Multiple sequence alignment - TraesCS6D01G108300

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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 TraesCS6D01G108300 chr6D 100.000 3050 0 0 1 3050 72353816 72356865 0 5633
1 TraesCS6D01G108300 chr6D 93.766 3080 150 24 1 3050 426967874 426964807 0 4586
2 TraesCS6D01G108300 chr5D 93.388 3070 162 16 13 3050 383616031 383612971 0 4506
3 TraesCS6D01G108300 chr5D 91.469 3071 212 28 6 3050 438205674 438202628 0 4174
4 TraesCS6D01G108300 chr5D 91.832 2571 163 24 1 2543 188362808 188365359 0 3541
5 TraesCS6D01G108300 chr2D 91.328 3079 209 33 6 3050 543503407 543500353 0 4154
6 TraesCS6D01G108300 chr2D 91.465 3023 213 27 53 3050 324886387 324883385 0 4111
7 TraesCS6D01G108300 chr2B 91.000 3089 225 32 4 3050 366596930 366593853 0 4115
8 TraesCS6D01G108300 chr3D 91.004 3079 209 31 1 3050 554292372 554289333 0 4089
9 TraesCS6D01G108300 chr4B 90.670 3076 237 29 1 3050 78621806 78624857 0 4045
10 TraesCS6D01G108300 chr7D 91.956 2822 173 23 1 2801 195581726 195578938 0 3904
11 TraesCS6D01G108300 chr7D 94.590 1830 75 11 1 1813 122819680 122817858 0 2809
12 TraesCS6D01G108300 chr7D 94.036 939 46 8 1 933 22994922 22995856 0 1415
13 TraesCS6D01G108300 chr1A 89.987 3056 236 46 48 3050 124221091 124218053 0 3884
14 TraesCS6D01G108300 chr4D 94.498 2072 100 11 991 3050 179912092 179914161 0 3182
15 TraesCS6D01G108300 chr4D 95.175 974 40 7 1 974 179897201 179898167 0 1531
16 TraesCS6D01G108300 chr1B 85.114 1881 213 44 50 1889 218460023 218458169 0 1860
17 TraesCS6D01G108300 chrUn 94.143 939 46 7 1 933 89954375 89955310 0 1421


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 TraesCS6D01G108300 chr6D 72353816 72356865 3049 False 5633 5633 100.000 1 3050 1 chr6D.!!$F1 3049
1 TraesCS6D01G108300 chr6D 426964807 426967874 3067 True 4586 4586 93.766 1 3050 1 chr6D.!!$R1 3049
2 TraesCS6D01G108300 chr5D 383612971 383616031 3060 True 4506 4506 93.388 13 3050 1 chr5D.!!$R1 3037
3 TraesCS6D01G108300 chr5D 438202628 438205674 3046 True 4174 4174 91.469 6 3050 1 chr5D.!!$R2 3044
4 TraesCS6D01G108300 chr5D 188362808 188365359 2551 False 3541 3541 91.832 1 2543 1 chr5D.!!$F1 2542
5 TraesCS6D01G108300 chr2D 543500353 543503407 3054 True 4154 4154 91.328 6 3050 1 chr2D.!!$R2 3044
6 TraesCS6D01G108300 chr2D 324883385 324886387 3002 True 4111 4111 91.465 53 3050 1 chr2D.!!$R1 2997
7 TraesCS6D01G108300 chr2B 366593853 366596930 3077 True 4115 4115 91.000 4 3050 1 chr2B.!!$R1 3046
8 TraesCS6D01G108300 chr3D 554289333 554292372 3039 True 4089 4089 91.004 1 3050 1 chr3D.!!$R1 3049
9 TraesCS6D01G108300 chr4B 78621806 78624857 3051 False 4045 4045 90.670 1 3050 1 chr4B.!!$F1 3049
10 TraesCS6D01G108300 chr7D 195578938 195581726 2788 True 3904 3904 91.956 1 2801 1 chr7D.!!$R2 2800
11 TraesCS6D01G108300 chr7D 122817858 122819680 1822 True 2809 2809 94.590 1 1813 1 chr7D.!!$R1 1812
12 TraesCS6D01G108300 chr7D 22994922 22995856 934 False 1415 1415 94.036 1 933 1 chr7D.!!$F1 932
13 TraesCS6D01G108300 chr1A 124218053 124221091 3038 True 3884 3884 89.987 48 3050 1 chr1A.!!$R1 3002
14 TraesCS6D01G108300 chr4D 179912092 179914161 2069 False 3182 3182 94.498 991 3050 1 chr4D.!!$F2 2059
15 TraesCS6D01G108300 chr4D 179897201 179898167 966 False 1531 1531 95.175 1 974 1 chr4D.!!$F1 973
16 TraesCS6D01G108300 chr1B 218458169 218460023 1854 True 1860 1860 85.114 50 1889 1 chr1B.!!$R1 1839
17 TraesCS6D01G108300 chrUn 89954375 89955310 935 False 1421 1421 94.143 1 933 1 chrUn.!!$F1 932

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
970 1021 0.886563 AAGTCCCGTACGAGGTGAAG 59.113 55.0 18.76 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2871 3025 0.034896 CCTTCTTACCACCTGCACGT 59.965 55.0 0.0 0.0 0.0 4.49 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
195 222 2.102252 AGTAGATTCTGCTAGCTGGCAC 59.898 50.000 22.10 11.50 37.29 5.01
200 227 4.765449 TGCTAGCTGGCACCTGCG 62.765 66.667 22.10 1.67 44.03 5.18
307 343 4.380841 ATGTTCAGCACATGGCAATTAG 57.619 40.909 8.58 0.00 45.12 1.73
442 485 4.615912 CGGATGTGTTTTCATTTCACCCTC 60.616 45.833 0.00 0.00 0.00 4.30
705 755 4.133013 AGAAACGTTATCGCAATAGGGT 57.867 40.909 0.00 0.00 41.18 4.34
784 834 1.350351 GCTAGTGAGATGGGGATGCAT 59.650 52.381 0.00 0.00 0.00 3.96
905 956 1.228552 GGAAGGCTGCCTTTGGACA 60.229 57.895 32.71 0.00 44.82 4.02
970 1021 0.886563 AAGTCCCGTACGAGGTGAAG 59.113 55.000 18.76 0.00 0.00 3.02
1121 1185 0.387239 GCTGTTTTTGCGCCTACCAG 60.387 55.000 4.18 5.87 0.00 4.00
1194 1266 6.347859 TCTCTACTCCTTTCTTCCTTCAAC 57.652 41.667 0.00 0.00 0.00 3.18
1277 1358 1.063031 GCTGATGCGGCAACTTTTTC 58.937 50.000 6.82 0.00 35.55 2.29
1326 1407 4.883083 AGCTGAAAGACGTGAAGAACATA 58.117 39.130 0.00 0.00 34.07 2.29
1449 1531 4.413495 TTTGCAAATACTCTTACCACGC 57.587 40.909 8.05 0.00 0.00 5.34
1497 1582 4.211389 GCAGTTGTTGATAAGTGTGAACG 58.789 43.478 0.00 0.00 34.29 3.95
1517 1602 2.738643 CGGTACAAGATCGTTCATGGCT 60.739 50.000 3.98 0.00 0.00 4.75
1588 1699 3.972133 TCTGTTTGATCCATGGCATCTT 58.028 40.909 6.96 0.00 0.00 2.40
1722 1839 6.435430 TGTGGCAACTATCATCATAACAAC 57.565 37.500 0.00 0.00 37.61 3.32
1770 1887 4.225042 TGGCAACTAACACAGATAGATGGT 59.775 41.667 0.00 0.00 37.61 3.55
1797 1914 4.522789 TCTTTTCCCTTTCATTCCCTTTCG 59.477 41.667 0.00 0.00 0.00 3.46
1860 1977 3.572632 ATAGCATGATGGCAACTGACT 57.427 42.857 0.00 0.00 35.83 3.41
1949 2071 1.077625 CTAGGATAGGAGGCCCGCT 59.922 63.158 0.00 0.00 34.22 5.52
2002 2124 1.202256 CGTACGATGCTGTCAAGGCTA 60.202 52.381 10.44 0.00 0.00 3.93
2047 2169 6.650120 ACTGATACGAAATATGGGAAACTGT 58.350 36.000 0.00 0.00 0.00 3.55
2200 2326 2.077579 ATGGCACCCATGTCTGACA 58.922 52.632 13.60 13.60 43.39 3.58
2367 2497 3.255969 AGACTACAACGTGTTTGGTGT 57.744 42.857 0.00 0.00 39.84 4.16
2610 2756 1.002502 GGGTAGTTTGCTTCCGGCT 60.003 57.895 0.00 0.00 42.39 5.52
2650 2796 0.768622 TTGGTTGAGGGTTGGACGAT 59.231 50.000 0.00 0.00 0.00 3.73
2710 2856 2.757314 TCACACCATTTGTTGCAGAACA 59.243 40.909 0.00 0.00 40.45 3.18
2720 2866 2.135139 GTTGCAGAACAGACACATCGA 58.865 47.619 0.00 0.00 31.78 3.59
2757 2903 1.935933 CCGGTATGACTACAACAGCC 58.064 55.000 0.00 0.00 0.00 4.85
2871 3025 6.704050 TGAAACTCGATGAACATGTTGAAGTA 59.296 34.615 17.58 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.037062 GGCACTTTAAAAATGTTCAAGTTGCT 59.963 34.615 0.00 0.00 0.00 3.91
116 138 3.622206 GCAAGATCATAGGAACACCCACA 60.622 47.826 0.00 0.00 37.41 4.17
195 222 1.134699 TGAGCTTATGAAGGACGCAGG 60.135 52.381 0.00 0.00 0.00 4.85
200 227 4.683832 ACGTGTATGAGCTTATGAAGGAC 58.316 43.478 0.32 0.00 0.00 3.85
274 309 2.137523 GCTGAACATGCACAAAAAGGG 58.862 47.619 0.00 0.00 0.00 3.95
361 402 8.491331 TTCACTTGATATCATCGATGAACAAA 57.509 30.769 30.41 19.89 40.69 2.83
362 403 8.667076 ATTCACTTGATATCATCGATGAACAA 57.333 30.769 30.41 28.56 40.69 2.83
442 485 6.130298 TGAGGTAAGAACAAAACACATGTG 57.870 37.500 24.25 24.25 0.00 3.21
502 545 2.000447 GCGGTAACTCCATGAAGTCAC 59.000 52.381 0.00 0.00 35.57 3.67
705 755 2.325583 AGTCAGGCGTTCTTGTGAAA 57.674 45.000 0.00 0.00 33.52 2.69
784 834 0.904649 ACCGAACATCCATCAGAGCA 59.095 50.000 0.00 0.00 0.00 4.26
892 943 1.203287 GATTCCTTGTCCAAAGGCAGC 59.797 52.381 0.00 0.00 37.34 5.25
905 956 1.523758 GTGCAGAACACGGATTCCTT 58.476 50.000 0.30 0.00 40.07 3.36
940 991 2.491675 ACGGGACTTTGATTTCTCCC 57.508 50.000 0.00 0.00 39.35 4.30
970 1021 0.879090 AAACGGGCGAACAAGGATTC 59.121 50.000 0.00 0.00 0.00 2.52
1121 1185 0.729690 GTTGCTTGGGCGAAGAGATC 59.270 55.000 13.81 0.00 42.25 2.75
1152 1216 5.649265 AGAGATAGAGCATTCACCAGGATA 58.351 41.667 0.00 0.00 0.00 2.59
1194 1266 9.350357 CTTACAGATGACATCAAAATCAAAAGG 57.650 33.333 17.57 0.00 0.00 3.11
1277 1358 4.466828 CTGCACGACACAAATTTTAGGAG 58.533 43.478 0.00 0.00 0.00 3.69
1326 1407 4.156922 TCCGCGATGAATTTACACCAATTT 59.843 37.500 8.23 0.00 0.00 1.82
1372 1453 2.237392 AGCCCTTCTGGTACATCTTGTC 59.763 50.000 0.00 0.00 38.20 3.18
1449 1531 7.308109 CCATGTTGATTTGGGAAAACATTCAAG 60.308 37.037 0.00 0.00 40.36 3.02
1497 1582 2.906354 AGCCATGAACGATCTTGTACC 58.094 47.619 7.61 0.00 0.00 3.34
1510 1595 3.838565 TGAAAACAAAGGGTAGCCATGA 58.161 40.909 19.83 0.00 0.00 3.07
1517 1602 8.696374 TCACATAAACAATGAAAACAAAGGGTA 58.304 29.630 0.00 0.00 39.07 3.69
1588 1699 3.034924 CCTTGTAGGCAGCAACCAA 57.965 52.632 0.00 0.00 0.00 3.67
1735 1852 0.604578 AGTTGCCATCATGTTGTGCC 59.395 50.000 12.03 2.26 0.00 5.01
1770 1887 8.504811 AAAGGGAATGAAAGGGAAAAGATTTA 57.495 30.769 0.00 0.00 0.00 1.40
1797 1914 4.799564 AGAGTCCTTCAGTCATCAAGTC 57.200 45.455 0.00 0.00 0.00 3.01
1949 2071 3.561143 ACAACAAACTTATGTGGAGGCA 58.439 40.909 0.00 0.00 32.81 4.75
2047 2169 4.426704 AGAAAGGAGGCAGAACTAACCTA 58.573 43.478 0.00 0.00 32.67 3.08
2367 2497 1.830477 ACTTGCCAAAGTTTTGAGGCA 59.170 42.857 12.77 12.77 44.47 4.75
2610 2756 2.032528 CCCGAGCAAGCTGGTCAA 59.967 61.111 0.00 0.00 44.51 3.18
2650 2796 4.380550 CGTCACTGTCAGAGCCATTAAGTA 60.381 45.833 6.91 0.00 0.00 2.24
2710 2856 3.914984 CCAGTTGGTCGATGTGTCT 57.085 52.632 0.00 0.00 0.00 3.41
2732 2878 1.783071 TGTAGTCATACCGGCCATGA 58.217 50.000 13.84 13.84 0.00 3.07
2777 2923 6.805016 ACATCTCCATCTAGTTCATCTTGT 57.195 37.500 0.00 0.00 0.00 3.16
2841 2990 7.433708 AACATGTTCATCGAGTTTCATGTTA 57.566 32.000 25.52 0.00 46.96 2.41
2852 3001 4.384547 CACGTACTTCAACATGTTCATCGA 59.615 41.667 8.48 0.00 0.00 3.59
2871 3025 0.034896 CCTTCTTACCACCTGCACGT 59.965 55.000 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.