Multiple sequence alignment - TraesCS5B01G152200

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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 TraesCS5B01G152200 chr5B 100.000 4712 0 0 1 4712 281582655 281577944 0 8702
1 TraesCS5B01G152200 chr5A 94.706 2701 95 22 7 2675 331111917 331114601 0 4152
2 TraesCS5B01G152200 chr5A 96.441 1995 45 8 2719 4712 331114847 331116816 0 3267
3 TraesCS5B01G152200 chr5D 97.139 1992 32 6 2721 4712 247074627 247076593 0 3339
4 TraesCS5B01G152200 chr5D 94.875 1834 68 7 877 2700 247072525 247074342 0 2843
5 TraesCS5B01G152200 chr5D 95.023 864 21 11 5 847 247071353 247072215 0 1338
6 TraesCS5B01G152200 chr3A 90.020 1012 76 9 2783 3788 95945634 95944642 0 1286
7 TraesCS5B01G152200 chr3A 84.712 1040 120 17 991 1993 95948646 95947609 0 1003
8 TraesCS5B01G152200 chr3B 89.631 1003 82 7 2793 3792 127856285 127855302 0 1256
9 TraesCS5B01G152200 chr3B 85.481 1040 112 16 991 1993 127862519 127861482 0 1048
10 TraesCS5B01G152200 chr3D 88.495 1043 94 9 2751 3786 81693319 81692296 0 1238
11 TraesCS5B01G152200 chr3D 85.243 1030 115 14 991 1985 81696338 81695311 0 1026


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 TraesCS5B01G152200 chr5B 281577944 281582655 4711 True 8702.000000 8702 100.0000 1 4712 1 chr5B.!!$R1 4711
1 TraesCS5B01G152200 chr5A 331111917 331116816 4899 False 3709.500000 4152 95.5735 7 4712 2 chr5A.!!$F1 4705
2 TraesCS5B01G152200 chr5D 247071353 247076593 5240 False 2506.666667 3339 95.6790 5 4712 3 chr5D.!!$F1 4707
3 TraesCS5B01G152200 chr3A 95944642 95948646 4004 True 1144.500000 1286 87.3660 991 3788 2 chr3A.!!$R1 2797
4 TraesCS5B01G152200 chr3B 127855302 127856285 983 True 1256.000000 1256 89.6310 2793 3792 1 chr3B.!!$R1 999
5 TraesCS5B01G152200 chr3B 127861482 127862519 1037 True 1048.000000 1048 85.4810 991 1993 1 chr3B.!!$R2 1002
6 TraesCS5B01G152200 chr3D 81692296 81696338 4042 True 1132.000000 1238 86.8690 991 3786 2 chr3D.!!$R1 2795

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
592 596 0.389296 TCGCCACCATGTCGTACAAG 60.389 55.0 0.00 0.00 0.00 3.16 F
1221 1572 0.391793 TCACGTCCACACTGCACAAA 60.392 50.0 0.00 0.00 0.00 2.83 F
1287 1638 0.615331 AGCAGAAGATTGCCGAGGAA 59.385 50.0 0.00 0.00 45.18 3.36 F
2691 3580 1.436600 CACTGCTGCAGTACCAAGAG 58.563 55.0 32.51 16.13 43.43 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 3196 0.036388 TCGGATCTTGCTGGTGTTCC 60.036 55.000 0.00 0.00 0.00 3.62 R
2662 3551 1.975407 GCAGCAGTGGGTCAGCATT 60.975 57.895 0.00 0.00 0.00 3.56 R
2716 4337 5.707495 AGAAGTGGTTATCTCCTAGGTAGG 58.293 45.833 9.08 0.00 45.02 3.18 R
4074 5748 0.702316 AAGGGAAAGGTACGCCCATT 59.298 50.000 12.44 1.36 44.55 3.16 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
30 31 2.360350 ACACCCCTTGCATCAGCG 60.360 61.111 0.00 0.00 46.23 5.18
37 38 0.729116 CCTTGCATCAGCGGTTACAG 59.271 55.000 0.00 0.00 46.23 2.74
196 199 3.077484 ACATGCCATCAGTAAACAGCT 57.923 42.857 0.00 0.00 0.00 4.24
592 596 0.389296 TCGCCACCATGTCGTACAAG 60.389 55.000 0.00 0.00 0.00 3.16
702 707 5.052298 CCATTTATCTGGGCTGAGCATCAT 61.052 45.833 6.82 0.00 37.25 2.45
705 710 9.178630 CCATTTATCTGGGCTGAGCATCATAAC 62.179 44.444 6.82 0.00 37.25 1.89
720 730 9.294030 GAGCATCATAACAGAAATTTTGTTAGG 57.706 33.333 19.98 19.98 42.40 2.69
732 742 7.619302 AGAAATTTTGTTAGGGATGCATAAGGA 59.381 33.333 0.00 0.00 0.00 3.36
853 1162 1.956678 GGGCCGCGCTTAATCTCTC 60.957 63.158 5.56 0.00 0.00 3.20
855 1164 1.956678 GCCGCGCTTAATCTCTCCC 60.957 63.158 5.56 0.00 0.00 4.30
982 1294 2.196229 CCACGAAAACCCCCACCA 59.804 61.111 0.00 0.00 0.00 4.17
1217 1568 2.279186 CGTCACGTCCACACTGCA 60.279 61.111 0.00 0.00 0.00 4.41
1221 1572 0.391793 TCACGTCCACACTGCACAAA 60.392 50.000 0.00 0.00 0.00 2.83
1287 1638 0.615331 AGCAGAAGATTGCCGAGGAA 59.385 50.000 0.00 0.00 45.18 3.36
1520 1871 2.507452 CATCTCCCGCATGCTCCA 59.493 61.111 17.13 0.00 0.00 3.86
1530 1881 1.919600 GCATGCTCCAGGAGAAGGGT 61.920 60.000 21.89 0.00 0.00 4.34
1644 1995 2.591429 CTGGTGTTCGTGCTGCCA 60.591 61.111 0.00 0.00 0.00 4.92
1689 2040 2.548707 GGAGATGCTGATGCCGATTGTA 60.549 50.000 0.00 0.00 38.71 2.41
2125 2908 3.127589 TCTGATCTTCACGAAAAACGCA 58.872 40.909 0.00 0.00 46.94 5.24
2137 2920 4.201783 ACGAAAAACGCAGGATACATTAGC 60.202 41.667 0.00 0.00 46.94 3.09
2184 2967 8.927675 TTTCTAATGGGTAAAACTTAAGAGCA 57.072 30.769 10.09 0.00 0.00 4.26
2189 2972 3.434641 GGGTAAAACTTAAGAGCACGGTC 59.565 47.826 10.09 0.00 0.00 4.79
2304 3094 6.351711 GGATGTAGGAGGAATATGAGACCATG 60.352 46.154 0.00 0.00 34.31 3.66
2406 3196 4.263462 TGTTATATTGCAGGCCCTCCTATG 60.263 45.833 0.00 0.00 41.93 2.23
2505 3366 4.813296 AACGACAATTTCAGTGTCCTTC 57.187 40.909 0.00 0.00 42.00 3.46
2507 3368 2.411547 CGACAATTTCAGTGTCCTTCGC 60.412 50.000 0.00 0.00 42.00 4.70
2573 3462 9.102757 AGCAATGTAGATGTAAACTTGTCTATG 57.897 33.333 0.00 0.00 0.00 2.23
2691 3580 1.436600 CACTGCTGCAGTACCAAGAG 58.563 55.000 32.51 16.13 43.43 2.85
3342 5011 3.777106 TTCCCTGATATCCAGCATGTC 57.223 47.619 0.00 0.00 41.57 3.06
3378 5047 2.030628 GCCTGCCGAGATAGAGAACTAC 60.031 54.545 0.00 0.00 0.00 2.73
3820 5493 6.980978 CCTTACCTTACATGTGTAGACATCAG 59.019 42.308 9.11 0.05 41.12 2.90
3865 5538 6.342111 CAGATACAGTAGGGAACTCCTTTTC 58.658 44.000 0.00 0.00 45.47 2.29
4074 5748 6.569127 TGTAGGGATCTTTAAAGGCATACA 57.431 37.500 15.13 14.86 0.00 2.29
4083 5757 2.428544 AAAGGCATACAATGGGCGTA 57.571 45.000 0.00 0.00 34.32 4.42
4188 5862 6.694447 ACTTTCAAATCCATCTGGTTCATTG 58.306 36.000 0.00 0.00 36.34 2.82
4447 6121 2.596452 CTTGCTTCTCTAGAACGCGAA 58.404 47.619 15.93 0.00 33.77 4.70
4524 6198 3.438087 CAGACAGTAGTCCAAAGCAATGG 59.562 47.826 1.50 1.50 46.15 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.596248 TGTCGTATACAAAGAAAGACTGTAACC 59.404 37.037 3.32 0.00 34.29 2.85
37 38 7.404139 AACTGTGTCGTATACAAAGAAAGAC 57.596 36.000 3.32 1.18 45.18 3.01
196 199 4.678256 AGTAGAGGAGAAGAATGTGGTGA 58.322 43.478 0.00 0.00 0.00 4.02
373 377 2.048503 CCCGACGTCTGGAACACC 60.049 66.667 20.35 0.00 0.00 4.16
592 596 2.476051 CTCAACCACGACATGCGC 59.524 61.111 0.00 0.00 46.04 6.09
702 707 7.531857 TGCATCCCTAACAAAATTTCTGTTA 57.468 32.000 17.37 17.37 38.05 2.41
705 710 7.707893 CCTTATGCATCCCTAACAAAATTTCTG 59.292 37.037 0.19 0.00 0.00 3.02
717 727 5.593909 CACACATTTTCCTTATGCATCCCTA 59.406 40.000 0.19 0.00 0.00 3.53
720 730 5.104374 CACACACATTTTCCTTATGCATCC 58.896 41.667 0.19 0.00 0.00 3.51
809 840 2.575532 CAGACCCAACAGTGTCATGTT 58.424 47.619 0.00 0.00 44.12 2.71
982 1294 0.921256 ATGGCTGGGGTTTAGAGGCT 60.921 55.000 0.00 0.00 33.56 4.58
1031 1343 1.546834 GTAGTTGTCCTCGTCATCGC 58.453 55.000 0.00 0.00 36.96 4.58
1195 1546 1.105167 AGTGTGGACGTGACGAGGAA 61.105 55.000 13.70 0.00 0.00 3.36
1231 1582 4.176752 GGTGGGGGTGATCTCCGC 62.177 72.222 19.63 19.63 39.30 5.54
1287 1638 3.450115 GTCGTGCGGTAGGAGGCT 61.450 66.667 0.00 0.00 0.00 4.58
1320 1671 1.134699 GTGATGTCCTTGGCGATCTCA 60.135 52.381 0.00 0.00 0.00 3.27
1520 1871 1.115467 CTGCACGATACCCTTCTCCT 58.885 55.000 0.00 0.00 0.00 3.69
1644 1995 1.450848 CAGCGCCACCATGATGAGT 60.451 57.895 2.29 0.00 0.00 3.41
1804 2155 0.108138 ATGCAGAGCAAGGGTCGTAC 60.108 55.000 0.00 0.00 43.62 3.67
2094 2875 4.449068 TCGTGAAGATCAGAAAAAGACAGC 59.551 41.667 0.00 0.00 0.00 4.40
2125 2908 1.416401 CCACCCACGCTAATGTATCCT 59.584 52.381 0.00 0.00 0.00 3.24
2184 2967 0.535335 ATAGACACGCCAATGACCGT 59.465 50.000 0.00 0.00 38.35 4.83
2189 2972 6.944557 TCGATAATTATAGACACGCCAATG 57.055 37.500 4.34 0.00 0.00 2.82
2304 3094 5.445964 TCTGAATTATTTTCTACCCAGGCC 58.554 41.667 0.00 0.00 0.00 5.19
2406 3196 0.036388 TCGGATCTTGCTGGTGTTCC 60.036 55.000 0.00 0.00 0.00 3.62
2505 3366 3.666883 TTGTAATCGTTGGCATTAGCG 57.333 42.857 0.00 0.00 43.41 4.26
2507 3368 5.238432 TGCCTATTGTAATCGTTGGCATTAG 59.762 40.000 0.00 0.00 43.09 1.73
2573 3462 9.965824 CAATGATGGGGATTAGTTGTTTAATAC 57.034 33.333 0.00 0.00 0.00 1.89
2662 3551 1.975407 GCAGCAGTGGGTCAGCATT 60.975 57.895 0.00 0.00 0.00 3.56
2716 4337 5.707495 AGAAGTGGTTATCTCCTAGGTAGG 58.293 45.833 9.08 0.00 45.02 3.18
2717 4338 7.663043 AAAGAAGTGGTTATCTCCTAGGTAG 57.337 40.000 9.08 5.31 0.00 3.18
3342 5011 5.178061 TCGGCAGGCATATCATAGTTAATG 58.822 41.667 0.00 0.00 36.88 1.90
3654 5323 1.280133 TCTCTTCTGGAACCAGCCATG 59.720 52.381 15.20 6.68 43.31 3.66
3820 5493 7.615582 TCTGGATTGTCATCTCATTGTTTAC 57.384 36.000 0.00 0.00 0.00 2.01
3865 5538 5.165961 TGTGAATACCCTCCAGAAAAGAG 57.834 43.478 0.00 0.00 0.00 2.85
4074 5748 0.702316 AAGGGAAAGGTACGCCCATT 59.298 50.000 12.44 1.36 44.55 3.16
4083 5757 8.499288 TGAAACCATTAAATAAAGGGAAAGGT 57.501 30.769 0.00 0.00 41.79 3.50
4245 5919 1.235724 GGACCTTTGAAACCTCCGTG 58.764 55.000 0.00 0.00 0.00 4.94
4524 6198 4.678509 TTTACGACAATGCAACCATCTC 57.321 40.909 0.00 0.00 0.00 2.75
4529 6203 3.987220 AGCAATTTTACGACAATGCAACC 59.013 39.130 0.00 0.00 0.00 3.77
4589 6263 6.508030 TTTCCTGCCATATGAGTAATGGTA 57.492 37.500 3.65 0.00 44.87 3.25
4622 6296 7.599998 ACATCAGGTGATTAAAAGTTGCATTTC 59.400 33.333 0.00 0.00 31.21 2.17


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

AutoCloner maintained by Alex Coulton.