Multiple sequence alignment - TraesCS4D01G260800

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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 TraesCS4D01G260800 chr4D 100.000 3155 0 0 1 3155 431418565 431415411 0.000000e+00 5827.0
1 TraesCS4D01G260800 chr4B 92.751 2814 102 43 4 2751 529852656 529849879 0.000000e+00 3973.0
2 TraesCS4D01G260800 chr4B 84.659 352 35 4 2752 3084 529849834 529849483 1.810000e-87 333.0
3 TraesCS4D01G260800 chr4A 93.501 2631 82 42 185 2750 32678236 32675630 0.000000e+00 3829.0
4 TraesCS4D01G260800 chr4A 85.161 155 11 6 1 144 32678563 32678410 7.050000e-32 148.0
5 TraesCS4D01G260800 chr7D 100.000 42 0 0 3114 3155 374567245 374567286 9.380000e-11 78.7
6 TraesCS4D01G260800 chr6D 100.000 42 0 0 3114 3155 79863096 79863137 9.380000e-11 78.7
7 TraesCS4D01G260800 chr6A 100.000 42 0 0 3114 3155 54943488 54943529 9.380000e-11 78.7
8 TraesCS4D01G260800 chr5D 100.000 42 0 0 3114 3155 298961361 298961402 9.380000e-11 78.7
9 TraesCS4D01G260800 chr5D 100.000 42 0 0 3114 3155 310265949 310265990 9.380000e-11 78.7
10 TraesCS4D01G260800 chr5D 100.000 42 0 0 3114 3155 459862110 459862069 9.380000e-11 78.7
11 TraesCS4D01G260800 chr1D 100.000 42 0 0 3114 3155 86214604 86214563 9.380000e-11 78.7
12 TraesCS4D01G260800 chr1D 100.000 42 0 0 3114 3155 460551920 460551879 9.380000e-11 78.7
13 TraesCS4D01G260800 chr1D 100.000 42 0 0 3114 3155 463475786 463475745 9.380000e-11 78.7


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 TraesCS4D01G260800 chr4D 431415411 431418565 3154 True 5827.0 5827 100.000 1 3155 1 chr4D.!!$R1 3154
1 TraesCS4D01G260800 chr4B 529849483 529852656 3173 True 2153.0 3973 88.705 4 3084 2 chr4B.!!$R1 3080
2 TraesCS4D01G260800 chr4A 32675630 32678563 2933 True 1988.5 3829 89.331 1 2750 2 chr4A.!!$R1 2749

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
124 136 0.248621 CATCCGCCAGCCGAATTTTC 60.249 55.0 0.00 0.00 40.02 2.29 F
423 597 0.524414 GCAATCATCACACTGCTGCA 59.476 50.0 0.88 0.88 0.00 4.41 F
688 871 0.947960 CGATCTCCTCGCTTGCTAGA 59.052 55.0 0.00 0.00 41.14 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2319 0.319211 TTTGTAGCACGACGGTCCTG 60.319 55.000 1.91 2.63 0.00 3.86 R
2127 2334 1.477558 GGATGCCGGATGATCCTTTGT 60.478 52.381 5.05 0.00 36.04 2.83 R
2612 2852 2.292267 AGCAACAAGAGACAACACCTG 58.708 47.619 0.00 0.00 0.00 4.00 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
42 43 1.070821 TCTGCAAGCATTTCGTCGAG 58.929 50.000 0.00 0.00 0.00 4.04
59 70 1.931841 CGAGAAGTGGATGATGTGCAG 59.068 52.381 0.00 0.00 0.00 4.41
61 72 3.196463 GAGAAGTGGATGATGTGCAGAG 58.804 50.000 0.00 0.00 0.00 3.35
73 85 3.683365 TGTGCAGAGATGTTTAGCTGA 57.317 42.857 0.00 0.00 0.00 4.26
124 136 0.248621 CATCCGCCAGCCGAATTTTC 60.249 55.000 0.00 0.00 40.02 2.29
133 145 3.445096 CCAGCCGAATTTTCCAAGAGAAT 59.555 43.478 0.00 0.00 33.44 2.40
135 147 4.860907 CAGCCGAATTTTCCAAGAGAATTG 59.139 41.667 0.00 0.00 33.44 2.32
136 148 4.524328 AGCCGAATTTTCCAAGAGAATTGT 59.476 37.500 0.00 0.00 33.44 2.71
137 149 5.710099 AGCCGAATTTTCCAAGAGAATTGTA 59.290 36.000 0.00 0.00 33.44 2.41
138 150 6.030228 GCCGAATTTTCCAAGAGAATTGTAG 58.970 40.000 0.00 0.00 33.44 2.74
144 156 7.435068 TTTTCCAAGAGAATTGTAGCAGTAC 57.565 36.000 0.00 0.00 33.44 2.73
145 157 6.360370 TTCCAAGAGAATTGTAGCAGTACT 57.640 37.500 0.00 0.00 0.00 2.73
146 158 7.476540 TTCCAAGAGAATTGTAGCAGTACTA 57.523 36.000 0.00 0.00 0.00 1.82
147 159 7.661536 TCCAAGAGAATTGTAGCAGTACTAT 57.338 36.000 0.00 0.00 32.15 2.12
148 160 8.762481 TCCAAGAGAATTGTAGCAGTACTATA 57.238 34.615 0.00 0.00 32.15 1.31
226 384 2.034305 CCAGATAATGCAGCCAGAAAGC 59.966 50.000 0.00 0.00 0.00 3.51
323 486 3.276091 CGGTGGTGCGTTGCTTCA 61.276 61.111 0.00 0.00 0.00 3.02
365 528 2.584835 AACTAATCAGGGCAGCAACA 57.415 45.000 0.00 0.00 0.00 3.33
366 529 1.826385 ACTAATCAGGGCAGCAACAC 58.174 50.000 0.00 0.00 0.00 3.32
401 572 2.624364 TGCTCGTGTGTTTACTCCACTA 59.376 45.455 0.00 0.00 33.92 2.74
404 575 4.227538 CTCGTGTGTTTACTCCACTACTG 58.772 47.826 0.00 0.00 33.92 2.74
423 597 0.524414 GCAATCATCACACTGCTGCA 59.476 50.000 0.88 0.88 0.00 4.41
688 871 0.947960 CGATCTCCTCGCTTGCTAGA 59.052 55.000 0.00 0.00 41.14 2.43
700 883 0.980754 TTGCTAGATTGCTCCCCCGA 60.981 55.000 0.00 0.00 0.00 5.14
769 957 2.511145 CGCAGCTTCTCCCTCTGC 60.511 66.667 3.59 3.59 46.98 4.26
774 972 2.041928 CTTCTCCCTCTGCCCCCT 59.958 66.667 0.00 0.00 0.00 4.79
874 1072 3.054503 CTGCTTGCTGAGGCGCTT 61.055 61.111 7.64 0.00 42.25 4.68
882 1080 1.086634 GCTGAGGCGCTTCTCGATTT 61.087 55.000 20.92 0.00 41.67 2.17
889 1087 1.470979 GCGCTTCTCGATTTGGTCCTA 60.471 52.381 0.00 0.00 41.67 2.94
922 1120 2.366533 CACCTGATCTGCTGCTGATTT 58.633 47.619 20.70 3.11 0.00 2.17
1461 1659 2.103143 CTCCAGCGCTTCGACGAT 59.897 61.111 7.50 0.00 34.06 3.73
1481 1688 4.688419 GGACGACAACGACGCCGA 62.688 66.667 0.00 0.00 42.66 5.54
2058 2265 1.558756 CTGGAGGCCTTCATGAAGAGT 59.441 52.381 32.49 18.03 40.79 3.24
2112 2319 4.933064 CGAGACATCCGCCGAGCC 62.933 72.222 0.00 0.00 0.00 4.70
2127 2334 3.755628 GCCAGGACCGTCGTGCTA 61.756 66.667 14.51 0.00 38.87 3.49
2294 2504 7.757526 TGAACGGGTCAGTTTGATATAAATTG 58.242 34.615 0.00 0.00 34.00 2.32
2316 2526 4.809958 TGTTGTTTGGCTCATTGATTTGTG 59.190 37.500 0.00 0.00 0.00 3.33
2546 2786 5.365605 TCAGAGGTCCAAGTTTTCTGAAGTA 59.634 40.000 4.24 0.00 40.75 2.24
2725 2966 6.935741 AGATATCTATATCTCAGCGGTGTC 57.064 41.667 15.22 0.00 44.58 3.67
2727 2968 3.510531 TCTATATCTCAGCGGTGTCCT 57.489 47.619 15.22 2.84 0.00 3.85
2794 3079 9.619316 CGACATGTACTTTTTGGATATTTTTGA 57.381 29.630 0.00 0.00 0.00 2.69
2847 3132 4.000988 CGTACTTTGGAGCAATTGTACCT 58.999 43.478 18.54 4.59 33.98 3.08
2851 3136 2.507407 TGGAGCAATTGTACCTTCCC 57.493 50.000 18.54 7.05 0.00 3.97
2852 3137 1.992557 TGGAGCAATTGTACCTTCCCT 59.007 47.619 18.54 2.07 0.00 4.20
2867 3152 8.867097 TGTACCTTCCCTAGTATGTCAAATATC 58.133 37.037 0.00 0.00 0.00 1.63
2870 3155 9.315363 ACCTTCCCTAGTATGTCAAATATCTAG 57.685 37.037 0.00 0.00 0.00 2.43
2871 3156 8.254508 CCTTCCCTAGTATGTCAAATATCTAGC 58.745 40.741 0.00 0.00 0.00 3.42
2908 3193 7.008440 TCATGTTTCTTTAGCAGAATGATCG 57.992 36.000 0.00 0.00 41.42 3.69
2909 3194 5.801350 TGTTTCTTTAGCAGAATGATCGG 57.199 39.130 0.00 0.00 41.42 4.18
2993 3294 5.193663 TCTGCTATTTCCTCTCGAATCTG 57.806 43.478 0.00 0.00 0.00 2.90
2999 3300 4.891992 TTTCCTCTCGAATCTGGACTTT 57.108 40.909 0.00 0.00 0.00 2.66
3012 3313 7.928706 CGAATCTGGACTTTACTATCTGGATTT 59.071 37.037 0.00 0.00 0.00 2.17
3029 3330 6.591062 TCTGGATTTTATGTTCTTGCATTTGC 59.409 34.615 0.00 0.00 42.50 3.68
3046 3350 5.062558 GCATTTGCATGTGAACTGGTATTTC 59.937 40.000 0.00 0.00 41.59 2.17
3050 3354 5.255687 TGCATGTGAACTGGTATTTCTCAT 58.744 37.500 0.00 0.00 37.56 2.90
3057 3361 7.552687 TGTGAACTGGTATTTCTCATTGTATCC 59.447 37.037 0.00 0.00 0.00 2.59
3058 3362 7.770897 GTGAACTGGTATTTCTCATTGTATCCT 59.229 37.037 0.00 0.00 0.00 3.24
3060 3364 9.262358 GAACTGGTATTTCTCATTGTATCCTAC 57.738 37.037 0.00 0.00 0.00 3.18
3115 3419 8.751302 TTTTCTTCCGCTTAATATTTTTGGTC 57.249 30.769 0.00 0.00 0.00 4.02
3116 3420 6.445357 TCTTCCGCTTAATATTTTTGGTCC 57.555 37.500 0.00 0.00 0.00 4.46
3117 3421 5.358725 TCTTCCGCTTAATATTTTTGGTCCC 59.641 40.000 0.00 0.00 0.00 4.46
3118 3422 4.862371 TCCGCTTAATATTTTTGGTCCCT 58.138 39.130 0.00 0.00 0.00 4.20
3119 3423 4.885325 TCCGCTTAATATTTTTGGTCCCTC 59.115 41.667 0.00 0.00 0.00 4.30
3120 3424 4.261031 CCGCTTAATATTTTTGGTCCCTCG 60.261 45.833 0.00 0.00 0.00 4.63
3121 3425 4.607955 GCTTAATATTTTTGGTCCCTCGC 58.392 43.478 0.00 0.00 0.00 5.03
3122 3426 4.788521 GCTTAATATTTTTGGTCCCTCGCG 60.789 45.833 0.00 0.00 0.00 5.87
3123 3427 2.413310 ATATTTTTGGTCCCTCGCGT 57.587 45.000 5.77 0.00 0.00 6.01
3124 3428 1.729284 TATTTTTGGTCCCTCGCGTC 58.271 50.000 5.77 0.00 0.00 5.19
3125 3429 1.296056 ATTTTTGGTCCCTCGCGTCG 61.296 55.000 5.77 0.00 0.00 5.12
3146 3450 4.517934 CTAGGGCGACTCGGGGGA 62.518 72.222 0.00 0.00 0.00 4.81
3147 3451 4.517934 TAGGGCGACTCGGGGGAG 62.518 72.222 0.00 0.00 0.00 4.30
3151 3455 2.124403 GCGACTCGGGGGAGTCTA 60.124 66.667 18.78 0.00 46.85 2.59
3152 3456 2.188161 GCGACTCGGGGGAGTCTAG 61.188 68.421 18.78 8.23 46.85 2.43
3153 3457 1.526455 CGACTCGGGGGAGTCTAGG 60.526 68.421 18.78 3.69 46.85 3.02
3154 3458 1.152715 GACTCGGGGGAGTCTAGGG 60.153 68.421 15.12 0.00 45.88 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.257469 TCTCTGCACATCATCCACTTC 57.743 47.619 0.00 0.00 0.00 3.01
59 70 4.113354 CCGTTACCTCAGCTAAACATCTC 58.887 47.826 0.00 0.00 0.00 2.75
61 72 4.113354 CTCCGTTACCTCAGCTAAACATC 58.887 47.826 0.00 0.00 0.00 3.06
73 85 1.163554 GTCGTCACTCTCCGTTACCT 58.836 55.000 0.00 0.00 0.00 3.08
116 128 6.611381 TGCTACAATTCTCTTGGAAAATTCG 58.389 36.000 0.00 0.00 37.49 3.34
124 136 8.634444 AGTATAGTACTGCTACAATTCTCTTGG 58.366 37.037 5.39 0.00 37.69 3.61
226 384 1.243342 TTCCTTCACAGCATTGCCCG 61.243 55.000 4.70 0.00 0.00 6.13
323 486 0.678048 GTCTCGGGGAAGCAAGCAAT 60.678 55.000 0.00 0.00 0.00 3.56
401 572 1.810755 CAGCAGTGTGATGATTGCAGT 59.189 47.619 0.00 0.00 35.45 4.40
404 575 0.524414 TGCAGCAGTGTGATGATTGC 59.476 50.000 0.00 0.00 35.45 3.56
423 597 6.998673 TCTGAATCTGATCTGATGATGCAATT 59.001 34.615 15.04 0.00 32.19 2.32
688 871 2.998949 GAGGTTCGGGGGAGCAAT 59.001 61.111 0.00 0.00 0.00 3.56
700 883 1.228657 GCGGTCAAGAAAGCGAGGTT 61.229 55.000 0.00 0.00 42.48 3.50
769 957 4.918201 GCGGATTCGAGCAGGGGG 62.918 72.222 0.00 0.00 39.00 5.40
774 972 2.186903 GGGAAGCGGATTCGAGCA 59.813 61.111 0.00 0.00 38.95 4.26
874 1072 2.022195 CGTCCTAGGACCAAATCGAGA 58.978 52.381 31.78 0.00 41.76 4.04
882 1080 3.129502 CGACGCGTCCTAGGACCA 61.130 66.667 31.78 0.00 41.76 4.02
903 1101 2.239150 AGAAATCAGCAGCAGATCAGGT 59.761 45.455 0.00 0.00 0.00 4.00
922 1120 2.353406 GGACTTTGACCGGATTTCGAGA 60.353 50.000 9.46 0.00 42.43 4.04
936 1134 0.739813 GGATGGACGGACGGACTTTG 60.740 60.000 0.00 0.00 0.00 2.77
996 1194 2.993471 GCTGGTGTTCCCCATTGCG 61.993 63.158 0.00 0.00 33.00 4.85
1101 1299 4.908877 GCCGCCTCGTACGAGCTC 62.909 72.222 34.54 26.16 40.69 4.09
1218 1416 1.357334 GAGGGAGTCGAGCGACATC 59.643 63.158 22.96 16.42 46.76 3.06
1461 1659 2.050714 GCGTCGTTGTCGTCCTCA 60.051 61.111 0.00 0.00 38.33 3.86
2112 2319 0.319211 TTTGTAGCACGACGGTCCTG 60.319 55.000 1.91 2.63 0.00 3.86
2127 2334 1.477558 GGATGCCGGATGATCCTTTGT 60.478 52.381 5.05 0.00 36.04 2.83
2294 2504 4.318974 GCACAAATCAATGAGCCAAACAAC 60.319 41.667 0.00 0.00 31.72 3.32
2316 2526 2.365293 ACAAAAGGGGTCATGAAACAGC 59.635 45.455 0.00 0.00 0.00 4.40
2557 2797 7.255625 GCTTAGACAATGACCTTTTCCTCTTTT 60.256 37.037 0.00 0.00 0.00 2.27
2562 2802 5.248380 AGCTTAGACAATGACCTTTTCCT 57.752 39.130 0.00 0.00 0.00 3.36
2612 2852 2.292267 AGCAACAAGAGACAACACCTG 58.708 47.619 0.00 0.00 0.00 4.00
2682 2922 8.871629 ATATCTCGTACATTCTGTCTTCCTAT 57.128 34.615 0.00 0.00 0.00 2.57
2725 2966 2.432628 GTTCTGCCGGACACGAGG 60.433 66.667 5.05 0.00 44.60 4.63
2727 2968 2.338620 CAGTTCTGCCGGACACGA 59.661 61.111 5.05 0.00 44.60 4.35
2825 3110 4.000988 AGGTACAATTGCTCCAAAGTACG 58.999 43.478 17.79 0.00 38.54 3.67
2847 3132 8.958060 AGCTAGATATTTGACATACTAGGGAA 57.042 34.615 0.00 0.00 0.00 3.97
2897 3182 6.551385 AATTTACTGATCCGATCATTCTGC 57.449 37.500 11.53 0.00 38.85 4.26
2948 3233 9.469807 CAGATATTCCTTGTGCTAGTTAGTTAG 57.530 37.037 0.00 0.00 0.00 2.34
2950 3235 6.763610 GCAGATATTCCTTGTGCTAGTTAGTT 59.236 38.462 0.00 0.00 0.00 2.24
2951 3236 6.098982 AGCAGATATTCCTTGTGCTAGTTAGT 59.901 38.462 0.00 0.00 42.63 2.24
2952 3237 6.520272 AGCAGATATTCCTTGTGCTAGTTAG 58.480 40.000 0.00 0.00 42.63 2.34
2954 3239 5.365021 AGCAGATATTCCTTGTGCTAGTT 57.635 39.130 0.00 0.00 42.63 2.24
2955 3240 6.678568 ATAGCAGATATTCCTTGTGCTAGT 57.321 37.500 8.21 0.00 46.81 2.57
2956 3241 7.118971 GGAAATAGCAGATATTCCTTGTGCTAG 59.881 40.741 8.21 0.00 46.81 3.42
2958 3243 5.767168 GGAAATAGCAGATATTCCTTGTGCT 59.233 40.000 0.28 0.28 46.10 4.40
2999 3300 9.851686 ATGCAAGAACATAAAATCCAGATAGTA 57.148 29.630 0.00 0.00 0.00 1.82
3029 3330 7.149569 ACAATGAGAAATACCAGTTCACATG 57.850 36.000 0.00 0.00 36.71 3.21
3039 3340 9.614792 ACAAAGTAGGATACAATGAGAAATACC 57.385 33.333 0.00 0.00 46.26 2.73
3046 3350 7.921786 TGGAAACAAAGTAGGATACAATGAG 57.078 36.000 0.00 0.00 40.64 2.90
3089 3393 9.198837 GACCAAAAATATTAAGCGGAAGAAAAA 57.801 29.630 0.00 0.00 0.00 1.94
3090 3394 7.815549 GGACCAAAAATATTAAGCGGAAGAAAA 59.184 33.333 0.00 0.00 0.00 2.29
3091 3395 7.317390 GGACCAAAAATATTAAGCGGAAGAAA 58.683 34.615 0.00 0.00 0.00 2.52
3092 3396 6.127563 GGGACCAAAAATATTAAGCGGAAGAA 60.128 38.462 0.00 0.00 0.00 2.52
3093 3397 5.358725 GGGACCAAAAATATTAAGCGGAAGA 59.641 40.000 0.00 0.00 0.00 2.87
3094 3398 5.359860 AGGGACCAAAAATATTAAGCGGAAG 59.640 40.000 0.00 0.00 0.00 3.46
3095 3399 5.265989 AGGGACCAAAAATATTAAGCGGAA 58.734 37.500 0.00 0.00 0.00 4.30
3096 3400 4.862371 AGGGACCAAAAATATTAAGCGGA 58.138 39.130 0.00 0.00 0.00 5.54
3097 3401 4.261031 CGAGGGACCAAAAATATTAAGCGG 60.261 45.833 0.00 0.00 0.00 5.52
3098 3402 4.788521 GCGAGGGACCAAAAATATTAAGCG 60.789 45.833 0.00 0.00 0.00 4.68
3099 3403 4.607955 GCGAGGGACCAAAAATATTAAGC 58.392 43.478 0.00 0.00 0.00 3.09
3100 3404 4.334481 ACGCGAGGGACCAAAAATATTAAG 59.666 41.667 15.93 0.00 0.00 1.85
3101 3405 4.263435 ACGCGAGGGACCAAAAATATTAA 58.737 39.130 15.93 0.00 0.00 1.40
3102 3406 3.872771 GACGCGAGGGACCAAAAATATTA 59.127 43.478 15.93 0.00 0.00 0.98
3103 3407 2.681344 GACGCGAGGGACCAAAAATATT 59.319 45.455 15.93 0.00 0.00 1.28
3104 3408 2.285977 GACGCGAGGGACCAAAAATAT 58.714 47.619 15.93 0.00 0.00 1.28
3105 3409 1.729284 GACGCGAGGGACCAAAAATA 58.271 50.000 15.93 0.00 0.00 1.40
3106 3410 1.296056 CGACGCGAGGGACCAAAAAT 61.296 55.000 15.93 0.00 0.00 1.82
3107 3411 1.957186 CGACGCGAGGGACCAAAAA 60.957 57.895 15.93 0.00 0.00 1.94
3108 3412 2.356553 CGACGCGAGGGACCAAAA 60.357 61.111 15.93 0.00 0.00 2.44
3129 3433 4.517934 TCCCCCGAGTCGCCCTAG 62.518 72.222 7.12 0.00 0.00 3.02
3130 3434 4.517934 CTCCCCCGAGTCGCCCTA 62.518 72.222 7.12 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.