Multiple sequence alignment - TraesCS5D01G168400

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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 TraesCS5D01G168400 chr5D 100.000 4075 0 0 1 4075 264020237 264016163 0.000000e+00 7526.0
1 TraesCS5D01G168400 chr5D 97.143 35 1 0 109 143 454103100 454103066 4.400000e-05 60.2
2 TraesCS5D01G168400 chr5D 96.970 33 1 0 2953 2985 339356061 339356093 5.690000e-04 56.5
3 TraesCS5D01G168400 chr5A 96.544 1389 36 5 1954 3335 350237269 350235886 0.000000e+00 2289.0
4 TraesCS5D01G168400 chr5A 91.582 1580 64 30 143 1687 350239019 350237474 0.000000e+00 2117.0
5 TraesCS5D01G168400 chr5A 82.306 746 125 7 3331 4073 600259861 600260602 1.240000e-179 640.0
6 TraesCS5D01G168400 chr5A 80.577 381 62 10 2389 2765 440263633 440264005 2.400000e-72 283.0
7 TraesCS5D01G168400 chr5A 77.011 174 32 5 3658 3827 18064424 18064255 4.340000e-15 93.5
8 TraesCS5D01G168400 chr5A 92.857 56 4 0 49 104 350239072 350239017 9.390000e-12 82.4
9 TraesCS5D01G168400 chr5A 96.970 33 1 0 2953 2985 440265579 440265611 5.690000e-04 56.5
10 TraesCS5D01G168400 chr5A 94.286 35 2 0 109 143 664782292 664782258 2.000000e-03 54.7
11 TraesCS5D01G168400 chr5B 92.736 1597 57 13 143 1704 296379840 296378268 0.000000e+00 2252.0
12 TraesCS5D01G168400 chr5B 93.237 1449 60 19 1905 3334 296378196 296376767 0.000000e+00 2098.0
13 TraesCS5D01G168400 chr5B 94.231 104 6 0 1 104 296379941 296379838 4.220000e-35 159.0
14 TraesCS5D01G168400 chr5B 96.970 33 1 0 2953 2985 398349949 398349981 5.690000e-04 56.5
15 TraesCS5D01G168400 chr4B 88.400 750 78 6 3331 4075 567009357 567010102 0.000000e+00 894.0
16 TraesCS5D01G168400 chr4D 86.400 750 94 4 3324 4073 434884238 434883497 0.000000e+00 813.0
17 TraesCS5D01G168400 chr2A 86.040 745 86 8 3333 4075 751763015 751763743 0.000000e+00 784.0
18 TraesCS5D01G168400 chr2B 85.606 528 63 4 3499 4025 760040713 760041228 3.580000e-150 542.0
19 TraesCS5D01G168400 chr2B 87.850 107 13 0 3969 4075 760041229 760041335 4.280000e-25 126.0
20 TraesCS5D01G168400 chr2B 96.774 31 1 0 116 146 125221528 125221498 7.000000e-03 52.8
21 TraesCS5D01G168400 chr6B 78.209 748 121 26 3334 4075 709029762 709029051 1.340000e-119 440.0
22 TraesCS5D01G168400 chr6B 82.387 511 72 12 3331 3835 683426642 683427140 2.910000e-116 429.0
23 TraesCS5D01G168400 chr4A 86.458 384 46 6 3330 3711 697495382 697495003 2.270000e-112 416.0
24 TraesCS5D01G168400 chr3D 88.530 279 29 3 3327 3605 43005250 43004975 6.530000e-88 335.0
25 TraesCS5D01G168400 chr3D 93.103 203 9 3 1694 1891 575732369 575732571 3.980000e-75 292.0
26 TraesCS5D01G168400 chr3D 95.161 186 5 2 1704 1885 299744490 299744305 1.430000e-74 291.0
27 TraesCS5D01G168400 chr3A 78.330 503 97 12 3329 3827 685113051 685113545 8.500000e-82 315.0
28 TraesCS5D01G168400 chr3A 77.095 179 32 6 3658 3832 719688483 719688310 1.210000e-15 95.3
29 TraesCS5D01G168400 chr6D 95.652 184 4 2 1704 1883 112815735 112815918 3.980000e-75 292.0
30 TraesCS5D01G168400 chr6D 95.628 183 4 2 1704 1882 348607387 348607205 1.430000e-74 291.0
31 TraesCS5D01G168400 chr6D 95.135 185 4 3 1703 1882 436404407 436404223 1.850000e-73 287.0
32 TraesCS5D01G168400 chr6D 86.486 74 7 2 1043 1114 104988303 104988231 1.210000e-10 78.7
33 TraesCS5D01G168400 chr2D 92.929 198 10 2 1698 1891 6929558 6929361 6.670000e-73 285.0
34 TraesCS5D01G168400 chr1D 94.149 188 7 2 1704 1887 458763409 458763222 2.400000e-72 283.0
35 TraesCS5D01G168400 chr1D 97.059 34 1 0 109 142 10440800 10440833 1.580000e-04 58.4
36 TraesCS5D01G168400 chr7D 92.821 195 9 3 1692 1882 179220085 179219892 1.120000e-70 278.0
37 TraesCS5D01G168400 chr7D 90.385 208 15 3 1688 1890 49310992 49310785 6.710000e-68 268.0
38 TraesCS5D01G168400 chrUn 82.377 244 35 8 3323 3561 76824550 76824790 5.340000e-49 206.0
39 TraesCS5D01G168400 chr6A 83.784 74 9 2 1043 1114 127192076 127192004 2.630000e-07 67.6
40 TraesCS5D01G168400 chr7B 97.143 35 1 0 109 143 213417534 213417568 4.400000e-05 60.2


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 TraesCS5D01G168400 chr5D 264016163 264020237 4074 True 7526.000000 7526 100.000000 1 4075 1 chr5D.!!$R1 4074
1 TraesCS5D01G168400 chr5A 350235886 350239072 3186 True 1496.133333 2289 93.661000 49 3335 3 chr5A.!!$R3 3286
2 TraesCS5D01G168400 chr5A 600259861 600260602 741 False 640.000000 640 82.306000 3331 4073 1 chr5A.!!$F1 742
3 TraesCS5D01G168400 chr5B 296376767 296379941 3174 True 1503.000000 2252 93.401333 1 3334 3 chr5B.!!$R1 3333
4 TraesCS5D01G168400 chr4B 567009357 567010102 745 False 894.000000 894 88.400000 3331 4075 1 chr4B.!!$F1 744
5 TraesCS5D01G168400 chr4D 434883497 434884238 741 True 813.000000 813 86.400000 3324 4073 1 chr4D.!!$R1 749
6 TraesCS5D01G168400 chr2A 751763015 751763743 728 False 784.000000 784 86.040000 3333 4075 1 chr2A.!!$F1 742
7 TraesCS5D01G168400 chr2B 760040713 760041335 622 False 334.000000 542 86.728000 3499 4075 2 chr2B.!!$F1 576
8 TraesCS5D01G168400 chr6B 709029051 709029762 711 True 440.000000 440 78.209000 3334 4075 1 chr6B.!!$R1 741

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
959 973 0.319125 GCCTGTCGATACCTGCTAGC 60.319 60.000 8.10 8.10 0.0 3.42 F
1234 1277 0.037697 TTGCCTGCTAACACGATCGT 60.038 50.000 16.60 16.60 0.0 3.73 F
1236 1279 0.645868 GCCTGCTAACACGATCGTTC 59.354 55.000 20.14 6.17 0.0 3.95 F
1723 1766 1.469308 GGTGTGTCTAGGTCTCAGTCG 59.531 57.143 0.00 0.00 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2391 0.318869 CAACAAAAGGAGCGCATGCA 60.319 50.0 19.57 0.00 46.23 3.96 R
2190 2392 0.318955 ACAACAAAAGGAGCGCATGC 60.319 50.0 11.47 7.91 43.24 4.06 R
2746 2953 1.490693 CTGCATGCGACGGACATACC 61.491 60.0 14.09 0.00 0.00 2.73 R
3433 3664 0.741915 AGTCTAAGCGAGCTACTGCC 59.258 55.0 0.00 0.00 40.80 4.85 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
104 105 8.331931 TGTCCCTGGTTCAGAAAATATATACT 57.668 34.615 0.00 0.00 32.44 2.12
105 106 8.210946 TGTCCCTGGTTCAGAAAATATATACTG 58.789 37.037 0.00 7.66 32.44 2.74
106 107 8.211629 GTCCCTGGTTCAGAAAATATATACTGT 58.788 37.037 11.53 0.00 32.44 3.55
107 108 8.210946 TCCCTGGTTCAGAAAATATATACTGTG 58.789 37.037 11.53 1.49 32.44 3.66
109 110 9.613428 CCTGGTTCAGAAAATATATACTGTGAA 57.387 33.333 11.53 7.82 32.44 3.18
131 132 9.916397 GTGAAAACACTCTTATATTATGGAACG 57.084 33.333 0.00 0.00 0.00 3.95
132 133 9.878667 TGAAAACACTCTTATATTATGGAACGA 57.121 29.630 0.00 0.00 0.00 3.85
135 136 8.888579 AACACTCTTATATTATGGAACGAAGG 57.111 34.615 0.00 0.00 0.00 3.46
136 137 7.442656 ACACTCTTATATTATGGAACGAAGGG 58.557 38.462 0.00 0.00 0.00 3.95
137 138 7.289317 ACACTCTTATATTATGGAACGAAGGGA 59.711 37.037 0.00 0.00 0.00 4.20
138 139 7.815068 CACTCTTATATTATGGAACGAAGGGAG 59.185 40.741 0.00 0.00 0.00 4.30
139 140 7.509659 ACTCTTATATTATGGAACGAAGGGAGT 59.490 37.037 0.00 0.00 0.00 3.85
140 141 8.945195 TCTTATATTATGGAACGAAGGGAGTA 57.055 34.615 0.00 0.00 0.00 2.59
141 142 8.800332 TCTTATATTATGGAACGAAGGGAGTAC 58.200 37.037 0.00 0.00 0.00 2.73
142 143 8.716674 TTATATTATGGAACGAAGGGAGTACT 57.283 34.615 0.00 0.00 0.00 2.73
143 144 9.812347 TTATATTATGGAACGAAGGGAGTACTA 57.188 33.333 0.00 0.00 0.00 1.82
144 145 5.841957 TTATGGAACGAAGGGAGTACTAC 57.158 43.478 0.00 0.00 0.00 2.73
145 146 3.159213 TGGAACGAAGGGAGTACTACA 57.841 47.619 7.57 0.00 0.00 2.74
146 147 3.705051 TGGAACGAAGGGAGTACTACAT 58.295 45.455 7.57 0.00 0.00 2.29
147 148 4.858850 TGGAACGAAGGGAGTACTACATA 58.141 43.478 7.57 0.00 0.00 2.29
148 149 5.452255 TGGAACGAAGGGAGTACTACATAT 58.548 41.667 7.57 0.00 0.00 1.78
149 150 6.604171 TGGAACGAAGGGAGTACTACATATA 58.396 40.000 7.57 0.00 0.00 0.86
150 151 6.488006 TGGAACGAAGGGAGTACTACATATAC 59.512 42.308 7.57 0.00 0.00 1.47
151 152 6.348050 GGAACGAAGGGAGTACTACATATACG 60.348 46.154 7.57 9.52 0.00 3.06
152 153 5.858381 ACGAAGGGAGTACTACATATACGA 58.142 41.667 16.51 0.00 0.00 3.43
153 154 6.471146 ACGAAGGGAGTACTACATATACGAT 58.529 40.000 16.51 3.53 0.00 3.73
154 155 6.939163 ACGAAGGGAGTACTACATATACGATT 59.061 38.462 16.51 0.00 0.00 3.34
191 192 4.400567 GCTAAAATGTGAAATCAGGGAGCT 59.599 41.667 0.00 0.00 0.00 4.09
192 193 5.590259 GCTAAAATGTGAAATCAGGGAGCTA 59.410 40.000 0.00 0.00 0.00 3.32
193 194 5.904362 AAAATGTGAAATCAGGGAGCTAC 57.096 39.130 0.00 0.00 0.00 3.58
194 195 2.672961 TGTGAAATCAGGGAGCTACG 57.327 50.000 0.00 0.00 0.00 3.51
274 279 1.699083 TCGTCCATATGCATGATGGGT 59.301 47.619 23.58 0.00 43.58 4.51
312 317 3.677156 ATACCCTGACGTTACCTAGGT 57.323 47.619 20.57 20.57 0.00 3.08
313 318 1.844687 ACCCTGACGTTACCTAGGTC 58.155 55.000 20.32 3.78 41.06 3.85
314 319 1.109609 CCCTGACGTTACCTAGGTCC 58.890 60.000 20.32 9.63 40.18 4.46
315 320 1.341778 CCCTGACGTTACCTAGGTCCT 60.342 57.143 20.32 0.00 40.18 3.85
316 321 2.092212 CCCTGACGTTACCTAGGTCCTA 60.092 54.545 20.32 2.04 40.18 2.94
317 322 3.212685 CCTGACGTTACCTAGGTCCTAG 58.787 54.545 20.32 17.97 40.18 3.02
388 397 4.814234 CCCACATAAAGCACATGTACGTAT 59.186 41.667 0.00 0.00 34.88 3.06
423 435 3.067601 TGACAACACACAGACGAGTACAT 59.932 43.478 0.00 0.00 0.00 2.29
424 436 3.381045 ACAACACACAGACGAGTACATG 58.619 45.455 0.00 0.00 0.00 3.21
425 437 2.065993 ACACACAGACGAGTACATGC 57.934 50.000 0.00 0.00 0.00 4.06
426 438 1.339929 ACACACAGACGAGTACATGCA 59.660 47.619 0.00 0.00 0.00 3.96
427 439 1.721389 CACACAGACGAGTACATGCAC 59.279 52.381 0.00 0.00 0.00 4.57
428 440 1.339929 ACACAGACGAGTACATGCACA 59.660 47.619 0.00 0.00 0.00 4.57
488 500 5.343593 CCTCACGAATCACGATTTCTATAGC 59.656 44.000 0.00 0.00 45.77 2.97
571 583 0.885196 GGCAAACGGCTGGTTATGAA 59.115 50.000 0.00 0.00 44.01 2.57
608 620 6.093633 GCTTAATCTCCGGTAAACAAATGAGT 59.906 38.462 0.00 0.00 0.00 3.41
704 716 5.801531 ATAAAGAAAGTTTCCCACCAACC 57.198 39.130 12.05 0.00 0.00 3.77
895 907 2.014128 GCAGTGTTGTGTGGTACTGTT 58.986 47.619 0.00 0.00 41.84 3.16
915 927 4.101898 TGTTGTAAGTAGCAGGGAAGAACA 59.898 41.667 0.00 0.00 0.00 3.18
954 968 1.066858 ACTTGTGCCTGTCGATACCTG 60.067 52.381 0.00 0.00 0.00 4.00
955 969 0.391130 TTGTGCCTGTCGATACCTGC 60.391 55.000 0.00 0.00 0.00 4.85
956 970 1.257750 TGTGCCTGTCGATACCTGCT 61.258 55.000 0.00 0.00 0.00 4.24
957 971 0.744874 GTGCCTGTCGATACCTGCTA 59.255 55.000 0.00 0.00 0.00 3.49
958 972 1.032794 TGCCTGTCGATACCTGCTAG 58.967 55.000 0.00 0.00 0.00 3.42
959 973 0.319125 GCCTGTCGATACCTGCTAGC 60.319 60.000 8.10 8.10 0.00 3.42
960 974 1.032794 CCTGTCGATACCTGCTAGCA 58.967 55.000 18.22 18.22 0.00 3.49
961 975 1.000827 CCTGTCGATACCTGCTAGCAG 60.001 57.143 33.58 33.58 43.26 4.24
962 976 0.385751 TGTCGATACCTGCTAGCAGC 59.614 55.000 34.82 21.62 42.35 5.25
981 1016 1.193203 GCATCTACATCGTGCCAATCG 59.807 52.381 0.00 0.00 32.88 3.34
983 1018 1.107945 TCTACATCGTGCCAATCGGA 58.892 50.000 0.00 0.00 0.00 4.55
1012 1055 1.234821 GAGAGAGATGCCGATCGAGT 58.765 55.000 18.66 1.09 33.34 4.18
1035 1078 2.806621 GACAACGTACCGGCCGAC 60.807 66.667 30.73 17.64 0.00 4.79
1122 1165 3.474570 CGCCTCCTCCAGAAGGGG 61.475 72.222 0.00 0.00 46.52 4.79
1168 1211 1.596934 CCTGGTACGTGTGGCATCT 59.403 57.895 0.00 0.00 0.00 2.90
1175 1218 2.586258 ACGTGTGGCATCTCATACTC 57.414 50.000 0.00 0.00 0.00 2.59
1233 1276 1.290203 ATTGCCTGCTAACACGATCG 58.710 50.000 14.88 14.88 0.00 3.69
1234 1277 0.037697 TTGCCTGCTAACACGATCGT 60.038 50.000 16.60 16.60 0.00 3.73
1235 1278 0.037697 TGCCTGCTAACACGATCGTT 60.038 50.000 20.14 7.98 0.00 3.85
1236 1279 0.645868 GCCTGCTAACACGATCGTTC 59.354 55.000 20.14 6.17 0.00 3.95
1354 1397 2.434359 GAGCCCGAAACCCTCGTG 60.434 66.667 0.00 0.00 46.65 4.35
1719 1762 4.764050 TTTTTGGTGTGTCTAGGTCTCA 57.236 40.909 0.00 0.00 0.00 3.27
1720 1763 4.336889 TTTTGGTGTGTCTAGGTCTCAG 57.663 45.455 0.00 0.00 0.00 3.35
1721 1764 2.677542 TGGTGTGTCTAGGTCTCAGT 57.322 50.000 0.00 0.00 0.00 3.41
1722 1765 2.515854 TGGTGTGTCTAGGTCTCAGTC 58.484 52.381 0.00 0.00 0.00 3.51
1723 1766 1.469308 GGTGTGTCTAGGTCTCAGTCG 59.531 57.143 0.00 0.00 0.00 4.18
1724 1767 2.424557 GTGTGTCTAGGTCTCAGTCGA 58.575 52.381 0.00 0.00 0.00 4.20
1725 1768 2.160022 GTGTGTCTAGGTCTCAGTCGAC 59.840 54.545 7.70 7.70 0.00 4.20
1726 1769 2.038689 TGTGTCTAGGTCTCAGTCGACT 59.961 50.000 13.58 13.58 34.38 4.18
1727 1770 2.417239 GTGTCTAGGTCTCAGTCGACTG 59.583 54.545 34.76 34.76 45.08 3.51
1756 1799 9.036980 ACTTAACCAAGTCTTGAGTGATATAGT 57.963 33.333 14.42 2.41 41.25 2.12
1833 1876 9.836076 ATGCAAGATCAATGAAATATAACATCG 57.164 29.630 0.00 0.00 0.00 3.84
1834 1877 9.054922 TGCAAGATCAATGAAATATAACATCGA 57.945 29.630 0.00 0.00 0.00 3.59
1835 1878 9.322776 GCAAGATCAATGAAATATAACATCGAC 57.677 33.333 0.00 0.00 0.00 4.20
1838 1881 9.987272 AGATCAATGAAATATAACATCGACTGA 57.013 29.630 0.00 0.00 0.00 3.41
1840 1883 9.987272 ATCAATGAAATATAACATCGACTGAGA 57.013 29.630 0.00 0.00 0.00 3.27
1841 1884 9.249457 TCAATGAAATATAACATCGACTGAGAC 57.751 33.333 0.00 0.00 0.00 3.36
1842 1885 9.034544 CAATGAAATATAACATCGACTGAGACA 57.965 33.333 0.00 0.00 0.00 3.41
1843 1886 9.770097 AATGAAATATAACATCGACTGAGACAT 57.230 29.630 0.00 0.00 0.00 3.06
1847 1890 8.729529 AATATAACATCGACTGAGACATAACG 57.270 34.615 0.00 0.00 0.00 3.18
1848 1891 4.696899 AACATCGACTGAGACATAACGA 57.303 40.909 0.00 0.00 0.00 3.85
1849 1892 4.696899 ACATCGACTGAGACATAACGAA 57.303 40.909 0.00 0.00 33.77 3.85
1850 1893 5.055642 ACATCGACTGAGACATAACGAAA 57.944 39.130 0.00 0.00 33.77 3.46
1851 1894 5.651530 ACATCGACTGAGACATAACGAAAT 58.348 37.500 0.00 0.00 33.77 2.17
1852 1895 5.744345 ACATCGACTGAGACATAACGAAATC 59.256 40.000 0.00 0.00 33.77 2.17
1853 1896 5.562506 TCGACTGAGACATAACGAAATCT 57.437 39.130 0.00 0.00 0.00 2.40
1854 1897 6.673154 TCGACTGAGACATAACGAAATCTA 57.327 37.500 0.00 0.00 0.00 1.98
1855 1898 7.080353 TCGACTGAGACATAACGAAATCTAA 57.920 36.000 0.00 0.00 0.00 2.10
1856 1899 7.187480 TCGACTGAGACATAACGAAATCTAAG 58.813 38.462 0.00 0.00 0.00 2.18
1857 1900 6.967767 CGACTGAGACATAACGAAATCTAAGT 59.032 38.462 0.00 0.00 35.87 2.24
1858 1901 7.164498 CGACTGAGACATAACGAAATCTAAGTC 59.836 40.741 7.33 7.33 42.70 3.01
1859 1902 6.967767 ACTGAGACATAACGAAATCTAAGTCG 59.032 38.462 0.00 0.00 42.91 4.18
1860 1903 7.080353 TGAGACATAACGAAATCTAAGTCGA 57.920 36.000 0.00 0.00 39.64 4.20
1861 1904 6.965500 TGAGACATAACGAAATCTAAGTCGAC 59.035 38.462 7.70 7.70 39.64 4.20
1862 1905 7.086230 AGACATAACGAAATCTAAGTCGACT 57.914 36.000 13.58 13.58 39.64 4.18
1863 1906 6.967767 AGACATAACGAAATCTAAGTCGACTG 59.032 38.462 20.85 7.79 39.64 3.51
1864 1907 6.849502 ACATAACGAAATCTAAGTCGACTGA 58.150 36.000 20.85 13.61 39.64 3.41
1865 1908 6.967767 ACATAACGAAATCTAAGTCGACTGAG 59.032 38.462 22.32 22.32 39.64 3.35
1866 1909 5.624344 AACGAAATCTAAGTCGACTGAGA 57.376 39.130 30.58 30.58 39.64 3.27
1867 1910 4.972201 ACGAAATCTAAGTCGACTGAGAC 58.028 43.478 30.97 18.96 36.33 3.36
1868 1911 4.023128 CGAAATCTAAGTCGACTGAGACG 58.977 47.826 30.97 25.25 45.26 4.18
1869 1912 4.435784 CGAAATCTAAGTCGACTGAGACGT 60.436 45.833 30.97 22.20 45.26 4.34
1870 1913 5.220359 CGAAATCTAAGTCGACTGAGACGTA 60.220 44.000 30.97 12.59 45.26 3.57
1871 1914 5.721876 AATCTAAGTCGACTGAGACGTAG 57.278 43.478 30.97 20.75 46.90 3.51
1872 1915 2.928757 TCTAAGTCGACTGAGACGTAGC 59.071 50.000 26.12 0.00 45.92 3.58
1873 1916 1.520494 AAGTCGACTGAGACGTAGCA 58.480 50.000 20.85 0.00 45.26 3.49
1874 1917 1.520494 AGTCGACTGAGACGTAGCAA 58.480 50.000 19.30 0.00 45.26 3.91
1875 1918 1.878088 AGTCGACTGAGACGTAGCAAA 59.122 47.619 19.30 0.00 45.26 3.68
1876 1919 2.292569 AGTCGACTGAGACGTAGCAAAA 59.707 45.455 19.30 0.00 45.26 2.44
1877 1920 2.404361 GTCGACTGAGACGTAGCAAAAC 59.596 50.000 8.70 0.00 0.00 2.43
1878 1921 2.292569 TCGACTGAGACGTAGCAAAACT 59.707 45.455 4.08 0.00 0.00 2.66
1879 1922 2.405357 CGACTGAGACGTAGCAAAACTG 59.595 50.000 0.00 0.00 0.00 3.16
1882 1925 4.189231 ACTGAGACGTAGCAAAACTGTTT 58.811 39.130 0.00 0.00 0.00 2.83
1929 2131 4.354587 GTTACTGCCAATGATTTGCTAGC 58.645 43.478 8.10 8.10 0.00 3.42
1948 2150 6.036300 TGCTAGCACGTACGCTTAATTAATTT 59.964 34.615 14.93 0.00 43.56 1.82
2002 2204 1.545582 CGTGGATGCAAAGGTGGAATT 59.454 47.619 0.00 0.00 0.00 2.17
2016 2218 4.720273 AGGTGGAATTCGTATAGAAAGGGT 59.280 41.667 0.00 0.00 42.91 4.34
2057 2259 3.209410 CTGAGGCCAATGAGGTATTGTC 58.791 50.000 5.01 0.00 43.78 3.18
2133 2335 3.738791 GCCATTTTTAACCACTCCAAACG 59.261 43.478 0.00 0.00 0.00 3.60
2378 2585 4.399303 AGCATGCATGATGATATCCATGTG 59.601 41.667 30.64 12.53 41.49 3.21
2379 2586 4.440112 GCATGCATGATGATATCCATGTGG 60.440 45.833 30.64 11.43 41.49 4.17
2675 2882 2.758327 TACATCTGCGCCGAGGGT 60.758 61.111 17.54 14.62 0.00 4.34
2746 2953 1.305549 AGTACCCCGTACCCACCAG 60.306 63.158 0.00 0.00 39.58 4.00
2802 3009 1.664321 CCGCTAGCTGGTTCTACCGT 61.664 60.000 13.93 0.00 42.58 4.83
2803 3010 1.019673 CGCTAGCTGGTTCTACCGTA 58.980 55.000 13.93 0.00 42.58 4.02
2822 3030 6.683715 ACCGTAGTATTTTTGGTTGATTTGG 58.316 36.000 0.00 0.00 0.00 3.28
2849 3058 1.065600 ACATGTGCGTTTGGTGTGC 59.934 52.632 0.00 0.00 0.00 4.57
3169 3392 5.729883 CGGTCTTATATATGCGTACACGTAC 59.270 44.000 3.44 0.00 42.22 3.67
3191 3414 1.713404 CACTTTTAATTGGTGCGTGCG 59.287 47.619 0.00 0.00 0.00 5.34
3214 3437 2.203294 GCGTGAGTGGGTGGGTTT 60.203 61.111 0.00 0.00 0.00 3.27
3304 3529 9.250246 TCCATATATAGTGATGTAAATCCACGA 57.750 33.333 0.00 0.00 36.06 4.35
3390 3621 6.948886 AGTTCATAGAGTTACAGTCAAGAGGA 59.051 38.462 0.00 0.00 0.00 3.71
3417 3648 3.910627 AGTCCTCAATACAAGGTGGAACT 59.089 43.478 0.00 0.00 36.74 3.01
3431 3662 1.078848 GAACTGAGCCGAGCCACAT 60.079 57.895 0.00 0.00 0.00 3.21
3433 3664 0.176680 AACTGAGCCGAGCCACATAG 59.823 55.000 0.00 0.00 0.00 2.23
3447 3678 1.115467 ACATAGGCAGTAGCTCGCTT 58.885 50.000 0.00 0.00 41.70 4.68
3452 3683 0.741915 GGCAGTAGCTCGCTTAGACT 59.258 55.000 0.00 0.00 41.70 3.24
3496 3727 3.114065 GGCGACTCTATTTTGAGTACGG 58.886 50.000 13.60 3.62 46.11 4.02
3523 3755 3.492102 TTCTGAGGAACAAACTCCCTG 57.508 47.619 0.00 0.00 35.95 4.45
3561 3793 6.013725 TCCTTAATCTCAAGAACTAACTGGCA 60.014 38.462 0.00 0.00 0.00 4.92
3562 3794 6.655003 CCTTAATCTCAAGAACTAACTGGCAA 59.345 38.462 0.00 0.00 0.00 4.52
3569 3801 3.670625 AGAACTAACTGGCAAATACGCA 58.329 40.909 0.00 0.00 0.00 5.24
3570 3802 4.261801 AGAACTAACTGGCAAATACGCAT 58.738 39.130 0.00 0.00 0.00 4.73
3596 3828 1.615392 ACCAAGGCTTCATTTGACAGC 59.385 47.619 0.00 6.32 0.00 4.40
3632 3864 4.398358 TCTGACGAATCCGATTGAAGTACT 59.602 41.667 0.00 0.00 39.50 2.73
3636 3868 4.400251 ACGAATCCGATTGAAGTACTACCA 59.600 41.667 0.00 0.00 39.50 3.25
3667 3899 2.817834 TTGTATCGCCAGCGCCAC 60.818 61.111 2.29 7.93 39.59 5.01
3714 3946 0.810648 TTCCAACGGATCATTGCAGC 59.189 50.000 0.00 0.00 0.00 5.25
3888 4124 1.277557 TCAGCTTCTTCTCTGAAGGCC 59.722 52.381 0.00 0.00 42.53 5.19
3891 4127 1.678425 GCTTCTTCTCTGAAGGCCTGG 60.678 57.143 5.69 0.00 42.53 4.45
3994 4287 0.679002 TCTAGGAACTCGACCGTGGG 60.679 60.000 0.00 0.00 41.75 4.61
4007 4300 2.450243 GTGGGGAGGACAGGAGGA 59.550 66.667 0.00 0.00 0.00 3.71
4037 4330 1.070786 ATGGGTCTTGTCGTTGCGT 59.929 52.632 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.478344 CAGCAAGAGATACATGAACTAGGAAC 59.522 42.308 0.00 0.00 0.00 3.62
10 11 5.939764 ACCAGCAAGAGATACATGAACTA 57.060 39.130 0.00 0.00 0.00 2.24
12 13 5.886960 AAACCAGCAAGAGATACATGAAC 57.113 39.130 0.00 0.00 0.00 3.18
106 107 9.878667 TCGTTCCATAATATAAGAGTGTTTTCA 57.121 29.630 0.00 0.00 0.00 2.69
109 110 9.326413 CCTTCGTTCCATAATATAAGAGTGTTT 57.674 33.333 0.00 0.00 0.00 2.83
110 111 7.931948 CCCTTCGTTCCATAATATAAGAGTGTT 59.068 37.037 0.00 0.00 0.00 3.32
113 114 7.509659 ACTCCCTTCGTTCCATAATATAAGAGT 59.490 37.037 0.00 0.00 0.00 3.24
114 115 7.897864 ACTCCCTTCGTTCCATAATATAAGAG 58.102 38.462 0.00 0.00 0.00 2.85
115 116 7.850935 ACTCCCTTCGTTCCATAATATAAGA 57.149 36.000 0.00 0.00 0.00 2.10
116 117 8.804204 AGTACTCCCTTCGTTCCATAATATAAG 58.196 37.037 0.00 0.00 0.00 1.73
117 118 8.716674 AGTACTCCCTTCGTTCCATAATATAA 57.283 34.615 0.00 0.00 0.00 0.98
118 119 9.236006 GTAGTACTCCCTTCGTTCCATAATATA 57.764 37.037 0.00 0.00 0.00 0.86
119 120 7.727186 TGTAGTACTCCCTTCGTTCCATAATAT 59.273 37.037 0.00 0.00 0.00 1.28
120 121 7.062322 TGTAGTACTCCCTTCGTTCCATAATA 58.938 38.462 0.00 0.00 0.00 0.98
121 122 5.895534 TGTAGTACTCCCTTCGTTCCATAAT 59.104 40.000 0.00 0.00 0.00 1.28
122 123 5.263599 TGTAGTACTCCCTTCGTTCCATAA 58.736 41.667 0.00 0.00 0.00 1.90
123 124 4.858850 TGTAGTACTCCCTTCGTTCCATA 58.141 43.478 0.00 0.00 0.00 2.74
124 125 3.705051 TGTAGTACTCCCTTCGTTCCAT 58.295 45.455 0.00 0.00 0.00 3.41
125 126 3.159213 TGTAGTACTCCCTTCGTTCCA 57.841 47.619 0.00 0.00 0.00 3.53
126 127 6.348050 CGTATATGTAGTACTCCCTTCGTTCC 60.348 46.154 0.00 0.00 0.00 3.62
127 128 6.425114 TCGTATATGTAGTACTCCCTTCGTTC 59.575 42.308 0.00 0.00 0.00 3.95
128 129 6.291377 TCGTATATGTAGTACTCCCTTCGTT 58.709 40.000 0.00 0.00 0.00 3.85
129 130 5.858381 TCGTATATGTAGTACTCCCTTCGT 58.142 41.667 0.00 0.00 0.00 3.85
130 131 6.981762 ATCGTATATGTAGTACTCCCTTCG 57.018 41.667 0.00 0.00 0.00 3.79
131 132 7.028361 GCAATCGTATATGTAGTACTCCCTTC 58.972 42.308 0.00 0.00 0.00 3.46
132 133 6.071503 GGCAATCGTATATGTAGTACTCCCTT 60.072 42.308 0.00 0.00 0.00 3.95
133 134 5.418209 GGCAATCGTATATGTAGTACTCCCT 59.582 44.000 0.00 0.00 0.00 4.20
134 135 5.184479 TGGCAATCGTATATGTAGTACTCCC 59.816 44.000 0.00 0.00 0.00 4.30
135 136 6.263516 TGGCAATCGTATATGTAGTACTCC 57.736 41.667 0.00 0.00 0.00 3.85
136 137 8.027189 TCAATGGCAATCGTATATGTAGTACTC 58.973 37.037 0.00 0.00 0.00 2.59
137 138 7.892609 TCAATGGCAATCGTATATGTAGTACT 58.107 34.615 0.00 0.00 0.00 2.73
138 139 8.433126 GTTCAATGGCAATCGTATATGTAGTAC 58.567 37.037 0.00 0.00 0.00 2.73
139 140 8.364894 AGTTCAATGGCAATCGTATATGTAGTA 58.635 33.333 0.00 0.00 0.00 1.82
140 141 7.171508 CAGTTCAATGGCAATCGTATATGTAGT 59.828 37.037 0.00 0.00 0.00 2.73
141 142 7.360353 CCAGTTCAATGGCAATCGTATATGTAG 60.360 40.741 0.00 0.00 32.48 2.74
142 143 6.426633 CCAGTTCAATGGCAATCGTATATGTA 59.573 38.462 0.00 0.00 32.48 2.29
143 144 5.239306 CCAGTTCAATGGCAATCGTATATGT 59.761 40.000 0.00 0.00 32.48 2.29
144 145 5.335113 CCCAGTTCAATGGCAATCGTATATG 60.335 44.000 0.00 0.00 39.17 1.78
145 146 4.761739 CCCAGTTCAATGGCAATCGTATAT 59.238 41.667 0.00 0.00 39.17 0.86
146 147 4.133820 CCCAGTTCAATGGCAATCGTATA 58.866 43.478 0.00 0.00 39.17 1.47
147 148 2.951642 CCCAGTTCAATGGCAATCGTAT 59.048 45.455 0.00 0.00 39.17 3.06
148 149 2.364632 CCCAGTTCAATGGCAATCGTA 58.635 47.619 0.00 0.00 39.17 3.43
149 150 1.176527 CCCAGTTCAATGGCAATCGT 58.823 50.000 0.00 0.00 39.17 3.73
150 151 0.179129 GCCCAGTTCAATGGCAATCG 60.179 55.000 0.00 0.00 44.70 3.34
151 152 3.746900 GCCCAGTTCAATGGCAATC 57.253 52.632 0.00 0.00 44.70 2.67
274 279 5.047847 GGGTATTTCTCGTCATCGATCAAA 58.952 41.667 0.00 0.00 45.21 2.69
312 317 1.692749 AAGAATGGCCGCCCTAGGA 60.693 57.895 11.48 0.00 0.00 2.94
313 318 1.526917 CAAGAATGGCCGCCCTAGG 60.527 63.158 7.03 0.06 0.00 3.02
314 319 0.815615 GTCAAGAATGGCCGCCCTAG 60.816 60.000 7.03 0.00 0.00 3.02
315 320 1.223487 GTCAAGAATGGCCGCCCTA 59.777 57.895 7.03 0.00 0.00 3.53
316 321 2.044946 GTCAAGAATGGCCGCCCT 60.045 61.111 7.03 0.00 0.00 5.19
317 322 2.361104 TGTCAAGAATGGCCGCCC 60.361 61.111 7.03 0.00 0.00 6.13
318 323 1.244019 AACTGTCAAGAATGGCCGCC 61.244 55.000 1.04 1.04 0.00 6.13
388 397 8.460428 TCTGTGTGTTGTCATATGTACGTATTA 58.540 33.333 4.78 0.00 0.00 0.98
423 435 0.528924 AGTATTCGCTACGGTGTGCA 59.471 50.000 8.28 0.00 35.35 4.57
424 436 1.636988 AAGTATTCGCTACGGTGTGC 58.363 50.000 0.00 0.00 35.35 4.57
425 437 3.924686 AGAAAAGTATTCGCTACGGTGTG 59.075 43.478 0.00 0.00 35.35 3.82
426 438 4.184079 AGAAAAGTATTCGCTACGGTGT 57.816 40.909 0.00 0.00 35.35 4.16
427 439 4.259292 CGAAGAAAAGTATTCGCTACGGTG 60.259 45.833 0.00 0.00 41.11 4.94
428 440 3.855950 CGAAGAAAAGTATTCGCTACGGT 59.144 43.478 0.00 0.00 41.11 4.83
571 583 3.430929 GGAGATTAAGCTCCGTGTCATGT 60.431 47.826 23.19 0.00 44.52 3.21
595 607 4.219033 CGTGCCAGAACTCATTTGTTTAC 58.781 43.478 0.00 0.00 0.00 2.01
608 620 1.548719 AGTACTACATGCGTGCCAGAA 59.451 47.619 5.64 0.00 0.00 3.02
895 907 3.901844 ACTGTTCTTCCCTGCTACTTACA 59.098 43.478 0.00 0.00 0.00 2.41
915 927 1.527034 TACGCTGTGTACTCGGAACT 58.473 50.000 7.94 0.00 0.00 3.01
939 953 1.032794 CTAGCAGGTATCGACAGGCA 58.967 55.000 0.00 0.00 0.00 4.75
940 954 0.319125 GCTAGCAGGTATCGACAGGC 60.319 60.000 10.63 0.00 0.00 4.85
954 968 2.057316 CACGATGTAGATGCTGCTAGC 58.943 52.381 8.10 8.10 42.82 3.42
955 969 2.057316 GCACGATGTAGATGCTGCTAG 58.943 52.381 0.00 0.00 36.40 3.42
956 970 1.269778 GGCACGATGTAGATGCTGCTA 60.270 52.381 0.00 0.00 39.38 3.49
957 971 0.531532 GGCACGATGTAGATGCTGCT 60.532 55.000 0.00 0.00 39.38 4.24
958 972 0.811219 TGGCACGATGTAGATGCTGC 60.811 55.000 0.00 0.00 39.38 5.25
959 973 1.655484 TTGGCACGATGTAGATGCTG 58.345 50.000 0.00 0.00 39.38 4.41
960 974 2.487934 GATTGGCACGATGTAGATGCT 58.512 47.619 0.00 0.00 39.38 3.79
961 975 1.193203 CGATTGGCACGATGTAGATGC 59.807 52.381 0.00 0.00 38.68 3.91
962 976 1.794701 CCGATTGGCACGATGTAGATG 59.205 52.381 0.00 0.00 0.00 2.90
963 977 1.686587 TCCGATTGGCACGATGTAGAT 59.313 47.619 0.00 0.00 34.14 1.98
964 978 1.107945 TCCGATTGGCACGATGTAGA 58.892 50.000 0.00 0.00 34.14 2.59
965 979 1.934589 TTCCGATTGGCACGATGTAG 58.065 50.000 0.00 0.00 34.14 2.74
969 1004 2.684001 TACTTTCCGATTGGCACGAT 57.316 45.000 0.00 0.00 34.14 3.73
981 1016 4.356289 GCATCTCTCTCGACTTACTTTCC 58.644 47.826 0.00 0.00 0.00 3.13
983 1018 3.181495 CGGCATCTCTCTCGACTTACTTT 60.181 47.826 0.00 0.00 0.00 2.66
1168 1211 4.439968 ACTCACGTACTGATCGAGTATGA 58.560 43.478 21.40 14.42 44.24 2.15
1175 1218 4.016113 TGATGAACTCACGTACTGATCG 57.984 45.455 0.00 0.00 0.00 3.69
1217 1260 0.645868 GAACGATCGTGTTAGCAGGC 59.354 55.000 23.51 0.00 30.75 4.85
1238 1281 0.445436 GCCAGAAGTCATGCGAACAG 59.555 55.000 0.00 0.00 0.00 3.16
1239 1282 0.250252 TGCCAGAAGTCATGCGAACA 60.250 50.000 0.00 0.00 0.00 3.18
1698 1741 4.163458 ACTGAGACCTAGACACACCAAAAA 59.837 41.667 0.00 0.00 0.00 1.94
1699 1742 3.709653 ACTGAGACCTAGACACACCAAAA 59.290 43.478 0.00 0.00 0.00 2.44
1700 1743 3.305720 ACTGAGACCTAGACACACCAAA 58.694 45.455 0.00 0.00 0.00 3.28
1701 1744 2.891580 GACTGAGACCTAGACACACCAA 59.108 50.000 0.00 0.00 0.00 3.67
1702 1745 2.515854 GACTGAGACCTAGACACACCA 58.484 52.381 0.00 0.00 0.00 4.17
1703 1746 1.469308 CGACTGAGACCTAGACACACC 59.531 57.143 0.00 0.00 0.00 4.16
1704 1747 2.160022 GTCGACTGAGACCTAGACACAC 59.840 54.545 8.70 0.00 35.22 3.82
1705 1748 2.038689 AGTCGACTGAGACCTAGACACA 59.961 50.000 19.30 0.00 41.83 3.72
1706 1749 2.417239 CAGTCGACTGAGACCTAGACAC 59.583 54.545 36.73 0.00 46.59 3.67
1707 1750 2.701107 CAGTCGACTGAGACCTAGACA 58.299 52.381 36.73 0.00 46.59 3.41
1717 1760 6.438740 ACTTGGTTAAGTCTCAGTCGACTGA 61.439 44.000 38.24 38.24 45.53 3.41
1718 1761 3.917329 TGGTTAAGTCTCAGTCGACTG 57.083 47.619 34.76 34.76 43.14 3.51
1719 1762 3.890147 ACTTGGTTAAGTCTCAGTCGACT 59.110 43.478 13.58 13.58 43.53 4.18
1720 1763 4.240175 ACTTGGTTAAGTCTCAGTCGAC 57.760 45.455 7.70 7.70 43.53 4.20
1807 1850 9.836076 CGATGTTATATTTCATTGATCTTGCAT 57.164 29.630 0.00 0.00 0.00 3.96
1808 1851 9.054922 TCGATGTTATATTTCATTGATCTTGCA 57.945 29.630 0.00 0.00 31.83 4.08
1809 1852 9.322776 GTCGATGTTATATTTCATTGATCTTGC 57.677 33.333 10.75 0.00 37.00 4.01
1812 1855 9.987272 TCAGTCGATGTTATATTTCATTGATCT 57.013 29.630 10.75 8.36 37.00 2.75
1814 1857 9.987272 TCTCAGTCGATGTTATATTTCATTGAT 57.013 29.630 10.75 2.37 37.00 2.57
1815 1858 9.249457 GTCTCAGTCGATGTTATATTTCATTGA 57.751 33.333 0.00 5.96 33.63 2.57
1816 1859 9.034544 TGTCTCAGTCGATGTTATATTTCATTG 57.965 33.333 0.00 0.00 0.00 2.82
1817 1860 9.770097 ATGTCTCAGTCGATGTTATATTTCATT 57.230 29.630 0.00 0.00 0.00 2.57
1821 1864 9.181805 CGTTATGTCTCAGTCGATGTTATATTT 57.818 33.333 0.00 0.00 0.00 1.40
1822 1865 8.565416 TCGTTATGTCTCAGTCGATGTTATATT 58.435 33.333 0.00 0.00 0.00 1.28
1823 1866 8.095937 TCGTTATGTCTCAGTCGATGTTATAT 57.904 34.615 0.00 0.00 0.00 0.86
1824 1867 7.486802 TCGTTATGTCTCAGTCGATGTTATA 57.513 36.000 0.00 0.00 0.00 0.98
1825 1868 6.373186 TCGTTATGTCTCAGTCGATGTTAT 57.627 37.500 0.00 0.00 0.00 1.89
1826 1869 5.806366 TCGTTATGTCTCAGTCGATGTTA 57.194 39.130 0.00 0.00 0.00 2.41
1827 1870 4.696899 TCGTTATGTCTCAGTCGATGTT 57.303 40.909 0.00 0.00 0.00 2.71
1828 1871 4.696899 TTCGTTATGTCTCAGTCGATGT 57.303 40.909 0.00 0.00 0.00 3.06
1829 1872 5.974158 AGATTTCGTTATGTCTCAGTCGATG 59.026 40.000 0.00 0.00 0.00 3.84
1830 1873 6.137794 AGATTTCGTTATGTCTCAGTCGAT 57.862 37.500 0.00 0.00 0.00 3.59
1831 1874 5.562506 AGATTTCGTTATGTCTCAGTCGA 57.437 39.130 0.00 0.00 0.00 4.20
1832 1875 6.967767 ACTTAGATTTCGTTATGTCTCAGTCG 59.032 38.462 0.00 0.00 0.00 4.18
1833 1876 7.164498 CGACTTAGATTTCGTTATGTCTCAGTC 59.836 40.741 0.00 0.00 38.03 3.51
1834 1877 6.967767 CGACTTAGATTTCGTTATGTCTCAGT 59.032 38.462 0.00 0.00 30.24 3.41
1835 1878 7.164498 GTCGACTTAGATTTCGTTATGTCTCAG 59.836 40.741 8.70 0.00 36.60 3.35
1836 1879 6.965500 GTCGACTTAGATTTCGTTATGTCTCA 59.035 38.462 8.70 0.00 36.60 3.27
1837 1880 7.164498 CAGTCGACTTAGATTTCGTTATGTCTC 59.836 40.741 17.26 0.00 36.60 3.36
1838 1881 6.967767 CAGTCGACTTAGATTTCGTTATGTCT 59.032 38.462 17.26 0.00 36.60 3.41
1839 1882 6.965500 TCAGTCGACTTAGATTTCGTTATGTC 59.035 38.462 17.26 0.00 36.60 3.06
1840 1883 6.849502 TCAGTCGACTTAGATTTCGTTATGT 58.150 36.000 17.26 0.00 36.60 2.29
1841 1884 7.164498 GTCTCAGTCGACTTAGATTTCGTTATG 59.836 40.741 27.34 8.71 36.60 1.90
1842 1885 7.188157 GTCTCAGTCGACTTAGATTTCGTTAT 58.812 38.462 27.34 0.00 36.60 1.89
1843 1886 6.541086 GTCTCAGTCGACTTAGATTTCGTTA 58.459 40.000 27.34 4.85 36.60 3.18
1844 1887 5.392286 GTCTCAGTCGACTTAGATTTCGTT 58.608 41.667 27.34 0.00 36.60 3.85
1845 1888 4.435784 CGTCTCAGTCGACTTAGATTTCGT 60.436 45.833 27.34 0.00 36.60 3.85
1846 1889 4.023128 CGTCTCAGTCGACTTAGATTTCG 58.977 47.826 27.34 22.28 36.55 3.46
1847 1890 4.972201 ACGTCTCAGTCGACTTAGATTTC 58.028 43.478 27.34 16.22 29.97 2.17
1848 1891 5.447548 GCTACGTCTCAGTCGACTTAGATTT 60.448 44.000 27.34 20.08 37.74 2.17
1849 1892 4.034279 GCTACGTCTCAGTCGACTTAGATT 59.966 45.833 27.34 20.36 37.74 2.40
1850 1893 3.556775 GCTACGTCTCAGTCGACTTAGAT 59.443 47.826 27.34 17.32 37.74 1.98
1851 1894 2.928757 GCTACGTCTCAGTCGACTTAGA 59.071 50.000 22.49 22.49 37.74 2.10
1852 1895 2.671888 TGCTACGTCTCAGTCGACTTAG 59.328 50.000 17.26 18.13 38.24 2.18
1853 1896 2.691927 TGCTACGTCTCAGTCGACTTA 58.308 47.619 17.26 7.41 0.00 2.24
1854 1897 1.520494 TGCTACGTCTCAGTCGACTT 58.480 50.000 17.26 2.43 0.00 3.01
1855 1898 1.520494 TTGCTACGTCTCAGTCGACT 58.480 50.000 13.58 13.58 0.00 4.18
1856 1899 2.327081 TTTGCTACGTCTCAGTCGAC 57.673 50.000 7.70 7.70 0.00 4.20
1857 1900 2.292569 AGTTTTGCTACGTCTCAGTCGA 59.707 45.455 0.00 0.00 0.00 4.20
1858 1901 2.405357 CAGTTTTGCTACGTCTCAGTCG 59.595 50.000 0.00 0.00 0.00 4.18
1859 1902 3.381949 ACAGTTTTGCTACGTCTCAGTC 58.618 45.455 0.00 0.00 0.00 3.51
1860 1903 3.454371 ACAGTTTTGCTACGTCTCAGT 57.546 42.857 0.00 0.00 0.00 3.41
1861 1904 4.795970 AAACAGTTTTGCTACGTCTCAG 57.204 40.909 0.00 0.00 0.00 3.35
1862 1905 5.554822 AAAAACAGTTTTGCTACGTCTCA 57.445 34.783 12.13 0.00 35.58 3.27
1887 1930 7.498900 CAGTAACCATTGGCTCTGTATATGAAA 59.501 37.037 1.54 0.00 0.00 2.69
1899 1942 1.826720 CATTGGCAGTAACCATTGGCT 59.173 47.619 1.54 0.00 40.13 4.75
1901 1944 4.741321 AATCATTGGCAGTAACCATTGG 57.259 40.909 0.00 0.00 40.12 3.16
1907 2109 4.142403 TGCTAGCAAATCATTGGCAGTAAC 60.142 41.667 16.84 0.00 37.02 2.50
1948 2150 5.608676 TCGACATTTGCGTACCATAAAAA 57.391 34.783 0.00 0.00 0.00 1.94
1952 2154 2.159156 AGCTCGACATTTGCGTACCATA 60.159 45.455 0.00 0.00 0.00 2.74
1995 2197 5.522824 GTCACCCTTTCTATACGAATTCCAC 59.477 44.000 0.00 0.00 0.00 4.02
2002 2204 3.758023 TCAACGTCACCCTTTCTATACGA 59.242 43.478 0.00 0.00 34.62 3.43
2016 2218 6.335471 TCAGTAGGTAAGAAATCAACGTCA 57.665 37.500 0.00 0.00 0.00 4.35
2057 2259 4.641645 TGACGCACTGGCCAAGGG 62.642 66.667 7.01 13.59 36.38 3.95
2094 2296 1.718757 GGCCGCAAGCTAGAATGGTG 61.719 60.000 0.00 0.00 43.05 4.17
2133 2335 2.700722 AGGTAGAGCTAGCAAAAGGC 57.299 50.000 18.83 1.57 45.30 4.35
2189 2391 0.318869 CAACAAAAGGAGCGCATGCA 60.319 50.000 19.57 0.00 46.23 3.96
2190 2392 0.318955 ACAACAAAAGGAGCGCATGC 60.319 50.000 11.47 7.91 43.24 4.06
2191 2393 1.788308 CAACAACAAAAGGAGCGCATG 59.212 47.619 11.47 0.72 0.00 4.06
2192 2394 1.680735 TCAACAACAAAAGGAGCGCAT 59.319 42.857 11.47 0.00 0.00 4.73
2746 2953 1.490693 CTGCATGCGACGGACATACC 61.491 60.000 14.09 0.00 0.00 2.73
2802 3009 8.472007 AGTGACCAAATCAACCAAAAATACTA 57.528 30.769 0.00 0.00 39.72 1.82
2803 3010 7.360113 AGTGACCAAATCAACCAAAAATACT 57.640 32.000 0.00 0.00 39.72 2.12
2822 3030 3.288242 CAAACGCACATGTGTTAGTGAC 58.712 45.455 26.01 7.44 46.75 3.67
2849 3058 1.669115 CACCTCGTCCTTGCACCTG 60.669 63.158 0.00 0.00 0.00 4.00
3293 3518 7.201582 CCTGGTTATTGTAGTTCGTGGATTTAC 60.202 40.741 0.00 0.00 0.00 2.01
3304 3529 4.082245 GCACATTGCCTGGTTATTGTAGTT 60.082 41.667 0.00 0.00 37.42 2.24
3345 3571 5.607119 ACTTGCAATACAACTCCGTTTAG 57.393 39.130 0.00 0.00 33.68 1.85
3350 3576 4.685169 ATGAACTTGCAATACAACTCCG 57.315 40.909 0.00 0.00 33.68 4.63
3357 3583 8.480643 ACTGTAACTCTATGAACTTGCAATAC 57.519 34.615 0.00 0.00 0.00 1.89
3390 3621 4.389374 CACCTTGTATTGAGGACTTGTGT 58.611 43.478 0.00 0.00 37.72 3.72
3417 3648 3.220222 CCTATGTGGCTCGGCTCA 58.780 61.111 0.00 0.00 0.00 4.26
3431 3662 1.948145 GTCTAAGCGAGCTACTGCCTA 59.052 52.381 0.00 0.00 40.80 3.93
3433 3664 0.741915 AGTCTAAGCGAGCTACTGCC 59.258 55.000 0.00 0.00 40.80 4.85
3447 3678 5.442391 GGTTGGCCAATTATAACCAGTCTA 58.558 41.667 23.66 0.00 41.64 2.59
3452 3683 3.367646 TCGGTTGGCCAATTATAACCA 57.632 42.857 23.66 5.81 42.01 3.67
3496 3727 6.382608 GGAGTTTGTTCCTCAGAAAATTAGC 58.617 40.000 0.00 0.00 34.27 3.09
3523 3755 7.865706 TGAGATTAAGGATCTTTTTGGTAGC 57.134 36.000 0.00 0.00 45.17 3.58
3561 3793 2.940410 CCTTGGTTCGGTATGCGTATTT 59.060 45.455 0.00 0.00 0.00 1.40
3562 3794 2.557317 CCTTGGTTCGGTATGCGTATT 58.443 47.619 0.00 0.00 0.00 1.89
3569 3801 3.366052 AATGAAGCCTTGGTTCGGTAT 57.634 42.857 2.08 0.00 42.15 2.73
3570 3802 2.817258 CAAATGAAGCCTTGGTTCGGTA 59.183 45.455 2.08 0.00 42.15 4.02
3596 3828 4.114659 ATTCGTCAGAAGCCTTGTCAAGG 61.115 47.826 25.05 25.05 43.94 3.61
3636 3868 3.130693 GCGATACAACACTCTAACCTCCT 59.869 47.826 0.00 0.00 0.00 3.69
3714 3946 3.483574 GCGGCATATCGGTTCATATTTCG 60.484 47.826 0.00 0.00 0.00 3.46
3784 4020 4.974438 AGGAGGCCAACGGGTCCA 62.974 66.667 5.01 0.00 40.78 4.02
3888 4124 1.172180 TCGCCCTTGACTTTTGCCAG 61.172 55.000 0.00 0.00 0.00 4.85
3891 4127 0.598065 ATGTCGCCCTTGACTTTTGC 59.402 50.000 0.00 0.00 39.64 3.68
4007 4300 1.686236 AGACCCATGGGAAGGACATT 58.314 50.000 38.07 12.42 38.96 2.71
4037 4330 3.720494 TGGCGGATCTGGCAGTTA 58.280 55.556 25.81 4.14 39.79 2.24


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

AutoCloner maintained by Alex Coulton.