Multiple sequence alignment - TraesCS2D01G396400

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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 TraesCS2D01G396400 chr2D 100.000 4334 0 0 1 4334 507748405 507752738 0.000000e+00 8004.0
1 TraesCS2D01G396400 chr2A 95.103 3921 119 23 63 3935 652287408 652291303 0.000000e+00 6109.0
2 TraesCS2D01G396400 chr2A 96.797 281 8 1 3989 4269 652291456 652291735 6.560000e-128 468.0
3 TraesCS2D01G396400 chr2A 94.118 68 4 0 4254 4321 652291764 652291831 2.130000e-18 104.0
4 TraesCS2D01G396400 chr2B 95.601 3546 124 19 397 3935 596409821 596413341 0.000000e+00 5655.0
5 TraesCS2D01G396400 chr2B 97.989 348 5 1 3989 4334 596413493 596413840 1.720000e-168 603.0
6 TraesCS2D01G396400 chr2B 94.583 240 10 3 1 239 596409571 596409808 6.850000e-98 368.0
7 TraesCS2D01G396400 chr2B 96.610 59 1 1 3933 3991 596413395 596413452 3.570000e-16 97.1
8 TraesCS2D01G396400 chr5A 74.930 714 149 28 1428 2126 593089878 593089180 2.530000e-77 300.0
9 TraesCS2D01G396400 chr4D 75.542 646 138 19 1435 2070 50641669 50642304 2.530000e-77 300.0
10 TraesCS2D01G396400 chr4D 74.595 370 67 24 2548 2902 387756418 387756775 2.100000e-28 137.0
11 TraesCS2D01G396400 chr5D 74.884 649 137 24 1435 2070 473117336 473116701 5.520000e-69 272.0
12 TraesCS2D01G396400 chr5B 74.017 712 159 24 1428 2126 580515084 580514386 2.570000e-67 267.0
13 TraesCS2D01G396400 chr6D 76.667 360 74 9 2548 2902 427569031 427568677 1.590000e-44 191.0
14 TraesCS2D01G396400 chr7A 87.970 133 15 1 3743 3874 65461698 65461566 5.800000e-34 156.0
15 TraesCS2D01G396400 chr7A 76.923 221 41 8 2559 2774 556299617 556299832 2.740000e-22 117.0
16 TraesCS2D01G396400 chr7A 87.037 54 7 0 2550 2603 33606952 33606899 1.300000e-05 62.1
17 TraesCS2D01G396400 chr7B 78.281 221 38 8 2559 2774 517394136 517394351 2.720000e-27 134.0
18 TraesCS2D01G396400 chr7D 77.376 221 40 8 2559 2774 489114491 489114706 5.890000e-24 122.0
19 TraesCS2D01G396400 chr6B 77.193 228 40 11 2548 2769 219570860 219571081 5.890000e-24 122.0
20 TraesCS2D01G396400 chr6A 81.481 135 23 2 2642 2775 156751702 156751569 4.580000e-20 110.0


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 TraesCS2D01G396400 chr2D 507748405 507752738 4333 False 8004.000 8004 100.000000 1 4334 1 chr2D.!!$F1 4333
1 TraesCS2D01G396400 chr2A 652287408 652291831 4423 False 2227.000 6109 95.339333 63 4321 3 chr2A.!!$F1 4258
2 TraesCS2D01G396400 chr2B 596409571 596413840 4269 False 1680.775 5655 96.195750 1 4334 4 chr2B.!!$F1 4333
3 TraesCS2D01G396400 chr5A 593089180 593089878 698 True 300.000 300 74.930000 1428 2126 1 chr5A.!!$R1 698
4 TraesCS2D01G396400 chr4D 50641669 50642304 635 False 300.000 300 75.542000 1435 2070 1 chr4D.!!$F1 635
5 TraesCS2D01G396400 chr5D 473116701 473117336 635 True 272.000 272 74.884000 1435 2070 1 chr5D.!!$R1 635
6 TraesCS2D01G396400 chr5B 580514386 580515084 698 True 267.000 267 74.017000 1428 2126 1 chr5B.!!$R1 698

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
436 455 0.110486 AAGGAGGCGGTGTCATTGTT 59.890 50.000 0.00 0.0 0.0 2.83 F
440 459 0.179032 AGGCGGTGTCATTGTTGTCA 60.179 50.000 0.00 0.0 0.0 3.58 F
540 559 0.320683 TGGCATATGAATCGCTCCCG 60.321 55.000 6.97 0.0 0.0 5.14 F
1255 1311 0.806868 CTACAACTACGAGACGGCCA 59.193 55.000 2.24 0.0 0.0 5.36 F
3053 3109 1.227089 CCATCTCCGCCGTCTTCAG 60.227 63.158 0.00 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2292 2348 1.202806 CCTGCTTCCTTGACAACCTGA 60.203 52.381 0.00 0.00 0.00 3.86 R
2415 2471 1.225376 TGGTGTACTTCTTTGCCGCG 61.225 55.000 0.00 0.00 0.00 6.46 R
2520 2576 2.532199 TAGTTTGGCCCCCGGGAA 60.532 61.111 26.32 4.79 37.50 3.97 R
3223 3279 3.672295 GAGCGGCCTTGGTCCTCAG 62.672 68.421 0.00 0.00 0.00 3.35 R
3970 4090 2.897326 GGTAACCATCCTGTTTTTGGCT 59.103 45.455 0.00 0.00 33.66 4.75 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
44 45 8.548877 TGTGGATTAACTTTATTCCTAGCTTCT 58.451 33.333 0.00 0.00 35.33 2.85
58 59 7.492352 TCCTAGCTTCTTTACTTTGTGTTTC 57.508 36.000 0.00 0.00 0.00 2.78
164 166 1.676529 ACTACGATCCAGTGTCCATCG 59.323 52.381 12.43 12.43 44.06 3.84
178 180 7.307989 CCAGTGTCCATCGTCCAATAATTTATC 60.308 40.741 0.00 0.00 0.00 1.75
201 203 1.344942 CGTACCGTCAAGTCAGCAGC 61.345 60.000 0.00 0.00 0.00 5.25
231 236 1.393883 GACGCTCCCGATGAAACTTTC 59.606 52.381 0.00 0.00 38.29 2.62
239 244 6.288941 TCCCGATGAAACTTTCTACATACA 57.711 37.500 3.22 0.00 0.00 2.29
240 245 6.884832 TCCCGATGAAACTTTCTACATACAT 58.115 36.000 3.22 0.00 0.00 2.29
241 246 6.761242 TCCCGATGAAACTTTCTACATACATG 59.239 38.462 3.22 0.00 0.00 3.21
380 399 5.532406 CGTACAATCCATTTCCATTCCATCT 59.468 40.000 0.00 0.00 0.00 2.90
385 404 8.995577 ACAATCCATTTCCATTCCATCTAAAAT 58.004 29.630 0.00 0.00 0.00 1.82
393 412 5.054477 CCATTCCATCTAAAATCGTACGGT 58.946 41.667 16.52 4.91 0.00 4.83
436 455 0.110486 AAGGAGGCGGTGTCATTGTT 59.890 50.000 0.00 0.00 0.00 2.83
437 456 0.606401 AGGAGGCGGTGTCATTGTTG 60.606 55.000 0.00 0.00 0.00 3.33
438 457 0.889186 GGAGGCGGTGTCATTGTTGT 60.889 55.000 0.00 0.00 0.00 3.32
439 458 0.517316 GAGGCGGTGTCATTGTTGTC 59.483 55.000 0.00 0.00 0.00 3.18
440 459 0.179032 AGGCGGTGTCATTGTTGTCA 60.179 50.000 0.00 0.00 0.00 3.58
441 460 0.665835 GGCGGTGTCATTGTTGTCAA 59.334 50.000 0.00 0.00 37.98 3.18
471 490 2.250924 ACCAAATTTTCCCCTCAGCAG 58.749 47.619 0.00 0.00 0.00 4.24
540 559 0.320683 TGGCATATGAATCGCTCCCG 60.321 55.000 6.97 0.00 0.00 5.14
544 563 2.332104 CATATGAATCGCTCCCGTGAG 58.668 52.381 0.00 0.00 41.84 3.51
588 608 1.003866 GACGAATCAATGCGCTAACCC 60.004 52.381 9.73 0.00 0.00 4.11
726 757 4.021544 CCCTCCTGAAATATCTCCGAGAAG 60.022 50.000 1.27 0.00 0.00 2.85
773 814 2.637872 AGCAAACCTACTCCAACAGCTA 59.362 45.455 0.00 0.00 0.00 3.32
877 918 1.143305 CTCACTGTTCAGCGGTTCAG 58.857 55.000 8.87 8.87 33.66 3.02
879 920 1.598130 ACTGTTCAGCGGTTCAGCC 60.598 57.895 9.95 0.00 38.01 4.85
1007 1060 1.449353 GCCTCTTCGCCATGGATCT 59.551 57.895 18.40 0.00 0.00 2.75
1016 1069 2.279451 CATGGATCTTCGCGGCGA 60.279 61.111 22.69 22.69 0.00 5.54
1255 1311 0.806868 CTACAACTACGAGACGGCCA 59.193 55.000 2.24 0.00 0.00 5.36
2292 2348 3.322466 CCTCGGGTGCAGAAGGGT 61.322 66.667 0.00 0.00 0.00 4.34
2310 2366 1.476833 GGTCAGGTTGTCAAGGAAGCA 60.477 52.381 0.00 0.00 0.00 3.91
2520 2576 4.719369 GTGGTCGCCGCGTTCTCT 62.719 66.667 13.39 0.00 0.00 3.10
2922 2978 1.927487 TTGGGCAGAACGAGTACCTA 58.073 50.000 0.00 0.00 0.00 3.08
3053 3109 1.227089 CCATCTCCGCCGTCTTCAG 60.227 63.158 0.00 0.00 0.00 3.02
3223 3279 1.067071 AGCTCGCCTACAAGGTTACAC 60.067 52.381 0.00 0.00 37.80 2.90
3366 3422 3.846360 AGTACTGTATCGTTGTTCTGCC 58.154 45.455 0.00 0.00 0.00 4.85
3378 3435 0.460459 GTTCTGCCTTAGTCGAGGGC 60.460 60.000 10.50 10.50 45.45 5.19
3463 3520 3.054503 CAGCCAGCTGCACAGGAC 61.055 66.667 8.66 0.00 44.83 3.85
3604 3668 4.720046 TGTGTGTGTACAACATATTGGGT 58.280 39.130 0.00 0.00 41.97 4.51
3619 3683 4.250305 GGTGTGACCCAGCGGTGT 62.250 66.667 14.40 0.00 44.88 4.16
3623 3687 3.625897 TGACCCAGCGGTGTGGAG 61.626 66.667 23.30 8.86 44.88 3.86
3660 3724 5.733373 GCGAATTTAGCTCGATTCCCAAATT 60.733 40.000 13.42 7.54 38.61 1.82
3705 3769 3.396260 TTCTTGTAGTTCTCCCCAACG 57.604 47.619 0.00 0.00 0.00 4.10
3840 3904 1.160137 CTGAAAACTGGGCTTCTCCG 58.840 55.000 0.00 0.00 34.94 4.63
3887 3951 0.260230 TCACCAAGGGGCTGTTTCAA 59.740 50.000 0.00 0.00 37.90 2.69
3928 3992 4.826274 AACTTGCTGCTGAACCTCTATA 57.174 40.909 0.00 0.00 0.00 1.31
3929 3993 4.130286 ACTTGCTGCTGAACCTCTATAC 57.870 45.455 0.00 0.00 0.00 1.47
3970 4090 7.444183 AGAACAATTTAAAGGATCGAACACTCA 59.556 33.333 0.00 0.00 0.00 3.41
3972 4092 5.803020 ATTTAAAGGATCGAACACTCAGC 57.197 39.130 0.00 0.00 0.00 4.26
4128 4291 3.189080 TGTTATGTTCTGACAGCACATGC 59.811 43.478 25.19 18.72 39.58 4.06
4187 4352 5.969435 CAGTGTGTCAATATTTGCAGCTATG 59.031 40.000 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.229506 AGCTAGGAATAAAGTTAATCCACATGC 59.770 37.037 7.70 6.02 35.58 4.06
44 45 7.981142 ACAATCTTCTCGAAACACAAAGTAAA 58.019 30.769 0.00 0.00 0.00 2.01
164 166 4.152938 GGTACGGGCGATAAATTATTGGAC 59.847 45.833 2.71 0.00 0.00 4.02
201 203 1.519455 GGGAGCGTCGGATGAAGTG 60.519 63.158 0.33 0.00 0.00 3.16
231 236 3.332919 GCTCCATGGCTCATGTATGTAG 58.667 50.000 6.96 0.00 39.94 2.74
239 244 3.248764 GAGGGCTCCATGGCTCAT 58.751 61.111 6.96 0.00 41.48 2.90
266 281 0.107456 CCTCGCCCAGCTGTATCATT 59.893 55.000 13.81 0.00 0.00 2.57
333 352 2.969950 TGATTAGGGTAATCTGGGACGG 59.030 50.000 7.90 0.00 43.79 4.79
380 399 3.487376 CGAGGCTGTACCGTACGATTTTA 60.487 47.826 18.76 0.00 46.52 1.52
385 404 2.753966 GCGAGGCTGTACCGTACGA 61.754 63.158 18.76 0.00 46.52 3.43
393 412 0.178068 GAAAGGGATGCGAGGCTGTA 59.822 55.000 0.00 0.00 0.00 2.74
436 455 7.040823 GGAAAATTTGGTAATGGCAAATTGACA 60.041 33.333 3.10 3.10 41.29 3.58
437 456 7.304735 GGAAAATTTGGTAATGGCAAATTGAC 58.695 34.615 0.00 0.00 38.19 3.18
438 457 6.432472 GGGAAAATTTGGTAATGGCAAATTGA 59.568 34.615 0.00 0.00 38.19 2.57
439 458 6.350027 GGGGAAAATTTGGTAATGGCAAATTG 60.350 38.462 0.00 0.00 38.19 2.32
440 459 5.714333 GGGGAAAATTTGGTAATGGCAAATT 59.286 36.000 0.00 0.00 39.36 1.82
441 460 5.015072 AGGGGAAAATTTGGTAATGGCAAAT 59.985 36.000 0.00 0.00 0.00 2.32
526 545 0.673985 CCTCACGGGAGCGATTCATA 59.326 55.000 9.89 0.00 39.96 2.15
540 559 2.435059 GTTGCTCGGGCTCCTCAC 60.435 66.667 9.62 0.00 39.59 3.51
726 757 4.972440 GCTTGTCACACATTCTTCTTTCAC 59.028 41.667 0.00 0.00 0.00 3.18
773 814 3.461773 CGGTGACCCTGCGAGGAT 61.462 66.667 0.00 0.00 37.67 3.24
877 918 2.606587 TTGAAGAGGAGCAGGGGGC 61.607 63.158 0.00 0.00 45.30 5.80
879 920 0.251634 GAGTTGAAGAGGAGCAGGGG 59.748 60.000 0.00 0.00 0.00 4.79
1007 1060 3.138128 TCCATCTCTCGCCGCGAA 61.138 61.111 17.53 2.08 34.74 4.70
1092 1148 3.865745 CCATGTGGACGATGTAAGTCTTC 59.134 47.826 0.00 0.00 38.58 2.87
1905 1961 1.246056 ACAGGCTGTCGCGGTAGTAA 61.246 55.000 15.88 0.00 36.88 2.24
2292 2348 1.202806 CCTGCTTCCTTGACAACCTGA 60.203 52.381 0.00 0.00 0.00 3.86
2310 2366 1.374190 GATCATGCCGATGCCTCCT 59.626 57.895 0.00 0.00 33.17 3.69
2415 2471 1.225376 TGGTGTACTTCTTTGCCGCG 61.225 55.000 0.00 0.00 0.00 6.46
2520 2576 2.532199 TAGTTTGGCCCCCGGGAA 60.532 61.111 26.32 4.79 37.50 3.97
2951 3007 3.909086 AAGCCCTTGAGCTGCGTCC 62.909 63.158 0.00 0.00 44.11 4.79
3223 3279 3.672295 GAGCGGCCTTGGTCCTCAG 62.672 68.421 0.00 0.00 0.00 3.35
3366 3422 1.381327 TCCCAGGCCCTCGACTAAG 60.381 63.158 0.00 0.00 0.00 2.18
3378 3435 2.438075 GCTGCTTCTGCTCCCAGG 60.438 66.667 0.00 0.00 39.61 4.45
3403 3460 1.519455 CTCGCTTACCAAGAGGCCG 60.519 63.158 0.00 0.00 39.06 6.13
3408 3465 2.565391 TCATCAACCTCGCTTACCAAGA 59.435 45.455 0.00 0.00 0.00 3.02
3454 3511 0.603707 GCAAGTGCTAGTCCTGTGCA 60.604 55.000 0.00 0.00 38.21 4.57
3463 3520 1.734465 CTTTCTTCCGGCAAGTGCTAG 59.266 52.381 0.00 0.00 41.70 3.42
3604 3668 4.248842 CCACACCGCTGGGTCACA 62.249 66.667 0.00 0.00 46.01 3.58
3619 3683 1.617018 CGCCCTGATGGAGTTCTCCA 61.617 60.000 21.55 21.55 44.85 3.86
3623 3687 2.044123 AATTCGCCCTGATGGAGTTC 57.956 50.000 0.00 0.00 35.07 3.01
3634 3698 1.531578 GGAATCGAGCTAAATTCGCCC 59.468 52.381 12.15 0.00 37.94 6.13
3660 3724 1.576451 GCACATGCGATGGTGTCACA 61.576 55.000 5.12 0.00 37.35 3.58
3840 3904 4.452795 GGAACACTAGAAGCTGGAGAAAAC 59.547 45.833 0.00 0.00 0.00 2.43
3970 4090 2.897326 GGTAACCATCCTGTTTTTGGCT 59.103 45.455 0.00 0.00 33.66 4.75
4128 4291 6.749578 CCTTCTTCTGTATATATGCTGTAGCG 59.250 42.308 2.37 1.31 45.83 4.26
4187 4352 5.473504 ACAATGACCAGATTCACCAAACTAC 59.526 40.000 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.