Multiple sequence alignment - TraesCS5D01G432500

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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 TraesCS5D01G432500 chr5D 100.000 3300 0 0 1 3300 488676423 488679722 0.000000e+00 6095.0
1 TraesCS5D01G432500 chr5B 91.932 2925 81 45 422 3285 601863972 601866802 0.000000e+00 3951.0
2 TraesCS5D01G432500 chr5B 94.595 37 2 0 49 85 601857460 601857496 1.280000e-04 58.4
3 TraesCS5D01G432500 chr5A 90.964 2335 85 47 687 2962 609618864 609621131 0.000000e+00 3027.0
4 TraesCS5D01G432500 chr5A 87.427 517 38 14 164 665 609618372 609618876 1.330000e-158 569.0
5 TraesCS5D01G432500 chr5A 82.647 340 35 17 2964 3300 609621161 609621479 2.510000e-71 279.0
6 TraesCS5D01G432500 chr2D 80.856 397 53 16 1200 1574 302253267 302252872 1.160000e-74 291.0
7 TraesCS5D01G432500 chr2A 79.901 403 52 17 1200 1574 379158733 379158332 5.430000e-68 268.0
8 TraesCS5D01G432500 chr2A 83.607 61 8 2 1195 1253 746932041 746931981 4.600000e-04 56.5
9 TraesCS5D01G432500 chr2B 86.000 250 30 3 1200 1445 357923704 357923456 2.530000e-66 263.0
10 TraesCS5D01G432500 chr6B 86.628 172 23 0 1315 1486 522646869 522647040 1.210000e-44 191.0
11 TraesCS5D01G432500 chr3D 100.000 28 0 0 1394 1421 22289609 22289636 6.000000e-03 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 TraesCS5D01G432500 chr5D 488676423 488679722 3299 False 6095.000000 6095 100.000000 1 3300 1 chr5D.!!$F1 3299
1 TraesCS5D01G432500 chr5B 601863972 601866802 2830 False 3951.000000 3951 91.932000 422 3285 1 chr5B.!!$F2 2863
2 TraesCS5D01G432500 chr5A 609618372 609621479 3107 False 1291.666667 3027 87.012667 164 3300 3 chr5A.!!$F1 3136

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
142 143 0.038343 GCATGAAAGGGCTTGCGAAA 60.038 50.0 0.00 0.0 30.8 3.46 F
275 282 0.038618 ACACAGACGATACAAGCGCA 60.039 50.0 11.47 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 1970 1.354040 GAGAACTGCGTCATCTGGTG 58.646 55.000 0.00 0.00 0.00 4.17 R
2364 2466 1.001181 ACCCAAGCATGATTTGTGCAC 59.999 47.619 10.75 10.75 44.87 4.57 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
26 27 4.680237 CGGCCGCACACTTCAGGA 62.680 66.667 14.67 0.00 0.00 3.86
27 28 2.743928 GGCCGCACACTTCAGGAG 60.744 66.667 0.00 0.00 0.00 3.69
28 29 3.426568 GCCGCACACTTCAGGAGC 61.427 66.667 0.00 0.00 0.00 4.70
29 30 2.031012 CCGCACACTTCAGGAGCA 59.969 61.111 0.00 0.00 0.00 4.26
30 31 2.320587 CCGCACACTTCAGGAGCAC 61.321 63.158 0.00 0.00 0.00 4.40
31 32 1.595109 CGCACACTTCAGGAGCACA 60.595 57.895 0.00 0.00 0.00 4.57
32 33 0.952497 CGCACACTTCAGGAGCACAT 60.952 55.000 0.00 0.00 0.00 3.21
33 34 0.801251 GCACACTTCAGGAGCACATC 59.199 55.000 0.00 0.00 0.00 3.06
34 35 1.073964 CACACTTCAGGAGCACATCG 58.926 55.000 0.00 0.00 0.00 3.84
35 36 0.671781 ACACTTCAGGAGCACATCGC 60.672 55.000 0.00 0.00 42.91 4.58
36 37 0.671472 CACTTCAGGAGCACATCGCA 60.671 55.000 0.00 0.00 46.13 5.10
37 38 0.390866 ACTTCAGGAGCACATCGCAG 60.391 55.000 0.00 0.00 46.13 5.18
38 39 1.078918 TTCAGGAGCACATCGCAGG 60.079 57.895 0.00 0.00 46.13 4.85
39 40 3.200593 CAGGAGCACATCGCAGGC 61.201 66.667 0.00 0.00 46.13 4.85
40 41 4.827087 AGGAGCACATCGCAGGCG 62.827 66.667 7.46 7.46 46.13 5.52
45 46 3.857854 CACATCGCAGGCGCAGTC 61.858 66.667 10.83 0.00 38.40 3.51
46 47 4.377708 ACATCGCAGGCGCAGTCA 62.378 61.111 10.83 0.00 38.40 3.41
47 48 3.857854 CATCGCAGGCGCAGTCAC 61.858 66.667 10.83 0.00 38.40 3.67
53 54 4.687215 AGGCGCAGTCACGTGCAT 62.687 61.111 11.67 0.00 44.21 3.96
54 55 4.450122 GGCGCAGTCACGTGCATG 62.450 66.667 11.67 12.83 44.21 4.06
56 57 3.714963 CGCAGTCACGTGCATGCA 61.715 61.111 30.87 18.46 44.21 3.96
57 58 2.872557 GCAGTCACGTGCATGCAT 59.127 55.556 28.72 5.67 43.41 3.96
58 59 1.226211 GCAGTCACGTGCATGCATC 60.226 57.895 28.72 16.09 43.41 3.91
59 60 1.914531 GCAGTCACGTGCATGCATCA 61.915 55.000 28.72 5.16 43.41 3.07
60 61 0.518195 CAGTCACGTGCATGCATCAA 59.482 50.000 25.64 7.29 0.00 2.57
61 62 0.800631 AGTCACGTGCATGCATCAAG 59.199 50.000 25.64 17.34 0.00 3.02
62 63 0.518636 GTCACGTGCATGCATCAAGT 59.481 50.000 25.64 17.98 0.00 3.16
63 64 0.518195 TCACGTGCATGCATCAAGTG 59.482 50.000 25.64 26.81 42.50 3.16
64 65 0.239082 CACGTGCATGCATCAAGTGT 59.761 50.000 25.64 12.54 38.50 3.55
65 66 1.464219 CACGTGCATGCATCAAGTGTA 59.536 47.619 25.64 0.00 38.50 2.90
66 67 1.733912 ACGTGCATGCATCAAGTGTAG 59.266 47.619 25.64 9.17 0.00 2.74
67 68 1.063027 CGTGCATGCATCAAGTGTAGG 59.937 52.381 25.64 0.00 0.00 3.18
68 69 2.086869 GTGCATGCATCAAGTGTAGGT 58.913 47.619 25.64 0.00 0.00 3.08
69 70 2.086094 TGCATGCATCAAGTGTAGGTG 58.914 47.619 18.46 0.00 0.00 4.00
70 71 1.402968 GCATGCATCAAGTGTAGGTGG 59.597 52.381 14.21 0.00 0.00 4.61
71 72 2.019249 CATGCATCAAGTGTAGGTGGG 58.981 52.381 0.00 0.00 0.00 4.61
72 73 1.357137 TGCATCAAGTGTAGGTGGGA 58.643 50.000 0.00 0.00 0.00 4.37
73 74 1.915489 TGCATCAAGTGTAGGTGGGAT 59.085 47.619 0.00 0.00 0.00 3.85
74 75 3.111484 TGCATCAAGTGTAGGTGGGATA 58.889 45.455 0.00 0.00 0.00 2.59
75 76 3.134623 TGCATCAAGTGTAGGTGGGATAG 59.865 47.826 0.00 0.00 0.00 2.08
76 77 3.495100 GCATCAAGTGTAGGTGGGATAGG 60.495 52.174 0.00 0.00 0.00 2.57
77 78 2.759355 TCAAGTGTAGGTGGGATAGGG 58.241 52.381 0.00 0.00 0.00 3.53
78 79 1.141053 CAAGTGTAGGTGGGATAGGGC 59.859 57.143 0.00 0.00 0.00 5.19
79 80 0.642710 AGTGTAGGTGGGATAGGGCT 59.357 55.000 0.00 0.00 0.00 5.19
80 81 0.759346 GTGTAGGTGGGATAGGGCTG 59.241 60.000 0.00 0.00 0.00 4.85
81 82 0.399949 TGTAGGTGGGATAGGGCTGG 60.400 60.000 0.00 0.00 0.00 4.85
82 83 1.461461 TAGGTGGGATAGGGCTGGC 60.461 63.158 0.00 0.00 0.00 4.85
83 84 2.264494 TAGGTGGGATAGGGCTGGCA 62.264 60.000 2.88 0.00 0.00 4.92
84 85 2.193248 GTGGGATAGGGCTGGCAC 59.807 66.667 2.88 0.00 0.00 5.01
85 86 3.096495 TGGGATAGGGCTGGCACC 61.096 66.667 2.88 0.74 0.00 5.01
95 96 1.897560 GGCTGGCACCCACTATTATC 58.102 55.000 0.00 0.00 0.00 1.75
96 97 1.142870 GGCTGGCACCCACTATTATCA 59.857 52.381 0.00 0.00 0.00 2.15
97 98 2.222027 GCTGGCACCCACTATTATCAC 58.778 52.381 0.00 0.00 0.00 3.06
98 99 2.158755 GCTGGCACCCACTATTATCACT 60.159 50.000 0.00 0.00 0.00 3.41
99 100 3.071023 GCTGGCACCCACTATTATCACTA 59.929 47.826 0.00 0.00 0.00 2.74
100 101 4.444306 GCTGGCACCCACTATTATCACTAA 60.444 45.833 0.00 0.00 0.00 2.24
101 102 5.290493 TGGCACCCACTATTATCACTAAG 57.710 43.478 0.00 0.00 0.00 2.18
102 103 4.719773 TGGCACCCACTATTATCACTAAGT 59.280 41.667 0.00 0.00 0.00 2.24
103 104 5.163343 TGGCACCCACTATTATCACTAAGTC 60.163 44.000 0.00 0.00 0.00 3.01
104 105 5.298347 GCACCCACTATTATCACTAAGTCC 58.702 45.833 0.00 0.00 0.00 3.85
105 106 5.529791 CACCCACTATTATCACTAAGTCCG 58.470 45.833 0.00 0.00 0.00 4.79
106 107 4.038883 ACCCACTATTATCACTAAGTCCGC 59.961 45.833 0.00 0.00 0.00 5.54
107 108 4.038763 CCCACTATTATCACTAAGTCCGCA 59.961 45.833 0.00 0.00 0.00 5.69
108 109 5.452776 CCCACTATTATCACTAAGTCCGCAA 60.453 44.000 0.00 0.00 0.00 4.85
109 110 6.046593 CCACTATTATCACTAAGTCCGCAAA 58.953 40.000 0.00 0.00 0.00 3.68
110 111 6.537301 CCACTATTATCACTAAGTCCGCAAAA 59.463 38.462 0.00 0.00 0.00 2.44
111 112 7.226720 CCACTATTATCACTAAGTCCGCAAAAT 59.773 37.037 0.00 0.00 0.00 1.82
112 113 8.612619 CACTATTATCACTAAGTCCGCAAAATT 58.387 33.333 0.00 0.00 0.00 1.82
113 114 9.826574 ACTATTATCACTAAGTCCGCAAAATTA 57.173 29.630 0.00 0.00 0.00 1.40
120 121 9.168451 TCACTAAGTCCGCAAAATTATAAATCA 57.832 29.630 0.00 0.00 0.00 2.57
121 122 9.438291 CACTAAGTCCGCAAAATTATAAATCAG 57.562 33.333 0.00 0.00 0.00 2.90
122 123 9.174166 ACTAAGTCCGCAAAATTATAAATCAGT 57.826 29.630 0.00 0.00 0.00 3.41
123 124 9.438291 CTAAGTCCGCAAAATTATAAATCAGTG 57.562 33.333 0.00 0.00 0.00 3.66
124 125 6.265577 AGTCCGCAAAATTATAAATCAGTGC 58.734 36.000 0.00 0.00 0.00 4.40
125 126 6.033341 GTCCGCAAAATTATAAATCAGTGCA 58.967 36.000 0.00 0.00 0.00 4.57
126 127 6.697019 GTCCGCAAAATTATAAATCAGTGCAT 59.303 34.615 0.00 0.00 0.00 3.96
127 128 6.696583 TCCGCAAAATTATAAATCAGTGCATG 59.303 34.615 0.00 0.00 0.00 4.06
128 129 6.696583 CCGCAAAATTATAAATCAGTGCATGA 59.303 34.615 0.00 0.00 43.70 3.07
129 130 7.222417 CCGCAAAATTATAAATCAGTGCATGAA 59.778 33.333 0.00 0.00 42.53 2.57
130 131 8.593842 CGCAAAATTATAAATCAGTGCATGAAA 58.406 29.630 0.00 0.00 42.53 2.69
131 132 9.910511 GCAAAATTATAAATCAGTGCATGAAAG 57.089 29.630 0.00 0.00 42.53 2.62
133 134 9.603921 AAAATTATAAATCAGTGCATGAAAGGG 57.396 29.630 0.00 0.00 42.53 3.95
134 135 4.660789 ATAAATCAGTGCATGAAAGGGC 57.339 40.909 0.00 0.00 42.53 5.19
135 136 2.226962 AATCAGTGCATGAAAGGGCT 57.773 45.000 0.00 0.00 42.53 5.19
136 137 2.226962 ATCAGTGCATGAAAGGGCTT 57.773 45.000 0.00 0.00 42.53 4.35
137 138 1.250328 TCAGTGCATGAAAGGGCTTG 58.750 50.000 0.00 0.00 34.02 4.01
138 139 0.389426 CAGTGCATGAAAGGGCTTGC 60.389 55.000 0.00 0.00 38.85 4.01
139 140 1.444895 GTGCATGAAAGGGCTTGCG 60.445 57.895 0.00 0.00 40.60 4.85
140 141 1.603171 TGCATGAAAGGGCTTGCGA 60.603 52.632 0.00 0.00 40.60 5.10
141 142 1.177895 TGCATGAAAGGGCTTGCGAA 61.178 50.000 0.00 0.00 40.60 4.70
142 143 0.038343 GCATGAAAGGGCTTGCGAAA 60.038 50.000 0.00 0.00 30.80 3.46
143 144 1.986698 CATGAAAGGGCTTGCGAAAG 58.013 50.000 0.00 0.00 0.00 2.62
144 145 1.270550 CATGAAAGGGCTTGCGAAAGT 59.729 47.619 4.74 0.00 0.00 2.66
145 146 0.667993 TGAAAGGGCTTGCGAAAGTG 59.332 50.000 4.74 0.00 0.00 3.16
146 147 0.039165 GAAAGGGCTTGCGAAAGTGG 60.039 55.000 4.74 0.00 0.00 4.00
147 148 2.087462 AAAGGGCTTGCGAAAGTGGC 62.087 55.000 4.74 0.00 0.00 5.01
148 149 3.294493 GGGCTTGCGAAAGTGGCA 61.294 61.111 4.74 0.00 38.93 4.92
149 150 2.639327 GGGCTTGCGAAAGTGGCAT 61.639 57.895 4.74 0.00 40.62 4.40
150 151 1.444895 GGCTTGCGAAAGTGGCATG 60.445 57.895 4.74 0.00 40.62 4.06
151 152 1.580942 GCTTGCGAAAGTGGCATGA 59.419 52.632 4.74 0.00 40.62 3.07
152 153 0.730494 GCTTGCGAAAGTGGCATGAC 60.730 55.000 4.74 0.00 40.62 3.06
153 154 0.453282 CTTGCGAAAGTGGCATGACG 60.453 55.000 0.00 0.00 40.62 4.35
154 155 0.882484 TTGCGAAAGTGGCATGACGA 60.882 50.000 0.00 0.00 40.62 4.20
155 156 0.882484 TGCGAAAGTGGCATGACGAA 60.882 50.000 0.00 0.00 35.04 3.85
156 157 0.179215 GCGAAAGTGGCATGACGAAG 60.179 55.000 0.00 0.00 0.00 3.79
181 182 7.782168 AGTGTAGTGATCAATCTCATCTCCTTA 59.218 37.037 0.00 0.00 0.00 2.69
210 211 3.692791 CACTCGTCGTGAATAGATGGA 57.307 47.619 0.56 0.00 46.81 3.41
211 212 3.364062 CACTCGTCGTGAATAGATGGAC 58.636 50.000 0.56 0.00 46.81 4.02
212 213 3.014623 ACTCGTCGTGAATAGATGGACA 58.985 45.455 0.56 0.00 0.00 4.02
213 214 3.442625 ACTCGTCGTGAATAGATGGACAA 59.557 43.478 0.56 0.00 0.00 3.18
214 215 3.766151 TCGTCGTGAATAGATGGACAAC 58.234 45.455 0.00 0.00 0.00 3.32
216 217 3.924073 CGTCGTGAATAGATGGACAACAA 59.076 43.478 0.00 0.00 0.00 2.83
219 220 6.307155 GTCGTGAATAGATGGACAACAAAAG 58.693 40.000 0.00 0.00 0.00 2.27
224 230 2.665165 AGATGGACAACAAAAGCACCA 58.335 42.857 0.00 0.00 0.00 4.17
227 233 4.832266 AGATGGACAACAAAAGCACCATTA 59.168 37.500 0.00 0.00 38.09 1.90
232 238 3.243839 ACAACAAAAGCACCATTAGCCAG 60.244 43.478 0.00 0.00 0.00 4.85
246 252 3.068881 CCAGGGTGGCGAAGAGAA 58.931 61.111 0.00 0.00 0.00 2.87
261 267 3.951979 AGAGAAAAAGCGACAACACAG 57.048 42.857 0.00 0.00 0.00 3.66
274 281 1.068474 AACACAGACGATACAAGCGC 58.932 50.000 0.00 0.00 0.00 5.92
275 282 0.038618 ACACAGACGATACAAGCGCA 60.039 50.000 11.47 0.00 0.00 6.09
283 290 1.599071 CGATACAAGCGCATGACCATT 59.401 47.619 20.91 0.00 0.00 3.16
293 300 2.797087 CGCATGACCATTTGATTCTGCC 60.797 50.000 0.00 0.00 0.00 4.85
310 317 3.276091 CGTTGCAACTCACCGGCA 61.276 61.111 26.09 0.00 35.41 5.69
351 358 7.603297 AAAATAGTGAAAAATCGAACACACG 57.397 32.000 0.00 0.00 35.97 4.49
355 362 3.246699 GTGAAAAATCGAACACACGGAGA 59.753 43.478 0.00 0.00 34.05 3.71
356 363 3.493129 TGAAAAATCGAACACACGGAGAG 59.507 43.478 0.00 0.00 0.00 3.20
358 365 0.389948 AATCGAACACACGGAGAGCC 60.390 55.000 0.00 0.00 0.00 4.70
359 366 2.227089 ATCGAACACACGGAGAGCCC 62.227 60.000 0.00 0.00 0.00 5.19
384 392 0.886563 AGGAAGACCCGAACGTGTAG 59.113 55.000 0.00 0.00 40.87 2.74
385 393 0.108945 GGAAGACCCGAACGTGTAGG 60.109 60.000 0.00 0.00 0.00 3.18
387 395 0.316204 AAGACCCGAACGTGTAGGTG 59.684 55.000 8.26 1.06 31.10 4.00
667 724 2.578178 CGCGTGCGGAGAGAGAAG 60.578 66.667 6.30 0.00 35.56 2.85
668 725 2.878429 GCGTGCGGAGAGAGAAGA 59.122 61.111 0.00 0.00 0.00 2.87
669 726 1.226547 GCGTGCGGAGAGAGAAGAG 60.227 63.158 0.00 0.00 0.00 2.85
670 727 1.649390 GCGTGCGGAGAGAGAAGAGA 61.649 60.000 0.00 0.00 0.00 3.10
671 728 0.805614 CGTGCGGAGAGAGAAGAGAA 59.194 55.000 0.00 0.00 0.00 2.87
672 729 1.202132 CGTGCGGAGAGAGAAGAGAAG 60.202 57.143 0.00 0.00 0.00 2.85
673 730 1.134175 GTGCGGAGAGAGAAGAGAAGG 59.866 57.143 0.00 0.00 0.00 3.46
674 731 0.102300 GCGGAGAGAGAAGAGAAGGC 59.898 60.000 0.00 0.00 0.00 4.35
675 732 1.468985 CGGAGAGAGAAGAGAAGGCA 58.531 55.000 0.00 0.00 0.00 4.75
676 733 1.405105 CGGAGAGAGAAGAGAAGGCAG 59.595 57.143 0.00 0.00 0.00 4.85
677 734 1.136891 GGAGAGAGAAGAGAAGGCAGC 59.863 57.143 0.00 0.00 0.00 5.25
678 735 0.817013 AGAGAGAAGAGAAGGCAGCG 59.183 55.000 0.00 0.00 0.00 5.18
679 736 0.805711 GAGAGAAGAGAAGGCAGCGC 60.806 60.000 0.00 0.00 0.00 5.92
680 737 2.125753 AGAAGAGAAGGCAGCGCG 60.126 61.111 0.00 0.00 0.00 6.86
681 738 2.433318 GAAGAGAAGGCAGCGCGT 60.433 61.111 8.43 0.00 0.00 6.01
682 739 2.734673 GAAGAGAAGGCAGCGCGTG 61.735 63.158 8.43 6.12 0.00 5.34
771 828 4.100084 CGATCAGGCAGGGGTGCA 62.100 66.667 0.00 0.00 36.33 4.57
773 830 2.937689 ATCAGGCAGGGGTGCAGT 60.938 61.111 0.00 0.00 36.33 4.40
774 831 3.278072 ATCAGGCAGGGGTGCAGTG 62.278 63.158 0.00 0.00 36.33 3.66
778 835 4.962836 GCAGGGGTGCAGTGCAGT 62.963 66.667 20.42 0.11 40.08 4.40
779 836 2.981909 CAGGGGTGCAGTGCAGTG 60.982 66.667 20.42 17.56 40.08 3.66
780 837 4.962836 AGGGGTGCAGTGCAGTGC 62.963 66.667 34.65 34.65 40.08 4.40
906 963 2.103042 CGTTGCCACTCTAGCCAGC 61.103 63.158 0.00 0.00 0.00 4.85
907 964 1.298014 GTTGCCACTCTAGCCAGCT 59.702 57.895 0.00 0.00 0.00 4.24
908 965 0.742635 GTTGCCACTCTAGCCAGCTC 60.743 60.000 0.00 0.00 0.00 4.09
909 966 1.903877 TTGCCACTCTAGCCAGCTCC 61.904 60.000 0.00 0.00 0.00 4.70
910 967 2.362369 GCCACTCTAGCCAGCTCCA 61.362 63.158 0.00 0.00 0.00 3.86
911 968 1.821936 CCACTCTAGCCAGCTCCAG 59.178 63.158 0.00 0.00 0.00 3.86
2010 2085 1.748879 CCGGTTACATGGGTGCCAG 60.749 63.158 0.00 0.00 36.75 4.85
2056 2134 1.968540 GCACTTCTCCAGCCACCAC 60.969 63.158 0.00 0.00 0.00 4.16
2124 2202 1.684734 GCCCTCCCTTCCTGTACGA 60.685 63.158 0.00 0.00 0.00 3.43
2190 2286 3.967715 GCTGTGGAACGGGTTCTC 58.032 61.111 11.02 6.08 45.56 2.87
2283 2385 6.782000 CCCCCTTATTACCATTGATTGATTGA 59.218 38.462 0.00 0.00 0.00 2.57
2284 2386 7.455638 CCCCCTTATTACCATTGATTGATTGAT 59.544 37.037 0.00 0.00 0.00 2.57
2285 2387 8.873144 CCCCTTATTACCATTGATTGATTGATT 58.127 33.333 0.00 0.00 0.00 2.57
2286 2388 9.701098 CCCTTATTACCATTGATTGATTGATTG 57.299 33.333 0.00 0.00 0.00 2.67
2364 2466 2.135933 GTGTCCTCGTGTCCTTCAAAG 58.864 52.381 0.00 0.00 0.00 2.77
2365 2467 1.760613 TGTCCTCGTGTCCTTCAAAGT 59.239 47.619 0.00 0.00 0.00 2.66
2383 2494 1.274167 AGTGCACAAATCATGCTTGGG 59.726 47.619 21.04 8.30 43.77 4.12
2636 2750 1.269723 GCTAGTTTTGGGCACAACCTC 59.730 52.381 0.00 0.00 39.10 3.85
2770 2891 7.105494 GCTTTAGCAAAACTGTTATTGAACC 57.895 36.000 15.01 3.36 41.59 3.62
2838 2967 1.483415 TCACCTAGACAATTACCCGCC 59.517 52.381 0.00 0.00 0.00 6.13
2859 2988 4.142752 GCCCAGTCTTATTGGTTTAACGTC 60.143 45.833 0.00 0.00 33.73 4.34
2903 3032 1.273324 TGGTTCCTGGTTGGTTGGTTT 60.273 47.619 0.00 0.00 37.07 3.27
2912 3041 3.089284 GGTTGGTTGGTTTGGGATCTAG 58.911 50.000 0.00 0.00 0.00 2.43
2913 3042 3.499745 GGTTGGTTGGTTTGGGATCTAGT 60.500 47.826 0.00 0.00 0.00 2.57
2914 3043 4.263594 GGTTGGTTGGTTTGGGATCTAGTA 60.264 45.833 0.00 0.00 0.00 1.82
2937 3066 5.065704 AGTGACTAAGTCTACATGTGCAG 57.934 43.478 9.11 0.00 33.15 4.41
3065 3236 3.212685 CCCTGAATCATCTTCCTGCTTC 58.787 50.000 0.00 0.00 0.00 3.86
3117 3288 5.126067 GTGCATTCCATCAGTAGGTACAAT 58.874 41.667 0.00 0.00 0.00 2.71
3118 3289 6.126911 TGTGCATTCCATCAGTAGGTACAATA 60.127 38.462 0.00 0.00 0.00 1.90
3119 3290 6.202954 GTGCATTCCATCAGTAGGTACAATAC 59.797 42.308 0.00 0.00 0.00 1.89
3120 3291 6.126911 TGCATTCCATCAGTAGGTACAATACA 60.127 38.462 9.40 0.00 0.00 2.29
3121 3292 6.765989 GCATTCCATCAGTAGGTACAATACAA 59.234 38.462 9.40 0.00 0.00 2.41
3132 3303 8.759782 AGTAGGTACAATACAAAAGCAGTAGAT 58.240 33.333 9.40 0.00 0.00 1.98
3133 3304 9.379791 GTAGGTACAATACAAAAGCAGTAGATT 57.620 33.333 0.00 0.00 0.00 2.40
3143 3314 5.886960 AAAGCAGTAGATTGGTGAATGTC 57.113 39.130 0.00 0.00 0.00 3.06
3158 3329 3.503363 TGAATGTCTCTGTTCATTGTGCC 59.497 43.478 0.00 0.00 34.92 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.680237 TCCTGAAGTGTGCGGCCG 62.680 66.667 24.05 24.05 0.00 6.13
10 11 2.743928 CTCCTGAAGTGTGCGGCC 60.744 66.667 0.00 0.00 0.00 6.13
11 12 3.426568 GCTCCTGAAGTGTGCGGC 61.427 66.667 0.00 0.00 0.00 6.53
12 13 2.031012 TGCTCCTGAAGTGTGCGG 59.969 61.111 0.00 0.00 0.00 5.69
13 14 0.952497 ATGTGCTCCTGAAGTGTGCG 60.952 55.000 0.00 0.00 0.00 5.34
14 15 0.801251 GATGTGCTCCTGAAGTGTGC 59.199 55.000 0.00 0.00 0.00 4.57
15 16 1.073964 CGATGTGCTCCTGAAGTGTG 58.926 55.000 0.00 0.00 0.00 3.82
16 17 0.671781 GCGATGTGCTCCTGAAGTGT 60.672 55.000 0.00 0.00 41.73 3.55
17 18 0.671472 TGCGATGTGCTCCTGAAGTG 60.671 55.000 0.00 0.00 46.63 3.16
18 19 0.390866 CTGCGATGTGCTCCTGAAGT 60.391 55.000 0.00 0.00 46.63 3.01
19 20 1.088340 CCTGCGATGTGCTCCTGAAG 61.088 60.000 0.00 0.00 46.63 3.02
20 21 1.078918 CCTGCGATGTGCTCCTGAA 60.079 57.895 0.00 0.00 46.63 3.02
21 22 2.580815 CCTGCGATGTGCTCCTGA 59.419 61.111 0.00 0.00 46.63 3.86
22 23 3.200593 GCCTGCGATGTGCTCCTG 61.201 66.667 0.00 0.00 46.63 3.86
23 24 4.827087 CGCCTGCGATGTGCTCCT 62.827 66.667 5.43 0.00 46.63 3.69
36 37 4.687215 ATGCACGTGACTGCGCCT 62.687 61.111 22.23 0.00 40.31 5.52
37 38 4.450122 CATGCACGTGACTGCGCC 62.450 66.667 22.23 0.00 40.31 6.53
39 40 2.891461 GATGCATGCACGTGACTGCG 62.891 60.000 25.37 10.96 40.31 5.18
40 41 1.226211 GATGCATGCACGTGACTGC 60.226 57.895 25.37 26.52 37.70 4.40
41 42 0.518195 TTGATGCATGCACGTGACTG 59.482 50.000 25.37 16.12 0.00 3.51
42 43 0.800631 CTTGATGCATGCACGTGACT 59.199 50.000 25.37 5.55 0.00 3.41
43 44 0.518636 ACTTGATGCATGCACGTGAC 59.481 50.000 25.37 11.46 0.00 3.67
44 45 0.518195 CACTTGATGCATGCACGTGA 59.482 50.000 25.37 8.59 37.61 4.35
45 46 0.239082 ACACTTGATGCATGCACGTG 59.761 50.000 25.37 26.03 40.21 4.49
46 47 1.733912 CTACACTTGATGCATGCACGT 59.266 47.619 25.37 14.74 0.00 4.49
47 48 1.063027 CCTACACTTGATGCATGCACG 59.937 52.381 25.37 14.07 0.00 5.34
48 49 2.086869 ACCTACACTTGATGCATGCAC 58.913 47.619 25.37 17.16 0.00 4.57
49 50 2.086094 CACCTACACTTGATGCATGCA 58.914 47.619 25.04 25.04 0.00 3.96
50 51 1.402968 CCACCTACACTTGATGCATGC 59.597 52.381 11.82 11.82 0.00 4.06
51 52 2.019249 CCCACCTACACTTGATGCATG 58.981 52.381 2.46 0.00 0.00 4.06
52 53 1.915489 TCCCACCTACACTTGATGCAT 59.085 47.619 0.00 0.00 0.00 3.96
53 54 1.357137 TCCCACCTACACTTGATGCA 58.643 50.000 0.00 0.00 0.00 3.96
54 55 2.717639 ATCCCACCTACACTTGATGC 57.282 50.000 0.00 0.00 0.00 3.91
55 56 3.071602 CCCTATCCCACCTACACTTGATG 59.928 52.174 0.00 0.00 0.00 3.07
56 57 3.318313 CCCTATCCCACCTACACTTGAT 58.682 50.000 0.00 0.00 0.00 2.57
57 58 2.759355 CCCTATCCCACCTACACTTGA 58.241 52.381 0.00 0.00 0.00 3.02
58 59 1.141053 GCCCTATCCCACCTACACTTG 59.859 57.143 0.00 0.00 0.00 3.16
59 60 1.009675 AGCCCTATCCCACCTACACTT 59.990 52.381 0.00 0.00 0.00 3.16
60 61 0.642710 AGCCCTATCCCACCTACACT 59.357 55.000 0.00 0.00 0.00 3.55
61 62 0.759346 CAGCCCTATCCCACCTACAC 59.241 60.000 0.00 0.00 0.00 2.90
62 63 0.399949 CCAGCCCTATCCCACCTACA 60.400 60.000 0.00 0.00 0.00 2.74
63 64 1.769716 GCCAGCCCTATCCCACCTAC 61.770 65.000 0.00 0.00 0.00 3.18
64 65 1.461461 GCCAGCCCTATCCCACCTA 60.461 63.158 0.00 0.00 0.00 3.08
65 66 2.774351 GCCAGCCCTATCCCACCT 60.774 66.667 0.00 0.00 0.00 4.00
66 67 3.096495 TGCCAGCCCTATCCCACC 61.096 66.667 0.00 0.00 0.00 4.61
67 68 2.193248 GTGCCAGCCCTATCCCAC 59.807 66.667 0.00 0.00 0.00 4.61
68 69 3.096495 GGTGCCAGCCCTATCCCA 61.096 66.667 0.00 0.00 0.00 4.37
69 70 3.890926 GGGTGCCAGCCCTATCCC 61.891 72.222 0.10 0.00 45.22 3.85
76 77 1.142870 TGATAATAGTGGGTGCCAGCC 59.857 52.381 5.84 5.84 32.34 4.85
77 78 2.158755 AGTGATAATAGTGGGTGCCAGC 60.159 50.000 0.00 0.00 32.34 4.85
78 79 3.845781 AGTGATAATAGTGGGTGCCAG 57.154 47.619 0.00 0.00 32.34 4.85
79 80 4.719773 ACTTAGTGATAATAGTGGGTGCCA 59.280 41.667 0.00 0.00 0.00 4.92
80 81 5.291905 ACTTAGTGATAATAGTGGGTGCC 57.708 43.478 0.00 0.00 0.00 5.01
81 82 5.298347 GGACTTAGTGATAATAGTGGGTGC 58.702 45.833 0.00 0.00 0.00 5.01
82 83 5.529791 CGGACTTAGTGATAATAGTGGGTG 58.470 45.833 0.00 0.00 0.00 4.61
83 84 4.038883 GCGGACTTAGTGATAATAGTGGGT 59.961 45.833 0.00 0.00 0.00 4.51
84 85 4.038763 TGCGGACTTAGTGATAATAGTGGG 59.961 45.833 0.00 0.00 0.00 4.61
85 86 5.196341 TGCGGACTTAGTGATAATAGTGG 57.804 43.478 0.00 0.00 0.00 4.00
86 87 7.534085 TTTTGCGGACTTAGTGATAATAGTG 57.466 36.000 0.00 0.00 0.00 2.74
87 88 8.732746 AATTTTGCGGACTTAGTGATAATAGT 57.267 30.769 0.00 0.00 0.00 2.12
94 95 9.168451 TGATTTATAATTTTGCGGACTTAGTGA 57.832 29.630 0.00 0.00 0.00 3.41
95 96 9.438291 CTGATTTATAATTTTGCGGACTTAGTG 57.562 33.333 0.00 0.00 0.00 2.74
96 97 9.174166 ACTGATTTATAATTTTGCGGACTTAGT 57.826 29.630 0.00 0.00 0.00 2.24
97 98 9.438291 CACTGATTTATAATTTTGCGGACTTAG 57.562 33.333 0.00 0.00 0.00 2.18
98 99 7.913297 GCACTGATTTATAATTTTGCGGACTTA 59.087 33.333 0.00 0.00 0.00 2.24
99 100 6.751888 GCACTGATTTATAATTTTGCGGACTT 59.248 34.615 0.00 0.00 0.00 3.01
100 101 6.127758 TGCACTGATTTATAATTTTGCGGACT 60.128 34.615 0.00 0.00 0.00 3.85
101 102 6.033341 TGCACTGATTTATAATTTTGCGGAC 58.967 36.000 0.00 0.00 0.00 4.79
102 103 6.201226 TGCACTGATTTATAATTTTGCGGA 57.799 33.333 0.00 0.00 0.00 5.54
103 104 6.696583 TCATGCACTGATTTATAATTTTGCGG 59.303 34.615 0.00 0.00 0.00 5.69
104 105 7.682593 TCATGCACTGATTTATAATTTTGCG 57.317 32.000 0.00 0.00 0.00 4.85
105 106 9.910511 CTTTCATGCACTGATTTATAATTTTGC 57.089 29.630 0.00 0.00 32.72 3.68
107 108 9.603921 CCCTTTCATGCACTGATTTATAATTTT 57.396 29.630 0.00 0.00 32.72 1.82
108 109 7.712205 GCCCTTTCATGCACTGATTTATAATTT 59.288 33.333 0.00 0.00 32.72 1.82
109 110 7.070322 AGCCCTTTCATGCACTGATTTATAATT 59.930 33.333 0.00 0.00 32.72 1.40
110 111 6.552350 AGCCCTTTCATGCACTGATTTATAAT 59.448 34.615 0.00 0.00 32.72 1.28
111 112 5.893255 AGCCCTTTCATGCACTGATTTATAA 59.107 36.000 0.00 0.00 32.72 0.98
112 113 5.448654 AGCCCTTTCATGCACTGATTTATA 58.551 37.500 0.00 0.00 32.72 0.98
113 114 4.284178 AGCCCTTTCATGCACTGATTTAT 58.716 39.130 0.00 0.00 32.72 1.40
114 115 3.700538 AGCCCTTTCATGCACTGATTTA 58.299 40.909 0.00 0.00 32.72 1.40
115 116 2.532843 AGCCCTTTCATGCACTGATTT 58.467 42.857 0.00 0.00 32.72 2.17
116 117 2.226962 AGCCCTTTCATGCACTGATT 57.773 45.000 0.00 0.00 32.72 2.57
117 118 1.822990 CAAGCCCTTTCATGCACTGAT 59.177 47.619 0.00 0.00 32.72 2.90
118 119 1.250328 CAAGCCCTTTCATGCACTGA 58.750 50.000 0.00 0.00 0.00 3.41
119 120 0.389426 GCAAGCCCTTTCATGCACTG 60.389 55.000 0.00 0.00 38.63 3.66
120 121 1.870055 CGCAAGCCCTTTCATGCACT 61.870 55.000 0.00 0.00 38.69 4.40
121 122 1.444895 CGCAAGCCCTTTCATGCAC 60.445 57.895 0.00 0.00 38.69 4.57
122 123 1.177895 TTCGCAAGCCCTTTCATGCA 61.178 50.000 0.00 0.00 38.69 3.96
123 124 0.038343 TTTCGCAAGCCCTTTCATGC 60.038 50.000 0.00 0.00 35.49 4.06
124 125 1.270550 ACTTTCGCAAGCCCTTTCATG 59.729 47.619 0.00 0.00 32.57 3.07
125 126 1.270550 CACTTTCGCAAGCCCTTTCAT 59.729 47.619 0.00 0.00 32.57 2.57
126 127 0.667993 CACTTTCGCAAGCCCTTTCA 59.332 50.000 0.00 0.00 32.57 2.69
127 128 0.039165 CCACTTTCGCAAGCCCTTTC 60.039 55.000 0.00 0.00 32.57 2.62
128 129 2.041153 CCACTTTCGCAAGCCCTTT 58.959 52.632 0.00 0.00 32.57 3.11
129 130 2.564721 GCCACTTTCGCAAGCCCTT 61.565 57.895 0.00 0.00 32.57 3.95
130 131 2.985847 GCCACTTTCGCAAGCCCT 60.986 61.111 0.00 0.00 32.57 5.19
131 132 2.639327 ATGCCACTTTCGCAAGCCC 61.639 57.895 0.00 0.00 40.22 5.19
132 133 1.444895 CATGCCACTTTCGCAAGCC 60.445 57.895 0.00 0.00 40.22 4.35
133 134 0.730494 GTCATGCCACTTTCGCAAGC 60.730 55.000 0.00 0.00 40.22 4.01
134 135 0.453282 CGTCATGCCACTTTCGCAAG 60.453 55.000 0.00 0.00 40.22 4.01
135 136 0.882484 TCGTCATGCCACTTTCGCAA 60.882 50.000 0.00 0.00 40.22 4.85
136 137 0.882484 TTCGTCATGCCACTTTCGCA 60.882 50.000 0.00 0.00 41.28 5.10
137 138 0.179215 CTTCGTCATGCCACTTTCGC 60.179 55.000 0.00 0.00 0.00 4.70
138 139 1.136252 CACTTCGTCATGCCACTTTCG 60.136 52.381 0.00 0.00 0.00 3.46
139 140 1.873591 ACACTTCGTCATGCCACTTTC 59.126 47.619 0.00 0.00 0.00 2.62
140 141 1.967319 ACACTTCGTCATGCCACTTT 58.033 45.000 0.00 0.00 0.00 2.66
141 142 2.037251 ACTACACTTCGTCATGCCACTT 59.963 45.455 0.00 0.00 0.00 3.16
142 143 1.618837 ACTACACTTCGTCATGCCACT 59.381 47.619 0.00 0.00 0.00 4.00
143 144 1.726791 CACTACACTTCGTCATGCCAC 59.273 52.381 0.00 0.00 0.00 5.01
144 145 1.616374 TCACTACACTTCGTCATGCCA 59.384 47.619 0.00 0.00 0.00 4.92
145 146 2.363788 TCACTACACTTCGTCATGCC 57.636 50.000 0.00 0.00 0.00 4.40
146 147 3.511699 TGATCACTACACTTCGTCATGC 58.488 45.455 0.00 0.00 0.00 4.06
147 148 6.038985 AGATTGATCACTACACTTCGTCATG 58.961 40.000 0.00 0.00 0.00 3.07
148 149 6.127619 TGAGATTGATCACTACACTTCGTCAT 60.128 38.462 0.00 0.00 0.00 3.06
149 150 5.183140 TGAGATTGATCACTACACTTCGTCA 59.817 40.000 0.00 0.00 0.00 4.35
150 151 5.641709 TGAGATTGATCACTACACTTCGTC 58.358 41.667 0.00 0.00 0.00 4.20
151 152 5.644977 TGAGATTGATCACTACACTTCGT 57.355 39.130 0.00 0.00 0.00 3.85
152 153 6.502652 AGATGAGATTGATCACTACACTTCG 58.497 40.000 0.00 0.00 30.46 3.79
153 154 6.922957 GGAGATGAGATTGATCACTACACTTC 59.077 42.308 0.00 0.00 30.46 3.01
154 155 6.610830 AGGAGATGAGATTGATCACTACACTT 59.389 38.462 0.00 0.00 30.46 3.16
155 156 6.135454 AGGAGATGAGATTGATCACTACACT 58.865 40.000 0.00 0.00 30.46 3.55
156 157 6.403866 AGGAGATGAGATTGATCACTACAC 57.596 41.667 0.00 0.00 30.46 2.90
157 158 8.583296 CATAAGGAGATGAGATTGATCACTACA 58.417 37.037 0.00 0.00 30.46 2.74
158 159 8.801299 TCATAAGGAGATGAGATTGATCACTAC 58.199 37.037 0.00 0.00 32.05 2.73
159 160 8.946797 TCATAAGGAGATGAGATTGATCACTA 57.053 34.615 0.00 0.00 32.05 2.74
160 161 7.852550 TCATAAGGAGATGAGATTGATCACT 57.147 36.000 0.00 0.00 32.05 3.41
161 162 9.806203 CTATCATAAGGAGATGAGATTGATCAC 57.194 37.037 0.00 0.00 39.18 3.06
162 163 9.765295 TCTATCATAAGGAGATGAGATTGATCA 57.235 33.333 0.00 0.00 39.18 2.92
165 166 9.765295 TGATCTATCATAAGGAGATGAGATTGA 57.235 33.333 0.00 0.00 39.18 2.57
166 167 9.806203 GTGATCTATCATAAGGAGATGAGATTG 57.194 37.037 0.00 0.00 39.18 2.67
167 168 9.772605 AGTGATCTATCATAAGGAGATGAGATT 57.227 33.333 0.00 0.00 39.18 2.40
168 169 9.412460 GAGTGATCTATCATAAGGAGATGAGAT 57.588 37.037 0.00 0.00 39.18 2.75
169 170 7.552330 CGAGTGATCTATCATAAGGAGATGAGA 59.448 40.741 0.00 0.00 39.18 3.27
170 171 7.336679 ACGAGTGATCTATCATAAGGAGATGAG 59.663 40.741 0.00 0.00 39.18 2.90
171 172 7.171653 ACGAGTGATCTATCATAAGGAGATGA 58.828 38.462 0.00 0.00 40.08 2.92
172 173 7.389803 ACGAGTGATCTATCATAAGGAGATG 57.610 40.000 0.00 0.00 39.30 2.90
207 208 3.243704 GCTAATGGTGCTTTTGTTGTCCA 60.244 43.478 0.00 0.00 0.00 4.02
208 209 3.317150 GCTAATGGTGCTTTTGTTGTCC 58.683 45.455 0.00 0.00 0.00 4.02
209 210 3.243704 TGGCTAATGGTGCTTTTGTTGTC 60.244 43.478 0.00 0.00 0.00 3.18
210 211 2.697751 TGGCTAATGGTGCTTTTGTTGT 59.302 40.909 0.00 0.00 0.00 3.32
211 212 3.319755 CTGGCTAATGGTGCTTTTGTTG 58.680 45.455 0.00 0.00 0.00 3.33
212 213 2.299867 CCTGGCTAATGGTGCTTTTGTT 59.700 45.455 0.00 0.00 0.00 2.83
213 214 1.895131 CCTGGCTAATGGTGCTTTTGT 59.105 47.619 0.00 0.00 0.00 2.83
214 215 1.205417 CCCTGGCTAATGGTGCTTTTG 59.795 52.381 0.00 0.00 0.00 2.44
216 217 0.409484 ACCCTGGCTAATGGTGCTTT 59.591 50.000 0.00 0.00 0.00 3.51
219 220 1.754234 CCACCCTGGCTAATGGTGC 60.754 63.158 11.65 0.00 46.54 5.01
232 238 0.241213 GCTTTTTCTCTTCGCCACCC 59.759 55.000 0.00 0.00 0.00 4.61
246 252 1.647346 TCGTCTGTGTTGTCGCTTTT 58.353 45.000 0.00 0.00 0.00 2.27
261 267 0.577269 GGTCATGCGCTTGTATCGTC 59.423 55.000 21.14 7.63 0.00 4.20
274 281 2.424601 ACGGCAGAATCAAATGGTCATG 59.575 45.455 0.00 0.00 0.00 3.07
275 282 2.726821 ACGGCAGAATCAAATGGTCAT 58.273 42.857 0.00 0.00 0.00 3.06
328 335 6.017770 TCCGTGTGTTCGATTTTTCACTATTT 60.018 34.615 0.00 0.00 0.00 1.40
329 336 5.467399 TCCGTGTGTTCGATTTTTCACTATT 59.533 36.000 0.00 0.00 0.00 1.73
330 337 4.992319 TCCGTGTGTTCGATTTTTCACTAT 59.008 37.500 0.00 0.00 0.00 2.12
331 338 4.370049 TCCGTGTGTTCGATTTTTCACTA 58.630 39.130 0.00 0.00 0.00 2.74
332 339 3.199677 TCCGTGTGTTCGATTTTTCACT 58.800 40.909 0.00 0.00 0.00 3.41
333 340 3.246699 TCTCCGTGTGTTCGATTTTTCAC 59.753 43.478 0.00 0.00 0.00 3.18
334 341 3.459145 TCTCCGTGTGTTCGATTTTTCA 58.541 40.909 0.00 0.00 0.00 2.69
335 342 3.664537 GCTCTCCGTGTGTTCGATTTTTC 60.665 47.826 0.00 0.00 0.00 2.29
355 362 4.083862 GTCTTCCTTCGCCGGGCT 62.084 66.667 18.34 0.00 0.00 5.19
358 365 4.814294 CGGGTCTTCCTTCGCCGG 62.814 72.222 0.00 0.00 0.00 6.13
359 366 3.291101 TTCGGGTCTTCCTTCGCCG 62.291 63.158 0.00 0.00 0.00 6.46
361 368 2.092882 CGTTCGGGTCTTCCTTCGC 61.093 63.158 0.00 0.00 0.00 4.70
362 369 1.007336 CACGTTCGGGTCTTCCTTCG 61.007 60.000 0.00 0.00 0.00 3.79
363 370 0.033090 ACACGTTCGGGTCTTCCTTC 59.967 55.000 0.00 0.00 0.00 3.46
365 372 0.886563 CTACACGTTCGGGTCTTCCT 59.113 55.000 2.68 0.00 0.00 3.36
366 373 0.108945 CCTACACGTTCGGGTCTTCC 60.109 60.000 2.68 0.00 0.00 3.46
368 375 0.316204 CACCTACACGTTCGGGTCTT 59.684 55.000 2.68 0.00 0.00 3.01
384 392 2.162754 CGACCCGAACGTATGCACC 61.163 63.158 0.00 0.00 0.00 5.01
385 393 2.795389 GCGACCCGAACGTATGCAC 61.795 63.158 0.00 0.00 0.00 4.57
387 395 3.259751 GGCGACCCGAACGTATGC 61.260 66.667 0.00 0.00 0.00 3.14
411 419 1.873863 CACCACGACACTAGCTCGA 59.126 57.895 15.42 0.00 35.08 4.04
655 712 0.102300 GCCTTCTCTTCTCTCTCCGC 59.898 60.000 0.00 0.00 0.00 5.54
656 713 1.405105 CTGCCTTCTCTTCTCTCTCCG 59.595 57.143 0.00 0.00 0.00 4.63
657 714 1.136891 GCTGCCTTCTCTTCTCTCTCC 59.863 57.143 0.00 0.00 0.00 3.71
658 715 1.202290 CGCTGCCTTCTCTTCTCTCTC 60.202 57.143 0.00 0.00 0.00 3.20
659 716 0.817013 CGCTGCCTTCTCTTCTCTCT 59.183 55.000 0.00 0.00 0.00 3.10
660 717 0.805711 GCGCTGCCTTCTCTTCTCTC 60.806 60.000 0.00 0.00 0.00 3.20
661 718 1.217779 GCGCTGCCTTCTCTTCTCT 59.782 57.895 0.00 0.00 0.00 3.10
662 719 2.164026 CGCGCTGCCTTCTCTTCTC 61.164 63.158 5.56 0.00 0.00 2.87
663 720 2.125753 CGCGCTGCCTTCTCTTCT 60.126 61.111 5.56 0.00 0.00 2.85
664 721 2.433318 ACGCGCTGCCTTCTCTTC 60.433 61.111 5.73 0.00 0.00 2.87
665 722 2.740055 CACGCGCTGCCTTCTCTT 60.740 61.111 5.73 0.00 0.00 2.85
750 807 2.202932 CCCCTGCCTGATCGTTCG 60.203 66.667 0.00 0.00 0.00 3.95
771 828 2.668889 GCTCAGCTGCACTGCACT 60.669 61.111 9.47 0.03 46.76 4.40
906 963 2.686470 TCAGGGCTGGAGCTGGAG 60.686 66.667 0.00 0.00 41.70 3.86
907 964 3.005539 GTCAGGGCTGGAGCTGGA 61.006 66.667 0.00 0.00 41.70 3.86
908 965 3.324930 TGTCAGGGCTGGAGCTGG 61.325 66.667 0.00 0.00 41.70 4.85
909 966 2.046507 GTGTCAGGGCTGGAGCTG 60.047 66.667 0.00 0.00 41.70 4.24
910 967 3.699894 CGTGTCAGGGCTGGAGCT 61.700 66.667 0.00 0.00 41.70 4.09
1519 1585 2.266055 CCCTTGCTGGTCTCCGAC 59.734 66.667 0.00 0.00 0.00 4.79
1895 1970 1.354040 GAGAACTGCGTCATCTGGTG 58.646 55.000 0.00 0.00 0.00 4.17
2364 2466 1.001181 ACCCAAGCATGATTTGTGCAC 59.999 47.619 10.75 10.75 44.87 4.57
2365 2467 1.340088 ACCCAAGCATGATTTGTGCA 58.660 45.000 0.00 0.00 44.87 4.57
2383 2494 1.154150 CGACACCCGTCCTTCGTAC 60.154 63.158 0.00 0.00 39.11 3.67
2554 2665 9.765295 ATACTACTATTACTGTATTACCAGGGG 57.235 37.037 0.00 0.00 36.75 4.79
2601 2715 1.352352 ACTAGCAACTGTGGCCTTGAT 59.648 47.619 3.32 0.56 0.00 2.57
2636 2750 8.671921 AGATGAAGCTGACAAATGTTGTTATAG 58.328 33.333 0.00 0.00 45.52 1.31
2694 2808 6.993175 ATGACGATAAATATCAGTGTCGTG 57.007 37.500 7.34 0.00 41.69 4.35
2770 2891 2.292267 GGCATATGTTGGACCTGTCAG 58.708 52.381 4.29 0.00 0.00 3.51
2807 2936 2.283604 TAGGTGACTGCGGCCAGA 60.284 61.111 2.24 0.00 43.88 3.86
2808 2937 2.185350 CTAGGTGACTGCGGCCAG 59.815 66.667 2.24 0.00 43.88 4.85
2809 2938 2.283604 TCTAGGTGACTGCGGCCA 60.284 61.111 2.24 0.00 43.88 5.36
2813 2942 3.187700 GGTAATTGTCTAGGTGACTGCG 58.812 50.000 0.00 0.00 45.54 5.18
2838 2967 4.435121 GCGACGTTAAACCAATAAGACTGG 60.435 45.833 0.00 0.00 40.05 4.00
2859 2988 1.712081 CCGACATCTGAAGCAAGCG 59.288 57.895 0.00 0.00 0.00 4.68
2903 3032 6.971340 AGACTTAGTCACTTACTAGATCCCA 58.029 40.000 15.23 0.00 41.70 4.37
2912 3041 6.387465 TGCACATGTAGACTTAGTCACTTAC 58.613 40.000 15.23 8.90 34.60 2.34
2913 3042 6.433093 TCTGCACATGTAGACTTAGTCACTTA 59.567 38.462 15.23 0.00 34.60 2.24
2914 3043 5.243954 TCTGCACATGTAGACTTAGTCACTT 59.756 40.000 15.23 6.38 34.60 3.16
2970 3134 9.657121 GCTCATCTGAAACTATGTTTTTATAGC 57.343 33.333 0.00 0.00 34.67 2.97
2975 3139 8.078596 GTGAAGCTCATCTGAAACTATGTTTTT 58.921 33.333 0.00 0.00 0.00 1.94
2994 3161 2.304180 AGCAGACTTATGTGGTGAAGCT 59.696 45.455 0.00 0.00 0.00 3.74
3065 3236 8.408601 CCTAGTGTTGATTGGATAGAAAATTGG 58.591 37.037 0.00 0.00 0.00 3.16
3117 3288 6.714810 ACATTCACCAATCTACTGCTTTTGTA 59.285 34.615 0.00 0.00 0.00 2.41
3118 3289 5.536161 ACATTCACCAATCTACTGCTTTTGT 59.464 36.000 0.00 0.00 0.00 2.83
3119 3290 6.017400 ACATTCACCAATCTACTGCTTTTG 57.983 37.500 0.00 0.00 0.00 2.44
3120 3291 6.006449 AGACATTCACCAATCTACTGCTTTT 58.994 36.000 0.00 0.00 0.00 2.27
3121 3292 5.564550 AGACATTCACCAATCTACTGCTTT 58.435 37.500 0.00 0.00 0.00 3.51
3132 3303 5.008911 CACAATGAACAGAGACATTCACCAA 59.991 40.000 0.00 0.00 37.64 3.67
3133 3304 4.516321 CACAATGAACAGAGACATTCACCA 59.484 41.667 0.00 0.00 37.64 4.17
3143 3314 1.800805 ACGAGGCACAATGAACAGAG 58.199 50.000 0.00 0.00 0.00 3.35
3229 3400 5.720371 AGCATCTGGATGTCTGATACTAC 57.280 43.478 11.52 0.00 40.80 2.73


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

AutoCloner maintained by Alex Coulton.