Multiple sequence alignment - TraesCS4B01G205800

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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 TraesCS4B01G205800 chr4B 100.000 3095 0 0 517 3611 438227883 438224789 0.000000e+00 5716
1 TraesCS4B01G205800 chr4B 100.000 123 0 0 1 123 438228399 438228277 1.010000e-55 228
2 TraesCS4B01G205800 chr4D 95.784 2965 77 17 517 3467 354147108 354144178 0.000000e+00 4739
3 TraesCS4B01G205800 chr4D 94.574 129 1 2 1 123 354147245 354147117 1.020000e-45 195
4 TraesCS4B01G205800 chr4D 85.714 161 6 5 3468 3611 354144126 354143966 1.740000e-33 154
5 TraesCS4B01G205800 chr4A 95.230 2977 89 22 517 3469 110378639 110381586 0.000000e+00 4662
6 TraesCS4B01G205800 chr4A 96.032 126 0 1 1 121 110378249 110378374 2.200000e-47 200
7 TraesCS4B01G205800 chr4A 84.337 166 4 5 3468 3611 110381636 110381801 3.760000e-30 143
8 TraesCS4B01G205800 chr3B 78.718 390 77 6 1542 1929 616182900 616183285 4.630000e-64 255
9 TraesCS4B01G205800 chr3A 78.442 385 79 4 1547 1929 606425501 606425883 7.740000e-62 248
10 TraesCS4B01G205800 chr3D 78.182 385 80 4 1547 1929 463082335 463081953 3.600000e-60 243


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 TraesCS4B01G205800 chr4B 438224789 438228399 3610 True 2972.000000 5716 100.000000 1 3611 2 chr4B.!!$R1 3610
1 TraesCS4B01G205800 chr4D 354143966 354147245 3279 True 1696.000000 4739 92.024000 1 3611 3 chr4D.!!$R1 3610
2 TraesCS4B01G205800 chr4A 110378249 110381801 3552 False 1668.333333 4662 91.866333 1 3611 3 chr4A.!!$F1 3610

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
569 581 1.153958 GCTTGATTGCAACTCCGCC 60.154 57.895 0.0 0.0 0.0 6.13 F
1470 1499 0.036306 CCCACTACTTCAAGCCGGTT 59.964 55.000 1.9 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1802 1.134340 ACTAAGTTTGGTGTCCGCACA 60.134 47.619 0.12 0.0 46.95 4.57 R
2977 3006 0.609957 TGGAAGCACATTGAGCAGGG 60.610 55.000 8.78 0.0 0.00 4.45 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
552 559 4.897224 TCGATTTGATTTCGACTGATTGC 58.103 39.130 0.00 0.00 40.44 3.56
569 581 1.153958 GCTTGATTGCAACTCCGCC 60.154 57.895 0.00 0.00 0.00 6.13
585 597 4.560856 CCGCGAGAGAGGCCTTCG 62.561 72.222 18.95 18.95 46.21 3.79
587 599 3.832492 GCGAGAGAGGCCTTCGCT 61.832 66.667 32.95 21.27 45.01 4.93
588 600 2.103934 CGAGAGAGGCCTTCGCTG 59.896 66.667 6.77 2.05 35.96 5.18
685 697 4.916314 TCCTCGGGCCGGATCTCC 62.916 72.222 27.98 0.00 0.00 3.71
687 699 4.924187 CTCGGGCCGGATCTCCCT 62.924 72.222 27.98 0.00 40.41 4.20
688 700 4.475444 TCGGGCCGGATCTCCCTT 62.475 66.667 27.98 0.00 40.41 3.95
689 701 3.930012 CGGGCCGGATCTCCCTTC 61.930 72.222 20.56 0.00 40.41 3.46
690 702 3.561241 GGGCCGGATCTCCCTTCC 61.561 72.222 5.05 0.00 39.46 3.46
691 703 2.446802 GGCCGGATCTCCCTTCCT 60.447 66.667 5.05 0.00 0.00 3.36
692 704 2.812619 GGCCGGATCTCCCTTCCTG 61.813 68.421 5.05 0.00 0.00 3.86
693 705 2.825264 CCGGATCTCCCTTCCTGC 59.175 66.667 0.00 0.00 0.00 4.85
714 726 2.281762 CGAATTCGTGGGATTTCTCGTC 59.718 50.000 19.67 0.00 32.80 4.20
750 762 3.620929 ATGCGAGATTGATTGATGTGC 57.379 42.857 0.00 0.00 0.00 4.57
1039 1068 2.981302 CGCTCTCCATGGACACCA 59.019 61.111 11.44 0.00 38.19 4.17
1107 1136 2.915659 ACTGCCTCCCACGACGAA 60.916 61.111 0.00 0.00 0.00 3.85
1470 1499 0.036306 CCCACTACTTCAAGCCGGTT 59.964 55.000 1.90 0.00 0.00 4.44
1489 1518 1.419381 TATGTCGGCTGATAAGGGCA 58.581 50.000 0.00 0.00 0.00 5.36
1560 1589 1.530013 ATGCTTTCCTGGTGCAGCAC 61.530 55.000 17.97 17.97 44.82 4.40
1773 1802 3.053095 AGTGCCTTCATGGGATTGAGATT 60.053 43.478 0.00 0.00 38.80 2.40
1780 1809 0.617935 TGGGATTGAGATTGTGCGGA 59.382 50.000 0.00 0.00 0.00 5.54
1827 1856 3.525199 AGGCTGATATGAAGAGGTGGTTT 59.475 43.478 0.00 0.00 0.00 3.27
2316 2345 3.916989 AGGTGAAGGTTACCTGGAAGAAT 59.083 43.478 3.99 0.00 46.48 2.40
2341 2370 3.081133 CGAATGGCGTCGTCAAGG 58.919 61.111 2.47 0.00 36.26 3.61
2458 2487 1.003233 AGTTCATCCGGGAAGTTCCAC 59.997 52.381 23.33 10.78 38.64 4.02
2687 2716 2.038164 TGTCAGCTGCTCTTGACTGATT 59.962 45.455 9.47 0.00 40.95 2.57
2857 2886 3.704061 GGAAATTTAGGGGCATGCTACAA 59.296 43.478 18.92 4.13 0.00 2.41
2891 2920 4.830046 ACATATCTGGATTACTCACTCGCT 59.170 41.667 0.00 0.00 0.00 4.93
2970 2999 8.482128 TGTGGAATTTTTCTTTGTATGAAAGGT 58.518 29.630 0.00 0.00 35.27 3.50
2974 3003 9.650371 GAATTTTTCTTTGTATGAAAGGTTTGC 57.350 29.630 0.00 0.00 35.27 3.68
2975 3004 7.546778 TTTTTCTTTGTATGAAAGGTTTGCC 57.453 32.000 0.00 0.00 35.27 4.52
2976 3005 4.497473 TCTTTGTATGAAAGGTTTGCCG 57.503 40.909 0.00 0.00 40.50 5.69
2977 3006 2.715737 TTGTATGAAAGGTTTGCCGC 57.284 45.000 0.00 0.00 40.50 6.53
3020 3054 2.026915 TGTGCATTACTCTGGTGAGCAT 60.027 45.455 0.00 0.00 43.85 3.79
3038 3072 6.694411 GTGAGCATTCTGTTTAGGCATTTATG 59.306 38.462 0.00 0.00 0.00 1.90
3045 3079 6.953101 TCTGTTTAGGCATTTATGGTCAGTA 58.047 36.000 0.00 0.00 0.00 2.74
3078 3112 1.490490 TGAGAAGTCTGCTTTGTGGGT 59.510 47.619 0.00 0.00 34.61 4.51
3086 3120 0.257328 TGCTTTGTGGGTGTTCCTGA 59.743 50.000 0.00 0.00 36.20 3.86
3238 3272 5.310451 TGAAGGTACCAGTGTAAACAATCC 58.690 41.667 15.94 0.00 0.00 3.01
3343 3377 3.020984 GTTCAGTTCAACTTCAACCCCA 58.979 45.455 0.00 0.00 0.00 4.96
3404 3439 4.508861 TCTGCATTTTTCTTTTGCTGAAGC 59.491 37.500 0.00 0.00 40.08 3.86
3405 3440 3.560896 TGCATTTTTCTTTTGCTGAAGCC 59.439 39.130 0.00 0.00 41.18 4.35
3446 3481 4.449229 GGATTAGCCCCATTTGGAGGTATT 60.449 45.833 0.00 0.00 37.39 1.89
3481 3567 2.295909 TGTCCTATGGCAACTGTTTTGC 59.704 45.455 0.00 0.17 44.22 3.68
3484 3570 4.217550 GTCCTATGGCAACTGTTTTGCTAA 59.782 41.667 8.76 0.00 44.36 3.09
3536 3623 2.560105 GCTCACCCTGCATCTTCTTTTT 59.440 45.455 0.00 0.00 0.00 1.94
3546 3650 6.317789 TGCATCTTCTTTTTAGAACCACTG 57.682 37.500 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
552 559 1.135315 CGGCGGAGTTGCAATCAAG 59.865 57.895 0.59 0.00 36.28 3.02
587 599 3.109547 CGGCAAGAACGTAGCGCA 61.110 61.111 11.47 0.00 0.00 6.09
588 600 3.849953 CCGGCAAGAACGTAGCGC 61.850 66.667 0.00 0.00 0.00 5.92
685 697 1.369091 CCCACGAATTCGCAGGAAGG 61.369 60.000 30.57 20.62 44.43 3.46
686 698 0.391130 TCCCACGAATTCGCAGGAAG 60.391 55.000 30.57 19.54 44.43 3.46
687 699 0.251916 ATCCCACGAATTCGCAGGAA 59.748 50.000 31.42 19.14 43.80 3.36
688 700 0.251916 AATCCCACGAATTCGCAGGA 59.748 50.000 30.47 30.47 44.39 3.86
689 701 1.064060 GAAATCCCACGAATTCGCAGG 59.936 52.381 27.03 25.92 44.43 4.85
690 702 2.009774 AGAAATCCCACGAATTCGCAG 58.990 47.619 27.03 19.06 44.43 5.18
691 703 2.006888 GAGAAATCCCACGAATTCGCA 58.993 47.619 27.03 9.59 44.43 5.10
692 704 1.004927 CGAGAAATCCCACGAATTCGC 60.005 52.381 27.03 8.62 44.43 4.70
693 705 2.268298 ACGAGAAATCCCACGAATTCG 58.732 47.619 25.64 25.64 46.33 3.34
714 726 2.161410 TCGCATTCGAAACCCAAATCTG 59.839 45.455 0.00 0.00 42.44 2.90
1107 1136 1.677637 GCGGGAGGAAGAGGTCGAAT 61.678 60.000 0.00 0.00 0.00 3.34
1137 1166 3.272364 ATGGAGGCAGCGCTGGAAA 62.272 57.895 36.47 5.01 0.00 3.13
1326 1355 4.394712 GACACTGGGGCCGAGGTG 62.395 72.222 20.28 18.21 35.99 4.00
1470 1499 1.344438 CTGCCCTTATCAGCCGACATA 59.656 52.381 0.00 0.00 0.00 2.29
1773 1802 1.134340 ACTAAGTTTGGTGTCCGCACA 60.134 47.619 0.12 0.00 46.95 4.57
1827 1856 1.482954 CATCTCTCCCAGTGAGCTCA 58.517 55.000 13.74 13.74 41.18 4.26
2337 2366 3.798878 CGACACTAGTGCATGATACCTTG 59.201 47.826 22.90 0.15 0.00 3.61
2341 2370 3.372954 GTCCGACACTAGTGCATGATAC 58.627 50.000 22.90 9.86 0.00 2.24
2458 2487 2.445845 TGGGATCCGGGTAGGCAG 60.446 66.667 5.45 0.00 40.77 4.85
2687 2716 2.627515 AGCAGACAAGACAGCAAAGA 57.372 45.000 0.00 0.00 0.00 2.52
2857 2886 2.846206 TCCAGATATGTTCCTTGTGGCT 59.154 45.455 0.00 0.00 0.00 4.75
2891 2920 4.634004 CCAGCAACGATACCAAAACATAGA 59.366 41.667 0.00 0.00 0.00 1.98
2970 2999 2.283101 ATTGAGCAGGGCGGCAAA 60.283 55.556 12.47 0.00 33.36 3.68
2973 3002 3.818787 CACATTGAGCAGGGCGGC 61.819 66.667 0.00 0.00 0.00 6.53
2974 3003 3.818787 GCACATTGAGCAGGGCGG 61.819 66.667 0.89 0.00 0.00 6.13
2975 3004 2.262471 GAAGCACATTGAGCAGGGCG 62.262 60.000 8.78 0.00 0.00 6.13
2976 3005 1.509923 GAAGCACATTGAGCAGGGC 59.490 57.895 8.78 0.00 0.00 5.19
2977 3006 0.609957 TGGAAGCACATTGAGCAGGG 60.610 55.000 8.78 0.00 0.00 4.45
3020 3054 6.245408 ACTGACCATAAATGCCTAAACAGAA 58.755 36.000 0.00 0.00 0.00 3.02
3038 3072 5.128827 TCTCACCAACCTATGAATACTGACC 59.871 44.000 0.00 0.00 0.00 4.02
3045 3079 5.738909 CAGACTTCTCACCAACCTATGAAT 58.261 41.667 0.00 0.00 0.00 2.57
3078 3112 5.726980 CCTGGATGAAATTTTCAGGAACA 57.273 39.130 16.34 11.12 45.66 3.18
3086 3120 6.554605 TGAACTCCTTTCCTGGATGAAATTTT 59.445 34.615 0.00 0.00 35.30 1.82
3313 3347 7.681939 TGAAGTTGAACTGAACATAATACCC 57.318 36.000 0.00 0.00 0.00 3.69
3404 3439 4.963318 TCCTATCCTTGCAGATACTTGG 57.037 45.455 0.00 0.00 0.00 3.61
3405 3440 6.593382 GCTAATCCTATCCTTGCAGATACTTG 59.407 42.308 0.00 0.00 0.00 3.16
3446 3481 5.163237 GCCATAGGACACCAGAATAGGTAAA 60.163 44.000 0.00 0.00 40.77 2.01
3481 3567 5.016831 AGTCCCAGGGCAAAAACTTATTAG 58.983 41.667 0.00 0.00 0.00 1.73
3484 3570 3.165071 CAGTCCCAGGGCAAAAACTTAT 58.835 45.455 0.00 0.00 0.00 1.73
3546 3650 4.747108 CCTCATTTACTCATCCACATCGTC 59.253 45.833 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.