Multiple sequence alignment - TraesCS5B01G387600

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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 TraesCS5B01G387600 chr5B 100.000 4096 0 0 629 4724 566683704 566687799 0.000000e+00 7564.0
1 TraesCS5B01G387600 chr5B 100.000 292 0 0 1 292 566683076 566683367 1.500000e-149 540.0
2 TraesCS5B01G387600 chr5D 95.908 3201 104 9 776 3958 460755283 460758474 0.000000e+00 5160.0
3 TraesCS5B01G387600 chr5D 95.460 771 21 3 3955 4724 460758634 460759391 0.000000e+00 1218.0
4 TraesCS5B01G387600 chr5D 97.260 292 7 1 1 292 460754749 460755039 1.180000e-135 494.0
5 TraesCS5B01G387600 chr5D 94.350 177 9 1 640 816 460755114 460755289 2.170000e-68 270.0
6 TraesCS5B01G387600 chr5A 94.666 3337 138 17 629 3958 580943935 580947238 0.000000e+00 5140.0
7 TraesCS5B01G387600 chr5A 97.090 756 19 3 3969 4724 580947428 580948180 0.000000e+00 1271.0
8 TraesCS5B01G387600 chr5A 95.745 282 8 2 1 279 580943585 580943865 7.210000e-123 451.0
9 TraesCS5B01G387600 chr5A 100.000 28 0 0 3955 3982 580947388 580947415 9.000000e-03 52.8


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 TraesCS5B01G387600 chr5B 566683076 566687799 4723 False 4052.0 7564 100.00000 1 4724 2 chr5B.!!$F1 4723
1 TraesCS5B01G387600 chr5D 460754749 460759391 4642 False 1785.5 5160 95.74450 1 4724 4 chr5D.!!$F1 4723
2 TraesCS5B01G387600 chr5A 580943585 580948180 4595 False 1728.7 5140 96.87525 1 4724 4 chr5A.!!$F1 4723

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
891 936 0.243636 CACCGTCCCAGATTTTTGGC 59.756 55.0 0.0 0.0 36.88 4.52 F
1839 1901 0.537188 ACGAGCAGATTGTCGGGATT 59.463 50.0 0.0 0.0 40.59 3.01 F
2935 3000 0.598562 TCTCTGTCGAACACTGGCTC 59.401 55.0 0.0 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 2384 1.276138 GCTTTTCCTTTGTCCCCCATG 59.724 52.381 0.0 0.0 0.00 3.66 R
3591 3656 1.034292 GCCTGAAATCCTGGTGCTCC 61.034 60.000 0.0 0.0 36.37 4.70 R
4591 4846 1.847328 CCATTCCCCAAAGGTACACC 58.153 55.000 0.0 0.0 36.75 4.16 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
715 719 3.328343 TGTCTCGAGGGGTAAAATGGAAA 59.672 43.478 13.56 0.00 0.00 3.13
758 762 2.184579 CTCCGGGAAGACGAAGCC 59.815 66.667 0.00 0.00 35.47 4.35
883 928 2.603473 CCCACTCACCGTCCCAGA 60.603 66.667 0.00 0.00 0.00 3.86
891 936 0.243636 CACCGTCCCAGATTTTTGGC 59.756 55.000 0.00 0.00 36.88 4.52
910 958 1.336702 GCTGATCCACATCGCTCTAGG 60.337 57.143 0.00 0.00 0.00 3.02
1695 1757 2.354604 CCTGGCTCTGAAGAAGGAAGAC 60.355 54.545 0.00 0.00 32.28 3.01
1839 1901 0.537188 ACGAGCAGATTGTCGGGATT 59.463 50.000 0.00 0.00 40.59 3.01
1991 2053 8.144478 TCTTCTTGATTTACTGATATCCCTTCG 58.856 37.037 0.00 0.00 0.00 3.79
2079 2141 2.669434 CGGACACAAATTACCAGTACGG 59.331 50.000 2.71 2.71 42.50 4.02
2122 2184 3.748083 TGCCATGCTTATCTTGGAGATC 58.252 45.455 0.00 0.00 41.25 2.75
2149 2211 1.423584 TGCTGAGGTGTTCCTTCAGA 58.576 50.000 5.73 0.00 45.24 3.27
2150 2212 1.345741 TGCTGAGGTGTTCCTTCAGAG 59.654 52.381 5.73 0.00 45.24 3.35
2202 2264 3.305720 TGATATGGTTAAGGAGGTCGCT 58.694 45.455 0.00 0.00 0.00 4.93
2254 2316 8.856153 TGAGTATGCACTAAAATTTTACTCCA 57.144 30.769 18.36 11.27 35.40 3.86
2256 2318 9.722056 GAGTATGCACTAAAATTTTACTCCATG 57.278 33.333 13.31 4.51 34.21 3.66
2277 2339 2.254546 TGGAAGACGTTGCTGTTCAT 57.745 45.000 0.00 0.00 0.00 2.57
2287 2349 4.142622 ACGTTGCTGTTCATAATGATGGTG 60.143 41.667 0.00 0.00 33.49 4.17
2289 2351 2.689471 TGCTGTTCATAATGATGGTGGC 59.311 45.455 0.00 0.00 33.49 5.01
2292 2354 3.205338 TGTTCATAATGATGGTGGCTCG 58.795 45.455 0.00 0.00 33.49 5.03
2322 2384 1.495878 CTGCTCGATGCTACATGGTC 58.504 55.000 0.00 0.00 43.37 4.02
2346 2408 3.181412 TGGGGGACAAAGGAAAAGCTATT 60.181 43.478 0.00 0.00 0.00 1.73
2418 2480 9.282569 GTACGGATAACCTTATCTTCTCTTCTA 57.717 37.037 5.28 0.00 39.53 2.10
2421 2483 8.508875 CGGATAACCTTATCTTCTCTTCTAGTC 58.491 40.741 5.28 0.00 39.53 2.59
2424 2486 9.802039 ATAACCTTATCTTCTCTTCTAGTCGAT 57.198 33.333 0.00 0.00 0.00 3.59
2428 2490 7.659799 CCTTATCTTCTCTTCTAGTCGATGAGA 59.340 40.741 6.25 6.25 45.75 3.27
2440 2502 8.093659 TCTAGTCGATGAGAATAAGAGTGATG 57.906 38.462 0.00 0.00 0.00 3.07
2442 2504 6.969366 AGTCGATGAGAATAAGAGTGATGAG 58.031 40.000 0.00 0.00 0.00 2.90
2450 2512 7.288621 TGAGAATAAGAGTGATGAGGCTATCAA 59.711 37.037 7.82 0.00 42.53 2.57
2451 2513 8.027524 AGAATAAGAGTGATGAGGCTATCAAA 57.972 34.615 7.82 0.00 42.53 2.69
2452 2514 7.930865 AGAATAAGAGTGATGAGGCTATCAAAC 59.069 37.037 7.82 6.14 42.53 2.93
2469 2534 3.072944 CAAACTGCTTTCTCCTCCTGAG 58.927 50.000 0.00 0.00 42.90 3.35
2499 2564 1.048160 TGCAGTCCGCTGATATCCCA 61.048 55.000 0.00 0.00 45.28 4.37
2524 2589 1.691196 TCAGAAACCTTGGTGGCTTG 58.309 50.000 0.00 0.00 40.22 4.01
2537 2602 2.369394 GTGGCTTGATGGGGAAGTAAG 58.631 52.381 0.00 0.00 0.00 2.34
2538 2603 2.026262 GTGGCTTGATGGGGAAGTAAGA 60.026 50.000 0.00 0.00 0.00 2.10
2826 2891 2.161211 GGCAGCAGAGTCAAATGAAGAC 59.839 50.000 0.00 0.00 36.26 3.01
2932 2997 4.082733 TGTTAGATCTCTGTCGAACACTGG 60.083 45.833 0.00 0.00 38.32 4.00
2935 3000 0.598562 TCTCTGTCGAACACTGGCTC 59.401 55.000 0.00 0.00 0.00 4.70
2984 3049 7.326305 GCTGCAAATTATCAATCATGCTCTTAG 59.674 37.037 0.00 0.00 35.71 2.18
2997 3062 6.656902 TCATGCTCTTAGACTTGGAAATGAT 58.343 36.000 0.00 0.00 0.00 2.45
3027 3092 5.272402 TCTGATGACATCAAGGAGGAACTA 58.728 41.667 18.49 0.00 37.65 2.24
3072 3137 1.703411 ACAGAGCTCTAGATCCCAGC 58.297 55.000 17.75 0.00 0.00 4.85
3147 3212 3.448686 CGCATGGAACTCCTACTACAAG 58.551 50.000 0.00 0.00 36.82 3.16
3160 3225 5.778241 TCCTACTACAAGGTGACATCAAGAA 59.222 40.000 0.00 0.00 37.91 2.52
3222 3287 1.380302 GGATCCCAAGTGTGTGCCT 59.620 57.895 0.00 0.00 0.00 4.75
3246 3311 4.637534 CCTAAAATCATATCTGGGCATCGG 59.362 45.833 0.00 0.00 0.00 4.18
3408 3473 2.046988 CAGTGCATCGTCCAGGCA 60.047 61.111 0.00 0.00 34.70 4.75
3411 3476 0.745845 AGTGCATCGTCCAGGCATTC 60.746 55.000 0.00 0.00 40.05 2.67
3591 3656 4.672587 TCCATTCGAGGAGGATTTACAG 57.327 45.455 0.00 0.00 32.77 2.74
3732 3797 8.612145 ACCTACTGTTCTATTTAGGAATTGGTT 58.388 33.333 0.49 0.00 35.56 3.67
3776 3841 0.620556 CTTGGCCCTGTCTATGTGGT 59.379 55.000 0.00 0.00 0.00 4.16
3784 3849 1.736126 CTGTCTATGTGGTTGCTGCTG 59.264 52.381 0.00 0.00 0.00 4.41
3786 3851 0.325933 TCTATGTGGTTGCTGCTGCT 59.674 50.000 17.00 0.00 40.48 4.24
3946 4011 6.971527 TTGATCATGAAACAAAATGGATGC 57.028 33.333 13.69 0.00 0.00 3.91
3994 4222 7.817418 AGTACATGAAAAGAACTGCCTAAAA 57.183 32.000 0.00 0.00 0.00 1.52
4128 4383 0.883833 GGTGGTGGCATCAGAGTTTG 59.116 55.000 0.00 0.00 0.00 2.93
4207 4462 2.285827 ACAGCATTGTCTAGAGCGTC 57.714 50.000 0.00 0.00 29.46 5.19
4301 4556 3.073062 ACAACAAGGGTCATCAAGCTAGT 59.927 43.478 0.00 0.00 0.00 2.57
4492 4747 2.355108 GGTGTAGAAGCAGCCTGATGAA 60.355 50.000 0.00 0.00 0.00 2.57
4526 4781 5.952347 TGTAGTGTCAAGATGATGAGTACCT 59.048 40.000 0.00 0.00 0.00 3.08
4529 4784 5.105554 AGTGTCAAGATGATGAGTACCTCAC 60.106 44.000 0.00 0.00 43.63 3.51
4531 4786 3.706594 TCAAGATGATGAGTACCTCACCC 59.293 47.826 0.00 0.00 43.63 4.61
4570 4825 3.157087 ACAAAGATGACATGGGTGAACC 58.843 45.455 0.00 0.00 40.81 3.62
4591 4846 4.216963 GCAACGCTGCTCTTTGTG 57.783 55.556 2.93 0.00 45.74 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 2.582978 GCCTACAACCTCGTCCCC 59.417 66.667 0.00 0.00 0.00 4.81
74 75 2.388232 CCGCAACGCCTACAACCTC 61.388 63.158 0.00 0.00 0.00 3.85
833 878 3.267974 GCCTTGAGCCCTTGAACG 58.732 61.111 0.00 0.00 34.35 3.95
876 921 2.428530 GGATCAGCCAAAAATCTGGGAC 59.571 50.000 0.00 0.00 36.92 4.46
891 936 1.336702 GCCTAGAGCGATGTGGATCAG 60.337 57.143 0.00 0.00 0.00 2.90
1281 1343 4.087892 TGCTGCCTCCTCCGCTTC 62.088 66.667 0.00 0.00 0.00 3.86
1839 1901 1.884075 CGACGGTGTTGGAGGGATGA 61.884 60.000 0.00 0.00 0.00 2.92
1991 2053 2.621998 CCATGGGCATCATTTCTCAGAC 59.378 50.000 2.85 0.00 32.92 3.51
2058 2120 2.669434 CCGTACTGGTAATTTGTGTCCG 59.331 50.000 0.00 0.00 0.00 4.79
2122 2184 2.227388 GGAACACCTCAGCATGTTTCAG 59.773 50.000 0.00 0.00 39.13 3.02
2149 2211 3.196207 AACGCCCCAGATGCACACT 62.196 57.895 0.00 0.00 0.00 3.55
2150 2212 2.672996 AACGCCCCAGATGCACAC 60.673 61.111 0.00 0.00 0.00 3.82
2202 2264 3.486383 CCCCAAACTTTGAAGAGTGCTA 58.514 45.455 2.87 0.00 0.00 3.49
2253 2315 2.079158 ACAGCAACGTCTTCCATCATG 58.921 47.619 0.00 0.00 0.00 3.07
2254 2316 2.479566 ACAGCAACGTCTTCCATCAT 57.520 45.000 0.00 0.00 0.00 2.45
2256 2318 2.143122 TGAACAGCAACGTCTTCCATC 58.857 47.619 0.00 0.00 0.00 3.51
2277 2339 3.494223 CCACATACGAGCCACCATCATTA 60.494 47.826 0.00 0.00 0.00 1.90
2287 2349 1.432270 GCAGCTTCCACATACGAGCC 61.432 60.000 0.00 0.00 35.79 4.70
2289 2351 1.565305 GAGCAGCTTCCACATACGAG 58.435 55.000 0.00 0.00 0.00 4.18
2292 2354 1.863454 CATCGAGCAGCTTCCACATAC 59.137 52.381 0.00 0.00 0.00 2.39
2322 2384 1.276138 GCTTTTCCTTTGTCCCCCATG 59.724 52.381 0.00 0.00 0.00 3.66
2346 2408 8.925338 CCTTCTAAAGCTTTATAGAGGTAAGGA 58.075 37.037 18.93 6.40 33.82 3.36
2418 2480 6.016360 CCTCATCACTCTTATTCTCATCGACT 60.016 42.308 0.00 0.00 0.00 4.18
2421 2483 4.922692 GCCTCATCACTCTTATTCTCATCG 59.077 45.833 0.00 0.00 0.00 3.84
2424 2486 6.779539 TGATAGCCTCATCACTCTTATTCTCA 59.220 38.462 0.00 0.00 29.93 3.27
2428 2490 7.714377 CAGTTTGATAGCCTCATCACTCTTATT 59.286 37.037 0.00 0.00 34.69 1.40
2440 2502 3.625313 GGAGAAAGCAGTTTGATAGCCTC 59.375 47.826 0.00 0.00 0.00 4.70
2442 2504 3.615155 AGGAGAAAGCAGTTTGATAGCC 58.385 45.455 0.00 0.00 0.00 3.93
2469 2534 1.661112 GCGGACTGCAACTCTGTATTC 59.339 52.381 0.00 0.00 45.45 1.75
2499 2564 3.875369 GCCACCAAGGTTTCTGATGATCT 60.875 47.826 0.00 0.00 40.61 2.75
2524 2589 2.620585 GCTGCATTCTTACTTCCCCATC 59.379 50.000 0.00 0.00 0.00 3.51
2712 2777 3.021269 TGAAATACGCTGTCTTGACGT 57.979 42.857 0.00 0.00 43.45 4.34
2769 2834 1.321474 TCCTTGCTCTGTTTGCCTTG 58.679 50.000 0.00 0.00 0.00 3.61
2826 2891 7.324856 GCTCTACGTGTATCATCTCTTATTGTG 59.675 40.741 0.00 0.00 0.00 3.33
2932 2997 1.933247 AAGTATCGCTGAAGCAGAGC 58.067 50.000 2.79 0.00 42.21 4.09
2935 3000 2.606725 CCTCAAAGTATCGCTGAAGCAG 59.393 50.000 2.79 0.00 42.21 4.24
2997 3062 2.854736 TGATGTCATCAGAGAGGGGA 57.145 50.000 11.62 0.00 33.59 4.81
3072 3137 1.949525 CGGACATAATCAAAGCCAGGG 59.050 52.381 0.00 0.00 0.00 4.45
3078 3143 9.093970 TGAACTACATAACGGACATAATCAAAG 57.906 33.333 0.00 0.00 0.00 2.77
3147 3212 4.887748 TCTCTTCTGTTCTTGATGTCACC 58.112 43.478 0.00 0.00 0.00 4.02
3160 3225 8.753497 AACTTAAAATGACCTTTCTCTTCTGT 57.247 30.769 0.00 0.00 0.00 3.41
3222 3287 5.491070 CGATGCCCAGATATGATTTTAGGA 58.509 41.667 0.00 0.00 0.00 2.94
3408 3473 2.607187 CACTTGTAGAGGAACGCGAAT 58.393 47.619 15.93 0.00 0.00 3.34
3411 3476 1.352156 GGCACTTGTAGAGGAACGCG 61.352 60.000 3.53 3.53 0.00 6.01
3591 3656 1.034292 GCCTGAAATCCTGGTGCTCC 61.034 60.000 0.00 0.00 36.37 4.70
3739 3804 9.476928 AGGGCCAAGTACTTGTATATAGTATAG 57.523 37.037 29.05 13.43 38.85 1.31
3784 3849 5.409520 TCACGATTATATGGAAATGCTGAGC 59.590 40.000 0.00 0.00 0.00 4.26
3786 3851 6.427853 CCTTCACGATTATATGGAAATGCTGA 59.572 38.462 0.00 0.00 0.00 4.26
3982 4210 6.198403 GCTAGTGTTTTTGTTTTAGGCAGTTC 59.802 38.462 0.00 0.00 0.00 3.01
3983 4211 6.040247 GCTAGTGTTTTTGTTTTAGGCAGTT 58.960 36.000 0.00 0.00 0.00 3.16
3994 4222 3.084070 GCTTGCAGCTAGTGTTTTTGT 57.916 42.857 5.72 0.00 38.45 2.83
4023 4277 9.296400 GCTTAGTTTGTTTTGTCTTTTGTATCA 57.704 29.630 0.00 0.00 0.00 2.15
4070 4324 4.017126 TCAGCCACCCTATATATGTCTCG 58.983 47.826 0.00 0.00 0.00 4.04
4086 4340 2.504175 GGTGGTAGAGGTTTATCAGCCA 59.496 50.000 0.00 0.00 0.00 4.75
4128 4383 5.228843 GCTGTAAGTTTACCGATACTCGAAC 59.771 44.000 0.00 0.00 38.18 3.95
4207 4462 7.782242 TGCATTTTATTTTTGAGCAGTTTACG 58.218 30.769 0.00 0.00 0.00 3.18
4492 4747 6.481976 TCATCTTGACACTACATTTTCGTTGT 59.518 34.615 0.00 0.00 0.00 3.32
4526 4781 6.099990 TGTTTGTATCCCTATAATTCGGGTGA 59.900 38.462 7.13 0.00 41.40 4.02
4529 4784 7.717875 TCTTTGTTTGTATCCCTATAATTCGGG 59.282 37.037 1.84 1.84 42.05 5.14
4559 4814 1.900981 TTGCCACGGTTCACCCATG 60.901 57.895 0.00 0.00 0.00 3.66
4591 4846 1.847328 CCATTCCCCAAAGGTACACC 58.153 55.000 0.00 0.00 36.75 4.16


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

AutoCloner maintained by Alex Coulton.