Multiple sequence alignment - TraesCS4A01G266800

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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 TraesCS4A01G266800 chr4A 100.000 2999 0 0 673 3671 578575269 578572271 0.000000e+00 5539
1 TraesCS4A01G266800 chr4A 100.000 295 0 0 1 295 578575941 578575647 2.490000e-151 545
2 TraesCS4A01G266800 chr4A 89.151 212 21 2 83 294 578582405 578582196 2.810000e-66 263
3 TraesCS4A01G266800 chr4B 97.628 2066 49 0 673 2738 35234518 35236583 0.000000e+00 3544
4 TraesCS4A01G266800 chr4B 93.326 914 41 13 2763 3671 35236795 35237693 0.000000e+00 1332
5 TraesCS4A01G266800 chr4B 96.759 216 7 0 80 295 35234205 35234420 9.690000e-96 361
6 TraesCS4A01G266800 chr4D 96.999 2066 62 0 673 2738 23305925 23307990 0.000000e+00 3472
7 TraesCS4A01G266800 chr4D 95.604 910 37 3 2763 3671 23308233 23309140 0.000000e+00 1456
8 TraesCS4A01G266800 chr4D 95.098 204 6 2 9 212 23305441 23305640 5.920000e-83 318


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 TraesCS4A01G266800 chr4A 578572271 578575941 3670 True 3042.000000 5539 100.000000 1 3671 2 chr4A.!!$R2 3670
1 TraesCS4A01G266800 chr4B 35234205 35237693 3488 False 1745.666667 3544 95.904333 80 3671 3 chr4B.!!$F1 3591
2 TraesCS4A01G266800 chr4D 23305441 23309140 3699 False 1748.666667 3472 95.900333 9 3671 3 chr4D.!!$F1 3662

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
854 855 1.414061 ATCCCTTCCCTCATCGCCTG 61.414 60.0 0.0 0.0 0.0 4.85 F
2286 2287 0.106819 GACAGCTCTGCCCCAATGAT 60.107 55.0 0.0 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2311 0.038744 CCATCTGGCCAAGACCTTGT 59.961 55.000 7.01 0.0 37.88 3.16 R
3092 3314 3.702045 GTCAGGATGGCACTAAGTACTCT 59.298 47.826 0.00 0.0 43.01 3.24 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
854 855 1.414061 ATCCCTTCCCTCATCGCCTG 61.414 60.000 0.00 0.00 0.00 4.85
962 963 4.785453 CCTCGCCCTGTCCAAGGC 62.785 72.222 0.00 0.00 45.89 4.35
1080 1081 2.032681 AAGTGGAAGCGCCTGGAC 59.967 61.111 2.29 0.00 37.63 4.02
1179 1180 4.024048 GTCATTCGTGTTCTTGTGATTGGT 60.024 41.667 0.00 0.00 0.00 3.67
1256 1257 1.069513 CCCAGACGTGTTCACTTACCA 59.930 52.381 0.00 0.00 0.00 3.25
1302 1303 0.652592 GTTTCAGGATGGATGACGCG 59.347 55.000 3.53 3.53 36.16 6.01
1368 1369 2.485903 GGTGTCGTGGTGTACAATTCA 58.514 47.619 0.00 0.00 0.00 2.57
1473 1474 1.000843 TCAGCGAGCACACATAACACT 59.999 47.619 0.00 0.00 0.00 3.55
1512 1513 3.249189 AACGGGAGGGCAGAAGCA 61.249 61.111 0.00 0.00 44.61 3.91
1569 1570 1.538512 CAGCTATTGGATGGGATTGCG 59.461 52.381 0.00 0.00 0.00 4.85
1578 1579 3.244078 TGGATGGGATTGCGTACAGTATC 60.244 47.826 0.00 0.00 0.00 2.24
1605 1606 1.301293 GGAGTTCTGCAAGGAGGGG 59.699 63.158 0.00 0.00 0.00 4.79
1641 1642 1.233019 CAGAGGCAGTCAGTTTGGTG 58.767 55.000 0.00 0.00 0.00 4.17
1644 1645 2.092429 AGAGGCAGTCAGTTTGGTGAAA 60.092 45.455 0.00 0.00 0.00 2.69
1656 1657 5.180868 CAGTTTGGTGAAAGAGATGGAAGAG 59.819 44.000 0.00 0.00 0.00 2.85
1843 1844 5.221263 GGACCACAAGATAGAGCGAAAGATA 60.221 44.000 0.00 0.00 0.00 1.98
1977 1978 1.318576 GGTCTTTGTCCCCACACTTG 58.681 55.000 0.00 0.00 29.76 3.16
2150 2151 3.758554 AGTGTAGCCTGCAAGTTATTTGG 59.241 43.478 0.00 0.00 37.26 3.28
2256 2257 1.004044 CAGGTCTGGGCAGTTCTTCAT 59.996 52.381 0.00 0.00 0.00 2.57
2286 2287 0.106819 GACAGCTCTGCCCCAATGAT 60.107 55.000 0.00 0.00 0.00 2.45
2331 2332 0.846427 AAGGTCTTGGCCAGATGGGA 60.846 55.000 5.11 0.00 40.01 4.37
2343 2344 3.561313 GCCAGATGGGAAAAACAGAGGTA 60.561 47.826 0.12 0.00 40.01 3.08
2436 2437 3.088532 CAATCAATTGGGAAAGGTCGGA 58.911 45.455 5.42 0.00 34.22 4.55
2677 2678 7.759489 AAACAGCAATCTAAATGAACTACCA 57.241 32.000 0.00 0.00 0.00 3.25
2754 2946 5.173854 GGCGAAAATGTAAAGATGCATAAGC 59.826 40.000 0.00 0.00 42.57 3.09
2807 3026 6.932356 TGCTTCCTTAGATCATTGAATGAC 57.068 37.500 10.45 4.98 43.01 3.06
2884 3103 9.244799 TCGTATGTGATTTATGAAGTCATGTAC 57.755 33.333 4.00 0.00 37.15 2.90
2989 3210 0.802494 ACGGCCATTAACTTGCTTCG 59.198 50.000 2.24 0.00 0.00 3.79
3070 3292 2.671070 GCTGGTTTACTCCCATTTTGCG 60.671 50.000 0.00 0.00 0.00 4.85
3082 3304 5.049167 TCCCATTTTGCGCATGAATATTTC 58.951 37.500 12.75 0.00 0.00 2.17
3124 3346 2.238521 GCCATCCTGACCTTTTGAACA 58.761 47.619 0.00 0.00 0.00 3.18
3174 3396 0.843984 GGGGCATAACTCCTGGCTTA 59.156 55.000 0.00 0.00 39.05 3.09
3295 3519 1.606668 TCACCGCATTCAGGAAAACAC 59.393 47.619 0.00 0.00 0.00 3.32
3348 3572 4.199310 TGTTGTCTTCTGCTTGTAGCTTT 58.801 39.130 0.00 0.00 42.97 3.51
3349 3573 5.364778 TGTTGTCTTCTGCTTGTAGCTTTA 58.635 37.500 0.00 0.00 42.97 1.85
3528 3752 9.880157 ATTTCTTTTGAATCAAATGGTCTATGG 57.120 29.630 17.73 0.36 38.37 2.74
3534 3758 5.044919 TGAATCAAATGGTCTATGGGACTGT 60.045 40.000 0.00 0.00 43.97 3.55
3553 3777 9.436957 GGGACTGTATGTAATCCAAATATGTAG 57.563 37.037 0.00 0.00 32.45 2.74
3619 3843 9.384764 GCTATAGAGTTTTCCAGTTGAAATAGT 57.615 33.333 3.21 0.00 42.38 2.12
3625 3849 4.439305 TTCCAGTTGAAATAGTGCATGC 57.561 40.909 11.82 11.82 0.00 4.06
3659 3883 4.016444 GAGCATTTCTGATTACACCCCAA 58.984 43.478 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.579768 TCGTTTCTTTTCTTTTGATGATTTTGA 57.420 25.926 0.00 0.00 0.00 2.69
36 37 0.452452 GAGTGTCTCGTTCGTCCGAC 60.452 60.000 0.00 0.00 32.57 4.79
962 963 3.686128 CAGAAGTCATCGTAGAGGTTCG 58.314 50.000 0.00 0.00 43.63 3.95
1080 1081 1.068954 GCGAAAAGCTTGAGGGACTTG 60.069 52.381 0.00 0.00 41.08 3.16
1113 1114 3.764466 ACAAGCGGAGGAGAGGCG 61.764 66.667 0.00 0.00 0.00 5.52
1256 1257 3.948719 ACCCATCCACAACCGCGT 61.949 61.111 4.92 0.00 0.00 6.01
1302 1303 2.010145 TCTCCTGAAACATACGCAGC 57.990 50.000 0.00 0.00 0.00 5.25
1349 1350 3.128349 AGTGAATTGTACACCACGACAC 58.872 45.455 13.34 9.97 38.82 3.67
1368 1369 6.299141 TGCTTTGAAGAGTCCATTTAGAAGT 58.701 36.000 0.00 0.00 0.00 3.01
1467 1468 1.831106 AGCCCATCGATCACAGTGTTA 59.169 47.619 0.00 0.00 0.00 2.41
1473 1474 0.612744 TGAACAGCCCATCGATCACA 59.387 50.000 0.00 0.00 0.00 3.58
1512 1513 1.482182 TCATAGAACAGCCGACATGCT 59.518 47.619 0.00 0.00 44.00 3.79
1569 1570 6.324254 AGAACTCCCTTACCATGATACTGTAC 59.676 42.308 0.00 0.00 0.00 2.90
1578 1579 2.787473 TGCAGAACTCCCTTACCATG 57.213 50.000 0.00 0.00 0.00 3.66
1605 1606 0.890996 CTGCAACTTGGTCCCCTGTC 60.891 60.000 0.00 0.00 0.00 3.51
1641 1642 1.474143 CCCCGCTCTTCCATCTCTTTC 60.474 57.143 0.00 0.00 0.00 2.62
1644 1645 2.439104 GCCCCGCTCTTCCATCTCT 61.439 63.158 0.00 0.00 0.00 3.10
1656 1657 2.929398 CAAATCAATAACAAAGCCCCGC 59.071 45.455 0.00 0.00 0.00 6.13
1977 1978 2.429610 AGCATGTTTGGCAAGATGATCC 59.570 45.455 19.80 7.16 36.02 3.36
2150 2151 5.755849 TCCTTCCCAGATTTGTAAAGATCC 58.244 41.667 0.00 0.00 0.00 3.36
2256 2257 1.610673 GAGCTGTCCACCCCTCTCA 60.611 63.158 0.00 0.00 0.00 3.27
2310 2311 0.038744 CCATCTGGCCAAGACCTTGT 59.961 55.000 7.01 0.00 37.88 3.16
2331 2332 4.891992 TGAGCTAGCTACCTCTGTTTTT 57.108 40.909 19.38 0.00 0.00 1.94
2343 2344 3.920231 TGTTCCATGATTGAGCTAGCT 57.080 42.857 19.45 19.45 0.00 3.32
2436 2437 5.405935 AACAGTTTGCTTCTTCAACCTTT 57.594 34.783 0.00 0.00 0.00 3.11
2474 2475 0.187117 TGGTTTCATGCCCCTTGTGA 59.813 50.000 0.00 0.00 0.00 3.58
2531 2532 2.708861 TCCTTCAACCTACCAGCTTTCA 59.291 45.455 0.00 0.00 0.00 2.69
2754 2946 3.756434 ACGGACTTTCCAACATTACCATG 59.244 43.478 0.00 0.00 35.91 3.66
2755 2947 4.028993 ACGGACTTTCCAACATTACCAT 57.971 40.909 0.00 0.00 35.91 3.55
2757 2949 3.816523 TCAACGGACTTTCCAACATTACC 59.183 43.478 0.00 0.00 35.91 2.85
2758 2950 5.237779 TCTTCAACGGACTTTCCAACATTAC 59.762 40.000 0.00 0.00 35.91 1.89
2760 2952 4.204012 TCTTCAACGGACTTTCCAACATT 58.796 39.130 0.00 0.00 35.91 2.71
2807 3026 5.371526 TGTAGTTCTAGGTACATACTCCCG 58.628 45.833 0.00 0.00 0.00 5.14
2823 3042 9.797556 AAACATAAAGAAAAACACCTGTAGTTC 57.202 29.630 0.00 0.00 0.00 3.01
3092 3314 3.702045 GTCAGGATGGCACTAAGTACTCT 59.298 47.826 0.00 0.00 43.01 3.24
3295 3519 7.799447 CCACATTTACAATGCTTTGATTTGTTG 59.201 33.333 18.35 10.02 36.64 3.33
3348 3572 5.777850 TCGATAAACCATGACGGAATCTA 57.222 39.130 0.00 0.00 38.63 1.98
3349 3573 4.665833 TCGATAAACCATGACGGAATCT 57.334 40.909 0.00 0.00 38.63 2.40
3377 3601 5.063817 TCACGTAAATCAGTGCAATGATCTG 59.936 40.000 28.03 19.31 39.00 2.90
3528 3752 9.998106 ACTACATATTTGGATTACATACAGTCC 57.002 33.333 0.00 0.00 0.00 3.85
3553 3777 6.039829 GGAATCTGGAATCCACAGGAATTTAC 59.960 42.308 0.00 0.00 34.34 2.01


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

AutoCloner maintained by Alex Coulton.