Multiple sequence alignment - TraesCS3D01G097200

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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 TraesCS3D01G097200 chr3D 100.000 4724 0 0 1 4724 49004431 49009154 0.000000e+00 8724
1 TraesCS3D01G097200 chr3D 86.580 231 20 5 1 229 170685265 170685044 1.310000e-60 244
2 TraesCS3D01G097200 chr3D 86.634 202 18 4 1 199 313674495 313674690 1.030000e-51 215
3 TraesCS3D01G097200 chr3A 94.710 3932 167 26 808 4724 61478413 61482318 0.000000e+00 6071
4 TraesCS3D01G097200 chr3A 88.815 599 45 13 231 813 61477764 61478356 0.000000e+00 715
5 TraesCS3D01G097200 chr3A 90.847 437 39 1 915 1350 61434377 61434813 6.810000e-163 584
6 TraesCS3D01G097200 chr3B 93.773 3774 180 26 808 4562 78594991 78598728 0.000000e+00 5616
7 TraesCS3D01G097200 chr3B 91.150 565 34 7 258 813 78594378 78594935 0.000000e+00 752
8 TraesCS3D01G097200 chr5B 93.023 215 6 3 1 214 477455290 477455496 5.940000e-79 305
9 TraesCS3D01G097200 chr4B 89.815 216 10 6 1 212 662533121 662532914 2.800000e-67 267
10 TraesCS3D01G097200 chr4B 88.073 218 13 6 1 214 562427231 562427439 3.650000e-61 246
11 TraesCS3D01G097200 chr2D 89.524 210 12 3 1 208 642135120 642135321 1.690000e-64 257
12 TraesCS3D01G097200 chr4A 87.850 214 12 9 1 209 29098668 29098872 6.110000e-59 239
13 TraesCS3D01G097200 chr7D 87.440 207 15 7 1 204 550937772 550937970 1.320000e-55 228
14 TraesCS3D01G097200 chr7D 85.520 221 17 9 1 214 600498627 600498415 2.860000e-52 217


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 TraesCS3D01G097200 chr3D 49004431 49009154 4723 False 8724 8724 100.0000 1 4724 1 chr3D.!!$F1 4723
1 TraesCS3D01G097200 chr3A 61477764 61482318 4554 False 3393 6071 91.7625 231 4724 2 chr3A.!!$F2 4493
2 TraesCS3D01G097200 chr3B 78594378 78598728 4350 False 3184 5616 92.4615 258 4562 2 chr3B.!!$F1 4304

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
68 69 0.033228 TGCCGGCCATCTTTGTTTTG 59.967 50.0 26.77 0.0 0.00 2.44 F
69 70 0.033366 GCCGGCCATCTTTGTTTTGT 59.967 50.0 18.11 0.0 0.00 2.83 F
1805 1902 0.099082 CTCGTAACCGTGAGCCTCTC 59.901 60.0 0.00 0.0 35.01 3.20 F
2477 2574 0.596082 AGCCGAAATTCCCAAACGTG 59.404 50.0 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1902 0.446222 CATACCGCTTGTCAAACCGG 59.554 55.000 17.97 17.97 45.80 5.28 R
1823 1920 1.338389 GCTGGCCTAAGGTAACGTTCA 60.338 52.381 2.82 0.00 46.39 3.18 R
3341 3438 3.855255 TGTCAGTCTGGGATGAAACAA 57.145 42.857 0.00 0.00 0.00 2.83 R
4134 4238 0.037139 GCTGTGCCAATGCCAATGAA 60.037 50.000 0.00 0.00 36.33 2.57 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
18 19 3.639162 CCTCAGAGTGCTAGAAGCG 57.361 57.895 0.00 0.00 46.26 4.68
24 25 3.188786 GTGCTAGAAGCGCGGTGG 61.189 66.667 13.41 3.94 46.26 4.61
25 26 3.691342 TGCTAGAAGCGCGGTGGT 61.691 61.111 13.41 4.47 46.26 4.16
26 27 2.344981 TGCTAGAAGCGCGGTGGTA 61.345 57.895 13.41 5.58 46.26 3.25
27 28 1.877165 GCTAGAAGCGCGGTGGTAC 60.877 63.158 13.41 4.18 0.00 3.34
28 29 1.807886 CTAGAAGCGCGGTGGTACT 59.192 57.895 13.41 11.81 0.00 2.73
29 30 0.172803 CTAGAAGCGCGGTGGTACTT 59.827 55.000 13.41 2.14 0.00 2.24
30 31 0.171903 TAGAAGCGCGGTGGTACTTC 59.828 55.000 13.41 12.66 39.03 3.01
31 32 1.080025 GAAGCGCGGTGGTACTTCT 60.080 57.895 13.41 0.00 36.45 2.85
32 33 1.077089 GAAGCGCGGTGGTACTTCTC 61.077 60.000 13.41 0.00 36.45 2.87
33 34 2.502692 AAGCGCGGTGGTACTTCTCC 62.503 60.000 13.41 0.00 0.00 3.71
34 35 2.202570 CGCGGTGGTACTTCTCCG 60.203 66.667 0.00 7.89 44.86 4.63
35 36 2.183555 GCGGTGGTACTTCTCCGG 59.816 66.667 12.49 0.00 42.71 5.14
36 37 2.345760 GCGGTGGTACTTCTCCGGA 61.346 63.158 2.93 2.93 42.71 5.14
37 38 1.807886 CGGTGGTACTTCTCCGGAG 59.192 63.158 26.32 26.32 39.41 4.63
62 63 3.061848 CGGTTGCCGGCCATCTTT 61.062 61.111 26.77 0.00 44.15 2.52
63 64 2.573340 GGTTGCCGGCCATCTTTG 59.427 61.111 26.77 0.00 0.00 2.77
64 65 2.275380 GGTTGCCGGCCATCTTTGT 61.275 57.895 26.77 0.00 0.00 2.83
65 66 1.665442 GTTGCCGGCCATCTTTGTT 59.335 52.632 26.77 0.00 0.00 2.83
66 67 0.033366 GTTGCCGGCCATCTTTGTTT 59.967 50.000 26.77 0.00 0.00 2.83
67 68 0.755686 TTGCCGGCCATCTTTGTTTT 59.244 45.000 26.77 0.00 0.00 2.43
68 69 0.033228 TGCCGGCCATCTTTGTTTTG 59.967 50.000 26.77 0.00 0.00 2.44
69 70 0.033366 GCCGGCCATCTTTGTTTTGT 59.967 50.000 18.11 0.00 0.00 2.83
70 71 1.934849 GCCGGCCATCTTTGTTTTGTC 60.935 52.381 18.11 0.00 0.00 3.18
71 72 1.665735 CCGGCCATCTTTGTTTTGTCG 60.666 52.381 2.24 0.00 0.00 4.35
72 73 1.265635 CGGCCATCTTTGTTTTGTCGA 59.734 47.619 2.24 0.00 0.00 4.20
73 74 2.095263 CGGCCATCTTTGTTTTGTCGAT 60.095 45.455 2.24 0.00 0.00 3.59
74 75 3.501950 GGCCATCTTTGTTTTGTCGATC 58.498 45.455 0.00 0.00 0.00 3.69
75 76 3.191371 GGCCATCTTTGTTTTGTCGATCT 59.809 43.478 0.00 0.00 0.00 2.75
76 77 4.161333 GCCATCTTTGTTTTGTCGATCTG 58.839 43.478 0.00 0.00 0.00 2.90
77 78 4.161333 CCATCTTTGTTTTGTCGATCTGC 58.839 43.478 0.00 0.00 0.00 4.26
78 79 3.896648 TCTTTGTTTTGTCGATCTGCC 57.103 42.857 0.00 0.00 0.00 4.85
79 80 2.223144 TCTTTGTTTTGTCGATCTGCCG 59.777 45.455 0.00 0.00 0.00 5.69
80 81 1.588674 TTGTTTTGTCGATCTGCCGT 58.411 45.000 0.00 0.00 0.00 5.68
81 82 1.588674 TGTTTTGTCGATCTGCCGTT 58.411 45.000 0.00 0.00 0.00 4.44
82 83 1.262950 TGTTTTGTCGATCTGCCGTTG 59.737 47.619 0.00 0.00 0.00 4.10
83 84 0.237235 TTTTGTCGATCTGCCGTTGC 59.763 50.000 0.00 0.00 38.26 4.17
84 85 1.573829 TTTGTCGATCTGCCGTTGCC 61.574 55.000 0.00 0.00 36.33 4.52
85 86 3.554692 GTCGATCTGCCGTTGCCG 61.555 66.667 0.00 0.00 36.33 5.69
86 87 4.063967 TCGATCTGCCGTTGCCGT 62.064 61.111 0.00 0.00 36.33 5.68
87 88 3.554692 CGATCTGCCGTTGCCGTC 61.555 66.667 0.00 0.00 36.33 4.79
88 89 3.554692 GATCTGCCGTTGCCGTCG 61.555 66.667 0.00 0.00 36.33 5.12
89 90 4.373116 ATCTGCCGTTGCCGTCGT 62.373 61.111 0.00 0.00 36.33 4.34
90 91 3.876589 ATCTGCCGTTGCCGTCGTT 62.877 57.895 0.00 0.00 36.33 3.85
91 92 4.368808 CTGCCGTTGCCGTCGTTG 62.369 66.667 0.00 0.00 36.33 4.10
103 104 3.757745 CCGTCGTTGGCATTTATTTCT 57.242 42.857 0.00 0.00 0.00 2.52
104 105 3.680789 CCGTCGTTGGCATTTATTTCTC 58.319 45.455 0.00 0.00 0.00 2.87
105 106 3.374058 CCGTCGTTGGCATTTATTTCTCT 59.626 43.478 0.00 0.00 0.00 3.10
106 107 4.142687 CCGTCGTTGGCATTTATTTCTCTT 60.143 41.667 0.00 0.00 0.00 2.85
107 108 5.390613 CGTCGTTGGCATTTATTTCTCTTT 58.609 37.500 0.00 0.00 0.00 2.52
108 109 5.508224 CGTCGTTGGCATTTATTTCTCTTTC 59.492 40.000 0.00 0.00 0.00 2.62
109 110 6.612306 GTCGTTGGCATTTATTTCTCTTTCT 58.388 36.000 0.00 0.00 0.00 2.52
110 111 7.084486 GTCGTTGGCATTTATTTCTCTTTCTT 58.916 34.615 0.00 0.00 0.00 2.52
111 112 7.595130 GTCGTTGGCATTTATTTCTCTTTCTTT 59.405 33.333 0.00 0.00 0.00 2.52
112 113 7.807907 TCGTTGGCATTTATTTCTCTTTCTTTC 59.192 33.333 0.00 0.00 0.00 2.62
113 114 7.809806 CGTTGGCATTTATTTCTCTTTCTTTCT 59.190 33.333 0.00 0.00 0.00 2.52
114 115 9.133627 GTTGGCATTTATTTCTCTTTCTTTCTC 57.866 33.333 0.00 0.00 0.00 2.87
115 116 8.641498 TGGCATTTATTTCTCTTTCTTTCTCT 57.359 30.769 0.00 0.00 0.00 3.10
116 117 8.734386 TGGCATTTATTTCTCTTTCTTTCTCTC 58.266 33.333 0.00 0.00 0.00 3.20
117 118 8.955388 GGCATTTATTTCTCTTTCTTTCTCTCT 58.045 33.333 0.00 0.00 0.00 3.10
118 119 9.986833 GCATTTATTTCTCTTTCTTTCTCTCTC 57.013 33.333 0.00 0.00 0.00 3.20
124 125 9.639563 ATTTCTCTTTCTTTCTCTCTCCTTTTT 57.360 29.630 0.00 0.00 0.00 1.94
140 141 3.467776 TTTTTGGGCTGGTTTGTGC 57.532 47.368 0.00 0.00 0.00 4.57
141 142 0.908198 TTTTTGGGCTGGTTTGTGCT 59.092 45.000 0.00 0.00 0.00 4.40
142 143 0.177604 TTTTGGGCTGGTTTGTGCTG 59.822 50.000 0.00 0.00 0.00 4.41
143 144 2.308968 TTTGGGCTGGTTTGTGCTGC 62.309 55.000 0.00 0.00 0.00 5.25
144 145 4.347453 GGGCTGGTTTGTGCTGCG 62.347 66.667 0.00 0.00 0.00 5.18
145 146 4.347453 GGCTGGTTTGTGCTGCGG 62.347 66.667 0.00 0.00 0.00 5.69
147 148 4.347453 CTGGTTTGTGCTGCGGCC 62.347 66.667 16.57 7.08 37.74 6.13
161 162 2.919328 GGCCCCAGCAAGCTTGTT 60.919 61.111 26.55 19.21 42.56 2.83
162 163 2.341176 GCCCCAGCAAGCTTGTTG 59.659 61.111 30.08 30.08 38.85 3.33
163 164 2.501602 GCCCCAGCAAGCTTGTTGT 61.502 57.895 32.71 15.42 37.65 3.32
164 165 1.178534 GCCCCAGCAAGCTTGTTGTA 61.179 55.000 32.71 0.00 37.65 2.41
165 166 1.549203 CCCCAGCAAGCTTGTTGTAT 58.451 50.000 32.71 12.07 37.65 2.29
166 167 1.474077 CCCCAGCAAGCTTGTTGTATC 59.526 52.381 32.71 15.16 37.65 2.24
167 168 2.161855 CCCAGCAAGCTTGTTGTATCA 58.838 47.619 32.71 0.00 37.65 2.15
168 169 2.163010 CCCAGCAAGCTTGTTGTATCAG 59.837 50.000 32.71 20.79 37.65 2.90
169 170 3.076621 CCAGCAAGCTTGTTGTATCAGA 58.923 45.455 32.71 0.00 37.65 3.27
170 171 3.693085 CCAGCAAGCTTGTTGTATCAGAT 59.307 43.478 32.71 1.26 37.65 2.90
171 172 4.438336 CCAGCAAGCTTGTTGTATCAGATG 60.438 45.833 32.71 16.75 37.65 2.90
172 173 4.393990 CAGCAAGCTTGTTGTATCAGATGA 59.606 41.667 29.07 0.00 35.09 2.92
173 174 5.066117 CAGCAAGCTTGTTGTATCAGATGAT 59.934 40.000 29.07 0.31 35.09 2.45
174 175 5.651139 AGCAAGCTTGTTGTATCAGATGATT 59.349 36.000 26.55 0.00 36.05 2.57
175 176 5.742453 GCAAGCTTGTTGTATCAGATGATTG 59.258 40.000 26.55 0.00 36.05 2.67
176 177 5.496133 AGCTTGTTGTATCAGATGATTGC 57.504 39.130 0.00 0.00 36.05 3.56
177 178 5.191426 AGCTTGTTGTATCAGATGATTGCT 58.809 37.500 0.00 0.00 36.05 3.91
178 179 5.651139 AGCTTGTTGTATCAGATGATTGCTT 59.349 36.000 0.00 0.00 36.05 3.91
179 180 6.152323 AGCTTGTTGTATCAGATGATTGCTTT 59.848 34.615 0.00 0.00 36.05 3.51
180 181 7.337689 AGCTTGTTGTATCAGATGATTGCTTTA 59.662 33.333 0.00 0.00 36.05 1.85
181 182 8.133627 GCTTGTTGTATCAGATGATTGCTTTAT 58.866 33.333 0.00 0.00 36.05 1.40
201 202 8.857694 CTTTATAATCTATAAAGCGGGGGAAA 57.142 34.615 11.35 0.00 45.98 3.13
202 203 8.625786 TTTATAATCTATAAAGCGGGGGAAAC 57.374 34.615 0.00 0.00 36.12 2.78
203 204 7.666804 TTTATAATCTATAAAGCGGGGGAAACC 59.333 37.037 0.00 0.00 41.43 3.27
227 228 4.839668 TTTTCTTACCCAACAACGGATG 57.160 40.909 0.00 0.00 0.00 3.51
228 229 3.495434 TTCTTACCCAACAACGGATGT 57.505 42.857 0.00 0.00 46.82 3.06
239 240 0.893727 AACGGATGTTTGGGCTGTCC 60.894 55.000 0.00 0.00 33.53 4.02
317 326 4.752101 AGACACAACCTCTGAATTTTCTCG 59.248 41.667 0.00 0.00 0.00 4.04
399 417 0.656205 CGTTGGAGACCAAAAACGCG 60.656 55.000 3.53 3.53 45.73 6.01
400 418 0.658897 GTTGGAGACCAAAAACGCGA 59.341 50.000 15.93 0.00 45.73 5.87
521 539 4.733725 CCCCTCCCTCCCGGACAA 62.734 72.222 0.73 0.00 34.86 3.18
613 631 1.445871 GGGGCGATTTTCAGTTACGT 58.554 50.000 0.00 0.00 0.00 3.57
620 638 5.202640 GCGATTTTCAGTTACGTGTTCTTT 58.797 37.500 0.00 0.00 0.00 2.52
642 660 2.733227 CGATTTCACTTTGGATGCTGGC 60.733 50.000 0.00 0.00 0.00 4.85
667 685 2.164865 CTCTGTGAGCAGCGGGAACT 62.165 60.000 0.00 0.00 42.29 3.01
686 704 4.086706 ACTAAGCTAGGCTGTTGTGTTT 57.913 40.909 0.00 0.00 39.62 2.83
705 723 4.764143 GGCACCCATGGTTTAGCT 57.236 55.556 11.73 0.00 31.02 3.32
706 724 2.976099 GGCACCCATGGTTTAGCTT 58.024 52.632 11.73 0.00 31.02 3.74
707 725 2.137810 GGCACCCATGGTTTAGCTTA 57.862 50.000 11.73 0.00 31.02 3.09
708 726 2.452505 GGCACCCATGGTTTAGCTTAA 58.547 47.619 11.73 0.00 31.02 1.85
733 751 1.846124 GTGGGAGTGAAGTGGGGGA 60.846 63.158 0.00 0.00 0.00 4.81
787 811 2.578981 GAGACGAACGGCGCCTAC 60.579 66.667 26.68 14.22 46.04 3.18
844 931 2.419297 CCTCTAGTTAGCTTGGCACCTG 60.419 54.545 0.00 0.00 0.00 4.00
852 939 2.283821 TTGGCACCTGGATTGGGC 60.284 61.111 0.00 0.00 0.00 5.36
856 943 2.440796 CACCTGGATTGGGCGCAT 60.441 61.111 10.83 0.00 0.00 4.73
863 950 0.532115 GGATTGGGCGCATGAACTTT 59.468 50.000 10.83 0.00 0.00 2.66
865 952 0.532115 ATTGGGCGCATGAACTTTCC 59.468 50.000 10.83 0.00 0.00 3.13
866 953 1.531739 TTGGGCGCATGAACTTTCCC 61.532 55.000 10.83 0.00 0.00 3.97
867 954 2.710902 GGGCGCATGAACTTTCCCC 61.711 63.158 10.83 0.00 0.00 4.81
868 955 2.710902 GGCGCATGAACTTTCCCCC 61.711 63.158 10.83 0.00 0.00 5.40
889 976 4.226168 CCCCTATTTTTGCCCAATTTGGTA 59.774 41.667 14.26 0.39 35.17 3.25
904 991 2.435372 TGGTACTCCATGATTTGCCC 57.565 50.000 0.00 0.00 39.03 5.36
905 992 1.638070 TGGTACTCCATGATTTGCCCA 59.362 47.619 0.00 0.00 39.03 5.36
906 993 2.024414 GGTACTCCATGATTTGCCCAC 58.976 52.381 0.00 0.00 0.00 4.61
910 997 0.825410 TCCATGATTTGCCCACATGC 59.175 50.000 0.00 0.00 39.68 4.06
911 998 0.828022 CCATGATTTGCCCACATGCT 59.172 50.000 0.00 0.00 39.68 3.79
912 999 2.033372 CCATGATTTGCCCACATGCTA 58.967 47.619 0.00 0.00 39.68 3.49
913 1000 2.035449 CCATGATTTGCCCACATGCTAG 59.965 50.000 0.00 0.00 39.68 3.42
917 1013 1.533625 TTTGCCCACATGCTAGTCAC 58.466 50.000 0.00 0.00 0.00 3.67
919 1015 2.464459 GCCCACATGCTAGTCACGC 61.464 63.158 0.00 0.00 0.00 5.34
990 1087 6.430616 CCTTTGAAATGGGTGCATTAATGTTT 59.569 34.615 16.61 8.03 0.00 2.83
1026 1123 5.689961 GGACAAATTTGTGCGAATTTACAGT 59.310 36.000 27.85 0.00 42.43 3.55
1185 1282 4.015406 AATGTCCGCGCACAGGGA 62.015 61.111 9.54 2.18 34.27 4.20
1225 1322 0.529337 CGCTCATCGGCACTTCATCT 60.529 55.000 0.00 0.00 33.78 2.90
1239 1336 3.389329 ACTTCATCTTGGTGCCTATCGAT 59.611 43.478 2.16 2.16 0.00 3.59
1318 1415 2.642311 TGCCTGGAGGTTTATGTTCAGA 59.358 45.455 0.00 0.00 37.57 3.27
1424 1521 1.513158 CACCGCGAGATCCAGAACT 59.487 57.895 8.23 0.00 0.00 3.01
1460 1557 1.519455 CTCCTTCGATGGTGACCGC 60.519 63.158 16.29 0.00 0.00 5.68
1494 1591 1.667724 GTTCATCCTCAACATGCTCGG 59.332 52.381 0.00 0.00 0.00 4.63
1513 1610 2.395654 GGCTACGAAGAATAAGGAGCG 58.604 52.381 0.00 0.00 0.00 5.03
1518 1615 1.202417 CGAAGAATAAGGAGCGCCAGA 60.202 52.381 9.88 0.00 36.29 3.86
1541 1638 4.657408 TGCTGGCATTCGTGGGCA 62.657 61.111 0.00 0.00 39.18 5.36
1572 1669 3.038280 TGAAGAGGTTCAGTCTGGTCAA 58.962 45.455 0.00 0.00 37.79 3.18
1613 1710 4.081420 AGGGACAGTTGATACAACTAGCTG 60.081 45.833 15.17 8.02 0.00 4.24
1696 1793 6.258727 GGTACATCAATGACAACCTGTATCAG 59.741 42.308 0.00 0.00 0.00 2.90
1734 1831 8.673711 GCAAACAAAATGTGGTATAGTGATAGA 58.326 33.333 0.00 0.00 0.00 1.98
1736 1833 8.964476 AACAAAATGTGGTATAGTGATAGAGG 57.036 34.615 0.00 0.00 0.00 3.69
1744 1841 7.448777 TGTGGTATAGTGATAGAGGACTGATTC 59.551 40.741 0.00 0.00 0.00 2.52
1745 1842 7.668052 GTGGTATAGTGATAGAGGACTGATTCT 59.332 40.741 0.00 0.00 0.00 2.40
1774 1871 4.418392 CTTGATTTGGCACAGCATCTAAC 58.582 43.478 0.00 0.00 42.39 2.34
1805 1902 0.099082 CTCGTAACCGTGAGCCTCTC 59.901 60.000 0.00 0.00 35.01 3.20
1925 2022 2.096013 CGTCTCTGCACTAGTTGATCGA 59.904 50.000 0.00 0.00 0.00 3.59
2387 2484 7.071698 AGGAGGCAATCAGATCAAAGTAATCTA 59.928 37.037 0.00 0.00 32.24 1.98
2477 2574 0.596082 AGCCGAAATTCCCAAACGTG 59.404 50.000 0.00 0.00 0.00 4.49
2681 2778 2.969950 TGCACCTATATGTACCCAGGAC 59.030 50.000 6.25 0.00 32.25 3.85
2856 2953 1.596603 TGTCTGTTGTCTGTGCATGG 58.403 50.000 0.00 0.00 0.00 3.66
2865 2962 2.757314 TGTCTGTGCATGGTTGTTTTCA 59.243 40.909 0.00 0.00 0.00 2.69
2906 3003 0.908910 TGTACCAGTAGCCACCCATG 59.091 55.000 0.00 0.00 0.00 3.66
3078 3175 2.030490 TTGCGGTGGTACAGACGGTT 62.030 55.000 0.00 0.00 41.80 4.44
3341 3438 6.118170 CACATGAATATTTCTGACACCTCCT 58.882 40.000 0.00 0.00 0.00 3.69
3513 3610 3.434319 ATTGCTGCTGCGGTTCCG 61.434 61.111 10.62 6.90 43.34 4.30
3818 3918 9.466497 TTCTATTTTATCATGCTCTCTTTGGTT 57.534 29.630 0.00 0.00 0.00 3.67
3844 3944 3.334691 TCTGCTTTAGTTGAACCATCGG 58.665 45.455 0.00 0.00 0.00 4.18
3872 3972 9.309516 CAAATGATTCTTGGACCATTATTTCTG 57.690 33.333 0.00 0.00 0.00 3.02
3891 3991 4.920376 TCTGTGCTTACTGCTTTTGTTTC 58.080 39.130 0.00 0.00 43.37 2.78
3924 4025 4.379813 GGGCTTGTGTGTTTCAGTCATATG 60.380 45.833 0.00 0.00 0.00 1.78
3928 4029 4.002982 TGTGTGTTTCAGTCATATGAGGC 58.997 43.478 5.42 0.00 0.00 4.70
3929 4030 4.256920 GTGTGTTTCAGTCATATGAGGCT 58.743 43.478 5.42 0.00 0.00 4.58
3934 4035 1.764723 TCAGTCATATGAGGCTGTGGG 59.235 52.381 18.05 0.00 0.00 4.61
3946 4047 1.871126 GCTGTGGGCTGAAGAAAGGC 61.871 60.000 0.00 0.00 41.86 4.35
3961 4062 0.255890 AAGGCCATGATGGTTAGCGT 59.744 50.000 13.84 0.00 40.46 5.07
3962 4063 0.464373 AGGCCATGATGGTTAGCGTG 60.464 55.000 13.84 0.00 40.46 5.34
3987 4088 3.817084 CAGAAGTTCATGCCTCTGACAAA 59.183 43.478 5.50 0.00 0.00 2.83
4003 4104 3.986572 TGACAAATTTAACATTGGCTGCG 59.013 39.130 6.77 0.00 35.53 5.18
4122 4223 4.511454 CCGTGTTTATATGTCCATGGTCTG 59.489 45.833 12.58 0.00 30.86 3.51
4134 4238 2.619849 CCATGGTCTGCAATGAACTCCT 60.620 50.000 2.57 0.00 0.00 3.69
4135 4239 2.957402 TGGTCTGCAATGAACTCCTT 57.043 45.000 0.00 0.00 0.00 3.36
4136 4240 2.783135 TGGTCTGCAATGAACTCCTTC 58.217 47.619 0.00 0.00 0.00 3.46
4137 4241 2.106338 TGGTCTGCAATGAACTCCTTCA 59.894 45.455 0.00 0.00 40.77 3.02
4216 4323 6.789262 ACTGAAACTTGAAGTGAACTCATTG 58.211 36.000 0.00 0.00 0.00 2.82
4391 4499 6.436261 CAAATGTGATGTATGATCAGCTTCC 58.564 40.000 0.09 1.04 0.00 3.46
4399 4507 1.266178 TGATCAGCTTCCCTTCGACA 58.734 50.000 0.00 0.00 0.00 4.35
4510 4619 4.540715 CTTCAGGGGATGAGGCTTTAATT 58.459 43.478 0.00 0.00 39.68 1.40
4513 4622 6.086011 TCAGGGGATGAGGCTTTAATTTTA 57.914 37.500 0.00 0.00 32.77 1.52
4556 4665 3.705051 ACTGAATTGGGCATGTTGATCT 58.295 40.909 0.00 0.00 0.00 2.75
4577 4686 3.710209 ATGTATCTCCTTGGCCATAGC 57.290 47.619 6.09 0.00 38.76 2.97
4601 4710 5.671742 GCAATTTGCAAAACCAATACTGT 57.328 34.783 17.19 0.00 44.26 3.55
4604 4713 6.657888 CAATTTGCAAAACCAATACTGTTCC 58.342 36.000 17.19 0.00 0.00 3.62
4605 4714 5.606348 TTTGCAAAACCAATACTGTTCCT 57.394 34.783 10.02 0.00 0.00 3.36
4616 4725 7.690256 ACCAATACTGTTCCTCAAGTATCTTT 58.310 34.615 0.00 0.00 0.00 2.52
4632 4742 0.469892 CTTTCCCCCAAACTGGCTGT 60.470 55.000 0.00 0.00 35.79 4.40
4637 4747 0.404040 CCCCAAACTGGCTGTTCCTA 59.596 55.000 10.31 0.00 38.03 2.94
4652 4762 6.207221 GGCTGTTCCTACTAGTATCTTAGACC 59.793 46.154 2.33 0.00 0.00 3.85
4656 4766 8.216423 TGTTCCTACTAGTATCTTAGACCGAAT 58.784 37.037 2.33 0.00 0.00 3.34
4686 4796 6.816134 TGTGCTAAATGATGTGTAATGTGT 57.184 33.333 0.00 0.00 0.00 3.72
4688 4798 7.656412 TGTGCTAAATGATGTGTAATGTGTTT 58.344 30.769 0.00 0.00 0.00 2.83
4691 4801 8.236586 TGCTAAATGATGTGTAATGTGTTTCTC 58.763 33.333 0.00 0.00 0.00 2.87
4718 4828 5.957842 TGAATTCACATGTACAGGGAAAC 57.042 39.130 12.79 10.75 0.00 2.78
4719 4829 5.380900 TGAATTCACATGTACAGGGAAACA 58.619 37.500 12.79 12.68 0.00 2.83
4720 4830 5.240623 TGAATTCACATGTACAGGGAAACAC 59.759 40.000 12.79 8.55 0.00 3.32
4721 4831 3.847671 TCACATGTACAGGGAAACACA 57.152 42.857 12.79 0.00 0.00 3.72
4722 4832 4.365514 TCACATGTACAGGGAAACACAT 57.634 40.909 12.79 0.00 31.91 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.527385 GCGCTTCTAGCACTCTGAGG 60.527 60.000 9.85 0.00 42.58 3.86
1 2 0.865218 CGCGCTTCTAGCACTCTGAG 60.865 60.000 5.56 2.45 42.58 3.35
2 3 1.137614 CGCGCTTCTAGCACTCTGA 59.862 57.895 5.56 0.00 42.58 3.27
3 4 1.875813 CCGCGCTTCTAGCACTCTG 60.876 63.158 5.56 0.00 42.58 3.35
4 5 2.344203 ACCGCGCTTCTAGCACTCT 61.344 57.895 5.56 0.00 42.58 3.24
5 6 2.161486 CACCGCGCTTCTAGCACTC 61.161 63.158 5.56 0.00 42.58 3.51
6 7 2.125912 CACCGCGCTTCTAGCACT 60.126 61.111 5.56 0.00 42.58 4.40
7 8 2.552585 TACCACCGCGCTTCTAGCAC 62.553 60.000 5.56 0.00 42.58 4.40
8 9 2.344981 TACCACCGCGCTTCTAGCA 61.345 57.895 5.56 0.00 42.58 3.49
9 10 1.877165 GTACCACCGCGCTTCTAGC 60.877 63.158 5.56 0.00 38.02 3.42
10 11 0.172803 AAGTACCACCGCGCTTCTAG 59.827 55.000 5.56 0.00 0.00 2.43
11 12 0.171903 GAAGTACCACCGCGCTTCTA 59.828 55.000 5.56 0.00 35.69 2.10
12 13 1.080025 GAAGTACCACCGCGCTTCT 60.080 57.895 5.56 0.00 35.69 2.85
13 14 1.077089 GAGAAGTACCACCGCGCTTC 61.077 60.000 5.56 12.24 38.01 3.86
14 15 1.080025 GAGAAGTACCACCGCGCTT 60.080 57.895 5.56 0.00 0.00 4.68
15 16 2.572284 GAGAAGTACCACCGCGCT 59.428 61.111 5.56 0.00 0.00 5.92
16 17 2.508663 GGAGAAGTACCACCGCGC 60.509 66.667 0.00 0.00 0.00 6.86
17 18 2.202570 CGGAGAAGTACCACCGCG 60.203 66.667 0.00 0.00 38.98 6.46
18 19 2.183555 CCGGAGAAGTACCACCGC 59.816 66.667 0.00 0.00 43.37 5.68
19 20 1.664321 CCTCCGGAGAAGTACCACCG 61.664 65.000 33.39 7.87 44.16 4.94
20 21 1.328430 CCCTCCGGAGAAGTACCACC 61.328 65.000 33.39 0.00 0.00 4.61
21 22 0.614134 ACCCTCCGGAGAAGTACCAC 60.614 60.000 33.39 0.00 0.00 4.16
22 23 0.613853 CACCCTCCGGAGAAGTACCA 60.614 60.000 33.39 0.00 0.00 3.25
23 24 1.957765 GCACCCTCCGGAGAAGTACC 61.958 65.000 33.39 17.83 0.00 3.34
24 25 1.255667 TGCACCCTCCGGAGAAGTAC 61.256 60.000 33.39 22.41 0.00 2.73
25 26 0.970937 CTGCACCCTCCGGAGAAGTA 60.971 60.000 33.39 18.66 0.00 2.24
26 27 2.203788 TGCACCCTCCGGAGAAGT 60.204 61.111 33.39 24.96 0.00 3.01
27 28 2.581354 CTGCACCCTCCGGAGAAG 59.419 66.667 33.39 24.29 0.00 2.85
28 29 3.706373 GCTGCACCCTCCGGAGAA 61.706 66.667 33.39 11.32 0.00 2.87
46 47 1.815817 AACAAAGATGGCCGGCAACC 61.816 55.000 30.85 8.48 0.00 3.77
47 48 0.033366 AAACAAAGATGGCCGGCAAC 59.967 50.000 30.85 18.26 0.00 4.17
48 49 0.755686 AAAACAAAGATGGCCGGCAA 59.244 45.000 30.85 20.37 0.00 4.52
49 50 0.033228 CAAAACAAAGATGGCCGGCA 59.967 50.000 30.85 15.30 0.00 5.69
50 51 0.033366 ACAAAACAAAGATGGCCGGC 59.967 50.000 21.18 21.18 0.00 6.13
51 52 1.665735 CGACAAAACAAAGATGGCCGG 60.666 52.381 0.00 0.00 0.00 6.13
52 53 1.265635 TCGACAAAACAAAGATGGCCG 59.734 47.619 0.00 0.00 0.00 6.13
53 54 3.191371 AGATCGACAAAACAAAGATGGCC 59.809 43.478 0.00 0.00 0.00 5.36
54 55 4.161333 CAGATCGACAAAACAAAGATGGC 58.839 43.478 0.00 0.00 0.00 4.40
55 56 4.161333 GCAGATCGACAAAACAAAGATGG 58.839 43.478 0.00 0.00 0.00 3.51
56 57 4.161333 GGCAGATCGACAAAACAAAGATG 58.839 43.478 0.00 0.00 0.00 2.90
57 58 3.120199 CGGCAGATCGACAAAACAAAGAT 60.120 43.478 0.00 0.00 0.00 2.40
58 59 2.223144 CGGCAGATCGACAAAACAAAGA 59.777 45.455 0.00 0.00 0.00 2.52
59 60 2.032030 ACGGCAGATCGACAAAACAAAG 60.032 45.455 0.00 0.00 0.00 2.77
60 61 1.944024 ACGGCAGATCGACAAAACAAA 59.056 42.857 0.00 0.00 0.00 2.83
61 62 1.588674 ACGGCAGATCGACAAAACAA 58.411 45.000 0.00 0.00 0.00 2.83
62 63 1.262950 CAACGGCAGATCGACAAAACA 59.737 47.619 0.00 0.00 0.00 2.83
63 64 1.950472 CAACGGCAGATCGACAAAAC 58.050 50.000 0.00 0.00 0.00 2.43
64 65 0.237235 GCAACGGCAGATCGACAAAA 59.763 50.000 0.00 0.00 40.72 2.44
65 66 1.573829 GGCAACGGCAGATCGACAAA 61.574 55.000 0.00 0.00 43.71 2.83
66 67 2.032634 GGCAACGGCAGATCGACAA 61.033 57.895 0.00 0.00 43.71 3.18
67 68 2.434185 GGCAACGGCAGATCGACA 60.434 61.111 0.00 0.00 43.71 4.35
83 84 3.374058 AGAGAAATAAATGCCAACGACGG 59.626 43.478 0.00 0.00 0.00 4.79
84 85 4.600012 AGAGAAATAAATGCCAACGACG 57.400 40.909 0.00 0.00 0.00 5.12
85 86 6.612306 AGAAAGAGAAATAAATGCCAACGAC 58.388 36.000 0.00 0.00 0.00 4.34
86 87 6.817765 AGAAAGAGAAATAAATGCCAACGA 57.182 33.333 0.00 0.00 0.00 3.85
87 88 7.809806 AGAAAGAAAGAGAAATAAATGCCAACG 59.190 33.333 0.00 0.00 0.00 4.10
88 89 9.133627 GAGAAAGAAAGAGAAATAAATGCCAAC 57.866 33.333 0.00 0.00 0.00 3.77
89 90 9.082313 AGAGAAAGAAAGAGAAATAAATGCCAA 57.918 29.630 0.00 0.00 0.00 4.52
90 91 8.641498 AGAGAAAGAAAGAGAAATAAATGCCA 57.359 30.769 0.00 0.00 0.00 4.92
91 92 8.955388 AGAGAGAAAGAAAGAGAAATAAATGCC 58.045 33.333 0.00 0.00 0.00 4.40
92 93 9.986833 GAGAGAGAAAGAAAGAGAAATAAATGC 57.013 33.333 0.00 0.00 0.00 3.56
98 99 9.639563 AAAAAGGAGAGAGAAAGAAAGAGAAAT 57.360 29.630 0.00 0.00 0.00 2.17
122 123 0.908198 AGCACAAACCAGCCCAAAAA 59.092 45.000 0.00 0.00 0.00 1.94
123 124 0.177604 CAGCACAAACCAGCCCAAAA 59.822 50.000 0.00 0.00 0.00 2.44
124 125 1.821936 CAGCACAAACCAGCCCAAA 59.178 52.632 0.00 0.00 0.00 3.28
125 126 2.795110 GCAGCACAAACCAGCCCAA 61.795 57.895 0.00 0.00 0.00 4.12
126 127 3.225798 GCAGCACAAACCAGCCCA 61.226 61.111 0.00 0.00 0.00 5.36
127 128 4.347453 CGCAGCACAAACCAGCCC 62.347 66.667 0.00 0.00 0.00 5.19
128 129 4.347453 CCGCAGCACAAACCAGCC 62.347 66.667 0.00 0.00 0.00 4.85
130 131 4.347453 GGCCGCAGCACAAACCAG 62.347 66.667 0.00 0.00 42.56 4.00
144 145 2.919328 AACAAGCTTGCTGGGGCC 60.919 61.111 26.27 0.00 37.74 5.80
145 146 1.178534 TACAACAAGCTTGCTGGGGC 61.179 55.000 28.37 0.00 39.26 5.80
146 147 1.474077 GATACAACAAGCTTGCTGGGG 59.526 52.381 28.37 15.64 0.00 4.96
147 148 2.161855 TGATACAACAAGCTTGCTGGG 58.838 47.619 28.37 17.17 0.00 4.45
148 149 3.076621 TCTGATACAACAAGCTTGCTGG 58.923 45.455 28.37 19.34 0.00 4.85
149 150 4.393990 TCATCTGATACAACAAGCTTGCTG 59.606 41.667 26.27 25.41 0.00 4.41
150 151 4.582869 TCATCTGATACAACAAGCTTGCT 58.417 39.130 26.27 11.98 0.00 3.91
151 152 4.952262 TCATCTGATACAACAAGCTTGC 57.048 40.909 26.27 9.35 0.00 4.01
152 153 5.742453 GCAATCATCTGATACAACAAGCTTG 59.258 40.000 24.84 24.84 33.73 4.01
153 154 5.651139 AGCAATCATCTGATACAACAAGCTT 59.349 36.000 0.00 0.00 33.73 3.74
154 155 5.191426 AGCAATCATCTGATACAACAAGCT 58.809 37.500 0.00 0.00 33.73 3.74
155 156 5.496133 AGCAATCATCTGATACAACAAGC 57.504 39.130 0.00 0.00 33.73 4.01
177 178 7.666804 GGTTTCCCCCGCTTTATAGATTATAAA 59.333 37.037 0.00 2.39 38.06 1.40
178 179 7.017850 AGGTTTCCCCCGCTTTATAGATTATAA 59.982 37.037 0.00 0.00 0.00 0.98
179 180 6.502863 AGGTTTCCCCCGCTTTATAGATTATA 59.497 38.462 0.00 0.00 0.00 0.98
180 181 5.312443 AGGTTTCCCCCGCTTTATAGATTAT 59.688 40.000 0.00 0.00 0.00 1.28
181 182 4.661709 AGGTTTCCCCCGCTTTATAGATTA 59.338 41.667 0.00 0.00 0.00 1.75
182 183 3.462205 AGGTTTCCCCCGCTTTATAGATT 59.538 43.478 0.00 0.00 0.00 2.40
183 184 3.053826 AGGTTTCCCCCGCTTTATAGAT 58.946 45.455 0.00 0.00 0.00 1.98
184 185 2.484602 AGGTTTCCCCCGCTTTATAGA 58.515 47.619 0.00 0.00 0.00 1.98
185 186 3.292492 AAGGTTTCCCCCGCTTTATAG 57.708 47.619 0.00 0.00 0.00 1.31
186 187 3.743092 AAAGGTTTCCCCCGCTTTATA 57.257 42.857 0.00 0.00 0.00 0.98
187 188 2.615986 AAAGGTTTCCCCCGCTTTAT 57.384 45.000 0.00 0.00 0.00 1.40
188 189 2.385135 AAAAGGTTTCCCCCGCTTTA 57.615 45.000 0.00 0.00 0.00 1.85
189 190 1.502690 AAAAAGGTTTCCCCCGCTTT 58.497 45.000 0.00 0.00 0.00 3.51
190 191 3.233953 AAAAAGGTTTCCCCCGCTT 57.766 47.368 0.00 0.00 0.00 4.68
205 206 4.645588 ACATCCGTTGTTGGGTAAGAAAAA 59.354 37.500 0.00 0.00 33.74 1.94
206 207 4.208746 ACATCCGTTGTTGGGTAAGAAAA 58.791 39.130 0.00 0.00 33.74 2.29
207 208 3.822940 ACATCCGTTGTTGGGTAAGAAA 58.177 40.909 0.00 0.00 33.74 2.52
208 209 3.495434 ACATCCGTTGTTGGGTAAGAA 57.505 42.857 0.00 0.00 33.74 2.52
209 210 3.495434 AACATCCGTTGTTGGGTAAGA 57.505 42.857 0.64 0.00 46.80 2.10
218 219 0.467290 ACAGCCCAAACATCCGTTGT 60.467 50.000 0.00 0.00 41.53 3.32
219 220 0.240945 GACAGCCCAAACATCCGTTG 59.759 55.000 0.00 0.00 34.86 4.10
220 221 0.893727 GGACAGCCCAAACATCCGTT 60.894 55.000 0.00 0.00 36.73 4.44
221 222 1.303317 GGACAGCCCAAACATCCGT 60.303 57.895 0.00 0.00 34.14 4.69
222 223 1.303236 TGGACAGCCCAAACATCCG 60.303 57.895 0.00 0.00 43.29 4.18
223 224 4.841441 TGGACAGCCCAAACATCC 57.159 55.556 0.00 0.00 43.29 3.51
231 232 0.039618 TCCCTCAAAATGGACAGCCC 59.960 55.000 0.00 0.00 0.00 5.19
232 233 2.149973 ATCCCTCAAAATGGACAGCC 57.850 50.000 0.00 0.00 32.36 4.85
239 240 3.278574 TCCTACGCAATCCCTCAAAATG 58.721 45.455 0.00 0.00 0.00 2.32
335 345 4.331968 AGGAAATGACGCATAACTTTCCA 58.668 39.130 17.25 0.00 44.67 3.53
339 349 5.705609 ACAAAGGAAATGACGCATAACTT 57.294 34.783 0.00 0.00 0.00 2.66
347 357 2.993899 AGCGTCTACAAAGGAAATGACG 59.006 45.455 8.65 8.65 46.45 4.35
395 413 2.867091 GCGTTTGTCACTGTCGCGT 61.867 57.895 5.77 0.00 37.74 6.01
399 417 1.332028 CGTCAAGCGTTTGTCACTGTC 60.332 52.381 11.93 0.00 35.73 3.51
400 418 0.650512 CGTCAAGCGTTTGTCACTGT 59.349 50.000 11.93 0.00 35.73 3.55
620 638 2.749076 CCAGCATCCAAAGTGAAATCGA 59.251 45.455 0.00 0.00 0.00 3.59
662 680 3.003480 CACAACAGCCTAGCTTAGTTCC 58.997 50.000 0.00 0.00 36.40 3.62
667 685 3.146066 CCAAACACAACAGCCTAGCTTA 58.854 45.455 0.00 0.00 36.40 3.09
705 723 5.245531 CACTTCACTCCCACTGCTAATTAA 58.754 41.667 0.00 0.00 0.00 1.40
706 724 4.323485 CCACTTCACTCCCACTGCTAATTA 60.323 45.833 0.00 0.00 0.00 1.40
707 725 3.560025 CCACTTCACTCCCACTGCTAATT 60.560 47.826 0.00 0.00 0.00 1.40
708 726 2.026822 CCACTTCACTCCCACTGCTAAT 60.027 50.000 0.00 0.00 0.00 1.73
733 751 5.739070 GCTGCAAACCCTAGCTAAACTTTTT 60.739 40.000 0.00 0.00 34.70 1.94
787 811 1.597663 GTATTCTTGGTCCCAATCGCG 59.402 52.381 0.00 0.00 35.20 5.87
789 814 5.277857 ACTAGTATTCTTGGTCCCAATCG 57.722 43.478 0.00 0.00 35.20 3.34
844 931 0.532115 AAAGTTCATGCGCCCAATCC 59.468 50.000 4.18 0.00 0.00 3.01
865 952 3.619419 CAAATTGGGCAAAAATAGGGGG 58.381 45.455 0.00 0.00 0.00 5.40
866 953 3.010027 ACCAAATTGGGCAAAAATAGGGG 59.990 43.478 17.27 0.00 43.37 4.79
867 954 4.299586 ACCAAATTGGGCAAAAATAGGG 57.700 40.909 17.27 0.00 43.37 3.53
868 955 6.048732 AGTACCAAATTGGGCAAAAATAGG 57.951 37.500 17.27 0.00 43.37 2.57
869 956 6.106003 GGAGTACCAAATTGGGCAAAAATAG 58.894 40.000 17.27 0.00 43.37 1.73
870 957 5.544176 TGGAGTACCAAATTGGGCAAAAATA 59.456 36.000 17.27 0.00 43.37 1.40
871 958 4.349342 TGGAGTACCAAATTGGGCAAAAAT 59.651 37.500 17.27 0.00 43.37 1.82
872 959 3.711704 TGGAGTACCAAATTGGGCAAAAA 59.288 39.130 17.27 0.00 43.37 1.94
873 960 3.309296 TGGAGTACCAAATTGGGCAAAA 58.691 40.909 17.27 0.00 43.37 2.44
874 961 2.964209 TGGAGTACCAAATTGGGCAAA 58.036 42.857 17.27 0.00 43.37 3.68
889 976 2.104967 CATGTGGGCAAATCATGGAGT 58.895 47.619 0.00 0.00 36.36 3.85
910 997 4.201753 CCAAGAAATGTGATGCGTGACTAG 60.202 45.833 0.00 0.00 0.00 2.57
911 998 3.684305 CCAAGAAATGTGATGCGTGACTA 59.316 43.478 0.00 0.00 0.00 2.59
912 999 2.485426 CCAAGAAATGTGATGCGTGACT 59.515 45.455 0.00 0.00 0.00 3.41
913 1000 2.226437 ACCAAGAAATGTGATGCGTGAC 59.774 45.455 0.00 0.00 0.00 3.67
917 1013 6.194508 CGTTATAAACCAAGAAATGTGATGCG 59.805 38.462 0.00 0.00 0.00 4.73
919 1015 8.964420 AACGTTATAAACCAAGAAATGTGATG 57.036 30.769 0.00 0.00 0.00 3.07
965 1061 5.490159 ACATTAATGCACCCATTTCAAAGG 58.510 37.500 15.48 0.00 41.68 3.11
1026 1123 2.449518 TTCACCAGCTCCCCACCA 60.450 61.111 0.00 0.00 0.00 4.17
1077 1174 3.496870 CCTTGAACCATATACCCTGCTCC 60.497 52.174 0.00 0.00 0.00 4.70
1125 1222 1.941476 GCTTCTTGTACACGGCGTCG 61.941 60.000 10.85 8.42 43.02 5.12
1185 1282 2.332654 GCCGCCAACATTCGTCCTT 61.333 57.895 0.00 0.00 0.00 3.36
1225 1322 1.107945 TCGTCATCGATAGGCACCAA 58.892 50.000 0.00 0.00 41.35 3.67
1318 1415 1.954362 GCAGATGGACGCTCCTCTGT 61.954 60.000 20.53 0.00 40.62 3.41
1424 1521 0.823356 AGCAAAAAGAGAAGCGCCCA 60.823 50.000 2.29 0.00 0.00 5.36
1460 1557 0.602562 ATGAACGGTTGGTGCATTGG 59.397 50.000 0.00 0.00 42.63 3.16
1494 1591 1.787731 GCGCTCCTTATTCTTCGTAGC 59.212 52.381 0.00 0.00 0.00 3.58
1541 1638 0.846693 AACCTCTTCACCTGCAACCT 59.153 50.000 0.00 0.00 0.00 3.50
1543 1640 1.876156 CTGAACCTCTTCACCTGCAAC 59.124 52.381 0.00 0.00 32.68 4.17
1572 1669 1.556911 CCTGAAGCTCCACACTGGTAT 59.443 52.381 0.00 0.00 39.03 2.73
1613 1710 5.353123 TCGTCATACAGCCCAATTAAAAGAC 59.647 40.000 0.00 0.00 0.00 3.01
1713 1810 8.424918 AGTCCTCTATCACTATACCACATTTTG 58.575 37.037 0.00 0.00 0.00 2.44
1714 1811 8.424918 CAGTCCTCTATCACTATACCACATTTT 58.575 37.037 0.00 0.00 0.00 1.82
1734 1831 5.310409 TCAAGGAAACAAGAATCAGTCCT 57.690 39.130 0.00 0.00 37.08 3.85
1735 1832 6.581171 AATCAAGGAAACAAGAATCAGTCC 57.419 37.500 0.00 0.00 0.00 3.85
1736 1833 6.865205 CCAAATCAAGGAAACAAGAATCAGTC 59.135 38.462 0.00 0.00 0.00 3.51
1744 1841 4.053295 CTGTGCCAAATCAAGGAAACAAG 58.947 43.478 0.00 0.00 0.00 3.16
1745 1842 3.740764 GCTGTGCCAAATCAAGGAAACAA 60.741 43.478 0.00 0.00 0.00 2.83
1774 1871 2.796383 CGGTTACGAGGATTGAGCTCAG 60.796 54.545 17.43 6.68 44.60 3.35
1805 1902 0.446222 CATACCGCTTGTCAAACCGG 59.554 55.000 17.97 17.97 45.80 5.28
1823 1920 1.338389 GCTGGCCTAAGGTAACGTTCA 60.338 52.381 2.82 0.00 46.39 3.18
1925 2022 1.620819 GTGTGTGTCTCAGGTCTCCAT 59.379 52.381 0.00 0.00 0.00 3.41
2192 2289 2.906389 CAGGCTAAGGATGTATGCCCTA 59.094 50.000 0.00 0.00 44.19 3.53
2477 2574 2.562298 CCTGTCATCCTCTAGCTCATCC 59.438 54.545 0.00 0.00 0.00 3.51
2642 2739 4.058124 GTGCAAGATGTAGTGTCTTCACA 58.942 43.478 0.00 0.00 46.01 3.58
2681 2778 4.142730 GCTTGAGTTAGCCACAAATGAGAG 60.143 45.833 0.00 0.00 35.06 3.20
2856 2953 5.458779 CCAACTTCCTCGAATTGAAAACAAC 59.541 40.000 0.00 0.00 0.00 3.32
2865 2962 7.703058 ACATAATTTCCAACTTCCTCGAATT 57.297 32.000 0.00 0.00 0.00 2.17
2906 3003 5.166398 CCTGCAAAATCATCAGAAAACCTC 58.834 41.667 0.00 0.00 0.00 3.85
3341 3438 3.855255 TGTCAGTCTGGGATGAAACAA 57.145 42.857 0.00 0.00 0.00 2.83
3513 3610 4.156556 TCAGCTGCAATAGTTGTTGAATCC 59.843 41.667 9.47 0.00 38.61 3.01
3807 3907 1.538950 GCAGAGGCAAACCAAAGAGAG 59.461 52.381 0.00 0.00 40.72 3.20
3818 3918 2.884639 GGTTCAACTAAAGCAGAGGCAA 59.115 45.455 0.00 0.00 44.61 4.52
3844 3944 4.476628 AATGGTCCAAGAATCATTTGCC 57.523 40.909 0.00 0.00 0.00 4.52
3891 3991 4.320608 ACACACAAGCCCTGTAATTTTG 57.679 40.909 0.00 0.00 36.10 2.44
3924 4025 0.250901 TTTCTTCAGCCCACAGCCTC 60.251 55.000 0.00 0.00 45.47 4.70
3928 4029 1.246737 GGCCTTTCTTCAGCCCACAG 61.247 60.000 0.00 0.00 41.00 3.66
3929 4030 1.228552 GGCCTTTCTTCAGCCCACA 60.229 57.895 0.00 0.00 41.00 4.17
3934 4035 1.407979 CCATCATGGCCTTTCTTCAGC 59.592 52.381 3.32 0.00 0.00 4.26
3946 4047 1.299541 GGACACGCTAACCATCATGG 58.700 55.000 0.54 0.54 45.02 3.66
3947 4048 1.935873 CTGGACACGCTAACCATCATG 59.064 52.381 0.00 0.00 33.08 3.07
3948 4049 1.831106 TCTGGACACGCTAACCATCAT 59.169 47.619 0.00 0.00 33.08 2.45
3961 4062 1.980765 AGAGGCATGAACTTCTGGACA 59.019 47.619 0.00 0.00 0.00 4.02
3962 4063 2.027745 TCAGAGGCATGAACTTCTGGAC 60.028 50.000 10.97 0.00 0.00 4.02
3987 4088 5.506317 GCTTCTATCGCAGCCAATGTTAAAT 60.506 40.000 0.00 0.00 0.00 1.40
4134 4238 0.037139 GCTGTGCCAATGCCAATGAA 60.037 50.000 0.00 0.00 36.33 2.57
4135 4239 1.592743 GCTGTGCCAATGCCAATGA 59.407 52.632 0.00 0.00 36.33 2.57
4136 4240 4.195308 GCTGTGCCAATGCCAATG 57.805 55.556 0.00 0.00 36.33 2.82
4142 4246 8.439870 ATAGTTCACTATATGGCTGTGCCAATG 61.440 40.741 15.52 9.00 45.25 2.82
4143 4247 6.466326 ATAGTTCACTATATGGCTGTGCCAAT 60.466 38.462 15.52 11.97 45.25 3.16
4159 4263 5.128919 GGGATGAATGAGCAATAGTTCACT 58.871 41.667 0.00 0.00 37.82 3.41
4169 4276 2.761767 CCACAAATGGGATGAATGAGCA 59.238 45.455 0.00 0.00 43.04 4.26
4325 4432 3.541632 GAAACTCCTTGAAGGTGTGACA 58.458 45.455 18.53 0.00 40.88 3.58
4327 4434 2.777692 AGGAAACTCCTTGAAGGTGTGA 59.222 45.455 18.53 0.00 46.91 3.58
4391 4499 1.880027 CTGTTTTTCCCCTGTCGAAGG 59.120 52.381 6.66 6.66 46.94 3.46
4399 4507 4.741928 ACAACCTATCTGTTTTTCCCCT 57.258 40.909 0.00 0.00 0.00 4.79
4556 4665 4.223700 CAGCTATGGCCAAGGAGATACATA 59.776 45.833 10.96 0.00 39.73 2.29
4601 4710 3.537337 TGGGGGAAAGATACTTGAGGAA 58.463 45.455 0.00 0.00 0.00 3.36
4604 4713 4.702131 CAGTTTGGGGGAAAGATACTTGAG 59.298 45.833 0.00 0.00 0.00 3.02
4605 4714 4.508405 CCAGTTTGGGGGAAAGATACTTGA 60.508 45.833 0.00 0.00 32.67 3.02
4616 4725 1.152830 GAACAGCCAGTTTGGGGGA 59.847 57.895 0.00 0.00 41.51 4.81
4632 4742 9.638176 AAATTCGGTCTAAGATACTAGTAGGAA 57.362 33.333 8.85 1.89 0.00 3.36
4652 4762 8.525876 CACATCATTTAGCACAATACAAATTCG 58.474 33.333 0.00 0.00 0.00 3.34
4686 4796 8.675705 TGTACATGTGAATTCAAGAAGAGAAA 57.324 30.769 10.35 0.00 0.00 2.52
4688 4798 6.875726 CCTGTACATGTGAATTCAAGAAGAGA 59.124 38.462 10.35 0.00 0.00 3.10
4691 4801 5.939883 TCCCTGTACATGTGAATTCAAGAAG 59.060 40.000 10.35 3.45 0.00 2.85


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

AutoCloner maintained by Alex Coulton.