Multiple sequence alignment - TraesCS6D01G287500

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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 TraesCS6D01G287500 chr6D 100.000 8362 0 0 1 8362 396846849 396838488 0.000000e+00 15442.0
1 TraesCS6D01G287500 chr6D 91.543 1348 104 5 2704 4042 441154264 441155610 0.000000e+00 1849.0
2 TraesCS6D01G287500 chr6D 90.456 241 19 4 4038 4276 441281381 441281619 1.750000e-81 315.0
3 TraesCS6D01G287500 chr6B 93.147 4071 210 37 4319 8362 593357166 593353138 0.000000e+00 5908.0
4 TraesCS6D01G287500 chr6B 90.293 2287 152 28 439 2702 593359392 593357153 0.000000e+00 2929.0
5 TraesCS6D01G287500 chr6B 93.166 439 8 5 1 423 593359808 593359376 7.130000e-175 625.0
6 TraesCS6D01G287500 chr6A 96.947 3439 87 12 4319 7742 543209096 543205661 0.000000e+00 5753.0
7 TraesCS6D01G287500 chr6A 91.875 2043 130 18 673 2702 543211102 543209083 0.000000e+00 2820.0
8 TraesCS6D01G287500 chr6A 95.781 474 20 0 7833 8306 543205335 543204862 0.000000e+00 765.0
9 TraesCS6D01G287500 chr6A 82.573 241 28 6 439 665 543211380 543211140 5.120000e-47 200.0
10 TraesCS6D01G287500 chr6A 82.629 213 17 5 230 423 543211575 543211364 4.010000e-38 171.0
11 TraesCS6D01G287500 chr6A 93.421 76 5 0 113 188 543211648 543211573 6.860000e-21 113.0
12 TraesCS6D01G287500 chr6A 96.875 64 2 0 8299 8362 543193706 543193643 3.190000e-19 108.0
13 TraesCS6D01G287500 chr3D 96.351 1617 54 1 2702 4313 537708749 537710365 0.000000e+00 2654.0
14 TraesCS6D01G287500 chr3D 95.565 1601 41 7 2703 4298 282938971 282937396 0.000000e+00 2536.0
15 TraesCS6D01G287500 chr2B 96.543 1591 49 2 2702 4287 178862661 178861072 0.000000e+00 2628.0
16 TraesCS6D01G287500 chr2B 95.578 1583 61 5 2702 4279 32134231 32132653 0.000000e+00 2527.0
17 TraesCS6D01G287500 chr2B 74.542 1037 184 56 4913 5889 57780957 57779941 6.130000e-101 379.0
18 TraesCS6D01G287500 chr2B 77.581 620 106 24 6277 6881 57680589 57679988 2.230000e-90 344.0
19 TraesCS6D01G287500 chr2B 89.437 142 12 2 991 1132 57781625 57781487 8.630000e-40 176.0
20 TraesCS6D01G287500 chr2B 80.455 220 41 2 7156 7374 57679795 57679577 5.190000e-37 167.0
21 TraesCS6D01G287500 chr2B 87.324 142 15 2 991 1132 57682666 57682528 8.690000e-35 159.0
22 TraesCS6D01G287500 chr2B 78.995 219 32 9 7162 7379 57778790 57778585 4.070000e-28 137.0
23 TraesCS6D01G287500 chr2B 96.078 51 2 0 6022 6072 57779798 57779748 5.380000e-12 84.2
24 TraesCS6D01G287500 chr2B 90.323 62 6 0 6011 6072 57680813 57680752 1.930000e-11 82.4
25 TraesCS6D01G287500 chr5D 93.112 1147 66 7 2702 3841 431901722 431900582 0.000000e+00 1668.0
26 TraesCS6D01G287500 chr2D 93.220 1121 52 9 3162 4259 497909241 497910360 0.000000e+00 1628.0
27 TraesCS6D01G287500 chr2D 77.583 629 102 28 6277 6892 35001196 35000594 2.230000e-90 344.0
28 TraesCS6D01G287500 chr2D 72.960 1054 187 59 4916 5889 35002605 35001570 2.300000e-70 278.0
29 TraesCS6D01G287500 chr2D 80.786 229 40 4 7154 7379 35000411 35000184 8.630000e-40 176.0
30 TraesCS6D01G287500 chr2D 88.732 142 13 2 991 1132 35003279 35003141 4.010000e-38 171.0
31 TraesCS6D01G287500 chr2D 73.931 491 81 27 5616 6072 35024300 35023823 4.040000e-33 154.0
32 TraesCS6D01G287500 chr2D 86.765 136 15 2 997 1132 35025735 35025603 1.880000e-31 148.0
33 TraesCS6D01G287500 chr2D 90.323 62 6 0 6011 6072 35001417 35001356 1.930000e-11 82.4
34 TraesCS6D01G287500 chr5B 91.878 1145 79 10 2702 3838 91465014 91466152 0.000000e+00 1587.0
35 TraesCS6D01G287500 chr5B 89.820 167 16 1 3912 4077 663077137 663076971 6.570000e-51 213.0
36 TraesCS6D01G287500 chr3B 91.812 1148 78 8 2702 3841 114203778 114202639 0.000000e+00 1585.0
37 TraesCS6D01G287500 chr3B 83.099 142 23 1 3912 4053 679506760 679506620 2.450000e-25 128.0
38 TraesCS6D01G287500 chr3A 91.790 1145 78 10 2702 3838 710949854 710950990 0.000000e+00 1580.0
39 TraesCS6D01G287500 chr2A 73.036 1031 201 50 4913 5895 38332074 38331073 8.210000e-75 292.0
40 TraesCS6D01G287500 chr2A 78.231 441 70 18 991 1423 38324850 38324428 8.330000e-65 259.0
41 TraesCS6D01G287500 chr2A 88.732 142 13 2 991 1132 38332750 38332612 4.010000e-38 171.0
42 TraesCS6D01G287500 chr2A 79.724 217 30 8 7162 7377 38329929 38329726 2.430000e-30 145.0
43 TraesCS6D01G287500 chr2A 90.476 63 6 0 6011 6073 38322900 38322838 5.380000e-12 84.2
44 TraesCS6D01G287500 chr7A 77.987 477 81 21 6276 6742 8750284 8749822 2.300000e-70 278.0
45 TraesCS6D01G287500 chr7A 72.694 813 151 44 5119 5886 8751380 8750594 1.100000e-48 206.0
46 TraesCS6D01G287500 chr7D 77.453 479 84 19 6272 6742 8292642 8292180 1.790000e-66 265.0
47 TraesCS6D01G287500 chr7D 73.201 806 146 45 5119 5880 8293728 8292949 2.350000e-55 228.0
48 TraesCS6D01G287500 chr4A 76.459 497 87 19 1568 2054 424362204 424362680 8.390000e-60 243.0
49 TraesCS6D01G287500 chr4A 85.652 230 32 1 6272 6500 731421446 731421675 3.020000e-59 241.0
50 TraesCS6D01G287500 chr4B 80.255 157 21 8 4136 4284 598570250 598570404 8.870000e-20 110.0
51 TraesCS6D01G287500 chr4B 100.000 37 0 0 3930 3966 21206979 21207015 1.510000e-07 69.4


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 TraesCS6D01G287500 chr6D 396838488 396846849 8361 True 15442.000000 15442 100.000000 1 8362 1 chr6D.!!$R1 8361
1 TraesCS6D01G287500 chr6D 441154264 441155610 1346 False 1849.000000 1849 91.543000 2704 4042 1 chr6D.!!$F1 1338
2 TraesCS6D01G287500 chr6B 593353138 593359808 6670 True 3154.000000 5908 92.202000 1 8362 3 chr6B.!!$R1 8361
3 TraesCS6D01G287500 chr6A 543204862 543211648 6786 True 1637.000000 5753 90.537667 113 8306 6 chr6A.!!$R2 8193
4 TraesCS6D01G287500 chr3D 537708749 537710365 1616 False 2654.000000 2654 96.351000 2702 4313 1 chr3D.!!$F1 1611
5 TraesCS6D01G287500 chr3D 282937396 282938971 1575 True 2536.000000 2536 95.565000 2703 4298 1 chr3D.!!$R1 1595
6 TraesCS6D01G287500 chr2B 178861072 178862661 1589 True 2628.000000 2628 96.543000 2702 4287 1 chr2B.!!$R2 1585
7 TraesCS6D01G287500 chr2B 32132653 32134231 1578 True 2527.000000 2527 95.578000 2702 4279 1 chr2B.!!$R1 1577
8 TraesCS6D01G287500 chr5D 431900582 431901722 1140 True 1668.000000 1668 93.112000 2702 3841 1 chr5D.!!$R1 1139
9 TraesCS6D01G287500 chr2D 497909241 497910360 1119 False 1628.000000 1628 93.220000 3162 4259 1 chr2D.!!$F1 1097
10 TraesCS6D01G287500 chr2D 35000184 35003279 3095 True 210.280000 344 82.076800 991 7379 5 chr2D.!!$R1 6388
11 TraesCS6D01G287500 chr5B 91465014 91466152 1138 False 1587.000000 1587 91.878000 2702 3838 1 chr5B.!!$F1 1136
12 TraesCS6D01G287500 chr3B 114202639 114203778 1139 True 1585.000000 1585 91.812000 2702 3841 1 chr3B.!!$R1 1139
13 TraesCS6D01G287500 chr3A 710949854 710950990 1136 False 1580.000000 1580 91.790000 2702 3838 1 chr3A.!!$F1 1136
14 TraesCS6D01G287500 chr2A 38329726 38332750 3024 True 202.666667 292 80.497333 991 7377 3 chr2A.!!$R2 6386
15 TraesCS6D01G287500 chr7A 8749822 8751380 1558 True 242.000000 278 75.340500 5119 6742 2 chr7A.!!$R1 1623
16 TraesCS6D01G287500 chr7D 8292180 8293728 1548 True 246.500000 265 75.327000 5119 6742 2 chr7D.!!$R1 1623

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
837 906 0.039617 TCGCCGTTGCCATTTTCTTG 60.040 50.000 0.00 0.00 0.00 3.02 F
947 1017 0.040157 TGCTTGCTTGTTCATGTCGC 60.040 50.000 0.00 0.00 0.00 5.19 F
2287 2407 0.393537 AGTAGGCCAGCATGAGCAAC 60.394 55.000 5.01 0.00 45.49 4.17 F
2338 2458 0.458543 CTAGAAAGGAGCTTGCGCGA 60.459 55.000 12.10 0.00 42.32 5.87 F
3033 3156 0.753111 GAGGCATTCCCATGGACACC 60.753 60.000 15.22 7.22 35.39 4.16 F
3682 3818 2.678336 GAGAAAACTACCCATCTTGCGG 59.322 50.000 0.00 0.00 0.00 5.69 F
4391 4556 2.946329 TCTTTGTAACCGTGCACACAAT 59.054 40.909 18.64 2.07 31.45 2.71 F
5873 6153 9.285770 CTCATGATATTCTTGTTGTTGAATGTG 57.714 33.333 0.00 0.00 35.01 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 1928 0.106769 TTGTCAAGAGCTGGTTGGCA 60.107 50.000 8.32 8.32 37.74 4.92 R
2499 2619 0.110373 GTAGCGCCACAACTTTTCCG 60.110 55.000 2.29 0.00 0.00 4.30 R
3443 3573 2.282603 GTTTGCGGGTGGCCCTAA 60.283 61.111 0.00 0.00 42.67 2.69 R
4108 4270 2.682494 AGATGGTACGGCGTGGGT 60.682 61.111 24.86 5.73 0.00 4.51 R
4112 4274 3.077519 GCTGGAGATGGTACGGCGT 62.078 63.158 19.64 19.64 0.00 5.68 R
4551 4716 4.221703 TCACACCAACAAATGTGGAGTTTT 59.778 37.500 4.66 0.00 45.16 2.43 R
5873 6153 3.258123 ACCATTGGTGATACAAACCTTGC 59.742 43.478 7.76 0.00 38.60 4.01 R
7779 8170 1.005450 TGCATTCTCTTTACCCACCCC 59.995 52.381 0.00 0.00 0.00 4.95 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
61 62 0.963355 TGCCATTTGGGTTCGGTAGC 60.963 55.000 0.00 0.00 39.65 3.58
84 85 0.604780 GCATGCATGCGATCTACCCT 60.605 55.000 33.99 0.00 44.67 4.34
102 103 0.376152 CTTGGATGTCGCATGCTCAC 59.624 55.000 17.13 12.62 0.00 3.51
104 105 1.450134 GGATGTCGCATGCTCACCA 60.450 57.895 17.13 7.00 0.00 4.17
227 230 0.984961 TCAGCCCCATGAGCTTAGCT 60.985 55.000 6.37 6.37 43.88 3.32
228 231 0.761187 CAGCCCCATGAGCTTAGCTA 59.239 55.000 6.75 0.00 39.88 3.32
229 232 1.141657 CAGCCCCATGAGCTTAGCTAA 59.858 52.381 6.75 0.00 39.88 3.09
230 233 1.419387 AGCCCCATGAGCTTAGCTAAG 59.581 52.381 26.20 26.20 39.88 2.18
411 431 4.580167 CCCTCGGAAGAATGAAATAATGCA 59.420 41.667 0.00 0.00 41.32 3.96
412 432 5.506317 CCCTCGGAAGAATGAAATAATGCAC 60.506 44.000 0.00 0.00 41.32 4.57
413 433 5.155509 TCGGAAGAATGAAATAATGCACG 57.844 39.130 0.00 0.00 37.03 5.34
414 434 4.035091 TCGGAAGAATGAAATAATGCACGG 59.965 41.667 0.00 0.00 37.03 4.94
415 435 4.201910 CGGAAGAATGAAATAATGCACGGT 60.202 41.667 0.00 0.00 0.00 4.83
416 436 5.007234 CGGAAGAATGAAATAATGCACGGTA 59.993 40.000 0.00 0.00 0.00 4.02
417 437 6.430451 GGAAGAATGAAATAATGCACGGTAG 58.570 40.000 0.00 0.00 0.00 3.18
418 438 6.038271 GGAAGAATGAAATAATGCACGGTAGT 59.962 38.462 0.00 0.00 0.00 2.73
499 526 2.266055 CCTCAGTGAACGCCCTCC 59.734 66.667 0.00 0.00 0.00 4.30
524 554 3.426323 CTGTTCGATCGAGATCAAACGA 58.574 45.455 18.54 10.86 37.50 3.85
534 564 1.173043 GATCAAACGACATTGGGCCA 58.827 50.000 0.00 0.00 0.00 5.36
593 623 0.250124 TTGGATCAAGCGTGACCGTT 60.250 50.000 3.91 0.00 36.31 4.44
724 791 2.582636 ACCAAATCCCATAGGTGAAGCT 59.417 45.455 0.00 0.00 32.04 3.74
725 792 3.011708 ACCAAATCCCATAGGTGAAGCTT 59.988 43.478 0.00 0.00 32.04 3.74
726 793 3.382546 CCAAATCCCATAGGTGAAGCTTG 59.617 47.826 2.10 0.00 0.00 4.01
727 794 3.303351 AATCCCATAGGTGAAGCTTGG 57.697 47.619 2.10 0.00 0.00 3.61
728 795 0.918983 TCCCATAGGTGAAGCTTGGG 59.081 55.000 2.10 7.48 46.99 4.12
729 796 0.106519 CCCATAGGTGAAGCTTGGGG 60.107 60.000 2.10 10.87 42.79 4.96
802 871 4.190772 CTGCAAAGTGTTTGGAAAATGGT 58.809 39.130 1.80 0.00 40.53 3.55
820 889 1.267532 GGTGAGCGCACATTGTAATCG 60.268 52.381 22.36 0.00 46.96 3.34
821 890 0.373370 TGAGCGCACATTGTAATCGC 59.627 50.000 11.47 17.09 45.34 4.58
837 906 0.039617 TCGCCGTTGCCATTTTCTTG 60.040 50.000 0.00 0.00 0.00 3.02
851 920 7.439056 TGCCATTTTCTTGATCTTGTTTTCTTC 59.561 33.333 0.00 0.00 0.00 2.87
876 945 2.745152 CGTGTTTTGGAGTGGACTTCCT 60.745 50.000 0.00 0.00 36.82 3.36
879 948 3.142174 GTTTTGGAGTGGACTTCCTCTG 58.858 50.000 4.56 0.00 39.71 3.35
881 950 2.992847 TGGAGTGGACTTCCTCTGTA 57.007 50.000 4.56 0.00 39.71 2.74
890 959 3.764972 GGACTTCCTCTGTACTAGTGCTT 59.235 47.826 12.42 0.00 0.00 3.91
919 988 6.987386 AGGACCATTATAAGTCGATCAAGAG 58.013 40.000 0.00 0.00 33.66 2.85
947 1017 0.040157 TGCTTGCTTGTTCATGTCGC 60.040 50.000 0.00 0.00 0.00 5.19
973 1046 6.499350 TGAGGAATACTAACAGTAACAAGGGT 59.501 38.462 0.00 0.00 33.89 4.34
974 1047 7.016858 TGAGGAATACTAACAGTAACAAGGGTT 59.983 37.037 0.00 0.00 41.06 4.11
975 1048 8.439964 AGGAATACTAACAGTAACAAGGGTTA 57.560 34.615 0.00 0.00 38.45 2.85
976 1049 8.883302 AGGAATACTAACAGTAACAAGGGTTAA 58.117 33.333 0.00 0.00 40.95 2.01
1150 1232 5.156608 GGTATACACACATACCCCATACC 57.843 47.826 5.01 0.00 43.19 2.73
1537 1638 1.517276 GTCGAACGTTCATATGAGCCG 59.483 52.381 26.71 19.40 0.00 5.52
1632 1735 6.185511 AGCATGAGGGATACAATCATAATGG 58.814 40.000 0.00 0.00 41.16 3.16
1636 1739 7.640577 TGAGGGATACAATCATAATGGGTAA 57.359 36.000 0.00 0.00 39.74 2.85
1637 1740 7.458397 TGAGGGATACAATCATAATGGGTAAC 58.542 38.462 0.00 0.00 39.74 2.50
1685 1797 1.221466 ACAATCGACACCAGCACACG 61.221 55.000 0.00 0.00 0.00 4.49
1712 1824 3.652274 GCAAAAGATAGCACCAGCAAAA 58.348 40.909 0.00 0.00 45.49 2.44
1800 1918 3.561310 AGCGATTGACGATATGCAACAAT 59.439 39.130 0.00 0.00 45.77 2.71
1810 1928 5.300034 ACGATATGCAACAATGACCATCAAT 59.700 36.000 0.00 0.00 0.00 2.57
1839 1957 2.171448 AGCTCTTGACAACACAAGGACT 59.829 45.455 0.00 0.00 44.84 3.85
1842 1960 4.058817 CTCTTGACAACACAAGGACTACC 58.941 47.826 0.00 0.00 44.84 3.18
1844 1962 3.469008 TGACAACACAAGGACTACCAG 57.531 47.619 0.00 0.00 38.94 4.00
1864 1982 3.985925 CAGCAAGATTCTTTGGAAGCAAC 59.014 43.478 0.00 0.00 39.98 4.17
1872 1990 1.338020 CTTTGGAAGCAACGCCTTTCT 59.662 47.619 0.00 0.00 0.00 2.52
1923 2041 3.181475 TGCCAGATCTAACCATCGAAGAC 60.181 47.826 0.00 0.00 42.51 3.01
1924 2042 3.068873 GCCAGATCTAACCATCGAAGACT 59.931 47.826 0.00 0.00 42.51 3.24
1955 2073 3.818773 GGTTTTCACCCGAAAGATCAAGA 59.181 43.478 0.00 0.00 42.00 3.02
1956 2074 4.459337 GGTTTTCACCCGAAAGATCAAGAT 59.541 41.667 0.00 0.00 42.00 2.40
1957 2075 5.392057 GGTTTTCACCCGAAAGATCAAGATC 60.392 44.000 1.81 1.81 42.00 2.75
1983 2101 1.377725 CTCCAAGCAATGCCCTCGT 60.378 57.895 0.00 0.00 0.00 4.18
2009 2127 3.000022 GCTAACAATCTAAAGACGCCGTC 60.000 47.826 9.71 9.71 0.00 4.79
2015 2133 1.067142 TCTAAAGACGCCGTCATTGCT 60.067 47.619 20.65 0.00 34.60 3.91
2063 2181 1.388837 GGTTTTCACCCGGTGCAAGT 61.389 55.000 13.19 0.00 37.03 3.16
2132 2250 2.063774 CGAGGTTGGGGTGGTAGTT 58.936 57.895 0.00 0.00 0.00 2.24
2181 2299 0.728129 CAACACAAGCTGCTCGCATG 60.728 55.000 1.00 0.00 42.74 4.06
2208 2327 1.672854 GCCACTGCATGCATCACCAT 61.673 55.000 22.97 0.00 37.47 3.55
2287 2407 0.393537 AGTAGGCCAGCATGAGCAAC 60.394 55.000 5.01 0.00 45.49 4.17
2300 2420 0.670162 GAGCAACTGCACCACATGTT 59.330 50.000 4.22 0.00 45.16 2.71
2338 2458 0.458543 CTAGAAAGGAGCTTGCGCGA 60.459 55.000 12.10 0.00 42.32 5.87
2499 2619 2.026822 TGAGATGAGAAAGGGGAGTTGC 60.027 50.000 0.00 0.00 0.00 4.17
2610 2730 7.062022 GCTATACTATTAACCTTGCTCTTACGC 59.938 40.741 0.00 0.00 0.00 4.42
2628 2748 1.230635 GCGTGCCCATATGCTTCGAT 61.231 55.000 0.00 0.00 33.67 3.59
2658 2778 2.103042 GCTGCCTGGTTGCTAGTCG 61.103 63.158 0.00 0.00 0.00 4.18
2677 2797 3.855379 GTCGGCGGGAACAATTTTAAATC 59.145 43.478 7.21 0.00 0.00 2.17
2748 2869 6.623114 GCTGGCATTCATTGATAATAGCAGAG 60.623 42.308 0.00 0.00 0.00 3.35
3001 3124 2.307309 CGCGGCTTCGACTTCACAA 61.307 57.895 0.00 0.00 35.61 3.33
3033 3156 0.753111 GAGGCATTCCCATGGACACC 60.753 60.000 15.22 7.22 35.39 4.16
3682 3818 2.678336 GAGAAAACTACCCATCTTGCGG 59.322 50.000 0.00 0.00 0.00 5.69
3972 4132 4.959596 GATCCTCCGCCTCGCAGC 62.960 72.222 0.00 0.00 0.00 5.25
4259 4421 3.965888 CTAGGTTTTGCTCCTGGCT 57.034 52.632 0.00 0.00 42.39 4.75
4313 4475 4.101448 CCTCCCCGGGTCTGCTTG 62.101 72.222 21.85 1.24 0.00 4.01
4314 4476 4.785453 CTCCCCGGGTCTGCTTGC 62.785 72.222 21.85 0.00 0.00 4.01
4317 4479 4.785453 CCCGGGTCTGCTTGCCTC 62.785 72.222 14.18 0.00 0.00 4.70
4380 4545 7.088272 ACAAGTCTGTGTTTTTCTTTGTAACC 58.912 34.615 0.00 0.00 33.30 2.85
4386 4551 4.030865 GTGTTTTTCTTTGTAACCGTGCAC 59.969 41.667 6.82 6.82 0.00 4.57
4387 4552 4.167268 GTTTTTCTTTGTAACCGTGCACA 58.833 39.130 18.64 0.00 0.00 4.57
4391 4556 2.946329 TCTTTGTAACCGTGCACACAAT 59.054 40.909 18.64 2.07 31.45 2.71
5873 6153 9.285770 CTCATGATATTCTTGTTGTTGAATGTG 57.714 33.333 0.00 0.00 35.01 3.21
5921 6201 1.134175 GTTATGGCCCATTCACAACCG 59.866 52.381 0.00 0.00 0.00 4.44
6216 6562 2.552315 CGCCAACCTTTACAGTGAACAT 59.448 45.455 0.00 0.00 0.00 2.71
6490 6846 5.106038 TGAGATTGCACTATTCTTTTGGCTG 60.106 40.000 0.00 0.00 0.00 4.85
6513 6869 8.290325 GCTGTTGGTAAGAATAATATGCTAACC 58.710 37.037 0.00 0.00 0.00 2.85
6595 6957 7.094334 TGCATAGACTATAAGTTTCCGATCGAT 60.094 37.037 18.66 0.00 0.00 3.59
7106 7475 6.710744 ACCATGTAGGCATTTACTAGCATAAC 59.289 38.462 0.00 0.00 43.14 1.89
7368 7738 4.074970 CTCATTGGTGCAGTAAAGGACTT 58.925 43.478 0.00 0.00 35.64 3.01
7760 8151 5.932303 AGAGCGAAGAATAACAACTAGCAAA 59.068 36.000 0.00 0.00 0.00 3.68
7775 8166 6.426646 ACTAGCAAATAAGTAGGAGATGGG 57.573 41.667 0.00 0.00 0.00 4.00
7776 8167 4.713792 AGCAAATAAGTAGGAGATGGGG 57.286 45.455 0.00 0.00 0.00 4.96
7777 8168 3.395941 AGCAAATAAGTAGGAGATGGGGG 59.604 47.826 0.00 0.00 0.00 5.40
7806 8197 4.892934 TGGGTAAAGAGAATGCAAACACTT 59.107 37.500 0.00 0.00 0.00 3.16
7807 8198 5.362430 TGGGTAAAGAGAATGCAAACACTTT 59.638 36.000 17.25 17.25 33.29 2.66
7821 8212 5.691305 GCAAACACTTTGTGATGCAAGAATA 59.309 36.000 19.52 0.00 43.43 1.75
7822 8213 6.366877 GCAAACACTTTGTGATGCAAGAATAT 59.633 34.615 19.52 0.00 43.43 1.28
7863 8489 6.789959 AGATAGTTGGCAATATCCTAAGTCCT 59.210 38.462 18.05 5.40 0.00 3.85
7888 8514 7.601856 TCATTGACGAAGGCTTCAAAATAAAT 58.398 30.769 25.66 13.02 36.12 1.40
8003 8629 0.692476 TCATCGGGCCCCATATTCAG 59.308 55.000 18.66 0.00 0.00 3.02
8151 8777 1.965754 AAGGCCTCGATCAGAGTGGC 61.966 60.000 5.23 13.46 45.44 5.01
8227 8853 4.219725 TCTTGGAACACATCGTAGTCATCA 59.780 41.667 0.00 0.00 39.29 3.07
8266 8892 4.021104 CCTCAAGCATAGGGATCGTATTCA 60.021 45.833 0.00 0.00 0.00 2.57
8281 8907 4.018779 TCGTATTCAGGGTCTGGGAAAATT 60.019 41.667 0.00 0.00 31.51 1.82
8328 8955 6.243216 TGTACTCCCAAGTAGACAAACTTT 57.757 37.500 0.00 0.00 38.66 2.66
8334 8961 4.499696 CCCAAGTAGACAAACTTTGGCAAG 60.500 45.833 10.08 0.00 42.71 4.01
8354 8981 6.293516 GGCAAGAAAAATGCACATTCAAATGA 60.294 34.615 9.62 0.00 45.60 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 1.442526 GAGCATGCGACATCCAAGGG 61.443 60.000 13.01 0.00 0.00 3.95
84 85 1.026182 GGTGAGCATGCGACATCCAA 61.026 55.000 20.30 0.00 0.00 3.53
102 103 4.518970 CCATTTCGGGGATATACAAGTTGG 59.481 45.833 7.96 0.00 0.00 3.77
104 105 4.142038 GCCATTTCGGGGATATACAAGTT 58.858 43.478 0.00 0.00 34.06 2.66
159 160 1.000506 GGCTGAGTTAGTTCACGTGGA 59.999 52.381 17.00 3.16 0.00 4.02
205 208 0.543277 TAAGCTCATGGGGCTGAGTG 59.457 55.000 13.24 0.00 43.75 3.51
208 211 0.984961 AGCTAAGCTCATGGGGCTGA 60.985 55.000 13.24 6.66 40.19 4.26
227 230 0.966875 TCGCCCGTGTCCTTAGCTTA 60.967 55.000 0.00 0.00 0.00 3.09
228 231 1.614241 ATCGCCCGTGTCCTTAGCTT 61.614 55.000 0.00 0.00 0.00 3.74
229 232 0.754217 TATCGCCCGTGTCCTTAGCT 60.754 55.000 0.00 0.00 0.00 3.32
230 233 0.596859 GTATCGCCCGTGTCCTTAGC 60.597 60.000 0.00 0.00 0.00 3.09
231 234 0.317603 CGTATCGCCCGTGTCCTTAG 60.318 60.000 0.00 0.00 0.00 2.18
426 446 7.062839 GCATTACCGTGCATTGATCTTTAAAAA 59.937 33.333 0.00 0.00 44.43 1.94
427 447 6.529829 GCATTACCGTGCATTGATCTTTAAAA 59.470 34.615 0.00 0.00 44.43 1.52
428 448 6.033341 GCATTACCGTGCATTGATCTTTAAA 58.967 36.000 0.00 0.00 44.43 1.52
429 449 5.577835 GCATTACCGTGCATTGATCTTTAA 58.422 37.500 0.00 0.00 44.43 1.52
430 450 5.168526 GCATTACCGTGCATTGATCTTTA 57.831 39.130 0.00 0.00 44.43 1.85
431 451 4.032703 GCATTACCGTGCATTGATCTTT 57.967 40.909 0.00 0.00 44.43 2.52
432 452 3.698029 GCATTACCGTGCATTGATCTT 57.302 42.857 0.00 0.00 44.43 2.40
499 526 1.066152 TGATCTCGATCGAACAGCTGG 59.934 52.381 19.92 5.59 40.63 4.85
524 554 4.349342 TGGTTTTATTTTCTGGCCCAATGT 59.651 37.500 0.00 0.00 0.00 2.71
534 564 8.743714 GTCCTTGATCATCTGGTTTTATTTTCT 58.256 33.333 0.00 0.00 0.00 2.52
593 623 1.535444 TCGGTCCTGGCCTTCTCAA 60.535 57.895 3.32 0.00 0.00 3.02
665 699 2.690497 CTGGTAGAGATTTCGAGGCTGA 59.310 50.000 0.00 0.00 0.00 4.26
724 791 3.104836 CTATGCCCCCAACCCCAA 58.895 61.111 0.00 0.00 0.00 4.12
725 792 3.749870 GCTATGCCCCCAACCCCA 61.750 66.667 0.00 0.00 0.00 4.96
726 793 4.894896 CGCTATGCCCCCAACCCC 62.895 72.222 0.00 0.00 0.00 4.95
727 794 2.748513 TACGCTATGCCCCCAACCC 61.749 63.158 0.00 0.00 0.00 4.11
728 795 1.525306 GTACGCTATGCCCCCAACC 60.525 63.158 0.00 0.00 0.00 3.77
729 796 0.179029 ATGTACGCTATGCCCCCAAC 60.179 55.000 0.00 0.00 0.00 3.77
802 871 0.373370 GCGATTACAATGTGCGCTCA 59.627 50.000 15.29 15.29 43.85 4.26
820 889 2.094545 AGATCAAGAAAATGGCAACGGC 60.095 45.455 0.00 0.00 42.51 5.68
821 890 3.855689 AGATCAAGAAAATGGCAACGG 57.144 42.857 0.00 0.00 42.51 4.44
837 906 5.169836 ACACGGTTGAAGAAAACAAGATC 57.830 39.130 0.00 0.00 0.00 2.75
851 920 1.064952 GTCCACTCCAAAACACGGTTG 59.935 52.381 0.00 0.00 0.00 3.77
876 945 4.815308 GTCCTCGATAAGCACTAGTACAGA 59.185 45.833 0.00 0.00 0.00 3.41
879 948 3.881688 TGGTCCTCGATAAGCACTAGTAC 59.118 47.826 0.00 0.00 0.00 2.73
881 950 3.014304 TGGTCCTCGATAAGCACTAGT 57.986 47.619 0.00 0.00 0.00 2.57
890 959 6.882678 TGATCGACTTATAATGGTCCTCGATA 59.117 38.462 8.01 0.00 37.82 2.92
919 988 0.957362 ACAAGCAAGCAAGGAGAAGC 59.043 50.000 0.00 0.00 0.00 3.86
947 1017 7.042335 CCCTTGTTACTGTTAGTATTCCTCAG 58.958 42.308 0.00 0.00 29.64 3.35
973 1046 3.308832 CCCCAAGGGTCACTGCTAATTAA 60.309 47.826 4.11 0.00 38.25 1.40
974 1047 2.241176 CCCCAAGGGTCACTGCTAATTA 59.759 50.000 4.11 0.00 38.25 1.40
975 1048 1.005924 CCCCAAGGGTCACTGCTAATT 59.994 52.381 4.11 0.00 38.25 1.40
976 1049 0.625849 CCCCAAGGGTCACTGCTAAT 59.374 55.000 4.11 0.00 38.25 1.73
1026 1102 1.773496 CGTCAACTCGAGCGGTTTC 59.227 57.895 13.61 0.00 0.00 2.78
1029 1105 4.719369 GGCGTCAACTCGAGCGGT 62.719 66.667 13.61 0.00 0.00 5.68
1149 1231 1.069765 CTTCGTCGATGGGATGGGG 59.930 63.158 4.48 0.00 32.24 4.96
1150 1232 1.595382 GCTTCGTCGATGGGATGGG 60.595 63.158 4.48 0.00 32.24 4.00
1300 1389 0.994247 TGAATCCCAGCACCATGAGT 59.006 50.000 0.00 0.00 0.00 3.41
1517 1618 1.517276 CGGCTCATATGAACGTTCGAC 59.483 52.381 22.48 8.93 0.00 4.20
1537 1638 5.574830 GTCTCATGATTCATACGGCTGATAC 59.425 44.000 0.00 0.00 0.00 2.24
1607 1710 6.662234 CCATTATGATTGTATCCCTCATGCTT 59.338 38.462 0.00 0.00 32.20 3.91
1632 1735 2.683859 GCAAAGACCGCGGGTTACC 61.684 63.158 31.76 12.62 35.25 2.85
1636 1739 1.003112 TTATGCAAAGACCGCGGGT 60.003 52.632 31.76 15.52 39.44 5.28
1637 1740 1.024579 AGTTATGCAAAGACCGCGGG 61.025 55.000 31.76 12.50 0.00 6.13
1639 1742 2.536365 TCTAGTTATGCAAAGACCGCG 58.464 47.619 0.00 0.00 0.00 6.46
1640 1743 4.786609 GCATTCTAGTTATGCAAAGACCGC 60.787 45.833 20.32 0.00 45.93 5.68
1665 1769 1.790755 GTGTGCTGGTGTCGATTGTA 58.209 50.000 0.00 0.00 0.00 2.41
1669 1773 2.738521 GCGTGTGCTGGTGTCGAT 60.739 61.111 0.00 0.00 38.39 3.59
1685 1797 3.013439 GCTATCTTTTGCGCGCGC 61.013 61.111 45.02 45.02 42.35 6.86
1687 1799 1.583709 GGTGCTATCTTTTGCGCGC 60.584 57.895 27.26 27.26 40.21 6.86
1701 1813 1.528161 GATGTTGCTTTTTGCTGGTGC 59.472 47.619 0.00 0.00 43.37 5.01
1712 1824 2.420022 GCGGTCTTGTATGATGTTGCTT 59.580 45.455 0.00 0.00 0.00 3.91
1761 1876 3.452474 TCGCTTGTTTGATTGTTTTGGG 58.548 40.909 0.00 0.00 0.00 4.12
1762 1877 5.433855 CAATCGCTTGTTTGATTGTTTTGG 58.566 37.500 6.75 0.00 44.00 3.28
1800 1918 1.548081 CTGGTTGGCATTGATGGTCA 58.452 50.000 0.00 0.00 0.00 4.02
1810 1928 0.106769 TTGTCAAGAGCTGGTTGGCA 60.107 50.000 8.32 8.32 37.74 4.92
1839 1957 3.758554 GCTTCCAAAGAATCTTGCTGGTA 59.241 43.478 12.08 3.91 0.00 3.25
1842 1960 3.928727 TGCTTCCAAAGAATCTTGCTG 57.071 42.857 0.00 0.00 0.00 4.41
1844 1962 2.982470 CGTTGCTTCCAAAGAATCTTGC 59.018 45.455 0.00 0.00 33.05 4.01
1872 1990 0.242825 CTAGCGTGTCGTTCCCTTCA 59.757 55.000 0.00 0.00 0.00 3.02
1923 2041 5.531122 TCGGGTGAAAACCTATGATCTAG 57.469 43.478 0.00 0.00 0.00 2.43
1924 2042 5.943349 TTCGGGTGAAAACCTATGATCTA 57.057 39.130 0.00 0.00 0.00 1.98
1955 2073 1.896220 TTGCTTGGAGTTTGCTCGAT 58.104 45.000 0.00 0.00 42.53 3.59
1956 2074 1.536766 CATTGCTTGGAGTTTGCTCGA 59.463 47.619 0.00 0.00 42.53 4.04
1957 2075 1.973138 CATTGCTTGGAGTTTGCTCG 58.027 50.000 0.00 0.00 42.53 5.03
1983 2101 4.630069 GGCGTCTTTAGATTGTTAGCTTGA 59.370 41.667 0.00 0.00 0.00 3.02
2009 2127 6.183361 ACCCTAGTTGGTTATACCTAGCAATG 60.183 42.308 0.00 0.00 39.58 2.82
2063 2181 0.474466 CATGGCCTCCTATCCCTCCA 60.474 60.000 3.32 0.00 0.00 3.86
2092 2210 2.348998 GCTGGACTCACCACCCTG 59.651 66.667 0.00 0.00 44.64 4.45
2147 2265 3.472652 TGTGTTGTATGGCGTTCTCTTT 58.527 40.909 0.00 0.00 0.00 2.52
2208 2327 3.986996 TCAGTGGAAGATCTTGCATGA 57.013 42.857 29.19 26.30 42.66 3.07
2287 2407 1.089920 GCCTCTAACATGTGGTGCAG 58.910 55.000 0.00 0.00 0.00 4.41
2421 2541 1.074850 TCCGGGGATGATGGCAGTA 60.075 57.895 0.00 0.00 0.00 2.74
2460 2580 0.461548 CATCGCTGCTAGAGGAACCA 59.538 55.000 0.00 0.00 0.00 3.67
2499 2619 0.110373 GTAGCGCCACAACTTTTCCG 60.110 55.000 2.29 0.00 0.00 4.30
2610 2730 1.229428 AATCGAAGCATATGGGCACG 58.771 50.000 4.56 2.15 37.25 5.34
2658 2778 4.180817 CTGGATTTAAAATTGTTCCCGCC 58.819 43.478 2.99 0.00 0.00 6.13
2748 2869 1.404035 ACCTTGTTGTTTCCGTTGCTC 59.596 47.619 0.00 0.00 0.00 4.26
3033 3156 2.052690 TCGGCTCTTCTTCTCCGGG 61.053 63.158 0.00 0.00 41.98 5.73
3443 3573 2.282603 GTTTGCGGGTGGCCCTAA 60.283 61.111 0.00 0.00 42.67 2.69
3749 3885 4.783621 GTGCAGATCTGGCGGGCA 62.784 66.667 23.89 12.46 0.00 5.36
4108 4270 2.682494 AGATGGTACGGCGTGGGT 60.682 61.111 24.86 5.73 0.00 4.51
4112 4274 3.077519 GCTGGAGATGGTACGGCGT 62.078 63.158 19.64 19.64 0.00 5.68
4313 4475 8.982091 AATTCCTACCTTAGAAATAAAGAGGC 57.018 34.615 0.00 0.00 0.00 4.70
4386 4551 4.494690 CGCTCCTGTAATTGTGCTATTGTG 60.495 45.833 0.00 0.00 0.00 3.33
4387 4552 3.623060 CGCTCCTGTAATTGTGCTATTGT 59.377 43.478 0.00 0.00 0.00 2.71
4391 4556 3.259064 GTTCGCTCCTGTAATTGTGCTA 58.741 45.455 0.00 0.00 0.00 3.49
4551 4716 4.221703 TCACACCAACAAATGTGGAGTTTT 59.778 37.500 4.66 0.00 45.16 2.43
5754 6017 9.643693 GAAATTATCAAAATTCCTGCTTCAGAA 57.356 29.630 0.00 0.00 32.44 3.02
5873 6153 3.258123 ACCATTGGTGATACAAACCTTGC 59.742 43.478 7.76 0.00 38.60 4.01
6120 6465 7.838079 AAAGGCTTGGCAATATTATGTATCA 57.162 32.000 0.00 0.00 0.00 2.15
6490 6846 8.784043 CCTGGTTAGCATATTATTCTTACCAAC 58.216 37.037 12.92 0.00 38.53 3.77
6513 6869 2.624838 AGTCAGTTTGATTTGGTGCCTG 59.375 45.455 0.00 0.00 0.00 4.85
6595 6957 8.740123 TTGGACTAACTTTGAAGATAACAACA 57.260 30.769 0.00 0.00 0.00 3.33
6722 7085 6.961360 ATGATACCTTATGACAACTCGAGA 57.039 37.500 21.68 0.00 0.00 4.04
7106 7475 5.983540 AGAGATTGAGGGCAGTTAGTTAAG 58.016 41.667 0.00 0.00 0.00 1.85
7640 8031 8.107095 TGCCAACATTAAACCTAGAAGTAGAAT 58.893 33.333 0.00 0.00 0.00 2.40
7778 8169 1.685180 GCATTCTCTTTACCCACCCCC 60.685 57.143 0.00 0.00 0.00 5.40
7779 8170 1.005450 TGCATTCTCTTTACCCACCCC 59.995 52.381 0.00 0.00 0.00 4.95
7780 8171 2.507407 TGCATTCTCTTTACCCACCC 57.493 50.000 0.00 0.00 0.00 4.61
7781 8172 3.572255 TGTTTGCATTCTCTTTACCCACC 59.428 43.478 0.00 0.00 0.00 4.61
7782 8173 4.278419 AGTGTTTGCATTCTCTTTACCCAC 59.722 41.667 0.00 0.00 0.00 4.61
7783 8174 4.469657 AGTGTTTGCATTCTCTTTACCCA 58.530 39.130 0.00 0.00 0.00 4.51
7863 8489 6.567687 TTATTTTGAAGCCTTCGTCAATGA 57.432 33.333 0.00 0.00 39.68 2.57
7888 8514 5.208294 AGGGATCTTGTACTCCTAGAACA 57.792 43.478 0.00 0.00 0.00 3.18
8060 8686 7.277098 TCAACTTCCTCGCTATTGTTGTAATAC 59.723 37.037 0.00 0.00 36.93 1.89
8151 8777 7.041780 ACTGTTATGCTTCCGCTTATTCTATTG 60.042 37.037 0.00 0.00 36.97 1.90
8227 8853 4.338879 CTTGAGGGGATGTCATTGAGTTT 58.661 43.478 0.00 0.00 0.00 2.66
8262 8888 4.089361 GTCAATTTTCCCAGACCCTGAAT 58.911 43.478 0.00 0.00 32.44 2.57
8266 8892 3.500343 CTTGTCAATTTTCCCAGACCCT 58.500 45.455 0.00 0.00 0.00 4.34
8281 8907 3.769739 ATGTACTCACTTGGCTTGTCA 57.230 42.857 0.00 0.00 0.00 3.58
8316 8943 7.621102 CATTTTTCTTGCCAAAGTTTGTCTAC 58.379 34.615 14.36 2.19 34.78 2.59
8317 8944 6.257630 GCATTTTTCTTGCCAAAGTTTGTCTA 59.742 34.615 14.36 0.00 34.78 2.59
8328 8955 4.069300 TGAATGTGCATTTTTCTTGCCA 57.931 36.364 0.00 0.00 39.39 4.92
8334 8961 6.081693 GCCTTCATTTGAATGTGCATTTTTC 58.918 36.000 0.00 0.00 37.65 2.29


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

AutoCloner maintained by Alex Coulton.