Multiple sequence alignment - TraesCS3D01G033900

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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 TraesCS3D01G033900 chr3D 100.000 2260 0 0 1 2260 12433632 12431373 0.000000e+00 4174.0
1 TraesCS3D01G033900 chr3D 90.417 240 20 3 1191 1430 12701160 12700924 1.950000e-81 313.0
2 TraesCS3D01G033900 chr3D 100.000 106 0 0 2509 2614 12431124 12431019 2.050000e-46 196.0
3 TraesCS3D01G033900 chr3D 88.732 71 8 0 1025 1095 12422372 12422302 1.290000e-13 87.9
4 TraesCS3D01G033900 chr3D 88.571 70 8 0 1029 1098 12454974 12454905 4.640000e-13 86.1
5 TraesCS3D01G033900 chr3A 88.598 1298 90 26 839 2104 24748073 24749344 0.000000e+00 1524.0
6 TraesCS3D01G033900 chr3A 94.650 243 11 1 579 819 24747845 24748087 2.460000e-100 375.0
7 TraesCS3D01G033900 chr3A 90.583 223 18 2 63 285 24747116 24747335 2.540000e-75 292.0
8 TraesCS3D01G033900 chr3A 92.222 180 12 2 410 587 24747323 24747502 1.200000e-63 254.0
9 TraesCS3D01G033900 chr3A 85.965 114 11 4 2152 2260 24749772 24749885 1.640000e-22 117.0
10 TraesCS3D01G033900 chr3A 93.846 65 4 0 1 65 24744593 24744529 5.950000e-17 99.0
11 TraesCS3D01G033900 chr3B 87.146 1307 99 32 839 2104 18026787 18025509 0.000000e+00 1419.0
12 TraesCS3D01G033900 chr3B 90.476 588 48 6 2 588 18120308 18119728 0.000000e+00 769.0
13 TraesCS3D01G033900 chr3B 94.558 147 8 0 587 733 18028772 18028626 7.280000e-56 228.0
14 TraesCS3D01G033900 chr3B 92.632 95 7 0 727 821 18026865 18026771 1.260000e-28 137.0
15 TraesCS3D01G033900 chr3B 78.750 160 26 5 942 1101 18570382 18570231 1.660000e-17 100.0
16 TraesCS3D01G033900 chr3B 91.429 70 1 4 2152 2217 18025046 18024978 9.960000e-15 91.6
17 TraesCS3D01G033900 chr3B 88.732 71 8 0 1028 1098 18128056 18127986 1.290000e-13 87.9
18 TraesCS3D01G033900 chrUn 85.965 57 8 0 1016 1072 430383202 430383258 7.810000e-06 62.1


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 TraesCS3D01G033900 chr3D 12431019 12433632 2613 True 2185.0 4174 100.00000 1 2614 2 chr3D.!!$R4 2613
1 TraesCS3D01G033900 chr3A 24747116 24749885 2769 False 512.4 1524 90.40360 63 2260 5 chr3A.!!$F1 2197
2 TraesCS3D01G033900 chr3B 18119728 18120308 580 True 769.0 769 90.47600 2 588 1 chr3B.!!$R1 586
3 TraesCS3D01G033900 chr3B 18024978 18028772 3794 True 468.9 1419 91.44125 587 2217 4 chr3B.!!$R4 1630

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
400 402 0.75085 ATCGCTTAGGGCATGTACGT 59.249 50.0 0.0 0.0 41.91 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 4083 0.03601 CACCTCCTTAGCAGTGGGTG 60.036 60.0 0.0 0.0 35.66 4.61 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
25 26 2.196776 CATCCCTCCATGGTGGGC 59.803 66.667 37.39 0.00 45.72 5.36
56 57 1.134753 CAAAGAGCACACAAACCTGCA 59.865 47.619 0.00 0.00 35.73 4.41
80 81 3.123050 CGCGGTATGAATCTTGATGTGA 58.877 45.455 0.00 0.00 0.00 3.58
88 89 9.553064 GGTATGAATCTTGATGTGACTAAATCT 57.447 33.333 0.00 0.00 0.00 2.40
95 96 9.730705 ATCTTGATGTGACTAAATCTCTCAAAA 57.269 29.630 0.00 0.00 0.00 2.44
96 97 9.559732 TCTTGATGTGACTAAATCTCTCAAAAA 57.440 29.630 0.00 0.00 0.00 1.94
178 180 8.861086 ACAACATGTGAGGTATTATCTAGTAGG 58.139 37.037 0.00 0.00 0.00 3.18
179 181 8.861086 CAACATGTGAGGTATTATCTAGTAGGT 58.139 37.037 0.00 0.00 0.00 3.08
319 321 3.571590 AGGATTGCCTTGTTTACCAACA 58.428 40.909 0.00 0.00 43.90 3.33
330 332 4.035441 TTGTTTACCAACAACGGAAGTAGC 59.965 41.667 0.00 0.00 46.06 3.58
341 343 1.014564 GGAAGTAGCTGTGCCGTCAC 61.015 60.000 0.00 0.00 43.40 3.67
355 357 1.137086 CCGTCACCACAATCTAGAGGG 59.863 57.143 0.00 0.00 0.00 4.30
399 401 1.139989 CATCGCTTAGGGCATGTACG 58.860 55.000 0.00 0.00 41.91 3.67
400 402 0.750850 ATCGCTTAGGGCATGTACGT 59.249 50.000 0.00 0.00 41.91 3.57
401 403 1.391577 TCGCTTAGGGCATGTACGTA 58.608 50.000 0.00 0.00 41.91 3.57
402 404 1.066002 TCGCTTAGGGCATGTACGTAC 59.934 52.381 18.90 18.90 41.91 3.67
403 405 1.066605 CGCTTAGGGCATGTACGTACT 59.933 52.381 25.12 9.27 41.91 2.73
483 485 4.401202 ACCACCGTTTCTGAAAATTTCTGT 59.599 37.500 4.09 0.00 0.00 3.41
507 509 2.506444 ACGGAGGCTACACTCTATAGC 58.494 52.381 0.00 0.00 43.66 2.97
508 510 2.158652 ACGGAGGCTACACTCTATAGCA 60.159 50.000 0.00 0.00 45.76 3.49
511 513 4.340617 GGAGGCTACACTCTATAGCAGAT 58.659 47.826 6.37 0.00 45.76 2.90
523 525 6.385467 ACTCTATAGCAGATCCACCTTTCTTT 59.615 38.462 0.00 0.00 31.13 2.52
566 568 5.690865 TCATTTCTCTCTACCTCTCTCCTC 58.309 45.833 0.00 0.00 0.00 3.71
820 2942 2.681344 TGATCATGCACAGCTCATTGTC 59.319 45.455 0.00 0.00 0.00 3.18
821 2943 2.484742 TCATGCACAGCTCATTGTCT 57.515 45.000 0.00 0.00 0.00 3.41
822 2944 2.786777 TCATGCACAGCTCATTGTCTT 58.213 42.857 0.00 0.00 0.00 3.01
823 2945 3.151554 TCATGCACAGCTCATTGTCTTT 58.848 40.909 0.00 0.00 0.00 2.52
824 2946 3.570975 TCATGCACAGCTCATTGTCTTTT 59.429 39.130 0.00 0.00 0.00 2.27
825 2947 4.038282 TCATGCACAGCTCATTGTCTTTTT 59.962 37.500 0.00 0.00 0.00 1.94
845 2967 3.182538 TTTTTGCGCTGATGCACAG 57.817 47.368 9.73 10.75 46.25 3.66
905 3028 0.960364 GCAATTGGCTCCTCGTGGAA 60.960 55.000 7.72 0.00 42.66 3.53
1010 3136 0.871057 GGCAAAGTCAGTGAGTGAGC 59.129 55.000 13.73 13.73 35.13 4.26
1011 3137 1.542108 GGCAAAGTCAGTGAGTGAGCT 60.542 52.381 18.81 0.00 35.13 4.09
1012 3138 1.530293 GCAAAGTCAGTGAGTGAGCTG 59.470 52.381 14.48 6.49 35.13 4.24
1016 3142 1.612950 AGTCAGTGAGTGAGCTGTGAG 59.387 52.381 0.00 0.00 35.13 3.51
1023 3149 0.598680 AGTGAGCTGTGAGCAACGAC 60.599 55.000 0.00 0.00 45.56 4.34
1025 3151 1.371758 GAGCTGTGAGCAACGACGA 60.372 57.895 0.00 0.00 45.56 4.20
1037 3163 2.987149 GCAACGACGAAGATGAAGAGAA 59.013 45.455 0.00 0.00 0.00 2.87
1081 3207 2.437897 CTTTCACTGGGGGCAGCT 59.562 61.111 0.00 0.00 0.00 4.24
1129 3291 0.700564 TTCTCCTGCCAAGCCAAGAT 59.299 50.000 0.00 0.00 0.00 2.40
1210 3372 1.373570 AACTTATCGCTGCTTGGCTC 58.626 50.000 0.00 0.00 0.00 4.70
1211 3373 0.807667 ACTTATCGCTGCTTGGCTCG 60.808 55.000 0.00 0.00 0.00 5.03
1212 3374 0.807667 CTTATCGCTGCTTGGCTCGT 60.808 55.000 0.00 0.00 0.00 4.18
1222 3384 1.151668 CTTGGCTCGTTGTTGAGGAG 58.848 55.000 0.00 0.00 41.97 3.69
1238 3403 1.518903 GGAGTTGCAGACCAAGTGGC 61.519 60.000 0.00 0.00 37.22 5.01
1279 3444 3.439513 AAGTGCTGCGACGTGACCA 62.440 57.895 0.00 0.00 0.00 4.02
1368 3533 3.792401 CGAGGACTGCAATGGTTATGTA 58.208 45.455 0.00 0.00 0.00 2.29
1468 3633 6.752351 CGGTAACTGAACTCTACGTACTACTA 59.248 42.308 0.00 0.00 0.00 1.82
1469 3634 7.436673 CGGTAACTGAACTCTACGTACTACTAT 59.563 40.741 0.00 0.00 0.00 2.12
1470 3635 9.751542 GGTAACTGAACTCTACGTACTACTATA 57.248 37.037 0.00 0.00 0.00 1.31
1474 3639 9.959749 ACTGAACTCTACGTACTACTATACTAC 57.040 37.037 0.00 0.00 0.00 2.73
1495 3673 3.993376 TACGCGCACCGGTTGGATC 62.993 63.158 2.97 0.00 42.52 3.36
1502 3680 0.524816 CACCGGTTGGATCGTCTACG 60.525 60.000 2.97 0.00 39.21 3.51
1504 3682 1.660560 CCGGTTGGATCGTCTACGGT 61.661 60.000 2.24 0.00 37.43 4.83
1518 3696 2.418280 TCTACGGTTATGCGAACGTACA 59.582 45.455 0.00 0.00 40.38 2.90
1569 3750 2.489971 ACTTATGTTGTGTGTGGTCCG 58.510 47.619 0.00 0.00 0.00 4.79
1722 3905 8.530269 TTTTCTTTTTCTAGATACGACAGTCC 57.470 34.615 0.00 0.00 0.00 3.85
1735 3918 1.197721 GACAGTCCACAAAAGCCGATG 59.802 52.381 0.00 0.00 0.00 3.84
1803 3986 9.936759 AAAAGAAAACAACATCCAGAAACTTAA 57.063 25.926 0.00 0.00 0.00 1.85
1844 4037 5.603596 ACTGGTACGTTAATTTCTGTCACA 58.396 37.500 0.00 0.00 0.00 3.58
1853 4046 6.587990 CGTTAATTTCTGTCACATCACTCTCT 59.412 38.462 0.00 0.00 0.00 3.10
1854 4047 7.201393 CGTTAATTTCTGTCACATCACTCTCTC 60.201 40.741 0.00 0.00 0.00 3.20
1862 4055 3.055458 TCACATCACTCTCTCGTCTCTCT 60.055 47.826 0.00 0.00 0.00 3.10
1863 4056 3.689161 CACATCACTCTCTCGTCTCTCTT 59.311 47.826 0.00 0.00 0.00 2.85
1864 4057 3.938963 ACATCACTCTCTCGTCTCTCTTC 59.061 47.826 0.00 0.00 0.00 2.87
1878 4071 2.190578 CTTCGGGGATGCCTCCAC 59.809 66.667 10.44 5.16 44.08 4.02
1890 4083 0.796927 GCCTCCACGTAGTCAAAAGC 59.203 55.000 0.00 0.00 41.61 3.51
1894 4087 0.872388 CCACGTAGTCAAAAGCACCC 59.128 55.000 0.00 0.00 41.61 4.61
1895 4088 1.588674 CACGTAGTCAAAAGCACCCA 58.411 50.000 0.00 0.00 41.61 4.51
1898 4091 1.531149 CGTAGTCAAAAGCACCCACTG 59.469 52.381 0.00 0.00 0.00 3.66
1928 4121 6.360370 AGGTGCAGAGTAGTAAATTTGAGA 57.640 37.500 0.00 0.00 0.00 3.27
1941 4134 2.163818 TTTGAGACATGACCGGTCAC 57.836 50.000 38.46 25.57 43.11 3.67
1945 4138 1.741770 GACATGACCGGTCACTGCC 60.742 63.158 38.46 24.19 43.11 4.85
1946 4139 2.436646 CATGACCGGTCACTGCCC 60.437 66.667 38.46 10.08 43.11 5.36
1980 4173 0.873721 GCCTACGCGGTTACCAAAAA 59.126 50.000 12.47 0.00 34.25 1.94
2033 4226 8.719560 ACTAAGAGCAAGGTTAATAGTTTAGC 57.280 34.615 0.00 0.00 0.00 3.09
2039 4232 5.675323 GCAAGGTTAATAGTTTAGCCAACCG 60.675 44.000 2.19 0.00 40.23 4.44
2082 4279 3.788937 TGTTACAGCGAACCTAATAGCC 58.211 45.455 0.00 0.00 0.00 3.93
2088 4285 1.138266 GCGAACCTAATAGCCCACTCA 59.862 52.381 0.00 0.00 0.00 3.41
2095 4292 7.470981 CGAACCTAATAGCCCACTCATAGTTAA 60.471 40.741 0.00 0.00 0.00 2.01
2096 4293 7.873699 ACCTAATAGCCCACTCATAGTTAAT 57.126 36.000 0.00 0.00 0.00 1.40
2104 4301 8.268878 AGCCCACTCATAGTTAATTCTATTCT 57.731 34.615 0.00 0.00 0.00 2.40
2105 4302 8.153550 AGCCCACTCATAGTTAATTCTATTCTG 58.846 37.037 0.00 0.00 0.00 3.02
2106 4303 7.389053 GCCCACTCATAGTTAATTCTATTCTGG 59.611 40.741 0.00 0.00 0.00 3.86
2126 4411 7.841282 TCTGGTCTTTTCTCTCTTCTCTTTA 57.159 36.000 0.00 0.00 0.00 1.85
2133 4418 9.757227 TCTTTTCTCTCTTCTCTTTACTTCAAG 57.243 33.333 0.00 0.00 0.00 3.02
2150 4776 7.759489 ACTTCAAGTAAAATCTAATGTGGCA 57.241 32.000 0.00 0.00 0.00 4.92
2154 4780 9.638239 TTCAAGTAAAATCTAATGTGGCATTTC 57.362 29.630 0.00 0.00 0.00 2.17
2157 4783 9.860898 AAGTAAAATCTAATGTGGCATTTCTTC 57.139 29.630 0.00 0.00 0.00 2.87
2171 4797 5.116882 GCATTTCTTCTAACCCGACTATGT 58.883 41.667 0.00 0.00 0.00 2.29
2172 4798 5.006746 GCATTTCTTCTAACCCGACTATGTG 59.993 44.000 0.00 0.00 0.00 3.21
2173 4799 4.730949 TTCTTCTAACCCGACTATGTGG 57.269 45.455 0.00 0.00 0.00 4.17
2217 4847 3.505293 ACCACTAACTCGTAGACAAGGAC 59.495 47.826 0.00 0.00 33.61 3.85
2219 4849 4.158025 CCACTAACTCGTAGACAAGGACAT 59.842 45.833 0.00 0.00 33.61 3.06
2234 4864 1.407437 GGACATTGGCAGAGGGTAGTG 60.407 57.143 0.00 0.00 0.00 2.74
2241 4871 1.379977 CAGAGGGTAGTGGAGGCGA 60.380 63.158 0.00 0.00 0.00 5.54
2244 4874 0.175989 GAGGGTAGTGGAGGCGAAAG 59.824 60.000 0.00 0.00 0.00 2.62
2249 4879 2.180159 TAGTGGAGGCGAAAGTGGGC 62.180 60.000 0.00 0.00 0.00 5.36
2532 5162 5.968676 ACCCAAATTACTAGGCATAGTCA 57.031 39.130 15.39 4.34 41.46 3.41
2533 5163 5.681639 ACCCAAATTACTAGGCATAGTCAC 58.318 41.667 15.39 0.00 41.46 3.67
2534 5164 5.063880 CCCAAATTACTAGGCATAGTCACC 58.936 45.833 15.39 0.00 41.46 4.02
2535 5165 5.163195 CCCAAATTACTAGGCATAGTCACCT 60.163 44.000 15.39 0.00 41.46 4.00
2536 5166 5.760253 CCAAATTACTAGGCATAGTCACCTG 59.240 44.000 15.39 8.67 41.46 4.00
2537 5167 6.349300 CAAATTACTAGGCATAGTCACCTGT 58.651 40.000 15.39 0.00 41.46 4.00
2538 5168 6.561519 AATTACTAGGCATAGTCACCTGTT 57.438 37.500 15.39 0.00 41.46 3.16
2539 5169 6.561519 ATTACTAGGCATAGTCACCTGTTT 57.438 37.500 15.39 0.00 41.46 2.83
2540 5170 7.670605 ATTACTAGGCATAGTCACCTGTTTA 57.329 36.000 15.39 0.00 41.46 2.01
2541 5171 5.599999 ACTAGGCATAGTCACCTGTTTAG 57.400 43.478 4.95 0.00 37.75 1.85
2542 5172 5.024118 ACTAGGCATAGTCACCTGTTTAGT 58.976 41.667 4.95 0.00 37.75 2.24
2543 5173 4.473477 AGGCATAGTCACCTGTTTAGTC 57.527 45.455 0.00 0.00 34.07 2.59
2544 5174 3.197983 AGGCATAGTCACCTGTTTAGTCC 59.802 47.826 0.00 0.00 34.07 3.85
2545 5175 3.055385 GGCATAGTCACCTGTTTAGTCCA 60.055 47.826 0.00 0.00 0.00 4.02
2546 5176 4.184629 GCATAGTCACCTGTTTAGTCCAG 58.815 47.826 0.00 0.00 0.00 3.86
2547 5177 2.841442 AGTCACCTGTTTAGTCCAGC 57.159 50.000 0.00 0.00 0.00 4.85
2548 5178 1.348036 AGTCACCTGTTTAGTCCAGCC 59.652 52.381 0.00 0.00 0.00 4.85
2549 5179 0.690762 TCACCTGTTTAGTCCAGCCC 59.309 55.000 0.00 0.00 0.00 5.19
2550 5180 0.400213 CACCTGTTTAGTCCAGCCCA 59.600 55.000 0.00 0.00 0.00 5.36
2551 5181 1.004745 CACCTGTTTAGTCCAGCCCAT 59.995 52.381 0.00 0.00 0.00 4.00
2552 5182 1.710809 ACCTGTTTAGTCCAGCCCATT 59.289 47.619 0.00 0.00 0.00 3.16
2553 5183 2.916934 ACCTGTTTAGTCCAGCCCATTA 59.083 45.455 0.00 0.00 0.00 1.90
2554 5184 3.332485 ACCTGTTTAGTCCAGCCCATTAA 59.668 43.478 0.00 0.00 0.00 1.40
2555 5185 4.017499 ACCTGTTTAGTCCAGCCCATTAAT 60.017 41.667 0.00 0.00 0.00 1.40
2556 5186 4.339247 CCTGTTTAGTCCAGCCCATTAATG 59.661 45.833 8.58 8.58 0.00 1.90
2589 5219 3.672808 CCTATAGGTACGATCGTGGACT 58.327 50.000 30.23 24.09 0.00 3.85
2590 5220 3.436015 CCTATAGGTACGATCGTGGACTG 59.564 52.174 30.23 13.33 0.00 3.51
2591 5221 2.408271 TAGGTACGATCGTGGACTGT 57.592 50.000 30.23 14.52 0.00 3.55
2592 5222 1.093159 AGGTACGATCGTGGACTGTC 58.907 55.000 30.23 9.08 0.00 3.51
2593 5223 1.093159 GGTACGATCGTGGACTGTCT 58.907 55.000 30.23 2.46 0.00 3.41
2594 5224 1.471684 GGTACGATCGTGGACTGTCTT 59.528 52.381 30.23 1.66 0.00 3.01
2595 5225 2.477525 GGTACGATCGTGGACTGTCTTC 60.478 54.545 30.23 4.27 0.00 2.87
2596 5226 0.526662 ACGATCGTGGACTGTCTTCC 59.473 55.000 22.06 0.00 36.03 3.46
2597 5227 0.523546 CGATCGTGGACTGTCTTCCG 60.524 60.000 7.03 7.70 38.69 4.30
2598 5228 0.802607 GATCGTGGACTGTCTTCCGC 60.803 60.000 7.85 0.00 42.01 5.54
2599 5229 2.227089 ATCGTGGACTGTCTTCCGCC 62.227 60.000 7.85 0.00 42.39 6.13
2600 5230 2.932234 CGTGGACTGTCTTCCGCCT 61.932 63.158 7.85 0.00 42.39 5.52
2601 5231 1.079750 GTGGACTGTCTTCCGCCTC 60.080 63.158 7.85 0.00 39.88 4.70
2602 5232 2.283529 TGGACTGTCTTCCGCCTCC 61.284 63.158 7.85 0.00 38.69 4.30
2603 5233 2.283529 GGACTGTCTTCCGCCTCCA 61.284 63.158 7.85 0.00 0.00 3.86
2604 5234 1.671742 GACTGTCTTCCGCCTCCAA 59.328 57.895 0.00 0.00 0.00 3.53
2605 5235 0.670854 GACTGTCTTCCGCCTCCAAC 60.671 60.000 0.00 0.00 0.00 3.77
2606 5236 1.376037 CTGTCTTCCGCCTCCAACC 60.376 63.158 0.00 0.00 0.00 3.77
2607 5237 1.831652 CTGTCTTCCGCCTCCAACCT 61.832 60.000 0.00 0.00 0.00 3.50
2608 5238 1.375326 GTCTTCCGCCTCCAACCTT 59.625 57.895 0.00 0.00 0.00 3.50
2609 5239 0.673956 GTCTTCCGCCTCCAACCTTC 60.674 60.000 0.00 0.00 0.00 3.46
2610 5240 1.125093 TCTTCCGCCTCCAACCTTCA 61.125 55.000 0.00 0.00 0.00 3.02
2611 5241 0.250727 CTTCCGCCTCCAACCTTCAA 60.251 55.000 0.00 0.00 0.00 2.69
2612 5242 0.404040 TTCCGCCTCCAACCTTCAAT 59.596 50.000 0.00 0.00 0.00 2.57
2613 5243 0.035439 TCCGCCTCCAACCTTCAATC 60.035 55.000 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.538977 CATGGAGGGATGTGATGGGC 60.539 60.000 0.00 0.00 0.00 5.36
13 14 0.622665 AAGAGAAGCCCACCATGGAG 59.377 55.000 21.47 11.19 40.96 3.86
14 15 1.075601 AAAGAGAAGCCCACCATGGA 58.924 50.000 21.47 0.00 40.96 3.41
45 46 2.352229 CGCGTGTGCAGGTTTGTG 60.352 61.111 0.00 0.00 42.97 3.33
56 57 2.665649 TCAAGATTCATACCGCGTGT 57.334 45.000 4.92 5.32 0.00 4.49
96 97 4.411256 TGTCTCAGTCGGGTAAGTTTTT 57.589 40.909 0.00 0.00 0.00 1.94
106 107 6.480524 TTGATTTAACAATGTCTCAGTCGG 57.519 37.500 0.00 0.00 0.00 4.79
152 154 8.861086 CCTACTAGATAATACCTCACATGTTGT 58.139 37.037 0.00 0.00 0.00 3.32
319 321 1.374252 CGGCACAGCTACTTCCGTT 60.374 57.895 7.46 0.00 35.75 4.44
330 332 0.603707 AGATTGTGGTGACGGCACAG 60.604 55.000 25.47 0.00 46.96 3.66
341 343 0.918983 TTGCCCCCTCTAGATTGTGG 59.081 55.000 0.00 0.00 0.00 4.17
375 377 4.827481 GCCCTAAGCGATGACGAA 57.173 55.556 0.00 0.00 42.66 3.85
483 485 0.251653 AGAGTGTAGCCTCCGTTGGA 60.252 55.000 0.00 0.00 31.53 3.53
507 509 4.701651 TGCATGTAAAGAAAGGTGGATCTG 59.298 41.667 0.00 0.00 0.00 2.90
508 510 4.922206 TGCATGTAAAGAAAGGTGGATCT 58.078 39.130 0.00 0.00 0.00 2.75
511 513 5.647658 CACTATGCATGTAAAGAAAGGTGGA 59.352 40.000 10.16 0.00 0.00 4.02
523 525 7.701539 AATGAAAGGAAACACTATGCATGTA 57.298 32.000 10.16 0.00 0.00 2.29
566 568 3.062042 TGAAGCTATGCTGATGTATGCG 58.938 45.455 0.00 0.00 39.62 4.73
706 1059 0.687427 GCATGGCCAATGGGTAGGTT 60.687 55.000 10.96 0.00 36.71 3.50
707 1060 1.076044 GCATGGCCAATGGGTAGGT 60.076 57.895 10.96 0.00 36.71 3.08
708 1061 3.860681 GCATGGCCAATGGGTAGG 58.139 61.111 10.96 0.00 36.71 3.18
835 2957 2.081462 TGACAATGAGCTGTGCATCAG 58.919 47.619 10.75 10.75 46.12 2.90
836 2958 2.081462 CTGACAATGAGCTGTGCATCA 58.919 47.619 0.00 0.00 0.00 3.07
837 2959 1.400846 CCTGACAATGAGCTGTGCATC 59.599 52.381 0.00 0.00 0.00 3.91
838 2960 1.271762 ACCTGACAATGAGCTGTGCAT 60.272 47.619 0.00 0.00 0.00 3.96
839 2961 0.109153 ACCTGACAATGAGCTGTGCA 59.891 50.000 0.00 0.00 0.00 4.57
840 2962 1.734465 GTACCTGACAATGAGCTGTGC 59.266 52.381 0.00 0.00 0.00 4.57
841 2963 2.350522 GGTACCTGACAATGAGCTGTG 58.649 52.381 4.06 0.00 0.00 3.66
842 2964 2.770164 GGTACCTGACAATGAGCTGT 57.230 50.000 4.06 0.00 0.00 4.40
905 3028 3.499048 CATTAACGTCTAGCAGTCGTGT 58.501 45.455 8.55 3.99 38.90 4.49
934 3057 1.842562 AGTGGATCAGCTAAGCATGGT 59.157 47.619 0.00 0.00 0.00 3.55
1010 3136 1.388093 CATCTTCGTCGTTGCTCACAG 59.612 52.381 0.00 0.00 0.00 3.66
1011 3137 1.000717 TCATCTTCGTCGTTGCTCACA 60.001 47.619 0.00 0.00 0.00 3.58
1012 3138 1.698165 TCATCTTCGTCGTTGCTCAC 58.302 50.000 0.00 0.00 0.00 3.51
1016 3142 2.596452 TCTCTTCATCTTCGTCGTTGC 58.404 47.619 0.00 0.00 0.00 4.17
1023 3149 5.461737 GGAATACTGCTTCTCTTCATCTTCG 59.538 44.000 0.00 0.00 0.00 3.79
1025 3151 6.558488 AGGAATACTGCTTCTCTTCATCTT 57.442 37.500 0.00 0.00 0.00 2.40
1129 3291 2.158871 GGCATGGATCACCGTACCTTTA 60.159 50.000 0.00 0.00 36.07 1.85
1161 3323 3.275999 ACTAGAGAGAAGAGAACGGAGC 58.724 50.000 0.00 0.00 0.00 4.70
1166 3328 9.968870 TTTAAACTGAACTAGAGAGAAGAGAAC 57.031 33.333 0.00 0.00 0.00 3.01
1210 3372 1.261619 GTCTGCAACTCCTCAACAACG 59.738 52.381 0.00 0.00 0.00 4.10
1211 3373 1.604278 GGTCTGCAACTCCTCAACAAC 59.396 52.381 0.00 0.00 0.00 3.32
1212 3374 1.211703 TGGTCTGCAACTCCTCAACAA 59.788 47.619 0.00 0.00 0.00 2.83
1222 3384 1.181098 ATGGCCACTTGGTCTGCAAC 61.181 55.000 8.16 0.00 41.34 4.17
1279 3444 1.690219 GGGATCGACCTGGTGCAGAT 61.690 60.000 2.82 6.41 38.98 2.90
1438 3603 1.183676 AGAGTTCAGTTACCGCCGGT 61.184 55.000 15.63 15.63 40.16 5.28
1468 3633 0.585357 CGGTGCGCGTAGAGTAGTAT 59.415 55.000 8.43 0.00 0.00 2.12
1469 3634 1.431488 CCGGTGCGCGTAGAGTAGTA 61.431 60.000 8.43 0.00 0.00 1.82
1470 3635 2.758089 CCGGTGCGCGTAGAGTAGT 61.758 63.158 8.43 0.00 0.00 2.73
1471 3636 2.024305 CCGGTGCGCGTAGAGTAG 59.976 66.667 8.43 0.00 0.00 2.57
1472 3637 2.334946 AACCGGTGCGCGTAGAGTA 61.335 57.895 8.52 0.00 0.00 2.59
1473 3638 3.677648 AACCGGTGCGCGTAGAGT 61.678 61.111 8.52 0.00 0.00 3.24
1474 3639 3.179265 CAACCGGTGCGCGTAGAG 61.179 66.667 8.52 0.00 0.00 2.43
1475 3640 4.728102 CCAACCGGTGCGCGTAGA 62.728 66.667 8.52 0.00 0.00 2.59
1495 3673 0.835740 CGTTCGCATAACCGTAGACG 59.164 55.000 0.00 0.00 39.44 4.18
1496 3674 1.900237 ACGTTCGCATAACCGTAGAC 58.100 50.000 0.00 0.00 0.00 2.59
1497 3675 2.418280 TGTACGTTCGCATAACCGTAGA 59.582 45.455 0.00 0.00 36.57 2.59
1502 3680 0.641783 CGGTGTACGTTCGCATAACC 59.358 55.000 8.04 0.00 37.93 2.85
1518 3696 1.069906 GTAGTAACACACGTCGACGGT 60.070 52.381 37.89 28.97 44.95 4.83
1569 3750 3.117372 CAAGCAGCTAGGCATGCC 58.883 61.111 30.12 30.12 43.60 4.40
1651 3834 1.009222 CATCGTACGTAGCCCGACC 60.009 63.158 16.05 0.00 40.70 4.79
1706 3889 5.621555 GCTTTTGTGGACTGTCGTATCTAGA 60.622 44.000 0.00 0.00 0.00 2.43
1709 3892 3.326747 GCTTTTGTGGACTGTCGTATCT 58.673 45.455 1.07 0.00 0.00 1.98
1722 3905 6.638873 TGTATTTTTGTACATCGGCTTTTGTG 59.361 34.615 0.00 0.00 30.00 3.33
1816 4009 1.632422 AATTAACGTACCAGTCCGCG 58.368 50.000 0.00 0.00 0.00 6.46
1844 4037 3.194861 CGAAGAGAGACGAGAGAGTGAT 58.805 50.000 0.00 0.00 0.00 3.06
1853 4046 1.384989 GCATCCCCGAAGAGAGACGA 61.385 60.000 0.00 0.00 0.00 4.20
1854 4047 1.066587 GCATCCCCGAAGAGAGACG 59.933 63.158 0.00 0.00 0.00 4.18
1878 4071 1.531149 CAGTGGGTGCTTTTGACTACG 59.469 52.381 0.00 0.00 0.00 3.51
1890 4083 0.036010 CACCTCCTTAGCAGTGGGTG 60.036 60.000 0.00 0.00 35.66 4.61
1898 4091 2.104170 ACTACTCTGCACCTCCTTAGC 58.896 52.381 0.00 0.00 0.00 3.09
1899 4092 5.916661 TTTACTACTCTGCACCTCCTTAG 57.083 43.478 0.00 0.00 0.00 2.18
1905 4098 6.166982 GTCTCAAATTTACTACTCTGCACCT 58.833 40.000 0.00 0.00 0.00 4.00
1928 4121 2.347490 GGCAGTGACCGGTCATGT 59.653 61.111 38.11 25.92 42.18 3.21
1961 4154 0.873721 TTTTTGGTAACCGCGTAGGC 59.126 50.000 4.92 0.00 46.52 3.93
1980 4173 5.011329 TCTGATGACTTTACAGTACCCGTTT 59.989 40.000 0.00 0.00 31.22 3.60
1983 4176 4.713824 TCTGATGACTTTACAGTACCCG 57.286 45.455 0.00 0.00 31.22 5.28
2033 4226 0.677288 TCATATAGTCGGCCGGTTGG 59.323 55.000 27.83 8.94 38.77 3.77
2039 4232 4.595762 TGGTAACTTCATATAGTCGGCC 57.404 45.455 0.00 0.00 37.61 6.13
2082 4279 9.482627 GACCAGAATAGAATTAACTATGAGTGG 57.517 37.037 0.00 0.00 35.80 4.00
2095 4292 9.045745 AGAAGAGAGAAAAGACCAGAATAGAAT 57.954 33.333 0.00 0.00 0.00 2.40
2096 4293 8.429237 AGAAGAGAGAAAAGACCAGAATAGAA 57.571 34.615 0.00 0.00 0.00 2.10
2104 4301 7.604657 AGTAAAGAGAAGAGAGAAAAGACCA 57.395 36.000 0.00 0.00 0.00 4.02
2105 4302 8.145122 TGAAGTAAAGAGAAGAGAGAAAAGACC 58.855 37.037 0.00 0.00 0.00 3.85
2106 4303 9.535878 TTGAAGTAAAGAGAAGAGAGAAAAGAC 57.464 33.333 0.00 0.00 0.00 3.01
2126 4411 7.759489 TGCCACATTAGATTTTACTTGAAGT 57.241 32.000 2.37 2.37 0.00 3.01
2140 4766 5.220854 CGGGTTAGAAGAAATGCCACATTAG 60.221 44.000 0.00 0.00 0.00 1.73
2141 4767 4.638421 CGGGTTAGAAGAAATGCCACATTA 59.362 41.667 0.00 0.00 0.00 1.90
2144 4770 2.039216 TCGGGTTAGAAGAAATGCCACA 59.961 45.455 0.00 0.00 0.00 4.17
2145 4771 2.418976 GTCGGGTTAGAAGAAATGCCAC 59.581 50.000 0.00 0.00 0.00 5.01
2146 4772 2.304761 AGTCGGGTTAGAAGAAATGCCA 59.695 45.455 0.00 0.00 0.00 4.92
2148 4774 5.006746 CACATAGTCGGGTTAGAAGAAATGC 59.993 44.000 0.00 0.00 0.00 3.56
2150 4776 5.671493 CCACATAGTCGGGTTAGAAGAAAT 58.329 41.667 0.00 0.00 0.00 2.17
2154 4780 2.483188 GGCCACATAGTCGGGTTAGAAG 60.483 54.545 0.00 0.00 0.00 2.85
2157 4783 0.106149 GGGCCACATAGTCGGGTTAG 59.894 60.000 4.39 0.00 0.00 2.34
2171 4797 9.043548 GGTATTAGAGAAAGTATAATAGGGCCA 57.956 37.037 6.18 0.00 0.00 5.36
2172 4798 9.043548 TGGTATTAGAGAAAGTATAATAGGGCC 57.956 37.037 0.00 0.00 0.00 5.80
2173 4799 9.872721 GTGGTATTAGAGAAAGTATAATAGGGC 57.127 37.037 0.00 0.00 0.00 5.19
2217 4847 0.911769 TCCACTACCCTCTGCCAATG 59.088 55.000 0.00 0.00 0.00 2.82
2219 4849 0.909610 CCTCCACTACCCTCTGCCAA 60.910 60.000 0.00 0.00 0.00 4.52
2224 4854 0.252103 TTTCGCCTCCACTACCCTCT 60.252 55.000 0.00 0.00 0.00 3.69
2508 5138 6.602009 GTGACTATGCCTAGTAATTTGGGTTT 59.398 38.462 1.26 0.00 38.33 3.27
2509 5139 6.120220 GTGACTATGCCTAGTAATTTGGGTT 58.880 40.000 1.26 0.00 38.33 4.11
2510 5140 5.397559 GGTGACTATGCCTAGTAATTTGGGT 60.398 44.000 1.26 0.00 38.33 4.51
2511 5141 5.063880 GGTGACTATGCCTAGTAATTTGGG 58.936 45.833 1.26 0.00 38.33 4.12
2512 5142 5.760253 CAGGTGACTATGCCTAGTAATTTGG 59.240 44.000 1.26 0.00 40.21 3.28
2513 5143 6.349300 ACAGGTGACTATGCCTAGTAATTTG 58.651 40.000 1.26 1.26 40.21 2.32
2514 5144 6.561519 ACAGGTGACTATGCCTAGTAATTT 57.438 37.500 1.26 0.00 40.21 1.82
2515 5145 6.561519 AACAGGTGACTATGCCTAGTAATT 57.438 37.500 1.26 0.00 40.21 1.40
2516 5146 6.561519 AAACAGGTGACTATGCCTAGTAAT 57.438 37.500 1.26 0.00 40.21 1.89
2517 5147 6.666546 ACTAAACAGGTGACTATGCCTAGTAA 59.333 38.462 1.26 0.00 40.21 2.24
2518 5148 6.192773 ACTAAACAGGTGACTATGCCTAGTA 58.807 40.000 1.26 0.00 40.21 1.82
2519 5149 5.024118 ACTAAACAGGTGACTATGCCTAGT 58.976 41.667 0.79 0.79 40.21 2.57
2520 5150 5.452077 GGACTAAACAGGTGACTATGCCTAG 60.452 48.000 0.00 0.00 40.21 3.02
2521 5151 4.404715 GGACTAAACAGGTGACTATGCCTA 59.595 45.833 0.00 0.00 40.21 3.93
2522 5152 3.197983 GGACTAAACAGGTGACTATGCCT 59.802 47.826 0.00 0.00 40.21 4.75
2523 5153 3.055385 TGGACTAAACAGGTGACTATGCC 60.055 47.826 0.00 0.00 40.21 4.40
2524 5154 4.184629 CTGGACTAAACAGGTGACTATGC 58.815 47.826 0.00 0.00 40.21 3.14
2525 5155 4.184629 GCTGGACTAAACAGGTGACTATG 58.815 47.826 0.00 0.00 40.21 2.23
2526 5156 3.197983 GGCTGGACTAAACAGGTGACTAT 59.802 47.826 0.00 0.00 40.21 2.12
2527 5157 2.565834 GGCTGGACTAAACAGGTGACTA 59.434 50.000 0.00 0.00 40.21 2.59
2528 5158 1.348036 GGCTGGACTAAACAGGTGACT 59.652 52.381 0.00 0.00 46.44 3.41
2529 5159 1.610886 GGGCTGGACTAAACAGGTGAC 60.611 57.143 0.00 0.00 36.48 3.67
2530 5160 0.690762 GGGCTGGACTAAACAGGTGA 59.309 55.000 0.00 0.00 36.48 4.02
2531 5161 0.400213 TGGGCTGGACTAAACAGGTG 59.600 55.000 0.00 0.00 36.48 4.00
2532 5162 1.372501 ATGGGCTGGACTAAACAGGT 58.627 50.000 0.00 0.00 36.48 4.00
2533 5163 2.514458 AATGGGCTGGACTAAACAGG 57.486 50.000 0.00 0.00 36.48 4.00
2534 5164 4.339247 CCATTAATGGGCTGGACTAAACAG 59.661 45.833 24.61 0.00 44.31 3.16
2535 5165 4.277476 CCATTAATGGGCTGGACTAAACA 58.723 43.478 24.61 0.00 44.31 2.83
2536 5166 4.918810 CCATTAATGGGCTGGACTAAAC 57.081 45.455 24.61 0.00 44.31 2.01
2568 5198 3.436015 CAGTCCACGATCGTACCTATAGG 59.564 52.174 22.26 17.73 42.17 2.57
2569 5199 4.063689 ACAGTCCACGATCGTACCTATAG 58.936 47.826 22.26 6.47 0.00 1.31
2570 5200 4.060900 GACAGTCCACGATCGTACCTATA 58.939 47.826 22.26 0.00 0.00 1.31
2571 5201 2.877168 GACAGTCCACGATCGTACCTAT 59.123 50.000 22.26 5.95 0.00 2.57
2572 5202 2.093288 AGACAGTCCACGATCGTACCTA 60.093 50.000 22.26 3.62 0.00 3.08
2573 5203 1.093159 GACAGTCCACGATCGTACCT 58.907 55.000 22.26 13.57 0.00 3.08
2574 5204 1.093159 AGACAGTCCACGATCGTACC 58.907 55.000 22.26 11.42 0.00 3.34
2575 5205 2.477525 GGAAGACAGTCCACGATCGTAC 60.478 54.545 22.26 16.63 37.65 3.67
2576 5206 1.741706 GGAAGACAGTCCACGATCGTA 59.258 52.381 22.26 2.95 37.65 3.43
2577 5207 0.526662 GGAAGACAGTCCACGATCGT 59.473 55.000 16.60 16.60 37.65 3.73
2578 5208 0.523546 CGGAAGACAGTCCACGATCG 60.524 60.000 14.88 14.88 37.56 3.69
2579 5209 0.802607 GCGGAAGACAGTCCACGATC 60.803 60.000 11.92 0.00 37.56 3.69
2580 5210 1.215647 GCGGAAGACAGTCCACGAT 59.784 57.895 11.92 0.00 37.56 3.73
2581 5211 2.649034 GCGGAAGACAGTCCACGA 59.351 61.111 11.92 0.00 37.56 4.35
2582 5212 2.432628 GGCGGAAGACAGTCCACG 60.433 66.667 0.00 0.81 40.66 4.94
2583 5213 1.079750 GAGGCGGAAGACAGTCCAC 60.080 63.158 0.00 0.00 46.78 4.02
2584 5214 2.283529 GGAGGCGGAAGACAGTCCA 61.284 63.158 0.00 0.00 46.78 4.02
2585 5215 1.827399 TTGGAGGCGGAAGACAGTCC 61.827 60.000 0.00 0.00 46.78 3.85
2586 5216 0.670854 GTTGGAGGCGGAAGACAGTC 60.671 60.000 0.00 0.00 46.78 3.51
2587 5217 1.371558 GTTGGAGGCGGAAGACAGT 59.628 57.895 0.00 0.00 46.78 3.55
2588 5218 1.376037 GGTTGGAGGCGGAAGACAG 60.376 63.158 0.00 0.00 46.78 3.51
2589 5219 1.415672 AAGGTTGGAGGCGGAAGACA 61.416 55.000 0.00 0.00 46.78 3.41
2590 5220 0.673956 GAAGGTTGGAGGCGGAAGAC 60.674 60.000 0.00 0.00 42.06 3.01
2591 5221 1.125093 TGAAGGTTGGAGGCGGAAGA 61.125 55.000 0.00 0.00 0.00 2.87
2592 5222 0.250727 TTGAAGGTTGGAGGCGGAAG 60.251 55.000 0.00 0.00 0.00 3.46
2593 5223 0.404040 ATTGAAGGTTGGAGGCGGAA 59.596 50.000 0.00 0.00 0.00 4.30
2594 5224 0.035439 GATTGAAGGTTGGAGGCGGA 60.035 55.000 0.00 0.00 0.00 5.54
2595 5225 2.482326 GATTGAAGGTTGGAGGCGG 58.518 57.895 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.