Multiple sequence alignment - TraesCS6D01G274700

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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 TraesCS6D01G274700 chr6D 100.000 3508 0 0 1 3508 383540699 383544206 0.000000e+00 6479.0
1 TraesCS6D01G274700 chr6A 92.021 3434 148 46 1 3381 525755046 525758406 0.000000e+00 4708.0
2 TraesCS6D01G274700 chr6A 90.610 213 18 2 1 211 525745883 525746095 7.410000e-72 281.0
3 TraesCS6D01G274700 chr6A 92.969 128 3 2 3382 3503 525758450 525758577 7.740000e-42 182.0
4 TraesCS6D01G274700 chr6B 92.595 3268 144 39 1 3214 573681281 573684504 0.000000e+00 4604.0
5 TraesCS6D01G274700 chr3B 100.000 35 0 0 3346 3380 6683705 6683671 8.130000e-07 65.8
6 TraesCS6D01G274700 chr2B 94.737 38 2 0 3343 3380 750063005 750063042 3.780000e-05 60.2
7 TraesCS6D01G274700 chr5D 100.000 28 0 0 3352 3379 298965733 298965706 6.000000e-03 52.8
8 TraesCS6D01G274700 chr4D 94.118 34 2 0 3346 3379 508584362 508584395 6.000000e-03 52.8
9 TraesCS6D01G274700 chr1B 100.000 28 0 0 3353 3380 654085546 654085573 6.000000e-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 TraesCS6D01G274700 chr6D 383540699 383544206 3507 False 6479 6479 100.000 1 3508 1 chr6D.!!$F1 3507
1 TraesCS6D01G274700 chr6A 525755046 525758577 3531 False 2445 4708 92.495 1 3503 2 chr6A.!!$F2 3502
2 TraesCS6D01G274700 chr6B 573681281 573684504 3223 False 4604 4604 92.595 1 3214 1 chr6B.!!$F1 3213

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
90 93 0.955428 GGATGTGTTTGCTCGGCAGA 60.955 55.0 0.00 0.00 40.61 4.26 F
536 562 1.100510 CAGGACGGACGTATCCTTGA 58.899 55.0 11.80 0.00 43.09 3.02 F
2051 2114 0.257039 ACTGGGGCTAGCAGGATTTG 59.743 55.0 18.24 2.12 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2080 1.134371 CCCAGTTAGCAAGGTAGAGCC 60.134 57.143 0.00 0.0 37.58 4.70 R
2318 2383 1.131883 GCTGCATTTGCTGTCCTGTAG 59.868 52.381 10.52 0.0 42.66 2.74 R
3424 3547 1.474077 CTACAACATTGCAGAAGCCCC 59.526 52.381 0.00 0.0 41.13 5.80 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
90 93 0.955428 GGATGTGTTTGCTCGGCAGA 60.955 55.000 0.00 0.00 40.61 4.26
129 132 2.616893 ATGGGGGCTTGGGCACTA 60.617 61.111 0.00 0.00 42.45 2.74
274 293 3.346315 TGTGTGGTCTTCAATATGGCTG 58.654 45.455 0.00 0.00 0.00 4.85
356 382 6.640907 CACTGTTTAAAGATAGGTGTTTTGGC 59.359 38.462 0.00 0.00 0.00 4.52
386 412 1.115930 AGCAAGTGGACAGGTCGAGT 61.116 55.000 0.00 0.00 0.00 4.18
408 434 2.165845 GGTAGTGAGTAGTCCGCATGTT 59.834 50.000 0.00 0.00 0.00 2.71
476 502 1.878948 GCCCTTGTGCCGTTGTAACTA 60.879 52.381 0.00 0.00 0.00 2.24
509 535 4.215827 GGCTTTCCTTCTATGAGCATGATG 59.784 45.833 0.00 0.00 35.12 3.07
536 562 1.100510 CAGGACGGACGTATCCTTGA 58.899 55.000 11.80 0.00 43.09 3.02
538 564 1.475682 AGGACGGACGTATCCTTGAAC 59.524 52.381 9.22 0.00 43.09 3.18
543 569 4.320870 ACGGACGTATCCTTGAACAAAAT 58.679 39.130 0.00 0.00 43.73 1.82
765 816 3.236003 GAGGTTTCTCGGCCGGTGT 62.236 63.158 27.83 2.76 0.00 4.16
766 817 3.047877 GGTTTCTCGGCCGGTGTG 61.048 66.667 27.83 13.38 0.00 3.82
767 818 3.047877 GTTTCTCGGCCGGTGTGG 61.048 66.667 27.83 10.73 42.50 4.17
768 819 3.552384 TTTCTCGGCCGGTGTGGT 61.552 61.111 27.83 0.00 41.21 4.16
769 820 3.109592 TTTCTCGGCCGGTGTGGTT 62.110 57.895 27.83 0.00 41.21 3.67
770 821 2.612095 TTTCTCGGCCGGTGTGGTTT 62.612 55.000 27.83 0.00 41.21 3.27
771 822 3.353836 CTCGGCCGGTGTGGTTTG 61.354 66.667 27.83 0.64 41.21 2.93
772 823 3.818121 CTCGGCCGGTGTGGTTTGA 62.818 63.158 27.83 0.00 41.21 2.69
1201 1253 3.305335 GGTCCGTCCGTCTGTTTACTTTA 60.305 47.826 0.00 0.00 0.00 1.85
1218 1270 1.971505 TTACCGATCTGCCTGCCTGG 61.972 60.000 0.00 0.00 39.35 4.45
1239 1291 3.581687 GATCTCTCATCCGCCGGGC 62.582 68.421 9.54 9.54 0.00 6.13
1656 1715 1.823250 GCTGAAGATGTTGGGGGTGTT 60.823 52.381 0.00 0.00 0.00 3.32
1883 1942 7.162082 ACCTGTTCAAGTTATATATGCTAGCC 58.838 38.462 13.29 0.00 0.00 3.93
1917 1980 1.934589 CACTGACGTGGTGTTTCTCA 58.065 50.000 0.00 0.00 37.50 3.27
2017 2080 1.375523 GTACTGACGGTTGGCCCTG 60.376 63.158 0.00 0.00 0.00 4.45
2047 2110 1.338136 GCTAACTGGGGCTAGCAGGA 61.338 60.000 18.24 0.00 40.27 3.86
2048 2111 1.428869 CTAACTGGGGCTAGCAGGAT 58.571 55.000 18.24 2.06 0.00 3.24
2049 2112 1.771255 CTAACTGGGGCTAGCAGGATT 59.229 52.381 18.24 6.40 0.00 3.01
2050 2113 1.002857 AACTGGGGCTAGCAGGATTT 58.997 50.000 18.24 0.48 0.00 2.17
2051 2114 0.257039 ACTGGGGCTAGCAGGATTTG 59.743 55.000 18.24 2.12 0.00 2.32
2052 2115 0.548031 CTGGGGCTAGCAGGATTTGA 59.452 55.000 18.24 0.00 0.00 2.69
2141 2205 9.472361 TCTACTATGAAACACAACTCTACAAAC 57.528 33.333 0.00 0.00 0.00 2.93
2182 2246 6.002062 GAATCAAATTCGGTTGTGAGTTCT 57.998 37.500 0.00 0.00 0.00 3.01
2250 2315 9.712305 TTTGTTCCTCAAAAAGAAATACAACAA 57.288 25.926 0.00 0.00 42.18 2.83
2296 2361 9.904198 TTGGAATCTTGAGACATATGACAAATA 57.096 29.630 10.38 4.94 0.00 1.40
2317 2382 7.855784 AATATGAAGAACTCCCCTTTGTTTT 57.144 32.000 0.00 0.00 0.00 2.43
2318 2383 5.791336 ATGAAGAACTCCCCTTTGTTTTC 57.209 39.130 0.00 0.00 0.00 2.29
2345 2410 3.113979 GCAAATGCAGCAACGCCC 61.114 61.111 0.00 0.00 41.59 6.13
2416 2481 2.186160 CGCCAGGAAGCACAACACA 61.186 57.895 0.00 0.00 0.00 3.72
2456 2521 3.118992 TGTCATGGTTCTTCGGAGATGAG 60.119 47.826 0.00 0.00 41.68 2.90
2504 2569 1.751351 CTGGACACGGAGCTCAAGATA 59.249 52.381 17.19 0.00 0.00 1.98
2674 2739 6.472016 TCTTCTTCTTTTGGTTTTGCCTTTT 58.528 32.000 0.00 0.00 38.35 2.27
2685 2750 4.050934 GCCTTTTGGGTTCGGCGG 62.051 66.667 7.21 0.00 40.82 6.13
2769 2834 1.931841 GATTTACGGGCTTCTTCGGAC 59.068 52.381 0.00 0.00 0.00 4.79
3044 3110 2.320745 ACCCTCTTCGTTTTGACGTT 57.679 45.000 0.00 0.00 0.00 3.99
3057 3124 3.524648 GACGTTGAGGTTCGCCCCA 62.525 63.158 0.00 0.00 38.27 4.96
3058 3125 2.742372 CGTTGAGGTTCGCCCCAG 60.742 66.667 0.00 0.00 38.27 4.45
3063 3130 1.281419 TGAGGTTCGCCCCAGATTTA 58.719 50.000 0.00 0.00 38.27 1.40
3110 3177 8.197592 TCAGGTTAGTTCACTATTTCAAGGTA 57.802 34.615 0.00 0.00 0.00 3.08
3117 3188 7.690256 AGTTCACTATTTCAAGGTACCTCATT 58.310 34.615 16.64 0.00 0.00 2.57
3227 3298 2.128035 CACAAATAGCCGTCGGATCTC 58.872 52.381 17.49 0.00 0.00 2.75
3232 3303 2.577020 TAGCCGTCGGATCTCCCCAA 62.577 60.000 17.49 0.00 0.00 4.12
3237 3308 1.961394 CGTCGGATCTCCCCAATAAGA 59.039 52.381 0.00 0.00 0.00 2.10
3246 3317 3.118775 TCTCCCCAATAAGATGTGTCACG 60.119 47.826 0.00 0.00 0.00 4.35
3261 3332 3.002862 GTGTCACGAATTGCAACAAGGTA 59.997 43.478 0.00 0.00 0.00 3.08
3266 3337 3.119849 ACGAATTGCAACAAGGTAGATGC 60.120 43.478 0.00 0.00 37.75 3.91
3268 3339 4.379813 CGAATTGCAACAAGGTAGATGCTT 60.380 41.667 0.00 0.00 38.05 3.91
3271 3342 2.030007 TGCAACAAGGTAGATGCTTTGC 60.030 45.455 0.00 0.00 38.05 3.68
3272 3343 2.030007 GCAACAAGGTAGATGCTTTGCA 60.030 45.455 0.00 0.00 44.86 4.08
3282 3353 0.250234 ATGCTTTGCAGGTCGCTCTA 59.750 50.000 0.00 0.00 43.65 2.43
3283 3354 0.670546 TGCTTTGCAGGTCGCTCTAC 60.671 55.000 0.00 0.00 43.06 2.59
3284 3355 0.670546 GCTTTGCAGGTCGCTCTACA 60.671 55.000 0.00 0.00 43.06 2.74
3331 3402 1.807742 TCGAGGTGTTATTTTTGCCCG 59.192 47.619 0.00 0.00 0.00 6.13
3348 3428 1.607148 CCCGAAACAGAAACTCCCAAC 59.393 52.381 0.00 0.00 0.00 3.77
3359 3439 6.176183 CAGAAACTCCCAACATAGATCTTGT 58.824 40.000 0.00 2.53 0.00 3.16
3424 3547 0.731174 GCGGTAAACAATGTTGCGGG 60.731 55.000 0.00 0.00 0.00 6.13
3459 3582 7.043192 GCAATGTTGTAGGAATTTATGTCATGC 60.043 37.037 0.00 0.00 0.00 4.06
3479 3607 2.287308 GCGTCACCTTGCAACATAAACA 60.287 45.455 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.660560 GGCATGCCTGTGGATGTGAC 61.661 60.000 29.98 0.00 0.00 3.67
10 11 2.043652 GGGCATGCCTGTGGATGT 60.044 61.111 34.70 0.00 36.10 3.06
90 93 1.526575 CCCAAGACTGCGTGCCAAAT 61.527 55.000 0.00 0.00 0.00 2.32
127 130 0.106335 CCTCAGGTGCAGGCATCTAG 59.894 60.000 6.74 5.57 34.77 2.43
129 132 1.614525 TCCTCAGGTGCAGGCATCT 60.615 57.895 0.15 0.15 38.01 2.90
274 293 1.873591 CACTACGCTCATTATTGGGGC 59.126 52.381 0.00 0.00 0.00 5.80
279 298 5.290493 TGGATTCCACTACGCTCATTATT 57.710 39.130 0.00 0.00 0.00 1.40
356 382 7.433680 ACCTGTCCACTTGCTTTAAAAATTAG 58.566 34.615 0.00 0.00 0.00 1.73
367 393 1.115930 ACTCGACCTGTCCACTTGCT 61.116 55.000 0.00 0.00 0.00 3.91
386 412 1.749063 CATGCGGACTACTCACTACCA 59.251 52.381 0.00 0.00 0.00 3.25
408 434 3.370104 TGGAGGCCAAGAAAAGAAAACA 58.630 40.909 5.01 0.00 0.00 2.83
454 480 0.887387 TTACAACGGCACAAGGGCTC 60.887 55.000 0.00 0.00 40.61 4.70
514 540 2.496291 GGATACGTCCGTCCTGGGG 61.496 68.421 0.00 0.00 38.76 4.96
765 816 2.422597 GATGACGACACCATCAAACCA 58.577 47.619 0.00 0.00 39.98 3.67
766 817 1.737793 GGATGACGACACCATCAAACC 59.262 52.381 0.00 0.00 41.52 3.27
767 818 2.699954 AGGATGACGACACCATCAAAC 58.300 47.619 0.00 0.00 41.52 2.93
768 819 3.073678 CAAGGATGACGACACCATCAAA 58.926 45.455 0.00 0.00 41.52 2.69
769 820 2.698803 CAAGGATGACGACACCATCAA 58.301 47.619 0.00 0.00 41.52 2.57
770 821 1.675714 GCAAGGATGACGACACCATCA 60.676 52.381 0.00 0.00 41.52 3.07
771 822 1.009829 GCAAGGATGACGACACCATC 58.990 55.000 0.00 0.00 39.61 3.51
772 823 0.740868 CGCAAGGATGACGACACCAT 60.741 55.000 0.00 0.00 0.00 3.55
817 868 1.442769 CCGTGCATGTAGCTTCTGTT 58.557 50.000 4.96 0.00 45.94 3.16
818 869 0.391661 CCCGTGCATGTAGCTTCTGT 60.392 55.000 4.96 0.00 45.94 3.41
819 870 1.709147 GCCCGTGCATGTAGCTTCTG 61.709 60.000 4.96 0.00 45.94 3.02
820 871 1.450312 GCCCGTGCATGTAGCTTCT 60.450 57.895 4.96 0.00 45.94 2.85
821 872 2.472909 GGCCCGTGCATGTAGCTTC 61.473 63.158 15.43 0.00 45.94 3.86
1201 1253 3.790437 CCAGGCAGGCAGATCGGT 61.790 66.667 0.00 0.00 0.00 4.69
1218 1270 2.048690 GGCGGATGAGAGATCGGC 60.049 66.667 0.00 0.00 41.68 5.54
1239 1291 2.475187 GCGTGCAGCTGAAGTCATTTAG 60.475 50.000 20.43 0.86 44.04 1.85
1883 1942 3.054878 GTCAGTGCAAGGCAAAATGAAG 58.945 45.455 0.00 0.00 41.47 3.02
2006 2069 3.399181 TAGAGCCAGGGCCAACCG 61.399 66.667 6.18 0.00 46.96 4.44
2017 2080 1.134371 CCCAGTTAGCAAGGTAGAGCC 60.134 57.143 0.00 0.00 37.58 4.70
2047 2110 7.530426 AGTAGAAGCCAGTTCAAATTCAAAT 57.470 32.000 0.00 0.00 37.67 2.32
2048 2111 6.959639 AGTAGAAGCCAGTTCAAATTCAAA 57.040 33.333 0.00 0.00 37.67 2.69
2049 2112 7.224297 ACTAGTAGAAGCCAGTTCAAATTCAA 58.776 34.615 3.59 0.00 37.67 2.69
2050 2113 6.769512 ACTAGTAGAAGCCAGTTCAAATTCA 58.230 36.000 3.59 0.00 37.67 2.57
2051 2114 7.010645 GCTACTAGTAGAAGCCAGTTCAAATTC 59.989 40.741 30.09 5.47 37.67 2.17
2052 2115 6.819146 GCTACTAGTAGAAGCCAGTTCAAATT 59.181 38.462 30.09 0.00 37.67 1.82
2122 2186 7.441890 TTCTTGTTTGTAGAGTTGTGTTTCA 57.558 32.000 0.00 0.00 0.00 2.69
2141 2205 8.781067 TTTGATTCGTCTGTTGTTATTTCTTG 57.219 30.769 0.00 0.00 0.00 3.02
2250 2315 5.591067 TCCAAACCTACACTTTTGATTCGTT 59.409 36.000 0.00 0.00 35.13 3.85
2296 2361 5.458595 AGAAAACAAAGGGGAGTTCTTCAT 58.541 37.500 0.00 0.00 0.00 2.57
2317 2382 2.703416 CTGCATTTGCTGTCCTGTAGA 58.297 47.619 3.94 0.00 42.66 2.59
2318 2383 1.131883 GCTGCATTTGCTGTCCTGTAG 59.868 52.381 10.52 0.00 42.66 2.74
2456 2521 4.760047 TCGCGGCTTCCCAGCTTC 62.760 66.667 6.13 0.00 46.44 3.86
2504 2569 2.438434 GGCTTGTGCACCGGCTAT 60.438 61.111 23.62 0.00 41.91 2.97
2641 2706 6.951062 ACCAAAAGAAGAAGAAGAAGAAGG 57.049 37.500 0.00 0.00 0.00 3.46
2642 2707 9.080915 CAAAACCAAAAGAAGAAGAAGAAGAAG 57.919 33.333 0.00 0.00 0.00 2.85
2643 2708 7.545615 GCAAAACCAAAAGAAGAAGAAGAAGAA 59.454 33.333 0.00 0.00 0.00 2.52
2644 2709 7.035612 GCAAAACCAAAAGAAGAAGAAGAAGA 58.964 34.615 0.00 0.00 0.00 2.87
2645 2710 6.256539 GGCAAAACCAAAAGAAGAAGAAGAAG 59.743 38.462 0.00 0.00 38.86 2.85
2646 2711 6.070824 AGGCAAAACCAAAAGAAGAAGAAGAA 60.071 34.615 0.00 0.00 43.14 2.52
2685 2750 2.031682 AGAAACTGTGAGCAAACATCGC 60.032 45.455 0.00 0.00 0.00 4.58
2769 2834 7.992033 AGGATTCTTAATCAGATTGAGGAACAG 59.008 37.037 13.57 0.00 39.71 3.16
2952 3017 4.199310 TGCCAATATTGCTCACCTAAGAC 58.801 43.478 10.11 0.00 0.00 3.01
3034 3099 1.596220 GGCGAACCTCAACGTCAAAAC 60.596 52.381 0.00 0.00 34.20 2.43
3057 3124 6.514947 TCAGCTTTGCAACAACATTAAATCT 58.485 32.000 0.00 0.00 0.00 2.40
3058 3125 6.768029 TCAGCTTTGCAACAACATTAAATC 57.232 33.333 0.00 0.00 0.00 2.17
3063 3130 4.325028 TCATCAGCTTTGCAACAACATT 57.675 36.364 0.00 0.00 0.00 2.71
3110 3177 8.635765 TTTTAGTAGAAGCAATCAAATGAGGT 57.364 30.769 0.00 0.00 0.00 3.85
3117 3188 5.185056 GGCCCTTTTTAGTAGAAGCAATCAA 59.815 40.000 0.00 0.00 0.00 2.57
3227 3298 3.260475 TCGTGACACATCTTATTGGGG 57.740 47.619 6.37 0.00 0.00 4.96
3232 3303 5.181056 TGTTGCAATTCGTGACACATCTTAT 59.819 36.000 0.59 0.00 0.00 1.73
3237 3308 3.550639 CCTTGTTGCAATTCGTGACACAT 60.551 43.478 0.59 0.00 0.00 3.21
3246 3317 4.708726 AGCATCTACCTTGTTGCAATTC 57.291 40.909 0.59 0.00 35.71 2.17
3261 3332 3.583383 GCGACCTGCAAAGCATCT 58.417 55.556 0.00 0.00 45.45 2.90
3271 3342 2.061773 CTGTTGTTGTAGAGCGACCTG 58.938 52.381 0.00 0.00 0.00 4.00
3272 3343 1.605712 GCTGTTGTTGTAGAGCGACCT 60.606 52.381 0.00 0.00 0.00 3.85
3331 3402 6.881602 AGATCTATGTTGGGAGTTTCTGTTTC 59.118 38.462 0.00 0.00 0.00 2.78
3424 3547 1.474077 CTACAACATTGCAGAAGCCCC 59.526 52.381 0.00 0.00 41.13 5.80
3459 3582 3.617540 TGTTTATGTTGCAAGGTGACG 57.382 42.857 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.