Multiple sequence alignment - TraesCS2A01G311100

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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 TraesCS2A01G311100 chr2A 100.000 4016 0 0 1 4016 534629136 534625121 0.000000e+00 7417
1 TraesCS2A01G311100 chr2D 97.399 2422 51 6 187 2605 396665421 396663009 0.000000e+00 4113
2 TraesCS2A01G311100 chr2D 92.404 1198 29 9 2881 4016 396662946 396661749 0.000000e+00 1652
3 TraesCS2A01G311100 chr2D 98.413 189 3 0 1 189 396666904 396666716 2.310000e-87 333
4 TraesCS2A01G311100 chr2B 96.607 1562 36 6 1 1558 470063172 470061624 0.000000e+00 2575
5 TraesCS2A01G311100 chr2B 94.981 1056 49 3 1557 2608 470061522 470060467 0.000000e+00 1653
6 TraesCS2A01G311100 chr2B 94.965 715 28 4 2710 3416 470060397 470059683 0.000000e+00 1114
7 TraesCS2A01G311100 chr2B 87.797 631 38 13 3398 4016 470059628 470059025 0.000000e+00 702
8 TraesCS2A01G311100 chr3A 86.612 366 45 3 2210 2575 293042622 293042261 6.250000e-108 401
9 TraesCS2A01G311100 chr5B 86.612 366 41 2 2210 2575 179796405 179796048 8.090000e-107 398
10 TraesCS2A01G311100 chr5B 90.435 115 9 2 2599 2712 508629656 508629543 2.500000e-32 150
11 TraesCS2A01G311100 chr5B 90.090 111 10 1 2600 2709 508629538 508629648 4.180000e-30 143
12 TraesCS2A01G311100 chr6B 86.066 366 47 1 2210 2575 356796099 356795738 1.350000e-104 390
13 TraesCS2A01G311100 chr6B 91.346 104 9 0 2609 2712 493033403 493033300 4.180000e-30 143
14 TraesCS2A01G311100 chr6B 100.000 40 0 0 3945 3984 353181479 353181440 1.550000e-09 75
15 TraesCS2A01G311100 chr1B 85.519 366 45 2 2210 2575 87188017 87188374 3.790000e-100 375
16 TraesCS2A01G311100 chr1B 81.953 338 35 5 2239 2576 10841076 10840765 3.080000e-66 263
17 TraesCS2A01G311100 chr7D 97.273 110 3 0 2600 2709 128138448 128138557 1.910000e-43 187
18 TraesCS2A01G311100 chr7D 97.000 100 3 0 2609 2708 128138556 128138457 6.900000e-38 169
19 TraesCS2A01G311100 chr6D 91.892 111 8 1 2599 2709 71537540 71537649 1.930000e-33 154
20 TraesCS2A01G311100 chr3B 90.090 111 11 0 2609 2719 786488618 786488728 1.160000e-30 145
21 TraesCS2A01G311100 chr3B 90.000 110 11 0 2614 2723 786488712 786488603 4.180000e-30 143
22 TraesCS2A01G311100 chr5A 88.696 115 11 2 2604 2716 544309553 544309667 5.410000e-29 139


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 TraesCS2A01G311100 chr2A 534625121 534629136 4015 True 7417.000000 7417 100.0000 1 4016 1 chr2A.!!$R1 4015
1 TraesCS2A01G311100 chr2D 396661749 396666904 5155 True 2032.666667 4113 96.0720 1 4016 3 chr2D.!!$R1 4015
2 TraesCS2A01G311100 chr2B 470059025 470063172 4147 True 1511.000000 2575 93.5875 1 4016 4 chr2B.!!$R1 4015

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
486 1788 3.324846 TCTTTAGTCAGATGGCGGCATAT 59.675 43.478 25.86 19.98 0.0 1.78 F
777 2079 5.590259 AGTCTACTTTGTGAATTGCAACAGT 59.410 36.000 0.00 0.00 0.0 3.55 F
2047 3454 1.896220 TGGGCACAAGACTGATTGAC 58.104 50.000 0.00 0.00 34.2 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 3454 3.011818 TGCATGGATGTGCTTACTTCTG 58.988 45.455 0.0 0.0 45.27 3.02 R
2690 4100 0.041684 CCCCTCCATCCCAAAAAGCT 59.958 55.000 0.0 0.0 0.00 3.74 R
3222 4681 0.840288 TAGCTGGAGGGGAAACTGCA 60.840 55.000 0.0 0.0 37.28 4.41 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
75 76 7.491682 TGCAAGTTTCTTGCTTTATTCTTCTT 58.508 30.769 26.88 0.00 45.13 2.52
263 1561 6.506538 AAACTTGCAGATAGGATGGAGTAT 57.493 37.500 0.00 0.00 0.00 2.12
264 1562 7.618019 AAACTTGCAGATAGGATGGAGTATA 57.382 36.000 0.00 0.00 0.00 1.47
486 1788 3.324846 TCTTTAGTCAGATGGCGGCATAT 59.675 43.478 25.86 19.98 0.00 1.78
777 2079 5.590259 AGTCTACTTTGTGAATTGCAACAGT 59.410 36.000 0.00 0.00 0.00 3.55
1767 3172 5.607119 ACTGGCATAACTTCGTTAACTTG 57.393 39.130 3.71 0.00 31.56 3.16
2047 3454 1.896220 TGGGCACAAGACTGATTGAC 58.104 50.000 0.00 0.00 34.20 3.18
2196 3603 3.162147 AGCTATATCTCCTTCTCCGCA 57.838 47.619 0.00 0.00 0.00 5.69
2311 3718 2.361610 CCAAGGTTGGCTCCGCAT 60.362 61.111 0.00 0.00 42.21 4.73
2327 3734 5.168526 TCCGCATGAAATTTTATTCCTCG 57.831 39.130 0.00 0.00 0.00 4.63
2416 3824 1.986882 CCTCTGTTTTGCAGGAAGGT 58.013 50.000 0.00 0.00 45.08 3.50
2431 3839 2.170607 GGAAGGTATACTGAAGGCTGCA 59.829 50.000 0.50 0.00 0.00 4.41
2434 3842 3.610911 AGGTATACTGAAGGCTGCAAAC 58.389 45.455 0.50 0.00 0.00 2.93
2542 3951 5.854010 AGGATAGCGTTCAGATCAGTTTA 57.146 39.130 0.00 0.00 0.00 2.01
2546 3955 2.668457 AGCGTTCAGATCAGTTTAAGCG 59.332 45.455 0.00 0.00 0.00 4.68
2613 4023 9.322773 TCGACTATATGAATAGTATTACCTCCG 57.677 37.037 0.00 0.00 46.71 4.63
2614 4024 9.107177 CGACTATATGAATAGTATTACCTCCGT 57.893 37.037 0.00 0.00 46.71 4.69
2616 4026 9.406113 ACTATATGAATAGTATTACCTCCGTCC 57.594 37.037 0.00 0.00 45.26 4.79
2617 4027 5.997384 ATGAATAGTATTACCTCCGTCCC 57.003 43.478 0.00 0.00 0.00 4.46
2618 4028 4.806892 TGAATAGTATTACCTCCGTCCCA 58.193 43.478 0.00 0.00 0.00 4.37
2619 4029 5.210430 TGAATAGTATTACCTCCGTCCCAA 58.790 41.667 0.00 0.00 0.00 4.12
2621 4031 6.156602 TGAATAGTATTACCTCCGTCCCAAAA 59.843 38.462 0.00 0.00 0.00 2.44
2622 4032 4.914177 AGTATTACCTCCGTCCCAAAAA 57.086 40.909 0.00 0.00 0.00 1.94
2623 4033 4.840271 AGTATTACCTCCGTCCCAAAAAG 58.160 43.478 0.00 0.00 0.00 2.27
2624 4034 3.801307 ATTACCTCCGTCCCAAAAAGT 57.199 42.857 0.00 0.00 0.00 2.66
2625 4035 3.581265 TTACCTCCGTCCCAAAAAGTT 57.419 42.857 0.00 0.00 0.00 2.66
2626 4036 2.447408 ACCTCCGTCCCAAAAAGTTT 57.553 45.000 0.00 0.00 0.00 2.66
2627 4037 2.028876 ACCTCCGTCCCAAAAAGTTTG 58.971 47.619 0.00 0.00 0.00 2.93
2628 4038 2.028876 CCTCCGTCCCAAAAAGTTTGT 58.971 47.619 0.00 0.00 0.00 2.83
2629 4039 2.034179 CCTCCGTCCCAAAAAGTTTGTC 59.966 50.000 0.00 0.00 0.00 3.18
2630 4040 2.949644 CTCCGTCCCAAAAAGTTTGTCT 59.050 45.455 0.00 0.00 0.00 3.41
2631 4041 3.358118 TCCGTCCCAAAAAGTTTGTCTT 58.642 40.909 0.00 0.00 38.10 3.01
2632 4042 4.525024 TCCGTCCCAAAAAGTTTGTCTTA 58.475 39.130 0.00 0.00 35.02 2.10
2633 4043 4.577283 TCCGTCCCAAAAAGTTTGTCTTAG 59.423 41.667 0.00 0.00 35.02 2.18
2634 4044 4.577283 CCGTCCCAAAAAGTTTGTCTTAGA 59.423 41.667 0.00 0.00 35.02 2.10
2635 4045 5.240844 CCGTCCCAAAAAGTTTGTCTTAGAT 59.759 40.000 0.00 0.00 35.02 1.98
2636 4046 6.238925 CCGTCCCAAAAAGTTTGTCTTAGATT 60.239 38.462 0.00 0.00 35.02 2.40
2637 4047 7.200455 CGTCCCAAAAAGTTTGTCTTAGATTT 58.800 34.615 0.00 0.00 35.02 2.17
2638 4048 7.167468 CGTCCCAAAAAGTTTGTCTTAGATTTG 59.833 37.037 0.00 0.00 35.02 2.32
2639 4049 7.979537 GTCCCAAAAAGTTTGTCTTAGATTTGT 59.020 33.333 0.00 0.00 33.26 2.83
2640 4050 8.194769 TCCCAAAAAGTTTGTCTTAGATTTGTC 58.805 33.333 0.00 0.00 33.26 3.18
2641 4051 8.197439 CCCAAAAAGTTTGTCTTAGATTTGTCT 58.803 33.333 0.00 0.00 33.26 3.41
2648 4058 9.790389 AGTTTGTCTTAGATTTGTCTAGATACG 57.210 33.333 0.00 0.00 0.00 3.06
2649 4059 9.021863 GTTTGTCTTAGATTTGTCTAGATACGG 57.978 37.037 0.00 0.00 0.00 4.02
2650 4060 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
2651 4061 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
2652 4062 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
2653 4063 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
2654 4064 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
2690 4100 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2702 4112 7.015584 ACAAATCTAAGACAAGCTTTTTGGGAT 59.984 33.333 16.28 6.42 36.69 3.85
2703 4113 5.964958 TCTAAGACAAGCTTTTTGGGATG 57.035 39.130 0.00 0.00 38.05 3.51
2756 4185 7.158021 TGGACCTAAATATTTGTTGGCAAAAG 58.842 34.615 11.05 0.00 46.23 2.27
2795 4224 0.610232 AGGGATGCAAGTGGTTCAGC 60.610 55.000 0.00 0.00 0.00 4.26
2825 4254 6.611613 CATCCCTCTATGCTGGTATTCTAA 57.388 41.667 0.00 0.00 0.00 2.10
2877 4306 9.984190 GGGACCTAACATAACAACATTTTTAAA 57.016 29.630 0.00 0.00 0.00 1.52
3048 4477 2.883026 ACCTATCAAGCTATCTCGCCT 58.117 47.619 0.00 0.00 0.00 5.52
3179 4638 9.586150 GTACATGCTTTTTCATATGTAGATTCG 57.414 33.333 1.90 0.00 36.87 3.34
3222 4681 3.534554 TCGCAGATTGCATGATGTTACT 58.465 40.909 0.00 0.00 45.36 2.24
3316 4775 4.770531 TCTCCTAGTTCCGATTTGAGTTCA 59.229 41.667 0.00 0.00 0.00 3.18
3355 4814 2.426024 GGACGTCTCATAGCCTTGTGTA 59.574 50.000 16.46 0.00 0.00 2.90
3356 4815 3.068307 GGACGTCTCATAGCCTTGTGTAT 59.932 47.826 16.46 0.00 0.00 2.29
3357 4816 4.045104 GACGTCTCATAGCCTTGTGTATG 58.955 47.826 8.70 0.00 0.00 2.39
3359 4818 4.643334 ACGTCTCATAGCCTTGTGTATGTA 59.357 41.667 0.00 0.00 0.00 2.29
3360 4819 5.126545 ACGTCTCATAGCCTTGTGTATGTAA 59.873 40.000 0.00 0.00 0.00 2.41
3361 4820 6.040247 CGTCTCATAGCCTTGTGTATGTAAA 58.960 40.000 0.00 0.00 0.00 2.01
3460 5006 8.902806 TGTAAATTCACTGTCTTTCAGATTGTT 58.097 29.630 1.79 0.00 46.27 2.83
3533 5079 6.037610 GTGCTGATTAGAGAACCATCGAAATT 59.962 38.462 0.00 0.00 0.00 1.82
3539 5085 9.314321 GATTAGAGAACCATCGAAATTACAGAA 57.686 33.333 0.00 0.00 0.00 3.02
3599 5145 3.902150 AGATCGATACGAACATGCGAAT 58.098 40.909 0.00 0.00 39.99 3.34
3602 5148 3.440228 TCGATACGAACATGCGAATTCA 58.560 40.909 6.22 0.00 31.06 2.57
3680 5226 2.821969 GAGGTTCACATTTGGCAGATGT 59.178 45.455 17.11 17.11 38.21 3.06
3832 5390 2.172082 CAGATTGGATGCCTTCCTCTCA 59.828 50.000 4.59 0.00 45.68 3.27
3871 5429 5.029807 TGTGGATCAGACACACAAGTTTA 57.970 39.130 6.55 0.00 43.35 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 4.832248 CCACTCCAGAAGTAGCAAATACA 58.168 43.478 0.00 0.00 36.07 2.29
263 1561 3.201266 ACACCAACCAAAAGAGTCTGGTA 59.799 43.478 3.14 0.00 45.39 3.25
486 1788 6.403049 TCCTTTCTTGTACGCTCATATTCAA 58.597 36.000 0.00 0.00 0.00 2.69
755 2057 5.588246 TCACTGTTGCAATTCACAAAGTAGA 59.412 36.000 0.59 0.00 0.00 2.59
777 2079 4.335315 GTGGAAGAGTCAAACAACACATCA 59.665 41.667 0.00 0.00 0.00 3.07
1191 2493 7.174946 TGGCTTTAAATCACTTAACAAGAGAGG 59.825 37.037 0.00 0.00 31.69 3.69
1767 3172 3.262420 AGGTATGTCGTCATTCAAGCAC 58.738 45.455 0.00 0.00 35.70 4.40
2047 3454 3.011818 TGCATGGATGTGCTTACTTCTG 58.988 45.455 0.00 0.00 45.27 3.02
2308 3715 8.131100 TCTCATTCGAGGAATAAAATTTCATGC 58.869 33.333 0.00 0.00 39.95 4.06
2341 3749 5.532406 TGCTCATCTTTCTACAAGCAAGTTT 59.468 36.000 0.00 0.00 36.86 2.66
2416 3824 3.259064 GTCGTTTGCAGCCTTCAGTATA 58.741 45.455 0.00 0.00 0.00 1.47
2431 3839 5.374071 ACCCTTTCTTGAAGTATGTCGTTT 58.626 37.500 0.00 0.00 33.29 3.60
2434 3842 5.721232 AGTACCCTTTCTTGAAGTATGTCG 58.279 41.667 0.00 0.00 33.29 4.35
2542 3951 3.437049 GCTCTGGTTGATTCTAAACGCTT 59.563 43.478 0.00 0.00 0.00 4.68
2546 3955 3.125316 CCGTGCTCTGGTTGATTCTAAAC 59.875 47.826 0.00 0.00 0.00 2.01
2578 3987 3.587797 TCATATAGTCGATTTCCCCGC 57.412 47.619 0.00 0.00 0.00 6.13
2579 3988 6.864342 ACTATTCATATAGTCGATTTCCCCG 58.136 40.000 0.00 0.00 42.61 5.73
2608 4018 2.028876 ACAAACTTTTTGGGACGGAGG 58.971 47.619 3.82 0.00 0.00 4.30
2609 4019 2.949644 AGACAAACTTTTTGGGACGGAG 59.050 45.455 3.82 0.00 0.00 4.63
2613 4023 7.979537 ACAAATCTAAGACAAACTTTTTGGGAC 59.020 33.333 3.82 0.00 37.77 4.46
2614 4024 8.073467 ACAAATCTAAGACAAACTTTTTGGGA 57.927 30.769 3.82 0.00 37.77 4.37
2615 4025 8.197439 AGACAAATCTAAGACAAACTTTTTGGG 58.803 33.333 3.82 0.00 37.77 4.12
2622 4032 9.790389 CGTATCTAGACAAATCTAAGACAAACT 57.210 33.333 0.00 0.00 36.98 2.66
2623 4033 9.021863 CCGTATCTAGACAAATCTAAGACAAAC 57.978 37.037 0.00 0.00 36.98 2.93
2624 4034 8.963725 TCCGTATCTAGACAAATCTAAGACAAA 58.036 33.333 0.00 0.00 36.98 2.83
2625 4035 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2626 4036 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
2627 4037 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
2628 4038 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
2663 4073 9.788889 TGTCTTAGATTTGTCTAGATACGGATA 57.211 33.333 0.00 0.00 0.00 2.59
2670 4080 9.732130 AAAAGCTTGTCTTAGATTTGTCTAGAT 57.268 29.630 0.00 0.00 34.28 1.98
2677 4087 6.748132 TCCCAAAAAGCTTGTCTTAGATTTG 58.252 36.000 0.00 4.37 34.28 2.32
2682 4092 4.766891 TCCATCCCAAAAAGCTTGTCTTAG 59.233 41.667 0.00 0.00 33.88 2.18
2690 4100 0.041684 CCCCTCCATCCCAAAAAGCT 59.958 55.000 0.00 0.00 0.00 3.74
2702 4112 9.871175 GTTATAAAATATAAAAGACCCCCTCCA 57.129 33.333 0.00 0.00 0.00 3.86
2729 4158 7.962995 TTGCCAACAAATATTTAGGTCCATA 57.037 32.000 0.00 0.00 31.21 2.74
2739 4168 8.835439 CAAAACTACCTTTTGCCAACAAATATT 58.165 29.630 0.00 0.00 44.96 1.28
2756 4185 5.592688 TCCCTTAAGCATATGCAAAACTACC 59.407 40.000 28.62 0.00 45.16 3.18
2766 4195 4.022589 CCACTTGCATCCCTTAAGCATATG 60.023 45.833 0.00 0.00 38.19 1.78
2775 4204 1.915141 CTGAACCACTTGCATCCCTT 58.085 50.000 0.00 0.00 0.00 3.95
2812 4241 4.816385 GCTGCACTAATTAGAATACCAGCA 59.184 41.667 24.66 18.05 41.85 4.41
3048 4477 2.712709 TGTTGAACTCAAACCCGAACA 58.287 42.857 0.00 0.00 37.63 3.18
3222 4681 0.840288 TAGCTGGAGGGGAAACTGCA 60.840 55.000 0.00 0.00 37.28 4.41
3390 4863 5.465532 ACAGATACAGATACAGATGCAGG 57.534 43.478 0.00 0.00 0.00 4.85
3460 5006 4.276678 GCCATATTGCAATCTGCTAACTGA 59.723 41.667 16.86 0.00 45.31 3.41
3533 5079 7.064609 GTCGAAATCATGTCAGGAAATTCTGTA 59.935 37.037 11.96 0.21 36.25 2.74
3539 5085 7.500227 ACATATGTCGAAATCATGTCAGGAAAT 59.500 33.333 1.41 0.00 0.00 2.17
3599 5145 5.179368 GCTGCAAACTGTATCAGTAAGTGAA 59.821 40.000 2.80 0.00 44.62 3.18
3602 5148 4.899502 AGCTGCAAACTGTATCAGTAAGT 58.100 39.130 1.02 0.00 44.62 2.24
3680 5226 7.086856 CCTTCCAGGAATCAGGATGAAAATGA 61.087 42.308 1.09 0.00 44.32 2.57
3712 5258 2.513666 TAAAGCATCCCAGCGGCG 60.514 61.111 0.51 0.51 40.15 6.46
3832 5390 2.849536 AGCAAAGCTGGAGGCCTT 59.150 55.556 6.77 0.00 43.05 4.35
3871 5429 6.465948 TGTTTTTGGAATGCTTATGCTGATT 58.534 32.000 1.96 0.00 40.48 2.57
3921 5479 4.201763 GGTAGAAGAGCAAATGAGCTTTCG 60.202 45.833 0.00 0.00 46.75 3.46
3985 5543 4.940046 AGTGCTAAAGAGTCCATCAATGTG 59.060 41.667 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.