Multiple sequence alignment - TraesCS3A01G170700

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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 TraesCS3A01G170700 chr3A 100.000 2811 0 0 770 3580 178987753 178984943 0.000000e+00 5192
1 TraesCS3A01G170700 chr3A 100.000 356 0 0 1 356 178988522 178988167 0.000000e+00 658
2 TraesCS3A01G170700 chr3D 94.367 2219 83 14 770 2970 151901275 151903469 0.000000e+00 3367
3 TraesCS3A01G170700 chr3D 96.594 323 10 1 3259 3580 151904072 151904394 5.260000e-148 534
4 TraesCS3A01G170700 chr3D 93.258 267 11 2 2993 3259 151903449 151903708 1.560000e-103 387
5 TraesCS3A01G170700 chr3D 94.512 164 3 2 1 163 151900498 151900656 7.680000e-62 248
6 TraesCS3A01G170700 chr3D 99.219 128 1 0 219 346 151901144 151901271 7.730000e-57 231
7 TraesCS3A01G170700 chr3B 94.060 2239 72 22 770 2970 222317979 222320194 0.000000e+00 3341
8 TraesCS3A01G170700 chr3B 94.407 590 16 6 2993 3580 222320174 222320748 0.000000e+00 891
9 TraesCS3A01G170700 chr3B 98.315 356 5 1 1 356 222317615 222317969 1.090000e-174 623
10 TraesCS3A01G170700 chr4D 90.050 402 40 0 1234 1635 433393653 433393252 4.100000e-144 521
11 TraesCS3A01G170700 chr4B 90.050 402 40 0 1234 1635 531580985 531580584 4.100000e-144 521
12 TraesCS3A01G170700 chr5D 89.826 403 41 0 1233 1635 442331797 442332199 5.300000e-143 518
13 TraesCS3A01G170700 chr5B 89.826 403 41 0 1233 1635 538542404 538542806 5.300000e-143 518
14 TraesCS3A01G170700 chr4A 89.681 407 41 1 1229 1635 34787862 34787457 5.300000e-143 518
15 TraesCS3A01G170700 chr5A 88.834 403 45 0 1233 1635 558543702 558544104 2.480000e-136 496
16 TraesCS3A01G170700 chr2B 88.177 406 45 3 1233 1635 605381366 605380961 6.950000e-132 481


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 TraesCS3A01G170700 chr3A 178984943 178988522 3579 True 2925.000000 5192 100.000 1 3580 2 chr3A.!!$R1 3579
1 TraesCS3A01G170700 chr3D 151900498 151904394 3896 False 953.400000 3367 95.590 1 3580 5 chr3D.!!$F1 3579
2 TraesCS3A01G170700 chr3B 222317615 222320748 3133 False 1618.333333 3341 95.594 1 3580 3 chr3B.!!$F1 3579

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
801 1235 0.175989 CTAACCCAGTTCCGCTCTCC 59.824 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2636 3094 0.179032 TACATGGCCGCGGATGAATT 60.179 50.0 33.48 11.3 0.0 2.17 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
195 197 1.529244 CGCCCTTTGATGATCCCCC 60.529 63.158 0.00 0.00 0.00 5.40
283 717 3.490933 GCACTCCTTTTCAACTTTCACCC 60.491 47.826 0.00 0.00 0.00 4.61
795 1229 1.402456 CGTCTCACTAACCCAGTTCCG 60.402 57.143 0.00 0.00 34.26 4.30
801 1235 0.175989 CTAACCCAGTTCCGCTCTCC 59.824 60.000 0.00 0.00 0.00 3.71
802 1236 1.262640 TAACCCAGTTCCGCTCTCCC 61.263 60.000 0.00 0.00 0.00 4.30
819 1253 5.105567 TCTCCCGCTCTCTCCTATATTAG 57.894 47.826 0.00 0.00 0.00 1.73
933 1370 5.163854 CCAAATCAAGACTAGTTAAGCACCG 60.164 44.000 0.00 0.00 0.00 4.94
953 1390 0.782384 GCAGTACGTCGACCAACAAG 59.218 55.000 10.58 6.52 0.00 3.16
1328 1776 4.660938 GGCAAGGGGTTCCAGCGT 62.661 66.667 0.00 0.00 37.26 5.07
1971 2422 0.692476 CCACCACATTGGAGGTCTCA 59.308 55.000 0.00 0.00 42.45 3.27
1988 2439 4.388499 ATGTCGTCCGGTGGTGGC 62.388 66.667 0.00 0.00 0.00 5.01
2379 2836 0.667487 CGACAGAGCTCTTTTCGGCA 60.667 55.000 26.68 0.00 0.00 5.69
2396 2853 4.025858 ACGAGCCAGCACCAGCAT 62.026 61.111 0.00 0.00 45.49 3.79
2471 2928 1.081906 GTACGACGTGTTCTCGGCA 60.082 57.895 11.56 0.00 38.97 5.69
2495 2952 4.473520 CACGCCGGCCTCAAGGAT 62.474 66.667 23.46 0.00 37.39 3.24
2526 2983 0.978667 GGAGGAGACCAGGGACTTCC 60.979 65.000 0.00 0.00 34.60 3.46
2564 3021 1.793532 GCACTCTGCTCATCATCGATG 59.206 52.381 19.61 19.61 40.96 3.84
2586 3043 4.709397 TGCATGGGTGGATTTAGTTTAAGG 59.291 41.667 0.00 0.00 0.00 2.69
2587 3044 4.709886 GCATGGGTGGATTTAGTTTAAGGT 59.290 41.667 0.00 0.00 0.00 3.50
2588 3045 5.394115 GCATGGGTGGATTTAGTTTAAGGTG 60.394 44.000 0.00 0.00 0.00 4.00
2590 3047 3.446161 GGGTGGATTTAGTTTAAGGTGGC 59.554 47.826 0.00 0.00 0.00 5.01
2591 3048 4.083565 GGTGGATTTAGTTTAAGGTGGCA 58.916 43.478 0.00 0.00 0.00 4.92
2592 3049 4.709886 GGTGGATTTAGTTTAAGGTGGCAT 59.290 41.667 0.00 0.00 0.00 4.40
2593 3050 5.889289 GGTGGATTTAGTTTAAGGTGGCATA 59.111 40.000 0.00 0.00 0.00 3.14
2616 3074 5.811399 CATGTTAATCATGTAACCGTGGT 57.189 39.130 4.32 0.00 46.18 4.16
2636 3094 5.124457 GTGGTGATACGAGGAGTAGTGTTTA 59.876 44.000 0.00 0.00 38.94 2.01
2639 3097 7.093640 TGGTGATACGAGGAGTAGTGTTTAATT 60.094 37.037 0.00 0.00 38.94 1.40
2660 3121 3.876198 CCGCGGCCATGTAAGCAC 61.876 66.667 14.67 0.00 0.00 4.40
2708 3173 5.176774 GCAACTTTACAAAATACCACAAGGC 59.823 40.000 0.00 0.00 39.06 4.35
2709 3174 6.276847 CAACTTTACAAAATACCACAAGGCA 58.723 36.000 0.00 0.00 39.06 4.75
2710 3175 6.664428 ACTTTACAAAATACCACAAGGCAT 57.336 33.333 0.00 0.00 39.06 4.40
2777 3242 5.059161 GTCTTAGCCAGCACATCATTCATA 58.941 41.667 0.00 0.00 0.00 2.15
2804 3269 8.967664 TTTTGTTACTTACAGTACTTGATGGT 57.032 30.769 0.00 0.00 38.19 3.55
2807 3272 9.865321 TTGTTACTTACAGTACTTGATGGTATC 57.135 33.333 0.00 0.00 38.19 2.24
2808 3273 9.251440 TGTTACTTACAGTACTTGATGGTATCT 57.749 33.333 0.00 0.00 28.93 1.98
2809 3274 9.517609 GTTACTTACAGTACTTGATGGTATCTG 57.482 37.037 0.00 0.00 28.93 2.90
2810 3275 7.719871 ACTTACAGTACTTGATGGTATCTGT 57.280 36.000 0.00 0.00 37.56 3.41
2811 3276 7.773149 ACTTACAGTACTTGATGGTATCTGTC 58.227 38.462 0.00 0.00 36.49 3.51
2812 3277 7.616150 ACTTACAGTACTTGATGGTATCTGTCT 59.384 37.037 0.00 0.00 36.49 3.41
2827 3292 6.926272 GGTATCTGTCTATCTGAACCATTCAC 59.074 42.308 0.00 0.00 35.46 3.18
2882 3347 7.795047 TCATATGGAGAAGAACTGAAGCAATA 58.205 34.615 2.13 0.00 0.00 1.90
2883 3348 8.435187 TCATATGGAGAAGAACTGAAGCAATAT 58.565 33.333 2.13 0.00 0.00 1.28
2884 3349 9.716531 CATATGGAGAAGAACTGAAGCAATATA 57.283 33.333 0.00 0.00 0.00 0.86
2896 3361 4.021807 TGAAGCAATATATGGCTGCAATGG 60.022 41.667 19.18 0.00 42.62 3.16
2917 3383 3.181476 GGCAGGCAAGTTGAAGAGAAAAA 60.181 43.478 7.16 0.00 0.00 1.94
2920 3386 3.638627 AGGCAAGTTGAAGAGAAAAAGGG 59.361 43.478 7.16 0.00 0.00 3.95
2921 3387 3.384789 GGCAAGTTGAAGAGAAAAAGGGT 59.615 43.478 7.16 0.00 0.00 4.34
2923 3389 4.737649 GCAAGTTGAAGAGAAAAAGGGTGG 60.738 45.833 7.16 0.00 0.00 4.61
2924 3390 2.959030 AGTTGAAGAGAAAAAGGGTGGC 59.041 45.455 0.00 0.00 0.00 5.01
2942 3408 0.311165 GCAGAGATCCATGCATGCAC 59.689 55.000 25.37 10.10 42.11 4.57
2951 3425 2.164827 TCCATGCATGCACATTCTCAAC 59.835 45.455 25.37 0.00 0.00 3.18
2952 3426 2.094442 CCATGCATGCACATTCTCAACA 60.094 45.455 25.37 0.00 0.00 3.33
2953 3427 3.580731 CATGCATGCACATTCTCAACAA 58.419 40.909 25.37 0.00 0.00 2.83
2954 3428 3.015934 TGCATGCACATTCTCAACAAC 57.984 42.857 18.46 0.00 0.00 3.32
2955 3429 2.624364 TGCATGCACATTCTCAACAACT 59.376 40.909 18.46 0.00 0.00 3.16
2956 3430 3.819902 TGCATGCACATTCTCAACAACTA 59.180 39.130 18.46 0.00 0.00 2.24
2957 3431 4.460034 TGCATGCACATTCTCAACAACTAT 59.540 37.500 18.46 0.00 0.00 2.12
2958 3432 5.047872 TGCATGCACATTCTCAACAACTATT 60.048 36.000 18.46 0.00 0.00 1.73
2959 3433 5.287752 GCATGCACATTCTCAACAACTATTG 59.712 40.000 14.21 0.00 0.00 1.90
2961 3435 6.000891 TGCACATTCTCAACAACTATTGTC 57.999 37.500 0.00 0.00 44.59 3.18
2962 3436 5.764686 TGCACATTCTCAACAACTATTGTCT 59.235 36.000 0.00 0.00 44.59 3.41
2963 3437 6.934083 TGCACATTCTCAACAACTATTGTCTA 59.066 34.615 0.00 0.00 44.59 2.59
2964 3438 7.607607 TGCACATTCTCAACAACTATTGTCTAT 59.392 33.333 0.00 0.00 44.59 1.98
2965 3439 8.119226 GCACATTCTCAACAACTATTGTCTATC 58.881 37.037 0.00 0.00 44.59 2.08
2966 3440 9.376075 CACATTCTCAACAACTATTGTCTATCT 57.624 33.333 0.00 0.00 44.59 1.98
2967 3441 9.950496 ACATTCTCAACAACTATTGTCTATCTT 57.050 29.630 0.00 0.00 44.59 2.40
2970 3444 9.862371 TTCTCAACAACTATTGTCTATCTTCTC 57.138 33.333 0.00 0.00 44.59 2.87
2971 3445 9.025041 TCTCAACAACTATTGTCTATCTTCTCA 57.975 33.333 0.00 0.00 44.59 3.27
2972 3446 8.988064 TCAACAACTATTGTCTATCTTCTCAC 57.012 34.615 0.00 0.00 44.59 3.51
2973 3447 8.585018 TCAACAACTATTGTCTATCTTCTCACA 58.415 33.333 0.00 0.00 44.59 3.58
2974 3448 9.208022 CAACAACTATTGTCTATCTTCTCACAA 57.792 33.333 0.00 0.00 44.59 3.33
2975 3449 9.778741 AACAACTATTGTCTATCTTCTCACAAA 57.221 29.630 0.00 0.00 44.59 2.83
2976 3450 9.778741 ACAACTATTGTCTATCTTCTCACAAAA 57.221 29.630 0.00 0.00 40.56 2.44
2978 3452 9.778741 AACTATTGTCTATCTTCTCACAAAACA 57.221 29.630 0.00 0.00 32.66 2.83
2979 3453 9.778741 ACTATTGTCTATCTTCTCACAAAACAA 57.221 29.630 0.00 0.00 32.66 2.83
3148 3622 1.871039 CCAGTCCACCACTTTACAACG 59.129 52.381 0.00 0.00 30.26 4.10
3190 3664 1.528129 ACCTTTTCAGTGCAGCTAGC 58.472 50.000 6.62 6.62 45.96 3.42
3191 3665 1.072965 ACCTTTTCAGTGCAGCTAGCT 59.927 47.619 12.68 12.68 45.94 3.32
3192 3666 1.467734 CCTTTTCAGTGCAGCTAGCTG 59.532 52.381 35.54 35.54 45.94 4.24
3193 3667 2.149578 CTTTTCAGTGCAGCTAGCTGT 58.850 47.619 37.91 21.35 45.24 4.40
3197 3671 1.747924 TCAGTGCAGCTAGCTGTCTAG 59.252 52.381 37.91 26.89 45.24 2.43
3353 4191 4.442706 TGTCAAAGAGTCTGAGGTTCAAC 58.557 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.217038 GCTCTGACCTGGACCCACA 61.217 63.158 0.00 0.00 0.00 4.17
78 80 3.108357 GAACCAACTATGCCGCCGC 62.108 63.158 0.00 0.00 0.00 6.53
165 167 0.966179 AAAGGGCGGTAAAAAGCTGG 59.034 50.000 0.00 0.00 0.00 4.85
195 197 4.475016 TGAGGAGAAAGATAGGGAAAAGGG 59.525 45.833 0.00 0.00 0.00 3.95
795 1229 0.251165 ATAGGAGAGAGCGGGAGAGC 60.251 60.000 0.00 0.00 37.41 4.09
801 1235 4.590918 TGGACTAATATAGGAGAGAGCGG 58.409 47.826 0.00 0.00 0.00 5.52
802 1236 4.095782 GCTGGACTAATATAGGAGAGAGCG 59.904 50.000 0.00 0.00 0.00 5.03
933 1370 0.598158 TTGTTGGTCGACGTACTGCC 60.598 55.000 9.92 0.00 0.00 4.85
953 1390 3.980775 GCTAGCTCTCGATGAGATTGTTC 59.019 47.826 7.70 0.00 45.39 3.18
1061 1503 3.124921 GGTGTTCATGGGACGGCG 61.125 66.667 4.80 4.80 0.00 6.46
1241 1689 4.194720 GCGATCACCTCCGCGTCT 62.195 66.667 4.92 0.00 42.02 4.18
1292 1740 0.987715 CGCAGATCTCACACACGAAG 59.012 55.000 0.00 0.00 0.00 3.79
1301 1749 2.586245 CCCTTGCCGCAGATCTCA 59.414 61.111 0.00 0.00 0.00 3.27
1328 1776 1.071987 CAGCTGCAGGTTCTGGTCA 59.928 57.895 17.45 0.00 31.21 4.02
1404 1852 2.943034 GACGTAGACGCGCTTCCG 60.943 66.667 10.66 10.40 44.43 4.30
1809 2257 4.711949 AGCAGGCTTGAGGTGCGG 62.712 66.667 0.00 0.00 42.26 5.69
1964 2415 1.304217 ACCGGACGACATGAGACCT 60.304 57.895 9.46 0.00 0.00 3.85
1971 2422 4.388499 GCCACCACCGGACGACAT 62.388 66.667 9.46 0.00 0.00 3.06
2379 2836 2.184020 TTATGCTGGTGCTGGCTCGT 62.184 55.000 0.00 0.00 40.48 4.18
2564 3021 4.709886 ACCTTAAACTAAATCCACCCATGC 59.290 41.667 0.00 0.00 0.00 4.06
2616 3074 8.058667 TGAATTAAACACTACTCCTCGTATCA 57.941 34.615 0.00 0.00 0.00 2.15
2636 3094 0.179032 TACATGGCCGCGGATGAATT 60.179 50.000 33.48 11.30 0.00 2.17
2639 3097 1.227527 CTTACATGGCCGCGGATGA 60.228 57.895 33.48 12.07 0.00 2.92
2708 3173 7.090173 AGTAAACCAATTGAAACGGAATGATG 58.910 34.615 7.12 0.00 0.00 3.07
2709 3174 7.040062 TGAGTAAACCAATTGAAACGGAATGAT 60.040 33.333 7.12 0.00 0.00 2.45
2710 3175 6.263392 TGAGTAAACCAATTGAAACGGAATGA 59.737 34.615 7.12 0.00 0.00 2.57
2790 3255 8.001875 AGATAGACAGATACCATCAAGTACTGT 58.998 37.037 0.00 0.00 37.33 3.55
2791 3256 8.296000 CAGATAGACAGATACCATCAAGTACTG 58.704 40.741 0.00 0.00 32.41 2.74
2804 3269 7.685398 GCAGTGAATGGTTCAGATAGACAGATA 60.685 40.741 0.00 0.00 41.01 1.98
2805 3270 6.580788 CAGTGAATGGTTCAGATAGACAGAT 58.419 40.000 0.00 0.00 41.01 2.90
2806 3271 5.625426 GCAGTGAATGGTTCAGATAGACAGA 60.625 44.000 0.00 0.00 41.01 3.41
2807 3272 4.569966 GCAGTGAATGGTTCAGATAGACAG 59.430 45.833 0.00 0.00 41.01 3.51
2808 3273 4.223700 AGCAGTGAATGGTTCAGATAGACA 59.776 41.667 0.00 0.00 41.01 3.41
2809 3274 4.764172 AGCAGTGAATGGTTCAGATAGAC 58.236 43.478 0.00 0.00 41.01 2.59
2810 3275 4.440663 CGAGCAGTGAATGGTTCAGATAGA 60.441 45.833 0.00 0.00 40.53 1.98
2811 3276 3.801050 CGAGCAGTGAATGGTTCAGATAG 59.199 47.826 0.00 0.00 40.53 2.08
2812 3277 3.447229 TCGAGCAGTGAATGGTTCAGATA 59.553 43.478 0.00 0.00 40.53 1.98
2827 3292 1.284657 CACTGGCACTAATCGAGCAG 58.715 55.000 0.00 0.00 0.00 4.24
2896 3361 3.715628 TTTTCTCTTCAACTTGCCTGC 57.284 42.857 0.00 0.00 0.00 4.85
2904 3369 2.693074 TGCCACCCTTTTTCTCTTCAAC 59.307 45.455 0.00 0.00 0.00 3.18
2917 3383 1.992519 GCATGGATCTCTGCCACCCT 61.993 60.000 8.35 0.00 38.44 4.34
2920 3386 0.952280 CATGCATGGATCTCTGCCAC 59.048 55.000 19.40 0.00 38.44 5.01
2921 3387 0.822121 GCATGCATGGATCTCTGCCA 60.822 55.000 27.34 0.00 40.24 4.92
2923 3389 0.311165 GTGCATGCATGGATCTCTGC 59.689 55.000 25.64 13.02 38.87 4.26
2924 3390 1.675552 TGTGCATGCATGGATCTCTG 58.324 50.000 25.64 1.74 0.00 3.35
2952 3426 9.778741 TGTTTTGTGAGAAGATAGACAATAGTT 57.221 29.630 0.00 0.00 0.00 2.24
2953 3427 9.778741 TTGTTTTGTGAGAAGATAGACAATAGT 57.221 29.630 0.00 0.00 0.00 2.12
2992 3466 6.122964 GCCAAGGAGATAGACCATAGTTTTT 58.877 40.000 0.00 0.00 0.00 1.94
2993 3467 5.685075 CGCCAAGGAGATAGACCATAGTTTT 60.685 44.000 0.00 0.00 0.00 2.43
2994 3468 4.202264 CGCCAAGGAGATAGACCATAGTTT 60.202 45.833 0.00 0.00 0.00 2.66
3010 3484 4.929211 CCCTTTTATTTTTCTTCGCCAAGG 59.071 41.667 0.00 0.00 0.00 3.61
3014 3488 5.048294 TGTCTCCCTTTTATTTTTCTTCGCC 60.048 40.000 0.00 0.00 0.00 5.54
3066 3540 6.479884 AGCTACTCTTTGATCAATGGTTCTT 58.520 36.000 18.33 4.65 0.00 2.52
3067 3541 6.059787 AGCTACTCTTTGATCAATGGTTCT 57.940 37.500 18.33 12.73 0.00 3.01
3148 3622 7.763985 AGGTAATTTGGTTTGTGCAATAATAGC 59.236 33.333 0.00 0.00 0.00 2.97
3197 3671 8.830580 TGTTCAAACAAGATCAAGCTATATAGC 58.169 33.333 24.55 24.55 41.84 2.97
3316 4154 4.341806 TCTTTGACATTTGGACAAGCACAT 59.658 37.500 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.