024200 chr2D 94.691 2317 118 2 360 2672 10512156 10509841 0.000000e+00 3592
2 TraesCS2D01G024200 chr2D 94.605 2317 120 2 360 2672 10495105 10492790 0.000000e+00 3581
3 TraesCS2D01G024200 chr2D 94.569 2320 114 3 357 2672 10293366 10295677 0.000000e+00 3576
4 TraesCS2D01G024200 chr2D 99.468 752 2 1 2672 3423 10250783 10251532 0.000000e+00 1365
5 TraesCS2D01G024200 chr2D 93.973 365 22 0 1 365 10512563 10512199 1.520000e-153 553
6 TraesCS2D01G024200 chr2D 93.646 362 23 0 1 362 10292962 10293323 3.280000e-150 542
7 TraesCS2D01G024200 chr2D 93.425 365 24 0 1 365 10495512 10495148 3.280000e-150 542
8 TraesCS2D01G024200 chr2D 94.379 338 0 1 3420 3738 10257122 10257459 5.570000e-138 501
9 TraesCS2D01G024200 chr2D 93.787 338 2 2 3420 3738 10286262 10286599 1.210000e-134 490
10 TraesCS2D01G024200 chr2D 93.787 338 2 1 3420 3738 10464018 10463681 1.210000e-134 490
11 TraesCS2D01G024200 chr2A 92.699 3424 186 18 357 3738 11310413 11307012 0.000000e+00 4879
12 TraesCS2D01G024200 chr2A 90.000 890 62 5 2869 3738 11043146 11042264 0.000000e+00 1125
13 TraesCS2D01G024200 chr2A 87.471 431 34 2 3327 3738 11237978 11237549 2.610000e-131 479
14 TraesCS2D01G024200 chr2B 91.780 3090 181 17 695 3738 15638861 15635799 0.000000e+00 4231
15 TraesCS2D01G024200 chr2B 90.320 2934 212 21 847 3738 15119809 15116906 0.000000e+00 3779
16 TraesCS2D01G024200 chr2B 89.550 2823 232 22 770 3565 15382573 15379787 0.000000e+00 3520
17 TraesCS2D01G024200 chr2B 93.612 2270 132 3 602 2871 15883327 15881071 0.000000e+00 3376
18 TraesCS2D01G024200 chr2B 93.568 2270 132 4 602 2871 15962722 15960467 0.000000e+00 3371
19 TraesCS2D01G024200 chr2B 93.395 2271 134 6 602 2871 15727504 15725249 0.000000e+00 3349
20 TraesCS2D01G024200 chr2B 93.354 2272 134 7 602 2871 15790571 15788315 0.000000e+00 3343
21 TraesCS2D01G024200 chr2B 93.917 822 39 2 602 1423 15983581 15982771 0.000000e+00 1230
22 TraesCS2D01G024200 chr2B 92.668 491 28 6 2869 3356 15725220 15724735 0.000000e+00 701
23 TraesCS2D01G024200 chr2B 92.668 491 28 6 2869 3356 15788286 15787801 0.000000e+00 701
24 TraesCS2D01G024200 chr2B 92.638 489 27 5 2872 3356 15881035 15880552 0.000000e+00 695
25 TraesCS2D01G024200 chr2B 89.770 391 20 2 3367 3738 15879199 15878810 2.020000e-132 483
26 TraesCS2D01G024200 chr2B 89.514 391 21 2 3367 3738 15979095 15978706 9.390000e-131 477
27 TraesCS2D01G024200 chr2B 88.747 391 24 2 3367 3738 15722691 15722302 9.460000e-126 460
28 TraesCS2D01G024200 chr2B 88.747 391 24 2 3367 3738 15723734 15723345 9.460000e-126 460
29 TraesCS2D01G024200 chrUn 93.700 2270 129 4 602 2871 339546441 339548696 0.000000e+00 3387
30 TraesCS2D01G024200 chrUn 93.568 2270 132 4 602 2871 339561602 339559347 0.000000e+00 3371
31 TraesCS2D01G024200 chrUn 93.945 2048 113 2 602 2649 349087491 349085455 0.000000e+00 3085
32 TraesCS2D01G024200 chrUn 93.799 2048 116 2 602 2649 349092566 349094602 0.000000e+00 3068
33 TraesCS2D01G024200 chrUn 94.379 338 0 1 3420 3738 393451548 393451211 5.570000e-138 501
34 TraesCS2D01G024200 chrUn 89.770 391 20 2 3367 3738 258350436 258350825 2.020000e-132 483
35 TraesCS2D01G024200 chrUn 89.514 391 21 2 3367 3738 250801722 250801333 9.390000e-131 477
36 TraesCS2D01G024200 chrUn 88.085 235 15 4 602 835 328699764 328699986 2.210000e-67 267
37 TraesCS2D01G024200 chrUn 87.815 238 16 4 602 838 433700886 433700661 2.210000e-67 267
38 TraesCS2D01G024200 chr3B 88.007 592 53 11 7 582 257779181 257778592 0.000000e+00 684
39 TraesCS2D01G024200 chr3B 87.780 491 40 7 1 473 747537035 747536547 1.170000e-154 556
40 TraesCS2D01G024200 chr3B 91.176 374 31 2 1 373 335830725 335831097 1.200000e-139 507
41 TraesCS2D01G024200 chr5B 90.909 374 32 2 1 373 26947147 26947519 5.570000e-138 501
42 TraesCS2D01G024200 chr5B 90.374 374 34 2 1 373 10171721 10172093 1.210000e-134 490
43 TraesCS2D01G024200 chr6D 90.541 370 35 0 1 370 10680007 10680376 1.210000e-134 490
44 TraesCS2D01G024200 chr3A 90.685 365 32 2 1 365 734150328 734150690 5.610000e-133 484
45 TraesCS2D01G024200 chr6B 91.064 235 21 0 362 596 205120865 205120631 6.020000e-83 318
46 TraesCS2D01G024200 chr4B 90.000 250 18 6 367 616 59852311 59852553 2.170000e-82 316
47 TraesCS2D01G024200 chr4B 88.186 237 25 3 360 593 412589115 412588879 2.840000e-71 279
48 TraesCS2D01G024200 chr1A 89.873 237 22 2 357 593 538778205 538778439 1.690000e-78 303
49 TraesCS2D01G024200 chr3D 87.815 238 27 2 357 594 498726617 498726382 1.020000e-70 278


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 TraesCS2D01G024200 chr2D 10797665 10801402 3737 True 6903.0 6903 100.000000 1 3738 1 chr2D.!!$R2 3737
1 TraesCS2D01G024200 chr2D 10509841 10512563 2722 True 2072.5 3592 94.332000 1 2672 2 chr2D.!!$R4 2671
2 TraesCS2D01G024200 chr2D 10492790 10495512 2722 True 2061.5 3581 94.015000 1 2672 2 chr2D.!!$R3 2671
3 TraesCS2D01G024200 chr2D 10292962 10295677 2715 False 2059.0 3576 94.107500 1 2672 2 chr2D.!!$F4 2671
4 TraesCS2D01G024200 chr2D 10250783 10251532 749 False 1365.0 1365 99.468000 2672 3423 1 chr2D.!!$F1 751
5 TraesCS2D01G024200 chr2A 11307012 11310413 3401 True 4879.0 4879 92.699000 357 3738 1 chr2A.!!$R3 3381
6 TraesCS2D01G024200 chr2A 11042264 11043146 882 True 1125.0 1125 90.000000 2869 3738 1 chr2A.!!$R1 869
7 TraesCS2D01G024200 chr2B 15635799 15638861 3062 True 4231.0 4231 91.780000 695 3738 1 chr2B.!!$R3 3043
8 TraesCS2D01G024200 chr2B 15116906 15119809 2903 True 3779.0 3779 90.320000 847 3738 1 chr2B.!!$R1 2891
9 TraesCS2D01G024200 chr2B 15379787 15382573 2786 True 3520.0 3520 89.550000 770 3565 1 chr2B.!!$R2 2795
10 TraesCS2D01G024200 chr2B 15960467 15962722 2255 True 3371.0 3371 93.568000 602 2871 1 chr2B.!!$R4 2269
11 TraesCS2D01G024200 chr2B 15787801 15790571 2770 True 2022.0 3343 93.011000 602 3356 2 chr2B.!!$R6 2754
12 TraesCS2D01G024200 chr2B 15878810 15883327 4517 True 1518.0 3376 92.006667 602 3738 3 chr2B.!!$R7 3136
13 TraesCS2D01G024200 chr2B 15722302 15727504 5202 True 1242.5 3349 90.889250 602 3738 4 chr2B.!!$R5 3136
14 TraesCS2D01G024200 chr2B 15978706 15983581 4875 True 853.5 1230 91.715500 602 3738 2 chr2B.!!$R8 3136
15 TraesCS2D01G024200 chrUn 339546441 339548696 2255 False 3387.0 3387 93.700000 602 2871 1 chrUn.!!$F3 2269
16 TraesCS2D01G024200 chrUn 339559347 339561602 2255 True 3371.0 3371 93.568000 602 2871 1 chrUn.!!$R2 2269
17 TraesCS2D01G024200 chrUn 349085455 349087491 2036 True 3085.0 3085 93.945000 602 2649 1 chrUn.!!$R3 2047
18 TraesCS2D01G024200 chrUn 349092566 349094602 2036 False 3068.0 3068 93.799000 602 2649 1 chrUn.!!$F4 2047
19 TraesCS2D01G024200 chr3B 257778592 257779181 589 True 684.0 684 88.007000 7 582 1 chr3B.!!$R1 575

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
400 452 0.169230 GATCGAGCGCGTCTCCATAT 59.831 55.000 19.89 13.10 38.62 1.78 F
1260 1314 3.375299 GGGCTACTCATGTCATTGTTGTC 59.625 47.826 0.00 0.00 0.00 3.18 F
1740 1795 1.265454 CCGACTACTTCCCAGCCCTT 61.265 60.000 0.00 0.00 0.00 3.95 F
2359 2644 1.308047 CAACTGTTGCTGGCTACACA 58.692 50.000 7.70 0.45 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1465 1519 0.252103 TGGCCGTACTCCTCTTTCCT 60.252 55.000 0.0 0.0 0.0 3.36 R
2443 2728 2.107204 AGTGTTCAAATGCCTCTCAGGT 59.893 45.455 0.0 0.0 37.8 4.00 R
2611 2896 3.380637 GGAGACTGATACTCTTAACGCCA 59.619 47.826 0.0 0.0 35.1 5.69 R
3595 6832 3.951037 TGCCCGTGTAATTCAGCAATAAT 59.049 39.130 0.0 0.0 0.0 1.28 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
29 30 2.721859 CGCCATCGTCCGATCTGA 59.278 61.111 0.00 0.00 31.62 3.27
52 53 2.319438 AGACCAGATCCTAGGGTTTCCT 59.681 50.000 9.46 0.00 46.96 3.36
96 97 1.057636 AACAGTTACACGACGATGCG 58.942 50.000 0.00 0.00 37.29 4.73
112 113 2.442212 TGCGTTCATCAAGGTAACGA 57.558 45.000 10.65 0.00 46.66 3.85
239 240 3.224324 GCGGGCCGACCATCTCTA 61.224 66.667 33.44 0.00 40.22 2.43
287 288 1.450312 CACCGGCCAGAACAGATCC 60.450 63.158 0.00 0.00 0.00 3.36
349 353 2.183300 CGTCGCCGATCCAAAGGA 59.817 61.111 0.00 0.00 35.63 3.36
355 359 1.473257 CGCCGATCCAAAGGAAGATGA 60.473 52.381 0.00 0.00 34.34 2.92
386 438 2.721859 CGCCACAGATCGGATCGA 59.278 61.111 12.08 0.00 41.13 3.59
400 452 0.169230 GATCGAGCGCGTCTCCATAT 59.831 55.000 19.89 13.10 38.62 1.78
549 601 4.770874 TGGCGGCGGCTAGGTTTC 62.771 66.667 33.21 0.38 39.81 2.78
1260 1314 3.375299 GGGCTACTCATGTCATTGTTGTC 59.625 47.826 0.00 0.00 0.00 3.18
1740 1795 1.265454 CCGACTACTTCCCAGCCCTT 61.265 60.000 0.00 0.00 0.00 3.95
1776 1831 2.352715 GGATGGCCAAGAAAAGGTTTCG 60.353 50.000 10.96 0.00 0.00 3.46
1902 1957 3.057736 CGAGAGACTTTTTGGACGTCCTA 60.058 47.826 33.39 24.89 36.82 2.94
1911 1966 5.988310 TTTTGGACGTCCTAGTTCATCTA 57.012 39.130 33.39 8.02 36.82 1.98
1966 2025 7.255451 CCCTACAAGAAATTAGAGCACAAACAA 60.255 37.037 0.00 0.00 0.00 2.83
1980 2039 4.212636 GCACAAACAACGGTTAGTATGTCT 59.787 41.667 0.00 0.00 35.82 3.41
1991 2051 5.521544 GGTTAGTATGTCTCCTTAAGCTCG 58.478 45.833 0.00 0.00 0.00 5.03
2061 2121 4.444536 ACCTTTTCTGTTGCGTTGTACTA 58.555 39.130 0.00 0.00 0.00 1.82
2067 2127 7.718272 TTTCTGTTGCGTTGTACTAATTACT 57.282 32.000 0.00 0.00 0.00 2.24
2231 2292 5.980698 TGTCGGTAAAGATAGACTAGTCG 57.019 43.478 17.07 2.22 34.92 4.18
2359 2644 1.308047 CAACTGTTGCTGGCTACACA 58.692 50.000 7.70 0.45 0.00 3.72
2443 2728 3.888930 GGACTGAACCATTGGAGTTTCAA 59.111 43.478 10.37 0.00 0.00 2.69
2539 2824 1.609783 GAGGGGTTGTCCTGGGATG 59.390 63.158 0.00 0.00 37.25 3.51
2611 2896 3.297134 TTCACTTGGACAAAGCTTCCT 57.703 42.857 0.00 0.00 39.76 3.36
2715 3002 7.035612 CGTTTGGCTGCACATCTCTATATATA 58.964 38.462 0.50 0.00 0.00 0.86
2716 3003 7.708322 CGTTTGGCTGCACATCTCTATATATAT 59.292 37.037 0.50 0.00 0.00 0.86
3532 6746 4.150897 TGTTTGGTTTGTACTCTCAGCT 57.849 40.909 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.523972 GGAAACCCTAGGATCTGGTCTTT 59.476 47.826 11.48 0.00 0.00 2.52
52 53 2.049156 CACTCGTGCTGCTTCGGA 60.049 61.111 14.88 1.47 0.00 4.55
96 97 2.063266 TGCGTCGTTACCTTGATGAAC 58.937 47.619 0.00 0.00 0.00 3.18
239 240 1.067776 GTGGTCGTCATCTCTTCCGTT 60.068 52.381 0.00 0.00 0.00 4.44
287 288 3.220999 TTGGTGGCACCTCGAGTCG 62.221 63.158 34.69 6.09 39.58 4.18
334 338 0.830648 ATCTTCCTTTGGATCGGCGA 59.169 50.000 13.87 13.87 0.00 5.54
386 438 1.667177 CGATTCATATGGAGACGCGCT 60.667 52.381 5.73 3.91 0.00 5.92
1260 1314 2.256591 GGCTATCTGTGGGCATGCG 61.257 63.158 12.44 0.00 0.00 4.73
1465 1519 0.252103 TGGCCGTACTCCTCTTTCCT 60.252 55.000 0.00 0.00 0.00 3.36
1510 1564 0.664224 CATGCCATGTCGCTGCAATA 59.336 50.000 0.00 0.00 38.69 1.90
1740 1795 2.040278 GCCATCCATGTCAAGGCCTATA 59.960 50.000 5.16 0.00 39.42 1.31
1753 1808 2.629017 ACCTTTTCTTGGCCATCCAT 57.371 45.000 6.09 0.00 43.05 3.41
1764 1819 2.820197 GGCATCCTTCGAAACCTTTTCT 59.180 45.455 0.00 0.00 0.00 2.52
1776 1831 1.547372 AGTGTTTGCATGGCATCCTTC 59.453 47.619 0.00 0.00 38.76 3.46
1911 1966 2.158475 TGGTTGTCCCTCTGCATCTTTT 60.158 45.455 0.00 0.00 0.00 2.27
1966 2025 4.954826 AGCTTAAGGAGACATACTAACCGT 59.045 41.667 4.29 0.00 0.00 4.83
1980 2039 6.525578 TGAACTTTCTATCGAGCTTAAGGA 57.474 37.500 4.29 0.00 0.00 3.36
2231 2292 2.737039 GCCGAGGAATGTCAGACTCTTC 60.737 54.545 1.31 5.17 0.00 2.87
2432 2717 2.487265 GCCTCTCAGGTTGAAACTCCAA 60.487 50.000 0.00 0.00 37.80 3.53
2443 2728 2.107204 AGTGTTCAAATGCCTCTCAGGT 59.893 45.455 0.00 0.00 37.80 4.00
2539 2824 5.401531 TTGTCATAGAGGTACCAAGTGAC 57.598 43.478 22.44 22.44 36.09 3.67
2611 2896 3.380637 GGAGACTGATACTCTTAACGCCA 59.619 47.826 0.00 0.00 35.10 5.69
2715 3002 9.046296 CGTATTAACTCTTTTTAGCTGGATCAT 57.954 33.333 0.00 0.00 0.00 2.45
2716 3003 7.011109 GCGTATTAACTCTTTTTAGCTGGATCA 59.989 37.037 0.00 0.00 0.00 2.92
3450 6664 5.700402 AGCCTGATAATAAACTGTCCTGT 57.300 39.130 0.00 0.00 0.00 4.00
3532 6746 4.314740 ACCTGCAGCAATAAACGAAAAA 57.685 36.364 8.66 0.00 0.00 1.94
3595 6832 3.951037 TGCCCGTGTAATTCAGCAATAAT 59.049 39.130 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.