Multiple sequence alignment - TraesCS1A01G129700

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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 TraesCS1A01G129700 chr1A 100.000 3726 0 0 1 3726 167799422 167803147 0.000000e+00 6881
1 TraesCS1A01G129700 chr1D 94.411 3006 124 19 748 3726 189886900 189883912 0.000000e+00 4580
2 TraesCS1A01G129700 chr1B 94.400 2268 99 9 748 2997 263749944 263747687 0.000000e+00 3459
3 TraesCS1A01G129700 chr1B 94.398 482 21 3 3247 3726 263747339 263746862 0.000000e+00 736
4 TraesCS1A01G129700 chr1B 90.278 288 17 5 2963 3248 263747682 263747404 2.110000e-97 366
5 TraesCS1A01G129700 chr5A 95.861 749 31 0 1 749 632350288 632351036 0.000000e+00 1212
6 TraesCS1A01G129700 chr7B 95.606 751 31 1 1 749 13848282 13847532 0.000000e+00 1203
7 TraesCS1A01G129700 chr7B 95.455 748 34 0 1 748 281380061 281380808 0.000000e+00 1194
8 TraesCS1A01G129700 chr2A 95.594 749 33 0 1 749 716824737 716823989 0.000000e+00 1201
9 TraesCS1A01G129700 chr5B 95.187 748 35 1 1 748 695819125 695818379 0.000000e+00 1181
10 TraesCS1A01G129700 chr6D 95.067 750 36 1 1 750 424765710 424764962 0.000000e+00 1179
11 TraesCS1A01G129700 chrUn 94.793 749 39 0 1 749 232151845 232152593 0.000000e+00 1168
12 TraesCS1A01G129700 chrUn 94.793 749 39 0 1 749 237970884 237971632 0.000000e+00 1168
13 TraesCS1A01G129700 chr3B 94.793 749 39 0 1 749 764444638 764445386 0.000000e+00 1168


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 TraesCS1A01G129700 chr1A 167799422 167803147 3725 False 6881.000000 6881 100.000000 1 3726 1 chr1A.!!$F1 3725
1 TraesCS1A01G129700 chr1D 189883912 189886900 2988 True 4580.000000 4580 94.411000 748 3726 1 chr1D.!!$R1 2978
2 TraesCS1A01G129700 chr1B 263746862 263749944 3082 True 1520.333333 3459 93.025333 748 3726 3 chr1B.!!$R1 2978
3 TraesCS1A01G129700 chr5A 632350288 632351036 748 False 1212.000000 1212 95.861000 1 749 1 chr5A.!!$F1 748
4 TraesCS1A01G129700 chr7B 13847532 13848282 750 True 1203.000000 1203 95.606000 1 749 1 chr7B.!!$R1 748
5 TraesCS1A01G129700 chr7B 281380061 281380808 747 False 1194.000000 1194 95.455000 1 748 1 chr7B.!!$F1 747
6 TraesCS1A01G129700 chr2A 716823989 716824737 748 True 1201.000000 1201 95.594000 1 749 1 chr2A.!!$R1 748
7 TraesCS1A01G129700 chr5B 695818379 695819125 746 True 1181.000000 1181 95.187000 1 748 1 chr5B.!!$R1 747
8 TraesCS1A01G129700 chr6D 424764962 424765710 748 True 1179.000000 1179 95.067000 1 750 1 chr6D.!!$R1 749
9 TraesCS1A01G129700 chrUn 232151845 232152593 748 False 1168.000000 1168 94.793000 1 749 1 chrUn.!!$F1 748
10 TraesCS1A01G129700 chrUn 237970884 237971632 748 False 1168.000000 1168 94.793000 1 749 1 chrUn.!!$F2 748
11 TraesCS1A01G129700 chr3B 764444638 764445386 748 False 1168.000000 1168 94.793000 1 749 1 chr3B.!!$F1 748

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
72 73 0.168788 GCTGTTAAGCGCATTCTGCA 59.831 50.0 11.47 0.0 45.36 4.41 F
1369 1375 0.908910 TCACCGCAACCATCCTGTAT 59.091 50.0 0.00 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1405 0.439985 CAAGATGCTCGGTCGTGTTG 59.560 55.0 0.00 0.0 0.00 3.33 R
2994 3033 0.250684 TTGCCTGCGAAGGACATTCA 60.251 50.0 15.89 0.0 37.83 2.57 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
72 73 0.168788 GCTGTTAAGCGCATTCTGCA 59.831 50.000 11.47 0.00 45.36 4.41
101 102 2.893424 AGGGAACATTGCAAACTGGAT 58.107 42.857 1.71 0.00 0.00 3.41
146 147 5.880332 TCCACCAGCATTAGTATTTTCACTC 59.120 40.000 0.00 0.00 0.00 3.51
250 251 3.554337 GGAGTTCTAAGAAGCAACCGACA 60.554 47.826 0.00 0.00 0.00 4.35
269 270 4.111198 GACAGTGTCGAGATCTAGTACGA 58.889 47.826 7.68 0.00 0.00 3.43
398 399 8.100791 GGTGTGATAATTTAGGAGCCACATATA 58.899 37.037 0.00 0.00 35.83 0.86
451 452 5.929992 CACCAAGCACATTGAGATTGATTTT 59.070 36.000 12.69 0.00 41.83 1.82
538 539 4.036027 CAGCTGGCTGATGTATTTACCAAG 59.964 45.833 16.59 0.00 46.30 3.61
543 544 3.947834 GCTGATGTATTTACCAAGCCAGT 59.052 43.478 0.00 0.00 0.00 4.00
587 588 8.761689 ACCGATTTAGTACCAATCTAAACCTTA 58.238 33.333 11.68 0.00 39.24 2.69
757 760 5.221342 ACCTATTCTCATACTGCTAGTGCAC 60.221 44.000 9.40 9.40 45.31 4.57
847 850 4.154918 CCTCTCCTTTTGAATGCACAGTAC 59.845 45.833 0.00 0.00 0.00 2.73
1362 1368 2.703798 GCAGCATCACCGCAACCAT 61.704 57.895 0.00 0.00 0.00 3.55
1369 1375 0.908910 TCACCGCAACCATCCTGTAT 59.091 50.000 0.00 0.00 0.00 2.29
1399 1405 2.024176 ATGCCGTACTGTGATTCACC 57.976 50.000 14.05 0.00 32.73 4.02
1402 1408 1.463444 GCCGTACTGTGATTCACCAAC 59.537 52.381 14.05 8.38 32.73 3.77
1428 1434 2.425312 CCGAGCATCTTGTAGTCTCACT 59.575 50.000 0.00 0.00 0.00 3.41
1429 1435 3.433709 CGAGCATCTTGTAGTCTCACTG 58.566 50.000 0.00 0.00 0.00 3.66
1430 1436 3.733380 CGAGCATCTTGTAGTCTCACTGG 60.733 52.174 0.00 0.00 0.00 4.00
1431 1437 2.093764 AGCATCTTGTAGTCTCACTGGC 60.094 50.000 0.00 0.00 0.00 4.85
1432 1438 2.534298 CATCTTGTAGTCTCACTGGCG 58.466 52.381 0.00 0.00 0.00 5.69
1433 1439 1.617322 TCTTGTAGTCTCACTGGCGT 58.383 50.000 0.00 0.00 0.00 5.68
1435 1441 2.061773 CTTGTAGTCTCACTGGCGTTG 58.938 52.381 0.00 0.00 0.00 4.10
1436 1442 0.319555 TGTAGTCTCACTGGCGTTGC 60.320 55.000 0.00 0.00 0.00 4.17
1549 1563 0.734889 GACCGCATCCTTTCCATGTG 59.265 55.000 0.00 0.00 0.00 3.21
1712 1726 0.951040 GCCTCAACTCCAGGTTCGTG 60.951 60.000 0.00 0.00 35.74 4.35
1715 1729 0.249868 TCAACTCCAGGTTCGTGCTG 60.250 55.000 0.00 0.00 35.74 4.41
1778 1792 2.844839 ACCAGGCTCGGGATAGGC 60.845 66.667 0.00 0.00 42.17 3.93
1868 1882 0.036732 TCAACCACTGGCTGTCCATC 59.963 55.000 0.00 0.00 42.51 3.51
1874 1888 0.545171 ACTGGCTGTCCATCATCCTG 59.455 55.000 0.00 0.00 42.51 3.86
1941 1959 1.272816 TGATCCAGGTAACGTCTCCCA 60.273 52.381 5.52 0.00 46.39 4.37
1947 1965 0.899720 GGTAACGTCTCCCATGTCCA 59.100 55.000 0.00 0.00 0.00 4.02
1950 1968 1.480212 AACGTCTCCCATGTCCAGCA 61.480 55.000 0.00 0.00 0.00 4.41
2002 2030 0.314302 ATCTCGGCGAGTTAATCCGG 59.686 55.000 33.31 8.70 43.10 5.14
2080 2108 2.676342 GTTCTCGGAACAACACAACTGT 59.324 45.455 10.67 0.00 0.00 3.55
2092 2120 1.008538 CAACTGTGCCGCTGGTTTC 60.009 57.895 0.00 0.00 0.00 2.78
2149 2177 0.035458 AGCTTGTCTTCGGTTCAGGG 59.965 55.000 0.00 0.00 0.00 4.45
2330 2358 1.960689 GCAGCCTAAAACCACAAAGGA 59.039 47.619 0.00 0.00 41.22 3.36
2363 2400 2.097825 ACATTCTTCTTGCTCCCATGC 58.902 47.619 0.00 0.00 0.00 4.06
2370 2407 3.329542 TTGCTCCCATGCCGAGGAC 62.330 63.158 9.37 0.00 0.00 3.85
2371 2408 3.785859 GCTCCCATGCCGAGGACA 61.786 66.667 9.37 0.00 0.00 4.02
2381 2418 3.374402 CGAGGACAGACCCTGCGT 61.374 66.667 0.00 0.00 40.05 5.24
2386 2423 1.069090 GACAGACCCTGCGTCACAA 59.931 57.895 0.00 0.00 44.66 3.33
2393 2430 2.738521 CTGCGTCACAAGGACCGG 60.739 66.667 0.00 0.00 43.95 5.28
2394 2431 4.308458 TGCGTCACAAGGACCGGG 62.308 66.667 6.32 0.00 43.95 5.73
2490 2527 1.614317 GGTTGAGATGGAAGGGTGGTG 60.614 57.143 0.00 0.00 0.00 4.17
2756 2793 2.094906 GCAGCTTCTTCACAATGCATGA 60.095 45.455 0.00 0.00 33.92 3.07
2961 3000 5.282055 TGGAAAGATGCTAGTACCTGATG 57.718 43.478 0.00 0.00 0.00 3.07
3016 3094 0.957395 ATGTCCTTCGCAGGCAACAG 60.957 55.000 0.00 0.00 40.58 3.16
3068 3146 9.326413 ACATGCCTACAAGATAATACAAACTAC 57.674 33.333 0.00 0.00 0.00 2.73
3069 3147 7.997107 TGCCTACAAGATAATACAAACTACG 57.003 36.000 0.00 0.00 0.00 3.51
3070 3148 7.774134 TGCCTACAAGATAATACAAACTACGA 58.226 34.615 0.00 0.00 0.00 3.43
3071 3149 8.252417 TGCCTACAAGATAATACAAACTACGAA 58.748 33.333 0.00 0.00 0.00 3.85
3072 3150 9.257651 GCCTACAAGATAATACAAACTACGAAT 57.742 33.333 0.00 0.00 0.00 3.34
3149 3229 6.874134 CACTATACAAGCACCAAGTCTAGTTT 59.126 38.462 0.00 0.00 0.00 2.66
3153 3233 5.621193 ACAAGCACCAAGTCTAGTTTGTAT 58.379 37.500 0.00 0.00 34.41 2.29
3175 3255 7.717875 TGTATATACTGCATTTTCCCCTGTTAC 59.282 37.037 13.89 0.00 0.00 2.50
3181 3261 3.864540 GCATTTTCCCCTGTTACAAAGCC 60.865 47.826 0.00 0.00 0.00 4.35
3192 3272 5.078411 TGTTACAAAGCCTTGCTCAAAAA 57.922 34.783 0.00 0.00 38.25 1.94
3215 3295 4.704540 ACCACAAACATTTCTCAACAGACA 59.295 37.500 0.00 0.00 0.00 3.41
3233 3313 6.119536 ACAGACAGGAGACATTTACACAAAA 58.880 36.000 0.00 0.00 0.00 2.44
3234 3314 6.601613 ACAGACAGGAGACATTTACACAAAAA 59.398 34.615 0.00 0.00 0.00 1.94
3297 3443 5.703130 GTCTGCAGTTTTCTCCAACTTATCT 59.297 40.000 14.67 0.00 34.60 1.98
3386 3532 3.586470 ACAACACACAGGTTCCCAATA 57.414 42.857 0.00 0.00 0.00 1.90
3568 3714 2.869101 TTCGAAACCATCCATCCACA 57.131 45.000 0.00 0.00 0.00 4.17
3594 3740 4.097741 TCCACAATTCACACCAAAACTCTG 59.902 41.667 0.00 0.00 0.00 3.35
3603 3749 4.754618 CACACCAAAACTCTGCTGTATACA 59.245 41.667 5.25 5.25 0.00 2.29
3633 3781 2.678786 ACCCATACGGTGCTTCTCA 58.321 52.632 0.00 0.00 46.09 3.27
3641 3789 3.746045 ACGGTGCTTCTCAGTTTTCTA 57.254 42.857 0.00 0.00 0.00 2.10
3674 3822 8.156820 CCGACTCATCCATCTATCTATCTATCT 58.843 40.741 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 6.493458 AGTTTGCAATGTTCCCTTTACATAGT 59.507 34.615 0.00 0.00 35.26 2.12
101 102 2.158813 AGACAGCCTTCCGAAACTTCAA 60.159 45.455 0.00 0.00 0.00 2.69
214 215 6.323482 TCTTAGAACTCCAGGAGATGAGATTG 59.677 42.308 24.45 6.19 33.32 2.67
250 251 4.121317 CCTTCGTACTAGATCTCGACACT 58.879 47.826 0.00 0.00 32.14 3.55
269 270 1.880027 CAAAGCTTTGTACTCGGCCTT 59.120 47.619 27.59 0.00 33.59 4.35
398 399 2.086610 AAAACTGGGTTGGCAGTCAT 57.913 45.000 0.00 0.00 0.00 3.06
451 452 1.520564 ACGCTCACGCACAAAGTGA 60.521 52.632 0.58 0.00 45.23 3.41
538 539 1.080995 GCATCTGTCGAGTGACTGGC 61.081 60.000 0.00 0.00 45.70 4.85
543 544 2.017782 GGTCTAGCATCTGTCGAGTGA 58.982 52.381 0.00 0.00 0.00 3.41
587 588 7.069331 CCCTCAATCTGAACTTCTACTCTGTAT 59.931 40.741 0.00 0.00 0.00 2.29
698 701 1.600916 GGCAAAGCCTCTCCACGTT 60.601 57.895 0.00 0.00 46.69 3.99
756 759 3.721087 AAGATCCGTTCATTTCTGGGT 57.279 42.857 0.00 0.00 0.00 4.51
757 760 4.737054 CAAAAGATCCGTTCATTTCTGGG 58.263 43.478 0.00 0.00 0.00 4.45
1005 1008 3.949980 TCAGGCTGCTGCTGCTGT 61.950 61.111 26.79 14.47 39.81 4.40
1131 1134 1.237285 GCAGCAAAAGAAGCGGAGGA 61.237 55.000 0.00 0.00 37.01 3.71
1350 1356 0.908910 ATACAGGATGGTTGCGGTGA 59.091 50.000 0.00 0.00 43.62 4.02
1362 1368 9.480053 GTACGGCATTATAAAAGTTATACAGGA 57.520 33.333 0.00 0.00 0.00 3.86
1369 1375 8.951787 ATCACAGTACGGCATTATAAAAGTTA 57.048 30.769 0.00 0.00 0.00 2.24
1390 1396 0.511221 CGGTCGTGTTGGTGAATCAC 59.489 55.000 4.51 4.51 0.00 3.06
1399 1405 0.439985 CAAGATGCTCGGTCGTGTTG 59.560 55.000 0.00 0.00 0.00 3.33
1402 1408 1.135373 ACTACAAGATGCTCGGTCGTG 60.135 52.381 0.00 0.00 0.00 4.35
1436 1442 1.005394 CTGCAGCCAAAGCCAAAGG 60.005 57.895 0.00 0.00 41.25 3.11
1643 1657 2.286523 CCTGGCCTGGTCGAACTCT 61.287 63.158 20.28 0.00 0.00 3.24
1712 1726 1.298014 CCTGGTCTTGGACTCCAGC 59.702 63.158 0.00 0.00 45.00 4.85
1715 1729 2.972819 GCCCCTGGTCTTGGACTCC 61.973 68.421 0.00 0.00 32.47 3.85
1778 1792 3.626680 TTCTTCCCTGACGCTCGCG 62.627 63.158 10.06 10.06 46.03 5.87
1788 1802 1.551452 CTCTCGGTGTCTTCTTCCCT 58.449 55.000 0.00 0.00 0.00 4.20
1815 1829 1.228245 GCAACCTGGTCAGCTCCAA 60.228 57.895 14.74 0.00 37.01 3.53
1915 1929 1.207329 ACGTTACCTGGATCAAGCTCC 59.793 52.381 0.00 0.00 35.74 4.70
1947 1965 1.509373 AAGATCTCTGGCCAGATGCT 58.491 50.000 35.11 26.57 40.92 3.79
2002 2030 6.293680 GGAGATTCTGACAAGAAAACCTCAAC 60.294 42.308 0.00 0.00 45.44 3.18
2080 2108 0.323302 TCATACTGAAACCAGCGGCA 59.677 50.000 1.45 0.00 35.09 5.69
2092 2120 1.584724 AGTTGGACCCCCTCATACTG 58.415 55.000 0.00 0.00 0.00 2.74
2149 2177 3.740128 ATGATCGCCGTCCTGTGCC 62.740 63.158 0.00 0.00 0.00 5.01
2215 2243 0.322816 TGAGCTTGACATCTTGGGCC 60.323 55.000 0.00 0.00 0.00 5.80
2264 2292 3.655481 GTTGAGCCGGGACAACAG 58.345 61.111 22.92 0.00 43.66 3.16
2276 2304 2.027625 GCGTCCCGAGGTTGTTGAG 61.028 63.158 0.00 0.00 0.00 3.02
2363 2400 4.135153 CGCAGGGTCTGTCCTCGG 62.135 72.222 0.00 0.00 34.31 4.63
2370 2407 1.669115 CCTTGTGACGCAGGGTCTG 60.669 63.158 17.85 6.40 46.24 3.51
2371 2408 1.837051 TCCTTGTGACGCAGGGTCT 60.837 57.895 17.85 0.00 46.24 3.85
2756 2793 6.118852 GCAGGGAAGAAGAGAGAACATAAAT 58.881 40.000 0.00 0.00 0.00 1.40
2932 2971 5.525378 GGTACTAGCATCTTTCCATTCTGTG 59.475 44.000 0.00 0.00 0.00 3.66
2933 2972 5.426833 AGGTACTAGCATCTTTCCATTCTGT 59.573 40.000 0.00 0.00 36.02 3.41
2949 2988 8.341892 TGCATAGAAGATACATCAGGTACTAG 57.658 38.462 0.00 0.00 36.02 2.57
2994 3033 0.250684 TTGCCTGCGAAGGACATTCA 60.251 50.000 15.89 0.00 37.83 2.57
3149 3229 6.260700 ACAGGGGAAAATGCAGTATATACA 57.739 37.500 15.18 0.00 0.00 2.29
3153 3233 6.068461 TGTAACAGGGGAAAATGCAGTATA 57.932 37.500 0.00 0.00 0.00 1.47
3175 3255 2.609002 GTGGTTTTTGAGCAAGGCTTTG 59.391 45.455 3.80 3.80 39.88 2.77
3181 3261 5.799681 AATGTTTGTGGTTTTTGAGCAAG 57.200 34.783 0.00 0.00 37.53 4.01
3192 3272 4.704540 TGTCTGTTGAGAAATGTTTGTGGT 59.295 37.500 0.00 0.00 0.00 4.16
3233 3313 7.549839 AGCTTGTAACATATGATGCATGTTTT 58.450 30.769 10.38 0.00 42.52 2.43
3234 3314 7.104043 AGCTTGTAACATATGATGCATGTTT 57.896 32.000 10.38 0.99 42.52 2.83
3297 3443 9.905713 AGCAGAAATTATCACCTTGAGTTTATA 57.094 29.630 0.00 0.00 0.00 0.98
3386 3532 2.485479 CCATGCTTGGCCTTATCTACGT 60.485 50.000 3.32 0.00 35.85 3.57
3410 3556 8.041323 TGTTTGGTTACATTTTATTGTTGGTGT 58.959 29.630 0.00 0.00 0.00 4.16
3568 3714 4.405358 AGTTTTGGTGTGAATTGTGGATGT 59.595 37.500 0.00 0.00 0.00 3.06
3594 3740 8.671384 TGGGTTAGTTAATCATTGTATACAGC 57.329 34.615 5.56 0.00 0.00 4.40
3633 3781 6.371825 GGATGAGTCGGTGAAAATAGAAAACT 59.628 38.462 0.00 0.00 0.00 2.66
3641 3789 4.494091 AGATGGATGAGTCGGTGAAAAT 57.506 40.909 0.00 0.00 0.00 1.82
3674 3822 6.934645 CCAGTTCTGTTCCAAGTAGTTTGATA 59.065 38.462 0.00 0.00 39.21 2.15
3675 3823 5.765182 CCAGTTCTGTTCCAAGTAGTTTGAT 59.235 40.000 0.00 0.00 39.21 2.57
3676 3824 5.104693 TCCAGTTCTGTTCCAAGTAGTTTGA 60.105 40.000 0.00 0.00 39.21 2.69
3677 3825 5.123227 TCCAGTTCTGTTCCAAGTAGTTTG 58.877 41.667 0.00 0.00 36.50 2.93
3678 3826 5.367945 TCCAGTTCTGTTCCAAGTAGTTT 57.632 39.130 0.00 0.00 0.00 2.66
3679 3827 4.202367 CCTCCAGTTCTGTTCCAAGTAGTT 60.202 45.833 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.