Multiple sequence alignment - TraesCS2D01G285900

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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 TraesCS2D01G285900 chr2D 100.000 4293 0 0 1 4293 364162965 364167257 0.000000e+00 7928
1 TraesCS2D01G285900 chr2D 80.451 532 91 12 1 525 52620431 52620956 1.120000e-105 394
2 TraesCS2D01G285900 chr2D 83.003 353 54 5 1 351 155776996 155777344 8.960000e-82 315
3 TraesCS2D01G285900 chr2B 93.414 4358 176 33 1 4293 432552723 432557034 0.000000e+00 6355
4 TraesCS2D01G285900 chr2A 97.207 3581 78 15 724 4293 490659311 490662880 0.000000e+00 6039
5 TraesCS2D01G285900 chr2A 84.105 648 84 11 1 647 490614285 490614914 3.670000e-170 608
6 TraesCS2D01G285900 chr7D 80.488 533 92 11 1 525 97639153 97638625 8.650000e-107 398
7 TraesCS2D01G285900 chr1B 80.566 530 90 10 1 525 666561519 666562040 3.110000e-106 396
8 TraesCS2D01G285900 chr6B 79.237 472 95 3 2 471 39175104 39174634 4.140000e-85 326
9 TraesCS2D01G285900 chr6D 77.778 540 107 7 2 538 24213929 24213400 1.930000e-83 320
10 TraesCS2D01G285900 chr7B 80.348 402 74 5 1 399 52509878 52509479 2.510000e-77 300
11 TraesCS2D01G285900 chr3D 76.923 299 54 13 237 525 48362681 48362388 5.750000e-34 156


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 TraesCS2D01G285900 chr2D 364162965 364167257 4292 False 7928 7928 100.000 1 4293 1 chr2D.!!$F3 4292
1 TraesCS2D01G285900 chr2D 52620431 52620956 525 False 394 394 80.451 1 525 1 chr2D.!!$F1 524
2 TraesCS2D01G285900 chr2B 432552723 432557034 4311 False 6355 6355 93.414 1 4293 1 chr2B.!!$F1 4292
3 TraesCS2D01G285900 chr2A 490659311 490662880 3569 False 6039 6039 97.207 724 4293 1 chr2A.!!$F2 3569
4 TraesCS2D01G285900 chr2A 490614285 490614914 629 False 608 608 84.105 1 647 1 chr2A.!!$F1 646
5 TraesCS2D01G285900 chr7D 97638625 97639153 528 True 398 398 80.488 1 525 1 chr7D.!!$R1 524
6 TraesCS2D01G285900 chr1B 666561519 666562040 521 False 396 396 80.566 1 525 1 chr1B.!!$F1 524
7 TraesCS2D01G285900 chr6D 24213400 24213929 529 True 320 320 77.778 2 538 1 chr6D.!!$R1 536

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
346 351 0.034896 AGAGGTCGCATCCGTTTTGT 59.965 50.000 0.00 0.0 35.54 2.83 F
392 397 0.454600 CTCCAGTGGCATGAATGTGC 59.545 55.000 3.51 0.0 44.31 4.57 F
1326 1407 0.747255 ACGACCCCGAAGATGATGAG 59.253 55.000 0.00 0.0 39.50 2.90 F
2462 2548 1.203300 TCTCCCATGGTTCCTCAGTCA 60.203 52.381 11.73 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2266 0.034616 GATCTGCCCGAGGATCCTTG 59.965 60.000 20.95 20.95 34.09 3.61 R
2235 2321 4.479158 TGAAGGCCAATTTTACCTGAACT 58.521 39.130 5.01 0.00 32.92 3.01 R
2591 2677 1.696336 TCTGCAAGAGCTCTCCTGTTT 59.304 47.619 18.55 0.00 38.67 2.83 R
3556 3651 1.876156 GCTGACAAGCTGTAGTTTGCT 59.124 47.619 8.16 0.00 46.60 3.91 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
88 89 1.883926 GGGTGTGGTACGATTTTTGCT 59.116 47.619 0.00 0.00 0.00 3.91
89 90 2.295070 GGGTGTGGTACGATTTTTGCTT 59.705 45.455 0.00 0.00 0.00 3.91
174 175 2.355837 TGGCTCACGAACAGACGC 60.356 61.111 0.00 0.00 36.70 5.19
180 181 2.105528 ACGAACAGACGCGTGGTT 59.894 55.556 20.70 21.29 39.56 3.67
206 211 2.936202 AGATTTCTTGGCACACACACT 58.064 42.857 0.00 0.00 39.29 3.55
232 237 4.035102 GGAGGAAGGCGGGCAGTT 62.035 66.667 3.78 0.00 0.00 3.16
260 265 2.359900 GTTTGAATGTGGCGAGGAGAT 58.640 47.619 0.00 0.00 0.00 2.75
346 351 0.034896 AGAGGTCGCATCCGTTTTGT 59.965 50.000 0.00 0.00 35.54 2.83
392 397 0.454600 CTCCAGTGGCATGAATGTGC 59.545 55.000 3.51 0.00 44.31 4.57
500 521 1.748122 CGCCTGCAAAGCCTCTCAT 60.748 57.895 2.96 0.00 0.00 2.90
558 579 2.856346 CGCGGTCCGAATGTAAGCG 61.856 63.158 17.49 1.81 40.02 4.68
569 590 3.123284 CGAATGTAAGCGGACGGTTTAAA 59.877 43.478 14.48 1.81 37.08 1.52
570 591 4.377226 CGAATGTAAGCGGACGGTTTAAAA 60.377 41.667 14.48 0.00 37.08 1.52
581 602 3.269178 ACGGTTTAAAAGTCGGTGTTGA 58.731 40.909 10.25 0.00 0.00 3.18
588 609 2.550830 AAGTCGGTGTTGAAGATGCT 57.449 45.000 0.00 0.00 0.00 3.79
667 709 6.446110 TGATTAGGGGCTGATTGATCTGATAT 59.554 38.462 0.00 0.00 0.00 1.63
694 736 2.092592 AGTTTAGGGGCTGGTTTATCCG 60.093 50.000 0.00 0.00 39.52 4.18
1326 1407 0.747255 ACGACCCCGAAGATGATGAG 59.253 55.000 0.00 0.00 39.50 2.90
1357 1438 3.432051 GATGTGAGGGGCGAGGACG 62.432 68.421 0.00 0.00 42.93 4.79
1372 1453 2.106857 GAGGACGATAGGAAGGAGGAGA 59.893 54.545 0.00 0.00 43.77 3.71
1450 1531 5.351740 CGGGAGGTGAGAGAAAAATAACTTC 59.648 44.000 0.00 0.00 0.00 3.01
1517 1598 5.627503 GCTTGTGGAAATTAGGGCATTGATT 60.628 40.000 0.00 0.00 0.00 2.57
1518 1599 6.406849 GCTTGTGGAAATTAGGGCATTGATTA 60.407 38.462 0.00 0.00 0.00 1.75
1519 1600 7.673641 TTGTGGAAATTAGGGCATTGATTAT 57.326 32.000 0.00 0.00 0.00 1.28
1520 1601 8.774546 TTGTGGAAATTAGGGCATTGATTATA 57.225 30.769 0.00 0.00 0.00 0.98
1682 1763 3.829886 TCGTTGTCATCAATTTGCTCC 57.170 42.857 0.00 0.00 35.92 4.70
1822 1906 4.651045 ACTGTTCATTTCTTTTGAAGGCCT 59.349 37.500 0.00 0.00 39.88 5.19
2171 2257 7.312415 TGATGATACCATTGATGAGATCTGT 57.688 36.000 0.00 0.00 32.09 3.41
2180 2266 6.206243 CCATTGATGAGATCTGTGGTTTATCC 59.794 42.308 0.00 0.00 33.08 2.59
2235 2321 3.261643 TGCAAGGCTCAGAGAAGACAATA 59.738 43.478 0.00 0.00 0.00 1.90
2242 2328 5.108517 GCTCAGAGAAGACAATAGTTCAGG 58.891 45.833 0.00 0.00 0.00 3.86
2462 2548 1.203300 TCTCCCATGGTTCCTCAGTCA 60.203 52.381 11.73 0.00 0.00 3.41
2491 2577 1.480545 GGTCACAACAAAGGGCAACTT 59.519 47.619 0.00 0.00 42.52 2.66
2562 2648 6.932400 CCCTTCAAAGTACACATGTTACACTA 59.068 38.462 15.75 0.00 0.00 2.74
2591 2677 3.440522 CACCAGAGAGTACTGACGAATCA 59.559 47.826 0.00 0.00 39.94 2.57
3162 3251 7.550906 AGTTGCACTCCTAGAATTCAATAAGTC 59.449 37.037 8.44 2.24 0.00 3.01
3368 3462 5.405269 GCCCTTTTGATGTACAACAAATGTC 59.595 40.000 25.94 18.37 42.70 3.06
3371 3465 7.656948 CCCTTTTGATGTACAACAAATGTCATT 59.343 33.333 25.94 0.00 42.70 2.57
3399 3493 3.675348 TGCATCTCCCATGAGGAAAAT 57.325 42.857 0.00 0.00 46.94 1.82
3456 3550 7.279615 TCAGAACCAGTCTACAAGAAAAATCA 58.720 34.615 0.00 0.00 33.56 2.57
3556 3651 4.814234 ACTTTGATCAAGACGTTTACAGCA 59.186 37.500 8.41 0.00 36.21 4.41
3938 4033 5.398169 TCATGCTTAAATTTAGGCGTTGTG 58.602 37.500 20.81 17.31 38.44 3.33
3981 4076 8.635765 ACTTCATCTTGCTGAAATAAGGTAAA 57.364 30.769 0.00 0.00 34.86 2.01
3982 4077 8.515414 ACTTCATCTTGCTGAAATAAGGTAAAC 58.485 33.333 0.00 0.00 34.86 2.01
4015 4110 8.087750 ACTCTTGTTTCTTCTCAACTCTCATAG 58.912 37.037 0.00 0.00 0.00 2.23
4058 4155 6.309737 GGCTCTGTTCTTATGCTTTTGATTTG 59.690 38.462 0.00 0.00 0.00 2.32
4077 4174 6.696583 TGATTTGTTTGTGAGTTGCATGTTAG 59.303 34.615 0.00 0.00 0.00 2.34
4082 4179 4.019792 TGTGAGTTGCATGTTAGACCAT 57.980 40.909 0.00 0.00 0.00 3.55
4083 4180 4.002982 TGTGAGTTGCATGTTAGACCATC 58.997 43.478 0.00 0.00 0.00 3.51
4094 4191 5.139435 TGTTAGACCATCTCTGTTCACTG 57.861 43.478 0.00 0.00 0.00 3.66
4179 4276 2.625790 GTGGGCAGAGGTAGTAGATGAG 59.374 54.545 0.00 0.00 0.00 2.90
4288 4385 5.587844 GCTGGATTGTCAGTGAAGTGAATAT 59.412 40.000 0.00 0.00 37.12 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 142 1.866237 CCACCCGTCATTGAACACG 59.134 57.895 0.00 0.00 35.72 4.49
169 170 0.892358 TCTACTCCAACCACGCGTCT 60.892 55.000 9.86 0.00 0.00 4.18
174 175 3.684788 CCAAGAAATCTACTCCAACCACG 59.315 47.826 0.00 0.00 0.00 4.94
180 181 3.072330 TGTGTGCCAAGAAATCTACTCCA 59.928 43.478 0.00 0.00 0.00 3.86
206 211 1.340600 CCGCCTTCCTCCATTAAACCA 60.341 52.381 0.00 0.00 0.00 3.67
232 237 1.066303 GCCACATTCAAACGACCACAA 59.934 47.619 0.00 0.00 0.00 3.33
445 464 1.153549 CCGCTCCTGACTACCTTGC 60.154 63.158 0.00 0.00 0.00 4.01
448 467 2.760385 GCCCGCTCCTGACTACCT 60.760 66.667 0.00 0.00 0.00 3.08
495 515 3.055458 TGCATACCGGAGACAAAATGAGA 60.055 43.478 9.46 0.00 0.00 3.27
500 521 3.410631 TTCTGCATACCGGAGACAAAA 57.589 42.857 9.46 0.00 42.55 2.44
525 546 0.650512 CCGCGCTGTTCGAATATGTT 59.349 50.000 5.56 0.00 41.67 2.71
526 547 0.459585 ACCGCGCTGTTCGAATATGT 60.460 50.000 5.56 0.00 41.67 2.29
549 570 4.516321 ACTTTTAAACCGTCCGCTTACATT 59.484 37.500 0.00 0.00 0.00 2.71
558 579 2.212652 ACACCGACTTTTAAACCGTCC 58.787 47.619 9.88 0.00 0.00 4.79
569 590 2.417719 GAGCATCTTCAACACCGACTT 58.582 47.619 0.00 0.00 0.00 3.01
570 591 2.086054 GAGCATCTTCAACACCGACT 57.914 50.000 0.00 0.00 0.00 4.18
588 609 6.839124 ATTGCAGATGGTTTTGATGTAAGA 57.161 33.333 0.00 0.00 0.00 2.10
621 643 1.026718 CAATCAACCCCTGAGCGGTC 61.027 60.000 7.89 7.89 37.52 4.79
634 656 2.241941 TCAGCCCCTAATCAGCAATCAA 59.758 45.455 0.00 0.00 0.00 2.57
667 709 0.541764 CCAGCCCCTAAACTTTGCCA 60.542 55.000 0.00 0.00 0.00 4.92
804 885 2.030958 CGGGCTTTGGTGTCGGTAC 61.031 63.158 0.00 0.00 0.00 3.34
947 1028 2.739379 CAGAAGCTTCTCGAAAGTTCCC 59.261 50.000 26.18 0.00 34.74 3.97
1233 1314 1.226603 GTAGAACGCGGACGAGCAT 60.227 57.895 12.47 0.00 43.93 3.79
1326 1407 1.969923 CTCACATCCTCCTCATCCTCC 59.030 57.143 0.00 0.00 0.00 4.30
1357 1438 2.888414 CGTCCTTCTCCTCCTTCCTATC 59.112 54.545 0.00 0.00 0.00 2.08
1372 1453 0.410270 ACCTCCTCTTCCTCGTCCTT 59.590 55.000 0.00 0.00 0.00 3.36
1450 1531 7.904461 GCAAATGGTCAAATCAAATAAAATCGG 59.096 33.333 0.00 0.00 0.00 4.18
1550 1631 4.469945 AGCAGTAGGGTATGAGTAGCAAAA 59.530 41.667 0.00 0.00 0.00 2.44
1682 1763 4.033129 CACAACAAGCAAACAACATGAAGG 59.967 41.667 0.00 0.00 0.00 3.46
2180 2266 0.034616 GATCTGCCCGAGGATCCTTG 59.965 60.000 20.95 20.95 34.09 3.61
2235 2321 4.479158 TGAAGGCCAATTTTACCTGAACT 58.521 39.130 5.01 0.00 32.92 3.01
2242 2328 5.659440 TGGAGAATGAAGGCCAATTTTAC 57.341 39.130 5.01 0.00 0.00 2.01
2462 2548 3.321682 CCTTTGTTGTGACCACATCCATT 59.678 43.478 3.47 0.00 41.52 3.16
2491 2577 4.329545 GCGTGGAGGAGTTGCCCA 62.330 66.667 0.00 0.00 37.37 5.36
2510 2596 2.188817 ACATAGTCAGGAACCCCAGAC 58.811 52.381 0.00 0.00 46.01 3.51
2562 2648 3.010696 TCAGTACTCTCTGGTGTCTCCAT 59.989 47.826 0.00 0.00 46.12 3.41
2591 2677 1.696336 TCTGCAAGAGCTCTCCTGTTT 59.304 47.619 18.55 0.00 38.67 2.83
3099 3188 3.703556 TCCCAGCACAAGAAATTCAAACA 59.296 39.130 0.00 0.00 0.00 2.83
3315 3409 6.118170 CCTTGTGTATTCTGGTGAATCTGAT 58.882 40.000 0.00 0.00 41.55 2.90
3368 3462 4.724074 TGGGAGATGCAAAAGCTTAATG 57.276 40.909 0.00 3.36 0.00 1.90
3371 3465 3.949754 CTCATGGGAGATGCAAAAGCTTA 59.050 43.478 0.00 0.00 44.26 3.09
3399 3493 2.270434 AACCTGAAGGAGATGGCCTA 57.730 50.000 3.32 0.00 37.26 3.93
3539 3633 2.766313 TGCTGCTGTAAACGTCTTGAT 58.234 42.857 0.00 0.00 0.00 2.57
3556 3651 1.876156 GCTGACAAGCTGTAGTTTGCT 59.124 47.619 8.16 0.00 46.60 3.91
3938 4033 5.901552 TGAAGTTCTCCCAAATCAACAAAC 58.098 37.500 4.17 0.00 0.00 2.93
3987 4082 6.536582 TGAGAGTTGAGAAGAAACAAGAGTTG 59.463 38.462 0.00 0.00 38.17 3.16
4015 4110 2.492088 AGCCCAAAACTTTAGATTCGCC 59.508 45.455 0.00 0.00 0.00 5.54
4058 4155 4.036262 TGGTCTAACATGCAACTCACAAAC 59.964 41.667 0.00 0.00 0.00 2.93
4077 4174 4.199432 ACATCAGTGAACAGAGATGGTC 57.801 45.455 15.60 0.00 41.55 4.02
4082 4179 4.760204 TCGTCTTACATCAGTGAACAGAGA 59.240 41.667 0.00 0.00 0.00 3.10
4083 4180 5.048153 TCGTCTTACATCAGTGAACAGAG 57.952 43.478 0.00 0.00 0.00 3.35
4094 4191 4.391830 TGAACTGCCAAATCGTCTTACATC 59.608 41.667 0.00 0.00 0.00 3.06
4267 4364 8.136057 CACTATATTCACTTCACTGACAATCC 57.864 38.462 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.