Multiple sequence alignment - TraesCS3B01G246000

Loading Multiple Alignment...

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 TraesCS3B01G246000 chr3B 100.000 3278 0 0 1 3278 390451630 390454907 0.000000e+00 6054
1 TraesCS3B01G246000 chr3A 93.772 1718 35 20 1599 3278 394026598 394028281 0.000000e+00 2514
2 TraesCS3B01G246000 chr3A 96.131 827 18 4 730 1547 394025777 394026598 0.000000e+00 1338
3 TraesCS3B01G246000 chr3A 86.450 738 65 21 5 713 394024974 394025705 0.000000e+00 776
4 TraesCS3B01G246000 chr3D 92.051 1711 58 15 1609 3278 296039965 296041638 0.000000e+00 2335
5 TraesCS3B01G246000 chr3D 96.259 1203 34 7 395 1594 296038785 296039979 0.000000e+00 1962
6 TraesCS3B01G246000 chr3D 92.701 411 24 4 3 412 296038358 296038763 3.640000e-164 588


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 TraesCS3B01G246000 chr3B 390451630 390454907 3277 False 6054.000000 6054 100.000000 1 3278 1 chr3B.!!$F1 3277
1 TraesCS3B01G246000 chr3A 394024974 394028281 3307 False 1542.666667 2514 92.117667 5 3278 3 chr3A.!!$F1 3273
2 TraesCS3B01G246000 chr3D 296038358 296041638 3280 False 1628.333333 2335 93.670333 3 3278 3 chr3D.!!$F1 3275

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
165 166 0.178958 AACACCCGTGGAGAGAGAGT 60.179 55.0 0.0 0.0 34.19 3.24 F
1290 1423 1.078759 CGGTGCTTCTGTCCATCGAC 61.079 60.0 0.0 0.0 37.76 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 2290 1.083015 CGCCGACAAAAGTGGAACG 60.083 57.895 0.0 0.0 45.86 3.95 R
2357 2518 0.107993 GCAGCAGACACAGCCTGATA 60.108 55.000 0.0 0.0 33.65 2.15 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
43 44 5.983118 ACAAAAACTTCAAAATCGGTCATCC 59.017 36.000 0.00 0.00 0.00 3.51
68 69 6.845302 TGTGCAAATATTCATCAGTTGAGAC 58.155 36.000 0.00 0.00 35.27 3.36
109 110 1.246294 AGGTATGGCCTCCCTAGTCT 58.754 55.000 3.32 0.00 46.96 3.24
115 116 3.596940 TGGCCTCCCTAGTCTACTAAG 57.403 52.381 3.32 0.00 0.00 2.18
123 124 6.039605 CCTCCCTAGTCTACTAAGCTAAACAC 59.960 46.154 0.00 0.00 0.00 3.32
142 143 1.759445 ACTATGTGCCACCTCTAGCTG 59.241 52.381 0.00 0.00 0.00 4.24
152 153 1.348036 ACCTCTAGCTGAACAACACCC 59.652 52.381 0.00 0.00 0.00 4.61
154 155 1.000955 CTCTAGCTGAACAACACCCGT 59.999 52.381 0.00 0.00 0.00 5.28
165 166 0.178958 AACACCCGTGGAGAGAGAGT 60.179 55.000 0.00 0.00 34.19 3.24
169 170 1.747367 CCGTGGAGAGAGAGTCGCT 60.747 63.158 0.00 0.00 0.00 4.93
235 236 3.803021 GCAAACATTGGAAGGCATGTGAA 60.803 43.478 0.00 0.00 33.76 3.18
259 260 3.624861 AGAAAGCCATATTGCGAGACTTG 59.375 43.478 0.00 0.00 36.02 3.16
276 277 3.305720 ACTTGATGTAATAGAGGGCGGA 58.694 45.455 0.00 0.00 0.00 5.54
277 278 3.904339 ACTTGATGTAATAGAGGGCGGAT 59.096 43.478 0.00 0.00 0.00 4.18
278 279 3.961480 TGATGTAATAGAGGGCGGATG 57.039 47.619 0.00 0.00 0.00 3.51
379 380 3.560636 ACGGGGAGAATGGTAAGATTG 57.439 47.619 0.00 0.00 0.00 2.67
515 583 4.219725 GGTGTTGCCCTAATAAAAGAAGCA 59.780 41.667 0.00 0.00 0.00 3.91
573 643 6.100004 AGTGTTGATTATACAACCTCGTGAG 58.900 40.000 0.00 0.00 46.32 3.51
621 692 1.377202 CAGGCCCTGCGCTCTAAAA 60.377 57.895 9.73 0.00 37.74 1.52
672 743 4.143179 GGAACATTCCTAACGAAGTTGACG 60.143 45.833 3.24 0.00 46.91 4.35
804 934 1.610379 ATCCACAGCCAAAAGGCCC 60.610 57.895 0.00 0.00 35.12 5.80
962 1092 1.528309 ACCCGCACCAAAAGACAGG 60.528 57.895 0.00 0.00 0.00 4.00
1245 1378 2.444256 GGCCCCTAGCTCCATCGTT 61.444 63.158 0.00 0.00 43.05 3.85
1290 1423 1.078759 CGGTGCTTCTGTCCATCGAC 61.079 60.000 0.00 0.00 37.76 4.20
1495 1630 5.588648 TCAGACCTTTTTGTACCTGAGTTTG 59.411 40.000 0.00 0.00 0.00 2.93
1500 1635 5.290885 CCTTTTTGTACCTGAGTTTGTTTGC 59.709 40.000 0.00 0.00 0.00 3.68
1501 1636 5.392767 TTTTGTACCTGAGTTTGTTTGCA 57.607 34.783 0.00 0.00 0.00 4.08
1555 1690 8.418597 ACTAATAAAGTCGCATTATCCCTCTA 57.581 34.615 0.00 0.00 30.33 2.43
1685 1821 2.566833 TGGTCCTTCTGTGAACATGG 57.433 50.000 0.00 0.00 0.00 3.66
2151 2311 1.161563 TTCCACTTTTGTCGGCGTCC 61.162 55.000 6.85 0.00 0.00 4.79
2491 2652 5.164254 CGTTGTTGATGTGTGTAGTACGTAC 60.164 44.000 18.10 18.10 0.00 3.67
2492 2653 4.465921 TGTTGATGTGTGTAGTACGTACG 58.534 43.478 19.49 15.01 33.87 3.67
2493 2654 4.024133 TGTTGATGTGTGTAGTACGTACGT 60.024 41.667 25.98 25.98 33.87 3.57
2494 2655 5.178438 TGTTGATGTGTGTAGTACGTACGTA 59.822 40.000 23.60 23.60 33.87 3.57
2543 2712 5.682943 TGTAAAAACCAGAATCTCCAACG 57.317 39.130 0.00 0.00 0.00 4.10
2580 2749 3.864686 CCACGCTACGCATGCACC 61.865 66.667 19.57 1.09 0.00 5.01
2590 2759 1.451207 GCATGCACCCGGATGTACA 60.451 57.895 14.21 0.00 42.60 2.90
2591 2760 1.029408 GCATGCACCCGGATGTACAA 61.029 55.000 14.21 0.00 42.60 2.41
2592 2761 1.016627 CATGCACCCGGATGTACAAG 58.983 55.000 0.73 0.00 36.29 3.16
2595 2764 1.206132 TGCACCCGGATGTACAAGTAG 59.794 52.381 0.73 0.00 0.00 2.57
2596 2765 1.206371 GCACCCGGATGTACAAGTAGT 59.794 52.381 0.73 0.00 0.00 2.73
2598 2767 3.490419 GCACCCGGATGTACAAGTAGTAG 60.490 52.174 0.73 0.00 32.19 2.57
2613 2782 7.479150 ACAAGTAGTAGTAGTAGAATTTCGGC 58.521 38.462 0.00 0.00 0.00 5.54
2821 2996 3.217743 CTACGCCTCCCTCCGGAC 61.218 72.222 0.00 0.00 33.32 4.79
2841 3016 1.048601 CTGGGATACGGTAGGTGCAT 58.951 55.000 0.00 0.00 37.60 3.96
3063 3238 1.820056 GGGAGAAAAGCTAGGCGGC 60.820 63.158 0.00 0.00 0.00 6.53
3092 3270 5.537300 CTTATCCAGCACAGTGGTACTAT 57.463 43.478 4.57 2.27 38.88 2.12
3130 3316 4.374702 CGCACCTGCAACAGACGC 62.375 66.667 0.00 0.00 42.21 5.19
3131 3317 2.974698 GCACCTGCAACAGACGCT 60.975 61.111 0.00 0.00 41.59 5.07
3198 3398 3.389329 AGAGTGTCTTCTTTGCTCCAAGA 59.611 43.478 0.00 0.00 0.00 3.02
3199 3399 3.737850 AGTGTCTTCTTTGCTCCAAGAG 58.262 45.455 0.00 0.00 0.00 2.85
3200 3400 2.810852 GTGTCTTCTTTGCTCCAAGAGG 59.189 50.000 0.00 0.00 0.00 3.69
3201 3401 1.809547 GTCTTCTTTGCTCCAAGAGGC 59.190 52.381 0.00 0.00 33.74 4.70
3202 3402 1.421268 TCTTCTTTGCTCCAAGAGGCA 59.579 47.619 0.00 0.00 36.62 4.75
3203 3403 2.158623 TCTTCTTTGCTCCAAGAGGCAA 60.159 45.455 0.00 0.00 45.06 4.52
3204 3404 1.901591 TCTTTGCTCCAAGAGGCAAG 58.098 50.000 0.00 0.00 46.75 4.01
3222 3422 4.380867 GGCAAGTGGACAATTAATCACCAG 60.381 45.833 7.98 1.28 0.00 4.00
3243 3443 1.425066 TCCATCCAACAAAGGCAGACT 59.575 47.619 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.448615 GTTTTTGTTAAATCTCGTACCAGCTAT 58.551 33.333 0.00 0.00 0.00 2.97
1 2 7.658575 AGTTTTTGTTAAATCTCGTACCAGCTA 59.341 33.333 0.00 0.00 0.00 3.32
43 44 6.965500 GTCTCAACTGATGAATATTTGCACAG 59.035 38.462 0.00 0.00 37.67 3.66
68 69 3.118629 TCATGGTCAGGATTCCTTTCTCG 60.119 47.826 1.28 0.00 0.00 4.04
109 110 6.103997 GTGGCACATAGTGTTTAGCTTAGTA 58.896 40.000 13.86 0.00 44.52 1.82
115 116 2.678336 GAGGTGGCACATAGTGTTTAGC 59.322 50.000 20.82 0.00 44.52 3.09
123 124 2.034878 TCAGCTAGAGGTGGCACATAG 58.965 52.381 20.82 17.56 44.52 2.23
142 143 0.391597 TCTCTCCACGGGTGTTGTTC 59.608 55.000 0.00 0.00 0.00 3.18
152 153 1.719117 GAGCGACTCTCTCTCCACG 59.281 63.158 0.00 0.00 38.78 4.94
154 155 0.036294 TTCGAGCGACTCTCTCTCCA 60.036 55.000 0.00 0.00 39.70 3.86
165 166 3.001533 GTGTTGGTTTTAGTTTCGAGCGA 59.998 43.478 0.00 0.00 0.00 4.93
169 170 4.033129 CGACTGTGTTGGTTTTAGTTTCGA 59.967 41.667 0.00 0.00 0.00 3.71
235 236 4.265073 AGTCTCGCAATATGGCTTTCTTT 58.735 39.130 0.00 0.00 0.00 2.52
259 260 2.832129 TCCATCCGCCCTCTATTACATC 59.168 50.000 0.00 0.00 0.00 3.06
276 277 6.923199 AAAACTCAATTCTCAACCATCCAT 57.077 33.333 0.00 0.00 0.00 3.41
277 278 6.462768 CCAAAAACTCAATTCTCAACCATCCA 60.463 38.462 0.00 0.00 0.00 3.41
278 279 5.928264 CCAAAAACTCAATTCTCAACCATCC 59.072 40.000 0.00 0.00 0.00 3.51
573 643 0.098728 CCATCGCCGTCATGTTTTCC 59.901 55.000 0.00 0.00 0.00 3.13
575 645 1.401552 CATCCATCGCCGTCATGTTTT 59.598 47.619 0.00 0.00 0.00 2.43
579 649 2.084610 ATACATCCATCGCCGTCATG 57.915 50.000 0.00 0.00 0.00 3.07
580 650 2.839486 AATACATCCATCGCCGTCAT 57.161 45.000 0.00 0.00 0.00 3.06
621 692 2.287129 GCCACCGTACACGTGAATTTTT 60.287 45.455 25.01 0.00 37.74 1.94
659 730 1.937278 TTGCACCGTCAACTTCGTTA 58.063 45.000 0.00 0.00 0.00 3.18
672 743 4.683781 TCTTTTGATGCGTAAATTTGCACC 59.316 37.500 5.42 0.00 45.07 5.01
804 934 8.642885 CACTATAAATATGCTGCTTCTACTTCG 58.357 37.037 0.00 0.00 0.00 3.79
962 1092 0.861837 CTAAATCGATCCGCACTGCC 59.138 55.000 0.00 0.00 0.00 4.85
1290 1423 4.168291 GCCCTCTCCAAGCCCTCG 62.168 72.222 0.00 0.00 0.00 4.63
1382 1515 7.960793 GTGTAACTGCGTATTTCTGTTTATCT 58.039 34.615 0.00 0.00 0.00 1.98
1500 1635 9.571810 GTCAAGATGAGATAGACTAGCATAATG 57.428 37.037 0.00 2.19 0.00 1.90
1501 1636 8.748412 GGTCAAGATGAGATAGACTAGCATAAT 58.252 37.037 0.00 0.00 0.00 1.28
1590 1725 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1591 1726 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1592 1727 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1593 1728 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1594 1729 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1595 1730 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1596 1731 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1597 1732 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1685 1821 1.474143 GCTCCATGGAACTCCTGTAGC 60.474 57.143 17.00 8.49 36.82 3.58
2130 2290 1.083015 CGCCGACAAAAGTGGAACG 60.083 57.895 0.00 0.00 45.86 3.95
2172 2332 0.540923 GAGGCTGCTCCATCAGAACT 59.459 55.000 0.00 0.00 36.19 3.01
2205 2365 2.357517 GAGCAGTGGTGACCGTGG 60.358 66.667 0.00 0.00 0.00 4.94
2352 2513 3.118956 AGCAGACACAGCCTGATAGTAAC 60.119 47.826 0.00 0.00 33.65 2.50
2353 2514 3.099905 AGCAGACACAGCCTGATAGTAA 58.900 45.455 0.00 0.00 33.65 2.24
2354 2515 2.428530 CAGCAGACACAGCCTGATAGTA 59.571 50.000 0.00 0.00 33.65 1.82
2355 2516 1.206610 CAGCAGACACAGCCTGATAGT 59.793 52.381 0.00 0.00 33.65 2.12
2356 2517 1.937278 CAGCAGACACAGCCTGATAG 58.063 55.000 0.00 0.00 33.65 2.08
2357 2518 0.107993 GCAGCAGACACAGCCTGATA 60.108 55.000 0.00 0.00 33.65 2.15
2440 2601 1.588404 CAATTAGCACTACTCGCACGG 59.412 52.381 0.00 0.00 0.00 4.94
2447 2608 5.593679 ACGTATCCACAATTAGCACTACT 57.406 39.130 0.00 0.00 0.00 2.57
2497 2658 2.749441 GGACCCAAGAGCAGCAGC 60.749 66.667 0.00 0.00 42.56 5.25
2543 2712 1.034292 GGGAACAGGAGCATGCTTCC 61.034 60.000 23.61 22.75 29.87 3.46
2580 2749 7.212976 TCTACTACTACTACTTGTACATCCGG 58.787 42.308 0.00 0.00 0.00 5.14
2590 2759 6.540189 TCGCCGAAATTCTACTACTACTACTT 59.460 38.462 0.00 0.00 0.00 2.24
2591 2760 6.051717 TCGCCGAAATTCTACTACTACTACT 58.948 40.000 0.00 0.00 0.00 2.57
2592 2761 6.292389 TCGCCGAAATTCTACTACTACTAC 57.708 41.667 0.00 0.00 0.00 2.73
2595 2764 6.142002 GTGATTCGCCGAAATTCTACTACTAC 59.858 42.308 2.60 0.00 0.00 2.73
2596 2765 6.204359 GTGATTCGCCGAAATTCTACTACTA 58.796 40.000 2.60 0.00 0.00 1.82
2598 2767 4.085721 CGTGATTCGCCGAAATTCTACTAC 60.086 45.833 2.60 0.00 0.00 2.73
2613 2782 1.209128 GTATGGACAGCCGTGATTCG 58.791 55.000 0.00 0.00 36.79 3.34
2651 2826 2.367894 TGAATGCCTGCATTTGGAACAA 59.632 40.909 17.66 0.00 45.50 2.83
2663 2838 4.149571 CGACGATAAGAATCTGAATGCCTG 59.850 45.833 0.00 0.00 0.00 4.85
2821 2996 1.046472 TGCACCTACCGTATCCCAGG 61.046 60.000 0.00 0.00 0.00 4.45
2841 3016 3.699538 AGGAATGAGCACTGTACGATACA 59.300 43.478 0.00 0.00 37.13 2.29
3088 3266 4.585162 CCGGAATCCTGAGACAGTAATAGT 59.415 45.833 0.00 0.00 0.00 2.12
3092 3270 2.758979 GACCGGAATCCTGAGACAGTAA 59.241 50.000 9.46 0.00 0.00 2.24
3130 3316 2.964464 ACATAGGCATCACTCAGAGGAG 59.036 50.000 1.53 0.00 46.96 3.69
3131 3317 2.961741 GACATAGGCATCACTCAGAGGA 59.038 50.000 1.53 0.00 0.00 3.71
3198 3398 3.763897 GGTGATTAATTGTCCACTTGCCT 59.236 43.478 5.34 0.00 0.00 4.75
3199 3399 3.509575 TGGTGATTAATTGTCCACTTGCC 59.490 43.478 5.34 0.00 0.00 4.52
3200 3400 4.218417 ACTGGTGATTAATTGTCCACTTGC 59.782 41.667 5.34 0.00 0.00 4.01
3201 3401 5.106157 GGACTGGTGATTAATTGTCCACTTG 60.106 44.000 14.72 7.71 42.32 3.16
3202 3402 5.010282 GGACTGGTGATTAATTGTCCACTT 58.990 41.667 14.72 3.81 42.32 3.16
3203 3403 4.042809 TGGACTGGTGATTAATTGTCCACT 59.957 41.667 16.73 5.75 45.86 4.00
3204 3404 4.331968 TGGACTGGTGATTAATTGTCCAC 58.668 43.478 16.73 9.15 45.86 4.02
3222 3422 1.541588 GTCTGCCTTTGTTGGATGGAC 59.458 52.381 0.00 0.00 0.00 4.02
3227 3427 2.435372 ACAAGTCTGCCTTTGTTGGA 57.565 45.000 0.00 0.00 0.00 3.53
3243 3443 5.903010 TGCTACCTTTCTCCATCCTATACAA 59.097 40.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.