Multiple sequence alignment - TraesCS6D01G118000

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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 TraesCS6D01G118000 chr6D 100.000 4220 0 0 1 4220 83539491 83543710 0.000000e+00 7793.0
1 TraesCS6D01G118000 chr6D 93.032 2741 167 6 1057 3795 83124785 83122067 0.000000e+00 3982.0
2 TraesCS6D01G118000 chr6D 86.667 2190 267 17 1063 3242 83057981 83055807 0.000000e+00 2403.0
3 TraesCS6D01G118000 chr6D 85.976 2132 278 19 1120 3242 83046859 83044740 0.000000e+00 2261.0
4 TraesCS6D01G118000 chr6D 93.726 1036 46 11 396 1419 83827238 83828266 0.000000e+00 1535.0
5 TraesCS6D01G118000 chr6D 88.595 605 39 11 3617 4217 84028491 84029069 0.000000e+00 708.0
6 TraesCS6D01G118000 chr6D 87.084 511 44 10 3536 4031 83104994 83104491 3.690000e-155 558.0
7 TraesCS6D01G118000 chr6D 90.294 340 19 4 510 836 83126095 83125757 2.330000e-117 433.0
8 TraesCS6D01G118000 chr6D 84.682 346 23 13 81 400 83820755 83821096 6.810000e-83 318.0
9 TraesCS6D01G118000 chr6D 84.034 238 20 11 444 669 83125091 83124860 3.310000e-51 213.0
10 TraesCS6D01G118000 chr6B 95.770 3333 116 13 510 3823 159401454 159404780 0.000000e+00 5350.0
11 TraesCS6D01G118000 chr6B 92.857 2940 202 4 1057 3993 158149854 158146920 0.000000e+00 4259.0
12 TraesCS6D01G118000 chr6B 85.675 2178 287 16 1063 3230 158103940 158101778 0.000000e+00 2270.0
13 TraesCS6D01G118000 chr6B 87.480 631 54 13 3588 4213 159574162 159574772 0.000000e+00 704.0
14 TraesCS6D01G118000 chr6B 96.059 406 13 1 3812 4217 159597188 159597590 0.000000e+00 658.0
15 TraesCS6D01G118000 chr6B 90.030 331 26 4 223 547 159401128 159401457 5.040000e-114 422.0
16 TraesCS6D01G118000 chr6B 89.527 296 18 3 510 793 158151143 158150849 3.100000e-96 363.0
17 TraesCS6D01G118000 chr6B 84.549 233 18 10 449 669 158150155 158149929 9.190000e-52 215.0
18 TraesCS6D01G118000 chr6B 93.600 125 5 2 81 205 159400950 159401071 2.590000e-42 183.0
19 TraesCS6D01G118000 chr6A 95.020 3032 126 10 865 3889 100802795 100805808 0.000000e+00 4739.0
20 TraesCS6D01G118000 chr6A 96.635 2556 78 7 865 3413 100760726 100763280 0.000000e+00 4237.0
21 TraesCS6D01G118000 chr6A 92.224 2842 188 16 1057 3895 100185143 100182332 0.000000e+00 3993.0
22 TraesCS6D01G118000 chr6A 85.714 602 53 13 3438 4030 100763260 100763837 4.670000e-169 604.0
23 TraesCS6D01G118000 chr6A 85.382 602 55 12 3438 4030 100809897 100810474 1.010000e-165 593.0
24 TraesCS6D01G118000 chr6A 85.211 568 42 17 510 1063 100186411 100185872 2.870000e-151 545.0
25 TraesCS6D01G118000 chr6A 92.330 339 13 3 510 836 100760390 100760727 1.780000e-128 470.0
26 TraesCS6D01G118000 chr6A 89.676 339 14 4 510 836 100802467 100802796 3.040000e-111 412.0
27 TraesCS6D01G118000 chr6A 87.283 346 35 3 206 547 100760053 100760393 1.840000e-103 387.0
28 TraesCS6D01G118000 chr6A 88.146 329 32 4 223 547 100802145 100802470 6.620000e-103 385.0
29 TraesCS6D01G118000 chr6A 85.377 212 16 8 444 643 100185393 100185185 5.530000e-49 206.0
30 TraesCS6D01G118000 chr6A 85.350 157 9 4 3883 4030 100808337 100808488 2.630000e-32 150.0
31 TraesCS6D01G118000 chr5D 88.235 85 8 2 1 83 527178561 527178477 2.680000e-17 100.0
32 TraesCS6D01G118000 chr5B 93.478 46 3 0 41 86 621593809 621593854 7.570000e-08 69.4
33 TraesCS6D01G118000 chr1B 81.395 86 10 5 1 82 486776061 486776144 9.790000e-07 65.8


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 TraesCS6D01G118000 chr6D 83539491 83543710 4219 False 7793.000000 7793 100.000000 1 4220 1 chr6D.!!$F1 4219
1 TraesCS6D01G118000 chr6D 83055807 83057981 2174 True 2403.000000 2403 86.667000 1063 3242 1 chr6D.!!$R2 2179
2 TraesCS6D01G118000 chr6D 83044740 83046859 2119 True 2261.000000 2261 85.976000 1120 3242 1 chr6D.!!$R1 2122
3 TraesCS6D01G118000 chr6D 83122067 83126095 4028 True 1542.666667 3982 89.120000 444 3795 3 chr6D.!!$R4 3351
4 TraesCS6D01G118000 chr6D 83827238 83828266 1028 False 1535.000000 1535 93.726000 396 1419 1 chr6D.!!$F3 1023
5 TraesCS6D01G118000 chr6D 84028491 84029069 578 False 708.000000 708 88.595000 3617 4217 1 chr6D.!!$F4 600
6 TraesCS6D01G118000 chr6D 83104491 83104994 503 True 558.000000 558 87.084000 3536 4031 1 chr6D.!!$R3 495
7 TraesCS6D01G118000 chr6B 158101778 158103940 2162 True 2270.000000 2270 85.675000 1063 3230 1 chr6B.!!$R1 2167
8 TraesCS6D01G118000 chr6B 159400950 159404780 3830 False 1985.000000 5350 93.133333 81 3823 3 chr6B.!!$F3 3742
9 TraesCS6D01G118000 chr6B 158146920 158151143 4223 True 1612.333333 4259 88.977667 449 3993 3 chr6B.!!$R2 3544
10 TraesCS6D01G118000 chr6B 159574162 159574772 610 False 704.000000 704 87.480000 3588 4213 1 chr6B.!!$F1 625
11 TraesCS6D01G118000 chr6A 100182332 100186411 4079 True 1581.333333 3993 87.604000 444 3895 3 chr6A.!!$R1 3451
12 TraesCS6D01G118000 chr6A 100760053 100763837 3784 False 1424.500000 4237 90.490500 206 4030 4 chr6A.!!$F1 3824
13 TraesCS6D01G118000 chr6A 100802145 100810474 8329 False 1255.800000 4739 88.714800 223 4030 5 chr6A.!!$F2 3807

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
21 22 0.109458 TGCTCGCGGGCGTAATATAG 60.109 55.000 28.15 2.75 40.74 1.31 F
22 23 0.169672 GCTCGCGGGCGTAATATAGA 59.830 55.000 18.60 0.00 40.74 1.98 F
64 65 0.456628 GAGGCGAGACTACCAACTCC 59.543 60.000 0.00 0.00 0.00 3.85 F
1084 1343 0.935831 CACAACACCATGCAGCAACG 60.936 55.000 0.00 0.00 0.00 4.10 F
1621 2651 1.347707 TGATGAAGAGCCTGGTCGTTT 59.652 47.619 0.00 0.00 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 2765 2.166459 CTGAGCAATTACCGAGTCCTGA 59.834 50.000 0.00 0.0 0.00 3.86 R
1961 2992 2.765699 AGCTCCTCCAATCTCTTCAGAC 59.234 50.000 0.00 0.0 0.00 3.51 R
2495 3526 4.540359 TTGCCTTGCAAAAATAGCATCT 57.460 36.364 0.00 0.0 45.96 2.90 R
2697 3728 1.130561 GGCGTGAGGTATTGCAGAAAC 59.869 52.381 0.00 0.0 0.00 2.78 R
3719 4763 0.034337 TTAGTGCTTCCTCGGCGTTT 59.966 50.000 6.85 0.0 0.00 3.60 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
17 18 2.661866 GATGCTCGCGGGCGTAAT 60.662 61.111 28.42 14.83 40.74 1.89
18 19 1.372499 GATGCTCGCGGGCGTAATA 60.372 57.895 28.42 8.35 40.74 0.98
19 20 0.736325 GATGCTCGCGGGCGTAATAT 60.736 55.000 28.42 13.93 40.74 1.28
20 21 0.528924 ATGCTCGCGGGCGTAATATA 59.471 50.000 27.17 5.40 40.74 0.86
21 22 0.109458 TGCTCGCGGGCGTAATATAG 60.109 55.000 28.15 2.75 40.74 1.31
22 23 0.169672 GCTCGCGGGCGTAATATAGA 59.830 55.000 18.60 0.00 40.74 1.98
23 24 1.794437 GCTCGCGGGCGTAATATAGAG 60.794 57.143 18.60 0.00 40.74 2.43
24 25 1.467734 CTCGCGGGCGTAATATAGAGT 59.532 52.381 13.21 0.00 40.74 3.24
25 26 1.881973 TCGCGGGCGTAATATAGAGTT 59.118 47.619 13.21 0.00 40.74 3.01
26 27 2.294233 TCGCGGGCGTAATATAGAGTTT 59.706 45.455 13.21 0.00 40.74 2.66
27 28 2.407361 CGCGGGCGTAATATAGAGTTTG 59.593 50.000 4.64 0.00 34.35 2.93
28 29 2.157085 GCGGGCGTAATATAGAGTTTGC 59.843 50.000 0.00 0.00 0.00 3.68
29 30 2.735134 CGGGCGTAATATAGAGTTTGCC 59.265 50.000 0.00 0.00 40.48 4.52
30 31 3.735591 GGGCGTAATATAGAGTTTGCCA 58.264 45.455 2.07 0.00 42.95 4.92
31 32 4.131596 GGGCGTAATATAGAGTTTGCCAA 58.868 43.478 2.07 0.00 42.95 4.52
32 33 4.213482 GGGCGTAATATAGAGTTTGCCAAG 59.787 45.833 2.07 0.00 42.95 3.61
33 34 4.213482 GGCGTAATATAGAGTTTGCCAAGG 59.787 45.833 0.00 0.00 40.88 3.61
34 35 4.213482 GCGTAATATAGAGTTTGCCAAGGG 59.787 45.833 0.00 0.00 0.00 3.95
35 36 5.607477 CGTAATATAGAGTTTGCCAAGGGA 58.393 41.667 0.00 0.00 0.00 4.20
36 37 6.231211 CGTAATATAGAGTTTGCCAAGGGAT 58.769 40.000 0.00 0.00 0.00 3.85
37 38 7.383687 CGTAATATAGAGTTTGCCAAGGGATA 58.616 38.462 0.00 0.00 0.00 2.59
38 39 7.876068 CGTAATATAGAGTTTGCCAAGGGATAA 59.124 37.037 0.00 0.00 0.00 1.75
39 40 9.740710 GTAATATAGAGTTTGCCAAGGGATAAT 57.259 33.333 0.00 0.00 0.00 1.28
40 41 8.641498 AATATAGAGTTTGCCAAGGGATAATG 57.359 34.615 0.00 0.00 0.00 1.90
41 42 3.635591 AGAGTTTGCCAAGGGATAATGG 58.364 45.455 0.00 0.00 0.00 3.16
42 43 3.269381 AGAGTTTGCCAAGGGATAATGGA 59.731 43.478 0.00 0.00 0.00 3.41
43 44 4.023291 GAGTTTGCCAAGGGATAATGGAA 58.977 43.478 0.00 0.00 0.00 3.53
44 45 4.623863 AGTTTGCCAAGGGATAATGGAAT 58.376 39.130 0.00 0.00 0.00 3.01
45 46 4.406649 AGTTTGCCAAGGGATAATGGAATG 59.593 41.667 0.00 0.00 0.00 2.67
46 47 3.969466 TGCCAAGGGATAATGGAATGA 57.031 42.857 0.00 0.00 0.00 2.57
47 48 3.836146 TGCCAAGGGATAATGGAATGAG 58.164 45.455 0.00 0.00 0.00 2.90
48 49 3.160269 GCCAAGGGATAATGGAATGAGG 58.840 50.000 0.00 0.00 0.00 3.86
49 50 3.160269 CCAAGGGATAATGGAATGAGGC 58.840 50.000 0.00 0.00 0.00 4.70
50 51 2.816087 CAAGGGATAATGGAATGAGGCG 59.184 50.000 0.00 0.00 0.00 5.52
51 52 2.338809 AGGGATAATGGAATGAGGCGA 58.661 47.619 0.00 0.00 0.00 5.54
52 53 2.304180 AGGGATAATGGAATGAGGCGAG 59.696 50.000 0.00 0.00 0.00 5.03
53 54 2.303022 GGGATAATGGAATGAGGCGAGA 59.697 50.000 0.00 0.00 0.00 4.04
54 55 3.330267 GGATAATGGAATGAGGCGAGAC 58.670 50.000 0.00 0.00 0.00 3.36
55 56 3.007398 GGATAATGGAATGAGGCGAGACT 59.993 47.826 0.00 0.00 0.00 3.24
56 57 4.220821 GGATAATGGAATGAGGCGAGACTA 59.779 45.833 0.00 0.00 0.00 2.59
57 58 3.460857 AATGGAATGAGGCGAGACTAC 57.539 47.619 0.00 0.00 0.00 2.73
58 59 1.112113 TGGAATGAGGCGAGACTACC 58.888 55.000 0.00 0.00 0.00 3.18
59 60 1.112113 GGAATGAGGCGAGACTACCA 58.888 55.000 0.00 0.00 0.00 3.25
60 61 1.480954 GGAATGAGGCGAGACTACCAA 59.519 52.381 0.00 0.00 0.00 3.67
61 62 2.541556 GAATGAGGCGAGACTACCAAC 58.458 52.381 0.00 0.00 0.00 3.77
62 63 1.853963 ATGAGGCGAGACTACCAACT 58.146 50.000 0.00 0.00 0.00 3.16
63 64 1.174783 TGAGGCGAGACTACCAACTC 58.825 55.000 0.00 0.00 0.00 3.01
64 65 0.456628 GAGGCGAGACTACCAACTCC 59.543 60.000 0.00 0.00 0.00 3.85
65 66 0.971447 AGGCGAGACTACCAACTCCC 60.971 60.000 0.00 0.00 0.00 4.30
66 67 1.516423 GCGAGACTACCAACTCCCC 59.484 63.158 0.00 0.00 0.00 4.81
67 68 0.971447 GCGAGACTACCAACTCCCCT 60.971 60.000 0.00 0.00 0.00 4.79
68 69 1.558233 CGAGACTACCAACTCCCCTT 58.442 55.000 0.00 0.00 0.00 3.95
69 70 1.900486 CGAGACTACCAACTCCCCTTT 59.100 52.381 0.00 0.00 0.00 3.11
70 71 3.094572 CGAGACTACCAACTCCCCTTTA 58.905 50.000 0.00 0.00 0.00 1.85
71 72 3.130693 CGAGACTACCAACTCCCCTTTAG 59.869 52.174 0.00 0.00 0.00 1.85
72 73 4.351127 GAGACTACCAACTCCCCTTTAGA 58.649 47.826 0.00 0.00 0.00 2.10
73 74 4.759953 AGACTACCAACTCCCCTTTAGAA 58.240 43.478 0.00 0.00 0.00 2.10
74 75 4.778427 AGACTACCAACTCCCCTTTAGAAG 59.222 45.833 0.00 0.00 0.00 2.85
75 76 4.500452 ACTACCAACTCCCCTTTAGAAGT 58.500 43.478 0.00 0.00 0.00 3.01
76 77 5.658474 ACTACCAACTCCCCTTTAGAAGTA 58.342 41.667 0.00 0.00 0.00 2.24
77 78 5.720520 ACTACCAACTCCCCTTTAGAAGTAG 59.279 44.000 0.00 0.00 0.00 2.57
78 79 4.759953 ACCAACTCCCCTTTAGAAGTAGA 58.240 43.478 0.00 0.00 0.00 2.59
79 80 4.778427 ACCAACTCCCCTTTAGAAGTAGAG 59.222 45.833 0.00 0.00 33.99 2.43
122 123 1.272480 GCCCCACAGGTTAAAGGTCAT 60.272 52.381 0.00 0.00 38.26 3.06
168 169 5.799827 CCTTTTTGAGGTCCATAAACCAA 57.200 39.130 0.00 0.00 42.12 3.67
174 175 6.648879 TTGAGGTCCATAAACCAAAAGAAG 57.351 37.500 0.00 0.00 42.12 2.85
178 179 5.074515 AGGTCCATAAACCAAAAGAAGAGGA 59.925 40.000 0.00 0.00 42.12 3.71
205 206 5.546499 ACCTCTTTGTCTAACCCACAAGATA 59.454 40.000 0.00 0.00 35.22 1.98
212 255 7.461182 TGTCTAACCCACAAGATAAAAATGG 57.539 36.000 0.00 0.00 0.00 3.16
217 260 6.493189 ACCCACAAGATAAAAATGGTTTGT 57.507 33.333 0.00 0.00 0.00 2.83
290 334 3.780850 CCCTACCTCTTTGTCTAACCCAT 59.219 47.826 0.00 0.00 0.00 4.00
306 350 9.403583 GTCTAACCCATAATATTTGAACCTCAA 57.596 33.333 0.00 0.00 34.03 3.02
323 368 4.768968 ACCTCAATCTTGCTGCTTAATTGT 59.231 37.500 15.65 1.77 0.00 2.71
339 384 8.296713 TGCTTAATTGTTAAAGGCTTACTCTTG 58.703 33.333 0.00 0.00 0.00 3.02
340 385 8.512138 GCTTAATTGTTAAAGGCTTACTCTTGA 58.488 33.333 0.00 0.00 0.00 3.02
343 392 8.635765 AATTGTTAAAGGCTTACTCTTGATGA 57.364 30.769 0.00 0.00 0.00 2.92
390 439 6.656270 TGTCAAAGACAATCTGCTATGTTCAT 59.344 34.615 0.00 0.00 39.78 2.57
437 486 1.493446 TGAGAGGTCCGGCTGTAGATA 59.507 52.381 0.00 0.00 0.00 1.98
440 489 2.091775 AGAGGTCCGGCTGTAGATACTT 60.092 50.000 0.00 0.00 0.00 2.24
442 491 2.431057 AGGTCCGGCTGTAGATACTTTG 59.569 50.000 0.00 0.00 0.00 2.77
563 680 1.784525 GAGACCTCCACAAAGTCGTG 58.215 55.000 0.00 0.00 35.65 4.35
617 735 4.058124 GTCTGTTGTCATGCTTCTGTACA 58.942 43.478 0.00 0.00 0.00 2.90
673 800 2.289882 TGCATCTGAGTAGCAGCAAACT 60.290 45.455 0.00 0.00 44.52 2.66
843 1015 4.142902 CGACTTAACACGGCATCAGAAATT 60.143 41.667 0.00 0.00 0.00 1.82
855 1027 8.465999 ACGGCATCAGAAATTTAATATTCAACA 58.534 29.630 0.00 0.00 0.00 3.33
1084 1343 0.935831 CACAACACCATGCAGCAACG 60.936 55.000 0.00 0.00 0.00 4.10
1115 2141 3.412386 ACAGCAGGTACACCAAGAAATC 58.588 45.455 0.38 0.00 38.89 2.17
1621 2651 1.347707 TGATGAAGAGCCTGGTCGTTT 59.652 47.619 0.00 0.00 0.00 3.60
1880 2911 2.952978 GGTTAGAAGGAGCTCTCGATGA 59.047 50.000 14.64 0.00 0.00 2.92
1938 2969 2.586792 GGGAATGAGCTCAGCGGT 59.413 61.111 22.96 7.13 0.00 5.68
1961 2992 7.148052 CGGTAATATTCCAGAGTCTATAGGTGG 60.148 44.444 0.00 2.87 0.00 4.61
2373 3404 6.015940 CCCTTTATATTGGATGCAACTTCCTC 60.016 42.308 0.12 0.00 34.17 3.71
2495 3526 5.355910 GGTTATCAAAGCTACCGAATTTGGA 59.644 40.000 19.20 1.47 35.21 3.53
2761 3792 9.804977 AGCTTAATCTAGCCATGAATAATTTCT 57.195 29.630 0.00 0.00 42.20 2.52
3129 4161 4.278310 ACCCCATAAAACAGATTGGTAGC 58.722 43.478 0.00 0.00 0.00 3.58
3303 4335 9.624373 AGAATATAAGAACATTTGACTCTGCAT 57.376 29.630 0.00 0.00 0.00 3.96
3429 4464 6.721318 AGCTGATTAGGTAAAGGACATTTCA 58.279 36.000 0.00 0.00 31.69 2.69
3446 4481 7.205515 ACATTTCATTCCATTCTCTCCTAGT 57.794 36.000 0.00 0.00 0.00 2.57
3586 4621 2.562298 CAAACCAGAAGCCTTGCCAATA 59.438 45.455 0.00 0.00 0.00 1.90
3620 4662 3.560068 GTGTCCCTGTTGTTGTCAAGTAG 59.440 47.826 0.00 0.00 33.97 2.57
3642 4684 3.733709 CCTGGAGCAGGTTGACTTT 57.266 52.632 0.00 0.00 45.82 2.66
3647 4689 4.082571 CCTGGAGCAGGTTGACTTTATTTG 60.083 45.833 0.00 0.00 45.82 2.32
3696 4738 1.831580 AAGCATCCTCTTGAACTGCC 58.168 50.000 0.00 0.00 33.34 4.85
3700 4742 2.352127 GCATCCTCTTGAACTGCCAAAC 60.352 50.000 0.00 0.00 0.00 2.93
3732 4776 4.506886 AGATATAGAAACGCCGAGGAAG 57.493 45.455 0.00 0.00 0.00 3.46
3805 9383 4.080863 CCTATTCTCCCACAAGCTAACAGT 60.081 45.833 0.00 0.00 0.00 3.55
3823 9401 3.623060 ACAGTATGGTGCATAAGAAAGCG 59.377 43.478 0.00 0.00 43.62 4.68
3826 9404 5.008019 CAGTATGGTGCATAAGAAAGCGAAT 59.992 40.000 0.00 0.00 0.00 3.34
3867 9446 5.616488 TCGATTGTGAATATGCATCATGG 57.384 39.130 0.19 0.00 0.00 3.66
4039 9627 9.998106 TGAATTACATAGGAAGGTAGCTTATTC 57.002 33.333 7.26 10.59 0.00 1.75
4067 9656 6.973229 AGAAAGCCAATTATGTTTCATTGC 57.027 33.333 7.80 0.00 32.38 3.56
4079 9668 4.236147 TGTTTCATTGCCAATGTCAATCG 58.764 39.130 16.55 0.00 39.87 3.34
4117 9706 6.047511 AGGCTAAATATGTCAGCTATCCAG 57.952 41.667 0.00 0.00 35.60 3.86
4132 9721 5.604650 AGCTATCCAGGCACTTAATACTCTT 59.395 40.000 0.00 0.00 34.60 2.85
4162 9753 8.752005 ACATAATATTACAACCTCAAGCATGT 57.248 30.769 0.00 0.00 0.00 3.21
4179 9770 3.485633 CATGTGAGATCTGTTTTGCACG 58.514 45.455 0.00 0.00 0.00 5.34
4185 9776 2.032894 AGATCTGTTTTGCACGAACACG 60.033 45.455 10.02 7.58 33.73 4.49
4187 9778 1.199852 CTGTTTTGCACGAACACGGC 61.200 55.000 10.02 0.00 33.73 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.736325 ATATTACGCCCGCGAGCATC 60.736 55.000 14.50 0.00 42.83 3.91
1 2 0.528924 TATATTACGCCCGCGAGCAT 59.471 50.000 14.50 0.00 42.83 3.79
2 3 0.109458 CTATATTACGCCCGCGAGCA 60.109 55.000 14.50 0.00 42.83 4.26
4 5 1.467734 ACTCTATATTACGCCCGCGAG 59.532 52.381 17.16 0.00 42.83 5.03
5 6 1.527034 ACTCTATATTACGCCCGCGA 58.473 50.000 17.16 0.00 42.83 5.87
6 7 2.342910 AACTCTATATTACGCCCGCG 57.657 50.000 7.69 7.69 46.03 6.46
7 8 2.157085 GCAAACTCTATATTACGCCCGC 59.843 50.000 0.00 0.00 0.00 6.13
8 9 2.735134 GGCAAACTCTATATTACGCCCG 59.265 50.000 0.00 0.00 32.01 6.13
9 10 3.735591 TGGCAAACTCTATATTACGCCC 58.264 45.455 0.00 0.00 37.49 6.13
10 11 4.213482 CCTTGGCAAACTCTATATTACGCC 59.787 45.833 0.00 0.00 38.79 5.68
11 12 4.213482 CCCTTGGCAAACTCTATATTACGC 59.787 45.833 0.00 0.00 0.00 4.42
12 13 5.607477 TCCCTTGGCAAACTCTATATTACG 58.393 41.667 0.00 0.00 0.00 3.18
13 14 9.740710 ATTATCCCTTGGCAAACTCTATATTAC 57.259 33.333 0.00 0.00 0.00 1.89
14 15 9.739276 CATTATCCCTTGGCAAACTCTATATTA 57.261 33.333 0.00 0.00 0.00 0.98
15 16 7.671398 CCATTATCCCTTGGCAAACTCTATATT 59.329 37.037 0.00 0.00 0.00 1.28
16 17 7.018550 TCCATTATCCCTTGGCAAACTCTATAT 59.981 37.037 0.00 0.00 32.80 0.86
17 18 6.331572 TCCATTATCCCTTGGCAAACTCTATA 59.668 38.462 0.00 0.00 32.80 1.31
18 19 5.134339 TCCATTATCCCTTGGCAAACTCTAT 59.866 40.000 0.00 0.00 32.80 1.98
19 20 4.476846 TCCATTATCCCTTGGCAAACTCTA 59.523 41.667 0.00 0.00 32.80 2.43
20 21 3.269381 TCCATTATCCCTTGGCAAACTCT 59.731 43.478 0.00 0.00 32.80 3.24
21 22 3.631250 TCCATTATCCCTTGGCAAACTC 58.369 45.455 0.00 0.00 32.80 3.01
22 23 3.756082 TCCATTATCCCTTGGCAAACT 57.244 42.857 0.00 0.00 32.80 2.66
23 24 4.405358 TCATTCCATTATCCCTTGGCAAAC 59.595 41.667 0.00 0.00 32.80 2.93
24 25 4.618635 TCATTCCATTATCCCTTGGCAAA 58.381 39.130 0.00 0.00 32.80 3.68
25 26 4.217510 CTCATTCCATTATCCCTTGGCAA 58.782 43.478 0.00 0.00 32.80 4.52
26 27 3.436906 CCTCATTCCATTATCCCTTGGCA 60.437 47.826 0.00 0.00 32.80 4.92
27 28 3.160269 CCTCATTCCATTATCCCTTGGC 58.840 50.000 0.00 0.00 32.80 4.52
28 29 3.160269 GCCTCATTCCATTATCCCTTGG 58.840 50.000 0.00 0.00 0.00 3.61
29 30 2.816087 CGCCTCATTCCATTATCCCTTG 59.184 50.000 0.00 0.00 0.00 3.61
30 31 2.711009 TCGCCTCATTCCATTATCCCTT 59.289 45.455 0.00 0.00 0.00 3.95
31 32 2.304180 CTCGCCTCATTCCATTATCCCT 59.696 50.000 0.00 0.00 0.00 4.20
32 33 2.303022 TCTCGCCTCATTCCATTATCCC 59.697 50.000 0.00 0.00 0.00 3.85
33 34 3.007398 AGTCTCGCCTCATTCCATTATCC 59.993 47.826 0.00 0.00 0.00 2.59
34 35 4.264460 AGTCTCGCCTCATTCCATTATC 57.736 45.455 0.00 0.00 0.00 1.75
35 36 4.021016 GGTAGTCTCGCCTCATTCCATTAT 60.021 45.833 0.00 0.00 0.00 1.28
36 37 3.321111 GGTAGTCTCGCCTCATTCCATTA 59.679 47.826 0.00 0.00 0.00 1.90
37 38 2.103263 GGTAGTCTCGCCTCATTCCATT 59.897 50.000 0.00 0.00 0.00 3.16
38 39 1.689273 GGTAGTCTCGCCTCATTCCAT 59.311 52.381 0.00 0.00 0.00 3.41
39 40 1.112113 GGTAGTCTCGCCTCATTCCA 58.888 55.000 0.00 0.00 0.00 3.53
40 41 1.112113 TGGTAGTCTCGCCTCATTCC 58.888 55.000 0.00 0.00 0.00 3.01
41 42 2.166664 AGTTGGTAGTCTCGCCTCATTC 59.833 50.000 0.00 0.00 0.00 2.67
42 43 2.166664 GAGTTGGTAGTCTCGCCTCATT 59.833 50.000 0.00 0.00 0.00 2.57
43 44 1.751924 GAGTTGGTAGTCTCGCCTCAT 59.248 52.381 0.00 0.00 0.00 2.90
44 45 1.174783 GAGTTGGTAGTCTCGCCTCA 58.825 55.000 0.00 0.00 0.00 3.86
45 46 0.456628 GGAGTTGGTAGTCTCGCCTC 59.543 60.000 0.00 0.00 0.00 4.70
46 47 0.971447 GGGAGTTGGTAGTCTCGCCT 60.971 60.000 0.00 0.00 37.57 5.52
47 48 1.516423 GGGAGTTGGTAGTCTCGCC 59.484 63.158 0.00 0.00 37.57 5.54
48 49 0.971447 AGGGGAGTTGGTAGTCTCGC 60.971 60.000 0.00 0.00 41.02 5.03
49 50 1.558233 AAGGGGAGTTGGTAGTCTCG 58.442 55.000 0.00 0.00 0.00 4.04
50 51 4.351127 TCTAAAGGGGAGTTGGTAGTCTC 58.649 47.826 0.00 0.00 0.00 3.36
51 52 4.415224 TCTAAAGGGGAGTTGGTAGTCT 57.585 45.455 0.00 0.00 0.00 3.24
52 53 4.531339 ACTTCTAAAGGGGAGTTGGTAGTC 59.469 45.833 0.00 0.00 0.00 2.59
53 54 4.500452 ACTTCTAAAGGGGAGTTGGTAGT 58.500 43.478 0.00 0.00 0.00 2.73
54 55 5.956563 TCTACTTCTAAAGGGGAGTTGGTAG 59.043 44.000 0.00 0.00 0.00 3.18
55 56 5.907421 TCTACTTCTAAAGGGGAGTTGGTA 58.093 41.667 0.00 0.00 0.00 3.25
56 57 4.759953 TCTACTTCTAAAGGGGAGTTGGT 58.240 43.478 0.00 0.00 0.00 3.67
57 58 5.024118 TCTCTACTTCTAAAGGGGAGTTGG 58.976 45.833 9.37 0.00 34.84 3.77
58 59 6.800072 ATCTCTACTTCTAAAGGGGAGTTG 57.200 41.667 9.37 0.00 34.84 3.16
78 79 9.830975 GGCAACCCATTTAAACAAATATAATCT 57.169 29.630 0.00 0.00 0.00 2.40
103 104 2.899303 ATGACCTTTAACCTGTGGGG 57.101 50.000 0.00 0.00 41.89 4.96
122 123 9.415008 AGGTTAATGCATGGTTAAATACATGTA 57.585 29.630 8.27 8.27 44.74 2.29
154 155 5.074515 TCCTCTTCTTTTGGTTTATGGACCT 59.925 40.000 0.00 0.00 40.47 3.85
178 179 3.201266 TGTGGGTTAGACAAAGAGGTGTT 59.799 43.478 0.00 0.00 0.00 3.32
225 268 1.681076 GTAGGGTCCCCGCAAGAAA 59.319 57.895 3.51 0.00 41.95 2.52
226 269 2.295602 GGTAGGGTCCCCGCAAGAA 61.296 63.158 3.51 0.00 41.95 2.52
227 270 2.686106 GGTAGGGTCCCCGCAAGA 60.686 66.667 3.51 0.00 41.95 3.02
228 271 2.687566 AGGTAGGGTCCCCGCAAG 60.688 66.667 3.51 0.00 41.95 4.01
263 307 3.277416 AGACAAAGAGGTAGGGTTCCT 57.723 47.619 0.00 0.00 38.09 3.36
290 334 7.340232 AGCAGCAAGATTGAGGTTCAAATATTA 59.660 33.333 0.00 0.00 40.12 0.98
306 350 6.071165 AGCCTTTAACAATTAAGCAGCAAGAT 60.071 34.615 0.00 0.00 0.00 2.40
323 368 7.001674 TGGTTTCATCAAGAGTAAGCCTTTAA 58.998 34.615 0.00 0.00 0.00 1.52
339 384 6.322491 GGTTGCAAAGTATAGTGGTTTCATC 58.678 40.000 0.00 0.00 0.00 2.92
340 385 5.106317 CGGTTGCAAAGTATAGTGGTTTCAT 60.106 40.000 0.00 0.00 0.00 2.57
343 392 4.023536 CACGGTTGCAAAGTATAGTGGTTT 60.024 41.667 0.00 0.00 0.00 3.27
390 439 1.218047 GCTGACGGGCATGTGTCTA 59.782 57.895 13.48 3.27 36.10 2.59
414 463 1.482593 CTACAGCCGGACCTCTCAAAT 59.517 52.381 5.05 0.00 0.00 2.32
437 486 1.933853 GTGTCTGTGAACGCTCAAAGT 59.066 47.619 5.92 0.00 38.03 2.66
440 489 1.866601 CATGTGTCTGTGAACGCTCAA 59.133 47.619 0.00 0.00 31.88 3.02
442 491 0.164647 GCATGTGTCTGTGAACGCTC 59.835 55.000 0.00 0.00 0.00 5.03
563 680 1.219522 AACTGCACGCGTACCACTTC 61.220 55.000 13.44 0.00 0.00 3.01
590 708 3.567164 AGAAGCATGACAACAGACTTTGG 59.433 43.478 0.00 0.00 0.00 3.28
652 778 2.079158 GTTTGCTGCTACTCAGATGCA 58.921 47.619 0.00 0.00 45.72 3.96
673 800 6.156519 ACATTTCAGCGTCGATGCTATTATA 58.843 36.000 30.57 15.02 45.23 0.98
940 1149 5.175859 GTCCATTCGGATTCTGTCAGTTTA 58.824 41.667 0.00 0.00 45.33 2.01
1084 1343 4.082949 GGTGTACCTGCTGTATGAAAAACC 60.083 45.833 0.00 0.00 0.00 3.27
1115 2141 2.877975 CCAAGGGAAGGCATGTGAG 58.122 57.895 0.00 0.00 0.00 3.51
1621 2651 6.418057 AAATCTGTTGGAACTGGCATTAAA 57.582 33.333 0.00 0.00 0.00 1.52
1735 2765 2.166459 CTGAGCAATTACCGAGTCCTGA 59.834 50.000 0.00 0.00 0.00 3.86
1880 2911 4.579340 CCAGATTTATGAGCTTGCTGATGT 59.421 41.667 0.00 0.00 0.00 3.06
1938 2969 8.679725 AGACCACCTATAGACTCTGGAATATTA 58.320 37.037 0.00 0.00 0.00 0.98
1961 2992 2.765699 AGCTCCTCCAATCTCTTCAGAC 59.234 50.000 0.00 0.00 0.00 3.51
2495 3526 4.540359 TTGCCTTGCAAAAATAGCATCT 57.460 36.364 0.00 0.00 45.96 2.90
2697 3728 1.130561 GGCGTGAGGTATTGCAGAAAC 59.869 52.381 0.00 0.00 0.00 2.78
2761 3792 2.177016 TCTCCTCCGGAATCATACCAGA 59.823 50.000 5.23 0.00 0.00 3.86
3129 4161 3.070018 GGTCATAAAGATGATGGCCTCG 58.930 50.000 3.32 0.00 44.30 4.63
3303 4335 4.766891 CCCTGTAGATTTTCTTTGCTGGAA 59.233 41.667 0.00 0.00 0.00 3.53
3429 4464 7.126421 TCAGCTTTAACTAGGAGAGAATGGAAT 59.874 37.037 0.00 0.00 0.00 3.01
3586 4621 2.025321 ACAGGGACACAAAGTTGGTCTT 60.025 45.455 10.48 0.00 38.10 3.01
3667 4709 2.897350 GGATGCTTTCGGGCGAGG 60.897 66.667 0.00 0.00 34.52 4.63
3719 4763 0.034337 TTAGTGCTTCCTCGGCGTTT 59.966 50.000 6.85 0.00 0.00 3.60
3727 4771 6.716628 TGATTGTTCTGAAATTAGTGCTTCCT 59.283 34.615 0.00 0.00 0.00 3.36
3732 4776 8.454106 AGTGTATGATTGTTCTGAAATTAGTGC 58.546 33.333 0.00 0.00 0.00 4.40
3783 9361 5.091261 ACTGTTAGCTTGTGGGAGAATAG 57.909 43.478 0.00 0.00 0.00 1.73
3784 9362 6.408092 CCATACTGTTAGCTTGTGGGAGAATA 60.408 42.308 0.00 0.00 0.00 1.75
3795 9373 5.989477 TCTTATGCACCATACTGTTAGCTT 58.011 37.500 0.00 0.00 0.00 3.74
3805 9383 6.204688 CCTAATTCGCTTTCTTATGCACCATA 59.795 38.462 0.00 0.00 0.00 2.74
3826 9404 9.337396 ACAATCGATAATAGATTTTGTGCCTAA 57.663 29.630 0.00 0.00 36.30 2.69
3865 9444 4.019950 ACATCTGTTGTGACATGATCTCCA 60.020 41.667 0.00 0.00 37.11 3.86
3867 9446 5.521735 GGTACATCTGTTGTGACATGATCTC 59.478 44.000 0.00 0.00 39.48 2.75
3942 9521 4.718961 ACCTGTGCTAGACATTTTCAACT 58.281 39.130 0.00 0.00 32.74 3.16
4057 9646 4.236147 CGATTGACATTGGCAATGAAACA 58.764 39.130 38.83 29.87 41.46 2.83
4058 9647 3.061161 GCGATTGACATTGGCAATGAAAC 59.939 43.478 38.83 28.18 41.46 2.78
4067 9656 1.328680 CTCGGAAGCGATTGACATTGG 59.671 52.381 0.00 0.00 0.00 3.16
4079 9668 9.250624 CATATTTAGCCTATAATACTCGGAAGC 57.749 37.037 0.00 0.00 0.00 3.86
4117 9706 9.780186 ATTATGTCCTTAAGAGTATTAAGTGCC 57.220 33.333 14.51 4.52 31.77 5.01
4132 9721 9.555727 GCTTGAGGTTGTAATATTATGTCCTTA 57.444 33.333 12.96 8.72 0.00 2.69
4162 9753 3.002246 GTGTTCGTGCAAAACAGATCTCA 59.998 43.478 14.40 0.00 37.30 3.27
4179 9770 0.462403 TATTTAGGCGGGCCGTGTTC 60.462 55.000 28.82 14.52 41.95 3.18
4185 9776 4.903054 AGTATTTACTATTTAGGCGGGCC 58.097 43.478 0.18 0.18 34.13 5.80
4187 9778 7.444299 TGGTTAGTATTTACTATTTAGGCGGG 58.556 38.462 0.00 0.00 38.48 6.13


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

AutoCloner maintained by Alex Coulton.