Multiple sequence alignment - TraesCS2D01G263100

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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 TraesCS2D01G263100 chr2D 100.000 4199 0 0 1 4199 320284652 320280454 0.000000e+00 7755
1 TraesCS2D01G263100 chr2B 95.307 4262 136 16 1 4199 388598590 388594330 0.000000e+00 6704
2 TraesCS2D01G263100 chr2A 94.911 3262 107 23 144 3361 410850696 410853942 0.000000e+00 5049
3 TraesCS2D01G263100 chr2A 92.075 858 47 7 3356 4199 410853986 410854836 0.000000e+00 1188
4 TraesCS2D01G263100 chr2A 87.129 101 12 1 1 101 410850600 410850699 3.430000e-21 113


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 TraesCS2D01G263100 chr2D 320280454 320284652 4198 True 7755.000000 7755 100.000000 1 4199 1 chr2D.!!$R1 4198
1 TraesCS2D01G263100 chr2B 388594330 388598590 4260 True 6704.000000 6704 95.307000 1 4199 1 chr2B.!!$R1 4198
2 TraesCS2D01G263100 chr2A 410850600 410854836 4236 False 2116.666667 5049 91.371667 1 4199 3 chr2A.!!$F1 4198

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
84 85 0.967662 TTGTTGTGGGGATGTGCATG 59.032 50.000 0.00 0.0 0.00 4.06 F
443 469 1.067199 CGGCGCTGCTTTCAATTGTC 61.067 55.000 7.64 0.0 0.00 3.18 F
1671 1727 0.676466 TCCGGCATTGCAGTTACCTG 60.676 55.000 11.39 0.0 41.91 4.00 F
2115 2171 1.081242 CAGCGGCAATGTTGGTCAC 60.081 57.895 1.45 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 1660 1.173913 GTTCCCGGACAATTCCAAGG 58.826 55.000 0.73 0.0 43.00 3.61 R
2263 2331 0.032017 TCCCTCTCCCTTCTAGTGCC 60.032 60.000 0.00 0.0 0.00 5.01 R
2861 2929 0.251634 TGTCATTGCATACTCCGGCA 59.748 50.000 0.00 0.0 38.46 5.69 R
4084 4215 1.204704 TCAGTAAGGACGGCATCAGTG 59.795 52.381 0.00 0.0 0.00 3.66 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
77 78 7.586349 ACTTGATTCTATATTGTTGTGGGGAT 58.414 34.615 0.00 0.00 0.00 3.85
84 85 0.967662 TTGTTGTGGGGATGTGCATG 59.032 50.000 0.00 0.00 0.00 4.06
109 110 1.906574 TCCCATGTTGGAGACAGTACC 59.093 52.381 0.00 0.00 40.96 3.34
124 125 5.428783 AGACAGTACCTTAATATGGTTGGCT 59.571 40.000 3.07 1.85 38.88 4.75
130 131 2.254546 TAATATGGTTGGCTGCTCGG 57.745 50.000 0.00 0.00 0.00 4.63
210 213 7.068103 ACACATTCTTTCTGGTGAACACATTTA 59.932 33.333 7.25 0.00 35.33 1.40
381 386 2.302260 CATGAGAAGAGCCGAGTAGGA 58.698 52.381 0.00 0.00 45.00 2.94
426 452 2.819595 CGCCTTGTGATGGGTCGG 60.820 66.667 0.00 0.00 0.00 4.79
431 457 4.758251 TGTGATGGGTCGGCGCTG 62.758 66.667 10.86 10.86 0.00 5.18
439 465 2.690778 GGTCGGCGCTGCTTTCAAT 61.691 57.895 12.58 0.00 0.00 2.57
443 469 1.067199 CGGCGCTGCTTTCAATTGTC 61.067 55.000 7.64 0.00 0.00 3.18
448 474 2.401720 CGCTGCTTTCAATTGTCGAAAC 59.598 45.455 5.13 0.00 0.00 2.78
449 475 3.632189 GCTGCTTTCAATTGTCGAAACT 58.368 40.909 5.13 0.00 0.00 2.66
450 476 3.665871 GCTGCTTTCAATTGTCGAAACTC 59.334 43.478 5.13 0.00 0.00 3.01
454 485 5.514914 TGCTTTCAATTGTCGAAACTCAAAC 59.485 36.000 5.13 0.00 0.00 2.93
493 524 1.821759 CGCCAAATACGATGGGCCA 60.822 57.895 9.61 9.61 43.50 5.36
552 583 2.031870 GCCTTTATGGTTGGGCCTAAG 58.968 52.381 0.00 0.00 38.77 2.18
605 642 2.489275 CGCCAAAAGGTGCACCACT 61.489 57.895 36.39 20.99 38.89 4.00
607 644 1.675720 GCCAAAAGGTGCACCACTGT 61.676 55.000 36.39 16.47 38.89 3.55
637 674 2.367241 TGCAGTGTAGAAACCTAGCACA 59.633 45.455 0.00 0.00 32.99 4.57
710 747 9.487790 AAAATCAAATATGAAACAAACGGTCAT 57.512 25.926 0.00 0.00 39.49 3.06
721 758 7.911205 TGAAACAAACGGTCATAAAACTAACAG 59.089 33.333 0.00 0.00 0.00 3.16
722 759 6.930667 ACAAACGGTCATAAAACTAACAGT 57.069 33.333 0.00 0.00 0.00 3.55
723 760 8.436046 AACAAACGGTCATAAAACTAACAGTA 57.564 30.769 0.00 0.00 0.00 2.74
724 761 8.436046 ACAAACGGTCATAAAACTAACAGTAA 57.564 30.769 0.00 0.00 0.00 2.24
725 762 8.891720 ACAAACGGTCATAAAACTAACAGTAAA 58.108 29.630 0.00 0.00 0.00 2.01
726 763 9.377383 CAAACGGTCATAAAACTAACAGTAAAG 57.623 33.333 0.00 0.00 0.00 1.85
727 764 7.125536 ACGGTCATAAAACTAACAGTAAAGC 57.874 36.000 0.00 0.00 0.00 3.51
886 939 1.645704 ATCACTCCCGAGTCGTCGTG 61.646 60.000 12.31 14.36 45.30 4.35
895 948 2.804090 GTCGTCGTGGCTTCGTCC 60.804 66.667 0.00 0.00 0.00 4.79
896 949 4.047059 TCGTCGTGGCTTCGTCCC 62.047 66.667 0.00 0.00 0.00 4.46
1059 1115 2.806945 TTGCCACCTTATTCCTCCTG 57.193 50.000 0.00 0.00 0.00 3.86
1104 1160 3.182967 CTCGCTAGTCCAAGAACATGAC 58.817 50.000 0.00 0.00 0.00 3.06
1106 1162 3.006430 TCGCTAGTCCAAGAACATGACAA 59.994 43.478 0.00 0.00 0.00 3.18
1113 1169 1.136252 CAAGAACATGACAAGTCGGCG 60.136 52.381 0.00 0.00 0.00 6.46
1382 1438 2.511373 TGAGTTATGGCGGCTGCG 60.511 61.111 12.29 0.00 44.10 5.18
1671 1727 0.676466 TCCGGCATTGCAGTTACCTG 60.676 55.000 11.39 0.00 41.91 4.00
2115 2171 1.081242 CAGCGGCAATGTTGGTCAC 60.081 57.895 1.45 0.00 0.00 3.67
2169 2225 2.411031 GGTGTTAGTCGTCATTGTTGCG 60.411 50.000 0.00 0.00 0.00 4.85
2256 2324 4.962836 GGCACTGGCACTGGCACT 62.963 66.667 14.26 0.00 43.71 4.40
2257 2325 2.032528 GCACTGGCACTGGCACTA 59.967 61.111 0.07 0.00 43.71 2.74
2258 2326 2.037136 GCACTGGCACTGGCACTAG 61.037 63.158 0.07 0.00 43.71 2.57
2259 2327 2.037136 CACTGGCACTGGCACTAGC 61.037 63.158 0.07 0.00 43.71 3.42
2260 2328 2.348620 CTGGCACTGGCACTAGCA 59.651 61.111 0.07 0.00 44.61 3.49
2261 2329 2.032528 TGGCACTGGCACTAGCAC 59.967 61.111 0.07 0.00 44.61 4.40
2262 2330 2.348998 GGCACTGGCACTAGCACT 59.651 61.111 0.00 0.00 44.61 4.40
2263 2331 2.037136 GGCACTGGCACTAGCACTG 61.037 63.158 0.00 0.00 44.61 3.66
2264 2332 2.037136 GCACTGGCACTAGCACTGG 61.037 63.158 0.00 0.00 44.61 4.00
2265 2333 2.037136 CACTGGCACTAGCACTGGC 61.037 63.158 0.00 0.00 44.61 4.85
2266 2334 2.348620 CTGGCACTAGCACTGGCA 59.651 61.111 7.69 7.69 44.61 4.92
2385 2453 1.959085 CAACTGCATCGGCTTTGGT 59.041 52.632 0.00 0.00 41.91 3.67
2646 2714 1.928868 AGAGGCAAATTGGTTGGAGG 58.071 50.000 0.00 0.00 37.73 4.30
2713 2781 1.992519 GCATGATGAGTGCTCCCCCT 61.993 60.000 0.00 0.00 39.45 4.79
2781 2849 7.281098 ACAATGACTTCAATGCATATCTCTCT 58.719 34.615 0.00 0.00 30.12 3.10
2861 2929 3.749609 GCTGGTACTTTTGGTTATGTCGT 59.250 43.478 0.00 0.00 0.00 4.34
2955 3023 6.333416 TGAACTGATCTCGGATAAGAAAGTG 58.667 40.000 5.53 0.00 30.75 3.16
3102 3170 6.351711 TGATGACCTGGTTGAGATTATGAAG 58.648 40.000 0.00 0.00 0.00 3.02
3165 3233 4.050553 CCAAAATGAAGCATGTTGTTCGT 58.949 39.130 8.92 0.00 37.37 3.85
3415 3532 7.722728 CCAGTATGTAGTGTCCTATGGTTAGTA 59.277 40.741 0.00 0.00 0.00 1.82
3416 3533 9.298250 CAGTATGTAGTGTCCTATGGTTAGTAT 57.702 37.037 0.00 0.00 0.00 2.12
3610 3730 2.418368 TTAGGCTGCCCTATGTGTTG 57.582 50.000 16.57 0.00 43.15 3.33
3694 3814 6.231211 CAAGAAACTGACATAGTACCCTGTT 58.769 40.000 0.00 0.00 39.18 3.16
3855 3975 7.996644 TGGTAGTCACACCTAGAAAAGAAAAAT 59.003 33.333 0.00 0.00 39.50 1.82
3873 3993 8.593492 AGAAAAATGCTCTTTTTGGTTGTATC 57.407 30.769 12.89 0.43 32.37 2.24
3899 4019 4.463539 TGAAGCTGCACATAATTGGTCATT 59.536 37.500 1.02 0.00 0.00 2.57
4011 4138 1.071699 GTGCGCTCTATTTATGGGGGA 59.928 52.381 9.73 0.00 0.00 4.81
4014 4141 2.814336 GCGCTCTATTTATGGGGGAAAG 59.186 50.000 0.00 0.00 0.00 2.62
4029 4156 5.714806 TGGGGGAAAGTCTGAAATAATTGTC 59.285 40.000 0.00 0.00 0.00 3.18
4105 4236 2.111384 ACTGATGCCGTCCTTACTGAT 58.889 47.619 0.00 0.00 0.00 2.90
4195 4326 0.579156 GCGATTCGAGGACAAGATGC 59.421 55.000 10.88 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.438651 GTGACAAGGTGCGCATTAGA 58.561 50.000 15.91 0.00 0.00 2.10
60 61 4.206375 TGCACATCCCCACAACAATATAG 58.794 43.478 0.00 0.00 0.00 1.31
62 63 3.098774 TGCACATCCCCACAACAATAT 57.901 42.857 0.00 0.00 0.00 1.28
109 110 2.549754 CCGAGCAGCCAACCATATTAAG 59.450 50.000 0.00 0.00 0.00 1.85
124 125 0.966875 ATGCCAGATTTTGCCGAGCA 60.967 50.000 0.00 0.00 36.47 4.26
130 131 3.357504 GCTCCATGCCAGATTTTGC 57.642 52.632 0.00 0.00 35.15 3.68
168 169 5.354234 AGAATGTGTCCTTATTTAGTTGCCG 59.646 40.000 0.00 0.00 0.00 5.69
178 179 6.126863 TCACCAGAAAGAATGTGTCCTTAT 57.873 37.500 0.00 0.00 0.00 1.73
341 344 6.245408 TCATGTGGGCTCAAATAACTAAACT 58.755 36.000 0.00 0.00 0.00 2.66
351 354 2.877300 GCTCTTCTCATGTGGGCTCAAA 60.877 50.000 0.00 0.00 0.00 2.69
388 394 1.623311 TCTCCGCAACCTCATTCTTCA 59.377 47.619 0.00 0.00 0.00 3.02
426 452 0.110238 TCGACAATTGAAAGCAGCGC 60.110 50.000 13.59 0.00 0.00 5.92
431 457 5.743872 AGTTTGAGTTTCGACAATTGAAAGC 59.256 36.000 13.59 5.69 36.10 3.51
448 474 1.028905 TGTTGGGCCGAAAGTTTGAG 58.971 50.000 0.01 0.00 0.00 3.02
449 475 1.475403 TTGTTGGGCCGAAAGTTTGA 58.525 45.000 0.01 0.00 0.00 2.69
450 476 2.524569 ATTGTTGGGCCGAAAGTTTG 57.475 45.000 0.01 0.00 0.00 2.93
454 485 2.293399 GCCTATATTGTTGGGCCGAAAG 59.707 50.000 0.01 0.00 38.77 2.62
493 524 6.434340 TGCTGATATCGACACATACTCCTAAT 59.566 38.462 0.00 0.00 0.00 1.73
605 642 7.284489 AGGTTTCTACACTGCATTTTCTTAACA 59.716 33.333 0.00 0.00 0.00 2.41
607 644 7.817418 AGGTTTCTACACTGCATTTTCTTAA 57.183 32.000 0.00 0.00 0.00 1.85
637 674 7.175990 CCATGTGGTTTGTTTGGTAACTATACT 59.824 37.037 0.00 0.00 35.24 2.12
705 742 7.303261 GTGGCTTTACTGTTAGTTTTATGACC 58.697 38.462 0.00 0.00 0.00 4.02
710 747 5.532032 GGTGGTGGCTTTACTGTTAGTTTTA 59.468 40.000 0.00 0.00 0.00 1.52
721 758 5.462530 AATTTAACTGGTGGTGGCTTTAC 57.537 39.130 0.00 0.00 0.00 2.01
722 759 5.740513 GCAAATTTAACTGGTGGTGGCTTTA 60.741 40.000 0.00 0.00 0.00 1.85
723 760 4.702831 CAAATTTAACTGGTGGTGGCTTT 58.297 39.130 0.00 0.00 0.00 3.51
724 761 3.494223 GCAAATTTAACTGGTGGTGGCTT 60.494 43.478 0.00 0.00 0.00 4.35
725 762 2.037121 GCAAATTTAACTGGTGGTGGCT 59.963 45.455 0.00 0.00 0.00 4.75
726 763 2.224161 TGCAAATTTAACTGGTGGTGGC 60.224 45.455 0.00 0.00 0.00 5.01
727 764 3.742433 TGCAAATTTAACTGGTGGTGG 57.258 42.857 0.00 0.00 0.00 4.61
807 860 8.594687 CGGATGGCTTTACTTGATTAATTTTTG 58.405 33.333 0.00 0.00 0.00 2.44
886 939 2.033424 GCATCATTAAAGGGACGAAGCC 59.967 50.000 0.00 0.00 0.00 4.35
895 948 5.591877 AGTGAAGGCTTAGCATCATTAAAGG 59.408 40.000 13.49 0.00 30.99 3.11
896 949 6.690194 AGTGAAGGCTTAGCATCATTAAAG 57.310 37.500 13.49 0.00 30.99 1.85
1104 1160 3.589654 TTGGAGGAGCGCCGACTTG 62.590 63.158 2.29 0.00 39.96 3.16
1106 1162 4.070552 GTTGGAGGAGCGCCGACT 62.071 66.667 2.29 0.00 39.96 4.18
1113 1169 1.363744 CGTTCATGAGTTGGAGGAGC 58.636 55.000 0.00 0.00 0.00 4.70
1272 1328 4.309950 GACAACACCCCGGCGAGT 62.310 66.667 9.30 1.73 0.00 4.18
1303 1359 1.371183 CTTTGAGGTCGGTGAGGCA 59.629 57.895 0.00 0.00 0.00 4.75
1604 1660 1.173913 GTTCCCGGACAATTCCAAGG 58.826 55.000 0.73 0.00 43.00 3.61
1961 2017 2.746362 GCTGTCACTTGGGAAATCTCAG 59.254 50.000 0.00 0.00 0.00 3.35
2010 2066 4.932200 ACTGTAAATACTTCAGCAGAGTGC 59.068 41.667 0.00 0.00 45.46 4.40
2115 2171 3.641434 ACAATCTCCATGGTCTTCAGG 57.359 47.619 12.58 0.00 0.00 3.86
2127 2183 4.082026 ACCAAAGCTATTGCAACAATCTCC 60.082 41.667 0.00 0.00 42.74 3.71
2169 2225 1.036707 TGGTGGCCACAACTAAAAGC 58.963 50.000 35.78 16.31 34.61 3.51
2214 2270 2.115266 CTTGGTTGCCTCGGGGTT 59.885 61.111 1.62 0.00 34.45 4.11
2255 2323 1.137872 CCCTTCTAGTGCCAGTGCTAG 59.862 57.143 0.00 0.00 38.71 3.42
2256 2324 1.195115 CCCTTCTAGTGCCAGTGCTA 58.805 55.000 0.00 0.00 38.71 3.49
2257 2325 0.545309 TCCCTTCTAGTGCCAGTGCT 60.545 55.000 0.00 0.00 38.71 4.40
2258 2326 0.107945 CTCCCTTCTAGTGCCAGTGC 60.108 60.000 0.00 0.00 38.26 4.40
2259 2327 1.480137 CTCTCCCTTCTAGTGCCAGTG 59.520 57.143 0.00 0.00 0.00 3.66
2260 2328 1.621072 CCTCTCCCTTCTAGTGCCAGT 60.621 57.143 0.00 0.00 0.00 4.00
2261 2329 1.118838 CCTCTCCCTTCTAGTGCCAG 58.881 60.000 0.00 0.00 0.00 4.85
2262 2330 0.325671 CCCTCTCCCTTCTAGTGCCA 60.326 60.000 0.00 0.00 0.00 4.92
2263 2331 0.032017 TCCCTCTCCCTTCTAGTGCC 60.032 60.000 0.00 0.00 0.00 5.01
2264 2332 1.408969 CTCCCTCTCCCTTCTAGTGC 58.591 60.000 0.00 0.00 0.00 4.40
2265 2333 1.289530 ACCTCCCTCTCCCTTCTAGTG 59.710 57.143 0.00 0.00 0.00 2.74
2266 2334 1.289530 CACCTCCCTCTCCCTTCTAGT 59.710 57.143 0.00 0.00 0.00 2.57
2385 2453 0.179070 TATATGTCGCGCCAAAGCCA 60.179 50.000 0.00 0.00 34.57 4.75
2646 2714 1.615392 AGAGCAATTTTGTGGAGCACC 59.385 47.619 0.00 0.00 32.73 5.01
2781 2849 7.594758 CGAAGAAGTTTTGCTAATCCAAAATCA 59.405 33.333 3.75 0.00 43.93 2.57
2861 2929 0.251634 TGTCATTGCATACTCCGGCA 59.748 50.000 0.00 0.00 38.46 5.69
2955 3023 1.270041 GGAGAGAACGATGGATCCAGC 60.270 57.143 20.38 20.38 0.00 4.85
3384 3501 3.107601 AGGACACTACATACTGGCACAT 58.892 45.455 0.00 0.00 38.20 3.21
3415 3532 8.798859 AGATGCTCTATTGTTAAAACTGACAT 57.201 30.769 0.00 0.00 0.00 3.06
3416 3533 8.621532 AAGATGCTCTATTGTTAAAACTGACA 57.378 30.769 0.00 0.00 0.00 3.58
3610 3730 4.261363 CCAAACTTGCTTCTTTCTCCAGTC 60.261 45.833 0.00 0.00 0.00 3.51
3694 3814 2.235155 TCTACCGCATTACCAAGAAGCA 59.765 45.455 0.00 0.00 0.00 3.91
3855 3975 6.707440 TCAAAGATACAACCAAAAAGAGCA 57.293 33.333 0.00 0.00 0.00 4.26
3873 3993 4.813027 ACCAATTATGTGCAGCTTCAAAG 58.187 39.130 0.00 0.00 0.00 2.77
3899 4019 2.102070 AACGCGGAAATACCACATCA 57.898 45.000 12.47 0.00 38.90 3.07
3986 4113 4.322725 CCCCATAAATAGAGCGCACATCTA 60.323 45.833 11.47 8.93 33.93 1.98
4029 4156 8.341173 GGATGCAACATTAATGAAACTAGAGAG 58.659 37.037 22.16 1.02 0.00 3.20
4084 4215 1.204704 TCAGTAAGGACGGCATCAGTG 59.795 52.381 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.