Multiple sequence alignment - TraesCS3D01G359300

Loading Multiple Alignment...

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 TraesCS3D01G359300 chr3D 100.000 7953 0 0 1 7953 473443809 473435857 0.000000e+00 14687.0
1 TraesCS3D01G359300 chr3D 92.493 3410 146 47 2978 6351 472949862 472946527 0.000000e+00 4778.0
2 TraesCS3D01G359300 chr3D 92.883 815 40 7 2142 2948 472950661 472949857 0.000000e+00 1168.0
3 TraesCS3D01G359300 chr3D 84.455 1010 58 49 681 1681 472951652 472950733 0.000000e+00 904.0
4 TraesCS3D01G359300 chr3D 90.476 630 30 10 6453 7082 472946523 472945924 0.000000e+00 804.0
5 TraesCS3D01G359300 chr3D 92.929 99 6 1 4102 4200 570265025 570265122 8.320000e-30 143.0
6 TraesCS3D01G359300 chr3D 97.015 67 2 0 7608 7674 473436136 473436070 6.520000e-21 113.0
7 TraesCS3D01G359300 chr3D 97.015 67 2 0 7674 7740 473436202 473436136 6.520000e-21 113.0
8 TraesCS3D01G359300 chr3B 98.031 5638 102 6 1819 7452 628402221 628396589 0.000000e+00 9788.0
9 TraesCS3D01G359300 chr3B 93.912 2283 94 17 4087 6351 628120032 628117777 0.000000e+00 3404.0
10 TraesCS3D01G359300 chr3B 90.108 1941 108 39 2129 4023 628121935 628120033 0.000000e+00 2444.0
11 TraesCS3D01G359300 chr3B 94.275 1048 39 12 561 1593 628403472 628402431 0.000000e+00 1583.0
12 TraesCS3D01G359300 chr3B 89.107 661 38 13 6453 7112 628117773 628117146 0.000000e+00 791.0
13 TraesCS3D01G359300 chr3B 84.894 801 50 45 681 1459 628122682 628121931 0.000000e+00 743.0
14 TraesCS3D01G359300 chr3B 93.617 282 16 1 7674 7953 628396512 628396231 3.430000e-113 420.0
15 TraesCS3D01G359300 chr3B 93.642 173 7 3 1588 1759 628402388 628402219 1.020000e-63 255.0
16 TraesCS3D01G359300 chr3B 84.564 149 23 0 7750 7898 763650144 763649996 1.790000e-31 148.0
17 TraesCS3D01G359300 chr3B 91.209 91 8 0 7584 7674 628396536 628396446 3.010000e-24 124.0
18 TraesCS3D01G359300 chr3B 96.552 58 2 0 7486 7543 628396592 628396535 6.570000e-16 97.1
19 TraesCS3D01G359300 chr3B 89.831 59 6 0 61 119 628404815 628404757 8.560000e-10 76.8
20 TraesCS3D01G359300 chr3A 95.701 6002 212 26 1977 7953 615706801 615700821 0.000000e+00 9612.0
21 TraesCS3D01G359300 chr3A 90.060 2334 156 37 4790 7112 615276735 615274467 0.000000e+00 2955.0
22 TraesCS3D01G359300 chr3A 88.340 2024 127 44 2819 4790 615278802 615276836 0.000000e+00 2329.0
23 TraesCS3D01G359300 chr3A 90.577 1231 71 31 543 1759 615708001 615706802 0.000000e+00 1589.0
24 TraesCS3D01G359300 chr3A 93.459 795 36 6 2142 2928 615279535 615278749 0.000000e+00 1166.0
25 TraesCS3D01G359300 chr3A 83.103 1012 80 48 681 1666 615280606 615279660 0.000000e+00 837.0
26 TraesCS3D01G359300 chr3A 85.185 81 12 0 39 119 615708556 615708476 5.110000e-12 84.2
27 TraesCS3D01G359300 chr2B 88.849 278 31 0 7674 7951 296017461 296017738 7.640000e-90 342.0
28 TraesCS3D01G359300 chr2B 97.917 48 1 0 3030 3077 282847248 282847201 5.110000e-12 84.2
29 TraesCS3D01G359300 chr5A 92.708 96 6 1 4108 4203 552861673 552861579 3.870000e-28 137.0
30 TraesCS3D01G359300 chr7D 97.143 35 1 0 1786 1820 526525602 526525636 8.620000e-05 60.2
31 TraesCS3D01G359300 chr4A 100.000 29 0 0 1794 1822 670946833 670946861 4.000000e-03 54.7
32 TraesCS3D01G359300 chrUn 94.118 34 2 0 1788 1821 30708138 30708171 1.400000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G359300 chr3D 473435857 473443809 7952 True 14687.000000 14687 100.000000 1 7953 1 chr3D.!!$R1 7952
1 TraesCS3D01G359300 chr3D 472945924 472951652 5728 True 1913.500000 4778 90.076750 681 7082 4 chr3D.!!$R2 6401
2 TraesCS3D01G359300 chr3B 628117146 628122682 5536 True 1845.500000 3404 89.505250 681 7112 4 chr3B.!!$R2 6431
3 TraesCS3D01G359300 chr3B 628396231 628404815 8584 True 1763.414286 9788 93.879571 61 7953 7 chr3B.!!$R3 7892
4 TraesCS3D01G359300 chr3A 615700821 615708556 7735 True 3761.733333 9612 90.487667 39 7953 3 chr3A.!!$R2 7914
5 TraesCS3D01G359300 chr3A 615274467 615280606 6139 True 1821.750000 2955 88.740500 681 7112 4 chr3A.!!$R1 6431

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
397 1020 0.032912 TGCCATGCTCCATGATGGTT 60.033 50.000 11.87 0.0 43.81 3.67 F
405 1028 0.113972 TCCATGATGGTTGTTGGGCA 59.886 50.000 11.87 0.0 39.03 5.36 F
1919 2989 0.538057 TTGGAGCTCAGCCTGTTTGG 60.538 55.000 17.19 0.0 39.35 3.28 F
2023 3093 1.039068 ATAGCAGCACGAGCAGATCT 58.961 50.000 7.77 0.0 45.49 2.75 F
2218 3291 2.485659 TGAATTCAGGAGAGGGATGCT 58.514 47.619 3.38 0.0 0.00 3.79 F
2654 3738 5.759506 TGACGCCTTCTAAATTCAAAACA 57.240 34.783 0.00 0.0 0.00 2.83 F
4324 5528 3.157087 CCTGGGCTGTCACAAATAAGTT 58.843 45.455 0.00 0.0 0.00 2.66 F
4495 5700 1.003545 CCGCGTCACATGGAAATCATC 60.004 52.381 4.92 0.0 32.92 2.92 F
5355 6676 2.579684 ATCTTCTCACCGGGCTTCGC 62.580 60.000 6.32 0.0 37.59 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 3026 0.040646 ACCAGTGATCTACGACCCCA 59.959 55.000 0.00 0.00 0.00 4.96 R
2010 3080 0.461961 ACCCTAAGATCTGCTCGTGC 59.538 55.000 1.71 1.71 40.20 5.34 R
2761 3850 5.466393 CGCTCAAATTTTCTGGACCAAAAAT 59.534 36.000 15.72 15.72 36.81 1.82 R
2847 3936 7.905604 TTTATCCAGTCTGATGTACAACAAG 57.094 36.000 7.28 2.26 0.00 3.16 R
4028 5230 4.377445 CCACGTTGTAACTGCGTAAAAATG 59.623 41.667 0.00 0.00 37.07 2.32 R
4495 5700 0.447801 CCCGCTTGTCAATTTCCTCG 59.552 55.000 0.00 0.00 0.00 4.63 R
5355 6676 3.057386 TGGAAGCATGCACACATACTTTG 60.057 43.478 21.98 0.00 39.51 2.77 R
6874 8213 2.110835 TCGCTGCTGAACTTGCCA 59.889 55.556 0.00 0.00 0.00 4.92 R
7685 9029 0.103026 TCCAGATCAATGTCGAGGCG 59.897 55.000 0.00 0.00 0.00 5.52 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
21 22 4.806056 GCATACGATCAAACAAGCAAAC 57.194 40.909 0.00 0.00 0.00 2.93
22 23 4.225984 GCATACGATCAAACAAGCAAACA 58.774 39.130 0.00 0.00 0.00 2.83
23 24 4.858692 GCATACGATCAAACAAGCAAACAT 59.141 37.500 0.00 0.00 0.00 2.71
24 25 6.027131 GCATACGATCAAACAAGCAAACATA 58.973 36.000 0.00 0.00 0.00 2.29
25 26 6.195244 GCATACGATCAAACAAGCAAACATAG 59.805 38.462 0.00 0.00 0.00 2.23
26 27 5.940192 ACGATCAAACAAGCAAACATAGA 57.060 34.783 0.00 0.00 0.00 1.98
27 28 6.312399 ACGATCAAACAAGCAAACATAGAA 57.688 33.333 0.00 0.00 0.00 2.10
28 29 6.142817 ACGATCAAACAAGCAAACATAGAAC 58.857 36.000 0.00 0.00 0.00 3.01
29 30 6.017109 ACGATCAAACAAGCAAACATAGAACT 60.017 34.615 0.00 0.00 0.00 3.01
30 31 7.172532 ACGATCAAACAAGCAAACATAGAACTA 59.827 33.333 0.00 0.00 0.00 2.24
31 32 7.689812 CGATCAAACAAGCAAACATAGAACTAG 59.310 37.037 0.00 0.00 0.00 2.57
32 33 7.801716 TCAAACAAGCAAACATAGAACTAGT 57.198 32.000 0.00 0.00 0.00 2.57
33 34 8.220755 TCAAACAAGCAAACATAGAACTAGTT 57.779 30.769 8.13 8.13 0.00 2.24
34 35 8.682710 TCAAACAAGCAAACATAGAACTAGTTT 58.317 29.630 10.02 2.79 36.00 2.66
35 36 9.944663 CAAACAAGCAAACATAGAACTAGTTTA 57.055 29.630 10.02 4.94 34.03 2.01
44 45 8.928270 AACATAGAACTAGTTTATCGTCCTTG 57.072 34.615 10.02 4.76 0.00 3.61
45 46 8.289939 ACATAGAACTAGTTTATCGTCCTTGA 57.710 34.615 10.02 0.00 0.00 3.02
49 50 7.540299 AGAACTAGTTTATCGTCCTTGAGAAG 58.460 38.462 10.02 0.00 0.00 2.85
54 55 2.322355 ATCGTCCTTGAGAAGCATGG 57.678 50.000 0.00 0.00 41.86 3.66
64 65 5.047519 CCTTGAGAAGCATGGAGAAAAATGT 60.048 40.000 0.00 0.00 42.85 2.71
76 77 6.898041 TGGAGAAAAATGTATGTGTTCTTCG 58.102 36.000 0.00 0.00 0.00 3.79
80 81 6.485313 AGAAAAATGTATGTGTTCTTCGTCCA 59.515 34.615 0.00 0.00 0.00 4.02
85 86 2.804697 TGTGTTCTTCGTCCATTCGA 57.195 45.000 0.00 0.00 38.08 3.71
89 90 4.209112 GTGTTCTTCGTCCATTCGAAAAC 58.791 43.478 0.00 0.00 46.55 2.43
137 142 5.471797 TGAGAATGTACCATTCGAGCAAAAA 59.528 36.000 10.39 0.00 33.51 1.94
140 145 4.742438 TGTACCATTCGAGCAAAAAGAC 57.258 40.909 0.00 0.00 0.00 3.01
143 148 4.853924 ACCATTCGAGCAAAAAGACATT 57.146 36.364 0.00 0.00 0.00 2.71
146 151 4.984161 CCATTCGAGCAAAAAGACATTTGT 59.016 37.500 2.21 0.00 41.34 2.83
149 154 7.329226 CCATTCGAGCAAAAAGACATTTGTTAT 59.671 33.333 2.21 0.00 41.34 1.89
155 160 8.947055 AGCAAAAAGACATTTGTTATTGAGTT 57.053 26.923 2.21 0.00 41.34 3.01
160 165 8.856490 AAAGACATTTGTTATTGAGTTCACAC 57.144 30.769 0.00 0.00 0.00 3.82
161 166 7.566760 AGACATTTGTTATTGAGTTCACACA 57.433 32.000 0.00 0.00 0.00 3.72
163 168 8.292448 AGACATTTGTTATTGAGTTCACACATC 58.708 33.333 0.00 0.00 0.00 3.06
164 169 7.370383 ACATTTGTTATTGAGTTCACACATCC 58.630 34.615 0.00 0.00 0.00 3.51
166 171 4.000325 TGTTATTGAGTTCACACATCCGG 59.000 43.478 0.00 0.00 0.00 5.14
173 178 3.750371 AGTTCACACATCCGGATTTTGA 58.250 40.909 23.88 18.57 0.00 2.69
175 180 4.766891 AGTTCACACATCCGGATTTTGATT 59.233 37.500 23.88 11.79 0.00 2.57
178 183 4.764308 TCACACATCCGGATTTTGATTTCA 59.236 37.500 23.88 1.64 0.00 2.69
183 188 4.678509 TCCGGATTTTGATTTCAAGTCG 57.321 40.909 0.00 0.00 37.15 4.18
184 189 4.320023 TCCGGATTTTGATTTCAAGTCGA 58.680 39.130 0.00 0.00 37.15 4.20
185 190 4.391830 TCCGGATTTTGATTTCAAGTCGAG 59.608 41.667 0.00 0.00 37.15 4.04
186 191 4.154195 CCGGATTTTGATTTCAAGTCGAGT 59.846 41.667 0.00 0.00 37.15 4.18
188 193 5.565259 CGGATTTTGATTTCAAGTCGAGTTG 59.435 40.000 24.19 24.19 37.15 3.16
189 194 6.438763 GGATTTTGATTTCAAGTCGAGTTGT 58.561 36.000 27.61 12.71 37.15 3.32
190 195 6.918022 GGATTTTGATTTCAAGTCGAGTTGTT 59.082 34.615 27.61 16.27 37.15 2.83
191 196 8.073768 GGATTTTGATTTCAAGTCGAGTTGTTA 58.926 33.333 27.61 18.59 37.15 2.41
192 197 9.107367 GATTTTGATTTCAAGTCGAGTTGTTAG 57.893 33.333 27.61 7.22 37.15 2.34
193 198 7.780008 TTTGATTTCAAGTCGAGTTGTTAGA 57.220 32.000 27.61 14.90 37.15 2.10
194 199 6.764877 TGATTTCAAGTCGAGTTGTTAGAC 57.235 37.500 27.61 17.74 35.30 2.59
195 200 5.401376 TGATTTCAAGTCGAGTTGTTAGACG 59.599 40.000 27.61 5.52 39.65 4.18
196 201 3.976793 TCAAGTCGAGTTGTTAGACGT 57.023 42.857 27.61 0.00 39.65 4.34
197 202 3.881795 TCAAGTCGAGTTGTTAGACGTC 58.118 45.455 27.61 7.70 39.65 4.34
198 203 2.978489 CAAGTCGAGTTGTTAGACGTCC 59.022 50.000 22.33 0.00 39.65 4.79
200 205 2.818432 AGTCGAGTTGTTAGACGTCCAT 59.182 45.455 13.01 0.00 39.65 3.41
201 206 2.915463 GTCGAGTTGTTAGACGTCCATG 59.085 50.000 13.01 0.00 0.00 3.66
203 349 2.661675 CGAGTTGTTAGACGTCCATGTG 59.338 50.000 13.01 0.00 0.00 3.21
205 351 1.126113 GTTGTTAGACGTCCATGTGCG 59.874 52.381 13.01 4.87 0.00 5.34
207 353 0.989890 GTTAGACGTCCATGTGCGAC 59.010 55.000 13.01 6.79 0.00 5.19
209 355 1.741528 TAGACGTCCATGTGCGACTA 58.258 50.000 13.01 11.91 35.20 2.59
211 357 1.476891 AGACGTCCATGTGCGACTATT 59.523 47.619 13.01 0.00 32.22 1.73
219 365 1.011968 TGTGCGACTATTGCGGTGAC 61.012 55.000 0.00 0.00 34.24 3.67
230 376 2.975536 CGGTGACCGCTCCCTTTA 59.024 61.111 12.53 0.00 41.17 1.85
231 377 1.153628 CGGTGACCGCTCCCTTTAG 60.154 63.158 12.53 0.00 41.17 1.85
232 378 1.601419 CGGTGACCGCTCCCTTTAGA 61.601 60.000 12.53 0.00 41.17 2.10
233 379 0.175989 GGTGACCGCTCCCTTTAGAG 59.824 60.000 0.00 0.00 36.92 2.43
237 383 2.233922 TGACCGCTCCCTTTAGAGAAAG 59.766 50.000 0.00 0.00 41.61 2.62
240 386 3.072622 ACCGCTCCCTTTAGAGAAAGTTT 59.927 43.478 0.00 0.00 40.53 2.66
242 388 5.045797 ACCGCTCCCTTTAGAGAAAGTTTAT 60.046 40.000 0.00 0.00 40.53 1.40
243 389 6.155737 ACCGCTCCCTTTAGAGAAAGTTTATA 59.844 38.462 0.00 0.00 40.53 0.98
245 391 7.715686 CCGCTCCCTTTAGAGAAAGTTTATAAT 59.284 37.037 0.00 0.00 40.53 1.28
247 393 9.614792 GCTCCCTTTAGAGAAAGTTTATAATGA 57.385 33.333 0.00 0.00 40.53 2.57
271 417 1.134189 TGGAGTCGCTAGATCGAAGGA 60.134 52.381 0.00 0.00 40.43 3.36
272 418 1.948145 GGAGTCGCTAGATCGAAGGAA 59.052 52.381 0.00 0.00 40.43 3.36
274 420 1.950909 AGTCGCTAGATCGAAGGAAGG 59.049 52.381 0.00 0.00 40.43 3.46
277 423 1.268352 CGCTAGATCGAAGGAAGGGAG 59.732 57.143 0.00 0.00 0.00 4.30
278 424 1.616374 GCTAGATCGAAGGAAGGGAGG 59.384 57.143 0.00 0.00 0.00 4.30
279 425 2.753507 GCTAGATCGAAGGAAGGGAGGA 60.754 54.545 0.00 0.00 0.00 3.71
280 426 2.785357 AGATCGAAGGAAGGGAGGAT 57.215 50.000 0.00 0.00 0.00 3.24
281 427 2.324541 AGATCGAAGGAAGGGAGGATG 58.675 52.381 0.00 0.00 0.00 3.51
283 429 0.691078 TCGAAGGAAGGGAGGATGGG 60.691 60.000 0.00 0.00 0.00 4.00
284 430 0.691078 CGAAGGAAGGGAGGATGGGA 60.691 60.000 0.00 0.00 0.00 4.37
285 431 1.596496 GAAGGAAGGGAGGATGGGAA 58.404 55.000 0.00 0.00 0.00 3.97
289 901 1.132500 GAAGGGAGGATGGGAACGAT 58.868 55.000 0.00 0.00 0.00 3.73
291 903 2.016905 AGGGAGGATGGGAACGATAG 57.983 55.000 0.00 0.00 46.19 2.08
319 935 4.083324 TGTTGCCTCGATGAATGTTTTCTC 60.083 41.667 0.00 0.00 32.78 2.87
325 941 6.109359 CCTCGATGAATGTTTTCTCCTTAGT 58.891 40.000 0.00 0.00 32.78 2.24
326 942 6.036517 CCTCGATGAATGTTTTCTCCTTAGTG 59.963 42.308 0.00 0.00 32.78 2.74
327 943 5.351465 TCGATGAATGTTTTCTCCTTAGTGC 59.649 40.000 0.00 0.00 32.78 4.40
331 949 2.489971 TGTTTTCTCCTTAGTGCCGTG 58.510 47.619 0.00 0.00 0.00 4.94
333 951 2.450609 TTTCTCCTTAGTGCCGTGTC 57.549 50.000 0.00 0.00 0.00 3.67
336 954 0.179161 CTCCTTAGTGCCGTGTCGAG 60.179 60.000 0.00 0.00 0.00 4.04
346 965 0.528901 CCGTGTCGAGTTTGTGTGGA 60.529 55.000 0.00 0.00 0.00 4.02
356 975 4.742167 CGAGTTTGTGTGGATAGCTAGATG 59.258 45.833 0.00 0.00 0.00 2.90
361 980 0.247736 GTGGATAGCTAGATGGGCCG 59.752 60.000 0.00 0.00 0.00 6.13
368 987 1.510480 GCTAGATGGGCCGTTGATGC 61.510 60.000 0.00 0.00 0.00 3.91
374 993 2.908015 GGCCGTTGATGCCCTCTA 59.092 61.111 0.00 0.00 43.33 2.43
375 994 1.227674 GGCCGTTGATGCCCTCTAG 60.228 63.158 0.00 0.00 43.33 2.43
376 995 1.227674 GCCGTTGATGCCCTCTAGG 60.228 63.158 0.00 0.00 39.47 3.02
377 996 1.686325 GCCGTTGATGCCCTCTAGGA 61.686 60.000 0.00 0.00 38.24 2.94
378 997 1.051812 CCGTTGATGCCCTCTAGGAT 58.948 55.000 0.00 0.00 38.24 3.24
379 998 1.270518 CCGTTGATGCCCTCTAGGATG 60.271 57.143 0.00 0.00 38.24 3.51
380 999 1.875576 CGTTGATGCCCTCTAGGATGC 60.876 57.143 0.00 0.00 38.24 3.91
393 1012 0.778083 AGGATGCCATGCTCCATGAT 59.222 50.000 6.77 0.00 43.81 2.45
397 1020 0.032912 TGCCATGCTCCATGATGGTT 60.033 50.000 11.87 0.00 43.81 3.67
405 1028 0.113972 TCCATGATGGTTGTTGGGCA 59.886 50.000 11.87 0.00 39.03 5.36
425 1048 4.335315 GGCATGTATCTCGGTTTTCATTCA 59.665 41.667 0.00 0.00 0.00 2.57
426 1049 5.009010 GGCATGTATCTCGGTTTTCATTCAT 59.991 40.000 0.00 0.00 0.00 2.57
429 1052 7.489113 GCATGTATCTCGGTTTTCATTCATTTT 59.511 33.333 0.00 0.00 0.00 1.82
520 1434 9.500785 TGTTTCTCAATTTTATTTGATTTCCCC 57.499 29.630 0.00 0.00 35.20 4.81
522 1436 7.805083 TCTCAATTTTATTTGATTTCCCCCA 57.195 32.000 0.00 0.00 35.20 4.96
523 1437 8.391305 TCTCAATTTTATTTGATTTCCCCCAT 57.609 30.769 0.00 0.00 35.20 4.00
525 1439 9.465199 CTCAATTTTATTTGATTTCCCCCATTT 57.535 29.630 0.00 0.00 35.20 2.32
526 1440 9.819754 TCAATTTTATTTGATTTCCCCCATTTT 57.180 25.926 0.00 0.00 30.82 1.82
529 1443 9.599056 ATTTTATTTGATTTCCCCCATTTTTGT 57.401 25.926 0.00 0.00 0.00 2.83
530 1444 7.992754 TTATTTGATTTCCCCCATTTTTGTG 57.007 32.000 0.00 0.00 0.00 3.33
531 1445 5.379706 TTTGATTTCCCCCATTTTTGTGT 57.620 34.783 0.00 0.00 0.00 3.72
532 1446 4.348863 TGATTTCCCCCATTTTTGTGTG 57.651 40.909 0.00 0.00 0.00 3.82
534 1448 2.478872 TTCCCCCATTTTTGTGTGGA 57.521 45.000 0.00 0.00 37.72 4.02
535 1449 2.478872 TCCCCCATTTTTGTGTGGAA 57.521 45.000 0.00 0.00 37.72 3.53
536 1450 2.983296 TCCCCCATTTTTGTGTGGAAT 58.017 42.857 0.00 0.00 37.72 3.01
537 1451 2.636893 TCCCCCATTTTTGTGTGGAATG 59.363 45.455 0.00 0.00 37.72 2.67
538 1452 2.371510 CCCCCATTTTTGTGTGGAATGT 59.628 45.455 0.00 0.00 37.72 2.71
540 1454 4.459330 CCCCATTTTTGTGTGGAATGTTT 58.541 39.130 0.00 0.00 37.72 2.83
541 1455 4.514816 CCCCATTTTTGTGTGGAATGTTTC 59.485 41.667 0.00 0.00 37.72 2.78
550 1465 9.883142 TTTTGTGTGGAATGTTTCTTTCTTAAT 57.117 25.926 0.00 0.00 0.00 1.40
661 1577 3.855668 TGACCCTTTCATGGAAAATGGT 58.144 40.909 10.58 10.58 38.54 3.55
670 1593 7.662669 CCTTTCATGGAAAATGGTGAGAAAAAT 59.337 33.333 0.00 0.00 30.84 1.82
1188 2137 3.726517 CTCCAGGTGCCGTTTGCG 61.727 66.667 0.00 0.00 45.60 4.85
1309 2271 1.197721 CTGCATTTCCACAAGACGGAC 59.802 52.381 0.00 0.00 30.29 4.79
1469 2443 2.109126 GTGAGCGATCCAAGTGCCC 61.109 63.158 0.00 0.00 0.00 5.36
1470 2444 2.268920 GAGCGATCCAAGTGCCCA 59.731 61.111 0.00 0.00 0.00 5.36
1484 2458 3.805207 AGTGCCCATCGTCCTAAATTAC 58.195 45.455 0.00 0.00 0.00 1.89
1508 2482 2.422127 TGTGCTTCGCTTAATTAAGGCC 59.578 45.455 23.37 13.30 33.95 5.19
1575 2557 4.974368 TGTTTGACCGTGACATTTTCTT 57.026 36.364 0.00 0.00 0.00 2.52
1579 2561 7.136119 TGTTTGACCGTGACATTTTCTTATTC 58.864 34.615 0.00 0.00 0.00 1.75
1614 2645 3.503891 ACGTTTTGTGTGGCTTTTGTAC 58.496 40.909 0.00 0.00 0.00 2.90
1723 2792 3.795639 CGTAGATCACTGCATGTCTCAAG 59.204 47.826 0.00 0.00 0.00 3.02
1727 2796 5.311265 AGATCACTGCATGTCTCAAGAAAA 58.689 37.500 0.00 0.00 0.00 2.29
1728 2797 5.411977 AGATCACTGCATGTCTCAAGAAAAG 59.588 40.000 0.00 0.00 0.00 2.27
1741 2810 3.638160 TCAAGAAAAGATTGTGCAAGGCT 59.362 39.130 0.00 0.00 0.00 4.58
1747 2816 5.789643 AAAGATTGTGCAAGGCTTAGAAA 57.210 34.783 0.00 0.00 0.00 2.52
1759 2828 5.941555 AGGCTTAGAAAGTGCACTATACT 57.058 39.130 22.01 20.14 0.00 2.12
1760 2829 7.265673 CAAGGCTTAGAAAGTGCACTATACTA 58.734 38.462 22.01 19.16 0.00 1.82
1761 2830 6.807789 AGGCTTAGAAAGTGCACTATACTAC 58.192 40.000 22.01 11.87 0.00 2.73
1762 2831 6.608002 AGGCTTAGAAAGTGCACTATACTACT 59.392 38.462 22.01 14.52 0.00 2.57
1763 2832 6.919115 GGCTTAGAAAGTGCACTATACTACTC 59.081 42.308 22.01 15.10 0.00 2.59
1764 2833 6.919115 GCTTAGAAAGTGCACTATACTACTCC 59.081 42.308 22.01 10.13 0.00 3.85
1765 2834 5.855740 AGAAAGTGCACTATACTACTCCC 57.144 43.478 22.01 0.00 0.00 4.30
1766 2835 5.520751 AGAAAGTGCACTATACTACTCCCT 58.479 41.667 22.01 0.00 0.00 4.20
1767 2836 5.595133 AGAAAGTGCACTATACTACTCCCTC 59.405 44.000 22.01 0.00 0.00 4.30
1768 2837 3.834938 AGTGCACTATACTACTCCCTCC 58.165 50.000 20.16 0.00 0.00 4.30
1769 2838 2.553172 GTGCACTATACTACTCCCTCCG 59.447 54.545 10.32 0.00 0.00 4.63
1770 2839 2.174210 TGCACTATACTACTCCCTCCGT 59.826 50.000 0.00 0.00 0.00 4.69
1771 2840 2.813172 GCACTATACTACTCCCTCCGTC 59.187 54.545 0.00 0.00 0.00 4.79
1772 2841 3.496515 GCACTATACTACTCCCTCCGTCT 60.497 52.174 0.00 0.00 0.00 4.18
1773 2842 4.262808 GCACTATACTACTCCCTCCGTCTA 60.263 50.000 0.00 0.00 0.00 2.59
1774 2843 5.571251 GCACTATACTACTCCCTCCGTCTAT 60.571 48.000 0.00 0.00 0.00 1.98
1775 2844 6.351711 GCACTATACTACTCCCTCCGTCTATA 60.352 46.154 0.00 0.00 0.00 1.31
1776 2845 7.619050 CACTATACTACTCCCTCCGTCTATAA 58.381 42.308 0.00 0.00 0.00 0.98
1777 2846 8.266473 CACTATACTACTCCCTCCGTCTATAAT 58.734 40.741 0.00 0.00 0.00 1.28
1778 2847 8.266473 ACTATACTACTCCCTCCGTCTATAATG 58.734 40.741 0.00 0.00 0.00 1.90
1779 2848 4.080687 ACTACTCCCTCCGTCTATAATGC 58.919 47.826 0.00 0.00 0.00 3.56
1780 2849 2.958818 ACTCCCTCCGTCTATAATGCA 58.041 47.619 0.00 0.00 0.00 3.96
1781 2850 3.305720 ACTCCCTCCGTCTATAATGCAA 58.694 45.455 0.00 0.00 0.00 4.08
1782 2851 3.322254 ACTCCCTCCGTCTATAATGCAAG 59.678 47.826 0.00 0.00 0.00 4.01
1783 2852 3.572642 TCCCTCCGTCTATAATGCAAGA 58.427 45.455 0.00 0.00 0.00 3.02
1784 2853 3.321111 TCCCTCCGTCTATAATGCAAGAC 59.679 47.826 6.25 6.25 39.00 3.01
1808 2877 6.539649 GCAATAACGTCTTGCATTATAGGA 57.460 37.500 23.39 0.00 46.44 2.94
1809 2878 6.363473 GCAATAACGTCTTGCATTATAGGAC 58.637 40.000 23.39 0.00 46.44 3.85
1812 2881 3.364889 CGTCTTGCATTATAGGACGGA 57.635 47.619 0.00 0.00 43.69 4.69
1813 2882 3.309388 CGTCTTGCATTATAGGACGGAG 58.691 50.000 0.00 0.00 43.69 4.63
1814 2883 3.654414 GTCTTGCATTATAGGACGGAGG 58.346 50.000 0.00 0.00 0.00 4.30
1815 2884 2.632996 TCTTGCATTATAGGACGGAGGG 59.367 50.000 0.00 0.00 0.00 4.30
1816 2885 2.391926 TGCATTATAGGACGGAGGGA 57.608 50.000 0.00 0.00 0.00 4.20
1817 2886 2.248248 TGCATTATAGGACGGAGGGAG 58.752 52.381 0.00 0.00 0.00 4.30
1818 2887 2.249139 GCATTATAGGACGGAGGGAGT 58.751 52.381 0.00 0.00 0.00 3.85
1819 2888 3.181426 TGCATTATAGGACGGAGGGAGTA 60.181 47.826 0.00 0.00 0.00 2.59
1820 2889 3.193056 GCATTATAGGACGGAGGGAGTAC 59.807 52.174 0.00 0.00 0.00 2.73
1895 2965 2.364324 TGTATCTGTTCCGGTATCTGCC 59.636 50.000 0.00 0.00 0.00 4.85
1905 2975 3.071023 TCCGGTATCTGCCTTTATTGGAG 59.929 47.826 0.00 0.00 0.00 3.86
1914 2984 2.295885 CCTTTATTGGAGCTCAGCCTG 58.704 52.381 17.19 0.00 0.00 4.85
1919 2989 0.538057 TTGGAGCTCAGCCTGTTTGG 60.538 55.000 17.19 0.00 39.35 3.28
1928 2998 3.084039 TCAGCCTGTTTGGTGATCATTC 58.916 45.455 0.00 0.00 38.35 2.67
1936 3006 5.559770 TGTTTGGTGATCATTCTAGAAGCA 58.440 37.500 11.53 3.97 0.00 3.91
1956 3026 5.535990 AGCACTTTTATACCCTACTACCCT 58.464 41.667 0.00 0.00 0.00 4.34
2010 3080 9.462174 TTGAAAATCAGTTGTTTACAATAGCAG 57.538 29.630 0.00 0.00 38.24 4.24
2023 3093 1.039068 ATAGCAGCACGAGCAGATCT 58.961 50.000 7.77 0.00 45.49 2.75
2054 3124 4.276678 TGCAAGATTGACAGTTTTCTCCTG 59.723 41.667 0.00 0.00 36.01 3.86
2171 3242 3.347077 ACATCTGGAGCCTCTTTTCAG 57.653 47.619 0.00 0.00 0.00 3.02
2212 3285 6.432162 TGAATTTGTCTTGAATTCAGGAGAGG 59.568 38.462 19.59 3.12 44.30 3.69
2218 3291 2.485659 TGAATTCAGGAGAGGGATGCT 58.514 47.619 3.38 0.00 0.00 3.79
2654 3738 5.759506 TGACGCCTTCTAAATTCAAAACA 57.240 34.783 0.00 0.00 0.00 2.83
2799 3888 9.502145 GAAAATTTGAGCGTGTATGAATGAATA 57.498 29.630 0.00 0.00 0.00 1.75
4028 5230 8.323567 TCCCGTTACATTTATATTATCCTTCCC 58.676 37.037 0.00 0.00 0.00 3.97
4324 5528 3.157087 CCTGGGCTGTCACAAATAAGTT 58.843 45.455 0.00 0.00 0.00 2.66
4495 5700 1.003545 CCGCGTCACATGGAAATCATC 60.004 52.381 4.92 0.00 32.92 2.92
4671 5876 6.992715 CGATGAGGGTTTTAGATAACAATCCT 59.007 38.462 0.00 0.00 0.00 3.24
4836 6142 5.943416 CCTACTGGACCATTTTACATTGTCA 59.057 40.000 0.00 0.00 34.57 3.58
5203 6524 3.944015 AGAGCTGTTTGCAGATTATGTCC 59.056 43.478 0.00 0.00 42.00 4.02
5355 6676 2.579684 ATCTTCTCACCGGGCTTCGC 62.580 60.000 6.32 0.00 37.59 4.70
6874 8213 0.468226 TCTTGAACACGGCTGGAAGT 59.532 50.000 0.00 0.00 35.30 3.01
6901 8240 4.704833 AGCAGCGACCGCACCATT 62.705 61.111 16.97 0.00 44.88 3.16
6996 8335 1.096967 TGGATGATGATGCGTGGCAC 61.097 55.000 7.79 7.79 43.04 5.01
7010 8349 2.936498 CGTGGCACTAATAAGGACCTTG 59.064 50.000 17.47 2.27 0.00 3.61
7084 8423 1.595794 CAACGTACGAAGCCTGTTGTT 59.404 47.619 24.41 0.00 36.17 2.83
7085 8424 1.214367 ACGTACGAAGCCTGTTGTTG 58.786 50.000 24.41 0.00 0.00 3.33
7086 8425 1.214367 CGTACGAAGCCTGTTGTTGT 58.786 50.000 10.44 0.00 0.00 3.32
7292 8631 6.992123 TCATGTTGCCTATGTAGTTAGGATTG 59.008 38.462 1.71 0.00 41.18 2.67
7422 8762 9.545105 AAAGACTCATATCTCATAAGCTGAAAG 57.455 33.333 0.00 0.00 32.14 2.62
7443 8783 2.948315 GCTCTTAGGCAGGATTTGAAGG 59.052 50.000 0.00 0.00 0.00 3.46
7486 8830 6.147000 GCTAGAATGAAGCTCCTAATAAGTGC 59.853 42.308 0.00 0.00 37.01 4.40
7553 8897 5.888161 CCTTTGTATAGGCAGGAGTTCAATT 59.112 40.000 0.00 0.00 0.00 2.32
7618 8962 3.423539 AAAGAGATGTACCAGCTGCAA 57.576 42.857 8.66 0.00 26.98 4.08
7659 9003 3.230245 CCTGGGCGCCACCAAAAA 61.230 61.111 30.85 2.91 40.68 1.94
7671 9015 4.260579 CGCCACCAAAAATGAAGTTTTTCC 60.261 41.667 0.00 0.00 45.70 3.13
7685 9029 3.005791 AGTTTTTCCATACCAGCTGCAAC 59.994 43.478 8.66 0.00 0.00 4.17
7788 9132 0.104855 TGTTGAGAGACTGCAACGCT 59.895 50.000 11.20 0.00 45.47 5.07
7797 9141 4.873810 TGCAACGCTGTGGCCTGT 62.874 61.111 3.32 0.00 30.14 4.00
7809 9153 3.646715 GCCTGTAGCACCACCCCA 61.647 66.667 0.00 0.00 42.97 4.96
7886 9232 1.115467 CCTTCTCGAGGCAGGTATGT 58.885 55.000 18.72 0.00 39.09 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.225984 TGTTTGCTTGTTTGATCGTATGC 58.774 39.130 0.00 0.00 0.00 3.14
1 2 7.463544 TCTATGTTTGCTTGTTTGATCGTATG 58.536 34.615 0.00 0.00 0.00 2.39
3 4 7.172532 AGTTCTATGTTTGCTTGTTTGATCGTA 59.827 33.333 0.00 0.00 0.00 3.43
4 5 5.940192 TCTATGTTTGCTTGTTTGATCGT 57.060 34.783 0.00 0.00 0.00 3.73
5 6 6.373779 AGTTCTATGTTTGCTTGTTTGATCG 58.626 36.000 0.00 0.00 0.00 3.69
6 7 8.507249 ACTAGTTCTATGTTTGCTTGTTTGATC 58.493 33.333 0.00 0.00 0.00 2.92
7 8 8.396272 ACTAGTTCTATGTTTGCTTGTTTGAT 57.604 30.769 0.00 0.00 0.00 2.57
8 9 7.801716 ACTAGTTCTATGTTTGCTTGTTTGA 57.198 32.000 0.00 0.00 0.00 2.69
9 10 8.856490 AAACTAGTTCTATGTTTGCTTGTTTG 57.144 30.769 8.95 0.00 35.23 2.93
12 13 8.656849 CGATAAACTAGTTCTATGTTTGCTTGT 58.343 33.333 8.95 0.00 35.77 3.16
13 14 8.656849 ACGATAAACTAGTTCTATGTTTGCTTG 58.343 33.333 8.95 0.00 35.77 4.01
14 15 8.773404 ACGATAAACTAGTTCTATGTTTGCTT 57.227 30.769 8.95 0.00 35.77 3.91
15 16 7.491696 GGACGATAAACTAGTTCTATGTTTGCT 59.508 37.037 8.95 0.00 35.77 3.91
16 17 7.491696 AGGACGATAAACTAGTTCTATGTTTGC 59.508 37.037 8.95 0.00 35.77 3.68
17 18 8.928270 AGGACGATAAACTAGTTCTATGTTTG 57.072 34.615 8.95 0.00 35.77 2.93
18 19 9.367444 CAAGGACGATAAACTAGTTCTATGTTT 57.633 33.333 8.95 0.00 37.60 2.83
19 20 8.746530 TCAAGGACGATAAACTAGTTCTATGTT 58.253 33.333 8.95 0.00 0.00 2.71
20 21 8.289939 TCAAGGACGATAAACTAGTTCTATGT 57.710 34.615 8.95 5.94 0.00 2.29
21 22 8.622157 TCTCAAGGACGATAAACTAGTTCTATG 58.378 37.037 8.95 2.66 0.00 2.23
22 23 8.749026 TCTCAAGGACGATAAACTAGTTCTAT 57.251 34.615 8.95 8.94 0.00 1.98
23 24 8.571461 TTCTCAAGGACGATAAACTAGTTCTA 57.429 34.615 8.95 4.47 0.00 2.10
24 25 7.463961 TTCTCAAGGACGATAAACTAGTTCT 57.536 36.000 8.95 0.00 0.00 3.01
25 26 6.253942 GCTTCTCAAGGACGATAAACTAGTTC 59.746 42.308 8.95 0.00 0.00 3.01
26 27 6.100668 GCTTCTCAAGGACGATAAACTAGTT 58.899 40.000 1.12 1.12 0.00 2.24
27 28 5.185249 TGCTTCTCAAGGACGATAAACTAGT 59.815 40.000 0.00 0.00 0.00 2.57
28 29 5.651530 TGCTTCTCAAGGACGATAAACTAG 58.348 41.667 0.00 0.00 0.00 2.57
29 30 5.654603 TGCTTCTCAAGGACGATAAACTA 57.345 39.130 0.00 0.00 0.00 2.24
30 31 4.537135 TGCTTCTCAAGGACGATAAACT 57.463 40.909 0.00 0.00 0.00 2.66
31 32 4.034510 CCATGCTTCTCAAGGACGATAAAC 59.965 45.833 0.00 0.00 35.62 2.01
32 33 4.081142 TCCATGCTTCTCAAGGACGATAAA 60.081 41.667 0.00 0.00 37.62 1.40
33 34 3.450817 TCCATGCTTCTCAAGGACGATAA 59.549 43.478 0.00 0.00 37.62 1.75
34 35 3.031013 TCCATGCTTCTCAAGGACGATA 58.969 45.455 0.00 0.00 37.62 2.92
35 36 1.833630 TCCATGCTTCTCAAGGACGAT 59.166 47.619 0.00 0.00 37.62 3.73
36 37 1.205655 CTCCATGCTTCTCAAGGACGA 59.794 52.381 0.00 0.00 37.62 4.20
37 38 1.205655 TCTCCATGCTTCTCAAGGACG 59.794 52.381 0.00 0.00 37.62 4.79
44 45 6.971184 CACATACATTTTTCTCCATGCTTCTC 59.029 38.462 0.00 0.00 0.00 2.87
45 46 6.435277 ACACATACATTTTTCTCCATGCTTCT 59.565 34.615 0.00 0.00 0.00 2.85
49 50 6.624423 AGAACACATACATTTTTCTCCATGC 58.376 36.000 0.00 0.00 0.00 4.06
54 55 7.015877 GGACGAAGAACACATACATTTTTCTC 58.984 38.462 0.00 0.00 0.00 2.87
56 57 6.664515 TGGACGAAGAACACATACATTTTTC 58.335 36.000 0.00 0.00 0.00 2.29
64 65 4.443913 TCGAATGGACGAAGAACACATA 57.556 40.909 0.00 0.00 39.34 2.29
76 77 4.481930 TCACATGTGTTTTCGAATGGAC 57.518 40.909 24.63 0.00 0.00 4.02
80 81 4.821805 AGAGGTTCACATGTGTTTTCGAAT 59.178 37.500 24.63 5.02 0.00 3.34
85 86 4.081752 TGCAAAGAGGTTCACATGTGTTTT 60.082 37.500 24.63 13.30 0.00 2.43
89 90 3.181488 TGTTGCAAAGAGGTTCACATGTG 60.181 43.478 20.18 20.18 0.00 3.21
127 132 7.421599 TCAATAACAAATGTCTTTTTGCTCGA 58.578 30.769 0.00 0.00 39.65 4.04
128 133 7.379529 ACTCAATAACAAATGTCTTTTTGCTCG 59.620 33.333 0.00 0.00 39.65 5.03
131 136 8.816144 TGAACTCAATAACAAATGTCTTTTTGC 58.184 29.630 0.00 0.00 39.65 3.68
137 142 7.566760 TGTGTGAACTCAATAACAAATGTCT 57.433 32.000 0.00 0.00 0.00 3.41
140 145 6.524239 CGGATGTGTGAACTCAATAACAAATG 59.476 38.462 0.00 0.00 0.00 2.32
143 148 4.454161 CCGGATGTGTGAACTCAATAACAA 59.546 41.667 0.00 0.00 0.00 2.83
146 151 4.545208 TCCGGATGTGTGAACTCAATAA 57.455 40.909 0.00 0.00 0.00 1.40
149 154 3.417069 AATCCGGATGTGTGAACTCAA 57.583 42.857 19.95 0.00 0.00 3.02
155 160 4.764308 TGAAATCAAAATCCGGATGTGTGA 59.236 37.500 19.95 20.60 0.00 3.58
160 165 5.030295 CGACTTGAAATCAAAATCCGGATG 58.970 41.667 19.95 7.57 35.15 3.51
161 166 4.941263 TCGACTTGAAATCAAAATCCGGAT 59.059 37.500 12.38 12.38 35.15 4.18
163 168 4.154195 ACTCGACTTGAAATCAAAATCCGG 59.846 41.667 0.00 0.00 35.15 5.14
164 169 5.283060 ACTCGACTTGAAATCAAAATCCG 57.717 39.130 0.00 0.02 35.15 4.18
166 171 7.914537 AACAACTCGACTTGAAATCAAAATC 57.085 32.000 11.17 0.00 35.15 2.17
173 178 5.287226 ACGTCTAACAACTCGACTTGAAAT 58.713 37.500 11.17 1.33 0.00 2.17
175 180 4.285292 GACGTCTAACAACTCGACTTGAA 58.715 43.478 8.70 0.00 0.00 2.69
178 183 2.620115 TGGACGTCTAACAACTCGACTT 59.380 45.455 16.46 0.00 0.00 3.01
183 188 2.412089 GCACATGGACGTCTAACAACTC 59.588 50.000 16.46 0.00 0.00 3.01
184 189 2.413837 GCACATGGACGTCTAACAACT 58.586 47.619 16.46 0.00 0.00 3.16
185 190 1.126113 CGCACATGGACGTCTAACAAC 59.874 52.381 16.46 0.00 0.00 3.32
186 191 1.000052 TCGCACATGGACGTCTAACAA 60.000 47.619 16.46 0.00 0.00 2.83
188 193 0.989890 GTCGCACATGGACGTCTAAC 59.010 55.000 16.46 0.00 0.00 2.34
189 194 0.885879 AGTCGCACATGGACGTCTAA 59.114 50.000 16.46 4.64 39.38 2.10
190 195 1.741528 TAGTCGCACATGGACGTCTA 58.258 50.000 16.46 10.40 39.38 2.59
191 196 1.103803 ATAGTCGCACATGGACGTCT 58.896 50.000 16.46 12.32 39.38 4.18
192 197 1.588404 CAATAGTCGCACATGGACGTC 59.412 52.381 7.13 7.13 39.38 4.34
193 198 1.640428 CAATAGTCGCACATGGACGT 58.360 50.000 9.11 0.00 39.38 4.34
194 199 0.301687 GCAATAGTCGCACATGGACG 59.698 55.000 0.00 0.00 39.38 4.79
195 200 0.301687 CGCAATAGTCGCACATGGAC 59.698 55.000 0.00 0.00 34.62 4.02
196 201 0.809636 CCGCAATAGTCGCACATGGA 60.810 55.000 0.00 0.00 0.00 3.41
197 202 1.089481 ACCGCAATAGTCGCACATGG 61.089 55.000 0.00 0.00 0.00 3.66
198 203 0.026674 CACCGCAATAGTCGCACATG 59.973 55.000 0.00 0.00 0.00 3.21
200 205 1.011968 GTCACCGCAATAGTCGCACA 61.012 55.000 0.00 0.00 0.00 4.57
201 206 1.693083 GGTCACCGCAATAGTCGCAC 61.693 60.000 0.00 0.00 0.00 5.34
203 349 2.514013 CGGTCACCGCAATAGTCGC 61.514 63.158 1.50 0.00 41.17 5.19
219 365 3.336138 AACTTTCTCTAAAGGGAGCGG 57.664 47.619 3.19 0.00 45.39 5.52
232 378 8.936864 CGACTCCAACTTCATTATAAACTTTCT 58.063 33.333 0.00 0.00 0.00 2.52
233 379 7.692705 GCGACTCCAACTTCATTATAAACTTTC 59.307 37.037 0.00 0.00 0.00 2.62
237 383 6.663944 AGCGACTCCAACTTCATTATAAAC 57.336 37.500 0.00 0.00 0.00 2.01
240 386 6.954487 TCTAGCGACTCCAACTTCATTATA 57.046 37.500 0.00 0.00 0.00 0.98
242 388 5.505819 CGATCTAGCGACTCCAACTTCATTA 60.506 44.000 0.00 0.00 0.00 1.90
243 389 4.688021 GATCTAGCGACTCCAACTTCATT 58.312 43.478 0.00 0.00 0.00 2.57
245 391 2.097629 CGATCTAGCGACTCCAACTTCA 59.902 50.000 0.00 0.00 0.00 3.02
247 393 2.366533 TCGATCTAGCGACTCCAACTT 58.633 47.619 0.00 0.00 35.01 2.66
250 396 1.676529 CCTTCGATCTAGCGACTCCAA 59.323 52.381 0.00 0.00 40.42 3.53
251 397 1.134189 TCCTTCGATCTAGCGACTCCA 60.134 52.381 0.00 0.00 40.42 3.86
271 417 2.330216 CTATCGTTCCCATCCTCCCTT 58.670 52.381 0.00 0.00 0.00 3.95
272 418 1.220750 ACTATCGTTCCCATCCTCCCT 59.779 52.381 0.00 0.00 0.00 4.20
274 420 2.040178 ACACTATCGTTCCCATCCTCC 58.960 52.381 0.00 0.00 0.00 4.30
277 423 2.093658 ACACACACTATCGTTCCCATCC 60.094 50.000 0.00 0.00 0.00 3.51
278 424 3.247006 ACACACACTATCGTTCCCATC 57.753 47.619 0.00 0.00 0.00 3.51
279 425 3.334691 CAACACACACTATCGTTCCCAT 58.665 45.455 0.00 0.00 0.00 4.00
280 426 2.761559 CAACACACACTATCGTTCCCA 58.238 47.619 0.00 0.00 0.00 4.37
281 427 1.463444 GCAACACACACTATCGTTCCC 59.537 52.381 0.00 0.00 0.00 3.97
283 429 2.412089 GAGGCAACACACACTATCGTTC 59.588 50.000 0.00 0.00 41.41 3.95
284 430 2.413837 GAGGCAACACACACTATCGTT 58.586 47.619 0.00 0.00 41.41 3.85
285 431 1.668919 CGAGGCAACACACACTATCGT 60.669 52.381 0.00 0.00 41.41 3.73
289 901 1.616374 TCATCGAGGCAACACACACTA 59.384 47.619 0.00 0.00 41.41 2.74
291 903 1.225855 TTCATCGAGGCAACACACAC 58.774 50.000 0.00 0.00 41.41 3.82
296 908 3.820467 AGAAAACATTCATCGAGGCAACA 59.180 39.130 0.00 0.00 41.41 3.33
297 909 4.406943 GAGAAAACATTCATCGAGGCAAC 58.593 43.478 0.00 0.00 0.00 4.17
299 911 3.009723 GGAGAAAACATTCATCGAGGCA 58.990 45.455 0.00 0.00 0.00 4.75
319 935 0.038526 AACTCGACACGGCACTAAGG 60.039 55.000 0.00 0.00 0.00 2.69
325 941 1.153529 ACACAAACTCGACACGGCA 60.154 52.632 0.00 0.00 0.00 5.69
326 942 1.275657 CACACAAACTCGACACGGC 59.724 57.895 0.00 0.00 0.00 5.68
327 943 0.528901 TCCACACAAACTCGACACGG 60.529 55.000 0.00 0.00 0.00 4.94
331 949 2.960819 AGCTATCCACACAAACTCGAC 58.039 47.619 0.00 0.00 0.00 4.20
333 951 4.371855 TCTAGCTATCCACACAAACTCG 57.628 45.455 0.00 0.00 0.00 4.18
336 954 4.130118 CCCATCTAGCTATCCACACAAAC 58.870 47.826 0.00 0.00 0.00 2.93
346 965 1.717032 TCAACGGCCCATCTAGCTAT 58.283 50.000 0.00 0.00 0.00 2.97
361 980 1.544314 GGCATCCTAGAGGGCATCAAC 60.544 57.143 0.58 0.00 38.72 3.18
368 987 0.324285 GAGCATGGCATCCTAGAGGG 59.676 60.000 0.00 0.00 35.41 4.30
369 988 0.324285 GGAGCATGGCATCCTAGAGG 59.676 60.000 0.00 0.00 32.51 3.69
370 989 1.054231 TGGAGCATGGCATCCTAGAG 58.946 55.000 0.00 0.00 36.50 2.43
371 990 1.350019 CATGGAGCATGGCATCCTAGA 59.650 52.381 0.00 0.00 38.11 2.43
372 991 1.350019 TCATGGAGCATGGCATCCTAG 59.650 52.381 0.00 0.00 41.66 3.02
374 993 0.778083 ATCATGGAGCATGGCATCCT 59.222 50.000 0.00 0.00 41.66 3.24
375 994 0.888619 CATCATGGAGCATGGCATCC 59.111 55.000 0.00 0.00 41.66 3.51
376 995 0.888619 CCATCATGGAGCATGGCATC 59.111 55.000 0.00 0.00 40.96 3.91
377 996 0.187606 ACCATCATGGAGCATGGCAT 59.812 50.000 11.90 0.00 43.16 4.40
378 997 0.032912 AACCATCATGGAGCATGGCA 60.033 50.000 11.90 0.00 43.16 4.92
379 998 0.387929 CAACCATCATGGAGCATGGC 59.612 55.000 11.90 0.00 43.16 4.40
380 999 1.771565 ACAACCATCATGGAGCATGG 58.228 50.000 11.90 9.12 40.96 3.66
393 1012 2.722094 GAGATACATGCCCAACAACCA 58.278 47.619 0.00 0.00 0.00 3.67
397 1020 0.908910 ACCGAGATACATGCCCAACA 59.091 50.000 0.00 0.00 0.00 3.33
497 1411 8.212259 TGGGGGAAATCAAATAAAATTGAGAA 57.788 30.769 0.00 0.00 42.21 2.87
508 1422 5.769162 CACACAAAAATGGGGGAAATCAAAT 59.231 36.000 0.00 0.00 0.00 2.32
509 1423 5.128919 CACACAAAAATGGGGGAAATCAAA 58.871 37.500 0.00 0.00 0.00 2.69
512 1426 3.326297 TCCACACAAAAATGGGGGAAATC 59.674 43.478 0.00 0.00 44.07 2.17
513 1427 3.321950 TCCACACAAAAATGGGGGAAAT 58.678 40.909 0.00 0.00 44.07 2.17
514 1428 2.764269 TCCACACAAAAATGGGGGAAA 58.236 42.857 0.00 0.00 44.07 3.13
517 1431 2.371510 ACATTCCACACAAAAATGGGGG 59.628 45.455 0.00 0.00 44.07 5.40
518 1432 3.767902 ACATTCCACACAAAAATGGGG 57.232 42.857 0.00 0.00 45.45 4.96
519 1433 5.367302 AGAAACATTCCACACAAAAATGGG 58.633 37.500 0.00 0.00 36.56 4.00
520 1434 6.923928 AAGAAACATTCCACACAAAAATGG 57.076 33.333 0.00 0.00 35.24 3.16
522 1436 8.791327 AAGAAAGAAACATTCCACACAAAAAT 57.209 26.923 0.00 0.00 0.00 1.82
523 1437 9.712305 TTAAGAAAGAAACATTCCACACAAAAA 57.288 25.926 0.00 0.00 0.00 1.94
525 1439 9.883142 AATTAAGAAAGAAACATTCCACACAAA 57.117 25.926 0.00 0.00 0.00 2.83
550 1465 5.814481 TGTGGTGGTTCATGATCTCATTAA 58.186 37.500 0.00 0.00 33.61 1.40
661 1577 9.801873 CTTGTTTTCTGAGGTTAATTTTTCTCA 57.198 29.630 0.00 0.00 35.32 3.27
670 1593 4.142038 GGCTCCTTGTTTTCTGAGGTTAA 58.858 43.478 0.00 0.00 32.33 2.01
894 1837 2.583441 CGGTGAACTCTGGAGGCCA 61.583 63.158 5.01 0.00 0.00 5.36
1309 2271 0.831307 GGTAGTAGGTCTGCTTGGGG 59.169 60.000 0.00 0.00 0.00 4.96
1469 2443 4.870426 AGCACACTGTAATTTAGGACGATG 59.130 41.667 0.00 0.00 0.00 3.84
1470 2444 5.086104 AGCACACTGTAATTTAGGACGAT 57.914 39.130 0.00 0.00 0.00 3.73
1575 2557 8.084073 ACAAAACGTAGTACTGCTACTTGAATA 58.916 33.333 5.39 0.00 45.00 1.75
1579 2561 5.461078 ACACAAAACGTAGTACTGCTACTTG 59.539 40.000 5.39 9.44 45.00 3.16
1614 2645 1.066143 ACCAGATACCTGAACCGCTTG 60.066 52.381 0.00 0.00 43.02 4.01
1723 2792 5.376854 TCTAAGCCTTGCACAATCTTTTC 57.623 39.130 0.00 0.00 0.00 2.29
1727 2796 4.217118 CACTTTCTAAGCCTTGCACAATCT 59.783 41.667 0.00 0.00 0.00 2.40
1728 2797 4.479619 CACTTTCTAAGCCTTGCACAATC 58.520 43.478 0.00 0.00 0.00 2.67
1741 2810 7.124052 AGGGAGTAGTATAGTGCACTTTCTAA 58.876 38.462 27.06 6.71 33.52 2.10
1747 2816 3.748027 CGGAGGGAGTAGTATAGTGCACT 60.748 52.174 25.12 25.12 33.52 4.40
1759 2828 4.108501 TGCATTATAGACGGAGGGAGTA 57.891 45.455 0.00 0.00 0.00 2.59
1760 2829 2.958818 TGCATTATAGACGGAGGGAGT 58.041 47.619 0.00 0.00 0.00 3.85
1761 2830 3.574396 TCTTGCATTATAGACGGAGGGAG 59.426 47.826 0.00 0.00 0.00 4.30
1762 2831 3.321111 GTCTTGCATTATAGACGGAGGGA 59.679 47.826 0.69 0.00 32.31 4.20
1763 2832 3.654414 GTCTTGCATTATAGACGGAGGG 58.346 50.000 0.69 0.00 32.31 4.30
1786 2855 6.346598 CCGTCCTATAATGCAAGACGTTATTG 60.347 42.308 16.15 9.42 46.62 1.90
1787 2856 5.694910 CCGTCCTATAATGCAAGACGTTATT 59.305 40.000 16.15 0.00 46.62 1.40
1788 2857 5.010314 TCCGTCCTATAATGCAAGACGTTAT 59.990 40.000 16.15 7.90 46.62 1.89
1789 2858 4.338964 TCCGTCCTATAATGCAAGACGTTA 59.661 41.667 16.15 1.71 46.62 3.18
1790 2859 3.131577 TCCGTCCTATAATGCAAGACGTT 59.868 43.478 16.15 0.00 46.62 3.99
1791 2860 2.691526 TCCGTCCTATAATGCAAGACGT 59.308 45.455 16.15 0.00 46.62 4.34
1793 2862 3.555168 CCCTCCGTCCTATAATGCAAGAC 60.555 52.174 0.00 0.00 0.00 3.01
1794 2863 2.632996 CCCTCCGTCCTATAATGCAAGA 59.367 50.000 0.00 0.00 0.00 3.02
1795 2864 2.632996 TCCCTCCGTCCTATAATGCAAG 59.367 50.000 0.00 0.00 0.00 4.01
1796 2865 2.632996 CTCCCTCCGTCCTATAATGCAA 59.367 50.000 0.00 0.00 0.00 4.08
1797 2866 2.248248 CTCCCTCCGTCCTATAATGCA 58.752 52.381 0.00 0.00 0.00 3.96
1798 2867 2.249139 ACTCCCTCCGTCCTATAATGC 58.751 52.381 0.00 0.00 0.00 3.56
1799 2868 4.404640 TGTACTCCCTCCGTCCTATAATG 58.595 47.826 0.00 0.00 0.00 1.90
1800 2869 4.736611 TGTACTCCCTCCGTCCTATAAT 57.263 45.455 0.00 0.00 0.00 1.28
1801 2870 4.166725 TCTTGTACTCCCTCCGTCCTATAA 59.833 45.833 0.00 0.00 0.00 0.98
1802 2871 3.718434 TCTTGTACTCCCTCCGTCCTATA 59.282 47.826 0.00 0.00 0.00 1.31
1803 2872 2.512896 TCTTGTACTCCCTCCGTCCTAT 59.487 50.000 0.00 0.00 0.00 2.57
1804 2873 1.918262 TCTTGTACTCCCTCCGTCCTA 59.082 52.381 0.00 0.00 0.00 2.94
1805 2874 0.702902 TCTTGTACTCCCTCCGTCCT 59.297 55.000 0.00 0.00 0.00 3.85
1806 2875 1.104630 CTCTTGTACTCCCTCCGTCC 58.895 60.000 0.00 0.00 0.00 4.79
1807 2876 2.125773 TCTCTTGTACTCCCTCCGTC 57.874 55.000 0.00 0.00 0.00 4.79
1808 2877 2.169330 GTTCTCTTGTACTCCCTCCGT 58.831 52.381 0.00 0.00 0.00 4.69
1809 2878 1.477295 GGTTCTCTTGTACTCCCTCCG 59.523 57.143 0.00 0.00 0.00 4.63
1810 2879 2.234168 GTGGTTCTCTTGTACTCCCTCC 59.766 54.545 0.00 0.00 0.00 4.30
1811 2880 3.056465 CAGTGGTTCTCTTGTACTCCCTC 60.056 52.174 0.00 0.00 0.00 4.30
1812 2881 2.900546 CAGTGGTTCTCTTGTACTCCCT 59.099 50.000 0.00 0.00 0.00 4.20
1813 2882 2.613223 GCAGTGGTTCTCTTGTACTCCC 60.613 54.545 0.00 0.00 0.00 4.30
1814 2883 2.037251 TGCAGTGGTTCTCTTGTACTCC 59.963 50.000 0.00 0.00 0.00 3.85
1815 2884 3.060602 GTGCAGTGGTTCTCTTGTACTC 58.939 50.000 0.00 0.00 0.00 2.59
1816 2885 2.700897 AGTGCAGTGGTTCTCTTGTACT 59.299 45.455 0.00 0.00 0.00 2.73
1817 2886 3.113260 AGTGCAGTGGTTCTCTTGTAC 57.887 47.619 0.00 0.00 0.00 2.90
1818 2887 5.483685 AATAGTGCAGTGGTTCTCTTGTA 57.516 39.130 3.69 0.00 0.00 2.41
1819 2888 4.357918 AATAGTGCAGTGGTTCTCTTGT 57.642 40.909 3.69 0.00 0.00 3.16
1820 2889 5.695851 AAAATAGTGCAGTGGTTCTCTTG 57.304 39.130 3.69 0.00 0.00 3.02
1895 2965 2.996631 ACAGGCTGAGCTCCAATAAAG 58.003 47.619 23.66 1.29 0.00 1.85
1905 2975 0.807496 GATCACCAAACAGGCTGAGC 59.193 55.000 23.66 0.00 43.14 4.26
1914 2984 5.645497 AGTGCTTCTAGAATGATCACCAAAC 59.355 40.000 5.44 0.00 0.00 2.93
1928 2998 8.358895 GGTAGTAGGGTATAAAAGTGCTTCTAG 58.641 40.741 0.00 0.00 0.00 2.43
1936 3006 5.222086 CCCAGGGTAGTAGGGTATAAAAGT 58.778 45.833 0.00 0.00 37.81 2.66
1956 3026 0.040646 ACCAGTGATCTACGACCCCA 59.959 55.000 0.00 0.00 0.00 4.96
2010 3080 0.461961 ACCCTAAGATCTGCTCGTGC 59.538 55.000 1.71 1.71 40.20 5.34
2023 3093 3.327757 ACTGTCAATCTTGCAGACCCTAA 59.672 43.478 16.09 0.00 36.50 2.69
2171 3242 6.158598 ACAAATTCACACCATCAATTACTGC 58.841 36.000 0.00 0.00 0.00 4.40
2212 3285 1.030457 CATTTCCCAGAGCAGCATCC 58.970 55.000 0.00 0.00 0.00 3.51
2218 3291 1.304381 GCCACCATTTCCCAGAGCA 60.304 57.895 0.00 0.00 0.00 4.26
2761 3850 5.466393 CGCTCAAATTTTCTGGACCAAAAAT 59.534 36.000 15.72 15.72 36.81 1.82
2773 3862 7.795431 TTCATTCATACACGCTCAAATTTTC 57.205 32.000 0.00 0.00 0.00 2.29
2847 3936 7.905604 TTTATCCAGTCTGATGTACAACAAG 57.094 36.000 7.28 2.26 0.00 3.16
4028 5230 4.377445 CCACGTTGTAACTGCGTAAAAATG 59.623 41.667 0.00 0.00 37.07 2.32
4477 5682 1.933181 TCGATGATTTCCATGTGACGC 59.067 47.619 0.00 0.00 35.17 5.19
4495 5700 0.447801 CCCGCTTGTCAATTTCCTCG 59.552 55.000 0.00 0.00 0.00 4.63
4671 5876 0.898326 TCCGCACTACTGGCTTCTCA 60.898 55.000 0.00 0.00 0.00 3.27
4926 6238 7.039923 ACAAGCAACATTTTCTCAGAGAATGAT 60.040 33.333 21.75 9.53 36.61 2.45
5022 6342 3.615155 AGCTCCAGAACTAATTGAAGCC 58.385 45.455 0.00 0.00 0.00 4.35
5203 6524 5.656416 TCTGGAATTTGTTAGGCCAAATAGG 59.344 40.000 5.01 0.00 42.63 2.57
5355 6676 3.057386 TGGAAGCATGCACACATACTTTG 60.057 43.478 21.98 0.00 39.51 2.77
6874 8213 2.110835 TCGCTGCTGAACTTGCCA 59.889 55.556 0.00 0.00 0.00 4.92
6901 8240 3.643320 AGATCTCCTTCGCATATTGGTCA 59.357 43.478 0.00 0.00 0.00 4.02
7010 8349 4.196971 GGTTATTCACCATGGACCAGTAC 58.803 47.826 21.47 9.27 46.42 2.73
7084 8423 2.290367 GTGCAGCAGAATACACAACACA 59.710 45.455 0.00 0.00 33.23 3.72
7085 8424 2.549754 AGTGCAGCAGAATACACAACAC 59.450 45.455 0.00 0.00 35.47 3.32
7086 8425 2.849942 AGTGCAGCAGAATACACAACA 58.150 42.857 0.00 0.00 35.47 3.33
7239 8578 8.663911 CACAAAACAACATTTTGATACCAAAGT 58.336 29.630 16.73 0.00 42.55 2.66
7250 8589 7.188157 GCAACATGATCACAAAACAACATTTT 58.812 30.769 0.00 0.00 0.00 1.82
7337 8676 3.744238 AAAACCTTCAATTTCCACCCG 57.256 42.857 0.00 0.00 0.00 5.28
7422 8762 2.948315 CCTTCAAATCCTGCCTAAGAGC 59.052 50.000 0.00 0.00 0.00 4.09
7618 8962 0.179100 CCAGATCAATGTCGAGGCGT 60.179 55.000 0.00 0.00 0.00 5.68
7645 8989 0.670239 CTTCATTTTTGGTGGCGCCC 60.670 55.000 26.77 15.53 36.04 6.13
7648 8992 4.873768 AAAAACTTCATTTTTGGTGGCG 57.126 36.364 0.00 0.00 46.53 5.69
7659 9003 4.082026 GCAGCTGGTATGGAAAAACTTCAT 60.082 41.667 17.12 0.00 0.00 2.57
7671 9015 1.709147 GAGGCGTTGCAGCTGGTATG 61.709 60.000 17.12 0.00 37.29 2.39
7685 9029 0.103026 TCCAGATCAATGTCGAGGCG 59.897 55.000 0.00 0.00 0.00 5.52
7809 9153 3.044305 GTCGCAAAGGACGCAGCT 61.044 61.111 0.00 0.00 0.00 4.24
7886 9232 1.933021 ACCAGACAAGGGTATCGTGA 58.067 50.000 0.00 0.00 36.72 4.35


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

AutoCloner maintained by Alex Coulton.