Multiple sequence alignment - TraesCS5D01G266200

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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 TraesCS5D01G266200 chr5D 100.000 4988 0 0 1 4988 370461879 370466866 0.000000e+00 9212.0
1 TraesCS5D01G266200 chr5A 92.550 4765 228 46 300 4988 473009089 473013802 0.000000e+00 6715.0
2 TraesCS5D01G266200 chr5B 93.155 4047 193 34 300 4281 439715175 439719202 0.000000e+00 5862.0
3 TraesCS5D01G266200 chr5B 89.481 732 31 12 4291 4988 439719245 439719964 0.000000e+00 883.0
4 TraesCS5D01G266200 chr5B 92.273 220 17 0 1591 1810 688589695 688589476 3.750000e-81 313.0
5 TraesCS5D01G266200 chr5B 92.373 118 4 1 126 238 439715040 439715157 4.000000e-36 163.0
6 TraesCS5D01G266200 chr5B 100.000 45 0 0 1497 1541 688590239 688590195 3.200000e-12 84.2
7 TraesCS5D01G266200 chr7B 76.479 2891 597 60 1140 3981 168074423 168077279 0.000000e+00 1495.0
8 TraesCS5D01G266200 chr7B 96.875 32 0 1 1446 1476 323817638 323817607 9.000000e-03 52.8
9 TraesCS5D01G266200 chr7D 76.369 2886 603 56 1140 3981 204109127 204111977 0.000000e+00 1478.0
10 TraesCS5D01G266200 chr7D 91.714 350 28 1 1455 1804 484694710 484694362 7.510000e-133 484.0
11 TraesCS5D01G266200 chr7A 76.025 2903 605 69 1140 3992 215934506 215937367 0.000000e+00 1421.0


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 TraesCS5D01G266200 chr5D 370461879 370466866 4987 False 9212.000000 9212 100.000000 1 4988 1 chr5D.!!$F1 4987
1 TraesCS5D01G266200 chr5A 473009089 473013802 4713 False 6715.000000 6715 92.550000 300 4988 1 chr5A.!!$F1 4688
2 TraesCS5D01G266200 chr5B 439715040 439719964 4924 False 2302.666667 5862 91.669667 126 4988 3 chr5B.!!$F1 4862
3 TraesCS5D01G266200 chr7B 168074423 168077279 2856 False 1495.000000 1495 76.479000 1140 3981 1 chr7B.!!$F1 2841
4 TraesCS5D01G266200 chr7D 204109127 204111977 2850 False 1478.000000 1478 76.369000 1140 3981 1 chr7D.!!$F1 2841
5 TraesCS5D01G266200 chr7A 215934506 215937367 2861 False 1421.000000 1421 76.025000 1140 3992 1 chr7A.!!$F1 2852

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
248 254 0.180406 GTACAATCCATGCCCCGACT 59.820 55.000 0.00 0.00 0.00 4.18 F
807 849 0.181587 TTGGTTCGGAGGTTCTTGCA 59.818 50.000 0.00 0.00 0.00 4.08 F
859 901 0.524862 CACTGCATGTTCTTGCCCTC 59.475 55.000 7.92 0.00 42.06 4.30 F
1783 1932 0.979665 TGCTCAGAAGAGGAACCTGG 59.020 55.000 0.00 0.00 39.45 4.45 F
1857 2006 1.135960 AGCCTGAAGATAAGGAGGGC 58.864 55.000 0.00 0.00 36.91 5.19 F
2081 2230 1.137675 TGCAGAGATCGAGGGAATGTG 59.862 52.381 0.00 0.00 0.00 3.21 F
2712 2864 1.301293 GGAAGGGAAGGACCTGCAG 59.699 63.158 6.78 6.78 40.87 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 1932 1.003839 TGTCGAACAGGATGGGCAC 60.004 57.895 0.00 0.00 43.62 5.01 R
2254 2406 0.605319 TCAACCGATGCCTCCAACAC 60.605 55.000 0.00 0.00 0.00 3.32 R
2343 2495 1.527034 TGCTGTTGCACCTGAATCTC 58.473 50.000 0.00 0.00 45.31 2.75 R
3540 3692 0.312102 GCTTGAGTTGAACCACAGGC 59.688 55.000 10.18 10.18 0.00 4.85 R
3607 3759 0.527565 AATGCCATGAACGCTTGGAC 59.472 50.000 0.00 0.00 40.77 4.02 R
3645 3797 0.536006 ACACCTTGAGCAACTCCAGC 60.536 55.000 0.00 0.00 0.00 4.85 R
4400 4591 0.037447 GCAAGGGAAGACTCAAGGCT 59.963 55.000 0.00 0.00 0.00 4.58 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
22 23 4.814294 CGGGAGCAGGCGTACCAC 62.814 72.222 0.00 0.00 39.06 4.16
23 24 4.468689 GGGAGCAGGCGTACCACC 62.469 72.222 0.00 0.00 39.06 4.61
24 25 3.702048 GGAGCAGGCGTACCACCA 61.702 66.667 2.63 0.00 39.06 4.17
25 26 2.434359 GAGCAGGCGTACCACCAC 60.434 66.667 2.63 0.00 39.06 4.16
26 27 2.923035 AGCAGGCGTACCACCACT 60.923 61.111 2.63 0.00 39.06 4.00
27 28 2.742372 GCAGGCGTACCACCACTG 60.742 66.667 2.63 0.00 39.06 3.66
28 29 3.056458 CAGGCGTACCACCACTGA 58.944 61.111 2.63 0.00 39.06 3.41
29 30 1.369692 CAGGCGTACCACCACTGAA 59.630 57.895 2.63 0.00 39.06 3.02
30 31 0.250124 CAGGCGTACCACCACTGAAA 60.250 55.000 2.63 0.00 39.06 2.69
31 32 0.250166 AGGCGTACCACCACTGAAAC 60.250 55.000 2.63 0.00 39.06 2.78
32 33 0.533308 GGCGTACCACCACTGAAACA 60.533 55.000 0.00 0.00 35.26 2.83
33 34 1.519408 GCGTACCACCACTGAAACAT 58.481 50.000 0.00 0.00 0.00 2.71
34 35 1.196808 GCGTACCACCACTGAAACATG 59.803 52.381 0.00 0.00 0.00 3.21
35 36 2.761559 CGTACCACCACTGAAACATGA 58.238 47.619 0.00 0.00 0.00 3.07
36 37 3.135225 CGTACCACCACTGAAACATGAA 58.865 45.455 0.00 0.00 0.00 2.57
37 38 3.751175 CGTACCACCACTGAAACATGAAT 59.249 43.478 0.00 0.00 0.00 2.57
38 39 4.215399 CGTACCACCACTGAAACATGAATT 59.785 41.667 0.00 0.00 0.00 2.17
39 40 4.853924 ACCACCACTGAAACATGAATTC 57.146 40.909 0.00 4.35 0.00 2.17
40 41 3.253188 ACCACCACTGAAACATGAATTCG 59.747 43.478 0.00 3.53 0.00 3.34
41 42 3.236816 CACCACTGAAACATGAATTCGC 58.763 45.455 0.00 0.00 0.00 4.70
42 43 2.228822 ACCACTGAAACATGAATTCGCC 59.771 45.455 0.00 0.00 0.00 5.54
43 44 2.415893 CCACTGAAACATGAATTCGCCC 60.416 50.000 0.00 0.00 0.00 6.13
44 45 2.489329 CACTGAAACATGAATTCGCCCT 59.511 45.455 0.00 0.00 0.00 5.19
45 46 2.489329 ACTGAAACATGAATTCGCCCTG 59.511 45.455 0.00 0.00 0.00 4.45
46 47 1.818060 TGAAACATGAATTCGCCCTGG 59.182 47.619 0.00 0.00 0.00 4.45
47 48 0.532115 AAACATGAATTCGCCCTGGC 59.468 50.000 0.00 0.00 37.85 4.85
48 49 0.323725 AACATGAATTCGCCCTGGCT 60.324 50.000 6.60 0.00 39.32 4.75
49 50 1.033746 ACATGAATTCGCCCTGGCTG 61.034 55.000 6.60 0.24 39.32 4.85
50 51 1.454479 ATGAATTCGCCCTGGCTGG 60.454 57.895 6.60 2.96 39.32 4.85
58 59 3.164269 CCCTGGCTGGCTCGGTAT 61.164 66.667 4.64 0.00 0.00 2.73
59 60 2.109799 CCTGGCTGGCTCGGTATG 59.890 66.667 2.00 0.00 0.00 2.39
60 61 2.590007 CTGGCTGGCTCGGTATGC 60.590 66.667 2.00 0.00 0.00 3.14
61 62 3.390183 CTGGCTGGCTCGGTATGCA 62.390 63.158 2.00 0.00 0.00 3.96
62 63 2.590007 GGCTGGCTCGGTATGCAG 60.590 66.667 0.00 0.00 0.00 4.41
63 64 2.501128 GCTGGCTCGGTATGCAGA 59.499 61.111 0.00 0.00 0.00 4.26
64 65 1.593750 GCTGGCTCGGTATGCAGAG 60.594 63.158 6.59 6.59 39.44 3.35
65 66 1.068753 CTGGCTCGGTATGCAGAGG 59.931 63.158 12.40 0.00 37.40 3.69
67 68 2.280457 GCTCGGTATGCAGAGGCC 60.280 66.667 12.40 0.00 40.13 5.19
68 69 3.094062 GCTCGGTATGCAGAGGCCA 62.094 63.158 5.01 0.00 40.13 5.36
69 70 1.068753 CTCGGTATGCAGAGGCCAG 59.931 63.158 5.01 0.00 40.13 4.85
70 71 2.109799 CGGTATGCAGAGGCCAGG 59.890 66.667 5.01 0.00 40.13 4.45
71 72 2.203266 GGTATGCAGAGGCCAGGC 60.203 66.667 5.01 1.26 40.13 4.85
86 87 4.243007 GCCAGGCCATTGATTAATGTAC 57.757 45.455 5.01 2.19 41.68 2.90
87 88 3.304659 GCCAGGCCATTGATTAATGTACG 60.305 47.826 5.01 0.00 41.68 3.67
88 89 3.882888 CCAGGCCATTGATTAATGTACGT 59.117 43.478 5.01 0.00 41.68 3.57
89 90 5.060506 CCAGGCCATTGATTAATGTACGTA 58.939 41.667 5.01 0.00 41.68 3.57
90 91 5.705441 CCAGGCCATTGATTAATGTACGTAT 59.295 40.000 5.01 0.00 41.68 3.06
91 92 6.348458 CCAGGCCATTGATTAATGTACGTATG 60.348 42.308 5.01 0.00 41.68 2.39
92 93 6.204688 CAGGCCATTGATTAATGTACGTATGT 59.795 38.462 5.01 0.00 41.68 2.29
93 94 6.426937 AGGCCATTGATTAATGTACGTATGTC 59.573 38.462 5.01 0.00 41.68 3.06
94 95 6.296605 GCCATTGATTAATGTACGTATGTCG 58.703 40.000 9.16 0.00 41.68 4.35
95 96 6.073980 GCCATTGATTAATGTACGTATGTCGT 60.074 38.462 9.16 3.55 45.76 4.34
96 97 7.115236 GCCATTGATTAATGTACGTATGTCGTA 59.885 37.037 9.16 1.82 44.85 3.43
105 106 2.129823 CGTATGTCGTATGGTCCACC 57.870 55.000 0.00 0.00 34.52 4.61
106 107 1.406180 CGTATGTCGTATGGTCCACCA 59.594 52.381 0.00 0.00 41.73 4.17
116 117 1.575419 TGGTCCACCATACTACCACC 58.425 55.000 0.00 0.00 42.01 4.61
117 118 1.203326 TGGTCCACCATACTACCACCA 60.203 52.381 0.00 0.00 42.01 4.17
118 119 1.485066 GGTCCACCATACTACCACCAG 59.515 57.143 0.00 0.00 35.64 4.00
119 120 2.185387 GTCCACCATACTACCACCAGT 58.815 52.381 0.00 0.00 0.00 4.00
120 121 2.093658 GTCCACCATACTACCACCAGTG 60.094 54.545 0.00 0.00 0.00 3.66
121 122 2.184533 CCACCATACTACCACCAGTGA 58.815 52.381 0.00 0.00 0.00 3.41
122 123 2.569853 CCACCATACTACCACCAGTGAA 59.430 50.000 0.00 0.00 0.00 3.18
123 124 3.199946 CCACCATACTACCACCAGTGAAT 59.800 47.826 0.00 0.00 0.00 2.57
124 125 4.191544 CACCATACTACCACCAGTGAATG 58.808 47.826 0.00 0.00 0.00 2.67
133 134 5.304686 ACCACCAGTGAATGAAAACTCTA 57.695 39.130 0.00 0.00 0.00 2.43
175 176 6.262207 ACTAGGTACTCCTCCATTAACAACT 58.738 40.000 0.00 0.00 43.94 3.16
185 186 2.290896 CCATTAACAACTCCCTCCTGCA 60.291 50.000 0.00 0.00 0.00 4.41
186 187 3.624777 CATTAACAACTCCCTCCTGCAT 58.375 45.455 0.00 0.00 0.00 3.96
207 213 7.760437 TGCATTTCATCTCGTTTCATTCAATA 58.240 30.769 0.00 0.00 0.00 1.90
238 244 0.767998 TGTGCACAGGGTACAATCCA 59.232 50.000 17.42 0.00 39.28 3.41
239 245 1.354031 TGTGCACAGGGTACAATCCAT 59.646 47.619 17.42 0.00 39.28 3.41
240 246 1.745087 GTGCACAGGGTACAATCCATG 59.255 52.381 13.17 0.00 43.73 3.66
244 250 0.468029 CAGGGTACAATCCATGCCCC 60.468 60.000 0.00 0.00 41.67 5.80
245 251 1.528309 GGGTACAATCCATGCCCCG 60.528 63.158 0.00 0.00 34.74 5.73
246 252 1.529796 GGTACAATCCATGCCCCGA 59.470 57.895 0.00 0.00 0.00 5.14
247 253 0.818040 GGTACAATCCATGCCCCGAC 60.818 60.000 0.00 0.00 0.00 4.79
248 254 0.180406 GTACAATCCATGCCCCGACT 59.820 55.000 0.00 0.00 0.00 4.18
249 255 0.468226 TACAATCCATGCCCCGACTC 59.532 55.000 0.00 0.00 0.00 3.36
250 256 1.526917 CAATCCATGCCCCGACTCC 60.527 63.158 0.00 0.00 0.00 3.85
254 260 3.411517 CATGCCCCGACTCCCCTT 61.412 66.667 0.00 0.00 0.00 3.95
255 261 3.411517 ATGCCCCGACTCCCCTTG 61.412 66.667 0.00 0.00 0.00 3.61
259 265 4.148825 CCCGACTCCCCTTGCGAG 62.149 72.222 0.00 0.00 0.00 5.03
260 266 4.821589 CCGACTCCCCTTGCGAGC 62.822 72.222 0.00 0.00 0.00 5.03
261 267 4.069232 CGACTCCCCTTGCGAGCA 62.069 66.667 0.00 0.00 0.00 4.26
262 268 2.586792 GACTCCCCTTGCGAGCAT 59.413 61.111 0.00 0.00 0.00 3.79
263 269 1.823295 GACTCCCCTTGCGAGCATA 59.177 57.895 0.00 0.00 0.00 3.14
264 270 0.530870 GACTCCCCTTGCGAGCATAC 60.531 60.000 0.00 0.00 0.00 2.39
265 271 1.227674 CTCCCCTTGCGAGCATACC 60.228 63.158 0.00 0.00 0.00 2.73
266 272 1.971505 CTCCCCTTGCGAGCATACCA 61.972 60.000 0.00 0.00 0.00 3.25
267 273 1.819632 CCCCTTGCGAGCATACCAC 60.820 63.158 0.00 0.00 0.00 4.16
268 274 1.819632 CCCTTGCGAGCATACCACC 60.820 63.158 0.00 0.00 0.00 4.61
269 275 1.078497 CCTTGCGAGCATACCACCA 60.078 57.895 0.00 0.00 0.00 4.17
270 276 0.464373 CCTTGCGAGCATACCACCAT 60.464 55.000 0.00 0.00 0.00 3.55
271 277 0.940126 CTTGCGAGCATACCACCATC 59.060 55.000 0.00 0.00 0.00 3.51
272 278 0.251634 TTGCGAGCATACCACCATCA 59.748 50.000 0.00 0.00 0.00 3.07
273 279 0.469494 TGCGAGCATACCACCATCAT 59.531 50.000 0.00 0.00 0.00 2.45
274 280 1.134128 TGCGAGCATACCACCATCATT 60.134 47.619 0.00 0.00 0.00 2.57
275 281 1.265095 GCGAGCATACCACCATCATTG 59.735 52.381 0.00 0.00 0.00 2.82
319 325 1.334556 GCATCATCATTGGCGTTGCTA 59.665 47.619 0.00 0.00 0.00 3.49
321 327 2.106477 TCATCATTGGCGTTGCTACA 57.894 45.000 0.00 0.00 0.00 2.74
322 328 2.431454 TCATCATTGGCGTTGCTACAA 58.569 42.857 0.00 0.00 0.00 2.41
323 329 2.161410 TCATCATTGGCGTTGCTACAAC 59.839 45.455 0.00 0.32 0.00 3.32
324 330 0.878416 TCATTGGCGTTGCTACAACC 59.122 50.000 4.96 0.00 0.00 3.77
325 331 0.881118 CATTGGCGTTGCTACAACCT 59.119 50.000 4.96 0.00 0.00 3.50
404 414 3.561960 CCTTTTGATGTCATCTCCCCACA 60.562 47.826 13.90 0.00 0.00 4.17
439 449 1.325476 CCCTGCTTTTGCCATCTCCC 61.325 60.000 0.00 0.00 46.87 4.30
485 495 1.693627 CAGATAGCGGTGGGAGTAGT 58.306 55.000 0.00 0.00 0.00 2.73
486 496 2.860009 CAGATAGCGGTGGGAGTAGTA 58.140 52.381 0.00 0.00 0.00 1.82
537 551 9.503399 CTCCCAAAGTTTCTTTACTTGTACTAT 57.497 33.333 0.00 0.00 38.33 2.12
577 607 2.412591 CTGGGACAAGATCATAGGGGT 58.587 52.381 0.00 0.00 38.70 4.95
755 797 3.077359 CGTCAGATTCTTGAAGGCCTTT 58.923 45.455 21.54 1.13 0.00 3.11
758 800 2.559668 CAGATTCTTGAAGGCCTTTGCA 59.440 45.455 21.54 11.45 40.13 4.08
778 820 4.096833 TGCAGGTAATTAGCTTGCTCAATG 59.903 41.667 25.38 12.95 32.80 2.82
794 836 4.737054 CTCAATGTGTGCCTATTTGGTTC 58.263 43.478 0.00 0.00 38.35 3.62
796 838 1.529226 TGTGTGCCTATTTGGTTCGG 58.471 50.000 0.00 0.00 38.35 4.30
798 840 1.737793 GTGTGCCTATTTGGTTCGGAG 59.262 52.381 0.00 0.00 38.35 4.63
807 849 0.181587 TTGGTTCGGAGGTTCTTGCA 59.818 50.000 0.00 0.00 0.00 4.08
812 854 1.878953 TCGGAGGTTCTTGCAAAGTC 58.121 50.000 0.00 0.00 46.34 3.01
828 870 5.580297 TGCAAAGTCCATGTTTTGTTTCTTC 59.420 36.000 12.99 1.36 36.81 2.87
829 871 5.006649 GCAAAGTCCATGTTTTGTTTCTTCC 59.993 40.000 12.99 0.00 36.81 3.46
830 872 6.340522 CAAAGTCCATGTTTTGTTTCTTCCT 58.659 36.000 0.00 0.00 31.36 3.36
831 873 6.544928 AAGTCCATGTTTTGTTTCTTCCTT 57.455 33.333 0.00 0.00 0.00 3.36
832 874 6.544928 AGTCCATGTTTTGTTTCTTCCTTT 57.455 33.333 0.00 0.00 0.00 3.11
835 877 7.549134 AGTCCATGTTTTGTTTCTTCCTTTTTC 59.451 33.333 0.00 0.00 0.00 2.29
859 901 0.524862 CACTGCATGTTCTTGCCCTC 59.475 55.000 7.92 0.00 42.06 4.30
872 914 3.202818 TCTTGCCCTCAATCCATACATGT 59.797 43.478 2.69 2.69 0.00 3.21
880 922 5.463499 TCAATCCATACATGTTCGTTTCG 57.537 39.130 2.30 0.00 0.00 3.46
881 923 4.932799 TCAATCCATACATGTTCGTTTCGT 59.067 37.500 2.30 0.00 0.00 3.85
883 925 4.914312 TCCATACATGTTCGTTTCGTTC 57.086 40.909 2.30 0.00 0.00 3.95
884 926 3.680937 TCCATACATGTTCGTTTCGTTCC 59.319 43.478 2.30 0.00 0.00 3.62
888 930 3.399330 ACATGTTCGTTTCGTTCCTGAT 58.601 40.909 0.00 0.00 0.00 2.90
889 931 3.186409 ACATGTTCGTTTCGTTCCTGATG 59.814 43.478 0.00 0.00 0.00 3.07
890 932 2.139917 TGTTCGTTTCGTTCCTGATGG 58.860 47.619 0.00 0.00 0.00 3.51
891 933 2.224090 TGTTCGTTTCGTTCCTGATGGA 60.224 45.455 0.00 0.00 41.36 3.41
903 945 4.226427 TCCTGATGGAATTTGACTCCTG 57.774 45.455 0.00 0.00 39.87 3.86
908 969 2.507484 TGGAATTTGACTCCTGCTGTG 58.493 47.619 0.00 0.00 33.77 3.66
945 1016 1.699634 CTGACAGGAAAAGGAGGACCA 59.300 52.381 0.00 0.00 38.94 4.02
946 1017 1.699634 TGACAGGAAAAGGAGGACCAG 59.300 52.381 0.00 0.00 38.94 4.00
1024 1095 2.775490 AGGGGGAGAGCAAAAAGTTT 57.225 45.000 0.00 0.00 0.00 2.66
1245 1364 2.280186 CCTCCTAATCCGCCGCAC 60.280 66.667 0.00 0.00 0.00 5.34
1783 1932 0.979665 TGCTCAGAAGAGGAACCTGG 59.020 55.000 0.00 0.00 39.45 4.45
1857 2006 1.135960 AGCCTGAAGATAAGGAGGGC 58.864 55.000 0.00 0.00 36.91 5.19
2064 2213 1.271597 GGAAGGGAGAAAGAGCTTGCA 60.272 52.381 0.00 0.00 0.00 4.08
2081 2230 1.137675 TGCAGAGATCGAGGGAATGTG 59.862 52.381 0.00 0.00 0.00 3.21
2254 2406 3.289834 ACAAGTGCAAGCGGCCTG 61.290 61.111 0.00 0.00 43.89 4.85
2343 2495 3.119173 AGAGATCAAAGCTCAGGAAGTCG 60.119 47.826 0.00 0.00 34.85 4.18
2712 2864 1.301293 GGAAGGGAAGGACCTGCAG 59.699 63.158 6.78 6.78 40.87 4.41
2749 2901 1.376424 ACTGGAGCAAGCCATGTCG 60.376 57.895 0.00 0.00 37.30 4.35
2961 3113 5.614308 TCACTGTTGTCTGAGTTGATGATT 58.386 37.500 0.00 0.00 0.00 2.57
2977 3129 7.718753 AGTTGATGATTGATCCTGGTATTCTTC 59.281 37.037 0.00 0.00 0.00 2.87
3022 3174 5.643348 TCGCTAAATGAGAACATGATTGTGT 59.357 36.000 0.00 0.00 35.83 3.72
3090 3242 2.262423 AGGTGTTGGTCTTCTGCTTC 57.738 50.000 0.00 0.00 0.00 3.86
3486 3638 7.805083 AAGGACTGGCAATATGTCTATCTAT 57.195 36.000 4.84 0.00 0.00 1.98
3492 3644 9.044646 ACTGGCAATATGTCTATCTATTCAGAT 57.955 33.333 0.00 0.00 44.04 2.90
3757 3909 0.036952 CTGGAAGAAGAAGCTGCGGA 60.037 55.000 0.00 0.00 34.07 5.54
3967 4119 2.171489 GACGCTCGCAAAGGTGGTTC 62.171 60.000 0.00 0.00 0.00 3.62
3992 4144 6.865726 CGATACAGGAGTAAAATCTGAGATGG 59.134 42.308 0.00 0.00 33.13 3.51
4046 4198 8.153550 AGGCAGTATCTAGATTTTGTATCTTGG 58.846 37.037 11.25 0.00 0.00 3.61
4185 4344 1.526887 CAACTTGCTGTGTACAGTCCG 59.473 52.381 13.08 4.90 45.45 4.79
4232 4391 9.720769 AATTTTCTTTGATGAAATTCTGAGCAT 57.279 25.926 0.00 0.00 36.07 3.79
4233 4392 9.720769 ATTTTCTTTGATGAAATTCTGAGCATT 57.279 25.926 0.00 0.00 36.07 3.56
4235 4394 9.550406 TTTCTTTGATGAAATTCTGAGCATTTT 57.450 25.926 0.00 0.00 31.81 1.82
4277 4436 3.181440 ACACATGTGACCTGGAGATGTTT 60.181 43.478 31.94 1.18 0.00 2.83
4284 4443 3.072330 TGACCTGGAGATGTTTTGTGCTA 59.928 43.478 0.00 0.00 0.00 3.49
4285 4444 3.412386 ACCTGGAGATGTTTTGTGCTAC 58.588 45.455 0.00 0.00 0.00 3.58
4288 4447 3.674997 TGGAGATGTTTTGTGCTACTCC 58.325 45.455 0.00 0.00 41.61 3.85
4289 4448 3.072330 TGGAGATGTTTTGTGCTACTCCA 59.928 43.478 0.00 0.00 46.29 3.86
4290 4449 4.263462 TGGAGATGTTTTGTGCTACTCCAT 60.263 41.667 0.00 0.00 44.53 3.41
4292 4451 5.392380 GGAGATGTTTTGTGCTACTCCATTG 60.392 44.000 0.00 0.00 41.12 2.82
4400 4591 2.612604 GCAACTGATTGATGCAATGCA 58.387 42.857 11.44 11.44 42.94 3.96
4401 4592 2.603110 GCAACTGATTGATGCAATGCAG 59.397 45.455 14.98 0.00 42.94 4.41
4402 4593 2.579207 ACTGATTGATGCAATGCAGC 57.421 45.000 17.34 17.34 45.81 5.25
4403 4594 1.136305 ACTGATTGATGCAATGCAGCC 59.864 47.619 21.20 11.85 44.94 4.85
4404 4595 1.409064 CTGATTGATGCAATGCAGCCT 59.591 47.619 21.20 8.21 44.94 4.58
4405 4596 1.828595 TGATTGATGCAATGCAGCCTT 59.171 42.857 21.20 8.01 44.94 4.35
4406 4597 2.201732 GATTGATGCAATGCAGCCTTG 58.798 47.619 21.20 6.07 44.94 3.61
4444 4635 7.414873 GCAATTCTGATGCTGAATTTAGTCTGA 60.415 37.037 8.83 0.00 39.02 3.27
4496 4690 7.826252 ACAGAGTAGCAGACATGATAAACAATT 59.174 33.333 0.00 0.00 0.00 2.32
4497 4691 8.121086 CAGAGTAGCAGACATGATAAACAATTG 58.879 37.037 3.24 3.24 0.00 2.32
4535 4729 6.623767 GCTTCTTCCTTATCGCAAACAATCTT 60.624 38.462 0.00 0.00 0.00 2.40
4543 4737 1.401409 CGCAAACAATCTTGTCGGCAT 60.401 47.619 14.97 0.00 41.31 4.40
4695 4915 2.224843 TGGCAACAGACAGATCCAATGT 60.225 45.455 0.00 0.00 46.17 2.71
4696 4916 2.821969 GGCAACAGACAGATCCAATGTT 59.178 45.455 0.00 0.00 34.56 2.71
4721 4943 1.089112 CGCAGTGCATTCTCATCCAA 58.911 50.000 16.83 0.00 0.00 3.53
4723 4945 1.404391 GCAGTGCATTCTCATCCAAGG 59.596 52.381 11.09 0.00 0.00 3.61
4759 4981 2.263540 CCATGCTTGCCTGGTTGC 59.736 61.111 8.46 0.00 0.00 4.17
4848 5073 1.006571 GCTTCTTCGACACCGTCCA 60.007 57.895 0.00 0.00 37.05 4.02
4920 5145 3.744719 CCTCTTCCACGACGGCGA 61.745 66.667 22.49 0.00 41.64 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.814294 GTGGTACGCCTGCTCCCG 62.814 72.222 0.00 0.00 35.27 5.14
14 15 1.196808 CATGTTTCAGTGGTGGTACGC 59.803 52.381 0.00 0.00 38.67 4.42
15 16 2.761559 TCATGTTTCAGTGGTGGTACG 58.238 47.619 0.00 0.00 0.00 3.67
16 17 5.616866 CGAATTCATGTTTCAGTGGTGGTAC 60.617 44.000 6.22 0.00 0.00 3.34
17 18 4.454161 CGAATTCATGTTTCAGTGGTGGTA 59.546 41.667 6.22 0.00 0.00 3.25
18 19 3.253188 CGAATTCATGTTTCAGTGGTGGT 59.747 43.478 6.22 0.00 0.00 4.16
19 20 3.825308 CGAATTCATGTTTCAGTGGTGG 58.175 45.455 6.22 0.00 0.00 4.61
20 21 3.236816 GCGAATTCATGTTTCAGTGGTG 58.763 45.455 6.22 0.00 0.00 4.17
21 22 2.228822 GGCGAATTCATGTTTCAGTGGT 59.771 45.455 6.22 0.00 0.00 4.16
22 23 2.415893 GGGCGAATTCATGTTTCAGTGG 60.416 50.000 6.22 0.00 0.00 4.00
23 24 2.489329 AGGGCGAATTCATGTTTCAGTG 59.511 45.455 6.22 0.00 0.00 3.66
24 25 2.489329 CAGGGCGAATTCATGTTTCAGT 59.511 45.455 6.22 0.00 0.00 3.41
25 26 2.159338 CCAGGGCGAATTCATGTTTCAG 60.159 50.000 6.22 5.76 0.00 3.02
26 27 1.818060 CCAGGGCGAATTCATGTTTCA 59.182 47.619 6.22 0.00 0.00 2.69
27 28 1.469767 GCCAGGGCGAATTCATGTTTC 60.470 52.381 6.22 0.00 0.00 2.78
28 29 0.532115 GCCAGGGCGAATTCATGTTT 59.468 50.000 6.22 0.00 0.00 2.83
29 30 2.192605 GCCAGGGCGAATTCATGTT 58.807 52.632 6.22 0.00 0.00 2.71
30 31 3.924507 GCCAGGGCGAATTCATGT 58.075 55.556 6.22 0.00 0.00 3.21
34 35 3.521796 GCCAGCCAGGGCGAATTC 61.522 66.667 4.37 0.00 45.40 2.17
41 42 3.164269 ATACCGAGCCAGCCAGGG 61.164 66.667 6.05 0.00 38.09 4.45
42 43 2.109799 CATACCGAGCCAGCCAGG 59.890 66.667 0.08 0.08 41.84 4.45
43 44 2.590007 GCATACCGAGCCAGCCAG 60.590 66.667 0.00 0.00 0.00 4.85
44 45 3.390183 CTGCATACCGAGCCAGCCA 62.390 63.158 0.00 0.00 0.00 4.75
45 46 2.590007 CTGCATACCGAGCCAGCC 60.590 66.667 0.00 0.00 0.00 4.85
46 47 1.593750 CTCTGCATACCGAGCCAGC 60.594 63.158 0.00 0.00 0.00 4.85
47 48 1.068753 CCTCTGCATACCGAGCCAG 59.931 63.158 0.00 0.00 0.00 4.85
48 49 3.094062 GCCTCTGCATACCGAGCCA 62.094 63.158 0.00 0.00 37.47 4.75
49 50 2.280457 GCCTCTGCATACCGAGCC 60.280 66.667 0.00 0.00 37.47 4.70
50 51 2.280457 GGCCTCTGCATACCGAGC 60.280 66.667 0.00 0.00 40.13 5.03
51 52 1.068753 CTGGCCTCTGCATACCGAG 59.931 63.158 3.32 0.00 40.13 4.63
52 53 2.434843 CCTGGCCTCTGCATACCGA 61.435 63.158 3.32 0.00 40.13 4.69
53 54 2.109799 CCTGGCCTCTGCATACCG 59.890 66.667 3.32 0.00 40.13 4.02
54 55 2.203266 GCCTGGCCTCTGCATACC 60.203 66.667 7.66 0.00 40.13 2.73
55 56 2.203266 GGCCTGGCCTCTGCATAC 60.203 66.667 30.42 0.00 46.69 2.39
65 66 3.304659 CGTACATTAATCAATGGCCTGGC 60.305 47.826 11.05 11.05 44.97 4.85
66 67 3.882888 ACGTACATTAATCAATGGCCTGG 59.117 43.478 3.32 0.00 44.97 4.45
67 68 6.204688 ACATACGTACATTAATCAATGGCCTG 59.795 38.462 3.32 0.00 44.97 4.85
68 69 6.296026 ACATACGTACATTAATCAATGGCCT 58.704 36.000 3.32 0.00 44.97 5.19
69 70 6.554334 ACATACGTACATTAATCAATGGCC 57.446 37.500 0.00 0.00 44.97 5.36
70 71 6.296605 CGACATACGTACATTAATCAATGGC 58.703 40.000 0.00 0.00 40.36 4.40
85 86 1.406539 GGTGGACCATACGACATACGT 59.593 52.381 0.00 0.00 46.12 3.57
86 87 1.406180 TGGTGGACCATACGACATACG 59.594 52.381 0.00 0.00 42.01 3.06
98 99 1.485066 CTGGTGGTAGTATGGTGGACC 59.515 57.143 0.00 0.00 0.00 4.46
99 100 2.093658 CACTGGTGGTAGTATGGTGGAC 60.094 54.545 0.00 0.00 0.00 4.02
100 101 2.184533 CACTGGTGGTAGTATGGTGGA 58.815 52.381 0.00 0.00 0.00 4.02
101 102 2.184533 TCACTGGTGGTAGTATGGTGG 58.815 52.381 0.70 0.00 0.00 4.61
102 103 3.973206 TTCACTGGTGGTAGTATGGTG 57.027 47.619 0.70 0.00 0.00 4.17
103 104 4.101114 TCATTCACTGGTGGTAGTATGGT 58.899 43.478 0.70 0.00 0.00 3.55
104 105 4.753516 TCATTCACTGGTGGTAGTATGG 57.246 45.455 0.70 0.00 0.00 2.74
105 106 6.655003 AGTTTTCATTCACTGGTGGTAGTATG 59.345 38.462 0.70 0.00 0.00 2.39
106 107 6.779860 AGTTTTCATTCACTGGTGGTAGTAT 58.220 36.000 0.70 0.00 0.00 2.12
107 108 6.042781 AGAGTTTTCATTCACTGGTGGTAGTA 59.957 38.462 0.70 0.00 0.00 1.82
108 109 5.048846 AGTTTTCATTCACTGGTGGTAGT 57.951 39.130 0.70 0.00 0.00 2.73
109 110 5.308825 AGAGTTTTCATTCACTGGTGGTAG 58.691 41.667 0.70 0.00 0.00 3.18
110 111 5.304686 AGAGTTTTCATTCACTGGTGGTA 57.695 39.130 0.70 0.00 0.00 3.25
111 112 4.170468 AGAGTTTTCATTCACTGGTGGT 57.830 40.909 0.70 0.00 0.00 4.16
112 113 6.430925 TCATTAGAGTTTTCATTCACTGGTGG 59.569 38.462 0.70 0.00 0.00 4.61
113 114 7.388776 TCTCATTAGAGTTTTCATTCACTGGTG 59.611 37.037 0.00 0.00 42.66 4.17
114 115 7.389053 GTCTCATTAGAGTTTTCATTCACTGGT 59.611 37.037 0.00 0.00 42.66 4.00
115 116 7.412346 CGTCTCATTAGAGTTTTCATTCACTGG 60.412 40.741 0.00 0.00 42.66 4.00
116 117 7.451429 CGTCTCATTAGAGTTTTCATTCACTG 58.549 38.462 0.00 0.00 42.66 3.66
117 118 6.091441 GCGTCTCATTAGAGTTTTCATTCACT 59.909 38.462 0.00 0.00 42.66 3.41
118 119 6.128553 TGCGTCTCATTAGAGTTTTCATTCAC 60.129 38.462 0.00 0.00 42.66 3.18
119 120 5.931724 TGCGTCTCATTAGAGTTTTCATTCA 59.068 36.000 0.00 0.00 42.66 2.57
120 121 6.408858 TGCGTCTCATTAGAGTTTTCATTC 57.591 37.500 0.00 0.00 42.66 2.67
121 122 6.037610 GGATGCGTCTCATTAGAGTTTTCATT 59.962 38.462 5.77 0.00 42.66 2.57
122 123 5.525378 GGATGCGTCTCATTAGAGTTTTCAT 59.475 40.000 5.77 0.00 42.66 2.57
123 124 4.870426 GGATGCGTCTCATTAGAGTTTTCA 59.130 41.667 5.77 0.00 42.66 2.69
124 125 4.870426 TGGATGCGTCTCATTAGAGTTTTC 59.130 41.667 5.77 0.00 42.66 2.29
133 134 3.895232 AGTACTTGGATGCGTCTCATT 57.105 42.857 5.77 0.00 35.05 2.57
175 176 1.139654 CGAGATGAAATGCAGGAGGGA 59.860 52.381 0.00 0.00 0.00 4.20
238 244 3.411517 CAAGGGGAGTCGGGGCAT 61.412 66.667 0.00 0.00 0.00 4.40
244 250 2.016393 TATGCTCGCAAGGGGAGTCG 62.016 60.000 11.25 0.00 46.54 4.18
245 251 0.530870 GTATGCTCGCAAGGGGAGTC 60.531 60.000 11.25 5.35 46.54 3.36
246 252 1.522569 GTATGCTCGCAAGGGGAGT 59.477 57.895 11.25 0.00 46.54 3.85
247 253 1.227674 GGTATGCTCGCAAGGGGAG 60.228 63.158 5.99 5.99 46.54 4.30
249 255 1.819632 GTGGTATGCTCGCAAGGGG 60.820 63.158 0.00 0.00 39.30 4.79
250 256 1.819632 GGTGGTATGCTCGCAAGGG 60.820 63.158 0.00 0.00 44.72 3.95
252 258 0.940126 GATGGTGGTATGCTCGCAAG 59.060 55.000 0.00 0.00 0.00 4.01
253 259 0.251634 TGATGGTGGTATGCTCGCAA 59.748 50.000 0.00 0.00 0.00 4.85
254 260 0.469494 ATGATGGTGGTATGCTCGCA 59.531 50.000 0.00 0.00 0.00 5.10
255 261 1.265095 CAATGATGGTGGTATGCTCGC 59.735 52.381 0.00 0.00 0.00 5.03
256 262 1.875514 CCAATGATGGTGGTATGCTCG 59.124 52.381 0.00 0.00 42.18 5.03
280 286 2.269172 GCCCGTTTCGAAAACCAAAAA 58.731 42.857 13.10 0.00 0.00 1.94
281 287 1.203994 TGCCCGTTTCGAAAACCAAAA 59.796 42.857 13.10 0.00 0.00 2.44
282 288 0.815734 TGCCCGTTTCGAAAACCAAA 59.184 45.000 13.10 0.00 0.00 3.28
283 289 1.001158 GATGCCCGTTTCGAAAACCAA 60.001 47.619 13.10 0.00 0.00 3.67
284 290 0.594110 GATGCCCGTTTCGAAAACCA 59.406 50.000 13.10 7.71 0.00 3.67
285 291 0.594110 TGATGCCCGTTTCGAAAACC 59.406 50.000 13.10 0.00 0.00 3.27
286 292 2.095466 TGATGATGCCCGTTTCGAAAAC 60.095 45.455 13.10 6.30 0.00 2.43
287 293 2.155279 TGATGATGCCCGTTTCGAAAA 58.845 42.857 13.10 0.00 0.00 2.29
288 294 1.814793 TGATGATGCCCGTTTCGAAA 58.185 45.000 6.47 6.47 0.00 3.46
289 295 2.036958 ATGATGATGCCCGTTTCGAA 57.963 45.000 0.00 0.00 0.00 3.71
290 296 1.670295 CAATGATGATGCCCGTTTCGA 59.330 47.619 0.00 0.00 0.00 3.71
291 297 1.268692 CCAATGATGATGCCCGTTTCG 60.269 52.381 0.00 0.00 0.00 3.46
292 298 1.536709 GCCAATGATGATGCCCGTTTC 60.537 52.381 0.00 0.00 0.00 2.78
293 299 0.461135 GCCAATGATGATGCCCGTTT 59.539 50.000 0.00 0.00 0.00 3.60
294 300 1.727511 CGCCAATGATGATGCCCGTT 61.728 55.000 0.00 0.00 0.00 4.44
295 301 2.188829 CGCCAATGATGATGCCCGT 61.189 57.895 0.00 0.00 0.00 5.28
296 302 1.727511 AACGCCAATGATGATGCCCG 61.728 55.000 0.00 0.00 0.00 6.13
297 303 0.249155 CAACGCCAATGATGATGCCC 60.249 55.000 0.00 0.00 0.00 5.36
298 304 0.872881 GCAACGCCAATGATGATGCC 60.873 55.000 0.00 0.00 0.00 4.40
319 325 1.101049 CAAGACCGGTTGCAGGTTGT 61.101 55.000 9.42 0.00 43.01 3.32
321 327 1.528309 CCAAGACCGGTTGCAGGTT 60.528 57.895 9.42 0.00 43.01 3.50
322 328 2.113139 CCAAGACCGGTTGCAGGT 59.887 61.111 9.42 0.00 46.16 4.00
323 329 1.966451 GACCAAGACCGGTTGCAGG 60.966 63.158 9.42 11.69 40.22 4.85
324 330 0.535102 AAGACCAAGACCGGTTGCAG 60.535 55.000 9.42 0.63 40.22 4.41
325 331 0.534203 GAAGACCAAGACCGGTTGCA 60.534 55.000 9.42 0.00 40.22 4.08
404 414 2.876079 GCAGGGGAGAAAAACAGATCGT 60.876 50.000 0.00 0.00 0.00 3.73
439 449 0.978146 AATGGAGGAGACCGAGTGGG 60.978 60.000 0.00 0.00 40.75 4.61
485 495 2.215196 GGCCGTTTGAACTGTCAAGTA 58.785 47.619 0.00 0.00 44.49 2.24
486 496 1.021968 GGCCGTTTGAACTGTCAAGT 58.978 50.000 0.00 0.00 44.49 3.16
537 551 0.979665 CTCCCAAGCAGTCAAGGAGA 59.020 55.000 0.00 0.00 45.83 3.71
646 687 2.060980 AGGAGAGCTTGTAGGGCCG 61.061 63.158 0.00 0.00 0.00 6.13
709 750 5.002464 GCCATTAGCATTGTGATTCTGTT 57.998 39.130 0.00 0.00 42.97 3.16
738 779 2.824341 CTGCAAAGGCCTTCAAGAATCT 59.176 45.455 20.79 0.00 40.13 2.40
755 797 3.348647 TGAGCAAGCTAATTACCTGCA 57.651 42.857 7.03 0.00 0.00 4.41
758 800 5.124457 CACACATTGAGCAAGCTAATTACCT 59.876 40.000 0.00 0.00 0.00 3.08
778 820 1.737793 CTCCGAACCAAATAGGCACAC 59.262 52.381 0.00 0.00 43.14 3.82
794 836 0.875059 GGACTTTGCAAGAACCTCCG 59.125 55.000 0.00 0.00 0.00 4.63
796 838 2.887152 ACATGGACTTTGCAAGAACCTC 59.113 45.455 15.25 2.34 32.81 3.85
798 840 3.733443 AACATGGACTTTGCAAGAACC 57.267 42.857 0.00 5.14 0.00 3.62
807 849 6.544928 AGGAAGAAACAAAACATGGACTTT 57.455 33.333 0.00 0.00 0.00 2.66
812 854 7.848223 AGAAAAAGGAAGAAACAAAACATGG 57.152 32.000 0.00 0.00 0.00 3.66
828 870 6.507023 AGAACATGCAGTGTAAAGAAAAAGG 58.493 36.000 0.00 0.00 41.14 3.11
829 871 7.515684 GCAAGAACATGCAGTGTAAAGAAAAAG 60.516 37.037 0.00 0.00 45.70 2.27
830 872 6.255453 GCAAGAACATGCAGTGTAAAGAAAAA 59.745 34.615 0.00 0.00 45.70 1.94
831 873 5.748152 GCAAGAACATGCAGTGTAAAGAAAA 59.252 36.000 0.00 0.00 45.70 2.29
832 874 5.280945 GCAAGAACATGCAGTGTAAAGAAA 58.719 37.500 0.00 0.00 45.70 2.52
859 901 5.216566 ACGAAACGAACATGTATGGATTG 57.783 39.130 0.00 0.00 0.00 2.67
872 914 2.823924 TCCATCAGGAACGAAACGAA 57.176 45.000 0.00 0.00 42.23 3.85
883 925 2.686915 GCAGGAGTCAAATTCCATCAGG 59.313 50.000 0.00 0.00 37.18 3.86
884 926 3.377485 CAGCAGGAGTCAAATTCCATCAG 59.623 47.826 0.00 0.00 37.18 2.90
888 930 2.158623 ACACAGCAGGAGTCAAATTCCA 60.159 45.455 0.00 0.00 37.18 3.53
889 931 2.508526 ACACAGCAGGAGTCAAATTCC 58.491 47.619 0.00 0.00 34.83 3.01
890 932 4.574599 AAACACAGCAGGAGTCAAATTC 57.425 40.909 0.00 0.00 0.00 2.17
891 933 4.646492 AGAAAACACAGCAGGAGTCAAATT 59.354 37.500 0.00 0.00 0.00 1.82
895 937 2.092968 ACAGAAAACACAGCAGGAGTCA 60.093 45.455 0.00 0.00 0.00 3.41
898 940 2.032550 CACACAGAAAACACAGCAGGAG 59.967 50.000 0.00 0.00 0.00 3.69
899 941 2.016318 CACACAGAAAACACAGCAGGA 58.984 47.619 0.00 0.00 0.00 3.86
900 942 1.066002 CCACACAGAAAACACAGCAGG 59.934 52.381 0.00 0.00 0.00 4.85
901 943 2.016318 TCCACACAGAAAACACAGCAG 58.984 47.619 0.00 0.00 0.00 4.24
903 945 3.715628 AATCCACACAGAAAACACAGC 57.284 42.857 0.00 0.00 0.00 4.40
908 969 5.499139 TGTCAGAAATCCACACAGAAAAC 57.501 39.130 0.00 0.00 0.00 2.43
945 1016 5.879223 CAGTGCAAGAACTTCATAGGAATCT 59.121 40.000 0.00 0.00 31.34 2.40
946 1017 5.877012 TCAGTGCAAGAACTTCATAGGAATC 59.123 40.000 0.00 0.00 31.34 2.52
1245 1364 2.269241 GAGGCCCTGGTTTCTCGG 59.731 66.667 0.00 0.00 0.00 4.63
1307 1435 2.116772 TGTCCTCCGACCGGAACT 59.883 61.111 9.46 0.00 44.66 3.01
1443 1592 1.901085 CACGGGGAAGGAGAAGGAG 59.099 63.158 0.00 0.00 0.00 3.69
1783 1932 1.003839 TGTCGAACAGGATGGGCAC 60.004 57.895 0.00 0.00 43.62 5.01
1857 2006 1.937546 GCCCCTCAAACGCTTCCATG 61.938 60.000 0.00 0.00 0.00 3.66
2064 2213 1.786937 AGCACATTCCCTCGATCTCT 58.213 50.000 0.00 0.00 0.00 3.10
2138 2290 3.629855 CACACCACTGGACACACAATTAA 59.370 43.478 0.71 0.00 0.00 1.40
2148 2300 1.609061 CCATCTGACACACCACTGGAC 60.609 57.143 0.71 0.00 0.00 4.02
2254 2406 0.605319 TCAACCGATGCCTCCAACAC 60.605 55.000 0.00 0.00 0.00 3.32
2343 2495 1.527034 TGCTGTTGCACCTGAATCTC 58.473 50.000 0.00 0.00 45.31 2.75
2500 2652 9.942850 TGATAAATTCAGTATGTTCTGTCTCAA 57.057 29.630 0.00 0.00 37.40 3.02
2712 2864 6.650120 TCCAGTGTTTCTAGGTATGAAATCC 58.350 40.000 0.00 0.00 36.10 3.01
2961 3113 4.141620 GCCTCAAGAAGAATACCAGGATCA 60.142 45.833 0.00 0.00 0.00 2.92
2977 3129 2.507992 CCGCTCGACAGCCTCAAG 60.508 66.667 0.00 0.00 43.56 3.02
3022 3174 4.422073 AGTTGTCATCACCAGAACAGAA 57.578 40.909 0.00 0.00 0.00 3.02
3090 3242 0.392863 TCACCTGGTCCATCAATGCG 60.393 55.000 0.00 0.00 0.00 4.73
3486 3638 2.840038 ACTAGCCCACATGTGATCTGAA 59.160 45.455 27.46 8.20 0.00 3.02
3492 3644 0.620030 ATGCACTAGCCCACATGTGA 59.380 50.000 27.46 6.09 41.13 3.58
3540 3692 0.312102 GCTTGAGTTGAACCACAGGC 59.688 55.000 10.18 10.18 0.00 4.85
3607 3759 0.527565 AATGCCATGAACGCTTGGAC 59.472 50.000 0.00 0.00 40.77 4.02
3642 3794 3.020026 CTTGAGCAACTCCAGCGCG 62.020 63.158 0.00 0.00 37.01 6.86
3645 3797 0.536006 ACACCTTGAGCAACTCCAGC 60.536 55.000 0.00 0.00 0.00 4.85
3684 3836 4.415332 GCGACCGACTTCTCCGCA 62.415 66.667 0.00 0.00 44.55 5.69
3840 3992 4.555709 AACAACCCGCCTCGCACA 62.556 61.111 0.00 0.00 0.00 4.57
3967 4119 6.865726 CCATCTCAGATTTTACTCCTGTATCG 59.134 42.308 0.00 0.00 0.00 2.92
4046 4198 3.561310 TGAATCACAGACACAGCAAAGAC 59.439 43.478 0.00 0.00 0.00 3.01
4236 4395 9.803507 ACATGTGTCATTAGATAATTCATCCAT 57.196 29.630 0.00 0.00 33.75 3.41
4247 4406 4.471025 TCCAGGTCACATGTGTCATTAGAT 59.529 41.667 24.63 2.10 0.00 1.98
4334 4525 7.936301 AGATCCCTTGCTAAATATTCTTCACTC 59.064 37.037 0.00 0.00 0.00 3.51
4400 4591 0.037447 GCAAGGGAAGACTCAAGGCT 59.963 55.000 0.00 0.00 0.00 4.58
4401 4592 0.250901 TGCAAGGGAAGACTCAAGGC 60.251 55.000 0.00 0.00 0.00 4.35
4402 4593 2.276732 TTGCAAGGGAAGACTCAAGG 57.723 50.000 0.00 0.00 0.00 3.61
4403 4594 4.077822 AGAATTGCAAGGGAAGACTCAAG 58.922 43.478 4.94 0.00 0.00 3.02
4404 4595 3.822735 CAGAATTGCAAGGGAAGACTCAA 59.177 43.478 4.94 0.00 0.00 3.02
4405 4596 3.072915 TCAGAATTGCAAGGGAAGACTCA 59.927 43.478 4.94 0.00 0.00 3.41
4406 4597 3.679389 TCAGAATTGCAAGGGAAGACTC 58.321 45.455 4.94 0.00 0.00 3.36
4444 4635 3.319122 GGAGAACTTTGCTGGTGAAATGT 59.681 43.478 0.00 0.00 0.00 2.71
4543 4737 2.488204 TCCATCTCACAAAATCGGCA 57.512 45.000 0.00 0.00 0.00 5.69
4721 4943 2.564062 GCATGGCATGGCATTTATACCT 59.436 45.455 30.44 6.98 0.00 3.08
4804 5029 2.509336 ATCTTGAACGGCGCCTCG 60.509 61.111 26.68 15.19 0.00 4.63


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

AutoCloner maintained by Alex Coulton.