Multiple sequence alignment - TraesCS2D01G384200

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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 TraesCS2D01G384200 chr2D 100.000 3235 0 0 1 3235 488554579 488551345 0.000000e+00 5975
1 TraesCS2D01G384200 chr2D 94.404 3145 106 24 149 3235 488455085 488451953 0.000000e+00 4769
2 TraesCS2D01G384200 chr2D 95.645 2549 69 6 1 2547 489370718 489368210 0.000000e+00 4054
3 TraesCS2D01G384200 chr2D 86.530 1804 166 33 746 2545 82143569 82145299 0.000000e+00 1914
4 TraesCS2D01G384200 chr2D 84.214 1495 159 33 1232 2688 450992708 450994163 0.000000e+00 1382
5 TraesCS2D01G384200 chr2D 94.695 754 36 1 1 750 82142762 82143515 0.000000e+00 1168
6 TraesCS2D01G384200 chr2D 89.875 721 37 13 2528 3233 489367851 489367152 0.000000e+00 894
7 TraesCS2D01G384200 chr2D 89.220 705 56 8 1 685 450990887 450991591 0.000000e+00 863
8 TraesCS2D01G384200 chr2D 83.358 673 97 10 1570 2228 450986090 450986761 2.760000e-170 608
9 TraesCS2D01G384200 chr2D 83.991 456 48 13 756 1196 450992179 450992624 6.460000e-112 414
10 TraesCS2D01G384200 chr2D 82.131 291 46 4 1233 1517 450984834 450985124 8.970000e-61 244
11 TraesCS2D01G384200 chr2D 99.194 124 0 1 1 124 488455193 488455071 4.200000e-54 222
12 TraesCS2D01G384200 chr2D 94.366 142 8 0 2405 2546 489368218 489368077 5.430000e-53 219
13 TraesCS2D01G384200 chr2B 96.348 2574 90 4 1 2574 572706218 572703649 0.000000e+00 4229
14 TraesCS2D01G384200 chr2B 84.754 2158 228 51 746 2896 133980073 133982136 0.000000e+00 2069
15 TraesCS2D01G384200 chr2B 83.311 1498 167 40 1232 2688 531131561 531133016 0.000000e+00 1304
16 TraesCS2D01G384200 chr2B 89.220 705 56 8 1 685 531129710 531130414 0.000000e+00 863
17 TraesCS2D01G384200 chr2B 88.937 696 40 21 2570 3235 572692785 572692097 0.000000e+00 824
18 TraesCS2D01G384200 chr2B 91.708 603 32 4 1 602 133979332 133979917 0.000000e+00 821
19 TraesCS2D01G384200 chr2B 87.719 285 31 4 915 1196 531131194 531131477 2.410000e-86 329
20 TraesCS2D01G384200 chr2B 93.421 76 4 1 641 715 133979914 133979989 9.490000e-21 111
21 TraesCS2D01G384200 chr2A 85.505 1366 142 29 1232 2575 598621591 598620260 0.000000e+00 1375
22 TraesCS2D01G384200 chr2A 89.124 708 57 8 1 688 598623373 598622666 0.000000e+00 863
23 TraesCS2D01G384200 chr2A 84.211 456 47 15 756 1196 598622120 598621675 1.390000e-113 420
24 TraesCS2D01G384200 chr3D 75.049 509 103 22 50 546 390658593 390659089 7.030000e-52 215


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 TraesCS2D01G384200 chr2D 488551345 488554579 3234 True 5975.000000 5975 100.000000 1 3235 1 chr2D.!!$R1 3234
1 TraesCS2D01G384200 chr2D 488451953 488455193 3240 True 2495.500000 4769 96.799000 1 3235 2 chr2D.!!$R2 3234
2 TraesCS2D01G384200 chr2D 489367152 489370718 3566 True 1722.333333 4054 93.295333 1 3233 3 chr2D.!!$R3 3232
3 TraesCS2D01G384200 chr2D 82142762 82145299 2537 False 1541.000000 1914 90.612500 1 2545 2 chr2D.!!$F1 2544
4 TraesCS2D01G384200 chr2D 450990887 450994163 3276 False 886.333333 1382 85.808333 1 2688 3 chr2D.!!$F3 2687
5 TraesCS2D01G384200 chr2D 450984834 450986761 1927 False 426.000000 608 82.744500 1233 2228 2 chr2D.!!$F2 995
6 TraesCS2D01G384200 chr2B 572703649 572706218 2569 True 4229.000000 4229 96.348000 1 2574 1 chr2B.!!$R2 2573
7 TraesCS2D01G384200 chr2B 133979332 133982136 2804 False 1000.333333 2069 89.961000 1 2896 3 chr2B.!!$F1 2895
8 TraesCS2D01G384200 chr2B 531129710 531133016 3306 False 832.000000 1304 86.750000 1 2688 3 chr2B.!!$F2 2687
9 TraesCS2D01G384200 chr2B 572692097 572692785 688 True 824.000000 824 88.937000 2570 3235 1 chr2B.!!$R1 665
10 TraesCS2D01G384200 chr2A 598620260 598623373 3113 True 886.000000 1375 86.280000 1 2575 3 chr2A.!!$R1 2574

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
384 385 2.181021 GACGCCGATGGACTCGTT 59.819 61.111 0.0 0.0 46.18 3.85 F
1190 1946 2.807967 TCAATGAGCAGGTGAGAAAACG 59.192 45.455 0.0 0.0 0.00 3.60 F
1525 3264 4.365514 TCAGTAACCATGAAGAAGCCAA 57.634 40.909 0.0 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 2252 0.537143 TTGTGTTGCCTAGCACCCTG 60.537 55.000 0.00 0.0 38.71 4.45 R
2175 3926 0.659957 GGAACGCTGGCAATCTGATC 59.340 55.000 0.00 0.0 0.00 2.92 R
3038 5218 2.170187 TGTTGCTGAATTGGGCAAGTTT 59.830 40.909 12.95 0.0 46.87 2.66 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
247 248 2.507102 CCGTCGAGATGCGCAACT 60.507 61.111 21.06 21.06 40.61 3.16
384 385 2.181021 GACGCCGATGGACTCGTT 59.819 61.111 0.00 0.00 46.18 3.85
647 673 9.519191 TGAATTCAATTCTCTCTTATGACCAAA 57.481 29.630 11.46 0.00 39.96 3.28
816 1471 4.626042 AGCGCACCATGAAAACAAAATAA 58.374 34.783 11.47 0.00 0.00 1.40
935 1661 6.425210 TCTACTATTTCATGGGTGGATCAG 57.575 41.667 0.00 0.00 0.00 2.90
1177 1933 3.795623 ATGTCAATGGCTTCAATGAGC 57.204 42.857 0.00 0.00 41.96 4.26
1190 1946 2.807967 TCAATGAGCAGGTGAGAAAACG 59.192 45.455 0.00 0.00 0.00 3.60
1198 1954 4.396166 AGCAGGTGAGAAAACGAATTATGG 59.604 41.667 0.00 0.00 0.00 2.74
1200 1956 5.673818 GCAGGTGAGAAAACGAATTATGGAC 60.674 44.000 0.00 0.00 0.00 4.02
1443 2252 6.212888 AGGCTTGTCAATAATCCAAATGTC 57.787 37.500 0.00 0.00 0.00 3.06
1525 3264 4.365514 TCAGTAACCATGAAGAAGCCAA 57.634 40.909 0.00 0.00 0.00 4.52
1544 3283 5.128827 AGCCAATTGATGATTTTGATGAGCT 59.871 36.000 7.12 0.00 0.00 4.09
1549 3288 5.571784 TGATGATTTTGATGAGCTTGGTC 57.428 39.130 0.00 0.00 0.00 4.02
1821 3571 5.879223 ACTGTTTGCCATCACAAAATTTTCA 59.121 32.000 0.00 0.00 40.99 2.69
1913 3663 7.847096 AGTTTAAATTTATCCTTTCCGCCATT 58.153 30.769 0.00 0.00 0.00 3.16
1970 3721 5.616866 CGCTTTGTACAAATTCGACTGGATT 60.617 40.000 25.91 0.00 32.08 3.01
2069 3820 8.970859 AACCATTGAAACAAAATAATGACCAA 57.029 26.923 0.00 0.00 33.50 3.67
2076 3827 8.260818 TGAAACAAAATAATGACCAACCAAAGA 58.739 29.630 0.00 0.00 0.00 2.52
2175 3926 3.131223 ACTCTCCATGTCGGACATTAGTG 59.869 47.826 20.52 20.30 39.64 2.74
2307 4062 8.804743 CATCGTTAGTGTTTTCTTGATATACGT 58.195 33.333 0.00 0.00 0.00 3.57
2626 4800 3.589988 ACTAACTACAGATGCAGTGCAC 58.410 45.455 22.44 9.40 43.04 4.57
2627 4801 2.549064 AACTACAGATGCAGTGCACA 57.451 45.000 22.44 0.00 43.04 4.57
2756 4935 1.681264 GCCAAGGGTATGCCAATGTAC 59.319 52.381 1.04 0.00 36.17 2.90
2970 5150 8.863872 AGCTATTACAAAAGAATACACTTGGT 57.136 30.769 0.00 0.00 0.00 3.67
3210 5431 6.901887 GCTTGTGTCATATAACAACAAGATCG 59.098 38.462 18.13 2.16 38.79 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
502 503 2.342279 CTGGTGAAGAACGCGGGA 59.658 61.111 12.47 0.00 0.00 5.14
647 673 7.787623 AGTTACACTAAGTATGGTGGTTAGT 57.212 36.000 0.00 0.00 41.94 2.24
816 1471 6.153680 TGGTTCCAAAGTGTGTAAAGACAAAT 59.846 34.615 0.00 0.00 37.31 2.32
935 1661 7.728847 ATTTAAATTTCTGGACCAAGTTTGC 57.271 32.000 0.00 0.00 0.00 3.68
973 1729 0.618458 TTGACATAGGGTCCACTGCC 59.382 55.000 0.00 0.00 46.38 4.85
1177 1933 5.163754 GGTCCATAATTCGTTTTCTCACCTG 60.164 44.000 0.00 0.00 0.00 4.00
1190 1946 7.385752 CACATATTTGGCAATGGTCCATAATTC 59.614 37.037 4.33 0.00 32.92 2.17
1198 1954 6.476380 CACAATACACATATTTGGCAATGGTC 59.524 38.462 0.00 0.00 0.00 4.02
1200 1956 6.256104 CACACAATACACATATTTGGCAATGG 59.744 38.462 0.00 0.00 0.00 3.16
1443 2252 0.537143 TTGTGTTGCCTAGCACCCTG 60.537 55.000 0.00 0.00 38.71 4.45
1525 3264 6.540438 ACCAAGCTCATCAAAATCATCAAT 57.460 33.333 0.00 0.00 0.00 2.57
1544 3283 6.183360 CGTATCCAATTGTTTATCACGACCAA 60.183 38.462 4.43 0.00 0.00 3.67
1549 3288 7.172654 TCATCGTATCCAATTGTTTATCACG 57.827 36.000 4.43 5.49 0.00 4.35
1821 3571 2.224548 GCTTCAGTCCACTGTAACCCTT 60.225 50.000 6.61 0.00 44.12 3.95
1857 3607 7.401955 TGGAGAGGTAGTAACTAAAGCTTAC 57.598 40.000 0.00 0.00 0.00 2.34
1859 3609 6.070710 CCTTGGAGAGGTAGTAACTAAAGCTT 60.071 42.308 0.00 0.00 40.95 3.74
1913 3663 2.946990 TCCGTATGTCGCTATGAACTCA 59.053 45.455 0.00 0.00 38.35 3.41
1970 3721 2.304761 CCTAAAGGTCCAGTTGCCAGTA 59.695 50.000 0.00 0.00 0.00 2.74
2069 3820 3.822735 CCATCATATCCGCAATCTTTGGT 59.177 43.478 0.00 0.00 0.00 3.67
2076 3827 4.202441 GGCTTATCCATCATATCCGCAAT 58.798 43.478 0.00 0.00 34.01 3.56
2175 3926 0.659957 GGAACGCTGGCAATCTGATC 59.340 55.000 0.00 0.00 0.00 2.92
2246 4000 7.974501 CGAGACACTCTACCAAGTTACATTATT 59.025 37.037 0.00 0.00 0.00 1.40
2813 4992 2.471815 TCCGAGGTGATAGGGTTGAT 57.528 50.000 0.00 0.00 0.00 2.57
2985 5165 9.729023 CAAGAATTGTGTATCAAGTTTGTGTTA 57.271 29.630 0.00 0.00 42.34 2.41
3038 5218 2.170187 TGTTGCTGAATTGGGCAAGTTT 59.830 40.909 12.95 0.00 46.87 2.66
3046 5226 8.586570 TTAGTTTTGTATTGTTGCTGAATTGG 57.413 30.769 0.00 0.00 0.00 3.16
3125 5305 5.863935 GCTGGATGGATCAAGTTTTTGTAAC 59.136 40.000 0.00 0.00 35.73 2.50
3126 5306 5.538053 TGCTGGATGGATCAAGTTTTTGTAA 59.462 36.000 0.00 0.00 35.73 2.41
3129 5337 4.524316 TGCTGGATGGATCAAGTTTTTG 57.476 40.909 0.00 0.00 35.57 2.44
3185 5406 6.901887 CGATCTTGTTGTTATATGACACAAGC 59.098 38.462 23.16 15.74 37.89 4.01


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

AutoCloner maintained by Alex Coulton.