Multiple sequence alignment - TraesCS2D01G153500

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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 TraesCS2D01G153500 chr2D 100.000 3545 0 0 1 3545 96291892 96295436 0.000000e+00 6547.0
1 TraesCS2D01G153500 chr2D 98.301 2825 36 6 1 2823 96082443 96085257 0.000000e+00 4940.0
2 TraesCS2D01G153500 chr2D 95.286 2800 78 20 754 3544 95786400 95789154 0.000000e+00 4390.0
3 TraesCS2D01G153500 chr2D 96.925 1561 35 7 1270 2823 95917196 95918750 0.000000e+00 2604.0
4 TraesCS2D01G153500 chr2D 95.173 1098 42 7 186 1281 95914331 95915419 0.000000e+00 1724.0
5 TraesCS2D01G153500 chr2D 93.400 697 36 2 2858 3544 96085477 96086173 0.000000e+00 1024.0
6 TraesCS2D01G153500 chr2D 93.276 699 35 2 2858 3544 95918972 95919670 0.000000e+00 1020.0
7 TraesCS2D01G153500 chr2D 96.216 185 4 2 1 183 95902432 95902615 2.070000e-77 300.0
8 TraesCS2D01G153500 chr2D 100.000 32 0 0 2822 2853 96085419 96085450 3.820000e-05 60.2
9 TraesCS2D01G153500 chr2A 87.353 2040 171 34 754 2758 94317135 94319122 0.000000e+00 2257.0
10 TraesCS2D01G153500 chr2A 91.589 856 69 2 1647 2502 94447034 94447886 0.000000e+00 1179.0
11 TraesCS2D01G153500 chr2A 92.459 663 46 4 2061 2723 94324405 94325063 0.000000e+00 944.0
12 TraesCS2D01G153500 chr2A 84.738 439 64 3 3100 3537 94320679 94321115 1.510000e-118 436.0
13 TraesCS2D01G153500 chr2A 85.575 409 43 8 756 1159 94323797 94324194 7.080000e-112 414.0
14 TraesCS2D01G153500 chr2A 84.580 441 39 14 3101 3537 94449628 94450043 9.160000e-111 411.0
15 TraesCS2D01G153500 chr2A 89.083 229 23 2 2533 2760 94447882 94448109 2.080000e-72 283.0
16 TraesCS2D01G153500 chr2A 81.933 238 22 7 1199 1421 94324189 94324420 7.820000e-42 182.0
17 TraesCS2D01G153500 chr2A 81.250 240 19 7 2759 2973 94449400 94449638 1.690000e-38 171.0
18 TraesCS2D01G153500 chr2A 80.508 236 19 9 2759 2971 94319813 94320044 4.740000e-34 156.0
19 TraesCS2D01G153500 chr2A 89.189 111 10 2 2994 3103 216837799 216837908 1.720000e-28 137.0
20 TraesCS2D01G153500 chr2A 86.486 74 8 2 754 826 94419445 94419517 2.930000e-11 80.5
21 TraesCS2D01G153500 chrUn 90.253 1026 78 15 1637 2658 17383308 17384315 0.000000e+00 1321.0
22 TraesCS2D01G153500 chrUn 87.882 916 64 20 754 1633 17382370 17383274 0.000000e+00 1033.0
23 TraesCS2D01G153500 chrUn 100.000 407 0 0 2216 2622 477994025 477993619 0.000000e+00 752.0
24 TraesCS2D01G153500 chr7D 86.817 311 37 3 338 646 630765844 630765536 9.420000e-91 344.0
25 TraesCS2D01G153500 chr7D 89.796 49 4 1 1520 1568 75947695 75947742 1.060000e-05 62.1
26 TraesCS2D01G153500 chr4A 87.097 310 33 6 339 645 535261387 535261082 9.420000e-91 344.0
27 TraesCS2D01G153500 chr6B 86.076 316 39 4 339 653 130939760 130940071 5.670000e-88 335.0
28 TraesCS2D01G153500 chr6B 75.490 306 60 13 1652 1948 679566753 679566454 6.170000e-28 135.0
29 TraesCS2D01G153500 chr4B 85.897 312 38 5 337 645 92021766 92021458 9.490000e-86 327.0
30 TraesCS2D01G153500 chr7A 85.761 309 40 3 339 645 383864838 383865144 1.230000e-84 324.0
31 TraesCS2D01G153500 chr7A 88.991 109 12 0 2992 3100 621569054 621568946 6.170000e-28 135.0
32 TraesCS2D01G153500 chr7A 91.489 47 2 2 1520 1566 80085900 80085944 2.950000e-06 63.9
33 TraesCS2D01G153500 chr5D 85.761 309 40 3 339 645 491336202 491335896 1.230000e-84 324.0
34 TraesCS2D01G153500 chr5D 89.286 112 10 2 2989 3100 386689204 386689095 4.770000e-29 139.0
35 TraesCS2D01G153500 chr5D 88.034 117 12 2 2982 3098 557611098 557611212 1.720000e-28 137.0
36 TraesCS2D01G153500 chr2B 84.024 338 46 6 319 653 637570520 637570188 5.710000e-83 318.0
37 TraesCS2D01G153500 chr3D 86.260 131 14 4 2972 3100 185070517 185070389 4.770000e-29 139.0
38 TraesCS2D01G153500 chr3D 92.500 40 3 0 1794 1833 109263177 109263216 1.370000e-04 58.4
39 TraesCS2D01G153500 chr4D 88.182 110 12 1 2983 3092 336131465 336131573 2.870000e-26 130.0
40 TraesCS2D01G153500 chr3B 77.064 109 19 5 1728 1833 160621887 160621992 1.370000e-04 58.4


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 TraesCS2D01G153500 chr2D 96291892 96295436 3544 False 6547.000000 6547 100.000000 1 3545 1 chr2D.!!$F3 3544
1 TraesCS2D01G153500 chr2D 95786400 95789154 2754 False 4390.000000 4390 95.286000 754 3544 1 chr2D.!!$F1 2790
2 TraesCS2D01G153500 chr2D 96082443 96086173 3730 False 2008.066667 4940 97.233667 1 3544 3 chr2D.!!$F5 3543
3 TraesCS2D01G153500 chr2D 95914331 95919670 5339 False 1782.666667 2604 95.124667 186 3544 3 chr2D.!!$F4 3358
4 TraesCS2D01G153500 chr2A 94317135 94325063 7928 False 731.500000 2257 85.427667 754 3537 6 chr2A.!!$F3 2783
5 TraesCS2D01G153500 chr2A 94447034 94450043 3009 False 511.000000 1179 86.625500 1647 3537 4 chr2A.!!$F4 1890
6 TraesCS2D01G153500 chrUn 17382370 17384315 1945 False 1177.000000 1321 89.067500 754 2658 2 chrUn.!!$F1 1904

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
953 971 1.076118 ATGCATGCGATTTCCCCCA 60.076 52.632 14.09 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2701 4633 1.013596 TTGCATGAAGGGATAACGCG 58.986 50.0 3.53 3.53 0.0 6.01 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
107 109 3.181469 GCATGAGTCCGGTCCAGTTTATA 60.181 47.826 0.00 0.00 0.00 0.98
245 247 1.691337 TGGTCCCCTTATCGGTGGG 60.691 63.158 0.00 0.00 42.98 4.61
252 254 3.515316 CTTATCGGTGGGCGGCGAT 62.515 63.158 12.98 2.38 0.00 4.58
361 363 8.024145 AGTACTCCCTTCATTTCCTTATACAG 57.976 38.462 0.00 0.00 0.00 2.74
663 666 2.036556 ACGATTTTTCGCAGCACAAG 57.963 45.000 0.00 0.00 36.44 3.16
953 971 1.076118 ATGCATGCGATTTCCCCCA 60.076 52.632 14.09 0.00 0.00 4.96
1008 1026 4.672801 GCAAGTTTTCTTCATCCCATCGTC 60.673 45.833 0.00 0.00 38.17 4.20
1539 3384 1.415659 CTCATCCGCCTCTTCTTCCAT 59.584 52.381 0.00 0.00 0.00 3.41
1765 3646 0.872021 GTGATAGACGCGGCCAAGAG 60.872 60.000 9.25 0.00 0.00 2.85
1814 3695 4.794439 TCCTGCGCCGACATCGTG 62.794 66.667 4.18 0.00 37.74 4.35
2095 3993 0.889186 GCCAACGACAACTCCACCAT 60.889 55.000 0.00 0.00 0.00 3.55
2701 4633 5.360144 TCTCTGCTGTAACATCCTTAGGTAC 59.640 44.000 0.00 0.00 0.00 3.34
3036 6710 5.484173 TGTACGAATCTCCATGCAAAATC 57.516 39.130 0.00 0.00 0.00 2.17
3114 7230 4.723754 GCCAAACTGAAACGAAAAACAAGC 60.724 41.667 0.00 0.00 0.00 4.01
3187 7303 0.693049 TTGGTGAGAGAAAGAGGGCC 59.307 55.000 0.00 0.00 0.00 5.80
3210 7326 6.605119 CCAAGGTGATATTCAAATCCCTAGT 58.395 40.000 0.00 0.00 30.74 2.57
3214 7330 5.827797 GGTGATATTCAAATCCCTAGTTGCA 59.172 40.000 0.00 0.00 30.81 4.08
3234 7350 0.671472 TGTCGCCGTCTTCTCGTCTA 60.671 55.000 0.00 0.00 0.00 2.59
3243 7359 0.532573 CTTCTCGTCTAGCCCAGCAA 59.467 55.000 0.00 0.00 0.00 3.91
3257 7373 1.071471 AGCAAGGTGGACCAGTTCG 59.929 57.895 0.00 0.00 38.89 3.95
3288 7404 1.501582 CTAGGGAAGTCTTGGAGGGG 58.498 60.000 0.00 0.00 0.00 4.79
3345 7461 0.896019 AGCAGCTACTCGACTGTGGT 60.896 55.000 0.00 0.00 36.26 4.16
3347 7463 0.734253 CAGCTACTCGACTGTGGTGC 60.734 60.000 0.00 0.00 0.00 5.01
3377 7493 1.079405 GTGGAAGACGGCCGAATCA 60.079 57.895 35.90 18.63 0.00 2.57
3445 7561 1.279496 ACAAGTGGCTCTAGATGGCA 58.721 50.000 12.33 12.33 37.66 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 70 1.482278 TGCAAACACGCCGAATTTTC 58.518 45.000 0.00 0.00 0.00 2.29
74 76 1.565156 GACTCATGCAAACACGCCGA 61.565 55.000 0.00 0.00 0.00 5.54
107 109 5.184864 TCATACAAACAAGGCCGATTTTCAT 59.815 36.000 0.00 0.00 0.00 2.57
245 247 0.179174 AAATTTTCGACCATCGCCGC 60.179 50.000 0.00 0.00 40.21 6.53
252 254 0.594110 GACCCGCAAATTTTCGACCA 59.406 50.000 11.88 0.00 0.00 4.02
361 363 9.816354 ATGTAAAATGTATTTTTGATAGTGCCC 57.184 29.630 7.78 0.00 40.24 5.36
953 971 6.473778 GCATGCGTATTTATAGTCTCGATCAT 59.526 38.462 0.00 0.00 0.00 2.45
1008 1026 2.627004 CTCGATCGAGGGACGTCG 59.373 66.667 32.81 9.62 42.19 5.12
1539 3384 1.765904 TGTACCTGGACAAAGCAGTCA 59.234 47.619 0.00 0.00 40.29 3.41
1765 3646 3.309954 CGGACATTTTTCCTCGATCTTCC 59.690 47.826 0.00 0.00 32.88 3.46
2042 3940 1.617947 GGTCACGGAAGGAGGAGCAT 61.618 60.000 0.00 0.00 0.00 3.79
2701 4633 1.013596 TTGCATGAAGGGATAACGCG 58.986 50.000 3.53 3.53 0.00 6.01
2957 6566 4.354662 TCACACCCTTTTTGTTTACCCTT 58.645 39.130 0.00 0.00 0.00 3.95
3010 6684 5.697473 TTGCATGGAGATTCGTACAAAAA 57.303 34.783 0.00 0.00 0.00 1.94
3036 6710 3.498777 TCAGTCGATGCTATAGTCCTTCG 59.501 47.826 0.84 5.63 0.00 3.79
3114 7230 6.074994 GGAGAAGTGTAATTTCACGCGTATAG 60.075 42.308 13.44 0.00 42.40 1.31
3187 7303 7.469181 GCAACTAGGGATTTGAATATCACCTTG 60.469 40.741 0.00 0.00 31.69 3.61
3214 7330 1.136984 GACGAGAAGACGGCGACAT 59.863 57.895 16.62 0.00 37.61 3.06
3234 7350 3.971702 GGTCCACCTTGCTGGGCT 61.972 66.667 0.00 0.00 41.11 5.19
3243 7359 1.913762 CCTCCGAACTGGTCCACCT 60.914 63.158 0.00 0.00 39.52 4.00
3257 7373 2.124695 CCCTAGCAAACCGCCTCC 60.125 66.667 0.00 0.00 44.04 4.30
3288 7404 2.156051 AACCTCTCCGACCGCAGAAC 62.156 60.000 0.00 0.00 0.00 3.01
3329 7445 0.896019 AGCACCACAGTCGAGTAGCT 60.896 55.000 0.00 0.00 0.00 3.32
3347 7463 0.397941 TCTTCCACCAGCTTCACCAG 59.602 55.000 0.00 0.00 0.00 4.00
3377 7493 1.082117 CGTAGAAGCCCATCGCGTTT 61.082 55.000 5.77 0.00 44.76 3.60
3445 7561 1.594331 GGTTTGAGACCGAACTTGCT 58.406 50.000 0.00 0.00 39.00 3.91


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

AutoCloner maintained by Alex Coulton.