Multiple sequence alignment - TraesCS6D01G192500

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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 TraesCS6D01G192500 chr6D 100.000 4278 0 0 1 4278 266448032 266443755 0.000000e+00 7901.0
1 TraesCS6D01G192500 chr6B 93.929 3706 120 38 371 4043 413955684 413952051 0.000000e+00 5500.0
2 TraesCS6D01G192500 chr6B 86.614 381 35 13 11 379 413956833 413956457 1.430000e-109 407.0
3 TraesCS6D01G192500 chr6A 95.646 2251 64 17 1810 4041 377864905 377862670 0.000000e+00 3583.0
4 TraesCS6D01G192500 chr6A 88.313 1891 88 40 1 1814 377866701 377864867 0.000000e+00 2145.0
5 TraesCS6D01G192500 chr4D 84.316 1001 103 30 1337 2317 364581163 364582129 0.000000e+00 929.0
6 TraesCS6D01G192500 chr3B 83.733 1002 109 31 1337 2317 229500563 229501531 0.000000e+00 898.0
7 TraesCS6D01G192500 chr5B 82.717 1001 106 33 1337 2317 579152033 579152986 0.000000e+00 828.0
8 TraesCS6D01G192500 chr2B 76.331 169 26 10 4051 4210 734326390 734326553 1.280000e-10 78.7
9 TraesCS6D01G192500 chr2B 89.286 56 6 0 4051 4106 236097637 236097582 2.130000e-08 71.3
10 TraesCS6D01G192500 chr1B 85.714 70 7 2 4051 4117 667540335 667540266 2.130000e-08 71.3


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 TraesCS6D01G192500 chr6D 266443755 266448032 4277 True 7901.0 7901 100.0000 1 4278 1 chr6D.!!$R1 4277
1 TraesCS6D01G192500 chr6B 413952051 413956833 4782 True 2953.5 5500 90.2715 11 4043 2 chr6B.!!$R1 4032
2 TraesCS6D01G192500 chr6A 377862670 377866701 4031 True 2864.0 3583 91.9795 1 4041 2 chr6A.!!$R1 4040
3 TraesCS6D01G192500 chr4D 364581163 364582129 966 False 929.0 929 84.3160 1337 2317 1 chr4D.!!$F1 980
4 TraesCS6D01G192500 chr3B 229500563 229501531 968 False 898.0 898 83.7330 1337 2317 1 chr3B.!!$F1 980
5 TraesCS6D01G192500 chr5B 579152033 579152986 953 False 828.0 828 82.7170 1337 2317 1 chr5B.!!$F1 980

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
37 38 0.179108 GGACCGCTATGAGGTGTGTC 60.179 60.0 0.00 0.00 43.01 3.67 F
1313 2152 0.104120 CCACCAATATCACGCTCCGA 59.896 55.0 0.00 0.00 0.00 4.55 F
1686 2558 0.250295 TGCAGCTTGCTCTTACCGTT 60.250 50.0 9.12 0.00 45.31 4.44 F
1782 2657 0.734889 GCCATGGTTGATCTTCCACG 59.265 55.0 14.67 4.24 36.50 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 2630 1.747355 GATCAACCATGGCAGGAACAG 59.253 52.381 13.04 0.0 0.00 3.16 R
2388 3304 0.449388 GCAGAGGTTTGCCATCGAAG 59.551 55.000 0.00 0.0 38.13 3.79 R
2947 3863 0.460987 CCGCCAGAAGGTCATCAGTC 60.461 60.000 0.00 0.0 37.19 3.51 R
3503 4419 1.070758 GAGACTCAGGTTGGAAGCACA 59.929 52.381 0.00 0.0 0.00 4.57 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
26 27 1.274167 ACATTTTCTGACGGACCGCTA 59.726 47.619 15.39 1.65 0.00 4.26
34 35 1.664321 GACGGACCGCTATGAGGTGT 61.664 60.000 15.39 0.00 43.01 4.16
37 38 0.179108 GGACCGCTATGAGGTGTGTC 60.179 60.000 0.00 0.00 43.01 3.67
49 50 1.376609 GGTGTGTCGGATTCCATGCC 61.377 60.000 3.09 0.00 0.00 4.40
55 56 2.092158 TGTCGGATTCCATGCCCAAATA 60.092 45.455 3.09 0.00 0.00 1.40
111 112 5.107220 ACGACTAAATGCTTCGTTTTGTAGG 60.107 40.000 0.00 4.46 43.23 3.18
130 131 0.603569 GCTCCCTTGAGAGTGAACGA 59.396 55.000 0.00 0.00 41.42 3.85
141 142 1.257155 GAGTGAACGAACGCGAACTTT 59.743 47.619 15.93 5.89 41.64 2.66
201 213 5.467035 TGTCAAATTCTGCTTTTTAGGGG 57.533 39.130 0.00 0.00 0.00 4.79
203 215 5.010617 TGTCAAATTCTGCTTTTTAGGGGTC 59.989 40.000 0.00 0.00 0.00 4.46
313 330 4.286032 CCCCCTCGGAATAGAATATGACAA 59.714 45.833 0.00 0.00 0.00 3.18
358 375 3.817148 GGATACTGCTCTACTCGTAGC 57.183 52.381 0.00 0.00 39.25 3.58
385 1186 4.081697 CCCAGTATTACCTTTTTGCAAGGG 60.082 45.833 7.81 10.06 41.71 3.95
524 1330 2.878406 CACGAGGACAAACAAAGACCAT 59.122 45.455 0.00 0.00 0.00 3.55
535 1341 5.659440 AACAAAGACCATCTCTCTCTCTC 57.341 43.478 0.00 0.00 0.00 3.20
536 1342 4.934356 ACAAAGACCATCTCTCTCTCTCT 58.066 43.478 0.00 0.00 0.00 3.10
538 1344 5.195940 CAAAGACCATCTCTCTCTCTCTCT 58.804 45.833 0.00 0.00 0.00 3.10
644 1458 2.175715 GTTCCCATAATCCCCTTGCTCT 59.824 50.000 0.00 0.00 0.00 4.09
664 1478 1.002274 GCCTCCTCCTCCTCCTCAA 59.998 63.158 0.00 0.00 0.00 3.02
721 1535 0.725117 GTCCGCAACCCTCGTATTTG 59.275 55.000 0.00 0.00 0.00 2.32
808 1627 3.628032 TGTCGACAACAAACAATTAGCCA 59.372 39.130 17.62 0.00 34.03 4.75
810 1629 4.439776 GTCGACAACAAACAATTAGCCAAC 59.560 41.667 11.55 0.00 0.00 3.77
1141 1966 3.858868 TTCTCACACCGCGTGGCTC 62.859 63.158 16.69 0.00 46.36 4.70
1310 2149 1.134521 TCCACCACCAATATCACGCTC 60.135 52.381 0.00 0.00 0.00 5.03
1311 2150 1.299541 CACCACCAATATCACGCTCC 58.700 55.000 0.00 0.00 0.00 4.70
1312 2151 0.179084 ACCACCAATATCACGCTCCG 60.179 55.000 0.00 0.00 0.00 4.63
1313 2152 0.104120 CCACCAATATCACGCTCCGA 59.896 55.000 0.00 0.00 0.00 4.55
1315 2154 2.029380 CCACCAATATCACGCTCCGATA 60.029 50.000 0.00 0.00 0.00 2.92
1351 2197 2.095718 CGGCAGGTTTCTGTTTTAGAGC 60.096 50.000 0.00 0.00 42.78 4.09
1442 2288 4.527038 TCTTTGATCTGTTTCGGTCCTACT 59.473 41.667 0.00 0.00 0.00 2.57
1682 2553 3.487574 CGTAGTATGCAGCTTGCTCTTAC 59.512 47.826 1.94 8.22 45.31 2.34
1686 2558 0.250295 TGCAGCTTGCTCTTACCGTT 60.250 50.000 9.12 0.00 45.31 4.44
1698 2570 6.582636 TGCTCTTACCGTTGATCTGAATTAT 58.417 36.000 0.00 0.00 0.00 1.28
1755 2630 9.620660 AAATAAACACAAATCGACTTGAATACC 57.379 29.630 14.37 0.00 0.00 2.73
1781 2656 1.747355 CTGCCATGGTTGATCTTCCAC 59.253 52.381 14.67 0.00 36.50 4.02
1782 2657 0.734889 GCCATGGTTGATCTTCCACG 59.265 55.000 14.67 4.24 36.50 4.94
1783 2658 1.678728 GCCATGGTTGATCTTCCACGA 60.679 52.381 14.67 0.00 36.50 4.35
1784 2659 2.283298 CCATGGTTGATCTTCCACGAG 58.717 52.381 2.57 5.58 36.50 4.18
1785 2660 2.355108 CCATGGTTGATCTTCCACGAGT 60.355 50.000 2.57 0.00 36.50 4.18
1786 2661 3.118775 CCATGGTTGATCTTCCACGAGTA 60.119 47.826 2.57 0.00 36.50 2.59
1787 2662 4.503910 CATGGTTGATCTTCCACGAGTAA 58.496 43.478 10.65 0.00 36.50 2.24
1788 2663 4.819105 TGGTTGATCTTCCACGAGTAAT 57.181 40.909 5.56 0.00 0.00 1.89
1789 2664 4.503910 TGGTTGATCTTCCACGAGTAATG 58.496 43.478 5.56 0.00 0.00 1.90
1790 2665 4.221924 TGGTTGATCTTCCACGAGTAATGA 59.778 41.667 5.56 0.00 0.00 2.57
1791 2666 4.567159 GGTTGATCTTCCACGAGTAATGAC 59.433 45.833 0.00 0.00 0.00 3.06
1792 2667 5.168569 GTTGATCTTCCACGAGTAATGACA 58.831 41.667 0.00 0.00 0.00 3.58
1793 2668 5.598416 TGATCTTCCACGAGTAATGACAT 57.402 39.130 0.00 0.00 0.00 3.06
1794 2669 6.709018 TGATCTTCCACGAGTAATGACATA 57.291 37.500 0.00 0.00 0.00 2.29
1795 2670 7.107639 TGATCTTCCACGAGTAATGACATAA 57.892 36.000 0.00 0.00 0.00 1.90
1796 2671 6.978659 TGATCTTCCACGAGTAATGACATAAC 59.021 38.462 0.00 0.00 0.00 1.89
1797 2672 6.275494 TCTTCCACGAGTAATGACATAACA 57.725 37.500 0.00 0.00 0.00 2.41
1798 2673 6.873997 TCTTCCACGAGTAATGACATAACAT 58.126 36.000 0.00 0.00 0.00 2.71
1799 2674 7.327975 TCTTCCACGAGTAATGACATAACATT 58.672 34.615 0.00 0.00 42.17 2.71
1800 2675 6.902224 TCCACGAGTAATGACATAACATTG 57.098 37.500 0.00 0.00 40.15 2.82
1801 2676 6.635755 TCCACGAGTAATGACATAACATTGA 58.364 36.000 0.00 0.00 40.15 2.57
1802 2677 7.272244 TCCACGAGTAATGACATAACATTGAT 58.728 34.615 0.00 0.00 40.15 2.57
1803 2678 7.768582 TCCACGAGTAATGACATAACATTGATT 59.231 33.333 0.00 0.00 40.15 2.57
1804 2679 8.397906 CCACGAGTAATGACATAACATTGATTT 58.602 33.333 0.00 0.00 40.15 2.17
1805 2680 9.773328 CACGAGTAATGACATAACATTGATTTT 57.227 29.630 0.00 0.00 40.15 1.82
1806 2681 9.773328 ACGAGTAATGACATAACATTGATTTTG 57.227 29.630 0.00 0.00 40.15 2.44
1807 2682 9.773328 CGAGTAATGACATAACATTGATTTTGT 57.227 29.630 0.00 0.00 40.15 2.83
1809 2684 9.357652 AGTAATGACATAACATTGATTTTGTGC 57.642 29.630 0.00 0.00 40.15 4.57
1810 2685 9.357652 GTAATGACATAACATTGATTTTGTGCT 57.642 29.630 0.00 0.00 40.15 4.40
1811 2686 8.836268 AATGACATAACATTGATTTTGTGCTT 57.164 26.923 0.00 0.00 38.76 3.91
1812 2687 7.872163 TGACATAACATTGATTTTGTGCTTC 57.128 32.000 0.00 0.00 0.00 3.86
1813 2688 6.867816 TGACATAACATTGATTTTGTGCTTCC 59.132 34.615 0.00 0.00 0.00 3.46
1814 2689 6.757237 ACATAACATTGATTTTGTGCTTCCA 58.243 32.000 0.00 0.00 0.00 3.53
2020 2932 6.787085 AGTTAGTTAAATCAGTGTGTGCTC 57.213 37.500 0.00 0.00 0.00 4.26
2097 3013 7.480760 AGATGGGTGTTTACTTGCATATTTT 57.519 32.000 0.00 0.00 0.00 1.82
2131 3047 2.595124 TCGTGCTTCTTGTGACTTCA 57.405 45.000 0.00 0.00 0.00 3.02
2284 3200 6.545666 TGATTGGTGTGCCGATTATAATCTTT 59.454 34.615 20.47 0.00 38.98 2.52
2388 3304 7.497249 ACTTCCTCACTACTATCATGAAAATGC 59.503 37.037 0.00 0.00 0.00 3.56
2494 3410 4.541779 ACGAGCTCGACATTCTTGATATC 58.458 43.478 40.58 0.00 43.02 1.63
2860 3776 6.418946 TCAGCTGAAGAACTATCTCTACTCA 58.581 40.000 15.67 0.00 33.77 3.41
2953 3869 0.469917 CCCATTACCGGCAGACTGAT 59.530 55.000 6.65 0.00 0.00 2.90
2965 3881 0.534412 AGACTGATGACCTTCTGGCG 59.466 55.000 0.00 0.00 36.63 5.69
2971 3887 1.949847 ATGACCTTCTGGCGGACTCG 61.950 60.000 0.00 0.00 36.63 4.18
3282 4198 2.225394 TGAGAGAAAGTGGGTAGCCTCT 60.225 50.000 13.11 11.33 34.11 3.69
3284 4200 1.208293 GAGAAAGTGGGTAGCCTCTGG 59.792 57.143 15.85 0.00 0.00 3.86
3297 4213 1.547372 GCCTCTGGTGTTTGCATCAAT 59.453 47.619 0.00 0.00 34.97 2.57
3501 4417 3.788227 TTTTGGAAGAGGAGCTTAGCA 57.212 42.857 7.07 0.00 36.83 3.49
3502 4418 3.788227 TTTGGAAGAGGAGCTTAGCAA 57.212 42.857 7.07 0.00 36.83 3.91
3503 4419 4.307032 TTTGGAAGAGGAGCTTAGCAAT 57.693 40.909 7.07 0.00 36.83 3.56
3504 4420 3.272574 TGGAAGAGGAGCTTAGCAATG 57.727 47.619 7.07 0.00 36.83 2.82
3505 4421 2.573462 TGGAAGAGGAGCTTAGCAATGT 59.427 45.455 7.07 0.00 36.83 2.71
3506 4422 2.941720 GGAAGAGGAGCTTAGCAATGTG 59.058 50.000 7.07 0.00 36.83 3.21
3507 4423 2.035530 AGAGGAGCTTAGCAATGTGC 57.964 50.000 7.07 0.00 45.46 4.57
3620 4538 3.058983 CGCAGCAGTTTCTCATTGTTACA 60.059 43.478 0.00 0.00 0.00 2.41
3691 4612 0.717784 CTGCAGTACATGTGCACTCG 59.282 55.000 19.41 11.37 45.96 4.18
3714 4635 1.001641 GTTCATGTCCTGCCTGCCT 60.002 57.895 0.00 0.00 0.00 4.75
3715 4636 1.028868 GTTCATGTCCTGCCTGCCTC 61.029 60.000 0.00 0.00 0.00 4.70
3716 4637 2.513204 CATGTCCTGCCTGCCTCG 60.513 66.667 0.00 0.00 0.00 4.63
3775 4703 8.375506 AGTGTCTTAATCCTCTTAACATGTGAA 58.624 33.333 0.00 0.00 0.00 3.18
3862 4794 4.204012 CAGTCACAGGTTTCCTTGGTAAA 58.796 43.478 0.00 0.00 0.00 2.01
3988 4920 2.668550 GGCTGTCCGTGTGGGTTC 60.669 66.667 0.00 0.00 37.00 3.62
4070 5002 4.776647 GCGCGCCGGCTGAAAAAT 62.777 61.111 26.68 0.00 36.88 1.82
4071 5003 2.576847 CGCGCCGGCTGAAAAATC 60.577 61.111 26.68 3.29 36.88 2.17
4072 5004 2.576847 GCGCCGGCTGAAAAATCG 60.577 61.111 26.68 6.32 35.83 3.34
4073 5005 2.100216 CGCCGGCTGAAAAATCGG 59.900 61.111 26.68 0.00 44.70 4.18
4075 5007 2.100216 CCGGCTGAAAAATCGGCG 59.900 61.111 0.00 0.00 42.62 6.46
4076 5008 2.686816 CCGGCTGAAAAATCGGCGT 61.687 57.895 6.85 0.00 43.95 5.68
4077 5009 1.511887 CGGCTGAAAAATCGGCGTG 60.512 57.895 6.85 0.00 42.62 5.34
4078 5010 1.154035 GGCTGAAAAATCGGCGTGG 60.154 57.895 6.85 0.00 42.62 4.94
4079 5011 1.154035 GCTGAAAAATCGGCGTGGG 60.154 57.895 6.85 0.00 31.87 4.61
4080 5012 1.154035 CTGAAAAATCGGCGTGGGC 60.154 57.895 6.85 0.00 38.90 5.36
4092 5024 3.861263 GTGGGCGCGATCGGTTTC 61.861 66.667 18.30 0.00 35.95 2.78
4096 5028 3.564027 GCGCGATCGGTTTCCCAG 61.564 66.667 18.30 0.00 35.95 4.45
4097 5029 3.564027 CGCGATCGGTTTCCCAGC 61.564 66.667 18.30 0.00 0.00 4.85
4098 5030 3.202706 GCGATCGGTTTCCCAGCC 61.203 66.667 18.30 0.00 0.00 4.85
4100 5032 3.202706 GATCGGTTTCCCAGCCGC 61.203 66.667 0.00 0.00 46.79 6.53
4101 5033 3.682292 GATCGGTTTCCCAGCCGCT 62.682 63.158 0.00 0.00 46.79 5.52
4102 5034 3.976701 ATCGGTTTCCCAGCCGCTG 62.977 63.158 13.82 13.82 46.79 5.18
4117 5049 3.384532 CTGCCCAGGCGCCATTTT 61.385 61.111 31.54 4.11 45.51 1.82
4118 5050 2.921972 TGCCCAGGCGCCATTTTT 60.922 55.556 31.54 3.61 45.51 1.94
4119 5051 1.603236 CTGCCCAGGCGCCATTTTTA 61.603 55.000 31.54 9.21 45.51 1.52
4120 5052 1.188219 TGCCCAGGCGCCATTTTTAA 61.188 50.000 31.54 4.51 45.51 1.52
4121 5053 0.036858 GCCCAGGCGCCATTTTTAAA 60.037 50.000 31.54 0.00 0.00 1.52
4122 5054 1.609320 GCCCAGGCGCCATTTTTAAAA 60.609 47.619 31.54 0.00 0.00 1.52
4123 5055 2.345876 CCCAGGCGCCATTTTTAAAAG 58.654 47.619 31.54 3.76 0.00 2.27
4124 5056 2.289382 CCCAGGCGCCATTTTTAAAAGT 60.289 45.455 31.54 0.00 0.00 2.66
4125 5057 3.398406 CCAGGCGCCATTTTTAAAAGTT 58.602 40.909 31.54 0.00 0.00 2.66
4126 5058 3.812609 CCAGGCGCCATTTTTAAAAGTTT 59.187 39.130 31.54 0.00 0.00 2.66
4127 5059 4.274705 CCAGGCGCCATTTTTAAAAGTTTT 59.725 37.500 31.54 6.06 0.00 2.43
4128 5060 5.220951 CCAGGCGCCATTTTTAAAAGTTTTT 60.221 36.000 31.54 0.00 0.00 1.94
4151 5083 8.664211 TTTTTAAAACATACTCGGCCAAAATT 57.336 26.923 2.24 0.00 0.00 1.82
4152 5084 8.664211 TTTTAAAACATACTCGGCCAAAATTT 57.336 26.923 2.24 0.00 0.00 1.82
4153 5085 7.644986 TTAAAACATACTCGGCCAAAATTTG 57.355 32.000 2.24 0.00 0.00 2.32
4165 5097 4.550577 CCAAAATTTGGCCAAACAAGAC 57.449 40.909 32.62 0.00 45.17 3.01
4166 5098 3.944015 CCAAAATTTGGCCAAACAAGACA 59.056 39.130 32.62 9.87 45.17 3.41
4167 5099 4.201901 CCAAAATTTGGCCAAACAAGACAC 60.202 41.667 32.62 0.00 45.17 3.67
4168 5100 3.902881 AATTTGGCCAAACAAGACACA 57.097 38.095 32.62 8.22 32.51 3.72
4169 5101 2.957491 TTTGGCCAAACAAGACACAG 57.043 45.000 27.13 0.00 0.00 3.66
4170 5102 2.136298 TTGGCCAAACAAGACACAGA 57.864 45.000 17.98 0.00 0.00 3.41
4171 5103 2.136298 TGGCCAAACAAGACACAGAA 57.864 45.000 0.61 0.00 0.00 3.02
4172 5104 2.665165 TGGCCAAACAAGACACAGAAT 58.335 42.857 0.61 0.00 0.00 2.40
4173 5105 3.030291 TGGCCAAACAAGACACAGAATT 58.970 40.909 0.61 0.00 0.00 2.17
4174 5106 3.068024 TGGCCAAACAAGACACAGAATTC 59.932 43.478 0.61 0.00 0.00 2.17
4175 5107 3.300009 GCCAAACAAGACACAGAATTCG 58.700 45.455 0.00 0.00 0.00 3.34
4176 5108 3.853307 GCCAAACAAGACACAGAATTCGG 60.853 47.826 3.87 3.87 0.00 4.30
4177 5109 3.300009 CAAACAAGACACAGAATTCGGC 58.700 45.455 5.43 0.00 0.00 5.54
4178 5110 2.254546 ACAAGACACAGAATTCGGCA 57.745 45.000 5.43 0.00 0.00 5.69
4179 5111 2.571212 ACAAGACACAGAATTCGGCAA 58.429 42.857 5.43 0.00 0.00 4.52
4180 5112 2.948979 ACAAGACACAGAATTCGGCAAA 59.051 40.909 5.43 0.00 0.00 3.68
4181 5113 3.380004 ACAAGACACAGAATTCGGCAAAA 59.620 39.130 5.43 0.00 0.00 2.44
4182 5114 4.037923 ACAAGACACAGAATTCGGCAAAAT 59.962 37.500 5.43 0.00 0.00 1.82
4183 5115 4.853924 AGACACAGAATTCGGCAAAATT 57.146 36.364 5.43 0.00 0.00 1.82
4184 5116 5.200368 AGACACAGAATTCGGCAAAATTT 57.800 34.783 5.43 0.00 0.00 1.82
4185 5117 6.325919 AGACACAGAATTCGGCAAAATTTA 57.674 33.333 5.43 0.00 0.00 1.40
4186 5118 6.744112 AGACACAGAATTCGGCAAAATTTAA 58.256 32.000 5.43 0.00 0.00 1.52
4187 5119 6.863126 AGACACAGAATTCGGCAAAATTTAAG 59.137 34.615 5.43 0.00 0.00 1.85
4188 5120 5.405269 ACACAGAATTCGGCAAAATTTAAGC 59.595 36.000 5.43 6.93 0.00 3.09
4189 5121 4.621034 ACAGAATTCGGCAAAATTTAAGCG 59.379 37.500 5.43 5.65 0.00 4.68
4190 5122 4.621034 CAGAATTCGGCAAAATTTAAGCGT 59.379 37.500 0.00 0.00 0.00 5.07
4191 5123 5.118510 CAGAATTCGGCAAAATTTAAGCGTT 59.881 36.000 0.00 3.12 0.00 4.84
4192 5124 5.344933 AGAATTCGGCAAAATTTAAGCGTTC 59.655 36.000 0.00 9.67 0.00 3.95
4193 5125 2.936316 TCGGCAAAATTTAAGCGTTCC 58.064 42.857 8.81 0.00 0.00 3.62
4194 5126 2.293677 TCGGCAAAATTTAAGCGTTCCA 59.706 40.909 8.81 0.00 0.00 3.53
4195 5127 3.057174 TCGGCAAAATTTAAGCGTTCCAT 60.057 39.130 8.81 0.00 0.00 3.41
4196 5128 3.303229 CGGCAAAATTTAAGCGTTCCATC 59.697 43.478 8.81 0.00 0.00 3.51
4197 5129 3.303229 GGCAAAATTTAAGCGTTCCATCG 59.697 43.478 8.81 0.00 0.00 3.84
4259 5191 5.607119 AAAAACAATCACTACTAGTGCCG 57.393 39.130 5.39 4.98 45.54 5.69
4260 5192 2.295253 ACAATCACTACTAGTGCCGC 57.705 50.000 5.39 0.00 45.54 6.53
4261 5193 1.134788 ACAATCACTACTAGTGCCGCC 60.135 52.381 5.39 0.00 45.54 6.13
4262 5194 0.464452 AATCACTACTAGTGCCGCCC 59.536 55.000 5.39 0.00 45.54 6.13
4263 5195 1.735376 ATCACTACTAGTGCCGCCCG 61.735 60.000 5.39 0.00 45.54 6.13
4264 5196 3.834799 ACTACTAGTGCCGCCCGC 61.835 66.667 5.39 0.00 38.31 6.13
4265 5197 4.587189 CTACTAGTGCCGCCCGCC 62.587 72.222 5.39 0.00 36.24 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.070783 GCGGTCCGTCAGAAAATGTTA 58.929 47.619 13.94 0.00 0.00 2.41
8 9 2.167693 TCATAGCGGTCCGTCAGAAAAT 59.832 45.455 13.94 0.00 0.00 1.82
18 19 0.179108 GACACACCTCATAGCGGTCC 60.179 60.000 0.00 0.00 30.82 4.46
26 27 1.275666 TGGAATCCGACACACCTCAT 58.724 50.000 0.00 0.00 0.00 2.90
34 35 0.038890 TTTGGGCATGGAATCCGACA 59.961 50.000 0.00 0.00 0.00 4.35
37 38 3.156293 TGATATTTGGGCATGGAATCCG 58.844 45.455 0.00 0.00 0.00 4.18
76 77 2.144833 TTTAGTCGTTCGCTCGGGCA 62.145 55.000 8.62 0.00 38.60 5.36
111 112 0.603569 TCGTTCACTCTCAAGGGAGC 59.396 55.000 0.00 0.00 41.13 4.70
151 163 9.895138 GGTCTTATAACCACTTGTTTAGGATTA 57.105 33.333 0.00 0.00 39.27 1.75
176 188 5.870978 CCCTAAAAAGCAGAATTTGACATGG 59.129 40.000 0.00 0.00 0.00 3.66
250 267 5.877564 ACAAAAACACCAGGTAACCAAAATG 59.122 36.000 0.00 0.00 37.17 2.32
251 268 6.056090 ACAAAAACACCAGGTAACCAAAAT 57.944 33.333 0.00 0.00 37.17 1.82
256 273 5.045215 GCTTTACAAAAACACCAGGTAACC 58.955 41.667 0.00 0.00 37.17 2.85
259 276 3.637694 GGGCTTTACAAAAACACCAGGTA 59.362 43.478 0.00 0.00 0.00 3.08
262 279 4.400529 AAGGGCTTTACAAAAACACCAG 57.599 40.909 0.00 0.00 0.00 4.00
313 330 2.132762 CCGTGTTTCGCTACTTGAACT 58.867 47.619 0.00 0.00 38.35 3.01
323 340 1.859080 GTATCCTCATCCGTGTTTCGC 59.141 52.381 0.00 0.00 38.35 4.70
324 341 3.116300 CAGTATCCTCATCCGTGTTTCG 58.884 50.000 0.00 0.00 39.52 3.46
358 375 4.764823 TGCAAAAAGGTAATACTGGGACTG 59.235 41.667 0.00 0.00 0.00 3.51
385 1186 7.921214 ACGATTTCCTTTCTTTTCTTTTCCTTC 59.079 33.333 0.00 0.00 0.00 3.46
524 1330 3.711704 GGGAAGAGAGAGAGAGAGAGAGA 59.288 52.174 0.00 0.00 0.00 3.10
535 1341 0.251634 GGCACAAGGGGAAGAGAGAG 59.748 60.000 0.00 0.00 0.00 3.20
536 1342 0.473694 TGGCACAAGGGGAAGAGAGA 60.474 55.000 0.00 0.00 31.92 3.10
538 1344 2.069776 CTGGCACAAGGGGAAGAGA 58.930 57.895 0.00 0.00 38.70 3.10
644 1458 1.002274 GAGGAGGAGGAGGAGGCAA 59.998 63.158 0.00 0.00 0.00 4.52
664 1478 0.824759 AGCGGAAAGGAATAGCGAGT 59.175 50.000 0.00 0.00 0.00 4.18
706 1520 0.179200 CGTGCAAATACGAGGGTTGC 60.179 55.000 9.72 9.72 46.46 4.17
721 1535 0.236187 TGTTGTGCGGAAATACGTGC 59.764 50.000 0.00 0.00 35.98 5.34
808 1627 2.446994 TGGTGTCCTCGGGGTGTT 60.447 61.111 0.00 0.00 0.00 3.32
810 1629 4.394712 GCTGGTGTCCTCGGGGTG 62.395 72.222 0.00 0.00 0.00 4.61
1110 1935 3.594134 GTGTGAGAAAGGGACAGATCTG 58.406 50.000 21.37 21.37 0.00 2.90
1141 1966 3.493350 CCAGGTAATCAATCCACCGAGAG 60.493 52.174 0.00 0.00 37.42 3.20
1310 2149 5.944049 CCGACGGAATAACAATATATCGG 57.056 43.478 8.64 0.00 40.44 4.18
1311 2150 4.860352 TGCCGACGGAATAACAATATATCG 59.140 41.667 20.50 0.00 0.00 2.92
1312 2151 5.291128 CCTGCCGACGGAATAACAATATATC 59.709 44.000 20.50 0.00 0.00 1.63
1313 2152 5.175859 CCTGCCGACGGAATAACAATATAT 58.824 41.667 20.50 0.00 0.00 0.86
1315 2154 3.181458 ACCTGCCGACGGAATAACAATAT 60.181 43.478 20.50 0.00 0.00 1.28
1351 2197 3.005554 AGGCAAATCTCATCGACACTTG 58.994 45.455 0.00 0.00 0.00 3.16
1682 2553 4.813161 AGACAGCATAATTCAGATCAACGG 59.187 41.667 0.00 0.00 0.00 4.44
1686 2558 6.475596 TCAGAGACAGCATAATTCAGATCA 57.524 37.500 0.00 0.00 0.00 2.92
1698 2570 8.097038 ACTATACAAAGAAAATCAGAGACAGCA 58.903 33.333 0.00 0.00 0.00 4.41
1755 2630 1.747355 GATCAACCATGGCAGGAACAG 59.253 52.381 13.04 0.00 0.00 3.16
1781 2656 9.773328 ACAAAATCAATGTTATGTCATTACTCG 57.227 29.630 3.80 0.00 36.44 4.18
1783 2658 9.357652 GCACAAAATCAATGTTATGTCATTACT 57.642 29.630 3.80 0.00 36.44 2.24
1784 2659 9.357652 AGCACAAAATCAATGTTATGTCATTAC 57.642 29.630 0.00 0.00 36.44 1.89
1785 2660 9.926158 AAGCACAAAATCAATGTTATGTCATTA 57.074 25.926 0.00 0.00 36.44 1.90
1786 2661 8.836268 AAGCACAAAATCAATGTTATGTCATT 57.164 26.923 0.00 0.00 38.38 2.57
1787 2662 7.546667 GGAAGCACAAAATCAATGTTATGTCAT 59.453 33.333 0.00 0.00 0.00 3.06
1788 2663 6.867816 GGAAGCACAAAATCAATGTTATGTCA 59.132 34.615 0.00 0.00 0.00 3.58
1789 2664 6.867816 TGGAAGCACAAAATCAATGTTATGTC 59.132 34.615 0.00 0.00 0.00 3.06
1790 2665 6.757237 TGGAAGCACAAAATCAATGTTATGT 58.243 32.000 0.00 0.00 0.00 2.29
1791 2666 7.546316 TCATGGAAGCACAAAATCAATGTTATG 59.454 33.333 0.00 0.00 0.00 1.90
1792 2667 7.613585 TCATGGAAGCACAAAATCAATGTTAT 58.386 30.769 0.00 0.00 0.00 1.89
1793 2668 6.990798 TCATGGAAGCACAAAATCAATGTTA 58.009 32.000 0.00 0.00 0.00 2.41
1794 2669 5.856156 TCATGGAAGCACAAAATCAATGTT 58.144 33.333 0.00 0.00 0.00 2.71
1795 2670 5.011329 ACTCATGGAAGCACAAAATCAATGT 59.989 36.000 0.00 0.00 0.00 2.71
1796 2671 5.475719 ACTCATGGAAGCACAAAATCAATG 58.524 37.500 0.00 0.00 0.00 2.82
1797 2672 5.733620 ACTCATGGAAGCACAAAATCAAT 57.266 34.783 0.00 0.00 0.00 2.57
1798 2673 6.647334 TTACTCATGGAAGCACAAAATCAA 57.353 33.333 0.00 0.00 0.00 2.57
1799 2674 6.839124 ATTACTCATGGAAGCACAAAATCA 57.161 33.333 0.00 0.00 0.00 2.57
1800 2675 9.241317 CATTATTACTCATGGAAGCACAAAATC 57.759 33.333 0.00 0.00 0.00 2.17
1801 2676 8.752187 ACATTATTACTCATGGAAGCACAAAAT 58.248 29.630 0.00 0.00 0.00 1.82
1802 2677 8.121305 ACATTATTACTCATGGAAGCACAAAA 57.879 30.769 0.00 0.00 0.00 2.44
1803 2678 7.701539 ACATTATTACTCATGGAAGCACAAA 57.298 32.000 0.00 0.00 0.00 2.83
1804 2679 8.673711 GTTACATTATTACTCATGGAAGCACAA 58.326 33.333 0.00 0.00 0.00 3.33
1805 2680 7.826744 TGTTACATTATTACTCATGGAAGCACA 59.173 33.333 0.00 0.00 0.00 4.57
1806 2681 8.208718 TGTTACATTATTACTCATGGAAGCAC 57.791 34.615 0.00 0.00 0.00 4.40
1807 2682 8.978874 ATGTTACATTATTACTCATGGAAGCA 57.021 30.769 0.00 0.00 0.00 3.91
1808 2683 9.669353 CAATGTTACATTATTACTCATGGAAGC 57.331 33.333 10.46 0.00 0.00 3.86
1938 2850 4.260620 GCTTACGGTGTATTGCATAACTGG 60.261 45.833 0.00 0.00 0.00 4.00
2020 2932 3.879295 CTGTACAAACTGCAGGGATATGG 59.121 47.826 19.93 2.58 0.00 2.74
2097 3013 4.305989 AGCACGAAATTGAGCTGAAAAA 57.694 36.364 0.00 0.00 34.40 1.94
2102 3018 3.231965 CAAGAAGCACGAAATTGAGCTG 58.768 45.455 0.00 0.00 35.90 4.24
2131 3047 4.401022 TGTGAGAAATCACTCAGGCAATT 58.599 39.130 9.57 0.00 45.67 2.32
2284 3200 5.565455 TCTGGCCATGAACATATATGACA 57.435 39.130 19.63 17.05 0.00 3.58
2388 3304 0.449388 GCAGAGGTTTGCCATCGAAG 59.551 55.000 0.00 0.00 38.13 3.79
2821 3737 3.443037 CAGCTGAAGGTGAAGTATCTCG 58.557 50.000 8.42 0.00 45.66 4.04
2947 3863 0.460987 CCGCCAGAAGGTCATCAGTC 60.461 60.000 0.00 0.00 37.19 3.51
2953 3869 2.636412 CGAGTCCGCCAGAAGGTCA 61.636 63.158 0.00 0.00 37.19 4.02
2965 3881 4.394712 CAGTGCCACCCCGAGTCC 62.395 72.222 0.00 0.00 0.00 3.85
2971 3887 4.982701 AAGCTGCAGTGCCACCCC 62.983 66.667 16.64 0.00 0.00 4.95
3282 4198 5.918426 ATCACATATTGATGCAAACACCA 57.082 34.783 0.00 0.00 43.87 4.17
3501 4417 2.107204 AGACTCAGGTTGGAAGCACATT 59.893 45.455 0.00 0.00 0.00 2.71
3502 4418 1.701847 AGACTCAGGTTGGAAGCACAT 59.298 47.619 0.00 0.00 0.00 3.21
3503 4419 1.070758 GAGACTCAGGTTGGAAGCACA 59.929 52.381 0.00 0.00 0.00 4.57
3504 4420 1.346068 AGAGACTCAGGTTGGAAGCAC 59.654 52.381 5.02 0.00 0.00 4.40
3505 4421 1.722034 AGAGACTCAGGTTGGAAGCA 58.278 50.000 5.02 0.00 0.00 3.91
3506 4422 2.224402 ACAAGAGACTCAGGTTGGAAGC 60.224 50.000 5.02 0.00 0.00 3.86
3507 4423 3.760580 ACAAGAGACTCAGGTTGGAAG 57.239 47.619 5.02 0.00 0.00 3.46
3508 4424 3.454447 TCAACAAGAGACTCAGGTTGGAA 59.546 43.478 26.01 13.80 39.33 3.53
3509 4425 3.038280 TCAACAAGAGACTCAGGTTGGA 58.962 45.455 26.01 16.35 39.33 3.53
3510 4426 3.475566 TCAACAAGAGACTCAGGTTGG 57.524 47.619 26.01 15.02 39.33 3.77
3511 4427 5.059161 TGAATCAACAAGAGACTCAGGTTG 58.941 41.667 23.09 23.09 40.00 3.77
3512 4428 5.296151 TGAATCAACAAGAGACTCAGGTT 57.704 39.130 5.02 5.64 0.00 3.50
3691 4612 1.678970 GGCAGGACATGAACCCACC 60.679 63.158 0.00 3.51 0.00 4.61
3723 4648 2.225791 GAAAAACGGATGGCCCCTGC 62.226 60.000 0.00 0.00 0.00 4.85
3862 4794 1.380302 CCTGCAGCAAACCTACCCT 59.620 57.895 8.66 0.00 0.00 4.34
3874 4806 3.131046 GGATTACCCAAATCAACCTGCAG 59.869 47.826 6.78 6.78 45.05 4.41
4053 4985 4.776647 ATTTTTCAGCCGGCGCGC 62.777 61.111 25.94 25.94 41.18 6.86
4054 4986 2.576847 GATTTTTCAGCCGGCGCG 60.577 61.111 23.20 17.14 41.18 6.86
4055 4987 2.576847 CGATTTTTCAGCCGGCGC 60.577 61.111 23.20 0.00 0.00 6.53
4056 4988 2.100216 CCGATTTTTCAGCCGGCG 59.900 61.111 23.20 16.49 35.29 6.46
4058 4990 2.100216 CGCCGATTTTTCAGCCGG 59.900 61.111 0.00 0.00 44.34 6.13
4059 4991 1.511887 CACGCCGATTTTTCAGCCG 60.512 57.895 0.00 0.00 0.00 5.52
4060 4992 1.154035 CCACGCCGATTTTTCAGCC 60.154 57.895 0.00 0.00 0.00 4.85
4061 4993 1.154035 CCCACGCCGATTTTTCAGC 60.154 57.895 0.00 0.00 0.00 4.26
4062 4994 1.154035 GCCCACGCCGATTTTTCAG 60.154 57.895 0.00 0.00 0.00 3.02
4063 4995 2.958576 GCCCACGCCGATTTTTCA 59.041 55.556 0.00 0.00 0.00 2.69
4064 4996 2.202427 CGCCCACGCCGATTTTTC 60.202 61.111 0.00 0.00 0.00 2.29
4075 5007 3.861263 GAAACCGATCGCGCCCAC 61.861 66.667 10.32 0.00 35.83 4.61
4102 5034 0.036858 TTTAAAAATGGCGCCTGGGC 60.037 50.000 29.70 0.00 42.69 5.36
4103 5035 2.289382 ACTTTTAAAAATGGCGCCTGGG 60.289 45.455 29.70 8.04 0.00 4.45
4104 5036 3.038788 ACTTTTAAAAATGGCGCCTGG 57.961 42.857 29.70 7.44 0.00 4.45
4105 5037 5.416862 AAAACTTTTAAAAATGGCGCCTG 57.583 34.783 29.70 6.96 0.00 4.85
4126 5058 8.664211 AATTTTGGCCGAGTATGTTTTAAAAA 57.336 26.923 1.31 0.00 0.00 1.94
4127 5059 8.552034 CAAATTTTGGCCGAGTATGTTTTAAAA 58.448 29.630 0.00 0.00 0.00 1.52
4128 5060 7.171678 CCAAATTTTGGCCGAGTATGTTTTAAA 59.828 33.333 14.96 0.00 45.17 1.52
4129 5061 6.647067 CCAAATTTTGGCCGAGTATGTTTTAA 59.353 34.615 14.96 0.00 45.17 1.52
4130 5062 6.159988 CCAAATTTTGGCCGAGTATGTTTTA 58.840 36.000 14.96 0.00 45.17 1.52
4131 5063 4.994217 CCAAATTTTGGCCGAGTATGTTTT 59.006 37.500 14.96 0.00 45.17 2.43
4132 5064 4.565022 CCAAATTTTGGCCGAGTATGTTT 58.435 39.130 14.96 0.00 45.17 2.83
4133 5065 4.186856 CCAAATTTTGGCCGAGTATGTT 57.813 40.909 14.96 0.00 45.17 2.71
4134 5066 3.866883 CCAAATTTTGGCCGAGTATGT 57.133 42.857 14.96 0.00 45.17 2.29
4145 5077 4.394300 TGTGTCTTGTTTGGCCAAATTTTG 59.606 37.500 32.52 21.48 32.36 2.44
4146 5078 4.583871 TGTGTCTTGTTTGGCCAAATTTT 58.416 34.783 32.52 0.00 32.36 1.82
4147 5079 4.081198 TCTGTGTCTTGTTTGGCCAAATTT 60.081 37.500 32.52 0.00 32.36 1.82
4148 5080 3.450457 TCTGTGTCTTGTTTGGCCAAATT 59.550 39.130 32.52 0.00 32.36 1.82
4149 5081 3.030291 TCTGTGTCTTGTTTGGCCAAAT 58.970 40.909 32.52 0.00 32.36 2.32
4150 5082 2.451490 TCTGTGTCTTGTTTGGCCAAA 58.549 42.857 27.13 27.13 0.00 3.28
4151 5083 2.136298 TCTGTGTCTTGTTTGGCCAA 57.864 45.000 16.05 16.05 0.00 4.52
4152 5084 2.136298 TTCTGTGTCTTGTTTGGCCA 57.864 45.000 0.00 0.00 0.00 5.36
4153 5085 3.642705 GAATTCTGTGTCTTGTTTGGCC 58.357 45.455 0.00 0.00 0.00 5.36
4154 5086 3.300009 CGAATTCTGTGTCTTGTTTGGC 58.700 45.455 3.52 0.00 0.00 4.52
4155 5087 3.853307 GCCGAATTCTGTGTCTTGTTTGG 60.853 47.826 3.52 0.00 0.00 3.28
4156 5088 3.243035 TGCCGAATTCTGTGTCTTGTTTG 60.243 43.478 3.52 0.00 0.00 2.93
4157 5089 2.948979 TGCCGAATTCTGTGTCTTGTTT 59.051 40.909 3.52 0.00 0.00 2.83
4158 5090 2.571212 TGCCGAATTCTGTGTCTTGTT 58.429 42.857 3.52 0.00 0.00 2.83
4159 5091 2.254546 TGCCGAATTCTGTGTCTTGT 57.745 45.000 3.52 0.00 0.00 3.16
4160 5092 3.624326 TTTGCCGAATTCTGTGTCTTG 57.376 42.857 3.52 0.00 0.00 3.02
4161 5093 4.853924 ATTTTGCCGAATTCTGTGTCTT 57.146 36.364 3.52 0.00 0.00 3.01
4162 5094 4.853924 AATTTTGCCGAATTCTGTGTCT 57.146 36.364 3.52 0.00 0.00 3.41
4163 5095 6.399986 GCTTAAATTTTGCCGAATTCTGTGTC 60.400 38.462 3.52 0.00 0.00 3.67
4164 5096 5.405269 GCTTAAATTTTGCCGAATTCTGTGT 59.595 36.000 3.52 0.00 0.00 3.72
4165 5097 5.443170 CGCTTAAATTTTGCCGAATTCTGTG 60.443 40.000 3.52 0.00 0.00 3.66
4166 5098 4.621034 CGCTTAAATTTTGCCGAATTCTGT 59.379 37.500 3.52 0.00 0.00 3.41
4167 5099 4.621034 ACGCTTAAATTTTGCCGAATTCTG 59.379 37.500 3.52 0.00 0.00 3.02
4168 5100 4.805219 ACGCTTAAATTTTGCCGAATTCT 58.195 34.783 3.52 0.00 0.00 2.40
4169 5101 5.444087 GGAACGCTTAAATTTTGCCGAATTC 60.444 40.000 0.00 0.00 0.00 2.17
4170 5102 4.387559 GGAACGCTTAAATTTTGCCGAATT 59.612 37.500 0.00 0.00 0.00 2.17
4171 5103 3.924073 GGAACGCTTAAATTTTGCCGAAT 59.076 39.130 0.00 0.00 0.00 3.34
4172 5104 3.243434 TGGAACGCTTAAATTTTGCCGAA 60.243 39.130 0.00 0.00 0.00 4.30
4173 5105 2.293677 TGGAACGCTTAAATTTTGCCGA 59.706 40.909 0.00 0.00 0.00 5.54
4174 5106 2.667137 TGGAACGCTTAAATTTTGCCG 58.333 42.857 0.00 0.00 0.00 5.69
4175 5107 3.303229 CGATGGAACGCTTAAATTTTGCC 59.697 43.478 0.00 0.00 0.00 4.52
4176 5108 4.483977 CGATGGAACGCTTAAATTTTGC 57.516 40.909 0.00 0.79 0.00 3.68
4247 5179 3.834799 GCGGGCGGCACTAGTAGT 61.835 66.667 12.47 0.00 42.87 2.73
4248 5180 4.587189 GGCGGGCGGCACTAGTAG 62.587 72.222 19.08 0.00 46.16 2.57


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

AutoCloner maintained by Alex Coulton.