Multiple sequence alignment - TraesCS2A01G395700

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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 TraesCS2A01G395700 chr2A 100.000 3632 0 0 1 3632 649486499 649482868 0.000000e+00 6708.0
1 TraesCS2A01G395700 chr2A 93.340 946 47 8 2562 3507 649478341 649477412 0.000000e+00 1384.0
2 TraesCS2A01G395700 chr2A 96.479 142 4 1 3491 3632 649477400 649477260 2.180000e-57 233.0
3 TraesCS2A01G395700 chr2A 86.096 187 23 1 3166 3352 745090584 745090401 7.950000e-47 198.0
4 TraesCS2A01G395700 chr2D 92.576 3098 110 50 5 3033 503438905 503435859 0.000000e+00 4337.0
5 TraesCS2A01G395700 chr2D 95.161 62 2 1 3391 3452 503435869 503435809 2.990000e-16 97.1
6 TraesCS2A01G395700 chr2B 93.129 2969 95 36 105 3033 591914872 591911973 0.000000e+00 4252.0
7 TraesCS2A01G395700 chr2B 87.281 228 27 2 3405 3632 591895151 591894926 3.600000e-65 259.0
8 TraesCS2A01G395700 chr2B 92.308 104 6 1 7 108 591915002 591914899 2.920000e-31 147.0
9 TraesCS2A01G395700 chr6B 85.406 1206 153 19 934 2133 479397431 479396243 0.000000e+00 1230.0
10 TraesCS2A01G395700 chr6B 88.272 162 14 2 3165 3326 436494902 436494746 4.790000e-44 189.0
11 TraesCS2A01G395700 chr6A 85.055 1191 154 15 946 2130 480805372 480806544 0.000000e+00 1192.0
12 TraesCS2A01G395700 chr6A 87.879 198 19 4 3164 3361 264774888 264774696 1.010000e-55 228.0
13 TraesCS2A01G395700 chr6D 84.971 1191 155 15 946 2130 341078253 341079425 0.000000e+00 1186.0
14 TraesCS2A01G395700 chr6D 89.005 191 16 3 3165 3355 274304553 274304368 7.840000e-57 231.0
15 TraesCS2A01G395700 chr1A 79.487 1170 199 31 964 2123 333499873 333498735 0.000000e+00 793.0
16 TraesCS2A01G395700 chr1D 79.316 1170 201 31 964 2123 269514801 269515939 0.000000e+00 782.0
17 TraesCS2A01G395700 chr4D 80.378 1004 160 30 1159 2145 497698157 497697174 0.000000e+00 728.0
18 TraesCS2A01G395700 chr4B 80.279 1004 161 31 1159 2145 639010509 639011492 0.000000e+00 723.0
19 TraesCS2A01G395700 chr4B 85.644 202 25 3 3152 3353 626391369 626391566 3.670000e-50 209.0
20 TraesCS2A01G395700 chr3D 89.071 183 17 2 3173 3355 16131706 16131527 1.310000e-54 224.0
21 TraesCS2A01G395700 chr3D 85.417 144 16 4 3026 3166 564006485 564006344 1.050000e-30 145.0
22 TraesCS2A01G395700 chr5D 90.798 163 12 3 3199 3360 551178325 551178165 7.900000e-52 215.0
23 TraesCS2A01G395700 chr5D 88.060 134 10 4 3037 3166 462454800 462454669 1.750000e-33 154.0
24 TraesCS2A01G395700 chr5D 85.496 131 18 1 3036 3166 246301832 246301961 6.330000e-28 135.0
25 TraesCS2A01G395700 chr3B 84.896 192 25 3 3161 3352 149471886 149472073 1.330000e-44 191.0
26 TraesCS2A01G395700 chr3A 75.271 461 82 22 1119 1572 598410860 598410425 1.330000e-44 191.0
27 TraesCS2A01G395700 chr4A 84.536 194 25 4 3163 3355 58873805 58873616 1.720000e-43 187.0
28 TraesCS2A01G395700 chr1B 88.618 123 11 3 3045 3165 577610461 577610340 2.920000e-31 147.0
29 TraesCS2A01G395700 chr5B 87.500 128 11 3 3041 3166 581220863 581220987 3.780000e-30 143.0
30 TraesCS2A01G395700 chr5B 86.719 128 14 2 3041 3166 616904560 616904686 4.890000e-29 139.0
31 TraesCS2A01G395700 chr7D 86.131 137 11 5 3036 3166 64007305 64007171 1.360000e-29 141.0
32 TraesCS2A01G395700 chr5A 85.821 134 14 4 3036 3166 362159280 362159411 1.760000e-28 137.0
33 TraesCS2A01G395700 chr7B 76.793 237 48 5 1122 1356 723395454 723395685 3.810000e-25 126.0


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 TraesCS2A01G395700 chr2A 649482868 649486499 3631 True 6708.00 6708 100.0000 1 3632 1 chr2A.!!$R1 3631
1 TraesCS2A01G395700 chr2A 649477260 649478341 1081 True 808.50 1384 94.9095 2562 3632 2 chr2A.!!$R3 1070
2 TraesCS2A01G395700 chr2D 503435809 503438905 3096 True 2217.05 4337 93.8685 5 3452 2 chr2D.!!$R1 3447
3 TraesCS2A01G395700 chr2B 591911973 591915002 3029 True 2199.50 4252 92.7185 7 3033 2 chr2B.!!$R2 3026
4 TraesCS2A01G395700 chr6B 479396243 479397431 1188 True 1230.00 1230 85.4060 934 2133 1 chr6B.!!$R2 1199
5 TraesCS2A01G395700 chr6A 480805372 480806544 1172 False 1192.00 1192 85.0550 946 2130 1 chr6A.!!$F1 1184
6 TraesCS2A01G395700 chr6D 341078253 341079425 1172 False 1186.00 1186 84.9710 946 2130 1 chr6D.!!$F1 1184
7 TraesCS2A01G395700 chr1A 333498735 333499873 1138 True 793.00 793 79.4870 964 2123 1 chr1A.!!$R1 1159
8 TraesCS2A01G395700 chr1D 269514801 269515939 1138 False 782.00 782 79.3160 964 2123 1 chr1D.!!$F1 1159
9 TraesCS2A01G395700 chr4D 497697174 497698157 983 True 728.00 728 80.3780 1159 2145 1 chr4D.!!$R1 986
10 TraesCS2A01G395700 chr4B 639010509 639011492 983 False 723.00 723 80.2790 1159 2145 1 chr4B.!!$F2 986

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
223 266 0.165944 CCTTTTAGCACAGCGAACCG 59.834 55.000 0.0 0.0 0.00 4.44 F
303 346 1.703438 CGATGCAGTGCAGAGGAAGC 61.703 60.000 24.2 0.0 43.65 3.86 F
2284 2367 1.546476 AGGTGGAGCGTGTAGAAGAAG 59.454 52.381 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2367 3.155167 CCCCTCACCGCCCTCTAC 61.155 72.222 0.00 0.0 0.00 2.59 R
2422 2511 0.034670 AGGAAGAGGCATTGTGAGGC 60.035 55.000 0.00 0.0 0.00 4.70 R
3498 3611 1.183030 AATGTCGGTCAGTCGGGACA 61.183 55.000 1.17 0.0 39.59 4.02 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
95 98 4.248859 CCCAATTTCACACACAAACACAA 58.751 39.130 0.00 0.00 0.00 3.33
104 107 2.124693 ACAAACACAAGCCCCCACG 61.125 57.895 0.00 0.00 0.00 4.94
168 201 1.484240 CCACCAAAGGCTGAAACCAAA 59.516 47.619 0.00 0.00 0.00 3.28
169 202 2.483538 CCACCAAAGGCTGAAACCAAAG 60.484 50.000 0.00 0.00 0.00 2.77
170 203 1.138859 ACCAAAGGCTGAAACCAAAGC 59.861 47.619 0.00 0.00 38.76 3.51
173 206 3.534554 CAAAGGCTGAAACCAAAGCTTT 58.465 40.909 5.69 5.69 40.08 3.51
223 266 0.165944 CCTTTTAGCACAGCGAACCG 59.834 55.000 0.00 0.00 0.00 4.44
226 269 2.997952 TTTAGCACAGCGAACCGGCA 62.998 55.000 0.00 0.00 34.64 5.69
303 346 1.703438 CGATGCAGTGCAGAGGAAGC 61.703 60.000 24.20 0.00 43.65 3.86
448 498 6.014242 TCCAGCAAGAATACAAGAAGAGAGAA 60.014 38.462 0.00 0.00 0.00 2.87
489 539 4.765856 GTCCTACAGTGTTCTCCTAACAGA 59.234 45.833 0.00 0.00 0.00 3.41
490 540 5.010933 TCCTACAGTGTTCTCCTAACAGAG 58.989 45.833 0.00 0.00 35.04 3.35
584 634 2.616458 CCCCTCCTTCCCCACCTTG 61.616 68.421 0.00 0.00 0.00 3.61
724 775 8.028938 ACACACATCAGCAATCCTTTATTAAAC 58.971 33.333 0.00 0.00 0.00 2.01
728 779 8.395633 ACATCAGCAATCCTTTATTAAACGTAC 58.604 33.333 0.00 0.00 0.00 3.67
729 780 6.996106 TCAGCAATCCTTTATTAAACGTACG 58.004 36.000 15.01 15.01 0.00 3.67
732 783 8.545420 CAGCAATCCTTTATTAAACGTACGTAT 58.455 33.333 23.12 14.16 0.00 3.06
733 784 8.545420 AGCAATCCTTTATTAAACGTACGTATG 58.455 33.333 23.12 13.27 0.00 2.39
777 835 5.996513 TCAACCAAACCTAGTACGCAATTAA 59.003 36.000 0.00 0.00 0.00 1.40
806 870 2.108168 ACGCTTCTCCTACCATTGCTA 58.892 47.619 0.00 0.00 0.00 3.49
856 920 9.838339 CATTCCTATCTTTGGACTGTATAGTTT 57.162 33.333 0.00 0.00 37.25 2.66
2284 2367 1.546476 AGGTGGAGCGTGTAGAAGAAG 59.454 52.381 0.00 0.00 0.00 2.85
2480 2569 1.298413 CTGACCGCGACTGGTATCG 60.298 63.158 8.23 0.00 44.01 2.92
2525 2615 6.659242 GTGAGATTTGGGAAGGAGATTTACAA 59.341 38.462 0.00 0.00 0.00 2.41
2529 2619 3.265489 TGGGAAGGAGATTTACAAGGGT 58.735 45.455 0.00 0.00 0.00 4.34
2679 2780 3.666253 GGGTTTTCGGGTGCGGTG 61.666 66.667 0.00 0.00 0.00 4.94
2680 2781 3.666253 GGTTTTCGGGTGCGGTGG 61.666 66.667 0.00 0.00 0.00 4.61
2681 2782 3.666253 GTTTTCGGGTGCGGTGGG 61.666 66.667 0.00 0.00 0.00 4.61
2682 2783 4.958897 TTTTCGGGTGCGGTGGGG 62.959 66.667 0.00 0.00 0.00 4.96
2773 2881 1.553248 TGTCCCGTCCCTATTCAAGTG 59.447 52.381 0.00 0.00 0.00 3.16
2798 2906 8.572185 TGCACATTTATTTTTCAACTACTGCTA 58.428 29.630 0.00 0.00 0.00 3.49
2927 3040 5.223449 TCTCTTTTACAGAAACGTGGGAT 57.777 39.130 0.00 0.00 0.00 3.85
2938 3051 4.455877 AGAAACGTGGGATGTTCTTCAATC 59.544 41.667 0.00 0.00 0.00 2.67
2981 3094 5.465390 CGCCGGAATAGTTGATTAGATTTCA 59.535 40.000 5.05 0.00 0.00 2.69
2988 3101 3.950395 AGTTGATTAGATTTCAGGCTGGC 59.050 43.478 15.73 2.14 0.00 4.85
3033 3146 0.811281 GATGCCCCGGCTATATTTGC 59.189 55.000 7.35 0.00 42.51 3.68
3043 3156 3.007635 GGCTATATTTGCGGGGTATGAC 58.992 50.000 0.00 0.00 0.00 3.06
3044 3157 3.307480 GGCTATATTTGCGGGGTATGACT 60.307 47.826 0.00 0.00 0.00 3.41
3053 3166 2.231529 CGGGGTATGACTAGGTCTCAG 58.768 57.143 0.00 0.00 33.15 3.35
3059 3172 3.637911 ATGACTAGGTCTCAGTCGACT 57.362 47.619 13.58 13.58 44.44 4.18
3088 3201 9.220767 GATTTAACCAAGTCTCAGTCAAGTAAT 57.779 33.333 0.00 0.00 0.00 1.89
3093 3206 9.654663 AACCAAGTCTCAGTCAAGTAATATAAC 57.345 33.333 0.00 0.00 0.00 1.89
3100 3213 9.317936 TCTCAGTCAAGTAATATAACATGCAAG 57.682 33.333 0.00 0.00 0.00 4.01
3101 3214 9.317936 CTCAGTCAAGTAATATAACATGCAAGA 57.682 33.333 0.00 0.00 0.00 3.02
3171 3284 5.833406 AGATCTCACGGATATAGAGCATG 57.167 43.478 0.00 0.00 34.33 4.06
3280 3393 8.385898 CAAGACAACTTGGTAACCAATTAGTA 57.614 34.615 0.00 0.00 46.67 1.82
3282 3395 9.582648 AAGACAACTTGGTAACCAATTAGTAAT 57.417 29.630 0.00 0.00 43.07 1.89
3356 3469 5.232838 GCACAAAACCAATTATGCTCATAGC 59.767 40.000 0.00 0.00 42.82 2.97
3373 3486 8.097078 GCTCATAGCATTGATTGAGACTTAAT 57.903 34.615 14.23 0.00 41.89 1.40
3471 3584 1.508808 GGACGCAAAAACGCTACCCA 61.509 55.000 0.00 0.00 36.19 4.51
3474 3587 1.068816 ACGCAAAAACGCTACCCAATC 60.069 47.619 0.00 0.00 36.19 2.67
3498 3611 1.608590 CTCCGCACAACCAACTCAAAT 59.391 47.619 0.00 0.00 0.00 2.32
3531 3672 5.006896 ACCGACATTCCCTATATCCTACA 57.993 43.478 0.00 0.00 0.00 2.74
3615 3756 3.548818 GCTTGCGTCAATTCACCCATATC 60.549 47.826 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.528127 TGTCGGGCAAGAGGGGAA 60.528 61.111 0.00 0.00 0.00 3.97
1 2 3.319198 GTGTCGGGCAAGAGGGGA 61.319 66.667 0.00 0.00 0.00 4.81
2 3 4.760047 CGTGTCGGGCAAGAGGGG 62.760 72.222 0.00 0.00 0.00 4.79
77 80 3.520569 GGCTTGTGTTTGTGTGTGAAAT 58.479 40.909 0.00 0.00 0.00 2.17
163 196 1.063266 TGGACTTGGGAAAGCTTTGGT 60.063 47.619 18.30 7.19 0.00 3.67
168 201 2.529632 GGATTTGGACTTGGGAAAGCT 58.470 47.619 0.00 0.00 0.00 3.74
169 202 1.550524 GGGATTTGGACTTGGGAAAGC 59.449 52.381 0.00 0.00 0.00 3.51
170 203 2.827921 CTGGGATTTGGACTTGGGAAAG 59.172 50.000 0.00 0.00 0.00 2.62
173 206 1.455822 ACTGGGATTTGGACTTGGGA 58.544 50.000 0.00 0.00 0.00 4.37
290 333 3.710722 CCGGGCTTCCTCTGCACT 61.711 66.667 0.00 0.00 0.00 4.40
294 337 3.567579 TTTGGCCGGGCTTCCTCTG 62.568 63.158 29.87 0.00 0.00 3.35
295 338 3.256960 TTTGGCCGGGCTTCCTCT 61.257 61.111 29.87 0.00 0.00 3.69
303 346 3.127533 CTCGAAGCTTTGGCCGGG 61.128 66.667 13.87 2.12 39.73 5.73
344 391 4.389576 GTGCTTTGCGCCTCACGG 62.390 66.667 4.18 0.00 43.93 4.94
361 408 0.379669 CGTACCTACTACCGTGCTGG 59.620 60.000 0.00 0.00 46.41 4.85
454 504 9.128404 AGAACACTGTAGGACGATACAATATTA 57.872 33.333 0.00 0.00 35.32 0.98
462 512 4.232188 AGGAGAACACTGTAGGACGATA 57.768 45.455 0.00 0.00 0.00 2.92
647 697 4.091424 GCGAGTTTGTTTACTGATGATGC 58.909 43.478 0.00 0.00 0.00 3.91
648 698 4.154015 TGGCGAGTTTGTTTACTGATGATG 59.846 41.667 0.00 0.00 0.00 3.07
649 699 4.323417 TGGCGAGTTTGTTTACTGATGAT 58.677 39.130 0.00 0.00 0.00 2.45
650 700 3.734463 TGGCGAGTTTGTTTACTGATGA 58.266 40.909 0.00 0.00 0.00 2.92
691 741 2.049888 TGCTGATGTGTGTGGAAACA 57.950 45.000 0.00 0.00 38.70 2.83
692 742 3.568538 GATTGCTGATGTGTGTGGAAAC 58.431 45.455 0.00 0.00 0.00 2.78
693 743 2.557924 GGATTGCTGATGTGTGTGGAAA 59.442 45.455 0.00 0.00 0.00 3.13
724 775 3.040795 AGCGAATGTTAGCATACGTACG 58.959 45.455 15.01 15.01 34.39 3.67
728 779 2.472861 CCTGAGCGAATGTTAGCATACG 59.527 50.000 0.00 0.00 34.39 3.06
729 780 3.458189 ACCTGAGCGAATGTTAGCATAC 58.542 45.455 0.00 0.00 34.39 2.39
732 783 2.496070 ACTACCTGAGCGAATGTTAGCA 59.504 45.455 0.91 0.00 35.48 3.49
733 784 3.117046 GACTACCTGAGCGAATGTTAGC 58.883 50.000 0.00 0.00 0.00 3.09
777 835 1.853963 AGGAGAAGCGTATCCACTGT 58.146 50.000 15.79 0.00 37.63 3.55
834 898 9.751542 CACTAAACTATACAGTCCAAAGATAGG 57.248 37.037 0.00 0.00 32.29 2.57
864 928 9.581099 CCCAATTGCTAATTAAAAACGAGTATT 57.419 29.630 0.00 0.00 0.00 1.89
871 936 7.389803 AATGGCCCAATTGCTAATTAAAAAC 57.610 32.000 0.00 0.00 0.00 2.43
2284 2367 3.155167 CCCCTCACCGCCCTCTAC 61.155 72.222 0.00 0.00 0.00 2.59
2422 2511 0.034670 AGGAAGAGGCATTGTGAGGC 60.035 55.000 0.00 0.00 0.00 4.70
2449 2538 4.910585 GTCAGCATACCCCGCCCG 62.911 72.222 0.00 0.00 0.00 6.13
2450 2539 4.564110 GGTCAGCATACCCCGCCC 62.564 72.222 0.00 0.00 33.02 6.13
2451 2540 4.910585 CGGTCAGCATACCCCGCC 62.911 72.222 2.19 0.00 36.03 6.13
2469 2558 1.734137 CACTCCCCGATACCAGTCG 59.266 63.158 0.00 0.00 41.13 4.18
2470 2559 1.400530 CCCACTCCCCGATACCAGTC 61.401 65.000 0.00 0.00 0.00 3.51
2480 2569 4.048470 GCCAGAACCCCACTCCCC 62.048 72.222 0.00 0.00 0.00 4.81
2644 2745 0.035056 CCCACTCAATCCCAGTCCAC 60.035 60.000 0.00 0.00 0.00 4.02
2773 2881 7.873739 AGCAGTAGTTGAAAAATAAATGTGC 57.126 32.000 0.00 0.00 0.00 4.57
2938 3051 1.267532 CGGACCGAAATCTGCAAATCG 60.268 52.381 8.64 0.00 35.19 3.34
2981 3094 1.077212 ATCTGCAAATCGCCAGCCT 60.077 52.632 0.00 0.00 41.33 4.58
2988 3101 1.590932 CCTCCCTGATCTGCAAATCG 58.409 55.000 0.00 0.00 0.00 3.34
3019 3132 1.674322 CCCCGCAAATATAGCCGGG 60.674 63.158 16.05 16.05 42.58 5.73
3033 3146 2.231529 CTGAGACCTAGTCATACCCCG 58.768 57.143 0.00 0.00 34.60 5.73
3053 3166 5.471257 AGACTTGGTTAAATCTCAGTCGAC 58.529 41.667 7.70 7.70 0.00 4.20
3059 3172 6.419484 TGACTGAGACTTGGTTAAATCTCA 57.581 37.500 3.03 3.03 44.05 3.27
3093 3206 9.938670 TTTCATTTTTCATTTTTCTCTTGCATG 57.061 25.926 0.00 0.00 0.00 4.06
3146 3259 7.777440 TCATGCTCTATATCCGTGAGATCTTAT 59.223 37.037 0.00 0.00 36.33 1.73
3157 3270 5.702670 ACAAACCAATCATGCTCTATATCCG 59.297 40.000 0.00 0.00 0.00 4.18
3171 3284 6.818142 AGCCAAATATTAGCAACAAACCAATC 59.182 34.615 11.71 0.00 0.00 2.67
3289 3402 5.163530 TGTTTAGCATTGTGCCAGATATTGG 60.164 40.000 0.00 0.94 46.52 3.16
3383 3496 9.539825 CTCTAACACAAATATCAGTCTTGCTAT 57.460 33.333 0.00 0.00 0.00 2.97
3498 3611 1.183030 AATGTCGGTCAGTCGGGACA 61.183 55.000 1.17 0.00 39.59 4.02
3531 3672 7.416890 GCATCTCTATGTTCGCCCTAGTTATAT 60.417 40.741 0.00 0.00 35.38 0.86
3596 3737 2.571212 GGATATGGGTGAATTGACGCA 58.429 47.619 16.53 16.53 42.34 5.24


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

AutoCloner maintained by Alex Coulton.