Multiple sequence alignment - TraesCS2A01G042300

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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 TraesCS2A01G042300 chr2A 100.000 6039 0 0 1 6039 16990573 16984535 0.000000e+00 11153.0
1 TraesCS2A01G042300 chr2A 82.081 519 77 14 3394 3901 16884201 16883688 4.320000e-116 429.0
2 TraesCS2A01G042300 chr2A 85.385 260 28 5 3013 3265 16884511 16884255 1.670000e-65 261.0
3 TraesCS2A01G042300 chr2A 88.083 193 20 1 3073 3265 16874658 16874469 6.090000e-55 226.0
4 TraesCS2A01G042300 chr2D 91.903 5891 383 40 1 5844 14829366 14823523 0.000000e+00 8150.0
5 TraesCS2A01G042300 chr2D 91.912 544 35 3 5496 6039 14823521 14822987 0.000000e+00 752.0
6 TraesCS2A01G042300 chr2D 81.633 588 92 13 3392 3966 14787581 14786997 1.970000e-129 473.0
7 TraesCS2A01G042300 chr2D 82.198 455 71 8 3521 3966 14802274 14801821 3.410000e-102 383.0
8 TraesCS2A01G042300 chr2D 81.857 463 75 6 3476 3931 14780833 14780373 1.230000e-101 381.0
9 TraesCS2A01G042300 chr2D 81.439 431 51 18 2857 3265 14788086 14787663 5.840000e-85 326.0
10 TraesCS2A01G042300 chr2D 80.769 416 61 14 877 1277 14803199 14802788 2.110000e-79 307.0
11 TraesCS2A01G042300 chr2D 78.337 457 74 15 4052 4497 14801699 14801257 7.710000e-69 272.0
12 TraesCS2A01G042300 chr2D 87.565 193 21 2 3073 3265 14781314 14781125 2.830000e-53 220.0
13 TraesCS2A01G042300 chr2D 83.085 201 25 6 2628 2821 14788815 14788617 2.240000e-39 174.0
14 TraesCS2A01G042300 chr2D 83.041 171 23 5 2158 2325 638722443 638722276 3.770000e-32 150.0
15 TraesCS2A01G042300 chr2D 87.500 112 11 2 5728 5839 164392484 164392592 6.350000e-25 126.0
16 TraesCS2A01G042300 chr2D 100.000 34 0 0 2116 2149 67195935 67195902 5.050000e-06 63.9
17 TraesCS2A01G042300 chr2B 90.536 6097 438 70 1 6039 26732607 26726592 0.000000e+00 7934.0
18 TraesCS2A01G042300 chr2B 90.535 6096 437 67 1 6039 26711960 26705948 0.000000e+00 7932.0
19 TraesCS2A01G042300 chr2B 83.117 462 62 13 3449 3901 26582969 26582515 2.030000e-109 407.0
20 TraesCS2A01G042300 chr2B 81.144 472 82 5 3476 3940 26576469 26575998 7.390000e-99 372.0
21 TraesCS2A01G042300 chr2B 82.558 344 45 7 4158 4486 26589478 26589135 7.660000e-74 289.0
22 TraesCS2A01G042300 chr2B 87.678 211 22 2 3052 3261 26583360 26583153 6.050000e-60 243.0
23 TraesCS2A01G042300 chr2B 84.483 232 32 3 3073 3302 26590094 26589865 6.090000e-55 226.0
24 TraesCS2A01G042300 chr2B 83.065 248 38 3 4793 5036 26589112 26588865 7.880000e-54 222.0
25 TraesCS2A01G042300 chr2B 78.873 284 41 13 4184 4449 26575243 26574961 2.240000e-39 174.0
26 TraesCS2A01G042300 chr2B 83.815 173 25 3 1979 2149 104305923 104306094 1.740000e-35 161.0
27 TraesCS2A01G042300 chr2B 79.909 219 41 3 2249 2464 714520542 714520760 2.250000e-34 158.0
28 TraesCS2A01G042300 chr5D 80.128 312 59 3 2194 2504 547455503 547455812 4.710000e-56 230.0
29 TraesCS2A01G042300 chr5D 78.292 281 51 9 2182 2457 293205101 293205376 8.050000e-39 172.0
30 TraesCS2A01G042300 chr4D 81.588 277 43 6 2226 2499 437288160 437288431 7.880000e-54 222.0
31 TraesCS2A01G042300 chr3D 80.000 180 34 2 2158 2337 601186644 601186467 1.370000e-26 132.0
32 TraesCS2A01G042300 chrUn 88.182 110 10 2 5730 5839 321894324 321894218 1.770000e-25 128.0
33 TraesCS2A01G042300 chr6B 88.182 110 10 1 5730 5839 93568454 93568348 1.770000e-25 128.0
34 TraesCS2A01G042300 chr6B 79.646 113 19 4 189 299 46071637 46071527 1.800000e-10 78.7
35 TraesCS2A01G042300 chr6A 88.182 110 10 2 5730 5839 295818514 295818408 1.770000e-25 128.0
36 TraesCS2A01G042300 chr7D 84.375 128 17 3 2354 2480 403559316 403559441 8.220000e-24 122.0
37 TraesCS2A01G042300 chr7D 83.333 138 15 5 5719 5852 607955400 607955267 2.960000e-23 121.0
38 TraesCS2A01G042300 chr5B 75.261 287 55 13 2155 2438 600320466 600320193 8.220000e-24 122.0
39 TraesCS2A01G042300 chr5A 80.795 151 22 7 2009 2155 558336119 558335972 1.780000e-20 111.0


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 TraesCS2A01G042300 chr2A 16984535 16990573 6038 True 11153.000000 11153 100.000000 1 6039 1 chr2A.!!$R2 6038
1 TraesCS2A01G042300 chr2A 16883688 16884511 823 True 345.000000 429 83.733000 3013 3901 2 chr2A.!!$R3 888
2 TraesCS2A01G042300 chr2D 14822987 14829366 6379 True 4451.000000 8150 91.907500 1 6039 2 chr2D.!!$R6 6038
3 TraesCS2A01G042300 chr2D 14786997 14788815 1818 True 324.333333 473 82.052333 2628 3966 3 chr2D.!!$R4 1338
4 TraesCS2A01G042300 chr2D 14801257 14803199 1942 True 320.666667 383 80.434667 877 4497 3 chr2D.!!$R5 3620
5 TraesCS2A01G042300 chr2D 14780373 14781314 941 True 300.500000 381 84.711000 3073 3931 2 chr2D.!!$R3 858
6 TraesCS2A01G042300 chr2B 26726592 26732607 6015 True 7934.000000 7934 90.536000 1 6039 1 chr2B.!!$R2 6038
7 TraesCS2A01G042300 chr2B 26705948 26711960 6012 True 7932.000000 7932 90.535000 1 6039 1 chr2B.!!$R1 6038
8 TraesCS2A01G042300 chr2B 26582515 26583360 845 True 325.000000 407 85.397500 3052 3901 2 chr2B.!!$R4 849
9 TraesCS2A01G042300 chr2B 26574961 26576469 1508 True 273.000000 372 80.008500 3476 4449 2 chr2B.!!$R3 973
10 TraesCS2A01G042300 chr2B 26588865 26590094 1229 True 245.666667 289 83.368667 3073 5036 3 chr2B.!!$R5 1963

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
687 691 0.251073 ATACCCGTTCCCTTTCGTGG 59.749 55.000 0.0 0.0 0.00 4.94 F
1723 1740 1.002201 TCAAATGCAAATGGTGGCAGG 59.998 47.619 0.0 0.0 44.24 4.85 F
1929 1946 0.392461 GTTAGCATGAACCTCGGGCA 60.392 55.000 0.0 0.0 0.00 5.36 F
2262 2282 0.604780 ATAGCATCACCTCGGCATGC 60.605 55.000 9.9 9.9 42.81 4.06 F
3239 3800 0.662619 CGTTTCTTGCAGTTGAGGCA 59.337 50.000 0.0 0.0 40.00 4.75 F
4133 5526 0.249120 CTCCGTCCCACACAATGCTA 59.751 55.000 0.0 0.0 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 1851 0.098025 ACCAACTCGCAACAACAACG 59.902 50.000 0.0 0.0 0.00 4.10 R
3468 4224 1.351017 TGATGCGGGAGAAGAAAAGGT 59.649 47.619 0.0 0.0 0.00 3.50 R
3657 4417 1.471287 CCATCAGACACTGTTGCATGG 59.529 52.381 0.0 0.0 31.91 3.66 R
4119 5511 0.249120 CGAGGTAGCATTGTGTGGGA 59.751 55.000 0.0 0.0 0.00 4.37 R
4983 6407 0.105862 TCCGGACGGTATCTTCCCAT 60.106 55.000 10.9 0.0 36.47 4.00 R
5942 7710 0.394352 ATTAGGCAGGACGGGCAAAG 60.394 55.000 0.0 0.0 35.46 2.77 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
33 34 2.729360 GCAAAACACGTTCCATTTAGCC 59.271 45.455 0.00 0.00 0.00 3.93
54 55 4.700213 GCCAGCCTATACTTGTTCTTTTCA 59.300 41.667 0.00 0.00 0.00 2.69
65 66 9.736023 ATACTTGTTCTTTTCAATGTCACTTTC 57.264 29.630 0.00 0.00 0.00 2.62
71 72 7.251704 TCTTTTCAATGTCACTTTCAGAGAC 57.748 36.000 0.00 0.00 36.54 3.36
75 76 7.389803 TTCAATGTCACTTTCAGAGACAAAA 57.610 32.000 7.91 2.13 46.03 2.44
82 83 6.038714 GTCACTTTCAGAGACAAAATTGGACT 59.961 38.462 0.00 0.00 36.13 3.85
96 97 8.585018 ACAAAATTGGACTTAAAGTAATCCAGG 58.415 33.333 0.00 0.00 42.12 4.45
110 111 3.788227 ATCCAGGCTTTGTAGAACACA 57.212 42.857 0.00 0.00 34.51 3.72
123 124 4.573201 TGTAGAACACACTTTGGTAGTTGC 59.427 41.667 0.00 0.00 33.85 4.17
133 135 7.326789 CACACTTTGGTAGTTGCAAAATGATAG 59.673 37.037 0.00 0.00 33.85 2.08
140 142 8.136800 TGGTAGTTGCAAAATGATAGCATATTG 58.863 33.333 0.00 0.00 38.19 1.90
222 224 6.094186 CCTTTCCAACTACTTAGGCATTTCTC 59.906 42.308 0.00 0.00 0.00 2.87
223 225 5.099042 TCCAACTACTTAGGCATTTCTCC 57.901 43.478 0.00 0.00 0.00 3.71
234 236 3.648067 AGGCATTTCTCCAATCGATCCTA 59.352 43.478 0.00 0.00 0.00 2.94
254 257 5.538813 TCCTAGACATATTTCCACTACGCAT 59.461 40.000 0.00 0.00 0.00 4.73
262 265 4.497473 TTTCCACTACGCATTTGAAAGG 57.503 40.909 0.00 0.00 0.00 3.11
263 266 3.134574 TCCACTACGCATTTGAAAGGT 57.865 42.857 0.00 0.00 0.00 3.50
331 334 1.569493 CTCGCAACCCAACAACTCG 59.431 57.895 0.00 0.00 0.00 4.18
332 335 0.878523 CTCGCAACCCAACAACTCGA 60.879 55.000 0.00 0.00 0.00 4.04
364 368 2.534231 GCTGCCTTTTAGCTTCTTCG 57.466 50.000 0.00 0.00 38.14 3.79
385 389 8.458843 TCTTCGAAACAGAACAATTCTCTTTTT 58.541 29.630 0.00 0.04 38.11 1.94
386 390 8.614994 TTCGAAACAGAACAATTCTCTTTTTC 57.385 30.769 0.00 12.03 38.11 2.29
415 419 8.421249 AATTAATTTTGAGACCCAACATCTGA 57.579 30.769 0.00 0.00 33.85 3.27
416 420 5.712152 AATTTTGAGACCCAACATCTGAC 57.288 39.130 0.00 0.00 33.85 3.51
418 422 0.608130 TGAGACCCAACATCTGACCG 59.392 55.000 0.00 0.00 0.00 4.79
474 478 6.513393 GCCTTTTCCGTGTCATATTCCATAAG 60.513 42.308 0.00 0.00 0.00 1.73
475 479 6.371809 TTTTCCGTGTCATATTCCATAAGC 57.628 37.500 0.00 0.00 0.00 3.09
524 528 5.885449 ATTGAGAGACCCTCCTCAATTAG 57.115 43.478 10.71 0.00 41.90 1.73
548 552 3.057386 TGTGGCACTATTCATGCAACTTG 60.057 43.478 19.83 0.00 45.70 3.16
554 558 4.629634 CACTATTCATGCAACTTGGTCGTA 59.370 41.667 0.00 0.00 0.00 3.43
600 604 7.944000 AGTATGGCCAACATATCAACATCAATA 59.056 33.333 10.96 0.00 43.55 1.90
636 640 9.790344 ATTAGAGAAAATGGATCATCCTAACAG 57.210 33.333 4.96 0.00 37.46 3.16
639 643 7.127032 AGAGAAAATGGATCATCCTAACAGACT 59.873 37.037 4.96 0.00 37.46 3.24
640 644 7.278875 AGAAAATGGATCATCCTAACAGACTC 58.721 38.462 4.96 0.00 37.46 3.36
641 645 5.559148 AATGGATCATCCTAACAGACTCC 57.441 43.478 4.96 0.00 37.46 3.85
671 675 1.824230 TGGAAGCAATGCCCAACATAC 59.176 47.619 0.00 0.00 38.34 2.39
674 678 1.037030 AGCAATGCCCAACATACCCG 61.037 55.000 0.00 0.00 38.34 5.28
683 687 2.089201 CCAACATACCCGTTCCCTTTC 58.911 52.381 0.00 0.00 0.00 2.62
687 691 0.251073 ATACCCGTTCCCTTTCGTGG 59.749 55.000 0.00 0.00 0.00 4.94
694 698 1.990160 TTCCCTTTCGTGGCCACACT 61.990 55.000 34.16 0.00 45.50 3.55
695 699 1.122632 TCCCTTTCGTGGCCACACTA 61.123 55.000 34.16 17.02 45.50 2.74
723 727 7.410174 TCACTAGGAAATTAATCAACCCACAT 58.590 34.615 0.00 0.00 0.00 3.21
733 737 8.846423 ATTAATCAACCCACATAACCCATTTA 57.154 30.769 0.00 0.00 0.00 1.40
749 753 4.385643 CCCATTTATCAGAGAAGCCCTTCA 60.386 45.833 10.37 0.00 41.84 3.02
754 758 4.858965 ATCAGAGAAGCCCTTCATTCTT 57.141 40.909 10.37 0.00 41.84 2.52
782 786 7.716998 TGTTTGCTAAATAAAAGGCCATTTGAA 59.283 29.630 16.08 0.00 0.00 2.69
835 839 9.995003 TTTTCAATACAACTATTCCATTTTGCT 57.005 25.926 0.00 0.00 0.00 3.91
842 846 7.318141 ACAACTATTCCATTTTGCTGAATCAG 58.682 34.615 5.78 5.78 31.55 2.90
848 852 3.863424 CCATTTTGCTGAATCAGATGTGC 59.137 43.478 15.38 0.00 32.44 4.57
1009 1023 2.685999 GGGCAGAAATGGAGGCCT 59.314 61.111 3.86 3.86 45.68 5.19
1010 1024 1.454663 GGGCAGAAATGGAGGCCTC 60.455 63.158 25.59 25.59 45.68 4.70
1041 1055 1.341531 GCTATGTATCCTCAGCACCGT 59.658 52.381 0.00 0.00 34.13 4.83
1362 1378 2.539476 CAAGGTGGTGCTTTTGTCAAC 58.461 47.619 0.00 0.00 0.00 3.18
1445 1461 6.707440 TGCTTTTTCTGTTATCTTTCACCA 57.293 33.333 0.00 0.00 0.00 4.17
1511 1527 2.809665 GCTCAGGGTATCAAGCCATCAG 60.810 54.545 0.00 0.00 46.32 2.90
1512 1528 1.141657 TCAGGGTATCAAGCCATCAGC 59.858 52.381 0.00 0.00 46.32 4.26
1528 1544 2.816689 TCAGCGGTACAATGTTATCCG 58.183 47.619 15.75 15.75 43.37 4.18
1652 1669 9.979270 CAAGATTCATTCACTTCACATACTAAC 57.021 33.333 0.00 0.00 0.00 2.34
1667 1684 6.980978 CACATACTAACAGGTCCTCACTTATG 59.019 42.308 0.00 0.00 0.00 1.90
1723 1740 1.002201 TCAAATGCAAATGGTGGCAGG 59.998 47.619 0.00 0.00 44.24 4.85
1739 1756 5.057149 GTGGCAGGGATTAGTAGTGTTATG 58.943 45.833 0.00 0.00 0.00 1.90
1745 1762 6.205464 CAGGGATTAGTAGTGTTATGGCAATG 59.795 42.308 0.00 0.00 0.00 2.82
1752 1769 9.674068 TTAGTAGTGTTATGGCAATGTTCATTA 57.326 29.630 0.00 0.00 0.00 1.90
1839 1856 6.252967 TCTTCATGCAAAATCATACGTTGT 57.747 33.333 0.00 0.00 0.00 3.32
1846 1863 4.660414 GCAAAATCATACGTTGTTGTTGCG 60.660 41.667 14.91 0.00 0.00 4.85
1856 1873 2.319136 TGTTGTTGCGAGTTGGTAGT 57.681 45.000 0.00 0.00 0.00 2.73
1857 1874 2.634600 TGTTGTTGCGAGTTGGTAGTT 58.365 42.857 0.00 0.00 0.00 2.24
1858 1875 2.610374 TGTTGTTGCGAGTTGGTAGTTC 59.390 45.455 0.00 0.00 0.00 3.01
1859 1876 2.605837 TGTTGCGAGTTGGTAGTTCA 57.394 45.000 0.00 0.00 0.00 3.18
1860 1877 2.206750 TGTTGCGAGTTGGTAGTTCAC 58.793 47.619 0.00 0.00 0.00 3.18
1861 1878 2.206750 GTTGCGAGTTGGTAGTTCACA 58.793 47.619 0.00 0.00 0.00 3.58
1862 1879 2.605837 TGCGAGTTGGTAGTTCACAA 57.394 45.000 0.00 0.00 0.00 3.33
1863 1880 2.206750 TGCGAGTTGGTAGTTCACAAC 58.793 47.619 0.00 0.00 45.45 3.32
1884 1901 4.406456 ACTTCACATGGTTCTTATTGCCA 58.594 39.130 0.00 0.00 36.64 4.92
1891 1908 5.185056 ACATGGTTCTTATTGCCACCTTAAC 59.815 40.000 0.00 0.00 34.84 2.01
1901 1918 6.610075 ATTGCCACCTTAACAGAAATGAAT 57.390 33.333 0.00 0.00 0.00 2.57
1904 1921 7.716799 TGCCACCTTAACAGAAATGAATTAT 57.283 32.000 0.00 0.00 0.00 1.28
1927 1944 1.338674 TGTGTTAGCATGAACCTCGGG 60.339 52.381 0.00 0.00 0.00 5.14
1929 1946 0.392461 GTTAGCATGAACCTCGGGCA 60.392 55.000 0.00 0.00 0.00 5.36
1980 1997 2.345760 CCAGGCAAGCACACATCCC 61.346 63.158 0.00 0.00 0.00 3.85
2077 2096 5.511571 CAAATGTGCATGCAAAATTTCACA 58.488 33.333 27.49 18.49 38.56 3.58
2078 2097 4.735662 ATGTGCATGCAAAATTTCACAC 57.264 36.364 24.58 6.29 37.28 3.82
2090 2109 9.734620 TGCAAAATTTCACACTATTATGCTATC 57.265 29.630 0.00 0.00 0.00 2.08
2208 2228 6.460123 CCACTAACCCATTTATCTCAACATGC 60.460 42.308 0.00 0.00 0.00 4.06
2257 2277 2.620251 TGGAAATAGCATCACCTCGG 57.380 50.000 0.00 0.00 0.00 4.63
2262 2282 0.604780 ATAGCATCACCTCGGCATGC 60.605 55.000 9.90 9.90 42.81 4.06
2318 2338 4.873827 GCAAACATGCATGAGAATTTCCAT 59.126 37.500 32.75 3.33 34.41 3.41
2320 2340 6.535865 GCAAACATGCATGAGAATTTCCATTA 59.464 34.615 32.75 0.00 34.41 1.90
2328 2348 9.304335 TGCATGAGAATTTCCATTATATCATGT 57.696 29.630 17.05 0.00 38.59 3.21
2559 2579 3.888930 ACACCGTCTTTTTGGATGACATT 59.111 39.130 0.00 0.00 33.27 2.71
2567 2587 7.573656 CGTCTTTTTGGATGACATTGAGATTCA 60.574 37.037 0.00 0.00 33.27 2.57
2568 2588 8.248945 GTCTTTTTGGATGACATTGAGATTCAT 58.751 33.333 0.00 0.00 33.74 2.57
2569 2589 8.248253 TCTTTTTGGATGACATTGAGATTCATG 58.752 33.333 0.00 0.00 29.93 3.07
2572 2592 7.797038 TTGGATGACATTGAGATTCATGTAG 57.203 36.000 0.00 0.00 29.93 2.74
2606 2630 1.611491 GGTCGTGAGCCCATTTGAAAA 59.389 47.619 0.00 0.00 0.00 2.29
2608 2632 1.885887 TCGTGAGCCCATTTGAAAAGG 59.114 47.619 0.00 0.00 0.00 3.11
2633 2657 9.559958 GGTCATTTTGAAGTCTTTATACACATG 57.440 33.333 0.00 0.00 0.00 3.21
2682 2714 6.728089 TCATTTAGCATTCCCAATTGCATA 57.272 33.333 0.00 0.00 0.00 3.14
2701 2733 8.854979 TTGCATAGATGTTAATTTACATGCAC 57.145 30.769 18.17 5.27 38.99 4.57
2719 2751 3.244735 TGCACTTGTAGGTTGATTGCCTA 60.245 43.478 0.00 0.00 37.54 3.93
2806 2840 5.045797 ACTGAGGTATAGTTTTCCTTGACCC 60.046 44.000 0.00 0.00 30.48 4.46
2813 2847 8.050930 GGTATAGTTTTCCTTGACCCTTTGATA 58.949 37.037 0.00 0.00 0.00 2.15
2878 3414 6.921914 TGAATATCATTGTTGTGTGCAATCA 58.078 32.000 0.00 0.00 36.92 2.57
2924 3460 7.283127 ACCCATGTGCACATAATCTAGTAAAAG 59.717 37.037 30.92 13.98 34.26 2.27
2925 3461 7.134815 CCATGTGCACATAATCTAGTAAAAGC 58.865 38.462 30.92 0.00 34.26 3.51
2969 3505 8.871629 TTCTTTTACACCCTTAATCATGCTTA 57.128 30.769 0.00 0.00 0.00 3.09
3009 3560 5.916661 TGAGAACTCCTATGTTGAGGTAC 57.083 43.478 0.00 0.00 37.88 3.34
3134 3692 4.999950 GTCTTTGGTCATGGGAGCTATATG 59.000 45.833 0.00 0.00 42.05 1.78
3145 3703 7.237471 TCATGGGAGCTATATGGATGAAGTAAA 59.763 37.037 0.00 0.00 0.00 2.01
3239 3800 0.662619 CGTTTCTTGCAGTTGAGGCA 59.337 50.000 0.00 0.00 40.00 4.75
3360 4004 5.648092 CCTTGTTTACATTGACCTCCCTTAG 59.352 44.000 0.00 0.00 0.00 2.18
3444 4121 2.907910 TCTAAGTCAACTACCGTCGC 57.092 50.000 0.00 0.00 0.00 5.19
3468 4224 6.037172 GCTTGAGAAATTGACGCCTCTATTTA 59.963 38.462 5.43 0.00 33.58 1.40
3469 4225 6.903883 TGAGAAATTGACGCCTCTATTTAC 57.096 37.500 5.43 4.70 33.58 2.01
3663 4423 2.636647 TCACAAGAACAGTCCATGCA 57.363 45.000 0.00 0.00 0.00 3.96
3679 4442 1.596603 TGCAACAGTGTCTGATGGTG 58.403 50.000 0.00 0.00 35.32 4.17
3768 4531 9.212641 CAGAAGTCAGAGAAACAATTGAATCTA 57.787 33.333 13.59 0.00 0.00 1.98
3776 4539 7.122353 AGAGAAACAATTGAATCTATTGCTGCT 59.878 33.333 13.59 8.75 36.65 4.24
3934 4706 6.778834 TCACGTCCTATATCACTTTTGGTA 57.221 37.500 0.00 0.00 0.00 3.25
3976 4796 4.350368 ACAATTTGTTCCCATGTTTCCC 57.650 40.909 0.00 0.00 0.00 3.97
4018 4887 9.620259 TGCCTTTACACATGTATTGACATATAA 57.380 29.630 0.00 0.00 44.82 0.98
4062 5454 7.496747 ACACAAAACCTAGTTGCATGTTTTAT 58.503 30.769 5.36 0.00 38.47 1.40
4119 5511 1.697982 GCCTTGGATAATACCCTCCGT 59.302 52.381 0.00 0.00 34.05 4.69
4133 5526 0.249120 CTCCGTCCCACACAATGCTA 59.751 55.000 0.00 0.00 0.00 3.49
4138 5531 0.249120 TCCCACACAATGCTACCTCG 59.751 55.000 0.00 0.00 0.00 4.63
4319 5732 3.295093 ACTGATCTCTGGATGTGATCGT 58.705 45.455 0.00 0.00 44.32 3.73
4462 5876 4.634199 CGGTAAGTACTTGTTTCCCTTGA 58.366 43.478 18.56 0.00 0.00 3.02
4504 5918 3.243301 CCACCATATCTGCAATCTTGTGC 60.243 47.826 0.00 0.00 45.15 4.57
4512 5926 2.022934 TGCAATCTTGTGCTGTTGTGA 58.977 42.857 0.00 0.00 45.17 3.58
4568 5982 5.757988 ACTTTAAACCCCACAAGTACAAGA 58.242 37.500 0.00 0.00 0.00 3.02
4580 5994 7.308589 CCCACAAGTACAAGAAAATTGGACTAG 60.309 40.741 5.93 0.77 42.44 2.57
4620 6035 9.739276 ACATGGAAAGAAGTATTGTATTCTTCA 57.261 29.630 0.00 0.00 43.25 3.02
4625 6040 9.766277 GAAAGAAGTATTGTATTCTTCAGCTTG 57.234 33.333 8.21 0.00 43.25 4.01
4642 6057 5.425217 TCAGCTTGGGATAACATGACTAGAA 59.575 40.000 0.00 0.00 0.00 2.10
4650 6065 7.344612 TGGGATAACATGACTAGAAAGAGCTAA 59.655 37.037 0.00 0.00 0.00 3.09
4655 6070 8.940768 AACATGACTAGAAAGAGCTAATTCTC 57.059 34.615 14.84 4.82 37.16 2.87
4678 6093 6.449698 TCCAGAGAAATTTTGTCTTGCAATC 58.550 36.000 6.09 0.00 36.89 2.67
4686 6101 8.752766 AAATTTTGTCTTGCAATCTCAGTATG 57.247 30.769 0.00 0.00 36.89 2.39
4775 6190 3.254411 GCTCACTTTTCCTTTTGAGAGGG 59.746 47.826 1.64 0.00 38.19 4.30
4776 6191 3.823304 CTCACTTTTCCTTTTGAGAGGGG 59.177 47.826 0.00 0.00 38.19 4.79
4777 6192 3.204382 TCACTTTTCCTTTTGAGAGGGGT 59.796 43.478 0.00 0.00 37.41 4.95
4778 6193 3.319122 CACTTTTCCTTTTGAGAGGGGTG 59.681 47.826 0.00 0.00 37.41 4.61
4779 6194 2.675658 TTTCCTTTTGAGAGGGGTGG 57.324 50.000 0.00 0.00 37.41 4.61
4780 6195 0.777446 TTCCTTTTGAGAGGGGTGGG 59.223 55.000 0.00 0.00 37.41 4.61
4781 6196 1.140134 TCCTTTTGAGAGGGGTGGGG 61.140 60.000 0.00 0.00 37.41 4.96
4782 6197 1.384191 CTTTTGAGAGGGGTGGGGG 59.616 63.158 0.00 0.00 0.00 5.40
4808 6227 3.056607 GGGTGCATGTTGCTAACTTTGAT 60.057 43.478 0.00 0.00 45.31 2.57
4829 6248 6.830912 TGATCTGGTTATATACAGCTTTGCT 58.169 36.000 0.00 0.00 40.77 3.91
4896 6315 6.865205 AGCTCTTGTTTTGCTTCAATGATTAC 59.135 34.615 0.00 0.00 32.61 1.89
4900 6320 8.845227 TCTTGTTTTGCTTCAATGATTACAGTA 58.155 29.630 0.00 0.00 0.00 2.74
4923 6347 8.819845 AGTACAGATGATGGATATTTCATAGCA 58.180 33.333 0.00 0.00 32.84 3.49
4931 6355 9.316594 TGATGGATATTTCATAGCATGGATTTT 57.683 29.630 0.00 0.00 0.00 1.82
4983 6407 6.889177 TCAGAAACCCATACATGCAATTTCTA 59.111 34.615 0.00 0.00 33.67 2.10
5027 6451 1.834188 TCTGCCTAGTGATGTCGTGA 58.166 50.000 0.00 0.00 0.00 4.35
5137 6561 2.310647 GGAACTTCCCCCTTAACCATGA 59.689 50.000 0.00 0.00 0.00 3.07
5183 6607 2.783135 AGACTGTTGACCGCATGATTT 58.217 42.857 0.00 0.00 0.00 2.17
5196 6620 7.094420 TGACCGCATGATTTTCTTTGATTCTTA 60.094 33.333 0.00 0.00 0.00 2.10
5212 6636 6.713276 TGATTCTTAAATCGAACCCCACTTA 58.287 36.000 0.00 0.00 43.61 2.24
5234 6658 4.888326 TGGCTGGCAAATAAGTTTGAAT 57.112 36.364 0.00 0.00 46.03 2.57
5239 6663 6.347644 GGCTGGCAAATAAGTTTGAATTGAAC 60.348 38.462 5.17 0.00 46.03 3.18
5255 6679 4.827304 TTGAACGACTGAAATTGATGCA 57.173 36.364 0.00 0.00 0.00 3.96
5349 6773 6.774673 TGACTGTTATCCCATTTGTTGTCTA 58.225 36.000 0.00 0.00 0.00 2.59
5352 6776 6.879458 ACTGTTATCCCATTTGTTGTCTAGAC 59.121 38.462 16.32 16.32 0.00 2.59
5368 6792 9.826574 GTTGTCTAGACACATACCCAAATTATA 57.173 33.333 25.13 1.86 41.67 0.98
5398 6823 5.429130 ACCTTCTTTTTATCCGAGGACATC 58.571 41.667 0.00 0.00 0.00 3.06
5400 6825 5.294552 CCTTCTTTTTATCCGAGGACATCAC 59.705 44.000 0.00 0.00 0.00 3.06
5505 6930 2.655364 CGCTAGGATCACGGTGCG 60.655 66.667 2.51 0.00 37.57 5.34
5506 6931 2.279517 GCTAGGATCACGGTGCGG 60.280 66.667 2.51 0.00 0.00 5.69
5519 6944 0.597637 GGTGCGGATAGTGGTCATCG 60.598 60.000 0.00 0.00 0.00 3.84
5529 6954 3.247006 AGTGGTCATCGTAATGTGGAC 57.753 47.619 0.00 0.00 34.32 4.02
5585 7010 2.431782 AGCACTGTGAACAAGGCATTTT 59.568 40.909 12.86 0.00 0.00 1.82
5587 7012 3.737663 GCACTGTGAACAAGGCATTTTCA 60.738 43.478 12.86 5.14 0.00 2.69
5722 7490 9.941664 GACATGATGAATAAAATACTTGACCAG 57.058 33.333 0.00 0.00 0.00 4.00
5737 7505 7.989947 ACTTGACCAGATAAAATACTCCCTA 57.010 36.000 0.00 0.00 0.00 3.53
5742 7510 9.837681 TGACCAGATAAAATACTCCCTATGATA 57.162 33.333 0.00 0.00 0.00 2.15
5778 7546 6.536582 GTCACTCAAACACATGTATCTAGCAT 59.463 38.462 0.00 0.00 0.00 3.79
5794 7562 9.849166 GTATCTAGCATTGAAATAGGTCTAGAC 57.151 37.037 14.87 14.87 35.38 2.59
5796 7564 5.854010 AGCATTGAAATAGGTCTAGACGA 57.146 39.130 16.56 7.63 0.00 4.20
5797 7565 6.412362 AGCATTGAAATAGGTCTAGACGAT 57.588 37.500 16.56 9.63 0.00 3.73
5798 7566 7.526142 AGCATTGAAATAGGTCTAGACGATA 57.474 36.000 16.56 12.06 0.00 2.92
5805 7573 3.488778 AGGTCTAGACGATACATCCGT 57.511 47.619 16.56 0.00 43.56 4.69
5840 7608 6.791371 AGTAATATGGATCGGAAGGAGTAGA 58.209 40.000 0.00 0.00 0.00 2.59
5880 7648 7.595819 AACCCACAATAGAAAGTTTGATTGA 57.404 32.000 19.57 0.00 34.18 2.57
5897 7665 5.386924 TGATTGAATCATCATATGGTGCCA 58.613 37.500 11.35 6.31 34.96 4.92
5914 7682 6.071728 ATGGTGCCATCTATTGCTTAATAAGC 60.072 38.462 17.42 17.42 43.06 3.09
5932 7700 3.041508 AGCGGAGTCCTAGTTTTTGTC 57.958 47.619 7.77 0.00 0.00 3.18
5935 7703 3.306156 GCGGAGTCCTAGTTTTTGTCTCT 60.306 47.826 7.77 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.820648 ACATTGAAAAGAACAAGTATAGGCTG 58.179 34.615 0.00 0.00 0.00 4.85
71 72 7.545615 GCCTGGATTACTTTAAGTCCAATTTTG 59.454 37.037 0.00 0.00 40.03 2.44
75 76 6.079712 AGCCTGGATTACTTTAAGTCCAAT 57.920 37.500 0.00 0.00 40.03 3.16
82 83 7.940137 TGTTCTACAAAGCCTGGATTACTTTAA 59.060 33.333 0.00 0.00 32.54 1.52
96 97 4.632538 ACCAAAGTGTGTTCTACAAAGC 57.367 40.909 0.00 0.00 41.89 3.51
110 111 6.015519 TGCTATCATTTTGCAACTACCAAAGT 60.016 34.615 0.00 0.00 41.49 2.66
123 124 9.060347 AGTACTCACCAATATGCTATCATTTTG 57.940 33.333 0.00 3.57 39.66 2.44
133 135 5.419542 TCAACTCAGTACTCACCAATATGC 58.580 41.667 0.00 0.00 0.00 3.14
140 142 6.861065 TTTTTGATCAACTCAGTACTCACC 57.139 37.500 7.89 0.00 34.68 4.02
180 182 4.831698 GCAAGTTGCTTTGTGCCA 57.168 50.000 20.71 0.00 40.96 4.92
182 184 1.594397 GAAAGGCAAGTTGCTTTGTGC 59.406 47.619 23.98 13.59 42.03 4.57
183 185 2.204237 GGAAAGGCAAGTTGCTTTGTG 58.796 47.619 23.98 0.00 42.03 3.33
184 186 1.830477 TGGAAAGGCAAGTTGCTTTGT 59.170 42.857 23.98 14.56 42.03 2.83
185 187 2.600470 TGGAAAGGCAAGTTGCTTTG 57.400 45.000 23.98 0.00 42.03 2.77
186 188 2.501316 AGTTGGAAAGGCAAGTTGCTTT 59.499 40.909 26.16 22.41 44.88 3.51
222 224 6.591834 GTGGAAATATGTCTAGGATCGATTGG 59.408 42.308 0.00 0.00 0.00 3.16
223 225 7.382110 AGTGGAAATATGTCTAGGATCGATTG 58.618 38.462 0.00 0.00 0.00 2.67
234 236 6.112734 TCAAATGCGTAGTGGAAATATGTCT 58.887 36.000 0.00 0.00 0.00 3.41
254 257 5.047660 CGAACCCATTATTGGACCTTTCAAA 60.048 40.000 5.18 0.00 46.92 2.69
262 265 5.451381 GGGAATTTCGAACCCATTATTGGAC 60.451 44.000 15.62 0.00 46.92 4.02
263 266 4.647399 GGGAATTTCGAACCCATTATTGGA 59.353 41.667 15.62 0.00 46.92 3.53
346 349 4.024048 TGTTTCGAAGAAGCTAAAAGGCAG 60.024 41.667 0.00 0.00 45.90 4.85
385 389 7.717568 TGTTGGGTCTCAAAATTAATTTTCGA 58.282 30.769 20.71 18.67 37.86 3.71
386 390 7.938563 TGTTGGGTCTCAAAATTAATTTTCG 57.061 32.000 20.71 16.16 37.86 3.46
448 452 3.279434 GGAATATGACACGGAAAAGGCT 58.721 45.455 0.00 0.00 0.00 4.58
458 462 6.425114 ACGATTCTGCTTATGGAATATGACAC 59.575 38.462 0.00 0.00 33.05 3.67
474 478 4.093998 CCATATGCAAGGATACGATTCTGC 59.906 45.833 0.00 0.00 46.39 4.26
475 479 4.093998 GCCATATGCAAGGATACGATTCTG 59.906 45.833 7.33 0.00 40.83 3.02
510 514 2.173569 GCCACATCTAATTGAGGAGGGT 59.826 50.000 7.62 0.00 37.61 4.34
524 528 3.379372 AGTTGCATGAATAGTGCCACATC 59.621 43.478 0.00 0.00 39.80 3.06
548 552 3.991773 TGAGTGTGCTAAACAATACGACC 59.008 43.478 0.00 0.00 41.57 4.79
554 558 7.148188 CCATACTGATTGAGTGTGCTAAACAAT 60.148 37.037 0.00 0.00 41.35 2.71
620 624 4.825445 AGGAGTCTGTTAGGATGATCCAT 58.175 43.478 14.90 1.51 39.61 3.41
647 651 1.126488 TTGGGCATTGCTTCCAAACA 58.874 45.000 14.62 0.00 37.58 2.83
657 661 1.134175 GAACGGGTATGTTGGGCATTG 59.866 52.381 0.00 0.00 38.94 2.82
671 675 3.053896 GCCACGAAAGGGAACGGG 61.054 66.667 0.00 0.00 35.60 5.28
674 678 1.527380 TGTGGCCACGAAAGGGAAC 60.527 57.895 30.07 3.38 35.60 3.62
683 687 2.890808 AGTGATATAGTGTGGCCACG 57.109 50.000 30.07 0.00 46.56 4.94
687 691 9.726438 ATTAATTTCCTAGTGATATAGTGTGGC 57.274 33.333 0.00 0.00 0.00 5.01
695 699 9.574516 GTGGGTTGATTAATTTCCTAGTGATAT 57.425 33.333 0.00 0.00 0.00 1.63
723 727 4.726825 AGGGCTTCTCTGATAAATGGGTTA 59.273 41.667 0.00 0.00 0.00 2.85
733 737 4.858965 AAGAATGAAGGGCTTCTCTGAT 57.141 40.909 0.00 0.00 40.14 2.90
749 753 9.599866 GGCCTTTTATTTAGCAAACATAAGAAT 57.400 29.630 0.00 0.00 0.00 2.40
754 758 9.160496 CAAATGGCCTTTTATTTAGCAAACATA 57.840 29.630 15.68 0.00 0.00 2.29
782 786 9.956720 CTCACTTTGAAAAGTCTTATGACAAAT 57.043 29.630 11.02 0.00 45.65 2.32
835 839 5.237815 ACTAAAAGACGCACATCTGATTCA 58.762 37.500 0.00 0.00 0.00 2.57
872 876 5.701224 ACAGGTTCTTAACTTTCCCATCAA 58.299 37.500 0.00 0.00 0.00 2.57
927 931 9.520515 AGTTAGACAGATAACAACAATGGAAAT 57.479 29.630 0.05 0.00 37.98 2.17
1009 1023 1.102978 TACATAGCAGTGCGAGCAGA 58.897 50.000 10.00 0.00 0.00 4.26
1010 1024 2.057316 GATACATAGCAGTGCGAGCAG 58.943 52.381 10.00 1.60 0.00 4.24
1041 1055 7.883833 TGTAGTACCAGGTATATGTTTTTGCAA 59.116 33.333 1.54 0.00 0.00 4.08
1429 1445 5.724370 TCCTATGGTGGTGAAAGATAACAGA 59.276 40.000 0.00 0.00 0.00 3.41
1430 1446 5.989477 TCCTATGGTGGTGAAAGATAACAG 58.011 41.667 0.00 0.00 0.00 3.16
1431 1447 6.575244 ATCCTATGGTGGTGAAAGATAACA 57.425 37.500 0.00 0.00 0.00 2.41
1511 1527 2.542597 TGTCGGATAACATTGTACCGC 58.457 47.619 18.52 15.17 42.73 5.68
1512 1528 6.698329 TCTTAATGTCGGATAACATTGTACCG 59.302 38.462 17.74 17.74 46.56 4.02
1652 1669 5.089970 TGAACATCATAAGTGAGGACCTG 57.910 43.478 0.00 0.00 38.38 4.00
1723 1740 7.282224 TGAACATTGCCATAACACTACTAATCC 59.718 37.037 0.00 0.00 0.00 3.01
1739 1756 6.646240 ACACAACAAAGATAATGAACATTGCC 59.354 34.615 9.87 2.62 32.50 4.52
1745 1762 7.141363 AGCTTGACACAACAAAGATAATGAAC 58.859 34.615 0.00 0.00 0.00 3.18
1752 1769 7.365741 CAATAGAAGCTTGACACAACAAAGAT 58.634 34.615 2.10 0.00 0.00 2.40
1834 1851 0.098025 ACCAACTCGCAACAACAACG 59.902 50.000 0.00 0.00 0.00 4.10
1839 1856 2.610374 GTGAACTACCAACTCGCAACAA 59.390 45.455 0.00 0.00 0.00 2.83
1846 1863 4.873827 TGTGAAGTTGTGAACTACCAACTC 59.126 41.667 5.59 1.74 41.91 3.01
1856 1873 7.424803 CAATAAGAACCATGTGAAGTTGTGAA 58.575 34.615 0.00 0.00 0.00 3.18
1857 1874 6.514870 GCAATAAGAACCATGTGAAGTTGTGA 60.515 38.462 0.00 0.00 0.00 3.58
1858 1875 5.630680 GCAATAAGAACCATGTGAAGTTGTG 59.369 40.000 0.00 0.00 0.00 3.33
1859 1876 5.278957 GGCAATAAGAACCATGTGAAGTTGT 60.279 40.000 0.00 0.00 0.00 3.32
1860 1877 5.163513 GGCAATAAGAACCATGTGAAGTTG 58.836 41.667 0.00 0.00 0.00 3.16
1861 1878 4.832266 TGGCAATAAGAACCATGTGAAGTT 59.168 37.500 0.00 0.00 0.00 2.66
1862 1879 4.218417 GTGGCAATAAGAACCATGTGAAGT 59.782 41.667 0.00 0.00 35.53 3.01
1863 1880 4.380867 GGTGGCAATAAGAACCATGTGAAG 60.381 45.833 0.00 0.00 35.53 3.02
1891 1908 9.961265 ATGCTAACACATGATAATTCATTTCTG 57.039 29.630 0.00 0.00 40.70 3.02
1956 1973 2.710377 TGTGTGCTTGCCTGGTAATAG 58.290 47.619 0.00 0.00 0.00 1.73
1960 1977 0.322456 GGATGTGTGCTTGCCTGGTA 60.322 55.000 0.00 0.00 0.00 3.25
1962 1979 2.345760 GGGATGTGTGCTTGCCTGG 61.346 63.158 0.00 0.00 0.00 4.45
2065 2084 9.956720 AGATAGCATAATAGTGTGAAATTTTGC 57.043 29.630 0.00 0.00 39.11 3.68
2070 2089 9.935241 CCAGTAGATAGCATAATAGTGTGAAAT 57.065 33.333 0.00 0.00 0.00 2.17
2073 2092 9.582648 TTACCAGTAGATAGCATAATAGTGTGA 57.417 33.333 0.00 0.00 0.00 3.58
2174 2194 1.076265 GGGTTAGTGGGGGCAATCC 60.076 63.158 0.00 0.00 0.00 3.01
2176 2196 0.715987 AATGGGTTAGTGGGGGCAAT 59.284 50.000 0.00 0.00 0.00 3.56
2216 2236 3.966979 TGCATGTTCCATGATAAGGTGT 58.033 40.909 8.34 0.00 0.00 4.16
2229 2249 4.980434 GTGATGCTATTTCCATGCATGTTC 59.020 41.667 24.58 8.01 45.90 3.18
2247 2267 0.309922 GATTGCATGCCGAGGTGATG 59.690 55.000 16.68 0.00 0.00 3.07
2433 2453 7.959658 ATTCAATGAGATTTGGTTGTATGGA 57.040 32.000 0.00 0.00 0.00 3.41
2465 2485 4.566360 ACACCTTTCTGCGAAAATGTTTTG 59.434 37.500 11.38 0.00 0.00 2.44
2567 2587 7.768582 TCACGACCATAAATGAATCAACTACAT 59.231 33.333 0.00 0.00 0.00 2.29
2568 2588 7.100409 TCACGACCATAAATGAATCAACTACA 58.900 34.615 0.00 0.00 0.00 2.74
2569 2589 7.534085 TCACGACCATAAATGAATCAACTAC 57.466 36.000 0.00 0.00 0.00 2.73
2572 2592 5.266242 GCTCACGACCATAAATGAATCAAC 58.734 41.667 0.00 0.00 0.00 3.18
2606 2630 8.918202 TGTGTATAAAGACTTCAAAATGACCT 57.082 30.769 0.00 0.00 0.00 3.85
2682 2714 8.677300 CCTACAAGTGCATGTAAATTAACATCT 58.323 33.333 2.03 0.00 38.01 2.90
2719 2751 4.261155 CCACATTTTGTCACATGTTCTCGT 60.261 41.667 0.00 0.00 30.90 4.18
2816 2850 9.596308 AACCCAACCTATAAAGTTTAGAACAAT 57.404 29.630 1.21 0.00 0.00 2.71
2831 2892 7.463431 TCATTAGTGTACAAAACCCAACCTAT 58.537 34.615 0.00 0.00 0.00 2.57
2924 3460 5.932661 AGAAGAGCTCAAACTAAATTTCGC 58.067 37.500 17.77 0.00 0.00 4.70
2925 3461 8.788409 AAAAGAAGAGCTCAAACTAAATTTCG 57.212 30.769 17.77 0.00 0.00 3.46
3009 3560 9.317936 ACTGTAATGCACCATCATATTATATCG 57.682 33.333 0.00 0.00 0.00 2.92
3134 3692 5.779529 ATGGTGATGCATTTACTTCATCC 57.220 39.130 0.00 0.00 36.64 3.51
3239 3800 1.987807 ATACCAAGCGCTCCCTGCAT 61.988 55.000 12.06 0.00 43.06 3.96
3335 3909 3.655777 AGGGAGGTCAATGTAAACAAGGA 59.344 43.478 0.00 0.00 0.00 3.36
3336 3910 4.034285 AGGGAGGTCAATGTAAACAAGG 57.966 45.455 0.00 0.00 0.00 3.61
3386 4031 8.930846 AGCGGAATAAGGTATTCTAGTAACTA 57.069 34.615 7.69 0.00 43.15 2.24
3391 4036 7.836479 ACTAAGCGGAATAAGGTATTCTAGT 57.164 36.000 7.69 5.39 43.15 2.57
3400 4045 5.875359 AGAGAACAAACTAAGCGGAATAAGG 59.125 40.000 0.00 0.00 0.00 2.69
3408 4053 6.641314 TGACTTAGAAGAGAACAAACTAAGCG 59.359 38.462 0.00 0.00 41.76 4.68
3444 4121 6.428385 AAATAGAGGCGTCAATTTCTCAAG 57.572 37.500 9.41 0.00 0.00 3.02
3468 4224 1.351017 TGATGCGGGAGAAGAAAAGGT 59.649 47.619 0.00 0.00 0.00 3.50
3469 4225 2.012673 CTGATGCGGGAGAAGAAAAGG 58.987 52.381 0.00 0.00 0.00 3.11
3537 4297 2.094026 GGGATGAACACCCTGCATTTTC 60.094 50.000 0.00 0.00 43.65 2.29
3657 4417 1.471287 CCATCAGACACTGTTGCATGG 59.529 52.381 0.00 0.00 31.91 3.66
3662 4422 5.749596 TTAAACACCATCAGACACTGTTG 57.250 39.130 0.00 0.00 32.74 3.33
3663 4423 9.905713 ATATATTAAACACCATCAGACACTGTT 57.094 29.630 0.00 0.00 32.61 3.16
3776 4539 5.192927 CAGTCAATAAACTTCATGCCCCTA 58.807 41.667 0.00 0.00 0.00 3.53
3908 4680 5.005394 CCAAAAGTGATATAGGACGTGAACG 59.995 44.000 0.00 0.40 46.33 3.95
3911 4683 5.670792 ACCAAAAGTGATATAGGACGTGA 57.329 39.130 0.00 0.00 0.00 4.35
3934 4706 9.639563 AATTGTTTTAAAGGACATGGGAAAATT 57.360 25.926 0.00 0.00 0.00 1.82
4009 4877 8.896320 ACACACACAAAGTAACTTATATGTCA 57.104 30.769 0.00 0.00 0.00 3.58
4048 4917 9.231297 TCTAGCTTTTCTATAAAACATGCAACT 57.769 29.630 0.00 0.00 29.96 3.16
4062 5454 7.336931 CCTTTGCCATTAGTTCTAGCTTTTCTA 59.663 37.037 0.00 0.00 0.00 2.10
4069 5461 5.048013 ACAAACCTTTGCCATTAGTTCTAGC 60.048 40.000 0.00 0.00 41.79 3.42
4119 5511 0.249120 CGAGGTAGCATTGTGTGGGA 59.751 55.000 0.00 0.00 0.00 4.37
4133 5526 4.351874 TGAGAAACAAGAAATCCGAGGT 57.648 40.909 0.00 0.00 0.00 3.85
4179 5572 9.091220 ACTAGGACTTTCTAGTGTCAAATAGTT 57.909 33.333 4.02 0.00 45.68 2.24
4319 5732 8.656806 TCTTTTTCTTCTCTTGTCCATAACCTA 58.343 33.333 0.00 0.00 0.00 3.08
4468 5882 7.611467 GCAGATATGGTGGGTTGATTATATGAA 59.389 37.037 0.00 0.00 0.00 2.57
4537 5951 3.452627 TGTGGGGTTTAAAGTTGTTGCAT 59.547 39.130 0.00 0.00 0.00 3.96
4539 5953 3.528597 TGTGGGGTTTAAAGTTGTTGC 57.471 42.857 0.00 0.00 0.00 4.17
4620 6035 5.957771 TTCTAGTCATGTTATCCCAAGCT 57.042 39.130 0.00 0.00 0.00 3.74
4625 6040 6.168270 AGCTCTTTCTAGTCATGTTATCCC 57.832 41.667 0.00 0.00 0.00 3.85
4642 6057 8.738106 CAAAATTTCTCTGGAGAATTAGCTCTT 58.262 33.333 12.93 0.00 45.78 2.85
4650 6065 6.266103 TGCAAGACAAAATTTCTCTGGAGAAT 59.734 34.615 12.93 0.00 45.78 2.40
4655 6070 6.453092 AGATTGCAAGACAAAATTTCTCTGG 58.547 36.000 4.94 0.00 42.86 3.86
4663 6078 7.692460 TCATACTGAGATTGCAAGACAAAAT 57.308 32.000 4.94 0.00 42.86 1.82
4678 6093 9.926158 ATCTAGCACAAGAATATTCATACTGAG 57.074 33.333 17.56 8.51 0.00 3.35
4779 6194 4.315264 AACATGCACCCCACCCCC 62.315 66.667 0.00 0.00 0.00 5.40
4780 6195 2.996734 CAACATGCACCCCACCCC 60.997 66.667 0.00 0.00 0.00 4.95
4781 6196 3.694538 GCAACATGCACCCCACCC 61.695 66.667 0.00 0.00 44.26 4.61
4808 6227 9.056005 CAATTAGCAAAGCTGTATATAACCAGA 57.944 33.333 1.04 0.00 40.10 3.86
4847 6266 2.677836 CCTTATGTCGACCAACACCATG 59.322 50.000 14.12 0.00 30.55 3.66
4896 6315 9.096160 GCTATGAAATATCCATCATCTGTACTG 57.904 37.037 0.00 0.00 37.46 2.74
4900 6320 7.556635 CCATGCTATGAAATATCCATCATCTGT 59.443 37.037 2.83 0.00 37.46 3.41
4917 6337 6.943981 CATTGCAAAGAAAATCCATGCTATG 58.056 36.000 1.71 11.67 41.29 2.23
4983 6407 0.105862 TCCGGACGGTATCTTCCCAT 60.106 55.000 10.90 0.00 36.47 4.00
5027 6451 3.556004 GGTGCTCTAGCTCACTTCTTGTT 60.556 47.826 3.26 0.00 42.66 2.83
5116 6540 2.310647 TCATGGTTAAGGGGGAAGTTCC 59.689 50.000 13.99 13.99 35.23 3.62
5117 6541 3.732048 TCATGGTTAAGGGGGAAGTTC 57.268 47.619 0.00 0.00 0.00 3.01
5168 6592 4.545610 TCAAAGAAAATCATGCGGTCAAC 58.454 39.130 0.00 0.00 0.00 3.18
5183 6607 6.717540 TGGGGTTCGATTTAAGAATCAAAGAA 59.282 34.615 0.00 0.00 41.43 2.52
5196 6620 2.025321 AGCCATAAGTGGGGTTCGATTT 60.025 45.455 0.00 0.00 46.14 2.17
5212 6636 4.888326 TTCAAACTTATTTGCCAGCCAT 57.112 36.364 0.00 0.00 44.22 4.40
5234 6658 4.827304 TGCATCAATTTCAGTCGTTCAA 57.173 36.364 0.00 0.00 0.00 2.69
5239 6663 6.690098 CCTTATCTTTGCATCAATTTCAGTCG 59.310 38.462 0.00 0.00 0.00 4.18
5255 6679 7.990055 CCTATCCATAGGTTTCCCTTATCTTT 58.010 38.462 4.61 0.00 43.95 2.52
5285 6709 1.898472 CACTCCAGAGTCACAGATGGT 59.102 52.381 0.00 0.00 40.20 3.55
5286 6710 1.898472 ACACTCCAGAGTCACAGATGG 59.102 52.381 0.00 0.00 40.20 3.51
5321 6745 6.095440 ACAACAAATGGGATAACAGTCATAGC 59.905 38.462 0.00 0.00 0.00 2.97
5327 6751 6.879458 GTCTAGACAACAAATGGGATAACAGT 59.121 38.462 18.20 0.00 0.00 3.55
5328 6752 6.878923 TGTCTAGACAACAAATGGGATAACAG 59.121 38.462 23.24 0.00 38.56 3.16
5349 6773 9.693739 TTTCATGTATAATTTGGGTATGTGTCT 57.306 29.630 0.00 0.00 0.00 3.41
5352 6776 8.912988 AGGTTTCATGTATAATTTGGGTATGTG 58.087 33.333 0.00 0.00 0.00 3.21
5368 6792 6.151144 CCTCGGATAAAAAGAAGGTTTCATGT 59.849 38.462 0.00 0.00 0.00 3.21
5386 6811 1.182667 TCAACGTGATGTCCTCGGAT 58.817 50.000 0.00 0.00 36.21 4.18
5387 6812 1.182667 ATCAACGTGATGTCCTCGGA 58.817 50.000 0.00 0.00 35.43 4.55
5388 6813 2.159296 TGTATCAACGTGATGTCCTCGG 60.159 50.000 9.77 0.00 37.70 4.63
5390 6815 6.422776 AAAATGTATCAACGTGATGTCCTC 57.577 37.500 9.77 0.00 37.70 3.71
5484 6909 0.530650 CACCGTGATCCTAGCGCATT 60.531 55.000 11.47 0.00 0.00 3.56
5505 6930 4.038763 TCCACATTACGATGACCACTATCC 59.961 45.833 0.00 0.00 36.73 2.59
5506 6931 4.982916 GTCCACATTACGATGACCACTATC 59.017 45.833 0.00 0.00 36.73 2.08
5519 6944 5.479027 ACAATAAACCCAAGGTCCACATTAC 59.521 40.000 0.00 0.00 33.12 1.89
5529 6954 6.993786 AAAACAACAACAATAAACCCAAGG 57.006 33.333 0.00 0.00 0.00 3.61
5632 7057 7.379529 GCATGTTAGTTGGTCATAATTATGCAC 59.620 37.037 18.89 16.37 36.01 4.57
5742 7510 8.506437 CATGTGTTTGAGTGACAAGTAATATGT 58.494 33.333 0.00 0.00 39.77 2.29
5746 7514 6.942532 ACATGTGTTTGAGTGACAAGTAAT 57.057 33.333 0.00 0.00 39.77 1.89
5778 7546 7.308408 CGGATGTATCGTCTAGACCTATTTCAA 60.308 40.741 17.23 0.00 0.00 2.69
5794 7562 1.517276 GTCGCTCAAACGGATGTATCG 59.483 52.381 0.00 0.00 0.00 2.92
5796 7564 2.665649 TGTCGCTCAAACGGATGTAT 57.334 45.000 0.00 0.00 0.00 2.29
5797 7565 2.288579 ACTTGTCGCTCAAACGGATGTA 60.289 45.455 0.00 0.00 35.48 2.29
5798 7566 1.148310 CTTGTCGCTCAAACGGATGT 58.852 50.000 0.00 0.00 35.48 3.06
5805 7573 5.462068 CGATCCATATTACTTGTCGCTCAAA 59.538 40.000 0.00 0.00 35.48 2.69
5880 7648 6.096423 GCAATAGATGGCACCATATGATGATT 59.904 38.462 0.00 0.00 36.70 2.57
5914 7682 4.487019 GAGAGACAAAAACTAGGACTCCG 58.513 47.826 0.00 0.00 0.00 4.63
5932 7700 0.600255 ACGGGCAAAGTTGTCGAGAG 60.600 55.000 13.06 0.00 32.44 3.20
5935 7703 1.595929 GGACGGGCAAAGTTGTCGA 60.596 57.895 13.06 0.00 32.44 4.20
5942 7710 0.394352 ATTAGGCAGGACGGGCAAAG 60.394 55.000 0.00 0.00 35.46 2.77


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

AutoCloner maintained by Alex Coulton.